Characterization of FFPE-induced bacterial DNA damage and development of a repair method

A critical spotlight on the paradigms of FFPE-DNA sequencing

In the late 19th century, formalin fixation with paraffin-embedding (FFPE) of tissues was developed as a fixation and conservation method and is still used to this day in routine clinical and pathological practice. The implementation of state-of-the-art nucleic acid sequencing technologies has sparked much interest for using historical FFPE samples stored in biobanks as they hold promise in extracting new information from these valuable samples. However, formalin fixation chemically modifies DNA, which potentially leads to incorrect sequences or misinterpretations in downstream processing and data analysis. Many publications have concentrated on one type of DNA damage, but few have addressed the complete spectrum of FFPE-DNA damage. Here, we review mitigation strategies in (I) pre-analytical sample quality control, (II) DNA repair treatments, (III) analytical sample preparation and (IV) bioinformatic analysis of FFPE-DNA. We then provide recommendations that are tested and illustrated with DNA from 13-year-old liver specimens, one FFPE preserved and one fresh frozen, applying target-enriched sequencing. Thus, we show how DNA damage can be compensated, even when using low quantities (50 ng) of fragmented FFPE-DNA (DNA integrity number 2.0) that cannot be amplified well (Q129 bp/Q41 bp = 5%). Finally, we provide a checklist called 'ERROR-FFPE-DNA' that summarises recommendations for the minimal information in publications required for assessing fitness-for-purpose and inter-study comparison when using FFPE samples.

Bladder cancer-associated microbiota: Recent advances and future perspectives

Recent evidence suggests that the human genitourinary microbiome plays a significant role in mediating the development and progression of urological tumors, including bladder cancer (BC). Clinicians widely recognize the role of Bacille Calmette Guérin (BCG), an attenuated Mycobacterium tuberculosis vaccine, in the management of intermediate- and high-risk NMIBC. However, compared to the large body of evidence on the gut microbiota and gastrointestinal tumors, limited information is available about the interaction between BC and the genitourinary microbiome. This is an expanding field that merits further investigation. Urologists will need to consider the potential impact of the microbiome in BC diagnosis, prevention of recurrence and progression, and treatment prospects in the future. This review highlights the approaches adopted for microbiome research and the findings and inadequacies of current research on BC.

Understanding and harnessing triple-negative breast cancer-related microbiota in oncology

Bacterial inhabitants of the body have the potential to play a role in various stages of cancer initiation, progression, and treatment. These bacteria may be distal to the primary tumour, such as gut microbiota, or local to the tissue, before or after tumour growth. Breast cancer is well studied in this context. Amongst breast cancer types, Triple Negative Breast Cancer (TNBC) is more aggressive, has fewer treatment options than receptor-positive breast cancers, has an overall worse prognosis and higher rates of reoccurrence. Thus, an in-depth understanding of the bacterial influence on TNBC progression and treatment is of high value. In this regard, the Gut Microbiota (GM) can be involved in various stages of tumour progression. It may suppress or promote carcinogenesis through the release of carcinogenic metabolites, sustenance of proinflammatory environments and/or the promotion of epigenetic changes in our genome. It can also mediate metastasis and reoccurrence through interactions with the immune system and has been recently shown to influence chemo-, radio-, and immune-therapies. Furthermore, bacteria have also been found to reside in normal and malignant breast tissue. Several studies have now described the breast and breast tumour microbiome, with the tumour microbiota of TNBC having the least taxonomic diversity among all breast cancer types. Here, specific conditions of the tumour microenvironment (TME) - low O2, leaky vasculature and immune suppression - are supportive of tumour selective bacterial growth. This innate bacterial ability could enable their use as delivery agents for various therapeutics or as diagnostics. This review aims to examine the current knowledge on bacterial relevance to TNBC and potential uses while examining some of the remaining unanswered questions regarding mechanisms underpinning observed effects.

An efficient procedure for the recovery of DNA from formalin-fixed paraffin-embedded tissue sections

With the advent of new molecular diagnostic techniques, retrieving DNA from the formalin-fixed paraffin-embedded (FFPE) tissues has become an essential yet challenging step for efficient downstream processes. Owing to low quality and quantity of DNA retrieved from the FFPE sections, the process is often impractical and needs significant improvements. Here, we established an efficient method for the purification of DNA from FFPE specimens by optimizing incubation temperature, incubation time, and the concentration of a formalin scavenger tris(hydroxymethyl)aminomethane (Tris) for reverse-crosslinking. The optimized method, named "Highly concentrated Tris-mediated DNA extraction" (HiTE), yielded three times the DNA yield per tissue slice compared with a representative DNA extraction kit. Moreover, the use of HiTE-extracted DNA increased the yield of the sequencing library three times and accordingly yielded a log higher and more reproducible sequencing library compared with that obtained using the commonly used commercial kit. The sequencing library prepared from HiTE-extracted FFPE-DNA had longer inserts and produced reads that evenly covered the reference genome. Successful application of HiTE-extracted FFPE-DNA for whole-genome and targeted gene panel sequencing indicates its practical usability.

Characterizing and Exploiting Tumor Microenvironments to Optimize Treatment Outcomes

Simple Summary

The Irish Association for Cancer Research (IACR) held its 57th annual conference from the 24–26 March 2021 in a virtual format due to the ongoing pandemic. This report provides a summary overview of the work presented at the conference, which had a particular focus on the tumor microenvironment. Tumors do not develop and grow in isolation, but rather within the context of their surrounding environment. The work presented at the conference outlined the complexity of the tumor microenvironment and highlighted several ways in which it influences tumor growth and progression. Moreover, the tumor microenvironment was discussed as a potential target for new cancer treatments. Traditionally, laboratory research has focused on the tumor only, but conference speakers highlighted the importance of modeling the surrounding microenvironment to gain a more physiologically relevant view of tumorigenesis. Finally, conference attendees heard from the patient’s perspective regarding the development of novel targeted therapies.

Abstract

Our understanding of cancer initiation, progression, and treatment is continually progressing through dedicated research achieved through laboratory investigation, clinical trials, and patient engagement. The importance and complexity of the microenvironment and its role in tumor development and behavior is pivotal to the understanding of tumor growth and the best course of treatment. The 57th Irish Association for Cancer Research (IACR) Annual Conference collected key researchers, clinicians, and patient advocates together to highlight and discuss the recognized importance of the microenvironment and treatment advances in cancer. In this article, we describe the key components of the microenvironment that influence tumor development and treatment, including the microbiome, metabolism, and immune response and the progress of preclinical models to reflect these complex environments. From a psycho-social oncology perspective, we highlight expert opinion and data on the process of shared decision-making in the context of emerging cancer treatments.