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*

Osteoporosis is a prevalent skeletal condition characterized by reduced bone mass and strength, leading to increased fragility. Buqi-Tongluo (BQTL) decoction, a traditional Chinese medicine (TCM) prescription, has yet to be fully evaluated for its potential in treating bone diseases such as osteoporosis. To investigate the mechanism by which BQTL decoction inhibits osteoclast differentiation in vitro and validate these findings through in vivo experiments. We employed MTS assays to assess the potential proliferative or toxic effects of BQTL on bone marrow macrophages (BMMs) at various concentrations. TRAcP experiments were conducted to examine BQTL's impact on osteoclast differentiation. RT-PCR and Western blot analyses were utilized to evaluate the relative expression levels of osteoclast-specific genes and proteins under BQTL stimulation. Finally, in vivo experiments were performed using an osteoporosis model to further validate the in vitro findings. This study revealed that BQTL suppressed receptor activator of NF-κB ligand (RANKL)-induced osteoclastogenesis and osteoclast resorption activity in vitro in a dose-dependent manner without observable cytotoxicity. The inhibitory effects of BQTL on osteoclast formation and function were attributed to the downregulation of NFATc1 and c-fos activity, primarily through attenuation of the MAPK, NF-κB, and Calcineurin signaling pathways. BQTL's inhibitory capacity was further examined in vivo using an ovariectomized (OVX) rat model, demonstrating a strong protective effect against bone loss. BQTL may serve as an effective therapeutic TCM for the treatment of postmenopausal osteoporosis and the alleviation of bone loss induced by estrogen deficiency and related conditions.
Animals ; NFATC Transcription Factors/genetics* ; Drugs, Chinese Herbal/pharmacology* ; Ovariectomy ; Osteoclasts/metabolism* ; Female ; Osteogenesis/drug effects* ; Rats, Sprague-Dawley ; Rats ; NF-kappa B/genetics* ; Osteoporosis/genetics* ; Signal Transduction/drug effects* ; Bone Resorption/genetics* ; Cell Differentiation/drug effects* ; Humans ; RANK Ligand/metabolism* ; Mitogen-Activated Protein Kinases/genetics* ; Transcription Factors

Aortic Valve/surgery* ; Aortic Valve Stenosis/surgery* ; China/epidemiology* ; Heart Valve Prosthesis Implantation ; Humans ; Severity of Illness Index ; Treatment Outcome

BACKGROUND: The past decade has witnessed an ever-increasing momentum of transcatheter aortic valve replacement (TAVR) and a subsequent paradigm shift in the contemporary management of severe aortic stenosis (AS). We conducted a multi-centric TAVR registry based on Chinese patients (the China Aortic valve tRanscatheter Replacement registrY [CARRY]) to delineate the clinical characteristics and outcomes of Chinese patients who underwent TAVR and compare the results between different valve types in different Chinese regions. METHODS: CARRY is an all-comer registry of aortic valve disease patients undergoing TAVR across China and was designed as an observational study that retrospectively included all TAVR patients at each participating site. Seven hospitals in China participated in the CARRY, and 1204 patients from April 2012 to November 2020 were included. Categorical variables were compared using the chi-squared test, and continuous variables were analyzed using a t test or analysis of variance (ANOVA) test. The Kaplan-Meier curve was used to estimate the risk of adverse events during follow-up. RESULTS: The mean age of the patients was 73.8 ± 6.5 years and 57.2% were male. The median Society of Thoracic Surgeon-Predicted Risk of Mortality score was 6.0 (3.7-8.9). Regarding the aortic valve, the proportion of bicuspid aortic valve (BAV) was 48.5%. During the hospital stay, the stroke rate was 0.7%, and the incidence of high-degree atrioventricular block indicating permanent pacemaker implantation was 11.0%. The in-hospital all-cause mortality rate was 2.2%. After 1 year, the overall mortality rate was 4.5%. Compared to patients with tricuspid aortic valve (TAV), those with BAV had similar in-hospital complication rates, but a lower incidence of in-hospital mortality (1.4% vs. 3.3%) and 1 year mortality (2.3% vs. 5.8%). CONCLUSIONS: TAVR candidates in China were younger, higher proportion of BAV, and had lower rates of post-procedural complications and mortality than other international all-comer registries. Given the use of early generation valves in the majority of the population, patients with BAV had similar rates of complications, but lower mortality than those with TAV. These findings further propel the extension of TAVR in low-risk patients. TRIAL REGISTRATION https://www.chictr.org.cn/ (No. ChiCTR2000038526).
Aged ; Aged, 80 and over ; Aortic Valve/surgery* ; Aortic Valve Stenosis/surgery* ; Humans ; Male ; Registries ; Retrospective Studies ; Risk Factors ; Transcatheter Aortic Valve Replacement/adverse effects* ; Treatment Outcome

Establishing an effective three-dimensional (3D) culture system to better model human neurological diseases is desirable, since the human brain is a 3D structure. Here, we demonstrated the development of a polydimethylsiloxane (PDMS) pillar-based 3D scaffold that mimicked the 3D microenvironment of the brain. We utilized this scaffold for the growth of human cortical glutamatergic neurons that were differentiated from human pluripotent stem cells. In comparison with the 2D culture, we demonstrated that the developed 3D culture promoted the maturation of human cortical glutamatergic neurons by showing significantly more MAP2 and less Ki67 expression. Based on this 3D culture system, we further developed an disease-like model of traumatic brain injury (TBI), which showed a robust increase of glutamate-release from the neurons, in response to mechanical impacts, recapitulating the critical pathology of TBI. The increased glutamate-release from our 3D culture model was attenuated by the treatment of neural protective drugs, memantine or nimodipine. The established 3D human neural culture system and TBI-like model may be used to facilitate mechanistic studies and drug screening for neurotrauma or other neurological diseases.

