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Dysregulation of Small Nucleolar RNAs in B-Cell Malignancies. Biomedicines 2022; 10:biomedicines10061229. [PMID: 35740251 PMCID: PMC9219770 DOI: 10.3390/biomedicines10061229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 01/17/2023] Open
Abstract
Small nucleolar RNAs (snoRNAs) are responsible for post-transcriptional modification of ribosomal RNAs, transfer RNAs and small nuclear RNAs, and thereby have important regulatory functions in mRNA splicing and protein translation. Several studies have shown that snoRNAs are dysregulated in human cancer and may play a role in cancer initiation and progression. In this review, we focus on the role of snoRNAs in normal and malignant B-cell development. SnoRNA activity appears to be essential for normal B-cell differentiation and dysregulated expression of sno-RNAs is determined in B-cell acute lymphoblastic leukemia, chronic lymphocytic leukemia, B-cell non-Hodgkin’s lymphoma, and plasma cell neoplasms. SnoRNA expression is associated with cytogenetic/molecular subgroups and clinical outcome in patients with B-cell malignancies. Translocations involving snoRNAs have been described as well. Here, we discuss the different aspects of snoRNAs in B-cell malignancies and report on their role in oncogenic transformation, which may be useful for the development of novel diagnostic biomarkers or therapeutic targets.
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Rehn JA, O’Connor MJ, White DL, Yeung DT. DUX Hunting-Clinical Features and Diagnostic Challenges Associated with DUX4-Rearranged Leukaemia. Cancers (Basel) 2020; 12:cancers12102815. [PMID: 33007870 PMCID: PMC7599557 DOI: 10.3390/cancers12102815] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 09/26/2020] [Accepted: 09/29/2020] [Indexed: 02/07/2023] Open
Abstract
Simple Summary DUX4-rearrangement (DUX4r) is a recently discovered recurrent genomic lesion reported in 4–7% of childhood B cell acute lymphoblastic leukaemia (B-ALL) cases. This subtype has favourable outcomes, especially in children and adolescents treated with intensive chemotherapy. The fusion most commonly links the hypervariable IGH gene to DUX4 a gene located within the D4Z4 macrosatellite repeat on chromosome 4. DUX4r is cryptic to most standard diagnostic techniques, and difficult to identify even with next generation sequencing assays. This review summarises the clinical features and molecular genetics of DUX4r B-ALL and proposes prospective new diagnostic methods. Abstract DUX4-rearrangement (DUX4r) is a recently discovered recurrent genomic lesion reported in 4–7% of childhood B cell acute lymphoblastic leukaemia (B-ALL) cases. This subtype has favourable outcomes, especially in children and adolescents treated with intensive chemotherapy. The fusion most commonly links the hypervariable IGH gene to DUX4 a gene located within the D4Z4 macrosatellite repeat on chromosome 4, with a homologous polymorphic repeat on chromosome 10. DUX4r is cryptic to most standard diagnostic techniques, and difficult to identify even with next generation sequencing assays. This review summarises the clinical features and molecular genetics of DUX4r B-ALL and proposes prospective new diagnostic methods.
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Affiliation(s)
- Jacqueline A. Rehn
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA 5000, Australia; (J.A.R.); (D.T.Y.)
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, SA 5000, Australia
| | - Matthew J. O’Connor
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA 5000, Australia; (J.A.R.); (D.T.Y.)
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, SA 5000, Australia
- Michael Rice Centre for Haematology and Oncology, Womens’s & Children’s Hospital, North Adelaide, SA 5006, Australia
| | - Deborah L. White
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA 5000, Australia; (J.A.R.); (D.T.Y.)
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, SA 5000, Australia
- Australian Genomics, The Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
- Australian and New Zealand Children’s Oncology Group (ANZCHOG), Clayton, VIC 3168, Australia
- Correspondence:
| | - David T. Yeung
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA 5000, Australia; (J.A.R.); (D.T.Y.)
