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1.  The gut microbiome in atherosclerotic cardiovascular disease 
Nature Communications  2017;8:845.
The gut microbiota has been linked to cardiovascular diseases. However, the composition and functional capacity of the gut microbiome in relation to cardiovascular diseases have not been systematically examined. Here, we perform a metagenome-wide association study on stools from 218 individuals with atherosclerotic cardiovascular disease (ACVD) and 187 healthy controls. The ACVD gut microbiome deviates from the healthy status by increased abundance of Enterobacteriaceae and Streptococcus spp. and, functionally, in the potential for metabolism or transport of several molecules important for cardiovascular health. Although drug treatment represents a confounding factor, ACVD status, and not current drug use, is the major distinguishing feature in this cohort. We identify common themes by comparison with gut microbiome data associated with other cardiometabolic diseases (obesity and type 2 diabetes), with liver cirrhosis, and rheumatoid arthritis. Our data represent a comprehensive resource for further investigations on the role of the gut microbiome in promoting or preventing ACVD as well as other related diseases.
The gut microbiota may play a role in cardiovascular diseases. Here, the authors perform a metagenome-wide association study on stools from individuals with atherosclerotic cardiovascular disease and healthy controls, identifying microbial strains and functions associated with the disease.
doi:10.1038/s41467-017-00900-1
PMCID: PMC5635030  PMID: 29018189
2.  Constitutive Lck activity drives sensitivity differences between CD8+ memory T cell subsets 
CD8+ T cells develop increased sensitivity following antigen experience, and differences in sensitivity exist between T cell memory subsets. How differential TCR signaling between memory subsets contributes to sensitivity differences is unclear. We show in mouse effector memory T cells (TEM) that more than 50% of lymphocyte-specific protein tyrosine kinase (Lck) exists in a constitutively active conformation, compared with less than 20% in central memory T cells (TCM). Immediately proximal to Lck signaling, we observed enhanced Zap-70 phosphorylation in TEM following TCR ligation compared with TCM. Further, we observed superior cytotoxic effector function in TEM compared with TCM, and provide evidence that this results from a lower probability of TCM reaching threshold signaling due to the decreased magnitude of TCR-proximal signaling. We provide evidence that the differences in Lck constitutive activity between CD8+ TCM and TEM are due to differential regulation by SH2 domain-containing phosphatase-1 (Shp-1) and C-terminal Src kinase (Csk), and use modeling of early TCR signaling to reveal the significance of these differences. We show that inhibition of Shp-1 results in increased constitutive Lck activity in TCM to levels similar to TEM, as well as increased cytotoxic effector function in TCM. Together, this work demonstrates a role for constitutive Lck activity in controlling antigen sensitivity, and suggests that differential activities of TCR-proximal signaling components may contribute to establishing the divergent effector properties of TCM and TEM. This work also identifies Shp-1 as a potential target to improve the cytotoxic effector functions of TCM for adoptive cell therapy applications.
doi:10.4049/jimmunol.1600178
PMCID: PMC4935560  PMID: 27271569
3.  Preparation and properties of a novel carbon nanotubes/poly(vinyl alcohol)/epidermal growth factor composite biological dressing 
Wound dressings with drug delivery system have drawn increasing attention in skin damage recombination. Herein, a novel composite biological dressing was prepared and based on poly(vinyl alcohol) (PVA) combined with carbon nanotubes (CNTs) and epidermal growth factor (EGF) by electrospinning on gauze. The properties of the CNTs/PVA/EGF composite dressing were systemically investigated by general observation, and scanning electron microscopy (SEM). In vitro, the cytotoxicity of this dressing was investigated using a methyl thiazolyl tetrazolium (MTT) assay on L929 fibroblasts. In order to study the sustained release of EGF from this dressing, the concentration of EGF at different times was tested by ELISA. Furthermore, the biological activity of the released EGF was also evaluated using the MTT assay. Moreover, an in vivo experiment was conducted to observe whether this dressing was capable of improving healing in the model of wounded skin on rats. It was revealed that this dressing had a well-distributed microstructure by SEM. Additionally, the grade of cytotoxicity was low, and the EGF had a sustained release rate from this dressing. Furthermore, a maximum accumulative release rate of 12.47% was identified at 12 h, and was retained at 9.4% after 48 h. Simultaneously, the relative growth rate of L929 fibroblasts in the 12 h experimental group and 48 h group was 291.24 and 211.3%, respectively. Next, the efficacy of these products was evaluated in vivo using Sprague-Dawley rats with a skin injury model. The healing of wounded skin of rats was sped up by this dressing based on the gross and histological appearances. From 7 to 10 days, the wounds in the experimental group were almost healed. In conclusion, this CNTs/PVA/EGF dressing had a well-distributed structure and an ability to release EGF at a sustained rate with the activity being favorable. On the basis of those results, a positive influence of designed dressing for accelerated wound healing was confirmed.
doi:10.3892/etm.2017.4752
PMCID: PMC5609095
biological dressing; poly(vinyl alcohol); carbon nanotubes; epidermal growth factor; nanofiber
4.  Log odds of positive lymph nodes is superior to the number- and ratio-based lymph node classification systems for colorectal cancer patients undergoing curative (R0) resection 
Molecular and Clinical Oncology  2017;6(5):782-788.
The metastatic lymph node status (N classification) is an important prognostic factor for patients with colorectal cancer (CRC). The aim of the present study was to evaluate and compare the prognostic assessment of three different lymph node staging methods, namely standard lymph node (pN) staging, metastatic lymph node ratio (LNR) and log odds of positive lymph nodes (LODDS) in CRC patients who undergo curative resection (R0). Data were retrospectively collected from 192 patients who had undergone R0 resection. Kaplan-Meier survival curves, Cox proportional hazards model and accuracy of the three methods (pN, LNR and LODDS) were compared to evaluate the prognostic effect. Univariate analysis demonstrated that pN, LNR and LODDS were all significantly correlated with survival (P=0.001, P<0.001 and P<0.001, respectively). The final result of the 3-step multivariate analysis demonstrated that LODDS was superior to the other two N categories. Patients in the same pN or LNR classifications may be classified into different LODDS stages with different prognoses. Thus, LODDS may be a meaningful prognostic indicator and superior to the pN and LNR classifications in CRC patients who undergo curative (R0) resection.
doi:10.3892/mco.2017.1203
PMCID: PMC5431519
colorectal cancer; lymph node; lymph node ratio; log odds of positive lymph nodes; survival
5.  GYY4137 stimulates osteoblastic cell proliferation and differentiation via an ERK1/2-dependent anti-oxidant mechanism 
Objective: Oxidative stress plays a critical role in the development of osteoporosis. Hydrogen sulfide (H2S), produces anti-oxidant effect in various biological systems. The present study found that GYY4137, a slow H2S releasing compound, stimulated both mRNA level and activity of alkaline phosphatase, the marker of osteoblast differentiation. This research aims to explore the mechanism on how GYY4137 stimulates osteoblastic cell proliferation and differentiation via an ERK1/2-dependent anti-oxidant approach. Methods: The MC3T3-E1 osteoblast-like cell line was cultured in plate. After pretreatment with GYY4137 (100 µM) for 30 min, the cells were washed twice with PBS solution and then incubated in freshly prepared low serum medium containing 400 μM H2O2 for 4 h. Cells viability was evaluated with the MTT. Cell apoptosis was evaluated by the Hoechst 33342. Then, ALP activity, NO and the superoxide dismutase (SOD) activity is determined by assay kit accordingly, ALP mRNA is identified by RT-PCR. ERK1/2 was analyzed by Western blot. The ROS production was measured with a fluorescence reader. All data was analyzed by SPSS 16.0. Results: We found in the present study that GYY4137, a slow H2S releasing compound, stimulated both mRNA level and activity of alkaline phosphatase, the marker of osteoblast differentiation. RT-PCR shows that GYY4137 stimulated the transcriptional levels of Runx2, a key transcription factor associated with osteoblast differentiation. These data suggest that GYY4137 may stimulate osteoblastic cell proliferation and differentiation. Moreover, GYY4137, which alone at 1-1000 µM had no significant effect, protected MC3T3-E1 osteoblastic cells against hydrogen peroxide (H2O2)-induced cell death and apoptosis. This was mediated by its anti-oxidant effect, as GYY4137 reversed the reduced superoxide dismutase activity and the elevated productions of reactive oxygen species and nitric oxide in the osteoblastic cells treated with H2O2. Western blotting analysis showed that the protective effects of GYY4137 were mediated by suppression of ERK1/2. Conclusions: GYY4137 stimulates osteoblastic cell proliferation and bone differentiation via an ERK1/2-dependent anti-oxidant mechanism. Our findings suggest that GYY4137 may have a potentially therapeutic value for osteoporosis.
