Background
Cervical cancer, frequently leading to death, is one of the most common gynecological malignancies among women globally [
1]. Fortunately, the incidence of advanced cervical cancer and cervical-cancer mortality has been dramatically reduced through screening for human papillomavirus (HPV) instead of a single conventional cytological test or visual inspection [
2]. Although efficient diagnosis during precancerous and early stages of cervical cancer is pivotal for the effective cure of cervical cancer [
3‐
5], the effectiveness of cervical cancer treatments has not been improved significantly over the past decades [
6‐
8]. The overall cervical-cancer incidence and mortality increased steadily from 1991 to 2013, which has been predicted to continue in the future [
9]. Therefore, it is very important to identify molecular markers and therapeutic targets to improve the effectiveness of cervical cancer treatment.
Alternative splicing is one of the key molecular mechanism contributing to the biological functional complexity of the human genome [
10]. The alternative processing of primary RNA transcripts of individual mammalian genes produces various mRNA and protein isoforms which have related, distinct or even opposing functions [
11‐
13]; These include both widespread homeostatic activities and cell-type-specific functions [
14]. It was reported that transcripts from ~ 95% of multiexon genes are alternatively spliced. In major human tissues, there are about 100,000 intermediate- to high-abundance alternative splicing events [
15]. In the past few years, emerging data suggest that the cancer progression and metastasis are specifically associated with a plethora of mRNA isoforms [
16‐
21]. Noncanonical and cancer-specific mRNA transcripts produced by the aberrant splicing can lead to loss of function of tumor suppressors or activator of oncogenes and cancer pathways [
21]. These cancer-specific isoforms may represent attractive cancer therapeutic targets. Recently, it was reported that alternative splicing regulates cervical cancer oncogenesis via miL1RAP-NF-κB-CD47 axis, indicative of an attractive therapeutic target for treatment of cervical cancer [
22].
The center of tumorigenesis is the activation of various signal transduction pathways, and key kinases in these pathways represent a large class of effective therapeutic targets [
23‐
26]. For example, a wide range of epithelial cancers have aberrant activation of EGFR signaling by overexpression or mutation, and targeting EGFR signaling network thus represents a rational for novel treatment approaches [
27‐
29]. Overexpression of components of cAMP/CREB pathway is related to a subset of human carcinomas, indicating a potential therapeutic strategies for this group of tumors [
25]. The activation of the PI3K/Akt pathway is associated with incomplete metabolic response in cervical cancer and therefore represents a therapeutic target in cervical cancer [
26].
Signaling adaptors connect the activated cell-surface receptors with down-stream effectors (kinases) in the signaling pathways, via their domains and motifs mediating molecular interactions [
30‐
33]. These adaptors are increasingly recognized as coordinators of the dynamic activation of signaling pathways in response to both external and intrinsic stimuli and/or changes [
34‐
38]. The cytoplasmic adaptor
CRKL (v-crk avian sarcoma virus CT10 oncogene homolog-like) is a CRK like proto-oncogene, which belongs to Crk family adaptors and encodes a SH2 and SH3 (src homology) domain-containing adaptor protein [
32]. This adaptor can form multi-protein complexes by selective interaction with a number of adaptor proteins, including paxillin (substrate for several normal and oncogenic tyrosine kinases), p130CAS (130 kDa Crk associated kinase substrate) and p120 c-cbl (maintenance of T-cell non-responsiveness), as well as insulin receptor substrate proteins (IRS), STAT5 and PI3K (phosphatidylinositol kinases) [
39‐
53]. These interactions rely on the specific recognition and binding via the SH2 and SH3 domains [
33,
54]. Many oncogenes, receptors, receptor ligands and other stimuli are proposed to induce Crk/CRKL complex formation, which links Crk/CRKL with a number of development and tumorigenesis-related signaling pathways [
33]. For example, the FGF and VEGF signaling pathways regulated by Crk function in cell proliferation, migration, and survival [
55‐
57]. CRKL modulates EGFR inhibitor resistance in small cell lung cancers and is essential in FGF8 signaling in a mouse disease model [
58,
59].