OBJECTIVETo study the expression of the ID3 protein in prostate cancer and its clinicopathological significance.

METHODSWe detected the expression of the ID3 protein in PC-3M cells by indirect immunofluorescence, and that in 29 prostate cancer and 15 prostate hyperplasia specimens by immunohistochemistry. Then we analyzed the correlation between the expression level of ID3 and the clinicopathological parameters.

RESULTSThe ID3 protein was expressed predominantly in the nucleus of PC-3M cells. Its expression rate was 82.7% (24/29) in the prostate cancer specimens, significantly higher than 6.6% (1/15) in prostate hyperplasia (P < 0.05), and was positively correlated with the Gleason score of prostate cancer (P < 0.05).

CONCLUSIONThe ID3 protein is expressed in prostate cancer, and is elevated with the increase of Gleason score.

Aged ; Aged, 80 and over ; Fluoroimmunoassay ; Humans ; Immunohistochemistry ; Inhibitor of Differentiation Proteins ; metabolism ; Male ; Middle Aged ; Neoplasm Proteins ; metabolism ; Prostatic Neoplasms ; metabolism ; pathology

OBJECTIVETo investigate the dynamic trend of specific antibody against severe acute respiratory syndrome (SARS)-CoV in serum collected at various periods among employees in Guangzhou Xinyuan animal market.

METHODSVolunteers from employees of the animal market were recruited and their serum specific antibody against SARS-CoV were determined by enzyme linked immunesorbent assay (ELISA) method.

RESULTSPositive SARS-CoV specific IgG antibody was found 25.61% (n = 328), 13.03% (n = 238), 12.59% (n = 135), 5.04% (n = 139) and 9.43% (n = 53) among volunteers, which were sampled in May 2003, Dec. 2003, Jan. 2004, July 2004 and June 2005 respectively. No specific IgM antibody was found in all of those samples. Among 129 samples which were tested twice or more, 97 were all negative, 18 all positive, 13 changed from positive to negative but only one sample from negative to positive. When the volunteers were divided by the duration of their working experiences as short-term or long-term, those who had worked at animal market for less than or more then 6 months when being tested, the positive rate for long-term employees were relatively constant, however, all of the persons employed after January 2004, when the palm civets and raccoon dogs were culled from the market, were tested negative.

CONCLUSIONThe prevalence of specific antibody against SARS-CoV in employees of the animal market were somehow related with the presence or absence of palm civet. No serum was tested positive for persons who were employed after palm civets and raccoon dogs were culled from market. This data indicated that the SARS-CoV might have been from the palm civets and raccoon dog, and the animal market seemed to serve as one of the sources of infection.

Animals ; Antibodies, Viral ; analysis ; Commerce ; Enzyme-Linked Immunosorbent Assay ; Humans ; Occupational Exposure ; Raccoon Dogs ; virology ; SARS Virus ; immunology ; Severe Acute Respiratory Syndrome ; Viverridae ; virology

OBJECTIVETo detect the RNA of severe acute respiratory syndrome virus (SARS-CoV) by using reverse transcription polymerase chain reaction (RT-PCR) targeted for a two loci and a modified nested real-time RT-PCR as to improving the reliability and sensitivity of tests.

METHODSA nested RT-PCR was used for detecting one fragment of SARS-CoV RNA in oropharyngeal swabs from 3 SARS probable patients, 4 SARS suspect patients and other 27 patients with fever in Hangzhou, and the nested RT-PCR product from one SARS probable patient was sequenced. Meanwhile in these 3 SARS probable patients, other three RT-PCR methods, including a hemi-nested RT-PCR targeted for another fragment of SARS-CoV RNA, a real-time RT-PCR and a modified nested real-time RT-PCR, were employed to detect SARS-CoV RNA.

RESULTSTwo positives were found in the 3 SARS probable patients, and none positive in 4 SARS suspect patients and other 27 patients with fever, using the nested RT-PCR. The sequence of the nested RT-PCR product from one SARS probable patient was identified with the counterpart of SARS-CoV genomes published in public database. The results of the hemi-nested RT-PCR, the real-time RT-PCR and the modified nested real-time RT-PCR in the 3 SARS patients were consistent with the one of the nested RT-PCR. During detecting specimen with low copies of RNA, a weak positive signal was produced after about 35 cycles in the real-time RT-PCR, but a strong positive signal was found only after 10 cycles in the modified nested real-time RT-PCR.

CONCLUSIONIt might improve the reliability of test by employing RT-PCR targeted for two or more fragments in SARS-CoV genome. The modified nested real-time RT-PCR might have higher sensitivity than the routine real-time RT-PCR.

Adolescent ; Adult ; Aged ; Aged, 80 and over ; Base Sequence ; Humans ; Middle Aged ; RNA, Viral ; genetics ; metabolism ; Reproducibility of Results ; Reverse Transcriptase Polymerase Chain Reaction ; methods ; SARS Virus ; genetics ; Sensitivity and Specificity ; Severe Acute Respiratory Syndrome ; diagnosis ; virology ; Young Adult