Protracted dormancy of pre-leukaemic stem cells

Abstract

Cancer stem cells can escape therapeutic kill by adopting a quiescent or dormant state. The reversibility of this condition provides the potential for later recurrence or relapse, potentially many years later. We describe the genomics of a rare case of childhood BCR-ABL1 positive, B cell precursor acute lymphoblastic leukaemia (ALL) that relapsed, with an AML immunophenotype, 22 years after the initial diagnosis, sustained remission and presumed cure. The primary and relapsed leukaemias shared the identical BCR-ABL1 fusion genomic sequence and two identical immunoglobulin gene rearrangements, indicating that the relapse was derivative of the founding clone. All other mutational changes (SNV, CNAs) were distinct in diagnostic or relapse samples. These data provide unambiguous evidence that leukaemia-propagating cells, most probably pre-leukaemic stem cells, can remain covert and silent but potentially reactivatable for more than two decades.

INTRODUCTION

Recurrence or relapse of cancer many years ^1-3 or occasionally decades ⁴ after an initial diagnosis has been frequently recorded. These observations raise difficult issues related to presumptions of cure, risk assessment and monitoring of residual disease. A plausible mechanism for persistent, covert cancer cells during and after treatment is provided by the observation that some cancer stem cells can adapt a reversible quiescent or dormant state in which they are relatively resistant to radiation and chemotherapy ^5-8. However, the assumption is usually made that late recurring cancer is a derivative of the original clone at diagnosis, evidence for which is very limited, with the exception of some acute leukaemias where physiological rearrangement of immunoglobulin genes (IGH/IGK) provide clone-specific markers ^9-11.

MATERIALS AND METHODS

Targeted capture libraries, cloning and sequencing of gene fusions

A cell line, MR-87, was established from the original leukaemic cells of the 4 year old patient and showed the same immunophenotype and karyotype of the diagnostic leukaemic cells. These cells were also shown to express the p190 BCR-ABL1 protein ¹². Illumina paired end libraries covering the entire genomic regions of the BCR, ABL1 and IKZF1 genes were prepared from MR87 cell line DNA (diagnosis) using the Agilent SureSelectXT 2 Custom (1kb-499kb) DNA bait library. The custom libraries were sequenced on a HiSeq2500 to a coverage depth of 99×. Casava software (v1.8, Illumina) was used to make base calls and demultiplex the sequencing data and the genomic fusion breakpoints of BCR-ABL1 and IKZF1 were roughly determined using Burrows-Wheeler Aligner (BWA) and Breakdancer software. The BCR-ABL1 breakpoint fusion was predicted based on the location of read pairs that mapped to the fusion partners and the average fragment size of the capture library (320bp). Using GRCh37.p13, the predicted breakpoint region in BCR was at chr22:23533568 – 23533950 (intron 1), and the breakpoint region in ABL1 was expected at chr9:133608500 – 133608811 (intron 1). A large deletion in IKZF1 (~50kb) was observed between regions chr7:50412887 - 50463541. PCR primers were then designed to span the putative breakpoints using Primer3 plus (www.primer3plus.com/). Primers used for cloning the BCR-ABL1 fusion were: 5′-GTCAAAGCATTTTCCCCTGC and 5′-TCTTGATACTGGGTTGGCTGC and for the IKZF1 deletion were: 5′-GTCCTGGGTTTAAGCTTCAGTTCTCTGCCT and 5′-GGGTTGATAAGGAGGGTTTTGTGTCCCAGT, respectively. Patient specific gene fusions were amplified using AccuPrime^™ Taq DNA Polymerase High Fidelity (Life Technologies) and PCR products sequenced using BigDye Terminator v1.1 and an ABI-3730xl Genetic Analyzer (Applied Biosystems, UK). Sequences were aligned by BLAST (http://blast.ncbi.nlm.nih.gov/Blast.cgi).

Screening for immunoglobulin (IG) and T-cell receptor (TCR) gene rearrangements

DNA was extracted from diagnostic (MR87) and relapse cells (PB and BM). PCR amplification of IG heavy chain variable-diversity-joining (IGH V(D)J; complete and incomplete), IG kappa variable-joining (IGK-VJ), IGK V-kappa deleting element (Kde), intron recombination signal sequence (IRSS)-Kde, IG lambda (IGL), TCR beta (TCRB), TCR gamma (TCRG) and TCR delta gene rearrangements were performed using primers and conditions recommended by the BIOMED-2 Consortium ¹³. The FAM-labelled products were analysed using an ABI 3500 Genetic Analyzer (Applied Biosystems,), clonality was assessed by GeneScan® software (Applied Biosystems) and the results were interpreted in accordance with the EuroClonality/BIOMED-2 guidelines ¹⁴. PCR products were cloned into pCR2.1 (Life), sequenced and analysed as above. Junction analyses were performed using IgBLAST (www.ncbi.nlm.nih.gov/igblast/) and the ImMunoGeneTics database (www.imgt.org/).

