key: cord-0020257-it3wfb53
authors: Chen, Miaomiao; Zhang, Chunhua; Hu, Zhiqing; Li, Zhuo; Li, Menglin; Wu, Lingqian; Zhou, Miaojin; Liang, Desheng
title: CRISPR/Cas12a-Based Ultrasensitive and Rapid Detection of JAK2 V617F Somatic Mutation in Myeloproliferative Neoplasms
date: 2021-07-24
journal: Biosensors (Basel)
DOI: 10.3390/bios11080247
sha: 82ab8ff63b18df4d5320f9ce4e273cfbd034edfa
doc_id: 20257
cord_uid: it3wfb53

The JAK2 V617F mutation is a major diagnostic, therapeutic, and monitoring molecular target of Philadelphia-negative myeloproliferative neoplasms (MPNs). To date, numerous methods of detecting the JAK2 V617F mutation have been reported, but there is no gold-standard diagnostic method for clinical applications. Here, we developed and validated an efficient Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR associated protein 12a (Cas12a)-based assay to detect the JAK2 V617F mutation. Our results showed that the sensitivity of the JAK2 V617F/Cas12a fluorescence detection system was as high as 0.01%, and the JAK2 V617F/Cas12a lateral flow strip assay could unambiguously detect as low as 0.5% of the JAK2 V617F mutation, which was much higher than the sensitivity required for clinical application. The minimum detectable concentration of genomic DNA achieved was 0.01 ng/μL (~5 aM, ~3 copies/μL). In addition, the whole process only took about 1.5 h, and the cost of an individual test was much lower than that of the current assays. Thus, our methods can be applied to detect the JAK2 V617F mutation, and they are highly sensitive, rapid, cost-effective, and convenient.

Philadelphia-negative myeloproliferative neoplasms (MPNs), including polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF), are a group of heterogeneous chronic diseases characterized by the clonal expansion of one or more myeloid lineages [1, 2] . It was reported that the crude annual incidence rate of classic MPNs ranged from 1.15 to 4.99 per 100,000, with a prevalence rate of 93.43 per 100,000 [3] . The JAK2 V617F mutation is the most common molecular event in the classic MPNs and presents in more than 95% of patients with PV and 50-60% of patients with ET or PMF [4] [5] [6] [7] . In 2016, the World Health Organization (WHO) classification of myeloproliferative neoplasms specifically recognized the JAK2 V617F mutation as one of the main diagnostic criteria of Philadelphia-negative MPNs [8] .

JAK2, a non-receptor-type tyrosine kinase belonging to the Janus kinase family, is encoded by the JAK2 gene located on chromosome 9p24, which plays an important role in the signal transduction of cytokines and several hematopoietic growth factor receptors [9, 10] . Structurally, JAK2 is characterized by the presence of seven homologous kinase domains (JH1-JH7), among which the JH1 domain is the catalytic active region of JAK2 and has tyrosine kinase activity. In contrast, the JH2 domain has no kinase activity, and it negatively regulates the kinase activity of JH1 domain [11] . The JAK2 V617F mutation is an acquired Gto-T transversion at nucleotide 1849 of exon 14, resulting in amino-acid substitution of valine

The study sample comprised a patient with essential thrombocythemia (ET) diagnosed according to the 2016 WHO criteria and 13 healthy volunteers. Peripheral blood samples of the patient and 13 healthy volunteers were obtained from The First Affiliated Hospital of Jinan University and Hunan Jiahui Genetics Hospital, respectively. Their genomic DNA (gDNA) was extracted from peripheral blood using the conventional phenol-chloroform method [43] . All study participants signed informed consent and the study was approved by the Ethics Committee of School of Life Sciences, Central South University.

The wild-type fragment containing exon 14 of the JAK2 gene (NM_004972) was amplified from normal human gDNA by PCR using primers F and R (Table S1 ). The JAK2 V617F mutation was introduced by overlap extension PCR with mutation-specific primers F, R, Fm, and Rm (Table S1 ). The wild-type and mutant amplified fragments were cloned into the pGEM-T Easy Vector; then, the plasmids were transformed into E. coli DH5α for amplification, before being extracted and verified by Sanger sequencing. All the inserted sequences in the resulting recombinant plasmids were shown in Figure S1 .

