Gout et al Ultra-mutation targets germline SNPs in an infant leukemia
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Retraction:
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This article should not be cited. We are currently investigating alternative
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constitutional patient DNA from this patient. She was treated upfront by stem
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cell transplantation. The timing of remission sample collection with respect to
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the transplantation requires confirmation. It is plausible the remission sample
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sequenced includes transplanted cells. We apologise for the inconvenience.
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.CC-BY-NC 4.0 International licenseavailable under a
not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
The copyright holder for this preprint (which wasthis version posted May 17, 2018. ; https://doi.org/10.1101/248690doi: bioRxiv preprint
Gout et al Ultra-mutation targets germline SNPs in an infant leukemia
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Recapitulation of human germline coding variation in an ultra-mutated
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infant leukemia
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Alexander M Gout
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, Rishi S Kotecha
2,3,4
, Parwinder Kaur
5,6
, Ana Abad
1
, Bree
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Foley
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, Kim W Carter
1,8
, Catherine H Cole
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, Charles S Bond
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, Ursula R Kees
2
,
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Jason Waithman
7,
*, Mark N Cruickshank
1,
*
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1
Cancer Genomics and Epigenetics Laboratory, Telethon Kids Cancer Centre,
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Telethon Kids Institute, University of Western Australia, Perth, Australia.
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2
Leukaemia and Cancer Genetics Program, Telethon Kids Cancer Centre,
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Telethon Kids Institute, Perth, Australia.
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3
Department of Haematology and Oncology, Princess Margaret Hospital for
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Children, Perth, Australia.
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School of Medicine, University of Western Australia, Perth, Australia.
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5
Personalised Medicine Centre for Children, Telethon Kids Institute, Australia.
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6
Centre for Plant Genetics & Breeding, UWA School of Agriculture &
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Environment.
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Cancer Immunology Unit, Telethon Kids Institute, Perth, Australia.
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McCusker Charitable Foundation Bioinformatics Centre, Telethon Kids
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Institute, Perth, Australia.
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School of Molecular Sciences, The University of Western Australia, Perth,
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Australia.
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* These authors contributed equally to this work. Correspondence and
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requests for materials should be addressed to J.W.
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(Jason.Waithman@telethonkids.org.au) or to M.N.C.
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(Mark.Cruickshank@telethonkids.org.au). Telethon Kids Institute, 100 Roberts
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Road, Subiaco, Western Australia, 6008. Phone: +61 8 9489 7777. Fax: +61
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8 9489 7700.
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Running title: Ultra-mutation targets germline SNPs in an infant leukemia.
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Total number of Figures/Tables: 5 figures and 2 tables.
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.CC-BY-NC 4.0 International licenseavailable under a
not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
The copyright holder for this preprint (which wasthis version posted May 17, 2018. ; https://doi.org/10.1101/248690doi: bioRxiv preprint
Gout et al Ultra-mutation targets germline SNPs in an infant leukemia
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Abstract:
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Mixed lineage leukemia/Histone-lysine N-methyltransferase 2A gene
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rearrangements occur in 80% of infant acute lymphoblastic leukemia, but the
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role of cooperating events is unknown. While infant leukemias typically carry
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few somatic lesions, we identified a case with over 100 somatic point
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mutations per megabase and here report unique molecular features of this
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peculiar case. The patient presented at 82 days of age, one of the earliest
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manifestations of cancer hypermutation recorded. The transcriptional profile
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showed global similarities to canonical cases. Coding lesions were
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predominantly clonal and almost entirely targeting alleles reported in human
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genetic variation databases with a notable exception in the mismatch repair
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gene, MSH2. There were no rare germline alleles or somatic mutations
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affecting proof-reading polymerase genes POLE or POLD1, however there
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was a predicted damaging mutation in the error prone replicative polymerase,
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POLK. The patient’s diagnostic leukemia transcriptome was depleted of rare
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and low-frequency germline alleles due to loss-of-heterozygosity, while
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somatic point mutations targeted low-frequency and common human alleles in
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proportions that offset this discrepancy. Somatic signatures of ultra-mutations
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were highly correlated with germline single nucleotide polymorphic sites
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indicating a common role for 5-methylcytosine deamination, DNA mismatch
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repair and DNA adducts. Thus, we document a novel somatic ultra-mutational
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signature that recapitulates population-scale human genome variation with
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unprecedented precision.