Genome-wide copy number analysis

SNP array analysis was carried out using Affymetrix SNP 6.0 arrays according to the manufacturer’s instructions on DNA extracted using standard methods from the diagnostic cell line (MR87) and from relapse bone marrow. Genotyping and generation of QC data was performed in Genotyping Console™ v4.1.4 software (Affymetrix). The sample files were scrutinised for copy number alterations by visual inspection and using Partek Genomics Suite 6.6 software (Partek®, USA). Copy number was determined by normalisation to Partek distributed baseline files which comprise 270 Hapmap files using a genomic segmentation algorithm.

Whole exome sequencing (WES)

Exome capture was performed using the Agilent SureSelect Human All Exon V5 kit following manufacturer’s instructions (Agilent) and sequenced by Illumina paired end sequencing (protocol v1.2). Briefly, DNA was sheared by fragmentation (Covaris), purified using Agencourt AMPure XP beads (Beckman Coulter) and the resulting fragments analysed on an Agilent 2100 Bioanalyzer. Fragment ends were repaired and adaptors ligated to the fragments and the library was purified using beads. After amplification and hybridisation with biotinylated RNA baits, bound genomic DNA was purified with streptavidin coated magnetic Dynabeads (Invitrogen) and re-amplified to include barcoding tags before finally pooling for sequencing on an Illumina HiSeq 2000.

Exome analysis was completed in Oxford Gene Technology’s (OGT, UK) exome pipeline. Briefly, reads were aligned to the human genome reference sequence GRCh37 using BWA 0.6.2. ¹⁵. Local realignment was performed around indels with the Genome Analysis Toolkit (GATK v1.6) IndelRealigner ¹⁶. Optical and PCR duplicates were marked in BAM files using Picard 1.107 (http://picard.sourceforge.net). Original HiSeq base quality scores were recalibrated using GATK TableRecalibration and per-sample variants called with GATK UnifiedGenotyper. Indels and SNVs were hard-filtered according to Broad Institute best-practice guidelines to eliminate false positive calls.

CNV’s, somatic SNV and somatic indels were identified between presentation and relapse samples using VarScan2 ¹⁷. Variant annotation was performed with a modified version of Ensembl Variant Effect Predictor (VEP) ¹⁸.

RESULTS

Clinical and haematological features of case

A brief case report of the patient was already published ¹⁹ and is summarised as follows. A 4 year old boy was diagnosed as having precursor B-cell ALL but with a mixed lympho-myeloid phenotype: positive for myeloperoxidase, CD13⁺, CD10⁺ and CD19⁺. Cytogenetics on leukaemic cells showed 46,XY,9p−,t(9q+;22q−) indicating Ph⁺ pre-B-ALL. RT-PCR confirmed presence of the minor breakpoint (p190) BCR-ABL1 fusion.

The patient was treated with chemotherapy and achieved complete remission. Eight weeks after the diagnosis, he developed a central nervous system relapse which was successfully treated with cranial irradiation and intrathecal drug administration. Three months after the diagnosis, he received a bone marrow transplant (BMT) from his human leucocyte antigen (HLA) identical (non-twin) brother when in the second complete remission (CR). BMT was successful and no major complications were observed.

At the age of 25 years (20 years after BMT) the patient presented with general fatigue. His white blood cell count was 16.7 × 10⁹/l with 7% blasts, and his bone marrow aspirates showed leukaemic cells with a myeloid immunophenotype positive for CD13 and CD33 and negative for CD10 and CD19. The leukaemic cell karyotype was 46,XY,t(9;22)(q34;q11) × 2 plus other complex abnormalities. He was tentatively diagnosed as having a relapse of the initial Ph⁺ pre-B-ALL and received intensive chemotherapy resulting in complete remission. He underwent the second BMT from an HLA-identical unrelated donor but had bone marrow relapse 35 weeks after the second BMT and subsequently died of the disease.

