1.Electroacupuncture Ameliorates NLRP3-mediated Pyroptosis in Spinal Cord Injury Rats by Reshaping The Gut Microbiota
Yin-Jie CUI ; Hong-Ru LI ; Jing-Yi LIU ; Hai-Lin DU ; Shu-Wen LIU ; Yuan YANG ; Chen-Guang ZHENG ; Jian-Qin XIANG ; Xiao-Juan SONG
Progress in Biochemistry and Biophysics 2026;53(5):1132-1153
ObjectiveSpinal cord injury (SCI) directly impairs the regulatory function of the autonomic nervous system, induces intestinal dysfunction, and significantly reduces patients’ quality of life. Preclinical studies have shown that electroacupuncture (EA) therapy can regulate the brain-gut axis and is used to treat central nervous system diseases such as major depressive disorder, Alzheimer’s disease and Parkinson’s disease. Recent research has established that fecal microbiota transplantation (FMT) from EA-treated SCI rats restored intestinal motility and colonic morphology. However, it remains unclear whether the regulation of gut microbiota by EA therapy directly contributes to neural repair after SCI. This study aims to explore whether gut microbiota mediates the neuroprotective effect of EA in the treatment of SCI and its possible mechanism. MethodsThe study employed RNA transcriptome analysis of spinal cord tissue to characterize gene expression profiles and to identify key signaling pathways following EA treatment for SCI. Hematoxylin-Eosin (HE) staining and Nissl staining were used to observe the morphological changes in spinal cord tissue. Western blot (WB) and enzyme-linked immunosorbent assay (ELISA) were applied to detect the effects of EA on the expression of proteins related to nucleotide-binding domain leucine-rich repeat and pyrin domain-containing receptor 3 (NLRP3) -dependent pyroptosis. Using 16S rDNA sequencing, the study observed alterations in gut microbiota diversity and community composition in SCI rats. Prior to establishing SCI models, rats were pretreated with an antibiotic cocktail to induce gut dysbiosis, and the effects on intestinal function and spinal cord neural repair were evaluated. FMT was performed to investigate the regulatory effects of post-EA FMT on motor function, general status, liver and spleen indices, and NLRP3-mediated pyroptosis in SCI rats. ResultsEA improved motor function and reduced regulated neuronal cell death in SCI rats. Transcriptomic analysis demonstrated the activation of immune- and inflammation-related pathways post-SCI, including NOD-like receptors, nuclear factor-kappa B(NF-κB), and Toll-like receptor (TLR) pathways. EA primarily influenced intestinal inflammation and autoimmune functions. 16S rDNA sequencing illustrated that EA did not alter the diversity of gut microbiota. However, EA altered the gut microbiota composition in SCI rats, increasing Lactobacillus and Akkermansia genera while rebalancing the Firmicutes/Bacteroidetes ratio. Furthermore, depletion of gut microbiota by antibiotics disrupted the intestinal barrier, reduced the expression of intestinal barrier proteins Zonula Occludens-1 (ZO-1) and Occludin, elevated serum lipopolysaccharide-binding protein (LBP) levels, exacerbated spinal cord tissue damage, and hindered motor function recovery in SCI rats. FMT from donors treated with EA reduced LBP levels in the intestine, blood, and spinal cord of rats, inhibited the TLR4 myeloid differentiation primary response protein 88 (MyD88)-NF‑κB pathway and NLRP3-dependent pyroptosis, and improved motor function. On the other hand, FMT treatment resulted in decreased body weight and food intake, whereas FMT using EA-treated donors effectively alleviated these alterations. ConclusionEA effectively alleviated neuroinflammatory responses in rats with SCI, primarily through regulating the gut microbiota and suppressing the NLRP3-dependent pyroptosis signaling pathway.
