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Ordoñez R, Zhang W, Ellis G, Zhu Y, Ashe HJ, Ribeiro-Dos-Santos AM, Brosh R, Huang E, Hogan MS, Boeke JD, Maurano MT. Genomic context sensitizes regulatory elements to genetic disruption. Mol Cell 2024; 84:1842-1854.e7. [PMID: 38759624 PMCID: PMC11104518 DOI: 10.1016/j.molcel.2024.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 03/11/2024] [Accepted: 04/18/2024] [Indexed: 05/19/2024]
Abstract
Genomic context critically modulates regulatory function but is difficult to manipulate systematically. The murine insulin-like growth factor 2 (Igf2)/H19 locus is a paradigmatic model of enhancer selectivity, whereby CTCF occupancy at an imprinting control region directs downstream enhancers to activate either H19 or Igf2. We used synthetic regulatory genomics to repeatedly replace the native locus with 157-kb payloads, and we systematically dissected its architecture. Enhancer deletion and ectopic delivery revealed previously uncharacterized long-range regulatory dependencies at the native locus. Exchanging the H19 enhancer cluster with the Sox2 locus control region (LCR) showed that the H19 enhancers relied on their native surroundings while the Sox2 LCR functioned autonomously. Analysis of regulatory DNA actuation across cell types revealed that these enhancer clusters typify broader classes of context sensitivity genome wide. These results show that unexpected dependencies influence even well-studied loci, and our approach permits large-scale manipulation of complete loci to investigate the relationship between regulatory architecture and function.
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Affiliation(s)
- Raquel Ordoñez
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Weimin Zhang
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Gwen Ellis
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Yinan Zhu
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Hannah J Ashe
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | | | - Ran Brosh
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Emily Huang
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Megan S Hogan
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Jef D Boeke
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA; Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Matthew T Maurano
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Pathology, NYU School of Medicine, New York, NY 10016, USA.
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2
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Alser M, Lawlor B, Abdill RJ, Waymost S, Ayyala R, Rajkumar N, LaPierre N, Brito J, Ribeiro-Dos-Santos AM, Almadhoun N, Sarwal V, Firtina C, Osinski T, Eskin E, Hu Q, Strong D, Kim BDBD, Abedalthagafi MS, Mutlu O, Mangul S. Packaging and containerization of computational methods. Nat Protoc 2024:10.1038/s41596-024-00986-0. [PMID: 38565959 DOI: 10.1038/s41596-024-00986-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 02/12/2024] [Indexed: 04/04/2024]
Abstract
Methods for analyzing the full complement of a biomolecule type, e.g., proteomics or metabolomics, generate large amounts of complex data. The software tools used to analyze omics data have reshaped the landscape of modern biology and become an essential component of biomedical research. These tools are themselves quite complex and often require the installation of other supporting software, libraries and/or databases. A researcher may also be using multiple different tools that require different versions of the same supporting materials. The increasing dependence of biomedical scientists on these powerful tools creates a need for easier installation and greater usability. Packaging and containerization are different approaches to satisfy this need by delivering omics tools already wrapped in additional software that makes the tools easier to install and use. In this systematic review, we describe and compare the features of prominent packaging and containerization platforms. We outline the challenges, advantages and limitations of each approach and some of the most widely used platforms from the perspectives of users, software developers and system administrators. We also propose principles to make the distribution of omics software more sustainable and robust to increase the reproducibility of biomedical and life science research.
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Affiliation(s)
- Mohammed Alser
- Department of Information Technology and Electrical Engineering, ETH Zürich, Zurich, Switzerland
| | - Brendan Lawlor
- Department of Computer Science, Munster Technological University, Cork, Ireland
- Department of Biological Sciences, Munster Technological University, Cork, Ireland
| | - Richard J Abdill
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Sharon Waymost
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ram Ayyala
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
- Titus Family Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Neha Rajkumar
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Nathan LaPierre
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Jaqueline Brito
- Titus Family Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | | | - Nour Almadhoun
- Department of Information Technology and Electrical Engineering, ETH Zürich, Zurich, Switzerland
| | - Varuni Sarwal
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA
| | - Can Firtina
- Department of Information Technology and Electrical Engineering, ETH Zürich, Zurich, Switzerland
| | - Tomasz Osinski
- Center for Advanced Research Computing, University of Southern California, Los Angeles, CA, USA
| | - Eleazar Eskin
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of California, Los Angeles, CA, USA
| | - Qiyang Hu
- Office of Advanced Research Computing, University of California, Los Angeles, CA, USA
| | - Derek Strong
- Center for Advanced Research Computing, University of Southern California, Los Angeles, CA, USA
| | - Byoung-Do B D Kim
- Center for Advanced Research Computing, University of Southern California, Los Angeles, CA, USA
| | - Malak S Abedalthagafi
- Department of Pathology & Laboratory Medicine, Emory University Hospital, Atlanta, GA, USA
- King Salman Center for Disability Research, Riyadh, Saudi Arabia
| | - Onur Mutlu
- Department of Information Technology and Electrical Engineering, ETH Zürich, Zurich, Switzerland
| | - Serghei Mangul
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
- Titus Family Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA.
