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1. A combined analysis of genome-wide association studies in breast cancer

Author

Li, Jingmei, Humphreys, Keith, Heikkinen, Tuomas, Aittomäki, Kristiina, Blomqvist, Carl, Pharoah, Paul D. P., Dunning, Alison M., Ahmed, Shahana, Hooning, Maartje J., Martens, John W. M., van den Ouweland, Ans M. W., Alfredsson, Lars, Palotie, Aarno, Peltonen-Palotie, Leena, Irwanto, Astrid, Low, Hui Qi, Teoh, Garrett H. K., Thalamuthu, Anbupalam, Easton, Douglas F., Nevanlinna, Heli, Liu, Jianjun, Czene, Kamila, and Hall, Per

Published
2011
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5. A genome-wide association scan on estrogen receptor-negative breast cancer

Author

Li, Jingmei, Humphreys, Keith, Darabi, Hatef, Rosin, Gustaf, Hannelius, Ulf, Heikkinen, Tuomas, Aittomäki, Kristiina, Blomqvist, Carl, Pharoah, Paul Dp, Dunning, Alison M, Ahmed, Shahana, Hooning, Maartje J, Hollestelle, Antoinette, Oldenburg, Rogier A, Alfredsson, Lars, Palotie, Aarno, Peltonen-Palotie, Leena, Irwanto, Astrid, Low, Hui Qi, Teoh, Garrett Hk, Thalamuthu, Anbupalam, Kere, Juha, D'Amato, Mauro, Easton, Douglas F, Nevanlinna, Heli, Liu, Jianjun, Czene, Kamila, Hall, Per, Li, Jingmei, Humphreys, Keith, Darabi, Hatef, Rosin, Gustaf, Hannelius, Ulf, Heikkinen, Tuomas, Aittomäki, Kristiina, Blomqvist, Carl, Pharoah, Paul Dp, Dunning, Alison M, Ahmed, Shahana, Hooning, Maartje J, Hollestelle, Antoinette, Oldenburg, Rogier A, Alfredsson, Lars, Palotie, Aarno, Peltonen-Palotie, Leena, Irwanto, Astrid, Low, Hui Qi, Teoh, Garrett Hk, Thalamuthu, Anbupalam, Kere, Juha, D'Amato, Mauro, Easton, Douglas F, Nevanlinna, Heli, Liu, Jianjun, Czene, Kamila, and Hall, Per

Abstract

INTRODUCTION: Breast cancer is a heterogeneous disease and may be characterized on the basis of whether estrogen receptors (ER) are expressed in the tumour cells. ER status of breast cancer is important clinically, and is used both as a prognostic indicator and treatment predictor. In this study, we focused on identifying genetic markers associated with ER-negative breast cancer risk.METHODS: We conducted a genome-wide association analysis of 285,984 single nucleotide polymorphisms (SNPs) genotyped in 617 ER-negative breast cancer cases and 4,583 controls. We also conducted a genome-wide pathway analysis on the discovery dataset using permutation-based tests on pre-defined pathways. The extent of shared polygenic variation between ER-negative and ER-positive breast cancers was assessed by relating risk scores, derived using ER-positive breast cancer samples, to disease state in independent, ER-negative breast cancer cases.RESULTS: Association with ER-negative breast cancer was not validated for any of the five most strongly associated SNPs followed up in independent studies (1,011 ER-negative breast cancer cases, 7,604 controls). However, an excess of small P-values for SNPs with known regulatory functions in cancer-related pathways was found (global P = 0.052). We found no evidence to suggest that ER-negative breast cancer shares a polygenic basis to disease with ER-positive breast cancer.CONCLUSIONS: ER-negative breast cancer is a distinct breast cancer subtype that merits independent analyses. Given the clinical importance of this phenotype and the likelihood that genetic effect sizes are small, greater sample sizes and further studies are required to understand the etiology of ER-negative breast cancers.

