1
|
Miner MD, deCamp A, Grunenberg N, De Rosa SC, Fiore-Gartland A, Bar K, Spearman P, Allen M, Yu PC, Manso B, Frahm N, Kalams S, Baden L, Keefer MC, Scott HM, Novak R, Van Tieu H, Tomaras GD, Kublin JG, McElrath MJ, Corey L, Frank I. Polytopic fractional delivery of an HIV vaccine alters cellular responses and results in increased epitope breadth in a phase 1 randomized trial. EBioMedicine 2024; 100:104987. [PMID: 38306894 PMCID: PMC10847480 DOI: 10.1016/j.ebiom.2024.104987] [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: 05/30/2023] [Revised: 12/20/2023] [Accepted: 01/15/2024] [Indexed: 02/04/2024] Open
Abstract
BACKGROUND Elicitation of broad immune responses is understood to be required for an efficacious preventative HIV vaccine. This Phase 1 randomized controlled trial evaluated whether administration of vaccine antigens separated at multiple injection sites vs combined, fractional delivery at multiple sites affected T-cell breadth compared to standard, single site vaccination. METHODS We randomized 90 participants to receive recombinant adenovirus 5 (rAd5) vector with HIV inserts gag, pol and env via three different strategies. The Standard group received vaccine at a single anatomic site (n = 30) compared to two polytopic (multisite) vaccination groups: Separated (n = 30), where antigens were separately administered to four anatomical sites, and Fractioned (n = 30), where fractions of each vaccine component were combined and administered at four sites. All groups received the same total dose of vaccine. FINDINGS CD8 T-cell response rates and magnitudes were significantly higher in the Fractioned group than Standard for several antigen pools tested. CD4 T-cell response magnitudes to Pol were higher in the Separated than Standard group. T-cell epitope mapping demonstrated greatest breadth in the Fractioned group (median 8.0 vs 2.5 for Standard, Wilcoxon p = 0.03; not significant after multiplicity adjustment for co-primary endpoints). IgG binding antibody response rates to Env were higher in the Standard and Fractioned groups vs Separated group. INTERPRETATION This study shows that the number of anatomic sites for which a vaccine is delivered and distribution of its antigenic components influences immune responses in humans. FUNDING National Institute of Allergy and Infectious Diseases, NIH.
Collapse
Affiliation(s)
- Maurine D Miner
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, WA, USA.
| | - Allan deCamp
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, WA, USA
| | - Nicole Grunenberg
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, WA, USA
| | - Stephen C De Rosa
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, WA, USA; Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, USA
| | | | | | - Paul Spearman
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Mary Allen
- Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Pei-Chun Yu
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, WA, USA
| | - Bryce Manso
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, WA, USA
| | - Nicole Frahm
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, WA, USA
| | - Spyros Kalams
- Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Michael C Keefer
- Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY, USA
| | - Hyman M Scott
- San Francisco Department of Public Health, San Francisco, CA, USA
| | | | - Hong Van Tieu
- Laboratory of Infectious Disease Prevention, Lindsley F. Kimball Research Institute, New York Blood Center, New York City, NY, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York City, NY, USA
| | | | - James G Kublin
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, WA, USA
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, WA, USA
| | - Lawrence Corey
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, WA, USA
| | - Ian Frank
- University of Pennsylvania, Philadelphia, PA, USA
| |
Collapse
|
2
|
Abouarab B, Bazarian C, Ben Chaouch Z, Lo AW, Mourenza Gonzalez G, Novak R, Vigneault F. Financing repurposed drugs for rare diseases: a case study of Unravel Biosciences. Orphanet J Rare Dis 2023; 18:287. [PMID: 37700316 PMCID: PMC10496212 DOI: 10.1186/s13023-023-02753-y] [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: 12/16/2021] [Accepted: 06/04/2023] [Indexed: 09/14/2023] Open
Abstract
BACKGROUND We consider two key challenges that early-stage biotechnology firms face in developing a sustainable financing strategy and a sustainable business model: developing a valuation model for drug compounds, and choosing an appropriate operating model and corporate structure. We use the specific example of Unravel Biosciences-a therapeutics platform company that identifies novel drug targets through off-target mechanisms of existing drugs and then develops optimized new molecules-throughout the paper and explore a specific scenario of drug repurposing for rare genetic diseases. RESULTS The first challenge consists of producing a realistic financial valuation of a potential rare disease repurposed drug compound, in this case targeting Rett syndrome. More generally, we develop a framework to value a portfolio of pairwise correlated rare disease compounds in early-stage development and quantify its risk profile. We estimate the probability of a negative return to be [Formula: see text] for a single compound and [Formula: see text] for a portfolio of 8 drugs. The probability of selling the project at a loss decreases from [Formula: see text] (phase 3) for a single compound to [Formula: see text] (phase 3) for the 8-drug portfolio. For the second challenge, we find that the choice of operating model and corporate structure is crucial for early-stage biotech startups and illustrate this point with three concrete examples. CONCLUSIONS Repurposing existing compounds offers important advantages that could help early-stage biotech startups better align their business and financing issues with their scientific and medical objectives, enter a space that is not occupied by large pharmaceutical companies, and accelerate the validation of their drug development platform.
Collapse
Affiliation(s)
- Bechara Abouarab
- Sloan School of Management, MIT, Cambridge, USA
- Laboratory for Financial Engineering, MIT, Cambridge, USA
| | - Christian Bazarian
- Sloan School of Management, MIT, Cambridge, USA
- Laboratory for Financial Engineering, MIT, Cambridge, USA
| | - Zied Ben Chaouch
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, USA
- Laboratory for Financial Engineering, MIT, Cambridge, USA
| | - Andrew W Lo
- Sloan School of Management, MIT, Cambridge, USA.
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, USA.
- Laboratory for Financial Engineering, MIT, Cambridge, USA.
- Santa Fe Institute, Santa Fe, USA.
| | | | - Richard Novak
- Wyss Institute, Harvard University, Boston, USA
- Unravel Biosciences, Boston, USA
| | - Frederic Vigneault
- Wyss Institute, Harvard University, Boston, USA
- Unravel Biosciences, Boston, USA
| |
Collapse
|
3
|
Rowell PD, Ferguson PC, Tsoi KM, Nevin JL, Novak R, Griffin AM, Wunder JS. Endoprosthetic reconstruction for lower extremity soft tissue sarcomas with bone involvement. J Surg Oncol 2023; 128:660-666. [PMID: 37144623 DOI: 10.1002/jso.27300] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/24/2023] [Accepted: 04/18/2023] [Indexed: 05/06/2023]
Abstract
BACKGROUND AND OBJECTIVES Bone resection and endoprosthetic reconstruction (EPR) in the setting of soft tissue sarcoma (STS) management is rare and incurs unique challenges. We aim to report on the surgical and oncological outcomes of this relatively previously undocumented cohort. METHODS This is a single-center retrospective review of prospectively collected data for patients who required EPRs following resection of STSs of the lower extremity. Following inclusion criteria, we assessed 29 cases of EPR for primary STS of the lower limb. RESULTS The mean age was 54 years (range 18-84). Of the 29 patients, there were 6 total femur, 11 proximal femur, 4 intercalary, and 8 distal femur EPRs. Fourteen of 29 patients (48%) underwent re-operations for surgical complications, with 9 relating to infection (31%). When a matched cohort analysis was performed comparing our cohort to STSs that did not necessitate EPR, a reduced rate of overall survival and metastasis-free survival was found in those requiring EPR. CONCLUSION This series identifies a high rate of complication from EPRs performed for STS. Patients should be cautioned about the high rate of infection, surgical complications, and lower overall survival in this setting.
Collapse
Affiliation(s)
- P D Rowell
- University of Toronto Musculoskeletal Oncology Unit, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - P C Ferguson
- University of Toronto Musculoskeletal Oncology Unit, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - K M Tsoi
- University of Toronto Musculoskeletal Oncology Unit, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - J L Nevin
- University of Toronto Musculoskeletal Oncology Unit, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - R Novak
- University of Toronto Musculoskeletal Oncology Unit, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - A M Griffin
- University of Toronto Musculoskeletal Oncology Unit, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - J S Wunder
- University of Toronto Musculoskeletal Oncology Unit, Mount Sinai Hospital, Toronto, Ontario, Canada
| |
Collapse
|
4
|
Branche A, Rouphael N, Diemert D, Falsey A, Losada C, Baden LR, Frey S, Whitaker J, Little S, Anderson E, Walter E, Novak R, Rupp R, Jackson L, Babu T, Kottkamp A, Luetkemeyer A, Immergluck L, Presti R, Backer M, Winokur P, Mahgoub S, Goepfert P, Fusco D, Malkin E, Bethony J, Walsh E, Graciaa D, Samaha H, Sherman A, Walsh S, Abate G, Oikonomopoulou Z, El Sahly H, Martin T, Kamidani S, Smith M, Ladner B, Porterfield L, Dunstan M, Wald A, Davis T, Atmar R, Mulligan M, Lyke K, Posavad C, Meagher M, Stephens D, Neuzil K, Abebe K, Hill H, Albert J, Telu K, Mu J, Lewis T, Giebeig L, Eaton A, Netzl A, Wilks S, Tureli S, Makhene M, Crandon S, Montefiori D, Makowski M, Smith D, Nayak S, Roberts P, Beigel J. Bivalent and Monovalent SARS-CoV-2 Variant Vaccine Boosters Improve coverage of the known Antigenic Landscape: Results of the COVID-19 Variant Immunologic Landscape (COVAIL) Trial. Res Sq 2023:rs.3.rs-2653179. [PMID: 37205592 PMCID: PMC10187423 DOI: 10.21203/rs.3.rs-2653179/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Vaccine protection against COVID-19 wanes over time and has been impacted by the emergence of new variants with increasing escape of neutralization. The COVID-19 Variant Immunologic Landscape (COVAIL) randomized clinical trial (clinicaltrials.gov NCT05289037) compares the breadth, magnitude and durability of antibody responses induced by a second COVID-19 vaccine boost with mRNA (Moderna mRNA-1273 and Pfizer-BioNTech BNT162b2), or adjuvanted recombinant protein (Sanofi CoV2 preS DTM-AS03) monovalent or bivalent vaccine candidates targeting ancestral and variant SARS-CoV-2 spike antigens (Beta, Delta and Omicron BA.1). We found that boosting with a variant strain is not associated with loss in neutralization against the ancestral strain. However, while variant vaccines compared to the prototype/wildtype vaccines demonstrated higher neutralizing activity against Omicron BA.1 and BA.4/5 subvariants for up to 3 months after vaccination, neutralizing activity was lower for more recent Omicron subvariants. Our study, incorporating both antigenic distances and serologic landscapes, can provide a framework for objectively guiding decisions for future vaccine updates.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Susan Little
- Department of Medicine, University of California, San Diego, CA 92903
| | | | | | | | | | - Lisa Jackson
- Kaiser Permanente Washington Health Research Institute
| | | | | | | | | | | | | | | | | | - Paul Goepfert
- Department of Medicine, Division of Infectious Diseases, University of Alabama at Birmingham
| | | | | | | | | | - Daniel Graciaa
- Department of Medicine, Emory University School of Medicine
| | | | | | | | | | | | | | | | - Satoshi Kamidani
- Center for Childhood Infections and Vaccines (CCIV) of Children's Healthcare of Atlanta and Emory University Department of Pediatrics
| | | | | | | | | | | | | | | | | | - Kirsten Lyke
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine
| | - Christine Posavad
- Department of Laboratory Medicine and Pathology, University of Washington
| | | | | | | | | | | | | | | | | | - Teri Lewis
- 29. Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research
| | - Lisa Giebeig
- 29. Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research
| | | | | | - Sam Wilks
- Centre for Pathogen Evolution, Department of Zoology, University of Cambridge
| | | | - Mamodikoe Makhene
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH)
| | - Sonja Crandon
- Division of Microbiology and Infectious Diseases, NIAID, NIH
| | | | | | | | - Seema Nayak
- Division of Microbiology and Infectious Diseases, NIAID, NIH
| | - Paul Roberts
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH)
| | | |
Collapse
|
5
|
Sperry MM, Oskotsky TT, Marić I, Kaushal S, Takeda T, Horvath V, Powers RK, Rodas M, Furlong B, Soong M, Prabhala P, Goyal G, Carlson KE, Wong RJ, Kosti I, Le BL, Logue J, Hammond H, Frieman M, Stevenson DK, Ingber DE, Sirota M, Novak R. Target-agnostic drug prediction integrated with medical record analysis uncovers differential associations of statins with increased survival in COVID-19 patients. PLoS Comput Biol 2023; 19:e1011050. [PMID: 37146076 DOI: 10.1371/journal.pcbi.1011050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 05/17/2023] [Accepted: 03/27/2023] [Indexed: 05/07/2023] Open
Abstract
Drug repurposing requires distinguishing established drug class targets from novel molecule-specific mechanisms and rapidly derisking their therapeutic potential in a time-critical manner, particularly in a pandemic scenario. In response to the challenge to rapidly identify treatment options for COVID-19, several studies reported that statins, as a drug class, reduce mortality in these patients. However, it is unknown if different statins exhibit consistent function or may have varying therapeutic benefit. A Bayesian network tool was used to predict drugs that shift the host transcriptomic response to SARS-CoV-2 infection towards a healthy state. Drugs were predicted using 14 RNA-sequencing datasets from 72 autopsy tissues and 465 COVID-19 patient samples or from cultured human cells and organoids infected with SARS-CoV-2. Top drug predictions included statins, which were then assessed using electronic medical records containing over 4,000 COVID-19 patients on statins to determine mortality risk in patients prescribed specific statins versus untreated matched controls. The same drugs were tested in Vero E6 cells infected with SARS-CoV-2 and human endothelial cells infected with a related OC43 coronavirus. Simvastatin was among the most highly predicted compounds (14/14 datasets) and five other statins, including atorvastatin, were predicted to be active in > 50% of analyses. Analysis of the clinical database revealed that reduced mortality risk was only observed in COVID-19 patients prescribed a subset of statins, including simvastatin and atorvastatin. In vitro testing of SARS-CoV-2 infected cells revealed simvastatin to be a potent direct inhibitor whereas most other statins were less effective. Simvastatin also inhibited OC43 infection and reduced cytokine production in endothelial cells. Statins may differ in their ability to sustain the lives of COVID-19 patients despite having a shared drug target and lipid-modifying mechanism of action. These findings highlight the value of target-agnostic drug prediction coupled with patient databases to identify and clinically evaluate non-obvious mechanisms and derisk and accelerate drug repurposing opportunities.
