Genomic Features of Ph-Like ALL

Genomic Features of Ph-Like ALL: Comparison

Please note this is a comparison between Version 1 by Ilaria Iacobucci and Version 2 by Nora Tang.

A wide spectrum of genetic alterations (>60), including translocations, cryptic rearrangements, sequence mutations and copy number changes have been described in Ph-like ALL, with slight differences in prevalence across age. These alterations drive constitutively active kinase or cytokine receptor signaling, many of which have been shown to be druggable with a variety of kinase inhibitors. The most commonly mutated pathways are the ABL and JAK-STAT pathways with multiple rearrangements and lesions that converge on downstream ABL/JAK-STAT signaling. Founder alterations may be grouped into three types: (i) JAK/STAT alterations including mutations activating cytokine receptors (e.g., CRLF2 and IL7R); gene fusions hijacking cytokine receptor expression (e.g.,

IGH-CRLF2

and

P2RY8–CRLF2

); gene fusions and/or mutations activating kinases (e.g.,

JAK1

JAK2

JAK3

TYK2

); and rearrangements hijacking and truncating cytokine receptor expression (e.g., cryptic

EPOR

rearrangements); (ii) fusions involving ABL-class genes (

ABL1

ABL2

CSF1R

LYN

PDGFRA

PDGFRB

); (iii) less common fusions (

FLT3

FGFR1

NTRK3

PTK2B

) whose number is growing with increasing sequencing studies of different cohorts.

acute lymphoblastic leukemia (ALL)
Ph-like ALL

1. JAK/STAT Alterations

Approximately 50% of patients with Ph-like ALL harbor rearrangements of the cytokine receptor- like factor 2 (

CRLF2

) gene, located on the pseudoautosomal region 1 (

PAR1) of chromosomes Xp22 and Yp11 ^[1][2][3][4]. In normal conditions CRLF2 dimerizes with the α- subunit of interleukin- 7 receptor (IL7RA) to form a heterodimeric thymic stromal lymphopoietin receptor (TSLPR) which actives downstream JAK2/STAT5 and thePI3K/AKT/mTOR pathways ^[5][6][7] and is implicated in early B-cell development ^[8].

) of chromosomes Xp22 and Yp11 [4,12,15,24]. In normal conditions CRLF2 dimerizes with the α- subunit of interleukin- 7 receptor (IL7RA) to form a heterodimeric thymic stromal lymphopoietin receptor (TSLPR) which actives downstream JAK2/STAT5 and thePI3K/AKT/mTOR pathways [26,27,28] and is implicated in early B-cell development [29].

CRLF2

deregulation results from three main mechanisms: (1) a cryptic rearrangement that juxtaposes

CRLF2

to the immunoglobulin heavy chain locus (

IGH

); (2) a focal deletion in the pseudoautosomal region of the sex chromosomes resulting in P2Y receptor family member 8 (

P2RY8

CRLF2

fusion that positions

CRLF2

under the control of the

P2RY8

promoter; (3) and less frequently by an activating

CRLF2 point mutation, F232C ^{[9][10][11][12][13][14][15][16][17]}. Rearrangements of

point mutation, F232C [13,17,22,23,25,30,31,32,33]. Rearrangements of

CRLF2 account for 24% of pediatric patients with NCI SR Ph-like ALL ^[18], 55% of children with HR disease ^[19] and 50% to 60% of adolescent and adult patients with Ph-like ALL cases ^{[1][20][2][9][10][21]}.

account for 24% of pediatric patients with NCI SR Ph-like ALL [9], 55% of children with HR disease [10] and 50% to 60% of adolescent and adult patients with Ph-like ALL cases [4,11,12,13,17,18].

P2RY8-CRLF2 fusions occur more commonly in younger children and in patients with Down syndrome (DS) ALL ^[11][13], while

fusions occur more commonly in younger children and in patients with Down syndrome (DS) ALL [22,25], while

IGH-CRLF2 fusions are detected more frequently in older patients and patients of Hispanic ethnicity ^[22]. In a genome-wide association study of

fusions are detected more frequently in older patients and patients of Hispanic ethnicity [34]. In a genome-wide association study of

