Show simple item record

A trans-omics assessment of gene–gene interaction in early-stage NSCLC

dc.contributor.authorChen, Jiajin
dc.contributor.authorSong, Yunjie
dc.contributor.authorLi, Yi
dc.contributor.authorWei, Yongyue
dc.contributor.authorShen, Sipeng
dc.contributor.authorZhao, Yang
dc.contributor.authorYou, Dongfang
dc.contributor.authorSu, Li
dc.contributor.authorBjaanæs, Maria Moksnes
dc.contributor.authorKarlsson, Anna
dc.contributor.authorPlanck, Maria
dc.contributor.authorStaaf, Johan
dc.contributor.authorHelland, Åslaug
dc.contributor.authorEsteller, Manel
dc.contributor.authorShen, Hongbing
dc.contributor.authorChristiani, David C.
dc.contributor.authorZhang, Ruyang
dc.contributor.authorChen, Feng
dc.date.accessioned2023-02-01T19:00:26Z
dc.date.available2024-02-01 14:00:23en
dc.date.available2023-02-01T19:00:26Z
dc.date.issued2023-01
dc.identifier.citationChen, Jiajin; Song, Yunjie; Li, Yi; Wei, Yongyue; Shen, Sipeng; Zhao, Yang; You, Dongfang; Su, Li; Bjaanæs, Maria Moksnes ; Karlsson, Anna; Planck, Maria; Staaf, Johan; Helland, Åslaug ; Esteller, Manel; Shen, Hongbing; Christiani, David C.; Zhang, Ruyang; Chen, Feng (2023). "A trans- omics assessment of gene- gene interaction in early- stage NSCLC." Molecular Oncology (1): 173-187.
dc.identifier.issn1574-7891
dc.identifier.issn1878-0261
dc.identifier.urihttps://hdl.handle.net/2027.42/175807
dc.publisherWiley Periodicals, Inc.
dc.subject.otherNSCLC
dc.subject.otheroverall survival
dc.subject.otherprognosis
dc.subject.othertrans-omics
dc.subject.otherG × G interactions
dc.titleA trans-omics assessment of gene–gene interaction in early-stage NSCLC
dc.typeArticle
dc.rights.robotsIndexNoFollow
dc.subject.hlbsecondlevelHematology and Oncology
dc.subject.hlbtoplevelHealth Sciences
dc.description.peerreviewedPeer Reviewed
dc.description.bitstreamurlhttp://deepblue.lib.umich.edu/bitstream/2027.42/175807/1/mol213345_am.pdf
dc.description.bitstreamurlhttp://deepblue.lib.umich.edu/bitstream/2027.42/175807/2/mol213345.pdf
dc.identifier.doi10.1002/1878-0261.13345
dc.identifier.sourceMolecular Oncology
dc.identifier.citedreferenceDimitrakopoulos FD, Kottorou AE, Kalofonou M, Kalofonos HP. The fire within: NF-κB involvement in non-small cell lung cancer. Cancer Res. 2020; 80: 4025 – 36.
dc.identifier.citedreferenceJi X, Lin L, Fan J, Li Y, Wei Y, Shen S, et al. Epigenome-wide three-way interaction study identifies a complex pattern between TRIM27, KIAA0226, and smoking associated with overall survival of early-stage NSCLC. Mol Oncol. 2022; 16: 717 – 31.
dc.identifier.citedreferenceJi X, Lin L, Shen S, Dong X, Chen C, Li Y, et al. Epigenetic-smoking interaction reveals histologically heterogeneous effects of TRIM27 DNA methylation on overall survival among early-stage NSCLC patients. Mol Oncol. 2020; 14: 2759 – 74.
dc.identifier.citedreferenceChu M, Zhang R, Zhao Y, Wu C, Guo H, Zhou B, et al. A genome-wide gene-gene interaction analysis identifies an epistatic gene pair for lung cancer susceptibility in Han Chinese. Carcinogenesis. 2014; 35: 572 – 7.
dc.identifier.citedreferenceZhang R, Shen S, Wei Y, Zhu Y, Li Y, Chen J, et al. A large-scale genome-wide gene-gene interaction study of lung cancer susceptibility in Europeans with a trans-ethnic validation in Asians. J Thorac Oncol. 2022; 17: 974 – 90.
dc.identifier.citedreferenceAsomaning K, Miller DP, Liu G, Wain JC, Lynch TJ, Su L, et al. Second hand smoke, age of exposure and lung cancer risk. Lung Cancer. 2008; 61: 13 – 20.
dc.identifier.citedreferenceSandoval J, Mendez-Gonzalez J, Nadal E, Chen G, Carmona FJ, Sayols S, et al. A prognostic DNA methylation signature for stage I non-small-cell lung cancer. J Clin Oncol. 2013; 31: 4140 – 7.
dc.identifier.citedreferenceBjaanæs MM, Fleischer T, Halvorsen AR, Daunay A, Busato F, Solberg S, et al. Genome-wide DNA methylation analyses in lung adenocarcinomas: association with EGFR, KRAS and TP53 mutation status, gene expression and prognosis. Mol Oncol. 2016; 10: 330 – 43.
dc.identifier.citedreferenceKarlsson A, Jönsson M, Lauss M, Brunnström H, Jönsson P, Borg Å, et al. Genome-wide DNA methylation analysis of lung carcinoma reveals one neuroendocrine and four adenocarcinoma epitypes associated with patient outcome. Clin Cancer Res. 2014; 20: 6127 – 40.
