The heterogeneity of cellular senescence: insights at the single-cell level

In the paper

“Senescent cells are highly associated with aging and pathological conditions and could be targeted to slow the aging process.”

• Also stated in: § The importance of understanding cellular senescence heterogeneity · hedged

  “Cellular senescence has emerged as a mechanism that could be targeted to delay the aging process.”

What the sources say

• Not checked yetcites [3] Gasek NS (2021) Strategies for targeting senescent cells in human disease. Nat Aging. 1, 870– 879 34841261 PMC8612694 source

In the paper

“At the transcript level, p16 and p21 are the two most commonly used markers for senescent cells [3,16].”

What the sources say

• Not checked yetcites [3] Gasek NS (2021) Strategies for targeting senescent cells in human disease. Nat Aging. 1, 870– 879 34841261 PMC8612694 source
• Not checked yetcites [16] Gorgoulis V (2019) Cellular senescence: defining a path forward. Cell 179, 813– 827 31675495 source

In the paper

“Studies have begun to reveal the remarkable heterogeneity of cellular senescence in different tissues, highlighting the importance of cellular senescence markers beyond p16 – including Cdkn1a (p21) [7–10], Cdkn2d (p19) [11], uPAR [12], and glycoprotein non-metastatic melanoma protein B (GPNMB) [13] – and emphasizing the urgent need for a better understanding of senescent cell heterogeneity.”

What the sources say

• Not checked yetcites [7] Sturmlechner I (2021) p21 produces a bioactive secretome that places stressed cells under immunosurveillance. Science 374 PMC8985214 34709885 source
• Not checked yetcites [8] Wang B (2020) Transplanting cells from old but not young donors causes physical dysfunction in older recipients. Aging Cell 19, e13106 31971661 PMC7059132 source
• Not checked yetcites [9] Wang B (2021) An inducible p21-Cre mouse model to monitor and manipulate p21-highly-expressing senescent cells in vivo. Nat Aging 1, 962– 973 35024619 PMC8746571 source
• Not checked yetcites [10] Wang L (2022) Targeting p21(Cip1) highly expressing cells in adipose tissue alleviates insulin resistance in obesity. Cell Metab. 34, 75– 89 e8 34813734 PMC8732323 source
• Not checked yetcites [11] Dehkordi SK (2021) Profiling senescent cells in human brains reveals neurons with CDKN2D/p19 and tau neuropathology. Nature Aging 1, 1107– 1116 35531351 PMC9075501 source
• Not checked yetcites [12] Amor C (2020) Senolytic CAR T cells reverse senescence-associated pathologies. Nature 583, 127– 132 32555459 PMC7583560 source

In the paper

“Also, senescent cells produce a characteristic proinflammatory secretome, collectively termed the senescence-associated secretory phenotype (SASP) [16].”

What the sources say

• Not checked yetcites [16] Gorgoulis V (2019) Cellular senescence: defining a path forward. Cell 179, 813– 827 31675495 source

In the paper

“However, p16 might not be a specific or sensitive marker for cellular senescence since not all p16 highly expressing (p16high) cells are necessarily senescent [4] and some senescent cells do not express p16 [5,6].”

• Also stated in: § Models for understanding senescent cell heterogeneity in vivo · hedged

  “Emerging evidence has indicated that p16 might be neither a sensitive nor a specific marker for senescence because some p16high cells are not senescent (e.g., pancreatic β-cells [24], macrophages [4], mesenchymal stem cells [25], endothelial cells [26]), while not all senescent cells express high levels of p16 [16].”

What the sources say

• Not checked yetcites [4] Hall BM (2017) p16(Ink4a) and senescence-associated beta-galactosidase can be induced in macrophages as part of a reversible response to physiological stimuli. Aging 9, 1867– 1884 28768895 PMC5611982 source
• Not checked yetcites [5] Yosef R (2017) p21 maintains senescent cell viability under persistent DNA damage response by restraining JNK and caspase signaling. EMBO J. 36, 2280– 2295 28607003 PMC5538795 source
• Not checked yetcites [6] Wang L (2021) Targeting p21Cip1 highly expressing cells in adipose tissue alleviates insulin resistance in obesity. Cell Metab. 34, 75– 89.e8 34813734 PMC8732323 source
• Not checked yetcites [16] Gorgoulis V (2019) Cellular senescence: defining a path forward. Cell 179, 813– 827 31675495 source

In the paper

“Elimination of uPAR-expressing cells with chimeric antigen receptor (CAR) T cells specifically kills senescent cells both in vivo and in vitro, and extends the lifespan of mice with lung adenocarcinoma [12].”

