B-ALL patients feature disease-specific mutations in the CD19 locus at initial diagnosis
The cellular mechanisms that potentially account for epitope loss are diverse, mutations in the gene encoding for the targeted antigen itself being one of them. As most CART-19 therapy-resistant protein variants identified so far result from exon 2 deletions or inaccurate excision of adjacent introns, we performed mutation analysis of the genomic sequence comprising exon 1 to 4 including introns. We analyzed 3 controls and 20 pediatric B-ALL patients at initial diagnosis and, out of those, 15 samples in remission by deep sequencing (Table S1). Strikingly, we identified a small deletion (NM_001178098.1:c.356 − 95_356-94delCT, derived from TTC > TTC/T at position 28944127) with an allele frequency of ~ 1% located in intron 2 (Tables S2, S3, Fig. 1A) in 35% of samples at diagnosis, both in common and pre-B-ALL, but not in the control group. Remission samples of the same patients did not harbor this genetic variant, indicating its specificity to leukemic blasts. In one sample from initial diagnosis another intronic mutation (NM_001178098.1:c.356-111A > G) was detected. It was located next to the NM_001178098.1:c.356 − 95 locus and featured an allele frequency of 50% in our sample while showing a particularly low allele frequency (0.12%) in the cohort of the 1000 Genomes Project (https://www.internationalgenome.org). However, as material of the same patient in remission was not available, we cannot judge whether the mutation is associated to leukemic blasts. Interestingly, our analysis did not reveal any blast-specific mutation affecting the coding region of CD19.
Thus, our results indicate that subclonal, intronic mutations already exist in leukemic blasts at diagnosis.
Disease-specific Mutations In Cd19 Affect Rbp Binding Sites
We next investigated whether the small deletion in CD19 intron 2 might overlap with recognition motifs for splicing factors and thereby alter the landscape of cis-regulatory elements. The ATtRACT database predicted PTBP1 and ZFP36 to bind to this locus (Fig. 1B). Although we found a high frequency of PTBP1 binding sites throughout the analyzed sequence, the abundance of long and thereby more specific motifs accumulate in intron regions and, remarkably, most prominently in intron 2 (Fig. S1, 1B). We assume an outstanding function of this dedicated locus, as the optimal binding site for PTBP1 is the core sequence TCTTCT embedded in a longer pyrimidine tract (15, 16). Exactly the same motif is affected by the NM_001178098.1:c.356 − 95_356-94delCT deletion, furthermore shortening the pyrimidine tract downstream of the consensus sequence. Thus, we conclude that this blast-specific mutation has a considerable impact on PTBP1 binding.
In order to determine the role of PTBP1 and ZFP36 in B cell leukemia and to figure out whether their expression might be associated with the disease state, qRT-PCR analysis was performed in sorted blasts and B cells (Fig. 1C). Although not reaching significance due to high patient-to-patient variability, PTBP1 showed lower mRNA abundance in blasts of 77% of patients compared to the average expression in B cells. Other than PTBP1, transcription of ZFP36 was rather low in all our samples. Yet, it was significantly less expressed in blasts than in B cells.
Expression Of Rbps Is Deregulated In B-all Patients
Single splicing factors have already been associated with CD19 exon 2 processing. In order to investigate other relevant RBPs that might impact CD19 protein processing, we extended the search for RBP binding sites to the genomic region spanning exon 1 to exon 3. We thereby considered only those motifs ranging between 4 and 10 nucleotides, resulting in a list of 54 RBPs (Fig. S1). Expression levels of the same splicing factors were analyzed by targeted RNA-Seq in 9 patient samples of initial B-ALL diagnosis, 16 in remission and of 2 healthy donors to investigate a disease-associated expression profile (Fig. 2A). Pairwise comparisons revealed 20 differentially expressed genes (DEGs) in blasts relative to B cells, while 10 and 40 DEGs were found comparing remission samples to blasts or B cells, respectively (Tables S4-S6). Overall, the majority of RBPs were highest expressed in B cells, which is most likely also a result of cell sorting of these specimens. Going along with a comparatively small amount of B cells in the remission samples indicated by low levels of CD19, expression relative to blasts and B cells was mostly decreased.
The z-score revealed that PTBP1 and ZFP36 were higher expressed in B cells than in leukemic blasts, corroborating our qRT-PCR data (Fig. 2B, Table S4). To validate the disease-associated expression pattern of selected RBPs, the RNA-Seq data was corroborated by qRT-PCR analysis of leukemic blasts of pediatric B-ALL patients and normal B cells (Fig. 2C, D). Isolation by FACS thereby allowed cell type-related conclusions (Fig. S2). Consistently, PTBP2, a well-described paralog of PTBP1, was in tendency less expressed in isolated leukemic blasts than in B cells. TIA1 did not significantly differ between both cohorts. While SRSF1 expression was unchanged, SRSF3 significantly decreased in blasts compared to B cells. This, however, was not confirmed by targeted RNA-Seq, where it did not appear as DEG. In contrast, RNA-Seq suggested SRSF7 as well as RBM5 to be decreased in blasts relative to B cells, which could not be confirmed in the sorted cells. Interestingly, NONO, which is associated with tumorigenesis in many types of cancer, was significantly less expressed in blasts than in B cells. RNA-Seq also implied differential expression of YTHDC1 and PABPN1. This, however, could not be corroborated by qRT-PCR analysis. Despite discrepancies between both types of analysis for some of the RBPs, explainable by variations in sample preparation, different patient cohorts used for the two types of experiments and a high patient-to-patient variability, our data reveal a disease- and patient-specific expression pattern of several RBPs that implies a correlation with the occurrence of particular CD19 isoforms.
