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Beshiri ML, Capaldo BJ, Lake R, Ku AT, Burner D, Tice CM, Tran C, Kostas J, Alilin AN, Yin JJ, Agarwal S, Morris SA, Karzai FH, Lotan TL, Dahut WL, Sowalsky AG, Kelly K. Stem cell dynamics and cellular heterogeneity across lineage subtypes of castrate resistant prostate cancer. Stem Cells 2024:sxae025. [PMID: 38563224 DOI: 10.1093/stmcls/sxae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Indexed: 04/04/2024]
Abstract
To resist lineage-dependent therapies such as androgen receptor inhibition, prostate luminal epithelial adenocarcinoma cells often adopt a stem-like state resulting in lineage-plasticity and phenotypic heterogeneity. Castrate resistant prostate adenocarcinoma can transition to neuroendocrine and occasionally to amphicrine, co-expressed luminal and neuroendocrine, phenotypes. We developed CRPC patient-derived organoid models that preserve heterogeneity of the originating tumor, including an amphicrine model displaying a range of luminal and neuroendocrine phenotypes. To gain biological insight and to identify potential treatment targets within heterogeneous tumor cell populations, we assessed the lineage hierarchy and molecular characteristics of various CRPC tumor subpopulations. Transcriptionally similar stem/progenitor cells were identified for all lineage populations. Lineage tracing in amphicrine CRPC showed that heterogeneity originated from distinct subclones of infrequent stem/progenitor cells that produced mainly quiescent differentiated amphicrine progeny. By contrast, adenocarcinoma CRPC progeny originated from stem/progenitor cells and self-renewing differentiated luminal cells. NEPC was composed almost exclusively of self-renewing stem/progenitor cells. Amphicrine subpopulations were enriched for secretory luminal, mesenchymal, and enzalutamide treatment persistent signatures that characterize clinical progression. Finally, the amphicrine stem/progenitor subpopulation was specifically depleted with an AURKA inhibitor, which blocked tumor growth. These data illuminate distinct stem cell characteristics for subtype-specific CRPC in addition to demonstrating a context for targeting differentiation-competent prostate stem cells.
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Affiliation(s)
- Michael L Beshiri
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Brian J Capaldo
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Ross Lake
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Anson T Ku
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Danielle Burner
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Caitlin M Tice
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Crystal Tran
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Julianna Kostas
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Aian Neil Alilin
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Juan Juan Yin
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Supreet Agarwal
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Samantha A Morris
- Department of Developmental Biology, Washington University School of Medicine in St Louis, St Louis, MO, USA
- Department of Genetics, Washington University School of Medicine in St Louis, St Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine in St Louis, St Louis, MO, USA
| | - Fatima H Karzai
- Genitourinary Malignancies Branch, National Cancer Institute, NIH, Bethesda, Maryland
| | - Tamara L Lotan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - William L Dahut
- Genitourinary Malignancies Branch, National Cancer Institute, NIH, Bethesda, Maryland
| | - Adam G Sowalsky
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Kathleen Kelly
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
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Jindal K, Adil MT, Yamaguchi N, Yang X, Wang HC, Kamimoto K, Rivera-Gonzalez GC, Morris SA. Single-cell lineage capture across genomic modalities with CellTag-multi reveals fate-specific gene regulatory changes. Nat Biotechnol 2023:10.1038/s41587-023-01931-4. [PMID: 37749269 DOI: 10.1038/s41587-023-01931-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 07/31/2023] [Indexed: 09/27/2023]
Abstract
Complex gene regulatory mechanisms underlie differentiation and reprogramming. Contemporary single-cell lineage-tracing (scLT) methods use expressed, heritable DNA barcodes to combine cell lineage readout with single-cell transcriptomics. However, reliance on transcriptional profiling limits adaptation to other single-cell assays. With CellTag-multi, we present an approach that enables direct capture of heritable random barcodes expressed as polyadenylated transcripts, in both single-cell RNA sequencing and single-cell Assay for Transposase Accessible Chromatin using sequencing assays, allowing for independent clonal tracking of transcriptional and epigenomic cell states. We validate CellTag-multi to characterize progenitor cell lineage priming during mouse hematopoiesis. Additionally, in direct reprogramming of fibroblasts to endoderm progenitors, we identify core regulatory programs underlying on-target and off-target fates. Furthermore, we reveal the transcription factor Zfp281 as a regulator of reprogramming outcome, biasing cells toward an off-target mesenchymal fate. Our results establish CellTag-multi as a lineage-tracing method compatible with multiple single-cell modalities and demonstrate its utility in revealing fate-specifying gene regulatory changes across diverse paradigms of differentiation and reprogramming.
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Affiliation(s)
- Kunal Jindal
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Mohd Tayyab Adil
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Naoto Yamaguchi
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Xue Yang
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Helen C Wang
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Kenji Kamimoto
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Guillermo C Rivera-Gonzalez
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Samantha A Morris
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA.
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Rivera-Gonzalez GC, Butka EG, Gonzalez CE, Kong W, Jindal K, Morris SA. Single-cell lineage tracing reveals hierarchy and mechanism of adipocyte precursor maturation. bioRxiv 2023:2023.06.01.543318. [PMID: 37398135 PMCID: PMC10312565 DOI: 10.1101/2023.06.01.543318] [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] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
White adipose tissue is crucial in various physiological processes. In response to high caloric intake, adipose tissue may expand by generating new adipocytes. Adipocyte precursor cells (progenitors and preadipocytes) are essential for generating mature adipocytes, and single-cell RNA sequencing provides new means to identify these populations. Here, we characterized adipocyte precursor populations in the skin, an adipose depot with rapid and robust generation of mature adipocytes. We identified a new population of immature preadipocytes, revealed a biased differentiation potential of progenitor cells, and identified Sox9 as a critical factor in driving progenitors toward adipose commitment, the first known mechanism of progenitor differentiation. These findings shed light on the specific dynamics and molecular mechanisms underlying rapid adipogenesis in the skin.
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Affiliation(s)
- Guillermo C. Rivera-Gonzalez
- Department of Developmental Biology, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Emily G. Butka
- Department of Developmental Biology, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Carolynn E. Gonzalez
- Department of Developmental Biology, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Wenjun Kong
- Department of Developmental Biology, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Kunal Jindal
- Department of Developmental Biology, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Samantha A. Morris
- Department of Developmental Biology, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
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Amrute JM, Lai L, Ma P, Koenig AL, Kamimoto K, Bredemeyer A, Shankar TS, Kuppe C, Kadyrov FF, Schulte LJ, Stoutenburg D, Kopecky BJ, Navankasattusas S, Visker J, Morris SA, Kramann R, Leuschner F, Mann DL, Drakos SG, Lavine KJ. Defining cardiac functional recovery in end-stage heart failure at single-cell resolution. Nat Cardiovasc Res 2023; 2:399-416. [PMID: 37583573 PMCID: PMC10426763 DOI: 10.1038/s44161-023-00260-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 03/01/2023] [Indexed: 08/17/2023]
Abstract
Recovery of cardiac function is the holy grail of heart failure therapy yet is infrequently observed and remains poorly understood. In this study, we performed single-nucleus RNA sequencing from patients with heart failure who recovered left ventricular systolic function after left ventricular assist device implantation, patients who did not recover and non-diseased donors. We identified cell-specific transcriptional signatures of recovery, most prominently in macrophages and fibroblasts. Within these cell types, inflammatory signatures were negative predictors of recovery, and downregulation of RUNX1 was associated with recovery. In silico perturbation of RUNX1 in macrophages and fibroblasts recapitulated the transcriptional state of recovery. Cardiac recovery mediated by BET inhibition in mice led to decreased macrophage and fibroblast Runx1 expression and diminished chromatin accessibility within a Runx1 intronic peak and acquisition of human recovery signatures. These findings suggest that cardiac recovery is a unique biological state and identify RUNX1 as a possible therapeutic target to facilitate cardiac recovery.
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Affiliation(s)
- Junedh M. Amrute
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- These authors contributed equally: Junedh M. Amrute, Lulu Lai
| | - Lulu Lai
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
- These authors contributed equally: Junedh M. Amrute, Lulu Lai
| | - Pan Ma
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Andrew L. Koenig
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Kenji Kamimoto
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Andrea Bredemeyer
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Thirupura S. Shankar
- Division of Cardiovascular Medicine & Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah Health & School of Medicine, Salt Lake City, UT, USA
| | - Christoph Kuppe
- Institute of Experimental Medicine and Systems Biology and Division of Nephrology, RWTH Aachen University, Aachen, Germany
| | - Farid F. Kadyrov
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Linda J. Schulte
- Division of Cardiothoracic Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Dylan Stoutenburg
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Benjamin J. Kopecky
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Sutip Navankasattusas
- Division of Cardiovascular Medicine & Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah Health & School of Medicine, Salt Lake City, UT, USA
| | - Joseph Visker
- Division of Cardiovascular Medicine & Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah Health & School of Medicine, Salt Lake City, UT, USA
| | - Samantha A. Morris
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Rafael Kramann
- Institute of Experimental Medicine and Systems Biology and Division of Nephrology, RWTH Aachen University, Aachen, Germany
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Florian Leuschner
- Department of Cardiology, University Hospital Heidelberg, Heidelberg, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Heidelberg, Heidelberg, Germany
| | - Douglas L. Mann
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Stavros G. Drakos
- Division of Cardiovascular Medicine & Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah Health & School of Medicine, Salt Lake City, UT, USA
| | - Kory J. Lavine
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
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5
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Kamimoto K, Adil MT, Jindal K, Hoffmann CM, Kong W, Yang X, Morris SA. Gene regulatory network reconfiguration in direct lineage reprogramming. Stem Cell Reports 2023; 18:97-112. [PMID: 36584685 PMCID: PMC9860067 DOI: 10.1016/j.stemcr.2022.11.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 12/31/2022] Open
Abstract
In direct lineage conversion, transcription factor (TF) overexpression reconfigures gene regulatory networks (GRNs) to reprogram cell identity. We previously developed CellOracle, a computational method to infer GRNs from single-cell transcriptome and epigenome data. Using inferred GRNs, CellOracle simulates gene expression changes in response to TF perturbation, enabling in silico interrogation of network reconfiguration. Here, we combine CellOracle analysis with lineage tracing of fibroblast to induced endoderm progenitor (iEP) conversion, a prototypical direct reprogramming paradigm. By linking early network state to reprogramming outcome, we reveal distinct network configurations underlying successful and failed fate conversion. Via in silico simulation of TF perturbation, we identify new factors to coax cells into successfully converting their identity, uncovering a central role for the AP-1 subunit Fos with the Hippo signaling effector, Yap1. Together, these results demonstrate the efficacy of CellOracle to infer and interpret cell-type-specific GRN configurations, providing new mechanistic insights into lineage reprogramming.
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Affiliation(s)
- Kenji Kamimoto
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA
| | - Mohd Tayyab Adil
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA
| | - Kunal Jindal
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA
| | - Christy M Hoffmann
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA
| | - Wenjun Kong
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA
| | - Xue Yang
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA
| | - Samantha A Morris
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA.
