1
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Boyle C, Lansdorp PM, Edelstein-Keshet L. Predicting the number of lifetime divisions for hematopoietic stem cells from telomere length measurements. iScience 2023; 26:107053. [PMID: 37360685 PMCID: PMC10285640 DOI: 10.1016/j.isci.2023.107053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 05/09/2023] [Accepted: 06/01/2023] [Indexed: 06/28/2023] Open
Abstract
How many times does a typical hematopoietic stem cell (HSC) divide to maintain a daily production of over 1011 blood cells over a human lifetime? It has been predicted that relatively few, slowly dividing HSCs occupy the top of the hematopoietic hierarchy. However, tracking HSCs directly is extremely challenging due to their rarity. Here, we utilize previously published data documenting the loss of telomeric DNA repeats in granulocytes, to draw inferences about HSC division rates, the timing of major changes in those rates, as well as lifetime division totals. Our method uses segmented regression to identify the best candidate representations of the telomere length data. Our method predicts that, on average, an HSC divides 56 times over an 85-year lifespan (with lower and upper bounds of 36 and 120, respectively), with half of these divisions during the first 24 years of life.
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Affiliation(s)
- Cole Boyle
- Department of Mathematics, University of British Columbia, Vancouver, BC V6T 1Z2 Canada
| | - Peter M. Lansdorp
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Leah Edelstein-Keshet
- Department of Mathematics, University of British Columbia, Vancouver, BC V6T 1Z2 Canada
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2
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Abstract
Dense local haplotypes can now readily be extracted from long-read or droplet-based sequence data. However, these methods struggle to combine subchromosomal haplotype blocks into global chromosome-length haplotypes. Strand-seq is a single cell sequencing technique that uses read orientation to capture sparse global phase information by sequencing only one of two DNA strands for each parental homolog. In combination with dense local haplotypes from other technologies, Strand-seq data can be used to obtain complete chromosome-length phase information. In this chapter, we run the R package StrandPhaseR to phase SNVs using publicly available sequence data for sample HG005 of the Genome in a Bottle project.
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Affiliation(s)
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
| | - Peter M Lansdorp
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
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3
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Akbari V, Hanlon VC, O’Neill K, Lefebvre L, Schrader KA, Lansdorp PM, Jones SJ. Parent-of-origin detection and chromosome-scale haplotyping using long-read DNA methylation sequencing and Strand-seq. Cell Genom 2022; 3:100233. [PMID: 36777186 PMCID: PMC9903809 DOI: 10.1016/j.xgen.2022.100233] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 09/08/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022]
Abstract
Hundreds of loci in human genomes have alleles that are methylated differentially according to their parent of origin. These imprinted loci generally show little variation across tissues, individuals, and populations. We show that such loci can be used to distinguish the maternal and paternal homologs for all human autosomes without the need for the parental DNA. We integrate methylation-detecting nanopore sequencing with the long-range phase information in Strand-seq data to determine the parent of origin of chromosome-length haplotypes for both DNA sequence and DNA methylation in five trios with diverse genetic backgrounds. The parent of origin was correctly inferred for all autosomes with an average mismatch error rate of 0.31% for SNVs and 1.89% for insertions or deletions (indels). Because our method can determine whether an inherited disease allele originated from the mother or the father, we predict that it will improve the diagnosis and management of many genetic diseases.
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Affiliation(s)
- Vahid Akbari
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada,Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | | | - Kieran O’Neill
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Louis Lefebvre
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Kasmintan A. Schrader
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | - Peter M. Lansdorp
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada,Corresponding author
| | - Steven J.M. Jones
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada,Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Corresponding author
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4
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Abstract
Telomeres and telomerase play a crucial role in human aging and cancer. Three "drivers" of human aging can be identified. The developmental program encoded in DNA is the primary determinant of lifespan. Faithful execution of the developmental program requires stability of the (epi-)genome which is challenged throughout life by damage to DNA as well as epigenetic 'scars' from error-free DNA repair and stochastic errors made during the establishment and maintenance of the "epigenome". Over time (epi-)mutations accumulate, compromising cellular function and causing (pre-)malignant alterations. Damage to the genome and epigenome can be considered the second "driver" of aging. A third driver of the aging process, important to suppress tumors in long-lived animals, is caused by progressive loss of telomeric DNA. Telomere erosion protects against cancer early in life but limits cell renewal late in life, in agreement with the Antagonistic Pleiotropy theory on the evolutionary origin of aging. Malignant tumors arise when mutations and/or epimutations in cells (clock 2) corrupt the developmental program (clock 1) as well as tumor suppression by telomere erosion (clock 3). In cancer cells clock 3 is typically inactivated by loss of p53 as well as increased expression of telomerase. Taken together, aging in humans can be described by the ticking of three clocks: the clock that directs development, the accumulation of (epi-)mutations over time and the telomere clock that limits the number of cell divisions in normal stem and immune cells.
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Affiliation(s)
- Peter M Lansdorp
- Terry Fox Laboratory, BC Cancer Research Institute, Vancouver, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, Canada.
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5
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Hanlon VCT, Lansdorp PM, Guryev V. A survey of current methods to detect and genotype inversions. Hum Mutat 2022; 43:1576-1589. [PMID: 36047337 DOI: 10.1002/humu.24458] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 11/11/2022]
Abstract
Polymorphic inversions are ubiquitous in humans, and they have been linked to both adaptation and disease. Following their discovery in Drosophila more than a century ago, inversions have proved to be more elusive than other structural variants. A wide variety of methods for the detection and genotyping of inversions have recently been developed: multiple techniques based on selective amplification by PCR, short- and long-read sequencing approaches, principal component analysis of small variant haplotypes, template strand sequencing, optical mapping, and various genome assembly methods. Many methods apply complex wet lab protocols or increasingly refined bioinformatic analyses. This review is an attempt to provide a practical summary and comparison of the methods that are in current use, with a focus on metrics such as the maximum size of segmental duplications at inversion breakpoints that each method can tolerate, the size range of inversions that they recover, their throughput, and whether the locations of putative inversions must be known beforehand. This article is protected by copyright. All rights reserved.
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Affiliation(s)
| | - Peter M Lansdorp
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV, Groningen, The Netherlands
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6
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Lansdorp PM. Sex differences in telomere length, lifespan, and embryonic dyskerin levels. Aging Cell 2022; 21:e13614. [PMID: 35441417 PMCID: PMC9124296 DOI: 10.1111/acel.13614] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/20/2022] [Accepted: 04/03/2022] [Indexed: 01/22/2023] Open
Abstract
Telomerase levels in most human cells are insufficient to prevent loss of telomeric DNA with each replication cycle. The resulting “Hayflick” limit may have allowed lifespan to increase by suppressing the development of tumors early in life be it at the expense of compromised cellular responses late in life. At any given age, the average telomere length in leukocytes shows considerably variation between individuals with females having, on average, longer telomeres than males. Sex differences in average telomere length are already present at birth and correspond to reported differences in the average life expectancy between the sexes. Levels of telomerase RNA and dyskerin, encoded by DKC1, are known to limit telomerase activity in embryonic stem cells. X‐linked DKC1 is expressed from both alleles in female embryo cells and higher levels of dyskerin and telomerase could elongate telomeres prior to embryo implantation. The hypothesis that embryonic telomerase levels set the stage for the sex differences in telomere length and lifespan deserves further study.
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Affiliation(s)
- Peter M. Lansdorp
- Terry Fox Laboratory BC Cancer Agency Vancouver BC Canada
- Department of Medical Genetics University of British Columbia Vancouver BC Canada
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7
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Hamadeh Z, Hanlon V, Lansdorp PM. Mapping of sister chromatid exchange events and genome alterations in single cells. Methods 2022; 204:64-72. [PMID: 35483548 DOI: 10.1016/j.ymeth.2022.04.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 04/08/2022] [Accepted: 04/22/2022] [Indexed: 12/14/2022] Open
Abstract
Mammalian genomes encode over a hundred different helicases, many of which are implicated in the repair of DNA lesions by acting on DNA structures arising during DNA replication, recombination or transcription. Defining the in vivo substrates of such DNA helicases is a major challenge given the large number of helicases in the genome, the breadth of potential substrates in the genome and the degree of genetic pleiotropy among DNA helicases in resolving diverse substrates. Helicases such as WRN, BLM and RECQL5 are implicated in the resolution of error-free recombination events known as sister chromatid exchange events (SCEs). Single cell Strand-seq can be used to map the genomic location of individual SCEs at a resolution that exceeds that of classical cytogenetic techniques by several orders of magnitude. By mapping the genomic locations of SCEs in the absence of different helicases, it should in principle be possible to infer the substrate specificity of specific helicases. Here we describe how the genome can be interrogated for such DNA repair events using single-cell template strand sequencing (Strand-seq) and bioinformatic tools. SCEs and copy-number alterations were mapped to genomic locations at kilobase resolution in haploid KBM7 cells. Strategies, possibilities, and limitations of Strand-seq to study helicase function are illustrated using these cells before and after CRISPR/Cas9 knock out of WRN, BLM and/or RECQL5.
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Affiliation(s)
- Zeid Hamadeh
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada; Department of Genome Science and Technology, University of British Columbia, Vancouver, BC, Canada
| | - Vincent Hanlon
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Peter M Lansdorp
- Departments of Medical Genetics and Hematology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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8
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Hanlon VC, Chan DD, Hamadeh Z, Wang Y, Mattsson CA, Spierings DC, Coope RJ, Lansdorp PM. Construction of Strand-seq libraries in open nanoliter arrays. Cell Rep Methods 2022; 2:100150. [PMID: 35474869 PMCID: PMC9017222 DOI: 10.1016/j.crmeth.2021.100150] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 10/22/2021] [Accepted: 12/17/2021] [Indexed: 12/22/2022]
Abstract
Single-cell Strand-seq generates directional genomic information to study DNA repair, assemble genomes, and map structural variation onto chromosome-length haplotypes. We report a nanoliter-volume, one-pot (OP) Strand-seq library preparation protocol in which reagents are added cumulatively, DNA purification steps are avoided, and enzymes are inactivated with a thermolabile protease. OP-Strand-seq libraries capture 10%-25% of the genome from a single-cell with reduced costs and increased throughput.
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Affiliation(s)
| | - Daniel D. Chan
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Zeid Hamadeh
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Yanni Wang
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | | | - Diana C.J. Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, the Netherlands
| | - Robin J.N. Coope
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Peter M. Lansdorp
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, the Netherlands
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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9
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Zwinderman MRH, Lobo TJ, van der Wouden PE, Spierings DCJ, van Vugt MATM, Lansdorp PM, Guryev V, Dekker FJ. Deposition Bias of Chromatin Proteins Inverts under DNA Replication Stress Conditions. ACS Chem Biol 2021; 16:2193-2201. [PMID: 34592816 PMCID: PMC8609521 DOI: 10.1021/acschembio.1c00321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
Following DNA replication,
equal amounts of chromatin proteins
are distributed over sister chromatids by re-deposition of parental
chromatin proteins and deposition of newly synthesized chromatin proteins.
Molecular mechanisms balancing the allocation of new and old chromatin
proteins remain largely unknown. Here, we studied the genome-wide
distribution of new chromatin proteins relative to parental DNA template
strands and replication initiation zones using the double-click-seq.
Under control conditions, new chromatin proteins were preferentially
found on DNA replicated by the lagging strand machinery. Strikingly,
replication stress induced by hydroxyurea or curaxin treatment and
inhibition of ataxia telangiectasia and Rad3-related protein (ATR)
or p53 inactivation inverted the observed chromatin protein deposition
bias to the strand replicated by the leading strand polymerase in
line with previously reported effects on replication protein A occupancy.
