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Pyatnitskiy MA, Poverennaya EV. Transcript-Level Biomarkers of Early Lung Carcinogenesis in Bronchial Lesions. Cancers (Basel) 2024; 16:2260. [PMID: 38927965 PMCID: PMC11202239 DOI: 10.3390/cancers16122260] [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: 05/10/2024] [Revised: 06/09/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Premalignant lesions within the bronchial epithelium signify the initial phases of squamous cell lung carcinoma, posing challenges for detection via conventional methods. Instead of focusing solely on gene expression, in this study, we explore transcriptomic alterations linked to lesion progression, with an emphasis on protein-coding transcripts. We reanalyzed a publicly available RNA-Seq dataset on airway epithelial cells from 82 smokers with and without premalignant lesions. Transcript and gene abundance were quantified using kallisto, while differential expression and transcript usage analysis was performed utilizing sleuth and RATs packages. Functional characterization involved overrepresentation analysis via clusterProfiler, weighted coexpression network analysis (WGCNA), and network analysis via Enrichr-KG. We detected 5906 differentially expressed transcripts and 4626 genes, exhibiting significant enrichment within pathways associated with oxidative phosphorylation and mitochondrial function. Remarkably, transcript-level WGCNA revealed a single module correlated with dysplasia status, notably enriched in cilium-related biological processes. Notable hub transcripts included RABL2B (ENST00000395590), DNAH1 (ENST00000420323), EFHC1 (ENST00000635996), and VWA3A (ENST00000563389) along with transcription factors such as FOXJ1 and ZNF474 as potential regulators. Our findings underscore the value of transcript-level analysis in uncovering novel insights into premalignant bronchial lesion biology, including identification of potential biomarkers associated with early lung carcinogenesis.
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Affiliation(s)
- Mikhail A. Pyatnitskiy
- Institute of Biomedical Chemistry, Moscow 119121, Russia;
- National Research University Higher School of Economics, Moscow 101000, Russia
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2
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Grätz C, Schuster M, Brandes F, Meidert AS, Kirchner B, Reithmair M, Schelling G, Pfaffl MW. A pipeline for the development and analysis of extracellular vesicle-based transcriptomic biomarkers in molecular diagnostics. Mol Aspects Med 2024; 97:101269. [PMID: 38552453 DOI: 10.1016/j.mam.2024.101269] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/11/2024] [Accepted: 03/17/2024] [Indexed: 06/12/2024]
Abstract
Extracellular vesicles are shed by every cell type and can be found in any biofluid. They contain different molecules that can be utilized as biomarkers, including several RNA species which they protect from degradation. Here, we present a pipeline for the development and analysis of extracellular vesicle-associated transcriptomic biomarkers that our group has successfully applied multiple times. We highlight the key steps of the pipeline and give particular emphasis to the necessary quality control checkpoints, which are linked to numerous available guidelines that should be considered along the workflow. Our pipeline starts with patient recruitment and continues with blood sampling and processing. The purification and characterization of extracellular vesicles is explained in detail, as well as the isolation and quality control of extracellular vesicle-associated RNA. We point out the possible pitfalls during library preparation and RNA sequencing and present multiple bioinformatic tools to pinpoint biomarker signature candidates from the sequencing data. Finally, considerations and pitfalls during the validation of the biomarker signature using RT-qPCR will be elaborated.
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Affiliation(s)
- Christian Grätz
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany.
| | - Martina Schuster
- Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Florian Brandes
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Agnes S Meidert
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Benedikt Kirchner
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany; Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Marlene Reithmair
- Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Gustav Schelling
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Michael W Pfaffl
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany.
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Dong W, Chen Q, He F. Transcriptome-based identification and validation of reference genes for corm growth stages, different tissues, and drought stress in Taro (Colocasia esculenta). BMC PLANT BIOLOGY 2024; 24:478. [PMID: 38816693 PMCID: PMC11137888 DOI: 10.1186/s12870-024-05199-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 05/24/2024] [Indexed: 06/01/2024]
Abstract
Taro is a widely utilized starch resource plant. It is essential to quantify the expression levels of functional genes associated with taro growth using real-time quantitative polymerase chain reaction (RT-qPCR). However, to obtain reliable RT-qPCR results, appropriate reference genes (RGs) are required for data normalization. In this study, we screened seven novel candidate RGs using transcriptome datasets from taro, encompassing data from growth corms and various tissues. The expression stability of these seven new RGs, along with the commonly used RGs Actin, EF1-α, and β-tubulin, was assessed using Delta Ct, BestKeeper, geNorm, and NormFinder algorithms. Furthermore, we conducted a comprehensive analysis using the RefFinder program and validated the results using the target gene, CeAGPL1. The findings revealed that ACY-1 and PIA2 were the optimal multiple RGs for normalization during corm growth, while COX10 and Armc8 were suitable for samples including various types of tissues. Furthermore, we found three RGs, Armc8, COX10 and CCX4L, were the optimal RGs for drought stress. This study assessed the suitability of RGs in taro for the first time. The identified RGs provide valuable resources for studying corm growth, diverse tissues, and drought stress. This study contributes to the advancement of our understanding of the underlying mechanisms that govern the growth of taro.
