Exploring landscapes of gene activity in tissue and disease

SciLifeLab have developed and pioneered a new molecular gene activity technology, Spatial Transcriptomics (ST), that has already demonstrated major impacts in many fields of biological sciences from plants to neurodegenerative disease.

ST is a molecular method that provides the possibility to investigate tissues using artificial intelligence (AI). This is expected to lead to a revolution in clinical care by providing an unbiased view of the gene expression landscape in for example tumors. ST has the potential to standardise and democratise disease diagnosis worldwide and replace the current analysis based on manual and highly variable interpretation of tissue sections under the microscope.

Research

Background

Traditional analysis of tissues is based on visual inspection of corresponding tissue sections under the microscope, a technology already used in the end of the 18th century. The images obtained from microscopy reveals the basic structural organization of healthy organs and the changes that take place in common pathologies and is still, strikingly, in routine use in hospitals today.

For several decades, it has been known that the genetic information is encapsulated within the cells. In 2001, a new era commenced with the completion of the total human genome. This was accomplished by an international collaboration and could not been achieved without concurrent technological breakthroughs. A few years later, the next transition in the field of genomics occurred by introduction of next generation DNA sequencing technology (NGS) that enable cost efficient and fast DNA sequencing. NGS was one of the rationales to form SciLifeLab allowing Swedish researchers access to these new powerful tools. Today SciLifeLab, is one of the main hubs in Europe for DNA sequencing.

In October 2016, the Human Cell Atlas (HCA) project was initiated as a new international project to describe and make an atlas of all human organs to essentially describe which genes are active in a tissue. Again, technology breakthroughs made HCA a reality. By encapsulating single cells from dissociated tissue in oil droplets and then perform RNA sequencing (gene activity) of these cells gives a dictionary of the cellular components in human organs.

The Spatial Transcriptomics technology is the first method that directly brings these tools of genomics into a tissue context that do not disrupt or dissociate the investigated tissues. The power of ST is that it can visualize and map gene activity by RNA sequencing to single cellular components of tissue structures.

Underpinning research

The ST technology was jointly invented by researchers at KTH (Joakim Lundeberg, Patrik Ståhl) and Karolinska Institutet (Jonas Frisen) and the technology development was primarily performed at SciLifeLab, Solna. The initial funding from Knut and Alice Wallenberg Foundation (KAW) was of paramount importance for the development of the technology and its initial applications to describe the molecular landscape of the odor system in mouse but also its applications to cancer. The first publication of the ST technology appeared in the prominent journal of Science in 2016.

KAW funding was also fundamental in our efforts to make the first molecular map of the mouse brain  in collaboration with Konstantinos Meletis, Karolinska Institute. More than 1000 full downloads of the recent mouse brain paper were done within the first two days demonstrating the wide interest of the ST based findings using machine learning (AI) to define the structures of brain. The KAW funding to development and application of the ST technology has reached >30 MSEK.

With the fundamental technology in place we have been able to use ST to address both neurological diseases and cancer. In collaboration with different groups (re: Hemali Phanti, Rich Bonneau) in the USA we have been able to use machine learning and ST to better understand the molecular mechanism in ALS. The findings were published in Science in 2019. Currently we are finalizing our studies of Alzheimer disease in a European (re: Bart de Strooper) and USA (re: Wilhelm Bohr) collaboration.

The first study is available at bioRxiv's webpage  and shows the molecular landscape of plaque accumulation in brain. The funding of >20 MSEK has been received by Target ALS (USA foundation), Thon Foundation (Norway), and EC JPND FP7 (Europe) for neurodegenerative disease.

The Swedish Foundation for Strategic Research (SSF), Swedish Cancer Society (CF), Swedish Pediatric Cancer Society (BCF) has allowed a deeper dive into tumors and machine learning tools and allowed us to describe the molecular events in particular leukemia, breast, brain and prostate cancer.

Scientific papers have been published in Science, Nature Communications and Cancer Research. The collected support for analysis of tumors is >20 MSEK.

Currently, the use of ST technology is the basis of several academic flagship projects such as making atlases of human tissues (www.humancellatlas.org) funded by national foundations such as KAW, Erling Persson family foundation (EP) and European council (H2020) as well an international funding (Helmsley foundation, Chen Zuckerberg Initiative). This demonstrates the impact and the international competitiveness of the developed technology and has received collective support >100 MSEK.

In 2013, together with groups in Umeå (re. Stefan Jansson, Ove Nilsson), we described the genome sequence of the Christmas tree, spruce, with a publication in Nature and this was the first description of the genome of a tree in the world. The fundamental work of the spruce genome enabled us to start performing a ‘Tree Cell Atlas’, i.e. an atlas of the genes being active in different parts of the plant. The pioneering work was published in Nature Plant in 2017. 

Fundamental to the ongoing research is to continue to develop technology and computational tools for the next phase of tissue-based genomics. An example of the development is presented in the recent publication in Nature Methods in which we show sub-cellular resolution of the ST technology. The development is primarily supported, >8 MSEK, by Swedish Scientific Council, SciLifeLab, and SFO Post Doc SciLifeLab.

Details of impact

We can demonstrate impact at different levels during the process from an initial idea to a commercial product:

Technology development

We have reported our experimental work in high profile peer reviewed publications (see below). The original submitted patents have been granted and additional patents are pending. A spin-off company, Spatial Transcriptomics AB , was established based on technology and IP and received funding primarily from venture capital.

International engagement

We have used the technology as a stepping stone to enter large international projects such as the Human Cell Atlas. The technology platform is currently being established worldwide through primarily the commercial provider, 10X Genomics Inc.

Open access

In addition to open access principles, with pre-publications in bioRxiv, we make computational tools available at GitHub. The tools are now being used by users worldwide as distributed way of impact.

