del(X)(p22p22) P2RY8/CRLF2
del(Y)(p11p11) P2RY8/CRLF2

2017-03-01   Daniel MartÍnez-Anaya , Patricia Pérez Vera , Rocío Juárez-Velázquez 

1.Laboratorio de Genética y Cáncer. Instituto Nacional de PediatrÍa, Mexico, Mexico; pperezvera@yahoo.com

Abstract

Review on del(X)(p22.33p22.33) or del(Y)(p11.32p11.32), with data on the genes involved, and clinics.

Clinics and Pathology

Disease

Provisional entity: B-lymphoblastic leukemia/lymphoma, BCR-ABL1-like (Arber et al., 2016)

Etiology

Among positive patients the PR2Y8/CRLF2 rearrangement has been detected in different proportions of cells, in principal clones and in minor subclones. Original major clones may persist, disappear, or revert to a minor clone; the minor clones may evolve into a major clone or loss, continue or substitute by a clone with different breakpoint. Based on this, it has been proposed that PR2Y8/CRLF2 is not a driver abnormality in the process of leukemogenesis. Instead, it is a secondary lesion and requires concomitant mutations to become functionally important. The presence of acquire CRLF2 rearrangements in constitutional trisomy 21, and the coexistence of the PR2Y8/CRLF2 and iAMP21 in non-Down syndrome B-cell precursor (BCP) acute lymphoblastic leukemia (ALL), also suggest that CRLF2 rearrangements requires cooperating mutations to activate JAK/STAT and PI3K/mTOR pathways (Morak et al., 2012).

Epidemiology

PR2Y8/CRLF2 positive patients are included in the Ph-like BCP-ALL subgroup, based on its characteristic gene expression signature (Arber et al., 2016). The prevalence of this subgroup is associated with age, high-risk stratification and ethnicity (Harvey et al., 2010). It presents in about 10% of standard-risk childhood ALL, and in >25% of young adults; CRLF2 is the most frequent deregulated gene in the Ph-like subgroup. Overexpression of CRLF2 results in constitutive JAK/STAT activation and cytokine-independent growth (Roberts et al., 2015). In the total of BCP-ALL patients 6% present over-expression of CRLF2, this deregulation is more prevalent among Down syndrome patients (54%). In an unselected cohort of pediatric patients, the Medical Research Council (MRC) found predominance of PR2Y8/CRLF2 (5%) in contrast to IGH/CRLF2 (1%). In comparison, the Childrens Oncology Group (COG) observed that IGH/CRLF2 is twice as prevalent as PR2Y8/CRLF2 (Ensor et al., 2011); this variability could be explained by the selection of high risk ALL patients analysed in this study, including a high proportion of older patients and Hispanic patients, who are 5 times more possible to have CRLF2 abnormalities compared with patients with other ethnicities. In children with BCP-ALL and Down syndrome PR2Y8/CRLF2 was identified in 54.5% of cases (Mullighan et al., 2009). In adults with BCP-ALL the prevalence of Ph-like is >20%, of this group, the IGH/CRLF2 (57.6%) is more prevalent than PR2Y8/CRLF2 (21.2%) (Roberts et al., 2017). In general, IGH/CRLF2 patients are older than PR2Y8/CRLF2 patients.

Clinics

ALL with BCP immunophenotype with rearrangement involving a cytokine receptor, included in the BCR-ABL1-like ALL subgroup.

Treatment

The PR2Y8/CRLF2 rearrangement results in kinase-activating lesion that causes the constitutive activation of the JAK/STAT signalling pathway. Therefore, patients with PR2Y8/CRLF2 ALL could benefit from the treatment with clinically approved tyrosine kinase inhibitors such as Ruxolitinib, which target these pathways. The treatment of these patients with the relevant tyrosine kinase inhibitor could potentially improve their survival (Harrison, 2013).

Prognosis

In different cohorts of children with high risk ALL, the presence of CRLF2 alterations have been associated with poor clinical outcome. However, not in all the study groups have been found positive correlations. The different treatment protocols, not standardized methods for diagnosis of CRLF2 alterations or over-expression, and limited prospective studies for analysing prognostic value are source of bias. A meta-analysis study including 5945 patients of seven different studies analysed the association between CRLF2 alterations and survival of children with ALL, the results showed that CRLF2 deregulation predicts poor prognosis. In adults, the outcome of patients with Ph-like ALL is inferior compared with the outcome of patients with non-Ph-like ALL, excluding BCR/ABL1 and MLL positive cases (Roberts et al., 2017).
It is expected that PR2Y8/CRLF2 positive clones contribute to disease progression. However, in children it has been found heterogeneity in PR2Y8/CRLF2 clone sizes, and no participation in relapses if the size is very small at diagnosis. In part, these may be the basis of the controversies about the prognostic value of this rearrangement and the over-expression of CRLF2 as risk markers. A revision of these parameters should be done.

