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*

Guided by molecular networking, nine novel curvularin derivatives (1-9) and 16 known analogs (10-25) were isolated from the hydrothermal vent sediment fungus Penicillium sp. HL-50. Notably, compounds 5-7 represented a hybrid of curvularin and purine. The structures and absolute configurations of compounds 1-9 were elucidated via nuclear magnetic resonance (NMR) spectroscopy, X-ray diffraction, electronic circular dichroism (ECD) calculations, ¹³C NMR calculation, modified Mosher's method, and chemical derivatization. Investigation of anti-inflammatory activities revealed that compounds 7-9, 11, 12, 14, 15, and 18 exhibited significant suppressive effects against lipopolysaccharide (LPS)-induced nitric oxide (NO) production in murine macrophage RAW264.7 cells, with IC₅₀ values ranging from 0.44 to 4.40 μmol·L^-1. Furthermore, these bioactive compounds were found to suppress the expression of inflammation-related proteins, including inducible NO synthase (iNOS), cyclooxygenase-2 (COX-2), NLR family pyrin domain-containing protein 3 (NLRP3), and nuclear factor kappa-B (NF-κB). Additional studies demonstrated that the novel compound 7 possessed potent anti-inflammatory activity by inhibiting the transcription of inflammation-related genes, downregulating the expression of inflammation-related proteins, and inhibiting the release of inflammatory cytokines, indicating its potential application in the treatment of inflammatory diseases.
Penicillium/chemistry* ; Mice ; Animals ; Anti-Inflammatory Agents/isolation & purification* ; RAW 264.7 Cells ; Nitric Oxide/metabolism* ; Hydrothermal Vents/microbiology* ; Macrophages/immunology* ; Molecular Structure ; Nitric Oxide Synthase Type II/immunology* ; Cyclooxygenase 2/immunology* ; Geologic Sediments/microbiology* ; NF-kappa B/immunology* ; NLR Family, Pyrin Domain-Containing 3 Protein/immunology*

Objective To investigate the clinical features of Menkes disease(MD)caused by ATP7A gene mutation.Methods Clinical data of one MD patient was retrospectively analyzed,and the literature on the MD cases was reviewed.Results The patient was a 7-month-old male.The initial symptoms were epilepsy,feeding difficulties and psychomotor retardation,followed by distinctive facial appearance,hair abnormality,pectus excavatum and hypotonia.Biochemical tests revealed reduced serum ceruloplasmin and copper.Brain MRI showed diffuse cerebral atrophy,cerebral dysplasia and subdural effusion.Genetic testing showed that there was a new hemizygous mutation c.2916+2(IVS14)T＞C in the ATP7A gene splicing site on the X chromosome,which verified that the mother was a heterozygous carrier with a normal phenotype.Conclusions MD often starts in infancy and childhood.MD may involve multi-system such as the nervous system and connective tissues,and should be diagnosed with genetic testing.

Objective:To investigate the efficacy and safety of separated R-CHOP in older patients with newly diagnosed diffuse large B-cell lymphoma(DLBCL).Methods:A total of 137 patients aged 65-80 years newly diagnosed with DLBCL between April 2013 and September 2022 at The First Affiliated Hospital of Zhengzhou University were enrolled.The patients were assigned into separated R-CHOP,full-dose R-CHOP,and reduced R-CHOP-like groups based on their different chemotherapy regimens.All individuals were treated in 21-day cycles for 4-8 cycles.The short-term and long-term efficacies and adverse reactions of the treatments were compared among the three groups,and factors influencing progression-free survival(PFS)and overall survival(OS)were analyzed.Results:The overall response rates(ORR)of patients in the separated R-CHOP,full-dose R-CHOP,and reduced R-CHOP-like groups were 89.7%,90.3%,and 86.1%,respectively,with no significant differences among them.The complete respond rate(CRR)of the separated R-CHOP group(64.1%)was significantly higher than that of the reduced R-CHOP-like group(33.3%)(P=0.008)but not significantly different from that of the full-dose R-CHOP group(66.1%).Survival curve analysis revealed no significant differences in PFS and OS between the separated and full-dose R-CHOP groups.Although the separated R-CHOP group showed improved PFS compared with the reduced R-CHOP-like group(P=0.036),there was no statistical difference in OS between these two groups.Multivariate analysis revealed that the international prognostic index(IPI)and separated R-CHOP had significant effects on PFS in patients with DLBCL(all P<0.05),whereas only IPI had a significant effect on OS(P<0.001).The incidence of leukopenia and grade 3-4 leukopenia in the separated R-CHOP group was significantly lower than that in the full-dose R-CHOP group(P=0.007,P=0.012),but there was no significant difference with the reduced R-CHOP-like group in this regard.Conclusions:In older patients with newly diagnosed DLBCL,separated R-CHOP showed good efficacy both in the short and long terms and had acceptable safety and tolerability profiles.