We propose that asymmetric deposition of newly synthesized chromatin
proteins onto sister chromatids reflects differences in the processivity
of leading and lagging strand synthesis.
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Affiliation(s)
- Martijn R. H. Zwinderman
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Thamar Jessurun Lobo
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
| | - Petra E. van der Wouden
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Diana C. J. Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
| | - Marcel A. T. M. van Vugt
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Peter M. Lansdorp
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, V5Z 1L3 British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, V6T 1Z4 British Columbia, Canada
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
| | - Frank J. Dekker
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands
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10
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Hanlon VCT, Mattsson CA, Spierings DCJ, Guryev V, Lansdorp PM. InvertypeR: Bayesian inversion genotyping with Strand-seq data. BMC Genomics 2021; 22:582. [PMID: 34332539 PMCID: PMC8325862 DOI: 10.1186/s12864-021-07892-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 07/15/2021] [Indexed: 11/23/2022] Open
Abstract
Background Single cell Strand-seq is a unique tool for the discovery and phasing of genomic inversions. Conventional methods to discover inversions with Strand-seq data are blind to known inversion locations, limiting their statistical power for the detection of inversions smaller than 10 Kb. Moreover, the methods rely on manual inspection to separate false and true positives. Results Here we describe “InvertypeR”, a method based on a Bayesian binomial model that genotypes inversions using fixed genomic coordinates. We validated InvertypeR by re-genotyping inversions reported for three trios by the Human Genome Structural Variation Consortium. Although 6.3% of the family inversion genotypes in the original study showed Mendelian discordance, this was reduced to 0.5% using InvertypeR. By applying InvertypeR to published inversion coordinates and predicted inversion hotspots (n = 3701), as well as coordinates from conventional inversion discovery, we furthermore genotyped 66 inversions not previously reported for the three trios. Conclusions InvertypeR discovers, genotypes, and phases inversions without relying on manual inspection. For greater accessibility, results are presented as phased chromosome ideograms with inversions linked to Strand-seq data in the genome browser. InvertypeR increases the power of Strand-seq for studies on the role of inversions in phenotypic variation, genome instability, and human disease. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07892-9.
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Affiliation(s)
- Vincent C T Hanlon
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada.
| | - Carl-Adam Mattsson
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Diana C J Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV, Groningen, The Netherlands
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV, Groningen, The Netherlands
| | - Peter M Lansdorp
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada.,European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV, Groningen, The Netherlands.,Departments of Medical Genetics and Hematology, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
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11
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Porubsky D, Ebert P, Audano PA, Vollger MR, Harvey WT, Marijon P, Ebler J, Munson KM, Sorensen M, Sulovari A, Haukness M, Ghareghani M, Lansdorp PM, Paten B, Devine SE, Sanders AD, Lee C, Chaisson MJP, Korbel JO, Eichler EE, Marschall T. Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads. Nat Biotechnol 2021; 39:302-308. [PMID: 33288906 PMCID: PMC7954704 DOI: 10.1038/s41587-020-0719-5] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 09/16/2020] [Indexed: 12/18/2022]
Abstract
Human genomes are typically assembled as consensus sequences that lack information on parental haplotypes. Here we describe a reference-free workflow for diploid de novo genome assembly that combines the chromosome-wide phasing and scaffolding capabilities of single-cell strand sequencing1,2 with continuous long-read or high-fidelity3 sequencing data. Employing this strategy, we produced a completely phased de novo genome assembly for each haplotype of an individual of Puerto Rican descent (HG00733) in the absence of parental data. The assemblies are accurate (quality value > 40) and highly contiguous (contig N50 > 23 Mbp) with low switch error rates (0.17%), providing fully phased single-nucleotide variants, indels and structural variants. A comparison of Oxford Nanopore Technologies and Pacific Biosciences phased assemblies identified 154 regions that are preferential sites of contig breaks, irrespective of sequencing technology or phasing algorithms.
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Affiliation(s)
- David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Peter Ebert
- Heinrich Heine University Düsseldorf, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Düsseldorf, Germany
| | - Peter A Audano
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Mitchell R Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - William T Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Pierre Marijon
- Heinrich Heine University Düsseldorf, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Düsseldorf, Germany
| | - Jana Ebler
- Heinrich Heine University Düsseldorf, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Düsseldorf, Germany
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Melanie Sorensen
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Arvis Sulovari
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Marina Haukness
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Maryam Ghareghani
- Heinrich Heine University Düsseldorf, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Düsseldorf, Germany
- Center for Bioinformatics, Saarland University, and Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Peter M Lansdorp
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Scott E Devine
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Ashley D Sanders
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- Department of Life Science, Ewha Womans University, Seoul, Republic of Korea
| | - Mark J P Chaisson
- Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Jan O Korbel
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
| | - Tobias Marschall
- Heinrich Heine University Düsseldorf, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Düsseldorf, Germany.
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12
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Porubsky D, Sanders AD, Taudt A, Colomé-Tatché M, Lansdorp PM, Guryev V. breakpointR: an R/Bioconductor package to localize strand state changes in Strand-seq data. Bioinformatics 2020; 36:1260-1261. [PMID: 31504176 DOI: 10.1093/bioinformatics/btz681] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 08/12/2019] [Accepted: 08/27/2019] [Indexed: 12/18/2022] Open
Abstract
MOTIVATION Strand-seq is a specialized single-cell DNA sequencing technique centered around the directionality of single-stranded DNA. Computational tools for Strand-seq analyses must capture the strand-specific information embedded in these data. RESULTS Here we introduce breakpointR, an R/Bioconductor package specifically tailored to process and interpret single-cell strand-specific sequencing data obtained from Strand-seq. We developed breakpointR to detect local changes in strand directionality of aligned Strand-seq data, to enable fine-mapping of sister chromatid exchanges, germline inversion and to support global haplotype assembly. Given the broad spectrum of Strand-seq applications we expect breakpointR to be an important addition to currently available tools and extend the accessibility of this novel sequencing technique. AVAILABILITY AND IMPLEMENTATION R/Bioconductor package https://bioconductor.org/packages/breakpointR. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- David Porubsky
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Ashley D Sanders
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, Canada.,European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Aaron Taudt
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Maria Colomé-Tatché
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Peter M Lansdorp
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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13
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Tamminga M, Andree KC, Hiltermann TJN, Jayat M, Schuuring E, van den Bos H, Spierings DCJ, Lansdorp PM, Timens W, Terstappen LWMM, Groen HJM. Detection of Circulating Tumor Cells in the Diagnostic Leukapheresis Product of Non-Small-Cell Lung Cancer Patients Comparing CellSearch ® and ISET. Cancers (Basel) 2020; 12:E896. [PMID: 32272669 PMCID: PMC7226321 DOI: 10.3390/cancers12040896] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 03/25/2020] [Accepted: 04/03/2020] [Indexed: 01/04/2023] Open
Abstract
Circulating tumor cells (CTCs) detected by CellSearch are prognostic in non-small-cell lung cancer (NSCLC), but rarely found. CTCs can be extracted from the blood together with mononuclear cell populations by diagnostic leukapheresis (DLA), therefore concentrating them. However, CellSearch can only process limited DLA volumes (≈2 mL). Therefore, we established a protocol to enumerate CTCs in DLA products with Isolation by SizE of Tumor cells (ISET), and compared CTC counts between CellSearch® and ISET. DLA was performed in NSCLC patients who started a new therapy. With an adapted protocol, ISET could process 10 mL of DLA. CellSearch detected CTCs in a volume equaling 2 × 108 leukocytes (mean 2 mL). CTC counts per mL were compared. Furthermore, the live cell protocol of ISET was tested in eight patients. ISET successfully processed all DLA products-16 with the fixed cell protocol and 8 with the live cell protocol. In total, 10-20 mL of DLA was processed. ISET detected CTCs in 88% (14/16), compared to 69% (11/16, p < 0.05) with CellSearch. ISET also detected higher number of CTCs (ISET median CTC/mL = 4, interquartile range [IQR] = 2-6, CellSearch median CTC/mL = 0.9, IQR = 0-1.8, p < 0.01). Cells positive for the epithelial cell adhesion molecule (EpCAM+) per mL were detected in similar counts by both methods. Eight patients were processed with the live cell protocol. All had EpCAM+, CD45-, CD235- cells isolated by fluorescence-activated cell sorting (FACS). Overall, ISET processed larger volumes and detected higher CTC counts compared to CellSearch. EpCAM+ CTCs were detected in comparable rates.
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Affiliation(s)
- Menno Tamminga
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands; (M.T.); (T.J.N.H.)
| | - Kiki C. Andree
- Department of Medical Cell BioPhysics, Faculty of Sciences and Technology, University of Twente, 7522 NB Enschede, The Netherlands; (K.C.A.); (L.W.M.M.T.)
| | - T. Jeroen N. Hiltermann
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands; (M.T.); (T.J.N.H.)
| | | | - Ed Schuuring
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands; (E.S.); (W.T.)
| | - Hilda van den Bos
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands; (H.v.d.B.); (D.C.J.S.); (P.M.L.)
| | - Diana C. J. Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands; (H.v.d.B.); (D.C.J.S.); (P.M.L.)
| | - Peter M. Lansdorp
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands; (H.v.d.B.); (D.C.J.S.); (P.M.L.)
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Wim Timens
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands; (E.S.); (W.T.)
| | - Leon W. M. M. Terstappen
- Department of Medical Cell BioPhysics, Faculty of Sciences and Technology, University of Twente, 7522 NB Enschede, The Netherlands; (K.C.A.); (L.W.M.M.T.)
| | - Harry J. M. Groen
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands; (M.T.); (T.J.N.H.)
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14
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Middelkamp S, van Tol HTA, Spierings DCJ, Boymans S, Guryev V, Roelen BAJ, Lansdorp PM, Cuppen E, Kuijk EW. Sperm DNA damage causes genomic instability in early embryonic development. Sci Adv 2020; 6:eaaz7602. [PMID: 32494621 PMCID: PMC7159919 DOI: 10.1126/sciadv.aaz7602] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/22/2020] [Indexed: 05/03/2023]
Abstract
Genomic instability is common in human embryos, but the underlying causes are largely unknown. Here, we examined the consequences of sperm DNA damage on the embryonic genome by single-cell whole-genome sequencing of individual blastomeres from bovine embryos produced with sperm damaged by γ-radiation. Sperm DNA damage primarily leads to fragmentation of the paternal chromosomes followed by random distribution of the chromosomal fragments over the two sister cells in the first cell division. An unexpected secondary effect of sperm DNA damage is the induction of direct unequal cleavages, which include the poorly understood heterogoneic cell divisions. As a result, chaotic mosaicism is common in embryos derived from fertilizations with damaged sperm. The mosaic aneuploidies, uniparental disomies, and de novo structural variation induced by sperm DNA damage may compromise fertility and lead to rare congenital disorders when embryos escape developmental arrest.
