• Like T lymphoblastic leukemia, a subset of T lymphoblastic lymphomas shows an early T-cell phenotype.

  • Early T-cell phenotype T lymphoblastic lymphomas show recurrent genomic changes distinct from other cases of T lymphoblastic lymphoma.

Early T-cell precursor phenotype acute lymphoblastic leukemia (ETP-ALL) is a subtype of T-ALL with a unique immunophenotype and genetic abnormalities distinct from conventional T-ALL. A subset of T lymphoblastic lymphoma (T-LLy) also demonstrates the early T-cell precursor immunophenotype and may be a counterpart of ETP-ALL. Unlike ETP-ALL, the incidence, clinical features, and genomic features of ETP-LLy are unknown. We reviewed the immunophenotyping data of 218 T-LLy patients who enrolled in the Children’s Oncology Group AALL0434 clinical trial and identified 9 cases (4%) exhibiting a definitive ETP immunophenotype. We performed single-nucleotide polymorphism array profiling on 9 ETP-LLy and 15 non-ETP T-LLy cases. Compared with non-ETP T-LLy, ETP-LLy showed less frequent deletion of 9p (CKDN2A/B), more frequent deletion of 12p (ETV6) and 1p (RPL22), and more frequent absence of biallelic T-cell receptor γ deletions. Recurrent abnormalities previously described in ETP-ALL such as deletions of 5q and 13q and gain of 6q were not observed in ETP-LLy cases. There were no failures of therapy among the ETP-LLy subtype with a 4-year event-free survival of 100%. Overall, ETP-LLy does not exhibit unifying genetic alterations but shows some distinct genomic features from non-ETP T-LLy suggesting that ETP-LLy may be a distinct entity from non-ETP T-LLy.

T- cell lymphoblastic lymphoma (T-LLy) is an aggressive neoplasm of immature T-cell precursors and represents 25% to 30% of childhood non-Hodgkin lymphoma.1 It is classified as an overlapping entity with T-cell acute lymphoblastic leukemia (T-ALL) in the 2017 World Health Organization classification because they share morphologic and immunophenotypic features and are treated with similar strategies.2 Despite these similarities, clinical and molecular differences have been established suggesting potential pathogenetic differences. T-LLy and T-ALL share many clinical features, often presenting with an extramedullary mass in the mediastinum and/or lymph nodes. T-ALL by definition displays primary bone marrow involvement (defined as >25% bone marrow blasts).2 Genomic and gene expression studies have shown that T-LLy and T-ALL have different transcriptional and genetic characteristics.3-5 For example, genes involved in chemotactic responses and angiogenesis are differentially expressed5 and a copy number gain on chromosome 22q including the PIM3 oncogene is specifically found in T-ALL. However, the genomic abnormalities of T-LLy are not well-characterized because of the lack of fresh or frozen samples required for most genomic studies.

Early T-cell precursor acute lymphoblastic leukemia (ETP-ALL) is a subtype of T-ALL that shows an early T-cell precursor immunophenotype (CD1a, CD8, CD5 or weakly positive, CD34/myeloid antigen positive).2,6 Initial reports suggested that ETP-ALL was a high risk T-ALL subset with poor survival, but outcomes are comparable to non-ETP T-ALL in more recent studies.7-9 ETP-ALL demonstrates genetic abnormalities distinct from conventional T-ALL including less frequent deletions of CDKN2A/B and more frequent absence of biallelic T-cell receptor (TCR) γ deletion (ABD).10-13 ETP-ALL also exhibits some genetic abnormalities also observed in acute myeloid leukemia with less frequent NOTCH1 mutations; frequent mutations in FLT3, DNMT3A, RAS, and IDH genes; and 5q and 13q deletions.14,15 The World Health Organization 2017 classification of ALL included ETP-ALL as a provisional entity.2 A subset of T-LLy with an ETP immunophenotype has been described, suggesting that there may be an early T-cell precursor lymphoblastic lymphoma (ETP-LLy) counterpart of ETP-ALL.16 Unlike ETP-ALL, the incidence, clinical features, and genomic features of ETP-LLy are unknown.

In the present study, we sought to assess the incidence of ETP-LLy among a large cohort of T-LLy patients treated on the Children’s Oncology Group (COG) AALL0434 trial,17,18 and to compare the copy number profiles of ETP-LLy and non-ETP T-LLy using DNA isolated from archival formalin-fixed, paraffin-embedded (FFPE) samples. Our study provides an initial understanding of the genetic landscape of ETP-LLy and indicates that the underlying pathogenic mechanisms of ETP-LLy may differ from non-ETP T-LLy.

COG AALL0434 was a phase 3 trial developed for children, adolescents, and young adults 1 to 30.99 years old with T-ALL and T-LLy. AALL0434 was approved by the National Cancer Institute, Cancer Therapy Evaluation Program, Food and Drug Administration, and the Pediatric Central institutional review board, and by institutional review boards at each participating center. In accordance with the Declaration of Helsinki, informed consent/assent was obtained before study entry. The details and results of AALL0434 have been reported previously.18-21 

Central pathology review of immunophenotyping data, including flow cytometry and immunohistochemistry, was performed for all T-LLy patients enrolled in AALL0434 to identify ETP cases according to the definition published by Costain-Smith et al.6 Cases were considered ETP if they were CD1a, CD8, CD5 or weak, and expressed at least 1 of the following stem/myeloid markers: CD34, CD13, CD33, CD117. Non-ETP T-LLy cases selected for comparison were required to express CD1a, CD5, and CD8. Clinical parameters including patient age, sex, and Murphy stage were extracted, and cytogenetic data were reviewed when available. The institutional review board of the University of Utah approved this study, and use of COG specimens was approved under study number ANHL17B1-Q.

Unstained slides leftover from central pathology review were used for DNA isolation. An hematoxylin and eosin stain was reviewed on each case to verify at least 80% tumor cells in sections. FFPE tissue from 10 slides per case was scraped into tubes, and DNA was isolated using the RecoverAll Total Nucleic Acid Isolation kit (Ambion/Applied Biosystems, Austin, TX) and quantitated with the PicoGreen assay (Invitrogen).

Genomic microarray hybridization was performed using OncoScan FFPE molecular inversion probe single-nucleotide polymorphism assay (MIP SNP, Affymetrix/ThermoFisher, Santa Clara, CA). The MIP SNP array was performed as previously described.22,23 Analysis was performed using Nexus copy number software version (version 8.0; BioDiscovery, El Segundo, CA) and Chromosome Analysis Suite (version 3.3; Applied Biosystems, Santa Clara, CA). Data that passed quality control criteria of the array (MAPD value < 0.6) were analyzed using Nexus Copy Number software and Chromosome Analysis Suite with NCBI build 37.0 of the human genome. The SNP-TuScan segmentation algorithm and default settings for significance and number of probes per segment were used. Minimal threshold setting of log2ratio for absence of biallelic ABD was −1.5 and a minimum of 5 probes per segment were required to determine the presence of ABD. Both number and size of copy number aberrations (CNAs) were used to measure the level of genomic instability in non-ETP T-LLy and ETP-LLy.6 The SNP array data have been deposited in NCBI's Gene Expression Omnibus24 and are accessible through GEO Series accession number GSE168884 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE168884).

