The authors would like to acknowledge Dr. Ellen Lauchnor, Dr. Phil Stewart, and Bengisu Kilic for their previous work and assistance with the O2 microsensors; Andy Sebrell for training in organoid culture and micromanipulation; Lexi Burcham for assistance in organoid culture, media preparation, data recording, and organization; and Dr. Susy Kohout for general advice in electrophysiology. We would like to thank Dr. Heidi Smith for her assistance with imaging and acknowledge the Center for Biofilm Engineering Bioimaging Facility at Montana State University, which is supported by funding from the National Science Foundation MRI Program (2018562), the M.J. Murdock Charitable Trust (202016116), the US Department of Defense (77369LSRIP &#38; W911NF1910288), and by the Montana Nanotechnology Facility (an NNCI member supported by NSF Grant ECCS-2025391).
Special thanks to the entire Unisense team who made this work possible, especially Dr. Andrew Cerskus, Dr. Laura Woods, Dr. Lars Larsen, Dr. Tage Dalsgaard, Dr. Line Daugaard, Dr. Karen Maegaard, and Mette Gammelgaard. Funding for our study was provided by the National Institutes of Health grants R01 GM13140801 (D.B., R.B.) and UL1 TR002319 (K.N.L), and a Research Expansion Award from the Montana State University Office for Research and Economic Development (D.B.). Figure 1A was created with BioRender.

This protocol requires 3D organoids of at least 200 &#181;m in diameter that have a distinct lumen and that are embedded in an artificial extracellular matrix (ECM, e.g., Matrigel). Human gastric tissues for organoid derivation were obtained with approval from the Institutional Review Board of Montana State University and informed consent from patients undergoing upper endoscopy at Bozeman Health (protocol # 2023-48-FCR, to D.B.) or as exempt whole stomach or sleeve gastrectomy specimens from the National Disease Researc...

Precise Luminal pH Measurement in 3D Gastric Organoids with Microelectrodes

<ol>
	<li>Zhang, N., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tissue+spatial+omics+dissects+organoid+biomimicry.">Tissue spatial omics dissects organoid biomimicry.</a> GEN Biotechnology. 2 (5), 372-383 (2023).</li><li>Sato, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single+lgr5+stem+cells+build+crypt-villus+structures+in+vitro+without+a+mesenchymal+niche.">Single lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche.</a> Nature. 459 (7244), 262-265 (2009).</li><li>Lancaster, M. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cerebral+organoids+model+human+brain+development+and+microcephaly.">Cerebral organoids model human brain development and microcephaly.</a> Nature. 501 (7467), 373-379 (2013).</li><li>Dutta, D., Heo, I., Clevers, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Disease+modeling+in+stem+cell-derived+3d+organoid+systems.">Disease modeling in stem cell-derived 3d organoid systems.</a> Trends Mol Med. 23 (5), 393-410 (2017).</li><li>Achberger, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Merging+organoid+and+organ-on-a-chip+technology+to+generate+complex+multi-layer+tissue+models+in+a+human+retina-on-a-chip+platform.">Merging organoid and organ-on-a-chip technology to generate complex multi-layer tissue models in a human retina-on-a-chip platform.</a> Elife. 8, e46188 (2019).</li><li>Bartfeld, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+vitro+expansion+of+human+gastric+epithelial+stem+cells+and+their+responses+to+bacterial+infection.">In vitro expansion of human gastric epithelial stem cells and their responses to bacterial infection.</a> Gastroenterology. 148 (1), 126-136 (2015).</li><li>Fatehullah, A., Tan, S. H., Barker, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Organoids+as+an+in+vitro+model+of+human+development+and+disease.">Organoids as an in vitro model of human development and disease.</a> Nat Cell Biol. 18 (3), 246-254 (2016).</li><li>Clevers, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Modeling+development+and+disease+with+organoids.">Modeling development and disease with organoids.</a> Cell. 165 (7), 1586-1597 (2016).