2.Electroacupuncture Ameliorates NLRP3-mediated Pyroptosis in Spinal Cord Injury Rats by Reshaping The Gut Microbiota
Yin-Jie CUI ; Hong-Ru LI ; Jing-Yi LIU ; Hai-Lin DU ; Shu-Wen LIU ; Yuan YANG ; Chen-Guang ZHENG ; Jian-Qin XIANG ; Xiao-Juan SONG
Progress in Biochemistry and Biophysics 2026;53(5):1132-1153
ObjectiveSpinal cord injury (SCI) directly impairs the regulatory function of the autonomic nervous system, induces intestinal dysfunction, and significantly reduces patients’ quality of life. Preclinical studies have shown that electroacupuncture (EA) therapy can regulate the brain-gut axis and is used to treat central nervous system diseases such as major depressive disorder, Alzheimer’s disease and Parkinson’s disease. Recent research has established that fecal microbiota transplantation (FMT) from EA-treated SCI rats restored intestinal motility and colonic morphology. However, it remains unclear whether the regulation of gut microbiota by EA therapy directly contributes to neural repair after SCI. This study aims to explore whether gut microbiota mediates the neuroprotective effect of EA in the treatment of SCI and its possible mechanism. MethodsThe study employed RNA transcriptome analysis of spinal cord tissue to characterize gene expression profiles and to identify key signaling pathways following EA treatment for SCI. Hematoxylin-Eosin (HE) staining and Nissl staining were used to observe the morphological changes in spinal cord tissue. Western blot (WB) and enzyme-linked immunosorbent assay (ELISA) were applied to detect the effects of EA on the expression of proteins related to nucleotide-binding domain leucine-rich repeat and pyrin domain-containing receptor 3 (NLRP3) -dependent pyroptosis. Using 16S rDNA sequencing, the study observed alterations in gut microbiota diversity and community composition in SCI rats. Prior to establishing SCI models, rats were pretreated with an antibiotic cocktail to induce gut dysbiosis, and the effects on intestinal function and spinal cord neural repair were evaluated. FMT was performed to investigate the regulatory effects of post-EA FMT on motor function, general status, liver and spleen indices, and NLRP3-mediated pyroptosis in SCI rats. ResultsEA improved motor function and reduced regulated neuronal cell death in SCI rats. Transcriptomic analysis demonstrated the activation of immune- and inflammation-related pathways post-SCI, including NOD-like receptors, nuclear factor-kappa B(NF-κB), and Toll-like receptor (TLR) pathways. EA primarily influenced intestinal inflammation and autoimmune functions. 16S rDNA sequencing illustrated that EA did not alter the diversity of gut microbiota. However, EA altered the gut microbiota composition in SCI rats, increasing Lactobacillus and Akkermansia genera while rebalancing the Firmicutes/Bacteroidetes ratio. Furthermore, depletion of gut microbiota by antibiotics disrupted the intestinal barrier, reduced the expression of intestinal barrier proteins Zonula Occludens-1 (ZO-1) and Occludin, elevated serum lipopolysaccharide-binding protein (LBP) levels, exacerbated spinal cord tissue damage, and hindered motor function recovery in SCI rats. FMT from donors treated with EA reduced LBP levels in the intestine, blood, and spinal cord of rats, inhibited the TLR4 myeloid differentiation primary response protein 88 (MyD88)-NF‑κB pathway and NLRP3-dependent pyroptosis, and improved motor function. On the other hand, FMT treatment resulted in decreased body weight and food intake, whereas FMT using EA-treated donors effectively alleviated these alterations. ConclusionEA effectively alleviated neuroinflammatory responses in rats with SCI, primarily through regulating the gut microbiota and suppressing the NLRP3-dependent pyroptosis signaling pathway.