PMCID: PMC5376009  PMID: 28386344
Oxidative stress; osteoporosis; bone formation; hydrogen sulfide; reactive oxygen species; ERK1/2
6.  Chronic Lymphocytic Leukemia Prognostic Index: A New Integrated Scoring System to Predict the Time to First Treatment in Chinese Patients with Chronic Lymphocytic Leukemia 
Chinese Medical Journal  2017;130(2):135-142.
Background:
The established clinical staging systems (Rai/Binet) of chronic lymphocytic leukemia (CLL) cannot accurately predict the appropriate treatment of patients in the earlier stages. In the past two decades, several prognostic factors have been identified to predict the outcome of patients with CLL, but only a few studies investigated more markers together. To predict the time to first treatment (TTFT) in patients of early stages, we evaluated the prognostic role of conventional markers as well as cytogenetic abnormalities and combined them together in a new prognostic scoring system, the CLL prognostic index (CLL-PI).
Methods:
Taking advantage of a population of 406 untreated Chinese patients with CLL at early and advanced stage of disease, we identified the strongest prognostic markers of TTFT and, subsequently, in a cohort of 173 patients who had complete data for all 3 variables, we integrated the data of traditional staging system, cytogenetic aberrations, and mutational status of immunoglobulin heavy chain variable region (IGHV) in CLL-PI. The median follow-up time was 45 months and the end point was TTFT.
Results:
The median TTFT was 38 months and the 5-year overall survival was 80%. According to univariate analysis, patients of advanced Rai stages (P < 0.001) or with 11q- (P = 0.002), 17p- (P < 0.001), unmutated IGHV (P < 0.001), negative 13q- (P = 0.007) and elevated lactate dehydrogenase levels (P = 0.001) tended to have a significantly shorter TTFT. And subsequently, based on multivariate Cox regression analysis, three independent factors for TTFT were identified: advanced clinical stage (P = 0.002), 17p- (P = 0.050) and unmutated IGHV (P = 0.049). Applying weighted grading of these independent factors, a CLL-PI was constructed based on regression parameters, which could categorize four different risk groups (low risk [score 0], intermediate low [score 1], intermediate high [score 2] and high risk [score 3–6]) with significantly different TTFT (median TTFT of not reached (NR), 65.0 months, 36.0 months and 19.0 months, respectively, P < 0.001).
Conclusions:
This study developed a weighted, integrated CLL-PI prognostic system of CLL patients which combines the critical genetic prognostic markers with traditional clinical stage. This novel modified PI system could be used to discriminate among groups and may help predict the TTFT and prognosis of patients with CLL.
doi:10.4103/0366-6999.197978
PMCID: PMC5282668  PMID: 28091403
17p Deletion; Chronic Lymphocytic Leukemia; Immunoglobulin Heavy Chain Variable Mutation; Prognostic Index; Time to First Treatment
7.  Immunotherapy Bridge 2016 and Melanoma Bridge 2016: meeting abstracts 
Hirsh, Vera | Pignata, Sandro | Bersanelli, Melissa | Gnetti, Letizia | Azzoni, Cinzia | Bottarelli, Lorena | Gasparro, Donatello | Leonardi, Francesco | Silini, Enrico Maria | Buti, Sebastiano | Wennerberg, Erik | Mediero, Aranzazu | Cronstein, Bruce | Formenti, Silvia | Demaria, Sandra | Vanpouille-Box, Claire | Pilones, Karsten | Rudqvist, Nils | Diamond, Julie | Formenti, Silvia | Demaria, Sandra | Morris, Zachary S. | Guy, Emily I. | Francis, David M. | Gressett, Monica M. | Armstrong, Eric A. | Huang, Shyhmin | Gilles, Stephen D. | Korman, Alan J. | Hank, Jacquelyn A. | Hoefges, Anna | Rakhmilevich, Alexander L. | Harari, Paul M. | Sondel, Paul M. | Hailemichael, Yared | Overwijk, Willem W. | Straten, Per thor | Lugli, Alessandro | Dawson, Heather | Blank, Annika | Zlobec, Inti | Fattore, Luigi | Costantini, Susan | Acunzo, Mario | Romano, Giulia | Nigita, Giovanni | Laganà, Alessandro | Malpicci, Debora | Ruggiero, Ciro Francesco | Pisanu, Maria Elena | Noto, Alessia | De Vitis, Claudia | Croce, Carlo Maria | Ascierto, Paolo Antonio | Mancini, Rita | Ciliberto, Gennaro | Postow, Michael | Luke, Jason | Stroncek, David | Castiello, Luciano | Chen, Wenjing | Jin, Ping | Ren, Jiaqiang | Sabatino, Marianna | Ferrone, Soldano | Duong, Connie PM | Vetizou, Marie | Zitvogel, Laurence | Pisanu, Maria Elena | Noto, Alessia | Fattore, Luigi | Malpicci, Debora | Ciliberto, Gennaro | Mancini, Rita | Occelli, Marcella | Cauchi, Carolina | Sciancalepore, Grazia | Lo Nigro, Cristiana | Rovera, Michela | Varamo, Chiara | Vivenza, Daniela | Seia, Zelda | Palazzini, Stefania | Errico, Fabiana | Basso, Davide | Quaranta, Laura | Forte, Giuseppe | Lavagna, Fulvio | Violante, Silvia | Bosio, Paolo | Lattanzio, Laura | Merlano, Marco Carlo | Moogk, Duane | Zhong, Shi | Yu, Zhiya | Liadi, Ivan | Rittase, William | Fang, Victoria | Dougherty, Janna | Perez-Garcia, Arianne | Osman, Iman | Zhu, Cheng | Varadarajan, Navin | Restifo, Nicholas P. | Frey, Alan | Krogsgaard, Michelle | Balatoni, Timea | Moho, Anita | Sebestyén, Timea | Varga, Anita | Oláh, Judit | Lengyel, Zsuzsanna | Emri, Gabriella | Liszkay, Gabriella | Ladányi, Andrea | Polini, Beatrice | Fogli, Stefano | Carpi, Sara | Pardini, Barbara | Naccarati, Alessio | Dubbini, Nevio | Breschi, Maria Cristina | Romanini, Antonella | Nieri, Paola | Morgese, Francesca | Soldato, Davide | Pagliaretta, Silvia | Giampieri, Riccardo | Brancorsini, Donatella | Rinaldi, Silvia | Torniai, Mariangela | Campanati, Anna | Ganzetti, Giulia | Offidani, Annamaria | Giacchetti, Alfredo | Ricotti, Giuseppe | Savini, Agnese | Onofri, Azzurra | Bianchi, Francesca | Berardi, Rossana | Galdo, Giovanna | Orlandino, Gianfranco | Serio, Salvatore | Massariello, Domenico | Fabrizio, Tommaso | Montagnani, Valentina | Benelli, Matteo | Apollo, Alessandro | Pescucci, Chiara | Licastro, Danilo | Urso, Carmelo | Gerlini, Gianni | Borgognoni, Lorenzo | Luzzatto, Lucio | Stecca, Barbara | Gambale, Elisabetta | Tinari, Camilla | Quinzii, Alberto | Cortellini, Alessio | Carella, Consiglia | De Tursi, Michele | De Francesco, Adele Emanuela | De Fina, Mariarosanna | Zito, Maria Cristina | Bisceglia, Maria Dezia | Esposito, Stefania | Fersini, Giuseppina | Morello, Silvana | Sorrentino, Claudia | Pinto, Aldo | Di Sarno, Antonella | Bianco, Antonella | D’Aniello, Carmine | Andreozzi, Francesca | Festina, Lucia | Vanella, Vito | Ascierto, Paolo Antonio | Montesarchio, Vincenzo | Kotlan, Beatrix | Godeny, Maria | Emil, Farkas | Toth, Laszlo | Horvath, Szabolcs | Eles, Klara | Balatoni, Timea | Savolt, Akos | Szollar, Andras | Kasler, Miklós | Liszkay, Gabriella | Yiu, Daniel | Grizzi, Fabio | Patrinicola, Federica | Chiriva-Internati, Maurizio | Motta, Stefania | Monti, Marcello | Benini, Lavinia | Ugel, Stefano | Cingarlini, Sara | Fiore, Alessandra | Grego, Elisabetta | Tortora, Giampaolo | Bronte, Vincenzo | Tondulli, Luca | Di Monta, Gianluca | Caracò, Corrado | Marone, Ugo | Festino, Lucia | Ascierto, Paolo Antonio | Mozzillo, Nicola
Journal of Translational Medicine  2017;15(Suppl 1):8.
