1
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March S, Nerurkar N, Jain A, Andrus L, Kim D, Whittaker CA, Tan EK, Thiberge S, Fleming HE, Mancio-Silva L, Rice CM, Bhatia SN. Autonomous circadian rhythms in the human hepatocyte regulate hepatic drug metabolism and inflammatory responses. Sci Adv 2024; 10:eadm9281. [PMID: 38657074 PMCID: PMC11042741 DOI: 10.1126/sciadv.adm9281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/22/2024] [Indexed: 04/26/2024]
Abstract
Critical aspects of physiology and cell function exhibit self-sustained ~24-hour variations termed circadian rhythms. In the liver, circadian rhythms play fundamental roles in maintaining organ homeostasis. Here, we established and characterized an in vitro liver experimental system in which primary human hepatocytes display self-sustained oscillations. By generating gene expression profiles of these hepatocytes over time, we demonstrated that their transcriptional state is dynamic across 24 hours and identified a set of cycling genes with functions related to inflammation, drug metabolism, and energy homeostasis. We designed and tested a treatment protocol to minimize atorvastatin- and acetaminophen-induced hepatotoxicity. Last, we documented circadian-dependent induction of pro-inflammatory cytokines when triggered by LPS, IFN-β, or Plasmodium infection in human hepatocytes. Collectively, our findings emphasize that the phase of the circadian cycle has a robust impact on the efficacy and toxicity of drugs, and we provide a test bed to study the timing and magnitude of inflammatory responses over the course of infection in human liver.
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Affiliation(s)
- Sandra March
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Niketa Nerurkar
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA
| | - Anisha Jain
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Linda Andrus
- Laboratory of Virology and Infectious Disease, The Rockefeller University, NY, New York, USA
| | - Daniel Kim
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA
| | - Charles A. Whittaker
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA
| | - Edward K.W. Tan
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA
| | - Sabine Thiberge
- Institut Pasteur, Université Paris Cité, Inserm U1201, CNRS EMR9195, Unité de Biologie des Interactions Hôte-Parasite, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Centre de Production et d’Infection des Anophèles, 75015 Paris, France
| | - Heather E. Fleming
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Liliana Mancio-Silva
- Institut Pasteur, Université Paris Cité, Inserm U1201, CNRS EMR9195, Unité de Biologie des Interactions Hôte-Parasite, 75015 Paris, France
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, NY, New York, USA
| | - Sangeeta N. Bhatia
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Wyss Institute at Harvard University, 201 Brookline Ave, Boston, MA 02215, USA
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2
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Hao L, Boehnke N, Elledge SK, Harzallah NS, Zhao RT, Cai E, Feng YX, Neaher S, Fleming HE, Gupta PB, Hammond PT, Bhatia SN. Targeting and monitoring ovarian cancer invasion with an RNAi and peptide delivery system. Proc Natl Acad Sci U S A 2024; 121:e2307802121. [PMID: 38437557 PMCID: PMC10945808 DOI: 10.1073/pnas.2307802121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 12/28/2023] [Indexed: 03/06/2024] Open
Abstract
RNA interference (RNAi) therapeutics are an emerging class of medicines that selectively target mRNA transcripts to silence protein production and combat disease. Despite the recent progress, a generalizable approach for monitoring the efficacy of RNAi therapeutics without invasive biopsy remains a challenge. Here, we describe the development of a self-reporting, theranostic nanoparticle that delivers siRNA to silence a protein that drives cancer progression while also monitoring the functional activity of its downstream targets. Our therapeutic target is the transcription factor SMARCE1, which was previously identified as a key driver of invasion in early-stage breast cancer. Using a doxycycline-inducible shRNA knockdown in OVCAR8 ovarian cancer cells both in vitro and in vivo, we demonstrate that SMARCE1 is a master regulator of genes encoding proinvasive proteases in a model of human ovarian cancer. We additionally map the peptide cleavage profiles of SMARCE1-regulated proteases so as to design a readout for downstream enzymatic activity. To demonstrate the therapeutic and diagnostic potential of our approach, we engineered self-assembled layer-by-layer nanoparticles that can encapsulate nucleic acid cargo and be decorated with peptide substrates that release a urinary reporter upon exposure to SMARCE1-related proteases. In an orthotopic ovarian cancer xenograft model, theranostic nanoparticles were able to knockdown SMARCE1 which was in turn reported through a reduction in protease-activated urinary reporters. These LBL nanoparticles both silence gene products by delivering siRNA and noninvasively report on downstream target activity by delivering synthetic biomarkers to sites of disease, enabling dose-finding studies as well as longitudinal assessments of efficacy.
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Affiliation(s)
- Liangliang Hao
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Natalie Boehnke
- Department of Chemical Engineering and Materials Science, University of Minnesota Twin Cities, Minneapolis, MN55455
| | - Susanna K. Elledge
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Nour-Saïda Harzallah
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Renee T. Zhao
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Eva Cai
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA02139
- Harvard University–Massachusetts Institute of Technology Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Yu-Xiong Feng
- Department of Biology, Whitehead Institute for Biomedical Research, Cambridge, MA02142
| | - Sofia Neaher
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Heather E. Fleming
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA02139
- Harvard University–Massachusetts Institute of Technology Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA02139
| | | | - Paula T. Hammond
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA02139
- Institute for Soldier Nanotechnologies, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- Marble Center for Cancer Nanomedicine, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Sangeeta N. Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA02139
- Harvard University–Massachusetts Institute of Technology Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA02139
- Marble Center for Cancer Nanomedicine, Massachusetts Institute of Technology, Cambridge, MA02139
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA02142
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA02115
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA02115
- HHMI, Massachusetts Institute of Technology, Cambridge, MA02139
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3
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Bhatia SN, Dahlman JE. RNA delivery systems. Proc Natl Acad Sci U S A 2024; 121:e2315789121. [PMID: 38437565 PMCID: PMC10945841 DOI: 10.1073/pnas.2315789121] [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: 03/06/2024] Open
Affiliation(s)
- Sangeeta N. Bhatia
- Harvard University–Massachusetts Institute of Technology Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115
- HHMI, Massachusetts Institute of Technology, Cambridge, MA02139
- Marble Center for Cancer Nanomedicine, Massachusetts Institute of Technology, Cambridge, MA02139
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA02142
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA02215
| | - James E. Dahlman
- Wallace H. Coulter Department of Biomedical Engineering, Emory School of Medicine and Georgia Institute of Technology, Atlanta, GA 30307
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4
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Martin-Alonso C, Tabrizi S, Xiong K, Blewett T, Sridhar S, Crnjac A, Patel S, An Z, Bekdemir A, Shea D, Wang ST, Rodriguez-Aponte S, Naranjo CA, Rhoades J, Kirkpatrick JD, Fleming HE, Amini AP, Golub TR, Love JC, Bhatia SN, Adalsteinsson VA. Priming agents transiently reduce the clearance of cell-free DNA to improve liquid biopsies. Science 2024; 383:eadf2341. [PMID: 38236959 DOI: 10.1126/science.adf2341] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/01/2023] [Indexed: 01/23/2024]
Abstract
Liquid biopsies enable early detection and monitoring of diseases such as cancer, but their sensitivity remains limited by the scarcity of analytes such as cell-free DNA (cfDNA) in blood. Improvements to sensitivity have primarily relied on enhancing sequencing technology ex vivo. We sought to transiently augment the level of circulating tumor DNA (ctDNA) in a blood draw by attenuating its clearance in vivo. We report two intravenous priming agents given 1 to 2 hours before a blood draw to recover more ctDNA. Our priming agents consist of nanoparticles that act on the cells responsible for cfDNA clearance and DNA-binding antibodies that protect cfDNA. In tumor-bearing mice, they greatly increase the recovery of ctDNA and improve the sensitivity for detecting small tumors.
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Affiliation(s)
- Carmen Martin-Alonso
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Shervin Tabrizi
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA 02114, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Kan Xiong
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Timothy Blewett
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Andjela Crnjac
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sahil Patel
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Division of Pulmonary and Critical Care, Department of Medicine, Massachusetts General Hospital, Boston, MA 02124, USA
| | - Zhenyi An
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ahmet Bekdemir
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Douglas Shea
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shih-Ting Wang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sergio Rodriguez-Aponte
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christopher A Naranjo
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Justin Rhoades
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jesse D Kirkpatrick
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Heather E Fleming
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ava P Amini
- Microsoft Research, Cambridge, MA 02142, USA
| | - Todd R Golub
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - J Christopher Love
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
- Wyss Institute at Harvard University, Boston, MA 02215, USA
- Howard Hughes Medical Institute, Cambridge, MA 02138, USA
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5
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Zhong Q, Tan EKW, Martin-Alonso C, Parisi T, Hao L, Kirkpatrick JD, Fadel T, Fleming HE, Jacks T, Bhatia SN. Inhalable point-of-care urinary diagnostic platform. Sci Adv 2024; 10:eadj9591. [PMID: 38181080 PMCID: PMC10776015 DOI: 10.1126/sciadv.adj9591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 12/01/2023] [Indexed: 01/07/2024]
Abstract
Although low-dose computed tomography screening improves lung cancer survival in at-risk groups, inequality remains in lung cancer diagnosis due to limited access to and high costs of medical imaging infrastructure. We designed a needleless and imaging-free platform, termed PATROL (point-of-care aerosolizable nanosensors with tumor-responsive oligonucleotide barcodes), to reduce resource disparities for early detection of lung cancer. PATROL formulates a set of DNA-barcoded, activity-based nanosensors (ABNs) into an inhalable format. Lung cancer-associated proteases selectively cleave the ABNs, releasing synthetic DNA reporters that are eventually excreted via the urine. The urinary signatures of barcoded nanosensors are quantified within 20 min at room temperature using a multiplexable paper-based lateral flow assay. PATROL detects early-stage tumors in an autochthonous lung adenocarcinoma mouse model with high sensitivity and specificity. Tailoring the library of ABNs may enable not only the modular PATROL platform to lower the resource threshold for lung cancer early detection tools but also the rapid detection of chronic pulmonary disorders and infections.
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Affiliation(s)
- Qian Zhong
- Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Marble Center of Cancer Nanomedicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Edward K. W. Tan
- Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Marble Center of Cancer Nanomedicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Carmen Martin-Alonso
- Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Harvard-MIT Division Health Sciences and Technology, Cambridge, MA 02139, USA
| | - Tiziana Parisi
- Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Liangliang Hao
- Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Marble Center of Cancer Nanomedicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jesse D. Kirkpatrick
- Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tarek Fadel
- Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Marble Center of Cancer Nanomedicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Heather E. Fleming
- Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tyler Jacks
- Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sangeeta N. Bhatia
- Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Marble Center of Cancer Nanomedicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Harvard-MIT Division Health Sciences and Technology, Cambridge, MA 02139, USA
- Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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6
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Van Heest AE, Deng F, Zhao RT, Harzallah NS, Fleming HE, Bhatia SN, Hao L. CRISPR-Cas-mediated Multianalyte Synthetic Urine Biomarker Test for Portable Diagnostics. J Vis Exp 2023:10.3791/66189. [PMID: 38145378 PMCID: PMC10840402 DOI: 10.3791/66189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2023] Open
Abstract
Creating synthetic biomarkers for the development of precision diagnostics has enabled detection of disease through pathways beyond those used for traditional biofluid measurements. Synthetic biomarkers generally make use of reporters that provide readable signals in the biofluid to reflect the biochemical alterations in the local disease microenvironment during disease incidence and progression. The pharmacokinetic concentration of the reporters and biochemical amplification of the disease signal are paramount to achieving high sensitivity and specificity in a diagnostic test. Here, a cancer diagnostic platform is built using one format of synthetic biomarkers: activity-based nanosensors carrying chemically stabilized DNA reporters that can be liberated by aberrant proteolytic signatures in the tumor microenvironment. Synthetic DNA as a disease reporter affords multiplexing capability through its use as a barcode, allowing for the readout of multiple proteolytic signatures at once. DNA reporters released into the urine are detected using CRISPR nucleases via hybridization with CRISPR RNAs, which in turn produce a fluorescent or colorimetric signal upon enzyme activation. In this protocol, DNA-barcoded, activity-based nanosensors are constructed and their application is exemplified in a preclinical mouse model of metastatic colorectal cancer. This system is highly modifiable according to disease biology and generates multiple disease signals simultaneously, affording a comprehensive understanding of the disease characteristics through a minimally invasive process requiring only nanosensor administration, urine collection, and a paper test which enables point-of-care diagnostics.
