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Article ; Online: Death-seq and ye shall find: A novel screening strategy for dying cells.

Wallis, Ryan / Bishop, Cleo L

2023 Volume 35, Issue 10, Page(s) 1675–1676

Abstract: Killing senescent cells to improve health-span holds great promise. However, screening for senescence-regulating genes and molecules is challenging because these cells do not proliferate. In this issue, Colville and Liu et al. develop Death-seq, a ... ...

Abstract	Killing senescent cells to improve health-span holds great promise. However, screening for senescence-regulating genes and molecules is challenging because these cells do not proliferate. In this issue, Colville and Liu et al. develop Death-seq, a positive selection screening tool that overcomes this hurdle to offer broad genetic and pharmacological utility.
MeSH term(s)	Apoptosis ; Cellular Senescence/genetics
Language	English
Publishing date	2023-10-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Comment
ZDB-ID	2176834-1
ISSN	1932-7420 ; 1550-4131
ISSN (online)	1932-7420
ISSN	1550-4131
DOI	10.1016/j.cmet.2023.09.003
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Article: Current Understanding of the Role of Senescent Melanocytes in Skin Ageing.

Hughes, Bethany K / Bishop, Cleo L

Biomedicines

2022 Volume 10, Issue 12

Abstract: Melanocytes reside within the basal epidermis of human skin, and function to protect the skin from ultraviolet light through the production of melanin. Prolonged exposure of the skin to UV light can induce irreparable DNA damage and drive cells into ... ...

Abstract	Melanocytes reside within the basal epidermis of human skin, and function to protect the skin from ultraviolet light through the production of melanin. Prolonged exposure of the skin to UV light can induce irreparable DNA damage and drive cells into senescence, a sustained cell cycle arrest that prevents the propagation of this damage. Senescent cells can also be detrimental and contribute to skin ageing phenotypes through their senescence-associated secretory phenotype. Senescent cells can act in both an autocrine and paracrine manner to produce widespread tissue inflammation and skin ageing. Recently, melanocytes have been identified as the main senescent cell population within the epidermis and have been linked to a variety of skin ageing phenotypes, such as epidermal thinning and the presence of wrinkles. However, the literature surrounding melanocyte senescence is limited and tends to focus on the role of senescence in the prevention of melanoma. Therefore, this review aims to explore the current understanding of the contribution of senescent melanocytes to human skin ageing.
Language	English
Publishing date	2022-12-02
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2720867-9
ISSN	2227-9059
ISSN	2227-9059
DOI	10.3390/biomedicines10123111
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Article ; Online: Yearning for machine learning: applications for the classification and characterisation of senescence.

Hughes, Bethany K / Wallis, Ryan / Bishop, Cleo L

Cell and tissue research

2023 Volume 394, Issue 1, Page(s) 1–16

Abstract: Senescence is a widely appreciated tumour suppressive mechanism, which acts as a barrier to cancer development by arresting cell cycle progression in response to harmful stimuli. However, senescent cell accumulation becomes deleterious in aging and ... ...

Abstract	Senescence is a widely appreciated tumour suppressive mechanism, which acts as a barrier to cancer development by arresting cell cycle progression in response to harmful stimuli. However, senescent cell accumulation becomes deleterious in aging and contributes to a wide range of age-related pathologies. Furthermore, senescence has beneficial roles and is associated with a growing list of normal physiological processes including wound healing and embryonic development. Therefore, the biological role of senescent cells has become increasingly nuanced and complex. The emergence of sophisticated, next-generation profiling technologies, such as single-cell RNA sequencing, has accelerated our understanding of the heterogeneity of senescence, with distinct final cell states emerging within models as well as between cell types and tissues. In order to explore data sets of increasing size and complexity, the senescence field has begun to employ machine learning (ML) methodologies to probe these intricacies. Most notably, ML has been used to aid the classification of cells as senescent, as well as to characterise the final senescence phenotypes. Here, we provide a background to the principles of ML tasks, as well as some of the most commonly used methodologies from both traditional and deep ML. We focus on the application of these within the context of senescence research, by addressing the utility of ML for the analysis of data from different laboratory technologies (microscopy, transcriptomics, proteomics, methylomics), as well as the potential within senolytic drug discovery. Together, we aim to highlight both the progress and potential for the application of ML within senescence research.
MeSH term(s)	Humans ; Cellular Senescence/genetics ; Aging/metabolism ; Neoplasms/genetics ; Phenotype ; Cell Division
Language	English
Publishing date	2023-04-05
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	125067-x
ISSN	1432-0878 ; 0302-766X
ISSN (online)	1432-0878
ISSN	0302-766X
DOI	10.1007/s00441-023-03768-4
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Article ; Online: Tissue engineering to better understand senescence: Organotypics come of age.

