Article
Cell Biology
Di Wu
Summary: The germinal vesicle (GV) stage is a critical transition point in mammalian oocyte development that determines oocyte quality through active RNA degradation and transcriptome reprofiling. Oocyte RNA-seq has revealed differences between non-surrounded nucleolus (NSN) and surrounded nucleolus (SN) phases. Single oocyte RNA-seq (soRNA-seq) shows higher reproducibility and a better illustration of gene changes during oocyte development.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Florian Le Billan, Julie Perrot, Elena Carceller, Simon Travers, Say Viengchareun, Peter Kolkhof, Marc Lombes, Jerome Fagart
Summary: The study analyzed the effects of two MRAs on the aldosterone-induced transcriptome in a human renal cell line, revealing the regulation of hundreds of genes by aldosterone and the quantitative efficiency of finerenone on certain aldosterone-induced genes. The data provides insights into the mechanisms of MR signaling pathway and potential therapeutic targets for renal dysfunction.
Review
Chemistry, Physical
Yingwen Chen, Jia Song, Qingyu Ruan, Xi Zeng, Lingling Wu, Linfeng Cai, Xuanqun Wang, Chaoyong Yang
Summary: Cells are fundamental building blocks of biological systems, and studying single cells can provide insights into cell diversity and disease processes. Single-cell RNA sequencing technologies allow cellular heterogeneity to be dissected at unprecedented resolution.
Article
Endocrinology & Metabolism
Pierre Moffatt, Iris Boraschi-Diaz, Ghalib Bardai, Frank Rauch
Summary: The study revealed that two severe OI mouse models share abnormalities in the expression of genes related to extracellular matrix proteins, lipid and energy metabolism, and structural proteins of type I muscle fibers. These muscle disturbances could be viewed as a mild form of muscle dystrophy caused by collagen type I mutations.
Article
Multidisciplinary Sciences
Balazs Gocz, Eva Rumpler, Miklos Sarvari, Katalin Skrapits, Szabolcs Takacs, Imre Farkas, Veronika Csillag, Sarolta H. Trinh, Zsuzsanna Bardoczi, Yvette Ruska, Norbert Solymosi, Szilard Poliska, Zsuzsanna Szoke, Lucia Bartoloni, Yassine Zouaghi, Andrea Messina, Nelly Pitteloud, Ross C. Anderson, Robert P. Millar, Richard Quinton, Stephen M. Manchishi, William H. Colledge, Erik Hrabovszky
Summary: This study provides a comprehensive characterization of the estrogen-dependent kisspeptin neuron transcriptome and sheds light on the molecular mechanisms of ovary-brain communication, which is important for genetic research on human fertility disorders.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Pierre Moffatt, Iris Boraschi-Diaz, Juliana Marulanda, Ghalib Bardai, Frank Rauch
Summary: Comparing the transcriptome of calvaria bone tissue in different types of OI mouse models revealed shared dysregulated genes that may play an important role in the pathophysiology of the disorder.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Cell Biology
Roman Perik-Zavodskii, Olga Perik-Zavodskaia, Julia Shevchenko, Vera Denisova, Saleh Alrhmoun, Marina Volynets, Valeriy Tereshchenko, Konstantin Zaitsev, Sergey Sennikov
Summary: The study found differential expression of immune-related genes in NECs from different origins, and early and late NECs also showed differences in multiple gene expressions.
Article
Genetics & Heredity
Mengyue Shang, Yi Hu, Huaming Cao, Qin Lin, Na Yi, Junfang Zhang, Yanqiong Gu, Yujie Yang, Siyu He, Min Lu, Luying Peng, Li Li
Summary: Normal heart development is crucial for maintaining its function, and the complex interactions between different cell lineages play a key role in this process. This study identified major types of cardiac cells and determined species-shared and species-specific marker genes, as well as consistent and different gene expression patterns, through single-cell transcriptome analysis of human and mouse embryonic hearts. Comparison of the developmental stage similarity revealed differences in the development of cardiomyocytes, fibroblasts, and endothelial cells/fibroblasts between humans and mice. These findings provide valuable resources for studying cardiac cell types and their developmental trajectories among different species.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Xirong Zhang, Yini Li, Xiaopan Chen, Bihui Jin, Chongyi Shu, Wanmao Ni, Yinshen Jiang, Jing Zhang, Lijia Ma, Jing Shu
Summary: Infertility is a global social and medical problem, and thin endometrium (TE) poses a great challenge to infertility treatment. This study used single-cell RNA sequencing to construct a transcriptomic atlas and identified cellular and molecular heterogeneity in TE. Differential expressed genes (DEGs) were found to affect cell-type ratio and impair endometrial receptivity in TE.
