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Bekaert B, Boel A, Rybouchkin A, Cosemans G, Declercq S, Chuva de Sousa Lopes SM, Parrington J, Stoop D, Coucke P, Menten B, Heindryckx B. Various repair events following CRISPR/Cas9-based mutational correction of an infertility-related mutation in mouse embryos. J Assist Reprod Genet 2024; 41:1605-1617. [PMID: 38557805 PMCID: PMC11224219 DOI: 10.1007/s10815-024-03095-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 03/12/2024] [Indexed: 04/04/2024] Open
Abstract
PURPOSE Unpredictable genetic modifications and chromosomal aberrations following CRISPR/Cas9 administration hamper the efficacy of germline editing. Repair events triggered by double-strand DNA breaks (DSBs) besides non-homologous end joining and repair template-driven homology-directed repair have been insufficiently investigated in mouse. In this work, we are the first to investigate the precise repair mechanisms triggered by parental-specific DSB induction in mouse for paternal mutational correction in the context of an infertility-related mutation. METHODS We aimed to correct a paternal 22-nucleotide deletion in Plcz1, associated with lack of fertilisation in vitro, by administrating CRISPR/Cas9 components during intracytoplasmic injection of Plcz1-null sperm in wild-type oocytes combined with assisted oocyte activation. Through targeted next-generation sequencing, 77 injected embryos and 26 blastomeres from seven injected embryos were investigated. In addition, low-pass whole genome sequencing was successfully performed on 17 injected embryo samples. RESULTS Repair mechanisms induced by two different CRISPR/Cas9 guide RNA (gRNA) designs were investigated. In 13.73% (7/51; gRNA 1) and 19.05% (4/21; gRNA 2) of the targeted embryos, only the wild-type allele was observed, of which the majority (85.71%; 6/7) showed integrity of the targeted chromosome. Remarkably, for both designs, only in one of these embryos (1/7; gRNA 1 and 1/4; gRNA2) could repair template use be detected. This suggests that alternative repair events have occurred. Next, various genetic events within the same embryo were detected after single-cell analysis of four embryos. CONCLUSION Our results suggest the occurrence of mosaicism and complex repair events after CRISPR/Cas9 DSB induction where chromosomal integrity is predominantly contained.
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Affiliation(s)
- B Bekaert
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - A Boel
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - A Rybouchkin
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - G Cosemans
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - S Declercq
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - S M Chuva de Sousa Lopes
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, 2333 ZA, the Netherlands
| | - J Parrington
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - D Stoop
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - P Coucke
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - B Menten
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - B Heindryckx
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium.
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Taitt CR, Leski TA, Compton JR, Chen A, Berk KL, Dorsey RW, Sozhamannan S, Dutt DL, Vora GJ. Impact of template denaturation prior to whole genome amplification on gene detection in high GC-content species, Burkholderia mallei and B. pseudomallei. BMC Res Notes 2024; 17:70. [PMID: 38475810 DOI: 10.1186/s13104-024-06717-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/13/2024] [Indexed: 03/14/2024] Open
Abstract
OBJECTIVE In this study, we sought to determine the types and prevalence of antimicrobial resistance determinants (ARDs) in Burkholderia spp. strains using the Antimicrobial Resistance Determinant Microarray (ARDM). RESULTS Whole genome amplicons from 22 B. mallei (BM) and 37 B. pseudomallei (BP) isolates were tested for > 500 ARDs using ARDM v.3.1. ARDM detected the following Burkholderia spp.-derived genes, aac(6), blaBP/MBL-3, blaABPS, penA-BP, and qacE, in both BM and BP while blaBP/MBL-1, macB, blaOXA-42/43 and penA-BC were observed in BP only. The method of denaturing template for whole genome amplification greatly affected the numbers and types of genes detected by the ARDM. BlaTEM was detected in nearly a third of BM and BP amplicons derived from thermally, but not chemically denatured templates. BlaTEM results were confirmed by PCR, with 81% concordance between methods. Sequences from 414-nt PCR amplicons (13 preparations) were 100% identical to the Klebsiella pneumoniae reference gene. Although blaTEM sequences have been observed in B. glumae, B. cepacia, and other undefined Burkholderia strains, this is the first report of such sequences in BM/BP/B. thailandensis (BT) clade. These results highlight the importance of sample preparation in achieving adequate genome coverage in methods requiring untargeted amplification before analysis.
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Affiliation(s)
- Chris R Taitt
- Nova Research Inc., Alexandria, VA, 22308, USA
- Center for Biomolecular Science & Engineering, US Naval Research Laboratory, Washington, DC, USA
| | - Tomasz A Leski
- Center for Biomolecular Science & Engineering, US Naval Research Laboratory, Washington, DC, USA
| | - Jaimee R Compton
- Center for Biomolecular Science & Engineering, US Naval Research Laboratory, Washington, DC, USA
| | - Amy Chen
- Karle's Fellow, US Naval Research Laboratory, Washington, DC, USA
| | - Kimberly L Berk
- US Army Combat Capabilities Development Command-Chemical Biological Center, Aberdeen Proving Ground, MD, USA
| | - Robert W Dorsey
- US Army Combat Capabilities Development Command-Chemical Biological Center, Aberdeen Proving Ground, MD, USA
| | - Shanmuga Sozhamannan
- Defense Biological Product Assurance Office, Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND), Frederick, MD, USA
- Joint Research and Development, Inc., Stafford, VA, USA
| | - Dianne L Dutt
- Defense Threat Reduction Agency, Joint Science and Technology Office, Ft. Belvoir, VA, USA
| | - Gary J Vora
- Center for Biomolecular Science & Engineering, US Naval Research Laboratory, Washington, DC, USA.
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3
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Yang Y, Ma B, Chen J, Liu D, Ma J, Li B, Hao J, Zhou X. Epigenetic regulation and factors that influence the effect of iPSCs-derived neural stem/progenitor cells (NS/PCs) in the treatment of spinal cord injury. Clin Epigenetics 2024; 16:30. [PMID: 38383473 PMCID: PMC10880347 DOI: 10.1186/s13148-024-01639-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/30/2024] [Indexed: 02/23/2024] Open
Abstract
Spinal cord injury (SCI) is a severe neurological disorder that causes neurological impairment and disability. Neural stem/progenitor cells (NS/PCs) derived from induced pluripotent stem cells (iPSCs) represent a promising cell therapy strategy for spinal cord regeneration and repair. However, iPSC-derived NS/PCs face many challenges and issues in SCI therapy; one of the most significant challenges is epigenetic regulation and that factors that influence this mechanism. Epigenetics refers to the regulation of gene expression and function by DNA methylation, histone modification, and chromatin structure without changing the DNA sequence. Previous research has shown that epigenetics plays a crucial role in the generation, differentiation, and transplantation of iPSCs, and can influence the quality, safety, and outcome of transplanted cells. In this study, we review the effects of epigenetic regulation and various influencing factors on the role of iPSC-derived NS/PCs in SCI therapy at multiple levels, including epigenetic reprogramming, regulation, and the adaptation of iPSCs during generation, differentiation, and transplantation, as well as the impact of other therapeutic tools (e.g., drugs, electrical stimulation, and scaffolds) on the epigenetic status of transplanted cells. We summarize our main findings and insights in this field and identify future challenges and directions that need to be addressed and explored.
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Affiliation(s)
- Yubiao Yang
- Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| | - Boyuan Ma
- The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, People's Republic of China
| | - Jinyu Chen
- The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, People's Republic of China
| | - Derong Liu
- Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| | - Jun Ma
- Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| | - Bo Li
- Department of Orthopedics, Beijing Luhe Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Jian Hao
- The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, People's Republic of China.
| | - Xianhu Zhou
- The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, People's Republic of China.
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Hård J, Mold JE, Eisfeldt J, Tellgren-Roth C, Häggqvist S, Bunikis I, Contreras-Lopez O, Chin CS, Nordlund J, Rubin CJ, Feuk L, Michaëlsson J, Ameur A. Long-read whole-genome analysis of human single cells. Nat Commun 2023; 14:5164. [PMID: 37620373 PMCID: PMC10449900 DOI: 10.1038/s41467-023-40898-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023] Open
Abstract
Long-read sequencing has dramatically increased our understanding of human genome variation. Here, we demonstrate that long-read technology can give new insights into the genomic architecture of individual cells. Clonally expanded CD8+ T-cells from a human donor were subjected to droplet-based multiple displacement amplification (dMDA) to generate long molecules with reduced bias. PacBio sequencing generated up to 40% genome coverage per single-cell, enabling detection of single nucleotide variants (SNVs), structural variants (SVs), and tandem repeats, also in regions inaccessible by short reads. 28 somatic SNVs were detected, including one case of mitochondrial heteroplasmy. 5473 high-confidence SVs/cell were discovered, a sixteen-fold increase compared to Illumina-based results from clonally related cells. Single-cell de novo assembly generated a genome size of up to 598 Mb and 1762 (12.8%) complete gene models. In summary, our work shows the promise of long-read sequencing toward characterization of the full spectrum of genetic variation in single cells.
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Affiliation(s)
- Joanna Hård
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
- ETH AI Center, ETH Zurich, Zurich, Switzerland.
| | - Jeff E Mold
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jesper Eisfeldt
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Christian Tellgren-Roth
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Susana Häggqvist
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Ignas Bunikis
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | | | | | - Jessica Nordlund
- Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Lars Feuk
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Jakob Michaëlsson
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Adam Ameur
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
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Bekaert B, Boel A, De Witte L, Vandenberghe W, Popovic M, Stamatiadis P, Cosemans G, Tordeurs L, De Loore AM, Chuva de Sousa Lopes SM, De Sutter P, Stoop D, Coucke P, Menten B, Heindryckx B. Retained chromosomal integrity following CRISPR-Cas9-based mutational correction in human embryos. Mol Ther 2023; 31:2326-2341. [PMID: 37376733 PMCID: PMC10422011 DOI: 10.1016/j.ymthe.2023.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 04/11/2023] [Accepted: 06/22/2023] [Indexed: 06/29/2023] Open
Abstract
Human germline gene correction by targeted nucleases holds great promise for reducing mutation transmission. However, recent studies have reported concerning observations in CRISPR-Cas9-targeted human embryos, including mosaicism and loss of heterozygosity (LOH). The latter has been associated with either gene conversion or (partial) chromosome loss events. In this study, we aimed to correct a heterozygous basepair substitution in PLCZ1, related to infertility. In 36% of the targeted embryos that originated from mutant sperm, only wild-type alleles were observed. By performing genome-wide double-digest restriction site-associated DNA sequencing, integrity of the targeted chromosome (i.e., no deletions larger than 3 Mb or chromosome loss) was confirmed in all seven targeted GENType-analyzed embryos (mutant editing and absence of mutation), while short-range LOH events (shorter than 10 Mb) were clearly observed by single-nucleotide polymorphism assessment in two of these embryos. These results fuel the currently ongoing discussion on double-strand break repair in early human embryos, making a case for the occurrence of gene conversion events or partial template-based homology-directed repair.
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Affiliation(s)
- Bieke Bekaert
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Annekatrien Boel
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Lisa De Witte
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Winter Vandenberghe
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Mina Popovic
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Panagiotis Stamatiadis
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Gwenny Cosemans
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Lise Tordeurs
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Athina-Maria De Loore
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Susana Marina Chuva de Sousa Lopes
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium; Department of Anatomy and Embryology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Petra De Sutter
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Dominic Stoop
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Paul Coucke
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Björn Heindryckx
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium.
