Int. J. Biol. Sci. 2021, Vol. 17 3133 Ivyspring International Publisher International Journal of Biological Sciences 2021; 17(12): 3133-3144. doi: 10.7150/ijbs.62393 Research Paper Genome-scale CRISPRa screening identifies MTX1 as a contributor for sorafenib resistance in hepatocellular carcinoma by augmenting autophagy Li Li, Shijun Yu, Qingqing Hu, Yanan Hai, Yandong Li Department of Oncology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai 200120, China Corresponding authors: Yandong Li and Yanan Hai, Department of Oncology, Shanghai East Hospital, School of Medicine, Tongji University, 150 Ji-Mo Rd., Shanghai 200120, China. Phone: 86-21-61569884; Fax: +86-21-58798999; E-mail: [email protected] and [email protected] © The author(s). This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/). See http://ivyspring.com/terms for full terms and conditions. Received: 2021.05.06; Accepted: 2021.07.09; Published: 2021.07.25 Abstract Sorafenib is the standard first-line drug for the treatment of advanced hepatocellular carcinoma (HCC), however, its therapeutic efficacy is not satisfactory due to primary or secondary resistance of HCC cells. In the present study, we identified Metaxin 1 (MTX1) as a new regulator of sorafenib resistance in HCC through genome-scale CRISPR activation (CRISPRa) screening. We found that MTX1 was frequently upregulated in HCC tissues and overexpression of MTX1 promoted HCC cell proliferation in vitro and in vivo. As well, MTX1 overexpression increased cell growth rate and decreased cell apoptosis upon sorafenib treatment. Consistently, the resistance induced by MTX1 was also observed in subcutaneous xenograft tumor model. Clinically, high expression of MTX1 was closely related with poor outcomes in HCC patients who received sorafenib treatment. Mechanistically, overexpression of MTX1 could promote HCC cell autophagy via interacting with and inhibiting CDGSH iron sulfur domain 1 (CISD1), an autophagy negative regulator. Taken together, our findings suggest that MTX1 is upregulated in HCC and contributes to sorafenib resistance via a possible mechanism involving CISD1 mediated autophagy. Key words: HCC, MTX1, sorafenib, autophagy, CISD1 Introduction Hepatocellular carcinoma (HCC) is one of the The clustered regularly interspaced short most common malignancies and the third cause of palindromic repeats/CRISPR-associated (CRISPR/ cancer-associated mortality worldwide [1]. Sorafenib, Cas) system has been rapidly developed as a powerful an oral multi-kinase inhibitor, has become a mainstay tool for gene editing in recent years [7]. The system of standard treatment for advanced HCC patients has currently innovated CRISPR interference since 2007 [2]. Its multi-kinase targets include RAF (CRISPRi) or CRISPR activation (CRISPRa) library, proto-oncogene (RAF), vascular endothelial growth which can quickly knock out or amplify any genes in factor (VEGF), platelet-derived growth factor (PDGF), the human genome [8, 9]. The genome-wide screening FMS-like tyrosine kinase 3 (FLT3) and KIT is an effective and unbiased approach to determine proto-oncogene (KIT) [3, 4]. The inhibition of these genes or pathways involved in biological processes kinases affects HCC cell growth, proliferation or [10]. To date, several studies have applied the survival. Nevertheless, the clinical efficacy of technique to successfully pick out the required genes sorafenib is frequently limited by drug resistance in a or pathways. For example, kinases that regulate considerable number of HCC patients [5, 6]. response to fibroblast growth factor receptor (FGFR) Therefore, understanding the molecular mechanism inhibitor have been found in gastric cancer [11], and of sorafenib resistance and searching for effective the Wnt-FZD5 signaling pathway that regulates drug biomarkers are crucial for predicting or overcoming sensitivity has been identified in RNF43-mutant sorafenib resistance for HCC patients. pancreatic tumors [12]. In the present work, in order http://www.ijbs.com Int. J. Biol. Sci. 2021, Vol. 17 3134 to identify genes which are essential to sorafenib Selleck Chemicals (Houston, TX, USA). Primary resistance in HCC, we conducted CRISPR-Pool™ antibodies used in this study were listed below: MTX1 SAM human library comprising 70,290 SAM-sgRNAs (15529-1-AP, Proteintech, Wuhan, China), CISD1 upon HCC cells to amplify genes for screening (16006-1-AP, Proteintech, Wuhan, China), Beclin1 purposes. Among the potential sorafenib resistance (11306-1-AP, Proteintech, Wuhan, China), LC3 factors, Metaxin 1 (MTX1) was considered as the most (14600-1-AP, Proteintech, Wuhan, China), GAPDH effective druggable target genes. (60004-1-Ig, Proteintech, Wuhan, China), β-Actin MTX1 