Yeast carries a strictly conserved branch point sequence (BPS) of UACUAAC, whereas the human BPS is degenerative and is less well characterized. The human consensus BPS has never been extensively explored in vitro to date. Here, we sequenced 367 clones of lariat RT-PCR products arising from 52 introns of 20 human housekeeping genes. Among the 367 clones, a misincorporated nucleotide at the branch point was observed in 181 clones, for which we can precisely pinpoint the branch point. The branch points were comprised of 92.3% A, 3.3% C, 1.7% G and 2.8% U. Our analysis revealed that the human consensus BPS is simply yUnAy, where the underlined is the branch point at position zero and the lowercase pyrimidines (‘y’) are not as well conserved as the uppercase U and A. We found that the branch points are located 21–34 nucleotides upstream of the 3′ end of an intron in 83% clones. We also found that the polypyrimidine tract spans 4–24 nucleotides downstream of the branch point. Our analysis demonstrates that the human BPSs are more degenerative than we have expected and that the human BPSs are likely to be recognized in combination with the polypyrimidine tract and/or the other splicing cis-elements.

Exosomal long noncoding RNA (lncRNA) has been found to be associated with the development of cancers. However, the expression characteristics and the biological roles of exosomal lncRNAs in hepatocellular carcinoma (HCC) remain unknown. Here, by RNA sequencing, we found 9440 mRNAs and 8572 lncRNAs were differentially expressed (DE‐) in plasma exosomes between HCC patients and healthy controls. Exosomal DE‐lncRNAs displayed higher expression levels and tissue specificity, lower expression variability and splicing efficiency than DE‐mRNAs. Six candidate DE‐lncRNAs (fold change 6 or more, P ≤ .01) were high in HCC cells and cell exosomes. The knockdown of these candidate DE‐lncRNAs significantly affected the migration, proliferation, and apoptosis in HCC cells. In particular, a novel DE‐lncRNA, RP11‐85G21.1 (lnc85), promoted HCC cellular proliferation and migration by targeted binding and regulating of miR‐324‐5p. More importantly, the level of serum lnc85 was highly expressed in both Alpha‐fetoprotein (AFP)‐positive and AFP‐negative HCC patients and allowed distinguishing AFP‐negative HCC from healthy control and liver cirrhosis (area under the receiver operating characteristic curve, 0.869; sensitivity, 80.0%; specificity, 76.5%) with high accuracy. Our finding offers a new insight into the association between the dysregulation of exosomal lncRNA and HCC, suggesting that lnc85 could be a potential biomarker of HCC.

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Background Transfer RNA-derived fragments (tRFs) are a new class of small non-coding RNAs. Recent studies suggest that tRFs participate in some pathological processes. However, the biological functions and mechanisms of tRFs in non-small cell lung cancer (NSCLC) are largely unknown. Methods Differentially expressed tRFs were identified by tRF and tiRNA sequencing using 9 pairs of pre- and post-operation plasma from patients with NSCLC. Quantitative real-time PCR (qRT-PCR) and fluorescence in situ hybridization (FISH) were used to determine the levels of tRF in tissues, plasma, and cells. Gain- and loss-of-function experiments were implemented to investigate the oncogenic effects of tRF on NSCLC cells in vitro and in vivo. Chromatin immunoprecipitation (ChIP), luciferase reporter, RNA pulldown, mass spectrum, RNA immunoprecipitation (RIP), Western blot, co-immunoprecipitation (Co-IP) assays, and rescue experiments were performed to explore the regulatory mechanisms of tRF in NSCLC. Results AS-tDR-007333 was an uncharacterized tRF and significantly up-regulated in NSCLC tissues, plasma, and cells. Clinically, AS-tDR-007333 overexpression could distinguish NSCLC patients from healthy controls and associated with poorer prognosis of NSCLC patients. Functionally, overexpression of AS-tDR-007333 enhanced proliferation and migration of NSCLC cells, whereas knockdown of AS-tDR-007333 resulted in opposite effects. Mechanistically, AS-tDR-007333 promoted the malignancy of NSCLC cells by activating MED29 through two distinct mechanisms. First, AS-tDR-007333 bound to and interacted with HSPB1, which activated MED29 expression by enhancing H3K4me1 and H3K27ac in MED29 promoter. Second, AS-tDR-007333 stimulated the expression of transcription factor ELK4, which bound to MED29 promoter and increased its transcription. Therapeutically, inhibition of AS-tDR-007333 suppressed NSCLC cell growth in vivo. Conclusions Our study identifies a new oncogenic tRF and uncovers a novel mechanism that AS-tDR-007333 promotes NSCLC malignancy through the HSPB1-MED29 and ELK4-MED29 axes. AS-tDR-007333 is a potential diagnostic or prognostic marker and therapeutic target for NSCLC.

There is currently no detailed evidence for the long-term effects of bariatric surgery on severely obese with type 2 diabetes, such as the risk of myocardial infarction and stroke. In order to provide evidence on the risks of macrovascular diseases and metabolic indicators of bariatric surgery follow-up for more than five years, we searched in the Cochrane library, Pubmed, and EMBASE databases from the earliest studies to January 31, 2019. Randomized clinical trials or cohort studies compared bariatric surgery and conventional medical therapy for long-term incidence of macrovascular events and metabolic outcomes in severely obese patients with T2DM. Fixed-effects and random-effects meta-analyses were performed to pool the relative risks (RRs), hazard ratios (HRs) and weighted mean difference (WMD). Publication bias and heterogeneity were examined. Four RCTs and six cohort studies were finally involved in this review. Patients in the bariatric surgery group as compared to the conventional treatment group had lower incidence of macrovascular complications (RR = 0.43, 95%CI = 0.27~0.70), cardiovascular events (CVEs) (HR = 0.52, 95%CI = 0.39~0.71), and myocardial infarction (MI) (RR = 0.40, 95%CI = 0.26~0.61). At the same time, the results demonstrate that bariatric surgery is associated with better weight and better glycemic control over the long-term than non-surgical therapies, and reveal that different surgical methods have different effects on various metabolic indicators. Bariatric surgery significantly decreases macrovascular complications over the long term and is associated with greater weight loss and better intermediate glucose outcomes among T2DM patients with severe obesity as compared to patients receiving only conservative medical measures.