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Genes
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Genomic Aberrations in Hematologic Malignancies
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Genomic Aberrations in Hematologic Malignancies

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Cytogenomics".

Deadline for manuscript submissions: closed (15 April 2024) | Viewed by 15175

Special Issue Editors

Dr. Zhenya Tang

E-Mail Website
Guest Editor
Departments of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
Interests: hematological malignancies; lung cancer; structural chromosomal abnormalities; advanced technologies in molecular diagnostics
Special Issues, Collections and Topics in MDPI journals
Dr. Zejuan Li

E-Mail Website
Guest Editor
Institute for Academic Medicine, Houston Methodist Research Institute, Weill Cornell Medical College, Houston Methodist Hospital, Houston, TX 77030, USA
Interests: cancer; diagnostics; biomarker
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Recurrent genomic alterations presenting in various forms are characteristics for a variety of hematological malignancies. In this issue, we would like to focus on recurrent structural alterations that either lead to oncogenic gene fusions, such as translocations and/or inversions-derived formation of fusion genes such as t(9;22)(q34.1;q11.2) and related BCR::ABL1, t(8;21)(q22;q22.1) and related RUNX1::RUNX1T1, inv(16)(p13.1q22)/(16;16)(p13.1;q22) and related CBFB::MYH11, t(15;17)(q24;q21) and related PML::RARA; t(12;21)(p13.2;q22.1) and ETV6::RUNX1, and a wide spectrum of 11q23 abnormalities/KMT2A(MLL) rearrangement and related fusion genes; and/or hijacking enhancers and super-enhancers to dysregulate gene expressions such as MECOM, MYC, and IGH rearrangement in both myeloid and lymphoid neoplasms. They are widely applied as biomarkers for the diagnosis of specific entities and/or sub-entities of hematological malignancies, targeted therapies, and prognostic predictions in the field of hemato-oncology. Attributed to the widespread application of advanced next-generation sequencing (NGS)-based technologies and genome-wide comprehensive studies, tremendous novel fusion genes associated with cryptic chromosomal abnormalities have been identified in hematological malignancies in the past several decades. They all play important roles in the era of precision medicine.

Dr. Zhenya Tang
Dr. Zejuan Li
Guest Editors

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Keywords

  • chromosomal abnormalities
  • fusion gene
  • hijacking super-enhancer
  • translocation
  • inversion
  • whole-genome sequencing (WGS)
  • whole-transcriptome sequencing (WTS)
  • whole-exome sequencing (WES)

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Published Papers (5 papers)

