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Shao J, Shah S, Ganguly S, Zu Y, He C, Li Z. Classification of Acute Myeloid Leukemia by Cell-Free DNA 5-Hydroxymethylcytosine. Genes (Basel) 2023; 14:1180. [PMID: 37372359 PMCID: PMC10298116 DOI: 10.3390/genes14061180] [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: 04/17/2023] [Revised: 05/23/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
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 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.
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Affiliation(s)
- Jianming Shao
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Shilpan Shah
- Neal Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA
- Weill Cornell Medical College, New York, NY 10065, USA
| | - Siddhartha Ganguly
- Neal Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA
- Weill Cornell Medical College, New York, NY 10065, USA
- Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Youli Zu
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
- Weill Cornell Medical College, New York, NY 10065, USA
- Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Chuan He
- Department of Chemistry, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Zejuan Li
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
- Weill Cornell Medical College, New York, NY 10065, USA
- Houston Methodist Research Institute, Houston, TX 77030, USA
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Pathak E, Mishra R. Deciphering the link between Diabetes mellitus and SARS-CoV-2 infection through differential targeting of microRNAs in the human pancreas. J Endocrinol Invest 2022; 45:537-550. [PMID: 34669152 PMCID: PMC8527307 DOI: 10.1007/s40618-021-01693-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/10/2021] [Indexed: 01/08/2023]
Abstract
PURPOSE Coronavirus Disease 2019 (COVID-19) severity and Diabetes mellitus affect each other bidirectionally. However, the cause of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) infection on the incidence of diabetes is unclear. In the SARS-CoV-2-infected cells, host microRNAs (miRNAs) may target the native gene transcripts as well as the viral genomic and subgenomic RNAs. Here, we investigated the role of miRNAs in linking Diabetes to SARS-CoV-2 infection in the human pancreas. METHODS Differential gene expression and disease enrichment analyses were performed on an RNA-Seq dataset of human embryonic stem cell-derived (hESC) mock-infected and SARS-CoV-2-infected pancreatic organoids to obtain the dysregulated Diabetes-associated genes. The miRNA target prediction for the Diabetes-associated gene transcripts and the SARS-CoV-2 RNAs has been made to determine the common miRNAs targeting them. Minimum Free Energy (MFE) analysis was done to identify the miRNAs, preferably targeting SARS-CoV-2 RNAs over the Diabetes-associated gene transcripts. RESULTS The gene expression and disease enrichment analyses of the RNA-Seq data have revealed five biomarker genes, i.e., CP, SOCS3, AGT, PSMB8 and CFB that are associated with Diabetes and get significantly upregulated in the pancreas following SARS-CoV-2-infection. Four miRNAs, i.e., hsa-miR-298, hsa-miR-3925-5p, hsa-miR-4691-3p and hsa-miR-5196-5p, showed preferential targeting of the SARS-CoV-2 genome over the cell's Diabetes-associated messenger RNAs (mRNAs) in the human pancreas. CONCLUSION Our study proposes that the differential targeting of the Diabetes-associated host genes by the miRNAs may lead to diabetic complications or new-onset Diabetes that can worsen the condition of COVID-19 patients.
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Affiliation(s)
| | - R Mishra
- Bioinformatics, MMV, Institute of Science, Banaras Hindu University, Varanasi, 221005, India.
