1
|
Investigating the impact of RNA integrity variation on the transcriptome of human leukemic cells. 3 Biotech 2022; 12:160. [PMID: 35814037 PMCID: PMC9259771 DOI: 10.1007/s13205-022-03223-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 06/17/2022] [Indexed: 11/12/2022] Open
Abstract
High RNA integrity is essential for good quality of transcriptomics profiling. Nevertheless, in some cases samples with low RNA integrity is the only available material to study. This work was set to investigate the impact of thermal-induced RNA degradation on the transcriptomic profiles of human leukemic cells. DNA microarray-based transcriptomics was conducted on two groups of samples; high RNA integrity samples (n = 4) and low RNA integrity samples (n = 5). RNA degradation caused limited but noticeable changes in the transcriptomes. Only 1945 (6.7%) of 29,230 genes showed altered quantitation (fold change ≥ two-fold, p value ≤ 0.03, corrected p value ≤ 0.05). RNA degradation had the most impact on short transcripts and those with short distance between their 5’end and the probe binding position. Overall, the present work identified the genes whose relative quantification is sensitive to RNA degradation. Therefore, altered expression of these genes should be interpreted with caution when studied in low integrity RNA samples.
Collapse
|
2
|
Guo X, Gao X, Keenan BT, Zhu J, Sarantopoulou D, Lian J, Galante RJ, Grant GR, Pack AI. RNA-seq analysis of galaninergic neurons from ventrolateral preoptic nucleus identifies expression changes between sleep and wake. BMC Genomics 2020; 21:633. [PMID: 32928100 PMCID: PMC7491139 DOI: 10.1186/s12864-020-07050-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 09/03/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Previous studies show that galanin neurons in ventrolateral preoptic nucleus (VLPO-Gal) are essential for sleep regulation. Here, we explored the transcriptional regulation of the VLPO-Gal neurons in sleep by comparing their transcriptional responses between sleeping mice and those kept awake, sacrificed at the same diurnal time. RESULTS RNA-sequencing (RNA-seq) analysis was performed on eGFP(+) galanin neurons isolated using laser captured microdissection (LCM) from VLPO. Expression of Gal was assessed in our LCM eGFP(+) neurons via real time qPCR and showed marked enrichment when compared to LCM eGFP(-) cells and to bulk VLPO samples. Gene set enrichment analysis utilizing data from a recent single-cell RNA-seq study of the preoptic area demonstrated that our VLPO-Gal samples were highly enriched with galanin-expressing inhibitory neurons, but not galanin-expressing excitatory neurons. A total of 263 genes were differentially expressed between sleep and wake in VLPO-Gal neurons. When comparing differentially expressed genes in VLPO-Gal neurons to differentially expressed genes in a wake-active neuronal region (the medial prefrontal cortex), evidence indicates that both systemic and cell-specific mechanisms contribute to the transcriptional regulation in VLPO-Gal neurons. In both wake-active and sleep-active neurons, ER stress pathways are activated by wake and cold-inducible RNA-binding proteins are activated by sleep. In contrast, expression of DNA repair genes is increased in VLPO-Gal during wakefulness, but increased in wake-active cells during sleep. CONCLUSION Our study identified transcriptomic responses of the galanin neurons in the ventrolateral preoptic nucleus during sleep and sleep deprivation. Data indicate that VLPO contains mainly sleep-active inhibitory galaninergic neurons. The VLPO galanin neurons show responses to sleep and wake similar to wake-active regions, indicating these responses, such as ER stress and cold-inducible RNA-binding proteins, are systemic affecting all neuronal populations. Region-specific differences in sleep/wake responses were also identified, in particular DNA repair. Our study expands knowledge about the transcriptional response of a distinct group of neurons essential for sleep.