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6
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Arya B, Donofrio MT, Freud LR, Hornberger LK, Moon-Grady AJ, Morris SA, Pinto N, Simpson LL, Cuneo BF, Divanovic A, Jaeggi E, Peyvandi S, Puchalski MD, Rychik J, Schidlow DN, Srivastava S, Tacy TA, Tworetzky W, Walsh MJ. Implications of United States Supreme Court's ruling on Dobbs vs Jackson Women's Health Organization: perspective of physicians caring for critically ill fetuses and newborns. Ultrasound Obstet Gynecol 2022; 60:812-813. [PMID: 36353858 DOI: 10.1002/uog.26107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Affiliation(s)
- B Arya
- Seattle Children's Hospital and the University of Washington School of Medicine, Seattle, WA, USA
| | - M T Donofrio
- Children's National Hospital and George Washington School of Medicine, Washington, DC, USA
| | - L R Freud
- The Hospital for Sick Children and the University of Toronto, Toronto, Canada
| | | | - A J Moon-Grady
- University of California at San Francisco, San Francisco, CA, USA
| | - S A Morris
- Texas Children's Hospital and Baylor College of Medicine, Houston, TX, USA
| | - N Pinto
- Seattle Children's Hospital and the University of Washington School of Medicine, Seattle, WA, USA
| | - L L Simpson
- Columbia University Irving Medical School, New York, NY, USA
| | - B F Cuneo
- Children's Hospital of Colorado, Aurora, CO, USA
| | - A Divanovic
- Cincinnati Children's Hospital and the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - E Jaeggi
- The Hospital for Sick Children and the University of Toronto, Toronto, Canada
| | - S Peyvandi
- University of California at San Francisco, San Francisco, CA, USA
| | - M D Puchalski
- Johns Hopkins All Children's Hospital, St Petersburg, FL, USA
| | - J Rychik
- The Children's Hospital of Philadelphia and Perelman, School of Medicine at University of Pennsylvania, Philadelphia, PA, USA
| | - D N Schidlow
- Boston Children's Hospital and Harvard School of Medicine, Boston, MA, USA
| | | | - T A Tacy
- Lucile Packard Children's Hospital at Stanford University, Palo Alto, CA, USA
| | - W Tworetzky
- Boston Children's Hospital and Harvard School of Medicine, Boston, MA, USA
| | - M J Walsh
- Atrium Health Wake Forest Baptist, Winston-Salem, NC, USA
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Weigel A, Caldas C, Meyer A, Morris SA. The impact of AI on research. Cell 2022; 185:2621-2622. [PMID: 35868265 DOI: 10.1016/j.cell.2022.06.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 06/10/2022] [Accepted: 06/10/2022] [Indexed: 10/17/2022]
Abstract
Large and complex datasets have made artificial intelligence (AI) an invaluable tool for discovery across biological research. We asked experts how AI has impacted their work. Their experiences and perspectives offer thoughtful insights into potential offered by AI for their fields.
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8
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Lancaster M, Morris SA, Takebe T, Qian L, Gao S, Huch M. Anniversary reflections: Inspiring discoveries and the future of the field. Cell Stem Cell 2022; 29:879-881. [PMID: 35659874 DOI: 10.1016/j.stem.2022.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Cell Stem Cell was launched in 2007, and this year marks its 15th anniversary. To recognize this occasion, we asked six advisory board members to reflect on inspiring discoveries reported in Cell Stem Cell and how these breakthroughs connect to their vision for the future of the field.
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9
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Affiliation(s)
- Alejo Rodriguez-Fraticelli
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Carrer de Baldiri Reixac 10, Barcelona 08028, Spain
| | - Samantha A Morris
- Washington University in St Louis, Washington University School of Medicine in St Louis, 660 South Euclid Avenue, Campus Box 8103, St Louis, MO 63110, USA
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10
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Luff SA, Creamer JP, Valsoni S, Dege C, Scarfò R, Dacunto A, Cascione S, Randolph LN, Cavalca E, Merelli I, Morris SA, Ditadi A, Sturgeon CM. Identification of a retinoic acid-dependent haemogenic endothelial progenitor from human pluripotent stem cells. Nat Cell Biol 2022; 24:616-624. [PMID: 35484246 PMCID: PMC9109599 DOI: 10.1038/s41556-022-00898-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 03/16/2022] [Indexed: 01/12/2023]
Abstract
The generation of haematopoietic stem cells (HSCs) from human pluripotent stem cells (hPSCs) is a major goal for regenerative medicine. During embryonic development, HSCs derive from haemogenic endothelium (HE) in a NOTCH- and retinoic acid (RA)-dependent manner. Although a WNT-dependent (WNTd) patterning of nascent hPSC mesoderm specifies clonally multipotent intra-embryonic-like HOXA+ definitive HE, this HE is functionally unresponsive to RA. Here we show that WNTd mesoderm, before HE specification, is actually composed of two distinct KDR+ CD34neg populations. CXCR4negCYP26A1+ mesoderm gives rise to HOXA+ multilineage definitive HE in an RA-independent manner, whereas CXCR4+ ALDH1A2+ mesoderm gives rise to HOXA+ multilineage definitive HE in a stage-specific, RA-dependent manner. Furthermore, both RA-independent (RAi) and RA-dependent (RAd) HE harbour transcriptional similarity to distinct populations found in the early human embryo, including HSC-competent HE. This revised model of human haematopoietic development provides essential resolution to the regulation and origins of the multiple waves of haematopoiesis. These insights provide the basis for the generation of specific haematopoietic populations, including the de novo specification of HSCs.
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Affiliation(s)
- Stephanie A Luff
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai School of Medicine, New York, NY, USA
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Hematology, Washington University School of Medicine, St Louis, MO, USA
| | - J Philip Creamer
- Department of Medicine, Division of Hematology, Washington University School of Medicine, St Louis, MO, USA
| | - Sara Valsoni
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Carissa Dege
- Department of Medicine, Division of Hematology, Washington University School of Medicine, St Louis, MO, USA
| | - Rebecca Scarfò
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Analisa Dacunto
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai School of Medicine, New York, NY, USA
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sara Cascione
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Lauren N Randolph
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Eleonora Cavalca
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Ivan Merelli
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Institute for Biomedical Technologies, National Research Council, Milan, Italy
| | - Samantha A Morris
- Department of Developmental Biology, Washington University in Saint Louis, St Louis, MO, USA
- Department of Genetics, Washington University in Saint Louis, St Louis, MO, USA
| | - Andrea Ditadi
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy.
| | - Christopher M Sturgeon
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai School of Medicine, New York, NY, USA.
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Medicine, Division of Hematology, Washington University School of Medicine, St Louis, MO, USA.
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11
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Venardos A, Colquitt J, Morris SA. Fetal growth of left-sided structures and postnatal surgical outcome in borderline left heart varies by cardiac phenotype. Ultrasound Obstet Gynecol 2022; 59:642-650. [PMID: 33998097 DOI: 10.1002/uog.23689] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 04/29/2021] [Accepted: 05/04/2021] [Indexed: 06/12/2023]
Abstract
OBJECTIVES There are two borderline left-heart phenotypes in the fetus: (1) severe aortic stenosis (AS), which is associated with a 'short, fat', globular left ventricle (LV), LV systolic dysfunction and LV growth arrest; and (2) severe left-heart hypoplasia (LHH), which is associated with a 'long, skinny' LV, laminar flow across hypoplastic mitral and aortic valves and arch hypoplasia. Both phenotypes may be counseled for possible single-ventricle palliation. We aimed to compare the rates of left-sided cardiac structure growth and Z-score change over gestation and to describe the postnatal outcomes associated with these two phenotypes. We hypothesized that the left-sided structures would grow faster in fetuses with LHH compared to those with AS, and that those with LHH would be more likely to achieve biventricular circulation. METHODS This was a retrospective cohort study using data collected in an institutional cardiology database between April 2001 and April 2018. We included fetuses with severe AS or severe LHH, and with at least two fetal echocardiograms. Inclusion criteria for the AS group included: aortic-annulus Z-score < -2.0, severe AS, depressed LV function, retrograde systolic flow in the aortic arch and endocardial fibroelastosis. Inclusion criteria for the LHH group included: aortic-annulus Z-score < -2.0, hypoplastic but apex-forming LV, normal LV function and retrograde systolic flow in the aortic arch. Exclusion criteria were: abnormal cardiac connections, other forms of structural congenital heart disease, cardiomyopathy, history of fetal aortic valvuloplasty and participation in a maternal hyperoxygenation study. Measurements and respective Z-scores for the aortic-valve annulus, mitral-valve annulus, LV long- and short-axis dimensions, along with aortic-arch measurements, were collected longitudinally for each fetus and plotted over time for both cohorts. Mean slopes of change in dimension and Z-scores over gestation were calculated and compared between the two groups using mixed generalized linear regression accounting for repeated measures. A subanalysis was performed, matching six fetuses from each group for initial aortic-annulus Z-score and gestational age, due to the significant differences in these two variables between the original cohorts. RESULTS In total, 53 fetuses with 158 echocardiograms were included. In the AS cohort, there were 20 (38%) fetuses with 65 echocardiograms, and in the LHH cohort there were 33 (62%) fetuses with 93 echocardiograms. On the first echocardiogram, LHH fetuses had a later gestational age and a larger aortic-annulus diameter. The rate of aortic-annulus growth was greater in the LHH group compared with the AS group (mean ± SD, 0.15 ± 0.01 mm/week for LHH vs 0.07 ± 0.01 mm/week for AS (P < 0.001)). While the LHH group had a decrease in aortic-annulus Z-score over time, this was at a slower rate than the decrease in the AS group (mean ± SD, -0.04 ± 0.02/week for LHH vs -0.13 ± 0.02/week for AS (P < 0.001)). A similar pattern was seen for the mitral-valve and LV short-axis-dimension Z-scores. Subanalysis of six fetuses from each group matched for initial aortic-annulus Z-score and gestational age demonstrated similar findings, with the LHH group Z-scores decreasing at a slower rate than those in the AS group. Fifty-two of the 53 fetuses were liveborn, one LHH fetus dying in utero. Of the 20 liveborn in the AS cohort, 15 (75%) infants underwent single-ventricle palliation, two (10%) underwent biventricular repair and three (15%) died prior to intervention. Of the 32 liveborn in the LHH cohort, three (9.4%) underwent single-ventricle palliation, 28 (87.5%) achieved biventricular circulation, of which six required no surgery, and one (3.1%) died prior to intervention. CONCLUSIONS The left-sided cardiac structures grow at a faster rate in fetuses with severe LHH than they do in fetuses with severe AS, and the Z-scores decrease at a slower rate in fetuses with severe LHH than they do in those with severe AS. The majority of infants in the LHH group did not undergo single-ventricle palliation. This information can be useful in counseling families on the expected growth potential of the fetus's aortic valve, mitral valve and LV, depending on the cardiac phenotype. © 2022 International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- A Venardos
- Texas Children's Hospital, Department of Pediatrics, Houston, TX, USA
| | - J Colquitt
- Texas Children's Hospital, Department of Pediatrics, Houston, TX, USA
| | - S A Morris
- Texas Children's Hospital, Department of Pediatrics, Houston, TX, USA
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12
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Kong W, Fu YC, Holloway EM, Garipler G, Yang X, Mazzoni EO, Morris SA. Capybara: A computational tool to measure cell identity and fate transitions. Cell Stem Cell 2022; 29:635-649.e11. [PMID: 35354062 PMCID: PMC9040453 DOI: 10.1016/j.stem.2022.03.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [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: 12/20/2021] [Revised: 02/18/2022] [Accepted: 03/03/2022] [Indexed: 01/14/2023]
Abstract
Measuring cell identity in development, disease, and reprogramming is challenging as cell types and states are in continual transition. Here, we present Capybara, a computational tool to classify discrete cell identity and intermediate "hybrid" cell states, supporting a metric to quantify cell fate transition dynamics. We validate hybrid cells using experimental lineage tracing data to demonstrate the multi-lineage potential of these intermediate cell states. We apply Capybara to diagnose shortcomings in several cell engineering protocols, identifying hybrid states in cardiac reprogramming and off-target identities in motor neuron programming, which we alleviate by adding exogenous signaling factors. Further, we establish a putative in vivo correlate for induced endoderm progenitors. Together, these results showcase the utility of Capybara to dissect cell identity and fate transitions, prioritizing interventions to enhance the efficiency and fidelity of stem cell engineering.
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Affiliation(s)
- Wenjun Kong
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA
| | - Yuheng C Fu
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA
| | - Emily M Holloway
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA
| | - Görkem Garipler
- Department of Biology, New York University, New York, NY 10003, USA
| | - Xue Yang
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA
| | | | - Samantha A Morris
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA.
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13
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Cable J, Elowitz MB, Domingos AI, Habib N, Itzkovitz S, Hamidzada H, Balzer MS, Yanai I, Liberali P, Whited J, Streets A, Cai L, Stergachis AB, Hong CKY, Keren L, Guilliams M, Alon U, Shalek AK, Hamel R, Pfau SJ, Raj A, Quake SR, Zhang NR, Fan J, Trapnell C, Wang B, Greenwald NF, Vento-Tormo R, Santos SDM, Spencer SL, Garcia HG, Arekatla G, Gaiti F, Arbel-Goren R, Rulands S, Junker JP, Klein AM, Morris SA, Murray JI, Galloway KE, Ratz M, Romeike M. Single cell biology-a Keystone Symposia report. Ann N Y Acad Sci 2021; 1506:74-97. [PMID: 34605044 DOI: 10.1111/nyas.14692] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 08/24/2021] [Indexed: 11/27/2022]
Abstract
Single cell biology has the potential to elucidate many critical biological processes and diseases, from development and regeneration to cancer. Single cell analyses are uncovering the molecular diversity of cells, revealing a clearer picture of the variation among and between different cell types. New techniques are beginning to unravel how differences in cell state-transcriptional, epigenetic, and other characteristics-can lead to different cell fates among genetically identical cells, which underlies complex processes such as embryonic development, drug resistance, response to injury, and cellular reprogramming. Single cell technologies also pose significant challenges relating to processing and analyzing vast amounts of data collected. To realize the potential of single cell technologies, new computational approaches are needed. On March 17-19, 2021, experts in single cell biology met virtually for the Keystone eSymposium "Single Cell Biology" to discuss advances both in single cell applications and technologies.
