Tuberculosis (TB) has one of the highest mortality rates among infectious diseases worldwide. The immune response in the host after infection is proposed to contribute significantly to the progression of TB, but the specific mechanisms involved remain to be elucidated. Single-cell RNA sequencing (scRNA-seq) provides unbiased transcriptome sequencing of large quantities of individual cells, thereby defining biological comprehension of cellular heterogeneity and dynamic transcriptome state of cell populations in the field of immunology and is therefore increasingly applied to lung disease research. Here, we first briefly introduce the concept of scRNA-seq, followed by a summarization on the application of scRNA-seq to TB. Furthermore, we underscore the potential of scRNA-seq for clinical biomarker exploration, host-directed therapy, and precision therapy research in TB and discuss the bottlenecks that need to be overcome for the broad application of scRNA-seq to TB-related research.
Humans ; Single-Cell Analysis/methods* ; Tuberculosis/genetics* ; Sequence Analysis, RNA/methods* ; Transcriptome/genetics*

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

Over the past decade, high-throughput RNA sequencing (RNA-seq) has vastly expanded our understanding of transcriptome dynamics in human physiology and disease. As a powerful tool for investigating systematic changes in RNA biology, RNA-seq has facilitated the discovery of novel functional RNA species. Mature RNA transcripts, which transmit genetic information from DNA to proteins, undergo intricate transcriptional and post-transcriptional regulation. This process allows a single gene to produce multiple RNA transcripts, each performing specific functions depending on the physiological or pathological context. Specific RNA transcripts (SRTs) are uniquely expressed in particular tissues or tumors and are closely associated with tissue-specific functions or disease states, particularly cancer. This review explores the generation of SRTs through key mechanisms, such as alternative splicing (AS), transcriptional regulation, polyadenylation (polyA), and the influence of transposable elements (TEs). We also examine their critical roles in normal tissue development and diseases, with an emphasis on their relevance to cancer. Furthermore, the potential applications of SRTs in diagnosing and treating diseases, especially malignancies, are discussed. By serving as diagnostic markers and therapeutic targets, SRTs hold significant promise in the development of personalized medicine and precision therapies. This review aims to provide new insights into the importance of SRTs in advancing the understanding and treatment of human diseases.
Humans ; Neoplasms/genetics* ; Alternative Splicing/genetics* ; RNA/genetics* ; Animals ; Sequence Analysis, RNA/methods* ; Polyadenylation/genetics*

Humans ; Consensus ; High-Throughput Nucleotide Sequencing/standards* ; Neoplasms/diagnosis* ; Quality Control ; Sequence Analysis, DNA/methods* ; Sequence Analysis, RNA/methods*

OBJECTIVES: Recent advancements in single-cell RNA sequencing (scRNA-seq) have revolutionized the study of cellular heterogeneity, particularly within the hematological system. However, accurately annotating cell types remains challenging due to the complexity of immune cells. To address this challenge, we develop a PAN-blood single-cell Data Annotator (scPANDA), which leverages a comprehensive 10-million-cell atlas to provide precise cell type annotation. METHODS: The atlas, constructed from data collected in 16 studies, incorporated rigorous quality control, preprocessing, and integration steps to ensure a high-quality reference for annotation. scPANDA utilizes a three-layer inference approach, progressively refining cell types from broad compartments to specific clusters. Iterative clustering and harmonization processes were employed to maintain cell type purity throughout the analysis. Furthermore, the performance of scPANDA was evaluated in three external datasets. RESULTS: The atlas was structured hierarchically, consisting of 16 compartments, 54 classes, 4,‍460 low-level clusters (pd_cc_cl_tfs), and 611 high-level clusters (pmid_cts). Robust performance of the tool was demonstrated in annotating diverse immune scRNA-seq datasets, analyzing immune-tumor coexisting clusters in renal cell carcinoma, and identifying conserved cell clusters across species. CONCLUSIONS scPANDA exemplifies effective reference mapping with a large-scale atlas, enhancing the accuracy and reliability of blood cell type identification.
Humans ; Single-Cell Analysis/methods* ; Sequence Analysis, RNA/methods* ; Blood Cells

