Article
Chemistry, Multidisciplinary
Yu-An Kuo, Cheulhee Jung, Yu-An Chen, Hung-Che Kuo, Oliver S. Zhao, Trung D. Nguyen, James R. Rybarski, Soonwoo Hong, Yuan- Chen, Dennis C. Wylie, John A. Hawkins, Jada N. Walker, Samuel W. J. Shields, Jennifer S. Brodbelt, Jeffrey T. Petty, Ilya J. Finkelstein, Hsin-Chih Yeh
Summary: The study revealed that the nucleobases at positions 7-12 of the 18-nucleotide-long activator are critical to creating bright NCBs, while positions 4-6 and 2-4 are hotspots to generate yellow-orange and red POTs.
ADVANCED MATERIALS
(2022)
Review
Chemistry, Multidisciplinary
Junyun Cheng, Gaole Lin, Tianhao Wang, Yunzhu Wang, Wenbo Guo, Jie Liao, Penghui Yang, Jie Chen, Xin Shao, Xiaoyan Lu, Ling Zhu, Yi Wang, Xiaohui Fan
Summary: CRISPR-based genetic screening is a powerful approach for unbiased functional genomics research. Single-cell CRISPR screening techniques allow the analysis of regulatory networks in complex biological systems at unprecedented resolution. These methods involve perturbing cells en masse using a pooled CRISPR library and high-content phenotyping.
Review
Biochemistry & Molecular Biology
Princess D. Rodriguez, Hana Paculova, Sophie Kogut, Jessica Heath, Hilde Schjerven, Seth Frietze
Summary: Studies have shown that non-coding RNAs (ncRNAs) play central roles in the pathogenesis of B-cell acute lymphoblastic leukemia (B-ALL), providing new insights into the molecular mechanisms of the disease.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Oncology
Junhun Cho, Sang Eun Yoon, Seok Jin Kim, Young Hyeh Ko, Won Seog Kim
Summary: Different types of lymphomas have varying mutation burdens, indicating that tumor mutation burden could potentially serve as a promising biomarker for immunotherapy in lymphomas.
Article
Biochemical Research Methods
James Gooch, Sireethorn Tungsirisurp, Hayley Costanzo, Richard Napier, Nunzianda Frascione
Summary: The study selected ssDNA aptamers against human sperm cells using Cell-SELEX and massively parallel sequencing technologies, revealing promising aptamer candidates that selectively bind sperm cells. These aptamers have the potential to increase the efficiency of sexual offence investigations by facilitating sperm detection.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Review
Endocrinology & Metabolism
Aideen M. McInerney-Leo, Emma L. Duncan
Summary: There have been two major eras in gene discovery history, from linkage analysis to massively parallel sequencing (MPS). MPS has greatly accelerated the identification of disease genes, reducing the time needed to determine disease genes from years to weeks.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Article
Chemistry, Analytical
Diana Wu, Trevor Feagin, Peter Mage, Alexandra Rangel, Leighton Wan, Dehui Kong, Anping Li, John Coller, Michael Eisenstein, Hyongsok Soh
Summary: Aptamers incorporating chemically modified bases can achieve superior affinity and specificity compared to natural aptamers. The non-natural aptamer array (N2A2) system offers a high-throughput method for generating and characterizing large libraries of base-modified DNA aptamers. The N2A2 system provides a broadly accessible tool for generating high-quality affinity reagents for diverse applications.
ANALYTICAL CHEMISTRY
(2023)
Article
Biotechnology & Applied Microbiology
David W. McKellar, Iwijn De Vlaminck
Summary: Spatial total RNA-sequencing (STRS) combines in situ polyadenylation with existing spatial transcriptomics technologies, providing a comprehensive view of the transcriptome in tissues. This technique was used to spatially map coding, noncoding and nonhost RNAs in skeletal muscle regeneration and viral myocarditis models.
