**1. Introduction**

With over 1.8 million new cases and around 800,000 fatalities recorded in 2018, colorectal cancer (CRC) is considered as one of the most common malignancies, worldwide [1,2]. In recent years, early age onset of CRC cases have increased dramatically [3]. Conventional chemotherapy, radiotherapy and surgery provide effective local control of colon cancer. However, serious side effects and resistance to therapies over time decrease the survival rate of patients [4]. Despite recent dramatic advances in early diagnosis and treatment, there still remains an unmet need to palliate CRC symptoms, develop novel therapeutic strategies with lower side effects, and prolong the overall survival of the patients [5]. Numerous studies have shown that different cellular pathways including cell cycle, cell proliferation, drug resistance, apoptosis and metastasis are modulated in CRC. Furthermore, recent findings show that metabolic pathways such as glycolysis can influence the apoptotic potential of cancer therapeutics. Therefore, therapies targeting various targets in cancer cells have recently raised more interest [6,7].

Herbal compounds and their derivatives have attracted huge attention and become a prominent contribution in novel drug discovery programs by exhibiting their therapeutic

**Citation:** Azeez, H.J.; Neri, F.; Hosseinpour Feizi, M.A.; Babaei, E. Transcriptome Profiling of HCT-116 Colorectal Cancer Cells with RNA Sequencing Reveals Novel Targets for Polyphenol Nano Curcumin. *Molecules* **2022**, *27*, 3470. https:// doi.org/10.3390/molecules27113470

Academic Editor: Nour Eddine Es-Safi

Received: 1 May 2022 Accepted: 24 May 2022 Published: 27 May 2022

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effects through a multi-targeted approach, which is a characteristic that is highly desirable in cancer malignancies [6]. Phytochemicals may illustrate their antitumor properties through promoting apoptosis, suppressing the cell cycle, inhibiting angiogenesis and regulating antioxidant activities. Moreover, numerous naturally bioactive compounds have been shown to modulate immune checkpoints and affect the activities of immune cells including T and B cells, Treg cells and NK cells [8]. More interestingly, these natural products have gained competing interests due to the absence of toxicity and harmful side effects commonly associated with current therapies [9].

Curcumin is a polyphenolic derivative of turmeric known to have dramatic anticancer effects on cancer cells rather than normal ones. It has been demonstrated that curcumin exerts its toxic effects through modulation of the function of multiple genes including apoptotic, metastatic, cell proliferation and transcription factors [10]. Studies reported that curcumin modulates cellular pathways involved in cancer pathogenesis including NF-kB, MAPK, PTEN, P53 and wnt [11]. Despite these tempting advantages of curcumin, the poor bioavailability limits its exploitation as a therapeutic compound [12]. Our team has recently formulated and characterized a nano-based encapsulated curcumin, gemini curcumin (Gemini-Cur), with significant anticancer effects on ovarian, gastric, breast and colorectal cancer [13–16]. Briefly, gemini surfactant nanoparticles belong to a surfactant family with two identical structures that are linked by a rigid or flexible spacer that could harbor and deliver drugs and genes into the cells and tissues. Gemini curcumin nanoparticles are spherical and well-dispersed vesicles that easily enter the cancer cells [15].

Exploration of the genes with abnormal expression during the treatment of colon cancer with Gemini-Cur is essential to provide a deeper understanding of the mechanisms involved. Because regulatory genes are affected by dietary compounds, the ability of curcumin to modulate the transcriptome profile has attracted much attention [8,17]. Based on our recent findings on the significant toxic properties of Gemini-Cur on cancer cells, here, we employed RNA sequencing and bioinformatics analysis to identify the key genes and related pathways modulated in colorectal HCT-116 cells treated with Gemini-Cur. The data of the current study help us to determine top Differentially Expressed Genes (DEGs) as possible cellular targets and figure out potential biological pathways in colon cancer that are modulated by curcumin.

#### **2. Materials and Methods**