Collapse
Affiliation(s)
- Megan M Sperry
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
- Department of Biology, Tufts University, Medford, Massachusetts, United States of America
| | - Tomiko T Oskotsky
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, California, United States of America
- Department of Pediatrics, University of California San Francisco, San Francisco, California, United States of America
| | - Ivana Marić
- Department of Pediatrics, School of Medicine, Stanford University, Stanford, California, United States of America
- Center for Academic Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Shruti Kaushal
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
| | - Takako Takeda
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
| | - Viktor Horvath
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
| | - Rani K Powers
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
| | - Melissa Rodas
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
| | - Brooke Furlong
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
| | - Mercy Soong
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
| | - Pranav Prabhala
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
| | - Girija Goyal
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
| | - Kenneth E Carlson
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
| | - Ronald J Wong
- Department of Pediatrics, School of Medicine, Stanford University, Stanford, California, United States of America
- Center for Academic Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Idit Kosti
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, California, United States of America
- Department of Pediatrics, University of California San Francisco, San Francisco, California, United States of America
| | - Brian L Le
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, California, United States of America
- Department of Pediatrics, University of California San Francisco, San Francisco, California, United States of America
| | - James Logue
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Holly Hammond
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Matthew Frieman
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - David K Stevenson
- Department of Pediatrics, School of Medicine, Stanford University, Stanford, California, United States of America
- Center for Academic Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Donald E Ingber
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
- Vascular Biology Program and Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Harvard John A. Paulson School of Engineering and Applied Sciences, Cambridge, Massachusetts, United States of America
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, California, United States of America
- Department of Pediatrics, University of California San Francisco, San Francisco, California, United States of America
| | - Richard Novak
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
| |
Collapse
|
6
|
Vagts CL, Chang YS, Ascoli C, Lee JM, Huang K, Huang Y, Cherian RA, Sarup N, Warpecha SR, Edafetanure-Ibeh R, Amin MR, Sultana T, Ghassemi M, Sweiss NJ, Novak R, Perkins DL, Finn PW. Trimer IgG and neutralising antibody response to COVID-19 mRNA vaccination in individuals with sarcoidosis. ERJ Open Res 2023; 9:00025-2022. [PMID: 36601311 PMCID: PMC9501840 DOI: 10.1183/23120541.00025-2022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 08/19/2022] [Indexed: 01/21/2023] Open
Abstract
Background Individuals with sarcoidosis are at higher risk for infection owing to underlying disease pathogenesis and need for immunosuppressive treatment. Current knowledge as to how subjects with sarcoidosis respond to different forms of vaccination is limited. We examined quantitative and functional antibody response to COVID-19 vaccination in infection-naive subjects with and without sarcoidosis. Methods Our prospective cohort study recruited 14 subjects with biopsy-proven sarcoidosis and 27 age-sex matched controls who underwent a two-shot series of the BNT162b2 mRNA vaccine at the University of Illinois at Chicago. Baseline, 4-week and 6-month trimer spike protein IgG and neutralising antibody (nAb) titres were assessed. Correlation and multivariate regression analysis was conducted. Results Sarcoidosis subjects had a significant increase in short-term antibody production to a level comparable to controls; however, IgG titres significantly declined back to baseline levels by 6 months. Corresponding neutralising assays revealed robust nAb titres in sarcoidosis subjects that persisted at 6 months. A significant and strong correlation between IgG and nAb titres across all time points was observed in the control group. However within the sarcoidosis group, a significant but weak correlation between antibody levels was found. Overall, IgG levels were poor predictors of nAb titres at short- or long-term time points. Conclusions Sarcoidosis subjects exhibit nAb induced by the BNT162b2 mRNA SARS-CoV-2 vaccine at levels comparable to controls that persists at 6 months indicating conferred immunity. Trimer IgG levels are poor predictors of nAb in subjects with sarcoidosis. Studies of further antibody immunoglobulins and subtypes warrant investigation.
Collapse
Affiliation(s)
- Christen L. Vagts
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Yi-Shin Chang
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA,Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Christian Ascoli
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Jessica M. Lee
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA,Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL, USA
| | - Kai Huang
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA,Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Yue Huang
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Ruth A. Cherian
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Nandini Sarup
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | | | | | - Md-Ruhul Amin
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Tasmin Sultana
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Mahmood Ghassemi
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Nadera J. Sweiss
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Richard Novak
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - David L. Perkins
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA,Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA,Department of Surgery, University of Illinois at Chicago, Chicago, IL, USA,These authors contributed equally
| | - Patricia W. Finn
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA,Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA,Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL, USA,These authors contributed equally,Corresponding author: Patricia Finn ()
| |
Collapse
|
7
|
Clifton C, Niemeyer BF, Novak R, Can UI, Hainline K, Benam KH. BPIFA1 is a secreted biomarker of differentiating human airway epithelium. Front Cell Infect Microbiol 2022; 12:1035566. [PMID: 36519134 PMCID: PMC9744250 DOI: 10.3389/fcimb.2022.1035566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/07/2022] [Indexed: 11/29/2022] Open
Abstract
In vitro culture and differentiation of human-derived airway basal cells under air-liquid interface (ALI) into a pseudostratified mucociliated mucosal barrier has proven to be a powerful preclinical tool to study pathophysiology of respiratory epithelium. As such, identifying differentiation stage-specific biomarkers can help investigators better characterize, standardize, and validate populations of regenerating epithelial cells prior to experimentation. Here, we applied longitudinal transcriptomic analysis and observed that the pattern and the magnitude of OMG, KRT14, STC1, BPIFA1, PLA2G7, TXNIP, S100A7 expression create a unique biosignature that robustly indicates the stage of epithelial cell differentiation. We then validated our findings by quantitative hemi-nested real-time PCR from in vitro cultures sourced from multiple donors. In addition, we demonstrated that at protein-level secretion of BPIFA1 accurately reflects the gene expression profile, with very low quantities present at the time of ALI induction but escalating levels were detectable as the epithelial cells terminally differentiated. Moreover, we observed that increase in BPIFA1 secretion closely correlates with emergence of secretory cells and an anti-inflammatory phenotype as airway epithelial cells undergo mucociliary differentiation under air-liquid interface in vitro.
Collapse
Affiliation(s)
- Clarissa Clifton
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Brian F. Niemeyer
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Richard Novak
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, United States
| | - Uryan Isik Can
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Kelly Hainline
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, United States
| | - Kambez H. Benam
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, United States,Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, United States,Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, United States,*Correspondence: Kambez H. Benam,
| |
Collapse
|
8
|
Sperry MM, Novak R, Keshari V, Dinis ALM, Cartwright MJ, Camacho DM, Paré J, Super M, Levin M, Ingber DE. Enhancers of Host Immune Tolerance to Bacterial Infection Discovered Using Linked Computational and Experimental Approaches. Adv Sci (Weinh) 2022; 9:e2200222. [PMID: 35706367 PMCID: PMC9475558 DOI: 10.1002/advs.202200222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/10/2022] [Indexed: 05/31/2023]
Abstract
Current therapeutic strategies against bacterial infections focus on reduction of pathogen load using antibiotics; however, stimulation of host tolerance to infection in the presence of pathogens might offer an alternative approach. Computational transcriptomics and Xenopus laevis embryos are used to discover infection response pathways, identify potential tolerance inducer drugs, and validate their ability to induce broad tolerance. Xenopus exhibits natural tolerance to Acinetobacter baumanii, Klebsiella pneumoniae, Staphylococcus aureus, and Streptococcus pneumoniae bacteria, whereas Aeromonas hydrophila and Pseudomonas aeruginosa produce lethal infections. Transcriptional profiling leads to definition of a 20-gene signature that discriminates between tolerant and susceptible states, as well as identification of a more active tolerance response to gram negative compared to gram positive bacteria. Gene pathways associated with active tolerance in Xenopus, including some involved in metal ion binding and hypoxia, are found to be conserved across species, including mammals, and administration of a metal chelator (deferoxamine) or a HIF-1α agonist (1,4-DPCA) in embryos infected with lethal A. hydrophila increased survival despite high pathogen load. These data demonstrate the value of combining the Xenopus embryo infection model with computational multiomics analyses for mechanistic discovery and drug repurposing to induce host tolerance to bacterial infections.
Collapse
Affiliation(s)
- Megan M. Sperry
- Wyss Institute for Biologically Inspired Engineering at Harvard UniversityBostonMA02115USA
- Department of BiologyTufts UniversityMedfordMA02155USA
| | - Richard Novak
- Wyss Institute for Biologically Inspired Engineering at Harvard UniversityBostonMA02115USA
- Present address:
Unravel Biosciences, Inc.BostonMA02125USA
| | - Vishal Keshari
- Wyss Institute for Biologically Inspired Engineering at Harvard UniversityBostonMA02115USA
| | - Alexandre L. M. Dinis
- Wyss Institute for Biologically Inspired Engineering at Harvard UniversityBostonMA02115USA
- Present address:
University of Massachusetts Medical SchoolWorcesterMA01655USA
| | - Mark J. Cartwright
- Wyss Institute for Biologically Inspired Engineering at Harvard UniversityBostonMA02115USA
| | - Diogo M. Camacho
- Wyss Institute for Biologically Inspired Engineering at Harvard UniversityBostonMA02115USA
- Present address:
Rheos MedicinesCambridgeMA02142USA
| | - Jean‐François Paré
- Department of BiologyTufts UniversityMedfordMA02155USA
- Present address:
Queen's UniversityKingstonON K7L 3N6Canada
| | - Michael Super
- Wyss Institute for Biologically Inspired Engineering at Harvard UniversityBostonMA02115USA
| | - Michael Levin
- Wyss Institute for Biologically Inspired Engineering at Harvard UniversityBostonMA02115USA
- Department of BiologyTufts UniversityMedfordMA02155USA
- Allen Discovery Center at Tufts UniversityMedfordMA02155USA
| | - Donald E. Ingber
- Wyss Institute for Biologically Inspired Engineering at Harvard UniversityBostonMA02115USA
- Vascular Biology Program and Department of SurgeryBoston Children's Hospital and Harvard Medical SchoolBostonMA02115USA
- Harvard John A. Paulson School of Engineering and Applied SciencesCambridgeMA02138USA
| |
Collapse
|
9
|
Sperry MM, Oskotsky T, MariÄ I, Kaushal S, Takeda T, Horvath V, Powers RK, Rodas M, Furlong B, Soong M, Prabhala P, Goyal G, Carlson KE, Wong RJ, Kosti I, Le BL, Logue J, Hammond H, Frieman M, Stevenson DK, Ingber DE, Sirota M, Novak R. Target-agnostic drug prediction integrated with medical record analysis uncovers differential associations of statins with increased survival in COVID-19 patients. medRxiv 2022:2022.04.12.22273802. [PMID: 35441166 PMCID: PMC9016655 DOI: 10.1101/2022.04.12.22273802] [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: 05/25/2023]
Abstract
Importance Drug repurposing requires distinguishing established drug class targets from novel molecule-specific mechanisms and rapidly derisking their therapeutic potential in a time-critical manner, particularly in a pandemic scenario. In response to the challenge to rapidly identify treatment options for COVID-19, several studies reported that statins, as a drug class, reduce mortality in these patients. However, it is unknown if different statins exhibit consistent function or may have varying therapeutic benefit. Objectives To test if different statins differ in their ability to exert protective effects based on molecular computational predictions and electronic medical record analysis. Main Outcomes and Measures A Bayesian network tool was used to predict drugs that shift the host transcriptomic response to SARS-CoV-2 infection towards a healthy state. Drugs were predicted using 14 RNA-sequencing datasets from 72 autopsy tissues and 465 COVID-19 patient samples or from cultured human cells and organoids infected with SARS-CoV-2, with a total of 2,436 drugs investigated. Top drug predictions included statins, which were then assessed using electronic medical records containing over 4,000 COVID-19 patients on statins to determine mortality risk in patients prescribed specific statins versus untreated matched controls. The same drugs were tested in Vero E6 cells infected with SARS-CoV-2 and human endothelial cells infected with a related OC43 coronavirus. Results Simvastatin was among the most highly predicted compounds (14/14 datasets) and five other statins, including atorvastatin, were predicted to be active in > 50% of analyses. Analysis of the clinical database revealed that reduced mortality risk was only observed in COVID-19 patients prescribed a subset of statins, including simvastatin and atorvastatin. In vitro testing of SARS-CoV-2 infected cells revealed simvastatin to be a potent direct inhibitor whereas most other statins were less effective. Simvastatin also inhibited OC43 infection and reduced cytokine production in endothelial cells. Conclusions and Relevance Different statins may differ in their ability to sustain the lives of COVID-19 patients despite having a shared drug target and lipid-modifying mechanism of action. These findings highlight the value of target-agnostic drug prediction coupled with patient databases to identify and clinically evaluate non-obvious mechanisms and derisk and accelerate drug repurposing opportunities.
Collapse
|
10
|
Abstract
It is impossible to analyze human-specific host-microbiome interactions using animal models and existing in vitro methods fail to support survival of human cells in direct contact with complex living microbiota for extended times. Here we describe a protocol for culturing human organ-on-a-chip (Organ Chip) microfluidic devices lined by human patient-derived primary intestinal epithelium in the presence of a physiologically relevant transluminal hypoxia gradient that enables their coculture with hundreds of different living aerobic and anaerobic bacteria found within the human gut microbiome. This protocol can be adapted to provide different levels of oxygen tension to facilitate coculturing of microbiome from different regions of gastrointestinal tract, and the same system can be applied with any other type of Organ Chip. This method can help to provide further insight into the host-microbiome interactions that contribute to human health and disease, enable discovery of new microbiome-related diagnostics and therapeutics, and provide a novel approach to advanced personalized medicine.
Collapse
Affiliation(s)
- Sasan Jalili-Firoozinezhad
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Amir Bein
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Francesca S Gazzaniga
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Immunology, Harvard Medical School, Boston, MA, USA
| | - Cicely W Fadel
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Neonatology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Richard Novak
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Donald E Ingber
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
- Vascular Biology Program and Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
- Harvard John A. Paulson School of Engineering and Applied Sciences, Cambridge, MA, USA.
| |
Collapse
|
11
|
Murugan NJ, Kaltman DH, Jin PH, Chien M, Martinez R, Nguyen CQ, Kane A, Novak R, Ingber DE, Levin M. Mechanosensation Mediates Long-Range Spatial Decision-Making in an Aneural Organism. Adv Mater 2021; 33:e2008161. [PMID: 34263487 DOI: 10.1002/adma.202008161] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 06/14/2021] [Indexed: 05/25/2023]
Abstract
The unicellular protist Physarum polycephalum is an important emerging model for understanding how aneural organisms process information toward adaptive behavior. Here, it is revealed that Physarum can use mechanosensation to reliably make decisions about distant objects in its environment, preferentially growing in the direction of heavier, substrate-deforming, but chemically inert masses. This long-range sensing is abolished by gentle rhythmic mechanical disruption, changing substrate stiffness, or the addition of an inhibitor of mechanosensitive transient receptor potential channels. Additionally, it is demonstrated that Physarum does not respond to the absolute magnitude of strain. Computational modeling reveales that Physarum may perform this calculation by sensing the fraction of its perimeter that is distorted above a threshold substrate strain-a fundamentally novel method of mechanosensation. Using its body as both a distributed sensor array and computational substrate, this aneural organism leverages its unique morphology to make long-range decisions. Together, these data identify a surprising behavioral preference relying on biomechanical features and quantitatively characterize how the Physarum exploits physics to adaptively regulate its growth and shape.
