Reference gene identification for reverse transcription-quantitative polymerase chain reaction analysis in an ischemic wound-healing model

Catechin, epicatechin, curcumin, garlic, pomegranate peel and neem extracts of Indian origin showed enhanced anti-inflammatory potential in human primary acute and chronic wound derived fibroblasts by decreasing TGF-β and TNF-α expression

BACKGROUND

Although chronic wounds are devastating and can cause burden at multiple levels, chronic wound research is still far behind. Chronic wound treatment is often less efficient due to delay in diagnosis and treatment, non-specific treatment mainly due to lack of knowledge of wound healing or healing resistance genes. It's known that chronic wounds do not progress towards healing, because it gets stalled in inflammatory phase of wound healing.

OBJECTIVE

We aimed to use phytoextracts possessing excellent anti-inflammatory properties to regulate the unbalanced levels of cytokines responsible for increased inflammation.

METHODS

Evaluation of anti-inflammatory activity of selected phytoextracts namely, Camellia sinensis (L.) Kuntze, Acacia catechu (L.f) Willd., Curcuma longa (L.), Allium sativum (L.), Punica granatum (L.) and Azadirachta indica A. hereafter, called as catechin, epicatechin, curcumin, garlic, pomegranate and neem extracts, respectively in Acute wound fibroblasts (AWFs) and Chronic wound fibroblasts (CWFs) using flow cytometry.

RESULTS

The phytoextracts exhibited no cytotoxicity below 100 μg/ml on normal Human Dermal fibroblasts (HDFs), while garlic extract showed highest cell viability followed by catechin, epicatechin, curcumin, pomegranate peel and neem based on IC₅₀ value. Garlic, catechin and epicatechin extracts showed highest anti-inflammatory activities for both TGF-β and TNF-α in both AWFs and CWFs treated cells. After treatment of AWFs with catechin, epicatechin and garlic extracts, TGF-β and TNF-α expression was significantly reduced compared to untreated AWFs and reached to almost normal HDFs level. Also, after treatment of CWFs with catechin, epicatechin and garlic extracts, TGF-β and TNF-α expression was significantly reduced compared to untreated CWFs and was lesser than untreated AWFs.

CONCLUSION

The present findings reveal the potential of catechin, epicatechin and garlic extracts for the treatment of acute and chronic wounds with excellent anti-inflammatory properties.

SARS-CoV-2 awakens ancient retroviral genes and the expression of proinflammatory HERV-W envelope protein in COVID-19 patients

Patients with COVID-19 may develop abnormal inflammatory response, followed in some cases by severe disease and long-lasting syndromes. We show here that in vitro exposure to SARS-CoV-2 activates the expression of the human endogenous retrovirus (HERV) HERV-W proinflammatory envelope protein (ENV) in peripheral blood mononuclear cells from a subset of healthy donors, in ACE2 receptor and infection-independent manner. Plasma and/or sera of 221 COVID-19 patients from different cohorts, infected with successive SARS-CoV-2 variants including the Omicron, had detectable HERV-W ENV, which correlated with ENV expression in T lymphocytes and peaked with the disease severity. HERV-W ENV was also found in postmortem tissues of lungs, heart, gastrointestinal tract, brain olfactory bulb, and nasal mucosa from COVID-19 patients. Altogether, these results demonstrate that SARS-CoV-2 could induce HERV-W envelope protein expression and suggest its involvement in the immunopathogenesis of certain COVID-19-associated syndromes and thereby its relevance in the development of personalized treatment of patients.

Challenges in Healing Wound: Role of Complementary and Alternative Medicine

Although the word wound sounds like a simple injury to tissue, individual's health status and other inherent factors may make it very complicated. Hence, wound healing has gained major attention in the healthcare. The biology wound healing is precise and highly programmed, through phases of hemostasis, inflammation, proliferation and remodeling. Current options for wound healing which includes, use of anti-microbial agents, healing promoters along with application of herbal and natural products. However, there is no efficient evidence-based therapy available for specific chronic wounds that can result in definitive clinical outcomes. Under co-morbid conditions, chronic would poses numerous challenges. Use of Complementary and Alternative Medicines (CAMs) in health care sector is increasing and its applications in wound management remains like to "separate the diamonds from ore." Attempts have been made to understand the wound at the molecular level, mainly through the analysis of signature genes and the influence of several synthetic and natural molecules on these. We have outlined a review of challenges in chronic wound healing and the role of CAMs in chronic wound management. The main focus is on the applications and limitations of currently available treatment options for a non-healing wound and the best possible alternates to consider. This information generates broader knowledge on challenges in chronic wound healing, which can be further addressed using multidisciplinary approach and combination therapies.

Identification of optimal endogenous reference RNAs for RT-qPCR normalization in hindgut of rat models with anorectal malformations

Background

Quantitative real-time polymerase chain reaction (RT-qPCR) is a sensitive method for quantifying mRNA abundance. With relative expression analysis, however, reliable data output is dependent on stably expressed reference genes across the samples being studied. In anorectal malformations (ARMs), there is limited data on the selection of appropriate reference genes.

Purpose

This study was aimed to investigate the optimal reference genes for PCR in ARM rat models.

