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Esquiaveto-Aun AM, de Mello MP, Guaragna MS, da Silva Lopes VLG, Francese-Santos AP, Dos Santos Cruz Piveta C, Mazolla TN, de Lemos-Marini SHV, Guerra-Junior G. X-linked congenital adrenal hypoplasia: Report of long clinical follow-up and description of a new complex variant in the NR0B1 gene. Am J Med Genet A 2024; 194:e63536. [PMID: 38243380 DOI: 10.1002/ajmg.a.63536] [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: 09/27/2023] [Revised: 12/15/2023] [Accepted: 12/26/2023] [Indexed: 01/21/2024]
Abstract
Adrenal hypoplasia congenita, attributed to NR0B1 pathogenic variants, accounts for more than 50% of the incidence of primary adrenal insufficiency in children. Although more than 250 different deleterious variations have been described, no genotype-phenotype correlation has been defined to date. We report a case of an adopted boy who reported the onset of an adrenal crisis at 2 weeks of age, requiring replacement therapy with mineralocorticoids and glucocorticoids for 4 months. For 3 years, he did well without treatment. At almost 4 years of age, the disorder was restarted. A long follow-up showed the evolution of hypogonadotropic hypogonadism. Molecular studies on NR0B1 revealed a novel and deleterious deletion-insertion-inversion-deletion complex rearrangement sorted in the 5'-3' direction, which is described as follows: (1) deletion of the intergenic region (between TASL and NR0B1 genes) and 5' region, (2) insertion of a sequence containing 37 bp at the junction of the intergenic region of the TASL gene and a part of exon 1 of the NR0B1 gene, (3) inversion of a part of exon 1, (4) deletion of the final portion of exon 1 and exon 2 and beginning of the 3'UTR region, (5) maintenance of part of the intergenic sequence (between genes MAGEB1 and NR0B1, telomeric sense), (6) large posterior deletion, in the same sense. The path to molecular diagnosis was challenging and involved several molecular biology techniques. Evaluating the breakpoints in our patient, we assumed that it was a nonrecurrent rearrangement that had not yet been described. It may involve a repair mechanism known as nonhomologous end-joining (NHEJ), which joins two ends of DNA in an imprecise manner, generating an "information scar," represented herein by the 37 bp insertion. In addition, the local Xp21 chromosome architecture with sequences capable of modifying the DNA structure could impact the formation of complex rearrangements.
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Affiliation(s)
- Adriana Mangue Esquiaveto-Aun
- Graduate Program in Child and Adolescent Health, Faculty of Medical Sciences (FCM), UNICAMP, Campinas, São Paulo, Brazil
| | - Maricilda Palandi de Mello
- Laboratory of Human Genetics, Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Mara Sanches Guaragna
- Laboratory of Human Genetics, Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Vera Lúcia Gil da Silva Lopes
- Department of Translational Medicine, Medical Genetics and Genomic Medicine, Faculty of Medical Sciences (FCM), UNICAMP, Campinas, São Paulo, Brazil
| | - Ana Paula Francese-Santos
- Department of Translational Medicine, Medical Genetics and Genomic Medicine, Faculty of Medical Sciences (FCM), UNICAMP, Campinas, São Paulo, Brazil
| | - Cristiane Dos Santos Cruz Piveta
- Laboratory of Human Genetics, Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Taís Nitsh Mazolla
- Laboratory of Human Genetics, Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Sofia Helena Valente de Lemos-Marini
- Laboratory of Human Genetics, Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
- Department of Pediatrics, Faculty of Medical Sciences (FCM), UNICAMP, Campinas, São Paulo, Brazil
| | - Gil Guerra-Junior
- Laboratory of Human Genetics, Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
- Department of Pediatrics, Faculty of Medical Sciences (FCM), UNICAMP, Campinas, São Paulo, Brazil
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2
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Jia M, Shi J, Shi W, Xue X. Factors affecting the reproductive outcome in reciprocal translocation carriers undergoing preimplantation genetic testing for structural rearrangements (PGTSR). Int J Gynaecol Obstet 2024; 165:709-716. [PMID: 38205866 DOI: 10.1002/ijgo.15307] [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: 04/28/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 01/12/2024]
Abstract
OBJECTIVE To investigate the reproductive outcomes of balanced reciprocal translocation carriers and evaluate the association between the number of metaphase-II oocytes retrieved and cumulative live birth rates (LBRs). METHODS This retrospective analysis included 344 preimplantation genetic testing (PGT) for structural rearrangement cycles of 281 couples with balanced reciprocal translocations between January 2018 and January 2021. All patients included in the analysis had either delivered a baby or had used all their embryos after one stimulation cycle. All women were followed up for at least 2 years. RESULTS After ovarian stimulation and oocyte fertilization, 44.2% of PGT for structural rearrangements cycles achieved a live birth. Carrier's sex and female age did not affect the cumulative LBR of reciprocal translocation carriers. Cumulative LBRs steadily increased with the number of oocytes, reaching 64% when >20 oocytes were retrieved. The cutoff values for achieving at least one live birth were 9.5 metaphase-II (MII) oocytes and 3.5 biopsied embryos. CONCLUSION Couples with reciprocal translocations have lower transferable embryo rates and cumulative LBRs. The MII oocytes retrieved may be a crucial factor for cumulative LBRs. A high ovarian response may further increase cumulative LBRs, but avoidance of ovarian hyperstimulation syndrome or other iatrogenic complications should be considered.
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Affiliation(s)
- Miaomiao Jia
- The ART Center, Northwest Women and Children's Hospital, Xi'an, China
| | - Juanzi Shi
- The ART Center, Northwest Women and Children's Hospital, Xi'an, China
| | - Wenhao Shi
- The ART Center, Northwest Women and Children's Hospital, Xi'an, China
| | - Xia Xue
- The ART Center, Northwest Women and Children's Hospital, Xi'an, China
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Emilius L, Bremm F, Binder AK, Schaft N, Dörrie J. Tumor Antigens beyond the Human Exome. Int J Mol Sci 2024; 25:4673. [PMID: 38731892 PMCID: PMC11083240 DOI: 10.3390/ijms25094673] [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: 03/27/2024] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
With the advent of immunotherapeutics, a new era in the combat against cancer has begun. Particularly promising are neo-epitope-targeted therapies as the expression of neo-antigens is tumor-specific. In turn, this allows the selective targeting and killing of cancer cells whilst healthy cells remain largely unaffected. So far, many advances have been made in the development of treatment options which are tailored to the individual neo-epitope repertoire. The next big step is the achievement of efficacious "off-the-shelf" immunotherapies. For this, shared neo-epitopes propose an optimal target. Given the tremendous potential, a thorough understanding of the underlying mechanisms which lead to the formation of neo-antigens is of fundamental importance. Here, we review the various processes which result in the formation of neo-epitopes. Broadly, the origin of neo-epitopes can be categorized into three groups: canonical, noncanonical, and viral neo-epitopes. For the canonical neo-antigens that arise in direct consequence of somatic mutations, we summarize past and recent findings. Beyond that, our main focus is put on the discussion of noncanonical and viral neo-epitopes as we believe that targeting those provides an encouraging perspective to shape the future of cancer immunotherapeutics.
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Affiliation(s)
- Lisabeth Emilius
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (L.E.); (F.B.); (A.K.B.); (J.D.)
- Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg (CCC ER-EMN), 91054 Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
- Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany
| | - Franziska Bremm
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (L.E.); (F.B.); (A.K.B.); (J.D.)
- Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg (CCC ER-EMN), 91054 Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
- Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany
| | - Amanda Katharina Binder
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (L.E.); (F.B.); (A.K.B.); (J.D.)
- Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg (CCC ER-EMN), 91054 Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
- Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany
| | - Niels Schaft
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (L.E.); (F.B.); (A.K.B.); (J.D.)
- Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg (CCC ER-EMN), 91054 Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
- Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany
| | - Jan Dörrie
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (L.E.); (F.B.); (A.K.B.); (J.D.)
- Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg (CCC ER-EMN), 91054 Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
- Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany
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Bouassida M, Molina‐Gomes D, Koraichi F, Hervé B, Lhuilier M, Duvillier C, Le Gall J, Gauthier‐Villars M, Serazin V, Quibel T, Dard R, Vialard F. The clinical value of optical genome mapping in the rapid characterization of RB1 duplication and 15q23q24.2 triplication, for more appropriate prenatal genetic counselling. Mol Genet Genomic Med 2024; 12:e2437. [PMID: 38588252 PMCID: PMC11000809 DOI: 10.1002/mgg3.2437] [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: 01/07/2024] [Revised: 03/21/2024] [Accepted: 03/27/2024] [Indexed: 04/10/2024] Open
Abstract
BACKGROUND Despite recent advances in prenatal genetic diagnosis, medical geneticists still face considerable difficulty in interpreting the clinical outcome of copy-number-variant duplications and defining the mechanisms underlying the formation of certain chromosomal rearrangements. Optical genome mapping (OGM) is an emerging cytogenomic tool with proved ability to identify the full spectrum of cytogenetic aberrations. METHODS Here, we report on the use of OGM in a prenatal diagnosis setting. Detailed breakpoint mapping was used to determine the relative orientations of triplicated and duplicated segments in two unrelated foetuses harbouring chromosomal aberrations: a de novo 15q23q24.2 triplication and a paternally inherited 13q14.2 duplication that overlapped partially with the RB1 gene. RESULTS OGM enabled us to suggest a plausible mechanism for the triplication and confirmed that the RB1 duplication was direct oriented and in tandem. This enabled us to predict the pathogenic consequences, refine the prognosis and adapt the follow-up and familial screening appropriately. CONCLUSION Along with an increase in diagnostic rates, OGM can rapidly highlight genotype-phenotype correlations, improve genetic counselling and significantly influence prenatal management.
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Affiliation(s)
- Malek Bouassida
- Genetics DepartmentCHI de Poissy‐St Germain en LayePoissyFrance
| | | | | | - Bérénice Hervé
- Genetics DepartmentCHI de Poissy‐St Germain en LayePoissyFrance
| | | | | | | | | | - Valérie Serazin
- Genetics DepartmentCHI de Poissy‐St Germain en LayePoissyFrance
| | - Thibaud Quibel
- Obstetrics DepartmentCHI de Poissy‐St Germain en LayePoissyFrance
| | - Rodolphe Dard
- Genetics DepartmentCHI de Poissy‐St Germain en LayePoissyFrance
- RHuMA TeamUMR‐BREED, UVSQ, INRAE, ENVAMontigny le BretonneuxFrance
| | - François Vialard
- Genetics DepartmentCHI de Poissy‐St Germain en LayePoissyFrance
- RHuMA TeamUMR‐BREED, UVSQ, INRAE, ENVAMontigny le BretonneuxFrance
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Gozashti L, Hartl DL, Corbett-Detig R. Universal signatures of transposable element compartmentalization across eukaryotic genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.17.562820. [PMID: 38585780 PMCID: PMC10996525 DOI: 10.1101/2023.10.17.562820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The evolutionary mechanisms that drive the emergence of genome architecture remain poorly understood but can now be assessed with unprecedented power due to the massive accumulation of genome assemblies spanning phylogenetic diversity1,2. Transposable elements (TEs) are a rich source of large-effect mutations since they directly and indirectly drive genomic structural variation and changes in gene expression3. Here, we demonstrate universal patterns of TE compartmentalization across eukaryotic genomes spanning ~1.7 billion years of evolution, in which TEs colocalize with gene families under strong predicted selective pressure for dynamic evolution and involved in specific functions. For non-pathogenic species these genes represent families involved in defense, sensory perception and environmental interaction, whereas for pathogenic species, TE-compartmentalized genes are highly enriched for pathogenic functions. Many TE-compartmentalized gene families display signatures of positive selection at the molecular level. Furthermore, TE-compartmentalized genes exhibit an excess of high-frequency alleles for polymorphic TE insertions in fruit fly populations. We postulate that these patterns reflect selection for adaptive TE insertions as well as TE-associated structural variants. This process may drive the emergence of a shared TE-compartmentalized genome architecture across diverse eukaryotic lineages.
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Affiliation(s)
- Landen Gozashti
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Daniel L. Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
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6
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Lesack KJ, Wasmuth JD. The impact of FASTQ and alignment read order on structural variant calling from long-read sequencing data. PeerJ 2024; 12:e17101. [PMID: 38500526 PMCID: PMC10946394 DOI: 10.7717/peerj.17101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 02/21/2024] [Indexed: 03/20/2024] Open
Abstract
Background Structural variant (SV) calling from DNA sequencing data has been challenging due to several factors, including the ambiguity of short-read alignments, multiple complex SVs in the same genomic region, and the lack of "truth" datasets for benchmarking. Additionally, caller choice, parameter settings, and alignment method are known to affect SV calling. However, the impact of FASTQ read order on SV calling has not been explored for long-read data. Results Here, we used PacBio DNA sequencing data from 15 Caenorhabditis elegans strains and four Arabidopsis thaliana ecotypes to evaluate the sensitivity of different SV callers on FASTQ read order. Comparisons of variant call format files generated from the original and permutated FASTQ files demonstrated that the order of input data affected the SVs predicted by each caller. In particular, pbsv was highly sensitive to the order of the input data, especially at the highest depths where over 70% of the SV calls generated from pairs of differently ordered FASTQ files were in disagreement. These demonstrate that read order sensitivity is a complex, multifactorial process, as the differences observed both within and between species varied considerably according to the specific combination of aligner, SV caller, and sequencing depth. In addition to the SV callers being sensitive to the input data order, the SAMtools alignment sorting algorithm was identified as a source of variability following read order randomization. Conclusion The results of this study highlight the sensitivity of SV calling on the order of reads encoded in FASTQ files, which has not been recognized in long-read approaches. These findings have implications for the replication of SV studies and the development of consistent SV calling protocols. Our study suggests that researchers should pay attention to the input order sensitivity of read alignment sorting methods when analyzing long-read sequencing data for SV calling, as mitigating a source of variability could facilitate future replication work. These results also raise important questions surrounding the relationship between SV caller read order sensitivity and tool performance. Therefore, tool developers should also consider input order sensitivity as a potential source of variability during the development and benchmarking of new and improved methods for SV calling.