</li><li>Davies, J. A., Davies, J. A., Lawrence, M. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Organoids and Mini-organs. , 3-40 (2018).</li><li>Ambrosini, Y. M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Recapitulation+of+the+accessible+interface+of+biopsy-derived+canine+intestinal+organoids+to+study+epithelial-luminal+interactions.">Recapitulation of the accessible interface of biopsy-derived canine intestinal organoids to study epithelial-luminal interactions.</a> PLoS One. 15 (4), e0231423 (2020).</li><li>Williams, S. E., Turnberg, L. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Demonstration+of+a+pH+gradient+across+mucus+adherent+to+rabbit+gastric+mucosa:+Evidence+for+a+'mucus-bicarbonate'+barrier.">Demonstration of a pH gradient across mucus adherent to rabbit gastric mucosa: Evidence for a 'mucus-bicarbonate' barrier.</a> Gut. 22 (2), 94-96 (1981).</li><li>Schubert, M. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Gastric+secretion.">Gastric secretion.</a> Curr Opin Gastroenterol. 20 (6), 519-525 (2004).</li><li>Celli, J. P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rheology+of+gastric+mucin+exhibits+a+pH-dependent+sol&#8722;gel+transition.">Rheology of gastric mucin exhibits a pH-dependent sol&#8722;gel transition.</a> Biomacromolecules. 8 (5), 1580-1586 (2007).</li><li>Takeshita, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Assessment+of+pH-dependent+errors+in+spectrophotometric+pH+measurements+of+seawater.">Assessment of pH-dependent errors in spectrophotometric pH measurements of seawater.</a> Marine Chemistry. 223, 103801 (2020).</li><li>Mccracken, K. W., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Wnt/&#946;-catenin+promotes+gastric+fundus+specification+in+mice+and+humans.">Wnt/&#946;-catenin promotes gastric fundus specification in mice and humans.</a> Nature. 541 (7636), 182-187 (2017).</li><li>Larsen, M., Borisov, S. M., Grunwald, B., Klimant, I., Glud, R. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+simple+and+inexpensive+high+resolution+color+ratiometric+planar+optode+imaging+approach:+Application+to+oxygen+and+ph+sensing.">A simple and inexpensive high resolution color ratiometric planar optode imaging approach: Application to oxygen and ph sensing.</a> Limnology and Oceanography: Methods. 9 (9), 348-360 (2011).</li><li>Jewell, M. P., Galyean, A. A., Kirk Harris, J., Zemanick, E. T., Cash, K. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Luminescent+nanosensors+for+ratiometric+monitoring+of+three-dimensional+oxygen+gradients+in+laboratory+and+clinical+pseudomonas+aeruginosa+biofilms.">Luminescent nanosensors for ratiometric monitoring of three-dimensional oxygen gradients in laboratory and clinical pseudomonas aeruginosa biofilms.</a> Appl Environ Microbiol. 85 (20), e01116-e01119 (2019).</li><li>Brooks, E. L., Hussain, K. K., Kotecha, K., Abdalla, A., Patel, B. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Three-dimensional-printed+electrochemical+multiwell+plates+for+monitoring+food+intolerance+from+intestinal+organoids.">Three-dimensional-printed electrochemical multiwell plates for monitoring food intolerance from intestinal organoids.</a> ACS Sens. 8 (2), 712-720 (2023).</li><li>pH and reference electrode manual. Unisense Available from: <a target="_blank" href="https://unisense.com/wp-content/uploads/2023/05/2023.05-pH-and-ref-sensor-manual.pdf">https://unisense.com/wp-content/uploads/2023/05/2023.05-pH-and-ref-sensor-manual.pdf</a> (2023)</li><li>Villahermosa, D., Corzo, A., Garcia-Robledo, E., Gonzalez, J. M., Papaspyrou, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Kinetics+of+indigenous+nitrate+reducing+sulfide+oxidizing+activity+in+microaerophilic+wastewater+biofilms.">Kinetics of indigenous nitrate reducing sulfide oxidizing activity in microaerophilic wastewater biofilms.</a> PLoS One. 11 (2), 0149096 (2016).</li><li>Pabst, B., Pitts, B., Lauchnor, E., Stewart, P. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Gel-entrapped+staphylococcus+aureus+bacteria+as+models+of+biofilm+infection+exhibit+growth+in+dense+aggregates,+oxygen+limitation,+antibiotic+tolerance,+and+heterogeneous+gene+expression.">Gel-entrapped staphylococcus aureus bacteria as models of biofilm infection exhibit growth in dense aggregates, oxygen limitation, antibiotic tolerance, and heterogeneous gene expression.