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3
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Ordoñez R, Zhang W, Ellis G, Zhu Y, Ashe HJ, Ribeiro-Dos-Santos AM, Brosh R, Huang E, Hogan MS, Boeke JD, Maurano MT. Genomic context sensitizes regulatory elements to genetic disruption. bioRxiv 2024:2023.07.02.547201. [PMID: 37781588 PMCID: PMC10541140 DOI: 10.1101/2023.07.02.547201] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Enhancer function is frequently investigated piecemeal using truncated reporter assays or single deletion analysis. Thus it remains unclear to what extent enhancer function at native loci relies on surrounding genomic context. Using the Big-IN technology for targeted integration of large DNAs, we analyzed the regulatory architecture of the murine Igf2 / H19 locus, a paradigmatic model of enhancer selectivity. We assembled payloads containing a 157-kb functional Igf2 / H19 locus and engineered mutations to genetically direct CTCF occupancy at the imprinting control region (ICR) that switches the target gene of the H19 enhancer cluster. Contrasting activity of payloads delivered at the endogenous Igf2 / H19 locus or ectopically at Hprt revealed that the Igf2 / H19 locus includes additional, previously unknown long-range regulatory elements. Exchanging components of the Igf2 / H19 locus with the well-studied Sox2 locus showed that the H19 enhancer cluster functioned poorly out of context, and required its native surroundings to activate Sox2 expression. Conversely, the Sox2 locus control region (LCR) could activate both Igf2 and H19 outside its native context, but its activity was only partially modulated by CTCF occupancy at the ICR. Analysis of regulatory DNA actuation across different cell types revealed that, while the H19 enhancers are tightly coordinated within their native locus, the Sox2 LCR acts more independently. We show that these enhancer clusters typify broader classes of loci genome-wide. Our results show that unexpected dependencies may influence even the most studied functional elements, and our synthetic regulatory genomics approach permits large-scale manipulation of complete loci to investigate the relationship between locus architecture and function. HIGHLIGHTS Composite enhancer elements are subject to genomic context effects mapped to a specific architecture of their endogenous loci. Igf2/H19 expression is affected by long-range regulatory elements beyond the canonically defined locus, and the H19 enhancer cluster in particular relies on the surrounding context at its endogenous locus. The Sox2 LCR functions as an autonomous enhancer without requiring additional surrounding context. The influence of genomic context is buffered at intact loci, but manifests more strongly as key regulatory elements are deleted or repositioned.
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Zhang W, Golynker I, Brosh R, Fajardo A, Zhu Y, Wudzinska AM, Ordoñez R, Ribeiro-Dos-Santos AM, Carrau L, Damani-Yokota P, Yeung ST, Khairallah C, Vela Gartner A, Chalhoub N, Huang E, Ashe HJ, Khanna KM, Maurano MT, Kim SY, tenOever BR, Boeke JD. Mouse genome rewriting and tailoring of three important disease loci. Nature 2023; 623:423-431. [PMID: 37914927 PMCID: PMC10632133 DOI: 10.1038/s41586-023-06675-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 09/25/2023] [Indexed: 11/03/2023]
Abstract
Genetically engineered mouse models (GEMMs) help us to understand human pathologies and develop new therapies, yet faithfully recapitulating human diseases in mice is challenging. Advances in genomics have highlighted the importance of non-coding regulatory genome sequences, which control spatiotemporal gene expression patterns and splicing in many human diseases1,2. Including regulatory extensive genomic regions, which requires large-scale genome engineering, should enhance the quality of disease modelling. Existing methods set limits on the size and efficiency of DNA delivery, hampering the routine creation of highly informative models that we call genomically rewritten and tailored GEMMs (GREAT-GEMMs). Here we describe 'mammalian switching antibiotic resistance markers progressively for integration' (mSwAP-In), a method for efficient genome rewriting in mouse embryonic stem cells. We demonstrate the use of mSwAP-In for iterative genome rewriting of up to 115 kb of a tailored Trp53 locus, as well as for humanization of mice using 116 kb and 180 kb human ACE2 loci. The ACE2 model recapitulated human ACE2 expression patterns and splicing, and notably, presented milder symptoms when challenged with SARS-CoV-2 compared with the existing K18-hACE2 model, thus representing a more human-like model of infection. Finally, we demonstrated serial genome writing by humanizing mouse Tmprss2 biallelically in the ACE2 GREAT-GEMM, highlighting the versatility of mSwAP-In in genome writing.
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Affiliation(s)
- Weimin Zhang
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Ilona Golynker
- Department of Microbiology, NYU Langone Health, New York, NY, USA
| | - Ran Brosh
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Alvaro Fajardo
- Department of Microbiology, NYU Langone Health, New York, NY, USA
| | - Yinan Zhu
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Aleksandra M Wudzinska
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Raquel Ordoñez
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - André M Ribeiro-Dos-Santos
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Lucia Carrau
- Department of Microbiology, NYU Langone Health, New York, NY, USA
| | | | - Stephen T Yeung
- Department of Microbiology, NYU Langone Health, New York, NY, USA
| | | | - Antonio Vela Gartner
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Noor Chalhoub
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Emily Huang
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Hannah J Ashe
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Kamal M Khanna
- Department of Microbiology, NYU Langone Health, New York, NY, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Matthew T Maurano
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
- Department of Pathology, NYU Langone Health, New York, NY, USA
| | - Sang Yong Kim
- Department of Pathology, NYU Langone Health, New York, NY, USA
| | - Benjamin R tenOever
- Department of Microbiology, NYU Langone Health, New York, NY, USA
- Department of Medicine, NYU Langone Health, New York, NY, USA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA.
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY, USA.
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5
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Brosh R, Coelho C, Ribeiro-Dos-Santos AM, Ellis G, Hogan MS, Ashe HJ, Somogyi N, Ordoñez R, Luther RD, Huang E, Boeke JD, Maurano MT. Synthetic regulatory genomics uncovers enhancer context dependence at the Sox2 locus. Mol Cell 2023; 83:1140-1152.e7. [PMID: 36931273 PMCID: PMC10081970 DOI: 10.1016/j.molcel.2023.02.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/20/2023] [Accepted: 02/23/2023] [Indexed: 03/18/2023]
Abstract
Sox2 expression in mouse embryonic stem cells (mESCs) depends on a distal cluster of DNase I hypersensitive sites (DHSs), but their individual contributions and degree of interdependence remain a mystery. We analyzed the endogenous Sox2 locus using Big-IN to scarlessly integrate large DNA payloads incorporating deletions, rearrangements, and inversions affecting single or multiple DHSs, as well as surgical alterations to transcription factor (TF) recognition sequences. Multiple mESC clones were derived for each payload, sequence-verified, and analyzed for Sox2 expression. We found that two DHSs comprising a handful of key TF recognition sequences were each sufficient for long-range activation of Sox2 expression. By contrast, three nearby DHSs were entirely context dependent, showing no activity alone but dramatically augmenting the activity of the autonomous DHSs. Our results highlight the role of context in modulating genomic regulatory element function, and our synthetic regulatory genomics approach provides a roadmap for the dissection of other genomic loci.
