CRISPR/Cas9 for overcoming drug resistance in solid tumors

Abstract

Objectives

In this review, we focus on the application of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated nuclease 9 (Cas9), as a powerful genome editing system, in the identification of resistance mechanisms and in overcoming drug resistance in the most frequent solid tumors.

Data acquisition

Data were collected by conducting systematic searching of scientific English literature using specific keywords such as “cancer”, “CRISPR” and related combinations.

Results

The review findings revealed the importance of CRISPR/Cas9 system in understanding drug resistance mechanisms and identification of resistance-related genes such as PBRM1, SLFN11 and ATPE1 in different cancers. We also provided an overview of genes, including RSF1, CDK5, and SGOL1, whose disruption can synergize with the currently available drugs such as paclitaxel and sorafenib.

Conclusion

The data suggest CRISPR/Cas9 system as a useful tool in elucidating the molecular basis of drug resistance and improving clinical outcomes.

Graphical abstract.

The mechanisms of CRISPR/Cas9-mediated genome editing and double-strand breaks (DSBs) repair.

Background

Cancer is a multi-factorial disease and genetics play an important role in the tumorigenesis process. The formation of cancer cells is a long-term process and it can take several years for a normal cell to turn into a cancer cell. Several genetic changes are accumulated in normal cells over time and this eventually results in cancer [1]. Sometimes, cancer cells can be “addicted” to a certain molecule. This means targeting a specific gene/molecule in tumor cells can lead to cell death. For instance, genomic aberrations in genes such as EGFR, HER2, MET and ALK can make a normal cell cancerous [2]. Therefore, targeting these molecules or related pathways by chemical inhibitors such as tyrosine kinase inhibitors (TKIs), i.e. gefitinib, afatinib or crizotinib, can lead to significant inhibition of tumor growth. However, eventually, tumor cells become resistant to the treatment due to the emergence of a new bypass mechanisms which could be via acquiring new genomic aberrations [3, 4]. For instance, acquiring EGFR mutation (T790 M), amplification of MET proto-oncogene (a receptor tyrosine kinase) and AXL activation are proven cause of resistance against EGFR-TKIs in lung cancer patients [5]. Overall, a wide range of cellular mechanisms including epithelial-mesenchymal transition (EMT), changes in autophagy and glycolysis, suppression of apoptosis, epigenetic modifications and alteration in the drug metabolism can lead to drug resistance in different types of cancer [3, 6]. These new genomic changes can be either induced by treatment or originated from intratumor heterogeneity [3, 7]. Thus, treatment strategy should be modified based on the new molecular signature of the tumor.

CRISPR/Cas9 gene editing technology has dramatically influenced the field of molecular biology. It is a very flexible, powerful and convenient gene manipulation tool which is used for a wide range of purposes including elucidation of protein function [8, 9], investigation of molecular basis of cancer by generating in vivo and in vitro models [10, 11] and identification of drug resistance mechanisms [12, 13]. Besides, one of the most valuable applications of CRISPR/Cas9 system is to investigate the role of different genes in the improvement of drug response. It can be employed to modify genomic DNA at single nucleotide level or to knockout a certain gene in cancer cells to functionally study the effect of these modifications in treatment response. Therefore, CRISPR/Cas9 can provide the opportunity to study drug resistance in different cancer types resulting in the identification of several resistance-related genes. These genes can be either genetically disrupted or pharmaceutically inhibited, if they are overexpressed in tumor cells resulting in resensitization of the cells to treatment.

Recently, few review articles have been published mainly focusing either on the application of CRISPR/Cas9 technology in cancer treatment and on drug resistance in breast cancer [14, 15]. In this review, we specifically focus on drug resistance and identification of different target genes to overcome drug resistance in different cancer types which can improve clinical outcomes. Thus, we present an overview of CRISPR-based pre-clinical studies associated with drug resistance in a number of solid tumors including lung, breast, liver and brain cancer.

Data acquisition

Data were collected from PubMed by using specific keywords such as “CRISPR” in combination with other related-keywords including lung, breast, liver, glioma, ovarian, colon and testicular cancer, tumor or malignancy. Our search resulted in 369 English articles containing both CRISPR and one of the cancers in either title or abstract. Only articles with a focus on drug resistance were included in this review. After skimming titles and scanning abstracts, 42 articles were included in this review.