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Affiliation(s)
| | - Feiyang Deng
- Department of Biomedical Engineering, Boston University
| | - Renee T Zhao
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology
| | - Nour Saida Harzallah
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology
| | - Heather E Fleming
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Howard Hughes Medical Institute
| | - Sangeeta N Bhatia
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Howard Hughes Medical Institute; Broad Institute of Massachusetts Institute of Technology and Harvard; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School
| | - Liangliang Hao
- Department of Biomedical Engineering, Boston University; Institute for Medical Engineering and Science, Massachusetts Institute of Technology; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology;
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7
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Babic A, Rosenthal MH, Sundaresan TK, Khalaf N, Lee V, Brais LK, Loftus M, Caplan L, Denning S, Gurung A, Harrod J, Schawkat K, Yuan C, Wang QL, Lee AA, Biller LH, Yurgelun MB, Ng K, Nowak JA, Aguirre AJ, Bhatia SN, Vander Heiden MG, Van Den Eeden SK, Caan BJ, Wolpin BM. Adipose tissue and skeletal muscle wasting precede clinical diagnosis of pancreatic cancer. Nat Commun 2023; 14:4317. [PMID: 37463915 DOI: 10.1038/s41467-023-40024-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 07/04/2023] [Indexed: 07/20/2023] Open
Abstract
Patients with pancreatic cancer commonly develop weight loss and muscle wasting. Whether adipose tissue and skeletal muscle losses begin before diagnosis and the potential utility of such losses for earlier cancer detection are not well understood. We quantify skeletal muscle and adipose tissue areas from computed tomography (CT) imaging obtained 2 months to 5 years before cancer diagnosis in 714 pancreatic cancer cases and 1748 matched controls. Adipose tissue loss is identified up to 6 months, and skeletal muscle wasting is identified up to 18 months before the clinical diagnosis of pancreatic cancer and is not present in the matched control population. Tissue losses are of similar magnitude in cases diagnosed with localized compared with metastatic disease and are not correlated with at-diagnosis circulating levels of CA19-9. Skeletal muscle wasting occurs in the 1-2 years before pancreatic cancer diagnosis and may signal an upcoming diagnosis of pancreatic cancer.
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Affiliation(s)
- Ana Babic
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael H Rosenthal
- Department of Radiology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Natalia Khalaf
- Center for Innovations in Quality, Effectiveness, and Safety (IQuESt), Michael E. DeBakey Veterans Affairs Medical Center; Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Valerie Lee
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Lauren K Brais
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Maureen Loftus
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Leah Caplan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sarah Denning
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anamol Gurung
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Joanna Harrod
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Khoschy Schawkat
- Department of Radiology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Chen Yuan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Qiao-Li Wang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Alice A Lee
- Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Leah H Biller
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Matthew B Yurgelun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kimmie Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jonathan A Nowak
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Andrew J Aguirre
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sangeeta N Bhatia
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Wyss Institute, Harvard University, Boston, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Matthew G Vander Heiden
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Bette J Caan
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Brian M Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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8
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Hao L, Zhao RT, Welch NL, Tan EKW, Zhong Q, Harzallah NS, Ngambenjawong C, Ko H, Fleming HE, Sabeti PC, Bhatia SN. CRISPR-Cas-amplified urinary biomarkers for multiplexed and portable cancer diagnostics. Nat Nanotechnol 2023; 18:798-807. [PMID: 37095220 PMCID: PMC10359190 DOI: 10.1038/s41565-023-01372-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 03/10/2023] [Indexed: 05/03/2023]
Abstract
Synthetic biomarkers, bioengineered sensors that generate molecular reporters in diseased microenvironments, represent an emerging paradigm in precision diagnostics. Despite the utility of DNA barcodes as a multiplexing tool, their susceptibility to nucleases in vivo has limited their utility. Here we exploit chemically stabilized nucleic acids to multiplex synthetic biomarkers and produce diagnostic signals in biofluids that can be 'read out' via CRISPR nucleases. The strategy relies on microenvironmental endopeptidase to trigger the release of nucleic acid barcodes and polymerase-amplification-free, CRISPR-Cas-mediated barcode detection in unprocessed urine. Our data suggest that DNA-encoded nanosensors can non-invasively detect and differentiate disease states in transplanted and autochthonous murine cancer models. We also demonstrate that CRISPR-Cas amplification can be harnessed to convert the readout to a point-of-care paper diagnostic tool. Finally, we employ a microfluidic platform for densely multiplexed, CRISPR-mediated DNA barcode readout that can potentially evaluate complex human diseases rapidly and guide therapeutic decisions.
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Affiliation(s)
- Liangliang Hao
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Renee T Zhao
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicole L Welch
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Harvard Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Edward Kah Wei Tan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Qian Zhong
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nour Saida Harzallah
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Chayanon Ngambenjawong
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Henry Ko
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Heather E Fleming
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Pardis C Sabeti
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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9
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Tabrizi S, Martin-Alonso C, Xiong K, Blewett T, Sridhar S, An Z, Patel S, Rodriguez-Aponte S, Naranjo C, Shea D, Golub T, Bhatia SN, Adalsteinsson VA, Love JC. Abstract 3371: A DNA-binding priming agent protects cell-free DNA and improves the sensitivity of liquid biopsies. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-3371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Liquid biopsies using cell-free DNA (cfDNA) enable non-invasive detection and characterization of disease. Advances in sequencing methods have significantly improved the performance of liquid biopsies. Yet, despite these advances, sensitivity remains a fundamental challenge. In oncology, circulating tumor DNA (ctDNA) screening tests only detect 20-40% of stage I tumors and tests for minimal residual disease have only 25-50% sensitivity after surgery. The major barrier to better sensitivity is the intrinsic low level of ctDNA in plasma. Physical absence of tumor DNA molecules in a blood draw from a patient with low disease burden will result in a negative test, no matter the sensitivity of the ex vivo detection platform. To overcome this barrier, here we report a first-in-class intravenous DNA-binding priming agent that is given 2 hours prior to a blood draw to recover more ctDNA, boosting the detection of tumor mutations in plasma by 19-fold and increasing sensitivity from 6% to 84%. Given the rapid clearance of cfDNA from circulation, we reasoned that a priming agent that could bind and protect cfDNA from clearance could increase the tumor DNA recovered from plasma. We selected monoclonal antibodies (mAbs) as the class of molecules to use as cfDNA protectors given their persistence in circulation and ease of engineering. We identify a mAb that binds double-stranded DNA (dsDNA) and find on electrophoretic mobility shift assays that it binds both free and histone-bound dsDNA, the constituent components of cfDNA. We then demonstrate that this mAb can delay the clearance of dsDNA from plasma in vivo through co-injection of the mAb with free- and histone-bound dsDNA in mice. We further identify interactions with Fc-gamma-receptors as a key mediator of early clearance of dsDNA bound to the priming mAb. To address this early clearance and limit potential immune interactions, we engineer the mAb to abrogate its Fc effector function. The engineered variant decreases clearance of injected dsDNA by over 150-fold at one hour post-injection compared to dsDNA alone. We next evaluate the effect of our priming mAb on cancer detection. We use a targeted panel against 1,822 mutations in the MC26 murine colon carcinoma cell line to detect tumor mutations in the plasma of tumor bearing mice. The priming mAb results in 19-fold higher recovery of tumor DNA molecules compared to a control mAb. This improved recovery leads to detection of 77% of targeted sites in plasma compared to only 15% in the control group. In sensitivity analyses, higher recovery of mutant molecules improves sensitivity for cancer detection from 6% to 84% at 0.001% tumor fraction. In summary, we demonstrate an approach to overcome a key barrier in liquid biopsies. We envision that similar to contrast agents in clinical imaging, priming agents could significantly boost the diagnostic sensitivity of liquid biopsies and enable further applications across biomedicine.
Citation Format: Shervin Tabrizi, Carmen Martin-Alonso, Kan Xiong, Timothy Blewett, Sainetra Sridhar, Zhenyi An, Sahil Patel, Sergio Rodriguez-Aponte, Christopher Naranjo, Douglas Shea, Todd Golub, Sangeeta N. Bhatia, Viktor A. Adalsteinsson, J. Christopher Love. A DNA-binding priming agent protects cell-free DNA and improves the sensitivity of liquid biopsies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3371.
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Affiliation(s)
- Shervin Tabrizi
- 1Harvard Medical School/Massachusetts General Hospital, Boston, MA
| | | | | | | | | | | | - Sahil Patel
- 1Harvard Medical School/Massachusetts General Hospital, Boston, MA
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10
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Aung A, Cui A, Maiorino L, Amini AP, Gregory JR, Bukenya M, Zhang Y, Lee H, Cottrell CA, Morgan DM, Silva M, Suh H, Kirkpatrick JD, Amlashi P, Remba T, Froehle LM, Xiao S, Abraham W, Adams J, Love JC, Huyett P, Kwon DS, Hacohen N, Schief WR, Bhatia SN, Irvine DJ. Low protease activity in B cell follicles promotes retention of intact antigens after immunization. Science 2023; 379:eabn8934. [PMID: 36701450 PMCID: PMC10041875 DOI: 10.1126/science.abn8934] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The structural integrity of vaccine antigens is critical to the generation of protective antibody responses, but the impact of protease activity on vaccination in vivo is poorly understood. We characterized protease activity in lymph nodes and found that antigens were rapidly degraded in the subcapsular sinus, paracortex, and interfollicular regions, whereas low protease activity and antigen degradation rates were detected in the vicinity of follicular dendritic cells (FDCs). Correlated with these findings, immunization regimens designed to target antigen to FDCs led to germinal centers dominantly targeting intact antigen, whereas traditional immunizations led to much weaker responses that equally targeted the intact immunogen and antigen breakdown products. Thus, spatially compartmentalized antigen proteolysis affects humoral immunity and can be exploited.
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Affiliation(s)
- Aereas Aung
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
| | - Ang Cui
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard-MIT Division of Health Sciences and Technology, MIT, Cambridge, MA, USA
| | - Laura Maiorino
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
| | - Ava P Amini
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Harvard-MIT Division of Health Sciences and Technology, MIT, Cambridge, MA, USA
- Program in Biophysics, Harvard University, Boston, MA, USA
- Microsoft Research New England, Cambridge, MA, USA
| | - Justin R Gregory
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
| | - Maurice Bukenya
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
| | - Yiming Zhang
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Heya Lee
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
| | - Christopher A Cottrell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
| | - Duncan M Morgan
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Murillo Silva
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
| | - Heikyung Suh
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
| | - Jesse D Kirkpatrick
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Harvard-MIT Division of Health Sciences and Technology, MIT, Cambridge, MA, USA
| | - Parastoo Amlashi
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
| | - Tanaka Remba
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
| | - Leah M Froehle
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Shuhao Xiao
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
| | - Wuhbet Abraham
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
| | - Josetta Adams
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
| | - J Christopher Love
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Phillip Huyett
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA, USA
| | - Douglas S Kwon
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - William R Schief
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
| | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard-MIT Division of Health Sciences and Technology, MIT, Cambridge, MA, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Wyss Institute at Harvard, Boston, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Darrell J Irvine
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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11
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Tabrizi S, Martin-Alonso C, Xiong K, Blewett T, Sridhar S, An Z, Patel S, Rodriguez-Aponte S, Naranjo CA, Wang ST, Shea D, Golub TR, Bhatia SN, Adalsteinsson V, Love JC. An intravenous DNA-binding priming agent protects cell-free DNA and improves the sensitivity of liquid biopsies. bioRxiv 2023:2023.01.13.523947. [PMID: 36711455 PMCID: PMC9882106 DOI: 10.1101/2023.01.13.523947] [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: 01/16/2023]
Abstract
Blood-based, or "liquid," biopsies enable minimally invasive diagnostics but have limits on sensitivity due to scarce cell-free DNA (cfDNA). Improvements to sensitivity have primarily relied on enhancing sequencing technology ex vivo . Here, we sought to augment the level of circulating tumor DNA (ctDNA) detected in a blood draw by attenuating the clearance of cfDNA in vivo . We report a first-in-class intravenous DNA-binding priming agent given 2 hours prior to a blood draw to recover more cfDNA. The DNA-binding antibody minimizes nuclease digestion and organ uptake of cfDNA, decreasing its clearance at 1 hour by over 150-fold. To improve plasma persistence and limit potential immune interactions, we abrogated its Fc-effector function. We found that it protects GC-rich sequences and DNase-hypersensitive sites, which are ordinarily underrepresented in cfDNA. In tumor-bearing mice, priming improved tumor DNA recovery by 19-fold and sensitivity for detecting cancer from 6% to 84%. These results suggest a novel method to enhance the sensitivity of existing DNA-based cancer testing using blood biopsies.
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12
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Martin-Alonso C, Tabrizi S, Xiong K, Blewett T, Patel S, An Z, Sridhar S, Bekdemir A, Shea D, Amini AP, Wang ST, Kirkpatrick J, Rhoades J, Golub TR, Love JC, Adalsteinsson VA, Bhatia SN. A nanoparticle priming agent reduces cellular uptake of cell-free DNA and enhances the sensitivity of liquid biopsies. bioRxiv 2023:2023.01.13.524003. [PMID: 36711603 PMCID: PMC9882213 DOI: 10.1101/2023.01.13.524003] [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: 01/16/2023]
Abstract
Liquid biopsies are enabling minimally invasive monitoring and molecular profiling of diseases across medicine, but their sensitivity remains limited by the scarcity of cell-free DNA (cfDNA) in blood. Here, we report an intravenous priming agent that is given prior to a blood draw to increase the abundance of cfDNA in circulation. Our priming agent consists of nanoparticles that act on the cells responsible for cfDNA clearance to slow down cfDNA uptake. In tumor-bearing mice, this agent increases the recovery of circulating tumor DNA (ctDNA) by up to 60-fold and improves the sensitivity of a ctDNA diagnostic assay from 0% to 75% at low tumor burden. We envision that this priming approach will significantly improve the performance of liquid biopsies across a wide range of clinical applications in oncology and beyond.
