Think Tank Summaries

Summary of Somatic Mosaicism and Retrotransposition Think Tanks

In the fall of 2019, the idea of a new Common Fund program to study the mechanisms of transposable elements (TEs), somatic mosaicism (SM), and somatic variation (SVs) was introduced to OSC staff, and the planning stage begun. In addition to OSC staff members (Richard Conroy, Tony Casco, Dena Procaccini), seventeen NIH staff members were recruited to become part of the workgroup from NCI, NIA, NIDA, NIDCR, NIMH, NICHD, NINDS, NIAMS, and NIEHS to ensure a broad range of expertise for the management of this potential program. The workgroup members convened and decided that the best way to develop a program that would have meaningful impact in the field of mobile elements would be to collect a group of experts and gather their feedback. The group decided that two “Think Tanks” – one on the drivers and consequences of mobile elements, and one on the tools, methods, and resources necessary to study mobile elements were necessary. Around 45 experts in the field were contacted and agreed to lead or participate in the workshops, and other members of the NIH community were welcome to listen to the discussion. Think Tank 1 was held on June 29, 2020, and chaired by John Moran, PhD and Kathy Burns, MD/PhD, and Think Tank 2 was held on July 2, 2020 and chaired by Molly Gale-Hammel, PhD and Alex Urban PhD. Approximately eighty people attended both workshops and said that they were very insightful and engaging.

SM-RT/SV: The Somatic Mosaicism by Retrotransposition/Structural Variation Initiative

Think Tank Session 1: Drivers and Consequences of Somatic Mosaicism and Retrotransposition – June 29, 2020

Chairs: John Moran, PhD and Kathy Burns, MD, PhD

The goals of this Think Tank were to identify the mechanisms that drive retrotransposition and somatic mosaicism, and to discover the molecular, epigenetic, and cellular processes across cell-types and developmental time periods. Four sessions were held during the workshop to discuss 1) drivers of somatic mosaicism and retrotransposition, 2) “normal” development and tissue function, 3) inherited variants as contributors to aging and disease, and 4) clinical implications. During the sessions, the researchers suggested the areas of study that would need to be focused on in order to truly advance the field of transposition and somatic mosaicism. Two overarching ideas had almost universal backing. One was that any initiative would need to move beyond simply cataloging the elements to understanding the phenotypic changes they cause, and the other was that in order to study the effects of volatile repetitive elements, the initiative will require the union of cutting-edge genome and computational approaches. In particular, the participants identified seven key areas of development that would benefit from investment from the NIH, and thus could provide long-lasting and critical opportunities to elucidate the scope, mechanism, and impact on human health of repetitive volatile elements.

Key areas of study –

1. The impact of the biological processes of volatile repetitive elements on human health and disease, such as mobilization, how those mechanisms change during the lifespan, contributing factors that drive TE expression and inhibition, variation and frequency between individuals, how many TEs do individuals normally carry, is there a threshold level at which point transposition or mosaicism becomes an issue for the cell, or are there differences between maternal and paternal repetitive element alleles are just some of the biological questions that the researchers suggested should be asked into order to understand the function and processes of TEs.

2. The role epigenetic and environmental influences play in regulating volatile repetitive elements. Will need to develop new epigenomic assays in order to thoroughly study these influences, and bioinformatic techniques to characterize, analyze, and visualize the data from these new assays.

3. Determining which disorders volatile elements play a role in. They have been implicated in many different kinds of disorders, such as neurological, aging, immune system responses, infertility, developmental disorders, and cancer. It was suggested that the new initiative should launch a comprehensive survey of TE/SM related diseases by investigating their mechanisms, biological processes, prevalence of TE/SM in various populations, and co-morbidities that affect disease susceptibility as just a few facets that would need to be understood to fully comprehend the role of these elements in human disease.

4. Develop therapeutics (RNAi, AAVs to deliver shRNA, reverse transcriptase inhibitors) as well as repurposing abandoned compounds were all suggested as ways to moderate the activity and expression of TEs/SMs

5. Develop new high-throughput, multiplexed proteomics and single-cell assays to study both the structural and functional processes that are occurring in response to the TEs. It was mentioned by the researchers that this would be the area that the Common Fund could do the most good, as the current technology is not sufficient to thoroughly study repetitive elements. Current technology ignores repetitive sequences, and any technology that is developed will need to be synergistic with other efforts to be effective. Once efficient, high-throughput sequencing pipelines are developed, it will be necessary to study how the sequences vary from cell to cell, and tissue to tissue.

