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Gao, G.

Publications and source records attributed to Gao, G..

At least 37 records · Page 2Linked to original sources

Exacerbation of a Subset of Behavioral Phenotypes by Early Treatment with AAV FOXG1 Gene Replacement Therapy in a Mouse Model of FOXG1 Syndrome

FOXG1 syndrome is a severe neurodevelopmental disorder characterized by microcephaly, profound intellectual disability with communication deficits including lack of speech, impaired social interaction, increased anxiety, hyperkinetic/dyskinetic movements, seizures and abnormal sleep patterns. Mutations in a single allele of the FOXG1 gene cause disease, likely due to loss-of-function. However, current therapies do not target this root cause of FOXG1 syndrome and have little to modest therapeutic benefit on only a small subset of symptoms. Recently, we reported the beneficial effects of adeno-associated virus (AAV) human FOXG1 gene replacement therapy administered by intracerebroventricular (ICV) injection at postnatal day 6 (P6) on several behavioral deficits that are relevant to key features of human FOXG1 syndrome, in male FOXG1 mice that were engineered with a highly prevalent, patient-specific Q84P mutation. Here, we report the behavioral effects of AAV human FOXG1 gene replacement therapy administered by ICV injection in female as well as male mice and at an earlier age - postnatal day 2 (P2). Although the earlier studies had suggested that AAV FOXG1 gene replacement therapy is a promising approach for the treatment of a subset of functional deficits in human FOXG1 syndrome with no toxicity observations, our current study shows that certain motor behaviors can be negatively impacted or exacerbated by P2 treatment with AAV FOXG1 gene replacement therapy, in female but not male FOXG1 mice. Given these results, the risk-benefit balance of AAV FOXG1 gene replacement therapy in patients with FOXG1 syndrome should be carefully considered, especially in female patients.

neuroscience↗

Exogenous Photoreceptor-Specific N-Glycosylated PROM1 Rescues Retinal Degeneration in Patient and Mouse Models

PROM1 is widely expressed across various tissues. However, its pathogenic mutations are exclusively associated with inherited retinal dystrophy (IRD). The mechanisms underlying this retina-specific vulnerability remain poorly understood, and no effective treatment currently exists for PROM1-IRD. Here, we utilized urine cells, hiPSCs, hiPSC-RPE cells, retinal organoids (ROs) and Prom1-/- mice to address these challenges. During photoreceptor development in ROs, PROM1 co-localized with ciliary marker ARL13B and outer segment (OS) marker PRPH2. It exhibited photoreceptor-specific mRNA splicing isoforms and unique N-glycosylation. In IRD patient-specific models with the PROM1 c.619G>T (p.E207X) homozygous mutation, we observed nonsense-mediated mRNA decay and altered splicing, leading to complete loss of PROM1 protein and OS-like structure disruption, faithfully recapitulating PROM1-IRD pathology. To rescue these defects, we engineered a photoreceptor-specific AAV7m8-CRXp-hPROM1, which successfully restored PROM1 expression and OS-like structures in patient-derived ROs. Therapeutic efficacy was further validated in Prom1-/- mice, where subretinal delivery of AAV8-CRXp-hPROM1 led to photoreceptor-specific expression of human PROM1, significantly preserving OS morphology and improving visual function. These findings not only provide the first solid preclinical evidence supporting gene therapy for PROM1-IRD, but also reveal photoreceptor-specific vulnerability to PROM1 mutations, offering a novel conceptual framework for investigating and treating related IRDs.

neuroscience↗

Deep-learning triage of 3D pathology datasets for comprehensive and efficient pathologist assessments

