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Feng HG, Wu CX, Zhong GC, Gong JP, Miao CM, Xiong B. Integrative analysis reveals that SLC38A1 promotes hepatocellular carcinoma development via PI3K/AKT/mTOR signaling via glutamine mediated energy metabolism. J Cancer Res Clin Oncol 2023; 149:15879-15898. [PMID: 37673823 DOI: 10.1007/s00432-023-05360-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 08/27/2023] [Indexed: 09/08/2023]
Abstract
Although hepatocellular carcinoma (HCC) is rather frequent, little is known about the molecular pathways underlying its development, progression, and prognosis. In the current study, we comprehensively analyzed the deferentially expressed metabolism-related genes (MRGs) in HCC based on TCGA datasets attempting to discover the potentially prognostic genes in HCC. The up-regulated MRGs were further subjected to analyze their prognostic values and protein expressions. Twenty-seven genes were identified because their high expressions were significant in OS, PFS, DFS, DSS, and HCC tumor samples. They were then used for GO, KEGG, methylation, genetics changes, immune infiltration analyses. Moreover, we established a prognostic model in HCC using univariate assays and LASSO regression based on these MRGs. Additionally, we also found that SLC38A1, an amino acid metabolism closely related transporter, was a potential prognostic gene in HCC, and its function in HCC was further studied using experiments. We found that the knockdown of SLC38A1 notably suppressed the growth and migration of HCC cells. Further studies revealed that SLC38A1 modulated the development of HCC cells by regulating PI3K/AKT/mTOR signaling via glutamine mediated energy metabolism. In conclusion, this study identified the potentially prognostic MRGs in HCC and uncovered that SLC38A1 regulated HCC development and progression by regulating PI3K/AKT/mTOR signaling via glutamine mediated energy metabolism, which might provide a novel marker and potential therapeutic target in HCC.
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Affiliation(s)
- Hua-Guo Feng
- Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, No. 74 Linjiang Road, Chongqing, China
| | - Chuan-Xin Wu
- Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, No. 74 Linjiang Road, Chongqing, China
| | - Guo-Chao Zhong
- Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, No. 74 Linjiang Road, Chongqing, China
| | - Jian-Ping Gong
- Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, No. 74 Linjiang Road, Chongqing, China
| | - Chun-Mu Miao
- Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, No. 74 Linjiang Road, Chongqing, China
| | - Bin Xiong
- Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, No. 74 Linjiang Road, Chongqing, China.
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2
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Zhang H, Xue F, Zhao H, Chen L, Wang T, Wu X. DNA methylation status of DNAJA4 is essential for human erythropoiesis. Epigenomics 2022; 14:1249-1267. [DOI: 10.2217/epi-2022-0341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Aims: To investigate DNA methylation patterns in early and terminal stages of erythropoiesis, and to explore the function of differentially methylated genes in erythropoiesis and erythroid disorders. Materials & methods: Differential analysis of DNA methylation and gene expression during erythropoiesis, as well as weighted gene coexpression network analysis of acute myeloid leukemia was performed. Results: We identified four candidate genes that possessed differential methylation in the promoter regions. DNAJA4 affected proliferation, apoptosis and enucleation during terminal erythropoiesis and was associated with the prognosis of acute myeloid leukemia. DNAJA4 was specifically highly expressed in erythroleukemia and is associated with DNA methylation. Conclusion: DNAJA4 plays a crucial role for erythropoiesis and is regulated via DNA methylation. Dysregulation of DNAJA4 expression is associated with erythroid disorders.
