1
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Tiniakou I, Hsu PF, Lopez-Zepeda LS, Garipler G, Esteva E, Adams NM, Jang G, Soni C, Lau CM, Liu F, Khodadadi-Jamayran A, Rodrick TC, Jones D, Tsirigos A, Ohler U, Bedford MT, Nimer SD, Kaartinen V, Mazzoni EO, Reizis B. Genome-wide screening identifies Trim33 as an essential regulator of dendritic cell differentiation. Sci Immunol 2024; 9:eadi1023. [PMID: 38608038 DOI: 10.1126/sciimmunol.adi1023] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 03/21/2024] [Indexed: 04/14/2024]
Abstract
The development of dendritic cells (DCs), including antigen-presenting conventional DCs (cDCs) and cytokine-producing plasmacytoid DCs (pDCs), is controlled by the growth factor Flt3 ligand (Flt3L) and its receptor Flt3. We genetically dissected Flt3L-driven DC differentiation using CRISPR-Cas9-based screening. Genome-wide screening identified multiple regulators of DC differentiation including subunits of TSC and GATOR1 complexes, which restricted progenitor growth but enabled DC differentiation by inhibiting mTOR signaling. An orthogonal screen identified the transcriptional repressor Trim33 (TIF-1γ) as a regulator of DC differentiation. Conditional targeting in vivo revealed an essential role of Trim33 in the development of all DCs, but not of monocytes or granulocytes. In particular, deletion of Trim33 caused rapid loss of DC progenitors, pDCs, and the cross-presenting cDC1 subset. Trim33-deficient Flt3+ progenitors up-regulated pro-inflammatory and macrophage-specific genes but failed to induce the DC differentiation program. Collectively, these data elucidate mechanisms that control Flt3L-driven differentiation of the entire DC lineage and identify Trim33 as its essential regulator.
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Affiliation(s)
- Ioanna Tiniakou
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Pei-Feng Hsu
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Lorena S Lopez-Zepeda
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Görkem Garipler
- Department of Biology, New York University, New York, NY, USA
| | - Eduardo Esteva
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Nicholas M Adams
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Geunhyo Jang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Chetna Soni
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Colleen M Lau
- Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Fan Liu
- Department of Biochemistry and Molecular Biology, Department of Medicine and Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Alireza Khodadadi-Jamayran
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Applied Bioinformatics Laboratories, New York University Grossman School of Medicine, New York, NY, USA
| | - Tori C Rodrick
- Metabolomics Laboratory, Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Drew Jones
- Metabolomics Laboratory, Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Applied Bioinformatics Laboratories, New York University Grossman School of Medicine, New York, NY, USA
| | - Uwe Ohler
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stephen D Nimer
- Department of Biochemistry and Molecular Biology, Department of Medicine and Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Vesa Kaartinen
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry, Ann Arbor, MI, USA
| | | | - Boris Reizis
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
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2
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Feng J, Jang G, Esteva E, Adams NM, Jin H, Reizis B. Clonal barcoding of endogenous adult hematopoietic stem cells reveals a spectrum of lineage contributions. Proc Natl Acad Sci U S A 2024; 121:e2317929121. [PMID: 38227649 PMCID: PMC10823160 DOI: 10.1073/pnas.2317929121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 12/11/2023] [Indexed: 01/18/2024] Open
Abstract
The hierarchical model of hematopoiesis posits that self-renewing, multipotent hematopoietic stem cells (HSCs) give rise to all blood cell lineages. While this model accounts for hematopoiesis in transplant settings, its applicability to steady-state hematopoiesis remains to be clarified. Here, we used inducible clonal DNA barcoding of endogenous adult HSCs to trace their contribution to major hematopoietic cell lineages in unmanipulated animals. While the majority of barcodes were unique to a single lineage, we also observed frequent barcode sharing between multiple lineages, specifically between lymphocytes and myeloid cells. These results suggest that both single-lineage and multilineage contributions by HSCs collectively drive continuous hematopoiesis, and highlight a close relationship of myeloid and lymphoid development.
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Affiliation(s)
- Jue Feng
- Department of Pathology, New York University Grossman School of Medicine, New York, NY10016
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY10029
| | - Geunhyo Jang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY10016
| | - Eduardo Esteva
- Department of Pathology, New York University Grossman School of Medicine, New York, NY10016
- Applied Bioinformatics Laboratories, New York University Grossman School of Medicine, New York, NY10016
| | - Nicholas M. Adams
- Department of Pathology, New York University Grossman School of Medicine, New York, NY10016
| | - Hua Jin
- Department of Pathology, New York University Grossman School of Medicine, New York, NY10016
| | - Boris Reizis
- Department of Pathology, New York University Grossman School of Medicine, New York, NY10016
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3
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Pearlman SI, Leelawong M, Richardson KA, Adams NM, Russ PK, Pask ME, Wolfe AE, Wessely C, Haselton FR. Correction to "Low-Resource Nucleic Acid Extraction Method Enabled by High-Gradient Magnetic Separation". ACS Appl Mater Interfaces 2024; 16:1953. [PMID: 38126871 PMCID: PMC11027509 DOI: 10.1021/acsami.3c18419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Indexed: 12/23/2023]
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4
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Sulczewski FB, Maqueda-Alfaro RA, Alcántara-Hernández M, Perez OA, Saravanan S, Yun TJ, Seong D, Arroyo Hornero R, Raquer-McKay HM, Esteva E, Lanzar ZR, Leylek RA, Adams NM, Das A, Rahman AH, Gottfried-Blackmore A, Reizis B, Idoyaga J. Transitional dendritic cells are distinct from conventional DC2 precursors and mediate proinflammatory antiviral responses. Nat Immunol 2023; 24:1265-1280. [PMID: 37414907 PMCID: PMC10683792 DOI: 10.1038/s41590-023-01545-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 05/26/2023] [Indexed: 07/08/2023]
Abstract
High-dimensional approaches have revealed heterogeneity amongst dendritic cells (DCs), including a population of transitional DCs (tDCs) in mice and humans. However, the origin and relationship of tDCs to other DC subsets has been unclear. Here we show that tDCs are distinct from other well-characterized DCs and conventional DC precursors (pre-cDCs). We demonstrate that tDCs originate from bone marrow progenitors shared with plasmacytoid DCs (pDCs). In the periphery, tDCs contribute to the pool of ESAM+ type 2 DCs (DC2s), and these DC2s have pDC-related developmental features. Different from pre-cDCs, tDCs have less turnover, capture antigen, respond to stimuli and activate antigen-specific naïve T cells, all characteristics of differentiated DCs. Different from pDCs, viral sensing by tDCs results in IL-1β secretion and fatal immune pathology in a murine coronavirus model. Our findings suggest that tDCs are a distinct pDC-related subset with a DC2 differentiation potential and unique proinflammatory function during viral infections.
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Affiliation(s)
- Fernando Bandeira Sulczewski
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Raul A Maqueda-Alfaro
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Marcela Alcántara-Hernández
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Oriana A Perez
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Sanjana Saravanan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Tae Jin Yun
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - David Seong
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
- Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Rebeca Arroyo Hornero
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Hayley M Raquer-McKay
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Eduardo Esteva
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Zachary R Lanzar
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Rebecca A Leylek
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicholas M Adams
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Annesa Das
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Adeeb H Rahman
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andres Gottfried-Blackmore
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Redwood City, CA, USA
| | - Boris Reizis
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA.
| | - Juliana Idoyaga
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
- Immunology Program, Stanford University School of Medicine, Stanford, CA, USA.
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5
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Jang G, Contreras Castillo S, Esteva E, Upadhaya S, Feng J, Adams NM, Richard E, Awatramani R, Sawai CM, Reizis B. Stem cell decoupling underlies impaired lymphoid development during aging. Proc Natl Acad Sci U S A 2023; 120:e2302019120. [PMID: 37216517 PMCID: PMC10236001 DOI: 10.1073/pnas.2302019120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/20/2023] [Indexed: 05/24/2023] Open
Abstract
Mammalian aging is associated with multiple defects of hematopoiesis, most prominently with the impaired development of T and B lymphocytes. This defect is thought to originate in hematopoietic stem cells (HSCs) of the bone marrow, specifically due to the age-dependent accumulation of HSCs with preferential megakaryocytic and/or myeloid potential ("myeloid bias"). Here, we tested this notion using inducible genetic labeling and tracing of HSCs in unmanipulated animals. We found that the endogenous HSC population in old mice shows reduced differentiation into all lineages including lymphoid, myeloid, and megakaryocytic. Single-cell RNA sequencing and immunophenotyping (CITE-Seq) showed that HSC progeny in old animals comprised balanced lineage spectrum including lymphoid progenitors. Lineage tracing using the aging-induced HSC marker Aldh1a1 confirmed the low contribution of old HSCs across all lineages. Competitive transplantations of total bone marrow cells with genetically marked HSCs revealed that the contribution of old HSCs was reduced, but compensated by other donor cells in myeloid cells but not in lymphocytes. Thus, the HSC population in old animals becomes globally decoupled from hematopoiesis, which cannot be compensated in lymphoid lineages. We propose that this partially compensated decoupling, rather than myeloid bias, is the primary cause of the selective impairment of lymphopoiesis in older mice.