NATURE BIOTECHNOLOGY
(2023)
Review
Genetics & Heredity
Cordula Haas, Jacqueline Neubauer, Andrea Patrizia Salzmann, Erin Hanson, Jack Ballantyne
Summary: Transcriptome analyses have seen significant growth in forensic genetics in recent years, with applications such as body fluid and tissue identification, determining stain and donor age, estimating post-mortem interval, and conducting post mortem death investigations. The introduction of Massively Parallel Sequencing (MPS) has opened up new possibilities for this field, allowing for high-resolution analyses and whole transcriptome sequencing of forensically relevant materials.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2021)
Article
Biochemical Research Methods
Pierre-Aurelien Gilliot, Thomas E. Gorochowski
Summary: This article develops a Python package called FORECAST that accurately simulates cell-sorting and sequencing-based MPRAs and performs robust inference of genetic design function from MPRA data. The capabilities of FORECAST reveal rules for accurate genotype-to-phenotype links in MPRA experimental design and demonstrate how simulation of MPRA experiments can improve prediction accuracy when training deep learning-based classifiers. As MPRAs continue to grow in scale and scope, tools like FORECAST will help inform decision-making during their development and maximize the utility of the data produced.
Review
Genetics & Heredity
Erin M. Gorden, Kimberly Sturk-Andreaggi, Charla Marshall
Summary: Hybridization capture technology has gained attention in the forensic field for its ability to process degraded DNA fragments and enrich mitochondrial DNA or nuclear genome polymorphisms through massively parallel sequencing. As the technology advances, hybridization capture becomes increasingly important in analyzing DNA from aged and degraded remains.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2021)
Article
Biotechnology & Applied Microbiology
Qianqin Li, Zezhou Xiao, Yongsheng Wang, Ximao Liu, Hao Liu, Zhiwen Luo, Shaoyi Zheng
Summary: In this study, RNA sequencing was used to identify various lncRNAs and mRNAs associated with vascular aging in the thoracic aortas of young and old rats. Differentially expressed mRNAs were found to be enriched in biological processes and signaling pathways related to angiogenesis. Specific lncRNAs and mRNAs, as well as signaling pathways, were identified as potential targets for improving vascular aging.
Article
Biochemistry & Molecular Biology
Keisuke Hitachi, Masashi Nakatani, Yuri Kiyofuji, Hidehito Inagaki, Hiroki Kurahashi, Kunihiro Tsuchida
Summary: Long non-coding RNAs (lncRNAs) play critical roles in muscle atrophy, and the study results provide new insights into the regulatory mechanisms of muscle atrophy, which may help identify potential therapeutic targets.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Obstetrics & Gynecology
Songchang Chen, Xuyang Yin, Sijia Zhang, Jun Xia, Ping Liu, Pingyuan Xie, Huijuan Yan, Xinming Liang, Junyu Zhang, Yiyao Chen, Hongjun Fei, Lanlan Zhang, Yuting Hu, Hui Jiang, Ge Lin, Fang Chen, Chenming Xu
Summary: WGS offers a cost-effective and reliable approach for genome-wide haplotyping and PGT for monogenic disorders, aneuploidy, and structural rearrangements without the need for additional family members, showing 100% concordance with traditional PGT methods.
HUMAN REPRODUCTION
(2021)
Article
Biotechnology & Applied Microbiology
Oana Ursu, James T. Neal, Emily Shea, Pratiksha Thakore, Livnat Jerby-Arnon, Lan Nguyen, Danielle Dionne, Celeste Diaz, Julia Bauman, Mariam Mounir Mosaad, Christian Fagre, April Lo, Maria McSharry, Andrew O. Giacomelli, Seav Huong Ly, Orit Rozenblatt-Rosen, William C. Hahn, Andrew J. Aguirre, Alice H. Berger, Aviv Regev, Jesse S. Boehm
Summary: The functional impact of somatic mutations in cancer genes was assessed in single cells using pooled Perturb-seq. Variants were categorized into phenotypic subsets based on their impact on RNA profiles, and it was found that KRAS variants displayed a continuum of gain-of-function phenotypes. The study highlights the limitations of predicting functional impact solely based on frequency in patient cohorts and provides a scalable method for assessing variant impact in multiple disease settings.