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Srivastava P, Prasad D. Isothermal nucleic acid amplification and its uses in modern diagnostic technologies. 3 Biotech 2023; 13:200. [PMID: 37215369 PMCID: PMC10193355 DOI: 10.1007/s13205-023-03628-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/10/2023] [Indexed: 05/24/2023] Open
Abstract
Nucleic acids are prominent biomarkers for diagnosing infectious pathogens using nucleic acid amplification techniques (NAATs). PCR, a gold standard technique for amplifying nucleic acids, is widely used in scientific research and diagnosis. Efficient pathogen detection is a key to adequate food safety and hygiene. However, using bulky thermal cyclers and costly laboratory setup limits its uses in developing countries, including India. The isothermal amplification methods are exploited to develop miniaturized sensors against viruses, bacteria, fungi and other pathogenic organisms and have been applied for in situ diagnosis. Isothermal amplification techniques have been found suitable for POC techniques and follow WHO's ASSURED criteria. LAMP, NASBA, SDA, RCA and RPA are some of the isothermal amplification techniques which are preferable for POC diagnostics. Furthermore, methods such as WGA, CPA, HDA, EXPAR, SMART, SPIA and DAMP were introduced for even more accuracy and robustness. Using recombinant polymerases and other nucleic acid-modifying enzymes has dramatically broadened the detection range of target pathogens under the scanner. The coupling of isothermal amplification methods with advanced technologies such as CRISPR/Cas systems, fluorescence-based chemistries, microfluidics and paper-based sensors has significantly influenced the biosensing and diagnosis field. This review comprehensively analyzed isothermal nucleic acid amplification methods, emphasizing their advantages, disadvantages and limitations.
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Affiliation(s)
- Pulkit Srivastava
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835215 India
| | - Dinesh Prasad
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835215 India
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Schmidt JK, Kim YH, Strelchenko N, Gierczic SR, Pavelec D, Golos TG, Slukvin II. Whole genome sequencing of CCR5 CRISPR-Cas9-edited Mauritian cynomolgus macaque blastomeres reveals large-scale deletions and off-target edits. Front Genome Ed 2023; 4:1031275. [PMID: 36714391 PMCID: PMC9877282 DOI: 10.3389/fgeed.2022.1031275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 12/15/2022] [Indexed: 01/15/2023] Open
Abstract
Introduction: Genome editing by CRISPR-Cas9 approaches offers promise for introducing or correcting disease-associated mutations for research and clinical applications. Nonhuman primates are physiologically closer to humans than other laboratory animal models, providing ideal candidates for introducing human disease-associated mutations to develop models of human disease. The incidence of large chromosomal anomalies in CRISPR-Cas9-edited human embryos and cells warrants comprehensive genotypic investigation of editing outcomes in primate embryos. Our objective was to evaluate on- and off-target editing outcomes in CCR5 CRISPR-Cas9-targeted Mauritian cynomolgus macaque embryos. Methods: DNA isolated from individual blastomeres of two embryos, along with paternal and maternal DNA, was subjected to whole genome sequencing (WGS) analysis. Results: Large deletions were identified in macaque blastomeres at the on-target site that were not previously detected using PCR-based methods. De novo mutations were also identified at predicted CRISPR-Cas9 off-target sites. Discussion: This is the first report of WGS analysis of CRISPR-Cas9-targeted nonhuman primate embryonic cells, in which a high editing efficiency was coupled with the incidence of editing errors in cells from two embryos. These data demonstrate that comprehensive sequencing-based methods are warranted for evaluating editing outcomes in primate embryos, as well as any resultant offspring to ensure that the observed phenotype is due to the targeted edit and not due to unidentified off-target mutations.
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Affiliation(s)
- Jenna Kropp Schmidt
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Yun Hee Kim
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Nick Strelchenko
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Sarah R. Gierczic
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Derek Pavelec
- University of Wisconsin Biotechnology Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Thaddeus G. Golos
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI, United States
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI, United States
| | - Igor I. Slukvin
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, United States
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8
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Patil N, Howe O, Cahill P, Byrne HJ. Monitoring and modelling the dynamics of the cellular glycolysis pathway: A review and future perspectives. Mol Metab 2022; 66:101635. [PMID: 36379354 PMCID: PMC9703637 DOI: 10.1016/j.molmet.2022.101635] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/28/2022] [Accepted: 11/06/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND The dynamics of the cellular glycolysis pathway underpin cellular function and dysfunction, and therefore ultimately health, disease, diagnostic and therapeutic strategies. Evolving our understanding of this fundamental process and its dynamics remains critical. SCOPE OF REVIEW This paper reviews the medical relevance of glycolytic pathway in depth and explores the current state of the art for monitoring and modelling the dynamics of the process. The future perspectives of label free, vibrational microspectroscopic techniques to overcome the limitations of the current approaches are considered. MAJOR CONCLUSIONS Vibrational microspectroscopic techniques can potentially operate in the niche area of limitations of other omics technologies for non-destructive, real-time, in vivo label-free monitoring of glycolysis dynamics at a cellular and subcellular level.
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Affiliation(s)
- Nitin Patil
- FOCAS Research Institute, Technological University Dublin, City Campus, Camden Row, Dublin 8, Ireland; School of Physics and Optometric & Clinical Sciences, Technological University Dublin, City Campus, Grangegorman, Dublin 7, Ireland.
| | - Orla Howe
- School of Biological and Health Sciences, Technological University Dublin, City Campus, Grangegorman, Dublin 7, Ireland
| | - Paul Cahill
- School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Hugh J Byrne
- FOCAS Research Institute, Technological University Dublin, City Campus, Camden Row, Dublin 8, Ireland
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9
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Bekaert B, Boel A, Cosemans G, De Witte L, Menten B, Heindryckx B. CRISPR/Cas gene editing in the human germline. Semin Cell Dev Biol 2022; 131:93-107. [PMID: 35305903 DOI: 10.1016/j.semcdb.2022.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 12/14/2022]
Abstract
The ease and efficacy of CRISPR/Cas9 germline gene editing in animal models paved the way to human germline gene editing (HGGE), by which permanent changes can be introduced into the embryo. Distinct genes can be knocked out to examine their function during embryonic development. Alternatively, specific sequences can be introduced which can be applied to correct disease-causing mutations. To date, it has been shown that the success of HGGE is dependent on various experimental parameters and that various hurdles (i.e. loss-of-heterozygosity and mosaicism) need to be overcome before clinical applications should be considered. Due to the shortage of human germline material and the ethical constraints concerning HGGE, alternative models such as stem cells have been evaluated as well, in terms of their predictive value on the genetic outcome for HGGE approaches. This review will give an overview of the state of the art of HGGE in oocytes and embryos, and its accompanying challenges.
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Affiliation(s)
- B Bekaert
- Ghent-Fertility And Stem cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - A Boel
- Ghent-Fertility And Stem cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - G Cosemans
- Ghent-Fertility And Stem cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - L De Witte
- Center for Medical Genetics Ghent, Ghent University, Department of Biomolecular Medicine, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - B Menten
- Center for Medical Genetics Ghent, Ghent University, Department of Biomolecular Medicine, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - B Heindryckx
- Ghent-Fertility And Stem cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium.
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10
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Gridina M, Taskina A, Lagunov T, Nurislamov A, Kulikova T, Krasikova A, Fishman V. Comparison and critical assessment of single-cell Hi-C protocols. Heliyon 2022; 8:e11023. [PMID: 36281413 PMCID: PMC9587272 DOI: 10.1016/j.heliyon.2022.e11023] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 08/13/2022] [Accepted: 10/06/2022] [Indexed: 01/24/2023] Open
Abstract
Advances in single-cell sequencing technologies make it possible to study the genome architecture in single cells. The rapid growth of the field has been fueled by the development of innovative single-cell Hi-C protocols. However, the protocols vary considerably in their efficiency, bias, scale and costs, and their relative advantages for different applications are unclear. Here, we compare the two most commonly used single-cell Hi-C protocols. We use long-read sequencing to analyze molecular products of the Hi-C assay and show that whole-genome amplification step results in increased number of artifacts, larger coverage biases, and increased amount of noise compared to PCR-based amplification. Our comparison provides guidance for researchers studying chromatin architecture in individual cells.
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11
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Whole-Genome Amplification—Surveying Yield, Reproducibility, and Heterozygous Balance, Reported by STR-Targeting MIPs. Int J Mol Sci 2022; 23:ijms23116161. [PMID: 35682839 PMCID: PMC9181316 DOI: 10.3390/ijms23116161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/27/2022] [Accepted: 05/27/2022] [Indexed: 02/01/2023] Open
Abstract
Whole-genome amplification is a crucial first step in nearly all single-cell genomic analyses, with the following steps focused on its products. Bias and variance caused by the whole-genome amplification process add numerous challenges to the world of single-cell genomics. Short tandem repeats are sensitive genomic markers used widely in population genetics, forensics, and retrospective lineage tracing. A previous evaluation of common whole-genome amplification targeting ~1000 non-autosomal short tandem repeat loci is extended here to ~12,000 loci across the entire genome via duplex molecular inversion probes. Other than its improved scale and reduced noise, this system detects an abundance of heterogeneous short tandem repeat loci, allowing the allelic balance to be reported. We show here that while the best overall yield is obtained using RepliG-SC, the maximum uniformity between alleles and reproducibility across cells are maximized by Ampli1, rendering it the best candidate for the comparative heterozygous analysis of single-cell genomes.
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12
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Bowes A, Tarabichi M, Pillay N, Van Loo P. Leveraging single cell sequencing to unravel intra-tumour heterogeneity and tumour evolution in human cancers. J Pathol 2022; 257:466-478. [PMID: 35438189 PMCID: PMC9322001 DOI: 10.1002/path.5914] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 11/11/2022]
Abstract
Intra-tumour heterogeneity and tumour evolution are well-documented phenomena in human cancers. While the advent of next-generation sequencing technologies has facilitated the large-scale capture of genomic data, the field of single cell genomics is nascent but rapidly advancing and generating many new insights into the complex molecular mechanisms of tumour biology. In this review, we provide an overview of current single cell DNA sequencing technologies, exploring how recent methodological advancements have enumerated new insights into intra-tumour heterogeneity and tumour evolution. Areas highlighted include the potential power of single cell genome sequencing studies to explore evolutionary dynamics contributing to tumourigenesis through to progression, metastasis and therapy resistance. We also explore the use of in-situ sequencing technologies to study intra-tumour heterogeneity in a spatial context, as well as examining the use of single cell genomics to perform lineage tracing in both normal and malignant tissues. Finally, we consider the use of multi-modal single cell sequencing technologies. Taken together, it is hoped that these many facets of single cell genome sequencing will improve our understanding of tumourigenesis, progression and lethality in cancer leading to the development of novel therapies. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Amy Bowes
- Cancer Genomics Group, The Francis Crick Institute, London, UK.,Sarcoma Biology and Genomics Group, UCL Cancer Institute, London, UK
| | - Maxime Tarabichi
- Cancer Genomics Group, The Francis Crick Institute, London, UK.,Institute for Interdisciplinary Research, Université Libre de Bruxelles, Brussels, Belgium
| | - Nischalan Pillay
- Sarcoma Biology and Genomics Group, UCL Cancer Institute, London, UK.,Department of Histopathology, The Royal National Orthopaedic Hospital NHS Trust, London, UK
| | - Peter Van Loo
- Cancer Genomics Group, The Francis Crick Institute, London, UK.,Department of Genetics, The University of Texas MD Anderson Cancer Centre, Houston, USA.,Department of Genomic Medicine, The University of Texas MD Anderson Cancer Centre, Houston, USA
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13
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14
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Kashyap A, Rapsomaniki MA, Barros V, Fomitcheva-Khartchenko A, Martinelli AL, Rodriguez AF, Gabrani M, Rosen-Zvi M, Kaigala G. Quantification of tumor heterogeneity: from data acquisition to metric generation. Trends Biotechnol 2021; 40:647-676. [PMID: 34972597 DOI: 10.1016/j.tibtech.2021.11.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 01/18/2023]
Abstract
Tumors are unique and complex ecosystems, in which heterogeneous cell subpopulations with variable molecular profiles, aggressiveness, and proliferation potential coexist and interact. Understanding how heterogeneity influences tumor progression has important clinical implications for improving diagnosis, prognosis, and treatment response prediction. Several recent innovations in data acquisition methods and computational metrics have enabled the quantification of spatiotemporal heterogeneity across different scales of tumor organization. Here, we summarize the most promising efforts from a common experimental and computational perspective, discussing their advantages, shortcomings, and challenges. With personalized medicine entering a new era of unprecedented opportunities, our vision is that of future workflows integrating across modalities, scales, and dimensions to capture intricate aspects of the tumor ecosystem and to open new avenues for improved patient care.