Collapse
Affiliation(s)
- Xiaofeng Guo
- Division of Sleep Medicine/Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, 19104, USA
| | - Xiaoling Gao
- Department of Respiratory and Critical Care Medicine, Second Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Brendan T Keenan
- Division of Sleep Medicine/Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, 19104, USA
| | - Jingxu Zhu
- Division of Sleep Medicine/Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, 19104, USA
| | - Dimitra Sarantopoulou
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, 19104, USA
- Present address at National Institute on Aging, National Institutes of Health, Baltimore, 21224, USA
| | - Jie Lian
- Division of Sleep Medicine/Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, 19104, USA
| | - Raymond J Galante
- Division of Sleep Medicine/Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, 19104, USA
| | - Gregory R Grant
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, 19104, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, 19104, USA
| | - Allan I Pack
- Division of Sleep Medicine/Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, 19104, USA.
| |
Collapse
|
3
|
İçöz K, Gerçek T, Murat A, Özcan S, Ünal E. Capturing B type acute lymphoblastic leukemia cells using two types of antibodies. Biotechnol Prog 2018; 35:e2737. [PMID: 30353996 DOI: 10.1002/btpr.2737] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 09/07/2018] [Accepted: 10/16/2018] [Indexed: 11/07/2022]
Abstract
One way to monitor minimal residual disease (MRD) is to screen cells for multiple surface markers using flow cytometry. In order to develop an alternative microfluidic based method, isolation of B type acute lymphoblastic cells using two types of antibodies should be investigated. The immunomagnetic beads coated with various antibodies are used to capture the B type acute lymphoblastic cells. Single beads, two types of beads and surface immobilized antibody were used to measure the capture efficiency. Both micro and nanosize immunomagnetic beads can be used to capture B type acute lymphoblastic cells with a minimum efficiency of 94% and maximum efficiency of 98%. Development of a microfluidic based biochip incorporating immunomagnetic beads and surface immobilized antibodies for monitoring MRD can be an alternative to current cost and time inefficient laboratory methods. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 35: e2737, 2019.
Collapse
Affiliation(s)
- Kutay İçöz
- BioMINDS (Bio Micro/Nano Devices and Sensors) Lab, Dept. of Electrical and Electronics Engineering, Abdullah Gül University, Kayseri, Turkey
- Bioengineering Dept., Abdullah Gül University, Kayseri, Turkey
| | - Tayyibe Gerçek
- BioMINDS (Bio Micro/Nano Devices and Sensors) Lab, Dept. of Electrical and Electronics Engineering, Abdullah Gül University, Kayseri, Turkey
- Bioengineering Dept., Abdullah Gül University, Kayseri, Turkey
| | - Ayşegül Murat
- Genome and Stem Cell Center (GENKOK), Erciyes University, Kayseri, Turkey
| | - Servet Özcan
- Biology Dept., Erciyes University, Kayseri, Turkey
- Genome and Stem Cell Center (GENKOK), Erciyes University, Kayseri, Turkey
| | - Ekrem Ünal
- Pediatric Oncology Dept., Erciyes University, Kayseri, Turkey
| |
Collapse
|
4
|
Liu H, Smith TPL, Nonneman DJ, Dekkers JCM, Tuggle CK. A high-quality annotated transcriptome of swine peripheral blood. BMC Genomics 2017. [PMID: 28646867 PMCID: PMC5483264 DOI: 10.1186/s12864-017-3863-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background High throughput gene expression profiling assays of peripheral blood are widely used in biomedicine, as well as in animal genetics and physiology research. Accurate, comprehensive, and precise interpretation of such high throughput assays relies on well-characterized reference genomes and/or transcriptomes. However, neither the reference genome nor the peripheral blood transcriptome of the pig have been sufficiently assembled and annotated to support such profiling assays in this emerging biomedical model organism. We aimed to assemble published and novel RNA-seq data to provide a comprehensive, well-annotated blood transcriptome for pigs by integrating a de novo assembly with a genome-guided assembly. Results A de novo and a genome-guided transcriptome of porcine whole peripheral blood was assembled with ~162 million pairs of paired-end and ~183 million single-end, trimmed and normalized Illumina RNA-seq reads (~6 billion initial reads from 146 RNA-seq libraries) from five independent studies by using the Trinity and Cufflinks software, respectively. We then removed putative transcripts (PTs) of low confidence from both assemblies and merged the remaining PTs into an integrated transcriptome consisting of 132,928 PTs, with 126,225 (~95%) PTs from the de novo assembly and more than 91% of PTs spliced. In the integrated transcriptome, ~90% and 63% of PTs had significant sequence similarity to sequences in