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Affiliation(s)
- Geunhyo Jang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY10016
| | | | - Eduardo Esteva
- Department of Pathology, New York University Grossman School of Medicine, New York, NY10016
- Applied Bioinformatics Laboratories, New York University Grossman School of Medicine, New York, NY10016
| | - Samik Upadhaya
- Department of Pathology, New York University Grossman School of Medicine, New York, NY10016
| | - Jue Feng
- Department of Pathology, New York University Grossman School of Medicine, New York, NY10016
| | - Nicholas M. Adams
- Department of Pathology, New York University Grossman School of Medicine, New York, NY10016
| | - Elodie Richard
- INSERM Unit 1312 Bordeaux Institute of Oncology, University of Bordeaux33076Bordeaux, France
| | - Rajeshwar Awatramani
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
| | - Catherine M. Sawai
- INSERM Unit 1312 Bordeaux Institute of Oncology, University of Bordeaux33076Bordeaux, France
| | - Boris Reizis
- Department of Pathology, New York University Grossman School of Medicine, New York, NY10016
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6
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Feng J, Pucella JN, Jang G, Alcántara-Hernández M, Upadhaya S, Adams NM, Khodadadi-Jamayran A, Lau CM, Stoeckius M, Hao S, Smibert P, Tsirigos A, Idoyaga J, Reizis B. Clonal lineage tracing reveals shared origin of conventional and plasmacytoid dendritic cells. Immunity 2022; 55:405-422.e11. [PMID: 35180378 PMCID: PMC9344860 DOI: 10.1016/j.immuni.2022.01.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [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: 03/17/2021] [Revised: 09/23/2021] [Accepted: 01/24/2022] [Indexed: 12/14/2022]
Abstract
Developmental origins of dendritic cells (DCs) including conventional DCs (cDCs, comprising cDC1 and cDC2 subsets) and plasmacytoid DCs (pDCs) remain unclear. We studied DC development in unmanipulated adult mice using inducible lineage tracing combined with clonal DNA "barcoding" and single-cell transcriptome and phenotype analysis (CITE-seq). Inducible tracing of Cx3cr1+ hematopoietic progenitors in the bone marrow showed that they simultaneously produce all DC subsets including pDCs, cDC1s, and cDC2s. Clonal tracing of hematopoietic stem cells (HSCs) and of Cx3cr1+ progenitors revealed clone sharing between cDC1s and pDCs, but not between the two cDC subsets or between pDCs and B cells. Accordingly, CITE-seq analyses of differentiating HSCs and Cx3cr1+ progenitors identified progressive stages of pDC development including Cx3cr1+ Ly-6D+ pro-pDCs that were distinct from lymphoid progenitors. These results reveal the shared origin of pDCs and cDCs and suggest a revised scheme of DC development whereby pDCs share clonal relationship with cDC1s.
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Affiliation(s)
- Jue Feng
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA.
| | - Joseph N Pucella
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Geunhyo Jang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Marcela Alcántara-Hernández
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Samik Upadhaya
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Nicholas M Adams
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Alireza Khodadadi-Jamayran
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; Applied Bioinformatics Laboratories, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Colleen M Lau
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Marlon Stoeckius
- Technology Innovation Laboratory, New York Genome Center, New York, NY 10013, USA
| | - Stephanie Hao
- Technology Innovation Laboratory, New York Genome Center, New York, NY 10013, USA
| | - Peter Smibert
- Technology Innovation Laboratory, New York Genome Center, New York, NY 10013, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; Applied Bioinformatics Laboratories, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Juliana Idoyaga
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Boris Reizis
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA.
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7
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McNaughton CD, Adams NM, Hirschie Johnson C, Ward MJ, Schmitz JE, Lasko TA. Diurnal Variation in SARS-CoV-2 PCR Test Results: Test Accuracy May Vary by Time of Day. J Biol Rhythms 2021; 36:595-601. [PMID: 34696614 PMCID: PMC8599649 DOI: 10.1177/07487304211051841] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
False negative tests for SARS-CoV-2 are common and have important public health and medical implications. We tested the hypothesis of diurnal variation in viral shedding by assessing the proportion of positive versus negative SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) tests and cycle time (Ct) values among positive samples by the time of day. Among 86,342 clinical tests performed among symptomatic and asymptomatic patients in a regional health care network in the southeastern United States from March to August 2020, we found evidence for diurnal variation in the proportion of positive SARS-CoV-2 tests, with a peak around 1400 h and 1.7-fold variation over the day after adjustment for age, sex, race, testing location, month, and day of week and lower Ct values during the day for positive samples. These findings have important implications for public health testing and vaccination strategies.
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Affiliation(s)
- Candace D McNaughton
- Department of Emergency Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Geriatric Research Education Clinical Center, Tennessee Valley Healthcare System VA Medical Center, Nashville, Tennessee, USA.,Institute for Clinical Evaluative Sciences, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, ON, Canada
| | - Nicholas M Adams
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | | | - Michael J Ward
- Department of Emergency Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Geriatric Research Education Clinical Center, Tennessee Valley Healthcare System VA Medical Center, Nashville, Tennessee, USA
| | - Jonathan E Schmitz
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Thomas A Lasko
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, Tennessee, USA
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8
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Zimmers ZA, Adams NM, Haselton FR. Addition of mirror-image L-DNA elements to DNA amplification circuits to distinguish leakage from target signal. Biosens Bioelectron 2021; 188:113354. [PMID: 34034212 DOI: 10.1016/j.bios.2021.113354] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 03/30/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 10/21/2022]
Abstract
DNA amplification circuits that rely on thermodynamically-driven hybridization events triggered by a target nucleic acid are becoming increasingly utilized due to their relative simplicity. A drawback of these circuits is that non-specific amplification, or circuit leakage, must be estimated using a separate "no-target" control reaction to eliminate false positives. Aside from requiring an additional reaction, the problem with this approach is the difficulty of creating a no-target control for biological specimens. To overcome this limitation, we propose a strategy that combines both reactions into the same tube using naturally-occurring right-handed D-DNA circuit elements for the target detection reaction and identical synthetic mirror-image left-handed L-DNA circuit elements for the no-target control reaction. We illustrate this approach using catalyzed hairpin assembly (CHA), one of the most studied DNA amplification circuits. In a dual-chirality CHA design, the right-handed circuit signal is produced by target-specific amplification and circuit leakage, whereas the left-handed circuit signal is produced only by circuit leakage. The target-specific amplification is calculated as the difference between the two signals. The limit of detection of this dual-chirality CHA reaction was found to be similar to that of traditional CHA (81 vs 92 pM, respectively). Furthermore, the left-handed no-target signal matched the right-handed leakage across a wide range of sample conditions including background DNA, increased salt concentration, increased temperature, and urine. These results demonstrate the robustness of a dual-chirality design and the potential utility of left-handed DNA in the development of new DNA amplification circuits better-suited for target detection applications in biological samples.
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Affiliation(s)
- Zackary A Zimmers
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37240, USA
| | - Nicholas M Adams
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37240, USA
| | - Frederick R Haselton
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37240, USA.
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9
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Wiedemann GM, Santosa EK, Grassmann S, Sheppard S, Le Luduec JB, Adams NM, Dang C, Hsu KC, Sun JC, Lau CM. Deconvoluting global cytokine signaling networks in natural killer cells. Nat Immunol 2021; 22:627-638. [PMID: 33859404 PMCID: PMC8476180 DOI: 10.1038/s41590-021-00909-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 02/24/2021] [Indexed: 01/31/2023]
Abstract
Cytokine signaling via signal transducer and activator of transcription (STAT) proteins is crucial for optimal antiviral responses of natural killer (NK) cells. However, the pleiotropic effects of both cytokine and STAT signaling preclude the ability to precisely attribute molecular changes to specific cytokine-STAT modules. Here, we employed a multi-omics approach to deconstruct and rebuild the complex interaction of multiple cytokine signaling pathways in NK cells. Proinflammatory cytokines and homeostatic cytokines formed a cooperative axis to commonly regulate global gene expression and to further repress expression induced by type I interferon signaling. These cytokines mediated distinct modes of epigenetic regulation via STAT proteins, and collective signaling best recapitulated global antiviral responses. The most dynamically responsive genes were conserved across humans and mice, which included a cytokine-STAT-induced cross-regulatory program. Thus, an intricate crosstalk exists between cytokine signaling pathways, which governs NK cell responses.
