Gene Manipulation Research Articles

Innovative PBMC-derived humanized mouse model reveals CD8+ T cell-intrinsic regulation during antitumor immunity.

The PBMC-derived humanized mouse model (PBMC model) may serve as an excellent tool in the field of immunology for both preclinical research and personalized therapeutic strategy development. However, single transplantation of complete PBMCs without modifications prevents the identification of cell type-specific factors that are potentially involved in modulating cell-intrinsic functions for the immune response. Here, we establish an innovative strategy for PBMC model generation, where two-step transplantations coupled with cell type-specific gene manipulation were conducted to evaluate the potential role of CD8+ T cell-intrinsic factors in regulating antitumor immunity toward PDX-based tumors. This method readily yields over 10% of human CD45+ cells within the PBMCs of humanized mice with high editing efficiency of gene expression in CD8+ T cells that can be subsequently detected in the tumor microenvironment (TME). Our work provides a new method to generate a PBMC-derived humanized mouse model for investigating regulators of interest during antitumor immunity in a cell type-specific manner.

Enhanced silk production and pupal weight in Bombyx mori through CRISPR/Cas9-mediated circadian Clock gene disruption.

The domesticated silkworm, Bombyx mori, is crucial for global silk production, which is a significant economic activity supporting millions of livelihoods worldwide. Beyond traditional silk production, the growing demand for insect larvae in cosmetics, biomedical products, and animal feed underscores the need to enhance B. mori productivity. This study investigates the role of the circadian clock gene Clock in B. mori using CRISPR/Cas9-mediated mutagenesis to establish the ClkΔ29 knock-out mutant strain. Dysregulation of the circadian clock in ClkΔ29 was demonstrated by altered temporal transcriptional profiles of core circadian clock genes in adult heads and disrupted circadian-controlled behaviors, including adult eclosion and egg hatching rhythms under constant darkness. By analysing larval development timing, as well as the weights of late instar larvae, pupae, and cocoon components in ClkΔ29 mutants and in ClkΔ1922 silkworms (carrying an independently generated Clk- null allele), we showed that CLK contributes to physiological processes regulating B. mori development and growth. Importantly, ClkΔ29 mutants reared on a standard sericulture diet exhibited significant increases in key economic traits, with silk production increasing by up to 7%, and pupal weight increasing by up to 25% compared to wild-type controls. This study highlights the potential of circadian clock gene manipulation to significantly enhance sericultural productivity. Future research should focus on elucidating the molecular mechanisms driving these phenotypes and determining whether they result from circadian clock functions or pleiotropic effects of B. mori Clk. These findings provide a foundation for advancing sustainable sericulture and developing new commercial applications for silkworm-derived products.

Luteinizing hormone receptor knockout mouse: What has it taught us?

Luteinizing hormone (LH), along with its agonist choriongonadotropin (hCG) in humans, is the key hormone responsible for the tropic regulation of the gonadal function. LH and hCG act through their cognate receptor, the luteinizing hormone/choriongonadotropin receptor (LHCGR; more appropriately LHR in rodents lacking CG), located in the testis in Leydig cells and in the ovary in theca, luteal, and luteinizing granulosa cells. Low levels in LHCGR are also expressed in numerous extragonadal sites. Hypogonadism is observed in humans expressing inactivating mutations in the LHβ-subunit (LHB)and LHCGR genes, confirming the crucial role of LH and LHCGR in gonadal development and function. Unraveling of the LHR structure and the advent of gene manipulation techniques enabled the production of mouse models with inactivated LHR function, that is, the LHR knockout (LuRKO) mouse, some 20 years ago. This mouse model has thereafter been instrumental in various experimental settings, alone or combined with other genetically modified mouse models, in providing novel, and in some cases unexpected, details about the LH/LHR function. We will review here the salient findings of these studies.

