Chronic kidney disease of unknown etiology (CKDu), having epidemic characteristics, is being diagnosed increasingly in certain tropical regions of the world, mainly Latin America and Sri Lanka. They have been observed primarily in farming communities and current hypotheses point toward many environmental and occupational triggers. CKDu does not have common etiologies of chronic kidney disease (CKD) such as hypertension, diabetes, or autoimmune disease. We aimed to understand the molecular processes underlying CKDu in Sri Lanka using transcriptome analysis.
RNA extracted from whole blood was reverse transcribed and used for microarray analysis using the Human HT-12 v.4 array (Illumina). Pathway analysis was carried out using ingenuity pathway analysis (IPA—Qiagen). Microarray results were validated using real-time PCR of five selected genes.
Pathways related to innate immune response, including interferon signaling, inflammasome signaling and TREM1 signaling had the most significant positive activation z scores, where as EIF2 signaling and mTOR signaling had the most significant negative activation z scores. Pathways previously linked to fluoride toxicity; G-protein activation, Cdc42 signaling, Rac signaling and RhoA signaling were activated in CKDu patients. The most significantly activated biological functions were cell death, cell movement and antimicrobial response. Significant toxicological functions were mitochondrial dysfunction, oxidative stress and apoptosis.
Based on the molecular pathway analysis in CKDu patients and review of literature, viral infections and fluoride toxicity appear to be contributing to the molecular mechanisms underlying CKDu.
This is a preview of subscription content, log in to check access.
Buy single article
Instant access to the full article PDF.
Tax calculation will be finalised during checkout.
Subscribe to journal
Immediate online access to all issues from 2019. Subscription will auto renew annually.
Tax calculation will be finalised during checkout.
Hamer RA, El Nahas AM (2006) The burden of chronic kidney disease: is rising rapidly worldwide. BMJ 332(7541):563–564
Jha V, Prasad N (2016) CKD and infectious diseases in Asia Pacific: challenges and opportunities. Am J Kidney Dis 68(1):148–160
Jha V, Garcia-Garcia G, Iseki K, Li Z, Naicker S, Plattner B et al (2013) Chronic kidney disease: global dimension and perspectives. Lancet 382(9888):260–272
Brooks DR, Ramirez-Rubio O, Amador JJ (2012) CKD in Central America: a hot issue. Am J Kidney Dis 59(4):481–484
El Minshawy O (2011) End-stage renal disease in the El-Minia Governorate, upper Egypt: an epidemiological study. Saudi J Kidney Dis Transpl 22(5):1048–1054
Reddy DV, Gunasekar A (2013) Chronic kidney disease in two coastal districts of Andhra Pradesh, India: role of drinking water. Environ Geochem Health 35(4):439–454
Dissanayake CB, Chandrajith R (2007) Medical geology in tropical countries with special reference to Sri Lanka. Environ Geochem Health 29(2):155–162
Liyanage M, Magana-arachchi D, Priyadarshika C, Abeysekara T, Guneratne L (2016) Cyanobacteria and cyanotoxins in well waters of the girandurukotte, ckdu endemic area in Sri Lanka; do they drink safe water? J Ecotechnol Res 18(1):17–21
Dharma-Wardana MW, Amarasiri SL, Dharmawardene N, Panabokke CR (2015) Chronic kidney disease of unknown aetiology and ground-water ionicity: study based on Sri Lanka. Environ Geochem Health 37(2):221–231
Jayatilake N, Mendis S, Maheepala P, Mehta FR, Team CKNRP. (2013) Chronic kidney disease of uncertain aetiology: prevalence and causative factors in a developing country. BMC Nephrol 14:180