Results

CRISPR/Cas9 technology

CRISPR/Cas9 is part of prokaryotic immune system, which is used as a defense mechanism to disrupt foreign plasmids and viruses. It consists of two main subunits: a single-guide RNA (sgRNA) and Cas9 nuclease. Cas9 is usually derived from Streptococcus pyogenes and contains two nuclease domains (HNH and RuvC-like nuclease domains) which can cut double stranded DNA. The HNH domain cleaves the complementary DNA strand while the RuvC-like domain cuts the non-complementary strand. Single-guide RNA is responsible for the recognition of the target site via a 20-nucleotide sequence which is complementary to the target sequence [16–18]. It directs Cas9 to the target site and then, Cas9 cleaves the genomic DNA resulting in a double stranded break (DSB). Subsequently, the genomic DNA is repaired either by non-homologous end joining (NHEJ) or homology directed DNA repair (HDR) (Fig. 1). NHEJ usually results in small insertion/deletions (indels) and gene knockout, whereas HDR works more precisely and results in point mutations or gene knockin [19]. Basically, any gene of interest can be targeted by small modifications in the sgRNA sequence. However, the selected target sequence must be immediately downstream of a protospacer adjacent motif (PAM), a short sequence (5’-NGG-3′), that is recognizable by Cas9 nuclease [16, 20].

Fig. 1.

The mechanisms of CRISPR/Cas9-mediated genome editing and double-strand breaks (DSBs) repair. CRISPR/Cas9 can introduce DSBs in DNA. The DSBs is repaired by either non-homologous end joining (NHEJ) or homology-directed repair (HDR). Insertions, deletions or other alterations of DNA will occur during this process to achieve gene modifications. PAM: protospacer adjacent motif; sgRNA: single-guide RNA

CRISPR/Cas9 system and drug response in solid tumors

Many genomic aberrations, such as chromosomal rearrangements, activating mutations in oncogenes, loss of function mutations in tumor suppressor genes and epigenetic events are needed to convert a normal cell to a cancer cell [21, 22]. Tumor cells may respond to treatment depending on their molecular signature. However, resistance inevitably arises and new treatment strategies are required. The CRISPR/Cas9 genome editing system can precisely introduce activating or loss of function mutations into the tumor genome enabling researchers to explore the role of different genes in tumorigenesis.

In addition, the CRISPR/Cas9 editing system can be utilized to get insight into the molecular mechanisms underlying drug resistance as well as targeting specific oncogenes either as monotherapy or in combination with currently available drugs (Table 1) [12, 13, 24, 42, 60]. CRISPR/Cas9 system can be used to correct resistant form of a certain targetable cancer-related gene and resensitize tumor cells to the treatment. Moreover, CRISPR/Cas9 can be engineered to disrupt resistance-related oncogenes such as KRAS or to correct certain tumor suppressor genes such as TP53 resulting in resensitization of tumor cells.

Table 1.

Pre-clinical studies in which CRISPR/Cas9 was used to investigate the role of different genes in response to treatment

