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The genetic basis of early T-cell precursor acute lymphoblastic leukaemia
Open accessAbstract
Early T-cell precursor acute lymphoblastic leukaemia (ETP ALL) is an aggressive malignancy of unknown genetic basis. We performed whole-genome sequencing of 12 ETP ALL cases and assessed the frequency of the identified somatic mutations in 94 T-cell acute lymphoblastic leukaemia cases. ETP ALL was characterized by activating mutations in genes regulating cytokine receptor and RAS signalling (67% of cases; NRAS, KRAS, FLT3, IL7R, JAK3, JAK1, SH2B3 and BRAF), inactivating lesions disrupting haematopoietic development (58%; GATA3, ETV6, RUNX1, IKZF1 and EP300) and histone-modifying genes (48%; EZH2, EED, SUZ12, SETD2 and EP300). We also identified new targets of recurrent mutation including DNM2, ECT2L and RELN. The mutational spectrum is similar to myeloid tumours, and moreover, the global transcriptional profile of ETP ALL was similar to that of normal and myeloid leukaemia haematopoietic stem cells. These findings suggest that addition of myeloid-directed therapies might improve the poor outcome of ETP ALL. This work shows that treatments used for acute myeloid leukaemia and targeted therapies could be used for early T-cell precursor acute lymphoblastic leukaemia. The early T-cell precursor (ETP) subtype of childhood acute lymphoblastic leukaemia (ALL) has a poor prognosis when treated with standard chemotherapy. Whole genome sequencing is used here to gain insights into the genetic basis of the condition. The results reveal a high frequency of activating mutations in genes regulating cytokine receptor and Ras signalling, lesions that disrupt haemopoiesis (many of which arise from chromosomal rearrangements that generate novel chimeric in-frame fusion genes), and inactivating mutations in histone modifying genes. This mutation pattern resembles that of myeloid malignancies, suggesting that myeloid-directed therapies such as high-dose cytarabine, or targeted therapies that inhibit cytokine receptor and JAK signalling, might be effective in ETP ALL.
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“High frequency of mutations in EZH2, EED, and SUZ12 are observed in patients with early T cell precursor ALL (ETP-ALL) [154, 155].”
From Proteolysis targeting chimeras (PROTACs) are emerging therapeutics for hematologic malignancies (2020) · cites this paper as [155]
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“[22] identified GATA3 mutation in 10% of early T cell precursor ALL (ETP-ALL) and was not present in any of patients with non-ETP ALL.”
BackgroundMutational Spectrum Of Adult T-ALL
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“com/oncotarget (12%), and BCL11B (10%) were in the range of previously reported frequencies[21,26,39,40].”
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“This may be related to their mutations in immature T-ALL ( 54).”
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“ETP-ALL has several genomic features similar to those of T/myeloid MPAL, such as an increased incidence of biallelic WT1 changes and mutations in transcriptional regulators; epigenetic regulators; and signaling pathways, including JAK/STAT, RAS, PI3K/AKT/mTOR, FLT3, and MAPK [121,124,125].”
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“…is a tumor suppressor that is functionally inhibited in B-cell precursor acute lymphoblastic leukemia (ALL), blocking differentiation and supporting the early B-cell phenotype [52], and in B-cell and early T-cell precursor ALL [53,54], with this impairment associated with leukemogenesis [51,52].”
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“Other recurrent CNAs observed in both ETP-ALL and non-ETP TALL 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.”