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Affiliation(s)
- Gabriela M. Wiedemann
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Department of Internal Medicine II, Technical University of Munich, Munich, Germany
| | - Endi K. Santosa
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Simon Grassmann
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sam Sheppard
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Nicholas M. Adams
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Celeste Dang
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Katharine C. Hsu
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joseph C. Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, New York, NY, USA,Correspondence and requests for materials should be addressed to J.C.S. or C.M.L. ;
| | - Colleen M. Lau
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Correspondence and requests for materials should be addressed to J.C.S. or C.M.L. ;
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10
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Adams NM, Diaz-Salazar C, Dang C, Lanier LL, Sun JC. Cutting Edge: Heterogeneity in Cell Age Contributes to Functional Diversity of NK Cells. J Immunol 2020; 206:465-470. [PMID: 33443057 DOI: 10.4049/jimmunol.2001163] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 11/25/2020] [Indexed: 11/19/2022]
Abstract
Heterogeneity among naive adaptive lymphocytes determines their individual functions and fate decisions during an immune response. NK cells are innate lymphocytes capable of generating "adaptive" responses during infectious challenges. However, the factors that govern various NK cell functions are not fully understood. In this study, we use a reporter mouse model to permanently "time stamp" NK cells and type 1 innate lymphoid cells (ILC1s) to characterize the dynamics of their homeostatic turnover. We found that the homeostatic turnover of tissue-resident ILC1s is much slower than that of circulating NK cells. NK cell homeostatic turnover is further accelerated without the transcription factor Eomes. Finally, heterogeneity in NK cell age diversifies NK cell function, with "older" NK cells exhibiting more potent IFN-γ production to activating stimuli and more robust adaptive responses during CMV infection. These results provide insight into how the functional response of an NK cell varies over its lifespan.
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Affiliation(s)
- Nicholas M Adams
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Carlos Diaz-Salazar
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065.,Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, New York, NY 10065
| | - Celeste Dang
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065.,Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Lewis L Lanier
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143; and.,Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065; .,Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, New York, NY 10065.,Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065
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11
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Adams NM, Leelawong M, Benton A, Quinn C, Haselton FR, Schmitz JE. COVID-19 diagnostics for resource-limited settings: Evaluation of "unextracted" qRT-PCR. J Med Virol 2020; 93:559-563. [PMID: 32779772 PMCID: PMC7405028 DOI: 10.1002/jmv.26328] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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] [Received: 05/12/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 12/19/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has created a precipitous increase in the need for molecular diagnostics. Unfortunately, access to RNA extraction reagents can represent a bottleneck for quantitative real-time reverse transcriptase-polymerase chain reaction (qRT-PCR)-based methodologies, stemming from both extraordinary supply-chain stresses and the global reach of the virus into resource-limited settings. To provide flexible diagnostic options for such environments, we report here an "unextracted modification" for qRT-PCR using the Centers for Disease Control's (CDC's) widely utilized primers/probe sets for severe acute respiratory syndrome coronavirus 2 (N1/N2/N3 targeting viral nucleocapsid and RP-control targeting human RNase P). This approach replaces RNA extraction/purification with a heat-inactivation step of viral transport media (VTM), followed by direct inoculation-with or without VTM spin concentration-into PCR master mixes. Using derivatives of care from our clinical workflow, we compared traditional and unextracted CDC methodologies. Although some decrease in analytic sensitivity was evident (by higher Ct values) without extraction, in particular for the N2 primer/probe-set, we observed high categorical positive agreement between extracted and unextracted results for N1 (unconcentrated VTM-38/40; concentrated VTM-39/41), N3 (unconcentrated VTM-38/40; concentrated VTM-41/41), and RP (unconcentrated and concentrated VTM-81/81). The negative categorical agreement for N1/N2/N3 was likewise high. Overall, these results suggest that laboratories could adapt and validate unextracted qRT-PCR protocols as a contingency to overcome supply limitations, with minimal impact on categorical results.
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Affiliation(s)
- Nicholas M Adams
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee
| | - Mindy Leelawong
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee
| | - Alison Benton
- Molecular Infectious Diseases Laboratory, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Criziel Quinn
- Molecular Infectious Diseases Laboratory, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Frederick R Haselton
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee
| | - Jonathan E Schmitz
- Molecular Infectious Diseases Laboratory, Vanderbilt University Medical Center, Nashville, Tennessee.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee.,Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee
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12
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Pearlman S, Leelawong M, Richardson KA, Adams NM, Russ PK, Pask ME, Wolfe AE, Wessely C, Haselton FR. Low-Resource Nucleic Acid Extraction Method Enabled by High-Gradient Magnetic Separation. ACS Appl Mater Interfaces 2020; 12:12457-12467. [PMID: 32039572 PMCID: PMC7082792 DOI: 10.1021/acsami.9b21564] [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] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 02/10/2020] [Indexed: 05/26/2023]
Abstract
Nucleic acid-based diagnostic tests often require isolation and concentration of nucleic acids from biological samples. Commercial purification kits are difficult to use in low-resource settings because of their cost and insufficient laboratory infrastructure. Several recent approaches based on the use of magnetic beads offer a potential solution but remain limited to small volume samples. We have developed a simple and low-cost nucleic acid extraction method suitable for isolation and concentration of nucleic acids from small or large sample volumes. The method uses magnetic beads, a transfer pipette, steel wool, and an external magnet to implement high-gradient magnetic separation (HGMS) to retain nucleic acid-magnetic bead complexes within the device's steel wool matrix for subsequent processing steps. We demonstrate the method's utility by extracting tuberculosis DNA from both sputum and urine, two typical large volume sample matrices (5-200 mL), using guanidine-based extraction chemistry. Our HGMS-enabled extraction method is statistically indistinguishable from commercial extraction kits when detecting a spiked 123-base DNA sequence. For our HGMS-enabled extraction method, we obtained extraction efficiencies for sputum and urine of approximately 10 and 90%, whereas commercial kits obtained 10-17 and 70-96%, respectively. We also used this method previously in a blinded sample preparation comparison study published by Beall et al., 2019. Our manual extraction method is insensitive to high flow rates and sample viscosity, with capture of ∼100% for flow rates up to 45 mL/min and viscosities up to 55 cP, possibly making it suitable for a wide variety of sample volumes and types and point-of-care users. This HGMS-enabled extraction method provides a robust instrument-free method for magnetic bead-based nucleic acid extraction, potentially suitable for field implementation of nucleic acid testing.
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Affiliation(s)
- Stephanie
I. Pearlman
- Department
of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Mindy Leelawong
- Department
of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Kelly A. Richardson
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Nicholas M. Adams
- Department
of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Patricia K. Russ
- Department
of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Megan E. Pask
- Department
of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Anna E. Wolfe
- Department
of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Cassandra Wessely
- Department
of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Frederick R. Haselton
- Department
of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
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13
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Geary CD, Krishna C, Lau CM, Adams NM, Gearty SV, Pritykin Y, Thomsen AR, Leslie CS, Sun JC. Non-redundant ISGF3 Components Promote NK Cell Survival in an Auto-regulatory Manner during Viral Infection. Cell Rep 2020; 24:1949-1957.e6. [PMID: 30134157 PMCID: PMC6153266 DOI: 10.1016/j.celrep.2018.07.060] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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] [Received: 02/16/2018] [Revised: 06/05/2018] [Accepted: 07/17/2018] [Indexed: 01/14/2023] Open
Abstract
Natural killer (NK) cells are innate lymphocytes that possess adaptive features, including antigen-specific clonal expansion and long-lived memory responses. Although previous work demonstrated that type I interferon (IFN) signaling is crucial for NK cell expansion and memory cell formation following mouse cytomegalovirus (MCMV) infection, the global transcriptional mechanisms underlying type I IFN-mediated responses remained to be determined. Here, we demonstrate that among the suite of transcripts induced in activated NK cells, IFN-α is necessary and sufficient to promote expression of its downstream transcription factors STAT1, STAT2, and IRF9, via an auto-regulatory, feedforward loop. Similar to STAT1 deficiency, we show that STAT2- or IRF9-deficient NK cells are defective in their ability to expand following MCMV infection, in part because of diminished survival rather than an inability to proliferate. Thus, our findings demonstrate that individual ISGF3 components are crucial cell-autonomous and non-redundant regulators of the NK cell response to viral infection. Using RNA-seq and ChIP-seq, Geary et al. investigate the impacts of type I interferon on NK cells during MCMV infection and demonstrate crucial and non-redundant roles for STAT1, STAT2, and IRF9 in promoting cytotoxicity and survival of antiviral NK cells.
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Affiliation(s)
- Clair D Geary
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Chirag Krishna
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Colleen M Lau
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nicholas M Adams
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sofia V Gearty
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yuri Pritykin
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Allan R Thomsen
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Christina S Leslie
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, New York, NY 10065, USA.
