Review
Cell Biology
Mohi Miah, Issac Goh, Muzlifah Haniffa
Summary: The human mononuclear phagocyte system plays a critical role in coordinating remodeling, maturation, and repair of target organs during embryonic and fetal development. However, the molecular regulation governing chemotaxis, homeostasis, and functional diversification of resident MP cells during development remains unclear. New experimental platforms like single-cell multi-omic approaches and ex-vivo organ-on-chip models offer potential to study human MPs in development and disease.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Dmitry Velmeshev, Yonatan Perez, Zihan Yan, Jonathan E. Valencia, David R. Castaneda-Castellanos, Li Wang, Lucas Schirmer, Simone Mayer, Brittney Wick, Shaohui Wang, Tomasz Jan Nowakowski, Mercedes Paredes, Eric J. Huang, Arnold R. Kriegstein
Summary: In this study, we analyzed over 700,000 single-nucleus RNA sequencing profiles to identify lineage-specific programs and gene expression networks that regulate the development of specific cortical cell types. By intersecting our results with genetic risk factors, we identified the vulnerable cell types and lineages associated with different brain disorders, particularly autism. Our study provides insights into the molecular progression of cortical lineages during human development.
Article
Cell Biology
Rui Gao, Shiyang Zeng, Dongxu Yang, Xiaocui Li, Wenqiang Liu, Yawei Gao, Dandan Bai, Linfeng Zhang, Chuan Chen, Yunzhe Kang, Beiying Wang, Wei Hong, Mingzhu Wang, Jiqing Yin, Hong Wang, Qiaolin Deng, Shaorong Gao, Yong Zhang, Jiayu Chen
Summary: Histone modifications play critical roles in regulating gene expression during early embryo development. This study provides the first genome-wide profiles of three key histone modifications in human primordial germ cells, revealing the positive correlation between H3K4me3 and gene expression, as well as the important roles of H3K27me3 in regulating specific promoters and X chromosome reactivation. The repressive marks of H3K9me3 and H3K27me3 jointly regulate demethylation-resistant regions in hPGCs.
Article
Allergy
Avery DeVries, Kathryn McCauley, Douglas Fadrosh, Kei E. Fujimura, Debra A. Stern, Susan Lynch, Donata Vercelli
Summary: This study examined the relationship between maternal prenatal immune dysfunction and childhood asthma risk, indicating associations with asthma development, neonatal immune training, and microbial colonization patterns in early life.
Article
Multidisciplinary Sciences
Christer Sylven, Eva Wärdell, Agneta Mänsson-Broberg, Eugenio Cingolani, Konstantinos Ampatzis, Ludvig Larsson, Asa Björklund, Stefania Giacomello
Summary: Human prenatal cardiomyocytes were characterized using single-cell RNA sequencing, spatial transcriptomics, and ligand-receptor interaction information. Eight types of developing cardiomyocytes were identified, more than double the ones in the Human Developmental Cell Atlas. These cells exhibit high variability in cell cycle activity, mitochondrial content, and connexin gene expression, and are differentially distributed in the ventricles and atria. The ligand-receptor crosstalk of cardiomyocytes is mainly with non-cardiomyocyte cell types and involves cardiogenesis-related pathways. Understanding the developmental dynamics of early prenatal human cardiomyocytes may lead to new therapies.
Article
Neurosciences
Goran Simic, Zeljka Krsnik, Vinka Knezovic, Zlatko Kelovic, Mathias Lysholt Mathiasen, Alisa Junakovic, Milan Rados, Damir Mulc, Ena Spanic, Giulia Quattrocolo, Vanessa Jane Hall, Laszlo Zaborszky, Mario Vuksic, Francisco Olucha Bordonau, Ivica Kostovic, Menno P. Witter, Patrick R. Hof
Summary: The development of the human entorhinal cortex (EC), a major hub in the brain, has been analyzed in this study. The results show that the cytoarchitectural differentiation of the EC begins early in fetal development and follows a specific pattern. These findings have implications for understanding the normal function of the EC and its role in brain disorders.
JOURNAL OF COMPARATIVE NEUROLOGY
(2022)
Article
Biology
Alexandra Proshchina, Anastasia Kharlamova, Yuliya Krivova, Olga Godovalova, Dmitriy Otlyga, Victoria Gulimova, Ekaterina Otlyga, Olga Junemann, Gleb Sonin, Sergey Saveliev
Summary: Recent data on human brain development are limited, but highly valuable for medical practices, education, and fundamental research in various fields. This paper introduces the new online Human Prenatal Brain Development Atlas (HBDA), which provides annotated hemisphere maps and immunophenotype profiles of human fetal brain at different stages of development. The HBDA serves as a reference database for neurological research, allowing comparison of data obtained from noninvasive techniques and analysis of individual brain variability. It also contributes to the understanding of prenatal neurogenesis and offers potential for new therapy methods for neurological pathologies. Preliminary data are accessible on the HBDA website.
