<p>XLSX file - 602KB, Supplementary Table 5. Cancer cell lines analyzed in this study. Supplementary Table 6. Tumor tissues analyzed in this study. Supplementary Table 7. List of 340 well characterized hotspot mutations interrogated by the amplicon libraries in this study. Variants also assayed by asPCR are indicated. Supplementary Table 8. Variants detected in 66 cancer cell lines, after applying post-processing filters. Note that indels and predicted deleterious SNVs are reported for all interrogated genes and transcripts. Supplementary Table 9. Variants detected in 73 FFPE endometrial tumor tissues, after applying post-processing filters. Note that indels and predicted deleterious SNVs are reported for all interrogated genes and transcripts. Supplementary Table 10. For cell line data, concordance with COSMIC somatic mutation annotation.</p>
We examined the effect of the beta 2-agonist terbutaline on dry airflow-induced bronchoconstriction (AIB) in the canine lung periphery. Using a wedged bronchoscope technique, collateral resistance (Rcs) and airway wall temperature (Taw) were measured before and after a 2-min exposure to dry air. When sublobar segments were challenged with dry air, Taw fell during challenge (p less than 0.001), and Rcs increased 5 min postchallenge (p less than 0.01). Pretreatment with terbutaline (100 micrograms/kg) reduced the fall induced by dry-air challenge in Taw by 37% and the subsequent rise in Rcs by 87%. Terbutaline significantly reduced the concentrations of thromboxane B2 (TxB2) and prostaglandin D2 (PGD2), and decreased the concentration of epithelial cells recovered in bronchoalveolar lavage fluid 5 min postchallenge. In addition, terbutaline attenuated histamine- and PGD2-induced constriction. Finally, peripheral lung sensitivity (as assessed by delta Rcs/delta Taw) to challenge after treatment with terbutaline was significantly less than that calculated for untreated control animals (p less than 0.05). These data are consistent with the idea that terbutaline attenuates AIB by (1) facilitating replacement of water lost during exposure to dry air, (2) inhibiting mediator production and release from osmosensitive cells, and (3) reducing smooth muscle responsiveness.
DNA hypermethylation of tumor suppressor genes has been frequently observed in cancer patients, and therefore, may provide a valuable biomarker for cancer prevention and treatment. DNA hypermethylation may also provide an important mechanism in cancer progression. Lung cancer is strongly associated with exposure to environmental carcinogens, especially tobacco smoke. DNA damage generated by tobacco smoke is believed to play an important role in lung cancer development. XPC is a DNA damage recognition protein required for DNA repair and other DNA damage responses and attenuated XPC protein levels have been detected in many lung cancer patients. We studied the role of XPC protein deficiency in tobacco smoke-caused DNA hypermethylation of important tumor suppressor genes. Using both normal human fibroblasts (NF) and XPC-deficient hu man fibroblasts (XPC), our DNA methylation studies demonstrated that the XPC deficiency caused elevated levels of DNA hypermethylation in both Brca1 and Mlh1 tumor suppressor genes following exposure to tobacco smoke condensate (TSC). The results of our ChIP studies revealed that the XPC deficiency led to an increased binding of DNA methyltransferase 3A (DNMT3A) at the promoter region CpG island-containing sequences of these genes under the TSC treatment; however, this increase was partially diminished with prior treatment with caffeine. The results of our immuno-precipitation (IP) studies demonstrated a protein-protein interaction of the ATR with DNMT3A. Our western blots revealed that the XPC deficiency caused an increase in TSC-induced ATR phosphorylation at serine 428, an indicator of ATR activation. All these results suggest that XPC deficiency causes an accelerated DNA hypermethylation in important tumor suppressor genes under tobacco smoke exposure and activation of the ATR signaling pathway is involved in this DNA hypermethylation process.
Rabdosia rubescens is a herbal root extract of traditional Chinese medicine (TCM) used to treat inflammatory diseases and oral cancers. A key principle of TCM is that multiple ingredients in a plant extract are more effective and less toxic than a single purified active ingredient or a purified drug derived from a plant product. Rabdosia rubescens extract (RRE) contains terpenoids and flavonoids, but the most active ingredient within the extract attributed to the inhibition of cancer is the kaurene diterpene, oridonin. In order to research synergy with a complete plant extract, the effects of RRE on the inhibition of prostate cancer cell proliferation were compared to the effects of pure oridonin alone in vitro. Three groups of 8 SCID mice bearing human prostate cancer xenografts (LAPC-4) were administered either RRE containing 0.02 mg/g oridonin, pure oridonin at a dose of 0.02 mg/g, or pure oridonin at a dose of 0.1 mg/g, by gavage for 5 days/week for 4 weeks. RRE and pure oridonin at 0.1 mg/g inhibited tumor growth to a similar extent, while oridonin at a dose of 0.02 mg/g did not. Therefore, in comparison to RRE, five times more pure oridonin was required to obtain equivalent prostate xenograft growth inhibition. Since the nuclear factor-κB signaling pathway and inflammation are implicated in prostate carcinogenesis, gene microarray analysis was conducted and demonstrated activation of genes by RRE that was not evident with oridonin treatment alone. This study demonstrated that genomic methods and xenograft studies are capable of demonstrating the benefits of the synergy of whole plant extracts rather than active ingredients isolated and purified as drugs.
