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Chilimoniuk J, Erol A, Rödiger S, Burdukiewicz M. Challenges and opportunities in processing NanoString nCounter data. Comput Struct Biotechnol J 2024; 23:1951-1958. [PMID: 38736697 PMCID: PMC11087919 DOI: 10.1016/j.csbj.2024.04.061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/14/2024] Open
Abstract
NanoString nCounter is a medium-throughput technology used in mRNA and miRNA differential expression studies. It offers several advantages, including the absence of an amplification step and the ability to analyze low-grade samples. Despite its considerable strengths, the popularity of the nCounter platform in experimental research stabilized in 2022 and 2023, and this trend may continue in the upcoming years. Such stagnation could potentially be attributed to the absence of a standardized analytical pipeline or the indication of optimal processing methods for nCounter data analysis. To standardize the description of the nCounter data analysis workflow, we divided it into five distinct steps: data pre-processing, quality control, background correction, normalization and differential expression analysis. Next, we evaluated eleven R packages dedicated to nCounter data processing to point out functionalities belonging to these steps and provide comments on their applications in studies of mRNA and miRNA samples.
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Affiliation(s)
| | - Anna Erol
- Clinical Research Centre, Medical University of Białystok, Białystok, Poland
| | - Stefan Rödiger
- Institute of Biotechnology, Faculty Environment and Natural Sciences, Brandenburg University of Technology Cottbus - Senftenberg, Senftenberg, Germany
| | - Michał Burdukiewicz
- Clinical Research Centre, Medical University of Białystok, Białystok, Poland
- Institute of Biotechnology and Biomedicine, Autonomous University of Barcelona, Barcelona, Spain
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2
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Tansey MG, Boles J, Holt J, Cole C, Neighbarger N, Urs N, Uriarte-Huarte O. Locus coeruleus injury modulates ventral midbrain neuroinflammation during DSS-induced colitis. RESEARCH SQUARE 2024:rs.3.rs-3952442. [PMID: 38559083 PMCID: PMC10980147 DOI: 10.21203/rs.3.rs-3952442/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Parkinson's disease (PD) is characterized by a decades-long prodrome, consisting of a collection of non-motor symptoms that emerges prior to the motor manifestation of the disease. Of these non-motor symptoms, gastrointestinal dysfunction and deficits attributed to central norepinephrine (NE) loss, including mood changes and sleep disturbances, are frequent in the PD population and emerge early in the disease. Evidence is mounting that injury and inflammation in the gut and locus coeruleus (LC), respectively, underlie these symptoms, and the injury of these systems is central to the progression of PD. In this study, we generate a novel two-hit mouse model that captures both features, using dextran sulfate sodium (DSS) to induce gut inflammation and N-(2-chloroethyl)-N-ethyl-2-bromobenzylamine (DSP-4) to lesion the LC. We first confirmed the specificity of DSP-4 for central NE using neurochemical methods and fluorescence light-sheet microscopy of cleared tissue, and established that DSS-induced outcomes in the periphery, including weight loss, gross indices of gut injury and systemic inflammation, the loss of tight junction proteins in the colonic epithelium, and markers of colonic inflammation, were unaffected with DSP-4 pre-administration. We then measured alterations in neuroimmune gene expression in the ventral midbrain in response to DSS treatment alone as well as the extent to which prior LC injury modified this response. In this two-hit model we observed that DSS-induced colitis activates the expression of key cytokines and chemokines in the ventral midbrain only in the presence of LC injury and the typical DSS-associated neuroimmune is blunted by pre-LC lesioning with DSP-4. In all, this study supports the growing appreciation for the LC as neuroprotective against inflammation-induced brain injury and draws attention to the potential for NEergic interventions to exert disease-modifying effects under conditions where peripheral inflammation may compromise ventral midbrain dopaminergic neurons and increase the risk for development of PD.