Engineered CRISPR-Cas9 for Streptomyces sp. genome editing to improve specialized metabolite production

The CRISPR-Cas9 system has frequently been used for genome editing in Streptomyces; however, cytotoxicity, caused by off-target cleavage, limits its application. In this study, we implement innovative modification to Cas9, strategically addressing challenges encountered during gene manipulation using Cas9 within strains possessing high GC content genome. The Cas9-BD, a modified Cas9 with the addition of polyaspartate to its N- and C-termini, is developed with decreased off-target binding and cytotoxicity compared with wild-type Cas9. Cas9-BD and similarly modified dCas9-BD have been successfully employed for simultaneous biosynthetic gene cluster (BGC) refactoring, multiple BGC deletions, or multiplexed gene expression modulations in Streptomyces. We also demonstrate improved secondary metabolite production using multiplexed genome editing with multiple single guide RNA libraries in several Streptomyces strains. Cas9-BD is also used to capture large BGCs using a developed in vivo cloning method. The modified CRISPR-Cas9 system is successfully applied to many Streptomyces sp., providing versatile and efficient genome editing tools for strain engineering of actinomycetes with high GC content genome.

Plasmid Gene Therapy for Monogenic Disorders: Challenges and Perspectives.

Monogenic disorders are a group of human diseases caused by mutations in single genes. While some disease-altering treatments offer relief and slow the progression of certain conditions, the majority of monogenic disorders still lack effective therapies. In recent years, gene therapy has appeared as a promising approach for addressing genetic disorders. However, despite advancements in gene manipulation tools and delivery systems, several challenges remain unresolved, including inefficient delivery, lack of sustained expression, immunogenicity, toxicity, capacity limitations, genomic integration risks, and limited tissue specificity. This review provides an overview of the plasmid-based gene therapy techniques and delivery methods currently employed for monogenic diseases, highlighting the challenges they face and exploring potential strategies to overcome these barriers.

Harnessing the Streptomyces-originating type I-E CRISPR/Cas system for efficient genome editing in Streptomyces.

Since their discovery, CRISPR/Cas systems have significantly expanded the genetic toolbox, aiding in the exploration and enhanced production of natural products across various microbes. Among these, class 2 CRISPR/Cas systems are simpler and more broadly used, but they frequently fail to function effectively in many Streptomyces strains. In this study, we present an engineered class 1 type I CRISPR/Cas system derived from Streptomyces avermitilis, which enables efficient gene editing in phylogenetically distant Streptomyces strains. Through a plasmid interference assay, we identified the effective protospacer adjacent motif as 5'-AAN-3'. Utilizing this system, we achieved targeted chromosomal deletions ranging from 8 bp to 100 kb, with efficiencies exceeding 92%. We further utilized this system to insert DNA fragments into different Streptomyces genomes, facilitating the heterologous expression of exogenous genes and the activation of endogenous natural product biosynthetic gene clusters. Overall, we established a type I CRISPR/Cas-based gene-editing methodology that significantly advances the exploration of Streptomyces, known for their rich natural product resources. This is the first report of a gene editing tool developed based on the endogenous class 1 type I CRISPR/Cas system in Streptomyces spp. Our work enriches the Streptomyces gene manipulation toolbox and advances the discovery of valuable natural products within these organisms.

Uncovering the genetic basis of antiviral polyketide limocrocin biosynthesis through heterologous expression

BackgroundStreptomyces roseochromogenes NRRL 3504 produces clorobiocin, an aminocoumarin antibiotic that inhibits DNA replication. No other natural products have been isolated from this bacterium so far, despite the presence of a rich repertoire of specialized metabolite biosynthesis gene clusters (smBGCs) within its genome. Heterologous expression of smBGCs in suitable chassis speeds up the discovery of the natural products hidden behind these sets of genes.ResultsIn this work we focus on one intriguing smBGC of NRRL 3504 bearing some similarity to gene clusters involved in production of manumycin family polyketides. Through heterologous expression in Streptomyces chassis strains S. albus Del14 and S. lividans ΔYA9, this smBGC (hereafter referred to as lim BGC) was shown to direct the production of unusual polyketide limocrocin (LIM) known for its ability to interfere with viral reverse transcriptases. The organization of lim BGC, data on the structures of revealed metabolites as well as manipulations of lim genes allowed us to put forward an initial hypothesis about a biosynthetic pathway leading to LIM. We provide initial data on two LIM derivatives as well as updated NMR spectra for the main product.ConclusionThis study reveals the genetic control of biosynthesis of LIM that remained hidden for the last 70 years. This, in turn, opens the door to biological routes towards overproduction of LIM as well as generation of its derivatives.

