We have demonstrated that subclones carrying driver mutations are more prone to release DNA. We have also demonstrated the quantitative ability of capture-based sequencing, paving its way for routine utilization in clinical settings.

Pitaya (Hylocereus) is the most economically important fleshy-fruited tree of the Cactaceae family that is grown worldwide, and it has attracted significant attention because of its betalain-abundant fruits. Nonetheless, the lack of a pitaya reference genome significantly hinders studies focused on its evolution, as well as the potential for genetic improvement of this crop. Herein, we employed various sequencing approaches, namely, PacBio-SMRT, Illumina HiSeq paired-end, 10× Genomics, and Hi-C (high-throughput chromosome conformation capture) to provide a chromosome-level genomic assembly of ‘GHB’ pitaya (H. undatus, 2n = 2x = 22 chromosomes). The size of the assembled pitaya genome was 1.41 Gb, with a scaffold N50 of ~127.15 Mb. In total, 27,753 protein-coding genes and 896.31 Mb of repetitive sequences in the H. undatus genome were annotated. Pitaya has undergone a WGT (whole-genome triplication), and a recent WGD (whole-genome duplication) occurred after the gamma event, which is common to the other species in Cactaceae. A total of 29,328 intact LTR-RTs (~696.45 Mb) were obtained in H. undatus, of which two significantly expanded lineages, Ty1/copia and Ty3/gypsy, were the main drivers of the expanded genome. A high-density genetic map of F1 hybrid populations of ‘GHB’ × ‘Dahong’ pitayas (H. monacanthus) and their parents were constructed, and a total of 20,872 bin markers were identified (56,380 SNPs) for 11 linkage groups. More importantly, through transcriptomic and WGCNA (weighted gene coexpression network analysis), a global view of the gene regulatory network, including structural genes and the transcription factors involved in pitaya fruit betalain biosynthesis, was presented. Our data present a valuable resource for facilitating molecular breeding programs of pitaya and shed novel light on its genomic evolution, as well as the modulation of betalain biosynthesis in edible fruits.

Background A suitable reference gene is an important prerequisite for guarantying accurate and reliable results in quantitative real-time PCR (qRT-PCR) analyses. However, there is no absolute universality in reference genes among different species. It’s hard to find an ideal reference gene to fit for different tissues and growth periods. Pitaya ( Hylocereus ) is commercially produced as a new fruit crop at a large scale in tropical and subtropical regions. To date, there is no report on the identification of the most reliable reference genes for qRT-PCR normalization in pitaya. Results In this study, six candidate reference genes i.e. Actin(1) , GAPDH , UBC(1) , UBC(2) EF1 - α(1) and histone(1) were selected from thirty-nine typical candidate reference genes to determine the most stable reference genes for qRT-PCR normalization in different tissues, temperature stresses and fruit developmental stages of pitaya. Among the six candidate reference genes, Actin(1) and EF1 - α(1) were the most stable gene according to calculations of three statistical methods (GeNorm, NormFinder and BestKeeper) while UBC(1) and UBC(2) showed the lowest expression stability. The six candidate reference genes were further validated by comparing expression profiles of key genes related to betalain biosynthesis at flesh coloration stages of Guanhuahong ( Hylocereus monacanthus ) and Guanhuabai ( H. undatus ) pitayas. Actin(1) was recommended the best reference gene for accurate normalization of qRT-PCR data. Conclusions In this study, the stability of the selected reference genes for normalizing the qRT-PCR data were identified from pitaya. Actin(1) was the most stably expressed genes in different tissues and fruit developmental stages in pitaya. The present work provides the first data of reference gene identification for pitaya and will facilitate further studies in molecular biology and gene function on Hylocereus and other closely related species. Electronic supplementary material The online version of this article (10.1186/s13007-019-0455-3) contains supplementary material, which is available to authorized users.