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Affiliation(s)
- Weiqing Dong
- Vegetable Research Institute, Guangxi Zhuang Autonomous Region Academy of Agricultural Sciences, Nanning, 530007, China
| | - Qi Chen
- New Technology Entrepreneur Center, Nanning, 530007, China
| | - Fanglian He
- Vegetable Research Institute, Guangxi Zhuang Autonomous Region Academy of Agricultural Sciences, Nanning, 530007, China.
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Moustakli E, Zikopoulos A, Skentou C, Stavros S, Sofikitis N, Georgiou I, Zachariou A. Integrative Assessment of Seminal Plasma Biomarkers: A Narrative Review Bridging the Gap between Infertility Research and Clinical Practice. J Clin Med 2024; 13:3147. [PMID: 38892858 PMCID: PMC11173072 DOI: 10.3390/jcm13113147] [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: 04/23/2024] [Revised: 05/21/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024] Open
Abstract
Infertility represents a significant global health challenge impacting millions of couples worldwide. Approximately half of all infertile couples exhibit compromised semen quality, indicative of diminished male fertility. While the diagnosis of male infertility traditionally relies on semen analysis, its limitations in providing a comprehensive assessment of male reproductive health have spurred efforts to identify novel biomarkers. Seminal plasma, a complex fluid containing proteins, lipids, and metabolites, has emerged as a rich source of such indicators. Reproduction depends heavily on seminal plasma, the primary transporter of chemicals from male reproductive glands. It provides a non-invasive sample for urogenital diagnostics and has demonstrated potential in the identification of biomarkers linked to illnesses of the male reproductive system. The abundance of seminal proteins has enabled a deeper understanding of their biological functions, origins, and differential expression in various conditions associated with male infertility, including azoospermia, asthenozoospermia, oligozoospermia, teratozoospermia, among others. The true prevalence of male infertility is understated due to the limitations of the current diagnostic techniques. This review critically evaluates the current landscape of seminal plasma biomarkers and their utility in assessing male infertility. Βy bridging the gap between research and clinical practice, the integrative assessment of seminal plasma biomarkers offers a multimodal approach to comprehensively evaluate male infertility.
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Affiliation(s)
- Efthalia Moustakli
- Laboratory of Medical Genetics, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece;
| | - Athanasios Zikopoulos
- Obstetrics and Gynecology, Royal Devon and Exeter Hospital, Barrack Rd, Exeter EX 25 DW, UK;
| | - Charikleia Skentou
- Department of Obstetrics and Gynecology, Medical School of Ioannina, University General Hospital, 45110 Ioannina, Greece;
| | - Sofoklis Stavros
- Third Department of Obstetrics and Gynecology, Attikon Hospital, Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece;
| | - Nikolaos Sofikitis
- Department of Urology, School of Medicine, Ioannina University, 45110 Ioannina, Greece; (N.S.); (A.Z.)
| | - Ioannis Georgiou
- Laboratory of Medical Genetics, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece;
| | - Athanasios Zachariou
- Department of Urology, School of Medicine, Ioannina University, 45110 Ioannina, Greece; (N.S.); (A.Z.)
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5
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Sadikan MZ, Abdul Nasir NA, Ibahim MJ, Iezhitsa I, Agarwal R. Identifying the stability of housekeeping genes to be used for the quantitative real-time PCR normalization in retinal tissue of streptozotocin-induced diabetic rats. Int J Ophthalmol 2024; 17:794-805. [PMID: 38766348 PMCID: PMC11074185 DOI: 10.18240/ijo.2024.05.02] [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: 08/03/2023] [Accepted: 02/23/2024] [Indexed: 05/22/2024] Open
Abstract
AIM To investigate the stability of the seven housekeeping genes: beta-actin (ActB), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), 18s ribosomal unit 5 (18s), cyclophilin A (CycA), hypoxanthine-guanine phosphoribosyl transferase (HPRT), ribosomal protein large P0 (36B4) and terminal uridylyl transferase 1 (U6) in the diabetic retinal tissue of rat model. METHODS The expression of these seven genes in rat retinal tissues was determined using real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) in two groups; normal control rats and streptozotocin-induced diabetic rats. The stability analysis of gene expression was investigated using geNorm, NormFinder, BestKeeper, and comparative delta-Ct (ΔCt) algorithms. RESULTS The 36B4 gene was stably expressed in the retinal tissues of normal control animals; however, it was less stable in diabetic retinas. The 18s gene was expressed consistently in both normal control and diabetic rats' retinal tissue. That this gene was the best reference for data normalisation in RT-qPCR studies that used the retinal tissue of streptozotocin-induced diabetic rats. Furthermore, there was no ideal gene stably expressed for use in all experimental settings. CONCLUSION Identifying relevant genes is a need for achieving RT-qPCR validity and reliability and must be appropriately achieved based on a specific experimental setting.