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3
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Mayr P, Grünewald T, Filippini Velazquez G, Rank A, Schmid C, Harloff M, Märkl B, Trepel M, Hirschbühl K, Pfeiffer T, Claus R. Transfusion‐refractory pancytopenia with
MDS
‐like morphologic alterations of the bone marrow in a 29‐year old man: A mimicry manifestation caused by scurvy. Br J Haematol 2022; 197:627-630. [DOI: 10.1111/bjh.18064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/13/2022] [Accepted: 01/14/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Patrick Mayr
- Hematology and Oncology, Medical Faculty University of Augsburg Augsburg Germany
| | - Tatiana Grünewald
- Hematology and Oncology, Medical Faculty University of Augsburg Augsburg Germany
| | | | - Andreas Rank
- Hematology and Oncology, Medical Faculty University of Augsburg Augsburg Germany
| | - Christoph Schmid
- Hematology and Oncology, Medical Faculty University of Augsburg Augsburg Germany
| | - Manuela Harloff
- General Pathology and Molecular Diagnostics, Medical Faculty University of Augsburg Augsburg Germany
| | - Bruno Märkl
- General Pathology and Molecular Diagnostics, Medical Faculty University of Augsburg Augsburg Germany
| | - Martin Trepel
- Hematology and Oncology, Medical Faculty University of Augsburg Augsburg Germany
| | - Klaus Hirschbühl
- Hematology and Oncology, Medical Faculty University of Augsburg Augsburg Germany
| | - Tim Pfeiffer
- Hematology and Oncology, Medical Faculty University of Augsburg Augsburg Germany
| | - Rainer Claus
- Hematology and Oncology, Medical Faculty University of Augsburg Augsburg Germany
- General Pathology and Molecular Diagnostics, Medical Faculty University of Augsburg Augsburg Germany
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He P, Lei J, Zou LX, Zhou GZ, Peng L, Deng Q, Liu XL. Effects of hypoxia on DNA hydroxymethylase Tet methylcytosine dioxygenase 2 in a KG-1 human acute myeloid leukemia cell line and its mechanism. Oncol Lett 2021; 22:692. [PMID: 34457047 PMCID: PMC8358611 DOI: 10.3892/ol.2021.12953] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 06/04/2021] [Indexed: 12/20/2022] Open
Abstract
Hypoxia is involved in the epigenetic modification of leukemia. As an important DNA hydroxymethylase and a tumor suppressor gene, the expression regulating mechanism of Tet methylcytosine dioxygenase 2 (TET2) remains unclear. The aim of the present study was to explore whether hypoxia and hypoxia-inducible factor 1α (HIF-1α) regulate TET2 gene expression and its demethylation function in acute myeloid leukemia (AML). The human AML cell line KG-1 was used in the present study. The results demonstrated that hypoxia could increase proliferation, enhance metabolism and inhibit apoptosis in KG-1 cells, as detected by the cell counting kit-8 assay, lactate dehydrogenase assay and Annexin V-FITC/propidium iodide staining, respectively. Hypoxia reduced the genome methylation status in KG-1 cells detected using 5-methylcytosine and 5-hydroxymethylcytosine detection kits. In addition, HIF-1α overexpression increased TET2 expression, 5-hmC level and cyclin-dependent kinase inhibitor 2B [p15(INK4B)] gene demethylation compared with the HIF-1α non-overexpression group in KG-1 cells detected by reverse transcription-quantitative PCR, western blotting, 5-hydroxymethylcytosine detection kits and methylation-specific PCR, respectively. The inhibition of HIF-1α by inhibitor YC-1 reduced demethylation in KG-1 cells by decreasing TET2 expression. It was also revealed that HIF-1α could enhance TET2 transcriptional activity by binding to the hypoxia response element of the TET2 gene promoter region using chromatin immunoprecipitation and luciferase reporter gene assays. TET2 may be a potential target gene regulated by HIF-1α. Hypoxia was demonstrated to regulate the expression of TET2 by HIF-1α, which in turn affected the methylation and expression of downstream target genes and served a role in the occurrence and progression of leukemia. In the present study, the association between hypoxia metabolism and epigenetic regulation in AML was investigated and the findings provided a new idea and experimental basis for the diagnosis and treatment of hematologic malignancies.