Objective Ovarian cancer (OC) is a common female disease with a poor prognosis. But the possible mechanism of OC tumor progression remains an active area of research. This study is intended to explore the effect of metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) on proliferation and apoptosis of OC and its mechanism. Materials and methods MALAT1 and miR-503-5p expressions in human OC cell lines and normal human ovarian epithelial (HOSE) cell line were measured using qRT-PCR. OC cell line SKOV3 is divided into 4 groups: pcDNA3.1 group, pcDNA3.1-MALAT1 group, si-NC group, and si-MALAT1 group. MTT assay and 5-ethynyl-2ʹ-deoxyuridine (EdU) assay were applied for the detection of cell proliferation. Relationship of MALAT1 with miR-503-5p was verified using luciferase assay and RNA pull-down. The luciferase activity in cells was normalized to RNA concentrations determined by Bradford assays. Results MALAT1 expression in OC cells was elevated compared with HOSE cells. MTT assay and EdU assay supported that si-MALAT1 could inhibit cell proliferation in OC cells. Treatment of si-MALAT1 results in increased cell apoptosis rate in both SKOV3 cells and OVCAR3 cells. The expression of lncRNA-MALAT1 was negatively associated with the expression of miR-503-5p in OC cells, while luciferase assay and RNA pull-down together supported the direct binding of MALAT1 with miR-503-5p. Knockdown of MALAT1 was able to inhibit the activation of JAK2/STAT3 signal pathway, and MALAT1 overexpression was accompanied by activation of these factors. Conclusion lncRNA-MALAT1 can negatively target miR-503-5p expression to further promote proliferation and depress apoptosis of OC cells through the JAK2-STAT3 pathway.

We have recently developed a flexible catheter electrode used for bronchoscopic radiofrequency ablation (RFA). Two patients with nonsurgical stage IA peripheral lung cancer and 1 with lung metastasis underwent treatment with flexible catheter RFA utilizing navigation bronchoscopy. Chest computed tomography (CT) and positron emission tomography/CT (PET/CT) were performed before and after RFA to assess the ablation response of the patients. One patient's tumor had no prior PET uptake and therefore no follow-up PET was obtained. The first and the third patient obtained partial response to RFA, and the second patient obtained complete response 3 months after RFA. The first patient developed progressive disease 6 months after RFA. The second and the third patient achieved one-year progression-free survival. No significant complications occurred in the 3 patients. Navigation bronchoscopy-guided RFA is a safe and feasible procedure for poor surgical candidates with stage IA lung cancer or lung metastasis.

KeywordsDiagnostic yield; electromagnetic navigation bronchoscopy (ENB); peripheral pulmonary lesions (PPLs); transbronchial lung biopsy (TBLB); virtual bronchoscopic navigation (VBN). Correspondence AbstractBackground: To compare the diagnostic yield of peripheral pulmonary lesions (PPLs) with and without navigation system. Methods: Studies dating from January 1990 to October 2019 were collected from databases. Diagnostic yield of navigation bronchoscopy and non-navigation bronchoscopy was extracted from comparative studies. Subgroup analysis was adopted to test diagnostic yield variation by lesion size, lobe location of the lesion, distance from the hilum, bronchus sign and nature of the lesion. Results: In total, 2131 patients from 10 studies were enrolled into the study. Diagnostic yield of navigation bronchoscopy was statistically higher than nonnavigation bronchoscopy for PPLs (odds ratio [OR] 1.69, 95% confidence interval [CI] 1.32, 2.18, P < 0.001), particularly for PPLs in the peripheral third lung (OR 2.26, 95% CI 1.48, 3.44, P < 0.001) and for bronchus sign positive PPLs (OR 2.26, 95% CI 1.21, 4.26, P = 0.011). Navigation bronchoscopy had better performance than non-navigation bronchoscopy when PPLs were ≤ 20 mm (OR 2.09, 95% CI 1.44, 3.03, P < 0.001). It also elevated diagnostic yield of malignant PPLs (OR 1.67, 95% CI 1.26, 2.22, P < 0.001) and PPLs in the bilateral upper lobes (OR 1.50, 95% CI 1.09, 2.08, P = 0.014). Conclusions: Navigation bronchoscopy enhanced diagnostic yield when compared to non-navigation bronchoscopy, particularly for PPLs in the peripheral third lung, PPLs being bronchus sign positive, PPLs ≤ 20 mm, malignant PPLs and PPLs in the bilateral upper lobes. Key pointsThe current study provided systematic evaluation on the diagnostic value of navigation bronchoscopy by comparing it with non-navigation bronchoscopy, and exploring the factors affecting the diagnostic yield.

