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Zhang X, Song B, Carlino MJ, Li G, Ferchen K, Chen M, Thompson EN, Kain BN, Schnell D, Thakkar K, Kouril M, Jin K, Hay SB, Sen S, Bernardicius D, Ma S, Bennett SN, Croteau J, Salvatori O, Lye MH, Gillen AE, Jordan CT, Singh H, Krause DS, Salomonis N, Grimes HL. An immunophenotype-coupled transcriptomic atlas of human hematopoietic progenitors. Nat Immunol 2024; 25:703-715. [PMID: 38514887 PMCID: PMC11003869 DOI: 10.1038/s41590-024-01782-4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 02/07/2024] [Indexed: 03/23/2024]
Abstract
Analysis of the human hematopoietic progenitor compartment is being transformed by single-cell multimodal approaches. Cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) enables coupled surface protein and transcriptome profiling, thereby revealing genomic programs underlying progenitor states. To perform CITE-seq systematically on primary human bone marrow cells, we used titrations with 266 CITE-seq antibodies (antibody-derived tags) and machine learning to optimize a panel of 132 antibodies. Multimodal analysis resolved >80 stem, progenitor, immune, stromal and transitional cells defined by distinctive surface markers and transcriptomes. This dataset enables flow cytometry solutions for in silico-predicted cell states and identifies dozens of cell surface markers consistently detected across donors spanning race and sex. Finally, aligning annotations from this atlas, we nominate normal marrow equivalents for acute myeloid leukemia stem cell populations that differ in clinical response. This atlas serves as an advanced digital resource for hematopoietic progenitor analyses in human health and disease.
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Affiliation(s)
- Xuan Zhang
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Baobao Song
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Immunology Graduate Program, University of Cincinnati, Cincinnati, OH, USA
| | - Maximillian J Carlino
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale University, New Haven, CT, USA
| | - Guangyuan Li
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kyle Ferchen
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Mi Chen
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale University, New Haven, CT, USA
| | - Evrett N Thompson
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale University, New Haven, CT, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Bailee N Kain
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Dan Schnell
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kairavee Thakkar
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Michal Kouril
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kang Jin
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Stuart B Hay
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Sidharth Sen
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - David Bernardicius
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Siyuan Ma
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Sierra N Bennett
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | | | | | | | - Austin E Gillen
- Division of Hematology, University of Colorado School of Medicine, Aurora, CO, USA
- Rocky Mountain Regional VA Medical Center, Aurora, CO, USA
| | - Craig T Jordan
- Division of Hematology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Harinder Singh
- Departments of Immunology and Computational and Systems Biology, Center for Systems Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Diane S Krause
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale University, New Haven, CT, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA.
| | - H Leighton Grimes
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA.
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
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Thompson EN, Carlino MJ, Scanlon VM, Grimes HL, Krause DS. Assay optimization for the objective quantification of human multilineage colony-forming units. Exp Hematol 2023; 124:36-44.e3. [PMID: 37271449 PMCID: PMC10527702 DOI: 10.1016/j.exphem.2023.05.007] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/06/2023]
Abstract
Colony-forming unit (CFU) assays are a powerful tool in hematopoietic research because they allow researchers to functionally test the lineage potential of individual stem and progenitor cells. Assaying for lineage potential is important for determining and validating the identity of progenitor populations isolated by methods such as fluorescence-activated cell sorting (FACS). However, current methods for CFU assays are limited in their ability to robustly assay multipotent progenitors with the ability to differentiate down the myeloid, erythroid, and megakaryocytic lineages because of the lack of specific growth factors necessary for certain lineage outputs. In addition, manual counting of colony types is subjective resulting in user to user variability in assessments of cell types based on colony and cell morphologies. We demonstrate that the addition of granulocyte colony-stimulating factor (G-CSF), macrophage (M)-CSF, and granulocyte-macrophage (GM)-CSF into a collagen-based MegaCult medium containing IL-3, IL-6, SCF, EPO, and TPO allows for the differentiation of common myeloid progenitors into expected proportions of colonies containing granulocytic (G), monocytic (M), erythroid (E), and megakaryocytic (Mk) cells. Additionally, we demonstrate an objective method using in situ immunofluorescence (IF) with anti-CD66b, anti-CD14, anti-CD235a, and anti-CD41 to detect G, M, E, and Mk cells, respectively. IF stained colonies can be analyzed individually at a microscope or using high-throughput microscopy. Thus, our improvements to the culture conditions and method for assay readout increase the accuracy, reproducibility, and throughput of the myeloid CFU assay.
