Transcriptomics and Proteomics Analyses Reveal JAK Signaling and Inflammatory Phenotypes during Cellular Senescence in Blind Mole Rats: The Reflections of Superior Biology.
Inci Kavum, Nurcan; Akyildiz, Erdogan Oguzhan; Bulbul, Abdullah Alperet al.
JAK–STAT; MMP; NF-κB; SASP; aging; anticancer; cancer; cellular senescence; inflammation; Biochemistry, Genetics and Molecular Biology (all); Immunology and Microbiology (all); Agricultural and Biological Sciences (all); General Agricultural and Biological Sciences; General Immunology and Microbiology; General Biochemistry, Genetics and Molecular Biology
Abstract :
[en] The blind mole rat (BMR), a long-living subterranean rodent, is an exceptional model for both aging and cancer research since they do not display age-related phenotypes or tumor formation. The Janus kinase-signal transducer and activator of transcription (JAK-STAT) signaling is a cytokine-stimulated pathway that has a crucial role in immune regulation, proliferation, and cytokine production. Therefore, the pathway has recently attracted interest in cellular senescence studies. Here, by using publicly available data, we report that JAK-STAT signaling was suppressed in the BMR in comparison to the mouse. Interestingly, our experimental results showed upregulated Jak1/2 expressions in BMR fibroblasts during the replicative senescence process. The transcriptomic analysis using publicly available data also demonstrated that various cytokines related to JAK-STAT signaling were upregulated in the late passage cells, while some other cytokines such as MMPs and SERPINs were downregulated, representing a possible balance of senescence-associated secretory phenotypes (SASPs) in the BMR. Finally, our proteomics data also confirmed cytokine-mediated signaling activation in senescent BMR fibroblasts. Together, our findings suggest the critical role of JAK-STAT and cytokine-mediated signaling pathways during cellular senescence, pointing to the possible contribution of divergent inflammatory factors to the superior resistance of aging and cancer in BMRs.
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Inci Kavum, Nurcan ✱; Université de Liège - ULiège > Département des sciences biomédicales et précliniques > Pharmacologie
Akyildiz, Erdogan Oguzhan ✱; Department of Molecular and Translational Biomedicine, Institute of Natural and Applied Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul 34752, Turkey
Bulbul, Abdullah Alper ; Department of Biostatistics and Bioinformatics, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul 34752, Turkey
Turanli, Eda Tahir; Department of Molecular and Translational Biomedicine, Institute of Natural and Applied Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul 34752, Turkey ; Department of Molecular Biology and Genetics, Faculty of Engineering and Natural Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul 34752, Turkey
Akgun, Emel; Department of Medical Biochemistry, Faculty of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul 34752, Turkey
Baykal, Ahmet Tarik ; Department of Medical Biochemistry, Faculty of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul 34752, Turkey
Colak, Faruk; Department of Biology, Faculty of Arts and Science, Zonguldak Bulent Ecevit University, Zonguldak 67100, Turkey
Bozaykut, Perinur ; Department of Molecular and Translational Biomedicine, Institute of Natural and Applied Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul 34752, Turkey ; Department of Molecular Biology and Genetics, Faculty of Engineering and Natural Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul 34752, Turkey
✱ These authors have contributed equally to this work.
Language :
English
Title :
Transcriptomics and Proteomics Analyses Reveal JAK Signaling and Inflammatory Phenotypes during Cellular Senescence in Blind Mole Rats: The Reflections of Superior Biology.
Scientific and Technological Research Council of Turkey ACU - Acıbadem University
Funding text :
The experimental parts of this research were funded by The Scientific and Technological Research Council of Turkey (TUBITAK), Grant Nos. 121N467 and 121Z564, and the Acibadem University Scientific Research Project Commission, Grant No. 2020/02/01, which were awarded to Perinur Bozaykut. BMR capture was supported by a grant from the Zonguldak Bülent Ecevit University Research Project Commission, Grant No. 2019-84906727-01, and was awarded to Faruk Colak.