Recent studies have shown that shorter periods of ejaculatory abstinence may enhance certain sperm parameters, but the molecular mechanisms underlying these improvements are still unclear. This study explored whether reduced abstinence periods could improve semen quality, particularly for use in assisted reproductive technologies (ART). We analyzed semen samples from men with normal sperm counts ( n = 101) and those with low sperm motility or concentration ( n = 53) after 3-7 days of abstinence and then after 1-3 h of abstinence, obtained from the Reproductive & Genetic Hospital of CITIC-Xiangya (Changsha, China). Physiological and biochemical sperm parameters were evaluated, and the dynamics of transfer RNA (tRNA)-derived fragments (tRFs) were analyzed using deep RNA sequencing in five consecutive samples from men with normal sperm counts. Our results revealed significant improvement in sperm motility and a decrease in the DNA fragmentation index after the 1- to 3-h abstinence period. Additionally, we identified 245 differentially expressed tRFs, and the mitogen-activated protein kinase (MAPK) signaling pathway was the most enriched. Further investigations showed significant changes in tRF-Lys-TTT and its target gene mitogen-activated protein kinase kinase 2 ( MAP2K2 ), which indicates a role of tRFs in improving sperm function. These findings provide new insights into how shorter abstinence periods influence sperm quality and suggest that tRFs may serve as biomarkers for male fertility. This research highlights the potential for optimizing ART protocols and improving reproductive outcomes through molecular approaches that target sperm function.
Male ; Humans ; Spermatozoa/metabolism* ; RNA, Transfer/genetics* ; Sperm Motility/genetics* ; Adult ; Semen Analysis ; Sexual Abstinence/physiology* ; Sperm Count ; DNA Fragmentation

OBJECTIVES: To study the expression of the transcription factor GATA1 in bronchial asthma (referred to as asthma) and its effect on the expression level of the asthma susceptibility gene orosomucoid 1-like protein 3 (ORMDL3), along with the underlying molecular mechanisms. METHODS: The study included 28 cases of moderate asthma, 46 cases of severe asthma, and 12 normal controls from the Gene Expression Omnibus (GEO) database. The mRNA expression levels of GATA1 and ORMDL3 were analyzed among the asthma patients and the normal controls, including their correlation. The pGL-185/58 plasmid was co-transfected with GATA1 gene siRNA (si-GATA1 group) and siRNA negative control (si-control group) into BEAS-2B cells. Bioinformatics methods were used to predict GATA1 binding sites in the promoter region of the ORMDL3 gene. The dual-luciferase reporter gene system was employed to assess the promoter activity of ORMDL3, while real-time quantitative PCR and Western blotting were used to measure the mRNA and protein expression levels of GATA1 and ORMDL3. Chromatin immunoprecipitation (ChIP) assays were conducted to determine whether GATA1 binds to the promoter region of ORMDL3. RESULTS: The expression levels of GATA1 and ORMDL3 mRNA were significantly higher in the severe asthma group compared to the normal control group (P<0.001). Positive correlations were observed between GATA1 mRNA and ORMDL3 mRNA expression levels in both the moderate and severe asthma groups (r=0.636 and 0.341, respectively; P<0.05). In BEAS-2B cells, the dual-luciferase reporter assay revealed that ORMDL3 promoter luciferase activity, as well as ORMDL3 mRNA and protein expression levels, were lower in the si-GATA1 group compared to the si-control group (P<0.05). ChIP assay results demonstrated that GATA1 could bind to the promoter region of ORMDL3. CONCLUSIONS The expression of GATA1 is increased in asthma patients, which may regulate the promoter activity and expression of the asthma susceptibility gene ORMDL3.
Humans ; Asthma/etiology* ; GATA1 Transcription Factor/analysis* ; Membrane Proteins/physiology* ; Male ; Female ; Promoter Regions, Genetic ; Child ; Transcription, Genetic ; Gene Expression Regulation ; Adolescent ; RNA, Messenger/analysis*

OBJECTIVES: To investigate the effects of hyperoxia on the expression of N-methyl-D-aspartate receptor 1 (NMDAR1) and its synapse-associated molecules, including cannabinoid receptor 1 (CB1R), postsynaptic density 95 (PSD95), and synapsin (SYN), in the hippocampus of neonatal rats. METHODS: One-day-old Sprague-Dawley neonatal rats were randomly divided into a hyperoxia group and a control group (n=8 per group). The hyperoxia group was exposed to 80% ± 5% oxygen continuously, while the control group was exposed to room air, for 7 days. At 1, 3, and 7 days after hyperoxia exposure, hematoxylin and eosin (HE) staining was used to observe histopathological changes in the brain. The expression levels of NMDAR1, CB1R, PSD95, and SYN proteins and mRNAs in the hippocampus were detected by immunohistochemistry, Western blotting, and quantitative real-time PCR. RESULTS: After 7 days of hyperoxia exposure, the hyperoxia group showed decreased neuronal density and disordered arrangement in brain tissue. Compared with the control group, after 1 day of hyperoxia exposure, CB1R mRNA and both NMDAR1 and CB1R protein expression in the hyperoxia group were significantly downregulated, while SYN protein expression was significantly upregulated (P<0.05). After 3 days, mRNA expression of NMDAR1, CB1R, and SYN was significantly decreased (P<0.05); NMDAR1 and CB1R protein expression was significantly downregulated (P<0.05), while PSD95 and SYN protein expression was significantly upregulated (P<0.05). After 7 days of hyperoxia, the protein expression of NMDAR1 and CB1R was significantly upregulated (P<0.05). CONCLUSIONS Continuous hyperoxia exposure induces time-dependent changes in the expression levels of NMDAR1 and its synapse-associated molecules in the hippocampus of neonatal rats.
Animals ; Receptors, N-Methyl-D-Aspartate/genetics* ; Rats, Sprague-Dawley ; Hippocampus/pathology* ; Rats ; Animals, Newborn ; Receptor, Cannabinoid, CB1/genetics* ; Hyperoxia/metabolism* ; Disks Large Homolog 4 Protein/genetics* ; Synapsins/genetics* ; Synapses ; Male ; Female ; RNA, Messenger/analysis*