BackgroundResultInfluentialSelf-citationChromothripsis in Chronic Lymphocytic Leukemia: A Driving Force of Genome Instability
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BackgroundInfluentialMYC fails to efficiently shape malignant transformation in T‐cell acute lymphoblastic leukemia
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“leukins 5 and 7 in other cells,(10-12) the proposed mechanism associating DNM2 loss-of-function mutations and ETPALL development.(5) Further, previous studies using pharmacological approaches have suggested that dynamin GTPase activity contributes to receptor desensitization in human platelets, as in the case of the p…”
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Self-citationGata3 restrains B cell proliferation and cooperates with p18INK4c to repress B cell lymphomagenesis
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“Clinical studies revealed that somatic mutations in GATA3 were frequently detected in early T cell precursor acute lymphoblastic leukemia [13] and that inherited genetic variation in GATA3 is associated with susceptibility to developing lymphoma and acute lymphoblastic leukemia [14, 15], suggesting that GATA3 may play…”
BackgroundSelf-citationETV6 and NOTCH1 germline variants in adult acute leukemia
Dirsė, V., Norvilas, R., Gineikienė, E., Matuzevičienė, R., Griškevičius, L., & Preikšaitienė, E. (2017) · Leukemia & lymphoma/Leukemia and lymphoma · doi:10.1080/10428194.2017.1359742 · Cited by 12
“Closely located somatic variant Y104fs was also associated with this disease [4], and adjacent F102fs variant was detected in a patient with acute lymphoblastic leukemia [5].”
BackgroundMiyashita, K., Kitajima, K., Goyama, S., Kitamura, T., & Hara, T. (2017) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2017.12.135 · Cited by 12
Canté-Barrett, K., Uitdehaag, J. C. M., & Meijerink, J. P. P. (2016) · Haematologica · doi:10.3324/haematol.2015.138248 · Cited by 12
Yim, J., Koh, J., Kim, S., Song, S. G., Bae, J. M., Yun, H., Sung, J., Kim, T. M., Park, S., & Jeon, Y. K. (2022) · PubMed Central · doi:10.1097/pas.0000000000001859 · Cited by 7
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Polycomb repressive complex 2 (PRC2) pathway’s role in cancer cell plasticity and drug resistance
Goleij, P., Heidari, M. M., Tabari, M. A. K., Hadipour, M., Rezaee, A., Javan, A., Sanaye, P. M., Larsen, D. S., Daglia, M., & Khan, H. (2025) · Functional & Integrative Genomics · doi:10.1007/s10142-025-01563-8 · Cited by 13
“…lysine 27 (H3K27) as a catalytic substrate (2012, De Raedt et al. 2014; Ernst et al. 2010; Khan et al. 2013; Lee et al. 2014; Nikoloski et al. 2010; Ntziachristos et al. 2012; Puda et al. 2012; Schwartzentruber et al. 2012; Score et al. 2012; Sturm et al. 2012; Ueda et al. 2012; Zhang et al. 2012).”
Identification of somatic alterations in stage I lung adenocarcinomas by next‐generation sequencing
Zhao, Y., Yang, J., Chen, Z., Gao, Z., Zhou, F., Li, X., Li, J., Shi, S., Feng, X., Sun, N., et al. (2014) · Genes Chromosomes and Cancer · doi:10.1002/gcc.22138 · Cited by 11
Ikoma, M. R. V., Sandes, A. F., Thiago, L. S., Cavalcanti, G. B., Lorand-Metze, I. G. H., da Costa, E. S., Pimenta, G., Santos‐Silva, M. C., Bacal, N. S., Yamamoto, M., et al. (2014) · Cytometry Part B Clinical Cytometry · doi:10.1002/cyto.b.21175 · Cited by 11
“This is a subset of thymocytes representing recent immigrants from the BM to the thymus, which retain multilineage differentiation potential (53,54).”
BackgroundWhich patients should I transplant with acute lymphoblastic leukemia?
