Review
Urology & Nephrology
Yoshiharu Muto, Benjamin D. Humphreys
Summary: Lineage tracing was originally developed to identify all progeny of a single cell during morphogenesis, but has since been applied to organ homeostasis and injury recovery. Modern techniques rely on reporter gene expression induced by cell-specific DNA recombination, and recent advances include intersectional genetics and sequencing-based genomic lineage tracing.
KIDNEY INTERNATIONAL
(2021)
Review
Cell Biology
Anna Konturek-Ciesla, David Bryder
Summary: Appropriate production of mature blood cells is essential for organismal health. This article describes tools and methods for tracing HSC lineage in mice and integrating them with single-cell molecular analysis. By combining new insights from experiments with past knowledge, we gain a better understanding of HSC-derived hematopoiesis in humans.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Mingze Yao, Tinglin Ren, Yuanqing Pan, Xiaoqing Xue, Rong Li, Lei Zhang, Yuhang Li, Ke Huang
Summary: This review presents the progress of the latest CbLT (CRISPR-based Lineage Tracing) and discusses the current limitations and potential technical pitfalls in their application and other emerging concepts.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Immunology
Miles B. Horton, HoChan Cheon, Ken R. Duffy, Daniel Brown, Shalin H. Naik, Carolina Alvarado, Joanna R. Groom, Susanne Heinzel, Philip D. Hodgkin
Summary: This study reveals that B lymphocytes generate plasma cells with diverse antibody isotypes, and their fate is regulated by discrete mechanisms. Founder cells have a major influence on clonal plasma-cell fate, while class switch recombination (CSR) shows variation within clones. The CSR patterns are determined by the independent all-or-none expression of activation-induced cytidine deaminase and IgH germline transcription.
Article
Multidisciplinary Sciences
Elijah R. Sommer, Giulia C. Napoli, Cindy H. Chau, Douglas K. Price, William D. Figg
Summary: Identification of actionable drug targets remains a bottleneck in successful drug development for metastatic cancers. The use of CRISPR-Cas9 for targeted genomic edits has accelerated discoveries in developmental biology. Recent work has integrated CRISPR-Cas9-based lineage tracing with single-cell transcriptomics in cancer metastasis, highlighting the importance of single-cell lineage tracing in oncology drug development and the potential of computational approaches in reshaping cancer drug discovery.
Article
Immunology
Catherine Gutierrez, Caroline K. Vilas, Catherine J. Wu, Aziz M. Al'Khafaji
Summary: The success of cancer treatment is often hindered by intratumoral heterogeneity and evolutionary capacity. Novel therapeutic approaches that reduce heterogeneity are needed. Recent advances in functionalized lineage tracing methods provide insights into the characteristics and fitness of tumor clones, which can guide the design of homogenization strategies.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Medicine, General & Internal
Louisa Hadj Abed, Tamar Tak, Jason Cosgrove, Leila Perie
Summary: Single-cell lineage tracing is a powerful technique that allows the tracking of individual cells and their progeny. However, the analysis of lineage tracing data has been challenging due to its inherent variability and technical noise. In this study, the authors introduce CellDestiny, a user-friendly toolkit that enables biologists to visualize and analyze single-cell lineage tracing data without coding skills. The functionality of CellDestiny is demonstrated using various datasets, showcasing its versatility and ease of use.
FRONTIERS IN MEDICINE
(2022)
Article
Oncology
Matthew G. Jones, Dian Yang, Jonathan S. Weissman
Summary: During tumor evolution, cancer cells acquire various abilities and events occur stochastically and over long times. Lineage tracing approaches provide critical insights into tumor evolution. Recent advances in single-cell lineage tracing greatly enhance the resolution and scale of lineage tracing toolkits for reconstructing tumor phylogenies. In this review, we discuss static and evolving lineage tracing methods, in vivo applications, and highlight outstanding questions in cancer evolution.
