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1. Author Correction: The NK cell granule protein NKG7 regulates cytotoxic granule exocytosis and inflammation

Author

Ng, Susanna S., De Labastida Rivera, Fabian, Yan, Juming, Corvino, Dillon, Das, Indrajit, Zhang, Ping, Kuns, Rachel, Chauhan, Shashi Bhushan, Hou, Jiajie, Li, Xian-Yang, Frame, Teija C. M., McEnroe, Benjamin A., Moore, Eilish, Na, Jinrui, Engel, Jessica A., Soon, Megan S. F., Singh, Bhawana, Kueh, Andrew J., Herold, Marco J., Montes de Oca, Marcela, Singh, Siddharth Sankar, Bunn, Patrick T., Aguilera, Amy Roman, Casey, Mika, Braun, Matthias, Ghazanfari, Nazanin, Wani, Shivangi, Wang, Yulin, Amante, Fiona H., Edwards, Chelsea L., Haque, Ashraful, Dougall, William C., Singh, Om Prakash, Baxter, Alan G., Teng, Michele W. L., Loukas, Alex, Daly, Norelle L., Cloonan, Nicole, Degli-Esposti, Mariapia A., Uzonna, Jude, Heath, William R., Bald, Tobias, Tey, Siok-Keen, Nakamura, Kyohei, Hill, Geoffrey R., Kumar, Rajiv, Sundar, Shyam, Smyth, Mark J., and Engwerda, Christian R.

Published
2024
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2. Targeting DNA Damage Response and Replication Stress in Pancreatic Cancer

Author

Allison, Sarah, Bailey, Peter J., Bailey, Ulla-Maja, Biankin, Andrew V., Beraldi, Dario, Brunton, Holly, Caligiuri, Giuseppina, Cameron, Euan, Chang, David K., Cooke, Susanna L., Cunningham, Richard, Dreyer, Stephan, Grimwood, Paul, Kelly, Shane, Lampraki, Eirini-Maria, Marshall, John, Martin, Sancha, McDade, Brian, McElroy, Daniel, Musgrove, Elizabeth A., Nourse, Craig, Paulus-Hock, Viola, Ramsay, Donna, Upstill-Goddard, Rosie, Wright, Derek, Jones, Marc D., Evers, Lisa, Rebus, Selma, Rahib, Lola, Serrels, Bryan, Hair, Jane, Jamieson, Nigel B., McKay, Colin J., Westwood, Paul, Williams, Nicola, Duthie, Fraser, Johns, Amber L., Mawson, Amanda, Scarlett, Christopher J., Brancato, Mary-Anne L., Rowe, Sarah J., Simpson, Skye H., Martyn-Smith, Mona, Thomas, Michelle T., Chantrill, Lorraine A., Chin, Venessa T., Chou, Angela, Cowley, Mark J., Humphris, Jeremy L., Mead, R. Scott, Nagrial, Adnan M., Pajic, Marina, Pettit, Jessica, Pinese, Mark, Rooman, Ilse, Wu, Jianmin, Tao, Jiang, DiPietro, Renee, Watson, Clare, Steinmann, Angela, Lee, Hong Ching, Wong, Rachel, Pinho, Andreia V., Giry-Laterriere, Marc, Daly, Roger J., Sutherland, Robert L., Grimmond, Sean M., Waddell, Nicola, Kassahn, Karin S., Miller, David K., Wilson, Peter J., Patch, Ann-Marie, Song, Sarah, Harliwong, Ivon, Idrisoglu, Senel, Nourbakhsh, Ehsan, Manning, Suzanne, Wani, Shivangi, Gongora, Milena, Anderson, Matthew, Holmes, Oliver, Leonard, Conrad, Taylor, Darrin, Wood, Scott, Xu, Christina, Nones, Katia, Fink, J. Lynn, Christ, Angelika, Bruxner, Tim, Cloonan, Nicole, Newell, Felicity, Pearson, John V., Bailey, Peter, Quinn, Michael, Nagaraj, Shivashankar, Kazakoff, Stephen, Waddell, Nick, Krisnan, Keerthana, Quek, Kelly, Wood, David, Samra, Jaswinder S., Gill, Anthony J., Pavlakis, Nick, Guminski, Alex, Toon, Christopher, Asghari, Ray, Merrett, Neil D., Pavey, Darren, Das, Amitabha, Cosman, Peter H., Ismail, Kasim, O’Connnor, Chelsie, Lam, Vincent W., McLeod, Duncan, Pleass, Henry C., Richardson, Arthur, James, Virginia, Kench, James G., Cooper, Caroline L., Joseph, David, Sandroussi, Charbel, Crawford, Michael, Gallagher, James, Texler, Michael, Forest, Cindy, Laycock, Andrew, Epari, Krishna P., Ballal, Mo, Fletcher, David R., Mukhedkar, Sanjay, Spry, Nigel A., DeBoer, Bastiaan, Chai, Ming, Zeps, Nikolajs, Beilin, Maria, Feeney, Kynan, Nguyen, Nan Q., Ruszkiewicz, Andrew R., Worthley, Chris, Tan, Chuan P., Debrencini, Tamara, Chen, John, Brooke-Smith, Mark E., Papangelis, Virginia, Tang, Henry, Barbour, Andrew P., Clouston, Andrew D., Martin, Patrick, O’Rourke, Thomas J., Chiang, Amy, Fawcett, Jonathan W., Slater, Kellee, Yeung, Shinn, Hatzifotis, Michael, Hodgkinson, Peter, Christophi, Christopher, Nikfarjam, Mehrdad, Mountain, Angela, Biobank, Victorian Cancer, Eshleman, James R., Hruban, Ralph H., Maitra, Anirban, Iacobuzio-Donahue, Christine A., Schulick, Richard D., Wolfgang, Christopher L., Morgan, Richard A., Hodgin, Mary, Scarpa, Aldo, Lawlor, Rita T., Beghelli, Stefania, Corbo, Vincenzo, Scardoni, Maria, Bassi, Claudio, Tempero, Margaret A., Graham, Janet S., Dreyer, Stephan B., Paris, Clara, Dray, Eloise, Plenker, Dennis, Galluzzo, Zachary, Tesson, Mathias, Jones, Marc, Moran-Jones, Kim, Wright, Derek W., Oien, Karin, McGregor, Grant A., Gulati, Aditi, Brough, Rachel, Bajrami, Ilirjana, Pettitt, Stephan, Dziubinski, Michele L., Candido, Juliana, Balkwill, Frances, Barry, Simon T., Grützmann, Robert, Johns, Amber, Froeling, Fieke E.M., Beer, Phillip, Petersen, Gloria M., Ashworth, Alan, Frame, Margaret C., Crawford, Howard C., Simeone, Diane M., Lord, Chris, Mukhopadhyay, Debabrata, Pilarsky, Christian, Tuveson, David A., Morton, Jennifer P., and Sansom, Owen J.

Published
2021
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3. HNF4A and GATA6 Loss Reveals Therapeutically Actionable Subtypes in Pancreatic Cancer