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14
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Euliano EM, Hardcastle AN, Victoriano CM, Gabella WE, Haselton FR, Adams NM. Multiplexed Adaptive RT-PCR Based on L-DNA Hybridization Monitoring for the Detection of Zika, Dengue, and Chikungunya RNA. Sci Rep 2019; 9:11372. [PMID: 31388071 PMCID: PMC6684530 DOI: 10.1038/s41598-019-47862-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 04/02/2019] [Accepted: 07/25/2019] [Indexed: 02/06/2023] Open
Abstract
Reverse transcription polymerase chain reaction (RT-PCR) is the gold standard for the molecular diagnosis of many infectious diseases, including RNA viruses, but is generally limited to settings with access to trained personnel and laboratory resources. We have previously reported a fundamentally simpler thermal cycling platform called Adaptive PCR, which dynamically controls thermal cycling conditions during each cycle by optically monitoring the annealing and melting of mirror-image L-DNA surrogates of the PCR primers and targets. In this report, we integrate optically-controlled reverse transcription and single-channel monitoring of L-DNAs to develop a multiplexed Adaptive RT-PCR instrument and assay for the detection of Zika, dengue, and chikungunya virus RNA with high target specific and low limits of detection. The assay is demonstrated to detect as low as 5 copies/reaction of Zika or chikungunya RNA and 50 copies/reaction of dengue RNA. The multiplexed Adaptive RT-PCR instrument is robust and has many of the features required to implement diagnostic assays for RNA viruses in settings that lack traditional laboratory resources.
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Affiliation(s)
- Erin M Euliano
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37235, USA
| | - Austin N Hardcastle
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37235, USA
| | - Christia M Victoriano
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37235, USA
| | - William E Gabella
- Department of Physics and Astronomy, Vanderbilt University, Nashville, TN, 37235, USA
| | - Frederick R Haselton
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37235, USA.
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA.
| | - Nicholas M Adams
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37235, USA.
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15
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Abstract
Group 1 innate lymphocytes consist of a phenotypically, spatially, and functionally heterogeneous population of NK cells and ILC1s that are engaged during pathogen invasion. We are only beginning to understand the context-dependent roles that different subsets of group 1 innate lymphocytes play during homeostatic perturbations. With a focus on viral infection, this review highlights the organization and regulation of spatially and temporally distinct waves of NK cell and ILC1 responses that collectively serve to achieve optimal viral control.
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Affiliation(s)
- Nicholas M Adams
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York.,Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York.,Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York.,Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, New York
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16
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Adams NM, Geary CD, Santosa EK, Lumaquin D, Le Luduec JB, Sottile R, van der Ploeg K, Hsu J, Whitlock BM, Jackson BT, Weizman OE, Huse M, Hsu KC, Sun JC. Cytomegalovirus Infection Drives Avidity Selection of Natural Killer Cells. Immunity 2019; 50:1381-1390.e5. [PMID: 31103381 PMCID: PMC6614060 DOI: 10.1016/j.immuni.2019.04.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [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: 10/03/2018] [Revised: 03/08/2019] [Accepted: 04/22/2019] [Indexed: 12/23/2022]
Abstract
The process of affinity maturation, whereby T and B cells bearing antigen receptors with optimal affinity to the relevant antigen undergo preferential expansion, is a key feature of adaptive immunity. Natural killer (NK) cells are innate lymphocytes capable of "adaptive" responses after cytomegalovirus (CMV) infection. However, whether NK cells are similarly selected on the basis of their avidity for cognate ligand is unknown. Here, we showed that NK cells with the highest avidity for the mouse CMV glycoprotein m157 were preferentially selected to expand and comprise the memory NK cell pool, whereas low-avidity NK cells possessed greater capacity for interferon-γ (IFN-γ) production. Moreover, we provide evidence for avidity selection occurring in human NK cells during human CMV infection. These results delineate how heterogeneity in NK cell avidity diversifies NK cell effector function during antiviral immunity, and how avidity selection might serve to produce the most potent memory NK cells.
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Affiliation(s)
- Nicholas M Adams
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Clair D Geary
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Endi K Santosa
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dianne Lumaquin
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Rosa Sottile
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Joy Hsu
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Benjamin M Whitlock
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Benjamin T Jackson
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Orr-El Weizman
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Morgan Huse
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Katharine C Hsu
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, New York, NY 10065, USA.
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17
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Zimmers ZA, Adams NM, Gabella WE, Haselton FR. Fluorophore-Quencher Interactions Effect on Hybridization Characteristics of Complementary Oligonucleotides. Anal Methods 2019; 11:2862-2867. [PMID: 32661463 PMCID: PMC7357715 DOI: 10.1039/c9ay00584f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Nucleic acids are often covalently modified with fluorescent reporter molecules to create a hybridization state-dependent optical signal. Designing such a nucleic acid reporter involves selecting a fluorophore, quencher, and fluorescence quenching design. This report outlines the effect that these choices have on the DNA hybridization characteristics by examining six fluorophores in four quenching schemes: a quencher molecule offset from the fluorophore by 0, 5, or 10 bases, and nucleotide quenching. The similar binding characteristics of left-handed L-DNA were evaluated in comparison with right-handed DNA to quantify the effect of each quenching scheme. These results were applied to the Adaptive PCR method, which monitors fluorescently-labeled L-DNA as a sentinel for analogous unlabeled D-DNA in the reaction. All of the tested fluorophores and quenching schemes increased the annealing temperature of the oligonucleotide pairs by values ranging from 0.5 to 8.5 °C relative to unlabeled oligonucleotides. The design with the smallest increase (0.5 °C) was a sense strand with a FAM fluorophore and an anti-sense strand with Black Hole Quencher 2 offset by 10 bases from the FAM. An identical design that did not offset the quencher molecules resulted in a shift in annealing temperature of 5 °C. PCR was performed using temperature switching based on each of these L-DNA designs, and efficiency was significantly increased for the 10-base offset design, which had the smallest shift in annealing temperature. These results highlight the importance of selecting an appropriate fluorescence quenching scheme for nucleic acid optical signals.
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Affiliation(s)
- Zackary A Zimmers
- 5932 Stevenson Center Science and Engineering, Vanderbilt University
| | - Nicholas M Adams
- 5932 Stevenson Center Science and Engineering, Vanderbilt University
| | - William E Gabella
- 5932 Stevenson Center Science and Engineering, Vanderbilt University
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18
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Leelawong M, Adams NM, Gabella WE, Wright DW, Haselton FR. Detection of Single-Nucleotide Polymorphism Markers of Antimalarial Drug Resistance Directly from Whole Blood. J Mol Diagn 2019; 21:623-631. [PMID: 31204166 DOI: 10.1016/j.jmoldx.2019.02.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/12/2018] [Accepted: 02/22/2019] [Indexed: 02/01/2023] Open
Abstract
Monitoring of antimalarial resistance is important to prevent its further spread, but the available options for assessing resistance are less than ideal for field settings. Although molecular detection is perhaps the most efficient method, it is also the most complex because it requires DNA extraction and PCR instrumentation. To develop a more deployable approach, we designed new probes, which, when used in combination with an inhibitor-tolerant Taq polymerase, enable single-nucleotide polymorphism genotyping directly from whole blood. The probes feature two strategic design elements: locked nucleic acids to enhance specificity and the reporter dyes Cy5 and TEX615, which have less optical overlap with the blood absorbance spectra than other commonly used dyes. Probe performance was validated on a traditional laboratory-based instrument and then further tested on a field-deployable Adaptive PCR instrument to develop a point-of-care platform appropriate for use in malaria settings. The probes discriminated between wild-type Plasmodium falciparum and the chloroquine-resistant CRT PF3D7_0709000:c.227A>C (p.Lys76Thr) mutant in the presence of 2% blood. Additionally, in allelic discrimination plots with the new probes, samples clustered more closely to their respective axes compared with samples using minor groove binder probes with 6-FAM and VIC reporter dyes. Our strategy greatly simplifies single-nucleotide polymorphism detection and provides a more accessible alternative for antimalarial resistance surveillance in the field.
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Affiliation(s)
- Mindy Leelawong
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee
| | - Nicholas M Adams
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee
| | - William E Gabella
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee
| | - David W Wright
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee.
| | - Frederick R Haselton
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee; Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee.
