capTEs enables locus-specific dissection of transcriptional outputs from reference and nonreference transposable elements.

Transposable elements (TEs) serve as both insertional mutagens and regulatory elements in cells, and their aberrant activity is increasingly being revealed to contribute to diseases and cancers. However, measuring the transcriptional consequences of nonreference and young TEs at individual loci remains challenging with current methods, primarily due to technical limitations, including short read lengths generated and insufficient coverage in target regions. Here, we introduce a long-read targeted RNA sequencing method, Cas9-assisted profiling TE expression sequencing (capTEs), for quantitative analysis of transcriptional outputs for individual TEs, including transcribed nonreference insertions, noncanonical transcripts from various transcription patterns and their correlations with expression changes in related genes.

Single-Cell Transcriptomics of Immune Cells Reveal Diversity and Exhaustion Signatures in Non-Small-Cell Lung Cancer.

Understanding immune cell phenotypes in the tumor microenvironment (TME) is essential for explaining and predicting progression of non-small cell lung cancer (NSCLC) and its response to immunotherapy. Here we describe the single-cell transcriptomics of CD45 immune cells from tumors, normal tissues and blood of NSCLC patients. We identified three clusters of immune cells exerting immunosuppressive effects: CD8 T cells with exhausted phenotype, tumor-associated macrophages (TAMs) with a pro-inflammatory M2 phenotype, and regulatory B cells (B regs) with tumor-promoting characteristics.

Single-cell exome sequencing reveals multiple subclones in metastatic colorectal carcinoma.

Background: Colorectal cancer (CRC) is a major cancer type whose mechanism of metastasis remains elusive.

Methods: In this study, we characterised the evolutionary pattern of metastatic CRC (mCRC) by analysing bulk and single-cell exome sequencing data of primary and metastatic tumours from 7 CRC patients with liver metastases. Here, 7 CRC patients were analysed by bulk whole-exome sequencing (WES); 4 of these were also analysed using single-cell sequencing.

Accurate single-cell genotyping utilizing information from the local genome territory.

Single-nucleotide variant (SNV) detection in the genome of single cells is affected by DNA amplification artefacts, including imbalanced alleles and early PCR errors. Existing single-cell genotyper accuracy often depends on the quality and coordination of both the target single-cell and external data, such as heterozygous profiles determined by bulk data. In most single-cell studies, information from different sources is not perfectly matched.

An antidiabetic nutraceutical combination of red yeast rice (), bitter gourd (), and chromium alleviates dedifferentiation of pancreatic β cells in db/db mice.

Antidiabetic properties of red yeast rice, bitter gourd, and chromium have gained scientific support. This study aimed to test whether a nutraceutical combination of these 3 materials prevented dedifferentiation of pancreatic β cells. Male db/db mice (8 weeks of age) were allocated into four groups (DB, DB/L, DB/M, and DB/H;  = 8-10) and fed a high-fat diet containing 0%, 0.

Transcriptomic and open chromatin atlas of high-resolution anatomical regions in the rhesus macaque brain.

The rhesus macaque is a prime model animal in neuroscience. A comprehensive transcriptomic and open chromatin atlas of the rhesus macaque brain is key to a deeper understanding of the brain. Here we characterize the transcriptome of 416 brain samples from 52 regions of 8 rhesus macaque brains.

The Open Chromatin Landscape of Non-Small Cell Lung Carcinoma.

Non-small cell lung carcinoma (NSCLC) is a major cancer type whose epigenetic alteration remains unclear. We analyzed open chromatin data with matched whole-genome sequencing and RNA-seq data of 50 primary NSCLC cases. We observed high interpatient heterogeneity of open chromatin profiles and the degree of heterogeneity correlated to several clinical parameters.