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Mitchell MI, Ben‐Dov IZ, Ye K, Liu C, Shi M, Sadoughi A, Shah C, Siddiqui T, Okorozo A, Gutierrez M, Unawane R, Biamonte L, Parikh K, Spivack S, Loudig O. Exhaled breath condensate contains extracellular vesicles (EVs) that carry miRNA cargos of lung tissue origin that can be selectively purified and analyzed. J Extracell Vesicles 2024; 13:e12440. [PMID: 38659349 PMCID: PMC11043690 DOI: 10.1002/jev2.12440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 03/24/2024] [Indexed: 04/26/2024] Open
Abstract
Lung diseases, including lung cancer, are rising causes of global mortality. Despite novel imaging technologies and the development of biomarker assays, the detection of lung cancer remains a significant challenge. However, the lung communicates directly with the external environment and releases aerosolized droplets during normal tidal respiration, which can be collected, stored and analzsed as exhaled breath condensate (EBC). A few studies have suggested that EBC contains extracellular vesicles (EVs) whose microRNA (miRNA) cargos may be useful for evaluating different lung conditions, but the cellular origin of these EVs remains unknown. In this study, we used nanoparticle tracking, transmission electron microscopy, Western blot analyses and super resolution nanoimaging (ONi) to detect and validate the identity of exhaled EVs (exh-EVs). Using our customizable antibody-purification assay, EV-CATCHER, we initially determined that exh-EVs can be selectively enriched from EBC using antibodies against three tetraspanins (CD9, CD63 and CD81). Using ONi we also revealed that some exh-EVs harbour lung-specific proteins expressed in bronchiolar Clara cells (Clara Cell Secretory Protein [CCSP]) and Alveolar Type II cells (Surfactant protein C [SFTPC]). When conducting miRNA next generation sequencing (NGS) of airway samples collected at five different anatomic levels (i.e., mouth rinse, mouth wash, bronchial brush, bronchoalveolar lavage [BAL] and EBC) from 18 subjects, we determined that miRNA profiles of exh-EVs clustered closely to those of BAL EVs but not to those of other airway samples. When comparing the miRNA profiles of EVs purified from matched BAL and EBC samples with our three tetraspanins EV-CATCHER assay, we captured significant miRNA expression differences associated with smoking, asthma and lung tumor status of our subjects, which were also reproducibly detected in EVs selectively purified with our anti-CCSP/SFTPC EV-CATCHER assay from the same samples, but that confirmed their lung tissue origin. Our findings underscore that enriching exh-EV subpopulations from EBC allows non-invasive sampling of EVs produced by lung tissues.
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Affiliation(s)
- Megan I. Mitchell
- Center for Discovery and InnovationHackensack Meridian HealthNutleyNew JerseyUSA
| | - Iddo Z. Ben‐Dov
- Laboratory of Medical Transcriptomics, Internal Medicine BHadassah‐Hebrew University Medical CenterJerusalemIsrael
| | - Kenny Ye
- The Albert Einstein College of MedicineMontefiore Medical CenterBronxNew JerseyUSA
| | - Christina Liu
- Center for Discovery and InnovationHackensack Meridian HealthNutleyNew JerseyUSA
| | - Miao Shi
- The Albert Einstein College of MedicineMontefiore Medical CenterBronxNew JerseyUSA
| | - Ali Sadoughi
- The Albert Einstein College of MedicineMontefiore Medical CenterBronxNew JerseyUSA
| | - Chirag Shah
- The Albert Einstein College of MedicineMontefiore Medical CenterBronxNew JerseyUSA
| | - Taha Siddiqui
- The Albert Einstein College of MedicineMontefiore Medical CenterBronxNew JerseyUSA
| | - Aham Okorozo
- The Albert Einstein College of MedicineMontefiore Medical CenterBronxNew JerseyUSA
| | - Martin Gutierrez
- Department of Thoracic OncologyHackensack University Medical Center, Hackensack Meridian HealthHackensackNew JerseyUSA
| | - Rashmi Unawane
- Department of Thoracic OncologyHackensack University Medical Center, Hackensack Meridian HealthHackensackNew JerseyUSA
| | - Lisa Biamonte
- Department of Thoracic OncologyHackensack University Medical Center, Hackensack Meridian HealthHackensackNew JerseyUSA
| | - Kaushal Parikh
- Department of Thoracic OncologyThe Mayo ClinicRochesterMinnesotaUSA
| | - Simon Spivack
- The Albert Einstein College of MedicineMontefiore Medical CenterBronxNew JerseyUSA
| | - Olivier Loudig
- Center for Discovery and InnovationHackensack Meridian HealthNutleyNew JerseyUSA
