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Wu Z, Song Q, Liu M, Hu Y, Peng X, Zhang Z, Yao X, Peng Q. Deciphering the role of HLF in idiopathic orbital inflammation: integrative analysis via bioinformatics and machine learning techniques. Sci Rep 2024; 14:19346. [PMID: 39164324 PMCID: PMC11336107 DOI: 10.1038/s41598-024-68890-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 07/29/2024] [Indexed: 08/22/2024] Open
Abstract
Idiopathic orbital inflammation, formerly known as NSOI (nonspecific orbital inflammation), is characterized as a spectrum disorder distinguished by the polymorphic infiltration of lymphoid tissue, presenting a complex and poorly understood etiology. Recent advancements have shed light on the HLF (Human lactoferrin), proposing its critical involvement in the regulation of hematopoiesis and the maintenance of innate mucosal immunity. This revelation has generated significant interest in exploring HLF's utility as a biomarker for NSOI, despite the existing gaps in our understanding of its biosynthetic pathways and operational mechanisms. Intersecting multi-omic datasets-specifically, common differentially expressed genes between GSE58331 and GSE105149 from the Gene Expression Omnibus and immune-related gene compendiums from the ImmPort database-we employed sophisticated analytical methodologies, including Lasso regression and support vector machine-recursive feature elimination, to identify HLF. Gene set enrichment analysis and gene set variation analysis disclosed significant immune pathway enrichment within gene sets linked to HLF. The intricate relationship between HLF expression and immunological processes was further dissected through the utilization of CIBERSORT and ESTIMATE algorithms, which assess characteristics of the immune microenvironment, highlighting a noteworthy association between increased HLF expression and enhanced immune cell infiltration. The expression levels of HLF were corroborated using data from the GSE58331 dataset, reinforcing the validity of our findings. Analysis of 218 HLF-related differentially expressed genes revealed statistically significant discrepancies. Fifteen hub genes were distilled using LASSO and SVM-RFE algorithms. Biological functions connected with HLF, such as leukocyte migration, ossification, and the negative regulation of immune processes, were illuminated. Immune cell analysis depicted a positive correlation between HLF and various cells, including resting mast cells, activated NK cells, plasma cells, and CD8 T cells. Conversely, a negative association was observed with gamma delta T cells, naive B cells, M0 and M1 macrophages, and activated mast cells. Diagnostic assessments of HLF in distinguishing NSOI showed promising accuracy. Our investigation delineates HLF as intricately associated with NSOI, casting light on novel biomarkers for diagnosis and progression monitoring of this perplexing condition.
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Affiliation(s)
- Zixuan Wu
- Hunan University of Traditional Chinese Medicine, Changsha, 410208, Hunan, China
| | - Qiujie Song
- Dongying People's Hospital (Dongying Hospital of Shandong Provincial Hospital Group), Dongying, Shandong, 257091, People's Republic of China
| | - Meiling Liu
- Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Yi Hu
- Hunan University of Traditional Chinese Medicine, Changsha, 410208, Hunan, China
| | - Xin Peng
- Hunan University of Traditional Chinese Medicine, Changsha, 410208, Hunan, China
| | - Zheyuan Zhang
- Hunan University of Traditional Chinese Medicine, Changsha, 410208, Hunan, China
| | - Xiaolei Yao
- Department of Ophthalmology, The First Affiliated Hospital of Hunan University of Traditional Chinese Medicine, Changsha, 410007, Hunan, China.
| | - Qinghua Peng
- Hunan University of Traditional Chinese Medicine, Changsha, 410208, Hunan, China.
- Department of Ophthalmology, The First Affiliated Hospital of Hunan University of Traditional Chinese Medicine, Changsha, 410007, Hunan, China.