Pairwise comparisons were made using the Fisher’s exact test, and continuous variable were comparted using the t test. Two-tailed P values are reported and were considered significant when P < .05. Survival analysis was performed using Kaplan-Meier curves.

A total of 24 patient samples were analyzed. Nine ETP-LLy cases were identified using the criteria previously presented, and 15 non-ETP-LLy cases were randomly selected for comparison from among the remaining cases with non-ETP phenotypes and adequate tissue.

The clinical characteristics of the T-LLy patients are shown in supplemental Table 1. The mean age was 10.7 years (range, 1-23) with a male:female ratio of 2.0 for all 24 patients in the study. Patients were classified as Murphy stage 2 (n = 1), 3 (n = 9), or 4 (n = 9); staging data were not available on 5 patients.

A subset of T-LLy shows an ETP phenotype

A total of 9/218 T-LLy cases (4%) showed a definitive ETP phenotype as defined in the methods section (complete immunophenotyping data in supplemental Table 2). An additional 15 non-ETP cases were selected for comparison. There were no differences between ETP and non-ETP cases in age (10.3 vs 10.9, P = .8), male:female ratio (1.25 vs 2.75, P = .4), or stage (P = .35). In addition to the defined differences in immunophenotype, fewer ETP cases expressed CD2 (3/9 vs 13/15, P = .021) or CD4 (0/9 vs 14/15, P < .0001) than non-ETP cases.

Similarities and differences in the genetics lesions between ETP-LLy and non-ETP T-LLy

MIP SNP array was performed on the 24 cases (9 ETP-LLy and 15 non-ETP T-LLy) and identified CNAs and copy-neutral loss-of-heterozygosity (CN-LOH) (Figure 1). CNAs and/or CN-LOH were identified in 8 of 9 ETP-LLy cases and in 15/15 non-ETP T-LLy cases. The genetic lesions found by MIP SNP array for all 24 cases, along with cytogenetic results available in a subset of cases, are listed in Table 1. Genetic lesions observed in 2 or more ETP and/or non-ETP T-LLy cases were considered recurrent abnormalities and are summarized in Table 2. ETP-LLy cases showed significantly less frequent 9p deletion/CN-LOH than non-ETP T-LLy (4/9, 44% vs 14/15, 93%, P = .015; Figure 2A). All of the 9p deletion/CN-LOH lesions except case 21 include both CDKN2A and CDKN2B genes (Figure 2B; Table 1). The 9p deletion in case 21 (chr9: 21901262-21971430, hg19) includes exons 2-3 of the CDKN2A gene (NM_058195) but not the CDKN2B gene. Deletions of 12p including the ETV6 gene were only observed in ETP-LLy (3/9, 33% in ETP-LLy vs 0/15, 0% in non-ETP T-LLy, P = .042; Figure 2C-D). The minimal common deleted region on 12p (chr12: 9c512c809-25c551,025, hg19; Figure 2D; Table 1) contains the ETV6 gene. Deletions of 1p including the RPL22 gene were only observed in ETP-LLy (4/9, 44% in ETP-LLy vs 0/15, 0% in non-ETP T-LLy, P = .012; Figure 2E-F). The minimal common deleted region on 1p (chr1: 3c921c449-7c050c061, hg19) seen in case 23 includes the RPL22 gene (Figure 2F; Table 1).

Deletions of the TCR gene regions are a normal part of TCR rearrangement and can be detected by SNP array in a clonal population. ABD at 7p14.1 is more frequent in ETP-LLy compared with non-ETP T-LLy (8/9, 88.9% in ETP-LLy vs 5/15, 33.3% in non-ETP T-LLy, P = .013).

Focal PHF6 deletions on Xq and gain of NUP214-ABL1 fusion on 9q were observed together in 2 cases, 1 non-ETP T-LLy case (case 11) and 1 ETP-LLy case (case 23) (Tables 1 and 2). Two non-ETP T-LLy cases (cases 14 and 15) were noted to have CHIC2 deletions. CHIC2 deletions result in FIP1L1-PDGFRA fusion and upregulated tyrosine kinase activity. They have been described in chronic eosinophilia as well as T/myeloid proliferations that can present as acute myeloid leukemia, T-LLy, or both, which are often associated with eosinophilia.2 Neither of the cases showed increased eosinophils in the blood (0.7 and 0.2 k/µL, respectively) or lymphoma tissue; however, the bone marrow pathology report for case 14 did note 17% eosinophils in the aspirate smear, whereas case 15 had 6%. A myeloid leukemia component was not reported in either case.

Previous SNP array analysis showed significantly more CNAs in ETP-ALL compared with non-ETP T-ALL, suggesting a higher genomic instability in ETP-ALL.6 In our study, ETP-LLy cases showed a trend but not significantly more or larger CNAs than the non-ETP T-LLy cases (Table 3).

Figure 1.

Summary of copy number aberrations (CNAs). (A-B) and copy-neutral loss-of-heterozygosity (CN-LOH) (C-D) in ETP-LLy (A,C) and non-ETP T-LLy (B,D). In panels A and B, losses are to the left and gains are to the right, and the amplitude reflects the incidence.

Figure 1.

Summary of copy number aberrations (CNAs). (A-B) and copy-neutral loss-of-heterozygosity (CN-LOH) (C-D) in ETP-LLy (A,C) and non-ETP T-LLy (B,D). In panels A and B, losses are to the left and gains are to the right, and the amplitude reflects the incidence.

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Figure 2.

Comparison of frequency and distributionof 9p, 12p, and 1p deletions in ETP-LLy and non-ETP T-LLy. (A,C,E) Frequency, (B,D,F) distribution.

Figure 2.

Comparison of frequency and distributionof 9p, 12p, and 1p deletions in ETP-LLy and non-ETP T-LLy. (A,C,E) Frequency, (B,D,F) distribution.

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Table 1.

Complete list of copy number abnormalities and loss of heterozygosity by SNP array for each case

