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Advances and applications of single-cell sequencing technologies. ​

Literature Information ​

PMID26000845
JournalMolecular cell
Impact Factor16.6
JCR QuartileQ1
Publication Year2015
Times Cited312
KeywordsSingle-cell sequencing, Technological advances, Biological applications
Literature TypeJournal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't, Review
ISSN1097-2765
Pages598-609
Issue58(4)
AuthorsYong Wang, Nicholas E Navin

TL;DR ​

Single-cell sequencing (SCS) has revolutionized the study of rare cells and complex populations across various biological fields, such as microbiology, neurobiology, and cancer research, over the past five years. This review explores the advancements in SCS technologies and their significant translational applications in clinical settings, highlighting their potential to enhance our understanding of cellular diversity and inform medical practices.

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Single-cell sequencing · Technological advances · Biological applications

Abstract ​

Single-cell sequencing (SCS) has emerged as a powerful new set of technologies for studying rare cells and delineating complex populations. Over the past 5 years, SCS methods for DNA and RNA have had a broad impact on many diverse fields of biology, including microbiology, neurobiology, development, tissue mosaicism, immunology, and cancer research. In this review, we will discuss SCS technologies and applications, as well as translational applications in the clinic.

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Primary Questions Addressed ​

  1. What are the specific challenges faced in the application of single-cell sequencing in cancer research?
  2. How do single-cell sequencing technologies differ in their approach to studying immune responses compared to traditional bulk sequencing methods?
  3. In what ways can single-cell sequencing contribute to our understanding of neurodevelopmental disorders?
  4. What are the potential translational applications of single-cell sequencing in clinical settings, particularly in personalized medicine?
  5. How can advancements in single-cell sequencing technologies improve our understanding of tissue mosaicism and its implications for health?

Key Findings ​

Research Background and Objectives ​

Single-cell sequencing (SCS) has become a transformative technology in the biological sciences, enabling the detailed study of rare cell types and the characterization of complex cellular populations. The objective of this review is to provide an overview of SCS technologies, their applications across various fields, and their potential translational impacts in clinical settings.

Main Methods/Materials/Experimental Design ​

The review covers various SCS technologies, primarily focusing on DNA and RNA sequencing methods. These techniques allow researchers to analyze genetic material at the single-cell level, providing insights into cellular heterogeneity and function.

Methodological Overview ​

The following flowchart illustrates the SCS methodologies discussed in the review:

Mermaid diagram

Key Results and Findings ​

The review highlights several key findings regarding the impact of SCS technologies:

  • Diverse Applications: SCS has been successfully applied in various biological fields, enhancing our understanding of complex biological systems.
  • Clinical Relevance: The ability to analyze single cells has implications for personalized medicine, particularly in cancer research and immunotherapy.
  • Technological Advancements: Recent improvements in SCS methodologies have increased throughput and reduced costs, making these technologies more accessible for widespread use.

Main Conclusions/Significance/Innovation ​

The review concludes that SCS technologies represent a significant advancement in the biological sciences, offering unprecedented insights into cellular diversity and function. The ability to study cells at the single level is revolutionizing our understanding of diseases and could lead to novel therapeutic strategies. The innovations in SCS methodologies are expected to facilitate further research and clinical applications, ultimately improving patient outcomes.

Research Limitations and Future Directions ​

Despite the advancements, the review acknowledges several limitations:

  • Technical Challenges: Issues such as cell handling, data complexity, and analysis remain significant hurdles.
  • Scalability: While SCS technologies have improved, scaling these methods for large-scale studies is still a challenge.
  • Standardization: There is a need for standardized protocols to ensure reproducibility and comparability across studies.

Future Directions ​

Future research should focus on:

  • Developing more robust and user-friendly SCS technologies.
  • Enhancing data analysis tools to handle the complexity of single-cell data.
  • Exploring new applications in emerging fields, such as synthetic biology and regenerative medicine.

In summary, single-cell sequencing is a rapidly evolving field with the potential to significantly advance our understanding of biology and medicine, although challenges remain that need to be addressed to fully realize its potential.

