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Nishio A, Bolte FJ, Takeda K, Park N, Yu ZX, Park H, Valdez K, Ghany MG, Rehermann B. Clearance of pegylated interferon by Kupffer cells limits NK cell activation and therapy response of patients with HBV infection. Sci Transl Med 2021; 13:13/587/eaba6322. [PMID: 33790025 DOI: 10.1126/scitranslmed.aba6322] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 02/24/2021] [Indexed: 12/12/2022]
Abstract
Pegylated interferon-α (PEG-IFN-α), where IFN-α is attached to polyethylene glycol (PEG), is an approved treatment for chronic hepatitis B virus (HBV) infection, a disease that causes liver-related morbidity and mortality in 257 million people worldwide. It is unknown why only a minority of patients respond to PEG-IFN-α. Using sequential blood samples and liver biopsies of patients with chronic HBV infection before, during, and after PEG-IFN-α treatment, we find that patients with early natural killer (NK) cell activation after PEG-IFN-α injection experienced greater liver inflammation, lysis of HBV-infected hepatocytes, and hepatitis B surface antigen (HBsAg) decline than those without. NK cell activation was associated with induction of interferon-stimulated genes and determined by PEG-IFN-α pharmacokinetics. Patients with delayed increases in PEG-IFN-α concentrations had greater amounts of PEG-specific immunoglobulin M (IgM) immune complexes in the blood and more PEG and IgM detected in the liver than patients with rapid increase in PEG-IFN-α concentration. This was associated with reduced NK cell activation. These results indicate that the immunomodulatory functions of PEG-IFN-α, particularly activation of NK cells, play a pivotal role in the response to treatment and further demonstrate that these functions are affected by PEG-IFN-α pharmacokinetics. Accelerated clearance of antibody-complexed pegylated drugs by Kupffer cells may be important beyond the field of HBV therapeutics. Thus, these findings may contribute to improving the efficacy of pegylated drugs that are now being developed for other chronic diseases and cancer.
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Affiliation(s)
- Akira Nishio
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Fabian J Bolte
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Kazuyo Takeda
- Pathology Core, National Heart, Lung and Blood Institute, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Nana Park
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Zu-Xi Yu
- Pathology Core, National Heart, Lung and Blood Institute, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Heiyoung Park
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Kristin Valdez
- Clinical Research Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Marc G Ghany
- Clinical Research Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Barbara Rehermann
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA.
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Russick J, Foy PE, Josseaume N, Meylan M, Hamouda NB, Kirilovsky A, Sissy CE, Tartour E, Smadja DM, Karras A, Hulot JS, Livrozet M, Fayol A, Arlet JB, Diehl JL, Dragon-Durey MA, Pagès F, Cremer I. Immune Signature Linked to COVID-19 Severity: A SARS-Score for Personalized Medicine. Front Immunol 2021; 12:701273. [PMID: 34322128 PMCID: PMC8312547 DOI: 10.3389/fimmu.2021.701273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/28/2021] [Indexed: 12/15/2022] Open
Abstract
SARS-CoV-2 infection leads to a highly variable clinical evolution, ranging from asymptomatic to severe disease with acute respiratory distress syndrome, requiring intensive care units (ICU) admission. The optimal management of hospitalized patients has become a worldwide concern and identification of immune biomarkers predictive of the clinical outcome for hospitalized patients remains a major challenge. Immunophenotyping and transcriptomic analysis of hospitalized COVID-19 patients at admission allow identifying the two categories of patients. Inflammation, high neutrophil activation, dysfunctional monocytic response and a strongly impaired adaptive immune response was observed in patients who will experience the more severe form of the disease. This observation was validated in an independent cohort of patients. Using in silico analysis on drug signature database, we identify differential therapeutics that specifically correspond to each group of patients. From this signature, we propose a score-the SARS-Score-composed of easily quantifiable biomarkers, to classify hospitalized patients upon arrival to adapt treatment according to their immune profile.
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Affiliation(s)
- Jules Russick
- Centre de Recherche des Cordeliers, Sorbonne Universite, Inserm, Universite de Paris, Team Inflammation, Complement and Cancer, Paris, France
| | - Pierre-Emmanuel Foy
- Centre de Recherche des Cordeliers, Sorbonne Universite, Inserm, Universite de Paris, Team Inflammation, Complement and Cancer, Paris, France
| | - Nathalie Josseaume
- Centre de Recherche des Cordeliers, Sorbonne Universite, Inserm, Universite de Paris, Team Inflammation, Complement and Cancer, Paris, France
| | - Maxime Meylan
- Centre de Recherche des Cordeliers, Sorbonne Universite, Inserm, Universite de Paris, Team Inflammation, Complement and Cancer, Paris, France
| | - Nadine Ben Hamouda
- Hopital Europeen Georges Pompidou, AP-HP, Paris, Universite de Paris, Paris, France
- Centre de Recherche des Cordeliers, Sorbonne Universite, Inserm, Universite de Paris, Team Integrative Cancer Immunology F-75006, Paris, France
- Sorbonne Universite, Paris, France
| | - Amos Kirilovsky
- Hopital Europeen Georges Pompidou, AP-HP, Paris, Universite de Paris, Paris, France
- Centre de Recherche des Cordeliers, Sorbonne Universite, Inserm, Universite de Paris, Team Integrative Cancer Immunology F-75006, Paris, France
- Sorbonne Universite, Paris, France
| | - Carine El Sissy
- Hopital Europeen Georges Pompidou, AP-HP, Paris, Universite de Paris, Paris, France
- Centre de Recherche des Cordeliers, Sorbonne Universite, Inserm, Universite de Paris, Team Integrative Cancer Immunology F-75006, Paris, France
- Sorbonne Universite, Paris, France
| | - Eric Tartour
- Department of Immunology, Hôpital Europeen Georges Pompidou, AP-HP, Paris, France
| | - David M. Smadja
- Université de Paris, Innovative Therapies in Hemostasis, INSERM, Hematology Department and Biosurgical Research Lab, (Carpentier Foundation) Assistance Publique Hôpitaux de Paris, Centre-Université de Paris (APHP-CUP), Paris, France
- F-CRIN INNOVTE, Saint-Étienne, France
| | - Alexandre Karras
- Department of Nephrology, Hopital Europeen Georges Pompidou, AP-HP, Paris, France
- Department of Nephrology, Universite de Paris, Paris, France
| | - Jean-Sébastien Hulot
- Université de Paris, INSERM, PARCC, Paris, France
- CIC1418 and DMU CARTE, AP-HP, Hôpital Européen Georges-Pompidou, Paris, France
| | - Marine Livrozet
- Université de Paris, INSERM, PARCC, Paris, France
- CIC1418 and DMU CARTE, AP-HP, Hôpital Européen Georges-Pompidou, Paris, France
| | - Antoine Fayol
- Université de Paris, INSERM, PARCC, Paris, France
- CIC1418 and DMU CARTE, AP-HP, Hôpital Européen Georges-Pompidou, Paris, France
| | - Jean-Benoit Arlet
- Department of Nephrology, Universite de Paris, Paris, France
- Department of Internal Medicine, Hopital Europeen Georges Pompidou, AP-HP, Paris, France
| | - Jean-Luc Diehl
- Université de Paris, Innovative Therapies in Haemostasis, INSERM, Paris, France
- Intensive Care Unit and Biosurgical Research Lab (Carpentier Foundation), AH-HP, Georges Pompidou European Hospital, Paris, France
| | - Marie-Agnès Dragon-Durey
- Centre de Recherche des Cordeliers, Sorbonne Universite, Inserm, Universite de Paris, Team Inflammation, Complement and Cancer, Paris, France
- Hopital Europeen Georges Pompidou, AP-HP, Paris, Universite de Paris, Paris, France
- Centre de Recherche des Cordeliers, Sorbonne Universite, Inserm, Universite de Paris, Team Integrative Cancer Immunology F-75006, Paris, France
- Sorbonne Universite, Paris, France
| | - Franck Pagès
- Hopital Europeen Georges Pompidou, AP-HP, Paris, Universite de Paris, Paris, France
- Centre de Recherche des Cordeliers, Sorbonne Universite, Inserm, Universite de Paris, Team Integrative Cancer Immunology F-75006, Paris, France
- Sorbonne Universite, Paris, France
| | - Isabelle Cremer
- Centre de Recherche des Cordeliers, Sorbonne Universite, Inserm, Universite de Paris, Team Inflammation, Complement and Cancer, Paris, France
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Laar RV, King S, McCoy R, Saad M, Fereday S, Winship I, Uzzell C, Landgren A. Translation of a circulating miRNA signature of melanoma into a solid tissue assay to improve diagnostic accuracy and precision. Biomark Med 2021; 15:1111-1122. [PMID: 34184547 DOI: 10.2217/bmm-2021-0289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: Successful treatment of cutaneous melanoma depends on early and accurate diagnosis of clinically suspicious melanocytic skin lesions. Multiple international studies have described the challenge of providing accurate and reproducible histopathological assessments of melanocytic lesions, highlighting the need for new diagnostic tools including disease-specific biomarkers. Previously, a 38-miRNA signature (MEL38) was identified in melanoma patient plasma and validated as a novel biomarker. In this study, MEL38 expression in solid tissue biopsies representing the benign nevi to metastatic melanoma spectrum is examined. Patients & methods: Nanostring digital gene expression assessment of the MEL38 signature was performed on 308 formalin-fixed paraffin-embedded biopsies of nevi, melanoma in situ and invasive melanoma. Genomic data were interrogated using hierarchical clustering, univariate and multivariate statistical approaches. Classification scores computed from the MEL38 signature were analyzed for their association with demographic data and histopathology results, including MPATH-DX class, AJCC disease stage and tissue subtype. Results: The MEL38 score can stratify higher-risk melanomas (MPATH-Dx class V or more advanced) from lower-risk skin lesions (class I-IV) with an area under the curve of 0.97 (p < 0.001). The genomic score ranges from 0 to 10 and is positively correlated with melanoma progression, with an intraclass correlation coefficient of 0.85 with stage 0-IV disease. Using an optimized classification threshold of ≥2.7 accurately identifies higher-risk melanomas with 89% sensitivity and 94% specificity. Multivariate analysis showed the score to be a significant predictor of malignancy, independent of technical and clinical covariates. Application of the MEL38 signature to Spitz nevi reveals an intrasubtype profile, with elements in common to both nevi and melanoma. Conclusion: Melanoma-specific circulating miRNAs maintain their association with malignancy when measured in the hypothesized tissue of origin. The MEL38 signature is an accurate and reproducible metric of melanoma status, based on changes in miRNA expression that occur as the disease develops and spreads. Inclusion of the MEL38 score into routine practice would provide physicians with previously unavailable, personalized genomic information about their patient's skin lesions. Combining molecular biomarker data with conventional histopathology data may improve diagnostic accuracy, healthcare resource utilization and patient outcomes.
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Affiliation(s)
- Ryan Van Laar
- Geneseq Biosciences, 555 St Kilda Road, Melbourne, Victoria, 3004, Australia
| | - Samuel King
- Australian Clinical Labs, 1868 Dandenong Road, Clayton, Victoria, 3168, Australia
| | - Richard McCoy
- Australian Clinical Labs, 1868 Dandenong Road, Clayton, Victoria, 3168, Australia
| | - Mirette Saad
- Australian Clinical Labs, 1868 Dandenong Road, Clayton, Victoria, 3168, Australia
| | - Sian Fereday
- Geneseq Biosciences, 555 St Kilda Road, Melbourne, Victoria, 3004, Australia
| | - Ingrid Winship
- Geneseq Biosciences, 555 St Kilda Road, Melbourne, Victoria, 3004, Australia
| | - Catherine Uzzell
- Australian Clinical Labs, 1868 Dandenong Road, Clayton, Victoria, 3168, Australia
| | - Anthony Landgren
- Australian Clinical Labs, 1868 Dandenong Road, Clayton, Victoria, 3168, Australia
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Mahurkar-Joshi S, Rankin CR, Videlock EJ, Soroosh A, Verma A, Khandadash A, Iliopoulos D, Pothoulakis C, Mayer EA, Chang L. The Colonic Mucosal MicroRNAs, MicroRNA-219a-5p, and MicroRNA-338-3p Are Downregulated in Irritable Bowel Syndrome and Are Associated With Barrier Function and MAPK Signaling. Gastroenterology 2021; 160:2409-2422.e19. [PMID: 33617890 PMCID: PMC8169529 DOI: 10.1053/j.gastro.2021.02.040] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 02/03/2021] [Accepted: 02/17/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS Alterations in microRNA (miRNA) and in the intestinal barrier are putative risk factors for irritable bowel syndrome (IBS). We aimed to identify differentially expressed colonic mucosal miRNAs, their targets in IBS compared to healthy controls (HCs), and putative downstream pathways. METHODS Twenty-nine IBS patients (15 IBS with constipation [IBS-C], 14 IBS with diarrhea [IBS-D]), and 15 age-matched HCs underwent sigmoidoscopy with biopsies. A nCounter array was used to assess biopsy specimen-associated miRNA levels. A false discovery rate (FDR) < 10% was considered significant. Real-time polymerase chain reaction (PCR) was used to validate differentially expressed genes. To assess barrier function, trans-epithelial electrical resistance (TEER) and dextran flux assays were performed on Caco-2 intestinal epithelial cells that were transfected with miRNA-inhibitors or control inhibitors. Protein expression of barrier function associated genes was confirmed using western blots. RESULTS Four out of 247 miRNAs tested were differentially expressed in IBS compared to HCs (FDR < 10%). Real-time PCR validation suggested decreased levels of miR-219a-5p and miR-338-3p in IBS (P = .026 and P = .004), and IBS-C (P = .02 and P = .06) vs. HCs as the strongest associations. Inhibition of miR-219a-5p resulted in altered expression of proteasome/barrier function genes. Functionally, miR-219a-5p inhibition enhanced the permeability of intestinal epithelial cells as TEER was reduced (25-50%, P < .05) and dextran flux was increased (P < .01). Additionally, inhibition of miR-338-3p in cells caused alterations in the mitogen-activated protein kinase (MAPK) signaling pathway genes. CONCLUSION Two microRNAs that potentially affect permeability and visceral nociception were identified to be altered in IBS patients. MiR-219a-5p and miR-338-3p potentially alter barrier function and visceral hypersensitivity via neuronal and MAPK signaling and could be therapeutic targets in IBS.
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Affiliation(s)
- Swapna Mahurkar-Joshi
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, Division of Digestive Diseases, Department of Medicine at UCLA
| | - Carl Robert Rankin
- UCLA Center for Inflammatory Bowel Diseases, Division of Digestive Diseases, Department of Medicine at UCLA
| | - Elizabeth Jane Videlock
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, Division of Digestive Diseases, Department of Medicine at UCLA
| | - Artin Soroosh
- UCLA Center for Inflammatory Bowel Diseases, Division of Digestive Diseases, Department of Medicine at UCLA
| | - Abhishek Verma
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, Division of Digestive Diseases, Department of Medicine at UCLA
| | - Ariela Khandadash
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, Division of Digestive Diseases, Department of Medicine at UCLA
| | - Dimitrios Iliopoulos
- UCLA Center for Inflammatory Bowel Diseases, Division of Digestive Diseases, Department of Medicine at UCLA
| | - Charalabos Pothoulakis
- UCLA Center for Inflammatory Bowel Diseases, Division of Digestive Diseases, Department of Medicine at UCLA
| | - Emeran A Mayer
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, Division of Digestive Diseases, Department of Medicine at UCLA
| | - Lin Chang
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, Division of Digestive Diseases, Department of Medicine, University of California, Los Angeles, Los Angeles, California.
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55
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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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56
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de Mingo Pulido Á, Hänggi K, Celias DP, Gardner A, Li J, Batista-Bittencourt B, Mohamed E, Trillo-Tinoco J, Osunmakinde O, Peña R, Onimus A, Kaisho T, Kaufmann J, McEachern K, Soliman H, Luca VC, Rodriguez PC, Yu X, Ruffell B. The inhibitory receptor TIM-3 limits activation of the cGAS-STING pathway in intra-tumoral dendritic cells by suppressing extracellular DNA uptake. Immunity 2021; 54:1154-1167.e7. [PMID: 33979578 DOI: 10.1016/j.immuni.2021.04.019] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 02/24/2021] [Accepted: 04/16/2021] [Indexed: 12/17/2022]
Abstract
Blockade of the inhibitory receptor TIM-3 shows efficacy in cancer immunotherapy clinical trials. TIM-3 inhibits production of the chemokine CXCL9 by XCR1+ classical dendritic cells (cDC1), thereby limiting antitumor immunity in mammary carcinomas. We found that increased CXCL9 expression by splenic cDC1s upon TIM-3 blockade required type I interferons and extracellular DNA. Chemokine expression as well as combinatorial efficacy of TIM-3 blockade and paclitaxel chemotherapy were impaired by deletion of Cgas and Sting. TIM-3 blockade increased uptake of extracellular DNA by cDC1 through an endocytic process that resulted in cytoplasmic localization. DNA uptake and efficacy of TIM-3 blockade required DNA binding by HMGB1, while galectin-9-induced cell surface clustering of TIM-3 was necessary for its suppressive function. Human peripheral blood cDC1s also took up extracellular DNA upon TIM-3 blockade. Thus, TIM-3 regulates endocytosis of extracellular DNA and activation of the cytoplasmic DNA sensing cGAS-STING pathway in cDC1s, with implications for understanding the mechanisms underlying TIM-3 immunotherapy.
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Affiliation(s)
- Álvaro de Mingo Pulido
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Kay Hänggi
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Daiana P Celias
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Alycia Gardner
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; Cancer Biology PhD Program, University of South Florida, Tampa, FL 33620, USA
| | - Jie Li
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; Cancer Biology PhD Program, University of South Florida, Tampa, FL 33620, USA
| | - Bruna Batista-Bittencourt
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; Cancer Biology PhD Program, University of South Florida, Tampa, FL 33620, USA
| | - Eslam Mohamed
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Jimena Trillo-Tinoco
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Olabisi Osunmakinde
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; Cancer Biology PhD Program, University of South Florida, Tampa, FL 33620, USA; Department of Health Science and Technology, Aalborg University, Aalborg 29220, Denmark
| | - Reymi Peña
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Alexis Onimus
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; Molecular Medicine PhD Program, University of South Florida, Tampa, FL 33620, USA
| | - Tsuneyasu Kaisho
- Institute for Advanced Medicine, Wakayama Medical University, Wakayama 641-8509, Japan
| | - Johanna Kaufmann
- Immuno-Oncology & Combinations Research Unit, GSK, Waltham, MA 02451, USA
| | | | - Hatem Soliman
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; Department of Breast Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Vincent C Luca
- Department of Drug Discovery, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Paulo C Rodriguez
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Xiaoqing Yu
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Brian Ruffell
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; Department of Breast Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.
