The aryl hydrocarbon receptor regulates epidermal differentiation through transient activation of TFAP2A.

The aryl hydrocarbon receptor (AHR) is an evolutionary conserved environmental sensor identified as indispensable regulator of epithelial homeostasis and barrier organ function. Molecular signaling cascade and target genes upon AHR activation and their contribution to cell and tissue function are however not fully understood. Multi-omics analyses using human skin keratinocytes revealed that, upon ligand activation, AHR binds open chromatin to induce expression of transcription factors (TFs), e.g., Transcription Factor AP-2α (TFAP2A), as a swift response to environmental stimuli. The terminal differentiation program including upregulation of barrier genes, filaggrin and keratins, was mediated by TFAP2A as a secondary response to AHR activation. The role of AHR-TFAP2A axis in controlling keratinocyte terminal differentiation for proper barrier formation was further confirmed using CRISPR/Cas9 in human epidermal equivalents. Overall, the study provides additional insights into the molecular mechanism behind AHR-mediated barrier function and identifies potential targets for the treatment of skin barrier diseases.

scANANSE gene regulatory network and motif analysis of single-cell clusters.

The recent development of single-cell techniques is essential to unravel complex biological systems. By measuring the transcriptome and the accessible genome on a single-cell level, cellular heterogeneity in a biological environment can be deciphered. Transcription factors act as key regulators activating and repressing downstream target genes, and together they constitute gene regulatory networks that govern cell morphology and identity. Dissecting these gene regulatory networks is crucial for understanding molecular mechanisms and disease, especially within highly complex biological systems. The gene regulatory network analysis software ANANSE and the motif enrichment software GimmeMotifs were both developed to analyse bulk datasets. We developed scANANSE, a software pipeline for gene regulatory network analysis and motif enrichment using single-cell RNA and ATAC datasets. The scANANSE pipeline can be run from either R or Python. First, it exports data from standard single-cell objects. Next, it automatically runs multiple comparisons of cell cluster data. Finally, it imports the results back to the single-cell object, where the result can be further visualised, integrated, and interpreted. Here, we demonstrate our scANANSE pipeline on a publicly available PBMC multi-omics dataset. It identifies well-known cell type-specific hematopoietic factors. Importantly, we also demonstrated that scANANSE combined with GimmeMotifs is able to predict transcription factors with both activating and repressing roles in gene regulation.

Interventions to treat patients with blood blister-like aneurysms of the internal carotid artery: a protocol for a network meta-analysis.

INTRODUCTION: Blood blister-like aneurysm (BBA) is a special type of intracranial aneurysm with relatively low morbidity and high mortality. Various microsurgical techniques and endovascular approaches have been reported, but the optimal management remains controversial. For a better understanding of the treatment of BBA patients, a network meta-analysis that comprehensively compares the effects of different therapies is necessary. METHODS AND ANALYSIS: This protocol has been reported following the Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols. Related studies in the following databases will be searched until November 2022: PubMed, Embase, Scopus, Web of Science, Cochrane Library, China National Knowledge Infrastructure (CNKI), VIP and Wanfang. Randomised controlled trials (RCTs) and non-randomised studies comparing at least two different interventions in BBA patients will be included. Quality assessment will be conducted using Cochrane Collaboration's tool or Newcastle-Ottawa Scale based on their study designs. The primary outcome is the composite of the incidences of intraoperative bleeding, postoperative bleeding and postoperative recurrence. The secondary outcome is an unfavourable functional outcome. Pairwise and network meta-analyses will be conducted using STATA V.14 (StataCorp, College Station, Texas, USA). Mean ranks and the surface under the cumulative ranking curve will be used to evaluate every intervention. Statistical inconsistency assessment, subgroup analysis, sensitivity analysis and publication bias assessment will be performed. ETHICS AND DISSEMINATION: Ethics approval is not necessary because this study will be based on publications. The results of this study will be published in a peer-reviewed journal. PROSPERO REGISTRATION NUMBER: CRD42022383699.

Identification of the regulatory circuit governing corneal epithelial fate determination and disease.