The HEL human erythroleukemia cell line harboring homozygous for JAK2 V617F mutation was purchased from the Cell Bank of the Chinese Academy of Sciences (Shanghai, China). The HEL cell line was cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) at 37 • C in a humidified atmosphere containing 95% air and 5% CO 2 . The human induced pluripotent stem (hiPS) cell line without JAK2 V617F mutation originated from our research group and was maintained in hiPSCs medium at 37 • C under 5% CO 2 . Then, many cells were harvested, and the gDNA was isolated from HEL cells and hiPSCs using the conventional phenol-chloroform method. We further authenticated the JAK2 V617F mutational status of two different cell lines by DNA sequencing analysis. In addition, the concentrations of DNA were measured with a NanoDrop 1000 spectrophotometer and adjusted to 100 ng/µL for storage at -20 • C until use.

To amplify exon 14 of the JAK2 gene from plasmids and gDNA, PCR primers (PCR-F, PCR-R) were designed using an NCBI PrimerBlast according to the JAK2 reference sequence (NM_004972). The primer sequences were provided in Table S1 . The PCR reaction was performed in 20 µL total volume, including 16 µL of Premix Ex Taq HS, 100 nM of forward and reverse primer, 1 µL of DNA template, and nuclease-free water to final reaction volume. When using plasmids as a template for PCR amplification, the PCR cycling parameters were as follows: pre-degeneration at 95 • C for 5 min, followed by 35 cycles of 95 • C for 30 s, 58 • C for 30 s, 72 • C for 30 s, and a final extension at 72 • C for 5 min. PCR amplification of gDNA was carried out using the same oligonucleotide primers and reaction conditions, except for reducing the number of cycles to 30.

According to the principle of designing RPA primers and the sequence of the target gene, we used the online software (NCBI PrimerBlast) to design five forward primers and four reverse primers ( Figure S2 and Table S1 ). A DNA sample from a healthy individual was amplified with 20 pairwise combinations of the RPA primers. All 20 amplicons were purified using the Cycle Pure Kit and screened by 1.2% agarose gel electrophoresis. We found that the RPA-F2/RPA-R3 combination was the best performing primer pair. In order to further confirm the reliability of amplification fragments, Sanger sequencing was applied to analyze the purified RPA products.

All RPA reactions were conducted by using the Twist-Dx RPA Kit according to the manufacturer's instructions. The amplification reactions were set up in a 50 µL volume, comprising 25 µL of 2× reaction buffer, 9.2 µL of dNTPs (10 µM), 5 µL of basic E-mix, 2.4 µL of each RPA primer (10 µM), 2.5 µL of 20× core reaction mix, 2.5 µL of MgOAc (280 mM), and 1 µL of target dsDNA; then, they were incubated at 40 • C for 40 min.

For the detection of JAK2 V617F by AS-PCR, AS-PCR primers (Table S1 ) were synthesized by following previous reports [4] . The volume of the AS-PCR reaction was 20 µL, containing 10 µL of ChamQ Universal SYBR qPCR Master Mix, 5 µL of nuclease-free water, 2 µL of reverse AS-PCR primer (10 µM), 1 µL of two forward primers (10 µM), and 1 µL of gDNA (100 ng/µL). Thermocycling conditions were 5 min at 95 • C, and then 30 cycles at 95 • C for 30 s, 58 • C for 30 s, 72 • C for 30 s, with elongation at 72 • C for 5 min. After amplification, we inspected the number of amplicon bands on 2.0% agarose gel electrophoresis. The primer AS-Fm was specific for the gene with JAK2 V617F mutation; hence, the AS-PCR amplification products for DNA samples with JAK2 V617F mutation were 203 bp and 364 bp, whereas the samples were considered to be negative for the JAK2 V617F point mutation if only a single 364 bp band was present.