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13
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Abstract
Antimicrobial peptides (AMPs) constitute a promising class of alternatives to antibiotics to curb antimicrobial resistance. Nonetheless, their utility as a systemic agent is hampered by short circulation time and toxicity. Infection sites, analogous to tumors, harbor an aberrant microenvironment that has the potential to be exploited to develop conditionally activated therapeutics with an improved therapeutic index. In particular, we identified strategies to prolong systemic circulation of small, cationic AMPs in a mouse model of bacterial pneumonia. Specifically, we report an albumin-binding domain (ABD)-AMP conjugate as a long-circulating conditional AMP therapeutic with a masked activity that can be liberated by proteases in the infected tissue microenvironment. Our systemically administered conjugate enhanced the pulmonary delivery of active AMP while also reducing AMP exposure to other off-target organs. Importantly, this reduction in off-target exposure improved the safety profile of the AMP. The framework we present can be generalized to quantify and optimize the performance of this emerging class of conditional therapeutics.
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Affiliation(s)
- Chayanon Ngambenjawong
- Koch
Institute for Integrative Cancer Research, Institute for Medical Engineering
and Science, and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Leslie W. Chan
- Koch
Institute for Integrative Cancer Research, Institute for Medical Engineering
and Science, and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather E. Fleming
- Koch
Institute for Integrative Cancer Research, Institute for Medical Engineering
and Science, and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Howard
Hughes Medical Institute, Cambridge, Massachusetts 02139, United States
| | - Sangeeta N. Bhatia
- Koch
Institute for Integrative Cancer Research, Institute for Medical Engineering
and Science, and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Howard
Hughes Medical Institute, Cambridge, Massachusetts 02139, United States
- Department
of Medicine, Brigham and Women’s
Hospital and Harvard Medical School, Boston Massachusetts 02115, United States
- Broad Institute
of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02139, United States
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14
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Amini AP, Kirkpatrick JD, Wang CS, Jaeger AM, Su S, Naranjo S, Zhong Q, Cabana CM, Jacks T, Bhatia SN. Multiscale profiling of protease activity in cancer. Nat Commun 2022; 13:5745. [PMID: 36192379 PMCID: PMC9530178 DOI: 10.1038/s41467-022-32988-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 08/24/2022] [Indexed: 11/09/2022] Open
Abstract
Diverse processes in cancer are mediated by enzymes, which most proximally exert their function through their activity. High-fidelity methods to profile enzyme activity are therefore critical to understanding and targeting the pathological roles of enzymes in cancer. Here, we present an integrated set of methods for measuring specific protease activities across scales, and deploy these methods to study treatment response in an autochthonous model of Alk-mutant lung cancer. We leverage multiplexed nanosensors and machine learning to analyze in vivo protease activity dynamics in lung cancer, identifying significant dysregulation that includes enhanced cleavage of a peptide, S1, which rapidly returns to healthy levels with targeted therapy. Through direct on-tissue localization of protease activity, we pinpoint S1 cleavage to the tumor vasculature. To link protease activity to cellular function, we design a high-throughput method to isolate and characterize proteolytically active cells, uncovering a pro-angiogenic phenotype in S1-cleaving cells. These methods provide a framework for functional, multiscale characterization of protease dysregulation in cancer. The activity of multiple enzymes is dysregulated in cancer, but this cannot always be measured through enzyme expression. Here, the authors develop methods to measure protease activity across the organism, tissue, and single cell scales, and identify protease dysregulation in lung cancer and its response to targeted therapy.
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Affiliation(s)
- Ava P Amini
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Harvard MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Program in Biophysics, Harvard University, Boston, MA, USA.,Microsoft Research New England, Cambridge, MA, USA
| | - Jesse D Kirkpatrick
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Harvard MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Cathy S Wang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alex M Jaeger
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Susan Su
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Santiago Naranjo
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Qian Zhong
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Christina M Cabana
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tyler Jacks
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Harvard MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA. .,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA. .,Wyss Institute at Harvard University, Boston, MA, USA. .,Howard Hughes Medical Institute, Cambridge, MA, USA.
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15
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Abstract
The field of cancer nanomedicine seeks to overcome the inherent shortcomings of conventional cancer diagnostics and therapies. Yet despite the surge of interest in and attractive attributes of nanotechnologies, challenges remain in their clinical translation, prompting some to argue that they have not yet reached their true potential. In this Viewpoint article, we asked four experts for their opinions on how we can fulfil the great promise of nanomedicine for the detection, diagnosis and treatment of patients with cancer.
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Affiliation(s)
- Sangeeta N Bhatia
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Xiaoyuan Chen
- Department of Diagnostic Radiology, Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, Singapore, Singapore.
- Department of Surgery, Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, Singapore, Singapore.
- Department of Chemical and Biomolecular Engineering, Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, Singapore, Singapore.
- Department of Biomedical Engineering, Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, Singapore, Singapore.
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
| | - Marina A Dobrovolskaia
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
| | - Twan Lammers
- Department of Nanomedicine and Theranostics, Institute for Experimental Molecular Imaging (ExMI), Center for Biohybrid Medical Systems (CBMS), RWTH Aachen University Clinic, Aachen, Germany.
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16
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Scoon WA, Mancio-Silva L, Suder EL, Villacorta-Martin C, Lindstrom-Vautrin J, Bernbaum JG, Mazur S, Johnson RF, Olejnik J, Flores EY, Mithal A, Wang F, Hume AJ, Kaserman JE, March-Riera S, Wilson AA, Bhatia SN, Mühlberger E, Mostoslavsky G. Ebola virus infection induces a delayed type I IFN response in bystander cells and the shutdown of key liver genes in human iPSC-derived hepatocytes. Stem Cell Reports 2022; 17:2286-2302. [PMID: 36084636 PMCID: PMC9561183 DOI: 10.1016/j.stemcr.2022.08.003] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 01/26/2023] Open
Abstract
Liver damage and an exacerbated inflammatory response are hallmarks of Ebola virus (EBOV) infection. Little is known about the intrinsic response to infection in human hepatocytes and their contribution to inflammation. Here, we present an induced pluripotent stem cell (iPSC)-derived hepatocyte-like cell (HLC) platform to define the hepato-intrinsic response to EBOV infection. We used this platform to show robust EBOV infection, with characteristic ultrastructural changes and evidence for viral replication. Transcriptomics analysis revealed a delayed response with minimal early transcriptomic changes, followed by a general downregulation of hepatic function and upregulation of interferon signaling, providing a potential mechanism by which hepatocytes participate in disease severity and liver damage. Using RNA-fluorescence in situ hybridization (FISH), we showed that IFNB1 and CXCL10 were mainly expressed in non-infected bystander cells. We did not observe an inflammatory signature during infection. In conclusion, iPSC-HLCs are an immune competent platform to study responses to EBOV infection.
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Affiliation(s)
- Whitney A. Scoon
- Center for Regenerative Medicine (CReM), Boston University and Boston Medical Center, 670 Albany Street, Suite 209, Boston, MA 02118, USA,National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, 620 Albany Street, Boston, MA 02118, USA,Department of Microbiology, Boston University School of Medicine, 620 Albany Street, Boston, MA 02118, USA
| | - Liliana Mancio-Silva
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, MA 02139, USA
| | - Ellen L. Suder
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, 620 Albany Street, Boston, MA 02118, USA,Department of Microbiology, Boston University School of Medicine, 620 Albany Street, Boston, MA 02118, USA
| | - Carlos Villacorta-Martin
- Center for Regenerative Medicine (CReM), Boston University and Boston Medical Center, 670 Albany Street, Suite 209, Boston, MA 02118, USA
| | - Jonathan Lindstrom-Vautrin
- Center for Regenerative Medicine (CReM), Boston University and Boston Medical Center, 670 Albany Street, Suite 209, Boston, MA 02118, USA
| | - John G. Bernbaum
- Integrated Research Facility, Division of Clinical Research, National Institute for Allergy and Infectious Disease, National Institutes of Health, Frederick, MD 21702, USA
| | - Steve Mazur
- Integrated Research Facility, Division of Clinical Research, National Institute for Allergy and Infectious Disease, National Institutes of Health, Frederick, MD 21702, USA
| | - Reed F. Johnson
- Integrated Research Facility, Division of Clinical Research, National Institute for Allergy and Infectious Disease, National Institutes of Health, Frederick, MD 21702, USA,Emerging Viral Pathogens Section, Laboratory of Immunoregulation, Division of Intramural Research, National Institute for Allergy and Infectious Disease, National Institutes of Health, Frederick, MD 21702, USA
| | - Judith Olejnik
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, 620 Albany Street, Boston, MA 02118, USA,Department of Microbiology, Boston University School of Medicine, 620 Albany Street, Boston, MA 02118, USA
| | - Elizabeth Y. Flores
- Center for Regenerative Medicine (CReM), Boston University and Boston Medical Center, 670 Albany Street, Suite 209, Boston, MA 02118, USA,National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, 620 Albany Street, Boston, MA 02118, USA,Department of Microbiology, Boston University School of Medicine, 620 Albany Street, Boston, MA 02118, USA
| | - Aditya Mithal
- Center for Regenerative Medicine (CReM), Boston University and Boston Medical Center, 670 Albany Street, Suite 209, Boston, MA 02118, USA,Department of Microbiology, Boston University School of Medicine, 620 Albany Street, Boston, MA 02118, USA
| | - Feiya Wang
- Center for Regenerative Medicine (CReM), Boston University and Boston Medical Center, 670 Albany Street, Suite 209, Boston, MA 02118, USA
| | - Adam J. Hume
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, 620 Albany Street, Boston, MA 02118, USA,Department of Microbiology, Boston University School of Medicine, 620 Albany Street, Boston, MA 02118, USA
| | - Joseph E. Kaserman
- Center for Regenerative Medicine (CReM), Boston University and Boston Medical Center, 670 Albany Street, Suite 209, Boston, MA 02118, USA,The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Sandra March-Riera
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, MA 02139, USA
| | - Andrew A. Wilson
- Center for Regenerative Medicine (CReM), Boston University and Boston Medical Center, 670 Albany Street, Suite 209, Boston, MA 02118, USA,The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Sangeeta N. Bhatia
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, MA 02139, USA,Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA,Broad Institute, Cambridge, MA 02139, USA,Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Elke Mühlberger
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, 620 Albany Street, Boston, MA 02118, USA; Department of Microbiology, Boston University School of Medicine, 620 Albany Street, Boston, MA 02118, USA.
| | - Gustavo Mostoslavsky
- Center for Regenerative Medicine (CReM), Boston University and Boston Medical Center, 670 Albany Street, Suite 209, Boston, MA 02118, USA; National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, 620 Albany Street, Boston, MA 02118, USA; Department of Microbiology, Boston University School of Medicine, 620 Albany Street, Boston, MA 02118, USA; Section of Gastroenterology, Department of Medicine, Boston University School of Medicine, 670 Albany Street, Suite 209, Boston, MA 02118, USA.
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17
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Connelly GG, Kirkland OO, Bohannon S, Lim DC, Wilson RM, Richards EJ, Tay DM, Jee H, Hellinger RD, Hoang NK, Hao L, Chhabra A, Martin-Alonso C, Tan EK, Koehler AN, Yaffe MB, London WB, Lee PY, Krammer F, Bohannon RC, Bhatia SN, Sikes HD, Li H. Direct capture of neutralized RBD enables rapid point-of-care assessment of SARS-CoV-2 neutralizing antibody titer. Cell Rep Methods 2022; 2:100273. [PMID: 35942328 PMCID: PMC9350670 DOI: 10.1016/j.crmeth.2022.100273] [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] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 06/13/2022] [Accepted: 07/22/2022] [Indexed: 11/26/2022]
Abstract
Neutralizing antibody (NAb) titer is a key biomarker of protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, but point-of-care methods for assessing NAb titer are not widely available. Here, we present a lateral flow assay that captures SARS-CoV-2 receptor-binding domain (RBD) that has been neutralized from binding angiotensin-converting enzyme 2 (ACE2). Quantification of neutralized RBD in this assay correlates with NAb titer from vaccinated and convalescent patients. This methodology demonstrated superior performance in assessing NAb titer compared with either measurement of total anti-spike immunoglobulin G titer or quantification of the absolute reduction in binding between ACE2 and RBD. Our testing platform has the potential for mass deployment to aid in determining at population scale the degree of protective immunity individuals may have following SARS-CoV-2 vaccination or infection and can enable simple at-home assessment of NAb titer.
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Affiliation(s)
- Guinevere G. Connelly
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Orville O. Kirkland
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Daniel C. Lim
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Robert M. Wilson
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Edward J. Richards
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Dragonfly Therapeutics, Waltham, MA 02451, USA
| | - Dousabel M. Tay
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hyuk Jee
- Division of Rheumatology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Riley D. Hellinger
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ngoc K. Hoang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Liang Hao
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Arnav Chhabra
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Satellite Bio, Cambridge, MA 02139, USA
| | - Carmen Martin-Alonso
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Edward K.W. Tan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Angela N. Koehler
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael B. Yaffe
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Wendy B. London
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Pui Y. Lee
- Division of Rheumatology, Boston Children’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Florian Krammer
- Department of Microbiology, and Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Sangeeta N. Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA
- Institute for Medical Engineering and Science, and Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Wyss Institute at Harvard, Boston, MA 02115, USA
| | - Hadley D. Sikes
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hojun Li
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02115, USA
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18
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Soleimany AP, Martin-Alonso C, Anahtar M, Wang CS, Bhatia SN. Protease Activity Analysis: A Toolkit for Analyzing Enzyme Activity Data. ACS Omega 2022; 7:24292-24301. [PMID: 35874224 PMCID: PMC9301967 DOI: 10.1021/acsomega.2c01559] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Analyzing the activity of proteases and their substrates is critical to defining the biological functions of these enzymes and to designing new diagnostics and therapeutics that target protease dysregulation in disease. While a wide range of databases and algorithms have been created to better predict protease cleavage sites, there is a dearth of computational tools to automate analysis of in vitro and in vivo protease assays. This necessitates individual researchers to develop their own analytical pipelines, resulting in a lack of standardization across the field. To facilitate protease research, here we present Protease Activity Analysis (PAA), a toolkit for the preprocessing, visualization, machine learning analysis, and querying of protease activity data sets. PAA leverages a Python-based object-oriented implementation that provides a modular framework for streamlined analysis across three major components. First, PAA provides a facile framework to query data sets of synthetic peptide substrates and their cleavage susceptibilities across a diverse set of proteases. To complement the database functionality, PAA also includes tools for the automated analysis and visualization of user-input enzyme-substrate activity measurements generated through in vitro screens against synthetic peptide substrates. Finally, PAA supports a set of modular machine learning functions to analyze in vivo protease activity signatures that are generated by activity-based sensors. Overall, PAA offers the protease community a breadth of computational tools to streamline research, taking a step toward standardizing data analysis across the field and in chemical biology and biochemistry at large.