CRLF2

-rearranged ALL, the inherited

GATA3

variant rs3824662 was associated with

CRLF2

rearrangement,

JAK

mutation,

IKZF1

deletion, variation in

GATA3 expression and increased risk of relapse ^[23]. This variant is markedly more common in patients of Hispanic ethnicity (~40%) or Native American (~50%) genetic ancestry, while is it detected in only 14% of Europeans ^[23][24]. The point mutation changing phenylalanine 232 to cysteine in CRLF2 has been identified in 9% of DS-ALL patients ^[13] and 21% of adult B-ALL patients ^[12]. In in vitro assays, the expression of CRLF2 F232C in the absence of co-expression of mutant JAK2 promotes JAK2 signaling activation and cell transformation ^[12][13][25].

expression and increased risk of relapse [35]. This variant is markedly more common in patients of Hispanic ethnicity (~40%) or Native American (~50%) genetic ancestry, while is it detected in only 14% of Europeans [35,36]. The point mutation changing phenylalanine 232 to cysteine in CRLF2 has been identified in 9% of DS-ALL patients [25] and 21% of adult B-ALL patients [23]. In in vitro assays, the expression of CRLF2 F232C in the absence of co-expression of mutant JAK2 promotes JAK2 signaling activation and cell transformation [23,25,37].

CRLF2

rearrangement and overexpression is associated with worse outcome compared to cases with lack of

CRLF2 alterations ^{[3][22][26][27]}. However, the poor prognostic impact of

alterations [15,34,38,39]. However, the poor prognostic impact of

CRLF2

overexpression is overcome by

BCR-ABL1

–like signature and

IKZF1 deletion in the Dutch Childhood Oncology Group trials and German Cooperative ALL trials ^[25]. In about half of

deletion in the Dutch Childhood Oncology Group trials and German Cooperative ALL trials [37]. In about half of

CRLF2

-rearranged pediatric Ph-like ALL cases, concomitant

JAK1

and

JAK2

(most commonly in the pseudokinase domain at R683) mutations occur. In adults, the frequency of

JAK

mutations in patients with

CRLF2

rearrangement is lower, with a ratio of 1:4 with

JAK wild type ^{[1][2][3][12]}. In

wild type [4,12,15,23]. In

JAK1

the most common mutation is represented by V658F which is the homolog of JAK2 V617F, hotspot in myeloproliferative neoplasms. Other alterations leading to JAK/STAT activation target

IL7RA

SH2B3

IL2RB

, and

TYK2 genes. Collectively these alterations are approximately two-fold higher in children (14%) compared to adolescents (5.0%), and adults (7.3%) ^[1][2][3].

genes. Collectively these alterations are approximately two-fold higher in children (14%) compared to adolescents (5.0%), and adults (7.3%) [4,12,15].

IL7RA mutations occur in exon 6 and are mainly in-frame insertion/deletions in the juxtamembrane-transmembrane domain or, rarely, a serine-to-cysteine substitution at amino acid 185 in the extracellular domain ^[26]. Independent of

mutations occur in exon 6 and are mainly in-frame insertion/deletions in the juxtamembrane-transmembrane domain or, rarely, a serine-to-cysteine substitution at amino acid 185 in the extracellular domain [38]. Independent of

CRLF2

rearrangements, JAK-STAT signaling activation can result from

JAK2

(~7%) or erythropoietin receptor (

EPOR,

5%) -rearrangements.

Over 20 different

JAK2

gene fusion partners have been reported (most commonly

EBF1

ETV6

PAX5

, and

BCR

), making

JAK2

the most promiscuous gene in Ph-like ALL. All fusions preserve the JAK2 kinase domain and result in STAT5 activation and growth factor independence, making cells expressing these fusions amenable to JAK2 inhibitors.

Common

EPOR

rearrangements involve juxtaposition or less frequently translocation of the

EPOR

gene in proximity of a strong enhancer, such as that of the immunoglobulin heavy (

IGH

) or kappa (

IGK

) loci, that drives its expression. Less frequent rearrangements involve insertion of

EPOR

into the upstream region of

LAIR1

or the

THADA loci ^[1][27]. All these rearrangements clip off the C-terminal cytoplasmic tail, thus preserving the proximal tyrosine requested for activation and removing almost all tyrosine sites required for shutting off the receptor signaling and down-regulate and internalize the receptor. This leads to transformation in in vivo models and sensitivity to a variety of different JAK2 inhibitors in in vitro and in vivo models. While

loci [4,39]. All these rearrangements clip off the C-terminal cytoplasmic tail, thus preserving the proximal tyrosine requested for activation and removing almost all tyrosine sites required for shutting off the receptor signaling and down-regulate and internalize the receptor. This leads to transformation in in vivo models and sensitivity to a variety of different JAK2 inhibitors in in vitro and in vivo models. While

