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Park SY, Lindner MS, Brick K, Noll N, Ounit R, Noa LJ, Sabzwari R, Trible R, Sniffen JC, Roth P, Khan A, Rodriguez A, Sahra S, Davis MJ, Brar IS, Balasundaram G, Nolte FS, Blauwkamp TA, Perkins BA, Bercovici S. Detection of Mpox Virus Using Microbial Cell-Free DNA: The Potential of Pathogen-Agnostic Sequencing for Rapid Identification of Emerging Pathogens. J Infect Dis 2024; 229:S144-S155. [PMID: 37824825 DOI: 10.1093/infdis/jiad452] [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] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/09/2023] [Accepted: 10/09/2023] [Indexed: 10/14/2023] Open
Abstract
BACKGROUND The 2022 global outbreak of Monkeypox virus (MPXV) highlighted challenges with polymerase chain reaction detection as divergent strains emerged and atypical presentations limited the applicability of swab sampling. Recommended testing in the United States requires a swab of lesions, which arise late in infection and may be unrecognized. We present MPXV detections using plasma microbial cell-free DNA (mcfDNA) sequencing. METHODS Fifteen plasma samples from 12 case-patients were characterized through mcfDNA sequencing. Assay performance was confirmed through in silico inclusivity and exclusivity assessments. MPXV isolates were genotyped using mcfDNA, and phylodynamic information was imputed using publicly available sequences. RESULTS MPXV mcfDNA was detected in 12 case-patients. Mpox was not suspected in 5, with 1 having documented resolution of mpox >6 months previously. Six had moderate to severe mpox, supported by high MPXV mcfDNA concentrations; 4 died. In 7 case-patients, mcfDNA sequencing detected coinfections. Genotyping by mcfDNA sequencing identified 22 MPXV mutations at 10 genomic loci in 9 case-patients. Consistent with variation observed in the 2022 outbreak, 21 of 22 variants were G > A/C > T. Phylogenetic analyses imputed isolates to sublineages arising at different time points and from different geographic locations. CONCLUSIONS We demonstrate the potential of plasma mcfDNA sequencing to detect, quantify, and, for acute infections with high sequencing coverage, subtype MPXV using a single noninvasive test. Sequencing plasma mcfDNA may augment existing mpox testing in vulnerable patient populations or in patients with atypical symptoms or unrecognized mpox. Strain type information may supplement disease surveillance and facilitate tracking emerging pathogens.
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Affiliation(s)
- Sarah Y Park
- Medical Affairs, Karius, Inc, Redwood City, California
| | | | - Kevin Brick
- Analytics, Karius, Inc., Redwood City, California
| | | | - Rachid Ounit
- Analytics, Karius, Inc., Redwood City, California
| | - Luis J Noa
- Infectious Disease Section, AdventHealth Orlando, Florida
| | - Rabeeya Sabzwari
- Infectious Diseases, Edward Hines Jr Veterans Affairs Hospital, Hines, Illinois
| | | | | | - Prerana Roth
- Infectious Diseases, Prisma Health-Upstate, Greenville, South Carolina
| | - Amir Khan
- Infectious Diseases, Carle Foundation Hospital, Urbana, Illinois
| | | | - Syeda Sahra
- Department of Infectious Diseases, Oklahoma University Medical Center, Oklahoma City
| | - Michael J Davis
- Department of Infectious Diseases and International Medicine, University of Minnesota, Minneapolis, MN
| | - Inderjeet S Brar
- Infectious Diseases, Baptist Memorial Health Care, Memphis, Tennessee
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Demirkan G, Merritt C, Hinerfeld D, Ong G, Sorg K, Balasundaram G, Dunaway D, Geiss GK, Beechem JM. Spatially-resolved, multiplexed quantification of protein and mRNA distribution and abundance in colorectal cancer tumor microenvironment with multiple modalities of NanoString GeoMx Digital Spatial Profiler. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.e14218] [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] [Indexed: 11/20/2022] Open
Abstract
e14218 Background: Characterization of the spatial distribution and abundance of proteins and mRNAs with morphological context within tissues enables a better understanding of biological systems in many research areas, including immunology and oncology. However, it has proven difficult to perform such studies in a highly multiplexed manner. To address this unmet need, we have developed a novel optical-barcode based microscope and tissue-sampling platform designed to simultaneously analyze hundreds of proteins or mRNAs on a single FFPE section from distinct tissue spatial regions. Methods: Using colorectal cancer FFPE sections we spatially resolve protein and mRNA expression of immune-oncology targets and present a series of modalities and associated applications for the GeoMx Digital Spatial Profiler platform. Results: Microsatellite stable (MSS) or instable (MSI) colorectal tumors will be characterized to evaluate active and suppressive immune mechanisms in both immune dense regions and tumor versus stroma by utilizing segment profiling. Regions from the invasive margins and tumor centers will be investigated with contour profiling to define different immunosuppressive and activated immune phenotypes. Evaluation of tumor versus stroma will also identify pathways related to each compartment that are different between MSI and MSS tumors. These techniques can be used to discover drug mechanism of action or immune activation status, as well as to facilitate prediction of treatment response and disease progression or investigation of specific rare cell populations’ molecular profiles. Conclusions: This study will demonstrate multiplexed pathway-level protein and gene expression analysis from discrete regions within a colorectal tumor (tumor center and immune invasive margin), enabling systematic interrogation of immune activity in FFPE samples. Further studies could eventually lead to the identification of unique localized immune characteristics to guide combination therapeutic approaches.