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Affiliation(s)
- Muhammad Zulfiqah Sadikan
- Department of Pharmacology, Faculty of Medicine, Manipal University College Malaysia (MUCM), Bukit Baru, Melaka 75150, Malaysia
| | - Nurul Alimah Abdul Nasir
- Centre for Neuroscience Research (NeuRon), Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Sungai Buloh, Selangor 47000, Malaysia
- Department of Medical Education, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Sungai Buloh, Selangor 47000, Malaysia
| | - Mohammad Johari Ibahim
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Sungai Buloh, Selangor 47000, Malaysia
| | - Igor Iezhitsa
- School of Medicine, International Medical University, Bukit Jalil, Kuala Lumpur 57000, Malaysia
- Department of Pharmacology and Bioinformatics, Volgograd State Medical University, Volgograd 400131, Russia
| | - Renu Agarwal
- School of Medicine, International Medical University, Bukit Jalil, Kuala Lumpur 57000, Malaysia
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Jang WS, Lee JM, Lee E, Park S, Lim CS. Loop-Mediated Isothermal Amplification and Lateral Flow Immunochromatography Technology for Rapid Diagnosis of Influenza A/B. Diagnostics (Basel) 2024; 14:967. [PMID: 38732380 PMCID: PMC11083224 DOI: 10.3390/diagnostics14090967] [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: 04/03/2024] [Revised: 04/25/2024] [Accepted: 05/05/2024] [Indexed: 05/13/2024] Open
Abstract
Influenza viruses cause highly contagious respiratory diseases that cause millions of deaths worldwide. Rapid detection of influenza viruses is essential for accurate diagnosis and the initiation of appropriate treatment. We developed a loop-mediated isothermal amplification and lateral flow assay (LAMP-LFA) capable of simultaneously detecting influenza A and influenza B. Primer sets for influenza A and influenza B were designed to target conserved regions of segment 7 and the nucleoprotein gene, respectively. Optimized through various primer set ratios, the assay operated at 62 °C for 30 min. For a total of 243 (85 influenza A positive, 58 influenza B positive and 100 negative) nasopharyngeal swab samples, the performance of the influenza A/B multiplex LAMP-LFA was compared with that of the commercial AllplexTM Respiratory Panel 1 assay (Seegene, Seoul, Korea). The influenza A/B multiplex LAMP-LFA demonstrated a specificity of 98% for the non-infected clinical samples, along with sensitivities of 94.1% for the influenza A clinical samples and 96.6% for the influenza B clinical samples, respectively. The influenza A/B multiplex LAMP-LFA showed high sensitivity and specificity, indicating that it is reliable for use in a low-resource environment.
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Affiliation(s)
- Woong Sik Jang
- Emergency Medicine, College of Medicine, Korea University Guro Hospital, 148, Gurodong-ro, Guro-gu, Seoul 08308, Republic of Korea;
| | - Jun Min Lee
- BK21 Graduate Program, Department of Biomedical Sciences, College of Medicine, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea;
| | - Eunji Lee
- Department of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, 148, Gurodong-ro, Guro-gu, Seoul 08308, Republic of Korea; (E.L.); (S.P.)
| | - Seoyeon Park
- Department of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, 148, Gurodong-ro, Guro-gu, Seoul 08308, Republic of Korea; (E.L.); (S.P.)
| | - Chae Seung Lim
- Department of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, 148, Gurodong-ro, Guro-gu, Seoul 08308, Republic of Korea; (E.L.); (S.P.)