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Ahmadi M, Mohajeri Khorasani A, Morshedzadeh F, Saffarzadeh N, Ghaderian SMH, Ghafouri-Fard S, Mousavi P. HLF is a promising prognostic, immunological, and therapeutic biomarker in human tumors. Biochem Biophys Rep 2024; 38:101725. [PMID: 38711550 PMCID: PMC11070826 DOI: 10.1016/j.bbrep.2024.101725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 04/14/2024] [Accepted: 04/27/2024] [Indexed: 05/08/2024] Open
Abstract
Despite past research linking HLF mutations to cancer development, no pan-cancer analyses of HLF have been published. As a result, we utilized multiple databases to illustrate the potential roles of HLF in diverse types of cancers. Several databases were used to assess HLF expression in the TCGA cancer samples. Additional assessments were undertaken to investigate the relationship between HLF and overall survival, immune cell infiltration, genetic alterations, promoter methylation, and protein-protein interaction. HLF's putative roles and the relationship between HLF expression and drug reactivity were investigated. HLF expression was shown to be lower in tumor tissues from a variety of malignancies when compared to normal tissues. There was a substantial link found between HLF expression and patient survival, genetic mutations, and immunological infiltration. HLF influenced the pathways of apoptosis, cell cycle, EMT, and PI3K/AKT signaling. Abnormal expression of HLF lowered sensitivity to numerous anti-tumor drugs and small compounds. According to our findings, reduced HLF expression drives cancer growth, and it has the potential to be identified as a vital biomarker for use in prognosis, immunotherapy, and targeted treatment of a range of malignancies.
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Affiliation(s)
- Mohsen Ahmadi
- Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Firouzeh Morshedzadeh
- Department of Genetics, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Negin Saffarzadeh
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Pegah Mousavi
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
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Gu Y, Xu ZJ, Zhou JD, Wen XM, Jin Y, Yuan Q, Xia PH, Feng Y, Yang L, Lin J, Qian J. SLC22A3 methylation-mediated gene silencing predicts adverse prognosis in acute myeloid leukemia. Clin Epigenetics 2022; 14:162. [PMID: 36461046 PMCID: PMC9716704 DOI: 10.1186/s13148-022-01373-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 11/09/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND We screened out several hypermethylated solute carrier (SLC) family genes in acute myeloid leukemia by reduced representation bisulfite sequencing. SLC22A3 encodes an organic cation transport protein, which is critical for drug transportation and cellular detoxification. SLC22A3 is significantly downregulated and associated with tumor progression and worse prognosis in a variety of solid tumors. However, there are no data available regarding the role of SLC22 in AML. This study aimed to explore the regulatory mechanism of DNA methylation on SLC22A3 expression, as well as its clinical significance in AML prognosis. RESULTS SLC22A3 was identified as the sole prognosis-associated gene among SLCs based on TCGA and Beat AML databases. Bone marrow mononuclear cells (BMMNCs) from AML, MDS patients, and healthy donors were enrolled in this study. SLC22A3 methylation was significantly increased in AML compared with controls and MDS patients; meanwhile, the expression level of SLC22A3 was decreased. SLC22A3 hypermethylation presented an obvious association with some specific clinical characteristics and affected the survival time of AML patients as an independent risk indicator. SLC22A3 expression changed regularly as the disease complete remissions and relapses. Demethylation drug 5-aza-2'-deoxycytidine (DAC) activated transcription and increased mRNA expression of SLC22A3 in leukemia cell lines and AML fresh BMMNCs. Knockdown of SLC22A3 in leukemia cells enhanced cell proliferation and suppressed cell apoptosis. Data from public programs were used for auxiliary screening of probable molecular mechanisms of SLC22A3 in the antileukemia effect. CONCLUSIONS Our results showed that increased methylation and decreased expression of SLC22A3 may be indicators of poor prognosis in AML. Methylation-silenced SLC22A3 expression may have potential guiding significance on antileukemia effect of DAC.