Published
2010

6. A genome-wide association scan on estrogen receptor-negative breast cancer

Author

Li, Jingmei, primary, Humphreys, Keith, additional, Darabi, Hatef, additional, Rosin, Gustaf, additional, Hannelius, Ulf, additional, Heikkinen, Tuomas, additional, Aittomäki, Kristiina, additional, Blomqvist, Carl, additional, Pharoah, Paul DP, additional, Dunning, Alison M, additional, Ahmed, Shahana, additional, Hooning, Maartje J, additional, Hollestelle, Antoinette, additional, Oldenburg, Rogier A, additional, Alfredsson, Lars, additional, Palotie, Aarno, additional, Peltonen-Palotie, Leena, additional, Irwanto, Astrid, additional, Low, Hui Qi, additional, Teoh, Garrett HK, additional, Thalamuthu, Anbupalam, additional, Kere, Juha, additional, D'Amato, Mauro, additional, Easton, Douglas F, additional, Nevanlinna, Heli, additional, Liu, Jianjun, additional, Czene, Kamila, additional, and Hall, Per, additional

Published
2010
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7. A combined analysis of genome-wide association studies in breast cancer

Author

Li, Jingmei, primary, Humphreys, Keith, additional, Heikkinen, Tuomas, additional, Aittomäki, Kristiina, additional, Blomqvist, Carl, additional, Pharoah, Paul D. P., additional, Dunning, Alison M., additional, Ahmed, Shahana, additional, Hooning, Maartje J., additional, Martens, John W. M., additional, van den Ouweland, Ans M. W., additional, Alfredsson, Lars, additional, Palotie, Aarno, additional, Peltonen-Palotie, Leena, additional, Irwanto, Astrid, additional, Low, Hui Qi, additional, Teoh, Garrett H. K., additional, Thalamuthu, Anbupalam, additional, Easton, Douglas F., additional, Nevanlinna, Heli, additional, Liu, Jianjun, additional, Czene, Kamila, additional, and Hall, Per, additional

Published
2010
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8. Transcriptional Profiling of Mycobacterium tuberculosisExposed to In VitroLysosomal Stress

Author

Lin, Wenwei, de Sessions, Paola Florez, Teoh, Garrett Hor Keong, Mohamed, Ahmad Naim Nazri, Zhu, Yuan O., Koh, Vanessa Hui Qi, Ang, Michelle Lay Teng, Dedon, Peter C., Hibberd, Martin Lloyd, and Alonso, Sylvie

Abstract

ABSTRACTIncreasing experimental evidence supports the idea that Mycobacterium tuberculosishas evolved strategies to survive within lysosomes of activated macrophages. To further our knowledge of M. tuberculosisresponse to the hostile lysosomal environment, we profiled the global transcriptional activity of M. tuberculosiswhen exposed to the lysosomal soluble fraction (SF) prepared from activated macrophages. Transcriptome sequencing (RNA-seq) analysis was performed using various incubation conditions, ranging from noninhibitory to cidal based on the mycobacterial replication or killing profile. Under inhibitory conditions that led to the absence of apparent mycobacterial replication, M. tuberculosisexpressed a unique transcriptome with modulation of genes involved in general stress response, metabolic reprogramming, respiration, oxidative stress, dormancy response, and virulence. The transcription pattern also indicates characteristic cell wall remodeling with the possible outcomes of increased infectivity, intrinsic resistance to antibiotics, and subversion of the host immune system. Among the lysosome-specific responses, we identified the glgE-mediated 1,4 α-glucan synthesis pathway and a defined group of VapBC toxin/anti-toxin systems, both of which represent toxicity mechanisms that potentially can be exploited for killing intracellular mycobacteria. A meta-analysis including previously reported transcriptomic studies in macrophage infection and in vitrostress models was conducted to identify overlapping and nonoverlapping pathways. Finally, the Tap efflux pump-encoding gene Rv1258cwas selected for validation. An M. tuberculosis ΔRv1258cmutant was constructed and displayed increased susceptibility to killing by lysosomal SF and the antimicrobial peptide LL-37, as well as attenuated survival in primary murine macrophages and human macrophage cell line THP-1.

Published
2016
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