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Mitchell MI, Ben-Dov IZ, Liu C, Wang T, Hazan RB, Bauer TL, Zakrzewski J, Donnelly K, Chow K, Ma J, Loudig O. Non-invasive detection of orthotopic human lung tumors by microRNA expression profiling of mouse exhaled breath condensates and exhaled extracellular vesicles. EXTRACELLULAR VESICLES AND CIRCULATING NUCLEIC ACIDS 2024; 5:138-164. [PMID: 38863869 PMCID: PMC11165456 DOI: 10.20517/evcna.2023.77] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Aim The lung is the second most frequent site of metastatic dissemination. Early detection is key to improving survival. Given that the lung interfaces with the external environment, the collection of exhaled breath condensate (EBC) provides the opportunity to obtain biological material including exhaled miRNAs that originate from the lung. Methods In this proof-of-principal study, we used the highly metastatic MDA-MB-231 subline 3475 breast cancer cell line (LM-3475) to establish an orthotopic lung tumor-bearing mouse model and investigate non-invasive detection of lung tumors by analysis of exhaled miRNAs. We initially conducted miRNA NGS and qPCR validation analyses on condensates collected from unrestrained animals and identified significant miRNA expression differences between the condensates of lung tumor-bearing and control mice. To focus our purification of EBC and evaluate the origin of these differentially expressed miRNAs, we developed a system to collect EBC directly from the nose and mouth of our mice. Results Using nanoparticle distribution analyses, TEM, and ONi super-resolution nanoimaging, we determined that human tumor EVs could be increasingly detected in mouse EBC during the progression of secondary lung tumors. Using our customizable EV-CATCHER assay, we purified human tumor EVs from mouse EBC and demonstrated that the bulk of differentially expressed exhaled miRNAs originate from lung tumors, which could be detected by qPCR within 1 to 2 weeks after tail vein injection of the metastatic cells. Conclusion This study is the first of its kind and demonstrates that lung tumor EVs are exhaled in mice and provide non-invasive biomarkers for detection of lung tumors.
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Affiliation(s)
- Megan I. Mitchell
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
- Hackensack University Medical Center, Hackensack Meridian Health, Hackensack, NJ 07601, USA
| | - Iddo Z. Ben-Dov
- Laboratory of Medical Transcriptomics, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Christina Liu
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - Tao Wang
- Department of Epidemiology and Population Health, The Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY 10461, USA
| | - Rachel B. Hazan
- Department of Pathology, The Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY 10461, USA
| | - Thomas L. Bauer
- Jersey Shore University Medical Center, Hackensack Meridian Health, Neptune City, NJ 07753, USA
| | - Johannes Zakrzewski
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
- Hackensack University Medical Center, Hackensack Meridian Health, Hackensack, NJ 07601, USA
| | - Kathryn Donnelly
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - Kar Chow
- Hackensack University Medical Center, Hackensack Meridian Health, Hackensack, NJ 07601, USA
| | - Junfeng Ma
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Olivier Loudig
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
- Hackensack University Medical Center, Hackensack Meridian Health, Hackensack, NJ 07601, USA
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Park JA, Pham D, Yalamanchili S, Twardus S, Suzuki K. Developing technologies and areas of interest in lung cancer screening adjuncts. J Thorac Dis 2024; 16:1552-1564. [PMID: 38505010 PMCID: PMC10944753 DOI: 10.21037/jtd-23-1326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/22/2023] [Indexed: 03/21/2024]
Abstract
Lung cancer remains the leading cause of cancer mortality. Screening guidelines have been implemented in the past decade to aid in earlier detection of at-risk groups. Nevertheless, computed tomography (CT) scans, the principal screening modality in use today, are still low yield, with 3.6% of lung cancer confirmed amongst 39.1% of lesions detected over a 3-year period. They also carry relatively high false positive rates, between 9% and 27%, which can bear unnecessary financial and emotional costs to patients. As such, research efforts have been dedicated to the development of lung cancer screening adjuncts to improve detection reliability. We herein review several emerging technologies in this specific arena and their efficacy. These include plasma markers (microDNA, DNA methylation, and tumor-associated antibodies), breath/sputum biomarkers [volatile organic compounds (VOCs) and exhaled breath condensate (EBC)], proteomics, metabolomics, and machine learning, such as radiomics technology. We find that, across the board, they offer promising results in terms of non-invasive diagnostics, genetic sequencing for higher-risk individuals, and accessibility for a diverse cohort of patients. While these screening adjuncts are unlikely to completely replace the current standard of care at the moment, continued research into these technologies is crucial to improve and personalize the identification, treatment, and outcome of lung cancer patients in the near future.