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Affiliation(s)
- Ran Brosh
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Camila Coelho
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | | | - Gwen Ellis
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Megan S Hogan
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Hannah J Ashe
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Nicolette Somogyi
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Raquel Ordoñez
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Raven D Luther
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Emily Huang
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Jef D Boeke
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA; Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Matthew T Maurano
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Pathology, NYU School of Medicine, New York, NY 10016, USA.
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Leitão LPC, de Carvalho DC, Rodrigues JCG, Fernandes MR, Wanderley AV, Vinagre LWMS, da Silva NM, Pastana LF, Gellen LPA, Assunção MCE, Fernandes SSM, Pereira EEB, Ribeiro-Dos-Santos AM, Guerreiro JF, Ribeiro-dos-Santos Â, de Assumpção PP, dos Santos SEB, dos Santos NPC. Identification of Genomic Variants Associated with the Risk of Acute Lymphoblastic Leukemia in Native Americans from Brazilian Amazonia. J Pers Med 2022; 12:jpm12060856. [PMID: 35743641 PMCID: PMC9224820 DOI: 10.3390/jpm12060856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/17/2022] [Accepted: 04/18/2022] [Indexed: 12/04/2022] Open
Abstract
A number of genomic variants related to native American ancestry may be associated with an increased risk of developing Acute Lymphoblastic Leukemia (ALL), which means that Latin American and hispanic populations from the New World may be relatively susceptible to this disease. However, there has not yet been any comprehensive investigation of the variants associated with susceptibility to ALL in traditional Amerindian populations from Brazilian Amazonia. We investigated the exomes of the 18 principal genes associated with susceptibility to ALL in samples of 64 Amerindians from this region, including cancer-free individuals and patients with ALL. We compared the findings with the data on populations representing five continents available in the 1000 Genomes database. The variation in the allele frequencies found between the different groups was evaluated using Fisher’s exact test. The analyses of the exomes of the Brazilian Amerindians identified 125 variants, seven of which were new. The comparison of the allele frequencies between the two Amerindian groups analyzed in the present study (ALL patients vs. cancer-free individuals) identified six variants (rs11515, rs2765997, rs1053454, rs8068981, rs3764342, and rs2304465) that may be associated with susceptibility to ALL. These findings contribute to the identification of genetic variants that represent a potential risk for ALL in Amazonian Amerindian populations and might favor precision oncology measures.
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Affiliation(s)
- Luciana P. C. Leitão
- Oncology Research Nucleus, Universidade Federal do Pará, Belém 66073-005, PA, Brazil; (L.P.C.L.); (D.C.d.C.); (J.C.G.R.); (M.R.F.); (L.W.M.S.V.); (N.M.d.S.); (L.F.P.); (L.P.A.G.); (M.C.E.A.); (P.P.d.A.)
- Faculdade de Ciências Médicas do Pará (FACIMPA), Marabá 68508-030, PA, Brazil
| | - Darlen C. de Carvalho
- Oncology Research Nucleus, Universidade Federal do Pará, Belém 66073-005, PA, Brazil; (L.P.C.L.); (D.C.d.C.); (J.C.G.R.); (M.R.F.); (L.W.M.S.V.); (N.M.d.S.); (L.F.P.); (L.P.A.G.); (M.C.E.A.); (P.P.d.A.)
| | - Juliana C. G. Rodrigues
- Oncology Research Nucleus, Universidade Federal do Pará, Belém 66073-005, PA, Brazil; (L.P.C.L.); (D.C.d.C.); (J.C.G.R.); (M.R.F.); (L.W.M.S.V.); (N.M.d.S.); (L.F.P.); (L.P.A.G.); (M.C.E.A.); (P.P.d.A.)
| | - Marianne R. Fernandes
- Oncology Research Nucleus, Universidade Federal do Pará, Belém 66073-005, PA, Brazil; (L.P.C.L.); (D.C.d.C.); (J.C.G.R.); (M.R.F.); (L.W.M.S.V.); (N.M.d.S.); (L.F.P.); (L.P.A.G.); (M.C.E.A.); (P.P.d.A.)
| | - Alayde V. Wanderley
- Pediatrics Department, Ophir Loyola Hospital, Belém 66063-240, PA, Brazil; (A.V.W.); (S.S.M.F.)
| | - Lui W. M. S. Vinagre
- Oncology Research Nucleus, Universidade Federal do Pará, Belém 66073-005, PA, Brazil; (L.P.C.L.); (D.C.d.C.); (J.C.G.R.); (M.R.F.); (L.W.M.S.V.); (N.M.d.S.); (L.F.P.); (L.P.A.G.); (M.C.E.A.); (P.P.d.A.)
| | - Natasha M. da Silva
- Oncology Research Nucleus, Universidade Federal do Pará, Belém 66073-005, PA, Brazil; (L.P.C.L.); (D.C.d.C.); (J.C.G.R.); (M.R.F.); (L.W.M.S.V.); (N.M.d.S.); (L.F.P.); (L.P.A.G.); (M.C.E.A.); (P.P.d.A.)
| | - Lucas F. Pastana
- Oncology Research Nucleus, Universidade Federal do Pará, Belém 66073-005, PA, Brazil; (L.P.C.L.); (D.C.d.C.); (J.C.G.R.); (M.R.F.); (L.W.M.S.V.); (N.M.d.S.); (L.F.P.); (L.P.A.G.); (M.C.E.A.); (P.P.d.A.)
| | - Laura P. A. Gellen
- Oncology Research Nucleus, Universidade Federal do Pará, Belém 66073-005, PA, Brazil; (L.P.C.L.); (D.C.d.C.); (J.C.G.R.); (M.R.F.); (L.W.M.S.V.); (N.M.d.S.); (L.F.P.); (L.P.A.G.); (M.C.E.A.); (P.P.d.A.)
| | - Matheus C. E. Assunção
- Oncology Research Nucleus, Universidade Federal do Pará, Belém 66073-005, PA, Brazil; (L.P.C.L.); (D.C.d.C.); (J.C.G.R.); (M.R.F.); (L.W.M.S.V.); (N.M.d.S.); (L.F.P.); (L.P.A.G.); (M.C.E.A.); (P.P.d.A.)
| | - Sweny S. M. Fernandes
- Pediatrics Department, Ophir Loyola Hospital, Belém 66063-240, PA, Brazil; (A.V.W.); (S.S.M.F.)
| | - Esdras E. B. Pereira
- Human and Medical Genetics Laboratory, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil; (E.E.B.P.); (A.M.R.-D.-S.); (J.F.G.); (Â.R.-d.-S.); (S.E.B.d.S.)