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Affiliation(s)
- Yu Gu
- grid.452247.2Department of Hematology, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,Zhenjiang Clinical Research Center of Hematology, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China
| | - Zi-jun Xu
- Zhenjiang Clinical Research Center of Hematology, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,grid.452247.2Laboratory Center, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China
| | - Jing-dong Zhou
- grid.452247.2Department of Hematology, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,Zhenjiang Clinical Research Center of Hematology, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China
| | - Xiang-mei Wen
- Zhenjiang Clinical Research Center of Hematology, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,grid.452247.2Laboratory Center, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China
| | - Ye Jin
- grid.452247.2Department of Hematology, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,Zhenjiang Clinical Research Center of Hematology, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China
| | - Qian Yuan
- Zhenjiang Clinical Research Center of Hematology, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,grid.452247.2Laboratory Center, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China
| | - Pei-hui Xia
- Zhenjiang Clinical Research Center of Hematology, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,grid.452247.2Laboratory Center, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China
| | - Yuan Feng
- grid.452247.2Department of Hematology, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,Zhenjiang Clinical Research Center of Hematology, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China
| | - Lei Yang
- grid.452247.2Department of Hematology, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,Zhenjiang Clinical Research Center of Hematology, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China
| | - Jiang Lin
- Zhenjiang Clinical Research Center of Hematology, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,grid.452247.2Laboratory Center, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China
| | - Jun Qian
- grid.452247.2Department of Hematology, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,Zhenjiang Clinical Research Center of Hematology, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China
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He GQ, Guo X, Jiang MY, Xu RR, Dai YL, Luo L, Gao J. Co-occurrence of TCF3-PBX1 gene fusion, and chromosomal aberration in a pediatric pre-B cell acute lymphoblastic leukemia with clitoris swelling: A case report and literature review. Medicine (Baltimore) 2021; 100:e24802. [PMID: 33663097 PMCID: PMC7909158 DOI: 10.1097/md.0000000000024802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/29/2021] [Indexed: 01/05/2023] Open
Abstract
RATIONALE Clitoris swelling as the initial clinical presentation of acute lymphoblastic leukemia (ALL) is extremely rare. These patients may be misdiagnosed with acute myeloid leukemia or solid tumor, and the main treatment can also be delayed. PATIENT CONCERNS A 2.10-year-old girl was referred to the pediatric surgery clinic with a worsening onset of clitoris swellings. The patient was afebrile and well appearing. Multiple retroperitoneal mass were confirmed by computed tomography (CT) and high serum neuron-specific enolase level was high. She was scheduled for an abdominal biopsy from the retroperitoneal mass suspicious of neuroblastoma. DIAGNOSES The child was eventually diagnosed as having precursor B cell ALL with central nervous system involved, with TCF3-PBX1 fusion gene and additional chromosomal aberrations, based on examinations of the bone marrow and brain magnetic resonance imaging. INTERVENTIONS Before the diagnosis of leukemia, the patient was given symptomatic treatment for 1 week. She was treated with chemotherapy in accordance with the Chinese Children's Cancer Group protocol 2015 after confirmed diagnosis. OUTCOMES After induction chemotherapy for ALL, although the girl had transiently clinical remission, the bone marrow aspirate indicated a poor outcome. Our patient discontinued treatment and discharged. From literature review, there was only 1 case of in acute myeloid leukemia with clitoris swelling as the initial symptom. LESSONS The clinical symptoms of ALL with clitoris swelling are not typical, with a high rate of misdiagnosis. When the cause of clitoris swelling is unknown, ALL should be considered. Bone marrow aspiration must be done before doing a more invasive investigation like biopsy.