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Affiliation(s)
- Sjors Middelkamp
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, Utrecht 3584 CG, Netherlands
| | - Helena T. A. van Tol
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, Utrecht 3584 CM, Netherlands
| | - Diana C. J. Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, Netherlands
| | - Sander Boymans
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, Utrecht 3584 CG, Netherlands
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, Netherlands
| | - Bernard A. J. Roelen
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, Utrecht 3584 CM, Netherlands
| | - Peter M. Lansdorp
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, Netherlands
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, Utrecht 3584 CG, Netherlands
- Hartwig Medical Foundation, Amsterdam, Netherlands
- Corresponding author.
| | - Ewart W. Kuijk
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, Utrecht 3584 CG, Netherlands
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15
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Tamminga M, de Wit S, van de Wauwer C, van den Bos H, Swennenhuis JF, Klinkenberg TJ, Hiltermann TJN, Andree KC, Spierings DCJ, Lansdorp PM, van den Berg A, Timens W, Terstappen LWMM, Groen HJM. Analysis of Released Circulating Tumor Cells During Surgery for Non-Small Cell Lung Cancer. Clin Cancer Res 2019; 26:1656-1666. [PMID: 31772122 DOI: 10.1158/1078-0432.ccr-19-2541] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 10/17/2019] [Accepted: 11/22/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE Tumor cells from patients with lung cancer are expelled from the primary tumor into the blood, but difficult to detect in the peripheral circulation. We studied the release of circulating tumor cells (CTCs) during surgery to test the hypothesis that CTC counts are influenced by hemodynamic changes (caused by surgical approach) and manipulation. EXPERIMENTAL DESIGN Patients undergoing video-assisted thoracic surgery (VATS) or open surgery for (suspected) primary lung cancer were included. Blood samples were taken before surgery (T0) from the radial artery (RA), from both the RA and pulmonary vein (PV) when the PV was located (T1) and when either the pulmonary artery (T2 open) or the PV (T2 VATS) was dissected. The CTCs were enumerated using the CellSearch system. Single-cell whole-genome sequencing was performed on isolated CTCs for aneuploidy. RESULTS CTCs were detected in 58 of 138 samples (42%) of 31 patients. CTCs were more often detected in the PV (70%) compared with the RA (22%, P < 0.01) and in higher counts (P < 0.01). After surgery, the RA but not the PV showed less often CTCs (P = 0.02). Type of surgery did not influence CTC release. Only six of 496 isolated CTCs showed aneuploidy, despite matched primary tumor tissue being aneuploid. Euploid so-called CTCs had a different morphology than aneuploid. CONCLUSIONS CTCs defined by CellSearch were identified more often and in higher numbers in the PV compared with the RA, suggesting central clearance. The majority of cells in the PV were normal epithelial cells and outnumbered CTCs. Release of CTCs was not influenced by surgical approach.
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Affiliation(s)
- Menno Tamminga
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
| | - Sanne de Wit
- Department of Medical Cell BioPhysics, Faculty of Sciences and Technology, University of Twente, Enschede, the Netherlands
| | - Caroline van de Wauwer
- Department of Cardiothoracic Surgery, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Hilda van den Bos
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Joost F Swennenhuis
- Department of Medical Cell BioPhysics, Faculty of Sciences and Technology, University of Twente, Enschede, the Netherlands
| | - Theo J Klinkenberg
- Department of Cardiothoracic Surgery, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - T Jeroen N Hiltermann
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Kiki C Andree
- Department of Medical Cell BioPhysics, Faculty of Sciences and Technology, University of Twente, Enschede, the Netherlands
| | - Diana C J Spierings
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Peter M Lansdorp
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.,Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Anke van den Berg
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Wim Timens
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Leon W M M Terstappen
- Department of Medical Cell BioPhysics, Faculty of Sciences and Technology, University of Twente, Enschede, the Netherlands
| | - Harry J M Groen
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
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16
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Bolhaqueiro ACF, Ponsioen B, Bakker B, Klaasen SJ, Kucukkose E, van Jaarsveld RH, Vivié J, Verlaan-Klink I, Hami N, Spierings DCJ, Sasaki N, Dutta D, Boj SF, Vries RGJ, Lansdorp PM, van de Wetering M, van Oudenaarden A, Clevers H, Kranenburg O, Foijer F, Snippert HJG, Kops GJPL. Ongoing chromosomal instability and karyotype evolution in human colorectal cancer organoids. Nat Genet 2019; 51:824-834. [PMID: 31036964 DOI: 10.1038/s41588-019-0399-6] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 03/19/2019] [Indexed: 11/09/2022]
Abstract
Chromosome segregation errors cause aneuploidy and genomic heterogeneity, which are hallmarks of cancer in humans. A persistent high frequency of these errors (chromosomal instability (CIN)) is predicted to profoundly impact tumor evolution and therapy response. It is unknown, however, how prevalent CIN is in human tumors. Using three-dimensional live-cell imaging of patient-derived tumor organoids (tumor PDOs), we show that CIN is widespread in colorectal carcinomas regardless of background genetic alterations, including microsatellite instability. Cell-fate tracking showed that, although mitotic errors are frequently followed by cell death, some tumor PDOs are largely insensitive to mitotic errors. Single-cell karyotype sequencing confirmed heterogeneity of copy number alterations in tumor PDOs and showed that monoclonal lines evolved novel karyotypes over time in vitro. We conclude that ongoing CIN is common in colorectal cancer organoids, and propose that CIN levels and the tolerance for mitotic errors shape aneuploidy landscapes and karyotype heterogeneity.
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Affiliation(s)
- Ana C F Bolhaqueiro
- Oncode Institute, Hubrecht Institute-KNAW, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Bas Ponsioen
- Oncode Institute, Center for Molecular Medicine, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Bjorn Bakker
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Sjoerd J Klaasen
- Oncode Institute, Hubrecht Institute-KNAW, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Emre Kucukkose
- Department of Surgical Oncology, UMC Utrecht Cancer Centre, University Medical Centre, Utrecht, the Netherlands
| | - Richard H van Jaarsveld
- Oncode Institute, Hubrecht Institute-KNAW, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Judith Vivié
- Oncode Institute, Hubrecht Institute-KNAW, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Ingrid Verlaan-Klink
- Oncode Institute, Center for Molecular Medicine, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Nizar Hami
- Oncode Institute, Center for Molecular Medicine, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Diana C J Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Nobuo Sasaki
- Oncode Institute, Hubrecht Institute-KNAW, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Devanjali Dutta
- Oncode Institute, Hubrecht Institute-KNAW, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Sylvia F Boj
- Foundation Hubrecht Organoid Technology (HUB), Utrecht, the Netherlands
| | - Robert G J Vries
- Foundation Hubrecht Organoid Technology (HUB), Utrecht, the Netherlands
| | - Peter M Lansdorp
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands.,Terry Fox Laboratory, BC Cancer Agency, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marc van de Wetering
- Oncode Institute, Princess Maxima Centre for Paediatric Oncology, Utrecht, the Netherlands
| | - Alexander van Oudenaarden
- Oncode Institute, Hubrecht Institute-KNAW, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Hans Clevers
- Oncode Institute, Hubrecht Institute-KNAW, University Medical Centre Utrecht, Utrecht, the Netherlands.,Oncode Institute, Princess Maxima Centre for Paediatric Oncology, Utrecht, the Netherlands
| | - Onno Kranenburg
- Department of Surgical Oncology, UMC Utrecht Cancer Centre, University Medical Centre, Utrecht, the Netherlands
| | - Floris Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Hugo J G Snippert
- Oncode Institute, Center for Molecular Medicine, University Medical Centre Utrecht, Utrecht, the Netherlands.
| | - Geert J P L Kops
- Oncode Institute, Hubrecht Institute-KNAW, University Medical Centre Utrecht, Utrecht, the Netherlands.
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17
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Henderson A, Wu Y, Huang YC, Chavez EA, Platt J, Johnson FB, Brosh RM, Sen D, Lansdorp PM. Detection of G-quadruplex DNA in mammalian cells. Nucleic Acids Res 2018; 45:6252. [PMID: 28449109 PMCID: PMC5449604 DOI: 10.1093/nar/gkx300] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- Alexander Henderson
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Yuliang Wu
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, Baltimore, MD 21224, USA
| | - Yu Chuan Huang
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Elizabeth A Chavez
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Jesse Platt
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104-6100, USA
| | - F Brad Johnson
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104-6100, USA
| | - Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, Baltimore, MD 21224, USA
| | - Dipankar Sen
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Peter M Lansdorp
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.,Division of Hematology, Department of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.,European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
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18
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Pilsworth JA, Cochrane DR, Xia Z, Aubert G, Färkkilä AEM, Horlings HM, Yanagida S, Yang W, Lim JLP, Wang Y, Bashashati A, Keul J, Wong A, Oliva E, Shah SP, Kommoss S, Kommoss F, Lansdorp PM, Baird DM, Huntsman DG. Abstract PR13: TERT is frequently mutated in adult-type granulosa cell tumors of the ovary compared to other malignant sex cord-stromal tumors. Clin Cancer Res 2018. [DOI: 10.1158/1557-3265.ovca17-pr13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The telomerase reverse transcriptase (TERT) gene is highly expressed in stem cells and silenced upon differentiation. Cancer cells can attain immortality by activating TERT to maintain telomere length and telomerase activity, a crucial step of tumorigenesis. Two somatic mutations in the TERT promoter (C228T; C250T) have been identified in multiple cancers, such as melanoma and glioblastoma, as gain-of-function mutations that promote transcriptional activation of TERT. A recent study investigating TERT promoter mutations in ovarian carcinomas found mutations in 15% of clear cell carcinomas. However, it is unknown whether these mutations are prevalent in adult-type granulosa cell tumors (AGCTs) of the ovary, Sertoli-Leydig cell tumors (SLCTs), and other malignant sex cord-stromal tumors.
We performed whole-genome sequencing on ten AGCT cases with matched normal and identified the TERT C228T promoter mutation in 50% of cases. We found that AGCT cases with mutated TERT promoter have increased expression of TERT mRNA compared to those with wild-type TERT promoter. All five TERT promoter mutated cases had high levels of TERT mRNA expression, whereas three of the five wild-type TERT cases had no measurable TERT mRNA expression. There was a tendency towards longer telomere lengths in AGCT cases with the TERT promoter mutation relative to those without, although it was not statistically significant. These results suggest that telomerase may be activated by a different method in the cases with no TERT promoter mutations but have TERT mRNA expression. The remaining cases with neither TERT promoter mutations nor TERT mRNA expression likely maintain their telomeres using a telomerase-independent method, such as the alternative lengthening of telomeres pathway. TERT C228T allelic discrimination analysis of 331 AGCTs, 5 SLCTs, and 18 other malignant sex cord-stromal tumors detected the mutation in 56/247 (23%) of primary AGCTs, 22/84 (26%) of recurrent AGCTs, 1/5 (20%) of SLCTs and (0/18) 0% of other malignant sex cord-stromal tumors. The single SLCT case with the TERT promoter mutation was poorly differentiated and harbored the pathognomonic FOXL2 mutation of AGCT, suggesting this SLCT case may actually be an AGCT. In 204 AGCT cases with available survival data, there was a trend towards worse disease-specific survival in patients with the TERT promoter mutation compared to those without; however, statistical significance was not reached (p = 0.128, log-ranked test). In 5 AGCT cases with primary and recurrent tissues, we found that the TERT promoter mutation was absent in the primary tumors but present in the recurrent tumors, suggesting that TERT C228T mutation may play an active role in progression of AGCTs.
Overall, we found that TERT C228T promoter mutation was most common in AGCTs among the different malignant sex cord-stromal tumors. Our data confirm the activation of telomerase in AGCTs via TERT C228T promoter mutation, although alternative telomerase activation methods in AGCTs may exist. Our results suggest that TERT activation may play a role in AGCT recurrence. As such, telomere biology may be important for the progression of AGCTs.
This abstract is also being presented as Poster B54.