Standard-of-care slide-based 2D histopathology severely undersamples spatially heterogeneous tissue specimens, with each thin 2D section representing <1% of the entire tissue volume (in the case of a biopsy). Recent advances in non-destructive 3D pathology, such as open-top light-sheet microscopy (OTLS), enable comprehensive high-resolution imaging of large clinical specimens. While fully automated computational analyses of such 3D pathology datasets are being explored, a potential low-risk route for accelerated clinical adoption would be to continue to rely upon pathologists to provide final diagnoses. Since manual review of these massive and complex 3D datasets is infeasible for routine clinical practice, we present CARP3D, a deep learning triage framework that identifies high-risk 2D cross sections within large 3D pathology datasets to enable time-efficient pathologist evaluation. CARP3D assigns risk scores to all 2D levels within a tissue volume by leveraging context from a subset of neighboring depth levels, outperforming models in which predictions are based on isolated 2D levels. In two use cases - risk stratification based on prostate cancer biopsies and screening for dysplasia/cancer in endoscopic biopsies of Barretts esophagus - AI-triaged 3D pathology, enabled by CARP3D, demonstrates the potential to improve the detection of high-risk diseases in comparison to slide-based 2D histopathology while optimizing pathologist workloads.

pathology↗

Surface-Tethering Enhances Precision in Measuring Diffusion Within 3D Protein Condensates

Biomolecular condensates, or membraneless organelles, play pivotal roles in cellular organization by compartmentalizing biochemical reactions and regulating diverse processes such as RNA metabolism, signal transduction, and stress response. Super-resolved imaging and single-molecule tracking are essential for probing the internal dynamics of these condensates, yet intrinsic Brownian (thermal capillary wave) motion of the entire condensate in vitro could introduce artifacts into diffusion measurements, confounding the interpretation of molecular mobility. Here, we systematically assess and address this question using both experiments and simulations. We deploy three surface-tethering strategies--using biotinylated DNA, protein, or antibody tethers--to immobilize FUS protein condensates on passivated glass surfaces. We show that tethering effectively suppresses the global translational and rotational Brownian motion of the entire condensate, eliminating inherent measurement artifacts while preserving their spherical appearance and native liquid-like properties. Quantitative analysis reveals that untethered condensates systematically overestimate or underestimate molecular diffusion coefficients and step sizes, particularly for slowly diffusing structured mRNAs, while rapidly diffusing unstructured RNAs are unaffected due to temporal scale separation. Comparative evaluation of tethering strategies demonstrates tunable control over condensate stability and internal dynamics, with implications for optimizing experimental design. Finally, simulations spanning the full physiological parameter space enable us to provide practical guidelines for assessing whether, and to what extent, tethering is beneficial, based on condensate size and the diffusion properties of the biomolecule of interest. Our findings establish surface tethering as a necessary and robust approach for accurate quantification of intra-condensate molecular dynamics, providing a methodological framework for future studies of membraneless organelles. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/659185v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@1f0ae11org.highwire.dtl.DTLVardef@341574org.highwire.dtl.DTLVardef@16c75daorg.highwire.dtl.DTLVardef@1ad5ed1_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

Efficient Cell Factory Design by Combining Meta-Heuristic Algorithm with Enzyme Constrained Metabolic Models

The rational design of high-performance microbial cell factories remains a central challenge in sustainable biomanufacturing due to the complexity of metabolic networks and the difficulty of predicting synergistic genetic interventions. Despite recent advances in strain design algorithms, predicting combinatorial targets remains computationally prohibitive due to the combinatorial explosion. Here, we present MetaStrain, a unified computational framework that integrates enzyme-constrained models (ecModels) with meta-heuristic algorithms to identify non-intuitive combinatorial gene targets for improving product yields. MetaStrain first performs pre-screening through a modified enforced objective flux scanning algorithm to reduce the dimensionality of candidate genes and annotate editing strategies. The subsequent search module employs flexible individual encodings compatible with diverse meta-heuristic algorithms and adopts a bottom-up phenotype evaluation strategy enabling efficient exploration of the combinatorial design space. Integrated redundancy analysis tools further identify single and fixed-size combinatorial strategies, facilitating direct experimental implementation. Computational simulation in Saccharomyces cerevisiae reveals significant enhancements in 2-phenylethanol and spermidine biosynthesis, while controlling target count and covering experimentally validated targets. Experimental validation in Escherichia coli further confirmed the algorithms predictive power, achieving up to a 61.25% increase in L-tryptophan titer of the five-target combination strain. Overall, MetaStrain achieves high computational efficiency, stable convergence, and broad adaptability across diverse metabolic targets. This study provides a powerful tool for metabolic engineering, bridging computational prediction and experimental realization, and highlighting the potential of meta-heuristic optimization in synthetic biology.