Case no.Chromosome regionCytobandEventLength (Mb)Cytogenetic study
chr9:204c738-36c232,413 p24.3-p13.3 CN-LOH 36.03 NA 
chr9:21c778,976-22c081,850 p21.3 Homozygous deletion 0.30  
chr9:133c510,616-133c730,353 q34.12 Deletion 0.22  
chr11:192c764-51c575,951 p15.5-p11.12 CN-LOH 51.38  
chr14:22c922,369-36c982,350 q11.2-q13.3 Deletion 14.06  
chr17:37c291,349-80c263,427 q12-q25.3 CN-LOH 42.97  
chr9:204c738-23c386,738 p24.3-p21.3 CN-LOH 23.18 NA 
chr9:21c856,470-22c176,560 p21.3 Homozygous deletion 0.32  
chr10:0-36c046,475 p15.3-p11.21 Gain 36.05  
chr10:89c617,344-90c167,065 q23.31 High copy gain, CN = 4 0.55  
chr14:98c086,294-99c793,689 q32.2 Gain 1.71  
chrX:0-155c270,560 p22.33-q28 Deletion 155.27  
chr9:204c738-27c123,260 p24.3-p21.2 CN-LOH 26.92 46,XY,t1,14(32P;q11.2)[6]/46XY[9] (TAL1-TCR fusion) 
chr9:21c331,119-22c549,702 p21.3 Homozygous deletion 1.22  
chr5:38c139-180c698,312 p15.33-q35.3 Gain 180.66 NA 
chr9:19c277,320-21c853,221 p22.1-p21.3 Deletion 2.58  
chr9:21c856,470-22c004,153 p21.3 Homozygous deletion 0.15  
chr9:22c004,669-23c897,432 p21.3 Deletion 1.89  
chr20:69c094-15c687,866 p13-p12.1 Gain 15.62  
chr20:15c691,240-15c792,451 p12.1 Gain 0.10  
chr20:15c795,175-62c912,463 p12.1-q13.33 Gain 47.12  
chr6:135c483,742-135c754,471 q23.3 High copy gain, CN = 4 0.27 47,XY,t11,19(q23;p13.3), +der(19)t11,19[5]/46,XY[21]; FISH positive for MLL rearrangement in 7.5% cells 
chr9:204c738-39c184,065 p24.3-p13.1 CN-LOH 38.98  
chr10:607c980-718c912 p15.3 Deletion 0.11  
chr11:118c411,424-134c938,847 q23.3-q25 Gain 16.53  
chr13:32c929,387-32c952,164 q13.1 Gain 0.02  
chr19:6c585c298-23c460,785 p13.3-p12 Gain 16.88  
chr19:28c462,580-59c093,239 q11-q13.43 Gain 30.63  
chrX:154c979,673-155c219,364 q28 Gain 0.24  
chr5:48c877,508-180c915,260 q11.1-q35.3 CN-LOH 132.04 NA 
chr9:204c738-21c951,040 p24.3-p21.3 Deletion 21.75  
chr9:21c953,099-25c029,497 p21.3 Homozygous deletion 3.08  
chr9:25c049,865-27c722,059 p21.3-p21.2 Gain 2.67  
chr13:48c984,722-49c065,037 q14.2 Homozygous deletion 0.08  
chr14:36c649,246-36c949,593 q13.3 Deletion 0.30  
chrX:154c979,673-155c219,364 q28 Deletion 0.24  
chr4:52c657,621-191c154,276 q11-q35.2 Deletion 138.50 FISH positive for nullisomy of CDKN2A (9p21) gene in 88% cells; karyotype NA 
chr8:0-146c364,022 p23.3-q24.3 Gain 146.36  
chr9:11c311,712-13c036,747 p23 Deletion 1.73  
chr9:21c242,161-21c813,718 p21.3 Deletion 0.57  
chr9:21c816,528-22c655,723 p21.3 Homozygous deletion 0.84  
chr9:22c669,166-23c694,188 p21.3 Deletion 1.03  
chr13:19c084,823-115c103,150 q11-q34 Gain 96.02  
chr15:22c752,399-102c397,317 q11.2-q26.3 CN-LOH 79.64  
chr17:0-81c195,210 p13.3-q25.3 CN-LOH 81.20  
chr19:247c232-10c976,405 p13.3-p13.2 CN-LOH 10.73  
chr21:9c648c315-48c097,610 p11.2-q22.3 Gain 38.45  
chr4:126c144,980-191c154,276 q28.1-q35.2 CN-LOH 65.01 FISH negative for BCR-ABL, karyotype NA 
chr9:204c738-33c282,392 p24.3-p13.3 CN-LOH 33.08  
chr9:21c901,263-21c993,964 p21.3 Homozygous deletion 0.09  
chr16:3c892c461-4c518c754 p13.3 Deletion 0.63  
chr9:62c209-19c471,279 p24.3-p22.1 CN-LOH 19.41 NA 
chr9:19c628,633-32c741,593 p22.1-p21.1 Deletion 13.11  
chr11:127c117,212-129c553,078 q24.2-q24.3 Deletion 2.44  
10 chr9:204c738-36c489,161 p24.3-p13.2 CN-LOH 36.28 NA 
chr9:21c827,992-22c008,313 p21.3 Homozygous deletion 0.18  
11 chr2:144c545,138-243c052,331 q22.3-q37.3 CN-LOH 98.51 NA 
chr2:213c584,595-214c009,831 q34 Deletion 0.43  
chr9:21c901,263-21c993,468 p21.3 Homozygous deletion 0.09  
chr9:21c993,964-22c098,619 p21.3 Deletion 0.10  
chr9:133c719,421-134c094,802 q34.12-q34.13 Gain 0.38  
chr13:48c984,722-49c065,037 q14.2 Homozygous deletion 0.08  
chr13:50c652,628-51c516,305 q14.2-q14.3 Deletion 0.86  
chrX:130c973,820-134c581,228 q26.2-q26.3 Deletion 3.61  
12 chr9:131c468,740-133c828,128 q34.11-q34.12 Deletion 2.36 NA 
13 chr5:162c623,390-170c762,448 q34-q35.1 Deletion 8.14 NA 
chr9:20c678,439-21c987,472 p21.3 Deletion 1.31  
chr9:21c988,896-22c207,037 p21.3 Homozygous deletion 0.22  
chr11:114c990,423-118c489,708 q23.3 CN-LOH 3.50  
chr14:22c187,584-107c282,024 q11.2-q32.33 CN-LOH 85.09  
14 chr4:54c296,381-55c130,682 q12 Deletion 0.83 Normal karyotype 
chr9:204c738-39c184,065 p24.3-p13.1 CN-LOH 38.98  
chr9:21c928,654-22c114,495 p21.3 Deletion 0.19  
chrX:44c810,604-44c896,206 p11.3 Homozygous deletion 0.09  
15 chr4:54c324,930-55c102,425 q12 Deletion 0.78 NA 
chr4:55c105,182-64c560,949 q12-q13.1 Deletion 9.46  
chr4:64c573,303-83c148,663 q13.1-q21.22 Deletion 18.58  
chr4:83c164,184-93c288,641 q21.22-q22.1 Deletion 10.12  
chr4:92c607,449-191c154,276 q22.1-q35.2 CN-LOH 98.55  
chr6:135c293,365-135c754,471 q23.3 High copy gain, CN = 4 0.46  
chr7:92c245,458-92c471,899 q21.2 High copy gain, CN = 4 − 5 0.23  
chr9:204c738-39c184,065 p24.3-p13.1 CN-LOH 38.98  
chr9:21c965,073-22c014,524 p21.3 Homozygous deletion 0.05  
chr9:80c446,364-80c704,731 q21.2 High copy gain, CN = 4 − 5 0.26  
