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Zhong FM, Yao FY, Liu J, Li MY, Jiang JY, Cheng Y, Xu S, Li SQ, Zhang N, Huang B, Wang XZ. Splicing factor-mediated regulation patterns reveals biological characteristics and aid in predicting prognosis in acute myeloid leukemia. J Transl Med 2023; 21:6. [PMID: 36611187 PMCID: PMC9824960 DOI: 10.1186/s12967-022-03868-9] [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: 10/17/2022] [Accepted: 12/29/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Alternative splicing (AS) of RNA is a fundamental biological process that shapes protein diversity. Many non-characteristic AS events are involved in the onset and development of acute myeloid leukemia (AML). Abnormal alterations in splicing factors (SFs), which regulate the onset of AS events, affect the process of splicing regulation. Hence, it is important to explore the relationship between SFs and the clinical features and biological processes of patients with AML. METHODS This study focused on SFs of the classical heterogeneous nuclear ribonucleoprotein (hnRNP) family and arginine and serine/arginine-rich (SR) splicing factor family. We explored the relationship between the regulation patterns associated with the expression of SFs and clinicopathological factors and biological behaviors of AML based on a multi-omics approach. The biological functions of SRSF10 in AML were further analyzed using clinical samples and in vitro experiments. RESULTS Most SFs were upregulated in AML samples and were associated with poor prognosis. The four splicing regulation patterns were characterized by differences in immune function, tumor mutation, signaling pathway activity, prognosis, and predicted response to chemotherapy and immunotherapy. A risk score model was constructed and validated as an independent prognostic factor for AML. Overall survival was significantly shorter in the high-risk score group. In addition, we confirmed that SRSF10 expression was significantly up-regulated in clinical samples of AML, and knockdown of SRSF10 inhibited the proliferation of AML cells and promoted apoptosis and G1 phase arrest during the cell cycle. CONCLUSION The analysis of splicing regulation patterns can help us better understand the differences in the tumor microenvironment of patients with AML and guide clinical decision-making and prognosis prediction. SRSF10 can be a potential therapeutic target and biomarker for AML.
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Affiliation(s)
- Fang-Min Zhong
- grid.412455.30000 0004 1756 5980Jiangxi Province Key Laboratory of Laboratory Medicine, Jiangxi Provincial Clinical Research Center for Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi China ,grid.260463.50000 0001 2182 8825School of Public Health, Nanchang University, No. 461 BaYi Boulevard, Nanchang, 330006 Jiangxi China
| | - Fang-Yi Yao
- grid.412455.30000 0004 1756 5980Jiangxi Province Key Laboratory of Laboratory Medicine, Jiangxi Provincial Clinical Research Center for Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi China
| | - Jing Liu
- grid.412455.30000 0004 1756 5980Jiangxi Province Key Laboratory of Laboratory Medicine, Jiangxi Provincial Clinical Research Center for Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi China
| | - Mei-Yong Li
- grid.412455.30000 0004 1756 5980Jiangxi Province Key Laboratory of Laboratory Medicine, Jiangxi Provincial Clinical Research Center for Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi China
| | - Jun-Yao Jiang
- grid.412455.30000 0004 1756 5980Jiangxi Province Key Laboratory of Laboratory Medicine, Jiangxi Provincial Clinical Research Center for Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi China
| | - Ying Cheng
- grid.412455.30000 0004 1756 5980Jiangxi Province Key Laboratory of Laboratory Medicine, Jiangxi Provincial Clinical Research Center for Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi China ,grid.260463.50000 0001 2182 8825School of Public Health, Nanchang University, No. 461 BaYi Boulevard, Nanchang, 330006 Jiangxi China
| | - Shuai Xu
- grid.412455.30000 0004 1756 5980Jiangxi Province Key Laboratory of Laboratory Medicine, Jiangxi Provincial Clinical Research Center for Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi China ,grid.260463.50000 0001 2182 8825School of Public Health, Nanchang University, No. 461 BaYi Boulevard, Nanchang, 330006 Jiangxi China
| | - Shu-Qi Li
- grid.412455.30000 0004 1756 5980Jiangxi Province Key Laboratory of Laboratory Medicine, Jiangxi Provincial Clinical Research Center for Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi China
| | - Nan Zhang
- grid.412455.30000 0004 1756 5980Jiangxi Province Key Laboratory of Laboratory Medicine, Jiangxi Provincial Clinical Research Center for Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi China
| | - Bo Huang
- grid.412455.30000 0004 1756 5980Jiangxi Province Key Laboratory of Laboratory Medicine, Jiangxi Provincial Clinical Research Center for Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi China
| | - Xiao-Zhong Wang
- grid.412455.30000 0004 1756 5980Jiangxi Province Key Laboratory of Laboratory Medicine, Jiangxi Provincial Clinical Research Center for Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi China ,grid.260463.50000 0001 2182 8825School of Public Health, Nanchang University, No. 461 BaYi Boulevard, Nanchang, 330006 Jiangxi China