dc.identifier.citedreferenceChen YA, Lemire M, Choufani S, Butcher DT, Grafodatskaya D, Zanke BW, et al. Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray. Epigenetics. 2013; 8: 203 – 9.
dc.identifier.citedreferenceMarabita F, Almgren M, Lindholm ME, Ruhrmann S, Fagerström-Billai F, Jagodic M, et al. An evaluation of analysis pipelines for DNA methylation profiling using the Illumina HumanMethylation450 BeadChip platform. Epigenetics. 2013; 8: 333 – 46.
dc.identifier.citedreferenceVanderWeele TJ. Mediation analysis: a practitioner’s guide. Annu Rev Public Health. 2016; 37: 17 – 32.
dc.identifier.citedreferenceWarde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, Chao P, et al. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res. 2010; 38: W214 – 20.
dc.identifier.citedreferenceNewman AM, Liu CL, Green MR, Gentles AJ, Feng W, Xu Y, et al. Robust enumeration of cell subsets from tissue expression profiles. Nat Methods. 2015; 12: 453 – 7.
dc.identifier.citedreferenceMascaux C, Tomasini P, Greillier L, Barlesi F. Personalised medicine for nonsmall cell lung cancer. Eur Respir Rev. 2017; 26: 170066.
dc.identifier.citedreferenceDeb D, Moore AC, Roy UB. 2021 Global lung cancer therapy landscape. J Thorac Oncol. 2022; 17: 931 – 6.
dc.identifier.citedreferenceShiina T, Hosomichi K, Inoko H, Kulski JK. The HLA genomic loci map: expression, interaction, diversity and disease. J Hum Genet. 2009; 54: 15 – 39.
dc.identifier.citedreferenceGu SS, Zhang W, Wang X, Jiang P, Traugh N, Li Z, et al. Therapeutically increasing MHC-I expression potentiates immune checkpoint blockade. Cancer Discov. 2021; 11: 1524 – 41.
dc.identifier.citedreferenceNeefjes J, Jongsma ML, Paul P, Bakke O. Towards a systems understanding of MHC class I and MHC class II antigen presentation. Nat Rev Immunol. 2011; 11: 823 – 36.
dc.identifier.citedreferenceYang S, Tang D, Zhao YC, Liu H, Luo S, Stinchcombe TE, et al. Potentially functional variants of ERAP1, PSMF1 and NCF2 in the MHC-I-related pathway predict non-small cell lung cancer survival. Cancer Immunol Immunother. 2021; 70: 2819 – 33.
dc.identifier.citedreferenceGyrd-Hansen M, Meier P. IAPs: from caspase inhibitors to modulators of NF-kappaB, inflammation and cancer. Nat Rev Cancer. 2010; 10: 561 – 74.
dc.identifier.citedreferenceVerzella D, Pescatore A, Capece D, Vecchiotti D, Ursini MV, Franzoso G, et al. Life, death, and autophagy in cancer: NF-κB turns up everywhere. Cell Death Dis. 2020; 11: 210.
dc.identifier.citedreferenceContini P, Murdaca G, Puppo F, Negrini S. HLA-G expressing immune cells in immune mediated diseases. Front Immunol. 2020; 11: 1613.
dc.identifier.citedreferenceXu HH, Gan J, Xu DP, Li L, Yan WH. Comprehensive transcriptomic analysis reveals the role of the immune checkpoint HLA-G molecule in cancers. Front Immunol. 2021; 12: 614773.
dc.identifier.citedreferenceYie SM, Yang H, Ye SR, Li K, Dong DD, Lin XM. Expression of human leucocyte antigen G (HLA-G) is associated with prognosis in non-small cell lung cancer. Lung Cancer. 2007; 58: 267 – 74.
dc.identifier.citedreferenceShalapour S, Karin M. Pas de Deux: control of anti-tumor immunity by cancer-associated inflammation. Immunity. 2019; 51: 15 – 26.
dc.identifier.citedreferenceBerraondo P, Minute L, Ajona D, Corrales L, Melero I, Pio R. Innate immune mediators in cancer: between defense and resistance. Immunol Rev. 2016; 274: 290 – 306.
dc.identifier.citedreferenceJordan MA, Wilson L. Microtubules as a target for anticancer drugs. Nat Rev Cancer. 2004; 4: 253 – 65.
dc.identifier.citedreferenceParker AL, Kavallaris M, McCarroll JA. Microtubules and their role in cellular stress in cancer. Front Oncol. 2014; 4: 153.
dc.identifier.citedreferenceAl-Mehdi AB, Pastukh VM, Swiger BM, Reed DJ, Patel MR, Bardwell GC, et al. Perinuclear mitochondrial clustering creates an oxidant-rich nuclear domain required for hypoxia-induced transcription. Sci Signal. 2012; 5: ra47.
dc.identifier.citedreferenceIdelchik M, Begley U, Begley TJ, Melendez JA. Mitochondrial ROS control of cancer. Semin Cancer Biol. 2017; 47: 57 – 66.
dc.identifier.citedreferenceAraiso Y, Imai K, Endo T. Role of the TOM complex in protein import into mitochondria: structural views. Annu Rev Biochem. 2022; 91: 679 – 703. https://doi.org/10.1146/annurev-biochem-032620-104527
