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2. Ssb1 and Ssb2 cooperate to regulate mouse hematopoietic stem and progenitor cells by resolving replicative stress

Author

Shi, Wei, Vu, Therese, Boucher, Didier, Biernacka, Anna, Nde, Jules, Pandita, Raj K., Straube, Jasmin, Boyle, Glen M., Al-Ejeh, Fares, Nag, Purba, Jeffery, Jessie, Harris, Janelle L., Bain, Amanda L., Grzelak, Marta, Skrzypczak, Magdalena, Mitra, Abhishek, Dojer, Norbert, Crosetto, Nicola, Cloonan, Nicole, Becherel, Olivier J., Finnie, John, Skaar, Jeffrey R., Walkley, Carl R., Pandita, Tej K., Rowicka, Maga, Ginalski, Krzysztof, Lane, Steven W., and Khanna, Kum Kum

Published
2017
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3. Corrigendum: Whole-genome landscape of pancreatic neuroendocrine tumours

Author

Scarpa, Aldo, Chang, David K., Nones, Katia, Corbo, Vincenzo, Patch, Ann-Marie, Bailey, Peter, Lawlor, Rita T., Johns, Amber L., Miller, David K., Mafficini, Andrea, Rusev, Borislav, Scardoni, Maria, Antonello, Davide, Barbi, Stefano, Sikora, Katarzyna O., Cingarlini, Sara, Vicentini, Caterina, McKay, Skye, Quinn, Michael C. J., Bruxner, Timothy J. C., Christ, Angelika N., Harliwong, Ivon, Idrisoglu, Senel, McLean, Suzanne, Nourse, Craig, Nourbakhsh, Ehsan, Wilson, Peter J., Anderson, Matthew J., Fink, Lynn J., Newell, Felicity, Waddell, Nick, Holmes, Oliver, Kazakoff, Stephen H., Leonard, Conrad, Wood, Scott, Xu, Qinying, Nagaraj, Shivashankar Hiriyur, Amato, Eliana, Dalai, Irene, Bersani, Samantha, Cataldo, Ivana, Dei Tos, Angelo P., Capelli, Paola, Davì, Maria Vittoria, Landoni, Luca, Malpaga, Anna, Miotto, Marco, Whitehall, Vicki L. J., Leggett, Barbara A., Harris, Janelle L., Harris, Jonathan, Jones, Marc D., Humphris, Jeremy, Chantrill, Lorraine A., Chin, Venessa, Nagrial, Adnan M., Pajic, Marina, Scarlett, Christopher J., Pinho, Andreia, Rooman, Ilse, Toon, Christopher, Wu, Jianmin, Pinese, Mark, Cowley, Mark, Barbour, Andrew, Mawson, Amanda, Humphrey, Emily S., Colvin, Emily K., Chou, Angela, Lovell, Jessica A., Jamieson, Nigel B., Duthie, Fraser, Gingras, Marie-Claude, Fisher, William E., Dagg, Rebecca A., Lau, Loretta M. S., Lee, Michael, Pickett, Hilda A., Reddel, Roger R., Samra, Jaswinder S., Kench, James G., Merrett, Neil D., Epari, Krishna, Nguyen, Nam Q., Zeps, Nikolajs, Falconi, Massimo, Simbolo, Michele, Butturini, Giovanni, Van Buren, George, Partelli, Stefano, Fassan, Matteo, Khanna, Kum Kum, Gill, Anthony J., Wheeler, David A., Gibbs, Richard A., Musgrove, Elizabeth A., Bassi, Claudio, Tortora, Giampaolo, Pederzoli, Paolo, Pearson, John V., Waddell, Nicola, Biankin, Andrew V., and Grimmond, Sean M.

