Introduction to our New Blog Series
Welcome to Lab Insights our new blog series, where we explore how researchers and professional laboratories are using our products in their daily workflows. In this first blog post of this series, we address the InviTrap® product line, comprising specialized RNA extraction kits renowned for their outstanding performance.
The Relevance of RNA Extraction in Molecular Research
RNA-based research is crucial for understanding gene expression, cellular mechanisms, and disease pathology. Its applications span across human, animal, and plant research, including disease diagnostics, therapeutic development, and crop biotechnology. RNA analysis provides insights into gene regulation and cellular responses, making the extraction of high-quality RNA essential for accurate results.
In particular, plant RNA research is vital for crop improvement, stress tolerance, and plant-pathogen interactions. However, RNA extraction from plant tissues is particularly challenging due to the presence of complex cell walls and interfering compounds such as polysaccharides and phenolics.
Why High-Quality RNA Extraction is Essential
Efficient RNA extraction is the foundation of reliable RNA-based experiments. The quality and quantity of RNA extracted directly impact the accuracy and reproducibility of downstream applications, such as RNA sequencing (RNA-Seq), quantitative reverse transcription PCR (RT-qPCR), and microarrays. Poor RNA extraction can result in contamination with genomic DNA, proteins, or degraded RNA, leading to erroneous results and compromised conclusions.
In plant research, the complexity of the sample matrix adds further challenges. Plant tissues often contain high concentrations of secondary metabolites, polysaccharides, and phenolic compounds that can interfere with the extraction process and negatively impact RNA quality. Thus, RNA extraction must be performed with care to ensure purity and integrity, enabling the accurate analysis of gene expression and other RNA-based assays.
What Makes or Breaks RNA Extraction?
- RNA Yield: sufficient RNA quantity to support analysis.
- RNA Purity: minimal contamination from proteins, polysaccharides, or phenolics.
- RNA Integrity: preserved full-length RNA, avoiding degradation.
- DNA contamination: critical to avoid false positives or skewed expression data, particularly in RT-qPCR or sequencing.
Selective Removal of DNA: A Distinct Feature of our InviTrap® Products
One major technical challenge in RNA extraction is the removal of genomic DNA. While DNase digestion is common, it adds time, cost, and a risk of RNA degradation.
The InviTrap® extraction kits offer a unique and elegant solution for selectively removing DNA: During lysis, the released DNA of the cell is bound to mineral particles. This particle-bound DNA is then efficiently removed through centrifugation, leaving the RNA in the supernatant. The RNA is subsequently purified, leaving high-pure RNA with only minimal DNA residuals, making the kits ideal for sensitive downstream applications such as RNA-seq and RT-qPCR.
Lab Insight: InviTrap® Spin Universal RNA Mini Kit Enables Transcriptomic Profiling of Intracellular Staphylococcus aureus Persisters
A compelling example of how the InviTrap® Spin Universal RNA Mini Kit supports complex research workflows comes from the study “Intracellular Staphylococcus aureus persisters upon antibiotic exposure” by Peyrusson et al., published in Nature Communications (2020) (1). This study demonstrates the power of combining innovative cell biology and transcriptomics to uncover bacterial persistence mechanisms, and it highlights the critical role of high-purity, DNA-free RNA obtained using the InviTrap® kit.
Study Background: A Hidden Reservoir of Antibiotic-Tolerant Bacteria
The researchers addressed a growing challenge in infectious disease treatment: the formation of persister cells—non-dividing, metabolically active subpopulations of bacteria that tolerate antibiotic exposure without acquiring genetic resistance (2). Staphylococcus aureus, a major human pathogen, is known to survive within host cells such as macrophages, where antibiotic accessibility is limited, and stress responses are activated. Often, a rapid recolonization soon after the end of antibiotic therapy, causing relapsing infections is observed (3). Understanding the gene expression profile of these intracellular persisters, and the factors leading to antibiotic persistence and tolerance, were central to the study.
Experimental Overview: From Infected Cells to RNA Sequencing
To examine bacterial persistence at the molecular level by RNA-Seq, Peyrusson et al. designed the following experimental procedure shown in Figure 1:
- Infection of macrophages with a GFP-labelled Staphylococcus aureus strain.