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Affiliation(s)
- Ava P. Soleimany
- Harvard-MIT
Division of Health Sciences and Technology, MIT, Cambridge, Massachusetts 02139, United States
- Program
in Biophysics, Harvard University, Boston, Massachusetts 02115, United States
- Microsoft
Research New England, Cambridge, Massachusetts 02142, United States
| | - Carmen Martin-Alonso
- Harvard-MIT
Division of Health Sciences and Technology, MIT, Cambridge, Massachusetts 02139, United States
| | - Melodi Anahtar
- Harvard-MIT
Division of Health Sciences and Technology, MIT, Cambridge, Massachusetts 02139, United States
| | - Cathy S. Wang
- Department
of Biological Engineering, MIT, Cambridge, Massachusetts 02139, United States
| | - Sangeeta N. Bhatia
- Harvard-MIT
Division of Health Sciences and Technology, MIT, Cambridge, Massachusetts 02139, United States
- Department
of Electrical Engineering and Computer Science, MIT, Cambridge, Massachusetts 02139, United States
- Howard Hughes
Medical Institute, Cambridge, Massachusetts 02139, United States
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19
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Anahtar M, Chan LW, Ko H, Rao A, Soleimany AP, Khatri P, Bhatia SN. Host protease activity classifies pneumonia etiology. Proc Natl Acad Sci U S A 2022; 119:e2121778119. [PMID: 35696579 PMCID: PMC9231472 DOI: 10.1073/pnas.2121778119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/18/2022] [Indexed: 01/26/2023] Open
Abstract
Community-acquired pneumonia (CAP) has been brought to the forefront of global health priorities due to the COVID-19 pandemic. However, classification of viral versus bacterial pneumonia etiology remains a significant clinical challenge. To this end, we have engineered a panel of activity-based nanosensors that detect the dysregulated activity of pulmonary host proteases implicated in the response to pneumonia-causing pathogens and produce a urinary readout of disease. The nanosensor targets were selected based on a human protease transcriptomic signature for pneumonia etiology generated from 33 unique publicly available study cohorts. Five mouse models of bacterial or viral CAP were developed to assess the ability of the nanosensors to produce etiology-specific urinary signatures. Machine learning algorithms were used to train diagnostic classifiers that could distinguish infected mice from healthy controls and differentiate those with bacterial versus viral pneumonia with high accuracy. This proof-of-concept diagnostic approach demonstrates a way to distinguish pneumonia etiology based solely on the host proteolytic response to infection.
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Affiliation(s)
- Melodi Anahtar
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Leslie W. Chan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA 30332
| | - Henry Ko
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Aditya Rao
- Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305
| | - Ava P. Soleimany
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Graduate Program in Biophysics, Harvard University, Boston, MA 02115
- Microsoft Research New England, Cambridge, MA 02142
| | - Purvesh Khatri
- Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305
| | - Sangeeta N. Bhatia
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
- Hansjörg Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA 02115
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20
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Bekdemir A, Tanner EEL, Kirkpatrick J, Soleimany AP, Mitragotri S, Bhatia SN. Ionic Liquid-Mediated Transdermal Delivery of Thrombosis-Detecting Nanosensors. Adv Healthc Mater 2022; 11:e2102685. [PMID: 35182107 DOI: 10.1002/adhm.202102685] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/23/2022] [Indexed: 01/14/2023]
Abstract
Blood clotting disorders such as pulmonary embolism are associated with high morbidity and mortality. A large portion of thrombotic events occur postoperative and after hospital discharge. Therefore, easily applicable, noninvasive, and long-term monitoring of thrombosis occurrence is critical for urgent clinical intervention. Here, the use is proposed of ionic liquids as a skin transport facilitator to deliver thrombin-sensitive nanosensors that enable prolonged monitoring of pulmonary embolism. Co-formulation of nanosensors with choline and geranic acid (CAGE) ionic liquids demonstrates significant transdermal diffusion into the dermis of the skin and provides sustained release into the blood throughout 72 h. Upon reaching the systemic circulation, the nanosensors release reporter molecules into the urine by responding to activation of the clotting cascade and retain a diagnostic power for 24 h in an acute pulmonary embolism mouse model. These results demonstrate a proof-of-concept disease monitoring system that can be topically applied by patients and potentially reduce mortality and high cost of hospitalization.
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Affiliation(s)
- Ahmet Bekdemir
- Harvard–MIT Division of Health Sciences and Technology Institute for Medical Engineering and Science Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Eden E. L. Tanner
- School of Engineering and Applied Sciences Harvard University Cambridge MA 02138 USA
- Now at Department of Chemistry and Biochemistry University of Mississippi Oxford MS 38677 USA
| | - Jesse Kirkpatrick
- Harvard–MIT Division of Health Sciences and Technology Institute for Medical Engineering and Science Massachusetts Institute of Technology Cambridge MA 02139 USA
- Koch Institute for Integrative Cancer Research Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Ava P. Soleimany
- Harvard–MIT Division of Health Sciences and Technology Institute for Medical Engineering and Science Massachusetts Institute of Technology Cambridge MA 02139 USA
- Koch Institute for Integrative Cancer Research Massachusetts Institute of Technology Cambridge MA 02139 USA
- Harvard Graduate Program in Biophysics Harvard University Cambridge MA 02138 USA
| | - Samir Mitragotri
- School of Engineering and Applied Sciences Harvard University Cambridge MA 02138 USA
- Wyss Institute of Biologically Inspired Engineering Harvard University Cambridge MA 02138 USA
| | - Sangeeta N. Bhatia
- Harvard–MIT Division of Health Sciences and Technology Institute for Medical Engineering and Science Massachusetts Institute of Technology Cambridge MA 02139 USA
- Koch Institute for Integrative Cancer Research Massachusetts Institute of Technology Cambridge MA 02139 USA
- Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge MA 02139 USA
- Broad Institute of Massachusetts Institute of Technology and Harvard Cambridge MA 02139 USA
- Department of Medicine, Brigham and Women's Hospital Harvard Medical School Boston MA 02115 USA
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21
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Smith Q, Bays J, Li L, Shareef H, Chen CS, Bhatia SN. Directing Cholangiocyte Morphogenesis in Natural Biomaterial Scaffolds. Adv Sci (Weinh) 2022; 9:e2201951. [PMID: 35570837 PMCID: PMC9109051 DOI: 10.1002/advs.202201951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
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22
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Mancio-Silva L, Gural N, Real E, Wadsworth MH, Butty VL, March S, Nerurkar N, Hughes TK, Roobsoong W, Fleming HE, Whittaker CA, Levine SS, Sattabongkot J, Shalek AK, Bhatia SN. A single-cell liver atlas of Plasmodium vivax infection. Cell Host Microbe 2022; 30:1048-1060.e5. [PMID: 35443155 DOI: 10.1016/j.chom.2022.03.034] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 01/31/2022] [Accepted: 03/25/2022] [Indexed: 12/15/2022]
Abstract
Malaria-causing Plasmodium vivax parasites can linger in the human liver for weeks to years and reactivate to cause recurrent blood-stage infection. Although they are an important target for malaria eradication, little is known about the molecular features of replicative and non-replicative intracellular liver-stage parasites and their host cell dependence. Here, we leverage a bioengineered human microliver platform to culture patient-derived P. vivax parasites for transcriptional profiling. Coupling enrichment strategies with bulk and single-cell analyses, we capture both parasite and host transcripts in individual hepatocytes throughout the course of infection. We define host- and state-dependent transcriptional signatures and identify unappreciated populations of replicative and non-replicative parasites that share features with sexual transmissive forms. We find that infection suppresses the transcription of key hepatocyte function genes and elicits an anti-parasite innate immune response. Our work provides a foundation for understanding host-parasite interactions and reveals insights into the biology of P. vivax dormancy and transmission.
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Affiliation(s)
- Liliana Mancio-Silva
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA; Institut Pasteur, Université Paris Cité, Inserm U1201, CNRS EMR9195, Unité de Biologie des Interactions Hôte-Parasite, 75015 Paris, France.
| | - Nil Gural
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA
| | - Eliana Real
- Institut Pasteur, Université Paris Cité, Inserm U1201, CNRS EMR9195, Unité de Biologie des Interactions Hôte-Parasite, 75015 Paris, France
| | - Marc H Wadsworth
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Department of Chemistry, MIT, Cambridge, MA 02139, USA
| | - Vincent L Butty
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA; BioMicro Center, MIT, Cambridge, MA 02139, USA
| | - Sandra March
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Niketa Nerurkar
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA
| | - Travis K Hughes
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Department of Chemistry, MIT, Cambridge, MA 02139, USA
| | - Wanlapa Roobsoong
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine Mahidol University, Bangkok 10400, Thailand
| | - Heather E Fleming
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA
| | - Charlie A Whittaker
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA; BioMicro Center, MIT, Cambridge, MA 02139, USA
| | - Stuart S Levine
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA; BioMicro Center, MIT, Cambridge, MA 02139, USA
| | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine Mahidol University, Bangkok 10400, Thailand
| | - Alex K Shalek
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA; Department of Chemistry, MIT, Cambridge, MA 02139, USA; Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA.
| | - Sangeeta N Bhatia
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; The Wyss Institute for Biologically Inspired Engineering Harvard University Boston, MA 02215, USA.
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23
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Kirkpatrick JD, Soleimany AP, Dudani JS, Liu HJ, Lam HC, Priolo C, Henske EP, Bhatia SN. Protease activity sensors enable real-time treatment response monitoring in lymphangioleiomyomatosis. Eur Respir J 2022; 59:2100664. [PMID: 34561286 PMCID: PMC9030069 DOI: 10.1183/13993003.00664-2021] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 08/14/2021] [Indexed: 11/14/2022]
Abstract
BACKGROUND Biomarkers of disease progression and treatment response are urgently needed for patients with lymphangioleiomyomatosis (LAM). Activity-based nanosensors, an emerging biosensor class, detect dysregulated proteases in vivo and release a reporter to provide a urinary readout of disease. Because proteases are dysregulated in LAM and may directly contribute to lung function decline, activity-based nanosensors may enable quantitative, real-time monitoring of LAM progression and treatment response. We aimed to assess the diagnostic utility of activity-based nanosensors in a pre-clinical model of pulmonary LAM. METHODS Tsc2-null cells were injected intravenously into female nude mice to establish a mouse model of pulmonary LAM. A library of 14 activity-based nanosensors, designed to detect proteases across multiple catalytic classes, was administered into the lungs of LAM mice and healthy controls, urine was collected, and mass spectrometry was performed to measure nanosensor cleavage products. Mice were then treated with rapamycin and monitored with activity-based nanosensors. Machine learning was performed to distinguish diseased from healthy and treated from untreated mice. RESULTS Multiple activity-based nanosensors (PP03 (cleaved by metallo, aspartic and cysteine proteases), padjusted<0.0001; PP10 (cleaved by serine, aspartic and cysteine proteases), padjusted=0.017)) were differentially cleaved in diseased and healthy lungs, enabling strong classification with a machine learning model (area under the curve (AUC) 0.95 from healthy). Within 2 days after rapamycin initiation, we observed normalisation of PP03 and PP10 cleavage, and machine learning enabled accurate classification of treatment response (AUC 0.94 from untreated). CONCLUSIONS Activity-based nanosensors enable noninvasive, real-time monitoring of disease burden and treatment response in a pre-clinical model of LAM.