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Affiliation(s)
- Ju Ae Park
- Department of Surgery, Inova Fairfax Medical Campus, Falls Church, VA, USA
| | - Duy Pham
- University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Sriya Yalamanchili
- Department of Surgery, Inova Fairfax Medical Campus, Falls Church, VA, USA
| | - Shaina Twardus
- University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Kei Suzuki
- Department of Surgery, Inova Fairfax Medical Campus, Falls Church, VA, USA
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4
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Gao Y, Du P. miR-4529-3p Promotes the Progression of Retinoblastoma by Inhibiting RB1 Expression and Activating the ERK Signaling Pathway. Mol Biotechnol 2024; 66:102-111. [PMID: 37041423 DOI: 10.1007/s12033-023-00738-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 03/26/2023] [Indexed: 04/13/2023]
Abstract
Retinoblastoma (RB) is a malignant ocular cancer that affects children. Several microRNAs (miRNAs) have been implicated in RB regulation. The present study aimed to investigate the role of miR-4529-3p in RB pathogenesis. Scratch, Transwell, and Cell Counting Kit (CCK)-8 assays were conducted to assess the migratory, invasive, and proliferative abilities of RB cells. The expression levels of miR-4529-3p, RB1, and ERK pathway-related proteins were analyzed using western blotting and real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR). Target relationships were verified using dual-luciferase reporter experiments. A murine RB model was developed to analyze the effects of miR-4529-3p on RB tumor growth in vivo. Our experiments revealed high levels of miR-4529-3p and low levels of RB1 in RB tissues. Functional analyses revealed that the migratory, invasive, and proliferative abilities of RB cells were repressed by miR-4529-3p inhibition. Similarly, p-ERK 1/2 protein levels were suppressed by miR-4529-3p inhibition. Furthermore, downregulation of miR-4529-3p limited tumor growth in vivo. Mechanistically, miR-4259-3p targets RB1. Interestingly, RB1 silencing abrogated the alleviative effects of miR-4529-3p downregulation in RB cells. MiR-4529-3p promotes RB progression by inhibiting RB1 and activating the ERK pathway. This evidence suggests that the miR-4529-3p/RB1 regulatory axis may be a prospective target for RB treatment in clinical settings.
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Affiliation(s)
- Yuan Gao
- Department of Ophthalmology, Wuhan No.1 Hospital, No. 215, Zhongshan Avenue, Qiaokou District, Wuhan, 430022, Hubei, China.
| | - Pei Du
- Department of Ophthalmology, Wuhan No.1 Hospital, No. 215, Zhongshan Avenue, Qiaokou District, Wuhan, 430022, Hubei, China
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5
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Rai D, Pattnaik B, Bangaru S, Tak J, Kumari J, Verma U, Vadala R, Yadav G, Dhaliwal RS, Kumar S, Kumar R, Jain D, Luthra K, Chosdol K, Palanichamy JK, Khan MA, Surendranath A, Mittal S, Tiwari P, Hadda V, Madan K, Agrawal A, Guleria R, Mohan A. microRNAs in exhaled breath condensate for diagnosis of lung cancer in a resource-limited setting: a concise review. Breathe (Sheff) 2023; 19:230125. [PMID: 38351949 PMCID: PMC10862127 DOI: 10.1183/20734735.0125-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 11/30/2023] [Indexed: 02/16/2024] Open
Abstract
Lung cancer is one of the common cancers globally with high mortality and poor prognosis. Most cases of lung cancer are diagnosed at an advanced stage due to limited diagnostic resources. Screening modalities, such as sputum cytology and annual chest radiographs, have not proved sensitive enough to impact mortality. In recent years, annual low-dose computed tomography has emerged as a potential screening tool for early lung cancer detection, but it may not be a feasible option for developing countries. In this context, exhaled breath condensate (EBC) analysis has been evaluated recently as a noninvasive tool for lung cancer diagnosis. The breath biomarkers also have the advantage of differentiating various types and stages of lung cancer. Recent studies have focused more on microRNAs (miRNAs) as they play a key role in tumourigenesis by regulating the cell cycle, metastasis and angiogenesis. In this review, we have consolidated the current published literature suggesting the utility of miRNAs in EBC for the detection of lung cancer.