Background. Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) can obtain a small amount of specimen. This study aims to evaluate the feasibility and robustness of using EBUS-EBNA samples to perform capture-based targeted nextgeneration sequencing (NGS).Methods. Tissue samples from patients with advanced non-small cell lung cancer were collected by EBUS-TBNA and were formalin-fixed paraffinembedded. Three representative genes, EGFR, ALK, and ROS1, were examined by amplification refractory mutation system polymerase chain reaction, immunohistochemistry, and quantitative reverse transcription polymerase chain reaction. The remaining samples were processed with NGS assay with a 56-gene panel. Classic driver mutations detected by NGS were verified by conventional methods.Results. Of the 85 samples from patients with advanced non-small cell lung cancer, 77 were performed successfully with all assays. Forty-one mutations in EGFR, ALK, and ROS1 were detected in both conventional methods and NGS, representing a 100% concordance. In contrast, four EGFR mutations detected by NGS were not covered in the targeted regions of amplification refractory mutation system polymerase chain reaction, leading to a negative call in these patients. Altogether, NGS detected 12 additional variants, including six KRAS mutations, one BRAF mutation, one RET fusion, one MET amplification concurrent with EGFR L858R, one KRAS amplification together with EGFR 19del, and one ERBB2 amplification. The mean number of needle passes per lymph node was 5.2 in samples successfully applied in all assays.Conclusions. NGS assay can be successfully conducted with limited tissue samples obtained from EBUS-TBNA. Compared with conventional methods, NGS assay provides more comprehensive information on genetic alterations in tumors, which greatly assists therapeutic decision making for advanced lung cancer.

Background Transbronchial lung biopsy (TBLB) is usually performed to obtain a definitive diagnosis for peripheral pulmonary lesions (PPLs). Ultrathin bronchoscopy combined with virtual bronchoscopic navigation (VBN) and radial endobronchial ultrasound (R‐EBUS) are generally considered appropriate diagnostic methods for PPLs; however, they have not yet been explored in combination with fluoroscopy. Therefore, the present prospective randomized controlled trial determined the role of fluoroscopy in ultrathin bronchoscopy combined with VBN and R‐EBUS for the diagnosis of PPLs. Methods Patients with potentially malignant PPLs were enrolled in the study and randomized into fluoroscopy or nonfluoroscopy groups. In both groups, a 3.0‐mm outer and 1.7‐mm internal diameter ultrathin bronchoscope was used for transbronchial lung biopsy combined with R‐EBUS and VBN. In addition, the fluoroscopy group (FG) underwent fluoroscopy, while the nonfluoroscopy group (NFG) did not. Results A total of 126 patients were enrolled and randomized in the study. Among them, 120 patients (60 in the NFG and 60 in the FG) were analyzed. The mean lesion sizes were 26.3 ± 11.4 mm and 29.0 ± 11.3 mm in the NFG and FG, respectively. The diagnostic yield was 73.3% (44/60) in the NFG and 81.7% (49/60) in the FG without statistically significant difference (p = 0.38). No obvious complications occurred in either group. Conclusions Ultrathin bronchoscope combined with VBN and R‐EBUS without fluoroscopy is a feasible and safe diagnostic method for PPLs.