1
|
Xu AM, Haro M, Walts AE, Hu Y, John J, Karlan BY, Merchant A, Orsulic S. Spatiotemporal architecture of immune cells and cancer-associated fibroblasts in high-grade serous ovarian carcinoma. Sci Adv 2024; 10:eadk8805. [PMID: 38630822 PMCID: PMC11023532 DOI: 10.1126/sciadv.adk8805] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 03/15/2024] [Indexed: 04/19/2024]
Abstract
High-grade serous ovarian carcinoma (HGSOC), the deadliest form of ovarian cancer, is typically diagnosed after it has metastasized and often relapses after standard-of-care platinum-based chemotherapy, likely due to advanced tumor stage, heterogeneity, and immune evasion and tumor-promoting signaling from the tumor microenvironment. To understand how spatial heterogeneity contributes to HGSOC progression and early relapse, we profiled an HGSOC tissue microarray of patient-matched longitudinal samples from 42 patients. We found spatial patterns associated with early relapse, including changes in T cell localization, malformed tertiary lymphoid structure (TLS)-like aggregates, and increased podoplanin-positive cancer-associated fibroblasts (CAFs). Using spatial features to compartmentalize the tissue, we found that plasma cells distribute in two different compartments associated with TLS-like aggregates and CAFs, and these distinct microenvironments may account for the conflicting reports about the role of plasma cells in HGSOC prognosis.
Collapse
Affiliation(s)
- Alexander M. Xu
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Division of Hematology and Cellular Therapy, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Marcela Haro
- Department of Obstetrics and Gynecology and Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ann E. Walts
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ye Hu
- Department of Obstetrics and Gynecology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Joshi John
- Department of Veterans Affairs, Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA
- Department of Medicine, Division of Geriatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Beth Y. Karlan
- Department of Obstetrics and Gynecology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Akil Merchant
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Division of Hematology and Cellular Therapy, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Sandra Orsulic
- Department of Obstetrics and Gynecology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Veterans Affairs, Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA 90095, USA
| |
Collapse
|
2
|
Figueiredo JC, Levy J, Choi SY, Xu AM, Merin NM, Hamid O, Lemos T, Nguyen N, Nadri M, Gonzalez A, Mahov S, Darrah JM, Gong J, Paquette RL, Mita AC, Vescio RA, Salvy SJ, Mehmi I, Hendifar AE, Natale R, Tourtellotte WG, Krishnan Ramanujan V, Huynh CA, Sobhani K, Reckamp KL, Merchant AA. Low booster uptake in cancer patients despite health benefits. medRxiv 2023:2023.10.25.23297483. [PMID: 37961284 PMCID: PMC10635201 DOI: 10.1101/2023.10.25.23297483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Patients with cancer are at increased risk of death from COVID-19 and have reduced immune responses to SARS-CoV2 vaccines, necessitating regular boosters. We performed comprehensive chart reviews, surveys of patients attitudes, serology for SARS-CoV-2 antibodies and T-cell receptor (TCR) β sequencing for cellular responses on a cohort of 982 cancer patients receiving active cancer therapy accrued between November-3-2020 and Mar-31-2023. We found that 92·3% of patients received the primer vaccine, 70·8% received one monovalent booster, but only 30·1% received a bivalent booster. Booster uptake was lower under age 50, and among African American or Hispanic patients. Nearly all patients seroconverted after 2+ booster vaccinations (>99%) and improved cellular responses, demonstrating that repeated boosters could overcome poor response to vaccination. Receipt of booster vaccinations was associated with a lower risk of all-cause mortality (HR=0·61, P=0·024). Booster uptake in high-risk cancer patients remains low and strategies to encourage booster uptake are needed. Highlights COVID-19 booster vaccinations increase antibody levels and maintain T-cell responses against SARS-CoV-2 in patients receiving various anti-cancer therapiesBooster vaccinations reduced all-cause mortality in patientsA significant proportion of patients remain unboosted and strategies are needed to encourage patients to be up-to-date with vaccinations.
Collapse
|
3
|
Li D, Pavlovitch-Bedzyk AJ, Ebinger JE, Khan A, Hamideh M, Merchant A, Figueiredo JC, Cheng S, Davis MM, McGovern DPB, Melmed GY, Xu AM, Braun J. A Paratope-Enhanced Method to Determine Breadth and Depth TCR Clonal Metrics of the Private Human T-Cell Vaccine Response after SARS-CoV-2 Vaccination. Int J Mol Sci 2023; 24:14223. [PMID: 37762524 PMCID: PMC10531868 DOI: 10.3390/ijms241814223] [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: 07/14/2023] [Revised: 09/04/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Quantitative metrics for vaccine-induced T-cell responses are an important need for developing correlates of protection and their use in vaccine-based medical management and population health. Molecular TCR analysis is an appealing strategy but currently requires a targeted methodology involving complex integration of ex vivo data (antigen-specific functional T-cell cytokine responses and TCR molecular responses) that uncover only public antigen-specific metrics. Here, we describe an untargeted private TCR method that measures breadth and depth metrics of the T-cell response to vaccine challenge using a simple pre- and post-vaccine subject sampling, TCR immunoseq analysis, and a bioinformatic approach using self-organizing maps and GLIPH2. Among 515 subjects undergoing SARS-CoV-2 mRNA vaccination, we found that breadth and depth metrics were moderately correlated between the targeted public TCR response and untargeted private TCR response methods. The untargeted private TCR method was sufficiently sensitive to distinguish subgroups of potential clinical significance also observed using public TCR methods (the reduced T-cell vaccine response with age and the paradoxically elevated T-cell vaccine response of patients on anti-TNF immunotherapy). These observations suggest the promise of this untargeted private TCR method to produce T-cell vaccine-response metrics in an antigen-agnostic and individual-autonomous context.
Collapse
Affiliation(s)
- Dalin Li
- Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (D.L.); (A.K.); (M.H.); (D.P.B.M.); (G.Y.M.)
| | - Ana Jimena Pavlovitch-Bedzyk
- Computational and Systems Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; (A.J.P.-B.); (M.M.D.)
| | - Joseph E. Ebinger
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (J.E.E.); (S.C.)
| | - Abdul Khan
- Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (D.L.); (A.K.); (M.H.); (D.P.B.M.); (G.Y.M.)
| | - Mohamed Hamideh
- Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (D.L.); (A.K.); (M.H.); (D.P.B.M.); (G.Y.M.)
| | - Akil Merchant
- Cedars-Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (A.M.); (J.C.F.); (A.M.X.)
| | - Jane C. Figueiredo
- Cedars-Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (A.M.); (J.C.F.); (A.M.X.)
| | - Susan Cheng
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (J.E.E.); (S.C.)
| | - Mark M. Davis
- Computational and Systems Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; (A.J.P.-B.); (M.M.D.)
