Intracellular Gene Research Articles

Olig2-enriched exosomes: A novel therapeutic approach for cuprizone-induced demyelination

The research aims to study the therapeutic impact of HEK293-XPack-Olig2 cell-derived exosomes on remyelination of the corpus callosum in a cuprizone-induced demyelinating disease model. A lentiviral vector expressing Olig2 was constructed using XPack technology. The highly abundant Olig2 exosomes (ExoOs) were isolated by centrifugation for subsequent experiments. Western blot, nanoparticle tracking analysis (NTA), and electron microscopy showed no significant difference in particle size and morphology between Exos and ExoOs, and a high level of Olig2 expression could be detected in ExoOs, indicating that exosome modification by XPack technology was successful. The Black Gold/Fluromyelin staining analysis showed that the ExoOs group significantly reduced the demyelination area in the corpus callosum compared to the PBS and Exos groups. Additionally, the PDGFRα/APC staining of the demyelinating region revealed an increase in APC+ oligodendrocytes and a decrease in PDGFRα+ oligodendrocyte progenitor cells (OPCs) in the ExoOs group. Furthermore, there was evident myelin regeneration in the demyelinated areas after ExoOs treatment, with better g-ratio and a higher number of intact myelin compared to the other treatment groups. The level of Sox10 expression in the brain tissue of the ExoOs group were higher compared to those of the PBS and Exos groups. The demyelination process can be significantly slowed down by the XPack-modified exosomes, the differentiation of OPCs promoted, and myelin regeneration accelerated under pathological conditions. This process is presumed to be achieved by changing the expression level of intracellular differentiation-related genes after exosomes transport Olig2 enriched into oligodendrocyte progenitors.

Melatonin as a Circadian Marker for Plasmodium Rhythms.

Plasmodium, a digenetic parasite, requires a host and a vector for its life cycle completion. Most Plasmodium species display circadian rhythmicity during their intraerythrocytic cycle within the host, aiding in immune evasion. This rhythmicity, however, diminishes in in vitro cultures, highlighting the importance of host-derived signals for synchronizing the parasite's asexual cycle. Studies indicate a species-specific internal clock in Plasmodium, dependent on these host signals. Melatonin, a hormone the pineal gland produces under circadian regulation, impacts various physiological functions and is extensively reviewed as the primary circadian marker affecting parasite rhythms. Research suggests that melatonin facilitates synchronization through the PLC-IP3 signaling pathway, activating phospholipase C, which triggers intracellular calcium release and gene expression modulation. This evidence strongly supports the role of melatonin as a key circadian marker for parasite synchronization, presenting new possibilities for targeting the melatonin pathway when developing novel therapeutic approaches.

Effects of polyvinyl chloride microplastics and benzylalkyldimethylethyl compounds on system performance, microbial community and resistance genes in sulfur autotrophic denitrification system

Benzylalkyldimethylethyl ammonium compounds (BAC) and polyvinyl chloride microplastics (PVC MPs), as the frequently detected pollutants in wastewater treatment plants (WWTPs), have attracted more concerns on their ecosystem risks. Therefore, this study investigated how the sulfur autotrophic denitrification (SAD) system responded to the single and joint stress of PVC MPs (1, 10 and 100 mg/L) and BAC (0.5, 5 and 10 mg/L). After 100 days of operation, the presence of 10 mg/L BAC led to obviously inhibitory effects on system performance and microbial metabolic activity. And the additions of PVC MPs or/and BAC stimulated the proliferation of intracellular resistance genes (RGs), whereas exposure to BAC increased the abundances of extracellular RGs and free RGs in water more significantly. Compared to the joint stress, BAC single stress resulted in higher abundances of free RGs in water, which further increased the risk of RGs propagation. Moreover, the interaction between mobile genetic elements and extracellular polymeric substances further increased the spread of RGs. Pathogens might be the potential hosts of RGs and enriched in SAD system and plastisphere, thereby leading to more serious ecological risks. This study will broaden the understanding of the environmental hazards posed by PVC MPs and BAC in WWTPs.