chr11:128c157,643-128c615,486 q24.3 Gain 0.46  
chr12:11c795,269-12c059,452 p13.2 Gain 0.26  
chr13:48c885,423-49c262,256 q14.2 Gain 0.38  
chr14:98c100,176-100c100,128 q32.2 Gain 2.00  
chr15:56c642,839-58c955,123 q21.3 Gain 2.31  
16 chr11:79c517,863-93c209,472 q14.1-q21 Deletion 13.69 46,XX,t7,12(p13;p13), ?add17(p11.2)[16]/46,XX[11] 
17 chr1:202c643,208-249c212,878 q32.1-q44 Gain 46.57 51,XY,+5,del5(q31),+6, +del9(p13),?inv9(p24q21)x2, der(11)t1,11(q32;q?230,+18, +19[9]; FISH positive for 9p21 homozygous deletion in 89% cells; negative for MLL rearrangement and BCR-ABL fusion. 
chr5:38c139-128c975,230 p15.33-q23.3 Gain 128.94  
chr5:128c846,774-180c698,312 q23.3-q35.3 CN-LOH 51.85  
chr6:204c909-31c553,468 p25.3-p21.33 Gain 31.35  
chr6:31c555,130-32c162,418 p21.33-p21.32 Gain 0.61  
chr6:32c167,778-170c913,051 p21.32-q27 Gain 138.75  
chr8:138c891,978-146c292,734 q24.23-q24.3 Gain 7.40  
chr9:0-12c042,349 p24.3-p23 CN-LOH 12.04  
chr9:12c054,659-13c345,642 p23 Homozygous deletion 1.29  
chr9:13c354,725-21c585,658 p23-p21.3 CN-LOH 8.23  
chr9:21c604,067-24c075,082 p21.3 Homozygous deletion 2.47  
chr9:24c044,951-38c802,685 p21.3-p13.1 CN-LOH 14.76  
chr9:68c170,421-141c054,761 q13-q34.3 Gain 72.88  
chr14:95c161,449-107c282,024 q32.13-q32.33 Gain 12.12  
chr18:0-78c077,248 p11.32-q23 Gain 78.08  
chr19:0-59c128,983 p13.3-q13.43 Gain 59.13  
18 Normal female    NA 
19 chr1:754c192-8c788c907 p36.33-p36.23 Deletion 8.03 NA 
chr1:91c967,341-99c114,927 p22.2-p21.3 Deletion 7.15  
chr8:172c417-17c835,685 p23.3-p22 Deletion 17.66  
chr10:89c432,286-90c306,376 q23.2-q23.31 Deletion 0.87  
chr11:28c057,957-49c688,837 p14.1-p11.12 Deletion 21.63  
chr12:189c400-25c551,025 p13.33-p12.1 Deletion 25.36  
chr12:27c498,107-32c164,030 p11.23-p11.21 Deletion 4.67  
chr17:400c959-1c461c125 p13.3 Gain 1.06  
chrX:41c201,762-41c531,564 p11.4 Homozygous deletion 0.33  
chrX:42c869,649-44c344,324 p11.3 Homozygous deletion 1.47  
chrX:45c481,094-48c206,911 p11.3-p11.23 Gain 2.73  
chrX:50c817,478-52c695,241 p11.22 Homozygous deletion 1.88  
chrX:154c979,673-155c219,364 q28 Gain 0.24  
20 chr6:108c974,746-110c936,144 q21 Deletion 1.96 NA 
chr12:189c400-29c877,262 p13.33-p11.22 Deletion 29.69  
21 chr9:148c341-21c900,510 p24.3-p21.3 CN-LOH 21.75 NA 
chr9:21c900,511-21c971,583 p21.3 Homozygous deletion 0.07  
chr9:21c971,584-34c406,287 p21.3-p13.3 CN-LOH 12.43  
22 chr1:754c192-33c899,167 p36.33-p35.1 Deletion 33.14 NA 
chr4:58c592,202-190c915,650 q12-q35.2 Deletion 132.32  
chr5:38c139-24c037,074 p15.33-p14.2 Deletion 24.00  
chr5:70c306,678-180c698,312 q13.2-q35.3 Deletion 110.39  
chr7:41c421-52c432,938 p22.3-p12.1 Deletion 52.39  
chr9:4c304c915-21c255,150 p24.2-p21.3 Deletion 16.95  
chr9:21c265,500-25c891,012 p21.3-p21.2 Homozygous deletion 4.63  
chr12:9c512c809-30c667,228 p13.31-p11.22 Deletion 21.15  
chr13:36c912,708-115c103,150 q13.3-q34 Deletion 78.19  
chr16:83c887-27c690,168 p13.3-p12.1 Deletion 27.61  
chr18:26c057,437-78c007,784 q12.1-q23 Gain 51.95  
23 tetraploidy    NA 
chr1:3c921c449-7c050c061 p36.32-p36.31 Deletion, CN = 2 3.13  
chr1:23c103,620-24c108,104 p36.12-p36.11 Deletion, CN = 2 1.00  
chr1:114c594,372-115c470,556 p13.2 Deletion, CN = 2 0.88  
chr2:54c374,691-55c005,224 p16.2-p16.1 Deletion, CN = 2 0.63  
chr5:133c415,731-134c917,467 q31.1 Deletion, CN = 2 1.50  
chr6:0-26c382,744 p25.3-p22.2 CN-LOH, CN = 4 26.38  
chr8:33c078,287-33c503,454 p12 Deletion, CN = 2 0.43  
chr9:30c001,529-30c721,717 p21.1 Deletion, CN = 2 0.72  
chr9:133c618,461-134c097,558 q34.12-q34.13 High copy gain, CN = 6 0.48  
chr10:104c369,298-104c562,842 q24.32 Deletion, CN = 2 0.19  
chr11:103c091,553-114c475,360 q22.3-q23.2 Deletion, CN = 2 11.38  
chr12:17c200,436-18c268,880 p12.3 Deletion, CN = 2 1.07  
chr12:110c067,819-111c370,885 q24.11 Deletion, CN = 2 1.30  
chr12:111c370,885-111c911,916 q24.11-q24.12 Homozygous deletion, CN = 0 0.54  
chr12:111c911,916-112c035,561 q24.12 Deletion, CN = 2 0.12  
chr14:91c600,426-94c111,212 q32.11-q32.12 Deletion, CN = 2 2.51  
chr16:0-2c210c796 p13.3 Deletion, CN = 2 2.21  
chr16:7c299c668-8c301c002 p13.3-p13.2 Deletion, CN = 2 1.00  
chr17:27c957,832-29c631,473 q11.2 Deletion, CN = 2 1.67  
chr17:29c631,473-29c897,502 q11.2 Homozygous deletion, CN = 0 0.27  
chr17:29c897,502-30c692,775 q11.2 Deletion, CN = 2 0.80  
chr18:76c375,122-77c458,776 q23 Deletion, CN = 2 1.08  
chr20:49c176,050-53c504,956 q13.13-q13.2 Deletion, CN = 2 4.33  
chr22:37c543,717-39c369,251 q12.3-q13.1 Deletion, CN = 2 1.83  
chrX:133c432,498-134c242,874 q26.2-q26.3 Deletion, CN = 2 0.81  
24 chr1:754c192-9c617c682 p36.33-p36.22 Deletion 8.86 NA 
chr2:42c280,854-50c636,065 p21-p16.3 Deletion 8.36  
chr9:204c738-38c495,131 p24.3-p13.1 Deletion 38.29  
chr9:68c170,421-141c054,761 q13-q34.3 Gain 72.88  
chr12:189c400-6c771c877 p13.33-p13.31 Gain 6.58  
chrX:154c979,673-155c219,364 q28 Gain 0.24  
