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Advances in Genetic Research and Molecular Diagnostics for Hematological Diseases
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Advances in Genetic Research and Molecular Diagnostics for Hematological Diseases

A special issue of Biomedicines (ISSN 2227-9059). This special issue belongs to the section "Molecular Genetics and Genetic Diseases".

Deadline for manuscript submissions: 31 August 2026 | Viewed by 9303

Editors

Dr. Ying S. Zou

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Guest Editor
Department of Genomic Medicine and Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
Interests: chromosomal abnormality; structural variant; copy number variant; gene fusion/rearrangement
Special Issues, Collections and Topics in MDPI journals
Dr. Leonard N. Yenwongfai

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Guest Editor
Department of Pathology, Division of Hematopathology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
Interests: hematologic malignancies; advanced genomic profiling techniques; computational pathology

Special Issue Information

Dear Colleagues,

This Special Issue is dedicated to exploring cutting-edge genetic research in hematological diseases, with a particular emphasis on both malignant and benign disorders, encompassing inherited and acquired conditions. The complex genetic landscape of these diseases poses significant challenges, underscoring the need for innovative technological approaches to advance our understanding and improve therapeutic outcomes.

Recent advancements in molecular diagnostic techniques—such as next-generation sequencing (NGS), CRISPR gene editing, microarray analysis, optical genome mapping, whole genome sequencing, long-read sequencing, whole transcriptomes, proteomics, digital pathology, and computational intelligence, particularly the use of deep convolutional neural networks (DCNNs)—have revolutionized diagnostic and treatment approaches in hematology. This issue will highlight key research that uncovers the genetic mechanisms driving a range of hematological conditions, including leukemias, lymphomas, and other benign disorders.

This Special Issue will focus on the practical application of advanced molecular methodologies and digital technologies in clinical settings. By highlighting their effectiveness in enhancing diagnostic accuracy and guiding treatment strategies, the issue aims to foster the integration of genetic insights into personalized medicine, ultimately advancing patient care and management in the context of hematological disorders.

Dr. Ying S. Zou
Dr. Leonard N. Yenwongfai
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-anonymized peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomedicines is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • hematological diseases
  • genetic research
  • benign hematology
  • inherited disorders
  • next-generation sequencing/long-read sequencing
  • optical genome mapping
  • transcriptome
  • proteomics
  • digital pathology
  • deep convolutional neural networks

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Published Papers (6 papers)