Graph attention network with convolutional layer for predicting gene regulations from single-cell ribonucleic acid sequence data

Reconstructing gene regulatory networks (GRNs) is an important task to reveal the regulatory relationship between genes and understand the mechanism of intracellular gene expression regulation. With the development of single-cell ribonucleic acid sequencing (scRNA-seq) technology, researchers begin to attempt to infer GRN within cells. In this paper, we propose graph attention network with convolutional layer (GATCL) to infer the latent interactions between transcription factors (TFs) and target genes in GRN. Firstly, GATCL uses graph attention network (GAT), which can effectively extract information about genes and TFs. Secondly, we combine multi-head attention layer with one-head attention layer and propose a new method of using convolution instead of weight matrix. Thirdly, we use the exponential linear unit (ELU) activation function to replace the leaky rectified linear unit (LReLU) commonly used in GAT, which further improves the accuracy of GATCL. The AUROC of our method on seven scRNA-seq datasets with four types of ground-truth networks reached an average of 0.827, which is higher than other state-of-the-art models. GATCL applies a supervised deep learning algorithm to solve the problems existing in the inference of GRN from scRNA-seq in the engineering field, and the effectiveness of this method is verified by a large number of experiments.

Glutamine enhances pneumococcal growth under methionine semi-starvation by elevating intracellular pH.

Bacteria frequently encounter nutrient limitation in nature. The ability of living in this nutrient shortage environment is vital for bacteria to preserve their population and important for some pathogenic bacteria to cause infectious diseases. Usually, we study how bacteria survive after nutrient depletion, a total starvation condition when bacteria almost cease growth and try to survive. However, nutrient limitation may not always lead to total starvation. Bacterial adaptation to nutrient shortage was studied by determining bacterial growth curves, intracellular pH, intracellular amino acid contents, gene transcription, protein expression, enzyme activity, and translation and replication activities. No exogenous supply of methionine results in growth attenuation of Streptococcus pneumoniae, a human pathogen. In this paper, we refer to this inhibited growth state between ceased growth under total starvation and full-speed growth with full nutrients as semi-starvation. Similar to total starvation, methionine semi-starvation also leads to intracellular acidification. Surprisingly, it is intracellular acidification but not insufficient methionine synthesis that causes growth attenuation under methionine semi-starvation. With excessive glutamine supply in the medium, intracellular methionine level was not changed, while bacterial intracellular pH was elevated to ~ 7.6 (the optimal intracellular pH for pneumococcal growth) by glutamine deamination, and bacterial growth under semi-starvation was restored fully. Our data suggest that intracellular acidification decreases translation level and glutamine supply increases intracellular pH to restore translation level, thus restoring bacterial growth. This growth with intracellular pH adjustment by glutamine is a novel strategy we found for bacterial adaptation to nutrient shortage, which may provide new drug targets to inhibit growth of pathogenic bacteria under semi-starvation.

Investigating Intracellular Signaling Pathway and Telomerase Gene Expression in Nonsmall Cell Lung Cancer Treated with miR-302/367

Investigating Intracellular Signaling Pathway and Telomerase Gene Expression in Nonsmall Cell Lung Cancer Treated with miR-302/367

Unraveling the complex evolutionary features of the Cinnamomum camphora mitochondrial genome.

We reported the mitochondrial genome of Cinnamomum camphora for the first time, revealing frequent rearrangement events in the non-coding regions of Magnoliids mitochondrial genomes. As one of the representative species in the Lauraceae family of Magnoliids, Cinnamomum camphora holds significant economic and ecological value. In this study, the mitochondrial genome (mitogenome) of C. camphora was complete assembled and annotated using PacBio HiFi sequencing. The C. camphora mitogenome is characterized by a branch structure, spans 900,894 bp, and contains 43 protein-coding genes (PCGs), 24 tRNAs, and 3 rRNAs. Most of these PCGs are under purifying selection, with only two (ccmFc and rps7) exhibiting signs of positive selection. The C. camphora mitogenome contains numerous repetitive sequences and intracellular gene transfers, with a total of 36 mitochondrial plastid DNAs, amounting to a combined length of 23,816 bp. Comparative analysis revealed that the non-coding regions of Magnoliids mitogenomes have undergone frequent rearrangements during evolution, but the coding sequences remain highly conserved (more than 98% similarity for protein-coding sequences). Furthermore, a maximum-likelihood phylogenetic tree was reconstructed based on 25 PCGs from 23 plant mitogenomes. The analysis supports the closest relationship between C. camphora and C. chekiangense, consistent with the APG IV classification system. This study elucidates the unique evolutionary features of the C. camphora mitogenome, which will provide valuable insights into the study of genetics and evolution of the family Lauraceae.