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Affiliation(s)
- Kyle J. Lesack
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
- Host-Parasite Interactions Research Training Network, University of Calgary, Calgary, Alberta, Canada
| | - James D. Wasmuth
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
- Host-Parasite Interactions Research Training Network, University of Calgary, Calgary, Alberta, Canada
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7
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Wang Y, Chen Y, Gao J, Xie H, Guo Y, Yang J, Liu J, Chen Z, Li Q, Li M, Ren J, Wen L, Tang F. Mapping crossover events of mouse meiotic recombination by restriction fragment ligation-based Refresh-seq. Cell Discov 2024; 10:26. [PMID: 38443370 PMCID: PMC10915157 DOI: 10.1038/s41421-023-00638-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 12/11/2023] [Indexed: 03/07/2024] Open
Abstract
Single-cell whole-genome sequencing methods have undergone great improvements over the past decade. However, allele dropout, which means the inability to detect both alleles simultaneously in an individual diploid cell, largely restricts the application of these methods particularly for medical applications. Here, we develop a new single-cell whole-genome sequencing method based on third-generation sequencing (TGS) platform named Refresh-seq (restriction fragment ligation-based genome amplification and TGS). It is based on restriction endonuclease cutting and ligation strategy in which two alleles in an individual cell can be cut into equal fragments and tend to be amplified simultaneously. As a new single-cell long-read genome sequencing method, Refresh-seq features much lower allele dropout rate compared with SMOOTH-seq. Furthermore, we apply Refresh-seq to 688 sperm cells and 272 female haploid cells (secondary polar bodies and parthenogenetic oocytes) from F1 hybrid mice. We acquire high-resolution genetic map of mouse meiosis recombination at low sequencing depth and reveal the sexual dimorphism in meiotic crossovers. We also phase the structure variations (deletions and insertions) in sperm cells and female haploid cells with high precision. Refresh-seq shows great performance in screening aneuploid sperm cells and oocytes due to the low allele dropout rate and has great potential for medical applications such as preimplantation genetic diagnosis.
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Affiliation(s)
- Yan Wang
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Yijun Chen
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Junpeng Gao
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
- Emergency Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Haoling Xie
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Yuqing Guo
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Jingwei Yang
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Jun'e Liu
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Zonggui Chen
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
- Changping Laboratory, Beijing, China
| | - Qingqing Li
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Mengyao Li
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Jie Ren
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Lu Wen
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Fuchou Tang
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China.
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
- Changping Laboratory, Beijing, China.
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Carpinteyro-Ponce J, Machado CA. The Complex Landscape of Structural Divergence Between the Drosophila pseudoobscura and D. persimilis Genomes. Genome Biol Evol 2024; 16:evae047. [PMID: 38482945 PMCID: PMC10980976 DOI: 10.1093/gbe/evae047] [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] [Accepted: 03/07/2024] [Indexed: 04/01/2024] Open
Abstract
Structural genomic variants are key drivers of phenotypic evolution. They can span hundreds to millions of base pairs and can thus affect large numbers of genetic elements. Although structural variation is quite common within and between species, its characterization depends upon the quality of genome assemblies and the proportion of repetitive elements. Using new high-quality genome assemblies, we report a complex and previously hidden landscape of structural divergence between the genomes of Drosophila persimilis and D. pseudoobscura, two classic species in speciation research, and study the relationships among structural variants, transposable elements, and gene expression divergence. The new assemblies confirm the already known fixed inversion differences between these species. Consistent with previous studies showing higher levels of nucleotide divergence between fixed inversions relative to collinear regions of the genome, we also find a significant overrepresentation of INDELs inside the inversions. We find that transposable elements accumulate in regions with low levels of recombination, and spatial correlation analyses reveal a strong association between transposable elements and structural variants. We also report a strong association between differentially expressed (DE) genes and structural variants and an overrepresentation of DE genes inside the fixed chromosomal inversions that separate this species pair. Interestingly, species-specific structural variants are overrepresented in DE genes involved in neural development, spermatogenesis, and oocyte-to-embryo transition. Overall, our results highlight the association of transposable elements with structural variants and their importance in driving evolutionary divergence.
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Affiliation(s)
| | - Carlos A Machado
- Department of Biology, University of Maryland, College Park, MD, USA
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Ban IO, Chabert A, Guignard T, Puechberty J, Cabello-Aguilar S, Pujol P, Vendrell JA, Solassol J. Characterizing PALB2 intragenic duplication breakpoints in a triple-negative breast cancer case using long-read sequencing. Front Oncol 2024; 14:1355715. [PMID: 38487723 PMCID: PMC10938850 DOI: 10.3389/fonc.2024.1355715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 02/08/2024] [Indexed: 03/17/2024] Open
Abstract
Introduction Accurate identification and characterization of Large Genomic Rearrangements (LGR), especially duplications, are crucial for precise diagnosis and risk assessment. In this report, we characterized an intragenic duplication breakpoint of PALB2 to determine its pathogenicity significance. Methods A 52-year-old female with triple-negative breast cancer was diagnosed with a novel PALB2 LGR. An efficient and accurate methodology was applied, combining long-read sequencing and transcript analysis for the rapid characterization of the duplication. Results Duplication of exons 5 and 6 of PALB2 was validated by transcript analysis. Long-read sequencing enabled the localization of breakpoints within Alu elements, providing insights into the mechanism of duplication via non-allelic homologous recombination. Conclusion Using our combined methodology, we reclassified the PALB2 duplication as a pathogenic variant. This reclassification suggests a possible causative link between this specific genetic alteration and the aggressive phenotype of the patient.
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Affiliation(s)
- Iulian O. Ban
- Laboratoire de Biologie des Tumeurs Solides, Département de Pathologie et Oncobiologie, Centre Hospitalier Universitaire (CHU) Montpellier, Université de Montpellier, Montpellier, France
| | - Alice Chabert
- Laboratoire de Biologie des Tumeurs Solides, Département de Pathologie et Oncobiologie, Centre Hospitalier Universitaire (CHU) Montpellier, Université de Montpellier, Montpellier, France
| | - Thomas Guignard
- Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier, France
- Laboratoire de Génétique Chromosomique, Plateforme ChromoStem, Centre Hospitalier Universitaire (CHU) de Montpellier, Université de Montpellier, Montpellier, France
| | - Jacques Puechberty
- Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier, France
- Laboratoire de Génétique Chromosomique, Plateforme ChromoStem, Centre Hospitalier Universitaire (CHU) de Montpellier, Université de Montpellier, Montpellier, France
| | - Simon Cabello-Aguilar
- Laboratoire de Biologie des Tumeurs Solides, Département de Pathologie et Oncobiologie, Centre Hospitalier Universitaire (CHU) Montpellier, Université de Montpellier, Montpellier, France
- Montpellier BioInformatics for Clinical Diagnosis (MOBIDIC), Molecular Medicine and Genomics Platform (PMMG), Centre Hospitalier Universitaire (CHU) Montpellier, Montpellier, France
| | - Pascal Pujol
- Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier, France
| | - Julie A. Vendrell
- Laboratoire de Biologie des Tumeurs Solides, Département de Pathologie et Oncobiologie, Centre Hospitalier Universitaire (CHU) Montpellier, Université de Montpellier, Montpellier, France
| | - Jérôme Solassol
- Laboratoire de Biologie des Tumeurs Solides, Département de Pathologie et Oncobiologie, Centre Hospitalier Universitaire (CHU) Montpellier, Université de Montpellier, Montpellier, France
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Univ Montpellier, Inserm, Institut du Cancer de Montpellier (ICM), Montpellier, France
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10
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Livnat A, Love AC. Mutation and evolution: Conceptual possibilities. Bioessays 2024; 46:e2300025. [PMID: 38254311 DOI: 10.1002/bies.202300025] [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: 02/08/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 01/24/2024]
Abstract
Although random mutation is central to models of evolutionary change, a lack of clarity remains regarding the conceptual possibilities for thinking about the nature and role of mutation in evolution. We distinguish several claims at the intersection of mutation, evolution, and directionality and then characterize a previously unrecognized category: complex conditioned mutation. Empirical evidence in support of this category suggests that the historically famous fluctuation test should be revisited, and new experiments should be undertaken with emerging experimental techniques to facilitate detecting mutation rates within specific loci at an ultra-high, individual base pair resolution.
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Affiliation(s)
- Adi Livnat
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Alan C Love
- Department of Philosophy and Minnesota Center for Philosophy of Science, University of Minnesota (Twin Cities), Minneapolis, Minnesota, USA
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11
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Baker TM, Waise S, Tarabichi M, Van Loo P. Aneuploidy and complex genomic rearrangements in cancer evolution. NATURE CANCER 2024; 5:228-239. [PMID: 38286829 DOI: 10.1038/s43018-023-00711-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/14/2023] [Indexed: 01/31/2024]
Abstract
Mutational processes that alter large genomic regions occur frequently in developing tumors. They range from simple copy number gains and losses to the shattering and reassembly of entire chromosomes. These catastrophic events, such as chromothripsis, chromoplexy and the formation of extrachromosomal DNA, affect the expression of many genes and therefore have a substantial effect on the fitness of the cells in which they arise. In this review, we cover large genomic alterations, the mechanisms that cause them and their effect on tumor development and evolution.
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Affiliation(s)
- Toby M Baker
- The Francis Crick Institute, London, UK
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sara Waise
- The Francis Crick Institute, London, UK
- Cancer Sciences Unit, University of Southampton, Southampton, UK
| | - Maxime Tarabichi
- The Francis Crick Institute, London, UK
- Institute for Interdisciplinary Research (IRIBHM), Université Libre de Bruxelles, Brussels, Belgium
| | - Peter Van Loo
- The Francis Crick Institute, London, UK.
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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12
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Martin R, Espinoza CY, Large CRL, Rosswork J, Van Bruinisse C, Miller AW, Sanchez JC, Miller M, Paskvan S, Alvino GM, Dunham MJ, Raghuraman MK, Brewer BJ. Template switching between the leading and lagging strands at replication forks generates inverted copy number variants through hairpin-capped extrachromosomal DNA. PLoS Genet 2024; 20:e1010850. [PMID: 38175823 PMCID: PMC10766183 DOI: 10.1371/journal.pgen.1010850] [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: 06/30/2023] [Accepted: 10/23/2023] [Indexed: 01/06/2024] Open
Abstract
Inherited and germ-line de novo copy number variants (CNVs) are increasingly found to be correlated with human developmental and cancerous phenotypes. Several models for template switching during replication have been proposed to explain the generation of these gross chromosomal rearrangements. We proposed a model of template switching (ODIRA-origin dependent inverted repeat amplification) in which simultaneous ligation of the leading and lagging strands at diverging replication forks could generate segmental inverted triplications through an extrachromosomal inverted circular intermediate. Here, we created a genetic assay using split-ura3 cassettes to trap the proposed inverted intermediate. However, instead of recovering circular inverted intermediates, we found inverted linear chromosomal fragments ending in native telomeres-suggesting that a template switch had occurred at the centromere-proximal fork of a replication bubble. As telomeric inverted hairpin fragments can also be created through double strand breaks we tested whether replication errors or repair of double stranded DNA breaks were the most likely initiating event. The results from CRISPR/Cas9 cleavage experiments and growth in the replication inhibitor hydroxyurea indicate that it is a replication error, not a double stranded break that creates the inverted junctions. Since inverted amplicons of the SUL1 gene occur during long-term growth in sulfate-limited chemostats, we sequenced evolved populations to look for evidence of linear intermediates formed by an error in replication. All of the data are compatible with a two-step version of the ODIRA model in which sequential template switching at short inverted repeats between the leading and lagging strands at a replication fork, followed by integration via homologous recombination, generates inverted interstitial triplications.
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Affiliation(s)
- Rebecca Martin
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Claudia Y. Espinoza
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Christopher R. L. Large
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Joshua Rosswork
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Cole Van Bruinisse
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Aaron W. Miller
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Joseph C. Sanchez
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Madison Miller
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Samantha Paskvan
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Gina M. Alvino
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Maitreya J. Dunham
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - M. K. Raghuraman
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Bonita J. Brewer
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
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13
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Oketch DJA, Giulietti M, Piva F. Copy Number Variations in Pancreatic Cancer: From Biological Significance to Clinical Utility. Int J Mol Sci 2023; 25:391. [PMID: 38203561 PMCID: PMC10779192 DOI: 10.3390/ijms25010391] [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: 11/24/2023] [Revised: 12/20/2023] [Accepted: 12/24/2023] [Indexed: 01/12/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the most common type of pancreatic cancer, characterized by high tumor heterogeneity and a poor prognosis. Inter- and intra-tumoral heterogeneity in PDAC is a major obstacle to effective PDAC treatment; therefore, it is highly desirable to explore the tumor heterogeneity and underlying mechanisms for the improvement of PDAC prognosis. Gene copy number variations (CNVs) are increasingly recognized as a common and heritable source of inter-individual variation in genomic sequence. In this review, we outline the origin, main characteristics, and pathological aspects of CNVs. We then describe the occurrence of CNVs in PDAC, including those that have been clearly shown to have a pathogenic role, and further highlight some key examples of their involvement in tumor development and progression. The ability to efficiently identify and analyze CNVs in tumor samples is important to support translational research and foster precision oncology, as copy number variants can be utilized to guide clinical decisions. We provide insights into understanding the CNV landscapes and the role of both somatic and germline CNVs in PDAC, which could lead to significant advances in diagnosis, prognosis, and treatment. Although there has been significant progress in this field, understanding the full contribution of CNVs to the genetic basis of PDAC will require further research, with more accurate CNV assays such as single-cell techniques and larger cohorts than have been performed to date.
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Affiliation(s)
| | - Matteo Giulietti
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Francesco Piva
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
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14
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Ling C, Dai Y, Geng C, Pan S, Quan W, Ding Q, Yang X, Shen D, Tao Q, Li J, Li J, Wang Y, Jiang S, Wang Y, Chen L, Cui L, Wang D. Uncovering the true features of dystrophin gene rearrangement and improving the molecular diagnosis of Duchenne and Becker muscular dystrophies. iScience 2023; 26:108365. [PMID: 38047063 PMCID: PMC10690541 DOI: 10.1016/j.isci.2023.108365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/19/2023] [Accepted: 10/26/2023] [Indexed: 12/05/2023] Open
Abstract
Duchenne and Becker muscular dystrophies (DMD/BMD) are caused by complex mutations in the dystrophin gene (DMD). Currently, there is no integrative method for the precise detection of all potential DMD variants, a gap which we aimed to address using long-read sequencing. The captured long-read sequencing panel developed in this study was applied to 129 subjects, including 11 who had previously unsolved cases. The results showed that this method accurately detected DMD mutations, ranging from single-nucleotide variations to structural variations. Furthermore, our findings revealed that continuous exon duplication/deletion in the DMD/BMD cohort may be attributed to complex segmental rearrangements and that noncontiguous duplication/deletion is generally attributed to intragenic inversion or interchromosome translocation. Mutations in the deep introns were confirmed to produce a pseudoexon. Moreover, variations in female carriers were precisely identified. The integrated and precise DMD gene screening method proposed in this study could improve the molecular diagnosis of DMD/BMD.