Trophectoderm-specific gene manipulation using adeno-associated viral vectors.

In mammals, blastocyst-stage trophectoderm (TE) contacts the maternal body at the time of implantation and forms the placenta after implantation, which supports the development of the fetus. Studying gene function in TE and placenta is important to understand normal implantation and pregnancy processes and their dysfunction. However, genetically modified mice are commonly generated by manipulating pronuclear-stage zygotes, which modify both the genome of the fetus and the placenta. Therefore, we previously developed TE/placenta-specific gene expression technology by transducing blastocysts with lentiviral vectors. However, the zona pellucida (ZP) needed to be removed before transduction. In this study, we examined various adeno-associated viral (AAV) vectors to develop a new TE/placenta-specific gene transduction method. As AAV1 can path through ZP, we succeeded in trophoblast-specific gene expression without ZP removal. Furthermore, TE cells genetically modified by AAV1-Cre contributed uniformly to the placenta. Our new technology contributes to advances in implantation and placenta research and leads to the development of new assisted reproductive technology.

The landscape of immunogenic cell death-related genes predicts the overall survival and immune infiltration status of non-small-cell lung carcinoma.

Non-small cell lung cancer (NSCLC), which accounts for about 85% of all lung cancers, currently exhibits insensitivity to most treatment regimens. Therefore, the identification of new and effective biomarkers for NSCLC is crucial for the development of treatment strategies. Immunogenic cell death (ICD), a form of regulated cell death capable of activating adaptive immune responses and generating long-term immune memory, holds promise for enhancing anti-tumor immunity and offering promising prospects for immunotherapy strategies in NSCLC. Clinical information and expressive profiles of NSCLC genes were retrieved from the GEO and TCGA databases. By combining these databases, the researchers were able to identify the appropriate genes for use in forecasting outcomes of patients with this type of cancer. We further performed functional enrichment, gene variants and immune privilege correlation analysis to determine the underlying mechanisms. This was followed by univariate and multivariate Cox regression and LASSO regression analyses, we developed a prognostic risk model based on the TCGA cohort, which included 17 gene labels. The results of the external validation were then used to identify the appropriate genes for use in predicting the survival outcome of patients with this type of cancer. In addition, a nomogram was created to help visualise the clinical presentation of the patients. For the analyses, we performed 50 functional and immunoinfiltration assessments for two risk groups. Using 17 genes (AIRE, APOH, CDKN2A, CEACAM4, COL4A3, CPA, DBH, F10, FCGRB, FGFR4, MMP1, PGLYRP1, SCGB2A2, SLC9A3, UGT2B17 and VIP), The researchers then created a gene signature that could be used to identify patients with an increased risk of contracting cancer. They divided the patients into two groups based on their risk score. The low-risk group exhibited a better prognosis (P<0.01). The survival curve demonstrated that ICD-related models could accurately predict patient prognosis. Conversely, high-risk subgroups were closely associated with immune-related signaling pathways. The analysis of immune infiltration also showed that the infiltration levels of most immune cells were higher in the high risk sub-group than in the low risk sub-group. In comparison to the low-risk group, the high-risk group was more susceptible to the immune-checkpoint blockade (ICB) treatment. Our researchers utilized a gene model to analyze the immune inflammation and prognosis of patients with non-small-cell lung cancer (NSCLC). The discovery of new ICD-related genes could lead to the development of new targeted treatments for this condition.

Exploring stress hormone effects on memory specificity and strength in mice using the dual-event inhibitory avoidance task.

