B-cell acute lymphoblastic leukemia with t(3;9)(q25;p13) involving the PAX-5 and MBNL1

Kruti Chaubal,Dhanlaxmi Shetty  

Department of Cancer Cytogenetics, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Center, Navi Mumbai, India.~Department of Cancer Cytogenetics, Advanced Centre for Treatment, Research and Education in Cancer (ACTR

This chromosome aberration is

This chromosome aberration is

Patient demographics


Clinical findings

Date of diagnosis

A population of blast expressing HLA-DR, CD 10, moderate CD 22, moderate CD 9, moderate CD15, Dim-mod CD 19, CD 20, Dim CD 5, CD 34, CD 38, CD 86, Dim-neg CD45, CD 123, variable CD 304, cCD 79u03b1, MPO negative

Bone marrow showed hypercellular bone marrow with 95% blasts.

Sample(s) submitted for testing

Sample(s) submitted for testing
Bone Marrow

Conventional cytogenetics

Cultures set up
Mitogen used
Banding used

GTG Banding

Karyotypic description

Figure 1

Conventional karyotype showing 46,XY,t(8;14)(p21;q24),der(9)t(3;9)(q25;p13)[18]/46,XY[2]

Provide karyogram


Describe probes used, chromosome location, and results

Fluorescence In Situ Hybridization (FISH) using commercial LSI PAX5 (chromosome 9p13) break apart probe (Empire genomics)u00a0 showed 90% cells with PAX5 rearrangement i.e.u00a0nuc ish (PAX5 u00d72)(5u2019 PAX5 sep 3u2019 PAX5 u00d71)[180/200]u00a0

Figure 2

A) Interphase FISH using LSI PAX5 break apart probe showing 1F1R1G indicative of PAX5 rearrangement

B) Metaphase FISH using whole chromosome paints for chromosome 3 (Green) and chromosome 9 (Red) showing translocation between chromosome 3 and 9

Provide fish image(s)

Follow up


Methotrexate, Vincristine, L- asparginase, Ara-C, 6-MP

Complete remission achieved
Time post diagnosis

Conclusions and relevant comments


This is a first reported case of paediatric B-cell acute lymphoblastic leukemia with PAX5::MBNL1. Chromosomal translocation involving PAX5 are common, has many possible partners and occur in ~10% of B- cell acute lymphoblastic leukemia.u00a0This novel partner -MBNL1 has not been reported earlier.u00a0

The resultsu00a0were confirmedu00a0by Next generation sequencing by Illumina Miseq using gene specific primers for fusions involving ABL1,u00a0ABL2, CSF1R, CRLF2, DUX4, EPOR, ETV6, EBF1, FGFR1, IKZF1, JAK2, KMT2A MLLT4, MEF2D, NTRK3, NUP214, NUP98, P2RY8, PAX5, PDGFRA, PDGFRB, RUNX1, TCF3, TYK2 and ZNF384 and showedu00a0t(3;9) as a result of translocation between exon 6 of PAX5 gene on chromosome 9 and exon 2 of MBNL1 gene on chromosome 3.u00a0

PAX5 (Paired box gene 5) gene is involved in various developmentalu00a0processes, and continuously required not only during early B-cell developmentu00a0but also for B lineage maintenance.u00a0MBNL1 (muscleblind like splicing regualtor 1) is RNA binding protein which regulates alternative splicing of pre-m RNAs and plays an important role in the developmentu00a0of myotonic dystrophy 1.

This PAX5::MBNL1u00a0 falls under PAX5-altered category and these patients have intermediate outcome, however our case showed poor outcome as the patient is deceased.u00a0The chromosomal t(8 ;14)(p21;q24) was found in a sideline as an additional anomaly to t(3;9)(q25;p13), however, there is no evidence of such abnormality in literature.


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Kruti Chaubal,Dhanlaxmi Shetty

B-cell acute lymphoblastic leukemia with t(3;9)(q25;p13) involving the PAX-5 and MBNL1

Atlas Genet Cytogenet Oncol Haematol. 2022-01-25

Online version: http://atlasgeneticsoncology.org/case-report/208947/b-cell-acute-lymphoblastic-leukemia-with-t(3;9)(q25;p13)-involving-the-pax-5-and-mbnl1