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Affiliation(s)
- Divyanjali Rai
- Breathomics in Respiratory Diseases Lab, Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Bijay Pattnaik
- Breathomics in Respiratory Diseases Lab, Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Sunil Bangaru
- Breathomics in Respiratory Diseases Lab, Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Jaya Tak
- Breathomics in Respiratory Diseases Lab, Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Jyoti Kumari
- Breathomics in Respiratory Diseases Lab, Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Umashankar Verma
- Breathomics in Respiratory Diseases Lab, Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Rohit Vadala
- Breathomics in Respiratory Diseases Lab, Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Geetika Yadav
- Indian Council of Medical Research, New Delhi, India
| | | | - Sunil Kumar
- Department of Surgical Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Rakesh Kumar
- Department of Nuclear Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Deepali Jain
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Kalpana Luthra
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Kunzang Chosdol
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | | | - Maroof Ahmad Khan
- Department of Biostatistics, All India Institute of Medical Sciences, New Delhi, India
| | - Addagalla Surendranath
- Breathomics in Respiratory Diseases Lab, Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Saurabh Mittal
- Breathomics in Respiratory Diseases Lab, Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Pawan Tiwari
- Breathomics in Respiratory Diseases Lab, Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Vijay Hadda
- Breathomics in Respiratory Diseases Lab, Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Karan Madan
- Breathomics in Respiratory Diseases Lab, Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Anurag Agrawal
- Trivedi School of Biosciences, Ashoka University, Sonipat, India
| | - Randeep Guleria
- Breathomics in Respiratory Diseases Lab, Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Anant Mohan
- Breathomics in Respiratory Diseases Lab, Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
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Shi M, Han W, Loudig O, Shah CD, Dobkin JB, Keller S, Sadoughi A, Zhu C, Siegel RE, Fernandez MK, DeLaRosa L, Patel D, Desai A, Siddiqui T, Gombar S, Suh Y, Wang T, Hosgood HD, Pradhan K, Ye K, Spivack SD. Initial development and testing of an exhaled microRNA detection strategy for lung cancer case-control discrimination. Sci Rep 2023; 13:6620. [PMID: 37095155 PMCID: PMC10126132 DOI: 10.1038/s41598-023-33698-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 04/18/2023] [Indexed: 04/26/2023] Open
Abstract
For detecting field carcinogenesis non-invasively, early technical development and case-control testing of exhaled breath condensate microRNAs was performed. In design, human lung tissue microRNA-seq discovery was reconciled with TCGA and published tumor-discriminant microRNAs, yielding a panel of 24 upregulated microRNAs. The airway origin of exhaled microRNAs was topographically "fingerprinted", using paired EBC, upper and lower airway donor sample sets. A clinic-based case-control study (166 NSCLC cases, 185 controls) was interrogated with the microRNA panel by qualitative RT-PCR. Data were analyzed by logistic regression (LR), and by random-forest (RF) models. Feasibility testing of exhaled microRNA detection, including optimized whole EBC extraction, and RT and qualitative PCR method evaluation, was performed. For sensitivity in this low template setting, intercalating dye-based URT-PCR was superior to fluorescent probe-based PCR (TaqMan). In application, adjusted logistic regression models identified exhaled miR-21, 33b, 212 as overall case-control discriminant. RF analysis of combined clinical + microRNA models showed modest added discrimination capacity (1.1-2.5%) beyond clinical models alone: all subjects 1.1% (p = 8.7e-04)); former smokers 2.5% (p = 3.6e-05); early stage 1.2% (p = 9.0e-03), yielding combined ROC AUC ranging from 0.74 to 0.83. We conclude that exhaled microRNAs are qualitatively measureable, reflect in part lower airway signatures; and when further refined/quantitated, can potentially help to improve lung cancer risk assessment.
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Affiliation(s)
- Miao Shi
- Pulmonary Medicine, Albert Einstein College of Medicine, Bronx, NY, USA.
| | - Weiguo Han
- Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, USA
| | | | - Chirag D Shah
- Pulmonary Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jay B Dobkin
- Pulmonary Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Ali Sadoughi
- Pulmonary Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Changcheng Zhu
- Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Robert E Siegel
- Pulmonary Medicine, Icahn School of Medicine at Mount Sinai, James J. Peters Veterans Affairs Medical Center, New York, USA
| | | | - Lizett DeLaRosa
- Pulmonary Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | | | - Taha Siddiqui
- Pulmonary Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Saurabh Gombar
- Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Yousin Suh
- Reproductive Sciences (in Obstetrics and Gynecology), Columbia University, New York, USA
- Genetics and Development, Columbia University, New York, USA
| | - Tao Wang
- Biostatistics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - H Dean Hosgood
- Epidemiology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Kith Pradhan
- Biostatistics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Kenny Ye
- Biostatistics, Albert Einstein College of Medicine, Bronx, NY, USA
- Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Simon D Spivack
- Pulmonary Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
- Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Epidemiology, Albert Einstein College of Medicine, Bronx, NY, USA
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7
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Cherchi R, Cusano R, Orrù S, Ferrari PA, Massidda M, Fotia G, De Matteis S, Cocco P. Next Generation Sequencing for miRNA Detection on the Exhaled Breath Condensate: A Pilot Study. Epigenet Insights 2023; 16:25168657231160985. [PMID: 37025420 PMCID: PMC10070752 DOI: 10.1177/25168657231160985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/14/2023] [Indexed: 04/05/2023] Open
Abstract
Introduction: Exhaled breath condensate (EBC) sampling has been suggested as a less-invasive and cost-effective method to detect biological macromolecules, including miRNA. To explore the feasibility of its use as a biomarker of early effects of asbestos exposure, we conducted a preliminary test on male volunteers by comparing the miRNA profile in the EBC and the plasma using 2 different sequencing platforms. Methods: Six male volunteers, all retired and unexposed to dust or fumes, participated in the test. RNA was extracted from 200 μL EBC samples and same-size plasma samples. Sample aliquots were processed in 2 laboratories using 2 different sequencing platforms: a MiSeq Illumina® platform and a more performing HiSeq Illumina® platform. Results: The HiSeq3000® sequencing platform identified twice as many unique molecular indexes (UMI)-validated miRNA as the MiSeq® platform. The Spearman’s correlation coefficient between EBC counts and plasma counts was significant in 5/6 subjects with either platform (MiSeq® = 0.128-0.508, P = .026-<.001; HiSeq® = 0.156-0.412, P = .001-<.001). The intraclass correlation coefficient confirmed the consistency of the miRNA profile over the 6 participants with both biospecimens. Exploring the agreement between the EBC and plasma samples with Bland-Altman plots showed that using the HiSeq3000® platform substantially improved the EBC miRNA detection rate. Conclusion: Our preliminary study confirms that, when using the HiSeq® sequencing platform, EBC sampling is a suitable, non-invasive method to detect the miRNA profile in healthy subjects.