bioinformatics↗

ER tethering and active transport govern condensate diffusion during hyperosmotic stress

BackgroundHyperosmotic shock and the resulting cell volume compression are commonly experienced by organs such as the kidneys, causing rapid formation of hyperosmotic phase separation (HOPS) condensates in the cytoplasm and nucleoplasm. Although the tight relationship between hyperosmotic shock and condensation has been characterized, the dynamics of biomolecular condensates in hyperosmotically compressed cells and their regulatory mechanisms remain largely unknown. ResultsWe used live-cell single-particle tracking (SPT) across different time scales to systematically characterize the dynamics of HOPS condensates formed by model protein mRNA decapping enzyme 1A (DCP1A). We found that HOPS condensates predominantly exhibited sub-diffusion rather than free diffusion, whereas some ([~]2%) exhibited short super-diffusion. Using tools measuring spatial accessibility inside cells and fluorescence labels for specific cellular organelles, we further revealed the origins of sub-diffusion and super-diffusion as endoplasmic reticulum (ER) attachment and coupling to microtubule-dependent active transport, respectively. Further, we reconstructed an accessibility map of the hyperosmotically compressed cell from trajectories of genetically encoded multimeric nanoparticles (GEMs), revealing that the cytoplasm of a compressed cell remains highly accessible without significant local corrals. ConclusionsIn contrast to prior portrayals of the cytosolic space as static and constrained, our data suggest that the cytosol of a hyperosmotically compressed cell remains dynamic and accessible. Meanwhile, hyperosmotic and potentially other condensates can be spatially organized through docking to membrane structures, with intermittent episodes of long-range transport. These insights broaden our understanding of the physical environment within cells under hyperosmotic shock and provide a model for spatiotemporal organization of condensates via docking or coupling to existing cellular structures and processes.

biophysics↗

A systematic delineation of 3'UTR regulatory elements and their contextual associations

The 3'UTR encodes regulatory information that shapes transcript abundance and subcellular distribution, yet the underlying sequence rules remain incompletely defined. Using SEERS, we quantified the effects of [~]2 million synthetic 3'UTR inserts in A549 and HCT116 cells on RNA output and nuclear-cytoplasmic partitioning. We identify a broad repertoire of short (2[~]8 nt) elements whose effects largely align along a major coupled axis that links high expression with cytoplasmic enrichment and low expression with nuclear enrichment, and contribute predominantly in an additive manner. A context-aware deep learning model (TALE) captures most of this behavior while revealing that strong context dependence is uncommon and emerges mainly in rare, extreme contexts consistent with higher-order constraints. Applying TALE to ClinVar 3'UTR variants prioritizes a subset of pathogenic SNVs with aberrant predicted effects, frequently explained by creation or disruption of splice-site-like U1 telescripting signals, highlighting a potent route to 3'UTR-driven disease mechanisms.

genomics↗

Gene therapies alleviate absence epilepsy associated with Scn2a deficiency in DBA/2J mice

