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Preuss I, Rosenberg M, Yakhini Z, Anavy L. Efficient DNA-based data storage using shortmer combinatorial encoding. Sci Rep 2024; 14:7731. [PMID: 38565928 DOI: 10.1038/s41598-024-58386-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 03/28/2024] [Indexed: 04/04/2024] Open
Abstract
Data storage in DNA has recently emerged as a promising archival solution, offering space-efficient and long-lasting digital storage solutions. Recent studies suggest leveraging the inherent redundancy of synthesis and sequencing technologies by using composite DNA alphabets. A major challenge of this approach involves the noisy inference process, obstructing large composite alphabets. This paper introduces a novel approach for DNA-based data storage, offering, in some implementations, a 6.5-fold increase in logical density over standard DNA-based storage systems, with near-zero reconstruction error. Combinatorial DNA encoding uses a set of clearly distinguishable DNA shortmers to construct large combinatorial alphabets, where each letter consists of a subset of shortmers. We formally define various combinatorial encoding schemes and investigate their theoretical properties. These include information density and reconstruction probabilities, as well as required synthesis and sequencing multiplicities. We then propose an end-to-end design for a combinatorial DNA-based data storage system, including encoding schemes, two-dimensional (2D) error correction codes, and reconstruction algorithms, under different error regimes. We performed simulations and show, for example, that the use of 2D Reed-Solomon error correction has significantly improved reconstruction rates. We validated our approach by constructing two combinatorial sequences using Gibson assembly, imitating a 4-cycle combinatorial synthesis process. We confirmed the successful reconstruction, and established the robustness of our approach for different error types. Subsampling experiments supported the important role of sampling rate and its effect on the overall performance. Our work demonstrates the potential of combinatorial shortmer encoding for DNA-based data storage and describes some theoretical research questions and technical challenges. Combining combinatorial principles with error-correcting strategies, and investing in the development of DNA synthesis technologies that efficiently support combinatorial synthesis, can pave the way to efficient, error-resilient DNA-based storage solutions.
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Affiliation(s)
- Inbal Preuss
- School of Computer Science, Reichman University, 4610101, Herzliya, Israel.
- Faculty of Computer Science, Technion, 3200003, Haifa, Israel.
| | - Michael Rosenberg
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002, Ramat Gan, Israel
| | - Zohar Yakhini
- School of Computer Science, Reichman University, 4610101, Herzliya, Israel
- Faculty of Computer Science, Technion, 3200003, Haifa, Israel
| | - Leon Anavy
- School of Computer Science, Reichman University, 4610101, Herzliya, Israel
- Faculty of Computer Science, Technion, 3200003, Haifa, Israel
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2
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Sabary O, Yucovich A, Shapira G, Yaakobi E. Reconstruction algorithms for DNA-storage systems. Sci Rep 2024; 14:1951. [PMID: 38263421 PMCID: PMC10806084 DOI: 10.1038/s41598-024-51730-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 01/09/2024] [Indexed: 01/25/2024] Open
Abstract
Motivated by DNA storage systems, this work presents the DNA reconstruction problem, in which a length-n string, is passing through the DNA-storage channel, which introduces deletion, insertion and substitution errors. This channel generates multiple noisy copies of the transmitted string which are called traces. A DNA reconstruction algorithm is a mapping which receives t traces as an input and produces an estimation of the original string. The goal in the DNA reconstruction problem is to minimize the edit distance between the original string and the algorithm's estimation. In this work, we present several new algorithms for this problem. Our algorithms look globally on the entire sequence of the traces and use dynamic programming algorithms, which are used for the shortest common supersequence and the longest common subsequence problems, in order to decode the original string. Our algorithms do not require any limitations on the input and the number of traces, and more than that, they perform well even for error probabilities as high as 0.27. The algorithms have been tested on simulated data, on data from previous DNA storage experiments, and on a new synthesized dataset, and are shown to outperform previous algorithms in reconstruction accuracy.
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Affiliation(s)
- Omer Sabary
- The Henry and Marilyn Taub Faculty of Computer Science, Technion, 3200003, Haifa, Israel.
| | - Alexander Yucovich
- The Henry and Marilyn Taub Faculty of Computer Science, Technion, 3200003, Haifa, Israel
| | - Guy Shapira
- The Henry and Marilyn Taub Faculty of Computer Science, Technion, 3200003, Haifa, Israel
| | - Eitan Yaakobi
- The Henry and Marilyn Taub Faculty of Computer Science, Technion, 3200003, Haifa, Israel
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Benedetti F, Silvestri G, Saadat S, Denaro F, Latinovic OS, Davis H, Williams S, Bryant J, Ippodrino R, Rathinam CV, Gallo RC, Zella D. Mycoplasma DnaK increases DNA copy number variants in vivo. Proc Natl Acad Sci U S A 2023; 120:e2219897120. [PMID: 37459550 PMCID: PMC10372619 DOI: 10.1073/pnas.2219897120] [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: 11/21/2022] [Accepted: 06/14/2023] [Indexed: 07/20/2023] Open
Abstract
The human microbiota affects critical cellular functions, although the responsible mechanism(s) is still poorly understood. In this regard, we previously showed that Mycoplasma fermentans DnaK, an HSP70 chaperone protein, hampers the activity of important cellular proteins responsible for DNA integrity. Here, we describe a novel DnaK knock-in mouse model generated in our laboratory to study the effect of M. fermentans DnaK expression in vivo. By using an array-based comparative genomic hybridization assay, we demonstrate that exposure to DnaK was associated with a higher number of DNA copy number variants (CNVs) indicative of unbalanced chromosomal alterations, together with reduced fertility and a high rate of fetal abnormalities. Consistent with their implication in genetic disorders, one of these CNVs caused a homozygous Grid2 deletion, resulting in an aberrant ataxic phenotype that recapitulates the extensive biallelic deletion in the Grid2 gene classified in humans as autosomal recessive spinocerebellar ataxia 18. Our data highlight a connection between components of the human urogenital tract microbiota, namely Mycoplasmas, and genetic abnormalities in the form of DNA CNVs, with obvious relevant medical, diagnostic, and therapeutic implications.
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Affiliation(s)
- Francesca Benedetti
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD21201
| | - Giovannino Silvestri
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
- Department of Medicine, School of Medicine, University of Maryland School of Medicine, Baltimore, MD21201
| | - Saman Saadat
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
| | - Frank Denaro
- Department of Biology, Morgan State University, Baltimore, MD21251
| | - Olga S. Latinovic
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD21201
| | - Harry Davis
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
| | - Sumiko Williams
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
| | - Joseph Bryant
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
| | | | - Chozha V. Rathinam
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
- Department of Medicine, School of Medicine, University of Maryland School of Medicine, Baltimore, MD21201
| | - Robert C. Gallo
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
- Department of Medicine, School of Medicine, University of Maryland School of Medicine, Baltimore, MD21201
| | - Davide Zella
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD21201
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Cuenca-Guardiola J, de la Morena-Barrio B, García JL, Sanchis-Juan A, Corral J, Fernández-Breis JT. Improvement of large copy number variant detection by whole genome nanopore sequencing. J Adv Res 2022:S2090-1232(22)00241-7. [PMID: 36323370 PMCID: PMC10403694 DOI: 10.1016/j.jare.2022.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 10/18/2022] [Accepted: 10/22/2022] [Indexed: 11/11/2022] Open
Abstract
INTRODUCTION Whole-genome sequencing using nanopore technologies can uncover structural variants, which are DNA rearrangements larger than 50 base pairs. Nanopore technologies can also characterize their boundaries with single-base accuracy, owing to the kilobase-long reads that encompass either full variants or their junctions. Other methods, such as next-generation short read sequencing or PCR assays, are limited in their capabilities to detect or characterize structural variants. However, the existing software for nanopore sequencing data analysis still reports incomplete variant sets, which also contain erroneous calls, a considerable obstacle for the molecular diagnosis or accurate genotyping of populations. METHODS We compared multiple factors affecting variant calling, such as reference genome version, aligner (minimap2, NGMLR, and lra) choice, and variant caller combinations (Sniffles, CuteSV, SVIM, and NanoVar), to find the optimal group of tools for calling large (>50 kb) deletions and duplications, using data from seven patients exhibiting gross gene defects on SERPINC1 and from a reference variant set as the control. The goal was to obtain the most complete, yet reasonably specific group of large variants using a single cell of PromethION sequencing, which yielded lower depth coverage than short-read sequencing. We also used a custom method for the statistical analysis of the coverage value to refine the resulting datasets. RESULTS We found that for large deletions and duplications (>50 kb), the existing software performed worse than for smaller ones, in terms of both sensitivity and specificity, and newer tools had not improved this. Our novel software, disCoverage, could polish variant callers' results, improving specificity by up to 62% and sensitivity by 15%, the latter requiring other data or samples. CONCLUSION We analyzed the current situation of >50-kb copy number variants with nanopore sequencing, which could be improved. The methods presented in this work could help to identify the known deletions and duplications in a set of patients, while also helping to filter out erroneous calls for these variants, which might aid the efforts to characterize a not-yet well-known fraction of genetic variability in the human genome.
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Mascaraque-Checa M, Gallego-Rentero M, Nicolás-Morala J, Portillo-Esnaola M, Cuezva JM, González S, Gilaberte Y, Juarranz Á. Metformin overcomes metabolic reprogramming-induced resistance of skin squamous cell carcinoma to photodynamic therapy. Mol Metab 2022; 60:101496. [PMID: 35405370 PMCID: PMC9048115 DOI: 10.1016/j.molmet.2022.101496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 04/04/2022] [Accepted: 04/05/2022] [Indexed: 11/25/2022] Open
Abstract
Objective Cancer metabolic reprogramming promotes resistance to therapies. In this study, we addressed the role of the Warburg effect in the resistance to photodynamic therapy (PDT) in skin squamous cell carcinoma (sSCC). Furthermore, we assessed the effect of metformin treatment, an antidiabetic type II drug that modulates metabolism, as adjuvant to PDT. Methods For that, we have used two human SCC cell lines: SCC13 and A431, called parental (P) and from these cell lines we have generated the corresponding PDT resistant cells (10GT). Results Here, we show that 10GT cells induced metabolic reprogramming to an enhanced aerobic glycolysis and reduced activity of oxidative phosphorylation, which could influence the response to PDT. This result was also confirmed in P and 10GT SCC13 tumors developed in mice. The treatment with metformin caused a reduction in aerobic glycolysis and an increase in oxidative phosphorylation in 10GT sSCC cells. Finally, the combination of metformin with PDT improved the cytotoxic effects on P and 10GT cells. The combined treatment induced an increase in the protoporphyrin IX production, in the reactive oxygen species generation and in the AMPK expression and produced the inhibition of AKT/mTOR pathway. The greater efficacy of combined treatments was also seen in vivo, in xenografts of P and 10GT SCC13 cells. Conclusions Altogether, our results reveal that PDT resistance implies, at least partially, a metabolic reprogramming towards aerobic glycolysis that is prevented by metformin treatment. Therefore, metformin may constitute an excellent adjuvant for PDT in sSCC. Cell resistant to Photodynamic therapy (PDT) is due to the metabolic reprogramming. Metformin modulates energetic metabolism in PDT-resistant cells, sensitizing to PDT. Metformin increases protoporphyrin IX and reactive oxygen species generation. Metformin+PDT is proposed as potential therapy against skin squamous cell carcinoma.