What the sources say

• Not checked yetcites [12] Amor C (2020) Senolytic CAR T cells reverse senescence-associated pathologies. Nature 583, 127– 132 32555459 PMC7583560 source

In the paper

“For example, dasatinib is most effective at eliminating senescent preadipocytes, while quercetin better targets endothelial cells [19].”

What the sources say

• Not checked yetcites [19] Zhu Y (2015) The Achilles’ heel of senescent cells: from transcriptome to senolytic drugs. Aging Cell 14, 644– 658 25754370 PMC4531078 source

In the paper

“In 2021, a p21-Cre transgenic mouse model was generated, containing a p21 promoter driving an inducible Cre. This model targets p21 highly expressing (p21high) cells in vivo, which comprise 1–10% of cells in various tissues in aged mice, and are distinct from p16high cells, with both displaying a number of key characteristics of senescence [9].”

What the sources say

• Not checked yetcites [9] Wang B (2021) An inducible p21-Cre mouse model to monitor and manipulate p21-highly-expressing senescent cells in vivo. Nat Aging 1, 962– 973 35024619 PMC8746571 source

In the paper

“Remarkably, clearance of p21high cells reduces senescence markers, improves physical function in aged mice [9], and alleviates metabolic dysfunction in obese mice [10].”

What the sources say

• Not checked yetcites [9] Wang B (2021) An inducible p21-Cre mouse model to monitor and manipulate p21-highly-expressing senescent cells in vivo. Nat Aging 1, 962– 973 35024619 PMC8746571 source
• Not checked yetcites [10] Wang L (2022) Targeting p21(Cip1) highly expressing cells in adipose tissue alleviates insulin resistance in obesity. Cell Metab. 34, 75– 89 e8 34813734 PMC8732323 source

In the paper

“In another study, urokinase plasminogen activator receptor (uPAR), was identified as a unique senescence marker by comparing differentially expressed genes in bulk RNA-seq datasets of three known mouse models of senescence, and was validated by flow cytometry [12].”

What the sources say

• Not checked yetcites [12] Amor C (2020) Senolytic CAR T cells reverse senescence-associated pathologies. Nature 583, 127– 132 32555459 PMC7583560 source

In the paper

“Both fisetin and navitoclax kill senescent fibroblasts and endothelial cells, yet have limited effect on senescent preadipocytes [20,21].”

What the sources say

• Not checked yetcites [20] Yousefzadeh MJ (2018) Fisetin is a senotherapeutic that extends health and lifespan. EBioMedicine 36, 18– 28 30279143 PMC6197652 source
• Not checked yetcites [21] Chang J (2016) Clearance of senescent cells by ABT263 rejuvenates aged hematopoietic stem cells in mice. Nat. Med 22, 78– 83 26657143 PMC4762215 source

In the paper

“In addition, as evidenced by the different senescence markers discovered earlier, it is possible that one marker may not be enough to define senescent cells as a whole, and that a combination of many markers and features will ensure that cells are in a senescent state.”

In the paper

“Furthermore, individual senescent cells within the same culture of human fibroblasts also demonstrate cell-to-cell transcriptomic variability, as evidenced by single-cell isolation and nanofluidic PCR experiments showing a lack of correlation of gene expression among several senescence-associated genes [23].”

What the sources say

• Not checked yetcites [23] Wiley CD (2017) Analysis of individual cells identifies cell-to-cell variability following induction of cellular senescence. Aging Cell 16, 1043– 1050 28699239 PMC5595671 source

In the paper

“Conversely, single-nucleus RNA-seq can potentially capture all cell types while the sequencing sensitivity might be lower due to lower mRNA abundance in the nuclei.”