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Boles JS, Holt J, Cole CL, Neighbarger NK, Urs NM, Huarte OU, Tansey MG. Locus coeruleus injury modulates ventral midbrain neuroinflammation during DSS-induced colitis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.12.580010. [PMID: 38405709 PMCID: PMC10888767 DOI: 10.1101/2024.02.12.580010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Parkinson's disease (PD) is characterized by a decades-long prodrome, consisting of a collection of non-motor symptoms that emerges prior to the motor manifestation of the disease. Of these non-motor symptoms, gastrointestinal dysfunction and deficits attributed to central norepinephrine (NE) loss, including mood changes and sleep disturbances, are frequent in the PD population and emerge early in the disease. Evidence is mounting that injury and inflammation in the gut and locus coeruleus (LC), respectively, underlie these symptoms, and the injury of these systems is central to the progression of PD. In this study, we generate a novel two-hit mouse model that captures both features, using dextran sulfate sodium (DSS) to induce gut inflammation and N-(2-chloroethyl)-N-ethyl-2-bromobenzylamine (DSP-4) to lesion the LC. We first confirmed the specificity of DSP-4 for central NE using neurochemical methods and fluorescence light-sheet microscopy of cleared tissue, and established that DSS-induced outcomes in the periphery, including weight loss, gross indices of gut injury and systemic inflammation, the loss of tight junction proteins in the colonic epithelium, and markers of colonic inflammation, were unaffected with DSP-4 pre-administration. We then measured alterations in neuroimmune gene expression in the ventral midbrain in response to DSS treatment alone as well as the extent to which prior LC injury modified this response. In this two-hit model we observed that DSS-induced colitis activates the expression of key cytokines and chemokines in the ventral midbrain only in the presence of LC injury and the typical DSS-associated neuroimmune is blunted by pre-LC lesioning with DSP-4. In all, this study supports the growing appreciation for the LC as neuroprotective against inflammation-induced brain injury and draws attention to the potential for NEergic interventions to exert disease-modifying effects under conditions where peripheral inflammation may compromise ventral midbrain dopaminergic neurons and increase the risk for development of PD.
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Affiliation(s)
- Jake Sondag Boles
- Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA
- Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, FL, USA
- McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - Jenny Holt
- Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA
- Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, FL, USA
- McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - Cassandra L. Cole
- Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA
- Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, FL, USA
- McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - Noelle K. Neighbarger
- Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA
- Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, FL, USA
- McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - Nikhil M. Urs
- McKnight Brain Institute, University of Florida, Gainesville, FL, USA
- Department of Pharmacology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Oihane Uriarte Huarte
- Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA
- Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Malú Gámez Tansey
- Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA
- Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, FL, USA
- McKnight Brain Institute, University of Florida, Gainesville, FL, USA
- Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
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4
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Peltzer A, Mohr C, Stadermann KB, Zwick M, Schmid R. nf-core/nanostring: a pipeline for reproducible NanoString nCounter analysis. Bioinformatics 2024; 40:btae019. [PMID: 38212989 PMCID: PMC10805338 DOI: 10.1093/bioinformatics/btae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 11/29/2023] [Accepted: 01/10/2024] [Indexed: 01/13/2024] Open
Abstract
MOTIVATION The NanoString™ nCounter® technology platform is a widely used targeted quantification platform for the analysis of gene expression of up to ∼800 genes. Whereas the software tools by the manufacturer can perform the analysis in an interactive and GUI driven approach, there is no portable and user-friendly workflow available that can be used to perform reproducible analysis of multiple samples simultaneously in a scalable fashion on different computing infrastructures. RESULTS Here, we present the nf-core/nanostring open-source pipeline to perform a comprehensive analysis including quality control and additional features such as expression visualization, annotation with additional metadata and input creation for differential gene expression analysis. The workflow features an easy installation, comprehensive documentation, open-source code with the possibility for further extensions, a strong portability across multiple computing environments and detailed quality metrics reporting covering all parts of the pipeline. nf-core/nanostring has been implemented in the Nextflow workflow language and supports Docker, Singularity, Podman container technologies as well as Conda environments, enabling easy deployment on any Nextflow supported compatible system, including most widely used cloud computing environments such as Google GCP or Amazon AWS. AVAILABILITY AND IMPLEMENTATION The source code, documentation and installation instructions as well as results for continuous tests are freely available at https://github.com/nf-core/nanostring and https://nf-co.re/nanostring.