Citation Format: Jessica A. Pilsworth, Dawn R. Cochrane, Zhouchunyang Xia, Geraldine Aubert, Anniina E. M. Färkkilä, Hugo M. Horlings, Satoshi Yanagida, Winnie Yang, Jamie L. P. Lim, Yikan Wang, Ali Bashashati, Jacqueline Keul, Adele Wong, Esther Oliva, Sohrab P. Shah, Stefan Kommoss, Friedrich Kommoss, Peter M. Lansdorp, Duncan M. Baird, David G. Huntsman. TERT is frequently mutated in adult-type granulosa cell tumors of the ovary compared to other malignant sex cord-stromal tumors. [abstract]. In: Proceedings of the AACR Conference: Addressing Critical Questions in Ovarian Cancer Research and Treatment; Oct 1-4, 2017; Pittsburgh, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(15_Suppl):Abstract nr PR13.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Yikan Wang
- 2BC Cancer Agency, Vancouver, BC, Canada,
| | | | | | - Adele Wong
- 5Massachusetts General Hospital, Boston, MA,
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19
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O'Neill K, Hills M, Gottlieb M, Borkowski M, Karsan A, Lansdorp PM. Assembling draft genomes using contiBAIT. Bioinformatics 2018; 33:2737-2739. [PMID: 28475666 PMCID: PMC5860061 DOI: 10.1093/bioinformatics/btx281] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 05/03/2017] [Indexed: 11/14/2022] Open
Abstract
Summary Massively parallel sequencing is now widely used, but data interpretation is only as good as the reference assembly to which it is aligned. While the number of reference assemblies has rapidly expanded, most of these remain at intermediate stages of completion, either as scaffold builds, or as chromosome builds (consisting of correctly ordered, but not necessarily correctly oriented scaffolds separated by gaps). Completion of de novo assemblies remains difficult, as regions that are repetitive or hard to sequence prevent the accumulation of larger scaffolds, and create errors such as misorientations and mislocalizations. Thus, complementary methods for determining the orientation and positioning of fragments are important for finishing assemblies. Strand-seq is a method for determining template strand inheritance in single cells, information that can be used to determine relative genomic distance and orientation between scaffolds, and find errors within them. We present contiBAIT, an R/Bioconductor package which uses Strand-seq data to repair and improve existing assemblies. Availability and Implementation contiBAIT is available on Bioconductor. Source files available from GitHub. Contact koneill@bcgsc.ca or mark.hills@stemcell.com. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Kieran O'Neill
- Michael Smith Genome Sciences Centre, BC Cancer Agency.,Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | | | - Mike Gottlieb
- Michael Smith Genome Sciences Centre, BC Cancer Agency.,Bioinformatics Training Program, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | | | - Aly Karsan
- Michael Smith Genome Sciences Centre, BC Cancer Agency.,Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Peter M Lansdorp
- Michael Smith Genome Sciences Centre, BC Cancer Agency.,Hematology Division, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.,European Research Institute for the Biology of Ageing, University Medical Centre Groningen, Groningen, The Netherlands
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20
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Ferronika P, van den Bos H, Taudt A, Spierings DCJ, Saber A, Hiltermann TJN, Kok K, Porubsky D, van der Wekken AJ, Timens W, Foijer F, Colomé-Tatché M, Groen HJM, Lansdorp PM, van den Berg A. Copy number alterations assessed at the single-cell level revealed mono- and polyclonal seeding patterns of distant metastasis in a small-cell lung cancer patient. Ann Oncol 2018; 28:1668-1670. [PMID: 28419234 DOI: 10.1093/annonc/mdx182] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Indexed: 11/14/2022] Open
Affiliation(s)
- P Ferronika
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands.,Department of Pathology, Faculty of Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - H van den Bos
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - A Taudt
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands.,Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - D C J Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - A Saber
- Department of Pathology and Medical Biology
| | - T J N Hiltermann
- Department of Pulmonary Diseases, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - K Kok
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - D Porubsky
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - A J van der Wekken
- Department of Pulmonary Diseases, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - W Timens
- Department of Pathology and Medical Biology
| | - F Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - M Colomé-Tatché
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands.,Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - H J M Groen
- Department of Pulmonary Diseases, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - P M Lansdorp
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands.,Department of Medical Genetics, University of British Columbia and Terry Fox Laboratory, BC Cancer Research Centre, Vancouver, Canada
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21
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Soto M, Raaijmakers JA, Bakker B, Spierings DCJ, Lansdorp PM, Foijer F, Medema RH. p53 Prohibits Propagation of Chromosome Segregation Errors that Produce Structural Aneuploidies. Cell Rep 2018. [PMID: 28636931 DOI: 10.1016/j.celrep.2017.05.055] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
The presence of an abnormal karyotype has been shown to be profoundly detrimental at the cellular and organismal levels but is an overt hallmark of cancer. Aneuploidy can lead to p53 activation and thereby prevents proliferation, but the exact trigger for p53 activation has remained controversial. Here, we have used a system to induce aneuploidy in untransformed human cells to explore how cells deal with different segregation errors. We show that p53 is activated only in a subset of the cells with altered chromosome content. Importantly, we find that at least a subset of whole-chromosome aneuploidies can be propagated in p53-proficient cells, indicating that aneuploidy does not always lead to activation of p53. Finally, we demonstrate that propagation of structural aneuploidies (gain or loss of part of a chromosome) induced by segregation errors is limited to p53-deficient cells.
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Affiliation(s)
- Mar Soto
- Department of Cell Biology and Cancer Genomics Center, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Jonne A Raaijmakers
- Department of Cell Biology and Cancer Genomics Center, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Bjorn Bakker
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen 9713 AV, the Netherlands
| | - Diana C J Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen 9713 AV, the Netherlands
| | - Peter M Lansdorp
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen 9713 AV, the Netherlands
| | - Floris Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen 9713 AV, the Netherlands
| | - René H Medema
- Department of Cell Biology and Cancer Genomics Center, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands.
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22
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van Wietmarschen N, Merzouk S, Halsema N, Spierings DCJ, Guryev V, Lansdorp PM. BLM helicase suppresses recombination at G-quadruplex motifs in transcribed genes. Nat Commun 2018; 9:271. [PMID: 29348659 PMCID: PMC5773480 DOI: 10.1038/s41467-017-02760-1] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/21/2017] [Indexed: 11/16/2022] Open
Abstract
Bloom syndrome is a cancer predisposition disorder caused by mutations in the BLM helicase gene. Cells from persons with Bloom syndrome exhibit striking genomic instability characterized by excessive sister chromatid exchange events (SCEs). We applied single-cell DNA template strand sequencing (Strand-seq) to map the genomic locations of SCEs. Our results show that in the absence of BLM, SCEs in human and murine cells do not occur randomly throughout the genome but are strikingly enriched at coding regions, specifically at sites of guanine quadruplex (G4) motifs in transcribed genes. We propose that BLM protects against genome instability by suppressing recombination at sites of G4 structures, particularly in transcribed regions of the genome. Bloom syndrome is characterized by high levels of sister chromatid exchanges (SCEs). Here, the authors use single-cell DNA template strand-sequencing to map SCEs in patient cells, and propose that the BLM helicase protects the genome against unwanted recombination at sites of G-quadruplex structures.
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Affiliation(s)
- Niek van Wietmarschen
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Sarra Merzouk
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Nancy Halsema
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Diana C J Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Peter M Lansdorp
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands. .,Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, V5Z 1L3, Canada. .,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
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23
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Claussin C, Porubský D, Spierings DCJ, Halsema N, Rentas S, Guryev V, Lansdorp PM, Chang M. Genome-wide mapping of sister chromatid exchange events in single yeast cells using Strand-seq. eLife 2017; 6:e30560. [PMID: 29231811 PMCID: PMC5734873 DOI: 10.7554/elife.30560] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 12/08/2017] [Indexed: 01/09/2023] Open
Abstract
Homologous recombination involving sister chromatids is the most accurate, and thus most frequently used, form of recombination-mediated DNA repair. Despite its importance, sister chromatid recombination is not easily studied because it does not result in a change in DNA sequence, making recombination between sister chromatids difficult to detect. We have previously developed a novel DNA template strand sequencing technique, called Strand-seq, that can be used to map sister chromatid exchange (SCE) events genome-wide in single cells. An increase in the rate of SCE is an indicator of elevated recombination activity and of genome instability, which is a hallmark of cancer. In this study, we have adapted Strand-seq to detect SCE in the yeast Saccharomyces cerevisiae. We provide the first quantifiable evidence that most spontaneous SCE events in wild-type cells are not due to the repair of DNA double-strand breaks.
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Affiliation(s)
- Clémence Claussin
- European Research Institute for the Biology of Ageing, University Medical Center GroningenUniversity of GroningenGroningenNetherlands
| | - David Porubský
- European Research Institute for the Biology of Ageing, University Medical Center GroningenUniversity of GroningenGroningenNetherlands
| | - Diana CJ Spierings
- European Research Institute for the Biology of Ageing, University Medical Center GroningenUniversity of GroningenGroningenNetherlands
| | - Nancy Halsema
- European Research Institute for the Biology of Ageing, University Medical Center GroningenUniversity of GroningenGroningenNetherlands
| | | | - Victor Guryev
- European Research Institute for the Biology of Ageing, University Medical Center GroningenUniversity of GroningenGroningenNetherlands
| | - Peter M Lansdorp
- European Research Institute for the Biology of Ageing, University Medical Center GroningenUniversity of GroningenGroningenNetherlands
- Terry Fox LaboratoryBC Cancer AgencyVancouverCanada
- Department of Medical GeneticsUniversity of British ColumbiaVancouverCanada
| | - Michael Chang
- European Research Institute for the Biology of Ageing, University Medical Center GroningenUniversity of GroningenGroningenNetherlands
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24
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Porubsky D, Garg S, Sanders AD, Korbel JO, Guryev V, Lansdorp PM, Marschall T. Dense and accurate whole-chromosome haplotyping of individual genomes. Nat Commun 2017; 8:1293. [PMID: 29101320 PMCID: PMC5670131 DOI: 10.1038/s41467-017-01389-4] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 09/14/2017] [Indexed: 12/15/2022] Open
Abstract
The diploid nature of the human genome is neglected in many analyses done today, where a genome is perceived as a set of unphased variants with respect to a reference genome. This lack of haplotype-level analyses can be explained by a lack of methods that can produce dense and accurate chromosome-length haplotypes at reasonable costs. Here we introduce an integrative phasing strategy that combines global, but sparse haplotypes obtained from strand-specific single-cell sequencing (Strand-seq) with dense, yet local, haplotype information available through long-read or linked-read sequencing. We provide comprehensive guidance on the required sequencing depths and reliably assign more than 95% of alleles (NA12878) to their parental haplotypes using as few as 10 Strand-seq libraries in combination with 10-fold coverage PacBio data or, alternatively, 10X Genomics linked-read sequencing data. We conclude that the combination of Strand-seq with different technologies represents an attractive solution to chart the genetic variation of diploid genomes.
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Affiliation(s)
- David Porubsky
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Building 3226, 9713 AV, Groningen, The Netherlands
- Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Shilpa Garg
- Center for Bioinformatics, Saarland University, Saarland Informatics Campus E2.1, 66123, Saarbrücken, Germany
- Max Planck Institute for Informatics, Saarland Informatics Campus E1.4, 66123, Saarbrücken, Germany
- Graduate School of Computer Science, Saarland University, Saarland Informatics Campus E1.3, 66123, Saarbrücken, Germany
| | - Ashley D Sanders
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117, Heidelberg, Germany
- Terry Fox Laboratory, BC Cancer Agency, 601 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Jan O Korbel
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Building 3226, 9713 AV, Groningen, The Netherlands
| | - Peter M Lansdorp
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Building 3226, 9713 AV, Groningen, The Netherlands
- Terry Fox Laboratory, BC Cancer Agency, 601 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Department of Medical Genetics, University of British Columbia, 2350 Health Science Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Tobias Marschall
- Center for Bioinformatics, Saarland University, Saarland Informatics Campus E2.1, 66123, Saarbrücken, Germany.