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19
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Adams NM, Lumaquin D, Santosa EK, Whitlock BM, Jackson BT, Le Luduec JB, Sottile R, Weizman OE, Huse M, Hsu KC, Sun JC. Cytomegalovirus infection drives avidity selection of natural killer cells. The Journal of Immunology 2019. [DOI: 10.4049/jimmunol.202.supp.76.3] [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] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Adaptive lymphocyte clones with the greatest receptor affinity tend to dominate primary and secondary immune responses. Strength of receptor signal and receptor abundance, along with competition for antigen and cytokines, drive preferential outgrowth of certain clones, shaping the effector and memory pool in selection processes known as affinity and avidity maturation. Natural killer (NK) cells are innate lymphocytes capable of “adaptive” responses following infectious challenges. However, whether NK cells undergo a similar selection process on the basis of their avidity for cognate ligand is not known. Here, we show that NK cells with a broad range of avidities for the mouse cytomegalovirus (MCMV) glycoprotein m157 are initially recruited after virus infection, but those with highest avidity are selected to undergo the greatest clonal expansion to comprise the memory NK cell population. Furthermore, pre-established levels of Ly49H receptor expression within the Ly49H+ NK cell pool dictated the functional contribution of a given NK cell during MCMV infection, with lower avidity NK cells possessing greater capacity for IFN-γ production, and higher avidity NK cells possessing greater capacity for cytotoxicity and adaptive responses. Moreover, we provide evidence for avidity selection also occurring in human NK cells during human CMV (HCMV) infection. These results provide a mechanistic understanding of how heterogeneity in NK cell avidity underlies the diversification of NK cell effector function during a primary antiviral immune response, and how the process of avidity selection may serve to produce the most potent memory NK cell pool.
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20
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Seelige R, Saddawi-Konefka R, Adams NM, Picarda G, Sun JC, Benedict CA, Bui JD. Interleukin-17D and Nrf2 mediate initial innate immune cell recruitment and restrict MCMV infection. Sci Rep 2018; 8:13670. [PMID: 30209334 PMCID: PMC6135835 DOI: 10.1038/s41598-018-32011-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [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: 03/16/2018] [Accepted: 08/31/2018] [Indexed: 12/26/2022] Open
Abstract
Innate immune cells quickly infiltrate the site of pathogen entry and not only stave off infection but also initiate antigen presentation and promote adaptive immunity. The recruitment of innate leukocytes has been well studied in the context of extracellular bacterial and fungal infection but less during viral infections. We have recently shown that the understudied cytokine Interleukin (IL)-17D can mediate neutrophil, natural killer (NK) cell and monocyte infiltration in sterile inflammation and cancer. Herein, we show that early immune cell accumulation at the peritoneal site of infection by mouse cytomegalovirus (MCMV) is mediated by IL-17D. Mice deficient in IL-17D or the transcription factor Nuclear factor (erythroid-derived 2)-like 2 (Nrf2), an inducer of IL-17D, featured an early decreased number of innate immune cells at the point of viral entry and were more susceptible to MCMV infection. Interestingly, we were able to artificially induce innate leukocyte infiltration by applying the Nrf2 activator tert-butylhydroquinone (tBHQ), which rendered mice less susceptible to MCMV infection. Our results implicate the Nrf2/IL-17D axis as a sensor of viral infection and suggest therapeutic benefit in boosting this pathway to promote innate antiviral responses.
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Affiliation(s)
- Ruth Seelige
- Department of Pathology, University of California, San Diego, CA, 92093, USA
| | | | - Nicholas M Adams
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Gaëlle Picarda
- Division of Immune Regulation, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Chris A Benedict
- Division of Immune Regulation, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA
- Center for Infectious Disease, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA
| | - Jack D Bui
- Department of Pathology, University of California, San Diego, CA, 92093, USA.
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21
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Rapp M, Lau CM, Adams NM, Weizman OE, O'Sullivan TE, Geary CD, Sun JC. Core-binding factor β and Runx transcription factors promote adaptive natural killer cell responses. Sci Immunol 2018; 2:2/18/eaan3796. [PMID: 29222089 DOI: 10.1126/sciimmunol.aan3796] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 09/12/2017] [Accepted: 11/02/2017] [Indexed: 01/03/2023]
Abstract
Natural killer (NK) cells are innate lymphocytes that have features of adaptive immunity such as clonal expansion and generation of long-lived memory. Interleukin-12 (IL-12) signaling through its downstream transcription factor signal transducer and activator of transcription 4 (STAT4) is required for the generation of memory NK cells after expansion. We identify gene loci that are highly enriched for STAT4 binding using chromatin immunoprecipitation sequencing for STAT4 and the permissive histone mark H3K4me3 in activated NK cells. We found that promoter regions of Runx1 and Runx3 are targets of STAT4 and that STAT4 binding during NK cell activation induces epigenetic modifications of Runx gene loci resulting in increased expression. Furthermore, specific ablation of Runx1, Runx3, or their binding partner Cbfb in NK cells resulted in defective clonal expansion and memory formation during viral infection, with evidence for Runx1-mediated control of a cell cycle program. Thus, our study reveals a mechanism whereby STAT4-mediated epigenetic control of individual Runx transcription factors promotes the adaptive behavior of antiviral NK cells.
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Affiliation(s)
- Moritz Rapp
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Colleen M Lau
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nicholas M Adams
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Orr-El Weizman
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Timothy E O'Sullivan
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Clair D Geary
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. .,Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, New York, NY 10065, USA
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22
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Adams NM, Lau CM, Fan X, Rapp M, Geary CD, Weizman OE, Diaz-Salazar C, Sun JC. Transcription Factor IRF8 Orchestrates the Adaptive Natural Killer Cell Response. Immunity 2018; 48:1172-1182.e6. [PMID: 29858012 PMCID: PMC6233715 DOI: 10.1016/j.immuni.2018.04.018] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [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: 08/29/2017] [Revised: 03/08/2018] [Accepted: 04/16/2018] [Indexed: 12/18/2022]
Abstract
Natural killer (NK) cells are innate lymphocytes that display features of adaptive immunity during viral infection. Biallelic mutations in IRF8 have been reported to cause familial NK cell deficiency and susceptibility to severe viral infection in humans; however, the precise role of this transcription factor in regulating NK cell function remains unknown. Here, we show that cell-intrinsic IRF8 was required for NK-cell-mediated protection against mouse cytomegalovirus infection. During viral exposure, NK cells upregulated IRF8 through interleukin-12 (IL-12) signaling and the transcription factor STAT4, which promoted epigenetic remodeling of the Irf8 locus. Moreover, IRF8 facilitated the proliferative burst of virus-specific NK cells by promoting expression of cell-cycle genes and directly controlling Zbtb32, a master regulator of virus-driven NK cell proliferation. These findings identify the function and cell-type-specific regulation of IRF8 in NK-cell-mediated antiviral immunity and provide a mechanistic understanding of viral susceptibility in patients with IRF8 mutations.
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Affiliation(s)
- Nicholas M Adams
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Colleen M Lau
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Xiying Fan
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Moritz Rapp
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Clair D Geary
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Orr-El Weizman
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Carlos Diaz-Salazar
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, New York, NY 10065, USA.
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Weizman OE, Adams NM, Schuster IS, Krishna C, Pritykin Y, Lau C, Degli-Esposti MA, Leslie CS, Sun JC, O'Sullivan TE. ILC1 Confer Early Host Protection at Initial Sites of Viral Infection. Cell 2017; 171:795-808.e12. [PMID: 29056343 DOI: 10.1016/j.cell.2017.09.052] [Citation(s) in RCA: 299] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 08/11/2017] [Accepted: 08/16/2017] [Indexed: 10/18/2022]
Abstract
Infection is restrained by the concerted activation of tissue-resident and circulating immune cells. Whether tissue-resident lymphocytes confer early antiviral immunity at local sites of primary infection prior to the initiation of circulating responses is not well understood. Furthermore, the kinetics of initial antiviral responses at sites of infection remain unclear. Here, we show that tissue-resident type 1 innate lymphoid cells (ILC1) serve an essential early role in host immunity through rapid production of interferon (IFN)-γ following viral infection. Ablation of Zfp683-dependent liver ILC1 lead to increased viral load in the presence of intact adaptive and innate immune cells critical for mouse cytomegalovirus (MCMV) clearance. Swift production of interleukin (IL)-12 by tissue-resident XCR1+ conventional dendritic cells (cDC1) promoted ILC1 production of IFN-γ in a STAT4-dependent manner to limit early viral burden. Thus, ILC1 contribute an essential role in viral immunosurveillance at sites of initial infection in response to local cDC1-derived proinflammatory cytokines.