Article
Cardiac & Cardiovascular Systems
Marie Gunthel, Karel van Duijvenboden, Dennis E. M. de Bakker, Ingeborg B. Hooijkaas, Jeroen Bakkers, Phil Barnett, Vincent M. Christoffels
Summary: Myocardial infarction leads to changes in gene expression and epigenetic states of border zone cardiomyocytes, which may play a crucial role in maintaining the metabolic switch in these cells.
JOURNAL OF CARDIOVASCULAR DEVELOPMENT AND DISEASE
(2021)
Article
Genetics & Heredity
Daiki Shikata, Shogo Matoba, Masashi Hada, Akihiko Sakashita, Kimiko Inoue, Atsuo Ogura
Summary: In this study, researchers identified RLTR45-int subfamily of ERVK as a strong reprogramming barrier for SCNT. This reprogramming barrier not only suppressed the expression of RLTR45-int elements, but also inhibited the expression of nearby genes, further affecting the development and survival of embryos.
FRONTIERS IN GENETICS
(2022)
Article
Clinical Neurology
Alejandra N. Martinez, Giovane G. Tortelote, Crissey L. Pascale, Isabella G. McCormack, Kristen D. Nordham, Natalie J. Suder, Mitchell W. Couldwell, Aaron S. Dumont
Summary: Using single-cell RNA sequencing, this study comprehensively analyzed the heterogeneity and transcriptional profiles of vascular cells in the circle of Willis (CoW) of mice with and without cerebral aneurysms. The results revealed distinct cell lineages and transcriptional signatures, and showed an increased population of macrophages and a massive spike of neutrophils in aneurysmal vessels. These findings provide valuable insights into the pathogenesis of cerebral aneurysms.
Article
Chemistry, Physical
Jingyu Qi, Haibin Zhu, Yijian Li, Xiangyu Guan, Ying He, Guanhua Ren, Qiang Guo, Longqi Liu, Ying Gu, Xuan Dong, Ya Liu
Summary: Cell-cell interaction is an important way for transmitting information and activating the effects of functional cells. Researchers propose a droplet-based microfluidic platform for cell-cell interaction sequencing and screening, which allows for efficient analysis and interpretation of single-cell transcriptomes in cell interactions. This work fills a gap in the current experimental platform for cell-cell interaction research and has significant practical implications in biomedicine.
Article
Cell Biology
Seongkyun Lim, David E. Lee, Francielly Morena da Silva, Pieter J. Koopmans, Ivan J. Vechetti Jr, Ferdinand von Walden, Nicholas P. Greene, Kevin A. Murach
Summary: MicroRNA-16 (miR-16) plays a crucial role in stem cell biology and fate. It is lowly expressed in muscle during developmental hypertrophy and regeneration, and its inhibition enhances myoblast differentiation and myotube formation. Global transcriptomic and proteomic analyses revealed that miR-16 knockdown affects ribosomal protein gene expression, p53 pathway-related gene abundance, and regulation of tricarboxylic acid (TCA) cycle proteins and RNA metabolism-related proteins. miR-16 inhibition also induces specific proteins associated with myogenic differentiation. Overall, miR-16 is involved in myogenic cell differentiation.
AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY
(2023)
Article
Biochemical Research Methods
Yichi Zhang, Xinsheng Nie, Yanan Jiang, Lijuan Wang, Zhuzhi Wan, Hao Jin, Ronghui Pu, Meihui Liang, Hailong Zhang, Qi Liu, Yuan Chang, Yang Gao, Ningning Yang, Shizhu Jin
Summary: This study comprehensively analyzed differentially expressed transcripts in CCl4-induced liver cirrhosis and identified potential key regulatory processes.