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Linnaranta O, Trontti KT, Honkanen J, Hovatta I, Keinänen J, Suvisaari J. Peripheral metabolic state and immune system in first-episode psychosis - A gene expression study with a prospective one-year follow-up. J Psychiatr Res 2021; 137:383-392. [PMID: 33765450 DOI: 10.1016/j.jpsychires.2021.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 03/02/2021] [Accepted: 03/05/2021] [Indexed: 12/19/2022]
Abstract
he excess availability of glucose and lipids can also have an impact on the dynamics of activation and regulation of peripheral immune cellsWe aimed at understanding the correlations between peripheral metabolic state and immune system during the first year in first-episode psychosis (FEP). Patients with FEP (n = 67) and matched controls (n = 38), aged 18-40 years, were met at baseline, 2 and 12 months. Fasting peripheral blood samples were collected. We applied the NanoString nCounter in-solution hybridization technology to determine gene expression levels of 178 candidate genes reflecting activation of the immune system. Serum triglycerides, high-density lipoprotein (HDL), low-density lipoprotein (LDL) cholesterol and insulin and plasma glucose (fP-Gluc) were measured. We applied Ingenuity Pathway Analysis (IPA) to visualize enrichment of genes to functional classes. Strength of positive or negative regulation of the disease and functional pathways was deduced from IPA activation Z-score at the three evaluation points. We correlated gene expression with plasma glucose, triglycerids and HDL and LDL, and used hierarchical clustering of the pairwise correlations to identify groups of genes with similar correlation patterns with metabolic markers. In patients, initially, genes associated with the innate immune system response pathways were upregulated, which decreased by 12 months. Furthermore, genes associated with apoptosis and T cell death were downregulated, and genes associated with lipid metabolism were increasingly downregulated by 12 months. The immune activation was thus an acute phase during illness onset. At baseline, after controlling for multiple testing, 31/178 genes correlated positively with fasting glucose levels, and 54/178 genes negatively with triglycerides in patients only. The gene clusters showed patterns of correlations with metabolic markers over time. The results suggest a functional link between peripheral immune system and metabolic state in FEP. Metabolic factors may have had an influence on the initial activation of the innate immune system. Future work is necessary to understand the role of metabolic state in the regulation of immune response in the early phases of psychosis.
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Affiliation(s)
- Outi Linnaranta
- Department of Psychiatry, McGill University, Montreal, QC, Canada; Douglas Centre for Sleep and Biological Rhythms, Douglas Mental Health University Institute, 6875 LaSalle Boulevard, H4H 1R3, Montreal, QC, Canada; Department of Public Health Solutions, Mental Health Unit, Finnish Institute for Health and Welfare, P.O. Box 30, FI-00271, Helsinki, Finland.
| | - Kalevi T Trontti
- Sleep Well Research Program, Faculty of Medicine, P.O. Box 21, FI-00014, University of Helsinki, Finland; Neuroscience Center, Helsinki Institute of Life Science HiLIFE, P.O. Box 21, FI-00014, University of Helsinki, Finland
| | - Jarno Honkanen
- Research Program for Clinical and Molecular Metabolism, P.O. Box 63, FI-00014, University of Helsinki, Helsinki, Finland
| | - Iiris Hovatta
- Sleep Well Research Program, Faculty of Medicine, P.O. Box 21, FI-00014, University of Helsinki, Finland; Neuroscience Center, Helsinki Institute of Life Science HiLIFE, P.O. Box 21, FI-00014, University of Helsinki, Finland; Department of Psychology and Logopedics, Medicum, P.O. Box 21, FI-00014, University of Helsinki, Finland
| | - Jaakko Keinänen
- Department of Public Health Solutions, Mental Health Unit, Finnish Institute for Health and Welfare, P.O. Box 30, FI-00271, Helsinki, Finland; Department of Psychiatry, University of Helsinki and Helsinki University Hospital, P.O. Box 590, FI-00029, Helsinki, Finland
| | - Jaana Suvisaari
- Department of Public Health Solutions, Mental Health Unit, Finnish Institute for Health and Welfare, P.O. Box 30, FI-00271, Helsinki, Finland
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Hatscher L, Lehmann CHK, Purbojo A, Onderka C, Liang C, Hartmann A, Cesnjevar R, Bruns H, Gross O, Nimmerjahn F, Ivanović-Burmazović I, Kunz M, Heger L, Dudziak D. Select hyperactivating NLRP3 ligands enhance the T H1- and T H17-inducing potential of human type 2 conventional dendritic cells. Sci Signal 2021; 14:14/680/eabe1757. [PMID: 33906973 DOI: 10.1126/scisignal.abe1757] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The detection of microorganisms and danger signals by pattern recognition receptors on dendritic cells (DCs) and the consequent formation of inflammasomes are pivotal for initiating protective immune responses. Although the activation of inflammasomes leading to secretion of the cytokine IL-1β is typically accompanied by pyroptosis (an inflammatory form of lytic programmed cell death), some cells can survive and exist in a state of hyperactivation. Here, we found that the conventional type 2 DC (cDC2) subset is the major human DC subset that is transcriptionally and functionally poised for inflammasome formation and response without pyroptosis. When cDC2 were stimulated with ligands that relatively weakly activated the inflammasome, the cells did not enter pyroptosis but instead secreted IL-12 family cytokines and IL-1β. These cytokines induced prominent T helper type 1 (TH1) and TH17 responses that were superior to those seen in response to Toll-like receptor (TLR) stimulation alone or to stronger, classical inflammasome ligands. These findings not only define the human cDC2 subpopulation as a prime target for the treatment of inflammasome-dependent inflammatory diseases but may also inform new approaches for adjuvant and vaccine development.
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Affiliation(s)
- Lukas Hatscher
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, 91052 Erlangen, Germany
| | - Christian H K Lehmann
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, 91052 Erlangen, Germany
| | - Ariawan Purbojo
- Department of Pediatric Cardiac Surgery, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Constantin Onderka
- Department of Chemistry and Pharmacy, Friedrich-Alexander University Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Chunguang Liang
- Chair of Medical Informatics, Friedrich-Alexander University Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Arndt Hartmann
- Department of Pathology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Robert Cesnjevar
- Department of Pediatric Cardiac Surgery, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Heiko Bruns
- Department of Internal Medicine 5-Hematology/Oncology, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Olaf Gross
- Institute of Neuropathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany.,Center for Basics in NeuroModulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Falk Nimmerjahn
- Institute of Genetics, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
| | - Ivana Ivanović-Burmazović
- Department of Chemistry and Pharmacy, Friedrich-Alexander University Erlangen-Nürnberg, 91058 Erlangen, Germany.,Department Chemistry, Ludwigs Maximilians University, 81377 Munich, Germany
| | - Meik Kunz
- Chair of Medical Informatics, Friedrich-Alexander University Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Lukas Heger
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, 91052 Erlangen, Germany
| | - Diana Dudziak
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, 91052 Erlangen, Germany. .,Institute of Genetics, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany.,Deutsches Zentrum Immuntherapie, 91054 Erlangen, Germany.,Comprehensive Cancer Center Erlangen-European Metropolitan Area of Nuremberg, 91054 Erlangen, Germany.,Medical Immunology Campus Erlangen, 91054 Erlangen, Germany
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59
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Crist AM, Hinkle KM, Wang X, Moloney CM, Matchett BJ, Labuzan SA, Frankenhauser I, Azu NO, Liesinger AM, Lesser ER, Serie DJ, Quicksall ZS, Patel TA, Carnwath TP, DeTure M, Tang X, Petersen RC, Duara R, Graff-Radford NR, Allen M, Carrasquillo MM, Li H, Ross OA, Ertekin-Taner N, Dickson DW, Asmann YW, Carter RE, Murray ME. Transcriptomic analysis to identify genes associated with selective hippocampal vulnerability in Alzheimer's disease. Nat Commun 2021; 12:2311. [PMID: 33875655 PMCID: PMC8055900 DOI: 10.1038/s41467-021-22399-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 03/03/2021] [Indexed: 12/14/2022] Open
Abstract
Selective vulnerability of different brain regions is seen in many neurodegenerative disorders. The hippocampus and cortex are selectively vulnerable in Alzheimer's disease (AD), however the degree of involvement of the different brain regions differs among patients. We classified corticolimbic patterns of neurofibrillary tangles in postmortem tissue to capture extreme and representative phenotypes. We combined bulk RNA sequencing with digital pathology to examine hippocampal vulnerability in AD. We identified hippocampal gene expression changes associated with hippocampal vulnerability and used machine learning to identify genes that were associated with AD neuropathology, including SERPINA5, RYBP, SLC38A2, FEM1B, and PYDC1. Further histologic and biochemical analyses suggested SERPINA5 expression is associated with tau expression in the brain. Our study highlights the importance of embracing heterogeneity of the human brain in disease to identify disease-relevant gene expression.
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Affiliation(s)
- Angela M Crist
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Kelly M Hinkle
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Xue Wang
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | | | | | | | - Isabelle Frankenhauser
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Paracelsus Medical Private University, Salzburg, Austria
| | - Nkem O Azu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Elizabeth R Lesser
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | - Daniel J Serie
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | | | - Tulsi A Patel
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Troy P Carnwath
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Michael DeTure
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Xiaojia Tang
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | | | - Ranjan Duara
- Wien Center for Alzheimer's Disease and Memory Disorders, Mount Sinai Medical Center, Miami Beach, FL, USA
| | | | - Mariet Allen
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Owen A Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Department of Neurology, Mayo Clinic, Jacksonville, FL, USA
| | | | - Yan W Asmann
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | - Rickey E Carter
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
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60
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Savage AK, Gutschow MV, Chiang T, Henderson K, Green R, Chaudhari M, Swanson E, Heubeck AT, Kondza N, Burley KC, Genge PC, Lord C, Smith T, Thomson Z, Beaubien A, Johnson E, Goldy J, Bolouri H, Buckner JH, Meijer P, Coffey EM, Skene PJ, Torgerson TR, Li XJ, Bumol TF. Multimodal analysis for human ex vivo studies shows extensive molecular changes from delays in blood processing. iScience 2021; 24:102404. [PMID: 34113805 PMCID: PMC8169801 DOI: 10.1016/j.isci.2021.102404] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/28/2021] [Accepted: 04/06/2021] [Indexed: 12/04/2022] Open
Abstract
Multi-omic profiling of human peripheral blood is increasingly utilized to identify biomarkers and pathophysiologic mechanisms of disease. The importance of these platforms in clinical and translational studies led us to investigate the impact of delayed blood processing on the numbers and state of peripheral blood mononuclear cells (PBMC) and on the plasma proteome. Similar to previous studies, we show minimal effects of delayed processing on the numbers and general phenotype of PBMC up to 18 hours. In contrast, profound changes in the single-cell transcriptome and composition of the plasma proteome become evident as early as 6 hours after blood draw. These reflect patterns of cellular activation across diverse cell types that lead to progressive distancing of the gene expression state and plasma proteome from native in vivo biology. Differences accumulating during an overnight rest (18 hours) could confound relevant biologic variance related to many underlying disease states. Studies of human blood cells and plasma are highly sensitive to process variability Time variability distorts biology in cutting-edge single-cell and multiplex assays Longitudinal, multi-modal, and aligned data enable data qualification and exploration Dataset holds potential novel, multi-modal biological correlations and hypotheses
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Affiliation(s)
- Adam K Savage
- Allen Institute for Immunology, Seattle, WA 98109, USA
| | | | - Tony Chiang
- Allen Institute for Immunology, Seattle, WA 98109, USA
| | | | - Richard Green
- Allen Institute for Immunology, Seattle, WA 98109, USA
| | | | | | | | - Nina Kondza
- Allen Institute for Immunology, Seattle, WA 98109, USA
| | | | - Palak C Genge
- Allen Institute for Immunology, Seattle, WA 98109, USA
| | - Cara Lord
- Allen Institute for Immunology, Seattle, WA 98109, USA
| | - Tanja Smith
- Allen Institute for Immunology, Seattle, WA 98109, USA
| | | | | | - Ed Johnson
- Allen Institute for Immunology, Seattle, WA 98109, USA
| | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Hamid Bolouri
- Center for Systems Immunology, Benaroya Research Institute, Seattle, WA 98101, USA
| | - Jane H Buckner
- Center for Translational Research, Benaroya Research Institute, Seattle, WA 98101, USA
| | - Paul Meijer
- Allen Institute for Immunology, Seattle, WA 98109, USA
| | | | - Peter J Skene
- Allen Institute for Immunology, Seattle, WA 98109, USA
| | | | - Xiao-Jun Li
- Allen Institute for Immunology, Seattle, WA 98109, USA
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61
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Feliciano RDS, Atum ALB, Ruiz ÉGDS, Serra AJ, Antônio EL, Manchini MT, Silva JMA, Tucci PJF, Nathanson L, Morris M, Chavantes MC, Silva Júnior JA. Photobiomodulation Therapy on Myocardial Infarction in Rats: Transcriptional and Posttranscriptional Implications to Cardiac Remodeling. Lasers Surg Med 2021; 53:1247-1257. [PMID: 33846991 DOI: 10.1002/lsm.23407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 03/15/2021] [Accepted: 03/22/2021] [Indexed: 01/29/2023]
Abstract
BACKGROUND AND OBJECTIVES Induction of myocardial infarction (MI) in rats by occlusion of the left anterior descending coronary artery is an experimental model used in research to elucidate functional, structural, and molecular modifications associated with ischemic heart disease. Photobiomodulation therapy (PBMT) has become a therapeutic alternative by modulating various biological processes eliciting several effects, including anti-inflammatory and pro-proliferative actions. The main objective of this work was to evaluate the effect of PBMT in the modulation of transcriptional and post-transcriptional changes that occurred in myocardium signal transduction pathways after MI. STUDY DESIGN/MATERIALS AND METHODS Continuous wave (CW) non-thermal laser parameters were: 660 nm wavelength, power 15 mW, with a total energy of 0.9 J, fluence of 1.15 J/cm2 , spot size of 0.785 cm2 , and time of 60 seconds. Using in silico analysis, we selected and then, quantified the expression of messenger RNA (mRNA) of 47 genes of 9 signaling pathways associated with MI (angiogenesis, cell survival, hypertrophy, oxidative stress, apoptosis, extracellular matrix, calcium kinetics, cell metabolism, and inflammation). Messenger RNA expression quantification was performed in myocardial samples by polymerase chain reaction real-time array using TaqMan customized plates. RESULTS Our results evidenced that MI modified mRNA expression of several well-known biomarkers related to detrimental cardiac activity in almost all signaling pathways analyzed. However, PBMT reverted most of these transcriptional changes. More expressively, PBMT provoked a robust decrease in mRNA expression of molecules that participate in post-MI inflammation and ECM composition, such as IL-6, TNF receptor, TGFb1, and collagen I and III. Global microRNA (miRNA) expression analysis revealed that PBMT decreased miR-221, miR-34c, and miR-93 expressions post-MI, which are related to deleterious effects in cardiac remodeling. CONCLUSION Thus, the identification of transcriptional and post-transcriptional changes induced by PBMT may be used to interfere in the molecular dynamics of cardiac remodeling post-MI.
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Affiliation(s)
| | | | | | - Andrey Jorge Serra
- Universidade Federal de São Paulo, Rua Pedro de Toledo 709, Vila Clementino, São Paulo, SP, 04039-001, Brazil
| | - Ednei Luiz Antônio
- Universidade Federal de São Paulo, Rua Pedro de Toledo 709, Vila Clementino, São Paulo, SP, 04039-001, Brazil
| | | | | | - Paulo José Ferreira Tucci
- Universidade Federal de São Paulo, Rua Pedro de Toledo 709, Vila Clementino, São Paulo, SP, 04039-001, Brazil
| | - Lubov Nathanson
- Nova Southeastern University, 3301 College Avenue, Fort Lauderdale, Florida, 33314
| | - Mariana Morris
- Nova Southeastern University, 3301 College Avenue, Fort Lauderdale, Florida, 33314
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62
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Brcic L, Mathilakathu A, Walter RFH, Wessolly M, Mairinger E, Beckert H, Kreidt D, Steinborn J, Hager T, Christoph DC, Kollmeier J, Mairinger T, Wohlschlaeger J, Schmid KW, Borchert S, Mairinger FD. Digital Gene Expression Analysis of Epithelioid and Sarcomatoid Mesothelioma Reveals Differences in Immunogenicity. Cancers (Basel) 2021; 13:1761. [PMID: 33917061 PMCID: PMC8067687 DOI: 10.3390/cancers13081761] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/29/2021] [Accepted: 04/02/2021] [Indexed: 02/08/2023] Open
Abstract
Malignant pleural mesothelioma (MPM) is an aggressive malignancy associated with asbestos exposure. Median survival ranges from 14 to 20 months after initial diagnosis. As of November 2020, the FDA approved a combination of immune checkpoint inhibitors after promising intermediate results. Nonetheless, responses remain unsatisfying. Adequate patient stratification to improve response rates is still lacking. This retrospective study analyzed formalin fixed paraffin embedded specimens from a cohort of 22 MPM. Twelve of those samples showed sarcomatoid, ten epithelioid differentiation. Complete follow-up, including radiological assessment of response by modRECIST and time to death, was available with reported deaths of all patients. RNA of all samples was isolated and subjected to digital gene expression pattern analysis. Our study revealed a notable difference between epithelioid and sarcomatoid mesothelioma, showing differential gene expression for 304/698 expressed genes. Whereas antigen processing and presentation to resident cytotoxic T cells as well as phagocytosis is highly affected in sarcomatoid mesothelioma, cell-cell interaction via cytokines seems to be of greater importance in epithelioid cases. Our work reveals the specific role of the immune system within the different histologic subtypes of MPM, providing a more detailed background of their immunogenic potential. This is of great interest regarding therapeutic strategies including immunotherapy in mesothelioma.