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Affiliation(s)
- Jesse D Kirkpatrick
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ava P Soleimany
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard Graduate Program in Biophysics, Harvard University, Boston, MA, USA
- Microsoft Research New England, Cambridge, MA, USA
| | - Jaideep S Dudani
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Dept of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Heng-Jia Liu
- Pulmonary and Critical Care Medicine, Dept of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Hilaire C Lam
- Pulmonary and Critical Care Medicine, Dept of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Carmen Priolo
- Pulmonary and Critical Care Medicine, Dept of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Elizabeth P Henske
- Pulmonary and Critical Care Medicine, Dept of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- E.P. Henske and S.N. Bhatia co-supervised the study
| | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
- Dept of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Dept of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Wyss Institute at Harvard, Boston, MA, USA
- E.P. Henske and S.N. Bhatia co-supervised the study
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24
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Smith Q, Bays J, Li L, Shareef H, Chen CS, Bhatia SN. Directing Cholangiocyte Morphogenesis in Natural Biomaterial Scaffolds. Adv Sci (Weinh) 2022; 9:e2102698. [PMID: 34786888 PMCID: PMC8787431 DOI: 10.1002/advs.202102698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 09/04/2021] [Indexed: 06/13/2023]
Abstract
Patients with Alagille syndrome carry monogenic mutations in the Notch signaling pathway and face complications such as jaundice and cholestasis. Given the presence of intrahepatic ductopenia in these patients, Notch2 receptor signaling is implicated in driving normal biliary development and downstream branching morphogenesis. As a result, in vitro model systems of liver epithelium are needed to further mechanistic insight of biliary tissue assembly. Here, primary human intrahepatic cholangiocytes as a candidate population for such a platform are systematically evaluated, and conditions that direct their branching morphogenesis are described. It is found that extracellular matrix presentation, coupled with mitogen stimulation, promotes biliary branching in a Notch-dependent manner. These results demonstrate the utility of using 3D scaffolds for mechanistic investigation of cholangiocyte branching and provide a gateway to integrate biliary architecture in additional in vitro models of liver tissue.
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Affiliation(s)
- Quinton Smith
- Howard Hughes Medical InstituteChevy ChaseMD20815USA
- David H. Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMA02142USA
| | - Jennifer Bays
- Department of BioengineeringBoston UniversityBostonMA02215USA
- The Wyss Institute for Biologically Inspired EngineeringHarvard UniversityBostonMA02215USA
| | - Linqing Li
- Department of BioengineeringBoston UniversityBostonMA02215USA
- The Wyss Institute for Biologically Inspired EngineeringHarvard UniversityBostonMA02215USA
| | - Haniyah Shareef
- David H. Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMA02142USA
| | - Christopher S. Chen
- Department of BioengineeringBoston UniversityBostonMA02215USA
- The Wyss Institute for Biologically Inspired EngineeringHarvard UniversityBostonMA02215USA
| | - Sangeeta N. Bhatia
- Howard Hughes Medical InstituteChevy ChaseMD20815USA
- David H. Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMA02142USA
- The Wyss Institute for Biologically Inspired EngineeringHarvard UniversityBostonMA02215USA
- Institute for Medical Engineering and ScienceMassachusetts Institute of TechnologyCambridgeMA02142USA
- Department of Electrical Engineering and Computer ScienceMassachusetts Institute of TechnologyCambridgeMA02142USA
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25
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Hao L, Rohani N, Zhao RT, Pulver EM, Mak H, Kelada OJ, Ko H, Fleming HE, Gertler FB, Bhatia SN. Microenvironment-triggered multimodal precision diagnostics. Nat Mater 2021; 20:1440-1448. [PMID: 34267368 DOI: 10.1038/s41563-021-01042-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 05/26/2021] [Indexed: 05/24/2023]
Abstract
Therapeutic outcomes in oncology may be aided by precision diagnostics that offer early detection, localization and the opportunity to monitor response to therapy. Here, we report a multimodal nanosensor engineered to target tumours through acidosis, respond to proteases in the microenvironment to release urinary reporters and (optionally) carry positron emission tomography probes to enable localization of primary and metastatic cancers in mouse models of colorectal cancer. We present a paradigm wherein this multimodal sensor can be employed longitudinally to assess burden of disease non-invasively, including tumour progression and response to chemotherapy. Specifically, we showed that acidosis-mediated tumour insertion enhanced on-target release of matrix metalloproteinase-responsive reporters in urine. Subsequent on-demand loading of the radiotracer 64Cu allowed pH-dependent tumour visualization, enabling enriched microenvironmental characterization when compared with the conventional metabolic tracer 18F-fluorodeoxyglucose. Through tailored target specificities, this modular platform has the capacity to be engineered as a pan-cancer test that may guide treatment decisions for numerous tumour types.
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Affiliation(s)
- Liangliang Hao
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nazanin Rohani
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Renee T Zhao
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Emilia M Pulver
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Howard Mak
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Henry Ko
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Heather E Fleming
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Frank B Gertler
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Cambridge, MA, USA.
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
- Ludwig Center at Massachusetts Institute of Technology's Koch Institute for Integrative Cancer Research, Cambridge, MA, USA.
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26
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Abstract
Detection of cancer at an early stage when it is still localized improves patient response to medical interventions for most cancer types. The success of screening tools such as cervical cytology to reduce mortality has spurred significant interest in new methods for early detection (for example, using non-invasive blood-based or biofluid-based biomarkers). Yet biomarkers shed from early lesions are limited by fundamental biological and mass transport barriers - such as short circulation times and blood dilution - that limit early detection. To address this issue, synthetic biomarkers are being developed. These represent an emerging class of diagnostics that deploy bioengineered sensors inside the body to query early-stage tumours and amplify disease signals to levels that could potentially exceed those of shed biomarkers. These strategies leverage design principles and advances from chemistry, synthetic biology and cell engineering. In this Review, we discuss the rationale for development of biofluid-based synthetic biomarkers. We examine how these strategies harness dysregulated features of tumours to amplify detection signals, use tumour-selective activation to increase specificity and leverage natural processing of bodily fluids (for example, blood, urine and proximal fluids) for easy detection. Finally, we highlight the challenges that exist for preclinical development and clinical translation of synthetic biomarker diagnostics.
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Affiliation(s)
- Gabriel A Kwong
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA, USA.
- Parker H. Petit Institute of Bioengineering and Bioscience, Atlanta, GA, USA.
- Institute for Electronics and Nanotechnology, Georgia Tech, Atlanta, GA, USA.
- The Georgia Immunoengineering Consortium, Emory University and Georgia Tech, Atlanta, GA, USA.
- Winship Cancer Institute, Emory University, Atlanta, GA, USA.
| | - Sharmistha Ghosh
- Division of Cancer Prevention, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Lena Gamboa
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA, USA
| | - Christos Patriotis
- Division of Cancer Prevention, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sudhir Srivastava
- Division of Cancer Prevention, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Sangeeta N Bhatia
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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27
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Schepers AG, Shan J, Cox AG, Huang A, Evans H, Walesky C, Fleming HE, Goessling W, Bhatia SN. Identification of NQO2 As a Protein Target in Small Molecule Modulation of Hepatocellular Function. ACS Chem Biol 2021; 16:1770-1778. [PMID: 34427427 DOI: 10.1021/acschembio.1c00503] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The utility of in vitro human disease models is mainly dependent on the availability and functional maturity of tissue-specific cell types. We have previously screened for and identified small molecules that can enhance hepatocyte function in vitro. Here, we characterize the functional effects of one of the hits, FH1, on primary human hepatocytes in vitro, and also in vivo on primary hepatocytes in a zebrafish model. Furthermore, we conducted an analogue screen to establish the structure-activity relationship of FH1. We performed affinity-purification proteomics that identified NQO2 to be a potential binding target for this small molecule, revealing a possible link between inflammatory signaling and hepatocellular function in zebrafish and human hepatocyte model systems.
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Affiliation(s)
- Arnout G. Schepers
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Jing Shan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Andrew G. Cox
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Ada Huang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Helen Evans
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Chad Walesky
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Heather E. Fleming
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Wolfram Goessling
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, United States
- Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Harvard−MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Sangeeta N. Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Harvard−MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02139, United States
- Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, United States
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28
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He J, Nissim L, Soleimany AP, Binder-Nissim A, Fleming HE, Lu TK, Bhatia SN. Synthetic Circuit-Driven Expression of Heterologous Enzymes for Disease Detection. ACS Synth Biol 2021; 10:2231-2242. [PMID: 34464083 DOI: 10.1021/acssynbio.1c00133] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The integration of nanotechnology and synthetic biology could lay the framework for new classes of engineered biosensors that produce amplified readouts of disease states. As a proof-of-concept demonstration of this vision, here we present an engineered gene circuit that, in response to cancer-associated transcriptional deregulation, expresses heterologous enzyme biomarkers whose activity can be measured by nanoparticle sensors that generate amplified detection readouts. Specifically, we designed an AND-gate gene circuit that integrates the activity of two ovarian cancer-specific synthetic promoters to drive the expression of a heterologous protein output, secreted Tobacco Etch Virus (TEV) protease, exclusively from within tumor cells. Nanoparticle probes were engineered to carry a TEV-specific peptide substrate in order to measure the activity of the circuit-generated enzyme to yield amplified detection signals measurable in the urine or blood. We applied our integrated sense-and-respond system in a mouse model of disseminated ovarian cancer, where we demonstrated measurement of circuit-specific TEV protease activity both in vivo using exogenously administered nanoparticle sensors and ex vivo using quenched fluorescent probes. We envision that this work will lay the foundation for how synthetic biology and nanotechnology can be meaningfully integrated to achieve next-generation engineered biosensors.
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Affiliation(s)
- Jiang He
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Harvard−MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Lior Nissim
- Synthetic Biology Group, Research Laboratory of Electronics, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Ava P. Soleimany
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Harvard−MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Harvard Graduate Program in Biophysics, Harvard University, Boston, Massachusetts 02115, United States
- Microsoft Research New England, Cambridge, Massachusetts 02142, United States
| | - Adina Binder-Nissim
- Synthetic Biology Group, Research Laboratory of Electronics, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Family Medicine, Meuhedet Health Maintenance Organization, Tel Aviv 62038, Israel
| | - Heather E. Fleming
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Harvard−MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Timothy K. Lu
- Synthetic Biology Group, Research Laboratory of Electronics, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Sangeeta N. Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Harvard−MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02139, United States
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29
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Soleimany AP, Amini A, Goldman S, Rus D, Bhatia SN, Coley CW. Evidential Deep Learning for Guided Molecular Property Prediction and Discovery. ACS Cent Sci 2021; 7:1356-1367. [PMID: 34471680 PMCID: PMC8393200 DOI: 10.1021/acscentsci.1c00546] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Indexed: 05/12/2023]
Abstract
While neural networks achieve state-of-the-art performance for many molecular modeling and structure-property prediction tasks, these models can struggle with generalization to out-of-domain examples, exhibit poor sample efficiency, and produce uncalibrated predictions. In this paper, we leverage advances in evidential deep learning to demonstrate a new approach to uncertainty quantification for neural network-based molecular structure-property prediction at no additional computational cost. We develop both evidential 2D message passing neural networks and evidential 3D atomistic neural networks and apply these networks across a range of different tasks. We demonstrate that evidential uncertainties enable (1) calibrated predictions where uncertainty correlates with error, (2) sample-efficient training through uncertainty-guided active learning, and (3) improved experimental validation rates in a retrospective virtual screening campaign. Our results suggest that evidential deep learning can provide an efficient means of uncertainty quantification useful for molecular property prediction, discovery, and design tasks in the chemical and physical sciences.
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Affiliation(s)
- Ava P. Soleimany
- Harvard-MIT
Division of Health Sciences and Technology, MIT, Cambridge, Massachusetts 02139, United States
- Graduate
Program in Biophysics, Harvard University, Boston, Massachusetts 02115, United States
- Microsoft
Research New England, Cambridge, Massachusetts 02142, United States
| | - Alexander Amini
- Department
of Electrical Engineering and Computer Science, MIT, Cambridge, Massachusetts 02139, United States
| | - Samuel Goldman
- Computational
and Systems Biology, MIT, Cambridge, Massachusetts 02139, United States
| | - Daniela Rus
- Department
of Electrical Engineering and Computer Science, MIT, Cambridge, Massachusetts 02139, United States
| | - Sangeeta N. Bhatia
- Harvard-MIT
Division of Health Sciences and Technology, MIT, Cambridge, Massachusetts 02139, United States
- Department
of Electrical Engineering and Computer Science, MIT, Cambridge, Massachusetts 02139, United States
- Howard
Hughes Medical Institute, Cambridge, Massachusetts 02139, United States
| | - Connor W. Coley
- Department
of Chemical Engineering, MIT, Cambridge, Massachusetts 02139, United States
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30
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Subudhi S, Drescher HK, Dichtel LE, Bartsch LM, Chung RT, Hutter MM, Gee DW, Meireles OR, Witkowski ER, Gelrud L, Masia R, Osganian SA, Gustafson JL, Rwema S, Bredella MA, Bhatia SN, Warren A, Miller KK, Lauer GM, Corey KE. Distinct Hepatic Gene-Expression Patterns of NAFLD in Patients With Obesity. Hepatol Commun 2021; 6:77-89. [PMID: 34558849 PMCID: PMC8710788 DOI: 10.1002/hep4.1789] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 06/13/2021] [Indexed: 02/06/2023] Open
Abstract
Approaches to manage nonalcoholic fatty liver disease (NAFLD) are limited by an incomplete understanding of disease pathogenesis. The aim of this study was to identify hepatic gene‐expression patterns associated with different patterns of liver injury in a high‐risk cohort of adults with obesity. Using the NanoString Technologies (Seattle, WA) nCounter assay, we quantified expression of 795 genes, hypothesized to be involved in hepatic fibrosis, inflammation, and steatosis, in liver tissue from 318 adults with obesity. Liver specimens were categorized into four distinct NAFLD phenotypes: normal liver histology (NLH), steatosis only (steatosis), nonalcoholic steatohepatitis without fibrosis (NASH F0), and NASH with fibrosis stage 1‐4 (NASH F1‐F4). One hundred twenty‐five genes were significantly increasing or decreasing as NAFLD pathology progressed. Compared with NLH, NASH F0 was characterized by increased inflammatory gene expression, such as gamma‐interferon‐inducible lysosomal thiol reductase (IFI30) and chemokine (C‐X‐C motif) ligand 9 (CXCL9), while complement and coagulation related genes, such as C9 and complement component 4 binding protein beta (C4BPB), were reduced. In the presence of NASH F1‐F4, extracellular matrix degrading proteinases and profibrotic/scar deposition genes, such as collagens and transforming growth factor beta 1 (TGFB1), were simultaneously increased, suggesting a dynamic state of tissue remodeling. Conclusion: In adults with obesity, distinct states of NAFLD are associated with intrahepatic perturbations in genes related to inflammation, complement and coagulation pathways, and tissue remodeling. These data provide insights into the dynamic pathogenesis of NAFLD in high‐risk individuals.