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Nevado JB, Cutiongco-de la Paz EMC, Paz-Pacheco ET, Jasul GV, Aman AYCL, Deguit CDT, San Pedro JVB, Francisco MDG. Transcriptional profiles associated with coronary artery disease in type 2 diabetes mellitus. Front Endocrinol (Lausanne) 2024; 15:1323168. [PMID: 38706700 PMCID: PMC11066158 DOI: 10.3389/fendo.2024.1323168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/25/2024] [Indexed: 05/07/2024] Open
Abstract
Background Coronary artery disease (CAD) is a common complication of Type 2 diabetes mellitus (T2DM). Understanding the pathogenesis of this complication is essential in both diagnosis and management. Thus, this study aimed to characterize the presence of CAD in T2DM using molecular markers and pathway analyses. Methods The study is a sex- and age-frequency matched case-control design comparing 23 unrelated adult Filipinos with T2DM-CAD to 23 controls (DM with CAD). Healthy controls served as a reference. Total RNA from peripheral blood mononuclear cells (PBMCs) underwent whole transcriptomic profiling using the Illumina HumanHT-12 v4.0 expression beadchip. Differential gene expression with gene ontogeny analyses was performed, with supporting correlational analyses using weighted correlation network analysis (WGCNA). Results The study observed that 458 genes were differentially expressed between T2DM with and without CAD (FDR<0.05). The 5 top genes the transcription factor 3 (TCF3), allograft inflammatory factor 1 (AIF1), nuclear factor, interleukin 3 regulated (NFIL3), paired immunoglobulin-like type 2 receptor alpha (PILRA), and cytoskeleton-associated protein 4 (CKAP4) with AUCs >89%. Pathway analyses show differences in innate immunity activity, which centers on the myelocytic (neutrophilic/monocytic) theme. SNP-module analyses point to a possible causal dysfunction in innate immunity that triggers the CAD injury in T2DM. Conclusion The study findings indicate the involvement of innate immunity in the development of T2DM-CAD, and potential immunity markers can reflect the occurrence of this injury. Further studies can verify the mechanistic hypothesis and use of the markers.
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Affiliation(s)
- Jose B. Nevado
- Institute of Human Genetics, National Institutes of Health-University of the Philippines Manila, Manila, Philippines
| | - Eva Maria C. Cutiongco-de la Paz
- Institute of Human Genetics, National Institutes of Health-University of the Philippines Manila, Manila, Philippines
- Philippine Genome Center, University of the Philippines System, Diliman, Quezon City, Philippines
| | - Elizabeth T. Paz-Pacheco
- Division of Endocrinology, Department of Medicine, University of the Philippines-Philippine General Hospital Medical Center, Manila, Philippines
| | - Gabriel V. Jasul
- Division of Endocrinology, Department of Medicine, University of the Philippines-Philippine General Hospital Medical Center, Manila, Philippines
| | - Aimee Yvonne Criselle L. Aman
- Institute of Human Genetics, National Institutes of Health-University of the Philippines Manila, Manila, Philippines
| | - Christian Deo T. Deguit
- Institute of Human Genetics, National Institutes of Health-University of the Philippines Manila, Manila, Philippines
| | - Jana Victoria B. San Pedro
- Institute of Human Genetics, National Institutes of Health-University of the Philippines Manila, Manila, Philippines
| | - Mark David G. Francisco
- Division of Endocrinology, Department of Medicine, University of the Philippines-Philippine General Hospital Medical Center, Manila, Philippines
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Bustin SA. Improving the quality of quantitative polymerase chain reaction experiments: 15 years of MIQE. Mol Aspects Med 2024; 96:101249. [PMID: 38290180 DOI: 10.1016/j.mam.2024.101249] [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: 10/24/2023] [Revised: 01/02/2024] [Accepted: 01/15/2024] [Indexed: 02/01/2024]
Abstract
The quantitative polymerase chain reaction (qPCR) is fundamental to molecular biology. It is not just a laboratory technique, qPCR is a bridge between research and clinical practice. Its theoretical foundations guide the design of experiments, while its practical implications extend to diagnostics, treatment, and research advancements in the life sciences, human and veterinary medicine, agriculture, and forensics. However, the accuracy, reliability and reproducibility of qPCR data face challenges arising from various factors associated with experimental design, execution, data analysis and inadequate reporting details. Addressing these concerns, the Minimum Information for the Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines have emerged as a cohesive framework offering a standardised set of recommendations that describe the essential information required for assessing qPCR experiments. By emphasising the importance of methodological rigour, the MIQE guidelines have made a major contribution to improving the trustworthiness, consistency, and transparency of many published qPCR results. However, major challenges related to awareness, resources, and publication pressures continue to affect their consistent application.
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Affiliation(s)
- Stephen A Bustin
- Medical Technology Research Centre, Anglia Ruskin University, Chelmsford, Essex, CM1 1SQ, UK.