Author

Allison, Sarah, Biankin, Andrew V., Chang, David K., Cooke, Susanna L., Dreyer, Stephan, Grimwood, Paul, Kelly, Shane, Marshall, John, McDade, Brian, McElroy, Daniel, Ramsay, Donna, Upstill-Goddard, Rosie, Rebus, Selma, Hair, Jane, Jamieson, Nigel B., McKay, Colin J., Westwood, Paul, Williams, Nicola, Duthie, Fraser, Johns, Amber L., Mawson, Amanda, Scarlett, Christopher J., Brancato, Mary-Anne L., Rowe, Sarah J., Simpson, Skye H., Martyn-Smith, Mona, Thomas, Michelle T., Chantrill, Lorraine A., Chin, Venessa T., Chou, Angela, Cowley, Mark J., Humphris, Jeremy L., Mead, R. Scott, Nagrial, Adnan M., Pajic, Marina, Pettit, Jessica, Pinese, Mark, Rooman, Ilse, Wu, Jianmin, Tao, Jiang, DiPietro, Renee, Watson, Clare, Steinmann, Angela, Lee, Hong Ching, Wong, Rachel, Pinho, Andreia V., Giry-Laterriere, Marc, Daly, Roger J., Musgrove, Elizabeth A., Sutherland, Robert L., Grimmond, Sean M., Waddell, Nicola, Kassahn, Karin S., Miller, David K., Wilson, Peter J., Patch, Ann-Marie, Song, Sarah, Harliwong, Ivon, Idrisoglu, Senel, Nourbakhsh, Ehsan, Manning, Suzanne, Wani, Shivangi, Gongora, Milena, Anderson, Matthew, Holmes, Oliver, Leonard, Conrad, Taylor, Darrin, Wood, Scott, Xu, Christina, Nones, Katia, Fink, J. Lynn, Christ, Angelika, Bruxner, Tim, Cloonan, Nicole, Newell, Felicity, Pearson, John V., Quinn, Michael, Nagaraj, Shivashankar, Kazakoff, Stephen, Waddell, Nick, Krisnan, Keerthana, Quek, Kelly, Wood, David, Samra, Jaswinder S., Gill, Anthony J., Pavlakis, Nick, Guminski, Alex, Toon, Christopher, Asghari, Ray, Merrett, Neil D., Pavey, Darren, Das, Amitabha, Cosman, Peter H., Ismail, Kasim, O’Connnor, Chelsie, Lam, Vincent W., McLeod, Duncan, Pleass, Henry C., Richardson, Arthur, James, Virginia, Kench, James G., Cooper, Caroline L., Joseph, David, Sandroussi, Charbel, Crawford, Michael, Gallagher, James, Texler, Michael, Forest, Cindy, Laycock, Andrew, Epari, Krishna P., Ballal, Mo, Fletcher, David R., Mukhedkar, Sanjay, Spry, Nigel A., DeBoer, Bastiaan, Chai, Ming, Zeps, Nikolajs, Beilin, Maria, Feeney, Kynan, Nguyen, Nan Q., Ruszkiewicz, Andrew R., Worthley, Chris, Tan, Chuan P., Debrencini, Tamara, Chen, John, Brooke-Smith, Mark E., Papangelis, Virginia, Tang, Henry, Barbour, Andrew P., Clouston, Andrew D., Martin, Patrick, O’Rourke, Thomas J., Chiang, Amy, Fawcett, Jonathan W., Slater, Kellee, Yeung, Shinn, Hatzifotis, Michael, Hodgkinson, Peter, Christophi, Christopher, Nikfarjam, Mehrdad, Mountain, Angela, Eshleman, James R., Hruban, Ralph H., Maitra, Anirban, Iacobuzio-Donahue, Christine A., Schulick, Richard D., Wolfgang, Christopher L., Morgan, Richard A., Hodgin, Mary, Scarpa, Aldo, Lawlor, Rita T., Beghelli, Stefania, Corbo, Vincenzo, Scardoni, Maria, Bassi, Claudio, Tempero, Margaret A., Nourse, Craig, Graham, Janet S., Brunton, Holly, Caligiuri, Giuseppina, Cunningham, Richard, Bailey, Ulla-Maja, Garner, Ian M., Jones, Marc, Moran-Jones, Kim, Wright, Derek W., Paulus-Hock, Viola, Nixon, Colin, Thomson, Gemma, McGregor, Grant A., Evers, Lisa, Gulati, Aditi, Brough, Rachel, Bajrami, Ilirjana, Pettitt, Stephen J., Dziubinski, Michele L., Barry, Simon T., Grützmann, Robert, Brown, Robert, Curry, Edward, Petersen, Gloria M., Shanks, Emma, Ashworth, Alan, Crawford, Howard C., Simeone, Diane M., Froeling, Fieke E.M., Lord, Christopher J., Mukhopadhyay, Debabrata, Pilarsky, Christian, Grimmond, Sean E., Morton, Jennifer P., Sansom, Owen J., and Bailey, Peter J.

Published
2020
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4. The NK cell granule protein NKG7 regulates cytotoxic granule exocytosis and inflammation

Author

Ng, Susanna S., De Labastida Rivera, Fabian, Yan, Juming, Corvino, Dillon, Das, Indrajit, Zhang, Ping, Kuns, Rachel, Chauhan, Shashi Bhushan, Hou, Jiajie, Li, Xian-Yang, Frame, Teija C. M., McEnroe, Benjamin A., Moore, Eilish, Na, Jinrui, Engel, Jessica A., Soon, Megan S. F., Singh, Bhawana, Kueh, Andrew J., Herold, Marco J., Montes de Oca, Marcela, Singh, Siddharth Sankar, Bunn, Patrick T., Aguilera, Amy Roman, Casey, Mika, Braun, Matthias, Ghazanfari, Nazanin, Wani, Shivangi, Wang, Yulin, Amante, Fiona H., Edwards, Chelsea L., Haque, Ashraful, Dougall, William C., Singh, Om Prakash, Baxter, Alan G., Teng, Michele W. L., Loukas, Alex, Daly, Norelle L., Cloonan, Nicole, Degli-Esposti, Mariapia A., Uzonna, Jude, Heath, William R., Bald, Tobias, Tey, Siok-Keen, Nakamura, Kyohei, Hill, Geoffrey R., Kumar, Rajiv, Sundar, Shyam, Smyth, Mark J., and Engwerda, Christian R.

Published
2020
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5. Whole genomes redefine the mutational landscape of pancreatic cancer

Author

Biankin, Andrew V, Johns, Amber L, Mawson, Amanda, Chang, David K, Scarlett, Christopher J, Brancato, Mary-Anne L, Rowe, Sarah J, Simpson, Skye H, Martyn-Smith, Mona, Thomas, Michelle T, Chantrill, Lorraine A, Chin, Venessa T, Chou, Angela, Cowley, Mark J, Humphris, Jeremy L, Jones, Marc D, Scott Mead, R, Nagrial, Adnan M, Pajic, Marina, Pettit, Jessica, Pinese, Mark, Rooman, Ilse, Wu, Jianmin, Tao, Jiang, DiPietro, Renee, Watson, Clare, Steinmann, Angela, Ching Lee, Hong, Wong, Rachel, Pinho, Andreia V, Giry-Laterriere, Marc, Daly, Roger J, Musgrove, Elizabeth A, Sutherland, Robert L, Grimmond, Sean M, Waddell, Nicola, Kassahn, Karin S, Miller, David K, Wilson, Peter J, Patch, Ann-Marie, Song, Sarah, Harliwong, Ivon, Idrisoglu, Senel, Nourse, Craig, Nourbakhsh, Ehsan, Manning, Suzanne, Wani, Shivangi, Gongora, Milena, Anderson, Matthew, Holmes, Oliver, Leonard, Conrad, Taylor, Darrin, Wood, Scott, Xu, Christina, Nones, Katia, Lynn Fink, J, Christ, Angelika, Bruxner, Tim, Cloonan, Nicole, Newell, Felicity, Pearson, John V, Bailey, Peter, Quinn, Michael, Nagaraj, Shivashankar, Kazakoff, Stephen, Waddell, Nick, Krisnan, Keerthana, Quek, Kelly, Wood, David, Fadlullah, Muhammad ZH, Samra, Jaswinder S, Gill, Anthony J, Pavlakis, Nick, Guminski, Alex, Toon, Christopher, Asghari, Ray, Merrett, Neil D, Pavey, Darren, Das, Amitabha, Cosman, Peter H, Ismail, Kasim, O’Connnor, Chelsie, Lam Duncan McLeod, Vincent W, Pleass, Henry C, Richardson, Arthur, James, Virginia, Kench, James G, Cooper, Caroline L, Joseph, David, Sandroussi, Charbel, Crawford, Michael, Gallagher, James, Texler, Michael, Forest, Cindy, Laycock, Andrew, Epari, Krishna P, Ballal, Mo, Fletcher, David R, Mukhedkar, Sanjay, and Spry, Nigel A

Subjects
Cancer, Human Genome, Pancreatic Cancer, Digestive Diseases, Genetics, Rare Diseases, 2.1 Biological and endogenous factors, Aetiology, Adenocarcinoma, Animals, Carcinoma, Pancreatic Ductal, DNA Mutational Analysis, DNA Repair, Female, Genes, BRCA1, Genes, BRCA2, Genetic Markers, Genome, Human, Genomic Instability, Genomics, Genotype, Humans, Mice, Mutation, Pancreatic Neoplasms, Platinum, Point Mutation, Poly(ADP-ribose) Polymerase Inhibitors, Xenograft Model Antitumor Assays, Australian Pancreatic Cancer Genome Initiative, General Science & Technology
Abstract

Pancreatic cancer remains one of the most lethal of malignancies and a major health burden. We performed whole-genome sequencing and copy number variation (CNV) analysis of 100 pancreatic ductal adenocarcinomas (PDACs). Chromosomal rearrangements leading to gene disruption were prevalent, affecting genes known to be important in pancreatic cancer (TP53, SMAD4, CDKN2A, ARID1A and ROBO2) and new candidate drivers of pancreatic carcinogenesis (KDM6A and PREX2). Patterns of structural variation (variation in chromosomal structure) classified PDACs into 4 subtypes with potential clinical utility: the subtypes were termed stable, locally rearranged, scattered and unstable. A significant proportion harboured focal amplifications, many of which contained druggable oncogenes (ERBB2, MET, FGFR1, CDK6, PIK3R3 and PIK3CA), but at low individual patient prevalence. Genomic instability co-segregated with inactivation of DNA maintenance genes (BRCA1, BRCA2 or PALB2) and a mutational signature of DNA damage repair deficiency. Of 8 patients who received platinum therapy, 4 of 5 individuals with these measures of defective DNA maintenance responded.

