Formalin-Fixed Paraffin-Embedded (FFPE) samples are not a beneficial replacement for frozen tissues in fetal membrane microbiota research

Molecular detection of Bartonella spp. DNA in dogs with hemangiosarcoma

INTRODUCTION

The potential role of pathogens, particularly vector-transmitted infectious agents, as a cofactor or cause of neoplasia has not been intensively investigated. We previously reported a potential link between Bartonella spp. bacteremia and splenic hemangiosarcoma (HSA) in dogs living in the United States. The purpose of this study was to: 1/ further determine the prevalence of Bartonella spp. DNA in dogs with splenic HSA from throughout the United States; 2/ assess the impact of sample preservation methods on Bartonella spp. DNA amplification using characterized tissue samples from dogs diagnosed with HSA.

METHODS

In a blinded manner, we determined the presence of Bartonella spp. DNA in scrolls from biorepository formalin-fixed paraffin-embedded (FFPE) spleens from dogs living in three distant locations geographically transecting the United States. DNA extracted from non-lesional spleens (n = 249), nodular lymphoid hyperplasia spleens (n = 248), and splenic HSA (n = 330) were tested by quantitative polymerase chain reaction (qPCR), and droplet digital PCR (ddPCR). Subsequently, Bartonella PCR results from FFPE tissues and formalin-fixed tissues were compared using previously tested fresh frozen tissues from an additional 48 dogs with HSA.

RESULTS

There was no significant difference in the proportion of Bartonella PCR positive FFPE tissues from dogs diagnosed with an alesional spleen, nodular lymphoid hyperplasia, and splenic HSA. Regardless of the histological diagnosis, the most common Bartonella species identified was B. henselae (32/38). Bartonella spp. DNA was detected in a significantly larger proportion of fresh frozen tissues compared to FFPE tissues, when tested by qPCR (22/48 versus 1/48; p <0.0001) or ddPCR (19/48 versus 1/48; p <0.0001). Using ddPCR, Bartonella DNA was more often amplified from formalin-fixed tissues compared to FFPE tissues (15/39 versus 1/39; p <0.0001). The sensitivity of qPCR on FFPE samples and formalin-fixed samples, when comparing to fresh frozen samples as the reference standard, was 4.5% and 11.8%, respectively.

CONCLUSION

Due to decreased DNA amplification efficiency, FFPE scrolls should not be used for the detection of Bartonella infection in spleen samples from dogs with HSA. PCR testing of fresh frozen tissues substantially improves the detection of Bartonella spp. infection. If fresh frozen tissues are not available, formalin-fixed tissues should be tested with digital PCR to enhance Bartonella DNA detection.

Microbiological investigation of pregnancies following vaginal radical trachelectomy using 16S rRNA sequencing of FFPE placental specimens

This study examined the risk of intrauterine infection associated with radical trachelectomy (RT) in early-stage cervical cancer patients. This procedure preserves fertility but is linked to increased risk of intrauterine infection due to cervical defects during pregnancy. DNA was extracted from the formalin-fixed paraffin-embedded (FFPE) placental specimens of 23 pregnant post-RT patients and 16S rRNA gene sequencing was used for bacterial identification. The prevalence of Lactobacillus crispatus and Burkholderia stabilis was significantly higher in the non-chorioamnionitis group. In contrast, alpha diversity analysis using the PD index showed significantly higher diversity in the chorioamnionitis group (P = 0.04). The demonstrated relationship between chorioamnionitis and microbial diversity affirms the importance of controlling the genital bacterial flora in pregnancies following RT.

Tumor-resident Lactobacillus iners confer chemoradiation resistance through lactate-induced metabolic rewiring

Tumor microbiota can produce active metabolites that affect cancer and immune cell signaling, metabolism, and proliferation. Here, we explore tumor and gut microbiome features that affect chemoradiation response in patients with cervical cancer using a combined approach of deep microbiome sequencing, targeted bacterial culture, and in vitro assays. We identify that an obligate L-lactate-producing lactic acid bacterium found in tumors, Lactobacillus iners, is associated with decreased survival in patients, induces chemotherapy and radiation resistance in cervical cancer cells, and leads to metabolic rewiring, or alterations in multiple metabolic pathways, in tumors. Genomically similar L-lactate-producing lactic acid bacteria commensal to other body sites are also significantly associated with survival in colorectal, lung, head and neck, and skin cancers. Our findings demonstrate that lactic acid bacteria in the tumor microenvironment can alter tumor metabolism and lactate signaling pathways, causing therapeutic resistance. Lactic acid bacteria could be promising therapeutic targets across cancer types.