Inbar, T., Rowe, J. M., & Horowitz, N. A. (2017) · Best Practice & Research Clinical Haematology · doi:10.1016/j.beha.2017.07.005 · Cited by 11
Kumar, A., Drusbosky, L. M., Meacham, A. M., Turcotte, M., Bhargav, P., Vasista, S. M., Usmani, S., Pampana, A., Basu, K., Tyagi, A., et al. (2019) · Leukemia Research · doi:10.1016/j.leukres.2019.01.003 · Cited by 11
Deregulated expression of NKL homeobox genes in T-cell lymphomas
Nagel, S., Pommerenke, C., MacLeod, R. A. F., Meyer, C., Kaufmann, M., Fähnrich, S., & Drexler, H. G. (2019) · Oncotarget · doi:10.18632/oncotarget.26929 · Cited by 11
“Accordingly, the T-cell line LOUCY is derived from ETP-ALL which also expresses T-cell markers and NK-cell genes including AUTS2, ID2 and MSX1 [19, 47, 48].”
BackgroundInsights into novel emerging epigenetic drugs in myeloid malignancies
Chandhok, N. S., & Prébet, T. (2019) · Therapeutic Advances in Hematology · doi:10.1177/2040620719866081 · Cited by 11
The genomic and biological complexity of mixed phenotype acute leukemia
Andrews, C. N., Tierens, A. M., & Minden, M. D. (2020) · Critical Reviews in Clinical Laboratory Sciences · doi:10.1080/10408363.2020.1829537 · Cited by 11
Chen, D., Camponeschi, A., Nordlund, J., Marincevic-Zuniga, Y., Abrahamsson, J., Lönnerholm, G., Fogelstrand, L., & Mårtensson, I. (2021) · Cancer Medicine · doi:10.1002/cam4.3928 · Cited by 12
“Healthy (Fetal BM) GSE45460 DS0M South Korea GPL6244 8 [7] BCPALL (Pediatric) GSE26281 DS1M USA GPL96 127 [8] GSE28497 DS2M USA GPL96 239 [9] GSE47051 DS3M Sweden GPL570 75 [10] GSE12995 DS4M USA GPL96 175 [11] GSE33315 DS5M USA GPL96 483 [12] GSE26366 DS6M USA GPL96 172 [13] RNAseq1 DS7R Sweden Hiseq2000/2500 116 [14…”
Weng, S., Wen, M., Hsieh, S.-L., Chen, N., & Tarng, D. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.879648 · Cited by 11
“FasR shRNA (shFasR) and pLKO_TRC001 control (both from RNAi core, Academia Sinica; Taipei, Taiwan) were electroporated into MOHITO cells using the Neon™ Electroporation Transfection system (100-µl transfection volume, 1 × 106–5 × 106 T-cells, and 6-well, 60-mm, or 10-cm culture dish).”
MethodInfluentialMolecular Diagnostic Testing for Hematopoietic Neoplasms
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González‐Gil, C., Morgades, M., Lopes, T., Fuster‐Tormo, F., García-Chica, J., Zhao, R., Montesinos, P., Torrent, A., Díaz‐Beyá, M., Coll, R., et al. (2022) · Haematologica · doi:10.3324/haematol.2022.281196 · Cited by 11
“…transcription factor tumor suppressor genes ( PTEN, BCL11B, RUNX1, GATA3, ETV6 ) 23–27 ; ii) epigenetic regulators ( PHF6, DNMT3A, EP300, KMT2C ) 27–29 ; iii) DNA mismatch repair genes ( MSH2 ) 30 ; iv) genes expressing ribosomal protein ( RPL5 ) 31 ; v) genes involved in RNA splicing ( U2AF1 ) 32…”
Shah, M. A., Denton, E., Liu, L., & Schapira, M. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt710 · Cited by 11
“…(Biankin et al. , 2012; Dalgliesh et al. , 2010; Ellis et al. , 2012; Ho et al. , 2013; Jones et al. , 2012; Le Gallo et al. , 2012; Morin et al. , 2011; Pugh et al. , 2012; Robinson et al. , 2012; Schwartzentruber et al. , 2012; Stephens et al. , 2012; Varela et al. , 2011; Zhang et al. , 2012).”