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Li N, Ren P, Wang J, Zhu X, Qiao X, Zeng Z, Ye T, Wang S, Meng Z, Gan H, Liu S, Sun Y, Zhu X, Dou G, Gu R. Immune-Related Molecules CD3G and FERMT3: Novel Biomarkers Associated with Sepsis. Int J Mol Sci 2024; 25:749. [PMID: 38255822 PMCID: PMC10815248 DOI: 10.3390/ijms25020749] [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: 11/08/2023] [Revised: 12/23/2023] [Accepted: 12/31/2023] [Indexed: 01/24/2024] Open
Abstract
Sepsis ranks among the most common health problems worldwide, characterized by organ dysfunction resulting from infection. Excessive inflammatory responses, cytokine storms, and immune-induced microthrombosis are pivotal factors influencing the progression of sepsis. Our objective was to identify novel immune-related hub genes for sepsis through bioinformatic analysis, subsequently validating their specificity and potential as diagnostic and prognostic biomarkers in an animal experiment involving a sepsis mice model. Gene expression profiles of healthy controls and patients with sepsis were obtained from the Gene Expression Omnibus (GEO) and analysis of differentially expressed genes (DEGs) was conducted. Subsequently, weighted gene co-expression network analysis (WGCNA) was used to analyze genes within crucial modules. The functional annotated DEGs which related to the immune signal pathways were used for constructing protein-protein interaction (PPI) analysis. Following this, two hub genes, FERMT3 and CD3G, were identified through correlation analyses associated with sequential organ failure assessment (SOFA) scores. These two hub genes were associated with cell adhesion, migration, thrombosis, and T-cell activation. Furthermore, immune infiltration analysis was conducted to investigate the inflammation microenvironment influenced by the hub genes. The efficacy and specificity of the two hub genes were validated through a mice sepsis model study. Concurrently, we observed a significant negative correlation between the expression of CD3G and IL-1β and GRO/KC. These findings suggest that these two genes probably play important roles in the pathogenesis and progression of sepsis, presenting the potential to serve as more stable biomarkers for sepsis diagnosis and prognosis, deserving further study.
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Affiliation(s)
- Nanxi Li
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Peng Ren
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Jingya Wang
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Xiaohui Zhu
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Xuan Qiao
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Zhirui Zeng
- Guizhou Provincial Key Laboratory of Pathogenesis & Drug Research on Common Chronic Diseases, Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang 550000, China
| | - Tong Ye
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Shanshan Wang
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Zhiyun Meng
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Hui Gan
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Shuchen Liu
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Yunbo Sun
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Xiaoxia Zhu
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Guifang Dou
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Ruolan Gu
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing 100850, China
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Petersen PHD, Lopacinska-Jørgensen J, Høgdall CK, Høgdall EV. Identification of stably expressed microRNAs in plasma from high-grade serous ovarian carcinoma and benign tumor patients. Mol Biol Rep 2023; 50:10235-10247. [PMID: 37934368 PMCID: PMC10676310 DOI: 10.1007/s11033-023-08795-6] [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: 07/21/2023] [Accepted: 09/01/2023] [Indexed: 11/08/2023]
Abstract
BACKGROUND Ovarian cancer is a lethal gynecological cancer and no reliable minimally invasive early diagnosis tools exist. High grade serous ovarian carcinoma (HGSOC) is often diagnosed at advanced stages, resulting in poorer outcome than those diagnosed in early stage. Circulating microRNAs have been investigated for their biomarker potential. However, due to lack of standardization methods for microRNA detection, there is no consensus, which microRNAs should be used as stable endogenous controls. We aimed to identify microRNAs that are stably expressed in plasma of HGSOC and benign ovarian tumor patients. METHODS AND RESULTS We isolated RNA from plasma samples of 60 HGSOC and 48 benign patients. RT-qPCR was accomplished with a custom panel covering 40 microRNAs and 8 controls. Stability analysis was performed using five algorithms: Normfinder, geNorm, Delta-Ct, BestKeeper and RefFinder using an R-package; RefSeeker developed by our study group [1]. Among 41 analyzed RNAs, 13 were present in all samples and eligible for stability analysis. Differences between stability rankings were observed across algorithms. In HGSOC samples, hsa-miR-126-3p and hsa-miR-23a-3p were identified as the two most stable miRNAs. In benign samples, hsa-miR-191-5p and hsa-miR-27a-3p were most stable. In the combined HGSOC and benign group, hsa-miR-23a-3p and hsa-miR-27a-3p were identified by both the RefFinder and Normfinder analysis as the most stable miRNAs. CONCLUSIONS Consensus regarding normalization approaches in microRNA studies is needed. The choice of endogenous microRNAs used for normalization depends on the histological content of the cohort. Furthermore, normalization also depends on the algorithms used for stability analysis.