Published
2017
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4. Whole-genome landscape of pancreatic neuroendocrine tumours

Author

Scarpa, Aldo, Chang, David K., Nones, Katia, Corbo, Vincenzo, Patch, Ann-Marie, Bailey, Peter, Lawlor, Rita T., Johns, Amber L., Miller, David K., Mafficini, Andrea, Rusev, Borislav, Scardoni, Maria, Antonello, Davide, Barbi, Stefano, Sikora, Katarzyna O., Cingarlini, Sara, Vicentini, Caterina, McKay, Skye, Quinn, Michael C. J., Bruxner, Timothy J. C., Christ, Angelika N., Harliwong, Ivon, Idrisoglu, Senel, McLean, Suzanne, Nourse, Craig, Nourbakhsh, Ehsan, Wilson, Peter J., Anderson, Matthew J., Fink, Lynn J., Newell, Felicity, Waddell, Nick, Holmes, Oliver, Kazakoff, Stephen H., Leonard, Conrad, Wood, Scott, Xu, Qinying, Nagaraj, Shivashankar Hiriyur, Amato, Eliana, Dalai, Irene, Bersani, Samantha, Cataldo, Ivana, Dei Tos, Angelo P., Capelli, Paola, Davì, Maria Vittoria, Landoni, Luca, Malpaga, Anna, Miotto, Marco, Whitehall, Vicki L. J., Leggett, Barbara A., Harris, Janelle L., Harris, Jonathan, Jones, Marc D., Humphris, Jeremy, Chantrill, Lorraine A., Chin, Venessa, Nagrial, Adnan M., Pajic, Marina, Scarlett, Christopher J., Pinho, Andreia, Rooman, Ilse, Toon, Christopher, Wu, Jianmin, Pinese, Mark, Cowley, Mark, Barbour, Andrew, Mawson, Amanda, Humphrey, Emily S., Colvin, Emily K., Chou, Angela, Lovell, Jessica A., Jamieson, Nigel B., Duthie, Fraser, Gingras, Marie-Claude, Fisher, William E., Dagg, Rebecca A., Lau, Loretta M. S., Lee, Michael, Pickett, Hilda A., Reddel, Roger R., Samra, Jaswinder S., Kench, James G., Merrett, Neil D., Epari, Krishna, Nguyen, Nam Q., Zeps, Nikolajs, Falconi, Massimo, Simbolo, Michele, Butturini, Giovanni, Van Buren, George, Partelli, Stefano, Fassan, Matteo, Khanna, Kum Kum, Gill, Anthony J., Wheeler, David A., Gibbs, Richard A., Musgrove, Elizabeth A., Bassi, Claudio, Tortora, Giampaolo, Pederzoli, Paolo, Pearson, John V., Waddell, Nicola, Biankin, Andrew V., and Grimmond, Sean M.

Published
2017
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8. Corrigendum: Whole-genome landscape of pancreatic neuroendocrine tumours (Nature (2017) 543 (65-71) DOI: 10.1038/nature21063)