Wasana HM, Aluthpatabendi D, Kularatne WM, Wijekoon P, Weerasooriya R, Bandara J (2016) Drinking water quality and chronic kidney disease of unknown etiology (CKDu): synergic effects of fluoride, cadmium and hardness of water. Environ Geochem Health 38(1):157–168
Weaver VM, Fadrowski JJ, Jaar BG (2015) Global dimensions of chronic kidney disease of unknown etiology (CKDu): a modern era environmental and/or occupational nephropathy? BMC Nephrol 16:145
Nanayakkara S, Senevirathna ST, Parahitiyawa NB, Abeysekera T, Chandrajith R, Ratnatunga N et al (2015) Whole-exome sequencing reveals genetic variants associated with chronic kidney disease characterized by tubulointerstitial damages in North Central Region, Sri Lanka. Environ Health Prev Med 20(5):354–359
Nanayakkara S, Senevirathna ST, Abeysekera T, Chandrajith R, Ratnatunga N, Gunarathne ED et al (2014) An integrative study of the genetic, social and environmental determinants of chronic kidney disease characterized by tubulointerstitial damages in the North Central Region of Sri Lanka. J Occup Health 56(1):28–38
Sayanthooran S, Magana-Arachchi DN, Gunerathne L, Abeysekera TDJ, Sooriyapathirana SS (2016) Upregulation of oxidative stress related genes in a chronic kidney disease attributed to specific geographical locations of Sri Lanka. Biomed Res Int. https://doi.org/10.1155/2016/7546265
Gamage CD, Yoshimatsu K, Sarathkumara YD, Kulendiran T, Nanayakkara N, Arikawa J (2017) Serological evidence of hantavirus infection in Girandurukotte, an area endemic for chronic kidney disease of unknown aetiology (CKDu) in Sri Lanka. Int J Infect Dis 57:77–78
Herath KRPK, Ileperuma OA, Dharmagunawardhane HA, Haller KJ (eds) (2005) Environmental health risk for the chronic renal failure in Sri Lanka. 31st Congress on Science and Technology of Thailand. Suranaree University of Technology, Nakhon Ratchasima
Bandara JM, Senevirathna DM, Dasanayake DM, Herath V, Bandara JM, Abeysekara T et al (2008) Chronic renal failure among farm families in cascade irrigation systems in Sri Lanka associated with elevated dietary cadmium levels in rice and freshwater fish (Tilapia). Environ Geochem Health 30(5):465–478
Wasana HM, Perera GD, Gunawardena PS, Fernando PS, Bandara J (2017) WHO water quality standards Vs Synergic effect(s) of fluoride, heavy metals and hardness in drinking water on kidney tissues. Sci Rep 7:42516
Athuraliya NT, Abeysekera TD, Amerasinghe PH, Kumarasiri R, Bandara P, Karunaratne U et al (2011) Uncertain etiologies of proteinuric-chronic kidney disease in rural Sri Lanka. Kidney Int 80(11):1212–1221
Gifford F, Kimmitt R, Herath C, Webb DJ, Melville V, Siribaddana S et al (2016) Arterial stiffness & Sri Lankan chronic kidney disease of unknown origin. Sci Rep 6:32599
Wittchen F, Suckau L, Witt H, Skurk C, Lassner D, Fechner H et al (2007) Genomic expression profiling of human inflammatory cardiomyopathy (DCMi) suggests novel therapeutic targets. J Mol Med 85(3):257–271
Sorlie T, Tibshirani R, Parker J, Hastie T, Marron JS, Nobel A et al (2003) Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci USA 100(14):8418–8423
Dunning MJ, Smith ML, Ritchie ME, Tavare S (2007) beadarray: R classes and methods for Illumina bead-based data. Bioinformatics 23(16):2183–2184
Huber W, Carey VJ, Gentleman R, Anders S (2015) Orchestrating high-throughput genomic analysis with bioconductor. Nat Methods 12(2):115–121
Wickham H, Francois R, Henry L (2017) Müller K. dplyr: a grammar of data manipulation. Available at: https://cran.r-project.org/web/packages/dplyr/index.html. Accessed version 0.7.5.2017