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Affiliation(s)
- Roberto Cherchi
- Operative Unit of Thoracic Surgery, Hospital G. Brotzu, Cagliari, Italy
| | - Roberto Cusano
- CRS4-NGS Core, POLARIS Research Park, Pula—Cagliari, Italy
| | - Sandro Orrù
- Operative Unit of Medical Genetics, Health Agency of Sardinia, Hospital Binaghi, Cagliari, Italy
- Department of Medical Sciences and Public Health, University of Cagliari, Monserrato—Cagliari, Italy
- Orrù S, Unit of Medical Genetics, Health Agency of Sardinia, Hospital Binaghi, Via Is Guadazzonis 3, Cagliari 09126, Italy.
| | - Paolo A Ferrari
- Operative Unit of Thoracic Surgery, Hospital G. Brotzu, Cagliari, Italy
| | | | - Giorgio Fotia
- CRS4-NGS Core, POLARIS Research Park, Pula—Cagliari, Italy
| | - Sara De Matteis
- Department of Medical Sciences and Public Health, University of Cagliari, Monserrato—Cagliari, Italy
| | - Pierluigi Cocco
- Centre for Occupational and Environmental Health, Division of Population Health, Health Services Research & Primary Care, University of Manchester, Manchester, UK
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Sulewska A, Pilz L, Manegold C, Ramlau R, Charkiewicz R, Niklinski J. A Systematic Review of Progress toward Unlocking the Power of Epigenetics in NSCLC: Latest Updates and Perspectives. Cells 2023; 12:cells12060905. [PMID: 36980246 PMCID: PMC10047383 DOI: 10.3390/cells12060905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/28/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
Epigenetic research has the potential to improve our understanding of the pathogenesis of cancer, specifically non-small-cell lung cancer, and support our efforts to personalize the management of the disease. Epigenetic alterations are expected to have relevance for early detection, diagnosis, outcome prediction, and tumor response to therapy. Additionally, epi-drugs as therapeutic modalities may lead to the recovery of genes delaying tumor growth, thus increasing survival rates, and may be effective against tumors without druggable mutations. Epigenetic changes involve DNA methylation, histone modifications, and the activity of non-coding RNAs, causing gene expression changes and their mutual interactions. This systematic review, based on 110 studies, gives a comprehensive overview of new perspectives on diagnostic (28 studies) and prognostic (25 studies) epigenetic biomarkers, as well as epigenetic treatment options (57 studies) for non-small-cell lung cancer. This paper outlines the crosstalk between epigenetic and genetic factors as well as elucidates clinical contexts including epigenetic treatments, such as dietary supplements and food additives, which serve as anti-carcinogenic compounds and regulators of cellular epigenetics and which are used to reduce toxicity. Furthermore, a future-oriented exploration of epigenetic studies in NSCLC is presented. The findings suggest that additional studies are necessary to comprehend the mechanisms of epigenetic changes and investigate biomarkers, response rates, and tailored combinations of treatments. In the future, epigenetics could have the potential to become an integral part of diagnostics, prognostics, and personalized treatment in NSCLC.
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Affiliation(s)
- Anetta Sulewska
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland
- Correspondence: (A.S.); (J.N.)
| | - Lothar Pilz
- Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Christian Manegold
- Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Rodryg Ramlau
- Department of Oncology, Poznan University of Medical Sciences, 60-569 Poznan, Poland
| | - Radoslaw Charkiewicz
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland
| | - Jacek Niklinski
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland
- Correspondence: (A.S.); (J.N.)