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6
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Shi Q, Miao T, Liu Y, Hu L, Yang H, Shen H, Piao M, Huang Z, Zhang Z. Fabrication and Decryption of a Microarray of Digital Dithiosuccinimide Oligomers. Macromol Rapid Commun 2022; 43:e2200029. [PMID: 35322486 DOI: 10.1002/marc.202200029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/11/2022] [Indexed: 11/11/2022]
Abstract
Digital polymer with precisely arranged binary units provides an important option for information storage. This is especially true if the digital polymers are assembled in a device, as it would be of great benefit to data writing and reading in practice. Herein, inspired by DNA microarray technique, the programmable information storing and reading on a mass spectrometry target plate is proposed. First, an array of 4-bit sequence-coded dithiosuccinimide oligomers was efficiently built through sequential thiol-maleimide Michael couplings with good sequence readability by tandem mass spectrometry (MS/MS). Then, toward engineering microarray for information storage, a programmed robotic arm was specifically designed for precisely loading sequence-coded oligomers onto the target plate, and a decoding software was developed for efficient readout of the data from MS/MS sequencing. Notably, short sequence-coded oligomers chains can be used to write long strings of information, and extra error-correction codes are not required as usual due to the inherent concomitant fragmentation signals. Not only text but also bitimages can be automatically stored and decoded with excellent accuracy. This work provides a promising platform of digital polymers for programmable information storing and reading. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Qiunan Shi
- Q. Shi, T. Miao, Y. Liu, Prof. H. Shen, Prof. Z. Huang, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, China
| | - Tengfei Miao
- Q. Shi, T. Miao, Y. Liu, Prof. H. Shen, Prof. Z. Huang, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, China
| | - Yuxin Liu
- Q. Shi, T. Miao, Y. Liu, Prof. H. Shen, Prof. Z. Huang, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, China
| | - Lihua Hu
- Dr. L. Hu, Analysis and Testing Center, Soochow University, Suzhou, 215123, China
| | - Hai Yang
- H. Yang, Eurosmart Intelligent Technology Research Institute, Nanjing, 211106, China
| | - Hang Shen
- Q. Shi, T. Miao, Y. Liu, Prof. H. Shen, Prof. Z. Huang, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, China
| | - Minghao Piao
- Prof. M. Piao, Collaborative Innovation Center of Novel Software Technology and Industrialization, School of Computer Science and Technology, Soochow University, Suzhou, 215123, China
| | - Zhihao Huang
- Q. Shi, T. Miao, Y. Liu, Prof. H. Shen, Prof. Z. Huang, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, China
| | - Zhengbiao Zhang
- Prof. Z. Zhang, College of Chemistry, Chemical Engineering and Materials Science, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, 215123, China
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7
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Gordeeva V, Sharova E, Arapidi G. Progress in Methods for Copy Number Variation Profiling. Int J Mol Sci 2022; 23:ijms23042143. [PMID: 35216262 PMCID: PMC8879278 DOI: 10.3390/ijms23042143] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/09/2022] [Accepted: 02/11/2022] [Indexed: 02/04/2023] Open
Abstract
Copy number variations (CNVs) are the predominant class of structural genomic variations involved in the processes of evolutionary adaptation, genomic disorders, and disease progression. Compared with single-nucleotide variants, there have been challenges associated with the detection of CNVs owing to their diverse sizes. However, the field has seen significant progress in the past 20–30 years. This has been made possible due to the rapid development of molecular diagnostic methods which ensure a more detailed view of the genome structure, further complemented by recent advances in computational methods. Here, we review the major approaches that have been used to routinely detect CNVs, ranging from cytogenetics to the latest sequencing technologies, and then cover their specific features.
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Affiliation(s)
- Veronika Gordeeva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (E.S.); (G.A.)
- Moscow Institute of Physics and Technology, National Research University, Moscow Oblast, 141701 Moscow, Russia
- Correspondence:
| | - Elena Sharova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (E.S.); (G.A.)
| | - Georgij Arapidi
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (E.S.); (G.A.)
- Moscow Institute of Physics and Technology, National Research University, Moscow Oblast, 141701 Moscow, Russia
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
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Yagi H, Takiguchi H, Takeda N, Inuzuka R, Taniguchi Y, Porto KJ, Ishiura H, Mitsui J, Morita H, Komuro I. Family with congenital contractural arachnodactyly due to a novel multiexon deletion of the FBN2 gene. Clin Case Rep 2022; 10:e05335. [PMID: 35154713 PMCID: PMC8826123 DOI: 10.1002/ccr3.5335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/10/2022] [Accepted: 01/14/2022] [Indexed: 11/21/2022] Open
Abstract
Congenital contractural arachnodactyly (CCA) is caused by pathogenic FBN2 variants; however, the contributions of copy number variations (CNVs) to CCA are still unknown. Here, we report on a familial case of CCA, in which a novel multiexon deletion of exons 35-39 in FBN2 was identified after simple CNV prediction.
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Affiliation(s)
- Hiroki Yagi
- Department of Cardiovascular MedicineThe University of Tokyo HospitalTokyoJapan
- Marfan Syndrome CenterThe University of Tokyo HospitalTokyoJapan
| | - Hiroshi Takiguchi
- Department of Cardiovascular MedicineThe University of Tokyo HospitalTokyoJapan
| | - Norifumi Takeda
- Department of Cardiovascular MedicineThe University of Tokyo HospitalTokyoJapan
- Marfan Syndrome CenterThe University of Tokyo HospitalTokyoJapan
| | - Ryo Inuzuka
- Marfan Syndrome CenterThe University of Tokyo HospitalTokyoJapan
- Department of PediatricsThe University of Tokyo HospitalTokyoJapan
| | - Yuki Taniguchi
- Marfan Syndrome CenterThe University of Tokyo HospitalTokyoJapan
- Department of Orthopedic SurgeryThe University of Tokyo HospitalTokyoJapan
| | | | - Hiroyuki Ishiura
- Department of NeurologyThe University of Tokyo HospitalTokyoJapan
| | - Jun Mitsui
- Department of NeurologyThe University of Tokyo HospitalTokyoJapan
| | - Hiroyuki Morita
- Department of Cardiovascular MedicineThe University of Tokyo HospitalTokyoJapan
| | - Issei Komuro
- Department of Cardiovascular MedicineThe University of Tokyo HospitalTokyoJapan
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Labib M, Kelley SO. Circulating tumor cell profiling for precision oncology. Mol Oncol 2021; 15:1622-1646. [PMID: 33448107 PMCID: PMC8169448 DOI: 10.1002/1878-0261.12901] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/19/2020] [Accepted: 01/11/2021] [Indexed: 02/06/2023] Open
Abstract
Analysis of circulating tumor cells (CTCs) collected from patient's blood offers a broad range of opportunities in the field of precision oncology. With new advances in profiling technology, it is now possible to demonstrate an association between the molecular profiles of CTCs and tumor response to therapy. In this Review, we discuss mechanisms of tumor resistance to therapy and their link to phenotypic and genotypic properties of CTCs. We summarize key technologies used to isolate and analyze CTCs and discuss recent clinical studies that examined CTCs for genomic and proteomic predictors of responsiveness to therapy. We also point out current limitations that still hamper the implementation of CTCs into clinical practice. We finally reflect on how these shortcomings can be addressed with the likely contribution of multiparametric approaches and advanced data analytics.
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Affiliation(s)
- Mahmoud Labib
- Department of Pharmaceutical SciencesUniversity of TorontoCanada
| | - Shana O. Kelley
- Department of Pharmaceutical SciencesUniversity of TorontoCanada
- Institute for Biomaterials and Biomedical EngineeringUniversity of TorontoCanada
- Department of BiochemistryUniversity of TorontoCanada
- Department of ChemistryUniversity of TorontoCanada
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10
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Kanda S, Ohmuraya M, Akagawa H, Horita S, Yoshida Y, Kaneko N, Sugawara N, Ishizuka K, Miura K, Harita Y, Yamamoto T, Oka A, Araki K, Furukawa T, Hattori M. Deletion in the Cobalamin Synthetase W Domain-Containing Protein 1 Gene Is associated with Congenital Anomalies of the Kidney and Urinary Tract. J Am Soc Nephrol 2020; 31:139-147. [PMID: 31862704 PMCID: PMC6934996 DOI: 10.1681/asn.2019040398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 10/02/2019] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Researchers have identified about 40 genes with mutations that result in the most common cause of CKD in children, congenital anomalies of the kidney and urinary tract (CAKUT), but approximately 85% of patients with CAKUT lack mutations in these genes. The anomalies that comprise CAKUT are clinically heterogenous, and thought to be caused by disturbances at different points in kidney development. However, identification of novel CAKUT-causing genes remains difficult because of their variable expressivity, incomplete penetrance, and heterogeneity. METHODS We investigated two generations of a family that included two siblings with CAKUT. Although the parents and another child were healthy, the two affected siblings presented the same manifestations, unilateral renal agenesis and contralateral renal hypoplasia. To search for a novel causative gene of CAKUT, we performed whole-exome and whole-genome sequencing of DNA from the family members. We also generated two lines of genetically modified mice with a gene deletion present only in the affected siblings, and performed immunohistochemical and phenotypic analyses of these mice. RESULTS We found that the affected siblings, but not healthy family members, had a homozygous deletion in the Cobalamin Synthetase W Domain-Containing Protein 1 (CBWD1) gene. Whole-genome sequencing uncovered genomic breakpoints, which involved exon 1 of CBWD1, harboring the initiating codon. Immunohistochemical analysis revealed high expression of Cbwd1 in the nuclei of the ureteric bud cells in the developing kidneys. Cbwd1-deficient mice showed CAKUT phenotypes, including hydronephrosis, hydroureters, and duplicated ureters. CONCLUSIONS The identification of a deletion in CBWD1 gene in two siblings with CAKUT implies a role for CBWD1 in the etiology of some cases of CAKUT.
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Affiliation(s)
- Shoichiro Kanda
- Department of Pediatrics, The University of Tokyo, Tokyo, Japan;
- Department of Pediatric Nephrology
| | - Masaki Ohmuraya
- Department of Genetics, Hyogo College of Medicine, Hyogo, Japan
| | - Hiroyuki Akagawa
- Tokyo Women's Medical University Institute for Integrated Medical Sciences, Tokyo, Japan
| | - Shigeru Horita
- Department of Pathology, Kidney Center, School of Medicine, and
| | | | | | | | | | | | - Yutaka Harita
- Department of Pediatrics, The University of Tokyo, Tokyo, Japan
| | - Toshiyuki Yamamoto
- Tokyo Women's Medical University Institute for Integrated Medical Sciences, Tokyo, Japan
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Akira Oka
- Department of Pediatrics, The University of Tokyo, Tokyo, Japan
| | - Kimi Araki
- Division of Developmental Genetics, Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan; and
| | - Toru Furukawa
- Tokyo Women's Medical University Institute for Integrated Medical Sciences, Tokyo, Japan
- Department of Investigative Pathology, Tohoku University Graduate School of Medicine, Sendai, Japan
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Data storage in DNA with fewer synthesis cycles using composite DNA letters. Nat Biotechnol 2019; 37:1229-1236. [PMID: 31501560 DOI: 10.1038/s41587-019-0240-x] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 07/25/2019] [Indexed: 12/24/2022]
Abstract
The density and long-term stability of DNA make it an appealing storage medium, particularly for long-term data archiving. Existing DNA storage technologies involve the synthesis and sequencing of multiple nominally identical molecules in parallel, resulting in information redundancy. We report the development of encoding and decoding methods that exploit this redundancy using composite DNA letters. A composite DNA letter is a representation of a position in a sequence that consists of a mixture of all four DNA nucleotides in a predetermined ratio. Our methods encode data using fewer synthesis cycles. We encode 6.4 MB into composite DNA, with distinguishable composition medians, using 20% fewer synthesis cycles per unit of data, as compared to previous reports. We also simulate encoding with larger composite alphabets, with distinguishable composition deciles, to show that 75% fewer synthesis cycles are potentially sufficient. We describe applicable error-correcting codes and inference methods, and investigate error patterns in the context of composite DNA letters.
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12
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Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities. mSystems 2019; 4:4/4/e00296-19. [PMID: 31213523 PMCID: PMC6581690 DOI: 10.1128/msystems.00296-19] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The rapid development of metagenomic technologies, including microarrays, over the past decade has greatly expanded our understanding of complex microbial systems. However, because of the ever-expanding number of novel microbial sequences discovered each year, developing a microarray that is representative of real microbial communities, is specific and sensitive, and provides quantitative information remains a challenge. The newly developed GeoChip 5.0 is the most comprehensive microarray available to date for examining the functional capabilities of microbial communities important to biogeochemistry, ecology, environmental sciences, and human health. The GeoChip 5 is highly specific, sensitive, and quantitative based on both computational and experimental assays. Use of the array on a contaminated groundwater sample provided novel insights on the impacts of environmental contaminants on groundwater microbial communities. While functional gene arrays (FGAs) have greatly expanded our understanding of complex microbial systems, specificity, sensitivity, and quantitation challenges remain. We developed a new generation of FGA, GeoChip 5.0, using the Agilent platform. Two formats were created, a smaller format (GeoChip 5.0S), primarily covering carbon-, nitrogen-, sulfur-, and phosphorus-cycling genes and others providing ecological services, and a larger format (GeoChip 5.0M) containing the functional categories involved in biogeochemical cycling of C, N, S, and P and various metals, stress response, microbial defense, electron transport, plant growth promotion, virulence, gyrB, and fungus-, protozoan-, and virus-specific genes. GeoChip 5.0M contains 161,961 oligonucleotide probes covering >365,000 genes of 1,447 gene families from broad, functionally divergent taxonomic groups, including bacteria (2,721 genera), archaea (101 genera), fungi (297 genera), protists (219 genera), and viruses (167 genera), mainly phages. Computational and experimental evaluation indicated that designed probes were highly specific and could detect as little as 0.05 ng of pure culture DNAs within a background of 1 μg community DNA (equivalent to 0.005% of the population). Additionally, strong quantitative linear relationships were observed between signal intensity and amount of pure genomic (∼99% of probes detected; r > 0.9) or soil (∼97%; r > 0.9) DNAs. Application of the GeoChip to a contaminated groundwater microbial community indicated that environmental contaminants (primarily heavy metals) had significant impacts on the biodiversity of the communities. This is the most comprehensive FGA to date, capable of directly linking microbial genes/populations to ecosystem functions. IMPORTANCE The rapid development of metagenomic technologies, including microarrays, over the past decade has greatly expanded our understanding of complex microbial systems. However, because of the ever-expanding number of novel microbial sequences discovered each year, developing a microarray that is representative of real microbial communities, is specific and sensitive, and provides quantitative information remains a challenge. The newly developed GeoChip 5.0 is the most comprehensive microarray available to date for examining the functional capabilities of microbial communities important to biogeochemistry, ecology, environmental sciences, and human health. The GeoChip 5 is highly specific, sensitive, and quantitative based on both computational and experimental assays. Use of the array on a contaminated groundwater sample provided novel insights on the impacts of environmental contaminants on groundwater microbial communities.
