February 21, 2012 u vol. 109 u no. 8 u 2685–3190 Cover image: An artistic rendition of combined immunofluorescence and FISH images of a breast tumor shows the antigens CD44 (blue) and CD24 (yellow), chromosome segment 8q24 (red), and the centromere of chromosome 8 (green). Kornelia Polyak and Peter K. Vogt present an overview of progress in major areas of current breast cancer research, including results that might lead to improved treatment outcomes for patients. See the introduction to the Breast Cancer Special Feature on pages 2715–2717. Image courtesy of Vanessa Almendro (Dana-Farber Cancer Institute, Harvard Medical School, Boston). From the Cover 2715 Intra-tumor diversity in breast cancer 2890 Nanoscale modeling and design 3077 microRNAs from RNA viruses 3101 Dopamine signaling and nicotine withdrawal Contents COMMENTARIES 2691 RNA modeling, naturally Eric Westhof THIS WEEK IN PNAS See companion article on page 2890 2693 Actin bends over backward for directional branching 2685 In This Issue Tatyana M. Svitkina See companion article on page 2913 2695 MicroRNA expression by an oncogenic retrovirus LETTERS (ONLINE ONLY) Bryan R. Cullen See companion article on page 3077 E461 Viruses do replicate in cell-free systems 2697 Shifting pharmacology of nicotine use and withdrawal: Yervand E. Karapetyan Breaking the cycle of drug abuse E462 Reply to Karapetyan: Viral synthesis and assembly is Thibaut Sesia and Anthony A. Grace unlikely to occur under cell-free PMCA conditions See companion article on page 3101 Bruce Chesebro, Mikael Klingeborn, and Brent Race 2699 AgRP neurons: The foes of reproduction in leptin-deficient obese subjects Marcelo O. Dietrich and Tamas L. Horvath QNAS See companion article on page 3155 2687 QnAs with Richard T. Durrett PNAS PLUS (AUTHOR SUMMARIES) Sandeep Ravindran PHYSICAL SCIENCES PROFILE CHEMISTRY 2688 Profile of Robert B. Goldberg 2705 Unusual macrocyclic lactone sex pheromone of Nicholette Zeliadt Parcoblatta lata, a primary food source of the See Inaugural Article on page 8063 in issue 18 of volume 107 endangered red-cockaded woodpecker Dorit Eliyahu, Satoshi Nojima, Richard G. Santangelo, Shannon Carpenter, Francis X. Webster, David J. Kiemle, Cesar Gemeno, Walter S. Leal, and Coby Schal Free online through the PNAS open access option. See full research article on page E490 of www.pnas.org PNAS u February 21, 2012 u vol. 109 u no. 8 u iii–ix Downloaded by guest on October 1, 2021 SOCIAL SCIENCES BREAST CANCER SPECIAL FEATURE ANTHROPOLOGY 2701 Heterogeneity of hunting ability and nutritional status INTRODUCTION among domestic dogs in lowland Nicaragua 2715 Progress in breast cancer research Jeremy M. Koster and Kenneth B. Tankersley Kornelia Polyak and Peter K. Vogt See full research article on page E463 of www.pnas.org RESEARCH ARTICLES BIOLOGICAL SCIENCES 2718 Feedback upregulation of HER3 (ErbB3) expression and CELL BIOLOGY activity attenuates antitumor effect of PI3K inhibitors Anindita Chakrabarty, Violeta Sánchez, María G. Kuba, 2702 Rabenosyn-5 defines the fate of the transferrin receptor Cammie Rinehart, and Carlos L. Arteaga following clathrin-mediated endocytosis Deanna M. Navaroli, Karl D. Bellvé, Clive