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Affiliation(s)
- Hengchao Zhang
- School of Life Sciences, Zhengzhou University, Science Road 100, Zhengzhou, 450001, China
| | - Fumin Xue
- Department of Gastroenterology, Children’s Hospital affiliated of Zhengzhou University, Zhengzhou, 450000, China
| | - Huizhi Zhao
- School of Life Sciences, Zhengzhou University, Science Road 100, Zhengzhou, 450001, China
| | - Lixiang Chen
- School of Life Sciences, Zhengzhou University, Science Road 100, Zhengzhou, 450001, China
| | - Ting Wang
- School of Life Sciences, Zhengzhou University, Science Road 100, Zhengzhou, 450001, China
| | - Xiuyun Wu
- School of Life Sciences, Zhengzhou University, Science Road 100, Zhengzhou, 450001, China
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Abstract
The World Health Organization estimates that approximately a quarter of the world's population suffers from anemia, including almost half of preschool-age children. Globally, iron deficiency anemia is the most common cause of anemia. Other important causes of anemia in children are hemoglobinopathies, infection, and other chronic diseases. Anemia is associated with increased morbidity, including neurologic complications, increased risk of low birth weight, infection, and heart failure, as well as increased mortality. When approaching a child with anemia, detailed historical information, particularly diet, environmental exposures, and family history, often yield important clues to the diagnosis. Dysmorphic features on physical examination may indicate syndromic causes of anemia. Diagnostic testing involves a stepwise approach utilizing various laboratory techniques. The increasing availability of genetic testing is providing new mechanistic insights into inherited anemias and allowing diagnosis in many previously undiagnosed cases. Population-based approaches are being taken to address nutritional anemias. Novel pharmacologic agents and advances in gene therapy-based therapeutics have the potential to ameliorate anemia-associated disease and provide treatment strategies even in the most difficult and complex cases.
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Affiliation(s)
- Patrick G Gallagher
- Departments of Pediatrics, Pathology, and Genetics, Yale University School of Medicine, New Haven, CT
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Liu Z, Zhao F, Tong X, Liu K, Wang B, Yang L, Ning T, Wang Y, Zhao F, Wang D, Wang D. Comparative transcriptomic analysis reveals the mechanism of leech environmental adaptation. Gene 2018; 664:70-77. [DOI: 10.1016/j.gene.2018.04.063] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 03/09/2018] [Accepted: 04/20/2018] [Indexed: 02/06/2023]
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Steinberg-Shemer O, Ulirsch JC, Noy-Lotan S, Krasnov T, Attias D, Dgany O, Laor R, Sankaran VG, Tamary H. Whole-exome sequencing identifies an α-globin cluster triplication resulting in increased clinical severity of β-thalassemia. Cold Spring Harb Mol Case Stud 2017; 3:a001941. [PMID: 28667000 PMCID: PMC5701307 DOI: 10.1101/mcs.a001941] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 05/18/2017] [Indexed: 12/15/2022] Open
Abstract
Whole-exome sequencing (WES) has been increasingly useful for the diagnosis of patients with rare causes of anemia, particularly when there is an atypical clinical presentation or targeted genotyping approaches are inconclusive. Here, we describe a 20-yr-old man with a lifelong moderate-to-severe anemia with accompanying splenomegaly who lacked a definitive diagnosis. After a thorough clinical workup and targeted genetic sequencing, we identified a paternally inherited β-globin mutation (HBB:c.93-21G>A, IVS-I-110:G>A), a known cause of β-thalassemia minor. As this mutation alone was inconsistent with the severity of the anemia, we performed WES. Although we could not identify any relevant pathogenic single-nucleotide variants (SNVs) or small indels, copy-number variant (CNV) analyses revealed a likely triplication of the entire α-globin cluster, which was subsequently confirmed by multiplex ligation-dependent probe amplification. Treatment and follow-up was redefined according to the diagnosis of β-thalassemia intermedia resulting from a single β-thalassemia mutation in combination with an α-globin cluster triplication. Thus, we describe a case where the typical WES-based analysis of SNVs and small indels was unrevealing, but WES-based CNV analysis resulted in a definitive diagnosis that informed clinical decision-making. More generally, this case illustrates the value of performing CNV analysis when WES is otherwise unable to elucidate a clear genetic diagnosis.