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Affiliation(s)
- Chao Ling
- The Laboratory of Clinical Genetics, Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Yi Dai
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Chang Geng
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Shirang Pan
- Grandomics Biosciences, Beijing 102200, China
| | | | - Qingyun Ding
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Xunzhe Yang
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Dongchao Shen
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Qing Tao
- Grandomics Biosciences, Beijing 102200, China
| | - Jingjing Li
- Grandomics Biosciences, Beijing 102200, China
| | - Jia Li
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Yinbing Wang
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Shan Jiang
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Yang Wang
- Grandomics Biosciences, Beijing 102200, China
| | - Lin Chen
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Liying Cui
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Depeng Wang
- Grandomics Biosciences, Beijing 102200, China
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15
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Shi J, Jia Z, Sun J, Wang X, Zhao X, Zhao C, Liang F, Song X, Guan J, Jia X, Yang J, Chen Q, Yu K, Jia Q, Wu J, Wang D, Xiao Y, Xu X, Liu Y, Wu S, Zhong Q, Wu J, Cui S, Bo X, Wu Z, Park M, Kellis M, He K. Structural variants involved in high-altitude adaptation detected using single-molecule long-read sequencing. Nat Commun 2023; 14:8282. [PMID: 38092772 PMCID: PMC10719358 DOI: 10.1038/s41467-023-44034-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 11/27/2023] [Indexed: 12/17/2023] Open
Abstract
Structural variants (SVs), accounting for a larger fraction of the genome than SNPs/InDels, are an important pool of genetic variation, enabling environmental adaptations. Here, we perform long-read sequencing data of 320 Tibetan and Han samples and show that SVs are highly involved in high-altitude adaptation. We expand the landscape of global SVs, apply robust models of selection and population differentiation combining SVs, SNPs and InDels, and use epigenomic analyses to predict enhancers, target genes and biological functions. We reveal diverse Tibetan-specific SVs affecting the regulatory circuitry of biological functions, including the hypoxia response, energy metabolism and pulmonary function. We find a Tibetan-specific deletion disrupts a super-enhancer and downregulates EPAS1 using enhancer reporter, cellular knock-out and DNA pull-down assays. Our study expands the global SV landscape, reveals the role of gene-regulatory circuitry rewiring in human adaptation, and illustrates the diverse functional roles of SVs in human biology.
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Affiliation(s)
- Jinlong Shi
- Medical Big Data Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 100853, China
- National Engineering Research Center of Medical Big Data, Chinese PLA General Hospital, Beijing, 100853, China
- Key Laboratory of Biomedical Engineering and Translational Medicine, Ministry of Industry and Information Technology, Chinese PLA General Hospital, Beijing, 100853, China
- Beijing Key Laboratory for Precision Medicine of Chronic Heart Failure, Chinese PLA General Hospital, Beijing, China
| | - Zhilong Jia
- Key Laboratory of Biomedical Engineering and Translational Medicine, Ministry of Industry and Information Technology, Chinese PLA General Hospital, Beijing, 100853, China
- Beijing Key Laboratory for Precision Medicine of Chronic Heart Failure, Chinese PLA General Hospital, Beijing, China
- Medical Artificial Intelligence Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 100853, China
| | - Jinxiu Sun
- Medical Big Data Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 100853, China
- National Engineering Research Center of Medical Big Data, Chinese PLA General Hospital, Beijing, 100853, China
| | - Xiaoreng Wang
- Laboratory of Nuclear and Radiation Injury, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 100853, China
- State Key Laboratory of Experimental Hematology, Beijing, 100853, China
| | - Xiaojing Zhao
- Beijing Key Laboratory for Precision Medicine of Chronic Heart Failure, Chinese PLA General Hospital, Beijing, China
- Translational Medicine Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 100853, China
| | - Chenghui Zhao
- Key Laboratory of Biomedical Engineering and Translational Medicine, Ministry of Industry and Information Technology, Chinese PLA General Hospital, Beijing, 100853, China
- Research Center for Biomedical Engineering, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 100853, China
| | - Fan Liang
- NextOmics Biosciences Inc, Wuhan, 430000, China
| | - Xinyu Song
- Key Laboratory of Biomedical Engineering and Translational Medicine, Ministry of Industry and Information Technology, Chinese PLA General Hospital, Beijing, 100853, China
- Medical Artificial Intelligence Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 100853, China
| | - Jiawei Guan
- Medical Big Data Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 100853, China
- National Engineering Research Center of Medical Big Data, Chinese PLA General Hospital, Beijing, 100853, China
| | - Xue Jia
- Laboratory of Nuclear and Radiation Injury, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 100853, China
| | - Jing Yang
- Laboratory of Nuclear and Radiation Injury, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 100853, China
| | - Qi Chen
- Medical Big Data Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 100853, China
- National Engineering Research Center of Medical Big Data, Chinese PLA General Hospital, Beijing, 100853, China
| | - Kang Yu
- Key Laboratory of Biomedical Engineering and Translational Medicine, Ministry of Industry and Information Technology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Qian Jia
- Key Laboratory of Biomedical Engineering and Translational Medicine, Ministry of Industry and Information Technology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Jing Wu
- Medical Big Data Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 100853, China
- National Engineering Research Center of Medical Big Data, Chinese PLA General Hospital, Beijing, 100853, China
| | - Depeng Wang
- NextOmics Biosciences Inc, Wuhan, 430000, China
| | - Yuhui Xiao
- NextOmics Biosciences Inc, Wuhan, 430000, China
| | - Xiaoman Xu
- NextOmics Biosciences Inc, Wuhan, 430000, China
| | - Yinzhe Liu
- NextOmics Biosciences Inc, Wuhan, 430000, China
| | - Shijing Wu
- Key Laboratory of Biomedical Engineering and Translational Medicine, Ministry of Industry and Information Technology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Qin Zhong
- Medical Big Data Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 100853, China
- National Engineering Research Center of Medical Big Data, Chinese PLA General Hospital, Beijing, 100853, China
| | - Jue Wu
- Key Laboratory of Biomedical Engineering and Translational Medicine, Ministry of Industry and Information Technology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Saijia Cui
- Beijing Key Laboratory for Precision Medicine of Chronic Heart Failure, Chinese PLA General Hospital, Beijing, China
| | - Xiaochen Bo
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | | | | | - Manolis Kellis
- Massachusetts Institute of Technology; MIT Computer Science and Artificial Intelligence Laboratory, Broad Institute of MIT and Harvard, Cambridge, 02139, MA, USA
| | - Kunlun He
- Medical Big Data Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 100853, China.
- National Engineering Research Center of Medical Big Data, Chinese PLA General Hospital, Beijing, 100853, China.
- Key Laboratory of Biomedical Engineering and Translational Medicine, Ministry of Industry and Information Technology, Chinese PLA General Hospital, Beijing, 100853, China.
- Beijing Key Laboratory for Precision Medicine of Chronic Heart Failure, Chinese PLA General Hospital, Beijing, China.
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16
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Ibarra-Ramírez M, Campos-Acevedo LD, Martínez de Villarreal LE. Chromosomal Abnormalities of Interest in Turner Syndrome: An Update. J Pediatr Genet 2023; 12:263-272. [PMID: 38162151 PMCID: PMC10756729 DOI: 10.1055/s-0043-1770982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/01/2023] [Indexed: 01/03/2024]
Abstract
Turner syndrome (TS) is caused by the total or partial loss of the second sex chromosome; it occurs in 1 every 2,500-3,000 live births. The clinical phenotype is highly variable and includes short stature and gonadal dysgenesis. In 1959, the chromosomal origin of the syndrome was recognized; patients had 45 chromosomes with a single X chromosome. TS presents numerical and structural abnormalities in the sex chromosomes, interestingly only 40% have a 45, X karyotype. The rest of the chromosomal abnormalities include mosaics, deletions of the short and long arms of the X chromosome, rings, and isochromosomes. Despite multiple studies to establish a relationship between the clinical characteristics and the different chromosomal variants in TS, a clear association cannot yet be established. Currently, different mechanisms involved in the phenotype have been explored. This review focuses to analyze the different chromosomal abnormalities and phenotypes in TS and discusses the possible mechanisms that lead to these abnormalities.
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Affiliation(s)
- Marisol Ibarra-Ramírez
- Department of Genetics, “Dr. José Eleuterio González” University Hospital of the Autonomous University of Nuevo León, Monterrey, México
| | - Luis Daniel Campos-Acevedo
- Department of Genetics, “Dr. José Eleuterio González” University Hospital of the Autonomous University of Nuevo León, Monterrey, México
| | - Laura E. Martínez de Villarreal
- Department of Genetics, “Dr. José Eleuterio González” University Hospital of the Autonomous University of Nuevo León, Monterrey, México
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17
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Shimojima Yamamoto K, Tamura T, Okamoto N, Nishi E, Noguchi A, Takahashi I, Sawaishi Y, Shimizu M, Kanno H, Minakuchi Y, Toyoda A, Yamamoto T. Identification of small-sized intrachromosomal segments at the ends of INV-DUP-DEL patterns. J Hum Genet 2023; 68:751-757. [PMID: 37423943 DOI: 10.1038/s10038-023-01181-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 06/14/2023] [Accepted: 06/27/2023] [Indexed: 07/11/2023]
Abstract
The mechanism of chromosomal rearrangement associated with inverted-duplication-deletion (INV-DUP-DEL) pattern formation has been investigated by many researchers, and several possible mechanisms have been proposed. Currently, fold-back and subsequent dicentric chromosome formation has been established as non-recurrent INV-DUP-DEL pattern formation mechanisms. In the present study, we analyzed the breakpoint junctions of INV-DUP-DEL patterns in five patients using long-read whole-genome sequencing and detected 2.2-6.1 kb copy-neutral regions in all five patients. At the end of the INV-DUP-DEL, two patients exhibited chromosomal translocations, which are recognized as telomere capture, and one patient showed direct telomere healing. The remaining two patients had additional small-sized intrachromosomal segments at the end of the derivative chromosomes. These findings have not been previously reported but they may only be explained by the presence of telomere capture breakage. Further investigations are required to better understand the mechanisms underlying this finding.
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Affiliation(s)
- Keiko Shimojima Yamamoto
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, 162-8666, Japan
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, 162-8666, Japan
| | - Takeaki Tamura
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, 173-8610, Japan
- Division of Gene Medicine, Graduate Scholl of Medical Science, Tokyo Women's Medical University, Tokyo, 162-8666, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Izumi, 594-1101, Japan
| | - Eriko Nishi
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Izumi, 594-1101, Japan
| | - Atsuko Noguchi
- Department of Pediatrics, Akita University Graduate School of Medicine, Akita, 010-8543, Japan
| | - Ikuko Takahashi
- Department of Pediatrics, Akita University Graduate School of Medicine, Akita, 010-8543, Japan
| | - Yukio Sawaishi
- Department of Pediatrics, Akita Prefectural Center on Development and Disability, Akita, 010-0000, Japan
| | - Masaki Shimizu
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
| | - Hitoshi Kanno
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, 162-8666, Japan
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, 162-8666, Japan
| | - Yohei Minakuchi
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, 411-0801, Japan
| | - Atsushi Toyoda
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, 411-0801, Japan
| | - Toshiyuki Yamamoto
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, 162-8666, Japan.
- Division of Gene Medicine, Graduate Scholl of Medical Science, Tokyo Women's Medical University, Tokyo, 162-8666, Japan.
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18
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Hansen MH, Cédile O, Kjeldsen MLG, Thomassen M, Preiss B, von Neuhoff N, Abildgaard N, Nyvold CG. Toward Cytogenomics: Technical Assessment of Long-Read Nanopore Whole-Genome Sequencing for Detecting Large Chromosomal Alterations in Mantle Cell Lymphoma. J Mol Diagn 2023; 25:796-805. [PMID: 37683892 DOI: 10.1016/j.jmoldx.2023.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 06/20/2023] [Accepted: 08/14/2023] [Indexed: 09/10/2023] Open
Abstract
The current advances and success of next-generation sequencing hold the potential for the transition of cancer cytogenetics toward comprehensive cytogenomics. However, the conventional use of short reads impedes the resolution of chromosomal aberrations. Thus, this study evaluated the detection and reproducibility of extensive copy number alterations and chromosomal translocations using long-read Oxford Nanopore Technologies whole-genome sequencing compared with short-read Illumina sequencing. Using the mantle cell lymphoma cell line Granta-519, almost 99% copy-number reproducibility at the 100-kilobase resolution between replicates was demonstrated, with 98% concordance to Illumina. Collectively, the performance of copy number calling from 1.5 million to 7.5 million long reads was comparable to 1 billion Illumina-based reads (50× coverage). Expectedly, the long-read resolution of canonical translocation t(11;14)(q13;q32) was superior, with a sequence similarity of 89% to the already published CCND1/IGH junction (9× coverage), spanning up to 69 kilobases. The cytogenetic profile of Granta-519 was in general agreement with the literature and karyotype, although several differences remained unresolved. In conclusion, contemporary long-read sequencing is primed for future cytogenomics or sequencing-guided cytogenetics. The combined strength of long- and short-read sequencing is apparent, where the high-precision junctional mapping complements and splits paired-end reads. The potential is emphasized by the flexible single-sample genomic data acquisition of Oxford Nanopore Technologies with the high resolution of allelic imbalances using Illumina short-read sequencing.
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Affiliation(s)
- Marcus H Hansen
- Hematology-Pathology Research Laboratory, Research Unit of Hematology and Research Unit of Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark; Department of Hematology, Odense University Hospital, Odense, Denmark.
| | - Oriane Cédile
- Hematology-Pathology Research Laboratory, Research Unit of Hematology and Research Unit of Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark; Department of Hematology, Odense University Hospital, Odense, Denmark; OPEN, Odense Patient Data Explorative Network, Odense University Hospital, Odense, Denmark
| | - Marie L G Kjeldsen
- Hematology-Pathology Research Laboratory, Research Unit of Hematology and Research Unit of Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Birgitte Preiss
- Hematology-Pathology Research Laboratory, Research Unit of Hematology and Research Unit of Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark; Department of Pathology, Odense University Hospital, Odense, Denmark
| | - Nils von Neuhoff
- Department of Pediatric Hematology and Oncology, Essen University Hospital and University of Duisburg-Essen, Essen, Germany
| | - Niels Abildgaard
- Hematology-Pathology Research Laboratory, Research Unit of Hematology and Research Unit of Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark; Department of Hematology, Odense University Hospital, Odense, Denmark
| | - Charlotte G Nyvold
- Hematology-Pathology Research Laboratory, Research Unit of Hematology and Research Unit of Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark; Department of Hematology, Odense University Hospital, Odense, Denmark; OPEN, Odense Patient Data Explorative Network, Odense University Hospital, Odense, Denmark
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19
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Bai W, Zhang Q, Lin Z, Ye J, Shen X, Zhou L, Cai W. Analysis of copy number variations and possible candidate genes in spontaneous abortion by copy number variation sequencing. Front Endocrinol (Lausanne) 2023; 14:1218793. [PMID: 37916154 PMCID: PMC10616874 DOI: 10.3389/fendo.2023.1218793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 09/20/2023] [Indexed: 11/03/2023] Open
Abstract
Introduction Embryonic chromosomal abnormalities represent a major causative factor in early pregnancy loss, highlighting the importance of understanding their role in spontaneous abortion. This study investigates the potential correlation between chromosomal abnormalities and spontaneous abortion using copy number variation sequencing (CNV-seq), a Next-Generation Sequencing (NGS) technology. Methods We analyzed Copy Number Variations (CNVs) in 395 aborted fetal specimens from spontaneous abortion patients by CNV-seq. And collected correlated data, including maternal age, gestational week, and Body Mass Index (BMI), and analyzed their relationship with the CNVs. Results Out of the 395 cases, 67.09% of the fetuses had chromosomal abnormalities, including numerical abnormalities, structural abnormalities, and mosaicisms. Maternal age was found to be an important risk factor for fetal chromosomal abnormalities, with the proportion of autosomal trisomy in abnormal karyotypes increasing with maternal age, while polyploidy decreased. The proportion of abnormal karyotypes with mosaic decreased as gestational age increased, while the frequency of polyploidy and sex chromosome monosomy increased. Gene enrichment analysis identified potential miscarriage candidate genes and functions, as well as pathogenic genes and pathways associated with unexplained miscarriage among women aged below or over 35 years old. Based on our study, it can be inferred that there is an association between BMI values and the risk of recurrent miscarriage caused by chromosomal abnormalities. Discussion Overall, these findings provide important insights into the understanding of spontaneous abortion and have implications for the development of personalized interventions for patients with abnormal karyotypes.