- Instituto Tocantinense Presidente Antônio Carlos (ITPAC), Abaetetuba 68440-000, PA, Brazil
| | - André M. Ribeiro-Dos-Santos
- Human and Medical Genetics Laboratory, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil; (E.E.B.P.); (A.M.R.-D.-S.); (J.F.G.); (Â.R.-d.-S.); (S.E.B.d.S.)
| | - João F. Guerreiro
- Human and Medical Genetics Laboratory, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil; (E.E.B.P.); (A.M.R.-D.-S.); (J.F.G.); (Â.R.-d.-S.); (S.E.B.d.S.)
| | - Ândrea Ribeiro-dos-Santos
- Human and Medical Genetics Laboratory, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil; (E.E.B.P.); (A.M.R.-D.-S.); (J.F.G.); (Â.R.-d.-S.); (S.E.B.d.S.)
| | - Paulo P. de Assumpção
- Oncology Research Nucleus, Universidade Federal do Pará, Belém 66073-005, PA, Brazil; (L.P.C.L.); (D.C.d.C.); (J.C.G.R.); (M.R.F.); (L.W.M.S.V.); (N.M.d.S.); (L.F.P.); (L.P.A.G.); (M.C.E.A.); (P.P.d.A.)
| | - Sidney E. B. dos Santos
- Human and Medical Genetics Laboratory, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil; (E.E.B.P.); (A.M.R.-D.-S.); (J.F.G.); (Â.R.-d.-S.); (S.E.B.d.S.)
| | - Ney P. C. dos Santos
- Oncology Research Nucleus, Universidade Federal do Pará, Belém 66073-005, PA, Brazil; (L.P.C.L.); (D.C.d.C.); (J.C.G.R.); (M.R.F.); (L.W.M.S.V.); (N.M.d.S.); (L.F.P.); (L.P.A.G.); (M.C.E.A.); (P.P.d.A.)
- Correspondence: ; Tel.: +55-(91)-3201-6778
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7
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Ribeiro-Dos-Santos AM, Hogan MS, Luther RD, Brosh R, Maurano MT. Genomic context sensitivity of insulator function. Genome Res 2022; 32:425-436. [PMID: 35082140 PMCID: PMC8896466 DOI: 10.1101/gr.276449.121] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/25/2022] [Indexed: 11/24/2022]
Abstract
The specificity of interactions between genomic regulatory elements and potential target genes is influenced by the binding of insulator proteins such as CTCF, which can act as potent enhancer blockers when interposed between an enhancer and a promoter in a reporter assay. But not all CTCF sites genome-wide function as insulator elements, depending on cellular and genomic context. To dissect the influence of genomic context on enhancer blocker activity, we integrated reporter constructs with promoter-only, promoter and enhancer, and enhancer blocker configurations at hundreds of thousands of genomic sites using the Sleeping Beauty transposase. Deconvolution of reporter activity by genomic position reveals distinct expression patterns subject to genomic context, including a compartment of enhancer blocker reporter integrations with robust expression. The high density of integration sites permits quantitative delineation of characteristic genomic context sensitivity profiles and their decomposition into sensitivity to both local and distant DNase I hypersensitive sites. Furthermore, using a single-cell expression approach to test the effect of integrated reporters for differential expression of nearby endogenous genes reveals that CTCF insulator elements do not completely abrogate reporter effects on endogenous gene expression. Collectively, our results lend new insight into genomic regulatory compartmentalization and its influence on the determinants of promoter–enhancer specificity.
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Affiliation(s)
| | - Megan S Hogan
- Institute for Systems Genetics, NYU Grossman School of Medicine
| | - Raven D Luther
- Institute for Systems Genetics, NYU Grossman School of Medicine
| | - Ran Brosh
- Institute for Systems Genetics, NYU Grossman School of Medicine
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8
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Vidal AF, Ferraz RS, El-Husny A, Silva CS, Vinasco-Sandoval T, Magalhães L, Raiol-Moraes M, Barra WF, Pereira CLBL, de Assumpção PP, de Brito LM, Vialle RA, Santos S, Ribeiro-Dos-Santos Â, Ribeiro-Dos-Santos AM. Comprehensive analysis of germline mutations in northern Brazil: a panel of 16 genes for hereditary cancer-predisposing syndrome investigation. BMC Cancer 2021; 21:363. [PMID: 33827469 PMCID: PMC8028728 DOI: 10.1186/s12885-021-08089-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 03/23/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Next generation sequencing (NGS) has been a handy tool in clinical practice, mainly due to its efficiency and cost-effectiveness. It has been widely used in genetic diagnosis of several inherited diseases, and, in clinical oncology, it may enhance the discovery of new susceptibility genes and enable individualized care of cancer patients. In this context, we explored a pan-cancer panel in the investigation of germline variants in Brazilian patients presenting clinical criteria for hereditary cancer syndromes or familial history. METHODS Seventy-one individuals diagnosed or with familial history of hereditary cancer syndromes were submitted to custom pan-cancer panel including 16 high and moderate penetrance genes previously associated with hereditary cancer syndromes (APC, BRCA1, BRCA2, CDH1, CDKN2A, CHEK2, MSH2, MSH6, MUTYH, PTEN, RB1, RET, TP53, VHL, XPA and XPC). All pathogenic variants were validated by Sanger sequencing. RESULTS We identified a total of eight pathogenic variants among 12 of 71 individuals (16.9%). Among the mutation-positive subjects, 50% were diagnosed with breast cancer and had mutations in BRCA1, CDH1 and MUTYH. Notably, 33.3% were individuals diagnosed with polyposis or who had family cases and harbored pathogenic mutations in APC and MUTYH. The remaining individuals (16.7%) were gastric cancer patients with pathogenic variants in CDH1 and MSH2. Overall, 54 (76.05%) individuals presented at least one variant uncertain significance (VUS), totalizing 81 VUS. Of these, seven were predicted to have disease-causing potential. CONCLUSION Overall, analysis of all these genes in NGS-panel allowed the identification not only of pathogenic variants related to hereditary cancer syndromes but also of some VUS that need further clinical and molecular investigations. The results obtained in this study had a significant impact on patients and their relatives since it allowed genetic counselling and personalized management decisions.
