Subcellular Feature-Based Classification of α and β Cells Using Soft X-ray Tomography

Deshmukh, Aneesh; Chang, Kevin; Cuala, Janielle; Vanslembrouck, Bieke; Georgia, Senta; Loconte, Valentina; White, Kate L.

doi:10.3390/cells13100869

Subcellular Feature-Based Classification of α and β Cells Using Soft X-ray Tomography

Journal Article · Sat May 18 00:00:00 EDT 2024 · Cells

DOI:https://doi.org/10.3390/cells13100869· OSTI ID:2471074

^[1]; ^[1]; ^[1]; Vanslembrouck, Bieke ^[2]; ^[1]; ^[2]; White, Kate L. ^[3]

Univ. of Southern California, Los Angeles, CA (United States)
Univ. of California, San Francisco, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Univ. of Southern California, Los Angeles, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

The dysfunction of α and β cells in pancreatic islets can lead to diabetes. Many questions remain on the subcellular organization of islet cells during the progression of disease. Existing three-dimensional cellular mapping approaches face challenges such as time-intensive sample sectioning and subjective cellular identification. To address these challenges, we have developed a subcellular feature-based classification approach, which allows us to identify α and β cells and quantify their subcellular structural characteristics using soft X-ray tomography (SXT). We observed significant differences in whole-cell morphological and organelle statistics between the two cell types. Additionally, we characterize subtle biophysical differences between individual insulin and glucagon vesicles by analyzing vesicle size and molecular density distributions, which were not previously possible using other methods. These sub-vesicular parameters enable us to predict cell types systematically using supervised machine learning. We also visualize distinct vesicle and cell subtypes using Uniform Manifold Approximation and Projection (UMAP) embeddings, which provides us with an innovative approach to explore structural heterogeneity in islet cells. This methodology presents an innovative approach for tracking biologically meaningful heterogeneity in cells that can be applied to any cellular system.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Advanced Light Source (ALS)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2471074

Journal Information:: Cells, Journal Name: Cells Journal Issue: 10 Vol. 13; ISSN 2073-4409

Publisher:: MDPICopyright Statement

Country of Publication:: United States

Language:: English

References (62)