ANNUAL REVIEW OF CANCER BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Qingcai Meng, Daniel Stoyko, Celine Marlin Andrews, Parthena Konstantinidou, Pavol Genzor, O. Timothy, Alexandra R. Elchert, Leif Benner, Sushil Sobti, Esther Y. Katz, Astrid D. Haase
Summary: The combination of genome-editing and epitope tagging provides a powerful strategy to study proteins while preserving their physiological expression patterns. A simple and fast strategy to generate stable, endogenously tagged alleles is presented, allowing for the emulation of wild type protein expression and functionality.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Yu Fu, Zhenglin Zhu, Geng Meng, Rijun Zhang, Yueping Zhang
Summary: Post-translational modifications of histone proteins play a crucial role in gene expression and cell fate decisions. Developing efficient methods for introducing mutations to histones is vital for studying these modifications. By utilizing a CRISPR-Cas9 based system in yeast cells, researchers successfully generated multiple histone mutants, presenting a valuable tool for the field of epigenetics.
SCIENTIFIC REPORTS
(2021)
Article
Neurosciences
July Carolina Romero, Cynthia Berlinicke, Sharon Chow, Yukan Duan, Yifei Wang, Xitiz Chamling, Lena Smirnova
Summary: In this study, a hiPSC line with tagged proteolipid protein 1 (PLP1) with super-fold GFP (sfGFP) was generated using CRISPR/Cas9 technology. The fidelity, specificity, and function of the tagged PLP protein in a 3D model were validated and confirmed. The differentiation stages of oligodendrogenesis were tracked based on the morphology of PLP1-sfGFP(+) cells and the presence of PLP1-sfGFP surrounding axons during bMPS differentiation. Finally, the bMPS was challenged with cuprizone, and changes in the percentage of PLP1-sfGFP expressing cells and the intensity of GFP expression were quantified.
FRONTIERS IN CELLULAR NEUROSCIENCE
(2023)
Article
Cell & Tissue Engineering
Chase A. Pagani, Amanda K. Huber, Charles Hwang, Simone Marini, Karthik Padmanabhan, Nicholas Livingston, Johanna Nunez, Yuxiao Sun, Nicole Edwards, Yu-Hao Cheng, Noelle Visser, Pauline Yu, Nicole Patel, Joseph A. Greenstein, Husain Rasheed, Reagan Nelson, Karen Kessel, Kaetlin Vasquez, Amy L. Strong, Geoffrey E. Hespe, Jane Y. Song, Deneen M. Wellik, Benjamin Levi
Summary: The research discovered a specific lineage of cells as ectopic bone progenitors in the zeugopod, providing a new perspective on fate specification and multipotency acquired after injury.
Article
Cell Biology
Richard de Reuver, Evelien Dierick, Bartosz Wiernicki, Katrien Staes, Leen Seys, Ellen De Meester, Tuur Muyldermans, Alexander Botzki, Bart N. Lambrecht, Filip Van Nieuwerburgh, Peter Vandenabeele, Jonathan Maelfait
Summary: Disruption of the interaction between ADAR1 and Z-RNA leads to reduced A-to-I editing of dsRNA structures, triggering an MDA5/MAVS-mediated type I interferon response and causing the development of lethal autoinflammation.
Article
Biochemistry & Molecular Biology
Emily C. Stow, Tiffany Kaul, Dawn L. DeHaro, Madeleine R. Dem, Anna G. Beletsky, Maria E. Morales, Qianhui Du, Alexis J. LaRosa, Hanlin Yang, Emily Smither, Melody Baddoo, Nathan Ungerleider, Prescott Deininger, Victoria P. Belancio