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Affiliation(s)
- Amanda Ferreira Vidal
- Laboratory of Human and Medical Genetics, Graduate Program Genetics and Molecular Biology, Federal University of Pará, Belém, Pará, Brazil
| | - Rafaella Sousa Ferraz
- Laboratory of Human and Medical Genetics, Graduate Program Genetics and Molecular Biology, Federal University of Pará, Belém, Pará, Brazil
| | - Antonette El-Husny
- Bettina Ferro de Souza University Hospital, Federal University of Pará, Belém, Pará, Brazil
| | - Caio Santos Silva
- Laboratory of Human and Medical Genetics, Graduate Program Genetics and Molecular Biology, Federal University of Pará, Belém, Pará, Brazil
| | - Tatiana Vinasco-Sandoval
- Laboratory of Human and Medical Genetics, Graduate Program Genetics and Molecular Biology, Federal University of Pará, Belém, Pará, Brazil
| | - Leandro Magalhães
- Laboratory of Human and Medical Genetics, Graduate Program Genetics and Molecular Biology, Federal University of Pará, Belém, Pará, Brazil
| | - Milene Raiol-Moraes
- Laboratory of Human and Medical Genetics, Graduate Program Genetics and Molecular Biology, Federal University of Pará, Belém, Pará, Brazil
| | - Williams Fernandes Barra
- João de Barros Barreto University Hospital, Federal University of Pará, Belém, Pará, Brazil
- Center of Oncology Research, Federal University of Pará, Belém, Pará, Brazil
| | - Cynthia Lara Brito Lins Pereira
- João de Barros Barreto University Hospital, Federal University of Pará, Belém, Pará, Brazil
- Center of Oncology Research, Federal University of Pará, Belém, Pará, Brazil
| | | | - Leonardo Miranda de Brito
- Laboratory of Human and Medical Genetics, Graduate Program Genetics and Molecular Biology, Federal University of Pará, Belém, Pará, Brazil
| | - Ricardo Assunção Vialle
- Laboratory of Human and Medical Genetics, Graduate Program Genetics and Molecular Biology, Federal University of Pará, Belém, Pará, Brazil
| | - Sidney Santos
- Laboratory of Human and Medical Genetics, Graduate Program Genetics and Molecular Biology, Federal University of Pará, Belém, Pará, Brazil
- Center of Oncology Research, Federal University of Pará, Belém, Pará, Brazil
| | - Ândrea Ribeiro-Dos-Santos
- Laboratory of Human and Medical Genetics, Graduate Program Genetics and Molecular Biology, Federal University of Pará, Belém, Pará, Brazil
- Center of Oncology Research, Federal University of Pará, Belém, Pará, Brazil
| | - André M Ribeiro-Dos-Santos
- Laboratory of Human and Medical Genetics, Graduate Program Genetics and Molecular Biology, Federal University of Pará, Belém, Pará, Brazil.
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9
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Reis LB, Bakos RM, Vianna FSL, Macedo GS, Jacovas VC, Ribeiro-Dos-Santos AM, Santos S, Bakos L, Ashton-Prolla P. Skin pigmentation polymorphisms associated with increased risk of melanoma in a case-control sample from southern Brazil. BMC Cancer 2020; 20:1069. [PMID: 33167923 PMCID: PMC7650158 DOI: 10.1186/s12885-020-07485-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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] [Received: 05/14/2019] [Accepted: 10/02/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Melanoma is the most aggressive type of skin cancer and is associated with environmental and genetic risk factors. It originates in melanocytes, the pigment-producing cells. Single nucleotide polymorphisms (SNPs) in pigmentation genes have been described in melanoma risk modulation, but knowledge in the field is still limited. METHODS In a case-control approach (107 cases and 119 controls), we investigated the effect of four pigmentation gene SNPs (TYR rs1126809, HERC2 rs1129038, SLC24A5 rs1426654, and SLC45A2 rs16891982) on melanoma risk in individuals from southern Brazil using a multivariate logistic regression model and multifactor dimensionality reduction (MDR) analysis. RESULTS Two SNPs were associated with an increased risk of melanoma in a dominant model: rs1129038AA and rs1426654AA [OR = 2.094 (95% CI: 1.106-3.966), P = 2.3 10- 2 and OR = 7.126 (95% CI: 1.873-27.110), P = 4.0 10- 3, respectively]. SNP rs16891982CC was associated with a lower risk to melanoma development in a log-additive model when the allele C was inherited [OR = 0.081 (95% CI: 0.008-0.782), P = 3 10- 2]. In addition, MDR analysis showed that the combination of the rs1426654AA and rs16891982GG genotypes was associated with a higher risk for melanoma (P = 3 10- 3), with a redundant effect. CONCLUSIONS These results contribute to the current knowledge and indicate that epistatic interaction of these SNPs, with an additive or correlational effect, may be involved in modulating the risk of melanoma in individuals from a geographic region with a high incidence of the disease.
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Affiliation(s)
- Larissa B Reis
- Serviço de Pesquisa Experimental, Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, Porto Alegre, Rio Grande do Sul, 2350, Brazil.,Programa de Pós-Graduação em Medicina: Ciências Médicas, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Renato M Bakos
- Programa de Pós-Graduação em Medicina: Ciências Médicas, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Serviço de Dermatologia, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Fernanda S L Vianna
- Serviço de Pesquisa Experimental, Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, Porto Alegre, Rio Grande do Sul, 2350, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Gabriel S Macedo
- Serviço de Pesquisa Experimental, Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, Porto Alegre, Rio Grande do Sul, 2350, Brazil
| | - Vanessa C Jacovas
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | | | - Sidney Santos
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Lúcio Bakos
- Serviço de Dermatologia, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Patricia Ashton-Prolla
- Serviço de Pesquisa Experimental, Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, Porto Alegre, Rio Grande do Sul, 2350, Brazil. .,Programa de Pós-Graduação em Medicina: Ciências Médicas, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil. .,Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.