VmRDR2 of Valsa mali mediates the generation of VmR2-siR1 that suppresses apple resistance by RNA interference.

Cross-kingdom RNA interference (RNAi) is a crucial mechanism in host-pathogen interactions, with RNA-dependent RNA polymerase (RdRP) playing a vital role in signal amplification during RNAi. However, the role of pathogenic fungal RdRP in siRNAs generation and the regulation of plant-pathogen interactions remains elusive. Using deep sequencing, molecular, genetic, and biochemical approaches, this study revealed that VmRDR2 of Valsa mali regulates VmR2-siR1 to suppress the disease resistance-related gene MdLRP14 in apple. Both VmRDR1 and VmRDR2 are essential for the pathogenicity of V. mali in apple, with VmRDR2 mediating the generation of endogenous siRNAs, including an infection-related siRNA, VmR2-siR1. This siRNA specifically degrades the apple intracellular LRR-RI protein gene MdLRP14 in a sequence-specific manner, and overexpression of MdLRP14 enhances apple resistance against V. mali, which can be suppressed by VmR2-siR1. Conversely, MdLRP14 knockdown reduces resistance. In summary, this study demonstrates that VmRDR2 contributes to the generation of VmR2-siR1, which silences the host's intracellular LRR protein gene, thereby inhibiting host resistance. These findings offer novel insights into the fungi-mediated pathogenicity mechanism through RNAi.

Removal of intracellular and extracellular antibiotic resistance genes and virulence factor genes using electricity-intensified constructed wetlands

Constructed wetland (CW) is considered a promising technology for the removal of emerging contaminants. However, its removal performance for antibiotic resistance genes (ARGs) is not efficient and influence of virulence factor genes (VFGs) have not been elucidated. Here, removal of intracellular and extracellular ARGs as well as VFGs by electricity-intensified CWs was comprehensively evaluated. The two electrolysis-intensified CWs can improve the removal of intracellular ARGs and MGEs to 0.96- and 0.85-logs, respectively. But cell-free extracellular ARGs (CF-eARGs) were significantly enriched with 1.8-logs in the electrolysis-intensified CW. Interestingly, adding Fe-C microelectrolysis to the electrolysis-intensified CW is conducive to the reduction of CF-eARGs. However, the detected number and relative abundances of intracellular and extracellular VFGs were increased in all of the three CWs. The biofilms attached onto the substrates and rhizosphere are also hotspots of both intracellular and particle-associated extracellular ARGs and VFGs. Structural equation models and correlation analysis indicated that ARGs and VFGs were significantly cooccurred, suggesting that VFGs may affect the dynamics of ARGs. The phenotypes of VFGs, such as biofilm, may act as protective matrix for ARGs, hindering the removal of resistance genes. Our results provide novel insights into the ecological remediation technologies to enhance the removal of ARGs.

A Hybrid Nanotube Stamp System in Intracellular Protein Delivery for Cancer Treatment and NMR Analytical Techniques.

In contrast to intracellular gene transfer, the direct delivery of expressed proteins is a significantly challenging yet essential technique for elucidating cellular functions, including protein complex structure, liquid-liquid phase separation, therapeutic applications, and reprogramming. In this study, we developed a hybrid nanotube (HyNT) stamp system that physically inserts the HyNTs into adhesive cells, enabling the injection of target molecules through HyNT ducts. This system demonstrates the capability to deliver multiple proteins, such as lactate oxidase (LOx) and ubiquitin (UQ), to approximately 1.8 × 107 adhesive cells with a delivery efficiency of 89.9% and a viability of 97.1%. The delivery of LOx enzyme into HeLa cancer cells induced cell death, while enzyme-delivered healthy cells remained viable. Furthermore, our stamp system can deliver an isotope-labeled UQ into adhesive cells for detection by nuclear magnetic resonance (NMR).