- Max Planck Institute for Informatics, Saarland Informatics Campus E1.4, 66123, Saarbrücken, Germany.
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25
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Kazemier HG, Paeschke K, Lansdorp PM. Guanine quadruplex monoclonal antibody 1H6 cross-reacts with restrained thymidine-rich single stranded DNA. Nucleic Acids Res 2017; 45:5913-5919. [PMID: 28449085 PMCID: PMC5449594 DOI: 10.1093/nar/gkx245] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 04/04/2017] [Indexed: 01/09/2023] Open
Abstract
Previously we reported the production and characterization of monoclonal antibody 1H6 raised against (T4G4)2 intermolecular guanine quadruplex (G4) DNA structures (Henderson A. et al. (2014) Nucleic Acids Res., 42, 860–869; Hoffmann R.F. et al. (2016) Nucleic Acids Res., 44, 152–163). It was shown that 1H6 strongly stains nuclei and has exquisite specificity for heterochromatin by immuno-electron microscopy. Here we extend our studies of 1H6 reactivity using enzyme-linked immunosorbent assay (ELISA) and microscale thermophoresis (MST). As previously reported, 1H6 was found to strongly bind intermolecular G4 structures with a (T4G4)2 sequence motif. However, using both methods we did not detect significant binding to G4 structures without thymidines in their sequence motif or to G4 structures made with (T2G4)2 oligonucleotides. In addition, we observed strong, sequence-specific binding of 1H6 by ELISA to immobilized single stranded poly(T) DNA but not to immobilized poly(C) or poly(A) homo-polymers. Cross-reactivity of 1H6 to poly(T) was not measured in solution using MST. 1H6 was furthermore found to bind to selected areas on DNA fibers but only after DNA denaturation. Based on these observations we propose that 1H6 binds with high affinity to adjacent T's that are restricted in their movement in selected G4 structures and denatured DNA. Cross-reactivity of 1H6 to immobilized single stranded T-rich DNA next to its previously reported specificity for bona fide G4 structures needs to be taken into account in the interpretation of 1H6 binding to (sub-) cellular structures.
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Affiliation(s)
- Hinke G Kazemier
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Katrin Paeschke
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Peter M Lansdorp
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands.,Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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26
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Cornish-Bowden A, Cornish-Bowden A, Rasnick D, Heng HH, Horne S, Abdallah B, Liu G, Ye CJ, Bloomfield M, Vincent MD, Aldaz CM, Karlsson J, Valind A, Jansson C, Gisselsson D, Graves JAM, Stepanenko AA, Andreieva SV, Korets KV, Mykytenko DO, Huleyuk NL, Baklaushev VP, Kovaleva OA, Chekhonin VP, Vassetzky YS, Avdieiev SS, Bakker B, Taudt AS, Belderbos ME, Porubsky D, Spierings DCJ, de Jong TV, Halsema N, Kazemier HG, Hoekstra-Wakker K, Bradley A, de Bont ESJM, van den Berg A, Guryev V, Lansdorp PM, Tatché MC, Foijer F, Liehr T, Baudoin NC, Nicholson JM, Soto K, Quintanilla I, Camps J, Cimini D, Dürrbaum M, Donnelly N, Passerini V, Kruse C, Habermann B, Storchová Z, Mandrioli D, Belpoggi F, Silbergeld EK, Perry MJ, Skotheim RI, Løvf M, Johannessen B, Hoff AM, Zhao S, SveeStrømme JM, Sveen A, Lothe RA, Hehlmann R, Voskanyan A, Fabarius A, Böcking A, Biesterfeld S, Berynskyy L, Börgermann C, Engers R, Dietz J, Fritz A, Sehgal N, Vecerova J, Stojkovicz B, Ding H, Page N, Tye C, Bhattacharya S, Xu J, Stein G, Stein J, Berezney R, Gong X, Grasedieck S, Swoboda J, Rücker FG, Bullinger L, Pollack JR, Roumelioti FM, Chiourea M, Raftopoulou C, Gagos S, Duesberg P, Bloomfield M, Hwang S, Gustafsson HT, O’Sullivan C, Acevedo-Colina A, Huang X, Klose C, Schevchenko A, Dickson RC, Cavaliere P, Dephoure N, Torres EM, Stampfer MR, Vrba L, LaBarge MA, Futscher B, Garbe JC, Zhou YH, Trinh AL, Zhou YH, Digman M. Abstracts from the 3rd Conference on Aneuploidy and Cancer: Clinical and Experimental Aspects. Mol Cytogenet 2017. [PMCID: PMC5499067 DOI: 10.1186/s13039-017-0320-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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27
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Hoffmann RF, Moshkin YM, Mouton S, Grzeschik NA, Kalicharan RD, Kuipers J, Wolters AHG, Nishida K, Romashchenko AV, Postberg J, Lipps H, Berezikov E, Sibon OCM, Giepmans BNG, Lansdorp PM. Guanine quadruplex structures localize to heterochromatin. Nucleic Acids Res 2017; 45:6253. [PMID: 28449026 PMCID: PMC5449592 DOI: 10.1093/nar/gkx301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Roland F Hoffmann
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Yuri M Moshkin
- Department of Biochemistry, Erasmus University Medical Center, Dr. Molewaterplein 50, NL-3015 GE Rotterdam, The Netherlands
| | - Stijn Mouton
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Nicola A Grzeschik
- Department of Cell Biology, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Ruby D Kalicharan
- Department of Cell Biology, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Jeroen Kuipers
- Department of Cell Biology, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Anouk H G Wolters
- Department of Cell Biology, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Kazuki Nishida
- Faculty of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Aleksander V Romashchenko
- Department of Biochemistry, Erasmus University Medical Center, Dr. Molewaterplein 50, NL-3015 GE Rotterdam, The Netherlands.,Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Jan Postberg
- Helios Medical Centre Wuppertal, Paediatrics Centre, Witten/Herdecke University, Wuppertal, Germany
| | - Hans Lipps
- Institute of Cell Biology, Centre for Biomedical Education and Research, Witten/Herdecke University, Witten, Germany
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands.,Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Ody C M Sibon
- Department of Cell Biology, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Ben N G Giepmans
- Department of Cell Biology, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Peter M Lansdorp
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands.,Terry Fox Laboratory, British Columbia Cancer Agency and Department of Medicine, University of British Columbia Vancouver, BC, V5Z 1L3, Canada
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28
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Sanders AD, Falconer E, Hills M, Spierings DCJ, Lansdorp PM. Single-cell template strand sequencing by Strand-seq enables the characterization of individual homologs. Nat Protoc 2017; 12:1151-1176. [PMID: 28492527 DOI: 10.1038/nprot.2017.029] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The ability to distinguish between genome sequences of homologous chromosomes in single cells is important for studies of copy-neutral genomic rearrangements (such as inversions and translocations), building chromosome-length haplotypes, refining genome assemblies, mapping sister chromatid exchange events and exploring cellular heterogeneity. Strand-seq is a single-cell sequencing technology that resolves the individual homologs within a cell by restricting sequence analysis to the DNA template strands used during DNA replication. This protocol, which takes up to 4 d to complete, relies on the directionality of DNA, in which each single strand of a DNA molecule is distinguished based on its 5'-3' orientation. Culturing cells in a thymidine analog for one round of cell division labels nascent DNA strands, allowing for their selective removal during genomic library construction. To preserve directionality of template strands, genomic preamplification is bypassed and labeled nascent strands are nicked and not amplified during library preparation. Each single-cell library is multiplexed for pooling and sequencing, and the resulting sequence data are aligned, mapping to either the minus or plus strand of the reference genome, to assign template strand states for each chromosome in the cell. The major adaptations to conventional single-cell sequencing protocols include harvesting of daughter cells after a single round of BrdU incorporation, bypassing of whole-genome amplification, and removal of the BrdU+ strand during Strand-seq library preparation. By sequencing just template strands, the structure and identity of each homolog are preserved.
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Affiliation(s)
- Ashley D Sanders
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Ester Falconer
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Mark Hills
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Diana C J Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Peter M Lansdorp
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.,European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
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29
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Foijer F, Albacker LA, Bakker B, Spierings DC, Yue Y, Xie SZ, Davis S, Lutum-Jehle A, Takemoto D, Hare B, Furey B, Bronson RT, Lansdorp PM, Bradley A, Sorger PK. Deletion of the MAD2L1 spindle assembly checkpoint gene is tolerated in mouse models of acute T-cell lymphoma and hepatocellular carcinoma. eLife 2017; 6. [PMID: 28318489 PMCID: PMC5400506 DOI: 10.7554/elife.20873] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 03/18/2017] [Indexed: 12/17/2022] Open
Abstract
Chromosome instability (CIN) is deleterious to normal cells because of the burden of aneuploidy. However, most human solid tumors have an abnormal karyotype implying that gain and loss of chromosomes by cancer cells confers a selective advantage. CIN can be induced in the mouse by inactivating the spindle assembly checkpoint. This is lethal in the germline but we show here that adult T cells and hepatocytes can survive conditional inactivation of the Mad2l1 SAC gene and resulting CIN. This causes rapid onset of acute lymphoblastic leukemia (T-ALL) and progressive development of hepatocellular carcinoma (HCC), both lethal diseases. The resulting DNA copy number variation and patterns of chromosome loss and gain are tumor-type specific, suggesting differential selective pressures on the two tumor cell types.
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Affiliation(s)
- Floris Foijer
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Lee A Albacker
- Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Bjorn Bakker
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Diana C Spierings
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Ying Yue
- Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Stephanie Z Xie
- Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Stephanie Davis
- Department of Systems Biology, Harvard Medical School, Boston, United States
| | | | - Darin Takemoto
- Vertex Pharmaceuticals Incorporated, Cambridge, United States
| | - Brian Hare
- Vertex Pharmaceuticals Incorporated, Cambridge, United States
| | - Brinley Furey
- Vertex Pharmaceuticals Incorporated, Cambridge, United States
| | - Roderick T Bronson
- Rodent Histopathology Core, Dana-Farber/Harvard Cancer Center, Harvard Medical School, Boston, United States
| | | | - Allan Bradley
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Peter K Sorger
- Department of Systems Biology, Harvard Medical School, Boston, United States
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30
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Levine MS, Bakker B, Boeckx B, Moyett J, Lu J, Vitre B, Spierings DC, Lansdorp PM, Cleveland DW, Lambrechts D, Foijer F, Holland AJ. Centrosome Amplification Is Sufficient to Promote Spontaneous Tumorigenesis in Mammals. Dev Cell 2017; 40:313-322.e5. [PMID: 28132847 DOI: 10.1016/j.devcel.2016.12.022] [Citation(s) in RCA: 237] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/14/2016] [Accepted: 12/23/2016] [Indexed: 12/14/2022]
Abstract
Centrosome amplification is a common feature of human tumors, but whether this is a cause or a consequence of cancer remains unclear. Here, we test the consequence of centrosome amplification by creating mice in which centrosome number can be chronically increased in the absence of additional genetic defects. We show that increasing centrosome number elevated tumor initiation in a mouse model of intestinal neoplasia. Most importantly, we demonstrate that supernumerary centrosomes are sufficient to drive aneuploidy and the development of spontaneous tumors in multiple tissues. Tumors arising from centrosome amplification exhibit frequent mitotic errors and possess complex karyotypes, recapitulating a common feature of human cancer. Together, our data support a direct causal relationship among centrosome amplification, genomic instability, and tumor development.
