PPP1R7 Is a Novel Translocation Partner of CBFB via t(2;16)(q37;q22) in Acute Myeloid Leukemia

In a subset of acute myeloid leukemia (AML) cases, the core binding factor beta subunit gene (CBFB) was rearranged via inv(16)(p13.1q22) or t(16;16)(p13.1;q22), in which the smooth muscle myosin heavy chain 11 gene (MYH11) was the partner (CBFB::MYH11). Rare variants of CBFB rearrangement occurring via non-classic chromosomal aberrations have been reported, such as t(1;16), t(2;16), t(3;16), t(5;16), and t(16;19), but the partners of CBFB have not been characterized. We report a case of AML with a complex karyotype, including t(2;16)(q37;q22), in which the protein phosphatase 1 regulatory subunit 7 gene (PPP1R7) at chromosome 2q37 was rearranged with CBFB (CBFB::PPP1R7). This abnormality was inconspicuous by conventional karyotype and interphase fluorescence in situ hybridization (FISH), thus leading to an initial interpretation of inv(16)(p13.1q22); however, metaphase FISH showed that the CBFB rearrangement involved chromosome 2. Using whole genome and Sanger sequencing, the breakpoints were identified as being located in intron 5 of CBFB and intron 7 of PPP1R7. A microhomology of CAG was found in the break and reconnection sites of CBFB and PPP1R7, thus supporting the formation of CBFB::PPP1R7 by microhomology-mediated end joining.


Introduction
Core binding factor beta subunit gene (CBFB) is located on chromosome 16q22 and encodes the beta subunit of core binding factor (CBF), a member of the PEBP2/CBF transcription factor family considered to be a master regulator of normal hematopoiesis [1][2][3][4][5]. CBF also has an alpha subunit (CBFA), which binds to DNA and is composed of three subunits, RUNX1, RUNX2, and RUNX3 [6,7]. By contrast, CBFB is a non-DNA binding unit that is required for DNA binding by CBFA. Genetic alterations of these genes (CBFB, RUNX1, RUNX2, and RUNX3) can alter normal binding to DNA by CBF, thus resulting in a failure of hematopoiesis or hematologic malignancies, particularly acute myeloid leukemia (AML) [8][9][10][11][12][13].
Recently, we reviewed our files for cases of AML with CBFB rearrangement and identified three unusual AML cases with t(1;16)(q21;q22), t(2;16)(q37;q22), or t(16;19)(q22;q13.3) [24]. Fluorescence in situ hybridization (FISH) analysis in these cases showed a 3 -CBFB signal located on the chromosomal loci 1q21, 2q37, and 19q13.3, respectively. In all three cases, a cryptic CBFB::MYH11 rearrangement was excluded by reverse transcriptase polymerase chain reaction (RT-PCR) methods. Therefore, a novel partner of CBFB rearrangement is very likely in these three AML cases. [24] In the current study, we performed whole genome sequencing (WGS) and Sanger sequencing in one of these AML cases, associated with t(2;16)(q37;q22), which had available DNA for further investigation. We identified the protein phosphatase 1 regulatory subunit 7 gene (PPP1R7) located on chromosome 2q37 as a novel partner of CBFB via the translocation [24]. As far as we know, this report is the first to discover a novel partner for CBFB, other than MYH11.

Patients
We searched the database of the Clinical Cytogenetics Laboratory in the Department of Hematopathology, the University of Texas MD Anderson Cancer Center, for cases assessed by CBFB break-apart (BAP) FISH testing performed from 1 June 2000 through 31 May 2021. From a cohort of 271 AML cases with a confirmed CBFB rearrangement by FISH and/or RT-PCR, 3 cases were identified as negative for CBFB::MYH11 fusion [24]. The CBFB rearrangement in these cases was derived from non-classic t(1;16), t(2;16), and t (16;19), respectively. Of these three cases, in one case DNA was available for additional analysis. The electronic medical records were reviewed, and clinicopathologic and other laboratory information were collected. We performed a literature search and identified 7 AML cases with potential and/or confirmed CBFB rearrangement via translocations other than inv(16)/t (16;16). This study was approved by the Institutional Review Board (IRB) of the University of Texas MD Anderson Cancer Center.