Standley, Lawrence M. Lifshitz, James Cardia, David Lambright, 2724 Subtype and pathway specific responses to anticancer Deborah Leonard, Kevin E. Fogarty, and Silvia Corvera compounds in breast cancer See full research article on page E471 of www.pnas.org Laura M. Heiser, Anguraj Sadanandam, Wen-Lin Kuo, Stephen C. Benz, Theodore C. Goldstein, Sam Ng, William J. Gibb, Nicholas J. Wang, Safiyyah Ziyad, Frances Tong, DEVELOPMENTAL BIOLOGY Nora Bayani, Zhi Hu, Jessica I. Billig, Andrea Dueregger, 2704 Compensatory functions of histone deacetylase 1 Sophia Lewis, Lakshmi Jakkula, James E. Korkola, Steffen (HDAC1) and HDAC2 regulate transcription and Durinck, François Pepin, Yinghui Guan, Elizabeth Purdom, apoptosis during mouse oocyte development Pierre Neuvial, Henrik Bengtsson, Kenneth W. Wood, Pengpeng Ma, Hua Pan, Rusty L. Montgomery, Peter G. Smith, Lyubomir T. Vassilev, Bryan T. Hennessy, Eric N. Olson, and Richard M. Schultz Joel Greshock, Kurtis E. Bachman, Mary Ann Hardwicke, See full research article on page E481 of www.pnas.org John W. Park, Laurence J. Marton, Denise M. Wolf, Eric A. Collisson, Richard M. Neve, Gordon B. Mills, Terence P. ECOLOGY Speed, Heidi S. Feiler, Richard F. Wooster, David Haussler, Joshua M. Stuart, Joe W. Gray, and Paul T. Spellman 2705 Unusual macrocyclic lactone sex pheromone of Parcoblatta lata, a primary food source of the fi endangered red-cockaded woodpecker 2730 Genome-wide functional screen identi es Dorit Eliyahu, Satoshi Nojima, Richard G. Santangelo, a compendium of genes affecting sensitivity Shannon Carpenter, Francis X. Webster, David J. Kiemle, to tamoxifen Cesar Gemeno, Walter S. Leal, and Coby Schal Ana M. Mendes-Pereira, David Sims, Tim Dexter, See full research article on page E490 of www.pnas.org Kerry Fenwick, Ioannis Assiotis, Iwanka Kozarewa, Costas Mitsopoulos, Jarle Hakas, Marketa Zvelebil, Christopher J. Lord, and Alan Ashworth MICROBIOLOGY 2707 Mevalonate governs interdependency of ergosterol and 2736 The HOXB7 protein renders breast cancer cells resistant siderophore biosyntheses in the fungal pathogen to tamoxifen through activation of the EGFR pathway Aspergillus fumigatus Kideok Jin, Xiangjun Kong, Tariq Shah, Marie-France Penet, Sabiha Yasmin, Laura Alcazar-Fuoli, Mario Gründlinger, Flonne Wildes, Dennis C. Sgroi, Xiao-Jun Ma, Yi Huang, Thomas Puempel, Timothy Cairns, Michael Blatzer, Jordi F. Anne Kallioniemi, Goran Landberg, Ivan Bieche, Xinyan Wu, Lopez, Joan O. Grimalt, Elaine Bignell, and Hubertus Haas Peter E. Lobie, Nancy E. Davidson, Zaver M. Bhujwalla, See full research article on page E497 of www.pnas.org Tao Zhu, and Saraswati Sukumar NEUROSCIENCE 2742 Maintenance of hormone responsiveness in luminal 2709 Phoneme and word recognition in the auditory breast cancers by suppression of Notch ventral stream James M. Haughian, Mauricio P. Pinto, J. Chuck Harrell, Iain DeWitt and Josef P. Rauschecker Brian S. Bliesner, Kristiina M. Joensuu, Wendy W. Dye, See full research article on page E505 of www.pnas.org Carol A. Sartorius, Aik Choon Tan, Päivi Heikkilä, Charles M. Perou, and Kathryn B. Horwitz 2711 Reduced release probability prevents vesicle depletion and transmission