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Ma SA, O'Day CP, Dentchev T, Takeshita J, Ridky TW, Seykora JT, Chu EY. Expression of p15 in a spectrum of spitzoid melanocytic neoplasms. J Cutan Pathol 2019; 46:310-316. [PMID: 30666677 DOI: 10.1111/cup.13424] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 12/17/2018] [Accepted: 01/14/2019] [Indexed: 01/06/2023]
Abstract
BACKGROUND Accurate classification of spitzoid melanocytic lesions is difficult due to overlapping clinical and histopathologic features between Spitz nevi, atypical Spitz tumors (ASTs), and spitzoid melanomas. Expression of p16 (CDKN2A) has been used as a marker of spitzoid lesions. However, its expression may be variable. p15 is a tumor suppressor encoded by CDKN2B, loss of which has been recently shown to promote transition from nevus to melanoma. We sought to determine whether p15 is a useful immunohistochemical marker to distinguish Spitz nevi from spitzoid melanomas and to compare p15 and p16 staining in this population. METHODS Immunohistochemistry for p15 and p16 was performed on Spitz nevi (n = 19), ASTs (n = 41), and spitzoid melanomas (n = 17). Immunoexpression was categorized by a four-tiered system: 0 (negative), 1+ (weak), 2+ (moderate), 3+ (strong). RESULTS 3+/strong p15 staining was observed in 68.4% of Spitz nevi, 34.2% of ASTs, and 17.7% of spitzoid melanomas. By contrast, we observed 3+ p16 staining in roughly equivalent percentages of Spitz nevi (57.9%), ASTs (56.1%), and spitzoid melanomas (58.8%). CONCLUSION These data illustrate that p15 may be more useful than p16 as a biomarker to help distinguish benign from malignant spitzoid lesions.
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Affiliation(s)
- Sophia A Ma
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Conor P O'Day
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Tzvete Dentchev
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Junko Takeshita
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Biostatistics Epidemiology and Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Todd W Ridky
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - John T Seykora
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Emily Y Chu
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
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14
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Duong T, Vo DN, Nakayama T, Mukaisho KI, Bamba M, Nguyen T, Sugihara H. Rapidly and Slowly Growing Lineages in Chromosomal Instability-Type Gland-Forming Gastric Carcinomas as Revealed by Multisampling Analysis of DNA Copy-Number Profile. Pathobiology 2019; 86:118-127. [DOI: 10.1159/000494926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 10/28/2018] [Indexed: 11/19/2022] Open
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15
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Belmont JW. Molecular Methods. Clin Immunol 2019. [DOI: 10.1016/b978-0-7020-6896-6.00096-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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16
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Kitamura M, Nakayama T, Mukaisho KI, Mori T, Umeda T, Moritani S, Kushima R, Tani M, Sugihara H. Progression Potential of Ductal Carcinoma in situ Assessed by Genomic Copy Number Profiling. Pathobiology 2018; 86:92-101. [PMID: 30332671 DOI: 10.1159/000492833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 08/06/2018] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Ductal carcinoma in situ (DCIS) of the breast is heterogeneous in terms of the risk of progression to invasive ductal carcinoma (IDC). To treat DCIS appropriately for its progression risk, we classified individual DCIS by its profile of genomic changes into 2 groups and correlated them with clinicopathological progression factors. METHODS We used surgically resected, formalin-fixed, paraffin-embedded tissues of 22 DCIS and 30 IDC lesions. We performed immunohistochemical intrinsic subtyping, array-based comparative genomic hybridization, and unsupervised clustering. RESULTS The samples were divided into 2 major clusters, A and B. Cluster A showed a greater number of gene and chromosome copy number alterations, a larger IDC/DCIS ratio, a higher frequency of nonluminal subtype, a lower frequency of luminal subtype, and a higher nuclear grade, when compared with cluster B. However, there was no difference in the frequencies of lymph node metastasis between clusters A and B. We identified 9 breast-cancer-related genes, including TP53 and GATA3, that highly contributed to the discrimination of A and B clusters. CONCLUSION Classification of breast tumors into rapidly progressive cluster A and the other (cluster B) may contribute to select the treatment appropriate for their progression risk.
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Affiliation(s)
- Mina Kitamura
- Division of Molecular Diagnostic Pathology, Department of Pathology, Shiga University of Medical Science, Otsu, Japan.,Division of Digestive, Breast and General Surgery, Department of Surgery, Shiga University of Medical Science, Otsu, Japan
| | - Takahisa Nakayama
- Division of Molecular Diagnostic Pathology, Department of Pathology, Shiga University of Medical Science, Otsu, Japan
| | - Ken-Ichi Mukaisho
- Division of Molecular Diagnostic Pathology, Department of Pathology, Shiga University of Medical Science, Otsu, Japan
| | - Tsuyoshi Mori
- Division of Digestive, Breast and General Surgery, Department of Surgery, Shiga University of Medical Science, Otsu, Japan
| | - Tomoko Umeda
- Division of Digestive, Breast and General Surgery, Department of Surgery, Shiga University of Medical Science, Otsu, Japan
| | - Suzuko Moritani
- Division of Diagnostic Pathology, Shiga University of Medical Science Hospital, Otsu, Japan
| | - Ryoji Kushima
- Division of Diagnostic Pathology, Shiga University of Medical Science Hospital, Otsu, Japan
| | - Masaji Tani
- Division of Digestive, Breast and General Surgery, Department of Surgery, Shiga University of Medical Science, Otsu, Japan
| | - Hiroyuki Sugihara
- Division of Molecular Diagnostic Pathology, Department of Pathology, Shiga University of Medical Science, Otsu, Japan,
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17
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Hofving T, Arvidsson Y, Almobarak B, Inge L, Pfragner R, Persson M, Stenman G, Kristiansson E, Johanson V, Nilsson O. The neuroendocrine phenotype, genomic profile and therapeutic sensitivity of GEPNET cell lines. Endocr Relat Cancer 2018; 25. [PMID: 29540494 PMCID: PMC8133373 DOI: 10.1530/erc-17-0445e] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Tobias Hofving
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
- Correspondence should be addressed to T Hofving:
| | - Yvonne Arvidsson
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Bilal Almobarak
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Linda Inge
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Roswitha Pfragner
- Institute of Pathophysiology and Immunology, Center for Molecular Medicine, Medical University of Graz, Graz, Austria
| | - Marta Persson
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Göran Stenman
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Viktor Johanson
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Ola Nilsson
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
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18
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Hofving T, Arvidsson Y, Almobarak B, Inge L, Pfragner R, Persson M, Stenman G, Kristiansson E, Johanson V, Nilsson O. The neuroendocrine phenotype, genomic profile and therapeutic sensitivity of GEPNET cell lines. Endocr Relat Cancer 2018; 25:367-380. [PMID: 29444910 PMCID: PMC5827037 DOI: 10.1530/erc-17-0445] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 01/15/2018] [Indexed: 12/23/2022]
Abstract
Experimental models of neuroendocrine tumour disease are scarce, and no comprehensive characterisation of existing gastroenteropancreatic neuroendocrine tumour (GEPNET) cell lines has been reported. In this study, we aimed to define the molecular characteristics and therapeutic sensitivity of these cell lines. We therefore performed immunophenotyping, copy number profiling, whole-exome sequencing and a large-scale inhibitor screening of seven GEPNET cell lines. Four cell lines, GOT1, P-STS, BON-1 and QGP-1, displayed a neuroendocrine phenotype while three others, KRJ-I, L-STS and H-STS, did not. Instead, these three cell lines were identified as lymphoblastoid. Characterisation of remaining authentic GEPNET cell lines by copy number profiling showed that GOT1, among other chromosomal alterations, harboured losses on chromosome 18 encompassing the SMAD4 gene, while P-STS had a loss on 11q. BON-1 had a homozygous loss of CDKN2A and CDKN2B, and QGP-1 harboured amplifications of MDM2 and HMGA2 Whole-exome sequencing revealed both disease-characteristic mutations (e.g. ATRX mutation in QGP-1) and, for patient tumours, rare genetic events (e.g. TP53 mutation in P-STS, BON-1 and QGP-1). A large-scale inhibitor screening showed that cell lines from pancreatic NETs to a greater extent, when compared to small intestinal NETs, were sensitive to inhibitors of MEK. Similarly, neuroendocrine NET cells originating from the small intestine were considerably more sensitive to a group of HDAC inhibitors. Taken together, our results provide a comprehensive characterisation of GEPNET cell lines, demonstrate their relevance as neuroendocrine tumour models and explore their therapeutic sensitivity to a broad range of inhibitors.
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Affiliation(s)
- Tobias Hofving
- Sahlgrenska Cancer CenterDepartment of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Yvonne Arvidsson
- Sahlgrenska Cancer CenterDepartment of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Bilal Almobarak
- Sahlgrenska Cancer CenterDepartment of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Linda Inge
- Sahlgrenska Cancer CenterDepartment of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Roswitha Pfragner
- Institute of Pathophysiology and ImmunologyCenter for Molecular Medicine, Medical University of Graz, Graz, Austria
| | - Marta Persson
- Sahlgrenska Cancer CenterDepartment of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Göran Stenman
- Sahlgrenska Cancer CenterDepartment of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Erik Kristiansson
- Department of Mathematical SciencesChalmers University of Technology, Gothenburg, Sweden
| | - Viktor Johanson
- Department of SurgeryInstitute of Clinical Sciences, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Ola Nilsson
- Sahlgrenska Cancer CenterDepartment of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
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19
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Ko JM. Chromosomal Microarray: Application for Congenital Heart Diseases. Korean Circ J 2018; 48:233-235. [PMID: 29557111 PMCID: PMC5861317 DOI: 10.4070/kcj.2018.0032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 01/29/2018] [Indexed: 11/16/2022] Open
Affiliation(s)
- Jung Min Ko
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea.
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20
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Chari R, Lockwood WW, Lam WL. Computational Methods for the Analysis of Array Comparative Genomic Hybridization. Cancer Inform 2017. [DOI: 10.1177/117693510600200007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Array comparative genomic hybridization (array CGH) is a technique for assaying the copy number status of cancer genomes. The widespread use of this technology has lead to a rapid accumulation of high throughput data, which in turn has prompted the development of computational strategies for the analysis of array CGH data. Here we explain the principles behind array image processing, data visualization and genomic profile analysis, review currently available software packages, and raise considerations for future software development.