Stressful and emotionally arousing experiences induce the release of noradrenergic and glucocorticoid hormones that synergistically strengthen memories but differentially regulate qualitative aspects of memory. This highlights the need for sophisticated behavioral tasks that allow for the assessment of memory quality. The dual-event inhibitory avoidance task for rats is such a behavioral task designed to evaluate both the strength and specificity of memory. The noradrenergic stimulant yohimbine given systemically immediately after the training session was found to enhance both the strength and specificity of memory, whereas the glucocorticoid corticosterone induced a generalized strengthening of memory. As mice are the preferred species for targeted gene and neural circuit manipulations, we here aimed to set up the dual-event inhibitory avoidance task for mice, and to replicate the effects of systemic yohimbine and corticosterone administration on memory strength and specificity. Whereas noninjected control mice efficiently acquired the task and selectively avoided the test context previously associated with footshock, the introduction of posttraining intraperitoneal injections induced testing order effects and substantially increased variability both within groups and across experiments, precluding a thorough investigation of stress hormone effects on memory specificity. Thus, whereas the dual-event inhibitory avoidance task can be used to test the specificity of memory in mice, our findings indicate that intraperitoneal injections impact performance. Therefore, this task is less suitable to assess stress hormone effects on memory specificity in mice.

Nano-assisted delivery tools for plant genetic engineering: a review on recent developments.

Conventional approaches like Agrobacterium-mediated transformation, viral transduction, biolistic particle bombardment, and polyethylene glycol (PEG)-facilitated delivery methods have been optimized for transporting specific genes to various plant cells. These conventional approaches in genetically modified crops are dependent on several factors like plant types, cell types, and genotype requirements, as well as numerous disadvantages such as time-consuming, untargeted distribution of genes, and high cost of cultivation. Therefore, it is suggested to develop novel techniques for the transportation of genes in crop plants using tailored nanoparticles (NPs) of manipulative and controlled high-performance features synthesized using green and chemical routes. It is observed that site-specific delivery of genes exhibits high efficacy in species-independent circumstances which leads to an increased level of productivity. Therefore, to achieve these outcomes, NPs can be utilized as gene nano-carriers for excellent delivery inside crops (i.e., cotton, tobacco, rice, wheat, okra, and maize) for desired genetic engineering modifications. As outcomes, this review provides an outline of the conventional techniques and current application of numerous nano-enabled gene delivery needed for crop gene manipulation, the benefits, and drawbacks associated with state-of-the-art techniques, which serve as a roadmap for the possible applicability of nanomaterials in plant genomic engineering as well as crop improvement in the future.

All Roads Lead to Rome: Pathways to Engineering Disease Resistance in Plants.

Unlike animals, plants are unable to move and lack specialized immune cells and circulating antibodies. As a result, they are always threatened by a large number of microbial pathogens and harmful pests that can significantly reduce crop yield worldwide. Therefore, the development of new strategies to control them is essential to mitigate the increasing risk of crops lost to plant diseases. Recent developments in genetic engineering, including efficient gene manipulation and transformation methods, gene editing and synthetic biology, coupled with the understanding of microbial pathogenicity and plant immunity, both at molecular and genomic levels, have enhanced the capabilities to develop disease resistance in plants. This review comprehensively explains the fundamental mechanisms underlying the tug-of-war between pathogens and hosts, and provides a detailed overview of different strategies for developing disease resistance in plants. Additionally, it provides a summary of the potential genes that can be employed in resistance breeding for key crops to combat a wide range of potential pathogens and pests, including fungi, oomycetes, bacteria, viruses, nematodes, and insects. Furthermore, this review addresses the limitations associated with these strategies and their possible solutions. Finally, it discusses the future perspectives for producing plants with durable and broad-spectrum disease resistance.

METTL4-Mediated Mitochondrial DNA N6-Methyldeoxyadenosine Promoting Macrophage Inflammation and Atherosclerosis.