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10
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Ribeiro-Dos-Santos AM, Vidal AF, Vinasco-Sandoval T, Guerreiro J, Santos S, Ribeiro-Dos-Santos Â, de Souza SJ. Exome Sequencing of Native Populations From the Amazon Reveals Patterns on the Peopling of South America. Front Genet 2020; 11:548507. [PMID: 33193622 PMCID: PMC7660019 DOI: 10.3389/fgene.2020.548507] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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] [Received: 04/02/2020] [Accepted: 10/09/2020] [Indexed: 02/05/2023] Open
Abstract
Studies on the peopling of South America have been limited by the paucity of sequence data from Native Americans, especially from the east part of the Amazon region. Here, we investigate the whole exome variation from 58 Native American individuals (eight different populations) from the Amazon region and draw insights into the peopling of South America. By using the sequence data generated here together with data from the public domain, we confirmed a strong genetic distinction between Andean and Amazonian populations. By testing distinct demographic models, our analysis supports a scenario of South America occupation that involves migrations along the Pacific and Atlantic coasts. Occupation of the southeast part of South America would involve migrations from the north, rather than from the west of the continent.
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Affiliation(s)
| | - Amanda Ferreira Vidal
- Genetics and Molecular Biology Graduate Program, Instituto de Ciências Biológicas, UFPA, Belém, Brazil
| | - Tatiana Vinasco-Sandoval
- Genetics and Molecular Biology Graduate Program, Instituto de Ciências Biológicas, UFPA, Belém, Brazil
| | - João Guerreiro
- Genetics and Molecular Biology Graduate Program, Instituto de Ciências Biológicas, UFPA, Belém, Brazil
| | - Sidney Santos
- Genetics and Molecular Biology Graduate Program, Instituto de Ciências Biológicas, UFPA, Belém, Brazil.,Oncology and Medical Science Graduate Program, Núcleo de Pesquisas em Oncologica, UFPA, Belém, Brazil
| | - Ândrea Ribeiro-Dos-Santos
- Genetics and Molecular Biology Graduate Program, Instituto de Ciências Biológicas, UFPA, Belém, Brazil.,Oncology and Medical Science Graduate Program, Núcleo de Pesquisas em Oncologica, UFPA, Belém, Brazil
| | - Sandro J de Souza
- Instituto do Cérebro, UFRN, Natal, Brazil.,Bioinformatics Multidisciplinary Environment (BioME), Instituto Metrópole Digital, UFRN, Natal, Brazil.,Institute of Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
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11
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Maurano MT, Ramaswami S, Zappile P, Dimartino D, Boytard L, Ribeiro-Dos-Santos AM, Vulpescu NA, Westby G, Shen G, Feng X, Hogan MS, Ragonnet-Cronin M, Geidelberg L, Marier C, Meyn P, Zhang Y, Cadley J, Ordoñez R, Luther R, Huang E, Guzman E, Arguelles-Grande C, Argyropoulos KV, Black M, Serrano A, Call ME, Kim MJ, Belovarac B, Gindin T, Lytle A, Pinnell J, Vougiouklakis T, Chen J, Lin LH, Rapkiewicz A, Raabe V, Samanovic MI, Jour G, Osman I, Aguero-Rosenfeld M, Mulligan MJ, Volz EM, Cotzia P, Snuderl M, Heguy A. Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City region. Genome Res 2020; 30:1781-1788. [PMID: 33093069 PMCID: PMC7706732 DOI: 10.1101/gr.266676.120] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/20/2020] [Indexed: 11/30/2022]
Abstract
Effective public response to a pandemic relies upon accurate measurement of the extent and dynamics of an outbreak. Viral genome sequencing has emerged as a powerful approach to link seemingly unrelated cases, and large-scale sequencing surveillance can inform on critical epidemiological parameters. Here, we report the analysis of 864 SARS-CoV-2 sequences from cases in the New York City metropolitan area during the COVID-19 outbreak in spring 2020. The majority of cases had no recent travel history or known exposure, and genetically linked cases were spread throughout the region. Comparison to global viral sequences showed that early transmission was most linked to cases from Europe. Our data are consistent with numerous seeds from multiple sources and a prolonged period of unrecognized community spreading. This work highlights the complementary role of genomic surveillance in addition to traditional epidemiological indicators.
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Affiliation(s)
- Matthew T Maurano
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, USA.,Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Sitharam Ramaswami
- Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, New York 10016, USA
| | - Paul Zappile
- Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, New York 10016, USA
| | - Dacia Dimartino
- Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, New York 10016, USA
| | - Ludovic Boytard
- Center for Biospecimen Research and Development, NYU Langone Health, New York, New York 10016, USA
| | - André M Ribeiro-Dos-Santos
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, USA.,Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Nicholas A Vulpescu
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, USA.,Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Gael Westby
- Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, New York 10016, USA
| | - Guomiao Shen
- Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Xiaojun Feng
- Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Megan S Hogan
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, USA.,Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Manon Ragonnet-Cronin
- MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, United Kingdom
| | - Lily Geidelberg
- MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, United Kingdom
| | - Christian Marier
- Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, New York 10016, USA
| | - Peter Meyn
- Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, New York 10016, USA
| | - Yutong Zhang
- Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, New York 10016, USA
| | - John Cadley
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, USA.,Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Raquel Ordoñez
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, USA.,Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Raven Luther
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, USA.,Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Emily Huang
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, USA.,Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Emily Guzman
- Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, New York 10016, USA
| | | | - Kimon V Argyropoulos
- Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Margaret Black
- Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Antonio Serrano
- Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Melissa E Call
- Department of Dermatology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Min Jae Kim
- Department of Dermatology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Brendan Belovarac
- Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Tatyana Gindin
- Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Andrew Lytle
- Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Jared Pinnell
- Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | | | - John Chen
- Medical Center IT, NYU Langone Health, New York, New York 10016, USA
| | - Lawrence H Lin
- Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Amy Rapkiewicz
- Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Vanessa Raabe
- Division of Infectious Diseases and Immunology, Department of Medicine and NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Marie I Samanovic
- Division of Infectious Diseases and Immunology, Department of Medicine and NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - George Jour
- Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.,Department of Dermatology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Iman Osman
- Center for Biospecimen Research and Development, NYU Langone Health, New York, New York 10016, USA.,Department of Dermatology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | | | - Mark J Mulligan
- Division of Infectious Diseases and Immunology, Department of Medicine and NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Erik M Volz
- MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, United Kingdom
| | - Paolo Cotzia
- Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.,Center for Biospecimen Research and Development, NYU Langone Health, New York, New York 10016, USA
| | - Matija Snuderl
- Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Adriana Heguy
- Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.,Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, New York 10016, USA
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12
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Vidal AF, Ribeiro-Dos-Santos AM, Vinasco-Sandoval T, Magalhães L, Pinto P, Anaissi AKM, Demachki S, de Assumpção PP, Dos Santos SEB, Ribeiro-Dos-Santos Â. The comprehensive expression analysis of circular RNAs in gastric cancer and its association with field cancerization. Sci Rep 2017; 7:14551. [PMID: 29109417 PMCID: PMC5673933 DOI: 10.1038/s41598-017-15061-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 10/18/2017] [Indexed: 12/12/2022] Open
Abstract
Circular RNAs comprise a new class of long noncoding RNAs characterized by their 5' and 3' ends covalently joined. Previous studies have demonstrated that some circular RNAs act as microRNA sponges, and are associated with cellular proliferation in cancer. We were the first to analyze the global expression of circular RNAs in samples of patients without gastric cancer, gastric cancer, and matched tumor-adjacent gastric tissue. Among the samples, we identified 736 previously annotated circular RNAs by RNA-Seq. The tumor-adjacent tissue presented the higher abundance of circular RNAs and could not be considered as a normal tissue, reinforcing the notion of field effect in gastric cancer. We identified five differentially expressed circular RNAs that may be potential biomarkers of this type of cancer. We also predicted candidate microRNAs targets of the highest expressed circular RNAs in gastric tissues and found five miRNAs. Overall, our results support the hypothesis of circular RNAs representing a novel factor in the dynamic epigenetic network of gene regulation, which involves the microRNAs, its mRNAs targets, and the circular RNAs-derived genes. Further studies are needed to elucidate the roles and the functional relevance of the circular RNAs in human diseases.
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Affiliation(s)
- Amanda Ferreira Vidal
- Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará, Brazil
| | | | | | - Leandro Magalhães
- Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará, Brazil
| | - Pablo Pinto
- Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará, Brazil
| | - Ana K M Anaissi
- Center of Oncology Research, Federal University of Pará, Belém, Pará, Brazil
| | - Samia Demachki
- Center of Oncology Research, Federal University of Pará, Belém, Pará, Brazil
| | | | - Sidney Emanuel Batista Dos Santos
- Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará, Brazil
- Center of Oncology Research, Federal University of Pará, Belém, Pará, Brazil
| | - Ândrea Ribeiro-Dos-Santos
- Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará, Brazil.
- Center of Oncology Research, Federal University of Pará, Belém, Pará, Brazil.
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13
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El-Husny A, Raiol-Moraes M, Amador M, Ribeiro-Dos-Santos AM, Montagnini A, Barbosa S, Silva A, Assumpção P, Ishak G, Santos S, Pinto P, Cruz A, Ribeiro-Dos-Santos Â. CDH1 mutations in gastric cancer patients from northern Brazil identified by Next- Generation Sequencing (NGS). Genet Mol Biol 2016; 39:189-98. [PMID: 27192129 PMCID: PMC4910547 DOI: 10.1590/1678-4685-gmb-2014-0342] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 07/23/2015] [Indexed: 12/20/2022] Open
Abstract
Gastric cancer is considered to be the fifth highest incident tumor worldwide and the third leading cause of cancer deaths. Developing regions report a higher number of sporadic cases, but there are only a few local studies related to hereditary cases of gastric cancer in Brazil to confirm this fact. CDH1 germline mutations have been described both in familial and sporadic cases, but there is only one recent molecular description of individuals from Brazil. In this study we performed Next Generation Sequencing (NGS) to assess CDH1 germline mutations in individuals who match the clinical criteria for Hereditary Diffuse Gastric Cancer (HDGC), or who exhibit very early diagnosis of gastric cancer. Among five probands we detected CDH1 germline mutations in two cases (40%). The mutation c.1023T > G was found in a HDGC family and the mutation c.1849G > A, which is nearly exclusive to African populations, was found in an early-onset case of gastric adenocarcinoma. The mutations described highlight the existence of gastric cancer cases caused by CDH1 germline mutations in northern Brazil, although such information is frequently ignored due to the existence of a large number of environmental factors locally. Our report represent the first CDH1 mutations in HDGC described from Brazil by an NGS platform.