Diagnostic and late relapse clones share an identical BCR-ABL1 fusion sequence

The putative breakpoint regions of the BCR and ABL1 genes were identified by targeted whole genome sequencing of DNA isolated from the cell line (MR87) derived from patient cells at diagnosis. PCR primers were designed 5′ to the putative breakpoint in BCR and 3′ to that in ABL1 and the patient–specific BCR-ABL1 gene fusion was amplified, cloned and sequenced. The breakpoint detected in the BCR gene occurred within intron 1 at GRCh37.p13 position ch22:23533768 and within intron 1 of the ABL1 gene at position ch9:133608599 (Figure 1). The breaks in both BCR and ABL1 are therefore outside the recognised cluster regions described for Ph+ leukaemia ²⁰. The same set of PCR primers were next used to interrogate DNA from PB and BM at relapse and an identical sized fusion product was obtained. Cloning and sequencing of the relapse fusion products proved the BCR-ABL1 fusion sequence to be identical to that present at diagnosis (Figure 1A).

Figure 1. Diagnostic and late relapse clones share an identical BCR-ABL1 fusion sequence with a discordant intra-gene deletion of IKZF1.

A) Upper Panel: PCR primers that span the BCR-ABL1 breakpoint identified in diagnostic material (MR87, CL) were used to interrogate DNA isolated at relapse (BM, PB). An identical product is seen in all patient samples but not in leukaemia controls. Lower Panel: DNA sequence of the BCR-ABL1 fusion and comparison with wild-type BCR and ABL1 gene sequences (GRCh37.p13). The DNA sequence was identical in both diagnostic and relapse samples.

B) Upper Panel: DNA fusion sequence (GRCh37.p13) of the IKZF1 deletion at diagnosis reveals a 50kb deletion between introns 2 and 7. Lower Panel: The deletion/fusion product present at diagnosis (MR87 and CL) is not observed at relapse (BM, PB) or in DNA from leukaemia controls.

Genome-wide copy number analysis

SNP 6.0 analysis on DNA isolated from the diagnostic cell line showed the following recurrent leukaemia CNA: deletion of MTAP, CDKN2A/B, PAX5, 6q14.1 - 6q16.1 and IKZF1. Additionally amplification of MDM2 was noted. Relapse material was discordant for the diagnostic CNA drivers (Table 1), however copy number loss of 9p was demonstrated (including loss of the same genes deleted at diagnosis: CDKN2A/B, MTAP and PAX5) but results clearly demonstrated that this 9p deletion was a re-iterative event with distinct breakpoints to the diagnostic sample (Table S1, S2 and Figures S1A-F, in supplementary material). Potential drivers newly acquired in the relapse material also included deletion of the majority of chromosome 21q, gain of chromosome 20 and deletion of 8p (Table S2).

Table 1. Summary of ‘driver’ CNAs present at diagnosis versus relapse detected by SNP analysis.

	chr	start	end	cytoband	CNA Loss/Gain	Diagnosis	Relapse	Genes (max 3 listed)
1	chr6	78095353	93349377	6q14.1 - 6q16.1	Loss	present	absent	IRAK1BP1, PHIP, SYNCRIP
2	chr7	50389071	50477011	7p12.2	Loss	present	absent	IKZF1
3	chr9	16523946	21901150	9p22.3 - 9p21.3	Loss	present	absent	MLLT3, MTAP, FOCAD
4	chr9	21901150	22347406	9p21.3	Homozygous Loss	present	absent	CDKN2A, CDKN2B
5	chr9	36412035	38493465	9p13.2 - 9p13.1	Loss	present	absent	MELK, PAX5, FRMPD1
6	chr12	68970862	69406845	12q15	Gain	present	absent	RAP1B, NUP107, MDM2
7	chr 7	50389060	50486601	7p12.2	Loss	absent	present	IKZF1
8	chr8	31254	43078119	8p23.3 - 8p11.21	Loss	absent	present	ZNF596, FBXO25, DLGAP2
9	chr9	6988784	21926959	9p24.1 - 9p21.3	Loss	absent	present	MPDZ, MLLT3, MTAP
10	chr9	21926959	22200408	9p21.3	Heterozygous Loss	absent	present	CDKN2A, CDKN2B
11	chr9	22200408	132070825	9p21.3 – 9q34.11	Loss	absent	present	MOB3B, LINGO2, PAX5
12	chr20	61305	62956154	20p13-20q13.33	Gain	absent	present	DEFB125, DEFB126, TOP1
13	chr21	15939316	48096958	21q11.2 - 21q22.3	Loss	absent	present	CHODL,CXADR,NCAM2

Based on NCBI37/hg19 Assembly

Given that deletions in the tumour suppressor gene IKZF1 are considered a driving force of leukaemogenesis, we used targeted sequencing of diagnostic DNA to design PCR primers that spanned the putative boundaries of the 50kb IKZF1 intra-gene deletion. Subsequent PCR produced a ~4kb amplification product that was further cloned and sequenced (Figure 1B). The 5′ breakpoint was determined at GRCh37.p13 position 7:50412893 and the 3′ breakpoint at position 7:50463650 with loss of 50,757bp of DNA and the random insertion of 3 nucleotides (Figure 1B). Using the same primer set, we could not detect a deletion in the IKZF1 gene by conventional PCR or sensitive Q-PCR in PB or BM at relapse (Figure 1B and Figure S2). These data indicate that some genes (IKZF1, CDKN2A) were subject to reiterated CNA in diagnosis and relapse but no CNA was preserved from diagnosis to relapse.