Disease

T-lymphoblastic leukemia/lymphoma (T-ALL)

Note

: It has been reported CRLF2 over-expression in T-ALL patients: however, PR2Y8/CRLF2 has not been found in these cases. Deregulation of CRLF2 in this entity is considered a poor prognosis marker (Palmi et al., 2016).

Cytogenetics

Atlas Image
FISH in interphases with the PR2Y8/CRLF2 (PAR 1) deletion probe (Cytocell Aquarius) on a bone marrow sample of a female patient with Down syndrome. A) The expected two normal signals (red/green): B) One normal signal (red/green) and one corresponding to the PAR1 deletion (green with white arrow). C) One normal signal (red/green) and two abnormal signals (green with white arrows) which indicate the presence of two X chromosomes with the PAR1 deletion.

Genes Involved and Proteins

Gene name
CRLF2 (cytokine receptor-like factor 2)
Location
Xp22.33
Note
It is located at the PAR1 of chromosome X, Xp22.33, and chromosome Y, Yp11.
Other names and symbols: Thymic Stromal Lymphopoietin Protein Receptor, TSLP Receptor, IL-XR, TSLPR, CRL2, Thymic Stromal-Derived Lymphopoietin Receptor, Cytokine Receptor-Like 2. , Other names and symbols: purinergic receptor P2Y, G-protein coupled, 8, P2Y8, G-protein coupled purinergic receptor P2Y8, P2Y purinoceptor 8.
Dna rna description
The genomic location of CRLF2 gene in chromosome X starts in 1,187, 549 bp from pter, and ends in 1, 212, 815 bp from pter. The size is 25, 267 bases, with minus strand orientation NC_018934.
Atlas Image
Chromosomal location of the CRLF2 gene.
Protein description
The cytokine receptor-like factor 2 has a size of 371 amino acids, with a molecular mass of 42013 Daltons. Cytokine receptor-like factor 2 is a transmembrane protein with an extracellular domain of 210 residues, and an intracellular domain of 119 residues (Zhang et al., 2001). CRLF2 heterodimerizes with IL7R constituting a functional receptor (Rochman et al., 2010; Bugarin C et al., 2015).
Somatic mutations
The CRLF2 711T>G (Phe232Cys) mutation has been found in ALL blasts. The CRLF2 Phe232 residue is near to the junction of the extracellular and transmembrane domains. The Phe232Cys mutation confers a constitutive dimerization through the cysteine residues inducing the growth of cells. This mutation also promotes the up-regulation of transcriptional targets downstream of the JAK/STAT pathway (Yoda et al., 2010).
Gene name
P2RY8 (purinergic receptor P2Y, G-protein coupled, 8)
Location
Xp22.33
Note
P2RY8 is located at the pseudoautosomal region 1 (PAR1) of chromosome X, Xp22.33 and chromosome Y, Yp11.
Dna rna description
The genomic location of P2RY8 gene in chromosome X starts in 1,462, 572 bp from pter and ends in 1,537,506 bp from pter. The size is 74,935 bases, with minus strand orientation NC_000023.
Atlas Image
Chromosomal location of the P2RY8 gene.
Protein description
The P2Y purinoceptor 8 protein has a size of 359 amino acids, with a molecular mass of 40635 Daltons.

Result of the Chromosomal Anomaly

Note

The PR2Y8/CRLF2 rearrangement results from an interstitial microdeletion involving the PAR1, which is located in the short arm of both sex chromosomes. This deletion causes the CRLF2 overexpression through the juxtaposition of the entire coding sequence of CRLF2 with the first non-coding exon of P2RY8, and their transcriptional control elements that are highly active in lymphoid cells (Morak et al., 2016; Vesely et al., 2016; Ensor et al; 2016; Mullighan et al; 2009).
Atlas Image
The PAR1 deletion results in the PR2Y8/CRLF2 rearrangement.