Published
2015

8. Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes.

Author

Biankin, Andrew, Waddell, Nicola, Kassahn, Karin, Gingras, Marie-Claude, Muthuswamy, Lakshmi, Johns, Amber, Miller, David, Wilson, Peter, Patch, Ann-Marie, Wu, Jianmin, Chang, David, Cowley, Mark, Gardiner, Brooke, Song, Sarah, Harliwong, Ivon, Idrisoglu, Senel, Nourse, Craig, Nourbakhsh, Ehsan, Manning, Suzanne, Wani, Shivangi, Gongora, Milena, Pajic, Marina, Scarlett, Christopher, Gill, Anthony, Pinho, Andreia, Rooman, Ilse, Anderson, Matthew, Holmes, Oliver, Leonard, Conrad, Taylor, Darrin, Wood, Scott, Xu, Qinying, Nones, Katia, Fink, J, Christ, Angelika, Bruxner, Tim, Cloonan, Nicole, Kolle, Gabriel, Newell, Felicity, Pinese, Mark, Mead, R, Humphris, Jeremy, Kaplan, Warren, Jones, Marc, Colvin, Emily, Nagrial, Adnan, Humphrey, Emily, Chou, Angela, Chin, Venessa, Chantrill, Lorraine, Mawson, Amanda, Samra, Jaswinder, Kench, James, Lovell, Jessica, Daly, Roger, Merrett, Neil, Toon, Christopher, Epari, Krishna, Nguyen, Nam, Barbour, Andrew, Zeps, Nikolajs, Kakkar, Nipun, Zhao, Fengmei, Wu, Yuan, Wang, Min, Muzny, Donna, Fisher, William, Brunicardi, F, Hodges, Sally, Reid, Jeffrey, Drummond, Jennifer, Chang, Kyle, Han, Yi, Lewis, Lora, Dinh, Huyen, Buhay, Christian, Beck, Timothy, Timms, Lee, Sam, Michelle, Begley, Kimberly, Brown, Andrew, Pai, Deepa, Panchal, Ami, Buchner, Nicholas, De Borja, Richard, Denroche, Robert, Yung, Christina, Serra, Stefano, Onetto, Nicole, Mukhopadhyay, Debabrata, Tsao, Ming-Sound, Shaw, Patricia, Petersen, Gloria, Gallinger, Steven, Hruban, Ralph, Maitra, Anirban, Iacobuzio-Donahue, Christine, Schulick, Richard, Wolfgang, Christopher, and Morgan, Richard

Subjects
Animals, Axons, Carcinoma, Pancreatic Ductal, Gene Dosage, Gene Expression Regulation, Neoplastic, Genome, Humans, Kaplan-Meier Estimate, Mice, Mutation, Pancreatic Neoplasms, Proteins, Signal Transduction
Abstract

Pancreatic cancer is a highly lethal malignancy with few effective therapies. We performed exome sequencing and copy number analysis to define genomic aberrations in a prospectively accrued clinical cohort (n = 142) of early (stage I and II) sporadic pancreatic ductal adenocarcinoma. Detailed analysis of 99 informative tumours identified substantial heterogeneity with 2,016 non-silent mutations and 1,628 copy-number variations. We define 16 significantly mutated genes, reaffirming known mutations (KRAS, TP53, CDKN2A, SMAD4, MLL3, TGFBR2, ARID1A and SF3B1), and uncover novel mutated genes including additional genes involved in chromatin modification (EPC1 and ARID2), DNA damage repair (ATM) and other mechanisms (ZIM2, MAP2K4, NALCN, SLC16A4 and MAGEA6). Integrative analysis with in vitro functional data and animal models provided supportive evidence for potential roles for these genetic aberrations in carcinogenesis. Pathway-based analysis of recurrently mutated genes recapitulated clustering in core signalling pathways in pancreatic ductal adenocarcinoma, and identified new mutated genes in each pathway. We also identified frequent and diverse somatic aberrations in genes described traditionally as embryonic regulators of axon guidance, particularly SLIT/ROBO signalling, which was also evident in murine Sleeping Beauty transposon-mediated somatic mutagenesis models of pancreatic cancer, providing further supportive evidence for the potential involvement of axon guidance genes in pancreatic carcinogenesis.

Published
2012

9. Long Noncoding RNAs CUPID1 and CUPID2 Mediate Breast Cancer Risk at 11q13 by Modulating the Response to DNA Damage

Author

Betts, Joshua A., Moradi Marjaneh, Mahdi, Al-Ejeh, Fares, Lim, Yi Chieh, Shi, Wei, Sivakumaran, Haran, Tropée, Romain, Patch, Ann-Marie, Clark, Michael B., Bartonicek, Nenad, Wiegmans, Adrian P., Hillman, Kristine M., Kaufmann, Susanne, Bain, Amanda L., Gloss, Brian S., Crawford, Joanna, Kazakoff, Stephen, Wani, Shivangi, Wen, Shu W., Day, Bryan, Möller, Andreas, Cloonan, Nicole, Pearson, John, Brown, Melissa A., Mercer, Timothy R., Waddell, Nicola, Khanna, Kum Kum, Dray, Eloise, Dinger, Marcel E., Edwards, Stacey L., and French, Juliet D.

Published
2017
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11. Genomic analyses identify molecular subtypes of pancreatic cancer

Author

Bailey, Peter, Chang, David K., Nones, Katia, Johns, Amber L., Patch, Ann-Marie, Gingras, Marie-Claude, Miller, David K., Christ, Angelika N., Bruxner, Tim J. C., Quinn, Michael C., Nourse, Craig, Murtaugh, L. Charles, Harliwong, Ivon, Idrisoglu, Senel, Manning, Suzanne, Nourbakhsh, Ehsan, Wani, Shivangi, Fink, Lynn, Holmes, Oliver, Chin, Venessa, Anderson, Matthew J., Kazakoff, Stephen, Leonard, Conrad, Newell, Felicity, Waddell, Nick, Wood, Scott, Xu, Qinying, Wilson, Peter J., Cloonan, Nicole, Kassahn, Karin S., Taylor, Darrin, Quek, Kelly, Robertson, Alan, Pantano, Lorena, Mincarelli, Laura, Sanchez, Luis N., Evers, Lisa, Wu, Jianmin, Pinese, Mark, Cowley, Mark J., Jones, Marc D., Colvin, Emily K., Nagrial, Adnan M., Humphrey, Emily S., Chantrill, Lorraine A., Mawson, Amanda, Humphris, Jeremy, Chou, Angela, Pajic, Marina, Scarlett, Christopher J., Pinho, Andreia V., Giry-Laterriere, Marc, Rooman, Ilse, Samra, Jaswinder S., Kench, James G., Lovell, Jessica A., Merrett, Neil D., Toon, Christopher W., Epari, Krishna, Nguyen, Nam Q., Barbour, Andrew, Zeps, Nikolajs, Moran-Jones, Kim, Jamieson, Nigel B., Graham, Janet S., Duthie, Fraser, Oien, Karin, Hair, Jane, Grützmann, Robert, Maitra, Anirban, Iacobuzio-Donahue, Christine A., Wolfgang, Christopher L., Morgan, Richard A., Lawlor, Rita T., Corbo, Vincenzo, Bassi, Claudio, Rusev, Borislav, Capelli, Paola, Salvia, Roberto, Tortora, Giampaolo, Mukhopadhyay, Debabrata, Petersen, Gloria M., Munzy, Donna M., Fisher, William E., Karim, Saadia A., Eshleman, James R., Hruban, Ralph H., Pilarsky, Christian, Morton, Jennifer P., Sansom, Owen J., Scarpa, Aldo, Musgrove, Elizabeth A., Bailey, Ulla-Maja Hagbo, Hofmann, Oliver, Sutherland, Robert L., Wheeler, David A., Gill, Anthony J., Gibbs, Richard A., Pearson, John V., Waddell, Nicola, Biankin, Andrew V., and Grimmond, Sean M.