The transparent corneal epithelium in the eye is maintained through the homeostasis regulated by limbal stem cells (LSCs), while the nontransparent epidermis relies on epidermal keratinocytes for renewal. Despite their cellular similarities, the precise cell fates of these two types of epithelial stem cells, which give rise to functionally distinct epithelia, remain unknown. We performed a multi-omics analysis of human LSCs from the cornea and keratinocytes from the epidermis and characterized their molecular signatures, highlighting their similarities and differences. Through gene regulatory network analyses, we identified shared and cell type-specific transcription factors (TFs) that define specific cell fates and established their regulatory hierarchy. Single-cell RNA-seq (scRNA-seq) analyses of the cornea and the epidermis confirmed these shared and cell type-specific TFs. Notably, the shared and LSC-specific TFs can cooperatively target genes associated with corneal opacity. Importantly, we discovered that FOSL2, a direct PAX6 target gene, is a novel candidate associated with corneal opacity, and it regulates genes implicated in corneal diseases. By characterizing molecular signatures, our study unveils the regulatory circuitry governing the LSC fate and its association with corneal opacity.

Comparison of surgical strategies in patients with chronic subdural haematoma: a protocol for a network meta-analysis.

INTRODUCTION: Chronic subdural haematoma (CSDH) is one of the most common neurosurgical emergencies, especially in the elderly population. Surgery is the mainstay of treatment for CSDH. Some studies have suggested that some specific surgical strategies can have potential benefits for patients with CSDH; however, the best surgical method is still controversial. For a better understanding of surgical treatment for these patients, it is necessary to conduct a network meta-analysis to comprehensively compare the effects of medical treatment and different surgical methods. METHODS AND ANALYSIS: This protocol has been reported following the Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols. Related studies published up to April 2023 will be searched in the following databases: PubMed, Embase, Scopus, Web of Science, the Cochrane Library, China National Knowledge Infrastructure, VIP and Wanfang. Randomised controlled trials and non-randomised prospective studies comparing at least two different interventions for patients with CSDH will be included. Quality assessment will be conducted using Cochrane Collaboration's tool or the Newcastle-Ottawa Scale based on study design. The primary outcome will be the recurrence rates, and the secondary outcome will be the functional outcome at the end of follow-up. Pairwise and network meta-analyses will be conducted using STATA V.14 (StataCorp, College Station, Texas, USA). Mean ranks and the surface under the cumulative ranking curve will be used to evaluate each intervention. Statistical inconsistency assessment, subgroup analysis, sensitivity analysis and publication bias assessment will be performed. ETHICS AND DISSEMINATION: Ethics approval is not necessary because this study will be based on publications. The results of this study will be published in a peer-reviewed journal. PROSPERO REGISTRATION NUMBER: CRD42022376829.

Isotopic Tracing of Nucleotide Sugar Metabolism in Human Pluripotent Stem Cells.

Metabolism not only produces energy necessary for the cell but is also a key regulator of several cellular functions, including pluripotency and self-renewal. Nucleotide sugars (NSs) are activated sugars that link glucose metabolism with cellular functions via protein N-glycosylation and O-GlcNAcylation. Thus, understanding how different metabolic pathways converge in the synthesis of NSs is critical to explore new opportunities for metabolic interference and modulation of stem cell functions. Tracer-based metabolomics is suited for this challenge, however chemically-defined, customizable media for stem cell culture in which nutrients can be replaced with isotopically labeled analogs are scarcely available. Here, we established a customizable flux-conditioned E8 (FC-E8) medium that enables stem cell culture with stable isotopes for metabolic tracing, and a dedicated liquid chromatography mass-spectrometry (LC-MS/MS) method targeting metabolic pathways converging in NS biosynthesis. By 13C6-glucose feeding, we successfully traced the time-course of carbon incorporation into NSs directly via glucose, and indirectly via other pathways, such as glycolysis and pentose phosphate pathways, in induced pluripotent stem cells (hiPSCs) and embryonic stem cells. Then, we applied these tools to investigate the NS biosynthesis in hiPSC lines from a patient affected by deficiency of phosphoglucomutase 1 (PGM1), an enzyme regulating the synthesis of the two most abundant NSs, UDP-glucose and UDP-galactose.