the NCBI NT and NR databases, respectively; 68,754 (~52%) PTs were annotated with 15,965 unique gene ontology (GO) terms; and 7618 PTs annotated with Enzyme Commission codes were assigned to 134 pathways curated by the Kyoto Encyclopedia of Genes and Genomes (KEGG). Full exon-intron junctions of 17,528 PTs were validated by PacBio IsoSeq full-length cDNA reads from 3 other porcine tissues, NCBI pig RefSeq mRNAs and transcripts from Ensembl Sscrofa10.2 annotation. Completeness of the 5’ termini of 37,569 PTs was validated by public cap analysis of gene expression (CAGE) data. By comparison to the Ensembl transcripts, we found that (1) the deduced precursors of 54,402 PTs shared at least one intron or exon with those of 18,437 Ensembl transcripts; (2) 12,262 PTs had both longer 5’ and 3’ termini than their maximally overlapping Ensembl transcripts; and (3) 41,838 spliced PTs were totally missing from the Sscrofa10.2 annotation. Similar results were obtained when the PTs were compared to the pig NCBI RefSeq mRNA collection. Conclusions We built, validated and annotated a comprehensive porcine blood transcriptome with significant improvement over the annotation of Ensembl Sscrofa10.2 and the pig NCBI RefSeq mRNAs, and laid a foundation for blood-based high throughput transcriptomic assays in pigs and for advancing annotation of the pig genome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3863-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Haibo Liu
- Bioinformatics and Computational Biology Program, Department of Animal Science, Iowa State University, 2258 Kildee Hall, Ames, IA, 50011, USA
| | - Timothy P L Smith
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Dan J Nonneman
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Jack C M Dekkers
- Department of Animal Science, Iowa State University, 239 Kildee Hall, Ames, IA, 50011, USA
| | - Christopher K Tuggle
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA, 50011, USA.
| |
Collapse
|
5
|
Masucci GV, Cesano A, Hawtin R, Janetzki S, Zhang J, Kirsch I, Dobbin KK, Alvarez J, Robbins PB, Selvan SR, Streicher HZ, Butterfield LH, Thurin M. Validation of biomarkers to predict response to immunotherapy in cancer: Volume I - pre-analytical and analytical validation. J Immunother Cancer 2016; 4:76. [PMID: 27895917 PMCID: PMC5109744 DOI: 10.1186/s40425-016-0178-1] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 10/20/2016] [Indexed: 12/31/2022] Open
Abstract
Immunotherapies have emerged as one of the most promising approaches to treat patients with cancer. Recently, there have been many clinical successes using checkpoint receptor blockade, including T cell inhibitory receptors such as cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) and programmed cell death-1 (PD-1). Despite demonstrated successes in a variety of malignancies, responses only typically occur in a minority of patients in any given histology. Additionally, treatment is associated with inflammatory toxicity and high cost. Therefore, determining which patients would derive clinical benefit from immunotherapy is a compelling clinical question. Although numerous candidate biomarkers have been described, there are currently three FDA-approved assays based on PD-1 ligand expression (PD-L1) that have been clinically validated to identify patients who are more likely to benefit from a single-agent anti-PD-1/PD-L1 therapy. Because of the complexity of the immune response and tumor biology, it is unlikely that a single biomarker will be sufficient to predict clinical outcomes in response to immune-targeted therapy. Rather, the integration of multiple tumor and immune response parameters, such as protein expression, genomics, and transcriptomics, may be necessary for accurate prediction of clinical benefit. Before a candidate biomarker and/or new technology can be used in a clinical setting, several steps are necessary to demonstrate its clinical validity. Although regulatory guidelines provide general roadmaps for the validation process, their applicability to biomarkers in the cancer immunotherapy field is somewhat limited. Thus, Working Group 1 (WG1) of the Society for Immunotherapy of Cancer (SITC) Immune Biomarkers Task Force convened to address this need. In this two volume series, we discuss pre-analytical and analytical (Volume I) as well as clinical and regulatory (Volume II) aspects of the validation process as applied to predictive biomarkers for cancer immunotherapy. To illustrate the requirements for validation, we discuss examples of biomarker assays that have shown preliminary evidence of an association with clinical benefit from immunotherapeutic interventions. The scope includes only those assays and technologies that have established a certain level of validation for clinical use (fit-for-purpose). Recommendations to meet challenges and strategies to guide the choice of analytical and clinical validation design for specific assays are also provided.
