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* ; Humans ; Chromatin/genetics* ; Animals ; Binding Sites ; Mice ; DNA Footprinting/methods*

OBJECTIVE: Hepatocellular carcinoma (HCC) is sensitive to ferroptosis, a new form of programmed cell death that occurs in most tumor types. However, the mechanism through which ferroptosis modulates HCC remains unclear. This study aimed to investigate the oncogenic role and prognostic value of FANCD2 and provide novel insights into the prognostic assessment and prediction of immunotherapy. METHODS: Using clinicopathological parameters and bioinformatic techniques, we comprehensively examined the expression of FANCD2 macroscopically and microcosmically. We conducted univariate and multivariate Cox regression analyses to identify the prognostic value of FANCD2 in HCC and elucidated the detailed molecular mechanisms underlying the involvement of FANCD2 in oncogenesis by promoting iron-related death. RESULTS: FANCD2 was significantly upregulated in digestive system cancers with abundant immune infiltration. As an independent risk factor for HCC, a high FANCD2 expression level was associated with poor clinical outcomes and response to immune checkpoint blockade. Gene set enrichment analysis revealed that FANCD2 was mainly involved in the cell cycle and CYP450 metabolism. CONCLUSION To the best of our knowledge, this is the first study to comprehensively elucidate the oncogenic role of FANCD2. FANCD2 has a tumor-promoting aspect in the digestive system and acts as an independent risk factor in HCC; hence, it has recognized value for predicting tumor aggressiveness and prognosis and may be a potential biomarker for poor responsiveness to immunotherapy.
Humans ; Carcinoma, Hepatocellular/diagnosis* ; Liver Neoplasms/diagnosis* ; Immunotherapy ; Fanconi Anemia Complementation Group D2 Protein/metabolism* ; Prognosis ; Male ; Female ; Middle Aged ; Biomarkers, Tumor/metabolism*

Objective:To investigate the current situation of the use of transjugular intrahepatic portosystemic shunt (TIPS) for portal hypertension, which should aid the development of TIPS in China.Methods:The China Portal Hypertension Alliance (CHESS) initiated this study that comprehensively investigated the basic situation of TIPS for portal hypertension in China through network research. The survey included the following: the number of surgical cases, main indications, the development of Early-TIPS, TIPS for portal vein cavernous transformation, collateral circulation embolization, intraoperative portal pressure gradient measurement, commonly used stent types, conventional anticoagulation and time, postoperative follow-up, obstacles, and the application of domestic instruments.Results:According to the survey, a total of 13 527 TIPS operations were carried out in 545 hospitals participating in the survey in 2021, and 94.1% of the hospital had the habit of routine follow-up after TIPS. Most hospitals believed that the main indications of TIPS were the control of acute bleeding (42.6%) and the prevention of rebleeding (40.7%). 48.1% of the teams carried out early or priority TIPS, 53.0% of the teams carried out TIPS for the cavernous transformation of the portal vein, and 81.0% chose routine embolization of collateral circulation during operation. Most of them used coils and biological glue as embolic materials, and 78.5% of the team routinely performed intraoperative portal pressure gradient measurements. In selecting TIPS stents, 57.1% of the hospitals woulel choose Viator-specific stents, 57.2% woulel choose conventional anticoagulation after TIPS, and the duration of anticoagulation was between 3-6 months (55.4%). The limitation of TIPS surgery was mainly due to cost (72.3%) and insufficient understanding of doctors in related departments (77.4%). Most teams accepted the domestic instruments used in TIPS (92.7%).Conclusions:This survey shows that TIPS treatment is an essential part of treating portal hypertension in China. The total number of TIPS cases is far from that of patients with portal hypertension. In the future, it is still necessary to popularize TIPS technology and further standardize surgical indications, routine operations, and instrument application.