- Department of Microbiology and Immunology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Dermot P. B. McGovern
- Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (D.L.); (A.K.); (M.H.); (D.P.B.M.); (G.Y.M.)
| | - Gil Y. Melmed
- Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (D.L.); (A.K.); (M.H.); (D.P.B.M.); (G.Y.M.)
| | - Alexander M. Xu
- Cedars-Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (A.M.); (J.C.F.); (A.M.X.)
| | - Jonathan Braun
- Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (D.L.); (A.K.); (M.H.); (D.P.B.M.); (G.Y.M.)
| |
Collapse
|
4
|
Chour W, Choi J, Xie J, Chaffee ME, Schmitt TM, Finton K, DeLucia DC, Xu AM, Su Y, Chen DG, Zhang R, Yuan D, Hong S, Ng AHC, Butler JZ, Edmark RA, Jones LC, Murray KM, Peng S, Li G, Strong RK, Lee JK, Goldman JD, Greenberg PD, Heath JR. Large libraries of single-chain trimer peptide-MHCs enable antigen-specific CD8+ T cell discovery and analysis. Commun Biol 2023; 6:528. [PMID: 37193826 PMCID: PMC10186326 DOI: 10.1038/s42003-023-04899-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 05/01/2023] [Indexed: 05/18/2023] Open
Abstract
The discovery and characterization of antigen-specific CD8+ T cell clonotypes typically involves the labor-intensive synthesis and construction of peptide-MHC tetramers. We adapt single-chain trimer (SCT) technologies into a high throughput platform for pMHC library generation, showing that hundreds can be rapidly prepared across multiple Class I HLA alleles. We use this platform to explore the impact of peptide and SCT template mutations on protein expression yield, thermal stability, and functionality. SCT libraries were an efficient tool for identifying T cells recognizing commonly reported viral epitopes. We then construct SCT libraries to capture SARS-CoV-2 specific CD8+ T cells from COVID-19 participants and healthy donors. The immunogenicity of these epitopes is validated by functional assays of T cells with cloned TCRs captured using SCT libraries. These technologies should enable the rapid analyses of peptide-based T cell responses across several contexts, including autoimmunity, cancer, or infectious disease.
Collapse
Affiliation(s)
- William Chour
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Jongchan Choi
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Jingyi Xie
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, 98195, USA
| | - Mary E Chaffee
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Thomas M Schmitt
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Kathryn Finton
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Diana C DeLucia
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Alexander M Xu
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Yapeng Su
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Daniel G Chen
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Department of Microbiology and Department of Informatics, University of Washington, Seattle, WA, 98195, USA
| | - Rongyu Zhang
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Dan Yuan
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Sunga Hong
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Alphonsus H C Ng
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Jonah Z Butler
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Rick A Edmark
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | | | - Kim M Murray
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | | | - Guideng Li
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
- Suzhou Institute of Systems Medicine, Suzhou, 215123, China
- Key Laboratory of Synthetic Biology Regulatory Element, Chinese Academy of Medical Sciences, Beijing, China
| | - Roland K Strong
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - John K Lee
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Jason D Goldman
- Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA, 98104, USA
- Division of Infectious Disease, Department of Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Philip D Greenberg
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA, 98195, USA
- Department of Immunology, University of Washington, Seattle, WA, 98195, USA
| | - James R Heath
- Institute for Systems Biology, Seattle, WA, 98109, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA.
| |
Collapse
|
5
|
Xu AM, Chour W, DeLucia DC, Su Y, Pavlovitch-Bedzyk AJ, Ng R, Rasheed Y, Davis MM, Lee JK, Heath JR. Entropic analysis of antigen-specific CDR3 domains identifies essential binding motifs shared by CDR3s with different antigen specificities. Cell Syst 2023; 14:273-284.e5. [PMID: 37001518 PMCID: PMC10355346 DOI: 10.1016/j.cels.2023.03.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 09/01/2022] [Accepted: 03/01/2023] [Indexed: 04/22/2023]
Abstract
Antigen-specific T cell receptor (TCR) sequences can have prognostic, predictive, and therapeutic value, but decoding the specificity of TCR recognition remains challenging. Unlike DNA strands that base pair, TCRs bind to their targets with different orientations and different lengths, which complicates comparisons. We present scanning parametrized by normalized TCR length (SPAN-TCR) to analyze antigen-specific TCR CDR3 sequences and identify patterns driving TCR-pMHC specificity. Using entropic analysis, SPAN-TCR identifies 2-mer motifs that decrease the diversity (entropy) of CDR3s. These motifs are the most common patterns that can predict CDR3 composition, and we identify "essential" motifs that decrease entropy in the same CDR3 α or β chain containing the 2-mer, and "super-essential" motifs that decrease entropy in both chains. Molecular dynamics analysis further suggests that these motifs may play important roles in binding. We then employ SPAN-TCR to resolve similarities in TCR repertoires against different antigens using public databases of TCR sequences.
Collapse
Affiliation(s)
- Alexander M Xu
- Institute for Systems Biology, Seattle, WA 98109, USA; Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
| | - William Chour
- Institute for Systems Biology, Seattle, WA 98109, USA; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA 91125, USA
| | - Diana C DeLucia
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Yapeng Su
- Institute for Systems Biology, Seattle, WA 98109, USA; Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Rachel Ng
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Yusuf Rasheed
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Mark M Davis
- Computational and Systems Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - John K Lee
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - James R Heath
- Institute for Systems Biology, Seattle, WA 98109, USA.
| |
Collapse
|
6
|
Huang Y, Shin JE, Xu AM, Yao C, Joung S, Wu M, Zhang R, Shin B, Foley J, Mahov SB, Modes ME, Ebinger JE, Driver M, Braun JG, Jefferies CA, Parimon T, Hayes C, Sobhani K, Merchant A, Gharib SA, Jordan SC, Cheng S, Goodridge HS, Chen P. Evidence of premature lymphocyte aging in people with low anti-spike antibody levels after BNT162b2 vaccination. iScience 2022; 25:105209. [PMID: 36188190 PMCID: PMC9510055 DOI: 10.1016/j.isci.2022.105209] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/22/2022] [Accepted: 09/22/2022] [Indexed: 11/26/2022] Open
Abstract
SARS-CoV-2 vaccines have unquestionably blunted the overall impact of the COVID-19 pandemic, but host factors such as age, sex, obesity, and other co-morbidities can affect vaccine efficacy. We identified individuals in a relatively healthy population of healthcare workers (CORALE study cohort) who had unexpectedly low peak anti-spike receptor binding domain (S-RBD) antibody levels after receiving the BNT162b2 vaccine. Compared to matched controls, "low responders" had fewer spike-specific antibody-producing B cells after the second and third/booster doses. Moreover, their spike-specific T cell receptor (TCR) repertoire had less depth and their CD4+ and CD8+T cell responses to spike peptide stimulation were less robust. Single cell transcriptomic evaluation of peripheral blood mononuclear cells revealed activation of aging pathways in low responder B and CD4+T cells that could underlie their attenuated anti-S-RBD antibody production. Premature lymphocyte aging may therefore contribute to a less effective humoral response and could reduce vaccination efficacy.