In the paper

“Genetic elimination of GPNMB-positive cells reduces the senescent cell burden and alleviates metabolic irregularities in obese mice. Vaccination against GPNMB also improves a number of conditions associated with aging [13].”

What the sources say

• Not checked yetcites [13] Suda M (2021) Senolytic vaccination improves normal and pathological age-related phenotypes and increases lifespan in progeroid mice. Nature Aging 1, 1117– 1126 37117524 source

In the paper

“However, these features might not be conserved in all senescent cells and might not be sufficient or accessible to examine senescence heterogeneity in vivo.”

In the paper

“Based on these in vitro findings, senescent cells in vivo are likely heterogeneous as well, which can come from diversity in terms of age and sex as well as varied pathological states, locations of the tissues, microenvironment, and accumulation kinetics.”

In the paper

“Although single-cell RNA-seq remains the most comprehensive method for capturing the transcriptome of individual cells, due to high sequencing depth, it may miss capturing cells that are large or sensitive to dissociation, which likely include some senescent cells due to their enlarged size and physical fragility [18].”

What the sources say

• Not checked yetcites [18] Di Micco R (2021) Cellular senescence in ageing: from mechanisms to therapeutic opportunities. Nat. Rev. Mol. Cell Biol 22, 75– 95 33328614 PMC8344376 source

In the paper

“In healthy and young mouse livers, p16high cells are mostly endothelial cells and a few Kupffer cells. In mouse livers with non-alcoholic steatohepatitis (NASH), p16high cells are mainly macrophages along with other cell types. In healthy and young kidneys, p16high cells are mainly epithelial cells.”

What the sources say

• Not checked yetcites [28] Omori S (2020) Generation of a p16 reporter mouse and its use to characterize and target p16(high) cells in vivo. Cell Metab. 32, 814– 828 e6 32949498 source

In the paper

“p19 upregulation was further validated by mFISH and mABI in human AD brains and additional experiments confirmed that p19-expressing cells had several key features, including larger nuclei and more lipofuscin-positive cells than non-p19-expressing cells.”

What the sources say

• Not checked yetcites [11] Dehkordi SK (2021) Profiling senescent cells in human brains reveals neurons with CDKN2D/p19 and tau neuropathology. Nature Aging 1, 1107– 1116 35531351 PMC9075501 source

In the paper

“For example, multiplexed antibody-based imaging (mABI) technologies such as imaging mass cytometry (IMC) [31] and codetection by indexing (CODEX) [32] can detect 20–50 selected genes simultaneously in each cell at the protein level, which is a useful complement to transcript-based detection – especially given the potential for poor correlation of transcriptomic and proteomic data sets implicated”

What the sources say

• Not checked yetcites [31] Giesen C (2014) Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nat. Methods 11, 417– 422 24584193 source
• Not checked yetcites [32] Goltsev Y (2018) Deep profiling of mouse splenic architecture with CODEX multiplexed imaging. Cell 174, 968– 981 e15 30078711 PMC6086938 source
• Not checked yetcites [33] Sullivan DI (2021) Transcriptional and proteomic characterization of telomere-induced senescence in a human alveolar epithelial cell line. Front Med. 8, 600626 PMC7902064 33634147 source

In the paper

“Tabula Muris Senis, or Mouse Ageing Cell Atlas, is a single-cell RNA-seq database, completed in 2020, that contains sequencing data from 23 mouse tissues across the lifespan [42].”

What the sources say

• Not checked yetcites [42] Tabula Muris C. (2020) A single-cell transcriptomic atlas characterizes ageing tissues in the mouse. Nature 583, 590– 595 32669714 PMC8240505 source

In the paper

“The senescent cells found in this dataset were mostly excitatory neurons with tau pathology commonly seen with AD.”

What the sources say

• Not checked yetcites [11] Dehkordi SK (2021) Profiling senescent cells in human brains reveals neurons with CDKN2D/p19 and tau neuropathology. Nature Aging 1, 1107– 1116 35531351 PMC9075501 source

In the paper

“These powerful RNA-seq-based methods can detect thousands of transcripts at the same time, a feature that is essential for discovering new senescent cell markers.”

In the paper

“In human brains, a single-nucleus RNA sequencing study using an eigengene approach found that p19/CDKN2D was the most significant marker of senescent cells in postmortem brains from patients with Alzheimer’s disease (AD), and also defined a unique group of senescent cells in human AD brains [11].”