Currently,human health due to corona virus disease 2019(COVID-19)pandemic has been seriously threatened.The coronavirus severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)spike(S)protein plays a crucial role in virus transmission and several S-based therapeutic approaches have been approved for the treatment of COVID-19.However,the efficacy is compromised by the SARS-CoV-2 evolvement and mutation.Here we report the SARS-CoV-2 S protein receptor-binding domain(RBD)inhibitor licorice-saponin A3(A3)could widely inhibit RBD of SARS-CoV-2 variants,including Beta,Delta,and Omicron BA.1,XBB and BQ1.1.Furthermore,A3 could potently inhibit SARS-CoV-2 Omicron virus in Vero E6 cells,with EC50 of 1.016 pM.The mechanism was related to binding with Y453 of RBD deter-mined by hydrogen-deuterium exchange mass spectrometry(HDX-MS)analysis combined with quan-tum mechanics/molecular mechanics(QM/MM)simulations.Interestingly,phosphoproteomics analysis and multi fluorescent immunohistochemistry(mIHC)respectively indicated that A3 also inhibits host inflammation by directly modulating the JNK and p38 mitogen-activated protein kinase(MAPK)path-ways and rebalancing the corresponding immune dysregulation.This work supports A3 as a promising broad-spectrum small molecule drug candidate for COVID-19.

Objective To explore characteristics of clinical parameters and cytokines in patients with drug-induced liver injury(DILI)caused by different drugs and their correlation with clinical indicators. Method The study was conducted on patients who were up to Review of Uncertainties in Confidence Assessment for Medical Tests(RUCAM)scoring criteria and clinically diagnosed with DILI.Based on Chinese herbal medicine,cardiovascular drugs,non-steroidal anti-inflammatory drugs(NSAIDs),anti-infective drugs,and other drugs,patients were divided into five groups.Cytokines were measured by Luminex technology.Baseline characteristics of clinical biochemical indicators and cytokines in DILI patients and their correlation were analyzed. Results 73 patients were enrolled.Age among five groups was statistically different(P=0.032).Alanine aminotransferase(ALT)(P=0.033)and aspartate aminotransferase(AST)(P=0.007)in NSAIDs group were higher than those in chinese herbal medicine group.Interleukin-6(IL-6)and tumor necrosis factor alpha(TNF-α)in patients with Chinese herbal medicine(IL-6:P<0.001;TNF-α:P<0.001)and cardiovascular medicine(IL-6:P=0.020;TNF-α:P=0.001)were lower than those in NSAIDs group.There was a positive correlation between ALT(r=0.697,P=0.025),AST(r=0.721,P=0.019),and IL-6 in NSAIDs group. Conclusion Older age may be more prone to DILI.Patients with NSAIDs have more severe liver damage in early stages of DILI,TNF-α and IL-6 may partake the inflammatory process of DILI.

Objective To explore and optimize the in vitro primary culture method of astrocytes in neonatal mouse cerebral cortex, which provides a better solution for the in vitro culture of astrocytes.Methods In order to opti-mize the in vitro culture method of mouse cerebral cortex astrocytes, 3-day-old C57BL/6J mouse cerebral cortex tis-sues were taken, meninges and blood vessels were removed, digested by pancreatic enzymes and centrifuged, and high-glucose dulbecco's modified eagle medium (DMEM) was added to form cell suspension, which was purified by differential adhesion method, cross hand method and constant temperature shaking method.The cells were inoc-ulated in poly-D-lysine-coated culture bottles with different culture densities, and the purity of astrocytes was deter-mined by morphological observation and immunofluorescence staining.Results The cells were inoculated at a den-sity of 5 × 106 cells per bottle with good effect and high activity.The purity of astrocytes reached 99％ by using high sugar DMEM medium combined with differential adhesion method, cross hand method and constant temperature shaking method.Conclusion The primary culture method of astrocytes in mouse cerebral cortex is successfully es-tablished and optimized.

