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174 results on '"Marciniak, Sj"'

1. Recommendations on scuba diving in Birt-Hogg-Dubé syndrome

Author

van Riel, L., primary, van Hulst, RA., additional, van Hest, L., additional, van Moorselaar, RJA., additional, Boerrigter, BG., additional, Franken, SM., additional, Wolthuis, RMF., additional, Dubbink, HJ., additional, Marciniak, SJ., additional, Gupta, N., additional, van de Beek, I., additional, and Houweling, AC., additional

Published
2023
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2. Meta-analysis of the association between emphysematous change on thoracic computerized tomography scan and recurrent pneumothorax

Author

Girish, M, Pharoah, PD, Marciniak, SJ, Marciniak, SJ [0000-0001-8472-7183], and Apollo - University of Cambridge Repository

Subjects
Lung Diseases, Recurrence, Thoracic Surgery, Video-Assisted, Humans, Pneumothorax, Tomography, X-Ray Computed, Retrospective Studies
Abstract

OBJECTIVES: At least a third of patients go on to suffer a recurrence following a first spontaneous pneumothorax. Surgical intervention reduces the risk of recurrence and has been advocated as a primary treatment for pneumothorax. But surgery exposes patients to the risks of anaesthesia and in some cases can cause chronic pain. Risk stratification of patients to identify those most at risk of recurrence would help direct the most appropriate patients to early intervention. Many studies have addressed the role of thoracic computerized tomography (CT) in identifying those individuals at increased risk of recurrence, but a consensus is lacking. AIM: Our objective was to clarify whether CT provides valuable prognostic information for recurrent pneumothorax. DESIGN: Meta-analysis. METHODS: We conducted an exhaustive search of the literature for thoracic CT imaging and pneumothorax, and then performed a meta-analysis using a random effects model to estimate the common odds ratio and standard error. RESULTS: Here, we show by meta-analysis of data from 2475 individuals that emphysematous change on CT scan is associated with a significant increased odds ratio for recurrent pneumothorax ipsilateral to the radiological abnormality (odds ratio 2.49, 95% confidence interval 1.51-4.13). CONCLUSIONS: The association holds true for primary spontaneous pneumothorax when considering emphysematous changes including blebs and bullae. Features, such as bullae at the azygoesophageal recess or increased Goddard score similarly predicted recurrent secondary pneumothorax, as shown by subgroup analysis. Our meta-analysis suggests that CT scanning has value in risk stratifying patients considering surgery for pneumothorax.

Published
2022

10. S91 Patterns of cytokines and growth factors in pulmonary arterial hypertension patients with BMPR2 mutations and PAH patients without driving mutations and their influence on survival

Author

Schwiening, M, primary, Pandya, D, additional, Swietlik, EM, additional, Burling, KA, additional, Barker, P, additional, Treacy, CM, additional, Wort, SJ, additional, Pepke-Zaba, J, additional, Graf, S, additional, Marciniak, SJ, additional, Morrell, NW, additional, and Soon, E, additional

Published
2021
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13. An Optical Technique for Mapping Microviscosity Dynamics in Cellular Organelles

Author

Chambers, Joseph, Kubankova, Marketa, Huber, Roland, Lopez-Duarte, Ismael, Avezov, Edward, Bond, Peter, Marciniak, SJ, Kuimova, Marina, Chambers, Joseph [0000-0003-4675-0053], Avezov, Edward [0000-0002-2894-0585], Marciniak, Stefan [0000-0001-8472-7183], Apollo - University of Cambridge Repository, and Engineering & Physical Science Research Council (EPSRC)

Subjects
Boron Compounds, Models, Molecular, Technology, FLIM, organelle, Chemistry, Multidisciplinary, Materials Science, ENDOPLASMIC-RETICULUM, BIOLOGY, Materials Science, Multidisciplinary, Ligands, molecular rotors, MITOCHONDRIA, Chlorocebus aethiops, Animals, microviscosity, Nanoscience & Nanotechnology, LIVING CELLS, Cells, Cultured, Fluorescent Dyes, Organelles, Science & Technology, Chemistry, Physical, Viscosity, diffusion, Optical Imaging, MICROSCOPY, LIVE CELLS, cell biophysics, Chemistry, Physical Sciences, COS Cells, Science & Technology - Other Topics, MEMBRANE MICROVISCOSITY, fluorescence
Abstract

Microscopic viscosity (microviscosity) is a key determinant of diffusion in the cell and defines the rate of biological processes occurring at the nanoscale, including enzyme-driven metabolism and protein folding. Here we establish a Rotor-based Organelle Viscosity Imaging (ROVI) methodology that enables real-time quantitative mapping of cell microviscosity. This approach uses environment sensitive dyes termed molecular rotors, covalently linked to genetically encoded probes to provide compartment specific microviscosity measurements via fluorescence lifetime imaging (FLIM). ROVI visualised spatial and temporal dynamics of microviscosity with sub-organellar resolution, reporting on a microviscosity difference of nearly an order of magnitude between subcellular compartments. In the mitochondrial matrix, ROVI revealed several striking findings: a broad heterogeneity of microviscosity amongst individual mitochondria, unparalleled resilience to osmotic stress, and real-time changes in microviscosity during mitochondrial depolarisation. These findings demonstrate the use of ROVI to explore the biophysical mechanisms underlying cell biological processes.

Published
2018
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14. PPP1R15A-mediated dephosphorylation of eIF2$\alpha$ is unaffected by Sephin1 or Guanabenz

Author

Crespillo-Casado, A, Chambers, JE, Fischer, PM, Marciniak, SJ, Ron, D, Chambers, Joseph [0000-0003-4675-0053], Marciniak, Stefan [0000-0001-8472-7183], Ron, David [0000-0002-3014-5636], and Apollo - University of Cambridge Repository

Subjects
protein synthesis, phosphorylation, cell biology, Cricetulus griseus, biochemistry, chemical biology, drug action, human
Abstract

Dephosphorylation of translation initiation factor 2 (eIF2$\alpha$) terminates signalling in the mammalian integrated stress response (ISR) and has emerged as a promising target for modifying the course of protein misfolding diseases. The [(o-chlorobenzylidene)amino]guanidines (Guanabenz and Sephin1) have been proposed to exert protective effects against misfolding by interfering with eIF2$\alpha$-P dephosphorylation through selective disruption of a PP1-PPP1R15A holophosphatase complex. Surprisingly, they proved inert in vitro affecting neither stability of the PP1-PPP1R15A complex nor substrate-specific dephosphorylation. Furthermore, eIF2$\alpha$-P dephosphorylation, assessed by a kinase shut-off experiment, progressed normally in Sephin1-treated cells. Consistent with its role in defending proteostasis, Sephin1 attenuated the IRE1 branch of the endoplasmic reticulum unfolded protein response. However, repression was noted in both wildtype and Ppp1r15a deleted cells and in cells rendered ISR-deficient by CRISPR editing of the Eif2s1 locus to encode a non-phosphorylatable eIF2$\alpha$ (eIF2$\alpha^{S51A}$)). These findings challenge the view that [(o-chlorobenzylidene)amino]guanidines restore proteostasis by interfering with eIF2$\alpha$-P dephosphorylation.

Published
2017

21. Evaluation of secondary spontaneous pneumothorax with multidetector CT

Author

Hilliard, NJ, Marciniak, SJ, Babar, JL, Balan, A, Marciniak, Stefan [0000-0001-8472-7183], and Apollo - University of Cambridge Repository

Subjects
Lung Diseases, Multidetector Computed Tomography, cardiovascular system, Humans, Pneumothorax, cardiovascular diseases
Abstract

The purpose of this article is to review the underlying causes of secondary pneumothoraces as observed on multidetector computed tomography (MDCT). Using examples from our institutional experience, we shall illustrate important diagnostic features to indicate the underlying lung disease. Understanding the varied range of conditions is important for accurate diagnosis and facilitation of patient management.

Published
2013

22. Coordinate regulation of eif2α phosphorylation by PPP1R15 and GCN2 is required during Drosophila development

Author

Malzer, E, Szajewska-Skuta, M, Dalton, LE, Thomas, SE, Hu, N, Skaer, H, Lomas, DA, Crowther, DC, Marciniak, SJ, Marciniak, Stefan [0000-0001-8472-7183], and Apollo - University of Cambridge Repository

Abstract

Phosphorylation of eukaryotic translation initiation factor 2 alpha (eIF2α) by the kinase GCN2 attenuates protein synthesis during amino acid starvation in yeast, whereas in mammals a family of related eIF2α kinases regulate translation in response to a variety of stresses. Unlike single-celled eukaryotes, mammals also possess two specific eIF2α phosphatases, PPP1R15a and PPP1R15b, whose combined deletion leads to a poorly understood early embryonic lethality. We report the characterisation of the first non-mammalian eIF2α phosphatase and the use of Drosophila to dissect its role during development. The Drosophila protein demonstrates features of both mammalian proteins, including limited sequence homology and association with the endoplasmic reticulum. Of note, although this protein is not transcriptionally regulated, its expression is controlled by the presence of upstream open reading frames in its 5'UTR, enabling induction in response to eIF2α phosphorylation. Moreover, we show that its expression is necessary for embryonic and larval development and that this is to oppose the inhibitory effects of GCN2 on anabolic growth. © 2013. Published by The Company of Biologists Ltd., This work was supported by the UK Medical Research Council (MRC); and the British Society for Cell Biology. S.J.M. is an MRC Senior Clinical Fellow [grant number G1002610]. Deposited in PMC for release after 6 months.