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Affiliation(s)
| | | | | | - Giang Ong
- NanoString Technologies, Inc., Seattle, WA
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Dennis L, Danaher P, Eagan M, White A, Elliot N, Ram N, Balasundaram G, Jeiranian A, Kaufmann S, Boykin R, Irving L, Buckingham W, Ferree S, Bailey C, Beechem J. Abstract A49: Building a comprehensive view of tumor biology in breast cancer by combining NanoString's Prosigna assay with the Pancancer Pathways, Immune Profiling, and Progression Panels. Mol Cancer Res 2016. [DOI: 10.1158/1557-3125.advbc15-a49] [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] [Indexed: 11/16/2022]
Abstract
Abstract
Recent advances in molecular profiling of breast cancer have given clinicians the tools required to make better treatment decisions for patients. Building an accurate representation of the biology of a particular tumor is key for: patient selection, therapeutic monitoring, and rational combination therapy design.
The NanoString PanCancer Pathways, PanCancer Immune Profiling and PanCancer Progression Panels enable researchers to quickly analyze the expression of up to 770 genes (per panel) and construct a comprehensive view of the biology of a particular tumor. The PanCancer Pathways Panel groups genes into 13 canonical driver pathways and provides both an expression value for each gene based on digital counts of transcripts and a Pathway Score that describes the relative dysregulation of each pathway. The Immune Profiling Panel measures the expression level of target genes that are specific to immune cell types and immune cell functions. Differential expression of each gene, relative abundance of immune cell types and abundance of tumor-specific antigens can be analyzed with the Immune Profiling panel. The Progression Panel analyzes the expression level of genes within four major biological processes that are associated with tumor growth and invasiveness. Together, these panels allow holistic characterization of the biologically meaningful attributes of a tumor.
In this proof-of-concept study, we analyzed 59 FFPE primary breast tumor samples along with 10 normal breast tissues using the PanCancer panels as well as the Prosigna Gene Signature Assay. We grouped the tumor samples by intrinsic subtype and explored pathway dysregulation using the PanCancer Pathways Panel, the immune landscape using the Immune Profiling Panel and the metastatic potential of the tumor using the Progression panel. For data analysis purposes, we used NanoString's PanCancer Advanced Analysis software. In each panel's data we compared the Prosigna subtypes at the single gene and the pathway level. We measured differential expression of various genes across subtypes as well as overall changes in pathway activation and suppression. Using the Immune Profiling Panel, we further compared relative abundance of the various immune cells across subtype.
The distribution of intrinsic subtype, as determined by the Prosigna Assay, in the 59 breast tumors was as follows: 16 (27.1%) Luminal A; 20 (33.9%) Luminal B; 13 (22.0%) Her2 Enriched; and 10 (17.0%) BasalLike. PanCancer Pathways analysis of these tumor samples along with 10 normal breast tissues revealed that dysregulation of certain canonical pathways characterizes each intrinsic subtype. In BasalLike tumors, we found that genes involved in the TGF-b pathway are significantly downregulated relative to Luminal A tumors and normal breast tissues. Further analysis with the Immune Profiling Panel revealed that the relative abundance of Mast cells is reduced while that of type 2 Th (Th2) cells is increased in Basal Like tumors relative to Luminal A and normal breast tissue. These results suggest that pathways associated with angiogenesis are downregulated in Basal Like breast cancer and favor the recruitment of immune cells associated with hypoxic conditions. These results confirm findings from multiple previous studies.
