Article
Oncology
Fereshteh Izadi, Benjamin P. Sharpe, Stella P. Breininger, Maria Secrier, Jane Gibson, Robert C. Walker, Saqib Rahman, Ginny Devonshire, Megan A. Lloyd, Zoe S. Walters, Rebecca C. Fitzgerald, Matthew J. J. Rose-Zerilli, Tim J. Underwood
Summary: Esophageal adenocarcinoma (EAC) patients receive pre-operative chemotherapy, but a significant portion do not respond to this treatment, exhibiting chromosomal instability and gene copy number alterations. Different genetic profiles, including mutations in the tumor suppressor NAV3, are associated with non-responders, presenting potential drug targets for alternative treatment pathways.
Article
Biochemistry & Molecular Biology
Thomas J. Colgan, Andres N. Arce, Richard J. Gill, Ana Ramos Rodrigues, Abdoulie Kanteh, Elizabeth J. Duncan, Li Li, Lars Chittka, Yannick Wurm
Summary: This study analyzed the genomes of Bombus terrestris bumblebees in Great Britain and found genetic diversity within the population as well as signatures of recent adaptation affecting key processes. Unusual genomic features were also discovered, indicating the resilience of this pollinator species to future pressures. Applying this approach to other species can help understand their adaptive potential and develop conservation strategies.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Yibo Hu, Lijun Yu, Huizhong Fan, Guangping Huang, Qi Wu, Yonggang Nie, Shuai Liu, Li Yan, Fuwen Wei
Summary: This study investigated the genomic mechanisms of coevolution between nonmodel mammals and their parasitic roundworms. The research revealed that the parasitic roundworms did not phylogenetically coevolve with their hosts but showed coevolution in specific proteins during protein interaction. Additionally, roundworms in both pandas exhibited unique genetic features related to metallopeptidase genes and fast larval development.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Leeban H. Yusuf, Yolitzi Saldivar Lemus, Peter Thorpe, Constantino Macias Garcia, Michael G. Ritchie
Summary: The transition from oviparity to viviparity has occurred independently multiple times across vertebrates, presenting a case of phenotypic convergence. Although there is striking similarity among the genes and molecular pathways involved in the evolution of viviparity across different vertebrate groups, the extent of molecular convergence in genomic divergence remains unclear. Our study on a group of ray-finned freshwater fish suggests that independent transitions to viviparity are not strongly associated with an excess of molecular convergence, but a few genes show evidence of convergent evolution.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Review
Biochemistry & Molecular Biology
Jason Tasoulas, Sonal Srivastava, Xiaonan Xu, Valentina Tarasova, Anastasios Maniakas, Florian A. Karreth, Antonio L. Amelio
Summary: The head and neck region is highly susceptible to cancer, with over 1.5 million new cases reported worldwide in 2020. Significant progress has been made in understanding the disease mechanisms and tailoring treatments to individual tumor characteristics using genetically engineered mouse models. These models have successfully replicated various aspects of head and neck cancers.
Review
Oncology
Reihaneh Alsadat Mahmoudian, Moein Farshchian, Mohammad Reza Abbaszadegan
Summary: Esophageal cancer is a leading cause of cancer-related deaths worldwide, and understanding the mechanisms of its development is crucial for improving patient outcomes. Genetically engineered mouse models provide valuable insights into cancer pathogenesis and treatment strategies, despite the differences between mice and humans. By addressing challenges in modeling and utilizing advanced technologies, researchers can maximize the value of studying esophageal cancer in GEMMs.
EXPERIMENTAL CELL RESEARCH
(2021)
Review
Cell Biology
William Hill, Deborah R. Caswell, Charles Swanton
Summary: Cancer undergoes clonal evolution with high intratumor heterogeneity, influenced by both internal and external factors. Advances in sequencing technology have enabled the creation of diverse mouse models to explore mechanisms of tumor evolution.
