Bioinformatics analysis of proteomics profiles in senescent human primary proximal tubule epithelial cells

Therapeutic Opportunities Presented by Modulation of Cellular Senescence

Cellular senescence is a permanent state of growth arrest coupled with profound changes in phenotype that can be triggered by multiple extrinsic or intrinsic stimuli. Senescence is a process-level example of the evolution of ageing mechanisms through antagonistic pleiotropy and plays a primary role in tumour suppression, although evidence is mounting for its involvement in other fundamental physiological processes. Evidence from human premature ageing diseases and from transgenic mice in which it is possible to specifically delete senescent cells is consistent with a model in which the accumulation of senescent cells through the life course is responsible for later life chronic disease and impairment. The removal of senescent cells or their reversion to a phenotypically benign state is thus an important emerging goal of translational medicine.Modern bioinformatic approaches based on text mining have compiled co-mentions of cell senescence and age-related diseases allowing an impartial ranking of the impairments most closely associated with this process. Following this schema, the evidence for the involvement of senescence in several highly ranked pathologies is reviewed, alongside potential methods for the ablation of senescent cells or their reversion to their primary phenotype with polyphenolics or inhibitors of p38 MAP kinase. Lastly, the potential for senescence to act as a barrier to the development of bioartificial organs designed to treat some of these conditions is discussed.

Comparative analysis of markers for H2O2-induced senescence in renal tubular cells

To address what marker(s) is/are most suitable for determining renal cell senescence, cell area, granularity, cycle shift/arrest, SA-β-Gal, SIRT1 and p16 were evaluated after inducing senescence in HK-2 cells with 0.2-0.8 mM H₂O₂. Only cell area and granularity concentration-dependently increased at all time-points, whereas SA-β-Gal, SIRT1 and p16 showed significant coefficient of determination (R²) at two time-points. Cell granularity had significant correlation coefficient (R) with other six, whereas SA-β-Gal had significant R with five, and cell area, SIRT1 and p16 had significant R with four others. Comparing to SA-β-Gal, other markers had significantly lower fold-changes only at 72-h with 0.8 mM H₂O₂, whereas p16 provided greater fold-changes at 48-h with 0.4 and 0.8 mM H₂O₂. Therefore, cell area, granularity, SA-β-Gal and p16 may serve as the most suitable markers for determining H₂O₂-induced senescence in HK-2 renal cells, whereas other markers can be also used but with inferior quantitative precision.

Hederagenin ameliorates cisplatin-induced acute kidney injury via inhibiting long non-coding RNA A330074k22Rik/Axin2/β-catenin signalling pathway

BACKGROUND

Acute kidney injury (AKI), a kidney disease with high morbidity and mortality, is characterized by a dramatic decline in renal function. Hederagenin (HDG), a pentacyclic triterpenoid saponin isolated from astragalus membranaceus, has been shown to have significant anti-inflammatory effects on various diseases. However, the effects of HDG on renal injury and inflammation in AKI has not been elucidated.

METHODS

In this research, mice model of AKI was established by intraperitoneal injection of cisplatin in vivo, the inflammatory model of renal tubular epithelial cells was established by LPS stimulation in vitro, and HDG was used to intervene in vitro and in vivo models. Transcriptome sequencing was used to analyze the alterations of LncRNA and mRNA expression in AKI model and LncRNA-A330074k22Rik (A33) knockdown cells, respectively. Renal in situ electrotransfer knockdown plasmid was used to establish mice model of AKI with low expression of A33 in kidney.

RESULTS

The results showed that HDG effectively alleviate cisplatin-induced kidney injury and inflammation in mice. Transcriptome sequencing results showed that multiple LncRNAs in kidney of AKI model exhibited significant changes, among which LncRNA-A33 had the most obvious change trend. Subsequent results showed that A33 was highly expressed in kidney of AKI mice and LPS-induced renal tubular cells. After in situ renal electroporation knockdown plasmid down-regulated A33 in kidney of AKI mice, it was found that inhibition of A33 could significantly relieve cisplatin-induced kidney injury and inflammation of AKI, while HDG could effectively suppress the expression of A33 in vitro and in vivo, respectively. Subsequently, transcriptome sequencing was again used to analyze the changes in mRNA expression of renal tubular cells after A33 knockdown by siRNA. The results showed that a large number of inflammation-related signaling pathways were down-regulated, Axin2 and its downstream β-catenin signal were significantly inhibited. Cell recovery test showed that HDG inhibited Axin2/β-catenin signal by down-regulating A33, and improved kidney injury and inflammation of AKI.

CONCLUSION

Taken together, HDG significantly ameliorated cisplatin-induced kidney injury through LncRNA-A330074k22Rik/Axin2/β-catenin signal axis, which providing a potential therapeutic approach for the treatment of AKI.

The Quasimesenchymal Pancreatic Ductal Epithelial Cell Line PANC-1-A Useful Model to Study Clonal Heterogeneity and EMT Subtype Shifting

Simple Summary

Malignant tumors often escape therapy due to clonal propagation of a subfraction of drug-resistant cancer cells. The underlying phenomenon of intratumoral heterogeneity is driven by epithelial–mesenchymal plasticity (EMP) involving the developmental programs, epithelial–mesenchymal transition (EMT), in which epithelial cells are converted to invasive mesenchymal cells, and the reverse process, mesenchymal–epithelial transition (MET), which allows for metastatic outgrowth at distant sites. For therapeutic targeting of EMP, a better understanding of this process is required; however, cellular models with which to study EMP in pancreatic ductal adenocarcinoma (PDAC) are scarce. Using single-cell clonal analysis, we have found the PDAC cell line, PANC-1, to consist of cells with different E/M phenotypes and functional attributes. Parental PANC-1 cultures could be induced in vitro to shift towards either a more mesenchymal or a more epithelial phenotype, and this bidirectional shift was controlled by the small GTPases RAC1 and RAC1b, together identifying PANC-1 cells as a useful model with which to study EMP.

Abstract

Intratumoral heterogeneity (ITH) is an intrinsic feature of malignant tumors that eventually allows a subfraction of resistant cancer cells to clonally evolve and cause therapy failure or relapse. ITH, cellular plasticity and tumor progression are driven by epithelial–mesenchymal transition (EMT) and the reverse process, MET. During these developmental programs, epithelial (E) cells are successively converted to invasive mesenchymal (M) cells, or back to E cells, by passing through a series of intermediate E/M states, a phenomenon termed E–M plasticity (EMP). The induction of MET has clinical potential as it can block the initial EMT stages that favor tumor cell dissemination, while its inhibition can curb metastatic outgrowth at distant sites. In pancreatic ductal adenocarcinoma (PDAC), cellular models with which to study EMP or MET induction are scarce. Here, we have generated single cell-derived clonal cultures of the quasimesenchymal PDAC-derived cell line, PANC-1, and found that these differ strongly with respect to cell morphology and EMT marker expression, allowing for their tentative classification as E, E/M or M. Interestingly, the different EMT phenotypes were found to segregate with differences in tumorigenic potential in vitro, as measured by colony forming and invasive activities, and in circadian clock function. Moreover, the individual clones the phenotypes of which remained stable upon prolonged culture also responded differently to treatment with transforming growth factor (TGF)β1 in regard to regulation of growth and individual TGFβ target genes, and to culture conditions that favour ductal-to-endocrine transdifferentiation as a more direct measure for cellular plasticity. Of note, stimulation with TGFβ1 induced a shift in parental PANC-1 cultures towards a more extreme M and invasive phenotype, while exposing the cells to a combination of the proinflammatory cytokines IFNγ, IL1β and TNFα (IIT) elicited a shift towards a more E and less invasive phenotype resembling a MET-like process. Finally, we show that the actions of TGFβ1 and IIT both converge on regulating the ratio of the small GTPase RAC1 and its splice isoform, RAC1b. Our data provide strong evidence for dynamic EMT–MET transitions and qualify this cell line as a useful model with which to study EMP.

Transient ACE (Angiotensin-Converting Enzyme) Inhibition Suppresses Future Fibrogenic Capacity and Heterogeneity of Cardiac Fibroblast Subpopulations

Transient ACE (angiotensin-converting enzyme) inhibition in spontaneously hypertensive rats is known to protect against future injury-induced cardiac inflammation, fibrosis, and dysfunction; however, the mechanisms of protection have not been delineated. Here, we used single-cell RNA sequencing to test the hypothesis that transient ACE inhibitor treatment would induce a persistent shift in cardiac fibroblast subpopulations. Adult male spontaneously hypertensive rats (11 weeks old, hypertensive with cardiac hypertrophy) were treated for 2 weeks with an ACE inhibitor, enalapril (30 mg/kg per day, PO), or water (untreated spontaneously hypertensive rats) followed by a 2-week washout period (n=7/group). Cardiac fibroblasts were isolated from the left ventricle and subjected to single-cell RNA sequencing. Nine clusters of fibroblasts were identified, with 98% of cells in clusters 0 to 6. The transient treatment produced significant changes both within and across clusters. Cluster 1 depicted a highly fibrogenic gene profile, with cluster 6 serving as a gateway to cluster 1. Transient ACE inhibition depleted the gateway and expanded cluster 0, which was the least fibrogenic profile. Moreover, within cluster 1 fibroblasts, ACE inhibition reduced expression of individual fibrosis genes (eg, COL1A1, COL3A1, and FN1; all P<1×10-35). Clusters 2 to 5 reflected proliferative, moderately fibrogenic, translationally active, and less inflammatory subsets of fibroblasts, all of which exhibited attenuated fibrogenic gene expression after transient ACE inhibition. In conclusion, transient ACE inhibition shifts cardiac fibroblast subpopulations and degree of activation resulting in an overall reduced fibrogenic phenotype.

Autophagy and heat-shock response impair stress granule assembly during cellular senescence

Stress granules (SGs) are membraneless organelles formed in response to insult. These granules are related to pathological granules found in age-related neurogenerative diseases such as Parkinson's and Alzheimer's. Previously, we demonstrated that senescent cells, which accumulate with age, exposed to chronic oxidative stress, are unable to form SGs. Here, we show that the senescent cells' inability to form SGs correlates with an upregulation in both the heat-shock response and autophagy pathways, both of which are well-established promoters of SG disassembly. Our data also reveals that the knockdown of HSP70 and ATG5, important components of the heat-shock response and autophagy pathways, respectively, restores the number of SGs formed in senescent cells exposed to chronic oxidative stress. Surprisingly, under these conditions, the depletion of HSP70 or ATG5 did not affect the clearance of these SGs during their recovery from chronic stress. These data reveal that senescent cells possess a unique heat-shock and autophagy-dependent ability to impair the formation of SGs in response to chronic stress, thereby expanding the existing understanding of SG dynamics in senescent cells and their potential contribution to age-related neurodegenerative diseases.

A cmap-enabled gene expression signature-matching approach identifies small-molecule inducers of accelerated cell senescence

BACKGROUND

Diverse stresses including genotoxic therapy can induce proliferating cancer cells to undergo cellular senescence and take on the characteristic phenotypes of replicative cellular aging. This accelerated or therapy-induced senescence has been alternatively proposed to contribute to therapeutic efficacy or resistance. Toward better understanding this cell state, we sought to define the core transcriptome of accelerated senescence in cancer cells.

RESULTS

We examined senescence induced by ionizing irradiation or ectopic overexpression of the stoichiometric cyclin-dependent kinase (CDK) inhibitor p21CIP/WAF1/SDI1 in the human breast cancer cell line MCF7. While radiation produces a strong DNA damage response, ectopic expression of p21 arrests cell cycle progression independently of DNA damage. Both conditions promoted senescence within 5 days. Microarray analysis revealed 378 up- and 391 down-regulated genes that were shared between the two conditions, representing a candidate signature. Systems analysis of the shared differentially expressed genes (DEGs) revealed strong signals for cell cycle control and DNA damage response pathways and predicted multiple upstream regulators previously linked to senescence. Querying the shared DEGs against the Connectivity Map (cmap) database of transcriptional responses to small molecules yielded 20 compounds that induce a similar gene expression pattern in MCF7 cells. Of 16 agents evaluated, six induced senescence on their own. Of these, the selective estrogen receptor degrader fulvestrant and the histone acetyltransferase inhibitor vorinostat did so without causing chromosomal damage.

CONCLUSIONS

Using a systems biology approach with experimental validation, we have defined a core gene expression signature for therapy-induced senescence.

Renal tubular epithelial cells: the neglected mediator of tubulointerstitial fibrosis after injury

Renal fibrosis, especially tubulointerstitial fibrosis, is the inevitable outcome of all progressive chronic kidney diseases (CKDs) and exerts a great health burden worldwide. For a long time, interests in renal fibrosis have been concentrated on fibroblasts and myofibroblasts. However, in recent years, growing numbers of studies have focused on the role of tubular epithelial cells (TECs). TECs, rather than a victim or bystander, are probably a neglected mediator in renal fibrosis, responding to a variety of injuries. The maladaptive repair mechanisms of TECs may be the key point in this process. In this review, we will focus on the role of TECs in tubulointerstitial fibrosis. We will follow the fate of a tubular cell and depict the intracellular changes after injury. We will then discuss how the repair mechanism of tubular cells becomes maladaptive, and we will finally discuss the intercellular crosstalk in the interstitium that ultimately proceeds tubulointerstitial fibrosis.

Epithelial cell senescence: an adaptive response to pre-carcinogenic stresses?

Senescence is a cell state occurring in vitro and in vivo after successive replication cycles and/or upon exposition to various stressors. It is characterized by a strong cell cycle arrest associated with several molecular, metabolic and morphologic changes. The accumulation of senescent cells in tissues and organs with time plays a role in organismal aging and in several age-associated disorders and pathologies. Moreover, several therapeutic interventions are able to prematurely induce senescence. It is, therefore, tremendously important to characterize in-depth, the mechanisms by which senescence is induced, as well as the precise properties of senescent cells. For historical reasons, senescence is often studied with fibroblast models. Other cell types, however, much more relevant regarding the structure and function of vital organs and/or regarding pathologies, are regrettably often neglected. In this article, we will clarify what is known on senescence of epithelial cells and highlight what distinguishes it from, and what makes it like, replicative senescence of fibroblasts taken as a standard.