The mutational landscape of human somatic and germline cells
Posted on: 11 December 2020
Preprint posted on 26 November 2020
Article now published in Yearbook of Paediatric Endocrinology at http://dx.doi.org/10.1530/ey.19.14.16
Through the looking glass: examining mutation rate in normal human tissues.
Selected by Kerryn Elliott
Categories: bioinformatics, cancer biology, cell biology, developmental biology, genetics, genomics
Background
Our bodies accumulate DNA damage as we age, due to imperfect cell divisions and other external influences such as UV light. These mutations occur at different rates in different tissues, and are usually dependent on the number of cell divisions. In recent years the amount of mutations present in “normal tissues” had been shown to be variable between sample types, and includes a surprisingly high number of mutations in genes which are thought to drive cancer (driver genes), which previously had only been found in tumour samples. In order to understand how this mutation rate varies between different tissues and importantly between somatic and germline tissues, the authors present an impressive #panbodymap where they combine histology and genomics to microdissect tiny regions of normal human tissues and perform whole genome sequencing to determine how different cell types accumulate mutations over time.
Main findings
The authors used laser capture microscopy to dissect samples from 29 microscopic structures in three individuals, and then performed whole genome sequencing on more than 500 samples (Figure 1). These whole genomes were then used to analyse mutational signatures, telomere length, clonal structures, cancer associated mutations and mutation rate in all tissues sampled.
Figure 1. Histological sections and variant allele frequencies (VAF) from the 29 tissues sampled. The black outline indicates the sectioned area. A high VAF indicates a more clonal population. Figure 1b made available by a CC-BY-NC-ND 4.0 International license.
Of the most notable findings, the clonality of the mutations, represented by a higher variant allele frequency (Fig 1) and the total mutation burden varied considerably between the tissue types, with the crypts in the intestine showing the highest mutation rate at 52 singe base substitutions (SBS) per year, and the spermatagonial stem cells showing the lowest mutation rate at 2.6 SBS/year.
In order to determine how these mutations arose, mutational signatures, which are indicative of various mutational processes that are active in the genome, were calculated. The most abundant mutational signatures in normal tissues were SBS1, which occurs due to deamination of 5-methyl cytosine as we age, and SBS5/SBS40 which accumulate with age with an as yet unknown mechanism (Fig 2). Although these two signatures were present in every tissue, the amount of each was variable between tissue type.
Other dominant signatures detected which were restricted to certain sample types were the UV damage-induced SBS7, found in all skin samples and hair follicles, but not in skin sebaceous glands, and SBS18, which is caused by oxidative damage and was found in 19/29 sample types and was a major source of mutations in intestinal crypt stem cells. Interestingly SBS 2 and 13, which are thought to result from the mutagenic properties of APOBEC deaminases where present only in a subset of intestinal samples. Additionally, telomere length, which is also considered a hallmark of aging, was also found to vary between tissues with the prostate showing the shortest telomere length and the thyroid follicle and seminiferous tubule in the testis having the longest telomere length.
Figure 2. Mutational signature analyses across the cohort showing the contribution of each signature in each tissue. Note that SBS1 (cyan) and SBS5/40 (blue) dominate. Figure 3a made available by a CC-BY-NC-ND 4.0 International license.
One of the more striking discoveries was the decreased mutation rate in the testis. In order to further investigate this, the authors sequenced an additional 162 microbiopsies from 11 men. SBS1 was used to correlate the number of mutations to the number of cell divisions, suggesting that sperm stem cells only go through a handful of cell divisions per year, as compared to around a hundred divisions per year as seen in colon crypts (Fig 3).
Figure 3. Model depicting the number of SBS1 mutations per cell division for each cell division. Figure 2d made available by a CC-BY-NC-ND 4.0 International license.
Finally, although previous studies of normal tissues revealed the presence of mutations in key driver genes, most of the tissues sampled in this study had no driver mutations, although there were a handful detected in some tissues.
Why I chose this paper
My research focuses on cancer genomics, and mutational signatures have been an interest. I have followed the papers from the Sanger on mutations in normal tissues for many years now with fascination as they have been a real game changer in how we think about mutations in cancer. It has been great to see this compilation of cell types in one paper!
Questions for the authors
The low mutation rate for the testis was very interesting, but this is expected as the germline cells should be protected from mutation by increased repair systems. How would you further explore this phenomenon?
Why do you think there were very few driver gene mutations detected in this study?
The contribution from SBS1 and SBS 5/40 is intriguing in its differences. Was there any pattern to the cancers which had more or less of either?
Can you postulate why APOBEC deaminases would only be detectable in the intestinal crypts? Is it purely because that is where you see the most mutations?