Extending Imaging Volume in Soft X‐Ray Tomography Ekman, Axel; Chen, Jian-Hua; Vanslembrouck, Bieke Advanced Photonics Research, Vol. 4, Issue 4 https://doi.org/10.1002/adpr.202200142	journal	March 2023
Visualizing and quantifying cell phenotype using soft X-ray tomography McDermott, Gerry; Fox, Douglas M.; Epperly, Lindsay BioEssays, Vol. 34, Issue 4 https://doi.org/10.1002/bies.201100125	journal	January 2012
GABA and pancreatic beta-cells: colocalization of glutamic acid decarboxylase (GAD) and GABA with synaptic-like microvesicles suggests their role in GABA storage and secretion. Reetz, A.; Solimena, M.; Matteoli, M. The EMBO Journal, Vol. 10, Issue 5 https://doi.org/10.1002/j.1460-2075.1991.tb08069.x	journal	May 1991
Utrastructural and morphometric studies of delta cells in pancreatic islets from C57BL/Ks diabetes mice Leiter, E. H.; Gapp, D. A.; Eppig, J. J. Diabetologia, Vol. 17, Issue 5 https://doi.org/10.1007/BF01235886	journal	November 1979
Fluorescent protein vectors for pancreatic islet cell identification in live-cell imaging Shuai, Hongyan; Xu, Yunjian; Yu, Qian Pflügers Archiv - European Journal of Physiology, Vol. 468, Issue 10 https://doi.org/10.1007/s00424-016-1864-z	journal	August 2016
Ultrastructure of islet ghrelin cells in the human fetus Wierup, Nils; Sundler, Frank Cell and Tissue Research, Vol. 319, Issue 3 https://doi.org/10.1007/s00441-004-1044-x	journal	January 2005
Characterization of obestatin- and ghrelin-producing cells in the gastrointestinal tract and pancreas of rats: an immunohistochemical and electron-microscopic study Zhao, Chun-Mei; Furnes, Marianne W.; Stenström, Björn Cell and Tissue Research, Vol. 331, Issue 3 https://doi.org/10.1007/s00441-007-0514-3	journal	December 2007
Quantitatively Imaging Chromosomes by Correlated Cryo-Fluorescence and Soft X-Ray Tomographies Smith, Elizabeth A.; McDermott, Gerry; Do, Myan Biophysical Journal, Vol. 107, Issue 8 https://doi.org/10.1016/j.bpj.2014.09.011	journal	October 2014
Opportunities and Challenges in Building a Spatiotemporal Multi-scale Model of the Human Pancreatic β Cell Singla, Jitin; McClary, Kyle M.; White, Kate L. Cell, Vol. 173, Issue 1 https://doi.org/10.1016/j.cell.2018.03.014	journal	March 2018
Soft X-Ray Tomography Reveals Gradual Chromatin Compaction and Reorganization during Neurogenesis In Vivo Le Gros, Mark A.; Clowney, E. Josephine; Magklara, Angeliki Cell Reports, Vol. 17, Issue 8 https://doi.org/10.1016/j.celrep.2016.10.060	journal	November 2016
A community approach to whole-cell modeling Singla, Jitin; White, Kate L. Current Opinion in Systems Biology, Vol. 26 https://doi.org/10.1016/j.coisb.2021.03.009	journal	June 2021
Automated 3D cytoplasm segmentation in soft X-ray tomography Erozan, Ayse; Lösel, Philipp D.; Heuveline, Vincent iScience, Vol. 27, Issue 6 https://doi.org/10.1016/j.isci.2024.109856	journal	June 2024
Automatic alignment and reconstruction of images for soft X-ray tomography Parkinson, Dilworth Y.; Knoechel, Christian; Yang, Chao Journal of Structural Biology, Vol. 177, Issue 2 https://doi.org/10.1016/j.jsb.2011.11.027	journal	February 2012
Quantitative analysis of mouse pancreatic islet architecture by serial block-face SEM Pfeifer, C. R.; Shomorony, A.; Aronova, M. A. Journal of Structural Biology, Vol. 189, Issue 1 https://doi.org/10.1016/j.jsb.2014.10.013	journal	January 2015
The use of soft X-ray tomography to explore mitochondrial structure and function Loconte, Valentina; White, Kate L. Molecular Metabolism, Vol. 57 https://doi.org/10.1016/j.molmet.2021.101421	journal	March 2022
X-ray tomography of whole cells Le Gros, Mark A.; McDermott, Gerry; Larabell, Carolyn A. Current Opinion in Structural Biology, Vol. 15, Issue 5 https://doi.org/10.1016/j.sbi.2005.08.008	journal	October 2005