Mutations in the voltage-gated sodium channel gene SCN2A, which encodes the NaV1.2 channel, cause severe epileptic seizures. Patients with SCN2A loss-of-function (LoF) mutations, such as protein-truncating mutations, often experience later-onset and drug-resistant epilepsy, highlighting an urgent unmet clinical need for new therapies. We previously developed a gene-trap Scn2a (Scn2agt/gt) mouse model with a global NaV1.2 reduction in the widely used C57BL/6N (B6) strain. Although these mice display multiple behavioral abnormalities, EEG recordings indicated only mild epileptiform discharges, possibly attributable to the seizure-resistant characteristics associated with the B6 strain. To enhance the epileptic phenotype, we derived congenic Scn2agt/gt mice in the seizure-susceptible DBA/2J (D2J) strain. Notably, we found that these mice exhibit prominent spontaneous absence seizures, marked by both short and long spike-wave discharges (SWDs). Restoring NaV1.2 expression in adult mice substantially reduced their SWDs, suggesting the possibility of SCN2A gene replacement therapy during adulthood. RNA sequencing revealed significant alterations in gene expression in the Scn2agt/gt mice, in particular a broad downregulation of voltage-gated potassium channel (KV) genes, including KV1.1. The reduction of KV1.1 expression was further validated in human cerebral organoids with SCN2A deficiency, highlighting KV1.1 as a promising therapeutic target for refractory seizures associated with SCN2A dysfunction. Importantly, delivery of exogenous human KV1.1 expression via adeno-associated virus (AAV) in D2J Scn2agt/gt mice substantially reduced absence seizures. Together, these findings underscore the influence of mouse strain on seizure severity and highlight the potential of targeted gene therapies for treating SCN2A deficiency-related epilepsies. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=91 SRC="FIGDIR/small/657652v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@35374eorg.highwire.dtl.DTLVardef@1c22197org.highwire.dtl.DTLVardef@2b4582org.highwire.dtl.DTLVardef@e06e68_HPS_FORMAT_FIGEXP M_FIG C_FIG In briefScn2a deficiency leads to absence seizures in D2J mice and neuronal hyperexcitability with compensatory KV reduction; restoring NaV1.2 or introducing human KV1.1 reduces seizure burden. HighlightsO_LIScn2a deficiency induces robust absence seizures in the DBA/2J but not the C57BL/6N strain. C_LIO_LICortical neurons in adult DBA/2J mice with Scn2a deficiency exhibit intrinsic hyperexcitability. C_LIO_LISevere Scn2a deficiency leads to downregulation of multiple potassium channel genes. C_LIO_LIGenetic restoration of NaV1.2 expression alleviates spike-wave discharges (SWDs). C_LIO_LIAAV-mediated human KV1.1 delivery substantially reduced absence seizures, demonstrating the therapeutic potential of targeted gene therapy. C_LI

neuroscience↗

Engineering novel AAV capsids by global de-targeting and subsequent muscle-specific tropism in mice and NHPs

Recombinant adeno-associated viral (rAAV) vectors are a potent tool, but their clinical application is restricted by insufficient target tissue transduction and liver toxicity. We employed a novel two-step engineering strategy to create novel rAAV capsids with global tissue de-targeting, then produced strong tissue-specific expression by adding a peptide sequence. We created a novel capsid, AAV.Zero1, with globally de-targeted transduction by loop swapping domains from AAV9 into AAV2. Making an R585A substitution (AAV.Zero2) re-targeted tissues but deleting residues 585-587 (AAV.Zero3) abrogated transduction. Inserting a myogenic peptide into AAV.Zero3 produced a novel capsid (AAV.eM) with strong muscle-specific transgene expression while maintaining minimal off-target expression, including in liver, which was conserved in two mouse strains and non-human primates. AAV.eM showed similar expression as the leading myotropic vector MyoAAV.4A but had a more favorable safety profile. Importantly, AAV.eM was able to functionally rescue a mouse model of Duchenne Muscular Dystrophy following systemic delivery of a micro-dystrophin gene. Thus, AAV.eM is an improved myotropic rAAV capsid that de-targets other tissues, especially the liver, and proof-of-concept for a platform to create capsids with specific properties that translate across species by addition of peptides onto low transduction backbones.

bioengineering↗

A Compact Base Editor Rescues AATD-associated Liver and Lung Disease in Mouse Models