6. Develop model systems to investigate mobilization of TEs in situ across species in order to study species variation. While mice are commonly used as animal models for TEs, they are not the best animal models to study human TEs. Transgenic marmosets were suggested, as well as other non-human primates, Drosophila, Xenopus, C. elegans, and dogs. Stem cells and organoids were also suggested.

7. Finally, the researchers suggested that this initiative study the whole organism, not just genomic changes, as well as broaden the scope of the program to investigate CNVs as thoroughly as TEs.

Think Tank #2 – Tools, Methods, and Technologies

SM-RT/SV: The Somatic Mosaicism by RetroTransposition/Structural Variation Initiative

Think Tank Session 2: Tools, Methods and Resources – July 2, 2020

Chairs: Molly Gale Hammell, PhD and Alex Urban, PhD

The goal of this Think Tank was to define the capabilities and limitations of tools and resources available for detecting: somatic activation and insertion of endogenous transposable elements (TEs), and somatic structural variant (SV) mutations of all types (e.g. deletions, duplications, inversions). Five sessions were held to discuss (1) Current and Emerging Technologies, (2) Capturing the Mobile DNA Genome, (3) Single Cell Analysis of TE/SVs, (4) Data Analysis of TE/SVs, and (5) Current Technical Limitations and Reproducibility. During the sessions, obstacles were identified that currently limit our ability to reliably detect somatic mosaicism from TE-insertions (TEIs) and other SV-generating mechanisms. However, all participants agreed that many emerging tools and technologies are at the cusp of being ready to quantitatively and reproducibly detect somatic mosaicism constituted by TEIs/SVs. In particular, the participants identified 12 key areas of development that, with sufficient and timely support from the NIH, could provide transformative opportunities to fundamentally understand TE/SV somatic mosaicism: its scope, mechanisms of formation, and importantly, its implications for human disease.

Key Areas of Development:

1. Improved experimental protocols and computational tools to enable reliable, efficient, scalable, and affordable generation of genome sequencing data from single-cells (including from linked-reads and long-reads).

2. Improved experimental protocols and computational tools to generate long-reads (and/or linked reads) data from single-cells for other data types, such as transcriptomes and epigenomes, which will enable both an exploration of the mechanisms that lead to somatic mutation as well as a readout of their molecular consequences (also as a tool of validation).

3. Computational tools to combine and integrate data from multiple detection platforms to boost reproducibility and bridge across the limits of individual detection strategies.

4. Computational tools to combine and integrate multi-omics data to facilitate an understanding of the genetic, epigenetic, and environmental cues that drive new mutations in somatic cells.

5. The development of benchmark, ‘gold standard’, references (both experimental and computational) to validate new technologies and analysis methods. This could include reference cell lines with known variants (created by titration/cell-mixing), reference cell lines clonally propagated with known, possibly engineered-in, somatic variants from the parental lines, and others.

6. A comprehensive reference atlas of TE/SV somatic mutations across key developmental timepoints and relevant tissues that would provide expected frequencies of TE/SV somatic mutations, and reveal potential hotspots, to use as a reference and baseline when analyzing disease-associated rates and patterns in patient tissues (combined with developing a stringent set of standards for quality control and experimental validation).

7. The adoption of a comprehensive reference map of known TE and SV locations, and relevant polymorphisms in the germline (e.g. active/hot LINE-1s and all their alleles, SegDup configurations predisposing to SV formation), and the use of a graph-based genome modeling format to represent areas of known variation that new software packages would be motivated to adopt for omics analysis.

8. The comprehensive TE/SV mapping of one or two model organisms (e.g. marmosets, naked mole rats) that could then be used as a platform for exploring mechanisms that drive somatic mutation and its effects on disease states and lifespan.

9. Imaging technologies to visualize TE activity / de novo SV formation, ideally in living cells, to better understand questions about interactions with cell cycle, the likelihood that increased mutations lead to cell death, and the potential interactions with immune cells and/or innate immune pathways that detect products of TE/SV activity.

10. Support for a comprehensive effort to combine the integration of existing resources (e.g. GTEx, ENTEx, TCGA, PsychENCODE, the Brain Somatic Mosaicism Network, The telomere-to-telomere (T2T) consortium, the Human Cell Atlas, and others). These could then be enhanced and filled-in as needed and where opportune, with newly generated resources.

11. Development of technologies to detect TE activity and SV formation in liquid biopsies (e.g. leaked cytoplasmic LINE-1-cDNA, leaked circular genomic DNA).

12. Carefully calibrated but sufficient support for key mechanistic and functional/basic biology studies that could provide pivotal additional resources, e.g. a crystal structure for the LINE-1 ORF2 proteins.

This page last reviewed on January 4, 2022