Human cancer genomes harbor the mutational signature of tobacco-specific nitrosamines NNN and NNK.

Tobacco usage is linked to multiple cancer types and accounts for a quarter of all cancer-related deaths. Tobacco smoke contains various carcinogenic compounds, including polycyclic aromatic hydrocarbons (PAH), though the mutagenic potential of many tobacco-related chemicals remains largely unexplored. In particular, the highly carcinogenic tobacco-specific nitrosamines NNN and NNK form pre-mutagenic pyridyloxobutyl (POB) DNA adducts. In the study presented here, we identified genome-scale POB-induced mutational signatures in cell lines and rat tumors, while also investigating their role in human cancer. These signatures are characterized by T>N and C>T mutations forming from specific POB adducts damaging dT and dC residues. Analysis of 2,780 cancer genomes uncovered POB signatures in ∼180 tumors; from cancer types distinct from the ones linked to smoking-related signatures SBS4 and SBS92. This suggests that, unlike PAH compounds, the POB pathway may contribute uniquely to the mutational landscapes of certain hematological malignancies and cancers of the kidney, breast, prostate and pancreas.

Complete amide cis-trans switching synchronized with disulfide bond formation and cleavage in a proline-mimicking system.

A typical naturally occurring disulfide structure in proteins is an 8-membered disulfide ring formed between two adjacent cysteine (Cys-Cys) residues. Based on this structure, we designed 7- to 9-membered disulfide ring molecules, embedded in the 7-azabicyclo[2.2.1]heptane skeleton, that switch their conformation from exclusively trans-amide to exclusively cis-amide upon redox transformation from dithiol to disulfide, and vice versa. Constrained shape of disulfide rings is rare in nature, and the present molecular structure is expected to be a useful fundamental component for the construction of new conformation-switching systems.

Control-independent mosaic single nucleotide variant detection with DeepMosaic.

Mosaic variants (MVs) reflect mutagenic processes during embryonic development and environmental exposure, accumulate with aging and underlie diseases such as cancer and autism. The detection of noncancer MVs has been computationally challenging due to the sparse representation of nonclonally expanded MVs. Here we present DeepMosaic, combining an image-based visualization module for single nucleotide MVs and a convolutional neural network-based classification module for control-independent MV detection. DeepMosaic was trained on 180,000 simulated or experimentally assessed MVs, and was benchmarked on 619,740 simulated MVs and 530 independent biologically tested MVs from 16 genomes and 181 exomes. DeepMosaic achieved higher accuracy compared with existing methods on biological data, with a sensitivity of 0.78, specificity of 0.83 and positive predictive value of 0.96 on noncancer whole-genome sequencing data, as well as doubling the validation rate over previous best-practice methods on noncancer whole-exome sequencing data (0.43 versus 0.18). DeepMosaic represents an accurate MV classifier for noncancer samples that can be implemented as an alternative or complement to existing methods.

Long noncoding RNA LINC00930 promotes PFKFB3-mediated tumor glycolysis and cell proliferation in nasopharyngeal carcinoma.

BACKGROUND: Metabolic reprogramming is a hallmark of cancer. However, the roles of long noncoding RNAs (lncRNAs) in cancer metabolism, especially glucose metabolism remain largely unknown. RESULTS: In this study, we identified and functionally characterized a novel metabolism-related lncRNA, LINC00930, which was upregulated and associated with tumorigenesis, lymphatic invasion, metastasis, and poor prognosis in nasopharyngeal carcinoma (NPC). Functionally, LINC00930 was required for increased glycolysis activity and cell proliferation in multiple NPC models in vitro and in vivo. Mechanistically, LINC00930 served as a scaffold to recruit the RBBP5 and GCN5 complex to the PFKFB3 promoter and increased H3K4 trimethylation and H3K9 acetylation levels in the PFKFB3 promoter region, which epigenetically transactivating PFKFB3, and thus promoting glycolytic flux and cell cycle progression. Clinically, targeting LINC00930 and PFKFB3 in combination with radiotherapy induced tumor regression. CONCLUSIONS: Collectively, LINC00930 is mechanistically, functionally and clinically oncogenic in NPC. Targeting LINC00930 and its pathway may be meaningful for treating patients with NPC.

[Effects of inner-heating acupuncture on apoptosis of chondrocytes and expression of Caspase-3 and Caspase-9 in rats with knee osteoarthritis].