OBJECTIVE: To explore the application of targeted mRNA sequencing in fusion gene diagnosis of hematologic diseases. METHODS: Bone marrow or peripheral blood samples of 105 patients with abnormally elevated eosinophil proportions and 291 acute leukemia patients from January 2015 to June 2023 in the First Affiliated Hospital of Soochow University were analyzed and gene structural variants were detected by targeted mRNA sequencing. RESULTS: Among 105 patients with abnormally elevated eosinophil proportions, 6 cases were detected with gene structural variants, among which fusion gene testing results in 5 cases could serve as diagnostic indicators for myeloid neoplasms with eosinophilia. In addition, a IL3∷ETV6 fusion gene was detected in one patient with chronic eosinophilic leukemia, not otherwise specified. Among 119 patients with acute myeloid leukemia (AML), 38 cases were detected structural variants by targeted mRNA sequencing, accounting for 31.9%, which was significantly higher than 20.2% (24/119) detected by multiple quantitative PCR (P < 0.05). We also found one patient with AML had both NUP98∷PRRX2 and KCTD5∷JAK2 fusion genes. A total of 104 patients were detected structural variants by targeted mRNA sequencing in 172 cases with acute B-lymphoblastic leukemia who were tested negative by multiple quantitative PCR, with a detection rate of 60.5% (102/172). CONCLUSION Targeted mRNA sequencing can effectively detect fusion gene and has potential clinical application value in diagnosis and classificatation in hematologic diseases.
Humans ; Hematologic Diseases/diagnosis* ; RNA, Messenger/genetics* ; Oncogene Proteins, Fusion/genetics* ; Sequence Analysis, RNA ; Leukemia, Myeloid, Acute/diagnosis*

OBJECTIVE: To investigate the molecular alterations of splenocytes associated with anti-factor Ⅷ (FⅧ) immune response and the underlying mechanisms based on hemophilia A (HA) murine model via RNA sequencing (RNA-seq) technology. METHODS: Severe HA mice were immunized with recombinant human factor Ⅷ (rhF8) weekly for 4 weeks to establish an FⅧ inhibitor model. High quality raw data were obtained by using bulk RNA-seq and CASAVA base identification technology, and the differentially expressed genes (DEGs) were identified. The DEGs were statistically classified by gene ontology (GO) annotation to obtain information on the major signaling pathways and biological processes involved in anti-FⅧ immune response in HA mouse splenocytes. The cell clusters, genes, and signaling pathway datasets were comprehensively analyzed by GO, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and single cell RNA-seq (ScRNA-seq) analysis, respectively. Flow cytometry analysis was used to verify the changes in T follicular helper cells (Tfh) and regulatory T cells (Treg). RESULTS: A total of 3731 DEGs was identified, including 2275 genes with up-regulated expression and 1456 genes with down-regulated expression. The DEGs were enriched in helper T cell differentiation, cytokine receptor, T cell receptor signaling pathway, ferroptosis, etc. Uniform Manifold Approximation and Project (UMAP) downscaling and visualization analysis yielded a total number of 11 T/NK cell subsets, visualizing the overall expression distribution of C-X-C chemokine-specific receptor gene cxcr5 among these T/NK cell subsets. Higher expression of cxcr5 was found in activated Tfh from FⅧ inhibitor mice, in comparison to the control group. The visualization using Upset plot R language showed a close interaction between Tfh and Treg. Moreover, the increased frequencies of Tfh and the decreased frequencies of Treg in inhibitor mouse splenocytes were further verified by flow cytometry analysis. CONCLUSION Multiple immune cell subsets, signaling pathways, and characteristic genes may be involved in the process of anti-FⅧ immune response in HA mouse splenocytes. The molecules involved in the regulation of Tfh/Treg may play key roles, which provide potential biological targets and therapeutic strategies for HA patients with inhibitors in the future.
Animals ; Hemophilia A/genetics* ; Mice ; Sequence Analysis, RNA ; Disease Models, Animal ; Spleen/cytology* ; T-Lymphocytes, Regulatory/immunology* ; Humans ; Signal Transduction ; Factor VIII/immunology* ; T-Lymphocytes, Helper-Inducer/immunology*