dc.identifier.citedreferenceBender A, Desplats P, Spencer B, Rockenstein E, Adame A, Elstner M, et al. TOM40 mediates mitochondrial dysfunction induced by α-synuclein accumulation in Parkinson’s disease. PLoS One. 2013; 8: e62277.
dc.identifier.citedreferenceYang W, Shin HY, Cho H, Chung JY, Lee EJ, Kim JH, et al. TOM40 inhibits ovarian cancer cell growth by modulating mitochondrial function including intracellular ATP and ROS levels. Cancers (Basel). 2020; 12: 1329.
dc.identifier.citedreferenceGreenberg MVC, Bourc’his D. The diverse roles of DNA methylation in mammalian development and disease. Nat Rev Mol Cell Biol. 2019; 20: 590 – 607.
dc.identifier.citedreferenceMattioli K, Oliveros W, Gerhardinger C, Andergassen D, Maass PG, Rinn JL, et al. Cis and trans effects differentially contribute to the evolution of promoters and enhancers. Genome Biol. 2020; 21: 210.
dc.identifier.citedreferenceWainberg M, Sinnott-Armstrong N, Mancuso N, Barbeira AN, Knowles DA, Golan D, et al. Opportunities and challenges for transcriptome-wide association studies. Nat Genet. 2019; 51: 592 – 9.
dc.identifier.citedreferenceSung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, et al. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2021; 71: 209 – 49.
dc.identifier.citedreferenceChen Z, Fillmore CM, Hammerman PS, Kim CF, Wong KK. Non-small-cell lung cancers: a heterogeneous set of diseases. Nat Rev Cancer. 2014; 14: 535 – 46.
dc.identifier.citedreferenceTang S, Pan Y, Wang Y, Hu L, Cao S, Chu M, et al. Genome-wide association study of survival in early-stage non-small cell lung cancer. Ann Surg Oncol. 2015; 22: 630 – 5.
dc.identifier.citedreferenceJones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet. 2012; 13: 484 – 92.
dc.identifier.citedreferenceKoch A, Joosten SC, Feng Z, de Ruijter TC, Draht MX, Melotte V, et al. Analysis of DNA methylation in cancer: location revisited. Nat Rev Clin Oncol. 2018; 15: 459 – 66.
dc.identifier.citedreferenceAnglim PP, Alonzo TA, Laird-Offringa IA. DNA methylation-based biomarkers for early detection of non-small cell lung cancer: an update. Mol Cancer. 2008; 7: 81.
dc.identifier.citedreferenceCordell HJ. Detecting gene-gene interactions that underlie human diseases. Nat Rev Genet. 2009; 10: 392 – 404.
dc.identifier.citedreferenceChen J, Shen S, Li Y, Fan J, Xiong S, Xu J, et al. APOLLO: an accurate and independently validated prediction model of lower-grade gliomas overall survival and a comparative study of model performance. EBioMedicine. 2022; 79: 104007.
dc.identifier.citedreferenceZhang R, Chen C, Dong X, Shen S, Lai L, He J, et al. Independent validation of early-stage non-small cell lung cancer prognostic scores incorporating epigenetic and transcriptional biomarkers with gene-gene interactions and main effects. Chest. 2020; 158: 808 – 19.
dc.identifier.citedreferenceZhang R, Lai L, He J, Chen C, You D, Duan W, et al. EGLN2 DNA methylation and expression interact with HIF1A to affect survival of early-stage NSCLC. Epigenetics. 2019; 14: 118 – 29.
dc.identifier.citedreferenceZhu J, Guan J, Ji X, Song Y, Xu X, Wang Q, et al. A two-phase comprehensive NSCLC prognostic study identifies lncRNAs with significant main effect and interaction. Mol Genet Genomics. 2022; 297: 591 – 600.
dc.identifier.citedreferenceChen C, Wei Y, Wei L, Chen J, Chen X, Dong X, et al. Epigenome-wide gene-age interaction analysis reveals reversed effects of PRODH DNA methylation on survival between young and elderly early-stage NSCLC patients. Aging (Albany NY). 2020; 12: 10642 – 62.
dc.working.doiNOen
dc.owningcollnameInterdisciplinary and Peer-Reviewed


Files in this item

Show simple item record

Remediation of Harmful Language

The University of Michigan Library aims to describe library materials in a way that respects the people and communities who create, use, and are represented in our collections. Report harmful or offensive language in catalog records, finding aids, or elsewhere in our collections anonymously through our metadata feedback form. More information at Remediation of Harmful Language.

Accessibility

If you are unable to use this file in its current format, please select the Contact Us link and we can modify it to make it more accessible to you.