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Affiliation(s)
- Wei Bai
- Department of Laboratory Medicine, Wenzhou Traditional Chinese Medicine Hospital of Zhejiang Chinese Medical University, Zhejiang, China
| | - Qi Zhang
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co., Ltd., Hangzhou, China
| | - Zhi Lin
- Department of Laboratory Medicine, Wenzhou Traditional Chinese Medicine Hospital of Zhejiang Chinese Medical University, Zhejiang, China
| | - Jin Ye
- Department of Laboratory Medicine, Wenzhou Traditional Chinese Medicine Hospital of Zhejiang Chinese Medical University, Zhejiang, China
| | - Xiaoqi Shen
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co., Ltd., Hangzhou, China
| | - Linshuang Zhou
- Department of Laboratory Medicine, Wenzhou Traditional Chinese Medicine Hospital of Zhejiang Chinese Medical University, Zhejiang, China
| | - Wenpin Cai
- Department of Laboratory Medicine, Wenzhou Traditional Chinese Medicine Hospital of Zhejiang Chinese Medical University, Zhejiang, China
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20
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Grochowski CM, Bengtsson JD, Du H, Gandhi M, Lun MY, Mehaffey MG, Park K, Höps W, Benito-Garagorri E, Hasenfeld P, Korbel JO, Mahmoud M, Paulin LF, Jhangiani SN, Muzny DM, Fatih JM, Gibbs RA, Pendleton M, Harrington E, Juul S, Lindstrand A, Sedlazeck FJ, Pehlivan D, Lupski JR, Carvalho CMB. Break-induced replication underlies formation of inverted triplications and generates unexpected diversity in haplotype structures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560172. [PMID: 37873367 PMCID: PMC10592851 DOI: 10.1101/2023.10.02.560172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Background The duplication-triplication/inverted-duplication (DUP-TRP/INV-DUP) structure is a type of complex genomic rearrangement (CGR) hypothesized to result from replicative repair of DNA due to replication fork collapse. It is often mediated by a pair of inverted low-copy repeats (LCR) followed by iterative template switches resulting in at least two breakpoint junctions in cis . Although it has been identified as an important mutation signature of pathogenicity for genomic disorders and cancer genomes, its architecture remains unresolved and is predicted to display at least four structural variation (SV) haplotypes. Results Here we studied the genomic architecture of DUP-TRP/INV-DUP by investigating the genomic DNA of 24 patients with neurodevelopmental disorders identified by array comparative genomic hybridization (aCGH) on whom we found evidence for the existence of 4 out of 4 predicted SV haplotypes. Using a combination of short-read genome sequencing (GS), long- read GS, optical genome mapping and StrandSeq the haplotype structure was resolved in 18 samples. This approach refined the point of template switching between inverted LCRs in 4 samples revealing a DNA segment of ∼2.2-5.5 kb of 100% nucleotide similarity. A prediction model was developed to infer the LCR used to mediate the non-allelic homology repair. Conclusions These data provide experimental evidence supporting the hypothesis that inverted LCRs act as a recombinant substrate in replication-based repair mechanisms. Such inverted repeats are particularly relevant for formation of copy-number associated inversions, including the DUP-TRP/INV-DUP structures. Moreover, this type of CGR can result in multiple conformers which contributes to generate diverse SV haplotypes in susceptible loci .
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21
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Allou L, Mundlos S. Disruption of regulatory domains and novel transcripts as disease-causing mechanisms. Bioessays 2023; 45:e2300010. [PMID: 37381881 DOI: 10.1002/bies.202300010] [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: 01/16/2023] [Revised: 05/24/2023] [Accepted: 06/06/2023] [Indexed: 06/30/2023]
Abstract
Deletions, duplications, insertions, inversions, and translocations, collectively called structural variations (SVs), affect more base pairs of the genome than any other sequence variant. The recent technological advancements in genome sequencing have enabled the discovery of tens of thousands of SVs per human genome. These SVs primarily affect non-coding DNA sequences, but the difficulties in interpreting their impact limit our understanding of human disease etiology. The functional annotation of non-coding DNA sequences and methodologies to characterize their three-dimensional (3D) organization in the nucleus have greatly expanded our understanding of the basic mechanisms underlying gene regulation, thereby improving the interpretation of SVs for their pathogenic impact. Here, we discuss the various mechanisms by which SVs can result in altered gene regulation and how these mechanisms can result in rare genetic disorders. Beyond changing gene expression, SVs can produce novel gene-intergenic fusion transcripts at the SV breakpoints.
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Affiliation(s)
- Lila Allou
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Stefan Mundlos
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin, Germany
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22
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Rao H, Zhang H, Zou Y, Ma P, Huang T, Yuan H, Zhou J, Lu W, Li Q, Huang S, Liu Y, Yang B. Analysis of chromosomal structural variations in patients with recurrent spontaneous abortion using optical genome mapping. Front Genet 2023; 14:1248755. [PMID: 37732322 PMCID: PMC10507169 DOI: 10.3389/fgene.2023.1248755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 08/21/2023] [Indexed: 09/22/2023] Open
Abstract
Background and aims: Certain chromosomal structural variations (SVs) in biological parents can lead to recurrent spontaneous abortions (RSAs). Unequal crossing over during meiosis can result in the unbalanced rearrangement of gamete chromosomes such as duplication or deletion. Unfortunately, routine techniques such as karyotyping, fluorescence in situ hybridization (FISH), chromosomal microarray analysis (CMA), and copy number variation sequencing (CNV-seq) cannot detect all types of SVs. In this study, we show that optical genome mapping (OGM) quickly and accurately detects SVs for RSA patients with a high resolution and provides more information about the breakpoint regions at gene level. Methods: Seven couples who had suffered RSA with unbalanced chromosomal rearrangements of aborted embryos were recruited, and ultra-high molecular weight (UHMW) DNA was isolated from their peripheral blood. The consensus genome map was created by de novo assembly on the Bionano Solve data analysis software. SVs and breakpoints were identified via alignments of the reference genome GRCh38/hg38. The exact breakpoint sequences were verified using either Oxford Nanopore sequencing or Sanger sequencing. Results: Various SVs in the recruited couples were successfully detected by OGM. Also, additional complex chromosomal rearrangement (CCRs) and four cryptic balanced reciprocal translocations (BRTs) were revealed, further refining the underlying genetic causes of RSA. Two of the disrupted genes identified in this study, FOXK2 [46,XY,t(7; 17)(q31.3; q25)] and PLXDC2 [46,XX,t(10; 16)(p12.31; q23.1)], had been previously shown to be associated with male fertility and embryo transit. Conclusion: OGM accurately detects chromosomal SVs, especially cryptic BRTs and CCRs. It is a useful complement to routine human genetic diagnostics, such as karyotyping, and detects cryptic BRTs and CCRs more accurately than routine genetic diagnostics.
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Affiliation(s)
- Huihua Rao
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Haoyi Zhang
- School of Public Health, Nanchang University, Nanchang, Jiangxi, China
| | - Yongyi Zou
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Pengpeng Ma
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Tingting Huang
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Huizhen Yuan
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Jihui Zhou
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Wan Lu
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Qiao Li
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Shuhui Huang
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Yanqiu Liu
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Bicheng Yang
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
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23
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Wang L, Dong B, Xie Y, Kang H, Wu Y. The molecular mechanisms of recombinant chromosome 18 with parental pericentric inversions and a review of the literature. J Hum Genet 2023; 68:625-634. [PMID: 37161033 DOI: 10.1038/s10038-023-01157-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 04/07/2023] [Accepted: 04/26/2023] [Indexed: 05/11/2023]
Abstract
Chromosomal rearrangements mostly result from non-allelic homologous recombination mediated by low-copy repeats (LCRs) or segmental duplications (SDs). Recent studies on recombinant chromosome 18 (rec (18)) have focused on diagnoses and clinical phenotypes. We diagnosed two cases of prenatal rec (18) and identified precise breakpoint intervals using karyotype and chromosomal microarray analyses. We analyzed the distribution characteristics of breakpoint repetitive elements to infer rearrangement mechanisms and reviewed relevant literature to identify genetic trends. Among the 12 families with 25 pregnancies analyzed, 68% rec (18), 24% spontaneous abortions, and 8% normal births were reported. In the 17 rec (18) cases, 65% presented maternal origin and 35% were paternal. Short-arm breakpoints at p11.31 were reported in 10 cases, whereas the long-arm breakpoints were located at q21.3 (6 cases) and q12 (4 cases). Breakpoints of pericentric inversions on chromosome 18 are concentrated in p11.31, q21.3, and q12 regions. Rearrangements at 18p11.31 are non-recurrent events. ALUs, LINE1s, and MIRs were enriched at the breakpoint regions (1.85 to 3.42-fold enrichment over the entire chromosome 18), while SDs and LCRs were absent. ALU subfamilies had sequence identities of 85.94% and 83.01% between two pair breakpoints. Small repetitive elements may mediate recombination-coupled DNA repair processes, facilitating rearrangements on chromosome 18. Maternal inversion carriers are more prone to abnormal recombination in prenatal families with rec (18). Recombinant chromosomes may present preferential segregation during gamete formation.
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Affiliation(s)
- Lingxi Wang
- Prenatal Diagnosis Center, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 611731, China.
| | - Bing Dong
- Department of Eugenics, Meishan Women and Children's Hospital, Alliance Hospital of West China Second University Hospital, Sichuan University, Meishan, 620000, China
| | - Yamei Xie
- Prenatal Diagnosis Center, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Han Kang
- Prenatal Diagnosis Center, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Yong Wu
- Prenatal Diagnosis Center, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 611731, China
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24
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Cerqueira PG, Meyer D, Zhang L, Mallory B, Liu J, Hua Fu BX, Zhang X, Heyer WD. Saccharomyces cerevisiae DNA polymerase IV overcomes Rad51 inhibition of DNA polymerase δ in Rad52-mediated direct-repeat recombination. Nucleic Acids Res 2023; 51:5547-5564. [PMID: 37070185 PMCID: PMC10287921 DOI: 10.1093/nar/gkad281] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 03/29/2023] [Accepted: 04/06/2023] [Indexed: 04/19/2023] Open
Abstract
Saccharomyces cerevisiae DNA polymerase IV (Pol4) like its homolog, human DNA polymerase lambda (Polλ), is involved in Non-Homologous End-Joining and Microhomology-Mediated Repair. Using genetic analysis, we identified an additional role of Pol4 also in homology-directed DNA repair, specifically in Rad52-dependent/Rad51-independent direct-repeat recombination. Our results reveal that the requirement for Pol4 in repeat recombination was suppressed by the absence of Rad51, suggesting that Pol4 counteracts the Rad51 inhibition of Rad52-mediated repeat recombination events. Using purified proteins and model substrates, we reconstituted in vitro reactions emulating DNA synthesis during direct-repeat recombination and show that Rad51 directly inhibits Polδ DNA synthesis. Interestingly, although Pol4 was not capable of performing extensive DNA synthesis by itself, it aided Polδ in overcoming the DNA synthesis inhibition by Rad51. In addition, Pol4 dependency and stimulation of Polδ DNA synthesis in the presence of Rad51 occurred in reactions containing Rad52 and RPA where DNA strand-annealing was necessary. Mechanistically, yeast Pol4 displaces Rad51 from ssDNA independent of DNA synthesis. Together our in vitro and in vivo data suggest that Rad51 suppresses Rad52-dependent/Rad51-independent direct-repeat recombination by binding to the primer-template and that Rad51 removal by Pol4 is critical for strand-annealing dependent DNA synthesis.
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Affiliation(s)
- Paula G Cerqueira
- Department of Microbiology and Molecular Genetics, University of California, Davis, One Shields Avenue, Davis, CA 95616-8665, USA
| | - Damon Meyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, One Shields Avenue, Davis, CA 95616-8665, USA
| | - Lilin Zhang
- Department of Microbiology and Molecular Genetics, University of California, Davis, One Shields Avenue, Davis, CA 95616-8665, USA
| | - Benjamin Mallory
- Department of Microbiology and Molecular Genetics, University of California, Davis, One Shields Avenue, Davis, CA 95616-8665, USA
| | - Jie Liu
- Department of Microbiology and Molecular Genetics, University of California, Davis, One Shields Avenue, Davis, CA 95616-8665, USA
| | - Becky Xu Hua Fu
- Department of Microbiology and Molecular Genetics, University of California, Davis, One Shields Avenue, Davis, CA 95616-8665, USA
| | - Xiaoping Zhang
- Department of Microbiology and Molecular Genetics, University of California, Davis, One Shields Avenue, Davis, CA 95616-8665, USA
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, One Shields Avenue, Davis, CA 95616-8665, USA
- Department of Molecular and Cellular Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616-8665, USA
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25
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Abondio P, Cilli E, Luiselli D. Human Pangenomics: Promises and Challenges of a Distributed Genomic Reference. Life (Basel) 2023; 13:1360. [PMID: 37374141 DOI: 10.3390/life13061360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/02/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
A pangenome is a collection of the common and unique genomes that are present in a given species. It combines the genetic information of all the genomes sampled, resulting in a large and diverse range of genetic material. Pangenomic analysis offers several advantages compared to traditional genomic research. For example, a pangenome is not bound by the physical constraints of a single genome, so it can capture more genetic variability. Thanks to the introduction of the concept of pangenome, it is possible to use exceedingly detailed sequence data to study the evolutionary history of two different species, or how populations within a species differ genetically. In the wake of the Human Pangenome Project, this review aims at discussing the advantages of the pangenome around human genetic variation, which are then framed around how pangenomic data can inform population genetics, phylogenetics, and public health policy by providing insights into the genetic basis of diseases or determining personalized treatments, targeting the specific genetic profile of an individual. Moreover, technical limitations, ethical concerns, and legal considerations are discussed.
