Periodic Reporting for period 5 - ReSOLUTE (Research empowerment on solute carriers (ReSOLUTE))
Okres sprawozdawczy: 2022-07-01 do 2023-12-31
Solute carrier (SLC) transporters are molecular “gatekeepers” that shuttle a diverse range of substances across cell membranes. They are the largest group of transporters, with more than 450 members, and are implicated in numerous diseases with unmet medical need, including neurological diseases, diabetes, and cancer. They also play a crucial role in mediating drug uptake. Despite their importance, SLCs have been relatively neglected by the scientific community and around 30% of SLCs remain “orphans”, meaning that their substrates and functions are unknown.
RESOLUTE’s mission was threefold: (1) empower the scientific community with biological tools for SLC research, (2) elucidate the substrates and functions of orphan SLCs, and (3) develop robust assays for measuring transport activity. To that end, we created nearly 2,100 genetically modified cell lines either lacking or overexpressing individual SLCs. We used these cell lines to systematically determine the subcellular localization of SLCs, identify their interacting partners, and profile gene expression and metabolites in their presence/absence for the entire SLC superfamily, providing unbiased clues as to their substrates and functions.
RESOLUTE’s mission was threefold: (1) empower the scientific community with biological tools for SLC research, (2) elucidate the substrates and functions of orphan SLCs, and (3) develop robust assays for measuring transport activity. To that end, we created nearly 2,100 genetically modified cell lines either lacking or overexpressing individual SLCs. We used these cell lines to systematically determine the subcellular localization of SLCs, identify their interacting partners, and profile gene expression and metabolites in their presence/absence for the entire SLC superfamily, providing unbiased clues as to their substrates and functions.
Specifically, RESOLUTE achieved the following results:
•The RESOLUTE plasmid collection is available in our web portal and at the open-access repository Addgene. This collection contains 894 codon-optimized sequences of human SLCs inserted in a vector compatible with the Gateway system, as well as expression vectors needed to generate cell lines over-expressing the SLCs. From all cell line generated, we were able to deposit around 400 HCT116 KO cell lines in the cell line repository ATCC (https://re-solute.eu/resources/reagents(odnośnik otworzy się w nowym oknie); https://www.addgene.org/depositor-collections/re-solute/(odnośnik otworzy się w nowym oknie); https://www.atcc.org/cell-products/cell-models/solute-transporter-carrier-cells(odnośnik otworzy się w nowym oknie)).
•Furthermore, the consortium integrated public and RESOLUTE-generated data to deorphanize and functionalize solute carriers in a systematic way. The RESOLUTE database (currently containing reagents, protocols, assays, data and dashboards) together with the RESOLUTE knowledgebase form the RESOLUTE web portal, a reference hub for research on solute carriers (https://re-solute.eu/resources(odnośnik otworzy się w nowym oknie)).
•During the project, we developed 119 proof of concept, medium or high-throughput transport assays for 74 SLCs. Some of which were implemented in our industry and SME partners and could be used in future drug discovery endeavors. Importantly, we gave open access to the data and the protocols for 36 assays in our web page and public repositories. We consider this an important step towards providing the scientific community with novel approaches to functionally investigate SLCs (https://re-solute.eu/resources/reagents(odnośnik otworzy się w nowym oknie); https://zenodo.org/communities/resolute(odnośnik otworzy się w nowym oknie)).
The resulting datasets—acquired for the entire SLC family—are freely available and have been disseminated through different channels:
•SLC Knowledgebase, where any researcher can now look up their SLC of interest and find information on its substrates, expression, variants, disease associations, and much more (https://re-solute.eu/knowledgebase(odnośnik otworzy się w nowym oknie)).
•Through scientific publications, as well as posters and oral presentations at scientific conferences, RESOLUTE boosted the visibility of the role of SLCs and the project’s mission. Importantly, we organized the “Unlocking Transporters for Drug Discovery” conference in September 2023, which had around 200 participants. It was the first big event at which the RESOLUTE consortium presented most of their results and interacted extensively with the broader scientific and medical communities (recorded talks available at https://re-solute.eu/conference(odnośnik otworzy się w nowym oknie)).
