1
|
Leija-Montoya AG, González-Ramírez J, Martínez-Coronilla G, Mejía-León ME, Isiordia-Espinoza M, Sánchez-Muñoz F, Chávez-Cortez EG, Pitones-Rubio V, Serafín-Higuera N. Roles of microRNAs and Long Non-Coding RNAs Encoded by Parasitic Helminths in Human Carcinogenesis. Int J Mol Sci 2022; 23:ijms23158173. [PMID: 35897749 PMCID: PMC9331937 DOI: 10.3390/ijms23158173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/15/2022] [Accepted: 07/21/2022] [Indexed: 12/14/2022] Open
Abstract
Infectious agents such as viruses, bacteria, and parasites can lead to cancer development. Infection with the helminthic parasite Schistosoma haematobium can cause cancer of the urinary bladder in humans, and infection with the parasites Clonorchis sinensis and Opisthorchis viverrini can promote cholangiocarcinoma. These three pathogens have been categorized as “group 1: carcinogenic to humans” by the International Agency for Research on Cancer (IARC). Additionally, the parasite Schistosoma japonicum has been associated with liver and colorectal cancer and classified as “group 2B: possibly carcinogenic to humans”. These parasites express regulatory non-coding RNAs as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), which modulate genic expression in different biological processes. In this review, we discuss the potential roles of miRNAS and lncRNAs encoded by helminthic parasites that are classified by the IARC as carcinogenic and possibly carcinogenic to humans. The miRNAs of these parasites may be involved in carcinogenesis by modulating the biological functions of the pathogen and the host and by altering microenvironments prone to tumor growth. miRNAs were identified in different host fluids. Additionally, some miRNAs showed direct antitumoral effects. Together, these miRNAs show potential for use in future therapeutic and diagnostic applications. LncRNAs have been less studied in these parasites, and their biological effects in the parasite–host interaction are largely unknown.
Collapse
Affiliation(s)
- Ana Gabriela Leija-Montoya
- Facultad de Medicina Mexicali, Universidad Autónoma de Baja California, Centro Cívico, Mexicali 21000, BC, Mexico; (A.G.L.-M.); (G.M.-C.); (M.E.M.-L.)
| | - Javier González-Ramírez
- Facultad de Enfermería, Universidad Autónoma de Baja California, Av. Álvaro Obregón y Calle “G” S/N, Col. Nueva, Mexicali 21100, BC, Mexico;
| | - Gustavo Martínez-Coronilla
- Facultad de Medicina Mexicali, Universidad Autónoma de Baja California, Centro Cívico, Mexicali 21000, BC, Mexico; (A.G.L.-M.); (G.M.-C.); (M.E.M.-L.)
| | - María Esther Mejía-León
- Facultad de Medicina Mexicali, Universidad Autónoma de Baja California, Centro Cívico, Mexicali 21000, BC, Mexico; (A.G.L.-M.); (G.M.-C.); (M.E.M.-L.)
| | - Mario Isiordia-Espinoza
- Instituto de Investigación en Ciencias Médicas, Departamento de Clínicas, División de Ciencias Biomédicas, Centro Universitario de Los Altos, Universidad de Guadalajara, Av. Rafael Casillas Aceves 1200, Tepatitlán de Morelos 47600, JAL, Mexico;
| | - Fausto Sánchez-Muñoz
- Departamento de Inmunología, Instituto Nacional de Cardiología, Juan Badiano No. 1, Col. Sección XVI, Tlapan 140080, DF, Mexico;
| | - Elda Georgina Chávez-Cortez
- Centro de Ciencias de la Salud, Facultad de Odontología, Universidad Autónoma de Baja California, Zotoluca s/n, Fracc. Calafia, Mexicali 21040, BC, Mexico; (E.G.C.-C.); (V.P.-R.)
| | - Viviana Pitones-Rubio
- Centro de Ciencias de la Salud, Facultad de Odontología, Universidad Autónoma de Baja California, Zotoluca s/n, Fracc. Calafia, Mexicali 21040, BC, Mexico; (E.G.C.-C.); (V.P.-R.)
| | - Nicolas Serafín-Higuera
- Centro de Ciencias de la Salud, Facultad de Odontología, Universidad Autónoma de Baja California, Zotoluca s/n, Fracc. Calafia, Mexicali 21040, BC, Mexico; (E.G.C.-C.); (V.P.-R.)