</a> Antimicrob Agents Chemother. 60 (10), 6294-6301 (2016).</li><li>Ploug, H., Stolte, W., Epping, E. H. G., J&#248;rgensen, B. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Diffusive+boundary+layers,+photosynthesis,+and+respiration+of+the+colony-forming+plankton+algae,+phaeocystis+sp.">Diffusive boundary layers, photosynthesis, and respiration of the colony-forming plankton algae, phaeocystis sp.</a> Limnology and Oceanography. 44 (8), 1949-1958 (1999).</li><li>Kolpen, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nitrous+oxide+production+in+sputum+from+cystic+fibrosis+patients+with+chronic+pseudomonas+aeruginosa+lung+infection.">Nitrous oxide production in sputum from cystic fibrosis patients with chronic pseudomonas aeruginosa lung infection.</a> PLoS One. 9 (1), 84353 (2014).</li><li>Murphy, K. C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Measurement+of+oxygen+tension+within+mesenchymal+stem+cell+spheroids.">Measurement of oxygen tension within mesenchymal stem cell spheroids.</a> J R Soc Interface. 14 (127), 20160851 (2017).</li><li>Sebrell, T. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+novel+gastric+spheroid+co-culture+model+reveals+chemokine-dependent+recruitment+of+human+dendritic+cells+to+the+gastric+epithelium.">A novel gastric spheroid co-culture model reveals chemokine-dependent recruitment of human dendritic cells to the gastric epithelium.</a> Cell Mol Gastroenterol Hepatol. 8 (1), 157-171 (2019).</li><li>Miyoshi, H., Stappenbeck, T. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+vitro+expansion+and+genetic+modification+of+gastrointestinal+stem+cells+in+spheroid+culture.">In vitro expansion and genetic modification of gastrointestinal stem cells in spheroid culture.</a> Nat Protoc. 8 (12), 2471-2482 (2013).</li><li>Takase, Y., Fujishima, K., Takahashi, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+3d+culturing+of+organoids+from+murine+intestinal+crypts+and+a+single+stem+cell+for+organoid+research.">The 3d culturing of organoids from murine intestinal crypts and a single stem cell for organoid research.</a> J Vis Exp. (194), e65219 (2023).</li><li>Cherne, M. D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+synthetic+hydrogel,+vitrogel((r))+organoid-3,+improves+immune+cell-epithelial+interactions+in+a+tissue+chip+co-culture+model+of+human+gastric+organoids+and+dendritic+cells.">A synthetic hydrogel, vitrogel((r)) organoid-3, improves immune cell-epithelial interactions in a tissue chip co-culture model of human gastric organoids and dendritic cells.</a> Front Pharmacol. 12, 707891 (2021).</li><li>Sebrell, T. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Live+imaging+analysis+of+human+gastric+epithelial+spheroids+reveals+spontaneous+rupture,+rotation+and+fusion+events.">Live imaging analysis of human gastric epithelial spheroids reveals spontaneous rupture, rotation and fusion events.</a> Cell Tissue Res. 371 (2), 293-307 (2018).</li><li>Sensortrace suite user manual. 3.3. Unisense Available from: <a target="_blank" href="https://unisense.com/wp-content/uploads/2021/10/SensorTrace-Suite-Manual.pdf">https://unisense.com/wp-content/uploads/2021/10/SensorTrace-Suite-Manual.pdf</a> (2023)</li><li>Microprofiling system user manual. Unisense Available from: <a target="_blank" href="https://unisense.com/wp-content/uploads/2021/09/2023.11-MicroProfiling-System-2.pdf">https://unisense.com/wp-content/uploads/2021/09/2023.11-MicroProfiling-System-2.pdf</a> (2023)</li><li>Wolffling, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Egf+and+bmps+govern+differentiation+and+patterning+in+human+gastric+glands.">Egf and bmps govern differentiation and patterning in human gastric glands.</a> Gastroenterology. 161 (2), 623-636 (2021).</li><li>Boccellato, F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Polarised+epithelial+monolayers+of+the+gastric+mucosa+reveal+insights+into+mucosal+homeostasis+and+defence+against+infection.">Polarised epithelial monolayers of the gastric mucosa reveal insights into mucosal homeostasis and defence against infection.