Literature DB >> 28965763

Single-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation Patterns.

Martin Enge1, H Efsun Arda2, Marco Mignardi3, John Beausang1, Rita Bottino4, Seung K Kim2, Stephen R Quake5.   

Abstract

As organisms age, cells accumulate genetic and epigenetic errors that eventually lead to impaired organ function or catastrophic transformation such as cancer. Because aging reflects a stochastic process of increasing disorder, cells in an organ will be individually affected in different ways, thus rendering bulk analyses of postmitotic adult cells difficult to interpret. Here, we directly measure the effects of aging in human tissue by performing single-cell transcriptome analysis of 2,544 human pancreas cells from eight donors spanning six decades of life. We find that islet endocrine cells from older donors display increased levels of transcriptional noise and potential fate drift. By determining the mutational history of individual cells, we uncover a novel mutational signature in healthy aging endocrine cells. Our results demonstrate the feasibility of using single-cell RNA sequencing (RNA-seq) data from primary cells to derive insights into genetic and transcriptional processes that operate on aging human tissue.
Copyright © 2017 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  glucagon; human aging; human pancreas; insulin; islet; mutational signatures; single-cell RNA-seq; somatic variation; transcriptional instability

Mesh:

Year:  2017        PMID: 28965763      PMCID: PMC6047899          DOI: 10.1016/j.cell.2017.09.004

Source DB:  PubMed          Journal:  Cell        ISSN: 0092-8674            Impact factor:   41.582


  53 in total

1.  Increased cell-to-cell variation in gene expression in ageing mouse heart.

Authors:  Rumana Bahar; Claudia H Hartmann; Karl A Rodriguez; Ashley D Denny; Rita A Busuttil; Martijn E T Dollé; R Brent Calder; Gary B Chisholm; Brad H Pollock; Christoph A Klein; Jan Vijg
Journal:  Nature       Date:  2006-06-22       Impact factor: 49.962

2.  Preferential repair of oxidized base damage in the transcribed genes of mammalian cells.

Authors:  Dibyendu Banerjee; Santi M Mandal; Aditi Das; Muralidhar L Hegde; Soumita Das; Kishor K Bhakat; Istvan Boldogh; Partha S Sarkar; Sankar Mitra; Tapas K Hazra
Journal:  J Biol Chem       Date:  2010-12-17       Impact factor: 5.157

3.  Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.

Authors:  Aravind Subramanian; Pablo Tamayo; Vamsi K Mootha; Sayan Mukherjee; Benjamin L Ebert; Michael A Gillette; Amanda Paulovich; Scott L Pomeroy; Todd R Golub; Eric S Lander; Jill P Mesirov
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-30       Impact factor: 11.205

Review 4.  UVR-induced G-C to C-G transversions from oxidative DNA damage.

Authors:  Katsuhito Kino; Hiroshi Sugiyama
Journal:  Mutat Res       Date:  2005-01-25       Impact factor: 2.433

5.  DNA instability in postmitotic neurons.

Authors:  Roman Gonitel; Hilary Moffitt; Kirupa Sathasivam; Ben Woodman; Peter J Detloff; Richard L M Faull; Gillian P Bates
Journal:  Proc Natl Acad Sci U S A       Date:  2008-02-25       Impact factor: 11.205

6.  Age-Dependent Pancreatic Gene Regulation Reveals Mechanisms Governing Human β Cell Function.

Authors:  H Efsun Arda; Lingyu Li; Jennifer Tsai; Eduardo A Torre; Yenny Rosli; Heshan Peiris; Robert C Spitale; Chunhua Dai; Xueying Gu; Kun Qu; Pei Wang; Jing Wang; Markus Grompe; Raphael Scharfmann; Michael S Snyder; Rita Bottino; Alvin C Powers; Howard Y Chang; Seung K Kim
Journal:  Cell Metab       Date:  2016-04-28       Impact factor: 27.287

7.  Single pancreatic beta cells co-express multiple islet hormone genes in mice.

Authors:  H Katsuta; T Akashi; R Katsuta; M Nagaya; D Kim; Y Arinobu; M Hara; S Bonner-Weir; A J Sharma; K Akashi; G C Weir
Journal:  Diabetologia       Date:  2009-10-23       Impact factor: 10.122

8.  HTSeq--a Python framework to work with high-throughput sequencing data.

Authors:  Simon Anders; Paul Theodor Pyl; Wolfgang Huber
Journal:  Bioinformatics       Date:  2014-09-25       Impact factor: 6.937

9.  Tissue-specific mutation accumulation in human adult stem cells during life.

Authors:  Francis Blokzijl; Joep de Ligt; Myrthe Jager; Valentina Sasselli; Sophie Roerink; Nobuo Sasaki; Meritxell Huch; Sander Boymans; Ewart Kuijk; Pjotr Prins; Isaac J Nijman; Inigo Martincorena; Michal Mokry; Caroline L Wiegerinck; Sabine Middendorp; Toshiro Sato; Gerald Schwank; Edward E S Nieuwenhuis; Monique M A Verstegen; Luc J W van der Laan; Jeroen de Jonge; Jan N M IJzermans; Robert G Vries; Marc van de Wetering; Michael R Stratton; Hans Clevers; Edwin Cuppen; Ruben van Boxtel
Journal:  Nature       Date:  2016-10-03       Impact factor: 49.962

10.  Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes.