- Correspondence:
| |
Collapse
|
2
|
Dai X, Shen L. Advances and Trends in Omics Technology Development. Front Med (Lausanne) 2022; 9:911861. [PMID: 35860739 PMCID: PMC9289742 DOI: 10.3389/fmed.2022.911861] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/09/2022] [Indexed: 12/11/2022] Open
Abstract
The human history has witnessed the rapid development of technologies such as high-throughput sequencing and mass spectrometry that led to the concept of “omics” and methodological advancement in systematically interrogating a cellular system. Yet, the ever-growing types of molecules and regulatory mechanisms being discovered have been persistently transforming our understandings on the cellular machinery. This renders cell omics seemingly, like the universe, expand with no limit and our goal toward the complete harness of the cellular system merely impossible. Therefore, it is imperative to review what has been done and is being done to predict what can be done toward the translation of omics information to disease control with minimal cell perturbation. With a focus on the “four big omics,” i.e., genomics, transcriptomics, proteomics, metabolomics, we delineate hierarchies of these omics together with their epiomics and interactomics, and review technologies developed for interrogation. We predict, among others, redoxomics as an emerging omics layer that views cell decision toward the physiological or pathological state as a fine-tuned redox balance.
Collapse
|
3
|
Khan P, Ebenezer NS, Siddiqui JA, Maurya SK, Lakshmanan I, Salgia R, Batra SK, Nasser MW. MicroRNA-1: Diverse role of a small player in multiple cancers. Semin Cell Dev Biol 2021; 124:114-126. [PMID: 34034986 DOI: 10.1016/j.semcdb.2021.05.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/07/2021] [Accepted: 05/16/2021] [Indexed: 12/12/2022]
Abstract
The process of cancer initiation and development is a dynamic and complex mechanism involving multiple genetic and non-genetic variations. With the development of high throughput techniques like next-generation sequencing, the field of cancer biology extended beyond the protein-coding genes. It brought the functional role of noncoding RNAs into cancer-associated pathways. MicroRNAs (miRNAs) are one such class of noncoding RNAs regulating different cancer development aspects, including progression and metastasis. MicroRNA-1 (miR-1) is a highly conserved miRNA with a functional role in developing skeletal muscle precursor cells and cardiomyocytes and acts as a consistent tumor suppressor gene. In humans, two discrete genes, MIR-1-1 located on 20q13.333 and MIR-1-2 located on 18q11.2 loci encode for a single mature miR-1. Downregulation of miR-1 has been demonstrated in multiple cancers, including lung, breast, liver, prostate, colorectal, pancreatic, medulloblastoma, and gastric cancer. A vast number of studies have shown that miR-1 affects the hallmarks of cancer like proliferation, invasion and metastasis, apoptosis, angiogenesis, chemosensitization, and immune modulation. The potential therapeutic applications of miR-1 in multiple cancer pathways provide a novel platform for developing anticancer therapies. This review focuses on the different antitumorigenic and therapeutic aspects of miR-1, including how it regulates tumor development and associated immunomodulatory functions.
Collapse
Affiliation(s)
- Parvez Khan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Nivetha Sarah Ebenezer
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Jawed Akhtar Siddiqui
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Shailendra Kumar Maurya
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Imayavaramban Lakshmanan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center and Beckman Research Institute, Duarte, CA 91010, USA
| | - Surinder Kumar Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA; Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA; Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Mohd Wasim Nasser
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA; Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA.