Collapse
Affiliation(s)
- Nirosha J Murugan
- Department of Biology, Tufts University, Medford, MA, 02155, USA
- Allen Discovery Center at Tufts University, 200 College Avenue, Medford, MA, 02155, USA
| | - Daniel H Kaltman
- Department of Biology, Tufts University, Medford, MA, 02155, USA
- Allen Discovery Center at Tufts University, 200 College Avenue, Medford, MA, 02155, USA
| | - Paul H Jin
- Department of Biology, Tufts University, Medford, MA, 02155, USA
- Allen Discovery Center at Tufts University, 200 College Avenue, Medford, MA, 02155, USA
| | - Melanie Chien
- Department of Biology, Tufts University, Medford, MA, 02155, USA
- Allen Discovery Center at Tufts University, 200 College Avenue, Medford, MA, 02155, USA
| | - Ramses Martinez
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA, 02115, USA
| | - Cuong Q Nguyen
- Department of Biology, Tufts University, Medford, MA, 02155, USA
- Allen Discovery Center at Tufts University, 200 College Avenue, Medford, MA, 02155, USA
| | - Anna Kane
- Department of Biology, Tufts University, Medford, MA, 02155, USA
- Allen Discovery Center at Tufts University, 200 College Avenue, Medford, MA, 02155, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA, 02115, USA
| | - Richard Novak
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA, 02115, USA
| | - Donald E Ingber
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA, 02115, USA
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02115, USA
- Vascular Biology Program and Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Michael Levin
- Department of Biology, Tufts University, Medford, MA, 02155, USA
- Allen Discovery Center at Tufts University, 200 College Avenue, Medford, MA, 02155, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA, 02115, USA
| |
Collapse
|
12
|
Delorey TM, Ziegler CGK, Heimberg G, Normand R, Yang Y, Segerstolpe Å, Abbondanza D, Fleming SJ, Subramanian A, Montoro DT, Jagadeesh KA, Dey KK, Sen P, Slyper M, Pita-Juárez YH, Phillips D, Biermann J, Bloom-Ackermann Z, Barkas N, Ganna A, Gomez J, Melms JC, Katsyv I, Normandin E, Naderi P, Popov YV, Raju SS, Niezen S, Tsai LTY, Siddle KJ, Sud M, Tran VM, Vellarikkal SK, Wang Y, Amir-Zilberstein L, Atri DS, Beechem J, Brook OR, Chen J, Divakar P, Dorceus P, Engreitz JM, Essene A, Fitzgerald DM, Fropf R, Gazal S, Gould J, Grzyb J, Harvey T, Hecht J, Hether T, Jané-Valbuena J, Leney-Greene M, Ma H, McCabe C, McLoughlin DE, Miller EM, Muus C, Niemi M, Padera R, Pan L, Pant D, Pe’er C, Pfiffner-Borges J, Pinto CJ, Plaisted J, Reeves J, Ross M, Rudy M, Rueckert EH, Siciliano M, Sturm A, Todres E, Waghray A, Warren S, Zhang S, Zollinger DR, Cosimi L, Gupta RM, Hacohen N, Hibshoosh H, Hide W, Price AL, Rajagopal J, Tata PR, Riedel S, Szabo G, Tickle TL, Ellinor PT, Hung D, Sabeti PC, Novak R, Rogers R, Ingber DE, Jiang ZG, Juric D, Babadi M, Farhi SL, Izar B, Stone JR, Vlachos IS, Solomon IH, Ashenberg O, Porter CB, Li B, Shalek AK, Villani AC, Rozenblatt-Rosen O, Regev A. COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets. Nature 2021; 595:107-113. [PMID: 33915569 PMCID: PMC8919505 DOI: 10.1038/s41586-021-03570-8] [Citation(s) in RCA: 427] [Impact Index Per Article: 142.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 04/19/2021] [Indexed: 02/02/2023]
Abstract
COVID-19, which is caused by SARS-CoV-2, can result in acute respiratory distress syndrome and multiple organ failure1-4, but little is known about its pathophysiology. Here we generated single-cell atlases of 24 lung, 16 kidney, 16 liver and 19 heart autopsy tissue samples and spatial atlases of 14 lung samples from donors who died of COVID-19. Integrated computational analysis uncovered substantial remodelling in the lung epithelial, immune and stromal compartments, with evidence of multiple paths of failed tissue regeneration, including defective alveolar type 2 differentiation and expansion of fibroblasts and putative TP63+ intrapulmonary basal-like progenitor cells. Viral RNAs were enriched in mononuclear phagocytic and endothelial lung cells, which induced specific host programs. Spatial analysis in lung distinguished inflammatory host responses in lung regions with and without viral RNA. Analysis of the other tissue atlases showed transcriptional alterations in multiple cell types in heart tissue from donors with COVID-19, and mapped cell types and genes implicated with disease severity based on COVID-19 genome-wide association studies. Our foundational dataset elucidates the biological effect of severe SARS-CoV-2 infection across the body, a key step towards new treatments.
Collapse
Affiliation(s)
- Toni M. Delorey
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Carly G. K. Ziegler
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Program in Health Sciences & Technology, Harvard
Medical School & Massachusetts Institute of Technology, Boston, MA 02115,
USA,Institute for Medical Engineering & Science,
Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA
02139, USA,Harvard Graduate Program in Biophysics, Harvard University,
Cambridge, MA 02138, USA
| | - Graham Heimberg
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Rachelly Normand
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Center for Immunology and Inflammatory Diseases, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Center for Cancer Research, Massachusetts General Hospital,
Harvard Medical School, Boston, MA 02114, USA,Harvard Medical School, Boston, MA 02115, USA,Massachusetts Institute of Technology, Cambridge, MA
02139, USA
| | - Yiming Yang
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Center for Immunology and Inflammatory Diseases, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Åsa Segerstolpe
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Domenic Abbondanza
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA
| | - Stephen J. Fleming
- Data Sciences Platform, Broad Institute of MIT and
Harvard, Cambridge, MA 02142,Precision Cardiology Laboratory, Broad Institute of MIT
and Harvard, Cambridge, MA 02142, USA
| | - Ayshwarya Subramanian
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | | | - Karthik A. Jagadeesh
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Kushal K. Dey
- Department of Epidemiology, Harvard School of Public
Health
| | - Pritha Sen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Center for Immunology and Inflammatory Diseases, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Division of Infectious Diseases, Department of Medicine,
Massachusetts General Hospital, Boston, MA 02114, USA,Department of Medicine, Harvard Medical School, Boston,
MA 02115, USA
| | - Michal Slyper
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Yered H. Pita-Juárez
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Harvard Medical School, Boston, MA 02115, USA,Department of Pathology, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA,Harvard Medical School Initiative for RNA Medicine,
Boston, MA 02115, USA,Cancer Research Institute, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA
| | - Devan Phillips
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Jana Biermann
- Department of Medicine, Division of Hematology/Oncology,
Columbia University Irving Medical Center, New York, NY,Columbia Center for Translational Immunology, New York,
NY
| | - Zohar Bloom-Ackermann
- Infectious Disease and Microbiome Program, Broad
Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nick Barkas
- Data Sciences Platform, Broad Institute of MIT and
Harvard, Cambridge, MA 02142
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, Helsinki,
Finland,Analytical & Translational Genetics Unit,
Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - James Gomez
- Infectious Disease and Microbiome Program, Broad
Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Johannes C. Melms
- Department of Medicine, Division of Hematology/Oncology,
Columbia University Irving Medical Center, New York, NY,Columbia Center for Translational Immunology, New York,
NY
| | - Igor Katsyv
- Department of Pathology and Cell Biology, Columbia
University Irving Medical Center, New York, NY
| | - Erica Normandin
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Harvard Medical School, Boston, MA 02115, USA
| | - Pourya Naderi
- Harvard Medical School, Boston, MA 02115, USA,Department of Pathology, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA,Harvard Medical School Initiative for RNA Medicine,
Boston, MA 02115, USA
| | - Yury V. Popov
- Harvard Medical School, Boston, MA 02115, USA,Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA,Division of Gastroenterology, Hepatology and Nutrition,
Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215,
USA
| | - Siddharth S. Raju
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Department of Systems Biology, Harvard Medical School,
Boston, MA 02115, USA,FAS Center for Systems Biology, Department of Organismic
and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sebastian Niezen
- Harvard Medical School, Boston, MA 02115, USA,Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA,Division of Gastroenterology, Hepatology and Nutrition,
Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215,
USA
| | - Linus T.-Y. Tsai
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Harvard Medical School, Boston, MA 02115, USA,Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA,Division of Endocrinology, Diabetes, and Metabolism, Beth
Israel Deaconess Medical Center, Boston, MA 02115,Boston Nutrition and Obesity Research Center Functional
Genomics and Bioinformatics Core Boston, MA 02115, USA
| | - Katherine J. Siddle
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Department of Organismic and Evolutionary Biology,
Harvard University, Cambridge, MA, USA
| | - Malika Sud
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Victoria M. Tran
- Infectious Disease and Microbiome Program, Broad
Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shamsudheen K. Vellarikkal
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Divisions of Cardiovascular Medicine and Genetics,
Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115,
USA
| | - Yiping Wang
- Department of Medicine, Division of Hematology/Oncology,
Columbia University Irving Medical Center, New York, NY,Columbia Center for Translational Immunology, New York,
NY
| | - Liat Amir-Zilberstein
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Deepak S. Atri
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Divisions of Cardiovascular Medicine and Genetics,
Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115,
USA
| | | | - Olga R. Brook
- Department of Radiology, Beth Israel Deaconess Medical
Center, Boston, MA 02215, USA
| | - Jonathan Chen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Department of Pathology, Massachusetts General Hospital,
Harvard Medical School, Boston, MA 02115, USA
| | | | - Phylicia Dorceus
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Jesse M. Engreitz
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Department of Genetics and BASE Initiative, Stanford
University School of Medicine
| | - Adam Essene
- Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA,Division of Endocrinology, Diabetes, and Metabolism, Beth
Israel Deaconess Medical Center, Boston, MA 02115,Boston Nutrition and Obesity Research Center Functional
Genomics and Bioinformatics Core Boston, MA 02115, USA
| | - Donna M. Fitzgerald
- Massachusetts General Hospital Cancer Center, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Robin Fropf
- NanoString Technologies Inc., Seattle, WA 98109,
USA
| | - Steven Gazal
- Center for Genetic Epidemiology, Department of Preventive
Medicine, Keck School of Medicine, University of Southern California, Los Angeles,
CA, USA
| | - Joshua Gould
- Data Sciences Platform, Broad Institute of MIT and
Harvard, Cambridge, MA 02142
| | - John Grzyb
- Department of Pathology, Brigham and Women’s
Hospital, Boston, MA 02115
| | - Tyler Harvey
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Jonathan Hecht
- Harvard Medical School, Boston, MA 02115, USA,Department of Pathology, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA
| | - Tyler Hether
- NanoString Technologies Inc., Seattle, WA 98109,
USA
| | - Judit Jané-Valbuena
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | | | - Hui Ma
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Center for Immunology and Inflammatory Diseases, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Cristin McCabe
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Daniel E. McLoughlin
- Massachusetts General Hospital Cancer Center, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Christoph Muus
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,John A. Paulson School of Engineering and Applied
Sciences, Harvard University, Cambridge, MA 02138
| | - Mari Niemi
- Institute for Molecular Medicine Finland, Helsinki,
Finland
| | - Robert Padera
- Department of Pathology, Brigham and Women’s
Hospital, Boston, MA 02115,Harvard-MIT Division of Health Sciences and Technology,
Cambridge MA,Department of Pathology, Harvard Medical School, Boston,
MA 02115, USA
| | - Liuliu Pan
- NanoString Technologies Inc., Seattle, WA 98109,
USA
| | - Deepti Pant
- Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA,Division of Endocrinology, Diabetes, and Metabolism, Beth
Israel Deaconess Medical Center, Boston, MA 02115,Boston Nutrition and Obesity Research Center Functional
Genomics and Bioinformatics Core Boston, MA 02115, USA
| | - Carmel Pe’er
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | | | - Christopher J. Pinto
- Department of Medicine, Harvard Medical School, Boston,
MA 02115, USA,Massachusetts General Hospital Cancer Center, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jacob Plaisted
- Department of Pathology, Brigham and Women’s
Hospital, Boston, MA 02115
| | - Jason Reeves
- NanoString Technologies Inc., Seattle, WA 98109,
USA
| | - Marty Ross
- NanoString Technologies Inc., Seattle, WA 98109,
USA
| | - Melissa Rudy
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA
| | | | | | - Alexander Sturm
- Infectious Disease and Microbiome Program, Broad
Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ellen Todres
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Avinash Waghray
- Harvard Stem Cell Institute, Cambridge, MA, USA,Center for Regenerative Medicine, Massachusetts General
Hospital, Boston, MA 02114, USA
| | - Sarah Warren
- NanoString Technologies Inc., Seattle, WA 98109,
USA
| | - Shuting Zhang
- Infectious Disease and Microbiome Program, Broad
Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Lisa Cosimi
- Infectious Diseases Division, Department of Medicine,
Brigham and Women’s Hospital, Boston, MA, USA
| | - Rajat M. Gupta
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Divisions of Cardiovascular Medicine and Genetics,
Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115,
USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Center for Cancer Research, Massachusetts General Hospital,
Harvard Medical School, Boston, MA 02114, USA,Department of Medicine, Massachusetts General Hospital,
Harvard Medical School, Boston, MA 02114, USA
| | - Hanina Hibshoosh
- Department of Pathology and Cell Biology, Columbia
University Irving Medical Center, New York, NY
| | - Winston Hide
- Harvard Medical School, Boston, MA 02115, USA,Department of Pathology, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA,Harvard Medical School Initiative for RNA Medicine,
Boston, MA 02115, USA,Cancer Research Institute, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA
| | - Alkes L. Price
- Department of Epidemiology, Harvard School of Public
Health
| | - Jayaraj Rajagopal
- Massachusetts General Hospital Cancer Center, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Stefan Riedel
- Harvard Medical School, Boston, MA 02115, USA,Department of Pathology, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA
| | - Gyongyi Szabo
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Harvard Medical School, Boston, MA 02115, USA,Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA
| | - Timothy L. Tickle
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Data Sciences Platform, Broad Institute of MIT and
Harvard, Cambridge, MA 02142
| | - Patrick T. Ellinor
- Cardiovascular Disease Initiative, The Broad Institute of
MIT and Harvard, Cambridge, MA
| | - Deborah Hung
- Infectious Disease and Microbiome Program, Broad
Institute of MIT and Harvard, Cambridge, MA 02142, USA,Department of Genetics, Harvard Medical School, Boston,
MA 02115, USA,Department of Molecular Biology and Center for
Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA
02114, USA
| | - Pardis C. Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Department of Organismic and Evolutionary Biology,
Harvard University, Cambridge, MA, USA,Department of Immunology and Infectious Diseases, Harvard
T.H. Chan School of Public Health, Harvard University, Boston, MA, USA,Howard Hughes Medical Institute, Chevy Chase, MD,
USA,Massachusetts Consortium on Pathogen Readiness, Boston,
MA, USA
| | - Richard Novak
- Wyss Institute for Biologically Inspired Engineering,
Harvard University
| | - Robert Rogers
- Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA,Massachusetts General Hospital, MA 02114, USA
| | - Donald E. Ingber
- John A. Paulson School of Engineering and Applied
Sciences, Harvard University, Cambridge, MA 02138,Wyss Institute for Biologically Inspired Engineering,
Harvard University,Vascular Biology Program and Department of Surgery,
Boston Children’s Hospital, Harvard Medical School, Boston, MA USA
| | - Z. Gordon Jiang
- Harvard Medical School, Boston, MA 02115, USA,Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA,Division of Gastroenterology, Hepatology and Nutrition,
Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215,
USA
| | - Dejan Juric
- Department of Medicine, Harvard Medical School, Boston,
MA 02115, USA,Massachusetts General Hospital Cancer Center, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Mehrtash Babadi
- Data Sciences Platform, Broad Institute of MIT and
Harvard, Cambridge, MA 02142,Precision Cardiology Laboratory, Broad Institute of MIT
and Harvard, Cambridge, MA 02142, USA
| | - Samouil L. Farhi
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA
| | - Benjamin Izar
- Department of Medicine, Division of Hematology/Oncology,
Columbia University Irving Medical Center, New York, NY,Columbia Center for Translational Immunology, New York,
NY,Herbert Irving Comprehensive Cancer Center, Columbia
University Irving Medical Center, New York, NY,Program for Mathematical Genomics, Columbia University
Irving Medical Center, New York, NY
| | - James R. Stone
- Department of Pathology, Massachusetts General Hospital,
Harvard Medical School, Boston, MA 02115, USA
| | - Ioannis S. Vlachos
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Harvard Medical School, Boston, MA 02115, USA,Department of Pathology, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA,Harvard Medical School Initiative for RNA Medicine,
Boston, MA 02115, USA,Cancer Research Institute, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA
| | - Isaac H. Solomon
- Department of Pathology, Brigham and Women’s
Hospital, Boston, MA 02115
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Caroline B.M. Porter
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Bo Li
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Center for Immunology and Inflammatory Diseases, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Medicine, Harvard Medical School, Boston,
MA 02115, USA
| | - Alex K. Shalek
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Program in Health Sciences & Technology, Harvard
Medical School & Massachusetts Institute of Technology, Boston, MA 02115,
USA,Institute for Medical Engineering & Science,
Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA
02139, USA,Harvard Graduate Program in Biophysics, Harvard University,
Cambridge, MA 02138, USA,Harvard Medical School, Boston, MA 02115, USA,Harvard Stem Cell Institute, Cambridge, MA, USA,Program in Computational & Systems Biology,
Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Program in Immunology, Harvard Medical School, Boston, MA
02115, USA,Department of Chemistry, Massachusetts Institute of
Technology, Cambridge, MA 02139, USA
| | - Alexandra-Chloé Villani
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Center for Immunology and Inflammatory Diseases, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Center for Cancer Research, Massachusetts General Hospital,
Harvard Medical School, Boston, MA 02114, USA,Department of Medicine, Harvard Medical School, Boston,
MA 02115, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Current address: Genentech, 1 DNA Way, South San
Francisco, CA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Howard Hughes Medical Institute, Chevy Chase, MD,
USA,Current address: Genentech, 1 DNA Way, South San
Francisco, CA, USA
| |
Collapse
|
13
|
Palella FJ, Armon C, Cole SR, Hart R, Tedaldi E, Novak R, Battalora L, Purinton S, Li J, Buchacz K. HIV viral exposure and mortality in a multicenter ambulatory HIV adult cohort, United States, 1995-2016. Medicine (Baltimore) 2021; 100:e26285. [PMID: 34160393 PMCID: PMC8238313 DOI: 10.1097/md.0000000000026285] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 05/20/2021] [Indexed: 01/04/2023] Open
Abstract
The aim of this study was to identify viral exposure (VE) measures and their relationship to mortality risk among persons with HIV.Prospective multicenter observational study to compare VE formulae.Eligible participants initiated first combination antiretroviral therapy (cART) between March 1, 1995 and June 30, 2015. We included 1645 participants followed for ≥6 months after starting first cART, with cART prescribed ≥75% of time, who underwent ≥2 plasma viral load (VL) and ≥1 CD4+ T-lymphocyte cell (CD4) measurement during observation. We evaluated all-cause mortality from 6 months after cART initiation until June 30, 2016. VE was quantified using 2 time-updated variables: viremia copy-years and percent of person-years (%PY) spent >200 or 50 copies/mL. Cox models were fit to estimate associations between VE and mortality.Participants contributed 10,453 person years [py], with median 14 VLs per patient. Median %PY >200 or >50 were 10% (interquartile range: 1%-47%) and 26% (interquartile range: 6%-72%), respectively. There were 115 deaths, for an overall mortality rate of 1.19 per 100 person years. In univariate models, each measure of VE was significantly associated with mortality risk, as were older age, public insurance, injection drug use HIV risk history, and lower pre-cART CD4. Based on model fit, most recent viral load and %PY >200 copies/mL provided the best combination of VE factors to predict mortality, although all VE combinations evaluated performed well.The combination of most recent VL and %PY >200 copies/mL best predicted mortality, although all evaluated VE measures performed well.