We manually designed three crRNAs ( Figure 1b and Table S1 ) to identify the JAK2 V617F mutation against the DNA sequences in the near proximity of the JAK2 V617F mutation site, as well as the presence of the appropriate protospacer adjacent motif (PAM) for Cas12a (5 -TTTN and 5 -TTN) [39] , and the specificity of these crRNAs was checked with the web tool CHOPCHOP [44] .

Each JAK2 V617F/Cas12a fluorescence assay contained 2 µL of NEBuffer 2.1, 100 nM of Lba Cas12a, 50 nM of crRNA, 500 nM of fluorophore-quencher (FQ) probe (Table S1 ), 2 µL of PCR products, and nuclease-free water to a 20 µL total volume. Then, the reaction solution was mixed thoroughly and incubated at 37 • C for 1 h in the fluorescence detection instrument. The fluorescence channel was set to FAM, and the fluorescence signal was recorded every minute.

Fluorescence signals were analyzed using GraphPad Prism 8 (GraphPad Software). The date of two groups were compared using a Student's t-test, and multigroup data were tested using one-way analysis of variance (ANOVA). For all analyses, statistical significance was defined as p < 0.05.

Compared with the fluorescence detection, the lateral flow strip assays were performed using FITC-ssDNA-Biotin probes (Table S1 ) with commercially available lateral flow dipsticks. To explore the optimal amount of the FITC-ssDNA-Biotin probe, concentrations of the FITC-ssDNA-Biotin probes were set at 1000 nM, 500 nM, 100 nM, 10 nM, and 1 nM, and they were separately added to the 100 µL Dipstick assay buffer. After blending, the reactions and readouts on lateral flow strips were run. Accordingly, the suitable concentration of the FITC-ssDNA-Biotin probes was determined to be 100 nM.

Under the optimized amount of FITC-ssDNA-Biotin probe, The JAK2 V617F/Cas12a lateral flow strip assay was carried out in a volume of 20 µL, including 2 µL of NEBuffer 2.1, 2500 nM of Lba Cas12a, 250 nM of crRNA, 100 nM of the FITC-ssDNA-Biotin probes, 2 µL of RPA products, and nuclease-free water to final volume. The reaction was incubated at 37 • C for 20 min. Then, 100 µL of Dipstick assay buffer was added and mixed. Subsequently, a lateral flow strip was put into the mixture vertically at room temperature. After approximately 2 min, the lateral flow strip was removed for inspection, and band intensity was directly read with naked eyes and recorded using a smartphone camera or a scanner. Both the mutant plasmid concentration and the wild-type plasmid concentration were 0.01 pg/μL. MUT, mutant plasmid; WT, wild-type plasmid. Data represent means ± SD, with n = 3 replicates (**** p < 0.0001, * p < 0.05).

Each JAK2 V617F/Cas12a fluorescence assay contained 2 μL of NEBuffer 2.1, 100 nM of Lba Cas12a, 50 nM of crRNA, 500 nM of fluorophore-quencher (FQ) probe (Table S1 ), 2 μL of PCR products, and nuclease-free water to a 20 μL total volume. Then, the reaction solution was mixed thoroughly and incubated at 37 °C for 1 h in the fluorescence detection instrument. The fluorescence channel was set to FAM, and the fluorescence signal was recorded every minute.

Fluorescence signals were analyzed using GraphPad Prism 8 (GraphPad Software). The date of two groups were compared using a Student's t-test, and multigroup data were tested using one-way analysis of variance (ANOVA). For all analyses, statistical significance was defined as p < 0.05.

Compared with the fluorescence detection, the lateral flow strip assays were performed using FITC-ssDNA-Biotin probes (Table S1 ) with commercially available lateral flow dipsticks. To explore the optimal amount of the FITC-ssDNA-Biotin probe, concentrations of the FITC-ssDNA-Biotin probes were set at 1000 nM, 500 nM, 100 nM, 10 nM, Both the mutant plasmid concentration and the wild-type plasmid concentration were 0.01 pg/µL. MUT, mutant plasmid; WT, wild-type plasmid. Data represent means ± SD, with n = 3 replicates (**** p < 0.0001, * p < 0.05).