Objective:To investigate the expression level and application value of anti-carbamylated protein(CarP)antibody in rheumatoid arthritis(RA).Methods:Demographic data and laboratory test results of RA patients,non-RA patients and healthy controls in the physical examination center were re-viewed from December 2018 to June 2019 in the Rheumatology and Immunology Department of the Peo-ple's Hospital of Xinjiang Uygur Autonomous Region.The serum concentrations of anti-CarP antibodies in all the subjects were measured by ELISA and statistically analyzed.Results:A total of 259 subjects were included in this study,including 158 in the RA group(45 serum-negative RA patients),59 in the non-RA group and 42 in the healthy control group.The concentration of anti-CarP antibody in RA group[8.31(5.22,15.26)U/mL]was higher than that in non-RA group[4.50(3.35,5.89)U/mL]and healthy control group[3.46(2.76,4.92)U/mL].The concentration of anti-CarP antibody in non-RA group was not significantly different from that in healthy control group(P=0.10).Receiver operating characteristic(ROC)curve analysis showed that the sensitivity of anti-CarP antibody in the diagnosis of RA was 58.2％,and the specificity was 93.1％.The sensitivity of the combined detection of anti-CarP antibody,anti-cyclic peptide containing citrulline(CCP)antibody and rheumatoid factor(RF)was 82.3％,and the specificity was 96.5％.The positive rate of anti-CarP antibody in serum-negative RA patients was 44.4％(20/45).Univariate Logisitic regression analysis showed that age,C-reactive pro-tein(CRP),erythrocyte sedimentation rate(ESR),RF,glucose-6-phosphate isomerase(GPI),anti-CCP antibody and anti-CarP antibody were risk factors for RA.Multivariate Logisitic regression analysis showed that anti-CCP antibody and anti-CarP antibody were independent risk factors for RA.Spearman correlation analysis showed that there was no significant correlation between anti-CarP antibody and swol-len joint count(SJC),tenderness joints count(TJC),ESR,disease activity score for 28 joints(DAS28),clinical disease activity index(CDAI),simplified disease activity index(SDAI).The concentration of anti-CarP antibody in RA with bone erosion(n=88)was higher than that in RA without bone erosion(n=70),and there was significant difference between the two groups(P＜0.05).Conclusion:Anti-CarP antibody is an effective serological marker for the diagnosis of RA.The combined detection of RF,anti-CCP antibody and anti-CarP antibody can improve its diagnostic value,and anti-CarP antibody may be an effective assistant diagnostic tool for serum negative RA.The high serum concentration of anti-CarP antibody in patients with RA may indicate an increased risk of bone erosion and should be treated early,but further cohort studies are needed for follow-up observation.

Objective:To investigate age-related characteristics of gait parameters in the elderly.Methods:From February 2023 to August 2023, a convenient sampling method was used to investigate the elderly over 60 years old in communities in Beijing.General characteristics and anthropometric data were collected.Gait parameters of the subjects during normal speed walking were measured using a wearable gait analyzer.Comparisons were made of the basic characteristics, physical status and gait parameters in different age groups.Linear regression analysis was used to evaluate the changes of physical status and gait parameters with age, with the 60-69-year-old group as the baseline standard.Results:A total of 670 elderly people were included, including 324(48.4%)aged 60-69 years, 285(42.5%)aged 70-79 years, and 61(9.1%)aged ≥80 years.Linear regression analysis showed that after adjusting for confounding factors, with increasing age, skeletal muscle mass index(SMI)( β=-0.018, 95% CI: -0.029--0.007), calf circumference( β=-0.096, 95% CI: -0.142--0.051), upper limb flexibility( β=-0.200, 95%, 95% CI: -0.355--0.046), lower limb flexibility( β=-0.244, 95% CI: -0.377--0.111), grip strength( β=-0.397, 95% CI: -0.491--0.303), the Short Physical Performance Battery(SPPB)( β=-0.080, 95% CI: -0.100--0.060)decreased( P<0.05), and the gait parameter such as speed( β=-0.010, 95% CI: -0.014--0.007), cadence( β=-0.398, 95% CI: -0.634--0.162), step length/height( β=-0.002, 95% CI: -0.003--0.002), stride length( β=-0.009, 95% CI: -0.011--0.007), swing power( β=-0.009, 95% CI: -0.012--0.006), ground impact( β=-0.020, 95% CI: -0.026--0.014), foot fall( β=-0.050, 95% CI: -0.064--0.036), pre-swing angle( β=-0.545, 95% CI: -0.714--0.377)all decreased( P<0.05), while stride time( β=0.005, 95% CI: 0.001-0.009), single limb support time( β=1.566, 95% CI: 0.499-2.633), terminal double limb support time( β=0.609, 95% CI: 0.084-1.134), swing duration( β=1.288, 95% CI: 0.024-2.552), single step time( β=2.417, 95% CI: 0.462-4.372)and support phase time( β=1.935, 95% CI: 0.421-3.449)all increased( P<0.05). Conclusions:The walking ability tends to decline with age in older people in the community who walk at a normal walking speed.