CRKL is tightly linked to leukemia via its binding partners BCR-ABL and TEL-ABL [
33,
60]. BCR-ABL is well known to phosphorylate CRKL which plays a role in fibroblast transformation by binding to other adaptor proteins [
61‐
63]. The first SH3 domain of CRKL and a proline-rich region in the C-terminal tail of the ABL kinase mediated the direct interaction of CRKL and BCR-ABL.
CRKL is overexpressed in various types of human cancer and can induce cancer cell proliferation and invasion [
64‐
67]. In addition, CRKL was demonstrated to be an oncoprotein contributing to malignant cell growth and chemoresistance and promoting cancer cell invasion through a Src-dependent pathway [
68].
Key kinases and adaptors in signaling transduction pathways are known to regulate gene transcription [
69]. Interestingly, it is emerging that kinases in signal transduction pathways can also modulate the phosphorylation state of SR proteins which are key regulators of alternative splicing [
70‐
74]. Regulation of alternative splicing by key kinases and adaptor proteins might represent a general role in coordinating the cell responses to external and internal signals. Recently, a number of such proteins were reported to be associated with mRNAs in living cells, including CRKL, indicating a previously unknown regulatory mechanisms of these signaling proteins [
75]. Nevertheless, it remains unclear whether signaling adaptors such as CRKL could regulate alternative splicing.
In this study, we analyzed the expression level of
CRKL in 305 cervical cancer tissue samples available in TCGA database, showing a significant increased expression in Stage I cancer samples (Stage I, the carcinoma is strictly confined to the cervix without invasion). We then selected 40 cancer samples with 20 showing high
CRKL expression and 20 showing low, which were analyzed for the potential impact of CRKL on alternative splicing regulation of cancer transcriptome. We further explored the potential function of CRKL in regulating alternative splicing in HeLa cells using shRNA to knock-down
CRKL expression. The results confirmed the role of CRKL in promoting cell proliferation in HeLa cell published recently [
68], and also showed that CRKL could regulate the alternative splicing of pre-mRNAs from hundreds of genes. We further showed that 94% of CRKL-regulated alternative splicing events detected in HeLa cells could be validated by RT-qPCR approach. Moreover, significantly more CRKL-regulated alternative splicing events detected in HeLa cells were positively than those negatively correlated with the
CRKL expression level in cervical cancers. These results together support the conclusion that CRKL adaptor protein extensively regulates alternative splicing of many genes which are important in development and tumorigenesis, which expands the functional importance of signaling adaptors in coordinating the dynamic activation of signaling pathways at the alternative splicing level upon cellular responses to various stimuli.
Methods
Cell culture and transfections
Human cervical cancer cell lines, HeLa (CCTCC@GDC0009) were obtained from CCTCC (China Center for Type Culture Collection, Wuhan, Hubei, China) in 2017. The HeLa cell line has been authenticated with STR analysis by Cell Bank, Type Culture Collection, Chinese Academy of Sciences (CBTCCCAS), and tested for the free of mycoplasma contamination by the provider. The genomic DNA were purified with Purelink@ Genomic DNA Kits in the Cell Bank. The DNA sample was analyzed in Beijing Microread Genetics Co., Ltd. The sample was amplified with Goldeneye™20A STR Complex Amplification Kit. The profiles STR loci and Amelogenin gene characterized on ABI 3100 Type Genetic Analysis Instrument.