doi:10.1186/s12967-016-1095-2
PMCID: PMC5267294
8.  31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016): part one 
Lundqvist, Andreas | van Hoef, Vincent | Zhang, Xiaonan | Wennerberg, Erik | Lorent, Julie | Witt, Kristina | Sanz, Laia Masvidal | Liang, Shuo | Murray, Shannon | Larsson, Ola | Kiessling, Rolf | Mao, Yumeng | Sidhom, John-William | Bessell, Catherine A. | Havel, Jonathan | Schneck, Jonathan | Chan, Timothy A. | Sachsenmeier, Eliot | Woods, David | Berglund, Anders | Ramakrishnan, Rupal | Sodre, Andressa | Weber, Jeffrey | Zappasodi, Roberta | Li, Yanyun | Qi, Jingjing | Wong, Philip | Sirard, Cynthia | Postow, Michael | Newman, Walter | Koon, Henry | Velcheti, Vamsidhar | Callahan, Margaret K. | Wolchok, Jedd D. | Merghoub, Taha | Lum, Lawrence G. | Choi, Minsig | Thakur, Archana | Deol, Abhinav | Dyson, Gregory | Shields, Anthony | Haymaker, Cara | Uemura, Marc | Murthy, Ravi | James, Marihella | Wang, Daqing | Brevard, Julie | Monaghan, Catherine | Swann, Suzanne | Geib, James | Cornfeld, Mark | Chunduru, Srinivas | Agrawal, Sudhir | Yee, Cassian | Wargo, Jennifer | Patel, Sapna P. | Amaria, Rodabe | Tawbi, Hussein | Glitza, Isabella | Woodman, Scott | Hwu, Wen-Jen | Davies, Michael A. | Hwu, Patrick | Overwijk, Willem W. | Bernatchez, Chantale | Diab, Adi | Massarelli, Erminia | Segal, Neil H. | Ribrag, Vincent | Melero, Ignacio | Gangadhar, Tara C. | Urba, Walter | Schadendorf, Dirk | Ferris, Robert L. | Houot, Roch | Morschhauser, Franck | Logan, Theodore | Luke, Jason J. | Sharfman, William | Barlesi, Fabrice | Ott, Patrick A. | Mansi, Laura | Kummar, Shivaani | Salles, Gilles | Carpio, Cecilia | Meier, Roland | Krishnan, Suba | McDonald, Dan | Maurer, Matthew | Gu, Xuemin | Neely, Jaclyn | Suryawanshi, Satyendra | Levy, Ronald | Khushalani, Nikhil | Wu, Jennifer | Zhang, Jinyu | Basher, Fahmin | Rubinstein, Mark | Bucsek, Mark | Qiao, Guanxi | MacDonald, Cameron | Hylander, Bonnie | Repasky, Elizabeth | Chatterjee, Shilpak | Daenthanasanmak, Anusara | Chakraborty, Paramita | Toth, Kyle | Meek, Megan | Garrett-Mayer, Elizabeth | Nishimura, Michael | Paulos, Chrystal | Beeson, Craig | Yu, Xuezhong | Mehrotra, Shikhar | Zhao, Fei | Evans, Kathy | Xiao, Christine | Holtzhausen, Alisha | Hanks, Brent A. | Scharping, Nicole | Menk, Ashley V. | Moreci, Rebecca | Whetstone, Ryan | Dadey, Rebekah | Watkins, Simon | Ferris, Robert | Delgoffe, Greg M. | Peled, Jonathan | Devlin, Sean | Staffas, Anna | Lumish, Melissa | Rodriguez, Kori Porosnicu | Ahr, Katya | Perales, Miguel | Giralt, Sergio | Taur, Ying | Pamer, Eric | van den Brink, Marcel R. M. | Jenq, Robert | Annels, Nicola | Pandha, Hardev | Simpson, Guy | Mostafid, Hugh | Harrington, Kevin | Melcher, Alan | Grose, Mark | Davies, Bronwyn | Au, Gough | Karpathy, Roberta | Shafren, Darren | Ricca, Jacob | Merghoub, Taha | Wolchok, Jedd D. | Zamarin, Dmitriy | Batista, Luciana | Marliot, Florence | Vasaturo, Angela | Carpentier, Sabrina | Poggionovo, Cécile | Frayssinet, Véronique | Fieschi, Jacques | Van den Eynde, Marc | Pagès, Franck | Galon, Jérôme | Hermitte, Fabienne | Smith, Sean G. | Nguyen, Khue | Ravindranathan, Sruthi | Koppolu, Bhanu | Zaharoff, David | Schvartsman, Gustavo | Bassett, Roland | McQuade, Jennifer L. | Haydu, Lauren E. | Davies, Michael A. | Tawbi, Hussein | Glitza, Isabella | Kline, Douglas | Chen, Xiufen | Fosco, Dominick | Kline, Justin | Overacre, Abigail | Chikina, Maria | Brunazzi, Erin | Shayan, Gulidanna | Horne, William | Kolls, Jay | Ferris, Robert L. | Delgoffe, Greg M. | Bruno, Tullia C. | Workman, Creg | Vignali, Dario | Adusumilli, Prasad S. | Ansa-Addo, Ephraim A | Li, Zihai | Gerry, Andrew | Sanderson, Joseph P. | Howe, Karen | Docta, Roslin | Gao, Qian | Bagg, Eleanor A. L. | Tribble, Nicholas | Maroto, Miguel | Betts, Gareth | Bath, Natalie | Melchiori, Luca | Lowther, Daniel E. | Ramachandran, Indu | Kari, Gabor | Basu, Samik | Binder-Scholl, Gwendolyn | Chagin, Karen | Pandite, Lini | Holdich, Tom | Amado, Rafael | Zhang, Hua | Glod, John | Bernstein, Donna | Jakobsen, Bent | Mackall, Crystal | Wong, Ryan | Silk, Jonathan D. | Adams, Katherine | Hamilton, Garth | Bennett, Alan D. | Brett, Sara | Jing, Junping | Quattrini, Adriano | Saini, Manoj | Wiedermann, Guy | Gerry, Andrew | Jakobsen, Bent | Binder-Scholl, Gwendolyn | Brewer, Joanna | Duong, MyLinh | Lu, An | Chang, Peter | Mahendravada, Aruna | Shinners, Nicholas | Slawin, Kevin | Spencer, David M. | Foster, Aaron E. | Bayle, J. 