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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Trachtenberg AJ, Robert JH, Abdalla AE, Fraser A, He SY, Lacy JN, Rivas-Morello C, Truong A, Hardiman G, Ohno-Machado L, Liu F, Hovig E, Kuo WP. A primer on the current state of microarray technologies. Methods Mol Biol 2012; 802:3-17. [PMID: 22130870 DOI: 10.1007/978-1-61779-400-1_1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
DNA microarray technology has been used for genome-wide gene expression studies that incorporate molecular genetics and computer science analyses on massive levels. The availability of microarrays permit the simultaneous analysis of tens of thousands of genes for the purposes of gene discovery, disease diagnosis, improved drug development, and therapeutics tailored to specific disease processes. In this chapter, we provide an overview on the current state of common microarray technologies and platforms. Since many genes contribute to normal functioning, research efforts are moving from the search for a disease-specific gene to the understanding of the biochemical and molecular functioning of a variety of genes whose disrupted interaction in complicated networks can lead to a disease state. The field of microarrays has evolved over the past decade and is now standardized with a high level of quality control, while providing a relatively inexpensive and reliable alternative to studying various aspects of gene expression.
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Affiliation(s)
- Alexander J Trachtenberg
- Harvard Catalyst - Laboratory for Innovative Translational Technologies, Harvard Medical School, Boston, MA, USA
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Perera M, Tsang CS, Distel RJ, Lacy JN, Ohno-Machado L, Ricchiuti V, Samaranayake LP, Smejkal GB, Smith MG, Trachtenberg AJ, Kuo WP. TGF-beta1 interactome: metastasis and beyond. Cancer Genomics Proteomics 2010; 7:217-229. [PMID: 20656987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023] Open
Abstract
The ubiquitous cytokine transforming growth factor-beta1 (TGF-beta1) is one of the most potent metastatic inducers. Functional interactomic mapping using high-throughput proteomic and genomic data provides valuable insights into the regulation of tumor suppressive and metastatic attributes of TGF-beta1. Polarity changes of the TGF-beta1 interactome at a given time contributes to these contrasting effects. Differential expression profiles of pivotal interactomic nodes contribute to these polarity changes. These insights are of immense value in the development of effective cancer therapeutics. Moreover, TGF-beta1 interactomic nodes are useful in discovering novel cancer biomarkers. This review describes an initial version of the TGF-beta1 interactome in relation to tumor progression and metastasis. Thus, this review embodies an important step towards the mapping of comprehensive and individualized TGF-beta1 interactomes that will assist in the development of personalized cancer therapeutics.
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Affiliation(s)
- M Perera
- University of Hong Kong, Hong Kong
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