Published
2013

23. Measurement of the bottom-strange meson mixing phase in the full CDF data set

Author

Aaltonen, T., Alvarez, González, Amerio, B., Amidei, S., Anastassov, D., Annovi, A., Antos, A., Apollinari, J., Appel, G., J. A., Arisawa, Artikov, T., Asaadi, A., Ashmanskas, J., Auerbach, W., Aurisano, B., Azfar, A., Badgett, F., Bae, W., Barbaro, Galtieri, Barnes, A., V. E., Barnett, B. A., Barria, Bartos, P., Bauce, P., Bedeschi, M., Behari, F., Bellettini, S., Bellinger, G., Benjamin, J., Beretvas, D., Bhatti, A., Bisello, A., Bizjak, D., Bland, I., K. R., Blumenfeld, Bocci, B., Bodek, A., Bortoletto, A., Boudreau, D., Boveia, J., Brigliadori, A., Bromberg, L., Brucken, C., Budagov, E., Budd, J., H. S., Burkett, Busetto, K., Bussey, G., Buzatu, P., Calamba, A., Calancha, A., Camarda, C., Campanelli, S., Campbell, M., Canelli, M., Carls, F., Carlsmith, B., Carosi, D., Carrillo, R., Carron, S., Casal, S., Casarsa, B., Castro, M., Catastini, A., Cauz, P., Cavaliere, D., Cavalli, Sforza, Cerri, M., Cerrito, A., Chen, L., Y. C., Chertok, Chiarelli, M., Chlachidze, G., Chlebana, G., Cho, F., Chokheli, K., Chung, D., W. H., Chung, Y. S., Ciocci, M. A., Clark, Clarke, A., Compostella, C., Convery, G., M. E., Conway, Corbo, J., Cordelli, M., Cox, M., C. A., Cox, D. J., Crescioli, Cuevas, F., Culbertson, J., Dagenhart, R., D'Ascenzo, D., Datta, N., Barbaro, De, Dell'Orso, Mauro, Demortier, M., Deninno, L., Devoto, M., D'Errico, F., Canto, Di, Ruzza, Di, Dittmann, B., J. R., D'Onofrio, Donati, Simone, Dong, P., Dorigo, M., Dorigo, T., Ebina, K., Elagin, A., Eppig, A., Erbacher, R., Errede, S., Ershaidat, N., Eusebi, R., Farrington, S., Feindt, M., Fernandez, J. P., Field, R., Flanagan, G., Forrest, R., Frank, M. J., Franklin, M., Freeman, J. C., Funakoshi, Y., Furic, I., Gallinaro, M., Garcia, J. E., Garfinkel, A. F., Garosi, P., Gerberich, H., Gerchtein, E., Giagu, S., Giakoumopoulou, V., Giannetti, P., Gibson, K., Ginsburg, C. M., Giokaris, N., Giromini, P., Giurgiu, G., Glagolev, V., Glenzinski, D., Gold, M., Goldin, D., Goldschmidt, N., Golossanov, A., Gomez, G., Gomez, Ceballos, Goncharov, G., González, M., Gorelov, O., Goshaw, I., A. T., Goulianos, Grillo, K., Grinstein, L., Grosso, Pilcher, Group, C., R. C., Guimaraes Da Costa, Hahn, J., S. R., Halkiadakis, Hamaguchi, E., Han, A., J. Y., Happacher, Hara, F., Hare, K., Hare, D., Harr, M., R. F., Hatakeyama, Hays, K., Heck, C., Heinrich, M., Herndon, J., Hewamanage, M., Hocker, S., Hopkins, A., Horn, W., Hou, D., Hughes, S., R. E., Hurwitz, Husemann, M., Hussain, U., Hussein, N., Huston, M., Introzzi, J., Iori, G., Ivanov, M., James, A., Jang, E., Jayatilaka, D., Jeon, B., E. J., Jindariani, Jones, S., Joo, M., K. K., Jun, S. Y., Junk, T. R., Kamon, Karchin, T., P. E., Kasmi, Kato, A., Ketchum, Y., Keung, W., Khotilovich, J., Kilminster, V., Kim, B., D. H., Kim, H. S., Kim, J. E., Kim, M. J., Kim, S. B., Kim, S. H., Kim, Y. K., Kim, Y. J., Kimura, Kirby, N., Klimenko, M., Knoepfel, S., Kondo, K., Kong, K., D. J., Konigsberg, Kotwal, J., A. V., Kreps, Kroll, M., Krop, J., Kruse, D., Krutelyov, M., Kuhr, V., Kurata, T., Kwang, M., Laasanen, S., A. T., Lami, Lammel, S., Lancaster, S., Lander, M., R. L., Lannon, Lath, K., Latino, A., Lecompte, G., Lee, T., Lee, E., H. S., Lee, J. S., Lee, S. W., Leo, Leone, S., Lewis, S., J. D., Limosani, Lin, A., C. J., Lindgren, Lipeles, M., Lister, E., Litvintsev, A., D. O., Liu, Liu, C., Liu, H., Liu, Q., Lockwitz, T., Loginov, S., Lucchesi, A., Lueck, D., Lujan, J., Lukens, P., Lungu, P., Lys, G., Lysak, J., Madrak, R., Maeshima, R., Maestro, K., Malik, P., Manca, S., Manousakis, Katsikakis, Margaroli, A., Marino, F., Martínez, C., Mastrandrea, M., Matera, P., Mattson, K., M. E., Mazzacane, Mazzanti, A., Mcfarland, P., K. S., Mcintyre, Mcnulty, P., Mehta, R., Mehtala, A., Mesropian, P., Miao, C., Mietlicki, T., Mitra, D., Miyake, A., Moed, H., Moggi, S., Mondragon, N., M. N., Moon, C. S., Moore, Morello, R., M. J., Morlock, Movilla, Fernandez, Mukherjee, P., Muller, A., Murat, T., Mussini, P., Nachtman, M., Nagai, J., Naganoma, Y., Nakano, J., Napier, I., Nett, A., Neu, J., Neubauer, C., M. S., Nielsen, Nodulman, J., Noh, L., S. Y., Norniella, Oakes, O., Oh, L., S. H., Oh, Y. D., Oksuzian, Okusawa, I., Orava, T., Ortolan, R., Pagan, Griso, Pagliarone, S., Palencia, C., Papadimitriou, E., Paramonov, V., A. A., Patrick, Pauletta, J., Paulini, G., Paus, M., Pellett, C., D. E., Penzo, Phillips, A., T. J., Piacentino, Pianori, G., Pilot, E., Pitts, J., Plager, K., Pondrom, C., Poprocki, L., Potamianos, S., Prokoshin, K., Pranko, F., Ptohos, A., Punzi, Giovanni, Rahaman, G., Ramakrishnan, A., Ranjan, V., Redondo, N., Renton, I., Rescigno, P., Riddick, M., Rimondi, T., Ristori, F., Robson, L., Rodrigo, A., Rodriguez, T., Rogers, T., Rolli, E., Roser, S., Ruffini, R., Ruiz, F., Russ, A., Rusu, J., Safonov, V., Sakumoto, A., W. K., Sakurai, Santi, Y., Sato, L., Saveliev, K., Savoy, Navarro, Schlabach, A., Schmidt, P., Schmidt, A., E. E., Schwarz, Scodellaro, T., Scribano, L., Scuri, A., Seidel, F., Seiya, S., Semenov, Y., Sforza, A., Shalhout, F., S. Z., Shears, Shepard, T., P. F., Shimojima, Shochet, M., Shreyber, Tecker, Simonenko, I., Sinervo, A., Sliwa, P., Smith, K., J. R., Snider, F. D., Soha, Sorin, A., Song, V., Squillacioti, H., Stancari, P., Denis, S. t., Stelzer, R., Stelzer, Chilton, Stentz, O., Strologas, D., Strycker, J., G. L., Sudo, Sukhanov, Y., Suslov, A., Takemasa, I., Takeuchi, K., Tang, Y., Tecchio, J., Teng, M., P. K., Thom, Thome, J., Thompson, J., G. A., Thomson, Toback, E., Tokar, D., Tollefson, S., Tomura, K., Tonelli, T., Torre, D., Torretta, S., Totaro, D., Trovato, P., Ukegawa, M., Uozumi, F., Varganov, S., Vázquez, A., Velev, F., Vellidis, G., Vidal, C., Vila, M., Vilar, I., Vizán, R., Vogel, J., Volpi, M., Wagner, G., Wagner, P., R. L., Wakisaka, Wallny, T., Wang, R., S. M., Warburton, Waters, A., Wester, D., W. C., Whiteson, Wicklund, D., A. B., Wicklund, Wilbur, E., Wick, S., Williams, F., H. H., Wilson, J. S., Wilson, Winer, P., B. L., Wittich, Wolbers, P., Wolfe, S., Wright, H., Wu, T., Wu, X., Yamamoto, Z., Yamato, K., Yang, D., Yang, T., U. K., Yang, Y. C., Yao, W. M., Yeh, G. P., Yi, Yoh, K., Yorita, J., Yoshida, K., Yu, T., G. B., Yu, Yu, I., S. S., Yun, J. C., Zanetti, Zeng, A., Zhou, Y., Zucchelli, C., Jy, S., Koh, Yh, Koike, M, Komatsu, M, Kominami, E, Kong, Hj, Kong, Wj, Korolchuk, Vi, Kotake, Y, Koukourakis, Mi, Kouri Flores JB, Kovács, Al, Kraft, C, Krainc, D, Krämer, H, Kretz Remy, C, Krichevsky, Am, Kroemer, G, Krüger, R, Krut, O, Ktistakis, Nt, Kuan, Cy, Kucharczyk, R, Kumar, A, Kumar, R, Kumar, S, Kundu, M, Kung, Hj, Kurz, T, Kwon, Hj, La Spada AR, Lafont, F, Lamark, T, Landry, J, Lane, Jd, Lapaquette, P, Laporte, Jf, László, L, Lavandero, S, Lavoie, Jn, Layfield, R, Lazo, Pa, Le, W, Le Cam, L, Ledbetter, Dj, Lee, Aj, Lee, Bw, Lee, Gm, Lee, J, Lee, Jh, Lee, M, Lee, Ms, Lee, Sh, Leeuwenburgh, C, Legembre, P, Legouis, R, Lehmann, M, Lei, Hy, Lei, Qy, Leib, Da, Leiro, J, Lemasters, Jj, Lemoine, A, Lesniak, Ms, Lev, D, Levenson, Vv, Levine, B, Levy, E, Li, F, Li, Jl, Li, L, Li, S, Li, W, Li, Xj, Li, Yb, Li, Yp, Liang, C, Liang, Q, Liao, Yf, Liberski, Pp, Lieberman, A, Lim, Hj, Lim, Kl, Lim, K, Lin, Cf, Lin, Fc, Lin, J, Lin, Jd, Lin, K, Lin, Ww, Lin, Wc, Lin, Yl, Linden, R, Lingor, P, Lippincott Schwartz, J, Lisanti, Mp, Liton, Pb, Liu, B, Liu, Cf, Liu, K, Liu, L, Liu, Qa, Liu, W, Liu, Yc, Liu, Y, Lockshin, Ra, Lok, Cn, Lonial, S, Loos, B, Lopez Berestein, G, López Otín, C, Lossi, L, Lotze, Mt, Lőw, P, Lu, B, Lu, Z, Luciano, F, Lukacs, Nw, Lund, Ah, Lynch Day MA, Ma, Y, Macian, F, Mackeigan, Jp, Macleod, Kf, Madeo, F, Maiuri, L, Maiuri, Mc, Malagoli, D, Malicdan, Mc, Malorni, W, Man, N, Mandelkow, Em, Manon, S, Manov, I, Mao, K, Mao, X, Mao, Z, Marambaud, P, Marazziti, D, Marcel, Yl, Marchbank, K, Marchetti, P, Marciniak, Sj, Marcondes, M, Mardi, M, Marfe, G, Mariño, G, Markaki, M, Marten, Mr, Martin, Sj, Martinand