Objective To monitor the susceptibility of clinical isolates to antimicrobial agents in tertiary hospitals in major regions of China in 2022.Methods Clinical isolates from 58 hospitals in China were tested for antimicrobial susceptibility using a unified protocol based on disc diffusion method or automated testing systems.Results were interpreted using the 2022 Clinical &Laboratory Standards Institute(CLSI)breakpoints.Results A total of 318 013 clinical isolates were collected from January 1,2022 to December 31,2022,of which 29.5％were gram-positive and 70.5％were gram-negative.The prevalence of methicillin-resistant strains in Staphylococcus aureus,Staphylococcus epidermidis and other coagulase-negative Staphylococcus species(excluding Staphylococcus pseudintermedius and Staphylococcus schleiferi)was 28.3％,76.7％and 77.9％,respectively.Overall,94.0％of MRSA strains were susceptible to trimethoprim-sulfamethoxazole and 90.8％of MRSE strains were susceptible to rifampicin.No vancomycin-resistant strains were found.Enterococcus faecalis showed significantly lower resistance rates to most antimicrobial agents tested than Enterococcus faecium.A few vancomycin-resistant strains were identified in both E.faecalis and E.faecium.The prevalence of penicillin-susceptible Streptococcus pneumoniae was 94.2％in the isolates from children and 95.7％in the isolates from adults.The resistance rate to carbapenems was lower than 13.1％in most Enterobacterales species except for Klebsiella,21.7％-23.1％of which were resistant to carbapenems.Most Enterobacterales isolates were highly susceptible to tigecycline,colistin and polymyxin B,with resistance rates ranging from 0.1％to 13.3％.The prevalence of meropenem-resistant strains decreased from 23.5％in 2019 to 18.0％in 2022 in Pseudomonas aeruginosa,and decreased from 79.0％in 2019 to 72.5％in 2022 in Acinetobacter baumannii.Conclusions The resistance of clinical isolates to the commonly used antimicrobial agents is still increasing in tertiary hospitals.However,the prevalence of important carbapenem-resistant organisms such as carbapenem-resistant K.pneumoniae,P.aeruginosa,and A.baumannii showed a downward trend in recent years.This finding suggests that the strategy of combining antimicrobial resistance surveillance with multidisciplinary concerted action works well in curbing the spread of resistant bacteria.

Aim To investigate the involvement of mesencephalic astrocyte-derived neurotrophic factor(MANF)in rifampicin(RFP)-induced cholestatic liv-er injury.Methods We investigated the impact of MANF gene deletion on rifampicin-induced BAT ex-pression in mice by the MANF gene knockout mouse model.We investigated the influence of MANF knock-down on nuclear factor erythroid 2-related factor 2(Nrf2)in HepG2 cells by the MANF knockdown cell model.Results Compared with the wild-type(WT)mice,the mRNA and protein expression levels of bile salt export pump(BSEP)and multidrug-resistant asso-ciated protein4(MRP4)significantly increased in WT mice treated with RFP.However,compared to the WT mice treated with RFP,the mRNA and protein expres-sion levels of BSEP,Multidrug resistance protein 1(MDR1),multidrug resistance associated proteins 2/3/4(MRP2/3/4),and organic solute transport pro-teins α(OST α)were significantly reduced.In cell experiments we found that MANF knockdown weakened the expression of Nrf2 and its nuclear translocation by RFP.Conclusion MANF may regulate adaptive BAT expression by modulating Nrf2 expression,thereby pla-ying a protective role in RFP-induced liver injury.