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Affiliation(s)
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California
| | - Ana I Domingos
- Department of Physiology, Anatomy & Genetics, Oxford University, Oxford, United Kingdom.,The Howard Hughes Medical Institute, New York, New York
| | - Naomi Habib
- Cell Circuits Program, Broad Institute, Cambridge, Massachusetts.,Edmond & Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Homaira Hamidzada
- Toronto General Hospital Research Institute, University Health Network; Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research and Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Michael S Balzer
- Renal, Electrolyte, and Hypertension Division, Department of Medicine and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Itai Yanai
- Institute for Computational Medicine, NYU Langone Health, New York, New York
| | - Prisca Liberali
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland
| | - Jessica Whited
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts
| | - Aaron Streets
- Department of Bioengineering and Center for Computational Biology, University of California, Berkeley, Berkeley, California.,Chan Zuckerberg Biohub, San Francisco, California
| | - Long Cai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
| | - Andrew B Stergachis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington; and Brotman Baty Institute for Precision Medicine, Seattle, Washington
| | - Clarice Kit Yee Hong
- Edison Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, Missouri.,Department of Genetics, Washington University in St. Louis, St. Louis, Missouri
| | - Leeat Keren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.,Department of Pathology, School of Medicine, Stanford University, Stanford, California
| | - Martin Guilliams
- Laboratory of Myeloid Cell Biology in Tissue Homeostasis and Regeneration, VIB-UGent Center for Inflammation Research, and Unit of Immunoregulation and Mucosal Immunology, VIB Inflammation Research Center, and Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Uri Alon
- Faculty of Sciences, Department of Human Biology, University of Haifa, Haifa, Israel
| | - Alex K Shalek
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
| | - Regan Hamel
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Sarah J Pfau
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts
| | - Arjun Raj
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Stephen R Quake
- Chan Zuckerberg Biohub, San Francisco, California.,Department of Bioengineering, Stanford University, Stanford, California.,Department of Applied Physics, Stanford University, Stanford, California
| | - Nancy R Zhang
- Graduate Group in Genomics and Computational Biology and Department of Statistics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jean Fan
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine; and Allen Discovery Center for Cell Lineage Tracing, Seattle, Washington
| | - Bo Wang
- Department of Bioengineering, Stanford University, Stanford, California.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, California
| | - Noah F Greenwald
- Department of Pathology, School of Medicine, Stanford University, Stanford, California
| | | | | | - Sabrina L Spencer
- Department of Biochemistry and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado
| | - Hernan G Garcia
- Department of Physics; Biophysics Graduate Group; Department of Molecular and Cell Biology; and Institute for Quantitative Biosciences-QB3, University of California at Berkeley, Berkeley, California
| | | | - Federico Gaiti
- New York Genome Center and Meyer Cancer Center, Weill Cornell Medicine, New York, New York
| | - Rinat Arbel-Goren
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Steffen Rulands
- Max Planck Institute for the Physics of Complex Systems, and Center for Systems Biology Dresden, Dresden, Germany
| | - Jan Philipp Junker
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Allon M Klein
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts
| | - Samantha A Morris
- Department of Genetics, Washington University in St. Louis, St. Louis, Missouri.,Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - John I Murray
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kate E Galloway
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Michael Ratz
- Department of Cell and Molecular Biology, Karolinska Institute, Solna, Sweden
| | - Merrit Romeike
- Max Perutz Laboratories Vienna, University of Vienna, Vienna, Austria
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14
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Wu K, Kamimoto K, Zhang Y, Yang K, Keeler SP, Gerovac BJ, Agapov EV, Austin SP, Yantis J, Gissy KA, Byers DE, Alexander-Brett J, Hoffmann CM, Wallace M, Hughes ME, Crouch EC, Morris SA, Holtzman MJ. Basal epithelial stem cells cross an alarmin checkpoint for postviral lung disease. J Clin Invest 2021; 131:e149336. [PMID: 34343135 PMCID: PMC8483760 DOI: 10.1172/jci149336] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [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: 03/05/2021] [Accepted: 07/28/2021] [Indexed: 11/17/2022] Open
Abstract
Epithelial cells are charged with protection at barrier sites, but whether this normally beneficial response might sometimes become dysfunctional still needs definition. Here, we recognized a pattern of imbalance marked by basal epithelial cell growth and differentiation that replaced normal airspaces in a mouse model of progressive postviral lung disease due to the Sendai virus. Single-cell and lineage-tracing technologies identified a distinct subset of basal epithelial stem cells (basal ESCs) that extended into gas-exchange tissue to form long-term bronchiolar-alveolar remodeling regions. Moreover, this cell subset was selectively expanded by crossing a cell-growth and survival checkpoint linked to the nuclear-localized alarmin IL-33 that was independent of IL-33 receptor signaling and instead connected to autocrine chromatin accessibility. This mechanism creates an activated stem-progenitor cell lineage with potential for physiological or pathological function. Thus, conditional loss of Il33 gene function in basal epithelial cells disrupted the homeostasis of the epithelial barrier at skin and gut sites but also markedly attenuated postviral disease in the lung based on the downregulation of remodeling and inflammation. Thus, we define a basal ESC strategy to deploy innate immune machinery that appears to overshoot the primordial goal of self-defense. Our findings reveal new targets to stratify and correct chronic and often deadly postviral disease.
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Affiliation(s)
- Kangyun Wu
- Pulmonary and Critical Care Medicine, Department of Medicine
| | - Kenji Kamimoto
- Department of Genetics
- Department of Developmental Biology
| | - Yong Zhang
- Pulmonary and Critical Care Medicine, Department of Medicine
| | - Kuangying Yang
- Pulmonary and Critical Care Medicine, Department of Medicine
- Division of Biostatistics
| | | | | | | | | | - Jennifer Yantis
- Pulmonary and Critical Care Medicine, Department of Medicine
| | - Kelly A. Gissy
- Pulmonary and Critical Care Medicine, Department of Medicine
| | - Derek E. Byers
- Pulmonary and Critical Care Medicine, Department of Medicine
| | - Jennifer Alexander-Brett
- Pulmonary and Critical Care Medicine, Department of Medicine
- Department of Pathology and Immunology
| | | | - Matthew Wallace
- Pulmonary and Critical Care Medicine, Department of Medicine
| | - Michael E. Hughes
- Pulmonary and Critical Care Medicine, Department of Medicine
- Department of Genetics
| | | | | | - Michael J. Holtzman
- Pulmonary and Critical Care Medicine, Department of Medicine
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, Missouri, USA
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15
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Bocchi VD, Conforti P, Vezzoli E, Besusso D, Cappadona C, Lischetti T, Galimberti M, Ranzani V, Bonnal RJP, De Simone M, Rossetti G, He X, Kamimoto K, Espuny-Camacho I, Faedo A, Gervasoni F, Vuono R, Morris SA, Chen J, Felsenfeld D, Pavesi G, Barker RA, Pagani M, Cattaneo E. The coding and long noncoding single-cell atlas of the developing human fetal striatum. Science 2021; 372:372/6542/eabf5759. [PMID: 33958447 DOI: 10.1126/science.abf5759] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 03/29/2021] [Indexed: 12/12/2022]
Abstract
Deciphering how the human striatum develops is necessary for understanding the diseases that affect this region. To decode the transcriptional modules that regulate this structure during development, we compiled a catalog of 1116 long intergenic noncoding RNAs (lincRNAs) identified de novo and then profiled 96,789 single cells from the early human fetal striatum. We found that D1 and D2 medium spiny neurons (D1- and D2-MSNs) arise from a common progenitor and that lineage commitment is established during the postmitotic transition, across a pre-MSN phase that exhibits a continuous spectrum of fate determinants. We then uncovered cell type-specific gene regulatory networks that we validated through in silico perturbation. Finally, we identified human-specific lincRNAs that contribute to the phylogenetic divergence of this structure in humans. This work delineates the cellular hierarchies governing MSN lineage commitment.
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Affiliation(s)
- Vittoria Dickinson Bocchi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy.,INGM, Istituto Nazionale Genetica Molecolare, Milan, Italy
| | - Paola Conforti
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy.,INGM, Istituto Nazionale Genetica Molecolare, Milan, Italy
| | - Elena Vezzoli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy.,INGM, Istituto Nazionale Genetica Molecolare, Milan, Italy
| | - Dario Besusso
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy.,INGM, Istituto Nazionale Genetica Molecolare, Milan, Italy
| | - Claudio Cappadona
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy.,INGM, Istituto Nazionale Genetica Molecolare, Milan, Italy
| | - Tiziana Lischetti
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy.,INGM, Istituto Nazionale Genetica Molecolare, Milan, Italy
| | - Maura Galimberti
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy.,INGM, Istituto Nazionale Genetica Molecolare, Milan, Italy
| | | | | | | | | | - Xiaoling He
- WT-MRC Cambridge Stem Cell Institute and Department of Clinical Neuroscience, University of Cambridge, Cambridge, UK
| | - Kenji Kamimoto
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.,Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ira Espuny-Camacho
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy.,INGM, Istituto Nazionale Genetica Molecolare, Milan, Italy
| | - Andrea Faedo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy.,INGM, Istituto Nazionale Genetica Molecolare, Milan, Italy
| | - Federica Gervasoni
- INGM, Istituto Nazionale Genetica Molecolare, Milan, Italy.,Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Romina Vuono
- WT-MRC Cambridge Stem Cell Institute and Department of Clinical Neuroscience, University of Cambridge, Cambridge, UK
| | - Samantha A Morris
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.,Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jian Chen
- CHDI Management/CHDI Foundation, New York, NY, USA
| | | | - Giulio Pavesi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Roger A Barker
- WT-MRC Cambridge Stem Cell Institute and Department of Clinical Neuroscience, University of Cambridge, Cambridge, UK
| | - Massimiliano Pagani
- INGM, Istituto Nazionale Genetica Molecolare, Milan, Italy. .,Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Elena Cattaneo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy. .,INGM, Istituto Nazionale Genetica Molecolare, Milan, Italy
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16
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Minn KT, Dietmann S, Waye SE, Morris SA, Solnica-Krezel L. Gene expression dynamics underlying cell fate emergence in 2D micropatterned human embryonic stem cell gastruloids. Stem Cell Reports 2021; 16:1210-1227. [PMID: 33891870 PMCID: PMC8185470 DOI: 10.1016/j.stemcr.2021.03.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 03/28/2021] [Accepted: 03/29/2021] [Indexed: 11/26/2022] Open
Abstract
Human embryonic stem cells cultured in 2D micropatterns with BMP4 differentiate into a radial arrangement of germ layers and extraembryonic cells. Single-cell transcriptomes demonstrate generation of cell types transcriptionally similar to their in vivo counterparts in Carnegie stage 7 human gastrula. Time-course analyses indicate sequential differentiation, where the epiblast arises by 12 h between the prospective ectoderm in the center and the cells initiating differentiation toward extraembryonic fates at the edge. Extraembryonic and mesendoderm precursors arise from the epiblast by 24 h, while nascent mesoderm, endoderm, and primordial germ cell-like cells form by 44 h. Dynamic changes in transcripts encoding signaling components support a BMP, WNT, and Nodal hierarchy underlying germ-layer specification conserved across mammals, and FGF and HIPPO pathways being active throughout differentiation. This work also provides a resource for mining genes and pathways expressed in a stereotyped 2D gastruloid model, common with other species or unique to human gastrulation.