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Affiliation(s)
- Ping He
- Department of Hematology, The Affiliated Changsha Hospital, Hunan Normal University, Changsha, Hunan 410006, P.R. China
| | - Jian Lei
- Department of Pathology, The Affiliated Tumor Hospital, Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, P.R. China
| | - Li-Xin Zou
- Department of Hematology, The Affiliated Changsha Hospital, Hunan Normal University, Changsha, Hunan 410006, P.R. China
| | - Gui-Zhen Zhou
- Department of Hematology, Changsha Central Hospital, Changsha, Hunan 410018, P.R. China
| | - Lang Peng
- Department of Hematology, The Affiliated Changsha Hospital, Hunan Normal University, Changsha, Hunan 410006, P.R. China
| | - Qian Deng
- Department of Hematology, The Affiliated Changsha Hospital, Hunan Normal University, Changsha, Hunan 410006, P.R. China
| | - Xiao-Liu Liu
- Department of Hematology, The Affiliated Changsha Hospital, Hunan Normal University, Changsha, Hunan 410006, P.R. China
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Seipel K, Graber C, Flückiger L, Bacher U, Pabst T. Rationale for a Combination Therapy with the STAT5 Inhibitor AC-4-130 and the MCL1 Inhibitor S63845 in the Treatment of FLT3-Mutated or TET2-Mutated Acute Myeloid Leukemia. Int J Mol Sci 2021; 22:ijms22158092. [PMID: 34360855 PMCID: PMC8347059 DOI: 10.3390/ijms22158092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/19/2021] [Accepted: 07/26/2021] [Indexed: 12/27/2022] Open
Abstract
The FMS-like tyrosine kinase 3 (FLT3) gene is mutated in one-third of patients with de novo acute myeloid leukemia (AML). Mutated FLT3 variants are constitutively active kinases signaling via AKT kinase, MAP kinases, and STAT5. FLT3 inhibitors have been approved for the treatment of FLT3-mutated AML. However, treatment response to FLT3 inhibitors may be short-lived, and resistance may emerge. Compounds targeting STAT5 may enhance and prolong effects of FLT3 inhibitors in this subset of patients with FLT3-mutated AML. Here STAT5-inhibitor AC-4-130, FLT3 inhibitor midostaurin (PKC412), BMI-1 inhibitor PTC596, MEK-inhibitor trametinib, MCL1-inhibitor S63845, and BCL-2 inhibitor venetoclax were assessed as single agents and in combination for their ability to induce apoptosis and cell death in leukemic cells grown in the absence or presence of bone marrow stroma. Synergistic effects on cell viability were detected in both FLT3-mutated and FLT3-wild-type AML cells treated with AC-4-130 in combination with the MCL1 inhibitor S63845. AML patient samples with a strong response to AC-4-130 and S63845 combination treatment were characterized by mutated FLT3 or mutated TET2 genes. Susceptibility of AML cells to AC-4-130, PTC596, trametinib, PKC412, and venetoclax was altered in the presence of HS-5 stroma. Only the MCL1 inhibitor S63845 induced cell death with equal efficacy in the absence or presence of bone marrow stroma. The combination of the STAT5-inhibitor AC-4-130 and the MCL1 inhibitor S63845 may be an effective treatment targeting FLT3-mutated or TET2-mutated AML.
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Affiliation(s)
- Katja Seipel
- Department for Biomedical Research, University of Bern, 2008 Bern, Switzerland; (C.G.); (L.F.)
- Correspondence: (K.S.); (T.P.); Tel.: +41-31-632-0934 (K.S.)
| | - Carolyn Graber
- Department for Biomedical Research, University of Bern, 2008 Bern, Switzerland; (C.G.); (L.F.)
| | - Laura Flückiger
- Department for Biomedical Research, University of Bern, 2008 Bern, Switzerland; (C.G.); (L.F.)
| | - Ulrike Bacher
- Department of Hematology, University Hospital Bern, 3010 Bern, Switzerland;
| | - Thomas Pabst
- Department of Medical Oncology, University Hospital Bern, 3010 Bern, Switzerland
- Correspondence: (K.S.); (T.P.); Tel.: +41-31-632-0934 (K.S.)
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