Chromosomal Analysis
Conventional G-banded chromosomal analysis (karyotyping) was performed on 24 and 48 h cell cultures of bone marrow (BM) aspirate without mitogens. Twenty metaphases were analyzed routinely for each specimen, and the final results were reported following the 2020 International System for Human Cytogenetics Nomenclature (ISCN 2020) guidelines [24,25].

FISH Analysis
The Vysis CBFB Dual Color Break Apart Rearrangement Probe (Abbott Molecular, Des Plaines, IL, USA) was applied for FISH analysis. To better understand the exact location of the 5 and 3 CBFB signals and correlate with findings of chromosomal analysis, mapback FISH analyses on G-banded and karyotyped metaphases were performed [24,25].

Whole Genome Sequencing
The QIAamp DNA mini kit (QIAGEN, Germantown, MD, USA) was used for genomic DNA (gDNA) extraction from bone marrow aspirate at diagnosis. A total of 50 ng of purified gDNA was fragmented to 600-1000 bp sizes and underwent adapter ligation, indexing, and amplification. The SureSelectQXT reagent kit (Agilent Technologies Inc., Santa Clara, CA, USA) was used for DNA library prep. Low-pass whole-genome sequencing (WGS) was performed as reported previously. Briefly, the mean target coverage was 8.86× with a mapping rate of 91.27%. Alignment to the GRCh38/hg38 reference genome was performed by using BWA13 and BWA-MEM, as reported previously [26]. The HMMcopy software (Bioconductor. DOI: 10.18129/B9.bioc.HMMcopy, (accessed on 20 June 2022)) [27] was applied to analyze the copy number status with focus on 2q, 3q, and 16q that were involved in translocations in our case.

PCR and Sanger Sequencing
The KOD Xtreme™ Hot Start DNA Polymerase (MilliporeSigma Life Science, Burlington, NJ, USA) was applied for PCR amplification. Approximately 30 ng gDNA was used in each PCR reaction. According to WGS analysis results, the following primer pair was designed and applied for PCR amplification: forward primer, PPP1R7_F1: 5 -CAGTCCTCAGTATGCAGGTACG-3 (chr2:241662491-241662512) and reverse primer, CBFB_R1: 5 -GCTGAAAACTCTTCATGGGAAA-3 (chr16:72887661-72887640) (all coordinates in this study are following the GRCh38/hg38, T2T-CHM13v2.0 assembly). The PCR products were recovered from 1.5% agarose gel and then purified with QIAquick Gel Extraction Kit (QIAGEN, Germantown, MD, USA). The purified PCR products were ligated to Zero Blunt TOPO PCR Cloning Kit (Life Technologies, Carlsbad, CA, USA); then, they were subjected to Sanger sequencing using the Sequencing Primer M13R at the core facility of our institution. The obtained DNA sequences were analyzed and aligned using DNASTAR Lasergene 17 SeqManPro (DNASTAR, Inc., Madison, WI, USA) and SnapGene Viewer (GSL Biotech LLC, San Diego, CA, USA).