Summary: Expression of L1 mRNA in rodents shows significant organ specificity, with less than 0.8% of loci shared between organs of the same organism. There are notable differences in L1 mRNA expression between sexes, with only 5% of expressed loci shared between male and female mice. Total L1 mRNA expression levels fluctuate with age independently of the number and spectrum of expressed loci, demonstrating varied patterns in different organs and sexes.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biotechnology & Applied Microbiology
Shuai Ma, Feiyu Wang, Zhang Xuejing, Qiao Liping, Guo Xueping, Xuemei Lu, Qingsheng Qi
Summary: In this study, we successfully achieved gene editing and knockout in S. thermophilus using self-targeting CRISPR sequences and DNA repair templates, providing new possibilities for industrial applications of this species.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
WooJae Choi, Eunji Kim, Soo-Young Yum, ChoongIl Lee, JiHyun Lee, JoonHo Moon, Sisitha Ramachandra, Buddika Oshadi Malaweera, JongKi Cho, Jin-Soo Kim, SeokJoong Kim, Goo Jang
Article
Multidisciplinary Sciences
Hyo Young Kim, Soo Young Yum, Goo Jang, Dae-Ro Ahn
SCIENTIFIC REPORTS
(2015)
Review
Veterinary Sciences
Soo-Young Yum, Ki-Young Yoon, Choong-Il Lee, Byeong-Chun Lee, Goo Jang
JOURNAL OF VETERINARY SCIENCE
(2016)
Article
Biotechnology & Applied Microbiology
Hyun-Kyung Chang, Pyung-Hwan Kim, Hyun-Min Cho, Soo-Young Yum, Young-Jin Choi, YeonSung Son, DaBin Lee, InSung Kang, Kyung-Sun Kang, Goo Jang, Je-Yoel Cho
Article
Reproductive Biology
Woo Jae Choi, Ji-Hyun Lee, Sang-Hee Lee, Soo Young Yum, Song-Jeon Lee, Chae-Woong Lim, Goo Jang
Correction
Multidisciplinary Sciences
Sei-Myoung Han, Ye-Rin Coh, Jin-Ok Ahn, Goo Jang, Soo Young Yum, Sung-Keun Kang, Hee-Woo Lee, Hwa-Young Youn
Article
Cell & Tissue Engineering
Hyun-Min Cho, Pyung-Hwan Kim, Hyun-Kyung Chang, Yi-Ming Shen, Kwaku Bonsra, Byung-Jae Kang, Soo-Young Yum, Joo-Hyun Kim, So-Yeong Lee, Min-Cheol Choi, Hyongbum (Henry) Kim, Goo Jang, Je-Yoel Cho
STEM CELLS TRANSLATIONAL MEDICINE
(2017)
Article
Biotechnology & Applied Microbiology
Soo-Young Yum, Song-Jeon Lee, Sin-Gi Park, In-Gang Shin, Sang-Eun Hahn, Woo-Jae Choi, Hee-Soo Kim, Hyeong-Jong Kim, Seong-Hun Bae, Je-Hyeong Lee, Joo-Yeong Moon, Woo-Sung Lee, Ji-Hyun Lee, Choong-Il Lee, Seong-Jin Kim, Goo Jang
Review
Agriculture, Dairy & Animal Science
Soo-Young Yum, Ki-Young Youn, Woo-Jae Choi, Goo Jang
JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY
(2018)
Article
Chemistry, Multidisciplinary
Hien Bao Dieu Thai, Fabienne Levi-Acobas, Soo-Young Yum, Goo Jang, Marcel Hollenstein, Dae-Ro Ahn
CHEMICAL COMMUNICATIONS
(2018)
Article
Multidisciplinary Sciences
Soo-Young Yum, Song-Jeon Lee, Hyun-Min Kim, Woo-Jae Choi, Ji-Hyun Park, Won-Wu Lee, Hee-Soo Kim, Hyeong-Jong Kim, Seong-Hun Bae, Je-Hyeong Lee, Joo-Yeong Moon, Ji-Hyun Lee, Choong-Il Lee, Bong-Jun Son, Sang-Hoon Song, Su-Min Ji, Seong-Jin Kim, Goo Jang
SCIENTIFIC REPORTS
(2016)
Article
Cell & Tissue Engineering
Su-Jin Kim, Hee-Sun Kwon, Dae-kee Kwon, Ok-Jae Koo, Joon-Ho Moon, Eun-Jung Park, Soo-Young Yum, Byeong-Chun Lee, Goo Jang
CELLULAR REPROGRAMMING
(2019)
Article
Agriculture, Dairy & Animal Science
Soo-Young Yum, Woojae Choi, Seokjoong Kim, Goo Jang, Okjae Koo
Summary: Gene integration at site-specific loci, such as pAAVS1, was achieved in porcine fibroblasts using TALEN and CRISPR/Cas9. The efficiency of CRISPR/Cas9 was found to be higher than TALEN. Recombinase-mediated cassette exchange (RMCE) was successfully induced to exchange transgenes at the pAAVS1 locus, demonstrating the usefulness of this technology for porcine transgenesis studies.
ANIMAL BIOTECHNOLOGY
(2023)