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Affiliation(s)
- Raj Chari
- Cancer Genetics and Developmental Biology, British Columbia Cancer Research Centre, Vancouver BC, Canada V5Z 1L3
- These authors contributed equally to this work
| | - William W. Lockwood
- Cancer Genetics and Developmental Biology, British Columbia Cancer Research Centre, Vancouver BC, Canada V5Z 1L3
- These authors contributed equally to this work
| | - Wan L. Lam
- Cancer Genetics and Developmental Biology, British Columbia Cancer Research Centre, Vancouver BC, Canada V5Z 1L3
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Ali H, Bitar MS, Al Madhoun A, Marafie M, Al-Mulla F. Functionally-focused algorithmic analysis of high resolution microarray-CGH genomic landscapes demonstrates comparable genomic copy number aberrations in MSI and MSS sporadic colorectal cancer. PLoS One 2017; 12:e0171690. [PMID: 28231327 PMCID: PMC5322957 DOI: 10.1371/journal.pone.0171690] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 01/23/2017] [Indexed: 12/25/2022] Open
Abstract
Array-based comparative genomic hybridization (aCGH) emerged as a powerful technology for studying copy number variations at higher resolution in many cancers including colorectal cancer. However, the lack of standardized systematic protocols including bioinformatic algorithms to obtain and analyze genomic data resulted in significant variation in the reported copy number aberration (CNA) data. Here, we present genomic aCGH data obtained using highly stringent and functionally relevant statistical algorithms from 116 well-defined microsatellites instable (MSI) and microsatellite stable (MSS) colorectal cancers. We utilized aCGH to characterize genomic CNAs in 116 well-defined sets of colorectal cancer (CRC) cases. We further applied the significance testing for aberrant copy number (STAC) and Genomic Identification of Significant Targets in Cancer (GISTIC) algorithms to identify functionally relevant (nonrandom) chromosomal aberrations in the analyzed colorectal cancer samples. Our results produced high resolution genomic landscapes of both, MSI and MSS sporadic CRC. We found that CNAs in MSI and MSS CRCs are heterogeneous in nature but may be divided into 3 distinct genomic patterns. Moreover, we show that although CNAs in MSI and MSS CRCs differ with respect to their size, number and chromosomal distribution, the functional copy number aberrations obtained from MSI and MSS CRCs were in fact comparable but not identical. These unifying CNAs were verified by MLPA tumor-loss gene panel, which spans 15 different chromosomal locations and contains 50 probes for at least 20 tumor suppressor genes. Consistently, deletion/amplification in these frequently cancer altered genes were identical in MSS and MSI CRCs. Our results suggest that MSI and MSS copy number aberrations driving CRC may be functionally comparable.
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Affiliation(s)
- Hamad Ali
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Kuwait University, Jabriya, Kuwait
- Research Division, Immunology Unit, Dasman Diabetes Institute (DDI), Dasman, Kuwait
- * E-mail: (HA); (FA)
| | - Milad S. Bitar
- Research Division, Immunology Unit, Dasman Diabetes Institute (DDI), Dasman, Kuwait
- Department of Pharmacology & Toxicology, Faculty of Medicine, Kuwait University, Jabriya, Kuwait
| | - Ashraf Al Madhoun
- Research Division, Immunology Unit, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | | | - Fahd Al-Mulla
- Molecular Pathology Unit, Department of Pathology, Faculty of Medicine, Kuwait University, Jabriya, Kuwait
- Research Division, Genomics Unit, Dasman Diabetes Institute (DDI), Dasman, Kuwait
- * E-mail: (HA); (FA)
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22
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Anjiki H, Mukaisho KI, Kadomoto Y, Doi H, Yoshikawa K, Nakayama T, Vo DTN, Hattori T, Sugihara H. Adenocarcinoma arising in multiple hyperplastic polyps in a patient with Helicobacter pylori infection and hypergastrinemia during long-term proton pump inhibitor therapy. Clin J Gastroenterol 2017; 10:128-136. [DOI: 10.1007/s12328-017-0714-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 01/17/2017] [Indexed: 12/18/2022]
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NEIL1 is a candidate gene associated with common variable immunodeficiency in a patient with a chromosome 15q24 deletion. Clin Immunol 2017; 176:71-76. [PMID: 28093361 DOI: 10.1016/j.clim.2017.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 01/11/2017] [Accepted: 01/12/2017] [Indexed: 02/07/2023]
Abstract
We report the first patient with an interstitial deletion of chromosome 15q24.1-q24.3 associated with common variable immunodeficiency (CVID). The 18-year old female patient's clinical and immunological phenotype was compared with 8 additional previously published patients with chr15q24 deletions. A CGH analysis estimated the deletion to be 3.767Mb in size (chr15: 74,410,916-78,178,418) and the result was confirmed using qRT-PCR. We defined an immune-related commonly deleted region (ICDR) within the chromosomal band 15q24.2, deleted in all four patients with different forms of antibody deficiencies. Mutations in the 14 genes within this ICDR were not identified in the remaining allele in our patient by WES and gene expression analyses showed haploinsufficiency of all the genes. Among these genes, we consider Nei Like DNA Glycosylase 1 (NEIL1) as a likely candidate gene due to its crucial role in B-cell activation and terminal differentiation.
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Chi C, Ajwad R, Kuang Q, Hu P. A Novel Graph-based Algorithm to Infer Recurrent Copy Number Variations in Cancer. Cancer Inform 2016; 15:43-50. [PMID: 27773988 PMCID: PMC5063805 DOI: 10.4137/cin.s39368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 09/08/2016] [Accepted: 09/09/2016] [Indexed: 12/17/2022] Open
Abstract
Many cancers have been linked to copy number variations (CNVs) in the genomic DNA. Although there are existing methods to analyze CNVs from individual samples, cancer-causing genes are more frequently discovered in regions where CNVs are common among tumor samples, also known as recurrent CNVs. Integrating multiple samples and locating recurrent CNV regions remain a challenge, both computationally and conceptually. We propose a new graph-based algorithm for identifying recurrent CNVs using the maximal clique detection technique. The algorithm has an optimal solution, which means all maximal cliques can be identified, and guarantees that the identified CNV regions are the most frequent and that the minimal regions have been delineated among tumor samples. The algorithm has successfully been applied to analyze a large cohort of breast cancer samples and identified some breast cancer-associated genes and pathways.
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Affiliation(s)
- Chen Chi
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Canada; Centre for Healthcare Innovation, Winnipeg Regional Health Authority/University of Manitoba, Winnipeg, Canada
| | - Rasif Ajwad
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Canada; Department of Computer Science, University of Manitoba, Winnipeg, Canada
| | - Qin Kuang
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Canada
| | - Pingzhao Hu
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Canada; Centre for Healthcare Innovation, Winnipeg Regional Health Authority/University of Manitoba, Winnipeg, Canada; Department of Electrical and Computer Engineering, University of Manitoba, Winnipeg, Canada
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Roychowdhury A, Samadder S, Das P, Mandloi S, Addya S, Chakraborty C, Basu PS, Mondal R, Roy A, Chakrabarti S, Roychoudhury S, Panda CK. Integrative genomic and network analysis identified novel genes associated with the development of advanced cervical squamous cell carcinoma. Biochim Biophys Acta Gen Subj 2016; 1861:2899-2911. [PMID: 27641506 DOI: 10.1016/j.bbagen.2016.09.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 08/17/2016] [Accepted: 09/12/2016] [Indexed: 12/11/2022]
Abstract
BACKGROUND CSCC is one of the most common cancer affecting women globally. Though it is caused by the infection of hrHPV but long latency period for malignant outcome in only a subset of hrHPV infected women indicates involvement of additional alterations, primarily CNVs. Here, we showed how CNVs played a crucial role in development of advanced tumors (stage III/IV) in Indian patients. METHODS Initially, high-resolution CGH-SNP microarray analysis pointed out frequent CNVs followed by significantly altered genes. After comparison with TCGA dataset, expressions of the genes were checked in three CSCC datasets to identify key genes followed by Ingenuity® Pathway analysis. Then node effect property analysis was applied on the constructed PPI network to rank the key proteins. Finally, validations in independent samples were performed. RESULTS For the first time, frequent chromosomal amplifications at 3q13.13-3q29, 1p36.11-1p31.1, 1q21.1-1q44 and 5p15.33-5p12 followed by common deletions at 11q14.1-11q25, 2q34-2q37.3, 4p16.3-4p12 and 13q13.3-13q14.3 were identified in Indian CSCC patients. Integrative analysis found 78 key genes including several novel ones, which were mostly associated with 'Cancer' and may regulate DNA repair and metabolic pathways. Analysis showed PARP1 and ATR were among the top ranking protein interactors. CONCLUSIONS Frequent amplification and over-expression of ATR and PARP1 were further confirmed in cervical lesions, indicating their association with poor prognosis of advanced CSCC patients. GENERAL SIGNIFICANCE Our novel approach identified precise CNVs along with several novel genes within these loci and showed that PARP1 and ATR, having biologically significant interactions, may be involved in development of advanced CSCC.
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Affiliation(s)
- Anirban Roychowdhury
- Department of Oncogene Regulation, Chittaranjan National Cancer Institute, Kolkata, India
| | - Sudip Samadder
- Department of Oncogene Regulation, Chittaranjan National Cancer Institute, Kolkata, India
| | - Pijush Das
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Sapan Mandloi
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Sankar Addya
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | | | - Partha Sarathi Basu
- India Screening Group (SCR), Early Detection and Prevention Section (EDP), International Agency for Research on Cancer (IARC), World Health Organization (WHO), Lyon, France
| | - Ranajit Mondal
- Department of Gynaecology Oncology, Chittaranjan National Cancer Institute, Kolkata, India
| | - Anup Roy
- North Bengal Medical College and Hospital, West Bengal, India
| | - Saikat Chakrabarti
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | | | - Chinmay Kumar Panda
- Department of Oncogene Regulation, Chittaranjan National Cancer Institute, Kolkata, India.
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Facchinetti F, Loriot Y, Kuo MS, Mahjoubi L, Lacroix L, Planchard D, Besse B, Farace F, Auger N, Remon J, Scoazec JY, André F, Soria JC, Friboulet L. Crizotinib-Resistant ROS1 Mutations Reveal a Predictive Kinase Inhibitor Sensitivity Model for ROS1- and ALK-Rearranged Lung Cancers. Clin Cancer Res 2016; 22:5983-5991. [DOI: 10.1158/1078-0432.ccr-16-0917] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 06/20/2016] [Accepted: 06/22/2016] [Indexed: 11/16/2022]
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Cho-Vega JH. A diagnostic algorithm for atypical spitzoid tumors: guidelines for immunohistochemical and molecular assessment. Mod Pathol 2016; 29:656-70. [PMID: 27102343 DOI: 10.1038/modpathol.2016.70] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Revised: 02/28/2016] [Accepted: 03/06/2016] [Indexed: 11/09/2022]
Abstract
Atypical spitzoid tumors are a morphologically diverse group of rare melanocytic lesions most frequently seen in children and young adults. As atypical spitzoid tumors bear striking resemblance to Spitz nevus and spitzoid melanomas clinically and histopathologically, it is crucial to determine its malignant potential and predict its clinical behavior. To date, many researchers have attempted to differentiate atypical spitzoid tumors from unequivocal melanomas based on morphological, immonohistochemical, and molecular diagnostic differences. A diagnostic algorithm is proposed here to assess the malignant potential of atypical spitzoid tumors by using a combination of immunohistochemical and cytogenetic/molecular tests. Together with classical morphological evaluation, this algorithm includes a set of immunohistochemistry assays (p16(Ink4a), a dual-color Ki67/MART-1, and HMB45), fluorescence in situ hybridization (FISH) with five probes (6p25, 8q24, 11q13, CEN9, and 9p21), and an array-based comparative genomic hybridization. This review discusses details of the algorithm, the rationale of each test used in the algorithm, and utility of this algorithm in routine dermatopathology practice. This algorithmic approach will provide a comprehensive diagnostic tool that complements conventional histological criteria and will significantly contribute to improve the diagnosis and prediction of the clinical behavior of atypical spitzoid tumors.