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Affiliation(s)
- Luka Brcic
- Diagnostic and Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria;
| | - Alexander Mathilakathu
- Institute of Pathology, University Hospital Essen, University of Duisburg Essen, 45147 Essen, Germany; (A.M.); (R.F.H.W.); (M.W.); (E.M.); (D.K.); (J.S.); (T.H.); (K.W.S.); (S.B.)
| | - Robert F. H. Walter
- Institute of Pathology, University Hospital Essen, University of Duisburg Essen, 45147 Essen, Germany; (A.M.); (R.F.H.W.); (M.W.); (E.M.); (D.K.); (J.S.); (T.H.); (K.W.S.); (S.B.)
| | - Michael Wessolly
- Institute of Pathology, University Hospital Essen, University of Duisburg Essen, 45147 Essen, Germany; (A.M.); (R.F.H.W.); (M.W.); (E.M.); (D.K.); (J.S.); (T.H.); (K.W.S.); (S.B.)
| | - Elena Mairinger
- Institute of Pathology, University Hospital Essen, University of Duisburg Essen, 45147 Essen, Germany; (A.M.); (R.F.H.W.); (M.W.); (E.M.); (D.K.); (J.S.); (T.H.); (K.W.S.); (S.B.)
| | - Hendrik Beckert
- Department of Pulmonary Medicine, University Hospital Essen—Ruhrlandklinik, 45239 Essen, Germany;
| | - Daniel Kreidt
- Institute of Pathology, University Hospital Essen, University of Duisburg Essen, 45147 Essen, Germany; (A.M.); (R.F.H.W.); (M.W.); (E.M.); (D.K.); (J.S.); (T.H.); (K.W.S.); (S.B.)
| | - Julia Steinborn
- Institute of Pathology, University Hospital Essen, University of Duisburg Essen, 45147 Essen, Germany; (A.M.); (R.F.H.W.); (M.W.); (E.M.); (D.K.); (J.S.); (T.H.); (K.W.S.); (S.B.)
| | - Thomas Hager
- Institute of Pathology, University Hospital Essen, University of Duisburg Essen, 45147 Essen, Germany; (A.M.); (R.F.H.W.); (M.W.); (E.M.); (D.K.); (J.S.); (T.H.); (K.W.S.); (S.B.)
| | - Daniel C. Christoph
- Department of Medical Oncology, Evang. Kliniken Essen-Mitte, 45136 Essen, Germany;
| | - Jens Kollmeier
- Department of Pneumology, Helios Klinikum Emil von Behring, 14165 Berlin, Germany;
| | - Thomas Mairinger
- Department of Tissue Diagnostics, Helios Klinikum Emil von Behring, 14165 Berlin, Germany;
| | | | - Kurt Werner Schmid
- Institute of Pathology, University Hospital Essen, University of Duisburg Essen, 45147 Essen, Germany; (A.M.); (R.F.H.W.); (M.W.); (E.M.); (D.K.); (J.S.); (T.H.); (K.W.S.); (S.B.)
| | - Sabrina Borchert
- Institute of Pathology, University Hospital Essen, University of Duisburg Essen, 45147 Essen, Germany; (A.M.); (R.F.H.W.); (M.W.); (E.M.); (D.K.); (J.S.); (T.H.); (K.W.S.); (S.B.)
| | - Fabian D. Mairinger
- Diagnostic and Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria;
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Budakoti M, Panwar AS, Molpa D, Singh RK, Büsselberg D, Mishra AP, Coutinho HDM, Nigam M. Micro-RNA: The darkhorse of cancer. Cell Signal 2021; 83:109995. [PMID: 33785398 DOI: 10.1016/j.cellsig.2021.109995] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 03/25/2021] [Accepted: 03/25/2021] [Indexed: 12/21/2022]
Abstract
The discovery of micro RNAs (miRNA) in cancer has opened up new vistas for researchers in recent years. Micro RNAs area set of small, endogenous, highly conserved, non-coding RNAs that control the expression of about 30% genes at post-transcriptional levels. Typically, microRNAs impede the translation and stability of messenger RNAs (mRNA), control genes associated with cellular processes namely inflammation, cell cycle regulation, stress response, differentiation, apoptosis, and migration. Compelling findings revealed that miRNA mutations or disruption correspond to diverse human cancers and suggest that miRNAs can function as tumor suppressors or oncogenes. Here we summarize the literature on these master regulators in clinical settings from last three decades as both abrupt cancer therapeutics and as an approach to sensitize tumors to chemotherapy. This review highlights (I) the prevailing perception of miRNA genomics, biogenesis, as well as function; (II) the significant advancements in regulatory mechanisms in the expression of carcinogenic genes; and (III) explains, how miRNA is utilized as a diagnostic and prognostic biomarker for the disease stage indicating survival as well as therapeutic targets in cancer.
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Affiliation(s)
- Mridul Budakoti
- Department of Biochemistry, H. N. B. Garhwal University, Srinagar Garhwal 246174, Uttarakhand, India
| | - Abhay Shikhar Panwar
- Department of Biochemistry, H. N. B. Garhwal University, Srinagar Garhwal 246174, Uttarakhand, India
| | - Diksha Molpa
- Department of Biochemistry, H. N. B. Garhwal University, Srinagar Garhwal 246174, Uttarakhand, India
| | - Rahul Kunwar Singh
- Department of Microbiology, H. N. B. Garhwal University, Srinagar Garhwal 246174, Uttarakhand, India
| | - Dietrich Büsselberg
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha 24144, Qatar.
| | - Abhay Prakash Mishra
- Department of Pharmaceutical Chemistry, H. N. B. Garhwal University, Srinagar Garhwal 246174, Uttarakhand, India.
| | | | - Manisha Nigam
- Department of Biochemistry, H. N. B. Garhwal University, Srinagar Garhwal 246174, Uttarakhand, India.
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64
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Howe CG, Foley HB, Kennedy EM, Eckel SP, Chavez TA, Faham D, Grubbs BH, Al-Marayati L, Lerner D, Suglia S, Bastain TM, Marsit CJ, Breton CV. Extracellular vesicle microRNA in early versus late pregnancy with birth outcomes in the MADRES study. Epigenetics 2021; 17:269-285. [PMID: 33734019 DOI: 10.1080/15592294.2021.1899887] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Circulating miRNA may contribute to the development of adverse birth outcomes. However, few studies have investigated extracellular vesicle (EV) miRNA, which play important roles in intercellular communication, or compared miRNA at multiple time points in pregnancy. In the current study, 800 miRNA were profiled for EVs from maternal plasma collected in early (median: 12.5 weeks) and late (median: 31.8 weeks) pregnancy from 156 participants in the MADRES Study, a health disparity pregnancy cohort. Associations between miRNA and birth weight, birth weight for gestational age (GA), and GA at birth were examined using covariate-adjusted robust linear regression. Differences by infant sex and maternal BMI were also investigated. Late pregnancy measures of 13 miRNA were associated with GA at birth (PFDR<0.050). Negative associations were observed for eight miRNA (miR-4454+ miR-7975, miR-4516, let-7b-5p, miR-126-3p, miR-29b-3p, miR-15a-5p, miR-15b-5p, miR-19b-3p) and positive associations for five miRNA (miR-212-3p, miR-584-5p, miR-608, miR-210-3p, miR-188-5p). Predicted target genes were enriched (PFDR<0.050) in pathways involved in organogenesis and placental development. An additional miRNA (miR-107), measured in late pregnancy, was positively associated with GA at birth in infants born to obese women (PFDR for BMI interaction = 0.011). In primary analyses, the associations between early pregnancy miRNA and birth outcomes were not statistically significant (PFDR≥0.05). However, sex-specific associations were observed for early pregnancy measures of 37 miRNA and GA at birth (PFDR for interactions<0.050). None of the miRNA were associated with fetal growth measures (PFDR≥0.050). Our findings suggest that EV miRNA in both early and late pregnancy may influence gestational duration.
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Affiliation(s)
- Caitlin G Howe
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Helen B Foley
- Department of Preventive Medicine, Keck School of Medicine at the University of Southern California, Los Angeles, CA, USA
| | - Elizabeth M Kennedy
- Gangarosa Department of Environmental Health, Emory Rollins School of Public Health, Atlanta, GA, USA
| | - Sandrah P Eckel
- Department of Preventive Medicine, Keck School of Medicine at the University of Southern California, Los Angeles, CA, USA
| | - Thomas A Chavez
- Department of Preventive Medicine, Keck School of Medicine at the University of Southern California, Los Angeles, CA, USA
| | - Dema Faham
- Department of Preventive Medicine, Keck School of Medicine at the University of Southern California, Los Angeles, CA, USA
| | - Brendan H Grubbs
- Department of Obstetrics and Gynecology, Keck School of Medicine, Los Angeles, CA, USA
| | - Laila Al-Marayati
- Department of Obstetrics and Gynecology, Keck School of Medicine, Los Angeles, CA, USA.,Eisner Health, Los Angeles, CA, USA
| | | | - Shakira Suglia
- Department of Epidemiology, Emory Rollins School of Public Health, Atlanta, GA, USA
| | - Theresa M Bastain
- Department of Preventive Medicine, Keck School of Medicine at the University of Southern California, Los Angeles, CA, USA
| | - Carmen J Marsit
- Gangarosa Department of Environmental Health, Emory Rollins School of Public Health, Atlanta, GA, USA.,Department of Epidemiology, Emory Rollins School of Public Health, Atlanta, GA, USA
| | - Carrie V Breton
- Department of Preventive Medicine, Keck School of Medicine at the University of Southern California, Los Angeles, CA, USA
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Santos PM, Adamik J, Howes TR, Du S, Vujanovic L, Warren S, Gambotto A, Kirkwood JM, Butterfield LH. Impact of checkpoint blockade on cancer vaccine-activated CD8+ T cell responses. J Exp Med 2021; 217:151736. [PMID: 32369107 PMCID: PMC7336310 DOI: 10.1084/jem.20191369] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/04/2019] [Accepted: 03/23/2020] [Indexed: 12/19/2022] Open
Abstract
Immune and molecular profiling of CD8 T cells of patients receiving DC vaccines expressing three full-length melanoma antigens (MAs) was performed. Antigen expression levels in DCs had no significant impact on T cell or clinical responses. Patients who received checkpoint blockade before DC vaccination had higher baseline MA-specific CD8 T cell responses but no evidence for improved functional responses to the vaccine. Patients who showed the best clinical responses had low PD-1 expression on MA-specific T cells before and after DC vaccination; however, blockade of PD-1 during antigen presentation by DC had minimal functional impact on PD-1high MA-specific T cells. Gene and protein expression analyses in lymphocytes and tumor samples identified critical immunoregulatory pathways, including CTLA-4 and PD-1. High immune checkpoint gene expression networks correlated with inferior clinical outcomes. Soluble serum PD-L2 showed suggestive positive association with improved outcome. These findings show that checkpoint molecular pathways are critical for vaccine outcomes and suggest specific sequencing of vaccine combinations.
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Affiliation(s)
- Patricia M Santos
- University of Pittsburgh Medical Center, Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA
| | - Juraj Adamik
- Parker Institute for Cancer Immunotherapy, San Francisco, CA
| | - Timothy R Howes
- Parker Institute for Cancer Immunotherapy, San Francisco, CA
| | - Samuel Du
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA
| | - Lazar Vujanovic
- University of Pittsburgh Medical Center, Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA
| | | | - Andrea Gambotto
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA
| | - John M Kirkwood
- University of Pittsburgh Medical Center, Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA.,Department of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Lisa H Butterfield
- University of Pittsburgh Medical Center, Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA.,Parker Institute for Cancer Immunotherapy, San Francisco, CA.,Department of Immunology, University of Pittsburgh, Pittsburgh, PA.,Department of Surgery, University of Pittsburgh, Pittsburgh, PA.,Department of Medicine, University of Pittsburgh, Pittsburgh, PA
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66
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Peck B, Bland P, Mavrommati I, Muirhead G, Cottom H, Wai PT, Maguire SL, Barker HE, Morrison E, Kriplani D, Yu L, Gibson A, Falgari G, Brennan K, Farnie G, Buus R, Marlow R, Novo D, Knight E, Guppy N, Kolarevic D, Susnjar S, Milijic NM, Naidoo K, Gazinska P, Roxanis I, Pancholi S, Martin LA, Holgersen EM, Cheang MCU, Noor F, Postel-Vinay S, Quinn G, McDade S, Krasny L, Huang P, Daley F, Wallberg F, Choudhary JS, Haider S, Tutt AN, Natrajan R. 3D Functional Genomics Screens Identify CREBBP as a Targetable Driver in Aggressive Triple-Negative Breast Cancer. Cancer Res 2021; 81:847-859. [PMID: 33509944 PMCID: PMC7611219 DOI: 10.1158/0008-5472.can-20-1822] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 10/12/2020] [Accepted: 11/25/2020] [Indexed: 11/16/2022]
Abstract
Triple-negative breast cancers (TNBC) are resistant to standard-of-care chemotherapy and lack known targetable driver gene alterations. Identification of novel drivers could aid the discovery of new treatment strategies for this hard-to-treat patient population, yet studies using high-throughput and accurate models to define the functions of driver genes in TNBC to date have been limited. Here, we employed unbiased functional genomics screening of the 200 most frequently mutated genes in breast cancer, using spheroid cultures to model in vivo-like conditions, and identified the histone acetyltransferase CREBBP as a novel tumor suppressor in TNBC. CREBBP protein expression in patient tumor samples was absent in 8% of TNBCs and at a high frequency in other tumors, including squamous lung cancer, where CREBBP-inactivating mutations are common. In TNBC, CREBBP alterations were associated with higher genomic heterogeneity and poorer patient survival and resulted in upregulation and dependency on a FOXM1 proliferative program. Targeting FOXM1-driven proliferation indirectly with clinical CDK4/6 inhibitors (CDK4/6i) selectively impaired growth in spheroids, cell line xenografts, and patient-derived models from multiple tumor types with CREBBP mutations or loss of protein expression. In conclusion, we have identified CREBBP as a novel driver in aggressive TNBC and identified an associated genetic vulnerability in tumor cells with alterations in CREBBP and provide a preclinical rationale for assessing CREBBP alterations as a biomarker of CDK4/6i response in a new patient population. SIGNIFICANCE: This study demonstrates that CREBBP genomic alterations drive aggressive TNBC, lung cancer, and lymphomas and may be selectively treated with clinical CDK4/6 inhibitors.
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Affiliation(s)
- Barrie Peck
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
- Division of Molecular Pathology, The Institute of Cancer Research, London, England, United Kingdom
| | - Philip Bland
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
- Division of Molecular Pathology, The Institute of Cancer Research, London, England, United Kingdom
| | - Ioanna Mavrommati
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
- Division of Molecular Pathology, The Institute of Cancer Research, London, England, United Kingdom
| | - Gareth Muirhead
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Hannah Cottom
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
- Division of Molecular Pathology, The Institute of Cancer Research, London, England, United Kingdom
| | - Patty T Wai
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
- Division of Molecular Pathology, The Institute of Cancer Research, London, England, United Kingdom
| | - Sarah L Maguire
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Holly E Barker
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
- Division of Stem Cells and Cancer, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Eamonn Morrison
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Divya Kriplani
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Lu Yu
- Division of Cancer Biology, The Institute of Cancer Research, London, England, United Kingdom
| | - Amy Gibson
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
- Division of Molecular Pathology, The Institute of Cancer Research, London, England, United Kingdom
| | - Giulia Falgari
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
- Division of Molecular Pathology, The Institute of Cancer Research, London, England, United Kingdom
| | - Keith Brennan
- Faculty of Life Sciences, University of Manchester, Manchester, England, United Kingdom
| | - Gillian Farnie
- SGC Oxford, University of Oxford, Oxford, England, United Kingdom
| | - Richard Buus
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Rebecca Marlow
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
- Breast Cancer Now Research Unit, King's College London, London, England, United Kingdom
| | - Daniela Novo
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Eleanor Knight
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Naomi Guppy
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Daniela Kolarevic
- The Royal Marsden NHS Foundation Trust, London, England, United Kingdom
| | - Snezana Susnjar
- Department of Medical Oncology, The Institute of Oncology and Radiology of Serbia, Belgrade, Serbia
| | - Natasa Medic Milijic
- Department of Pathology and Cytology, The Institute of Oncology and Radiology of Serbia, Belgrade, Serbia
| | - Kalnisha Naidoo
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Patrycja Gazinska
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Ioannis Roxanis
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Sunil Pancholi
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Lesley-Ann Martin
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Erle M Holgersen
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Maggie C U Cheang
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, England, United Kingdom
| | - Farzana Noor
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Sophie Postel-Vinay
- Department of Drug Development (DITEP), Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- UMR981, ATIP-Avenir team, INSERM, Villejuif, France
| | - Gerard Quinn
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Simon McDade
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Lukas Krasny
- Division of Molecular Pathology, The Institute of Cancer Research, London, England, United Kingdom
| | - Paul Huang
- Division of Molecular Pathology, The Institute of Cancer Research, London, England, United Kingdom
| | - Frances Daley
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Fredrik Wallberg
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Jyoti S Choudhary
- Division of Cancer Biology, The Institute of Cancer Research, London, England, United Kingdom
| | - Syed Haider
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Andrew N Tutt
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
- Breast Cancer Now Research Unit, King's College London, London, England, United Kingdom
| | - Rachael Natrajan
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom.
- Division of Molecular Pathology, The Institute of Cancer Research, London, England, United Kingdom
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Buus R, Szijgyarto Z, Schuster EF, Xiao H, Haynes BP, Sestak I, Cuzick J, Paré L, Seguí E, Chic N, Prat A, Dowsett M, Cheang MCU. Development and validation for research assessment of Oncotype DX® Breast Recurrence Score, EndoPredict® and Prosigna®. NPJ Breast Cancer 2021; 7:15. [PMID: 33579961 PMCID: PMC7881187 DOI: 10.1038/s41523-021-00216-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 12/17/2020] [Indexed: 12/22/2022] Open
Abstract
Multi-gene prognostic signatures including the Oncotype® DX Recurrence Score (RS), EndoPredict® (EP) and Prosigna® (Risk Of Recurrence, ROR) are widely used to predict the likelihood of distant recurrence in patients with oestrogen-receptor-positive (ER+), HER2-negative breast cancer. Here, we describe the development and validation of methods to recapitulate RS, EP and ROR scores from NanoString expression data. RNA was available from 107 tumours from postmenopausal women with early-stage, ER+, HER2- breast cancer from the translational Arimidex, Tamoxifen, Alone or in Combination study (TransATAC) where previously these signatures had been assessed with commercial methodology. Gene expression was measured using NanoString nCounter. For RS and EP, conversion factors to adjust for cross-platform variation were estimated using linear regression. For ROR, the steps to perform subgroup-specific normalisation of the gene expression data and calibration factors to calculate the 46-gene ROR score were assessed and verified. Training with bootstrapping (n = 59) was followed by validation (n = 48) using adjusted, research use only (RUO) NanoString-based algorithms. In the validation set, there was excellent concordance between the RUO scores and their commercial counterparts (rc(RS) = 0.96, 95% CI 0.93-0.97 with level of agreement (LoA) of -7.69 to 8.12; rc(EP) = 0.97, 95% CI 0.96-0.98 with LoA of -0.64 to 1.26 and rc(ROR) = 0.97 (95% CI 0.94-0.98) with LoA of -8.65 to 10.54). There was also a strong agreement in risk stratification: (RS: κ = 0.86, p < 0.0001; EP: κ = 0.87, p < 0.0001; ROR: κ = 0.92, p < 0.001). In conclusion, the calibrated algorithms recapitulate the commercial RS and EP scores on individual biopsies and ROR scores on samples based on subgroup-centreing method using NanoString expression data.
