HumanIslets.com: Improving accessibility, integration, and usability of human research islet data

Jessica D Ewald¹, Yao Lu², Cara E Ellis³, Jessica Worton⁴, Jelena Kolic⁵, Shugo Sasaki⁶, Dahai Zhang⁶, Theodore Dos Santos³, Aliya F Spigelman³, Austin Bautista⁷, Xiao-Qing Dai³, James G Lyon⁷, Nancy P Smith³, Jordan M Wong⁴, Varsha Rajesh⁸, Han Sun⁸, Seth A Sharp⁸, Jason C Rogalski⁹, Renata Moravcova⁹, Haoning H Cen⁵, Jocelyn E Manning Fox³; HumanIslets.com Consortium; Ella Atlas¹⁰, Jennifer E Bruin¹¹, Erin E Mulvihill¹², C Bruce Verchere¹³, Leonard J Foster⁹, Anna L Gloyn¹⁴, James D Johnson⁵, Andrew R Pepper⁴, Francis C Lynn⁶, Jianguo Xia¹⁵, Patrick E MacDonald¹⁶

Affiliations

¹ Institute of Parasitology, McGill University, Montreal, QC, Canada; Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
² Institute of Parasitology, McGill University, Montreal, QC, Canada.
³ Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada; Department of Pharmacology, University of Alberta, Edmonton, AB, Canada.
⁴ Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada; Department of Surgery, University of Alberta, Edmonton, AB, Canada.
⁵ Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada.
⁶ Diabetes Research Group, BC Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Surgery, School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada.
⁷ Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada.
⁸ Department of Pediatrics, Division of Endocrinology, Stanford School of Medicine, Stanford, CA, USA.
⁹ Department of Biochemistry & Molecular Biology, Michael Smith Laboratories, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada.
¹⁰ Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada.
¹¹ Department of Biology & Institute of Biochemistry, Carleton University, Ottawa, ON, Canada.
¹² Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada; University of Ottawa Heart Institute, Ottawa, ON, Canada.
¹³ Department of Surgery, BC Children's Hospital Research Institute and University of British Columbia, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, BC Children's Hospital Research Institute and University of British Columbia, Vancouver, BC, Canada; Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada.
¹⁴ Department of Pediatrics, Division of Endocrinology, Stanford School of Medicine, Stanford, CA, USA; Stanford Diabetes Research Center, Stanford School of Medicine, Stanford, CA, USA; Department of Genetics, Stanford School of Medicine, Stanford, CA, USA.
¹⁵ Institute of Parasitology, McGill University, Montreal, QC, Canada. Electronic address: jeff.xia@mcgill.ca.
¹⁶ Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada; Department of Pharmacology, University of Alberta, Edmonton, AB, Canada; Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI, USA. Electronic address: pmacdonald@ualberta.ca.

PMID: 39357523
PMCID: PMC12577030
DOI: 10.1016/j.cmet.2024.09.001

HumanIslets.com: Improving accessibility, integration, and usability of human research islet data

Jessica D Ewald et al. Cell Metab. 2025.

. 2025 Jan 7;37(1):7-11.

doi: 10.1016/j.cmet.2024.09.001. Epub 2024 Oct 1.

Authors

Affiliations

¹ Institute of Parasitology, McGill University, Montreal, QC, Canada; Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
² Institute of Parasitology, McGill University, Montreal, QC, Canada.
³ Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada; Department of Pharmacology, University of Alberta, Edmonton, AB, Canada.
⁴ Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada; Department of Surgery, University of Alberta, Edmonton, AB, Canada.
⁵ Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada.
⁶ Diabetes Research Group, BC Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Surgery, School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada.
⁷ Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada.
⁸ Department of Pediatrics, Division of Endocrinology, Stanford School of Medicine, Stanford, CA, USA.
⁹ Department of Biochemistry & Molecular Biology, Michael Smith Laboratories, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada.
¹⁰ Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada.
¹¹ Department of Biology & Institute of Biochemistry, Carleton University, Ottawa, ON, Canada.
¹² Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada; University of Ottawa Heart Institute, Ottawa, ON, Canada.
¹³ Department of Surgery, BC Children's Hospital Research Institute and University of British Columbia, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, BC Children's Hospital Research Institute and University of British Columbia, Vancouver, BC, Canada; Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada.
¹⁴ Department of Pediatrics, Division of Endocrinology, Stanford School of Medicine, Stanford, CA, USA; Stanford Diabetes Research Center, Stanford School of Medicine, Stanford, CA, USA; Department of Genetics, Stanford School of Medicine, Stanford, CA, USA.
¹⁵ Institute of Parasitology, McGill University, Montreal, QC, Canada. Electronic address: jeff.xia@mcgill.ca.
¹⁶ Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada; Department of Pharmacology, University of Alberta, Edmonton, AB, Canada; Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI, USA. Electronic address: pmacdonald@ualberta.ca.