Collapse
Affiliation(s)
- Giuseppe V Masucci
- Department of Oncology-Pathology, Karolinska Institutet, 171 76 Stockholm, Sweden
| | | | - Rachael Hawtin
- Nodality, Inc, 170 Harbor Way, South San Francisco, 94080 CA USA
| | - Sylvia Janetzki
- ZellNet Consulting, Inc, 555 North Avenue, Fort Lee, 07024 NJ USA
| | - Jenny Zhang
- Covaris Inc, 14 Gill St, Woburn, MA 01801 USA
| | - Ilan Kirsch
- Adaptive Biotechnologies, Inc, 1551 Eastlake Ave. E, Seattle, WA 98102 USA
| | - Kevin K Dobbin
- Department of Epidemiology and Biostatistics, College of Public Health, The University of Georgia, 101 Buck Road, Athens, 30602 GA USA
| | - John Alvarez
- Janssen Research & Development, LLC, Spring House, PA 19477 USA
| | | | - Senthamil R Selvan
- Omni Array Biotechnology, 15601 Crabbs Branch Way, Rockville, 20855 MD USA
| | - Howard Z Streicher
- National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Bethesda, 20892 MD USA
| | - Lisa H Butterfield
- Department of Medicine, Surgery and Immunology, University of Pittsburgh Cancer Institute, 5117 Centre Avenue, Pittsburgh, PA 15213 USA
| | - Magdalena Thurin
- National Cancer Institute, Cancer Diagnosis Program, DCTD, National Institutes of Health, 9609 Medical Center Drive, Bethesda, 20892 MD USA ; Adaptive Biotechnologies, Inc, 1551 Eastlake Ave. E, Seattle, WA 98102 USA
| |
Collapse
|
6
|
Abstract
Inflammatory cells and mediators are essential components in tumor microenvironment and play decisive roles in the initiation, proliferation, survival, promotion, invasion, or metastasis of lung cancer. Clinical and epidemiologic studies suggested a strong association between inflammation and lung cancer and an influence of immune surveillances and tumor responses to chemotherapeutic drugs, although roles of inflammation in lung cancer remain unclear. The present review outlined roles of inflammation in lung cancer, with particular focus on inflammatory components, types, biomarkers, or principal mechanisms by which the inflammation contributes to the development of lung cancer. The cancer-associated inflammatory cells (CICs) should be furthermore defined and include cancer-specific and interacted cells with inflammatory or inflammation-like characteristics, e.g., innate or adaptive immune cells and cancer tissue cells. We also discuss targeting potentials of inflammation in the prevention and treatment of lung cancer. The diversity of cancer-related inflammatory microenvironment is instrumental to design novel therapeutic approaches for lung cancer.