Milligan, Deborah A / Tyler, Eleanor J / Bishop, Cleo L

Mechanisms of ageing and development

2020 Volume 190, Page(s) 111261

Abstract: The recent advent of 'organs in a dish' has revolutionised the research landscape. These 3D culture systems have paved the way for translational, post genomics research by enabling scientists to model diseases in the laboratory, grow patient-derived ... ...

Abstract	The recent advent of 'organs in a dish' has revolutionised the research landscape. These 3D culture systems have paved the way for translational, post genomics research by enabling scientists to model diseases in the laboratory, grow patient-derived organoids, and unite this technology with other cutting-edge methodologies such as drug discovery. Fields such as dermatology and neuroscience have revolutionised the development of robust 3D models, which faithfully recapitulate native physiology in vivo to provide important functional and mechanistic insights. These models have underpinned a rapid growth in the number of organs and myriad of human diseases that can be modelled in 3D, which currently includes breast, cerebral cortex, heart, intestine, kidney, liver, lung, neural tube, pancreas, prostate, skin and stomach, as well as patient derived tumours. However, so far, they have not yet been employed extensively in the study of fundamental cellular programmes such as senescence. Thus, tissue engineering and 3D culture offer an exciting opportunity to further understand the bright and dark sides of senescence in a more complex and physiologically relevant environment. Below, we will discuss previous approaches to investigating senescence and ageing using organotypic models, and some potential opportunities for future research.
MeSH term(s)	Biomedical Research/methods ; Biomedical Research/trends ; Biomedical Technology/methods ; Biomedical Technology/trends ; Cellular Senescence/physiology ; Humans ; Models, Biological ; Organ Culture Techniques/methods ; Organoids/physiology ; Organoids/physiopathology ; Tissue Engineering/methods
Language	English
Publishing date	2020-05-24
Publishing country	Ireland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	183915-9
ISSN	1872-6216 ; 0047-6374
ISSN (online)	1872-6216
ISSN	0047-6374
DOI	10.1016/j.mad.2020.111261
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Article ; Online: The bright and dark side of extracellular vesicles in the senescence-associated secretory phenotype.

Wallis, Ryan / Mizen, Hannah / Bishop, Cleo L

Mechanisms of ageing and development

2020 Volume 189, Page(s) 111263

Abstract: Senescence is a state of proliferative arrest which has been described as a protective mechanism against the malignant transformation of cells. However, senescent cells have also been demonstrated to accumulate with age and to contribute to a variety of ... ...

Abstract	Senescence is a state of proliferative arrest which has been described as a protective mechanism against the malignant transformation of cells. However, senescent cells have also been demonstrated to accumulate with age and to contribute to a variety of age-related pathologies. These pathological effects have been attributed to the acquisition of an enhanced secretory profile geared towards inflammatory molecules and tissue remodelling agents - known as the senescence-associated secretory phenotype (SASP). Whilst the SASP has long been considered to be comprised predominantly of soluble mediators, growing evidence has recently emerged for the role of extracellular vesicles (EVs) as key players within the secretome of senescent cells. This review is intended to consolidate recent evidence for the roles of senescent cell-derived EVs to both the beneficial (Bright) and detrimental (Dark) effects of the SASP.
MeSH term(s)	Aging/metabolism ; Cellular Senescence ; Extracellular Vesicles/metabolism ; Humans
Language	English
Publishing date	2020-05-24
Publishing country	Ireland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	183915-9
ISSN	1872-6216 ; 0047-6374
ISSN (online)	1872-6216
ISSN	0047-6374
DOI	10.1016/j.mad.2020.111263
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Article: Isolation methodology is essential to the evaluation of the extracellular vesicle component of the senescence-associated secretory phenotype.

Wallis, Ryan / Josipovic, Natasa / Mizen, Hannah / Robles-Tenorio, Arturo / Tyler, Eleanor J / Papantonis, Argyris / Bishop, Cleo L

Journal of extracellular vesicles

2021 Volume 10, Issue 4, Page(s) e12041

Abstract: A hallmark of senescence is the acquisition of an enhanced secretome comprising inflammatory mediators and tissue remodelling agents - the senescence-associated secretory phenotype (SASP). Through the SASP, senescent cells are hypothesised to contribute ... ...