</a> Gut. 68 (3), 400-413 (2019).</li><li>Mccracken, K. W., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Modelling+human+development+and+disease+in+pluripotent+stem-cell-derived+gastric+organoids.">Modelling human development and disease in pluripotent stem-cell-derived gastric organoids.</a> Nature. 516 (7531), 400-404 (2014).</li><li>Schumacher, M. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+use+of+murine-derived+fundic+organoids+in+studies+of+gastric+physiology.">The use of murine-derived fundic organoids in studies of gastric physiology.</a> J Physiol. 593 (8), 1809-1827 (2015).</li><li>. Unisense Available from: <a target="_blank" href="https://unisense.com/products/ph-microelectrode/">https://unisense.com/products/ph-microelectrode/</a> (2024)</li><li>Mccracken, K. W., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Wnt/beta-catenin+promotes+gastric+fundus+specification+in+mice+and+humans.">Wnt/beta-catenin promotes gastric fundus specification in mice and humans.</a> Nature. 541 (7636), 182-187 (2017).</li><li>Schreiber, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+situ+measurement+of+ph+in+the+secreting+canaliculus+of+the+gastric+parietal+cell+and+adjacent+structures.">In situ measurement of ph in the secreting canaliculus of the gastric parietal cell and adjacent structures.</a> Cell Tissue Res. 329 (2), 313-320 (2007).</li><li>Xu, H., Li, J., Chen, H., Wang, C., Ghishan, F. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nhe8+plays+important+roles+in+gastric+mucosal+protection.">Nhe8 plays important roles in gastric mucosal protection.</a> Am J Physiol Gastrointest Liver Physiol. 304 (3), G257-G261 (2013).</li><li>Gawenis, L. R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Impaired+gastric+acid+secretion+in+mice+with+a+targeted+disruption+of+the+nhe4+na+/h++exchanger.">Impaired gastric acid secretion in mice with a targeted disruption of the nhe4 na+/h+ exchanger.</a> J Biol Chem. 280 (13), 12781-12789 (2005).</li><li>Lewis, O. L., Keener, J. P., Fogelson, A. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+physics-based+model+for+maintenance+of+the+ph+gradient+in+the+gastric+mucus+layer.">A physics-based model for maintenance of the ph gradient in the gastric mucus layer.</a> Am J Physiol-Gastrointest Liver Physiol. 313 (6), G599-G612 (2017).</li><li>Okkelman, I. A., Neto, N., Papkovsky, D. B., Monaghan, M. G., Dmitriev, R. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+deeper+understanding+of+intestinal+organoid+metabolism+revealed+by+combining+fluorescence+lifetime+imaging+microscopy+(flim)+and+extracellular+flux+analyses.">A deeper understanding of intestinal organoid metabolism revealed by combining fluorescence lifetime imaging microscopy (flim) and extracellular flux analyses.</a> Redox Biol. 30, 101420 (2020).</li><li>Pleguezuelos-Manzano, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Establishment+and+culture+of+human+intestinal+organoids+derived+from+adult+stem+cells.">Establishment and culture of human intestinal organoids derived from adult stem cells.</a> Curr Protoc Immunol. 130 (1), e106 (2020).</li><li>Guimera, X., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+minimally+invasive+microsensor+specially+designed+for+simultaneous+dissolved+oxygen+and+ph+biofilm+profiling.">A minimally invasive microsensor specially designed for simultaneous dissolved oxygen and ph biofilm profiling.</a> Sensors (Basel). 19 (21), 4747 (2019).</li></ol>

Limited access to the luminal space of organoids has severely restricted our understanding of the physiological dynamics of this microenvironment. A reliable tool for functional analyses of luminal physiology will expand our ability to leverage organoids as in vitro models for physiology, pharmacology, and disease research. Organoids are highly tunable, physiologically relevant models with the added potential to replicate genetic variability within the human population. Existing methods for pH measurement inside...