Mari, C, Martinet, W, Martinez Vicente, M, Masini, M, Matarrese, P, Matsuo, S, Matteoni, R, Mayer, A, Mazure, Nm, Mcconkey, Dj, Mcconnell, Mj, Mcdermott, C, Mcdonald, C, Mcinerney, Gm, Mckenna, Sl, Mclaughlin, B, Mclean, Pj, Mcmaster, Cr, Mcquibban, Ga, Meijer, Aj, Meisler, Mh, Meléndez, A, Melia, Tj, Melino, G, Mena, Ma, Menendez, Ja, Menna Barreto RF, Menon, Mb, Menzies, Fm, Mercer, Ca, Merighi, A, Merry, De, Meschini, S, Meyer, Cg, Meyer, Tf, Miao, Cy, Miao, Jy, Michels, Pa, Michiels, C, Mijaljica, D, Milojkovic, A, Minucci, S, Miracco, C, Miranti, Ck, Mitroulis, I, Miyazawa, K, Mizushima, N, Mograbi, B, Mohseni, S, Molero, X, Mollereau, B, Mollinedo, F, Momoi, T, Monastyrska, I, Monick, Mm, Monteiro, Mj, Moore, Mn, Mora, R, Moreau, K, Moreira, Pi, Moriyasu, Y, Moscat, J, Mostowy, S, Mottram, Jc, Motyl, T, Moussa, Ce, Müller, S, Muller, S, Münger, K, Münz, C, Murphy, Lo, Murphy, Me, Musarò, A, Mysorekar, I, Nagata, E, Nagata, K, Nahimana, A, Nair, U, Nakagawa, T, Nakahira, K, Nakano, H, Nakatogawa, H, Nanjundan, M, Naqvi, Ni, Narendra, Dp, Narita, M, Navarro, M, Nawrocki, St, Nazarko, Ty, Nemchenko, A, Netea, Mg, Neufeld, Tp, Ney, Pa, Nezis, Ip, Nguyen, Hp, Nie, D, Nishino, I, Nislow, C, Nixon, Ra, Noda, T, Noegel, Aa, Nogalska, A, Noguchi, S, Notterpek, L, Novak, I, Nozaki, T, Nukina, N, Nürnberger, T, Nyfeler, B, Obara, K, Oberley, Td, Oddo, S, Ogawa, M, Ohashi, T, Okamoto, K, Oleinick, Nl, Oliver, Fj, Olsen, Lj, Olsson, S, Opota, O, Osborne, Tf, Ostrander, Gk, Otsu, K, Ou, Jh, Ouimet, M, Overholtzer, M, Ozpolat, B, Paganetti, P, Pagnini, U, Pallet, N, Palmer, Ge, Palumbo, C, Pan, T, Panaretakis, T, Pandey, Ub, Papackova, Z, Papassideri, I, Paris, I, Park, J, Park, Ok, Parys, Jb, Parzych, Kr, Patschan, S, Patterson, C, Pattingre, S, Pawelek, Jm, Peng, J, Perlmutter, Dh, Perrotta, I, Perry, G, Pervaiz, S, Peter, M, Peters, Gj, Petersen, M, Petrovski, G, Phang, Jm, Piacentini, M, Pierre, P, Pierrefite Carle, V, Pierron, G, Pinkas Kramarski, R, Piras, A, Piri, N, Platanias, Lc, Pöggeler, S, Poirot, M, Poletti, A, Poüs, C, Pozuelo Rubio, M, Prætorius Ibba, M, Prasad, A, Prescott, M, Priault, M, Produit Zengaffinen, N, Progulske Fox, A, Proikas Cezanne, T, Przedborski, S, Przyklenk, K, Puertollano, R, Puyal, J, Qian, Sb, Qin, L, Qin, Zh, Quaggin, Se, Raben, N, Rabinowich, H, Rabkin, Sw, Rahman, I, Rami, A, Ramm, G, Randall, G, Randow, F, Rao, Va, Rathmell, Jc, Ravikumar, B, Ray, Sk, Reed, Bh, Reed, Jc, Reggiori, F, Régnier Vigouroux, A, Reichert, As, Reiners JJ Jr, Reiter, Rj, Ren, J, Revuelta, Jl, Rhodes, Cj, Ritis, K, Rizzo, E, Robbins, J, Roberge, M, Roca, H, Roccheri, Mc, Rocchi, S, Rodemann, Hp, Rodríguez de Córdoba, S, Rohrer, B, Roninson, Ib, Rosen, K, Rost Roszkowska MM, Rouis, M, Rouschop, Km, Rovetta, F, Rubin, Bp, Rubinsztein, Dc, Ruckdeschel, K, Rucker EB 3rd, Rudich, A, Rudolf, E, Ruiz Opazo, N, Russo, R, Rusten, Te, Ryan, Km, Ryter, Sw, Sabatini, Dm, Sadoshima, J, Saha, T, Saitoh, T, Sakagami, H, Sakai, Y, Salekdeh, Gh, Salomoni, P, Salvaterra, Pm, Salvesen, G, Salvioli, R, Sanchez, Am, Sánchez Alcázar JA, Sánchez Prieto, R, Sandri, M, Sankar, U, Sansanwal, P, Santambrogio, L, Saran, S, Sarkar, S, Sarwal, M, Sasakawa, C, Sasnauskiene, A, Sass, M, Sato, K, Sato, M, Schapira, Ah, Scharl, M, Schätzl, Hm, Scheper, W, Schiaffino, S, Schneider, C, Schneider, Me, Schneider Stock, R, Schoenlein, Pv, Schorderet, Df, Schüller, C, Schwartz, Gk, Scorrano, L, Sealy, L, Seglen, Po, Segura Aguilar, J, Seiliez, I, Seleverstov, O, Sell, C, Seo, Jb, Separovic, D, Setaluri, V, Setoguchi, T, Settembre, C, Shacka, Jj, Shanmugam, M, Shapiro, Im, Shaulian, E, Shaw, Rj, Shelhamer, Jh, Shen, Hm, Shen, Wc, Sheng, Zh, Shi, Y, Shibuya, K, Shidoji, Y, Shieh, Jj, Shih, Cm, Shimada, Y, Shimizu, S, Shintani, T, Shirihai, Os, Shore, Gc, Sibirny, Aa, Sidhu, Sb, Sikorska, B, Silva Zacarin EC, Simmons, A, Simon, Ak, Simon, Hu, Simone, C, Simonsen, A, Sinclair, Da, Singh, R, Sinha, D, Sinicrope, Fa, Sirko, A, Siu, Pm, Sivridis, E, Skop, V, Skulachev, Vp, Slack, Rs, Smaili, Ss, Smith, Dr, Soengas, Ms, Soldati, T, Song, X, Sood, Ak, Soong, Tw, Sotgia, F, Spector, Sa, Spies, Cd, Springer, W, Srinivasula, Sm, Stefanis, L, Steffan, Js, Stendel, R, Stenmark, H, Stephanou, A, Stern, St, Sternberg, C, Stork, B, Strålfors, P, Subauste, Cs, Sui, X, 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Han, F. Happacher, K. Hara, D. Hare, M. Hare, R. Harr, K. Hatakeyama, C. Hay, M. Heck, J. Heinrich, M. Herndon, S. Hewamanage, A. Hocker, W. Hopkin, D. Horn, S. Hou, R. Hughe, M. Hurwitz, U. Husemann, N. Hussain, M. Hussein, J. Huston, G. Introzzi, M. Iori, A. Ivanov, E. Jame, D. Jang, B. Jayatilaka, E. Jeon, S. Jindariani, M. Jone, K. Joo, S. Jun, T. Junk, T. Kamon, P. Karchin, A. Kasmi, Y. Kato, W. Ketchum, J. Keung, V. Khotilovich, B. Kilminster, D. Kim, H. Kim, J. Kim, M. Kim, S. Kim, Y. Kim, N. Kimura, M. Kirby, S. Klimenko, K. Knoepfel, K. Kondo, D. Kong, J. Konigsberg, A. Kotwal, M. Krep, J. Kroll, D. Krop, M. Kruse, V. Krutelyov, T. Kuhr, M. Kurata, S. Kwang, A. Laasanen, S. Lami, S. Lammel, M. Lancaster, R. Lander, K. Lannon, A. Lath, G. Latino, T. LeCompte, E. Lee, H. Lee, J. Lee, S. Lee, S. Leo, S. Leone, J. Lewi, A. Limosani, C.-J. Lin, M. Lindgren, E. Lipele, A. Lister, D. Litvintsev, C. Liu, H. Liu, Q. Liu, T. Liu, S. Lockwitz, A. Loginov, D. Lucchesi, J. Lueck, P. Lujan, P. Luken, G. Lungu, J. Ly, R. Lysak, R. Madrak, K. Maeshima, P. Maestro, S. Malik, G. Manca, A. Manousakis-Katsikaki, F. Margaroli, C. Marino, M. Martínez, P. Mastrandrea, K. Matera, M. Mattson, A. Mazzacane, P. Mazzanti, K. McFarland, P. McIntyre, R. McNulty, A. Mehta, P. Mehtala, C. Mesropian, T. Miao, D. Mietlicki, A. Mitra, H. Miyake, S. Moed, N. Moggi, M. Mondragon, C. Moon, R. Moore, M. Morello, J. Morlock, P. Movilla Fernandez, A. Mukherjee, Th. Muller, P. Murat, M. Mussini, J. Nachtman, Y. Nagai, J. Naganoma, I. Nakano, A. Napier, J. Nett, C. Neu, M. Neubauer, J. Nielsen, L. Nodulman, S. Noh, O. Norniella, L. Oake, S. Oh, Y. Oh, I. Oksuzian, T. Okusawa, R. Orava, L. Ortolan, S. Pagan Griso, C. Pagliarone, E. Palencia, V. Papadimitriou, A. Paramonov, J. Patrick, G. Pauletta, M. Paulini, C. Pau, D. Pellett, A. Penzo, T. Phillip, G. Piacentino, E. Pianori, J. Pilot, K. Pitt, C. Plager, L. Pondrom, S. Poprocki, K. Potamiano, F. Prokoshin, A. Pranko, F. Ptoho, G. Punzi, A. Rahaman, V. Ramakrishnan, N. Ranjan, I. Redondo, P. Renton, M. Rescigno, T. Riddick, F. Rimondi, L. Ristori, A. Robson, T. Rodrigo, T. Rodriguez, E. Roger, S. Rolli, R. Roser, F. Ruffini, A. Ruiz, J. Ru, V. Rusu, A. Safonov, W. Sakumoto, Y. Sakurai, L. Santi, K. Sato, V. Saveliev, A. Savoy-Navarro, P. Schlabach, A. Schmidt, E. Schmidt, T. Schwarz, L. Scodellaro, A. Scribano, F. Scuri, S. Seidel, Y. Seiya, A. Semenov, F. Sforza, S. Shalhout, T. Shear, P. Shepard, M. Shimojima, M. Shochet, I. Shreyber-Tecker, A. Simonenko, P. Sinervo, K. Sliwa, J. Smith, F. Snider, A. Soha, V. Sorin, H. Song, P. Squillacioti, M. Stancari, R. St. Deni, B. Stelzer, O. Stelzer-Chilton, D. Stentz, J. Strologa, G. Strycker, Y. Sudo, A. Sukhanov, I. Suslov, K. Takemasa, Y. Takeuchi, J. Tang, M. Tecchio, P. Teng, J. Thom, J. Thome, G. Thompson, E. Thomson, D. Toback, S. Tokar, K. Tollefson, T. Tomura, D. Tonelli, S. Torre, D. Torretta, P. Totaro, M. Trovato, F. Ukegawa, S. Uozumi, A. Varganov, F. Vázquez, G. Velev, C. Vellidi, M. Vidal, I. Vila, R. Vilar, J. Vizán, M. Vogel, G. Volpi, P. Wagner, R. Wagner, T. Wakisaka, R. Wallny, S. Wang, A. Warburton, D. Water, W. Wester, D. Whiteson, A. Wicklund, E. Wicklund, S. Wilbur, F. Wick, H. William, J. Wilson, P. Wilson, B. Winer, P. Wittich, S. Wolber, H. Wolfe, T. Wright, X. Wu, Z. Wu, K. Yamamoto, D. Yamato, T. Yang, U. Yang, Y. Yang, W.-M. Yao, G. Yeh, K. Yi, J. Yoh, K. Yorita, T. Yoshida, G. Yu, I. Yu, S. Yu, J. Yun, A. Zanetti, Y. Zeng, C. Zhou, S. Zucchelli, and Universidad de Cantabria