Published
2016
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12. Integrated genomic and transcriptomic analysis of human brain metastases identifies alterations of potential clinical significance

Author

Saunus, Jodi M, Quinn, Michael CJ, Patch, Ann-Marie, Pearson, John V, Bailey, Peter J, Nones, Katia, McCart Reed, Amy E, Miller, David, Wilson, Peter J, Al-Ejeh, Fares, Mariasegaram, Mythily, Lau, Queenie, Withers, Teresa, Jeffree, Rosalind L, Reid, Lynne E, Da Silva, Leonard, Matsika, Admire, Niland, Colleen M, Cummings, Margaret C, Bruxner, Timothy JC, Christ, Angelika N, Harliwong, Ivon, Idrisoglu, Senel, Manning, Suzanne, Nourse, Craig, Nourbakhsh, Ehsan, Wani, Shivangi, Anderson, Matthew J, Fink, Lynn J, Holmes, Oliver, Kazakoff, Stephen, Leonard, Conrad, Newell, Felicity, Taylor, Darrin, Waddell, Nick, Wood, Scott, Xu, Qinying, Kassahn, Karin S, Narayanan, Vairavan, Taib, Nur Aishah, Teo, Soo-Hwang, Chow, Yock Ping, kConFab, Jat, Parmjit S, Brandner, Sebastian, Flanagan, Adrienne M, Khanna, Kum Kum, Chenevix-Trench, Georgia, Grimmond, Sean M, Simpson, Peter T, Waddell, Nicola, and Lakhani, Sunil R

Published
2015
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13. Whole genomes redefine the mutational landscape of pancreatic cancer

Author

Waddell, Nicola, Pajic, Marina, Patch, Ann-Marie, Chang, David K., Kassahn, Karin S., Bailey, Peter, Johns, Amber L., Miller, David, Nones, Katia, Quek, Kelly, Quinn, Michael C. J., Robertson, Alan J., Fadlullah, Muhammad Z. H., Bruxner, Tim J. C., Christ, Angelika N., Harliwong, Ivon, Idrisoglu, Senel, Manning, Suzanne, Nourse, Craig, Nourbakhsh, Ehsan, Wani, Shivangi, Wilson, Peter J., Markham, Emma, Cloonan, Nicole, Anderson, Matthew J., Fink, Lynn J., Holmes, Oliver, Kazakoff, Stephen H., Leonard, Conrad, Newell, Felicity, Poudel, Barsha, Song, Sarah, Taylor, Darrin, Waddell, Nick, Wood, Scott, Xu, Qinying, Wu, Jianmin, Pinese, Mark, Cowley, Mark J., Lee, Hong C., Jones, Marc D., Nagrial, Adnan M., Humphris, Jeremy, Chantrill, Lorraine A., Chin, Venessa, Steinmann, Angela M., Mawson, Amanda, Humphrey, Emily S., Colvin, Emily K., Chou, Angela, Scarlett, Christopher J., Pinho, Andreia V., Giry-Laterriere, Marc, Rooman, Ilse, Samra, Jaswinder S., Kench, James G., Pettitt, Jessica A., Merrett, Neil D., Toon, Christopher, Epari, Krishna, Nguyen, Nam Q., Barbour, Andrew, Zeps, Nikolajs, Jamieson, Nigel B., Graham, Janet S., Niclou, Simone P., Bjerkvig, Rolf, Grützmann, Robert, Aust, Daniela, Hruban, Ralph H., Maitra, Anirban, Iacobuzio-Donahue, Christine A., Wolfgang, Christopher L., Morgan, Richard A., Lawlor, Rita T., Corbo, Vincenzo, Bassi, Claudio, Falconi, Massimo, Zamboni, Giuseppe, Tortora, Giampaolo, Tempero, Margaret A., Gill, Anthony J., Eshleman, James R., Pilarsky, Christian, Scarpa, Aldo, Musgrove, Elizabeth A., Pearson, John V., Biankin, Andrew V., Grimmond, Sean M., Brancato, Mary-Anne L., Rowe, Sarah J., Simpson, Skye H., Martyn-Smith, Mona, Thomas, Michelle T., Chin, Venessa T., Humphris, Jeremy L., Mead, Scott R., Pettit, Jessica, Tao, Jiang, DiPietro, Renee, Watson, Clare, Steinmann, Angela, Lee, Hong Ching, Wong, Rachel, Daly, Roger J., Sutherland, Robert L., Miller, David K., Gongora, Milena, Anderson, Matthew, Xu, Christina, Christ, Angelika, Bruxner, Tim, Quinn, Michael, Nagaraj, Shivashankar, Kazakoff, Stephen, Krisnan, Keerthana, Wood, David, Pavlakis, Nick, Guminski, Alex, Asghari, Ray, Pavey, Darren, Das, Amitabha, Cosman, Peter H., Ismail, Kasim, OʼConnnor, Chelsie, Lam Duncan McLeod, Vincent W., Pleass, Henry C., Richardson, Arthur, James, Virginia, Cooper, Caroline L., Joseph, David, Sandroussi, Charbel, Crawford, Michael, Gallagher, James, Texler, Michael, Forest, Cindy, Laycock, Andrew, Epari, Krishna P., Ballal, Mo, Fletcher, David R., Mukhedkar, Sanjay, Spry, Nigel A., DeBoer, Bastiaan, Chai, Ming, Beilin, Maria, Feeney, Kynan, Nguyen, Nan Q., Ruszkiewicz, Andrew R., Worthley, Chris, Tan, Chuan P., Debrencini, Tamara, Chen, John, Brooke-Smith, Mark E., Papangelis, Virginia, Tang, Henry, Barbour, Andrew P., Clouston, Andrew D., Martin, Patrick, OʼRourke, Thomas J., Chiang, Amy, Fawcett, Jonathan W., Slater, Kellee, Yeung, Shinn, Hatzifotis, Michael, Hodgkinson, Peter, Christophi, Christopher, Nikfarjam, Mehrdad, Mountain, Angela, Schulick, Richard D., Hodgin, Mary, Beghelli, Stefania, Scardoni, Maria, Oien, Karen, and Hair, Jane

Published
2015
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14. Caveolin‐1‐driven membrane remodelling regulates hnRNPK‐mediated exosomal microRNA sorting in cancer

Author

Robinson, Harley, primary, Ruelcke, Jayde E., additional, Lewis, Amanda, additional, Bond, Charles S., additional, Fox, Archa H., additional, Bharti, Vandhana, additional, Wani, Shivangi, additional, Cloonan, Nicole, additional, Lai, Andrew, additional, Margolin, David, additional, Li, Li, additional, Salomon, Carlos, additional, Richards, Renée S., additional, Farrell, Aine, additional, Gardiner, Robert A., additional, Parton, Robert G., additional, Cristino, Alexandre S., additional, and Hill, Michelle M., additional

Published
2021
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15. The deubiquitinase USP9X suppresses pancreatic ductal adenocarcinoma

Author

Pérez-Mancera, Pedro A., Rust, Alistair G., van der Weyden, Louise, Kristiansen, Glen, Li, Allen, Sarver, Aaron L., Silverstein, Kevin A. T., Grützmann, Robert, Aust, Daniela, Rümmele, Petra, Knösel, Thomas, Herd, Colin, Stemple, Derek L., Kettleborough, Ross, Brosnan, Jacqueline A., Li, Ang, Morgan, Richard, Knight, Spencer, Yu, Jun, Stegeman, Shane, Collier, Lara S., ten Hoeve, Jelle J., de Ridder, Jeroen, Klein, Alison P., Goggins, Michael, Hruban, Ralph H., Chang, David K., Biankin, Andrew V., Grimmond, Sean M., Johns, Amber L., Mawson, Amanda, Brancato, Mary-Anne L., Rowe, Sarah J., Simpson, Skye L., Martyn-Smith, Mona, Chantrill, Lorraine A., Chin, Venessa T., Chou, Angela, Cowley, Mark J., Humphris, Jeremy L., Jones, Marc D., Mead, Scott R., Nagrial, Adnan M., Pajic, Marina, Pettit, Jessica, Pinese, Mark, Rooman, Ilse, Wu, Jianmin, Daly, Roger J., Musgrove, Elizabeth A., Sutherland, Robert L., Waddell, Nicola, Kassahn, Karin S., Miller, David K., Wilson, Peter J., Patch, Ann-Marie, Song, Sarah, Harliwong, Ivon, Idrisoglu, Senel, Nourse, Craig, Nourbakhsh, Ehsan, Manning, Suzanne, Wani, Shivangi, Gongora, Milena, Anderson, Matthew, Holmes, Oliver, Leonard, Conrad, Taylor, Darrin, Wood, Scott, Xu, Christina, Nones, Katia, Fink, Lynn J., Christ, Angelika, Bruxner, Tim, Cloonan, Nicole, Newell, Felicity, Pearson, John V., Samra, Jaswinder S., Gill, Anthony J., Pavlakis, Nick, Guminski, Alex, Toon, Christopher, Blankin, Andrew V., Asghari, Ray, Merrett, Neil D., Pavey, Darren A., Das, Amithabad, Cosman, Peter H., Ismail, Kasim, O’Connor, Chelsie, Lam, Vincent W., McLeod, Duncan, Pleass, Henry C., James, Virginia, Kench, James G., Cooper, Caroline L., Joseph, David, Sandroussi, Charbel, Crawford, Michael, Texler, Michael, Forrest, Cindy, Laycock, Andrew, Epari, Krishna P., Ballal, Mo, Fletcher, David R., Mukhedkar, Sanjay, Spry, Nigel A., DeBoer, Bastiaan, Chai, Ming, Feeney, Kynan, Zeps, Nikolajs, Beilin, Maria, Nguyen, Nam Q., Ruszkiewicz, Andrew R., Worthley, Chris, Tan, Chuan P., Debrencini, Tamara, Chen, John, Brooke-Smith, Mark E., Papangelis, Virginia, Tang, Henry, Barbour, Andrew P., Clouston, Andrew D., Martin, Patrick, O’Rourke, Thomas J., Chiang, Amy, Fawcett, Jonathan W., Slater, Kellee, Yeung, Shinn, Hatzifotis, Michael, Hodgkinson, Peter, Christophi, Christopher, Nikfarjam, Mehrdad, Biobank, Victorian Cancer, Eshleman, James R., Maitra, Anirban, Iacobuzio-Donahue, Christine A., Schulick, Richard D., Wolfgang, Christopher L., Morgan, Richard A., Lawlor, Rita T., Beghelli, Stefania, Corbo, Vincenzo, Scardoni, Maria, Bassi, Claudio, Tempero, Margaret A., Wessels, Lodewyk F. A., Wood, Stephen A., Pilarsky, Christian, Largaespada, David A., Adams, David J., and Tuveson, David A.