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Affiliation(s)
- Richard Buus
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, UK
| | - Zsolt Szijgyarto
- Clinical Trials and Statistics Unit (ICR-CTSU), Division of Clinical Studies, The Institute of Cancer Research, London, UK
| | - Eugene F Schuster
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, UK
| | - Hui Xiao
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, UK
| | - Ben P Haynes
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, UK
| | | | | | - Laia Paré
- Department of Medical Oncology, Hospital Clinic, Barcelona, Spain
- Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
| | - Elia Seguí
- Department of Medical Oncology, Hospital Clinic, Barcelona, Spain
- Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
| | - Nuria Chic
- Department of Medical Oncology, Hospital Clinic, Barcelona, Spain
- Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
| | - Aleix Prat
- Department of Medical Oncology, Hospital Clinic, Barcelona, Spain
- Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
| | - Mitch Dowsett
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, UK
| | - Maggie Chon U Cheang
- Clinical Trials and Statistics Unit (ICR-CTSU), Division of Clinical Studies, The Institute of Cancer Research, London, UK.
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Bracht JWP, Gimenez-Capitan A, Huang CY, Potie N, Pedraz-Valdunciel C, Warren S, Rosell R, Molina-Vila MA. Analysis of extracellular vesicle mRNA derived from plasma using the nCounter platform. Sci Rep 2021; 11:3712. [PMID: 33580122 PMCID: PMC7881020 DOI: 10.1038/s41598-021-83132-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 01/29/2021] [Indexed: 12/24/2022] Open
Abstract
Extracellular vesicles (EVs) are double-layered phospholipid membrane vesicles that are released by most cells and can mediate intercellular communication through their RNA cargo. In this study, we tested if the NanoString nCounter platform can be used for the analysis of EV-mRNA. We developed and optimized a methodology for EV enrichment, EV-RNA extraction and nCounter analysis. Then, we demonstrated the validity of our workflow by analyzing EV-RNA profiles from the plasma of 19 cancer patients and 10 controls and developing a gene signature to differentiate cancer versus control samples. TRI reagent outperformed automated RNA extraction and, although lower plasma input is feasible, 500 μL provided highest total counts and number of transcripts detected. A 10-cycle pre-amplification followed by DNase treatment yielded reproducible mRNA target detection. However, appropriate probe design to prevent genomic DNA binding is preferred. A gene signature, created using a bioinformatic algorithm, was able to distinguish between control and cancer EV-mRNA profiles with an area under the ROC curve of 0.99. Hence, the nCounter platform can be used to detect mRNA targets and develop gene signatures from plasma-derived EVs.
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Affiliation(s)
- Jillian W P Bracht
- Pangaea Oncology, Laboratory of Oncology, Quirón Dexeus University Hospital, Sabino Arana 5-19, 08028, Barcelona, Spain.
- Department of Biochemistry, Molecular Biology and Biomedicine, Universitat Autónoma de Barcelona (UAB), 08193, Cerdanyola, Spain.
| | - Ana Gimenez-Capitan
- Pangaea Oncology, Laboratory of Oncology, Quirón Dexeus University Hospital, Sabino Arana 5-19, 08028, Barcelona, Spain
| | | | - Nicolas Potie
- Department of Genetics, Faculty of Science, University of Granada, 18071, Granada, Spain
- Bioinformatics Laboratory, Biotechnology Institute, Centro de Investigacion Biomedica, PTS, Avda. del Conocimiento s/n, 18100, Granada, Spain
| | - Carlos Pedraz-Valdunciel
- Department of Biochemistry, Molecular Biology and Biomedicine, Universitat Autónoma de Barcelona (UAB), 08193, Cerdanyola, Spain
- Germans Trias i Pujol Health Sciences Institute and Hospital (IGTP), Badalona, Barcelona, Spain
| | | | - Rafael Rosell
- Germans Trias i Pujol Health Sciences Institute and Hospital (IGTP), Badalona, Barcelona, Spain
| | - Miguel A Molina-Vila
- Pangaea Oncology, Laboratory of Oncology, Quirón Dexeus University Hospital, Sabino Arana 5-19, 08028, Barcelona, Spain.
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Herbst RS, Arkenau HT, Bendell J, Arrowsmith E, Wermke M, Soriano A, Penel N, Santana-Davila R, Bischoff H, Chau I, Mi G, Wang H, Rasmussen E, Ferry D, Chao BH, Paz-Ares L. Phase 1 Expansion Cohort of Ramucirumab Plus Pembrolizumab in Advanced Treatment-Naive NSCLC. J Thorac Oncol 2021; 16:289-298. [PMID: 33068794 DOI: 10.1016/j.jtho.2020.10.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/30/2020] [Accepted: 10/03/2020] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Data of first-line ramucirumab plus pembrolizumab treatment of programmed death-ligand 1 (PD-L1)-positive NSCLC (cohort E) are reported (NCT02443324). METHODS In this multicenter, open-label phase 1a/b trial, patients received ramucirumab 10 mg/kg and pembrolizumab 200 mg every 21 days for up to 35 cycles. PD-L1 positivity was defined as tumor proportion score (TPS) greater than or equal to 1%. Exploratory NanoString biomarker analyses included three T-cell signatures (T-cell-inflamed, Gajewski, and effector T cells) and CD274 gene expression. RESULTS Cohort E included 26 patients. Treatment-related adverse events of any grade occurred in 22 patients (84.6%). Treatment-related adverse events of grade greater than or equal to 3 were reported in 11 patients (42.3%); the most frequent was hypertension (n = 4, 15.4%). Objective response rate was 42.3% in the treated population and 56.3% and 22.2% for patients with high (TPS ≥ 50%) and lower levels (TPS 1%-49%) of PD-L1 expression, respectively. Median progression-free survival (PFS) in the treated population was 9.3 months, and 12-month and 18-month PFS rates were 45% each. Median PFS was not reached in patients with PD-L1 TPS greater than or equal to 50% and was 4.2 months in patients with PD-L1 TPS 1% to 49%. Median overall survival was not reached in the treated population, and 12-month and 18-month overall survival rates were 73% and 64%, respectively. Biomarker data suggested a positive association among clinical response, three T-cell signatures, CD274 gene expression, and PD-L1 immunohistochemistry. CONCLUSIONS First-line therapy with ramucirumab plus pembrolizumab has a manageable safety profile in patients with NSCLC, and the efficacy signal seems to be strongest in tumors with high PD-L1 expression.
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Affiliation(s)
- Roy S Herbst
- Yale University School of Medicine, Yale Cancer Center, New Haven, Connecticut.
| | - Hendrik Tobias Arkenau
- Drug Development Unit, Sarah Cannon Research Institute United Kingdom, London, United Kingdom; Cancer Institute, University College London, London, United Kingdom
| | - Johanna Bendell
- Drug Development Unit, Tennessee Oncology/Sarah Cannon Research Institute, Nashville, Tennessee
| | - Edward Arrowsmith
- Tennessee Oncology/Sarah Cannon Research Institute, Chattanooga, Tennessee
| | - Martin Wermke
- NCT/UCC-ECTU, Medical Faculty Carl Gustav Carus, Technical University, Dresden, Germany
| | - Andres Soriano
- Florida Cancer Specialists/Sarah Cannon Research Institute, Englewood, Florida
| | - Nicolas Penel
- Centre Oscar Lambret, Lille University, Lille, France
| | | | - Helge Bischoff
- Department of Thoracic Oncology, Thoraxklinik Heidelberg, Heidelberg, Germany
| | - Ian Chau
- Department of Medicine, Royal Marsden Hospital, London and Surrey, United Kingdom
| | - Gu Mi
- Eli Lilly and Company, Indianapolis, Indiana
| | - Hong Wang
- Eli Lilly and Company, Indianapolis, Indiana
| | | | | | - Bo H Chao
- Eli Lilly and Company, New York, New York
| | - Luis Paz-Ares
- CNIO-H12o Lung Cancer Unit, Hospital Universitario 12 de Octubre, Universidad Complutense & CIBERONC, Madrid, Spain
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Veneziani I, Infante P, Ferretti E, Melaiu O, Battistelli C, Lucarini V, Compagnone M, Nicoletti C, Castellano A, Petrini S, Ognibene M, Pezzolo A, Di Marcotullio L, Bei R, Moretta L, Pistoia V, Fruci D, Barnaba V, Locatelli F, Cifaldi L. Nutlin-3a Enhances Natural Killer Cell-Mediated Killing of Neuroblastoma by Restoring p53-Dependent Expression of Ligands for NKG2D and DNAM-1 Receptors. Cancer Immunol Res 2021; 9:170-183. [PMID: 33303573 DOI: 10.1158/2326-6066.cir-20-0313] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 09/17/2020] [Accepted: 12/04/2020] [Indexed: 11/16/2022]
Abstract
In this study, we explored whether Nutlin-3a, a well-known, nontoxic small-molecule compound antagonizing the inhibitory interaction of MDM2 with the tumor suppressor p53, may restore ligands for natural killer (NK) cell-activating receptors (NK-AR) on neuroblastoma cells to enhance the NK cell-mediated killing. Neuroblastoma cell lines were treated with Nutlin-3a, and the expression of ligands for NKG2D and DNAM-1 NK-ARs and the neuroblastoma susceptibility to NK cells were evaluated. Adoptive transfer of human NK cells in a xenograft neuroblastoma-bearing NSG murine model was assessed. Two data sets of neuroblastoma patients were explored to correlate p53 expression with ligand expression. Luciferase assays and chromatin immunoprecipitation analysis of p53 functional binding on PVR promoter were performed. Primary neuroblastoma cells were also treated with Nutlin-3a, and neuroblastoma spheroids obtained from one high-risk patient were assayed for NK-cell cytotoxicity. We provide evidence showing that the Nutlin-3a-dependent rescue of p53 function in neuroblastoma cells resulted in (i) increased surface expression of ligands for NK-ARs, thus rendering neuroblastoma cell lines significantly more susceptible to NK cell-mediated killing; (ii) shrinkage of human neuroblastoma tumor masses that correlated with overall survival upon adoptive transfer of NK cells in neuroblastoma-bearing mice; (iii) and increased expression of ligands in primary neuroblastoma cells and boosting of NK cell-mediated disaggregation of neuroblastoma spheroids. We also found that p53 was a direct transcription factor regulating the expression of PVR ligand recognized by DNAM-1. Our findings demonstrated an immunomodulatory role of Nutlin-3a, which might be prospectively used for a novel NK cell-based immunotherapy for neuroblastoma.
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Affiliation(s)
- Irene Veneziani
- Department of Paediatric Haematology/Oncology and of Cell and Gene Therapy, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Paola Infante
- Center for Life NanoScience@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Elisa Ferretti
- Department of Experimental Medicine, University of Genoa, Genova, Italy
- Centre of Excellence for Biomedical Research, University of Genoa, Genova, Italy
| | - Ombretta Melaiu
- Department of Paediatric Haematology/Oncology and of Cell and Gene Therapy, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Cecilia Battistelli
- Istituto Pasteur-Fondazione Cenci Bolognetti, Rome, Italy
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Valeria Lucarini
- Department of Paediatric Haematology/Oncology and of Cell and Gene Therapy, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Mirco Compagnone
- Department of Paediatric Haematology/Oncology and of Cell and Gene Therapy, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Carmine Nicoletti
- Istituto Pasteur-Fondazione Cenci Bolognetti, Rome, Italy
- DAHFMO-Unit of Histology and Medical Embryology, Sapienza University of Rome, Rome, Italy
| | - Aurora Castellano
- Department of Paediatric Haematology/Oncology and of Cell and Gene Therapy, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Stefania Petrini
- Confocal Microscopy, Core Facility, Research Laboratories, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Marzia Ognibene
- Laboratorio Cellule Staminali Post Natali e Terapie Cellulari, IRCCS Giannina Gaslini Institute, Genoa, Italy
| | - Annalisa Pezzolo
- Laboratorio Cellule Staminali Post Natali e Terapie Cellulari, IRCCS Giannina Gaslini Institute, Genoa, Italy
| | - Lucia Di Marcotullio
- Istituto Pasteur-Fondazione Cenci Bolognetti, Rome, Italy
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Roberto Bei
- Department of Clinical Sciences and Translational Medicine, University of Rome "Tor Vergata," Rome, Italy
| | - Lorenzo Moretta
- Department of Immunology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Vito Pistoia
- Department of Immunology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Doriana Fruci
- Department of Paediatric Haematology/Oncology and of Cell and Gene Therapy, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Vincenzo Barnaba
- Istituto Pasteur-Fondazione Cenci Bolognetti, Rome, Italy
- Cellular and Molecular Immunology Unit, Dipartimento di Scienze Cliniche, Internistiche, Anestesiologiche e Cardiovascolari, Sapienza University of Rome, Rome, Italy
| | - Franco Locatelli
- Department of Paediatric Haematology/Oncology and of Cell and Gene Therapy, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
- Department of Pediatrics, Sapienza University of Rome, Rome, Italy
| | - Loredana Cifaldi
- Department of Paediatric Haematology/Oncology and of Cell and Gene Therapy, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy.
- Department of Clinical Sciences and Translational Medicine, University of Rome "Tor Vergata," Rome, Italy
- Academic Department of Pediatrics (DPUO), Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
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Low MGMT digital expression is associated with a better outcome of IDH1 wildtype glioblastomas treated with temozolomide. J Neurooncol 2021; 151:135-144. [PMID: 33400009 DOI: 10.1007/s11060-020-03675-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 12/10/2020] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Glioblastoma (GBM) is the deadliest primary brain tumor. The standard treatment consists of surgery, radiotherapy, and temozolomide (TMZ). TMZ response is heterogeneous, and MGMT promoter (MGMTp) methylation has been the major predictive biomarker. We aimed to describe the clinical and molecular data of GBMs treated with TMZ, compare MGMT methylation with MGMT expression, and further associate with patient's outcome. METHODS We evaluate 112 FFPE adult GBM cases. IDH1 and ATRX expression was analyzed by immunohistochemistry, hotspot TERT promoter (TERTp) mutations were evaluated by Sanger or pyrosequencing, and MGMTp methylation was assessed by pyrosequencing and MGMT mRNA expression using the nCounter® Vantage 3D™ DNA damage and repair panel. RESULTS Of the 112 GBMs, 96 were IDH1WT, and 16 were IDH1MUT. Positive ATRX expression was found in 91.6% (88/96) of IDHWT and 43.7% (7/16) of IDHMUT. TERTp mutations were detected in 70.4% (50/71) of IDHWT. MGMTp methylation was found in 55.5% (35/63) of IDHWT and 84.6% (11/13) of IDHMUT, and as expected, MGMTp methylation was significantly associated with a better response to TMZ. MGMT expression was inversely correlated with MGMTp methylation levels (- 0.506, p < 0.0001), and MGMT low expression were significantly associated with better patient survival. It was also observed that integrating MGMTp methylation and expression, significantly improved the prognostication value. CONCLUSIONS MGMT mRNA levels evaluated by digital expression were associated with the outcome of TMZ-treated GBM patients. The combination of MGMT methylation and mRNA expression may provide a more accurate prediction of TMZ response in GBM patients.
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Lambracht-Washington D, Fu M, Hynan LS, Rosenberg RN. Changes in the brain transcriptome after DNA Aβ42 trimer immunization in a 3xTg-AD mouse model. Neurobiol Dis 2021; 148:105221. [PMID: 33316368 PMCID: PMC7845550 DOI: 10.1016/j.nbd.2020.105221] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 11/23/2020] [Accepted: 12/07/2020] [Indexed: 12/23/2022] Open
Abstract
Alzheimer's disease (AD) has been associated with accumulation of amyloid beta (Aβ) peptides in brain, and immunotherapy targeting Aβ provides potential for AD prevention. We have used a DNA Aβ42 trimer construct for immunization of 3xTg-AD mice and found previously significant reduction of amyloid and tau pathology due to the immunotherapy. We show here that DNA Aβ42 immunized 3xTg-AD mice showed better performance in nest building activities and had a higher 24 months survival rate compared to the non-treated AD controls. The analysis of differently expressed genes in brains from 24 months old mice showed significant increases transcript levels between non-immunized AD mice and wild-type controls for genes involved in microglia and astrocyte function, cytokine and inflammatory signaling, apoptosis, the innate and adaptive immune response and are consistent with an inflammatory phenotype in AD. Most of these upregulated genes were downregulated in the DNA Aβ42 immunized 3xTg-AD mice due to the vaccine. Transcript numbers for the immediate early genes, Arc, Bdnf, Homer1, Egr1 and cfos, involved in neuronal and neurotransmission pathways which were much lower in the non-immunized 3xTg-AD mice, were restored to wild-type mouse brain levels in DNA Aβ42 immunized 3xTg-AD mice indicating positive effects of DNA Aβ42 immunotherapy on synapse stability and plasticity. The immune response after immunization is complex, but the multitude of changes after DNA Aβ42 immunization shows that this response moves beyond the amyloid hypothesis and into direction of disease prevention.
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Affiliation(s)
- Doris Lambracht-Washington
- Department of Neurology, UT Southwestern Medical Center Dallas, USA; Doris Lambracht Washington, UT Southwestern Medical Center Dallas, Department of Neurology , 5323 Harry Hines Blvd, Dallas, TX 75390-8813, USA.
| | - Min Fu
- Department of Neurology, UT Southwestern Medical Center Dallas, USA.
| | - Linda S Hynan
- Departments of Population and Data Sciences (Biostatistics) & Psychiatry, UT Southwestern Medical Center Dallas, USA.
| | - Roger N Rosenberg
- Department of Neurology, UT Southwestern Medical Center Dallas, USA.
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73
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Whole blood mRNA expression-based targets to discriminate active tuberculosis from latent infection and other pulmonary diseases. Sci Rep 2020; 10:22072. [PMID: 33328540 PMCID: PMC7745039 DOI: 10.1038/s41598-020-78793-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 11/30/2020] [Indexed: 01/22/2023] Open
Abstract
Current diagnostic tests for tuberculosis (TB) are not able to predict reactivation disease progression from latent TB infection (LTBI). The main barrier to predicting reactivation disease is the lack of our understanding of host biomarkers associated with progression from latent infection to active disease. Here, we applied an immune-based gene expression profile by NanoString platform to identify whole blood markers that can distinguish active TB from other lung diseases (OPD), and that could be further evaluated as a reactivation TB predictor. Among 23 candidate genes that differentiated patients with active TB from those with OPD, nine genes (CD274, CEACAM1, CR1, FCGR1A/B, IFITM1, IRAK3, LILRA6, MAPK14, PDCD1LG2) demonstrated sensitivity and specificity of 100%. Seven genes (C1QB, C2, CCR2, CCRL2, LILRB4, MAPK14, MSR1) distinguished TB from LTBI with sensitivity and specificity between 82 and 100%. This study identified single gene candidates that distinguished TB from OPD and LTBI with high sensitivity and specificity (both > 82%), which may be further evaluated as diagnostic for disease and as predictive markers for reactivation TB.