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, SA 5000, Australia
- Department of Haematology, Royal Adelaide Hospital, Adelaide, SA 5000, Australia
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Zaliova M, Potuckova E, Hovorkova L, Musilova A, Winkowska L, Fiser K, Stuchly J, Mejstrikova E, Starkova J, Zuna J, Stary J, Trka J. ERG deletions in childhood acute lymphoblastic leukemia with DUX4 rearrangements are mostly polyclonal, prognostically relevant and their detection rate strongly depends on screening method sensitivity. Haematologica 2019; 104:1407-1416. [PMID: 30630977 PMCID: PMC6601096 DOI: 10.3324/haematol.2018.204487] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 01/07/2019] [Indexed: 11/15/2022] Open
Abstract
ERG-deletions occur recurrently in acute lymphoblastic leukemia, especially in the DUX4-rearranged subtype. The ERG-deletion was shown to positively impact prognosis of patients with IKZF1-deletion and its presence precludes assignment into IKZF1plus group, a novel high-risk category on AIEOP-BFM ALL trials. We analyzed the impact of different methods on ERG-deletion detection rate, evaluated ERG-deletion as a potential marker for DUX4-rearranged leukemia, studied its associations with molecular and clinical characteristics within this leukemia subtype, and analyzed its clonality. Using single-nucleotide-polymorphism array, genomic polymerase chain reaction (PCR) and amplicon-sequencing we found ERG-deletion in 34% (16 of 47), 66% (33 of 50) and 78% (39 of 50) of DUX4-rearranged leukemia, respectively. False negativity of ERG-deletion by single-nucleotide-polymorphism array caused IKZF1plus misclassification in 5 patients. No ERG-deletion was found outside the DUX4-rearranged cases. Within DUX4-rearranged leukemia, the ERG-deletion was associated with higher total number of copy-number aberrations, and, importantly, the ERG-deletion positivity by PCR was associated with better outcome [5-year event-free survival (EFS), ERG-deletion-positive 93% vs. ERG-deletion-negative 68%, P=0.022; 5-year overall survival (OS), ERG-deletion-positive 97% vs. ERG-deletion-negative 75%, P=0.029]. Ultra-deep amplicon-sequencing revealed distinct co-existing ERG-deletions in 22 of 24 patients. In conclusion, our data demonstrate inadequate sensitivity of single-nucleotide-polymorphism array for ERG-deletion detection, unacceptable for proper IKZF1plus classification. Even using more sensitive methods (PCR/amplicon-sequencing) for its detection, ERG-deletion is absent in 22-34% of DUX4-rearranged leukemia and does not represent an adequately sensitive marker of this leukemia subtype. Importantly, the ERG-deletion potentially stratifies the DUX4-rearranged leukemia into biologically/clinically distinct subsets. Frequent polyclonal pattern of ERG-deletions shows that late origin of this lesion is more common than has been previously described.
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Affiliation(s)
- Marketa Zaliova
- CLIP - Childhood Leukaemia Investigation Prague .,Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague.,University Hospital Motol, Prague, Czech Republic
| | - Eliska Potuckova
- CLIP - Childhood Leukaemia Investigation Prague.,Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague
| | - Lenka Hovorkova
- CLIP - Childhood Leukaemia Investigation Prague.,Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague
| | - Alena Musilova
- CLIP - Childhood Leukaemia Investigation Prague.,Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague
| | - Lucie Winkowska
- CLIP - Childhood Leukaemia Investigation Prague.,Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague
| | - Karel Fiser
- CLIP - Childhood Leukaemia Investigation Prague.,Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague
| | - Jan Stuchly
- CLIP - Childhood Leukaemia Investigation Prague.,Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague
| | - Ester Mejstrikova
- CLIP - Childhood Leukaemia Investigation Prague.,Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague.,University Hospital Motol, Prague, Czech Republic
| | - Julia Starkova
- CLIP - Childhood Leukaemia Investigation Prague.,Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague
| | - Jan Zuna
- CLIP - Childhood Leukaemia Investigation Prague.,Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague.,University Hospital Motol, Prague, Czech Republic
| | - Jan Stary
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague.,University Hospital Motol, Prague, Czech Republic
| | - Jan Trka
- CLIP - Childhood Leukaemia Investigation Prague.,Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague.,University Hospital Motol, Prague, Czech Republic
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Lukes J, Potuckova E, Sramkova L, Stary J, Starkova J, Trka J, Votava F, Zuna J, Zaliova M. Two novel fusion genes, AIF1L-ETV6 and ABL1-AIF1L, result together with ETV6-ABL1 from a single chromosomal rearrangement in acute lymphoblastic leukemia with prenatal origin. Genes Chromosomes Cancer 2018; 57:471-477. [PMID: 29726059 DOI: 10.1002/gcc.6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/30/2018] [Accepted: 04/30/2018] [Indexed: 01/19/2023] Open
Abstract