Published
2012
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16. Targeting DNA Damage Response and Replication Stress in Pancreatic Cancer

Author

Dreyer, Stephan B., primary, Upstill-Goddard, Rosie, additional, Paulus-Hock, Viola, additional, Paris, Clara, additional, Lampraki, Eirini-Maria, additional, Dray, Eloise, additional, Serrels, Bryan, additional, Caligiuri, Giuseppina, additional, Rebus, Selma, additional, Plenker, Dennis, additional, Galluzzo, Zachary, additional, Brunton, Holly, additional, Cunningham, Richard, additional, Tesson, Mathias, additional, Nourse, Craig, additional, Bailey, Ulla-Maja, additional, Jones, Marc, additional, Moran-Jones, Kim, additional, Wright, Derek W., additional, Duthie, Fraser, additional, Oien, Karin, additional, Evers, Lisa, additional, McKay, Colin J., additional, McGregor, Grant A., additional, Gulati, Aditi, additional, Brough, Rachel, additional, Bajrami, Ilirjana, additional, Pettitt, Stephan, additional, Dziubinski, Michele L., additional, Candido, Juliana, additional, Balkwill, Frances, additional, Barry, Simon T., additional, Grützmann, Robert, additional, Rahib, Lola, additional, Johns, Amber, additional, Pajic, Marina, additional, Froeling, Fieke E.M., additional, Beer, Phillip, additional, Musgrove, Elizabeth A., additional, Petersen, Gloria M., additional, Ashworth, Alan, additional, Frame, Margaret C., additional, Crawford, Howard C., additional, Simeone, Diane M., additional, Lord, Chris, additional, Mukhopadhyay, Debabrata, additional, Pilarsky, Christian, additional, Tuveson, David A., additional, Cooke, Susanna L., additional, Jamieson, Nigel B., additional, Morton, Jennifer P., additional, Sansom, Owen J., additional, Bailey, Peter J., additional, Biankin, Andrew V., additional, Chang, David K., additional, Allison, Sarah, additional, Beraldi, Dario, additional, Cameron, Euan, additional, Dreyer, Stephan, additional, Grimwood, Paul, additional, Kelly, Shane, additional, Marshall, John, additional, Martin, Sancha, additional, McDade, Brian, additional, McElroy, Daniel, additional, Ramsay, Donna, additional, Wright, Derek, additional, Jones, Marc D., additional, Hair, Jane, additional, Westwood, Paul, additional, Williams, Nicola, additional, Johns, Amber L., additional, Mawson, Amanda, additional, Scarlett, Christopher J., additional, Brancato, Mary-Anne L., additional, Rowe, Sarah J., additional, Simpson, Skye H., additional, Martyn-Smith, Mona, additional, Thomas, Michelle T., additional, Chantrill, Lorraine A., additional, Chin, Venessa T., additional, Chou, Angela, additional, Cowley, Mark J., additional, Humphris, Jeremy L., additional, Mead, R. Scott, additional, Nagrial, Adnan M., additional, Pettit, Jessica, additional, Pinese, Mark, additional, Rooman, Ilse, additional, Wu, Jianmin, additional, Tao, Jiang, additional, DiPietro, Renee, additional, Watson, Clare, additional, Steinmann, Angela, additional, Lee, Hong Ching, additional, Wong, Rachel, additional, Pinho, Andreia V., additional, Giry-Laterriere, Marc, additional, Daly, Roger J., additional, Sutherland, Robert L., additional, Grimmond, Sean M., additional, Waddell, Nicola, additional, Kassahn, Karin S., additional, Miller, David K., additional, Wilson, Peter J., additional, Patch, Ann-Marie, additional, Song, Sarah, additional, Harliwong, Ivon, additional, Idrisoglu, Senel, additional, Nourbakhsh, Ehsan, additional, Manning, Suzanne, additional, Wani, Shivangi, additional, Gongora, Milena, additional, Anderson, Matthew, additional, Holmes, Oliver, additional, Leonard, Conrad, additional, Taylor, Darrin, additional, Wood, Scott, additional, Xu, Christina, additional, Nones, Katia, additional, Fink, J. Lynn, additional, Christ, Angelika, additional, Bruxner, Tim, additional, Cloonan, Nicole, additional, Newell, Felicity, additional, Pearson, John V., additional, Bailey, Peter, additional, Quinn, Michael, additional, Nagaraj, Shivashankar, additional, Kazakoff, Stephen, additional, Waddell, Nick, additional, Krisnan, Keerthana, additional, Quek, Kelly, additional, Wood, David, additional, Samra, Jaswinder S., additional, Gill, Anthony J., additional, Pavlakis, Nick, additional, Guminski, Alex, additional, Toon, Christopher, additional, Asghari, Ray, additional, Merrett, Neil D., additional, Pavey, Darren, additional, Das, Amitabha, additional, Cosman, Peter H., additional, Ismail, Kasim, additional, O’Connnor, Chelsie, additional, Lam, Vincent W., additional, McLeod, Duncan, additional, Pleass, Henry C., additional, Richardson, Arthur, additional, James, Virginia, additional, Kench, James G., additional, Cooper, Caroline L., additional, Joseph, David, additional, Sandroussi, Charbel, additional, Crawford, Michael, additional, Gallagher, James, additional, Texler, Michael, additional, Forest, Cindy, additional, Laycock, Andrew, additional, Epari, Krishna P., additional, Ballal, Mo, additional, Fletcher, David R., additional, Mukhedkar, Sanjay, additional, Spry, Nigel A., additional, DeBoer, Bastiaan, additional, Chai, Ming, additional, Zeps, Nikolajs, additional, Beilin, Maria, additional, Feeney, Kynan, additional, Nguyen, Nan Q., additional, Ruszkiewicz, Andrew R., additional, Worthley, Chris, additional, Tan, Chuan P., additional, Debrencini, Tamara, additional, Chen, John, additional, Brooke-Smith, Mark E., additional, Papangelis, Virginia, additional, Tang, Henry, additional, Barbour, Andrew P., additional, Clouston, Andrew D., additional, Martin, Patrick, additional, O’Rourke, Thomas J., additional, Chiang, Amy, additional, Fawcett, Jonathan W., additional, Slater, Kellee, additional, Yeung, Shinn, additional, Hatzifotis, Michael, additional, Hodgkinson, Peter, additional, Christophi, Christopher, additional, Nikfarjam, Mehrdad, additional, Mountain, Angela, additional, Biobank, Victorian Cancer, additional, Eshleman, James R., additional, Hruban, Ralph H., additional, Maitra, Anirban, additional, Iacobuzio-Donahue, Christine A., additional, Schulick, Richard D., additional, Wolfgang, Christopher L., additional, Morgan, Richard A., additional, Hodgin, Mary, additional, Scarpa, Aldo, additional, Lawlor, Rita T., additional, Beghelli, Stefania, additional, Corbo, Vincenzo, additional, Scardoni, Maria, additional, Bassi, Claudio, additional, Tempero, Margaret A., additional, and Graham, Janet S., additional

Published
2021
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17. HNF4A and GATA6 Loss Reveals Therapeutically Actionable Subtypes in Pancreatic Cancer

