Abstract Background Patient stratification based on molecular subtypes is an important strategy for cancer precision medicine. Deriving clinically informative cancer molecular subtypes from transcriptomic data generated on whole tumor tissue samples is a non-trivial task, especially given the various non-cancer cellular elements intertwined with cancer cells in the tumor microenvironment. Methods We developed a computational deconvolution method, DeClust, that stratifies patients into subtypes based on cancer cell-intrinsic signals identified by distinguishing cancer-type-specific signals from non-cancer signals in bulk tumor transcriptomic data. DeClust differs from most existing methods by directly incorporating molecular subtyping of solid tumors into the deconvolution process and outputting molecular subtype-specific tumor reference profiles for the cohort rather than individual tumor profiles. In addition, DeClust does not require reference expression profiles or signature matrices as inputs and estimates cancer-type-specific microenvironment signals from bulk tumor transcriptomic data. Results DeClust was evaluated on both simulated data and 13 solid tumor datasets from The Cancer Genome Atlas (TCGA). DeClust performed among the best, relative to existing methods, for estimation of cellular composition. Compared to molecular subtypes reported by TCGA or other similar approaches, the subtypes generated by DeClust had higher correlations with cancer-intrinsic genomic alterations (e.g., somatic mutations and copy number variations) and lower correlations with tumor purity. While DeClust-identified subtypes were not more significantly associated with survival in general, DeClust identified a poor prognosis subtype of clear cell renal cancer, papillary renal cancer, and lung adenocarcinoma, all of which were characterized by CDKN2A deletions. As a reference profile-free deconvolution method, the tumor-type-specific stromal profiles and cancer cell-intrinsic subtypes generated by DeClust were supported by single-cell RNA sequencing data. Conclusions DeClust is a useful tool for cancer cell-intrinsic molecular subtyping of solid tumors. DeClust subtypes, together with the tumor-type-specific stromal profiles generated by this pan-cancer study, may lead to mechanistic and clinical insights across multiple tumor types.
Abstract RNA polymerase II (Pol II)-mediated transcription in metazoan requires precise regulation. RNA polymerase II-associated protein 2 (RPAP2) was previously identified to transport Pol II from cytoplasm to nucleus and dephosphorylates Pol II C-terminal domain (CTD). We found that RPAP2 binds hypo/hyper-phosphorylated Pol II with undetectable phosphatase activity. Structure of RPAP2-Pol II shows mutually exclusive assembly of RPAP2-Pol II and pre-initiation complex (PIC) due to three steric clashes. RPAP2 prevents/disrupts Pol II-TFIIF interaction and impairs in vitro transcription initiation, suggesting a function in prohibiting PIC assembly. Loss of RPAP2 in cells leads to global accumulation of TFIIF and Pol II at promoters, indicating critical role of RPAP2 in inhibiting PIC assembly independent of its putative phosphatase activity. Our study indicates that RPAP2 functions as a gatekeeper to prohibit PIC assembly and transcription initiation and suggests a novel transcription checkpoint.
To investigate the mutation spectrum of phosphodiesterase beta subunit (PDE6B) gene and incidence in Chinese retinitis pigmentosa (RP) patients.Genomic DNA was extracted from the blood samples of 38 patients from 35 autosomal recessive retinitis pigmentosa (ARRP) families and 55 sporadic cases. The mutation of the PDE6B gene was detected using PCR-SSCP, and the amplified PCR product of abnormal bands was sequenced.Within intron 10 of PDE6B gene, a mutation was found in an ARRP family, a G --> A transition at 19th base upstream 5'-end of exon 11. A novel complex heterozygous variant of PDE6B gene in a sporadic case, a T to C transition in codon 323 resulting in the substitution of Gly by Ser and two bp(TG) inserted between the 27th-28th bp upstream of the 5'-end of exon 10 were both present in the same isolate RP. But they were not found in 100 unrelated normal individuals. A sporadic RP was found carrying a sequence variant of PDE6B gene, a G to C transversion in intron 18, the 15th base adjacent to the 3'end of exon 18. Another isolate RP was found to have 2 bp inserted between 31st and 32nd base upstream 5'end of exon 4 (in intron 3) of PDE6B gene.There is a complex heterozygous mutation of PDE6B gene responsible for a sporadic RP patient in China. Several DNA variants were found in intron of PDE6B gene in the national population.
Macrophages are a class of innate immune cells with strong plasticity. They can polarize into different phenotypes, serving with various functions, such as phagocytosis and chemotaxis, which is involved in the development of diseases. RNA-binding protein quaking (QKI) regulates monocyte differentiation, macrophage polarization and various cellular functions through RNA splicing, translocation and expression. QKI regulates the differentiation of monocytes into macrophages, and QKI deficiency promotes the polarization of macrophages into M1 type, which exerts a pro-inflammatory phenotype. In contrast, QKI overexpression promotes macrophage polarization into M2 type. Additionally, QKI affects macrophage phagocytic receptor and chemokine expression. Due to the variations in tissue-resident macrophages' features, QKI modulates macrophages in the pathogenesis of diseases (atherosclerosis, inflammatory bowel disease, etc.) through diverse mechanisms, which mainly involves cyclicAMP response element binding protein (CREB) transcription factor regulation, signal transducer and activator of transcription 1/nuclear factor κB (STAT1/NF-κB) inflammatory signaling pathway and pre-mRNA splicing of phagocytic receptor.
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