NATURE BIOTECHNOLOGY
(2022)
Article
Sport Sciences
Anne Hecksteden, Georges Pierre Schmartz, Yanni Egyptien, Karen Aus der Fuenten, Andreas Keller, Tim Meyer
Summary: This study aimed to forecast non-contact time-loss injuries in professional male football using machine learning techniques. The results showed promising performance of the gradient boosted model in predicting injuries, with potential for generalizability to new cases. However, the relatively low number of events highlights the need for external validation and model development.
SCIENCE AND MEDICINE IN FOOTBALL
(2023)
Article
Biochemistry & Molecular Biology
Ernesto Aparicio-Puerta, Pascal Hirsch, Georges P. Schmartz, Tobias Fehlmann, Verena Keller, Annika Engel, Fabian Kern, Michael Hackenberg, Andreas Keller
Summary: This article presents isomiRdb, a comprehensive resource that collects and organizes miRNA expression data at the isomiR resolution from various sources. It provides online access to millions of isomiR information and can be used to answer questions regarding the presence/absence of miRNA/isomiR in tissues.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Cell Biology
Caroline Diener, Martin Hart, Tim Kehl, Anouck Becker-Dorison, Tanja Taenzer, David Schub, Lena Krammes, Martina Sester, Andreas Keller, Marcus Unger, Barbara Walch-Rueckheim, Hans-Peter Lenhof, Eckart Meese
Summary: Parkinson's disease is a complex and multifactorial disease in which dysregulated T cells play a central role in the pathogenesis. This study used time-resolved RNA expression analysis of peripheral CD4+ T cells to uncover changes in cellular signaling during different stages of Parkinson's disease. The findings revealed altered expression of specific genes and highlighted the involvement of the IL-17 pathway, including an increased prevalence of Th17 cells and a specific subtype of IL-17 producing gamma delta-T cells.
CELL DEATH DISCOVERY
(2023)
Article
Biotechnology & Applied Microbiology
Viktoria Wagner, Fabian Kern, Oliver Hahn, Nicholas Schaum, Nicole Ludwig, Tobias Fehlmann, Annika Engel, Dominic Henn, Shusruto Rishik, Alina Isakova, Michelle Tan, Rene Sit, Norma Neff, Martin Hart, Eckart Meese, Steve Quake, Tony Wyss-Coray, Andreas Keller
Summary: By studying the expression of noncoding RNA (ncRNA) in aging and rejuvenated mice, we found that the molecular aging trajectories are mostly tissue-specific, except for eight broadly deregulated microRNAs (miRNAs). These miRNAs were also found in circulating plasma and extracellular vesicles (EVs), while tissue-specific ncRNAs were less present. MiR-29c-3p had the strongest correlation with aging in solid organs, plasma, and EVs. In mice rejuvenated by heterochronic parabiosis, the level of miR-29c-3p was restored to a similar level as in young liver. MiR-29c-3p targets pathways related to the extracellular matrix and secretion, which are known to be involved in aging.
NATURE BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Ernesto Aparicio-Puerta, Pascal Hirsch, Georges P. Schmartz, Fabian Kern, Tobias Fehlmann, Andreas Keller
Summary: miEAA is a flexible and comprehensive miRNA enrichment analysis tool based on direct and indirect miRNA annotation. It includes 19 miRNA repositories, covering 10 different organisms and 139,399 functional categories. miEAA has added information on the cellular context of miRNAs, isomiRs, and high-confidence miRNAs to improve the accuracy of results. It also improves the representation of aggregated results, including interactive Upset plots. Finally, miEAA demonstrates its functionality in the context of ageing and emphasizes the importance of carefully considering the miRNA input list. miEAA is free to use and publicly available.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Nutrition & Dietetics
Jacqueline Rehner, Georges P. Schmartz, Tabea Kramer, Verena Keller, Andreas Keller, Soeren L. Becker
Summary: Researchers conducted a study on the human gut microbiome of healthy volunteers following the Planetary Health diet and found a slight increase in probiotic-associated bacteria after 4 weeks.