In this study, we show that the NanoString PanCancer Pathways, Immune Profiling and Progression panels reveal associations between intrinsic breast cancer subtype and specific pathway dysregulation as well as related changes in the immune landscape of the tumor. We demonstrate that a comprehensive view of the biology of a tumor can be readily obtained with the NanoString platform and the PanCancer Panels.
Citation Format: Lucas Dennis, Patrick Danaher, Maribeth Eagan, Andrew White, Nathan Elliot, Namratha Ram, Gayathri Balasundaram, Arthur Jeiranian, Seely Kaufmann, Rich Boykin, Lindy Irving, Wesley Buckingham, Sean Ferree, Christina Bailey, Joseph Beechem. Building a comprehensive view of tumor biology in breast cancer by combining NanoString's Prosigna assay with the Pancancer Pathways, Immune Profiling, and Progression Panels. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research; Oct 17-20, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(2_Suppl):Abstract nr A49.
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Neph S, Vierstra J, Stergachis AB, Reynolds AP, Haugen E, Vernot B, Thurman RE, Sandstrom R, Johnson AK, Maurano MT, Humbert R, Rynes E, Wang H, Vong S, Lee K, Bates D, Diegel M, Roach V, Dunn D, Neri J, Schafer A, Hansen RS, Kutyavin T, Giste E, Weaver M, Canfield T, Sabo P, Zhang M, Balasundaram G, Byron R, MacCoss MJ, Akey JM, Bender M, Groudine M, Kaul R, Stamatoyannopoulos JA. An expansive human regulatory lexicon encoded in transcription factor footprints. Nature 2012; 489:83-90. [PMID: 22955618 PMCID: PMC3736582 DOI: 10.1038/nature11212] [Citation(s) in RCA: 566] [Impact Index Per Article: 47.2] [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: 12/11/2011] [Accepted: 05/10/2012] [Indexed: 01/04/2023]
Abstract
Regulatory factor binding to genomic DNA protects the underlying sequence from cleavage by DNase I, leaving nucleotide-resolution footprints. Using genomic DNase I footprinting across 41 diverse cell and tissue types, we detected 45 million transcription factor occupancy events within regulatory regions, representing differential binding to 8.4 million distinct short sequence elements. Here we show that this small genomic sequence compartment, roughly twice the size of the exome, encodes an expansive repertoire of conserved recognition sequences for DNA-binding proteins that nearly doubles the size of the human cis-regulatory lexicon. We find that genetic variants affecting allelic chromatin states are concentrated in footprints, and that these elements are preferentially sheltered from DNA methylation. High-resolution DNase I cleavage patterns mirror nucleotide-level evolutionary conservation and track the crystallographic topography of protein-DNA interfaces, indicating that transcription factor structure has been evolutionarily imprinted on the human genome sequence. We identify a stereotyped 50-base-pair footprint that precisely defines the site of transcript origination within thousands of human promoters. Finally, we describe a large collection of novel regulatory factor recognition motifs that are highly conserved in both sequence and function, and exhibit cell-selective occupancy patterns that closely parallel major regulators of development, differentiation and pluripotency.