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Affiliation(s)
- Orna Steinberg-Shemer
- Departments of Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tivka 49202, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jacob C Ulirsch
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Sharon Noy-Lotan
- Pediatric Hematology Laboratory, Felsenstein Medical Research Center, Petach Tikva 49414, Israel
| | - Tanya Krasnov
- Pediatric Hematology Laboratory, Felsenstein Medical Research Center, Petach Tikva 49414, Israel
| | - Dina Attias
- Pediatric Hematology/Oncology Unit, Bnai Zion Medical Center, Haifa 31048, Israel
| | - Orly Dgany
- Pediatric Hematology Laboratory, Felsenstein Medical Research Center, Petach Tikva 49414, Israel
| | - Ruth Laor
- Pediatric Hematology/Oncology Unit, Bnai Zion Medical Center, Haifa 31048, Israel
| | - Vijay G Sankaran
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Hannah Tamary
- Departments of Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tivka 49202, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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Kim Y, Park J, Kim M. Diagnostic approaches for inherited hemolytic anemia in the genetic era. Blood Res 2017; 52:84-94. [PMID: 28698843 PMCID: PMC5503903 DOI: 10.5045/br.2017.52.2.84] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 05/24/2017] [Accepted: 05/25/2017] [Indexed: 02/06/2023] Open
Abstract
Inherited hemolytic anemias (IHAs) are genetic diseases that present with anemia due to the increased destruction of circulating abnormal RBCs. The RBC abnormalities are classified into the three major disorders of membranopathies, hemoglobinopathies, and enzymopathies. Traditional diagnosis of IHA has been performed via a step-wise process combining clinical and laboratory findings. Nowadays, the etiology of IHA accounts for germline mutations of the responsible genes coding for the structural components of RBCs. Recent advances in molecular technologies, including next-generation sequencing, inspire us to apply these technologies as a first-line approach for the identification of potential mutations and to determine the novel causative genes in patients with IHAs. We herein review the concept and strategy for the genetic diagnosis of IHAs and provide an overview of the preparations for clinical applications of the new molecular technologies.
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Affiliation(s)
- Yonggoo Kim
- Department of Laboratory Medicine, Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Joonhong Park
- Department of Laboratory Medicine, Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Myungshin Kim
- Department of Laboratory Medicine, Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
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Lacy JN, Ulirsch JC, Grace RF, Towne MC, Hale J, Mohandas N, Lux SE, Agrawal PB, Sankaran VG. Exome sequencing results in successful diagnosis and treatment of a severe congenital anemia. Cold Spring Harb Mol Case Stud 2016; 2:a000885. [PMID: 27551681 PMCID: PMC4990811 DOI: 10.1101/mcs.a000885] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Whole-exome sequencing is increasingly used for diagnosis and identification of appropriate therapies in patients. Here, we present the case of a 3-yr-old male with a lifelong and severe transfusion-dependent anemia of unclear etiology, despite an extensive clinical workup. Given the difficulty of making the diagnosis and the potential side effects from performing interventions in patients with a congenital anemia of unknown etiology, we opted to perform whole-exome sequencing on the patient and his parents. This resulted in the identification of homozygous loss-of-function mutations in the EPB41 gene, encoding erythrocyte protein band 4.1, which therefore causes a rare and severe form of hereditary elliptocytosis in the patient. Based on prior clinical experience in similar patients, a surgical splenectomy was performed that resulted in subsequent transfusion independence in the patient. This case illustrates how whole-exome sequencing can lead to accurate diagnoses (and exclusion of diagnoses where interventions, such as splenectomy, would be contraindicated), thereby resulting in appropriate and successful therapeutic intervention—a major goal of precision medicine.
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Affiliation(s)
- Jessica N Lacy
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA;; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA;; Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Jacob C Ulirsch
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA;; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA;; Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Rachael F Grace
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA;; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Meghan C Towne
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - John Hale
- New York Blood Center, New York, New York 10065, USA
| | | | - Samuel E Lux
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA;; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Pankaj B Agrawal
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA;; Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA;; Division of Newborn Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA;; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA;; Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
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8
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Bertier G, Hétu M, Joly Y. Unsolved challenges of clinical whole-exome sequencing: a systematic literature review of end-users' views. BMC Med Genomics 2016; 9:52. [PMID: 27514372 PMCID: PMC4982236 DOI: 10.1186/s12920-016-0213-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 07/28/2016] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Whole-exome sequencing (WES) consists in the capture, sequencing and analysis of all exons in the human genome. Originally developed in the research context, this technology is now increasingly used clinically to inform patient care. The implementation of WES into healthcare poses significant organizational, regulatory, and ethical hurdles, which are widely discussed in the literature. METHODS In order to inform future policy decisions on the integration of WES into standard clinical practice, we performed a systematic literature review to identify the most important challenges directly reported by technology users. RESULTS Out of 2094 articles, we selected and analyzed 147 which reported a total of 23 different challenges linked to the production, analysis, reporting and sharing of patients' WES data. Interpretation of variants of unknown significance, incidental findings, and the cost and reimbursement of WES-based tests were the most reported challenges across all articles. CONCLUSIONS WES is already used in the clinical setting, and may soon be considered the standard of care for specific medical conditions. Yet, technology users are calling for certain standards and guidelines to be published before this technology replaces more focused approaches such as gene panels sequencing. In addition, a number of infrastructural adjustments will have to be made for clinics to store, process and analyze the amounts of data produced by WES.
