**3. Novel diagnostics in ALL**

The recent WHO 2016 classification has incorporated morphological, immunophenotypic and the existing cytogenetic features with the new molecular features associated with the various subgroups of ALL [28]. Cytogenetic/molecular abnormalities have been identified in 60–80% of patients with ALL using traditional methods [29]; however, with the advent of genome-wide analysis, this number is expected to increase. Evolution of the diagnostics from morphology, immunohistochemistry, and banding techniques to genome-wide analysis and epigenomics has led to an increased appreciation of the biology of leukemia. Genome-wide studies have also provided insight into the variation in the response to chemotherapy drugs among patients, explaining both the differences in toxicities and response to therapy [30]. In the near future, it can be envisioned that ALL will be molecularly characterized and defined, thus enabling us to deliver tailored therapy.

#### **4. Existing and novel genomics of ALL**

Cytogenetic aberrations in ALL have emerged as one of the most important prognostic factors driving the biology of the disease and patient outcomes [29]. Existing and recently identified novel prognostic markers are illustrated in **Figure 4** [31]. Children carrying either high hyperdiploidy (51–65 chromosomes) or ETV6- RUNX1 as their cytogenetic drivers have an excellent prognosis with survival of >90% at 5 years. Adverse prognostic factors include t(9; 22), MLL translocation, t(17; 19), complex karyotype, low hypodiploidy (31–39 chromosomes), near haploidy (24–30 chromosomes), and near triploidy (60–78 chromosomes) [13]. Germline TP53 mutations are seen in children with ALL and low hypodiploidy (chromosomes 31–39) and confer a poor prognosis [32]. New additions to the list of adverse prognostic factors include BCR-ABL-1 like mutations, iAMP21, CRFL2 overexpression, JAK mutations, and translocations involving immunoglobulin heavy chain (IGH), TCF-PBX1, IKZF1, PAX5, ERG and EBF1 mutations [31, 33–37]. Association of CDKN2A/2B deletions with Ph + ALL have emerged as a poor prognostic factor with guarded prognosis even with SCT [33]. FLT3 mutations have been found in KMT2A rearranged infant ALL and confer a poor prognosis [38–40]. Growing understanding of the biology of the disease allows better risk stratification and in some cases alterations to therapy to improve outcomes. For example, therapy intensification has resulted in improved outcomes in children harboring the iAMP21 mutation [41, 42].

**35**

**4.1 Novel genomics**

**Figure 4.**

*permission from Elsevier).*

*4.1.1 Ph-like ALL*

*Pediatric Acute Lymphoblastic Leukemia: Recent Advances for a Promising Future*

In T-cell ALL, mutations commonly found are those involved in T-cell development. Mutations of the NOTCH-1 activating gene are seen in approximately 50–60% of all the T-ALL cases, while mutations involving the tumor suppressor gene FBXW7 are found in approximately 15% of cases [43]. The French group (FRALLE) has demonstrated favorable outcomes in those with NOTCH/FBXW7 mutations along with wild-type PTEN/RAS [44]. However, the prognostic significance of these in T-ALL is not well defined [45, 46]. Genome-wide association studies have recently identified a number of inherited genetic polymorphisms that are associated with an increased predisposition to develop ALL. These novel genes include ARID5B, GATA3, IKZF1, CDKN2A, CDKN2B, PIP4K2A and TP63 [47–53].

*Sub-classification of childhood ALL. Blue wedges refer to B-progenitor ALL, yellow to recently identified subtypes of B-ALL, and red wedges to T-lineage ALL (reprinted from Ref. [31], copyright (2013) with* 

Salient features of the novel prognostic factors are described below:

BCR-ABL1-like ALL has recently been recognized by sequencing studies by the COG-St Jude consortium (TARGET) and the DCOG, and disease shows a similar gene expression profile to that of Ph + ALL in the absence of the BCR-ABL-1 gene translocation [54–56]. This accounts for 10% of pediatric and 15–20% of AYA ALL and confers an extremely poor prognosis with 5-year disease free survival (DFS) of 25% in AYA patients [34, 54]. The AALL0331 study showed decrease prevalence of Ph-like ALL in children with NCI standard risk (SR) compared to high risk (HR) ALL [57]. Ph-like ALL harbors two types of genomic alterations namely *kinase activating* and *cytokine receptor alterations* [58]*.* The kinase alterations which can be inhibited by ABL inhibitors include *ABL1*, *ABL2*, colony stimulating factor 1 receptor (*CSF1R*), platelet-derived growth factor receptor alfa and beta (*PDGFRA*, *PDGFRB*) [34]. Cytokine receptor alterations include alterations that act via the *JAK/STAT* pathway. This includes membrane-bound thymic stromal

*DOI: http://dx.doi.org/10.5772/intechopen.87092*

*Pediatric Acute Lymphoblastic Leukemia: Recent Advances for a Promising Future DOI: http://dx.doi.org/10.5772/intechopen.87092*

#### **Figure 4.**

*Advances in Hematologic Malignancies*

**3. Novel diagnostics in ALL**

deliver tailored therapy.