HeLa cells were cultured with 5% CO2 at 37 °C in DMEM (Dulbecco’s modified Eagle’s medium), which were with 10% FBS (fetal bovine serum), 100 U/mL penicillin and 100 μg/mL streptomycin. To silencing the expression of CRKL in HeLa cell, we constructed a shRNA-containing plasmid using the vector pGFP-B-RS. The shRNA sense strand against CRKL mRNA sequence was GACCTGTCTTTGCGAAAGCAA. According to the manufacturer’s protocol, shRNA was transfected into HeLa cells using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA), which were harvested after 48 h for following RT-qPCR analysis.
Assessment of the knockdown of CRKL by shRNA
We used housekeeping gene
GAPDH (glyceraldehyde-3-phosphate dehydrogenase) as a control gene for assessing the effects of shRNA targeting CRKL. cDNA synthesis was conducted by standard procedures for following real-time quantification PCR, which was performed on the HieffTM qPCR SYBR® Green Master Mix (Low Rox Plus) (YEASEN, Shanghai, China) to evaluate the knockdown of
CRKL by shRNA. The information of primers used for RT-qPCR is presented in Additional file
1. The concentration of transcript was then compared with
GAPDH mRNA level using 2
- ΔΔCT method [
76] to measure the transcript level of
CRKL.
MTT assay
The MTT assay was used to measure cell proliferation. We seeded indicated HeLa cells (1 × 104) in 96-well culture plates with 200 μl of cell growth medium. The vector was transfected into HeLa cells using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) after cells reached at 70% confluence according to the manufacturer’s protocol. Then, the cells were incubated at 37 °C for 48 h. Subsequently, each well of culture plates was added with 25 μl of MTT solution (5 mg/mL), following another 4 h incubation. The supernatant was removed from each well after centrifugation. DMSO was used to dissolved the colored formazan crystals produced from MTT in each well (0.15 mL/well), and the optical density (OD) values were measured at 490 nm.
RNA extraction and high-throughput sequencing
Total RNA was extracted by the TRIZOL (Ambion) and was further purified with two phenol-chloroform treatments. To remove DNA, the purified RNA was then treated with RQ1 DNase (RNase free) (Promega, Madison, WI, USA) and its quality and quantity were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad, USA). The integrity of RNA was then verified by 1.5% agarose gel electrophoresis.
We used 10 μg of the total RNA for each sample to preparing directional RNA-seq library. Before that, the polyadenylated mRNAs were concentrated with oligo (dT)-conjugated magnetic beads (Invitrogen, Carlsbad, CA, USA). Then, the concentrated mRNAs were iron fragmented at 95 °C, end repaired and 5′ adaptor ligated with 5′ adaptor. Then, reverse transcription (RT) was performed with RT primer harboring 3′ adaptor sequence and randomized hexamer. The purified cDNAs were amplified and stored at − 80 °C until they were used for sequencing [
77]. According to the manufacturer’s instructions, the libraries were prepared for high-throughput sequencing. Illumina HiSeq4000 system was used to collect data from 151-bp pair-end sequencing (ABlife Inc., Wuhan, China).
RNA-Seq raw data clean and alignment
Raw sequencing reads containing more than 2-N bases were first discarded. Then, the raw reads were trimmed off adaptors and low-quality bases using FASTX-Toolkit (Version 0.0.13). Besides, the short reads less than 16 nt were dropped to gain clean reads, which were subsequently aligned to the GRch38 genome by tophat2 [
78] with 4 mismatches. Uniquely mapped reads were ultimately used to calculate reads number and FPKM (paired-end fragments per kilobase of exon per million fragments mapped) value for each gene.
Differentially expressed genes (DEGs) analysis
The expression level of genes was evaluated using FPKM. We applied the software edgeR [
79], which is specifically used to analyze the differential expression of genes, to evaluate the FPKM value and screen out the DEGs (differentially expressed genes) using RNA-Seq data. We analyzed the results based on the fold change (fold change ≥2 or ≤ 0.5) and false discovery rate (FDR < 0.05) to determine whether a gene was differentially expressed.
