Eprobe-mediated screening system for somatic mutations in the KRAS locus

Concomitant knockdown resistance allele, L982W + F1534C, in Aedes aegypti has the potential to impose fitness costs without selection pressure

The Aedes aegypti mosquito, is an arbovirus vector that can spread dengue, chikungunya, Zika, and yellow fever. Pyrethroids are widely used to control mosquitoes. The voltage-gated sodium channel (Vgsc) is the target of pyrethroids, and amino acid substitutions in this channel attenuate the effects of pyrethroids. This is known as knockdown resistance (kdr). Recently, we found that Ae. aegypti with concomitant Vgsc mutations L982W + F1534C exhibit extremely high levels of pyrethroid resistance. L982 is located in a highly conserved region of Vgsc in vertebrates and invertebrates. This study aimed to evaluate the viability of Ae. aegypti, with concomitant L982W + F1534C mutations in Vgsc. We crossed a resistant strain (FTWC) with a susceptible strain (SMK) and reared it up to 15 generations. We developed a rapid and convenient genotyping method using a fluorescent probe (Eprobe) to easily and accurately distinguish between three genotypes: wild-type and mutant homozygotes, and heterozygotes. As generations progressed, the proportion of wild-type homozygotes increased, and only 2.9% of mutant homozygotes were present at the 15th generation; the allele frequencies of L982W + F1534C showed a decreasing trend over generations. These observations show that these concomitant mutations have some fitness costs, suggesting that mosquitoes can potentially recover pyrethroid susceptibility over time without pyrethroid selection pressure in the field.

SEB genotyping: SmartAmp-Eprimer binary code genotyping for complex, highly variable targets applied to HBV

Background

SmartAmp-Eprimer Binary code (SEB) Genotyping is a novel isothermal amplification method for rapid genotyping of any variable target of interest.

Methods

After in silico alignment of a large number of sequences and computational analysis to determine the smallest number of regions to be targeted by SEB Genotyping, SmartAmp primer sets were designed to obtain a binary code of On/Off fluorescence signals, each code corresponding to a unique genotype.

Results

Applied to HBV, we selected 4 targets for which fluorescence amplification signals produce a specific binary code unique to each of the 8 main genotypes (A–H) found in patients worldwide.

Conclusions

We present here the proof of concept of a new genotyping method specifically designed for complex and highly variable targets. Applied here to HBV, SEB Genotyping can be adapted to any other pathogen or disease carrying multiple known mutations. Using simple preparation steps, SEB Genotyping provides accurate results quickly and will enable physicians to choose the best adapted treatment for each of their patients.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07458-4.

Significance of RAS mutations in pulmonary metastases of patients with colorectal cancer

BACKGROUND

RAS/BRAF mutations of colorectal cancer (CRC) play a crucial role in carcinogenesis and cancer progression and need to be considered for the therapeutic strategy choice. We used next-generation-sequencing (NGS) technology to assess RAS/BRAF mutation differences between primary CRC and corresponding pulmonary metastases (PMs).

METHODS

We examined the mutation statuses of the KRAS 12/13/61/146, NRAS 12/13/61/146, and BRAF 600 codons in genomic DNA from fresh-frozen or formalin-fixed paraffin-embedded tissues derived from 34 primary lesions and 52 corresponding PMs from 36 patients with CRC.

RESULTS

We found RAS mutations in 76% (26/34) of primary CRC lesions and in 86% (31/36) of PMs. While 27% (7/26) of the primary CRC RAS mutations were heterogeneous, all the RAS mutations in PMs were homogeneous. Of the mutations in PMs, 71% (22/31) were KRAS G>A transitions, of which 82% (18/22) were KRAS G12D or G13D. The RAS mutation discordance between primary tumors and PMs was 12.1% (4/33). RAS mutations with the same genotyping were detected in all synchronous and metachronous PMs from 9 patients. We found no BRAF mutations in either primary or pulmonary tissues.