| |
Collapse
|
4
|
Navarro E, Mallén A, Cruzado JM, Torras J, Hueso M. Unveiling ncRNA regulatory axes in atherosclerosis progression. Clin Transl Med 2020; 9:5. [PMID: 32009226 PMCID: PMC6995802 DOI: 10.1186/s40169-020-0256-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/05/2020] [Indexed: 02/06/2023] Open
Abstract
Completion of the human genome sequencing project highlighted the richness of the cellular RNA world, and opened the door to the discovery of a plethora of short and long non-coding RNAs (the dark transcriptome) with regulatory or structural potential, which shifted the balance of pathological gene alterations from coding to non-coding RNAs. Thus, disease risk assessment currently has to also evaluate the expression of new RNAs such as small micro RNAs (miRNAs), long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), competing endogenous RNAs (ceRNAs), retrogressed elements, 3'UTRs of mRNAs, etc. We are interested in the pathogenic mechanisms of atherosclerosis (ATH) progression in patients suffering Chronic Kidney Disease, and in this review, we will focus in the role of the dark transcriptome (non-coding RNAs) in ATH progression. We will focus in miRNAs and in the formation of regulatory axes or networks with their mRNA targets and with the lncRNAs that function as miRNA sponges or competitive inhibitors of miRNA activity. In this sense, we will pay special attention to retrogressed genomic elements, such as processed pseudogenes and Alu repeated elements, that have been recently seen to also function as miRNA sponges, as well as to the use or miRNA derivatives in gene silencing, anti-ATH therapies. Along the review, we will discuss technical developments associated to research in lncRNAs, from sequencing technologies to databases, repositories and algorithms to predict miRNA targets, as well as new approaches to miRNA function, such as integrative or enrichment analysis and their potential to unveil RNA regulatory networks.
Collapse
Affiliation(s)
- Estanislao Navarro
- Independent Researcher, Barcelona, Spain. .,Department of Nephrology, Hospital Universitari Bellvitge and Bellvitge Research Institute (IDIBELL), C/Feixa Llarga, s/n; L'Hospitalet de Llobregat, 08907, Barcelona, Spain.
| | - Adrian Mallén
- Department of Nephrology, Hospital Universitari Bellvitge and Bellvitge Research Institute (IDIBELL), C/Feixa Llarga, s/n; L'Hospitalet de Llobregat, 08907, Barcelona, Spain
| | - Josep M Cruzado
- Department of Nephrology, Hospital Universitari Bellvitge and Bellvitge Research Institute (IDIBELL), C/Feixa Llarga, s/n; L'Hospitalet de Llobregat, 08907, Barcelona, Spain
| | - Joan Torras
- Department of Nephrology, Hospital Universitari Bellvitge and Bellvitge Research Institute (IDIBELL), C/Feixa Llarga, s/n; L'Hospitalet de Llobregat, 08907, Barcelona, Spain
| | - Miguel Hueso
- Department of Nephrology, Hospital Universitari Bellvitge and Bellvitge Research Institute (IDIBELL), C/Feixa Llarga, s/n; L'Hospitalet de Llobregat, 08907, Barcelona, Spain.