Article
Biochemistry & Molecular Biology
Zeshuai Wang, Zhisheng Wu, Hao Wang, Ruoqing Feng, Guanlin Wang, Muxi Li, Shuang-Yin Wang, Xiaoyan Chen, Yiyi Su, Jun Wang, Weiwen Zhang, Yuzhou Bao, Zhenwei Lan, Zhuo Song, Yiheng Wang, Xianyang Luo, Lingyu Zhao, Anli Hou, Shuye Tian, Hongliang Gao, Wenbin Miao, Yingyu Liu, Huilin Wang, Cui Yin, Zhi-Liang Ji, Mingqian Feng, Hongkun Liu, Lianghui Diao, Ido Amit, Yun Chen, Yong Zeng, Florent Ginhoux, Xueqing Wu, Yuanfang Zhu, Hanjie Li
Summary: Macrophages in human development exhibit diversity and developmental dynamics. The study identifies the presence of microglia-like cells in the fetal epidermis and proangiogenic macrophages around fetal organs.
Article
Biology
Darshana Z. Narayanan, Daniel Y. Takahashi, Lauren M. Kelly, Sabina Hlavaty, Junzhou Huang, Asif A. Ghazanfar
Summary: Human and non-human primates produce rhythmical sounds as soon as they are born to solicit the attention of caregivers. This study shows, through dense and longitudinal sampling of fetal head and orofacial movements in marmoset monkeys, that the orofacial movements necessary for producing rhythmical vocalizations differentiate from larger movement patterns and that signature features of marmoset infant contact calls emerge prenatally as a distinct pattern of orofacial movements.
Article
Multidisciplinary Sciences
Yunjiang Zheng, Esen Sefik, John Astle, Kutay Karatepe, Hasan H. OZ, Angel G. Solis, Ruaidhri Jackson, Hongbo R. Luo, Emanuela M. Bruscia, Stephanie Halene, Liang Shan, Richard A. Flavell
Summary: MISTRGGR mice, a humanized mouse model, were generated by replacing mouse G-CSF with human G-CSF and deleting the mouse G-CSF receptor gene. This model significantly improves the reconstitution of mature and functional human neutrophils in mice, which can be recruited during inflammatory and infectious challenges to reduce bacterial burden. It provides a unique tool to study human neutrophils in health and disease.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Hematology
Nicole A. Tseng, Anna E. Beaudin
Summary: This review highlights the role of inflammation in regulating hematopoietic stem cell function. Acute infection and inflammation can adaptively modulate adult hematopoietic stem cells, while prolonged inflammation can impair their function and lead to disease. The effects of prenatal inflammation on developing hematopoietic stem cells are less understood.
CURRENT OPINION IN HEMATOLOGY
(2023)
Article
Psychology, Developmental
Megan E. Norr, Jasmine L. Hect, Carly J. Lenniger, Martijn Van den Heuvel, Moriah E. Thomason
Summary: This study explores the impact of high maternal prenatal BMI on macrocircuitry in the human fetal brain. The findings suggest that maternal BMI is associated with connectivity between the left anterior insula/inferior frontal gyrus (aIN/IFG) and bilateral prefrontal cortex (PFC), with increased within-hemisphere connectivity and reduced cross-hemisphere connectivity in higher BMI pregnancies.
JOURNAL OF CHILD PSYCHOLOGY AND PSYCHIATRY
(2021)
Article
Multidisciplinary Sciences
Nidal S. Khatib, James Monsen, Saima Ahmed, Yuming Huang, David A. Hoey, Niamh C. Nowlan
Summary: This study investigates the role of TRPV4 in mechanical regulation of cartilage and bone formation. The researchers found that mechanical stimulation of mouse embryo hindlimbs induces knee cartilage growth and expression of TRPV4. They also demonstrated that TRPV4 activity is necessary for loading-driven joint cartilage growth and shape, and this is mediated by control of cell proliferation and matrix biosynthesis.
Article
Anatomy & Morphology
Yuliya S. Krivova, Alexandra E. Proshchina, Dmitry A. Otlyga, Ol'ga G. Leonova, Sergey V. Saveliev
Summary: The study revealed extensive prenatal development of sympathetic innervation in the human pancreas, including the formation of nerve plexuses, with some processes potentially occurring postnatally. Close interactions between TH-positive nerves and endocrine cells were observed in the fetal pancreas.