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74
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Souza AGD, Bastos VAF, Fujimura PT, Ferreira ICC, Leal LF, da Silva LS, Laus AC, Reis RM, Martins MM, Santos PS, Corrêa NCR, Marangoni K, Thomé CH, Colli LM, Goulart LR, Goulart VA. Cell-free DNA promotes malignant transformation in non-tumor cells. Sci Rep 2020; 10:21674. [PMID: 33303880 PMCID: PMC7728762 DOI: 10.1038/s41598-020-78766-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 11/30/2020] [Indexed: 12/16/2022] Open
Abstract
Cell-free DNA is present in different biological fluids and when released by tumor cells may contribute to pro-tumor events such as malignant transformation of cells adjacent to the tumor and metastasis. Thus, this study analyzed the effect of tumor cell-free DNA, isolated from the blood of prostate cancer patients, on non-tumor prostate cell lines (RWPE-1 and PNT-2). To achieve this, we performed cell-free DNA quantification and characterization assays, evaluation of gene and miRNA expression profiling focused on cancer progression and EMT, and metabolomics by mass spectrometry and cellular migration. The results showed that tumor-free cell DNA was able to alter the gene expression of MMP9 and CD44, alter the expression profile of nine miRNAs, and increased the tryptophan consumption and cell migration rates in non-tumor cells. Therefore, tumor cell-free DNA was capable of altering the receptor cell phenotype, triggering events related to malignant transformation in these cells, and can thus be considered a potential target for cancer diagnosis and therapy.
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Affiliation(s)
- Aline Gomes de Souza
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, MG, Brazil.
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School - University of São Paulo, Ribeirão Preto, Brazil.
| | - Victor Alexandre F Bastos
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, MG, Brazil
| | - Patricia Tieme Fujimura
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, MG, Brazil
| | - Izabella Cristina C Ferreira
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, MG, Brazil
| | - Letícia Ferro Leal
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil
| | | | - Ana Carolina Laus
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil
- Life and Health Sciences Research Institute (ICVS), Medical School, University of Minho, Braga, Portugal
- 3ICVS/3B's-PT Government Associate Laboratory, Braga, Portugal
| | - Mario Machado Martins
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, MG, Brazil
| | - Paula Souza Santos
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, MG, Brazil
| | - Natássia C Resende Corrêa
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, MG, Brazil
| | - Karina Marangoni
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, MG, Brazil
| | - Carolina Hassibe Thomé
- Center for Cell Based Therapy, Hemotherapy Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Leandro Machado Colli
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School - University of São Paulo, Ribeirão Preto, Brazil
| | - Luiz Ricardo Goulart
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, MG, Brazil
- Department of Medical Microbiology and Immunology, University of California-Davis, Davis, USA
| | - Vivian Alonso Goulart
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, MG, Brazil
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75
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Cellular and gene signatures of tumor-infiltrating dendritic cells and natural-killer cells predict prognosis of neuroblastoma. Nat Commun 2020; 11:5992. [PMID: 33239635 PMCID: PMC7689423 DOI: 10.1038/s41467-020-19781-y] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 10/26/2020] [Indexed: 12/19/2022] Open
Abstract
Tumor-infiltrating lymphocytes play an essential role in improving clinical outcome of neuroblastoma (NB) patients, but their relationship with other tumor-infiltrating immune cells in the T cell-inflamed tumors remains poorly investigated. Here we show that dendritic cells (DCs) and natural killer (NK) cells are positively correlated with T-cell infiltration in human NB, both at transcriptional and protein levels, and associate with a favorable prognosis. Multiplex imaging displays DC/NK/T cell conjugates in the tumor microenvironment of low-risk NB. Remarkably, this connection is further strengthened by the identification of gene signatures related to DCs and NK cells able to predict survival of NB patients and strongly correlate with the expression of PD-1 and PD-L1. In summary, our findings unveil a key prognostic role of DCs and NK cells and indicate their related gene signatures as promising tools for the identification of clinical biomarkers to better define risk stratification and survival of NB patients. Tumour-infiltrating lymphocytes play a crucial role in neuroblastoma, but their relationship to other immune cells is poorly understood. Here the authors identify the cellular and gene signatures of intratumoural dendritic cells and natural killer cells that predict the clinical outcome of neuroblastoma.
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76
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Lim GB, Kim YA, Seo JH, Lee HJ, Gong G, Park SH. Prediction of prognostic signatures in triple-negative breast cancer based on the differential expression analysis via NanoString nCounter immune panel. BMC Cancer 2020; 20:1052. [PMID: 33138797 PMCID: PMC7607642 DOI: 10.1186/s12885-020-07399-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 09/10/2020] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Triple-Negative Breast Cancer (TNBC) is an aggressive and complex subtype of breast cancer. The current biomarkers used in the context of breast cancer treatment are highly dependent on the targeting of oestrogen receptor, progesterone receptor, or HER2, resulting in treatment failure and disease recurrence and creating clinical challenges. Thus, there is still a crucial need for the improvement of TNBC treatment; the discovery of effective biomarkers that can be easily translated to the clinics is essential. METHODS We report an approach for the discovery of biomarkers that can predict tumour relapse and pathologic complete response (pCR) in TNBC on the basis of mRNA expression quantified using the NanoString nCounter Immunology Panel. To overcome the limited sample size, prediction models based on random Forest were constructed using the differentially expressed genes (DEGs) as selected features. We also evaluated the differences between pre- and post-treatment groups aiming for the combinatorial assessment of pCR and relapse using additive models in edgeR. RESULTS We identify nine and 13 DEGs strongly associated with pCR and relapse, respectively, from 579 immune genes in a small number of samples (n = 55) using edgeR. An additive model for the comparison of pre- and post-treatment groups via the adjustment of the independent subject in the relapse group revealed associations for 41 genes. Comprehensive analysis indicated that our prediction models outperformed those constructed using features extracted from the existing feature selection model Elastic Net in terms of accuracy. The prediction models were assessed using a randomization test to validate the robustness (empirical P for the model of pCR = 0.015 and empirical P for the model of relapse = 0.018). Furthermore, three DEGs (FCER1A, EDNRB, and TGFBI) in the model of relapse showed prognostic significance for predicting the survival of patients with cancer through Cox proportional hazards regression model-based survival analysis. CONCLUSION Gene expression quantified via the NanoString nCounter Immunology Panel can be seamlessly analysed using edgeR, even considering small sample sizes. Our approach provides a scalable framework that can easily be applied for the discovery of biomarkers based on the NanoString nCounter Immunology Panel. DATA AVAILABILITY The source code will be available from github at https://github.com/sungheep/nanostring .
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Affiliation(s)
- Gyeong Back Lim
- Department of Bioinformatics and Life Science, Soongsil University, Seoul, 06978 Republic of Korea
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505 Republic of Korea
| | - Young-Ae Kim
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505 Republic of Korea
| | - Jeong-Han Seo
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505 Republic of Korea
| | - Hee Jin Lee
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505 Republic of Korea
| | - Gyungyub Gong
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505 Republic of Korea
| | - Sung Hee Park
- Department of Bioinformatics and Life Science, Soongsil University, Seoul, 06978 Republic of Korea
- Foundation of University-Industry Cooperation, Soongsil University, Seoul, 06978 Republic of Korea
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77
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Ramucirumab in Combination with Pembrolizumab in Treatment-Naïve Advanced Gastric or GEJ Adenocarcinoma: Safety and Antitumor Activity from the Phase 1a/b JVDF Trial. Cancers (Basel) 2020; 12:cancers12102985. [PMID: 33076423 PMCID: PMC7602637 DOI: 10.3390/cancers12102985] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/05/2020] [Accepted: 10/13/2020] [Indexed: 02/08/2023] Open
Abstract
Simple Summary The prognosis for gastric cancer remains poor, with a median overall survival of approximately 1 year. Ramucirumab and pembrolizumab have each demonstrated antitumor activity and a favorable safety profile as treatments for patients with advanced gastric/gastroesophageal junction (G/GEJ) cancer in the second and third-line setting respectively. However, both agents failed to demonstrate survival benefit over chemotherapy in the first-line setting. Twenty-eight treatment-naïve patients with advanced/metastatic G/GEJ adenocarcinoma were treated with ramucirumab plus pembrolizumab in this phase 1a/b trial. Our results showed that this combination was well tolerated with no unexpected toxicities, and promising durable survival results, particularly among patients with PD-ligand 1 positive tumors. The results of our study therefore support modulating the tumor microenvironment with dual inhibition of VEGFR2 and PD-1 pathways in the first-line patients with advanced G/GEJ cancer. Abstract Ramucirumab (anti-VEGFR2) plus pembrolizumab (anti-PD1) demonstrated promising antitumor activity and tolerability among patients with previously treated advanced cancers, supporting growing evidence that combination therapies modulating the tumor microenvironment may expand the spectrum of patients who respond to checkpoint inhibitors. Here we present the results of this combination in first-line patients with metastatic G/GEJ cancer. Twenty-eight patients (≥18 years) with no prior systemic chemotherapy in the advanced/metastatic setting received ramucirumab (8 mg/kg days 1 and 8) plus pembrolizumab (200 mg day 1) every 3 weeks as part of JVDF phase 1a/b study. The primary endpoint was safety. Secondary endpoints included progression-free survival (PFS), objective response rate (ORR), and overall survival (OS). Tumors were PD-L1-positive (combined positive score ≥ 1) in 19 and -negative in 6 patients. Eighteen patients experienced grade 3 treatment-related adverse events, most commonly hypertension (14%) and elevated alanine/aspartate aminotransferase (11% each), with no grade 4 or 5 reported. The ORR was 25% (PD-L1-positive, 32%; PD-L1-negative, 17%) with duration of response not reached. PFS was 5.6 months (PD-L1-positive, 8.6 months; PD-L1-negative, 4.3 months), and OS 14.6 months (PD-L1-positive, 17.3 months; PD-L1-negative, 11.3 months). Acknowledging study design limitations, ramucirumab plus pembrolizumab had encouraging durable clinical activity with no unexpected toxicities in treatment-naïve biomarker-unselected metastatic G/GEJ cancer, and improved outcomes in patients with PD-L1-positive tumors.
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78
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Jeon J, Olkhov-Mitsel E, Xie H, Yao CQ, Zhao F, Jahangiri S, Cuizon C, Scarcello S, Jeyapala R, Watson JD, Fraser M, Ray J, Commisso K, Loblaw A, Fleshner NE, Bristow RG, Downes M, Vesprini D, Liu S, Bapat B, Boutros PC. Temporal Stability and Prognostic Biomarker Potential of the Prostate Cancer Urine miRNA Transcriptome. J Natl Cancer Inst 2020; 112:247-255. [PMID: 31161221 DOI: 10.1093/jnci/djz112] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 03/01/2019] [Accepted: 05/30/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The development of noninvasive tests for the early detection of aggressive prostate tumors is a major unmet clinical need. miRNAs are promising noninvasive biomarkers: they play essential roles in tumorigenesis, are stable under diverse analytical conditions, and can be detected in body fluids. METHODS We measured the longitudinal stability of 673 miRNAs by collecting serial urine samples from 10 patients with localized prostate cancer. We then measured temporally stable miRNAs in an independent training cohort (n = 99) and created a biomarker predictive of Gleason grade using machine-learning techniques. Finally, we validated this biomarker in an independent validation cohort (n = 40). RESULTS We found that each individual has a specific urine miRNA fingerprint. These fingerprints are temporally stable and associated with specific biological functions. We identified seven miRNAs that were stable over time within individual patients and integrated them with machine-learning techniques to create a novel biomarker for prostate cancer that overcomes interindividual variability. Our urine biomarker robustly identified high-risk patients and achieved similar accuracy as tissue-based prognostic markers (area under the receiver operating characteristic = 0.72, 95% confidence interval = 0.69 to 0.76 in the training cohort, and area under the receiver operating characteristic curve = 0.74, 95% confidence interval = 0.55 to 0.92 in the validation cohort). CONCLUSIONS These data highlight the importance of quantifying intra- and intertumoral heterogeneity in biomarker development. This noninvasive biomarker may usefully supplement invasive or expensive radiologic- and tissue-based assays.
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Affiliation(s)
- Jouhyun Jeon
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Honglei Xie
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Cindy Q Yao
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Fang Zhao
- Lunenfeld-Tannenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Sahar Jahangiri
- Sunnybrook Research Institute and Department of Radiation Oncology, Sunnybrook-Odette Cancer Centre, Toronto, ON, Canada
| | - Carmelle Cuizon
- Lunenfeld-Tannenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Seville Scarcello
- Sunnybrook Research Institute and Department of Radiation Oncology, Sunnybrook-Odette Cancer Centre, Toronto, ON, Canada
| | - Renu Jeyapala
- Lunenfeld-Tannenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - John D Watson
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Michael Fraser
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Jessica Ray
- Sunnybrook Research Institute and Department of Radiation Oncology, Sunnybrook-Odette Cancer Centre, Toronto, ON, Canada
| | - Kristina Commisso
- Sunnybrook Research Institute and Department of Radiation Oncology, Sunnybrook-Odette Cancer Centre, Toronto, ON, Canada
| | - Andrew Loblaw
- Sunnybrook Research Institute and Department of Radiation Oncology, Sunnybrook-Odette Cancer Centre, Toronto, ON, Canada
| | - Neil E Fleshner
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Robert G Bristow
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Manchester Cancer Research Centre, University of Manchester, Manchester, UK
| | | | - Danny Vesprini
- Sunnybrook Research Institute and Department of Radiation Oncology, Sunnybrook-Odette Cancer Centre, Toronto, ON, Canada
| | - Stanley Liu
- Sunnybrook Research Institute and Department of Radiation Oncology, Sunnybrook-Odette Cancer Centre, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Bharati Bapat
- Lunenfeld-Tannenbaum Research Institute, Sinai Health System, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Paul C Boutros
- Ontario Institute for Cancer Research, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Department of Pharmacology & Toxicology, University of Toronto, Toronto, ON, Canada.,Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA.,Department of Urology, University of California, Los Angeles, Los Angeles, CA.,Broad Stem Cell Research Centre, University of California, Los Angeles, Los Angeles, CA.,Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA.,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA
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79
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Martínez C, Lasitschka F, Thöni C, Wohlfarth C, Braun A, Granzow M, Röth R, Dizdar V, Rappold GA, Hausken T, Langeland N, Hanevik K, Niesler B. Comparative expression profiling in the intestine of patients with Giardia-induced postinfectious functional gastrointestinal disorders. Neurogastroenterol Motil 2020; 32:e13868. [PMID: 32391639 DOI: 10.1111/nmo.13868] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/13/2020] [Accepted: 04/07/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND A Giardia outbreak in Bergen, Norway, caused postinfectious functional gastrointestinal disorders (PI-FGIDs). Despite the devastating effects of this outbreak, it presented a unique chance to investigate the implication on the dysregulation of genetic pathways in PI-FGID. METHODS We performed the first comparative expression profiling of miRNAs and their potential target genes in microdissected rectal biopsies from 20 Giardia-induced PI-FGID patients vs 18 healthy controls by nCounter analysis. Subsequently, candidates were validated on protein level by immunostaining. KEY RESULTS miRNA profiling on rectal biopsy samples from 5 diarrhea-predominant PI-IBS cases compared to 10 healthy controls revealed differential expression in the epithelial layer. The top five regulated miRNAs were implicated in GI disease, inflammatory response, and immunological disease. Subsequently, these miRNAs and 100 potential mRNA targets were examined in 20 PI-FGID cases and 18 healthy controls in both the mucosal epithelium and the lamina propria. Although deregulation of the selected miRNAs could not be verified in the larger sample set, mRNAs involved in barrier function were downregulated in the epithelium. Pro-inflammatory genes and genes implicated in epigenetic modifications were upregulated in the lamina propria. Immunostaining for selected candidates on 17 PI-FGID cases and 16 healthy controls revealed increased tryptase levels as well as a decreased and aberrant subcellular expression of occludin. CONCLUSIONS AND INFERENCES Genes relevant to immune and barrier function as well as stress response and epigenetic modulation are differentially expressed in PI-FGIDs and may contribute to disease manifestation.
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Affiliation(s)
- Cristina Martínez
- Department of Human Molecular Genetics, Institute of Human Genetics, Heidelberg University, Heidelberg, Germany.,Lleida Institute for Biomedical Research Dr. Pifarré Foundation (IRBLleida), Lleida, Spain.,Genes in Irritable Bowel Syndrome (GENIEUR) Research Network Europe, Heidelberg, Germany
| | - Felix Lasitschka
- Institute of Pathology, Heidelberg University, Heidelberg, Germany
| | - Cornelia Thöni
- Institute of Pathology, Heidelberg University, Heidelberg, Germany
| | - Carolin Wohlfarth
- Department of Human Molecular Genetics, Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Alexander Braun
- Department of Human Molecular Genetics, Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Martin Granzow
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Ralph Röth
- Department of Human Molecular Genetics, Institute of Human Genetics, Heidelberg University, Heidelberg, Germany.,nCounter Core Facility Heidelberg, Institute of Human Genetics, Heidelberg, Germany
| | - Vernesa Dizdar
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Gudrun A Rappold
- Department of Human Molecular Genetics, Institute of Human Genetics, Heidelberg University, Heidelberg, Germany.,nCounter Core Facility Heidelberg, Institute of Human Genetics, Heidelberg, Germany
| | - Trygve Hausken
- Genes in Irritable Bowel Syndrome (GENIEUR) Research Network Europe, Heidelberg, Germany.,Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Nina Langeland
- Genes in Irritable Bowel Syndrome (GENIEUR) Research Network Europe, Heidelberg, Germany.,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Kurt Hanevik
- Genes in Irritable Bowel Syndrome (GENIEUR) Research Network Europe, Heidelberg, Germany.,Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Medicine, National Advisory Center for Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway
| | - Beate Niesler
- Department of Human Molecular Genetics, Institute of Human Genetics, Heidelberg University, Heidelberg, Germany.,Genes in Irritable Bowel Syndrome (GENIEUR) Research Network Europe, Heidelberg, Germany.,nCounter Core Facility Heidelberg, Institute of Human Genetics, Heidelberg, Germany
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80
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Romualdo GR, Prata GB, da Silva TC, Evangelista AF, Reis RM, Vinken M, Moreno FS, Cogliati B, Barbisan LF. The combination of coffee compounds attenuates early fibrosis-associated hepatocarcinogenesis in mice: involvement of miRNA profile modulation. J Nutr Biochem 2020; 85:108479. [PMID: 32795656 DOI: 10.1016/j.jnutbio.2020.108479] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 06/19/2020] [Accepted: 08/03/2020] [Indexed: 12/12/2022]
Abstract
Aberrant microRNA expression implicates on hepatocellular carcinoma (HCC) development. Conversely, coffee consumption reduces by ~40% the risk for fibrosis/cirrhosis and HCC, while decaffeinated coffee does not. It is currently unknown whether these protective effects are related to caffeine (CAF), or to its combination with other common and/or highly bioavailable coffee compounds, such as trigonelline (TRI) and chlorogenic acid (CGA). We evaluated whether CAF individually or combined with TRI and/or CGA alleviates fibrosis-associated hepatocarcinogenesis, examining the involvement of miRNA profile modulation. Then, male C3H/HeJ mice were submitted to a diethylnitrosamine/carbon tetrachloride-induced model. Animals received CAF (50 mg/kg), CAF+TRI (50 and 25 mg/kg), CAF+CGA (50 and 25 mg/kg) or CAF+TRI+CGA (50, 25 and 25 mg/kg), intragastrically, 5×/week, for 10 weeks. Only CAF+TRI+CGA combination reduced the incidence, number and proliferation (Ki-67) of hepatocellular preneoplastic foci while enhanced apoptosis (cleaved caspase-3) in adjacent parenchyma. CAF+TRI+CGA treatment also decreased hepatic oxidative stress and enhanced the antioxidant Nrf2 axis. CAF+TRI+CGA had the most pronounced effects on decreasing hepatic pro-inflammatory IL-17 and NFκB, contributing to reduce CD68-positive macrophage number, stellate cell activation, and collagen deposition. In agreement, CAF+TRI+CGA upregulated tumor suppressors miR-144-3p, miR-376a-3p and antifibrotic miR-15b-5p, frequently deregulated in human HCC. CAF+TRI+CGA reduced the hepatic protein levels of pro-proliferative EGFR (miR-144-3p target), antiapoptotic Bcl-2 family members (miR-15b-5p targets), and the number of PCNA (miR-376a-3p target) positive hepatocytes in preneoplastic foci. Our results suggest that the combination of most common and highly bioavailable coffee compounds, rather than CAF individually, attenuates fibrosis-associated hepatocarcinogenesis by modulating miRNA expression profile.