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Research

15 pages, 11141 KB  
Article
Genetic Spectrum of Hemoglobinopathies in Reproductive-Age Individuals from a Hospital-Based Cohort in Guangdong, China: A 7-Year Retrospective Analysis
by Yanchao Wang, Jiajia Xian, Jianchun He, Shaoying Li, Zhenlan Xia and Ding Wang
Biomedicines 2026, 14(6), 1326; https://doi.org/10.3390/biomedicines14061326 - 11 Jun 2026
Viewed by 425
Abstract
Background: Hemoglobinopathies, including thalassemia and structural hemoglobin variants, are among the most prevalent inherited disorders worldwide and represent a major public health concern in southern China. Accurate characterization of both common and rare variants is essential for carrier screening, genetic counseling, and [...] Read more.
Background: Hemoglobinopathies, including thalassemia and structural hemoglobin variants, are among the most prevalent inherited disorders worldwide and represent a major public health concern in southern China. Accurate characterization of both common and rare variants is essential for carrier screening, genetic counseling, and prevention. However, routine molecular screening is generally restricted to common pathogenic variants, potentially overlooking rare hemoglobinopathy subtypes. This study aimed to characterize the spectrum of hemoglobinopathies in a large hospital-based cohort of reproductive-age individuals from Guangdong, China, and to evaluate a genotype–phenotype discordance-guided secondary testing strategy. Methods: A retrospective hospital-based study was conducted in 71,676 reproductive-age individuals who underwent hemoglobinopathy screening at our hospital in Guangdong, China, between 2018 and 2024. Hematological and routine genetic analyses were performed in parallel. Cases exhibiting genotype–phenotype discordance were further investigated using tailored secondary molecular approaches selected according to specific hematological findings. Results: In this cohort, 10,412 hemoglobinopathies were identified. Thalassemia accounted for 10,217 cases (98.13%), including α-thalassemia (8026), β-thalassemia (2561), δβ-thalassemia (17), γ-thalassemia (10), and δ-thalassemia (4). Structural hemoglobin variants comprised 195 cases (1.91%). Among the 788 genotype–phenotype discordant cases, secondary analysis yielded a positive detection rate of 36.80% (290/788). Conclusions: This study provides large-scale hospital-based data on the distribution of hemoglobinopathies among reproductive-age individuals in Guangdong. Review of genotype–phenotype discordance improved the detection of rare variants beyond routine screening and may facilitate the development of tailored secondary testing strategies. Further studies are warranted to validate its clinical utility and applicability. Full article
(This article belongs to the Special Issue Advances in Genetic Research and Molecular Diagnostics for Hematological Diseases)
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13 pages, 723 KB  
Article
Associations of rs55829688 and rs145204276 Promoter Variants with lncRNA GAS5 Expression in AML: Prognostic Significance and Functional Analysis
by Djordje Pavlovic, Natasa Tosic, Isidora Curic, Bojan Ristivojevic, Zlatko Pravdic, Nada Suvajdzic Vukovic, Sonja Pavlovic, Branka Zukic and Vladimir Gasic
Biomedicines 2026, 14(3), 504; https://doi.org/10.3390/biomedicines14030504 - 25 Feb 2026
Viewed by 812
Abstract
Background/Objectives: Acute myeloid leukemia is a genetically diverse hematological malignancy where patient outcomes vary significantly. Long non-coding RNA (lncRNA) GAS5 acts as a tumor suppressor and is frequently downregulated in various cancers, as well as in AML. In the current study, we [...] Read more.
Background/Objectives: Acute myeloid leukemia is a genetically diverse hematological malignancy where patient outcomes vary significantly. Long non-coding RNA (lncRNA) GAS5 acts as a tumor suppressor and is frequently downregulated in various cancers, as well as in AML. In the current study, we aimed to explore the effects of GAS5 promoter variants on its expression levels in AML patients, their prognostic significance, and to investigate their functional effects. Methods: The GAS5 promoter region containing rs55829688 and rs145204276 was sequenced in 75 AML patients. Statistical analyses were performed to assess their associations with GAS5 expression and outcomes. An in vitro functional study in K562 cells evaluated the effects of these variants on the transcriptional activity of constructs containing each variant. In silico analysis was used to predict changes to transcription factor binding sites. Results: Patients carrying the rs55829688 TC/CC genotype exhibited lower GAS5 expression and were more frequently categorized into the adverse risk group. In intermediate-risk patients, this genotype trended toward lower overall survival and higher bone marrow blast percentages. In vitro, the construct harboring the rs55829688 C allele showed a two-fold decrease in reporter gene activity compared to the construct bearing both wild type alleles. In silico analysis identified RUNX3 as the most likely transcription factor affected by this variant. The variant rs145204276 was considered for the first time in AML; however, no significant clinical associations or transcriptional effects were found. Conclusions: Taken together, our findings provide evidence that the rs55829688 promoter variant reduces GAS5 expression in AML and could potentially be a prognostic marker. Full article