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.CC-BY-NC 4.0 International licenseavailable under a
not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
The copyright holder for this preprint (which wasthis version posted May 17, 2018. ; https://doi.org/10.1101/248690doi: bioRxiv preprint
Gout et al Ultra-mutation targets germline SNPs in an infant leukemia
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Author Summary:
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The mutational burden of human cancer varies widely. Infant cancers typically
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have few somatic alterations. In contrast, some tumours including 16% of
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adult cases and 6% of childhood cases, display an elevated mutation rate due
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to either environmental exposures or genetics. The most highly mutated
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human cancers (“ultra-mutated”) typically involve mutations and/or inherited
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defects in a DNA mismatch repair gene (commonly MSH2, MSH6, MLH1 or
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PMS1) and a proof-reading DNA polymerase gene (either POLE or POLD1).
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Infant leukemias typically carry few somatic lesions, and as a step to
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characterise the combined germline and somatic variations we analysed the
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coding sequences and transcriptomes of six patients’ remission-diagnosis
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samples. Most infant samples showed a “silent” genome with few somatic
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lesions. However, we observed a case diagnosed at 82 days of age with an
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ultra-mutated phenotype - the earliest manifestation on record. The sample
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had a mutation in the DNA-mismatch repair gene, MSH2 but there were no
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co-mutations affecting proof-reading polymerase genes POLE or POLD1. An
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alternative secondary hit, was observed in the replicative error-prone DNA
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polymerase POLK. Remarkably, the somatic ultra-mutations in this patient
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precisely targeted rare and common human germline alleles effectively
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causing a widespread “shuffling” of germline alleles without increasing the
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rare allele burden. Thus, the ultra-mutations in this sample mirror important
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aspects of human genome evolution and represent a novel somatic
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mutational mechanism.
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.CC-BY-NC 4.0 International licenseavailable under a
not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
The copyright holder for this preprint (which wasthis version posted May 17, 2018. ; https://doi.org/10.1101/248690doi: bioRxiv preprint
Gout et al Ultra-mutation targets germline SNPs in an infant leukemia
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Introduction:
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Histone-lysine N-methyltransferase 2A (KMT2A) (also known as Mixed
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lineage leukemia) gene rearrangements (KMT2A-R) at 11q23 occur in infant,
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pediatric, adult and therapy-induced acute leukemias and are associated with
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a poor prognosis. KMT2A-R occurs in around 80% of infant acute
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lymphoblastic leukemia (ALL) and 35-50% of infant acute myeloid leukemia
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(AML) involving more than 60 distinct partner genes
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. KMT2A-R infant ALL
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(iALL) genomes have an exceedingly low somatic mutation burden, with
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recurring mutations in RAS-PI3K complex genes. Compared to wild-type
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KMT2A, the fusion oncoprotein has altered histone-methyltransferase activity,
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causing epigenetic and transcriptional deregulation. While KMT2A-
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oncoproteins are strong drivers of leukemogenesis, several lines of evidence
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suggest that KMT2A-R alone is insufficient for tumor initiation. For example,
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there is significant variability in latency of disease onset in experimental
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models of KMT2A-fusions
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and in patients with KMT2A-R detected in
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neonatal blood spots
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. Furthermore, KMT2A-R acute leukemias
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in children
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are enriched for mutations affecting epigenetic regulatory genes and on
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average harbor more somatic lesions than infants. These observations have
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prompted speculation that iALL is a distinct developmental and genetic entity
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and pre-leukemic transformation occurs in utero, targeting a cell of origin with
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a genetic/epigenetic permissive predisposition
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.
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As a step towards defining cooperating events we performed next-
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generation sequencing on a KMT2A-R iALL patient cohort and integrated the
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data with a larger set of acute leukemias. We investigated the combined
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germline and somatic mutation profiles, identifying a highly mutated specimen
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.CC-BY-NC 4.0 International licenseavailable under a
not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
The copyright holder for this preprint (which wasthis version posted May 17, 2018. ; https://doi.org/10.1101/248690doi: bioRxiv preprint