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Affiliation(s)
- Aditya Kashyap
- IBM Research Europe -Säumerstrasse 4, Rüschlikon CH-8803, Zurich, Switzerland
| | | | - Vesna Barros
- Department of Healthcare Informatics, IBM Research, IBM R&D Labs, University of Haifa Campus, Mount Carmel, Haifa, 3498825, Israel; The Hebrew University, The Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Anna Fomitcheva-Khartchenko
- IBM Research Europe -Säumerstrasse 4, Rüschlikon CH-8803, Zurich, Switzerland; Eidgenössische Technische Hochschule (ETH-Zurich), Vladimir-Prelog-Weg 1-5/10, 8099 Zurich, Switzerland
| | | | | | - Maria Gabrani
- IBM Research Europe -Säumerstrasse 4, Rüschlikon CH-8803, Zurich, Switzerland
| | - Michal Rosen-Zvi
- Department of Healthcare Informatics, IBM Research, IBM R&D Labs, University of Haifa Campus, Mount Carmel, Haifa, 3498825, Israel; The Hebrew University, The Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Govind Kaigala
- IBM Research Europe -Säumerstrasse 4, Rüschlikon CH-8803, Zurich, Switzerland.
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15
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Xu Q, Wang Z, Kong Q, Wang X, Huang A, Li C, Liu X. Evaluating the effects of whole genome amplification strategies for amplifying trace DNA using capillary electrophoresis and massive parallel sequencing. Forensic Sci Int Genet 2021; 56:102599. [PMID: 34656831 DOI: 10.1016/j.fsigen.2021.102599] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 09/20/2021] [Accepted: 09/24/2021] [Indexed: 11/04/2022]
Abstract
To draw robust conclusions when trace DNA samples are detected in complex cases, it is essential to successfully recover and genotype short tandem repeats (STRs) from trace DNA. However, obtaining complete STR profiles by the conventional polymerase chain reaction-capillary electrophoresis (PCR-CE) method is generally difficult as trace DNA is often less than 100 pg. Previous studies have proven that through whole-genome amplification (WGA), the yield of DNA from trace DNA samples could be improved. In this study, we used two WGA kits, namely, REPLI-g® Single Cell kit and MALBAC® Single Cell DNA Quick-Amp Kit (hereafter referred to as REPLI and MALBAC), to amplify DNA samples with a series of dilutions (from 5.00 ng/μL to 0.391 pg/μL). Typing of STR markers in samples with and without WGA were then performed on a CE platform by the application of Goldeneye® DNA ID System 20 A kit, as well as directly calling sequences from massive parallel sequencing (MPS) for WGA samples with 1.00 ng, 125 pg and 25.0 pg as DNA inputs. Quantification results demonstrated that the yield of samples with WGA could reach the microgram level. The amplification fold was at least > 2000 and > 200 for REPLI and MALBAC, respectively. CE results showed that the number of correctly called loci was improved for trace DNA after WGA when the DNA inputs were lower than 25.0 pg for REPLI and 6.25 pg for MALBAC, respectively. WGA remarkably improved the percentage of called loci with DNA inputs lower than 50.0 pg, although poor performance in repeatability was observed. MPS results suggested that the correctly called loci calculated by MPS reads were mostly more than those calculated by CE, particularly for those of short length, implying MPS of samples after WGA is worth testing in the future. In conclusion, WGA has the potential usability for forensic trace DNA analysis at the single-cell level with good fidelity, although its repeatability requires further improvement.
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Affiliation(s)
- Qiannan Xu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, PR China; Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China
| | - Ziwei Wang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China; Department of Forensic Science, Medical School of Soochow University, Suzhou 215123, PR China
| | - Qianqian Kong
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China; School of Basic Medicine, Inner Mongolia Medical University, Hohhot 010030, PR China
| | - Xiaoxiao Wang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China; School of Forensic Medicine, Shanxi Medical University, Taiyuan 030001, PR China
| | - Ao Huang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China; Department of Forensic Science, Medical School of Soochow University, Suzhou 215123, PR China
| | - Chengtao Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, PR China; Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China.
| | - Xiling Liu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China.
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16
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Vitali V, Rothering R, Catania F. Fifty Generations of Amitosis: Tracing Asymmetric Allele Segregation in Polyploid Cells with Single-Cell DNA Sequencing. Microorganisms 2021; 9:1979. [PMID: 34576874 PMCID: PMC8467633 DOI: 10.3390/microorganisms9091979] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 01/04/2023] Open
Abstract
Amitosis is a widespread form of unbalanced nuclear division whose biomedical and evolutionary significance remain unclear. Traditionally, insights into the genetics of amitosis have been gleaned by assessing the rate of phenotypic assortment. Though powerful, this experimental approach relies on the availability of phenotypic markers. Leveraging Paramecium tetraurelia, a unicellular eukaryote with nuclear dualism and a highly polyploid somatic nucleus, we probe the limits of single-cell whole-genome sequencing to study the consequences of amitosis. To this end, we first evaluate the suitability of single-cell sequencing to study the AT-rich genome of P. tetraurelia, focusing on common sources of genome representation bias. We then asked: can alternative rearrangements of a given locus eventually assort after a number of amitotic divisions? To address this question, we track somatic assortment of developmentally acquired Internal Eliminated Sequences (IESs) up to 50 amitotic divisions post self-fertilization. To further strengthen our observations, we contrast empirical estimates of IES retention levels with in silico predictions obtained through mathematical modeling. In agreement with theoretical expectations, our empirical findings are consistent with a mild increase in variation of IES retention levels across successive amitotic divisions of the macronucleus. The modest levels of somatic assortment in P. tetraurelia suggest that IESs retention levels are largely sculpted at the time of macronuclear development, and remain fairly stable during vegetative growth. In forgoing the requirement for phenotypic assortment, our approach can be applied to a wide variety of amitotic species and could facilitate the identification of environmental and genetic factors affecting amitosis.
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Affiliation(s)
- Valerio Vitali
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany; (R.R.); (F.C.)
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17
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Zhou X, Kurywchak P, Wolf-Dennen K, Che SP, Sulakhe D, D’Souza M, Xie B, Maltsev N, Gilliam TC, Wu CC, McAndrews KM, LeBleu VS, McConkey DJ, Volpert OV, Pretzsch SM, Czerniak BA, Dinney CP, Kalluri R. Unique somatic variants in DNA from urine exosomes of individuals with bladder cancer. Mol Ther Methods Clin Dev 2021; 22:360-376. [PMID: 34514028 PMCID: PMC8408559 DOI: 10.1016/j.omtm.2021.05.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/21/2021] [Indexed: 01/03/2023]
Abstract
Bladder cancer (BC), a heterogeneous disease characterized by high recurrence rates, is diagnosed and monitored by cystoscopy. Accurate clinical staging based on biopsy remains a challenge, and additional, objective diagnostic tools are needed urgently. We used exosomal DNA (exoDNA) as an analyte to examine cancer-associated mutations and compared the diagnostic utility of exoDNA from urine and serum of individuals with BC. In contrast to urine exosomes from healthy individuals, urine exosomes from individuals with BC contained significant amounts of DNA. Whole-exome sequencing of DNA from matched urine and serum exosomes, bladder tumors, and normal tissue (peripheral blood mononuclear cells) identified exonic and 3' UTR variants in frequently mutated genes in BC, detectable in urine exoDNA and matched tumor samples. Further analyses identified somatic variants in driver genes, unique to urine exoDNA, possibly because of the inherent intra-tumoral heterogeneity of BC, which is not fully represented in random small biopsies. Multiple variants were also found in untranslated portions of the genome, such as microRNA (miRNA)-binding regions of the KRAS gene. Gene network analyses revealed that exoDNA is associated with cancer, inflammation, and immunity in BC exosomes. Our findings show utility of exoDNA as an objective, non-invasive strategy to identify novel biomarkers and targets for BC.
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Affiliation(s)
- Xunian Zhou
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paul Kurywchak
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kerri Wolf-Dennen
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sara P.Y. Che
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dinanath Sulakhe
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Mark D’Souza
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Bingqing Xie
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Natalia Maltsev
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - T. Conrad Gilliam
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Chia-Chin Wu
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kathleen M. McAndrews
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Valerie S. LeBleu
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - David J. McConkey
- Johns Hopkins Greenberg Bladder Cancer Institute, Baltimore, MD, USA
| | - Olga V. Volpert
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shanna M. Pretzsch
- Department of Urology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bogdan A. Czerniak
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Colin P. Dinney
- Department of Urology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Raghu Kalluri
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- School of Bioengineering, Rice University, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
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18
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Comparison of seven single cell whole genome amplification commercial kits using targeted sequencing. Sci Rep 2021; 11:17171. [PMID: 34433869 PMCID: PMC8387353 DOI: 10.1038/s41598-021-96045-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 07/26/2021] [Indexed: 11/08/2022] Open
Abstract
Advances in whole genome amplification (WGA) techniques enable understanding of the genomic sequence at a single cell level. Demand for single cell dedicated WGA kits (scWGA) has led to the development of several commercial kit. To this point, no robust comparison of all available kits was performed. Here, we benchmark an economical assay, comparing all commercially available scWGA kits. Our comparison is based on targeted sequencing of thousands of genomic loci, including highly mutable regions, from a large cohort of human single cells. Using this approach we have demonstrated the superiority of Ampli1 in genome coverage and of RepliG in reduced error rate. In summary, we show that no single kit is optimal across all categories, highlighting the need for a dedicated kit selection in accordance with experimental requirements.
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19
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Abstract
Tumour evolution is a complex interplay between the acquisition of somatic (epi)genomic changes in tumour cells and the phenotypic consequences they cause, all in the context of a changing microenvironment. Single-cell sequencing offers a window into this dynamic process at the ultimate resolution of individual cells. In this review, we discuss the transformative insight offered by single-cell sequencing technologies for understanding tumour evolution.
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Affiliation(s)
- Maximilian Mossner
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Ann-Marie C Baker
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Trevor A Graham
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
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20
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Frequent loss of heterozygosity in CRISPR-Cas9-edited early human embryos. Proc Natl Acad Sci U S A 2021; 118:2004832117. [PMID: 34050011 DOI: 10.1073/pnas.2004832117] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
CRISPR-Cas9 genome editing is a promising technique for clinical applications, such as the correction of disease-associated alleles in somatic cells. The use of this approach has also been discussed in the context of heritable editing of the human germ line. However, studies assessing gene correction in early human embryos report low efficiency of mutation repair, high rates of mosaicism, and the possibility of unintended editing outcomes that may have pathologic consequences. We developed computational pipelines to assess single-cell genomics and transcriptomics datasets from OCT4 (POU5F1) CRISPR-Cas9-targeted and control human preimplantation embryos. This allowed us to evaluate on-target mutations that would be missed by more conventional genotyping techniques. We observed loss of heterozygosity in edited cells that spanned regions beyond the POU5F1 on-target locus, as well as segmental loss and gain of chromosome 6, on which the POU5F1 gene is located. Unintended genome editing outcomes were present in ∼16% of the human embryo cells analyzed and spanned 4-20 kb. Our observations are consistent with recent findings indicating complexity at on-target sites following CRISPR-Cas9 genome editing. Our work underscores the importance of further basic research to assess the safety of genome editing techniques in human embryos, which will inform debates about the potential clinical use of this technology.