(This article belongs to the Special Issue Advances in Genetic Research and Molecular Diagnostics for Hematological Diseases)
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13 pages, 2358 KB  
Article
Low-VAF TP53-Mutated AML Displays Distinct Biological Features in a Single-Center Cohort
by Xiaoxuan Lu, Xiaohang Ma, Kainan Zhang, Shun Zhang, Fangfang Wei, Hao Jiang, Qian Jiang, Yingjun Chang, Xiaojun Huang and Xiaosu Zhao
Biomedicines 2026, 14(1), 180; https://doi.org/10.3390/biomedicines14010180 - 14 Jan 2026
Cited by 1 | Viewed by 1155
Abstract
Background: The International Consensus Classification (ICC) currently proposes an empirical variant allele frequency (VAF) threshold of 10% to define TP53-mutated acute myeloid leukemia (AML) and to distinguish oncogenic driver from concomitant mutations. However, the optimal cutoff remains uncertain, and the biological and [...] Read more.
Background: The International Consensus Classification (ICC) currently proposes an empirical variant allele frequency (VAF) threshold of 10% to define TP53-mutated acute myeloid leukemia (AML) and to distinguish oncogenic driver from concomitant mutations. However, the optimal cutoff remains uncertain, and the biological and clinical features of low-VAF cases have not been systematically characterized. Methods: In this single-center retrospective cohort study, we stratified TP53-mutated AML by a 10% VAF cutoff and compared clinical characteristics, cytogenetic and molecular profiles, and survival outcomes between groups. Results: The VAF < 10% group exhibited a distinctive profile: fewer adverse cytogenetic abnormalities [complex karyotype, −7, −5/del(5q)], a more adverse molecular profile (EVI1 overexpression, greater co-mutation burden, higher frequencies of ASXL1 and SRSF2 mutations), and a higher proportion of CD34+CD38− blast immunophenotype. TP53 hotspot mutations were also more common. Survival analyses showed poor prognosis in both groups, and the VAF < 10% group showed numerically longer survival without statistical significance, indicating no clear survival advantage for low VAF. Conclusions: These data support the clinical relevance of the ICC 10% threshold. TP53-mutated AML with VAF < 10% may represent a biologically distinct subgroup. Further multicenter studies with larger cohorts are needed to validate and refine the VAF threshold for prognostic evaluation and individualized management. Full article
(This article belongs to the Special Issue Advances in Genetic Research and Molecular Diagnostics for Hematological Diseases)
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16 pages, 2252 KB  
Article
Racial Differences in the Molecular Genetic Biomarkers of Diffuse Large B-Cell Lymphoma
by Marco D. Gomes, Kevin Sun, Ji Li, William Middlezong, Victoria Stinnett, Laura Morsberger, Ying S. Zou and Yi Huang
Biomedicines 2025, 13(11), 2782; https://doi.org/10.3390/biomedicines13112782 - 14 Nov 2025
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Abstract
Background/Objectives: Diffuse large B-cell lymphoma (DLBCL) exhibits pronounced racial disparities in incidence and outcomes, yet the molecular basis remains poorly understood. Here, we examined racial differences in gene rearrangements (MYC, BCL2, BCL6), fusions (IGH::MYC, IGH [...] Read more.
Background/Objectives: Diffuse large B-cell lymphoma (DLBCL) exhibits pronounced racial disparities in incidence and outcomes, yet the molecular basis remains poorly understood. Here, we examined racial differences in gene rearrangements (MYC, BCL2, BCL6), fusions (IGH::MYC, IGH::BCL2), and their interactions among White, Black, Asian, and Other-race groups in patients with DLBCL to uncover genetic drivers of disparities. Methods: We analyzed 919 DLBCL cases (2006–2023) from Johns Hopkins Hospital using fluorescence in situ hybridization to detect gene abnormalities. We used logistic regression and proportional odds models, adjusted for age and sex, to evaluate racial differences in five gene abnormalities and 10 gene–gene interaction pairs. Pearson’s Chi-squared and Goodman–Kruskal’s gamma tests assessed prevalence and interaction severity across racial groups. Results: MYC rearrangements and the MYC*IGH::MYC interaction were marginally more frequent in the White group than in Black and Other groups (p = 0.092, p = 0.098, respectively). IGH::BCL2 fusions were more prevalent in the Asian group than in the White group (p = 0.095), and the BCL2*IGH::BCL2 interaction was significantly higher in the Asian group (p = 0.049) than in the White group. Although high-grade B-cell lymphoma (HGBCL) prevalence showed no significant racial differences (p = 0.16), the Asian group exhibited a higher proportion of aggressive HGBCL with concurrent IGH::MYC and IGH::BCL2 fusions compared with the White group (p = 0.076). Age significantly influenced all gene abnormalities and interactions (p < 0.001–0.052), except for MYC rearrangements and specific pairs. Sex and sex–race interactions showed no significant effects. Conclusions: This study highlights molecular contributions to the racial differences in DLBCL disease. Further research collecting ancestry-specific biomarkers, treatment regimens, and clinical variables and outcomes is needed to advance personalized treatment strategies. Full article
