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1.  Escherichia coli of sequence type 3835 carrying blaNDM-1, blaCTX-M-15, blaCMY-42 and blaSHV-12 
Scientific Reports  2015;5:12275.
New Delhi metallo-β-lactamase (NDM) represents a serious challenge for treatment and public health. A carbapenem-resistant Escherichia coli clinical strain WCHEC13-8 was subjected to antimicrobial susceptibility tests, whole genome sequencing and conjugation experiments. It was resistant to imipenem (MIC, >256 μg/ml) and meropenem (MIC, 128 μg/ml) and belonged to ST3835. blaNDM-1 was the only carbapenemase gene detected. Strain WCHEC13-8 also had a plasmid-borne AmpC gene (blaCMY-42) and two extended-spectrum β-lactamase genes (blaCTX-M-15 and blaSHV-12). blaNDM-1 and blaSHV-12 were carried by a 54-kb IncX3 self-transmissible plasmid, which is identical to plasmid pNDM-HF727 from Enterobacter cloacae. blaCMY-42 was carried by a 64-kb IncI1 plasmid and blaCTX-M-15 was located on a 141-kb plasmid with multiple F replicons (replicon type: F36:A4:B1). blaCMY-42 was in a complicated context and the mobilisation of blaCMY-42 was due to the transposition of ISEcp1 by misidentifying its right-end boundary. Genetic context of blaNDM-1 in strain WCHEC13-8 was closely related to those on IncX3 plasmids in various Enterobacteriaceae species in China. In conclusion, a multidrug-resistant ST3835 E. coli clinical strain carrying blaNDM-1, blaCTX-M-15, blaCMY-42 and blaSHV-12 was identified. IncX3 plasmids may be making a significant contribution to the dissemination of blaNDM among Enterobacteriaceae in China.
doi:10.1038/srep12275
PMCID: PMC4508618  PMID: 26194736
2.  Evidence that the lung adenocarcinoma EML4-ALK fusion gene is not caused by exposure to secondhand tobacco smoke during childhood 
Background
The EML4-ALK fusion gene is more frequently found in younger, never smoking, lung cancer patients. Meanwhile, never smokers exposed to secondhand tobacco smoke (SHS) during childhood are diagnosed at a younger age compared with never smoking lung cancer patients that are not exposed. We therefore hypothesized that SHS, which can induce DNA damage, is associated with the EML4-ALK fusion gene.
Methods
We compared the frequency of the EML4-ALK fusion gene among 197 never smoker lung cancer patients with and without a history of exposure to SHS during childhood at Mayo Clinic.
Results
The EML4-ALK fusion gene was detected in 33% of cases from never smokers with a history of SHS exposure during childhood, while 47% of never smoking lung cancer cases without a history of childhood SHS exposure tested positive for the fusion gene.
Conclusions
The EML4-ALK fusion gene is not enriched in tumors from individuals exposed to SHS during childhood.
Impact
These data suggest that childhood exposure to SHS is not a significant etiologic cause of the EML4-ALK fusion gene in lung cancer.
doi:10.1158/1055-9965.EPI-14-0224
PMCID: PMC4082445  PMID: 24755712
3.  Renal Cell Carcinoma in Tuberous Sclerosis Complex 
Renal cell carcinoma (RCC) occurs in 2-4% of patients with tuberous sclerosis complex (TSC). Previous reports have noted a variety of histologic appearances in these cancers, but the full spectrum of morphologic and molecular features has not been fully elucidated. We encountered 46 renal epithelial neoplasms from 19 TSC patients and analyzed their clinical, pathological and molecular features, enabling separation of these 46 tumors into three groups. The largest subset of tumors (n=24) had a distinct morphological, immunological and molecular profile, including prominent papillary architecture and uniformly deficient SDHB expression prompting the novel term “TSC-associated papillary RCC.” The second group (n=15) was morphologically similar to a hybrid oncocytic/chromophobe tumor (HOCT) while the last 7 renal epithelial neoplasms of group 3 remained unclassifiable. The TSC-associated papillary RCCs (PRCC) had prominent papillary architecture lined by clear cells with delicate eosinophilic cytoplasmic thread-like strands that occasionally appeared more prominent and aggregated to form eosinophilic globules. All 24 (100%) of these tumors were the International Society of Urological Pathology (ISUP) nucleolar grade 2 or 3 with mostly basally located nuclei. Tumor cells from 17 of 24 TSC-associated PRCC showed strong, diffuse labeling for CA-IX (100%), CK7 (94%), vimentin (88%), CD10 (83%), and were uniformly negative for succinate dehydrogenase subunit B (SDHB), TFE3 and AMACR. Gains of chromosomes 7 and 17 were found in 2 tumors, whereas chromosome 3p deletion and TFE3 translocations were not detected. In this study, we reported a sizable cohort of renal tumors seen in TSC and were able to identify them as different morphotypes which may help to expand the morphologic spectrum of TSC-associated RCC.
doi:10.1097/PAS.0000000000000237
PMCID: PMC4139167  PMID: 24832166
Renal cell carcinoma; tuberous sclerosis complex; succinate dehydrogenase; hybrid oncocytic/chromophobe tumor; immunohistochemistry; molecular genetics
4.  Cx3cr1 deficiency in mice attenuates hepatic granuloma formation during acute schistosomiasis by enhancing the M2-type polarization of macrophages 
Disease Models & Mechanisms  2015;8(7):691-700.