Cancer	Target	in vitro	Cell line	in vivo	CRISPR	Vector	Treatment	Effect	Ref
Lung	EGFR	+	H2073	+	Inducing nucleotide change	Non-viral	Osimertinib (AZ5104)	Sensitized the cells	[23]
	MED1, CREBBP & EP300	+	PC9	–	Genome-wide CRISPR screening knockout	LV	Erlotinib/THZ1	Sensitized the cells	[24]
	AURKB (Aurora-B)	+	NA	NA	Both allele knockout	NA	Cisplatin or paclitaxel	Sensitized the cells	[25]
	RSF1	+	A460 & H1299	+	Both allele knockout	Non-viral	Paclitaxel	Sensitized the cells	[26]
	KEAP1	+	H1299, HCC827, CALU1 & HCC364	+	Genome-wide CRISPR screening knockout	LV	Erlotinib, trametinib or vemurafenib	Induced resistance	[12]
	PBRM1	+	PC9	–	Both allele knockout	LV	Gefitinib or AZD9291	Induced resistance	[27]
	IGF1R	+	HCC827	–	Both allele knockout	Non-viral	Erlotinib	Induced resistance	[28]
	MUC16	+	A549, H460, H292, H446 & 10 additional cell lines	–	Both allele knockout	Non-viral	Cisplatin	Induced resistance	[29]
	CDKN1A	+	A549	–	Both allele knockout	Non-viral	Radiation therapy	Induced resistance	[30]
	SLFN11	+	H526	+	Both allele knockout	LV	Talazoparib	Induced resistance	[31]
Breast	ZNF423	+	ZR75–1	+	Inducing nucleotide change (rs9940645 SNP)	Non-viral	Raloxifene, olaparib, 4-OHT or cisplatin	Sensitized the cells	[32]
	PSMB7 (Proteasome β2)	+	MDA-MB-231	+	Both allele knockout	LV	Bortezomib or carfilzomib	Sensitized the cells	[33]
	CDH1 (E-cadherin)	+	MCF7	+	Both allele knockout	Non-viral	Foretinib or crizotinib	Sensitized the cells	[34]
	Linc-RoR	+	MCF7	–	Both allele knockout	Non-viral	Tamoxifen	Sensitized the cells	[35]
	ESR1	+	T47D & MCF7	–	Inducing nucleotide change (Y537S)	Non-viral & AAV	Fulvestrant, raloxifene, 4-OHT or AZD9496	Induced resistance	[36–38]
	ATPE1	+	HCC1937	–	Both allele knockout	Non-viral	Olaparib	Induced resistance	[39]
	MAP3K1	+	MCF7	+	Both allele knockout	Non-viral	AZD5363	Induced resistance	[40]
	BAK	+	SK-BR-3	+	Genome-wide CRISPR screening knockout	LV	S63845	Induced resistance	[41]
	MAD2L1BP, ANAPC4 & ANAPC13	+	MDA-MB-231, MDA-MB-436 & MDA-MB-468	–	Genome-wide CRISPR screening knockout	LV	CFI-402257	Induced resistance	[13]
	Ctc1, Stn1 & Ten1	+	NA	+	Genome wide CRISPR drug resistance screening	NA	PARP inhibitors	Induced resistance	[42]
Liver	CDK5	+	NA	+	Both allele knockout	NA	Sorafenib	Sensitized the cells	[43]
	FGFR4	+	MHCC97L	–	Both allele knockout	LV	Sorafenib	Sensitized the cells	[44]
	MAPK1	+	HuH7	+	Kinome CRISPR screens	LV	Sorafenib or Sorafenib/Selumetinib	Sensitized the cells	[45]
	SGOL1	+	HuH7	+	Genome-wide CRISPR screening knockout	LV	Sorafenib	Induced resistance	[46]
Glioma	ATRX	+	U251, HG6 & LN229	+	Both allele knockout	LV	Temozolomide	Sensitized the cells	[47]
	NOTCH1	+	U87 & U251	+	Knockdown	LV	Radiation therapy	Sensitized the cells	[48]
	PCM1	+	NA	–	Both allele knockout	NA	Temozolomide	Sensitized the cells	[49]
	GLI1	+	GBM28 (primary cells)	–	Both allele knockout	Non-viral	Penfluridol	Sensitized the cells	[50]
Ovarian	PARP1	+	UWB1.289 & OVCAR8	+	Both alleles knockout	LV	Veliparib, olaparib, rucaparib, niraparib, talazoparib or cisplatin	Induced resistance	[51]
	BIRC5	+	SKOV3 & OVCAR3	–	Both alleles knockout	LV	Paclitaxel	Sensitized the cells	[52]
	ATG5	+	OVCAR3	+	Both alleles knockout	LV	Carboplatin	Sensitized the cells	[53]
	BMI1	+	SKOV3	+	Both alleles knockout	Non-viral	Cisplatin or carboplatin	Sensitized the cells	[54]
Colon	TP53	+	SW48	+	Inducing nucleotide change (R273H)	NA	Doxorubicin	Induced resistance	[55]
	MARCH2	+	HCT116	+	Both alleles knockout	NA	Etoposide and cisplatin	Sensitized the cells	[56]
	CASP3	+	HCT116	+	Both alleles knockout	NA	Radiation therapy or mitomycin C	Sensitized the cells	[57]
	RBX2	+	HCT116 & SW480	+	Both alleles knockout	Non-viral	Paclitaxel	Sensitized the cells	[58]
Testicular	HMGB4	+	NTera2	–	Both alleles knockout	Non-viral	Cisplatin	Induced resistance	[59]

LV Lentivirus, AAV Adeno-associated virus, NA Not available

Although CRISPR/Cas9 is a powerful tool for gene manipulation at the single base pair resolution, the vast majority of studies are focused on the knockout of certain genes in different cancers. Below, we only focus on CRISPR-based studies associated with drug response and resistance in the most frequent solid tumors including lung, breast, liver and brain cancers.