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Affiliation(s)
- Guo-qian He
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education
- Department of Pediatrics
| | - Xia Guo
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education
- Department of Pediatrics
| | - Ming-yan Jiang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education
- Department of Pediatrics
| | - Rong-rong Xu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education
- Department of Radiology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Yi-ling Dai
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education
- Department of Pediatrics
| | - Lili Luo
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education
- Department of Pediatrics
| | - Ju Gao
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education
- Department of Pediatrics
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Ehrlich KC, Baribault C, Ehrlich M. Epigenetics of Muscle- and Brain-Specific Expression of KLHL Family Genes. Int J Mol Sci 2020; 21:E8394. [PMID: 33182325 PMCID: PMC7672584 DOI: 10.3390/ijms21218394] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/02/2020] [Accepted: 11/06/2020] [Indexed: 02/07/2023] Open
Abstract
KLHL and the related KBTBD genes encode components of the Cullin-E3 ubiquitin ligase complex and typically target tissue-specific proteins for degradation, thereby affecting differentiation, homeostasis, metabolism, cell signaling, and the oxidative stress response. Despite their importance in cell function and disease (especially, KLHL40, KLHL41, KBTBD13, KEAP1, and ENC1), previous studies of epigenetic factors that affect transcription were predominantly limited to promoter DNA methylation. Using diverse tissue and cell culture whole-genome profiles, we examined 17 KLHL or KBTBD genes preferentially expressed in skeletal muscle or brain to identify tissue-specific enhancer and promoter chromatin, open chromatin (DNaseI hypersensitivity), and DNA hypomethylation. Sixteen of the 17 genes displayed muscle- or brain-specific enhancer chromatin in their gene bodies, and most exhibited specific intergenic enhancer chromatin as well. Seven genes were embedded in super-enhancers (particularly strong, tissue-specific clusters of enhancers). The enhancer chromatin regions typically displayed foci of DNA hypomethylation at peaks of open chromatin. In addition, we found evidence for an intragenic enhancer in one gene upregulating expression of its neighboring gene, specifically for KLHL40/HHATL and KLHL38/FBXO32 gene pairs. Many KLHL/KBTBD genes had tissue-specific promoter chromatin at their 5' ends, but surprisingly, two (KBTBD11 and KLHL31) had constitutively unmethylated promoter chromatin in their 3' exons that overlaps a retrotransposed KLHL gene. Our findings demonstrate the importance of expanding epigenetic analyses beyond the 5' ends of genes in studies of normal and abnormal gene regulation.
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Affiliation(s)
- Kenneth C. Ehrlich
- Center for Biomedical Informatics and Genomics, Tulane University Health Sciences Center, New Orleans, LA 70112, USA;
| | - Carl Baribault
- Center for Research and Scientific Computing (CRSC), Tulane University Information Technology, Tulane University, New Orleans, LA 70112, USA;
| | - Melanie Ehrlich
- Center for Biomedical Informatics and Genomics, Tulane Cancer Center, Hayward Genetics Program, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
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Replication timing alterations in leukemia affect clinically relevant chromosome domains. Blood Adv 2020; 3:3201-3213. [PMID: 31698451 DOI: 10.1182/bloodadvances.2019000641] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 08/18/2019] [Indexed: 12/29/2022] Open
Abstract
Human B-cell precursor acute lymphoid leukemias (BCP-ALLs) comprise a group of genetically and clinically distinct disease entities with features of differentiation arrest at known stages of normal B-lineage differentiation. We previously showed that BCP-ALL cells display unique and clonally heritable, stable DNA replication timing (RT) programs (ie, programs describing the variable order of replication and subnuclear 3D architecture of megabase-scale chromosomal units of DNA in different cell types). To determine the extent to which BCP-ALL RT programs mirror or deviate from specific stages of normal human B-cell differentiation, we transplanted immunodeficient mice with quiescent normal human CD34+ cord blood cells and obtained RT signatures of the regenerating B-lineage populations. We then compared these with RT signatures for leukemic cells from a large cohort of BCP-ALL patients with varied genetic subtypes and outcomes. The results identify BCP-ALL subtype-specific features that resemble specific stages of B-cell differentiation and features that seem to be associated with relapse. These results suggest that the genesis of BCP-ALL involves alterations in RT that reflect biologically significant and potentially clinically relevant leukemia-specific epigenetic changes.