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Affiliation(s)
- Kyaw Thu Minn
- Department of Biomedical Engineering, Washington University, St. Louis, MO 63130, USA; Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sabine Dietmann
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Division of Nephrology, Washington University School of Medicine, St. Louis, MO 63110, USA; Institute for Informatics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sarah E Waye
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Samantha A Morris
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Lilianna Solnica-Krezel
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
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17
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Russo ML, Gandhi M, Al-Kouatly HB, Morris SA. Prenatal ultrasound features of Loeys-Dietz syndrome Type 4. Ultrasound Obstet Gynecol 2021; 57:504-506. [PMID: 32119163 PMCID: PMC8274625 DOI: 10.1002/uog.22003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 02/21/2020] [Accepted: 02/26/2020] [Indexed: 06/10/2023]
Affiliation(s)
- M L Russo
- Department of Obstetrics and Gynecology, Warren Alpert Medical School of Brown University, Women and Infants Hospital of Rhode Island, Providence, RI, USA
| | - M Gandhi
- Department of Obstetrics and Gynecology, Texas Children's Pavilion for Women and Baylor College of Medicine, Houston, TX, USA
| | - H B Al-Kouatly
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, PA, USA
| | - S A Morris
- Section of Cardiology, Department of Pediatrics, Texas Children's Hospital and Baylor College of Medicine, Houston, TX, USA
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18
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Klatt Shaw D, Saraswathy VM, Zhou L, McAdow AR, Burris B, Butka E, Morris SA, Dietmann S, Mokalled MH. Localized EMT reprograms glial progenitors to promote spinal cord repair. Dev Cell 2021; 56:613-626.e7. [PMID: 33609461 DOI: 10.1016/j.devcel.2021.01.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 11/17/2020] [Accepted: 01/22/2021] [Indexed: 02/06/2023]
Abstract
Anti-regenerative scarring obstructs spinal cord repair in mammals and presents a major hurdle for regenerative medicine. In contrast, adult zebrafish possess specialized glial cells that spontaneously repair spinal cord injuries by forming a pro-regenerative bridge across the severed tissue. To identify the mechanisms that regulate differential regenerative capacity between mammals and zebrafish, we first defined the molecular identity of zebrafish bridging glia and then performed cross-species comparisons with mammalian glia. Our transcriptomics show that pro-regenerative zebrafish glia activate an epithelial-to-mesenchymal transition (EMT) gene program and that EMT gene expression is a major factor distinguishing mammalian and zebrafish glia. Functionally, we found that localized niches of glial progenitors undergo EMT after spinal cord injury in zebrafish and, using large-scale CRISPR-Cas9 mutagenesis, we identified the gene regulatory network that activates EMT and drives functional regeneration. Thus, non-regenerative mammalian glia lack an essential EMT-driving gene regulatory network that reprograms pro-regenerative zebrafish glia after injury.
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Affiliation(s)
- Dana Klatt Shaw
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Lili Zhou
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Anthony R McAdow
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Brooke Burris
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Emily Butka
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Samantha A Morris
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sabine Dietmann
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Mayssa H Mokalled
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
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19
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Cahan P, Cacchiarelli D, Dunn SJ, Hemberg M, de Sousa Lopes SMC, Morris SA, Rackham OJL, Del Sol A, Wells CA. Computational Stem Cell Biology: Open Questions and Guiding Principles. Cell Stem Cell 2021; 28:20-32. [PMID: 33417869 PMCID: PMC7799393 DOI: 10.1016/j.stem.2020.12.012] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Computational biology is enabling an explosive growth in our understanding of stem cells and our ability to use them for disease modeling, regenerative medicine, and drug discovery. We discuss four topics that exemplify applications of computation to stem cell biology: cell typing, lineage tracing, trajectory inference, and regulatory networks. We use these examples to articulate principles that have guided computational biology broadly and call for renewed attention to these principles as computation becomes increasingly important in stem cell biology. We also discuss important challenges for this field with the hope that it will inspire more to join this exciting area.
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Affiliation(s)
- Patrick Cahan
- Institute for Cell Engineering, Department of Biomedical Engineering, Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
| | - Davide Cacchiarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy d Department of Translational Medicine, University of Naples "Federico II," Naples, Italy
| | - Sara-Jane Dunn
- DeepMind, 14-18 Handyside Street, London N1C 4DN, UK; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge CB2 0AW, UK
| | - Martin Hemberg
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | | | - Samantha A Morris
- Department of Developmental Biology, Department of Genetics, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Owen J L Rackham
- Centre for Computational Biology and The Program for Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Antonio Del Sol
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, Belvaux 4366, Luxembourg; CIC bioGUNE, Bizkaia Technology Park, 801 Building, 48160 Derio, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao 48013, Spain
| | - Christine A Wells
- Centre for Stem Cell Systems, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia
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20
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Cates K, McCoy MJ, Kwon JS, Liu Y, Abernathy DG, Zhang B, Liu S, Gontarz P, Kim WK, Chen S, Kong W, Ho JN, Burbach KF, Gabel HW, Morris SA, Yoo AS. Deconstructing Stepwise Fate Conversion of Human Fibroblasts to Neurons by MicroRNAs. Cell Stem Cell 2021; 28:127-140.e9. [PMID: 32961143 PMCID: PMC7796891 DOI: 10.1016/j.stem.2020.08.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [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: 11/06/2019] [Revised: 07/11/2020] [Accepted: 08/21/2020] [Indexed: 12/14/2022]
Abstract
Cell-fate conversion generally requires reprogramming effectors to both introduce fate programs of the target cell type and erase the identity of starting cell population. Here, we reveal insights into the activity of microRNAs miR-9/9∗ and miR-124 (miR-9/9∗-124) as reprogramming agents that orchestrate direct conversion of human fibroblasts into motor neurons by first eradicating fibroblast identity and promoting uniform transition to a neuronal state in sequence. We identify KLF-family transcription factors as direct target genes for miR-9/9∗-124 and show their repression is critical for erasing fibroblast fate. Subsequent gain of neuronal identity requires upregulation of a small nuclear RNA, RN7SK, which induces accessibilities of chromatin regions and neuronal gene activation to push cells to a neuronal state. Our study defines deterministic components in the microRNA-mediated reprogramming cascade.
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Affiliation(s)
- Kitra Cates
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Program in Molecular Genetics and Genomics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Matthew J McCoy
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Program in Molecular Genetics and Genomics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ji-Sun Kwon
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Program in Computational and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yangjian Liu
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Daniel G Abernathy
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Program in Developmental, Regenerative, and Stem Cell Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Bo Zhang
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Shaopeng Liu
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Paul Gontarz
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Woo Kyung Kim
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Shawei Chen
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Wenjun Kong
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Program in Computational and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joshua N Ho
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Program in Developmental, Regenerative, and Stem Cell Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kyle F Burbach
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Program in Molecular Genetics and Genomics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Harrison W Gabel
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Samantha A Morris
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Andrew S Yoo
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
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21
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Minn KT, Fu YC, He S, Dietmann S, George SC, Anastasio MA, Morris SA, Solnica-Krezel L. High-resolution transcriptional and morphogenetic profiling of cells from micropatterned human ESC gastruloid cultures. eLife 2020. [PMID: 33206048 DOI: 10.1101/2020.1101.1122.915777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023] Open
Abstract
During mammalian gastrulation, germ layers arise and are shaped into the body plan while extraembryonic layers sustain the embryo. Human embryonic stem cells, cultured with BMP4 on extracellular matrix micro-discs, reproducibly differentiate into gastruloids, expressing markers of germ layers and extraembryonic cells in radial arrangement. Using single-cell RNA sequencing and cross-species comparisons with mouse, cynomolgus monkey gastrulae, and post-implantation human embryos, we reveal that gastruloids contain cells transcriptionally similar to epiblast, ectoderm, mesoderm, endoderm, primordial germ cells, trophectoderm, and amnion. Upon gastruloid dissociation, single cells reseeded onto micro-discs were motile and aggregated with the same but segregated from distinct cell types. Ectodermal cells segregated from endodermal and extraembryonic but mixed with mesodermal cells. Our work demonstrates that the gastruloid system models primate-specific features of embryogenesis, and that gastruloid cells exhibit evolutionarily conserved sorting behaviors. This work generates a resource for transcriptomes of human extraembryonic and embryonic germ layers differentiated in a stereotyped arrangement.
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Affiliation(s)
- Kyaw Thu Minn
- Department of Biomedical Engineering, Washington University, St. Louis, United States
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, United States
| | - Yuheng C Fu
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, United States
- Department of Genetics, Washington University School of Medicine, St. Louis, United States
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, United States
| | - Shenghua He
- Department of Computer Science & Engineering, Washington University, St. Louis, United States
| | - Sabine Dietmann
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, United States
- Division of Nephrology, Washington University School of Medicine, St. Louis, United States
- Institute for Informatics, Washington University School of Medicine, St. Louis, United States
| | - Steven C George
- Department of Biomedical Engineering, University of California, Davis, Davis, United States
| | - Mark A Anastasio
- Department of Biomedical Engineering, Washington University, St. Louis, United States
- Department of Bioengineering, University of Illinois, Urbana-Champaign, United States
| | - Samantha A Morris
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, United States
- Department of Genetics, Washington University School of Medicine, St. Louis, United States
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, United States
| | - Lilianna Solnica-Krezel
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, United States
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, United States
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22
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Minn KT, Fu YC, He S, Dietmann S, George SC, Anastasio MA, Morris SA, Solnica-Krezel L. High-resolution transcriptional and morphogenetic profiling of cells from micropatterned human ESC gastruloid cultures. eLife 2020; 9:e59445. [PMID: 33206048 PMCID: PMC7728446 DOI: 10.7554/elife.59445] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 11/17/2020] [Indexed: 12/29/2022] Open
Abstract
During mammalian gastrulation, germ layers arise and are shaped into the body plan while extraembryonic layers sustain the embryo. Human embryonic stem cells, cultured with BMP4 on extracellular matrix micro-discs, reproducibly differentiate into gastruloids, expressing markers of germ layers and extraembryonic cells in radial arrangement. Using single-cell RNA sequencing and cross-species comparisons with mouse, cynomolgus monkey gastrulae, and post-implantation human embryos, we reveal that gastruloids contain cells transcriptionally similar to epiblast, ectoderm, mesoderm, endoderm, primordial germ cells, trophectoderm, and amnion. Upon gastruloid dissociation, single cells reseeded onto micro-discs were motile and aggregated with the same but segregated from distinct cell types. Ectodermal cells segregated from endodermal and extraembryonic but mixed with mesodermal cells. Our work demonstrates that the gastruloid system models primate-specific features of embryogenesis, and that gastruloid cells exhibit evolutionarily conserved sorting behaviors. This work generates a resource for transcriptomes of human extraembryonic and embryonic germ layers differentiated in a stereotyped arrangement.
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Affiliation(s)
- Kyaw Thu Minn
- Department of Biomedical Engineering, Washington UniversitySt. LouisUnited States
- Department of Developmental Biology, Washington University School of MedicineSt. LouisUnited States
| | - Yuheng C Fu
- Department of Developmental Biology, Washington University School of MedicineSt. LouisUnited States
- Department of Genetics, Washington University School of MedicineSt. LouisUnited States
- Center of Regenerative Medicine, Washington University School of MedicineSt. LouisUnited States
| | - Shenghua He
- Department of Computer Science & Engineering, Washington UniversitySt. LouisUnited States
| | - Sabine Dietmann
- Department of Developmental Biology, Washington University School of MedicineSt. LouisUnited States
- Division of Nephrology, Washington University School of MedicineSt. LouisUnited States
- Institute for Informatics, Washington University School of MedicineSt. LouisUnited States
| | - Steven C George
- Department of Biomedical Engineering, University of California, DavisDavisUnited States
| | - Mark A Anastasio
- Department of Biomedical Engineering, Washington UniversitySt. LouisUnited States
- Department of Bioengineering, University of IllinoisUrbana-ChampaignUnited States
| | - Samantha A Morris
- Department of Developmental Biology, Washington University School of MedicineSt. LouisUnited States
- Department of Genetics, Washington University School of MedicineSt. LouisUnited States
- Center of Regenerative Medicine, Washington University School of MedicineSt. LouisUnited States
| | - Lilianna Solnica-Krezel
- Department of Developmental Biology, Washington University School of MedicineSt. LouisUnited States
- Center of Regenerative Medicine, Washington University School of MedicineSt. LouisUnited States
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23
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Li Y, Kong W, Yang W, Patel RM, Casey EB, Okeyo-Owuor T, White JM, Porter SN, Morris SA, Magee JA. Single-Cell Analysis of Neonatal HSC Ontogeny Reveals Gradual and Uncoordinated Transcriptional Reprogramming that Begins before Birth. Cell Stem Cell 2020; 27:732-747.e7. [PMID: 32822583 PMCID: PMC7655695 DOI: 10.1016/j.stem.2020.08.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [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: 10/01/2019] [Revised: 06/21/2020] [Accepted: 07/31/2020] [Indexed: 12/14/2022]
Abstract
Fetal and adult hematopoietic stem cells (HSCs) have distinct proliferation rates, lineage biases, gene expression profiles, and gene dependencies. Although these differences are widely recognized, it is not clear how the transition from fetal to adult identity is coordinated. Here we show that murine HSCs and committed hematopoietic progenitor cells (HPCs) undergo a gradual, rather than precipitous, transition from fetal to adult transcriptional states. The transition begins prior to birth and is punctuated by a late prenatal spike in type I interferon signaling that promotes perinatal HPC expansion and sensitizes progenitors to the leukemogenic FLT3ITD mutation. Most other changes in gene expression and enhancer activation are imprecisely timed and poorly coordinated. Thus, heterochronic enhancer elements, and their associated transcripts, are activated independently of one another rather than as part of a robust network. This simplifies the regulatory programs that guide neonatal HSC/HPC ontogeny, but it creates heterogeneity within these populations.