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Eric | Fry, Terry | Rao, Arjun A. | Teyssier, Noam | Pfeil, Jacob | Sgourakis, Nikolaos | Salama, Sofie | Haussler, David | Richman, Sarah A. | Nunez-Cruz, Selene | Gershenson, Zack | Mourelatos, Zissimos | Barrett, David | Grupp, Stephan | Milone, Michael | Rodriguez-Garcia, Alba | Robinson, Matthew K. | Adams, Gregory P. | Powell, Daniel J. | Santos, João | Havunen, Riikka | Siurala, Mikko | Cervera-Carrascón, Víctor | Parviainen, Suvi | Antilla, Marjukka | Hemminki, Akseli | Sethuraman, Jyothi | Santiago, Laurelis | Chen, Jie Qing | Dai, Zhimin | Wardell, Seth | Bender, James | Lotze, Michael T. | Sha, Huizi | Su, Shu | Ding, Naiqing | Liu, Baorui | Stevanovic, Sanja | Pasetto, Anna | Helman, Sarah R. | Gartner, Jared J. | Prickett, Todd D. | Robbins, Paul F. | Rosenberg, Steven A. | Hinrichs, Christian S. | Bhatia, Shailender | Burgess, Melissa | Zhang, Hui | Lee, Tien | Klingemann, Hans | Soon-Shiong, Patrick | Nghiem, Paul | Kirkwood, John M. | Rossi, John M. | Sherman, Marika | Xue, Allen | Shen, Yueh-wei | Navale, Lynn | Rosenberg, Steven A. | Kochenderfer, James N. | Bot, Adrian | Veerapathran, Anandaraman | Gokuldass, Aishwarya | Stramer, Amanda | Sethuraman, Jyothi | Blaskovich, Michelle A. | Wiener, Doris | Frank, Ian | Santiago, Laurelis | Rabinovich, Brian | Fardis, Maria | Bender, James | Lotze, Michael T. | Waller, Edmund K. | Li, Jian-Ming | Petersen, Christopher | Blazar, Bruce R. | Li, Jingxia | Giver, Cynthia R. | Wang, Ziming | Grossenbacher, Steven K. | Sturgill, Ian | Canter, Robert J. | Murphy, William J. | Zhang, Congcong | Burger, Michael C. | Jennewein, Lukas | Waldmann, Anja | Mittelbronn, Michel | Tonn, Torsten | Steinbach, Joachim P. | Wels, Winfried S. | Williams, Jason B. | Zha, Yuanyuan | Gajewski, Thomas F. | Williams, LaTerrica C. | Krenciute, Giedre | Kalra, Mamta | Louis, Chrystal | Gottschalk, Stephen | Xin, Gang | Schauder, David | Jiang, Aimin | Joshi, Nikhil | Cui, Weiguo | Zeng, Xue | Menk, Ashley V. | Scharping, Nicole | Delgoffe, Greg M. | Zhao, Zeguo | Hamieh, Mohamad | Eyquem, Justin | Gunset, Gertrude | Bander, Neil | Sadelain, Michel | Askmyr, David | Abolhalaj, Milad | Lundberg, Kristina | Greiff, Lennart | Lindstedt, Malin | Angell, Helen K. | Kim, Kyoung-Mee | Kim, Seung-Tae | Kim, Sung | Sharpe, Alan D. | Ogden, Julia | Davenport, Anna | Hodgson, Darren R. | Barrett, Carl | Lee, Jeeyun | Kilgour, Elaine | Hanson, Jodi | Caspell, Richard | Karulin, Alexey | Lehmann, Paul | Ansari, Tameem | Schiller, Annemarie | Sundararaman, Srividya | Lehmann, Paul | Hanson, Jodi | Roen, Diana | Karulin, Alexey | Lehmann, Paul | Ayers, Mark | Levitan, Diane | Arreaza, Gladys | Liu, Fang | Mogg, Robin | Bang, Yung-Jue | O’Neil, Bert | Cristescu, Razvan | Friedlander, Philip | Wassman, Karl | Kyi, Chrisann | Oh, William | Bhardwaj, Nina | Bornschlegl, Svetlana | Gustafson, Michael P. | Gastineau, Dennis A. | Parney, Ian F. | Dietz, Allan B. | Carvajal-Hausdorf, Daniel | Mani, Nikita | Velcheti, Vamsidhar | Schalper, Kurt | Rimm, David | Chang, Serena | Levy, Ronald | Kurland, John | Krishnan, Suba | Ahlers, Christoph Matthias | Jure-Kunkel, Maria | Cohen, Lewis | Maecker, Holden | Kohrt, Holbrook | Chen, Shuming | Crabill, George | Pritchard, Theresa | McMiller, Tracee | Pardoll, Drew | Pan, Fan | Topalian, Suzanne | Danaher, Patrick | Warren, Sarah | Dennis, Lucas | White, Andrew M. | D’Amico, Leonard | Geller, Melissa | Disis, Mary L. | Beechem, Joseph | Odunsi, Kunle | Fling, Steven | Derakhshandeh, Roshanak | Webb, Tonya J. | Dubois, Sigrid | Conlon, Kevin | Bryant, Bonita | Hsu, Jennifer | Beltran, Nancy | Müller, Jürgen | Waldmann, Thomas | Duhen, Rebekka | Duhen, Thomas | Thompson, Lucas | Montler, Ryan | Weinberg, Andrew | Kates, Max | Early, Brandon | Yusko, Erik | Schreiber, Taylor H. | Bivalacqua, Trinity J. | Ayers, Mark | Lunceford, Jared | Nebozhyn, Michael | Murphy, Erin | Loboda, Andrey | Kaufman, David R. | Albright, Andrew | Cheng, Jonathan | Kang, S. Peter | Shankaran, Veena | Piha-Paul, Sarina A. | Yearley, Jennifer | Seiwert, Tanguy | Ribas, Antoni | McClanahan, Terrill K. | Cristescu, Razvan | Mogg, Robin | Ayers, Mark | Albright, Andrew | Murphy, Erin | Yearley, Jennifer | Sher, Xinwei | Liu, Xiao Qiao | Nebozhyn, Michael | Lunceford, Jared | Joe, Andrew | Cheng, Jonathan | Plimack, Elizabeth | Ott, Patrick A. | McClanahan, Terrill K. | Loboda, Andrey | Kaufman, David R. | Forrest-Hay, Alex | Guyre, Cheryl A. | Narumiya, Kohei | Delcommenne, Marc | Hirsch, Heather A. | Deshpande, Amit | Reeves, Jason | Shu, Jenny | Zi, Tong | Michaelson, Jennifer | Law, Debbie | Trehu, Elizabeth | Sathyanaryanan, Sriram | Hodkinson, Brendan P. | Hutnick, Natalie A. | Schaffer, Michael E. | Gormley, Michael | Hulett, Tyler | Jensen, Shawn | Ballesteros-Merino, Carmen | Dubay, Christopher | Afentoulis, Michael | Reddy, Ashok | David, Larry | Fox, Bernard | Jayant, Kumar | Agrawal, Swati | Agrawal, Rajendra | Jeyakumar, Ghayathri | Kim, Seongho | Kim, Heejin | Silski, Cynthia | Suisham, Stacey | Heath, Elisabeth | Vaishampayan, Ulka | Vandeven, Natalie | Viller, Natasja Nielsen | O’Connor, Alison | Chen, Hui | Bossen, Bolette | Sievers, Eric | Uger, Robert | Nghiem, Paul | Johnson, Lisa | Kao, Hsiang-Fong | Hsiao, Chin-Fu | Lai, Shu-Chuan | Wang, Chun-Wei | Ko, Jenq-Yuh | Lou, Pei-Jen | Lee, Tsai-Jan | Liu, Tsang-Wu | Hong, Ruey-Long | Kearney, Staci J. | Black, Joshua C. | Landis, Benjamin J. | Koegler, Sally | Hirsch, Brooke | Gianani, Roberto | Kim, Jeffrey | He, Ming-Xiao | Zhang, Bingqing | Su, Nan | Luo, Yuling | Ma, Xiao-Jun | Park, Emily | Kim, Dae Won | Copploa, Domenico | Kothari, Nishi | doo Chang, Young | Kim, Richard | Kim, Namyong | Lye, Melvin | Wan, Ee | Kim, Namyong | Lye, Melvin | Wan, Ee | Kim, Namyong | Lye, Melvin | Wan, Ee | Knaus, Hanna A. | Berglund, Sofia | Hackl, Hubert | Karp, Judith E. | Gojo, Ivana | Luznik, Leo | Hong, Henoch S. | Koch, Sven D. | Scheel, Birgit | Gnad-Vogt, Ulrike | Kallen, Karl-Josef | Wiegand, Volker | Backert, Linus | Kohlbacher, Oliver | Hoerr, Ingmar | Fotin-Mleczek, Mariola | Billingsley, James M. | Koguchi, Yoshinobu | Conrad, Valerie | Miller, William | Gonzalez, Iliana | Poplonski, Tomasz | Meeuwsen, Tanisha | Howells-Ferreira, Ana | Rattray, Rogan | Campbell, Mary | Bifulco, Carlo | Dubay, Christopher | Bahjat, Keith | Curti, Brendan | Urba, Walter | Vetsika, E-K | Kallergi, G. | Aggouraki, Despoina | Lyristi, Z. | Katsarlinos, P. | Koinis, Filippos | Georgoulias, V. | Kotsakis, Athanasios | Martin, Nathan T. | Aeffner, Famke | Kearney, Staci J. | Black, Joshua C. | Cerkovnik, Logan | Pratte, Luke | Kim, Rebecca | Hirsch, Brooke | Krueger, Joseph | Gianani, Roberto | Martínez-Usatorre, Amaia | Jandus, Camilla | Donda, Alena | Carretero-Iglesia, Laura | Speiser, Daniel E. | Zehn, Dietmar | Rufer, Nathalie | Romero, Pedro | Panda, Anshuman | Mehnert, Janice | Hirshfield, Kim M. | Riedlinger, Greg | Damare, Sherri | Saunders, Tracie | Sokol, Levi | Stein, Mark | Poplin, Elizabeth | Rodriguez-Rodriguez, Lorna | Silk, Ann | Chan, Nancy | Frankel, Melissa | Kane, Michael | Malhotra, Jyoti | Aisner, Joseph | Kaufman, Howard L. | Ali, Siraj | Ross, Jeffrey | White, Eileen | Bhanot, Gyan | Ganesan, Shridar | Monette, Anne | Bergeron, Derek | Amor, Amira Ben | Meunier, Liliane | Caron, Christine | Morou, Antigoni | Kaufmann, Daniel | Liberman, Moishe | Jurisica, Igor | Mes-Masson, Anne-Marie | Hamzaoui, Kamel | Lapointe, Rejean | Mongan, Ann | Ku, Yuan-Chieh | Tom, Warren | Sun, Yongming | Pankov, Alex | Looney, Tim | Au-Young, Janice | Hyland, Fiona | Conroy, Jeff | Morrison, Carl | Glenn, Sean | Burgher, Blake | Ji, He | Gardner, Mark | Mongan, Ann | Omilian, Angela R. | Conroy, Jeff | Bshara, Wiam | Angela, Omilian | Burgher, Blake | Ji, He | Glenn, Sean | Morrison, Carl | Mongan, Ann | Obeid, Joseph M. | Erdag, Gulsun | Smolkin, Mark E. | Deacon, Donna H. | Patterson, James W. | Chen, Lieping | Bullock, Timothy N. | Slingluff, Craig L. | Obeid, Joseph M. | Erdag, Gulsun | Deacon, Donna H. | Slingluff, Craig L. | Bullock, Timothy N. | Loffredo, John T. | Vuyyuru, Raja | Beyer, Sophie | Spires, Vanessa M. | Fox, Maxine | Ehrmann, Jon M. | Taylor, Katrina A. | Korman, Alan J. | Graziano, Robert F. | Page, David | Sanchez, Katherine | Ballesteros-Merino, Carmen | Martel, Maritza | Bifulco, Carlo | Urba, Walter | Fox, Bernard | Patel, Sapna P. | De Macedo, Mariana Petaccia | Qin, Yong | Reuben, Alex | Spencer, Christine | Guindani, Michele | Bassett, Roland | Wargo, Jennifer | Racolta, Adriana | Kelly, Brian | Jones, Tobin | Polaske, Nathan | Theiss, Noah | Robida, Mark | Meridew, Jeffrey | Habensus, Iva | Zhang, Liping | Pestic-Dragovich, Lidija | Tang, Lei | Sullivan, Ryan J. | Logan, Theodore | Khushalani, Nikhil | Margolin, Kim | Koon, Henry | Olencki, Thomas | Hutson, Thomas | Curti, Brendan | Roder, Joanna | Blackmon, Shauna | Roder, Heinrich | Stewart, John | Amin, Asim | Ernstoff, Marc S. | Clark, Joseph I. | Atkins, Michael B. | Kaufman, Howard L. | Sosman, Jeffrey | Weber, Jeffrey | McDermott, David F. | Weber, Jeffrey | Kluger, Harriet | Halaban, Ruth | Snzol, Mario | Roder, Heinrich | Roder, Joanna | Asmellash, Senait | Steingrimsson, Arni | Blackmon, Shauna | Sullivan, Ryan J. | Wang, Chichung | Roman, Kristin | Clement, Amanda | Downing, Sean | Hoyt, Clifford | Harder, Nathalie | Schmidt, Guenter | Schoenmeyer, Ralf | Brieu, Nicolas | Yigitsoy, Mehmet | Madonna, Gabriele | Botti, Gerardo | Grimaldi, Antonio | Ascierto, Paolo A. | Huss, Ralf | Athelogou, Maria | Hessel, Harald | Harder, Nathalie | Buchner, Alexander | Schmidt, Guenter | Stief, Christian | Huss, Ralf | Binnig, Gerd | Kirchner, Thomas | Sellappan, Shankar | Thyparambil, Sheeno | Schwartz, Sarit | Cecchi, Fabiola | Nguyen, Andrew | Vaske, Charles | Hembrough, Todd
Journal for Immunotherapy of Cancer  2016;4(Suppl 1):1-106.
doi:10.1186/s40425-016-0172-7
PMCID: PMC5123387
9.  Structural Transitions in Nanosized Zn0.97Al0.03O Powders under High Pressure Analyzed by in Situ Angle-Dispersive X-ray Diffraction 
Materials  2016;9(7):561.