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21
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Nakamura IT, Ikegami M, Hasegawa N, Hayashi T, Ueno T, Kawazu M, Yagishita S, Goto Y, Shinno Y, Kojima Y, Takamochi K, Takahashi F, Takahashi K, Mano H, Kohsaka S. Development of an optimal protocol for molecular profiling of tumor cells in pleural effusions at single-cell level. Cancer Sci 2021; 112:2006-2019. [PMID: 33484069 PMCID: PMC8088920 DOI: 10.1111/cas.14821] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 01/12/2021] [Accepted: 01/18/2021] [Indexed: 12/11/2022] Open
Abstract
Liquid biopsy analyzes the current status of primary tumors and their metastatic regions. We aimed to develop an optimized protocol for single-cell sequencing of floating tumor cells (FTCs) in pleural effusion as a laboratory test. FTCs were enriched using a negative selection of white blood cells by a magnetic-activated cell sorting system, and CD45-negative and cytokeratin-positive selection using a microfluidic cell separation system with a dielectrophoretic array. The enriched tumor cells were subjected to whole-genome amplification (WGA) followed by genome sequencing. The FTC analysis detected an EGFR exon 19 deletion in Case 1 (12/19 cells, 63.2%), and EML4-ALK fusion (17/20 cells, 85%) with an alectinib-resistant mutation of ALK (p.G1202R) in Case 2. To eliminate WGA-associated errors and increase the uniformity of the WGA product, the protocol was revised to sequence multiple single FTCs individually. An analytical pipeline, accurate single-cell mutation detector (ASMD), was developed to identify somatic mutations of FTCs. The large numbers of WGA-associated errors were cleaned up, and the somatic mutations detected in FTCs by ASMD were concordant with those found in tissue specimens. This protocol is applicable to circulating tumor cells analysis of peripheral blood and expands the possibility of utilizing molecular profiling of cancers.
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Affiliation(s)
- Ikuko Takeda Nakamura
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan.,Department of Respiratory Medicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Masachika Ikegami
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan.,Department of Orthopedic Surgery, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nobuhiko Hasegawa
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan.,Department of Orthopedic Surgery, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Takuo Hayashi
- Department of Human Pathology, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Toshihide Ueno
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Masahito Kawazu
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Shigehiro Yagishita
- Division of Molecular Pharmacology, National Cancer Center Research Institute, Tokyo, Japan
| | - Yasushi Goto
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Yuki Shinno
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Yuki Kojima
- Department of Breast and Medical Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Kazuya Takamochi
- Department of General Thoracic Surgery, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Fumiyuki Takahashi
- Department of Respiratory Medicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Kazuhisa Takahashi
- Department of Respiratory Medicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Hiroyuki Mano
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Shinji Kohsaka
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
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22
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Bisulfite-free epigenomics and genomics of single cells through methylation-sensitive restriction. Commun Biol 2021; 4:153. [PMID: 33526904 PMCID: PMC7851132 DOI: 10.1038/s42003-021-01661-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 01/06/2021] [Indexed: 12/15/2022] Open
Abstract
Single-cell multi-omics are powerful means to study cell-to-cell heterogeneity. Here, we present a single-tube, bisulfite-free method for the simultaneous, genome-wide analysis of DNA methylation and genetic variants in single cells: epigenomics and genomics of single cells analyzed by restriction (epi-gSCAR). By applying this method, we obtained DNA methylation measurements of up to 506,063 CpGs and up to 1,244,188 single-nucleotide variants from single acute myeloid leukemia-derived cells. We demonstrate that epi-gSCAR generates accurate and reproducible measurements of DNA methylation and allows to differentiate between cell lines based on the DNA methylation and genetic profiles.
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23
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Tu J, Qiao Y, Luo Y, Long N, Lu Z. Quantifying genome DNA during whole-genome amplification via quantitative real-time multiple displacement amplification. RSC Adv 2021; 11:4617-4621. [PMID: 35424416 PMCID: PMC8694541 DOI: 10.1039/d0ra09021b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/28/2020] [Indexed: 12/02/2022] Open
Abstract
DNA quantification is important in the research of life sciences. In an independent quantification process, the extracted part of a DNA sample is usually difficult to be recycled for further use while the widely used real-time PCR is used to count the copies with certain sequences. Based on the popular multiple displacement amplification (MDA), we proposed and performed quantitative real-time MDA to obtain the information of template amount based on fluorescence signals while amplifying whole-genome DNA. The detection limit of real-time MDA was as low as 0.5 pg μl-1 (5 pg DNA input), offering the whole-genome research a promising tool to quantify the entire DNA during amplification without sacrificing sample completeness or introducing redundant steps.
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Affiliation(s)
- Jing Tu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University Nanjing 210096 China +86-25-83792396
| | - Yi Qiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University Nanjing 210096 China +86-25-83792396
| | - Yuhan Luo
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University Nanjing 210096 China +86-25-83792396
| | - Naiyun Long
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University Nanjing 210096 China +86-25-83792396
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University Nanjing 210096 China +86-25-83792396
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24
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Tan JHJ, Kong SL, Tai JA, Poh HM, Yao F, Sia YY, Lim EKH, Takano AM, Tan DSW, Javed A, Hillmer AM. Experimental and bioinformatics considerations in cancer application of single cell genomics. Comput Struct Biotechnol J 2020; 19:343-354. [PMID: 33489004 PMCID: PMC7788095 DOI: 10.1016/j.csbj.2020.12.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 01/12/2023] Open
Abstract
Single cell genomics offers an unprecedented resolution to interrogate genetic heterogeneity in a patient's tumour at the intercellular level. However, the DNA yield per cell is insufficient for today's sequencing library preparation protocols. This necessitates DNA amplification which is a key source of experimental noise. We provide an evaluation of two protocols using micro-fluidics based amplification for whole exome sequencing, which is an experimental scenario commonly used in single cell genomics. The results highlight their respective biases and relative strengths in identification of single nucleotide variations. Towards this end, we introduce a workflow SoVaTSiC, which allows for quality evaluation and somatic variant identification of single cell data. As proof of concept, the framework was applied to study a lung adenocarcinoma tumour. The analysis provides insights into tumour phylogeny by identifying key mutational events in lung adenocarcinoma evolution. The consequence of this inference is supported by the histology of the tumour and demonstrates usefulness of the approach.
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Affiliation(s)
- Joanna Hui Juan Tan
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore 138672, Singapore
- Department of Biochemistry, National University of Singapore, Singapore 117597, Singapore
| | - Say Li Kong
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Joyce A. Tai
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Huay Mei Poh
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Fei Yao
- Genome Innovation Lab, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Yee Yen Sia
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Edwin Kok Hao Lim
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Angela Maria Takano
- Department of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Daniel Shao-Weng Tan
- Department of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Asif Javed
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore 138672, Singapore
- School of Biomedical Sciences, University of Hong Kong, Hong Kong Special Administrative Region
| | - Axel M. Hillmer
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore 138672, Singapore
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
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25
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González RD, Gomes I, Gomes C, Rocha R, Durães L, Sousa P, Figueruelo M, Rodríguez M, Pita C, Hornero R, Gómez C, Lopes AM, Pinto N, Martins S. APOE Variants in an Iberian Alzheimer Cohort Detected through an Optimized Sanger Sequencing Protocol. Genes (Basel) 2020; 12:genes12010004. [PMID: 33375167 PMCID: PMC7822120 DOI: 10.3390/genes12010004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/10/2020] [Accepted: 12/19/2020] [Indexed: 01/03/2023] Open
Abstract
The primary genetic risk factor for late onset Alzheimer’s disease (LOAD) is the APOE4 allele of Apolipoprotein E (APOE) gene. The three most common variants of APOE are determined by single nucleotide polymorphisms (SNPs) rs429358 and rs7412. Our aim was to estimate allele and genotype frequencies of APOE variants in an Iberian cohort, thus helping to understand differences in APOE-related LOAD risk observed across populations. We analyzed saliva or buccal swab samples from 229 LOAD patients and 89 healthy elderly controls (≥68 years old) from Northern Portugal and Castile and León region, Spain. The genotyping was performed by Sanger sequencing, optimized to overcome GC content drawbacks. Results obtained in our Iberian LOAD and control cohorts are in line with previous large meta-analyses on APOE frequencies in Caucasian populations; however, we found differences in allele frequencies between our Portuguese and Spanish subgroups of AD patients. Moreover, when comparing studies from Iberian and other Caucasian cohorts, differences in APOE2 and APOE4 frequencies and subsequent different APOE-related LOAD risks must be clarified. These results show the importance of studying genetic variation at the APOE gene in different populations (including analyses at a regional level) to increase our knowledge about its clinical significance.
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Affiliation(s)
- Ricardo D. González
- IPATIMUP–Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal; (R.D.G.); (I.G.); (C.G.); (R.R.); (A.M.L.); (S.M.)
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Iva Gomes
- IPATIMUP–Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal; (R.D.G.); (I.G.); (C.G.); (R.R.); (A.M.L.); (S.M.)
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Catarina Gomes
- IPATIMUP–Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal; (R.D.G.); (I.G.); (C.G.); (R.R.); (A.M.L.); (S.M.)
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Rita Rocha
- IPATIMUP–Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal; (R.D.G.); (I.G.); (C.G.); (R.R.); (A.M.L.); (S.M.)
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Luís Durães
- Associação Portuguesa de Familiares e Amigos de Doentes de Alzheimer, 4455-301 Lavra, Portugal; (L.D.); (P.S.)
| | - Patrícia Sousa
- Associação Portuguesa de Familiares e Amigos de Doentes de Alzheimer, 4455-301 Lavra, Portugal; (L.D.); (P.S.)
| | - Manuel Figueruelo
- Asociación de Familiares y Amigos de Enfermos de Alzheimer y Otras Demencias de Zamora, 49021 Zamora, Spain; (M.F.); (M.R.); (C.P.)
| | - Maria Rodríguez
- Asociación de Familiares y Amigos de Enfermos de Alzheimer y Otras Demencias de Zamora, 49021 Zamora, Spain; (M.F.); (M.R.); (C.P.)
| | - Carmen Pita
- Asociación de Familiares y Amigos de Enfermos de Alzheimer y Otras Demencias de Zamora, 49021 Zamora, Spain; (M.F.); (M.R.); (C.P.)
| | - Roberto Hornero
- Grupo de Ingeniería Biomédica, Universidad de Valladolid, 47011 Valladolid, Spain; (R.H.); (C.G.)
- Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 47011 Valladolid, Spain
- Instituto de Investigación en Matemáticas (IMUVA), Universidad de Valladolid, 47011 Valladolid, Spain
| | - Carlos Gómez
- Grupo de Ingeniería Biomédica, Universidad de Valladolid, 47011 Valladolid, Spain; (R.H.); (C.G.)
- Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 47011 Valladolid, Spain
| | - Alexandra M. Lopes
- IPATIMUP–Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal; (R.D.G.); (I.G.); (C.G.); (R.R.); (A.M.L.); (S.M.)
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Nádia Pinto
- IPATIMUP–Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal; (R.D.G.); (I.G.); (C.G.); (R.R.); (A.M.L.); (S.M.)