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Affiliation(s)
- Alexander Peltzer
- Clinical Bioinformatics and Systems Pharmacology, Translational Medicine and Clinical Pharmacology, Boehringer Ingelheim Pharma GmbH & Co. KG, 88400 Biberach/Riss, Germany
| | - Christopher Mohr
- Clinical Bioinformatics and Systems Pharmacology, Translational Medicine and Clinical Pharmacology, Boehringer Ingelheim Pharma GmbH & Co. KG, 88400 Biberach/Riss, Germany
| | - Kai B Stadermann
- Clinical Bioinformatics and Systems Pharmacology, Translational Medicine and Clinical Pharmacology, Boehringer Ingelheim Pharma GmbH & Co. KG, 88400 Biberach/Riss, Germany
| | - Matthias Zwick
- Clinical Bioinformatics and Systems Pharmacology, Translational Medicine and Clinical Pharmacology, Boehringer Ingelheim Pharma GmbH & Co. KG, 88400 Biberach/Riss, Germany
| | - Ramona Schmid
- Clinical Bioinformatics and Systems Pharmacology, Translational Medicine and Clinical Pharmacology, Boehringer Ingelheim Pharma GmbH & Co. KG, 88400 Biberach/Riss, Germany
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Schöffski P, Machiels JP, Rottey S, Sadrolhefazi B, Musa H, Marzin K, Awada A. Phase Ia dose-escalation trial with the BET protein inhibitor BI 894999 in patients with advanced or metastatic solid tumours. Eur J Cancer 2023; 191:112987. [PMID: 37556913 DOI: 10.1016/j.ejca.2023.112987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/30/2023] [Accepted: 07/05/2023] [Indexed: 08/11/2023]
Abstract
BACKGROUND Bromodomain and extraterminal domain (BET) inhibitors have demonstrated efficacy in solid tumours and haematological malignancies. BI 894999 is a novel oral BET inhibitor that has demonstrated potent antitumour activity in preclinical studies. PATIENTS AND METHODS 1367.1 was an open-label, Phase Ia/Ib dose-finding study evaluating BI 894999 once daily in patients with advanced solid tumours (Schedule A: 0.2, 0.5, 1.0, 1.5, 2.0, and 5.0 mg, Days 1-21/21-d cycle; Schedule B: 1.5, 2.0, and 2.5 mg, Days 1-15/21-d cycle; Schedule C: loading dose 5.0, 6.0, or 7.0 mg on Day 1 followed by maintenance dose 2.5, 3.0, or 3.5 mg, Days 2-7 and 15-21/28-d cycle); 77 patients were enrolled. NCT02516553. RESULTS Grade ≥3 dose-limiting toxicities (DLTs) were reported in 8/21, 5/25, and 9/31 patients for Schedules A, B, and C, respectively. Thrombocytopenia was reported as a DLT in 28.6%, 4.8%, and 9.7% for Schedules A, B, and C, respectively. Other DLTs occurring in ≥1 patient were troponin T increase (13.6%), hypophosphataemia (4.5%), and elevated creatine phosphokinase (3.0%). Disease control was achieved in 23.8%, 24.0%, and 29.0% of patients for Schedules A, B, and C, respectively. A partial response was achieved in 9.5% and 4% of patients with Schedules A and B, respectively. The best response with Schedule C was stable disease. CONCLUSION The 1.5, 2.5, and 6.0/3.0 mg doses in Schedules A, B, and C, respectively, were declared as maximum tolerated dose. Based on the strength of these data, BI 894999 was further evaluated in a Phase Ib trial.