Subjects
FERMILAB TEVATRON COLLIDER, Particle physics, CP-violating asymmetries, Meson, B physic, General Physics and Astronomy, FOS: Physical sciences, B physics, Angle distribution, Branching ratio, CDF experiments, CP violations, CP-violating asymmetries, Data sample, Fermilab Tevatron collider, Integrated luminosity, Longitudinal polarization, Vector meson, Longitudinal polarization, 7. Clean energy, 01 natural sciences, High Energy Physics - Experiment, Vector meson, Physics and Astronomy (all), High Energy Physics - Experiment (hep-ex), High Energy Physics - Phenomenology (hep-ph), Mixing (mathematics), Strange b mesons, Phase (matter), 0103 physical sciences, STRANGE QUARK, mixing, Bottom-Strange Meson Mixing Phase, proton antiproton collisions, 010306 general physics, TEVATRON, Nuclear Experiment, BOTTOM QUARK, Physics, Integrated luminosity, 010308 nuclear & particles physics, Branching ratio, High Energy Physics - Phenomenology, CDF experiments, CP violations, Full data, Content (measure theory), Angle distribution, CDF, Production (computer science), High Energy Physics::Experiment, Data sample
Abstract

We report a measurement of the bottom-strange meson mixing phase βs using the time evolution of Bs0→J/ψ(→μ+μ-)ϕ(→K+K-) decays in which the quark-flavor content of the bottom-strange meson is identified at production. This measurement uses the full data set of proton-antiproton collisions at s=1.96 TeV collected by the Collider Detector experiment at the Fermilab Tevatron, corresponding to 9.6 fb-1 of integrated luminosity. We report confidence regions in the two-dimensional space of βs and the Bs0 decay-width difference ΔΓs and measure βs∈[-π/2,-1.51]∪[-0.06,0.30]∪[1.26,π/2] at the 68% confidence level, in agreement with the standard model expectation. Assuming the standard model value of βs, we also determine ΔΓs=0.068±0.026(stat)±0.009(syst) ps-1 and the mean Bs0 lifetime τs=1.528±0.019(stat)±0.009(syst) ps, which are consistent and competitive with determinations by other experiments., This work was supported by the U.S. Department of Energy and National Science Foundation; the Italian Istituto Nazionale di Fisica Nucleare; the Ministry of Education, Culture, Sports, Science and Technology of Japan; the Natural Sciences and Engineering Research Council of Canada; the National Science Council of the Republic of China; the Swiss National Science Foundation; the A. P. Sloan Foundation; the Bundesministerium für Bildung und Forschung, Germany; the Korean World Class University Program, the National Research Foundation of Korea; the Science and Technology Facilities Council and the Royal Society, UK; the Russian Foundation for Basic Research; the Ministerio de Ciencia e Innovación, and Programa Consolider-Ingenio 2010, Spain; the Slovak R&D Agency; the Academy of Finland; and the Australian Research Council (ARC).

Published
2012

27. Guidelines for the use and interpretation of assays for monitoring autophagy.

Author

Klionsky, Dj, Abdalla, Fc, Abeliovich, H, Abraham, Rt, Acevedo-Arozena, A, Adeli, K, Agholme, L, Agnello, M, Agostinis, P, Aguirre-Ghiso, Ja, Ahn, Hj, Ait-Mohamed, O, Ait-Si-Ali, S, Akematsu, T, Akira, S, Al-Younes, Hm, Al-Zeer, Ma, Albert, Ml, Albin, Rl, Alegre-Abarrategui, J, Aleo, Mf, Alirezaei, M, Almasan, A, Almonte-Becerril, M, Amano, A, Amaravadi, R, Amarnath, S, Amer, Ao, Andrieu-Abadie, N, Anantharam, V, Ann, Dk, Anoopkumar-Dukie, S, Aoki, H, Apostolova, N, Arancia, G, Aris, Jp, Asanuma, K, Asare, Ny, Ashida, H, Askanas, V, Askew, D, Auberger, P, Baba, M, Backues, Sk, Baehrecke, Eh, Bahr, Ba, Bai, Xy, Bailly, Y, Baiocchi, R, Baldini, G, Balduini, W, Ballabio, A, Bamber, Ba, Bampton, Et, Bánhegyi, G, Bartholomew, Cr, Bassham, Dc, Bast RC, Jr, Batoko, H, Bay, Bh, Beau, I, Béchet, Dm, Begley, Tj, Behl, C, Behrends, C, Bekri, S, Bellaire, B, Bendall, Lj, Benetti, L, Berliocchi, L, Bernardi, H, Bernassola, F, Besteiro, S, Bhatia-Kissova, I, Bi, X, Biard-Piechaczyk, M, Blum, J, 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Zuckerbraun, B., and Viscomi M. T. (ORCID:0000-0002-9096-4967)

Abstract

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused o

Published
2012

28. S64 Circulating polymers are found in alpha-1-antitrypsin deficiency and are associated with lung disease

Author

Dickens, JA, primary, Tan, L, additional, DeMeo, DL, additional, Miranda, E, additional, Perez, J, additional, Rashid, ST, additional, Day, J, additional, Ordonez, A, additional, Marciniak, SJ, additional, Haq, I, additional, Barker, AF, additional, Campbell, EJ, additional, Eden, E, additional, McElvaney, NG, additional, Rennard, SI, additional, Sandhaus, RA, additional, Stocks, JM, additional, Stoller, JK, additional, Strange, C, additional, Turino, G, additional, Rouhani, FN, additional, Brantly, M, additional, and Lomas, DA, additional

Published
2013
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29. S82 Multi-centre prospective comparison of the BTS and ACCP guidelines to determine size in primary spontaneous pneumothorax

Author

Nikolic, M, primary, Lok, L, additional, Mattishent, K, additional, Barth, S, additional, Yung, B, additional, Cummings, N, additional, Shulgina, L, additional, Wade, D, additional, Shittu, M, additional, Vali, Y, additional, Chong, K, additional, Wilkinson, A, additional, Mikolasch, T, additional, Brij, S, additional, Jenkins, S, additional, Kamath, A, additional, Pasteur, M, additional, Wason, J, additional, and Marciniak, SJ, additional

Published
2013
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30. Pharmacokinetics and Safety of Golimumab, a Fully Human Anti-TNF-{alpha} Monoclonal Antibody, in Subjects With Rheumatoid Arthritis.

