With the rapid development of sequencing technologies, the detection of alternative polyadenylation (APA) in mammals has become more precise. APA precisely regulates gene expression by altering the length and position of the poly(A) tail, and is involved in various biological processes such as disease occurrence and embryonic development. The research on APA in mammals mainly focuses on the following aspects:(1) identifying APA based on transcriptome data and elucidating their characteristics; (2) investigating the relationship between APA and gene expression regulation to reveal its important role in life regulation;(3) exploring the intrinsic connections between APA and disease occurrence, embryonic development, differentiation, and other life processes to provide new perspectives and methods for disease diagnosis and treatment, as well as uncovering embryonic development regulatory mechanisms. In this review, the classification, mechanisms and functions of APA were elaborated in detail and the methods for APA identifying and APA data resources based on various transcriptome data were systematically summarized. Moreover, we epitomized and provided an outlook on research on APA, emphasizing the role of sequencing technologies in driving studies on APA in mammals. In the future, with the further development of sequencing technology, the regulatory mechanisms of APA in mammals will become clearer.

BACKGROUND: Several studies have demonstrated the occurrence of secondary tumors as a rare but significant complication of chimeric antigen receptor T (CAR-T) cell therapy, underscoring the need for a detailed investigation. Given the limited variety of secondary tumor types reported to date, a comprehensive characterization of the various secondary tumors arising after CAR-T therapy is essential to understand the associated risks and to define the role of the immune microenvironment in malignant transformation. This study aims to characterize the immune microenvironment of a newly identified secondary tumor post-CAR-T therapy, to clarify its pathogenesis and potential therapeutic targets. METHODS: In this study, the bone marrow (BM) samples were collected by aspiration from the primary and secondary tumors before and after CD19 CAR-T treatment. The CD45 + BM cells were enriched with human CD45 microbeads. The CD45 + cells were then sent for 10× genomics single-cell RNA sequencing (scRNA-seq) to identify cell populations. The Cell Ranger pipeline and CellChat were used for detailed analysis. RESULTS: In this study, a rare type of secondary chronic myelomonocytic leukemia (CMML) were reported in a patient with diffuse large B-cell lymphoma (DLBCL) who had previously received CD19 CAR-T therapy. The scRNA-seq analysis revealed increased inflammatory cytokines, chemokines, and an immunosuppressive state of monocytes/macrophages, which may impair cytotoxic activity in both T and natural killer (NK) cells in secondary CMML before treatment. In contrast, their cytotoxicity was restored in secondary CMML after treatment. CONCLUSIONS This finding delineates a previously unrecognized type of secondary tumor, CMML, after CAR-T therapy and provide a framework for defining the immune microenvironment of secondary tumor occurrence after CAR-T therapy. In addition, the results provide a rationale for targeting macrophages to improve treatment strategies for CMML treatment.
Humans ; Lymphoma, Large B-Cell, Diffuse/therapy* ; Tumor Microenvironment/genetics* ; Antigens, CD19/metabolism* ; Leukemia, Myelomonocytic, Chronic/genetics* ; Immunotherapy, Adoptive/adverse effects* ; Male ; Single-Cell Analysis/methods* ; Female ; Sequence Analysis, RNA/methods* ; Receptors, Chimeric Antigen ; Middle Aged

Objective:To assess the current situation, advantages, and difficulties of standardized management in Investigator-Initiated Clinical Trials (IIT).Methods:This article summarized the requirements and policies for clinical research management, the development of clinical research domestically and internationally, the achievements and advantages of clinical research management development in China, and the main problems and difficulties with the standardized IIT management in China, and compiled the experiences and models of several medical institutions in IIT management.Results:While China has a large number of clinical medical publications and is ranked high in the world, the quality of the publications needs to be further improved. Domestic management requirements for IIT were gradually improving, providing a basis for medical institutions to implement standardized management throughout the lifecycle of IIT, and achieve certain progress. However, there were still challenges in the departmental divisions, the unification of management standards, whole-process management and quality control, the scientific review, high-risk project management, and registration.Conclusions:Drawing on the excellent experience of domestic medical institutions, measures including identifying a primary responsible department, establishing unified supervision and inspection standards, and implementing a whole life cycle management may help overcome the challenges in IIT management and improve the quality and efficiency of IIT management.