Imaging cellular architecture with X-rays Larabell, Carolyn A.; Nugent, Keith A. Current Opinion in Structural Biology, Vol. 20, Issue 5 https://doi.org/10.1016/j.sbi.2010.08.008	journal	October 2010
Soft X-ray tomography to map and quantify organelle interactions at the mesoscale Loconte, Valentina; Singla, Jitin; Li, Angdi Structure, Vol. 30, Issue 4 https://doi.org/10.1016/j.str.2022.01.006	journal	April 2022
Soft X-ray tomography and cryogenic light microscopy: the cool combination in cellular imaging McDermott, Gerry; Le Gros, Mark A.; Knoechel, Christian G. Trends in Cell Biology, Vol. 19, Issue 11 https://doi.org/10.1016/j.tcb.2009.08.005	journal	November 2009
Correlative cryogenic tomography of cells using light and soft x-rays Smith, Elizabeth A.; Cinquin, Bertrand P.; Do, Myan Ultramicroscopy, Vol. 143 https://doi.org/10.1016/j.ultramic.2013.10.013	journal	August 2014
A protocol for full-rotation soft X-ray tomography of single cells Chen, Jian-Hua; Vanslembrouck, Bieke; Loconte, Valentina STAR Protocols, Vol. 3, Issue 1 https://doi.org/10.1016/j.xpro.2022.101176	journal	March 2022
Soft X-ray microscopes and their biological applications Kirz, Janos; Jacobsen, Chris; Howells, Malcolm Quarterly Reviews of Biophysics, Vol. 28, Issue 1 https://doi.org/10.1017/S0033583500003139	journal	February 1995
Integrative structural modelling and visualisation of a cellular organelle Autin, Ludovic; Barbaro, Brett A.; Jewett, Andrew I. QRB Discovery, Vol. 3 https://doi.org/10.1017/qrd.2022.10	journal	January 2022
Three-dimensional cellular ultrastructure resolved by X-ray microscopy Schneider, Gerd; Guttmann, Peter; Heim, Stefan Nature Methods, Vol. 7, Issue 12 https://doi.org/10.1038/nmeth.1533	journal	November 2010
Fiji: an open-source platform for biological-image analysis Schindelin, Johannes; Arganda-Carreras, Ignacio; Frise, Erwin Nature Methods, Vol. 9, Issue 7 https://doi.org/10.1038/nmeth.2019	journal	June 2012
Gastric ghrelin cells in obese patients are hyperactive Castorina, Sergio; Barresi, Vincenza; Luca, Tonia International Journal of Obesity, Vol. 45, Issue 1 https://doi.org/10.1038/s41366-020-00711-3	journal	November 2020
Structural basis for delta cell paracrine regulation in pancreatic islets Arrojo e. Drigo, Rafael; Jacob, Stefan; García-Prieto, Concha F. Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-11517-x	journal	August 2019
Large-scale electron microscopy database for human type 1 diabetes de Boer, Pascal; Pirozzi, Nicole M.; Wolters, Anouk H. G. Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-16287-5	journal	May 2020
Introducing Biomedisa as an open-source online platform for biomedical image segmentation Lösel, Philipp D.; van de Kamp, Thomas; Jayme, Alejandra Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-19303-w	journal	November 2020
Spatial Transcriptomics-correlated Electron Microscopy maps transcriptional and ultrastructural responses to brain injury Androvic, Peter; Schifferer, Martina; Perez Anderson, Katrin Nature Communications, Vol. 14, Issue 1 https://doi.org/10.1038/s41467-023-39447-9	journal	July 2023
The somatostatin-secreting pancreatic δ-cell in health and disease Rorsman, Patrik; Huising, Mark O. Nature Reviews Endocrinology, Vol. 14, Issue 7 https://doi.org/10.1038/s41574-018-0020-6	journal	May 2018
The physiological role of β-cell heterogeneity in pancreatic islet function Benninger, Richard K. P.; Kravets, Vira Nature Reviews Endocrinology, Vol. 18, Issue 1 https://doi.org/10.1038/s41574-021-00568-0	journal	October 2021
A guide to machine learning for biologists Greener, Joe G.; Kandathil, Shaun M.; Moffat, Lewis Nature Reviews Molecular Cell Biology, Vol. 23, Issue 1 https://doi.org/10.1038/s41580-021-00407-0	journal	September 2021
