Granulopoiesis, the process by which neutrophilic granulocytes develop, is essential for innate immunity. A key feature of this process is the transformation of the nucleus from a round shape in progenitor cells to a segmented, lobulated structure in mature neutrophils. This segmentation serves as a hallmark for staging neutrophil development in clinical diagnostics. However, the molecular mechanisms underlying this dramatic nuclear remodeling and its impact on neutrophil function remain poorly understood.
In mature neutrophils, increased chromatin compaction and nuclear segmentation are believed to be regulated, at least in part, by lamins. The nuclear lamina, composed primarily of Lamin B receptor (LBR) and Lamin A/C, plays a vital role in organizing chromatin through lamina-associated domains, which tether heterochromatin to the nuclear periphery. These structural changes have functional implications, influencing gene silencing, nuclear stiffness, and immune competence (1). Mutations in human LBR gene cause marked alterations in neutrophil nuclear shape, observed in Pelger-Huët anomaly. Equivalent mutations in mouse Lbr gene on a lupus-prone genetic background promoted autoimmunity.
Neutrophils acquire key immune functions such as reactive oxygen species (ROS) production, NETosis, cytokine secretion, and migration as they mature (2,3). Our recent work has identified transcriptional regulators that simultaneously control nuclear morphology and immune function, indicating a link between chromatin remodeling and functional specification (4). Chromatin topology also plays a role in shaping gene expression patterns during differentiation (5). We hypothesise that lamins guide genome reorganisation, gene expression, and acquisition of immune functions during neutrophil differentiation. This project will investigate the molecular mechanisms behind these events:
- Objective 1: the structural role of nuclear lamins in neutrophil nuclear segmentation. High-resolution confocal and 3D lattice light sheet imaging will be used to assess localization of lamins during neutrophil differentiation. The impact of genetically altered lamin levels (shRNA, CRISPR-Cas9, mut/KO mice) on nuclear morphology will be quantified.
- Objective 2: lamin-dependent heterochromatinization. ChIP-seq for histone modifications (such as H3K9me3, H3K27me3) will map heterochromatin in control and lamin-perturbed cells. ATAC-seq will provide complementary data on chromatin accessibility. These datasets will be integrated to define how lamins influence chromatin compaction and accessibility.
- Objective 3: functional consequences of lamin-dependent chromatin remodeling. RNA-seq will identify genes affected by changes in chromatin state and lamin function. Functional assays (ROS production, NET formation, and chemotaxis) will assess the biological relevance of structural changes. Immunopathology development in the Lbr-mut mice will be investigated.
Overall, this study will elucidate how nuclear lamins coordinate chromatin dynamics, nuclear architecture, and immune function in neutrophils, offering insight into dysregulated granulopoiesis in disease contexts.
KEYWORDS:
Neutrophils, nuclear-segmentation, Nuclear-lamins, Heterochromatin, Epigenomics.
TRAINING OPPORTUNITIES:
The Kennedy Institute is a world-renowned research centre and is housed in a state-of-the-art research facility. Training will be provided in a wide range of functional genomics approaches (e.g. RNA-Seq, ATAC-Seq, ChIP-Seq etc), immunological (cell isolation, tissue culture, FACS), and imaging (immunofluorescence on tissue sections) approaches, as well as cutting edge single cell platforms (10x, Nanostring GeoMx, Nanostring CosMx) and computational pipelines. Recently developed novel in vivo models of inflammatory diseases will be extensively used and new models will be generated. A core curriculum of lectures will be taken in the first term to provide a strong foundation across a broad range of subjects, including musculoskeletal biology, inflammation, epigenetics, translational immunology and data analysis. The student will attend weekly seminars within the department and those relevant in the wider University. They will present their research regularly to the department and the Genomics of Inflammation group, and at the Computational Genomics Forum. They will also attend external conferences at which they will present their research to a global audience. The student will also have the opportunity to work closely with members of the Genome Biology laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Multidimensional Imaging of Molecular Structures Laboratory, Rosalind Franklin Institute, and to further broaden their experimental expertise and theoretical knowledge of the chromatin organisation in health and disease.
KEY PUBLICATIONS:
- Zheng, X., Hu, J., Yue, S., Kristiani, L., Kim, M., Sauria, M. E. G., ... Zhao, K. (2018). Lamins organize the global three-dimensional genome from the nuclear periphery. Molecular Cell, 71(5), 802–815.e7. https://doi.org/10.1016/j.molcel.2018.07.005
- Ballesteros, I., Rubio-Ponce, A., Genua, M., Lusito, E., Kwok, I., Fernández-Calero, T., ... Hidalgo, A. (2020). Co-option of neutrophil fates by tissue environments. Cell, 183(5), 1282–1297.e18. https://doi.org/10.1016/j.cell.2020.09.055
- Wang, L., Luqmani, R., & Udalova, I. A. (2022). The role of neutrophils in rheumatic disease-associated vascular inflammation. Nature Reviews Rheumatology, 18(3), 158–170. https://doi.org/10.1038/s41584-021-00710-z
- Khoyratty, T. E., Ai, Z., Ballesteros, I., Tickner, J., Fontana, M. F., Khiabanian, H., ... Udalova, I. A. (2021). Distinct transcription factor networks control neutrophil-driven inflammation. Nature Immunology, 22(9), 1093–1106. https://doi.org/10.1038/s41590-021-00987-5
- Zhu, Y., Gong, K., Denholtz, M., Chandra, V., Kamps, M. P., Alber, F., & Murre, C. (2017). Comprehensive characterization of neutrophil genome topology. Genes & Development, 31(2), 141–153. https://doi.org/10.1101/gad.290510.116
THEMES:
Innate immunity, granulopoiesis, chromatin regulation, epigenetics.
SUPERVISORS:
