The analysis of expression levels between SPATA31 over-expression cells and senescent cells.
Student: Selin Altunkara
Supervisor: Cemalettin Beckpen
The aim of my project is to find overlapping genes between genes that are significantly up or downregulated within the primary fibroblast cells that are ectopically overexpressing SPATA31A1 gene (Bekpen et al., 2018) and the genes that are significantly up or downregulated during cellular senescence Senescence Associated Secretory Phenotype (SASP)s.
Cellular senescence is a cell cycle arrest mechanism that occurs as a response to different stress signals. Senescence is a potential anti-tumor mechanism that inhibits the proliferation of damaged and mutated cells by arresting the cell cycle. Senescent cells are different than non-dividing cells morphologically and according to the expression patterns. There are some features/markers that can be used to characterize the cellular senescence such as β- galactosidase activity, expression of tumor suppressor genes, inhibitors of the cell cycle, secretion of inflammatory signaling molecules, DNA damage markers, etc. Senescent cells secrete a group of molecules called Senescence Associated Secretory Phenotype (SASP). SASP composition is highly heterogenous and most of the secretion includes chemokines, cytokines, and proteinases. Senescent cells accumulate in time with aging and the SASP levels are increasing accordingly. Irrecoverable and constant secretion of inflammatory signals by senescent cells which are not destroyed by the immune system and accumulated with aging enhances the chronic inflammation in the body consistently (Campisi J., 2012).
In the “Involvement of SPATA31 copy number variable genes in human lifespan” article (Bekpen et al., 2018), it is stated that SPATA31 overexpression has an impact on human lifespan and induces premature senescence. According to the Bekpen and coworkers, SPATA31A1 overexpressing cells were showing a premature senescence phenotype. In their experiment, they show that the staining of β- galactosidase (a marker for senescence cells) showed that senescent cell number is almost twice as higher for SPATA31A1 overexpressing cells than for the control ones. In my project, I have used the data from (Bekpen et al., 2018) to collect the significantly up and down-regulated upon overexpression of SPATA31A1 in primary fibroblast cell line and find whether any of these genes previously reported being SASP. To find the list of SASPs, I have used CellAge The Database of cell senescence genes which is a database used to identify the significantly expressed genes while cellular senescence (https://genomics.senescence.info/cells/). As a result of my analysis, between 66 genes (taken from SPATA31 overexpressed data) and 1259 genes (taken from CellAge data), 4 genes were overlapped. Consequently, it is found that CD36, SERPINB2, and L1CAM genes are overexpressed, and the CYTL1 gene is down expressed in both data. The overlapping analysis was done by using the R Studio program (RStudio Desktop 2022.02.3+492).
CD36 receptor is upregulated in response to oncogenic, replicative, and chemical senescent signals in several cell types (Chong et al., 2018). Also, CD36 is one of the important genes that trigger the NF-κB transcription factor and initiate the production of SASP molecules and a senescent state. L1CAM is a cell surface protein that is significantly upregulated in several cancer types such as breast, lung, gastric, and pancreatic cancers. SERPINB2 has a crucial role in senescence that stabilizes the p21 levels in the cell to maintain the senescence state as much as it is needed for the organism. CYTL1 is downregulated in most types of tumors. CYTL1 is potentially a novel tumor suppressor gene that is downregulated in the cancer cells to enhance metabolic reprogramming. In the article CYTL1 and SERPINB2 expressions were underlined because SERPINB2 was significantly high and CYTL1 was significantly down expressed in the SPATA31A1 overexpressing cells. Moreover, it is also stated that these genes are related to aging or age-related diseases.
- Bekpen C, Xie C, Nebel A, Tautz D. Involvement of SPATA31 copy number variable genes in human lifespan. Aging (Albany NY). 2018 Apr 19;10(4):674-688. doi: 10.18632/aging.101421. PMID: 29676996; PMCID: PMC5940121.
- Campisi J. Aging, cellular senescence, and cancer. Annu Rev Physiol. 2013;75:685-705. doi: 10.1146/annurev-physiol-030212-183653. Epub 2012 Nov 8. PMID: 23140366; PMCID: PMC4166529.
- Chong M, Yin T, Chen R, Xiang H, Yuan L, Ding Y, Pan CC, Tang Z, Alexander PB, Li QJ, Wang XF. CD36 initiates the secretory phenotype during the establishment of cellular senescence. EMBO Rep. 2018 Jun;19(6):e45274. doi: 10.15252/embr.201745274. Epub 2018 May 18. PMID: 29777051; PMCID: PMC5989758.