CURRENT BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Gurdeep Singh, Shanelle Mullany, Sakthi D. Moorthy, Richard Zhang, Tahmid Mehdi, Ruxiao Tian, Alan M. Moses, Jennifer A. Mitchell, Andrew G. Duncan
Summary: Transcriptional enhancers play a critical role in development and phenotype evolution, and a diverse repertoire of TFBS sequences is necessary for constructing synthetic enhancers with comparable activity to native enhancers. A threshold of TFBS sequence diversity overrides the need for optimized regulatory grammar and specific master regulators' recruitment by individual TFBSs. At least 10 different TFBSs are required for enhancer activity, with some specific TFBSs being dispensable.
Article
Infectious Diseases
Emelissa J. Valcourt, Kathy Manguiat, Alyssia Robinson, Julie Chih-Yu Chen, Kristina Dimitrova, Clark Philipson, Lise Lamoureux, Elizabeth McLachlan, Zachary Schiffman, Michael A. Drebot, Heidi Wood
Summary: The study evaluated the sensitivity, specificity, and cross-reactivity of sVNT compared with PRNT for SARS-CoV-2 neutralizing antibodies, finding sVNT to be a high-throughput screening tool for evaluation prior to confirmatory PRNT testing.
DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE
(2021)
Review
Developmental Biology
Nawrah Khader, Virlana M. Shchuka, Oksana Shynlova, Jennifer A. Mitchell
Summary: The onset of labour involves a transition of smooth muscle cells in the muscular layer of the uterus from quiescent to contractile phenotypes, facilitated by various transcription factors. Understanding the role of transcription factors in labour-associated gene expression changes may lead to new therapeutic treatments for preventing preterm labour.
MOLECULAR HUMAN REPRODUCTION
(2021)
Article
Biology
Patrick Morley Willoughby, Molly Allen, Jessica Yu, Roman Korytnikov, Tianhui Chen, Yupeng Liu, Isis So, Neil Macpherson, Jennifer A. Mitchell, Rodrigo Fernandez-Gonzalez, Ashley E. E. Bruce
Summary: In developing epithelial tissues, Rab GTPase Rab25 plays a key role in coordinating cytokinetic bridge abscission and cortical actin density, impacting cell shape changes and tissue-scale forces. Dysfunction of Rab25 leads to defective cytokinesis, resulting in anisotropic cell morphologies and delayed tissue development.
Article
Health Care Sciences & Services
Ieuan Clay, Christian Angelopoulos, Anne Lord Bailey, Aaron Blocker, Simona Carini, Rodrigo Carvajal, David Drummond, Kimberly F. McManus, Ingrid Oakley-Girvan, Krupal B. Patel, Phillip Szepietowski, Jennifer C. Goldsack
Summary: Data integration is crucial for the development and growth of technological solutions, but the cultural adoption of sensor data integration in healthcare is lacking, hindering its potential to transform health outcomes.
JOURNAL OF MEDICAL INTERNET RESEARCH
(2021)
Article
Health Care Sciences & Services
Mariko Makhmutova, Raghu Kainkaryam, Marta Ferreira, Jae Min, Martin Jaggi, Ieuan Clay
Summary: This study presents the development of a predictive model using person-generated health data (PGHD) to forecast the long-term increase in depression severity. The results demonstrate that low-burden PGHD can be the basis of accurate and timely warnings of deteriorating mental health.
JMIR MHEALTH AND UHEALTH
(2022)
Article
Microbiology
Christy-Lynn Peterson, David Alexander, Julie Chih-Yu Chen, Heather Adam, Matthew Walker, Jennifer Ali, Jessica Forbes, Eduardo Taboada, Dillon O. R. Barker, Morag Graham, Natalie Knox, Aleisha R. Reimer
Summary: This study evaluated the use of shotgun metagenomics for detecting enteric bacterial pathogens in stool samples. The results showed that KAT-SECT analysis provided the best sensitivity and specificity among the compared analysis tools and databases. The cost of metagenomics is getting closer to the combined cost of PCR, culture, and whole genome sequencing for pathogen detection and subtyping.
Article
Cell Biology
Divyaa Srinivasan, Tarak Shisode, Jatin Shrinet, Peter Fraser
Summary: Genome organization and the folding of chromosomes play significant roles in nuclear functions, such as gene regulation, replication, and repair. Chromosomes undergo continuous conformational changes throughout the cell cycle, with differential dynamics in various structures. Understanding these changes is crucial for interpreting genome conformation data and identifying the driving molecules and mechanisms behind chromosomal conformational changes.