CONCLUSION

Our NGS analysis suggests that RAS mutations of PM of patients with CRC are more common than initially thought. The presence of KRAS mutations in CRC specimens, especially G12D or G13D mutations, seems to promote PM formation.

Eprobe mediated RT-qPCR for the detection of leukemia-associated fusion genes

The detection and quantification of leukemia-associated fusion gene transcripts play important roles in the diagnosis and follow-up of leukemias. To establish a standardized method without interlaboratory discrepancies, we developed a novel one-step reverse transcription quantitative PCR (RT-qPCR) assay, called “the Eprobe leukemia assay,” for major and minor BCR-ABL1, RUNX1-RUNX1T1, and various isoforms of PML-RARA. This assay is comprised of Eprobes that are exciton-controlled hybridization-sensitive fluorescent oligonucleotides. Melting curve analyses were performed on synthetic quantitative standard RNAs with strict quality control. Quantification capacity was evaluated by comparison with TaqMan RT-qPCR using 67 primary leukemia patient samples. The lower limit of detection and the limit of quantification of this assay were less than 31.3 copies/reaction and 62.5 copies/reaction, respectively. This assay correctly detected the fusion genes in samples with 100% sensitivity and specificity. The specificity of the reactions was confirmed by melting curve analyses. The assay detected low-level expression of minor BCR-ABL1 co-expressed with major BCR-ABL1. These results illustrate the feasibility and high accuracy of the Eprobe leukemia assay, even for minimal residual disease monitoring.

Prognostic impact of stathmin 1 expression in patients with lung adenocarcinoma

OBJECTIVE

Stathmin 1 is a major cytosolic phosphoprotein that regulates microtubule dynamics and is associated with malignant phenotypes in various cancers, including non-small cell lung cancer. We aimed to determine differences in overall survival and disease-free proportion in patients with lung adenocarcinoma stratified by stathmin 1 tumor expression.

METHODS

With the use of immunohistochemistry, stathmin 1 expression was determined in resection specimens from 303 patients with adenocarcinoma. Associations between stathmin 1 protein expression and overall and disease-free proportion were assessed (Kaplan-Meier survival curves compared with log-rank statistics). Cox proportional hazards regression determined the hazard for death stratified by stathmin 1, adjusting for clinicopathologic characteristics.

RESULTS

During follow-up, 74 (24.4%) recurrences and 73 (24.1%) all-cause deaths were recorded. Expressed in 53.8% of adenocarcinoma cases, overall survival and disease-free proportion were significantly worse in stathmin 1-positive patients (log-rank P < .001 and P < .001, respectively). When adjusted for clinical and pathologic factors, stathmin 1 expression was an independent prognostic variable for both overall survival (hazard ratio, 2.21; 95% confidence interval, 1.28-3.80) and disease-free proportion (hazard ratio, 2.02; 95% confidence interval, 1.13-3.63) and for disease-free proportion even in the subset of patients with stage I (hazard ratio, 2.79; 95% confidence interval, 1.07-7.27). There was no significant difference between the stathmin 1-positive patients with stage IA and patients with stage IB in overall survival (P = .975) and disease-free proportion (P = .490), respectively.

CONCLUSIONS

Stathmin 1 expression was an independent prognostic factor for adenocarcinoma, even when restricted to patients with early-stage cancer.

Highly sensitive detection of a HER2 12-base pair duplicated insertion mutation in lung cancer using the Eprobe-PCR method