Clonality of immunoglobulin gene rearrangements at diagnosis and relapse

Screening for clonal IG and TCR gene rearrangements to assess clonality was performed on both the diagnostic and relapse DNA using multiplex PCR reactions and ABI GeneScan® profiling. Clonal rearrangements were identified in both IGH VDJ (FR 1 and 2) and IGL VJK reactions (Figure 2 and S3) with weaker clonal rearrangements observed in TCRBB/C and in TRG1 (data not shown). A V(N)JK light chain rearrangement was shown to be identical between diagnosis and relapse (Figure 2) and the two major IGH V(N)D(N)J peaks identified at 294 and 335bp at diagnosis were similarly shown to have identical sequences to the respective minor peaks observed at relapse (Figure S3). However, the two major peaks identified in relapse at 330 and 341bp were not detected in diagnostic material by conventional or Q-PCR (Figure S4). One interpretation of these data is that the ‘founder’ IGH rearrangement present in the diagnostic samples underwent further rearrangement in relapse. Taken together, these data further suggest that the diagnostic and relapse clones may have arisen from a pre-leukaemic progenitor cell already partially committed to the B cell lineage. However, the myeloid or AML immunophenotype seen in relapse indicates that the leukaemia was essentially ‘mixed lympho-myeloid’ and may have arisen in a cell with some myeloid differentiation capacity despite the clonal IGH rearrangements present in the bulk cell progeny.

Figure 2. Clonality of immunoglobulin light chain gene rearrangements at diagnosis and relapse.

Upper Panel: PCR amplifications of IGL V(N)J rearrangements at diagnosis and relapse were assessed by GeneScan® software. Lower Panel: DNA sequence analysis of the major V(N)J rearrangement identified at diagnosis shows an identical sequence to that observed at relapse.

N region insertion is shown in bold italics.

WES analysis

We performed WES on patient DNAs isolated at diagnosis, remission (germline) and relapse. All possible cross-comparisons between these three time points were assessed in the data analyses. In terms of somatic alterations, at diagnosis we identified, prior to filtering, a total of 2189 SNVs and 648 insertions and/or deletions. At relapse we identified 7320 SNVs and 1567 indels.

In further analyses, we highlighted relevant functional alterations. In the diagnostic sample, after filtering the data by read depth (between 30-170×), coding areas only and SNVs predicted to alter protein structure and deleterious/possibly damaging at protein level (VEP-Ensembl), we detected 92 somatic SNVs and 59 indels. We selected those genes with functions known to be associated with cancer of which there were twelve: SNVs; NOTCH2, PIK3CG, IL2RB, BAI3, FREM2 and RERE and indels; UTRN, CDHR3, NCOA5, CABYR, HOTAIR and FOLH1 (Table 2). In the relapse sample after a similar filtration, we identified 156 SNVs and 46 indels and identified ten potential ‘driver’ genes: SNVs; THOC6, VANGL2, THBS1, STAT2, ACY1, and indels; NBEAL1, SMG7, TRIM29, FANCG, FAM186A (Table 2). All 22 genes have previously been shown to play a relevant role in tumourigenesis or have potential to be a ‘driver’ of leukaemogenesis. We confirmed selected heterozygous point mutations or indels by Sanger sequencing, i.e. NOTCH2, HOTAIR, STAT2 and FANCG (data not shown). None were shared between the diagnostic and relapse samples and absent in remission (control, constitutive DNA)

Table 2. Principal mutations detected by whole exome sequencing of the patient DNA at diagnosis and relapse.

	Genes	Diagnosis	Relapse
SNV1	NOTCH2
SNV2	PIK3CG
SNV3	IL2RB
SNV4	BAI3
SNV5	FREM2
SNV6	RERE
Ind1	UTRN
Ind2	CDHR3
Ind3	NCOA5
Ind4	CABYR
Ind5	HOTAIR
Ind6	FOLH1
SV7	THOC6
SV8	VANGL2
SV9	THBS1
SV10	STAT2
SV11	ACY1
Ind7	NBEAL1
Ind8	SMG7
Ind9	TRIM29
Ind10	FANCG
Ind11	FAM186A

Somatic SNV

Somatic Inddel

WT

List of the relevant genes affected by somatic mutations (SNVs and indels) at diagnosis and relapse. The remission (germline) sample was also evaluated and did not harbour any of these mutations thus confirming their somatic/clonal origin. The colours differentiate SNVs (light grey) from indels (dark grey).