As shown in Figure 1a , the scheme of the JAK2 V617F/Cas12a fluorescence detection system involved the integration of PCR amplification with Cas12a-mediated cleavage. In more detail, the specific crRNA guided the Cas12a endonuclease to bind and cleave the amplified target dsDNA. Afterward, the nonspecific ssDNA trans cleavage activity of Cas12a was activated, which cut the ssDNA-FQ probes, leading to the generation of strong fluorescence signals. Then, statistical analyses of fluorescence dates were used to determine whether the target DNA was in the DNA sample.

Cas12a activity has been shown to be strongly affected by the sequence of the PAM and crRNA [31, 45, 46] . Therefore, we manually designed three different crRNAs (Figure 1b  and Table S1 ), crRNA-1, crRNA-2, and crRNA-3. The three Cas12a/crRNA complexes all recognized the sequences with JAK2 V617F mutation. Afterward, we constructed two plasmids containing JAK2 V617F mutation (MUT) and wild-type (WT) JAK2. The successful construction of the two plasmids was confirmed through Sanger sequencing (Figure 1c) . We tested the three crRNAs on PCR products of the recombinant plasmids carrying exon 14 of the JAK2 gene. The results indicated that all crRNAs were able to distinguish between mutant and wild-type JAK2, while the group with crRNA-1 revealed a higher specificity than the others (Figure 1d) . As a result, crRNA-1 was adopted for the rest of the study.

To determine the assay sensitivity, the successfully constructed recombinant plasmids were diluted to 0.01 pg/µL using nuclease-free water (the copies of 0.01 pg of recombinant plasmid DNA are comparable to the copies of 100 ng of human gDNA), and 0.01 pg/µL mutant and wild-type plasmid DNA was mixed in 10 different ratios (proportion of the mutant plasmids: 12.5%, 5%, 2%, 1%, 0.5%, 0.25%, 0.125%, 0.05%, 0.01%, and 0%). Subsequently, the 10 mixed plasmids and blank control group (nuclease-free water) were amplified by PCR with primers PCR-F and PCR-R (Table S1) , and the PCR products were detected using the JAK2 V617F/Cas12a fluorescence detection system. Measurement with the fluorescence detection instrument showed that the mixed plasmids containing 0.01% mutant plasmid DNA could be effectively detected by the JAK2 V617F/Cas12a fluorescence detection system when the concentration of plasmid was 0.01 pg/µL (Figure 2a ). The concentration of plasmid DNA in each sample was 0.01 pg/μL. The mutation ratio range in which the calibration cure was linear was 0-78% (R 2 = 0.9723). 0%, wild-type plasmid DNA.

In order to better mimic the JAK2 V617F mutation status within human gDNA, we directly exploited the gDNA derived from cells as the input and further studied the utility of the JAK2 V617F/Cas12a fluorescence detection system for detection of the JAK2 V617F mutation. We selected the HEL cell line homozygous for JAK2 V617F mutation as the positive standard and the hiPS cell line homozygous for wild-type JAK2 as the negative control, whereby the JAK2 V617F mutation status of gDNA derived from both cell lines was confirmed by Sanger sequencing (Figure 3a) . The sensitivity of the system was assessed using serial dilutions of the gDNA from the HEL cell line mixed to gDNA from hiPS cell line (the ratio of the HEL cell line gDNA in mixed gDNA: 2%, 1%, 0.5%, 0.25%, 0.125%, 0.05%, 0.01%, and 0%), where the concentration of gDNA extracted from two cell lines was 100 ng/μL. The results suggested that the system was able to reliably detect 100 ng/μL of mixed gDNA with 0.01% JAK2 V617F allele burden (Figure 3b) , and it was largely consistent with the results of the recombinant plasmids mentioned above.