Colorectal Cancer Archaeome: A Metagenomic Exploration, Tunisia

Colorectal cancer (CRC) is a serious public health problem known to have a multifactorial etiology. The association between gut microbiota and CRC has been widely studied; however, the link between archaea and CRC has not been sufficiently studied. To investigate the involvement of archaea in colorectal carcinogenesis, we performed a metagenomic analysis of 68 formalin-embedded paraffin fixed tissues from tumoral (n = 33) and healthy mucosa (n = 35) collected from 35 CRC Tunisian patients. We used two DNA extraction methods: Generead DNA FFPE kit (Qiagen, Germantown, MD, USA) and Chelex. We then sequenced the samples using Illumina Miseq. Interestingly, DNA extraction exclusively using Chelex generated enough DNA for sequencing of all samples. After data filtering and processing, we reported the presence of archaeal sequences, which represented 0.33% of all the reads generated. In terms of abundance, we highlighted a depletion in methanogens and an enrichment in Halobacteria in the tumor tissues, while the correlation analysis revealed a significant association between the Halobacteria and the tumor mucosa (p < 0.05). We reported a strong correlation between Natrialba magadii, Sulfolobus acidocaldarius, and tumor tissues, and a weak correlation between Methanococcus voltae and healthy adjacent mucosa. Here, we demonstrated the feasibility of archaeome analysis from formol fixed paraffin-embedded (FFPE) tissues using simple protocols ranging from sampling to data analysis, and reported a significant association between Halobacteria and tumor tissues in Tunisian patients with CRC. The importance of our study is that it represents the first metagenomic analysis of Tunisian CRC patients' gut microbiome, which consists of sequencing DNA extracted from paired tumor-adjacent FFPE tissues collected from CRC patients. The detection of archaeal sequences in our samples confirms the feasibility of carrying out an archaeome analysis from FFPE tissues using a simple DNA extraction protocol. Our analysis revealed the enrichment of Halobacteria, especially Natrialba magadii, in tumor mucosa compared to the normal mucosa in CRC Tunisian patients. Other species were also associated with CRC, including Sulfolobus acidocaldarius and Methanococcus voltae, which is a methanogenic archaea; both species were found to be correlated with adjacent healthy tissues.

Immunohistochemical Differentiation between Western and East Asian Types of CagA-Positive Helicobacter pylori in Gastric Biopsy Samples

BACKGROUND

Cag A-positive Helicobacter pylori isolated from human gastric mucosa is categorized as a Western or East Asian allele-type based on whether the cagA gene encodes an EPIYA-C or EPIYA-D motif. We aimed to differentiate between the 2 types of H. pylori by immunohistochemistry (IHC) using formalin-fixed paraffin-embedded (FFPE) gastric biopsy samples.

MATERIALS AND METHODS

We developed 2 monoclonal antibodies (mAbs) that detect either the EPIYA-C or EPIYA-D motif of the H. pylori CagA protein by IHC using FFPE tissues. FFPE tissue sections from 30 Japanese and 39 Brazilian gastric biopsy samples with H. pylori infection confirmed by Giemsa staining (moderate/severe in the Sydney classification system) were examined by IHC with the novel mAbs followed by polymerase chain reaction (PCR) for EPIYA-C or EPIYA-D using DNA extracted from adjacent tissue sections.

RESULTS

Differentiation among Western and East Asian types and CagA-negative H. pylori was successful in most (97%) samples by IHC with the novel mAbs and commercially available mAbs that react with a species-specific lipopolysaccharide or a common CagA motif of H. pylori. The detection status of EPIYA-C/D motifs by IHC with the novel mAbs was consistent with the PCR results in 61 (88%) of 69 samples: EPIYA-C(+)/D(-) in zero Japanese and 26 Brazilian samples, EPIYA-C(-)/D(+) in 26 Japanese and 1 Brazilian sample, and EPIYA-C(-)/D(-) in 1 Japanese and 7 Brazilian samples. The detection sensitivity and specificity of IHC with each novel mAb compared with the PCR results were, respectively, 84% and 97% for EPIYA-C, and 97% and 95% for EPIYA-D.

CONCLUSIONS

The novel mAbs specific to each EPIYA-C or EPIYA-D motif differentiated between Western and East Asian types of CagA-positive H. pylori by IHC using FFPE tissues. Applying these novel mAbs to large numbers of archived pathology samples will contribute to elucidating the association of these allele types with gastric cancer.