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Affiliation(s)
- Evrett N Thompson
- Department of Cell Biology, Yale School of Medicine, New Haven, CT; Yale Stem Cell Center, New Haven, CT
| | - Maximillian J Carlino
- Yale Stem Cell Center, New Haven, CT; Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
| | - Vanessa M Scanlon
- Yale Stem Cell Center, New Haven, CT; Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT; Center for Regenerative Medicine and Skeletal Development, University of Connecticut Health, Farmington, CT
| | - H Leighton Grimes
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Diane S Krause
- Department of Cell Biology, Yale School of Medicine, New Haven, CT; Yale Stem Cell Center, New Haven, CT; Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT; Department of Pathology, Yale School of Medicine, New Haven, CT.
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Elkhadragy L, Dasteh Goli K, Totura WM, Carlino MJ, Regan MR, Guzman G, Schook LB, Gaba RC, Schachtschneider KM. Effect of CRISPR Knockout of AXIN1 or ARID1A on Proliferation and Migration of Porcine Hepatocellular Carcinoma. Front Oncol 2022; 12:904031. [PMID: 35669430 PMCID: PMC9163418 DOI: 10.3389/fonc.2022.904031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 04/19/2022] [Indexed: 11/17/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is an aggressive disease lacking effective treatment. Animal models of HCC are necessary for preclinical evaluation of the safety and efficacy of novel therapeutics. Large animal models of HCC allow testing image-guided locoregional therapies, which are widely used in the management of HCC. Models with precise tumor mutations mimicking human HCC provide valuable tools for testing precision medicine. AXIN1 and ARID1A are two of the most frequently mutated genes in human HCC. Here, we investigated the effects of knockout of AXIN1 and/or ARID1A on proliferation, migration, and chemotherapeutic susceptibility of porcine HCC cells and we developed subcutaneous tumors harboring these mutations in pigs. Gene knockout was achieved by CRISPR/Cas9 and was validated by Next Generation Sequencing. AXIN1 knockout increased the migration of porcine HCC cells but did not alter the cell proliferation. Knockout of ARID1A increased both the proliferation and migration of porcine HCC cells. Simultaneous knockout of AXIN1 and ARID1A increased the migration, but did not alter the proliferation of porcine HCC cells. The effect of gene knockout on the response of porcine HCC cells to two of the most commonly used systemic and locoregional HCC treatments was investigated; sorafenib and doxorubicin, respectively. Knockout of AXIN1 and/or ARID1A did not alter the susceptibility of porcine HCC cells to sorafenib or doxorubicin. Autologous injection of CRISPR edited HCC cells resulted in development of subcutaneous tumors in pigs, which harbored the anticipated edits in AXIN1 and/or ARID1A. This study elucidates the effects of CRISPR-mediated knockout of HCC-associated genes in porcine HCC cells, and lays the foundation for development and utilization of genetically-tailored porcine HCC models for in vivo testing of novel therapeutic approaches in a clinically-relevant large animal model.
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Affiliation(s)
- Lobna Elkhadragy
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, United States
| | - Kimia Dasteh Goli
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, United States
| | - William M. Totura
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, United States
| | | | - Maureen R. Regan
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, United States
| | - Grace Guzman
- Department of Pathology, University of Illinois at Chicago, Chicago, IL, United States
| | - Lawrence B. Schook
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, United States
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Ron C. Gaba
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, United States
- Department of Pathology, University of Illinois at Chicago, Chicago, IL, United States
| | - Kyle M. Schachtschneider
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, United States
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, United States
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- *Correspondence: Kyle M. Schachtschneider,
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Carlino MJ, Kralicek SE, Santiago SA, Sitaraman LM, Harrington AT, Hecht GA. Quantitative analysis and virulence phenotypes of atypical enteropathogenic Escherichia coli (EPEC) acquired from diarrheal stool samples from a Midwest US hospital. Gut Microbes 2020; 12:1-21. [PMID: 33131419 PMCID: PMC7644165 DOI: 10.1080/19490976.2020.1824562] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Infectious diarrhea causes approximately 179 million illnesses annually in the US. Multiplex PCR assays for enteric pathogens detect enteropathogenic Escherichia coli (EPEC) in 12-29% of diarrheal stool samples from all age groups in developed nations. The aim of this study was to isolate and characterize EPEC from diarrhea samples identified as EPEC positive by BioFire Gastrointestinal Panel (GIP). EPEC is the second most common GIP-detected pathogen, equally present in sole and mixed infections peaking during summer months. EPEC bacterial load is higher in samples with additional pathogens. EPEC-GIP-positive stool samples were cultured on MacConkey II agar and analyzed by colony PCR for eaeA and bfpA to identify and classify EPEC isolates as typical (tEPEC) or atypical (aEPEC). EPEC were not recovered from the majority of stool samples with only 61 isolates obtained from 277 samples; most were aEPEC from adults. bfpA-mRNA was severely diminished in 3 of 4 bfpA-positive isolates. HeLa and SKCO-15 epithelial cells were infected with EPEC isolates and virulence-associated phenotypes, including adherence pattern, attachment level, pedestal formation, and tight junction disruption, were assessed. All aEPEC adherence patterns were represented with diffuse adherence predominating. Attachment rates of isolates adhering with defined adherence patterns were higher than tEPEC lacking bfpA (ΔbfpA). The majority of isolates formpedestals. All but one isolate initially increases but ultimately decreases transepithelial electrical resistance of SKCO-15 monolayers, similar to ΔbfpA. Most isolates severely disrupt occludin; ZO-1 disruption is variable. Most aEPEC isolates induce more robust virulence-phenotypes in vitro than ΔbfpA, but less than tEPEC-E2348/69.