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Affiliation(s)
- Jeong Hee Cho-Vega
- Department of Pathology, Dermatopathology, University of Miami Miller School of Medicine, Miami, FL, USA
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Jenkins GM, Goddard ME, Black MA, Brauning R, Auvray B, Dodds KG, Kijas JW, Cockett N, McEwan JC. Copy number variants in the sheep genome detected using multiple approaches. BMC Genomics 2016; 17:441. [PMID: 27277319 PMCID: PMC4898393 DOI: 10.1186/s12864-016-2754-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 05/19/2016] [Indexed: 02/07/2023] Open
Abstract
Background Copy number variants (CNVs) are a type of polymorphism found to underlie phenotypic variation, both in humans and livestock. Most surveys of CNV in livestock have been conducted in the cattle genome, and often utilise only a single approach for the detection of copy number differences. Here we performed a study of CNV in sheep, using multiple methods to identify and characterise copy number changes. Comprehensive information from small pedigrees (trios) was collected using multiple platforms (array CGH, SNP chip and whole genome sequence data), with these data then analysed via multiple approaches to identify and verify CNVs. Results In total, 3,488 autosomal CNV regions (CNVRs) were identified in this study, which substantially builds on an initial survey of the sheep genome that identified 135 CNVRs. The average length of the identified CNVRs was 19 kb (range of 1 kb to 3.6 Mb), with shorter CNVRs being more frequent than longer CNVRs. The total length of all CNVRs was 67.6Mbps, which equates to 2.7 % of the sheep autosomes. For individuals this value ranged from 0.24 to 0.55 %, and the majority of CNVRs were identified in single animals. Rather than being uniformly distributed throughout the genome, CNVRs tended to be clustered. Application of three independent approaches for CNVR detection facilitated a comparison of validation rates. CNVs identified on the Roche-NimbleGen 2.1M CGH array generally had low validation rates with lower density arrays, while whole genome sequence data had the highest validation rate (>60 %). Conclusions This study represents the first comprehensive survey of the distribution, prevalence and characteristics of CNVR in sheep. Multiple approaches were used to detect CNV regions and it appears that the best method for verifying CNVR on a large scale involves using a combination of detection methodologies. The characteristics of the 3,488 autosomal CNV regions identified in this study are comparable to other CNV regions reported in the literature and provide a valuable and sizeable addition to the small subset of published sheep CNVs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2754-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gemma M Jenkins
- AbacusBio Limited, 442 Moray Place, PO Box 5585, Dunedin, 9058, New Zealand.
| | - Michael E Goddard
- Victorian Department of Economic Development, Jobs, Transport and Resources, Bundoora, VIC, 3083, Australia
| | - Michael A Black
- Department of Biochemistry, University of Otago, 710 Cumberland St, Dunedin, 9054, New Zealand
| | - Rudiger Brauning
- AgResearch, Invermay Agricultural Centre, PB 50034, Mosgiel, 9053, New Zealand
| | - Benoit Auvray
- Department of Biochemistry, University of Otago, 710 Cumberland St, Dunedin, 9054, New Zealand
| | - Ken G Dodds
- AgResearch, Invermay Agricultural Centre, PB 50034, Mosgiel, 9053, New Zealand
| | - James W Kijas
- CSIRO Animal, Food and Health Sciences, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, QLD 4067, Australia
| | - Noelle Cockett
- Utah State University, 1435 Old Main Hill, Logan, UT, 84322-1435-1435, USA
| | - John C McEwan
- AgResearch, Invermay Agricultural Centre, PB 50034, Mosgiel, 9053, New Zealand
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Andreasen S, Persson M, Kiss K, Homøe P, Heegaard S, Stenman G. Genomic profiling of a combined large cell neuroendocrine carcinoma of the submandibular gland. Oncol Rep 2016; 35:2177-82. [PMID: 26883388 DOI: 10.3892/or.2016.4621] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 01/05/2016] [Indexed: 11/06/2022] Open
Abstract
A 69-year-old female with no previous medical history presented with a rapidly growing submandibular mass. Fine needle aspiration cytology suggested a small-cell carcinoma and PET-CT showed increased 18-FDG uptake in the submandibular mass as well as in a lung mass. Submandibular resection and selective neck dissection was performed and histopathologic examination revealed a combined large-cell neuroendocrine carcinoma (LCNEC) with a squamous component and without lymph node metastases. Resection of the lung tumor revealed a papillary adenocarcinoma that was morphologically distinctly different from the LCNEC. The patient died of her lung cancer after 19 months without evidence of recurrence of the LCNEC. Genomic profiling of the salivary gland LCNEC revealed a hypodiploid genome predominated by losses of whole chromosomes or chromosome arms involving chromosomes 3p, 4, 7q, 10, 11, 13, 16q and gains of 3q and 16p. In addition, there was a segmental gain of 9p23-p22.3 including the NFIB oncogene. Continued studies of salivary gland LCNEC may provide new knowledge concerning potential diagnostic biomarkers and may ultimately also lead to the identification of new treatment targets for patients with these aggressive carcinomas.
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Affiliation(s)
- Simon Andreasen
- Department of Otorhinolaryngology Head and Neck Surgery and Audiology, Rigshospitalet, Copenhagen, Denmark
| | - Marta Persson
- Sahlgrenska Cancer Center, Department of Pathology, University of Gothenburg, Gothenburg, Sweden
| | - Katalin Kiss
- Department of Pathology, Rigshospitalet, Copenhagen, Denmark
| | - Preben Homøe
- Department of Otorhinolaryngology and Maxillofacial Surgery, Køge University Hospital, Køge, Denmark
| | | | - Göran Stenman
- Sahlgrenska Cancer Center, Department of Pathology, University of Gothenburg, Gothenburg, Sweden
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Wu Y, Fan H, Jing S, Xia J, Chen Y, Zhang L, Gao X, Li J, Gao H, Ren H. A genome-wide scan for copy number variations using high-density single nucleotide polymorphism array in Simmental cattle. Anim Genet 2015; 46:289-98. [PMID: 25917301 DOI: 10.1111/age.12288] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2015] [Indexed: 12/14/2022]
Abstract
Copy number variations (CNVs) have recently been identified as promising sources of genetic variation, complementary to single nucleotide polymorphisms (SNPs). As a result, detection of CNVs has attracted a great deal of attention. In this study, we performed genome-wide CNV detection using Illumina Bovine HD BeadChip (770k) data on 792 Simmental cattle. A total of 263 CNV regions (CNVRs) were identified, which included 137 losses, 102 gains and 24 regions classified as both loss and gain, covering 35.48 Mb (1.41%) of the bovine genome. The length of these CNVRs ranged from 10.18 kb to 1.76 Mb, with an average length of 134.78 kb and a median length of 61.95 kb. In 136 of these regions, a total of 313 genes were identified related to biological functions such as transmembrane activity and olfactory transduction activity. To validate the results, we performed quantitative PCR to detect nine randomly selected CNVRs and successfully confirmed seven (77.6%) of them. Our results present a map of cattle CNVs derived from high-density SNP data, which expands the current CNV map of the cattle genome and provides useful information for investigation of genomic structural variation in cattle.
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Affiliation(s)
- Yang Wu
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, 100193, China
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Perez-Nanclares G, Velayos T, Vela A, Muñoz-Torres M, Castaño L. Pseudohypoparathyroidism type Ib associated with novel duplications in the GNAS locus. PLoS One 2015; 10:e0117691. [PMID: 25710380 PMCID: PMC4339194 DOI: 10.1371/journal.pone.0117691] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 12/30/2014] [Indexed: 12/18/2022] Open
Abstract
Context Pseudohypoparathyroidism type 1b (PHP-Ib) is characterized by renal resistance to PTH (and, sometimes, a mild resistance to TSH) and absence of any features of Albright's hereditary osteodystrophy. Patients with PHP-Ib suffer of defects in the methylation pattern of the complex GNAS locus. PHP-Ib can be either sporadic or inherited in an autosomal dominant pattern. Whereas familial PHP-Ib is well characterized at the molecular level, the genetic cause of sporadic PHP-Ib cases remains elusive, although some molecular mechanisms have been associated with this subtype. Objective The aim of the study was to investigate the molecular and imprinting defects in the GNAS locus in two unrelated patients with PHP-Ib. Design We have analyzed the GNAS locus by direct sequencing, Methylation-Specific Multiplex Ligation-dependent Probe Amplification, microsatellites, Quantitative Multiplex PCR of Short Fluorescent fragments and array-Comparative Genomic Hybridization studies in order to characterize two unrelated families with clinical features of PHP-Ib. Results We identified two duplications in the GNAS region in two patients with PHP-Ib: one of them, comprising ∼320 kb, occurred ‘de novo’ in the patient, whereas the other one, of ∼179 kb in length, was inherited from the maternal allele. In both cases, no other known genetic cause was observed. Conclusion In this article, we describe the to-our-knowledge biggest duplications reported so far in the GNAS region. Both are associated to PHP-Ib, one of them occurring ‘de novo’ and the other one being maternally inherited.
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Affiliation(s)
- Gustavo Perez-Nanclares
- Endocrinology and Diabetes Research Group, Hospital Universitario Cruces, BioCruces, CIBERER, CIBERDEM, UPV-EHU, Barakaldo, Basque Country, Spain
| | - Teresa Velayos
- Endocrinology and Diabetes Research Group, Hospital Universitario Cruces, BioCruces, CIBERER, CIBERDEM, UPV-EHU, Barakaldo, Basque Country, Spain
| | - Amaya Vela
- Endocrinology and Diabetes Research Group, Hospital Universitario Cruces, BioCruces, CIBERER, CIBERDEM, UPV-EHU, Barakaldo, Basque Country, Spain
| | - Manuel Muñoz-Torres
- Clinical Management Unit of Endocrinology and Nutrition, Hospital Universitario San Cecilio, Instituto de Investigacion Biosanitaria de Granada, Granada, Spain
| | - Luis Castaño
- Endocrinology and Diabetes Research Group, Hospital Universitario Cruces, BioCruces, CIBERER, CIBERDEM, UPV-EHU, Barakaldo, Basque Country, Spain
- * E-mail:
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Vo DTN, Nakayama T, Yamamoto H, Mukaisho KI, Hattori T, Sugihara H. Progression risk assessments of individual non-invasive gastric neoplasms by genomic copy-number profile and mucin phenotype. BMC Med Genomics 2015; 8:6. [PMID: 25881098 PMCID: PMC4346124 DOI: 10.1186/s12920-015-0080-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Accepted: 02/03/2015] [Indexed: 12/18/2022] Open
Abstract
Background Early detection and treatment of non-invasive neoplasms can effectively reduce the incidence of advanced gastric carcinoma (GC), but only when the lineage is continuous between non-invasive and advanced tumours. Although a fraction of non-invasive neoplasms progress to invasive GC, it is difficult to identify individual progression-prone non-invasive neoplasms. To classify non-invasive gland-forming gastric neoplasms into clusters of different levels of progression risk, we applied mucin phenotyping and genomic DNA microarray analyses to intramucosal gland-forming gastric neoplasms. Methods Formalin-fixed, paraffin-embedded tissues from 19 non-invasive and 24 invasive gland-forming neoplasms were obtained via endoscopic submucosal dissection or surgical excision. According to the Vienna classification, intramucosal neoplasms were classified as low-grade or high-grade non-invasive neoplasms (LGNs [category 3] and HGNs [category 4], respectively) or invasive carcinomas (intramucosal GCs and mucosal parts of submucosal or deeper GCs [category 5]). Neoplastic lesions were characterized by mucin phenotypes determined using monoclonal antibodies against MUC2, MUC5AC, MUC6, and CD10. Genomic DNA samples from mucosal neoplasms were subjected to array-based comparative genomic hybridization and subsequent unsupervised, hierarchical clustering with selected large-sized genes. Results There was no significant difference in mucin phenotype between HGNs/LGNs and invasive carcinomas. The clustering classified samples into stable, unstable, and intermediate. The histological tumour grade or mucin phenotype of non-invasive neoplasms did not correlate with the clustering results. Each cluster may represent an independent lineage of different outcome because the size distribution of non-invasive tumours among the 3 clusters almost overlapped. In contrast, the unstable cluster alone included invasive carcinomas. Conclusions These findings suggest that the outcome of individual tumours is not stochastically determined but can be predicted from the genomic copy-number profile even at the non-invasive stage. Non-invasive neoplasms of the unstable clusters, which accounted for 21% of non-invasive neoplasms, may progress to invasive carcinomas, whereas those of stable cluster may not. Electronic supplementary material The online version of this article (doi:10.1186/s12920-015-0080-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Diem Thi-Ngoc Vo
- Department of Pathology, Division of Molecular and Diagnostic Pathology, Shiga University of Medical Science, Otsu, 520-2192, Japan.
| | - Takahisa Nakayama
- Department of Pathology, Division of Molecular and Diagnostic Pathology, Shiga University of Medical Science, Otsu, 520-2192, Japan.
| | - Hiroto Yamamoto
- Department of Pathology, Division of Molecular and Diagnostic Pathology, Shiga University of Medical Science, Otsu, 520-2192, Japan.
| | - Ken-ichi Mukaisho
- Department of Pathology, Division of Molecular and Diagnostic Pathology, Shiga University of Medical Science, Otsu, 520-2192, Japan.
| | - Takanori Hattori
- Department of Pathology, Division of Molecular and Diagnostic Pathology, Shiga University of Medical Science, Otsu, 520-2192, Japan.
| | - Hiroyuki Sugihara
- Department of Pathology, Division of Molecular and Diagnostic Pathology, Shiga University of Medical Science, Otsu, 520-2192, Japan.