ABSTRACT
Acute schistosomiasis is characterized by pro-inflammatory responses against tissue- or organ-trapped parasite eggs along with granuloma formation. Here, we describe studies in Cx3cr1−/− mice and demonstrate the role of Cx3cr1 in the pathoetiology of granuloma formation during acute schistosomiasis. Mice deficient in Cx3cr1 were protected from granuloma formation and hepatic injury induced by Schistosoma japonicum eggs, as manifested by reduced body weight loss and attenuated hepatomegaly along with preserved liver function. Notably, S. japonicum infection induced high levels of hepatic Cx3cr1 expression, which was predominantly expressed by infiltrating macrophages. Loss of Cx3cr1 rendered macrophages preferentially towards M2 polarization, which then led to a characteristic switch of the host immune defense from a conventional Th1 to a typical Th2 response during acute schistosomiasis. This immune switch caused by Cx3cr1 deficiency was probably associated with enhanced STAT6/PPAR-γ signaling and increased expression of indoleamine 2,3-dioxygenase (IDO), an enzyme that promotes M2 polarization of macrophages. Taken together, our data provide evidence suggesting that CX3CR1 could be a viable therapeutic target for treatment of acute schistosomiasis.
Highlighted Article: A reduction in CX3CR1 signaling provides protection for mice against pro-inflammatory responses and hepatic granuloma formation during acute schistosomiasis.
doi:10.1242/dmm.018242
PMCID: PMC4486856  PMID: 26035381
CX3CR1; Schistosomiasis; Granuloma formation; Macrophage; STAT-6; PPAR-γ
5.  Tumor-specific Th2 responses inhibit growth of CT26 colon-cancer cells in mice via converting intratumor regulatory T cells to Th9 cells 
Scientific Reports  2015;5:10665.
The abnormality of immune regulation plays a critical role in the pathogenesis of cancer; the underlying mechanism has not been fully understood yet. This study aims to investigate the role of cancer specific T helper (Th)2 response in the inhibition of colon cancer (Cca) cell growth. The results showed that with Cca cell (CT26 cell) extracts as an antigen, the Cca-extract specific Th2 response was induced in the Cca-bearing mice. The Cca mass size was significantly reduced, or radically disappeared (5 out of 10; or 50%); the survival rate was markedly improved in mice immunized with Cca-extract, but not in those immunized with another tumor cell (U87 cell) extracts or to bovine serum albumin. The immunization with Cca-extract also induced Cca cell apoptosis and converted the intra-Cca Tregs to T helper (Th) 9 cells. In conclusion, Cca-specific Th2 responses inhibit Cca growth in a mouse model via inducing Cca cell apoptosis and converting intra-Cca Tregs to Th9 cells.
doi:10.1038/srep10665
PMCID: PMC4451845  PMID: 26035423
6.  Genetic variants of the Wnt signaling pathway as predictors of recurrence and survival in early-stage non-small cell lung cancer patients 
Carcinogenesis  2014;35(6):1284-1291.
Summary
NSCLC is often a lethal disease but potentially curative at early stages. In this study, we showed that genetic variants in the developmental and stem cell-related Wnt signaling pathway may influence disease recurrence and survival in early-stage NSCLC patients.
Early-stage non-small cell lung cancer (NSCLC) is potentially curative. Nevertheless, many patients will show disease recurrence after curative treatment. The Wnt signaling pathway is a developmental and stem cell pathway that plays an important role in tumorigenesis and may affect cancer progression. We hypothesize that genetic variants of the Wnt pathway may influence clinical outcome in early-stage NSCLC patients. We genotyped 441 functional and tagging single nucleotide polymorphisms (SNPs) from 54 genes of the Wnt pathway in 535 early-stage NSCLC patients treated with curative intent therapy including surgery and chemotherapy. For validation, 4 top SNPs were genotyped in 301 early-stage NSCLC patients from the Mayo Clinic. Cox proportional hazard model and combined SNP analyses were performed to identify significant SNPs correlated with recurrence-free and overall survival. Results from discovery group showed a total of 40 SNPs in 20 genes correlated with disease recurrence (P < 0.05). After correction for multiple comparisons, rs2536182 near Wnt16 remained significant (q < 0.1), which was validated in the replication population. Thirty-nine SNPs in 16 genes correlated with overall survival (P < 0.05) in the discovery group, and seven remained significant after multiple comparisons were considered (q < 0.1). In patients receiving surgery-only treatment, rs10898563 of FZD4 gene was associated with both recurrence-free and overall survival. Joint SNP analyses identified predictive markers for recurrence stratified by treatment. Our findings suggest inherited genetic variation in the Wnt signaling pathway may contribute to variable clinical outcomes for patients with early-stage NSCLC.
doi:10.1093/carcin/bgu034
PMCID: PMC4043238  PMID: 24517998
7.  Wnt Signaling Pathway Pharmacogenetics in Non-Small Cell Lung Cancer 
The pharmacogenomics journal  2014;14(6):509-522.
