Tumor-Associated Microbiome: Where Do We Stand?

Dysbiosis; Gut microbiome; TumorDisbiosis; Microbioma intestinal; TumorDisbiosi; Microbioma intestinal; TumorThe study of the human microbiome in oncology is a growing and rapidly evolving field. In the past few years, there has been an exponential increase in the number of studies investigating associations of microbiome and cancer, from oncogenesis and cancer progression to resistance or sensitivity to specific anticancer therapies. The gut microbiome is now known to play a significant role in antitumor immune responses and in predicting the efficacy of immune-checkpoint inhibitors in cancer patients. Beyond the gut, the tumor-associated microbiome-microbe communities located either in the tumor or within its body compartment-seems to interact with the local microenvironment and the tumor immune contexture, ultimately impacting cancer progression and treatment outcome. However, pre-clinical research focusing on causality and mechanistic pathways as well as proof-of-concept studies are still needed to fully understand the potential clinical utility of microbiome in cancer patients. Moreover, there is a need for the standardization of methodology and the implementation of quality control across microbiome studies to allow for a better interpretation and greater comparability of the results reported between them. This review summarizes the accumulating evidence in the field and discusses the current and upcoming challenges of microbiome studies

Gut microbiome diversity detected by high-coverage 16S and shotgun sequencing of paired stool and colon sample

The gut microbiome has a fundamental role in human health and disease. However, studying the complex structure and function of the gut microbiome using next generation sequencing is challenging and prone to reproducibility problems. Here, we obtained cross-sectional colon biopsies and faecal samples from nine participants in our COLSCREEN study and sequenced them in high coverage using Illumina pair-end shotgun (for faecal samples) and IonTorrent 16S (for paired feces and colon biopsies) technologies. The metagenomes consisted of between 47 and 92 million reads per sample and the targeted sequencing covered more than 300 k reads per sample across seven hypervariable regions of the 16S gene. Our data is freely available and coupled with code for the presented metagenomic analysis using up-to-date bioinformatics algorithms. These results will add up to the informed insights into designing comprehensive microbiome analysis and also provide data for further testing for unambiguous gut microbiome analysis

Tumor-Associated Microbiome: Where Do We Stand?

The study of the human microbiome in oncology is a growing and rapidly evolving field. In the past few years, there has been an exponential increase in the number of studies investigating associations of microbiome and cancer, from oncogenesis and cancer progression to resistance or sensitivity to specific anticancer therapies. The gut microbiome is now known to play a significant role in antitumor immune responses and in predicting the efficacy of immune-checkpoint inhibitors in cancer patients. Beyond the gut, the tumor-associated microbiome-microbe communities located either in the tumor or within its body compartment-seems to interact with the local microenvironment and the tumor immune contexture, ultimately impacting cancer progression and treatment outcome. However, pre-clinical research focusing on causality and mechanistic pathways as well as proof-of-concept studies are still needed to fully understand the potential clinical utility of microbiome in cancer patients. Moreover, there is a need for the standardization of methodology and the implementation of quality control across microbiome studies to allow for a better interpretation and greater comparability of the results reported between them. This review summarizes the accumulating evidence in the field and discusses the current and upcoming challenges of microbiome studies

Meta-Analysis and Validation of a Colorectal Cancer Risk Prediction Model Using Deep Sequenced Fecal Metagenomes

Simple Summary Colorectal cancer (CRC) is the third most common cancer in the world. The gut microbiome, which includes a collection of microbes, is a potential modifiable risk factor. The study of the microbiome is complex and many issues remain unsolved despite the scientific efforts that have been recently made. The present study aimed to build a CRC predictive model performing a meta-analyses of previously published shotgun metagenomics data, and to validate it in a new study. For that purpose, 156 participants of a CRC screening program were recruited, with an even distribution of CRCs, high-risk colonic precancerous lesions, and a control group with normal colonic mucosa. We have identified a signature of 32 bacterial species that have a good predictive accuracy to identify CRC but not precancerous lesions. This suggests that the identified microbes that were enriched or depleted in CRC are merely a consequence of the tumor. The gut microbiome is a potential modifiable risk factor for colorectal cancer (CRC). We re-analyzed all eight previously published stool sequencing data and conducted an MWAS meta-analysis. We used cross-validated LASSO predictive models to identify a microbiome signature for predicting the risk of CRC and precancerous lesions. These models were validated in a new study, Colorectal Cancer Screening (COLSCREEN), including 156 participants that were recruited in a CRC screening context. The MWAS meta-analysis identified 95 bacterial species that were statistically significantly associated with CRC (FDR < 0.05). The LASSO CRC predictive model obtained an area under the receiver operating characteristic curve (aROC) of 0.81 (95%CI: 0.78-0.83) and the validation in the COLSCREEN dataset was 0.75 (95%CI: 0.66-0.84). This model selected a total of 32 species. The aROC of this CRC-trained model to predict precancerous lesions was 0.52 (95%CI: 0.41-0.63). We have identified a signature of 32 bacterial species that have a good predictive accuracy to identify CRC but not precancerous lesions, suggesting that the identified microbes that were enriched or depleted in CRC are merely a consequence of the tumor. Further studies should focus on CRC as well as precancerous lesions with the intent to implement a microbiome signature in CRC screening programs