National outreach

The National Genomics Infrastructure (NGI) is the major platform at SciLifeLab and supports thousands of national projects and have a turnover of >250 MSEK per year. From 2019 the ST technology will be offered to Swedish researchers, through NGI. The integration is supported by funds from SciLifeLab. Furthermore, NGI will provide ST to European research groups through the EASI project (EC2020).

In summary, the researchers at KTH have and will continue to provide impact through multiple layers of expertise in the field of spatial technology such as continued molecular development and improved computational tools in the biological context of humans, model organisms and plants. 

References

Research

Vickovic S*, Eraslan G, Salmén F, Klughammer J, Stenbeck L, Schapiro D, Äijö T, Bonneau R, Bergenstråhle L, Navarro JF, Gould J, Griffin GK, Borg Å, Ronaghi M, Frisén J, Lundeberg J*, Regev A, Ståhl PL. (* corresponding authors). High-definition spatial transcriptomics for in situ tissue profiling. Nat Methods. 2019 Oct;16(10):987-990.

Maniatis S, Äijö T, Vickovic S, Braine C, Kang K, Mollbrink A, Fagegaltier D, Andrusivová Ž, Saarenpää S, Saiz-Castro G, Cuevas M, Watters A, Lundeberg J*, Bonneau R*, Phatnani H*. (* corresponding authors. Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis. Science. 2019 Apr 5;364(6435):89-93.

Berglund E, Maaskola J, Schultz N, Friedrich S, Marklund M, Bergenstråhle J, Tarish F, Tanoglidi A, Vickovic S, Larsson L, Salmén F, Ogris C, Wallenborg K, Lagergren J, Ståhl P, Sonnhammer E, Helleday T, Lundeberg J. Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity. Nat Commun. 2018 Jun 20;9(1):2419.

Giacomello S, Salmén F, Terebieniec BK, Vickovic S, Navarro JF, Alexeyenko A, Reimegård J, McKee LS, Mannapperuma C, Bulone V, Ståhl PL, Sundström JF, Street NR, Lundeberg J. Spatially resolved transcriptome profiling in model plant species. Nat Plants. 2017 May 8;3:17061.

Vickovic S, Ståhl PL, Salmén F, Giatrellis S, Westholm JO, Mollbrink A, Navarro JF, Custodio J, Bienko M, Sutton LA, Rosenquist R, Frisén J, Lundeberg J. Massive and parallel expression profiling using microarrayed single-cell sequencing. Nat Commun. 2016 Oct 14;7:13182

Ståhl PL, Salmén F, Vickovic S, Lundmark A, Navarro JF, Magnusson J, Giacomello S, Asp M, Westholm JO, Huss M, Mollbrink A, Linnarsson S, Codeluppi S, Borg Å, Pontén F, Costea PI, Sahlén P, Mulder J, Bergmann O, Lundeberg J*, Frisén J. (* corresponding author) Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science. 2016 Jul 1;353(6294):78-82.

Impact

International impact

The Spatial Transcriptomics platform is one the technologies used in the international Human Cell Atlas , HCA, aiming to create a molecular map of all human organs. We were part of the start-up meeting held in London 13-14 October, 2016. A white paper describing the project, Regev et al  is available at and the international project has received wide attention, such as in this WIRED article.

We are specifically contributing to the HCA project by characterizing human lung (Prof Martijn Nawijn, discovAir, EC H2020), gonad (Prof Alain Chedotal, funding by HUGODECA, EC H2020) starting in January 2020 and intestine (Prof Guy Boeckxstaens, funding Hemsley Foundation, USA) that started in 2019. We are received two start up HCA grants from the Chan Zuckerberg Initiative (CZI) in 2018.

We have also used the developed technology to describe disease progression in neurodegeneration (ALS) in a collaboration with New York Genome Center (PI Phatani), Columbia and New York University. A landmark paper was published in Science in April 2019  with accompanying broad attention in multiple media such as The Science Times in April 2019 .

The technology has been presented as keynote and plenary lectures, by invitation, at well-established conferences throughout the world and during 2019 these have been taking place in Japan (EMBO, HCA), Australia (Oz Single Cell), Singapore (Cell Symposia), USA (CZI SF, ISCB NY), Canada (Keystone Symposia) and Europe (EMBL/Welcome trust, VIB Brain Mosaicism, Eur of Pathology, Single Cell Genomics 2019).

National impact

The technology platform is currently being offered to all Swedish researchers through the National Genomics Infrastructure, NGI (ngisweden.scilifelab.se). This infrastructure is funded by SciLifeLab and the Swedish Scientific Council and is also part of one of KTH technology platforms.

NGI recently received funding from EC H2020 (Prof Ivo Gut, EASI) to also provide access to the ST technology on a European level ( www.easi-genomics.eu/about ).

With funding from Knut and Alice Wallenberg Foundation and Erling Persson Family Foundation we have also initiated a Swedish effort within the Human Cell Atlas project, the Human Developmental Cell Atlas  in which we will describe development of brain, lung and heart tissue. The main PIs are from KTH: Joakim Lundeberg, Emma Lundberg; KI: Sten Linnarsson, Erik Sundström, and SU: Mats Nilsson).

We received an additional reagent support, in competition, from Swedish Cancer Society to enable a full-scale ST analysis of cancer specimens over three years.

Industrial impact

We have received industrial support from AstraZenca to investigate prostate cancer and kidney tissue, Bayer AS to investigate crops to explore the potential of the technology.

A spin-off company was formed in 2012, Spatial Transcriptomics AB  with headquarters in Stockholm and this was acquired in 2018 by 10X Genomics Inc . A full commercial launch of products, reagents and software was done in October 2019 with accompanying release material .