Author

Zhou H, Jang H, Fleischmann RM, Bouman-Thio E, Xu Z, Marini JC, Pendley C, Jiao Q, Shankar G, Marciniak SJ, Cohen SB, Rahman MU, Baker D, Mascelli MA, Davis HM, and Everitt DE

Abstract

Golimumab is a fully human antitumor necrosis factor alpha (TNF-alpha) monoclonal antibody that is being developed for intravenous and subcutaneous administration. To assess the pharmacokinetics and safety of the intravenous formulation of golimumab, 36 adult subjects with rheumatoid arthritis were randomly assigned to receive a single infusion of placebo or golimumab (0.1, 0.3, 1, 3, 6, or 10 mg/kg). Serum concentrations of golimumab were determined using a validated enzyme-linked immunosorbent assay method. In addition to the noncompartmental analysis and compartmental modeling, a population pharmacokinetics analysis using NONMEM was also conducted. Both the maximum serum concentration and the area under the serum concentrationtime curve appeared to increase in a dose-proportional manner. The median half-life ranged from 7 to 20 days. A 2-compartment population pharmacokinetic model adequately described the pharmacokinetics of golimumab. The following pharmacokinetic parameters (typical value [% coefficient of variation]) were estimated from the population pharmacokinetic model: clearance (CL: 0.40 [10.1%] L/d), volume of distribution in the central compartment (V(c): 3.07 [6.4%] L), intercompartmental clearance (Q: 0.42 [15.5%] L/d), and volume of distribution in the peripheral compartment (V(p): 3.68 [11.8%] L). Interindividual variability of the pharmacokinetic parameters was quantified for CL (44.3%), V(c) (25.5%), Q (44.6%), and V(p) (44.6%). Residual variability was estimated to be 15.0%. Body weight was found to be an important covariate on V(c). Golimumab was generally well tolerated. The pharmacokinetics of golimumab appeared to be linear over the dose range evaluated in this study. [ABSTRACT FROM AUTHOR]

Published
2007
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31. The endoplasmic reticulum stress marker CHOP predicts survival in malignant mesothelioma

Author

Dalton, LE, Clarke, HJ, Knight, J, Lawson, MH, Wason, J, Lomas, DA, Howat, WJ, Rintoul, RC, Rassl, DM, and Marciniak, SJ

Subjects
Male, Mesothelioma, Cell Differentiation, Endoplasmic Reticulum Stress, Prognosis, 3. Good health, Immunoenzyme Techniques, Survival Rate, Tissue Array Analysis, Protein Phosphatase 1, Biomarkers, Tumor, Humans, Female, Endoplasmic Reticulum Chaperone BiP, Heat-Shock Proteins, Transcription Factor CHOP, Follow-Up Studies, Neoplasm Staging, Signal Transduction
Abstract

BACKGROUND: Mesothelioma is an incurable cancer originating from the mesothelial cells that line the pleural, peritoneal and pericardial cavities. These cells synthesise large quantities of surface glycoproteins, rendering them dependent upon efficient endoplasmic reticulum (ER) function. When faced with elevated levels of secretory protein load, cells are said to experience ER stress, which has been implicated in the pathogenesis of many human diseases including cancer. METHOD: We set out to measure markers of ER stress in malignant mesothelioma and to determine whether ER stress signalling correlates with clinical parameters. RESULTS: We observed that expression of the ER stress-responsive transcription factor C/EBP homologous protein (CHOP) correlated with patient survival and remained an independent prognostic variable in pairwise comparisons with all clinical variables tested. The most parsimonious multivariate model in our study comprised only performance status and CHOP staining. In contrast, expression of the ER stress-responsive phosphatase growth arrest and DNA damage 34 (GADD34) correlated with the degree of mesothelial differentiation, being lost progressively in biphasic and sarcomatoid mesotheliomas. CONCLUSION: Our findings suggest that staining for CHOP provides prognostic information that may be useful in the stratification of patients with mesothelioma. Staining for GADD34 may prove useful in classification of mesothelioma histopathology.

34. T6 Understanding the cellular dysfunction caused by pathogenic surfactant protein c mutant i73t

Author

Dickens, JA, Ellis, MO, and Marciniak, SJ

Abstract

Introduction and ObjectivesOur understanding of the pathogenesis of interstitial pulmonary disease is limited largely to its late, fibrotic stages. Inherited forms offer the potential to understand earlier pathogenic events. Autosomal dominant mutations in surfactant protein C (SFTPC) cause some cases of familial pulmonary fibrosis; the most common mutation is I73T, which is said to be mistrafficked within the type 2 pneumocyte. We hypothesise that mistrafficking of SFTPC I73T is causal in triggering type 2 pneumocyte dysfunction in familial pulmonary fibrosis. This work aims to understand the mechanism of SFTPC I73T mistrafficking such that type 2 pneumocyte dysfunction in familial, and sporadic disease can be better understood.MethodsWe overexpressed GFP tagged wild-type (WT) and I73T SFTPC in HeLa cells to study their localisation and trafficking. Subcellular localisation and co-localisation with organelle markers was assessed using confocal microscopy and immunofluorescence. Western blotting was used to assess expression of SFTPC isoforms and GFP traps to study SFTPC interactors, including ubiquitin. Mass spectrometry was used to assess the interactome of WT and I73T SFTPC.ResultsIn HeLa cells overexpressing GFP-SFTPC, we observed mistrafficking of SFTPC I73T; WT SFTPC is trafficked to the multivesicular body (MVB), while I73T mistrafficks to the cell surface and into tubular structures (figure 1A) which co-localise with a marker of recycling endosomes Rab8 (figure 1B). Correct trafficking of WT SFTPC to the MVB depends on ubiquitination of lysine-6 (K6). We see an absence of ubiquitination in the I73T mutant and a subcellular distribution similar to that seen in a SFTPC mutant (K6R) which cannot be ubiquitinated. Mass spectrometry revealed differential binding between WT and I73T SFTPC of a number of cell surface proteins.ConclusionWe have shown that pathogenic SFTPC mutant I73T mistrafficks not only to the cell surface, but also into recycling endosomes. We propose that this occurs as a result of failure of ubiquitination and internalisation into the MVB. Trafficking defects appear to impact upon binding of WT vs I73T to cell surface markers, the functional significance of which is the focus of our ongoing work.[Figure]

Published
2017
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35. S74 Endoplasmic stress is associated with fibrosis in interstitial lung disease

Author

Parfrey, H, Moseley, E, Beardsley, B, Knight, J, Marciniak, SJ, and Rassl, D

Abstract

Interstitial lung diseases (ILD) are a heterogeneous group characterised by variable amounts of inflammation and fibrosis. However, the development of pulmonary fibrosis is associated with a poorer prognosis. Although distinct histological features differentiate between the ILDs, it is unknown if there are shared pathogenic mechanisms involved in the development of fibrosis. Endoplasmic reticulum (ER) stress has been implicated in the pathogenesis of familial and sporadic idiopathic pulmonary fibrosis (IPF). In response to ER stress, cells trigger the unfolded protein response (UPR) and upregulate chaperones, such as BiP, and the phosphatase GADD34, which can regulate epithelial to mesenchyme transition, cell proliferation, apoptosis and cell survival.AimsWe hypothesise that ER stress may be involved in the pathogenesis of fibrosis in all interstitial lung diseases.MethodsParaffin embedded sections, obtained from video assisted thoracoscopic diagnostic lung biopsies, from 8 patients with familial pulmonary fibrosis, 11 sporadic idiopathic pulmonary fibrosis (IPF), 12 non-specific interstitial pneumonia (NSIP) and 10 hypersensitivity pneumonitis (HP) were evaluated for BiP and GADD34 by immunohistochemistry. Using light microscopy, 6 high power fields were scored for fibrosis, inflammation, BiP and GADD34 using semi-quantitative analysis by 2 blinded, independent investigators. Data were analysed by linear regression using Prism software.ResultsOf the 41 biopsy samples analysed, 20 (49%) were non-smokers and 18 (44%) were male. BiP and GADD34 were localised to reactive type II pneumocytes and columnar epithelium within areas of fibrosis. GADD34 was also evident in the endothelium. No staining was detected within fibroblasts or fibroblastic foci. Epithelial GADD34 correlated with extent of fibrosis in familial pulmonary fibrosis (r2=0.72 p<0.001), IPF (r2=0.51 p<0.0001) and NSIP (r2=0.46 p<0.0001). In contrast, BiP was associated with fibrosis in IPF (r2=0.49 p<0.0001) and HP (r2=0.59 p<0.0001). There was no association with inflammation.ConclusionThese data show that ER stress and the UPR are associated with fibrotic ILDs. Hence targeting ER stress may be a novel therapeutic option for pulmonary fibrosis. Work is on going to identify a peripheral biomarker signature for ER stress.