Wnt/β-catenin pathway alterations in non-small cell lung cancer (NSCLC) are associated with poor prognosis and resistance. In 598 stage III-IV NSCLC patients receiving platinum-based chemotherapy at MD Anderson Cancer Center (MDACC), we correlated survival with 441 host SNPs in 50 Wnt pathway genes. We then assessed the most significant SNPs in 240 Mayo Clinic patients receiving platinum-based chemotherapy for advanced NSCLC, 127 MDACC patients receiving platinum-based adjuvant chemotherapy and 340 early stage MDACC patients undergoing surgery alone (cohorts 2–4). In multivariate analysis, survival correlates with SNPs for AXIN2 (rs11868547 and rs4541111, of which rs11868547 was assessed in cohorts 2–4), Wnt-5B (rs12819505), CXXC4 (rs4413407) and WIF-1 (rs10878232). Median survival was 19.7, 15.6, and 10.7 months for patients with 1, 2, and 3–5 unfavorable genotypes, respectively (p= 3.8×10−9). Survival tree analysis classified patients into two groups (MST 11.3 vs 17.3 months, p=4.7×10−8). None of the SNPs achieved significance in cohorts 2–4; however, there was a trend in the same direction as cohort 1 for 3 of the SNPs. Using online databases, we found rs10878232 displayed expression quantitative trait loci (eQTL) correlation with the expression of LEMD3, a neighboring gene previously associated with NSCLC survival. In conclusion, results from cohort 1 provide further evidence for an important role for Wnt in NSCLC. Investigation of Wnt inhibitors in advanced NSCLC would be reasonable. Lack of a SNP association with outcome in cohorts 2–4 could be due to low statistical power, impact of patient heterogeneity, or false positive observations in cohort 1.
doi:10.1038/tpj.2014.21
PMCID: PMC4237616  PMID: 24980784
Wnt; pharmacogenetics; NSCLC
8.  blaNDM-5 Carried by an IncX3 Plasmid in Escherichia coli Sequence Type 167 
Antimicrobial Agents and Chemotherapy  2014;58(12):7548-7552.
blaNDM-5 was found in Escherichia coli strain 0215 from a Chinese patient without travel history. Genomic sequencing and conjugation experiments were performed. Strain 0215 belonged to sequence type 167 (ST167) and had other resistance determinants, including blaTEM-135, blaCTX-M-14, and aac(6′)-Ib. blaNDM-5 was carried by a 47-kb self-transmissible IncX3 plasmid and was in a complex genetic context similar to that of blaNDM-1 on IncX3 plasmids. IncX3 plasmids might have emerged as a common vehicle mediating the spread of blaNDM.
doi:10.1128/AAC.03911-14
PMCID: PMC4249565  PMID: 25246393
9.  Strain Engineering of Octahedral Rotations and Physical Properties of SrRuO3 Films 
Scientific Reports  2015;5:10245.
Strain engineering is an effective way to modify functional properties of thin films. Recently, the importance of octahedral rotations in pervoskite films has been recognized in discovering and designing new functional phases. Octahedral behavior of SrRuO3 film as a popular electrode in heterostructured devices is of particular interest for its probable interfacial coupling of octahedra with the functional overlayers. Here we report the strain engineering of octahedral rotations and physical properties that has been achieved in SrRuO3 films in response to the substrate-induced misfit strains of almost the same amplitude but of opposite signs. It shows that the compressively strained film on NdGaO3 substrate displays a rotation pattern of a tetragonal phase whilst the tensilely strained film on KTaO3 substrate has the rotation pattern of the bulk orthorhombic SrRuO3 phase. In addition, the compressively strained film displays a perpendicular magnetic anisotropy while the tensilely strained film has the magnetic easy axis lying in the film plane. The results show the prospect of strain engineered octahedral architecture in producing desired property and novel functionality in the class of perovskite material.
doi:10.1038/srep10245
PMCID: PMC4446894  PMID: 26018639
10.  Intrathecal Delivery of IL-6 Reactivates the Intrinsic Growth Capacity of Pyramidal Cells in the Sensorimotor Cortex after Spinal Cord Injury 
PLoS ONE  2015;10(5):e0127772.