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Exploring the Leukemogenic Potential of GATA-1 S, the Shorter Isoform of GATA-1: Novel Insights into Mechanisms Hampering Respiratory Chain Complex II Activity and Limiting Oxidative Phosphorylation Efficiency. Antioxidants (Basel) 2021; 10:antiox10101603. [PMID: 34679737 PMCID: PMC8533167 DOI: 10.3390/antiox10101603] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/05/2021] [Accepted: 10/07/2021] [Indexed: 12/02/2022] Open
Abstract
GATA-1 is a key regulator of hematopoiesis. A balanced ratio of its two isoforms, GATA-1FL and GATA-1S, contributes to normal hematopoiesis, whereas aberrant expression of GATA-1S alters the differentiation/proliferation potential of hematopoietic precursors and represents a poor prognostic factor in myeloid leukemia. We previously reported that GATA-1S over-expression correlates with high levels of the succinate dehydrogenase subunit C (SDHC). Alternative splicing variants of the SDHC transcript are over-expressed in several tumors and act as potent dominant negative inhibitors of SDH activity. With this in mind, we investigated the levels of SDHC variants and the oxidative mitochondrial metabolism in myeloid leukemia K562 cells over-expressing GATA-1 isoforms. Over-expression of SDHC variants accompanied by decreased SDH complex II activity and oxidative phosphorylation (OXPHOS) efficiency was found associated only with GATA-1S. Given the tumor suppressor role of SDH and the effects of OXPHOS limitations in leukemogenesis, identification of a link between GATA-1S and impaired complex II activity unveils novel pro-leukemic mechanisms triggered by GATA-1S. Abnormal levels of GATA-1S and SDHC variants were also found in an acute myeloid leukemia patient, thus supporting in vitro results. A better understanding of these mechanisms can contribute to identify novel promising therapeutic targets in myeloid leukemia.
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Im H, Rao V, Sridhar K, Bentley J, Mishra T, Chen R, Hall J, Graber A, Zhang Y, Li X, Mias GI, Snyder MP, Greenberg PL. Distinct transcriptomic and exomic abnormalities within myelodysplastic syndrome marrow cells. Leuk Lymphoma 2018; 59:2952-2962. [PMID: 29616851 DOI: 10.1080/10428194.2018.1452210] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
To provide biologic insights into mechanisms underlying myelodysplastic syndromes (MDS) we evaluated the CD34+ marrow cells transcriptome using high-throughput RNA sequencing (RNA-Seq). We demonstrated significant differential gene expression profiles (GEPs) between MDS and normal and identified 41 disease classifier genes. Additionally, two main clusters of GEPs distinguished patients based on their major clinical features, particularly between those whose disease remained stable versus patients who transformed into acute myeloid leukemia within 12 months. The genes whose expression was associated with disease outcome were involved in functional pathways and biologic processes highly relevant for MDS. Combined with exomic analysis we identified differential isoform usage of genes in MDS mutational subgroups, with consequent dysregulation of distinct biologic functions. This combination of clinical, transcriptomic and exomic findings provides valuable understanding of mechanisms underlying MDS and its progression to a more aggressive stage and also facilitates prognostic characterization of MDS patients.
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Affiliation(s)
- Hogune Im
- a Department of Genetics , Stanford University School of Medicine , Stanford , CA , USA
| | - Varsha Rao
- a Department of Genetics , Stanford University School of Medicine , Stanford , CA , USA
| | - Kunju Sridhar
- b Hematology Division , Stanford University School of Medicine, Stanford Cancer Institute , Stanford , CA , USA
| | - Jason Bentley
- c Quantitative Science Unit , Stanford University , Stanford , CA , USA
| | - Tejaswini Mishra
- a Department of Genetics , Stanford University School of Medicine , Stanford , CA , USA
| | - Rui Chen
- a Department of Genetics , Stanford University School of Medicine , Stanford , CA , USA
| | - Jeff Hall
- d Genoptix Inc. , Carlsbad , CA , USA
| | | | - Yan Zhang
- e Department of Hematology , Jiaotong University, 6th Hospital , Shanghai , China
| | - Xiao Li
- e Department of Hematology , Jiaotong University, 6th Hospital , Shanghai , China
| | - George I Mias
- f Department of Biochemistry and Molecular Biology , Michigan State University , East Lansing , MI , USA
| | - Michael P Snyder
- a Department of Genetics , Stanford University School of Medicine , Stanford , CA , USA
| | - Peter L Greenberg
- b Hematology Division , Stanford University School of Medicine, Stanford Cancer Institute , Stanford , CA , USA
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de Necochea-Campion R, Shouse GP, Zhou Q, Mirshahidi S, Chen CS. Aberrant splicing and drug resistance in AML. J Hematol Oncol 2016; 9:85. [PMID: 27613060 PMCID: PMC5018179 DOI: 10.1186/s13045-016-0315-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/02/2016] [Indexed: 02/08/2023] Open
Abstract
The advent of next-generation sequencing technologies has unveiled a new window into the heterogeneity of acute myeloid leukemia (AML). In particular, recurrent mutations in spliceosome machinery and genome-wide aberrant splicing events have been recognized as a prominent component of this disease. This review will focus on how these factors influence drug resistance through altered splicing of tumor suppressor and oncogenes and dysregulation of the apoptotic signaling network. A better understanding of these factors in disease progression is necessary to design appropriate therapeutic strategies recognizing specific alternatively spliced or mutated oncogenic targets.