TRENDS IN CELL BIOLOGY
(2021)
Article
Ecology
Elizabeth Ortega-Mayagoitia, Jose Arturo Alcantara-Rodriguez, Javier Urban-Olivares, Jorge E. Campos, Jorge Ciros-Perez
Summary: The study reveals that ecological divergence in copepod populations is influenced by salinity and the permanence/ephemerality of the lakes. Adaptation leads to reduced gene flow and accumulation of genomic differentiation through neutral evolution, ultimately promoting diversification and speciation.
FRESHWATER BIOLOGY
(2022)
Review
Oncology
Yuriko Saiki, Can Jiang, Masaki Ohmuraya, Toru Furukawa
Summary: Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy and a major cause of cancer-related deaths worldwide. Recent multi-gene analysis methods have provided valuable insight into the molecular characteristics of pancreatic tumors, with different types of pancreatic cancer and precursor lesions showing specific molecular alterations. Genetically engineered mouse models (GEMMs) driven by oncogenic Kras have proven to be useful in understanding the roles of altered genes and recapitulating key features of human PDAC.
Review
Biochemistry & Molecular Biology
Niat T. Gebru, Shannon E. Hill, Laura J. Blair
Summary: FK506 binding protein 51 (FKBP51) is a molecular chaperone involved in stress response and various biological processes. Genetic and epigenetic alterations in the FKBP5 gene are associated with neuropsychiatric disorders. Animal models, such as mouse models, have played a crucial role in understanding the function of FKBP51. This review examines different mouse models of FKBP5, discussing their generation, observations, and potential implications for stress-related disorders.
JOURNAL OF CELLULAR BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Lauric Reynes, Thierry Thibaut, Stephane Mauger, Aurelie Blanfune, Florian Holon, Corinne Cruaud, Arnaud Couloux, Myriam Valero, Didier Aurelle
Summary: The study identified genomic signatures of partial clonality in the deep water kelp species Laminaria rodriguezii and compared them with a closely related species Laminaria digitata. The findings showed distinct genetic distributions and different impacts of clonality and genetic drift on population diversity. These results provide insights into the genetic study of asexuality in natural populations and highlight potential applications of RAD-sequencing in investigating partial clonality in various non-model species.
Article
Biochemistry & Molecular Biology
Felix E. G. Beaudry, Joanna L. Rifkin, Amanda L. Peake, Deanna Kim, Madeline Jarvis-Cross, Spencer C. H. Barrett, Stephen Wright
Summary: This study investigates the gene flow between different geographic types of the plant species Rumex hastatulus, revealing that hybrids readily form and survive multiple backcross generations in the field. The study also suggests that the neo-sex chromosomes play a role in reproductive isolation between different geographic types.
Review
Oncology
Kajal Biswas, Altaf Mohammed, Shyam K. Sharan, Robert H. Shoemaker
Summary: Advances in molecular diagnostics have improved the diagnosis and understanding of hereditary cancers. Preclinical experimental models, such as genetically engineered mouse (GEM) models, play a crucial role in studying and preventing cancer in high-risk populations.
Article
Biotechnology & Applied Microbiology
Shaghayegh Soudi, Marc Crepeau, Travis C. Collier, Yoosook Lee, Anthony J. Cornel, Gregory C. Lanzaro
Summary: By integrating whole-genome sequencing data and topo-climate variables, this study identifies 112 genes associated with local environmental adaptation in Ae. aegypti populations in southern and central California. These findings provide insights into how environmental adaptation impacts the arboviral disease landscape and population control efforts.
Article
Multidisciplinary Sciences
Johannes C. van der Mijn, Kristian B. Laursen, Leiping Fu, Francesca Khani, Lukas E. Dow, Dawid G. Nowak, Qiuying Chen, Steven S. Gross, David M. Nanus, Lorraine J. Gudas
Summary: Genetically engineered mouse models (GEMMs) are important for cancer research and therapy development. In this study, researchers developed two GEMMs using inducible CRISPR-Cas9 systems to simulate common chromosome deletions in kidney cancer. The models induced somatic mutations in the kidneys but did not cause tissue transformation. Further research is needed.