The roses ocean and human health chair: A new way to engage the public in oceans and human health challenges

Involving and engaging stakeholders is crucial for studying and managing the complex interactions between marine ecosystems and human health and wellbeing. The Oceans and Human Health Chair was founded in the town of Roses (Catalonia, Spain, NW Mediterranean) in 2018, the fruit of a regional partnership between various stakeholders, and for the purpose of leading the way to better health and wellbeing through ocean research and conservation. The Chair is located in an area of the Mediterranean with a notable fishing, tourist, and seafaring tradition and is close to a marine reserve, providing the opportunity to observe diverse environmental conditions and coastal and maritime activities. The Chair is a case study demonstrating that local, collaborative, transdisciplinary, trans-sector, and bottom-up approaches offer tremendous opportunities for engaging coastal communities to help support long-lasting solutions that benefit everyone, and especially those living by the sea or making their living from the goods and services provided by the sea. Furthermore, the Chair has successfully integrated most of its experts in oceans and human health from the most prestigious institutions in Catalonia. The Chair focuses on three main topics identified by local stakeholders: Fish and Health; Leisure, Health, and Wellbeing; and Medicines from the Sea. Led by stakeholder engagement, the Chair can serve as a novel approach within the oceans and human health field of study to tackle a variety of environmental and public health challenges related to both communicable and non-communicable diseases, within the context of sociocultural issues. Drawing on the example provided by the Chair, four principles are established to encourage improved participatory processes in the oceans and human health field: bottom-up, “think local”, transdisciplinary and trans-sectorial, and “balance the many voices”.info:eu-repo/semantics/publishedVersio

The Roses Ocean and Human Health Chair: A New Way to Engage the Public in Oceans and Human Health Challenges

Involving and engaging stakeholders is crucial for studying and managing the complex interactions between marine ecosystems and human health and wellbeing. The Oceans and Human Health Chair was founded in the town of Roses (Catalonia, Spain, NW Mediterranean) in 2018, the fruit of a regional partnership between various stakeholders, and for the purpose of leading the way to better health and wellbeing through ocean research and conservation. The Chair is located in an area of the Mediterranean with a notable fishing, tourist, and seafaring tradition and is close to a marine reserve, providing the opportunity to observe diverse environmental conditions and coastal and maritime activities. The Chair is a case study demonstrating that local, collaborative, transdisciplinary, trans-sector, and bottom-up approaches offer tremendous opportunities for engaging coastal communities to help support long-lasting solutions that benefit everyone, and especially those living by the sea or making their living from the goods and services provided by the sea. Furthermore, the Chair has successfully integrated most of its experts in oceans and human health from the most prestigious institutions in Catalonia. The Chair focuses on three main topics identified by local stakeholders: Fish and Health; Leisure, Health, and Wellbeing; and Medicines from the Sea. Led by stakeholder engagement, the Chair can serve as a novel approach within the oceans and human health field of study to tackle a variety of environmental and public health challenges related to both communicable and non-communicable diseases, within the context of sociocultural issues. Drawing on the example provided by the Chair, four principles are established to encourage improved participatory processes in the oceans and human health field: bottom-up, "think local", transdisciplinary and trans-sectorial, and "balance the many voices"

Production and characterization of monoclonal antibodies for the detection of the hepatitis C core antigen