Lung cancer

Lung cancer is the main cause of cancer-related death in the word with a very poor prognosis [5]. As abovementioned, primary or secondary drug resistance in lung cancer patients is the main reason for researchers to look for new treatment strategies. Therefore, CRISPR/Cas9 technology would be of great benefit to directly target certain genes or to improve the drug response.

EGFR ex20isn is responsible for less than 10% of the EGFR mutations in non-small cell lung cancer (NSCLC) patients. However, unlike EGFR ex19del and L858R activating mutations, conventional chemotherapy is still the standard treatment for this subset of patients. A recent study investigated the potential therapeutic activity of osimertinib, a TKI used against resistant tumor cells harboring T790 M mutation, on NSCLC cells containing ex20ins. They established an EGFR ex20ins adenocarcinoma cell line using CRISPR/Cas9 and showed that osimertinib can inhibit the proliferation in tumor cells harboring this specific mutation in vitro as well as inhibition of the ex20ins-mediated pathway in vivo [23].

Recently, it has been shown that proteins involved in transcriptional complexes play a role in drug response. Terai et al. (2018) exploited a genome-wide CRISPR approach in combination with erlotinib (an EGFR-TKI) and THZ1 (CDK7/12 inhibitor) to overcome drug resistance in an EGFR-dependent lung cancer cell line (PC9). Interestingly, deletion of multiple genes involved in transcriptional complex including MED1, CREBBP and EP300 increased erlotinib/THZ1 synergy [24]. Thus, multiple sgRNAs that can target one or more of the abovementioned genes in combination with EGFR-TKIs such as erlotinib might be a better treatment option for EGFR-dependent tumors as compared to monotherapy. A combination of sgRNAs and shRNAs was used in lung cancer cells (PC9) treated with gefitinib resulted in the identification of several subunits of the SWI/SNF complex (a nucleosome remodeling complex) including PBRM1, ARID2, and ARID1A as a role player in cell survival and drug resistance. Furthermore, loss of PBRM1 attenuated the effect of gefitinib and prolonged survival of the cells treated with erlotinib [27]. In another study, deletion of insulin-like growth factor 1 receptor (IGF1R) in HCC827 lung cancer cells selectively induced erlotinib resistance via MET amplification as compared to the wildtype resistant cells [28].

KEAP1 is mutated in 20% of lung adenocarcinoma tumors and is involved in the oxidative stress response. KEAP1 targets NFE2L2/NRF2 for ubiquitination and proteasomal degradation. A genome wide CRISPR/Cas9 drug resistance screening study revealed that loss of KEAP1 confers multiple drug resistance to different lung cancer cells, i.e. H1299, CALU1 and HCC364, through elevated NRF2 activity [12]. In addition, CRISPR-mediated loss of function of Keap1 promoted lung cancer in a Kras-driven mouse models and caused glutaminolysis dependent lung tumors which can be inhibited by anti-glutaminase drugs [61]. As loss of KEAP1 is involved in drug resistance, restoring its expression in KEAP1 mutated tumors may resensitize tumor cells to the treatment. However, further in vivo studies are needed to investigate the effect of NRF2 depletion on KEAP1 mutated tumors.

Wright et al. (2017) showed that polo-like kinase 1 (PLK1) can be targeted by AZD1775, a WEE1 tyrosine kinase inhibitor. They showed that CRISPR-mediated knockout of WEE1 sensitized lung cancer cells (H322) to AZD1775 to a similar level as BI-2536, a potent PLK1 inhibitor [62]. Aurora-B is a protein kinase which is involved in the regulation of cell division. A recent study investigated the role of this protein in NSCLC resistance to chemotherapy. It was shown that ablation of Aurora-B resensitized NSCLC cancer cells to cisplatin [25]. Remodeling and spacing factor 1 (RSF1) is a protein involved in chromatin remodeling and transcriptional regulation. Disruption of RSF1 in A549 and H1299 lung cancer cells promoted apoptosis, reduced cell proliferation and increased sensitivity to paclitaxel, a chemotherapeutic compound [26]. Taken together, it seems that the origin of the tumor cells, their genetic makeup and whether the tumor cells rely on a specific molecule for proliferation play important roles in the selection of right targets for lung cancer treatment.