Collapse
Affiliation(s)
- Yapei Huang
- Women’s Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Juliana E. Shin
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Research Division of Immunology in the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Alexander M. Xu
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Division of Hematology and Cellular Therapy, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Changfu Yao
- Women’s Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Sandy Joung
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Min Wu
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ruan Zhang
- Comprehensive Transplant Center, Transplant Immunology Laboratory, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Bongha Shin
- Comprehensive Transplant Center, Transplant Immunology Laboratory, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Joslyn Foley
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Division of Hematology and Cellular Therapy, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Simeon B. Mahov
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Division of Hematology and Cellular Therapy, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Matthew E. Modes
- Women’s Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Joseph E. Ebinger
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Matthew Driver
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jonathan G. Braun
- Research Division of Immunology in the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Caroline A. Jefferies
- Research Division of Immunology in the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Medicine, Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Tanyalak Parimon
- Women’s Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Chelsea Hayes
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Kimia Sobhani
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Akil Merchant
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Division of Hematology and Cellular Therapy, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Sina A. Gharib
- Computational Medicine Core at Center for Lung Biology, Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA 98109, USA
| | - Stanley C. Jordan
- Comprehensive Transplant Center, Transplant Immunology Laboratory, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Susan Cheng
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Helen S. Goodridge
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Research Division of Immunology in the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Peter Chen
- Women’s Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| |
Collapse
|
7
|
Xu AM, Li D, Ebinger JE, Mengesha E, Elyanow R, Gittelman RM, Chapman H, Joung S, Botwin GJ, Pozdnyakova V, Debbas P, Mujukian A, Prostko JC, Frias EC, Stewart JL, Horizon AA, Merin N, Sobhani K, Figueiredo JC, Cheng S, Kaplan IM, McGovern DPB, Merchant A, Melmed GY, Braun J. Differences in SARS-CoV-2 Vaccine Response Dynamics Between Class-I- and Class-II-Specific T-Cell Receptors in Inflammatory Bowel Disease. Front Immunol 2022; 13:880190. [PMID: 35464463 PMCID: PMC9024211 DOI: 10.3389/fimmu.2022.880190] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 03/18/2022] [Indexed: 12/01/2022] Open
Abstract
T-cells specifically bind antigens to induce adaptive immune responses using highly specific molecular recognition, and a diverse T-cell repertoire with expansion of antigen-specific clones can indicate robust immune responses after infection or vaccination. For patients with inflammatory bowel disease (IBD), a spectrum of chronic intestinal inflammatory diseases usually requiring immunomodulatory treatment, the T-cell response has not been well characterized. Understanding the patient factors that result in strong vaccination responses is critical to guiding vaccination schedules and identifying mechanisms of T-cell responses in IBD and other immune-mediated conditions. Here we used T-cell receptor sequencing to show that T-cell responses in an IBD cohort were influenced by demographic and immune factors, relative to a control cohort of health care workers (HCWs). Subjects were sampled at the time of SARS-CoV-2 vaccination, and longitudinally afterwards; TCR Vβ gene repertoires were sequenced and analyzed for COVID-19-specific clones. We observed significant differences in the overall strength of the T-cell response by age and vaccine type. We further stratified the T-cell response into Class-I- and Class-II-specific responses, showing that Ad26.COV2.S vector vaccine induced Class-I-biased T-cell responses, whereas mRNA vaccine types led to different responses, with mRNA-1273 vaccine inducing a more Class-I-deficient T-cell response compared to BNT162b2. Finally, we showed that these T-cell patterns were consistent with antibody levels from the same patients. Our results account for the surprising success of vaccination in nominally immuno-compromised IBD patients, while suggesting that a subset of IBD patients prone to deficiencies in T-cell response may warrant enhanced booster protocols.
Collapse
Affiliation(s)
- Alexander M. Xu
- Cedars Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Dalin Li
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Joseph E. Ebinger
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Emebet Mengesha
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | | | | | - Heidi Chapman
- Adaptive Biotechnologies, Seattle, WA, United States
| | - Sandy Joung
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Gregory J. Botwin
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Valeriya Pozdnyakova
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Philip Debbas
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Angela Mujukian
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - John C. Prostko
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, United States
| | - Edwin C. Frias
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, United States
| | - James L. Stewart
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, United States
| | - Arash A. Horizon
- Center for Rheumatology Medical Group, Los Angeles, CA, United States
| | - Noah Merin
- Cedars Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Kimia Sobhani
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Jane C. Figueiredo
- Cedars Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Susan Cheng
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Ian M. Kaplan
- Adaptive Biotechnologies, Seattle, WA, United States
| | - Dermot P. B. McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Akil Merchant
- Cedars Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Gil Y. Melmed
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Jonathan Braun
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| |
Collapse
|
8
|
Guo T, Yuan X, Liu DF, Peng SH, Xu AM. LncRNA HOXA11-AS promotes migration and invasion through modulating miR-148a/WNT1/β-catenin pathway in gastric cancer. Neoplasma 2020; 67:492-500. [PMID: 32009419 DOI: 10.4149/neo_2020_190722n653] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 08/21/2019] [Indexed: 11/08/2022]
Abstract
Increasing researches have focused on the biological functions of long noncoding RNAs (lncRNAs) in human cancers. HOXA11-AS, a widely known lncRNA, has been confirmed to be involved in the progression of several cancers, including gastric cancer (GC). Whereas, the detailed mechanism of this lncRNA in GC remains to be further illuminated. The abundances of HOXA11-AS, miR-148a and WNT1 in GC tissues and cell lines were examined by qRT-PCR. Clinicopathological and Kaplan-Meier survival analyses were determined to explore the relationship between HOXA11-AS expression and outcomes of patients. Transwell assay was performed for the evaluation of cell migration and invasion. Bioinformatics, dual-luciferase reporter and RNA immunoprecipitation assays were employed to analyze the correlation between HOXA11-AS and miR-148a or miR-148a and WNT1. The protein levels of WNT1 and β-catenin were assessed by western blot assay. Results showed that HOXA11-AS and WNT1 expression levels were upregulated, while miR-148a level was downregulated in GC tissues and cell lines relative to matched controls. Elevated expression of HOXA11-AS was associated with increased tumor size, lymph node metastasis, advanced TNM stage, as well as reduced survival of GC patients. HOXA11-AS induced migration and invasion of GC cells through serving as a molecular sponge for miR-148a. Furthermore, miR-148a inactivated WNT1/β-catenin signaling pathway via directly targeting WNT1. HOXA11-AS increased WNT1/β-catenin pathway activity, which was abolished by miR-148a overexpression in GC cells. In conclusion, overexpression of HOXA11-AS contributed to migration and invasion of GC cells via activation of WNT1/β-catenin signaling pathway through repressing miR-148a, providing a prospective therapeutic target for GC.
Collapse
Affiliation(s)
- T Guo
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Department of Gastrointestinal Surgery, The Fourth Affiliated Hospital of Anhui Medical University, Hefei, China
| | - X Yuan
- Department of General Surgery, The Fourth Affiliated Hospital of Anhui Medical University, Hefei, China
| | - D F Liu
- Department of General Surgery, The Fourth Affiliated Hospital of Anhui Medical University, Hefei, China
| | - S H Peng
- Department of General Surgery, The Fourth Affiliated Hospital of Anhui Medical University, Hefei, China
| | - A M Xu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| |
Collapse
|
9
|
Ng AHC, Peng S, Xu AM, Noh WJ, Guo K, Bethune MT, Chour W, Choi J, Yang S, Baltimore D, Heath JR. MATE-Seq: microfluidic antigen-TCR engagement sequencing. Lab Chip 2019; 19:3011-3021. [PMID: 31502632 DOI: 10.1039/c9lc00538b] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Adaptive immunity is based on peptide antigen recognition. Our ability to harness the immune system for therapeutic gain relies on the discovery of the T cell receptor (TCR) genes that selectively target antigens from infections, mutated proteins, and foreign agents. Here we present a method that selectively labels peptide antigen-specific CD8+ T cells using magnetic nanoparticles functionalized with peptide-MHC tetramers, isolates these specific cells within an integrated microfluidic device, and directly amplifies the TCR genes for sequencing. Critically, the identity of the peptide recognized by the TCR is preserved, providing the link between peptide and gene. The platform requires inputs on the order of just 100 000 CD8+ T cells, can be multiplexed for simultaneous analysis of multiple peptides, and performs sorting and isolation on chip. We demonstrate 1000-fold sensitivity enhancement of detecting antigen-specific TCRs relative to bulk analysis and simultaneous capture of two virus antigen-specific TCRs from a population of T cells.
