Article
Multidisciplinary Sciences
Alecia-Jane Twigger, Lisa K. Engelbrecht, Karsten Bach, Isabel Schultz-Pernice, Sara Pensa, Jack Stenning, Stefania Petricca, Christina H. Scheel, Walid T. Khaled
Summary: This study characterizes cells in human milk and identifies epithelial cells similar to luminal progenitors and immune cells. The findings contribute to understanding the remodelling of human mammary tissue during pregnancy and lactation, and provide insights into the interplay between pregnancy, lactation, and breast cancer.
NATURE COMMUNICATIONS
(2022)
Article
Neurosciences
Ugomma C. Eze, Aparna Bhaduri, Maximilian Haeussler, Tomasz J. Nowakowski, Arnold R. Kriegstein
Summary: Through single-cell RNA sequencing, nine progenitor populations at the earliest stages of human brain development were identified, including a highly prevalent mesenchymal-like population that disappears once neurogenesis begins. Comparison with mouse progenitor populations revealed two clusters enriched in the early stages of human cortical development. Organoid systems displayed low fidelity to neuroepithelial and early radial glia cell types, but improved as neurogenesis progressed.
NATURE NEUROSCIENCE
(2021)
Article
Cell Biology
Ahmed K. Elsayed, Ihab Younis, Gowher Ali, Khalid Hussain, Essam M. Abdelalim
Summary: This study reveals the crucial role of FOXA2 in human pancreatic endocrine development and suggests that defects in FOXA2 may lead to diabetes. Generating induced pluripotent stem cells from a patient with FOXA2 haploinsufficiency and subsequent beta-cell differentiation provided insights into the impact of FOXA2 on pancreatic development.
CELL DEATH & DISEASE
(2021)
Article
Multidisciplinary Sciences
Sahar J. Alothman, Keunsoo Kang, Xuefeng Liu, Ewa Krawczyk, Redha Azhar, Rong Hu, David Goerlitz, Bhaskar Kallakury, Priscilla A. Furth
Summary: This study explores the biology and transcriptomes of non-cancerous human mammary epithelial cells at risk for breast cancer development. The findings suggest that high-risk cells exhibit diverse behavioral and gene expression patterns, potentially indicating different risk profiles.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Saeed Farjami, Karen Camargo Sosa, Jonathan H. P. Dawes, Robert N. Kelsh, Andrea Rocco
Summary: The article presents biologically motivated mathematical models for cell differentiation that generate oscillations, providing alternative explanations to Waddington's epigenetic landscape. Two generic dynamical scenarios for describing the differentiation process are proposed, involving gradual variation of control parameters. Analyses on repressilator and its variants indicate that gene regulatory networks with repressilator-like characteristics may play a role in cell fate selection through oscillatory processes.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2021)
Article
Cell & Tissue Engineering
Kyungtae Lim, Alex P. A. Donovan, Walfred Tang, Dawei Sun, Peng He, J. Patrick Pett, Sarah A. Teichmann, John C. Marioni, Kerstin B. Meyer, Andrea H. Brand, Emma L. Rawlins
Summary: Variation in lung alveolar development is linked to disease susceptibility. Researchers have identified an alveolar-fated epithelial progenitor in human fetal lungs and have grown them as self-organizing organoids to study cell lineage commitment. Using this system, they have discovered the role of Wnt signaling and the Wnt-NKX2.1 axis in alveolar differentiation, as well as the effects of genetic variation on this process.
Article
Multidisciplinary Sciences
Elizabeth F. Maughan, Robert E. Hynds, Adam Pennycuick, Ersilia Nigro, Kate H. C. Gowers, Celine Denais, Sandra Gomez-Lopez, Kyren A. Lazarus, Jessica C. Orr, David R. Pearce, Sarah E. Clarke, Dani Do Hyang Lee, Maximillian N. J. Woodall, Tereza Masonou, Katie-Marie Case, Vitor H. Teixeira, Benjamin E. Hartley, Richard J. Hewitt, Chadwan Al Yaghchi, Gurpreet S. Sandhu, Martin A. Birchall, Christopher O'Callaghan, Claire M. Smith, Paolo De Coppi, Colin R. Butler, Sam M. Janes
Summary: This study found cell-intrinsic differences between airway epithelial cells from children and adults in both homeostatic and proliferative states, with pediatric cells showing higher colony formation ability and outcompeting adult cells in cell culture.