Authors:  Åsa Segerstolpe; Athanasia Palasantza; Pernilla Eliasson; Eva-Marie Andersson; Anne-Christine Andréasson; Xiaoyan Sun; Simone Picelli; Alan Sabirsh; Maryam Clausen; Magnus K Bjursell; David M Smith; Maria Kasper; Carina Ämmälä; Rickard Sandberg
Journal:  Cell Metab       Date:  2016-09-22       Impact factor: 27.287

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  146 in total

Review 1.  Pancreatic Progenitors: There and Back Again.

Authors:  Juan Domínguez-Bendala; Mirza Muhammad Fahd Qadir; Ricardo Luis Pastori
Journal:  Trends Endocrinol Metab       Date:  2018-11-28       Impact factor: 12.015

2.  Single-Cell Chromatin Modification Profiling Reveals Increased Epigenetic Variations with Aging.

Authors:  Peggie Cheung; Francesco Vallania; Hayley C Warsinske; Michele Donato; Steven Schaffert; Sarah E Chang; Mai Dvorak; Cornelia L Dekker; Mark M Davis; Paul J Utz; Purvesh Khatri; Alex J Kuo
Journal:  Cell       Date:  2018-04-26       Impact factor: 41.582

Review 3.  SOX1 Is a Backup Gene for Brain Neurons and Glioma Stem Cell Protection and Proliferation.

Authors:  Kouminin Kanwore; Xiao-Xiao Guo; Ayanlaja Abiola Abdulrahman; Piniel Alphayo Kambey; Iqra Nadeem; Dianshuai Gao
Journal:  Mol Neurobiol       Date:  2021-01-22       Impact factor: 5.590

4.  Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts.

Authors:  Mohan Bolisetty; Pasquale Laise; William F Flynn; Ela Elyada; Elise T Courtois; Richard A Burkhart; Jonathan A Teinor; Pascal Belleau; Giulia Biffi; Matthew S Lucito; Santhosh Sivajothi; Todd D Armstrong; Dannielle D Engle; Kenneth H Yu; Yuan Hao; Christopher L Wolfgang; Youngkyu Park; Jonathan Preall; Elizabeth M Jaffee; Andrea Califano; Paul Robson; David A Tuveson
Journal:  Cancer Discov       Date:  2019-06-13       Impact factor: 39.397

Review 5.  The RNA world of human ageing.

Authors:  J C Gomez-Verjan; E R Vazquez-Martinez; N A Rivero-Segura; R H Medina-Campos
Journal:  Hum Genet       Date:  2018-11-01       Impact factor: 4.132

Review 6.  Power in Numbers: Single-Cell RNA-Seq Strategies to Dissect Complex Tissues.

Authors:  Kenneth D Birnbaum
Journal:  Annu Rev Genet       Date:  2018-09-07       Impact factor: 16.830

Review 7.  Tissue aging: the integration of collective and variant responses of cells to entropic forces over time.

Authors:  Michael E Todhunter; Rosalyn W Sayaman; Masaru Miyano; Mark A LaBarge
Journal:  Curr Opin Cell Biol       Date:  2018-06-19       Impact factor: 8.382

8.  Pitx2 maintains mitochondrial function during regeneration to prevent myocardial fat deposition.

Authors:  Lele Li; Ge Tao; Matthew C Hill; Min Zhang; Yuka Morikawa; James F Martin
Journal:  Development       Date:  2018-09-26       Impact factor: 6.868

9.  A Chromatin Basis for Cell Lineage and Disease Risk in the Human Pancreas.

Authors:  H Efsun Arda; Jennifer Tsai; Yenny R Rosli; Paul Giresi; Rita Bottino; William J Greenleaf; Howard Y Chang; Seung K Kim
Journal:  Cell Syst       Date:  2018-08-22       Impact factor: 10.304

10.  CSEA-DB: an omnibus for human complex trait and cell type associations.

Authors:  Yulin Dai; Ruifeng Hu; Astrid Marilyn Manuel; Andi Liu; Peilin Jia; Zhongming Zhao
Journal:  Nucleic Acids Res       Date:  2021-01-08       Impact factor: 16.971

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