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Affiliation(s)
- Shane Neph
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Jeff Vierstra
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | | | - Alex P. Reynolds
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Eric Haugen
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Benjamin Vernot
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Robert E. Thurman
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Richard Sandstrom
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Audra K. Johnson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Matthew T. Maurano
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Richard Humbert
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Eric Rynes
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Hao Wang
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Shinny Vong
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Kristen Lee
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Daniel Bates
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Morgan Diegel
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Vaughn Roach
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Douglas Dunn
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Jun Neri
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Anthony Schafer
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - R. Scott Hansen
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195
| | - Tanya Kutyavin
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Erika Giste
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Molly Weaver
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Theresa Canfield
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Peter Sabo
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Miaohua Zhang
- Basic Sciences Division, Fred Hutchison Cancer Research Center, Seattle, WA 98109
| | | | - Rachel Byron
- Basic Sciences Division, Fred Hutchison Cancer Research Center, Seattle, WA 98109
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Joshua M. Akey
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Michael Bender
- Basic Sciences Division, Fred Hutchison Cancer Research Center, Seattle, WA 98109
| | - Mark Groudine
- Basic Sciences Division, Fred Hutchison Cancer Research Center, Seattle, WA 98109
| | - Rajinder Kaul
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195
| | - John A. Stamatoyannopoulos
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
- Division of Oncology, Deparment of Medicine, University of Washington, Seattle, WA 98195
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5
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Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T, Giste E, Johnson A, Zhang M, Balasundaram G, Byron R, Roach V, Sabo PJ, Sandstrom R, Stehling AS, Thurman RE, Weissman SM, Cayting P, Hariharan M, Lian J, Cheng Y, Landt SG, Ma Z, Wold BJ, Dekker J, Crawford GE, Keller CA, Wu W, Morrissey C, Kumar SA, Mishra T, Jain D, Byrska-Bishop M, Blankenberg D, Lajoie1 BR, Jain G, Sanyal A, Chen KB, Denas O, Taylor J, Blobel GA, Weiss MJ, Pimkin M, Deng W, Marinov GK, Williams BA, Fisher-Aylor KI, Desalvo G, Kiralusha A, Trout D, Amrhein H, Mortazavi A, Edsall L, McCleary D, Kuan S, Shen Y, Yue F, Ye Z, Davis CA, Zaleski C, Jha S, Xue C, Dobin A, Lin W, Fastuca M, Wang H, Guigo R, Djebali S, Lagarde J, Ryba T, Sasaki T, Malladi VS, Cline MS, Kirkup VM, Learned K, Rosenbloom KR, Kent WJ, Feingold EA, Good PJ, Pazin M, Lowdon RF, Adams LB. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol 2012; 13:418. [PMID: 22889292 PMCID: PMC3491367 DOI: 10.1186/gb-2012-13-8-418] [Citation(s) in RCA: 343] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
To complement the human Encyclopedia of DNA Elements (ENCODE) project and to enable a broad range of mouse genomics efforts, the Mouse ENCODE Consortium is applying the same experimental pipelines developed for human ENCODE to annotate the mouse genome.
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Affiliation(s)
- John A Stamatoyannopoulos
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Ross Hardison
- Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Bing Ren
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California San Diego, La Jolla, California, USA
| | - Thomas Gingeras
- Dept. of Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Mark Groudine
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Michael Bender
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Rajinder Kaul
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Theresa Canfield
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Erica Giste
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Audra Johnson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Mia Zhang
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Gayathri Balasundaram
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Rachel Byron
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Vaughan Roach
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Peter J Sabo
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Richard Sandstrom
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - A Sandra Stehling
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Robert E Thurman
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | | | - Philip Cayting
- Department of Genetics, Yale University, New Haven, Connecticut, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Manoj Hariharan
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Jin Lian
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA
| | - Yong Cheng
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Stephen G Landt
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Zhihai Ma
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Barbara J Wold
- Div. of Biology, California Institute of Technology, Pasadena, California, USA
| | - Job Dekker
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachussetts, USA
| | - Gregory E Crawford
- Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, USA
- Department of Pediatrics, Duke University, Durham, North Carolina, USA
| | - Cheryl A Keller
- Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Weisheng Wu
- Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Christopher Morrissey
- Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Swathi A Kumar
- Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Tejaswini Mishra
- Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Deepti Jain
- Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Marta Byrska-Bishop
- Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Daniel Blankenberg
- Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Bryan R Lajoie1
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Gaurav Jain