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Affiliation(s)
- Paolo Abondio
- Laboratory of Ancient DNA, Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121 Ravenna, Italy
| | - Elisabetta Cilli
- Laboratory of Ancient DNA, Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121 Ravenna, Italy
| | - Donata Luiselli
- Laboratory of Ancient DNA, Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121 Ravenna, Italy
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26
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Delourme M, Charlene C, Gerard L, Ganne B, Perrin P, Vovan C, Bertaux K, Nguyen K, Bernard R, Magdinier F. Complex 4q35 and 10q26 Rearrangements: A Challenge for Molecular Diagnosis of Patients With Facioscapulohumeral Dystrophy. Neurol Genet 2023; 9:e200076. [PMID: 37200893 PMCID: PMC10188231 DOI: 10.1212/nxg.0000000000200076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/23/2023] [Indexed: 05/20/2023]
Abstract
Background and Objectives After clinical evaluation, the molecular diagnosis of type 1 facioscapulohumeral dystrophy (FSHD1) relies in most laboratories on the detection of a shortened D4Z4 array at the 4q35 locus by Southern blotting. In many instances, this molecular diagnosis remains inconclusive and requires additional experiments to determine the number of D4Z4 units or identify somatic mosaicism, 4q-10q translocations, and proximal p13E-11 deletions. These limitations highlight the need for alternative methodologies, illustrated by the recent emergence of novel technologies such as molecular combing (MC), single molecule optical mapping (SMOM), or Oxford Nanopore-based long-read sequencing providing a more comprehensive analysis of 4q and 10q loci. Over the last decade, MC revealed a further increasing complexity in the organization of the 4q and 10q distal regions in patients with FSHD with cis-duplication of D4Z4 arrays in approximately 1%-2% of cases. Methods By using MC, we investigated in our center 2,363 cases for molecular diagnosis of FSHD. We also evaluated whether previously reported cis-duplications might be identified by SMOM using the Bionano EnFocus FSHD 1.0 algorithm. Results In our cohort of 2,363 samples, we identified 147 individuals carrying an atypical organization of the 4q35 or 10q26 loci. Mosaicism is the most frequent category followed by cis-duplications of the D4Z4 array. We report here chromosomal abnormalities of the 4q35 or 10q26 loci in 54 patients clinically described as FSHD, which are not present in the healthy population. In one-third of the 54 patients, these rearrangements are the only genetic defect suggesting that they might be causative of the disease. By analyzing DNA samples from 3 patients carrying a complex rearrangement of the 4q35 region, we further showed that the SMOM direct assembly of the 4q and 10q alleles failed to reveal these abnormalities and lead to negative results for FSHD molecular diagnosis. Discussion This work further highlights the complexity of the 4q and 10q subtelomeric regions and the need of in-depth analyses in a significant number of cases. This work also highlights the complexity of the 4q35 region and interpretation issues with consequences on the molecular diagnosis of patients or genetic counseling.
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Affiliation(s)
- Megane Delourme
- From the Aix Marseille University (M.D., B.G., P.P., K.N., R.B., F.M.), INSERM; Département de Génétique Médicale (C.C., L.G., C.V., K.B., K.N., R.B.), and Centre de Ressources Biologiques (K.B.), AP-HM, Hôpital d'enfants de la Timone, Marseille, France
| | - Chaix Charlene
- From the Aix Marseille University (M.D., B.G., P.P., K.N., R.B., F.M.), INSERM; Département de Génétique Médicale (C.C., L.G., C.V., K.B., K.N., R.B.), and Centre de Ressources Biologiques (K.B.), AP-HM, Hôpital d'enfants de la Timone, Marseille, France
| | - Laurene Gerard
- From the Aix Marseille University (M.D., B.G., P.P., K.N., R.B., F.M.), INSERM; Département de Génétique Médicale (C.C., L.G., C.V., K.B., K.N., R.B.), and Centre de Ressources Biologiques (K.B.), AP-HM, Hôpital d'enfants de la Timone, Marseille, France
| | - Benjamin Ganne
- From the Aix Marseille University (M.D., B.G., P.P., K.N., R.B., F.M.), INSERM; Département de Génétique Médicale (C.C., L.G., C.V., K.B., K.N., R.B.), and Centre de Ressources Biologiques (K.B.), AP-HM, Hôpital d'enfants de la Timone, Marseille, France
| | - Pierre Perrin
- From the Aix Marseille University (M.D., B.G., P.P., K.N., R.B., F.M.), INSERM; Département de Génétique Médicale (C.C., L.G., C.V., K.B., K.N., R.B.), and Centre de Ressources Biologiques (K.B.), AP-HM, Hôpital d'enfants de la Timone, Marseille, France
| | - Catherine Vovan
- From the Aix Marseille University (M.D., B.G., P.P., K.N., R.B., F.M.), INSERM; Département de Génétique Médicale (C.C., L.G., C.V., K.B., K.N., R.B.), and Centre de Ressources Biologiques (K.B.), AP-HM, Hôpital d'enfants de la Timone, Marseille, France
| | - Karine Bertaux
- From the Aix Marseille University (M.D., B.G., P.P., K.N., R.B., F.M.), INSERM; Département de Génétique Médicale (C.C., L.G., C.V., K.B., K.N., R.B.), and Centre de Ressources Biologiques (K.B.), AP-HM, Hôpital d'enfants de la Timone, Marseille, France
| | - Karine Nguyen
- From the Aix Marseille University (M.D., B.G., P.P., K.N., R.B., F.M.), INSERM; Département de Génétique Médicale (C.C., L.G., C.V., K.B., K.N., R.B.), and Centre de Ressources Biologiques (K.B.), AP-HM, Hôpital d'enfants de la Timone, Marseille, France
| | - Rafaëlle Bernard
- From the Aix Marseille University (M.D., B.G., P.P., K.N., R.B., F.M.), INSERM; Département de Génétique Médicale (C.C., L.G., C.V., K.B., K.N., R.B.), and Centre de Ressources Biologiques (K.B.), AP-HM, Hôpital d'enfants de la Timone, Marseille, France
| | - Frederique Magdinier
- From the Aix Marseille University (M.D., B.G., P.P., K.N., R.B., F.M.), INSERM; Département de Génétique Médicale (C.C., L.G., C.V., K.B., K.N., R.B.), and Centre de Ressources Biologiques (K.B.), AP-HM, Hôpital d'enfants de la Timone, Marseille, France
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27
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Jourdain J, Barasc H, Faraut T, Calgaro A, Bonnet N, Marcuzzo C, Suin A, Barbat A, Hozé C, Besnard F, Taussat S, Grohs C, Kuchly C, Iampietro C, Donnadieu C, Pinton A, Boichard D, Capitan A. Large-scale detection and characterization of interchromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets. Genome Res 2023; 33:957-971. [PMID: 37414574 PMCID: PMC10519396 DOI: 10.1101/gr.277787.123] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/19/2023] [Indexed: 07/08/2023]
Abstract
In this paper, we developed a highly sensitive approach to detect interchromosomal rearrangements in cattle by searching for abnormal linkage disequilibrium patterns between markers located on different chromosomes in large paternal half-sib families genotyped as part of routine genomic evaluations. We screened 5571 families of artificial insemination sires from 15 breeds and revealed 13 putative interchromosomal rearrangements, 12 of which were validated by cytogenetic analysis and long-read sequencing. These consisted of one Robertsonian fusion, 10 reciprocal translocations, and the first case of insertional translocation reported in cattle. Taking advantage of the wealth of data available in cattle, we performed a series of complementary analyses to define the exact nature of these rearrangements, investigate their origins, and search for factors that may have favored their occurrence. We also evaluated the risks to the livestock industry and showed significant negative effects on several traits in the sires and in their balanced or aneuploid progeny compared with wild-type controls. Thus, we present the most comprehensive and thorough screen for interchromosomal rearrangements compatible with normal spermatogenesis in livestock species. This approach is readily applicable to any population that benefits from large genotype data sets, and will have direct applications in animal breeding. Finally, it also offers interesting prospects for basic research by allowing the detection of smaller and rarer types of chromosomal rearrangements than GTG banding, which are interesting models for studying gene regulation and the organization of genome structure.
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Affiliation(s)
- Jeanlin Jourdain
- Eliance, 75012 Paris, France;
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, G2B, 78350 Jouy-en-Josas, France
| | - Harmonie Barasc
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31320 Castanet-Tolosan, France
| | - Thomas Faraut
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31320 Castanet-Tolosan, France
| | - Anne Calgaro
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31320 Castanet-Tolosan, France
| | - Nathalie Bonnet
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31320 Castanet-Tolosan, France
| | - Camille Marcuzzo
- INRAE, US 1426, GeT-PlaGe, Genotoul, France Génomique, Université Fédérale de Toulouse, 31320 Castanet-Tolosan, France
| | - Amandine Suin
- INRAE, US 1426, GeT-PlaGe, Genotoul, France Génomique, Université Fédérale de Toulouse, 31320 Castanet-Tolosan, France
| | - Anne Barbat
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, G2B, 78350 Jouy-en-Josas, France
| | - Chris Hozé
- Eliance, 75012 Paris, France
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, G2B, 78350 Jouy-en-Josas, France
| | - Florian Besnard
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, G2B, 78350 Jouy-en-Josas, France
- Idele, 75012 Paris, France
| | - Sébastien Taussat
- Eliance, 75012 Paris, France
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, G2B, 78350 Jouy-en-Josas, France
| | - Cécile Grohs
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, G2B, 78350 Jouy-en-Josas, France
| | - Claire Kuchly
- INRAE, US 1426, GeT-PlaGe, Genotoul, France Génomique, Université Fédérale de Toulouse, 31320 Castanet-Tolosan, France
| | - Carole Iampietro
- INRAE, US 1426, GeT-PlaGe, Genotoul, France Génomique, Université Fédérale de Toulouse, 31320 Castanet-Tolosan, France
| | - Cécile Donnadieu
- INRAE, US 1426, GeT-PlaGe, Genotoul, France Génomique, Université Fédérale de Toulouse, 31320 Castanet-Tolosan, France
| | - Alain Pinton
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31320 Castanet-Tolosan, France
| | - Didier Boichard
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, G2B, 78350 Jouy-en-Josas, France
| | - Aurélien Capitan
- Eliance, 75012 Paris, France;
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, G2B, 78350 Jouy-en-Josas, France
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28
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Comaills V, Castellano-Pozo M. Chromosomal Instability in Genome Evolution: From Cancer to Macroevolution. BIOLOGY 2023; 12:biology12050671. [PMID: 37237485 DOI: 10.3390/biology12050671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023]
Abstract
The integrity of the genome is crucial for the survival of all living organisms. However, genomes need to adapt to survive certain pressures, and for this purpose use several mechanisms to diversify. Chromosomal instability (CIN) is one of the main mechanisms leading to the creation of genomic heterogeneity by altering the number of chromosomes and changing their structures. In this review, we will discuss the different chromosomal patterns and changes observed in speciation, in evolutional biology as well as during tumor progression. By nature, the human genome shows an induction of diversity during gametogenesis but as well during tumorigenesis that can conclude in drastic changes such as the whole genome doubling to more discrete changes as the complex chromosomal rearrangement chromothripsis. More importantly, changes observed during speciation are strikingly similar to the genomic evolution observed during tumor progression and resistance to therapy. The different origins of CIN will be treated as the importance of double-strand breaks (DSBs) or the consequences of micronuclei. We will also explain the mechanisms behind the controlled DSBs, and recombination of homologous chromosomes observed during meiosis, to explain how errors lead to similar patterns observed during tumorigenesis. Then, we will also list several diseases associated with CIN, resulting in fertility issues, miscarriage, rare genetic diseases, and cancer. Understanding better chromosomal instability as a whole is primordial for the understanding of mechanisms leading to tumor progression.
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Affiliation(s)
- Valentine Comaills
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, University of Pablo de Olavide-University of Seville-CSIC, Junta de Andalucía, 41092 Seville, Spain
| | - Maikel Castellano-Pozo
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, University of Pablo de Olavide-University of Seville-CSIC, Junta de Andalucía, 41092 Seville, Spain
- Genetic Department, Faculty of Biology, University of Seville, 41080 Seville, Spain
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29
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Shi S, Huang P, Yan R, Li R. Identification of complex and cryptic chromosomal rearrangements by optical genome mapping. Mol Cytogenet 2023; 16:5. [PMID: 37101225 PMCID: PMC10134526 DOI: 10.1186/s13039-023-00636-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 04/12/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND Optical genome mapping (OGM) has developed into a highly promising method for detecting structural variants (SVs) in human genomes. Complex chromosomal rearrangements (CCRs) and cryptic translocations are rare events that are considered difficult to detect by routine cytogenetic methods. In this study, OGM was applied to delineate the precise chromosomal rearrangements in three cases with uncertain or unconfirmed CCRs detected by conventional karyotyping and one case with a cryptic translocation suggested by fetal chromosomal microarray analysis (CMA). RESULTS In the three cases with CCRs, OGM not only confirmed or revised the original karyotyping results but also refined the precise chromosomal structures. In the case with a suspected translocation not detected by karyotyping, OGM efficiently identified the cryptic translocation and defined the genomic breakpoints with relatively high accuracy. CONCLUSIONS Our study confirmed OGM as a robust alternative approach to karyotyping for the detection of chromosomal structural rearrangements, including CCRs and cryptic translocations.
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Affiliation(s)
- Shanshan Shi
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Jinan University, No. 613 Huangpu West Road, Guangzhou, 510630, People's Republic of China
| | - Peizhi Huang
- Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Ruiling Yan
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Jinan University, No. 613 Huangpu West Road, Guangzhou, 510630, People's Republic of China.
| | - Ruiman Li
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Jinan University, No. 613 Huangpu West Road, Guangzhou, 510630, People's Republic of China.