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Affiliation(s)
- Michelle S Levine
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Bjorn Bakker
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, the Netherlands
| | - Bram Boeckx
- Laboratory of Translational Genetics, Vesalius Research Center, VIB, 3000 Leuven, Belgium; Laboratory of Translational Genetics, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Julia Moyett
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - James Lu
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Benjamin Vitre
- CNRS UMR-5237, Centre de Recherche en Biochimie Macromoleculaire, University of Montpellier, Montpellier 34093, France
| | - Diana C Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, the Netherlands
| | - Peter M Lansdorp
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, the Netherlands
| | - Don W Cleveland
- San Diego Branch, Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA; Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Diether Lambrechts
- Laboratory of Translational Genetics, Vesalius Research Center, VIB, 3000 Leuven, Belgium; Laboratory of Translational Genetics, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Floris Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, the Netherlands
| | - Andrew J Holland
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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Aubert G, Strauss KA, Lansdorp PM, Rider NL. Defects in lymphocyte telomere homeostasis contribute to cellular immune phenotype in patients with cartilage-hair hypoplasia. J Allergy Clin Immunol 2017; 140:1120-1129.e1. [PMID: 28126377 DOI: 10.1016/j.jaci.2016.11.051] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 10/18/2016] [Accepted: 11/01/2016] [Indexed: 12/20/2022]
Abstract
BACKGROUND Mutations in the long noncoding RNA RNase component of the mitochondrial RNA processing endoribonuclease (RMRP) give rise to the autosomal recessive condition cartilage-hair hypoplasia (CHH). The CHH disease phenotype has some overlap with dyskeratosis congenita, a well-known "telomere disorder." RMRP binds the telomerase reverse transcriptase (catalytic subunit) in some cell lines, raising the possibility that RMRP might play a role in telomere biology. OBJECTIVE We sought to determine whether a telomere phenotype is present in immune cells from patients with CHH and explore mechanisms underlying these observations. METHODS We assessed proliferative capacity and telomere length using flow-fluorescence in situ hybridization (in situ hybridization and flow cytometry) of primary lymphocytes from patients with CHH, carrier relatives, and control subjects. The role of telomerase holoenzyme components in gene expression and activity were assessed by using quantitative PCR and the telomere repeat amplification protocol from PBMCs and enriched lymphocyte cultures. RESULTS Lymphocyte cultures from patients with CHH display growth defects in vitro, which is consistent with an immune deficiency cellular phenotype. Here we show that telomere length and telomerase activity are impaired in primary lymphocyte subsets from patients with CHH. Notably, telomerase activity is affected in a gene dose-dependent manner when comparing heterozygote RMRP carriers with patients with CHH. Telomerase deficiency in patients with CHH is not mediated by abnormal telomerase gene transcript levels relative to those of endogenous genes. CONCLUSION These findings suggest that telomere deficiency is implicated in the CHH disease phenotype through an as yet unidentified mechanism.
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Affiliation(s)
- Geraldine Aubert
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Peter M Lansdorp
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada; Division of Hematology, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; European Research Institute on the Biology of Aging, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands.
| | - Nicholas L Rider
- Section of Immunology, Allergy and Rheumatology, Texas Children's Hospital, Baylor College of Medicine, Houston, Tex.
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Porubský D, Sanders AD, van Wietmarschen N, Falconer E, Hills M, Spierings DCJ, Bevova MR, Guryev V, Lansdorp PM. Direct chromosome-length haplotyping by single-cell sequencing. Genome Res 2016; 26:1565-1574. [PMID: 27646535 PMCID: PMC5088598 DOI: 10.1101/gr.209841.116] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 09/15/2016] [Indexed: 11/25/2022]
Abstract
Haplotypes are fundamental to fully characterize the diploid genome of an individual, yet methods to directly chart the unique genetic makeup of each parental chromosome are lacking. Here we introduce single-cell DNA template strand sequencing (Strand-seq) as a novel approach to phasing diploid genomes along the entire length of all chromosomes. We demonstrate this by building a complete haplotype for a HapMap individual (NA12878) at high accuracy (concordance 99.3%), without using generational information or statistical inference. By use of this approach, we mapped all meiotic recombination events in a family trio with high resolution (median range ∼14 kb) and phased larger structural variants like deletions, indels, and balanced rearrangements like inversions. Lastly, the single-cell resolution of Strand-seq allowed us to observe loss of heterozygosity regions in a small number of cells, a significant advantage for studies of heterogeneous cell populations, such as cancer cells. We conclude that Strand-seq is a unique and powerful approach to completely phase individual genomes and map inheritance patterns in families, while preserving haplotype differences between single cells.
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Affiliation(s)
- David Porubský
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
| | - Ashley D Sanders
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Niek van Wietmarschen
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
| | - Ester Falconer
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Mark Hills
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Diana C J Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
| | - Marianna R Bevova
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
| | - Peter M Lansdorp
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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Sanders AD, Hills M, Porubský D, Guryev V, Falconer E, Lansdorp PM. Characterizing polymorphic inversions in human genomes by single-cell sequencing. Genome Res 2016; 26:1575-1587. [PMID: 27472961 PMCID: PMC5088599 DOI: 10.1101/gr.201160.115] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 06/13/2016] [Indexed: 12/23/2022]
Abstract
Identifying genomic features that differ between individuals and cells can help uncover the functional variants that drive phenotypes and disease susceptibilities. For this, single-cell studies are paramount, as it becomes increasingly clear that the contribution of rare but functional cellular subpopulations is important for disease prognosis, management, and progression. Until now, studying these associations has been challenged by our inability to map structural rearrangements accurately and comprehensively. To overcome this, we coupled single-cell sequencing of DNA template strands (Strand-seq) with custom analysis software to rapidly discover, map, and genotype genomic rearrangements at high resolution. This allowed us to explore the distribution and frequency of inversions in a heterogeneous cell population, identify several polymorphic domains in complex regions of the genome, and locate rare alleles in the reference assembly. We then mapped the entire genomic complement of inversions within two unrelated individuals to characterize their distinct inversion profiles and built a nonredundant global reference of structural rearrangements in the human genome. The work described here provides a powerful new framework to study structural variation and genomic heterogeneity in single-cell samples, whether from individuals for population studies or tissue types for biomarker discovery.
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Affiliation(s)
- Ashley D Sanders
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Mark Hills
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - David Porubský
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, NL-9713 AV Groningen, The Netherlands
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, NL-9713 AV Groningen, The Netherlands
| | - Ester Falconer
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Peter M Lansdorp
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada.,European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, NL-9713 AV Groningen, The Netherlands.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
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Bakker B, Taudt A, Belderbos ME, Porubsky D, Spierings DCJ, de Jong TV, Halsema N, Kazemier HG, Hoekstra-Wakker K, Bradley A, de Bont ESJM, van den Berg A, Guryev V, Lansdorp PM, Colomé-Tatché M, Foijer F. Single-cell sequencing reveals karyotype heterogeneity in murine and human malignancies. Genome Biol 2016; 17:115. [PMID: 27246460 PMCID: PMC4888588 DOI: 10.1186/s13059-016-0971-7] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 04/29/2016] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Chromosome instability leads to aneuploidy, a state in which cells have abnormal numbers of chromosomes, and is found in two out of three cancers. In a chromosomal instable p53 deficient mouse model with accelerated lymphomagenesis, we previously observed whole chromosome copy number changes affecting all lymphoma cells. This suggests that chromosome instability is somehow suppressed in the aneuploid lymphomas or that selection for frequently lost/gained chromosomes out-competes the CIN-imposed mis-segregation. RESULTS To distinguish between these explanations and to examine karyotype dynamics in chromosome instable lymphoma, we use a newly developed single-cell whole genome sequencing (scWGS) platform that provides a complete and unbiased overview of copy number variations (CNV) in individual cells. To analyse these scWGS data, we develop AneuFinder, which allows annotation of copy number changes in a fully automated fashion and quantification of CNV heterogeneity between cells. Single-cell sequencing and AneuFinder analysis reveals high levels of copy number heterogeneity in chromosome instability-driven murine T-cell lymphoma samples, indicating ongoing chromosome instability. Application of this technology to human B cell leukaemias reveals different levels of karyotype heterogeneity in these cancers. CONCLUSION Our data show that even though aneuploid tumours select for particular and recurring chromosome combinations, single-cell analysis using AneuFinder reveals copy number heterogeneity. This suggests ongoing chromosome instability that other platforms fail to detect. As chromosome instability might drive tumour evolution, karyotype analysis using single-cell sequencing technology could become an essential tool for cancer treatment stratification.
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Affiliation(s)
- Bjorn Bakker
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Aaron Taudt
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Mirjam E Belderbos
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713 AV, The Netherlands
- Department of Paediatrics, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - David Porubsky
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Diana C J Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Tristan V de Jong
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Nancy Halsema
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Hinke G Kazemier
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Karina Hoekstra-Wakker
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Allan Bradley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
| | - Eveline S J M de Bont
- Department of Paediatrics, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Anke van den Berg
- Department of Pathology & Medical Biology, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Peter M Lansdorp
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713 AV, The Netherlands
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada
- Division of Hematology, Department of Medicine, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Maria Colomé-Tatché
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713 AV, The Netherlands.
- Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg, 85764, Germany.
| | - Floris Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713 AV, The Netherlands.
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35
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Affiliation(s)
- Peter M Lansdorp
- From the European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; and the Terry Fox Laboratory, BC Cancer Agency, and Division of Hematology, Department of Medicine, University of British Columbia - both in Vancouver, BC, Canada
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van Wietmarschen N, Lansdorp PM. Bromodeoxyuridine does not contribute to sister chromatid exchange events in normal or Bloom syndrome cells. Nucleic Acids Res 2016; 44:6787-93. [PMID: 27185886 PMCID: PMC5001594 DOI: 10.1093/nar/gkw422] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 05/05/2016] [Indexed: 12/12/2022] Open
Abstract
Sister chromatid exchanges (SCEs) are considered sensitive indicators of genome instability. Detection of SCEs typically requires cells to incorporate bromodeoxyuridine (BrdU) during two rounds of DNA synthesis. Previous studies have suggested that SCEs are induced by DNA replication over BrdU-substituted DNA and that BrdU incorporation alone could be responsible for the high number of SCE events observed in cells from patients with Bloom syndrome (BS), a rare genetic disorder characterized by marked genome instability and high SCE frequency. Here we show using Strand-seq, a single cell DNA template strand sequencing technique, that the presence of variable BrdU concentrations in the cell culture medium and in DNA template strands has no effect on SCE frequency in either normal or BS cells. We conclude that BrdU does not induce SCEs and that SCEs detected in either normal or BS cells reflect DNA repair events that occur spontaneously.
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Affiliation(s)
- Niek van Wietmarschen
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Peter M Lansdorp
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, The Netherlands Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada Division of Hematology, Department of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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Hoffmann RF, Moshkin YM, Mouton S, Grzeschik NA, Kalicharan RD, Kuipers J, Wolters AHG, Nishida K, Romashchenko AV, Postberg J, Lipps H, Berezikov E, Sibon OCM, Giepmans BNG, Lansdorp PM. Guanine quadruplex structures localize to heterochromatin. Nucleic Acids Res 2015; 44:152-63. [PMID: 26384414 PMCID: PMC4705689 DOI: 10.1093/nar/gkv900] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/21/2015] [Indexed: 12/27/2022] Open
Abstract
Increasing amounts of data support a role for guanine quadruplex (G4) DNA and RNA structures in various cellular processes. We stained different organisms with monoclonal antibody 1H6 specific for G4 DNA. Strikingly, immuno-electron microscopy showed exquisite specificity for heterochromatin. Polytene chromosomes from Drosophila salivary glands showed bands that co-localized with heterochromatin proteins HP1 and the SNF2 domain-containing protein SUUR. Staining was retained in SUUR knock-out mutants but lost upon overexpression of SUUR. Somatic cells in Macrostomum lignano were strongly labeled, but pluripotent stem cells labeled weakly. Similarly, germline stem cells in Drosophila ovaries were weakly labeled compared to most other cells. The unexpected presence of G4 structures in heterochromatin and the difference in G4 staining between somatic cells and stem cells with germline DNA in ciliates, flatworms, flies and mammals point to a conserved role for G4 structures in nuclear organization and cellular differentiation.