Fusion genes resulting from chromosomal rearrangements represent a hallmark of childhood acute lymphoblastic leukemia (ALL). Unlike more common fusion genes generated via simple reciprocal chromosomal translocations, formation of the ETV6-ABL1 fusion gene requires 3 DNA breaks and usually results from an interchromosomal insertion. We report a child with ALL in which a single interchromosomal insertion led to the formation of ETV6-ABL1 and 2 novel fusion genes: AIF1L-ETV6 and ABL1-AIF1L. We demonstrate the prenatal origin of this complex chromosomal rearrangement, which apparently initiated the leukemogenic process, by successful backtracking of the ETV6-ABL1 fusion into the patient's archived neonatal blood. We cloned coding sequences of AIF1L-ETV6 and ABL1-AIF1L in-frame fusion transcripts from the patient's leukemic blasts and we show that the chimeric protein containing the DNA binding domain of ETV6 is expressed from the AIF1L-ETV6 transcript and localized in both the cytoplasm and nucleus of transfected HEK293T cells. Transcriptomic and genomic profiling of the diagnostic bone marrow sample revealed Ph-like gene expression signature and loss of the IKZF1 and CDKN2A/B genes, the typical genetic lesions accompanying ETV6-ABL1-positive ALL. The prenatal origin of the rearrangement confirms that ETV6-ABL1 is not sufficient to cause overt leukemia, even when combined with the 2 novel fusions. We did not find the AIF1L-ETV6 and ABL1-AIF1L fusions in other ETV6-ABL1-positive ALL. Nevertheless, functional studies would be needed to establish the biological role of AIF1L-ETV6 and ABL1-AIF1L and to determine whether they contribute to leukemogenesis and/or to the final leukemia phenotype.
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Affiliation(s)
- Julius Lukes
- CLIP - Childhood Leukaemia Investigation Prague, Prague, Czech Republic
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Eliska Potuckova
- CLIP - Childhood Leukaemia Investigation Prague, Prague, Czech Republic
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Lucie Sramkova
- CLIP - Childhood Leukaemia Investigation Prague, Prague, Czech Republic
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
- University Hospital Motol, Prague, Czech Republic
| | - Jan Stary
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
- University Hospital Motol, Prague, Czech Republic
| | - Julia Starkova
- CLIP - Childhood Leukaemia Investigation Prague, Prague, Czech Republic
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jan Trka
- CLIP - Childhood Leukaemia Investigation Prague, Prague, Czech Republic
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
- University Hospital Motol, Prague, Czech Republic
| | - Felix Votava
- Department of Pediatrics, 3rd Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jan Zuna
- CLIP - Childhood Leukaemia Investigation Prague, Prague, Czech Republic
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
- University Hospital Motol, Prague, Czech Republic
| | - Marketa Zaliova
- CLIP - Childhood Leukaemia Investigation Prague, Prague, Czech Republic
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
- University Hospital Motol, Prague, Czech Republic
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Advances in B-cell Precursor Acute Lymphoblastic Leukemia Genomics. Hemasphere 2018; 2:e53. [PMID: 31723781 PMCID: PMC6746003 DOI: 10.1097/hs9.0000000000000053] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/13/2018] [Accepted: 04/20/2018] [Indexed: 01/07/2023] Open
Abstract
In childhood B-cell precursor acute lymphoblastic leukemia (BCP-ALL), cytogenetic abnormalities remain important diagnostic and prognostic tools. A number of well-established abnormalities are routinely used in risk stratification for treatment. These include high hyperdiploidy and ETV6-RUNX1 fusion, classified as good risk, while Philadelphia chromosome (Ph) positive ALL and rearrangements of the KMT2A (MLL) gene define poor risk. A poor risk subgroup of intrachromosomal amplification of chromosome 21 (iAMP21-ALL) has been described, in which intensification of therapy has greatly improved outcome. Until recently, no consistent molecular features were defined in around 30% of BCP-ALL (known as B-other-ALL). Recent studies are classifying them into distinct subgroups, some with clear potential for novel therapeutic approaches. For example, in 1 poor risk subtype, known as Ph-like/BCR-ABL1-like ALL, approximately 10% have rearrangements of ABL-class tyrosine kinases: including ABL1, ABL2, PDGFRB, PDGFRA, and CSF1R. Notably, they show a poor response to standard chemotherapy, while they respond to treatment with tyrosine kinase inhibitors, such as imatinib. In other Ph-like-ALL patients, deregulation of the cytokine receptor, CRLF2, and JAK2 rearrangements lead to activation of the JAK-STAT signaling pathway, implicating a specific role for JAK inhibitors in their treatment. Other novel subgroups within B-other-ALL are defined by the IGH-DUX4 translocation, related to deletions of the ERG gene and a good outcome, while fusions involving ZNF384, MEF2D, and intragenic PAX5 amplification (PAX5AMP) are linked to a poor outcome. Continued genetic screening will eventually lead to complete genomic classification of BCP-ALL and define more molecular targets for less toxic therapies.