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachussetts, USA
| | - Amartya Sanyal
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachussetts, USA
| | - Kaun-Bei Chen
- Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, USA
| | - Olgert Denas
- Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, USA
| | - James Taylor
- Department of Mathematics and Computer Science, Emory University, Atlanta, Georgia, USA
| | - Gerd A Blobel
- Div. of Hematology, Children's Hospital of Philadelphia, Abramson Research Center, Philadelphia, Pennsylvania, USA
| | - Mitchell J Weiss
- Div. of Hematology, Children's Hospital of Philadelphia, Abramson Research Center, Philadelphia, Pennsylvania, USA
| | - Max Pimkin
- Div. of Hematology, Children's Hospital of Philadelphia, Abramson Research Center, Philadelphia, Pennsylvania, USA
| | - Wulan Deng
- Div. of Hematology, Children's Hospital of Philadelphia, Abramson Research Center, Philadelphia, Pennsylvania, USA
| | - Georgi K Marinov
- Div. of Biology, California Institute of Technology, Pasadena, California, USA
| | - Brian A Williams
- Div. of Biology, California Institute of Technology, Pasadena, California, USA
| | | | - Gilberto Desalvo
- Div. of Biology, California Institute of Technology, Pasadena, California, USA
| | - Anthony Kiralusha
- Div. of Biology, California Institute of Technology, Pasadena, California, USA
| | - Diane Trout
- Div. of Biology, California Institute of Technology, Pasadena, California, USA
| | - Henry Amrhein
- Div. of Biology, California Institute of Technology, Pasadena, California, USA
| | - Ali Mortazavi
- Dept. of Developmental and Cell Biology, University of California Irvine, Irvine California, USA
| | - Lee Edsall
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California San Diego, La Jolla, California, USA
| | - David McCleary
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California San Diego, La Jolla, California, USA
| | - Samantha Kuan
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California San Diego, La Jolla, California, USA
| | - Yin Shen
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California San Diego, La Jolla, California, USA
| | - Feng Yue
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California San Diego, La Jolla, California, USA
| | - Zhen Ye
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California San Diego, La Jolla, California, USA
| | - Carrie A Davis
- Dept. of Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Chris Zaleski
- Dept. of Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Sonali Jha
- Dept. of Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Chenghai Xue
- Dept. of Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Alex Dobin
- Dept. of Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Wei Lin
- Dept. of Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Meagan Fastuca
- Dept. of Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Huaien Wang
- Dept. of Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Roderic Guigo
- Division of Bioinformatics and Genomics, Center for Genomic Regulation, Barcelona, Catalunya, Spain
| | - Sarah Djebali
- Division of Bioinformatics and Genomics, Center for Genomic Regulation, Barcelona, Catalunya, Spain
| | - Julien Lagarde
- Division of Bioinformatics and Genomics, Center for Genomic Regulation, Barcelona, Catalunya, Spain
| | - Tyrone Ryba
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Takayo Sasaki
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Venkat S Malladi
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, California, USA
| | - Melissa S Cline
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, California, USA
| | - Vanessa M Kirkup
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, California, USA
| | - Katrina Learned
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, California, USA
| | - Kate R Rosenbloom
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, California, USA
| | - W James Kent
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, California, USA
| | - Elise A Feingold
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Peter J Good
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael Pazin
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Rebecca F Lowdon
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Leslie B Adams
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
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6
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Janebodin K, Horst OV, Ieronimakis N, Balasundaram G, Reesukumal K, Pratumvinit B, Reyes M. Isolation and characterization of neural crest-derived stem cells from dental pulp of neonatal mice. PLoS One 2011; 6:e27526. [PMID: 22087335 PMCID: PMC3210810 DOI: 10.1371/journal.pone.0027526] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [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: 11/10/2010] [Accepted: 10/19/2011] [Indexed: 01/09/2023] Open
Abstract
Dental pulp stem cells (DPSCs) are shown to reside within the tooth and play an important role in dentin regeneration. DPSCs were first isolated and characterized from human teeth and most studies have focused on using this adult stem cell for clinical applications. However, mouse DPSCs have not been well characterized and their origin(s) have not yet been elucidated. Herein we examined if murine DPSCs are neural crest derived and determined their in vitro and in vivo capacity. DPSCs from neonatal murine tooth pulp expressed embryonic stem cell and neural crest related genes, but lacked expression of mesodermal genes. Cells isolated from the Wnt1-Cre/R26R-LacZ model, a reporter of neural crest-derived tissues, indicated that DPSCs were Wnt1-marked and therefore of neural crest origin. Clonal DPSCs showed multi-differentiation in neural crest lineage for odontoblasts, chondrocytes, adipocytes, neurons, and smooth muscles. Following in vivo subcutaneous transplantation with hydroxyapatite/tricalcium phosphate, based on tissue/cell morphology and specific antibody staining, the clones differentiated into odontoblast-like cells and produced dentin-like structure. Conversely, bone marrow stromal cells (BMSCs) gave rise to osteoblast-like cells and generated bone-like structure. Interestingly, the capillary distribution in the DPSC transplants showed close proximity to odontoblasts whereas in the BMSC transplants bone condensations were distant to capillaries resembling dentinogenesis in the former vs. osteogenesis in the latter. Thus we demonstrate the existence of neural crest-derived DPSCs with differentiation capacity into cranial mesenchymal tissues and other neural crest-derived tissues. In turn, DPSCs hold promise as a source for regenerating cranial mesenchyme and other neural crest derived tissues.