We have previously demonstrated the growth-promoting effect of intrathecal delivery of recombinant rat IL-6 immediately after corticospinal tract (CST) injury. Our present study aims to further clarify whether intrathecal delivery of IL-6 after CST injury could reactivate the intrinsic growth capacity of pyramidal cells in the sensorimotor cortex which project long axons to the spinal cord. We examined, by ELISA, levels of cyclic adenosine monophosphate (cAMP), adenylyl cyclase (AC, which synthesizes cAMP), phosphodiesterases (PDE, which degrades cAMP), and, by RT-PCR, the expression of regeneration-associated genes in the rat sensorimotor cortex after intrathecal delivery of IL-6 for 7 days, started immediately after CST injury. Furthermore, we injected retrograde neuronal tracer Fluorogold (FG) to the spinal cord to label pyramidal cells in the sensorimotor cortex, layers V and VI, combined with βIII-tubulin immunostaining, then we analyzed by immunohistochemisty and western blot the expression of the co-receptor gp-130 of IL-6 family, and pSTAT3 and mTOR, downstream IL-6/JAK/STAT3 and PI3K/AKT/mTOR signaling pathways respectively. We showed that intrathecal delivery of IL-6 elevated cAMP level and upregulated the expression of regeneration-associated genes including GAP-43, SPRR1A, CAP-23 and JUN-B, and the expression of pSTAT3 and mTOR in pyramidal cells of the sensorimotor cortex. In contrast, AG490, an inhibitor of JAK, partially blocked these effects of IL-6. All these results indicate that intrathecal delivery of IL-6 immediately after spinal cord injury can reactivate the intrinsic growth capacity of pyramidal cells in the sensorimotor cortex and these effects of IL-6 were partially JAK/STAT3-dependent.
doi:10.1371/journal.pone.0127772
PMCID: PMC4437647  PMID: 25992975
11.  Common Oncogene Mutations and Novel SND1-BRAF Transcript Fusion in Lung Adenocarcinoma from Never Smokers 
Scientific Reports  2015;5:9755.
Lung adenocarcinomas from never smokers account for approximately 15 to 20% of all lung cancers and these tumors often carry genetic alterations that are responsive to targeted therapy. Here we examined mutation status in 10 oncogenes among 89 lung adenocarcinomas from never smokers. We also screened for oncogene fusion transcripts in 20 of the 89 tumors by RNA-Seq. In total, 62 tumors had mutations in at least one of the 10 oncogenes, including EGFR (49 cases, 55%), K-ras (5 cases, 6%), BRAF (4 cases, 5%), PIK3CA (3 cases, 3%), and ERBB2 (4 cases, 5%). In addition to ALK fusions identified by IHC/FISH in four cases, two previously known fusions involving EZR- ROS1 and KIF5B-RET were identified by RNA-Seq as well as a third novel fusion transcript that was formed between exons 1–9 of SND1 and exons 2 to 3′ end of BRAF. This in-frame fusion was observed in 3/89 tested tumors and 2/64 additional never smoker lung adenocarcinoma samples. Ectopic expression of SND1-BRAF in H1299 cells increased phosphorylation levels of MEK/ERK, cell proliferation, and spheroid formation compared to parental mock-transfected control. Jointly, our results suggest a potential role of the novel BRAF fusion in lung cancer development and therapy.
doi:10.1038/srep09755
PMCID: PMC4434945  PMID: 25985019
12.  Chronic inflammation aggravates metabolic disorders of hepatic fatty acids in high-fat diet-induced obese mice 
Scientific Reports  2015;5:10222.
The prevalence of nonalcoholic fatty liver disease (NAFLD) increases with increasing body mass index (BMI). However, approximately 40–50% of obese adults do not develop hepatic steatosis. The level of inflammatory biomarkers is higher in obese subjects with NAFLD compared to BMI-matched subjects without hepatic steatosis. We used a casein injection in high-fat diet (HFD)-fed C57BL/6J mice to induce inflammatory stress. Although mice on a HFD exhibited apparent phenotypes of obesity and hyperlipidemia regardless of exposure to casein injection, only the HFD+Casein mice showed increased hepatic vacuolar degeneration accompanied with elevated inflammatory cytokines in the liver and serum, compared to mice on a normal chow diet. The expression of genes related to hepatic fatty acid synthesis and oxidation were upregulated in the HFD-only mice. The casein injection further increased baseline levels of lipogenic genes and decreased the levels of oxidative genes in HFD-only mice. Inflammatory stress induced both oxidative stress and endoplasmic reticulum stress in HFD-fed mice livers. We conclude that chronic inflammation precedes hepatic steatosis by disrupting the balance between fatty acid synthesis and oxidation in the livers of HFD-fed obese mice. This mechanism may operate in obese individuals with chronic inflammation, thus making them more prone to NAFLD.
doi:10.1038/srep10222
PMCID: PMC4431481  PMID: 25974206
13.  The Effects and Molecular Mechanisms of MiR-106a in Multidrug Resistance Reversal in Human Glioma U87/DDP and U251/G Cell Lines 
PLoS ONE  2015;10(5):e0125473.