Collapse
Affiliation(s)
- Alphonsus H C Ng
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd, Pasadena, CA 91125, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Peng S, Zaretsky JM, Ng AHC, Chour W, Bethune MT, Choi J, Hsu A, Holman E, Ding X, Guo K, Kim J, Xu AM, Heath JE, Noh WJ, Zhou J, Su Y, Lu Y, McLaughlin J, Cheng D, Witte ON, Baltimore D, Ribas A, Heath JR. Sensitive Detection and Analysis of Neoantigen-Specific T Cell Populations from Tumors and Blood. Cell Rep 2019; 28:2728-2738.e7. [PMID: 31484081 PMCID: PMC6774618 DOI: 10.1016/j.celrep.2019.07.106] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 05/04/2019] [Accepted: 07/29/2019] [Indexed: 12/30/2022] Open
Abstract
Neoantigen-specific T cells are increasingly viewed as important immunotherapy effectors, but physically isolating these rare cell populations is challenging. Here, we describe a sensitive method for the enumeration and isolation of neoantigen-specific CD8+ T cells from small samples of patient tumor or blood. The method relies on magnetic nanoparticles that present neoantigen-loaded major histocompatibility complex (MHC) tetramers at high avidity by barcoded DNA linkers. The magnetic particles provide a convenient handle to isolate the desired cell populations, and the barcoded DNA enables multiplexed analysis. The method exhibits superior recovery of antigen-specific T cell populations relative to literature approaches. We applied the method to profile neoantigen-specific T cell populations in the tumor and blood of patients with metastatic melanoma over the course of anti-PD1 checkpoint inhibitor therapy. We show that the method has value for monitoring clinical responses to cancer immunotherapy and might help guide the development of personalized mutational neoantigen-specific T cell therapies and cancer vaccines.
Collapse
Affiliation(s)
- Songming Peng
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Jesse M Zaretsky
- Department of Medicine, University of California Los Angeles and Jonsson Comprehensive Cancer Center, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA
| | - Alphonsus H C Ng
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Institute for Systems Biology, Seattle, WA 98109, USA
| | - William Chour
- Institute for Systems Biology, Seattle, WA 98109, USA; Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Michael T Bethune
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Jongchan Choi
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Alice Hsu
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Elizabeth Holman
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Xiaozhe Ding
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Katherine Guo
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Jungwoo Kim
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Alexander M Xu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Institute for Systems Biology, Seattle, WA 98109, USA
| | - John E Heath
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Won Jun Noh
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Jing Zhou
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Yapeng Su
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Institute for Systems Biology, Seattle, WA 98109, USA
| | - Yue Lu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Institute for Systems Biology, Seattle, WA 98109, USA
| | - Jami McLaughlin
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Donghui Cheng
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Owen N Witte
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - David Baltimore
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Antoni Ribas
- Department of Medicine, University of California Los Angeles and Jonsson Comprehensive Cancer Center, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA
| | - James R Heath
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Institute for Systems Biology, Seattle, WA 98109, USA.
| |
Collapse
|
11
|
Xu AM, Liu Q, Takata KL, Jeoung S, Su Y, Antoshechkin I, Chen S, Thomson M, Heath JR. Integrated measurement of intracellular proteins and transcripts in single cells. Lab Chip 2018; 18:3251-3262. [PMID: 30178802 PMCID: PMC6752714 DOI: 10.1039/c8lc00639c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Biological function arises from the interplay of proteins, transcripts, and metabolites. An ongoing revolution in miniaturization technologies has created tools to analyze any one of these species in single cells, thus resolving the heterogeneity of tissues previously invisible to bulk measurements. An emerging frontier is single cell multi-omics, which is the measurement of multiple classes of analytes from single cells. Here, we combine bead-based transcriptomics with microchip-based proteomics to measure intracellular proteins and transcripts from single cells and defined small numbers of cells. The transcripts and proteins are independently measured by sequencing and fluorescent immunoassays respectively, to preserve their optimal measurement modes, and linked by encoding the physical address locations of the cells into digital sequencing space using spatially patterned DNA barcodes. We resolve cell-type-specific protein and transcript signatures and present a path forward to scaling the platform to high-throughput.
Collapse
Affiliation(s)
- Alexander M. Xu
- California Institute of Technology, Division of Chemistry and Chemical Engineering, Pasadena, CA, USA
- Institute for Systems Biology, Seattle, WA, USA
| | - Qianhe Liu
- California Institute of Technology, Division of Chemistry and Chemical Engineering, Pasadena, CA, USA
| | - Kaitlyn L. Takata
- California Institute of Technology, Division of Chemistry and Chemical Engineering, Pasadena, CA, USA
| | - Sarah Jeoung
- California Institute of Technology, Division of Chemistry and Chemical Engineering, Pasadena, CA, USA
| | - Yapeng Su
- California Institute of Technology, Division of Chemistry and Chemical Engineering, Pasadena, CA, USA
| | - Igor Antoshechkin
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, CA, USA
| | - Sisi Chen
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, CA, USA
| | - Matthew Thomson
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, CA, USA
| | - James R. Heath
- California Institute of Technology, Division of Chemistry and Chemical Engineering, Pasadena, CA, USA
- Institute for Systems Biology, Seattle, WA, USA
| |
Collapse
|
12
|
Tian HL, Shi W, Zhou HF, Yuan L, Yao KH, Rexiati D, Xu AM. [Serotype distribution and drug resistance of Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis isolated from nasopharynx of Uygur children]. Zhonghua Er Ke Za Zhi 2018; 56:279-283. [PMID: 29614568 DOI: 10.3760/cma.j.issn.0578-1310.2018.04.008] [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] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To investigate the serotype distribution and antimicrobial susceptibility pattern of Streptococcus pneumoniae (S. pneumoniae), Haemophilus influenzae (H. influenzae) and Moraxella catarrhalis (M. catarrhalis) isolates collected from nasopharyngeal swabs from Uygur children in Kashi. Methods: Nasopharyngeal swabs were collected from inpatient Uygur children aged from 1 month to 5 years with respiratory infections from the pediatric department, the First People's Hospital of Kashi, Xinjiang Uygur Autonomous Region. Antimicrobial susceptibilities of the isolates were determined with E-test and KB disk diffusion methods. The production of β-lactamase was detected for H. influenzae and M. catarrhalisisolates using nitrocefin disc method. Quellung test and latex agglutination test were adopted to identify serotypes of S. pneumoniae and H. influenzae isolates. Results: Forty-seven S. pneumoniae, 13 H. influenzae and 16 M. catarrhalis isolates were detected. All of the 47 S. pneumoniae isolates were sensitive to parenteral penicillin, amoxicillin-clavulanic acid, vancomycin and levofloxacin; the susceptibility rates to cefotaxime, imipenem and chloramphenicol were 94% (44/47), 89% (42/47), and 98% (46/47). The resistance rate to erythromycin was 74% (35/47). The most common serotype of S. pneumoniae was serotype 19A (10 strains, 21%). The coverage rate of 13-valent conjugate vaccine (PCV13) was 70% (33/47). None of the 13 H. influenzae isolates could be typed. They were highly susceptible to tested β-lactams antibiotics, except ampicillin. Only one H. influenzae isolate could produce β-lactamase, and two isolates were identified as β-lactamase-negative-ampicillin-resistant ones. The sixteen M. catarrhalis isolates were all positive in β-lactamase detection, but sensitive to amoxicillin-clavulanic acid, cephalosporins and meropenem. Conclusions: In Kashi, Xinjiang Uygur Autonmous Region, S. pneumoniae isolates from Uygur children were highly sensitive to parenteral penicillin and other β-lactams antibiotics. H. influenzae isolates from Uygur children were highly susceptible to amoxicillin-clavulanic acid, cephalosporins and ciprofloxacin. All M. catarrhalis isolates from Uygur children could produce β-lactamase, but were sensitive to the enzyme inhibitors and cephalosporins.