Single-Cell RNA Sequencing: Opportunities and Challenges for Studies on Corneal Biology in Health and Disease.

The structure and major cell types of the multi-layer human cornea have been extensively studied. However, various cell states in specific cell types and key genes that define the cell states are not fully understood, hindering our comprehension of corneal homeostasis, related diseases, and therapeutic discovery. Single-cell RNA sequencing is a revolutionary and powerful tool for identifying cell states within tissues such as the cornea. This review provides an overview of current single-cell RNA sequencing studies on the human cornea, highlighting similarities and differences between them, and summarizing the key genes that define corneal cell states reported in these studies. In addition, this review discusses the opportunities and challenges of using single-cell RNA sequencing to study corneal biology in health and disease.

The aryl hydrocarbon receptor regulates epidermal differentiation through transient activation of TFAP2A.

The aryl hydrocarbon receptor (AHR) is an evolutionary conserved environmental sensor identified as indispensable regulator of epithelial homeostasis and barrier organ function. Molecular signaling cascade and target genes upon AHR activation and their contribution to cell and tissue function are however not fully understood. Multi-omics analyses using human skin keratinocytes revealed that, upon ligand activation, AHR binds open chromatin to induce expression of transcription factors (TFs), e.g., Transcription Factor AP-2α (TFAP2A), as a swift response to environmental stimuli. The terminal differentiation program including upregulation of barrier genes, filaggrin and keratins, was mediated by TFAP2A as a secondary response to AHR activation. The role of AHR-TFAP2A axis in controlling keratinocyte terminal differentiation for proper barrier formation was further confirmed using CRISPR/Cas9 in human epidermal equivalents. Overall, the study provides novel insights into the molecular mechanism behind AHR-mediated barrier function and potential novel targets for the treatment of skin barrier diseases.

Disease-related p63 DBD mutations impair DNA binding by distinct mechanisms and varying degree.

The transcription factor p63 shares a high sequence identity with the tumour suppressor p53 which manifests itself in high structural similarity and preference for DNA sequences. Mutations in the DNA binding domain (DBD) of p53 have been studied in great detail, enabling a general mechanism-based classification. In this study we provide a detailed investigation of all currently known mutations in the p63 DBD, which are associated with developmental syndromes, by measuring their impact on transcriptional activity, DNA binding affinity, zinc binding capacity and thermodynamic stability. Some of the mutations we have further characterized with respect to their ability to convert human dermal fibroblasts into induced keratinocytes. Here we propose a classification of the p63 DBD mutations based on the four different mechanisms of DNA binding impairment which we identified: direct DNA contact, zinc finger region, H2 region, and dimer interface mutations. The data also demonstrate that, in contrast to p53 cancer mutations, no p63 mutation induces global unfolding and subsequent aggregation of the domain. The dimer interface mutations that affect the DNA binding affinity by disturbing the interaction between the individual DBDs retain partial DNA binding capacity which correlates with a milder patient phenotype.

Lateral ventricle ectopic schwannoma: Case report and literature review.

Background: Cases of lateral ventricular ectopic schwannomas (LVES) are extremely rare, with only 23 cases reported thus far. This study aimed to obtain a better understanding of the disease. Methods: We reported a rare case of LVES, in which the patient was admitted to our hospital, and reviewed the relevant literature on LVES to summarize and analyze the clinical manifestations, pathologies, imaging features and progress. Results: Of the 23 patients, LVES was more common in men (74%, 17/23) than in women and was mostly located on the right side (78%, 18/23). The average age at clinical presentation was 28 years, with an age range between 8 and 68 years. Moreover, most cases were histologically benign, except in one case of malignancy. In all the benign cases, there were 2 cases of subtotal resection, but no recurrence was found during follow-up. Conclusions: The origin of LVES could be the tumor transformation of autonomic nerve tissue in the perivascular choroid plexus. For lateral ventricle tumors,which are rare benign lesions with good prognosis after surgical resection, LVES should be considered in the differential diagnosis. Moreover, whether LVES could be considered for gamma knife treatment, similar to a small acoustic neuromas,requires further investigation.