Bozaykut P. Sozen E. Kaga E. Ece A. Ozaltin E. Bergquist J. Ozer N.K. Yilmaz B.K. HSP70 Inhibition Leads to the Activation of Proteasomal System under Mild Hyperthermia Conditions in Young and Senescent Fibroblasts Oxidative Med. Cell. Longev. 2020 2020 9369524 10.1155/2020/9369524 32190179
Gorbunova V. Hine C. Tian X. Ablaeva J. Gudkov A.V. Nevo E. Seluanov A. Cancer resistance in the blind mole rat is mediated by concerted necrotic cell death mechanism Proc. Natl. Acad. Sci. USA 2012 109 19392 19396 10.1073/pnas.1217211109 23129611
Manov I. Hirsh M. Iancu T.C. Malik A. Sotnichenko N. Band M. Avivi A. Shams I. Pronounced cancer resistance in a subterranean rodent, the blind mole-rat, Spalax: In vivo and in vitroevidence BMC Biol. 2013 11 91 10.1186/1741-7007-11-91
Zhao Y. Oreskovic E. Zhang Q. Lu Q. Gilman A. Lin Y.S. He J. Zheng Z. Lu J.Y. Lee J. et al. Transposon-triggered innate immune response confers cancer resistance to the blind mole rat Nat. Immunol. 2021 22 1219 1230 10.1038/s41590-021-01027-8 34556881
Tchkonia T. Zhu Y. Van Deursen J. Campisi J. Kirkland J.L. Cellular senescence and the senescent secretory phenotype: Therapeutic opportunities J. Clin. Investig. 2013 123 966 972 10.1172/JCI64098
Michaud M. Balardy L. Moulis G. Gaudin C. Peyrot C. Vellas B. Cesari M. Nourhashemi F. Proinflammatory Cytokines, Aging, and Age-Related Diseases J. Am. Med. Dir. Assoc. 2013 14 877 882 10.1016/j.jamda.2013.05.009
Duraisingham S.S. Rouphael N. Cavanagh M.M. Nakaya H.I. Goronzy J.J. Pulendran B. Systems Biology of Vaccination in the Elderly Systems Biology. Current Topics in Microbiology and Immunology Katze M. Springer Berlin/Heidelberg, Germany 2012 363 117 142 10.1007/82_2012_250
Chakraborti S. Nirmal D. Dikshit M. Role of INOS in Insulin Resistance and Endothelial Dysfunction Oxidative Stress in Heart Diseases Chakraborti S. Dhalla N. Ganguly N. Dikshit M. Springer Singapore 2019 10.1007/978-981-13-8273-4_21
Campisi J. d’Adda di Fagagna F. Cellular senescence: When bad things happen to good cells Nat. Rev. Mol. Cell Biol. 2007 8 729 740 10.1038/nrm2233 17667954
Meyer S.C. Levine R.L. Molecular Pathways: Molecular Basis for Sensitivity and Resistance to JAK Kinase Inhibitors Clin. Cancer Res. 2014 20 2051 2059 10.1158/1078-0432.CCR-13-0279
Yu H. Pardoll D. Jove R. STATs in cancer inflammation and immunity: A leading role for STAT3 Nat. Cancer 2009 9 798 809 10.1038/nrc2734
Kiu H. Nicholson S.E. Biology and significance of the JAK/STAT signalling pathways Growth Factors 2012 30 88 106 10.3109/08977194.2012.660936 22339650
Bose S. Banerjee S. Mondal A. Chakraborty U. Pumarol J. Croley C. Bishayee A. Targeting the JAK/STAT Signaling Pathway Using Phytocompounds for Cancer Prevention and Therapy Cells 2020 9 1451 10.3390/cells9061451
Di Micco R. Krizhanovsky V. Baker D. di Fagagna F.D. Cellular senescence in ageing: From mechanisms to therapeutic opportunities Nat. Rev. Mol. Cell Biol. 2021 22 75 95 10.1038/s41580-020-00314-w 33328614
Odeh A. Dronina M. Domankevich V. Shams I. Manov I. Downregulation of the inflammatory network in senescent fibroblasts and aging tissues of the long-lived and cancer-resistant subterranean wild rodent Spalax. Aging Cell 2020 19 e13045 10.1111/acel.13045
Lee S.-G. Mikhalchenko A.E. Yim S.H. Gladyshev V.N. A naked mole rat iPSC line expressing drug-inducible mouse pluripotency factors developed from embryonic fibroblasts Stem Cell Res. 2018 31 197 200 10.1016/j.scr.2018.06.010