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Self-citationGenetics and epigenetics of pediatric leukemia in the era of precision medicine
Ramos, K. N., Ramos, I. N., Zeng, Y., & Ramos, K. S. (2018) · F1000Research · doi:10.12688/f1000research.14634.1 · Cited by 11
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Mutations that collaborate with IL-7Ra signaling pathways to drive ALL
Rodrigues, G. O. L., Cramer, S. D., Winer, H. Y., Hixon, J. A., Li, W., Yunes, J. A., & Durum, S. K. (2021) · Advances in Biological Regulation · doi:10.1016/j.jbior.2021.100788 · Cited by 11
Epigenetic and metabolic interplay in cutaneous squamous cell carcinoma
Pacella, G., & Capell, B. C. (2021) · Experimental Dermatology · doi:10.1111/exd.14354 · Cited by 11
Oncogenic Cooperation Between IL7R-JAK-STAT Pathway Mutations
Lodewijckx, I., Mentens, N., Jacobs, K., & Cools, J. (2021) · HemaSphere · doi:10.1097/hs9.0000000000000637 · Cited by 11
“13 Moreover, JAK1 was demonstrated to be more important than JAK3 for IL7R-JAK-STAT signaling pathway activation.”
Self-citationMathisen, M. S., Jabbour, E. J., & Kantarjian, H. M. (2012) · PubMed · Cited by 11
DNA sequencing methods in human genetics and disease research
Lehrach, H. (2013) · F1000Prime Reports · doi:10.12703/p5-34 · Cited by 12
“Significant progress has been made, but there are obvious limitations due to the inherent technical and biological noise in this type of data [136-140].”
BackgroundChaer, F. E., Holtzman, N. G., Binder, E. L., Porter, N. C., Singh, Z. N., Koka, R. M., Rapoport, A. P., & Emadi, A. (2017) · Bone Marrow Transplantation · doi:10.1038/bmt.2017.191 · Cited by 11
Wang, P., Peng, X., Deng, X., Gao, L., Zhang, X., & Feng, Y. (2018) · Medicine · doi:10.1097/md.0000000000012743 · Cited by 11
“, CD13, CD33, CD34, and CD117), weak or absent expression of CD5, lack of expression of the T-lineage cell surface markers CD1a and CD8, and a gene expression profile reminiscent of the murine early Tcell precursor,([9]) but MPO .”
The genomic landscape of teenage and young adult T‐cell acute lymphoblastic leukemia
Mansur, M. B., Furness, C. L., Nakjang, S., Enshaei, A., Alpár, D., Colman, S., Minto, L., Irving, J. A. E., Poole, B., Noronha, E. P., et al. (2021) · Cancer Medicine · doi:10.1002/cam4.4024 · Cited by 11
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Polyamines at the crossroad between cell metabolism and epigenetic regulation in acute leukemias
Pirini, F., Ferrari, A., Jandoubi, M., Azzali, I., Angeli, D., Mondrone, R., Bracci, C., Ruggieri, F., Martinelli, G., & Simonetti, G. (2025) · Cell Death Discovery · doi:10.1038/s41420-025-02573-y · Cited by 11
“CREBBP and EP300 are frequently targeted by loss of function mutations in B/T-ALL [52 – 54], or rearranged with KMT2A or zinc fi nger protein 384 ( ZNF384 ) [55, 56].”
Fischer, A., Lersch, R., Krätzig, N. D. A., Strong, A., Friedrich, M., Weber, J., Engleitner, T., Öllinger, R., Yen, H.-Y., Kohlhofer, U., et al. (2023) · Cell Genomics · doi:10.1016/j.xgen.2023.100276 · Cited by 10
“However, in the latest WHO classification one subset with unique biology has been recognized as a distinct sub-entity: ETP-ALL is characterized by the retention of myeloid and stem cell markers 32–34 , 67 (Figure 6A).”