ANNALS OF ANATOMY-ANATOMISCHER ANZEIGER
(2022)
Review
Oncology
Yanshan Ge, Xinhui Wang, Yali Guo, Junting Yan, Aliya Abuduwaili, Kasimujiang Aximujiang, Jie Yan, Minghua Wu
Summary: Recent scientific advances have shown the complex relationship between the gut microbiome and cancer. Changes in gut microbiota composition can lead to immune dysregulation, promoting chronic inflammation and tumor development. Gut microorganisms and their metabolites can affect inflammation and tumorigenesis in specific organs through various axes of interaction.
JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH
(2021)
Article
Biotechnology & Applied Microbiology
Emma Dann, Neil C. Henderson, Sarah A. Teichmann, Michael D. Morgan, John C. Marioni
Summary: Milo is a scalable statistical framework that performs differential abundance testing by assigning cells to partially overlapping neighborhoods on a k-nearest neighbor graph. It can identify perturbations obscured by discretizing cells into clusters and outperforms alternative testing strategies. Milo is based on cell-cell similarity structure and may be applicable to various single-cell data beyond scRNA-seq.
NATURE BIOTECHNOLOGY
(2022)
Correction
Multidisciplinary Sciences
Tim H. H. Coorens, Thomas R. W. Oliver, Rashesh Sanghvi, Ulla Sovio, Emma Cook, Roser Vento-Tormo, Muzlifah Haniffa, Matthew D. Young, Raheleh Rahbari, Neil Sebire, Peter J. Campbell, D. Stephen Charnock-Jones, Gordon C. S. Smith, Sam Behjati
Article
Biochemistry & Molecular Biology
Eleonora Khabirova, Laura Jardine, Tim H. H. Coorens, Simone Webb, Taryn D. Treger, Justin Engelbert, Tarryn Porter, Elena Prigmore, Grace Collord, Alice Piapi, Sarah A. Teichmann, Sarah Inglott, Owen Williams, Olaf Heidenreich, Matthew D. Young, Karin Straathof, Simon Bomken, Jack Bartram, Muzlifah Haniffa, Sam Behjati
Summary: This study investigates the developmental state of KMT2A-rearranged infant B-ALL and reveals its unique features compared to other childhood B-ALLs. The research shows that this leukemia harbors hybrid myeloid-lymphoid characteristics and suggests potential targetable antigens for specific cancer treatment.
Review
Genetics & Heredity
Rasa Elmentaite, Cecilia Dominguez Conde, Lu Yang, Sarah A. Teichmann
Summary: The development of single-cell and spatial transcriptomics methods has enabled the conception of the Human Cell Atlas initiative, aiming to generate an integrated map of all cells in the human body. By studying human tissues using single-cell gene expression data, we are gaining insights into the commonalities and tissue-specific features of major and supportive cell types within human organs.
NATURE REVIEWS GENETICS
(2022)
Article
Multidisciplinary Sciences
Jarrod Shilts, Yannik Severin, Francis Galaway, Nicole Mueller-Sienerth, Zheng-Shan Chong, Sophie Pritchard, Sarah Teichmann, Roser Vento-Tormo, Berend Snijder, Gavin J. Wright
Summary: In this study, we systematically mapped the direct protein interactions across a recombinant library that includes most of the surface proteins on human leukocytes, providing a high-confidence and quantitative view of the receptor wiring that connects human immune cells. By integrating our interactome with expression data, we identified trends in the dynamics of immune interactions and constructed a mathematical model that predicts cellular connectivity. We also developed an interactive multi-tissue single-cell atlas to infer immune interactions throughout the body and linked our receptor interactions to functional roles through protein stimulation and microscopy.
Editorial Material
Multidisciplinary Sciences
Sarah A. Teichmann, Muzlifah Haniffa, Jasmin Fisher
Summary: Diversity is a creative force that broadens views and enhances ideas, increasing productivity and the impact of science. Every research organization, whether in academia or industry, needs better inclusion policies to harness the benefits of diversity. We share our suggestions on promoting inclusion in academia and creating a better research culture for all, drawing from our experiences as women in science.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Jennifer E. Rood, Aidan Maartens, Anna Hupalowska, Sarah A. Teichmann, Aviv Regev
Summary: Single-cell atlases have the potential to bridge the gap between genes, diseases, and therapies. By understanding disease mechanisms at the cellular and tissue levels, they can aid in disease diagnostics, drug target identification, and the development of new therapies.