Integrating genetics with single-cell multiomic measurements across disease states identifies mechanisms of beta cell dysfunction in type 2 diabetes Wang, Gaowei; Chiou, Joshua; Zeng, Chun Nature Genetics, Vol. 55, Issue 6 https://doi.org/10.1038/s41588-023-01397-9	journal	May 2023
SciPy 1.0: fundamental algorithms for scientific computing in Python Virtanen, Pauli; Gommers, Ralf; Oliphant, Travis E. Nature Methods https://doi.org/10.1038/s41592-019-0686-2	journal	February 2020
Live-cell imaging of glucose-induced metabolic coupling of β and α cell metabolism in health and type 2 diabetes Wang, Zhongying; Gurlo, Tatyana; Matveyenko, Aleksey V. Communications Biology, Vol. 4, Issue 1 https://doi.org/10.1038/s42003-021-02113-1	journal	May 2021
Multi-omic profiling of primary mouse neutrophils predicts a pattern of sex- and age-related functional regulation Lu, Ryan J.; Taylor, Shalina; Contrepois, Kévin Nature Aging, Vol. 1, Issue 8 https://doi.org/10.1038/s43587-021-00086-8	journal	July 2021
The unique cytoarchitecture of human pancreatic islets has implications for islet cell function Cabrera, Over; Berman, Dora M.; Kenyon, Norma S. Proceedings of the National Academy of Sciences, Vol. 103, Issue 7 https://doi.org/10.1073/pnas.0510790103	journal	February 2006
Bayesian metamodeling of complex biological systems across varying representations Raveh, Barak; Sun, Liping; White, Kate L. Proceedings of the National Academy of Sciences, Vol. 118, Issue 35 https://doi.org/10.1073/pnas.2104559118	journal	August 2021
3D FIB-SEM reconstruction of microtubule–organelle interaction in whole primary mouse β cells Müller, Andreas; Schmidt, Deborah; Xu, C. Shan Journal of Cell Biology, Vol. 220, Issue 2 https://doi.org/10.1083/jcb.202010039	journal	December 2020
Isolation and Properties of Secretory Granules from rat Islets of Langerhans Greider, Marie H.; Howell, S. L.; Lacy, P. E. Journal of Cell Biology, Vol. 41, Issue 1 https://doi.org/10.1083/jcb.41.1.162	journal	April 1969
Comparative Analysis of Inter-Centroid K-Means Performance using Euclidean Distance, Canberra Distance and Manhattan Distance Faisal, M.; Zamzami, E. M. Journal of Physics: Conference Series, Vol. 1566, Issue 1 https://doi.org/10.1088/1742-6596/1566/1/012112	journal	June 2020
Soft X‐ray tomograms provide a structural basis for whole‐cell modeling Loconte, Valentina; Chen, Jian‐Hua; Vanslembrouck, Bieke The FASEB Journal, Vol. 37, Issue 1 https://doi.org/10.1096/fj.202200253R	journal	December 2022
Biological soft X-ray tomography on beamline 2.1 at the Advanced Light Source Le Gros, Mark A.; McDermott, Gerry; Cinquin, Bertrand P. Journal of Synchrotron Radiation, Vol. 21, Issue 6 https://doi.org/10.1107/S1600577514015033	journal	October 2014
Mesoscale imaging with cryo-light and X-rays: Larger than molecular machines, smaller than a cell: Mesoscale imaging with cryo-light and X-rays Ekman, Axel A.; Chen, Jian-Hua; Guo, Jessica Biology of the Cell, Vol. 109, Issue 1 https://doi.org/10.1111/boc.201600044	journal	November 2016
High-aperture cryogenic light microscopy Le Gros, M. A.; McDERMOTT, G.; Uchida, M. Journal of Microscopy, Vol. 235, Issue 1 https://doi.org/10.1111/j.1365-2818.2009.03184.x	journal	July 2009
Combining quantitative 2D and 3D image analysis in the serial block face SEM: application to secretory organelles of pancreatic islet cells: IMAGE ANALYSIS IN THE SERIAL BLOCK FACE SEM Shomorony, A.; Pfeifer, C. R.; Aronova, M. A. Journal of Microscopy, Vol. 259, Issue 2 https://doi.org/10.1111/jmi.12276	journal	July 2015
Visualizing subcellular rearrangements in intact β cells using soft x-ray tomography White, Kate L.; Singla, Jitin; Loconte, Valentina Science Advances, Vol. 6, Issue 50 https://doi.org/10.1126/sciadv.abc8262	journal	December 2020