Mitochondrial dysfunction is a key factor in the development of atherogenesis. METTL4 (methyltransferase-like protein 4) mediates N6- methyldeoxyadenosine (6mA) of mammalian mitochondrial DNA (mtDNA). However, the role of METTL4-mediated mitoepigenetic regulation in atherosclerosis is still unknown. This study aims to investigate the potential involvement of METTL4 in atherosclerosis, explore the underlying mechanism, and develop targeted strategies for treating atherosclerosis. Expression levels of mtDNA 6mA and METTL4 were determined in atherosclerotic lesions. We explored the mechanism of METTL4 involvement in atherosclerosis using Mettl4Mac-KO-Apoe-/- and Mettl4MUT-Apoe-/- mice and cell models, as well as bone marrow transplantation. Natural compound libraries were screened to identify potent METTL4 antagonists. In addition, bioinspired proteolysis targeting chimera technology targeting macrophages within plaques was used to increase the efficacy of the METTL4 antagonist. The expression levels of mtDNA 6mA and METTL4 were significantly increased in plaque macrophages. Mettl4Mac-KO-Apoe-/- mice displayed suppressed mtDNA 6mA levels and atherosclerotic progression, which were reversed by METTL4 restoration through bone marrow transplantation (n=6). Mechanistically, elevated METTL4 expression reduces MT-ATP6 expression by suppressing its transcription, thereby impairing the activity of mitochondrial respiration chain complex V. This disruption leads to the accumulation of excess protons in the mitochondrial intermembrane space, causing mitochondrial dysfunction. Consequently, mtDNA is released into the cytoplasm, ultimately triggering inflammasome activation. All results were reversed by the mutation in the METTL4 methyltransferase active site. Mettl4MUT-Apoe-/- mice showed suppressed mtDNA 6mA levels and atherosclerotic progression and repaired mitochondrial function of macrophage, which were reversed by METTL4 restoration through bone marrow transplantation (n=6). Pemetrexed was identified as the first METTL4 antagonist to effectively alleviate atherosclerotic progression. Furthermore, we generated a proteolysis targeting chimera drug based on pemetrexed that specifically targeted METTL4 in macrophages within plaques, showing a promising therapeutic effect on atherosclerosis. This study revealed a novel mechanism by which mtDNA 6mA orchestrated mitochondrial function-related gene expression in macrophages, thereby promoting atherosclerosis. Through various experimental techniques, such as gene manipulation, pharmacological inhibition, and proteolysis targeting chimera, this study demonstrated that mtDNA 6mA and its specific enzyme METTL4 hold potential as therapeutic targets for atherosclerosis.

SerpinB1 targeting safeguards against pathological cardiac hypertrophy and remodelling by suppressing cardiomyocyte pyroptosis and inflammation initiation.

While the pivotal role of inflammation in pathological cardiac hypertrophy and remodelling is widely acknowledged, the mechanisms triggering inflammation initiation remain largely obscure. This study aims to elucidate the role and mechanism of serpin family B member 1 (SerpinB1) in pro-inflammatory cardiomyocyte pyroptosis, heart inflammation, and cardiac remodelling. C57BL/6J wild-type, inducible cardiac-specific SerpinB1 overexpression or knockout mice underwent transverse aortic constriction (TAC) surgery. Cardiac hypertrophy and remodelling were assessed through echocardiography and histology. Cardiomyocyte pyroptosis and heart inflammation were monitored. Adeno-associated virus 9 -mediated gene manipulations and molecular assays were employed to explore the mechanisms through which SerpinB1 regulates cardiomyocyte pyroptosis and heart inflammation. Finally, recombinant mouse SerpinB1 protein (rSerpinB1) was administrated both in vivo through osmotic minipump delivery and in vitro to investigate the therapeutic potential of SerpinB1 in cardiac remodelling. Myocardial SerpinB1 overexpression was up-regulated shortly upon TAC or phenylephrine challenge, with no further elevation during prolonged hypertrophic stimuli. It is important to note that cardiac-specific overexpression of SerpinB1 markedly attenuated TAC-induced cardiac remodelling, while deletion of SerpinB1 exacerbated it. At the mechanistic level, SerpinB1 gain-of-function inhibited cardiomyocyte pyroptosis and inflammation in hypertrophic hearts; the protective effect was nullified by overexpression of either cleaved N-terminal gasdermin D or cleaved caspase-1. Co-immunoprecipitation and confocal assays confirmed that SerpinB1 directly interacts with caspase-1 in cardiomyocytes. Remarkably, rSerpinB1 replicated the cardioprotective effect against cardiac hypertrophy and remodelling. SerpinB1 safeguards against pathological cardiac hypertrophy and remodelling by impeding cardiomyocyte pyroptosis to suppress inflammation initiation, achieved through interaction with caspase-1 to inhibit its activation. Targeting SerpinB1 could represent a novel therapeutic strategy for treating pathological cardiac hypertrophy and remodelling.

