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Meah A, Vedarethinam V, Bronstein R, Gujarati N, Jain T, Mallipattu SK, Li Y, Wang J. Single-Cell Spatial MIST for Versatile, Scalable Detection of Protein Markers. Biosensors (Basel) 2023; 13:852. [PMID: 37754086 PMCID: PMC10526469 DOI: 10.3390/bios13090852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/21/2023] [Accepted: 08/25/2023] [Indexed: 09/28/2023]
Abstract
High-multiplex detection of protein biomarkers across tissue regions has been an attractive spatial biology approach due to significant advantages over traditional immunohistochemistry (IHC) methods. Different from most methods, spatial multiplex in situ tagging (MIST) transfers the spatial protein expression information to an ultrahigh-density, large-scale MIST array. This technique has been optimized to reach single-cell resolution by adoption of smaller array units and 30% 8-arm PEG polymer as transfer medium. Tissue cell nuclei stained with lamin B have been clearly visualized on the MIST arrays and are colocalized with detection of nine mouse brain markers. Pseudocells defined at 10 μm in size have been used to fully profile tissue regions including cells and the intercellular space. We showcased the versatility of our technology by successfully detecting 20 marker proteins in kidney samples with the addition of five minutes atop the duration of standard immunohistochemistry protocols. Spatial MIST is amenable to iterative staining and detection on the same tissue samples. When 25 proteins were co-detected on 1 mouse brain section for each round and 5 rounds were executed, an ultrahigh multiplexity of 125 proteins was obtained for each pseudocell. With its unique abilities, this single-cell spatial MIST technology has the potential to become an important method in advanced diagnosis of complex diseases.
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Affiliation(s)
- Arafat Meah
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
| | - Vadanasundari Vedarethinam
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
| | - Robert Bronstein
- Division of Nephrology and Hypertension, Department of Medicine, Stony Brook School of Medicine, Stony Brook, NY 11794, USA
| | - Nehaben Gujarati
- Division of Nephrology and Hypertension, Department of Medicine, Stony Brook School of Medicine, Stony Brook, NY 11794, USA
| | - Tanya Jain
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Programs of Neurosciences, Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10065, USA
| | - Sandeep K. Mallipattu
- Division of Nephrology and Hypertension, Department of Medicine, Stony Brook School of Medicine, Stony Brook, NY 11794, USA
- Renal Section, Northport VA Medical Center, Northport, NY 11768, USA
| | - Yueming Li
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Programs of Neurosciences, Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10065, USA
- Programs of Pharmacology, Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10021, USA
| | - Jun Wang
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
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Pace JA, Bronstein R, Guo Y, Yang Y, Estrada CC, Gujarati N, Salant DJ, Haley J, Bialkowska AB, Yang VW, He JC, Mallipattu SK. Podocyte-specific KLF4 is required to maintain parietal epithelial cell quiescence in the kidney. Sci Adv 2021; 7:eabg6600. [PMID: 34516901 PMCID: PMC8442927 DOI: 10.1126/sciadv.abg6600] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 07/13/2021] [Indexed: 06/06/2023]
Abstract
Podocyte loss triggering aberrant activation and proliferation of parietal epithelial cells (PECs) is a central pathogenic event in proliferative glomerulopathies. Podocyte-specific Krüppel-like factor 4 (KLF4), a zinc-finger transcription factor, is essential for maintaining podocyte homeostasis and PEC quiescence. Using mice with podocyte-specific knockdown of Klf4, we conducted glomerular RNA-sequencing, tandem mass spectrometry, and single-nucleus RNA-sequencing to identify cell-specific transcriptional changes that trigger PEC activation due to podocyte loss. Integration with in silico chromatin immunoprecipitation identified key ligand-receptor interactions, such as fibronectin 1 (FN1)–αVβ6, between podocytes and PECs dependent on KLF4 and downstream signal transducer and activator of transcription 3 (STAT3) signaling. Knockdown of Itgb6 in PECs attenuated PEC activation. Additionally, podocyte-specific induction of human KLF4 or pharmacological inhibition of downstream STAT3 activation reduced FN1 and integrin β 6 (ITGB6) expression and mitigated podocyte loss and PEC activation in mice. Targeting podocyte-PEC crosstalk might be a critical therapeutic strategy in proliferative glomerulopathies.
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Affiliation(s)
- Jesse A. Pace
- Division of Nephrology and Hypertension, Department of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Robert Bronstein
- Division of Nephrology and Hypertension, Department of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Yiqing Guo
- Division of Nephrology and Hypertension, Department of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Yaqi Yang
- Division of Nephrology and Hypertension, Department of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Chelsea C. Estrada
- Division of Nephrology and Hypertension, Department of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Nehaben Gujarati
- Division of Nephrology and Hypertension, Department of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - David J. Salant
- Division of Nephrology, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - John Haley
- Department of Pharmacology, Stony Brook University, Stony Brook, NY, USA
| | - Agnieszka B. Bialkowska
- Division of Gastroenterology, Department of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Vincent W. Yang
- Division of Gastroenterology, Department of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - John C. He
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sandeep K. Mallipattu
- Division of Nephrology and Hypertension, Department of Medicine, Stony Brook University, Stony Brook, NY, USA
- Renal Section, Northport VA Medical Center, Northport, NY, USA
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