Case no.Chromosome regionCytobandEventLength (Mb)Cytogenetic study
chr9:204c738-36c232,413 p24.3-p13.3 CN-LOH 36.03 NA 
chr9:21c778,976-22c081,850 p21.3 Homozygous deletion 0.30  
chr9:133c510,616-133c730,353 q34.12 Deletion 0.22  
chr11:192c764-51c575,951 p15.5-p11.12 CN-LOH 51.38  
chr14:22c922,369-36c982,350 q11.2-q13.3 Deletion 14.06  
chr17:37c291,349-80c263,427 q12-q25.3 CN-LOH 42.97  
chr9:204c738-23c386,738 p24.3-p21.3 CN-LOH 23.18 NA 
chr9:21c856,470-22c176,560 p21.3 Homozygous deletion 0.32  
chr10:0-36c046,475 p15.3-p11.21 Gain 36.05  
chr10:89c617,344-90c167,065 q23.31 High copy gain, CN = 4 0.55  
chr14:98c086,294-99c793,689 q32.2 Gain 1.71  
chrX:0-155c270,560 p22.33-q28 Deletion 155.27  
chr9:204c738-27c123,260 p24.3-p21.2 CN-LOH 26.92 46,XY,t1,14(32P;q11.2)[6]/46XY[9] (TAL1-TCR fusion) 
chr9:21c331,119-22c549,702 p21.3 Homozygous deletion 1.22  
chr5:38c139-180c698,312 p15.33-q35.3 Gain 180.66 NA 
chr9:19c277,320-21c853,221 p22.1-p21.3 Deletion 2.58  
chr9:21c856,470-22c004,153 p21.3 Homozygous deletion 0.15  
chr9:22c004,669-23c897,432 p21.3 Deletion 1.89  
chr20:69c094-15c687,866 p13-p12.1 Gain 15.62  
chr20:15c691,240-15c792,451 p12.1 Gain 0.10  
chr20:15c795,175-62c912,463 p12.1-q13.33 Gain 47.12  
chr6:135c483,742-135c754,471 q23.3 High copy gain, CN = 4 0.27 47,XY,t11,19(q23;p13.3), +der(19)t11,19[5]/46,XY[21]; FISH positive for MLL rearrangement in 7.5% cells 
chr9:204c738-39c184,065 p24.3-p13.1 CN-LOH 38.98  
chr10:607c980-718c912 p15.3 Deletion 0.11  
chr11:118c411,424-134c938,847 q23.3-q25 Gain 16.53  
chr13:32c929,387-32c952,164 q13.1 Gain 0.02  
chr19:6c585c298-23c460,785 p13.3-p12 Gain 16.88  
chr19:28c462,580-59c093,239 q11-q13.43 Gain 30.63  
chrX:154c979,673-155c219,364 q28 Gain 0.24  
chr5:48c877,508-180c915,260 q11.1-q35.3 CN-LOH 132.04 NA 
chr9:204c738-21c951,040 p24.3-p21.3 Deletion 21.75  
chr9:21c953,099-25c029,497 p21.3 Homozygous deletion 3.08  
chr9:25c049,865-27c722,059 p21.3-p21.2 Gain 2.67  
chr13:48c984,722-49c065,037 q14.2 Homozygous deletion 0.08  
chr14:36c649,246-36c949,593 q13.3 Deletion 0.30  
chrX:154c979,673-155c219,364 q28 Deletion 0.24  
chr4:52c657,621-191c154,276 q11-q35.2 Deletion 138.50 FISH positive for nullisomy of CDKN2A (9p21) gene in 88% cells; karyotype NA 
chr8:0-146c364,022 p23.3-q24.3 Gain 146.36  
chr9:11c311,712-13c036,747 p23 Deletion 1.73  
chr9:21c242,161-21c813,718 p21.3 Deletion 0.57  
chr9:21c816,528-22c655,723 p21.3 Homozygous deletion 0.84  
chr9:22c669,166-23c694,188 p21.3 Deletion 1.03  
chr13:19c084,823-115c103,150 q11-q34 Gain 96.02  
chr15:22c752,399-102c397,317 q11.2-q26.3 CN-LOH 79.64  
chr17:0-81c195,210 p13.3-q25.3 CN-LOH 81.20  
chr19:247c232-10c976,405 p13.3-p13.2 CN-LOH 10.73  
chr21:9c648c315-48c097,610 p11.2-q22.3 Gain 38.45  
chr4:126c144,980-191c154,276 q28.1-q35.2 CN-LOH 65.01 FISH negative for BCR-ABL, karyotype NA 
chr9:204c738-33c282,392 p24.3-p13.3 CN-LOH 33.08  
chr9:21c901,263-21c993,964 p21.3 Homozygous deletion 0.09  
chr16:3c892c461-4c518c754 p13.3 Deletion 0.63  
chr9:62c209-19c471,279 p24.3-p22.1 CN-LOH 19.41 NA 
chr9:19c628,633-32c741,593 p22.1-p21.1 Deletion 13.11  
chr11:127c117,212-129c553,078 q24.2-q24.3 Deletion 2.44  
10 chr9:204c738-36c489,161 p24.3-p13.2 CN-LOH 36.28 NA 
chr9:21c827,992-22c008,313 p21.3 Homozygous deletion 0.18  
11 chr2:144c545,138-243c052,331 q22.3-q37.3 CN-LOH 98.51 NA 
chr2:213c584,595-214c009,831 q34 Deletion 0.43  
chr9:21c901,263-21c993,468 p21.3 Homozygous deletion 0.09  
chr9:21c993,964-22c098,619 p21.3 Deletion 0.10  
chr9:133c719,421-134c094,802 q34.12-q34.13 Gain 0.38  
chr13:48c984,722-49c065,037 q14.2 Homozygous deletion 0.08  
chr13:50c652,628-51c516,305 q14.2-q14.3 Deletion 0.86  
chrX:130c973,820-134c581,228 q26.2-q26.3 Deletion 3.61  
12 chr9:131c468,740-133c828,128 q34.11-q34.12 Deletion 2.36 NA 
13 chr5:162c623,390-170c762,448 q34-q35.1 Deletion 8.14 NA 
chr9:20c678,439-21c987,472 p21.3 Deletion 1.31  
chr9:21c988,896-22c207,037 p21.3 Homozygous deletion 0.22  
chr11:114c990,423-118c489,708 q23.3 CN-LOH 3.50  
chr14:22c187,584-107c282,024 q11.2-q32.33 CN-LOH 85.09  
14 chr4:54c296,381-55c130,682 q12 Deletion 0.83 Normal karyotype 
chr9:204c738-39c184,065 p24.3-p13.1 CN-LOH 38.98  
chr9:21c928,654-22c114,495 p21.3 Deletion 0.19  
chrX:44c810,604-44c896,206 p11.3 Homozygous deletion 0.09  
15 chr4:54c324,930-55c102,425 q12 Deletion 0.78 NA 
chr4:55c105,182-64c560,949 q12-q13.1 Deletion 9.46  
chr4:64c573,303-83c148,663 q13.1-q21.22 Deletion 18.58  
chr4:83c164,184-93c288,641 q21.22-q22.1 Deletion 10.12  
chr4:92c607,449-191c154,276 q22.1-q35.2 CN-LOH 98.55  
chr6:135c293,365-135c754,471 q23.3 High copy gain, CN = 4 0.46  
chr7:92c245,458-92c471,899 q21.2 High copy gain, CN = 4 − 5 0.23  
chr9:204c738-39c184,065 p24.3-p13.1 CN-LOH 38.98  
chr9:21c965,073-22c014,524 p21.3 Homozygous deletion 0.05  
chr9:80c446,364-80c704,731 q21.2 High copy gain, CN = 4 − 5 0.26  