BackgroundAcute Leukemia of Ambiguous Lineage: Diagnosis and Evaluation by Flow Cytometry
Fuda, F. S., & Chen, W. (2025) · Cancers · doi:10.3390/cancers17050871 · Cited by 10
“T/myeloid MPAL is the second most common MPAL immunophenotype, representing ~20–30% of MPAL cases, and possess a heterogeneous group of gene alterations in transcription factors ( WT1 , ETV6 , and RUNX1 ) , epigenetic/chromatin modi fi ers ( PHF6 and DNMT3A ), NOTCH ( NOTCH1 ), signaling pathways…”
(2013) · Transcriptomics Open Access · doi:10.4172/2329-8936.1000104 · Cited by 10
“Genome sequencing has been applied for the development of a variety of research areas such as, characterization of ancient genomes [1], sequencing of different species [2], risk assessment of genetic diseases [3], molecular diagnosis of various diseases including cancer [4,5] among other, leading to a road for persona…”
BackgroundMcGinn, O. J., Krishnan, S., Bourquin, J., Sapra, P., Dempsey, C. E., Saha, V., & Stern, P. L. (2017) · Haematologica · doi:10.3324/haematol.2016.158485 · Cited by 9
Ruxolitinib is effective in the treatment of a patient with refractory T‐ALL
Jaramillo, S., Hennemann, H., Horak, P., Teleanu, V., Heilig, C. E., Hutter, B., Stenzinger, A., Glimm, H., Goeppert, B. F., Müller‐Tidow, C., et al. (2020) · eJHaem · doi:10.1002/jha2.143 · Cited by 10
“JAK3mutations have been reported in 10-16% of T-ALL patients, with JAK3 M511I being the most frequently identified mutation [9].”
BackgroundDovat, E., Song, C., Hu, T., Rahman, M. A., Dhanyamraju, P. K., Klink, M., Bogush, D., Soliman, M., Kane, S., McGrath, M., et al. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22020819 · Cited by 10
Metadata
- Authors
- Zhang, J., Ding, L., Holmfeldt, L., Wu, G., Heatley, S. L., Payne-Turner, D., Easton, J., Chen, X., Wang, J., Rusch, M., Lu, C., Chen, S.-C., Wei, L., Collins-Underwood, J. R., Ma, J., Roberts, K. G., Pounds, S. B., Ulyanov, A., Becksfort, J., Gupta, P., Huether, R., Kriwacki, R. W., Parker, M., McGoldrick, D. J., Zhao, D., Alford, D., Espy, S., Bobba, K. C., Song, G., Pei, D., Cheng, C., Roberts, S., Barbato, M. I., Campana, D., Coustan-Smith, E., Shurtleff, S. A., Raimondi, S. C., Kleppe, M., Cools, J., Shimano, K. A., Hermiston, M. L., Doulatov, S., Eppert, K., Laurenti, E., Notta, F., Dick, J. E., Basso, G., Hunger, S. P., Loh, M. L., Devidas, M., Wood, B., Winter, S., Dunsmore, K. P., Fulton, R. S., Fulton, L. L., Hong, X., Harris, C. C., Dooling, D. J., Ochoa, K., Johnson, K. J., Obenauer, J. C., Evans, W. E., Pui, C.-H., Naeve, C. W., Ley, T. J., Mardis, E. R., Wilson, R. K., Downing, J. R., & Mullighan, C. G.
- Affiliations
- St. Jude Children's Research Hospital (US)
- Washington University in St. Louis (US)
- KU Leuven (BE)
- University of California, San Francisco (US)
- University Health Network (CA)
- University of Padua (IT)
- Children's Hospital Colorado (US)
- University of Florida Health (US)
- Seattle Children's Hospital (US)
- University of New Mexico (US)
- Corresponding author
- Downing, James R.
- Mullighan, Charles G.
- ORCID
- Zhang, Jinghui
- Ding, Li
- Holmfeldt, Linda
- Wu, Gang
- Payne-Turner, Debbie
- Easton, John
- Chen, Xiang
- Wang, Jianmin
- Rusch, Michael
- Lu, Charles
- Chen, Shann-Ching
- Wei, Lei
- Ma, Jing
- Roberts, Kathryn G.