Collapse
Affiliation(s)
- Frank J. Palella
- Northwestern University Feinberg School of Medicine, Chicago, IL
| | | | | | | | - Ellen Tedaldi
- Lewis Katz School of Medicine at Temple University, Philadelphia, PA
| | | | - Linda Battalora
- Cerner Corporation, Kansas City, MO
- Colorado School of Mines, Golden, CO
| | | | - Jun Li
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | - Kate Buchacz
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| |
Collapse
|
14
|
McNulty M, Schmitt J, Friedman E, Hunt B, Tobin A, Maheswaran AB, Lin J, Novak R, Sha B, Rolfsen N, Moswin A, Rose B, Pitrak D, Glick N. Implementing Rapid Initiation of Antiretroviral Therapy for Acute HIV Infection Within a Routine Testing and Linkage to Care Program in Chicago. J Int Assoc Provid AIDS Care 2021; 19:2325958220939754. [PMID: 32734805 PMCID: PMC7401059 DOI: 10.1177/2325958220939754] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Growing evidence suggests that rapid initiation of antiretroviral therapy for HIV improves care continuum outcomes. We evaluated process and clinical outcomes for rapid initiation in acute HIV infection within a multisite health care–based HIV testing and linkage to care program in Chicago. Through retrospective analysis of HIV testing data (2016-2017), we assessed linkage to care, initiation of antiretroviral therapy, and viral suppression. Of 334 new HIV diagnoses, 33 (9.9%) individuals had acute HIV infection. Median time to linkage was 11 (interquartile range [IQR]: 5-19.5) days, with 15 days (IQR 5-27) to initiation of antiretroviral therapy. Clients achieved viral suppression at a median of 131 (IQR: 54-188) days. Of all, 69.7% were retained in care, all of whom were virally suppressed. Sites required few additional resources to incorporate rapid initiation into existing processes. Integration of rapid initiation of antiretroviral therapy into existing HIV screening programs is a promising strategy for scaling up this important intervention.
Collapse
Affiliation(s)
- Moira McNulty
- Section of Infectious Diseases and Global Health, University of Chicago, IL, USA
| | - Jessica Schmitt
- Section of Infectious Diseases and Global Health, University of Chicago, IL, USA
| | - Eleanor Friedman
- Section of Infectious Diseases and Global Health, University of Chicago, IL, USA
| | - Bijou Hunt
- Sinai Infectious Disease Center, Sinai Health System, Chicago, IL, USA
| | - Audra Tobin
- Sinai Infectious Disease Center, Sinai Health System, Chicago, IL, USA
| | | | - Janet Lin
- University of Illinois Hospital and Health Sciences and Systems, Chicago, IL, USA
| | - Richard Novak
- University of Illinois Hospital and Health Sciences and Systems, Chicago, IL, USA
| | - Beverly Sha
- Division of Infectious Diseases, Rush University Medical Center, Chicago, IL, USA
| | | | - Arthur Moswin
- Mercy Hospital and Medical Center, Chicago, IL, USA.,Michael Reese Research and Education Foundation, Chicago, IL, USA
| | | | - David Pitrak
- Section of Infectious Diseases and Global Health, University of Chicago, IL, USA
| | - Nancy Glick
- Sinai Infectious Disease Center, Sinai Health System, Chicago, IL, USA
| |
Collapse
|
15
|
Pettit ME, Boswell SA, Qian J, Novak R, Springer M. Accessioning and automation compatible anterior nares swab design. J Virol Methods 2021; 294:114153. [PMID: 33984398 PMCID: PMC8108477 DOI: 10.1016/j.jviromet.2021.114153] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/26/2021] [Accepted: 04/06/2021] [Indexed: 11/18/2022]
Abstract
The COVID-19 pandemic has resulted in an unparalleled need for viral testing capacity across the world and is a critical requirement for successful re-opening of economies. The logistical barriers to near-universal testing are considerable. We have designed an injection molded polypropylene anterior nares swab, the Rhinostic, with a screw cap integrated into the swab handle that is compatible with fully automated sample accessioning and processing. The ability to collect and release both human and viral material is comparable to that of several commonly used swabs on the market. SARS-CoV-2 is stable on dry Rhinostic swabs for at least 3 days, even at 42 °C, and elution can be achieved with small volumes. To test the performance of the Rhinostic in patients, 119 samples were collected with Rhinostic and the positive and negative determinations were 100 % concordant with samples collected using Clinical Laboratory Improvement Amendments (CLIA) use approved nasal swabs at a clinical lab. The Rhinostic swab and barcoded tube set can be produced, sterilized, and packaged cost effectively and is designed to be adopted by clinical laboratories using automation to increase throughput and dramatically reduce the cost of a standard SARS-CoV-2 detection pipeline.
Collapse
Affiliation(s)
- Mary E Pettit
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Sarah A Boswell
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Jason Qian
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA; Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA, 02115, USA
| | - Richard Novak
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Michael Springer
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA; Massachusetts Consortium on Pathogen Readiness, Boston, MA, 20115, USA.
| |
Collapse
|
16
|
Abstract
PURPOSE OF REVIEW Patients on chronic immunosuppressive treatments at baseline are at increased risk of opportunistic infections. These patients are at especially increased risk of morbidity and mortality during the coronavirus-19 (COVID-19) pandemic. This review will focus on patients with diseases in which immunosuppression is a vital part of the treatment regimen, including those with solid organ transplants, rheumatologic disorders, sarcoidosis, and inflammatory bowel disease (IBD). We will summarize the current knowledge of immunosuppression in these diseases and the risk of contracting COVID-19. Furthermore, we will discuss if immunosuppression increases severity of COVID-19 presentation. RECENT FINDINGS Since the start of the COVID-19 pandemic, a large number patients receiving chronic immunosuppression have been infected with SARS-CoV-2. Moreover, our understanding of the immunology of SARS-CoV-2 is advancing at a rapid pace. Currently, a number of clinical trials are underway to investigate the role of immunosuppressive treatments in the management of this disease. SUMMARY Currently, there is no conclusive evidence to suggest that solid organ transplant recipients on chronic immunosuppression are at increased risk of contracting COVID-19. Solid organ transplant recipients may be at increased risk for worse COVID-19 outcomes but the data are not consistent. There is evidence to suggest that patients with rheumatologic disorders or IBDs are not at increased risk of contracting COVID-19 and do not necessarily experience worse clinical outcomes. Patients with sarcoidosis are not necessarily at increased risk of COVID-19, although there is limited data available to determine if immunosuppression worsens outcomes in this population.
Collapse
Affiliation(s)
- Michael Manansala
- Department of Medicine, Academic Internal Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Robert Baughman
- Department of Medicine, University of Cincinnati Medical Center, Cincinnati, Ohio
| | - Richard Novak
- Division of Infectious Disease, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Marc Judson
- Department of Medicine, Albany Medical College, Albany, New York
| | - Nadera Sweiss
- Division of Rheumatology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| |
Collapse
|
17
|
Manansala M, Chopra A, Baughman RP, Novak R, Lower EE, Culver DA, Korsten P, Drake WP, Judson MA, Sweiss N. COVID-19 and Sarcoidosis, Readiness for Vaccination: Challenges and Opportunities. Front Med (Lausanne) 2021; 8:672028. [PMID: 33996868 PMCID: PMC8119656 DOI: 10.3389/fmed.2021.672028] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/06/2021] [Indexed: 12/19/2022] Open
Abstract
Sarcoidosis is an immune mediated chronic inflammatory disorder that is best characterized by non-caseating granulomas found in one or more affected organs. The COVID-19 pandemic poses a challenge for clinicians caring for sarcoidosis patients who may be at increased risk of infection compared to the general population. With the recent availability of COVID-19 vaccines, it is expected that clinicians raise questions regarding efficacy and safety in sarcoidosis. However, studies examining safety and efficacy of vaccines in sarcoidosis are lacking. In this review, we examine the current literature regarding vaccination in immunocompromised populations and apply them to sarcoidosis patients. The available literature suggests that vaccines are safe and effective in patients with autoimmune disorders and in those taking immunosuppressive medications. We strongly recommend the administration of COVID-19 vaccines in patients with sarcoidosis. We also present a clinical decision algorithm to provide guidance on vaccination of sarcoidosis patients against COVID-19.
Collapse
Affiliation(s)
- Michael Manansala
- Department of Medicine, Academic Internal Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - Amit Chopra
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Albany Medical College, Albany, NY, United States
| | - Robert P Baughman
- Department of Medicine, University of Cincinnati Medical Center, Cincinnati, OH, United States
| | - Richard Novak
- Division of Infectious Disease, Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - Elyse E Lower
- Department of Medicine, University of Cincinnati Medical Center, Cincinnati, OH, United States
| | - Daniel A Culver
- Cleveland Clinic, Department of Pulmonary Medicine, Cleveland, OH, United States
| | - Peter Korsten
- Department of Nephrology and Rheumatology, University Medical Center Göttingen, Göttingen, Germany
| | - Wonder P Drake
- Division of Infectious Disease, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Marc A Judson
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Albany Medical College, Albany, NY, United States
| | - Nadera Sweiss
- Division of Rheumatology, Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| |
Collapse
|
18
|
Delorey TM, Ziegler CGK, Heimberg G, Normand R, Yang Y, Segerstolpe A, Abbondanza D, Fleming SJ, Subramanian A, Montoro DT, Jagadeesh KA, Dey KK, Sen P, Slyper M, Pita-Juárez YH, Phillips D, Bloom-Ackerman Z, Barkas N, Ganna A, Gomez J, Normandin E, Naderi P, Popov YV, Raju SS, Niezen S, Tsai LTY, Siddle KJ, Sud M, Tran VM, Vellarikkal SK, Amir-Zilberstein L, Atri DS, Beechem J, Brook OR, Chen J, Divakar P, Dorceus P, Engreitz JM, Essene A, Fitzgerald DM, Fropf R, Gazal S, Gould J, Grzyb J, Harvey T, Hecht J, Hether T, Jane-Valbuena J, Leney-Greene M, Ma H, McCabe C, McLoughlin DE, Miller EM, Muus C, Niemi M, Padera R, Pan L, Pant D, Pe’er C, Pfiffner-Borges J, Pinto CJ, Plaisted J, Reeves J, Ross M, Rudy M, Rueckert EH, Siciliano M, Sturm A, Todres E, Waghray A, Warren S, Zhang S, Zollinger DR, Cosimi L, Gupta RM, Hacohen N, Hide W, Price AL, Rajagopal J, Tata PR, Riedel S, Szabo G, Tickle TL, Hung D, Sabeti PC, Novak R, Rogers R, Ingber DE, Jiang ZG, Juric D, Babadi M, Farhi SL, Stone JR, Vlachos IS, Solomon IH, Ashenberg O, Porter CB, Li B, Shalek AK, Villani AC, Rozenblatt-Rosen O, Regev A. A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2. bioRxiv 2021:2021.02.25.430130. [PMID: 33655247 PMCID: PMC7924267 DOI: 10.1101/2021.02.25.430130] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The SARS-CoV-2 pandemic has caused over 1 million deaths globally, mostly due to acute lung injury and acute respiratory distress syndrome, or direct complications resulting in multiple-organ failures. Little is known about the host tissue immune and cellular responses associated with COVID-19 infection, symptoms, and lethality. To address this, we collected tissues from 11 organs during the clinical autopsy of 17 individuals who succumbed to COVID-19, resulting in a tissue bank of approximately 420 specimens. We generated comprehensive cellular maps capturing COVID-19 biology related to patients' demise through single-cell and single-nucleus RNA-Seq of lung, kidney, liver and heart tissues, and further contextualized our findings through spatial RNA profiling of distinct lung regions. We developed a computational framework that incorporates removal of ambient RNA and automated cell type annotation to facilitate comparison with other healthy and diseased tissue atlases. In the lung, we uncovered significantly altered transcriptional programs within the epithelial, immune, and stromal compartments and cell intrinsic changes in multiple cell types relative to lung tissue from healthy controls. We observed evidence of: alveolar type 2 (AT2) differentiation replacing depleted alveolar type 1 (AT1) lung epithelial cells, as previously seen in fibrosis; a concomitant increase in myofibroblasts reflective of defective tissue repair; and, putative TP63+ intrapulmonary basal-like progenitor (IPBLP) cells, similar to cells identified in H1N1 influenza, that may serve as an emergency cellular reserve for severely damaged alveoli. Together, these findings suggest the activation and failure of multiple avenues for regeneration of the epithelium in these terminal lungs. SARS-CoV-2 RNA reads were enriched in lung mononuclear phagocytic cells and endothelial cells, and these cells expressed distinct host response transcriptional programs. We corroborated the compositional and transcriptional changes in lung tissue through spatial analysis of RNA profiles in situ and distinguished unique tissue host responses between regions with and without viral RNA, and in COVID-19 donor tissues relative to healthy lung. Finally, we analyzed genetic regions implicated in COVID-19 GWAS with transcriptomic data to implicate specific cell types and genes associated with disease severity. Overall, our COVID-19 cell atlas is a foundational dataset to better understand the biological impact of SARS-CoV-2 infection across the human body and empowers the identification of new therapeutic interventions and prevention strategies.