Case Report
The patient was a 58-year-old man who had a history of thyroiditis and intermittent cardiac arrhythmia. He was diagnosed initially with AML associated with inv(16) at another hospital and treated with cytarabine and mitoxantrone for induction chemotherapy, followed by two courses of high-dose cytarabine and mitoxantrone for consolidation chemotherapy. He achieved a complete remission for approximately one year. He then developed relapsed disease and was referred to our institution. The complete blood count at this time showed hemoglobin 14.5 g/dL (normal, 12.5-17.3 g/dL), hematocrit 41.9% (normal, 38.3-51.2%), platelets 95 K/uL (140-400 K/uL), and white blood cell (WBC) count 4.9 K/uL (normal, 4-11 K/uL), with 74% neutrophils, 18% lymphocytes, 7% monocytes, and 1% eosinophils. The patient underwent bone marrow (BM) examination at this time.
BM aspirate smears showed 12% blasts and 1% eosinophils. The blasts were intermediate to large size with oval-to-irregular nuclei and small-to-moderate amounts of cytoplasm. Some blasts had numerous cytoplasmic granules, and a few had vacuoles. Atypical eosinophil precursors with basophilic granules were seen but were rare ( Figure 1). Blasts were partially positive for myeloperoxidase by cytochemical staining. The bone marrow biopsy specimen showed 20% cellularity, with decreased megakaryocytes and increased immature cells consistent with blasts presenting in small clusters. Flow cy-tometry immunophenotypic analysis showed increased blasts positive for CD13, CD33, CD34, CD38 (bright), CD117, HLA-DR, and myeloperoxidase, as well as negative for CD14, CD41, CD56, CD64, TdT, and B-and T-cell markers. These findings were diagnostic for recurrent/relapsed AML. The patient was treated with a regimen of cytarabine plus/minus cisplatin plus/minus cloretazine, followed by a matched related-donor peripheral blood stem cell transplant (SCT) during second remission. The patient had several follow-up visits with no evidence of disease relapse. However, he died from unknown causes approximately 10 months after his discharge from our hospital.