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7
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Lejman M, Włodarczyk M, Zawitkowska J, Kowalczyk JR. Comprehensive chromosomal aberrations in a case of a patient with TCF3-HLF-positive BCP-ALL. BMC Med Genomics 2020; 13:58. [PMID: 32245383 PMCID: PMC7118981 DOI: 10.1186/s12920-020-0709-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/24/2020] [Indexed: 12/16/2022] Open
Abstract
Background The use of high-throughput analytical techniques has enabled the description of acute lymphoblastic leukaemia (ALL) subtypes. The TCF3-HLF translocation is a very rare rearrangement in ALL that is associated with an extremely poor prognosis. The TCF3-HLF fusion gene in the described case resulted in the fusion of the homeobox-related gene of TCF3 to the leucine zipper domain of HLF. The TCF3-HLF fusion gene product acts as a transcriptional factor leading to the dedifferentiation of mature B lymphocytes into an immature state (lymphoid stem cells). This process initiates the formation of pre-leukaemic cells. Due to the rarity of this chromosomal aberration, only a few cases have been described in the literature. The advantage of this work is the presentation of an interesting case of clonal evolution of cancer cells and the cumulative implications (diagnostic and prognostic) of the patient’s genetic alterations. Case presentation This work presents a patient with diagnosed with TCF3-HLF-positive ALL. Moreover, the additional genetic alterations, which play a key role in the pathogenesis of ALL, were detected in this patient: deletion of a fragment from the long arm of chromosome 13 (13q12.2-q21.1) containing the RB1 gene, intragenic deletions within the PAX5 gene and NOTCH1 intragenic duplication. Conclusions A patient with coexistence of chromosomal alterations and the TCF3-HLF fusion has not yet been described. Identifying all these chromosomal aberrations at the time of diagnosis could be sufficient to determine the cumulative effects of the described deletions on the activity of other oncogenes or tumour suppressors, as well as on the clinical course of the disease. On the other hand, complex changes in the patient’s karyotype and clonal evolution of cancer cells call into question the effectiveness of experimental therapy.
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Affiliation(s)
- Monika Lejman
- Laboratory of Genetic Diagnostics, Department of Pediatric Hematology, Oncology, and Transplantology, Medical University of Lublin, ul. Antoniego Gębali 6, Lublin, Poland.
| | - Monika Włodarczyk
- Laboratory of Genetic Diagnostics, Medical University of Lublin, Lublin, Poland
| | - Joanna Zawitkowska
- Department of Pediatric Hematology, Oncology, and Transplantology, Medical University of Lublin, Lublin, Poland
| | - Jerzy R Kowalczyk
- Department of Pediatric Hematology, Oncology, and Transplantology, Medical University of Lublin, Lublin, Poland
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Implementation of RNA sequencing and array CGH in the diagnostic workflow of the AIEOP-BFM ALL 2017 trial on acute lymphoblastic leukemia. Ann Hematol 2020; 99:809-818. [PMID: 32078009 PMCID: PMC7069912 DOI: 10.1007/s00277-020-03953-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 02/06/2020] [Indexed: 11/03/2022]
Abstract
Risk-adapted therapy has significantly contributed to improved survival rates in pediatric acute lymphoblastic leukemia (ALL) and reliable detection of chromosomal aberrations is mandatory for risk group stratification. This study evaluated the applicability of panel-based RNA sequencing and array CGH within the diagnostic workflow of the German study group of the international AIEOP-BFM ALL 2017 trial. In a consecutive cohort of 117 children with B cell precursor (BCP) ALL, array analysis identified twelve cases with an IKZF1plus profile of gene deletions and one case of masked hypodiploidy. Genetic markers BCR-ABL1 (n = 1), ETV6-RUNX1 (n = 25), and rearrangements involving KMT2A (n = 3) or TCF3 (n = 3) were assessed by established conventional techniques such as karyotyping, FISH, and RT-PCR. Comparison of these results with RNA sequencing analysis revealed overall consistency in n=115/117 cases, albeit with one undetected AFF1-KMT2A fusion in RNA sequencing and one undetected ETV6-RUNX1 fusion in conventional analyses. The combined application of RNA sequencing, FISH, and CGH+SNP array reliably detected all genetic markers necessary for risk stratification and will be used as the diagnostic standard workflow for BCP-ALL patients enrolled in the AIEOP-BFM ALL 2017 study. Prospectively, consistent collection of genome-wide CGH+SNP array as well as RNA sequencing data will be a valuable source to elucidate new prognostic lesions beyond established markers of pediatric ALL. In this respect, RNA sequencing identified various gene fusions in up to half of the IKZF1plus (n = 6/12) and B-other (n = 19/36) cases but not in cases with hyperdiploid karyotypes (n = 35). Among these fusions, this study reports several previously undescribed in frame PAX5 fusions, including PAX5-MYO1G and PAX5-NCOA6.