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Oliveira PH, da Silva CL, Cabral JM. Concise Review: Genomic Instability in Human Stem Cells: Current Status and Future Challenges. Stem Cells 2014; 32:2824-32. [DOI: 10.1002/stem.1796] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 06/03/2014] [Accepted: 06/09/2014] [Indexed: 12/26/2022]
Affiliation(s)
- Pedro H. Oliveira
- Institut Pasteur; Microbial Evolutionary Genomics, Département Génomes et Génétique; Paris France
- CNRS; UMR3525 Paris France
| | - Cláudia Lobato da Silva
- Institute for Biotechnology and Bioengineering, Department of Bioengineering; Instituto Superior Técnico, Universidade de Lisboa; Lisboa Portugal
| | - Joaquim M.S. Cabral
- Institute for Biotechnology and Bioengineering, Department of Bioengineering; Instituto Superior Técnico, Universidade de Lisboa; Lisboa Portugal
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Cappi C, Hounie AG, Mariani DB, Diniz JB, Silva ART, Reis VNS, Busso AF, Silva AG, Fidalgo F, Rogatto SR, Miguel EC, Krepischi AC, Brentani H. An inherited small microdeletion at 15q13.3 in a patient with early-onset obsessive-compulsive disorder. PLoS One 2014; 9:e110198. [PMID: 25303678 PMCID: PMC4193873 DOI: 10.1371/journal.pone.0110198] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 09/18/2014] [Indexed: 01/22/2023] Open
Abstract
Copy number variations (CNVs) have been previously associated with several different neurodevelopmental psychiatric disorders, such as autism, schizophrenia, and attention deficit hyperactivity disorder (ADHD). The present study consisted of a pilot genome-wide screen for CNVs in a cohort of 16 patients with early-onset obsessive-compulsive disorder (OCD) and 12 mentally healthy individuals, using array-based comparative genomic hybridization (aCGH) on 44K arrays. A small rare paternal inherited microdeletion (∼64 kb) was identified in chromosome 15q13.3 of one male patient with very early onset OCD. The father did not have OCD. The deletion encompassed part of the FMN1 gene, which is involved with the glutamatergic system. This finding supports the hypothesis of a complex network of several genes expressed in the brain contributing for the genetic risk of OCD, and also supports the glutamatergic involvement in OCD, which has been previously reported in the literature.
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Affiliation(s)
- Carolina Cappi
- Institute and Department of Psychiatry, São Paulo University Medical School, São Paulo, Brazil
| | - Ana Gabriela Hounie
- Institute and Department of Psychiatry, São Paulo University Medical School, São Paulo, Brazil
- Federal University of São Paulo-UPIA-UNIFESP, São Paulo, Brazil
| | - Daniel B. Mariani
- Inter-institutional Grad Program on Bioinformatics, Institute of Mathematics and Statistics, São Paulo University, São Paulo, Brazil
| | - Juliana Belo Diniz
- Institute and Department of Psychiatry, São Paulo University Medical School, São Paulo, Brazil
| | - Aderbal R. T. Silva
- Institute and Department of Psychiatry, São Paulo University Medical School, São Paulo, Brazil
| | - Viviane N. S. Reis
- Institute and Department of Psychiatry, São Paulo University Medical School, São Paulo, Brazil
| | - Ariane F. Busso
- International Research Center, AC Camargo Cancer Center, São Paulo, Brazil
| | | | - Felipe Fidalgo
- International Research Center, AC Camargo Cancer Center, São Paulo, Brazil
| | | | - Euripedes C. Miguel
- Institute and Department of Psychiatry, São Paulo University Medical School, São Paulo, Brazil
| | - Ana C. Krepischi
- International Research Center, AC Camargo Cancer Center, São Paulo, Brazil
| | - Helena Brentani
- Institute and Department of Psychiatry, São Paulo University Medical School, São Paulo, Brazil
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Navarro S, Moleiro V, Molina-Estevez FJ, Lozano ML, Chinchon R, Almarza E, Quintana-Bustamante O, Mostoslavsky G, Maetzig T, Galla M, Heinz N, Schiedlmeier B, Torres Y, Modlich U, Samper E, Río P, Segovia JC, Raya A, Güenechea G, Izpisua-Belmonte JC, Bueren JA. Generation of iPSCs from genetically corrected Brca2 hypomorphic cells: implications in cell reprogramming and stem cell therapy. Stem Cells 2014; 32:436-46. [PMID: 24420904 DOI: 10.1002/stem.1586] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Revised: 09/02/2013] [Accepted: 09/05/2013] [Indexed: 12/24/2022]
Abstract
Fanconi anemia (FA) is a complex genetic disease associated with a defective DNA repair pathway known as the FA pathway. In contrast to many other FA proteins, BRCA2 participates downstream in this pathway and has a critical role in homology-directed recombination (HDR). In our current studies, we have observed an extremely low reprogramming efficiency in cells with a hypomorphic mutation in Brca2 (Brca2(Δ) (27/) (Δ27)), that was associated with increased apoptosis and defective generation of nuclear RAD51 foci during the reprogramming process. Gene complementation facilitated the generation of Brca2(Δ) (27/) (Δ27) induced pluripotent stem cells (iPSCs) with a disease-free FA phenotype. Karyotype analyses and comparative genome hybridization arrays of complemented Brca2(Δ) (27/) (Δ27) iPSCs showed, however, the presence of different genetic alterations in these cells, most of which were not evident in their parental Brca2(Δ) (27/) (Δ27) mouse embryonic fibroblasts. Gene-corrected Brca2(Δ) (27/) (Δ27) iPSCs could be differentiated in vitro toward the hematopoietic lineage, although with a more limited efficacy than WT iPSCs or mouse embryonic stem cells, and did not engraft in irradiated Brca2(Δ) (27/) (Δ27) recipients. Our results are consistent with previous studies proposing that HDR is critical for cell reprogramming and demonstrate that reprogramming defects characteristic of Brca2 mutant cells can be efficiently overcome by gene complementation. Finally, based on analysis of the phenotype, genetic stability, and hematopoietic differentiation potential of gene-corrected Brca2(Δ) (27/) (Δ) (27) iPSCs, achievements and limitations in the application of current reprogramming approaches in hematopoietic stem cell therapy are also discussed.
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Affiliation(s)
- S Navarro
- Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBER-ER), Madrid, Spain
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Meta-analyses of Dehalococcoides mccartyi strain 195 transcriptomic profiles identify a respiration rate-related gene expression transition point and interoperon recruitment of a key oxidoreductase subunit. Appl Environ Microbiol 2014; 80:6062-72. [PMID: 25063656 DOI: 10.1128/aem.02130-14] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
A cDNA-microarray was designed and used to monitor the transcriptomic profile of Dehalococcoides mccartyi strain 195 (in a mixed community) respiring various chlorinated organics, including chloroethenes and 2,3-dichlorophenol. The cultures were continuously fed in order to establish steady-state respiration rates and substrate levels. The organization of array data into a clustered heat map revealed two major experimental partitions. This partitioning in the data set was further explored through principal component analysis. The first two principal components separated the experiments into those with slow (1.6±0.6 μM Cl-/h)- and fast (22.9±9.6 μM Cl-/h)-respiring cultures. Additionally, the transcripts with the highest loadings in these principal components were identified, suggesting that those transcripts were responsible for the partitioning of the experiments. By analyzing the transcriptomes (n=53) across experiments, relationships among transcripts were identified, and hypotheses about the relationships between electron transport chain members were proposed. One hypothesis, that the hydrogenases Hup and Hym and the formate dehydrogenase-like oxidoreductase (DET0186-DET0187) form a complex (as displayed by their tight clustering in the heat map analysis), was explored using a nondenaturing protein separation technique combined with proteomic sequencing. Although these proteins did not migrate as a single complex, DET0112 (an FdhB-like protein encoded in the Hup operon) was found to comigrate with DET0187 rather than with the catalytic Hup subunit DET0110. On closer inspection of the genome annotations of all Dehalococcoides strains, the DET0185-to-DET0187 operon was found to lack a key subunit, an FdhB-like protein. Therefore, on the basis of the transcriptomic, genomic, and proteomic evidence, the place of the missing subunit in the DET0185-to-DET0187 operon is likely filled by recruiting a subunit expressed from the Hup operon (DET0112).
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Rasmussen JØ, von Holstein SL, Prause JU, Vainer B, Hansen AB, Fehr A, Stenman G, Heegaard S. Genetic analysis of an orbital metastasis from a primary hepatic neuroendocrine carcinoma. Oncol Rep 2014; 32:1447-50. [PMID: 25051214 DOI: 10.3892/or.2014.3345] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 06/16/2014] [Indexed: 11/06/2022] Open
Abstract
A 71-year-old female with a known history of primary hepatic neuroendocrine carcinoma, presented with a visual defect, proptosis and restricted eye movements of the right eye. Biopsies from the orbit and from the primary hepatic neuroendocrine carcinoma showed similar morphological and immunohistochemical features, and high-resolution, array-based comparative genomic hybridization demonstrated loss of one copy each of chromosomes 3 and 18, and gain of 1q both in the primary hepatic neuroendocrine carcinoma and in the orbital tumour. The orbital mass was diagnosed as a metastasis from the primary hepatic neuroendocrine carcinoma. Primary hepatic neuroendocrine tumours are extremely rare, and the orbit is an extremely rare location for a neuroendocrine carcinoma metastasis. This is the first reported case of an orbital metastasis with origin from a primary hepatic neuroendocrine carcinoma.
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Affiliation(s)
- Jacob Ø Rasmussen
- Eye Pathology Institute, Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Sarah L von Holstein
- Eye Pathology Institute, Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Jan U Prause
- Eye Pathology Institute, Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Ben Vainer
- Department of Pathology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Alastair B Hansen
- Department of Pathology, Herlev Hospital, University of Copenhagen, Herlev, Denmark
| | - André Fehr
- Sahlgrenska Cancer Center, Department of Pathology, University of Gothenburg, Gothenburg, Sweden
| | - Göran Stenman
- Sahlgrenska Cancer Center, Department of Pathology, University of Gothenburg, Gothenburg, Sweden
| | - Steffen Heegaard
- Eye Pathology Institute, Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark
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Xiao J, Zhang L, Wang J, Jiang Y, Jin L, Lu J, Jin L, Zhong C, Xu X, Zhang F. Rearrangement structure-independent strategy of CNV breakpoint analysis. Mol Genet Genomics 2014; 289:755-63. [PMID: 24737421 DOI: 10.1007/s00438-014-0850-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 03/28/2014] [Indexed: 12/21/2022]
Abstract
Rare copy number variations (CNVs) generated by human genomic rearrangements have been shown to play an important role in pathogenesis of human diseases and cancers. CNV breakpoint analysis can help define genomic location, genetic content and sequence structure of pathogenic CNVs. This process is vital to elucidate CNV mutational mechanism and etiology of CNV-associated disorders. However, it is technically challenging to map CNV breakpoints at base-pair level, especially in the genomic regions with sequence complexity. In this study, we developed a new method of capture and breakpoint approaching sequencing (CBAS) to efficiently obtain CNV breakpoint sequences. This strategy is independent of CNV structures and applicable to various CNV types. As was demonstrated in CNV-associated patients with neurological disorders, CBAS achieved fine mapping of breakpoint sequences for compound deletion, complex duplication, and translocation. Intriguingly, CBAS also revealed unexpected CNV complexity involving long-range DNA rearrangement. Our observations showed that CBAS is an efficient method for obtaining CNV breakpoint sequence and mapping insertional events as well. This method can facilitate the researches on CNV-associated human diseases and cancers. CBAS is also applicable to mapping the integration sites of retrovirus (such as HIV) and transgenes in model organisms.
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Affiliation(s)
- Jianqiu Xiao
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, 220 Handan Road, Shanghai, 200433, China
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39
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Cellular intrinsic factors involved in the resistance of squamous cell carcinoma to photodynamic therapy. J Invest Dermatol 2014; 134:2428-2437. [PMID: 24717244 DOI: 10.1038/jid.2014.178] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 03/03/2014] [Accepted: 03/14/2014] [Indexed: 11/09/2022]
Abstract
Photodynamic therapy (PDT) is widely used to treat non-melanoma skin cancer. However, some patients affected with squamous cell carcinoma (SCC) do not respond adequately to PDT with methyl-δ-aminolevulinic acid (MAL-PDT) and the tumors acquire an infiltrative phenotype and became histologically more aggressive, less differentiated, and more fibroblastic. To search for potential factors implicated in SCC resistance to PDT, we have used the SCC-13 cell line (parental) and resistant SCC-13 cells obtained by repeated MAL-PDT treatments (5th and 10th PDT-resistant generations). Xenografts assays in immunodeficient mice showed that the tumors generated by resistant cells were bigger than those induced by parental cells. Comparative genomic hybridization array (aCGH) showed that the three cell types presented amplicons in 3p12.1 CADM2, 7p11.2 EFGR, and 11q13.3 CCND1 genes. The 5th and 10th PDT-resistant cells showed an amplicon in 5q11.2 MAP3K1, which was not present in parental cells. The changes detected by aCGH on CCND1, EFGR, and MAP3K1 were confirmed in extracts of SCC-13 cells by reverse-transcriptase PCR and by western blot, and by immunohistochemistry in human biopsies from persistent tumors after MAL-PDT. Our data suggest that genomic imbalances related to CCND1, EFGR, and particularly MAP3K1 seem to be involved in the development of the resistance of SCC to PDT.