Using KOBAS 2.0 server [
80], Gene Ontology (GO) analyses and enriched KEGG pathway were identified to predict functions of genes and calculate the functional category distribution frequency. The enrichment of each pathway (corrected
p-value< 0.05) was defined using hypergeometric test and Benjamini-Hochberg FDR controlling procedure.
Alternative splicing analysis
The ABLas pipeline as described previously [
81,
82] was used to define and quantify the ASEs (alternative splicing events) and RASEs (regulated alternative splicing events) between the samples. In brief, detection of seven types of canonical ASEs in each sample was based on the splice junction reads. These ASEs were exon skipping (ES), cassette exon (cassetteExon, CE), alternative 5′splice site (A5SS), alternative 3′splice site (A3SS), mutual exclusive exon skipping (MXE), the MXE combined with alternative polyadenylation site (3pMXE), and with alternative 5′ promoter (5pMXE).
After that, the significant p-value was calculated using fisher’s exact test, with the model reads of samples and alternative reads as input data, respectively. We calculated the changed ratio of alternatively spliced reads and constitutively spliced reads between compared samples, which was defined as the RASE ratio. The RASE ratio > 0.2 and p-value < 0.05 were set as the threshold for RASEs detection.
Reverse transcription qPCR validation of alternative splicing events
To elucidate the validity of ASEs in HeLa cells, quantitative reverse-transcription polymerase chain reaction (RT-qPCR) was performed in this study for some selected RASEs, and normalized with the reference gene GAPDH. The primers for detecting the pre-mRNA splicing are shown in Additional file
1. To quantitatively analyzing the two different splicing isoforms of a specific ASE using a qPCR approach, we designed two pairs of primers to specifically amplify each of these two isoforms after the initial synthesis of the first strand cDNA using random primers. To achieve this specificity, we designed a primer pairing the splice junction of the constitutive exon and alternative exon (Additional file
11). The RNA samples used for RT-qPCR were same to that for RNA-seq. The PCR conditions are consisted of denaturing at 95 °C for 10 min, 40 cycles of denaturing at 95 °C for 15 s, annealing and extension at 60 °C for 1 min. PCR amplifications were respectively performed in triplicate for control and CRKL-KD samples.
Western blotting analysis
Protein samples were loaded into 10% or 12% SDS-PAGE gels depending on molecular weight and transferred onto 0.45 mm PVDF membranes. The PVDF membranes were then blocked with 5% skim milk (in a buffer containing 10 mM Tris, pH 8.0, 150 mM NaCl, 0.05% Tween 20) for an hour, incubated overnight with primary antibody at 4 °C and then incubated with horseradish peroxidase-conjugated secondary antibody for 1 h at room temperature. Then, membranes were visualized through chemiluminescence. We also have quantitated some of the WB bands by the software Image J. Antibodies: The following antibodies were purchased from commercial sources including anti-AKT2 (Polyclonal Antibody, AB clonal; A0336), anti-phospho-AKT2 (Polyclonal Antibody, Affinity MT; AF3264); anti-CRKL (Polyclonal Antibody, AB clonal; A0511); anti-GAPDH (Polyclonal Antibody, AB clonal; AC001).
Downloading RNA-seq data of cervical cancer samples
The RNA-seq data of cervical cancer samples were downloaded from TCGA database to analyze the expression of CRKL and regulation of alternative splicing in cervical cancer.
Discussion
CRKL is a signaling adaptor protein containing SH2 and SH3 domains, which can connect the activated cell-surface receptors with down-stream effectors (kinases) in signaling pathways via mediating molecular interactions [
33,
54]. Many oncogenes, receptors, receptor ligands and other stimuli are proposed to link Crk/CRKL with a number of development and tumorigenesis-related signaling pathways, such as FGF, VEGF and EGFR signaling pathways [
55‐
59]. CRKL is overexpressed in a number of types of human malignant tumors, including cervical cancer, lung cancer, breast cancer, gastric cancer, and pancreatic carcinoma. It plays crucial roles in tumorigenesis and cancer progression [
65‐
68,
87]. Regulation of gene transcription and alternative splicing by key kinases and adaptors protein in signaling transduction pathways has been extensively studied [
69‐
74]. A number of such proteins were reported recently to be associated with mRNAs in living cell, including CRKL, indicating a previously unknown regulatory mechanism of these signaling proteins [
75]. Nevertheless, it remains unclear whether signaling adaptors such as CRKL could regulate alternative splicing. In the present study, we performed experiments to identify what role CRKL plays in cervical carcinoma and explore whether CRKL could regulate alternative splicing.