Organoids-miniature multicellular structures derived from stem cells-have revolutionized our ability to study human physiology and are starting to replace animal models, even in regulatory settings1. Since the initial description of intestinal organoids by Sato et al. in 2009, organoid technology has become immensely popular2. A large number of studies have characterized the cellular composition and function of organoid models in great detail3,4,5,6. However, the luminal space of these 3D multicellular structures remains largely undefined7,8. The lumen is the central cavity of organoids derived from mucosal tissues that is surrounded by the apical portions of polarized epithelial cells. Since cellular secretion and absorption predominantly occur at the apical epithelial surface, the luminal microenvironment of organoids is controlled by these important physiological processes. Currently used organoid models demonstrate variations in cell signaling patterns, overall stemness, metabolite concentration gradients, and environmental conditions9. Understanding organoid luminal physiology is therefore necessary for the accurate modeling of organ function and pathology. Unfortunately, the relative inaccessibility of the lumen significantly hinders functional analyses of luminal physiology in 3D organoids10.
The ability to examine pH profiles is especially important in the stomach, which is notorious for having the steepest proton gradient in the body, ranging from approximately 1-3 in the lumen, to near neutral at the epithelium11,12,13.There remains a significant gap in our understanding of the microscale maintenance of the gastric pH gradient, and the relevance of organoid models in recapitulating this dynamic milieu across the gastric mucus layer. Traditional approaches for the analysis of organoid pH have involved the use of pH-sensitive dyes, which can be fluorescent or colorimetric indicators. McCracken et al. used a luminal injection of SNARF-5F-a ratiometric pH indicator-into organoids to analyze a drop in luminal pH in response to histamine treatment. Such dyes can be incorporated into the culture media, allowing for real-time, non-invasive monitoring of pH. Not only do pH-sensitive dyes require complex calibration steps that contribute to poor reliability and accuracy with measurements, but such dyes also tend to operate within specific detection ranges that may not be representative of the full pH range within the microenvironment of interest14,15. It could be considered reasonable, however, to use indicator dyes for confirmatory experiments. Optical nanosensors that use fluorescent optode-based, pH-sensing approaches have also been developed; however, such sensing techniques require microscopic imaging and are also susceptible to photobleaching, phototoxicity, as well as imaging bias16,17. Additionally, Brooks et al. have 3D-printed multiwell plates containing microelectrodes on top of which organoids may be plated18. This approach, however, does not allow for measurements directly inside the organoid lumen.
Electrode-based pH measurements can achieve improved accuracy compared to other methods, as well as provide real-time pH monitoring. In addition, pH electrodes mounted on micromanipulators allow for superior spatial resolution of pH measurements as the precise location of the electrode tip can be finely controlled. This enables the highest possible flexibility and reproducibility in the analyses of organoid models. The electrodes used here are miniaturized pH microelectrodes that operate based on the diffusion of protons through selective pH glass that surrounds a thin platinum wire. The microelectrode is connected to an external Ag-AgCl reference electrode and then connected to a high-impedance millivolt meter. The electrical potential between the two electrode tips when submerged in the same solution will reflect the pH of the solution19. Such microprofiling systems have been used in the metabolic analysis of biofilms20,21, planktonic algae22, human sputum samples23, and even in mesenchymal stem cell spheroids24. Both our lab and Murphy et al. have previously used micromanipulator-controlled O2 microelectrodes to evaluate the oxygen concentrations in the luminal spaces of organoids. Murphy et al. paired this method with mathematical modeling to reveal an oxygen gradient within their spheroids. Our group was able to find reduced luminal oxygen levels in tissue-derived gastric organoids compared to the surrounding extracellular matrix25.