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Affiliation(s)
- Guilherme Ribeiro Romualdo
- Department of Pathology, Botucatu Medical School, São Paulo State University (UNESP), Botucatu, - SP, Brazil
| | - Gabriel Bacil Prata
- Department of Structural and Functional Biology, Biosciences Institute, São Paulo State University (UNESP), Botucatu, - SP, Brazil
| | - Tereza Cristina da Silva
- Department of Pathology, School of Veterinary Medicine and Animal Science, University of São Paulo (USP), São Paulo, - SP, Brazil
| | | | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, - SP, Brazil; Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal; 3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Mathieu Vinken
- Department of In Vitro Toxicology and Dermato-Cosmetology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Fernando Salvador Moreno
- Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, University of São Paulo (USP), São Paulo, - SP, Brazil
| | - Bruno Cogliati
- Department of Pathology, School of Veterinary Medicine and Animal Science, University of São Paulo (USP), São Paulo, - SP, Brazil
| | - Luís Fernando Barbisan
- Department of Structural and Functional Biology, Biosciences Institute, São Paulo State University (UNESP), Botucatu, - SP, Brazil.
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Crespo-Rodriguez E, Bergerhoff K, Bozhanova G, Foo S, Patin EC, Whittock H, Buus R, Haider S, Muirhead G, Thway K, Newbold K, Coffin RS, Vile RG, Kim D, McLaughlin M, Melcher AA, Harrington KJ, Pedersen M. Combining BRAF inhibition with oncolytic herpes simplex virus enhances the immune-mediated antitumor therapy of BRAF-mutant thyroid cancer. J Immunother Cancer 2020; 8:e000698. [PMID: 32759235 PMCID: PMC7445339 DOI: 10.1136/jitc-2020-000698] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The aggressive clinical behavior of poorly differentiated and anaplastic thyroid cancers (PDTC and ATC) has proven challenging to treat, and survival beyond a few months from diagnosis is rare. Although 30%-60% of these tumors contain mutations in the BRAF gene, inhibitors designed specifically to target oncogenic BRAF have shown limited and only short-lasting therapeutic benefits as single agents, thus highlighting the need for improved treatment strategies, including novel combinations. METHODS Using a BRAFV600E-driven mouse model of ATC, we investigated the therapeutic efficacy of the combination of BRAF inhibition and oncolytic herpes simplex virus (oHSV). Analyses of samples from tumor-bearing mice were performed to immunologically characterize the effects of different treatments. These immune data were used to inform the incorporation of immune checkpoint inhibitors into triple combination therapies. RESULTS We characterized the immune landscape in vivo following BRAF inhibitor treatment and detected only modest immune changes. We, therefore, hypothesized that the addition of oncolytic virotherapy to BRAF inhibition in thyroid cancer would create a more favorable tumor immune microenvironment, boost the inflammatory status of tumors and improve BRAF inhibitor therapy. First, we showed that thyroid cancer cells were susceptible to infection with oHSV and that this process was associated with activation of the immune tumor microenvironment in vivo. Next, we showed improved therapeutic responses when combining oHSV and BRAF inhibition in vivo, although no synergistic effects were seen in vitro, further confirming that the dominant effect of oHSV in this context was likely immune-mediated. Importantly, both gene and protein expression data revealed an increase in activation of T cells and natural killer (NK) cells in the tumor in combination-treated samples. The benefit of combination oHSV and BRAF inhibitor therapy was abrogated when T cells or NK cells were depleted in vivo. In addition, we showed upregulation of PD-L1 and CTLA-4 following combined treatment and demonstrated that blockade of the PD-1/PD-L1 axis or CTLA-4 further improved combination therapy. CONCLUSIONS The combination of oHSV and BRAF inhibition significantly improved survival in a mouse model of ATC by enhancing immune-mediated antitumor effects, and triple combination therapies, including either PD-1 or CTLA-4 blockade, further improved therapy.
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Affiliation(s)
| | | | - Galabina Bozhanova
- Translational Immunotherapy Team, The Institute of Cancer Research, London, United Kingdom
| | - Shane Foo
- Translational Immunotherapy Team, The Institute of Cancer Research, London, United Kingdom
| | - Emmanuel C Patin
- Targeted Therapy Team, The Institute of Cancer Research, London, United Kingdom
| | - Harriet Whittock
- Targeted Therapy Team, The Institute of Cancer Research, London, United Kingdom
| | - Richard Buus
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, United Kingdom
| | - Syed Haider
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Gareth Muirhead
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Khin Thway
- Sarcoma Unit, The Royal Marsden Hospital, London, United Kingdom
| | - Kate Newbold
- Head and Neck/Thyroid Oncology Department, The Royal Marsden Hospital, London, United Kingdom
| | | | - Richard G Vile
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, United States
| | - Dae Kim
- Head and Neck Department, St George's University Hospital, London, United Kingdom
| | - Martin McLaughlin
- Targeted Therapy Team, The Institute of Cancer Research, London, United Kingdom
| | - Alan A Melcher
- Translational Immunotherapy Team, The Institute of Cancer Research, London, United Kingdom
| | - Kevin J Harrington
- Targeted Therapy Team, The Institute of Cancer Research, London, United Kingdom
| | - Malin Pedersen
- Translational Immunotherapy Team, The Institute of Cancer Research, London, United Kingdom
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82
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Jin X, Guan Y, Zhang Z, Wang H. Microarray data analysis on gene and miRNA expression to identify biomarkers in non-small cell lung cancer. BMC Cancer 2020; 20:329. [PMID: 32299382 PMCID: PMC7164187 DOI: 10.1186/s12885-020-06829-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 04/05/2020] [Indexed: 01/22/2023] Open
Abstract
Background The aim of this study was to gain further investigation of non-small cell lung cancer (NSCLC) tumorigenesis and identify biomarkers for clinical management of patients through comprehensive bioinformatics analysis. Methods miRNA and mRNA microarray datasets were downloaded from GEO (Gene Expression Omnibus) database under the accession number GSE102286 and GSE101929, respectively. Genes and miRNAs with differential expression were identified in NSCLC samples compared with controls, respectively. The interaction between differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmiRs) was predicted, followed by functional enrichment analysis, and construction of miRNA-gene regulatory network, protein-protein interaction (PPI) network, and competing endogenous RNA (ceRNA) network. Through comprehensive bioinformatics analysis, we anticipate to find novel therapeutic targets and biomarkers for NSCLC. Results A total of 123 DEmiRs (5 up- and 118 down-regulated miRNAs) and 924 DEGs (309 up- and 615 down-regulated genes) were identified. These genes and miRNAs were significantly involved in different pathways including adherens junction, relaxin signaling pathway, and axon guidance. Furthermore, hsa-miR-9-5p, has-miR-196a-5p and hsa-miR-31-5p, as well as hsa-miR-1, hsa-miR-218-5p and hsa-miR-135a-5p were shown to have higher degree in the miRNA-gene regulatory network and ceRNA network, respectively. Furthermore, BIRC5 and FGF2, as well as RTKN2 and SLIT3 were hubs in the PPI network and ceRNA network, respectively. Conclusion Several pathways (adherens junction, relaxin signaling pathway, and axon guidance) miRNAs (hsa-miR-9-5p, has-miR-196a-5p, hsa-miR-31-5p, hsa-miR-1, hsa-miR-218-5p and hsa-miR-135a-5p) and genes (BIRC5, FGF2, RTKN2 and SLIT3) may play important roles in the pathogenesis of NSCLC.
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Affiliation(s)
- Xiang Jin
- Department of Respiration, The First Hospital of Jilin University, No. 1 Xinminda Street, Changchun, 130021, China
| | - Yinghui Guan
- Department of Respiration, The First Hospital of Jilin University, No. 1 Xinminda Street, Changchun, 130021, China.
| | - Zhen Zhang
- PICU, The First Hospital of Jilin University, Changchun, 130021, China
| | - Hongyue Wang
- Department of Nephrology, The First Hospital of Jilin University, Changchun, 130021, China
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83
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Immune subtyping of extranodal NK/T-cell lymphoma: a new biomarker and an immune shift during disease progression. Mod Pathol 2020; 33:603-615. [PMID: 31653980 DOI: 10.1038/s41379-019-0392-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 09/22/2019] [Accepted: 09/22/2019] [Indexed: 11/08/2022]
Abstract
Extranodal NK/T-cell lymphoma is an aggressive lymphoma that is strongly associated with Epstein-Barr virus infection. Although some extranodal NK/T-cell lymphoma patients have shown responses to immune checkpoint blockade, biomarkers for predicting extranodal NK/T-cell lymphoma patient response to immunotherapy have not yet been defined. To understand the tumor immune microenvironment, we analyzed the expression of 579 immune-related genes and characterized the immune cells using immunohistochemistries and in situ hybridization for EBER. Based on comprehensive analyses, we developed an immune subtyping model that classifies extranodal NK/T-cell lymphoma patients into four tumor immune microenvironment subgroups using three immunohistochemical markers (FoxP3, PD-L1, and CD68). The four tumor immune microenvironment subgroups were named immune tolerance, immune evasion-A, immune evasion-B, and immune silenced. The immune tolerance group was characterized by high-Treg counts and was frequently observed in early stage, and nasal extranodal NK/T-cell lymphoma. The immune evasion group showed high cytotoxic T-cell counts and high PD-L1 expression but low Treg counts. In the immune-silenced group, almost all immune responses were exhausted, most patients were at an advanced stage, and had the poorest disease prognosis among the tumor immune microenvironment subgroups. In some patients (n = 3), a shift in the tumor immune microenvironment subgroup classification was observed in sequential biopsies. The response rate to pembrolizumab, an anti-PD-1 antibody, was 100% (1/1) in the immune tolerance group, 60% (3/5) in the immune evasion group, and 0% (0/5) in the immune-silenced group. We classified extranodal NK/T-cell lymphoma into four tumor immune microenvironment subgroups using a new classification system. In conclusion, we propose that the tumor immune microenvironment of extranodal NK/T-cell lymphoma may change during disease progression and may serve as a useful biomarker for immunotherapy.
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84
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Molania R, Gagnon-Bartsch JA, Dobrovic A, Speed TP. A new normalization for Nanostring nCounter gene expression data. Nucleic Acids Res 2020; 47:6073-6083. [PMID: 31114909 PMCID: PMC6614807 DOI: 10.1093/nar/gkz433] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 04/25/2019] [Accepted: 05/07/2019] [Indexed: 12/18/2022] Open
Abstract
The Nanostring nCounter gene expression assay uses molecular barcodes and single molecule imaging to detect and count hundreds of unique transcripts in a single reaction. These counts need to be normalized to adjust for the amount of sample, variations in assay efficiency and other factors. Most users adopt the normalization approach described in the nSolver analysis software, which involves background correction based on the observed values of negative control probes, a within-sample normalization using the observed values of positive control probes and normalization across samples using reference (housekeeping) genes. Here we present a new normalization method, Removing Unwanted Variation-III (RUV-III), which makes vital use of technical replicates and suitable control genes. We also propose an approach using pseudo-replicates when technical replicates are not available. The effectiveness of RUV-III is illustrated on four different datasets. We also offer suggestions on the design and analysis of studies involving this technology.
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Affiliation(s)
- Ramyar Molania
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria 3084, Australia.,Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.,Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, Victoria 3084, Australia
| | | | - Alexander Dobrovic
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria 3084, Australia.,School of Cancer Medicine and Molecular Cancer Prevention Program, La Trobe University, Bundoora, Victoria 3086, Australia.,Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria 3010, Australia.,Department of Surgery, The University of Melbourne, Austin Health, Heidelberg, Victoria, 3084, Australia
| | - Terence P Speed
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.,Department of Mathematics and Statistics, University of Melbourne, Victoria 3010, Australia
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85
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Pessôa-Pereira D, Evangelista AF, Causin RL, da Costa Vieira RA, Abrahão-Machado LF, Santana IVV, da Silva VD, de Souza KCB, de Oliveira-Silva RJ, Fernandes GC, Reis RM, Palmero EI, Marques MMC. miRNA expression profiling of hereditary breast tumors from BRCA1- and BRCA2-germline mutation carriers in Brazil. BMC Cancer 2020; 20:143. [PMID: 32087690 PMCID: PMC7036228 DOI: 10.1186/s12885-020-6640-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 02/17/2020] [Indexed: 12/15/2022] Open
Abstract
Background MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional gene expression regulation and have been described as key regulators of carcinogenesis. Aberrant miRNA expression has been frequently reported in sporadic breast cancers, but few studies have focused on profiling hereditary breast cancers. In this study, we aimed to identify specific miRNA signatures in hereditary breast tumors and to compare with sporadic breast cancer and normal breast tissues. Methods Global miRNA expression profiling using NanoString technology was performed on 43 hereditary breast tumors (15 BRCA1, 14 BRCA2, and 14 BRCAX), 23 sporadic breast tumors and 8 normal breast tissues. These normal breast tissues derived from BRCA1- and BRCA2- mutation carriers (n = 5) and non-mutation carriers (n = 3). Subsequently, we performed receiver operating characteristic (ROC) curve analyses to evaluate the diagnostic performance of differentially expressed miRNAs. Putative target genes of each miRNAs considered as potential biomarkers were identified using miRDIP platform and used for pathway enrichment analysis. Results miRNA expression analyses identified several profiles that were specific to hereditary breast cancers. A total of 25 miRNAs were found to be differentially expressed (fold change: > 2.0 and p < 0.05) and considered as potential biomarkers (area under the curve > 0.75) in hereditary breast tumors compared to normal breast tissues, with an expressive upregulation among BRCAX cases. Furthermore, bioinformatic analysis revealed that these miRNAs shared target genes involved in ErbB, FoxO, and PI3K-Akt signaling pathways. Conclusions Our results showed that miRNA expression profiling can differentiate hereditary from sporadic breast tumors and normal breast tissues. These miRNAs were remarkably deregulated in BRCAX hereditary breast cancers. Therefore, miRNA signatures can be used as potential novel diagnostic biomarkers for the prediction of BRCA1/2- germline mutations and may be useful for future clinical management.
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Affiliation(s)
| | | | - Rhafaela Lima Causin
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil
| | | | | | | | | | | | | | | | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil.,Life and Health Sciences Research Institute (ICVS), Medical School, University of Minho, Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Edenir Inêz Palmero
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil.,Center of Molecular Diagnosis, Barretos Cancer Hospital, Barretos, SP, Brazil.,Department of Oncogenetics, Barretos Cancer Hospital, Barretos, SP, Brazil.,Barretos School of Health Sciences, Dr. Paulo Prata - FACISB, Barretos, SP, Brazil
| | - Márcia Maria Chiquitelli Marques
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil. .,Barretos School of Health Sciences, Dr. Paulo Prata - FACISB, Barretos, SP, Brazil. .,Tumor Biobank, Barretos Cancer Hospital, Barretos, SP, Brazil.
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86
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Loss of 5'-Methylthioadenosine Phosphorylase (MTAP) is Frequent in High-Grade Gliomas; Nevertheless, it is Not Associated with Higher Tumor Aggressiveness. Cells 2020; 9:cells9020492. [PMID: 32093414 PMCID: PMC7072758 DOI: 10.3390/cells9020492] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/04/2020] [Accepted: 02/10/2020] [Indexed: 12/12/2022] Open
Abstract
The 5’-methylthioadenosine phosphorylase (MTAP) gene is located in the chromosomal region 9p21. MTAP deletion is a frequent event in a wide variety of human cancers; however, its biological role in tumorigenesis remains unclear. The purpose of this study was to characterize the MTAP expression profile in a series of gliomas and to associate it with patients’ clinicopathological features. Moreover, we sought to evaluate, through glioma gene-edited cell lines, the biological impact of MTAP in gliomas. MTAP expression was evaluated in 507 glioma patients by immunohistochemistry (IHC), and the expression levels were associated with patients’ clinicopathological features. Furthermore, an in silico study was undertaken using genomic databases totalizing 350 samples. In glioma cell lines, MTAP was edited, and following MTAP overexpression and knockout (KO), a transcriptome analysis was performed by NanoString Pan-Cancer Pathways panel. Moreover, MTAP’s role in glioma cell proliferation, migration, and invasion was evaluated. Homozygous deletion of 9p21 locus was associated with a reduction of MTAP mRNA expression in the TCGA (The Cancer Genome Atlas) - glioblastoma dataset (p < 0.01). In addition, the loss of MTAP expression was markedly high in high-grade gliomas (46.6% of cases) determined by IHC and Western blotting (40% of evaluated cell lines). Reduced MTAP expression was associated with a better prognostic in the adult glioblastoma dataset (p < 0.001). Nine genes associated with five pathways were differentially expressed in MTAP-knockout (KO) cells, with six upregulated and three downregulated in MTAP. Analysis of cell proliferation, migration, and invasion did not show any significant differences between MTAP gene-edited and control cells. Our results integrating data from patients as well as in silico and in vitro models provide evidence towards the lack of strong biological importance of MTAP in gliomas. Despite the frequent loss of MTAP, it seems not to have a clinical impact in survival and does not act as a canonic tumor suppressor gene in gliomas.
