Revealing the grammar of small RNA secretion using interpretable machine learning.

Small non-coding RNAs can be secreted through a variety of mechanisms, including exosomal sorting, in small extracellular vesicles, and within lipoprotein complexes. However, the mechanisms that govern their sorting and secretion are not well understood. Here, we present ExoGRU, a machine learning model that predicts small RNA secretion probabilities from primary RNA sequences. We experimentally validated the performance of this model through ExoGRU-guided mutagenesis and synthetic RNA sequence analysis. Additionally, we used ExoGRU to reveal cis and trans factors that underlie small RNA secretion, including known and novel RNA-binding proteins (RBPs), e.g., YBX1, HNRNPA2B1, and RBM24. We also developed a novel technique called exoCLIP, which reveals the RNA interactome of RBPs within the cell-free space. Together, our results demonstrate the power of machine learning in revealing novel biological mechanisms. In addition to providing deeper insight into small RNA secretion, this knowledge can be leveraged in therapeutic and synthetic biology applications.

Immune landscape and risk prediction based on pyroptosis-related molecular subtypes in triple-negative breast cancer.

The survival outcome of triple-negative breast cancer (TNBC) remains poor, with difficulties still existing in prognosis assessment and patient stratification. Pyroptosis, a newly discovered form of programmed cell death, is involved in cancer pathogenesis and progression. The role of pyroptosis in the tumor microenvironment (TME) of TNBC has not been fully elucidated. In this study, we disclosed global alterations in 58 pyroptosis-related genes at somatic mutation and transcriptional levels in TNBC samples collected from The Cancer Genome Atlas and Gene Expression Omnibus databases. Based on the expression patterns of genes related to pyroptosis, we identified two molecular subtypes that harbored different TME characteristics and survival outcomes. Then, based on differentially expressed genes between two subtypes, we established a 12-gene score with robust efficacy in predicting short- and long-term overall survival of TNBC. Patients at low risk exhibited a significantly better prognosis, more antitumor immune cell infiltration, and higher expression of immune checkpoints including PD-1, PD-L1, CTLA-4, and LAG3. The comprehensive analysis of the immune landscape in TNBC indicated that alterations in pyroptosis-related genes were closely related to the formation of the immune microenvironment and the intensity of the anticancer response. The 12-gene score provided new information on the risk stratification and immunotherapy strategy for highly heterogeneous patients with TNBC.

Effects of core needle biopsy and subsequent neoadjuvant chemotherapy on molecular alterations and outcome in breast cancer.

OBJECTIVES: The aim of our study is to evaluate the effect of core needle biopsy (CNB) and subsequent neoadjuvant chemotherapy (NAC) on the expression of estrogen receptor (ER), progesterone receptor (PR), human epidermal growth hormone receptor 2 (HER2) and Ki67 in breast cancer, and the associated influencing factors. MATERIALS AND METHODS: In this retrospective cohort study, 143 patients with primary operable breast cancer who received NAC were included. ER, PR, HER2 and Ki67 statuses were compared between pretreatment and posttreatment residual samples. A control group of paired core and excision tumors from 123 patients who did not receive NAC within the same study period was also assessed. Data on patients' clinicopathologic features were collected to identify associated influencing factors. RESULTS: Ki67 value significantly increased in excision tumors compared with paired core samples in controls without presurgery treatment (P<0.01), which was associated with the pathologic lymph node status and the interaction of PR and HER2 status (P=0.008 and 0.028, respectively). In 143 patients who underwent NAC, a significant decrease was observed in the expression of PR and Ki67 after NAC (P=0.003 and P<0.01, respectively). Further subgroup analysis showed that PR decrease was more obvious in premenopausal patients and Luminal A patients (P=0.006 and 0.002, respectively). CONCLUSION: Core samples could provide more reliable information on determination of molecular subtype than surgical excisions. Decreases in PR and Ki67 expression following NAC could be used as positive prognostic factors. We recommend repeat testing of these biologic markers following NAC for the sake of better disease management. To the best of our knowledge, this is the most comprehensive study to analyze the effect of neoadjuvant chemotherapy on molecular alteration and its associated influencing factors after reporting a CNB-associated Ki67 increase in the same study.

End-to-End Invaginated Pancreaticojejunostomy with Three Overlapping U-Sutures--A Safe and Simple Method of Pancreaticoenteric Anastomosis.