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Affiliation(s)
- Sonu Subudhi
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Hannah K Drescher
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Laura E Dichtel
- Neuroendocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Lea M Bartsch
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Raymond T Chung
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Matthew M Hutter
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Denise W Gee
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ozanan R Meireles
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Elan R Witkowski
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Louis Gelrud
- Department of Medicine, St. Mary's Hospital Bon Secours, Richmond, VA, USA
| | - Ricard Masia
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Stephanie A Osganian
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jenna L Gustafson
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Steve Rwema
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Miriam A Bredella
- Division of Musculoskeletal Radiology and Interventions, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Sangeeta N Bhatia
- Ludwig Center for Molecular Oncology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Andrew Warren
- Ludwig Center for Molecular Oncology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Karen K Miller
- Neuroendocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Georg M Lauer
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Kathleen E Corey
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
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31
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Suscovich TJ, Fallon JK, Das J, Demas AR, Crain J, Linde CH, Michell A, Natarajan H, Arevalo C, Broge T, Linnekin T, Kulkarni V, Lu R, Slein MD, Luedemann C, Marquette M, March S, Weiner J, Gregory S, Coccia M, Flores-Garcia Y, Zavala F, Ackerman ME, Bergmann-Leitner E, Hendriks J, Sadoff J, Dutta S, Bhatia SN, Lauffenburger DA, Jongert E, Wille-Reece U, Alter G. Mapping functional humoral correlates of protection against malaria challenge following RTS,S/AS01 vaccination. Sci Transl Med 2021; 12:12/553/eabb4757. [PMID: 32718991 DOI: 10.1126/scitranslmed.abb4757] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/02/2020] [Indexed: 12/13/2022]
Abstract
Vaccine development has the potential to be accelerated by coupling tools such as systems immunology analyses and controlled human infection models to define the protective efficacy of prospective immunogens without expensive and slow phase 2b/3 vaccine studies. Among human challenge models, controlled human malaria infection trials have long been used to evaluate candidate vaccines, and RTS,S/AS01 is the most advanced malaria vaccine candidate, reproducibly demonstrating 40 to 80% protection in human challenge studies in malaria-naïve individuals. Although antibodies are critical for protection after RTS,S/AS01 vaccination, antibody concentrations are inconsistently associated with protection across studies, and the precise mechanism(s) by which vaccine-induced antibodies provide protection remains enigmatic. Using a comprehensive systems serological profiling platform, the humoral correlates of protection against malaria were identified and validated across multiple challenge studies. Rather than antibody concentration, qualitative functional humoral features robustly predicted protection from infection across vaccine regimens. Despite the functional diversity of vaccine-induced immune responses across additional RTS,S/AS01 vaccine studies, the same antibody features, antibody-mediated phagocytosis and engagement of Fc gamma receptor 3A (FCGR3A), were able to predict protection across two additional human challenge studies. Functional validation using monoclonal antibodies confirmed the protective role of Fc-mediated antibody functions in restricting parasite infection both in vitro and in vivo, suggesting that these correlates may mechanistically contribute to parasite restriction and can be used to guide the rational design of an improved vaccine against malaria.
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Affiliation(s)
- Todd J Suscovich
- Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
| | | | - Jishnu Das
- Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
| | - Allison R Demas
- Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jonathan Crain
- Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
| | - Caitlyn H Linde
- Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
| | - Ashlin Michell
- Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
| | - Harini Natarajan
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
| | - Claudia Arevalo
- Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
| | - Thomas Broge
- Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
| | - Thomas Linnekin
- Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
| | - Viraj Kulkarni
- Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
| | - Richard Lu
- Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
| | - Matthew D Slein
- Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
| | | | - Meghan Marquette
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sandra March
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Joshua Weiner
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
| | - Scott Gregory
- PATH's Malaria Vaccine Initiative, Washington, DC 20001, USA
| | | | - Yevel Flores-Garcia
- Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Fidel Zavala
- Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | | | - Elke Bergmann-Leitner
- Malaria Vaccine Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Jenny Hendriks
- Janssen Vaccines & Prevention B.V., 2333CN Leiden, Netherlands
| | - Jerald Sadoff
- Janssen Vaccines & Prevention B.V., 2333CN Leiden, Netherlands
| | - Sheetij Dutta
- Malaria Vaccine Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Sangeeta N Bhatia
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA.,Broad Institute, Cambridge, MA 02139, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Douglas A Lauffenburger
- Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | | | - Galit Alter
- Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA.
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32
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Kirkpatrick JD, Warren AD, Soleimany AP, Westcott PMK, Voog JC, Martin-Alonso C, Fleming HE, Tammela T, Jacks T, Bhatia SN. Urinary detection of lung cancer in mice via noninvasive pulmonary protease profiling. Sci Transl Med 2021; 12:12/537/eaaw0262. [PMID: 32238573 DOI: 10.1126/scitranslmed.aaw0262] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 08/06/2019] [Accepted: 03/11/2020] [Indexed: 12/15/2022]
Abstract
Lung cancer is the leading cause of cancer-related death, and patients most commonly present with incurable advanced-stage disease. U.S. national guidelines recommend screening for high-risk patients with low-dose computed tomography, but this approach has limitations including high false-positive rates. Activity-based nanosensors can detect dysregulated proteases in vivo and release a reporter to provide a urinary readout of disease activity. Here, we demonstrate the translational potential of activity-based nanosensors for lung cancer by coupling nanosensor multiplexing with intrapulmonary delivery and machine learning to detect localized disease in two immunocompetent genetically engineered mouse models. The design of our multiplexed panel of sensors was informed by comparative transcriptomic analysis of human and mouse lung adenocarcinoma datasets and in vitro cleavage assays with recombinant candidate proteases. Intrapulmonary administration of the nanosensors to a Kras- and Trp53-mutant lung adenocarcinoma mouse model confirmed the role of metalloproteases in lung cancer and enabled accurate detection of localized disease, with 100% specificity and 81% sensitivity. Furthermore, this approach generalized to an alternative autochthonous model of lung adenocarcinoma, where it detected cancer with 100% specificity and 95% sensitivity and was not confounded by lipopolysaccharide-driven lung inflammation. These results encourage the clinical development of activity-based nanosensors for the detection of lung cancer.
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Affiliation(s)
- Jesse D Kirkpatrick
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Andrew D Warren
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ava P Soleimany
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Harvard Graduate Program in Biophysics, Harvard University, Boston, MA 02115, USA
| | - Peter M K Westcott
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Justin C Voog
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Carmen Martin-Alonso
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Heather E Fleming
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tuomas Tammela
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Tyler Jacks
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Howard Hughes Medical Institute, Cambridge, MA 02139, USA
| | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. .,Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Howard Hughes Medical Institute, Cambridge, MA 02139, USA.,Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02139, USA.,Wyss Institute at Harvard, Boston, MA 02115, USA
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33
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Chan LW, Hern KE, Ngambenjawong C, Lee K, Kwon EJ, Hung DT, Bhatia SN. Selective Permeabilization of Gram-Negative Bacterial Membranes Using Multivalent Peptide Constructs for Antibiotic Sensitization. ACS Infect Dis 2021; 7:721-732. [PMID: 33689277 PMCID: PMC8043124 DOI: 10.1021/acsinfecdis.0c00805] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The drug-impermeable bacterial membrane in Gram-negative pathogens limits antibiotic access to intracellular drug targets. To expand our rapidly waning antibiotic arsenal, one approach is to improve the intracellular delivery of drugs with historically poor accumulation in Gram-negative bacteria. To do so, we engineered macromolecular potentiators to permeabilize the Gram-negative membrane to facilitate drug influx. Potentiators, known as WD40, were synthesized by grafting multiple copies of a cationic α-helical antimicrobial peptide, WLBU2, onto a dextran polymer scaffold. WD40 enabled drug uptake in the model pathogen P. aeruginosa, a capability that was not observed with unmodified WLBU2 peptide. WD40 was able to reduce minimum inhibitory concentrations of a drug panel by up to 3 orders of magnitude. Hydrophobic and highly three-dimensional antibiotics exhibited the greatest potentiation. Antibiotic activity was potentiated in several clinical strains and resulted in sensitization of drug-resistant strains to rifampin, a drug not previously used for Gram-negative infections.
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Affiliation(s)
- Leslie W. Chan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kelsey E. Hern
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Chayanon Ngambenjawong
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Katie Lee
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02139, United States
| | - Ester J. Kwon
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Deborah T. Hung
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02139, United States
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Sangeeta N. Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02139, United States
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
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34
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Kim B, Yang Q, Chan LW, Bhatia SN, Ruoslahti E, Sailor MJ. Fusogenic porous silicon nanoparticles as a broad-spectrum immunotherapy against bacterial infections. Nanoscale Horiz 2021; 6:330-340. [PMID: 33599221 PMCID: PMC8098644 DOI: 10.1039/d0nh00624f] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Bacterial infections are re-emerging as substantial threats to global health due to the limited selection of antibiotics that are capable of overcoming antibiotic-resistant strains. By deterring such mutations whilst minimizing the need to develop new pathogen-specific antibiotics, immunotherapy offers a broad-spectrum therapeutic solution against bacterial infections. In particular, pathology resulting from excessive immune response (i.e. fibrosis, necrosis, exudation, breath impediment) contributes significantly to negative disease outcome. Herein, we present a nanoparticle that is targeted to activated macrophages and loaded with siRNA against the Irf5 gene. This formulation is able to induce >80% gene silencing in activated macrophages in vivo, and it inhibits the excessive inflammatory response, generating a significantly improved therapeutic outcome in mouse models of bacterial infection. The versatility of the approach is demonstrated using mice with antibiotic-resistant Gram-positive (methicillin-resistant Staphylococcus aureus) and Gram-negative (Pseudomonas aeruginosa) muscle and lung infections, respectively. Effective depletion of the Irf5 gene in macrophages is found to significantly improve the therapeutic outcome of infected mice, regardless of the bacteria strain and type.
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Affiliation(s)
- Byungji Kim
- Materials Science and Engineering Program, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA.
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35
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Abstract
During the SARS-CoV-2 pandemic, experimental research groups face a unique challenge: how to train undergraduates without access to labs. We share our experience developing entirely virtual undergraduate research internships and make a case for virtual research as a complement to traditional undergraduate mentoring, even after the resolution of the pandemic.
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Affiliation(s)
- Tahoura Samad
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Heather E Fleming
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Wyss Institute at Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
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36
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Chen AX, Chhabra A, Song HHG, Fleming HE, Chen CS, Bhatia SN. Controlled Apoptosis of Stromal Cells to Engineer Human Microlivers. Adv Funct Mater 2020; 30:1910442. [PMID: 33776613 PMCID: PMC7996305 DOI: 10.1002/adfm.201910442] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/29/2020] [Indexed: 05/02/2023]
Abstract
Engineered tissue models comprise a variety of multiplexed ensembles in which combinations of epithelial, stromal, and immune cells give rise to physiologic function. Engineering spatiotemporal control of cell-cell and cell-matrix interactions within these 3D multicellular tissues would represent a significant advance for tissue engineering. In this work, a new method, entitled CAMEO (Controlled Apoptosis in Multicellular tissues for Engineered Organogenesis) enables the non-invasive triggering of controlled apoptosis to eliminate genetically-engineered cells from a pre-established culture. Using this approach, the contribution of stromal cells to the phenotypic stability of primary human hepatocytes is examined. 3D hepatic microtissues, in which fibroblasts can enhance phenotypic stability and accelerate aggregation into spheroids, were found to rely only transiently on fibroblast interaction to support multiple axes of liver function, such as protein secretion and drug detoxification. Due to its modularity, CAMEO has the promise to be readily extendable to other applications that are tied to the complexity of 3D tissue biology, from understanding in vitro organoid models to building artificial tissue grafts.
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Affiliation(s)
- Amanda X Chen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Arnav Chhabra
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - H-H Greco Song
- Harvard-MIT Program in Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Heather E Fleming
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christopher S Chen
- Biological Design Center, Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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37
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Song HHG, Lammers A, Sundaram S, Rubio L, Chen AX, Li L, Eyckmans J, Bhatia SN, Chen CS. Transient Support from Fibroblasts is Sufficient to Drive Functional Vascularization in Engineered Tissues. Adv Funct Mater 2020; 30:2003777. [PMID: 33613149 PMCID: PMC7891457 DOI: 10.1002/adfm.202003777] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Indexed: 05/05/2023]
Abstract
Formation of capillary blood vasculature is a critical requirement for native as well as engineered organs and can be induced in vitro by co-culturing endothelial cells with fibroblasts. However, whether these fibroblasts are required only in the initial morphogenesis of endothelial cells or needed throughout is unknown, and the ability to remove these stromal cells after assembly could be useful for clinical translation. In this study, we introduce a technique termed CAMEO (Controlled Apoptosis in Multicellular Tissues for Engineered Organogenesis), whereby fibroblasts are selectively ablated on demand, and utilize it to probe the dispensability of fibroblasts in vascular morphogenesis. The presence of fibroblasts is shown to be necessary only during the first few days of endothelial cell morphogenesis, after which they can be ablated without significantly affecting the structural and functional features of the developed vasculature. Furthermore, we demonstrate the use of CAMEO to vascularize a construct containing primary human hepatocytes that improved tissue function. In conclusion, this study suggests that transient, initial support from fibroblasts is sufficient to drive vascular morphogenesis in engineered tissues, and this strategy of engineering-via-elimination may provide a new general approach for achieving desired functions and cell compositions in engineered organs.