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9
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MicroRNAs in exhaled breath condensate: A pilot study of biomarker detection for lung cancer. Cancer Treat Res Commun 2023; 35:100689. [PMID: 36773435 DOI: 10.1016/j.ctarc.2023.100689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 12/19/2022] [Accepted: 01/19/2023] [Indexed: 02/12/2023]
Abstract
INTRODUCTION Quantitation of microRNAs secreted by lung cells can provide valuable information regarding lung health. Exhaled breath condensate (EBC) offers a non-invasive way to sample the secreted microRNAs, and could be used as diagnostic tools for lung cancer. MATERIALS & METHODS EBC samples from twenty treatment-naïve patients with pathologically confirmed lung cancer and twenty healthy subjects were profiled for miRNAs expression. Selected microRNAs were further validated, using quantitative-PCR, in an independent set of 10 subjects from both groups. RESULTS A total of 78 miRNAs were found to be significantly upregulated in the EBC of lung cancer patients compared to the control group. Six of these 78 miRNAs were shortlisted for validation. Of these, miR-31-3p, let7i, and miR-449c were significantly upregulated, exhibited good discriminatory power. DISCUSSION Differential expression of miRNAs secreted by lung cells could be quantitated in EBC samples, and could be used as a potential non-invasive tool for early diagnosis of lung cancer.
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Non-Coding RNAs in Pulmonary Diseases: Comparison of Different Airway-Derived Biosamples. Int J Mol Sci 2023; 24:ijms24032006. [PMID: 36768329 PMCID: PMC9916756 DOI: 10.3390/ijms24032006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/15/2023] [Accepted: 01/16/2023] [Indexed: 01/20/2023] Open
Abstract
Due to their structural conservation and functional role in critical signalling pathways, non-coding RNA (ncRNA) is a promising biomarker and modulator of pathological conditions. Most research has focussed on the role of microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs). These molecules have been investigated both in a cellular and an extracellular context. Sources of ncRNAs may include organ-specific body fluids. Therefore, studies on ncRNAs in respiratory diseases include those on sputum, bronchoalveolar lavage fluid (BALF) and exhaled breath condensate (EBC). It is worth identifying the limitations of these biosamples in terms of ncRNA abundance, processing and diagnostic potential. This review describes the progress in the literature on the role of ncRNAs in the pathogenesis and progression of severe respiratory diseases, including cystic fibrosis, asthma and interstitial lung disease. We showed that there is a deficit of information on lncRNAs and circRNAs in selected diseases, despite attempts to functionally bind them to miRNAs. miRNAs remain the most well-studied, but only a few investigations have been conducted on the least invasive biosample material, i.e., EBC. To summarise the studies conducted to date, we also performed a preliminary in silico analysis of the reported miRNAs, demonstrating the complexity of their role and interactions in selected respiratory diseases.
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11
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Keogh RJ, Riches JC. The Use of Breath Analysis in the Management of Lung Cancer: Is It Ready for Primetime? Curr Oncol 2022; 29:7355-7378. [PMID: 36290855 PMCID: PMC9600994 DOI: 10.3390/curroncol29100578] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/22/2022] [Accepted: 09/28/2022] [Indexed: 11/07/2022] Open
Abstract
Breath analysis is a promising non-invasive method for the detection and management of lung cancer. Exhaled breath contains a complex mixture of volatile and non-volatile organic compounds that are produced as end-products of metabolism. Several studies have explored the patterns of these compounds and have postulated that a unique breath signature is emitted in the setting of lung cancer. Most studies have evaluated the use of gas chromatography and mass spectrometry to identify these unique breath signatures. With recent advances in the field of analytical chemistry and machine learning gaseous chemical sensing and identification devices have also been created to detect patterns of odorant molecules such as volatile organic compounds. These devices offer hope for a point-of-care test in the future. Several prospective studies have also explored the presence of specific genomic aberrations in the exhaled breath of patients with lung cancer as an alternative method for molecular analysis. Despite its potential, the use of breath analysis has largely been limited to translational research due to methodological issues, the lack of standardization or validation and the paucity of large multi-center studies. It is clear however that it offers a potentially non-invasive alternative to investigations such as tumor biopsy and blood sampling.
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12
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Zhang C, Sun C, Zhao Y, Wang Q, Guo J, Ye B, Yu G. Overview of MicroRNAs as Diagnostic and Prognostic Biomarkers for High-Incidence Cancers in 2021. Int J Mol Sci 2022; 23:ijms231911389. [PMID: 36232692 PMCID: PMC9570028 DOI: 10.3390/ijms231911389] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 12/24/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs (ncRNAs) about 22 nucleotides in size, which play an important role in gene regulation and are involved in almost all major cellular physiological processes. In recent years, the abnormal expression of miRNAs has been shown to be associated with human diseases including cancer. In the past ten years, the link between miRNAs and various cancers has been extensively studied, and the abnormal expression of miRNAs has been reported in various malignant tumors, such as lung cancer, gastric cancer, colorectal cancer, liver cancer, breast cancer, and prostate cancer. Due to the high malignancy grade of these cancers, it is more necessary to develop the related diagnostic and prognostic methods. According to the study of miRNAs, many potential cancer biomarkers have been proposed for the diagnosis and prognosis of diseases, especially cancer, thus providing a new theoretical basis and perspective for cancer screening. The use of miRNAs as biomarkers for diagnosis or prognosis of cancer has the advantages of being less invasive to patients, with better accuracy and lower price. In view of the important clinical significance of miRNAs in human cancer research, this article reviewed the research status of miRNAs in the above-mentioned cancers in 2021, especially in terms of diagnosis and prognosis, and provided some new perspectives and theoretical basis for the diagnosis and treatment of cancers.