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Affiliation(s)
- Patrick Schöffski
- Department of General Medical Oncology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.
| | - Jean-Pascal Machiels
- Department of Medical Oncology, Institut Roi Albert II, Cliniques Universitaires Saint-Luc, and Institute for Experimental and Clinical Research (IREC, pôle MIRO), Université Catholique de Louvain (UCLouvain), Brussels, Belgium
| | - Sylvie Rottey
- Department of Medical Oncology, Ghent University Hospital, Ghent, Belgium
| | | | - Hanny Musa
- Boehringer Ingelheim International GmbH, Ingelheim am Rhein, Germany
| | - Kristell Marzin
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Ahmad Awada
- Oncology Medicine Department, Jules Bordet Institute, Brussels, Belgium
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Novak T, Crawford JC, Hahn G, Hall MW, Thair SA, Newhams MM, Chou J, Mourani PM, Tarquinio KM, Markovitz B, Loftis LL, Weiss SL, Higgerson R, Schwarz AJ, Pinto NP, Thomas NJ, Gedeit RG, Sanders RC, Mahapatra S, Coates BM, Cvijanovich NZ, Ackerman KG, Tellez DW, McQuillen P, Kurachek SC, Shein SL, Lange C, Thomas PG, Randolph AG. Transcriptomic profiles of multiple organ dysfunction syndrome phenotypes in pediatric critical influenza. Front Immunol 2023; 14:1220028. [PMID: 37533854 PMCID: PMC10390830 DOI: 10.3389/fimmu.2023.1220028] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 06/19/2023] [Indexed: 08/04/2023] Open
Abstract
Background Influenza virus is responsible for a large global burden of disease, especially in children. Multiple Organ Dysfunction Syndrome (MODS) is a life-threatening and fatal complication of severe influenza infection. Methods We measured RNA expression of 469 biologically plausible candidate genes in children admitted to North American pediatric intensive care units with severe influenza virus infection with and without MODS. Whole blood samples from 191 influenza-infected children (median age 6.4 years, IQR: 2.2, 11) were collected a median of 27 hours following admission; for 45 children a second blood sample was collected approximately seven days later. Extracted RNA was hybridized to NanoString mRNA probes, counts normalized, and analyzed using linear models controlling for age and bacterial co-infections (FDR q<0.05). Results Comparing pediatric samples collected near admission, children with Prolonged MODS for ≥7 days (n=38; 9 deaths) had significant upregulation of nine mRNA transcripts associated with neutrophil degranulation (RETN, TCN1, OLFM4, MMP8, LCN2, BPI, LTF, S100A12, GUSB) compared to those who recovered more rapidly from MODS (n=27). These neutrophil transcripts present in early samples predicted Prolonged MODS or death when compared to patients who recovered, however in paired longitudinal samples, they were not differentially expressed over time. Instead, five genes involved in protein metabolism and/or adaptive immunity signaling pathways (RPL3, MRPL3, HLA-DMB, EEF1G, CD8A) were associated with MODS recovery within a week. Conclusion Thus, early increased expression of neutrophil degranulation genes indicated worse clinical outcomes in children with influenza infection, consistent with reports in adult cohorts with influenza, sepsis, and acute respiratory distress syndrome.
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Affiliation(s)
- Tanya Novak
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children’s Hospital, Boston, MA, United States
- Department of Anaesthesia, Harvard Medical School, Boston, MA, United States
- National Institute of Allergy and Infectious Diseases (NIAID), Centers of Excellence for Influenza Research and Response (CEIRR), Center for Influenza Disease and Emergence Response (CIDER), Athens, GA, United States
| | - Jeremy Chase Crawford
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children’s Hospital, Boston, MA, United States
- National Institute of Allergy and Infectious Diseases (NIAID), Centers of Excellence for Influenza Research and Response (CEIRR), St. Jude Children's Research Hospital, Memphis, TN, United States
- Department of Immunology, St Jude Children’s Research Hospital, Memphis, TN, United States
| | - Georg Hahn
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Mark W. Hall
- Division of Critical Care Medicine, Department of Pediatrics, Nationwide Children’s Hospital, Columbus, OH, United States
| | - Simone A. Thair
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children’s Hospital, Boston, MA, United States
- Division of Biomedical Informatics Research, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Margaret M. Newhams
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children’s Hospital, Boston, MA, United States
- National Institute of Allergy and Infectious Diseases (NIAID), Centers of Excellence for Influenza Research and Response (CEIRR), Center for Influenza Disease and Emergence Response (CIDER), Athens, GA, United States
| | - Janet Chou
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States
- Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Peter M. Mourani
- Department of Pediatrics, Section of Critical Care Medicine, University of Arkansas for Medical Sciences and Arkansas Children’s Research Institute, Little Rock, AR, United States