Description

The PAR1 deletion measures approximately 320 Kb and deletes the complete coding sequence of P2RY8 along with ASMTL , SLC25A6, IL3RA and CSF2RA genes, bringing together the first exon of P2RY8 to exon 1 of CRLF2. The breakpoints of the deletion are highly conserved and are located 3.4 Kb upstream of the CRLF2 exon 1 and 0.3-1 Kb distal to P2RY8 exon 1 (Mullighan et al., 2009). Two new alternative breakpoints have been described, 2.1 Kb and 0.1 Kb upstream of CRLF2 exon 1, but in all cases the deletion place the full CRLF2 open reading frame under transcriptional control of the P2RY8 promoter (Morak et al., 2016). The presence of recombination signal sequences immediately internal to the deletion breakpoints suggests that the PAR1 deletion may arise as a result of aberrant activity of the RAG recombinases, this phenomenon has been described for other chromosomal rearrangements in B- ALL (Mullighan et al; 2009).

Transcript

The chimeric transcript contains the 5-UTR region of P2RY8 joined to exon 1 of CRLF2, prior to the transcription start codon (Hertzberg et al., 2016). The PR2Y8 5-UTR region measures approximately 226 bp, and the open reading frame of CRLF2, which is approximately of 1116 bp, remains complete; therefore the chimeric transcript size is 1342 bp (Yap et al., 2016).

Detection protocole

The PR2Y8/CRLF2 positive cases can be detected at genomic level by long range PCR or MLPA techniques using genomic DNA extracted from leukemic cells, however, these assays only reveal the presence of the rearrangement. On the other hand, FISH assay informs about the proportion of abnormal cells, it has been designed deletion probes for covering the telomeric end of P2RY8 and a region distal to the gene, and a control probe that covers a region of the proximal side of P2RY8 (Morak et al., 2016). At RNA level, RT-PCR can confirm the presence of chimeric transcripts. The overexpression of CRLF2 can be measured by qRT-PCR using different methods of absolute and relative measurement (Mullighan et al; 2009).

Oncogenesis

The overexpression of CRLF2 produced by the PR2Y8/CRLF2 rearrangement causes the constitutive activation of JAK/SAT signaling and the PI3K/mTOR, Ras, MAPK and Bcl-2 downstream related pathways in the leukemic blast. These signaling pathways have a central role in the regulation of the cell proliferation, survival, differentiation and immune response; hence its malfunction contributes to the leukemic transformation (Roberts KG et al., 2015).