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Affiliation(s)
- Gabrielle Bertier
- Center of Genomics and Policy, McGill University, 740 Dr. Penfield Avenue, Montreal, Quebec H3A 0G1 Canada
- UMR 1027, Inserm, University of Toulouse III - Paul Sabatier, 37 allées Jules Guesde, F-31000 Toulouse, France
| | - Martin Hétu
- Center of Genomics and Policy, McGill University, 740 Dr. Penfield Avenue, Montreal, Quebec H3A 0G1 Canada
| | - Yann Joly
- Center of Genomics and Policy, McGill University, 740 Dr. Penfield Avenue, Montreal, Quebec H3A 0G1 Canada
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9
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Polfus L, Khajuria R, Schick U, Pankratz N, Pazoki R, Brody J, Chen MH, Auer P, Floyd J, Huang J, Lange L, van Rooij F, Gibbs R, Metcalf G, Muzny D, Veeraraghavan N, Walter K, Chen L, Yanek L, Becker L, Peloso G, Wakabayashi A, Kals M, Metspalu A, Esko T, Fox K, Wallace R, Franceschini N, Matijevic N, Rice K, Bartz T, Lyytikäinen LP, Kähönen M, Lehtimäki T, Raitakari O, Li-Gao R, Mook-Kanamori D, Lettre G, van Duijn C, Franco O, Rich S, Rivadeneira F, Hofman A, Uitterlinden A, Wilson J, Psaty B, Soranzo N, Dehghan A, Boerwinkle E, Zhang X, Johnson A, O’Donnell C, Johnsen J, Reiner A, Ganesh S, Sankaran V. Whole-Exome Sequencing Identifies Loci Associated with Blood Cell Traits and Reveals a Role for Alternative GFI1B Splice Variants in Human Hematopoiesis. Am J Hum Genet 2016; 99:481-8. [PMID: 27486782 DOI: 10.1016/j.ajhg.2016.06.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 06/20/2016] [Indexed: 01/26/2023] Open
Abstract
Circulating blood cell counts and indices are important indicators of hematopoietic function and a number of clinical parameters, such as blood oxygen-carrying capacity, inflammation, and hemostasis. By performing whole-exome sequence association analyses of hematologic quantitative traits in 15,459 community-dwelling individuals, followed by in silico replication in up to 52,024 independent samples, we identified two previously undescribed coding variants associated with lower platelet count: a common missense variant in CPS1 (rs1047891, MAF = 0.33, discovery + replication p = 6.38 × 10(-10)) and a rare synonymous variant in GFI1B (rs150813342, MAF = 0.009, discovery + replication p = 1.79 × 10(-27)). By performing CRISPR/Cas9 genome editing in hematopoietic cell lines and follow-up targeted knockdown experiments in primary human hematopoietic stem and progenitor cells, we demonstrate an alternative splicing mechanism by which the GFI1B rs150813342 variant suppresses formation of a GFI1B isoform that preferentially promotes megakaryocyte differentiation and platelet production. These results demonstrate how unbiased studies of natural variation in blood cell traits can provide insight into the regulation of human hematopoiesis.