chr11:128c157,643-128c615,486 q24.3 Gain 0.46  
chr12:11c795,269-12c059,452 p13.2 Gain 0.26  
chr13:48c885,423-49c262,256 q14.2 Gain 0.38  
chr14:98c100,176-100c100,128 q32.2 Gain 2.00  
chr15:56c642,839-58c955,123 q21.3 Gain 2.31  
16 chr11:79c517,863-93c209,472 q14.1-q21 Deletion 13.69 46,XX,t7,12(p13;p13), ?add17(p11.2)[16]/46,XX[11] 
17 chr1:202c643,208-249c212,878 q32.1-q44 Gain 46.57 51,XY,+5,del5(q31),+6, +del9(p13),?inv9(p24q21)x2, der(11)t1,11(q32;q?230,+18, +19[9]; FISH positive for 9p21 homozygous deletion in 89% cells; negative for MLL rearrangement and BCR-ABL fusion. 
chr5:38c139-128c975,230 p15.33-q23.3 Gain 128.94  
chr5:128c846,774-180c698,312 q23.3-q35.3 CN-LOH 51.85  
chr6:204c909-31c553,468 p25.3-p21.33 Gain 31.35  
chr6:31c555,130-32c162,418 p21.33-p21.32 Gain 0.61  
chr6:32c167,778-170c913,051 p21.32-q27 Gain 138.75  
chr8:138c891,978-146c292,734 q24.23-q24.3 Gain 7.40  
chr9:0-12c042,349 p24.3-p23 CN-LOH 12.04  
chr9:12c054,659-13c345,642 p23 Homozygous deletion 1.29  
chr9:13c354,725-21c585,658 p23-p21.3 CN-LOH 8.23  
chr9:21c604,067-24c075,082 p21.3 Homozygous deletion 2.47  
chr9:24c044,951-38c802,685 p21.3-p13.1 CN-LOH 14.76  
chr9:68c170,421-141c054,761 q13-q34.3 Gain 72.88  
chr14:95c161,449-107c282,024 q32.13-q32.33 Gain 12.12  
chr18:0-78c077,248 p11.32-q23 Gain 78.08  
chr19:0-59c128,983 p13.3-q13.43 Gain 59.13  
18 Normal female    NA 
19 chr1:754c192-8c788c907 p36.33-p36.23 Deletion 8.03 NA 
chr1:91c967,341-99c114,927 p22.2-p21.3 Deletion 7.15  
chr8:172c417-17c835,685 p23.3-p22 Deletion 17.66  
chr10:89c432,286-90c306,376 q23.2-q23.31 Deletion 0.87  
chr11:28c057,957-49c688,837 p14.1-p11.12 Deletion 21.63  
chr12:189c400-25c551,025 p13.33-p12.1 Deletion 25.36  
chr12:27c498,107-32c164,030 p11.23-p11.21 Deletion 4.67  
chr17:400c959-1c461c125 p13.3 Gain 1.06  
chrX:41c201,762-41c531,564 p11.4 Homozygous deletion 0.33  
chrX:42c869,649-44c344,324 p11.3 Homozygous deletion 1.47  
chrX:45c481,094-48c206,911 p11.3-p11.23 Gain 2.73  
chrX:50c817,478-52c695,241 p11.22 Homozygous deletion 1.88  
chrX:154c979,673-155c219,364 q28 Gain 0.24  
20 chr6:108c974,746-110c936,144 q21 Deletion 1.96 NA 
chr12:189c400-29c877,262 p13.33-p11.22 Deletion 29.69  
21 chr9:148c341-21c900,510 p24.3-p21.3 CN-LOH 21.75 NA 
chr9:21c900,511-21c971,583 p21.3 Homozygous deletion 0.07  
chr9:21c971,584-34c406,287 p21.3-p13.3 CN-LOH 12.43  
22 chr1:754c192-33c899,167 p36.33-p35.1 Deletion 33.14 NA 
chr4:58c592,202-190c915,650 q12-q35.2 Deletion 132.32  
chr5:38c139-24c037,074 p15.33-p14.2 Deletion 24.00  
chr5:70c306,678-180c698,312 q13.2-q35.3 Deletion 110.39  
chr7:41c421-52c432,938 p22.3-p12.1 Deletion 52.39  
chr9:4c304c915-21c255,150 p24.2-p21.3 Deletion 16.95  
chr9:21c265,500-25c891,012 p21.3-p21.2 Homozygous deletion 4.63  
chr12:9c512c809-30c667,228 p13.31-p11.22 Deletion 21.15  
chr13:36c912,708-115c103,150 q13.3-q34 Deletion 78.19  
chr16:83c887-27c690,168 p13.3-p12.1 Deletion 27.61  
chr18:26c057,437-78c007,784 q12.1-q23 Gain 51.95  
23 tetraploidy    NA 
chr1:3c921c449-7c050c061 p36.32-p36.31 Deletion, CN = 2 3.13  
chr1:23c103,620-24c108,104 p36.12-p36.11 Deletion, CN = 2 1.00  
chr1:114c594,372-115c470,556 p13.2 Deletion, CN = 2 0.88  
chr2:54c374,691-55c005,224 p16.2-p16.1 Deletion, CN = 2 0.63  
chr5:133c415,731-134c917,467 q31.1 Deletion, CN = 2 1.50  
chr6:0-26c382,744 p25.3-p22.2 CN-LOH, CN = 4 26.38  
chr8:33c078,287-33c503,454 p12 Deletion, CN = 2 0.43  
chr9:30c001,529-30c721,717 p21.1 Deletion, CN = 2 0.72  
chr9:133c618,461-134c097,558 q34.12-q34.13 High copy gain, CN = 6 0.48  
chr10:104c369,298-104c562,842 q24.32 Deletion, CN = 2 0.19  
chr11:103c091,553-114c475,360 q22.3-q23.2 Deletion, CN = 2 11.38  
chr12:17c200,436-18c268,880 p12.3 Deletion, CN = 2 1.07  
chr12:110c067,819-111c370,885 q24.11 Deletion, CN = 2 1.30  
chr12:111c370,885-111c911,916 q24.11-q24.12 Homozygous deletion, CN = 0 0.54  
chr12:111c911,916-112c035,561 q24.12 Deletion, CN = 2 0.12  
chr14:91c600,426-94c111,212 q32.11-q32.12 Deletion, CN = 2 2.51  
chr16:0-2c210c796 p13.3 Deletion, CN = 2 2.21  
chr16:7c299c668-8c301c002 p13.3-p13.2 Deletion, CN = 2 1.00  
chr17:27c957,832-29c631,473 q11.2 Deletion, CN = 2 1.67  
chr17:29c631,473-29c897,502 q11.2 Homozygous deletion, CN = 0 0.27  
chr17:29c897,502-30c692,775 q11.2 Deletion, CN = 2 0.80  
chr18:76c375,122-77c458,776 q23 Deletion, CN = 2 1.08  
chr20:49c176,050-53c504,956 q13.13-q13.2 Deletion, CN = 2 4.33  
chr22:37c543,717-39c369,251 q12.3-q13.1 Deletion, CN = 2 1.83  
chrX:133c432,498-134c242,874 q26.2-q26.3 Deletion, CN = 2 0.81  
24 chr1:754c192-9c617c682 p36.33-p36.22 Deletion 8.86 NA 
chr2:42c280,854-50c636,065 p21-p16.3 Deletion 8.36  
chr9:204c738-38c495,131 p24.3-p13.1 Deletion 38.29  
chr9:68c170,421-141c054,761 q13-q34.3 Gain 72.88  
chr12:189c400-6c771c877 p13.33-p13.31 Gain 6.58  
chrX:154c979,673-155c219,364 q28 Gain 0.24  

