Editorial Material
Cell & Tissue Engineering
Rohan Bhattacharya, Makenzie G. Bonner, Samira Musah
Summary: In this study, Howden et al. identified transcriptionally distinct cell populations in human induced pluripotent stem cell-derived distal nephron epithelia that could be induced to ureteric epithelium phenotype.
Review
Cell Biology
Christine Lang, Lisa Conrad, Dagmar Iber
Summary: This review compares branching morphogenesis and its regulation in the lungs and kidneys, discussing the role of signaling pathways, mesenchyme, extracellular matrix, and cytoskeleton as potential determinants of branch position, orientation, and shape. Understanding the determinants of branch and organ shape in different organs may reveal how a highly conserved developmental process can adapt to various structural and functional frameworks.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Margaret E. Magaletta, Macrina Lobo, Eric M. Kernfeld, Hananeh Aliee, Jack D. Huey, Teagan J. Parsons, Fabian J. Theis, Rene Maehr
Summary: The authors used single cell transcriptomic and chromatin landscapes to study the regulatory programs driving pharyngeal endoderm development and define the immunodeficiency-associated developmental defects due to Foxn1 dysfunction. Maldevelopment of the pharyngeal endoderm may contribute to various human developmental syndromes and disorders, characterized by a spectrum of phenotypes that cannot be fully explained by known mutations or genetic variants.
NATURE COMMUNICATIONS
(2022)
Article
Developmental Biology
Adam Packard, William H. Klein, Frank Costantini
Summary: Research has shown that Ret signaling in kidney development is crucial for maintaining tip cells in the ureteric bud. Cells genetically forced to maintain Ret expression exhibit a tip-seeking behavior and self-organize into dense clusters in organoids. This suggests that Ret-dependent cell behaviors play a significant role in normal branching morphogenesis.
Article
Multidisciplinary Sciences
Kuan Zhang, Erica Yao, Ethan Chuang, Biao Chen, Evelyn Y. Chuang, Pao-Tien Chuang
Summary: Lung branching requires coordination between the differentiation of progenitor cells and morphogenetic events, with mTORC1 signaling playing a crucial role. Loss of mTORC1 signaling in lung progenitors disrupts the formation of the conducting airways without affecting gas exchange unit development. Additionally, compromised mitochondrial capacity also leads to lung developmental defects. These findings highlight the selective utilization of energy and regulatory programs during stem cell differentiation to produce distinct structures of the mammalian lungs.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Isao Matsui, Ayumi Matsumoto, Kazunori Inoue, Yusuke Katsuma, Seiichi Yasuda, Karin Shimada, Yusuke Sakaguchi, Masayuki Mizui, Jun-ya Kaimori, Yoshitsugu Takabatake, Yoshitaka Isaka
Summary: The coordinated growth and differentiation of multiple cells in kidney development were examined through re-analysis of single-cell RNA sequencing data, revealing lineage relationships and insights into differentiation processes. RNA velocity and NicheNet analyses provided insights into the self-renewal processes of nephron progenitors and the potential influence factors on cells involved in nephron development.
SCIENTIFIC REPORTS
(2021)
Article
Oncology
Shashwat Sharad, Travis C. Allemang, Hua Li, Darryl Nousome, Anson Tai Ku, Nichelle C. Whitlock, Adam G. Sowalsky, Jennifer Cullen, Isabell A. Sesterhenn, David G. McLeod, Shiv Srivastava, Albert Dobi
Summary: Prostate cancer incidence in young men is increasing, with patients diagnosed at an earlier age more likely to have aggressive cancer. Differences in gene expression associated with age and tumor differentiation suggest potential for age-specific and tumor differentiation-based therapeutic stratification of prostate cancer treatments. This study identified differentially expressed genes between young and old prostate cancer patients, indicating a significant age and tumor dependent heterogeneity among patients.