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Affiliation(s)
- Chunyan Zhang
- State Key Laboratory Cell Differentiation and Regulation, Henan Normal University, Xinxiang 453007, China
- Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Normal University, Xinxiang 453007, China
- Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Henan Normal University, Xinxiang 453007, China
- College of Life Science, Henan Normal University, Xinxiang 453007, China
- Institute of Biomedical Science, Henan Normal University, Xinxiang 453007, China
| | - Caifang Sun
- State Key Laboratory Cell Differentiation and Regulation, Henan Normal University, Xinxiang 453007, China
- College of Life Science, Henan Normal University, Xinxiang 453007, China
| | - Yabin Zhao
- State Key Laboratory Cell Differentiation and Regulation, Henan Normal University, Xinxiang 453007, China
- College of Life Science, Henan Normal University, Xinxiang 453007, China
| | - Qiwen Wang
- State Key Laboratory Cell Differentiation and Regulation, Henan Normal University, Xinxiang 453007, China
- Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Normal University, Xinxiang 453007, China
- Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Henan Normal University, Xinxiang 453007, China
- College of Life Science, Henan Normal University, Xinxiang 453007, China
- Institute of Biomedical Science, Henan Normal University, Xinxiang 453007, China
| | - Jianlin Guo
- State Key Laboratory Cell Differentiation and Regulation, Henan Normal University, Xinxiang 453007, China
- Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Normal University, Xinxiang 453007, China
- Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Henan Normal University, Xinxiang 453007, China
- College of Life Science, Henan Normal University, Xinxiang 453007, China
- Institute of Biomedical Science, Henan Normal University, Xinxiang 453007, China
| | - Bingyu Ye
- State Key Laboratory Cell Differentiation and Regulation, Henan Normal University, Xinxiang 453007, China
- Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Normal University, Xinxiang 453007, China
- Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Henan Normal University, Xinxiang 453007, China
- College of Life Science, Henan Normal University, Xinxiang 453007, China
- Institute of Biomedical Science, Henan Normal University, Xinxiang 453007, China
- Correspondence: (B.Y.); (G.Y.)
| | - Guoying Yu
- State Key Laboratory Cell Differentiation and Regulation, Henan Normal University, Xinxiang 453007, China
- Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Normal University, Xinxiang 453007, China
- Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Henan Normal University, Xinxiang 453007, China
- College of Life Science, Henan Normal University, Xinxiang 453007, China
- Institute of Biomedical Science, Henan Normal University, Xinxiang 453007, China
- Correspondence: (B.Y.); (G.Y.)
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13
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Kazeminasab S, Ghanbari R, Emamalizadeh B, Jouyban-Gharamaleki V, Taghizadieh A, Jouyban A, Khoubnasabjafari M. Exhaled breath condensate efficacy to identify mutations in patients with lung cancer: A pilot study. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2022; 41:370-383. [PMID: 35249462 DOI: 10.1080/15257770.2022.2046278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Exhaled breath condensate (EBC) is used to investigate the efficacy of EBC to detect the genetic mutations in patients with lung cancer. Samples of 5 patients and 5 healthy volunteers were collected. DNA was extracted and used for amplification of hotspot regions of TP53 and KRAS genes by using PCR. We performed the mutation analysis by direct sequencing in all subjects. Detected mutations in EBC samples were compared with those of corresponding tumor tissues and there was complete agreement within the detected mutations in EBC and tumorous tissue. EBC can be used as an efficient and noninvasive source for the assessment of gene mutations in patients with lung cancer.