Chemotherapy resistance is one of the major obstacles to effective glioma therapy. Currently, the mechanism underlying chemotherapy resistance is unclear. A recent study showed that miR-106a is an important molecule involved in chemotherapy resistance. To explore the effects and mechanisms of miR-106a on multidrug resistance reversal in human glioma cells, we silenced miR-106a expression in the cisplatin-resistant U87 (U87/DDP) and the gefitinib-resistant U251 (U251/G) glioma cell lines and measured the resulting drug sensitivity, cell apoptosis rate and rhodamine 123 content. In addition, we detected decreased expression of P-glycoprotein, MDR1, MRP1, GST-π, CDX2, ERCC1, RhoE, Bcl-2, Survivin and Topo-II, as well as reduced production of IL-6, IL-8 and TGF-β in these cell lines. Furthermore, we found decreased expression of p-AKT and transcriptional activation of NF-κB, Twist, AP-1 and Snail in these cell lines. These results suggest that miR-106a is a promising therapeutic target for the treatment of human multidrug resistant glioma.
doi:10.1371/journal.pone.0125473
PMCID: PMC4423781  PMID: 25950430
14.  Correlation of Regional Emphysema and Lung Cancer: A Lung Tissue Research Consortium Based Study 
Background
Chronic obstructive pulmonary disease (COPD) and lung cancer are linked since both airflow obstruction and emphysema, on computer tomography (CT), are independent risk factors for lung cancer. However, the local risk of malignancy relative to development of regional emphysema has not yet been defined. Specifically, it is not known if primary lung cancers are associated with regions of worse emphysema within individual patients.
Methods
We performed a database analysis evaluating the association between the degree of regional emphysema as scored on CT and development of primary lung cancer. We also studied the association between regional emphysema and benign lung nodules. We assembled two distinct cohorts using the National Heart, Lung, and Blood Institute’s Lung Tissue Research Consortium (LTRC) database, hypothesizing that lung malignancy will preferentially locate in the regions of the most severe emphysema.
Results
In the LTRC database, 624 cases met criteria for the malignant nodule cohort, and 64 were included in the benign nodule cohort. When comparing location of a malignant nodule to other lung regions within the same person, the odds of having a more severe emphysema score in the location of lung cancer was 1.342 (95% CI 1.112–1.620; p=0.0022). When comparing location of a benign nodule to other lung regions within the same person, the odds of having a more severe emphysema score in the location of the benign nodule was 1.118 (95% CI 0.725–1.725; p=0.6137).
Conclusions
Primary lung cancers are associated with areas of worse regional emphysema.
doi:10.1097/JTO.0000000000000144
PMCID: PMC3984592  PMID: 24662456
15.  Low bone mineral density is associated with increased arterial stiffness in participants of a health records based study 
Journal of Thoracic Disease  2015;7(5):790-798.
Aims
Many epidemiological studies have shown that low bone mineral density (BMD) and atherosclerosis appear to be related. However, their precise correlation is not completely understood after full adjustment the shared confounders of atherosclerosis and bone metabolism. The aim of this cross-sectional study was to investigate the relationship between BMD and subclinical atherosclerosis in a healthy Chinese population and the difference in gender.
Methods
The study population consisted of 2,487 subjects (1,467 men, 1,020 women) who participated in health check-up programs and were selected to be free of major diseases which might affect atherosclerosis and bone metabolism. Bone status was assessed by BMD in lumbar spine. The brachial-ankle PWV (baPWV) was assessed as a functional marker of atherosclerosis. The ankle-brachial index (ABI), carotid artery intima-media thickness (CIMT), estimated glomerular filtration rate (eGRF) and microalbuminuria were evaluated as indexes of structural markers of atherosclerosis.
Results
After adjustment for risk factors, significant association was shown between baPWV and BMD in both genders (male: r=−0.084, P=0.035; female: r=−0.088, P=0.014). The correlation was stronger in females than in males, and in females, the correlation was stronger after menopause. Similarly, mean baPWV differed significantly according to the decreased BMD (normal BMD, Osteopenia, Osteoporosis). In contrast, no significant differences were observed for ABI, CIMT, eGFR or microalbuminuria with BMD.