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Affiliation(s)
- Yanan Li
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Wenjun Kong
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA; Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Wei Yang
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Riddhi M Patel
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Emily B Casey
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Theresa Okeyo-Owuor
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - J Michael White
- Department of Pathology and Immunobiology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Shaina N Porter
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Samantha A Morris
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA; Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA.
| | - Jeffrey A Magee
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA.
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24
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Moudgil A, Wilkinson MN, Chen X, He J, Cammack AJ, Vasek MJ, Lagunas T, Qi Z, Lalli MA, Guo C, Morris SA, Dougherty JD, Mitra RD. Self-Reporting Transposons Enable Simultaneous Readout of Gene Expression and Transcription Factor Binding in Single Cells. Cell 2020; 182:992-1008.e21. [PMID: 32710817 PMCID: PMC7510185 DOI: 10.1016/j.cell.2020.06.037] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [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: 02/21/2019] [Revised: 04/14/2020] [Accepted: 06/23/2020] [Indexed: 12/13/2022]
Abstract
Cellular heterogeneity confounds in situ assays of transcription factor (TF) binding. Single-cell RNA sequencing (scRNA-seq) deconvolves cell types from gene expression, but no technology links cell identity to TF binding sites (TFBS) in those cell types. We present self-reporting transposons (SRTs) and use them in single-cell calling cards (scCC), a novel assay for simultaneously measuring gene expression and mapping TFBS in single cells. The genomic locations of SRTs are recovered from mRNA, and SRTs deposited by exogenous, TF-transposase fusions can be used to map TFBS. We then present scCC, which map SRTs from scRNA-seq libraries, simultaneously identifying cell types and TFBS in those same cells. We benchmark multiple TFs with this technique. Next, we use scCC to discover BRD4-mediated cell-state transitions in K562 cells. Finally, we map BRD4 binding sites in the mouse cortex at single-cell resolution, establishing a new method for studying TF biology in situ.
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Affiliation(s)
- Arnav Moudgil
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Medical Scientist Training Program, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Michael N Wilkinson
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Xuhua Chen
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - June He
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Alexander J Cammack
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Michael J Vasek
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Tomás Lagunas
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Zongtai Qi
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Matthew A Lalli
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Chuner Guo
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Medical Scientist Training Program, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Samantha A Morris
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Joseph D Dougherty
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Robi D Mitra
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA.
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25
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Abstract
ABSTRACT
Fueled by recent advances in single cell biology, we are moving away from qualitative and undersampled assessments of cell identity, toward building quantitative, high-resolution cell atlases. However, it remains challenging to precisely define cell identity, leading to renewed debate surrounding this concept. Here, I present three pillars that I propose are central to the notion of cell identity: phenotype, lineage and state. I explore emerging technologies that are enabling the systematic and unbiased quantification of these properties, and outline how these efforts will enable the construction of a high-resolution, dynamic landscape of cell identity, potentially revealing its underlying molecular regulation to provide new opportunities for understanding and manipulating cell fate.
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Affiliation(s)
- Samantha A. Morris
- Department of Developmental Biology, Washington University School of Medicine in St Louis, St Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine in St Louis, St Louis, MO 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine in St Louis, St Louis, MO 63110, USA
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26
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Abstract
Here, we outline p-Creode, a new algorithm to construct multi-branching cell lineage trajectories from single-cell data. Application of this platform to diverse sources of single-cell data demonstrates its robustness and scalability, while the discovery of a new origin for rare gut tuft cells showcases the utility of p-Creode.
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Affiliation(s)
- Kenji Kamimoto
- Department of Developmental Biology, Washington University School of Medicine in St. Louis. 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine in St. Louis. 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis. 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA
| | - Samantha A Morris
- Department of Developmental Biology, Washington University School of Medicine in St. Louis. 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine in St. Louis. 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis. 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA.
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Seiler KM, Waye SE, Kong W, Kamimoto K, Bajinting A, Goo WH, Onufer EJ, Courtney C, Guo J, Warner BW, Morris SA. Single-Cell Analysis Reveals Regional Reprogramming During Adaptation to Massive Small Bowel Resection in Mice. Cell Mol Gastroenterol Hepatol 2019; 8:407-426. [PMID: 31195149 PMCID: PMC6718927 DOI: 10.1016/j.jcmgh.2019.06.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 05/29/2019] [Accepted: 06/03/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS The small intestine (SI) displays regionality in nutrient and immunological function. Following SI tissue loss (as occurs in short gut syndrome, or SGS), remaining SI must compensate, or "adapt"; the capacity of SI epithelium to reprogram its regional identity has not been described. Here, we apply single-cell resolution analyses to characterize molecular changes underpinning adaptation to SGS. METHODS Single-cell RNA sequencing was performed on epithelial cells isolated from distal SI of mice following 50% proximal small bowel resection (SBR) vs sham surgery. Single-cell profiles were clustered based on transcriptional similarity, reconstructing differentiation events from intestinal stem cells (ISCs) through to mature enterocytes. An unsupervised computational approach to score cell identity was used to quantify changes in regional (proximal vs distal) SI identity, validated using immunofluorescence, immunohistochemistry, qPCR, western blotting, and RNA-FISH. RESULTS Uniform Manifold Approximation and Projection-based clustering and visualization revealed differentiation trajectories from ISCs to mature enterocytes in sham and SBR. Cell identity scoring demonstrated segregation of enterocytes by regional SI identity: SBR enterocytes assumed more mature proximal identities. This was associated with significant upregulation of lipid metabolism and oxidative stress gene expression, which was validated via orthogonal analyses. Observed upstream transcriptional changes suggest retinoid metabolism and proximal transcription factor Creb3l3 drive proximalization of cell identity in response to SBR. CONCLUSIONS Adaptation to proximal SBR involves regional reprogramming of ileal enterocytes toward a proximal identity. Interventions bolstering the endogenous reprogramming capacity of SI enterocytes-conceivably by engaging the retinoid metabolism pathway-merit further investigation, as they may increase enteral feeding tolerance, and obviate intestinal failure, in SGS.
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Affiliation(s)
- Kristen M Seiler
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Sarah E Waye
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri; Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Wenjun Kong
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri; Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Kenji Kamimoto
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri; Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Adam Bajinting
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - William H Goo
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Emily J Onufer
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Cathleen Courtney
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Jun Guo
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Brad W Warner
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Samantha A Morris
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri; Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri.
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Guo C, Kong W, Kamimoto K, Rivera-Gonzalez GC, Yang X, Kirita Y, Morris SA. CellTag Indexing: genetic barcode-based sample multiplexing for single-cell genomics. Genome Biol 2019; 20:90. [PMID: 31072405 PMCID: PMC6509836 DOI: 10.1186/s13059-019-1699-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 04/23/2019] [Indexed: 12/15/2022] Open
Abstract
High-throughput single-cell assays increasingly require special consideration in experimental design, sample multiplexing, batch effect removal, and data interpretation. Here, we describe a lentiviral barcode-based multiplexing approach, CellTag Indexing, which uses predefined genetic barcodes that are heritable, enabling cell populations to be tagged, pooled, and tracked over time in the same experimental replicate. We demonstrate the utility of CellTag Indexing by sequencing transcriptomes using a variety of cell types, including long-term tracking of cell engraftment and differentiation in vivo. Together, this presents CellTag Indexing as a broadly applicable genetic multiplexing tool that is complementary with existing single-cell technologies.
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Affiliation(s)
- Chuner Guo
- Department of Developmental Biology, Washington University School of Medicine in St Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
| | - Wenjun Kong
- Department of Developmental Biology, Washington University School of Medicine in St Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
| | - Kenji Kamimoto
- Department of Developmental Biology, Washington University School of Medicine in St Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
| | - Guillermo C Rivera-Gonzalez
- Department of Developmental Biology, Washington University School of Medicine in St Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
| | - Xue Yang
- Department of Developmental Biology, Washington University School of Medicine in St Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
| | - Yuhei Kirita
- Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Division of Nephrology, Department of Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
| | - Samantha A Morris
- Department of Developmental Biology, Washington University School of Medicine in St Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA.
- Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA.
- Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA.
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Guo C, Kong W, Kamimoto K, Rivera-Gonzalez GC, Yang X, Kirita Y, Morris SA. CellTag Indexing: genetic barcode-based sample multiplexing for single-cell genomics. Genome Biol 2019. [PMID: 31072405 DOI: 10.1101/335547] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023] Open
Abstract
High-throughput single-cell assays increasingly require special consideration in experimental design, sample multiplexing, batch effect removal, and data interpretation. Here, we describe a lentiviral barcode-based multiplexing approach, CellTag Indexing, which uses predefined genetic barcodes that are heritable, enabling cell populations to be tagged, pooled, and tracked over time in the same experimental replicate. We demonstrate the utility of CellTag Indexing by sequencing transcriptomes using a variety of cell types, including long-term tracking of cell engraftment and differentiation in vivo. Together, this presents CellTag Indexing as a broadly applicable genetic multiplexing tool that is complementary with existing single-cell technologies.
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Affiliation(s)
- Chuner Guo
- Department of Developmental Biology, Washington University School of Medicine in St Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
| | - Wenjun Kong
- Department of Developmental Biology, Washington University School of Medicine in St Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
| | - Kenji Kamimoto
- Department of Developmental Biology, Washington University School of Medicine in St Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
| | - Guillermo C Rivera-Gonzalez
- Department of Developmental Biology, Washington University School of Medicine in St Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
| | - Xue Yang
- Department of Developmental Biology, Washington University School of Medicine in St Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
| | - Yuhei Kirita
- Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Division of Nephrology, Department of Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
| | - Samantha A Morris
- Department of Developmental Biology, Washington University School of Medicine in St Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA.
- Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA.
- Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA.