Collapse
Affiliation(s)
- H L Tian
- Pediatric Department, First People's Hospital of Kashi, Xinjiang Uygur Autonomous Region, Kashi 844000, China
| | - W Shi
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Laboratory of Microbiology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | | | | | | | | | | |
Collapse
|
13
|
Sander J, Schmidt SV, Cirovic B, McGovern N, Papantonopoulou O, Hardt AL, Aschenbrenner AC, Kreer C, Quast T, Xu AM, Schmidleithner LM, Theis H, Thi Huong LD, Sumatoh HRB, Lauterbach MAR, Schulte-Schrepping J, Günther P, Xue J, Baßler K, Ulas T, Klee K, Katzmarski N, Herresthal S, Krebs W, Martin B, Latz E, Händler K, Kraut M, Kolanus W, Beyer M, Falk CS, Wiegmann B, Burgdorf S, Melosh NA, Newell EW, Ginhoux F, Schlitzer A, Schultze JL. Cellular Differentiation of Human Monocytes Is Regulated by Time-Dependent Interleukin-4 Signaling and the Transcriptional Regulator NCOR2. Immunity 2017; 47:1051-1066.e12. [PMID: 29262348 PMCID: PMC5772172 DOI: 10.1016/j.immuni.2017.11.024] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 09/15/2017] [Accepted: 11/28/2017] [Indexed: 12/24/2022]
Abstract
Human in vitro generated monocyte-derived dendritic cells (moDCs) and macrophages are used clinically, e.g., to induce immunity against cancer. However, their physiological counterparts, ontogeny, transcriptional regulation, and heterogeneity remains largely unknown, hampering their clinical use. High-dimensional techniques were used to elucidate transcriptional, phenotypic, and functional differences between human in vivo and in vitro generated mononuclear phagocytes to facilitate their full potential in the clinic. We demonstrate that monocytes differentiated by macrophage colony-stimulating factor (M-CSF) or granulocyte macrophage colony-stimulating factor (GM-CSF) resembled in vivo inflammatory macrophages, while moDCs resembled in vivo inflammatory DCs. Moreover, differentiated monocytes presented with profound transcriptomic, phenotypic, and functional differences. Monocytes integrated GM-CSF and IL-4 stimulation combinatorically and temporally, resulting in a mode- and time-dependent differentiation relying on NCOR2. Finally, moDCs are phenotypically heterogeneous and therefore necessitate the use of high-dimensional phenotyping to open new possibilities for better clinical tailoring of these cellular therapies. In vitro monocyte cultures model in vivo inflammatory dendritic cells and macrophages Monocyte-derived dendritic cells integrate interleukin-4 signaling time dependently NCOR2 controls differentiation of in vitro generated monocyte-derived dendritic cells In vitro generated monocyte-derived cells are phenotypically heterogeneous
Collapse
Affiliation(s)
- Jil Sander
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Susanne V Schmidt
- Institute of Innate Immunity, University Hospital Bonn, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | - Branko Cirovic
- Myeloid Cell Biology, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Naomi McGovern
- Agency for Science, Technology and Research (A(∗)STAR), Singapore Immunology Network (SIgN), 138648 Singapore, Singapore; Department of Pathology and Center for Trophoblast Research, University of Cambridge, CB2 1QP Cambridge, UK
| | | | - Anna-Lena Hardt
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Anna C Aschenbrenner
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Christoph Kreer
- Cellular Immunology, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Thomas Quast
- Molecular Immunology & Cell Biology, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Alexander M Xu
- Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305, USA
| | - Lisa M Schmidleithner
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Heidi Theis
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Lan Do Thi Huong
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Hermi Rizal Bin Sumatoh
- Agency for Science, Technology and Research (A(∗)STAR), Singapore Immunology Network (SIgN), 138648 Singapore, Singapore
| | - Mario A R Lauterbach
- Institute of Innate Immunity, University Hospital Bonn, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | | | - Patrick Günther
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Jia Xue
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Kevin Baßler
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Thomas Ulas
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Kathrin Klee
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Natalie Katzmarski
- Myeloid Cell Biology, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Stefanie Herresthal
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Wolfgang Krebs
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Bianca Martin
- Institute of Innate Immunity, University Hospital Bonn, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | - Eicke Latz
- Institute of Innate Immunity, University Hospital Bonn, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany; Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA; German Center for Neurodegenerative Diseases, 53127 Bonn, Germany
| | - Kristian Händler
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Michael Kraut
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Waldemar Kolanus
- Molecular Immunology & Cell Biology, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Marc Beyer
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany; Molecular Immunology, German Center for Neurodegenerative Diseases (DZNE), Sigmund-Freud-Str. 27, 53127 Bonn, Germany
| | - Christine S Falk
- Institute of Transplant Immunology, Integrated Research and Treatment Center Transplantation, Hannover Medical School, 30625 Hannover, Germany
| | - Bettina Wiegmann
- Department of Cardiothoracic, Transplantation and Vascular Surgery, Hannover Medical School, 30625 Hannover, Germany
| | - Sven Burgdorf
- Cellular Immunology, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Nicholas A Melosh
- Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305, USA
| | - Evan W Newell
- Agency for Science, Technology and Research (A(∗)STAR), Singapore Immunology Network (SIgN), 138648 Singapore, Singapore
| | - Florent Ginhoux
- Agency for Science, Technology and Research (A(∗)STAR), Singapore Immunology Network (SIgN), 138648 Singapore, Singapore
| | - Andreas Schlitzer
- Myeloid Cell Biology, LIMES-Institute, University of Bonn, 53115 Bonn, Germany; Agency for Science, Technology and Research (A(∗)STAR), Singapore Immunology Network (SIgN), 138648 Singapore, Singapore.
