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The landscape of somatic mutations in infant MLL-rearranged acute lymphoblastic leukemias.

Andersson AK, Ma J, Wang J, Chen X, Gedman AL, Dang J, Nakitandwe J, Holmfeldt L, Parker M, Easton J, Huether R, Kriwacki R, Rusch M, Wu G, Li Y, Mulder H, Raimondi S, Pounds S, Kang G, Shi L, Becksfort J, Gupta P, Payne-Turner D, Vadodaria B, Boggs K, Yergeau D, Manne J, Song G, Edmonson M, Nagahawatte P, Wei L, Cheng C, Pei D, Sutton R, Venn NC, Chetcuti A, Rush A, Catchpoole D, Heldrup J, Fioretos T, Lu C, Ding L, Pui CH, Shurtleff S, Mullighan CG, Mardis ER, Wilson RK, Gruber TA, Zhang J, Downing JR, St. Jude Children's Research Hospital–Washington University Pediatric Cancer Genome Proje - Nat. Genet. (2015)

Bottom Line: Our data show that infant MLL-R ALL has one of the lowest frequencies of somatic mutations of any sequenced cancer, with the predominant leukemic clone carrying a mean of 1.3 non-silent mutations.Despite this paucity of mutations, we detected activating mutations in kinase-PI3K-RAS signaling pathway components in 47% of cases.Surprisingly, these mutations were often subclonal and were frequently lost at relapse.

View Article: PubMed Central - PubMed

Affiliation: 1] Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA. [2] Department of Clinical Genetics, Lund University, Lund, Sweden.

ABSTRACT
Infant acute lymphoblastic leukemia (ALL) with MLL rearrangements (MLL-R) represents a distinct leukemia with a poor prognosis. To define its mutational landscape, we performed whole-genome, exome, RNA and targeted DNA sequencing on 65 infants (47 MLL-R and 18 non-MLL-R cases) and 20 older children (MLL-R cases) with leukemia. Our data show that infant MLL-R ALL has one of the lowest frequencies of somatic mutations of any sequenced cancer, with the predominant leukemic clone carrying a mean of 1.3 non-silent mutations. Despite this paucity of mutations, we detected activating mutations in kinase-PI3K-RAS signaling pathway components in 47% of cases. Surprisingly, these mutations were often subclonal and were frequently lost at relapse. In contrast to infant cases, MLL-R leukemia in older children had more somatic mutations (mean of 6.5 mutations/case versus 1.3 mutations/case, P = 7.15 × 10(-5)) and had frequent mutations (45%) in epigenetic regulators, a category of genes that, with the exception of MLL, was rarely mutated in infant MLL-R ALL.

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Mutational profiles of infant and non-infant MLL-R leukemia. (a) The number of non-silent SNVs and indels in the dominant leukemia clone affecting annotated genes in infant MLL-R ALL and non-infant MLL-R leukemia. (b) Distribution of somatic SNVs, indels, and CNAs in epigenetic regulatory genes in infant MLL-R ALL and non-infant MLL-R leukemias showing that these genes are significantly more often mutated in non-infant MLL-R leukemia (two-sided Fishers exact test, P=0.04). The black line between SJMLL002 and SJMLL021 indicate the separation between the lymphoblastic and myeloid non-infant leukemias. The only gene mutation that was found not to be expressed at the detection limit of our RNAseq analysis was the one in L3MBTL3.
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Figure 4: Mutational profiles of infant and non-infant MLL-R leukemia. (a) The number of non-silent SNVs and indels in the dominant leukemia clone affecting annotated genes in infant MLL-R ALL and non-infant MLL-R leukemia. (b) Distribution of somatic SNVs, indels, and CNAs in epigenetic regulatory genes in infant MLL-R ALL and non-infant MLL-R leukemias showing that these genes are significantly more often mutated in non-infant MLL-R leukemia (two-sided Fishers exact test, P=0.04). The black line between SJMLL002 and SJMLL021 indicate the separation between the lymphoblastic and myeloid non-infant leukemias. The only gene mutation that was found not to be expressed at the detection limit of our RNAseq analysis was the one in L3MBTL3.