The resistance to EGF receptor (EGFR) tyrosine kinase inhibitors (TKI) is a major challenge in the treatment of non-small cell lung cancer (NSCLC). Understanding the molecular mechanisms behind resistance is therefore an important issue. Here we assessed the role of EGFR pathway substrate 8 (EPS8) and Forkhead box O 3a (FoxO3a) as potentially valuable targets in the resistance of NSCLC .The expression levels of EPS8 and FoxO3a in patients with NSCLC (n = 75) were examined by immunohistochemistry staining, while in cells were detected by qPCR and western blot. The effects of EPS8 and FoxO3a on resistance, migration and invasion, cell cycle arrest were detected by MTT, transwell and flow cytometry, respectively. Chromatin immunoprecipitation and luciferase reporter assays were performed to determine the mechanisms of EPS8 expression and FoxO3a regulation.We observed that the expression of EPS8 inversely correlated with FoxO3a in NSCLC cell lines and NSCLC patients. FoxO3a levels were significantly decreased in tumor tissues compared with para-carcinoma tissues, while EPS8 is opposite. Besides, they play reverse roles in the resistance to gefitinib, the migration and invasion abilities, the cell cycle arrest in vitro and the tumor growth in vivo. Mechanistically, FoxO3a inhibits EPS8 levels by directly binding its gene promoter and they form a negative loop in EGFR pathway.Targeting FoxO3a and EPS8 in EGFR signaling pathway prevents the progression of NSCLC, which implied that the negative loop they formed could served as a therapeutic target for overcoming resistance in NSCLC.National Natural Science Foundation of China, Science and Technology Project of Henan, Outstanding Young Talent Research Fund of Zhengzhou University and the National Scholarship Fund.
Recent developments of single-cell RNA-seq (scRNA-seq) technologies have led to enormous biological discoveries. As the scale of scRNA-seq studies increases, a major challenge in analysis is batch effects, which are inevitable in studies involving human tissues. Most existing methods remove batch effects in a low-dimensional embedding space. Although useful for clustering, batch effects are still present in the gene expression space, leaving downstream gene-level analysis susceptible to batch effects. Recent studies have shown that batch effect correction in the gene expression space is much harder than in the embedding space. Methods such as Seurat 3.0 rely on the mutual nearest neighbor (MNN) approach to remove batch effects in gene expression, but MNN can only analyze two batches at a time, and it becomes computationally infeasible when the number of batches is large. Here, we present CarDEC, a joint deep learning model that simultaneously clusters and denoises scRNA-seq data while correcting batch effects both in the embedding and the gene expression space. Comprehensive evaluations spanning different species and tissues showed that CarDEC outperforms Scanorama, DCA + Combat, scVI, and MNN. With CarDEC denoising, non-highly variable genes offer as much signal for clustering as the highly variable genes (HVGs), suggesting that CarDEC substantially boosted information content in scRNA-seq. We also showed that trajectory analysis using CarDEC's denoised and batch-corrected expression as input revealed marker genes and transcription factors that are otherwise obscured in the presence of batch effects. CarDEC is computationally fast, making it a desirable tool for large-scale scRNA-seq studies.
<p>PDF file - 731KB, Supplementary Figure 1. Schematic workflow of MMP-seq. Supplementary Figure 2. Examples of tiling and hotspot amplicon designs. Supplementary Figure 3. Consistent target enrichment and variant allele quantification in FF biological replicates. Supplementary Figure 4. Correlation between called variant frequencies in paired FF and FFPE samples. Supplementary Figure 5. UDG treatment improves sequencing specificity but has no impact on sensitivity. Supplementary Figure 6. PIK3R1 mutation profiles from TCGA endometrial cancer study. Supplementary Table 1. MMP-seq target genes. Supplementary Table 2. Latin Square Design. Supplementary Table 3. Latin square mutation read frequency detected when sequencing input cell lines for Latin square cross-dilutions. Supplementary Table 4. Pretreatment of FFPE DNA samples with uracil-DNA glycosylase (UDG) resulted in markedly reduction of false positives.</p>
Endonuclease III of Escherichia coli excises a broad range of oxidized, hydrated and ring-fragmented pyrimidines from DNA. The kinetic parameters were compared for repair of three potentially mutagenic oxidized cytosine lesions: 5,6-dihydroxy-5,6-dihydro-2'-deoxyuridine (uracil glycol or Ug), 5-hydroxy-2'-deoxycytidine (5-ohC), and 5-hydroxy-2'-deoxyuridine (5-ohU). Site-specifically modified 40-mer oligonucleotides containing each of the three lesions in the same sequence context were synthesized chemically or by a combination of chemical and enzymatic methods. Appropriately protected phosphoramidites of 5-ohC and 5-ohU were synthesized and incorporated into oligonucleotides by standard solid-phase synthetic methods. The lability of Ug made it necessary to use an alternative approach to prepare the analogous 40-mers containing Ug. An uracil containing pentamer oligonucleotide was oxidized with OsO4 to generate the corresponding Ug containing product, which was then ligated into an oligonucleotide scaffold to generate 40 base pair duplexes. Using 32P-labeled substrates and a gel electrophoresis based assay, the values of Km and Vmax for excision of 5-ohC, 5-ohU, and Ug were determined. In this experimental system, the order of repair efficiency is Ug > 5-ohC > 5-ohU based on ratios of Vmax/Km. Modest effects were observed when the base paired opposite the lesion was changed from G to A.
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