| |
Collapse
|
5
|
Huson KM, Morphew RM, Allen NR, Hegarty MJ, Worgan HJ, Girdwood SE, Jones EL, Phillips HC, Vickers M, Swain M, Smith D, Kingston-Smith AH, Brophy PM. Polyomic tools for an emerging livestock parasite, the rumen fluke Calicophoron daubneyi; identifying shifts in rumen functionality. Parasit Vectors 2018; 11:617. [PMID: 30509301 PMCID: PMC6278170 DOI: 10.1186/s13071-018-3225-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 11/20/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Diseases caused by parasitic flatworms of rumen tissues (paramphistomosis) are a significant threat to global food security as a cause of morbidity and mortality in ruminant livestock in subtropical and tropical climates. Calicophoron daubneyi is currently the only paramphistome species commonly infecting ruminant livestock in temperate European climates. However, recorded incidences of C. daubneyi infection in European livestock have been increasing over the last decade. Whilst clinical paramphistomosis caused by adult worms has not been confirmed in Europe, fatalities have been attributed to severe haemorrhagic enteritis of the small intestine resulting from the migration of immature paramphistomes. Large numbers of mature adults can reside in the rumen, yet to date, the impact on rumen fermentation, and consequently on productivity and economic management of infected livestock, have not been resolved. Limited publicly available nucleotide and protein sequences for C. daubneyi underpin this lack of biological and economic understanding. Here we present for the first time a de novo assembled transcriptome, with functional annotations, for adult C. daubneyi, which provides a reference database for protein and nucleotide sequence identification to facilitate fundamental biology, anthelmintic, vaccine and diagnostics discoveries. RESULTS This dataset identifies a number of genes potentially unique to C. daubneyi and, by comparison to an existing transcriptome for the related Paramphistomum cervi, identifies novel genes which may be unique to the paramphistome group of platyhelminthes. Additionally, we present the first coverage of the excretory/secretory and soluble somatic proteome profiles for adult C. daubneyi and identify the release of extracellular vesicles from adult C. daubneyi parasites during in vitro, ex-host culture. Finally, we have performed the first analysis of rumen fluke impacting upon rumen fermentation parameters using an in vitro gas production study resulting in a significant increase in propionate production. CONCLUSIONS The resulting data provide a discovery platform (transcriptome, proteomes, EV isolation pipeline and in vitro fermentation system) to further study C. daubneyi-host interaction. In addition, the acetate: propionate ratio has been demonstrated to decrease with rumen fluke infection suggesting that acidotic conditions in the rumen may occur.
Collapse
Affiliation(s)
- Kathryn M Huson
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Ceredigion, Aberystwyth, SY23 3DA, UK
| | - Russell M Morphew
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Ceredigion, Aberystwyth, SY23 3DA, UK.
| | - Nathan R Allen
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Ceredigion, Aberystwyth, SY23 3DA, UK
| | - Matthew J Hegarty
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Ceredigion, Aberystwyth, SY23 3DA, UK
| | - Hillary J Worgan
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Ceredigion, Aberystwyth, SY23 3DA, UK
| | - Susan E Girdwood
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Ceredigion, Aberystwyth, SY23 3DA, UK
| | - Eleanor L Jones
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Ceredigion, Aberystwyth, SY23 3DA, UK
| | - Helen C Phillips
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Ceredigion, Aberystwyth, SY23 3DA, UK
| | - Martin Vickers
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Ceredigion, Aberystwyth, SY23 3DA, UK
| | - Martin Swain
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Ceredigion, Aberystwyth, SY23 3DA, UK
| | - Daniel Smith
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Ceredigion, Aberystwyth, SY23 3DA, UK
| | - Alison H Kingston-Smith
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Ceredigion, Aberystwyth, SY23 3DA, UK
| | - Peter M Brophy
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Ceredigion, Aberystwyth, SY23 3DA, UK
| |
Collapse
|
6
|
Cloning and Identification of Recombinant Argonaute-Bound Small RNAs Using Next-Generation Sequencing. Methods Mol Biol 2018; 1680:1-28. [PMID: 29030838 DOI: 10.1007/978-1-4939-7339-2_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Argonaute proteins (AGOs) are loaded with small RNAs as guides to recognize target mRNAs. Since the target specificity heavily depends on the base complementarity between two strands, it is important to identify small guide and long target RNAs bound to AGOs. For this purpose, next-generation sequencing (NGS) technologies have extended our appreciation truly to the nucleotide level. However, the identification of RNAs via NGS from scarce RNA samples remains a challenge. Further, most commercial and published methods are compatible with either small RNAs or long RNAs, but are not equally applicable to both. Therefore, a single method that yields quantitative, bias-free NGS libraries to identify small and long RNAs from low levels of input will be of wide interest. Here, we introduce such a procedure that is based on several modifications of two published protocols and allows robust, sensitive, and reproducible cloning and sequencing of small amounts of RNAs of variable lengths. The method was applied to the identification of small RNAs bound to a purified eukaryotic AGO. Following ligation of a DNA adapter to RNA 3'-end, the key feature of this method is to use the adapter for priming reverse transcription (RT) wherein biotinylated deoxyribonucleotides specifically incorporated into the extended complementary DNA. Such RT products are enriched on streptavidin beads, circularized while immobilized on beads and directly used for PCR amplification. We provide a stepwise guide to generate RNA-Seq libraries, their purification, quantification, validation, and preparation for next-generation sequencing. We also provide basic steps in post-NGS data analyses using Galaxy, an open-source, web-based platform.