Characterizing dysregulations via cell-cell communications in Alzheimer’s brains using single-cell transcriptomes

BackgroundAlzheimer’s disease (AD) is a devastating neurodegenerative disorder affecting 44 million people worldwide, leading to cognitive decline, memory loss, and significant impairment in daily functioning. The recent single-cell sequencing technology has revolutionized genetic and genomic resolution by enabling scientists to explore the diversity of gene expression patterns at the finest resolution. Most existing studies have solely focused on molecular perturbations within each cell, but cells live in microenvironments rather than in isolated entities. Here, we leveraged the large-scale and publicly available single-nucleus RNA sequencing in the human prefrontal cortex to investigate cell-to-cell communication in healthy brains and their perturbations in AD. We uniformly processed the snRNA-seq with strict QCs and labeled canonical cell types consistent with the definitions from the BRAIN Initiative Cell Census Network. From ligand and receptor gene expression, we built a high-confidence cell-to-cell communication network to investigate signaling differences between AD and healthy brains.ResultsSpecifically, we first performed broad communication pattern analyses to highlight that biologically related cell types in normal brains rely on largely overlapping signaling networks and that the AD brain exhibits the irregular inter-mixing of cell types and signaling pathways. Secondly, we performed a more focused cell-type-centric analysis and found that excitatory neurons in AD have significantly increased their communications to inhibitory neurons, while inhibitory neurons and other non-neuronal cells globally decreased theirs to all cells. Then, we delved deeper with a signaling-centric view, showing that canonical signaling pathways CSF, TGFβ, and CX3C are significantly dysregulated in their signaling to the cell type microglia/PVM and from endothelial to neuronal cells for the WNT pathway. Finally, after extracting 23 known AD risk genes, our intracellular communication analysis revealed a strong connection of extracellular ligand genes APP, APOE, and PSEN1 to intracellular AD risk genes TREM2, ABCA1, and APP in the communication from astrocytes and microglia to neurons.ConclusionsIn summary, with the novel advances in single-cell sequencing technologies, we show that cellular signaling is regulated in a cell-type-specific manner and that improper regulation of extracellular signaling genes is linked to intracellular risk genes, giving the mechanistic intra- and inter-cellular picture of AD.

Posttraumatic stress disorder is characterized by functional dysregulation of dermal fibroblasts

Incidence of mental health disorders are rising in modernity, with psychological stress linked to a propensity for developing various chronic diseases due to a relative inability of the body to counter the allostatic load on cellular level. Despite these high rates of comorbidities associated with posttraumatic stress disorder (PTSD), there is still a lack of understanding in terms of the peripheral effects of PTSD on tissue level. Therefore, the purpose of this study was to profile basal dermal fibroblast functional status in PTSD using a wide range of markers involved in the cell-to-cell communication facilitated by fibroblasts. Primary dermal fibroblasts derived from patients diagnosed with PTSD (n = 11) and matched trauma exposed controls (i.e. who did not develop PTSD, n = 10) were cultured using standard techniques. The patients and controls were matched based on age, sex, body-mass index (BMI) and lifestyle. The growth rate, population doubling time, cell surface marker expression (CD31, FNDC5) (flow cytometry), secretome (TIMP-2, MMP-9) (ELISAs), intracellular signalling capacity (Fluo-4 Ca2+ flux) and gene expression (IL-6, IL-10, PTX-3, iNOS, Arg1) were compared between groups. The data illustrated significant PTSD-associated fibroblast conditioning resulting in a blunted signalling capacity. This observation highlights the importance of including tissue-specific investigations in future studies focused on elucidating the association between PTSD and subsequent risk for somatic disease.

The correlation between fecal microbiota profiles and intracellular junction genes expression in young Iranian patients with celiac disease