Thus, beyond the appearance of intron-specific mutations that may affect the binding of certain RBPs, we show that the expression of such RBPS is generally deregulated in B-ALL.
Ptbp1 Is A Regulator Of Cd19 Intron 2 Splicing
Focusing on PTBP1, we observed a positive correlation between PTBP1 and CD19 mRNA expression in blasts at diagnosis (Fig. 3A). In order to investigate whether this effect might result from alternative CD19 splicing mediated by PTBP1, we performed CRISPR/Cas9-mediated knockdown in the leukemic cell line 697 (Fig. 3B). As PTBP2 has similar function as PTBP1 and both factors can compensate for each other, we also performed a knockdown of PTBP2 (Fig. S3A). qRT-PCR revealed that downregulation of PTBP1 induced an increase in PTBP2 expression, confirming the functional relevance of the reduction of PTBP1 levels (Fig. 3C). It is known that PTBP1 regulates PTBP2 levels by alternative splicing mediating nonsense-mediated decay, which potentially holds true also in our cellular model (17). Consistent with the positive correlation seen in our patient cohort, levels of CD19 total protein were approximately halved upon PTBP1 knockdown while a decrease in PTBP2 expression did not significantly change CD19 expression (Fig. 3D). Moreover, levels of CD19 surface expression were markedly reduced after PTBP1 knockdown (Fig. S3B). Decreased CD19 protein abundance due to PTBP1 KD was accompanied by an altered isoform composition (Fig. 3E). While the exon 2 WT variant as well as isoforms harboring exon 2 complete or partial deletion were less abundant, intron 2 retention (In2Ret) was significantly upregulated (Fig. 3F). Knockdown of PTBP2, however, did not affect isoform distribution. These data clearly suggest that deregulation of PTBP1, caused either by expression changes or alteration in binding capabilities, imply an accumulation of epitope-negative splicing variants that finally result in decreased levels of CD19 protein.
Intron 2 Retention Is Increased In Blasts Compared To Normal B Cells
In order to investigate whether leukemic blasts from patients at diagnosis and normal B cells generally differ in the expression of CD19 isoforms, we analyzed the occurrence of CD19 variants focusing on exon 2 processing. Consistent with previous results, in leukemic blasts both exon2-deleted CD19 variants (ΔEx2 and ΔEx2part), were already present at diagnosis (Fig. 4A). Additionally, we detected intron 2 retention, which has so far been analyzed only in pre- and post-CART-19 samples. All three mis-spliced CD19 isoforms were expressed also in B cells (Fig. 4B), suggesting that aberrant splicing does equally occur in healthy people. Consequently, the mere presence of the CD19 variants analyzed here is not per se predictive for the disease. However, the accumulation of dedicated isoforms might make a big difference by shifting their ratio and disbalance their regular equilibrium. To investigate this issue in our patient cohort, we precisely quantified the expression of CD19 variants by qRT-PCR using isoform-specific primers (Fig. 4C, Table S7). The high patient-to-patient variability observed before was equally visible in the present analysis, wherefore we did not detect significant differences in isoform expression between blasts and B cells. However, the majority of blast samples showed lower levels of Ex2 WT compared to B cells. Abundance of ΔEx2 and ΔEx2part did not show apparent differences between groups and ΔEx5-6 was hardly expressed in all of our samples. Levels of total CD19 were, similar to the Ex2 WT variant, extremely different across sample groups. For better interpretation of isoform distribution, we calculated the percentage of each exon 2-related variant showing that leukemic blasts had elevated levels of In2Ret compared to B cells (Fig. 4D). At the same time, the regularly spliced WT isoform was in tendency less expressed, suggesting that the shift toward the mis-spliced variant happens at the expense of the regular one. Further analysis corroborated this finding, revealing negative correlation of the percentage of the exon 2 WT isoform related to intron 2 retention (Fig. 4E). Although the increase in In2Ret could not be decidedly attributed to the expression levels of PTBP1 in the patient samples (Fig. 4F), we assume a prominent role of PTBP1 for CD19 exon 2 splicing. The effects of single RBPs might at least partially be masked by the general deregulation of the CD19 splicing machinery that we observe in the patient cohort. We show that the abnormal RBP expression profile in leukemic blasts already establishes at onset of the disease.