Objective:To improve the therapeutic regimen for mantle cell lymphoma,we investigated the efficacy and safety of adding a BTK inhibitor to a regimen including rituximab,bendamustine,cytarabine,and prednisone to treat patients with mantle cell lymphoma(MCL).Methods:Twenty-six patients newly diagnosed with MCL who were admitted to The First Affiliated Hospital of Zhengzhou University from March 2021 to November 2023 were treated with a regimen of rituximab,bendamustine,cytarabine and prednisone combined with a BTK inhibitor,and the efficacy and adverse effects of this regiment were retrospectively analyzed.Results:The median age of the 26 newly dia-gnosed MCL patients was 59(41-72)years.The cohort included 22 males and 4 females,and the median follow-up time was 12(3-28)months.The overall response rate(ORR)was 92.3%and the complete response rate(CRR)was 88.5%.Median progression-free survival(PFS)and median overall survival(OS)endpoints were not achieved,with a 1-year PFS rate of 81.25%and a 1-year OS rate of 92.3%.A bet-ter PFS was achieved in the low mantle cell lymphoma International Prognostic Index(MIPI)score(0-3 points)group than in the high MIPI score(4-11 points)group(P=0.020).PFS was better in the group without B symptoms than in the group with B symptoms(P=0.002).PFS was better in the classical group than in the pleomorphic-blastoid subtype group(P=0.009).The main adverse effects were lymphopenia and thrombocytopenia.No treatment-related serious adverse events were observed during the follow-up period.Conclusions:The regimen of rituximab,bendamustine,cytarabine,and prednisone in combination with BTK inhibitors is safe and effective for the treatment of newly dia-gnosed patients with MCL.

Objective To explore the prognostic factors of primary mediastinal large B-cell lymphoma (PMBCL) and the effects of chemoradiotherapy versus chemotherapy alone on patients' prognosis before and after rituximab era. Methods We extracted the data of PMBCL patients diagnosed from 2001 to 2015 from SEER database. SEER Stat software was used to calculate the incidence rate. Kaplan-Meier method and Cox regression model were used to analyze the impact of various clinical variables on prognosis. Results We included 635 patients with PMBCL. Multivariate Cox regression analysis showed that age, stage and chemotherapy were independent prognostic factors. Kaplan-Meier survival analysis showed that OS of the patients receiving chemotherapy only in 2006-2015 was significantly better than that in 2001-2005 (χ²=10.002, P=0.002). The patients who received chemoradiotherapy had better OS than those who received chemotherapy alone from 2001 to 2005. The OS and DSS of patients receiving chemoradiotherapy were not significantly different from those of chemotherapy alone from 2006 to 2015. Conclusion The application of rituximab improves the long-term survival of PMBCL patients. The prognosis of patients who received chemoradiotherapy is comparable to that of chemotherapy alone from 2006 to 2015.