A Chemical Reprogramming Approach Efficiently Producing Human Retinal Pigment Epithelium Cells for Retinal Disease Therapies.

Human induced pluripotent stem cells (hiPSCs) represent a promising cell source for generating functional cells suitable for clinical therapeutic applications, particularly in the context of autologous cell therapies. However, the production of hiPSCs through genetic manipulation, especially involving oncogenes, may raise safety concerns. Furthermore, the complexity and high costs associated with hiPSCs generation have hindered their broad clinical use. In this study, we utilised a recently developed chemical reprogramming method in conjunction with a guided differentiation protocol, introducing a chemically defined strategy for generating functional human retinal pigment epithelium (RPE) cells from adipose tissue, bypassing conventional hiPSCs generation challenges. By utilising small molecule-based chemical cocktails, we reprogrammed somatic adipose cells into human chemically induced pluripotent stem cells (hCiPSCs) in a safer and more streamlined manner, entirely free from gene manipulation. Subsequent differentiation of hCiPSCs into functional RPE cells demonstrated their capability for secretion and phagocytosis, emphasising their vital role in maintaining retinal homeostasis and underscoring their therapeutic potential. Our findings highlight the transformative potential of hCiPSCs as a safer, more efficient option for personalised cell therapies, with applications extending beyond ocular disease to a wide range of medical conditions.

Establishment of Nile Tilapia Primary Cell Culture Methods and In Vitro Cell Knockdown Techniques.

As an important aquaculture species and research model, Nile tilapia (Oreochromis niloticus) has not yet been systematically studied for the isolation, culture, and in vitro gene manipulation techniques of primary cells from various tissues. This study aimed to explore methods for isolating primary cells from various tissues, as well as developing in vitro gene manipulation techniques in Nile tilapia. Four different Nile tilapia tissues were enzymatically digested and separated using trypsin or collagenase. Collagenase (0.1%) was used for the digestion of the gonads, liver, and heart, while trypsin (0.25%) showed better adhesion efficiency for spleen tissue. Moreover, we assessed EGFP fluorescence intensity and cell survival rates following transfection with empty siRNA (siRNA-NC), lentivirus (LV-NC), and six adeno-associated virus (AAV-NC) serotypes (AAV2-NC, AAV5-NC, AAV6-NC, AAV8-NC, AAV9-NC, AAV-DJ-NC) in gonadal cells. The results demonstrated that cells transfected with siRNA-NC and LV-NC showed the highest levels of green fluorescent protein expression and survival rates in primary gonadal cells, compared to AAC-NC. Subsequently, we knocked down the Kdm6bb gene in Nile tilapia primary gonadal cells by transfecting them with LV-Kdm6bb and siRNA-Kdm6bb. qPCR and immunofluorescence analyses demonstrated a significant reduction in Kdm6bb mRNA levels following transfection with siRNA-Kdm6bb compared to siRNA-NC, and with LV-Kdm6bb compared to LV-NC. This study offers valuable tools for the validation of primary cell isolation and in vitro molecular regulatory mechanisms and functions in Nile tilapia.

Microtubule-Rab5 mutual-influential system screening based on gene-regulatory networks map in Rab5 RNAi eye-degeneration model

Rabs are involved in neuronal development and protrusion formation. Existing studies support the notion that manipulation or mutation of Rab genes could lead to functional changes in neurons. However, whether Rabs gene-manipulation induced Drosophila eye-degeneration remains unknown. By down-regulating Rab5, but not Rab7, we first constructed a compound eye injury model in Drosophila. As the distribution, content, and even maturation of Rab5-positive endosomes are influenced by cytoskeletal proteins, like actin or tubulin-related proteins, the existence of a bidirectional regulatory relationship between Rab5 and the cytoskeleton remains unclear and worth researching. Through complete transcriptome sequencing combined immunofluorescence testing, we confirmed that down-regulation of Rab5 affected the increase of α-Tub84B (alternatively named TubA84B) but not γ-tubulin. Based on Weighted Gene Co-Expression Network Analysis (WGCNA) and multi-tissue screening verification, this study proposes that the apoptosis-related factors–Rab5–TubA84B have conserved regulatory functions with cooperative expression. Gene manipulation confirmed that apoptotic factors, especially rpr, strongly regulate Rab5, and may ultimately influence microtubule structure through complex routes, including the Rab5 variance and the intracellular configuration ratio of α-Tubulin to Glyceraldehyde-3-phosphate dehydrogenase.