Alpha-1 antitrypsin deficiency (AATD) is commonly caused by a G-to-A mutation in the SERPINA1 gene (the PiZ mutation). The mutant PiZ AAT protein is sequestered in hepatocytes, causing lung emphysema due to insufficient AAT protein to inhibit neutrophil elastase in the lung. Here we show that a compact adenine base editor (ABE) with an evolved Cas9 nickase derived from Neisseria meningitidis (eNme2.C) can be packaged in a single AAV and correct the PiZ mutation in mouse models of AATD. An all-in-one eNme2.C-TadA8e/guide 2 plasmid achieved approximately 20% on-target editing in PiZ reporter cells. TadA9e, which has a narrower editing window than TadA8e, reduced bystander editing without significantly affecting the on-target edit. In PiZ transgenic mice, eNme2.C-TadA9e AAV showed approximately 23% editing efficiency after 8 weeks and reduced liver disease burden in treated mice. In a new AAT-null;PiZ transgenic mouse model, ABE restored serum levels of AAT to beyond the 570 g/mL therapeutic level. Moreover, ABE treatment was able to significantly correct lung functions in AAT-null;PiZ animals with emphysema. This study demonstrates the feasibility of an eNme2.C-based ABE in a single AAV to treat both AATD-associated liver and lung disease.

bioengineering↗

Behavioral Efficacy of AAV FOXG1 Gene Replacement Therapy in a Mouse Model of FOXG1 Syndrome

FOXG1 syndrome is a severe neurodevelopmental disorder characterized by microcephaly, profound intellectual disability with communication deficits including lack of speech, impaired social interaction, increased anxiety, hyperkinetic/dyskinetic movements, seizures and abnormal sleep patterns. Mutations in a single allele of the FOXG1 gene cause disease, likely due to loss-of-function. However, current therapies do not target this root cause of FOXG1 syndrome and have little to modest therapeutic benefit on only a small subset of symptoms. To date, the therapeutic potential of restoring FOXG1 levels in the brain with adeno-associated virus (AAV) FOXG1 gene replacement therapy has only been reported in a Foxg1fl/+;NexCre mouse model that lacks one Foxg1 allele but does not express mutant FOXG1, and with only neuroanatomical endpoints evaluated. Here, in a FOXG1 mouse model that contains a highly prevalent, patient-specific Q84P mutation, we describe the beneficial effects of AAV human FOXG1 gene replacement therapy administered by intracerebroventricular (ICV) injection at postnatal day 6 (P6) on several behavioral deficits that are relevant to key features of human FOXG1 syndrome. Our studies demonstrate that AAV FOXG1 gene replacement therapy is a promising approach for the treatment of a subset of functional deficits in human FOXG1 syndrome.

neuroscience↗

Identifying Key Cells for Fibrosis by Systematically Calling Cell Type-Phenotype Associations across Massive Heterogenous Datasets

Fibrotic diseases pose a significant burden on health care, yet the key pathogenic fibroblasts involved remain unclear. We developed the fibrotic disease fibroblast atlas (FDFA), which comprises 394 single-cell and 38 spatial transcriptomic samples from 11 common fibrotic diseases. To perform a cell-type phenotype association study in large-scale heterogeneous datasets, we developed the single-cell phenotype association research kit for large-scale dataset exploration (SPARKLE). SPARKLE handles heterogeneity by incorporating confounding information into its generalized linear mixed models (GLMMs). The application of SPARKLE to FDFA revealed that matrix fibroblasts (MTFs) constitute a crucial pathogenic cell group in fibrosis. Their increased proportion correlate with the fibrotic process. MTFs also synergize with MYO-Fs, increasing their degree of fibrosis. Based on MTF, we identified 25 potential antifibrotic targets for broad-spectrum antifibrotic therapies. This study enhances our understanding of fibrosis and provides a reliable framework for large-scale cell type-phenotype association research. HighlightsO_LIA cross-tissue, multidisease fibrotic disease fibroblast atlas (FDFA) reveals diverse fibroblast subtypes in fibrosis diseases. C_LIO_LIA new toolkit, SPARKLE, is introduced for detecting robust cell type-phenotype associations in large-scale heterogeneous datasets. C_LIO_LIMultiple pathogenic fibroblasts associated with common fibrosis disease (MTF) onset and progression have been identified, suggesting potential cell-specific therapeutic strategies for fibrosis-related diseases. C_LI

bioinformatics↗

Longitudinal analysis of retinal cell state transitions in RB1-deficient retinal organoids reveals the nascent cone precursors are the earliest cell-origin of human retinoblastoma