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30
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Steensma MJ, Lee YL, Bouwman AC, Pita Barros C, Derks MFL, Bink MCAM, Harlizius B, Huisman AE, Crooijmans RPMA, Groenen MAM, Mulder HA, Rochus CM. Identification and characterisation of de novo germline structural variants in two commercial pig lines using trio-based whole genome sequencing. BMC Genomics 2023; 24:208. [PMID: 37072725 PMCID: PMC10114323 DOI: 10.1186/s12864-023-09296-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 04/04/2023] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND De novo mutations arising in the germline are a source of genetic variation and their discovery broadens our understanding of genetic disorders and evolutionary patterns. Although the number of de novo single nucleotide variants (dnSNVs) has been studied in a number of species, relatively little is known about the occurrence of de novo structural variants (dnSVs). In this study, we investigated 37 deeply sequenced pig trios from two commercial lines to identify dnSVs present in the offspring. The identified dnSVs were characterised by identifying their parent of origin, their functional annotations and characterizing sequence homology at the breakpoints. RESULTS We identified four swine germline dnSVs, all located in intronic regions of protein-coding genes. Our conservative, first estimate of the swine germline dnSV rate is 0.108 (95% CI 0.038-0.255) per generation (one dnSV per nine offspring), detected using short-read sequencing. Two detected dnSVs are clusters of mutations. Mutation cluster 1 contains a de novo duplication, a dnSNV and a de novo deletion. Mutation cluster 2 contains a de novo deletion and three de novo duplications, of which one is inverted. Mutation cluster 2 is 25 kb in size, whereas mutation cluster 1 (197 bp) and the other two individual dnSVs (64 and 573 bp) are smaller. Only mutation cluster 2 could be phased and is located on the paternal haplotype. Mutation cluster 2 originates from both micro-homology as well as non-homology mutation mechanisms, where mutation cluster 1 and the other two dnSVs are caused by mutation mechanisms lacking sequence homology. The 64 bp deletion and mutation cluster 1 were validated through PCR. Lastly, the 64 bp deletion and the 573 bp duplication were validated in sequenced offspring of probands with three generations of sequence data. CONCLUSIONS Our estimate of 0.108 dnSVs per generation in the swine germline is conservative, due to our small sample size and restricted possibilities of dnSV detection from short-read sequencing. The current study highlights the complexity of dnSVs and shows the potential of breeding programs for pigs and livestock species in general, to provide a suitable population structure for identification and characterisation of dnSVs.
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Affiliation(s)
- Marije J Steensma
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, Wageningen, 6700 AH, the Netherlands.
| | - Y L Lee
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, Wageningen, 6700 AH, the Netherlands
| | - A C Bouwman
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, Wageningen, 6700 AH, the Netherlands
| | - C Pita Barros
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, Wageningen, 6700 AH, the Netherlands
| | - M F L Derks
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, Wageningen, 6700 AH, the Netherlands
- Topigs Norsvin Research Center, Schoenaker 6, Beuningen, 6641 SZ, the Netherlands
| | - M C A M Bink
- Hendrix Genetics, P.O. Box 114, Boxmeer, 5830 AC, the Netherlands
| | - B Harlizius
- Topigs Norsvin Research Center, Schoenaker 6, Beuningen, 6641 SZ, the Netherlands
| | - A E Huisman
- Hendrix Genetics, P.O. Box 114, Boxmeer, 5830 AC, the Netherlands
| | - R P M A Crooijmans
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, Wageningen, 6700 AH, the Netherlands
| | - M A M Groenen
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, Wageningen, 6700 AH, the Netherlands
| | - H A Mulder
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, Wageningen, 6700 AH, the Netherlands
| | - C M Rochus
- University of Guelph, Centre for Genetic Improvement of Livestock, 50 Stone Rd E, Guelph, O N, N1G 2W1, Canada
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31
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Zheng W, He Y, Guo Y, Yue T, Zhang H, Li J, Zhou B, Zeng X, Li L, Wang B, Cao J, Chen L, Li C, Li H, Cui C, Bai C, Qi X, Su B. Large-scale genome sequencing redefines the genetic footprints of high-altitude adaptation in Tibetans. Genome Biol 2023; 24:73. [PMID: 37055782 PMCID: PMC10099689 DOI: 10.1186/s13059-023-02912-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/29/2023] [Indexed: 04/15/2023] Open
Abstract
BACKGROUND Tibetans are genetically adapted to high-altitude environments. Though many studies have been conducted, the genetic basis of the adaptation remains elusive due to the poor reproducibility for detecting selective signatures in the Tibetan genomes. RESULTS Here, we present whole-genome sequencing (WGS) data of 1001 indigenous Tibetans, covering the major populated areas of the Qinghai-Tibetan Plateau in China. We identify 35 million variants, and more than one-third of them are novel variants. Utilizing the large-scale WGS data, we construct a comprehensive map of allele frequency and linkage disequilibrium and provide a population-specific genome reference panel, referred to as 1KTGP. Moreover, with the use of a combined approach, we redefine the signatures of Darwinian-positive selection in the Tibetan genomes, and we characterize a high-confidence list of 4320 variants and 192 genes that have undergone selection in Tibetans. In particular, we discover four new genes, TMEM132C, ATP13A3, SANBR, and KHDRBS2, with strong signals of selection, and they may account for the adaptation of cardio-pulmonary functions in Tibetans. Functional annotation and enrichment analysis indicate that the 192 genes with selective signatures are likely involved in multiple organs and physiological systems, suggesting polygenic and pleiotropic effects. CONCLUSIONS Overall, the large-scale Tibetan WGS data and the identified adaptive variants/genes can serve as a valuable resource for future genetic and medical studies of high-altitude populations.
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Affiliation(s)
- Wangshan Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Yaoxi He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Yongbo Guo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Tian Yue
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Hui Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Jun Li
- Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang Hospital, Lhasa, 850000, China
| | - Bin Zhou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Xuerui Zeng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Liya Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Bin Wang
- Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang Hospital, Lhasa, 850000, China
| | - Jingxin Cao
- Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang Hospital, Lhasa, 850000, China
| | - Li Chen
- Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang Hospital, Lhasa, 850000, China
| | - Chunxia Li
- Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang Hospital, Lhasa, 850000, China
| | - Hongyan Li
- Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang Hospital, Lhasa, 850000, China
| | - Chaoying Cui
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa, 850000, China
| | - Caijuan Bai
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa, 850000, China
| | - Xuebin Qi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
- Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang Hospital, Lhasa, 850000, China.
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
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32
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Kosik P, Skorvaga M, Belyaev I. Preleukemic Fusion Genes Induced via Ionizing Radiation. Int J Mol Sci 2023; 24:ijms24076580. [PMID: 37047553 PMCID: PMC10095576 DOI: 10.3390/ijms24076580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 04/05/2023] Open
Abstract
Although the prevalence of leukemia is increasing, the agents responsible for this increase are not definitely known. While ionizing radiation (IR) was classified as a group one carcinogen by the IARC, the IR-induced cancers, including leukemia, are indistinguishable from those that are caused by other factors, so the risk estimation relies on epidemiological data. Several epidemiological studies on atomic bomb survivors and persons undergoing IR exposure during medical investigations or radiotherapy showed an association between radiation and leukemia. IR is also known to induce chromosomal translocations. Specific chromosomal translocations resulting in preleukemic fusion genes (PFGs) are generally accepted to be the first hit in the onset of many leukemias. Several studies indicated that incidence of PFGs in healthy newborns is up to 100-times higher than childhood leukemia with the same chromosomal aberrations. Because of this fact, it has been suggested that PFGs are not able to induce leukemia alone, but secondary mutations are necessary. PFGs also have to occur in specific cell populations of hematopoetic stem cells with higher leukemogenic potential. In this review, we describe the connection between IR, PFGs, and cancer, focusing on recurrent PFGs where an association with IR has been established.
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Affiliation(s)
- Pavol Kosik
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia
| | - Milan Skorvaga
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia
| | - Igor Belyaev
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia
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33
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Wang G, Vasquez KM. Dynamic alternative DNA structures in biology and disease. Nat Rev Genet 2023; 24:211-234. [PMID: 36316397 DOI: 10.1038/s41576-022-00539-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2022] [Indexed: 11/06/2022]
Abstract
Repetitive elements in the human genome, once considered 'junk DNA', are now known to adopt more than a dozen alternative (that is, non-B) DNA structures, such as self-annealed hairpins, left-handed Z-DNA, three-stranded triplexes (H-DNA) or four-stranded guanine quadruplex structures (G4 DNA). These dynamic conformations can act as functional genomic elements involved in DNA replication and transcription, chromatin organization and genome stability. In addition, recent studies have revealed a role for these alternative structures in triggering error-generating DNA repair processes, thereby actively enabling genome plasticity. As a driving force for genetic variation, non-B DNA structures thus contribute to both disease aetiology and evolution.
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Affiliation(s)
- Guliang Wang
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Paediatric Research Institute, Austin, TX, USA
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Paediatric Research Institute, Austin, TX, USA.
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34
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Chen D, Liang Y, Wang H, Wang H, Su F, Zhang P, Wang S, Liu W, Li Z. CRISPR-Cas-Driven Single Micromotor (Cas-DSM) Enables Direct Detection of Nucleic Acid Biomarkers at the Single-Molecule Level. Anal Chem 2023; 95:5729-5737. [PMID: 36944919 DOI: 10.1021/acs.analchem.2c05767] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
The target-dependent endonuclease activity (also known as the trans-cleavage activity) of CRISPR-Cas systems has stimulated great interest in the development of nascent sensing strategies for nucleic acid diagnostics. Despite many attempts, the majority of the sensitive CRISPR-Cas diagnostics strategies mainly rely on nucleic acid preamplification, which generally needs complex probes/primers designs, multiple experimental steps, and a longer testing time, as well as introducing the risk of false-positive results. In this work, we propose the CRISPR-Cas-Driven Single Micromotor (Cas-DSM), which can directly detect the nucleic acid targets at a single-molecule level with high specificity. We have demonstrated that the Cas-DSM is a reliable and practical method for the quantitative detection of DNA/RNA in various complex clinical samples as well as in individual cells without any preamplification processes. Due to the excellent features of the CRISPR/Cas system, including constant temperature, simple design, high specificity, and flexible programmability, the Cas-DSM could serve as a simple and universal platform for nucleic acid detection. More importantly, this work will provide a breakthrough for the development of next-generation amplification-free CRISPR/Cas sensing toolboxes.
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Affiliation(s)
- Desheng Chen
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Yuanwen Liang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Honghong Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Hui Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Fengxia Su
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Pengbo Zhang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Shuhui Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Weiliang Liu
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Zhengping Li
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
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35
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Stricker E, Peckham-Gregory EC, Scheurer ME. HERVs and Cancer-A Comprehensive Review of the Relationship of Human Endogenous Retroviruses and Human Cancers. Biomedicines 2023; 11:936. [PMID: 36979914 PMCID: PMC10046157 DOI: 10.3390/biomedicines11030936] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/03/2023] [Accepted: 03/10/2023] [Indexed: 03/30/2023] Open
Abstract
Genomic instability and genetic mutations can lead to exhibition of several cancer hallmarks in affected cells such as sustained proliferative signaling, evasion of growth suppression, activated invasion, deregulation of cellular energetics, and avoidance of immune destruction. Similar biological changes have been observed to be a result of pathogenic viruses and, in some cases, have been linked to virus-induced cancers. Human endogenous retroviruses (HERVs), once external pathogens, now occupy more than 8% of the human genome, representing the merge of genomic and external factors. In this review, we outline all reported effects of HERVs on cancer development and discuss the HERV targets most suitable for cancer treatments as well as ongoing clinical trials for HERV-targeting drugs. We reviewed all currently available reports of the effects of HERVs on human cancers including solid tumors, lymphomas, and leukemias. Our review highlights the central roles of HERV genes, such as gag, env, pol, np9, and rec in immune regulation, checkpoint blockade, cell differentiation, cell fusion, proliferation, metastasis, and cell transformation. In addition, we summarize the involvement of HERV long terminal repeat (LTR) regions in transcriptional regulation, creation of fusion proteins, expression of long non-coding RNAs (lncRNAs), and promotion of genome instability through recombination.
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Affiliation(s)
- Erik Stricker
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77047, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77047, USA
| | | | - Michael E. Scheurer
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77047, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77047, USA
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36
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Tamura T, Shimojima Yamamoto K, Imaizumi T, Yamamoto H, Miyamoto Y, Yagasaki H, Morioka I, Kanno H, Yamamoto T. Breakpoint analysis for cytogenetically balanced translocation revealed unexpected complex structural abnormalities and suggested the position effect for MEF2C. Am J Med Genet A 2023; 191:1632-1638. [PMID: 36916329 DOI: 10.1002/ajmg.a.63182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/27/2023] [Accepted: 03/02/2023] [Indexed: 03/15/2023]
Abstract
Many disease-causing genes have been identified by determining the breakpoints of balanced chromosomal translocations. Recent progress in genomic analysis has accelerated the analysis of chromosomal translocation-breakpoints at the nucleotide level. Using a long-read whole-genome sequence, we analyzed the breakpoints of the cytogenetically balanced chromosomal translocation t(5;15)(q21;26.3), which was confirmed to be of de novo origin, in a patient with a neurodevelopmental disorder. The results showed complex rearrangements with seven fragments consisting of five breakpoint-junctions (BJs). Four of the five BJs showed microhomologies of 1-3-bp, and only one BJ displayed a signature of blunt-end ligation, indicating chromothripsis as the underlying mechanism. Although the BJs did not disrupt any disease-causing gene, the clinical features of the patient were compatible with MEF2C haploinsufficiency syndrome. Complex rearrangements were located approximately 2.5-Mb downstream of MEF2C. Therefore, position effects were considered the mechanism of the occurrence of MEF2C haploinsufficiency syndrome.
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Affiliation(s)
- Takeaki Tamura
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan.,Division of Gene Medicine, Graduate School of Medical Science, Tokyo Women's Medical University, Tokyo, Japan.,Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan
| | - Keiko Shimojima Yamamoto
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan.,Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Taichi Imaizumi
- Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Hisako Yamamoto
- Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Yusaku Miyamoto
- Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Hiroshi Yagasaki
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
| | - Ichiro Morioka
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
| | - Hitoshi Kanno
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan.,Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Toshiyuki Yamamoto
- Division of Gene Medicine, Graduate School of Medical Science, Tokyo Women's Medical University, Tokyo, Japan.,Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
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37
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Burssed B, Zamariolli M, Favilla BP, Meloni VA, Goloni-Bertollo EM, Bellucco FT, Melaragno MI. Fold-back mechanism originating inv-dup-del rearrangements in chromosomes 13 and 15. Chromosome Res 2023; 31:10. [PMID: 36826604 DOI: 10.1007/s10577-023-09720-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/09/2023] [Accepted: 02/09/2023] [Indexed: 02/25/2023]
Abstract
Intrachromosomal rearrangements involve a single chromosome and can be formed by several proposed mechanisms. We reported two patients with intrachromosomal duplications and deletions, whose rearrangements and breakpoints were characterized through karyotyping, chromosomal microarray, fluorescence in situ hybridization, whole-genome sequencing, and Sanger sequencing. Inverted duplications associated with terminal deletions, known as inv-dup-del rearrangements, were found in 13q and 15q in these patients. The presence of microhomology at the junction points led to the proposal of the Fold-back mechanism for their formation. The use of different high-resolution techniques allowed for a better characterization of the rearrangements, with Sanger sequencing of the junction points being essential to infer the mechanisms of formation as it revealed microhomologies that were missed by the previous techniques. A karyotype-phenotype correlation was also performed for the characterized rearrangements.
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Affiliation(s)
- Bruna Burssed
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Malú Zamariolli
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Bianca Pereira Favilla
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Vera Ayres Meloni
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Eny Maria Goloni-Bertollo
- Genetics and Molecular Biology Research Unit, Department of Molecular Biology, São José Do Rio Preto Medical School, São José Do Rio Preto, Brazil
| | - Fernanda Teixeira Bellucco
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Maria Isabel Melaragno
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil.