Mentions: Although MLL-R occur at a high frequency in infant ALL, this genetic lesion is also seen in older children with ALL or AML39. To compare the MLL-R mutational profile between infants and older children, we performed whole exome sequencing (WES) and SNP array analysis on 20 non-infant MLL-R patients (7–19 years of age, 9 ALLs, 10 AMLs, and 1 case of acute undifferentiated leukemia), as well as RNAseq on 18/20 cases (Supplementary Tables 9–11, 17, 31–32, and Supplementary Figs. 4 and 40). This analysis revealed that the major clone in non-infant MLL-R leukemia harbor a significantly higher number of non-silent somatic SNVs/indels than infant MLL-R ALL (mean 6.5/case versus 1.3/case, P=7.15×10−5, and for expressed genes: mean 3.2/case versus 0.6/case, P=1.6×10−3, Fig. 4a and Supplementary Tables 33 and 34, see Supplementary Table 35 for a mutation summary of all three cohorts). Although there was a trend towards a lower basal mutation rate in infants compared to non-infants (P=0.15), multiple linear regression analysis demonstrated that the significantly higher number of mutations in older children could not be solely attributed to the difference in the basal mutation rates (Supplementary Notes, Supplementary Figs. 41 and 42). This suggests that overt leukemia in older children with MLL-R may require more cooperating mutations. Similar to infants with MLL-R, activating mutations in tyrosine kinase/PI3K/RAS pathways were identified in 50% of the non-infant leukemias, with recurrent mutations in FLT3 (n=3), KRAS (n=3), NRAS (n=3), and non-recurrent mutations in CBL, PIK3CD, PTPN11, and PPM1J; all of which were expressed at the RNA level (Supplementary Tables 11, 36 and Supplementary Figs. 43 and 44). In contrast to infant MLL-R ALL cases, the majority of the tyrosine kinase/PI3K/RAS pathway mutations in the non-infant MLL-R leukemias were present in the major clone (Supplementary Table 25 and Supplementary Fig. 44). This observation extended to all identified somatic exonic mutations, whereas in infant MLL-R ALLs these mutations are more commonly seen in minor clones (P<0.0001, Supplementary Fig. 45). Non-infant MLL-R leukemias had a significantly higher number of CNAs as compared to infant MLL-R ALL (average 2.6/case versus 1.0/case, P=0.0234) (Supplementary Fig. 46). Deletions in CDKN2A/B were noted in 3/9 ALL cases (33%), but in none of the AML cases. None of the 20 non-infant MLL-R leukemias harbored a focal PAX5 lesion, which is in contrast to MLL-R infant ALL where PAX5 alterations were present in 5/22 cases (23%) (Supplementary Figs. 39, 44 and 47 and Supplementary Tables 37–39). RNAseq identified two novel in-frame non-MLL fusions, SETD2-CCDC12 (SJMLL009) and PABPC1L-YWHAB (SJMLL019). In addition, eight events identified in six cases resulted in out-of-frame fusions, one of which included MLL and four of which included MLL-partner genes (Supplementary Table 17). At the RNA level, a unique gene expression signature was noted in older children with MLL-AFF1 B-lineage disease (Supplementary Fig. 48 and Supplementary Tables 40 and 41).


The landscape of somatic mutations in infant MLL-rearranged acute lymphoblastic leukemias.

Andersson AK, Ma J, Wang J, Chen X, Gedman AL, Dang J, Nakitandwe J, Holmfeldt L, Parker M, Easton J, Huether R, Kriwacki R, Rusch M, Wu G, Li Y, Mulder H, Raimondi S, Pounds S, Kang G, Shi L, Becksfort J, Gupta P, Payne-Turner D, Vadodaria B, Boggs K, Yergeau D, Manne J, Song G, Edmonson M, Nagahawatte P, Wei L, Cheng C, Pei D, Sutton R, Venn NC, Chetcuti A, Rush A, Catchpoole D, Heldrup J, Fioretos T, Lu C, Ding L, Pui CH, Shurtleff S, Mullighan CG, Mardis ER, Wilson RK, Gruber TA, Zhang J, Downing JR, St. Jude Children's Research Hospital–Washington University Pediatric Cancer Genome Proje - Nat. Genet. (2015)

Mutational profiles of infant and non-infant MLL-R leukemia. (a) The number of non-silent SNVs and indels in the dominant leukemia clone affecting annotated genes in infant MLL-R ALL and non-infant MLL-R leukemia. (b) Distribution of somatic SNVs, indels, and CNAs in epigenetic regulatory genes in infant MLL-R ALL and non-infant MLL-R leukemias showing that these genes are significantly more often mutated in non-infant MLL-R leukemia (two-sided Fishers exact test, P=0.04). The black line between SJMLL002 and SJMLL021 indicate the separation between the lymphoblastic and myeloid non-infant leukemias. The only gene mutation that was found not to be expressed at the detection limit of our RNAseq analysis was the one in L3MBTL3.
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Related In: Results  -  Collection