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10
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Badar S, Busti F, Ferrarini A, Xumerle L, Bozzini P, Capelli P, Pozzi-Mucelli R, Campostrini N, De Matteis G, Marin Vargas S, Giorgetti A, Delledonne M, Olivieri O, Girelli D. Identification of novel mutations in hemochromatosis genes by targeted next generation sequencing in Italian patients with unexplained iron overload. Am J Hematol 2016; 91:420-5. [PMID: 26799139 DOI: 10.1002/ajh.24304] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 01/08/2016] [Accepted: 01/13/2016] [Indexed: 12/14/2022]
Abstract
Hereditary hemochromatosis, one of the commonest genetic disorder in Caucasians, is mainly associated to homozygosity for the C282Y mutation in the HFE gene, which is highly prevalent (allele frequency up to near 10% in Northern Europe) and easily detectable through a widely available "first level" molecular test. However, in certain geographical regions like the Mediterranean area, up to 30% of patients with a HH phenotype has a negative or non-diagnostic (i.e. simple heterozygosity) test, because of a known heterogeneity involving at least four other genes (HAMP, HJV, TFR2, and SLC40A1). Mutations in such genes are generally rare/private, making the diagnosis of atypical HH essentially a matter of exclusion in clinical practice (from here the term of "non-HFE" HH), unless cumbersome traditional sequencing is applied. We developed a Next Generation Sequencing (NGS)-based test targeting the five HH genes, and applied it to patients with clinically relevant iron overload (IO) and a non-diagnostic first level genetic test. We identified several mutations, some of which were novel (i.e. HFE W163X, HAMP R59X, and TFR2 D555N) and allowed molecular reclassification of "non-HFE" HH clinical diagnosis, particularly in some highly selected IO patients without concurring acquired risk factors. This NGS-based "second level" genetic test may represent a useful tool for molecular diagnosis of HH in patients in whom HH phenotype remains unexplained after the search of common HFE mutations.
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Affiliation(s)
- Sadaf Badar
- Department of Medicine; Section of Internal Medicine, University of Verona; Verona Italy
| | - Fabiana Busti
- Department of Medicine; Section of Internal Medicine, University of Verona; Verona Italy
| | | | - Luciano Xumerle
- Department of Biotechnology; University of Verona; Verona Italy
| | - Paolo Bozzini
- Department of Medicine; Section of Internal Medicine, University of Verona; Verona Italy
| | - Paola Capelli
- Unit of Pathology, Azienda Ospedaliera Universitaria Integrata Verona; Verona Italy
| | - Roberto Pozzi-Mucelli
- Department of Diagnostics and Public Health; Section of Radiology, University of Verona; Verona Italy
| | - Natascia Campostrini
- Department of Medicine; Section of Internal Medicine, University of Verona; Verona Italy
| | - Giovanna De Matteis
- Unit of Clinical Chemistry, Azienda Ospedaliera Universitaria Integrata Verona; Verona Italy
| | | | | | | | - Oliviero Olivieri
- Department of Medicine; Section of Internal Medicine, University of Verona; Verona Italy
| | - Domenico Girelli
- Department of Medicine; Section of Internal Medicine, University of Verona; Verona Italy
- Veneto Regional Referral Center for Iron Metabolism Disorders, GIMFer (Gruppo Interdisciplinare Sulle Malattie Del Ferro); Azienda Ospedaliera Uiversitaria Integrata Verona; Verona Italy
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11
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Insight into GATA1 transcriptional activity through interrogation of cis elements disrupted in human erythroid disorders. Proc Natl Acad Sci U S A 2016; 113:4434-9. [PMID: 27044088 DOI: 10.1073/pnas.1521754113] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Whole-exome sequencing has been incredibly successful in identifying causal genetic variants and has revealed a number of novel genes associated with blood and other diseases. One limitation of this approach is that it overlooks mutations in noncoding regulatory elements. Furthermore, the mechanisms by which mutations in transcriptionalcis-regulatory elements result in disease remain poorly understood. Here we used CRISPR/Cas9 genome editing to interrogate three such elements harboring mutations in human erythroid disorders, which in all cases are predicted to disrupt a canonical binding motif for the hematopoietic transcription factor GATA1. Deletions of as few as two to four nucleotides resulted in a substantial decrease (>80%) in target gene expression. Isolated deletions of the canonical GATA1 binding motif completely abrogated binding of the cofactor TAL1, which binds to a separate motif. Having verified the functionality of these three GATA1 motifs, we demonstrate strong evolutionary conservation of GATA1 motifs in regulatory elements proximal to other genes implicated in erythroid disorders, and show that targeted disruption of such elements results in altered gene expression. By modeling transcription factor binding patterns, we show that multiple transcription factors are associated with erythroid gene expression, and have created predictive maps modeling putative disruptions of their binding sites at key regulatory elements. Our study provides insight into GATA1 transcriptional activity and may prove a useful resource for investigating the pathogenicity of noncoding variants in human erythroid disorders.