Author

Brunton, Holly, primary, Caligiuri, Giuseppina, additional, Cunningham, Richard, additional, Upstill-Goddard, Rosie, additional, Bailey, Ulla-Maja, additional, Garner, Ian M., additional, Nourse, Craig, additional, Dreyer, Stephan, additional, Jones, Marc, additional, Moran-Jones, Kim, additional, Wright, Derek W., additional, Paulus-Hock, Viola, additional, Nixon, Colin, additional, Thomson, Gemma, additional, Jamieson, Nigel B., additional, McGregor, Grant A., additional, Evers, Lisa, additional, McKay, Colin J., additional, Gulati, Aditi, additional, Brough, Rachel, additional, Bajrami, Ilirjana, additional, Pettitt, Stephen J., additional, Dziubinski, Michele L., additional, Barry, Simon T., additional, Grützmann, Robert, additional, Brown, Robert, additional, Curry, Edward, additional, Pajic, Marina, additional, Musgrove, Elizabeth A., additional, Petersen, Gloria M., additional, Shanks, Emma, additional, Ashworth, Alan, additional, Crawford, Howard C., additional, Simeone, Diane M., additional, Froeling, Fieke E.M., additional, Lord, Christopher J., additional, Mukhopadhyay, Debabrata, additional, Pilarsky, Christian, additional, Grimmond, Sean E., additional, Morton, Jennifer P., additional, Sansom, Owen J., additional, Chang, David K., additional, Bailey, Peter J., additional, Biankin, Andrew V., additional, Allison, Sarah, additional, Cooke, Susanna L., additional, Grimwood, Paul, additional, Kelly, Shane, additional, Marshall, John, additional, McDade, Brian, additional, McElroy, Daniel, additional, Ramsay, Donna, additional, Rebus, Selma, additional, Hair, Jane, additional, Westwood, Paul, additional, Williams, Nicola, additional, Duthie, Fraser, additional, Johns, Amber L., additional, Mawson, Amanda, additional, Scarlett, Christopher J., additional, Brancato, Mary-Anne L., additional, Rowe, Sarah J., additional, Simpson, Skye H., additional, Martyn-Smith, Mona, additional, Thomas, Michelle T., additional, Chantrill, Lorraine A., additional, Chin, Venessa T., additional, Chou, Angela, additional, Cowley, Mark J., additional, Humphris, Jeremy L., additional, Mead, R. Scott, additional, Nagrial, Adnan M., additional, Pettit, Jessica, additional, Pinese, Mark, additional, Rooman, Ilse, additional, Wu, Jianmin, additional, Tao, Jiang, additional, DiPietro, Renee, additional, Watson, Clare, additional, Steinmann, Angela, additional, Lee, Hong Ching, additional, Wong, Rachel, additional, Pinho, Andreia V., additional, Giry-Laterriere, Marc, additional, Daly, Roger J., additional, Sutherland, Robert L., additional, Grimmond, Sean M., additional, Waddell, Nicola, additional, Kassahn, Karin S., additional, Miller, David K., additional, Wilson, Peter J., additional, Patch, Ann-Marie, additional, Song, Sarah, additional, Harliwong, Ivon, additional, Idrisoglu, Senel, additional, Nourbakhsh, Ehsan, additional, Manning, Suzanne, additional, Wani, Shivangi, additional, Gongora, Milena, additional, Anderson, Matthew, additional, Holmes, Oliver, additional, Leonard, Conrad, additional, Taylor, Darrin, additional, Wood, Scott, additional, Xu, Christina, additional, Nones, Katia, additional, Fink, J. Lynn, additional, Christ, Angelika, additional, Bruxner, Tim, additional, Cloonan, Nicole, additional, Newell, Felicity, additional, Pearson, John V., additional, Quinn, Michael, additional, Nagaraj, Shivashankar, additional, Kazakoff, Stephen, additional, Waddell, Nick, additional, Krisnan, Keerthana, additional, Quek, Kelly, additional, Wood, David, additional, Samra, Jaswinder S., additional, Gill, Anthony J., additional, Pavlakis, Nick, additional, Guminski, Alex, additional, Toon, Christopher, additional, Asghari, Ray, additional, Merrett, Neil D., additional, Pavey, Darren, additional, Das, Amitabha, additional, Cosman, Peter H., additional, Ismail, Kasim, additional, O’Connnor, Chelsie, additional, Lam, Vincent W., additional, McLeod, Duncan, additional, Pleass, Henry C., additional, Richardson, Arthur, additional, James, Virginia, additional, Kench, James G., additional, Cooper, Caroline L., additional, Joseph, David, additional, Sandroussi, Charbel, additional, Crawford, Michael, additional, Gallagher, James, additional, Texler, Michael, additional, Forest, Cindy, additional, Laycock, Andrew, additional, Epari, Krishna P., additional, Ballal, Mo, additional, Fletcher, David R., additional, Mukhedkar, Sanjay, additional, Spry, Nigel A., additional, DeBoer, Bastiaan, additional, Chai, Ming, additional, Zeps, Nikolajs, additional, Beilin, Maria, additional, Feeney, Kynan, additional, Nguyen, Nan Q., additional, Ruszkiewicz, Andrew R., additional, Worthley, Chris, additional, Tan, Chuan P., additional, Debrencini, Tamara, additional, Chen, John, additional, Brooke-Smith, Mark E., additional, Papangelis, Virginia, additional, Tang, Henry, additional, Barbour, Andrew P., additional, Clouston, Andrew D., additional, Martin, Patrick, additional, O’Rourke, Thomas J., additional, Chiang, Amy, additional, Fawcett, Jonathan W., additional, Slater, Kellee, additional, Yeung, Shinn, additional, Hatzifotis, Michael, additional, Hodgkinson, Peter, additional, Christophi, Christopher, additional, Nikfarjam, Mehrdad, additional, Mountain, Angela, additional, Eshleman, James R., additional, Hruban, Ralph H., additional, Maitra, Anirban, additional, Iacobuzio-Donahue, Christine A., additional, Schulick, Richard D., additional, Wolfgang, Christopher L., additional, Morgan, Richard A., additional, Hodgin, Mary, additional, Scarpa, Aldo, additional, Lawlor, Rita T., additional, Beghelli, Stefania, additional, Corbo, Vincenzo, additional, Scardoni, Maria, additional, Bassi, Claudio, additional, Tempero, Margaret A., additional, and Graham, Janet S., additional

Published
2020
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18. Refining transcriptional programs in kidney development by integration of deep RNA-sequencing and array-based spatial profiling

Author

Rumballe Bree A, Georgas Kylie M, Krishnan Keerthana, Tang Dave, Wani Shivangi, Nourbakhsh Ehsan, Kolle Gabriel, Mercer Tim R, Gardiner Brooke B, Cloonan Nicole, Thiagarajan Rathi D, Chiu Han S, Steen Jason A, Mattick John S, Little Melissa H, and Grimmond Sean M

Subjects
RNA-Seq, kidney development, microarray, Six2, Wt1, sense-antisense transcripts, alternative splicing, mesenchymal-epithelial transition, miR-214, microRNA, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The developing mouse kidney is currently the best-characterized model of organogenesis at a transcriptional level. Detailed spatial maps have been generated for gene expression profiling combined with systematic in situ screening. These studies, however, fall short of capturing the transcriptional complexity arising from each locus due to the limited scope of microarray-based technology, which is largely based on "gene-centric" models. Results To address this, the polyadenylated RNA and microRNA transcriptomes of the 15.5 dpc mouse kidney were profiled using strand-specific RNA-sequencing (RNA-Seq) to a depth sufficient to complement spatial maps from pre-existing microarray datasets. The transcriptional complexity of RNAs arising from mouse RefSeq loci was catalogued; including 3568 alternatively spliced transcripts and 532 uncharacterized alternate 3' UTRs. Antisense expressions for 60% of RefSeq genes was also detected including uncharacterized non-coding transcripts overlapping kidney progenitor markers, Six2 and Sall1, and were validated by section in situ hybridization. Analysis of genes known to be involved in kidney development, particularly during mesenchymal-to-epithelial transition, showed an enrichment of non-coding antisense transcripts extended along protein-coding RNAs. Conclusion The resulting resource further refines the transcriptomic cartography of kidney organogenesis by integrating deep RNA sequencing data with locus-based information from previously published expression atlases. The added resolution of RNA-Seq has provided the basis for a transition from classical gene-centric models of kidney development towards more accurate and detailed "transcript-centric" representations, which highlights the extent of transcriptional complexity of genes that direct complex development events.