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Affiliation(s)
- Roland F Hoffmann
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Yuri M Moshkin
- Department of Biochemistry, Erasmus University Medical Center, Dr. Molewaterplein 50, NL-3015 GE Rotterdam, The Netherlands
| | - Stijn Mouton
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Nicola A Grzeschik
- Department of Cell Biology, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Ruby D Kalicharan
- Department of Cell Biology, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Jeroen Kuipers
- Department of Cell Biology, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Anouk H G Wolters
- Department of Cell Biology, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Kazuki Nishida
- Faculty of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Aleksander V Romashchenko
- Department of Biochemistry, Erasmus University Medical Center, Dr. Molewaterplein 50, NL-3015 GE Rotterdam, The Netherlands Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Jan Postberg
- Helios Medical Centre Wuppertal, Paediatrics Centre, Witten/Herdecke University, Wuppertal, Germany
| | - Hans Lipps
- Institute of Cell Biology, Centre for Biomedical Education and Research, Witten/Herdecke University, Witten, Germany
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Ody C M Sibon
- Department of Cell Biology, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Ben N G Giepmans
- Department of Cell Biology, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Peter M Lansdorp
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands Terry Fox Laboratory, British Columbia Cancer Agency and Department of Medicine, University of British Columbia Vancouver, BC, V5Z 1L3, Canada
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Buganim Y, Markoulaki S, van Wietmarschen N, Hoke H, Wu T, Ganz K, Akhtar-Zaidi B, He Y, Abraham BJ, Porubsky D, Kulenkampff E, Faddah DA, Shi L, Gao Q, Sarkar S, Cohen M, Goldmann J, Nery JR, Schultz MD, Ecker JR, Xiao A, Young RA, Lansdorp PM, Jaenisch R. The developmental potential of iPSCs is greatly influenced by reprogramming factor selection. Cell Stem Cell 2015; 15:295-309. [PMID: 25192464 DOI: 10.1016/j.stem.2014.07.003] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 03/09/2014] [Accepted: 07/15/2014] [Indexed: 01/31/2023]
Abstract
Induced pluripotent stem cells (iPSCs) are commonly generated by transduction of Oct4, Sox2, Klf4, and Myc (OSKM) into cells. Although iPSCs are pluripotent, they frequently exhibit high variation in terms of quality, as measured in mice by chimera contribution and tetraploid complementation. Reliably high-quality iPSCs will be needed for future therapeutic applications. Here, we show that one major determinant of iPSC quality is the combination of reprogramming factors used. Based on tetraploid complementation, we found that ectopic expression of Sall4, Nanog, Esrrb, and Lin28 (SNEL) in mouse embryonic fibroblasts (MEFs) generated high-quality iPSCs more efficiently than other combinations of factors including OSKM. Although differentially methylated regions, transcript number of master regulators, establishment of specific superenhancers, and global aneuploidy were comparable between high- and low-quality lines, aberrant gene expression, trisomy of chromosome 8, and abnormal H2A.X deposition were distinguishing features that could potentially also be applicable to human.
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Affiliation(s)
- Yosef Buganim
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel.
| | | | - Niek van Wietmarschen
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, AV Groningen 9713, the Netherlands
| | - Heather Hoke
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tao Wu
- Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
| | - Kibibi Ganz
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | | | - Yupeng He
- Genomic Analysis Laboratory, Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - David Porubsky
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, AV Groningen 9713, the Netherlands
| | | | - Dina A Faddah
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Linyu Shi
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Qing Gao
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Sovan Sarkar
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Malkiel Cohen
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Johanna Goldmann
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Joseph R Nery
- Genomic Analysis Laboratory, Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Matthew D Schultz
- Genomic Analysis Laboratory, Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Andrew Xiao
- Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Skolkovo Institute of Science and Technology (Skoltech), Novaya strazha 100, Skolkovo Moscow Region 143025, Russia
| | - Peter M Lansdorp
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, AV Groningen 9713, the Netherlands; Skolkovo Institute of Science and Technology (Skoltech), Novaya strazha 100, Skolkovo Moscow Region 143025, Russia
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Skolkovo Institute of Science and Technology (Skoltech), Novaya strazha 100, Skolkovo Moscow Region 143025, Russia.
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Bakker B, van den Bos H, Lansdorp PM, Foijer F. How to count chromosomes in a cell: An overview of current and novel technologies. Bioessays 2015; 37:570-7. [PMID: 25739518 DOI: 10.1002/bies.201400218] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 02/05/2015] [Accepted: 02/13/2015] [Indexed: 12/25/2022]
Abstract
Aneuploidy, an aberrant number of chromosomes in a cell, is a feature of several syndromes associated with cognitive and developmental defects. In addition, aneuploidy is considered a hallmark of cancer cells and has been suggested to play a role in neurodegenerative disease. To better understand the relationship between aneuploidy and disease, various methods to measure the chromosome numbers in cells have been developed, each with their own advantages and limitations. While some methods rely on dividing cells and thus bias aneuploidy rates to that population, other, more unbiased methods can only detect the average aneuploidy rates in a cell population, cloaking cell-to-cell heterogeneity. Furthermore, some techniques are more prone to technical artefacts, which can result in over- or underestimation of aneuploidy rates. In this review, we provide an overview of several "traditional" karyotyping methods as well as the latest high throughput next generation sequencing karyotyping protocols with their respective advantages and disadvantages.
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Affiliation(s)
- Bjorn Bakker
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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Abstract
Telomere associations have been observed during key cellular processes such as mitosis, meiosis, and carcinogenesis and must be resolved before cell division to prevent genome instability. Here we establish that telomeric repeat-binding factor 1 (TRF1), a core component of the telomere protein complex, is a mediator of telomere associations in mammalian cells. Using live-cell imaging, we show that expression of TRF1 or yellow fluorescent protein (YFP)-TRF1 fusion protein above endogenous levels prevents proper telomere resolution during mitosis. TRF1 overexpression results in telomere anaphase bridges and aggregates containing TRF1 protein and telomeric DNA. Site-specific protein cleavage of YFP-TRF1 by tobacco etch virus protease resolves telomere aggregates, indicating that telomere associations are mediated by TRF1. This study provides novel insight into the formation and resolution of telomere associations.
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Affiliation(s)
- Kathleen Lisaingo
- Terry Fox Laboratory, BC Cancer Research Centre, University of British Columbia, Vancouver, BC V5Z 1L3, Canada
| | - Evert-Jan Uringa
- Terry Fox Laboratory, BC Cancer Research Centre, University of British Columbia, Vancouver, BC V5Z 1L3, CanadaEuropean Research Institute for the Biology of Ageing, University of Groningen, University Medical CentreGroningen, NL-9713 AV Groningen, Netherlands
| | - Peter M Lansdorp
- Terry Fox Laboratory, BC Cancer Research Centre, University of British Columbia, Vancouver, BC V5Z 1L3, CanadaEuropean Research Institute for the Biology of Ageing, University of Groningen, University Medical CentreGroningen, NL-9713 AV Groningen, Netherlands
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Henderson A, Wu Y, Huang YC, Chavez EA, Platt J, Johnson FB, Brosh RM, Sen D, Lansdorp PM. Detection of G-quadruplex DNA in mammalian cells. Nucleic Acids Res 2013; 42:860-9. [PMID: 24163102 PMCID: PMC3902944 DOI: 10.1093/nar/gkt957] [Citation(s) in RCA: 356] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
It has been proposed that guanine-rich DNA forms four-stranded structures in vivo called G-quadruplexes or G4 DNA. G4 DNA has been implicated in several biological processes, but tools to study G4 DNA structures in cells are limited. Here we report the development of novel murine monoclonal antibodies specific for different G4 DNA structures. We show that one of these antibodies designated 1H6 exhibits strong nuclear staining in most human and murine cells. Staining intensity increased on treatment of cells with agents that stabilize G4 DNA and, strikingly, cells deficient in FANCJ, a G4 DNA-specific helicase, showed stronger nuclear staining than controls. Our data strongly support the existence of G4 DNA structures in mammalian cells and indicate that the abundance of such structures is increased in the absence of FANCJ. We conclude that monoclonal antibody 1H6 is a valuable tool for further studies on the role of G4 DNA in cell and molecular biology.
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Affiliation(s)
- Alexander Henderson
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, Baltimore, MD 21224, USA, Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104-6100, USA, Division of Hematology, Department of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada and European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
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42
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Frumento G, Zheng Y, Aubert G, Raeiszadeh M, Lansdorp PM, Moss P, Lee SP, Chen FE. Cord blood T cells retain early differentiation phenotype suitable for immunotherapy after TCR gene transfer to confer EBV specificity. Am J Transplant 2013; 13:45-55. [PMID: 23016879 DOI: 10.1111/j.1600-6143.2012.04286.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Revised: 08/20/2012] [Accepted: 08/20/2012] [Indexed: 01/25/2023]
Abstract
Adoptive T cell therapy can be effective for Epstein-Barr virus (EBV)-associated posttransplant lymphoproliferative disease and melanoma. Transducing high-affinity TCR genes into T lymphocytes is an emerging method to improve potency and specificity of tumor-specific T cells. However, both methods necessitate in vitro lymphocyte proliferation, generating highly differentiated effector cells that display reduced survival and antitumor efficacy postinfusion. TCR-transduction of naive lymphocytes isolated from peripheral blood is reported to provide superior in vivo survival and function. We utilized cord blood (CB) lymphocytes, which comprise mainly naive cells, for transducing EBV-specific TCR. Comparable TCR expression was achieved in adult and CB cells, but the latter expressed an earlier differentiation profile. Further antigen-driven stimulation skewed adult lymphocytes to a late differentiation phenotype associated with immune exhaustion. In contrast, CB T cells retained a less differentiated phenotype after antigen stimulation, remaining CD57-negative but were still capable of antigen-specific polyfunctional cytokine expression and cytotoxicity in response to EBV antigen. CB T cells also retained longer telomeres and in general possessed higher telomerase activity indicative of greater proliferative potential. CB lymphocytes therefore have qualities indicating prolonged survival and effector function favorable to immunotherapy, especially in settings where donor lymphocytes are unavailable such as in solid organ and CB transplantation.
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Affiliation(s)
- G Frumento
- NHS Blood and Transplant, Birmingham, UK
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43
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van Wietmarschen N, Moradian A, Morin GB, Lansdorp PM, Uringa EJ. The mammalian proteins MMS19, MIP18, and ANT2 are involved in cytoplasmic iron-sulfur cluster protein assembly. J Biol Chem 2012; 287:43351-8. [PMID: 23150669 DOI: 10.1074/jbc.m112.431270] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Iron-sulfur (Fe-S) clusters are essential cofactors of proteins with a wide range of biological functions. A dedicated cytosolic Fe-S cluster assembly (CIA) system is required to assemble Fe-S clusters into cytosolic and nuclear proteins. Here, we show that the mammalian nucleotide excision repair protein homolog MMS19 can simultaneously bind probable cytosolic iron-sulfur protein assembly protein CIAO1 and Fe-S proteins, confirming that MMS19 is a central protein of the CIA machinery that brings Fe-S cluster donor proteins and the receiving apoproteins into proximity. In addition, we show that mitotic spindle-associated MMXD complex subunit MIP18 also interacts with both CIAO1 and Fe-S proteins. Specifically, it binds the Fe-S cluster coordinating regions in Fe-S proteins. Furthermore, we show that ADP/ATP translocase 2 (ANT2) interacts with Fe-S apoproteins and MMS19 in the CIA complex but not with the individual proteins. Together, these results elucidate the composition and interactions within the late CIA complex.