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38
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Leffler M, Christie L, Hackett A, Bennetts B, Goel H, Amor DJ, Peters GB, Field M, Dudding-Byth T. Further delineation of dosage-sensitive K/L mediated Xq28 duplication syndrome includes incomplete penetrance. Clin Genet 2023; 103:681-687. [PMID: 36688272 DOI: 10.1111/cge.14303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/07/2023] [Accepted: 01/17/2023] [Indexed: 01/24/2023]
Abstract
The low copy tandem repeat area at Xq28 is prone to recurrent copy number gains, including the K/L mediated duplications of 300 kb size (herein described as the K/L mediated Xq28 duplication syndrome). We describe five families, including nine males with K/L mediated Xq28 duplications, some with regions of greater copy number variation (CNV). We summarise findings in 25 affected males reported to date. Within the five families, males were variably affected by seizures, intellectual disability, and neurological features; however, one male with a familial K/L mediated Xq28 duplication has normal intelligence, suggesting that this CNV is not 100% penetrant. Including our five families, 13 carrier females have been identified, with nine presenting phenotypically normal. Three carrier females reported mild learning difficulties, and all of them had duplications containing regions with at least four copies. Delineation of the spectrum of K/L mediated Xq28 duplication syndrome highlights GDI1 as the most likely candidate gene contributing to the phenotype. For patients identified with CNVs in this region, high-resolution microarray is required to define copy number gains and provide families with accurate information.
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Affiliation(s)
- Melanie Leffler
- NSW Genetics of Learning Disability (GOLD) Service, Hunter New England Local Health District, Waratah, New South Wales, Australia
| | - Louise Christie
- NSW Genetics of Learning Disability (GOLD) Service, Hunter New England Local Health District, Waratah, New South Wales, Australia
| | - Anna Hackett
- NSW Genetics of Learning Disability (GOLD) Service, Hunter New England Local Health District, Waratah, New South Wales, Australia
| | - Bruce Bennetts
- Department of Molecular Genetics, Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, New South Wales, Australia.,Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Himanshu Goel
- Hunter Genetics, Hunter New England Local Health District, Waratah, New South Wales, Australia.,University of Newcastle, Callaghan, New South Wales, Australia
| | - David J Amor
- Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia.,Department of Paediatrics, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Greg B Peters
- Formerly of Sydney Genome Diagnostics, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Michael Field
- NSW Genetics of Learning Disability (GOLD) Service, Hunter New England Local Health District, Waratah, New South Wales, Australia
| | - Tracy Dudding-Byth
- NSW Genetics of Learning Disability (GOLD) Service, Hunter New England Local Health District, Waratah, New South Wales, Australia.,Hunter Genetics, Hunter New England Local Health District, Waratah, New South Wales, Australia.,University of Newcastle, Callaghan, New South Wales, Australia
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39
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Kweon J, Hwang HY, Ryu H, Jang AH, Kim D, Kim Y. Targeted genomic translocations and inversions generated using a paired prime editing strategy. Mol Ther 2023; 31:249-259. [PMID: 36114670 PMCID: PMC9840113 DOI: 10.1016/j.ymthe.2022.09.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 09/12/2022] [Accepted: 09/12/2022] [Indexed: 01/26/2023] Open
Abstract
A variety of cancers have been found to have chromosomal rearrangements, and the genomic abnormalities often induced expression of fusion oncogenes. To date, a pair of engineered nucleases including ZFNs, TALENs, and CRISPR-Cas9 nucleases have been used to generate chromosomal rearrangement in living cells and organisms for disease modeling. However, these methods induce unwanted indel mutations at the DNA break junctions, resulting in incomplete disease modeling. Here, we developed prime editor nuclease-mediated translocation and inversion (PETI), a method for programmable chromosomal translocation and inversion using prime editor 2 nuclease (PE2 nuclease) and paired pegRNA. Using PETI method, we successfully introduced DNA recombination in episomal fluorescence reporters as well as precise chromosomal translocations in human cells. We applied PETI to create cancer-associated translocations and inversions such as NPM1-ALK and EML4-ALK in human cells. Our findings show that PETI generated chromosomal translocation and inversion in a programmable manner with efficiencies comparable of Cas9. PETI methods, we believe, could be used to create disease models or for gene therapy.
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Affiliation(s)
- Jiyeon Kweon
- Department of Biomedical Sciences, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea; Stem Cell Immunomodulation Research Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Hye-Yeon Hwang
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Haesun Ryu
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - An-Hee Jang
- Department of Biomedical Sciences, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea; Stem Cell Immunomodulation Research Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Daesik Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea.
| | - Yongsub Kim
- Department of Biomedical Sciences, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea; Stem Cell Immunomodulation Research Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea.
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40
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Xia Q, Li S, Ding T, Liu Z, Liu J, Li Y, Zhu H, Yao Z. Nanopore sequencing for detecting reciprocal translocation carrier status in preimplantation genetic testing. BMC Genomics 2023; 24:1. [PMID: 36593441 PMCID: PMC9809107 DOI: 10.1186/s12864-022-09103-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Balanced reciprocal translocation (BRT) is one of the most common chromosomal abnormalities that causes infertility, recurrent miscarriage, and birth defects. Preimplantation genetic testing (PGT) is widely used to select euploid embryos for BRT carriers to increase the chance of a healthy live birth. Several strategies can be used to distinguish reciprocal translocation carrier embryos from those with a normal karyotype; however, these techniques are time-consuming and difficult to implement in clinical laboratories. In this study, nanopore sequencing was performed in two reciprocal translocation carriers, and the results were validated using the next-generation sequencing-based method named, "Mapping Allele with Resolved Carrier Status" (MaReCs). RESULTS The translocation breakpoints in both reciprocal translocation carriers were accurately identified by nanopore sequencing and were in accordance with the results obtained using MaReCs. More than one euploid non-balanced translocation carrier embryo was identified in both patients. Amniocentesis results revealed normal karyotypes, consistent with the findings by MaReCs and nanopore sequencing. CONCLUSION Our results suggest that nanopore sequencing is a powerful strategy for accurately distinguishing non-translocation embryos from translocation carrier embryos and precisely localizing translocation breakpoints, which is essential for PGT and aids in reducing the propagation of reciprocal translocation in the population.
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Affiliation(s)
- Qiuping Xia
- grid.216417.70000 0001 0379 7164Reproductive Medicine Center, Xiangya Hospital, Central South University, 410008 Changsha, Hunan China
| | - Shenglan Li
- grid.216417.70000 0001 0379 7164Department of Gastroenterology, Xiangya Hospital, Central South University, 410008 Changsha, Hunan China
| | - Taoli Ding
- Yikon Genomics Co., Ltd, 215000 Suzhou, Jiangsu China
| | - Zhen Liu
- Yikon Genomics Co., Ltd, 215000 Suzhou, Jiangsu China
| | - Jiaqi Liu
- Yikon Genomics Co., Ltd, 215000 Suzhou, Jiangsu China
| | - Yanping Li
- grid.216417.70000 0001 0379 7164Reproductive Medicine Center, Xiangya Hospital, Central South University, 410008 Changsha, Hunan China
| | - Huimin Zhu
- grid.216417.70000 0001 0379 7164Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, 410008 Changsha, Hunan China
| | - Zhongyuan Yao
- grid.216417.70000 0001 0379 7164Reproductive Medicine Center, Xiangya Hospital, Central South University, 410008 Changsha, Hunan China
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41
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Guo W, Comai L, Henry IM. Chromoanagenesis in plants: triggers, mechanisms, and potential impact. Trends Genet 2023; 39:34-45. [PMID: 36055901 DOI: 10.1016/j.tig.2022.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/30/2022]
Abstract
Chromoanagenesis is a single catastrophic event that involves, in most cases, localized chromosomal shattering and reorganization, resulting in a dramatically restructured chromosome. First discovered in cancer cells, it has since been observed in various other systems, including plants. In this review, we discuss the origin, characteristics, and potential mechanisms underlying chromoanagenesis in plants. We report that multiple processes, including mutagenesis and genetic engineering, can trigger chromoanagenesis via a variety of mechanisms such as micronucleation, breakage-fusion-bridge (BFB) cycles, or chain-like translocations. The resulting rearranged chromosomes can be preserved during subsequent plant growth, and sometimes inherited to the next generation. Because of their high tolerance to genome restructuring, plants offer a unique system for investigating the evolutionary consequences and potential practical applications of chromoanagenesis.
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Affiliation(s)
- Weier Guo
- Genome Center and Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA
| | - Luca Comai
- Genome Center and Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA
| | - Isabelle M Henry
- Genome Center and Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA.
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42
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Tamura T, Yamamoto Shimojima K, Okamoto N, Yagasaki H, Morioka I, Kanno H, Minakuchi Y, Toyoda A, Yamamoto T. Long-read sequence analysis for clustered genomic copy number aberrations revealed architectures of intricately intertwined rearrangements. Am J Med Genet A 2023; 191:112-119. [PMID: 36282026 DOI: 10.1002/ajmg.a.62997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 07/13/2022] [Accepted: 08/24/2022] [Indexed: 12/14/2022]
Abstract
Most chromosomal aberrations revealed by chromosomal microarray testing (CMA) are simple; however, very complex chromosomal structural rearrangements can also be found. Although the mechanism of structural rearrangements has been gradually revealed, not all mechanisms have been elucidated. We analyzed the breakpoint-junctions (BJs) of two or more clustered copy number variations (CNVs) in the same chromosome arms to understand their conformation and the mechanism of complex structural rearrangements. Combining CMA with long-read whole-genome sequencing (WGS) analysis, we successfully determined all BJs for the clustered CNVs identified in four patients. Multiple CNVs were intricately intertwined with each other, and clustered CNVs in four patients were involved in global complex chromosomal rearrangements. The BJs of two clustered deletions identified in two patients showed microhomologies, and their characteristics were explained by chromothripsis. In contrast, the BJs in the other two patients, who showed clustered deletions and duplications, consisted of blunt-end and nontemplated insertions. These findings could be explained only by alternative nonhomologous end-joining, a mechanism related to polymerase theta. All the patients had at least one inverted segment. Three patients showed cryptic aberrations involving a disruption and a deletion/duplication, which were not detected by CMA but were first identified by WGS. This result suggested that complex rearrangements should be considered if clustered CNVs are observed in the same chromosome arms. Because CMA has potential limitations in genotype-phenotype correlation analysis, a more detailed analysis by whole genome examination is recommended in cases of suspected complex structural aberrations.
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Affiliation(s)
- Takeaki Tamura
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan.,Division of Gene Medicine, Graduate School of Medical Science, Tokyo Women's Medical University, Tokyo, Japan.,Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan
| | - Keiko Yamamoto Shimojima
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan.,Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Izumi, Japan
| | - Hiroshi Yagasaki
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
| | - Ichiro Morioka
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
| | - Hitoshi Kanno
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan.,Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Yohei Minakuchi
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Atsushi Toyoda
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Toshiyuki Yamamoto
- Division of Gene Medicine, Graduate School of Medical Science, Tokyo Women's Medical University, Tokyo, Japan.,Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
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43
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Dutta UR, Bhattacherjee A, Bahal A, Posanapally LP, Lone KA, Bathula S, Dalal A. Cytogenomic Characterization of a Novel de novo Balanced Reciprocal Translocation t(1;12) by Genome Sequencing Leading to Fusion Gene Formation of EYA3/EFCAB4b. Mol Syndromol 2022; 13:370-380. [PMID: 36588754 PMCID: PMC9801327 DOI: 10.1159/000522011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 01/17/2022] [Indexed: 01/04/2023] Open
Abstract
Introduction The accurate detection of breakpoint regions of disease-associated chromosomal rearrangements helps understand the molecular mechanisms and identify the risks involved with disrupted genes. Methods In this study, a girl with growth retardation is characterized using positional cloning and genome sequencing. The techniques include fluorescence in situ hybridization (FISH) with paint (WCP) and bacterial-artificial chromosomes (BAC) probes, PCR, real-time PCR, and short and long-read sequencing. Results The translocation was identified by GTG banding and confirmed by WCP FISH. Microarray ruled out the involvement of other copy number variations except for 6 homozygous regions which are not disease-causing variants. Fine mapping with FISH showed split signals with BAC clone RP11-312A3. Genome sequencing of short-read with an average 30× depth and long-read sequencing technology with a 3.8× coverage identified both breakpoints, confirmed by Sanger sequencing, that showed microhomology. The breakpoint at 1p and 12p regions disrupted EYA3 and EFCAB4B genes. Expression analysis of EYA3 showed a 7-fold increase, suggesting the formation of a fusion gene with EFCAB4B. EYA3 is involved in skeleton development, and EFCAB4B plays a role in calcium metabolism, which may be relevant for the patient's phenotype. Conclusion The systematic application of genome techniques to translocations and their advantages is discussed.
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Affiliation(s)
- Usha R. Dutta
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India,*Usha R Dutta,
| | - Amrita Bhattacherjee
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Ashish Bahal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Laxmi P. Posanapally
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | | | - Siddardha Bathula
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
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44
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Salzberg LI, Martos AAR, Lombardi L, Jermiin LS, Blanco A, Byrne KP, Wolfe KH. A widespread inversion polymorphism conserved among Saccharomyces species is caused by recurrent homogenization of a sporulation gene family. PLoS Genet 2022; 18:e1010525. [PMID: 36441813 PMCID: PMC9731477 DOI: 10.1371/journal.pgen.1010525] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 12/08/2022] [Accepted: 11/12/2022] [Indexed: 11/29/2022] Open
Abstract
Saccharomyces genomes are highly collinear and show relatively little structural variation, both within and between species of this yeast genus. We investigated the only common inversion polymorphism known in S. cerevisiae, which affects a 24-kb 'flip/flop' region containing 15 genes near the centromere of chromosome XIV. The region exists in two orientations, called reference (REF) and inverted (INV). Meiotic recombination in this region is suppressed in crosses between REF and INV orientation strains such as the BY x RM cross. We find that the inversion polymorphism is at least 17 million years old because it is conserved across the genus Saccharomyces. However, the REF and INV isomers are not ancient alleles but are continually being re-created by re-inversion of the region within each species. Inversion occurs due to continual homogenization of two almost identical 4-kb sequences that form an inverted repeat (IR) at the ends of the flip/flop region. The IR consists of two pairs of genes that are specifically and strongly expressed during the late stages of sporulation. We show that one of these gene pairs, YNL018C/YNL034W, codes for a protein that is essential for spore formation. YNL018C and YNL034W are the founder members of a gene family, Centroid, whose members in other Saccharomycetaceae species evolve fast, duplicate frequently, and are preferentially located close to centromeres. We tested the hypothesis that Centroid genes are a meiotic drive system, but found no support for this idea.