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Research

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11 pages, 1596 KiB  
Article
Classification of Acute Myeloid Leukemia by Cell-Free DNA 5-Hydroxymethylcytosine
by Jianming Shao, Shilpan Shah, Siddhartha Ganguly, Youli Zu, Chuan He and Zejuan Li
Genes 2023, 14(6), 1180; https://doi.org/10.3390/genes14061180 - 28 May 2023
Cited by 4 | Viewed by 2266
Abstract
Epigenetic abnormality is a hallmark of acute myeloid leukemia (AML), and aberrant 5-hydroxymethylcytosine (5hmC) levels are commonly observed in AML patients. As epigenetic subgroups of AML correlate with different clinical outcomes, we investigated whether plasma cell-free DNA (cfDNA) 5hmC could categorize AML patients [...] Read more.
Epigenetic abnormality is a hallmark of acute myeloid leukemia (AML), and aberrant 5-hydroxymethylcytosine (5hmC) levels are commonly observed in AML patients. As epigenetic subgroups of AML correlate with different clinical outcomes, we investigated whether plasma cell-free DNA (cfDNA) 5hmC could categorize AML patients into subtypes. We profiled the genome-wide landscape of 5hmC in plasma cfDNA from 54 AML patients. Using an unbiased clustering approach, we found that 5hmC levels in genomic regions with a histone mark H3K4me3 classified AML samples into three distinct clusters that were significantly associated with leukemia burden and survival. Cluster 3 showed the highest leukemia burden, the shortest overall survival of patients, and the lowest 5hmC levels in the TET2 promoter. 5hmC levels in the TET2 promoter could represent TET2 activity resulting from mutations in DNA demethylation genes and other factors. The novel genes and key signaling pathways associated with aberrant 5hmC patterns could add to our understanding of DNA hydroxymethylation and highlight the potential therapeutic targets in AML. Our results identify a novel 5hmC-based AML classification system and further underscore cfDNA 5hmC as a highly sensitive marker for AML. Full article
(This article belongs to the Special Issue Genomic Aberrations in Hematologic Malignancies)
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8 pages, 641 KiB  
Article
Chronic Myelogenous Leukemia with Double Philadelphia Chromosome and Coexpression of p210 and p190 Fusion Transcripts
by Samara Silveira da Cruz, Aline Damasceno Seabra, Lais Helena Rescinho Macambira, Débora Monteiro Carneiro, Patrícia Ferreira Nunes, Thais Brilhante Pontes, Fernando Augusto Rodrigues Mello-Junior, Lucyana Barbosa Cardoso Leão, Fernanda de Nazaré Cardoso dos Santos Cordeiro, Thiago Xavier Carneiro, Caroline Aquino Moreira-Nunes and Rommel Mario Rodríguez Burbano
Genes 2022, 13(4), 580; https://doi.org/10.3390/genes13040580 - 25 Mar 2022
Viewed by 3105
Abstract
The Philadelphia (Ph+) chromosome, t(9;22)(q34;q11.2), originates from a chimeric gene called BCR-ABL and is present in more than 90% of CML patients. Most patients with CML express the protein p210 BCR-ABL and, with a frequency lower than 5%, express rare isoforms, the main [...] Read more.
The Philadelphia (Ph+) chromosome, t(9;22)(q34;q11.2), originates from a chimeric gene called BCR-ABL and is present in more than 90% of CML patients. Most patients with CML express the protein p210 BCR-ABL and, with a frequency lower than 5%, express rare isoforms, the main one being p190. In the transition from the chronic phase to the blast phase (BP), additional chromosomal abnormalities, such as the presence of the double Ph+ chromosome, are revealed. Of the 1132 patients analyzed via molecular biology in this study, two patients (0.17%) showed the co-expression of the p210 and p190 isoforms for the BCR-ABL transcript, with the concomitant presence of a double Ph+ chromosome, which was observed via conventional cytogenetics and confirmed by fluorescent in situ hybridization. The BCR-ABL/ABL% p210 and p190 ratio increased in these two patients from diagnosis to progression to blast crisis. To our knowledge, this is the first report in the literature of patients who co-expressed the two main BCR-ABL transcript isoforms and concomitantly presented Ph+ chromosome duplication. The evolution from the chronic phase to BP often occurs within 5 to 7 years, and, in this study, the evolution to BP was earlier, since disease-free survival was on average 4.5 months and overall survival was on average 9.5 months. The presence of the p190 transcript and the double Ph+ chromosome in CML may be related to the vertiginous progression of the disease. Full article
(This article belongs to the Special Issue Genomic Aberrations in Hematologic Malignancies)
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Review

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13 pages, 746 KiB  
Review
Commonly Assessed Markers in Childhood BCP-ALL Diagnostic Panels and Their Association with Genetic Aberrations and Outcome Prediction
by Jan Kulis, Łukasz Sędek, Łukasz Słota, Bartosz Perkowski and Tomasz Szczepański
Genes 2022, 13(8), 1374; https://doi.org/10.3390/genes13081374 - 31 Jul 2022
Cited by 9 | Viewed by 3168
Abstract
Immunophenotypic characterization of leukemic cells with the use of flow cytometry (FC) is a fundamental tool in acute lymphoblastic leukemia (ALL) diagnostics. A variety of genetic aberrations underlie specific B-cell precursor ALL (BCP-ALL) subtypes and their identification is of great importance for risk [...] Read more.
Immunophenotypic characterization of leukemic cells with the use of flow cytometry (FC) is a fundamental tool in acute lymphoblastic leukemia (ALL) diagnostics. A variety of genetic aberrations underlie specific B-cell precursor ALL (BCP-ALL) subtypes and their identification is of great importance for risk group stratification. These aberrations include: ETV6::RUNX1 fusion gene, Philadelphia chromosome (BCR::ABL1 fusion gene), rearrangements of the KMT2A, TCF3::PBX1 fusion gene and changes in chromosome number (hyperdiploidy and hypodiploidy). Diagnostic panels for BCP-ALL usually include B-cell lineage specific antigens: CD19, CD10, CD20, maturation stage markers: CD34, CD10, CD38, TdT, IgM and other markers useful for possible genetic subtype indication. Some genetic features of leukemic cells (blasts) are associated with expression of certain antigens. This review comprehensively summarizes all known research data on genotype-immunophenotype correlations in BCP-ALL. In some cases, single molecules are predictive of particular genetic subtypes, i.e., NG2 with KMT2A gene rearrangements or CD123 with hyperdiploidy. However, much more information on possible genotype or prognosis can be obtained with wider (≥8-color) panels. In several studies, a quantitative antigen expression scale and advanced statistical analyses were used to further increase the specificity and sensitivity of genotype/immunophenotype correlation detection. Fast detection of possible genotype/immunophenotype correlations makes multicolor flow cytometry an essential tool for initial leukemia diagnostics and stratification. Full article
(This article belongs to the Special Issue Genomic Aberrations in Hematologic Malignancies)
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Other