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Watanabe K, Yokota K, Yoshida K, Matsumoto A, Iwamoto S. Kbtbd11 contributes to adipocyte homeostasis through the activation of upstream stimulatory factor 1. Heliyon 2019; 5:e02777. [PMID: 31844712 PMCID: PMC6895693 DOI: 10.1016/j.heliyon.2019.e02777] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/17/2019] [Accepted: 10/29/2019] [Indexed: 12/27/2022] Open
Abstract
The present study aimed to investigate the transcriptional regulation of Kbtbd11 in adipose tissue. To elucidate the physiological role of Kbtbd11 gene expression, adipose Kbtbd11 mRNA expression levels were estimated under various feeding states in wild-type mice. Kbtbd11 expression increased in a time-dependent manner in the adipose tissue in mice fed on chow diet, whereas the promotion of Kbtbd11 mRNA expression by refeeding was attenuated in mice fed on high-fat (HF) diet, suggesting the suppression of Kbtbd11 mRNA expression under HF diets and that changes in mRNA levels were associated with regulation of the transcription activity of Kbtbd11 by some transcription factors. To investigate the transcriptional regulation of Kbtbd11, the fragment upstream of either mouse Kbtbd11 or human KBTBD11 promoter was inserted into a luciferase vector. Luciferase reporter assays revealed that both mouse and human KBTBD11 promoter activity was increased by USF1. Direct USF1 binding to the Ebox in the Kbtbd11 promoter was confirmed by electrophoretic mobility shift and chromatin immunoprecipitation assays. In addition, the adipocyte differentiation marker levels increased instantly in Kbtbd11-overexpressing Usf1 knockdown cells than in Usf1 knockdown cells. These results imply an association of between Kbtbd11 with Usf1 expression and suggest the involvement of Kbtbd11 in a novel adipogenesis pathway.
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Hepatic leukemia factor is a novel leukemic stem cell regulator in DNMT3A, NPM1, and FLT3-ITD triple-mutated AML. Blood 2019; 134:263-276. [PMID: 31076446 DOI: 10.1182/blood.2018862383] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 05/02/2019] [Indexed: 12/20/2022] Open
Abstract
FLT3, DNMT3A, and NPM1 are the most frequently mutated genes in cytogenetically normal acute myeloid leukemia (AML), but little is known about how these mutations synergize upon cooccurrence. Here we show that triple-mutated AML is characterized by high leukemia stem cell (LSC) frequency, an aberrant leukemia-specific GPR56 highCD34low immunophenotype, and synergistic upregulation of Hepatic Leukemia Factor (HLF). Cell sorting based on the LSC marker GPR56 allowed isolation of triple-mutated from DNMT3A/NPM1 double-mutated subclones. Moreover, in DNMT3A R882-mutated patients, CpG hypomethylation at the HLF transcription start site correlated with high HLF mRNA expression, which was itself associated with poor survival. Loss of HLF via CRISPR/Cas9 significantly reduced the CD34+GPR56+ LSC compartment of primary human triple-mutated AML cells in serial xenotransplantation assays. HLF knockout cells were more actively cycling when freshly harvested from mice, but rapidly exhausted when reintroduced in culture. RNA sequencing of primary human triple-mutated AML cells after shRNA-mediated HLF knockdown revealed the NOTCH target Hairy and Enhancer of Split 1 (HES1) and the cyclin-dependent kinase inhibitor CDKN1C/p57 as novel targets of HLF, potentially mediating these effects. Overall, our data establish HLF as a novel LSC regulator in this genetically defined high-risk AML subgroup.
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