CRISPR/Cas9 has been exploited in several studies to investigate potential resistance mechanisms to conventional therapies including chemotherapy and radiotherapy. Inducing specific mutations in MUC16, a member of the mucin family glycoproteins, resulted in resistance to chemotherapy (cisplatin) and conferred more aggressive characteristics to the cells [29]. In another study, disruption of CDKN1A (P21) resulted in resistance of lung cancer cells to radiation therapy suggesting its crucial role in lung cancer treatment response [30]. Expression analysis of more than 12,000 genes revealed SLFN11 as a significant potential determinant of poly-(ADP)-ribose polymerase (PARP) inhibitor activity in small cell lung cancer. In addition, CRISPR-mediated deletion of SLFN11 caused resistance to talazoparib, a PARP inhibitor, in vitro. Moreover, the response to talazoparib was strongly depended on the expression level of SLFN11 [31]. Overall, these findings indicate how resistance mechanisms can be defined by different molecules in tumor cells. Therefore, depending on the effect of the protein on the treatment outcomes, restoration or deletion of that specific protein could be beneficial for the patients. In addition, sgRNAs targeting certain genes could concomitantly be used with the currently available drugs to improve clinical outcomes. However, as lung tumors are very heterogeneous [7, 63], outgrowth of a minor resistant clone might occur.

Breast cancer

Breast cancer is the most common type of cancer and the main cause of cancer-related death in women worldwide [64]. It is classified into four main molecular subtypes based on the expression of different markers, i.e. progesterone receptor (PR), estrogen receptor (ER), ERBB2 (HER2), p53 and Ki-67 [65]. Drug resistance occurs in almost 30% of the cases with ER-positive luminal subtypes which are the most common type of breast cancer. Thus, identification of new strategies that can fundamentally influence drug resistance is critical. This can be done either by direct depletion of driver genes or resensitizing tumor cells to the treatment by suppression of drug resistance-related genes that can synergize with specific drugs.

Pharmacogenetics studies have shown that germline genetic variants can have a great impact on the metabolism of specific drugs. In other word, the response to treatment can be influenced by the inherited genetic variants. A single nucleotide polymorphisms (SNP) (rs9940645) in ZNF423 gene predicts the response to the selective estrogen receptor modulators (SERMs) in breast cancer patients. ZR75–1 cells, which are positive for ERα and contain the rs9940645 variant, were CRISPR-engineered to generate wildtype cells by Qin et al. (2017). The authors showed that the cells containing the variant are more sensitive to raloxifene, olaparib and cisplatin [32]. Beside the germline variants, somatic mutations in the frequently mutated genes such as ESR1 (ERα) in breast tumor cells can also affect the response to treatment. For instance, genetically modified T47D and MCF7 breast cancer cells containing mutations in ESR1 (Y537S and D538G mutations) showed estrogen-independent growth and resistance to fulvestrant, raloxifene and 4-Hydroxytamoxifen (4-OHT) in vitro [36–38]. Further in vivo studies are needed to investigate the role of different genetic variants on the response of tumor cells to specific drugs. Hence, inducing specific nucleotide changes in the breast cancer tumor cells may improve treatment outcomes in the near future.

CRISPR/Cas9 genome editing tools have been used in different studies to identify whether clinically available drugs for other cancer types can also be effective in breast cancer. Weyburne and colleagues genetically ablated proteasome β2 resulting in the sensitization of triple-negative breast cancer (TNBC) cells to the proteasome inhibitors bortezomib and carfilzomib, drugs commonly used for the treatment of multiple myeloma, in vitro and in vivo [33]. Another study revealed strong synergy of E-cadherin inhibition with clinically available ROS1 inhibitors, foretinib and crizotinib, in breast cancer cells both and in vivo [34]. These sorts of studies can save considerable amount of time for the development of new drugs in different types of cancer.

Non-coding RNAs play important roles in the cells and their dysregulation in various types of cancer including breast tumors have been reported previously. Knockout of long non-coding RNA RoR (linc-RoR) in MCF7 breast cancer cells promoted the MAPK/ERK signaling pathway indicating its oncogenic role in breast cancer. Furthermore, depletion of linc-RoR sensitized breast cancer cells to tamoxifen, a drug commonly used for the treatment of breast cancer [35]. These data suggest that suppression of non-coding RNAs could be an effective approach to improve clinical outcomes.