Author

Scarpa, Aldo, Chang, David K, Nones, Katia, Corbo, Vincenzo, Patch, Ann-Marie, Bailey, Peter, Lawlor, Rita T, Johns, Amber L, Miller, David K, Mafficini, Andrea, Rusev, Borislav, Scardoni, Maria, Antonello, Davide, Barbi, Stefano, Sikora, Katarzyna O, Cingarlini, Sara, Vicentini, Caterina, McKay, Skye, Quinn, Michael C J, Bruxner, Timothy J C, Christ, Angelika N, Harliwong, Ivon, Idrisoglu, Senel, McLean, Suzanne, Nourse, Craig, Nourbakhsh, Ehsan, Wilson, Peter J, Anderson, Matthew J, Fink, J Lynn, Newell, Felicity, Waddell, Nick, Holmes, Oliver, Kazakoff, Stephen H, Leonard, Conrad, Wood, Scott, Xu, Qinying, Hiriyur Nagaraj, Shivashankar, Amato, Eliana, Dalai, Irene, Bersani, Samantha, Cataldo, Ivana, Dei Tos, Angelo P, Capelli, Paola, Vittoria Davì, Maria, Landoni, Luca, Malpaga, Anna, Miotto, Marco, Whitehall, Vicki L J, Leggett, Barbara A, Harris, Janelle L, Harris, Jonathan, Jones, Marc D, Humphris, Jeremy, Chantrill, Lorraine A, Chin, Venessa, Nagrial, Adnan M, Pajic, Marina, Scarlett, Christopher J, Pinho, Andreia, Rooman, Ilse, Toon, Christopher, Wu, Jianmin, Pinese, Mark, Cowley, Mark, Barbour, Andrew, Mawson, Amanda, Humphrey, Emily S, Colvin, Emily K, Chou, Angela, Lovell, Jessica A, Jamieson, Nigel B, Duthie, Fraser, Gingras, Marie-Claude, Fisher, William E, Dagg, Rebecca A, Lau, Loretta M S, Lee, Michael, Pickett, Hilda A, Reddel, Roger R, Samra, Jaswinder S, Kench, James G, Merrett, Neil D, Epari, Krishna, Nguyen, Nam Q, Zeps, Nikolajs, Falconi, Massimo, Simbolo, Michele, Butturini, Giovanni, Van Buren, George, Partelli, Stefano, Fassan, Matteo, Khanna, Kum Kum, Gill, Anthony J, Wheeler, David A, Gibbs, Richard A, Musgrove, Elizabeth A, Bassi, Claudio, Tortora, Giampaolo, Pederzoli, Paolo, Pearson, John V, Waddell, Nicola, Biankin, Andrew V, Grimmond, Sean M, Scarpa, Aldo, Chang, David K, Nones, Katia, Corbo, Vincenzo, Patch, Ann-Marie, Bailey, Peter, Lawlor, Rita T, Johns, Amber L, Miller, David K, Mafficini, Andrea, Rusev, Borislav, Scardoni, Maria, Antonello, Davide, Barbi, Stefano, Sikora, Katarzyna O, Cingarlini, Sara, Vicentini, Caterina, Mckay, Skye, Quinn, Michael C J, Bruxner, Timothy J C, Christ, Angelika N, Harliwong, Ivon, Idrisoglu, Senel, Mclean, Suzanne, Nourse, Craig, Nourbakhsh, Ehsan, Wilson, Peter J, Anderson, Matthew J, Fink, J Lynn, Newell, Felicity, Waddell, Nick, Holmes, Oliver, Kazakoff, Stephen H, Leonard, Conrad, Wood, Scott, Xu, Qinying, Hiriyur Nagaraj, Shivashankar, Amato, Eliana, Dalai, Irene, Bersani, Samantha, Cataldo, Ivana, Dei Tos, Angelo P, Capelli, Paola, Vittoria Davì, Maria, Landoni, Luca, Malpaga, Anna, Miotto, Marco, Whitehall, Vicki L J, Leggett, Barbara A, Harris, Janelle L, Harris, Jonathan, Jones, Marc D, Humphris, Jeremy, Chantrill, Lorraine A, Chin, Venessa, Nagrial, Adnan M, Pajic, Marina, Scarlett, Christopher J, Pinho, Andreia, Rooman, Ilse, Toon, Christopher, Wu, Jianmin, Pinese, Mark, Cowley, Mark, Barbour, Andrew, Mawson, Amanda, Humphrey, Emily S, Colvin, Emily K, Chou, Angela, Lovell, Jessica A, Jamieson, Nigel B, Duthie, Fraser, Gingras, Marie-Claude, Fisher, William E, Dagg, Rebecca A, Lau, Loretta M S, Lee, Michael, Pickett, Hilda A, Reddel, Roger R, Samra, Jaswinder S, Kench, James G, Merrett, Neil D, Epari, Krishna, Nguyen, Nam Q, Zeps, Nikolaj, Falconi, Massimo, Simbolo, Michele, Butturini, Giovanni, Van Buren, George, Partelli, Stefano, Fassan, Matteo, Khanna, Kum Kum, Gill, Anthony J, Wheeler, David A, Gibbs, Richard A, Musgrove, Elizabeth A, Bassi, Claudio, Tortora, Giampaolo, Pederzoli, Paolo, Pearson, John V, Waddell, Nicola, Biankin, Andrew V, and Grimmond, Sean M