ABSTRACT Celiac disease (CD) is characterized by the disruption of the intestinal barrier integrity and alterations in the microbiota composition. This study aimed to evaluate the changes in the fecal microbiota profile and mRNA expressions of intracellular junction-related genes in pediatric patients with CD compared to healthy controls (HCs). Thirty treated CD patients, 10 active CD, and 40 HCs were recruited. Peripheral blood (PB) and fecal samples were collected. Microbiota analysis was performed using quantitative real-time PCR (qPCR) test. The mRNA expressions of ZO-1, occludin, β-catenin, E-cadherin, and COX-2 were also evaluated. In active and treated CD patients, the PB expression levels of ZO-1 (p = 0.04 and 0.002, respectively) and β-catenin (p = 0.006 and 0.02, respectively) were lower than in HCs. PB Occludin’s level was upregulated in both active and treated CD patients compared to HCs (p = 0.04 and 0.02, respectively). However, PB E-cadherin and COX-2 expression levels and fecal mRNA expressions of ZO-1, occludin, and COX-2 did not differ significantly between cases and HCs (P˃0.05). Active CD patients had a higher relative abundance of the Firmicutes (p = 0.04) and Actinobacteria (p = 0.03) phyla compared to treated subjects. The relative abundance of Veillonella (p = 0.04) and Staphylococcus (p = 0.01) genera was lower in active patients in comparison to HCs. Researchers should explore the precise impact of the gut microbiome on the molecules and mechanisms involved in intestinal damage of CD. Special attention should be given to Bifidobacteria and Enterobacteriaceae, as they have shown a significant correlation with the expression of tight junction-related genes.

Removal of intracellular antibiotic resistance genes by activating peroxymonosulfate with Co3O4@CNT catalytic membrane

The removal of antibiotic resistance genes (ARGs) is crucial to prevent the proliferation of antibiotic resistance. In this study, we successfully removed intracellular ARGs using the PMS/Co@CM system, which involved activating peroxymonosulfate (PMS) with a catalytic membrane composed of Co3O4 and carbon nanotubes. In the PMS/Co@CM system, 1O2 was the primary reactive oxygen species (ROS) responsible for intracellular ARGs removal. However, the presence of sulfamethoxazole (SMX) in the water samples significantly reduced the efficiency of removing intracellular ARGs in the PMS/Co@CM system although SMX was degraded by •SO4−. This can be attributed to the selective pressure of SMX, which elevated intracellular Superoxide Dismutase (SOD) levels while decreasing Propidium Iodide (PI) levels in cells. Consequently, this led to heightened antioxidant defense and reduced membrane permeability, thereby enhancing cell resistance to 1O2 generated by the PMS/Co@CM system. Encouragingly, a typical UV disinfection process facilitated the removal of residual intracellular ARGs in the effluent of the PMS/Co@CM system, attributed to decreased SOD levels and increased intracellular 1O2 by UV irradiation. These findings contribute to the theoretical understanding of effective ARGs removal and aid in the development of more efficient removal technologies.

The combination of ciprofloxacin and dialkyldimethyl ammonium compound synergistically proliferated intracellular resistance genes in nitrifying system

Antibiotics and quaternary ammonium compounds (QACs) usually co-exist in wastewater treatment plants. Hence, three sequencing batch reactors were established and named as R1, R2 and R3, to investigate the effects of individual and combined exposure of different concentrations of ciprofloxacin (CIP) (0.2, 1.0 and 2.0 mg/L) and dialkyldimethyl ammonium compound (DADMAC) (0.4, 2.0 and 4.0 mg/L) on the performance, microbial community structures and resistance genes (RGs) in nitrifying system during 150 days. Results showed that CIP had a slight effect on ammonia oxidation activity, while 2.0 and 4.0 mg/L DADAMAC could obviously inhibit it, and the combination of CIP and DADMAC had a synergistic inhibitory effect. Besides, both CIP and DADMAC caused partial nitrification, and the order of nitrite accumulation rate was ranked as R3 > R2 > R1. The combination of CIP and DADMAC had an antagonistic effect on the increase of sludge particle size and α-Helix/(β-Sheet + Random coil) was lowest in R3 (0.40). The combination of CIP and DADMAC synergistically stimulated most intracellular RGs in sludge, and the relative abundances of target RGs (e.g., qacEdelta1-01, qacH-01 and qnrS) at the end of operation in R3 were increased by 4.61–18.19 folds compared with those in CK, which were 1.34–5.57 folds higher than the R1 and R2. Moreover, the combination of CIP and DADMAC also promoted the transfer of RGs from sludge to water and enriched more potential hosts of RGs, further promoting the spread of RGs in nitrifying system. Thus, the combined pollution of CIP and DADMAC in wastewaters should attract more attentions.