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Affiliation(s)
- Letal I. Salzberg
- Conway Institute, University College Dublin, Dublin, Ireland
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Alexandre A. R. Martos
- Conway Institute, University College Dublin, Dublin, Ireland
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Lisa Lombardi
- Conway Institute, University College Dublin, Dublin, Ireland
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Lars S. Jermiin
- School of Medicine, University College Dublin, Dublin, Ireland
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Earth Institute, University College Dublin, Dublin, Ireland
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Alfonso Blanco
- Conway Institute, University College Dublin, Dublin, Ireland
| | - Kevin P. Byrne
- Conway Institute, University College Dublin, Dublin, Ireland
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Kenneth H. Wolfe
- Conway Institute, University College Dublin, Dublin, Ireland
- School of Medicine, University College Dublin, Dublin, Ireland
- * E-mail:
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45
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Wang F, Zhang R, Sun X, Wang J, Liu H, Zhang K, Wang C. An intelligent recognition method of chromosome rearrangement patterns based on information entropy. Sci Rep 2022; 12:19707. [PMID: 36385139 PMCID: PMC9668828 DOI: 10.1038/s41598-022-22046-x] [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: 06/09/2022] [Accepted: 10/07/2022] [Indexed: 11/17/2022] Open
Abstract
Chromosome rearrangements play an important role in the speciation of plants and animals, and the recognition of chromosome rearrangement patterns is helpful to elucidate the mechanism of species differentiation at the chromosome level. However, the existing chromosome rearrangement recognition methods have some major limitations, such as low quality, barriers to parental selection, and inability to identify specific rearrangement patterns. Based on the whole genome protein sequences, we constructed the combined figure according to the slope of the collinear fragment, the number of homologous genes, the coordinates in the top left and bottom right of the collinear fragment. The standardized combination figure is compared with the four standard pattern figures, and then combined with the information entropy analysis strategy to automatically classify the chromosome images and identify the chromosome rearrangement pattern. This paper proposes an automatic karyotype analysis method EntroCR (intelligent recognition method of chromosome rearrangement based on information entropy), which integrates rearrangement pattern recognition, result recommendation and related chromosome determination, so as to infer the evolution process of ancestral chromosomes to the existing chromosomes. Validation experiments were conducted using whole-genome data of Gossypium raimondii and Gossypium arboreum, Oryza sativa and Sorghum bicolor. The conclusions were consistent with previous results. EntroCR provides a reference for researchers in species evolution and molecular marker assisted breeding as well as new methods for analyzing karyotype evolution in other species.
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Affiliation(s)
- Fushun Wang
- grid.274504.00000 0001 2291 4530College of Information Science and Technology, Hebei Agricultural University, Baoding, 071000 People’s Republic of China ,grid.274504.00000 0001 2291 4530Hebei Key Laboratory of Agricultural Big Data, Baoding, 071000 People’s Republic of China
| | - Ruolan Zhang
- grid.274504.00000 0001 2291 4530College of Information Science and Technology, Hebei Agricultural University, Baoding, 071000 People’s Republic of China
| | - Xiaohua Sun
- grid.484109.00000 0004 1758 9755Department of Digital Media, Hebei Software Institute, Baoding, 071000 People’s Republic of China
| | - Junhao Wang
- grid.274504.00000 0001 2291 4530College of Information Science and Technology, Hebei Agricultural University, Baoding, 071000 People’s Republic of China
| | - Hongquan Liu
- grid.274504.00000 0001 2291 4530Department of Urban and Rural Construction, Hebei Agricultural University, Baoding, 071000 People’s Republic of China
| | - Kang Zhang
- grid.274504.00000 0001 2291 4530College of Life Science, Hebei Agricultural University, Baoding, 071000 People’s Republic of China ,grid.274504.00000 0001 2291 4530State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071000 People’s Republic of China ,grid.274504.00000 0001 2291 4530Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, 071000 People’s Republic of China
| | - Chunyang Wang
- grid.274504.00000 0001 2291 4530College of Life Science, Hebei Agricultural University, Baoding, 071000 People’s Republic of China ,grid.274504.00000 0001 2291 4530State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071000 People’s Republic of China
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46
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Huang S, Huang Y, Li S, He Y. Chromosome 17 translocation affects sperm morphology: Two case studies and literature review. Andrologia 2022; 54:e14620. [PMID: 36270636 DOI: 10.1111/and.14620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/14/2022] [Accepted: 09/28/2022] [Indexed: 11/30/2022] Open
Abstract
We present two cases of infertile males with teratozoospermia stemming from chromosome 17 translocation. The patients present karyotypes that have not been previously reported. Genes located on breakpoints (17p11.2, 9q31, and 11p15) were analysed to find the probable mechanism affecting sperm morphology. Our results suggest that ALKBH5, TOP3A, and LLGL1 interactions may be an underlying cause of abnormal sperm head morphology. Translocation of chromosome 17 occurred in conjunction with chromosome 9 and chromosome 11 translocation in the two cases, resulting in oligozoospermia and asthenozoospermia, respectively. These abnormal phenotypes may involve meiosis- and motility-related genes such as LDHC, DNHD1, UBQLN3, and NUP98. Translocation is thus a risk factor for sperm morphological abnormalities and motility deficiency. The interaction network of 22 genes on breakpoints suggests that they contribute to spermatogenesis as a group. In conclusion, this study highlighted the importance of investigating genes linked to sperm morphology, together with chromosome 17 translocation and reproductive risks. For patients interested in screening before a future pregnancy, we recommend preimplantation genetic diagnosis to reduce the risk of karyotypically unbalanced foetuses and birth defects.
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Affiliation(s)
- Shan Huang
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yingting Huang
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Shan Li
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yu He
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning, China
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47
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Farley BJ, Awad ME, Anderson P, Esseili AS, Hruska J, Mostafa G, Saleh KJ. Opioid-Related Genetic Polymorphisms of Cytochrome P450 Enzymes after Total Joint Arthroplasty: A Focus on Drug-Drug-Gene Interaction with Commonly Coprescribed Medications. Orthop Clin North Am 2022; 53:361-375. [PMID: 36208880 DOI: 10.1016/j.ocl.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Pharmacogenomic testing, together with the early detection of drug-drug-gene interactions (DDGI) before initiating opioids, can improve the selection of dosage and reduce the risk of adverse drug interactions and therapeutic failures following Total Joint Arthroplasty. The variants of CYP genes can mediate DDGI. Orthopedic surgeons should become familiar with the genetic aspect of opioid use and abuse, as well as the influence of the patient genetic makeup in opioid selection and response, and polymorphic variants in pain modulation.
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Affiliation(s)
- Brendan J Farley
- FAJR Scientific, Resident Research Partnership, 9308 Hickory Ridge Rd, Suite 301, Northville, MI, 48167, USA; Department of Orthopaedic Surgery, West Virginia University, 6040 University Town Centre Dr Drive, Morgantown, WV 26501, USA
| | - Mohamed E Awad
- FAJR Scientific, Resident Research Partnership, 9308 Hickory Ridge Rd, Suite 301, Northville, MI, 48167, USA; NorthStar Anesthesia, Detroit Medical Center, 4201 St Antoine Street, Detroit, MI 48201, USA; Michigan State University College of Osteopathic Medicine, 965 Wilson Rd, East Lansing, MI 48824, USA
| | - Paige Anderson
- FAJR Scientific, Resident Research Partnership, 9308 Hickory Ridge Rd, Suite 301, Northville, MI, 48167, USA; Cedarville University, 251 N Main St, Cedarville, OH 45314, USA
| | - Ali S Esseili
- FAJR Scientific, Resident Research Partnership, 9308 Hickory Ridge Rd, Suite 301, Northville, MI, 48167, USA; University of Michigan, 4901 Evergreen Rd, Dearborn, MI 48128, USA
| | - Justin Hruska
- NorthStar Anesthesia, Detroit Medical Center, 4201 St Antoine Street, Detroit, MI 48201, USA; Department of Anesthesiology, Wayne State University- Detroit Medical Center, 4201 St Antoine Street, Detroit, MI, 48201, USA
| | - Gamal Mostafa
- Wayne State University, School of Medicine, 3990 John R St, Detroit, MI 48201, USA
| | - Khaled J Saleh
- FAJR Scientific, Resident Research Partnership, 9308 Hickory Ridge Rd, Suite 301, Northville, MI, 48167, USA; Michigan State University College of Osteopathic Medicine, 965 Wilson Rd, East Lansing, MI 48824, USA; Department of Surgery, John D. Dingell VA Medical Center, 4646 John R St, Detroit, MI 48201, USA..
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48
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Gao Z, Rice SM, Wodoslawsky S, Long SC, Wang ZX, Torkzaban M, Angarita Africano AM, Liu J, Al-Kouatly HB. A Systematic Review of Reproductive Counseling in Cases of Parental Constitutional Reciprocal Translocation (9;22) Mimicking BCR-ABL1. Front Genet 2022; 13:921910. [PMID: 35991550 PMCID: PMC9386180 DOI: 10.3389/fgene.2022.921910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 06/02/2022] [Indexed: 11/17/2022] Open
Abstract
We aim to determine the spectrum of cytogenetic abnormalities and outcomes in unbalanced offspring of asymptomatic constitutional balanced t(9;22) carriers through a systematic literature review. We also include a case of a constitutional balanced t(9;22) carrier from our institution. Among the 16 balanced t(9;22) carriers in our review, 13 were maternal and 3 were paternal. Of the 15 unbalanced translocation cases identified, 13 were live births, one was a missed abortion, and one resulted in pregnancy termination. The spectrum of established syndromes reported among the live births was the following: trisomy 9p syndrome (6/13), dual trisomy 9p and DiGeorge syndrome (3/13), dual 9q subtelomere deletion syndrome and DiGeorge syndrome (1/13), 9q subtelomere deletion syndrome (1/13), and DiGeorge syndrome (1/13). One unbalanced case did not have a reported syndrome. The phenotype of the unbalanced cases included cardiac abnormalities (5/13), neurological findings (7/13), intellectual disability (6/10), urogenital anomalies (3/13), respiratory or immune dysfunction (3/13), and facial or skeletal dysmorphias (13/13). Any constitutional balanced reciprocal t(9;22) carrier should be counseled regarding the increased risk of having a child with an unbalanced translocation, the spectrum of possible cytogenetic abnormalities, and predicted clinical phenotype for the unbalanced derivative.
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Affiliation(s)
- Zimeng Gao
- Department of Obstetrics and Gynecology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, United States
| | - Stephanie M. Rice
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, United States
| | - Sascha Wodoslawsky
- Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, United States
| | - Sara C. Long
- Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, United States
| | - Zi-Xuan Wang
- Department of Pathology, Clinical Cytogenomics, Anatomy, and Cell Biology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, United States
| | - Mehnoosh Torkzaban
- Department of Radiology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, United States
| | - Ana Milena Angarita Africano
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, United States
| | - Jinglan Liu
- Department of Pathology, Clinical Cytogenomics, Anatomy, and Cell Biology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, United States
| | - Huda B. Al-Kouatly
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, United States
- *Correspondence: Huda B. Al-Kouatly,
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49
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Ren H, Yin A, Wu P, Zhou H, Zhou J, Yu Y, Lu H. Establishment of a Cre-loxP System Based on a Leaky LAC4 Promoter and an Unstable panARS Element in Kluyveromyces marxianus. Microorganisms 2022; 10:microorganisms10061240. [PMID: 35744758 PMCID: PMC9227491 DOI: 10.3390/microorganisms10061240] [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: 05/26/2022] [Revised: 06/12/2022] [Accepted: 06/15/2022] [Indexed: 02/01/2023] Open
Abstract
The Cre-loxP system produces structural variations, such as deletion, duplication, inversion and translocation, at specific loci and induces chromosomal rearrangements in the genome. To achieve chromosomal rearrangements in Kluyveromyces marxianus, the positions and sequences of centromeres were identified in this species for the first time. Next, a Cre-loxP system was established in K. marxianus. In this system, the Cre recombinase was expressed from a leaky LAC4 promoter in a plasmid to alleviate the cytotoxicity of Cre, and the unstable plasmid contained a panARS element to facilitate the clearance of the plasmid from the cells. By using LAC4 as a reporter gene, the recombination frequencies between loxP sites or loxPsym sites were 99% and 73%, respectively. A K. marxianus strain containing 16 loxPsym sites in the genome was constructed. The recombination frequency of large-scale chromosomal rearrangements between 16 loxPsym sites was up to 38.9%. Our study provides valuable information and tools for studying chromosomal structures and functions in K. marxianus.
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Affiliation(s)
- Haiyan Ren
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China; (H.R.); (A.Y.); (P.W.); (H.Z.); (J.Z.)
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200438, China
| | - Anqi Yin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China; (H.R.); (A.Y.); (P.W.); (H.Z.); (J.Z.)
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200438, China
| | - Pingping Wu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China; (H.R.); (A.Y.); (P.W.); (H.Z.); (J.Z.)
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200438, China
| | - Huanyu Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China; (H.R.); (A.Y.); (P.W.); (H.Z.); (J.Z.)
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200438, China
| | - Jungang Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China; (H.R.); (A.Y.); (P.W.); (H.Z.); (J.Z.)
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200438, China
| | - Yao Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China; (H.R.); (A.Y.); (P.W.); (H.Z.); (J.Z.)
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200438, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
- Correspondence: (Y.Y.); (H.L.)
| | - Hong Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China; (H.R.); (A.Y.); (P.W.); (H.Z.); (J.Z.)
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200438, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Shanghai 200237, China
- Correspondence: (Y.Y.); (H.L.)
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50
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Burssed B, Zamariolli M, Bellucco FT, Melaragno MI. Mechanisms of structural chromosomal rearrangement formation. Mol Cytogenet 2022; 15:23. [PMID: 35701783 PMCID: PMC9199198 DOI: 10.1186/s13039-022-00600-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/31/2022] [Indexed: 12/31/2022] Open
Abstract
Structural chromosomal rearrangements result from different mechanisms of formation, usually related to certain genomic architectural features that may lead to genetic instability. Most of these rearrangements arise from recombination, repair, or replication mechanisms that occur after a double-strand break or the stalling/breakage of a replication fork. Here, we review the mechanisms of formation of structural rearrangements, highlighting their main features and differences. The most important mechanisms of constitutional chromosomal alterations are discussed, including Non-Allelic Homologous Recombination (NAHR), Non-Homologous End-Joining (NHEJ), Fork Stalling and Template Switching (FoSTeS), and Microhomology-Mediated Break-Induced Replication (MMBIR). Their involvement in chromoanagenesis and in the formation of complex chromosomal rearrangements, inverted duplications associated with terminal deletions, and ring chromosomes is also outlined. We reinforce the importance of high-resolution analysis to determine the DNA sequence at, and near, their breakpoints in order to infer the mechanisms of formation of structural rearrangements and to reveal how cells respond to DNA damage and repair broken ends.
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Affiliation(s)
- Bruna Burssed
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Malú Zamariolli
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Fernanda Teixeira Bellucco
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Maria Isabel Melaragno
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
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