The last column includes karyotype and/or FISH data when available. Cases 1-15 are non-ETP T-LLy; cases 16-24 are ETP-LLy.

NA, not available.

Table 2.

Recurrent CNAs and CN-LOHs in T-LLy with the incidence in ETP and non-ETP cases along with the genomic coordinates

ChromosomeCasesIncidence in ETP-LLyIncidence in Non-ETP T-LLyP value (ETP vs non ETP)Minimal common regionStart genomic coordinatesStop genomic coordinatesAffected genes
Recurrent gains 
 6 5, 15 0/9 2/15 .511 6q23.3 135c483,742 135c754,471 MYB 
 9 11, 23 1/9 1/15 1.000 9q34.12q34.13 133c719,421 134c094,802 NUP14-ABL1 
Recurrent losses 
 1 19, 22, 23, 24 4/9 0/15 .012* 1p36.32p36.31 3c921c449 7c050c061 RPL11 
 12 19, 20, 22 3/9 0/15 .042* 12p12.3 17c200,436 18c268,880 RERGL 
 13 6, 11 0/9 2/15 .511 13q14.2 48c984,722 49c065,037 RB1 
 4 14, 15 0/9 2/15 .511 4q12 54c324,930 55c102,425 FIP1L1, CHIC, PDGFRa 
 X 11, 23 1/9 1/15 1.000 Xq26.2q26.3 130c973,820 134c242,874 PHF6 
Recurrent LOHs 
 4 8, 15 0/9 2/15 .511 4q28.1q35.2 126c144,980 191c154,276 FBXW7 
Recurrent losses and/or LOHs 
 9 1-11, 13-15, 17, 21, 22, 24 4/9 14/15 .015* 9p21.3 21c901,263 21c993,468 CDKN2A, CDKN2B 
ChromosomeCasesIncidence in ETP-LLyIncidence in Non-ETP T-LLyP value (ETP vs non ETP)Minimal common regionStart genomic coordinatesStop genomic coordinatesAffected genes
Recurrent gains 
 6 5, 15 0/9 2/15 .511 6q23.3 135c483,742 135c754,471 MYB 
 9 11, 23 1/9 1/15 1.000 9q34.12q34.13 133c719,421 134c094,802 NUP14-ABL1 
Recurrent losses 
 1 19, 22, 23, 24 4/9 0/15 .012* 1p36.32p36.31 3c921c449 7c050c061 RPL11 
 12 19, 20, 22 3/9 0/15 .042* 12p12.3 17c200,436 18c268,880 RERGL 
 13 6, 11 0/9 2/15 .511 13q14.2 48c984,722 49c065,037 RB1 
 4 14, 15 0/9 2/15 .511 4q12 54c324,930 55c102,425 FIP1L1, CHIC, PDGFRa 
 X 11, 23 1/9 1/15 1.000 Xq26.2q26.3 130c973,820 134c242,874 PHF6 
Recurrent LOHs 
 4 8, 15 0/9 2/15 .511 4q28.1q35.2 126c144,980 191c154,276 FBXW7 
Recurrent losses and/or LOHs 
 9 1-11, 13-15, 17, 21, 22, 24 4/9 14/15 .015* 9p21.3 21c901,263 21c993,468 CDKN2A, CDKN2B 

Cases 1-15 are non-ETP T-LLy, and cases 16-24 are ETP-LLy.

*

P < .05. 

Table 3.

Comparison of average number and size of CNAs between non-ETP T-LLy and ETP-LLy

Average no. of CNAs per case
One copy gainTwo or more copy gainHeterozygous lossBiallelic lossTotal CNAsAverage size of CNAs per case (Mb)
Non-ETP T-LLy 1.40 0.33 1.93 0.93 4.6 70.30 
ETP-LLy 1.89 0.11 4.78 7.78 160.66 
P value 0.65 0.45 0.13 0.85 0.19 0.23 
Average no. of CNAs per case
One copy gainTwo or more copy gainHeterozygous lossBiallelic lossTotal CNAsAverage size of CNAs per case (Mb)
Non-ETP T-LLy 1.40 0.33 1.93 0.93 4.6 70.30 
ETP-LLy 1.89 0.11 4.78 7.78 160.66 
P value 0.65 0.45 0.13 0.85 0.19 0.23 

Mb, megabases of genome involved.

Correlation between cytogenetic and MIP SNP array studies

Chromosome and/or fluorescence in situ hybridization (FISH) results are available for 7 cases including 5 non-ETP T-LLy and 2 ETP-LLy cases (Table 1). MIP SNP array detected unbalanced rearrangements observed by chromosome or FISH studies including the unbalanced KMT2A (MLL) rearrangement in case 5, CDKN2A deletion in case 7, and complex numerical and structural rearrangements in case 17. In case 5, the breakpoints of CNAs on chromosomes 11 and 19 are located at the KMT2A and MLLT1 genes supporting the translocation involving the KMT2A and MLLT1. This translocation is associated with acute leukemia including T-ALL.25 

Balanced rearrangements including translocation between chromosomes 1 and 14 resulting in TAL1-TCRαδ fusion in case 3 and balanced translocation between chromosomes 7 and 12 in case 16 were not detected by MIP SNP array as expected. MIP SNP array detected additional CNAs and CN-LOH in all cases with chromosome and/or FISH results (cases 3, 5, 7, 8, 14, 16, and 17). In addition, MIP array was able to detect CNAs and CN-LOH in 15 of 17 cases without chromosomal analysis or FISH results.

Comparison of patient outcome

Patient outcomes were assessed after a median follow-up of 6.3 years (range, 0.7-8.4 years). Patients with ETP-LLy had an excellent outcome with no failures or treatment related deaths leading to a 4-year event-free survival (EFS) of 100%. This is in comparison with 1 relapse and 2 remission deaths in the 15 non-ETP LLy patients in this small cohort leading to a 4-year EFS of 79%. EFS and overall survival were not different between ETP and non-ETP T-LLy in our cohort (supplemental Figure 1). However, these findings must be interpreted with appropriate caution because of the small number of patients, the missing stage data in 5 patients, and the selection of patients based on availability of immunophenotyping data and unstained slides.