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Affiliation(s)
- Antonette El-Husny
- Laboratório de Genética Humana e Médica (LGHM), Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, PA, Brazil.,Rede de Pesquisa em Genômica Populacional Humana, Universidade Federal do Pará (UFPA), Belém, PA, Brazil
| | - Milene Raiol-Moraes
- Laboratório de Genética Humana e Médica (LGHM), Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, PA, Brazil.,Rede de Pesquisa em Genômica Populacional Humana, Universidade Federal do Pará (UFPA), Belém, PA, Brazil
| | - Marcos Amador
- Laboratório de Genética Humana e Médica (LGHM), Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, PA, Brazil.,Rede de Pesquisa em Genômica Populacional Humana, Universidade Federal do Pará (UFPA), Belém, PA, Brazil
| | - André M Ribeiro-Dos-Santos
- Laboratório de Genética Humana e Médica (LGHM), Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, PA, Brazil.,Rede de Pesquisa em Genômica Populacional Humana, Universidade Federal do Pará (UFPA), Belém, PA, Brazil
| | - André Montagnini
- Instituto Sírio-Libanês de Ensino e Pesquisa, Hospital Sírio-Libanês, São Paulo, SP, Brazil
| | - Silvanira Barbosa
- Laboratório de Polimorfismo de DNA - Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, PA, Brazil
| | - Artur Silva
- Rede de Pesquisa em Genômica Populacional Humana, Universidade Federal do Pará (UFPA), Belém, PA, Brazil.,Laboratório de Polimorfismo de DNA - Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, PA, Brazil
| | - Paulo Assumpção
- Rede de Pesquisa em Genômica Populacional Humana, Universidade Federal do Pará (UFPA), Belém, PA, Brazil.,Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará (UFPA), Belém, PA, Brazil
| | - Geraldo Ishak
- Rede de Pesquisa em Genômica Populacional Humana, Universidade Federal do Pará (UFPA), Belém, PA, Brazil.,Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará (UFPA), Belém, PA, Brazil.,Hospital Universitário João de Barros Barreto, Universidade Federal do Pará (UFPA), Belém, PA, Brazil
| | - Sidney Santos
- Laboratório de Genética Humana e Médica (LGHM), Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, PA, Brazil.,Rede de Pesquisa em Genômica Populacional Humana, Universidade Federal do Pará (UFPA), Belém, PA, Brazil.,Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará (UFPA), Belém, PA, Brazil
| | - Pablo Pinto
- Laboratório de Genética Humana e Médica (LGHM), Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, PA, Brazil.,Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará (UFPA), Belém, PA, Brazil
| | - Aline Cruz
- Laboratório de Genética Humana e Médica (LGHM), Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, PA, Brazil.,Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará (UFPA), Belém, PA, Brazil
| | - Ândrea Ribeiro-Dos-Santos
- Laboratório de Genética Humana e Médica (LGHM), Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, PA, Brazil.,Rede de Pesquisa em Genômica Populacional Humana, Universidade Federal do Pará (UFPA), Belém, PA, Brazil.,Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará (UFPA), Belém, PA, Brazil
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14
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Moreira FC, Dustan B, Hamoy IG, Ribeiro-Dos-Santos AM, Dos Santos AR. TargetCompare: A web interface to compare simultaneous miRNAs targets. Bioinformation 2014; 10:602-5. [PMID: 25352731 PMCID: PMC4209372 DOI: 10.6026/97320630010602] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [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] [Received: 07/29/2014] [Accepted: 08/01/2014] [Indexed: 12/19/2022] Open
Abstract
UNLABELLED MicroRNAs (miRNAs) are small non-coding nucleotide sequences between 17 and 25 nucleotides in length that primarily function in the regulation of gene expression. A since miRNA has thousand of predict targets in a complex, regulatory cell signaling network. Therefore, it is of interest to study multiple target genes simultaneously. Hence, we describe a web tool (developed using Java programming language and MySQL database server) to analyse multiple targets of pre-selected miRNAs. We cross validated the tool in eight most highly expressed miRNAs in the antrum region of stomach. This helped to identify 43 potential genes that are target of at least six of the referred miRNAs. The developed tool aims to reduce the randomness and increase the chance of selecting strong candidate target genes and miRNAs responsible for playing important roles in the studied tissue. AVAILABILITY http://lghm.ufpa.br/targetcompare.
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Affiliation(s)
- Fabiano Cordeiro Moreira
- Laboratorio de Genética Humana e Medica, Instituto de Ciências Biológicas, Universidade Federal do Para, Belem, PA, Brasil ; Centro Universitário do Pará - Área de Ciências Exatas e Tecnologia, , Belém, PA, Brasil
| | - Bruno Dustan
- Laboratorio de Genética Humana e Medica, Instituto de Ciências Biológicas, Universidade Federal do Para, Belem, PA, Brasil ; Centro Universitário do Pará - Área de Ciências Exatas e Tecnologia, , Belém, PA, Brasil
| | - Igor G Hamoy
- Laboratorio de Genética Humana e Medica, Instituto de Ciências Biológicas, Universidade Federal do Para, Belem, PA, Brasil ; Universidade Federal Rural da Amazônia, Campus de Capanema, PA, Brasil
| | - André M Ribeiro-Dos-Santos
- Laboratorio de Genética Humana e Medica, Instituto de Ciências Biológicas, Universidade Federal do Para, Belem, PA, Brasil
| | - Andrea Ribeiro Dos Santos
- Laboratorio de Genética Humana e Medica, Instituto de Ciências Biológicas, Universidade Federal do Para, Belem, PA, Brasil ; Nucleo de Pesquisa em Oncologia, Universidade Federal do Para, Belem, PA, Brasil
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15
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Hamoy IG, Ribeiro-Dos-Santos AM, Alvarez L, Barbosa S, Silva A, Santos S, Gusmão L, Ribeiro-Dos-Santos A. A Protocol for mtGenome Analysis on Large Sample Numbers. Bioinform Biol Insights 2014; 8:127-34. [PMID: 25002812 PMCID: PMC4069038 DOI: 10.4137/bbi.s14623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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] [Received: 01/31/2014] [Revised: 03/09/2014] [Accepted: 03/10/2014] [Indexed: 01/04/2023] Open
Abstract
The mitochondrial genome is widely studied in a variety of fields, such as population, forensic, and human and medical genetics. Most studies have been limited to a small portion of the sequence that, although highly diverse, does not describe the total variability. The arrival of modern high-throughput sequencing technologies has made it possible to investigate larger sequences in a shorter amount of time as well as in a more affordable fashion. This work aims to describe a protocol for sequencing and analyzing the complete mitochondrial genome with the Ion PGM™ platform. To evaluate the protocol, the mitochondrial genome was sequenced to approximately 210 Mbp, with high-quality sequences distributed between 12 samples that had an average coverage of 1023× per sample. Several variant callers were compared to improve the protocol outcome. The results suggest that it is possible to run up to 120 samples per run without any loss of any significant quality. Therefore, this protocol is an efficient and accurate tool for full mitochondrial genome analysis.
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Affiliation(s)
- Igor G Hamoy
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil. ; Universidade Federal Rural da Amazônia, Campus de Capanema, PA, Brazil
| | | | - Luiz Alvarez
- Institute of Molecular Pathology and Immunology of the University of Porto, Universidade do Porto. Porto, Portugal
| | - Silvanira Barbosa
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
| | - Artur Silva
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
| | - Sidney Santos
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil. ; Núcleo de Pesquisa em Oncologia, Universidade Federal do Pará, Belém, PA, Brazil
| | - Leonor Gusmão
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil. ; Institute of Molecular Pathology and Immunology of the University of Porto, Universidade do Porto. Porto, Portugal
| | - Andrea Ribeiro-Dos-Santos
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil. ; Núcleo de Pesquisa em Oncologia, Universidade Federal do Pará, Belém, PA, Brazil
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