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- Centro de Matemática da Universidade do Porto, 4169-007 Porto, Portugal
- Correspondence: ; Tel.: +351-220408800
| | - Sandra Martins
- IPATIMUP–Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal; (R.D.G.); (I.G.); (C.G.); (R.R.); (A.M.L.); (S.M.)
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
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26
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Lamanna J, Scott EY, Edwards HS, Chamberlain MD, Dryden MDM, Peng J, Mair B, Lee A, Chan C, Sklavounos AA, Heffernan A, Abbas F, Lam C, Olson ME, Moffat J, Wheeler AR. Digital microfluidic isolation of single cells for -Omics. Nat Commun 2020; 11:5632. [PMID: 33177493 PMCID: PMC7658233 DOI: 10.1038/s41467-020-19394-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 10/02/2020] [Indexed: 11/28/2022] Open
Abstract
We introduce Digital microfluidic Isolation of Single Cells for -Omics (DISCO), a platform that allows users to select particular cells of interest from a limited initial sample size and connects single-cell sequencing data to their immunofluorescence-based phenotypes. Specifically, DISCO combines digital microfluidics, laser cell lysis, and artificial intelligence-driven image processing to collect the contents of single cells from heterogeneous populations, followed by analysis of single-cell genomes and transcriptomes by next-generation sequencing, and proteomes by nanoflow liquid chromatography and tandem mass spectrometry. The results described herein confirm the utility of DISCO for sequencing at levels that are equivalent to or enhanced relative to the state of the art, capable of identifying features at the level of single nucleotide variations. The unique levels of selectivity, context, and accountability of DISCO suggest potential utility for deep analysis of any rare cell population with contextual dependencies. Multi-Omic approaches are a powerful way for obtaining in-depth understanding of a cell’s state. Here the authors present DISCO, combining digital microfluidics, laser cell lysis, and artificial intelligence-driven image processing to analyze single-cell genomes, transcriptomes and proteomes in a mixed population.
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Affiliation(s)
- Julian Lamanna
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, M5S 3E1, Canada
| | - Erica Y Scott
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, M5S 3E1, Canada
| | - Harrison S Edwards
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, M5S 3E1, Canada.,Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada
| | - M Dean Chamberlain
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, M5S 3E1, Canada
| | - Michael D M Dryden
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - Jiaxi Peng
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - Barbara Mair
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, M5S 3E1, Canada
| | - Adam Lee
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada
| | - Calvin Chan
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - Alexandros A Sklavounos
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, M5S 3E1, Canada
| | - Austin Heffernan
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, M5S 3E1, Canada
| | - Farhana Abbas
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, M5S 3E1, Canada
| | - Charis Lam
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - Maxwell E Olson
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - Jason Moffat
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, M5S 3E1, Canada.,Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 3H6, Canada
| | - Aaron R Wheeler
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada. .,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, M5S 3E1, Canada. .,Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada.
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27
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Single Cell Sequencing: A New Dimension in Cancer Diagnosis and Treatment. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1255:109-121. [PMID: 32949394 DOI: 10.1007/978-981-15-4494-1_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Cancer is one of the leading causes of death worldwide and well known for its complexity. Cancer cells within the same tumor or from different tumors are highly heterogeneous. Furthermore, stromal and immune cells within tumor microenvironment interact with cancer cells to play important roles in how tumors progress and respond to different treatments. Recent advances in single cell technologies, especially massively parallel single cell sequencing, have made it possible to analyze cancer cells and cells in its tumor microenvironment in parallel with unprecedented high resolution. In this chapter, we will review recent developments in single cell sequencing technologies and their applications in cancer research. We will also explain how insights generated from single cell sequencing can be used to develop novel diagnostic and therapeutic approaches to conquer cancer.
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28
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Su X, Gong Y, Gou H, Jing X, Xu T, Zheng X, Chen R, Li Y, Ji Y, Ma B, Xu J. Rational Optimization of Raman-Activated Cell Ejection and Sequencing for Bacteria. Anal Chem 2020; 92:8081-8089. [PMID: 32401011 DOI: 10.1021/acs.analchem.9b05345] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In Raman-activated cell ejection and sequencing (RACE-Seq), success rate and sequence coverage have generally been low for shotgun sequencing of individual post-RACE cells. Here we quantitatively evaluated the influence of cell lysis condition, nucleic acid amplification condition, and parameters of Raman measurement on RACE-Seq performance. Variations in laser energy input during Raman signal acquisition, but not duration of alkaline lysate lysis, temperature, or measurement under dry or aqueous conditions, are vital to the success of multiple displacement amplification (MDA). In fact, laser irradiation is reversely linked to MDA product quality. However, introduction of oils prior to MDA, by mitigating such negative effects of Raman irradiation, elevates genome coverage of post-RACE Escherichia coli cells from <20% to ∼50%, while greatly improving the success rate of RACE-Seq for soil microbiota. Our findings provide a practical solution for enhancing RACE-Seq performance and pinpoint protection of cells from laser irradiation as a priority in method development.
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Affiliation(s)
- Xiaolu Su
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | - Yanhai Gong
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | - Honglei Gou
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | - Xiaoyan Jing
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | - Teng Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China.,University of Chinese Academy of Sciences, Beijing 100000, China
| | - Xiaoshan Zheng
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | - Rongze Chen
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China.,University of Chinese Academy of Sciences, Beijing 100000, China
| | - Yuandong Li
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | - Yuetong Ji
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | - Bo Ma
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China.,University of Chinese Academy of Sciences, Beijing 100000, China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China.,University of Chinese Academy of Sciences, Beijing 100000, China
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29
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Cackowski FC, Wang Y, Decker JT, Sifuentes C, Weindorf S, Jung Y, Wang Y, Decker AM, Yumoto K, Szerlip N, Buttitta L, Pienta KJ, Morgan TM, Taichman RS. Detection and isolation of disseminated tumor cells in bone marrow of patients with clinically localized prostate cancer. Prostate 2019; 79:1715-1727. [PMID: 31449673 PMCID: PMC8177057 DOI: 10.1002/pros.23896] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 08/05/2019] [Indexed: 01/27/2023]
Abstract
BACKGROUND Disseminated tumor cells (DTCs) have been reported in the bone marrow (BM) of patients with localized prostate cancer (PCa). However, the existence of these cells continues to be questioned, and few methods exist for viable DTC isolation. Therefore, we sought to develop novel approaches to identify and, if detected, analyze localized PCa patient DTCs. METHODS We used fluorescence-activated cell sorting (FACS) to isolate a putative DTC population, which was negative for CD45, CD235a, alkaline phosphatase, and CD34, and strongly expressed EPCAM. We examined tumor cell content by bulk cell RNA sequencing (RNA-Seq) and whole-exome sequencing after whole genome amplification. We also enriched for BM DTCs with α-EPCAM immunomagnetic beads and performed quantitative reverse trancriptase polymerase chain reaction (qRT-PCR) for PCa markers. RESULTS At a threshold of 4 cells per million BM cells, the putative DTC population was present in 10 of 58 patients (17%) with localized PCa, 4 of 8 patients with metastatic PCa of varying disease control, and 1 of 8 patients with no known cancer, and was positively correlated with patients' plasma PSA values. RNA-Seq analysis of the putative DTC population collected from samples above (3 patients) and below (5 patients) the threshold of 4 putative DTCs per million showed increased expression of PCa marker genes in 4 of 8 patients with localized PCa, but not the one normal donor who had the putative DTC population present. Whole-exome sequencing also showed the presence of single nucleotide polymorphisms and structural variants in the gene characteristics of PCa in 2 of 3 localized PCa patients. To examine the likely contaminating cell types, we used a myeloid colony formation assay, differential counts of cell smears, and analysis of the RNA-Seq data using the CIBERSORT algorithm, which most strongly suggested the presence of B-cell lineages as a contaminant. Finally, we used EPCAM enrichment and qRT-PCR for PCa markers to estimate DTC prevalence and found evidence of DTCs in 21 of 44 samples (47%). CONCLUSION These data support the presence of DTCs in the BM of a subset of patients with localized PCa and describe a novel FACS method for isolation and analysis of viable DTCs.
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Affiliation(s)
- Frank C. Cackowski
- Division of Hematology and Oncology, University of Michigan School of Medicine, Ann Arbor, Michigan
- Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, Michigan
| | - Yugang Wang
- Department of Urology, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Joseph T. Decker
- Department of Bioengineering, University of Michigan College of Engineering, Ann Arbor, Michigan
| | - Christopher Sifuentes
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Steven Weindorf
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Younghun Jung
- Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, Michigan
| | - Yu Wang
- Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, Michigan
| | - Ann M. Decker
- Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, Michigan
| | - Kenji Yumoto
- Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, Michigan
| | - Nicholas Szerlip
- Department of Neurological Surgery, University of Michigan and AAVAMC, Ann Arbor, Michigan
| | - Laura Buttitta
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - Kenneth J. Pienta
- Department of Urology and Oncology, James Buchannan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Todd M. Morgan
- Department of Urology, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Russell S. Taichman
- Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, Michigan
- School of Dentistry, University of Alabama at Birmingham, Birmingham, Alabama
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30
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Sherman MA, Barton AR, Lodato MA, Vitzthum C, Coulter ME, Walsh CA, Park PJ. PaSD-qc: quality control for single cell whole-genome sequencing data using power spectral density estimation. Nucleic Acids Res 2019; 46:e20. [PMID: 29186545 PMCID: PMC5829578 DOI: 10.1093/nar/gkx1195] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/17/2017] [Indexed: 11/13/2022] Open
Abstract
Single cell whole-genome sequencing (scWGS) is providing novel insights into the nature of genetic heterogeneity in normal and diseased cells. However, the whole-genome amplification process required for scWGS introduces biases into the resulting sequencing that can confound downstream analysis. Here, we present a statistical method, with an accompanying package PaSD-qc (Power Spectral Density-qc), that evaluates the properties and quality of single cell libraries. It uses a modified power spectral density to assess amplification uniformity, amplicon size distribution, autocovariance and inter-sample consistency as well as to identify chromosomes with aberrant read-density profiles due either to copy alterations or poor amplification. These metrics provide a standard way to compare the quality of single cell samples as well as yield information necessary to improve variant calling strategies. We demonstrate the usefulness of this tool in comparing the properties of scWGS protocols, identifying potential chromosomal copy number variation, determining chromosomal and subchromosomal regions of poor amplification, and selecting high-quality libraries from low-coverage data for deep sequencing. The software is available free and open-source at https://github.com/parklab/PaSDqc.
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Affiliation(s)
- Maxwell A Sherman
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Alison R Barton
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Michael A Lodato
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Carl Vitzthum
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Michael E Coulter
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.,Ludwig Center at Harvard, Boston, MA 02115, USA
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31
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Clonal heterogeneity of melanoma in a paradigmatic case study: future prospects for circulating melanoma cells. Melanoma Res 2019; 29:89-94. [PMID: 30222690 DOI: 10.1097/cmr.0000000000000510] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The management of metastatic melanoma is a difficult matter. Nevertheless, the advent of target therapy has significantly improved patient outcome, provided that tumor molecular characteristics become available: the detection of drug-resistant clones can contribute to understanding the reasons for resistance onset, influencing the choice of subsequent therapy. This work aimed to provide a possible explanation for the early resistance to vemurafenib developed by a patient with melanoma, and concurrently to assess the extent, and role, of the tumor clonal heterogeneity. We analyzed tissue samples from different sites and time points: first/second primary, three lymph node metastases, and circulating melanoma cells (CMCs). We first investigated these samples by the routine Sanger sequencing for BRAF, NRAS, and KIT, and then, we focused on specific hotspots by droplet digital PCR. We detected a BRAF V600E mutation by Sanger sequencing in the second primary and distant lymph node metastases, but not in the first primary or sentinel lymph node. Interestingly, by droplet digital PCR, the V600E mutation was also detected in the first primary, and the V600K in the second primary and metastases. Moreover, we identified a rare KIT V569G mutation, appearing to be CMC exclusive. This finding confirms the potential of CMCs as a source of tumor material for genetic analysis, reflecting real-time systemic disease evolution and, most likely, the most aggressive, treatment-resistant clones. In summary, this work underlines the importance of CMCs in the early identification of tumor clones putatively responsible for therapy resistance.