Conventional Cytogenetics, FISH and Molecular Results
Conventional chromosomal analysis of the BM showed a complex karyotype: 50, XY, t(2;16)(q37;q22), t(3;16)(p21;p13), +8, +21, +22, +mar [5]/51, idem[cp2]/46, XY [13]. A representative karyogram is illustrated in Figure 2. Concurrent CBFB BAP FISH showed CBFB rearrangement in 40 of 200 (20%) cells analyzed. Interestingly, a captured metaphase FISH image showed that split 5 CBFB (red) and 3 CBFB (green) signals were located on different chromosomes, with evidence against inv (16) with CBFB rearrangement, as had been reported elsewhere. Mapback FISH was then performed with the same probe on a previously G-banded slide, and the results indicated the 5 CBFB (red) signal was located on a morphologically normal chromosome 16, the 3 CBFB (green) signal was located on an abnormal chromosome 2, and an intact CBFB signal (orange) was located on an abnormal chromosome 16 on its short (p) arm with material from chromosome 3 (Figure 3). RT-PCR testing performed on the BM showed no evidence of CBFB::MYH11 transcripts. In the aggregate, these results show that CBFB rearrangement did not occur via CBFB::MYH11 fusion; instead, CBFB had a novel partner most likely located on chromosome 2q. Sanger sequencing, in this case, also showed no evidence of RAS and JAK2 mutation, and a PCR assay showed no evidence of FLT3 internal tandem duplication (ITD) or mutation.   The breakpoints and the microhomology of CAG described were located in intron 5 of CBFB and intron 7 of PPP1R7, thus confirming what was postulated from the WGS results. The putative CBFB::PPP1R7 fusion transcript was postulated to consist of exons 1 to 5 of CBFB and exons of 8 to 11 of PPP1R7 (the variant 1 as example), whereas the reciprocal PPP1R7::CBFB transcript was postulated to be a recombination of exons 1 to 7 of PPP1R7 and exon 6 of CBFB, as illustrated in Figure 5.
We retrospectively searched our database within a timeframe of 21 years (from 1 June 2000 through 31 May 2021) [24] and found only 10 AML cases showed clonal t(2;16) aberrations, but involving various band levels of both chromosome 2 and chromosome 16. Among the seven cases tested with CBFB BAP FISH, only the case included in this study showed a positive CBFB rearrangement. Therefore, the t(2;16) aberrations with/without CBFB::PPP1R7 are extremely rare in AML. We also searched our database for the t(1;16)(q43;q22) [18], t(3;16)(q21;q22) [20], t(3;16)(q24;q22) [19], t(5;16)(q13;q22) [22], and t(5;16)(q33;q22) [22,23] that have been reported as rare CBFB rearrangement cases ( Table 1). None of these cases has been found in our database. The clinicopathologic and cytogenetic features of all these cases with rare CBFB rearrangement, including our patient with t(2;16)/CBFB::PPP1R7, mimicked that of classic inv(16)/t(16;16) AML with CBFB::MYH11 (Figure 1), except the AML case with t(1;16)(q43;q22)/CBFB rearrangement reported by Gupta et al. [18], which initially presented as a deceptive acute promyelocytic leukemia (APL) with multiple Auer rods in the abnormal promyelocytes, which has been finally diagnosed and treated as CBF AML. From a practice point of view, it should be pointed out that the t(2;16)(q37;q22) alteration in the case we report was subtle (Figures 2 and 3). This abnormality could be easily missed when metaphase cells of low resolution are obtained for chromosomal analysis or misinterpreted as inv(16) when a positive CBFB BAP FISH result is obtained without a metaphase FISH image, as well as mapback FISH to show the exact locations of the 5 CBFB and 3 CBFB signals. A t(3;16)(p21;p13) was coexistent in our case. The low-pass WGS did not show any potential gene rearrangement(s) through this translocation. Therefore, the t(2;16)(q37;q22)/CBFB::PPP1R7 rearrangement is likely the driver mutation in the AML case we report. The frequency of rare CBFB rearrangements is low in AML, but they can present in various forms of chromosomal aberrations with different partners. A confirmation of CBFB rearrangements by FISH test is necessary and relevant for clinical diagnosis and management in all these cases.
PPP1R7 protein, also called as Sds22, is an important unit of protein phosphatase-1 which physiologically regulates the activity and function of a serine/threonine phosphatase. PPP1R7 is also involved in signal transduction pathways, such as the activation of the cAMP-dependent protein kinase and GPCR pathways [32]. Chiang et al. also reported that PPP1R7 knock-out caused cardiac dysfunction and disruption of calcium release from the sarcoplasmic reticulum in both animal models and cell lines [33]. PPP1R7 protein also plays an important role in accurate chromosome segregation [34][35][36][37], although the association between the PPP1R7 protein and carcinogenesis/tumorigenesis, especially leukemogenesis in hematologic malignancies, generally remains unknown. PPP1R7 has been reported to be a tumor suppressor gene, since the allelic loss of 2q37, where this gene is seated, is associated with oral squamous cell carcinoma [38][39][40]. An in vitro study has shown that PPP1R7 can induce apoptosis and, consequently, inhibit breast cancer tumorigenesis, mainly through the negative regulation of the AKT signaling pathway [41]. In the current study, a microhomology of CAG at the break and reconnection sites of CBFB and PPP1R7 was identified. As reported in the literature, microhomology-mediated end joining (MMEJ) is one of the mechanisms of double-strand DNA break repair. This process plays a physiological role in normal cells, but it is highly error-prone and can cause gene deletion and chromosomal rearrangement [42][43][44]. For example, microhomology-mediated recurrent deletions of CALR, ASXL1, and SRSF2 and non-recurrent deletions in TET2, DNMT3a, CEBPA, and RUNX1 have been reported in myeloid neoplasms [45]. In addition, microhomology-mediated recurrent MYC and other complex gene rearrangements have been reported in myeloma [46].
One limitation of this study is that we are unable to characterize the t(2;16)(q37;q22)/ CBFB::PPP1R7 at the mRNA level, due to a lack of stocked purified RNA and suboptimal quality of RNA purified from paraffin-embedded tissue blocks. Therefore, we cannot explore the exact function(s) of CBFB::PPP1R7 and how they may be applied to understand the pathogenesis of this case of AML.
In conclusion, we have successfully identified PPP1R7 as a new partner of CBFB in a case of AML associated with t(2;16)(q37;q22). This case had clinicopathologic features of classic inv(16)/t(16;16) associated AML, suggesting that the novel CBFB::PPP1R7 potentially plays a role similar to CBFB::MYH11 in leukemogenesis.  Data Availability Statement: Data presented in this study are available on request from the corresponding author.
Acknowledgments: All authors acknowledge Su Yang, Anamaria Fals, and Lisa F. Honore for their restoration and preparation of the excellent chromosome and FISH images from archives.

Conflicts of Interest:
The authors declare no conflict of interest.