A high neutrophil-to-platelet ratio is associated with hematoma expansion in patients with spontaneous intracerebral hemorrhage: a retrospective study.

BACKGROUND: Early hematoma expansion (HE) occurs in 20 to 40% of spontaneous intracerebral hemorrhage (ICH) patients and is a primary determinant of early deterioration and poor prognosis. Previous studies have shown that inflammation is a major pathological feature of ICH, and the neutrophil-to-platelet ratio (NPR) is a marker of systemic inflammation. Therefore, we aimed to assess the association between the NPR and HE in ICH patients. METHODS: We retrospectively collected and analyzed data from ICH patients who received treatment at our institution from January 2018 to November 2019. The NPR was calculated from the admission blood test. Brain computed tomography (CT) scans were performed at admission and repeated within 24 h. Hematoma growth was defined as relative growth > 33% or absolute growth > 6 ml. RESULTS: A total of 317 patients were enrolled in our study. Multivariate logistic regression analysis indicated that the NPR was an independent predictor of HE [odds ratio (OR) = 1.742; 95% CI: 1.508-2.012, p < 0.001]. Receiver operating characteristic (ROC) curve analysis revealed that the NPR could predict HE, with an area under the curve of 0.838 (95% CI, 0.788-0.888, p < 0.001). The best predictive cut-off of the NPR for HE was 5.47 (sensitivity, 75.3%; specificity, 77.6%). CONCLUSIONS: A high NPR was associated with an increased risk of HE in patients with ICH.

Effects of enhanced recovery after surgery plus pulmonary rehabilitation on complications after video-assisted lung cancer surgery: a multicentre randomised controlled trial.

BACKGROUND: Lung cancer surgery is associated with a high incidence of postoperative pulmonary complications (PPCs). We evaluated whether enhanced recovery after surgery plus pulmonary rehabilitation was superior over enhanced recovery after surgery alone in reducing the incidence of postoperative PPCs and length of hospital stay. METHODS: In this pragmatic multicentre, randomised controlled, parallel-group clinical trial, eligible patients scheduled for video-assisted lung cancer surgery were randomly assigned (1:1) to either a newly developed programme that integrated preoperative and postoperative pulmonary rehabilitation components into a generic thoracic enhanced recovery after surgery pathway, or routine thoracic enhanced recovery after surgery. Primary outcome was the overall occurrence of PPCs within 2 weeks after surgery. Secondary outcomes were the occurrence of specific complications, time to removal of chest drain, and length of hospital stay (LOS). RESULTS: Of 428 patients scheduled for lung cancer surgery, 374 were randomised with 187 allocated to the experimental programme and 187 to control. Incidence of PPCs at 14 Days was 18.7% (35/187) in the experimental group and 33.2% (62/187) in the control group (intention-to-treat, unadjusted HR 0.524, 95% CI 0.347 to 0.792, p=0.002). Particularly, significant risk reduction was observed regarding pleural effusion, pneumonia and atelectasis. Time to removal of chest drain and LOS were not significantly reduced in the experimental group. CONCLUSIONS: Adding pulmonary rehabilitation to enhanced recovery after surgery appears to be effective in reducing the incidence of PPCs, but not LOS. Standard integration of pulmonary rehabilitation into thoracic enhanced recovery after surgery is a promising approach to PPC prophylaxis. TRIAL REGISTRATION NUMBER: ChiCTR1900024646.

Fibroblast growth factor-2 bound to specific dermal fibroblast-derived extracellular vesicles is protected from degradation.