DISCUSSION

The identity of shared and clone-specific genotypic sequences in this patient’s diagnostic and very late relapse leukaemia cell population provides unambiguous evidence that the relapse derived, after 22 years, from descendent progeny of the original founder clone (Figure 3). Late relapses derived from the founder diagnostic clones in ALL have been described before ^{9, 10} but this is the longest dormancy interval recorded with the possible exception of a case relapsing after 34 years in which the genetic evidence was very limited ²¹. It is striking that although the BCR-ABL1 fusion gene was identical in the paired diagnostic/relapse samples, all other genetic abnormalities detected by SNP arrays as CNA or by exomic sequencing as SNVs were distinctive although the same gene was in some reiteratively mutated (e.g. CDKN2A, IKZF1). Reiterative CNA have been reported before in ALL ^{22, 23} and the predominant mutational mechanism for these structural changes appears to be driven by the lymphoid recombinases RAG1/2 ²⁴. SNV in ALL have a different mutational mechanism involving APOBEC’s ²⁴. It is unclear if the predominance of CNA as recurrent changes in ALL is a reflection of the relative activity of these different mutational mechanisms, the prevalence of different selective pressures or differential functional impacts of CNA versus SNV on cellular fitness.

Figure 3. Model for the pre-leukaemic origins of very late relapse.

CNA, SNV and indel numbers – distinctive mutations found in diagnostic and relapse clones (numbers 1-13 refer to aberrations noted in Tables 1 and 2).

ALLs have multiple, genetically distinct stem cells at diagnosis ²². Our interpretation of the genomic data on this patient is that the long term surviving stem cells that spawned very late relapse derived from stem cells of a minor clone at diagnosis and most likely from a pre-leukaemic clone that harboured a founder BCR-ABL1 lesion but not other secondary genetic changes (Figure 3). Evidence for such pre-malignant clones in ALL with BCR-ABL or other founder lesions have been provided by comparative genetics of monozygotic twins with discordant ALL ^25-27. Sharing of identical or clonotypic BCR-ABL1 genomic fusions in monozygotic twins with concordant or discordant ALL but discordance of other genetic changes ²⁷ suggests that the BCR-ABL1 fusion in such cases is an early or likely founder or initiation event spawning a pre-leukaemic clone. Limited comparative genetics had previously suggested that some late relapses in ALL might be spawned by persistent pre-leukaemic clones ^{28, 29}. Immunophenotypically or genetically defined pre-leukaemic cells have previously been shown to preferentially survive chemotherapy in ALL ³⁰ and acute myeloblastic leukaemia (AML) ³¹. Recently, Zhang et al ³² reported a relapse after 17 years in a case of acute promyelocytic leukaemia (APML). The comparative genetics in this case was also compatible with the relapse originating from pre-leukaemic stem cells.

Many mechanisms have been proposed to explain protracted clinical dormancy of cancer including balanced proliferation, cell death, non-angiogenic phenotypes, negative signalling within stromal niches maintaining cells out of cycle and immune-surveillance ^{6, 7, 33}. Whatever the prevailing restraints, a late recurrence derived from the original clone requires that cells with self-renewal or stem cell potential survive to re-establish disease. In this respect, the recognised therapeutic resistance of quiescent cancer stem cells and residence in specialised bone marrow niches ³³ provides a basis for their survival in a dormant state as we assume occurred in our patient.

Adopting dormancy as a survival strategy is not unique to cancer stem cells. Normal blood stem cells fluctuate between proliferative and quiescent or out of cycle phases ³⁴. Bacteria ‘hunker down’ or adopt a non-proliferative state when confronted with stressful conditions ³⁵. The capacity of cancer stem cells to avoid lethal therapy by switching to a dormant state can be seen as a legacy of evolutionary programming of protective mechanisms for essential normal stem cells.

The case reported here reflects an extremely rare occurrence and does not conflict with the suggestion that cure in childhood ALL can be operationally defined by remission of four years post cessation of treatment when the risk of relapse is <1% ^{10, 36}.

Although many very late (>20 years) recurrences or relapses of cancer have been recorded, the assumption that this reflects re-awakening of the original clone or one of its subclones requires genetic scrutiny. Provided the diagnostic sample or biopsy is archived, this can be resolved, as in the current case, by comparative genomics.