- Antibiotic exposure using high concentrations of Oxacillin for 24h to induce the persister phenotype.
- Cell sorting using flow cytometry to isolate viable, non-dividing bacteria, directly from host cells.
- Plate re-growth of intact bacterial persisters and control samples.
- RNA extraction from this enriched intracellular subpopulation using the InviTrap® Spin Universal RNA Mini Kit.
Figure 1: Experimental procedure performed by Peyrusson et al. to analyse the gene expression of persistent Staphylococcus aureus cells. Macrophages were infected with a GFP-labelled S. aureus strain. Formation of persisters was induced by antibiotic exposure for 24h using Oxacillin. The subset of intact persisters and control samples were collected and sorted by FACS. After re-growth of the collected bacterial cells, total RNA was extracted using the InviTrap® Spin Universal RNA Mini Kit and analysed by RNA sequencing. Differentially expressed genes (DEG) were then analysed by hierarchical clustering and over-representation analysis. (Figure from Peyrusson et al., 2020)
Key Finding: Active Stress Response Pathways in Persisters is causing Antibiotic Resistance
The RNA sequencing data revealed that intracellular Staphylococcus aureus persisters exhibit an active and highly adaptive gene expression profile rather than a dormant state. The transcriptional analysis showed that persisters activate multiple stress response pathways, including the stringent response, cell wall stress stimulon (CWSS), SOS DNA repair response, and heat shock response. These pathways help the bacteria survive antibiotic pressure by reducing metabolic activity, enhancing damage repair, and stabilizing essential cellular functions.
The Role of the InviTrap® Spin Universal RNA Mini Kit in the Workflow
For RNA isolation, the researchers selected the InviTrap® Spin Universal RNA Mini Kit, which proved to be a reliable tool for obtaining high-quality RNA from clinical samples. The kit delivered RNA with the integrity and purity required for RNA sequencing, enabling accurate gene expression analysis. Its ease of use and consistent performance made it a valuable component of the study’s transcriptomic workflow.
Summary
RNA extraction is a critical step in modern molecular biology, and its success directly influences the reliability of downstream applications such as RNA sequencing and RT-qPCR. As demonstrated in the study above, high-quality RNA is essential for uncovering complex biological mechanisms—in this case, the adaptive responses of intracellular S. aureus persisters under antibiotic stress.
The InviTrap® kits provide researchers with robust, easy-to-use tools for extracting RNA with high yield, purity and integrity across a range of challenging sample types. Whether working with plant tissues, human cells, or enriched bacterial populations, these kits help ensure that RNA-based experiments begin with a solid foundation.
This Lab Insight highlights how a reliable RNA extraction method can play a key role in supporting high-impact research and advancing our understanding of gene expression in health, disease, and microbial persistence.
| Product | Description |
| InviTrap® Spin Universal RNA Mini Kit (CE-IVD) |
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| InviTrap® Spin Plant RNA Mini Kit |
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References
[1] Peyrusson F, Varet H, Nguyen TK, Legendre R, Sismeiro O, Coppée JY, Wolz C, Tenson T, Van Bambeke F. Intracellular Staphylococcus aureus persisters upon antibiotic exposure. Nat Commun. 2020 May 4;11(1):2200. doi: 10.1038/s41467-020-15966-7. PMID: 32366839; PMCID: PMC7198484
[2] Fauvart M, De Groote VN, Michiels J. Role of persister cells in chronic infections: clinical relevance and perspectives on anti-persister therapies. J Med Microbiol. 2011 Jun;60(Pt 6):699-709. doi: 10.1099/jmm.0.030932-0. Epub 2011 Apr 1. PMID: 21459912.
[3] Rollin G, Tan X, Tros F, Dupuis M, Nassif X, Charbit A, Coureuil M. Intracellular Survival of Staphylococcus aureus in Endothelial Cells: A Matter of Growth or Persistence. Front Microbiol. 2017 Jul 19;8:1354. doi: 10.3389/fmicb.2017.01354. PMID: 28769913; PMCID: PMC5515828.