Methods

We selected 15 commonly used reference genes (Rps18, Actb, B2m, Gapdh, Ppia, Hprt1, Pgk1, Ywhaz, Tbp, Ubc, Rps16, Rpl13a, Rplp1, Sdha, and Hmbs) as candidate reference genes and detected their mRNA expression in ARM samples by RT-qPCR. The expression stability and variability of these transcripts were subsequently evaluated using four methods (geNorm, NormFinder, comparative ΔCt, and BestKeeper).

Results

The abundance of the candidate reference genes was qualified by RT-qPCR and the cycle threshold (Ct) values ranged between 14.07 (Rplp1) and 21.89 (Sdha). In the overall candidate genes, different variations existed across the different algorithms. A comprehensive analysis revealed that Rpl13a ranked first among the relatively stable genes, followed by Ywhaz, Rps18, Sdha, and Hmbs.

Conclusions

The most stable reference genes for RT-qPCR were Rpl13a, Ywhaz, and Rps18 in ETU-induced ARMs in rat fetus. This study provided a foundation for reference gene selection for future gene expression analyses.

Development and Characterisation of a Human Chronic Skin Wound Cell Line-Towards an Alternative for Animal Experimentation

Background: Chronic skin wounds are a growing financial burden for healthcare providers, causing discomfort/immobility to patients. Whilst animal chronic wound models have been developed to allow for mechanistic studies and to develop/test potential therapies, such systems are not good representations of the human chronic wound state. As an alternative, human chronic wound fibroblasts (CWFs) have permitted an insight into the dysfunctional cellular mechanisms that are associated with these wounds. However, such cells strains have a limited replicative lifespan and therefore a limited reproducibility/usefulness. Objectives: To develop/characterise immortalised cell lines of CWF and patient-matched normal fibroblasts (NFs). Methods and Results: Immortalisation with human telomerase resulted in both CWF and NF proliferating well beyond their replicative senescence end-point (respective cell strains senesced as normal). Gene expression analysis demonstrated that, whilst proliferation-associated genes were up-regulated in the cell lines (as would be expected), the immortalisation process did not significantly affect the disease-specific genotype. Immortalised CWF (as compared to NF) also retained a distinct impairment in their wound repopulation potential (in line with CWF cell strains). Conclusions: These novel CWF cell lines are a credible animal alternative and could be a valuable research tool for understanding both the aetiology of chronic skin wounds and for therapeutic pre-screening.

Laser capture microdissection of intestinal tissue from sea bass larvae using an optimized RNA integrity assay and validated reference genes

The increasing demand for a sustainable larviculture has promoted research regarding environmental parameters, diseases and nutrition, intersecting at the mucosal surface of the gastrointestinal tract of fish larvae. The combination of laser capture microdissection (LCM) and gene expression experiments allows cell specific expression profiling. This study aimed at optimizing an LCM protocol for intestinal tissue of sea bass larvae. Furthermore, a 3′/5′ integrity assay was developed for LCM samples of fish tissue, comprising low RNA concentrations. Furthermore, reliable reference genes for performing qPCR in larval sea bass gene expression studies were identified, as data normalization is critical in gene expression experiments using RT-qPCR. We demonstrate that a careful optimization of the LCM procedure allows recovery of high quality mRNA from defined cell populations in complex intestinal tissues. According to the geNorm and Normfinder algorithms, ef1a, rpl13a, rps18 and faua were the most stable genes to be implemented as reference genes for an appropriate normalization of intestinal tissue from sea bass across a range of experimental settings. The methodology developed here, offers a rapid and valuable approach to characterize cells/tissues in the intestinal tissue of fish larvae and their changes following pathogen exposure, nutritional/environmental changes, probiotic supplementation or a combination thereof.

Selection of reference genes for quantitative RT-PCR (RT-qPCR) analysis of rat tissues under physiological and toxicological conditions

In biological research the analysis of gene expression levels in cells and tissues can be a powerful tool to gain insights into biological processes. For this, quantitative RT-PCR (RT-qPCR) is a popular method that often involve the use of constitutively expressed endogenous reference (or ‘housekeeping’) gene for normalization of data. Thus, it is essential to use reference genes that have been verified to be stably expressed within the specific experimental setting. Here, we have analysed the expression stability of 12 commonly used reference genes (Actb, B2m, Gapdh, Hprt, Pgk1, Rn18s, Rpl13a, Rps18, Rps29, Sdha, Tbp and Ubc) across several juvenile and adult rat tissues (liver, adrenal, prostate, fat pad, testis and ovaries), both under normal conditions and following exposure to various chemicals during development. Employing NormFinder and BestKeeper softwares, we found Hprt and Sdha to be amongst the most stable genes across normal and manipulated tissues, with several others also being suitable for most tissues. Tbp and B2m displayed highest variability in transcript levels between tissues and developmental stages. It was also observed that the reference genes were most unstable in liver and testis following toxicological exposure. For future studies, we propose the use of more than one verified reference gene and the continuous monitoring of their suitability under various experimental conditions, including toxicological studies, based on changes in threshold (Ct) values from cDNA samples having been reverse-transcribed from a constant input concentration of RNA.