Patel et al first reported ETP-LLy having an incidence of 4% with an additional 7% that showed ETP features but were incompletely immunophenotyped.16 In the present study, we have confirmed 4% incidence of pediatric ETP-LLy in a separate cohort and further assessed the immunophenotypic and genomic characteristics of this subtype. ETP-LLy patients were not different in terms of age or sex, but the lymphomas were less likely to express CD2 and CD4 than non-ETP T-LLy. Lack of CD4 in ETP-ALL has been described and proposed as part of an alternative immunophenotypic definition.9 

In our study, ETP-LLy showed less frequent 9p deletions including the CDKN2A/CDKN2B genes and more frequent 12p deletions including the ETV6 gene compared with non-ETP T-LLy. Similar findings have been reported in ETP-ALL.10-12,14,15,26 Deletions of 9p were identified in 93% (14/15 cases) in non-ETP T-LLy cases in our cohort, which is higher than 33% frequency (3/9 cases) reported previously in a smaller cohort of T-LLy4 but closer to the 75% (12/16) recently reported in T-LLy27 and the 75% to 83% frequency reported previously in T-ALL.10,11,14 The higher incidence of 9p deletion in our selected non-ETP patients thus may not be representative, and the true incidence should be assessed in future studies of larger cohorts.

In our study, 1p deletions including the RPL22 gene were frequent in ETP-LLy (44%) but not seen in non-ETP T-LLy. The RPL22 gene encodes a component of the RNA-binding 60S ribosomal subunit. Autosomal dominant germline mutations in multiple ribosomal protein family members result in impaired ribosome biogenesis and function, termed ribosomopathies, and bone marrow failure syndrome such as Diamond-Blackfan syndrome with subsequent risk of development MDS and AML.28 Somatic mutations in the ribosomal proteins RPM5 and RPL10 are reported in ?10% of pediatric T-ALL patients.29,RPL22 is a component of the TCR signaling pathway and is essential during T-cell development.30 RPL22 haploinsufficiency has been reported in 10% T-ALL, but this study did not specify the immunophenotype of the patients so it is not known if some of the patients had ETP-ALL.31 Our study is the first to specifically associate RPL22 gene deletion with ETP-LLy, and may provide novel insights in the pathogenesis of ETP-LLy. Additional studies are needed to determine if RPL22 gene deletion is also characteristic of ETP-ALL.

ABD characterizes early thymocyte precursors before V(D)J recombination and is associated with early treatment failure in both pediatric T-ALL and T-LLy,3,32 although a more recent study showed no difference in outcomes.9 We noted more frequent ABD in ETP-LLy, similar to previous studies in ETP-ALL.9,10,13 

Other recurrent CNAs observed in both ETP-ALL and non-ETP T-ALL include 6q gains involving the MYB gene, 13q deletions including the RB1 genes.11,14,33,34 The 6q gain, 13q deletion, and CHIC2 deletions are each present in 2 non-ETP T-LLy cases but not in ETP-LLy patients in our study. The 4q deletion involving CHIC2 resulting in fusion between FIP1L1 and PDGFRα is previously reported in T-ALL, but this abnormality was not present in the in ETP-ALL patients.14 Additional independent studies are needed to confirm if these abnormalities are limited in non-ETP T-ALL or can be present in both subtypes. Multiple complex rearrangements suggesting chromothripsis previously reported in ETP-ALL were not seen in ETP-LLy samples in this study. ETP-LLy cases may exhibit less genomic instability than ETP-ALL,6 but this was not directly assessed in our study. Such differences may correspond to the difference in outcome that we observed in this study compared with reports suggesting ETP-ALL was associated with an inferior outcome compared with non-ETP-ALL.6 

Some recurrent CNAs are seen in both ETP and non-ETP T-LLy cases. Focal PHF6 deletions on the long arm of chromosome X and NUP214-ABL1 fusion amplification were observed in non-ETP T-LLy case 11 and ETP-LLy case 23. PHF6 plays a role in epigenetic regulation of gene expression and was identified as a key tumor suppressor gene in T-ALL. PHF6 mutation and/or deletion was reported almost exclusively in male T-ALL patients by Van Vlierberghe et al.35 However, the PHF6 deletion in case 23 (female) is heterozygous, affecting 1 copy of chromosome X. It is possible that the PHF6 copy on the other chromosome X homolog may be silenced by X-inactivation or carry mutation resulting in loss of function in both copies. Co-occurrence of PHF6 deletion and NUP214-ABL1 fusion amplification has not been reported previously, to the best of our knowledge.36 The presence of both abnormalities in 1 ETP-LLy case and 1 non-ETP T-LLy case suggests that these 2 abnormalities may be associated with each other and are not specific for the ETP-LLy subtype.

The 6q CN-LOH, deletion of the CASP8AP2 gene on chromosome 6 (also known as FLASH deletion), and PTEN deletion have been previously reported in T-LLy and T-ALL and shown to have prognostic association.3,27 These abnormalities were not observed in our study in either ETP or non-ETP T-LLy.

In comparing MIP SNP array data to cytogenetic and FISH data when available, the MIP SNP array detected all cytogenetic and FISH abnormalities except the balanced translocations. In each case, additional CNAs and CN-LOH were detected by MIP SNP array highlighting that it is a superior test for CNA and LOH detection than conventional chromosome and FISH analysis. In addition, MIP array can be used in LLy patients without access to fresh tissue for chromosomal analysis or when the chromosome analysis fails.

The outcomes for the ETP patients in our cohort were excellent and not significantly different than the outcomes for patients with non-ETP phenotype T-LLy. These findings are in line with recent studies that demonstrated noninferior outcomes of ETP-ALL7-9 but should also be interpreted with appropriate caution because of the small number of patients.

One important limitation of our study may be the classification of ETP-LLy based on immunophenotyping rather than gene expression profiling. The ETP-ALL entity was originally defined by gene expression profiling, and Zuurbier et al demonstrated that ETP classification by immunophenotyping likely underestimates the actual incidence relative to gene expression profiling.9 In addition, we used a strict definition of ETP/non-ETP and thus excluded near-ETP cases from our assessment.15 

In conclusion, we have established an incidence of ETP-LLy of 4% and demonstrated that ETP-LLy exhibit distinct features from non-ETP T-LLy at the genomic level including less frequent 9p deletion including CDK2A/B and more frequent 12p deletion including ETV6. We identified RPL22 deletion on 1p as a recurrent finding in ETP-LLy suggesting ribosomal biogenesis dysfunction may play a role in the pathogenesis of some ETP-LLy. Finally, the MIP SNP array may have clinical utility for assessment of T-LLy specimens, especially when only fixed tissue is available.

This work was supported by the National Institutes of Health, National Cancer Institute’s National Clinical Trials Network (NCTN) Operations Center Grant U10CA180886, the NCTN Statistics & Data Center Grant U10CA180899, and the Children’s Oncology Group Biospecimen Bank Grant U24CA196173.

The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Contribution: X.X., C.N.P., S.L.P., and R.R.M. designed the study, performed the research, and analyzed the data; M.D. performed the statistical analysis; and R.J.H., K.P.D., S.S.W., S.P.H., N.J.W., W.L.C., M.L.L., T.G.G., and C.M.B. designed and supported the AALL0434 clinical trial through the Children’s Oncology Group acute lymphoblastic leukemia and non-Hodgkin lymphoma disease committees.

Conflict-of-interest disclosure: M.L.L. served on the advisory board of MediSix Therapeutics. The remaining authors declare no competing financial interests.

The current affiliation for X.X. is Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN.

Correspondence: Rodney R. Miles, University of Utah Department of Pathology, 15 N Medical Dr E, JMRB Room 2100, Salt Lake City, UT 84112; e-mail: rodney.miles@path.utah.edu.

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Author notes

The SNP array data have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE168884 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE168884).

The full-text version of this article contains a data supplement.

Supplemental data