| | - Joachim L Schultze
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany; Platform for Single Cell Genomics and Epigenomics (PRECISE) at the German Center for Neurodegenerative Diseases and the University of Bonn, 53127 Bonn, Germany
| |
Collapse
|
14
|
Xu AM, Wang DS, Shieh P, Cao Y, Melosh NA. Direct Intracellular Delivery of Cell-Impermeable Probes of Protein Glycosylation by Using Nanostraws. Chembiochem 2017; 18:623-628. [PMID: 28130882 DOI: 10.1002/cbic.201600689] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Indexed: 12/24/2022]
Abstract
Bioorthogonal chemistry is an effective tool for elucidating metabolic pathways and measuring cellular activity, yet its use is currently limited by the difficulty of getting probes past the cell membrane and into the cytoplasm, especially if more complex probes are desired. Here we present a simple and minimally perturbative technique to deliver functional probes of glycosylation into cells by using a nanostructured "nanostraw" delivery system. Nanostraws provide direct intracellular access to cells through fluid conduits that remain small enough to minimize cell perturbation. First, we demonstrate that our platform can deliver an unmodified azidosugar, N-azidoacetylmannosamine, into cells with similar effectiveness to a chemical modification strategy (peracetylation). We then show that the nanostraw platform enables direct delivery of an azidosugar modified with a charged uridine diphosphate group (UDP) that prevents intracellular penetration, thereby bypassing multiple enzymatic processing steps. By effectively removing the requirement for cell permeability from the probe, the nanostraws expand the toolbox of bioorthogonal probes that can be used to study biological processes on a single, easy-to-use platform.
Collapse
Affiliation(s)
- Alexander M Xu
- Department of Materials Science and Engineering, Stanford University, 476 Lomita Mall, Stanford, CA, 94305, USA.,Present address: Chemistry and Chemical Engineering Division, California Institute of Technology, 1200 E California Boulevard, Pasadena, CA, 91106, USA
| | - Derek S Wang
- Department of Materials Science and Engineering, Stanford University, 476 Lomita Mall, Stanford, CA, 94305, USA
| | - Peyton Shieh
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, CA, 94305, USA
| | - Yuhong Cao
- Department of Materials Science and Engineering, Stanford University, 476 Lomita Mall, Stanford, CA, 94305, USA
| | - Nicholas A Melosh
- Department of Materials Science and Engineering, Stanford University, 476 Lomita Mall, Stanford, CA, 94305, USA
| |
Collapse
|
15
|
Xu AM, Kim SA, Wang DS, Aalipour A, Melosh NA. Temporally resolved direct delivery of second messengers into cells using nanostraws. Lab Chip 2016; 16:2434-2439. [PMID: 27292263 DOI: 10.1039/c6lc00463f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Second messengers are biomolecules with the critical role of conveying information to intracellular targets. They are typically membrane-impermeable and only enter cells through tightly regulated transporters. Current methods for manipulating second messengers in cells require preparation of modified cell lines or significant disruptions in cell function, especially at the cell membrane. Here we demonstrate that 100 nm diameter 'nanostraws' penetrate the cell membrane to directly modulate second messenger concentrations within cells. Nanostraws are hollow vertical nanowires that provide a fluidic conduit into cells to allow time-resolved delivery of the signaling ion Ca(2+) without chemical permeabilization or genetic modification, minimizing cell perturbation. By integrating the nanostraw platform into a microfluidic device, we demonstrate coordinated delivery of Ca(2+) ions into hundreds of cells at the time scale of several seconds with the ability to deliver complex signal patterns, such as oscillations over time. The diffusive nature of nanostraw delivery gives the platform unique versatility, opening the possibility for time-resolved delivery of any freely diffusing molecules.
Collapse
Affiliation(s)
- Alexander M Xu
- Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305, USA.
| | | | | | | | | |
Collapse
|
16
|
Fox CB, Cao Y, Nemeth CL, Chirra HD, Chevalier RW, Xu AM, Melosh NA, Desai TA. Fabrication of Sealed Nanostraw Microdevices for Oral Drug Delivery. ACS Nano 2016; 10:5873-81. [PMID: 27268699 PMCID: PMC5435488 DOI: 10.1021/acsnano.6b00809] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [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: 05/24/2023]
Abstract
The oral route is preferred for systemic drug administration and provides direct access to diseased tissue of the gastrointestinal (GI) tract. However, many drugs have poor absorption upon oral administration due to damaging enzymatic and pH conditions, mucus and cellular permeation barriers, and limited time for drug dissolution. To overcome these limitations and enhance oral drug absorption, micron-scale devices with planar, asymmetric geometries, termed microdevices, have been designed to adhere to the lining of the GI tract and release drug at high concentrations directly toward GI epithelium. Here we seal microdevices with nanostraw membranes-porous nanostructured biomolecule delivery substrates-to enhance the properties of these devices. We demonstrate that the nanostraws facilitate facile drug loading and tunable drug release, limit the influx of external molecules into the sealed drug reservoir, and increase the adhesion of devices to epithelial tissue. These findings highlight the potential of nanostraw microdevices to enhance the oral absorption of a wide range of therapeutics by binding to the lining of the GI tract, providing prolonged and proximal drug release, and reducing the exposure of their payload to drug-degrading biomolecules.
Collapse
Affiliation(s)
- Cade B. Fox
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94158, United States
| | - Yuhong Cao
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
| | - Cameron L. Nemeth
- Graduate Program in Bioengineering, University of California at Berkeley and San Francisco, UCSF Mission Bay Campus, San Francisco, California 94158, United States
| | - Hariharasudhan D. Chirra
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94158, United States
| | - Rachel W. Chevalier
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94158, United States
- Department of Pediatrics, Division of Pediatric Gastroenterology, School of Medicine, University of California, San Francisco, California 94158, United States
| | - Alexander M. Xu
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
| | - Nicholas A. Melosh
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
| | - Tejal A. Desai
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94158, United States
- Graduate Program in Bioengineering, University of California at Berkeley and San Francisco, UCSF Mission Bay Campus, San Francisco, California 94158, United States
| |
Collapse
|
17
|
Aalipour A, Xu AM, Leal-Ortiz S, Garner CC, Melosh NA. Plasma membrane and actin cytoskeleton as synergistic barriers to nanowire cell penetration. Langmuir 2014; 30:12362-7. [PMID: 25244597 DOI: 10.1021/la502273f] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Nanowires are a rapidly emerging platform for manipulation of and material delivery directly into the cell cytosol. These high aspect ratio structures can breach the lipid membrane; however, the yield of penetrant structures is low, and the mechanism is largely unknown. In particular, some nanostructures appear to defeat the membrane transiently, while others can retain long-term access. Here, we examine if local dissolution of the lipid membrane, actin cytoskeleton, or both can enhance nanowire penetration. It is possible that, during cell contact, membrane rupture occurs; however, if the nanostructures do not penetrate the cytoskeleton, the membrane may reclose over a relatively short time frame. We show with quantitative analysis of the number of penetrating nanowires that the lipid bilayer and actin cytoskeleton are synergistic barriers to nanowire cell access, yet chemical poration through both is still insufficient to increase long-term access for adhered cells.