Response of nitrification system to co-exposure of sucralose and single or combined disinfectants: Reducing damage to nitrification performance and aggravating the spread of intracellular resistance genes

Sucralose (SUC) is an artificial sweetener for everyday consumption and often co-exists with disinfectants such as triclosan (TCS) and dialkyldimethyl ammonium compound (DAC) in sewage. Considering their continuous accumulation in sewage, it is essential to understand the impacts of their single and combined stress on the evolution of resistance genes (RGs) and microorganisms. In this study, three sequencing batch reactors (SBRs) were established, which were added with SUC, disinfectant, SUC and disinfectant, respectively, and named SSBR, DSBR and SDSBR in turn. There were four stages in total, the first two stages and the latter two stages were set to explore the effects of co-exposure of SUC and single disinfectant (TCS), SUC and combined disinfectants (TCS and DAC) on nitrification system, respectively. SSBR showed excellent ammonia oxidation performance in the whole operation stages. Compared with DSBR, the microorganisms in SDSBR under the combined stress of SUC and TCS were less inhibited. TCS and DAC destroyed the ammonia oxidation performance of DSBR and SDSBR. Within 120 days, the removal efficiency of TCS reached 90 %. In SSBR, 1 mg/L SUC promoted the proliferation of RGs, especially induced free RGs in water (w-RGs) to maintain high abundance and persistence. Compared with single stress, the abundances of intracellular RGs in sludge were higher under the combined stress of SUC and TCS, and the risk of RGs transmission was greater. The combined stress of SUC and disinfectants (TCS and DAC) led to a higher enrichment of w-RGs, exacerbating the risk of w-RGs transmission.

Intraocular mRNA delivery with endogenous MmPEG10-based virus-like particles

Virus-like particles (VLP) are a promising tool for intracellular gene delivery, yet their potential in ocular gene therapy remains underexplored. In this study, we bridged this knowledge gap by demonstrating the successful generation and application of vesicular stomatitis virus glycoprotein (VSVG)-pseudotyped mouse PEG10 (MmPEG10)-VLP for intraocular mRNA delivery. Our findings revealed that PEG10-VLP can efficiently deliver GFP mRNA to adult retinal pigment epithelial cell line-19 (ARPE-19) cells, leading to transient expression. Moreover, we showed that MmPEG10-VLP can transfer SMAD7 to inhibit epithelial-mesenchymal transition (EMT) in RPE cells effectively. In vivo experiments further substantiated the potential of these vectors, as subretinal delivery into adult mice resulted in efficient transduction of retinal pigment epithelial (RPE) cells and GFP reporter gene expression without significant immune response. However, intravitreal injection did not yield efficient ocular expression. We also evaluated the transduction characteristics of MmPEG10-VLP following intracameral delivery, revealing transient GFP protein expression in corneal endothelial cells without significant immunotoxicities. In summary, our study established that VSVG pseudotyped MmPEG10-based VLP can transduce mitotically inactive RPE cells and corneal endothelial cells in vivo without triggering an inflammatory response, underscoring their potential utility in ocular gene therapy.

Intracellular acidification and glycolysis modulate inflammatory pathway in senescent cells.

Senescent cells accumulate in various organs with ageing, and its accumulation induces chronic inflammation and age-related physiological dysfunctions. Several remodelling of intracellular environments have been identified in senescent cells, including enlargement of cell/nuclear size and intracellular acidification. Although these alterations of intracellular environments were reported to be involved in the unique characteristics of senescent cells, the contribution of intracellular acidification to senescence-associated cellular phenotypes is poorly understood. Here, we identified that the upregulation of TXNIP and its paralog ARRDC4 as a hallmark of intracellular acidification in addition to KGA-type GLS1. These genes were also upregulated in response to senescence-associated intracellular acidification. Neutralization of the intracellular acidic environment ameliorated not only senescence-related upregulation of TXNIP, ARRDC4 and KGA but also inflammation-related genes, possibly through suppression of PDK-dependent anaerobic glycolysis. Furthermore, we found that expression of the intracellular acidification-induced genes, TXNIP and ARRDC4, correlated with inflammatory gene expression in heterogeneous senescent cell population in vitro and even in vivo, implying that the contribution of intracellular pH to senescence-associated cellular features, such as SASP.

A High-Throughput Microdroplet-Based Single Cell Transfection Method for Gene Knockout Based on the CRISPR/Cas9 System.