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Affiliation(s)
- Orr-El Weizman
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nicholas M Adams
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Iona S Schuster
- Immunology and Virology Program, Centre for Ophthalmology and Visual Science, The University of Western Australia, Crawley, WA, Australia; Centre for Experimental Immunology, Lions Eye Institute, Nedlands, WA, Australia
| | - Chirag Krishna
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yuri Pritykin
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Colleen Lau
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Mariapia A Degli-Esposti
- Immunology and Virology Program, Centre for Ophthalmology and Visual Science, The University of Western Australia, Crawley, WA, Australia; Centre for Experimental Immunology, Lions Eye Institute, Nedlands, WA, Australia
| | - Christina S Leslie
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, New York, NY 10065, USA.
| | - Timothy E O'Sullivan
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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Bauer WS, Gulka CP, Silva-Baucage L, Adams NM, Haselton FR, Wright DW. Metal Affinity-Enabled Capture and Release Antibody Reagents Generate a Multiplex Biomarker Enrichment System that Improves Detection Limits of Rapid Diagnostic Tests. Anal Chem 2017; 89:10216-10223. [DOI: 10.1021/acs.analchem.7b01513] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Westley S. Bauer
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Christopher P. Gulka
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Lidalee Silva-Baucage
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Nicholas M. Adams
- Department
of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Frederick R. Haselton
- Department
of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - David W. Wright
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
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Adams NM, O'Sullivan TE, Geary CD, Karo JM, Amezquita RA, Joshi NS, Kaech SM, Sun JC. NK Cell Responses Redefine Immunological Memory. J Immunol 2017; 197:2963-2970. [PMID: 27824591 DOI: 10.4049/jimmunol.1600973] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 06/30/2016] [Indexed: 01/16/2023]
Abstract
Immunological memory has traditionally been regarded as a unique trait of the adaptive immune system. Nevertheless, there is evidence of immunological memory in lower organisms and invertebrates, which lack an adaptive immune system. Despite their innate ability to rapidly produce effector cytokines and kill virally infected or transformed cells, NK cells also exhibit adaptive characteristics such as clonal expansion, longevity, self-renewal, and robust recall responses to antigenic or nonantigenic stimuli. In this review, we highlight the intracellular and extracellular requirements for memory NK cell generation and describe the emerging evidence for memory precursor NK cells and their derivation.
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Affiliation(s)
- Nicholas M Adams
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | | | - Clair D Geary
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Jenny M Karo
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Robert A Amezquita
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520; and
| | - Nikhil S Joshi
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520; and
| | - Susan M Kaech
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520; and
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065; .,Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, New York, NY 10065
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Bauer WS, Kimmel DW, Adams NM, Gibson LE, Scherr TF, Richardson KA, Conrad JA, Matakala HK, Haselton FR, Wright DW. Magnetically-enabled biomarker extraction and delivery system: towards integrated ASSURED diagnostic tools. Analyst 2017; 142:1569-1580. [PMID: 28386613 PMCID: PMC5674985 DOI: 10.1039/c7an00278e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [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] [Indexed: 11/21/2022]
Abstract
Diagnosis of asymptomatic malaria poses a great challenge to global disease elimination efforts. Healthcare infrastructure in rural settings cannot support existing state-of-the-art tools necessary to diagnose asymptomatic malaria infections. Instead, lateral flow immunoassays (LFAs) are widely used as a diagnostic tool in malaria endemic areas. While LFAs are simple and easy to use, they are unable to detect low levels of parasite infection. We have developed a field deployable Magnetically-enabled Biomarker Extraction And Delivery System (mBEADS) that significantly improves limits of detection for several commercially available LFAs. Integration of mBEADS with leading commercial Plasmodium falciparum malaria LFAs improves detection limits to encompass an estimated 95% of the disease reservoir. This user-centered mBEADS platform makes significant improvements to a previously cumbersome malaria biomarker enrichment strategy by improving reagent stability, decreasing the processing time 10-fold, and reducing the assay cost 10-fold. The resulting mBEADS process adds just three minutes and less than $0.25 to the total cost of a single LFA, thus balancing sensitivity and practicality to align with the World Health Organization's ASSURED criteria for point-of-care (POC) testing.
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Affiliation(s)
- Westley S Bauer
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA.
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Bauer WS, Richardson KA, Adams NM, Ricks KM, Gasperino DJ, Ghionea SJ, Rosen M, Nichols KP, Weigl BH, Haselton FR, Wright DW. Rapid concentration and elution of malarial antigen histidine-rich protein II using solid phase Zn(II) resin in a simple flow-through pipette tip format. Biomicrofluidics 2017; 11:034115. [PMID: 28652885 PMCID: PMC5457299 DOI: 10.1063/1.4984788] [Citation(s) in RCA: 7] [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: 04/05/2017] [Accepted: 05/18/2017] [Indexed: 05/31/2023]
Abstract
Rapid diagnostic tests (RDTs) designed to function at the point of care are becoming more prevalent in malaria diagnostics because of their low cost and simplicity. While many of these tests function effectively with high parasite density samples, their poor sensitivity can often lead to misdiagnosis when parasitemia falls below 100 parasites/μl. In this study, a flow-through pipette-based column was explored as a cost-effective means to capture and elute more Plasmodium falciparum histidine-rich protein II (HRPII) antigen, concentrating the biomarker available in large-volume lysed whole blood samples into volumes compatible with Plasmodium falciparum-specific RDTs. A systematic investigation of immobilized metal affinity chromatography divalent metal species and solid phase supports established the optimal design parameters necessary to create a flow-through column incorporated into a standard pipette tip. The bidirectional flow inherent to this format maximizes mixing efficiency so that in less than 5 min of sample processing, the test band signal intensity was increased up to a factor of twelve from HRPII concentrations as low as 25 pM. In addition, the limit of detection per sample was decreased by a factor of five when compared to the RDT manufacturer's suggested protocol. Both the development process and commercial viability of this application are explored, serving as a potential model for future applications.
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Affiliation(s)
- Westley S Bauer
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Kelly A Richardson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Nicholas M Adams
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Keersten M Ricks
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - David J Gasperino
- Intellectual Ventures Laboratory, 14360 SE Eastgate Way, Bellevue, Washington 98007, USA
| | - Simon J Ghionea
- Intellectual Ventures Laboratory, 14360 SE Eastgate Way, Bellevue, Washington 98007, USA
| | - Mathew Rosen
- Intellectual Ventures Laboratory, 14360 SE Eastgate Way, Bellevue, Washington 98007, USA
| | - Kevin P Nichols
- Intellectual Ventures Laboratory, 14360 SE Eastgate Way, Bellevue, Washington 98007, USA
| | - Bernhard H Weigl
- Intellectual Ventures Laboratory, 14360 SE Eastgate Way, Bellevue, Washington 98007, USA
| | | | - David W Wright
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
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Abstract
Polymerase chain reaction (PCR) is dependent on two key hybridization events during each cycle of amplification, primer annealing and product melting. To ensure that these hybridization events occur, current PCR approaches rely on temperature set points and reaction contents that are optimized and maintained using rigid thermal cycling programs and stringent sample preparation procedures. This report describes a fundamentally simpler and more robust PCR design that dynamically controls thermal cycling by more directly monitoring the two key hybridization events during the reaction. This is achieved by optically sensing the annealing and melting of mirror-image l-DNA analogs of the reaction's primers and targets. Because the properties of l-DNA enantiomers parallel those of natural d-DNAs, the l-DNA reagents indicate the cycling conditions required for effective primer annealing and product melting during each cycle without interfering with the reaction. This hybridization-sensing approach adapts in real time to variations in reaction contents and conditions that impact primer annealing and product melting and eliminates the requirement for thermal calibrations and cycling programs. Adaptive PCR is demonstrated to amplify DNA targets with high efficiency and specificity under both controlled conditions and conditions that are known to cause traditional PCR to fail. The advantages of this approach promise to make PCR-based nucleic acid analysis simpler, more robust, and more accessible outside of well-controlled laboratory settings.
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Affiliation(s)
- Nicholas M Adams
- Department of Biomedical Engineering, ‡Department of Physics and Astronomy, and §Department of Chemistry, Vanderbilt University , Nashville, Tennessee 37235, United States
| | - William E Gabella
- Department of Biomedical Engineering, ‡Department of Physics and Astronomy, and §Department of Chemistry, Vanderbilt University , Nashville, Tennessee 37235, United States
| | - Austin N Hardcastle
- Department of Biomedical Engineering, ‡Department of Physics and Astronomy, and §Department of Chemistry, Vanderbilt University , Nashville, Tennessee 37235, United States
| | - Frederick R Haselton
- Department of Biomedical Engineering, ‡Department of Physics and Astronomy, and §Department of Chemistry, Vanderbilt University , Nashville, Tennessee 37235, United States
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Ricks KM, Adams NM, Scherr TF, Haselton FR, Wright DW. Direct transfer of HRPII-magnetic bead complexes to malaria rapid diagnostic tests significantly improves test sensitivity. Malar J 2016; 15:399. [PMID: 27495329 PMCID: PMC4975893 DOI: 10.1186/s12936-016-1448-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [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] [Received: 04/15/2016] [Accepted: 07/20/2016] [Indexed: 12/24/2022] Open
Abstract
Background The characteristic ease of use, rapid time to result, and low cost of malaria rapid diagnostic tests (RDTs) promote their widespread use at the point-of-care for malaria detection and surveillance. However, in many settings, the success of malaria elimination campaigns depends on point-of-care diagnostics with greater sensitivity than currently available RDTs. To address this need, a sample preparation method was developed to deliver more biomarkers onto a malaria RDT by concentrating the biomarker from blood sample volumes that are too large to be directly applied to a lateral flow strip. Methods In this design, Ni–NTA-functionalized magnetic beads captured the Plasmodium falciparum biomarker HRPII from a P. falciparum D6 culture spiked blood sample. This transfer of magnetic beads to the RDT was facilitated by an inexpensive 3D-printed apparatus that aligned the sample tube with the sample deposition pad and a magnet beneath the RDT. Biomarkers were released from the bead surface onto the lateral flow strip using imidazole-spiked running buffer. Kinetics of HRPII binding to the Ni–NTA beads as a function of blood sample volume were explored prior to determining the effect of the proposed method on the limit of detection of Paracheck RDTs. Results More than 80 % of HRPII biomarkers were extracted from blood sample volumes ranging from 25 to 250 µL. The time required to reach 80 % binding ranged from 5 to 60 min, depending on sample volume. Using 250 μL of blood and a 30-min biomarker binding time, the limit of detection of the Paracheck Pf RDT brand was improved by 21-fold, resulting in a limit of detection below 1 parasite/μL. Conclusions This approach has the sensitivity and simplicity required to assist in malaria elimination campaigns in settings with limited access to clinical and laboratory resources. Electronic supplementary material The online version of this article (doi:10.1186/s12936-016-1448-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Keersten M Ricks
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
| | - Nicholas M Adams
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37235, USA
| | - Thomas F Scherr
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37235, USA
| | - Frederick R Haselton
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA.,Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37235, USA
| | - David W Wright
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA.