CRISPR/Cas9 technology, either as a single gene manipulation tool or as a genome wide screening method, has been extensively used to understand resistance mechanisms in breast cancer. This has led to the identification of several molecules with a role in drug resistance. Genetic ablation of ATPE1, a base excision repair enzyme, in TNBC cells (HCC1937) led to resistance to olaparib [39]. Disruption of WAVE3, a member of the WASP/WAVE actin-cytoskeleton remodeling family, substantially attenuated cancer stem cell (CSC) populations in TNBC cell lines through suppressing CSC self-renewal capacity and transcriptional regulation of CSC-specific genes. These results support the critical role of WAVE protein in TNBC chemoresistance [66]. CRISPR-based knockout of MAP3K1 in mutant PIK3CA breast cancer cell lines resulted in an increased proliferation rate and decreased sensitivity to an AKT inhibitor (AZD5363) through enhanced phosphorylation of AKT in vitro as well as in vivo [40]. In addition, disruption of FUT8 significantly reduced cell invasion and metastatic abilities in vivo by suppressing EMT which is a well-known drug resistance mechanism [67].

A genome-wide CRISPR screening revealed that single deletion of BAK or double deletion of BAK/BOX confers resistance of the cells against S63845, a MCL-1 inhibitor [41]. Thu and colleagues (2018) used the same method and revealed that genetic ablation of any components of the anaphase-promoting complex/cyclosome (APC/C), i.e. MAD2L1BP, ANAPC4 and ANAPC13 can confer resistance to CFI-402257, a TTK protein kinase inhibitor [13]. Another genome wide CRISPR/Cas9 screening study revealed that ablation of any CST complex member, i.e. Ctc1, Stn1 or Ten1, confers resistance to PARP inhibitors in BRCA1 deficient breast cancer cells in vivo [42]. In summary, CRISPR/Cas9 helped to identify several novel resistance mechanisms to a wide range of drugs including PARP inhibitors. It can also significantly improve the drug response to SERMs in breast cancer. These findings may push pharmaceutical companies to generate new compounds which can overcome drug resistance.

Liver cancer

Liver cancer is the second cause of cancer-related death in the world. It has limited treatment options and the majority of the patients experience tumor recurrence [68]. Therefore, a better understanding of drug resistance mechanisms and identification of new treatment options in this cancer seems vital.

Sorafenib is a multikinase inhibitor which is commonly used for treatment of liver cancer patients. Recently, several research groups have utilized CRISPR-based methods to understand the potential resistance mechanisms and increase the efficacy of sorafenib in hepatocellular carcinoma (HCC). Suppression of cyclin dependent kinase 5 (CDK5) combined with sorafenib resulted in a reduced cell proliferation and migration as well as suppression of HCC progression both in vitro and in vivo by interfering with intracellular trafficking mechanisms [43]. It has been shown that knockout of the fibroblast growth factor receptor (FGFR4) using CRISPR technology sensitizes HCC cancer cells to sorafenib [44]. A CRISPR-based screening study, with focus on kinases, revealed that disruption of MAPK1 (ERK2) has a synergistic effect with sorafenib alone or a combination of sorafenib and selumetinib in HCC cell line (HuH7) by suppression of cell proliferation [45].

A genome wide CRISPR screening study revealed that loss of SGOL1, a protein involved in mitosis, is the main cause of resistance to sorafenib in HuH7 and SMMC-7721 HCC cells. Further in vivo studies showed decreased sorafenib cytotoxicity and increased tumor size supporting contribution of SGOL1 to sorafenib resistance [46]. These findings suggest that SGOL1 might be a suitable therapeutic target for HCC patients and individuals with SGOL1 overexpression might be appropriate candidates to be treated with sorafenib. In addition, serial sampling during treatment and assessment of SGOL1 expression levels might be used as a putative resistance biomarker in HCC patients which demands further investigation. Together, these data show that clinical outcomes in liver cancer patients may be improved by suppression of specific proteins such as CDK5, FGFR4 and MAPK1, especially when it is combined with drugs like sorafenib.

Gliomas

Malignant glioma is the most common type of brain primary tumor and is divided into different subtypes. Glioblastoma multiforme (GBM) is responsible for approximately 70% of all gliomas and it is the most aggressive form of brain cancer with a poor prognosis. GBM is highly heterogeneous which may promote the chance of drug resistance [69, 70]. Thus, CRISPR/Cas9 would be a valuable method to identify genes involved in glioma pathogenesis and drug resistance.