The efficient application of the newly developed gene-editing method CRISPR/Cas9 requires more accurate intracellular gene delivery. Traditional delivery approaches, such as lipotransfection and non-viral delivery methods, must contend with major problems to overcome the drawbacks of low efficiency, high toxicity, and cell-type dependency. The high-throughput microdroplet-based single-cell transfection method presented herein provides an alternative method for delivering genome-editing reagents into single living cells. By accurately controlling the number of exogenous plasmids in microdroplets, this method can achieve high-efficiency delivery of nucleic acids to different types of single cells. This paper presents a high-throughput quantitative DNA transfection method for single cells and explores the optimal DNA transfection conditions for specific cell lines. The transfection efficiency of cells at different concentrations of DNA in microdroplets is measured. Under the optimized transfection conditions, the method is used to construct gene-knockout cancer cell lines to determine specific gene functions through the CRISPR/Cas9 knockout system. In a case study, the migration ability of TRIM72 knockout cancer cells is inhibited, and the tumorigenicity of cells in a zebrafish tumor model is reduced. A single-cell microfluidic chip is designed to achieve CRISPR/Cas9 DNA transfection, dramatically improving the transfection efficiency of difficult-to-transfect cells. This research demonstrates that the microdroplet method developed herein has a unique advantage in CRISPR/Cas9 gene-editing applications.

Abstract 6383: Targeting radiation-induced fibrosis: Exploring promising therapeutic avenues and innovative assessment methods

Abstract Introduction: Radiation therapy is a vital cancer treatment for nearly 50% of patients, yet it poses a significant challenge in the form of radiation-induced fibrosis (RF). RF affects about 60% of those undergoing radiation, leading to painful scarring from excessive collagen accumulation. In head and neck cancer patients, as an example, RF reduces tissue flexibility, causing limited neck mobility and impaired swallowing. Furthermore, approximately 30% of patients also face disease recurrence post-radiation, with RF increasing surgical complications. Our laboratory previously identified the role of reduced fatty acid oxidation in RF (Zhao et al; Nat Metab;1(1):147 2019), offering a promising avenue for future drug development. We described the potential therapeutic benefit of caffeic acid phenethyl ester (CAPE) in countering pro-fibrotic metabolic changes. Our current objective is to develop more effective lead compounds to mitigate RF. Methods: Collagen expression, utilized as a surrogate marker for fibrosis, was quantified using ELISA, Western blot analysis, and RT-qPCR. Metabolic changes were assessed by examining the expression levels of PPARG and CD36. CAPE-like analogs were derived from an in-house collection, a commercially available library, and structure-activity relationship (SAR) analyses. In vivo, RF was induced in the hindlimbs of mice through exposure to 40 Gy, followed by weekly X-ray evaluations of hindlimb angles for 16 weeks. During X-ray assessments, both hindlimbs were subjected to a 5 g weight to enable measurement of the joint angle between the femur and tibia (wherein higher acute angles were a measure of worsening fibrosis). Skin samples from irradiated and unirradiated limbs were collected for the evaluation of collagen deposition, utilizing Picro Sirius staining followed by polarized microscopy. Results: Amongst 200 newly synthesized analogs, approximately one-third successfully reduced collagen secretion in human primary dermal fibroblasts. The most promising compounds exhibited a half-maximum inhibition concentration (IC50) for collagen secretion from 1 to 5µM. They also decreased intracellular collagen production and gene expression, associated with upregulation of PPARG and CD36 transcripts. The joint angle measurements in vivo revealed three distinct phases in the development of dermal fibrosis: 1) inflammatory; 2) recovery; and 3) fibrotic phases. Conclusions: We have successfully synthesized novel and potent analogs of CAPE which were able to reduce secretion of collagen. Furthermore, a novel method for the in vivo assessment of fibrosis was also developed. This innovative approach will facilitate the detailed assessments of future compounds capable of reducing collagen deposition in vivo, thereby providing an innovative avenue to mitigate one of the most pressing late normal tissue toxicities of radiation therapy. Citation Format: Pierre-Antoine Bissey, Leonardo Massignan, Ross Mancini, Wei Shi, Justin Williams, Mark Reed, Kenneth W. Yip, Fei-Fei Liu. Targeting radiation-induced fibrosis: Exploring promising therapeutic avenues and innovative assessment methods [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6383.