•To gain visibility worldwide and create awareness around SLC research, we produced a total of 18 videos describing the project in general and of specific project activities in particular. Furthermore, we created the SLC family card game with information on the current SLC families. We continuously updated the web portal and increased the transparency on our activities and progress. To date we published in total 16 open-access scientific publications in peer-reviewed journals, which are also listed in our web page. More than 20 manuscripts are still in preparation or in the publishing process (https://re-solute.eu/communications(odnośnik otworzy się w nowym oknie)).
•The RESOLUTE plasmid collection is available in our web portal and at the open-access repository Addgene. This collection contains 894 codon-optimized sequences of human SLCs inserted in a vector compatible with the Gateway system, as well as expression vectors needed to generate cell lines over-expressing the SLCs. From all cell line generated, we were able to deposit around 400 HCT116 KO cell lines in the cell line repository ATCC (https://re-solute.eu/resources/reagents(odnośnik otworzy się w nowym oknie); https://www.addgene.org/depositor-collections/re-solute/(odnośnik otworzy się w nowym oknie); https://www.atcc.org/cell-products/cell-models/solute-transporter-carrier-cells(odnośnik otworzy się w nowym oknie)).
•Furthermore, the consortium integrated public and RESOLUTE-generated data to deorphanize and functionalize solute carriers in a systematic way. The RESOLUTE database (currently containing reagents, protocols, assays, data and dashboards) together with the RESOLUTE knowledgebase form the RESOLUTE web portal, a reference hub for research on solute carriers (https://re-solute.eu/resources(odnośnik otworzy się w nowym oknie)).
•During the project, we developed 119 proof of concept, medium or high-throughput transport assays for 74 SLCs. Some of which were implemented in our industry and SME partners and could be used in future drug discovery endeavors. Importantly, we gave open access to the data and the protocols for 36 assays in our web page and public repositories. We consider this an important step towards providing the scientific community with novel approaches to functionally investigate SLCs (https://re-solute.eu/resources/reagents(odnośnik otworzy się w nowym oknie); https://zenodo.org/communities/resolute(odnośnik otworzy się w nowym oknie)).
The resulting datasets—acquired for the entire SLC family—are freely available and have been disseminated through different channels:
•SLC Knowledgebase, where any researcher can now look up their SLC of interest and find information on its substrates, expression, variants, disease associations, and much more (https://re-solute.eu/knowledgebase(odnośnik otworzy się w nowym oknie)).
•Through scientific publications, as well as posters and oral presentations at scientific conferences, RESOLUTE boosted the visibility of the role of SLCs and the project’s mission. Importantly, we organized the “Unlocking Transporters for Drug Discovery” conference in September 2023, which had around 200 participants. It was the first big event at which the RESOLUTE consortium presented most of their results and interacted extensively with the broader scientific and medical communities (recorded talks available at https://re-solute.eu/conference(odnośnik otworzy się w nowym oknie)).
•To gain visibility worldwide and create awareness around SLC research, we produced a total of 18 videos describing the project in general and of specific project activities in particular. Furthermore, we created the SLC family card game with information on the current SLC families. We continuously updated the web portal and increased the transparency on our activities and progress. To date we published in total 16 open-access scientific publications in peer-reviewed journals, which are also listed in our web page. More than 20 manuscripts are still in preparation or in the publishing process (https://re-solute.eu/communications(odnośnik otworzy się w nowym oknie)).
Beyond these achievements, RESOLUTE stands as a model for collaborative biomedical research and showcases effective partnerships between academia and the pharmaceutical industry. Many of the professional connections formed are independent of organizations and may give rise to more formal collaborations on SLC research in the future.
In summary, RESOLUTE has transformed the field of SLC research, and the ripple effects will be far-reaching. The challenge now lies in leveraging the amassed resources to systematically identify specific chemical probes for each SLC and design effective therapeutics.
In summary, RESOLUTE has transformed the field of SLC research, and the ripple effects will be far-reaching. The challenge now lies in leveraging the amassed resources to systematically identify specific chemical probes for each SLC and design effective therapeutics.