Published
2011
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20. A workflow to increase verification rate of chromosomal structural rearrangements using high-throughput next-generation sequencing

Author

Quek, Kelly, primary, Nones, Katia, additional, Patch, Ann-Marie, additional, Fink, J. Lynn, additional, Newell, Felicity, additional, Cloonan, Nicole, additional, Miller, David, additional, Fadlullah, Muhammad Z. H., additional, Kassahn, Karin, additional, Christ, Angelika N., additional, Bruxner, Timothy J. C., additional, Manning, Suzanne, additional, Harliwong, Ivon, additional, Idrisoglu, Senel, additional, Nourse, Craig, additional, Nourbakhsh, Ehsan, additional, Wani, Shivangi, additional, Steptoe, Anita, additional, Anderson, Matthew, additional, Holmes, Oliver, additional, Leonard, Conrad, additional, Taylor, Darrin, additional, Wood, Scott, additional, Xu, Qinying, additional, Wilson, Peter, additional, Biankin, Andrew V., additional, Pearson, John V., additional, Waddell, Nic, additional, and Grimmond, Sean M., additional

Published
2014
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22. Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human embryonic stem cells

Author

Kolle, Gabriel, Shepherd, Jill L, Gardiner, Brooke, Kassahn, Karin, Cloonan, Nicole, Wood, David L, Nourbakhsh, Ehsan, Taylor, Darren F, Wani, Shivangi, Chy, Hun S, Zhou, Qi, McKernan, Kevin, Kuersten, Scott, Laslett, Andrew L, Grimmond, Sean M, Kolle, Gabriel, Shepherd, Jill L, Gardiner, Brooke, Kassahn, Karin, Cloonan, Nicole, Wood, David L, Nourbakhsh, Ehsan, Taylor, Darren F, Wani, Shivangi, Chy, Hun S, Zhou, Qi, McKernan, Kevin, Kuersten, Scott, Laslett, Andrew L, and Grimmond, Sean M

Abstract

Recent RNA-sequencing studies have shown remarkable complexity in the mammalian transcriptome. The ultimate impact of this complexity on the predicted proteomic output is less well defined. We have undertaken strand-specific RNA sequencing of multiple cellular RNA fractions (>20 Gb) to uncover the transcriptional complexity of human embryonic stem cells (hESCs). We have shown that human embryonic stem (ES) cells display a high degree of transcriptional diversity, with more than half of active genes generating RNAs that differ from conventional gene models. We found evidence that more than 1000 genes express long 5′ and/or extended 3′UTRs, which was confirmed by “virtual Northern” analysis. Exhaustive sequencing of the membrane-polysome and cytosolic/untranslated fractions of hESCs was used to identify RNAs encoding peptides destined for secretion and the extracellular space and to demonstrate preferential selection of transcription complexity for translation in vitro. The impact of this newly defined complexity on known gene-centric network models such as the Plurinet and the cell surface signaling machinery in human ES cells revealed a significant expansion of known transcript isoforms at play, many predicting possible alternative functions based on sequence alterations within key functional domains.

Published
2011

23. MicroRNAs and their isomiRs function cooperatively to target common biological pathways

Author

Cloonan, Nicole, Wani, Shivangi, Xu, Qinying, Gu, Jian, Lea, Kristi, Heater, Sheila, Barbaciouru, Catalin, Steptoe, Anita, Martin, Hilary, Nourbakhsh, Ehsan, Krishnan, Keerthana, Gardiner, Brooke, Wang, Xiaohui, Nones, Katia, Steen, Jason A, Matigan, Nick A, Wood, Dave L, Kasshan, Karin, Waddell, Nic, Shepherd, Jill L, Lee, Clarence, Ichikawa, Jeff, McKernan, Kevin, Bramlett, Kelli, Kuersten, Scott, Grimmond, Sean M, Cloonan, Nicole, Wani, Shivangi, Xu, Qinying, Gu, Jian, Lea, Kristi, Heater, Sheila, Barbaciouru, Catalin, Steptoe, Anita, Martin, Hilary, Nourbakhsh, Ehsan, Krishnan, Keerthana, Gardiner, Brooke, Wang, Xiaohui, Nones, Katia, Steen, Jason A, Matigan, Nick A, Wood, Dave L, Kasshan, Karin, Waddell, Nic, Shepherd, Jill L, Lee, Clarence, Ichikawa, Jeff, McKernan, Kevin, Bramlett, Kelli, Kuersten, Scott, and Grimmond, Sean M

Abstract

Background: Variants of microRNAs (miRNAs), called isomiRs, are commonly reported in deep-sequencing studies; however, the functional significance of these variants remains controversial. Observational studies show that isomiR patterns are non-random, hinting that these molecules could be regulated and therefore functional, although no conclusive biological role has been demonstrated for these molecules. Results: To assess the biological relevance of isomiRs, we have performed ultra-deep miRNA-seq on ten adult human tissues, and created an analysis pipeline called miRNA-MATE to align, annotate, and analyze miRNAs and their isomiRs. We find that isomiRs share sequence and expression characteristics with canonical miRNAs, and are generally strongly correlated with canonical miRNA expression. A large proportion of isomiRs potentially derive from AGO2 cleavage independent of Dicer. We isolated polyribosome-associated mRNA, captured the mRNA-bound miRNAs, and found that isomiRs and canonical miRNAs are equally associated with translational machinery. Finally, we transfected cells with biotinylated RNA duplexes encoding isomiRs or their canonical counterparts and directly assayed their mRNA targets. These studies allow us to experimentally determine genome-wide mRNA targets, and these experiments showed substantial overlap in functional mRNA networks suppressed by both canonical miRNAs and their isomiRs. Conclusions: Together, these results find isomiRs to be biologically relevant and functionally cooperative partners of canonical miRNAs that act coordinately to target pathways of functionally related genes. This work exposes the complexity of the miRNA-transcriptome, and helps explain a major miRNA paradox: how specific regulation of biological processes can occur when the specificity of miRNA targeting is mediated by only 6 to 11 nucleotides.

Published
2011

25. Somatic Point Mutation Calling in Low Cellularity Tumors

Author

Kassahn, Karin S., primary, Holmes, Oliver, additional, Nones, Katia, additional, Patch, Ann-Marie, additional, Miller, David K., additional, Christ, Angelika N., additional, Harliwong, Ivon, additional, Bruxner, Timothy J., additional, Xu, Qinying, additional, Anderson, Matthew, additional, Wood, Scott, additional, Leonard, Conrad, additional, Taylor, Darrin, additional, Newell, Felicity, additional, Song, Sarah, additional, Idrisoglu, Senel, additional, Nourse, Craig, additional, Nourbakhsh, Ehsan, additional, Manning, Suzanne, additional, Wani, Shivangi, additional, Steptoe, Anita, additional, Pajic, Marina, additional, Cowley, Mark J., additional, Pinese, Mark, additional, Chang, David K., additional, Gill, Anthony J., additional, Johns, Amber L., additional, Wu, Jianmin, additional, Wilson, Peter J., additional, Fink, Lynn, additional, Biankin, Andrew V., additional, Waddell, Nicola, additional, Grimmond, Sean M., additional, and Pearson, John V., additional

Published
2013
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26. MicroRNA-182-5p targets a network of genes involved in DNA repair

Author

Krishnan, Keerthana, primary, Steptoe, Anita L., additional, Martin, Hilary C., additional, Wani, Shivangi, additional, Nones, Katia, additional, Waddell, Nic, additional, Mariasegaram, Mythily, additional, Simpson, Peter T., additional, Lakhani, Sunil R., additional, Gabrielli, Brian, additional, Vlassov, Alexander, additional, Cloonan, Nicole, additional, and Grimmond, Sean M., additional

Published
2012
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27. Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human embryonic stem cells

Author

Kolle, Gabriel, primary, Shepherd, Jill L., additional, Gardiner, Brooke, additional, Kassahn, Karin S., additional, Cloonan, Nicole, additional, Wood, David L.A., additional, Nourbakhsh, Ehsan, additional, Taylor, Darrin F., additional, Wani, Shivangi, additional, Chy, Hun S., additional, Zhou, Qi, additional, McKernan, Kevin, additional, Kuersten, Scott, additional, Laslett, Andrew L., additional, and Grimmond, Sean M., additional

Published
2011
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28. Refining transcriptional programs in kidney development by integration of deep RNA-sequencing and array-based spatial profiling

Author

Thiagarajan, Rathi D, primary, Cloonan, Nicole, additional, Gardiner, Brooke B, additional, Mercer, Tim R, additional, Kolle, Gabriel, additional, Nourbakhsh, Ehsan, additional, Wani, Shivangi, additional, Tang, Dave, additional, Krishnan, Keerthana, additional, Georgas, Kylie M, additional, Rumballe, Bree A, additional, Chiu, Han S, additional, Steen, Jason A, additional, Mattick, John S, additional, Little, Melissa H, additional, and Grimmond, Sean M, additional

Published
2011
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29. MicroRNAs and their isomiRs function cooperatively to target common biological pathways

Author

Cloonan, Nicole, primary, Wani, Shivangi, additional, Xu, Qinying, additional, Gu, Jian, additional, Lea, Kristi, additional, Heater, Sheila, additional, Barbacioru, Catalin, additional, Steptoe, Anita L, additional, Martin, Hilary C, additional, Nourbakhsh, Ehsan, additional, Krishnan, Keerthana, additional, Gardiner, Brooke, additional, Wang, Xiaohui, additional, Nones, Katia, additional, Steen, Jason A, additional, Matigian, Nicholas A, additional, Wood, David L, additional, Kassahn, Karin S, additional, Waddell, Nic, additional, Shepherd, Jill, additional, Lee, Clarence, additional, Ichikawa, Jeff, additional, McKernan, Kevin, additional, Bramlett, Kelli, additional, Kuersten, Scott, additional, and Grimmond, Sean M, additional

Published
2011
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30. The regulated retrotransposon transcriptome of mammalian cells