We analyzed the expression level of
CRKL in 305 cervical cancer tissue samples and 3 normal samples by referring to the RNA-seq data available from TCGA database and found a significant increased expression in cervical tumor, especially in Stage I cancer samples (Fig.
1). What cause that
CRKL has highest expression in Stage I tumor need to be further explored. We then selected 40 cancer samples with 20 showing high
CRKL expression and 20 showing low, which were analyzed for the potential impact of CRKL on alternative splicing regulation of cancer transcriptome. Alternative splicing of pre-mRNAs from 461 genes, which were enriched in DNA repair, mitotic cell cycle and a number of signaling pathways, were shown to be correlated with the CRKL expression level.
In order to explore whether CRKL is directly involved in regulating alternative splicing in HeLa cells, we established
CRKL-knockdown (KD) cells by transient transfection of
CRKL-shRNA and performed cell proliferation experiment. A significant decrease in cell proliferation level in
CRKL-KD HeLa cells confirmed the role of CRKL in promoting cell proliferation in HeLa cell published recently [
68] (Fig.
3). In addition, RNA-seq analysis on
CRKL-KD and control HeLa cells showed that CRKL could extensively regulate alternative splicing of pre-mRNA from hundreds of genes, which enriched in protein autophosphorylation, embryonic development, DNA repair, mitotic cell cycle, and cell proliferation (Fig.
4). These functional pathways that CRKL-regulated alternative splicing events enriched in are similar as those in cervical cancer samples (Fig.
2). This indicated that the effect of CRKL on alternative splicing might be significantly related to tumorigenesis in cervical cancer. More importantly, we showed that 34 (87%) of CRKL-regulated alternative splicing events detected in HeLa cells could be validated by RT-qPCR approach. SR proteins are well known splicing factors extensively regulate alternative splicing [
74,
84]. We and another group have demonstrated that CRKL expression level regulates the phosphorylation of an SR protein AKT (Additional file
10) [
68]. These results together suggested that CRKL is directly involved in alternative splicing regulation, and CRKL might achieve this regulation via its positive regulation of AKT2 activity.
Furthermore, we reported that more than a half of the qPCR-validated CRKL-regulated ASEs detected in HeLa cells were also correlated with the
CRKL expression level in cervical cancers (Fig.
7 and Additional file
12). We noticed that the expression difference between the CRKL-high and CRKL-low samples was relatively small, this small difference could at least partially explain the relative low correlation of the RASEs between HeLa cells and cervical tumor samples.
Here we noted that validated alternative splicing events regulated by CRKL mostly located in genes encoding kinases or adaptor proteins in various signaling pathways or transcription regulation factor, including
RAC3 (Rac Family Small GTPase 3),
PTK2B (Protein Tyrosine Kinase 2 Beta),
MELK (Maternal Embryonic Leucine Zipper Kinase),
ATM (ATM Serine/Threonine Kinase),
TSC2 (Tuberous Sclerosis 2, a tumor suppressor),
EPS15 (Epidermal Growth Factor Receptor Pathway Substrate 15),
RACGAP1 (Rac GTPase Activating Protein 1),
APC (WNT Signaling Pathway Regulator),
TRAIP (TRAF Interacting Protein),
SIN3A (SIN3 Transcription Regulator Family Member A),
CHEK2 (checkpoint kinase),
EIF4E2 (Eukaryotic Translation Initiation Factor 4E Family Member 2) and
UBE2A (Ubiquitin Conjugating Enzyme E2 A) (Fig.
