UNSEG: unsupervised segmentation of cells and their nuclei in complex tissue samples

Autor: Bogdan Kochetov, Phoenix D. Bell, Paulo S. Garcia, Akram S. Shalaby, Rebecca Raphael, Benjamin Raymond, Brian J. Leibowitz, Karen Schoedel, Rhonda M. Brand, Randall E. Brand, Jian Yu, Lin Zhang, Brenda Diergaarde, Robert E. Schoen, Aatur Singhi, Shikhar Uttam

Publikováno v: Communications Biology, Vol 7, Iss 1, Pp 1-14 (2024)

Abstract Multiplexed imaging technologies have made it possible to interrogate complex tissue microenvironments at sub-cellular resolution within their native spatial context. However, proper quantification of this complexity requires the ability to

Externí odkaz: https://doaj.org/article/874dc85ae11740acb138f7e5d23648d4

Fine-mapping analysis including over 254,000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes

Autor: Zhishan Chen, Xingyi Guo, Ran Tao, Jeroen R. Huyghe, Philip J. Law, Ceres Fernandez-Rozadilla, Jie Ping, Guochong Jia, Jirong Long, Chao Li, Quanhu Shen, Yuhan Xie, Maria N. Timofeeva, Minta Thomas, Stephanie L. Schmit, Virginia Díez-Obrero, Matthew Devall, Ferran Moratalla-Navarro, Juan Fernandez-Tajes, Claire Palles, Kitty Sherwood, Sarah E. W. Briggs, Victoria Svinti, Kevin Donnelly, Susan M. Farrington, James Blackmur, Peter G. Vaughan-Shaw, Xiao-Ou Shu, Yingchang Lu, Peter Broderick, James Studd, Tabitha A. Harrison, David V. Conti, Fredrick R. Schumacher, Marilena Melas, Gad Rennert, Mireia Obón-Santacana, Vicente Martín-Sánchez, Jae Hwan Oh, Jeongseon Kim, Sun Ha Jee, Keum Ji Jung, Sun-Seog Kweon, Min-Ho Shin, Aesun Shin, Yoon-Ok Ahn, Dong-Hyun Kim, Isao Oze, Wanqing Wen, Keitaro Matsuo, Koichi Matsuda, Chizu Tanikawa, Zefang Ren, Yu-Tang Gao, Wei-Hua Jia, John L. Hopper, Mark A. Jenkins, Aung Ko Win, Rish K. Pai, Jane C. Figueiredo, Robert W. Haile, Steven Gallinger, Michael O. Woods, Polly A. Newcomb, David Duggan, Jeremy P. Cheadle, Richard Kaplan, Rachel Kerr, David Kerr, Iva Kirac, Jan Böhm, Jukka-Pekka Mecklin, Pekka Jousilahti, Paul Knekt, Lauri A. Aaltonen, Harri Rissanen, Eero Pukkala, Johan G. Eriksson, Tatiana Cajuso, Ulrika Hänninen, Johanna Kondelin, Kimmo Palin, Tomas Tanskanen, Laura Renkonen-Sinisalo, Satu Männistö, Demetrius Albanes, Stephanie J. Weinstein, Edward Ruiz-Narvaez, Julie R. Palmer, Daniel D. Buchanan, Elizabeth A. Platz, Kala Visvanathan, Cornelia M. Ulrich, Erin Siegel, Stefanie Brezina, Andrea Gsur, Peter T. Campbell, Jenny Chang-Claude, Michael Hoffmeister, Hermann Brenner, Martha L. Slattery, John D. Potter, Kostas K. Tsilidis, Matthias B. Schulze, Marc J. Gunter, Neil Murphy, Antoni Castells, Sergi Castellví-Bel, Leticia Moreira, Volker Arndt, Anna Shcherbina, D. Timothy Bishop, Graham G. Giles, Melissa C. Southey, Gregory E. Idos, Kevin J. McDonnell, Zomoroda Abu-Ful, Joel K. Greenson, Katerina Shulman, Flavio Lejbkowicz, Kenneth Offit, Yu-Ru Su, Robert Steinfelder, Temitope O. Keku, Bethany van Guelpen, Thomas J. Hudson, Heather Hampel, Rachel Pearlman, Sonja I. Berndt, Richard B. Hayes, Marie Elena Martinez, Sushma S. Thomas, Paul D. P. Pharoah, Susanna C. Larsson, Yun Yen, Heinz-Josef Lenz, Emily White, Li Li, Kimberly F. Doheny, Elizabeth Pugh, Tameka Shelford, Andrew T. Chan, Marcia Cruz-Correa, Annika Lindblom, David J. Hunter, Amit D. Joshi, Clemens Schafmayer, Peter C. Scacheri, Anshul Kundaje, Robert E. Schoen, Jochen Hampe, Zsofia K. Stadler, Pavel Vodicka, Ludmila Vodickova, Veronika Vymetalkova, Christopher K. Edlund, W. James Gauderman, David Shibata, Amanda Toland, Sanford Markowitz, Andre Kim, Stephen J. Chanock, Franzel van Duijnhoven, Edith J. M. Feskens, Lori C. Sakoda, Manuela Gago-Dominguez, Alicja Wolk, Barbara Pardini, Liesel M. FitzGerald, Soo Chin Lee, Shuji Ogino, Stephanie A. Bien, Charles Kooperberg, Christopher I. Li, Yi Lin, Ross Prentice, Conghui Qu, Stéphane Bézieau, Taiki Yamaji, Norie Sawada, Motoki Iwasaki, Loic Le Marchand, Anna H. Wu, Chenxu Qu, Caroline E. McNeil, Gerhard Coetzee, Caroline Hayward, Ian J. Deary, Sarah E. Harris, Evropi Theodoratou, Stuart Reid, Marion Walker, Li Yin Ooi, Ken S. Lau, Hongyu Zhao, Li Hsu, Qiuyin Cai, Malcolm G. Dunlop, Stephen B. Gruber, Richard S. Houlston, Victor Moreno, Graham Casey, Ulrike Peters, Ian Tomlinson, Wei Zheng