Abstract

It has been brought to our attention that in Fig. 2d of this Article, an incorrect Sanger trace was used to represent the breakpoint of the EWSR1 and FLI1 type 2 fusion. This was due to an error during manuscript preparation, when we inadvertently inserted the electrophoretic trace referring to EWSR1 splicing variants. Figure 2d has been corrected in the online versions of the Article. We apologize for the confusion. In addition, in the first sentence of the 'Somatic driver mutation' section on page 67, the sentence: 'A total of 15,751 somatic coding mutations (7,703 non-silent) were detected in 2,787 genes (Supplementary Tables 4, 5)", should have stated "A total of 3,097 somatic coding mutations (2,498 non-silent) were detected in 2,567 genes (Supplementary Tables 4, 5)". Note that the numbers in the Supplementary Tables are correct. This sentence has been corrected in the online versions of the Article.

Published
2017

9. Enhanced dependency of KRAS ‐mutant colorectal cancer cells on RAD 51‐dependent homologous recombination repair identified from genetic interactions in Saccharomyces cerevisiae

Author

Kalimutho, Murugan, primary, Bain, Amanda L., additional, Mukherjee, Bipasha, additional, Nag, Purba, additional, Nanayakkara, Devathri M., additional, Harten, Sarah K., additional, Harris, Janelle L., additional, Subramanian, Goutham N., additional, Sinha, Debottam, additional, Shirasawa, Senji, additional, Srihari, Sriganesh, additional, Burma, Sandeep, additional, and Khanna, Kum Kum, additional

Published
2017
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10. Enhanced dependency of KRAS-mutant colorectal cancer cells on RAD51-dependent homologous recombination repair identified from genetic interactions in Saccharomyces cerevisiae.

Author

Kalimutho, Murugan, Bain, Amanda L., Mukherjee, Bipasha, Nag, Purba, Nanayakkara, Devathri M., Harten, Sarah K., Harris, Janelle L., Subramanian, Goutham N., Sinha, Debottam, Shirasawa, Senji, Srihari, Sriganesh, Burma, Sandeep, and Khanna, Kum Kum

Abstract

Activating KRAS mutations drive colorectal cancer tumorigenesis and influence response to anti- EGFR-targeted therapy. Despite recent advances in understanding Ras signaling biology and the revolution in therapies for melanoma using BRAF inhibitors, no targeted agents have been effective in KRAS-mutant cancers, mainly due to activation of compensatory pathways. Here, by leveraging the largest synthetic lethal genetic interactome in yeast, we identify that KRAS-mutated colorectal cancer cells have augmented homologous recombination repair ( HRR) signaling. We found that KRAS mutation resulted in slowing and stalling of the replication fork and accumulation of DNA damage. Moreover, we found that KRAS-mutant HCT116 cells have an increase in MYC-mediated RAD51 expression with a corresponding increase in RAD51 recruitment to irradiation-induced DNA double-strand breaks ( DSBs) compared to genetically complemented isogenic cells. MYC depletion using RNA interference significantly reduced IR-induced RAD51 foci formation and HRR. On the contrary, overexpression of either HA-tagged wild-type (WT) MYC or phospho-mutant S62A increased RAD51 protein levels and hence IR-induced RAD51 foci. Likewise, depletion of RAD51 selectively induced apoptosis in HCT116-mutant cells by increasing DSBs. Pharmacological inhibition targeting HRR signaling combined with PARP inhibition selectivity killed KRAS-mutant cells. Interestingly, these differences were not seen in a second isogenic pair of KRAS WT and mutant cells ( DLD-1), likely due to their nondependency on the KRAS mutation for survival. Our data thus highlight a possible mechanism by which KRAS-mutant-dependent cells drive HRR in vitro by upregulating MYC- RAD51 expression. These data may offer a promising therapeutic vulnerability in colorectal cancer cells harboring otherwise nondruggable KRAS mutations, which warrants further investigation in vivo. [ABSTRACT FROM AUTHOR]