**4. Existing and novel genomics of ALL**

are treated.

however long-term survival is only 40–50% [26, 27]. Moreover, the outcomes are worse in patients with primary refractory or relapse and refractory disease (r/r) as well as relapse post SCT; hence the unmet need for durable therapies for such children. The incorporation of newer therapies including monoclonal antibodies and Chimeric Antigen Receptor (CAR) T-cell therapy offer an alternative approach to the management of relapsed/refractory pediatric B ALL. The increasing use of upfront genome-based characterization of disease, and incorporation of drugs against identified actionable targets, will ultimately lead to improved clinical outcomes and deceased toxicity of therapy. This chapter will focus on the recent diagnostic and therapeutic advances which are changing the way children with ALL

The recent WHO 2016 classification has incorporated morphological, immunophenotypic and the existing cytogenetic features with the new molecular features associated with the various subgroups of ALL [28]. Cytogenetic/molecular abnormalities have been identified in 60–80% of patients with ALL using traditional methods [29]; however, with the advent of genome-wide analysis, this number is expected to increase. Evolution of the diagnostics from morphology, immunohistochemistry, and banding techniques to genome-wide analysis and epigenomics has led to an increased appreciation of the biology of leukemia. Genome-wide studies have also provided insight into the variation in the response to chemotherapy drugs among patients, explaining both the differences in toxicities and response to therapy [30]. In the near future, it can be envisioned that ALL will be molecularly characterized and defined, thus enabling us to

Cytogenetic aberrations in ALL have emerged as one of the most important prognostic factors driving the biology of the disease and patient outcomes [29]. Existing and recently identified novel prognostic markers are illustrated in **Figure 4** [31]. Children carrying either high hyperdiploidy (51–65 chromosomes) or ETV6- RUNX1 as their cytogenetic drivers have an excellent prognosis with survival of >90% at 5 years. Adverse prognostic factors include t(9; 22), MLL translocation, t(17; 19), complex karyotype, low hypodiploidy (31–39 chromosomes), near haploidy (24–30 chromosomes), and near triploidy (60–78 chromosomes) [13]. Germline TP53 mutations are seen in children with ALL and low hypodiploidy (chromosomes 31–39) and confer a poor prognosis [32]. New additions to the list of adverse prognostic factors include BCR-ABL-1 like mutations, iAMP21, CRFL2 overexpression, JAK mutations, and translocations involving immunoglobulin heavy chain (IGH), TCF-PBX1, IKZF1, PAX5, ERG and EBF1 mutations [31, 33–37].

Association of CDKN2A/2B deletions with Ph + ALL have emerged as a poor prognostic factor with guarded prognosis even with SCT [33]. FLT3 mutations have been found in KMT2A rearranged infant ALL and confer a poor prognosis [38–40]. Growing understanding of the biology of the disease allows better risk stratification and in some cases alterations to therapy to improve outcomes. For example, therapy intensification has resulted in improved outcomes in children harboring the

**34**

iAMP21 mutation [41, 42].

*Sub-classification of childhood ALL. Blue wedges refer to B-progenitor ALL, yellow to recently identified subtypes of B-ALL, and red wedges to T-lineage ALL (reprinted from Ref. [31], copyright (2013) with permission from Elsevier).*

In T-cell ALL, mutations commonly found are those involved in T-cell development. Mutations of the NOTCH-1 activating gene are seen in approximately 50–60% of all the T-ALL cases, while mutations involving the tumor suppressor gene FBXW7 are found in approximately 15% of cases [43]. The French group (FRALLE) has demonstrated favorable outcomes in those with NOTCH/FBXW7 mutations along with wild-type PTEN/RAS [44]. However, the prognostic significance of these in T-ALL is not well defined [45, 46]. Genome-wide association studies have recently identified a number of inherited genetic polymorphisms that are associated with an increased predisposition to develop ALL. These novel genes include ARID5B, GATA3, IKZF1, CDKN2A, CDKN2B, PIP4K2A and TP63 [47–53].

#### **4.1 Novel genomics**

Salient features of the novel prognostic factors are described below:

#### *4.1.1 Ph-like ALL*

BCR-ABL1-like ALL has recently been recognized by sequencing studies by the COG-St Jude consortium (TARGET) and the DCOG, and disease shows a similar gene expression profile to that of Ph + ALL in the absence of the BCR-ABL-1 gene translocation [54–56]. This accounts for 10% of pediatric and 15–20% of AYA ALL and confers an extremely poor prognosis with 5-year disease free survival (DFS) of 25% in AYA patients [34, 54]. The AALL0331 study showed decrease prevalence of Ph-like ALL in children with NCI standard risk (SR) compared to high risk (HR) ALL [57]. Ph-like ALL harbors two types of genomic alterations namely *kinase activating* and *cytokine receptor alterations* [58]*.* The kinase alterations which can be inhibited by ABL inhibitors include *ABL1*, *ABL2*, colony stimulating factor 1 receptor (*CSF1R*), platelet-derived growth factor receptor alfa and beta (*PDGFRA*, *PDGFRB*) [34]. Cytokine receptor alterations include alterations that act via the *JAK/STAT* pathway. This includes membrane-bound thymic stromal

lymphopoietin receptor *(TSLRP)/CRLF2*. Other pathways involving CRLF2 include *PI3K* and the *mTOR* pathways [58]. *CRLF2* gene rearrangements have been associated with 50% of the cases of Ph-like ALL, of which another 50% also show positivity for *JAK* mutations [33, 56]. Additionally, *IKZF1*deletions (28%), *EPOR, RAS* pathway (10%) are also seen in this group. Patients harboring the *CRLF2* alterations fare poorly with high risk of relapse [59]. Similarly, increased expression of *IKZF1* possibly translates into high post induction MRD as well as higher risk of relapse [60, 61].
