Changes in gene expression patterns are a hallmark of the aging process. Important insight into the mechanisms controlling such gene expression programs has come from the study of replicative senescence of cultured cells (eg, human diploid fibroblasts), which recapitulates many features of cells from aging individuals. This Project has traditionally studied changes in RNA-binding protein (RBP) expression and function during replicative senescence. It has also examined the influence of RBPs in replicative senescence by interventions to elevate or reduce RBP levels, followed by the analysis of changes in senescence-associated mRNA expression patterns. We have studied if a given RBP binds a senescence-associated mRNA using a variety of in vitro binding assays (biotin pulldown, RNA EMSA, etc) and assays to measure binding of endogenous molecules ribonucleoprotein immunoprecipitation (RIP) or crosslinking IP (CLIP). In recent years, we have included the analysis of noncoding RNAs microRNAs (mi)RNAs, long noncoding (lnc)RNAs, and circular (circ)RNAs that influence senescence and aging. To investigate RBP and ncRNAs function during senescence, we employ approaches such as silencing of the RBP or ncRNA, overexpression of the same, analysis or mutant RBPs/ncRNAs, and RBP/ncRNA-associated RNA identification (using microarrays, RNAseq, and RT-qPCR). To investigate whether RBPs and ncRNAs affect the stability of target mRNAs during senescence, we measure the steady-state levels and half-lives of the mRNAs of interest as a function of RBP/ncRNA abundance. We investigate whether RBPs and ncRNAs affect the translation of target mRNAs by studying the relative association of the mRNA with translating polysomes and by quantifying the nascent translation rates of the encoded proteins. We also employ reporter constructs to gain additional insight into the processes modulated by the RBPs and ncRNAs and use various senescence-associated markers to examine changes in the senescence phenotype. Over the past 12 months, this Project has examined the changes in gene expression that occur in human tissues as part of physiologic aging. Much of our effort in this Project has been directed at understanding how proteins of different types (including RBPs) and ncRNAs affect the process of cellular senescence, which is increasingly recognized as underlying age-related changes in tissue physiology and pathology. The studies in this Project examine the proteins and RNAs that modulate cellular senescence and the consequences of their influence on the senescent phenotype. Among the cell systems used for these studies, human diploid fibroblasts have been particularly informative. SENESCENCE-ASSOCIATED CELL SURFACE MARKERS. With increasing evidence that senescent cell accumulation in aging tissues is linked to age-associated diseases and declining function, we have initiated efforts to remove senescent cells selectively. Mass spectrometry analysis revealed that secretory carrier membrane protein 4 (SCAMP4) levels were strikingly elevated on the surface of senescent cells compared with proliferating cells. Interestingly, silencing SCAMP4 in senescent fibroblasts reduced the secretion of SASP factors, including interleukin 6 (IL6), IL8, growth differentiation factor 15 (GDF-15), C-X-C motif chemokine ligand 1 (CXCL1), and IL7, while, conversely, SCAMP4 overexpression in proliferating fibroblasts increased SASP factor secretion. Our results indicate that SCAMP4 accumulates on the surface of senescent cells, promotes SASP factor secretion, and critically enhances the SASP phenotype (Kim et al., Genes & Development, 2018). Experiments are underway to identify other senescence-associated membrane markers, as well as RNA markers (coding and noncoding) of senescence. SENESCENCE-ASSOCIATED noncoding RNAs. A new area of study has continued in earnest during this review cycle: the analysis of circular RNAs and microRNAs associated with the senescent program. During the past twelve months, we have continued to investigate the influence of ncRNAs in senescence. During this review cycle, we have looked at microRNAs more closely. In collaboration with LEPS, we examined the role of metformin in the production of DICER1, a key protein in the biosynthesis of microRNAs, in senescent cells (Noren Hooten et al., Aging Cell, 2016). Together with the Slack team, we identified microRNAs associated with longevity using samples from the Baltimore Longitudinal Study of Aging (BLSA) (Smith-Vikos et al., Aging, 2016). The impact of miR-16 on the production of BAFF, a protein component of the senescence-associated secretory phenotype (SASP) was examined in collaboration with investigators in the SardiNIA consortium (Steri et al., The New England Journal of Medicine, 2017). Other SASP regulators were reviewed (Panda et al., Mechanisms of Ageing and Development, 2017). Ongoing experiments continue to focus on elucidating the function of specific linear and circular RNAs in cell senescence. SENESCENCE-ASSOCIATED RBPs. Following a long-established line of research in our group, we have continued the characterization of several RBPs implicated in aspects of cellular senescence, including the loss of proliferation, the impaired ability to respond to stress, and the implementation of a senescence-associated secretory phenotype. In collaboration with the Wang laboratory, we have investigated RBPs that methylate RNA via methylation at m6C and m5C (METTL3, METTL14, NSUN2) (Cai et al., Oncotarget, 2016; Xing et al., J. Cell Biochem. 2017). Ongoing efforts have been aimed at identifying the specific role of GRSF1 in senescence. A manuscript has been submitted manuscript reporting that GRSF1 prevents premature senescence by preserving mitochondrial function.

Agency
National Institute of Health (NIH)
Institute
National Institute on Aging (NIA)
Type
Investigator-Initiated Intramural Research Projects (ZIA)
Project #
1ZIAAG000393-11
Application #
9770124
Study Section
Project Start
Project End
Budget Start
Budget End
Support Year
11
Fiscal Year
2018
Total Cost
Indirect Cost
Name
Aging
Department
Type
DUNS #
City
State
Country
Zip Code
Omer, Amr; Patel, Devang; Lian, Xian Jin et al. (2018) Stress granules counteract senescence by sequestration of PAI-1. EMBO Rep 19:
Kim, Kyoung Mi; Noh, Ji Heon; Bodogai, Monica et al. (2018) SCAMP4 enhances the senescent cell secretome. Genes Dev 32:909-914
Tang, Hao; Wang, Hu; Cheng, Xiaolei et al. (2018) HuR regulates telomerase activity through TERC methylation. Nat Commun 9:2213
Tang, Hao; Wang, Hu; Cheng, Xiaolei et al. (2018) Author Correction: HuR regulates telomerase activity through TERC methylation. Nat Commun 9:2721
Noh, Ji Heon; Kim, Kyoung Mi; McClusky, Waverly G et al. (2018) Cytoplasmic functions of long noncoding RNAs. Wiley Interdiscip Rev RNA 9:e1471
Basu, Sandip K; Gonit, Mesfin; Salotti, Jacqueline et al. (2018) A RAS-CaMKK?-AMPK?2 pathway promotes senescence by licensing post-translational activation of C/EBP? through a novel 3'UTR mechanism. Oncogene 37:3528-3548
Kim, Jiyoung; Noh, Ji Heon; Lee, Seung-Kyu et al. (2017) LncRNA OIP5-AS1/cyrano suppresses GAK expression to control mitosis. Oncotarget 8:49409-49420
Abdelmohsen, Kotb; Panda, Amaresh C; Munk, Rachel et al. (2017) Identification of HuR target circular RNAs uncovers suppression of PABPN1 translation by CircPABPN1. RNA Biol 14:361-369
Li, Qiu; Li, Xiu; Tang, Hao et al. (2017) NSUN2-Mediated m5C Methylation and METTL3/METTL14-Mediated m6A Methylation Cooperatively Enhance p21 Translation. J Cell Biochem 118:2587-2598
Kim, Kyoung Mi; Noh, Ji Heon; Bodogai, Monica et al. (2017) Identification of senescent cell surface targetable protein DPP4. Genes Dev 31:1529-1534

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