IGH-EPOR fusion due the translocation t(14;19)(q32;p13) can be detected by fluorescence in situ hybridization (FISH) ^[28], the other

fusion due the translocation t(14;19)(q32;p13) can be detected by fluorescence in situ hybridization (FISH) [40], the other

EPOR

rearrangements are cryptic and challenging to detect without using next-generation sequencing (NGS) technologies. The prevalence of

EPOR rearrangements has a peak in young adults (9%) compared to children and adolescents (5% and 3%, respectively). They are rarely detected in adults (1%) ^[9][27].

rearrangements has a peak in young adults (9%) compared to children and adolescents (5% and 3%, respectively). They are rarely detected in adults (1%) [13,39].

JAK2

and

EPOR rearrangements are associated with the poorest outcome compared with the other molecular Ph-like subtypes ^[2][9].

rearrangements are associated with the poorest outcome compared with the other molecular Ph-like subtypes [12,13].

2. Fusions Involving ABL-Class Genes

The ABL-class gene fusions include rearrangements of ABL proto-oncogene 1 (

ABL1;

e.g., to

RCSD1, NUP214, LSM14A, ETV6, RANBP2, CENPC, FOXP1, SFPQ, SNX1, SNX2, SPTNA1, ZMIZ1, NUP153

), ABL proto-oncogene 2 (

ABL2;

e.g., to

RCSD2, PAG1, ZC3HAV1

), colony-stimulating factor 1 receptor (

CSF1R;

e.g., to

SSBP2

MEF2D, TBL1XR1

), platelet-derived growth factor receptor beta (

PDGFRB;

e.g., to

EBF1, ETV6, ATF7IP, SNX29, SSBP2, TNIP1, ZEB2, ZMYND8, NUMA1

) and

LYN (GATAD2A-LYN, NCOR1-LYN ^[29]), with multiple partner genes, with

[41]), with multiple partner genes, with

ABL1

and

PDGFRB being the most common. The prevalence of these rearrangements is 17% in children, 9% in adolescents, 10% young adults and 9% older adults ^{[1][2][30][3]}. Patients with ABL-class fusions respond poorly to chemotherapy regimens, and the

being the most common. The prevalence of these rearrangements is 17% in children, 9% in adolescents, 10% young adults and 9% older adults [4,12,14,15]. Patients with ABL-class fusions respond poorly to chemotherapy regimens, and the

EBF1-PDGFRB fusion in particular is associated with induction failure ^[31][32][33]. All fusions preserve the tyrosine kinase of the ABL-class gene and promote constitutive kinase signaling that confers the ability to survive and grow independently of cytokine in vitro ^[34]. Imatinib, the dual ABL1/SRC inhibitor dasatinib or other TKIs inhibit the downstream signaling induced by each of these chimeric fusion proteins ^[1][35][36] and are currently used in clinical trials. The best and first example is provided by the inhibition of

fusion in particular is associated with induction failure [42,43,44]. All fusions preserve the tyrosine kinase of the ABL-class gene and promote constitutive kinase signaling that confers the ability to survive and grow independently of cytokine in vitro [45]. Imatinib, the dual ABL1/SRC inhibitor dasatinib or other TKIs inhibit the downstream signaling induced by each of these chimeric fusion proteins [4,46,47] and are currently used in clinical trials. The best and first example is provided by the inhibition of

EBF1-PDGFRB fusion by imatinib ^{[33][35][36][37][38]}. The emergence of kinase domain point mutations may represent a potential mechanism of relapse in

fusion by imatinib [44,46,47,48,49]. The emergence of kinase domain point mutations may represent a potential mechanism of relapse in

EBF1-PDGFRB

or other kinase driven-subtypes in Ph-like ALL. Recently, the T681I gatekeeper mutation has been demonstrated to be the most common resistant mutation in

EBF1-PDGFRB Ph-like ALL to both imatinib and dasatinib in in vitro screens and it was associated with a trend towards increased risk of relapse in patients harboring T681I subclones at diagnosis compared to T681I-negative patients ^[39].

Ph-like ALL to both imatinib and dasatinib in in vitro screens and it was associated with a trend towards increased risk of relapse in patients harboring T681I subclones at diagnosis compared to T681I-negative patients [50].