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Morris SA. Pinpointing a spatial address for RNA profiles in tissues. Nature 2019; 569:197-199. [DOI: 10.1038/d41586-019-01405-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Belfort MA, Morris SA, Espinoza J, Shamshirsaz AA, Sanz Cortes M, Justino H, Ayres NA, Qureshi AM. Thulium laser-assisted atrial septal stent placement: first use in fetal hypoplastic left heart syndrome and intact atrial septum. Ultrasound Obstet Gynecol 2019; 53:417-418. [PMID: 30353586 DOI: 10.1002/uog.20161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 08/16/2018] [Indexed: 06/08/2023]
Affiliation(s)
- M A Belfort
- Departments of Obstetrics and Gynecology, Division of Fetal Therapy and Surgery, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas, USA
| | - S A Morris
- Department of Pediatrics, Division of Pediatric Cardiology, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas, USA
| | - J Espinoza
- Departments of Obstetrics and Gynecology, Division of Fetal Therapy and Surgery, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas, USA
| | - A A Shamshirsaz
- Departments of Obstetrics and Gynecology, Division of Fetal Therapy and Surgery, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas, USA
| | - M Sanz Cortes
- Departments of Obstetrics and Gynecology, Division of Fetal Therapy and Surgery, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas, USA
| | - H Justino
- Department of Pediatrics, Division of Pediatric Cardiology, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas, USA
| | - N A Ayres
- Department of Pediatrics, Division of Pediatric Cardiology, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas, USA
| | - A M Qureshi
- Department of Pediatrics, Division of Pediatric Cardiology, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas, USA
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Biddy BA, Kong W, Kamimoto K, Guo C, Waye SE, Sun T, Morris SA. Single-cell mapping of lineage and identity in direct reprogramming. Nature 2018; 564:219-224. [PMID: 30518857 PMCID: PMC6635140 DOI: 10.1038/s41586-018-0744-4] [Citation(s) in RCA: 194] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 10/03/2018] [Indexed: 12/19/2022]
Abstract
Direct lineage reprogramming involves the conversion of cellular identity. Single-cell technologies are useful for deconstructing the considerable heterogeneity that emerges during lineage conversion. However, lineage relationships are typically lost during cell processing, complicating trajectory reconstruction. Here we present 'CellTagging', a combinatorial cell-indexing methodology that enables parallel capture of clonal history and cell identity, in which sequential rounds of cell labelling enable the construction of multi-level lineage trees. CellTagging and longitudinal tracking of fibroblast to induced endoderm progenitor reprogramming reveals two distinct trajectories: one leading to successfully reprogrammed cells, and one leading to a 'dead-end' state, paths determined in the earliest stages of lineage conversion. We find that expression of a putative methyltransferase, Mettl7a1, is associated with the successful reprogramming trajectory; adding Mettl7a1 to the reprogramming cocktail increases the yield of induced endoderm progenitors. Together, these results demonstrate the utility of our lineage-tracing method for revealing the dynamics of direct reprogramming.
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Affiliation(s)
- Brent A Biddy
- Department of Developmental Biology, Washington University School of Medicine in St Louis, St Louis, MO, USA
- Department of Genetics, Washington University School of Medicine in St Louis, St Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine in St Louis, St Louis, MO, USA
| | - Wenjun Kong
- Department of Developmental Biology, Washington University School of Medicine in St Louis, St Louis, MO, USA
- Department of Genetics, Washington University School of Medicine in St Louis, St Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine in St Louis, St Louis, MO, USA
| | - Kenji Kamimoto
- Department of Developmental Biology, Washington University School of Medicine in St Louis, St Louis, MO, USA
- Department of Genetics, Washington University School of Medicine in St Louis, St Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine in St Louis, St Louis, MO, USA
| | - Chuner Guo
- Department of Developmental Biology, Washington University School of Medicine in St Louis, St Louis, MO, USA
- Department of Genetics, Washington University School of Medicine in St Louis, St Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine in St Louis, St Louis, MO, USA
| | - Sarah E Waye
- Department of Developmental Biology, Washington University School of Medicine in St Louis, St Louis, MO, USA
- Department of Genetics, Washington University School of Medicine in St Louis, St Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine in St Louis, St Louis, MO, USA
| | - Tao Sun
- Department of Developmental Biology, Washington University School of Medicine in St Louis, St Louis, MO, USA
- Department of Genetics, Washington University School of Medicine in St Louis, St Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine in St Louis, St Louis, MO, USA
- Nanomedicine Research Center, Department of Neurosurgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Samantha A Morris
- Department of Developmental Biology, Washington University School of Medicine in St Louis, St Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine in St Louis, St Louis, MO, USA.
- Center of Regenerative Medicine, Washington University School of Medicine in St Louis, St Louis, MO, USA.
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Wu H, Uchimura K, Donnelly EL, Kirita Y, Morris SA, Humphreys BD. Comparative Analysis and Refinement of Human PSC-Derived Kidney Organoid Differentiation with Single-Cell Transcriptomics. Cell Stem Cell 2018; 23:869-881.e8. [PMID: 30449713 DOI: 10.1016/j.stem.2018.10.010] [Citation(s) in RCA: 337] [Impact Index Per Article: 56.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 08/09/2018] [Accepted: 10/06/2018] [Indexed: 12/18/2022]
Abstract
Kidney organoids derived from human pluripotent stem cells have great utility for investigating organogenesis and disease mechanisms and, potentially, as a replacement tissue source, but how closely organoids derived from current protocols replicate adult human kidney is undefined. We compared two directed differentiation protocols by single-cell transcriptomics of 83,130 cells from 65 organoids with single-cell transcriptomes of fetal and adult kidney cells. Both protocols generate a diverse range of kidney cells with differing ratios, but organoid-derived cell types are immature, and 10%-20% of cells are non-renal. Reconstructing lineage relationships by pseudotemporal ordering identified ligands, receptors, and transcription factor networks associated with fate decisions. Brain-derived neurotrophic factor (BDNF) and its cognate receptor NTRK2 were expressed in the neuronal lineage during organoid differentiation. Inhibiting this pathway improved organoid formation by reducing neurons by 90% without affecting kidney differentiation, highlighting the power of single-cell technologies to characterize and improve organoid differentiation.
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Affiliation(s)
- Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Kohei Uchimura
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Erinn L Donnelly
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Yuhei Kirita
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Samantha A Morris
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA.
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Abstract
We know a great deal about the development of the mammalian embryo until the time that the blastocyst implants into the uterus. With model organisms such as the mouse, we have also developed a considerable understanding of development immediately around gastrulation as embryos can be recovered at this stage for short-term in vitro culture. However, the intervening period of development remained a ‘black box’ because it takes place as the blastocyst is implanting into the uterus. Over the past 6 years, techniques pioneered and developed in Magdalena Zernicka-Goetz's laboratory for the in vitro culture of embryos through these implantation stages have opened up this box, affording the first glimpse of embryonic development through these previously hidden stages. Remarkably, the techniques developed with mouse embryos are equally applicable to human embryos, ushering the very first opportunities for studying our own development throughout this time. Here, I outline how the culture methods were developed, paving the way to culture of the human embryo to the point of gastrulation, an accomplishment recognized as the People's Choice for the Scientific Breakthrough of 2016 in Science magazine. I also discuss the new ethical challenges raised by the possibility of extending the time limits for human embryo culture.
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Affiliation(s)
- Samantha A Morris
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA .,Department of Genetics, Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA
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Lara DA, Morris SA, Maskatia SA, Becker J, Challman M, Nguyen M, Feagin DK, Schoppe L, Zhang J, Bhatt A, Sexson-Tejtel SK, Lopez KN, Lawrence EJ, Andreas S, Wang Y, Belfort MA, Ruano R, Ayres NA, Altman CA, Aagaard KM. Reply. Ultrasound Obstet Gynecol 2016; 48:405-406. [PMID: 27593405 DOI: 10.1002/uog.15909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Affiliation(s)
- D A Lara
- Division of Pediatric Cardiology, Baylor College of Medicine, Texas Children's Hospital, 6621 Fannin St., MC 19345-C, Houston, TX, 77030, USA
- Fetal Center, Texas Children's Hospital, Houston, TX, USA
| | - S A Morris
- Division of Pediatric Cardiology, Baylor College of Medicine, Texas Children's Hospital, 6621 Fannin St., MC 19345-C, Houston, TX, 77030, USA
- Fetal Center, Texas Children's Hospital, Houston, TX, USA
| | - S A Maskatia
- Division of Pediatric Cardiology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - J Becker
- Division of Pediatric Cardiology, Baylor College of Medicine, Texas Children's Hospital, 6621 Fannin St., MC 19345-C, Houston, TX, 77030, USA
- Fetal Center, Texas Children's Hospital, Houston, TX, USA
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Lara DA, Morris SA, Maskatia SA, Challman M, Nguyen M, Feagin DK, Schoppe L, Zhang J, Bhatt A, Sexson-Tejtel SK, Lopez KN, Lawrence EJ, Andreas S, Wang Y, Belfort MA, Ruano R, Ayres NA, Altman CA, Aagaard KM, Becker J. Pilot study of chronic maternal hyperoxygenation and effect on aortic and mitral valve annular dimensions in fetuses with left heart hypoplasia. Ultrasound Obstet Gynecol 2016; 48:365-372. [PMID: 26700848 DOI: 10.1002/uog.15846] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 12/14/2015] [Accepted: 12/18/2015] [Indexed: 06/05/2023]
Abstract
OBJECTIVE Acute maternal hyperoxygenation (AMH) results in increased fetal left heart blood flow. Our aim was to perform a pilot study to determine the safety, feasibility and direction and magnitude of effect of chronic maternal hyperoxygenation (CMH) on mitral and aortic valve annular dimensions in fetuses with left heart hypoplasia (LHH) after CMH. METHODS Gravidae with fetal LHH were eligible for inclusion in a prospective evaluation of CMH. LHH was defined as: sum of aortic and mitral valve annuli Z-scores < -4.5, arch flow reversal and left-to-right or bidirectional atrial level shunting without hypoplastic left heart syndrome or severe aortic stenosis. Gravidae with an affected fetus and with ≥ 10% increase in aortic/combined cardiac output flow after 10 min of AMH at 8 L/min 100% fraction of inspired oxygen were offered enrollment. Nine gravidae were enrolled from February 2014 to January 2015. The goal therapy was ≥ 8 h daily CMH from enrollment until delivery. Gravidae who were cared for from July 2012 to October 2014 with fetal LHH and no CMH were identified as historical controls (n = 9). Rates of growth in aortic and mitral annuli over the final trimester were compared between groups using longitudinal regression. RESULTS There were no significant maternal or fetal complications in the CMH cohort. Mean gestational age at study initiation was 29.6 ± 3.2 weeks for the intervention group and 28.4 ± 1.8 weeks for controls (P = 0.35). Mean relative increase in aortic/combined cardiac output after AMH was 35.3% (range, 18.1-47.9%). Median number of hours per day on CMH therapy was 9.3 (range, 6.5-14.6) and median duration of CMH was 48 (range, 33-84) days. Mean mitral annular growth was 0.19 ± 0.05 mm/week compared with 0.14 ± 0.05 mm/week in CMH vs controls (mean difference 0.05 ± 0.05 mm/week, P = 0.33). Mean aortic annular growth was 0.14 ± 0.03 mm/week compared with 0.13 ± 0.03 mm/week in CMH vs controls (mean difference 0.01 ± 0.03 mm/week, P = 0.75). More than 9 h CMH daily (n = 6) was associated with better growth of the aortic annulus in intervention fetuses (0.16 ± 0.03 vs 0.08 ± 0.02 mm/week, P = 0.014). CONCLUSIONS CMH is both safe and feasible for continued research. In this pilot study, the effect estimates of annular growth, using the studied method of delivery and dose of oxygen, were small. Copyright © 2015 ISUOG. Published by John Wiley & Sons Ltd.
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Affiliation(s)
- D A Lara
- Division of Pediatric Cardiology, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | - S A Morris
- Division of Pediatric Cardiology, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | - S A Maskatia
- Division of Pediatric Cardiology, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
- Texas Children's Fetal Center, Texas Children's Hospital, Houston, TX, USA
| | - M Challman
- Division of Pediatric Cardiology, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | - M Nguyen
- Texas Children's Fetal Center, Texas Children's Hospital, Houston, TX, USA
| | - D K Feagin
- Division of Pediatric Cardiology, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | - L Schoppe
- Texas Children's Fetal Center, Texas Children's Hospital, Houston, TX, USA
| | - J Zhang
- Division of Pediatric Cardiology, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
- Texas Children's Fetal Center, Texas Children's Hospital, Houston, TX, USA
| | - A Bhatt
- Department of Ophthalmology, Baylor College of Medicine, Houston, TX, USA
| | - S K Sexson-Tejtel
- Division of Pediatric Cardiology, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | - K N Lopez
- Division of Pediatric Cardiology, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | - E J Lawrence
- Division of Pediatric Cardiology, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | - S Andreas
- Division of Pediatric Cardiology, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | - Y Wang
- Division of Pediatric Cardiology, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | - M A Belfort
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA
| | - R Ruano
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA
| | - N A Ayres
- Division of Pediatric Cardiology, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | - C A Altman
- Division of Pediatric Cardiology, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | - K M Aagaard
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA
| | - J Becker
- Division of Pediatric Cardiology, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
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Abstract
Although many approaches have been employed to generate defined fate in vitro, the resultant cells often appear developmentally immature or incompletely specified, limiting their utility. Growing evidence suggests that current methods of direct lineage conversion may rely on the transition through a developmental intermediate. Here, I hypothesize that complete conversion between cell fates is more probable and feasible via reversion to a developmentally immature state. I posit that this is due to the role of pioneer transcription factors in engaging silent, unmarked chromatin and activating hierarchical gene regulatory networks responsible for embryonic patterning. Understanding these developmental contexts will be essential for the precise engineering of cell identity.