Identifying specific functional roles for senescence across cell types.

Cellular senescence plays critical roles in aging, regeneration, and disease; yet, the ability to discern its contributions across various cell types to these biological processes remains limited. In this study, we generated an invivo genetic toolbox consisting of three p16Ink4a-related intersectional genetic systems, enabling pulse-chase tracing (Sn-pTracer), Cre-based tracing and ablation (Sn-cTracer), and gene manipulation combined with tracing (Sn-gTracer) of defined p16Ink4a+ cell types. Using liver injury and repair as an example, we found that macrophages and endothelial cells (ECs) represent distinct senescent cell populations with different fates and functions during liver fibrosis and repair. Notably, clearance of p16Ink4a+ macrophages significantly mitigates hepatocellular damage, whereas eliminating p16Ink4a+ ECs aggravates liver injury. Additionally, targeted reprogramming of p16Ink4a+ ECs through Kdr overexpression markedly reduces liver fibrosis. This study illuminates the functional diversity of p16Ink4a+ cells and offers insights for developing cell-type-specific senolytic therapies in the future.

Population dynamics of engineered microbes under metabolic stress and reward in batch and continuous reactors

Metabolic engineering involves the manipulation of multiple genes from different sources to produce desired compounds. Engineered cells typically suffer from metabolic effects associated with product accumulation resulting in abortive production phenotype or strain degeneration. The revertant cells post a major barrier for repetitive or continuous culture, lowering both productivity and cost-efficiency of large-scale fermentation. Herein we formulated a set of kinetic models to reveal the population dynamics of strain degeneration in batch and continuous culture. By introducing a dimensionless metabolic coupling coefficient, we analyzed the effects of metabolic stress and reward on strain performance. Only limited metabolic coupling effect was found in batch culture, nevertheless, metabolic reward can significantly enrich the productive population and alleviates strain degeneration in repetitive batch culture. In continuous bioreactors, metabolic coupling strength and dilution rate synergistically dictate the productive and abortive strain population. The region where productive population is dominant is characterized by a critical metabolic coupling coefficient and tipping dilution rate. We identified a metabolic-reward mediated positive feedback loop with bistability and hysteresis behavior which allows the productive cell outcompetes the abortive population, even under strong competitive exclusion. Our results emphasize the theoretical basis to engineer product-rewarded growth to suppress mutation and stabilize long-term strain performance, which should be adopted as a general guideline to deploy strain engineering strategies.

ScGO: interpretable deep neural network for cell status annotation and disease diagnosis.

Machine learning has emerged as a transformative tool for elucidating cellular heterogeneity in single-cell RNA sequencing. However, a significant challenge lies in the "black box" nature of deep learning models, which obscures the decision-making process and limits interpretability in cell status annotation. In this study, we introduced scGO, a Gene Ontology (GO)-inspired deep learning framework designed to provide interpretable cell status annotation for scRNA-seq data. scGO employs sparse neural networks to leverage the intrinsic biological relationships among genes, transcription factors, and GO terms, significantly augmenting interpretability and reducing computational cost. scGO outperforms state-of-the-art methods in the precise characterization of cell subtypes across diverse datasets. Our extensive experimentation across a spectrum of scRNA-seq datasets underscored the remarkable efficacy of scGO in disease diagnosis, prediction of developmental stages, and evaluation of disease severity and cellular senescence status. Furthermore, we incorporated in silico individual gene manipulations into the scGO model, introducing an additional layer for discovering therapeutic targets. Our results provide an interpretable model for accurately annotating cell status, capturing latent biological knowledge, and informing clinical practice.