Author

Faulkner, Geoffrey J, primary, Kimura, Yasumasa, additional, Daub, Carsten O, additional, Wani, Shivangi, additional, Plessy, Charles, additional, Irvine, Katharine M, additional, Schroder, Kate, additional, Cloonan, Nicole, additional, Steptoe, Anita L, additional, Lassmann, Timo, additional, Waki, Kazunori, additional, Hornig, Nadine, additional, Arakawa, Takahiro, additional, Takahashi, Hazuki, additional, Kawai, Jun, additional, Forrest, Alistair R R, additional, Suzuki, Harukazu, additional, Hayashizaki, Yoshihide, additional, Hume, David A, additional, Orlando, Valerio, additional, Grimmond, Sean M, additional, and Carninci, Piero, additional

Published
2009
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32. Stem cell transcriptome profiling via massive-scale mRNA sequencing

Author

Cloonan, Nicole, primary, Forrest, Alistair R R, additional, Kolle, Gabriel, additional, Gardiner, Brooke B A, additional, Faulkner, Geoffrey J, additional, Brown, Mellissa K, additional, Taylor, Darrin F, additional, Steptoe, Anita L, additional, Wani, Shivangi, additional, Bethel, Graeme, additional, Robertson, Alan J, additional, Perkins, Andrew C, additional, Bruce, Stephen J, additional, Lee, Clarence C, additional, Ranade, Swati S, additional, Peckham, Heather E, additional, Manning, Jonathan M, additional, McKernan, Kevin J, additional, and Grimmond, Sean M, additional

Published
2008
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34. MicroRNA-182-5p targets a network of genes involved in DNA repair

Author

Krishnan, Keerthana, Steptoe, Anita L., Martin, Hilary C., Wani, Shivangi, Nones, Katia, Waddell, Nic, Mariasegaram, Mythily, Simpson, Peter T., Lakhani, Sunil R., Gabrielli, Brian, Vlassov, Alexander, Cloonan, Nicole, and Grimmond, Sean M.

Abstract

In this paper the authors use a pull-down strategy with biotinylated miR-182-5p to identify mRNA targets of this medically relevant miRNA. This results in the identification of a closely interacting network of more than 30 targets, all directly involved in the DNA damage response pathway. They experimentally verify the functional relevance of this targeting and show that miR-182-5p modulates PARP inhibitor sensitivity by targeting multiple components of the DNA repair pathway. They also show that this miRNA is highly expressed in a panel of human breast cancer samples, suggesting a potential role as an oncomir.

Published
2013
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35. HNF4Aand GATA6Loss Reveals Therapeutically Actionable Subtypes in Pancreatic Cancer

Author

Brunton, Holly, Caligiuri, Giuseppina, Cunningham, Richard, Upstill-Goddard, Rosie, Bailey, Ulla-Maja, Garner, Ian M., Nourse, Craig, Dreyer, Stephan, Jones, Marc, Moran-Jones, Kim, Wright, Derek W., Paulus-Hock, Viola, Nixon, Colin, Thomson, Gemma, Jamieson, Nigel B., McGregor, Grant A., Evers, Lisa, McKay, Colin J., Gulati, Aditi, Brough, Rachel, Bajrami, Ilirjana, Pettitt, Stephen J., Dziubinski, Michele L., Barry, Simon T., Grützmann, Robert, Brown, Robert, Curry, Edward, Allison, Sarah, Biankin, Andrew V., Chang, David K., Cooke, Susanna L., Dreyer, Stephan, Grimwood, Paul, Kelly, Shane, Marshall, John, McDade, Brian, McElroy, Daniel, Ramsay, Donna, Upstill-Goddard, Rosie, Rebus, Selma, Hair, Jane, Jamieson, Nigel B., McKay, Colin J., Westwood, Paul, Williams, Nicola, Duthie, Fraser, Biankin, Andrew V., Johns, Amber L., Mawson, Amanda, Chang, David K., Scarlett, Christopher J., Brancato, Mary-Anne L., Rowe, Sarah J., Simpson, Skye H., Martyn-Smith, Mona, Thomas, Michelle T., Chantrill, Lorraine A., Chin, Venessa T., Chou, Angela, Cowley, Mark J., Humphris, Jeremy L., Mead, R. Scott, Nagrial, Adnan M., Pajic, Marina, Pettit, Jessica, Pinese, Mark, Rooman, Ilse, Wu, Jianmin, Tao, Jiang, DiPietro, Renee, Watson, Clare, Steinmann, Angela, Lee, Hong Ching, Wong, Rachel, Pinho, Andreia V., Giry-Laterriere, Marc, Daly, Roger J., Musgrove, Elizabeth A., Sutherland, Robert L., Grimmond, Sean M., Waddell, Nicola, Kassahn, Karin S., Miller, David K., Wilson, Peter J., Patch, Ann-Marie, Song, Sarah, Harliwong, Ivon, Idrisoglu, Senel, Nourbakhsh, Ehsan, Manning, Suzanne, Wani, Shivangi, Gongora, Milena, Anderson, Matthew, Holmes, Oliver, Leonard, Conrad, Taylor, Darrin, Wood, Scott, Xu, Christina, Nones, Katia, Fink, J. Lynn, Christ, Angelika, Bruxner, Tim, Cloonan, Nicole, Newell, Felicity, Pearson, John V., Quinn, Michael, Nagaraj, Shivashankar, Kazakoff, Stephen, Waddell, Nick, Krisnan, Keerthana, Quek, Kelly, Wood, David, Samra, Jaswinder S., Gill, Anthony J., Pavlakis, Nick, Guminski, Alex, Toon, Christopher, Asghari, Ray, Merrett, Neil D., Pavey, Darren, Das, Amitabha, Cosman, Peter H., Ismail, Kasim, O’Connnor, Chelsie, Lam, Vincent W., McLeod, Duncan, Pleass, Henry C., Richardson, Arthur, James, Virginia, Kench, James G., Cooper, Caroline L., Joseph, David, Sandroussi, Charbel, Crawford, Michael, Gallagher, James, Texler, Michael, Forest, Cindy, Laycock, Andrew, Epari, Krishna P., Ballal, Mo, Fletcher, David R., Mukhedkar, Sanjay, Spry, Nigel A., DeBoer, Bastiaan, Chai, Ming, Zeps, Nikolajs, Beilin, Maria, Feeney, Kynan, Nguyen, Nan Q., Ruszkiewicz, Andrew R., Worthley, Chris, Tan, Chuan P., Debrencini, Tamara, Chen, John, Brooke-Smith, Mark E., Papangelis, Virginia, Tang, Henry, Barbour, Andrew P., Clouston, Andrew D., Martin, Patrick, O’Rourke, Thomas J., Chiang, Amy, Fawcett, Jonathan W., Slater, Kellee, Yeung, Shinn, Hatzifotis, Michael, Hodgkinson, Peter, Christophi, Christopher, Nikfarjam, Mehrdad, Mountain, Angela, Eshleman, James R., Hruban, Ralph H., Maitra, Anirban, Iacobuzio-Donahue, Christine A., Schulick, Richard D., Wolfgang, Christopher L., Morgan, Richard A., Hodgin, Mary, Scarpa, Aldo, Lawlor, Rita T., Beghelli, Stefania, Corbo, Vincenzo, Scardoni, Maria, Bassi, Claudio, Tempero, Margaret A., Nourse, Craig, Jamieson, Nigel B., Graham, Janet S., Pajic, Marina, Musgrove, Elizabeth A., Petersen, Gloria M., Shanks, Emma, Ashworth, Alan, Crawford, Howard C., Simeone, Diane M., Froeling, Fieke E.M., Lord, Christopher J., Mukhopadhyay, Debabrata, Pilarsky, Christian, Grimmond, Sean E., Morton, Jennifer P., Sansom, Owen J., Chang, David K., Bailey, Peter J., and Biankin, Andrew V.

Abstract

Pancreatic ductal adenocarcinoma (PDAC) can be divided into transcriptomic subtypes with two broad lineages referred to as classical (pancreatic) and squamous. We find that these two subtypes are driven by distinct metabolic phenotypes. Loss of genes that drive endodermal lineage specification, HNF4Aand GATA6, switch metabolic profiles from classical (pancreatic) to predominantly squamous, with glycogen synthase kinase 3 beta (GSK3β) a key regulator of glycolysis. Pharmacological inhibition of GSK3β results in selective sensitivity in the squamous subtype; however, a subset of these squamous patient-derived cell lines (PDCLs) acquires rapid drug tolerance. Using chromatin accessibility maps, we demonstrate that the squamous subtype can be further classified using chromatin accessibility to predict responsiveness and tolerance to GSK3β inhibitors. Our findings demonstrate that distinct patterns of chromatin accessibility can be used to identify patient subgroups that are indistinguishable by gene expression profiles, highlighting the utility of chromatin-based biomarkers for patient selection in the treatment of PDAC.

Published
2020
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