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87
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A 4-gene signature from histologically normal surgical margins predicts local recurrence in patients with oral carcinoma: clinical validation. Sci Rep 2020; 10:1713. [PMID: 32015424 PMCID: PMC6997450 DOI: 10.1038/s41598-020-58688-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 01/17/2020] [Indexed: 12/24/2022] Open
Abstract
Prognostic biomarkers for recurrence of Oral Squamous Cell Carcinoma (OSCC) are urgently needed. We aimed to independently validate a 4-gene expression signature (MMP1, COL4A1, P4HA2, THBS2) predictive of OSCC recurrence risk. Gene expression was measured using Nanostring nCounter® in 245 histologically normal surgical resection margins from 62 patients. Association between risk scores for individual patients and recurrence was assessed by Kaplan-Meier analysis. Signature performance was quantified by concordance index (CI), hazard ratio (HR) and the area under receiver operating characteristics (AUC). Risk scores for recurrence were significantly higher than recurrence-free patients (p = 9.58e-7, Welch’s t-test). A solid performance of the 4-gene signature was determined: CI = 0.64, HR = 3.38 (p = 1.4E-4; log-rank test), AUC = 0.71. We showed that three margins per patient are sufficient to preserve predictive performance (CI = 0.65; HR = 2.92; p = 2.94e-3; AUC = 0.71). Association between the predicted risk scores and recurrence was assessed and showed HR = 2.44 (p = 9.6E-3; log-rank test, N = 62). Signature performance analysis was repeated using an optimized threshold (70th percentile of risks), resulting in HR = 3.38 (p = 1.4E-4; log-rank test, N = 62). The 4-gene signature was validated as predictive of recurrence risk in an independent cohort of patients with resected OSCC and histologically negative margins, and is potentially applicable for clinical decision making on adjuvant treatment and disease monitoring.
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88
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Zhang W, Ham J, Li Q, Deyssenroth MA, Lambertini L, Huang Y, Tsuchiya KJ, Chen J, Nomura Y. Moderate prenatal stress may buffer the impact of Superstorm Sandy on placental genes: Stress in Pregnancy (SIP) Study. PLoS One 2020; 15:e0226605. [PMID: 31995614 PMCID: PMC6988921 DOI: 10.1371/journal.pone.0226605] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 11/29/2019] [Indexed: 12/26/2022] Open
Abstract
The placenta plays a central role in the epigenetic programming of neurodevelopment by prenatal stress (PS), but this pathway is not fully understood. It difficult to study in humans because the conditions for intense, traumatic PS are almost impossible to create ethically. This study was able to capitalize on a 2012 disaster that hit New York, Superstorm Sandy, to examine the impact of traumatic stress on placental gene expression while also examining normative PS, and compare the two. Of the 303 expectant mothers participating in the Stress in Pregnancy Study, 95 women were pregnant when Superstorm Sandy struck. During their pregnancy, participants completed self-report measures of PS and distress that were combined, using latent profile analysis, into one global indicator of normative PS. Placental tissue was collected at delivery and frozen for storage. RNA expression was assessed for 40 placental genes known to associate with the stress response system and neurodevelopment in offspring. Results showed that normative PS increased expression of just MECP2, HSD11B2, and ZNF507, whereas Superstorm Sandy PS decreased expression of CDKL5, CFL1, DYRK1A, HSD11B2, MAOA, MAOB, NCOR1, and ZNF507. Interaction analyses indicated that Superstorm Sandy PS was associated with decreased gene expression for the low and high PS group for CFL1, DYRK1A, HSD11B2, MAOA, and NCOR1 and increased expression for the moderate PS group for FOXP1, NR3C1, and NR3C2. This study supports the idea that a moderate amount of normative PS may buffer the impact of traumatic PS, in this case caused by Superstorm Sandy, on placental gene expression, which suggests that the placenta itself mirrors the organism's ability to develop an epigenetic resilience to, and inoculation from, stress.
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Affiliation(s)
- Wei Zhang
- Department of Psychology, Queens College, CUNY, New York, NY, United States of America
- Department of Psychology, New Jersey City University, Jersey City, NJ, United States of America
| | - Jacob Ham
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Qian Li
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Maya A. Deyssenroth
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Luca Lambertini
- Department of Medicine, Endocrinology, Diabetes and Bone Disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Yonglin Huang
- Department of Psychology, Queens College, CUNY, New York, NY, United States of America
- Department of Psychology, The Graduate Center, CUNY, New York, NY, United States of America
| | - Kenji J. Tsuchiya
- Research Center for Child Mental Development, Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Jia Chen
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Yoko Nomura
- Department of Psychology, Queens College, CUNY, New York, NY, United States of America
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Psychology, The Graduate Center, CUNY, New York, NY, United States of America
- Research Center for Child Mental Development, Hamamatsu University School of Medicine, Shizuoka, Japan
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89
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Barrow-McGee R, Procter J, Owen J, Woodman N, Lombardelli C, Kothari A, Kovacs T, Douek M, George S, Barry PA, Ramsey K, Gibson A, Buus R, Holgersen E, Natrajan R, Haider S, Shattock MJ, Gillett C, Tutt AN, Pinder SE, Naidoo K. Real-time ex vivo perfusion of human lymph nodes invaded by cancer (REPLICANT): a feasibility study. J Pathol 2019; 250:262-274. [PMID: 31755096 PMCID: PMC7065097 DOI: 10.1002/path.5367] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 11/06/2019] [Accepted: 11/18/2019] [Indexed: 01/18/2023]
Abstract
Understanding how breast cancer (BC) grows in axillary lymph nodes (ALNs), and refining how therapies might halt that process, is clinically important. However, modelling the complex ALN microenvironment is difficult, and no human models exist at present. We harvested ALNs from ten BC patients, and perfused them at 37 °C ex vivo for up to 24 h. Controlled autologous testing showed that ALNs remain viable after 24 h of ex vivo perfusion: haematoxylin and eosin-stained histological appearance and proliferation (by Ki67 immunohistochemistry) did not change significantly over time for any perfused ALN compared with a control from time-point zero. Furthermore, targeted gene expression analysis (NanoString PanCancer IO360 panel) showed that only 21/750 genes were differentially expressed between control and perfused ALNs (|log2 FC| > 1 and q < 0.1): none were involved in apoptosis and metabolism, but rather all 21 genes were involved in immune function and angiogenesis. During perfusion, tissue acid-base balance remained stable. Interestingly, the flow rate increased (p < 0.001) in cancer-replaced (i.e. metastasis occupied more than 90% of the surface area on multiple levels) compared to cancer-free nodes (i.e. nodes with no metastasis on multiple sections). CXCL11 transcripts were significantly more abundant in cancer-replaced nodes, while CXCL12 transcripts were significantly more abundant in cancer-free nodes. These cytokines were also detected in the circulating perfusate. Monoclonal antibodies (nivolumab and trastuzumab) were administered into a further three ALNs to confirm perfusion efficacy. These drugs saturated the nodes; nivolumab even induced cancer cell death. Normothermic ALN perfusion is not only feasible but sustains the tumour microenvironment ex vivo for scientific investigation. This model could facilitate the identification of actionable immuno-oncology targets. © 2019 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Rachel Barrow-McGee
- Toby Robins Breast Cancer Now Research Centre, Breast Cancer Research Division, The Institute of Cancer Research, London, UK
| | - Julia Procter
- Toby Robins Breast Cancer Now Research Centre, Breast Cancer Research Division, The Institute of Cancer Research, London, UK
| | - Julie Owen
- King's Health Partners Cancer Biobank, Guy's Comprehensive Cancer Centre, London, UK
| | - Natalie Woodman
- King's Health Partners Cancer Biobank, Guy's Comprehensive Cancer Centre, London, UK
| | - Cristina Lombardelli
- King's Health Partners Cancer Biobank, Guy's Comprehensive Cancer Centre, London, UK
| | | | - Tibor Kovacs
- Guy's and St. Thomas' Hospital NHS Foundation Trust, London, UK
| | - Michael Douek
- School of Cancer and Pharmaceutical Sciences, King's College London, Guy's Comprehensive Cancer Centre, London, UK
| | - Simi George
- Department of Cellular Pathology, Guy's and St. Thomas' Hospital NHS Foundation Trust, London, UK
| | | | | | - Amy Gibson
- Toby Robins Breast Cancer Now Research Centre, Breast Cancer Research Division, The Institute of Cancer Research, London, UK
| | - Richard Buus
- Toby Robins Breast Cancer Now Research Centre, Breast Cancer Research Division, The Institute of Cancer Research, London, UK.,Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, UK
| | - Erle Holgersen
- Toby Robins Breast Cancer Now Research Centre, Breast Cancer Research Division, The Institute of Cancer Research, London, UK
| | - Rachael Natrajan
- Toby Robins Breast Cancer Now Research Centre, Breast Cancer Research Division, The Institute of Cancer Research, London, UK
| | - Syed Haider
- Toby Robins Breast Cancer Now Research Centre, Breast Cancer Research Division, The Institute of Cancer Research, London, UK
| | - Michael J Shattock
- British Heart Foundation Centre of Research Excellence, King's College London, St Thomas' Hospital, London, UK
| | - Cheryl Gillett
- King's Health Partners Cancer Biobank, Guy's Comprehensive Cancer Centre, London, UK
| | - Andrew Nj Tutt
- Toby Robins Breast Cancer Now Research Centre, Breast Cancer Research Division, The Institute of Cancer Research, London, UK
| | - Sarah E Pinder
- School of Cancer and Pharmaceutical Sciences, King's College London, Guy's Comprehensive Cancer Centre, London, UK
| | - Kalnisha Naidoo
- Toby Robins Breast Cancer Now Research Centre, Breast Cancer Research Division, The Institute of Cancer Research, London, UK.,Department of Cellular Pathology, Guy's and St. Thomas' Hospital NHS Foundation Trust, London, UK
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90
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Leal MF, Haynes BP, Schuster E, Yeo B, Afentakis M, Zabaglo L, Martins V, Buus R, Dodson A, Cheang MCU, Smith IE, Martin LA, Dowsett M. Early Enrichment of ESR1 Mutations and the Impact on Gene Expression in Presurgical Primary Breast Cancer Treated with Aromatase Inhibitors. Clin Cancer Res 2019; 25:7485-7496. [PMID: 31548345 DOI: 10.1158/1078-0432.ccr-19-1129] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/24/2019] [Accepted: 09/09/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE To investigate the presence of ESR1 mutations in primary estrogen-receptor-positive (ER+) breast cancer treated with extended (>4 weeks) neoadjuvant (presurgical) aromatase inhibitor (NAI) therapy and to identify patients who may gain less benefit from aromatase inhibition (AI) alone based upon on-treatment changes in gene expression. EXPERIMENTAL DESIGN We evaluated ER, progesterone receptor, and Ki67 by immunostaining, ESR1 mutations by droplet-digital PCR and expression of over 800 key breast cancer genes in paired pre- and post-NAI tumor samples from 87 ER+ breast cancer patients. RESULTS Cell proliferation and estrogen-regulated genes (ERG) remained suppressed in most tumors indicative of persistent response to NAI. Enrichment of ESR1 mutations was found in five tumors and predominantly in patients receiving therapy for >6 months. ESR1-mutant tumors showed increased expression of ESR1 transcript and limited suppression of ERGs and proliferation-associated genes in response to NAI. ESR1 wild-type tumors with high residual proliferation (Ki67r ≥10%; 15/87 tumors) showed lower ESR1/ER expression pre- and post-therapy and lower ERGs. Tumors with ESR1 mutations or Ki67r ≥10% showed less inhibition of estrogen response, cell cycle, and E2F-target genes. CONCLUSIONS Ligand-independent ER signaling, as a result of ESR1 mutation or reduced ER dependence, identified after extended NAI therapy, can guide early selection of patients who would benefit from combination therapy.
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Affiliation(s)
- Mariana Ferreira Leal
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital NHS Trust, London, United Kingdom.
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Ben P Haynes
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital NHS Trust, London, United Kingdom
| | - Eugene Schuster
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Belinda Yeo
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital NHS Trust, London, United Kingdom
| | - Maria Afentakis
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital NHS Trust, London, United Kingdom
| | - Lila Zabaglo
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital NHS Trust, London, United Kingdom
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Vera Martins
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Richard Buus
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Andrew Dodson
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital NHS Trust, London, United Kingdom
| | - Maggie C U Cheang
- Clinical Trials and Statistic Unit, The Institute of Cancer Research, Sutton, United Kingdom
| | - Ian E Smith
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital NHS Trust, London, United Kingdom
- Breast Unit, The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Lesley-Ann Martin
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Mitch Dowsett
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital NHS Trust, London, United Kingdom
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
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91
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Mairinger F, Bankfalvi A, Schmid KW, Mairinger E, Mach P, Walter RF, Borchert S, Kasimir-Bauer S, Kimmig R, Buderath P. Digital Immune-Related Gene Expression Signatures In High-Grade Serous Ovarian Carcinoma: Developing Prediction Models For Platinum Response. Cancer Manag Res 2019; 11:9571-9583. [PMID: 31814759 PMCID: PMC6858803 DOI: 10.2147/cmar.s219872] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/28/2019] [Indexed: 12/18/2022] Open
Abstract
Purpose Response to platinum-based therapy is a major prognostic factor in high-grade serous ovarian cancer (HGSOC). While the exact mechanisms of platinum-resistance remain unclear, evidence is accumulating for a connection between the organism’s immune-response and response to platinum. However, predictive tools are missing. This study was performed to examine the putative role of the genetic tumor immune-microenvironment in mediating differential chemotherapy response in HGSOC patients. Patients and methods Expression profiling of 770 immune-related genes was performed in tumor tissues from 23 HGSOC cases. Tumors were screened for prognostic and predictive biomarkers using the NanoString nCounter platform for digital gene expression analysis with the appurtenant PanCancer Immune Profiling panel. As validation cohort, gene expression data (RNA Seq) of 303 patients with epithelial ovarian carcinoma (EOC) were retrieved from the The Cancer Genome Atlas (TCGA) database. Different scoring-systems were computed for prediction of risk-of-resistance to cisplatin, disease-free survival (DFS) and overall survival (OS). Results Validated on the TCGA-dataset, the developed scores identified 11 significantly differentially expressed genes (p <0.01**) associated with platinum response. HSD11B1 was highly significantly associated with lower risk of recurrence and 7 targets were found highly significantly influencing OS time (p <0.01**). Conclusion Our results suggest that response to platinum-based therapy and DFS in ovarian HGSOC is associated with distinct gene-expression patterns related to the tumor immune-system. We generated predictive scoring systems which proved valid when applied to a set of 303 EOC patients.
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Affiliation(s)
- Fabian Mairinger
- Institute for Pathology, University Hospital Essen, Essen, Germany
| | - Agnes Bankfalvi
- Institute for Pathology, University Hospital Essen, Essen, Germany
| | | | - Elena Mairinger
- Ruhrlandklinik, West German Lung Centre, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Pawel Mach
- Department of Gynecology and Obstetrics, University Hospital Essen, Essen, Germany
| | - Robert Fh Walter
- Ruhrlandklinik, West German Lung Centre, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Sabrina Borchert
- Institute for Pathology, University Hospital Essen, Essen, Germany
| | - Sabine Kasimir-Bauer
- Department of Gynecology and Obstetrics, University Hospital Essen, Essen, Germany
| | - Rainer Kimmig
- Department of Gynecology and Obstetrics, University Hospital Essen, Essen, Germany
| | - Paul Buderath
- Department of Gynecology and Obstetrics, University Hospital Essen, Essen, Germany
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92
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Roberto D, Selvarajah S, Park PC, Berman D, Venkateswaran V. Functional validation of metabolic genes that distinguish Gleason 3 from Gleason 4 prostate cancer foci. Prostate 2019; 79:1777-1788. [PMID: 31503357 DOI: 10.1002/pros.23903] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 08/14/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND Gleason grade is among the most powerful clinicopathological classification systems used to assess risk of lethal potential in prostate cancer, yet its biologic basis is poorly understood. Notably, pure low-grade cancers, comprised predominantly of Gleason pattern 3 (G3) are typically indolent, with lethal potential emerging with the progression of higher-grade Gleason patterns 4 (G4) or 5. One of the hallmarks of more aggressive cancer phenotypes is the stereotyped set of metabolic characteristics that transformed cells acquire to facilitate unregulated growth. In the present study, we profiled expression signatures of metabolic genes that are differentially expressed between G3 and G4 cancer foci and investigated the functional role of two of the profiled genes, PGRMC1 and HSD17B4, in prostate cancer cells. METHODS Gene expression profiling was conducted using 32 G3 and 32 G4 cancer foci from patients with 3+3 and ≥4+3 tumors, respectively. A 95-gene Nanostring probe set was used to probe genes associated with energy metabolism. Two out of five genes (PGRMC1 and HSD17B4) that significantly distinguish between G3 and G4 were functionally validated in vitro using established prostate cancer cells (PC3, DU145). Expression of PGRMC1 and HSD17B4 was knocked down and subsequent studies were performed to analyze cell proliferation, migration, invasion, and apoptosis. Mechanistic studies that explored the epidermal growth factor receptor (EGFR) pathway were performed by Western blot. RESULTS Multivariate analysis identified five metabolic genes that were differentially expressed between G3 and G4 stroma (P < .05). Functional validation studies revealed that knockdown of PGRMC1 and HSD17B4 significantly decreased cell proliferation, migration, and invasion, and increased apoptosis in PC3 and DU145 cells. Mechanistic studies showed that these effects, after PGRMC1 knockdown, were possibly mediated through alterations in downstream components of the EGFR, protein kinase B, and nuclear factor kappa-light-chain-enhancer of activated B cells pathways. CONCLUSION The following study provides evidence supporting the use of metabolic genes PGRMC1 and HSD17B4 as a prognostic biomarker for the distinction between G3 and G4 prostate cancers.
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Affiliation(s)
- Domenica Roberto
- Department of Surgery (Urology), Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Shamini Selvarajah
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada
| | - Paul C Park
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - David Berman
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
- Division of Cancer Biology and Genetics, Cancer Research Institute, Queen's University, Kingston, Ontario, Canada
| | - Vasundara Venkateswaran
- Department of Surgery (Urology), Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
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93
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Dietary tryptophan links encephalogenicity of autoreactive T cells with gut microbial ecology. Nat Commun 2019; 10:4877. [PMID: 31653831 PMCID: PMC6814758 DOI: 10.1038/s41467-019-12776-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 09/27/2019] [Indexed: 01/07/2023] Open
Abstract
The interaction between the mammalian host and its resident gut microbiota is known to license adaptive immune responses. Nutritional constituents strongly influence composition and functional properties of the intestinal microbial communities. Here, we report that omission of a single essential amino acid - tryptophan – from the diet abrogates CNS autoimmunity in a mouse model of multiple sclerosis. Dietary tryptophan restriction results in impaired encephalitogenic T cell responses and is accompanied by a mild intestinal inflammatory response and a profound phenotypic shift of gut microbiota. Protective effects of dietary tryptophan restriction are abrogated in germ-free mice, but are independent of canonical host sensors of intracellular tryptophan metabolites. We conclude that dietary tryptophan restriction alters metabolic properties of gut microbiota, which in turn have an impact on encephalitogenic T cell responses. This link between gut microbiota, dietary tryptophan and adaptive immunity may help to develop therapeutic strategies for protection from autoimmune neuroinflammation. Food intake shapes intestinal microbiome composition, which in turn shapes adaptive immune responses. Here the authors show that dietary tryptophan restriction (DTR) protects mice from subsequent autoimmune neuropathology challenge by altering intestinal microbiota, highlighting the potential of diet-regulated microbiota to prevent immune pathology.