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12
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Society for Pediatric Research 2015 Young Investigator Award: genetics of human hematopoiesis-what patients can teach us about blood cell production. Pediatr Res 2016; 79:366-70. [PMID: 26575596 DOI: 10.1038/pr.2015.245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 09/30/2015] [Indexed: 11/09/2022]
Abstract
Blood cell production or hematopoiesis is one of the most well-understood paradigms of cell differentiation in the body. The majority of work on hematopoiesis comes from studies that have primarily been conducted in mice, zebrafish, or other valuable model systems. However, it is clear that such model organisms may not consistently and faithfully mimic what is observed in humans with blood disorders. Moreover, there is significant divergence between species that is increasingly being appreciated at the genomic level. As a result, there is an opportunity to use observations in humans to provide a refined view of hematopoiesis. Here, we discuss vignettes from our work that illustrate how insight from human genetics can improve our understanding of blood cell production and identify promising therapeutic approaches for blood disorders.
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Abstract
PURPOSE OF REVIEW Research into the fundamental mechanisms of erythropoiesis has provided critical insights into inherited and acquired disorders of the erythrocyte. Studies of human erythropoiesis have primarily utilized in-vitro systems, whereas murine models have provided insights from in-vivo studies. This report reviews recent insights into human and murine erythropoiesis gained from transcriptome-based analyses. RECENT FINDINGS The availability of high-throughput genomic methodologies has allowed attainment of detailed gene expression data from cells at varying developmental and differentiation stages of erythropoiesis. Transcriptome analyses of human and murine reveal both stage and species-specific similarities and differences across terminal erythroid differentiation. Erythroid-specific long noncoding RNAs exhibit poor sequence conservation between human and mouse. Genome-wide analyses of alternative splicing reveal that complex, dynamic, stage-specific programs of alternative splicing program are utilized during terminal erythroid differentiation. Transcriptome data provide a significant resource for understanding mechanisms of normal and perturbed erythropoiesis. Understanding these processes will provide innovative strategies to detect, diagnose, prevent, and treat hematologic disease. SUMMARY Understanding the shared and different mechanisms controlling human and murine erythropoiesis will allow investigators to leverage the best model system to provide insights in normal and perturbed erythropoiesis.
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Sankaran VG, Ulirsch JC, Tchaikovskii V, Ludwig LS, Wakabayashi A, Kadirvel S, Lindsley RC, Bejar R, Shi J, Lovitch SB, Bishop DF, Steensma DP. X-linked macrocytic dyserythropoietic anemia in females with an ALAS2 mutation. J Clin Invest 2015; 125:1665-9. [PMID: 25705881 DOI: 10.1172/jci78619] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 01/08/2015] [Indexed: 01/19/2023] Open
Abstract
Macrocytic anemia with abnormal erythropoiesis is a common feature of megaloblastic anemias, congenital dyserythropoietic anemias, and myelodysplastic syndromes. Here, we characterized a family with multiple female individuals who have macrocytic anemia. The proband was noted to have dyserythropoiesis and iron overload. After an extensive diagnostic evaluation that did not provide insight into the cause of the disease, whole-exome sequencing of multiple family members revealed the presence of a mutation in the X chromosomal gene ALAS2, which encodes 5'-aminolevulinate synthase 2, in the affected females. We determined that this mutation (Y365C) impairs binding of the essential cofactor pyridoxal 5'-phosphate to ALAS2, resulting in destabilization of the enzyme and consequent loss of function. X inactivation was not highly skewed in wbc from the affected individuals. In contrast, and consistent with the severity of the ALAS2 mutation, there was a complete skewing toward expression of the WT allele in mRNA from reticulocytes that could be recapitulated in primary erythroid cultures. Together, the results of the X inactivation and mRNA studies illustrate how this X-linked dominant mutation in ALAS2 can perturb normal erythropoiesis through cell-nonautonomous effects. Moreover, our findings highlight the value of whole-exome sequencing in diagnostically challenging cases for the identification of disease etiology and extension of the known phenotypic spectrum of disease.