Published
2017
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15. Ssb1 and Ssb2 cooperate to regulate mouse hematopoietic stem and progenitor cells by resolving replicative stress.

Author

Wei Shi, Therese Vu, Boucher, Didier, Biernacka, Anna, Nde, Jules, Pandita, Raj K., Straube, Jasmin, Boyle, Glen M., Al-Ejeh, Fares, Nag, Purba, Jeffery, Jessie, Harris, Janelle L., Bain, Amanda L., Grzelak, Marta, Skrzypczak, Magdalena, Mitra, Abhishek, Dojer, Norbert, Crosetto, Nicola, Cloonan, Nicole, and Becherel, Olivier J.

Subjects
*CARRIER proteins, *DNA repair, *BONE marrow, *HEMATOPOIETIC system, *PROGENITOR cells
Abstract

Hematopoietic stem and progenitor cells (HSPCs) are vulnerable to endogenous damage and defects in DNA repair can limit their function. The 2 single-stranded DNA (ssDNA) binding proteins SSB1 and SSB2 are crucial regulators of the DNA damage response; however, their overlapping roles during normal physiology are incompletely understood. We generated mice in which both Ssb1 and Ssb2 were constitutively or conditionally deleted. Constitutive Ssb1/Ssb2 double knockout (DKO) caused early embryonic lethality, whereas conditional Ssb1/Ssb2 double knockout (cDKO) in adult mice resulted in acute lethality due to bone marrow failure and intestinal atrophy featuring stem and progenitor cell depletion, a phenotype unexpected from the previously reported single knockout models of Ssb1 or Ssb2. Mechanistically, cDKO HSPCs showed altered replication fork dynamics, massive accumulation of DNA damage, genome-wide doublestrand breaks enriched at Ssb-binding regions and CpG islands, together with the accumulation of R-loops and cytosolic ssDNA. Transcriptional profiling of cDKO HSPCs revealed the activation of p53 and interferon (IFN) pathways, which enforced cell cycling in quiescent HSPCs, resulting in their apoptotic death. Therapid cell death phenotypewas reproducible in invitroculturedcDKO-hematopoietic stemcells, which were significantly rescued by nucleotide supplementationor after depletion of p53. Collectively, Ssb1 and Ssb2 control crucial aspects of HSPC function, including proliferation and survival in vivo by resolving replicative stress to maintain genomic stability. [ABSTRACT FROM AUTHOR]

Published
2017
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16. Identification of ATM-Interacting Proteins by Co-immunoprecipitation and Glutathione-S-Transferase (GST) Pull-Down Assays.

Author

Bain AL, Harris JL, and Khanna KK

Subjects
DNA Damage genetics, Humans, Immunoprecipitation, Protein Binding, Transcription Factors metabolism, Glutathione Transferase metabolism
Abstract

The ATM kinase is a master regulator of the DNA damage response, and can interact with more than 700 proteins in response to DNA damage. These interactions play a critical role in fine-tuning the response of ATM to multiple cellular stressors, and can play both a positive or negative role in regulating its activity. Here, we detail using protein-protein interaction methods, including co-immunoprecipitation and Glutathione-S-transferase (GST) fusion protein pull-down assays to understand the molecular interactions of ATM. These assays give valuable functional insights into the role of ATM, as they are easy to establish within the laboratory, are not overly laborious, and are easily reproducible.

Published
2017
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