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Affiliation(s)
- MJ Carlino
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, USA
| | - SE Kralicek
- Department of Medicine, Division of Gastroenterology and Nutrition, Loyola University Chicago, Maywood, IL, USA
| | - SA Santiago
- Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - LM Sitaraman
- Department of Medicine, Division of Gastroenterology and Nutrition, Loyola University Chicago, Maywood, IL, USA
| | - AT Harrington
- Department of Pathology and Laboratory Medicine, Loyola University Chicago, Maywood, IL, USA
| | - Gail A. Hecht
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, USA,Department of Medicine, Division of Gastroenterology and Nutrition, Loyola University Chicago, Maywood, IL, USA,Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA,Department of Medical Service, Edward Hines Jr. VA Hospital, Hines, IL,CONTACT Gail A. Hecht Department of Medicine, Division of Gastroenterology, Loyola University Chicago, IL, USA
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Tapia R, Perez-Yepez EA, Carlino MJ, Karandikar UC, Kralicek SE, Estes MK, Hecht GA. Sperm Flagellar 1 Binds Actin in Intestinal Epithelial Cells and Contributes to Formation of Filopodia and Lamellipodia. Gastroenterology 2019; 157:1544-1555.e3. [PMID: 31473225 PMCID: PMC7016487 DOI: 10.1053/j.gastro.2019.08.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 08/21/2019] [Accepted: 08/23/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND & AIMS Sperm flagellar 1 (also called CLAMP) is a microtubule-associated protein that regulates microtubule dynamics and planar cell polarity in multi-ciliated cells. We investigated the localization and function of sperm flagellar 1, or CLAMP, in human intestinal epithelia cells (IECs). METHODS We performed studies with SKCO-15 and human intestinal enteroids established from biopsies from different intestinal segments (duodenal, jejunum, ileal, and colon) of a single donor. Enteroids were induced to differentiation after incubation with growth factors. The distribution of endogenous CLAMP in IECs was analyzed by immunofluorescence microscopy using total internal reflection fluorescence-ground state depletion and confocal microscopy. CLAMP localization was followed during the course of intestinal epithelial cell polarization as cells progressed from flat to compact, confluent monolayers. Protein interactions with endogenous CLAMP were determined in SKCO-15 cells using proximity ligation assays and co-immunoprecipitation. CLAMP was knocked down in SKCO-15 monolayers using small hairpin RNAs and cells were analyzed by immunoblot and immunofluorescence microscopy. The impact of CLAMP knock-down in migrating SKCO-15 cells was assessed using scratch-wound assays. RESULTS CLAMP bound to actin and apical junctional complex proteins but not microtubules in IECs. In silico analysis predicted the calponin-homology domain of CLAMP to contain conserved amino acids required for actin binding. During IEC polarization, CLAMP distribution changed from primarily basal stress fibers and cytoplasm in undifferentiated cells to apical membranes and microvilli in differentiated monolayers. CLAMP accumulated in lamellipodia and filopodia at the leading edge of migrating cells in association with actin. CLAMP knock-down reduced the number of filopodia, perturbed filopodia polarity, and altered the organization of actin filaments within lamellipodia. CONCLUSIONS CLAMP is an actin-binding protein, rather than a microtubule-binding protein, in IECs. CLAMP distribution changes during intestinal epithelial cell polarization, regulates the formation of filopodia, and appears to assist in the organization of actin bundles within lamellipodia of migrating IECs. Studies are needed to define the CLAMP domains that interact with actin and whether its loss from IECs affects intestinal function.
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Affiliation(s)
- Rocio Tapia
- Department of Medicine, Division of Gastroenterology and Nutrition
| | | | | | | | | | - Mary K. Estes
- Department of Molecular Virology and Microbiology,Department of Medicine - Gastroenterology and Hepatology and Infectious Diseases, Baylor College of Medicine, Houston, Texas
| | - Gail A. Hecht
- Department of Medicine, Division of Gastroenterology and Nutrition,Department of Microbiology and Immunology, Loyola University Chicago,Edward Hines Jr. VA Hospital, Hines, Illinois
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