MicroRNA modulated networks of adaptive and innate immune response in pancreatic ductal adenocarcinoma

RESEARCH ARTICLE MicroRNA modulated networks of adaptive and innate immune response in pancreatic ductal adenocarcinoma Tainara F. Felix1,2, Rainer M. Lopez Lapa2,3, Márcio de Carvalho4, Natália Bertoni1,2, Tomas Tokar5, Rogério A. Oliveira6, Maria A. M. Rodrigues7, Cláudia N. Hasimoto1, Walmar K. Oliveira1, Leonardo Pelafsky1, César T. Spadella1, Juan C. Llanos1, Giovanni F. Silva8, Wan L. Lam9, Silvia Regina Rogatto10, Luciana Schultz Amorim11, Sandra A. Drigo1,2, Robson F. Carvalho12, Patricia P. Reis ID1,2* a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 OPEN ACCESS Citation: Felix TF, Lopez Lapa RM, de Carvalho M, Bertoni N, Tokar T, Oliveira RA, et al. (2019) MicroRNA modulated networks of adaptive and innate immune response in pancreatic ductal adenocarcinoma. PLoS ONE 14(5): e0217421. https://doi.org/10.1371/journal.pone.0217421 Editor: Surinder K. Batra, University of Nebraska Medical Center, UNITED STATES Received: January 16, 2019 Accepted: May 10, 2019 Published: May 31, 2019 Copyright: © 2019 Felix et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: Original, raw data are publicly available on Gene Expression Omnibus (GEO), under accession number GSE125179. Funding: Research funds were obtained from São Paulo Research Foundation (FAPESP) (grant #2016/03905-2 to P. P. Reis). T.F.F. was funded, in separate time periods, through the Coordination for the Improvement of Higher Level Education (CAPES) and FAPESP - fellowship #2014/00367-4. The funders had no role in study design, data 1 Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University (UNESP), Botucatu, SP, Brazil, 2 Experimental Research Unity (UNIPEX), Faculty of Medicine, São Paulo State University (UNESP), Botucatu, SP, Brazil, 3 Department of Genetics, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, SP, Brazil, 4 Department of Veterinary Clinic, School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, SP, Brazil, 5 Krembil Research Institute, University Health Network, Toronto, ON, Canada, 6 Department of Biostatistics, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, SP, Brazil, 7 Department of Pathology, Faculty of Medicine, São Paulo State University (UNESP), Botucatu, SP, Brazil, 8 Department of Clinics and Gastroenterology, Faculty of Medicine, São Paulo State University (UNESP), Botucatu, SP, Brazil, 9 Genetics Unity, Integrative Oncology, British Columbia Cancer Center, Vancouver, BC, Canada, 10 Department of Clinical Genetics, Vejle Hospital, Institute of Regional Health Research, University of Southern Denmark, Denmark, DK, 11 Institute of Pathological Anatomy, Piracicaba, SP, Brazil, 12 Department of Morphology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, SP, Brazil * Abstract Despite progress in treatment strategies, only ~24% of pancreatic ductal adenocarcinoma (PDAC) patients survive >1 year. Our goal was to elucidate deregulated pathways modulated by microRNAs (miRNAs) in PDAC and Vater ampulla (AMP) cancers. Global miRNA expression was identified in 19 PDAC, 6 AMP and 25 paired, histologically normal pancreatic tissues using the GeneChip 4.0 miRNA arrays. Computational approaches were used for miRNA target prediction/identification of miRNA-regulated pathways. Target gene expression was validated in 178 pancreatic cancer and 4 pancreatic normal tissues from The Cancer Genome Atlas (TCGA). 20 miRNAs were significantly deregulated (FC�2 and p<0.05) (15 down- and 5 up-regulated) in PDAC. miR-216 family (miR-216a-3p, miR-216a5p, miR-216b-3p and miR-216b-5p) was consistently down-regulated in PDAC. miRNAmodulated pathways are associated with innate and adaptive immune system responses in PDAC. AMP cancers showed 8 down- and 1 up-regulated miRNAs (FDR p<0.05). Most enriched pathways (p<0.01) were RAS and Nerve Growth Factor signaling. PDAC and AMP display different global miRNA expression profiles and miRNA regulated networks/tumorigenesis pathways. The immune response was enriched in PDAC, suggesting the existence of immune checkpoint pathways more relevant to PDAC than AMP. PLOS ONE | https://doi.org/10.1371/journal.pone.0217421 May 31, 2019 1 / 20 MicroRNAs in pancreatic cancer collection and analysis, decision to publish, or preparation of the manuscript. Competing interests: The authors have declared that no competing interests exist. Introduction Pancreatic cancer is the fourth most frequent cause of cancer death, worldwide [1,2]. The majority of pancreatic cancers (~96%) comprise exocrine ductal adenocarcinomas (PDAC) [2]. Other pancreatic tumors include periampullary carcinomas; of these, ~12% are adenocarcinomas of Vater ampulla (AMP). AMP patients have a better prognosis (5-year survival of >45%) [3,4] compared to PDAC, mainly due to early disease detection. The asymptomatic nature of PDAC is often associated with late diagnosis and poor patient prognosis. This disease is characterized by very aggressive and rapid tumor growth and high incidence of distant metastasis [5]. Despite progress in treatment strategies (surgery, chemo and radiation therapies) in the past 5 years, only 24% of patients with PDAC survive more than a year and <5% are expected to survive more than 5 years after diagnosis [6]. More recently developed immunotherapy treatment strategies have failed to succeed for patients with PDAC. Therefore, there is a need to identify clinically useful biomarkers for early disease detection, as well as to further develop combinations of precision therapeutics for patients diagnosed with the late-stage disease [7]. Molecular mechanisms underlying pancreatic oncogenesis involve both genetic and epigenetic changes [8]. The role of microRNAs (miRNAs) has been widely reported as regulatory molecules associated with tumorigenesis [9]. miRNAs are potent gene expression regulators involved in biological processes including embryonic development, differentiation, apoptosis and cell proliferation [10,11]. An increasing number of non-coding RNAs, including miRNAs, have been reported to regulate immune system homeostasis and immune system development and function [12,13]. miRNAs have roles in the regulation of both innate and adaptive immune responses, in which they control early development of immune cell progenitors, maintenance and differentiation and mature immune cell function [12,14]. Considering that miRNAs have been shown as biomarkers for diagnosis, prognosis, and treatment of patients with cancer [15] they may have potential use as combination therapeutic molecules in PDAC, targeting immune system pathways. Previous studies compared global miRNA expression profiles in PDAC and AMP and showed (...truncated)