Fibroblast growth factor-2 (FGF2) has multiple roles in cutaneous wound healing but its natural low stability prevents the development of its use in skin repair therapies. Here we show that FGF2 binds the outer surface of dermal fibroblast (DF)-derived extracellular vesicles (EVs) and this association protects FGF2 from fast degradation. EVs isolated from DF cultured in the presence of FGF2 harbor FGF2 on their surface and FGF2 can bind purified EVs in absence of cells. Remarkably, FGF2 binding to EVs is restricted to a specific subpopulation of EVs, which do not express CD63 and CD81 markers. Treatment of DF with FGF2-EVs activated ERK and STAT signaling pathways and increased cell proliferation and migration. Local injection of FGF2-EVs improved wound healing in mice. We further demonstrated that binding to EVs protects FGF2 from both thermal and proteolytic degradation, thus maintaining FGF2 function. This suggests that EVs protect soluble factors from degradation and increase their stability and half-life. These results reveal a novel aspect of EV function and suggest EVs as a potential tool for delivering FGF2 in skin healing therapies.

Mutant Ras and inflammation-driven skin tumorigenesis is suppressed via a JNK-iASPP-AP1 axis.

Concurrent mutation of a RAS oncogene and the tumor suppressor p53 is common in tumorigenesis, and inflammation can promote RAS-driven tumorigenesis without the need to mutate p53. Here, we show, using a well-established mutant RAS and an inflammation-driven mouse skin tumor model, that loss of the p53 inhibitor iASPP facilitates tumorigenesis. Specifically, iASPP regulates expression of a subset of p63 and AP1 targets, including genes involved in skin differentiation and inflammation, suggesting that loss of iASPP in keratinocytes supports a tumor-promoting inflammatory microenvironment. Mechanistically, JNK-mediated phosphorylation regulates iASPP function and inhibits iASPP binding with AP1 components, such as JUND, via PXXP/SH3 domain-mediated interaction. Our results uncover a JNK-iASPP-AP1 regulatory axis that is crucial for tissue homeostasis. We show that iASPP is a tumor suppressor and an AP1 coregulator.

Measuring thermodynamic preferences to form non-native conformations in nucleic acids using ultraviolet melting.

Thermodynamic preferences to form non-native conformations are crucial for understanding how nucleic acids fold and function. However, they are difficult to measure experimentally because this requires accurately determining the population of minor low-abundance (<10%) conformations in a sea of other conformations. Here, we show that melting experiments enable facile measurements of thermodynamic preferences to adopt nonnative conformations in DNA and RNA. The key to this "delta-melt" approach is to use chemical modifications to render specific minor non-native conformations the major state. The validity and robustness of delta-melt is established for four different non-native conformations under various physiological conditions and sequence contexts through independent measurements of thermodynamic preferences using NMR. Delta-melt is faster relative to NMR, simple, and cost-effective and enables thermodynamic preferences to be measured for exceptionally low-populated conformations. Using delta-melt, we obtained rare insights into conformational cooperativity, obtaining evidence for significant cooperativity (1.0 to 2.5 kcal/mol) when simultaneously forming two adjacent Hoogsteen base pairs. We also measured the thermodynamic preferences to form G-C+ and A-T Hoogsteen and A-T base open states for nearly all 16 trinucleotide sequence contexts and found distinct sequence-specific variations on the order of 2 to 3 kcal/mol. This rich landscape of sequence-specific non-native minor conformations in the DNA double helix may help shape the sequence specificity of DNA biochemistry. Thus, melting experiments can now be used to access thermodynamic information regarding regions of the free energy landscape of biomolecules beyond the native folded and unfolded conformations.

Development of Mild Chemical Catalysis Conditions for m1A-to-m6A Rearrangement on RNA.

The conversion of N1-methyladenosine (m1A) to N6-methyladenosine (m6A) on RNA is an important step for both allowing efficient reverse transcription read-though for sequencing analysis and mapping modifications in the transcriptome. Enzymatic transformation is often used, but the efficiency of the removal can depend on local sequence context. Chemical conversion through the application of the Dimroth rearrangement, in which m1A rearranges into m6A under heat and alkaline conditions, is an alternative, but the required alkaline conditions result in significant RNA degradation by hydrolysis of the phosphodiester backbone. Here, we report novel, mild pH conditions that catalyze m1A-to-m6A arrangement using 4-nitrothiophenol as a catalyst. We demonstrate the efficient rearrangement in mononucleosides, synthetic RNA oligonucleotides, and RNAs isolated from human cell lines, thereby validating a new approach for converting m1A-to-m6A in RNA samples for sequencing analyses.