Furthermore, the gDNAs from the HEL and hiPS cell lines were diluted from 100 ng/μL to 0.01 ng/μL by 10-fold gradient dilution. The JAK2 V617F/Cas12a fluorescence detection system combined with PCR pre-amplification could detect as low as 0.01 ng/μL (~5 aM, ~3 copies/μL) of target gDNA according to the concentration gradient test results (Figure 3c ). This suggested that the limit of detection (LOD) in gDNA could reach ~3 copies/μL, showing an ultrahigh sensitivity close to single-copy level. Then, we further investigated the potential of quantitative analysis using the JAK2 V617F/Cas12a fluorescence detection system. According to six scaled standards of JAK2 V617F mutant allele (2%, 5%, 12.5%, 31%, 50%, and 78%), the recombinant plasmid pair was mixed at various proportions to obtain the six diluents to create standard curves, with correlation coefficients of 0.9723 (Figure 2b ). This demonstrated that the JAK2 V617F/Cas12a fluorescence detection system had great potential in the quantitative analysis of the JAK2 V617F allele burden.

In order to better mimic the JAK2 V617F mutation status within human gDNA, we directly exploited the gDNA derived from cells as the input and further studied the utility of the JAK2 V617F/Cas12a fluorescence detection system for detection of the JAK2 V617F mutation. We selected the HEL cell line homozygous for JAK2 V617F mutation as the positive standard and the hiPS cell line homozygous for wild-type JAK2 as the negative control, whereby the JAK2 V617F mutation status of gDNA derived from both cell lines was confirmed by Sanger sequencing (Figure 3a) . The sensitivity of the system was assessed using serial dilutions of the gDNA from the HEL cell line mixed to gDNA from hiPS cell line (the ratio of the HEL cell line gDNA in mixed gDNA: 2%, 1%, 0.5%, 0.25%, 0.125%, 0.05%, 0.01%, and 0%), where the concentration of gDNA extracted from two cell lines was 100 ng/µL. The results suggested that the system was able to reliably detect 100 ng/µL of mixed gDNA with 0.01% JAK2 V617F allele burden (Figure 3b) , and it was largely consistent with the results of the recombinant plasmids mentioned above. 

To more simply and rapidly detect JAK2 V617F mutation from the clinical samples in the field, we combined RPA with lateral flow strip detection to realize instrument-free visualization. The working principle of the JAK2 V617F/Cas12a lateral flow strip assay is illustrated in Figure 4a . All lateral flow strips contained a control band with biotin ligand and a test band with anti-rabbit antibody, in addition to carrying gold particle-labeled anti-FITC antibodies to show the readout. When the amplified DNA did not contain JAK2 V617F mutation, without trans cleavage, all FITC-ssDNA-Biotin probes remained intact and were captured by the biotin ligands at the control band, and then the FITCs were recognized and bound by all gold particle-labeled anti-FITC antibodies. Therefore, the control band generated a color signal, but the test band did not. When the amplified DNA contained JAK2 V617F mutation, upon recognition of the matching target, the Cas12a/crRNA-1 complex cleaved the ssDNA probes. The cleaved ssDNA with the gold particle-labeled anti-FITC antibodies flowed to the test band and were captured by the anti-rabbit antibodies, followed by the formation of a color deposit on the test band. In short, the JAK2 V617F/Cas12a lateral flow strip assay showed a negative result with a Furthermore, the gDNAs from the HEL and hiPS cell lines were diluted from 100 ng/µL to 0.01 ng/µL by 10-fold gradient dilution. The JAK2 V617F/Cas12a fluorescence detection system combined with PCR pre-amplification could detect as low as 0.01 ng/µL (~5 aM,~3 copies/µL) of target gDNA according to the concentration gradient test results (Figure 3c ). This suggested that the limit of detection (LOD) in gDNA could reach 3 copies/µL, showing an ultrahigh sensitivity close to single-copy level.

