Determining the utility of veterinary tissue archives for retrospective DNA analysis

Evaluating the potential of anti-dsRNA antibodies as an alternative viral sensing tool in encephalitides of different species

Although laboratory methods have advanced, the cause of many encephalitides is still unknown. Molecular methods like multiplex PCR and microarrays are considered to be often less sensitive than Next Generation Sequencing, whereas the latter is time-consuming and costly. These analyses require appropriate tissue preparations and are more difficult to perform on formalin-fixed, paraffin-embedded (FFPE) tissues. Anti-double-stranded RNA (dsRNA) antibodies could potentially identify virus infections independently of the viral genome and can be applied to FFPE material. This study examined the applicability of monoclonal anti-dsRNA antibodies by immunohistochemistry to confirm encephalitides caused by different RNA viruses and comparing the findings with those obtained using monoclonal and polyclonal virus-specific antibodies. The viruses studied included negative-sense (Borna disease virus 1, BoDV-1; canine distemper virus, CDV; Rift Valley fever virus, RVFV) and positive-sense single stranded RNA viruses (severe acute respiratory disease syndrome coronavirus 2, SARS-CoV-2; tick-borne encephalitis virus, TBEV; Theiler's murine encephalomyelitis virus, TMEV). Interestingly, dsRNA was detected in both infected and non-infected animals and inconsistently co-localized to BoDV-1, TBEV, and TMEV antigen. Strict co-localization was lacking in CDV, SARS-CoV-2 and RVFV. Despite the co-localization of dsRNA with virus antigen for some RNA viruses, anti-dsRNA antibodies were unreliable as markers for unknown virus infections. Future studies should explore the upstream components of the immune response, including the interferon signaling cascade to assess their potential as effective virus-sensing tool.

DNA purification increases PCR-amplifiable DNA extracted from formalin-fixed, paraffin-embedded canine mast cell tumors for routine KIT mutation detection

DNA amplification by PCR detects KIT exon 11 internal tandem duplications in canine mast cell tumors (MCTs). Tissue-specific inhibitors often contaminate DNA extracted from formalin-fixed, paraffin-embedded (FFPE) canine MCTs, blocking PCR amplification and, consequently, preventing mutation detection. We used a commercial kit to extract DNA from FFPE canine MCTs. Two independent PCR assays, each with one primer set, were used to amplify target genes (HPRT and KIT) directly after FFPE DNA extraction. PCR amplification failed with at least one primer set in 153 of 280 samples (54.6%, 95% CI: 48.8-60.5%). One or 2 DNA washing steps were required to remove PCR inhibitors in 130 of 280 (46.4%) and 23 of 280 (8.2%) of these cases, respectively. DNA concentration and quality (A₂₆₀/A₂₈₀ and A₂₆₀/A₂₃₀) either pre- or post-washing were not associated with ability of the samples to be amplified by PCR using both HPRT and KIT primer sets. Low-grade and subcutaneous MCTs were less likely to amplify directly after DNA extraction and without any washing steps compared to high-grade MCTs using KIT gene primers.

Optimization of RNA extraction protocol for long-term archived formalin-fixed paraffin-embedded tissues of horses

A suitable RNA extraction protocol was established to gain high quality RNA from formalin-fixed paraffin-embedded tissues to perform reliable molecular assays either applicable for using FFPE tissue archives or tissues with harsh formalin-fixation. Eighteen FFPE samples from the central nervous system of horses, stored up to 11 years, were used as archive cases. To test the influence of the fixation period, brain, liver, kidney, and skeletal muscle tissue fragments from another horse, were treated either with water or tris-acetate-EDTA buffer after fixation under different timepoints with 10% unbuffered formalin. Two deparaffinization methods and three proteinase K-based lysis step were tested and translated into three protocols. After detailed statistical analysis it was determined that a longer period and increase in volume of proteinase K incubation provide higher yields and purity of RNA (P < 0.01) of archived samples. Alongside, amplification of equid-housekeeping gene up to 298 bp was successful with the protocol adaptations. For different formalin-fixation timepoints, it was demonstrated that the right choice for treatment and formalin-fixation period is organ-related (P ≤ 0.05). Essentially, little alterations to pre-existing extraction protocols unwound the RNA of up to 11-year-old samples, enabling the use of FFPE tissue archives or e.g. harshly fixed material needed in infection research under high biosafety levels for a variety of molecular analysis.