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Figure 4: Mutational profiles of infant and non-infant MLL-R leukemia. (a) The number of non-silent SNVs and indels in the dominant leukemia clone affecting annotated genes in infant MLL-R ALL and non-infant MLL-R leukemia. (b) Distribution of somatic SNVs, indels, and CNAs in epigenetic regulatory genes in infant MLL-R ALL and non-infant MLL-R leukemias showing that these genes are significantly more often mutated in non-infant MLL-R leukemia (two-sided Fishers exact test, P=0.04). The black line between SJMLL002 and SJMLL021 indicate the separation between the lymphoblastic and myeloid non-infant leukemias. The only gene mutation that was found not to be expressed at the detection limit of our RNAseq analysis was the one in L3MBTL3.
Mentions: Although MLL-R occur at a high frequency in infant ALL, this genetic lesion is also seen in older children with ALL or AML39. To compare the MLL-R mutational profile between infants and older children, we performed whole exome sequencing (WES) and SNP array analysis on 20 non-infant MLL-R patients (7–19 years of age, 9 ALLs, 10 AMLs, and 1 case of acute undifferentiated leukemia), as well as RNAseq on 18/20 cases (Supplementary Tables 9–11, 17, 31–32, and Supplementary Figs. 4 and 40). This analysis revealed that the major clone in non-infant MLL-R leukemia harbor a significantly higher number of non-silent somatic SNVs/indels than infant MLL-R ALL (mean 6.5/case versus 1.3/case, P=7.15×10−5, and for expressed genes: mean 3.2/case versus 0.6/case, P=1.6×10−3, Fig. 4a and Supplementary Tables 33 and 34, see Supplementary Table 35 for a mutation summary of all three cohorts). Although there was a trend towards a lower basal mutation rate in infants compared to non-infants (P=0.15), multiple linear regression analysis demonstrated that the significantly higher number of mutations in older children could not be solely attributed to the difference in the basal mutation rates (Supplementary Notes, Supplementary Figs. 41 and 42). This suggests that overt leukemia in older children with MLL-R may require more cooperating mutations. Similar to infants with MLL-R, activating mutations in tyrosine kinase/PI3K/RAS pathways were identified in 50% of the non-infant leukemias, with recurrent mutations in FLT3 (n=3), KRAS (n=3), NRAS (n=3), and non-recurrent mutations in CBL, PIK3CD, PTPN11, and PPM1J; all of which were expressed at the RNA level (Supplementary Tables 11, 36 and Supplementary Figs. 43 and 44). In contrast to infant MLL-R ALL cases, the majority of the tyrosine kinase/PI3K/RAS pathway mutations in the non-infant MLL-R leukemias were present in the major clone (Supplementary Table 25 and Supplementary Fig. 44). This observation extended to all identified somatic exonic mutations, whereas in infant MLL-R ALLs these mutations are more commonly seen in minor clones (P<0.0001, Supplementary Fig. 45). Non-infant MLL-R leukemias had a significantly higher number of CNAs as compared to infant MLL-R ALL (average 2.6/case versus 1.0/case, P=0.0234) (Supplementary Fig. 46). Deletions in CDKN2A/B were noted in 3/9 ALL cases (33%), but in none of the AML cases. None of the 20 non-infant MLL-R leukemias harbored a focal PAX5 lesion, which is in contrast to MLL-R infant ALL where PAX5 alterations were present in 5/22 cases (23%) (Supplementary Figs. 39, 44 and 47 and Supplementary Tables 37–39). RNAseq identified two novel in-frame non-MLL fusions, SETD2-CCDC12 (SJMLL009) and PABPC1L-YWHAB (SJMLL019). In addition, eight events identified in six cases resulted in out-of-frame fusions, one of which included MLL and four of which included MLL-partner genes (Supplementary Table 17). At the RNA level, a unique gene expression signature was noted in older children with MLL-AFF1 B-lineage disease (Supplementary Fig. 48 and Supplementary Tables 40 and 41).

Bottom Line: Our data show that infant MLL-R ALL has one of the lowest frequencies of somatic mutations of any sequenced cancer, with the predominant leukemic clone carrying a mean of 1.3 non-silent mutations.Despite this paucity of mutations, we detected activating mutations in kinase-PI3K-RAS signaling pathway components in 47% of cases.Surprisingly, these mutations were often subclonal and were frequently lost at relapse.

View Article: PubMed Central - PubMed

Affiliation: 1] Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA. [2] Department of Clinical Genetics, Lund University, Lund, Sweden.

ABSTRACT
Infant acute lymphoblastic leukemia (ALL) with MLL rearrangements (MLL-R) represents a distinct leukemia with a poor prognosis. To define its mutational landscape, we performed whole-genome, exome, RNA and targeted DNA sequencing on 65 infants (47 MLL-R and 18 non-MLL-R cases) and 20 older children (MLL-R cases) with leukemia. Our data show that infant MLL-R ALL has one of the lowest frequencies of somatic mutations of any sequenced cancer, with the predominant leukemic clone carrying a mean of 1.3 non-silent mutations. Despite this paucity of mutations, we detected activating mutations in kinase-PI3K-RAS signaling pathway components in 47% of cases. Surprisingly, these mutations were often subclonal and were frequently lost at relapse. In contrast to infant cases, MLL-R leukemia in older children had more somatic mutations (mean of 6.5 mutations/case versus 1.3 mutations/case, P = 7.15 × 10(-5)) and had frequent mutations (45%) in epigenetic regulators, a category of genes that, with the exception of MLL, was rarely mutated in infant MLL-R ALL.

Show MeSH
Related in: MedlinePlus