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Affiliation(s)
- Samantha A Morris
- Departments of Developmental Biology and Genetics, Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA
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Wallace S, Guo DC, Regalado E, Mellor-Crummey L, Bamshad M, Nickerson DA, Dauser R, Hanchard N, Marom R, Martin E, Berka V, Sharina I, Ganesan V, Saunders D, Morris SA, Milewicz DM. Disrupted nitric oxide signaling due to GUCY1A3 mutations increases risk for moyamoya disease, achalasia and hypertension. Clin Genet 2016; 90:351-60. [PMID: 26777256 DOI: 10.1111/cge.12739] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/11/2016] [Accepted: 01/13/2016] [Indexed: 12/23/2022]
Abstract
Moyamoya disease (MMD) is a progressive vasculopathy characterized by occlusion of the terminal portion of the internal carotid arteries and its branches, and the formation of compensatory moyamoya collateral vessels. Homozygous mutations in GUCY1A3 have been reported as a cause of MMD and achalasia. Probands (n = 96) from unrelated families underwent sequencing of GUCY1A3. Functional studies were performed to confirm the pathogenicity of identified GUCY1A3 variants. Two affected individuals from the unrelated families were found to have compound heterozygous mutations in GUCY1A3. MM041 was diagnosed with achalasia at 4 years of age, hypertension and MMD at 18 years of age. MM149 was diagnosed with MMD and hypertension at the age of 20 months. Both individuals carry one allele that is predicted to lead to haploinsufficiency and a second allele that is predicted to produce a mutated protein. Biochemical studies of one of these alleles, GUCY1A3 Cys517Tyr, showed that the mutant protein (a subunit of soluble guanylate cyclase) has a significantly blunted signaling response with exposure to nitric oxide (NO). GUCY1A3 missense and haploinsufficiency mutations disrupt NO signaling leading to MMD and hypertension, with or without achalasia.
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Affiliation(s)
- S Wallace
- Division of Medical Genetics, Cardiology, and Hematology, Department of Internal Medicine, University of Texas Health Science Center, Houston, TX, USA
| | - D-C Guo
- Division of Medical Genetics, Cardiology, and Hematology, Department of Internal Medicine, University of Texas Health Science Center, Houston, TX, USA
| | - E Regalado
- Division of Medical Genetics, Cardiology, and Hematology, Department of Internal Medicine, University of Texas Health Science Center, Houston, TX, USA
| | - L Mellor-Crummey
- Division of Medical Genetics, Cardiology, and Hematology, Department of Internal Medicine, University of Texas Health Science Center, Houston, TX, USA
| | - M Bamshad
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - D A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - R Dauser
- Department of Neurosurgery, Texas Children's Hospital, Houston, TX, USA
| | - N Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - R Marom
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - E Martin
- Division of Medical Genetics, Cardiology, and Hematology, Department of Internal Medicine, University of Texas Health Science Center, Houston, TX, USA
| | - V Berka
- Division of Medical Genetics, Cardiology, and Hematology, Department of Internal Medicine, University of Texas Health Science Center, Houston, TX, USA
| | - I Sharina
- Division of Medical Genetics, Cardiology, and Hematology, Department of Internal Medicine, University of Texas Health Science Center, Houston, TX, USA
| | - V Ganesan
- Neuroscience Unit, University College of London Institute of Child Health, London, UK
| | - D Saunders
- Department of Radiology, Great Ormond Street Hospital, London, UK
| | - S A Morris
- Department of Pediatrics - Cardiology, Texas Children's Hospital and Baylor College of Medicine, Houston, TX, USA
| | - D M Milewicz
- Division of Medical Genetics, Cardiology, and Hematology, Department of Internal Medicine, University of Texas Health Science Center, Houston, TX, USA.
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40
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Affiliation(s)
- Patrick Cahan
- a Stem Cell Transplantation Program; Division of Pediatric Hematology/Oncology ; Manton Center for Orphan Disease Research ; Howard Hughes Medical Institute; Children's Hospital Boston and Dana Farber Cancer Institute ; Division of Hematology ; Brigham and Women's Hospital ; Boston , MA USA
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Diaz MF, Li N, Lee HJ, Adamo L, Evans SM, Willey HE, Arora N, Torisawa YS, Vickers DA, Morris SA, Naveiras O, Murthy SK, Ingber DE, Daley GQ, García-Cardeña G, Wenzel PL. Biomechanical forces promote blood development through prostaglandin E 2and the cAMP–PKA signaling axis. J Gen Physiol 2015. [DOI: 10.1085/jgp.1455oia20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Diaz MF, Li N, Lee HJ, Adamo L, Evans SM, Willey HE, Arora N, Torisawa YS, Vickers DA, Morris SA, Naveiras O, Murthy SK, Ingber DE, Daley GQ, García-Cardeña G, Wenzel PL. Biomechanical forces promote blood development through prostaglandin E 2and the cAMP–PKA signaling axis. J Biophys Biochem Cytol 2015. [DOI: 10.1083/jcb.2092oia69] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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43
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Diaz MF, Li N, Lee HJ, Adamo L, Evans SM, Willey HE, Arora N, Torisawa YS, Vickers DA, Morris SA, Naveiras O, Murthy SK, Ingber DE, Daley GQ, García-Cardeña G, Wenzel PL. Biomechanical forces promote blood development through prostaglandin E2 and the cAMP-PKA signaling axis. ACTA ACUST UNITED AC 2015; 212:665-80. [PMID: 25870199 PMCID: PMC4419354 DOI: 10.1084/jem.20142235] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/17/2015] [Indexed: 12/12/2022]
Abstract
Blood flow promotes emergence of definitive hematopoietic stem cells (HSCs) in the developing embryo, yet the signals generated by hemodynamic forces that influence hematopoietic potential remain poorly defined. Here we show that fluid shear stress endows long-term multilineage engraftment potential upon early hematopoietic tissues at embryonic day 9.5, an embryonic stage not previously described to harbor HSCs. Effects on hematopoiesis are mediated in part by a cascade downstream of wall shear stress that involves calcium efflux and stimulation of the prostaglandin E2 (PGE2)-cyclic adenosine monophosphate (cAMP)-protein kinase A (PKA) signaling axis. Blockade of the PGE2-cAMP-PKA pathway in the aorta-gonad-mesonephros (AGM) abolished enhancement in hematopoietic activity. Furthermore, Ncx1 heartbeat mutants, as well as static cultures of AGM, exhibit lower levels of expression of prostaglandin synthases and reduced phosphorylation of the cAMP response element-binding protein (CREB). Similar to flow-exposed cultures, transient treatment of AGM with the synthetic analogue 16,16-dimethyl-PGE2 stimulates more robust engraftment of adult recipients and greater lymphoid reconstitution. These data provide one mechanism by which biomechanical forces induced by blood flow modulate hematopoietic potential.
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Affiliation(s)
- Miguel F Diaz
- Program in Children's Regenerative Medicine, Department of Pediatric Surgery, Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine, and Immunology Program, Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030 Program in Children's Regenerative Medicine, Department of Pediatric Surgery, Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine, and Immunology Program, Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030 Program in Children's Regenerative Medicine, Department of Pediatric Surgery, Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine, and Immunology Program, Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030
| | - Nan Li
- Program in Children's Regenerative Medicine, Department of Pediatric Surgery, Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine, and Immunology Program, Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030 Program in Children's Regenerative Medicine, Department of Pediatric Surgery, Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine, and Immunology Program, Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030 Program in Children's Regenerative Medicine, Department of Pediatric Surgery, Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine, and Immunology Program, Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030
| | - Hyun Jung Lee
- Program in Children's Regenerative Medicine, Department of Pediatric Surgery, Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine, and Immunology Program, Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030 Program in Children's Regenerative Medicine, Department of Pediatric Surgery, Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine, and Immunology Program, Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030 Program in Children's Regenerative Medicine, Department of Pediatric Surgery, Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine, and Immunology Program, Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030
| | - Luigi Adamo
- Center for Excellence in Vascular Biology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Siobahn M Evans
- Program in Children's Regenerative Medicine, Department of Pediatric Surgery, Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine, and Immunology Program, Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030 Program in Children's Regenerative Medicine, Department of Pediatric Surgery, Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine, and Immunology Program, Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030 Program in Children's Regenerative Medicine, Department of Pediatric Surgery, Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine, and Immunology Program, Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030
| | - Hannah E Willey
- Department of Bioengineering, Rice University, Houston, TX 77030
| | - Natasha Arora
- Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Manton Center for Orphan Disease Research, and Howard Hughes Medical Institute, Children's Hospital Boston and Dana-Farber Cancer Institute, Boston, MA 02115 Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Manton Center for Orphan Disease Research, and Howard Hughes Medical Institute, Children's Hospital Boston and Dana-Farber Cancer Institute, Boston, MA 02115 Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Manton Center for Orphan Disease Research, and Howard Hughes Medical Institute, Children's Hospital Boston and Dana-Farber Cancer Institute, Boston, MA 02115 Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Manton Center for Orphan Disease Research, and Howard Hughes Medical Institute, Children's Hospital Boston and Dana-Farber Cancer Institute, Boston, MA 02115 Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 Harvard Stem Cell Institute and School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138
| | - Yu-Suke Torisawa
- Harvard Stem Cell Institute and School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138 Wyss Institute for Biologically Inspired Engineering at Harvard University and Vascular Biology Program, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115 Wyss Institute for Biologically Inspired Engineering at Harvard University and Vascular Biology Program, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115
| | - Dwayne A Vickers
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA 02115
| | - Samantha A Morris
- Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Manton Center for Orphan Disease Research, and Howard Hughes Medical Institute, Children's Hospital Boston and Dana-Farber Cancer Institute, Boston, MA 02115 Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Manton Center for Orphan Disease Research, and Howard Hughes Medical Institute, Children's Hospital Boston and Dana-Farber Cancer Institute, Boston, MA 02115 Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Manton Center for Orphan Disease Research, and Howard Hughes Medical Institute, Children's Hospital Boston and Dana-Farber Cancer Institute, Boston, MA 02115 Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Manton Center for Orphan Disease Research, and Howard Hughes Medical Institute, Children's Hospital Boston and Dana-Farber Cancer Institute, Boston, MA 02115 Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 Harvard Stem Cell Institute and School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138
| | - Olaia Naveiras
- Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Manton Center for Orphan Disease Research, and Howard Hughes Medical Institute, Children's Hospital Boston and Dana-Farber Cancer Institute, Boston, MA 02115 Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Manton Center for Orphan Disease Research, and Howard Hughes Medical Institute, Children's Hospital Boston and Dana-Farber Cancer Institute, Boston, MA 02115 Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Manton Center for Orphan Disease Research, and Howard Hughes Medical Institute, Children's Hospital Boston and Dana-Farber Cancer Institute, Boston, MA 02115 Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Manton Center for Orphan Disease Research, and Howard Hughes Medical Institute, Children's Hospital Boston and Dana-Farber Cancer Institute, Boston, MA 02115 Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 Harvard Stem Cell Institute and School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138
| | - Shashi K Murthy
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA 02115
| | - Donald E Ingber
- Harvard Stem Cell Institute and School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138 Wyss Institute for Biologically Inspired Engineering at Harvard University and Vascular Biology Program, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115 Wyss Institute for Biologically Inspired Engineering at Harvard University and Vascular Biology Program, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115
| | - George Q Daley
- Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Manton Center for Orphan Disease Research, and Howard Hughes Medical Institute, Children's Hospital Boston and Dana-Farber Cancer Institute, Boston, MA 02115 Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Manton Center for Orphan Disease Research, and Howard Hughes Medical Institute, Children's Hospital Boston and Dana-Farber Cancer Institute, Boston, MA 02115 Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Manton Center for Orphan Disease Research, and Howard Hughes Medical Institute, Children's Hospital Boston and Dana-Farber Cancer Institute, Boston, MA 02115 Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Manton Center for Orphan Disease Research, and Howard Hughes Medical Institute, Children's Hospital Boston and Dana-Farber Cancer Institute, Boston, MA 02115 Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 Harvard Stem Cell Institute and School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138
| | - Guillermo García-Cardeña
- Center for Excellence in Vascular Biology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115 Harvard Stem Cell Institute and School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138
| | - Pamela L Wenzel
- Program in Children's Regenerative Medicine, Department of Pediatric Surgery, Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine, and Immunology Program, Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030 Program in Children's Regenerative Medicine, Department of Pediatric Surgery, Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine, and Immunology Program, Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030 Program in Children's Regenerative Medicine, Department of Pediatric Surgery, Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine, and Immunology Program, Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030
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Cahan P, Li H, Morris SA, Lummertz da Rocha E, Daley GQ, Collins JJ. CellNet: network biology applied to stem cell engineering. Cell 2014; 158:903-915. [PMID: 25126793 DOI: 10.1016/j.cell.2014.07.020] [Citation(s) in RCA: 369] [Impact Index Per Article: 36.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 05/28/2014] [Accepted: 07/17/2014] [Indexed: 02/07/2023]
Abstract
Somatic cell reprogramming, directed differentiation of pluripotent stem cells, and direct conversions between differentiated cell lineages represent powerful approaches to engineer cells for research and regenerative medicine. We have developed CellNet, a network biology platform that more accurately assesses the fidelity of cellular engineering than existing methodologies and generates hypotheses for improving cell derivations. Analyzing expression data from 56 published reports, we found that cells derived via directed differentiation more closely resemble their in vivo counterparts than products of direct conversion, as reflected by the establishment of target cell-type gene regulatory networks (GRNs). Furthermore, we discovered that directly converted cells fail to adequately silence expression programs of the starting population and that the establishment of unintended GRNs is common to virtually every cellular engineering paradigm. CellNet provides a platform for quantifying how closely engineered cell populations resemble their target cell type and a rational strategy to guide enhanced cellular engineering.