Published
2017
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36. S54 Automating the analysis of thoracic ct scans in cystic lung disease

Author

Maharajan, V, Karia, S, Maher, ER, Taraskin, SN, Johnson, SR, and Marciniak, SJ

Abstract

IntroductionCertain disorders of the lung, such as Birt-Hogg-Dubé syndrome (BHD) and lymphangioleiomyomatosis (LAM), are characterised by the presence of multiple pulmonary cysts. Radiological analysis using thoracic computed tomography (CT) is the mainstay of diagnosis and follow-up of these disorders. The rate of change of the cysts contributes to therapeutic decisions including the prescription of potentially toxic therapies, most notably mTOR inhibitors in LAM. At present, cyst parameters including their location, size, shape and number are determined by the review of CT images by radiologists. Despite expert training, this process is prone to human error and susceptible to inter-observer disparity.ObjectiveWe wished to determine if automation of cyst analysis could provide robust data to aid the radiologists in their reporting of thoracic CT scans.Methods and ResultsSoftware was developed using C++to extract data from standard Digital Imaging and Communications in Medicine (DICOM) CT files. For each scan, voxels in lung parenchyma or cysts were detected by radiodensity being in the range from −935 HU to −610 HU or below −935 HU, respectively. The 3D-cyst boundaries were identified by means of novel recursive algorithm (figure 1). Trachea and airways were automatically detected and excluded from further analysis. Number of cysts per patient was recorded and each cyst analysed in terms of volume, spatial location, sphericity and cylindricity (calculated by using eigenvalues of gyration tensor for corresponding cyst) and opacity. The software was calibrated empirically through iterative adjustment of the above threshold values and comparison with scores generated by an expert thoracic radiologist thus enabling the reliable differentiation of cysts from noise. As proof-of-principle, the scans of 10 individuals with BHD and 10 with LAM were analysed in a blinded manner by the computer and compared with independent radiology reports.ConclusionAutomated image analysis provides a new set of objective cyst parameters and offers added value to the thoracic radiology reporting process. Future studies will determine the relative sensitivities of human vs. automated CT analysis in the diagnosis and monitoring of cystic lung diseases including BHD and LAM.[Figure]

Published
2017
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37. A novel human fetal lung-derived alveolar organoid model reveals mechanisms of surfactant protein C maturation relevant to interstitial lung disease.

Author

Lim K, Rutherford EN, Delpiano L, He P, Lin W, Sun D, Van den Boomen DJH, Edgar JR, Bang JH, Predeus A, Teichmann SA, Marioni JC, Matesic LE, Lee JH, Lehner PJ, Marciniak SJ, Rawlins EL, and Dickens JA

Subjects
Humans, Alveolar Epithelial Cells metabolism, Cell Differentiation, Lung metabolism, Lung embryology, Lung pathology, Fetus metabolism, Ubiquitin-Protein Ligases metabolism, Ubiquitin-Protein Ligases genetics, Organoids metabolism, Organoids pathology, Pulmonary Surfactant-Associated Protein C metabolism, Pulmonary Surfactant-Associated Protein C genetics, Lung Diseases, Interstitial metabolism, Lung Diseases, Interstitial pathology, Lung Diseases, Interstitial genetics
Abstract

Alveolar type 2 (AT2) cells maintain lung health by acting as stem cells and producing pulmonary surfactant. AT2 dysfunction underlies many lung diseases, including interstitial lung disease (ILD), in which some inherited forms result from the mislocalization of surfactant protein C (SFTPC) variants. Lung disease modeling and dissection of the underlying mechanisms remain challenging due to complexities in deriving and maintaining human AT2 cells ex vivo. Here, we describe the development of mature, expandable AT2 organoids derived from human fetal lungs which are phenotypically stable, can differentiate into AT1-like cells, and are genetically manipulable. We use these organoids to test key effectors of SFTPC maturation identified in a forward genetic screen including the E3 ligase ITCH, demonstrating that their depletion phenocopies the pathological SFTPC redistribution seen for the SFTPC-I73T variant. In summary, we demonstrate the development of a novel alveolar organoid model and use it to identify effectors of SFTPC maturation necessary for AT2 health., Competing Interests: Disclosure and competing interests statement. SAT is a remunerated member of the scientific advisory boards of Qiagen, Foresite Labs, and Element Biosciences, a co-founder and equity holder of TransitionBio, and a part-time employee of GlaxoSmithKline since January 2024. JCM has been an employee of Genentech, Inc. since September 2022. The remaining authors declare no competing interests., (© 2025. The Author(s).)

Published
2025
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39. GDF15 antagonism limits severe heart failure and prevents cardiac cachexia.

Author

Takaoka M, Tadross JA, Al-Hadithi ABAK, Zhao X, Villena-Gutiérrez R, Tromp J, Absar S, Au M, Harrison J, Coll AP, Marciniak SJ, Rimmington D, Oliver E, Ibáñez B, Voors AA, O'Rahilly S, Mallat Z, and Goodall JC

Subjects
Animals, Humans, Male, Protein Phosphatase 1 metabolism, Protein Phosphatase 1 genetics, Female, Weight Loss drug effects, Cardiomyopathy, Dilated metabolism, Cardiomyopathy, Dilated genetics, Cardiomyopathy, Dilated physiopathology, Myocardium metabolism, Myocardium pathology, Signal Transduction drug effects, Severity of Illness Index, Middle Aged, Aged, Mice, Bone Marrow Transplantation, Growth Differentiation Factor 15 metabolism, Growth Differentiation Factor 15 genetics, Cachexia metabolism, Cachexia prevention & control, Cachexia etiology, Cachexia physiopathology, Cachexia genetics, Heart Failure metabolism, Heart Failure physiopathology, Heart Failure prevention & control, Heart Failure genetics, Heart Failure drug therapy, Mice, Inbred C57BL, Disease Models, Animal, Mice, Knockout
Abstract

Aims: Heart failure and associated cachexia is an unresolved and important problem. This study aimed to determine the factors that contribute to cardiac cachexia in a new model of heart failure in mice that lack the integrated stress response (ISR) induced eIF2α phosphatase, PPP1R15A., Methods and Results: Mice were irradiated and reconstituted with bone marrow cells. Mice lacking functional PPP1R15A, exhibited dilated cardiomyopathy and severe weight loss following irradiation, whilst wild-type mice were unaffected. This was associated with increased expression of Gdf15 in the heart and increased levels of GDF15 in circulation. We provide evidence that the blockade of GDF15 activity prevents cachexia and slows the progression of heart failure. We also show the relevance of GDF15 to lean mass and protein intake in patients with heart failure., Conclusion: Our data suggest that cardiac stress mediates a GDF15-dependent pathway that drives weight loss and worsens cardiac function. Blockade of GDF15 could constitute a novel therapeutic option to limit cardiac cachexia and improve clinical outcomes in patients with severe systolic heart failure., Competing Interests: Conflict of interest: S.O.R. is an employee of the University of Cambridge and has provided remunerated consultancy services to the following pharmaceutical companies with an active or potential interest in GDF15: Pfizer, AstraZeneca, MedImmune, and Novo-Nordisk. A.A.V. and J.T received consultancy fees and research support from Roche Diagnostics. The employer of AAV received consultancy fees and/or research support from AnaCardio, AstraZeneca, BMS, Boehringer Ingelheim, Bayer, Corteria, EliLilly, Moderna, Novartis, NovoNordisk, Roche Diagnostics., (© The Author(s) 2024. Published by Oxford University Press on behalf of the European Society of Cardiology.)

Published
2024
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40. CT features associated with contralateral recurrence of spontaneous pneumothorax.

Author

Burn LA, Wetscherek MT, Pharoah PD, and Marciniak SJ

Subjects
Humans, Male, Female, Adult, Young Adult, Middle Aged, Cysts diagnostic imaging, Cysts complications, Retrospective Studies, Adolescent, Age Factors, Risk Factors, Pneumothorax diagnostic imaging, Recurrence, Tomography, X-Ray Computed
Abstract

Introduction: Spontaneous pneumothorax recurs in 30-54% of patients without surgery. Identifying individuals likely to suffer a recurrence, who might benefit from pre-emptive surgery, is challenging. Previous meta-analysis suggested a relationship between contralateral recurrence and specific CT findings., Methods: We analysed CT images and recurrence rates of 243 patients seen by our tertiary referral pneumothorax service., Results: We validated the meta-analysis observation that contralateral lung cysts are associated with a higher risk of contralateral recurrence in younger individuals. Furthermore, we observed that the size of contralateral cysts to be associated with increased contralateral recurrence in younger patients., Conclusion: The detection of contralateral lung cysts might therefore help identify younger patients more likely to benefit from pre-emptive surgery., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Association of Physicians.)

Published
2024
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41. Functional validation of EIF2AK4 (GCN2) missense variants associated with pulmonary arterial hypertension.

Author

Emanuelli G, Zhu J, Li W, Morrell NW, and Marciniak SJ

Subjects
Humans, Genetic Predisposition to Disease, Hypertension, Pulmonary genetics, Computational Biology methods, Protein Serine-Threonine Kinases genetics, Mutation, Missense genetics, Pulmonary Arterial Hypertension genetics
Abstract

Pulmonary arterial hypertension (PAH) is a disorder with a large genetic component. Biallelic mutations of EIF2AK4, which encodes the kinase GCN2, are causal in two ultra-rare subtypes of PAH, pulmonary veno-occlusive disease and pulmonary capillary haemangiomatosis. EIF2AK4 variants of unknown significance have also been identified in patients with classical PAH, though their relationship to disease remains unclear. To provide patients with diagnostic information and enable family testing, the functional consequences of such rare variants must be determined, but existing computational methods are imperfect. We applied a suite of bioinformatic and experimental approaches to sixteen EIF2AK4 variants that had been identified in patients. By experimentally testing the functional integrity of the integrated stress response (ISR) downstream of GCN2, we determined that existing computational tools have insufficient sensitivity to reliably predict impaired kinase function. We determined experimentally that several EIF2AK4 variants identified in patients with classical PAH had preserved function and are therefore likely to be non-pathogenic. The dysfunctional variants of GCN2 that we identified could be subclassified into three groups: misfolded, kinase-dead, and hypomorphic. Intriguingly, members of the hypomorphic group were amenable to paradoxical activation by a type-1½ GCN2 kinase inhibitor. This experiment approach may aid in the clinical stratification of EIF2AK4 variants and potentially identify hypomorophic alleles receptive to pharmacological activation., (© The Author(s) 2024. Published by Oxford University Press.)

Published
2024
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43. Leveraging the pleural space for anticancer therapies in pleural mesothelioma.