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Affiliation(s)
- H-H Greco Song
- Harvard-MIT Program in Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alex Lammers
- Biological Design Center, Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Subramanian Sundaram
- Biological Design Center, Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Logan Rubio
- Biological Design Center, Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Amanda X Chen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Linqing Li
- Biological Design Center, Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Jeroen Eyckmans
- Biological Design Center, Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Sangeeta N Bhatia
- Harvard-MIT Program in Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christopher S Chen
- Biological Design Center, Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
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38
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Soleimany AP, Kirkpatrick JD, Su S, Dudani JS, Zhong Q, Bekdemir A, Bhatia SN. Activatable Zymography Probes Enable In Situ Localization of Protease Dysregulation in Cancer. Cancer Res 2020; 81:213-224. [PMID: 33106334 DOI: 10.1158/0008-5472.can-20-2410] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/16/2020] [Accepted: 10/21/2020] [Indexed: 12/25/2022]
Abstract
Recent years have seen the emergence of conditionally activated diagnostics and therapeutics that leverage protease-cleavable peptide linkers to enhance their specificity for cancer. However, due to a lack of methods to measure and localize protease activity directly within the tissue microenvironment, the design of protease-activated agents has been necessarily empirical, yielding suboptimal results when translated to patients. To address the need for spatially resolved protease activity profiling in cancer, we developed a new class of in situ probes that can be applied to fresh-frozen tissue sections in a manner analogous to immunofluorescence staining. These activatable zymography probes (AZP) detected dysregulated protease activity in human prostate cancer biopsy samples, enabling disease classification. AZPs were leveraged within a generalizable framework to design conditional cancer diagnostics and therapeutics and showcased in the Hi-Myc mouse model of prostate cancer, which models features of early pathogenesis. Multiplexed screening against barcoded substrates yielded a peptide, S16, that was robustly and specifically cleaved by tumor-associated metalloproteinases in the Hi-Myc model. In situ labeling with an AZP incorporating S16 revealed a potential role of metalloproteinase dysregulation in proliferative, premalignant Hi-Myc prostatic glands. Systemic administration of an in vivo imaging probe incorporating S16 perfectly classified diseased and healthy prostates, supporting the relevance of ex vivo activity assays to in vivo translation. We envision AZPs will enable new insights into the biology of protease dysregulation in cancer and accelerate the development of conditional diagnostics and therapeutics for multiple cancer types. SIGNIFICANCE: Visualization of protease activity within the native tissue context using AZPs provides new biological insights into protease dysregulation in cancer and guides the design of conditional diagnostics and therapeutics.
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Affiliation(s)
- Ava P Soleimany
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Harvard Graduate Program in Biophysics, Harvard University, Boston, Massachusetts
| | - Jesse D Kirkpatrick
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Susan Su
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Jaideep S Dudani
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Qian Zhong
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Ahmet Bekdemir
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts. .,Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Howard Hughes Medical Institute, Cambridge, Massachusetts.,Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts.,Wyss Institute at Harvard, Boston, Massachusetts.,Ludwig Center at the MIT Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts
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39
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Chan LW, Anahtar MN, Ong TH, Hern KE, Kunz RR, Bhatia SN. Engineering synthetic breath biomarkers for respiratory disease. Nat Nanotechnol 2020; 15:792-800. [PMID: 32690884 PMCID: PMC8173716 DOI: 10.1038/s41565-020-0723-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 06/02/2020] [Indexed: 05/10/2023]
Abstract
Human breath contains many volatile metabolites. However, few breath tests are currently used in the clinic to monitor disease due to bottlenecks in biomarker identification. Here we engineered breath biomarkers for respiratory disease by local delivery of protease-sensing nanoparticles to the lungs. The nanosensors shed volatile reporters upon cleavage by neutrophil elastase, an inflammation-associated protease with elevated activity in lung diseases such as bacterial infection and alpha-1 antitrypsin deficiency. After intrapulmonary delivery into mouse models with acute lung inflammation, the volatile reporters are released and expelled in breath at levels detectable by mass spectrometry. These breath signals can identify diseased mice with high sensitivity as early as 10 min after nanosensor administration. Using these nanosensors, we performed serial breath tests to monitor dynamic changes in neutrophil elastase activity during lung infection and to assess the efficacy of a protease inhibitor therapy targeting neutrophil elastase for the treatment of alpha-1 antitrypsin deficiency.
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Affiliation(s)
- Leslie W Chan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Melodi N Anahtar
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ta-Hsuan Ong
- Biological and Chemical Technologies Group, Massachusetts Institute of Technology Lincoln Laboratory, Lexington, MA, USA
| | - Kelsey E Hern
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Roderick R Kunz
- Biological and Chemical Technologies Group, Massachusetts Institute of Technology Lincoln Laboratory, Lexington, MA, USA
| | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Broad Institute, Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Cambridge, MA, USA.
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40
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Abstract
Therapeutic nucleic acids hold great promise for the treatment of genetic diseases, yet the delivery of this highly charged macromolecular drug remains a challenge in the field. Peptides are promising agents to mediate nucleic acid delivery because they can encode a biological function to overcome the trafficking barriers. Electrostatic nanocomplexes of nucleic acid and peptides can achieve effective delivery, but the balance between their stability and biological function must be finely tuned. In this work, we explore two peptide building blocks that have been studied in the literature: targeting ligands and intracellular trafficking peptides. We grafted these peptides on a polyethylene glycol (PEG) backbone with eight sites for substitution to create so-called "peptide spiders". These conjugates achieve stability via the well-known hydrophilic shielding effect of PEG. In addition, the coordination of peptide building blocks into multimers may create new biological properties, such as the well-known phenomena of increased binding avidity with multivalent ligands. In this work, we linked two trafficking peptides to the PEG backbone using either nonreducible or reducible chemistries and investigated the ability of these materials to carry silencing RNAs into mammalian cells. We then investigated these nanomaterials for their pharmacokinetic properties and silencing of undruggable targets in a mouse model of cancer. While reducible linkages were more potent at silencing in vitro, this effect was reversed when applied in the context of living animals. This work offers an insight into peptide-based delivery materials and investigates peptide-polymer linkages.
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Affiliation(s)
- Ester J Kwon
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Henry Ko
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Sangeeta N Bhatia
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Electrical and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Marble Center for Cancer Nanomedicine, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States.,Broad Institute of Massachusetts of Technology and Harvard, Cambridge, Massachusetts 02139, United States.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, United States
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41
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Mehta NK, Pradhan RV, Soleimany AP, Moynihan KD, Rothschilds AM, Momin N, Rakhra K, Mata-Fink J, Bhatia SN, Wittrup KD, Irvine DJ. Pharmacokinetic tuning of protein-antigen fusions enhances the immunogenicity of T-cell vaccines. Nat Biomed Eng 2020; 4:636-648. [PMID: 32483299 DOI: 10.1038/s41551-020-0563-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 04/27/2020] [Indexed: 12/21/2022]
Abstract
The formulations of peptide-based antitumour vaccines being tested in clinical studies are generally associated with weak potency. Here, we show that pharmacokinetically tuning the responses of peptide vaccines by fusing the peptide epitopes to carrier proteins optimizes vaccine immunogenicity in mice. In particular, we show in immunized mice that the carrier protein transthyretin simultaneously optimizes three factors: efficient antigen uptake in draining lymphatics from the site of injection, protection of antigen payloads from proteolytic degradation and reduction of antigen presentation in uninflamed distal lymphoid organs. Optimizing these factors increases vaccine immunogenicity by up to 90-fold and maximizes the responses to viral antigens, tumour-associated antigens, oncofetal antigens and shared neoantigens. Protein-peptide epitope fusions represent a facile and generalizable strategy for enhancing the T-cell responses elicited by subunit vaccines.
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Affiliation(s)
- Naveen K Mehta
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Roma V Pradhan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ava P Soleimany
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Harvard Graduate Program in Biophysics, Harvard University, Boston, MA, USA
| | - Kelly D Moynihan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Adrienne M Rothschilds
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Noor Momin
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kavya Rakhra
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jordi Mata-Fink
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Harvard-MIT Health Sciences and Technology Program, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute, Cambridge, MA, USA
| | - K Dane Wittrup
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Darrell J Irvine
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. .,The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA. .,Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Howard Hughes Medical Institute, Cambridge, MA, USA.
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42
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Soleimany AP, Bhatia SN. Activity-Based Diagnostics: An Emerging Paradigm for Disease Detection and Monitoring. Trends Mol Med 2020; 26:450-468. [PMID: 32359477 DOI: 10.1016/j.molmed.2020.01.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/20/2020] [Accepted: 01/28/2020] [Indexed: 12/26/2022]
Abstract
Diagnostics to accurately detect disease and monitor therapeutic response are essential for effective clinical management. Bioengineering, chemical biology, molecular biology, and computer science tools are converging to guide the design of diagnostics that leverage enzymatic activity to measure or produce biomarkers of disease. We review recent advances in the development of these 'activity-based diagnostics' (ABDx) and their application in infectious and noncommunicable diseases. We highlight efforts towards both molecular probes that respond to disease-specific catalytic activity to produce a diagnostic readout, as well as diagnostics that use enzymes as an engineered component of their sense-and-respond cascade. These technologies exemplify how integrating techniques from multiple disciplines with preclinical validation has enabled ABDx that may realize the goals of precision medicine.
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Affiliation(s)
- Ava P Soleimany
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard Graduate Program in Biophysics, Harvard University, Boston, MA, USA
| | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA; Wyss Institute at Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, Cambridge, MA, USA.
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43
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Tian C, Öhlund D, Rickelt S, Lidström T, Huang Y, Hao L, Zhao RT, Franklin O, Bhatia SN, Tuveson DA, Hynes RO. Cancer Cell-Derived Matrisome Proteins Promote Metastasis in Pancreatic Ductal Adenocarcinoma. Cancer Res 2020; 80:1461-1474. [PMID: 32029550 PMCID: PMC7127978 DOI: 10.1158/0008-5472.can-19-2578] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [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: 08/23/2019] [Revised: 12/20/2019] [Accepted: 01/30/2020] [Indexed: 12/23/2022]
Abstract
The prognosis for pancreatic ductal adenocarcinoma (PDAC) remains poor despite decades of effort. The abundant extracellular matrix (ECM) in PDAC comprises a major fraction of the tumor mass and plays various roles in promoting resistance to therapies. However, nonselective depletion of ECM has led to poor patient outcomes. Consistent with that observation, we previously showed that individual matrisome proteins derived from stromal cells correlate with either long or short patient survival. In marked contrast, those derived from cancer cells correlate strongly with poor survival. Here, we studied three cancer cell-derived matrisome proteins that are significantly overrepresented during PDAC progression, AGRN (agrin), SERPINB5 (serine protease inhibitor B5), and CSTB (cystatin B). Using both overexpression and knockdown experiments, we demonstrate that all three are promoters of PDAC metastasis. Furthermore, these proteins operate at different metastatic steps. AGRN promoted epithelial-to-mesenchymal transition in primary tumors, whereas SERPINB5 and CSTB enhanced late steps in the metastatic cascade by elevating invadopodia formation and in vivo extravasation. All three genes were associated with a poor prognosis in human patients and high levels of SERPINB5, secreted by cancer cells and deposited in the ECM, correlated with poor patient prognosis. This study provides strong evidence that cancer cell-derived matrisome proteins can be causal in promoting tumorigenesis and metastasis and lead to poor patient survival. Therefore, compared with the bulk matrix, mostly made by stromal cells, precise interventions targeting cancer cell-derived matrisome proteins, such as AGRN, SERPINB5, and CSTB, may represent preferred potential therapeutic targets. SIGNIFICANCE: This study provides insights into the biological roles of cancer cell-derived matrisome proteins in PDAC and supports the notion that these proteins are protumorigenic and better therapeutic targets.
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Affiliation(s)
- Chenxi Tian
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Daniel Öhlund
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
- Department of Radiation Sciences, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Steffen Rickelt
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Tommy Lidström
- Department of Radiation Sciences, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Ying Huang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Liangliang Hao
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Renee T Zhao
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Oskar Franklin
- Department of Surgical and Perioperative Sciences, Umeå University, Umeå, Sweden
| | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Howard Hughes Medical Institute, Chevy Chase, Maryland
| | | | - Richard O Hynes
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts.