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MESH Headings
- 5-Aminolevulinate Synthetase/genetics
- 5-Aminolevulinate Synthetase/metabolism
- Adult
- Anemia, Dyserythropoietic, Congenital/genetics
- Anemia, Macrocytic/genetics
- Cells, Cultured
- Erythropoiesis/genetics
- Exome/genetics
- Female
- Genes, Dominant
- Genes, X-Linked
- Genetic Diseases, X-Linked/blood
- Genetic Diseases, X-Linked/genetics
- Hemorrhage/etiology
- Humans
- Iron Overload/etiology
- Male
- Models, Molecular
- Molecular Sequence Data
- Mutation, Missense
- Point Mutation
- Pregnancy
- Pregnancy Complications, Hematologic/genetics
- Protein Binding
- Protein Conformation
- Puerperal Disorders/etiology
- Pyridoxal Phosphate/metabolism
- RNA, Messenger/genetics
- Reticulocytes/metabolism
- X Chromosome Inactivation
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15
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Ulirsch JC, Lacy JN, An X, Mohandas N, Mikkelsen TS, Sankaran VG. Altered chromatin occupancy of master regulators underlies evolutionary divergence in the transcriptional landscape of erythroid differentiation. PLoS Genet 2014; 10:e1004890. [PMID: 25521328 PMCID: PMC4270484 DOI: 10.1371/journal.pgen.1004890] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 11/13/2014] [Indexed: 12/20/2022] Open
Abstract
Erythropoiesis is one of the best understood examples of cellular differentiation. Morphologically, erythroid differentiation proceeds in a nearly identical fashion between humans and mice, but recent evidence has shown that networks of gene expression governing this process are divergent between species. We undertook a systematic comparative analysis of six histone modifications and four transcriptional master regulators in primary proerythroblasts and erythroid cell lines to better understand the underlying basis of these transcriptional differences. Our analyses suggest that while chromatin structure across orthologous promoters is strongly conserved, subtle differences are associated with transcriptional divergence between species. Many transcription factor (TF) occupancy sites were poorly conserved across species (∼25% for GATA1, TAL1, and NFE2) but were more conserved between proerythroblasts and cell lines derived from the same species. We found that certain cis-regulatory modules co-occupied by GATA1, TAL1, and KLF1 are under strict evolutionary constraint and localize to genes necessary for erythroid cell identity. More generally, we show that conserved TF occupancy sites are indicative of active regulatory regions and strong gene expression that is sustained during maturation. Our results suggest that evolutionary turnover of TF binding sites associates with changes in the underlying chromatin structure, driving transcriptional divergence. We provide examples of how this framework can be applied to understand epigenomic variation in specific regulatory regions, such as the β-globin gene locus. Our findings have important implications for understanding epigenomic changes that mediate variation in cellular differentiation across species, while also providing a valuable resource for studies of hematopoiesis. The process whereby blood progenitor cells differentiate into red blood cells, known as erythropoiesis, is very similar between mice and humans. Yet, while studies of this process in mouse have substantially improved our knowledge of human erythropoiesis, recent work has shown a significant divergence in global gene expression across species, suggesting that extrapolation from mouse models to human is not always straightforward. In order to better understand these differences, we have performed a comparative epigenomic analysis of six histone modifications and four master transcription factors. By globally comparing chromatin structure across primary cells and model cell lines in both species, we discovered that while chromatin structure is well conserved at orthologous promoters, subtle changes are predictive of species-specific gene expression. Furthermore, we discovered that the genomic localizations of master transcription factors are poorly conserved, and species-specific losses or gains are associated with changes to the underlying chromatin structure and concomitant gene expression. By using our comparative epigenomics framework, we identified a putative human-specific cis-regulatory module that drives expression of human, but not mouse, GDF15, a gene implicated in iron homeostasis. Our results provide a resource to aid researchers in interpreting genetic and epigenetic differences between species.