Conclusions
Independent of confounding factors, low BMD is associated with the functional marker of subclinical atherosclerosis (increased baPWV), but not with structural markers (ABI, CIMT, eGFR or microalbuminuria) among healthy females and males.
doi:10.3978/j.issn.2072-1439.2015.04.47
PMCID: PMC4454857  PMID: 26101634
Low bone mineral density (BMD); atherosclerosis; health check-up; arterial stiffness
16.  Pulmonary Adenocarcinoma With Signet Ring Cell Features 
Comprehensive biological characteristics of pulmonary adenocarcinomas with signet ring cell features (SRC+) are not well known. Herein, we systematically evaluated clinical and molecular features of SRC+ cases with particular attention to smoking status. Surgically treated lung adenocarcinomas (n=763) with follow-up ≥5 years in 3 cohorts were reviewed: all patients in 2006 to 2007 (“all-comers,” n=222; 168 ever-smokers), a never-smoker cohort (n=266), and a cohort of ever-smokers (n=275). SRC+ tumors had ≥10% of SRCs agreed by 2 pathologists. SRC+ cases were tested for rearrangement of ALK and ROS1, as well as 187 known mutations in 10 oncogenes including EGFR, KRAS, BRAF, ERBB2, JAK2, AKT1, AKT2, KIT, MET, and PIK3CA. Overall, 53 of 763 cases (7%) were SRC+. In the 2006 to 2007 “all comer” cohort, 9% were SRC+. In the never-smoker cohort, 9% were SRC+. In the smoker cohort, 3% were SRC+. Univariable analysis showed that SRC+ never-smokers had shorter overall and disease-free survival (P=0.006 and 0.0004, respectively), but the significance faded in the multivariable analysis. For the other 2 cohorts, crude 5-year survival was decreased by 6% to 27% in SRC+ cases without reaching statistical significance. In SRC+ tumors, KRAS mutation was most common (29%), followed by ALK (26%), EGFR (18%), ROS1 (6%), BRAF (6%), and PIK3CA (3%). In summary, SRC+ tumors in never-smokers had a worse survival by univariable analysis only. SRC+ cases seemed enriched for ALK+ and ROS1+, and other mutations were generally in keeping with the patient’s smoking status.
doi:10.1097/PAS.0000000000000280
PMCID: PMC4410841  PMID: 25007143
signet ring cell; ALK; ROS1; lung; adenocarcinoma; smoking status; mutations; survival
17.  Genomic Rearrangements Define Lineage Relationships between Adjacent Lepidic and Invasive Components in Lung Adenocarcinoma 
Cancer research  2014;74(11):3157-3167.
The development of adenocarcinoma of the lung is believed to proceed from in situ disease (adenocarcinoma in situ, AIS) to minimally invasive disease with prominent lepidic growth (minimally invasive adenocarcinoma, MIA), then to fully invasive adenocarcinoma (AD), but direct evidence for this model has been lacking. Because some lung adenocarcinomas show prominent lepidic growth (AD-L), we designed a study to address the lineage relationship between the lepidic (noninvasive) component (L) and the adjacent nonlepidic growth component representing invasive disease within individual tumors. Lineage relationships were evaluated by next-generation DNA sequencing to define large genomic rearrangements in microdissected tissue specimens collected by laser capture. We found a strong lineage relationship between the majority of adjacent lepidic and invasive components, supporting a putative AIS–AD transition. Notably, many rearrangements were detected in the less aggressive lepidic component, although the invasive component exhibited an overall higher rate of genomic rearrangement. Furthermore, a significant number of genomic rearrangements were present in histologically normal lung adjacent to tumor, but not in host germline DNA, suggesting field defects restricted to zonal regions near a tumor. Our results offer a perspective on the genetic pathogenesis underlying adenocarcinoma development and its clinical management.
doi:10.1158/0008-5472.CAN-13-1727
PMCID: PMC4399556  PMID: 24879567
18.  Changes in proinflammatory cytokines and white matter in chronically stressed rats 
Although the pathogenesis of depression, an incapacitating psychiatric ailment, remains largely unknown, previous human and animal studies have suggested that both proinflammatory cytokines and altered oligodendrocytes play important roles in the condition. This study examined these two factors in the brains of rats following unpredictable chronic mild stress for 4 weeks, with the hypothesis that chronic stress may affect oligodendrocytes and elevate proinflammatory cytokines in the brain. After suffering unpredictable stressors for 4 weeks, the rats showed depression-like behaviors, including decreased locomotion in the open field, increased immobility time in the forced swim test, and decreased sucrose consumption and less sucrose preference when compared with controls. Immunohistochemical staining of brain sections showed higher immunoreactivity of proinflammatory cytokines in certain brain regions of stressed rats compared with controls; lower immunoreactivity of myelin basic protein and fewer mature oligodendrocytes were seen in the prefrontal cortex, but no demyelination was detected. These results are interpreted and discussed in the context of recent findings from human and animal studies.
doi:10.2147/NDT.S78131
PMCID: PMC4358419  PMID: 25834438
cytokines; depression; myelination; oligodendrocytes; stress
19.  SNPs in PTGS2 and LTA Predict Pain and Quality of Life in Long Term Lung Cancer Survivors 
PURPOSE
Lung cancer survivors report the lowest quality of life relative to other cancer survivors. Pain is one of the most devastating, persistent, and incapacitating symptoms for lung cancer survivors. Prevalence rates vary with 80–100% of survivors experiencing cancer pain and healthcare costs are five times higher in cancer survivors with uncontrolled pain. Cancer pain often has a considerable impact on quality of life among cancer patients and cancer survivors. Therefore, early identification, and treatment is important. Although recent studies have suggested a relationship between single nucleotide polymorphisms (SNPs) in several cytokine and inflammation genes with cancer prognosis, associations with cancer pain are not clear. Therefore, the primary aim of this study was to identify SNPs related to pain in long term lung cancer survivors.