6 and Additional file
11). Meanwhile, these genes generally involved in tumorigenesis functions including cell proliferation, migration and apoptosis.
RAC3 encodes a GTPase which is a member of the RAS proto-oncogene superfamily of small GTP-binding proteins. Studies have reported that its related pathways, ERK and RAC signaling, are key regulators in leukocyte and cancer cell migration [
88] and
RAC3 was further proved to regulate cell proliferation, differentiation and migration in several cancers [
89‐
91]. More interestingly,
RAC1 as the paralog of
RAC3 was reported to play an important role in cervical cancer progression [
92].
CRKL depletion significantly alters the retention of variable introns of
RAC3 (Fig.
6), which was changed in the opposite in clinical samples (Additional file
12). This underlines that the functional mechanism of RAC3 in cervical cancer sample maybe need to be further investigated. The
CRKL-dependent alternative splicing of
APC and
SCRIB resulted from the use of a cryptic donor site in respective intron and generate a changed isoform in
CRKL-knockdown cells (Additional file
11). They both function in tumor suppression pathways involved in cell proliferation, migration and apoptosis [
93,
94], which could be affected by their altered isoforms.
Several CRKL-regulated alternative splicing events involved in genes encoding protein kinase, such as
PTK2B,
MELK,
TSC2 and
ATM, which play roles in different signaling pathways or cellular processes. The protein tyrosine kinase PTK2B involved in Ca
2+-induced regulation of ion channel and MAP kinase activation [
61,
95], which has underlying relationship with cervical cancer [
96].
MELK encodes a protein Serine/Threonine kinase which plays a role in cell proliferation and carcinogenesis [
97,
98] and TSC2 as a protein phosphatase regulating mTOR and downstream signaling [
99].
CRKL depletion significantly alters the retention of variable introns of
PTK2B and
TSC2 (Additional file
11), and the inclusion of variable exons of
MELK (Fig.
6), and these tumorigenesis involving genes might then affect development or progression of cervical carcinoma. ATM is emerging as a serine/threonine protein kinase, which belongs to the PI3K/PI4K family and acts as a DNA damage sensor activating checkpoint signaling upon double strand breaks (DBSs) [
100]. This is an important cell cycle checkpoint kinase regulating a wide variety of downstream proteins [
101,
102], including tumor suppressor proteins p53 and BRCA1, checkpoint kinase CHK2, checkpoint proteins RAD17 and RAD9, oncogenic protein MDM2, and DNA repair protein NBS1. By phosphorylating these substrates, ATM responds swiftly and vigorously to DBSs and affects specific processes in which these proteins are involved. The AS regulation of
ATM might affect its response functions to DBSs in the process of carcinogenesis (Fig.
6, and Additional file
12).
The alternative spliced
BCL2L1 can modulate cell apoptosis to escape from cell death in cancer, which is critical for tumorigenesis [
103].
CRKL-depletion regulates alternative splicing to produce shorter isoforms of BCL2L1 which was reported to function as apoptosis activator (Additional file
11). This result indicates that CRKL could contribute to tumorigenesis via regulating the alternative splicing of
BCL2L1, an inhibitor of cell death. In addition, CRKL regulated alternative splicing of genes encoding proteins function in various cellular process. For example,
SIN3A as a transcriptional regulator,
UHRF1 as epigenetic regulatory factors,
EPS15 as epidermal Growth Factor Receptor Pathway Substrate,
RACGAP1 as a GTPase-activating protein (GAP),
CDC16 as a component of the anaphase promoting complex/cyclosome (APC/C) and
TUBG2 as a tubulin were all proved to be targeted (Additional file
11), which altogether influence the way CRKL regulates cervical cancer.