Nanosized aluminum-doped zinc oxide Zn1−xAlxO (AZO) powders (AZO-NPs) with x = 0.01, 0.03, 0.06, 0.09 and 0.11 were synthesized by chemical precipitation method. The thermogravimetric analysis (TGA) indicated that the precursors were converted to oxides from hydroxides near 250 °C, which were then heated to 500 °C for subsequent thermal processes to obtain preliminary powders. The obtained preliminary powders were then calcined at 500 °C for three hours. The structure and morphology of the products were measured and characterized by angle-dispersive X-ray diffraction (ADXRD) and scanning electron microscopy (SEM). ADXRD results showed that AZO-NPs with Al content less than 11% exhibited würtzite zinc oxide structure and there was no other impurity phase in the AZO-NPs, suggesting substitutional doping of Al on Zn sites. The Zn0.97Al0.03O powders (A3ZO-NPs) with grain size of about 21.4 nm were used for high-pressure measurements. The in situ ADXRD measurements revealed that, for loading run, the pressure-induced würtzite (B4)-to-rocksalt (B1) structural phase transition began at 9.0(1) GPa. Compared to the predicted phase-transition pressure of ~12.7 GPa for pristine ZnO nanocrystals of similar grain size (~21.4 nm), the transition pressure for the present A3ZO-NPs exhibited a reduction of ~3.7 GPa. The significant reduction in phase-transition pressure is attributed to the effects of highly selective site occupation, namely Zn2+ and Al3+, were mainly found in tetrahedral and octahedral sites, respectively.
doi:10.3390/ma9070561
PMCID: PMC5456907
aluminum-doped zinc oxide; zinc-blende; phase transition; angle-dispersive X-ray diffraction
10.  The independent contribution of miRNAs to the missing heritability in CYP3A4/5 functionality and the metabolism of atorvastatin 
Scientific Reports  2016;6:26544.
To evaluate the independent contribution of miRNAs to the missing heritability in CYP3A4/5 functionality and atorvastatin metabolism, the relationships among three levels of factors, namely (1) clinical characteristics, CYP3A4/5 genotypes, and miRNAs, (2) CYP3A4 and CYP3A5 mRNAs, and (3) CYP3A activity, as well as their individual impacts on atorvastatin metabolism, were assessed in 55 human liver tissues. MiR-27b, miR-206, and CYP3A4 mRNA respectively accounted for 20.0%, 5.8%, and 9.5% of the interindividual variations in CYP3A activity. MiR-142 was an independent contributor to the expressions of CYP3A4 mRNA (partial R2 = 0.12, P = 0.002) and CYP3A5 mRNA (partial R2 = 0.09, P = 0.005) but not CYP3A activity or atorvastatin metabolism. CYP3A activity was a unique independent predictor of variability of atorvastatin metabolism, explaining the majority of the variance in reduction of atorvastatin (60.0%) and formation of ortho-hydroxy atorvastatin (78.8%) and para-hydroxy atorvastatin (83.9%). MiR-27b and miR-206 were found to repress CYP3A4 gene expression and CYP3A activity by directly binding to CYP3A4 3′-UTR, while miR-142 was found to indirectly repress CYP3A activity. Our study indicates that miRNAs play significant roles in bridging the gap between epigenetic effects and missing heritability in CYP3A functionality.
doi:10.1038/srep26544
PMCID: PMC4876377  PMID: 27211076
11.  A Comparison between Three-Dimensional Visualization Guided Hepatectomy and Ultrasonography Guided Radiofrequency Ablation in the Treatment of Small Hepatocellular Carcinoma within the Milan Criteria 
BioMed Research International  2016;2016:8931732.
Background. Treatment selection for small hepatocellular carcinoma (sHCC) is controversial. We aimed to compare the outcomes of medical imaging three-dimensional visualization system (MI-3DVS) guided surgical resection (SR) and ultrasonography guided radiofrequency ablation (RFA) for sHCC. Methods. In total, 194 patients who underwent SR or RFA in our hospital between January 2006 and May 2010 were retrospectively enrolled. Overall survival (OS), recurrence-free survival (RFS), and postoperative complications were compared. Cox regression was used to estimate the benefits of MI-3DVS-guided SR on OS and RFS. Results. Ninety-two patients underwent SR and 102 underwent RFA. The SR group experienced more complications (41.3% versus 19.6%) and longer hospital stay (18.04 ± 7.11 versus 13.06 ± 5.59) (both p < 0.05). The 1-, 2-, 3-, 4-, and 5-year OS was 96.7%, 95.7%, 93.5%, 83.5%, and 61.1% in the SR group and 95.0%, 88.1%, 72.7%, 56.9%, and 39.5% in the RFA group. Corresponding RFS was 95.7%, 94.6%, 84.7%, 59.8%, and 40.2% in SR group and 91.2%, 80.3%, 60.5%, 32.3%, and 22.3% in RFA group. The 5-year OS and RFS were higher in SR group (both p < 0.001). Interestingly, there was no significance in OS and RFS among subgroups aged >60 years. Independent predictors of OS and RFS, respectively, were intervention (HR, 2.769 and 1.933), tumor number (HR, 5.128 and 3.903), and serum alpha-fetoprotein (AFP) (HR, 1.871 and 1.474) (all p < 0.05). Conclusions. MI-3DVS based hepatectomy should be considered primary treatment while RFA can be treated as alternative therapy for older patients. Intervention, tumor number, and AFP are independent predictors for both survival and recurrence.
doi:10.1155/2016/8931732
PMCID: PMC4880684  PMID: 27294142
12.  The native ant, Tapinoma melanocephalum, improves the survival of an invasive mealybug, Phenacoccus solenopsis, by defending it from parasitoids 
Scientific Reports  2015;5:15691.
Mutualistic ants can protect their partners from natural enemies in nature. Aenasius bambawalei is an important parasitoid of the the invasive mealybug Phenacoccus solenopsis. We hypothesized that mutualism between native ants and mealybugs would favor survival of mealybugs. To test this, we examined effects of tending by the native mutualistic ant Tapinoma melanocephalum on growth of P. solenopsis colonies on Chinese hibiscus, Hibiscus rosa-sinensis, in a field setting. Ant workers with access to honeydew of mealybugs lived much longer than those provisioned only with water in the laboratory, and number of ant workers foraging increased significantly with growth of mealybug colonies in the field. In later observations, there were significant differences in densities of mealybugs between ant-tended and -excluded treatments. Survival rate of mealybugs experiencing parasitoid attack was significantly higher on ant-tended plants than on ant-excluded plants. When the parasitoid was excluded, there was no difference in survival rate of mealybugs between ant-tended and -excluded plants. In most cases, ants directly attacked the parasitoid, causing the parasitoid to take evasive action. We conclude that native ants such as T. melanocephalum have the potential to facilitate invasion and spread of P. solenopsis in China by providing them with protection from parasitoids.