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Affiliation(s)
- Patrick Cahan
- Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Hu Li
- Center for Individualized Medicine, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Samantha A Morris
- Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Edroaldo Lummertz da Rocha
- Howard Hughes Medical Institute, Department of Biomedical Engineering and Center of Synthetic Biology, Boston University, Boston, MA 02215, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Graduate Program in Materials Science and Engineering, Federal University of Santa Catarina, 88040-900 Florianópolis, Brazil
| | - George Q Daley
- Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
| | - James J Collins
- Howard Hughes Medical Institute, Department of Biomedical Engineering and Center of Synthetic Biology, Boston University, Boston, MA 02215, USA.
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Morris SA, Cahan P, Li H, Zhao AM, San Roman AK, Shivdasani RA, Collins JJ, Daley GQ. Dissecting engineered cell types and enhancing cell fate conversion via CellNet. Cell 2014; 158:889-902. [PMID: 25126792 DOI: 10.1016/j.cell.2014.07.021] [Citation(s) in RCA: 194] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 05/28/2014] [Accepted: 07/17/2014] [Indexed: 12/16/2022]
Abstract
Engineering clinically relevant cells in vitro holds promise for regenerative medicine, but most protocols fail to faithfully recapitulate target cell properties. To address this, we developed CellNet, a network biology platform that determines whether engineered cells are equivalent to their target tissues, diagnoses aberrant gene regulatory networks, and prioritizes candidate transcriptional regulators to enhance engineered conversions. Using CellNet, we improved B cell to macrophage conversion, transcriptionally and functionally, by knocking down predicted B cell regulators. Analyzing conversion of fibroblasts to induced hepatocytes (iHeps), CellNet revealed an unexpected intestinal program regulated by the master regulator Cdx2. We observed long-term functional engraftment of mouse colon by iHeps, thereby establishing their broader potential as endoderm progenitors and demonstrating direct conversion of fibroblasts into intestinal epithelium. Our studies illustrate how CellNet can be employed to improve direct conversion and to uncover unappreciated properties of engineered cells.
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Affiliation(s)
- Samantha A Morris
- Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Patrick Cahan
- Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Hu Li
- Center for Individualized Medicine, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Anna M Zhao
- Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Adrianna K San Roman
- Department of Medical Oncology Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Ramesh A Shivdasani
- Department of Medical Oncology Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - James J Collins
- Howard Hughes Medical Institute, Department of Biomedical Engineering and Center for BioDynamics, Boston University; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA
| | - George Q Daley
- Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
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Abstract
Unstable bicondylar tibial plateau fractures are rare and there is little guidance in the literature as to the best form of treatment. We examined the short- to medium-term outcome of this injury in a consecutive series of patients presenting to two trauma centres. Between December 2005 and May 2010, a total of 55 fractures in 54 patients were treated by fixation, 34 with peri-articular locking plates and 21 with limited access direct internal fixation in combination with circular external fixation using a Taylor Spatial Frame (TSF). At a minimum of one year post-operatively, patient-reported outcome measures including the WOMAC index and SF-36 scores showed functional deficits, although there was no significant difference between the two forms of treatment. Despite low outcome scores, patients were generally satisfied with the outcome. We achieved good clinical and radiological outcomes, with low rates of complication. In total, only three patients (5%) had collapse of the joint of > 4 mm, and metaphysis to diaphysis angulation of 75º, and five patients (9%) with displacement of > 4 mm. All patients in our study went on to achieve full union. This study highlights the serious nature of this injury and generally poor patient-reported outcome measures following surgery, despite treatment by experienced surgeons using modern surgical techniques. Our findings suggest that treatment of complex bicondylar tibial plateau fractures with either a locking plate or a TSF gives similar clinical and radiological outcomes.
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Affiliation(s)
- N Ahearn
- University Hospitals Bristol NHS Foundation Trust, Bristol Royal Infirmary, Upper Maudlin Street, Bristol BS2 8HW, UK
| | - A Oppy
- Royal Melbourne Hospital, Grattan Street, Parkville, Victoria 3052, Australia
| | - R Halliday
- North Bristol NHS Trust, Frenchay Hospital, Frenchay Park Rd, Bristol, BS16 1LE, UK
| | - J Rowett-Harris
- University Hospitals Bristol NHS Foundation Trust, Bristol Royal Infirmary, Upper Maudlin Street, Bristol BS2 8HW, UK
| | - S A Morris
- North Bristol NHS Trust, Frenchay Hospital, Frenchay Park Rd, Bristol, BS16 1LE, UK
| | - T J Chesser
- North Bristol NHS Trust, Frenchay Hospital, Frenchay Park Rd, Bristol, BS16 1LE, UK
| | - J A Livingstone
- University Hospitals Bristol NHS Foundation Trust, Bristol Royal Infirmary, Upper Maudlin Street, Bristol BS2 8HW, UK
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Morris SA, Graham SJL, Jedrusik A, Zernicka-Goetz M. The differential response to Fgf signalling in cells internalized at different times influences lineage segregation in preimplantation mouse embryos. Open Biol 2013; 3:130104. [PMID: 24258274 PMCID: PMC3843820 DOI: 10.1098/rsob.130104] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Lineage specification in the preimplantation mouse embryo is a regulative process. Thus, it has been difficult to ascertain whether segregation of the inner-cell-mass (ICM) into precursors of the pluripotent epiblast (EPI) and the differentiating primitive endoderm (PE) is random or influenced by developmental history. Here, our results lead to a unifying model for cell fate specification in which the time of internalization and the relative contribution of ICM cells generated by two waves of asymmetric divisions influence cell fate. We show that cells generated in the second wave express higher levels of Fgfr2 than those generated in the first, leading to ICM cells with varying Fgfr2 expression. To test whether such heterogeneity is enough to bias cell fate, we upregulate Fgfr2 and show it directs cells towards PE. Our results suggest that the strength of this bias is influenced by the number of cells generated in the first wave and, mostly likely, by the level of Fgf signalling in the ICM. Differences in the developmental potential of eight-cell- and 16-cell-stage outside blastomeres placed in the inside of chimaeric embryos further support this conclusion. These results unite previous findings demonstrating the importance of developmental history and Fgf signalling in determining cell fate.
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Affiliation(s)
- Samantha A Morris
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
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Collins CT, Reid J, Makrides M, Lingwood BE, McPhee AJ, Morris SA, Gibson RA, Ward LC. Prediction of body water compartments in preterm infants by bioelectrical impedance spectroscopy. Eur J Clin Nutr 2013; 67 Suppl 1:S47-53. [DOI: 10.1038/ejcn.2012.164] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Abstract
Human diseases such as heart failure, diabetes, neurodegenerative disorders, and many others result from the deficiency or dysfunction of critical cell types. Strategies for therapeutic tissue repair or regeneration require the in vitro manufacture of clinically relevant quantities of defined cell types. In addition to transplantation therapy, the generation of otherwise inaccessible cells also permits disease modeling, toxicology testing and drug discovery in vitro. In this review, we discuss current strategies to manipulate the identity of abundant and accessible cells by differentiation from an induced pluripotent state or direct conversion between differentiated states. We contrast these approaches with recent advances employing partial reprogramming to facilitate lineage switching, and discuss the mechanisms underlying the engineering of cell fate. Finally, we address the current limitations of the field and how the resulting cell types can be assessed to ensure the production of medically relevant populations.
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Affiliation(s)
- Samantha A Morris
- Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Children's Hospital Boston and Dana Farber Cancer Institute, Boston, MA, USA
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Jones MR, Blahna MT, Kozlowski E, Matsuura KY, Ferrari JD, Morris SA, Powers JT, Daley GQ, Quinton LJ, Mizgerd JP. Zcchc11 uridylates mature miRNAs to enhance neonatal IGF-1 expression, growth, and survival. PLoS Genet 2012; 8:e1003105. [PMID: 23209448 PMCID: PMC3510031 DOI: 10.1371/journal.pgen.1003105] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 10/04/2012] [Indexed: 11/17/2022] Open
Abstract
The Zcchc11 enzyme is implicated in microRNA (miRNA) regulation. It can uridylate let-7 precursors to decrease quantities of the mature miRNA in embryonic stem cell lines, suggested to mediate stem cell maintenance. It can uridylate mature miR-26 to relieve silencing activity without impacting miRNA content in cancer cell lines, suggested to mediate cytokine and growth factor expression. Broader roles of Zcchc11 in shaping or remodeling the miRNome or in directing biological or physiological processes remain entirely speculative. We generated Zcchc11-deficient mice to address these knowledge gaps. Zcchc11 deficiency had no impact on embryogenesis or fetal development, but it significantly decreased survival and growth immediately following birth, indicating a role for this enzyme in early postnatal fitness. Deep sequencing of small RNAs from neonatal livers revealed roles of this enzyme in miRNA sequence diversity. Zcchc11 deficiency diminished the lengths and terminal uridine frequencies for diverse mature miRNAs, but it had no influence on the quantities of any miRNAs. The expression of IGF-1, a liver-derived protein essential to early growth and survival, was enhanced by Zcchc11 expression in vitro, and miRNA silencing of IGF-1 was alleviated by uridylation events observed to be Zcchc11-dependent in the neonatal liver. In neonatal mice, Zcchc11 deficiency significantly decreased IGF-1 mRNA in the liver and IGF-1 protein in the blood. We conclude that the Zcchc11-mediated terminal uridylation of mature miRNAs is pervasive and physiologically significant, especially important in the neonatal period for fostering IGF-1 expression and enhancing postnatal growth and survival. We propose that the miRNA 3′ terminus is a regulatory node upon which multiple enzymes converge to direct silencing activity and tune gene expression. MicroRNAs (miRNAs) are molecules that regulate gene expression, usually serving silencing functions. Mechanisms regulating miRNAs are poorly understood. In test tube experiments, the enzyme Zcchc11 adds uridines to the ends of miRNAs and their precursors, with uridyation of miRNA precursors decreasing the quantities of mature miRNAs and uridylation of mature miRNAs decreasing their silencing activity. Whether, when, and to what effect Zcchc11 alters miRNA in living animals has never previously been reported. To understand functions of Zcchc11 in integrative biology, we generated mice deficient in Zcchc11. Mutant mice were born normally, but some died soon after birth and survivors grew poorly. No miRNA quantities were changed in tissues sampled from these mice, but mature miRNAs were less likely to have additional uridines on their ends. Some miRNAs that were uridylated by Zcchc11 targeted a critical growth factor known as insulin-like growth factor 1 (IGF-1), but they did so less effectively when uridylated. Zcchc11-deficient mice had decreased amounts of IGF-1 in the liver and blood. These data reveal that Zcchc11 is an important enzyme in living animals for uridylating mature miRNAs, enhancing IGF-1 expression, and promoting neonatal growth and survival, suggesting a novel mode of gene regulation that is biologically significant.
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Affiliation(s)
- Matthew R Jones
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, United States of America
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