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Kodama S, Yamada T, Imai J, Sawada S, Takahashi K, Tsukita S, Kaneko K, Uno K, Ishigaki Y, Oka Y, Katagiri H. Simultaneous copy number losses within multiple subtelomeric regions in early-onset type 2 diabetes mellitus. PLoS One 2014; 9:e88602. [PMID: 24709989 PMCID: PMC3977841 DOI: 10.1371/journal.pone.0088602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 01/13/2014] [Indexed: 11/23/2022] Open
Abstract
Genetic factors play very important roles in the onset and progression of type 2 diabetes mellitus (T2DM). However, the genetic factors correlating with T2DM onset have not as yet been fully clarified. We previously found that copy number losses in the subtelomeric region on chromosome 4p16.3 were detected in early-onset Japanese T2DM patients (onset age <35 years) at a high frequency. Herein, we additionally found two novel copy number losses within the subtelomeric regions on chromosomes 16q24.2-3 and 22q13.31-33, which have significant associations with early-onset Japanese T2DM. The associations were statistically significant by Fisher's exact tests with P values of 5.19×10−3 and 1.81×10−3 and odds ratios of 5.7 and 4.4 for 16q24.2-3 and 22q13.31-33, respectively. Furthermore, copy number variation (CNV) analysis of the whole genome using the CNV BeadChip system verified simultaneous copy number losses in all three subtelomeric regions in 11 of our 100 T2DM subjects, while none of 100 non-diabetic controls showed the copy number losses in all three regions. Our results suggest that the mechanism underlying induction of CNVs is involved in the pathogenesis of early-onset T2DM. Thus, copy number losses within multiple subtelomeric regions are strongly associated with early-onset T2DM and examination of simultaneous CNVs in these three regions may lead to the development of an accurate and selective procedure for detecting genetic susceptibility to T2DM.
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Affiliation(s)
- Shinjiro Kodama
- Division of Metabolism and Diabetes, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tetsuya Yamada
- Division of Metabolism and Diabetes, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Junta Imai
- Division of Metabolism and Diabetes, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Shojiro Sawada
- Division of Metabolism and Diabetes, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kei Takahashi
- Division of Metabolism and Diabetes, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Sohei Tsukita
- Division of Metabolism and Diabetes, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Keizo Kaneko
- Division of Metabolism and Diabetes, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kenji Uno
- Division of Metabolism and Diabetes, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yasushi Ishigaki
- Division of Metabolism and Diabetes, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoshitomo Oka
- Division of Metabolism and Diabetes, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hideki Katagiri
- Division of Metabolism and Diabetes, Tohoku University Graduate School of Medicine, Sendai, Japan
- Japan Science and Technology Agency, CREST, Tokyo, Japan
- * E-mail:
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Ishiura H, Takahashi Y, Hayashi T, Saito K, Furuya H, Watanabe M, Murata M, Suzuki M, Sugiura A, Sawai S, Shibuya K, Ueda N, Ichikawa Y, Kanazawa I, Goto J, Tsuji S. Molecular epidemiology and clinical spectrum of hereditary spastic paraplegia in the Japanese population based on comprehensive mutational analyses. J Hum Genet 2014; 59:163-72. [PMID: 24451228 DOI: 10.1038/jhg.2013.139] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 11/16/2013] [Accepted: 11/29/2013] [Indexed: 12/12/2022]
Abstract
Hereditary spastic paraplegia (HSP) is one of the most genetically heterogeneous neurodegenerative disorders characterized by progressive spasticity and pyramidal weakness of lower limbs. Because >30 causative genes have been identified, screening of multiple genes is required for establishing molecular diagnosis of individual patients with HSP. To elucidate molecular epidemiology of HSP in the Japanese population, we have conducted mutational analyses of 16 causative genes of HSP (L1CAM, PLP1, ATL1, SPAST, CYP7B1, NIPA1, SPG7, KIAA0196, KIF5A, HSPD1, BSCL2, SPG11, SPG20, SPG21, REEP1 and ZFYVE27) using resequencing microarrays, array-based comparative genomic hybridization and Sanger sequencing. The mutational analysis of 129 Japanese patients revealed 49 mutations in 46 patients, 32 of which were novel. Molecular diagnosis was accomplished for 67.3% (33/49) of autosomal dominant HSP patients. Even among sporadic HSP patients, mutations were identified in 11.1% (7/63) of them. The present study elucidated the molecular epidemiology of HSP in the Japanese population and further broadened the mutational and clinical spectra of HSP.
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Affiliation(s)
- Hiroyuki Ishiura
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yuji Takahashi
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Toshihiro Hayashi
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kayoko Saito
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Hirokazu Furuya
- Department of Neurology, Neuro-Muscular Center, National Omuta Hospital, Fukuoka, Japan
| | - Mitsunori Watanabe
- Department of Neurology, Institute of Brain Science, Hirosaki University Graduate School of Medicine, Aomori, Japan
| | - Miho Murata
- Department of Neurology, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Mikiya Suzuki
- Department of Neurology, Higashisaitama Hospital, National Hospital Organization, Saitama, Japan
| | - Akira Sugiura
- Department of Neurology, Shizuoka Institute of Epilepsy and Neurological Disorders, Shizuoka, Japan
| | - Setsu Sawai
- 1] Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan [2] Division of Laboratory Medicine and Clinical Genetics, Chiba University Hospital, Chiba, Japan
| | - Kazumoto Shibuya
- Department of Neurology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Naohisa Ueda
- 1] Department of Neurology, Chigasaki Municipal Hospital, Kanagawa, Japan [2] Department of Neurology, Yokohama City University School of Medicine, Kanagawa, Japan
| | - Yaeko Ichikawa
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ichiro Kanazawa
- Graduate School, International University of Health and Welfare, Tokyo, Japan
| | - Jun Goto
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shoji Tsuji
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Differentially expressed genes in response to gamma-irradiation during the vegetative stage in Arabidopsis thaliana. Mol Biol Rep 2014; 41:2229-41. [PMID: 24442319 DOI: 10.1007/s11033-014-3074-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 01/04/2014] [Indexed: 10/25/2022]
Abstract
Biochemical and physiological processes in plants are affected by gamma-irradiation, which causes significant changes in gene transcripts and expression. To identify the differentially expressed Arabidopsis genes in response to gamma-irradiation, we performed a microarray analysis with rosette leaves during the vegetative stage. Arabidopsis plants were exposed to a wide spectrum doses of gamma ray (100, 200, 300, 400, 800, 1200, 1600 or 2000 Gy) for 24 h. At the dose range from 100 to 400 Gy, irradiated plants were found to be shorter than controls after 8 days of irradiation, while doses over 800 Gy caused severe growth retardation. Therefore, 100 and 800 Gy were selected as adequate doses for microarray analysis to identify differentially expressed genes. Among the 20,993 genes used as microarray probes, a total number of 496 and 1,042 genes were up-regulated and down-regulated by gamma-irradiation, respectively (P < 0.05). We identified the characteristics of the genes that were up-and down-regulated fourfold higher genes by gamma irradiation according to The arabidopsis information resource gene ontology. To confirm the microarray results, we performed a northern blot and quantitative real-time PCR with several selected genes that had a large difference in expression after irradiation. In particular, genes associated with lipid transfer proteins, histones and transposons were down-regulated by 100 and/or 800 Gy of gamma irradiation. The expression patterns of selected genes were generally in agreement with the microarray results, although there were quantitative differences in the expression levels.
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43
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Josephson R. Molecular cytogenetics: making it safe for human embryonic stem cells to enter the clinic. Expert Rev Mol Diagn 2014; 7:395-406. [PMID: 17620047 DOI: 10.1586/14737159.7.4.395] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Regenerative therapies based on transplantation of cells derived from human embryonic stem cells (hESC) are currently being prepared for clinical trials. Unfortunately, recent evidence indicates that many kinds of changes can occur to hESC during expansion in culture, and alterations to the growth control mechanisms may be required to establish hESC lines at all. Changes in the genome and epigenome can affect the validity of in vitro and animal studies, and put transplant recipients at increased risk of cancer. New molecular cytogenetic technologies enable us to examine the whole human genome with ever-finer resolution. This review describes several techniques for whole-genome analysis and the information they can provide about hESC lines. Adoption of high-resolution genotyping into routine characterization may prevent highly discouraging clinical outcomes.
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44
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Ahmed FE. Microarray RNA transcriptional profiling: Part I. Platforms, experimental design and standardization. Expert Rev Mol Diagn 2014; 6:535-50. [PMID: 16824028 DOI: 10.1586/14737159.6.4.535] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This review summarizes, in a balanced and comprehensive manner, the various components of microarrays and their types, substrate architecture, platforms for microarray probe implementation, standardizations and confounders. The review is intended to familiarize the beginner with the principles of experimental design and the selection of an appropriate microarray platform. This parallel technology has revolutionized transcriptomic approaches to data profiling and has a major role in the identification of expressed genes, classification and diagnosis studies. The technology is still evolving and guidelines for standardization and reporting have been developed and are being improved.
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Affiliation(s)
- Farid E Ahmed
- Leo W Jenkins Cancer Center, Department of Radiation Oncology, LSB 014, The Brody School of Medicine at East Carolina University, Greenville, NC 27858, USA.
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He W, Sun X, Liu L, Li M, Jin H, Wang WH. The prevalence of chromosomal deletions relating to developmental delay and/or intellectual disability in human euploid blastocysts. PLoS One 2014; 9:e85207. [PMID: 24409323 PMCID: PMC3883698 DOI: 10.1371/journal.pone.0085207] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 11/21/2013] [Indexed: 11/22/2022] Open
Abstract
Chromosomal anomalies in human embryos produced by in vitro fertilization are very common, which include numerical (aneuploidy) and structural (deletion, duplication or others) anomalies. Our previous study indicated that chromosomal deletion(s) is the most common structural anomaly accounting for approximately 8% of euploid blastocysts. It is still unknown if these deletions in human euploid blastocysts have clinical significance. In this study, we analyzed 15 previously diagnosed euploid blastocysts that had chromosomal deletion(s) using Agilent oligonucleotide DNA microarray platform and localized the gene location in each deletion. Then, we used OMIM gene map and phenotype database to investigate if these deletions are related with some important genes that cause genetic diseases, especially developmental delay or intellectual disability. As results, we found that the detectable chromosomal deletion size with Agilent microarray is above 2.38 Mb, while the deletions observed in human blastocysts are between 11.6 to 103 Mb. With OMIM gene map and phenotype database information, we found that deletions can result in loss of 81-464 genes. Out of these genes, 34–149 genes are related with known genetic problems. Furthermore, we found that 5 out of 15 samples lost genes in the deleted region, which were related to developmental delay and/or intellectual disability. In conclusion, our data indicates that all human euploid blastocysts with chromosomal deletion(s) are abnormal and transfer of these embryos may cause birth defects and/or developmental and intellectual disabilities. Therefore, the embryos with chromosomal deletion revealed by DNA microarray should not be transferred to the patients, or further gene map and/or phenotype seeking is necessary before making a final decision.