Article
Immunology
Susanne Herppich, Lisa Hoenicke, Fabian Kern, Friederike Kruse, Justine Smout, Marina C. Greweling-Pils, Robert Geffers, Oliver T. Burton, Adrian Liston, Andreas Keller, Stefan Floess, Jochen Huehn
Summary: Zfp362 deficiency increases colonic inflammation but does not directly promote Th17 cell differentiation. Instead, it regulates the effector function of Treg cells, suggesting an important role in promoting colonic inflammation.
EUROPEAN JOURNAL OF IMMUNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Fabian Kern, Thomas Kuhn, Nicole Ludwig, Martin Simon, Laura Groeger, Natalie Fabis, Ernesto Aparicio-Puerta, Abdulrahman Salhab, Tobias Fehlmann, Oliver Hahn, Annika Engel, Viktoria Wagner, Marcus Koch, Katarzyna Winek, Hermona Soreq, Irina Nazarenko, Gregor Fuhrmann, Tony Wyss-Coray, Eckart Meese, Verena Keller, Matthias W. Laschke, Andreas Keller
Summary: Previous studies have shown that RNA molecules exhibit global and tissue-specific ageing patterns in both murine models and humans. In this study, we focused on extracellular vesicles (EVs), which are membrane vesicles that mediate the transfer of genetic information between tissues. We sequenced small regulatory RNAs (sncRNAs) in two fractions of mouse plasma at different time points, and observed unique ageing patterns in different sncRNA classes between the free-circulating (fc-RNA) and EV-bound (EV-RNA) fractions. Furthermore, we found that miR-29 family in adipose tissues, particularly in the EV-RNA fraction, was strongly associated with ageing.
Article
Multidisciplinary Sciences
Dominic Henn, Dehua Zhao, Dharshan Sivaraj, Artem Trotsyuk, Clark Andrew Bonham, Katharina S. Fischer, Tim Kehl, Tobias Fehlmann, Autumn H. Greco, Hudson C. Kussie, Sylvia E. Moortgat Illouz, Jagannath Padmanabhan, Janos A. Barrera, Ulrich Kneser, Hans-Peter Lenhof, Michael Januszyk, Benjamin Levi, Andreas Keller, Michael T. Longaker, Kellen Chen, Lei S. Qi, Geoffrey C. Gurtner
Summary: Chronic wounds pose a significant healthcare burden, but cell-based therapies have not been widely adopted. Researchers applied CRISPR/Cas9 to edit murine dendritic cells and enhance their therapeutic potential for healing chronic wounds.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Pascal Hirsch, Azat Tagirdzhanov, Aleksandra Kushnareva, Ilia Olkhovskii, Simon Graf, Georges P. Schmartz, Julian D. Hegemann, Kenan A. J. Bozhueyuek, Rolf Mueller, Andreas Keller, Alexey Gurevich
Summary: ABC-HuMi is an atlas of biosynthetic gene clusters (BGCs) in the human microbiome, integrating data from major human microbiome sequence databases and providing accurate annotation and enhanced prediction capabilities. This database empowers researchers to efficiently explore and discover novel bioactive compounds.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Matthias Flotho, Jeremy Amand, Pascal Hirsch, Friederike Grandke, Tony Wyss-Coray, Andreas Keller, Fabian Kern
Summary: The molecular causes and mechanisms of neurodegenerative diseases are still not well understood. This study introduces ZEBRA, a large single-cell and single-nucleus RNA-seq database, which integrates gene expression and metadata from multiple studies to enhance our understanding of mammalian brain function during aging and disease.
NUCLEIC ACIDS RESEARCH
(2023)