BACKGROUND: Postoperative pancreatic fistula associated with mortality and morbidity remains an intractable problem after pancreaticoduodenectomy. To date it still carries a notable incidence of roughly 10% to 30% in large series in spite of numerous pharmacological and technical methods that have been proposed to achieve a leakproof pancreatic remnant. METHODS: In order to perform a safe anastomosis to pancreatic remnant with less sophisticated sutures and shorter operative duration, a fast and simple technique of end-to-end invaginated pancreaticojejunostomy with three overlapping U-sutures was devised in our institution. RESULTS: Between April 2011 and July 2013, end-to-end invaginated pancreaticojejunostomy with three overlapping U-sutures technique was used in 23 consecutive cases that underwent pancreaticoduodenectomy in our institute. The median operative time for pancreaticojejunostomy was 12 min. The incidence of pancreatic fistula was 8.7% (n = 2) and both cases were grade A fistula with no clinical impact or delayed hospital discharge. Neither relaparotomy nor postoperative mortality was observed. CONCLUSIONS: The technique of using three overlapping U-sutures in an end-to-end invaginated pancreaticojejunostomy represents a simple management of pancreaticoenteric anastomosis with reliability and applicability, and provides an alternative choice for pancreaticojejunostomy to senior pancreatic surgeons as well as those without experience.

Laparoscopic hepatectomy for liver metastases from colorectal cancer: a meta-analysis.

BACKGROUND: Liver resection can improve long-term survival for liver metastases from colorectal cancer. Laparoscopic hepatectomy is gaining increasing applications in colorectal liver metastases. We conducted a meta-analysis to investigate the safety, feasibility, and efficacy of laparoscopic liver resection compared with open hepatectomy for patients with colorectal liver metastases. MATERIALS AND METHODS: We performed both database and manual searching for comparative studies published before June 2013 without language or region restriction. Outcomes of interest consisted of perioperative outcomes and oncologic outcomes. RESULTS: Seven observational studies including 624 patients (241 in the laparoscopic group, 383 in the open group) were included. No randomized controlled trials were available. Pooled long-term oncologic outcomes of overall survival (hazard ratio=0.844; 95% confidence interval [CI] 0.412, 1.730; P=.644; I(2)=80.6%) and disease-free survival (hazard ratio=1.234; 95% CI 0.652, 2.333; P=.518; I(2)=79.6%) were similar in both groups. Subgroup analyses of studies with high quality and homogeneity confirmed the above outcomes. However, a lower incidence of R1 resection was observed in the laparoscopic group (relative risk [RR]=0.357; 95% CI 0.180, 0.708; P=.003; I(2)=0.0%) than in the open group. As for perioperative outcomes, laparoscopic hepatectomy presented a lower occurrence of postoperative complications (RR=0.647; 95% CI 0.477, 0.877; P=.005; I(2)=0.0%) and similar mortality (RR=0.625; 95% CI 0.12, 3.25; P=.576; I(2)=0.0%); less blood loss and less need for transfusion were also found in laparoscopic patients, whereas comparable operative time and length of hospital stay were required in the two groups. CONCLUSIONS: Laparoscopic hepatectomy is a safe procedure for colorectal liver metastases with long-term survival comparable to that of open hepatectomy. More prospective studies with adequate subgroup analyses are awaited to construct defined criteria for patient selection. Future randomized controlled trials are needed to eliminate potential selection bias and to confirm this conclusion.

Expression of microRNA-150 targeting vascular endothelial growth factor-A is downregulated under hypoxia during liver regeneration.

Vascular endothelial growth factor (VEGF) is a factor that stimulates the proliferation of sinusoidal endothelial cells and hepatocytes during liver regeneration (LR). The present study aimed to screen and validate a microRNA (miRNA) that targets VEGF-A with relative specificity and to elucidate the potential association between hypoxia-inducible factor-1α (HIF­1α) and miRNA expression in the early phase of LR. Changes in the expression of miRNAs, which were predicted to target VEGF-A using online databases, were detected at 12, 24 and 48 h following a 70% partial hepatectomy (PHx) using quantitative PCR (qPCR). An inhibitor of the most downregulated miRNA was transfected into the primary hepatocytes in order to observe changes in the expression of the VEGF-A gene. The expression of HIF-1α protein in the regenerating liver was investigated using western blot analysis. The expression levels of HIF-1α mRNA (messenger RNA), the selected miRNA and VEGF-A mRNA in an anoxic model of hepatocytes was examined with qPCR. Of seven putative miRNAs, the expression of miR-150 exhibited the sharpest downregulation from 12-48 h. The micrOFF™ miR-150 inhibitor significantly elevated the expression levels of VEGF-A mRNA and protein 48 h after transfection. Thus, VEGF-A may be a downstream target of miR-150 during LR. Furthermore, HIF-1α protein expression increased to its highest level 24 h following PHx. miR-150 expression was inhibited and the expression of VEGF-A mRNA increased accordingly in the hypoxia-induced hepatocytes. Our results suggest that miR-150 expression is subject to negative regulation by HIF-1α.