Gu Z, Eils R, Schlesner M (2016) Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics 32:2847–2849
Johnson WE, Rabinovic A, Li C (2007) Adjusting batch effects in microarray expression data using Empirical Bayes methods. Biostatistics 8(1):118–127
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-delta delta C(T)) method. Methods 25(4):402–408
Lodish H, Berk A, Zipursky SL, Matsudaira P, Baltimore D, Darnell J (2004) Molecular cell biology, 5th edn. W. H. Freeman & Company, New York
Nanayakkara S, Komiya T, Ratnatunga N, Senevirathna ST, Harada KH, Hitomi T et al (2012) Tubulointerstitial damage as the major pathological lesion in endemic chronic kidney disease among farmers in North Central Province of Sri Lanka. Environ Health Prev Med 17(3):213–221
Fogo AB, Cohen HC, Colvin RB, Jennette JC, Alpers CE (2014) Fundamentals of renal pathology, 2nd edn. Springer, Berlin
Farris AB, Colvin RB (2012) Renal interstitial fibrosis: mechanisms and evaluation in: current opinion in nephrology and hypertension. Curr Opin Nephrol Hypertens 21(3):289–300
Stark GR, Kerr IM, Williams BR, Silverman RH, Schreiber RD (1998) How cells respond to interferons. Annu Rev Biochem 67:227–264
Schoggins JW, Rice CM (2011) Interferon-stimulated genes and their antiviral effector functions. Curr Opin Virol 1(6):519–525
Schneider WM, Chevillotte MD, Rice CM (2014) Interferon-stimulated genes: a complex web of host defenses. Annu Rev Immunol 32:513–545
Der SD, Zhou A, Williams BRG, Silverman RH (1998) Identification of genes differentially regulated by interferon α, β, or γ using oligonucleotide arrays. Proc Natl Acad Sci 95(26):15623–15628
Hervas-Stubbs S, Perez-Gracia JL, Rouzaut A, Sanmamed MF, Le Bon A, Melero I (2011) Direct effects of type I interferons on cells of the immune system. Clin Cancer Res 17(9):2619–2627
Barsoum RS (2006) Chronic kidney disease in the developing world. N Engl J Med 354(10):997–999
Shrestha N, Bahnan W, Wiley DJ, Barber G, Fields KA, Schesser K (2012) Eukaryotic initiation factor 2 (eIF2) signaling regulates proinflammatory cytokine expression and bacterial invasion. J Biol Chem 287(34):28738–28744
Toribio R, Ventoso I (2010) Inhibition of host translation by virus infection in vivo. Proc Natl Acad Sci 107(21):9837–9842
Zhang J, Zhu Y, Shi Y, Han Y, Liang C, Feng Z et al (2017) Fluoride-induced autophagy via the regulation of phosphorylation of mammalian targets of rapamycin in mice leydig cells. J Agric Food Chem 65(40):8966–8976
Carpenter RL, Jiang BH (2013) Roles of EGFR, PI3K, AKT, and mTOR in heavy metal-induced cancer. Curr Cancer Drug Targets 13(3):252–266
Liang Q, Luo Z, Zeng J, Chen W, Foo S-S, Lee S-A et al (2016) Zika virus NS4A and NS4B proteins deregulate Akt-mTOR signaling in human fetal neural stem cells to inhibit neurogenesis and induce autophagy. Cell Stem Cell 19(5):663–671
Buchkovich NJ, Yu Y, Zampieri CA, Alwine JC (2008) The TORrid affairs of viruses: effects of mammalian DNA viruses on the PI3K-Akt-mTOR signalling pathway. Nat Rev Microbiol 6(4):266–275
Fillerova R, Gallo J, Radvansky M, Kraiczova V, Kudelka M, Kriegova E (2017) Excellent diagnostic characteristics for ultrafast gene profiling of DEFA1-IL1B-LTF in detection of prosthetic joint infections. J Clin Microbiol 55(9):2686–2697
Kamińska T, Tustanowska-Stachura A, Słotwińska M, Szuster-Ciesielska A, Stasiak M, Kandefer-Szerszeń M (2007) Cell death and cytokine production induced by cadmium in leukocytes of cord blood and peripheral blood of adults. J Pre Clin Clin Res 1(1):30–34