Here, we provide a detailed method for the manual microelectrode profiling of the luminal pH in spherical gastrointestinal tract organoids that will enable enhanced physiological understanding of their complex luminal microenvironment. We anticipate that this technique will add a new dimension to the exploration of organoid physiology through real-time, high-resolution measurements of pH levels at a microscale. Furthermore, the following protocol could be easily adapted for the analysis of O2, N2O, H2, NO, H2S, redox, and temperature in various types of organoid models. Physiological profiling serves as a valuable tool for optimizing organoid culture conditions to better mimic in vivo environments, thereby enhancing the relevance and utility of organoid models in biomedical research.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>3 M KCl</td>
			<td>Unisense</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>5 mL Wobble-not Serological Pipet, Individually Wrapped, Paper/Plastic, Bag, Sterile</td>
			<td>CellTreat</td>
			<td>229091B</td>
			<td></td>
		</tr>
		<tr>
			<td>10 mL Wobble-not Serological Pipet, Individually Wrapped, Paper/Plastic, Bag, Sterile</td>
			<td>CellTreat</td>
			<td>229092B</td>
			<td></td>
		</tr>
		<tr>
			<td>15 mL Centrifuge Tube - Foam Rack, Sterile</td>
			<td>CellTreat</td>
			<td>229412</td>
			<td></td>
		</tr>
		<tr>
			<td>24 Well Tissue Culture Plate, Sterile</td>
			<td>CellTreat</td>
			<td>229124</td>
			<td></td>
		</tr>
		<tr>
			<td>25 mL Wobble-not Serological Pipet, Individually Wrapped, Paper/Plastic, Bag, Sterile</td>
			<td>CellTreat</td>
			<td>229093B</td>
			<td></td>
		</tr>
		<tr>
			<td>35 mm Dish | No. 1.5 Coverslip | 20 mm Glass Diameter | Uncoated</td>
			<td>MatTek</td>
			<td>P35G-1.5-20-C</td>
			<td></td>
		</tr>
		<tr>
			<td>50 mL Centrifuge Tube - Foam Rack, Sterile</td>
			<td>CellTreat</td>
			<td>229422</td>
			<td></td>
		</tr>
		<tr>
			<td>70% Ethanol</td>
			<td>BP82031GAL</td>
			<td>BP82031GAL</td>
			<td></td>
		</tr>
		<tr>
			<td>70 &#956;m Cell Strainer, Individually Wrapped, Sterile</td>
			<td>CellTreat</td>
			<td>229483&#160;</td>
			<td></td>
		</tr>
		<tr>
			<td>1,000 &#181;L Extended Length Low Retention Pipette Tips, Racked, Sterile</td>
			<td>CellTreat</td>
			<td>229037</td>
			<td></td>
		</tr>
		<tr>
			<td>Amphotericin B (Fungizone) Solution</td>
			<td>HyClone Laboratories, Inc</td>
			<td>SV30078.01</td>
			<td></td>
		</tr>
		<tr>
			<td>Biosafety Cabinet</td>
			<td>Nuaire&#160;</td>
			<td>NU-425-600</td>
			<td>Class II Type A/B3</td>
		</tr>
		<tr>
			<td>Bovine Serum Albumin</td>
			<td>Fisher Bioreagents</td>
			<td>BP1605-100</td>
			<td></td>
		</tr>
		<tr>
			<td>Cell recovery solution</td>
			<td>Corning</td>
			<td>354253</td>
			<td>Cell dissociation solution</td>
		</tr>
		<tr>
			<td>DMEM/F-12 (Advanced DMEM)</td>
			<td>Gibco</td>
			<td>12-491-015</td>
			<td></td>
		</tr>
		<tr>
			<td>Dulbecco&#39;s Modification of Eagles Medium (DMEM)</td>
			<td>Fisher Scientific</td>
			<td>15017CV</td>
			<td></td>
		</tr>
		<tr>
			<td>Fetal Bovine Serum</td>
			<td>HyClone Laboratories, Inc</td>
			<td>SH30088</td>
			<td></td>
		</tr>
		<tr>
			<td>G418 Sulfate</td>
			<td>Corning</td>
			<td>30-234-CR</td>
			<td></td>
		</tr>
		<tr>
			<td>Gentamycin sulfate</td>
			<td>IBI Scientific</td>
			<td>IB02030</td>
			<td></td>
		</tr>
		<tr>
			<td>HEPES, Free Acid</td>
			<td>Cytiva</td>
			<td>SH30237.01</td>
			<td></td>
		</tr>
		<tr>
			<td>HP Pavillion 2-in-1 14&#34; Laptop Intel Core i3</td>