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Affiliation(s)
- Patrick H D Petersen
- Department of Pathology, Herlev Hospital, University of Copenhagen, Borgmester Ib Juuls Vej 25, Herlev, 2730, Denmark
| | - Joanna Lopacinska-Jørgensen
- Department of Pathology, Herlev Hospital, University of Copenhagen, Borgmester Ib Juuls Vej 25, Herlev, 2730, Denmark
| | - Claus K Høgdall
- Department of Gynecology, The Juliane Marie Centre, Rigshospitalet, University of Copenhagen, Copenhagen, 2100, Denmark
| | - Estrid V Høgdall
- Department of Pathology, Herlev Hospital, University of Copenhagen, Borgmester Ib Juuls Vej 25, Herlev, 2730, Denmark.
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Benedetto A, Šťastný K, Giaccio N, Marturella M, Biasibetti E, Arigoni M, Calogero R, Gili M, Pezzolato M, Tošnerová K, Hodkovicová N, Faldyna M, Puleio R, Bozzo G, Bozzetta E. RNAseq Analysis of Livers from Pigs Treated with Testosterone and Nandrolone Esters: Selection and Field Validation of Transcriptional Biomarkers. Animals (Basel) 2023; 13:3495. [PMID: 38003113 PMCID: PMC10668810 DOI: 10.3390/ani13223495] [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: 09/25/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
The use of anabolic-androgenic steroids (AASs) as growth promoters in farm animals is banned in the European Union, representing both an illicit practice and a risk for consumer health. However, these compounds are still illegally administered, often in the form of synthetic esters. This work aimed to characterize significant coding RNA perturbations related to the illicit administration of testosterone and nandrolone esters in fattening pigs. A total of 27 clinically healthy 90-day-old pigs were randomly assigned to test and control groups. Nine animals were treated with testosterone esters (Sustanon®) and other nine with nandrolone esters (Myodine®). At the end of the trial, liver samples were collected and analyzed using RNAseq, allowing the identification of 491 differentially expressed genes (DEGs). The transcriptional signature was further characterized by a smaller sub-cluster of 143 DEGs, from which a selection of 16 genes was made. The qPCR analysis confirmed that the identified cluster could still give good discrimination between untreated gilt and barrows compared to the relative testosterone-treated counterparts. A conclusive field survey on 67 liver samples collected from pigs of different breeds and weight categories confirmed, in agreement with testosterone residue profiles, the specificity of selected transcriptional biomarkers, showing their potential applications for screening purposes when AAS treatment is suspected, allowing to focus further investigations of competent authorities and confirmatory analysis where needed.
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Affiliation(s)
- Alessandro Benedetto
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Turin, Italy; (N.G.); (M.M.); (E.B.); (M.G.); (M.P.); (E.B.)
| | - Kamil Šťastný
- Department of Infectious Diseases and Preventive Medicine, Veterinary Research Institute, 621 00 Brno, Czech Republic; (K.Š.); (K.T.); (N.H.); (M.F.)
| | - Nunzia Giaccio
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Turin, Italy; (N.G.); (M.M.); (E.B.); (M.G.); (M.P.); (E.B.)
| | - Marianna Marturella
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Turin, Italy; (N.G.); (M.M.); (E.B.); (M.G.); (M.P.); (E.B.)
| | - Elena Biasibetti
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Turin, Italy; (N.G.); (M.M.); (E.B.); (M.G.); (M.P.); (E.B.)
| | - Maddalena Arigoni
- Dipartimento di Biotecnologie e Scienze della Salute, Core-Lab di Bioinformatica e Genomica, Università degli Studi di Torino, 10124 Turin, Italy; (M.A.); (R.C.)
| | - Raffaele Calogero
- Dipartimento di Biotecnologie e Scienze della Salute, Core-Lab di Bioinformatica e Genomica, Università degli Studi di Torino, 10124 Turin, Italy; (M.A.); (R.C.)
| | - Marilena Gili
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Turin, Italy; (N.G.); (M.M.); (E.B.); (M.G.); (M.P.); (E.B.)
| | - Marzia Pezzolato
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Turin, Italy; (N.G.); (M.M.); (E.B.); (M.G.); (M.P.); (E.B.)
| | - Kristína Tošnerová
- Department of Infectious Diseases and Preventive Medicine, Veterinary Research Institute, 621 00 Brno, Czech Republic; (K.Š.); (K.T.); (N.H.); (M.F.)
| | - Nikola Hodkovicová
- Department of Infectious Diseases and Preventive Medicine, Veterinary Research Institute, 621 00 Brno, Czech Republic; (K.Š.); (K.T.); (N.H.); (M.F.)