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Affiliation(s)
- Jacob C. Ulirsch
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jessica N. Lacy
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Xiuli An
- New York Blood Center, New York, New York, United States of America
| | - Narla Mohandas
- New York Blood Center, New York, New York, United States of America
| | - Tarjei S. Mikkelsen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Harvard Stem Cell Institute, Cambridge, Massachusetts, United States of America
| | - Vijay G. Sankaran
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail:
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16
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Global transcriptome analysis and enhancer landscape of human primary T follicular helper and T effector lymphocytes. Blood 2014; 124:3719-29. [PMID: 25331115 DOI: 10.1182/blood-2014-06-582700] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
T follicular helper (Tfh) cells are a subset of CD4(+) T helper cells that migrate into germinal centers and promote B-cell maturation into memory B and plasma cells. Tfh cells are necessary for promotion of protective humoral immunity following pathogen challenge, but when aberrantly regulated, drive pathogenic antibody formation in autoimmunity and undergo neoplastic transformation in angioimmunoblastic T-cell lymphoma and other primary cutaneous T-cell lymphomas. Limited information is available on the expression and regulation of genes in human Tfh cells. Using a fluorescence-activated cell sorting-based strategy, we obtained primary Tfh and non-Tfh T effector cells from tonsils and prepared genome-wide maps of active, intermediate, and poised enhancers determined by chromatin immunoprecipitation-sequencing, with parallel transcriptome analyses determined by RNA sequencing. Tfh cell enhancers were enriched near genes highly expressed in lymphoid cells or involved in lymphoid cell function, with many mapping to sites previously associated with autoimmune disease in genome-wide association studies. A group of active enhancers unique to Tfh cells associated with differentially expressed genes was identified. Fragments from these regions directed expression in reporter gene assays. These data provide a significant resource for studies of T lymphocyte development and differentiation and normal and perturbed Tfh cell function.
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17
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Abstract
Most heritable anemias are caused by mutations in genes encoding globins, red blood cell (RBC) membrane proteins, or enzymes in the glycolytic and hexose monophosphate shunt pathways. A less common class of genetic anemia is caused by mutations that alter the functions of erythroid transcription factors (TFs). Many TF mutations associated with heritable anemia cause truncations or amino acid substitutions, resulting in the production of functionally altered proteins. Characterization of these mutant proteins has provided insights into mechanisms of gene expression, hematopoietic development, and human disease. Mutations within promoter or enhancer regions that disrupt TF binding to essential erythroid genes also cause anemia and heritable variations in RBC traits, such as fetal hemoglobin content. Defining the latter may have important clinical implications for de-repressing fetal hemoglobin synthesis to treat sickle cell anemia and β thalassemia. Functionally important alterations in genes encoding TFs or their cognate cis elements are likely to occur more frequently than currently appreciated, a hypothesis that will soon be tested through ongoing genome-wide association studies and the rapidly expanding use of global genome sequencing for human diagnostics. Findings obtained through such studies of RBCs and associated diseases are likely generalizable to many human diseases and quantitative traits.
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18
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Abstract
We recently developed fluorescence-activated cell sorting (FACS)-based methods to purify morphologically and functionally discrete populations of cells, each representing specific stages of terminal erythroid differentiation. We used these techniques to obtain pure populations of both human and murine erythroblasts at distinct developmental stages. RNA was prepared from these cells and subjected to RNA sequencing analyses, creating unbiased, stage-specific transcriptomes. Tight clustering of transcriptomes from differing stages, even between biologically different replicates, validated the utility of the FACS-based assays. Bioinformatic analyses revealed that there were marked differences between differentiation stages, with both shared and dissimilar gene expression profiles defining each stage within transcriptional space. There were vast temporal changes in gene expression across the differentiation stages, with each stage exhibiting unique transcriptomes. Clustering and network analyses revealed that varying stage-specific patterns of expression observed across differentiation were enriched for genes of differing function. Numerous differences were present between human and murine transcriptomes, with significant variation in the global patterns of gene expression. These data provide a significant resource for studies of normal and perturbed erythropoiesis, allowing a deeper understanding of mechanisms of erythroid development in various inherited and acquired erythroid disorders.
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