			<td>HP</td>
			<td>M03840-001</td>
			<td></td>
		</tr>
		<tr>
			<td>Hydrochloric acid</td>
			<td>Fisher Scientific</td>
			<td>A144C-212</td>
			<td></td>
		</tr>
		<tr>
			<td>Incubator</td>
			<td>Fisher Scientific</td>
			<td>11676604</td>
			<td></td>
		</tr>
		<tr>
			<td>iPhone 12 camera</td>
			<td>Apple</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>L-glutamine</td>
			<td>Cytiva</td>
			<td>SH3003401</td>
			<td></td>
		</tr>
		<tr>
			<td>Large Kimberly-Clark Professional Kimtech Science Kimwipes Delicate Task Wipers, 1-Ply</td>
			<td>Fisher Scientific</td>
			<td>34133</td>
			<td></td>
		</tr>
		<tr>
			<td>M 205 FA Stereomicroscope</td>
			<td>Leica</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Matrigel Membrane Matrix 354234</td>
			<td>Corning</td>
			<td>CB-40234</td>
			<td></td>
		</tr>
		<tr>
			<td>MC-1 UniMotor Controller</td>
			<td>Unisense</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Methyl red</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>MM33 Micromanipulator</td>
			<td>Marzhauser Wetzlar</td>
			<td>61-42-113-0000</td>
			<td>Right handed</td>
		</tr>
		<tr>
			<td>MS-15 Motorized Stage</td>
			<td>Unisense</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Nanoject-II</td>
			<td>Drummond</td>
			<td>3-000-204</td>
			<td>nanoliter autoinjector</td>
		</tr>
		<tr>
			<td>Penicillin/Streptomycin (10,000 U/mL)</td>
			<td>Gibco</td>
			<td>15-140-148</td>
			<td></td>
		</tr>
		<tr>
			<td>pH Microelectrodes</td>
			<td>Unisense</td>
			<td>50-109158, 25-203452, 25-205272, 25-111626, 25-109160</td>
			<td>SensorTrace software is not compatible with Apple computers</td>
		</tr>
		<tr>
			<td>Reference Electrode</td>
			<td>Unisense</td>
			<td>REF-RM-001652</td>
			<td>SensorTrace software is not compatible with Apple computers</td>
		</tr>
		<tr>
			<td>SB 431542</td>
			<td>Tocris Bioscience</td>
			<td>16-141-0</td>
			<td></td>
		</tr>
		<tr>
			<td>Smartphone Camera Adapter</td>
			<td>Gosky</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Specifications Laboratory Stand LS</td>
			<td>Unisense</td>
			<td>LS-009238</td>
			<td></td>
		</tr>
		<tr>
			<td>Trypsin-EDTA 0.025%, phenol red</td>
			<td>Gibco</td>
			<td>25-200-056</td>
			<td></td>
		</tr>
		<tr>
			<td>UniAmp</td>
			<td>Unisense</td>
			<td>11632</td>
			<td></td>
		</tr>
		<tr>
			<td>United Biosystems Inc&#160;MINI CELL SCRAPERS 200/PK</td>
			<td>Fisher</td>
			<td>MCS-200</td>
			<td></td>
		</tr>
		<tr>
			<td>Y-27632 dihydrochloride</td>
			<td>Tocris Bioscience</td>
			<td>12-541-0</td>
			<td></td>
		</tr>
		<tr>
			<td>&#181;Sensor Calibration Kit</td>
			<td>Unisense/ Mettler Toledo</td>
			<td>51-305-070, 51-302-069</td>
			<td>pH 4.01 and 9.21, 20 mL packets</td>
		</tr>
	</tbody>
</table>

profiling luminal ph in three-dimensional gastrointestinal organoids using microelectrodes

The optimization and detailed characterization of gastrointestinal organoid models require advanced methods for analyzing their luminal environments. This paper presents a highly reproducible method for the precise measurement of pH within the lumina of 3D human gastric organoids via micromanipulator-controlled microelectrodes. The pH microelectrodes are commercially available and consist of beveled glass tips of 25 &#181;m in diameter. For measurements, the pH microelectrode is advanced into the lumen of an organoid (&gt;200 &#181;m) that is suspended in Matrigel, while a reference electrode rests submerged in the surrounding medium in the culture plate. 