3.Differences in deltamethrin resistance and kdr gene mutation in Culex tritaeniorhynchus population in and outside the Yellow Sea wetland
Xiao-er ZHANG ; Zhi-ming WU ; Ye TIAN ; Qian CUI ; Yu-qian JI ; Huan WANG ; Shu-juan YANG ; Yi-chao ZHAO ; Yu WANG ; Hua-yu YIN ; Yu DING ; Guo-jin YAN ; Min-sen ZHAO ; Shou-gang ZHANG ; Bing-dong SONG ; Hong-na CHEN ; Jian GAO ; Wei-fang YANG ; Yu-fu ZHANG ; Hui LIU ; Hong-liang CHU
Acta Parasitologica et Medica Entomologica Sinica 2026;33(2):101-107
Objective To gain insights into the biological characteristics of different populations of Culex tritaeniorhynchus within and around the Yellow Sea wetland from the perspective of the occurrence of resistance, we investigated the levels of resistance to deltamethrin and kdr gene mutation in the wetland and its peripheral areas. Methods Specimens were collected from Cx. tritaeniorhynchus populations at two monitoring sites in the Rare Bird National Nature Reserve and Tiaozi Ni Wetland Scenic Area, and also from two populations in Yancheng City and the Liuhe District of Nanjing, and the resistance of these mosquitoes to deltamethrin was determined using the CDC biotest bottle method. For each concentration of deltamethrin assessed, a random subset of exposed specimens was selected for amplification of the kdr gene fragment, followed by Sanger sequencing to identify and analyze resistance-associated mutations. Results The LC50 levels of deltamethrin among mosquitoes from the four populations in Luhe, Yancheng, the Rare Bird National Nature Reserve and the Tiaozi Ni Wetland Scenic Area were 2.048 5, 7.798 2, 3.473 3, and 17.695 5 mg/mL, respectively, with corresponding concentrations of deltamethrin ranging from 0.005 to 5.000,0.050 to 50.000,0.050 to 25.000 and 0.050 to 50.000 mg/mL, respectively. Furthermore, the ranges of the KT50 values were 11.76-107.43, 67.05-216.30,29.77-107.43 and 28.40-329.51 min; the 1-h knockdown rates were 34.58%-99.15%, 9.52%-43.80%, 55.09%-73.01%, and 10.09%-68.07%; and the 24-h mortality rates were 12.15%-67.52%,9.52%-79.56%,13.17%-82.21%, and 11.01%-78.99%, respectively. With respect to kdr gene mutation, we assayed a total of 63,70,59, and 57 mosquitoes for the four populations, for which we detected L1014F mutation frequencies of 14.29%, 35.00%, 20.34%, and 31.58%, respectively, with a majority of these mutations being heterozygous for resistance. In addition, five adult mosquitoes were identified has having synonymous mutations at site 1011[i. e. , AAT(asparagine)mutation to AAC(asparagine)]. Conclusions Our findings revealed the clear resistance of Cx. tritaeniorhynchus to deltamethrin in the Yancheng region of the Yellow Sea wetland, and the resistance phenotype and kdr frequency of Cx. tritaeniorhynchus in the wetland environment were comparable to those of Cx. tritaeniorhynchus in the wetland environment, thereby indicating that the resistance of different populations of Cx. tritaeniorhynchus was homogeneous under the pressure of different insecticide selection within and around the wetland. However, the underlying mechanisms need to be further studied.