Background: Despite highly effective treatments to cure hepatitis C, almost 80% of chronically HCV-infected people are not treated, as they are unaware of their infection. Diagnostic rates and linkage to care must be substantially improved to reverse this situation. The HCV core antigen (HCVcAg) is a highly conserved protein that can be detected in the blood of HCV-infected patients and indicates active infection. Aim: To produce murine monoclonal antibodies against HCVcAg suitable for rapid and inexpensive tests to detect HCV infection. Methods: BALB/c mice were sequentially inoculated with purified recombinant HCVcAg from Gt1a, Gt3a, Gt4a, and Gt1b genotypes. Hybridomas producing the desired monoclonal antibodies were selected, and the reactivity of antibodies against HCVcAg from various genotypes was tested by Western blotting and dot blotting. The binding kinetics of the antibodies to purified HCVcAg was analyzed by surface plasmon resonance (SPR), and their ability to detect HCVcAg was tested by double antibody sandwich ELISA (DAS-ELISA). Results: Four specific monoclonal antibodies (1C, 2C, 4C, and 8C) were obtained. 1C, 2C, and 4C recognized HCVcAg of all genotypes tested (Gt1a, Gt1b, Gt2a, Gt3a, and Gt4a), while 8C did not recognize the Gt2a and Gt3a genotypes. Based on SPR data, the antibody-HCVcAg complexes formed are stable, with 2C having the strongest binding properties. DAS-ELISA with different antibody combinations easily detected HCVcAg in culture supernatants from HCV-infected cells. Conclusion: Specific and cross-reactive anti-HCVcAg monoclonal antibodies with strong binding properties were obtained that may be useful for detecting HCVcAg in HCV-infected samples.This study was supported by a grant from Instituto de Salud Carlos III (ISCIII, PI19CIII/00009). The study was also funded by the Centro de Investigación Biomédica en Red de Enfermedades infecciosas (CIBERINFEC) [CB21/13/00044 (SR and IM)].S

Rapid profiling of RSV antibody repertoires from the memory B cells of naturally infected adult donors

Respiratory syncytial virus (RSV) causes substantial morbidity and mortality in young children and the elderly. There are currently no licensed RSV vaccines, and passive prophylaxis with the monoclonal antibody palivizumab is restricted to high-risk infants in part due to its modest efficacy. Although it is widely agreed that an effective RSV vaccine will require the induction of a potent neutralizing antibody response against the RSV fusion (F) glycoprotein, little is known about the specificities and functional activities of RSV F-specific antibodies induced by natural infection. Here, we have comprehensively profiled the human antibody response to RSV F by isolating and characterizing 364 RSV F-specific monoclonal antibodies from the memory B cells of three healthy adult donors. In all donors, the antibody response to RSV F is comprised of a broad diversity of clones that target several antigenic sites. Nearly half of the most potent antibodies target a previously undefined site of vulnerability near the apex of the prefusion conformation of RSV F (preF), providing strong support for the development of RSV vaccine candidates that preserve the membrane-distal hemisphere of the preF protein. Additionally, the antibodies targeting this new site display convergent sequence features, thus providing a future means to rapidly detect the presence of these antibodies in human vaccine samples. Many of the antibodies that bind preF-specific surfaces are over 100 times more potent than palivizumab, and several cross-neutralize human metapneumovirus (HMPV). Taken together, the results have implications for the design and evaluation of RSV vaccine candidates and offer new options for passive prophylaxis.We thank Tushar Jain for guidance on statistical analyses, Todd Boland for assistance with antibody sequence analysis, Emilie Shipman for assistance with protein expression, Wen Li for technical assistance, Cody Williams and S.M. Eagol for assistance with figure preparation, and Margaret Ackerman for use of the magnetic microplate washer (BioTek) and the FLEXMAP 3D flow cytometer (Luminex). PBMC processing was carried out in DartLab, the Immune Monitoring and Flow Cytometry Shared Resource, supported by a National Cancer Institute Cancer Center Support Grant to the Norris Cotton Cancer Center (P30CA023108-37) and an Immunology COBRE Grant (P30GM103415-15) from the National Institute of General Medical Sciences. All the IgGs were sequenced by Adimab's Molecular Core and produced by the High Throughput Expression group. Biolayer interferometry binding experiments were performed by Adimab's protein analytics group. Funding: Support for this work was provided by the National Institute of General Medical Sciences of the National Institutes of Health award T32GM008704 (M.S.A.G.) and P20GM113132 (J.S.M.) and intramural funding from the National Institute of Allergy and Infectious Diseases to support work at the Vaccine Research Center (B.S.G.). This work was partially supported by grant SAF2015-67033-R to J.A.M. from Plan Nacional I+D+i.S