| | - Keiko M. Tarquinio
- Division of Critical Care Medicine, Department of Pediatrics, Emory University School of Medicine, Children’s Healthcare of Atlanta, Atlanta, GA, United States
| | - Barry Markovitz
- Department of Anesthesiology Critical Care Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | - Laura L. Loftis
- Division of Critical Care Medicine, Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - Scott L. Weiss
- Nemours Children’s Hospital Delaware, Critical Care Medicine, Wilmington, DE, United States
| | - Renee Higgerson
- Pediatric Critical Care Medicine, St. David’s Children’s Hospital, Austin, TX, United States
| | - Adam J. Schwarz
- Department of Pediatrics, Children’s Hospital of Orange County, Orange, CA, United States
| | - Neethi P. Pinto
- Department of Anesthesiology and Critical Care Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Neal J. Thomas
- Department of Pediatrics, Penn State Health Children’s Hospital, Penn State University College of Medicine, Hershey, PA, United States
| | - Rainer G. Gedeit
- Pediatric Critical Care, Milwaukee Hospital-Children’s Wisconsin, Milwaukee, WI, United States
| | - Ronald C. Sanders
- Section of Pediatric Critical Care, Department of Pediatrics, University of Arkansas for Medical Sciences and Arkansas Children’s Research Institute, Little Rock, AR, United States
| | - Sidharth Mahapatra
- Pediatric Critical Care Medicine, Children’s Hospital & Medical Center Omaha, University of Nebraska Medical Center, Omaha, NE, United States
| | - Bria M. Coates
- Division of Critical Care Medicine, Department of Pediatrics, Northwestern University Feinberg School of Medicine, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, United States
| | - Natalie Z. Cvijanovich
- Division of Critical Care Medicine, UCSF Benioff Children’s Hospital, Oakland, CA, United States
| | - Kate G. Ackerman
- Department of Pediatrics, University of Rochester/UR Medicine Golisano Children’s Hospital, Rochester, NY, United States
| | - David W. Tellez
- Pediatric Critical Care Medicine, Phoenix Children’s Hospital, Phoenix, AZ, United States
| | - Patrick McQuillen
- Department of Pediatrics, Benioff Children’s Hospital, University of California, San Francisco, San Francisco, CA, United States
| | - Stephen C. Kurachek
- Department of Critical Care, Children’s Specialty Center, Children’s Minnesota, Minneapolis, MN, United States
| | - Steven L. Shein
- Division of Pediatric Critical Care Medicine, University Hospitals Rainbow Babies and Children’s Hospital, Cleveland, OH, United States
| | - Christoph Lange
- Department of Biostatistics, T.H. Chan School of Public Health, Harvard University, Boston, MA, United States
| | - Paul G. Thomas
- National Institute of Allergy and Infectious Diseases (NIAID), Centers of Excellence for Influenza Research and Response (CEIRR), St. Jude Children's Research Hospital, Memphis, TN, United States
- Department of Immunology, St Jude Children’s Research Hospital, Memphis, TN, United States
| | - Adrienne G. Randolph
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children’s Hospital, Boston, MA, United States
- Department of Anaesthesia, Harvard Medical School, Boston, MA, United States
- National Institute of Allergy and Infectious Diseases (NIAID), Centers of Excellence for Influenza Research and Response (CEIRR), Center for Influenza Disease and Emergence Response (CIDER), Athens, GA, United States
- Department of Pediatrics, Harvard Medical School, Boston, MA, United States
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7
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Tontsch-Grunt U, Traexler PE, Baum A, Musa H, Marzin K, Wang S, Trapani F, Engelhardt H, Solca F. Therapeutic impact of BET inhibitor BI 894999 treatment: backtranslation from the clinic. Br J Cancer 2022; 127:577-586. [PMID: 35444289 PMCID: PMC9346113 DOI: 10.1038/s41416-022-01815-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/24/2022] [Accepted: 03/31/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND BET inhibitors have been tested in several clinical trials where, despite encouraging preclinical results, substantial clinical benefit in monotherapy remains limited. This work illustrates the translational challenges and reports new data around the novel BET inhibitor, BI 894999. At clinically achievable concentrations, mechanistic studies were carried out to study pathway modulation and rational drug combinations. METHODS BRD-NUT fusions are oncogenic drivers in NUT carcinoma (NC). The effects of BI 894999 on proliferation, chromatin binding and pathway modulation were studied in NC in vitro. These studies were complemented by efficacy studies either as a single agent or in combination with the clinical p300/CBP inhibitor CCS1477. RESULTS Based on the modelling of preclinical and clinical data, we proposed and implemented a new clinical scheduling regimen. This led to plasma levels sufficient to fully dislodge BRD-NUT from chromatin and to sustained and pronounced pharmacodynamic (PD) modulation of HEXIM1 and HIST2H2BF. Platelet counts in patient blood samples were improved compared to previous schedules. Rational combination studies of BI 894999 performed at clinically meaningful concentrations led to tumour regressions in all NC xenograft models tested. CONCLUSIONS BI 894999 holds significant potential as a combination drug and CCS1477 p300/CBP inhibitor is a promising partner for future clinical trials.