Review
Cardiac & Cardiovascular Systems
Antonio M. A. Miranda, Vaibhao Janbandhu, Henrike Maatz, Kazumasa Kanemaru, James Cranley, Sarah A. Teichmann, Norbert Huebner, Michael D. Schneider, Richard P. Harvey, Michela Noseda
Summary: Cardiovascular disease is the leading cause of death globally. Understanding its mechanisms through advanced single-cell and single-nucleus transcriptomics studies is crucial for improving therapeutic strategies and patient risk assessment. This review provides an overview of the challenges and inferences in experimental design, as well as novel findings and applications in cardiac cell types and states. It also discusses the need for standardization and the translational and clinical implications of these technologies in diagnosing and treating heart disease.
NATURE REVIEWS CARDIOLOGY
(2023)
Article
Multidisciplinary Sciences
Jia-Ru Wei, Zhao-Zhe Hao, Chuan Xu, Mengyao Huang, Lei Tang, Nana Xu, Ruifeng Liu, Yuhui Shen, Sarah A. Teichmann, Zhichao Miao, Sheng Liu
Summary: The study describes a single-cell RNA sequencing dataset of macaque V1 cortex cells, revealing similarities and specific markers compared to human cortex. Differences in gene expression profiles and neuron diversity across species were found, providing insights into cognitive functions.
NATURE COMMUNICATIONS
(2022)
Review
Immunology
Johanna Strobl, Muzlifah Haniffa
Summary: The human skin contains a diverse population of memory T cells, which can quickly respond to pathogens and cancer antigens. Tissue-resident memory T cells (T-RM) have been linked to various allergic, autoimmune, and inflammatory skin diseases. The clonal expansion of T-RM cells is also known to contribute to cutaneous T-cell lymphoma. This review article discusses the phenotypes, transcriptional programs, and effector functions of skin T-RM cells, summarizes recent studies on T-RM formation, longevity, plasticity, and retrograde migration, and contextualizes the findings in relation to skin homeostasis and altered functions in skin disease.
IMMUNOLOGICAL REVIEWS
(2023)
Article
Dermatology
Chunhui Jiang, Renee M. Mckay, Sang Y. Lee, Carlos G. Romo, Jaishri O. Blakeley, Muzlifah Haniffa, Eduard Serra, Matthew R. Steensma, David Largaespada, Lu Q. Le
Summary: Neurofibromatosis type 1 is a common genetic disorder that predisposes patients to develop tumors. Cutaneous neurofibromas significantly impact patients' quality of life due to their unaesthetic appearance and physical discomfort. Understanding the factors involved in the heterogeneity of cNF can help develop personalized treatment regimens.
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Hannah K. Neikes, Katarzyna W. Kliza, Cathrin Grawe, Roelof A. Wester, Pascal W. T. C. Jansen, Lieke A. Lamers, Marijke P. Baltissen, Simon J. van Heeringen, Colin Logie, Sarah A. Teichmann, Rik G. H. Lindeboom, Michiel Vermeulen
Summary: BANC-seq is a method to determine the absolute binding affinities of transcription factors to native DNA across the genome. It adds a quantitative dimension to transcription factor biology and allows prediction of binding sites under non-physiological conditions.
NATURE BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Peerapat Khamwachirapithak, David Guillaume-Schoepfer, Pakkanan Chansongkrow, Sarah A. Teichmann, Philip A. Wigge, Varodom Charoensawan
Summary: This study combines ChIP-seq and RNA-seq to investigate the effects of global and local H3 depletion on gene transcription, as well as the interaction between the transcription factor Rap1 and H3. The results provide a working model and testable hypotheses regarding the impact of H3 depletion on transcriptional changes.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Genetics & Heredity
Emma Dann, Ana-Maria Cujba, Amanda J. Oliver, Kerstin B. Meyer, Sarah A. Teichmann, John C. Marioni
Summary: Joint analysis of diseased tissues and healthy reference data can reveal altered cell states. Using a reference atlas for latent space learning followed by differential analysis against controls improves identification of disease-associated cells, especially with multiple perturbed cell types. Reducing control sample numbers does not increase false discovery rates.
Correction
Multidisciplinary Sciences
Tim H. H. Coorens, Thomas R. W. Oliver, Rashesh Sanghvi, Ulla Sovio, Emma Cook, Roser Vento-Tormo, Muzlifah Haniffa, Matthew D. Young, Raheleh Rahbari, Neil Sebire, Peter J. Campbell, D. Stephen Charnock-Jones, Gordon C. S. Smith, Sam Behjati