PMID: 39357523
PMCID: PMC12577030
DOI: 10.1016/j.cmet.2024.09.001

Abstract

HumanIslets.com supports diabetes research by offering easy access to islet phenotyping data, analysis tools, and data download. It includes molecular omics, islet and cellular function assays, tissue processing metadata, and phenotypes from 547 donors. As it expands, the resource aims to improve human islet data quality, usability, and accessibility.

PubMed Disclaimer

Conflict of interest statement

Declaration of interests A.L.G.’s spouse is an employee of Genentech and holds stock options in Roche. A.R.P. serves on the Scientific Advisory Committee for Encellin Inc. J.X. is founder of XiaLab Analytics, which provides omics data science training and support.

Figures

**Figure 1.. Corrections for culture time and non-endocrine cell proportions**
(A–C) Impact of culture time on expression of *FGF2* measured by RNA-seq (A), NanoString (B), or proteomics (C). (D) Impact of adjusting for culture time on gene-level p values for the association of bulk RNA-seq data and diabetes status (T2D vs. none). Transcripts were significant (FDR < 0.05) both with and without adjusting for culture time (dark gray), only when adjusting for culture time (red), only when not adjusting for culture time (blue), or not significant in either scenario (light gray). (E) Cell-type distributions computed from proteomic data across donors, ranked by ‘‘non-endocrine’’ cell proportions. (F) Impact of adjusting for the proportion of non-endocrine cells on protein-level p values for the association of bulk proteomics data and diabetes status (T2D vs. none). Proteins were significant (FDR < 0.05) both with and without adjusting for non-endocrine cells (dark gray), only when adjusting for non-endocrine cells (red), only when not adjusting for non-endocrine cells (blue), or not significant in either scenario (light gray). (G) Adjusting for the proportion of non-endocrine cells increases the proportion of α and β cell-linked RNA-seq and proteomics features (adjusted p < 0.05) when comparing T2D versus no diabetes (non-adjusted RNA-seq, n = 117; adjusted RNA-seq, n = 90; non-adjusted proteomics, n = 134; adjusted proteomics, n = 134).

See this image and copyright information in PMC

References

1. Gloyn AL, Ibberson M, Marchetti P, Powers AC, Rorsman P, Sander M, and Solimena M (2022). Every islet matters: improving the impact of human islet research. Nat. Metab 4, 970–977. 10.1038/s42255-022-00607-8. - DOI - PMC - PubMed
1. Hart NJ, and Powers AC (2019). Use of human islets to understand islet biology and diabetes: progress, challenges and suggestions. Diabetologia 62, 212–222. 10.1007/s00125-018-4772-2. - DOI - PMC - PubMed
1. Wilkinson MD, Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten J-W, da Silva Santos LB, Bourne PE, et al. (2016). The FAIR Guiding Principles for scientific data management and stewardship. Sci. Data 3, 160018. 10.1038/sdata.2016.18. - DOI - PMC - PubMed
1. Shapira SN, Naji A, Atkinson MA, Powers AC, and Kaestner KH (2022). Understanding islet dysfunction in type 2 diabetes through multidimensional pancreatic phenotyping: The Human Pancreas Analysis Program. Cell Metab 34, 1906–1913. 10.1016/j.cmet.2022.09.013. - DOI - PMC - PubMed
1. Lyon J, Manning Fox JE, Spigelman AF, Kim R, Smith N, O’Gorman D, Kin T, Shapiro AMJ, Rajotte RV, and MacDonald PE (2016). Research-focused isolation of human islets from donors with and without diabetes at the Alberta Diabetes Institute IsletCore. Endocrinology 157, 560–569. 10.1210/en.2015-1562. - DOI - PubMed

MeSH terms

Actions
Actions
Actions
Actions
Actions

Grants and funding

LinkOut - more resources

Full Text Sources
- Elsevier Science
- PubMed Central
Research Materials
- NCI CPTC Antibody Characterization Program

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

HumanIslets.com: Improving accessibility, integration, and usability of human research islet data

Affiliations

HumanIslets.com: Improving accessibility, integration, and usability of human research islet data

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources

Research Materials