Somatic mutation in human epidermal growth factor receptor-related 2 gene (HER2) is one of the driver mutations in lung cancer. HER2 mutations are found in about 2% of lung adenocarcinomas (ADCs). Previous reports have been based mainly on diagnostic screening by Sanger sequencing or next-generation sequencing (NGS); however, these methods are time-consuming and complicated. We developed a rapid, simple, sensitive mutation detection assay for detecting HER2 12 base pair-duplicated insertion mutation based on the Eprobe-mediated PCR method (Eprobe-PCR) and validated the sensitivity of this assay system for clinical diagnostics. We examined 635 tumor samples and analyzed HER2 mutations using the Eprobe-PCR method, NGS, and Sanger sequencing. In a serial dilution study, the Eprobe-PCR was able to detect mutant plasmid DNA when its concentration was reduced to 0.1% by mixing with wild-type DNA. We also confirmed amplification of the mutated plasmid DNA with only 10 copies per reaction. In ADCs, Eprobe-PCR detected the HER2 mutation in 2.02% (9/446), while Sanger sequencing detected it in 1.57% (7/446). Eprobe-PCR was able to detect the mutation in two samples that were undetectable by Sanger sequencing. All non-ADC samples were wild-type. There were no discrepancies between frozen and formalin-fixed paraffin-embedded tissues in the nine samples. HER2 mutations detected by NGS data validated the high sensitivity of the method. Therefore, this new technique can lead to precise molecular-targeted therapies.

A novel E1B55kDa-deleted oncolytic adenovirus carrying microRNA-143 exerts specific antitumor efficacy on colorectal cancer cells

The KRAS is an important and frequently mutated gene during colorectal carcinogenesis. The expression of miR-143 is often down-regulated and it might play an important role by targeting KRAS in colorectal cancer (CRC). The purpose of this study was to investigate the antitumor effects of miR-143 with an intermediate oncolytic adenovirus (Ad) in CRC. We constructed the recombinant virus Ad-ZD55-miR-143 and verified its expression by qPCR and western blot assays. Oncolytic potency of Ad-ZD55-miR-143 was determined by cytopathic effect assays using human SW480 CRC cells and L-02 normal liver cells. MTT and cell apoptosis assays were applied to explore the biological functions of Ad-ZD55-miR-143 within SW480 cells. Dual-luciferase reporter assays were performed to validate whether KRAS was regulated by miR-143. The expression level of KRAS was measured by qPCR and western blot assays. Results showed that infection of SW480 cells with Ad-ZD55-miR-143 induced high level expression of miR-143. Furthermore, Ad-ZD55-miR-143 significantly suppressed the viability of SW480 cells in a dose-dependent pattern, but did not influence L-02 cells. Ad-ZD55-miR-143 also inhibited cell growth and induced cell apoptosis in SW480 cells. Dual-luciferase assays indicated that KRAS was a direct target of miR-143, as subsequently demonstrated by qPCR and western blot analysis showing that infection of SW480 cells with Ad-ZD55-miR-143 resulted in the down-regulation of KRAS at both mRNA and protein levels. Taken together, the recombinant virus Ad-ZD55-miR-143 exhibited specific antitumor effects by targeting KRAS, and might be a promising agent for the treatment of CRC.

Edesign: Primer and Enhanced Internal Probe Design Tool for Quantitative PCR Experiments and Genotyping Assays

Analytical PCR experiments preferably use internal probes for monitoring the amplification reaction and specific detection of the amplicon. Such internal probes have to be designed in close context with the amplification primers, and may require additional considerations for the detection of genetic variations. Here we describe Edesign, a new online and stand-alone tool for designing sets of PCR primers together with an internal probe for conducting quantitative real-time PCR (qPCR) and genotypic experiments. Edesign can be used for selecting standard DNA oligonucleotides like for instance TaqMan probes, but has been further extended with new functions and enhanced design features for Eprobes. Eprobes, with their single thiazole orange-labelled nucleotide, allow for highly sensitive genotypic assays because of their higher DNA binding affinity as compared to standard DNA oligonucleotides. Using new thermodynamic parameters, Edesign considers unique features of Eprobes during primer and probe design for establishing qPCR experiments and genotyping by melting curve analysis. Additional functions in Edesign allow probe design for effective discrimination between wild-type sequences and genetic variations either using standard DNA oligonucleotides or Eprobes. Edesign can be freely accessed online at http://www.dnaform.com/edesign2/, and the source code is available for download.