Collapse
Affiliation(s)
- Amin Aalipour
- Department of Materials Science and Engineering, Stanford University , 476 Lomita Mall, Stanford, California 94305, United States
| | | | | | | | | |
Collapse
|
18
|
Xiao J, Liong EC, Ching YP, Chang RCC, Fung ML, Xu AM, So KF, Tipoe GL. Lycium barbarum polysaccharides protect rat liver from non-alcoholic steatohepatitis-induced injury. Nutr Diabetes 2013; 3:e81. [PMID: 23877747 PMCID: PMC3730220 DOI: 10.1038/nutd.2013.22] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 05/26/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Lycium barbarum polysaccharides (LBPs) are antioxidant and neuroprotective derivative from Wolfberry. However, whether LBP has a protective effect in non-alcoholic steatohepatitis (NASH)-induced hepatic injury is still unknown. OBJECTIVE We aimed to study the possible hepatoprotective effects and mechanisms of LBP on a diet-induced NASH rat model. METHODS AND DESIGN In this study, female rats were fed a high-fat diet to induce NASH with or without an oral 1 mg kg(-1) LBP feeding daily for 8 weeks. After 8 weeks, blood serum and liver samples from each rat were subjected to histological analysis, biochemical and molecular measurements. RESULTS Compared with control rats, NASH rats showed typical NASH features including an increase in liver injury, lipid content, fibrosis, oxidative stress, inflammation and apoptosis. In contrast, NASH+LBP-co-treated rats showed (1) improved histology and free fatty acid levels; (2) re-balance of lipid metabolism; (3) reduction in profibrogenic factors through the TGF-β/SMAD pathway; (4) improved oxidative stress through cytochrome P450 2E1-dependent pathway; (5) reduction in hepatic pro-inflammatory mediators and chemokines production; and (6) amelioration of hepatic apoptosis through the p53-dependent intrinsic and extrinsic pathways. The preventive effects of LBP were partly modulated through the PI3K/Akt/FoxO1, LKB1/AMPK, JNK/c-Jun and MEK/ERK pathways and the downregulation of transcription factors in the liver, such as nuclear factor-κB and activator protein-1. CONCLUSION LBP is a novel hepatoprotective agent against NASH caused by abnormal liver metabolic functions.
Collapse
Affiliation(s)
- J Xiao
- 1] Department of Anatomy, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China [2] Gene and Cell Engineering Research Center, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | | | | | | | | | | | | | | |
Collapse
|
19
|
Xie X, Xu AM, Leal-Ortiz S, Cao Y, Garner CC, Melosh NA. Nanostraw-electroporation system for highly efficient intracellular delivery and transfection. ACS Nano 2013; 7:4351-8. [PMID: 23597131 DOI: 10.1021/nn400874a] [Citation(s) in RCA: 184] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Nondestructive introduction of genes, proteins, and small molecules into mammalian cells with high efficiency is a challenging, yet critical, process. Here we demonstrate a simple nanoelectroporation platform to achieve highly efficient molecular delivery and high transfection yields with excellent uniformity and cell viability. The system is built on alumina nanostraws extending from a track-etched membrane, forming an array of hollow nanowires connected to an underlying microfluidic channel. Cellular engulfment of the nanostraws provides an intimate contact, significantly reducing the necessary electroporation voltage and increasing homogeneity over a large area. Biomolecule delivery is achieved by diffusion through the nanostraws and enhanced by electrophoresis during pulsing. The system was demonstrated to offer excellent spatial, temporal, and dose control for delivery, as well as providing high-yield cotransfection and sequential transfection.
Collapse
Affiliation(s)
- Xi Xie
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
| | | | | | | | | | | |
Collapse
|
20
|
Abstract
Direct access into cells' interiors is essential for biomolecular delivery, gene transfection, and electrical recordings yet is challenging due to the cell membrane barrier. Recently, molecular delivery using vertical nanowires (NWs) has been demonstrated for introducing biomolecules into a large number of cells in parallel. However, the microscopic understanding of how and when the nanowires penetrate cell membranes is still lacking, and the degree to which actual membrane penetration occurs is controversial. Here we present results from a mechanical continuum model of elastic cell membrane penetration through two mechanisms, namely through "impaling" as cells land onto a bed of nanowires, and through "adhesion-mediated" penetration, which occurs as cells spread on the substrate and generate adhesion force. Our results reveal that penetration is much more effective through the adhesion mechanism, with NW geometry and cell stiffness being critically important. Stiffer cells have higher penetration efficiency, but are more sensitive to NW geometry. These results provide a guide to designing nanowires for applications in cell membrane penetration.
Collapse
Affiliation(s)
- Xi Xie
- Department of Materials Science and Engineering, Stanford University , Stanford, California 94305, United States
| | | | | | | | | | | |
Collapse
|
21
|
|
22
|
Abstract
Nanomaterials are promising candidates to improve the delivery efficiency and control of active agents such as DNA or drugs directly into cells. Here we demonstrate cell-culture platforms of nanotemplated "nanostraws" that pierce the cell membrane, providing a permanent fluidic pipeline into the cell for direct cytosolic access. Conventional polymeric track-etch cell culture membranes are alumina coated and etched to produce fields of nanostraws with controllable diameter, thickness, and height. Small molecules and ions were successfully transported into the cytosol with 40 and 70% efficiency, respectively, while GFP plasmids were successfully delivered and expressed. These platforms open the way for active, reproducible delivery of a wide variety of species into cells without endocytosis.
Collapse
Affiliation(s)
- Jules J VanDersarl
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, USA
| | | | | |
Collapse
|
23
|
|
24
|
Abstract
Controlled chemical delivery in microfluidic cell culture devices often relies on slowly evolving diffusive gradients, as the spatial and temporal control provided by fluid flow results in significant cell-perturbation. In this paper we introduce a microfluidic device architecture that allows for rapid spatial and temporal soluble signal delivery over large cell culture areas without fluid flow over the cells. In these devices the cell culture well is divided from a microfluidic channel located directly underneath the chamber by a nanoporous membrane. This configuration requires chemical signals in the microchannel to only diffuse through the thin membrane into large cell culture area, rather than diffuse in from the sides. The spatial chemical pattern within the microfluidic channel was rapidly transferred to the cell culture area with good fidelity through diffusion. The cellular temporal response to a step-function signal showed that dye reached the cell culture surface within 45 s, and achieved a static concentration in under 6 min. Chemical pulses of less than one minute were possible by temporally alternating the signal within the microfluidic channel, enabling rapid flow-free chemical microenvironment control for large cell culture areas.