4.Fluorescence Suppression Method of Raman Spectroscopy and Its Application in Skin and Cosmetics Analysis
Yun-Xia CHEN ; Jia-Rong WANG ; Jian-Yu ZHU ; Shi-Wen LIN ; Ya-Nan LIU ; Xiao-Yue MA ; Guang-Cheng XI ; Juan LIU
Progress in Biochemistry and Biophysics 2026;53(7):1914-1926
Owing to its inherent advantages—such as being non-destructive, rapid, highly molecule-specific, and minimally interfered with by moisture—Raman spectroscopy has been widely adopted in the fields of skin barrier function assessment, monitoring the transdermal penetration of active cosmetic ingredients, and the identification and quality control of cosmetic products. Despite these strengths, the practical application of this technique faces a significant bottleneck: the strong fluorescence background generated by endogenous skin components and exogenous cosmetic additives. Endogenous skin substances, such as structural proteins (e.g., collagen and elastin), metabolic coenzymes (e.g., nicotinamide adenine dinucleotide), and pigments (e.g., melanin), together with exogenous cosmetic constituents like organic colorants, chemical sunscreens, and fragrances, often possess strong absorption and emission characteristics. When excited by lasers, these components produce a fluorescence background that can be 106 to 108 times stronger than the Raman scattering signals, effectively masking the inherently weak vibrational fingerprint information. In recent years, driven by the rapid development of optoelectronic hardware and artificial intelligence algorithms, fluorescence suppression strategies have evolved from isolated, single-method approaches into comprehensive, multi-level synergistic systems. These systems are categorized into three distinct tiers: sample preparation, signal acquisition, and data processing. At the sample preparation level, techniques such as photobleaching and surface-enhanced Raman spectroscopy (SERS) are employed to eliminate or bypass the generation of fluorescence at the source. At the signal acquisition level, instrumental improvements—including the use of long-wavelength near-infrared excitation (typically 785 nm or 1 064 nm), confocal spatial filtering, and shifted excitation Raman difference spectroscopy (SERDS)— are utilized to physically isolate Raman signals from the fluorescence background. Furthermore, at the data processing level, numerical baseline correction methods such as polynomial fitting, penalized least squares (e.g., airPLS, arPLS), wavelet transform, and derivative algorithms are increasingly integrated into the analytical pipeline to extract Raman spectral features from mixed signals without increasing hardware costs or acquisition time. This review provides a systematic categorization and critical evaluation of these fluorescence suppression methods, detailing their underlying principles, technical advantages, and inherent limitations in diverse experimental setups. By focusing on critical application scenarios—including skin barrier assessment, percutaneous absorption monitoring, the routine quality control of cosmetics, and the emerging field of portable on-site detection—this paper explores the current state of technique selection and optimization. Finally, the article discusses future development trends, emphasizing the necessity of constructing adaptive, tiered suppression strategies, developing intelligent and automated data processing algorithms, and promoting the integration of portable, multi-modal diagnostic devices. The objective of this review is to provide a comprehensive technical reference to facilitate the transition of Raman spectroscopy from a specialized laboratory tool into a routine, robust analytical platform for advancements in skin science and cosmetic research.
5.Effect Analysis of Different Interventions to Improve Neuroinflammation in The Treatment of Alzheimer’s Disease
Jiang-Hui SHAN ; Chao-Yang CHU ; Shi-Yu CHEN ; Zhi-Cheng LIN ; Yu-Yu ZHOU ; Tian-Yuan FANG ; Chu-Xia ZHANG ; Biao XIAO ; Kai XIE ; Qing-Juan WANG ; Zhi-Tao LIU ; Li-Ping LI
Progress in Biochemistry and Biophysics 2025;52(2):310-333
Alzheimer’s disease (AD) is a central neurodegenerative disease characterized by progressive cognitive decline and memory impairment in clinical. Currently, there are no effective treatments for AD. In recent years, a variety of therapeutic approaches from different perspectives have been explored to treat AD. Although the drug therapies targeted at the clearance of amyloid β-protein (Aβ) had made a breakthrough in clinical trials, there were associated with adverse events. Neuroinflammation plays a crucial role in the onset and progression of AD. Continuous neuroinflammatory was considered to be the third major pathological feature of AD, which could promote the formation of extracellular amyloid plaques and intracellular neurofibrillary tangles. At the same time, these toxic substances could accelerate the development of neuroinflammation, form a vicious cycle, and exacerbate disease progression. Reducing neuroinflammation could break the feedback loop pattern between neuroinflammation, Aβ plaque deposition and Tau tangles, which might be an effective therapeutic strategy for treating AD. Traditional Chinese herbs such as Polygonum