FRONTIERS IN ONCOLOGY
(2021)
Article
Multidisciplinary Sciences
Andrea B. Alber, Hector A. Marquez, Liang Ma, George Kwong, Bibek R. Thapa, Carlos Villacorta-Martin, Jonathan Lindstrom-Vautrin, Pushpinder Bawa, Feiya Wang, Yongfeng Luo, Laertis Ikonomou, Wei Shi, Darrell N. Kotton
Summary: This study successfully generated a mouse induced pluripotent stem cell (iPSC) line carrying a lung-specific mesenchymal reporter/lineage tracer, and identified the signaling pathways necessary for specifying lung mesenchyme. Through co-culture with lung epithelial cells, three-dimensional organoids with juxtaposed layers of epithelium and mesenchyme were formed, and functional crosstalk between the two cell types was observed.
NATURE COMMUNICATIONS
(2023)
Article
Cell Biology
Justine Lai, Jing Li, Robert Gniadecki, Raymond Lai
Summary: A subset of MF patients progress to the tumor stage, which is associated with a worse clinical outcome. The study demonstrates that single-cell microdissection/GEP technology can be applied to archival tissues to identify key drivers of MF disease progression.
Article
Biochemical Research Methods
Camille Cassel de Camps, Stephanie Mok, Emily Ashby, Chen Li, Paula Lepine, Thomas M. M. Durcan, Christopher Moraes
Summary: Biofabrication of tissues is improved by using microfabricated smart hydrogel platforms to compress and mold microtissues into customized shapes. These Compressive Hydrogel Molders (CHyMs) can temporarily compress tissues, force them into new shapes, and then release them for downstream applications. The platform is demonstrated by molding breast cancer spheroids and brain organoids, resulting in shape changes and appropriate tissue differentiation. This new tool allows for the exploration of alternative organoid geometries as building blocks for bioassembly applications.
Article
Biochemical Research Methods
Daniel Almeida, Gustavo Turecki
Summary: The transcriptome of a cell plays a vital role in the complexity and heterogeneity of cell-types in the mammalian brain. However, using bulk-tissue homogenates makes it difficult to distinguish whether observed differences in gene expression are due to disease or cellular composition. Laser capture microdissection (LCM) is a strategy that allows for the capture of specific cell-types or regions of interest.
Article
Cell Biology
David Warburton
Summary: Branching of the upper airway and alveolarization in the lower airway rely on the fundamental physical process of epithelial extrusion through an orifice. The orientation and stiffness of the orifice boundary determine the stereotypy of upper airway branching and orientation of alveolar components. Alveoli do not arise by erection of interalveolar septae, but through ring or purse string structures containing elastin and collagen.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Janice L. Walker, Weihao Wang, Edith Lin, Alison Romisher, Meghan P. Bouchie, Brigid Bleaken, A. Sue Menko, Maria A. Kukuruzinska
Summary: The development of ductal structures during branching morphogenesis relies on cellular asymmetries defined by F-actin and ZO-1, with aPKC zeta and ROCK signaling establishing apical-basal polarity of ductal progenitors. Myosin IIB drives duct maturation by localizing to vertices linking apical domains of multiple ductal epithelial cells.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Mir Ali, Ryan LaCanna, Zhaorui Lian, Jian Huang, Yinfei Tan, Wenna Shao, Xiang Yu, Ying Tian
Summary: The proliferation of alveolar epithelial type 2 (AT2) cells is crucial for lung epithelial homeostasis and regeneration after injury. Through single-cell RNA sequencing and genetic lineage labeling, the study identifies all proliferative AT2 cells in healthy and injured lungs. These cells exhibit a unique transcriptional program regulated by activating transcription factor 3 (ATF3) and thyroid hormone receptor alpha (THRA) transcription factors. Overexpression of these factors in AT2 cells promotes their proliferation and improves lung function after injury.
Article
Biochemical Research Methods
Min Shi, Ping Fu, Joseph V. Bonventre, Kyle W. McCracken
Summary: Developing in vitro models of human kidney tissue using human pluripotent stem cells (hPSCs) is challenging but essential for regenerative nephrology research. This article describes a step-by-step protocol for differentiating hPSCs into three-dimensional ureteric bud (UB) organoids, which exhibit complex morphological development and can differentiate into functional collecting duct tissues. This approach provides a robust and reproducible method for generating UB tissues that can be used to study kidney development, model disease processes, and aid in the engineering of functional kidney tissue.