OBJECTIVE: To investigate the effect of inner-heating acupuncture on apoptosis of chondrocytes and expression of Caspase-3 and Caspase-9 in rats with knee osteoarthritis (KOA). METHODS: A total of 32 rats were divided into a normal group, a model group, a control treatment group and a treatment group by random number grouping method, 8 rats in each one. The rats in the normal group received no intervention. The rats in the remaining three groups adopted modified Videman method to develop KOA model, the ankle joint of left posterior leg was fully extended and fixed with a resin bandage for 6 weeks. After successful modeling, the rats in the model group received no intervention. The rats in the control treatment group were treated with medium-frequency pulse electrotherapy. The rats in the treatment group were treated with inner- heating acupuncture, 30 min each treatment, once a day, five days per week, and totally 3-week treatment was given. After 3 weeks, the damaged cartilage tissue was collected, and HE staining was used to observe the pathological changes of the cartilage tissue of the knee joint. ELISA was used to detect the content of cytochrome-C in the tissue homogenate supernatant. The chondrocytes in damaged cartilage tissue were isolated, flow cytometer was used to detect the changes of apoptosis and mitochondrial membrane potential. The mRNA and protein expression of Caspase-3 and Caspase-9 in chondrocytes were detected by real-time quantitative PCR (qRT-PCR) and Western blot (WB), respectively. RESULTS: Compared with the normal group, the damage of cartilage tissue in the model group was significant, and the expression level of Cyt-C in the homogenate supernatant of damaged cartilage tissue was increased (P<0.01); the chondrocyte apoptosis was increased significantly (P<0.01); the chondrocyte mitochondrial membrane potential was decreased significantly (P<0.01); the mRNA and protein expression of Caspase-3 and Caspase-9 was increased significantly (all P<0.01). Compared with the model group, the cartilage injury in the control treatment group and the treatment group was significantly relieved; the expression level of Cyt-C in the supernatant of damaged cartilage tissue homogenate was decreased (both P<0.01); the chondrocyte apoptosis was significantly reduced (both P<0.01); the chondrocyte mitochondrial membrane potential was increased significantly (both P<0.01). Moreover, the mRNA and protein expression of Caspase-3 and Caspase-9 was significantly reduced (all P<0.01). Compared with the control treatment group, the treatment group was more effective in the treatment of KOA. CONCLUSION: The inner-heating acupuncture could significantly improve the pathological changes of KOA rats, inhibit the apoptosis of chondrocytes, which may be closely related to the suppression of Caspase-3 and Caspase-9 expression.

[Effects of electroacupuncture on the expression of GDNF and Ret in Parkinson's disease model rats].

OBJECTIVE: To explore the mechanism of electroacupuncture therapy on Parkinson's disease (PD). METHODS: Fifty Wistar rats were randomly divided into a normal group, a sham-operation group, a model group, a Fengfu-Taichong group and a Shuanggu Yitong group. PD model was duplicated by microinjection of 6-Hydroxyl-Dopamine into right corpora striata, and by microinjection of normal saline in sham-operation group. Rats in normal group, sham-operation group and model group were not treated. In Fengfu-Taichong group, the rats were treated by electroacupuncture at "Fengfu" (GV 16) and "Taichong" (LR 3) on the basis of the PD model, and by electroacupuncture at "Fengfu" (GV 16), "Taichong" (LR 3), "Guanyuan" (CV 4) and "Zusanli" (ST 36) in Shuanggu Yitong group, once daily for 2 weeks. GDNF and Ret expression were detected by immunohistochemistry and western blotting, respectively. RESULTS: The number of GDNF positive cells and the content of Ret receptor increased significantly in the two electroacupuncture groups compared with those in the other groups (all P < 0.01), and the expression of GDNF increased significantly in Shuanggu Yitong group compared with that in Fengfu-Taichong group (P < 0.01). CONCLUSION: Electroacupuncture can not only increase the expression of GDNF, but also enhance its effect. "Shuanggu Yitong" method is better than simple acupuncture at "Fengfu" (GV 16) and "Taichong" (LR 3) in increasing expression of GDNF.

[Effect of electroacupuncture on morphological changes and apoptosis of substantia nigra cells in Parkinson's disease rats].

OBJECTIVE: To observe the influence of electroacupuncture (EA) of "Fengfu" (GV16) and "Taichong" (LR3) on morphological changes and apoptotic percentage of substantia nigra cells so as to explore its underlying mechanism in relieving Parkinson's disease. METHODS: Forty Wistar rats were randomly divided into normal control, sham-operation (sham), model and EA groups, with 10 rats in each. The Parkinson's disease model was established by micro-injection of 6-hydroxyl-dopamine (6-OHDA) into the right striatum. EA (2 Hz, 1 mA) was applied to "Fengfu"(GV16) and "Taichong" (LR3) for 30 min, once daily for 2 weeks. HE staining, Nissl staining and immunohistochemical staining were conducted for observing the morphological changes of substantia nigra pars compacta (SNc) and striatum, and the tyrosine hydroxylase(TH) immuno-reaction (IR) positive neurons and nerve fibers. The apoptosis was detected by flow cytometry. RESULTS: Compared to the normal control and sham groups, the total number of TH-IR positive neurons and Nissl-stained cells, and OD value of TH-IR positive nerve fibers in the SNc on the 6-OHDA-lesioned side were significantly lower in the model group (P < 0.01). Compared with the model group, the aforementioned 3 indexes of the EA group were increased obviously (P < 0.01). The percentage of apoptosis of SNc on the 6-OHDA-lesioned side was obviously lower in the EA group than in the model group (P < 0.01), but still obviously higher than in the normal group and sham group (P < 0.01). CONCLUSION: Electroacupuncture therapy can significantly increase the number of neurons of substantia nigra and the density of striatum nerve fibers,and reduce the apoptotic percentage of substantia nigra cells in the Parkinsonian rats, which may contribute to its effect in relieving Parkinson's disease.