Using single-cell multiple omics approaches to resolve tumor heterogeneity

Clinical and Translational Medicine
Michael A OrtegaLana X Garmire

Abstract

It has become increasingly clear that both normal and cancer tissues are composed of heterogeneous populations. Genetic variation can be attributed to the downstream effects of inherited mutations, environmental factors, or inaccurately resolved errors in transcription and replication. When lesions occur in regions that confer a proliferative advantage, it can support clonal expansion, subclonal variation, and neoplastic progression. In this manner, the complex heterogeneous microenvironment of a tumour promotes the likelihood of angiogenesis and metastasis. Recent advances in next-generation sequencing and computational biology have utilized single-cell applications to build deep profiles of individual cells that are otherwise masked in bulk profiling. In addition, the development of new techniques for combining single-cell multi-omic strategies is providing a more precise understanding of factors contributing to cellular identity, function, and growth. Continuing advancements in single-cell technology and computational deconvolution of data will be critical for reconstructing patient specific intra-tumour features and developing more personalized cancer treatments.

References

Apr 3, 2001·Nature Reviews. Genetics·T Cremer, C Cremer
Sep 17, 2005·Cancer Research·David J AratenLucio Luzzatto
Apr 8, 2009·Nature Methods·Fuchou TangM Azim Surani
Feb 16, 2011·Cell Research·Andrew J Bannister, Tony Kouzarides
Mar 15, 2011·Nature·Nicholas NavinMichael Wigler
Apr 16, 2011·Bioinformatics·Felix Krueger, Simon R Andrews
Dec 29, 2011·Proceedings of the National Academy of Sciences of the United States of America·Qihui ShiJames R Heath
Mar 9, 2012·The New England Journal of Medicine·Marco GerlingerCharles Swanton
Jul 24, 2012·Nature Biotechnology·Daniel RamsköldRickard Sandberg
Sep 4, 2012·Cell Reports·Tamar HashimshonyItai Yanai
Oct 30, 2012·Bioinformatics·Alexander DobinThomas R Gingeras
Jan 25, 2013·Proceedings of the National Academy of Sciences of the United States of America·Cristian TomasettiGiovanni Parmigiani
Mar 30, 2013·Science·Bert VogelsteinKenneth W Kinzler
Sep 24, 2013·Nature Methods·Simone PicelliRickard Sandberg
Dec 24, 2013·Nature Methods·Saiful IslamSten Linnarsson
Jun 14, 2014·Science·Anoop P PatelBradley E Bernstein
Jul 22, 2014·Nature Methods·Sébastien A SmallwoodGavin Kelsey
Aug 20, 2014·PloS One·Charles F A de BourcyStephen R Quake
Oct 18, 2014·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Fumihito Miura, Takashi Ito
Jan 20, 2015·Nature Biotechnology·Siddharth S DeyAlexander van Oudenaarden
Jan 24, 2015·Science·Mathias UhlénFredrik Pontén
Mar 31, 2015·PloS One·Alec R ChapmanX Sunney Xie
Apr 29, 2015·Nature Methods·Iain C MacaulayThierry Voet
May 23, 2015·Molecular Cell·Yong Wang, Nicholas E Navin
Jun 17, 2015·Annual Review of Genomics and Human Genetics·Lei HuangXiaoliang Sunney Xie
Sep 8, 2015·Nature Methods·Tyler GarvinMichael C Schatz

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Citations

Mar 11, 2018·Clinical Science·Alberto M MartelliJames A McCubrey
Jul 18, 2019·Epigenetics : Official Journal of the DNA Methylation Society·Boyang ZhangWentao Xu
Mar 16, 2019·Clinical Chemistry·Carmela PaolilloPaolo Fortina
Mar 30, 2020·G3 : Genes - Genomes - Genetics·Yuheng DuLana X Garmire
Jul 4, 2019·Scientific Reports·Erik FasteriusCristina Al-Khalili Szigyarto
Jul 6, 2020·Clinical and Translational Medicine·Jiaqiang ZhangYiming Zeng
Jul 14, 2020·Bioinformatics·Qiuyu LianKong Chen
May 11, 2018·Acta Biotheoretica·Angélique StéphanouAnnabelle Ballesta
Sep 9, 2018·Journal of Mammary Gland Biology and Neoplasia·Vidya C Sinha, Helen Piwnica-Worms
Nov 5, 2019·Frontiers in Genetics·Elisabetta Rossi, Rita Zamarchi
Apr 8, 2020·Frontiers in Oncology·Maria-Fernanda Senosain, Pierre P Massion
Dec 18, 2018·International Journal of Particle Therapy·Sally A Amundson
Jun 23, 2020·NPJ Precision Oncology·George AdamAnna Goldenberg
May 26, 2018·The Cancer Journal·Karin D RodlandRichard D Smith
Apr 5, 2019·Wiley Interdisciplinary Reviews. Developmental Biology·Q Richard LuXianyao Zhou
Aug 19, 2020·Genome Biology·Xian F MalloryLuay Nakhleh
May 8, 2018·Frontiers in Cell and Developmental Biology·Youjin HuYing Guo
Feb 18, 2021·NPJ Precision Oncology·George AdamAnna Goldenberg
Oct 21, 2020·The Korean Journal of Internal Medicine·Jisoo Kim, Jihwan Park
Aug 14, 2020·Journal of Thoracic Oncology : Official Publication of the International Association for the Study of Lung Cancer·Raul CasoDavid R Jones
Dec 29, 2020·Genomics, Proteomics & Bioinformatics·Qianhui HuangLana X Garmire

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Methods Mentioned

BETA
RNA-seq
chips
biopsies
chemical stress
biopsy
PCR
FACS
chip
exome
exome sequencing

Software Mentioned

Phenograph
ddSeq
Ginkgo
Monocle2
SynthEx
Integrate
scRRBS
Smart
scTrio
scHi

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