McKinney W. Data structures for statistical computing in python Proceedings of the 9th Python in Science Conference Austin, TX, USA 28 June–3 July 2010 Volume 445 51 56
Emmert-Streib F. Glazko G.V. Pathway Analysis of Expression Data: Deciphering Functional Building Blocks of Complex Diseases PLoS Comput. Biol. 2011 7 e1002053 10.1371/journal.pcbi.1002053 21637797
Maity P. Singh K. Krug L. Koroma A. Hainzl A. Bloch W. Kochanek S. Wlaschek M. Schorpp-Kistner M. Angel P. et al. Persistent JunB activation in fibroblasts disrupts stem cell niche interactions enforcing skin aging Cell Rep. 2021 36 10.1016/j.celrep.2021.109634
Altwasser R. Paz A. Korol A. Manov I. Avivi A. Shams I. The transcriptome landscape of the carcinogenic treatment response in the blind mole rat: Insights into cancer resistance mechanisms BMC Genom. 2019 20 17 10.1186/s12864-018-5417-z
Marthandan S. Priebe S. Baumgart M. Groth M. Cellerino A. Guthke R. Hemmerich P. Diekmann S. Similarities in Gene Expression Profiles during In Vitro Aging of Primary Human Embryonic Lung and Foreskin Fibroblasts BioMed Res. Int. 2015 2015 731938 10.1155/2015/731938
Leinonen R. Sugawara H. Shumway M. On behalf of the International Nucleotide Sequence Database Collaboration The Sequence Read Archive Nucleic Acids Res. 2011 39 D19 D21 10.1093/nar/gkq1019 21062823
Patro R. Duggal G. Love M. Irizarry R. Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression Nat Methods 2017 14 417 419 10.1038/nmeth.4197
Frankish A. Diekhans M. Jungreis I. Lagarde J. E Loveland J. Mudge J.M. Sisu C. Wright J.C. Armstrong J. Barnes I. et al. GENCODE 2021 Nucleic Acids Res. 2021 49 D916 D923 10.1093/nar/gkaa1087
Soneson C. Love M.I. Robinson M.D. Differential Analyses for RNA-Seq: Transcript-Level Estimates Improve Gene-Level Inferences F1000Research 2016 4 1521 10.12688/f1000research.7563.2
Biragyn A. Aliseychik M. Rogaev E. Potential importance of B cells in aging and aging-associated neurodegenerative diseases Semin. Immunopathol. 2017 39 283 294 10.1007/s00281-016-0615-8
Subramanian A. Tamayo P. Mootha V.K. Mukherjee S. Ebert B.L. Gillette M.A. Paulovich A. Pomeroy S.L. Golub T.R. Lander E.S. et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles Proc. Natl. Acad. Sci. USA 2005 102 15545 15550 10.1073/pnas.0506580102
Wu T. Hu E. Xu S. Chen M. Guo P. Dai Z. Feng T. Zhou L. Tang W. Zhan L. et al. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data Innovation 2021 2 100141 10.1016/j.xinn.2021.100141
Ben-David U. Benvenisty N. The tumorigenicity of human embryonic and induced pluripotent stem cells Nat. Cancer 2011 11 268 277 10.1038/nrc3034 21390058
Seluanov A. Gladyshev V.N. Vijg J. Gorbunova V. Mechanisms of cancer resistance in long-lived mammals Nat. Cancer 2018 18 433 441 10.1038/s41568-018-0004-9 29622806
Furman D. Jojic V. Kidd B. Shen-Orr S. Price J. Jarrell J. Tse T. Huang H. Lund P. Maecker H.T. et al. Apoptosis and other immune biomarkers predict influenza vaccine responsiveness Mol. Syst. Biol. 2013 9 659 10.1038/msb.2013.15
Weiskopf D. Weinberger B. Grubeck-Loebenstein B. The aging of the immune system Transpl. Int. 2009 22 1041 1050 10.1111/j.1432-2277.2009.00927.x 19624493