(This article belongs to the Special Issue Advances in Genetic Research and Molecular Diagnostics for Hematological Diseases)
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16 pages, 4142 KB  
Article
Acute Myeloid Leukemia Genome Characterization Study and Subtype Classification Employing Feature Selection and Bayesian Networks
by Zhenzhen Li, Jingwen Li, Sifan Li, Yangyang Wang and Jihan Wang
Biomedicines 2025, 13(5), 1067; https://doi.org/10.3390/biomedicines13051067 - 28 Apr 2025
Cited by 1 | Viewed by 2774
Abstract
Background: The precise diagnosis and classification of acute myeloid leukemia (AML) has important implications for clinical management and medical research. Methods: We investigated the expression of protein-coding genes in blood samples from AML patients and controls using The Cancer Genome Atlas (TCGA) and [...] Read more.
Background: The precise diagnosis and classification of acute myeloid leukemia (AML) has important implications for clinical management and medical research. Methods: We investigated the expression of protein-coding genes in blood samples from AML patients and controls using The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases. Subsequently, we applied the feature selection method of the least absolute shrinkage and selection operator (LASSO) to select the optimal gene subset for classifying AML patients and controls as well as between a particular FAB subtype and other subtypes of AML. Results: Using LASSO method, we identified a subset of 101 genes that could effectively distinguish between AML patients and control individuals; these genes included 70 up-regulated and 31 down-regulated genes in AML. Functional annotation and pathway analysis indicated the involvement of these genes in RNA-related pathways, which was also consistent with the epigenetic changes observed in AML. Results from survival analysis revealed that several genes are correlated with the overall survival in AML patients. Additionally, LASSO-based gene subset analysis successfully revealed differences between certain AML subtypes, providing valuable insights into subtype-specific molecular mechanisms and differentiation therapy. Conclusions: This study demonstrated the application of machine learning in genomic data analysis for identifying gene subsets relevant to AML diagnosis and classification, which could aid in improving the understanding of the molecular landscape of AML. The identification of survival-related genes and subtype-specific markers may lead to the identification of novel targets for personalized medicine in the treatment of AML. Full article
(This article belongs to the Special Issue Advances in Genetic Research and Molecular Diagnostics for Hematological Diseases)
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18 pages, 2132 KB  
Article
Functional Role of Fatty Acid Synthase for Signal Transduction in Core-Binding Factor Acute Myeloid Leukemia with an Activating c-Kit Mutation
by Ruimeng Zhuang, Bente Siebels, Konstantin Hoffer, Anna Worthmann, Stefan Horn, Nikolas Christian Cornelius von Bubnoff, Cyrus Khandanpour, Niklas Gebauer, Sivahari Prasad Gorantla, Hanna Voss, Hartmut Schlüter, Malte Kriegs, Walter Fiedler, Carsten Bokemeyer, Manfred Jücker and Maxim Kebenko
Biomedicines 2025, 13(3), 619; https://doi.org/10.3390/biomedicines13030619 - 3 Mar 2025
Cited by 3 | Viewed by 2322
Abstract
Background/Objectives: Acute myeloid leukemia (AML) is a rare hematological malignancy with a poor prognosis. Activating c-Kit (CD117) mutations occur in 5% of de novo AML and 30% of core-binding factor (CBF) AML, leading to worse clinical outcomes. Posttranslational modifications, particularly with myristic [...] Read more.
Background/Objectives: Acute myeloid leukemia (AML) is a rare hematological malignancy with a poor prognosis. Activating c-Kit (CD117) mutations occur in 5% of de novo AML and 30% of core-binding factor (CBF) AML, leading to worse clinical outcomes. Posttranslational modifications, particularly with myristic and palmitic acid, are crucial for various cellular processes, including membrane organization, signal transduction, and apoptosis regulation. However, most research has focused on solid tumors, with limited understanding of these mechanisms in AML. Fatty acid synthase (FASN), a key palmitoyl-acyltransferase, regulates the subcellular localization, trafficking, and degradation of target proteins, such as H-Ras, N-Ras, and FLT3-ITDmut receptors in AML. Methods: In this study, we investigated the role of FASN in two c-Kit-N822K-mutated AML cell lines using FASN knockdown via shRNA and the FASN inhibitor TVB-3166. Functional implications, including cell proliferation, were assessed through Western blotting, mass spectrometry, and PamGene. Results: FASN inhibition led to an increased phosphorylation of c-Kit (p-c-Kit), Lyn kinase (pLyn), MAP kinase (pMAPK), and S6 kinase (pS6). Furthermore, we observed sustained high expression of Gli1 in Kasumi1 cells following FASN inhibition, which is well known to be mediated by the upregulation of pS6. Conclusions: The combination of TVB-3166 and the Gli inhibitor GANT61 resulted in a significant reduction in the survival of Kasumi1 cells. Full article
(This article belongs to the Special Issue Advances in Genetic Research and Molecular Diagnostics for Hematological Diseases)
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