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Affiliation(s)
- Niek van Wietmarschen
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
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Abstract
Semi-conservative replication ensures that the DNA sequence of sister chromatids is identical except for replication errors and variation in the length of telomere repeats resulting from replicative losses and variable end processing. What happens with the various epigenetic marks during DNA replication is less clear. Many chromatin marks are likely to be copied onto both sister chromatids in conjunction with DNA replication, whereas others could be distributed randomly between sister chromatids. Epigenetic differences between sister chromatids could also emerge in a more predictable manner, for example, following processes that are associated with lagging strand DNA replication. The resulting epigenetic differences between sister chromatids could result in different gene expression patterns in daughter cells. This possibility has been difficult to test because techniques to distinguish between parental sister chromatids require analysis of single cells and are not obvious. Here, we briefly review the topic of sister chromatid epigenetics and discuss how the identification of sister chromatids in cells could change the way we think about asymmetric cell divisions and stochastic variation in gene expression between cells in general and paired daughter cells in particular.
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Affiliation(s)
- Peter M Lansdorp
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada.
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45
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Aubert G, Baerlocher GM, Vulto I, Poon SS, Lansdorp PM. Collapse of telomere homeostasis in hematopoietic cells caused by heterozygous mutations in telomerase genes. PLoS Genet 2012; 8:e1002696. [PMID: 22661914 PMCID: PMC3355073 DOI: 10.1371/journal.pgen.1002696] [Citation(s) in RCA: 167] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Accepted: 03/20/2012] [Indexed: 01/03/2023] Open
Abstract
Telomerase activity is readily detectable in extracts from human hematopoietic stem and progenitor cells, but appears unable to maintain telomere length with proliferation in vitro and with age in vivo. We performed a detailed study of the telomere length by flow FISH analysis in leukocytes from 835 healthy individuals and 60 individuals with reduced telomerase activity. Healthy individuals showed a broad range in average telomere length in granulocytes and lymphocytes at any given age. The average telomere length declined with age at a rate that differed between age-specific breakpoints and between cell types. Gender differences between leukocyte telomere lengths were observed for all cell subsets studied; interestingly, this trend could already be detected at birth. Heterozygous carriers for mutations in either the telomerase reverse transcriptase (hTERT) or the telomerase RNA template (hTERC) gene displayed striking and comparable telomere length deficits. Further, non-carrier relatives of such heterozygous individuals had somewhat shorter leukocyte telomere lengths than expected; this difference was most profound for granulocytes. Failure to maintain telomere homeostasis as a result of partial telomerase deficiency is thought to trigger cell senescence or cell death, eventually causing tissue failure syndromes. Our data are consistent with these statements and suggest that the likelihood of similar processes occurring in normal individuals increases with age. Our work highlights the essential role of telomerase in the hematopoietic system and supports the notion that telomerase levels in hematopoietic cells, while limiting and unable to prevent overall telomere shortening, are nevertheless crucial to maintain telomere homeostasis with age. Human blood cells all originate from a common precursor, the hematopoietic stem cell. Telomerase, the enzyme responsible for adding telomere repeats to chromosome ends, is active in human hematopoietic stem cells but appears unable to maintain a constant telomere length with age. We first document the telomere length of different blood cell subsets from 835 healthy individuals between birth and 100 years, to delineate the normal rate of telomere attrition with age. Telomere lengths of blood cells were found to be slightly longer in women than in men, from birth and throughout life. We then compared this reference data to the telomere length in similar blood cell subsets from individuals with reduced telomerase activity as a result of a mutation in one of the genes encoding telomerase and from their direct relatives. Strikingly short telomeres were found in telomerase-deficient individuals, consistent with their cellular pathology and disease susceptibility, and somewhat shorter telomeres than expected were found in cells of relatives with normal telomerase maintenance. Our data can be used as a reference for blood cell telomere length in studies of normal and accelerated aging.
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Affiliation(s)
- Geraldine Aubert
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Gabriela M. Baerlocher
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
- Experimental Hematology, Department of Clinical Research, University of Bern, Bern, Switzerland
| | - Irma Vulto
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Steven S. Poon
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Peter M. Lansdorp
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
- Division of Hematology, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
- * E-mail: ;
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Uringa EJ, Lisaingo K, Pickett HA, Brind'Amour J, Rohde JH, Zelensky A, Essers J, Lansdorp PM. RTEL1 contributes to DNA replication and repair and telomere maintenance. Mol Biol Cell 2012; 23:2782-92. [PMID: 22593209 PMCID: PMC3395665 DOI: 10.1091/mbc.e12-03-0179] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Telomere maintenance and DNA repair are important processes that protect the genome. The essential helicase mRtel1 functions in homologous recombination repair and replication. In addition, telomeres in mRtel-deficient ES cells appear relatively stable in length, suggesting that mRtel1 is required to allow extension by telomerase. Telomere maintenance and DNA repair are important processes that protect the genome against instability. mRtel1, an essential helicase, is a dominant factor setting telomere length in mice. In addition, mRtel1 is involved in DNA double-strand break repair. The role of mRtel1 in telomere maintenance and genome stability is poorly understood. Therefore we used mRtel1-deficient mouse embryonic stem cells to examine the function of mRtel1 in replication, DNA repair, recombination, and telomere maintenance. mRtel1-deficient mouse embryonic stem cells showed sensitivity to a range of DNA-damaging agents, highlighting its role in replication and genome maintenance. Deletion of mRtel1 increased the frequency of sister chromatid exchange events and suppressed gene replacement, demonstrating the involvement of the protein in homologous recombination. mRtel1 localized transiently at telomeres and is needed for efficient telomere replication. Of interest, in the absence of mRtel1, telomeres in embryonic stem cells appeared relatively stable in length, suggesting that mRtel1 is required to allow extension by telomerase. We propose that mRtel1 is a key protein for DNA replication, recombination, and repair and efficient elongation of telomeres by telomerase.
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Alter BP, Rosenberg PS, Giri N, Baerlocher GM, Lansdorp PM, Savage SA. Telomere length is associated with disease severity and declines with age in dyskeratosis congenita. Haematologica 2011; 97:353-9. [PMID: 22058220 DOI: 10.3324/haematol.2011.055269] [Citation(s) in RCA: 151] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Dyskeratosis congenita is a cancer-prone bone marrow failure syndrome caused by aberrations in telomere biology. DESIGN AND METHODS We studied 65 patients with dyskeratosis congenita and 127 unaffected relatives. Telomere length was measured by automated multicolor flow fluorescence in situ hybridization in peripheral blood leukocyte subsets. We age-adjusted telomere length using Z-scores (standard deviations from the mean for age). RESULTS We confirmed that telomere lengths below the first percentile for age are very sensitive and specific for the diagnosis of dyskeratosis congenita. We provide evidence that lymphocytes alone and not granulocytes may suffice for clinical screening, while lymphocyte subsets may be required for challenging cases, including identification of silent carriers. We show for the first time using flow fluorescence in situ hybridization that the shortest telomeres are associated with severe variants (Hoyeraal-Hreidarsson and Revesz syndromes), mutations in DKC1, TINF2, or unknown genes, and moderate or severe aplastic anemia. In the first longitudinal follow up of dyskeratosis congenita patients, we demonstrate that telomere lengths decline with age, in contrast to the apparent stable telomere length observed in cross-sectional data. CONCLUSIONS Telomere length by flow fluorescence in situ hybridization is an important diagnostic test for dyskeratosis congenita; age-adjusted values provide a quantitative measure of disease severity (clinical subset, mutated gene, and degree of bone marrow failure). Patients with dyskeratosis congenita have accelerated telomere shortening. This study is registered at www.clinicaltrials.gov (identifier: NCT00027274).
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Affiliation(s)
- Blanche P Alter
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, MD 20852-7231, USA.
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Abstract
We developed a flow cytometry method, chromosome flow fluorescence in situ hybridization (FISH), called CFF, to analyze repetitive DNA in chromosomes using FISH with directly labeled peptide nucleic acid (PNA) probes. We used CFF to measure the abundance of interstitial telomeric sequences in Chinese hamster chromosomes and major satellite sequences in mouse chromosomes. Using CFF we also identified parental homologs of human chromosome 18 with different amounts of repetitive DNA.
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Affiliation(s)
- Julie Brind'Amour
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
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Alder JK, Cogan JD, Brown AF, Anderson CJ, Lawson WE, Lansdorp PM, Phillips JA, Loyd JE, Chen JJL, Armanios M. Ancestral mutation in telomerase causes defects in repeat addition processivity and manifests as familial pulmonary fibrosis. PLoS Genet 2011; 7:e1001352. [PMID: 21483807 PMCID: PMC3069110 DOI: 10.1371/journal.pgen.1001352] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2010] [Accepted: 02/23/2011] [Indexed: 01/05/2023] Open
Abstract
The telomerase reverse transcriptase synthesizes new telomeres onto chromosome ends by copying from a short template within its integral RNA component. During telomere synthesis, telomerase adds multiple short DNA repeats successively, a property known as repeat addition processivity. However, the consequences of defects in processivity on telomere length maintenance are not fully known. Germline mutations in telomerase cause haploinsufficiency in syndromes of telomere shortening, which most commonly manifest in the age-related disease idiopathic pulmonary fibrosis. We identified two pulmonary fibrosis families that share two non-synonymous substitutions in the catalytic domain of the telomerase reverse transcriptase gene hTERT: V791I and V867M. The two variants fell on the same hTERT allele and were associated with telomere shortening. Genealogy suggested that the pedigrees shared a single ancestor from the nineteenth century, and genetic studies confirmed the two families had a common founder. Functional studies indicated that, although the double mutant did not dramatically affect first repeat addition, hTERT V791I-V867M showed severe defects in telomere repeat addition processivity in vitro. Our data identify an ancestral mutation in telomerase with a novel loss-of-function mechanism. They indicate that telomere repeat addition processivity is a critical determinant of telomere length and telomere-mediated disease.
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Affiliation(s)
- Jonathan K. Alder
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Joy D. Cogan
- Department of Pediatrics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Andrew F. Brown
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, United States of America
| | - Collin J. Anderson
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - William E. Lawson
- Department of Medicine, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Peter M. Lansdorp
- Terry Fox Laboratory and Department of Medicine, University of British Columbia, Vancouver, Canada
| | - John A. Phillips
- Department of Pediatrics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - James E. Loyd
- Department of Medicine, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Julian J.-L. Chen
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, United States of America
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Mary Armanios
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
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50
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Shlush LI, Skorecki KL, Itzkovitz S, Yehezkel S, Segev Y, Shachar H, Berkovitz R, Adir Y, Vulto I, Lansdorp PM, Selig S. Telomere elongation followed by telomere length reduction, in leukocytes from divers exposed to intense oxidative stress – Implications for tissue and organismal aging. Mech Ageing Dev 2011; 132:123-30. [DOI: 10.1016/j.mad.2011.01.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Revised: 01/26/2011] [Accepted: 01/29/2011] [Indexed: 12/14/2022]
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