Objective To explore the effect of task-oriented training of intelligent mirror gloves combined with low-frequency repeti-tive transcranial magnetic stimulation(rTMS)on hand function recovery in stroke patients. Methods From October 1st,2022 to June 30th,2023,136 stroke patients in Northern Jiangsu People's Hospital were ran-domly divided into control group,mirror group,rTMS group and combination group,with 34 patients in each group.All the groups received routine rehabilitation treatment.In addition,the mirror group received task-orient-ed training of intelligent mirror gloves,rTMS group received low-frequency rTMS,and the combination group received task-oriented training combined with low-frequency rTMS,for four weeks.The Fugl-Meyer Assess-ment-Upper Extremities(FMA-UE)score,Wolf Motor Function Test(WMFT)score,and surface electromyo-graphic root mean square(RMS)of forearm extensor and flexor muscle groups on the affected/healthy side be-fore and after treatment were compared.And the differences of transcranial magnetic stimulation-motor-evoked potentials(MEP)between rTMS group and combination group before and after treatment were also compared. Results Four cases in the control group,seven in the mirror group,five in rTMS group and six in the combination group dropped off.The intra-group effect(F>996.656,P<0.001),inter-group effect(F>20.333,P<0.001)and inter-action effect(F>72.796,P<0.001)were significant in the scores of FMA-UE and WMFT,and the RMS ratio of forearm extensor and flexor muscle groups among four groups,in which the combination group was the best.After treatment,the amplitude of MEP increased in rTMS group and combination group(|t|>3.842,P<0.05),and was higher in the combination group than in rTMS group(t=-3.060,P<0.01). Conclusion The task-oriented training of intelligent mirror gloves combined with low-frequency rTMS could effectively promote the recovery of hand function in stroke patients.

Objective: To investigate the rifampicin resistance status and its influencing factors among elderly patients with pulmonary tuberculosis in Changzhou City, Jiangsu Province, so as to provide the basis for improving drug-resistant pulmonary tuberculosis prevention and control strategies. Methods: Patients aged over 60 years with pulmonary tuberculosis treated in tuberculosis designated hospital was selected. Demographic information, history of previous disease, history of diagnosis and treatment and drug sensitivity test were collected. Rifampicin resistance among elderly patients with pulmonary tuberculosis and its influencing factors was analyzed. Results: Totally 249 elderly patients with pulmonary tuberculosis were included, with an average of (69.75±4.36) years. There were 147 males and 102 females, with a gender ratio of 1.44∶1. There were 183 treatment-naïve patients (73.49%) and 66 retreated patients (26.51%). Rifampicin resistance was found in 21 cases, with a drug resistance rate of 8.43%. Among them, there were 7 treatment-naïve patients (3.83%), and 14 retreated patients (21.21%). Multivariable logistic regression analysis showed that retreated elderly patients with pulmonary tuberculosis had a higher risk of rifampicin resistance (OR=10.551, 95%CI: 1.344-82.857). Conclusion The rifampicin resistance rate of 249 elderly patients with pulmonary tuberculosis was 8.43% and was associated with the type of treatment.

The Hedgehog(Hh) signaling pathway has the functions of improving embryogenesis and maintaining tissue homeostasis. By influencing the tumor microenvironment, intervening in cell apoptosis, and regulating angiogenesis, it is pivotal in the occurrence, progression, and recovery of various tumors. Therefore, targeting and inhibiting the abnormal activation of the Hh pathway has become a potential research strategy for alleviating and treating cancer. Currently, traditional Chinese medicine(TCM) is highly favored for treating cancer and other challenging and severe diseases due to its advantages, such as minimal side effects, high efficacy, lack of dependency, and the ability to address both symptoms and underlying causes. This review aimed to provide a scientific foundation and research ideas for the prevention and treatment of cancer with TCM by summarizing and reviewing the correlation between the Hh pathway and tumors, as well as the feasibility of using TCM to modulate the Hh pathway for anti-tumor effects.
Hedgehog Proteins/genetics* ; Humans ; Signal Transduction/drug effects* ; Neoplasms/metabolism* ; Animals ; Drugs, Chinese Herbal/pharmacology* ; Medicine, Chinese Traditional

Objective:To explore the development, application and practical experience of investigator-initiated integrated clinical research information platform.Methods:The process of developing and constructing an integrated clinical research platform in a tertiary hospital in Beijing was introduced, the functions and advantages of the platform were described and displayed, and the main problems and risk points in the development and construction process were analyzed.Results:The integrated clinical research platform meets the management requirements of clinical research initiated by investigators, and the standardized management of the whole life cycle of the project can be realized through the platform, and the key issues of data security, information capture, sharing and interoperability need to be further explored in terms of platform docking.Conclusions:The integrated clinical research platform effectively improves the standardization, management quality and efficiency of investigator-initiated clinical research.