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Affiliation(s)
- Somayeh Kazeminasab
- Pharmaceutical Analysis Research Center and Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Reza Ghanbari
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Babak Emamalizadeh
- Molecular Medicine Research Center and Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Vahid Jouyban-Gharamaleki
- Liver and Gastrointestinal Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Kimia Idea Pardaz Azarbayjan (KIPA) Science Based Company, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Taghizadieh
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Abolghasem Jouyban
- Pharmaceutical Analysis Research Center and Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.,Faculty of Pharmacy, Near East University, Mersin 10, Turkey
| | - Maryam Khoubnasabjafari
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Anesthesiology and Intensive Care, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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14
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Haince JF, Joubert P, Bach H, Ahmed Bux R, Tappia PS, Ramjiawan B. Metabolomic Fingerprinting for the Detection of Early-Stage Lung Cancer: From the Genome to the Metabolome. Int J Mol Sci 2022; 23:ijms23031215. [PMID: 35163138 PMCID: PMC8835988 DOI: 10.3390/ijms23031215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/17/2022] [Accepted: 01/17/2022] [Indexed: 12/19/2022] Open
Abstract
The five-year survival rate of lung cancer patients is very low, mainly because most newly diagnosed patients present with locally advanced or metastatic disease. Therefore, early diagnosis is key to the successful treatment and management of lung cancer. Unfortunately, early detection methods of lung cancer are not ideal. In this brief review, we described early detection methods such as chest X-rays followed by bronchoscopy, sputum analysis followed by cytological analysis, and low-dose computed tomography (LDCT). In addition, we discussed the potential of metabolomic fingerprinting, compared to that of other biomarkers, including molecular targets, as a low-cost, high-throughput blood-based test that is both feasible and affordable for early-stage lung cancer screening of at-risk populations. Accordingly, we proposed a paradigm shift to metabolomics as an alternative to molecular and proteomic-based markers in lung cancer screening, which will enable blood-based routine testing and be accessible to those patients at the highest risk for lung cancer.
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Affiliation(s)
| | - Philippe Joubert
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Department of Pathology, Laval University, Quebec, QC G1V 4G5, Canada;
| | - Horacio Bach
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, BC V6H 3Z6, Canada;
| | - Rashid Ahmed Bux
- BioMark Diagnostics Inc., Richmond, BC V6X 2W8, Canada; (J.-F.H.); (R.A.B.)
| | - Paramjit S. Tappia
- Asper Clinical Research Institute, St. Boniface Hospital, Winnipeg, MB R2H 2A6, Canada;
- Correspondence: ; Tel.: +1-204-258-1230
| | - Bram Ramjiawan
- Asper Clinical Research Institute, St. Boniface Hospital, Winnipeg, MB R2H 2A6, Canada;
- Department of Pharmacology & Therapeutics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0T6, Canada
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Zhou XP, Li QW, Shu ZZ, Liu Y. TP53-mediated miR-2861 promotes osteogenic differentiation of BMSCs by targeting Smad7. Mol Cell Biochem 2021; 477:283-293. [PMID: 34709507 DOI: 10.1007/s11010-021-04276-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 10/11/2021] [Indexed: 12/20/2022]
Abstract
Bone defect seriously affects the quality of life. Meanwhile, osteogenic differentiation in BMSCs could regulate the progression of bone defect. Transcription factors are known to regulate the osteogenic differentiation in BMSCs. The study aimed to investigate the detailed mechanism by which TP53 regulates the osteogenic differentiation. To study bone defect in vitro, BMSCs were isolated from spinal cord injury rats. CCK-8 assay was applied to test the cell viability. The mineralized nodules in BMSCs was tested by alizarin red staining. Meanwhile, TUNEL staining and flow cytometry were performed to test the cell apoptosis. mRNA expression was tested by qRT-PCR. Starbase and dual-luciferase reporter assay were used to predict the downstream mRNA of miR-2861. Moreover, western blot was applied to detect the protein expressions (TP53 and Smad7). BMSCs were successfully isolated from rats. The expressions of miR-2861 were significantly upregulated in osteogenic medium, compared with growth medium. MiR-2861 inhibitor significantly decreased the levels of OCN, ALP, BSP, and Runx2 in BMSCs. In addition, miR-2861 inhibitor notably inhibited the mineralized nodules, viability, and induced the apoptosis of BMSCs. Smad7 was identified to be the downstream target of miR-2861, and knockdown of Smad7 notably reversed miR-2861 inhibitor-induced inhibition of osteogenic differentiation and promotion of apoptosis in BMSCs. Moreover, miR-2861 was transcriptionally regulated by TP53 in BMSCs. TP53-meidiated miR-2861 promotes osteogenic differentiation of BMSCs by targeting Smad7. Thereby, our research might provide new methods for bone defect treatment.
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Affiliation(s)
- Xian-Pei Zhou
- Department of Hand and Foot Surgery, Brain Hospital of Hunan Province, No. 427, Section 3 of Furong Middle Road, Changsha, 410007, Hunan Province, China.
| | - Qi-Wei Li
- Department of Hand and Foot Surgery, Brain Hospital of Hunan Province, No. 427, Section 3 of Furong Middle Road, Changsha, 410007, Hunan Province, China
| | - Zi-Zhen Shu
- Department of Hand and Foot Surgery, Brain Hospital of Hunan Province, No. 427, Section 3 of Furong Middle Road, Changsha, 410007, Hunan Province, China
| | - Yang Liu
- Department of Gastrointestinal Surgery, Second Xiangaya Hospital, Central South University, No. 139 Renmin Road, Furong District, Changsha, 410011, Hunan Province, China.
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