Article
Cell Biology
Ryan J. Petrie, Heather M. Harlin, Lulu I. T. Korsak, Kenneth M. Yamada
JOURNAL OF CELL BIOLOGY
(2017)
Review
Cell Biology
Shaohe Wang, Rei Sekiguchi, William P. Daley, Kenneth M. Yamada
JOURNAL OF CELL BIOLOGY
(2017)
Article
Cell Biology
Ryan J. Petrie, Nuria Gavara, Richard S. Chadwick, Kenneth M. Yamada
JOURNAL OF CELL BIOLOGY
(2012)
Article
Cell Biology
Andrew D. Doyle, Matthew L. Kutys, Mary Anne Conti, Kazue Matsumoto, Robert S. Adelstein, Kenneth M. Yamada
JOURNAL OF CELL SCIENCE
(2012)
Review
Pathology
Kenneth M. Yamada, Joshua W. Collins, David A. Cruz Walma, Andrew D. Doyle, Shaimar Gonzalez Morales, Jiaoyang Lu, Kazue Matsumoto, Shayan S. Nazari, Rei Sekiguchi, Yoshinari Shinsato, Shaohe Wang
INTERNATIONAL JOURNAL OF EXPERIMENTAL PATHOLOGY
(2019)
Review
Cell Biology
Kenneth M. Yamada, Michael Sixt
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2019)
Review
Developmental Biology
David A. Cruz Walma, Kenneth M. Yamada
Review
Dentistry, Oral Surgery & Medicine
D. A. Cruz Walma, K. M. Yamada
Summary: The extracellular matrix (ECM) plays a crucial role in shaping the development of craniofacial organs by coordinating cell movements and behaviors. Understanding how ECM regulates craniofacial development and contributes to disease and disorders is important for promoting regeneration and preventing degenerative outcomes.
JOURNAL OF DENTAL RESEARCH
(2022)
Review
Cell Biology
David A. Cruz Walma, Zhuoyao Chen, Alex N. Bullock, Kenneth M. Yamada
Summary: This review discusses the critical roles of E3 ubiquitin ligases during key steps of early mammalian development and in human disease. It also considers how new methods to manipulate the ubiquitin regulatory machinery may facilitate clinical therapy, such as the development of molecular glues and PROTACs.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2022)
Review
Cell Biology
Kenneth M. Yamada, Andrew D. Doyle, Jiaoyang Lu
Summary: Cell-ECM interactions are essential in development, diseases, and tissue remodeling. Recent advances in research have provided detailed descriptions of ECM molecules, identified distinct modes of cell migration in different ECM environments, and offered new insights into organ formation mechanisms. The dynamic nature of these interactions and the feedback loops involved can contribute to disease progression.
TRENDS IN CELL BIOLOGY
(2022)
Article
Cell Biology
Minghan Hu, Andrew D. Doyle, Kenneth M. Yamada, Ashok B. Kulkarni
Summary: The mechanisms underlying facial pain are not fully understood, but this study explores the role of Cdk5 in pain signaling and its potential as a therapeutic target. The researchers use intravital imaging to study trigeminal neuronal activities and find that a Cdk5 inhibitor can alleviate facial inflammatory pain and inflammation-induced allodynia. This suggests that Cdk5 inhibitors may be promising non-opioid candidates for pain treatment.
Article
Cell Biology
Derek Cui Xu, Li Wang, Kenneth M. Yamada, Luis Alberto Baena-Lopez
Summary: This study reveals that, besides apoptosis, caspases also have tumor-suppressing activities and regulate the tumor microenvironment. These findings provide molecular details about the role of caspases in tumor progression and contribute to further understanding of their functions.
Article
Polymer Science
Shayan S. Nazari, Andrew D. Doyle, Kenneth M. Yamada
Summary: Through a 3D in vitro model, it was found that human cancer cells primarily use proteolysis and actin polymerization to breach the basement membrane and expand perforations, with relatively small contribution from myosin II contractility.
Article
Oncology
Yoshinari Shinsato, Andrew D. Doyle, Weimin Li, Kenneth M. Yamada
Article
Developmental Biology
William P. Daley, Kazue Matsumoto, Andrew D. Doyle, Shaohe Wang, Brian J. DuChez, Kenn Holmbeck, Kenneth M. Yamada