Collapse
Affiliation(s)
- Toni M. Delorey
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Carly G. K. Ziegler
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Health Sciences & Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA 02115, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA
| | - Graham Heimberg
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Rachelly Normand
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Harvard Medical School, Boston, MA 02115, USA
- Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yiming Yang
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Asa Segerstolpe
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Domenic Abbondanza
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Stephen J. Fleming
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ayshwarya Subramanian
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | | | - Karthik A. Jagadeesh
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Kushal K. Dey
- Department of Epidemiology, Harvard School of Public Health
| | - Pritha Sen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Michal Slyper
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Yered H. Pita-Juárez
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
- Harvard Medical School Initiative for RNA Medicine, Boston, MA 02115, USA
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Devan Phillips
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Zohar Bloom-Ackerman
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nick Barkas
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, Helsinki, Finland
- Analytical & Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - James Gomez
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Erica Normandin
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Pourya Naderi
- Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
- Harvard Medical School Initiative for RNA Medicine, Boston, MA 02115, USA
| | - Yury V. Popov
- Harvard Medical School, Boston, MA 02115, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Siddharth S. Raju
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sebastian Niezen
- Harvard Medical School, Boston, MA 02115, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Linus T.-Y. Tsai
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA 02115
- Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core Boston, MA 02115, USA
| | - Katherine J. Siddle
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Malika Sud
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Victoria M. Tran
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shamsudheen K. Vellarikkal
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Divisions of Cardiovascular Medicine and Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Liat Amir-Zilberstein
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Deepak S. Atri
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Divisions of Cardiovascular Medicine and Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Olga R. Brook
- Department of Radiology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Jonathan Chen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Phylicia Dorceus
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Jesse M. Engreitz
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics and BASE Initiative, Stanford University School of Medicine
| | - Adam Essene
- Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA 02115
- Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core Boston, MA 02115, USA
| | - Donna M. Fitzgerald
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Robin Fropf
- NanoString Technologies Inc., Seattle, WA 98109, USA
| | - Steven Gazal
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Joshua Gould
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - John Grzyb
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
| | - Tyler Harvey
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Jonathan Hecht
- Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Tyler Hether
- NanoString Technologies Inc., Seattle, WA 98109, USA
| | - Judit Jane-Valbuena
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | | | - Hui Ma
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Cristin McCabe
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Daniel E. McLoughlin
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Christoph Muus
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138
| | - Mari Niemi
- Institute for Molecular Medicine Finland, Helsinki, Finland
| | - Robert Padera
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
- Harvard-MIT Division of Health Sciences and Technology, Cambridge MA
- Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Liuliu Pan
- NanoString Technologies Inc., Seattle, WA 98109, USA
| | - Deepti Pant
- Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA 02115
- Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core Boston, MA 02115, USA
| | - Carmel Pe’er
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | | | - Christopher J. Pinto
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jacob Plaisted
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
| | - Jason Reeves
- NanoString Technologies Inc., Seattle, WA 98109, USA
| | - Marty Ross
- NanoString Technologies Inc., Seattle, WA 98109, USA
| | - Melissa Rudy
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - Alexander Sturm
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ellen Todres
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Avinash Waghray
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Sarah Warren
- NanoString Technologies Inc., Seattle, WA 98109, USA
| | - Shuting Zhang
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Lisa Cosimi
- Infectious Diseases Division, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Rajat M. Gupta
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Divisions of Cardiovascular Medicine and Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Winston Hide
- Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
- Harvard Medical School Initiative for RNA Medicine, Boston, MA 02115, USA
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Alkes L. Price
- Department of Epidemiology, Harvard School of Public Health
| | - Jayaraj Rajagopal
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Stefan Riedel
- Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Gyongyi Szabo
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA
| | - Timothy L. Tickle
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Deborah Hung
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Pardis C. Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA
| | - Richard Novak
- Wyss Institute for Biologically Inspired Engineering, Harvard University
| | - Robert Rogers
- Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA
- Massachusetts General Hospital, MA 02114, USA
| | - Donald E. Ingber
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138
- Wyss Institute for Biologically Inspired Engineering, Harvard University
- Vascular Biology Program and Department of Surgery, Boston Children’s Hospital, Harvard Medical School, Boston, MA USA
| | - Z. Gordon Jiang
- Harvard Medical School, Boston, MA 02115, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Dejan Juric
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Mehrtash Babadi
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Samouil L. Farhi
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - James R. Stone
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ioannis S. Vlachos
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
- Harvard Medical School Initiative for RNA Medicine, Boston, MA 02115, USA
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Isaac H. Solomon
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Caroline B.M. Porter
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Bo Li
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Alex K. Shalek
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Health Sciences & Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA 02115, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA
- Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Program in Computational & Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alexandra-Chloé Villani
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
- Current address: Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Current address: Genentech, 1 DNA Way, South San Francisco, CA, USA
| |
Collapse
|
19
|
Hernandez Cordero AI, Yang CX, Obeidat M, Yang J, MacIsaac J, McEwen L, Lin D, Kobor M, Novak R, Hudson F, Klinker H, Dharan N, Man SP, Sin DD, Kunisaki K, Leung J. DNA methylation is associated with airflow obstruction in patients living with HIV. Thorax 2020; 76:448-455. [PMID: 33443234 PMCID: PMC8070606 DOI: 10.1136/thoraxjnl-2020-215866] [Citation(s) in RCA: 12] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 11/30/2022]
Abstract
Introduction People living with HIV (PLWH) suffer from age-related comorbidities such as COPD. The processes responsible for reduced lung function in PLWH are largely unknown. We performed an epigenome-wide association study to investigate whether blood DNA methylation is associated with impaired lung function in PLWH. Methods Using blood DNA methylation profiles from 161 PLWH, we tested the effect of methylation on FEV1, FEV1/FVC ratio and FEV1 decline over a median of 5 years. We evaluated the global methylation of PLWH with airflow obstruction by testing the differential methylation of transposable elements Alu and LINE-1, a well-described marker of epigenetic ageing. Results Airflow obstruction as defined by a FEV1/FVC<0.70 was associated with 1393 differentially methylated positions (DMPs), while 4676 were associated with airflow obstruction based on the FEV1/FVC<lower limit of normal. These DMPs were enriched for biological pathways associated with chronic viral infections. The airflow obstruction group was globally hypomethylated compared with those without airflow obstruction. 103 and 7112 DMPs were associated with FEV1 and FEV1/FVC, respectively. No positions were associated with FEV1 decline. Conclusion A large number of DMPs were associated with airflow obstruction and lung function in a unique cohort of PLWH. Airflow obstruction in even relatively young PLWH is associated with global hypomethylation, suggesting advanced epigenetic ageing compared with those with normal lung function. The disturbance of the epigenetic regulation of key genes not previously identified in non-HIV COPD cohorts could explain the unique risk of COPD in PLWH.
Collapse
Affiliation(s)
- Ana I Hernandez Cordero
- Centre for Heart Lung Innovation, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Chen Xi Yang
- Centre for Heart Lung Innovation, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Maen Obeidat
- Centre for Heart Lung Innovation, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Julia Yang
- Centre for Heart Lung Innovation, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Julie MacIsaac
- Center for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Lisa McEwen
- Center for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - David Lin
- Center for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael Kobor
- Center for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Richard Novak
- Section of Infectious Diseases, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Fleur Hudson
- MRC Clinical Trials Unit, University College London, London, UK
| | - Hartwig Klinker
- Medizinische Klinik und Poliklinik II, Universitatsklinikum Wurzburg, Wurzburg, Germany
| | - Nila Dharan
- The Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Sf Paul Man
- Centre for Heart Lung Innovation, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Don D Sin
- Centre for Heart Lung Innovation, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Ken Kunisaki
- Minneapolis Veterans Affairs Health Care System, Section of Pulmonary, Critical Care and Sleep Medicine and the Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Janice Leung
- Centre for Heart Lung Innovation, The University of British Columbia, Vancouver, British Columbia, Canada
| | | |
Collapse
|
20
|
Feng D, Kumar M, Muntel J, Gurley SB, Birrane G, Stillman IE, Ding L, Wang M, Ahmed S, Schlondorff J, Alper SL, Ferrante T, Marquez SL, Ng CF, Novak R, Ingber DE, Steen H, Pollak MR. Phosphorylation of ACTN4 Leads to Podocyte Vulnerability and Proteinuric Glomerulosclerosis. J Am Soc Nephrol 2020; 31:1479-1495. [PMID: 32540856 PMCID: PMC7351002 DOI: 10.1681/asn.2019101032] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 03/23/2020] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Genetic mutations in α-actinin-4 (ACTN4)-an important actin crosslinking cytoskeletal protein that provides structural support for kidney podocytes-have been linked to proteinuric glomerulosclerosis in humans. However, the effect of post-translational modifications of ACTN4 on podocyte integrity and kidney function is not known. METHODS Using mass spectrometry, we found that ACTN4 is phosphorylated at serine (S) 159 in human podocytes. We used phosphomimetic and nonphosphorylatable ACTN4 to comprehensively study the effects of this phosphorylation in vitro and in vivo. We conducted x-ray crystallography, F-actin binding and bundling assays, and immunofluorescence staining to evaluate F-actin alignment. Microfluidic organ-on-a-chip technology was used to assess for detachment of podocytes simultaneously exposed to fluid flow and cyclic strain. We then used CRISPR/Cas9 to generate mouse models and assessed for renal injury by measuring albuminuria and examining kidney histology. We also performed targeted mass spectrometry to determine whether high extracellular glucose or TGF-β levels increase phosphorylation of ACTN4. RESULTS Compared with the wild type ACTN4, phosphomimetic ACTN4 demonstrated increased binding and bundling activity with F-actin in vitro. Phosphomimetic Actn4 mouse podocytes exhibited more spatially correlated F-actin alignment and a higher rate of detachment under mechanical stress. Phosphomimetic Actn4 mice developed proteinuria and glomerulosclerosis after subtotal nephrectomy. Moreover, we found that exposure to high extracellular glucose or TGF-β stimulates phosphorylation of ACTN4 at S159 in podocytes. CONCLUSIONS These findings suggest that increased phosphorylation of ACTN4 at S159 leads to biochemical, cellular, and renal pathology that is similar to pathology resulting from human disease-causing mutations in ACTN4. ACTN4 may mediate podocyte injury as a consequence of both genetic mutations and signaling events that modulate phosphorylation.
Collapse
Affiliation(s)
- Di Feng
- Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts,Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts
| | - Mukesh Kumar
- Department of Pathology, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts,F.M. Kirby Neurobiology Center, Department of Neurobiology, Boston Children’s Hospital, Boston, Massachusetts
| | | | - Susan B. Gurley
- Division of Nephrology and Hypertension, Oregon Health & Science University, Portland, Oregon
| | - Gabriel Birrane
- Division of Experimental Medicine, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - Isaac E. Stillman
- Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts,Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - Lai Ding
- NeuroTechnology Studio, Program for Interdisciplinary Neuroscience, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Minxian Wang
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Saima Ahmed
- Department of Pathology, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Johannes Schlondorff
- Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - Seth L. Alper
- Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Tom Ferrante
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts
| | - Susan L. Marquez
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts
| | - Carlos F. Ng
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts
| | - Richard Novak
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts
| | - Donald E. Ingber
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts,Vascular Biology Program, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts,Department of Surgery, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts,Harvard John A. Paulson School of Engineering and Applied Sciences, Cambridge, Massachusetts
| | - Hanno Steen
- Department of Pathology, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Martin R. Pollak
- Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| |
Collapse
|
21
|
Syed H, Ascoli C, Linssen CF, Vagts C, Iden T, Syed A, Kron J, Polly K, Perkins D, Finn PW, Novak R, Drent M, Baughman R, Sweiss NJ. Infection prevention in sarcoidosis: proposal for vaccination and prophylactic therapy. Sarcoidosis Vasc Diffuse Lung Dis 2020; 37:87-98. [PMID: 33093774 PMCID: PMC7569559 DOI: 10.36141/svdld.v37i2.9599] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 04/24/2020] [Indexed: 12/11/2022]
Abstract
Sarcoidosis is a systemic inflammatory disease characterized by granuloma formation in affected organs and caused by dysregulated immune response to an unknown antigen. Sarcoidosis patients receiving immunosuppressive medications are at increased risk of infection. Lymphopenia is also commonly seen among patient with sarcoidosis. In this review, risk of infections, including opportunistic infections, will be outlined. Recommendations for vaccinations and prophylactic therapy based on literature review will also be summarized. (Sarcoidosis Vasc Diffuse Lung Dis 2020; 37 (2): 87-98).
Collapse
Affiliation(s)
- Huzaefah Syed
- Division of Rheumatology, Allergy, and Immunology, Virginia Commonwealth University, Richmond, VA, USA
| | - Christian Ascoli
- Division of Pulmonary, Critical Care, Sleep, and Allergy, University of Illinois at Chicago, Chicago, IL, USA
| | - Catharina Fm Linssen
- Department of Medical Microbiology, Zuyderland Medical Centre, Heerlen/Sittard-Geleen, the Netherlands
| | - Christen Vagts
- Division of Pulmonary, Critical Care, Sleep, and Allergy, University of Illinois at Chicago, Chicago, IL, USA
| | - Thomas Iden
- Division of Pulmonary and Critical Care, Virginia Commonwealth University, Richmond, VA, USA
| | - Aamer Syed
- Division of Pulmonary and Critical Care, Virginia Commonwealth University, Richmond, VA, USA
| | - Jordana Kron
- Pauley Heart Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Kelly Polly
- Division of Pulmonary and Critical Care, Virginia Commonwealth University, Richmond, VA, USA
| | - David Perkins
- Division of Nephrology, University of Illinois at Chicago, Chicago, IL, USA
| | - Patricia W Finn
- Division of Pulmonary, Critical Care, Sleep, and Allergy, University of Illinois at Chicago, Chicago, IL, USA
| | - Richard Novak
- Division of Infectious Diseases, University of Illinois at Chicago, Chicago, IL, USA
| | - Marjolein Drent
- ILD Center of Excellence, St. Antonius Hospital, Nieuwegein, The Netherlands.,Department of Pharmacology and Toxicology, FHML, Maastricht University, Maastricht, The Netherlands
| | - Robert Baughman
- Department of Internal Medicine, University of Cincinnati Medical Center, Cincinnati, OH, USA
| | - Nadera J Sweiss
- Division of Pulmonary, Critical Care, Sleep, and Allergy, University of Illinois at Chicago, Chicago, IL, USA.,Division of Rheumatology, University of Illinois at Chicago, Chicago, IL, USA
| |
Collapse
|
22
|
Herland A, Maoz BM, Das D, Somayaji MR, Prantil-Baun R, Novak R, Cronce M, Huffstater T, Jeanty SSF, Ingram M, Chalkiadaki A, Benson Chou D, Marquez S, Delahanty A, Jalili-Firoozinezhad S, Milton Y, Sontheimer-Phelps A, Swenor B, Levy O, Parker KK, Przekwas A, Ingber DE. Quantitative prediction of human pharmacokinetic responses to drugs via fluidically coupled vascularized organ chips. Nat Biomed Eng 2020; 4:421-436. [PMID: 31988459 PMCID: PMC8011576 DOI: 10.1038/s41551-019-0498-9] [Citation(s) in RCA: 222] [Impact Index Per Article: 55.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 11/25/2019] [Indexed: 01/15/2023]
Abstract
Analyses of drug pharmacokinetics (PKs) and pharmacodynamics (PDs) performed in animals are often not predictive of drug PKs and PDs in humans, and in vitro PK and PD modelling does not provide quantitative PK parameters. Here, we show that physiological PK modelling of first-pass drug absorption, metabolism and excretion in humans-using computationally scaled data from multiple fluidically linked two-channel organ chips-predicts PK parameters for orally administered nicotine (using gut, liver and kidney chips) and for intravenously injected cisplatin (using coupled bone marrow, liver and kidney chips). The chips are linked through sequential robotic liquid transfers of a common blood substitute by their endothelium-lined channels (as reported by Novak et al. in an associated Article) and share an arteriovenous fluid-mixing reservoir. We also show that predictions of cisplatin PDs match previously reported patient data. The quantitative in-vitro-to-in-vivo translation of PK and PD parameters and the prediction of drug absorption, distribution, metabolism, excretion and toxicity through fluidically coupled organ chips may improve the design of drug-administration regimens for phase-I clinical trials.