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Affiliation(s)
| | | | - Anke Baum
- Boehringer Ingelheim RCV GmbH & Co KG, A-1120, Vienna, Austria
| | - Hanny Musa
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Kristell Marzin
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Shaonan Wang
- Boehringer Ingelheim Pharma GmbH & Co. KG, Ingelheim am Rhein, Germany
| | | | | | - Flavio Solca
- Boehringer Ingelheim RCV GmbH & Co KG, A-1120, Vienna, Austria
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8
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Saraji A, Offermann A, Stegmann-Frehse J, Hempel K, Kang D, Krupar R, Watermann C, Jonigk D, Kühnel MP, Kirfel J, Perner S, Sailer V. Cracking it - successful mRNA extraction for digital gene expression analysis from decalcified, formalin-fixed and paraffin-embedded bone tissue. PLoS One 2021; 16:e0257416. [PMID: 34529723 PMCID: PMC8445430 DOI: 10.1371/journal.pone.0257416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/31/2021] [Indexed: 11/18/2022] Open
Abstract
With the advance of precision medicine, the availability of tumor tissue for molecular analysis has become a limiting factor. This is particularly the case for bone metastases which are frequently occurring in cancer types such as prostate cancer. Due to the necessary decalcification process it was long thought that transcriptome analysis will not be feasible from decalcified formalin-fixed, paraffin-embedded (DFFPE) in a large manner. Here we demonstrate that mRNA extraction from DFFPE is feasible, quick, robust and reproducible and that decalcification does not hamper subsequent gene expression analysis. This might assist in implementing transcriptome analysis from DFFPE into every day practice.
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Affiliation(s)
- Alireza Saraji
- Pathology of the University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Anne Offermann
- Pathology of the University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Janine Stegmann-Frehse
- Pathology of the University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Katharina Hempel
- Pathology of the University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Duan Kang
- Pathology of the University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | | | - Christian Watermann
- Pathology of the University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Danny Jonigk
- Institute of Pathology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), German Center for Lung Research, Hannover, Germany
| | - Mark Philipp Kühnel
- Institute of Pathology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), German Center for Lung Research, Hannover, Germany
| | - Jutta Kirfel
- Pathology of the University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Sven Perner
- Pathology of the University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
- Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Verena Sailer
- Pathology of the University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
- * E-mail:
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9
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Bhattacharya A, Hamilton AM, Furberg H, Pietzak E, Purdue MP, Troester MA, Hoadley KA, Love MI. An approach for normalization and quality control for NanoString RNA expression data. Brief Bioinform 2021; 22:bbaa163. [PMID: 32789507 PMCID: PMC8138885 DOI: 10.1093/bib/bbaa163] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 01/10/2023] Open
Abstract
The NanoString RNA counting assay for formalin-fixed paraffin embedded samples is unique in its sensitivity, technical reproducibility and robustness for analysis of clinical and archival samples. While commercial normalization methods are provided by NanoString, they are not optimal for all settings, particularly when samples exhibit strong technical or biological variation or where housekeeping genes have variable performance across the cohort. Here, we develop and evaluate a more comprehensive normalization procedure for NanoString data with steps for quality control, selection of housekeeping targets, normalization and iterative data visualization and biological validation. The approach was evaluated using a large cohort ($N=\kern0.5em 1649$) from the Carolina Breast Cancer Study, two cohorts of moderate sample size ($N=359$ and$130$) and a small published dataset ($N=12$). The iterative process developed here eliminates technical variation (e.g. from different study phases or sites) more reliably than the three other methods, including NanoString's commercial package, without diminishing biological variation, especially in long-term longitudinal multiphase or multisite cohorts. We also find that probe sets validated for nCounter, such as the PAM50 gene signature, are impervious to batch issues. This work emphasizes that systematic quality control, normalization and visualization of NanoString nCounter data are an imperative component of study design that influences results in downstream analyses.