Collapse
|
7
|
Fromm B, Ovchinnikov V, Høye E, Bernal D, Hackenberg M, Marcilla A. On the presence and immunoregulatory functions of extracellular microRNAs in the trematode Fasciola hepatica. Parasite Immunol 2017; 39. [PMID: 27809346 DOI: 10.1111/pim.12399] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 10/28/2016] [Indexed: 12/16/2022]
Abstract
Liver flukes represent a paraphyletic group of endoparasitic flatworms that significantly affect man either indirectly due to economic damage on livestock or directly as pathogens. A range of studies have focussed on how these macroscopic organisms can evade the immune system and live inside a hostile environment such as the mammalian liver and bile ducts. Recently, microRNAs, a class of short noncoding gene regulators, have been proposed as likely candidates to play roles in this scenario. MicroRNAs (miRNAs) are key players in development and pathogenicity and are highly conserved between metazoans: identical miRNAs can be found in flatworms and mammalians. Interestingly, miRNAs are enriched in extracellular vesicles (EVs) which are secreted by most cells. EVs constitute an important mode of parasite/host interaction, and recent data illustrate that miRNAs play a vital part. We have demonstrated the presence of miRNAs in the EVs of the trematode species Dicrocoelium dendriticum and Fasciola hepatica (Fhe) and identified potential immune-regulatory miRNAs with targets in the host. After our initial identification of miRNAs expressed by F. hepatica, an assembled genome and additional miRNA data became available. This has enabled us to update the known complement of miRNAs in EVs and speculate on potential immune-regulatory functions that we review here.
Collapse
Affiliation(s)
- B Fromm
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Nydalen, Oslo, Norway
| | - V Ovchinnikov
- Department of Human and Animal Genetics, The Federal Research Center, Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - E Høye
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Nydalen, Oslo, Norway
| | - D Bernal
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Burjassot, Valencia, Spain
| | - M Hackenberg
- Facultad de Ciencias, Departamento de Genética, Universidad de Granada, Granada, Spain.,Laboratorio de Bioinformática, Instituto de Biotecnología, Centro de Investigación Biomédica, Granada, Spain
| | - A Marcilla
- Área de Parasitología, Departamento de Farmacia y Tecnologia Farmacéutica y Parasitología, Universitat de València, Burjassot, Valencia, Spain.,Joint Research Unit on Endocrinology, Nutrition and Clinical Dietetics, Health Research Institute-La Fe, Universitat de Valencia, Valencia, Spain
| |
Collapse
|
8
|
Jiang S, Li X, Wang X, Ban Q, Hui W, Jia B. MicroRNA profiling of the intestinal tissue of Kazakh sheep after experimental Echinococcus granulosus infection, using a high-throughput approach. ACTA ACUST UNITED AC 2016; 23:23. [PMID: 27235195 PMCID: PMC4884269 DOI: 10.1051/parasite/2016023] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 04/30/2016] [Indexed: 12/15/2022]
Abstract
Cystic echinococcosis (CE), caused by infection with the larval stage of the cestode Echinococcus granulosus, is a chronic zoonosis, to which sheep are highly susceptible. Previously, we found that Kazakh sheep with different MHC haplotypes differed in CE infection. Sheep with haplotype MHCMvaIbc-SacIIab-Hin1Iab were resistant to CE infection, while their counterparts without this haplotype were not. MicroRNAs (miRNAs), a class of small non-coding RNAs, are key regulators of gene expression at the post-transcriptional level and play essential roles in fundamental biological processes such as development and metabolism. To identify microRNA controlling resistance to CE in the early stage of infection, microRNA profiling was conducted in the intestinal tissue of sheep with resistant and non-resistant MHC haplotypes after peroral infection with E. granulosus eggs. A total of 351 known and 186 novel miRNAs were detected in the resistant group, against 353 known and 129 novel miRNAs in the non-resistant group. Among these miRNAs, 83 known miRNAs were significantly differentially expressed, including 75 up-regulated and 8 down-regulated miRNAs. Among these known microRNAs, miR-21-3p, miR-542-5p, miR-671, miR-134-5p, miR-26b, and miR-27a showed a significantly higher expression in CE-resistant sheep compared to the CE-non-resistant library, with the FC > 3. Functional analysis showed that they were NF-kB pathway-responsive miRNAs, which are involved in the inflammation process. The results suggest that these microRNAs may play important roles in the response of intestinal tissue to E. granulosus.