What the sources say

• Not checked yetcites [11] Dehkordi SK (2021) Profiling senescent cells in human brains reveals neurons with CDKN2D/p19 and tau neuropathology. Nature Aging 1, 1107– 1116 35531351 PMC9075501 source

In the paper

“To note, E2f2 and Lmnb1 are typically downregulated in senescent cells [43].”

What the sources say

• Not checked yetcites [43] Shimi T (2011) The role of nuclear lamin B1 in cell proliferation and senescence. Genes Dev. 25, 2579– 2593 22155925 PMC3248680 source

In the paper

“Spatial transcriptomics is another newly developed method which allows for transcriptomic detection in small tissue sections by RNA-seq while maintaining the histological information of these sections [30].”

What the sources say

• Not checked yetcites [30] Stahl PL (2016) Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science 353, 78– 82 27365449 source

In the paper

“One component of this large database was an examination of senescence in older mouse populations which showed that p16 expression increased significantly with aging as did E2f2, Lmnb1, Tnf, and Itgaf [42].”

What the sources say

• Not checked yetcites [42] Tabula Muris C. (2020) A single-cell transcriptomic atlas characterizes ageing tissues in the mouse. Nature 583, 590– 595 32669714 PMC8240505 source

In the paper

“These features include SA-β-gal staining, cell size, proliferation, DNA damage foci, and cytosolic DNA presence, all of which are currently not measurable by sequencing-based methods.”

In the paper

“One method that has yet to be used to study senescence is single-cell mass spectrometry, including single-cell proteomics and single-cell metabolomics which provide protein (including post-translational modification) and metabolite identification on a large scale [37] and could have enormous implications for studying senescent cells.”

What the sources say

• Not checked yetcites [37] Perkel JM (2021) Single-cell proteomics takes centre stage. Nature 597, 580– 582 34545225 source

In the paper

“They identified a subset of senescent endothelial cells in the retina, which highly express Col1a1, that can be specifically eliminated by a senolytic drug [41].”

What the sources say

• Not checked yetcites [41] Crespo-Garcia S (2021) Pathological angiogenesis in retinopathy engages cellular senescence and is amenable to therapeutic elimination via BCL-xL inhibition. Cell Metab. 33, 818– 832 e7 33548171 source

In the paper

“However, the sequencing depth of current methods remains relatively low, and only up to 50–60% of transcripts can be sequenced and detected in each cell.”

In the paper

“Moreover, by performing single-cell RNA-seq on adipose-derived mesenchymal stem cells isolated from young and aged mice, another study demonstrated that p21high cells accumulate more with aging and exhibit a number of altered pathways commonly seen in senescent cells induced in vitro, including upregulation of SCAPs, SASP, NF-κB, HMGB1, and FOXO pathways [8].”

What the sources say

• Not checked yetcites [8] Wang B (2020) Transplanting cells from old but not young donors causes physical dysfunction in older recipients. Aging Cell 19, e13106 31971661 PMC7059132 source

In the paper

“Another study used single-cell RNA-seq to compare transcriptomic differences in the kidney, lung, and spleen between aged and young mice [44] and found that various cell types express unique genes with aging, and similar cell types exhibit similar aging trajectories in terms of gene enrichment, while dissimilar cell types have distinct trajectories.”

What the sources say

• Not checked yetcites [44] Kimmel JC Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging. Genome Res. 29, 2088– 2103 PMC6886498 31754020 source

In the paper

“Due to the high therapeutic value of targeting senescent cells, understanding the heterogeneity of senescence will also play a major role in improving precision medicine approaches for older populations.”

In the paper

“Additionally, the tissue-specific differences in senescent cells described in this review suggest that a combination of many markers, rather than just one marker, could more accurately detect senescent cells.”

In the paper

“The study did show common genes differentially expressed with age among the three tissues studied, including decreased expression of genes in SRP-dependent protein translation and upregulated expression of genes related to inflammation [44].”

What the sources say

• Not checked yetcites [44] Kimmel JC Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging. Genome Res. 29, 2088– 2103 PMC6886498 31754020 source