failure at dynamin mutant synapses 2748 Transducin-like enhancer protein 1 mediates estrogen Xuelin Lou, Fan Fan, Mirko Messa, Andrea Raimondi, receptor binding and transcriptional activity in breast Yumei Wu, Loren L. Looger, Shawn M. Ferguson, cancer cells and Pietro De Camilli Kelly A. Holmes, Antoni Hurtado, Gordon D. Brown, See full research article on page E515 of www.pnas.org Rosalind Launchbury, Caryn S. Ross-Innes, James Hadfield, Duncan T. Odom, and Jason S. Carroll PHYSIOLOGY 2713 Sweet taste receptor signaling in beta cells mediates 2754 Cyclin-dependent kinase subunit (Cks) 1 or Cks2 fructose-induced potentiation of glucose-stimulated overexpression overrides the DNA damage response insulin secretion barrier triggered by activated oncoproteins George A. Kyriazis, Mangala M. Soundarapandian, Vasco Liberal, Hanna-Stina Martinsson-Ahlzén, Jennifer and Björn Tyrberg Liberal, Charles H. Spruck, Martin Widschwendter, See full research article on page E524 of www.pnas.org Clare H. McGowan, and Steven I. Reed iv u www.pnas.org Downloaded by guest on October 1, 2021 2760 Homeobox B9 induces epithelial-to-mesenchymal 2820 Altered antisense-to-sense transcript ratios in transition-associated radioresistance by accelerating breast cancer DNA damage responses Reo Maruyama, Michail Shipitsin, Sibgat Choudhury, Naokazu Chiba, Valentine Comaills, Bunsyo Shiotani, Zhenhua Wu, Alexei Protopopov, Jun Yao, Pang-Kuo Lo, Fumiyuki Takahashi, Toshiyuki Shimada, Ken Tajima, Marina Bessarabova, Alex Ishkin, Yuri Nikolsky, X. Shirley Daniel Winokur, Tetsu Hayashida, Henning Willers, Liu, Saraswati Sukumar, and Kornelia Polyak Elena Brachtel, Maria d. M. Vivanco, Daniel A. Haber, Lee Zou, and Shyamala Maheswaran PHYSICAL SCIENCES 2766 Sensitization of BCL-2–expressing breast tumors to chemotherapy by the BH3 mimetic ABT-737 APPLIED PHYSICAL SCIENCES Samantha R. Oakes, François Vaillant, Elgene Lim, Lily Lee, Kelsey Breslin, Frank Feleppa, Siddhartha Deb, Matthew E. 2825 A small world of weak ties provides optimal global Ritchie, Elena Takano, Teresa Ward, Stephen B. Fox, Daniele integration of self-similar modules in functional Generali, Gordon K. Smyth, Andreas Strasser, David C. S. brain networks Huang, Jane E. Visvader, and Geoffrey J. Lindeman Lazaros K. Gallos, Hernán A. Makse, and Mariano Sigman 3059 The heterogeneous motility of the Lyme disease 2772 Defining the cellular precursors to human breast cancer spirochete in gelatin mimics dissemination through tissue Patricia J. Keller, Lisa M. Arendt, Adam Skibinski, Tanya Michael W. Harman, Star M. Dunham-Ems, Melissa J. Logvinenko, Ina Klebba, Shumin Dong, Avi E. Smith, Caimano, Alexia A. Belperron, Linda K. Bockenstedt, Aleix Prat, Charles M. Perou, Hannah Gilmore, Henry C. Fu, Justin D. Radolf, and Charles W. Wolgemuth Stuart Schnitt, Stephen P. Naber, Jonathan A. Garlick, and Charlotte Kuperwasser EARTH, ATMOSPHERIC, AND PLANETARY SCIENCES 2778 Comparative oncogenomics identifies breast tumors 2831 A serpentinite-hosted ecosystem in the Southern enriched in functional tumor-initiating cells Mariana Forearc Jason I. Herschkowitz, Wei Zhao, Mei Zhang, Jerry Yasuhiko Ohara, Mark K. Reagan, Katsunori Fujikura,