Publikováno v: Nature Communications, Vol 15, Iss 1, Pp 1-17 (2024)

Abstract Genome-wide association studies (GWAS) have identified more than 200 common genetic variants independently associated with colorectal cancer (CRC) risk, but the causal variants and target genes are mostly unknown. We sought to fine-map all k

Externí odkaz: https://doaj.org/article/a9c9d74556364a62b1ef09719244a952

FAK loss reduces BRAFV600E-induced ERK phosphorylation to promote intestinal stemness and cecal tumor formation

Autor: Chenxi Gao, Huaibin Ge, Shih-Fan Kuan, Chunhui Cai, Xinghua Lu, Farzad Esni, Robert E Schoen, Jing H Wang, Edward Chu, Jing Hu

Publikováno v: eLife, Vol 13 (2024)

BRAFV600E mutation is a driver mutation in the serrated pathway to colorectal cancers. BRAFV600E drives tumorigenesis through constitutive downstream extracellular signal-regulated kinase (ERK) activation, but high-intensity ERK activation can also t

Externí odkaz: https://doaj.org/article/e2a122bab7f34dd78f4661a9fc648667

Prospective and Mendelian randomization analyses on the association of circulating fatty acid binding protein 4 (FABP-4) and risk of colorectal cancer

Autor: Katharina Nimptsch, Krasimira Aleksandrova, Thu Thi Pham, Nikos Papadimitriou, Jürgen Janke, Sofia Christakoudi, Alicia Heath, Anja Olsen, Anne Tjønneland, Matthias B. Schulze, Verena Katzke, Rudolf Kaaks, Bethany van Guelpen, Justin Harbs, Domenico Palli, Alessandra Macciotta, Fabrizio Pasanisi, Sandra Milena Colorado Yohar, Marcela Guevara, Pilar Amiano, Sara Grioni, Paula Gabriela Jakszyn, Jane C. Figueiredo, N. Jewel Samadder, Christopher I. Li, Victor Moreno, John D. Potter, Robert E. Schoen, Caroline Y. Um, Elisabete Weiderpass, Mazda Jenab, Marc J. Gunter, Tobias Pischon

Publikováno v: BMC Medicine, Vol 21, Iss 1, Pp 1-16 (2023)

Abstract Background Fatty acid binding protein 4 (FABP-4) is a lipid-binding adipokine upregulated in obesity, which may facilitate fatty acid supply for tumor growth and promote insulin resistance and inflammation and may thus play a role in colorec

Externí odkaz: https://doaj.org/article/39470599b6c34cc8a9ff758b8ae4253f

Enrollee characteristics and receipt of colorectal cancer testing in Pennsylvania after adoption of the Affordable Care Act Medicaid expansion

Autor: Kirsten Y. Eom, Scott D. Rothenberger, Marian P. Jarlenski, Robert E. Schoen, Evan S. Cole, Lindsay M. Sabik

Publikováno v: Cancer Medicine, Vol 12, Iss 14, Pp 15455-15467 (2023)

Abstract Background Colorectal cancer (CRC) is the fourth most common cancer and the second leading cause of cancer‐related death in the U.S. Despite increased CRC screening rates, they remain low among low‐income non‐older adults, including Me

Externí odkaz: https://doaj.org/article/677189ee34ab4101a07ed2d59fcd9375