doi:10.1038/srep15691
PMCID: PMC4621601  PMID: 26503138
13.  Correlation of lymphovascular invasion with clinicopathological factors in invasive breast cancer: a meta-analysis 
Objectives: Lymphovascular invasion (LVI) has been associated with a poor outcome in patients with breast cancer, but it is not included in international TNM staging system and molecular subtype criterion. The current studies have reported the relation between LVI and the tumor size (T), the status of axillary lymph node (ALN), age, histological grade in invasive breast cancer, but the results were debatable. So the meta-analysis was conducted to confirm the relation between LVI and the four clinicopathological factors. Methods: Literature was searched by entering the terms: breast AND (neoplasm OR cancer OR carcinoma) AND (lymphovascular OR “lymphatic vessel” OR “vascular vessel” OR “blood vessel” OR “lymph vessel”) AND (invasion OR “carcinoma embolus”) AND (lymph node OR grade OR size OR clinicopathological) in PubMed, The merged odds ratio (OR) and 95% confidence interval (CI) were estimated using fixed-effect or random-effect model, RevMan 5.3 was used to analyze the relation between LVI and tumor size, status of ALN, age, histological grade in invasive breast cancer respectively. The fail-safe number was used to estimate publication bias. Results: The analysis included 6 studies, LVI positive rate was significant lower in T≤2 cm, ALN negative, age >50 y and histological grade 1 groups statistically. The OR and 95% CI were 0.53 [0.46, 0.61], 0.23 [0.15, 0.35], 1.62 [1.42, 1.85], 0.36 [0.17, 0.77] respectively. Conclusions: LVI was significantly correlated with the expression status of the tumor size, status of ALN, age, histological grade in invasive breast cancer, and was consistent with adverse features of the four factors.
PMCID: PMC4694270  PMID: 26770370
Lymphovascular invasion; histological grade; axillary lymph node; clinicopathological factors; breast cancer
14.  Specific increase in potency via structure-based design of a T cell receptor 
Adoptive immunotherapy with antigen-specific T lymphocytes is a powerful strategy for cancer treatment. However, most tumor antigens are non-reactive “self” proteins, which presents an immunotherapy design challenge. Recent studies have shown that tumor-specific T cell receptors (TCRs) can be transduced into normal peripheral blood lymphocytes, which persist after transfer in about 30% of patients and effectively destroy tumor cells in vivo. Although encouraging, the limited clinical responses underscore the need for enrichment of T cells with desirable anti-tumor capabilities prior to patient transfer.
In this study, we used structure-based design to predict point mutations of a TCR (DMF5) that enhance its binding affinity for an agonist tumor antigen-major histocompatibility complex (pMHC), Mart-1(27L)-HLA-A2, which elicits full T cell activation to trigger immune responses. We analyzed the effects of selected TCR point mutations on T cell activation potency and analyzed cross-reactivity with related antigens. Our results showed that the mutated TCRs had improved T cell activation potency, while retaining a high degree of specificity. Such affinity-optimized TCRs have demonstrated to be very specific for Mart-1 (27L), the epitope for which they were structurally designed. And even though of limited clinical relevance, these studies open the possibility for future structural-based studies that could potentially be used in adoptive immunotherapy to treat melanoma while avoiding adverse autoimmunity-derived effects.
doi:10.4049/jimmunol.1302344
PMCID: PMC4205480  PMID: 25070852
15.  Anomalous origin of the right pulmonary artery from the ascending aorta: results of direct implantation surgical repair in 6 infants 
Background
Anomalous origin of the right pulmonary artery from the ascending aorta (AORPA) is a rare and potential fatal kind of congenital heart disease. This study summarizes the techniques and outcomes of 6 infants with AORPA who underwent the surgical repair.
Methods
Between November 2012 and November 2014, 6 infants with AORPA received surgical repair in the Second Xiangya Hospital and were included in the present study.
Results
Six infants (4 male, 66.7 %) with a median age of 101.5 ± 70.0 days, and a median body weight of 4.13 ± 0.62 kg underwent the surgical repair at our institute. There were no operative, in-hospital or follow-up deaths. Clinical symptoms of all 6 patients relieved at time of discharge, and mean pulmonary artery pressure (MPAP) decreased significantly after surgery. During follow-up, there were no further operations or interventions, mild stenosis at the anastomotic site presented in one patient, and all patients were asymptomatic and in stable clinical condition.
Conclusions
The short and mid-term surgical outcomes of AORPA are excellent in this group of operations. Moreover, we believe the direct implantation to be the optimal surgical strategy for the patients with the proximal form of AORPA.
doi:10.1186/s13019-015-0307-9
PMCID: PMC4499180  PMID: 26162911
Anomalous origin of the right pulmonary artery from the ascending aorta; Infant; Direct implantation; Pulmonary hypertension
16.  LDA-SVM-Based EGFR Mutation Model for NSCLC Brain Metastases 
Medicine  2015;94(5):e375.
Supplemental Digital Content is available in the text
Abstract
Epidermal growth factor receptor (EGFR) activating mutations are a predictor of tyrosine kinase inhibitor effectiveness in the treatment of non–small-cell lung cancer (NSCLC). The objective of this study is to build a model for predicting the EGFR mutation status of brain metastasis in patients with NSCLC.
Observation and model set-up.
This study was conducted between January 2003 and December 2011 in 6 medical centers in Southwest China.
The study included 31 NSCLC patients with brain metastases.
Eligibility requirements were histological proof of NSCLC, as well as sufficient quantity of paraffin-embedded lung and brain metastases specimens for EGFR mutation detection. The linear discriminant analysis (LDA) method was used for analyzing the dimensional reduction of clinical features, and a support vector machine (SVM) algorithm was employed to generate an EGFR mutation model for NSCLC brain metastases. Training-testing-validation (3 : 1 : 1) processes were applied to find the best fit in 12 patients (validation test set) with NSCLC and brain metastases treated with a tyrosine kinase inhibitor and whole-brain radiotherapy.
Primary and secondary outcome measures: EGFR mutation analysis in patients with NSCLC and brain metastases and the development of a LDA-SVM-based EGFR mutation model for NSCLC brain metastases patients.
EGFR mutation discordance between the primary lung tumor and brain metastases was found in 5 patients. Using LDA, 13 clinical features were transformed into 9 characteristics, and 3 were selected as primary vectors. The EGFR mutation model constructed with SVM algorithms had an accuracy, sensitivity, and specificity for determining the mutation status of brain metastases of 0.879, 0.886, and 0.875, respectively. Furthermore, the replicability of our model was confirmed by testing 100 random combinations of input values.
The LDA-SVM-based model developed in this study could predict the EGFR status of brain metastases in this small cohort of patients with NSCLC. Further studies with larger cohorts should be carried out to validate our findings in the clinical setting.
doi:10.1097/MD.0000000000000375
PMCID: PMC4602717  PMID: 25654374
17.  2D TCR–pMHC–CD8 kinetics determines T-cell responses in a self-antigen-specific TCR system 
European journal of immunology  2013;44(1):239-250.
Summary
Two-dimensional (2D) kinetic analysis directly measures molecular interactions at cell-cell junctions, thereby incorporating inherent cellular effects. By comparison, three-dimensional (3D) analysis probes the intrinsic physical chemistry of interacting molecules isolated from the cell. To understand how T-cell tumor reactivity relates to 2D and 3D binding parameters and to directly compare them, we performed kinetic analyses of a panel of human T-cell receptors (TCR) interacting with a melanoma self-antigen peptide (gp100209–217) bound to major histocompatibility complex (pMHC) in the absence and presence of coreceptor CD8. We found that while 3D parameters are inadequate to predict T-cell function, 2D parameters (which do not correlate with their 3D counterparts) show a far broader dynamic range and significantly improved correlation with T-cell function. Thus, our data support the general notion that 2D parameters of TCR–pMHC–CD8 interactions determine T-cell responsiveness and suggest a potential 2D-based strategy to screen TCRs for tumor immunotherapy.
doi:10.1002/eji.201343774
PMCID: PMC3941036  PMID: 24114747
2D kinetics; T cell activation; micropipette adhesion frequency assay; thermal fluctuation assay
20.  Vitellogenin Recognizes Cell Damage through Membrane Binding and Shields Living Cells from Reactive Oxygen Species* 
The Journal of Biological Chemistry  2013;288(39):28369-28381.