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O'Sullivan TE, Rapp M, Fan X, Weizman OE, Bhardwaj P, Adams NM, Walzer T, Dannenberg AJ, Sun JC. Adipose-Resident Group 1 Innate Lymphoid Cells Promote Obesity-Associated Insulin Resistance. Immunity 2016; 45:428-41. [PMID: 27496734 DOI: 10.1016/j.immuni.2016.06.016] [Citation(s) in RCA: 207] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 04/05/2016] [Accepted: 05/02/2016] [Indexed: 01/20/2023]
Abstract
Innate lymphoid cells (ILCs) function to protect epithelial barriers against pathogens and maintain tissue homeostasis in both barrier and non-barrier tissues. Here, utilizing Eomes reporter mice, we identify a subset of adipose group 1 ILC (ILC1) and demonstrate a role for these cells in metabolic disease. Adipose ILC1s were dependent on the transcription factors Nfil3 and T-bet but phenotypically and functionally distinct from adipose mature natural killer (NK) and immature NK cells. Analysis of parabiotic mice revealed that adipose ILC1s maintained long-term tissue residency. Diet-induced obesity drove early production of interleukin (IL)-12 in adipose tissue depots and led to the selective proliferation and accumulation of adipose-resident ILC1s in a manner dependent on the IL-12 receptor and STAT4. ILC1-derived interferon-γ was necessary and sufficient to drive proinflammatory macrophage polarization to promote obesity-associated insulin resistance. Thus, adipose-resident ILC1s contribute to obesity-related pathology in response to dysregulated local proinflammatory cytokine production.
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Affiliation(s)
- Timothy E O'Sullivan
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Moritz Rapp
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Xiying Fan
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Orr-El Weizman
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Priya Bhardwaj
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Nicholas M Adams
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Thierry Walzer
- Centre International de Recherche en Infectiologie (CIRI), 69007 Lyon, France
| | - Andrew J Dannenberg
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, New York, NY 10065, USA.
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Adams NM, Rapp M, Sun JCY. The transcription factor IRF8 regulates natural killer cell development and response to cytomegalovirus infection. The Journal of Immunology 2016. [DOI: 10.4049/jimmunol.196.supp.129.1] [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] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Interferon regulatory factor 8 (IRF8) is a transcription factor critical for specifying monocyte and dendritic cell lineage fate and for directing B cell development, yet its function in natural killer (NK) cells is not understood. NK cells are innate lymphocytes that develop in the bone marrow and are capable of antigen-specific clonal proliferation. We observe in mixed bone marrow chimeric mice that despite a prevalent NK progenitor (NKP) population compared to wild-type, peripheral Irf8−/− NK cells exhibit proper maturation and full functionality. However, using an adoptive transfer system, we demonstrate that IRF8 is indispensable for robust expansion of NK cells in response to mouse cytomegalovirus (MCMV). Consistent with this finding, Ly49H+ NK cells upregulate Irf8 transcript during the early stages of MCMV infection. Furthermore, the Irf8 locus is dynamically regulated upon activation, showing extensive STAT4 binding at promoter and enhancer regions, and upregulation of the activating epigenetic marks H3K4me3 and H3K4Ac27. Thus, our work elucidates the functional contribution of IRF8 during NK cell development and antiviral responses.
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Adams NM, Bordelon H, Wang KKA, Albert LE, Wright DW, Haselton FR. Comparison of three magnetic bead surface functionalities for RNA extraction and detection. ACS Appl Mater Interfaces 2015; 7:6062-9. [PMID: 25710198 DOI: 10.1021/am506374t] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Magnetic beads are convenient for extracting nucleic acid biomarkers from biological samples prior to molecular detection. These beads are available with a variety of surface functionalities designed to capture particular subsets of RNA. We hypothesized that bead surface functionality affects binding kinetics, processing simplicity, and compatibility with molecular detection strategies. In this report, three magnetic bead surface chemistries designed to bind nucleic acids, silica, oligo (dT), and a specific oligonucleotide sequence were evaluated. Commercially available silica-coated and oligo (dT) beads, as well as beads functionalized with oligonucleotides complementary to respiratory syncytial virus (RSV) nucleocapsid gene, respectively recovered ∼75, ∼71, and ∼7% target RSV mRNA after a 1 min of incubation time in a surrogate patient sample spiked with the target. RSV-specific beads required much longer incubation times to recover amounts of the target comparable to the other beads (∼77% at 180 min). As expected, silica-coated beads extracted total RNA, oligo (dT) beads selectively extracted total mRNA, and RSV-specific beads selectively extracted RSV N gene mRNA. The choice of bead functionality is generally dependent on the target detection strategy. The silica-coated beads are most suitable for applications that require nucleic acids other than mRNA, especially with detection strategies that are tolerant of a high concentration of nontarget background nucleic acids, such as RT-PCR. On the other hand, oligo (dT) beads are best-suited for mRNA targets, as they bind biomarkers rapidly, have relatively high recovery, and enable detection strategies to be performed directly on the bead surface. Sequence-specific beads may be best for applications that are not tolerant of a high concentration of nontarget nucleic acids that require short RNA sequences without poly(A) tails, such as microRNAs, or that perform RNA detection directly on the bead surface.
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Affiliation(s)
- Nicholas M Adams
- †Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
- ‡Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Hali Bordelon
- †Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Kwo-Kwang A Wang
- ‡Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Laura E Albert
- †Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - David W Wright
- ‡Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Frederick R Haselton
- †Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
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Adams NM, Wang KKA, Caprioli AC, Thomas LC, Kankia B, Haselton FR, Wright DW. Quadruplex priming amplification for the detection of mRNA from surrogate patient samples. Analyst 2014; 139:1644-52. [PMID: 24503712 DOI: 10.1039/c3an02261g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Simple and rapid methods for detecting mRNA biomarkers from patient samples are valuable in settings with limited access to laboratory resources. In this report, we describe the development and evaluation of a self-contained assay to extract and quantify mRNA biomarkers from complex samples using a novel nucleic acid-based molecular sensor called quadruplex priming amplification (QPA). QPA is a simple and robust isothermal nucleic acid amplification method that exploits the stability of the G-quadruplex nucleotide structure to drive spontaneous strand melting from a specific DNA template sequence. Quantification of mRNA was enabled by integrating QPA with a magnetic bead-based extraction method using an mRNA-QPA interface reagent. The assay was found to maintain >90% of the maximum signal over a 4 °C range of operational temperatures (64-68 °C). QPA had a dynamic range spanning four orders of magnitude, with a limit of detection of ~20 pM template molecules using a highly controlled heating and optical system and a limit of detection of ~250 pM using a less optimal water bath and plate reader. These results demonstrate that this integrated approach has potential as a simple and effective mRNA biomarker extraction and detection assay for use in limited resource settings.
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Affiliation(s)
- N M Adams
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA.
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Adams NM, Olmsted IR, Haselton FR, Bornhop DJ, Wright DW. The effect of hybridization-induced secondary structure alterations on RNA detection using backscattering interferometry. Nucleic Acids Res 2013; 41:e103. [PMID: 23519610 PMCID: PMC3643578 DOI: 10.1093/nar/gkt165] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [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] [Indexed: 01/30/2023] Open
Abstract
Backscattering interferometry (BSI) has been used to successfully monitor molecular interactions without labeling and with high sensitivity. These properties suggest that this approach might be useful for detecting biomarkers of infection. In this report, we identify interactions and characteristics of nucleic acid probes that maximize BSI signal upon binding the respiratory syncytial virus nucleocapsid gene RNA biomarker. The number of base pairs formed upon the addition of oligonucleotide probes to a solution containing the viral RNA target correlated with the BSI signal magnitude. Using RNA folding software mfold, we found that the predicted number of unpaired nucleotides in the targeted regions of the RNA sequence generally correlated with BSI sensitivity. We also demonstrated that locked nucleic acid (LNA) probes improved sensitivity approximately 4-fold compared to DNA probes of the same sequence. We attribute this enhancement in BSI performance to the increased A-form character of the LNA:RNA hybrid. A limit of detection of 624 pM, corresponding to ∼10(5) target molecules, was achieved using nine distinct ∼23-mer DNA probes complementary to regions distributed along the RNA target. Our results indicate that BSI has promise as an effective tool for sensitive RNA detection and provides a road map for further improving detection limits.