Xu M. Tchkonia T. Ding H. Ogrodnik M. Lubbers E.R. Pirtskhalava T. White T.A. Johnson K.O. Stout M.B. Mezera V. et al. JAK inhibition alleviates the cellular senescence-associated secretory phenotype and frailty in old age Proc. Natl. Acad. Sci. USA 2015 112 E6301 E6310 10.1073/pnas.1515386112 26578790
He S. Sharpless N.E. Senescence in Health and Disease Cell 2017 169 1000 1011 10.1016/j.cell.2017.05.015 28575665
Rodier F. Campisi J. Four faces of cellular senescence J. Cell Biol. 2011 192 547 556 10.1083/jcb.201009094
Baker D.J. Wijshake T. Tchkonia T. Lebrasseur N.K. Childs B.G. Van De Sluis B. Kirkland J.L. Van Deursen J.M. Clearance of p16Ink4a-positive senescent cells delays ageing-associated disorders Nature 2011 479 232 236 10.1038/nature10600
Freitas-Rodríguez S. Folgueras A.R. López-Otín C. The role of matrix metalloproteinases in aging: Tissue remodeling and beyond Biochim. Biophys. Acta (BBA) Bioenerg. 2017 1864 2015 2025 10.1016/j.bbamcr.2017.05.007
Zeng G. Millis A.J. Differential Regulation of Collagenase and Stromelysin mRNA in Late Passage Cultures of Human Fibroblasts Exp. Cell Res. 1996 222 150 156 10.1006/excr.1996.0019
Basisty N. Kale A. Jeon O.H. Kuehnemann C. Payne T. Rao C. Holtz A. Shah S. Sharma V. Ferrucci L. et al. A proteomic atlas of senescence-associated secretomes for aging biomarker development PLoS Biol. 2020 18 e3000599 10.1371/journal.pbio.3000599 31945054
Sun D. Novotny M. Bulek K. Liu C. Li X. A Hamilton T. Treatment with IL-17 prolongs the half-life of chemokine CXCL1 mRNA via the adaptor TRAF5 and the splicing-regulatory factor SF2 (ASF) Nat. Immunol. 2011 12 853 860 10.1038/ni.2081
Herjan T. Hong L. Bubenik J. Bulek K. Qian W. Liu C. Li X. Chen X. Yang H. Ouyang S. et al. IL-17-receptor-associated adaptor Act1 directly stabilizes mRNAs to mediate IL-17 inflammatory signaling Nat. Immunol. 2018 19 354 365 10.1038/s41590-018-0071-9
Liu Y. Lagowski J.P. Gao S. Raymond J.H. White C.R. Kulesz-Martin M.F. Regulation of the Psoriatic Chemokine CCL20 by E3 Ligases Trim32 and Piasy in Keratinocytes J. Investig. Dermatol. 2010 130 1384 1390 10.1038/jid.2009.416
Albor A. El-Hizawi S. Horn E.J. Laederich M. Frosk P. Wrogemann K. Kulesz-Martin M. The Interaction of Piasy with Trim32, an E3-Ubiquitin Ligase Mutated in Limb-girdle Muscular Dystrophy Type 2H, Promotes Piasy Degradation and Regulates UVB-induced Keratinocyte Apoptosis through NFκB J. Biol. Chem. 2006 281 25850 25866 10.1074/jbc.M601655200 16816390
Zhao M. Gao Y. Wang L. Liu S. Han B. Ma L. Ling Y. Mao S. Wang X. Overexpression of Integrin-linked Kinase Promotes Lung Cancer Cell Migration and Invasion via NF-κB-mediated Upregulation of Matrix Metalloproteinase-9 Int. J. Med. Sci. 2013 10 995 1002 10.7150/ijms.5963 23801886
Heo I. Joo C. Kim Y.-K. Ha M. Yoon M.-J. Cho J. Yeom K.-H. Han J. Kim V.N. TUT4 in Concert with Lin28 Suppresses MicroRNA Biogenesis through Pre-MicroRNA Uridylation Cell 2009 138 696 708 10.1016/j.cell.2009.08.002 19703396
Chen X. Li Z. Feng Z. Wang J. Ouyang C. Liu W. Fu B. Cai G. Wu C. Wei R. et al. Integrin-Linked Kinase Induces Both Senescence-Associated Alterations and Extracellular Fibronectin Assembly in Aging Cardiac Fibroblasts J. Gerontol. Ser. A 2006 61 1232 1245 10.1093/gerona/61.12.1232 17234816
Salminen A. Kauppinen A. Kaarniranta K. Emerging role of NF-κB signaling in the induction of senescence-associated secretory phenotype (SASP) Cell. Signal. 2012 24 835 845 10.1016/j.cellsig.2011.12.006