Author

Blyth KG, Adusumilli PS, Astoul P, Darlison L, Lee YCG, Mansfield AS, Marciniak SJ, Maskell N, Panou V, Peikert T, Rahman NM, Zauderer MG, Sterman D, and Fennell DA

Subjects
Humans, Mesothelioma, Malignant drug therapy, Mesothelioma, Malignant therapy, Antineoplastic Agents therapeutic use, Pleural Effusion, Malignant therapy, Pleural Neoplasms therapy, Pleural Neoplasms drug therapy, Pleural Neoplasms pathology, Mesothelioma drug therapy, Mesothelioma therapy, Mesothelioma pathology, Pleura pathology, Pleura diagnostic imaging
Abstract

Most patients with pleural mesothelioma (PM) present with symptomatic pleural effusion. In some patients, PM is only detectable on the pleural surfaces, providing a strong rationale for intrapleural anticancer therapy. In modern prospective studies involving expert radiological staging and specialist multidisciplinary teams, the population incidence of stage I PM (an approximate surrogate of pleura-only PM) is higher than in historical retrospective series. In this Viewpoint, we advocate for the expansion of intrapleural trials to serve these patients, given the paucity of data supporting licensed systemic therapies in this setting and the uncertainties involved in surgical therapy. We begin by reviewing the unique anatomical and physiological features of the PM-bearing pleural space, before critically appraising the evidence for systemic therapies in stage I PM and previous intrapleural PM trials. We conclude with a summary of key challenges and potential solutions, including optimal trial designs, repurposing of indwelling pleural catheters, and new technologies., Competing Interests: Declaration of interests KGB declares institutional grant funding from Rocket Medical and RS Oncology; lecture honoraria from Bristol-Myers Squibb; and the role of chief investigator of the PREDICT-Meso International Accelerator Network. PSA declares research funding from ATARA Biotherapeutics; patents, royalties, and intellectual property on therapies licensed to ATARA Biotherapeutics; and scientific advisory board membership and consulting fees from ATARA Biotherapeutics, Bayer, Bio4T2, Carisma Therapeutics, Imugene, ImmPactBio, Johnson & Johnson, Orion Pharma, and Outpace Bio. PA declares equipment loans for courses from Novatech, Wolf, and Olympus. LD declares lecture honoraria from Bristol-Myers Squibb. YCGL declares receipt of equipment from Rocket Medical for use in clinical trials. ASM declares institutional grant funding from Novartis and Verily; consulting fees from Rising Tide and TRIPTYCH Health Partners; institutional payments or honoraria from Janssen, BeiGene, Chugai Pharmaceutical (Roche), Ideology Health (formerly Health Media), Antoni van Leeuwenhoek Kanker Instituut, AXIS Medical Education, Johnson & Johnson Global Services, Intellisphere, Answers in CME, University of Miami International Mesothelioma Symposium, and Immunocore; support for attending meetings from Shanghai Roche; membership of scientific advisory boards for AbbVie, AstraZeneca, Bristol-Myers Squibb, Genentech/Roche, Takeda Oncology, and Sanofi Genzyme; and study funding from Bristol-Myers Squibb. SJM is co-principal investigator of the Engineering and Physical Sciences Research Council Interdisciplinary Research Collaboration in Targeted Delivery for Hard-to-Treat Cancers; he declares consulting fees from DefiniGEN, and support for attending meetings from Alpha-1 Foundation, Federation of American Societies for Experimental Biology, and Mesothelioma UK. NM declares consulting fees from Rocket Medical UK, Cook Medical UK, and Becton Dickinson. VP declares grant funding from the Danish Comprehensive Cancer Center and no conflicts of interest within the scope of this Viewpoint. NMR declares consulting fees from Rocket Medical UK, Cook Medical UK, and LTI USA. MGZ declares institutional grant funding from Medimmune, Precog, GSK, Epizyme, Polaris, Sellas Life Sciences, Bristol-Myers Squibb, Millenium, Curis, and Atara; consulting fees from Curis, Ikena, Takeda, GSK, and Novocure; and honoraria from PER and Medscape. DS declares support including research funding and consulting fees from AstraZeneca, Boehringer Ingelheim, Exigo Management, Flame Biosciences, HitchBio, Intuitive Surgical, Janssen, Johnson & Johnson, Medscape, Olympus Corporation of the Americas (also known as Spiration), Sensei Biotherapeutics, Trizell, Trustees of the University of Pennsylvania, Verismo, and Wolters Kluwer Health. DAF declares institutional grants from Aldeyra, Astex Therapeutics, Bayer Oncology, Bergen Bio, Boehringer Ingelheim, Clovis Oncology, Eli Lilly, Lovance, MSD, Owkin, Roche Oncology, and RS Oncology; consulting fees from Cambridge Clinical Laboratories and RS Oncology; honoraria from MSD and Bristol-Myers Squibb; support for attending meetings from RS Oncology; and participation on data monitoring or advisory boards for AstraZeneca and RS Oncology. TP declares no competing interests., (Copyright © 2024 Elsevier Ltd. All rights reserved, including those for text and data mining, AI training, and similar technologies.)

Published
2024
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44. Mutations causing premature termination codons discriminate and generate cellular and clinical variability in HHT.

Author

Bernabéu-Herrero ME, Patel D, Bielowka A, Zhu J, Jain K, Mackay IS, Chaves Guerrero P, Emanuelli G, Jovine L, Noseda M, Marciniak SJ, Aldred MA, and Shovlin CL

Subjects
Humans, Smad4 Protein genetics, Endothelial Cells metabolism, Endothelial Cells pathology, Mutation, Male, Female, Nonsense Mediated mRNA Decay, Codon, Nonsense, Telangiectasia, Hereditary Hemorrhagic genetics, Telangiectasia, Hereditary Hemorrhagic pathology, Endoglin genetics, Endoglin metabolism, Activin Receptors, Type II genetics
Abstract

Abstract: For monogenic diseases caused by pathogenic loss-of-function DNA variants, attention focuses on dysregulated gene-specific pathways, usually considering molecular subtypes together within causal genes. To better understand phenotypic variability in hereditary hemorrhagic telangiectasia (HHT), we subcategorized pathogenic DNA variants in ENG/endoglin, ACVRL1/ALK1, and SMAD4 if they generated premature termination codons (PTCs) subject to nonsense-mediated decay. In 3 patient cohorts, a PTC-based classification system explained some previously puzzling hemorrhage variability. In blood outgrowth endothelial cells (BOECs) derived from patients with ACVRL1+/PTC, ENG+/PTC, and SMAD4+/PTC genotypes, PTC-containing RNA transcripts persisted at low levels (8%-23% expected, varying between replicate cultures); genes differentially expressed to Bonferroni P < .05 in HHT+/PTC BOECs clustered significantly only to generic protein terms (isopeptide-bond/ubiquitin-like conjugation) and pulse-chase experiments detected subtle protein maturation differences but no evidence for PTC-truncated protein. BOECs displaying highest PTC persistence were discriminated in unsupervised hierarchical clustering of near-invariant housekeeper genes, with patterns compatible with higher cellular stress in BOECs with >11% PTC persistence. To test directionality, we used a HeLa reporter system to detect induction of activating transcription factor 4 (ATF4), which controls expression of stress-adaptive genes, and showed that ENG Q436X but not ENG R93X directly induced ATF4. AlphaFold accurately modeled relevant ENG domains, with AlphaMissense suggesting that readthrough substitutions would be benign for ENG R93X and other less rare ENG nonsense variants but more damaging for Q436X. We conclude that PTCs should be distinguished from other loss-of-function variants, PTC transcript levels increase in stressed cells, and readthrough proteins and mechanisms provide promising research avenues., (© 2024 American Society of Hematology. Published by Elsevier Inc. Licensed under Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0), permitting only noncommercial, nonderivative use with attribution. All other rights reserved.)

Published
2024
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45. Enhancing Drug Delivery Efficacy Through Bilayer Coating of Zirconium-Based Metal-Organic Frameworks: Sustained Release and Improved Chemical Stability and Cellular Uptake for Cancer Therapy.

Author

Liu X, Obacz J, Emanuelli G, Chambers JE, Abreu S, Chen X, Linnane E, Mehta JP, Wheatley AEH, Marciniak SJ, and Fairen-Jimenez D

Abstract

The development of nanoparticle (NP)-based drug carriers has presented an exciting opportunity to address challenges in oncology. Among the 100,000 available possibilities, zirconium-based metal-organic frameworks (MOFs) have emerged as promising candidates in biomedical applications. Zr-MOFs can be easily synthesized as small-size NPs compatible with intravenous injection, whereas the ease of decorating their external surfaces with functional groups allows for targeted treatment. Despite these benefits, Zr-MOFs suffer degradation and aggregation in real, in vivo conditions, whereas the loaded drugs will suffer the burst effect-i.e., the fast release of drugs in less than 48 h. To tackle these issues, we developed a simple but effective bilayer coating strategy in a generic, two-step process. In this work, bilayer-coated MOF NU-901 remained well dispersed in biologically relevant fluids such as buffers and cell growth media. Additionally, the coating enhances the long-term stability of drug-loaded MOFs in water by simultaneously preventing sustained leakage of the drug and aggregation of the MOF particles. We evaluated our materials for the encapsulation and transport of pemetrexed, the standard-of-care chemotherapy in mesothelioma. The bilayer coating allowed for a slowed release of pemetrexed over 7 days, superior to the typical 48 h release found in bare MOFs. This slow release and the related performance were studied in vitro using both A549 lung cancer and 3T mesothelioma cells. Using high-resolution microscopy, we found the successful uptake of bilayer-coated MOFs by the cells with an accumulation in the lysosomes. The pemetrex-loaded NU-901 was indeed cytotoxic to 3T and A549 cancer cells. Finally, we demonstrated the general approach by extending the coating strategy using two additional lipids and four surfactants. This research highlights how a simple yet effective bilayer coating provides new insights into the design of promising MOF-based drug delivery systems., Competing Interests: The authors declare the following competing financial interest(s): D.F.-J. has commercial interests in Vector Bioscience Cambridge, a spin-out for the commercialization of MOFs in healthcare applications., (© 2024 The Authors. Published by American Chemical Society.)

Published
2024
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46. Single-cell transcriptomic analysis of human pleura reveals stromal heterogeneity and informs in vitro models of mesothelioma.