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Vendramini E, Giordan M, Giarin E, Michielotto B, Fazio G, Cazzaniga G, Biondi A, Silvestri D, Valsecchi MG, Muckenthaler MU, Kulozik AE, Gattei V, Izraeli S, Basso G, Te Kronnie G. High expression of miR-125b-2 and SNORD116 noncoding RNA clusters characterize ERG-related B cell precursor acute lymphoblastic leukemia. Oncotarget 2018; 8:42398-42413. [PMID: 28415578 PMCID: PMC5522075 DOI: 10.18632/oncotarget.16392] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 03/04/2017] [Indexed: 12/19/2022] Open
Abstract
ERG-related leukemia is a B cell precursor acute lymphoblastic leukemia (BCP ALL) subtype characterized by aberrant expression of DUX4 and ERG transcription factors, and highly recurrent ERG intragenic deletions. ERG-related patients have remarkably favorable outcome despite a high incidence of inauspicious IKZF1 aberrations. We describe clinical and genomic features of the ERG-related cases in an unselected cohort of B-other BCP ALL pediatric patients enrolled in the AIEOP ALL 2000 therapeutic protocol. We report a small noncoding RNA signature specific of ERG-related group, with up-regulation of miR-125b-2 cluster on chromosome 21 and several snoRNAs in the Prader-Willi locus at 15q11.2, including the orphan SNORD116 cluster.
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Affiliation(s)
- Elena Vendramini
- Department of Women's and Children's Health, University of Padova, Padova, Italy.,Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel.,Tel Aviv University, Tel Aviv, Israel
| | - Marco Giordan
- Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Emanuela Giarin
- Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Barbara Michielotto
- Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Grazia Fazio
- Centro Ricerca Tettamanti, Clinica Pediatrica, University of Milano-Bicocca, Monza, Italy
| | - Gianni Cazzaniga
- Centro Ricerca Tettamanti, Clinica Pediatrica, University of Milano-Bicocca, Monza, Italy
| | - Andrea Biondi
- Centro Ricerca Tettamanti, Clinica Pediatrica, University of Milano-Bicocca, Monza, Italy
| | - Daniela Silvestri
- Centro Ricerca Tettamanti, Clinica Pediatrica, University of Milano-Bicocca, Monza, Italy
| | | | - Martina U Muckenthaler
- Department of Pediatric Oncology Hematology, University of Heidelberg, Heidelberg, Germany
| | - Andreas E Kulozik
- Department of Pediatric Oncology Hematology, University of Heidelberg, Heidelberg, Germany
| | - Valter Gattei
- Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico, I.R.C.C.S., Aviano (PN), Italy
| | - Shai Izraeli
- Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel.,Tel Aviv University, Tel Aviv, Israel
| | - Giuseppe Basso
- Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Geertruy Te Kronnie
- Department of Women's and Children's Health, University of Padova, Padova, Italy
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New oncogenic subtypes in pediatric B-cell precursor acute lymphoblastic leukemia. Blood 2017; 130:1395-1401. [PMID: 28778863 DOI: 10.1182/blood-2017-05-742643] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 07/27/2017] [Indexed: 12/22/2022] Open
Abstract
Until recently, 20% to 30% of pediatric B-cell precursor acute lymphoblastic leukemia (BCP-ALL) could not be classified into any of the established molecular subtypes. Recent molecular studies of such cases have, however, further clarified their mutational spectrum and identified new oncogenic subtypes consisting of cases with DUX4 rearrangements, ETV6-RUNX1-like gene expression, MEF2D rearrangements, and ZNF384 rearrangements. In this review, we describe these new subtypes, which account for up to 50% of previously unclassified pediatric BCP-ALL cases.
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