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Affiliation(s)
- Kajohnkiart Janebodin
- Department of Oral Health Sciences, School of Dentistry, University of Washington, Seattle, Washington, United States of America
- Department of Anatomy, Faculty of Dentistry, Mahidol University, Bangkok, Thailand
| | - Orapin V. Horst
- Departments of Dental Public Health Sciences and Endodontics, School of Dentistry, University of Washington, Seattle, Washington, United States of America
| | - Nicholas Ieronimakis
- Department of Pathology, Institute for Stem Cell and Regenerative Medicine, School of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Gayathri Balasundaram
- Department of Pathology, Institute for Stem Cell and Regenerative Medicine, School of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Kanit Reesukumal
- Department of Clinical Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Busadee Pratumvinit
- Department of Clinical Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Morayma Reyes
- Department of Oral Health Sciences, School of Dentistry, University of Washington, Seattle, Washington, United States of America
- Department of Pathology, Institute for Stem Cell and Regenerative Medicine, School of Medicine, University of Washington, Seattle, Washington, United States of America
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Ieronimakis N, Balasundaram G, Rainey S, Srirangam K, Yablonka-Reuveni Z, Reyes M. Absence of CD34 on murine skeletal muscle satellite cells marks a reversible state of activation during acute injury. PLoS One 2010; 5:e10920. [PMID: 20532193 PMCID: PMC2880004 DOI: 10.1371/journal.pone.0010920] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [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: 01/12/2010] [Accepted: 04/27/2010] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Skeletal muscle satellite cells are myogenic progenitors that reside on myofiber surface beneath the basal lamina. In recent years satellite cells have been identified and isolated based on their expression of CD34, a sialomucin surface receptor traditionally used as a marker of hematopoietic stem cells. Interestingly, a minority of satellite cells lacking CD34 has been described. METHODOLOGY/PRINCIPAL FINDINGS In order to elucidate the relationship between CD34+ and CD34- satellite cells we utilized fluorescence-activated cell sorting (FACS) to isolate each population for molecular analysis, culture and transplantation studies. Here we show that unless used in combination with alpha7 integrin, CD34 alone is inadequate for purifying satellite cells. Furthermore, the absence of CD34 marks a reversible state of activation dependent on muscle injury. CONCLUSIONS/SIGNIFICANCE Following acute injury CD34- cells become the major myogenic population whereas the percentage of CD34+ cells remains constant. In turn activated CD34- cells can reverse their activation to maintain the pool of CD34+ reserve cells. Such activation switching and maintenance of reserve pool suggests the satellite cell compartment is tightly regulated during muscle regeneration.
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Affiliation(s)
- Nicholas Ieronimakis
- Department of Pathology, School of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Gayathri Balasundaram
- Department of Pathology, School of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Sabrina Rainey
- Department of Pathology, School of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Kiran Srirangam
- Department of Pathology, School of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Zipora Yablonka-Reuveni
- Department of Biological Structure, School of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Morayma Reyes
- Department of Pathology, School of Medicine, University of Washington, Seattle, Washington, United States of America
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Ieronimakis N, Balasundaram G, Reyes M. Direct isolation, culture and transplant of mouse skeletal muscle derived endothelial cells with angiogenic potential. PLoS One 2008; 3:e0001753. [PMID: 18335025 PMCID: PMC2262143 DOI: 10.1371/journal.pone.0001753] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [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: 11/14/2007] [Accepted: 02/03/2008] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Although diseases associated with microvascular endothelial dysfunction are among the most prevalent illnesses to date, currently no method exists to isolate pure endothelial cells (EC) from skeletal muscle for in vivo or in vitro study. METHODOLOGY By utilizing multicolor fluorescent-activated cell sorting (FACS), we have isolated a distinct population of Sca-1(+), CD31(+), CD34(dim) and CD45(- )cells from skeletal muscles of C57BL6 mice. Characterization of this population revealed these cells are functional EC that can be expanded several times in culture without losing their phenotype or capabilities to uptake acetylated low-density lipoprotein (ac-LDL), produce nitric oxide (NO) and form vascular tubes. When transplanted subcutaneously or intramuscularly into the tibialis anterior muscle, EC formed microvessels and integrated with existing vasculature. CONCLUSION This method, which is highly reproducible, can be used to study the biology and role of EC in diseases such as peripheral vascular disease. In addition this method allows us to isolate large quantities of skeletal muscle derived EC with potential for therapeutic angiogenic applications.