Article
Multidisciplinary Sciences
Ana Catarina Menezes, Christabel Dixon, Anna Scholz, Rachael Nicholson, Adam Leckenby, Aleksandra Azevedo, Sarah Baker, Amanda F. Gilkes, Sara Davies, Richard L. Darley, Alex Tonks
Summary: This study demonstrates the regulatory role of RUNX3 in normal human erythropoiesis. RUNX3 has a modest impact on early erythroid growth and development, but promotes growth and inhibits terminal differentiation in late-stage erythroid development. Overexpression of RUNX3 increases colony formation in liquid culture.
SCIENTIFIC REPORTS
(2022)
Article
Cell Biology
Long Wang, Mu-Chun Wan, Ren-Yu Liao, Jie Xu, Zhou-Geng Xu, Hao-Chen Xue, Yan-Xia Mai, Jia-Wei Wang
Summary: Using time-resolved single-cell RNA sequencing, the cellular taxonomy of Marchantia polymorpha during asexual reproduction phases is defined. Two maturation and aging trajectories of the main plant body are identified: gradual maturation of tissues and organs along the tip-to-base axis of the midvein and progressive decline of meristem activities in the tip along the chronological axis. The observed aging trajectory is temporally correlated with the formation of clonal propagules, suggesting an ancient strategy to optimize resource allocation for producing offspring.
DEVELOPMENTAL CELL
(2023)
Article
Biochemistry & Molecular Biology
Qianhui Yu, Umut Kilik, Emily M. Holloway, Yu-Hwai Tsai, Christoph Harmel, Angeline Wu, Joshua H. Wu, Michael Czerwinski, Charlie J. Childs, Zhisong He, Meghan M. Capeling, Sha Huang, Ian A. Glass, Peter D. R. Higgins, Barbara Treutlein, Jason R. Spence, J. Gray Camp
Summary: This study utilized a single-cell transcriptome atlas to investigate the diversity of multiple human endodermal organs and implemented a high-dimensional search space on HIOs to evaluate pluripotent stem cell-derived intestinal organoids. Experimental results showed that HIOs reconstructed the molecular dynamics of intestinal epithelium and mesenchyme in vitro, contributing to the understanding of human organ development.
Review
Cardiac & Cardiovascular Systems
Crystal C. Kennedy, Erin E. Brown, Nadia O. Abutaleb, George A. Truskey
Summary: The vascular endothelium plays a crucial role in maintaining healthy vessel function throughout the body. Differentiated endothelial cells from induced pluripotent stem cells are widely used in in vitro models and in vivo applications. Furthermore, the use of pluripotent stem cells offers advantages in avoiding difficulties associated with sourcing primary endothelial cells.
FRONTIERS IN CARDIOVASCULAR MEDICINE
(2021)
Article
Cell Biology
Xiu Yu, Shiqi Liang, Manqi Chen, Hanwen Yu, Ruiqi Li, Yuliang Qu, Xuhui Kong, Ruirui Guo, Rongyan Zheng, Zsuzsanna Izsvak, Chuanbo Sun, Mingzhu Yang, Jichang Wang
Summary: In this study, a cell model mimicking human 8-cell stage embryos was developed to study the mechanisms of early human development. This model successfully isolated and maintained a population of cells resembling the 8-cell state, which expressed key genes involved in zygotic genome activation. The findings provide valuable insights into early human development.
Article
Cell & Tissue Engineering
Nadia Rajab, Paul W. Angel, Yidi Deng, Jennifer Gu, Vanta Jameson, Mariola Kurowska-Stolarska, Simon Milling, Chris M. Pacheco, Matt Rutar, Andrew L. Laslett, Kim-Anh Le Cao, Jarny Choi, Christine A. Wells
Summary: The Stemformatics myeloid atlas provides an integrated transcriptome atlas of human macrophages and dendritic cells, comparing different sources of myeloid cells. The study found that culture significantly impacted primary cell phenotypes, and identified characteristic features in pluripotent stem cell-derived macrophages. The reproducibility of myeloid subsets and phenotypes across experimental series, including single-cell data, demonstrates the robust reference that the atlas provides.