PATIENTS AND METHODS
Participants were enrolled in the Mayo Clinic Lung Cancer Cohort upon diagnosis of their lung cancer. 1149 Caucasian lung cancer survivors, (440 surviving < 3 years; 354 surviving 3–5 years; and 355 surviving> 5 years) completed study questionnaires and had genetic samples available. Ten SNPS from PTGS2 and LTA genes were selected based on the serum literature. Outcomes included pain, and quality of life as measured by the SF-8.
RESULTS
Of the 10 SNPs evaluated in LTA and PTGS2 genes, 3 were associated with pain severity (rs5277; rs1799964), social function (rs5277) and mental health (rs5275). These results suggested both specificity and consistency of these inflammatory gene SNPs in predicting pain severity in long term lung cancer survivors.
CONCLUSION
These results provide support for genetic predisposition to pain severity and may aid in identification of lung cancer survivors at high risk for morbidity and poor QOL.
doi:10.1016/j.lungcan.2012.02.017
PMCID: PMC4314090  PMID: 22464751
genetics; SNPs; pain; quality of life; lung cancer; cytokines; LTA; PTGS2
20.  Asparaginase induces apoptosis and cytoprotective autophagy in chronic myeloid leukemia cells 
Oncotarget  2015;6(6):3861-3873.
The antitumor enzyme asparaginase, which targets essential amino acid L-asparagine and catalyzes it to L-aspartic acid and ammonia, has been used for years in the treatment of acute lymphoblastic leukemia (ALL), subtypes of myeloid leukemia and T-cell lymphomas, whereas the anti-chronic myeloid leukemia (CML) effect of asparaginase and its underlying mechanism has not been completely elucidated. We have shown here that asparaginase induced significant growth inhibition and apoptosis in K562 and KU812 cells. Apart from induction of apoptosis, we reported for the first time that asparaginase induced autophagic response in K562 and KU812 cells as evidenced by the formation of autophagosome, microtubule-associated protein light chain 3 (LC3)-positive autophagy-like vacuoles, and the upregulation of LC3-II. Further study suggested that the Akt/mTOR (mammalian target of rapamycin) and Erk (extracellular signal-regulated kinase) signaling pathway were involved in asparaginase-induced autophagy in K562 cells. Moreover, blocking autophagy using pharmacological inhibitors LY294002, chloroquine (CQ) and quinacrine (QN) enhanced asparaginase-induced cell death and apoptosis, indicating the cytoprotective role of autophagy in asparaginase-treated K562 and KU812 cells. Together, these findings provide a rationale that combination of asparaginase anticancer activity and autophagic inhibition might be a promising new therapeutic strategy for CML.
PMCID: PMC4414159  PMID: 25738356
asparaginase; autophagy; apoptosis; chronic myeloid leukemia
21.  Effects of α-enolase (ENO1) over-expression on malignant biological behaviors of AGS cells 
Objective: To investigate the effects of α-Enolase (ENO1) over-expression on the proliferative and migratory abilities of AGS cells. Methods: The target gene was cloned and mounted to the eukaryotic expression vector pcDNA3.1(+), then was transfected into gastric cancer cell lines AGS. mRNA and protein level of ENO1 in AGS cells were verified by real-time quantitative RT-PCR and Western Blot, respectively. The effects of over-expression of ENO1 on proliferative and migratory abilities of AGS cells were detected by the experiments of CCK-8, colony formation and wound healing assays. Results: The eukaryotic expression vector pcDNA3.1(+)/eno1 was successfully constructed, and verified by sequencing. It was shown from the cell proliferation curves that the proliferative ability of AGS-ENO1 transfected group was higher than that of the control group after 72 hours (t = 3.44, P = 0.04), meanwhile, the number of the cell-colonies of the AGS-ENO1 group were significantly greater than that of the control group (t = 5.26, P = 0.01). For the ability of migration, it was significantly enhanced in the over-expression ENO1 cells than in the negative cells (t = 7.35, P < 0.001). Conclusion: The over-expression of ENO1 protein can enhance the abilities of proliferation and migration in gastric cancer cells of AGS, which indicates that ENO1 may be an important potential tumor-marker associated with the development of gastric cancer.
PMCID: PMC4358447  PMID: 25784992
α-enolase; gastric cancer; proliferation; migration
22.  Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes 
Nature Communications  2014;5:5896.