Background: Vitellogenin is a central regulator of honey bee life span by largely unknown mechanisms.
Results: Honey bee vitellogenin has membrane affinity that is connected to cell damage recognition and antioxidant function.
Conclusion: Membrane binding documents a new molecular behavior among vitellogenins.
Significance: Vitellogenins are widespread phylogenetically, and their molecular behavior is essential for fitness traits in many animals.
Large lipid transfer proteins are involved in lipid transportation and diverse other molecular processes. These serum proteins include vitellogenins, which are egg yolk precursors and pathogen pattern recognition receptors, and apolipoprotein B, which is an anti-inflammatory cholesterol carrier. In the honey bee, vitellogenin acts as an antioxidant, and elevated vitellogenin titer is linked to prolonged life span in this animal. Here, we show that vitellogenin has cell and membrane binding activity and that it binds preferentially to dead and damaged cells. Vitellogenin binds directly to phosphatidylcholine liposomes and with higher affinity to liposomes containing phosphatidylserine, a lipid of the inner leaflet of cell membranes that is exposed in damaged cells. Vitellogenin binding to live cells, furthermore, improves cell oxidative stress tolerance. This study can shed more light on why large lipid transfer proteins have a well conserved α-helical domain, because we locate the lipid bilayer-binding ability of vitellogenin largely to this region. We suggest that recognition of cell damage and oxidation shield properties are two mechanisms that allow vitellogenin to extend honey bee life span.
doi:10.1074/jbc.M113.465021
PMCID: PMC3784755  PMID: 23897804
Cell Death; Insect; Lipoprotein; Liposomes; Reactive Oxygen Species (ROS)
21.  Engineering improved T cell receptors using an alanine-scan guided T cell display selection system 
T cell receptors (TCRs) on T cells recognize peptide-major histocompatibility complex (pMHC) molecules on the surface of antigen presenting cells and this interaction determines the T cell immune response. Due to negative selection, naturally occurring TCRs bind self (tumor) peptides with low affinity and have a much higher affinity for foreign antigens. This complicates isolation of naturally occurring, high affinity TCRs that mediate more effective tumor rejection for therapeutic purposes. An attractive approach to resolve this issue is to engineer high affinity TCRs in vitro using phage, yeast or mammalian TCR display systems. A caveat of these systems is that they rely on a large library by random mutagenesis due to the lack of knowledge regarding the specific interactions between the TCR and pMHC. We have focused on the mammalian retroviral display system because it uniquely allows for direct comparison of TCR-pMHC-binding properties with T-cell activation outcomes. Through an alanine-scanning approach, we are able to quickly map the key amino acid residues directly involved in TCR-pMHC interactions thereby significantly reducing the library size. Using this method, we demonstrate that for a self-antigen-specific human TCR (R6C12) the key residues for pMHC binding are located in the CDR3β region. This information was used as a basis for designing an efficacious TCR CDR3α library that allowed for selection of TCRs with higher avidity than the wild-type as evaluated through binding and activation experiments. This is a direct approach to target specific TCR residues in TCR library design to efficiently engineer high avidity TCRs that may potentially be used to enhance adoptive immunotherapy treatments.
doi:10.1016/j.jim.2013.02.018
PMCID: PMC3668434  PMID: 23500145
T cell receptor; T cell clones; Mammalian TCR display system; CDR3 alanine scanning mutagenesis; Combinatorial library design
22.  Low-Dose Levodopa Protects Nerve Cells from Oxidative Stress and Up-Regulates Expression of pCREB and CD39 
PLoS ONE  2014;9(4):e95387.
Objective
This study aimed to investigate the influence of low-dose levodopa (L-DOPA) on neuronal cell death under oxidative stress.
Methods
PC12 cells were treated with L-DOPA at different concentrations. We detected the L-DOPA induced reactive oxygen species (ROS). Meanwhile, MTT and LDH assay were performed to determine the proliferation and growth of PC12 cells with or without ROS scavenger. In addition, after pretreatment with L-DOPA at different concentrations alone or in combination with CD39 inhibitor, PC12 cells were incubated with hydrogen peroxide (H2O2) and the cell viability was evaluated by MTT and LDH assay. In addition, the expression of pCREB and CD39 was detected by immunofluorescence staining and Western blot assay in both cells and rat’s brain after L-DOPA treatment.
Results
After treatment with L-DOPA for 3 days, the cell proliferation and growth were promoted when the L-DOPA concentration was <30 µM, while cell proliferation was comparable to that in control group when the L-DOPA concentration was >30 µM. Low dose L-DOPA could protect the PC12 cells from H2O2 induced oxidative stress, which was compromised by CD39 inhibitor. In addition, the expression of CD39 and pCREB increased in both PC12 cells and rats’ brain after L-DOPA treatment.
Conclusions
L-DOPA at different concentrations has distinct influence on proliferation and growth of PC12 cells, and low dose (<30 µM) L-DOPA protects PC12 cells against oxidative stress which might be related to the up-regulation of CD39 and pCREB expression.
doi:10.1371/journal.pone.0095387
PMCID: PMC3990701  PMID: 24743653
23.  A Comparison of Growth and Development of Three Major Agricultural Insect Pests Infected with Heliothis virescens ascovirus 3h (HvAV-3h) 
PLoS ONE  2013;8(12):e85704.
Ascoviruses are double-stranded DNA viruses that are pathogenic to lepidopteran hosts, particularly noctuid larvae. Infection of a larva is characterized by retarded growth, reduced feeding and yellowish body color. In this paper, we reported the growth and development of three major agricultural noctuid insect pests, Helicoverpa armigera (Hübner), Spodoptera exigua (Hübner) and Spodoptera litura (Fabricius), infected with Heliothis virescens ascovirus 3h (HvAV-3h). Using 10-fold serial dilutions (0 to 7) of HvAV-3h-containing hemolymph to infect S. litura larvae, we found no significant difference in larval mortalities from 0 to 103-fold dilutions; however, significant differences were observed at 104-fold dilution and above. Using a 10-fold dilution of HvAV-3h-containing hemolymph to infect H. armigera, S. exigua and S. litura larvae, we found that the growth and development were significantly affected. All infected larvae could not pupate; the survival times of treated H. armigera, S. litura and S. exigua larvae were significantly longer than untreated control larvae. Body weight showed significant difference between treated and untreated control group from day 1 after inoculation in H. armigera and S. exigua, but day 2 in S. litura. Additionally, food intake also showed significant difference between treated and untreated control group from day 2 after inoculation in H. armigera and S. litura, but day 3 in S. exigua.
doi:10.1371/journal.pone.0085704
PMCID: PMC3875588  PMID: 24386488
25.  Correction: Probing the Effector and Suppressive Functions of Human T Cell Subsets Using Antigen-Specific Engineered T Cell Receptors 
PLoS ONE  2013;8(10):10.1371/annotation/cbc71d72-f1a2-45de-9d4a-cb0c8dc076b5.
doi:10.1371/annotation/cbc71d72-f1a2-45de-9d4a-cb0c8dc076b5
PMCID: PMC3815353

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