Article
Biology
Wai Hoe Ng, Elizabeth K. Johnston, Jun Jie Tan, Jacqueline M. Bliley, Adam W. Feinberg, Donna B. Stolz, Ming Sun, Piyumi Wijesekara, Finn Hawkins, Darrell N. Kotton, Xi Ren
Summary: The interaction between the developing heart and lung is crucial for their proper formation. Researchers have developed a new human model using pluripotent stem cells to investigate this relationship, creating microtissues containing both heart and lung cells. The presence of developing heart cells was found to accelerate lung maturation in the microtissues, and the heart and lung tissues were observed to automatically separate from each other during later stages.
Article
Chemistry, Multidisciplinary
Wanchuan Ding, Xuan Yang, Huoyue Lin, Zixing Xu, Jun Wang, Jie Dai, Can Xu, Feng Chen, Xiaowei Wen, Weiran Chai, Gang Ruan
Summary: Hard-to-transfect cells, such as BMSCs, present challenges in intracellular delivery due to vesicle trapping. We found that coating nanoparticles with PDS1 can effectively avoid vesicle trapping in BMSCs and significantly enhance transfection efficiency and osteoblastic differentiation. Mechanistic studies suggest that higher cholesterol content in BMSCs' plasma membranes may contribute to the difficulty of vesicle escape.
Article
Multidisciplinary Sciences
Swapan Mallick, Heng Li, Mark Lipson, Iain Mathieson, Melissa Gymrek, Fernando Racimo, Mengyao Zhao, Niru Chennagiri, Susanne Nordenfelt, Arti Tandon, Pontus Skoglund, Iosif Lazaridis, Sriram Sankararaman, Qiaomei Fu, Nadin Rohland, Gabriel Renaud, Yaniv Erlich, Thomas Willems, Carla Gallo, Jeffrey P. Spence, Yun S. Song, Giovanni Poletti, Francois Balloux, George van Driem, Peter de Knijff, Irene Gallego Romero, Aashish R. Jha, Doron M. Behar, Claudio M. Bravi, Cristian Capelli, Tor Hervig, Andres Moreno-Estrada, Olga L. Posukh, Elena Balanovska, Oleg Balanovsky, Sena Karachanak-Yankova, Hovhannes Sahakyan, Draga Toncheva, Levon Yepiskoposyan, Chris Tyler-Smith, Yali Xue, M. Syafiq Abdullah, Andres Ruiz-Linares, Cynthia M. Beall, Anna Di Rienzo, Choongwon Jeong, Elena B. Starikovskaya, Ene Metspalu, Juri Parik, Richard Villems, Brenna M. Henn, Ugur Hodoglugil, Robert Mahley, Antti Sajantila, George Stamatoyannopoulos, Joseph T. S. Wee, Rita Khusainova, Elza Khusnutdinova, Sergey Litvinov, George Ayodo, David Comas, Michael F. Hammer, Toomas Kivisild, William Klitz, Cheryl A. Winkler, Damian Labuda, Michael Bamshad, Lynn B. Jorde, Sarah A. Tishkoff, W. Scott Watkins, Mait Metspalu, Stanislav Dryomov, Rem Sukernik, Lalji Singh, Kumarasamy Thangaraj, Svante Paeaebo, Janet Kelso, Nick Patterson, David Reich
Article
Genetics & Heredity
Courtney K. Burrows, Nicholas E. Banovich, Bryan J. Pavlovic, Kristen Patterson, Irene Gallego Romero, Jonathan K. Pritchard, Yoav Gilad
Article
Biochemistry & Molecular Biology
Nicholas E. Banovich, Yang I. Li, Anil Raj, Michelle C. Ward, Peyton Greenside, Diego Calderon, Po Yuan Tung, Jonathan E. Burnett, Marsha Myrthil, Samantha M. Thomas, Courtney K. Burrows, Irene Gallego Romero, Bryan J. Pavlovic, Anshul Kundaje, Jonathan K. Pritchard, Yoav Gilad
Review
Cell Biology
Michael Dannemann, Fernando Racimo
CURRENT OPINION IN GENETICS & DEVELOPMENT
(2018)
Article
Biochemistry & Molecular Biology
Burak Yelmen, Mayukh Mondal, Davide Marnetto, Ajai K. Pathak, Francesco Montinaro, Irene Gallego Romero, Toomas Kivisild, Mait Metspalu, Luca Pagani
