SCInter: A comprehensive single-cell transcriptome integration database for human and mouse.

Single-cell RNA sequencing (scRNA-seq), which profiles gene expression at the cellular level, has effectively explored cell heterogeneity and reconstructed developmental trajectories. With the increasing research on diseases and biological processes, scRNA-seq datasets are accumulating rapidly, highlighting the urgent need for collecting and processing these data to support comprehensive and effective annotation and analysis. Here, we have developed a comprehensive Single-Cell transcriptome integration database for human and mouse (SCInter, https://bio.liclab.net/SCInter/index.php), which aims to provide a manually curated database that supports the provision of gene expression profiles across various cell types at the sample level. The current version of SCInter includes 115 integrated datasets and 1016 samples, covering nearly 150 tissues/cell lines. It contains 8016,646 cell markers in 457 identified cell types. SCInter enabled comprehensive analysis of cataloged single-cell data encompassing quality control (QC), clustering, cell markers, multi-method cell type automatic annotation, predicting cell differentiation trajectories and so on. At the same time, SCInter provided a user-friendly interface to query, browse, analyze and visualize each integrated dataset and single cell sample, along with comprehensive QC reports and processing results. It will facilitate the identification of cell type in different cell subpopulations and explore developmental trajectories, enhancing the study of cell heterogeneity in the fields of immunology and oncology.

The value of 3D T2-weighted SPACE sequence in the differential diagnosis of spinal arteriovenous fistula and acute transverse myelitis.

OBJECTIVE: Spinal arteriovenous fistulas (SAVF) was often neglected and misdiagnosed as acute transverse myelitis (ATM) due to its insidious onset and non-specific clinical symptoms. This study aims to investigate the differential diagnostic value of high-resolution T2-weighted volumetric sequence (3D sampling perfection with application-optimized contrasts using different flip-angle evolutions [SPACE]) in patients with SAVF and ATM. METHODS: Retrospectively analyzed the clinical and radiological findings of 32 SDAVF patients and 32 ATM patients treated at our institutions from May 2018 to January 2023. They all underwent conventional spinal MRI and T2-SPACE examination, compared their performance in identifying lesions, to estimate the value of T2 SPACE sequence in the diagnosis of SAVF and ATM patients. RESULTS: The clue of cauda equina area change (CEAC) in conventional MRI and T2-SPACE sequences is specific for the diagnosis of SAVF. The diagnostic model composed of perimedullary flow voids (PFV) and CEAC has good diagnostic performance (AUCMRI = 0.95; AUCSPACE = 0.935). Compared with conventional MRI, the T2-SPACE sequence has a higher detection rate, sensitivity, and negative predictive value for PFV and CEAC in SAVF patients, but lower specificity and positive predictive value. In T2-SPACE images, there are significant differences in the distribution range, quadrant, and maximum diameter of PFV vessels between SAVF and ATM patients. Moreover, T2-SPACE sequence can determine the site of fistula in most SAVF patients preferably, and the inter-rater agreement was good in the assessment of the fistula. CONCLUSION: The CEAC is a new and useful clue for the diagnosis of thoracolumbar SAVF. And T2-SPACE sequence can more intuitively observe the lesions of SAVF, has good differential diagnostic value for SAVF and ATM patients.

Landscape and significance of human super enhancer-driven core transcription regulatory circuitry.

A core transcription regulatory circuitry (CRC) is an interconnected self-regulatory circuitry that is formed by a group of core transcription factors (TFs). These core TFs collectively regulate gene expression by binding not only to their own super enhancers (SEs) but also to the SEs of one another. For most human tissue/cell types, a global view of CRCs and core TFs has not been generated. Here, we identified numerous CRCs using two identification methods and detailed the landscape of the CRCs driven by SEs in large cell/tissue samples. The comprehensive biological analyses, including sequence conservation, CRC activity and genome binding affinity were conducted for common TFs, moderate TFs, and specific TFs, which exhibit different biological features. The local module located from the common CRC network highlighted the essential functions and prognostic performance. The tissue-specific CRC network was highly related to cell identity. Core TFs in tissue-specific CRC networks exhibited disease markers, and had regulatory potential for cancer immunotherapy. Moreover, a user-friendly resource named CRCdb (http://www.licpathway.net/crcdb/index.html) was developed, which contained the detailed information of CRCs and core TFs used in this study, as well as other interesting results, such as the most representative CRC, frequency of TFs, and indegree/outdegree of TFs.

Engineering Yarrowia lipolytica to produce nutritional fatty acids: Current status and future perspectives.

Due to their vital physiological functions, nutritional fatty acids have great potential as nutraceutical food supplements for preventing an array of diseases such as inflammation, depression, arthritis, osteoporosis, diabetes and cancer. Microbial biosynthesis of fatty acids follows the trend of sustainable development, as it enables green, environmentally friendly and efficient production. As a natural oleaginous yeast, Yarrowia lipolytica is especially well-suited for the production of fatty acids. Moreover, it has a variety of genetic engineering tools and novel metabolic engineering strategies that make it a robust workhorse for the production of an array of value-added products. In this review, we summarize recent advances in metabolic engineering strategies for accumulating nutritional fatty acids in Y. lipolytica, including conjugated fatty acids and polyunsaturated fatty acids. In addition, the future prospects of nutritional fatty acid production using the Y. lipolytica platform are discussed in light of the current progress, challenges, and trends in this field. Finally, guidelines for future studies are also emphasized.