Collapse
Affiliation(s)
- Jules J VanDersarl
- Department of Materials Science and Engineering, Stanford University, Stanford, CA, USA
| | | | | |
Collapse
|
25
|
Huang PH, Miraldi ER, Xu AM, Kundukulam VA, Del Rosario AM, Flynn RA, Cavenee WK, Furnari FB, White FM. Phosphotyrosine signaling analysis of site-specific mutations on EGFRvIII identifies determinants governing glioblastoma cell growth. Mol Biosyst 2010; 6:1227-37. [PMID: 20461251 DOI: 10.1039/c001196g] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
To evaluate the role of individual EGFR phosphorylation sites in activating components of the cellular signaling network we have performed a mass spectrometry-based analysis of the phosphotyrosine network downstream of site-specific EGFRvIII mutants, enabling quantification of network-level effects of site-specific point mutations. Mutation at Y845, Y1068 or Y1148 resulted in diminished receptor phosphorylation, while mutation at Y1173 led to increased phosphorylation on multiple EGFRvIII residues. Altered phosphorylation at the receptor was recapitulated in downstream signaling network activation levels, with Y1173F mutation leading to increased phosphorylation throughout the network. Computational modeling of GBM cell growth as a function of network phosphorylation levels highlights the Erk pathway as crucial for regulating EGFRvIII-driven U87MG GBM cell behavior, with the unexpected finding that Erk1/2 is negatively correlated to GBM cell growth. Genetic manipulation of this pathway supports the model, demonstrating that EGFRvIII-expressing U87MG GBM cells are sensitive to Erk activation levels. Additionally, we developed a model describing glioblastoma cell growth based on a reduced set of phosphoproteins, which represent potential candidates for future development as therapeutic targets for EGFRvIII-positive glioblastoma patients.
Collapse
Affiliation(s)
- Paul H Huang
- Protein Networks Team, Section for Cell and Molecular Biology, Institute of Cancer Research, London, UK
| | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Abstract
Cancer cells employ multiple mechanisms to evade tightly regulated cellular processes such as proliferation, apoptosis, and senescence. Systems-wide analyses of tumors have recently identified receptor tyrosine kinase (RTK) coactivation as an important mechanism by which cancer cells achieve chemoresistance. This mini-review discusses our current understanding of the complex and dynamic process of RTK coactivation. We highlight how systems biology and computational modeling have been employed to predict integrated signaling outcomes and cancer phenotypes downstream of RTK coactivation. We conclude by providing an outlook on the feasibility of targeting RTK networks to overcome chemoresistance in cancer.
Collapse
Affiliation(s)
- Alexander M Xu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | |
Collapse
|
27
|
Abstract
The epidermal growth factor receptor (EGFR) is a primary contributor to glioblastoma (GBM) initiation and progression. Here, we examine how EGFR and key downstream signaling networks contribute to the hallmark characteristics of GBM such as rapid cancer cell proliferation and diffused invasion. Additionally, we discuss current therapeutic options for GBM patients and elaborate on the mechanisms through which EGFR promotes chemoresistance. We conclude by offering a perspective on how the potential of integrative systems biology may be harnessed to develop safe and effective treatment strategies for this disease.
Collapse
Affiliation(s)
- Paul H Huang
- Protein Networks Team, Section of Cell and Molecular Biology, Institute of Cancer Research, London, UK.
| | | | | |
Collapse
|
28
|
Gao XF, Chen W, Kong XP, Xu AM, Wang ZG, Sweeney G, Wu D. Enhanced susceptibility of Cpt1c knockout mice to glucose intolerance induced by a high-fat diet involves elevated hepatic gluconeogenesis and decreased skeletal muscle glucose uptake. Diabetologia 2009; 52:912-20. [PMID: 19224198 DOI: 10.1007/s00125-009-1284-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2008] [Accepted: 01/12/2009] [Indexed: 12/18/2022]
Abstract
AIMS/HYPOTHESIS Carnitine palmitoyltransferase-1 (CPT1)c is a novel isoform in the CPT1 family and is found specifically in the brain. Cpt1c knockout (KO) mice are more susceptible to high-fat diet (HFD)-induced obesity. However, the underlying mechanism of this phenotype and the question of whether CPT1c is involved in the pathogenesis of diet-induced insulin resistance are unclear. METHODS To assess the potential role of CPT1c in the regulation of whole-body glucose homeostasis, we generated Cpt1c KO mice and challenged them with HFD or standard chow. Glucose homeostasis of each group was assessed weekly. RESULTS After 8 weeks of HFD feeding, Cpt1c KO mice developed a phenotype of more severe insulin resistance than that in wild-type controls. The increased susceptibility of Cpt1c KO mice to HFD-induced insulin resistance was independent of obesity. Impaired glucose tolerance in Cpt1c KO mice was attributable to elevated hepatic gluconeogenesis and decreased glucose uptake in skeletal muscle. These effects correlated with decreased hepatic and intramuscular fatty acid oxidation and expression of oxidative genes as well as with elevated triacylglycerol content in these tissues. Interestingly, Cpt1c deletion caused a specific elevation of hypothalamic CPT1a and CPT1b isoform expression and activity. We demonstrated that elevated plasma NEFA concentration is one mechanism via which this compensatory effect is induced. CONCLUSIONS/INTERPRETATION These results further establish the role of CPT1c in controlling whole-body glucose homeostasis and in the regulation of hypothalamic Cpt1 isoform expression. We identify changes in hepatic and skeletal muscle glucose metabolism as important mechanisms determining the phenotype of Cpt1c KO mice.
Collapse
Affiliation(s)
- X F Gao
- Key Laboratory of Regenerative Biology, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | | | | | | | | | | | | |
Collapse
|
29
|
Zhang YY, Xu AM, Nomen M, Walsh M, Keaney JF, Loscalzo J. Nitrosation of tryptophan residue(s) in serum albumin and model dipeptides. Biochemical characterization and bioactivity. J Biol Chem 1996. [PMID: 8662958 DOI: 10.1074/jbc.271.24.14271 june 14, 1996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nitrosation of bovine serum albumin with acidified NaNO2 was compared to that of carboxymethyl-bovine serum albumin in which the thiol group is covalently blocked. Differential ultraviolet-visible (UV-Vis) spectroscopy and a modified Saville assay indicated that a non-cysteine residue(s) in carboxymethyl-bovine serum albumin was nitrosated. The nitrosated carboxymethyl-bovine serum albumin exhibited similar vasorelaxation activity as that observed with nitrosated bovine serum albumin. Identification of the nitrosated non-cysteine residue(s) was studied using 16 model dipeptides, each of which contained a glycyl residue and a variable residue. Using photolysis-chemiluminescence analysis, modified Saville assay, differential UV-Vis spectroscopy, and bioassays, L-glycyl-L-tryptophan (Gly-Trp) was found to be the only dipeptide that underwent significant nitrosation under these conditions. Liquid chromatography-UV-Vis spectroscopy-mass spectrometry showed that the NO group was attached to the indole nitrogen of tryptophan. Nitrosated Gly-Trp exhibited dose-dependent vasorelaxation and platelet inhibiting activity with apparent EC50 values of 1.1 +/- 0. 3 and 3.5 +/- 0.9 microM, respectively. Because N-nitroso-Gly-Trp does not release NO radical via spontaneous homolytic N-NO bond fission nor freely diffuse through cellular membranes, the ability of this compound to induce NO.-like biological effects suggests the existence of a (membrane-associated) transnitrosation system that facilitates delivery of -NO to its specific biologic target(s).
Collapse
Affiliation(s)
- Y Y Zhang
- Whitaker Cardiovascular Institute, Evans Department of Medicine, Boston University School of Medicine, Boston, Massachusetts 02118-2394, USA
| | | | | | | | | | | |
Collapse
|