References ​

  1. Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution. - Peter Eirew;Adi Steif;Jaswinder Khattra;Gavin Ha;Damian Yap;Hossein Farahani;Karen Gelmon;Stephen Chia;Colin Mar;Adrian Wan;Emma Laks;Justina Biele;Karey Shumansky;Jamie Rosner;Andrew McPherson;Cydney Nielsen;Andrew J L Roth;Calvin Lefebvre;Ali Bashashati;Camila de Souza;Celia Siu;Radhouane Aniba;Jazmine Brimhall;Arusha Oloumi;Tomo Osako;Alejandra Bruna;Jose L Sandoval;Teresa Algara;Wendy Greenwood;Kaston Leung;Hongwei Cheng;Hui Xue;Yuzhuo Wang;Dong Lin;Andrew J Mungall;Richard Moore;Yongjun Zhao;Julie Lorette;Long Nguyen;David Huntsman;Connie J Eaves;Carl Hansen;Marco A Marra;Carlos Caldas;Sohrab P Shah;Samuel Aparicio - Nature (2015)
  2. EGFR variant heterogeneity in glioblastoma resolved through single-nucleus sequencing. - Joshua M Francis;Cheng-Zhong Zhang;Cecile L Maire;Joonil Jung;Veronica E Manzo;Viktor A Adalsteinsson;Heather Homer;Sam Haidar;Brendan Blumenstiel;Chandra Sekhar Pedamallu;Azra H Ligon;J Christopher Love;Matthew Meyerson;Keith L Ligon - Cancer discovery (2014)
  3. Complex tumor genomes inferred from single circulating tumor cells by array-CGH and next-generation sequencing. - Ellen Heitzer;Martina Auer;Christin Gasch;Martin Pichler;Peter Ulz;Eva Maria Hoffmann;Sigurd Lax;Julie Waldispuehl-Geigl;Oliver Mauermann;Carolin Lackner;Gerald Höfler;Florian Eisner;Heinz Sill;Hellmut Samonigg;Klaus Pantel;Sabine Riethdorf;Thomas Bauernhofer;Jochen B Geigl;Michael R Speicher - Cancer research (2013)
  4. Dissecting genomic diversity, one cell at a time. - Paul C Blainey;Stephen R Quake - Nature methods (2014)
  5. Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing. - Dmitry Usoskin;Alessandro Furlan;Saiful Islam;Hind Abdo;Peter Lönnerberg;Daohua Lou;Jens Hjerling-Leffler;Jesper Haeggström;Olga Kharchenko;Peter V Kharchenko;Sten Linnarsson;Patrik Ernfors - Nature neuroscience (2015)
  6. Reproducible copy number variation patterns among single circulating tumor cells of lung cancer patients. - Xiaohui Ni;Minglei Zhuo;Zhe Su;Jianchun Duan;Yan Gao;Zhijie Wang;Chenghang Zong;Hua Bai;Alec R Chapman;Jun Zhao;Liya Xu;Tongtong An;Qi Ma;Yuyan Wang;Meina Wu;Yu Sun;Shuhang Wang;Zhenxiang Li;Xiaodan Yang;Jun Yong;Xiao-Dong Su;Youyong Lu;Fan Bai;X Sunney Xie;Jie Wang - Proceedings of the National Academy of Sciences of the United States of America (2013)
  7. Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis. - Fuchou Tang;Catalin Barbacioru;Siqin Bao;Caroline Lee;Ellen Nordman;Xiaohui Wang;Kaiqin Lao;M Azim Surani - Cell stem cell (2010)
  8. Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer. - Jens G Lohr;Viktor A Adalsteinsson;Kristian Cibulskis;Atish D Choudhury;Mara Rosenberg;Peter Cruz-Gordillo;Joshua M Francis;Cheng-Zhong Zhang;Alex K Shalek;Rahul Satija;John J Trombetta;Diana Lu;Naren Tallapragada;Narmin Tahirova;Sora Kim;Brendan Blumenstiel;Carrie Sougnez;Alarice Lowe;Bang Wong;Daniel Auclair;Eliezer M Van Allen;Mari Nakabayashi;Rosina T Lis;Gwo-Shu M Lee;Tiantian Li;Matthew S Chabot;Amy Ly;Mary-Ellen Taplin;Thomas E Clancy;Massimo Loda;Aviv Regev;Matthew Meyerson;William C Hahn;Philip W Kantoff;Todd R Golub;Gad Getz;Jesse S Boehm;J Christopher Love - Nature biotechnology (2014)
  9. Entering the era of single-cell transcriptomics in biology and medicine. - Rickard Sandberg - Nature methods (2014)
  10. Degenerate oligonucleotide-primed PCR: general amplification of target DNA by a single degenerate primer. - H Telenius;N P Carter;C E Bebb;M Nordenskjöld;B A Ponder;A Tunnacliffe - Genomics (1992)

Literatures Citing This Work ​

  1. Cancer Molecular Evolution. - David Posada - Journal of molecular evolution (2015)
  2. Uniform and accurate single-cell sequencing based on emulsion whole-genome amplification. - Yusi Fu;Chunmei Li;Sijia Lu;Wenxiong Zhou;Fuchou Tang;X Sunney Xie;Yanyi Huang - Proceedings of the National Academy of Sciences of the United States of America (2015)
  3. Stem Cell Differentiation and Therapeutic Use. - Matthew S Alexander;Juan Carlos Casar;Norio Motohashi - Stem cells international (2015)
  4. The first five years of single-cell cancer genomics and beyond. - Nicholas E Navin - Genome research (2015)
  5. Revealing the Complexity of Breast Cancer by Next Generation Sequencing. - John Verigos;Angeliki Magklara - Cancers (2015)
  6. Microfluidic Sample Preparation for Single Cell Analysis. - Sanjin Hosic;Shashi K Murthy;Abigail N Koppes - Analytical chemistry (2016)
  7. Precision Medicine for Molecularly Targeted Agents and Immunotherapies in Early-Phase Clinical Trials. - Juanita Lopez;Sam Harris;Desam Roda;Timothy A Yap - Translational oncogenomics (2015)
  8. Highly multiplexed targeted DNA sequencing from single nuclei. - Marco L Leung;Yong Wang;Charissa Kim;Ruli Gao;Jerry Jiang;Emi Sei;Nicholas E Navin - Nature protocols (2016)
  9. Medoidshift clustering applied to genomic bulk tumor data. - Theodore Roman;Lu Xie;Russell Schwartz - BMC genomics (2016)
  10. Single-cell transcriptome sequencing: recent advances and remaining challenges. - Serena Liu;Cole Trapnell - F1000Research (2016)

... (302 more literatures)

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