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Tellez-Gabriel M, Heymann MF, Heymann D. Circulating Tumor Cells as a Tool for Assessing Tumor Heterogeneity. Am J Cancer Res 2019; 9:4580-4594. [PMID: 31367241 PMCID: PMC6643448 DOI: 10.7150/thno.34337] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 04/23/2019] [Indexed: 12/18/2022] Open
Abstract
Tumor heterogeneity is the major cause of failure in cancer prognosis and prediction. Accurately detecting heterogeneity for the development of biomarkers and the detection of the clones resistant to therapy is one of the main goals of contemporary medicine. Metastases belong to the natural history of cancer. The present review gives an overview on the origin of tumor heterogeneity. Recent progress has made it possible to isolate and characterize circulating tumor cells (CTCs), which are the drivers of the disease between the primary sites and metastatic foci. The most recent methods for characterizing CTCs are summarized and we discuss the power of CTC profiling for analyzing tumor heterogeneity in early and advanced diseases.
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Abstract
Precision medicine is emerging as a cornerstone of future cancer care with the objective of providing targeted therapies based on the molecular phenotype of each individual patient. Traditional bulk-level molecular phenotyping of tumours leads to significant information loss, as the molecular profile represents an average phenotype over large numbers of cells, while cancer is a disease with inherent intra-tumour heterogeneity at the cellular level caused by several factors, including clonal evolution, tissue hierarchies, rare cells and dynamic cell states. Single-cell sequencing provides means to characterize heterogeneity in a large population of cells and opens up opportunity to determine key molecular properties that influence clinical outcomes, including prognosis and probability of treatment response. Single-cell sequencing methods are now reliable enough to be used in many research laboratories, and we are starting to see applications of these technologies for characterization of human primary cancer cells. In this review, we provide an overview of studies that have applied single-cell sequencing to characterize human cancers at the single-cell level, and we discuss some of the current challenges in the field.
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Affiliation(s)
- Mattias Rantalainen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Nobels Vag 12A, Stockholm, Sweden
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Scerri J, Baldacchino S, Saliba C, Scerri C, Grech G. Bead-based RNA multiplex panels for biomarker detection in oncology samples. Methods 2019; 158:86-91. [PMID: 30352255 DOI: 10.1016/j.ymeth.2018.10.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 09/29/2018] [Accepted: 10/16/2018] [Indexed: 12/17/2022] Open
Abstract
Patient stratification, prognosis and disease monitoring are three important aspects of personalized cancer medicine. With traditional serum tumour protein biomarkers showing lack of specificity and sensitivity, and tumour heterogeneity affecting the response to targeted therapy based on tissue biomarkers, the focus has shifted to the use of molecular tumour signatures as specific biomarkers. Multiplex microsphere-based panels are robust and cost-effective, high throughput molecular assays, which can accurately characterize tumours even from small amounts of poor quality nucleic acids. Only few studies have reported the use of microspheres (beads) to quantify RNA expression of targets of interest simultaneously (multiplexing). This review is an overview of the various applications of bead-based RNA panels in molecular oncology, with focus on the Invitrogen™ QuantiGene™ Plex Assay (Thermo Fisher Scientific), and provides a comparison with PCR-based and other methodologies. The advantages of multiplex bead assays are exemplified by the quantification of RNA expression in formalin-fixed, paraffin embedded (FFPE) archival tissue and the simultaneous detection of biomarkers in low input samples, including quantification of markers in microdissected tissue material, to characterise heterogeneous tumour sites within a sample, and by the detection of markers in low numbers of circulating tumour cells.
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Affiliation(s)
- Jeanesse Scerri
- Department of Physiology & Biochemistry, Faculty of Medicine and Surgery, University of Malta, Malta.
| | - Shawn Baldacchino
- Department of Pathology, Faculty of Medicine & Surgery, University of Malta, Malta.
| | - Christian Saliba
- Centre for Molecular Medicine and Biobanking, University of Malta, Malta.
| | - Christian Scerri
- Department of Physiology & Biochemistry, Faculty of Medicine and Surgery, University of Malta, Malta.
| | - Godfrey Grech
- Department of Pathology, Faculty of Medicine & Surgery, University of Malta, Malta.
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Martí-Carreras J, Maes P. Human cytomegalovirus genomics and transcriptomics through the lens of next-generation sequencing: revision and future challenges. Virus Genes 2019; 55:138-164. [PMID: 30604286 PMCID: PMC6458973 DOI: 10.1007/s11262-018-1627-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 12/14/2018] [Indexed: 12/13/2022]
Abstract
The human cytomegalovirus (HCMV) genome was sequenced by hierarchical shotgun almost 30 years ago. Over these years, low and high passaged strains have been sequenced, improving, albeit still far from complete, the understanding of the coding potential, expression dynamics and diversity of wild-type HCMV strains. Next-generation sequencing (NGS) platforms have enabled a huge advancement, facilitating the comparison of differentially passaged strains, challenging diagnostics and research based on a single or reduced gene set genotyping. In addition, it allowed to link genetic features to different viral phenotypes as for example, correlating large genomic re-arrangements to viral attenuation or different mutations to antiviral resistance and cell tropism. NGS platforms provided the first high-resolution experiments to HCMV dynamics, allowing the study of intra-host viral population structures and the description of rare transcriptional events. Long-read sequencing has recently become available, helping to identify new genomic re-arrangements, partially accounting for the genetic variability displayed in clinical isolates, as well as, in changing the understanding of the HCMV transcriptome. Better knowledge of the transcriptome resulted in a vast number of new splicing events and alternative transcripts, although most of them still need additional validation. This review summarizes the sequencing efforts reached so far, discussing its approaches and providing a revision and new nuances on HCMV sequence variability in the sequencing field.
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Affiliation(s)
- Joan Martí-Carreras
- Zoonotic Infectious Diseases Unit, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, Box 1040, 3000, Leuven, Belgium
| | - Piet Maes
- Zoonotic Infectious Diseases Unit, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, Box 1040, 3000, Leuven, Belgium.
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Sequencing and Phylogenetic Analysis of Chloroplast Genes in Freshwater Raphidophytes. Genes (Basel) 2019; 10:genes10030245. [PMID: 30909525 PMCID: PMC6471398 DOI: 10.3390/genes10030245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/19/2019] [Accepted: 03/20/2019] [Indexed: 11/30/2022] Open
Abstract
The complex evolution of chloroplasts in microalgae has resulted in highly diverse pigment profiles. Freshwater raphidophytes, for example, display a very different pigment composition to marine raphidophytes. To investigate potential differences in the evolutionary origin of chloroplasts in these two groups of raphidophytes, the plastid genomes of the freshwater species Gonyostomum semen and Vacuolaria virescens were sequenced. To exclusively sequence the organelle genomes, chloroplasts were manually isolated and amplified using single-cell whole-genome-amplification. Assembled and annotated chloroplast genes of the two species were phylogenetically compared to the marine raphidophyte Heterosigma akashiwo and other evolutionarily more diverse microalgae. These phylogenetic comparisons confirmed the high relatedness of all investigated raphidophyte species despite their large differences in pigment composition. Notable differences regarding the presence of light-independent protochlorophyllide oxidoreductase (LIPOR) genes among raphidophyte algae were also revealed in this study. The whole-genome amplification approach proved to be useful for isolation of chloroplast DNA from nuclear DNA. Although only approximately 50% of the genomes were covered, this was sufficient for a multiple gene phylogeny representing large parts of the chloroplast genes.
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Belandres D, Shamonki M, Arrach N. Current status of spent embryo media research for preimplantation genetic testing. J Assist Reprod Genet 2019; 36:819-826. [PMID: 30895497 DOI: 10.1007/s10815-019-01437-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/07/2019] [Indexed: 12/20/2022] Open
Abstract
In recent years, a growing body of literature has emerged investigating the clinical utility of spent embryo media (SEM) for preimplantation genetic testing for aneuploidy (PGT-A) (Hammond et al. in Fertil Steril. 107(1):220-8, 2017; Xu et al. in Proc Natl Acad Sci USA. 113(42):11907-12, 2016; Shamonki et al. in Fertil Steril. 106(6):1312-8, 2016; Feichtinger et al. in Reprod BioMed Online. 34(6):583-9, 2017; Vera-Rodriguez et al. in Hum Reprod. 33(4):745-56, 2018; Kuznyetsov et al. in PLoS One. 13(5):e0197262, 2018; Ho et al. in Fertil Steril. 110(3):467-75, 2018; Capalbo et al. in Fertil Steril. 110(5):870-9, 2018). Most of these studies have reported moderate success rates, suggesting the need for improvements in sensitivity and specificity. The concordance between spent media and embryo biopsy or whole embryo was reported to be between 30.4 and 90%, with 50-70% correlation being the most representative (Xu et al. in Proc Natl Acad Sci USA. 113(42):11907-12, 2016; Shamonki et al. in Fertil Steril. 106(6):1312-8, 2016; Feichtinger et al. in Reprod BioMed Online. 34(6):583-9, 2017; Vera-Rodriguez et al. in Hum Reprod. 33(4):745-56, 2018; Kuznyetsov et al. in PLoS One. 13(5):e0197262, 2018; Ho et al. in Fertil Steril. 110(3):467-75, 2018). Here, we will analyze all spent media testing strategies including SEM collection methods, whole genome amplification (WGA) strategies, chromosome copy number detection, and bioinformatics analysis tools. We will propose improvements to further increase the accuracy and sensitivity of the assay before bringing PGT-A with SEM into the clinical sphere.
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Affiliation(s)
- Denice Belandres
- Progenesis Inc., 4150 Regents Park Row, Suite 245, La Jolla, CA, 92037, USA
| | - Mousa Shamonki
- Fertility and Surgical Associates of California, 325 Rolling Oaks Drive, Suite 110, Thousand Oaks, CA, 91361, USA.,University of California, Los Angeles, CA, 90095, USA
| | - Nabil Arrach
- Progenesis Inc., 4150 Regents Park Row, Suite 245, La Jolla, CA, 92037, USA.
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Huss WJ, Hu Q, Glenn ST, Gangavarapu KJ, Wang J, Luce JD, Quinn PK, Brese EA, Zhan F, Conroy JM, Paragh G, Foster BA, Morrison CD, Liu S, Wei L. Comparison of SureSelect and Nextera Exome Capture Performance in Single-Cell Sequencing. Hum Hered 2019; 83:153-162. [PMID: 30669152 DOI: 10.1159/000490506] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Advances in single-cell sequencing provide unprecedented opportunities for clinical examination of circulating tumor cells, cancer stem cells, and other rare cells responsible for disease progression and drug resistance. On the genomic level, single-cell whole exome sequencing (scWES) started to gain popularity with its unique potentials in characterizing mutational landscapes at a single-cell level. Currently, there is little known about the performance of different exome capture kits in scWES. Nextera rapid capture (NXT; Illumina, Inc.) has been the only exome capture kit recommended for scWES by Fluidigm C1, a widely accessed system in single-cell preparation. RESULTS In this study, we compared the performance of NXT following Fluidigm's protocol with Agilent SureSelectXT Target Enrichment System (AGL), another exome capture kit widely used for bulk sequencing. We created DNA libraries of 192 single cells isolated from spheres grown from a melanoma specimen using Fluidigm C1. Twelve high-yield cells were selected to perform dual-exome capture and sequencing using AGL and NXT in parallel. After mapping and coverage analysis, AGL outperformed NXT in coverage uniformity, mapping rates of reads, exome capture rates, and low PCR duplicate rates. For germline variant calling, AGL achieved better performance in overlap with known variants in dbSNP and transition-transversion ratios. Using calls from high coverage bulk sequencing from blood DNA as the golden standard, AGL-based scWES demonstrated high positive predictive values, and medium to high sensitivity. Lastly, we evaluated somatic mutation calling by comparing single-cell data with the matched blood sequence as control. On average, 300 mutations were identified in each cell. In 10 of 12 cells, higher numbers of mutations were identified using AGL than NXT, probably caused by coverage depth. When mutations are adequately covered in both AGL and NXT data, the two methods showed very high concordance (93-100% per cell). CONCLUSIONS Our results suggest that AGL can also be used for scWES when there is sufficient DNA, and it yields better data quality than the current Fluidigm's protocol using NXT.