| | - Martin Faldyna
- Department of Infectious Diseases and Preventive Medicine, Veterinary Research Institute, 621 00 Brno, Czech Republic; (K.Š.); (K.T.); (N.H.); (M.F.)
| | - Roberto Puleio
- Istituto Zooprofilattico Sperimentale della Sicilia, 90129 Palermo, Italy;
| | - Giancarlo Bozzo
- Dipartimento di Medicina Veterinaria, Università degli Studi di Bari Aldo Moro, 70121 Bari, Italy;
| | - Elena Bozzetta
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Turin, Italy; (N.G.); (M.M.); (E.B.); (M.G.); (M.P.); (E.B.)
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Čelešnik H, Potočnik U. Blood-Based mRNA Tests as Emerging Diagnostic Tools for Personalised Medicine in Breast Cancer. Cancers (Basel) 2023; 15:1087. [PMID: 36831426 PMCID: PMC9954278 DOI: 10.3390/cancers15041087] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Molecular diagnostic tests help clinicians understand the underlying biological mechanisms of their patients' breast cancer (BC) and facilitate clinical management. Several tissue-based mRNA tests are used routinely in clinical practice, particularly for assessing the BC recurrence risk, which can guide treatment decisions. However, blood-based mRNA assays have only recently started to emerge. This review explores the commercially available blood mRNA diagnostic assays for BC. These tests enable differentiation of BC from non-BC subjects (Syantra DX, BCtect), detection of small tumours <10 mm (early BC detection) (Syantra DX), detection of different cancers (including BC) from a single blood sample (multi-cancer blood test Aristotle), detection of BC in premenopausal and postmenopausal women and those with high breast density (Syantra DX), and improvement of diagnostic outcomes of DNA testing (variant interpretation) (+RNAinsight). The review also evaluates ongoing transcriptomic research on exciting possibilities for future assays, including blood transcriptome analyses aimed at differentiating lymph node positive and negative BC, distinguishing BC and benign breast disease, detecting ductal carcinoma in situ, and improving early detection further (expression changes can be detected in blood up to eight years before diagnosing BC using conventional approaches, while future metastatic and non-metastatic BC can be distinguished two years before BC diagnosis).
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Affiliation(s)
- Helena Čelešnik
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova Ulica 17, 2000 Maribor, Slovenia
- Center for Human Genetics & Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia
| | - Uroš Potočnik
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova Ulica 17, 2000 Maribor, Slovenia
- Center for Human Genetics & Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia
- Department for Science and Research, University Medical Centre Maribor, Ljubljanska Ulica 5, 2000 Maribor, Slovenia
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13
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Sabbaghian A, Mussack V, Kirchner B, Bui MLU, Kalani MR, Pfaffl MW, Golalipour M. A panel of blood-derived miRNAs with a stable expression pattern as a potential pan-cancer detection signature. Front Mol Biosci 2022; 9:1030749. [PMID: 36589227 PMCID: PMC9798419 DOI: 10.3389/fmolb.2022.1030749] [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: 08/29/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022] Open
Abstract
Introduction: MicroRNAs have a significant role in the regulation of the transcriptome. Several miRNAs have been proposed as potential biomarkers in different malignancies. However, contradictory results have been reported on the capability of miRNA biomarkers in cancer detection. The human biological clock involves molecular mechanisms that regulate several genes over time. Therefore, the sampling time becomes one of the significant factors in gene expression studies. Method: In the present study, we have tried to find miRNAs with minimum fluctuation in expression levels at different time points that could be more accurate candidates as diagnostic biomarkers. The small RNA-seq raw data of ten healthy individuals across nine-time points were analyzed to identify miRNAs with stable expression. Results: We have found five oscillation patterns. The stable miRNAs were investigated in 779 small-RNA-seq datasets of eleven cancer types. All miRNAs with the highest differential expression were selected for further analysis. The selected miRNAs were explored for functional pathways. The predominantly enriched pathways were miRNA in cancer and the P53-signaling pathway. Finally, we have found seven miRNAs, including miR-142-3p, miR-199a-5p, miR-223-5p, let-7d-5p, miR-148b-3p, miR-340-5p, and miR-421. These miRNAs showed minimum fluctuation in healthy blood and were dysregulated in the blood of eleven cancer types. Conclusion: We have found a signature of seven stable miRNAs which dysregulate in several cancer types and may serve as potential pan-cancer biomarkers.