Author

Obacz J, Valer JA, Nibhani R, Adams TS, Schupp JC, Veale N, Lewis-Wade A, Flint J, Hogan J, Aresu G, Coonar AS, Peryt A, Biffi G, Kaminski N, Francies H, Rassl DM, Garnett MJ, Rintoul RC, and Marciniak SJ

Subjects
Humans, Pleura pathology, Gene Expression Profiling, Mesothelioma genetics, Mesothelioma pathology, Mesothelioma, Malignant pathology, Pleural Neoplasms genetics, Pleural Neoplasms pathology
Abstract

The pleural lining of the thorax regulates local immunity, inflammation and repair. A variety of conditions, both benign and malignant, including pleural mesothelioma, can affect this tissue. A lack of knowledge concerning the mesothelial and stromal cells comprising the pleura has hampered the development of targeted therapies. Here, we present the first comprehensive single-cell transcriptomic atlas of the human parietal pleura and demonstrate its utility in elucidating pleural biology. We confirm the presence of known universal fibroblasts and describe novel, potentially pleural-specific, fibroblast subtypes. We also present transcriptomic characterisation of multiple in vitro models of benign and malignant mesothelial cells, and characterise these through comparison with in vivo transcriptomic data. While bulk pleural transcriptomes have been reported previously, this is the first study to provide resolution at the single-cell level. We expect our pleural cell atlas will prove invaluable to those studying pleural biology and disease. It has already enabled us to shed light on the transdifferentiation of mesothelial cells, allowing us to develop a simple method for prolonging mesothelial cell differentiation in vitro ., Competing Interests: Conflicts of interest: In addition to the funding acknowledged in the support statement, the following conflicts are declared by the authors. J. Obacz reports grants from Victor Dahdaleh Charitable Foundation. A.S. Coonar reports grants from Innovate UK, consultancy for Viderigen, honoraria for lectures from AstraZeneca, book royalties from Springer Nature, payment for expert testimony from Medicolegal reports, leadership or fiduciary roles for Society for Cardiothoracic Surgery of GB and Ireland, and is Chair of the Thoracic Surgery Committee, NHS, National Clinical Lead for NHS England and a Governor of Royal Papworth Hospital. A. Peryt reports lecture honoraria from AstraZeneca, and travel support from Albyn Medical. N. Kaminski is a scientific founder at Thyron, served as a consultant to Biogen Idec, Boehringer Ingelheim, Third Rock, Pliant, Samumed, NuMedii, Theravance, LifeMax, Three Lake Partners, Optikira, AstraZeneca, RohBar, Veracyte, Augmanity, CSL Behring, Galapagos, Gilead, Chiesi, Arrowhead, Sofinnova and Thyron over the last 3 years, reports Equity in Pliant and Thyron, and grants from Veracyte, Boehringer Ingelheim, BMS and Three Lakes Foundation, and non-financial support from MiRagen and Astra Zeneca; N. Kaminski also has the following patents licensed to biotech: New therapies for IPF, New Therapies for ARDS and New Biomarkers in IPF. M.J. Garnett reports consultancy fees from and equity in Mosaic Therapeutics, and has a patent pending for describing suspension organoid cultures. R.C. Rintoul is chief investigator of Mesobank UK and is part funded by Asthma+Lung UK. The remaining authors have no potential conflicts of interest to disclose., (Copyright ©The authors 2024.)

Published
2024
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47. What's new in pleural disease?

Author

Rintoul RC and Marciniak SJ

Subjects
Humans, Pleural Diseases therapy, Empyema, Pleural
Abstract

Competing Interests: Competing interests: None declared.

Published
2023
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48. Cigarette smoke restricts the ability of mesenchymal cells to support lung epithelial organoid formation.

Author

Khedoe PPSJ, van Schadewijk WAAM, Schwiening M, Ng-Blichfeldt JP, Marciniak SJ, Stolk J, Gosens R, and Hiemstra PS

Abstract

Adequate lung epithelial repair relies on supportive interactions within the epithelial niche, including interactions with WNT-responsive fibroblasts. In fibroblasts from patients with chronic obstructive pulmonary disease (COPD) or upon in vitro cigarette smoke exposure, Wnt/β-catenin signalling is distorted, which may affect interactions between epithelial cells and fibroblasts resulting in inadequate lung repair. We hypothesized that cigarette smoke (CS), the main risk factor for COPD, interferes with Wnt/β-catenin signalling in fibroblasts through induction of cellular stress responses, including oxidative- and endoplasmic reticulum (ER) stress, and thereby alters epithelial repair support potential. Therefore, we assessed the effect of CS-exposure and the ER stress inducer Thapsigargin (Tg) on Wnt/β-catenin signalling activation in MRC-5 fibroblasts, and on their ability to support lung epithelial organoid formation. Exposure of MRC-5 cells for 15 min with 5 AU/mL CS extract (CSE), and subsequent 6 h incubation induced oxidative stress ( HMOX1 ). Whereas stimulation with 100 nM Tg increased markers of both the integrated stress response (ISR - GADD34 / PPP1R15A , CHOP ) and the unfolded protein response (UPR - XBP1spl , GADD34/PPP1R15A , CHOP and HSPA5/BIP ), CSE only induced GADD34 / PPP1R15A expression. Strikingly, although treatment of MRC-5 cells with the Wnt activator CHIR99021 upregulated the Wnt/β-catenin target gene AXIN2, this response was diminished upon CSE or Tg pre-exposure, which was confirmed using a Wnt-reporter. Furthermore, pre-exposure of MRC-5 cells to CSE or Tg, restricted their ability to support organoid formation upon co-culture with murine pulmonary EpCam + cells in Matrigel at day 14. This restriction was alleviated by pre-treatment with CHIR99021. We conclude that exposure of MRC-5 cells to CSE increases oxidative stress, GADD34/PPP1R15A expression and impairs their ability to support organoid formation. This inhibitory effect may be restored by activating the Wnt/β-catenin signalling pathway., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The reviewer GT declared a past co-authorship with the authors RG to the handling Editor, (Copyright © 2023 Khedoe, van Schadewijk, Schwiening, Ng-Blichtfeldt, Marciniak, Stolk, Gosens and Hiemstra.)

Published
2023
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49. A novel human fetal lung-derived alveolar organoid model reveals mechanisms of surfactant protein C maturation relevant to interstitial lung disease.

Author

Lim K, Rutherford EN, Sun D, Van den Boomen DJH, Edgar JR, Bang JH, Matesic LE, Lee JH, Lehner PJ, Marciniak SJ, Rawlins EL, and Dickens JA

Abstract

Alveolar type 2 (AT2) cells maintain lung health by acting as stem cells and producing pulmonary surfactant 1-3 . AT2 dysfunction underlies many lung diseases including interstitial lung disease (ILD), in which some inherited forms result from mislocalisation of surfactant protein C (SFTPC) variants 4,5 . Disease modelling and dissection of mechanisms remains challenging due to complexities in deriving and maintaining AT2 cells ex vivo. Here, we describe the development of expandable adult AT2-like organoids derived from human fetal lung which are phenotypically stable, can differentiate into AT1-like cells and are genetically manipulable. We use these organoids to test key effectors of SFTPC maturation identified in a forward genetic screen including the E3 ligase ITCH, demonstrating that their depletion phenocopies the pathological SFTPC redistribution seen for the SFTPC-I73T variant. In summary, we demonstrate the development of a novel alveolar organoid model and use it to identify effectors of SFTPC maturation necessary for AT2 health.

Published
2023
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50. BAP1 Loss Is Associated with Higher ASS1 Expression in Epithelioid Mesothelioma: Implications for Therapeutic Stratification.

Author

Barnett SE, Kenyani J, Tripari M, Butt Z, Grosman R, Querques F, Shaw L, Silva LC, Goate Z, Marciniak SJ, Rassl DM, Jackson R, Lian LY, Szlosarek PW, Sacco JJ, and Coulson JM

Subjects
Humans, Argininosuccinate Synthase genetics, Argininosuccinate Synthase metabolism, Ubiquitin Thiolesterase genetics, Amino Acids, Arginine metabolism, Cell Line, Tumor, Tumor Suppressor Proteins genetics, Mesothelioma, Malignant, Mesothelioma drug therapy, Mesothelioma genetics
Abstract

The nuclear deubiquitylase BRCA1-associated protein 1 (BAP1) is frequently inactivated in malignant pleural mesothelioma (MPM) and germline BAP1 mutation predisposes to cancers including MPM. To explore the influence on cell physiology and drug sensitivity, we sequentially edited a predisposition mutation (w-) and a promoter trap (KO) into human mesothelial cells. BAP1w-/KO MeT5A cells express less BAP1 protein and phenocopy key aspects of BAP1 loss in MPM. Stable isotope labeling with amino acids in cell culture-mass spectrometry revealed evidence of metabolic adaptation, with concomitant alteration of cellular metabolites. In MeT5A, BAP1 deficiency reduces glycolytic enzyme levels but increases enzymes involved in the tricarboxylic acid cycle and anaplerotic pathways. Notably both argininosuccinate synthase 1 (ASS1), essential for cellular synthesis of arginine, and its substrate aspartate, are elevated in BAP1w-/KO MeT5A cells. Likewise, ASS1 expression is higher in BAP1-altered MPM cell lines, and inversely correlates with BAP1 in The Cancer Genome Atlas MESO dataset. Elevated ASS1 is also evident by IHC staining in epithelioid MPM lacking nuclear BAP1 expression, with improved survival among patients with BAP1-negative/ASS1-expressing tumors. Alterations in arginine metabolism may sensitize cells to metabolic drugs and we find that BAP1-negative/ASS1-expressing MPM cell lines are more sensitive to ASS1 inhibition, although not to inhibition of purine synthesis by mizoribine. Importantly, BAP1w-/KO MeT5A become desensitized to arginine deprivation by pegylated arginine deiminase (ADI-PEG20), phenocopying BAP1-negative/ASS1-expressing MPM cell lines., Implications: Our data reveal an interrelationship between BAP1 and arginine metabolism, providing a potential means of identifying patients with epithelioid MPM likely to benefit from ADI-PEG20., (©2023 The Authors; Published by the American Association for Cancer Research.)

Published
2023
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