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94
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A Distinct Pretreatment Immune Gene Signature in Lentigo Maligna Is Associated with Imiquimod Response. J Invest Dermatol 2019; 140:869-877.e16. [PMID: 31580843 DOI: 10.1016/j.jid.2019.07.725] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/26/2019] [Accepted: 07/30/2019] [Indexed: 12/24/2022]
Abstract
Lentigo maligna (LM) is a common subtype of in situ melanoma on chronically sun-exposed skin, particularly the head and neck of older patients. Although surgery is the standard treatment, there is associated morbidity, and options such as imiquimod cream or radiotherapy may be used if surgery is refused or inappropriate. Complete response rates following imiquimod treatment are variable in the literature. The aim of this study was to evaluate the host immune response both before and following treatment with imiquimod to better identify likely responders. Paired pre- and post-imiquimod treatment specimens were available for 27 patients. Patients were treated with imiquimod 5 days per week for 12 weeks; at 16 weeks, lesions were excised for histological assessment. Of the 27 patients, 16 were responders and 11 failed to clear the disease. PDL1 protein expression was increased, accompanied by a unique gene signature in lesions from patients that subsequently histologically cleared LM by 16 weeks. This comprised 57 upregulated immune genes in signaling networks for antigen presentation, type I interferon signaling, and T-cell activation. This may represent an early responder group to imiquimod, and this unique gene signature potentially can be used as a biomarker of LM response to imiquimod.
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95
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Chakrabarty P, Li A, Ladd TB, Strickland MR, Koller EJ, Burgess JD, Funk CC, Cruz PE, Allen M, Yaroshenko M, Wang X, Younkin C, Reddy J, Lohrer B, Mehrke L, Moore BD, Liu X, Ceballos-Diaz C, Rosario AM, Medway C, Janus C, Li HD, Dickson DW, Giasson BI, Price ND, Younkin SG, Ertekin-Taner N, Golde TE. TLR5 decoy receptor as a novel anti-amyloid therapeutic for Alzheimer's disease. J Exp Med 2019; 215:2247-2264. [PMID: 30158114 PMCID: PMC6122970 DOI: 10.1084/jem.20180484] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/09/2018] [Accepted: 05/09/2018] [Indexed: 12/22/2022] Open
Abstract
Chakrabarty et al. show that human TLR5 ectodomain reduces amyloid β (Aβ) plaques by direct interaction with Aβ, demonstrating the feasibility of such immune decoy receptor strategies as potential biotherapies in Alzheimer’s disease. There is considerable interest in harnessing innate immunity to treat Alzheimer’s disease (AD). Here, we explore whether a decoy receptor strategy using the ectodomain of select TLRs has therapeutic potential in AD. AAV-mediated expression of human TLR5 ectodomain (sTLR5) alone or fused to human IgG4 Fc (sTLR5Fc) results in robust attenuation of amyloid β (Aβ) accumulation in a mouse model of Alzheimer-type Aβ pathology. sTLR5Fc binds to oligomeric and fibrillar Aβ with high affinity, forms complexes with Aβ, and blocks Aβ toxicity. Oligomeric and fibrillar Aβ modulates flagellin-mediated activation of human TLR5 but does not, by itself, activate TLR5 signaling. Genetic analysis shows that rare protein coding variants in human TLR5 may be associated with a reduced risk of AD. Further, transcriptome analysis shows altered TLR gene expression in human AD. Collectively, our data suggest that TLR5 decoy receptor–based biologics represent a novel and safe Aβ-selective class of biotherapy in AD.
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Affiliation(s)
- Paramita Chakrabarty
- Center for Translational Research in Neurodegenerative Disease, Department of Neuroscience, University of Florida, Gainesville, FL .,McKnight Brain Institute, University of Florida, Gainesville, FL
| | - Andrew Li
- Center for Translational Research in Neurodegenerative Disease, Department of Neuroscience, University of Florida, Gainesville, FL
| | - Thomas B Ladd
- Center for Translational Research in Neurodegenerative Disease, Department of Neuroscience, University of Florida, Gainesville, FL
| | - Michael R Strickland
- Center for Translational Research in Neurodegenerative Disease, Department of Neuroscience, University of Florida, Gainesville, FL
| | - Emily J Koller
- Center for Translational Research in Neurodegenerative Disease, Department of Neuroscience, University of Florida, Gainesville, FL
| | | | | | - Pedro E Cruz
- Center for Translational Research in Neurodegenerative Disease, Department of Neuroscience, University of Florida, Gainesville, FL
| | - Mariet Allen
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL
| | - Mariya Yaroshenko
- Center for Translational Research in Neurodegenerative Disease, Department of Neuroscience, University of Florida, Gainesville, FL
| | - Xue Wang
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL
| | - Curtis Younkin
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL
| | - Joseph Reddy
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL
| | | | - Leonie Mehrke
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL
| | - Brenda D Moore
- Center for Translational Research in Neurodegenerative Disease, Department of Neuroscience, University of Florida, Gainesville, FL
| | - Xuefei Liu
- Center for Translational Research in Neurodegenerative Disease, Department of Neuroscience, University of Florida, Gainesville, FL
| | - Carolina Ceballos-Diaz
- Center for Translational Research in Neurodegenerative Disease, Department of Neuroscience, University of Florida, Gainesville, FL
| | - Awilda M Rosario
- Center for Translational Research in Neurodegenerative Disease, Department of Neuroscience, University of Florida, Gainesville, FL
| | | | - Christopher Janus
- Center for Translational Research in Neurodegenerative Disease, Department of Neuroscience, University of Florida, Gainesville, FL
| | | | | | - Benoit I Giasson
- Center for Translational Research in Neurodegenerative Disease, Department of Neuroscience, University of Florida, Gainesville, FL.,McKnight Brain Institute, University of Florida, Gainesville, FL
| | | | | | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL.,Department of Neurology, Mayo Clinic, Jacksonville, FL
| | - Todd E Golde
- Center for Translational Research in Neurodegenerative Disease, Department of Neuroscience, University of Florida, Gainesville, FL .,McKnight Brain Institute, University of Florida, Gainesville, FL
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96
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Sustained Type I interferon signaling as a mechanism of resistance to PD-1 blockade. Cell Res 2019; 29:846-861. [PMID: 31481761 PMCID: PMC6796942 DOI: 10.1038/s41422-019-0224-x] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 08/05/2019] [Indexed: 01/05/2023] Open
Abstract
PD-1 blockade represents a major therapeutic avenue in anticancer immunotherapy. Delineating mechanisms of secondary resistance to this strategy is increasingly important. Here, we identified the deleterious role of signaling via the type I interferon (IFN) receptor in tumor and antigen presenting cells, that induced the expression of nitric oxide synthase 2 (NOS2), associated with intratumor accumulation of regulatory T cells (Treg) and myeloid cells and acquired resistance to anti-PD-1 monoclonal antibody (mAb). Sustained IFNβ transcription was observed in resistant tumors, in turn inducing PD-L1 and NOS2 expression in both tumor and dendritic cells (DC). Whereas PD-L1 was not involved in secondary resistance to anti-PD-1 mAb, pharmacological or genetic inhibition of NOS2 maintained long-term control of tumors by PD-1 blockade, through reduction of Treg and DC activation. Resistance to immunotherapies, including anti-PD-1 mAb in melanoma patients, was also correlated with the induction of a type I IFN signature. Hence, the role of type I IFN in response to PD-1 blockade should be revisited as sustained type I IFN signaling may contribute to resistance to therapy.
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97
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Jia G, Wang X, Li Q, Lu W, Tang X, Wistuba I, Xie Y. RCRnorm: An integrated system of random-coefficient hierarchical regression models for normalizing NanoString nCounter data. Ann Appl Stat 2019; 13:1617-1647. [PMID: 33564347 PMCID: PMC7869841 DOI: 10.1214/19-aoas1249] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) samples have great potential for biomarker discovery, retrospective studies, and diagnosis or prognosis of diseases. Their application, however, is hindered by the unsatisfactory performance of traditional gene expression profiling techniques on damaged RNAs. NanoString nCounter platform is well suited for profiling of FFPE samples and measures gene expression with high sensitivity, which may greatly facilitate realization of scientific and clinical values of FFPE samples. However, methodological development for normalization, a critical step when analyzing this type of data, is far behind. Existing methods designed for the platform use information from different types of internal controls separately and rely on an overly-simplified assumption that expression of housekeeping genes is constant across samples for global scaling. Thus, these methods are not optimized for the nCounter system, not mentioning that they were not developed for FFPE samples. We construct an integrated system of random-coefficient hierarchical regression models to capture main patterns and characteristics observed from NanoString data of FFPE samples, and develop a Bayesian approach to estimate parameters and normalize gene expression across samples. Our method, labeled RCRnorm, incorporates information from all aspects of the experimental design and simultaneously removes biases from various sources. It eliminates the unrealistic assumption on housekeeping genes and offers great interpretability. Furthermore, it is applicable to freshly frozen or like samples that can be generally viewed as a reduced case of FFPE samples. Simulation and applications showed the superior performance of RCRnorm.
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Affiliation(s)
- Gaoxiang Jia
- Department of Statistical Science, Southern Methodist University, 3225 Daniel Avenue, P O Box 750332, Dallas, Texas 75275
- Quantitative Biomedical Research Center, Department of Clinical Sciences, The University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Xinlei Wang
- Department of Statistical Science, Southern Methodist University, 3225 Daniel Avenue, P O Box 750332, Dallas, Texas 75275
| | - Qiwei Li
- Quantitative Biomedical Research Center, Department of Clinical Sciences, The University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Wei Lu
- Department of Translational Molecular Pathology, University of Texas, MD Anderson Cancer Center, Houston, Texas 77030
| | - Ximing Tang
- Department of Translational Molecular Pathology, University of Texas, MD Anderson Cancer Center, Houston, Texas 77030
| | - Ignacio Wistuba
- Department of Translational Molecular Pathology, University of Texas, MD Anderson Cancer Center, Houston, Texas 77030
| | - Yang Xie
- Quantitative Biomedical Research Center, Department of Clinical Sciences, The University of Texas Southwestern Medical Center, Dallas, Texas 75390
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98
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Canouil M, Bouland GA, Bonnefond A, Froguel P, ’t Hart LM, Slieker RC. NACHO: an R package for quality control of NanoString nCounter data. Bioinformatics 2019; 36:970-971. [PMID: 31504159 PMCID: PMC9883715 DOI: 10.1093/bioinformatics/btz647] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/24/2019] [Accepted: 08/14/2019] [Indexed: 02/02/2023] Open
Abstract
SUMMARY The NanoStringTM nCounter® is a platform for the targeted quantification of expression data in biofluids and tissues. While software by the manufacturer is available in addition to third parties packages, they do not provide a complete quality control (QC) pipeline. Here, we present NACHO ('NAnostring quality Control dasHbOard'), a comprehensive QC R-package. The package consists of three subsequent steps: summarize, visualize and normalize. The summarize function collects all the relevant data and stores it in a tidy format, the visualize function initiates a dashboard with plots of the relevant QC outcomes. It contains QC metrics that are measured by default by the manufacturer, but also calculates other insightful measures, including the scaling factors that are needed in the normalization step. In this normalization step, different normalization methods can be chosen to optimally preprocess data. Together, NACHO is a comprehensive method that optimizes insight and preprocessing of nCounter® data. AVAILABILITY AND IMPLEMENTATION NACHO is available as an R-package on CRAN and the development version on GitHub https://github.com/mcanouil/NACHO. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | - Amélie Bonnefond
- Université de Lille, CNRS, Institut Pasteur de Lille, UMR 8199 - EGID, F-59000 Lille, France,Department of Medicine, Section of Genomics of Common Disease, Imperial College London, London SW7 2AZ, UK
| | - Philippe Froguel
- Université de Lille, CNRS, Institut Pasteur de Lille, UMR 8199 - EGID, F-59000 Lille, France,Department of Medicine, Section of Genomics of Common Disease, Imperial College London, London SW7 2AZ, UK
| | - Leen M ’t Hart
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands,Department of Epidemiology and Biostatistics, Amsterdam Public Health Institute, Amsterdam UMC, VU University Medical Center, Amsterdam 1081 HV, The Netherlands,Molecular Epidemiology Section, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden 2333 ZC, The Netherlands
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99
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Cho E, Park IJ, Yeom SS, Hong SM, Lee JB, Kim YW, Kim MJ, Lim HM, Lim SB, Yu CS, Kim JC. A Multigene Model for Predicting Tumor Responsiveness After Preoperative Chemoradiotherapy for Rectal Cancer. Int J Radiat Oncol Biol Phys 2019; 105:834-842. [PMID: 31419511 DOI: 10.1016/j.ijrobp.2019.07.058] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 07/25/2019] [Accepted: 07/30/2019] [Indexed: 12/29/2022]
Abstract
PURPOSE Although preoperative chemoradiotherapy (PCRT) is regarded as a standard treatment for locally advanced rectal cancer, there is no reliable biomarker for predicting responsiveness to PCRT. We aimed to develop a biomarker model for predicting response to PCRT. METHODS AND MATERIALS We included 184 patients who received PCRT followed by surgical resection and categorized them as good responders (complete or near-complete regression) or poor responders (all other patients). Candidate gene mRNAs were isolated from formalin-fixed paraffin-embedded tumor specimens and analyzed using the NanoString nCounter gene expression assay. Stepwise logistic regression analysis was used to select genes in discovery and training phases. A quantitative radio-responsiveness prediction model was developed and validated using internal cross-validation groups, and the model's predictive value was assessed based on the area under the receiver operating characteristic curve (AUC). RESULTS By comparing the gene expressions between good and poor responders, we created a multigene mRNA model using FZD9, HRAS, ITGA7, MECOM, MMP3, NKD1, PIK3CD, and PRKCB. This panel showed good ability to predict treatment response (AUC: 0.846 for the whole data set). Internal cross-validation was performed to evaluate the model's predictive stability among 3 cohorts, which provided AUC values of 0.808-0.909. The satisfactory diagnostic performance of the radio-response prediction index persisted regardless of other clinicopathologic features such as clinical T or N stage, interval between radiation and surgery, and pretreatment carcinoembryonic antigen levels (P = .001, 95% CI, 0.686-0.905). CONCLUSIONS We developed a multigene mRNA-based biomarker model that allows prediction of rectal cancer response to PCRT, which may help identify patients who will benefit most from PCRT.
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Affiliation(s)
- Eunhae Cho
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - In Ja Park
- Department of Colon and Rectal Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
| | - Seung-Seop Yeom
- Department of Colon and Rectal Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Seung Mo Hong
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Jung Bok Lee
- Clinical Epidemiology and Biostatistics, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Yeon Wook Kim
- Asan Institute for Life Science, Asan Medical Center, Seoul, Korea
| | - Mi-Ju Kim
- Asan Institute for Life Science, Asan Medical Center, Seoul, Korea
| | - Hye Min Lim
- Asan Institute for Life Science, Asan Medical Center, Seoul, Korea
| | - Seok-Byung Lim
- Department of Colon and Rectal Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Chang Sik Yu
- Department of Colon and Rectal Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Jin Cheon Kim
- Department of Colon and Rectal Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
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100
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Izzy S, Liu Q, Fang Z, Lule S, Wu L, Chung JY, Sarro-Schwartz A, Brown-Whalen A, Perner C, Hickman SE, Kaplan DL, Patsopoulos NA, El Khoury J, Whalen MJ. Time-Dependent Changes in Microglia Transcriptional Networks Following Traumatic Brain Injury. Front Cell Neurosci 2019; 13:307. [PMID: 31440141 PMCID: PMC6694299 DOI: 10.3389/fncel.2019.00307] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 06/24/2019] [Indexed: 12/21/2022] Open
Abstract
The neuroinflammatory response to traumatic brain injury (TBI) is critical to both neurotoxicity and neuroprotection, and has been proposed as a potentially modifiable driver of secondary injury in animal and human studies. Attempts to broadly target immune activation have been unsuccessful in improving outcomes, in part because the precise cellular and molecular mechanisms driving injury and outcome at acute, subacute, and chronic time points after TBI remain poorly defined. Microglia play a critical role in neuroinflammation and their persistent activation may contribute to long-term functional deficits. Activated microglia are characterized by morphological transformation and transcriptomic changes associated with specific inflammatory states. We analyzed the temporal course of changes in inflammatory genes of microglia isolated from injured brains at 2, 14, and 60 days after controlled cortical impact (CCI) in mice, a well-established model of focal cerebral contusion. We identified a time dependent, injury-associated change in the microglial gene expression profile toward a reduced ability to sense tissue damage, perform housekeeping, and maintain homeostasis in the early stages following CCI, with recovery and transition to a specialized inflammatory state over time. This later state starts at 14 days post-injury and is characterized by a biphasic pattern of IFNγ, IL-4, and IL-10 gene expression changes, with concurrent proinflammatory and anti-inflammatory gene changes. Our transcriptomic data sets are an important step to understand microglial role in TBI pathogenesis at the molecular level and identify common pathways that affect outcome. More studies to evaluate gene expression at the single cell level and focusing on subacute and chronic timepoint are warranted.
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Affiliation(s)
- Saef Izzy
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States.,Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States.,Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, United States.,Harvard Medical School, Boston, MA, United States
| | - Qiong Liu
- Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, Shanghai, China
| | - Zhou Fang
- Harvard Medical School, Boston, MA, United States.,Systems Biology and Computer Science Program, Ann Romney Center for Neurological Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA, United States.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Sevda Lule
- Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, United States.,Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Limin Wu
- Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, United States.,Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Joon Yong Chung
- Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, United States.,Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Aliyah Sarro-Schwartz
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States.,Harvard Medical School, Boston, MA, United States
| | - Alexander Brown-Whalen
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States.,Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, United States
| | - Caroline Perner
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States.,Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, United States.,Harvard Medical School, Boston, MA, United States
| | - Suzanne E Hickman
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States.,Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, United States.,Harvard Medical School, Boston, MA, United States
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, Medford, MA, United States
| | - Nikolaos A Patsopoulos
- Harvard Medical School, Boston, MA, United States.,Systems Biology and Computer Science Program, Ann Romney Center for Neurological Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA, United States.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Joseph El Khoury
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States.,Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, United States.,Harvard Medical School, Boston, MA, United States
| | - Michael J Whalen
- Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, United States.,Harvard Medical School, Boston, MA, United States.,Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
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