JP-UK Joint Symposium for Senescence Research

November 11 (Mon), 2024
On-site：Audiovisual hall, collaboration stationⅠ-2F

16:00 – 16:05

Remarks by Yasuyuki Ohkawa（Kyushu University, Japan）

16:05～16:25

01. Daiki Maejima（Institute of Science Tokyo, Japan）

Development of functional modification-specific intracellular antibodies (mintbodies)
by AI-based design for tracking chromatin modifications in vivo

16:25～16:45

02. Ioana Olan（University of Cambridge, the UK）

Principles of chromatin organisation across cellular senescence, cancer, and differentiation

16:45～17:05

03. Kosuke Tomimatsu（Kyushu University, Japan）

Highly multiplexed imaging to analyze senescence dynamics

Break for 15 minutes 17:05 – 17:20

17:20 - 17:50

03. Aiko Sada（Kyushu University, Japan）

Stem cell heterogeneity: Implications for skin inflammation and aging

17:50 - 18:20

04. Masashi Narita（University of Cambridge, the UK）

The Senescence Spectrum and Tumour Initiation

18:20 - 18:25

Closing by Yasuyuki Ohkawa（Kyushu University, Japan）

Session 1-1   Daiki　Maejima（Institute of Science Tokyo, Japan）

Development of functional modification-specific intracellular antibodies (mintbodies) by AI-based design for tracking chromatin modifications in vivo

Posttranslational modifications of histones are involved in the regulation of gene expression in various biological phenomena such as senescence and cancer development. While some histone modifications on specific genome loci are stably maintained to secure epigenomic gene regulation, others exhibit dynamic changes. To analyze histone modification dynamics, we have developed a genetically encoded live-cell imaging probe named mintbody (modification-specific intracellular antibody), which is a fusion protein consisting of the single chain variable fragment (scFv) of a modification-specific antibody and a fluorescent protein. However, most (>90%) of scFvs failed to be expressed as functional molecules to detect the target modification in cells, resulting in a low-throughput development. To improve the mintbody development throughput, we have established a platform for designing scFvs with high structural stability using proteinMPNN, which is a deep leaning-based tool and predicts protein sequences expected to fold into the same 3D structure as the input. We synthesized DNA fragments coding designed mintbody and transfected into cells to evaluate whether the mintbody is localized to the nucleus. Unlike the original mintbodies that have the same amino acid sequences as the hybridoma genome, most ProteinMPNN-designed mintbodies showed nuclear enrichments, resulting in acquiring more than ten new functional mintbodies for different modifications. As expected, some histone acetylation specific mintbodies were more concentrated in the nucleus when cells were treated with a histone deacetylase inhibitor, ensuring that these mintbodies bind to the target acetylation. For some functional designed mintbodies, improvements of biochemical properties such as solubility and thermal stability were confirmed, consistent with their cellular function. These new mintbodies will be useful for analyzing spatiotemporal dynamics of histone modifications that have not been previously observed in living cells.

Session 1-2   Ioana Olan（University of Cambridge, the UK）

Principles of chromatin organisation across cellular senescence, cancer, and differentiation

Current constructs used to characterise chromatin interactions derived from Hi-C experiments are insufficient for capturing the complexity of the epigenetic environments within the cell nucleus. We propose a more integrative chromatin compartment model called the 'chromatin gradient' which supports a detailed characterisation of chromatin states and their interplay within the chromatin network. The chromatin gradient is distorted in cancer cell lines, which show a predominantly modular 3D organisation, similar to embryonic stem cells. In contrast, differentiation and cellular senescence are associated with a stronger chromatin gradient. We show that this is a useful tool for inferring crucial insights regarding chromatin rewiring during senescence and building a universal model of chromatin organisation and its modulation during development and cancer.

Session 1-3   Kosuke Tomimatsu（Kyushu University, Japan）

Highly multiplexed imaging to analyze senescence dynamics

Cell states are regulated by responsive signal pathways on inter-cellular interactions. Multiplexed imaging has been introduced to profile the cell state by the acquisition of comprehensive spatial protein information in the cells. However, it is still challenging to extract the dynamics of multiple signal activations due to compromised resolution for visualising the molecules. We have developed a fluo-erasable antibody ‘Precise Emission Canceling Antibody (PECAb)’ for multiplexed imaging and applied it to single-cell analysis. To analyse cell state dynamics, we used IMR90 oncogene-induced senescence (OIS) as a model. The PECAbs allowed high-resolution sequential imaging using 206 antibodies and it allowed reconstruction of the spatiotemporal dynamics of signaling pathways during OIS. Additionally, combining this approach with a spatial transcriptome method, seq-smFISH, can effectively classify cells and identify their signal activation states in tissue. Overall, the PECAb system serves as a comprehensive platform for analysing complex cell processes.

Session 2-1   Aiko Sada（Kyushu University, Japan）

Stem cell heterogeneity: Implications for skin inflammation and aging

Tissue stem cells divide infrequently to minimize the risk of replication stress and DNA damage; however, it remains unclear whether the "slow cycling" nature of stem cells affects skin aging and inflammatory conditions. Using a model with slow- and fast-cycling stem cell populations identified in the mouse skin, we demonstrate that during aging, the number of fast-cycling clones gradually decreases, and the unique lineage identities of distinct stem cell populations are impaired. A similar stem cell imbalance is observed in the mouse models of IL1-dependent acute skin inflammation. The aging and inflammatory environment alters the expressions of epidermal stem cell niche factors, such as the canonical Wnt pathway. We also show that the extracellular matrix (ECM), fibulin-7, localized in the basement membrane, maintains epidermal stem cell heterogeneity, thereby protecting the skin from the detrimental effects of aging and preserving tissue resilience over time. Mice lacking fibulin-7 show early impairments resembling epidermal stem cell aging, such as the loss of fast-cycling clones, delayed wound healing, and increased expression of inflammation- and differentiation-related genes. Fibulin-7 interacts with structural ECM and matricellular proteins, and the overexpression of fibulin-7 in primary keratinocytes results in slower proliferation in the absence or presence of inflammatory cytokines. These results provide new insights into age- and inflammation-induced impairment in the epidermal stem cell identity and suggest that signal crosstalk maintains the balance of heterogeneous stem cell populations.

Session 2-2　Masashi Narita（University of Cambridge, the UK）

The Senescence Spectrum and Tumour Initiation

Cellular senescence can be induced by various stimuli, including oncogenic stress, leading to characteristic morphological changes and a stable exit from the cell cycle. Although senescent cells contribute to tissue homeostasis, their accumulation in vivo accelerates individual ageing and age-related diseases such as cancer. The harmful effects of senescent cells are often linked to the loss of their original functions. However, they also acquire new functions, which also play a critical role. I will discuss senescence as a dynamic process involving a shift in cellular functional identity, introducing the emerging concept of the senescence spectrum.

 Plane

• Fukuoka Airport → (Subway Kuko Line) → Nakasu-Kawabata Station（Transfer Subway Hakozaki Line towards Kaizuka) → Maidashi-Kyudaibyoinmae Station

 JR Train

• JR Hakata Station → (Subway Kuko Line) → Nakasu-Kawabata Station（Transfer Subway Hakozaki Line towards Kaizuka) → Maidashi-Kyudaibyoinmae Station
• JR Hakata Station → JR Yoshizuka Station

 Nishitetsu Train

• Fukuoka-Tenjin Station → (Subway) → Maidashi-Kyudaibyoinmae Station

 Highway Bus

• Nishitetsu Tenjin Bus Center → (Subway) → Maidashi-Kyudaibyoinmae Station