SCIENTIFIC REPORTS
(2023)
Article
Genetics & Heredity
Sunny Z. Wu, Ghamdan Al-Eryani, Daniel Lee Roden, Simon Junankar, Kate Harvey, Alma Andersson, Aatish Thennavan, Chenfei Wang, James R. Torpy, Nenad Bartonicek, Taopeng Wang, Ludvig Larsson, Dominik Kaczorowski, Neil Weisenfeld, Cedric R. Uytingco, Jennifer G. Chew, Zachary W. Bent, Chia-Ling Chan, Vikkitharan Gnanasambandapillai, Charles-Antoine Dutertre, Laurence Gluch, Mun N. Hui, Jane Beith, Andrew Parker, Elizabeth Robbins, Davendra Segara, Caroline Cooper, Cindy Mak, Belinda Chan, Sanjay Warrier, Florent Ginhoux, Ewan Millar, Joseph E. Powell, Stephen R. Williams, X. Shirley Liu, Sandra O'Toole, Elgene Lim, Joakim Lundeberg, Charles M. Perou, Alexander Swarbrick
Summary: This study presents a comprehensive transcriptional atlas of the cellular architecture of breast cancer, identifying recurrent neoplastic cell heterogeneity and new immune cell populations associated with clinical outcomes. A multi-omic atlas integrates single-cell RNA sequencing, spatial transcriptomics, and immunophenotyping to stratify breast cancer into nine ecotypes with unique cellular compositions and clinical outcomes.
Article
Oncology
Amber N. Hurson, Mustapha Abubakar, Alina M. Hamilton, Kathleen Conway, Katherine A. Hoadley, Michael Love, Andrew F. Olshan, Charles M. Perou, Montserrat Garcia-Closas, Melissa A. Troester
Summary: This study identified breast cancer risk factors associated with RNA-based TP53 and ER, providing a new etiologic schema of interest in breast cancer prevention research.
CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION
(2022)
Article
Oncology
Achal Patel, Montserrat Garcia-Closas, Andrew F. Olshan, Charles M. Perou, Melissa A. Troester, Michael Love, Arjun Bhattacharya
Summary: This study identifies race-specific genetic associations with breast cancer risk of recurrence scores and suggests mediation of these associations by PAM50 subtype and expression, with implications for clinical interpretation of these scores.
Article
Oncology
Carey K. Anders, Mark G. Woodcock, Amanda E. D. Van Swearingen, Dominic T. Moore, Maria J. Sambade, Sonia Laurie, Alexander Robeson, Oleg Kolupaev, Luz A. Cuaboy, Amy L. Garrett, Karen McKinnon, Kristen Cowens, Dante Bortone, Benjamin C. Calhoun, Alec D. Wilkinson, Lisa Carey, Trevor Jolly, Hyman Muss, Katherine Reeder-Hayes, Rebecca Kaltman, Rachel Jankowitz, Vinay Gudena, Oludamilola Olajide, Charles Perou, E. Claire Dees, Benjamin G. Vincent, Jonathan S. Serody
Summary: This study evaluated the efficacy of using a low dose of cyclophosphamide (Cy) to deplete regulatory T cells (T-regs) before initiating pembrolizumab in patients with triple negative breast cancer (TNBC). The results showed that Cy did not significantly decrease T-regs before pembrolizumab and there was a rapid recovery in T-regs after the first cycle of therapy. Baseline samples with increased B cell gene expression were associated with clinical response and immune-related toxicity (IRT).
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2022)
Article
Oncology
Alina M. Hamilton, Amber N. Hurson, Linnea T. Olsson, Andrea Walens, Joseph Nsonwu-Farley, Erin L. Kirk, Yara Abdou, Stephanie M. Downs-Canner, Jonathan S. Serody, Charles M. Perou, Benjamin C. Calhoun, Melissa A. Troester, Katherine A. Hoadley
Summary: The immune microenvironment in breast cancer is closely related to race, age, tumor subtype, and grade. Black and young women have higher immune response, which may be associated with higher recurrence risk.
CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION
(2022)
Article
Oncology
Sonam Bhatia, Melissa Kramer, Suzanne Russo, Payal Naik, Gayatri Arun, Kyle Brophy, Peter Andrews, Cheng Fan, Charles M. Perou, Jonathan Preall, Taehoon Ha, Dennis Plenker, David A. Tuveson, Arvind Rishi, John E. Wilkinson, W. Richard McCombie, Karen Kostroff, David L. Spector
Summary: This study developed a diverse biobank of patient-derived organoids of triple-negative breast cancer (TNBC) and provided comprehensive insights into TNBC biology and progression. The organoids successfully recapitulated patient tumor characteristics and identified potential mechanisms of tumorigenesis at the single-cell level.
Editorial Material
Oncology
Sarah Asad, Kathryn Kananen, Kurt R. Mueller, W. Fraser Symmans, Yujia Wen, Charles M. Perou, James S. Blachly, James Chen, Benjamin G. Vincent, Daniel G. Stover
JCO CLINICAL CANCER INFORMATICS
(2022)
Article
Oncology
Youli Xia, Xiaping He, Lorna Renshaw, Carlos Martinez-Perez, Charlene Kay, Mark Gray, James Meehan, Joel S. Parker, Charles M. Perou, Lisa A. Carey, J. Michael Dixon, Arran Turnbull
Summary: This study identified molecular mechanisms underlying endocrine therapy resistance (ETR) in hormone receptor-positive breast cancer through in-depth genomic analysis. The results showed that ETR involves diverse changes in somatic genetic and transcriptomic profiles, including mutations, gene expression changes, and activation of signaling pathways. Overcoming resistance will require an individualized approach utilizing genomic and genetic biomarkers and drugs tailored to each patient.
CLINICAL CANCER RESEARCH
(2022)
Article
Cell Biology
Grace Orstad, Gabriela Fort, Timothy J. Parnell, Alex Jones, Chris Stubben, Brian Lohman, Katherine L. Gillis, Walter Orellana, Rushmeen Tariq, Olaf Klingbeil, Klaus Kaestner, Christopher R. Vakoc, Benjamin T. Spike, Eric L. Snyder
Summary: Changes in cellular identity can drive malignant progression and resistance to therapy in lung adenocarcinoma. Loss of FoxA1/2 impairs tumorigenesis in NKX2-1-positive LUAD and leads to collapse of a dual-identity state, driving alternative cellular identity programs associated with non-proliferative states.
DEVELOPMENTAL CELL
(2022)
Article
Oncology
Audrey Y. Jung, Thomas U. Ahearn, Sabine Behrens, Pooja Middha, Manjeet K. Bolla, Qin Wang, Volker Arndt, Kristan J. Aronson, Annelie Augustinsson, Laura E. Beane Freeman, Heiko Becher, Hermann Brenner, Federico Canzian, Lisa A. Carey, Cts Consortium, Kamila Czene, A. Heather Eliassen, Mikael Eriksson, D. Gareth Evans, Jonine D. Figueroa, Lin Fritschi, Marike Gabrielson, Graham G. Giles, Pascal Guenel, Andreas Hadjisavvas, Christopher A. Haiman, Niclas Hakansson, Per Hall, Ute Hamann, Reiner Hoppe, John L. Hopper, Anthony Howell, David J. Hunter, Anika Huesing, Rudolf Kaaks, Veli-Matti Kosma, Stella Koutros, Peter Kraft, James Lacey, Loic Le Marchand, Jolanta Lissowska, Maria A. Loizidou, Arto Mannermaa, Tabea Maurer, Rachel A. Murphy, Andrew F. Olshan, Hakan Olsson, Alpa Patel, Charles M. Perou, Gad Rennert, Rana Shibli, Xiao-Ou Shu, Melissa C. Southey, Jennifer Stone, Rulla M. Tamimi, Lauren R. Teras, Melissa A. Troester, Therese Truong, Celine M. Vachon, Sophia S. Wang, Alicja Wolk, Anna H. Wu, Xiaohong R. Yang, Wei Zheng, Alison M. Dunning, Paul D. P. Pharoah, Douglas F. Easton, Roger L. Milne, Nilanjan Chatterjee, Marjanka K. Schmidt, Montserrat Garcia-Closas, Jenny Chang-Claude
Summary: Reproductive factors are differentially associated with risk of breast cancer subtypes, and triple-negative breast cancer has a distinct reproductive risk factor profile.
JNCI-JOURNAL OF THE NATIONAL CANCER INSTITUTE
(2022)
Article
Oncology
Aatish Thennavan, Susana Garcia-Recio, Siyao Liu, Xiaping He, Charles M. Perou
Summary: Ductal carcinoma in situ (DCIS) of the breast is a precursor of invasive ductal carcinoma (IDC). This study utilizes mouse models and human samples to identify features associated with DCIS progression. The analysis reveals malignant cells and tumor microenvironmental changes in DCIS and IDC, and suggests the existence of intrinsic subtype unique DCIS features. The findings may contribute to the identification and treatment of progression-prone DCIS in human basal-like breast cancers.
Article
Biology
Edward R. Polanco, Tarek E. Moustafa, Andrew Butterfield, Sandra D. Scherer, Emilio Cortes-Sanchez, Tyler Bodily, Benjamin T. Spike, Bryan E. Welm, Philip S. Bernard, Thomas A. Zangle
Summary: This article introduces a real-time and label-free approach based on quantitative phase imaging to determine drug sensitivity, which has significant advantages over endpoint viability or metabolic assays, and reveals single cell response heterogeneity.
COMMUNICATIONS BIOLOGY
(2022)
Article
Oncology
Frederick M. Howard, James Dolezal, Sara Kochanny, Galina Khramtsova, Jasmine Vickery, Andrew Srisuwananukorn, Anna Woodard, Nan Chen, Rita Nanda, Charles M. Perou, Olufunmilayo I. Olopade, Dezheng Huo, Alexander T. Pearson
Summary: Gene expression-based recurrence assays are recommended for guiding chemotherapy in hormone receptor-positive, HER2-negative breast cancer, but their high cost and limited availability pose challenges. This study presents a deep learning model that utilizes digital histology and clinical risk factors to predict recurrence assay results and the risk of recurrence, surpassing the performance of established clinical nomograms. The model can identify patients with excellent prognoses who may not require further genomic testing.
Article
Oncology
Jiehui Deng, Aatish Thennavan, Igor Dolgalev, Ting Chen, Jie Li, Antonio Marzio, John T. Poirier, David H. Peng, Mirna Bulatovic, Subhadip Mukhopadhyay, Heather Silver, Eleni Papadopoulos, Val Pyon, Cassandra Thakurdin, Han Han, Fei Li, Shuai Li, Hailin Ding, Hai Hu, Yuanwang Pan, Vajira Weerasekara, Baishan Jiang, Eric S. Wang, Ian Ahearn, Mark Philips, Thales Papagiannakopoulos, Aristotelis Tsirigos, Eli Rothenberg, Justin Gainor, Gordon J. Freeman, Charles M. Rudin, Nathanael S. Gray, Peter S. Hammerman, Michele Pagano, John V. Heymach, Charles M. Perou, Nabeel Bardeesy, Kwok-Kin Wong
Summary: The study found that LKB1-deficient lung tumors are sensitive to autophagy inhibition, which can restore impaired antigen presentation and antitumor immune responses, enhancing the effectiveness of PD-1 immunotherapy. Additionally, LKB1 deficiency inhibits antigen processing and presentation, but this can be reversed by targeting the autophagy pathway to restore immunoproteasome activity and antigen presentation.
Article
Oncology
Halei C. Benefield, Katherine E. Reeder-Hayes, Hazel B. Nichols, Benjamin C. Calhoun, Michael Love, Erin L. Kirk, Joseph Geradts, Katherine A. Hoadley, Stephen R. Cole, H. Shelton Earp, Andrew F. Olshan, Lisa A. Carey, Charles M. Perou, Melissa A. Troester
Summary: Black women with HR+/HER2-negative breast cancer have a higher risk of recurrence compared to White women, especially among those with aggressive tumors. Racial disparities in recurrence rates may be influenced by differences in treatment approaches. Identifying the causes of variations in cancer treatment is important for reducing outcome disparities.
JNCI CANCER SPECTRUM
(2021)