Finally, what do you think was the most surprising finding?
doi: https://doi.org/10.1242/prelights.25983
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SDB 78th Annual Meeting 2019
A curation of the preprints presented at the SDB meeting in Boston, July 26-30 2019. The preList will be updated throughout the duration of the meeting.
| List by | Alex Eve |
Lung Disease and Regeneration
This preprint list compiles highlights from the field of lung biology.
| List by | Rob Hynds |
Young Embryologist Network Conference 2019
Preprints presented at the Young Embryologist Network 2019 conference, 13 May, The Francis Crick Institute, London
| List by | Alex Eve |
Pattern formation during development
The aim of this preList is to integrate results about the mechanisms that govern patterning during development, from genes implicated in the processes to theoritical models of pattern formation in nature.
| List by | Alexa Sadier |
BSCB/BSDB Annual Meeting 2019
Preprints presented at the BSCB/BSDB Annual Meeting 2019
| List by | Dey Lab |
Zebrafish immunology
A compilation of cutting-edge research that uses the zebrafish as a model system to elucidate novel immunological mechanisms in health and disease.
| List by | Shikha Nayar |
Also in the genetics category:
June in preprints – the CellBio edition
A group of preLighters, with expertise in different areas of cell biology, have worked together to create this preprint reading lists for researchers with an interest in cell biology. This month, categories include: (1) Cell organelles and organisation (2) Cell signaling and mechanosensation (3) Genetics/gene expression (4) Biochemistry (5) Cytoskeleton
| List by | Barbora Knotkova et al. |
May in preprints – the CellBio edition
A group of preLighters, with expertise in different areas of cell biology, have worked together to create this preprint reading lists for researchers with an interest in cell biology. This month, categories include: 1) Biochemistry/metabolism 2) Cancer cell Biology 3) Cell adhesion, migration and cytoskeleton 4) Cell organelles and organisation 5) Cell signalling and 6) Genetics
| List by | Barbora Knotkova et al. |
Keystone Symposium – Metabolic and Nutritional Control of Development and Cell Fate
This preList contains preprints discussed during the Metabolic and Nutritional Control of Development and Cell Fate Keystone Symposia. This conference was organized by Lydia Finley and Ralph J. DeBerardinis and held in the Wylie Center and Tupper Manor at Endicott College, Beverly, MA, United States from May 7th to 9th 2025. This meeting marked the first in-person gathering of leading researchers exploring how metabolism influences development, including processes like cell fate, tissue patterning, and organ function, through nutrient availability and metabolic regulation. By integrating modern metabolic tools with genetic and epidemiological insights across model organisms, this event highlighted key mechanisms and identified open questions to advance the emerging field of developmental metabolism.
| List by | Virginia Savy, Martin Estermann |
April in preprints – the CellBio edition
A group of preLighters, with expertise in different areas of cell biology, have worked together to create this preprint reading lists for researchers with an interest in cell biology. This month, categories include: 1) biochemistry/metabolism 2) cell cycle and division 3) cell organelles and organisation 4) cell signalling and mechanosensing 5) (epi)genetics
| List by | Vibha SINGH et al. |
March in preprints – the CellBio edition
A group of preLighters, with expertise in different areas of cell biology, have worked together to create this preprint reading lists for researchers with an interest in cell biology. This month, categories include: 1) cancer biology 2) cell migration 3) cell organelles and organisation 4) cell signalling and mechanosensing 5) genetics and genomics 6) other
| List by | Girish Kale et al. |
Biologists @ 100 conference preList
This preList aims to capture all preprints being discussed at the Biologists @100 conference in Liverpool, UK, either as part of the poster sessions or the (flash/short/full-length) talks.
| List by | Reinier Prosee, Jonathan Townson |
Early 2025 preprints – the genetics & genomics edition
In this community-driven preList, a group of preLighters, with expertise in different areas of genetics and genomics have worked together to create this preprint reading list. Categories include: 1) bioinformatics 2) epigenetics 3) gene regulation 4) genomics 5) transcriptomics
| List by | Chee Kiang Ewe et al. |
January in preprints – the CellBio edition
A group of preLighters, with expertise in different areas of cell biology, have worked together to create this preprint reading lists for researchers with an interest in cell biology. This month, categories include: 1) biochemistry/metabolism 2) cell migration 3) cell organelles and organisation 4) cell signalling and mechanosensing 5) genetics/gene expression
| List by | Barbora Knotkova et al. |
End-of-year preprints – the genetics & genomics edition
In this community-driven preList, a group of preLighters, with expertise in different areas of genetics and genomics have worked together to create this preprint reading list. Categories include: 1) genomics 2) bioinformatics 3) gene regulation 4) epigenetics
| List by | Chee Kiang Ewe et al. |
BSDB/GenSoc Spring Meeting 2024
A list of preprints highlighted at the British Society for Developmental Biology and Genetics Society joint Spring meeting 2024 at Warwick, UK.
| List by | Joyce Yu, Katherine Brown |
BSCB-Biochemical Society 2024 Cell Migration meeting
This preList features preprints that were discussed and presented during the BSCB-Biochemical Society 2024 Cell Migration meeting in Birmingham, UK in April 2024. Kindly put together by Sara Morais da Silva, Reviews Editor at Journal of Cell Science.
| List by | Reinier Prosee |
9th International Symposium on the Biology of Vertebrate Sex Determination
This preList contains preprints discussed during the 9th International Symposium on the Biology of Vertebrate Sex Determination. This conference was held in Kona, Hawaii from April 17th to 21st 2023.
