Bacterial and Fungal Characterization of Pancreatic Adenocarcinoma from Endoscopic Ultrasound-guided Biopsies

Overview

Journal Front Immunol

Specialty Allergy & Immunology

Date 2023 Oct 30

PMID 37901238

Authors

Robin D Wright

Thais F Bartelli

Seyda Baydogan

James Robert White

Michael P Kim

Manoop S Bhutani

Florencia McAllister

Affiliations

Soon will be listed here.

Abstract

Introduction: The tumor microbiome (TM) has been linked to pancreatic cancer prognosis. Specific microbes can confer tumor resistance to therapies. Early knowledge of the TM at time of diagnosis would be clinically relevant for precision therapy based on microbial composition. However, it is difficult to define the TM prior to surgical resection.

Methods: In this pilot feasibility study, patients underwent Endoscopic Ultrasound-Fine Needle Aspiration (EUS-FNA) biopsy of pancreatic adenocarcinoma. These samples were analyzed using 16S rRNA and internal transcribed spacer (ITS) sequencing for characterization of the tumor bacteria and fungi.

Result: After in silico decontamination and comparison to non-matched tumor, we were able to characterize the TM in biopsies, which was comparable to the TM from surgical specimens.

Discussion: EUS-FNA biopsy may represent a feasible modality to characterize the pancreatic TM prior to surgical resection with proper decontamination strategies and improvements in matched controls.

Citing Articles

Metagenomic analysis reveals the community composition of the microbiome in different segments of the digestive tract in donkeys and cows: implications for microbiome research.

Su L, Guo J, Shi W, Tong W, Li X, Yang B BMC Microbiol. 2024; 24(1):530.

PMID: 39695983 PMC: 11656932. DOI: 10.1186/s12866-024-03696-5.

References

Kuczynski J, Stombaugh J, Walters W, Gonzalez A, Caporaso J, Knight R . Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Curr Protoc Bioinformatics. 2011; Chapter 10:10.7.1-10.7.20. PMC: 3249058. DOI: 10.1002/0471250953.bi1007s36. View

Chandra V, McAllister F . Therapeutic potential of microbial modulation in pancreatic cancer. Gut. 2021; . PMC: 8292583. DOI: 10.1136/gutjnl-2019-319807. View

Thompson L, Sanders J, McDonald D, Amir A, Ladau J, Locey K . A communal catalogue reveals Earth's multiscale microbial diversity. Nature. 2017; 551(7681):457-463. PMC: 6192678. DOI: 10.1038/nature24621. View

Drewes J, White J, Dejea C, Fathi P, Iyadorai T, Vadivelu J . High-resolution bacterial 16S rRNA gene profile meta-analysis and biofilm status reveal common colorectal cancer consortia. NPJ Biofilms Microbiomes. 2017; 3:34. PMC: 5707393. DOI: 10.1038/s41522-017-0040-3. View

Parhi L, Alon-Maimon T, Sol A, Nejman D, Shhadeh A, Fainsod-Levi T . Breast cancer colonization by Fusobacterium nucleatum accelerates tumor growth and metastatic progression. Nat Commun. 2020; 11(1):3259. PMC: 7320135. DOI: 10.1038/s41467-020-16967-2. View

Heberle H, Meirelles G, da Silva F, Telles G, Minghim R . InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams. BMC Bioinformatics. 2015; 16:169. PMC: 4455604. DOI: 10.1186/s12859-015-0611-3. View

Siegel R, Miller K, Fuchs H, Jemal A . Cancer statistics, 2022. CA Cancer J Clin. 2022; 72(1):7-33. DOI: 10.3322/caac.21708. View

Edgar R . Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010; 26(19):2460-1. DOI: 10.1093/bioinformatics/btq461. View

Das K, Early D . Pancreatic Cancer Screening. Curr Treat Options Gastroenterol. 2017; 15(4):562-575. DOI: 10.1007/s11938-017-0149-8. View

10.

Li X, Saxena D . The mycobiome-immune axis: The next frontier in pancreatic cancer. Cancer Cell. 2022; 40(2):120-122. PMC: 10191147. DOI: 10.1016/j.ccell.2022.01.009. View

11.

Gevers D, Knight R, Petrosino J, Huang K, McGuire A, Birren B . The Human Microbiome Project: a community resource for the healthy human microbiome. PLoS Biol. 2012; 10(8):e1001377. PMC: 3419203. DOI: 10.1371/journal.pbio.1001377. View

12.

Daquigan N, Seekatz A, Greathouse K, Young V, White J . High-resolution profiling of the gut microbiome reveals the extent of burden. NPJ Biofilms Microbiomes. 2017; 3:35. PMC: 5717231. DOI: 10.1038/s41522-017-0043-0. View

13.

Kulakov L, McAlister M, Ogden K, Larkin M, OHanlon J . Analysis of bacteria contaminating ultrapure water in industrial systems. Appl Environ Microbiol. 2002; 68(4):1548-55. PMC: 123900. DOI: 10.1128/AEM.68.4.1548-1555.2002. View

14.

Cervantes J, Michael M, Hong B, Springer A, Guo H, Mendoza B . Investigation of oral, gastric, and duodenal microbiota in patients with upper gastrointestinal symptoms. J Investig Med. 2020; . DOI: 10.1136/jim-2020-001642. View

15.

Kartal E, Schmidt T, Molina-Montes E, Rodriguez-Perales S, Wirbel J, Maistrenko O . A faecal microbiota signature with high specificity for pancreatic cancer. Gut. 2022; 71(7):1359-1372. PMC: 9185815. DOI: 10.1136/gutjnl-2021-324755. View

16.

Caporaso J, Kuczynski J, Stombaugh J, Bittinger K, Bushman F, Costello E . QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010; 7(5):335-6. PMC: 3156573. DOI: 10.1038/nmeth.f.303. View

17.

Nakano S, Kawamoto Y, Komatsu Y, Saito R, Ito K, Yamamura T . Analysis of the Pancreatic Cancer Microbiome Using Endoscopic Ultrasound-Guided Fine-Needle Aspiration-Derived Samples. Pancreas. 2022; 51(4):351-357. PMC: 9257056. DOI: 10.1097/MPA.0000000000002028. View

18.

Seo Y, Katz M . Preoperative therapy for pancreatic adenocarcinoma-precision beyond anatomy. Cancer. 2022; 128(16):3041-3056. DOI: 10.1002/cncr.34273. View

19.

Salter S, Cox M, Turek E, Calus S, Cookson W, Moffatt M . Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 2014; 12:87. PMC: 4228153. DOI: 10.1186/s12915-014-0087-z. View

20.

Tang Q, Jin G, Wang G, Liu T, Liu X, Wang B . Current Sampling Methods for Gut Microbiota: A Call for More Precise Devices. Front Cell Infect Microbiol. 2020; 10:151. PMC: 7161087. DOI: 10.3389/fcimb.2020.00151. View