JOURNAL OF CELL SCIENCE
(2022)
Article
Health Care Sciences & Services
Ieuan Clay, Francesca Cormack, Szymon Fedor, Luca Foschini, Giovanni Gentile, Chris van Hoof, Priya Kumar, Florian Lipsmeier, Akane Sano, Benjamin Smarr, Benjamin Vandendriessche, Valeria De Luca
Summary: The ability to objectively measure performance and behavior is crucial for digital health, and multimodal technologies have emerged to expand this capability. Experts in digital health convened to discuss the progress of multimodal digital measurements in disease detection and quality of life, highlighting the importance of collaboration, data sharing, and robust evaluation in advancing these capabilities.
JOURNAL OF MEDICAL INTERNET RESEARCH
(2022)
Correction
Biology
Patrick Morley Willoughby, Molly Allen, Jessica Yu, Roman Korytnikov, Tianhui Chen, Yupeng Liu, Isis So, Haoyu Wan, Neil Macpherson, Jennifer A. Mitchell, Rodrigo Fernandez-Gonzalez, Ashley E. E. Bruce
Article
Virology
Kerry Dust, Michael Carpenter, Julie Chih-yu Chen, Chris Grant, Stuart McCorrister, Garret R. Westmacott, Alberto Severini
Summary: This study investigates the effects of HPV16 viral proteins E6 and E7 on the host proteome in human neonatal keratinocytes. The results show that the expression of E6 and E7 leads to dysregulation in pathways related to interferon response, inflammation, and DNA damage repair. The study also identifies potential biomarkers associated with HPV oncoproteins in primary keratinocytes.
Article
Multidisciplinary Sciences
Virlana M. Shchuka, Nawrah A. Khader, Anna Dorogin, Oksana Shynlova, Jennifer A. Mitchell
Summary: Spontaneous uterine contractions during pregnancy are regulated by various transcription factors, including AP-1, NF-kappa beta, ER, and PR. This study reveals the roles of MYB and ELF3 proteins in promoting labor-driving gene transcription in mouse and human myometrial tissues.
Article
Biochemistry & Molecular Biology
Luis E. Abatti, Patricia Lado-Fernandez, Linh Huynh, Manuel Collado, Michael M. Hoffman, Jennifer A. Mitchell
Summary: This research identifies an enhancer cluster that is aberrantly activated in breast and lung adenocarcinoma, disrupting normal development and leading to dysregulated gene expression and reduced ability of cancer cells to form colonies. The study also reveals the correlation between chromatin accessibility at this cluster and SOX2 overexpression in breast and lung cancer patients. The authors demonstrate the roles of FOXA1 and NFIB in regulating the activity of the enhancer cluster and SOX2 transcription in cancer cells. The conserved regions within the cluster are shown to be essential for mouse development.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Medical Informatics
Ariel D. Stern, Jan Broenneke, Jorg F. Debatin, Julia Hagen, Henrik Matthies, Smit Patel, Ieuan Clay, Bjoern Eskofier, Annika Herr, Kurt Hoeller, Ashley Jaksa, Daniel B. Kramer, Mattias Kyhlstedt, Katherine T. Lofgren, Nirosha Mahendraratnam, Holger Muehlan, Simon Reif, Lars Riedemann, Jennifer C. Goldsack
Summary: Germany passed the Digital Healthcare Act to create a pathway for regulatory and reimbursement of digital health applications. The Act provides flexibility in evidence presentation for new digital products. The Digital Medicine Society and the Health Innovation Hub of the German Federal Ministry of Health organized roundtable discussions to advance innovative approaches to digital medical product evaluation and promote international harmonization of best evidentiary practices.
LANCET DIGITAL HEALTH
(2022)
Article
Computer Science, Artificial Intelligence
Allison Shapiro, Nicole Marinsek, Ieuan Clay, Benjamin Bradshaw, Ernesto Ramirez, Jae Min, Andrew Trister, Yuedong Wang, Tim Althoff, Luca Foschini
Summary: The study examined health data from 230 individuals who reported a COVID-19 diagnosis, finding that COVID-19 patients had distinct symptoms lasting longer and peaking later compared to flu patients. Wearable data showed significant changes in daily steps and anomalous resting heart rate measurements for both flu and COVID-19 cohorts.