Collapse
Affiliation(s)
- Anna Herland
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Division of Micro and Nanosystems, KTH Royal Institute of Technology, Stockholm, Sweden
- AIMES, Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Ben M Maoz
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Debarun Das
- CFD Research Corporation, Huntsville, AL, USA
| | | | - Rachelle Prantil-Baun
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Richard Novak
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Michael Cronce
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Tessa Huffstater
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Sauveur S F Jeanty
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Miles Ingram
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Angeliki Chalkiadaki
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - David Benson Chou
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Susan Marquez
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Aaron Delahanty
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Sasan Jalili-Firoozinezhad
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Bioengineering and Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Portugal Graduate Program, Universidade de Lisboa, Lisbon, Portugal
| | - Yuka Milton
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Alexandra Sontheimer-Phelps
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Ben Swenor
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Oren Levy
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Kevin K Parker
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | | | - Donald E Ingber
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
- Division of Micro and Nanosystems, KTH Royal Institute of Technology, Stockholm, Sweden.
- Vascular Biology Program and Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
23
|
Feng D, Kumar M, Muntel J, Gurley SB, Birrane G, Stillman IE, Ding L, Wang MB, Ahmed S, Schlondorff J, Alper SL, Novak R, Ingber DE, Steen H, Pollak MR. Increased phosphorylation of ACTN4 leads to podocyte vulnerability and proteinuric kidney disease and is stimulated by high glucose and TGF‐b. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.02190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Di Feng
- Beth Israel Deaconess Medical Center, and Harvard Medical School
| | - Mukesh Kumar
- Boston Children’s Hospital, and Harvard Medical School
| | | | | | - Gabriel Birrane
- Beth Israel Deaconess Medical Center, and Harvard Medical School
| | | | | | | | - Saima Ahmed
- Boston Children’s Hospital, and Harvard Medical School
| | | | - Seth L. Alper
- Beth Israel Deaconess Medical Center, and Harvard Medical School
| | - Richard Novak
- Wyss Institute for Biologically Inspired Engineering Harvard University
| | - Donald E. Ingber
- Wyss Institute for Biologically Inspired Engineering Harvard University
| | - Hanno Steen
- Boston Children’s Hospital, and Harvard Medical School
| | - Martin R. Pollak
- Beth Israel Deaconess Medical Center, and Harvard Medical School
| |
Collapse
|
24
|
Novak R, Ingram M, Marquez S, Das D, Delahanty A, Herland A, Maoz BM, Jeanty SSF, Somayaji MR, Burt M, Calamari E, Chalkiadaki A, Cho A, Choe Y, Chou DB, Cronce M, Dauth S, Divic T, Fernandez-Alcon J, Ferrante T, Ferrier J, FitzGerald EA, Fleming R, Jalili-Firoozinezhad S, Grevesse T, Goss JA, Hamkins-Indik T, Henry O, Hinojosa C, Huffstater T, Jang KJ, Kujala V, Leng L, Mannix R, Milton Y, Nawroth J, Nestor BA, Ng CF, O'Connor B, Park TE, Sanchez H, Sliz J, Sontheimer-Phelps A, Swenor B, Thompson G, Touloumes GJ, Tranchemontagne Z, Wen N, Yadid M, Bahinski A, Hamilton GA, Levner D, Levy O, Przekwas A, Prantil-Baun R, Parker KK, Ingber DE. Robotic fluidic coupling and interrogation of multiple vascularized organ chips. Nat Biomed Eng 2020; 4:407-420. [PMID: 31988458 DOI: 10.1038/s41551-019-0497-x] [Citation(s) in RCA: 209] [Impact Index Per Article: 52.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 11/25/2019] [Indexed: 02/08/2023]
Abstract
Organ chips can recapitulate organ-level (patho)physiology, yet pharmacokinetic and pharmacodynamic analyses require multi-organ systems linked by vascular perfusion. Here, we describe an 'interrogator' that employs liquid-handling robotics, custom software and an integrated mobile microscope for the automated culture, perfusion, medium addition, fluidic linking, sample collection and in situ microscopy imaging of up to ten organ chips inside a standard tissue-culture incubator. The robotic interrogator maintained the viability and organ-specific functions of eight vascularized, two-channel organ chips (intestine, liver, kidney, heart, lung, skin, blood-brain barrier and brain) for 3 weeks in culture when intermittently fluidically coupled via a common blood substitute through their reservoirs of medium and endothelium-lined vascular channels. We used the robotic interrogator and a physiological multicompartmental reduced-order model of the experimental system to quantitatively predict the distribution of an inulin tracer perfused through the multi-organ human-body-on-chips. The automated culture system enables the imaging of cells in the organ chips and the repeated sampling of both the vascular and interstitial compartments without compromising fluidic coupling.
Collapse
Affiliation(s)
- Richard Novak
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Miles Ingram
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Susan Marquez
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Debarun Das
- CFD Research Corporation, Huntsville, AL, USA
| | - Aaron Delahanty
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Anna Herland
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.,Division of Micro and Nanosystems, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Ben M Maoz
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.,Disease Biophysics Group, Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA.,Department of Biomedical Engineering and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Sauveur S F Jeanty
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.,Emulate, Inc., Boston, MA, USA
| | | | - Morgan Burt
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Elizabeth Calamari
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Angeliki Chalkiadaki
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | | | - Youngjae Choe
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - David Benson Chou
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Michael Cronce
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Stephanie Dauth
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.,Disease Biophysics Group, Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Toni Divic
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Jose Fernandez-Alcon
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.,Emulate, Inc., Boston, MA, USA
| | - Thomas Ferrante
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - John Ferrier
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.,Disease Biophysics Group, Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Edward A FitzGerald
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Rachel Fleming
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Sasan Jalili-Firoozinezhad
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.,Department of Bioengineering and iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Thomas Grevesse
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.,Disease Biophysics Group, Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Josue A Goss
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.,Disease Biophysics Group, Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Tiama Hamkins-Indik
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Olivier Henry
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Chris Hinojosa
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.,Emulate, Inc., Boston, MA, USA
| | - Tessa Huffstater
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Kyung-Jin Jang
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.,Emulate, Inc., Boston, MA, USA
| | - Ville Kujala
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.,Disease Biophysics Group, Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA.,Emulate, Inc., Boston, MA, USA
| | - Lian Leng
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.,Emulate, Inc., Boston, MA, USA
| | - Robert Mannix
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.,Vascular Biology Program and Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Yuka Milton
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Janna Nawroth
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.,Disease Biophysics Group, Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA.,Emulate, Inc., Boston, MA, USA
| | - Bret A Nestor
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Carlos F Ng
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Blakely O'Connor
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.,Disease Biophysics Group, Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Tae-Eun Park
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Henry Sanchez
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Josiah Sliz
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.,Emulate, Inc., Boston, MA, USA
| | - Alexandra Sontheimer-Phelps
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.,Department of Biology, University of Freiburg, Freiburg, Germany
| | - Ben Swenor
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Guy Thompson
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.,Emulate, Inc., Boston, MA, USA
| | - George J Touloumes
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.,Disease Biophysics Group, Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | | | - Norman Wen
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.,Emulate, Inc., Boston, MA, USA
| | - Moran Yadid
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.,Disease Biophysics Group, Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Anthony Bahinski
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.,GlaxoSmithKline, Collegeville, PA, USA
| | - Geraldine A Hamilton
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.,Emulate, Inc., Boston, MA, USA
| | - Daniel Levner
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.,Emulate, Inc., Boston, MA, USA
| | - Oren Levy
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | | | - Rachelle Prantil-Baun
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Kevin K Parker
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.,Disease Biophysics Group, Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Donald E Ingber
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA. .,Vascular Biology Program and Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA. .,Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA.
| |
Collapse
|
25
|
Benam KH, Novak R, Ferrante TC, Choe Y, Ingber DE. Biomimetic smoking robot for in vitro inhalation exposure compatible with microfluidic organ chips. Nat Protoc 2020; 15:183-206. [PMID: 31925401 DOI: 10.1038/s41596-019-0230-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 07/24/2019] [Indexed: 01/22/2023]
Abstract
Exposure of lung tissues to cigarette smoke is a major cause of human disease and death worldwide. Unfortunately, adequate model systems that can reliably recapitulate disease biogenesis in vitro, including exposure of the human lung airway to fresh whole cigarette smoke (WCS) under physiological breathing airflow, are lacking. This protocol extension builds upon, and can be used with, our earlier protocol for microfabrication of human organs-on-chips. Here, we describe the engineering, assembly and operation of a microfluidically coupled, multi-compartment platform that bidirectionally 'breathes' WCS through microchannels of a human lung small airway microfluidic culture device, mimicking how lung cells may experience smoke in vivo. Several WCS-exposure systems have been developed, but they introduce smoke directly from above the cell cultures, rather than tangentially as naturally occurs in the lung due to lateral airflow. We detail the development of an organ chip-compatible microrespirator and a smoke machine to simulate breathing behavior and smoking topography parameters such as puff time, inter-puff interval and puffs per cigarette. Detailed design files, assembly instructions and control software are provided. This novel platform can be fabricated and assembled in days and can be used repeatedly. Moderate to advanced engineering and programming skills are required to successfully implement this protocol. When coupled with the small airway chip, this protocol can enable prediction of patient-specific biological responses in a matched-comparative manner. We also demonstrate how to adapt the protocol to expose living ciliated airway epithelial cells to smoke generated by electronic cigarettes (e-cigarettes) on-chip.
Collapse
Affiliation(s)
- Kambez H Benam
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.,Division of Pulmonary Sciences and Critical Care Medicine, Departments of Medicine and Bioengineering, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Richard Novak
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Thomas C Ferrante
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Youngjae Choe
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Donald E Ingber
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA. .,Harvard John A. Paulson School of Engineering and Applied Sciences, Cambridge, MA, USA. .,Vascular Biology Program and Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
26
|
Jiang Y, Li X, Morrow BR, Pothukuchy A, Gollihar J, Novak R, Reilly CB, Ellington AD, Walt DR. Single-Molecule Mechanistic Study of Enzyme Hysteresis. ACS Cent Sci 2019; 5:1691-1698. [PMID: 31660437 PMCID: PMC6813718 DOI: 10.1021/acscentsci.9b00718] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Indexed: 05/04/2023]
Abstract
Hysteresis is an important feature of enzyme-catalyzed reactions, as it reflects the influence of enzyme regulation in the presence of ligands such as substrates or allosteric molecules. In typical kinetic studies of enzyme activity, hysteretic behavior is observed as a "lag" or "burst" in the time course of the catalyzed reaction. These lags and bursts are due to the relatively slow transition from one state to another state of the enzyme molecule, with different states having different kinetic properties. However, it is difficult to understand the underlying mechanism of hysteresis by observing bulk reactions because the different enzyme molecules in the population behave stochastically. In this work, we studied the hysteretic behavior of mutant β-glucuronidase (GUS) using a high-throughput single-molecule array platform and investigated the effect of thermal treatment on the hysteresis.
Collapse
Affiliation(s)
- Yu Jiang
- Department
of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss
Institute, Harvard University, Boston, Massachusetts 02115, United States
| | - Xiang Li
- Department
of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss
Institute, Harvard University, Boston, Massachusetts 02115, United States
| | - Barrett R. Morrow
- Institute
for Cellular and Molecular Biology, University
of Texas at Austin, Austin, Texas 78712, United States
| | - Arti Pothukuchy
- Institute
for Cellular and Molecular Biology, University
of Texas at Austin, Austin, Texas 78712, United States
| | - Jimmy Gollihar
- Institute
for Cellular and Molecular Biology, University
of Texas at Austin, Austin, Texas 78712, United States
| | - Richard Novak
- Wyss
Institute, Harvard University, Boston, Massachusetts 02115, United States
| | - Charles B. Reilly
- Wyss
Institute, Harvard University, Boston, Massachusetts 02115, United States
| | - Andrew D. Ellington
- Institute
for Cellular and Molecular Biology, University
of Texas at Austin, Austin, Texas 78712, United States
- E-mail:
| | - David R. Walt
- Department
of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss
Institute, Harvard University, Boston, Massachusetts 02115, United States
- E-mail:
| |
Collapse
|
27
|
Patel M, Tedaldi E, Armon C, Nesheim S, Lampe M, Palella F, Novak R, Sutton M, Buchacz K. HIV RNA Suppression during and after Pregnancy among Women in the HIV Outpatient Study, 1996 to 2015. J Int Assoc Provid AIDS Care 2019; 17:2325957417752259. [PMID: 29357772 PMCID: PMC6748471 DOI: 10.1177/2325957417752259] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVE To examine HIV viral suppression during/after pregnancy. DESIGN Prospective observational cohort. METHODS We identified pregnancies from 1996 to 2015. We examined HIV RNA viral load (VL), VL suppression (≤500 copies/mL), and antiretroviral therapy (ART) status at pregnancy start, end, and 6 months postpartum. We estimated risk ratios (RRs) and 95% confidence intervals (CIs) for VL nonsuppression. RESULTS Among 253 pregnancies analyzed, 34.8% of women exhibited VL suppression at pregnancy start, 60.1% at pregnancy end, and 42.7% at 6 months postpartum. Median VL (log10 copies/mL) was 2.80 (interquartile range [IQR]: 1.40-3.85) at pregnancy start, 1.70 (IQR: 1.40-2.82) at pregnancy end, and 2.30 (IQR: 1.40-3.86) at postpartum. Risk of postpartum VL nonsuppression was also lower among women on ART and with VL suppression at pregnancy end (versus those not; adjusted RR = 0.30, 95% CI: 0.17-0.53). CONCLUSIONS Maintaining VL suppression among US women remains a challenge, particularly during postpartum. Achieving VL suppression earlier during pregnancy benefits women subsequently.
Collapse
Affiliation(s)
- Monita Patel
- 1 Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ellen Tedaldi
- 2 Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Carl Armon
- 3 Cerner Corporation, Kansas City, MO, USA
| | - Steven Nesheim
- 1 Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Margaret Lampe
- 1 Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Frank Palella
- 4 Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Richard Novak
- 5 University of Illinois at Chicago, Chicago, IL, USA
| | - Madeline Sutton
- 1 Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Kate Buchacz
- 1 Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | |
Collapse
|
28
|
Prantil-Baun R, Novak R, Das D, Somayaji MR, Przekwas A, Ingber DE. Physiologically Based Pharmacokinetic and Pharmacodynamic Analysis Enabled by Microfluidically Linked Organs-on-Chips. Annu Rev Pharmacol Toxicol 2019; 58:37-64. [PMID: 29309256 DOI: 10.1146/annurev-pharmtox-010716-104748] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [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: 11/09/2022]
Abstract
Physiologically based pharmacokinetic (PBPK) modeling and simulation approaches are beginning to be integrated into drug development and approval processes because they enable key pharmacokinetic (PK) parameters to be predicted from in vitro data. However, these approaches are hampered by many limitations, including an inability to incorporate organ-specific differentials in drug clearance, distribution, and absorption that result from differences in cell uptake, transport, and metabolism. Moreover, such approaches are generally unable to provide insight into pharmacodynamic (PD) parameters. Recent development of microfluidic Organ-on-a-Chip (Organ Chip) cell culture devices that recapitulate tissue-tissue interfaces, vascular perfusion, and organ-level functionality offer the ability to overcome these limitations when multiple Organ Chips are linked via their endothelium-lined vascular channels. Here, we discuss successes and challenges in the use of existing culture models and vascularized Organ Chips for PBPK and PD modeling of human drug responses, as well as in vitro to in vivo extrapolation (IVIVE) of these results, and how these approaches might advance drug development and regulatory review processes in the future.