- Pounds, Stanley B.
- Ulyanov, Anatoly
- Becksfort, Jared
- Gupta, Pankaj
- Huether, Robert
- Kriwacki, Richard W.
- Parker, Matthew
- Zhao, David
- Espy, Stephen
- Song, Guangchun
- Cheng, Cheng
- Barbato, Michael I.
- Campana, Dario
- Raimondi, Susana C.
- Cools, Jan
- Shimano, Kristin A.
- Hermiston, Michelle L.
- Doulatov, Sergei
- Eppert, Kolja
- Laurenti, Elisa
- Notta, Faiyaz
- Dick, John E.
- Basso, Giuseppe
- Hunger, Stephen P.
- Loh, Mignon L.
- Devidas, Meenakshi
- Wood, Brent
- Winter, Stuart
- Fulton, Robert S.
- Fulton, Lucinda L.
- Johnson, Kimberly J.
- Obenauer, John C.
- Evans, William E.
- Pui, Ching-Hon
- Ley, Timothy J.
- Mardis, Elaine R.
- Wilson, Richard K.
- Downing, James R.
- Mullighan, Charles G.
- Venue
- Nature
- Published
- 2012-01
- Volume
- 481
- Issue
- 7380
- Pages
- 157-163
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3267575
- OpenAlex
- W2060605982
- Cited by
- 1,596
- References
- 45
- Citations by year
- 2026: 28 · 2025: 61 · 2024: 85 · 2023: 72 · 2022: 98 · 2021: 131 · 2020: 106 · 2019: 123 · 2018: 100 · 2017: 119 · 2016: 138 · 2015: 122 · 2014: 156 · 2013: 162 · 2012: 90
- FWCI
- 164.44
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Nature (publishedVersion, cc-by-nc-sa)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Padua Research Archive (University of Padova) (submittedVersion, cc-by-nc-sa)
- RePEc: Research Papers in Economics (submittedVersion)
- Adelaide Research & Scholarship (AR&S) (University of Adelaide) (submittedVersion)
- Funders
- Alex's Lemonade Stand Foundation for Childhood Cancer
- Washington University in St. Louis
- American Lebanese Syrian Associated Charities (CA021765)
- Alvin J. Siteman Cancer Center
- Children’s Oncology Group
- National Institutes of Health (CA 021765, CA98543)
- National Human Genome Research Institute (U54HG003079, HG003079, NHGRI U54 HG003079)
- National Cancer Institute (CA114766, CA‐98413, U10CA098413, U24CA114766, CA021765, U10CA098543, CA-98543, R25CA023944, T32CA128583, P30CA021765)
- National Institute of General Medical Sciences (U01GM92666, U01GM092666)
- Topics
- Health Sciences › Medicine › Hematology › Acute Lymphoblastic Leukemia research
- Health Sciences › Medicine › Hematology › Acute Myeloid Leukemia Research
- Health Sciences › Medicine › Pathology and Forensic Medicine › Lymphoma Diagnosis and Treatment
- Keywords
- somatic mutations, Ras signaling, cytokine receptor signalling, chromosomal rearrangements, mutation spectrum, high-dose cytarabine, gene expression profiling, hematopoietic stem cells, pediatric leukemia
- MeSH terms
- Reelin Protein, Child, Hematopoiesis, Histones, Humans, Molecular Sequence Data, Mutation, Genes, ras, Stem Cells, T-Lymphocytes, Translocation, Genetic, Signal Transduction, Leukemia, Myeloid, Acute, Genome, Human, Sequence Analysis, DNA, Age of Onset, Genetic Predisposition to Disease, Receptors, Interleukin-7, Genomics, Janus Kinases, Precursor T-Cell Lymphoblastic Leukemia-Lymphoma, DNA Copy Number Variations
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