3. Other Kinase Fusions and Genetic Aberrations

Around 5% of Ph-like ALL cases harbor gene fusions or mutations involving

NTRK3, BLNK, DGKH, PTK2B, FLT3, FGFR1, TYK2

and

SH2B3

. Among those, one percent of cases harbor the fusion between

ETV6

and

NTRK3 encoding a member of the tropomyosin receptor tyrosine kinase (TRK) family ^[40]. This fusion is not unique of Ph-like ALL since it has been identified in a range of hematological malignancies, such as acute myeloid leukemia ^[41], infantile sarcoma ^[42][43] and solid tumors ^{[44][45][46][47]}. In preclinical models, ETV6-NTRK3 has been shown to promote the development of an aggressive B-ALL and to be exquisitely sensitive to the TRK inhibitors larotrectinib (LOXO-101) or PLX7486 (Plexxikon) in both patient derived xenograft models and in B-ALL patients with

encoding a member of the tropomyosin receptor tyrosine kinase (TRK) family [51]. This fusion is not unique of Ph-like ALL since it has been identified in a range of hematological malignancies, such as acute myeloid leukemia [52], infantile sarcoma [53,54] and solid tumors [55,56,57,58]. In preclinical models, ETV6-NTRK3 has been shown to promote the development of an aggressive B-ALL and to be exquisitely sensitive to the TRK inhibitors larotrectinib (LOXO-101) or PLX7486 (Plexxikon) in both patient derived xenograft models and in B-ALL patients with

ETV6-NTRK3 ^[44][48][49]. Recently, a clinical response to larotrectinib has been reported in an adult Ph-like ALL with cryptic

[55,59,60]. Recently, a clinical response to larotrectinib has been reported in an adult Ph-like ALL with cryptic

ETV6-NTRK3

rearrangement and NRASGly12Asp mutation. The patient failed to respond to multiagent chemotherapy and relapse after investigational CD19-directed chimeric antigen receptor T-cell therapy with a clone positive for

ETV6-NTRK3 but not anymore for the NRASGly12Asp mutation. The relapsed leukemia progressed with further chemo- and immunotherapy but showed substantial leukemic cytoreduction using the TRK inhibitor larotrectinib ^[50]. Fusions of the B Cell Linker Protein (

but not anymore for the NRASGly12Asp mutation. The relapsed leukemia progressed with further chemo- and immunotherapy but showed substantial leukemic cytoreduction using the TRK inhibitor larotrectinib [61]. Fusions of the B Cell Linker Protein (

BLNK

) or

SLP65

gene to

DNTT

(also known as

TDT) have been also described ^[9][51].

) have been also described [13,62].

BLNK encodes a cytoplasmic adapter protein important for B-cell development and function by activating BCR downstream signaling ^[52], while

encodes a cytoplasmic adapter protein important for B-cell development and function by activating BCR downstream signaling [63], while

DNTT encodes a encodes a template-independent DNA polymerase that catalyzes the addition of deoxynucleotides and that is highly expressed in normal and malignant pre-B and pre-T lymphocytes during early differentiation ^[53].

encodes a encodes a template-independent DNA polymerase that catalyzes the addition of deoxynucleotides and that is highly expressed in normal and malignant pre-B and pre-T lymphocytes during early differentiation [64].

In addition to gene fusions, RAS pathway activating mutations or deletions (

KRAS, NRAS, NF1, PTPN11

) and copy number aberrations in genes involved in B-cell development (

IKZF1, PAX5, EBF1,

and

ETV6

) and cell cycle regulators (

CDKN2A/B

TP53

BTG1

, and

RB1

) are recurrent. Deletions in

IKZF1 occur in around 27% of pediatric cases and in approximately 70% of high-risk pediatric patients with ALL ^[1]. As in

occur in around 27% of pediatric cases and in approximately 70% of high-risk pediatric patients with ALL [4]. As in

BCR-ABL positive ALL ^[54][48],

positive ALL [6,59],

IKZF1 deletions confer a poor prognostic outcome ^[55].

deletions confer a poor prognostic outcome [20].

IKZF1

deletions are significantly more common in patients carrying kinase or cytokine receptor rearrangement (

IGH-CRLF2) than a sequence mutation ^[1][9], especially in Hispanic/Latino (H/L) children with B-ALL (29% in H/L compared to 15% of non-Hispanic Whites) where both

) than a sequence mutation [4,13], especially in Hispanic/Latino (H/L) children with B-ALL (29% in H/L compared to 15% of non-Hispanic Whites) where both

IGH-CRLF2

translocation and

IKZF1 deletion provide a strong biological rationale for the higher death-rate H/L experience due to B-ALL ^[49].

deletion provide a strong biological rationale for the higher death-rate H/L experience due to B-ALL [60].