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Affiliation(s)
- Wendy J Huss
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Qiang Hu
- Departments of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Sean T Glenn
- Center of Personalized Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA.,Department of Cancer Genetics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Kalyan J Gangavarapu
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Jianmin Wang
- Departments of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Jesse D Luce
- Center of Personalized Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Paul K Quinn
- Center of Personalized Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Elizabeth A Brese
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Fenglin Zhan
- PET/CT Center, The First Affiliated Hospital of the University of Science and Technology of China, Hefei, China
| | - Jeffrey M Conroy
- Center of Personalized Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Gyorgy Paragh
- Department of Dermatology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA.,Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Barbara A Foster
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Carl D Morrison
- Center of Personalized Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Song Liu
- Departments of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Lei Wei
- Departments of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA,
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Negishi R, Iwata R, Tanaka T, Kisailus D, Maeda Y, Matsunaga T, Yoshino T. Gel-based cell manipulation method for isolation and genotyping of single-adherent cells. Analyst 2019; 144:990-996. [DOI: 10.1039/c8an01456f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The simple and rapid method for isolation of single-adherent cells from a culture dish was developed and applied to genetic analysis of single-cells.
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Affiliation(s)
- Ryo Negishi
- Division of Biotechnology and Life Science
- Institute of Engineering
- Tokyo University of Agriculture and Technology
- Tokyo
- Japan
| | - Reito Iwata
- Division of Biotechnology and Life Science
- Institute of Engineering
- Tokyo University of Agriculture and Technology
- Tokyo
- Japan
| | - Tsuyoshi Tanaka
- Division of Biotechnology and Life Science
- Institute of Engineering
- Tokyo University of Agriculture and Technology
- Tokyo
- Japan
| | - David Kisailus
- Department of Chemical and Environmental Engineering
- University of California
- Riverside
- Riverside
- USA
| | - Yoshiaki Maeda
- Division of Biotechnology and Life Science
- Institute of Engineering
- Tokyo University of Agriculture and Technology
- Tokyo
- Japan
| | - Tadashi Matsunaga
- Division of Biotechnology and Life Science
- Institute of Engineering
- Tokyo University of Agriculture and Technology
- Tokyo
- Japan
| | - Tomoko Yoshino
- Division of Biotechnology and Life Science
- Institute of Engineering
- Tokyo University of Agriculture and Technology
- Tokyo
- Japan
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Hou Z, An L, Han J, Yuan Y, Chen D, Tian J. Revolutionize livestock breeding in the future: an animal embryo-stem cell breeding system in a dish. J Anim Sci Biotechnol 2018; 9:90. [PMID: 30568797 PMCID: PMC6298008 DOI: 10.1186/s40104-018-0304-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/30/2018] [Indexed: 12/21/2022] Open
Abstract
Meat and milk production needs to increase ~ 70–80% relative to its current levels for satisfying the human needs in 2050. However, it is impossible to achieve such genetic gain by conventional animal breeding systems. Based on recent advances with regard to in vitro induction of germ cell from pluripotent stem cells, herein we propose a novel embryo-stem cell breeding system. Distinct from the conventional breeding system in farm animals that involves selecting and mating individuals, the novel breeding system completes breeding cycles from parental to offspring embryos directly by selecting and mating embryos in a dish. In comparison to the conventional dairy breeding scheme, this system can rapidly achieve 30–40 times more genetic gain by significantly shortening generation interval and enhancing selection intensity. However, several major obstacles must be overcome before we can fully use this system in livestock breeding, which include derivation and mantaince of pluripotent stem cells in domestic animals, as well as in vitro induction of primordial germ cells, and subsequent haploid gametes. Thus, we also discuss the potential efforts needed in solving the obstacles for application this novel system, and elaborate on their groundbreaking potential in livestock breeding. This novel system would provide a revolutionary animal breeding system by offering an unprecedented opportunity for meeting the fast-growing meat and milk demand of humans.
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Affiliation(s)
- Zhuocheng Hou
- 1Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lei An
- 1Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jianyong Han
- 2State Key Laboratories for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ye Yuan
- 3Colorado Center for Reproductive Medicine, Denver, USA
| | - Dongbao Chen
- 4Department of Obstetrics and Gynecology, University of California Irvine, Irvine, USA
| | - Jianhui Tian
- 1Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Rezaei M, Winter M, Zander-Fox D, Whitehead C, Liebelt J, Warkiani ME, Hardy T, Thierry B. A Reappraisal of Circulating Fetal Cell Noninvasive Prenatal Testing. Trends Biotechnol 2018; 37:632-644. [PMID: 30501925 DOI: 10.1016/j.tibtech.2018.11.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/04/2018] [Accepted: 11/05/2018] [Indexed: 01/09/2023]
Abstract
New tools for higher-resolution fetal genome analysis including microarray and next-generation sequencing have revolutionized prenatal screening. This article provides commentary on this rapidly advancing field and a future perspective emphasizing circulating fetal cell (CFC) utility. Despite the tremendous technological challenges associated with their reliable and cost-effective isolation from maternal blood, CFCs have a strong potential to bridge the gap between the diagnostic sensitivity of invasive procedures and the desirable noninvasive nature of cell-free fetal DNA (cffDNA). Considering the rapid advances in both rare cell isolation and low-input DNA analysis, we argue here that CFC-based noninvasive prenatal testing is poised to be implemented clinically in the near future.
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Affiliation(s)
- Meysam Rezaei
- Future Industries Institute and ARC Centre of Excellence in Convergent Bio and Nano Science and Technology, University of South Australia, Mawson Lakes Campus, Mawson Lakes, South Australia, Australia; Joint first authors. https://twitter.com/@CBNSSA
| | - Marnie Winter
- Future Industries Institute and ARC Centre of Excellence in Convergent Bio and Nano Science and Technology, University of South Australia, Mawson Lakes Campus, Mawson Lakes, South Australia, Australia; Joint first authors. https://twitter.com/@CBNSSA
| | | | - Clare Whitehead
- Department of Obstetrics and Gynaecology, University of Toronto, Toronto, ON, Canada
| | - Jan Liebelt
- South Australian Clinical Genetics Service, Women's and Children's Hospital, Adelaide, Australia
| | - Majid Ebrahimi Warkiani
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Ultimo NSW 2007, Australia; Institute of Molecular Medicine, Sechenov First Moscow State University, Moscow 119991, Russia
| | - Tristan Hardy
- SA Pathology, Adelaide, Australia; Repromed, Dulwich, South Australia, Australia.
| | - Benjamin Thierry
- Future Industries Institute and ARC Centre of Excellence in Convergent Bio and Nano Science and Technology, University of South Australia, Mawson Lakes Campus, Mawson Lakes, South Australia, Australia; http://bionanoengineering.com/. https://twitter.com/@CBNSSA
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Tumour heterogeneity and metastasis at single-cell resolution. Nat Cell Biol 2018; 20:1349-1360. [PMID: 30482943 DOI: 10.1038/s41556-018-0236-7] [Citation(s) in RCA: 343] [Impact Index Per Article: 57.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/24/2018] [Indexed: 02/07/2023]
Abstract
Tumours comprise a heterogeneous collection of cells with distinct genetic and phenotypic properties that can differentially promote progression, metastasis and drug resistance. Emerging single-cell technologies provide a new opportunity to profile individual cells within tumours and investigate what roles they play in these processes. This Review discusses key technological considerations for single-cell studies in cancer, new findings using single-cell technologies and critical open questions for future applications.
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Novel Double Factor PGT strategy analyzing blastocyst stage embryos in a single NGS procedure. PLoS One 2018; 13:e0205692. [PMID: 30332465 PMCID: PMC6192598 DOI: 10.1371/journal.pone.0205692] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 09/28/2018] [Indexed: 12/16/2022] Open
Abstract
In families at risk from monogenic diseases affected offspring, it is fundamental the development of a suitable Double Factor Preimplantation Genetic Testing (DF-PGT) method for both single-gene analysis and chromosome complement screening. Aneuploidy is not only a major issue in advanced-maternal-age patients and balanced translocation carriers, but also the aneuploidy rate is extremely high in patients undergoing in vitro fertilization (IVF), even in young donors. To adequate NGS technology to the DF-PGT strategy four different whole genome amplification systems (Sureplex, MALBAC, and two multiple displacement amplification systems-MDA) were tested using TruSight One panel on cell lines and blastocyst trophectoderm biopsies-TE. Embryo cytogenetic status was analyzed by Nexus software. Sureplex and MALBAC DNA products were considered not suitable for PGT diagnosis due to inconsistent and poor results on Trusight one (TSO) panel. Results obtained with both MDA based methods (GEH-MDA and RG-MDA) were appropriate for direct mutation detection by TSO NGS platform. Nevertheless, RG-MDA amplification products showed better coverage and lower ADO rates than GEH-MDA. The present work also demonstrates that the same TSO sequencing data is suitable not only for the direct mutation detection, but also for the indirect mutation detection by linkage analysis of informative SNPs. The present work also demonstrates that Nexus software is competent for the detection of CNV by using with TSO sequencing data from RG-MDA products, allowing for the whole cytogenetic characterization of the embryos. In conclusion, successfully development of an innovative and promising DF-PGT strategy using TSO-NGS technology in TE biopsies, performed in-house in a single laboratory experience, has been done in the present work. Additional studies should be performed before it could be used as a diagnostic alternative in order to validate this approach for the detection of chromosomal aneuploidies.
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Transcriptomic but not genomic variability confers phenotype of breast cancer stem cells. Cancer Commun (Lond) 2018; 38:56. [PMID: 30231942 PMCID: PMC6146522 DOI: 10.1186/s40880-018-0326-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 09/08/2018] [Indexed: 12/19/2022] Open
Abstract
Background Breast cancer stem cells (BCSCs) are considered responsible for cancer relapse and drug resistance. Understanding the identity of BCSCs may open new avenues in breast cancer therapy. Although several discoveries have been made on BCSC characterization, the factors critical to the origination of BCSCs are largely unclear. This study aimed to determine whether genomic mutations contribute to the acquisition of cancer stem-like phenotype and to investigate the genetic and transcriptional features of BCSCs. Methods We detected potential BCSC phenotype-associated mutation hotspot regions by using whole-genome sequencing on parental cancer cells and derived serial-generation spheres in increasing order of BCSC frequency, and then performed target deep DNA sequencing at bulk-cell and single-cell levels. To identify the transcriptional program associated with BCSCs, bulk-cell and single-cell RNA sequencing was performed. Results By using whole-genome sequencing of bulk cells, potential BCSC phenotype-associated mutation hotspot regions were detected. Validation by target deep DNA sequencing, at both bulk-cell and single-cell levels, revealed no genetic changes specifically associated with BCSC phenotype. Moreover, single-cell RNA sequencing showed profound transcriptomic variability in cancer cells at the single-cell level that predicted BCSC features. Notably, this transcriptomic variability was enriched during the transcription of 74 genes, revealed as BCSC markers. Breast cancer patients with a high risk of relapse exhibited higher expression levels of these BCSC markers than those with a low risk of relapse, thereby highlighting the clinical significance of predicting breast cancer prognosis with these BCSC markers. Conclusions Transcriptomic variability, not genetic mutations, distinguishes BCSCs from non-BCSCs. The identified 74 BCSC markers have the potential of becoming novel targets for breast cancer therapy. Electronic supplementary material The online version of this article (10.1186/s40880-018-0326-8) contains supplementary material, which is available to authorized users.