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Affiliation(s)
- Amir Sabbaghian
- Department of Molecular Medicine, Advanced Technologies Faculty, Golestan University of Medical Science, Gorgan, Iran
| | - Veronika Mussack
- Department of Animal Physiology and Immunology, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Benedikt Kirchner
- Department of Animal Physiology and Immunology, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Maria L. U. Bui
- Department of Animal Physiology and Immunology, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Mohammad Reza Kalani
- Department of Molecular Medicine, Advanced Technologies Faculty, Golestan University of Medical Science, Gorgan, Iran
| | - Michael W. Pfaffl
- Department of Animal Physiology and Immunology, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Masoud Golalipour
- Department of Molecular Medicine, Advanced Technologies Faculty, Golestan University of Medical Science, Gorgan, Iran
- Cellular and Molecular Research Center, Golestan University of Medical Science, Gorgan, Iran
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14
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Stefanizzi FM, Zhang L, Salgado-Somoza A, Dankiewicz J, Stammet P, Hassager C, Wise MP, Friberg H, Cronberg T, Hundt A, Kjaergaard J, Nielsen N, Devaux Y. Circular RNAs to predict clinical outcome after cardiac arrest. Intensive Care Med Exp 2022; 10:41. [PMID: 36303007 PMCID: PMC9613847 DOI: 10.1186/s40635-022-00470-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 10/05/2022] [Indexed: 11/12/2022] Open
Abstract
Background Cardiac arrest (CA) represents the third leading cause of death worldwide. Among patients resuscitated and admitted to hospital, death and severe neurological sequelae are frequent but difficult to predict. Blood biomarkers offer clinicians the potential to improve prognostication. Previous studies suggest that circulating non-coding RNAs constitute a reservoir of novel biomarkers. Therefore, this study aims to identify circulating circular RNAs (circRNAs) associated with clinical outcome after CA. Results Whole blood samples obtained 48 h after return of spontaneous circulation in 588 survivors from CA enrolled in the Target Temperature Management trial (TTM) were used in this study. Whole transcriptome RNA sequencing in 2 groups of 23 sex-matched patients identified 28 circRNAs associated with neurological outcome and survival. The circRNA circNFAT5 was selected for further analysis using quantitative PCR. In the TTM-trial (n = 542), circNFAT5 was upregulated in patients with poor outcome as compared to patients with good neurological outcome (p < 0.001). This increase was independent of TTM regimen and sex. The adjusted odds ratio of circNFAT5 to predict neurological outcome was 1.39 [1.07–1.83] (OR [95% confidence interval]). CircNFAT5 predicted 6-month survival with an adjusted hazard ratio of 1.31 [1.13–1.52].
Conclusion We identified circulating circRNAs associated with clinical outcome after CA, among which circNFAT5 may have potential to aid in predicting neurological outcome and survival when used in combination with established biomarkers of CA. Supplementary Information The online version contains supplementary material available at 10.1186/s40635-022-00470-7.
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Affiliation(s)
- Francesca M Stefanizzi
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, 1A-B rue Edison, 1445, Strassen, Luxembourg
| | - Lu Zhang
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, 1A-B rue Edison, 1445, Strassen, Luxembourg
| | - Antonio Salgado-Somoza
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, 1A-B rue Edison, 1445, Strassen, Luxembourg
| | - Josef Dankiewicz
- Department of Cardiology, Clinical Sciences, Lund University and Skane University Hospital, 221 85, Lund, Sweden
| | - Pascal Stammet
- Department of Intensive Care Medicine, Centre Hospitalier de Luxembourg, 1210, Luxembourg, Luxembourg.,Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, 4365, Esch-sur-Alzette, Luxembourg
| | - Christian Hassager
- Department of Cardiology B, The Heart Centre, Rigshospitalet University Hospital, 2100, Copenhagen, Denmark
| | - Matthew P Wise
- Department of Intensive Care, University Hospital of Wales, Cardiff, CF14 4XW, UK
| | - Hans Friberg
- Department of Anesthesia and Intensive Care, Clinical Sciences, Lund University and Skane University Hospital, 221 85, Malmö, Sweden
| | - Tobias Cronberg
- Department of Neurology and Rehabilitation Medicine, Clinical Sciences, Lund University and Skane University Hospital, 221 85, Lund, Sweden
| | - Alexander Hundt
- Integrated BioBank of Luxembourg, Luxembourg Institute of Health, Dudelange, Luxembourg
| | - Jesper Kjaergaard
- Department of Cardiology B, The Heart Centre, Rigshospitalet University Hospital, 2100, Copenhagen, Denmark
| | - Niklas Nielsen
- Department of Anesthesia and Intensive Care, Clinical Sciences, Lund University and Helsingborg Hospital, 25187, Lund, Sweden
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, 1A-B rue Edison, 1445, Strassen, Luxembourg.
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