To more simply and rapidly detect JAK2 V617F mutation from the clinical samples in the field, we combined RPA with lateral flow strip detection to realize instrument-free visualization. The working principle of the JAK2 V617F/Cas12a lateral flow strip assay is illustrated in Figure 4a . All lateral flow strips contained a control band with biotin ligand and a test band with anti-rabbit antibody, in addition to carrying gold particlelabeled anti-FITC antibodies to show the readout. When the amplified DNA did not contain JAK2 V617F mutation, without trans cleavage, all FITC-ssDNA-Biotin probes remained intact and were captured by the biotin ligands at the control band, and then the FITCs were recognized and bound by all gold particle-labeled anti-FITC antibodies. Therefore, the control band generated a color signal, but the test band did not. When the amplified DNA contained JAK2 V617F mutation, upon recognition of the matching target, the Cas12a/crRNA-1 complex cleaved the ssDNA probes. The cleaved ssDNA with the gold particle-labeled anti-FITC antibodies flowed to the test band and were captured by the anti-rabbit antibodies, followed by the formation of a color deposit on the test band. In short, the JAK2 V617F/Cas12a lateral flow strip assay showed a negative result with a pink-colored line only at the control band and a positive result with coloration of both control and test bands. Before establishing the assay, we optimized the RPA primers and the concentration of the FITC-ssDNA-Biotin probes. Primer pair RPA-F2/RPA-R3 was screened from 20 primer pairs, and the RPA product amplified with the primer pair RPA-F2/RPA-R3 was confirmed by Sanger sequencing (Figure 4b and Figure S2 ). For optimizing the concentrations of the FITC-ssDNA-Biotin probes, we set several different concentrations from 1 nM to 1000 nM and found that only the group with the FITC-ssDNA-Biotin probe concentration of 100 nM did not produce a false-positive signal (Figure 4c) . Therefore, we chose primer pair RPA-F2/RPA-R3 as the primer for RPA amplification and 100 nM as the concentration of the FITC-ssDNA-Biotin probes to establish the JAK2 V617F/Cas12a lateral flow strip assay. Before establishing the assay, we optimized the RPA primers and the concentration of the FITC-ssDNA-Biotin probes. Primer pair RPA-F2/RPA-R3 was screened from 20 primer pairs, and the RPA product amplified with the primer pair RPA-F2/RPA-R3 was confirmed by Sanger sequencing (Figures 4b and S2 ). For optimizing the concentrations of the FITC-ssDNA-Biotin probes, we set several different concentrations from 1 nM to 1000 nM and found that only the group with the FITC-ssDNA-Biotin probe concentration of 100 nM did not produce a false-positive signal (Figure 4c) . Therefore, we chose primer pair RPA-F2/RPA-R3 as the primer for RPA amplification and 100 nM as the concentration of the FITC-ssDNA-Biotin probes to establish the JAK2 V617F/Cas12a lateral flow strip assay.

Similarly, we analyzed the viability and sensitivity of the JAK2 V617F/Cas12a lateral flow strip assay using mixed gDNA with different the JAK2 V617F allele burden. The assay was proven to be able to detect the mutation of JAK2 V617F at a low ratio of 0.5% (Figure 4d) , which far exceeded the sensitivity of 1-3% required in the clinic [23] . An ultrahigh sensitivity is essential for the early diagnosis and monitoring of MPNs with JAK2 V617F mutation.

To evaluate the feasibility of the JAK2 V617F/Cas12a lateral flow strip assay on the diagnosis of clinical samples, we carried out the analysis of the gDNA extracted from the peripheral blood of 13 healthy donors and one patient with essential thrombocythemia (ET), where the patient was diagnosed with ET according to the 2016 WHO criteria and was demonstrated to have the JAK2 V617F mutation through next-generation sequencing (NGS). The resulting images are shown in Figure 5a . A clear test line was detected in positive samples; in contrast, no detectable test line was observed from the negative samples. In parallel, as a reference method for JAK2 V617F detection, AS-PCR was also performed with gDNA extracted from those samples (Figure 5b) . The results were consistent with the results of the JAK2 V617F/Cas12a lateral flow strip assay. 

