藉著比較幹細胞和癌細胞的基因和表觀遺傳因子的細胞週期調控網路來調查其中的癌化機制

Investigating Carcinogenesis Mechanisms by Comparing Genetic-and-epigenetic Cell Cycle Networks between Stem and Cancer Cells using NGS and Microarray Data

蔡琨偉(Kun-Wei Tsai)

指導教授 ： 陳博現

國立清華大學/電機資訊學院/電機工程學系/碩士(2015年)

https://doi.org/10.6843/NTHU.2015.00560

摘要

背景
誘導多能幹細胞(iPSCs)的發現證明了再生醫學的潛力，然而有一些證據顯示了iPSCs相似於致癌病灶(OF)，一種在體外產生的腫瘤細胞。這些證據顯示了幹細胞和癌細胞有著強烈的關係。而最近的研究展示了細胞週期對於發育和癌化過程的重要性。因此，如何利用大資料庫辨識出的基因和表觀遺傳因子調節來揭開在幹細胞和癌細胞細胞週期進行中所產生的癌化機制，仍然是一個值得探討的問題。

結果
藉著利用系統模型、系統識別以及大資料庫探勘所建構幹細胞(胚胎幹細胞, ESCs)和癌細胞(海拉細胞, HeLa cells)真實基因和表觀遺傳因子細胞週期調控網路(GECCN)。為了方便分析，真實的GECCN被主網路投影方法(PNP)簡化成HeLa cells和ESCs的核心GECCN。在這裡，我們藉著利用HeLa cells和ESCs共同的核心網路來調查細胞週期進行中所產生的癌化機制，並以此來釐清iPSCs (類ESC)潛在的癌化機制。更進一步，我們藉著HeLa cells特有的核心網路的大機制分析來調查子宮頸癌的癌化機制。藉著整合藥物資料庫的資訊以及HeLa cells 特有的核心網路分析的結果設計出治療子宮頸癌的複合藥物並最小化這個複合藥物對ESCs和HeLa cells核心網路中的其他成員的影響。

結論
結果顯示了iPSCs誘導因子，LIN28和OCT4分別使LET7B和HIF1A失調，造成了iPSCs癌化的風險。此外，在G1、S、G2時期基因突變和DNA甲基化的累積以及MIR29C、MIR34A、MIR98、MIR215、MIR935的失調，所造成的異常細胞增生。而異常的增生也會被M失調的MIR17所導致。在G1和G2時期，MIR192的失調會導致子宮頸癌的轉移。在S和G2時期，基因突變和DNA甲基化的累積、S中MIR34A的失調以及G2中MIR192的失調會促發無效的DNA的修復因此誘導細胞的凋亡。但在G2和S時期，基因突變和DNA甲基化的累積以及G2中MIR192的失調會提高了子宮頸癌細胞對抗凋亡的能力來防止癌細胞中不正常的DNA突變量被減少。我們最後提出了治療子宮頸癌的複合藥物，其中包含了METHOTREXATE、 QUERCETIN 和 MIMOSINE，並分別會影響ARID5B、STK17B 和 CCL2這幾個關鍵的基因。

關鍵字

細胞週期進程 ； 真實基因和表觀遺傳因子的細胞週期調控網路 ； 癌化機制 ； 大機制 ； 子宮頸癌 ； 胚胎幹細胞 ； 大資料庫挖掘 ； 複合藥物 ； 次世代定序和微陣列檢測 ； 主網路投影

並列摘要

Background
Discovery of induced pluripotent stem cells (iPSCs) has shed light on the potential of regenerative medicine, but some evidences reveal iPSCs are similar to oncogenic foci (OF), a form of in vitro produced tumor cells. These evidences indicate that stem cells and cancer cells have intensive relation. Also, recent studies exhibit that the cell cycle play a central roles in development and carcinogenesis. Thus, how to unravel the mechanism of cell cycle progression in stem and cancer cells through genetic-and-epigenetic regulations using big databases is a big issue.

Results
The real genetic-and-epigenetic cell cycle networks (GECCNs) of stem cells (embryonic stem cells, ESCs) and cancer cells (HeLa cells) are constructed by applying the system modeling, system identification and big database mining. For convenience of analysis, the real GECCNs are reduced into the core GECCNs of HeLa cells and ESCs by applying principal network projection (PNP). In this study, we investigated carcinogenic mechanisms during cell cycle progression by using common core GECCNs between HeLa cells and ESCs to clarify the potential carcinogenic mechanisms of iPSCs (ESC-like cells). Furthermore, we investigated cervical carcinogenic mechanisms by applying the big mechanism analysis of the specific core GECCN in HeLa cells. By integrating information of drug databases, the result in the specific core GECCNs of HeLa cells could provide the multiple drug for cervical cancer treatment with minimal side effects on the other genes in the core GECCN of ESCs and HeLa cells.

Conclusions
The results indicated that the iPSC induction factors, LIN28 and OCT4, dysregulating LET7B and HIF1A, respectively, results in the carcinogenic risk of iPSCs. Additionally, the accumulated genetic mutations and DNA methylation, and dysregulations of MIR29C, MIR34A, MIR98, MIR215 and MIR935 during the G1, S, and G2 phases resulted in aberrant cell proliferation which also resulted from dysregulations of MIR17 during the M phases. Dysregulation of MIR192 led to metastatic cervical cancer during the G1 and G2 phases. Moreover, the accumulated genetic mutations and DNA methylation during the S and G2 phases, dysregulations of MIR34A during the S phases and dysregulations of MIR192 during the G2 phases could trigger ineffectively DNA repair, which could induce apoptosis. Thus, the accumulated genetic mutations and DNA methylation during the G2 and S phases and dysregulation of MIR192 during the G2 phase gave rise anti-apoptosis of cervical cancer cells to prevent the decrease of genetic mutation. We finally proposed the multiple drug, including METHOTREXATE, QUERCETIN and MIMOSINE that affect ARID5B, STK17B and CCL2, respectively, for the treatment of cervical cancer.

並列關鍵字

cell cycle progression ； real genetic-and-epigenetic cell cycle network ； carcinogenic mechanism ； big mechanism ； cervical cancer ； embryonic stem cells ； big database mining ； multiple drug ； NGS and microarray ； principal network projection

參考文獻

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