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11 pages, 1816 KiB  
Case Report
Case Report: Rare IKZF1 Gene Fusions Identified in Neonate with Congenital KMT2A-Rearranged Acute Lymphoblastic Leukemia
by Laura N. Eadie, Jacqueline A. Rehn, James Breen, Michael P. Osborn, Sophie Jessop, Charlotte E. J. Downes, Susan L. Heatley, Barbara J. McClure, David T. Yeung, Tamas Revesz, Benjamin Saxon and Deborah L. White
Genes 2023, 14(2), 264; https://doi.org/10.3390/genes14020264 - 19 Jan 2023
Cited by 1 | Viewed by 2648
Abstract
Chromosomal rearrangements involving the KMT2A gene occur frequently in acute lymphoblastic leukaemia (ALL). KMT2A-rearranged ALL (KMT2Ar ALL) has poor long-term survival rates and is the most common ALL subtype in infants less than 1 year of age. KMT2Ar ALL frequently occurs [...] Read more.
Chromosomal rearrangements involving the KMT2A gene occur frequently in acute lymphoblastic leukaemia (ALL). KMT2A-rearranged ALL (KMT2Ar ALL) has poor long-term survival rates and is the most common ALL subtype in infants less than 1 year of age. KMT2Ar ALL frequently occurs with additional chromosomal abnormalities including disruption of the IKZF1 gene, usually by exon deletion. Typically, KMT2Ar ALL in infants is accompanied by a limited number of cooperative le-sions. Here we report a case of aggressive infant KMT2Ar ALL harbouring additional rare IKZF1 gene fusions. Comprehensive genomic and transcriptomic analyses were performed on sequential samples. This report highlights the genomic complexity of this particular disease and describes the novel gene fusions IKZF1::TUT1 and KDM2A::IKZF1. Full article
(This article belongs to the Special Issue Genomic Aberrations in Hematologic Malignancies)
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9 pages, 1472 KiB  
Case Report
Acute Promyelocytic Leukemia with Rare Genetic Aberrations: A Report of Three Cases
by Guang Liu, Lanting Liu, Daniel Di Bartolo, Katie Y. Li and Xia Li
Genes 2023, 14(1), 46; https://doi.org/10.3390/genes14010046 - 23 Dec 2022
Cited by 2 | Viewed by 2787
Abstract
Acute promyelocytic leukemia (APL) is a unique subtype of acute myeloid leukemia (AML) that is characterized by the PML::RARA fusion or, more rarely, a variant RARA translocation. While APL can be clinically suspected, diagnosis of APL requires genetic confirmation. Targeted therapy such as [...] Read more.
Acute promyelocytic leukemia (APL) is a unique subtype of acute myeloid leukemia (AML) that is characterized by the PML::RARA fusion or, more rarely, a variant RARA translocation. While APL can be clinically suspected, diagnosis of APL requires genetic confirmation. Targeted therapy such as all-trans-retinoic acid (ATRA) and arsenic trioxide (ATO) has dramatically improved the prognosis of APL patients, but this is dependent on timely genetic testing as different fusions and/or mutations can affect therapeutic outcomes. Here we report three APL cases with various genetic aberrations: cryptic PML::RARA fusion, variant RARA rearrangement, and typical PML::RARA fusion with co-existing FLT3-ITD mutation. They serve to illustrate the utility of integrating genetic testing, using chromosome analysis, fluorescence in situ hybridization (FISH), reverse transcriptase-polymerase chain reaction (RT-PCR), and next-generation sequencing (NGS) in providing a detailed understanding of the genetic alterations underlying each patient’s disease. Full article
(This article belongs to the Special Issue Genomic Aberrations in Hematologic Malignancies)
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