Similarly, we analyzed the viability and sensitivity of the JAK2 V617F/Cas12a lateral flow strip assay using mixed gDNA with different the JAK2 V617F allele burden. The assay was proven to be able to detect the mutation of JAK2 V617F at a low ratio of 0.5% (Figure 4d ), which far exceeded the sensitivity of 1-3% required in the clinic [23] . An ultrahigh sensitivity is essential for the early diagnosis and monitoring of MPNs with JAK2 V617F mutation.

To evaluate the feasibility of the JAK2 V617F/Cas12a lateral flow strip assay on the diagnosis of clinical samples, we carried out the analysis of the gDNA extracted from the peripheral blood of 13 healthy donors and one patient with essential thrombocythemia (ET), where the patient was diagnosed with ET according to the 2016 WHO criteria and was demonstrated to have the JAK2 V617F mutation through next-generation sequencing (NGS). The resulting images are shown in Figure 5a . A clear test line was detected in positive samples; in contrast, no detectable test line was observed from the negative samples. In parallel, as a reference method for JAK2 V617F detection, AS-PCR was also performed with gDNA extracted from those samples (Figure 5b) . The results were consistent with the results of the JAK2 V617F/Cas12a lateral flow strip assay. 

MPNs are hematological malignancies, which seriously threaten human health and place great mental and economic pressure on society and patients. The JAK2 V617F mutation is one of the key somatic driver mutations associated with MPNs; thus, it is a potential therapeutic target for MPNs [4] [5] [6] 47] . In recent years, the United States Food and Drug Administration (FDA) approved JAK2 inhibitors, including ruxolitinib and fedratinib, for the treatment of MPNs [48] [49] [50] [51] [52] [53] . Thus, the detection of JAK2 V617F mutation is of significant social value and practical importance for the diagnosis and treatment of MPNs and allogeneic bone marrow transplantation (allo-BMT).

The sensitivity was reported to reach at least 1-3% for the detection of JAK2 V617F allele burden, because this threshold was shown to be correlated with pathogenicity and carried important clinical interest [23, 54, 55] . However, in existing methods, some of these are not sensitive enough to detect a minority of patients with low-level JAK2 V617F mutation, while some are sufficiently sensitive but yield frequent false-positive signals [23, 25] . In the method developed in this study, the maximum attainable sensitivity was 0.01% and the minimum detectable concentration of gDNA could reach 0.01 ng/µL, which is two orders of magnitude higher than the sensitivity required for clinical application. In addition, when it was used to validate clinical samples, there were no false-positive results. Hence, the assay is expected to provide clinicians with a powerful and effective means for companion diagnostic of MPNs.

In the present study, we report for the first time a CRISPR/Cas12a-based nucleic-acid detection system used to detect the JAK2 V617F mutation. The whole process can be divided into three steps: (1) DNA pre-amplification (PCR or RPA); (2) CRISPR/Cas12a-based target detection (the JAK2 V617F/Cas12a fluorescence detection system or the JAK2 V617F/Cas12a lateral flow strip assay); (3) reading and analysis of the results (fluorescence signal or lateral flow strip). Compared with current detection methods for the JAK2 V617F mutation, our methods offer several features and advantages. Firstly, the sensitivity reached the extremely high value of 0.01%, such that the detection ratio of JAK2 V617F mutation would not tend to differ between peripheral blood and granulocytes as sample sources [23, 56, 57] . As a result, the assay did not require isolating granulocytes from peripheral blood. Secondly, in addition to the JAK2 V617F mutation, there may be other somatic mutations in MPNs patients, such as exon 12 of JAK2, CALR, and MPL [8, [58] [59] [60] [61] [62] . Likewise, it is also possible that these different mutations can be assayed by simply adjusting the crRNA, thus embodying the method's simplicity and versatility. Thirdly, the test process was highly efficient, requiring only 1.5 h. Fourthly, our methods are more economical [34, 63] . Fifthly, the JAK2 V617F/Cas12a fluorescence detection system not only is capable of highly sensitive qualitative detection, but also has the potential of quantitative detection. Lastly, the JAK2 V617F/Cas12a lateral flow strip assay does not rely on sophisticated instruments and skilled technicians, and it is expected to be further integrated into a miniature portable diagnostic device, enabling its application for on-site, point-of-care, low-resource settings, and even home detection. Accordingly, our assays have obvious advantages in the detection of JAK2 V617F mutation.