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Affiliation(s)
| | | | | | | | - Mark P Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute
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Reinfeld BI, Madden MZ, Wolf MM, Chytil A, Bader JE, Patterson AR, Sugiura A, Cohen AS, Ali A, Do BT, Muir A, Lewis CA, Hongo RA, Young KL, Brown RE, Todd VM, Huffstater T, Abraham A, O'Neil RT, Wilson MH, Xin F, Tantawy MN, Merryman WD, Johnson RW, Williams CS, Mason EF, Mason FM, Beckermann KE, Vander Heiden MG, Manning HC, Rathmell JC, Rathmell WK. Cell-programmed nutrient partitioning in the tumour microenvironment. Nature 2021; 593:282-288. [PMID: 33828302 PMCID: PMC8122068 DOI: 10.1038/s41586-021-03442-1] [Citation(s) in RCA: 494] [Impact Index Per Article: 164.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 03/10/2021] [Indexed: 02/01/2023]
Abstract
Cancer cells characteristically consume glucose through Warburg metabolism1, a process that forms the basis of tumour imaging by positron emission tomography (PET). Tumour-infiltrating immune cells also rely on glucose, and impaired immune cell metabolism in the tumour microenvironment (TME) contributes to immune evasion by tumour cells2-4. However, whether the metabolism of immune cells is dysregulated in the TME by cell-intrinsic programs or by competition with cancer cells for limited nutrients remains unclear. Here we used PET tracers to measure the access to and uptake of glucose and glutamine by specific cell subsets in the TME. Notably, myeloid cells had the greatest capacity to take up intratumoral glucose, followed by T cells and cancer cells, across a range of cancer models. By contrast, cancer cells showed the highest uptake of glutamine. This distinct nutrient partitioning was programmed in a cell-intrinsic manner through mTORC1 signalling and the expression of genes related to the metabolism of glucose and glutamine. Inhibiting glutamine uptake enhanced glucose uptake across tumour-resident cell types, showing that glutamine metabolism suppresses glucose uptake without glucose being a limiting factor in the TME. Thus, cell-intrinsic programs drive the preferential acquisition of glucose and glutamine by immune and cancer cells, respectively. Cell-selective partitioning of these nutrients could be exploited to develop therapies and imaging strategies to enhance or monitor the metabolic programs and activities of specific cell populations in the TME.