All cancers develop from malignant transformation of normal cells, while it is challenging to identify these "cells-of-origin" since it is impossible to witness the dynamic changes in human cancers. Retinoblastoma (Rb), an intraocular malignant cancer, is a typical model for study the molecular and cellular mechanisms of cancers. Although the maturing cone precursors (CPs) are proposed as the cellular origin of human Rb, it is unknow whether other retinal cells are also sensitive to RB1 inactivation. Here we developed RB1-deficient human retinal organoids (ROs) models from RB1-/- or RB1+/- human induced pluripotent stem cells (hiPSCs). RB1-/- hiPSCs developed into Rb tumors which recapitulated the features of human native Rb and had the ability to form consecutive orthotopic xenografts in mice. Importantly, RB1 loss induced the overproliferation of ATOH7+ neurogenic retinal progenitor cells (nRPCs), which disrupted the retinal development by generating proliferative, nascent retinal cells including retinal ganglion cells and CPs. scRNA-seq analysis verified the ATOH7+/RXR{gamma}+ nascent CPs survived and finally drove Rb development. In contrast, monoallelic RB1 inactivation with low pRB expression did not induce nascent CPs proliferation, but only induced nRPCs overproliferation which caused retinocytoma-like phenotype. Finally, a potential therapeutic agent for Rb was identified from multi-omics data. Our findings firstly indicate that nRPCs are the most sensitive cells to RB1 loss inducing nascent retinal cells abnormal proliferation, and ATOH7+ nascent CPs are the earliest cellular origin of human Rb, facilitating drug development for Rb.

cell biology↗

A single amino acid variant in the variable region I of AAV capsid confers liver detargeting

AAV capsid serotypes isolated from nature have been widely used in gene delivery and gene therapy. Recently, more than 1,000 distinct AAV capsids were identified from human clinical samples by high-throughput, long-read DNA sequencing. In this study, we tap into this broad natural biodiversity of AAV capsids to develop liver-tropic AAV capsids. We initially screened a subset of variants derived from AAV8 (n=159) for packaging efficiency. The high-yielding variants were subjected to a barcoded vector library screen in mice and ferrets for their ability to mediate liver gene transfer. Although no variant surpassed AAV8 for liver targeting, several exhibited a liver detargeting phenotype. Among these, we focused on the N271D variant (AAV8 VP1 numbering), located in the variable region I (VR-1), which has been previously implicated in influencing liver tropism. The liver detargeting phenotype of AAV8.N271D was confirmed by single vector administration in mice. Additionally, we grafted the N271D variant onto AAV9 and MyoAAV capsids (N270D by AAV9 VP1 numbering). The AAV9.N270D and MyoAAV.N270D vectors showed a similar liver-detargeting phenotype, although muscle targeting was moderately reduced. Although we did not identify any capsid variants that outperform AAV8 in liver transduction, this study reinforces the important role of VR-1 in modulating liver tropism and highlights the potential of engineering VR-1 residues to reduce liver gene transfer and associated toxicity observed in several gene therapy studies.

molecular biology↗

AAVone: A Cost-Effective, Single-Plasmid Solution for Efficient AAV Production with Reduced DNA Impurities

Currently, the most common approach for manufacturing GMP-grade adeno-associated virus (AAV) vectors involves transiently transfecting mammalian cells with three plasmids that carry the essential components for production. The requirement for all three plasmids to be transfected into a single cell and the necessity for high quantities of input plasmid DNA, limits AAV production efficiency, introduces variability between production batches, and increases time and labor costs. Here, we developed an all-in-one, single-plasmid AAV production system, called AAVone. In this system, the adenovirus helper genes (E2A, E4orf6, and VA RNA), packaging genes (rep and cap), and the vector transgene cassette are consolidated into a single compact plasmid with a 13-kb backbone. The AAVone system achieves a two- to four-fold increase in yields compared to the traditional triple-plasmid system. Furthermore, the AAVone system exhibits low batch-to-batch variation and eliminates the need for fine-tuning the ratios of the three plasmids, simplifying the production process. In terms of vector quality, AAVs generated by the AAVone system show similar in vitro and in vivo transduction efficiency, but a substantial reduction in sequences attributed to plasmid backbones and a marked reduction in non-functional snap-back genomes. In Summary, the AAVone platform is a straightforward, cost-effective, and highly consistent AAV production system - making it particularly suitable for GMP-grade AAV vectors.