Objective: To develop a multi-classification orthodontic image recognition system using the SqueezeNet deep learning model for automatic classification of orthodontic image data. Methods: A total of 35 000 clinical orthodontic images were collected in the Department of Orthodontics, Capital Medical University School of Stomatology, from October to November 2020 and June to July 2021. The images were from 490 orthodontic patients with a male-to-female ratio of 49∶51 and the age range of 4 to 45 years. After data cleaning based on inclusion and exclusion criteria, the final image dataset included 17 453 face images (frontal, smiling, 90° right, 90° left, 45° right, and 45° left), 8 026 intraoral images [frontal occlusion, right occlusion, left occlusion, upper occlusal view (original and flipped), lower occlusal view (original and flipped) and coverage of occlusal relationship], 4 115 X-ray images [lateral skull X-ray from the left side, lateral skull X-ray from the right side, frontal skull X-ray, cone-beam CT (CBCT), and wrist bone X-ray] and 684 other non-orthodontic images. A labeling team composed of orthodontic doctoral students, associate professors, and professors used image labeling tools to classify the orthodontic images into 20 categories, including 6 face image categories, 8 intraoral image categories, 5 X-ray image categories, and other images. The data for each label were randomly divided into training, validation, and testing sets in an 8∶1∶1 ratio using the random function in the Python programming language. The improved SqueezeNet deep learning model was used for training, and 13 000 natural images from the ImageNet open-source dataset were used as additional non-orthodontic images for algorithm optimization of anomaly data processing. A multi-classification orthodontic image recognition system based on deep learning models was constructed. The accuracy of the orthodontic image classification was evaluated using precision, recall, F1 score, and confusion matrix based on the prediction results of the test set. The reliability of the model's image classification judgment logic was verified using the gradient-weighted class activation mapping (Grad-CAM) method to generate heat maps. Results: After data cleaning and labeling, a total of 30 278 orthodontic images were included in the dataset. The test set classification results showed that the precision, recall, and F1 scores of most classification labels were 100%, with only 5 misclassified images out of 3 047, resulting in a system accuracy of 99.84%(3 042/3 047). The precision of anomaly data processing was 100% (10 500/10 500). The heat map showed that the judgment basis of the SqueezeNet deep learning model in the image classification process was basically consistent with that of humans. Conclusions: This study developed a multi-classification orthodontic image recognition system for automatic classification of 20 types of orthodontic images based on the improved SqueezeNet deep learning model. The system exhibitted good accuracy in orthodontic image classification.
Humans ; Male ; Female ; Child, Preschool ; Child ; Adolescent ; Young Adult ; Adult ; Middle Aged ; Deep Learning ; Reproducibility of Results ; Radiography ; Algorithms ; Cone-Beam Computed Tomography

The Myh3 (myosin heavy chain 3) gene is a marker gene of muscle cell differentiation and regulates the utilization of energy in muscle cells, but whether it affects the glycolysis process of muscle cells in different states is rarely reported. In this paper, the expression patterns of Myh3 and glycolysis-related genes Pkm (M-type pyruvate kinse), Prkag3 (protein kinase adenosine monophosphate-activated γ3-subunit), and Gsk3β (glycogen synthase kinase-3β) were studied by the qRT-PCR (quantitative-Real-Time-PCR) method using C2C12 cells at different stages of myoblast and adipogenic differentiation as models. It was found that in the process of myoblast differentiation of C2C12 cells, the relative expression trends of Myh3 and glycolysis genes Prkag3 and Pkm were basically the same, and the relative expression levels first increased, reached the peak on the second day of differentiation, and then decreased; glycogen synthase the expression trend of the inhibitory gene Gsk3β was relatively stable. In the process of adipogenic differentiation of C2C12 cells, the relative expression trend of Myh3 and glycolysis genes Prkag3 and Pkm remained basically the same, and the relative expression gradually increased, reaching the highest value on the 8th day of differentiation; glycogen synthase inhibitory gene Gsk3β expression remained stable. In the myogenic differentiation state of C2C12 cells, qRT-PCR and Western blotting were used to detect the effects of interfering Myh3 on the mRNA and protein expressions of glycolysis-related genes Pkm, Prkag3, and Gsk3β. The results showed that after interfering with Myh3, the mRNA expressions of glycolysis genes Pkm and Prkag3 were significantly decreased (P<0.01), while the mRNA expression of glycogen synthase inhibitory gene Gsk3β had no significant change (P > 0.05). The protein levels of Myh3 and Pkm were significantly lower than those in the blank group and NC group. Under the adipogenic differentiation state of C2C12 cells, after interfering with Myh3, the mRNA levels of glycogen synthase inhibitor Gsk3β and glycolysis gene Prkag3 were significantly increased (P<0.01), and the mRNA level of glycolysis gene Pkm was decreased; the protein levels of Myh3 and Pkm in the Myh3 interference group were also lower than those in the blank group and NC group. Based on the above studies, there are significant differences in the levels of glycolysis in C2C12 cells in the myogenic and adipogenic states, and the expression patterns of Myh3 and glycolysis genes are similar. Further results showed that Myh3 suppression could inhibit the glycolysis of C2C12 cells in the myogenic state without affecting the glycogen synthesis. Unlike in the myogenic state, interfering expression of Myh3 in the adipogenic state of C2C12 cells inhibited both glycogen synthesis and glycolysis.