multiflorum and Curcuma were utilized in the treatment of AD due to their ability to mitigate neuroinflammation. Non-steroidal anti-inflammatory drugs such as ibuprofen and indomethacin had been shown to reduce the level of inflammasomes in the body, and taking these drugs was associated with a low incidence of AD. Biosynthetic nanomaterials loaded with oxytocin were demonstrated to have the capability to anti-inflammatory and penetrate the blood-brain barrier effectively, and they played an anti-inflammatory role via sustained-releasing oxytocin in the brain. Transplantation of mesenchymal stem cells could reduce neuroinflammation and inhibit the activation of microglia. The secretion of mesenchymal stem cells could not only improve neuroinflammation, but also exert a multi-target comprehensive therapeutic effect, making it potentially more suitable for the treatment of AD. Enhancing the level of TREM2 in microglial cells using gene editing technologies, or application of TREM2 antibodies such as Ab-T1, hT2AB could improve microglial cell function and reduce the level of neuroinflammation, which might be a potential treatment for AD. Probiotic therapy, fecal flora transplantation, antibiotic therapy, and dietary intervention could reshape the composition of the gut microbiota and alleviate neuroinflammation through the gut-brain axis. However, the drugs of sodium oligomannose remain controversial. Both exercise intervention and electromagnetic intervention had the potential to attenuate neuroinflammation, thereby delaying AD process. This article focuses on the role of drug therapy, gene therapy, stem cell therapy, gut microbiota therapy, exercise intervention, and brain stimulation in improving neuroinflammation in recent years, aiming to provide a novel insight for the treatment of AD by intervening neuroinflammation in the future.
6.Impact factor selection for non-fatal occupational injuries among manufacturing workers by LASSO regression
Yingheng XIAO ; Chunhua LU ; Juan QIAN ; Ying CHEN ; Yishuo GU ; Zeyun YANG ; Daozheng DING ; Liping LI ; Xiaojun ZHU
Journal of Environmental and Occupational Medicine 2025;42(2):133-139
Background As a pillar industry in China, the manufacturing sector has a high incidence of non-fatal occupational injuries. The factors influencing non-fatal occupational injuries in this industry are closely related at various levels, including individual, equipment, environment, and management, making the analysis of these influencing factors complex. Objective To identify influencing factors of non-fatal occupational injuries among manufacturing workers, providing a basis for targeted interventions and surveillance. Methods A total of
7.Comparison the application of Del nido cardioplegia and microplegia in the isolated coronary artery bypass grafting underwent the cardiopulmonary bypass
Xiangzhou CHEN ; Lin CHEN ; Jia HAO ; Juan XIAO ; Lan ZHANG
Chongqing Medicine 2025;54(5):1180-1186
Objective To compare the myocardial protective effects of Del nido cardioplegia(DC)and microplegia(MP)in the isolated coronary artery bypass grafting(CABG)underwent the cardiopulmonary by-pass(CPB),and evaluate the safety and efficacy of DC in isolated CABG.Methods A retrospective analysis was performed on 128 patients with isolated CABG by the same surgical team form January 2018 to April 2021 at the Second Affiliated Hospital of Army Medical University.The patients were divided into MP group(n=57)and DC group(n=71)according to the use of intraoperative cardioplegia during the surgery.Preoper-ative baseline data,blood gas at 4 time points of CPB 20 min(T1),CPB 60 min(T2),end of CPB(T3),and re-turning of ICU(T4),as well as perioperative data,major postoperative complications,mortality,medium and long-terms survival rate were collected.Results Compared with preoperative baseline data,the lactate(Lac)level in the DC group was lower;During the operation,the DC group had fewer times of cardiac arrest fluid perfusion and a larger amount volume of cardioplegia(P<0.001);In CPB,there was a higher fluid balance and a higher rate of spontaneous rebeating(88.7%vs.52.6%),differences were statistically significant(P<0.05).Blood gas at all 4 time points showed that the DC group had lower blood glucose level(P<0.05).The cardiac troponin Ⅰ(cTnⅠ)concentration 24 h postoperative was higher(P<0.05),and the ICU duration was shorter(P<0.05).Correlation analysis indicated that there was no correlation between cTnⅠ concentration 24 h postoperative and aortic cross clamping time(ACCT)in both groups(P>0.05).There was a positive correlation between the concentration of cTnⅠ 24 h postoperative and the numbers of cardioplegia deliveries(r=0.331,P=0.005)in DC group,but there was no correlation in MP group(r=0.023,P=0.866).There was no significant difference in perioperative period,postoperative complications and mortality between the two group(P>0.05).Kaplan-Meier analysis showed that there was no statistically significant difference in the 5 years survival rate between two groups(P=0.966).Conclusion Compared with MP,DC provides a comparable myocardial protection effect in the isolated CABG,with higher security,without affecting the short and medium-term clinical outcomes in patients.