Loftenius A, Andersson B, Butler J, Ekstrand J (1999) Fluoride augments the mitogenic and antigenic response of human blood lymphocytes in vitro. Caries Res 33(2):148–155
Tatin F, Grise F, Reuzeau E, Genot E, Moreau V (2010) Sodium fluoride induces podosome formation in endothelial cells. Biol Cell 102(9):489–498
Yokel AR, Golub MS (eds) (1997) Research issues in aluminium toxicity: proceedings of the workshop on research issues in aluminium toxicity. International symposium on aluminium toxicity, 1995. CRC Press, Vancouver
Agalakova NI, Gusev GP (2012) Molecular mechanisms of cytotoxicity and apoptosis induced by inorganic fluoride. ISRN Cell Biol 2012:1–16
Alarcon-Herrera MT, Bundschuh J, Nath B, Nicolli HB, Gutierrez M, Reyes-Gomez VM et al (2013) Co-occurrence of arsenic and fluoride in groundwater of semi-arid regions in Latin America: genesis, mobility and remediation. J Hazard Mater 262:960–969
González-Horta C, Ballinas-Casarrubias L, Sánchez-Ramírez B, Ishida MC, Barrera-Hernández A, Gutiérrez-Torres D et al (2015) A concurrent exposure to arsenic and fluoride from drinking water in Chihuahua, Mexico. Int J Environ Res Public Health 12(5):4587–4601
Shanthi M, Reddy BV, Venkataramana V, Gowrisankar S, Reddy BVT, Chennupati S (2014) Relationship between drinking water fluoride levels, dental fluorosis, dental caries and associated risk factors in 9–12 years old school children of Nelakondapally Mandal of Khammam District, Andhra Pradesh, India: a cross-sectional survey. J Int Oral Health 6(3):106–110
Rani A, Kumar A, Lal A, Pant M (2014) Cellular mechanisms of cadmium-induced toxicity: a review. Int J Environ Health Res 24(4):378–399
Niess H, Camaj P, Mair R, Renner A, Zhao Y, Jackel C et al (2015) Overexpression of IFN-induced protein with tetratricopeptide repeats 3 (IFIT3) in pancreatic cancer: cellular "pseudoinflammation" contributing to an aggressive phenotype. Oncotarget 6(5):3306–3318
Zhao B, Wang H, Zong G, Li P (2013) The role of IFITM3 in the growth and migration of human glioma cells. BMC Neurol 13(1):210
Martinez JM, Afshari CA, Bushel PR, Masuda A, Takahashi T, Walker NJ (2002) Differential toxicogenomic responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin in malignant and nonmalignant human airway epithelial cells. Toxicol Sci 69(2):409–423
Tang K-F, Ren H, Cao J, Zeng G-L, Xie J, Chen M et al (2008) Decreased Dicer expression elicits DNA damage and up-regulation of MICA and MICB. J Cell Biol 182(2):233–239
Hedl M, Abraham C (2011) Distinct roles for Nod2 protein and autocrine interleukin-1beta in muramyl dipeptide-induced mitogen-activated protein kinase activation and cytokine secretion in human macrophages. J Biol Chem 286(30):26440–26449
Koop K, Eikmans M, Baelde HJ, Kawachi H, De Heer E, Paul LC et al (2003) Expression of podocyteassociated molecules in acquired human kidney diseases. J Am Soc Nephrol 14(8):2063–2071
The authors thank the staff of the Renal Research Centre, District Hospital, Girandurukotte for their support in sample collection.
The real-time PCR machine used in this study was funded by the National Research Council, Sri Lanka (NRC Grant 11-059).
Conflict of interest
The authors declare that they have no conflict of interest.
Electronic supplementary material
About this article
Cite this article
Sayanthooran, S., Gunerathne, L., Abeysekera, T.D.J. et al. Transcriptome analysis supports viral infection and fluoride toxicity as contributors to chronic kidney disease of unknown etiology (CKDu) in Sri Lanka. Int Urol Nephrol 50, 1667–1677 (2018). https://doi.org/10.1007/s11255-018-1892-z
- EIF2 signaling
- Innate immunity
- Interferon signaling
- mTOR signaling