bioengineering↗

High-fidelity disentangled cellular embeddings for large-scale heterogeneous spatial omics via DECIPHER

The functional role of a cell, shaped by the sophisticated interplay between its molecular identity and spatial context, is often obscured in current spatial modeling. Aiming to model large-scale heterogeneous spatial data in silico properly, DECIPHER produces high-fidelity disentangled embeddings, not only achieving superior performance in systematic benchmarks, but also empowering various real-world applications. We further demonstrated that DECIPHER is scalable to atlas-scale datasets, enabling global analysis which is largely infeasible to current state-of-the-arts.

bioinformatics↗

Vaginal Microbiome and Inflammation Among Chinese Women.

Human papillomavirus (HPV) infection, cervical intraepithelial neoplasia (CIN), pelvic organ prolapse (POP), cervical polyps (CP), abnormal uterine bleeding (AUB), and vaginitis are common conditions encountered in gynecological practice. In this study, we collected vaginal secretions from patients diagnosed with these diseases (n = 310) and from healthy donors (n = 112) to analyze their vaginal microbiome using 16S rRNA sequencing and cytokine expression using a cytometric bead array (CBA). Our findings revealed that the vaginal microbiome in POP patients exhibited higher complexity compared to other groups. Regarding cytokine expression, levels of IL-1, IL-1{beta}, IL-6, IL-8, MCP-1, and MIG were significantly elevated in HPV and CIN patients. Analysis of microbial associations showed that Lactobacillus crispatus and Lactobacillus iners were significantly negatively correlated with IL-1 and IL-1{beta} expression. In contrast, non-Lactobacillus bacteria, including Bifidobacterium breve, Prevotella bivia, Gardnerella vaginalis, Sneathia amnii, Sneathia sanguinegens, Prevotella amnii, Escherichia coli, and Chlamydia trachomatis, were positively correlated with IL-1, IL-1{beta}, IL-6, IL-8, MCP-1, and MIG levels. Furthermore, Lactobacillus iners exhibited a significant negative effect in the HPV and CIN patient groups.

microbiology↗

Tissue-specific responses to TFAM and mtDNA copy number manipulation in prematurely ageing mice

Somatic mitochondrial DNA (mtDNA) mutations are heavily implicated as important drivers of ageing and age-related diseases. Their pathological effect can be partially counteracted by increasing the absolute amount of wild-type mtDNA via moderately upregulating TFAM, a protein important for mtDNA packaging and expression. However, strong TFAM overexpression can also have detrimental effects as it results in hypercompaction of the mtDNA and subsequent impairment of mtDNA gene expression. In this study, we have experimentally addressed the propensity of moderate TFAM modulation to improve the premature ageing phenotypes of mtDNA mutator mice, carrying random mtDNA mutations. Surprisingly, we detect tissue-specific endogenous compensatory mechanisms acting in mtDNA mutator mice which largely affects the outcome of TFAM modulation. Accordingly, moderate overexpression of TFAM can have both negative and beneficial effects in different tissues of mtDNA mutator mice. We see a similar behavior for moderate TFAM reduction, which improves brown adipocyte tissue homeostasis, while other tissues are largely unaffected. Our findings highlight that regulation of copy number and gene expression of mtDNA is complex and cause tissue-specific effects that should be considered when modulating TFAM levels. Additionally, we suggest that TFAM is not the sole determinant of mtDNA copy number in situations where oxidative phosphorylation (OXPHOS) is compromised but other important players must be involved.

genetics↗