Using such microelectrodes to profile organoids derived from the human gastric body, we demonstrate that luminal pH is relatively consistent within each culture well at ~7.7 &plusmn; 0.037 and that continuous measurements can be obtained for a minimum of 15 min. In some larger organoids, the measurements revealed a pH gradient between the epithelial surface and the lumen, suggesting that pH measurements in organoids can be achieved with high spatial resolution. In a previous study, microelectrodes were successfully used to measure luminal oxygen concentrations in organoids, demonstrating the versatility of this method for organoid analyses. In summary, this protocol describes an important tool for the functional characterization of the complex luminal space within 3D organoids.

Author Spotlight: Gastric Epithelial Cell Responses in &lt;em&gt;Helicobacter pylori&lt;/em&gt; infection

Profiling Luminal pH in Three-Dimensional Gastrointestinal Organoids Using Microelectrodes

The overall goal of our research is to understand how gastric epithelial cells, immune cells, stromal cells and their products, such as cytokines and mucus, work together to respond to infection with gastric pathogen helicobacter pylori. To that end, we are trying to build complex physiologically relevant models of the human gastric mucosa. Previous studies with gastric organoids have shown conflicting results regarding the ability of these models to maintain acid-secreting parietal cells.Using the pH microelectrodes, we demonstrated that in the absence of specific differentiation or stimulation protocols, human gastric organoids maintain a near neutral pH in the lumen. Relative in accessibility, the organoid lumen has long restricted our understanding of the microenvironment within. We demonstrate the first successful microelectrode pH measurements for the functional characterization of organoids.Our microelectrode-based method could provide researchers with a reliable tool that can be adapted to their specific needs. Until now, pH measurement within gastrointestinal organoids has involved the use of pH-sensitive dyes that rely on microscopic imaging for quantification. The main advantage of using microelectrodes is that they provide accurate numerical pH readings.In addition, intraluminal pH can be recorded in real time and with superior spatial resolution. We are working toward a fully functional model of the human gastric mucus layer with the physiological pH gradient so we can study the role of this barrier in helicobacter pylori infection. The ultimate goal is to develop new cytoprotective treatments that strengthen the mucus layer and prevent bacterial invasion.

Secretion of acid is a crucial function of the human stomach. However, to what extent acid secretion can be modeled in organoids is still a matter of debate6,32,33,34. We therefore developed the protocol detailed above to accurately measure acid production in gastric organoids. Notably, we used unstimulated adult stem cell-derived organoids cultured under standard expansion conditions that had ...

The present protocol describes pH measurements in human tissue-derived gastric organoids using microelectrodes for spatiotemporal characterization of intraluminal physiology.

The optimization and detailed characterization of gastrointestinal organoid models require advanced methods for analyzing their luminal environments. This ...

profiling-luminal-ph-three-dimensional-gastrointestinal-organoids