Collapse
Affiliation(s)
- Rachelle Prantil-Baun
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA;
| | - Richard Novak
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA;
| | - Debarun Das
- CFD Research Corporation, Huntsville, Alabama 35806, USA
| | | | | | - Donald E Ingber
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA; .,Vascular Biology Program and Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA.,Harvard John A. Paulson School of Engineering and Applied Sciences, Cambridge, Massachusetts 02139, USA
| |
Collapse
|
29
|
Jalili-Firoozinezhad S, Gazzaniga FS, Calamari EL, Camacho DM, Fadel CW, Bein A, Swenor B, Nestor B, Cronce MJ, Tovaglieri A, Levy O, Gregory KE, Breault DT, Cabral JMS, Kasper DL, Novak R, Ingber DE. Author Correction: A complex human gut microbiome cultured in an anaerobic intestine-on-a-chip. Nat Biomed Eng 2019; 3:583. [PMID: 31213704 DOI: 10.1038/s41551-019-0428-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the version of this Article originally published, the authors mistakenly cited Fig. 5d in the sentence beginning 'Importantly, the microbiome cultured in these primary Intestine Chips...'; the correct citation is Supplementary Table 2. This has now been amended.
Collapse
Affiliation(s)
- Sasan Jalili-Firoozinezhad
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.,Department of Bioengineering and Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Francesca S Gazzaniga
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.,Department of Immunology, Harvard Medical School, Boston, MA, USA
| | - Elizabeth L Calamari
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Diogo M Camacho
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Cicely W Fadel
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Amir Bein
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Ben Swenor
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Bret Nestor
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Michael J Cronce
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Alessio Tovaglieri
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.,Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Oren Levy
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Katherine E Gregory
- Department of Pediatric Newborn Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - David T Breault
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.,Department of Endocrinology, Boston Children's Hospital, Boston, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Joaquim M S Cabral
- Department of Bioengineering and Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Dennis L Kasper
- Department of Immunology, Harvard Medical School, Boston, MA, USA
| | - Richard Novak
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Donald E Ingber
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA. .,Vascular Biology Program and Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA. .,Harvard John A. Paulson School of Engineering and Applied Sciences, Cambridge, MA, USA.
| |
Collapse
|
30
|
Rothbauer M, Charwat V, Bachmann B, Sticker D, Novak R, Wanzenböck H, Mathies RA, Ertl P. Monitoring transient cell-to-cell interactions in a multi-layered and multi-functional allergy-on-a-chip system. Lab Chip 2019; 19:1916-1921. [PMID: 31070645 DOI: 10.1039/c9lc00108e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We have developed a highly integrated lab-on-a-chip containing embedded electrical microsensors, μdegassers and pneumatically-actuated micropumps to monitor allergic hypersensitivity. Rapid antigen-mediated histamine release (e.g. s to min) and resulting muscle contraction (<30 min) is detected by connecting an immune compartment containing sensitized basophile cells to a vascular co-culture model.
Collapse
Affiliation(s)
- Mario Rothbauer
- Faculty of Technical Chemistry, Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria. and Austrian Cluster for Tissue Regeneration, 1200 Vienna, Austria
| | - Verena Charwat
- Department of Biotechnology, University of Agricultural Resources and Life Sciences, Muthgasse 18, 1090 Vienna, Austria
| | - Barbara Bachmann
- Faculty of Technical Chemistry, Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria. and Austrian Cluster for Tissue Regeneration, 1200 Vienna, Austria and AUVA Research Centre, Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, 1200 Vienna, Austria
| | - Drago Sticker
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Richard Novak
- Department of Chemistry, University of California at Berkeley, Lewis Hall, Berkeley, California, USA
| | - Heinz Wanzenböck
- Faculty of Electrical Engineering, Vienna University of Technology, Gußhausstr. 25-25a, 1040 Vienna, Austria
| | - Richard A Mathies
- Department of Chemistry, University of California at Berkeley, Lewis Hall, Berkeley, California, USA
| | - Peter Ertl
- Faculty of Technical Chemistry, Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria. and Austrian Cluster for Tissue Regeneration, 1200 Vienna, Austria
| |
Collapse
|
31
|
McNulty MC, Schmitt J, Friedman E, Hunt B, Tobin A, Maheswaran AB, Lin J, Novak R, Sha B, Moswin A, Rose B, Pitrak D, Glick N. 562. Management and Outcomes of Patients With Acute HIV Infection in an Expanded Testing and Linkage to Care Program. Open Forum Infect Dis 2018. [PMCID: PMC6255002 DOI: 10.1093/ofid/ofy210.570] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Background Methods Results Conclusion Disclosures
Collapse
Affiliation(s)
- Moira C McNulty
- Section of Infectious Diseases and Global Health, University of Chicago Medicine, Chicago, Illinois
| | - Jessica Schmitt
- Section of Infectious Diseases and Global Health, University of Chicago Medicine, Chicago, Illinois
| | - Eleanor Friedman
- Section of Infectious Diseases and Global Health, University of Chicago Medicine, Chicago, Illinois
| | | | - Audra Tobin
- Infectious Diseases, Mount Sinai Hospital, Chicago, Illinois
| | | | - Janet Lin
- University of Illinois at Chicago, Chicago, Illinois
| | - Richard Novak
- University of Illinois at Chicago, Chicago, Illinois
| | - Beverly Sha
- Rush University Medical Center, Division of Infectious Diseases, Chicago, Illinois
| | - Arthur Moswin
- Michael Reese Research and Education Foundation, Chicago, Illinois
| | - Breon Rose
- Friend Family Health Center, Chicago, Illinois
| | - David Pitrak
- Section of Infectious Diseases and Global Health, University of Chicago Medicine, Chicago, Illinois
| | - Nancy Glick
- Infectious Diseases, SINAI HEALTH SYSTEM, Chicago, Illinois
| |
Collapse
|
32
|
Novak R, Didier M, Calamari E, Ng CF, Choe Y, Clauson SL, Nestor BA, Puerta J, Fleming R, Firoozinezhad SJ, Ingber DE. Scalable Fabrication of Stretchable, Dual Channel, Microfluidic Organ Chips. J Vis Exp 2018. [PMID: 30394380 DOI: 10.3791/58151] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
A significant number of lead compounds fail in the pharmaceutical pipeline because animal studies often fail to predict clinical responses in human patients. Human Organ-on-a-Chip (Organ Chip) microfluidic cell culture devices, which provide an experimental in vitro platform to assess efficacy, toxicity, and pharmacokinetic (PK) profiles in humans, may be better predictors of therapeutic efficacy and safety in the clinic compared to animal studies. These devices may be used to model the function of virtually any organ type and can be fluidically linked through common endothelium-lined microchannels to perform in vitro studies on human organ-level and whole body-level physiology without having to conduct experiments on people. These Organ Chips consist of two perfused microfluidic channels separated by a permeable elastomeric membrane with organ-specific parenchymal cells on one side and microvascular endothelium on the other, which can be cyclically stretched to provide organ-specific mechanical cues (e.g., breathing motions in lung). This protocol details the fabrication of flexible, dual channel, Organ Chips through casting of parts using 3D printed molds, enabling combination of multiple casting and post-processing steps. Porous poly (dimethyl siloxane) (PDMS) membranes are cast with micrometer sized through-holes using silicon pillar arrays under compression. Fabrication and assembly of Organ Chips involves equipment and steps that can be implemented outside of a traditional cleanroom. This protocol provides researchers with access to Organ Chip technology for in vitro organ- and body-level studies in drug discovery, safety and efficacy testing, as well as mechanistic studies of fundamental biological processes.
Collapse
Affiliation(s)
- Richard Novak
- Wyss Institute for Biologically Inspired Engineering, Harvard University;
| | - Meredyth Didier
- Wyss Institute for Biologically Inspired Engineering, Harvard University; Apple, Inc
| | - Elizabeth Calamari
- Wyss Institute for Biologically Inspired Engineering, Harvard University
| | - Carlos F Ng
- Wyss Institute for Biologically Inspired Engineering, Harvard University
| | - Youngjae Choe
- Wyss Institute for Biologically Inspired Engineering, Harvard University
| | - Susan L Clauson
- Wyss Institute for Biologically Inspired Engineering, Harvard University
| | - Bret A Nestor
- Wyss Institute for Biologically Inspired Engineering, Harvard University
| | - Jefferson Puerta
- Wyss Institute for Biologically Inspired Engineering, Harvard University
| | - Rachel Fleming
- Wyss Institute for Biologically Inspired Engineering, Harvard University
| | | | - Donald E Ingber
- Wyss Institute for Biologically Inspired Engineering, Harvard University; Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University; Vascular Biology Program and Department of Surgery, Boston Children's Hospital and Harvard Medical School
| |
Collapse
|
33
|
Dworkin MS, Chakraborty A, Zychowski D, Donenberg G, Novak R, Garofalo R. Self-efficacy and ability to read as factors associated with antiretroviral therapy adherence in an HIV-infected population. Int J STD AIDS 2018; 29:1154-1164. [PMID: 29890903 DOI: 10.1177/0956462418776073] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Determining the barriers and facilitators of antiretroviral adherence among former and current substance users may be useful in the creation of successful interventions that target this hard-to-reach population. We performed a cross-sectional study of HIV-infected patients (N = 123) prescribed antiretroviral therapy at four Chicago healthcare venues. Bivariate and multivariable analyses were performed to determine factors associated with non-adherence based on definitions of non-adherence (any missed doses) within the past 4-day, 14-day, and 1-month time periods. Factors consistently associated with non-adherence in bivariate and multivariate analyses, regardless of duration of non-adherence definition, were lower confidence in taking medication consistently and less self-reported ability to read. These data reveal the importance of self-efficacy and ability to read (rather than specific knowledge of CD4 and viral load definitions) in the design of interventions in a population of HIV-infected persons with significant substance use.
Collapse
Affiliation(s)
- Mark S Dworkin
- 1 Division of Epidemiology and Biostatistics, University of Illinois at Chicago School of Public Health, Chicago, IL, USA
| | - Apurba Chakraborty
- 1 Division of Epidemiology and Biostatistics, University of Illinois at Chicago School of Public Health, Chicago, IL, USA
| | - Diana Zychowski
- 1 Division of Epidemiology and Biostatistics, University of Illinois at Chicago School of Public Health, Chicago, IL, USA
| | - Geri Donenberg
- 1 Division of Epidemiology and Biostatistics, University of Illinois at Chicago School of Public Health, Chicago, IL, USA
| | - Richard Novak
- 2 Section of Infectious Diseases, University of Illinois at Chicago College of Medicine, Chicago, IL USA
| | - Robert Garofalo
- 3 Department of Pediatrics, Northwestern University/Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| |
Collapse
|
34
|
Abstract
Microfluidic systems can be applied to develop unique tools for cell culture, low-cost diagnostics, and precision experimentation by leveraging microscale fluid flow. As the field has expanded and matured, there is a need for rapid prototyping that is both accessible to most research groups and can readily translate toward scalable commercial manufacturing. Here, we describe a protocol that incorporates rapid computer numerical control (CNC) milling of positive molds, casting of a negative high-durometer silicone mold, and hot embossing to produce microfluidic devices composed of virtually any thermoplastic material. The method bypasses the need for high-precision machining of the bonding surfaces by using a cast acrylic stock and only milling channels, thus expanding this protocol to any CNC platform This technique represents a versatile, high-fidelity prototyping method that enables fast turnaround of prototype devices in a standard laboratory setting, while offering scalability for commercial manufacturing.
Collapse
Affiliation(s)
- Richard Novak
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Carlos F Ng
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Donald E Ingber
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.
- Harvard John A. Paulson School of Engineering and Applied Sciences, Cambridge, MA, USA.
- Vascular Biology Program, Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
35
|
Abstract
Organs-on-chips are microfluidic cell culture devices created using microchip manufacturing techniques that contain hollow microchannels lined by living cells, which recreate specialized tissue-tissue interfaces, physical microenvironments, and vascular perfusion necessary to recapitulate organ-level physiology in vitro. Here we describe a protocol for fabrication, culture, and operation of a human lung "small airway-on-a-chip," which contains a differentiated, mucociliary bronchiolar epithelium exposed to air and an underlying microvascular endothelium that experiences fluid flow. First, microengineering is used to fabricate a multilayered microfluidic device that contains two parallel elastomeric microchannels separated by a thin rigid porous membrane; this requires less than 1 day to complete. Next, primary human airway bronchiolar epithelial cells isolated from healthy normal donors or patients with respiratory disease are cultured on the porous membrane within one microchannel while lung microvascular endothelial cells are cultured on the opposite side of the same membrane in the second channel to create a mucociliated epithelium-endothelium interface; this process take about 4-6 weeks to complete. Finally, culture medium containing neutrophils isolated from fresh whole human blood are flowed through the microvascular channel of the device to enable real-time analysis of capture and recruitment of circulating leukocytes by endothelium under physiological shear; this step requires less than 1 day to complete. The small airway-on-a-chip represents a new microfluidic tool to model complex and dynamic inflammatory responses of healthy and diseased lungs in vitro.
Collapse
Affiliation(s)
- Kambez H Benam
- Wyss Institute for Biologically Inspired Engineering, Center for Life Science Building, 5th Floor, 3 Blackfan Circle, Boston, MA, 02115, USA
| | - Marc Mazur
- Wyss Institute for Biologically Inspired Engineering, Center for Life Science Building, 5th Floor, 3 Blackfan Circle, Boston, MA, 02115, USA.,University Medical Center Utrecht, Utrecht, 3584, CX, Netherlands
| | - Youngjae Choe
- Wyss Institute for Biologically Inspired Engineering, Center for Life Science Building, 5th Floor, 3 Blackfan Circle, Boston, MA, 02115, USA
| | - Thomas C Ferrante
- Wyss Institute for Biologically Inspired Engineering, Center for Life Science Building, 5th Floor, 3 Blackfan Circle, Boston, MA, 02115, USA
| | - Richard Novak
- Wyss Institute for Biologically Inspired Engineering, Center for Life Science Building, 5th Floor, 3 Blackfan Circle, Boston, MA, 02115, USA
| | - Donald E Ingber
- Wyss Institute for Biologically Inspired Engineering, Center for Life Science Building, 5th Floor, 3 Blackfan Circle, Boston, MA, 02115, USA. .,Harvard John A. Paulson School of Engineering and Applied Sciences, Cambridge, MA, 02139, USA. .,Vascular Biology Program, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
| |
Collapse
|
36
|
Abstract
The pressure at dedicated mammographic units, indicated by a manometer, shows the pressure in the hydraulic system. The reading of this instrument is misleading because the pressure in the breast caused by the compression plate is considerably lower. Appropriate compression during mammographic examination may, however, rupture cysts.
Collapse
|
37
|
Abstract
A 40-year-old patient underwent mammography for evaluation of a mass. Atypical calcifications were observed in the opposite breast. Two types of calcification were observed: one type was spiral-shaped and the other type rod-shaped. These calcifications were caused by Filaria loa. Parasitic calcifications in the breast are uncommon.