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Affiliation(s)
- Nicholas M Adams
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
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Perez JW, Adams NM, Zimmerman GR, Haselton FR, Wright DW. Detecting respiratory syncytial virus using nanoparticle-amplified immuno-PCR. Methods Mol Biol 2013; 1026:93-110. [PMID: 23749572 DOI: 10.1007/978-1-62703-468-5_8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Early-stage detection is essential for effective treatment of pediatric virus infections. In traditional -immuno-PCR, a single antibody recognition event is associated with one to three DNA tags, which are subsequently amplified by PCR. In this protocol, we describe a nanoparticle-amplified immuno-PCR assay that combines antibody recognition of traditional ELISA with a 50-fold nanoparticle valence amplification step followed by amplification by traditional PCR. The assay detects a respiratory syncytial virus (RSV) surface fusion protein using a Synagis antibody bound to a 15 nm gold nanoparticle co-functionalized with thiolated DNA complementary to a hybridized 76-base Tag DNA. The Tag DNA to Synagis ratio is 50 to 1. The presence of virus particles triggers the formation of a "sandwich" complex comprised of the gold nanoparticle construct, virus, and a 1 μm antibody-functionalized magnetic particle used for extraction. Virus-containing complexes are isolated using a magnet, DNA tags released by heating to 95 °C, and detected via real-time PCR. The limit of detection of the nanoparticle-amplified immuno-PCR assay was compared to traditional ELISA and traditional RT-PCR using RSV-infected HEp-2 cell extracts. Nanoparticle-amplified immuno-PCR showed a ∼4,000-fold improvement in the limit of detection compared to ELISA and a fourfold improvement in the limit of detection compared to traditional RT-PCR. Nanoparticle-amplified immuno-PCR offers a viable platform for the development of an early-stage diagnostics requiring an exceptionally low limit of detection.
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Affiliation(s)
- Jonas W Perez
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
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Adams NM, Creecy AE, Majors CE, Wariso BA, Short PA, Wright DW, Haselton FR. Design criteria for developing low-resource magnetic bead assays using surface tension valves. Biomicrofluidics 2013; 7:14104. [PMID: 24403996 PMCID: PMC3562276 DOI: 10.1063/1.4788922] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Accepted: 01/08/2013] [Indexed: 05/12/2023]
Abstract
Many assays for biological sample processing and diagnostics are not suitable for use in settings that lack laboratory resources. We have recently described a simple, self-contained format based on magnetic beads for extracting infectious disease biomarkers from complex biological samples, which significantly reduces the time, expertise, and infrastructure required. This self-contained format has the potential to facilitate the application of other laboratory-based sample processing assays in low-resource settings. The technology is enabled by immiscible fluid barriers, or surface tension valves, which stably separate adjacent processing solutions within millimeter-diameter tubing and simultaneously permit the transit of magnetic beads across the interfaces. In this report, we identify the physical parameters of the materials that maximize fluid stability and bead transport and minimize solution carryover. We found that fluid stability is maximized with ≤0.8 mm i.d. tubing, valve fluids of similar density to the adjacent solutions, and tubing with ≤20 dyn/cm surface energy. Maximizing bead transport was achieved using ≥2.4 mm i.d. tubing, mineral oil valve fluid, and a mass of 1-3 mg beads. The amount of solution carryover across a surface tension valve was minimized using ≤0.2 mg of beads, tubing with ≤20 dyn/cm surface energy, and air separators. The most favorable parameter space for valve stability and bead transport was identified by combining our experimental results into a single plot using two dimensionless numbers. A strategy is presented for developing additional self-contained assays based on magnetic beads and surface tension valves for low-resource diagnostic applications.
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Affiliation(s)
- Nicholas M Adams
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, USA ; Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Amy E Creecy
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Catherine E Majors
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Bathsheba A Wariso
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Philip A Short
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - David W Wright
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Frederick R Haselton
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, USA
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Adams NM, Jackson SR, Haselton FR, Wright DW. Design, synthesis, and characterization of nucleic-acid-functionalized gold surfaces for biomarker detection. Langmuir 2012; 28:1068-82. [PMID: 21905721 PMCID: PMC4211628 DOI: 10.1021/la2028862] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Nucleic-acid-functionalized gold surfaces have been used extensively for the development of biological sensors. The development of an effective biomarker detection assay requires careful design, synthesis, and characterization of probe components. In this Feature Article, we describe fundamental probe development constraints and provide a critical appraisal of the current methodologies and applications in the field. We discuss critical issues and obstacles that impede the sensitivity and reliability of the sensors to underscore the challenges that must be met to advance the field of biomarker detection.
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Affiliation(s)
- Nicholas M. Adams
- VU Station B 351822, Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA. VU Station B 351631, Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37235, USA
| | - Stephen R. Jackson
- VU Station B 351822, Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Frederick R. Haselton
- VU Station B 351631, Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37235, USA
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Bordelon H, Adams NM, Klemm AS, Russ PK, Williams JV, Talbot HK, Wright DW, Haselton FR. Development of a low-resource RNA extraction cassette based on surface tension valves. ACS Appl Mater Interfaces 2011; 3:2161-8. [PMID: 21604768 PMCID: PMC3129697 DOI: 10.1021/am2004009] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Nucleic acid-based diagnostics are highly sensitive and specific, but are easily disrupted by the presence of interferents in biological samples. In a laboratory or hospital setting, the influence of these interferents can be minimized using an RNA or DNA extraction procedure prior to analysis. However, in low-resource settings, limited access to specialized instrumentation and trained personnel presents challenges that impede sample preparation. We have developed a self-contained nucleic acid extraction cassette suitable for operation in a low-resource setting. This simple design contains processing solutions preloaded within a continuous length of 1.6 mm inner diameter Tygon tubing. Processing solutions are separated by air gaps and held in place during processing by the surface tension forces at the liquid-air interface, viz. surface tension valves. Nucleic acids preferentially adsorbed to silica-coated magnetic particles are separated from sample interferents using an external magnet to transfer the nucleic acid biomarker through successive solutions to precipitate, wash and elute in the final cassette solution. The efficiency of the extraction cassette was evaluated using quantitative reverse transcriptase PCR (qRT-PCR) following extraction of respiratory syncytial virus (RSV) RNA. RNA was recovered from TE buffer or from lysates of RSV infected HEp-2 cells with 55 and 33% efficiency, respectively, of the Qiagen RNeasy kit. Recovery of RSV RNA from RSV infected HEp-2 cells was similar at 30% of the RNeasy kit. An overall limit of detection after extraction was determined to be nearly identical (97.5%) to a laboratory-based commercially available kit. These results indicate that this extraction cassette design has the potential to be an effective sample preparation device suitable for use in a low-resource setting.
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Affiliation(s)
- Hali Bordelon
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37235
| | - Nicholas M. Adams
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37235
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235
| | - Amy S. Klemm
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37235
| | - Patricia K. Russ
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37235
| | - John V. Williams
- Department of Pediatric Infectious Diseases, Vanderbilt University, Nashville, TN 37235
| | - H. Keipp Talbot
- Department of Pediatric Infectious Diseases, Vanderbilt University, Nashville, TN 37235
- Department of Internal Medicine, Vanderbilt University, Nashville, TN 37235
| | - David W. Wright
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235
| | - Frederick R. Haselton
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37235
- To whom correspondence should be addressed: Rick Haselton, Biomedical Engineering, VU Station B - Box 351631, Vanderbilt University, Nashville, TN 37235, Tel: 615-322-6622; Fax: 615-343-7919,
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Abstract
We present a loss based method for comparing the predictive performance of diagnostic tests. Unlike standard assessment mechanisms, like the area under the receiver-operating characteristic curve and the misclassification rate, our method takes specific advantage of any information that can be obtained about misclassification costs. We argue that not taking costs into account can lead to incorrect conclusions, and illustrate with two examples.
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Affiliation(s)
- N M Adams
- Department of Mathematics, Imperial College, London, UK.
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Abstract
In this note we use examples from the literature to illustrate some poor practices in assessing the performance of supervised classification rules, and we suggest guidelines for better methodology. We also describe a new assessment criterion that is suitable for the needs of many practical problems.
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Affiliation(s)
- N M Adams
- Department of Mathematics, Imperial College, Huxley Building, 180 Queen's Gate, London, SW7 2BZ, UK
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