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Affiliation(s)
- Nicholas Ieronimakis
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Gayathri Balasundaram
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Morayma Reyes
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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Mello A, Hong Z, Rossi AM, Luan L, Farina M, Querido W, Eon J, Terra J, Balasundaram G, Webster T, Feinerman A, Ellis DE, Ketterson JB, Ferreira CL. Osteoblast proliferation on hydroxyapatite thin coatings produced by right angle magnetron sputtering. Biomed Mater 2007; 2:67-77. [PMID: 18458438 DOI: 10.1088/1748-6041/2/2/003] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Right angle magnetron sputtering (RAMS) was used to produce hydroxyapatite (HA) film coatings on pure titanium substrates and oriented silicon wafer (Si(0 0 1)) substrates with flat surfaces as well as engineered surfaces having different forms. Analyses using synchrotron XRD, AFM, XPS, FTIR and SEM with EDS showed that as-sputtered thin coatings consist of highly crystalline hydroxyapatite. The HA coatings induced calcium phosphate precipitation when immersed in simulated body fluid, suggesting in vivo bioactive behavior. In vitro experiments, using murine osteoblasts, showed that cells rapidly adhere, spread and proliferate over the thin coating surface, while simultaneously generating strong in-plane stresses, as observed on SEM images. Human osteoblasts were seeded at a density of 2500 cells cm(-2) on silicon and titanium HA coated substrates by RAMS. Uncoated glass was used as a reference substrate for further counting of cells. The highest proliferation of human osteoblasts was achieved on HA RAMS-coated titanium substrates. These experiments demonstrate that RAMS is a promising coating technique for biomedical applications.
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Affiliation(s)
- A Mello
- Instituto Militar de Engenharia, IME, Rio de Janeiro, 22290-270, RJ, Brazil.
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Tian J, Yam C, Balasundaram G, Wang H, Gore A, Sampath K. A temperature-sensitive mutation in the nodal-related gene cyclops reveals that the floor plate is induced during gastrulation in zebrafish. Development 2003; 130:3331-42. [PMID: 12783802 DOI: 10.1242/dev.00544] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The floor plate, a specialized group of cells in the ventral midline of the neural tube of vertebrates, plays crucial roles in patterning the central nervous system. Recent work from zebrafish, chick, chick-quail chimeras and mice to investigate the development of the floor plate have led to several models of floor-plate induction. One model suggests that the floor plate is formed by inductive signalling from the notochord to the overlying neural tube. The induction is thought to be mediated by notochord-derived Sonic hedgehog (Shh), a secreted protein, and requires direct cellular contact between the notochord and the neural tube. Another model proposes a role for the organizer in generating midline precursor cells that produce floor plate cells independent of notochord specification, and proposes that floor plate specification occurs early, during gastrulation. We describe a temperature-sensitive mutation that affects the zebrafish Nodal-related secreted signalling factor, Cyclops, and use it to address the issue of when the floor plate is induced in zebrafish. Zebrafish cyclops regulates the expression of shh in the ventral neural tube. Although null mutations in cyclops result in the lack of the medial floor plate, embryos homozygous for the temperature-sensitive mutation have floor plate cells at the permissive temperature and lack floor plate cells at the restrictive temperature. We use this mutant allele in temperature shift-up and shift-down experiments to answer a central question pertaining to the timing of vertebrate floor plate induction. Abrogation of Cyc/Nodal signalling in the temperature-sensitive mutant embryos at various stages indicates that the floor plate in zebrafish is induced early in development, during gastrulation. In addition, continuous Cyclops signalling is required through gastrulation for a complete ventral neural tube throughout the length of the neuraxis. Finally, by modulation of Nodal signalling levels in mutants and in ectopic overexpression experiments, we show that, similar to the requirements for prechordal plate mesendoderm fates, uninterrupted and high levels of Cyclops signalling are required for induction and specification of a complete ventral neural tube.