Collapse
|
7
|
Niu F, Wang DC, Lu J, Wu W, Wang X. Potentials of single-cell biology in identification and validation of disease biomarkers. J Cell Mol Med 2016; 20:1789-95. [PMID: 27113384 PMCID: PMC4988278 DOI: 10.1111/jcmm.12868] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 03/10/2016] [Indexed: 12/23/2022] Open
Abstract
Single-cell biology is considered a new approach to identify and validate disease-specific biomarkers. However, the concern raised by clinicians is how to apply single-cell measurements for clinical practice, translate the message of single-cell systems biology into clinical phenotype or explain alterations of single-cell gene sequencing and function in patient response to therapies. This study is to address the importance and necessity of single-cell gene sequencing in the identification and development of disease-specific biomarkers, the definition and significance of single-cell biology and single-cell systems biology in the understanding of single-cell full picture, the development and establishment of whole-cell models in the validation of targeted biological function and the figure and meaning of single-molecule imaging in single cell to trace intra-single-cell molecule expression, signal, interaction and location. We headline the important role of single-cell biology in the discovery and development of disease-specific biomarkers with a special emphasis on understanding single-cell biological functions, e.g. mechanical phenotypes, single-cell biology, heterogeneity and organization of genome function. We have reason to believe that such multi-dimensional, multi-layer, multi-crossing and stereoscopic single-cell biology definitely benefits the discovery and development of disease-specific biomarkers.
Collapse
Affiliation(s)
- Furong Niu
- Huzhou Central Hospital, Huzhou, Zhejiang Province, China
| | - Diane C Wang
- Department of Pulmonary Medicine, The First affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Jiapei Lu
- Department of Pulmonary Medicine, The First affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Wei Wu
- Huzhou Central Hospital, Huzhou, Zhejiang Province, China
| | - Xiangdong Wang
- Huzhou Central Hospital, Huzhou, Zhejiang Province, China
| |
Collapse
|
8
|
Rifatbegovic F, Abbasi MR, Taschner-Mandl S, Kauer M, Weinhäusel A, Handgretinger R, Ambros PF. Enriched Bone Marrow Derived Disseminated Neuroblastoma Cells Can Be a Reliable Source for Gene Expression Studies-A Validation Study. PLoS One 2015; 10:e0137995. [PMID: 26360775 PMCID: PMC4567134 DOI: 10.1371/journal.pone.0137995] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 08/25/2015] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Metastases in the bone marrow (BM) in form of disseminated tumor cells (DTCs) are frequent events at diagnosis and also at relapse in high-risk neuroblastoma patients. The frequently highly diluted occurrence of DTCs requires adequate enrichment strategies to enable their detailed characterization. However, to avoid methodical artifacts we tested whether pre-analytical processing steps-including transport duration, temperature and, importantly, tumor cell enrichment techniques-are confounding factors for gene expression analysis in DTCs. METHODS LAN-1 neuroblastoma cells were spiked into tumor free BM and/or peripheral blood and: i) kept at room temperature or at 4°C for 24, 48 and 72 hours; ii) frozen down at -80°C and thawed; iii) enriched via magnetic beads. The effect on the gene expression signature of LAN-1 cells was analyzed by qPCR arrays and gene expression microarrays. RESULTS Neither storage at -80°C in DMSO and subsequent thawing nor enrichment of spiked-in neuroblastoma cells changed the expression of the analyzed genes significantly. Whereas storage at 4°C altered the expression of analyzed genes (14.3%) only at the 72h-timepoint in comparison to the 0h-timepoint, storage at room temperature had a much more profound effect on gene expression by affecting 20% at 24h, 26% at 48h and 43% at 72h of the analyzed genes. CONCLUSION Using neuroblastoma as a model, we show that tumor cell enrichment by magnetic bead separation has virtually no effect on gene expression in DTCs. However, transport time and temperature can influence the expression profile remarkably. Thus, the expression profile of routinely collected BM samples can be analyzed without concern as long as the transport conditions are monitored.
Collapse
Affiliation(s)
- Fikret Rifatbegovic
- CCRI, Children’s Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
- * E-mail: (FR); (PFA)
| | - M. Reza Abbasi
- CCRI, Children’s Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Sabine Taschner-Mandl
- CCRI, Children’s Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Maximilian Kauer
- CCRI, Children’s Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Andreas Weinhäusel
- Molecular Diagnostics, Health & Environment Department, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | | | - Peter F. Ambros
- CCRI, Children’s Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria
- * E-mail: (FR); (PFA)
| |
Collapse
|