Objective:To explore the protective effect of sodium channels antagonists HOE642 on lung ischemia reperfusion and the role of the p38 mitogen activated protein kinase (p38MAPK) signaling pathway in this process.Methods:A total of 36 mice were randomly divided into a sham operation group (SHAM group),a lung ischemia reperfusion group (I/R group) and a lung ischemia reperfusion+HOE642 group (HOE group).The water content was detected by electronic scales,and the lung tissue pathological changes were observed under optical microscope.The inflammatory cytokines including IL-6 and TNF-α were examined by ELISA.The intracellular calcium fluorescence intensity was examined and observed under fluorescence microscope,and the protein expression of p38MAPK was detected by Western blot.Results:Lung water content in the HOE group was lower than that in the I/R group,but higher than that in the SHAM group (both P＜0.05).Lung interstitial edema,hemorrhage,lung tissue inflammatory cells infiltration were significantly alleviated in the HOE group than those in the I/R group,while the injury in the HOE group was aggravated than those in the SHAM group (both P＜0.05).T he IL-6 and TNF-α in lung tissues in the HOE group were lower than those in the I/R group,but higher than those in the SHAM group (both P＜0.05).Intracellular calcium fluorescence intensity in the HOE group was lower than that in the I/R group,but higher than that in the SHAM group (both P＜0.05).The protein expression of p38MAPK in lung tissues in the HOE group was lower than that in the I/R group,but higher than that in the SHAM group (both P＜0.05).Conclusion:HOE642 may exert protective effect on pulmonary I/R injury through regulation of the p38MAPK signaling pathway,resulting in reduction of intracellular calcium ion concentration and calcium overload,and decrease of inflammatory response.

Objective To explore clinical effects and operative experience of transanal pull-through procedure for Hirschsprung's disease (HD).Methods The clinical data of 126 children aged from 13 days to 14 years with HD were reviewed.There were 30 cases of short-segment type,85 of common type,and 11 of long-segment type.A total of 95 cases was operated with modified Soave and the other 31 cases were operated with modified Swenson.Results Except two-stage resection in 7(5.6％) cases who already underwent transanal Soave procedure early,one-stage transanal pull-through procedure was performed in the other cases.Laparotomy assisted operation was used for 5 cases and laparoscope assisted operation for 12 cases.The complications were occurred in 35 (27.8％) cases post-operation,including 15 perianatitis,9 enterocolitis,5 anastomotic stenosis,2 soiling,and 4 reoperation.The statistical analysis indicated no difference between two procedures and postoperative complications could be noted between different types (P ＞0.05).A total of 103 patients were followed up from 1 to 10 (mean 2) years.Of all patients,96 (93.2％) were cured,5 (4.9％) symptoms were improved and 2(1.9％) were failed.There were no significant differences in two procedure and the excellent rate of defecation function(P ＞ 0.05).Conclusions Two transanal procedures for HD both had a good efficacy and similar complications.By comparison,transanal Swenson procedure was simpler than Soave procedure,and did not need to enlarge anus post-operation as well.

AIM To investigate whether tubeimosides induce apoptosis in CNE-2Z. METHODS Growth inhibition by tubeimosides was measured using MTT assay. The effect of tubeimosides on apoptosis induction of CNE-2Z cell line was studied by the fluorescent microscopy, electronic microscopy, DNA agarose gel electrophoresis, flow cytometry analysis. Western blotting was performed for detecting the apoptosis-related gene. RESULTS The growth of CNE-2Z cells was inhibited obviously by tubeimosides. CNE-2Z cells showed typical apoptotic features observed by fluorescent microscopy, electronic microscopy. DNA fragmentation into multiples of low molecular weight DNA(180～200 bp) was detected by agarose gel electrophoresis of DNA; Sub-G 1 peak was found by flow cytometry analysis, and the apoptosis index was 58 0%. The expression of bcl-2, inhibitor of apoptosis, decreased apparently; while that of bax, inducer of apoptosis, increased notably at 1, 3, 5 h after the addition of tubeimosides. The cleavage of caspase-3 was noticed at 1, 3, 5 h after the treatment of tubeimosides. CONCLUSION Tubeimosides could induce the apoptosis of CNE-2Z cells. The induction of apoptotic by tubeimosides was closely associated with bcl-2, bax and caspase-3.