Collapse
|
38
|
Wagoner NV, Koltun W, Lucksinger G, Warren T, Tyring S, Bernstein D, Leone P, Panther L, Lalezari J, Fife K, Novak R, Beigi R, Kriesel J, Chan J, Tasker S, Hetherington S, Wald A. GEN-003 Phase 2 Interim Results: Therapeutic Vaccine for Genital Herpes Significantly Reduces Viral Shedding and Genital Lesions. Open Forum Infect Dis 2015. [DOI: 10.1093/ofid/ofv133.615] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
39
|
Abstract
Telomerase is a reverse transcriptase that maintains telomeres on the ends of chromosomes, allowing rapidly dividing cells to proliferate while avoiding senescence and apoptosis. Understanding telomerase gene expression and splicing at the single cell level could yield insights into the roles of telomerase during normal cell growth as well as cancer development. Here we use droplet-based single cell culture followed by single cell or colony transcript abundance analysis to investigate the relationship between cell growth and transcript abundance of the telomerase genes encoding the RNA component (hTR) and protein component (hTERT) as well as hTERT splicing. Jurkat and K562 cells were examined under normal cell culture conditions and during exposure to curcumin, a natural compound with anti-carcinogenic and telomerase activity-reducing properties. Individual cells predominantly express single hTERT splice variants, with the α+/β− variant exhibiting significant transcript abundance bimodality that is sustained through cell division. Sub-lethal curcumin exposure results in reduced bimodality of all hTERT splice variants and significant upregulation of alpha splicing, suggesting a possible role in cellular stress response. The single cell culture and transcript abundance analysis method presented here provides the tools necessary for multiparameter single cell analysis which will be critical for understanding phenotypes of heterogeneous cell populations, disease cell populations and their drug response.
Collapse
Affiliation(s)
- Richard Novak
- UCSF/UC Berkeley Graduate Program in Bioengineering, University of California, Berkeley, CA 94720, USA
| | - Kristina Hart
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Richard A Mathies
- UCSF/UC Berkeley Graduate Program in Bioengineering, University of California, Berkeley, CA 94720, USA Department of Chemistry, University of California, Berkeley, CA 94720, USA
| |
Collapse
|
40
|
Makinde H, Novak R, Landay A, Spear G. Increased expression of antimicrobial peptides in the cervix during Trichomonas vaginalis infection (MUC2P.923). The Journal of Immunology 2015. [DOI: 10.4049/jimmunol.194.supp.65.6] [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
The lower genital tract is a unique mucosal environment and further studies are needed to define the types of immune responses that occur during genital infections. We investigated the expression of antimicrobial proteins/peptides (AMP) and cytokines produced in response to Trichomonas vaginalis (TV) infection. A cohort of women (30 TV+, 30 TV-) aged 18-45 that was at high risk of acquiring HIV was studied. mRNA was isolated from cervical cytobrush samples, reverse transcribed, and real time PCR used to determine AMP and cytokine expression. Cytokines were measured by ELISA in cervical vaginal lavage (CVL). TV+ samples had significantly higher mRNA levels of S100A7, S100A8, S100A9 and Muc1 than TV- samples. In contrast, lactoferrin was lower in the TV+ group. For defensins (HBDs), mRNA for HBD4 was significantly higher in TV+ samples, while HBD103 was lower in TV+ samples, but there was no difference in HBD1. Cathelicidin was not different between TV+ and TV- samples. mRNA for RegIIIγ was detected in only four samples. Although a role in inducing expression of AMPs has been shown for IL-22 and IL-17A, these two cytokines, as well as IFNγ, were not different in TV+ and TV- groups. However, IL-17 protein, but not IL-22 was higher in TV+ CVL samples (p < 0.05). Our data identify AMPs that have altered expression in the cervix during TV infection suggesting that these AMPs might have an important role in immunity against TV infection.
Collapse
Affiliation(s)
| | | | - Alan Landay
- 1Rush University Medical Center, Chicago, IL
| | | |
Collapse
|
41
|
Novak R, Wartmann D, Mathies RA, Dostálek J, Ertl P. Microfluidic Platform for Multiplexed Cell Sampling and Time-Resolved SPR-Based Cytokine Sensing. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/978-3-319-11128-5_195] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
|
42
|
Novak R, Käfer A, Hölbfer S, Puchstein B, Zyadeh-Jinniate S, Salzer H. Schwangere im Substitutionsprogramm – Geburtshilfliches Outcome bei Müttern und Kindern. Eine Analyse aus dem Wilhelminenspital. Geburtshilfe Frauenheilkd 2014. [DOI: 10.1055/s-0034-1374781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
|
43
|
Abstract
A short tandem repeat (STR) typing method is developed for forensic identification of individual cells. In our strategy, monodisperse 1.5 nL agarose-in-oil droplets are produced with a high frequency using a microfluidic droplet generator. Statistically dilute single cells, along with primer-functionalized microbeads, are randomly compartmentalized in the droplets. Massively parallel single-cell droplet polymerase chain reaction (PCR) is performed to transfer replicas of desired STR targets from the single-cell genomic DNA onto the coencapsulated microbeads. These DNA-conjugated beads are subsequently harvested and reamplified under statistically dilute conditions for conventional capillary electrophoresis (CE) STR fragment size analysis. The 9-plex STR profiles of single cells from both pure and mixed populations of GM09947 and GM09948 human lymphoid cells show that all alleles are correctly called and allelic drop-in/drop-out is not observed. The cell mixture study exhibits a good linear relationship between the observed and input cell ratios in the range of 1:1 to 10:1. Additionally, the STR profile of GM09947 cells could be deduced even in the presence of a high concentration of cell-free contaminating 9948 genomic DNA. Our method will be valuable for the STR analysis of samples containing mixtures of cells/DNA from multiple contributors and for low-concentration samples.
Collapse
Affiliation(s)
- Tao Geng
- Department of Chemistry, University of California , Berkeley, California 94720, United States
| | | | | |
Collapse
|
44
|
Shuga J, Zeng Y, Novak R, Lan Q, Tang X, Rothman N, Vermeulen R, Li L, Hubbard A, Zhang L, Mathies RA, Smith MT. Single molecule quantitation and sequencing of rare translocations using microfluidic nested digital PCR. Nucleic Acids Res 2013; 41:e159. [PMID: 23873959 PMCID: PMC3763562 DOI: 10.1093/nar/gkt613] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [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: 01/12/2023] Open
Abstract
Cancers are heterogeneous and genetically unstable. New methods are needed that provide the sensitivity and specificity to query single cells at the genetic loci that drive cancer progression, thereby enabling researchers to study the progression of individual tumors. Here, we report the development and application of a bead-based hemi-nested microfluidic droplet digital PCR (dPCR) technology to achieve ‘quantitative’ measurement and single-molecule sequencing of somatically acquired carcinogenic translocations at extremely low levels (<10−6) in healthy subjects. We use this technique in our healthy study population to determine the overall concentration of the t(14;18) translocation, which is strongly associated with follicular lymphoma. The nested dPCR approach improves the detection limit to 1 × 10−7 or lower while maintaining the analysis efficiency and specificity. Further, the bead-based dPCR enabled us to isolate and quantify the relative amounts of the various clonal forms of t(14;18) translocation in these subjects, and the single-molecule sensitivity and resolution of dPCR led to the discovery of new clonal forms of t(14;18) that were otherwise masked by the conventional quantitative PCR measurements. In this manner, we created a quantitative map for this carcinogenic mutation in this healthy population and identified the positions on chromosomes 14 and 18 where the vast majority of these t(14;18) events occur.
Collapse
Affiliation(s)
- Joe Shuga
- School of Public Health, University of California, Berkeley, CA 94720, USA, Department of Chemistry, University of California, Berkeley, CA 94720, USA, Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA, UC San Francisco/UC Berkeley Graduate Program in Bioengineering, University of California, Berkeley, CA 94720, USA, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Department of Health and Human Services, Bethesda, MD 20852, USA, Guangdong Poison Control Center, Guangzhou 510300, China and Environmental Epidemiology Division, Institute for Risk Assessment Sciences, Utrecht University, Utrecht, NL-3508, The Netherlands
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Prince WT, Ivezic-Schoenfeld Z, Lell C, Tack KJ, Novak R, Obermayr F, Talbot GH. Phase II clinical study of BC-3781, a pleuromutilin antibiotic, in treatment of patients with acute bacterial skin and skin structure infections. Antimicrob Agents Chemother 2013; 57:2087-94. [PMID: 23422913 PMCID: PMC3632892 DOI: 10.1128/aac.02106-12] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [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: 10/17/2012] [Accepted: 02/12/2013] [Indexed: 01/22/2023] Open
Abstract
This study investigated the potential of the novel systemic pleuromutilin antibiotic BC-3781 to treat patients with an acute bacterial skin and skin structure infection (ABSSSI) caused by a Gram-positive pathogen. Patients were randomized to intravenous BC-3781 100 mg, BC-3781 150 mg, or vancomycin 1 g every 12 h. Response to treatment was assessed daily and at test of cure (TOC). The primary endpoint was the clinical success rate at TOC in the modified intent-to-treat (MITT) and clinically evaluable (CE) analysis populations. Baseline characteristics, including the frequency of methicillin-resistant Staphylococcus aureus (MRSA), were comparable between the different treatment groups. Of 210 patients randomized, 186 (88.6%) patients completed the study. Clinical success at TOC in the CE population occurred in 54 (90.0%) patients in the BC-3781 100-mg group, 48 (88.9%) in the BC-3781 150-mg group, and 47 (92.2%) in the vancomycin group. At day 3, the clinical response rate was similar across the three treatment groups. Six patients discontinued study medication following an adverse event. The incidence rate for drug-related adverse events was lower for patients receiving BC-3781 (34.3% and 39.4% in the 100-mg and 150-mg groups, respectively) than those receiving vancomycin (53.0%). When BC-3781 was used to treat ABSSSIs caused by a Gram-positive pathogen, including MRSA, clinical success rates were comparable to those of the comparator, vancomycin. BC-3781 was generally well tolerated. These results provide the first proof of concept for the systemic use of a pleuromutilin antibiotic for the treatment of ABSSSIs.
Collapse
Affiliation(s)
- W T Prince
- Nabriva Therapeutics AG, Vienna, Austria.
| | | | | | | | | | | | | |
Collapse
|
46
|
Abstract
The production of hot embossed plastic microfluidic devices is demonstrated in 1-2 h by exploiting vinyl adhesive stickers as masks for electroplating nickel molds. The sticker masks are cut directly from a CAD design using a cutting plotter and transferred to steel wafers for nickel electroplating. The resulting nickel molds are used to hot emboss a variety of plastic substrates, including cyclo-olefin copolymer and THV fluorinated thermoplastic elastomer. Completed devices are formed by bonding a blank sheet to the embossed layer using a solvent-assisted lamination method. For example, a microfluidic valve array or automaton and a droplet generator were fabricated with less than 100 μm x-y plane feature resolution, to within 9% of the target height, and with 90 ± 11% height uniformity over 5 cm. This approach for mold fabrication, embossing, and bonding reduces fabrication time and cost for research applications by avoiding photoresists, lithography masks, and the cleanroom.
Collapse
Affiliation(s)
- Richard Novak
- Program in Bioengineering, UC Berkeley, Berkeley, CA, USA.
| | - Navpreet Ranu
- Department of Bioengineering, MIT, Cambridge, MA, USA;
| | - Richard A. Mathies
- Program in Bioengineering, UC Berkeley, Berkeley, CA, USA.
- Department of Chemistry, UC Berkeley, Berkeley, CA, 94720 USA
- Tel.: (510) 642-4192,
| |
Collapse
|
47
|
Metch B, Frank I, Novak R, Swann E, Metzger D, Morgan C, Lucy D, Dunbar D, Graham P, Madenwald T, Escamilia G, Koblin B. Recruitment of urban US women at risk for HIV infection and willingness to participate in future HIV vaccine trials. AIDS Behav 2013; 17:760-72. [PMID: 23090677 DOI: 10.1007/s10461-012-0351-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Enrollment of US women with sufficient risk of HIV infection into HIV vaccine efficacy trials has proved challenging. A cohort of 799 HIV-negative women, aged 18-45, recruited from three US cities was enrolled to assess recruitment strategies based on geographic risk pockets, social and sexual networks and occurrence of sexual concurrency and to assess HIV seroincidence during follow-up (to be reported later). Among enrolled women, 90 % lived or engaged in risk behaviors within a local risk pocket, 64 % had a male partner who had concurrent partners and 50 % had a male partner who had been recently incarcerated. Nearly half (46 %) were recruited through peer referral. At enrollment, 86 % of women said they were willing to participate in a vaccine efficacy trial. Results indicate that participant and partner risk behaviors combined with a peer referral recruitment strategy may best identify an at-risk cohort willing to participate in future trials.
Collapse
|
48
|
Koblin B, Metch B, Morgan C, Novak R, Swann E, Metzger D, Lucy D, Dunbar D, Graham P, Madenwald T, Escamia G, Frank I. Feasibility of recruiting high-risk women in the US for HIV vaccine efficacy trials (HVTN 906). Retrovirology 2012. [PMCID: PMC3441717 DOI: 10.1186/1742-4690-9-s2-p123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
|
49
|
Kessel A, Peri R, Perricone R, Guarino MD, Vadasz Z, Novak R, Haj T, Kivity S, Toubi E. The autoreactivity of B cells in hereditary angioedema due to C1 inhibitor deficiency. Clin Exp Immunol 2012; 167:422-8. [PMID: 22288585 PMCID: PMC3374274 DOI: 10.1111/j.1365-2249.2011.04527.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2011] [Indexed: 01/29/2023] Open
Abstract
Patients with hereditary angioedema (HAE) tend to produce autoantibodies and have a propensity to develop immunoregulatory disorders. We characterize the profile of autoantibodies in a group of HAE patients and investigate their memory B cells' phenotype and activation status. We studied the activity status phenotype, Toll-like receptor (TLR)-9 expression and total phosphotyrosine in B cells isolated from HAE patients. Additionally, the following autoantibodies were assessed in the serum of 61 HAE patients: anti-nuclear, rheumatoid factor, anti-cardiolipin, anti-tissue transglutaminase, anti-endomysial, anti-Saccharomyces cerevisiae, anti-thyroid and anti-neutrophil cytoplasmic antibodies. In 47·5% of HAE patients we detected at least one of the tested autoantibodies. Expression of CD69, CD5 and CD21 was found to be significantly higher on memory B cells from HAE patients compared to healthy controls (4·59 ± 4·41 versus 2·06 ± 1·81, P = 0·04, 8·22 ± 7·17 versus 3·65 ± 3·78, P = 0·05, 2·43 ± 0·54 versus 1·92 ± 0·41, P = 0·01, respectively). Total phosphotyrosine in B cells from HAE patients was significantly higher compared to healthy controls (4·8 ± 1·1 versus 2·7 ± 1·3, P = 0·0003). Memory B cells isolated from the HAE group contained higher amounts of TLR-9 compared to healthy controls (8·17 ± 4·1 versus 4·56 ± 1·6, P = 0·0027). Furthermore, the expression of TLR-9 in memory B cells from HAE patients with autoantibodies was significantly higher than the control group (10 ± 4·7 versus 4·56 ± 1·6, P = 0·0002) and from that in HAE patients without autoantibodies (10 ± 4·7 versus 5·8 ± 0·9, P = 0·036). HAE patients have enhanced production of autoantibodies due most probably to the increased activation of B cells, which was found to be in association with a high expression of TLR-9.
Collapse
Affiliation(s)
- A Kessel
- Division of Allergy and Clinical Immunology, Bnai Zion Medical Center, Technion Faculty of Medicine, Haifa, Israel.
| | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Novak R, Zeng Y, Shuga J, Venugopalan G, Fletcher DA, Smith MT, Mathies RA. Single-cell multiplex gene detection and sequencing with microfluidically generated agarose emulsions. Angew Chem Int Ed Engl 2011; 50:390-5. [PMID: 21132688 DOI: 10.1002/anie.201006089] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Richard Novak
- Center for Exposure Biology, University of California, Berkeley, 307 Lewis Hall, Berkeley, CA 94720, USA
| | | | | | | | | | | | | |
Collapse
|