Highly cited references

Pubmed IDYearTitleCitations
198381942009Rearrangement of CRLF2 in B-progenitor- and Down syndrome-associated acute lymphoblastic leukemia.219
201390932010Rearrangement of CRLF2 is associated with mutation of JAK kinases, alteration of IKZF1, Hispanic/Latino ethnicity, and a poor outcome in pediatric B-progenitor acute lymphoblastic leukemia.199
199656412010Down syndrome acute lymphoblastic leukemia, a highly heterogeneous disease in which aberrant expression of CRLF2 is associated with mutated JAK2: a report from the International BFM Study Group.123
284084642017Targetable kinase gene fusions in high-risk B-ALL: a study from the Children's Oncology Group.95
223682722012Outcome modeling with CRLF2, IKZF1, JAK, and minimal residual disease in pediatric acute lymphoblastic leukemia: a Children's Oncology Group study.88
203787522010Presence of the P2RY8-CRLF2 rearrangement is associated with a poor prognosis in non-high-risk precursor B-cell acute lymphoblastic leukemia in children treated according to the ALL-BFM 2000 protocol.77
228756272013IKZF1 deletion is an independent predictor of outcome in pediatric acute lymphoblastic leukemia treated according to the ALL-BFM 2000 protocol.52
211069842011Demographic, clinical, and outcome features of children with acute lymphoblastic leukemia and CRLF2 deregulation: results from the MRC ALL97 clinical trial.46
228515632012IGH@ translocations, CRLF2 deregulation, and microdeletions in adolescents and adults with acute lymphoblastic leukemia.44
215275302011Genomic characterization implicates iAMP21 as a likely primary genetic event in childhood B-cell precursor acute lymphoblastic leukemia.40
224844212012Poor prognosis for P2RY8-CRLF2 fusion but not for CRLF2 over-expression in children with intermediate risk B-cell precursor acute lymphoblastic leukemia.38
283951182017ETV6/RUNX1-like acute lymphoblastic leukemia: A novel B-cell precursor leukemia subtype associated with the CD27/CD44 immunophenotype.25
230912962012Small sizes and indolent evolutionary dynamics challenge the potential role of P2RY8-CRLF2-harboring clones as main relapse-driving force in childhood ALL.25
239302172013IKZF1 deletion is associated with a poor outcome in pediatric B-cell precursor acute lymphoblastic leukemia in Japan.20
280336482017Characterisation of the genomic landscape of CRLF2-rearranged acute lymphoblastic leukemia.19
251058412014Frequent cases of RAS-mutated Down syndrome acute lymphoblastic leukaemia lack JAK2 mutations.19
228166142012Treatment outcome of CRLF2-rearranged childhood acute lymphoblastic leukaemia: a comparative analysis of the AIEOP-BFM and UK NCRI-CCLG study groups.17
278998022017Genomic and transcriptional landscape of P2RY8-CRLF2-positive childhood acute lymphoblastic leukemia.15
295070762018Prognostic impact of kinase-activating fusions and IKZF1 deletions in pediatric high-risk B-lineage acute lymphoblastic leukemia.12
291945622018A risk score including microdeletions improves relapse prediction for standard and medium risk precursor B-cell acute lymphoblastic leukaemia in children.11
288660952017Differential expression of MUC4, GPR110 and IL2RA defines two groups of CRLF2-rearranged acute lymphoblastic leukemia patients with distinct secondary lesions.11
260183352015The clinical impact of IKZF1 deletions in paediatric B-cell precursor acute lymphoblastic leukaemia is independent of minimal residual disease stratification in Nordic Society for Paediatric Haematology and Oncology treatment protocols used between 1992 and 2013.11
304875982019Single-cell analysis identifies CRLF2 rearrangements as both early and late events in Down syndrome and non-Down syndrome acute lymphoblastic leukaemia.9
283713172017Molecular characterization of acute lymphoblastic leukemia with high CRLF2 gene expression in childhood.9
267545562016CRLF2 overexpression identifies an unfavourable subgroup of adult B-cell precursor acute lymphoblastic leukemia lacking recurrent genetic abnormalities.9
249350702014An overall characterization of pediatric acute lymphoblastic leukemia with CRLF2 overexpression.9
299824392018Clinker: visualizing fusion genes detected in RNA-seq data.7
285979422017Copy number alterations determined by single nucleotide polymorphism array testing in the clinical laboratory are indicative of gene fusions in pediatric cancer patients.7
278555582017Diagnostic evaluation of RNA sequencing for the detection of genetic abnormalities associated with Ph-like acute lymphoblastic leukemia (ALL).7
276370122017Prognostic significance of P2RY8-CRLF2 and CRLF2 overexpression may vary across risk subgroups of childhood B-cell acute lymphoblastic leukemia.6
292285392017The enigmatic role(s) of P2RY8-CRLF2.5
250443582014Gene alterations involving the CRLF2-JAK pathway and recurrent gene deletions in Down syndrome-associated acute lymphoblastic leukemia in Japan.4
297867572018Copy number abnormality of acute lymphoblastic leukemia cell lines based on their genetic subtypes.3
337502582021Genomic landscape of B-other acute lymphoblastic leukemia in an adult retrospective cohort with a focus on BCR-ABL1-like subtype.2
308596362019GATA3 germline variant is associated with CRLF2 expression and predicts outcome in pediatric B-cell precursor acute lymphoblastic leukemia.2
291404082017Philadelphia Chromosome-like Mixed-Phenotype Acute Leukemia Demonstrating P2RY8-CRLF2 Fusion and JAK1 Mutation.2
231459002013No prognostic impact of P2RY8-CRLF2 fusion in intermediate cytogenetic risk childhood B-cell acute lymphoblastic leukaemia.2
337075992021Philadelphia chromosome-negative B-cell acute lymphoblastic leukaemia with kinase fusions in Taiwan.1
323956812020P2RY8-CRLF2Fusion-Positive Acute Myeloid Leukemia With Myelodysplasia-Related Changes: Response to Novel Therapy.1
341594012021Hematological characteristics, cytogenetic features, and post-induction measurable residual disease in thymic stromal lymphopoietin receptor (TSLPR) overexpressed B-cell acute lymphoblastic leukemia in an Indian cohort.0
338907262021CRLF2 and IKZF1 abnormalities in Mexican children with acute lymphoblastic leukemia and recurrent gene fusions: exploring surrogate markers of signaling pathways.0
336157102021Effects of different aberrations in the CRLF2 gene on the biological characteristics and drug sensitivities of Nalm6 cells.0
338123922021[Clinical Features and Prognosis of Acute Lymphoblastic Leukemia Children with P2RY8-CRLF2 Gene Rearrangement].0
337812172021Low incidence of ABL-class and JAK-STAT signaling pathway alterations in uniformly treated pediatric and adult B-cell acute lymphoblastic leukemia patients using MRD risk-directed approach - a population-based study.0
354840802022Clinico-hematological and Outcome Profile of Pediatric B-other-ALL and BCR::ABL1-like pre-B-ALL: An Integrated Genomic Study From North India.0
355373302022High occurrence of CRLF2 abnormalities in Mexican children with B-cell acute lymphoblastic leukemia.0
348578872022HMGN1 plays a significant role in CRLF2 driven Down Syndrome leukemia and provides a potential therapeutic target in this high-risk cohort.0
347326182021[Down syndrome and acute lymphoblastic leukemia].0