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Affiliation(s)
- Jing Tian
- Laboratory of Fish Embryology, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604
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Balasundaram G, Takahashi T, Ueno A, Mihara H. Construction of peptide conjugates with peptide nucleic acids containing an anthracene probe and their interactions with DNA. Bioorg Med Chem 2001; 9:1115-21. [PMID: 11377169 DOI: 10.1016/s0968-0896(00)00329-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We designed and synthesized the peptide nucleic acid (PNA)-peptide conjugates having anthracene chromophores and investigated their interactions with calf thymus DNA, [d(AT)(10)](2), [d(GC)(10)](2), and [d(AT)(10)dA(6)](2). Considering the synthesis compatibility and expecting that a novel DNA analogue, PNA, can improve DNA binding properties of alpha-helix peptides, we attempted to attach thymine PNA oligomers at the C-terminus of a 14 amino acid alpha-helix peptide that contained a pair of artificial intercalators, anthracene, as a probe, and to examine their interactions with DNA using anthracene UV, fluorescence and circular dichroism properties. The results observed in this study showed that the designed peptide folded in an alpha-helix structure in the presence of calf thymus DNA, [d(AT)(10)](2), and [d(AT)(10)dA(6)](2) with the chromophores at the side-chain being fixed with a left-handed chiral-sense orientation. The alpha-helix and the anthracene signals were not observed for [d(GC)(10)](2). Incorporation of thymine PNA oligomers into the designed alpha-helix peptide increased the DNA binding ability to [d(AT)(10)dA(6)](2) with increasing the length of the PNA without changing the conformations of the peptide backbone and the anthracene side-chains.
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Affiliation(s)
- G Balasundaram
- Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta, Yokohama 226-8501, Japan
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Agarwal A, Sarkar S, Nazabal C, Balasundaram G, Rao KV. B cell responses to a peptide epitope. I. The cellular basis for restricted recognition. J Immunol 1996; 157:2779-88. [PMID: 8816380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Primary humoral responses in BALB/c mice to a variety of peptide constructs containing a common 15-amino acid residue antigenic determinant (PS1) in conjunction with one or more Th cell epitopes were examined. In all cases, the mature IgG response was found to focus primarily on a tetrapeptide sequence, Asp-Pro-Ala-Phe. The dominance of this segment was independent of the position of the PS1 determinant in the peptide sequence and was also observed in constructs with a random secondary structure. In contrast to the mature IgG response, the early primary IgM response was constituted by multiple specificities that collectively spanned a major proportion of the PS1 sequence. However, subsequent progression of this response entailed a strict selection for only those Abs directed against the Asp-Pro-Ala-Phe segment and apparently occurred at or around the time of the IgM to IgG class switch. Studies of murine responses to peptide analogs containing single amino acid substitutions within the Asp-Pro-Ala-Phe sequence revealed that emergence of this segment as the dominant epitope was a consequence of active suppression of B cells directed against alternate determinants. Positive selection of this subset of Abs correlated with overall higher avidity for epitope binding and was the outcome of a competitive process enforced by the limiting amounts of Th cell help available in the early stages of the primary response.
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Affiliation(s)
- A Agarwal
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
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Agarwal A, Sarkar S, Nazabal C, Balasundaram G, Rao KV. B cell responses to a peptide epitope. I. The cellular basis for restricted recognition. The Journal of Immunology 1996. [DOI: 10.4049/jimmunol.157.7.2779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Abstract
Primary humoral responses in BALB/c mice to a variety of peptide constructs containing a common 15-amino acid residue antigenic determinant (PS1) in conjunction with one or more Th cell epitopes were examined. In all cases, the mature IgG response was found to focus primarily on a tetrapeptide sequence, Asp-Pro-Ala-Phe. The dominance of this segment was independent of the position of the PS1 determinant in the peptide sequence and was also observed in constructs with a random secondary structure. In contrast to the mature IgG response, the early primary IgM response was constituted by multiple specificities that collectively spanned a major proportion of the PS1 sequence. However, subsequent progression of this response entailed a strict selection for only those Abs directed against the Asp-Pro-Ala-Phe segment and apparently occurred at or around the time of the IgM to IgG class switch. Studies of murine responses to peptide analogs containing single amino acid substitutions within the Asp-Pro-Ala-Phe sequence revealed that emergence of this segment as the dominant epitope was a consequence of active suppression of B cells directed against alternate determinants. Positive selection of this subset of Abs correlated with overall higher avidity for epitope binding and was the outcome of a competitive process enforced by the limiting amounts of Th cell help available in the early stages of the primary response.
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Affiliation(s)
- A Agarwal
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - S Sarkar
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - C Nazabal
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - G Balasundaram
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - K V Rao
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
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