Objective: To investigate the functional changes of key gut microbiota (GM) that produce lipopolysaccharide (LPS) in atrial fibrillation (AF) patients and to explore their potential role in the pathogenesis of AF. Methods: This was a prospective cross-sectional study. Patients with AF admitted to Beijing Chaoyang Hospital of Capital Medical University were enrolled from March 2016 to December 2018. Subjects with matched genetic backgrounds undergoing physical examination during the same period were selected as controls. Clinical baseline data and fecal samples were collected. Bacterial DNA was extracted and metagenomic sequencing was performed by using Illumina Novaseq. Based on metagenomic data, the relative abundances of KEGG Orthology (KO), enzymatic genes and species that harbored enzymatic genes were acquired. The key features were selected via the least absolute shrinkage and selection operator (LASSO) analysis. The role of GM-derived LPS biosynthetic feature in the development of AF was assessed by receiver operating characteristic (ROC) curve, partial least squares structural equation modeling (PLS-SEM) and logistic regression analysis. Results: Fifty nonvalvular AF patients (mean age: 66.0 (57.0, 71.3), 32 males(64%)) were enrolled as AF group. Fifty individuals (mean age 55.0 (50.5, 57.5), 41 males(82%)) were recruited as controls. Compared with the controls, AF patients showed a marked difference in the GM genes underlying LPS-biosynthesis, including 20 potential LPS-synthesis KO, 7 LPS-biosynthesis enzymatic genes and 89 species that were assigned as taxa harbored nine LPS-enzymatic genes. LASSO regression analysis showed that 5 KO, 3 enzymatic genes and 9 species could be selected to construct the KO, enzyme and species scoring system. Genes enriched in AF group included 2 KO (K02851 and K00972), 3 enzymatic genes (LpxH, LpxC and LpxK) and 7 species (Intestinibacter bartlettii、Ruminococcus sp. JC304、Coprococcus catus、uncultured Eubacterium sp.、Eubacterium sp. CAG:251、Anaerostipes hadrus、Dorea longicatena). ROC curve analysis revealed the predictive capacity of differential GM-derived LPS signatures to distinguish AF patients in terms of above KO, enzymatic and species scores: area under curve (AUC)=0.957, 95%CI: 0.918-0.995, AUC=0.940, 95%CI 0.889-0.991, AUC=0.972, 95%CI 0.948-0.997. PLS-SEM showed that changes in lipopolysaccharide-producing bacteria could be involved in the pathogenesis of AF. The key KO mediated 35.17% of the total effect of key bacteria on AF. After incorporating the clinical factors of AF, the KO score was positively associated with the significantly increased risk of AF (OR<0.001, 95%CI:<0.001-0.021, P<0.001). Conclusion: Microbes involved in LPS synthesis are enriched in the gut of AF patients, accompanied with up-regulated LPS synthesis function by encoding the LPS-enzymatic biosynthesis gene.
Aged ; Atrial Fibrillation/complications* ; Cross-Sectional Studies ; Gastrointestinal Microbiome ; Humans ; Lipopolysaccharides ; Male ; Middle Aged ; Prospective Studies