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Affiliation(s)
- Rosalia de Necochea-Campion
- Biospecimen Laboratory, Loma Linda University Cancer Center, Loma Linda University School of Medicine, Loma Linda, CA, 92354, USA
| | - Geoffrey P Shouse
- Division of Hematology/Oncology, Loma Linda University School of Medicine, 11175 Campus Street, Chan Shun Pavilion 11015, Loma Linda, CA, 92354, USA
| | - Qi Zhou
- Biospecimen Laboratory, Loma Linda University Cancer Center, Loma Linda University School of Medicine, Loma Linda, CA, 92354, USA
| | - Saied Mirshahidi
- Biospecimen Laboratory, Loma Linda University Cancer Center, Loma Linda University School of Medicine, Loma Linda, CA, 92354, USA
| | - Chien-Shing Chen
- Biospecimen Laboratory, Loma Linda University Cancer Center, Loma Linda University School of Medicine, Loma Linda, CA, 92354, USA. .,Division of Hematology/Oncology, Loma Linda University School of Medicine, 11175 Campus Street, Chan Shun Pavilion 11015, Loma Linda, CA, 92354, USA.
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Pediatric asthma and autism-genomic perspectives. Clin Transl Med 2015; 4:37. [PMID: 26668064 PMCID: PMC4678135 DOI: 10.1186/s40169-015-0078-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 11/29/2015] [Indexed: 02/06/2023] Open
Abstract
High-throughput technologies, ranging from microarrays to NexGen sequencing of RNA and genomic DNA, have opened new avenues for exploration of the pathobiology of human disease. Comparisons of the architecture of the genome, identification of mutated or modified sequences, and pre-and post- transcriptional regulation of gene expression as disease specific biomarkers are revolutionizing our understanding of the causes of disease and are guiding the development of new therapies. There is enormous heterogeneity in types of genomic variation that occur in human disease. Some are inherited, while others are the result of new somatic or germline mutations or errors in chromosomal replication. In this review, we provide examples of changes that occur in the human genome in two of the most common chronic pediatric disorders, autism and asthma. The incidence and economic burden of both of these disorders are increasing worldwide. Genomic variations have the potential to serve as biomarkers for personalization of therapy and prediction of outcomes.
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Iqbal Z. Molecular genetic studies on 167 pediatric ALL patients from different areas of Pakistan confirm a low frequency of the favorable prognosis fusion oncogene TEL-AML1 (t 12; 21) in underdeveloped countries of the region. Asian Pac J Cancer Prev 2015; 15:3541-6. [PMID: 24870754 DOI: 10.7314/apjcp.2014.15.8.3541] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
TEL-AML1 fusion oncogene (t 12; 21) is the most common chromosomal abnormality in childhood acute lymphoblastic leukemia (ALL). This translocation is associated with a good prognosis and rarely shows chemotherapeutic resistance to 3-drug based remission induction phase of treatment as well as overall treatment. Thus, the higher the frequency of this fusion oncogene, the easier to manage childhood ALL in a given region with less intensive chemotherapy. Although global frequency of TEL-AML1 has been reported to be 20-30%, a very low frequency has been found in some geographical regions, including one study from Lahore, Punjab, Pakistan and others from India. The objective of present study was to investigate if this low frequency of TEL- AML1 in pediatric ALL is only in Lahore region or similar situation exists at other representative oncology centers of Pakistan. A total of 167 pediatric ALL patients were recruited from major pediatric oncology centers situated in Lahore, Faisalabad, Peshawar and Islamabad. Patients were tested for TEL-AML1 using nested reverse transcription polymerase chain reaction (RT-PCR). Only 17 out of 167 (10.2%) patients were found to be TEL-AML1 positive. TEL-AML1+ALL patients had favorable prognosis, most of them (82.4%, 14/17) showing early remission and good overall survival. Thus, our findings indicate an overall low frequency of TEL-AML1 in Pakistan pediatric ALL patients, in accordance with lower representation of this prognostically important genetic abnormality in other less developed countries, specifically in south Asia, thus associating it with poor living standards in these ethnic groups. It also indicates ethnic and geographical differences in the distribution of this prognostically important genetic abnormality among childhood ALL patients, which may have a significant bearing on ALL management strategies in different parts of the world.
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Affiliation(s)
- Zafar Iqbal
- CAMS, King Saud Bin Abdulaziz University for Health Sciences, National Guard Health Affairs, Riyadh, Saudi Arabia E-mail : , ,
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