OpenCell: Endogenous tagging for the cartography of human cellular organization Cho, Nathan H.; Cheveralls, Keith C.; Brunner, Andreas-David Science, Vol. 375, Issue 6585 https://doi.org/10.1126/science.abi6983	journal	March 2022
XGBoost: A Scalable Tree Boosting System Chen, Tianqi; Guestrin, Carlos Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining - KDD '16 https://doi.org/10.1145/2939672.2939785	conference	January 2016
Pancreatic β-cell heterogeneity in health and diabetes: classes, sources, and subtypes Miranda, Mario A.; Macias-Velasco, Juan F.; Lawson, Heather A. American Journal of Physiology-Endocrinology and Metabolism, Vol. 320, Issue 4 https://doi.org/10.1152/ajpendo.00649.2020	journal	April 2021
Essential role of Skp2-mediated p27 degradation in growth and adaptive expansion of pancreatic β cells Zhong, Lingwen; Georgia, Senta; Tschen, Shuen-ing Journal of Clinical Investigation, Vol. 117, Issue 10 https://doi.org/10.1172/JCI32198	journal	October 2007
Gene Signature of Proliferating Human Pancreatic α Cells Dominguez Gutierrez, Giselle; Xin, Yurong; Okamoto, Haruka Endocrinology, Vol. 159, Issue 9 https://doi.org/10.1210/en.2018-00469	journal	July 2018
Impaired Crosstalk between Pulsatile Insulin and Glucagon Secretion in Prediabetic Individuals Rohrer, Stefan; Menge, Björn A.; Grüber, Lena The Journal of Clinical Endocrinology & Metabolism, Vol. 97, Issue 5 https://doi.org/10.1210/jc.2011-3439	journal	May 2012
Alpha-, Delta- and PP-cells Brereton, Melissa F.; Vergari, Elisa; Zhang, Quan Journal of Histochemistry & Cytochemistry, Vol. 63, Issue 8 https://doi.org/10.1369/0022155415583535	journal	July 2015
The human α cell in health and disease Pettway, Yasminye D.; Saunders, Diane C.; Brissova, Marcela Journal of Endocrinology, Vol. 258, Issue 1 https://doi.org/10.1530/JOE-22-0298	journal	April 2023
UMAP: Uniform Manifold Approximation and Projection McInnes, Leland; Healy, John; Saul, Nathaniel Journal of Open Source Software, Vol. 3, Issue 29 https://doi.org/10.21105/joss.00861	journal	September 2018
Monitoring C-Peptide Storage and Secretion in Islet β-Cells In Vitro and In Vivo Zhu, Shuaishuai; Larkin, Dennis; Lu, Shusheng Diabetes, Vol. 65, Issue 3 https://doi.org/10.2337/db15-1264	journal	December 2015
Brief, Irregular Oscillations of Basal Plasma Insulin and Glucose Concentrations in Diabetic Man Lang, D. A.; Matthews, D. R.; Burnett, M. Diabetes, Vol. 30, Issue 5 https://doi.org/10.2337/diab.30.5.435	journal	May 1981
Heterogeneity of the Pancreatic Beta Cell Gutierrez, Giselle Dominguez; Gromada, Jesper; Sussel, Lori Frontiers in Genetics, Vol. 8 https://doi.org/10.3389/fgene.2017.00022	journal	March 2017
Bioactive Molecule Prediction Using Extreme Gradient Boosting Babajide Mustapha, Ismail; Saeed, Faisal Molecules, Vol. 21, Issue 8 https://doi.org/10.3390/molecules21080983	journal	July 2016
Pancreatic islet plasticity: Interspecies comparison of islet architecture and composition Steiner, Donald J.; Kim, Abraham; Miller, Kevin Islets, Vol. 2, Issue 3 https://doi.org/10.4161/isl.2.3.11815	journal	May 2010

Similar Records

Soft X-ray tomography to map and quantify organelle interactions at the mesoscale

Journal Article · Wed Feb 09 19:00:00 EST 2022 · Structure · OSTI ID:1882845

Visualizing subcellular rearrangements in intact β cells using soft x-ray tomography

Journal Article · Tue Dec 08 19:00:00 EST 2020 · Science Advances · OSTI ID:1734835

Related Subjects

3D cell mapping
59 BASIC BIOLOGICAL SCIENCES
Uniform Manifold Approximation and Projection (UMAP)
cryogenic fluorescence microscopy
machine learning
pancreatic islets
soft X-ray tomography
α cells
β cells

Subcellular Feature-Based Classification of α and β Cells Using Soft X-ray Tomography

Citation Formats

References (62)

Similar Records

Related Subjects