- Howard Hughes Medical Institute, Chevy Chase, Maryland
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44
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Schuerle S, Furubayashi M, Soleimany AP, Gwisai T, Huang W, Voigt C, Bhatia SN. Genetic Encoding of Targeted Magnetic Resonance Imaging Contrast Agents for Tumor Imaging. ACS Synth Biol 2020; 9:392-401. [PMID: 31922737 DOI: 10.1021/acssynbio.9b00416] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Tumor-selective contrast agents have the potential to aid in the diagnosis and treatment of cancer using noninvasive imaging modalities such as magnetic resonance imaging (MRI). Such contrast agents can consist of magnetic nanoparticles incorporating functionalities that respond to cues specific to tumor environments. Genetically engineering magnetotactic bacteria to display peptides has been investigated as a means to produce contrast agents that combine the robust image contrast effects of magnetosomes with the transgenic-targeting peptides displayed on their surface. This work reports the first use of magnetic nanoparticles that display genetically encoded pH low insertion peptide (pHLIP), a long peptide intended to enhance MRI contrast by targeting the extracellular acidity associated with the tumors. To demonstrate the modularity of this versatile platform to incorporate diverse targeting ligands by genetic engineering, we also incorporated the cyclic αv integrin-binding peptide iRGD into separate magnetosomes. Specifically, we investigate their potential for enhanced binding and tumor imaging both in vitro and in vivo. Our experiments indicate that these tailored magnetosomes retain their magnetic properties, making them well suited as T2 contrast agents, while exhibiting an increased binding compared to the binding in wild-type magnetosomes.
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Affiliation(s)
- Simone Schuerle
- Institute for Translational Medicine, Department of Health Sciences and Technology, ETH Zurich, CH-8092 Zurich, Switzerland
| | - Maiko Furubayashi
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Japan
| | - Ava P. Soleimany
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Harvard Graduate Program in Biophysics, Harvard University, Boston, Massachusetts 02115, United States
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Tinotenda Gwisai
- Institute for Translational Medicine, Department of Health Sciences and Technology, ETH Zurich, CH-8092 Zurich, Switzerland
| | - Wei Huang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Christopher Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Sangeeta N. Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Marble Center for Cancer Nanomedicine, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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45
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Boehnke N, Correa S, Hao L, Wang W, Straehla JP, Bhatia SN, Hammond PT. Back Cover: Theranostic Layer‐by‐Layer Nanoparticles for Simultaneous Tumor Detection and Gene Silencing (Angew. Chem. Int. Ed. 7/2020). Angew Chem Int Ed Engl 2020. [DOI: 10.1002/anie.201916374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Natalie Boehnke
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of Technology Cambridge MA 02139 USA
| | - Santiago Correa
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of Technology Cambridge MA 02139 USA
- Department of BioengineeringKoch Institute for Integrative Cancer ResearchMassachusetts Institute of Technology Cambridge MA 02139 USA
- Current address: Materials Science and EngineeringStanford University 496 Lomita Mall Stanford CA 94305 USA
| | - Liangliang Hao
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of Technology Cambridge MA 02139 USA
- Institute for Medical Engineering and ScienceMassachusetts Institute of Technology Cambridge MA 02139 USA
| | - Wade Wang
- Department of ChemistryKoch Institute for Integrative Cancer ResearchMassachusetts Institute of Technology Cambridge MA 02139 USA
| | - Joelle P. Straehla
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of Technology Cambridge MA 02139 USA
- Department of Pediatric OncologyDana-Farber/Boston Children's Cancer and Blood Disorders Center Boston MA 02115 USA
| | - Sangeeta N. Bhatia
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of Technology Cambridge MA 02139 USA
- Institute for Medical Engineering and ScienceMassachusetts Institute of Technology Cambridge MA 02139 USA
- Department of MedicineBrigham and Women's Hospital and Harvard Medical School Boston MA 02115 USA
- Broad Institute of Massachusetts Institute of Technology and Harvard Cambridge MA 02139 USA
- Howard Hughes Medical Institute Cambridge MA 02139 USA
| | - Paula T. Hammond
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of Technology Cambridge MA 02139 USA
- Department of Chemical EngineeringMassachusetts Institute of Technology Cambridge MA 02139 USA
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46
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Boehnke N, Correa S, Hao L, Wang W, Straehla JP, Bhatia SN, Hammond PT. Rücktitelbild: Theranostic Layer‐by‐Layer Nanoparticles for Simultaneous Tumor Detection and Gene Silencing (Angew. Chem. 7/2020). Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Natalie Boehnke
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of Technology Cambridge MA 02139 USA
| | - Santiago Correa
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of Technology Cambridge MA 02139 USA
- Department of BioengineeringKoch Institute for Integrative Cancer ResearchMassachusetts Institute of Technology Cambridge MA 02139 USA
- Current address: Materials Science and EngineeringStanford University 496 Lomita Mall Stanford CA 94305 USA
| | - Liangliang Hao
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of Technology Cambridge MA 02139 USA
- Institute for Medical Engineering and ScienceMassachusetts Institute of Technology Cambridge MA 02139 USA
| | - Wade Wang
- Department of ChemistryKoch Institute for Integrative Cancer ResearchMassachusetts Institute of Technology Cambridge MA 02139 USA
| | - Joelle P. Straehla
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of Technology Cambridge MA 02139 USA
- Department of Pediatric OncologyDana-Farber/Boston Children's Cancer and Blood Disorders Center Boston MA 02115 USA
| | - Sangeeta N. Bhatia
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of Technology Cambridge MA 02139 USA
- Institute for Medical Engineering and ScienceMassachusetts Institute of Technology Cambridge MA 02139 USA
- Department of MedicineBrigham and Women's Hospital and Harvard Medical School Boston MA 02115 USA
- Broad Institute of Massachusetts Institute of Technology and Harvard Cambridge MA 02139 USA
- Howard Hughes Medical Institute Cambridge MA 02139 USA
| | - Paula T. Hammond
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of Technology Cambridge MA 02139 USA
- Department of Chemical EngineeringMassachusetts Institute of Technology Cambridge MA 02139 USA
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47
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Boehnke N, Correa S, Hao L, Wang W, Straehla JP, Bhatia SN, Hammond PT. Theranostic Layer-by-Layer Nanoparticles for Simultaneous Tumor Detection and Gene Silencing. Angew Chem Int Ed Engl 2020; 59:2776-2783. [PMID: 31747099 DOI: 10.1002/anie.201911762] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [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: 09/13/2019] [Revised: 10/28/2019] [Indexed: 12/28/2022]
Abstract
Layer-by-layer nanoparticles (NPs) are modular drug delivery vehicles that incorporate multiple functional materials through sequential deposition of polyelectrolytes onto charged nanoparticle cores. Herein, we combined the multicomponent features and tumor targeting capabilities of layer-by-layer assembly with functional biosensing peptides to create a new class of nanotheranostics. These NPs encapsulate a high weight percentage of siRNA while also carrying a synthetic biosensing peptide on the surface that is cleaved into a urinary reporter upon exposure to specific proteases overexpressed in the tumor microenvironment. Importantly, this biosensor reports back on a molecular signature characteristic to metastatic tumors and associated with poor prognosis, MMP9 protease overexpression. This nanotheranostic mediates noninvasive urinary-based diagnostics in mouse models of three different cancers with simultaneous gene silencing in flank and metastatic mouse models of ovarian cancer.
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Affiliation(s)
- Natalie Boehnke
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Santiago Correa
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Bioengineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Current address: Materials Science and Engineering, Stanford University, 496 Lomita Mall, Stanford, CA, 94305, USA
| | - Liangliang Hao
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Wade Wang
- Department of Chemistry, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Joelle P Straehla
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02115, USA
| | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02139, USA.,Howard Hughes Medical Institute, Cambridge, MA, 02139, USA
| | - Paula T Hammond
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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48
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Boehnke N, Correa S, Hao L, Wang W, Straehla JP, Bhatia SN, Hammond PT. Theranostic Layer‐by‐Layer Nanoparticles for Simultaneous Tumor Detection and Gene Silencing. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201911762] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Natalie Boehnke
- Koch Institute for Integrative Cancer Research Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Santiago Correa
- Koch Institute for Integrative Cancer Research Massachusetts Institute of Technology Cambridge MA 02139 USA
- Department of Bioengineering Koch Institute for Integrative Cancer Research Massachusetts Institute of Technology Cambridge MA 02139 USA
- Current address: Materials Science and Engineering Stanford University 496 Lomita Mall Stanford CA 94305 USA
| | - Liangliang Hao
- Koch Institute for Integrative Cancer Research Massachusetts Institute of Technology Cambridge MA 02139 USA
- Institute for Medical Engineering and Science Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Wade Wang
- Department of Chemistry Koch Institute for Integrative Cancer Research Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Joelle P. Straehla
- Koch Institute for Integrative Cancer Research Massachusetts Institute of Technology Cambridge MA 02139 USA
- Department of Pediatric Oncology Dana-Farber/Boston Children's Cancer and Blood Disorders Center Boston MA 02115 USA
| | - Sangeeta N. Bhatia
- Koch Institute for Integrative Cancer Research Massachusetts Institute of Technology Cambridge MA 02139 USA
- Institute for Medical Engineering and Science Massachusetts Institute of Technology Cambridge MA 02139 USA
- Department of Medicine Brigham and Women's Hospital and Harvard Medical School Boston MA 02115 USA
- Broad Institute of Massachusetts Institute of Technology and Harvard Cambridge MA 02139 USA
- Howard Hughes Medical Institute Cambridge MA 02139 USA
| | - Paula T. Hammond
- Koch Institute for Integrative Cancer Research Massachusetts Institute of Technology Cambridge MA 02139 USA
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA
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49
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Vera IM, Grilo Ruivo MT, Lemos Rocha LF, Marques S, Bhatia SN, Mota MM, Mancio-Silva L. Targeting liver stage malaria with metformin. JCI Insight 2019; 4:127441. [PMID: 31852843 DOI: 10.1172/jci.insight.127441] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 11/13/2019] [Indexed: 12/29/2022] Open
Abstract
Despite an unprecedented 2 decades of success, the combat against malaria - the mosquito-transmitted disease caused by Plasmodium parasites - is no longer progressing. Efforts toward eradication are threatened by the lack of an effective vaccine and a rise in antiparasite drug resistance. Alternative approaches are urgently needed. Repurposing of available, approved drugs with distinct modes of action are being considered as viable and immediate adjuncts to standard antimicrobial treatment. Such strategies may be well suited to the obligatory and clinically silent first phase of Plasmodium infection, where massive parasite replication occurs within hepatocytes in the liver. Here, we report that the widely used antidiabetic drug, metformin, impairs parasite liver stage development of both rodent-infecting Plasmodium berghei and human-infecting P. falciparum parasites. Prophylactic treatment with metformin curtails parasite intracellular growth in vitro. An additional effect was observed in mice with a decrease in the numbers of infected hepatocytes. Moreover, metformin provided in combination with conventional liver- or blood-acting antimalarial drugs further reduced the total burden of P. berghei infection and substantially lessened disease severity in mice. Together, our findings indicate that repurposing of metformin in a prophylactic regimen could be considered for malaria chemoprevention.
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Affiliation(s)
- Iset Medina Vera
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina Universidade de Lisboa, Lisboa, Portugal
| | - Margarida T Grilo Ruivo
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina Universidade de Lisboa, Lisboa, Portugal
| | - Leonardo F Lemos Rocha
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina Universidade de Lisboa, Lisboa, Portugal
| | - Sofia Marques
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina Universidade de Lisboa, Lisboa, Portugal
| | - Sangeeta N Bhatia
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Cambridge, Masschusetts, USA
| | - Maria M Mota
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina Universidade de Lisboa, Lisboa, Portugal
| | - Liliana Mancio-Silva
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina Universidade de Lisboa, Lisboa, Portugal.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA
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50
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Jain PK, Lo JH, Rananaware S, Downing M, Panda A, Tai M, Raghavan S, Fleming HE, Bhatia SN. Non-viral delivery of CRISPR/Cas9 complex using CRISPR-GPS nanocomplexes. Nanoscale 2019; 11:21317-21323. [PMID: 31670340 PMCID: PMC7709491 DOI: 10.1039/c9nr01786k] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
There is a critical need for the development of safe and efficient delivery technologies for CRISPR/Cas9 to advance translation of genome editing to the clinic. Non-viral methods that are simple, efficient, and completely based on biologically-derived materials could offer such potential. Here we report a simple and modular tandem peptide-based nanocomplex system with cell-targeting capacity that efficiently combines guide RNA (sgRNA) with Cas9 protein, and facilitates internalization of sgRNA/Cas9 ribonucleoprotein complexes to yield robust genome editing across multiple cell lines.
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Affiliation(s)
- Piyush K Jain
- Department of Chemical Engineering, University of Florida, Gainesville, FL 32611, USA and Marble Center for Cancer Nanomedicine, Institute for Medical Engineering & Science, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA and UF Health Cancer Center, University of Florida, Gainesville, FL 32608.
| | - Justin H Lo
- Marble Center for Cancer Nanomedicine, Institute for Medical Engineering & Science, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA and Division of Hematology and Oncology, Department of Internal Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Santosh Rananaware
- Department of Chemical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Marco Downing
- Department of Chemical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Apekshya Panda
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA and Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02139, USA
| | - Michelle Tai
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Srivatsan Raghavan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA and Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02139, USA
| | - Heather E Fleming
- Marble Center for Cancer Nanomedicine, Institute for Medical Engineering & Science, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sangeeta N Bhatia
- Marble Center for Cancer Nanomedicine, Institute for Medical Engineering & Science, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA and Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02139, USA and Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA and Howard Hughes Medical Institute, Cambridge, MA 02139, USA.
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