Collapse
Affiliation(s)
- Song Jiang
- College of Animal Science and Technology, Shihezi University, Road Beisi, Shihezi 832003, Xinjiang, PR China
| | - Xin Li
- College of Animal Science and Technology, Shihezi University, Road Beisi, Shihezi 832003, Xinjiang, PR China
| | - Xuhai Wang
- College of Animal Science and Technology, Shihezi University, Road Beisi, Shihezi 832003, Xinjiang, PR China
| | - Qian Ban
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Road Jiulong, Hefei 230000, Anhui, PR China
| | - Wenqiao Hui
- College of Animal Science and Technology, Shihezi University, Road Beisi, Shihezi 832003, Xinjiang, PR China - Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agriculture Sciences, Road Nongkenan, Hefei 230031, Anhui, PR China
| | - Bin Jia
- College of Animal Science and Technology, Shihezi University, Road Beisi, Shihezi 832003, Xinjiang, PR China
| |
Collapse
|
9
|
Cai P, Liu S, Piao X, Hou N, Gobert GN, McManus DP, Chen Q. Comprehensive Transcriptome Analysis of Sex-Biased Expressed Genes Reveals Discrete Biological and Physiological Features of Male and Female Schistosoma japonicum. PLoS Negl Trop Dis 2016; 10:e0004684. [PMID: 27128440 PMCID: PMC4851400 DOI: 10.1371/journal.pntd.0004684] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 04/12/2016] [Indexed: 12/23/2022] Open
Abstract
Schistosomiasis is a chronic and debilitating disease caused by blood flukes (digenetic trematodes) of the genus Schistosoma. Schistosomes are sexually dimorphic and exhibit dramatic morphological changes during a complex lifecycle which requires subtle gene regulatory mechanisms to fulfil these complex biological processes. In the current study, a 41,982 features custom DNA microarray, which represents the most comprehensive probe coverage for any schistosome transcriptome study, was designed based on public domain and local databases to explore differential gene expression in S. japonicum. We found that approximately 1/10 of the total annotated genes in the S. japonicum genome are differentially expressed between adult males and females. In general, genes associated with the cytoskeleton, and motor and neuronal activities were readily expressed in male adult worms, whereas genes involved in amino acid metabolism, nucleotide biosynthesis, gluconeogenesis, glycosylation, cell cycle processes, DNA synthesis and genome fidelity and stability were enriched in females. Further, miRNAs target sites within these gene sets were predicted, which provides a scenario whereby the miRNAs potentially regulate these sex-biased expressed genes. The study significantly expands the expressional and regulatory characteristics of gender-biased expressed genes in schistosomes with high accuracy. The data provide a better appreciation of the biological and physiological features of male and female schistosome parasites, which may lead to novel vaccine targets and the development of new therapeutic interventions.
Collapse
Affiliation(s)
- Pengfei Cai
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Shuai Liu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
| | - Xianyu Piao
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
| | - Nan Hou
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
| | - Geoffrey N. Gobert
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Donald P. McManus
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Qijun Chen
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
- Key Laboratory of Zoonosis, Shenyang Agriculture University, Shenyang, P.R. China
| |
Collapse
|