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Burbulis IE, Wierman MB, Wolpert M, Haakenson M, Lopes MB, Schiff D, Hicks J, Loe J, Ratan A, McConnell MJ. Improved molecular karyotyping in glioblastoma. Mutat Res 2018; 811:16-26. [PMID: 30055482 DOI: 10.1016/j.mrfmmm.2018.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/22/2018] [Accepted: 06/24/2018] [Indexed: 06/08/2023]
Abstract
Uneven replication creates artifacts during whole genome amplification (WGA) that confound molecular karyotype assignment in single cells. Here, we present an improved WGA recipe that increased coverage and detection of copy number variants (CNVs) in single cells. We examined serial resections of glioblastoma (GBM) tumor from the same patient and found low-abundance clones containing CNVs in clinically relevant loci that were not observable using bulk DNA sequencing. We discovered extensive genomic variability in this class of tumor and provide a practical approach for investigating somatic mosaicism.
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Affiliation(s)
- Ian E Burbulis
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States; Escuela de Medicina, Universidad San Sebastian, Puerto Montt, Chile
| | - Margaret B Wierman
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - Matt Wolpert
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - Mark Haakenson
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - Maria-Beatriz Lopes
- Department of Pathology, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - David Schiff
- Department of Neurology, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - James Hicks
- Michelson Center, University of Southern California, Los Angeles, CA, United States; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Justin Loe
- Full Genomes Corp, Inc., Rockville, MD, United States
| | - Aakrosh Ratan
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States; Center for Public Health Genomics, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - Michael J McConnell
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States; Department of Neuroscience, University of Virginia, School of Medicine, Charlottesville, VA, United States; Center for Public Health Genomics, University of Virginia, School of Medicine, Charlottesville, VA, United States; Center for Brain Immunology and Glia, University of Virginia, School of Medicine, Charlottesville, VA, United States.
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46
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Mincarelli L, Lister A, Lipscombe J, Macaulay IC. Defining Cell Identity with Single-Cell Omics. Proteomics 2018; 18:e1700312. [PMID: 29644800 PMCID: PMC6175476 DOI: 10.1002/pmic.201700312] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 03/23/2018] [Indexed: 01/17/2023]
Abstract
Cells are a fundamental unit of life, and the ability to study the phenotypes and behaviors of individual cells is crucial to understanding the workings of complex biological systems. Cell phenotypes (epigenomic, transcriptomic, proteomic, and metabolomic) exhibit dramatic heterogeneity between and within the different cell types and states underlying cellular functional diversity. Cell genotypes can also display heterogeneity throughout an organism, in the form of somatic genetic variation-most notably in the emergence and evolution of tumors. Recent technical advances in single-cell isolation and the development of omics approaches sensitive enough to reveal these aspects of cell identity have enabled a revolution in the study of multicellular systems. In this review, we discuss the technologies available to resolve the genomes, epigenomes, transcriptomes, proteomes, and metabolomes of single cells from a wide variety of living systems.
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Affiliation(s)
- Laura Mincarelli
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZUnited Kingdom
| | - Ashleigh Lister
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZUnited Kingdom
| | - James Lipscombe
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZUnited Kingdom
| | - Iain C. Macaulay
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZUnited Kingdom
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47
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Volozonoka L, Perminov D, Korņejeva L, Alkšere B, Novikova N, Pīmane EJ, Blumberga A, Kempa I, Miskova A, Gailīte L, Fodina V. Performance comparison of two whole genome amplification techniques in frame of multifactor preimplantation genetic testing. J Assist Reprod Genet 2018; 35:1457-1472. [PMID: 29687370 PMCID: PMC6086788 DOI: 10.1007/s10815-018-1187-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 04/12/2018] [Indexed: 11/29/2022] Open
Abstract
PURPOSE To compare multiple displacement amplification and OmniPlex whole genome amplification technique performance during array comparative genome hybridization (aCGH), Sanger sequencing, SNaPshot and fragment size analysis downstream applications in frame of multifactor embryo preimplantation genetic testing. METHODS Preclinical workup included linked short tandem repeat (STR) marker selection and primer design for loci of interest. It was followed by a family haplotyping, after which an in vitro fertilization preimplantation genetic testing (IVF-PGT) cycle was carried out. A total of 62 embryos were retrieved from nine couples with a confirmed single gene disorder being transmitted in their family with various inheritance traits-autosomal dominant (genes-ACTA2, HTT, KRT14), autosomal recessive (genes-ALOX12B, TPP1, GLB1) and X-linked (genes-MTM1, DMD). Whole genome amplification (WGA) for the day 5 embryo trophectoderm single biopsies was carried out by multiple displacement amplification (MDA) or polymerase chain reaction (PCR)-based technology OmniPlex and was used for direct (Sanger sequencing, fragment size analysis, SNaPshot) and indirect mutation assessment (STR marker haplotyping), and embryo aneuploidy testing by array comparative genome hybridization (aCGH). RESULTS Family haplotyping revealed informative/semi-informative microsatellite markers for all clinical cases for all types of inheritance. Indirect testing gave a persuasive conclusion for all embryos assessed, which was confirmed through direct testing. The overall allele dropout (ADO) rate was higher for PCR-based WGA, and MDA shows a better genomic recovery scale. Five euploid embryos were subjected to elective single embryo transfer (eSET), which resulted in four clinical pregnancies and birth of two healthy children, which proved free of disease causative variants running in the family postnataly. CONCLUSIONS A developed multifactor PGT protocol can be adapted and applied to virtually any genetic condition and is capable of improving single gene disorder preimplantation genetic testing in a patient-tailored manner thus increasing pregnancy rates, saving costs and increasing patient reliability.
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Affiliation(s)
- Ludmila Volozonoka
- Scientific Laboratory of Molecular Genetics, Riga Stradins University, Dzirciema street 16, Riga, LV-1007, Latvia.
- Centre of Genetics, "IVF Riga" Reproductive Genetics Clinic, Riga, LV-1010, Latvia.
| | - Dmitry Perminov
- Centre of Genetics, "IVF Riga" Reproductive Genetics Clinic, Riga, LV-1010, Latvia
- Department of Molecular Biology, "E. Gulbja Laboratory", Riga, LV-1006, Latvia
| | - Liene Korņejeva
- Centre of Genetics, "IVF Riga" Reproductive Genetics Clinic, Riga, LV-1010, Latvia
| | - Baiba Alkšere
- Centre of Genetics, "IVF Riga" Reproductive Genetics Clinic, Riga, LV-1010, Latvia
| | - Natālija Novikova
- Centre of Genetics, "IVF Riga" Reproductive Genetics Clinic, Riga, LV-1010, Latvia
- Faculty of Medicine, University of Latvia, Riga, LV-1586, Latvia
| | - Evija Jokste Pīmane
- Centre of Genetics, "IVF Riga" Reproductive Genetics Clinic, Riga, LV-1010, Latvia
| | - Arita Blumberga
- Centre of Genetics, "IVF Riga" Reproductive Genetics Clinic, Riga, LV-1010, Latvia
| | - Inga Kempa
- Scientific Laboratory of Molecular Genetics, Riga Stradins University, Dzirciema street 16, Riga, LV-1007, Latvia
| | - Anna Miskova
- Department of Obstetrics and Gynecology, Riga Stradins University, Riga, LV-1007, Latvia
| | - Linda Gailīte
- Scientific Laboratory of Molecular Genetics, Riga Stradins University, Dzirciema street 16, Riga, LV-1007, Latvia
| | - Violeta Fodina
- Centre of Genetics, "IVF Riga" Reproductive Genetics Clinic, Riga, LV-1010, Latvia
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48
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Genotyping DNA isolated from UV irradiated human bloodstains using whole genome amplification. Mol Biol Rep 2018; 45:925-929. [DOI: 10.1007/s11033-018-4240-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 07/05/2018] [Indexed: 10/28/2022]
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49
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Deleye L, Gansemans Y, De Coninck D, Van Nieuwerburgh F, Deforce D. Massively parallel sequencing of micro-manipulated cells targeting a comprehensive panel of disease-causing genes: A comparative evaluation of upstream whole-genome amplification methods. PLoS One 2018; 13:e0196334. [PMID: 29698522 PMCID: PMC5919401 DOI: 10.1371/journal.pone.0196334] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 04/11/2018] [Indexed: 12/28/2022] Open
Abstract
Single Gene Disorders (SGD) are still routinely diagnosed using PCR-based assays that need to be developed and validated for each individual disease-specific gene fragment. The TruSight One sequencing panel currently covers 12 Mb of genomic content, including 4813 genes associated with a clinical phenotype. When only a limited number of cells are available, whole genome amplification (WGA) is required prior to DNA target capture techniques such as the TruSight One panel. In this study, we compared 4 different WGA methods in combination with the TruSight One sequencing panel to perform single nucleotide polymorphism (SNP) genotyping starting from 3 micro-manipulated cells. This setting simulates clinical settings such as day-5 blastocyst biopsy for Preimplantation Genetic Testing (PGT), liquid biopsy of circulating tumor cells (CTCs) and cancer-cell profiling. Bulk cell samples were processed alongside these WGA samples to serve as a performance reference. Target coverage, coverage uniformity and SNP calling accuracy obtained using any of the WGA, is inferior to the results obtained on bulk cell samples. However, results after REPLI-g come close. Compared to the other WGA methods, the method using REPLI-g WGA results in a better coverage of the targeted genomic regions with a more uniform read depth. Consequently, this method also results in a more accurate SNP calling and could be considered for clinical genotyping of a limited number of cells.
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Affiliation(s)
- Lieselot Deleye
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Yannick Gansemans
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Dieter De Coninck
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | | | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
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50
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Abstract
BACKGROUND Querying cancer genomes at single-cell resolution is expected to provide a powerful framework to understand in detail the dynamics of cancer evolution. However, given the high costs currently associated with single-cell sequencing, together with the inevitable technical noise arising from single-cell genome amplification, cost-effective strategies that maximize the quality of single-cell data are critically needed. Taking advantage of previously published single-cell whole-genome and whole-exome cancer datasets, we studied the impact of sequencing depth and sampling effort towards single-cell variant detection. METHODS Five single-cell whole-genome and whole-exome cancer datasets were independently downscaled to 25, 10, 5, and 1× sequencing depth. For each depth level, ten technical replicates were generated, resulting in a total of 6280 single-cell BAM files. The sensitivity of variant detection, including structural and driver mutations, genotyping, clonal inference, and phylogenetic reconstruction to sequencing depth was evaluated using recent tools specifically designed for single-cell data. RESULTS Altogether, our results suggest that for relatively large sample sizes (25 or more cells) sequencing single tumor cells at depths > 5× does not drastically improve somatic variant discovery, characterization of clonal genotypes, or estimation of single-cell phylogenies. CONCLUSIONS We suggest that sequencing multiple individual tumor cells at a modest depth represents an effective alternative to explore the mutational landscape and clonal evolutionary patterns of cancer genomes.
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