8.Paraventricular nucleus p-ERK neurons involving in the anorectic effect of amylin
Guo-Jun LI ; Hao-Dong LIU ; Xiao-Juan CAO ; Chen-Guang DU
Acta Anatomica Sinica 2025;56(6):651-657
Objective To explore the regulatory effect of amylin on the feeding behavior of mice through the ERK pathway of paraventricular nucleus of the hypothalamus(PVN).Methods A total of 54 C57BL/6J mice were randomly divided into multiple groups for experiments.First,immunofluorescence was used to detect the distribution of ERK and calcitonin receptor(CTR)neurons in the brains of 4 mice.A chemical lesion model of PVN neurons was established,and 16 mice were divided into four groups(4 mice per group):control(Ctrl)group,ibotenic acid(IBO)-lesioned group,amylin group,and amylin+IBO group.The number of ERK-positive neurons in the PVN region and food intake were then measured.Subsequently,16 mice were divided into four groups(4 mice per group),Ctrl group,amylin group,ERK antagonist U0126 group,and amylin+U0126 group.The expression level of the immediate early gene c-fos in the PVN was detected by Real-time PCR.Immunofluorescence was used to detect the distribution of p-ERK positive neurons in the brains of 4 saline-treated mice and 4 amylin-treated mice.Finally,18 mice were randomly divided into three groups(6 mice per group)through intracerebroventricular injection,Ctrl group,amylin group,and amylin+receptor antagonist AC 187 group.Then,triple immunofluorescence was used to detect the co-expression of p-ERK,neuronal nitric oxide synthase(nNOS),and CTR-immunopositive neurons in the PVN region,and food intake within 3 hours after treatment was recorded simultaneously.Results ERK-positive neurons were mainly distributed in the suprachiasmatic nucleus(SCN),arcuate nucleus(ARC),and locus coeruleus(LC),while ERK and CTR co-expressing positive neurons were specifically enriched in the PVN(P=0.0012).Lesion of PVN neurons led to a decrease in the number of ERK-positive neurons(P<0.001)and blocked the anorectic effect of amylin(P<0.001).Amylin activated the expression of the c-fos gene in the PVN region(P<0.05),and this effect was inhibited by U0126(P<0.05).After intracerebroventricular injection of amylin,the number of triple-positive neurons for p-ERK,nNOS,and CTR in the PVN increased(P<0.05).Addition of AC 187 blocked the activation effect of amylin(P<0.01)and reversed the anorectic effect of amylin(1 h,P=0.2218;2 h,P=0.2218;3 h,P=0.6974).Conclusion P-ERK neurons in the PVN regulate feeding behavior through an amylin receptor-dependent ERK signaling pathway.