In this study, we first developed and validated an efficient JAK2 V617F/Cas12a fluorescence detection system and a JAK2 V617F/Cas12a lateral flow strip assay for the rapid, specific, sensitive, robust, simple, and economical detection of the JAK2 V617F mutation, which has significant implications for the diagnosis, treatment, and prevention of MPNs. As a proof of concept, these two systems are adaptable and scalable for detecting somatic mutations in tumor-related genes.

Supplementary Materials: The following are available online at https://www.mdpi.com/article/10 .3390/bios11080247/s1, Figure S1 . The sequences of inserts in the recombinant plasmids; Figure S2 . Schematic representation of the locations of RPA primers; Table S1 . Detailed sequences of primers, crRNAs, and probes in this study. Informed Consent Statement: Informed consent was obtained from all subjects involved in the study.

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Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System

CRISPR-Cas12a-assisted nucleic acid detection

CRISPR-Cas fluorescent cleavage assay coupled with recombinase polymerase amplification for sensitive and specific detection of Enterocytozoon hepatopenaei

Cas12a and Lateral Flow Strip-Based Test for Rapid and Ultrasensitive Detection of Spinal Muscular Atrophy

Molecular Cloning-A Laboratory Manual

CHOPCHOP v2: A web tool for the next generation of CRISPR genome engineering

Structural Basis for Guide RNA Processing and Seed-Dependent DNA Targeting by CRISPR-Cas12a

Real-time observation of DNA target interrogation and product release by the RNA-guided endonuclease CRISPR Cpf1 (Cas12a)

Activating mutation in the tyrosine kinase JAK2 in polycythemia vera, essential thrombocythemia, and myeloid metaplasia with myelofibrosis

Ruxolitinib versus Standard Therapy for the Treatment of Polycythemia Vera

Inhibition with Ruxolitinib versus Best Available Therapy for Myelofibrosis

A Double-Blind, Placebo-Controlled Trial of Ruxolitinib for Myelofibrosis

Patient-Reported Outcomes Labeling for Products Approved by the Office of Hematology and Oncology Products of the US Food and Drug Administration (2010-2014)

Fedratinib Becomes New Option in Myelofibrosis. Cancer Discov. 2019, 9

Properties of FDA-approved small molecule protein kinase inhibitors: A 2020 update

JAK2 Mutations are present in all cases of polycythemia vera

Pitfalls in molecular diagnosis in haemato-oncology

Comparison of whole blood vs purified blood granulocytes for the detection and quantitation of JAK2 V617F

Clinical Performance of JAK2 V617F Mutation Detection Assays in a Molecular Diagnostics Laboratory: Evaluation of Screening and Quantitation Methods

JAK2 Exon 12 Mutations in Polycythemia Vera and Idiopathic Erythrocytosis

Somatic Mutations of Calreticulin in Myeloproliferative Neoplasms

Somatic CALR Mutations in Myeloproliferative Neoplasms with Nonmutated JAK2

MPL mutations in myeloproliferative disorders: Analysis of the PT-1 cohort

Adaptor protein Lnk negatively regulates the mutant MPL, MPLW515L associated with myeloproliferative disorders

SPRINT: A Cas13a-based platform for detection of small molecules

The following reagents and instruments were used: primers (Sangon Biotech, Shanghai, China), CRISPR RNAs (crRNAs) (Sangon Biotech, Shanghai, China), probes (Sangon Biotech, Shanghai, China), pGEM-T Easy Vector (Promega, Madison, WI, USA), E. coli 

The authors thank the staff of The First Affiliated Hospital of Jinan University (Hui Zeng and Huien Zhan) and Hunan Jiahui Genetics Hospital (Jingyi Cui) for assistance with samples collection. We also thank all subjects who participated in this study.

The authors declare no conflict of interest.