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Affiliation(s)
- Bradley I Reinfeld
- Medical Scientist Training Program, Vanderbilt University, Nashville, TN, USA
- Department of Medicine, Vanderbilt University Medical Center (VUMC), Nashville, TN, USA
- Graduate Program in Cancer Biology, Vanderbilt University, Nashville, TN, USA
| | - Matthew Z Madden
- Medical Scientist Training Program, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, VUMC, Nashville, TN, USA
| | - Melissa M Wolf
- Department of Medicine, Vanderbilt University Medical Center (VUMC), Nashville, TN, USA
- Graduate Program in Cancer Biology, Vanderbilt University, Nashville, TN, USA
| | - Anna Chytil
- Department of Medicine, Vanderbilt University Medical Center (VUMC), Nashville, TN, USA
| | - Jackie E Bader
- Department of Pathology, Microbiology and Immunology, VUMC, Nashville, TN, USA
| | - Andrew R Patterson
- Department of Pathology, Microbiology and Immunology, VUMC, Nashville, TN, USA
| | - Ayaka Sugiura
- Medical Scientist Training Program, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, VUMC, Nashville, TN, USA
| | - Allison S Cohen
- Department of Radiology and Radiological Sciences, VUMC, Nashville, TN, USA
- Vanderbilt University Institute of Imaging Science, VUMC, Nashville, TN, USA
| | - Ahmed Ali
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Brian T Do
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Alexander Muir
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA
| | - Caroline A Lewis
- Whitehead Institute for Biomedical Research, MIT, Cambridge, MA, USA
| | - Rachel A Hongo
- Department of Medicine, Vanderbilt University Medical Center (VUMC), Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, VUMC, Nashville, TN, USA
| | - Kirsten L Young
- Department of Medicine, Vanderbilt University Medical Center (VUMC), Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, VUMC, Nashville, TN, USA
| | - Rachel E Brown
- Medical Scientist Training Program, Vanderbilt University, Nashville, TN, USA
- Department of Medicine, Vanderbilt University Medical Center (VUMC), Nashville, TN, USA
- Graduate Program in Cancer Biology, Vanderbilt University, Nashville, TN, USA
| | - Vera M Todd
- Department of Medicine, Vanderbilt University Medical Center (VUMC), Nashville, TN, USA
- Graduate Program in Cancer Biology, Vanderbilt University, Nashville, TN, USA
| | - Tessa Huffstater
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Abin Abraham
- Medical Scientist Training Program, Vanderbilt University, Nashville, TN, USA
- Vanderbilt Genetics Institute, VUMC, Nashville, TN, USA
| | - Richard T O'Neil
- Department of Medicine, Vanderbilt University Medical Center (VUMC), Nashville, TN, USA
- Department of Veterans Affairs, Tennessee Valley Health System, Nashville, TN, USA
| | - Matthew H Wilson
- Department of Medicine, Vanderbilt University Medical Center (VUMC), Nashville, TN, USA
- Department of Veterans Affairs, Tennessee Valley Health System, Nashville, TN, USA
| | - Fuxue Xin
- Department of Radiology and Radiological Sciences, VUMC, Nashville, TN, USA
- Vanderbilt University Institute of Imaging Science, VUMC, Nashville, TN, USA
| | - M Noor Tantawy
- Department of Radiology and Radiological Sciences, VUMC, Nashville, TN, USA
- Vanderbilt University Institute of Imaging Science, VUMC, Nashville, TN, USA
| | - W David Merryman
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Rachelle W Johnson
- Department of Medicine, Vanderbilt University Medical Center (VUMC), Nashville, TN, USA
| | - Christopher S Williams
- Department of Medicine, Vanderbilt University Medical Center (VUMC), Nashville, TN, USA
- Department of Veterans Affairs, Tennessee Valley Health System, Nashville, TN, USA
| | - Emily F Mason
- Department of Pathology, Microbiology and Immunology, VUMC, Nashville, TN, USA
| | - Frank M Mason
- Department of Medicine, Vanderbilt University Medical Center (VUMC), Nashville, TN, USA
| | | | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - H Charles Manning
- Department of Radiology and Radiological Sciences, VUMC, Nashville, TN, USA
- Vanderbilt University Institute of Imaging Science, VUMC, Nashville, TN, USA
| | - Jeffrey C Rathmell
- Department of Pathology, Microbiology and Immunology, VUMC, Nashville, TN, USA.
- Vanderbilt Center for Immunobiology and Vanderbilt-Ingram Cancer Center, VUMC, Nashville, TN, USA.
| | - W Kimryn Rathmell
- Department of Medicine, Vanderbilt University Medical Center (VUMC), Nashville, TN, USA.
- Vanderbilt Center for Immunobiology and Vanderbilt-Ingram Cancer Center, VUMC, Nashville, TN, USA.
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