Abstract	A hallmark of senescence is the acquisition of an enhanced secretome comprising inflammatory mediators and tissue remodelling agents - the senescence-associated secretory phenotype (SASP). Through the SASP, senescent cells are hypothesised to contribute to both ageing and pathologies associated with age. Whilst soluble factors have been the most widely investigated components of the SASP, there is growing evidence that small extracellular vesicles (EVs) comprise functionally important constituents. Thus, dissecting the contribution of the soluble SASP from the vesicular component is crucial to elucidating the functional significance of senescent cell derived EVs. Here, we take advantage of a systematic proteomics based approach to determine that soluble SASP factors co-isolate with EVs following differential ultracentrifugation (dUC). We present size-exclusion chromatography (SEC) as a method for separation of the soluble and vesicular components of the senescent secretome and thus EV purification. Furthermore, we demonstrate that SEC EVs isolated from senescent cells contribute to non-cell autonomous paracrine senescence. Therefore, this work emphasises the requirement for methodological rigor due to the propensity of SASP components to co-isolate during dUC and provides a framework for future investigations of the vesicular component of the SASP.
MeSH term(s)	Aging/metabolism ; Cell Line, Tumor ; Cells, Cultured ; Cellular Senescence ; Chromatography, Gel ; Exosomes/chemistry ; Exosomes/metabolism ; Extracellular Vesicles/chemistry ; Extracellular Vesicles/metabolism ; Humans ; Phenotype ; Proteins/analysis ; Proteomics/methods ; Secretome/metabolism ; Senescence-Associated Secretory Phenotype
Chemical Substances	Proteins
Language	English
Publishing date	2021-02-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2683797-3
ISSN	2001-3078
ISSN	2001-3078
DOI	10.1002/jev2.12041
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Article ; Online: Senescence-associated morphological profiles (SAMPs): an image-based phenotypic profiling method for evaluating the inter and intra model heterogeneity of senescence.

Wallis, Ryan / Milligan, Deborah / Hughes, Bethany / Mizen, Hannah / López-Domínguez, José Alberto / Eduputa, Ugochim / Tyler, Eleanor J / Serrano, Manuel / Bishop, Cleo L

Aging

2022 Volume 14, Issue 10, Page(s) 4220–4246

Abstract: Senescence occurs in response to a number of damaging stimuli to limit oncogenic transformation and cancer development. As no single, universal senescence marker has been discovered, the confident classification of senescence induction requires the ... ...

Abstract	Senescence occurs in response to a number of damaging stimuli to limit oncogenic transformation and cancer development. As no single, universal senescence marker has been discovered, the confident classification of senescence induction requires the parallel assessment of a series of hallmarks. Therefore, there is a growing need for "first-pass" tools of senescence identification to streamline experimental workflows and complement conventional markers. Here, we utilise a high content, multidimensional phenotypic profiling-based approach, to assess the morphological profiles of senescent cells induced via a range of stimuli. In the context of senescence, we refer to these as senescence-associated morphological profiles (SAMPs), as they facilitate distinction between senescent and proliferating cells. The complexity of the profiles generated also allows exploration of the heterogeneity both between models of senescence and within an individual senescence model, providing a level of insight at the single cell level. Furthermore, we also demonstrate that these models are applicable to the assessment of senescence
MeSH term(s)	Biomarkers ; Carcinogenesis ; Cellular Senescence ; Humans ; Neoplasms/genetics ; Oncogenes
Chemical Substances	Biomarkers
Language	English
Publishing date	2022-05-16
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1945-4589
ISSN (online)	1945-4589
DOI	10.18632/aging.204072
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Article: Expression of p16 Within Myenteric Neurons of the Aged Colon: A Potential Marker of Declining Function.

Palmer, Alexandra / Epton, Sarah / Crawley, Ellie / Straface, Marilisa / Gammon, Luke / Edgar, Meghan M / Xu, Yichen / Elahi, Shezan / Chin-Aleong, Joanne / Martin, Joanne E / Bishop, Cleo L / Knowles, Charles H / Sanger, Gareth J

Frontiers in neuroscience

2021 Volume 15, Page(s) 747067

Abstract: Human colonic neuromuscular functions decline among the elderly. The aim was to explore the involvement of senescence. A preliminary PCR study looked for age-dependent differences in expression ... ...

Abstract	Human colonic neuromuscular functions decline among the elderly. The aim was to explore the involvement of senescence. A preliminary PCR study looked for age-dependent differences in expression of
Language	English
Publishing date	2021-10-07
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2411902-7
ISSN	1662-453X ; 1662-4548
ISSN (online)	1662-453X
ISSN	1662-4548
DOI	10.3389/fnins.2021.747067
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Article ; Online: Early growth response 2 (EGR2) is a novel regulator of the senescence programme.

Tyler, Eleanor J / Gutierrez Del Arroyo, Ana / Hughes, Bethany K / Wallis, Ryan / Garbe, James C / Stampfer, Martha R / Koh, Jim / Lowe, Robert / Philpott, Michael P / Bishop, Cleo L

Aging cell

2021 Volume 20, Issue 3, Page(s) e13318

Abstract: Senescence, a state of stable growth arrest, plays an important role in ageing and age-related diseases in vivo. Although the INK4/ARF locus is known to be essential for senescence programmes, the key regulators driving p16 and ARF transcription remain ... ...