Vertebrates diverged from other chordates ~500 Myr ago and experienced successful innovations and adaptations, but the genomic basis underlying vertebrate origins are not fully understood. Here we suggest, through comparison with multiple lancelet (amphioxus) genomes, that ancient vertebrates experienced high rates of protein evolution, genome rearrangement and domain shuffling and that these rates greatly slowed down after the divergence of jawed and jawless vertebrates. Compared with lancelets, modern vertebrates retain, at least relatively, less protein diversity, fewer nucleotide polymorphisms, domain combinations and conserved non-coding elements (CNE). Modern vertebrates also lost substantial transposable element (TE) diversity, whereas lancelets preserve high TE diversity that includes even the long-sought RAG transposon. Lancelets also exhibit rapid gene turnover, pervasive transcription, fastest exon shuffling in metazoans and substantial TE methylation not observed in other invertebrates. These new lancelet genome sequences provide new insights into the chordate ancestral state and the vertebrate evolution.
The lancelet, or amphioxus, is an extant basal chordate that diverged from other chordate lineages about 550 million years ago. Here the authors sequence and assemble the diploid genome of a male adult of the Chinese lancelet, B. belcheri, and highlight genomic features that may have played an important role in the origin and evolution of vertebrates.
doi:10.1038/ncomms6896
PMCID: PMC4284660  PMID: 25523484
23.  Inhibitory effect of isothiocyanate derivant targeting AGPS by computer-aid drug design on proliferation of glioma and hepatic carcinoma cells 
Lipids metabolism was involved in the process of many types of tumor and alkylglycerone phosphate synthase (AGPS) was considered implicated in tumor process. Benzyl isothiocyanate (BITC) showed the inhibitory effect of tumor and AGPS activity, therefore, we screened a group of small molecular compound based on BITC by computer-aid design targeting AGPS and the results showed that the derivants could suppress the proliferation, the expression of tumor related genes such as survivin and Bcl-2, and the level of ether lipids such as lysophosphatidic acid ether (LPAe) and platelet activating factor ether (PAFe); however, the activity of caspase-3/8 was improved in glioma U87MG and hepatic carcinoma HepG2 cells in vitro.
PMCID: PMC4348851  PMID: 25755779
Computer-aid drug design; alkylglycerone phosphate synthase; glioma; hepatic carcinoma
24.  Silencing of CXCR4 sensitizes triple-negative breast cancer cells to cisplatin 
Oncotarget  2014;6(2):1020-1030.
Triple-negative breast cancer (TNBC) is an aggressive form of breast cancer for which there is no effective treatment. Previously, we and others demonstrated that CXCR4 surface expression is an independent prognostic factor for disease relapse and survival in breast cancer. In this study, we investigated the effects of CXCR4 gene silencing on cisplatin chemosensitivity in human triple-negative breast cancer cell lines. We found that CXCR4 silencing significantly inhibited cell growth, decreased colony formation, and enhanced cisplatin sensitivity while overexpression of CXCR4 rendered cells more resistant to cisplatin. Moreover, the percentage of apoptosis and cell cycle arrest at the G2/M phase of cisplatin-treated CXCR4 knockdown cells was significantly higher than control cells. Furthermore, we demonstrated CXCR4 knockdown cells showed lower levels of mutant p53 and Bcl-2 protein than the control group, while also having higher levels of caspase-3 and Bax. However overexpression of CXCR4 had the reverse effect. In vivo experiments confirmed that downregulation of CXCR4 enhanced cisplatin anticancer activity in tumor-bearing mice, and that this enhanced anticancer activity is attributable to tumor cell apoptosis. Thus, this study indicates that CXCR4 can modulate cisplatin sensitivity in TNBC cells and suggests that CXCR4 may be a therapeutic target for TNBC.
PMCID: PMC4359214  PMID: 25544759
CXCR4; triple-negative breast cancer; cisplatin; chemosensitivity; apoptosis
25.  Investigation on the IL-18 -607A/C and -137C/G on the susceptibility of ischemic stroke 
Objective:
We conducted a case-control study with 322 cases and 322 controls to assess the role of the two common SNPs in the promoter of IL-18 gene.
Methods:
Polymerase chain reaction restriction fragment length of polymorphism (PCR-RFLP) was taken to genotype -607A/C and -137C/G in the promoter of the IL-18 gene.
Results:
By comparing cases and control subjects, we found that IS cases were more likely to have higher BMI, higher proportion of hypertension, and have higher proportion of smokers and drinkers. We found that IL-18 -607CC genotype (OR=1.70, 95% CI=1.03-2.81) and C allele (OR=1.26, 95% CI=1.01-1.58) were significantly more frequent in IS patients when compared with AA genotype. We did not find significant association between IL-18 -607A/C gene polymorphism and BMI, hypertension, smoking and drinking on the risk of IS.
Conclusion:
Our study suggests that polymorphisms in IL-18 -607A/C can influence the development of IS, and this gene polymorphism is associated with risk of IS in a Chinese population.
doi:10.12669/pjms.311.5997
PMCID: PMC4386186  PMID: 25878643
IL-18; Ischemic stroke; Polymorphism

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