MOLECULAR BIOLOGY AND EVOLUTION
(2019)
Article
Cell & Tissue Engineering
Michael Dannemann, Zhisong He, Christian Heide, Benjamin Vernot, Leila Sidow, Sabina Kanton, Anne Weigert, Barbara Treutlein, Svante Paabo, Janet Kelso, J. Gray Camp
Article
Evolutionary Biology
Michael Dannemann
Summary: Research has found associations between Neandertal-derived DNA and autoimmune diseases, prostate cancer, and type 2 diabetes, with many of these disease associations linked to specific populations' Neandertal DNA.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Genetics & Heredity
Heini M. Natri, Georgi Hudjashov, Guy Jacobs, Pradiptajati Kusuma, Lauri Saag, Chelzie Crenna Darusallam, Mait Metspalu, Herawati Sudoyo, Murray P. Cox, Irene Gallego Romero, Nicholas E. Banovich
Summary: The lack of diversity in human genomics hampers our understanding of the genetic basis of complex traits and contributes to health disparities. Through studying gene regulation in the Indonesian population, we found that population-specific genetic architecture, local ancestry, and archaic introgression play a role in gene regulation variation.
AMERICAN JOURNAL OF HUMAN GENETICS
(2022)
Editorial Material
Genetics & Heredity
Irene Gallego Romero
Summary: The article recalls a landmark publication by Rosenberg et al., which examined the fine-scale structure within and between human populations.
NATURE REVIEWS GENETICS
(2022)
Article
Genetics & Heredity
Davide M. Vespasiani, Guy S. Jacobs, Laura E. Cook, Nicolas Brucato, Matthew Leavesley, Christopher Kinipi, Francois-Xavier Ricaut, Murray P. Cox, Irene Gallego Romero
Summary: Modern humans have admixed with multiple archaic hominins, and Papuans owe up to 5% of their genome to Denisovans. Investigation of Papuan genomes reveals that Denisovan alleles strongly affect immune-related cells and potentially alter the binding affinity of multiple transcription factors to DNA, impacting phenotypic traits.
Article
Genetics & Heredity
Danat Yermakovich, Vasili Pankratov, Urmo Vosa, Bayazit Yunusbayev, Andres Metspalu, Mari Nelis, Lili Milani, Reedik Magi, Tonu Esko, Michael Dannemann, Sohini Ramachandran
Summary: The interbreeding between modern humans and Neandertals has resulted in about 2% of the genomes of present-day non-Africans consisting of Neandertal DNA. This Neandertal DNA significantly affects the transcriptomic landscape and influences phenotypic variation in people today. Through analyzing cis-eQTL SNPs, we identified 60 transcription factors of Neandertal ancestry, which form a connected protein-protein interaction network and have predicted long-range regulatory effects.
Review
Biotechnology & Applied Microbiology
Irene Gallego Romero, Amanda J. Lea
Summary: A long-standing goal of evolutionary biology is to understand how gene regulation contributes to organismal diversity. Massively parallel reporter assays (MPRAs) provide a powerful tool for testing the regulatory activity of thousands to millions of sequences simultaneously. This article discusses the execution, advantages, and limitations of MPRAs, with a focus on their potential for addressing evolutionary questions and enabling functional studies across diverse organisms.
Article
Biotechnology & Applied Microbiology
Michael Dannemann, Kay Pruefer, Janet Kelso