9.CURRENT SITUATION OF HUMAN INTESTINAL PARASITIC INFECTION IN JINUO INHABITED AREAS OF YUNNAN PROVINCE IN 2023
Juan ZHANG ; Hong TAO ; Yan-Zhong LI ; Meng CHEN ; Xiao-Mei ZHOU
Acta Parasitologica et Medica Entomologica Sinica 2025;32(2):78-83
Objective To investigate the infection with key intestinal parasites in the Jinuo-inhabited areas of Yunnan Province in 2023 and provide a scientific basis for preventing and controlling local parasitic diseases.Methods A cluster random sampling method was used to conduct a survey on human intestinal parasitic diseases in Jinuoshan Township,Jinghong City,Xishuangbanna Dai Autonomous Prefecture,Yunnan Province,from October to November 2023.Fecal samples and information on epidemiological factors were collected from permanent residents of the Jinuo ethnic group.Intestinal helminth eggs were detected and counted using the modified Kato-Katz technique(two slides per fecal sample).Intestinal protozoa were identified via iodine-stained smears.Each fecal sample was subjected to hookworm larval culture using the test tube filter paper method for species identification.Additionally,transparent adhesive tape anal swabs were used to detect Enterobius vermicularis eggs in children aged 3-9 years.Results A total of 1 367 individuals was examined,with 11 species of parasites detected,including 5 helminth species and 6 protozoan species.The overall intestinal parasite infection rate was 25.97%,with helminth and protozoan infection rates at 17.63%and 9.07%,respectively.The infection rate of E.vermicularis in children(via anal swabs)was 16.35%.The infection rates of specific parasites were as follows:Ascaris lumbricoides 0.07%,hookworm 13.97%,Trichuris sp.0.29%,Taenia solium 0.15%,Entamoeba nana 1.68%,Giardia lamblia 1.61%,Entamoeba histolytica 0.07%,Entamoeba coli 0.07%,Iodamolbe butschlii 1.61%,and Blastocystis hominis 4.10%.The degree of Acaris lumbricoides,hookworm,and Trichuris sp.infection was mainly mild.Hookworm species were identified as Necator americanus and Ancylostoma duodenale.No statistically significant differences in infection rates were observed across different village committees,genders,age groups,or occupations(P>0.05).The infection rates of preschool children and illiterate people were higher at 82.61%and 67.02%,respectively(χ2=344.798,P<0.01).The infection rate of the Jinuo people was 32.49%,which is higher than that of other ethnic groups(χ2=109.493,P<0.01).Conclusions The prevalence of intestinal parasitic infections among the Jinuo ethnic group in Yunnan Province remains relatively high.Strengthened prevention and control measures targeting relevant populations are urgently needed,with a particular focus on hookworm infections and E.vermicularis infections in children.
10.Genome-wide investigation of transcription factor footprints and dynamics using cFOOT-seq.
Heng WANG ; Ang WU ; Meng-Chen YANG ; Di ZHOU ; Xiyang CHEN ; Zhifei SHI ; Yiqun ZHANG ; Yu-Xin LIU ; Kai CHEN ; Xiaosong WANG ; Xiao-Fang CHENG ; Baodan HE ; Yutao FU ; Lan KANG ; Yujun HOU ; Kun CHEN ; Shan BIAN ; Juan TANG ; Jianhuang XUE ; Chenfei WANG ; Xiaoyu LIU ; Jiejun SHI ; Shaorong GAO ; Jia-Min ZHANG
Protein & Cell 2025;16(11):932-952
Gene regulation relies on the precise binding of transcription factors (TFs) at regulatory elements, but simultaneously detecting hundreds of TFs on chromatin is challenging. We developed cFOOT-seq, a cytosine deaminase-based TF footprinting assay, for high-resolution, quantitative genome-wide assessment of TF binding in both open and closed chromatin regions, even with small cell numbers. By utilizing the dsDNA deaminase SsdAtox, cFOOT-seq converts accessible cytosines to uracil while preserving genomic integrity, making it compatible with techniques like ATAC-seq for sensitive and cost-effective detection of TF occupancy at the single-molecule and single-cell level. Our approach enables the delineation of TF footprints, quantification of occupancy, and examination of chromatin influences on TF binding. Notably, cFOOT-seq, combined with FootTrack analysis, enables de novo prediction of TF binding sites and tracking of TF occupancy dynamics. We demonstrate its application in capturing cell type-specific TFs, analyzing TF dynamics during reprogramming, and revealing TF dependencies on chromatin remodelers. Overall, cFOOT-seq represents a robust approach for investigating the genome-wide dynamics of TF occupancy and elucidating the cis-regulatory architecture underlying gene regulation.
Transcription Factors/genetics*
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Humans
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Mice
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DNA Footprinting/methods*


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