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Affiliation(s)
- Wenyin He
- Key Laboratory of Major Obstetrics Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangdong, China
| | - Xiaofang Sun
- Key Laboratory of Major Obstetrics Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangdong, China
| | - Lian Liu
- Pacgenomics Inc., Village Medical Center, Thousand Oaks, California, United States of America
| | - Man Li
- Pacgenomics Inc., Village Medical Center, Thousand Oaks, California, United States of America
| | - Hua Jin
- Pacgenomics Inc., Village Medical Center, Thousand Oaks, California, United States of America
| | - Wei-Hua Wang
- New Houston Health, Houston, Texas, United States of America
- Vivere Health, Franklin, Tennessee, United States of America
- * E-mail:
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von Holstein SL. Tumours of the lacrimal gland. Epidemiological, clinical and genetic characteristics. Acta Ophthalmol 2013; 91 Thesis 6:1-28. [PMID: 24893972 DOI: 10.1111/aos.12271] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Tumours of the lacrimal gland are rare, but the prognosis may be grave. To date, no population-based incidence and distribution data on lacrimal gland tumours exist. In addition, almost nothing is known about the genetic profile of epithelial tumours of the lacrimal gland. We collected specimens and clinical files on all biopsied lacrimal gland lesions in Denmark over a 34-year period and re-evaluated the diagnosis to provide updated population-based incidence rates and epidemiological characteristics. Clinical data regarding symptoms, clinical examinations, treatment and follow-up were collected for patients with adenoid cystic carcinoma (ACC), pleomorphic adenoma (PA), carcinoma ex pleomorphic adenoma (Ca-ex-PA) and mucoepidermoid carcinoma (MEC). Using RT-PCR, FISH, immunohistochemistry, Q-PCR and high-resolution array-based comparative genomic hybridization (arrayCGH) we explored the genetic characteristics including copy number alterations (CNA) in ACC, PA, Ca-ex-PA and MEC. The incidence of biopsied lacrimal gland lesions was 1.3/1,000,000/year, and ~50% were neoplastic lesions. Of these, 55% were malignant tumours with epithelial tumours as the most frequent. The overall incidence was increasing, and this was caused by an increase in biopsied non-neoplastic lesions. We found that 10/14 ACCs either expressed the MYB-NFIB fusion gene and/or had rearrangements of MYB. All ACCs expressed the MYB protein. ACC was characterized by recurrent copy number losses involving 6q, 12q and 17q and gains involving 19q, 8q and 11q. ArrayCGH revealed an apparently normal genomic profile in 11/19 PAs. The remaining 8 PAs had recurrent copy number losses involving 1p, 6q, 8q and 13q and gain involving 9p. PA expressed PLAG1 in all tumours whereas only 2/29 tumours expressed HMGA2. Ca-ex-PA was characterized by recurrent copy number gain involving 22q. PLAG1 was expressed in 3/5 Ca-ex-PA whereas none of these tumours expressed HMGA2. MEC expressed the CRTC1-MAML2, and this fusion was found to be tumour-specific for lacrimal gland MEC. In conclusion, lacrimal gland lesions that require pathological evaluation are rare in the Danish population, and the incidence rate of biopsied benign lesions is increasing. Epithelial tumours of the lacrimal gland are molecularly very similar to their salivary gland counterparts in the expression of the tumour-specific fusion genes and in their genomic imbalances as demonstrated by arrayCGH. MYB-NFIB is a useful biomarker for ACC and MYB, and its downstream target genes may be potential therapeutic targets for these tumours.
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Tortajada A, Yébenes H, Abarrategui-Garrido C, Anter J, García-Fernández JM, Martínez-Barricarte R, Alba-Domínguez M, Malik TH, Bedoya R, Cabrera Pérez R, López Trascasa M, Pickering MC, Harris CL, Sánchez-Corral P, Llorca O, Rodríguez de Córdoba S. C3 glomerulopathy-associated CFHR1 mutation alters FHR oligomerization and complement regulation. J Clin Invest 2013; 123:2434-46. [PMID: 23728178 DOI: 10.1172/jci68280] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 03/06/2013] [Indexed: 02/06/2023] Open
Abstract
C3 glomerulopathies (C3G) are a group of severe renal diseases with distinct patterns of glomerular inflammation and C3 deposition caused by complement dysregulation. Here we report the identification of a familial C3G-associated genomic mutation in the gene complement factor H–related 1 (CFHR1), which encodes FHR1. The mutation resulted in the duplication of the N-terminal short consensus repeats (SCRs) that are conserved in FHR2 and FHR5. We determined that native FHR1, FHR2, and FHR5 circulate in plasma as homo- and hetero-oligomeric complexes, the formation of which is likely mediated by the conserved N-terminal domain. In mutant FHR1, duplication of the N-terminal domain resulted in the formation of unusually large multimeric FHR complexes that exhibited increased avidity for the FHR1 ligands C3b, iC3b, and C3dg and enhanced competition with complement factor H (FH) in surface plasmon resonance (SPR) studies and hemolytic assays. These data revealed that FHR1, FHR2, and FHR5 organize a combinatorial repertoire of oligomeric complexes and demonstrated that changes in FHR oligomerization influence the regulation of complement activation. In summary, our identification and characterization of a unique CFHR1 mutation provides insights into the biology of the FHRs and contributes to our understanding of the pathogenic mechanisms underlying C3G.
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Affiliation(s)
- Agustín Tortajada
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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Carrascosa-Romero MC, Suela J, Pardal-Fernández JM, Bermejo-Sánchez E, Vidal-Company A, MacDonald A, Tébar-Gil R, Martínez-Fernández ML, Martínez-Frías ML. A 2.84 Mb deletion at 21q22.11 in a patient clinically diagnosed with Marden-Walker syndrome. Am J Med Genet A 2013; 161A:2281-90. [PMID: 23894067 DOI: 10.1002/ajmg.a.35862] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 12/23/2012] [Indexed: 11/10/2022]
Abstract
We present a girl with the characteristic clinical picture associated with Marden-Walker syndrome (MWS; OMIM 248700), including mask-like face with blepharophimosis, joint contractures, intellectual disability, a multicystic dysplastic kidney and cerebral dysgenesis. The long-term follow-up allowed us to monitor the evolution of the phenotype in this patient, and among the main findings we highlight the following: demyelination of the pyramidal tract demonstrated by transcranial magnetic stimulation and the involvement of the levator muscles of angle of mouth in fixed facial expression with relative integrity of the rest of the facial expression muscles. A 244 k array comparative genomic hybridization (aCGH) was carried out and showed a de novo interstitial deletion of approximately 2.84 Mb affecting only the cytoband 21q22.11 (genome coordinates chr21:31,874,016-34,711,763). We selected 10 of the most recent published cases with either total or partial deletions of cytoband 21q22.11 that provided good characterization of the genomic size or the genes in the deleted regions. We observed that in nine of the 10 cases the deleted regions included the RUNX1 gene in 21q22.12, which is not affected in the current patient's deletion or in that of Patient 3 from Roberson et al. [2011]. After a comparison of shared deleted genes between cases, and correlation of their potential phenotypes, we concluded that the pattern of defects considered for a diagnosis of MWS may represent part of the phenotypic expression of a partial or total deletion of 21q22.11.
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Alsolami R, Knight SJ, Schuh A. Clinical application of targeted and genome-wide technologies: can we predict treatment responses in chronic lymphocytic leukemia? Per Med 2013; 10:361-376. [PMID: 24611071 DOI: 10.2217/pme.13.33] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Chronic lymphocytic leukemia (CLL) is low-grade lymphoma of mature B cells and it is considered to be the most common type of hematological malignancy in the western world. CLL is characterized by a chronically relapsing course and clinical and biological heterogeneity. Many patients do not require any treatment for years. Although important progress has been made in the treatment of CLL, none of the conventional treatment options are curative. Recurrent chromosomal abnormalities have been identified and are associated with prognosis and pathogenesis of the disease. More recently, unbiased genome-wide technologies have identified multiple additional recurrent aberrations. The precise predictive value of these has not been established, but it is likely that the genetic heterogeneity observed at least partly reflects the clinical variability. The present article reviews our current knowledge of predictive markers in CLL using whole-genome technologies.
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Affiliation(s)
- Reem Alsolami
- Oxford National Institute for Health Research Biomedical Research Centre, University of Oxford, Oxford, UK ; King Abdulaziz University, Faculty of Applied Medical Sciences, Jeddah, Saudi Arabia
| | - Samantha Jl Knight
- Oxford National Institute for Health Research Biomedical Research Centre, University of Oxford, Oxford, UK ; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Anna Schuh
- Oxford National Institute for Health Research Biomedical Research Centre, University of Oxford, Oxford, UK
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50
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Caruso N, Herberth B, Bartoli M, Puppo F, Dumonceaux J, Zimmermann A, Denadai S, Lebossé M, Roche S, Geng L, Magdinier F, Attarian S, Bernard R, Maina F, Levy N, Helmbacher F. Deregulation of the protocadherin gene FAT1 alters muscle shapes: implications for the pathogenesis of facioscapulohumeral dystrophy. PLoS Genet 2013; 9:e1003550. [PMID: 23785297 PMCID: PMC3681729 DOI: 10.1371/journal.pgen.1003550] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 04/23/2013] [Indexed: 01/01/2023] Open
Abstract
Generation of skeletal muscles with forms adapted to their function is essential for normal movement. Muscle shape is patterned by the coordinated polarity of collectively migrating myoblasts. Constitutive inactivation of the protocadherin gene Fat1 uncoupled individual myoblast polarity within chains, altering the shape of selective groups of muscles in the shoulder and face. These shape abnormalities were followed by early onset regionalised muscle defects in adult Fat1-deficient mice. Tissue-specific ablation of Fat1 driven by Pax3-cre reproduced muscle shape defects in limb but not face muscles, indicating a cell-autonomous contribution of Fat1 in migrating muscle precursors. Strikingly, the topography of muscle abnormalities caused by Fat1 loss-of-function resembles that of human patients with facioscapulohumeral dystrophy (FSHD). FAT1 lies near the critical locus involved in causing FSHD, and Fat1 mutant mice also show retinal vasculopathy, mimicking another symptom of FSHD, and showed abnormal inner ear patterning, predictive of deafness, reminiscent of another burden of FSHD. Muscle-specific reduction of FAT1 expression and promoter silencing was observed in foetal FSHD1 cases. CGH array-based studies identified deletion polymorphisms within a putative regulatory enhancer of FAT1, predictive of tissue-specific depletion of FAT1 expression, which preferentially segregate with FSHD. Our study identifies FAT1 as a critical determinant of muscle form, misregulation of which associates with FSHD.
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Affiliation(s)
- Nathalie Caruso
- Aix-Marseille Université, CNRS, IBDML UMR 7288, Parc Scientifique de Luminy, Case 907, Marseille, France
| | - Balàzs Herberth
- Aix-Marseille Université, CNRS, IBDML UMR 7288, Parc Scientifique de Luminy, Case 907, Marseille, France
| | - Marc Bartoli
- Aix-Marseille Université, Faculté de Médecine de la Timone, INSERM UMR 910, Marseille, France
| | - Francesca Puppo
- Aix-Marseille Université, Faculté de Médecine de la Timone, INSERM UMR 910, Marseille, France
| | - Julie Dumonceaux
- INSERM U974, UMR 7215 CNRS, Institut de Myologie, UM 76 Université Pierre et Marie Curie, Paris, France
| | - Angela Zimmermann
- Aix-Marseille Université, CNRS, IBDML UMR 7288, Parc Scientifique de Luminy, Case 907, Marseille, France
| | - Simon Denadai
- Aix-Marseille Université, CNRS, IBDML UMR 7288, Parc Scientifique de Luminy, Case 907, Marseille, France
| | - Marie Lebossé
- Aix-Marseille Université, CNRS, IBDML UMR 7288, Parc Scientifique de Luminy, Case 907, Marseille, France
| | - Stephane Roche
- Aix-Marseille Université, Faculté de Médecine de la Timone, INSERM UMR 910, Marseille, France
| | - Linda Geng
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Frederique Magdinier
- Aix-Marseille Université, Faculté de Médecine de la Timone, INSERM UMR 910, Marseille, France
| | - Shahram Attarian
- Aix-Marseille Université, Faculté de Médecine de la Timone, INSERM UMR 910, Marseille, France
- AP-HM, Neurologie, maladies neuro-musculaires, Hôpital de la Timone, Marseille, France
| | - Rafaelle Bernard
- Aix-Marseille Université, Faculté de Médecine de la Timone, INSERM UMR 910, Marseille, France
- AP-HM, Département de Génétique Médicale, Hôpital d'enfants Timone, Marseille, France
| | - Flavio Maina
- Aix-Marseille Université, CNRS, IBDML UMR 7288, Parc Scientifique de Luminy, Case 907, Marseille, France
| | - Nicolas Levy
- Aix-Marseille Université, Faculté de Médecine de la Timone, INSERM UMR 910, Marseille, France
- AP-HM, Département de Génétique Médicale, Hôpital d'enfants Timone, Marseille, France
| | - Françoise Helmbacher
- Aix-Marseille Université, CNRS, IBDML UMR 7288, Parc Scientifique de Luminy, Case 907, Marseille, France
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