Bibliography

Pubmed IDLast YearTitleAuthors
270692542016The 2016 revision to the World Health Organization classification of myeloid neoplasms and acute leukemia.Arber DA et al
260452942015BCR-ABL1-like cases in pediatric acute lymphoblastic leukemia: a comparison between DCOG/Erasmus MC and COG/St. Jude signatures.Boer JM et al
258627052015Fine tuning of surface CRLF2 expression and its associated signaling profile in childhood B-cell precursor acute lymphoblastic leukemia.Bugarin C et al
211069842011Demographic, clinical, and outcome features of children with acute lymphoblastic leukemia and CRLF2 deregulation: results from the MRC ALL97 clinical trial.Ensor HM et al
243191722013Targeting signaling pathways in acute lymphoblastic leukemia: new insights.Harrison CJ et al
201390932010Rearrangement of CRLF2 is associated with mutation of JAK kinases, alteration of IKZF1, Hispanic/Latino ethnicity, and a poor outcome in pediatric B-progenitor acute lymphoblastic leukemia.Harvey RC et al
199656412010Down syndrome acute lymphoblastic leukemia, a highly heterogeneous disease in which aberrant expression of CRLF2 is associated with mutated JAK2: a report from the International BFM Study Group.Hertzberg L et al
259205912015Prognostic significance of cytokine receptor-like factor 2 alterations in acute lymphoblastic leukemia: a meta-analysis.Jia M et al
230912962012Small sizes and indolent evolutionary dynamics challenge the potential role of P2RY8-CRLF2-harboring clones as main relapse-driving force in childhood ALL.Morak M et al
198381942009Rearrangement of CRLF2 in B-progenitor- and Down syndrome-associated acute lymphoblastic leukemia.Mullighan CG et al
274492872016CRLF2 over-expression is a poor prognostic marker in children with high risk T-cell acute lymphoblastic leukemia.Palmi C et al
209749632010Thymic stromal lymphopoietin-mediated STAT5 phosphorylation via kinases JAK1 and JAK2 reveals a key difference from IL-7-induced signaling.Rochman Y et al
278998022017Genomic and transcriptional landscape of P2RY8-CRLF2-positive childhood acute lymphoblastic leukemia.Vesely C et al
264048922015Identification of novel kinase fusion transcripts in paediatric B cell precursor acute lymphoblastic leukaemia with IKZF1 deletion.Yano M et al
278555582017Diagnostic evaluation of RNA sequencing for the detection of genetic abnormalities associated with Ph-like acute lymphoblastic leukemia (ALL).Yap KL et al
200187602010Functional screening identifies CRLF2 in precursor B-cell acute lymphoblastic leukemia.Yoda A et al
112377412001Identification of a novel type I cytokine receptor CRL2 preferentially expressed by human dendritic cells and activated monocytes.Zhang W et al

Summary

Fusion gene

P2RY8/CRLF2

Citation

Daniel MartÍnez-Anaya ; Patricia Pérez Vera ; Rocío Juárez-Velázquez

del(X)(p22p22) P2RY8/CRLF2
del(Y)(p11p11) P2RY8/CRLF2

Atlas Genet Cytogenet Oncol Haematol. 2017-03-01

Online version: http://atlasgeneticsoncology.org/haematological/1599/del(x)(p22p22)

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