belongs to Metaxins family, which also (sc-8432, Santa Cruz Biotechnology, USA) and FLAG includes another member Metaxin 2 (MTX2). As the (abs830005, Absin, China). outer membrane proteins of mitochondria, the Metaxins family participates in the import of Lenti CRISPR/cas9 screening and sequencing nuclear-encoded proteins into mitochondria and is CRISPR-Pool™SAM-Human-Dual vector was thought to be the member of Sorting and Assembly purchased from Shanghai Genechem Co., Ltd Machinery (SAM) [13, 14]. Some studies reveal that (Shanghai, China). The CRISPR/Cas9 synergistic MTX1 is essential for the proapoptotic protein Bak activator (SAM) system can activate gene (BCL2 antagonist/killer 1) activation during tumor transcription by using dCas9-VP64 to achieve the necrosis factor (TNFα)-induced cell death [14, 15]. In upregulation of coding genes. More specifically, addition, genome-wide association studies (GWASs) HCC-LM3 cells were transduced with have reported that MTX1 is one of the high-quality EF1α-MS2-p65-HSF1-2A-Hygro-WPRE lentivirus, biomarkers of gastric cancer susceptibility [16], and the successfully infected cells were screened with implicating the key role of MTX1 in promoting cancer Hygromycin B (200 µg/ml). Next, the cells were progression. However, the precise biological function infected with CRISPR-Pool™SAM human/Dual of MTX1 in HCC remains unclear. lentivirus. Two days later, Blasticidin S (10 µg/ml) In the present study, we identified MTX1 as a and Hygromycin B (100 µg/ml) were added to the new regulatory factor involving sorafenib resistance medium to select stably transduced cells. We by CRISPR/Cas9 activation library screening. Further classified the surviving cells into control or investigations indicated that MTX1 was upregulated experimental group. For experimental group, the cells in HCC tissues and enhanced sorafenib resistance of were continuously treated with sorafenib (7.5 µM) for HCC cells in vitro and in vivo. Finally, CISD1 was 14 days. The viable cells from control or experimental found to be interacted with MIX1, which may group respectively were harvested to extract genomic antagonize MTX1-caused autophagy during sorafenib DNA using DNA extraction kit (DP304, Tiangen treatment. Biotech, Beijing, China). And genomic DNA was performed to amply sgRNA targeted region using Materials and methods PCR technology. The enrichments of sgRNAs were identified by next generation sequencing (Oebiotech, Human HCC tissue specimens Shanghai, China). Forty paired tumor and corresponding normal liver samples derived from HCC patients were RNA interference and gene overexpression collected from Shanghai East Hospital in Shanghai, Short-interfering RNAs (siRNAs) targeting China. Following approval by the Ethics Committee MTX1 or CISD1 were synthesized by Shanghai of Shanghai East Hospital, each patient signed an Genepharma Co., Ltd, Shanghai, China. The informed consent before participating in the study. sequences were as follows: siNC: 5′-UUCU All fresh tissues were preserved in liquid nitrogen CCGAACGUGUCACGU-3′; siMTX1: 5’-CCCACA before use. UUCUCAGUCUCUA-3’; siCISD1-1: 5’-CAGCUGCA AUUGGUUAUCU-3’; siCISD1-2: 5’-CGUGAAGUUA Cell culture, reagents, and antibodies CCUGAUUGU-3’. Human HCC cell lines PLC/PRF/5 and Huh7 For gene overexpression, FLAG-tagged MTX1 were purchased from the Type Culture Collection of plasmid was constructed through cloning MTX1 the Chinese Academy of Sciences, Shanghai, China. cDNA (GeneBank Accession Number: NM_002455.5) HCC-LM3 cells were taken from our laboratory into pcDNA3.1 vector. CISD1 overexpression plasmid stocks. All the HCC cells were cultured in Dulbecco's (also FLAG tagged) was constructed based on modified Eagle's medium (DMEM; Corning, Inc., pENTER vector, which was obtained from Vigene Corning, NY, USA) with 10% fetal bovine serum (FBS) Biosciences, Shandong, China. MTX1-overexpressing and 1% penicillin/streptomycin, and were lentivirus was prepared by Shanghai Genepharma maintained in an incubator with 5% CO2 at 37 °C. Co., Ltd, Shanghai, China. Sorafenib and Bafilomycin A1 were obtained from http://www.ijbs.com Int. J. Biol. Sci. 2021, Vol. 17 3135 Cell proliferation assays AT-3’; Cell growth ability was measured by Cell MTX1-R: 5’-GTAGCCGTTCCATGTACTGCC-3’; Counting Kit-8 (CCK-8, Dojindo Laboratories, Japan) β-actin-F: 5’-AGAGCCTCGCCTTTGCCGAT according to the manufacturer’s instructions. Briefly, CC-3’; cells were seeded into 96-well plates with a density of β-actin-R: 5’-CTGGGCCTCGTCGCCCACA 3×103 cells per well in triplicate, and absorbance was TA-3’. read at 450 nm by spectrophotometer. For the Mouse model clonogenic assay, cells (1×103 cells /well) were plated Athymic nude mice aged 6 weeks were in