| List by | Martin Estermann |
Alumni picks – preLights 5th Birthday
This preList contains preprints that were picked and highlighted by preLights Alumni - an initiative that was set up to mark preLights 5th birthday. More entries will follow throughout February and March 2023.
| List by | Sergio Menchero et al. |
Semmelweis Symposium 2022: 40th anniversary of international medical education at Semmelweis University
This preList contains preprints discussed during the 'Semmelweis Symposium 2022' (7-9 November), organised around the 40th anniversary of international medical education at Semmelweis University covering a wide range of topics.
| List by | Nándor Lipták |
20th “Genetics Workshops in Hungary”, Szeged (25th, September)
In this annual conference, Hungarian geneticists, biochemists and biotechnologists presented their works. Link: http://group.szbk.u-szeged.hu/minikonf/archive/prg2021.pdf
| List by | Nándor Lipták |
2nd Conference of the Visegrád Group Society for Developmental Biology
Preprints from the 2nd Conference of the Visegrád Group Society for Developmental Biology (2-5 September, 2021, Szeged, Hungary)
| List by | Nándor Lipták |
EMBL Conference: From functional genomics to systems biology
Preprints presented at the virtual EMBL conference "from functional genomics and systems biology", 16-19 November 2020
| List by | Jesus Victorino |
TAGC 2020
Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20
| List by | Maiko Kitaoka et al. |
ECFG15 – Fungal biology
Preprints presented at 15th European Conference on Fungal Genetics 17-20 February 2020 Rome
| List by | Hiral Shah |
Autophagy
Preprints on autophagy and lysosomal degradation and its role in neurodegeneration and disease. Includes molecular mechanisms, upstream signalling and regulation as well as studies on pharmaceutical interventions to upregulate the process.
| List by | Sandra Malmgren Hill |
Also in the genomics category:
May in preprints – the CellBio edition
A group of preLighters, with expertise in different areas of cell biology, have worked together to create this preprint reading lists for researchers with an interest in cell biology. This month, categories include: 1) Biochemistry/metabolism 2) Cancer cell Biology 3) Cell adhesion, migration and cytoskeleton 4) Cell organelles and organisation 5) Cell signalling and 6) Genetics
| List by | Barbora Knotkova et al. |
March in preprints – the CellBio edition
A group of preLighters, with expertise in different areas of cell biology, have worked together to create this preprint reading lists for researchers with an interest in cell biology. This month, categories include: 1) cancer biology 2) cell migration 3) cell organelles and organisation 4) cell signalling and mechanosensing 5) genetics and genomics 6) other
| List by | Girish Kale et al. |
Biologists @ 100 conference preList
This preList aims to capture all preprints being discussed at the Biologists @100 conference in Liverpool, UK, either as part of the poster sessions or the (flash/short/full-length) talks.
| List by | Reinier Prosee, Jonathan Townson |
Early 2025 preprints – the genetics & genomics edition
In this community-driven preList, a group of preLighters, with expertise in different areas of genetics and genomics have worked together to create this preprint reading list. Categories include: 1) bioinformatics 2) epigenetics 3) gene regulation 4) genomics 5) transcriptomics
| List by | Chee Kiang Ewe et al. |
End-of-year preprints – the genetics & genomics edition
In this community-driven preList, a group of preLighters, with expertise in different areas of genetics and genomics have worked together to create this preprint reading list. Categories include: 1) genomics 2) bioinformatics 3) gene regulation 4) epigenetics
| List by | Chee Kiang Ewe et al. |
BSCB-Biochemical Society 2024 Cell Migration meeting
This preList features preprints that were discussed and presented during the BSCB-Biochemical Society 2024 Cell Migration meeting in Birmingham, UK in April 2024. Kindly put together by Sara Morais da Silva, Reviews Editor at Journal of Cell Science.
| List by | Reinier Prosee |
9th International Symposium on the Biology of Vertebrate Sex Determination
This preList contains preprints discussed during the 9th International Symposium on the Biology of Vertebrate Sex Determination. This conference was held in Kona, Hawaii from April 17th to 21st 2023.
| List by | Martin Estermann |
Semmelweis Symposium 2022: 40th anniversary of international medical education at Semmelweis University
This preList contains preprints discussed during the 'Semmelweis Symposium 2022' (7-9 November), organised around the 40th anniversary of international medical education at Semmelweis University covering a wide range of topics.
| List by | Nándor Lipták |
20th “Genetics Workshops in Hungary”, Szeged (25th, September)
In this annual conference, Hungarian geneticists, biochemists and biotechnologists presented their works. Link: http://group.szbk.u-szeged.hu/minikonf/archive/prg2021.pdf
| List by | Nándor Lipták |
EMBL Conference: From functional genomics to systems biology
Preprints presented at the virtual EMBL conference "from functional genomics and systems biology", 16-19 November 2020
| List by | Jesus Victorino |
TAGC 2020
Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20
| List by | Maiko Kitaoka et al. |
Zebrafish immunology
A compilation of cutting-edge research that uses the zebrafish as a model system to elucidate novel immunological mechanisms in health and disease.
| List by | Shikha Nayar |