Several studies have investigated the role of different proteins such as ATRX, NOTCH1, PCM1 and GLI1 in the response to various types of treatment such as chemo- and radiation therapy in gliomas using CRISPR/Cas9 system. Deletion of ATRX increased the sensitivity of the tumor cells both in vitro and in vivo to temozolomide, a commonly used chemotherapeutic agent [47]. Overexpression of NOTCH1, which is a transmembrane protein, is associated with poorer overall survival in GBM patients. NOTCH1 CRISPR-mediated knockout in U87 and U251 glioblastoma cells showed a significant synergistic effect with radiation therapy [48]. Depletion of PCM1, a component of centriolar satellites, resulted in the inhibition of glioblastoma cell proliferation. In addition, PCM1 ablation promoted apoptosis and increased the sensitivity to temozolomide in patient-derived GBM cell lines [49]. Knockout of GLI1, also known as glioma-associated oncogene, in combination with penfluridol (an antipsychotic drug) showed increased apoptosis in primary glioblastoma cells [50]. These findings indicate that combination of genetic modifications as a supplementary treatment with conventional therapies may increase the efficacy of the treatment in glioma patients.

Discussion and conclusion

Based on the data presented here, several drug response-related genes have been identified using CRISPR/Cas9 genome editing system. Reactivation or suppression of these genes/proteins may resensitize tumor cells to treatment and improve the drug response.

It has been shown that deletion of genes such as KEAP1 and CDKN1A results in drug resistance [12, 30]. Thus, maybe restoration of these proteins specifically in the tumor cells can resensitize them to the treatment. This can also be applied conversely. For instance, CRISPR-mediated deletion of a specific gene such as MAPK1 and CDK5 in cancer cells leads to suppression of the tumor cell growth and sensitization of the cells to treatment [43, 45]. Inducing loss of function mutations in these genes in the tumor cells may inhibit tumor growth and have a synergistic effect with a specific drug. However, how we can deliver the Cas9/sgRNAs only to the tumor cells without hurting normal cells still remains challenging. Therefore, one of the core topics of delivery is minimizing off-target effects by strategies that can specifically target tumor cells, such as using specific promoters and highly expressed surface receptors on cancer cells.

In addition, certain genetic variants can influence treatment outcomes. Thus, another strategy which might be useful is to induce specific nucleotide changes in certain genes in cancer cells to make them more vulnerable to treatment. For example, inducing specific genetic changes in ESR1 and ZNF423 in breast cancer cells followed by fulvestrant, raloxifene or olaparib treatment can significantly affect the tumor response [32, 36–38] which may be an option to improve the clinical outcomes in patients. Moreover, emerging new mutations in EGFR (p.T790 M) and ALK-EML4 (p.G1269A) can lead to acquired drug resistance in NSCLC patients [71–73]. Replacing these drug resistance causing mutations with the responsive variants can resensitize tumor cells to the same treatment.

Tumor heterogeneity is another challenge in using CRISPR/Cas9 technology as a therapeutic tool in cancer patients. Tumors usually contain one or more dominant clones and several minor subclones [7, 74, 75]. When patients are treated with a specific drug, tumor cell populations go through selection pressure. Thus, the dominant clones which are sensitive to the treatment are killed leading to the outgrowth of one or more resistant subclones. This can also happen if the tumor cells are treated with specific Cas9/sgRNAs targeting a certain gene and eventually resistance arises. However, treatment of the tumor cells with multiple Cas9/sgRNAs, targeting a number of resistance-related genes, might be an option to tackle this problem.

Despite all opportunities provided by CRISPR/Cas9 system in cancer therapy, there are still some social and ethical concerns that have to be addressed. Safety is the primary issue for the application of CRISPR-based technologies due to possible off-target effects as well as continuous activity of Cas9. In addition, lack of an efficient in vivo delivery method with high specificity is another issue that has to be solved. Therefore, safety of CRISPR/Cas9 system must be confirmed and validated before it is clinically available. Justice and equity is another concern; whether CRISPR-based treatments are available and affordable for everyone. Meanwhile, genome editing research involving embryos and clinical germline genome editing are other ethical issues related to CRISPR/Cas9 technologies that need to be taken into account.

In conclusion, although delivery of the CRISPR/Cas9 and off-target effects remains a challenge, CRISPR-based methods are promising and useful tools for cancer treatment, identification of resistance mechanisms and overcoming drug resistance.

Compliance with ethical standards

Competing interests

The authors declare that they have no competing interests.