New Advances in Nano-Drug Delivery Systems: Helicobacter pylori and Gastric Cancer.

With the development of materials science and biomedicine, the application of nanomaterials in the medical field is further promoted. In the process of the diagnosis and treatment of diseases, a variety of drugs need to be used. It is an ideal state to make these drugs arrive at a specific location at a specific time and release at a specific speed, which can improve the bioavailability of drugs and reduce the adverse effects of drugs on normal tissues. Traditional drug delivery methods such as tablets, capsules, syrups, and ointments have certain limitations. The emergence of a new nano-drug delivery system further improves the accuracy of drug delivery and the efficacy of drugs. It is well known that the development of the cancer of the stomach is the most serious consequence for the infection of Helicobacter pylori. For the patients who are suffering from gastric cancer, the treatments are mainly surgery, chemotherapy, targeted and immune therapy, and other comprehensive treatments. Although great progress has been made, the diagnosis and prognosis of gastric cancer are still poor with patients usually diagnosed with cancer at an advanced stage. Current treatments are of limited benefits for patients, resulting in a poor 5-year survival rate. Nanomaterials may play a critical role in early diagnosis. A nano-drug delivery system can significantly improve the chemotherapy, targeted therapy, and immunotherapy of advanced gastric cancer, reduce the side effects of the original treatment plan and provide patients with better benefits. It is a promising treatment for gastric cancer. This article introduces the application of nanomaterials in the diagnosis and treatment of H. pylori and gastric cancer.

Measuring healthy female nulliparous pubovisceral muscle from diffusion kurtosis imaging.

This study explores the feasibility of using diffusion kurtosis imaging (DKI) in the pelvic floor region and assesses the water diffusivity of the pubovisceral muscle. Twenty-seven healthy young nulliparous females underwent DKI at 3.0 T that included 15 gradient directions and three b values (0, 750, and 1500 s/mm2 ). The diffusion tensor and diffusion kurtosis metrics values of the pubovisceral muscle were measured after image processing. Two independent sample t-tests, a paired-samples t-test, and a nonparametric hypothesis test were performed as appropriate to compare the differences among different metrics. Twenty-six subjects (mean ± standard deviation age, 25 ± 2 years) were successfully analyzed by measuring the diffusion tensor and diffusion kurtosis metrics of the bilateral pubovisceral muscles. The metrics included mean kurtosis, axial kurtosis, radial kurtosis, fractional anisotropy, mean diffusivity, axial diffusivity, and radial diffusivity. We found no statistically significant differences for these measurement values between the left and right pubovisceral muscles (p = 0.271-0.931). However, radial kurtosis was greater than axial kurtosis in both pubovisceral muscles (p < 0.001) and axial diffusivity was lower than radial diffusivity in both pubovisceral muscles (p < 0.001). We deem the application of DKI technology to the pelvic floor region to be feasible.

Enhanced pro-apoptosis gene signature following the activation of TAp63α in oocytes upon γ irradiation.

Specialized surveillance mechanisms are essential to maintain the genetic integrity of germ cells, which are not only the source of all somatic cells but also of the germ cells of the next generation. DNA damage and chromosomal aberrations are, therefore, not only detrimental for the individual but affect the entire species. In oocytes, the surveillance of the structural integrity of the DNA is maintained by the p53 family member TAp63α. The TAp63α protein is highly expressed in a closed and inactive state and gets activated to the open conformation upon the detection of DNA damage, in particular DNA double-strand breaks. To understand the cellular response to DNA damage that leads to the TAp63α triggered oocyte death we have investigated the RNA transcriptome of oocytes following irradiation at different time points. The analysis shows enhanced expression of pro-apoptotic and typical p53 target genes such as CDKn1a or Mdm2, concomitant with the activation of TAp63α. While DNA repair genes are not upregulated, inflammation-related genes become transcribed when apoptosis is initiated by activation of STAT transcription factors. Furthermore, comparison with the transcriptional profile of the ΔNp63α isoform from other studies shows only a minimal overlap, suggesting distinct regulatory programs of different p63 isoforms.