Abstract	Senescence, a state of stable growth arrest, plays an important role in ageing and age-related diseases in vivo. Although the INK4/ARF locus is known to be essential for senescence programmes, the key regulators driving p16 and ARF transcription remain largely underexplored. Using siRNA screening for modulators of the p16/pRB and ARF/p53/p21 pathways in deeply senescent human mammary epithelial cells (DS HMECs) and fibroblasts (DS HMFs), we identified EGR2 as a novel regulator of senescence. EGR2 expression is up-regulated during senescence, and its ablation by siRNA in DS HMECs and HMFs transiently reverses the senescent phenotype. We demonstrate that EGR2 activates the ARF and p16 promoters and directly binds to both the ARF and p16 promoters. Loss of EGR2 down-regulates p16 levels and increases the pool of p16- p21- 'reversed' cells in the population. Moreover, EGR2 overexpression is sufficient to induce senescence. Our data suggest that EGR2 is a direct transcriptional activator of the p16/pRB and ARF/p53/p21 pathways in senescence and a novel marker of senescence.
MeSH term(s)	Adolescent ; Adult ; Cells, Cultured ; Cellular Senescence ; Cyclin-Dependent Kinase Inhibitor p16/metabolism ; Cyclin-Dependent Kinase Inhibitor p21/metabolism ; Early Growth Response Protein 2/metabolism ; Epithelial Cells/cytology ; Epithelial Cells/metabolism ; Fibroblasts/cytology ; Fibroblasts/metabolism ; Gene Knockdown Techniques ; Humans ; Mammary Glands, Human/cytology ; Protein Binding ; RNA, Small Interfering/metabolism ; Retinoblastoma Protein/metabolism ; Tumor Suppressor Protein p53/metabolism ; Up-Regulation ; Young Adult
Chemical Substances	Cyclin-Dependent Kinase Inhibitor p16 ; Cyclin-Dependent Kinase Inhibitor p21 ; Early Growth Response Protein 2 ; RNA, Small Interfering ; Retinoblastoma Protein ; Tumor Suppressor Protein p53
Language	English
Publishing date	2021-02-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2113083-8
ISSN	1474-9726 ; 1474-9718
ISSN (online)	1474-9726
ISSN	1474-9718
DOI	10.1111/acel.13318
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Article: High-Content Analysis of Cell Migration Dynamics within a Micropatterned Screening Platform.

Almeida, Filipe V / Gammon, Luke / Laly, Ana C / Pundel, Oscar J / Bishop, Cleo L / Connelly, John T

Advanced biosystems

2019 Volume 3, Issue 8, Page(s) e1900011

Abstract: Cell migration is a fundamental biological process that is dynamically regulated by complex interactions between the microenvironment and intrinsic gene expression programs. Here, a high-throughput cell migration assay is developed using micropatterned ... ...

Abstract	Cell migration is a fundamental biological process that is dynamically regulated by complex interactions between the microenvironment and intrinsic gene expression programs. Here, a high-throughput cell migration assay is developed using micropatterned and dynamically adhesive polymer brush substrates, which support highly precise and consistent control over cell-matrix interactions within a 96-well cell culture plate format. This system is combined with automated imaging and quantitation of both cell motility and organization of the F-actin cytoskeleton for high-content analysis of cell migration phenotypes. Using this platform to screen a library of 147 epigenetic inhibitors identifies a set of EZH2-specific compounds that promote cytoskeletal remodeling and accelerates keratinocyte migration through derepression of an epithelial to mesenchymal transition-like gene expression program. Together, these studies establish the high-throughput, micropatterned assay as a powerful tool for discovery of novel therapeutic targets and for dissecting complex gene-environment interactions involved in wound repair.
MeSH term(s)	Cell Line ; Cell Movement/physiology ; Cytological Techniques/methods ; Cytoskeleton/genetics ; Cytoskeleton/metabolism ; Enhancer of Zeste Homolog 2 Protein/genetics ; Enhancer of Zeste Homolog 2 Protein/metabolism ; Epigenesis, Genetic/genetics ; Equipment Design ; High-Throughput Screening Assays/instrumentation ; High-Throughput Screening Assays/methods ; Humans
Chemical Substances	Enhancer of Zeste Homolog 2 Protein (EC 2.1.1.43)
Language	English
Publishing date	2019-06-13
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2366-7478
ISSN	2366-7478
DOI	10.1002/adbi.201900011
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