Genome-Scale Methylation Analysis Identifies Immune Profiles and Age Acceleration Associations with Bladder Cancer Outcomes

Immune profiles have been associated with bladder cancer outcomes and may have clinical applications for prognosis. However, associations of detailed immune cell subtypes with patient outcomes remain underexplored and may contribute crucial prognostic information for better managing bladder cancer r...

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Published inCancer epidemiology, biomarkers & prevention Vol. 32; no. 10; pp. 1328 - 1337
Main Authors Chen, Ji-Qing, Salas, Lucas A., Wiencke, John K., Koestler, Devin C., Molinaro, Annette M., Andrew, Angeline S., Seigne, John D., Karagas, Margaret R., Kelsey, Karl T., Christensen, Brock C.
Format Journal Article
LanguageEnglish
Published United States American Association for Cancer Research 02.10.2023
Subjects
DNA Methylation
Humans
Lymphocytes
Neoplasm Recurrence, Local - genetics
Prognosis
Proportional Hazards Models
Urinary Bladder Neoplasms
Online AccessGet full text
ISSN1055-9965
1538-7755
1538-7755
DOI10.1158/1055-9965.EPI-23-0331

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Abstract Immune profiles have been associated with bladder cancer outcomes and may have clinical applications for prognosis. However, associations of detailed immune cell subtypes with patient outcomes remain underexplored and may contribute crucial prognostic information for better managing bladder cancer recurrence and survival. Bladder cancer case peripheral blood DNA methylation was measured using the Illumina HumanMethylationEPIC array. Extended cell-type deconvolution quantified 12 immune cell-type proportions, including memory, naïve T and B cells, and granulocyte subtypes. DNA methylation clocks determined biological age. Cox proportional hazards models tested associations of immune cell profiles and age acceleration with bladder cancer outcomes. The partDSA algorithm discriminated 10-year overall survival groups from clinical variables and immune cell profiles, and a semi-supervised recursively partitioned mixture model (SS-RPMM) with DNA methylation data was applied to identify a classifier for 10-year overall survival. Higher CD8T memory cell proportions were associated with better overall survival [HR = 0.95, 95% confidence interval (CI) = 0.93-0.98], while higher neutrophil-to-lymphocyte ratio (HR = 1.36, 95% CI = 1.23-1.50), CD8T naïve (HR = 1.21, 95% CI = 1.04-1.41), neutrophil (HR = 1.04, 95% CI = 1.03-1.06) proportions, and age acceleration (HR = 1.06, 95% CI = 1.03-1.08) were associated with worse overall survival in patient with bladder cancer. partDSA and SS-RPMM classified five groups of subjects with significant differences in overall survival. We identified associations between immune cell subtypes and age acceleration with bladder cancer outcomes. The findings of this study suggest that bladder cancer outcomes are associated with specific methylation-derived immune cell-type proportions and age acceleration, and these factors could be potential prognostic biomarkers.
AbstractList Immune profiles have been associated with bladder cancer outcomes and may have clinical applications for prognosis. However, associations of detailed immune cell subtypes with patient outcomes remain underexplored and may contribute crucial prognostic information for better managing bladder cancer recurrence and survival.BACKGROUNDImmune profiles have been associated with bladder cancer outcomes and may have clinical applications for prognosis. However, associations of detailed immune cell subtypes with patient outcomes remain underexplored and may contribute crucial prognostic information for better managing bladder cancer recurrence and survival.Bladder cancer case peripheral blood DNA methylation was measured using the Illumina HumanMethylationEPIC array. Extended cell-type deconvolution quantified 12 immune cell-type proportions, including memory, naïve T and B cells, and granulocyte subtypes. DNA methylation clocks determined biological age. Cox proportional hazards models tested associations of immune cell profiles and age acceleration with bladder cancer outcomes. The partDSA algorithm discriminated 10-year overall survival groups from clinical variables and immune cell profiles, and a semi-supervised recursively partitioned mixture model (SS-RPMM) with DNA methylation data was applied to identify a classifier for 10-year overall survival.METHODSBladder cancer case peripheral blood DNA methylation was measured using the Illumina HumanMethylationEPIC array. Extended cell-type deconvolution quantified 12 immune cell-type proportions, including memory, naïve T and B cells, and granulocyte subtypes. DNA methylation clocks determined biological age. Cox proportional hazards models tested associations of immune cell profiles and age acceleration with bladder cancer outcomes. The partDSA algorithm discriminated 10-year overall survival groups from clinical variables and immune cell profiles, and a semi-supervised recursively partitioned mixture model (SS-RPMM) with DNA methylation data was applied to identify a classifier for 10-year overall survival.Higher CD8T memory cell proportions were associated with better overall survival [HR = 0.95, 95% confidence interval (CI) = 0.93-0.98], while higher neutrophil-to-lymphocyte ratio (HR = 1.36, 95% CI = 1.23-1.50), CD8T naïve (HR = 1.21, 95% CI = 1.04-1.41), neutrophil (HR = 1.04, 95% CI = 1.03-1.06) proportions, and age acceleration (HR = 1.06, 95% CI = 1.03-1.08) were associated with worse overall survival in patient with bladder cancer. partDSA and SS-RPMM classified five groups of subjects with significant differences in overall survival.RESULTSHigher CD8T memory cell proportions were associated with better overall survival [HR = 0.95, 95% confidence interval (CI) = 0.93-0.98], while higher neutrophil-to-lymphocyte ratio (HR = 1.36, 95% CI = 1.23-1.50), CD8T naïve (HR = 1.21, 95% CI = 1.04-1.41), neutrophil (HR = 1.04, 95% CI = 1.03-1.06) proportions, and age acceleration (HR = 1.06, 95% CI = 1.03-1.08) were associated with worse overall survival in patient with bladder cancer. partDSA and SS-RPMM classified five groups of subjects with significant differences in overall survival.We identified associations between immune cell subtypes and age acceleration with bladder cancer outcomes.CONCLUSIONSWe identified associations between immune cell subtypes and age acceleration with bladder cancer outcomes.The findings of this study suggest that bladder cancer outcomes are associated with specific methylation-derived immune cell-type proportions and age acceleration, and these factors could be potential prognostic biomarkers.IMPACTThe findings of this study suggest that bladder cancer outcomes are associated with specific methylation-derived immune cell-type proportions and age acceleration, and these factors could be potential prognostic biomarkers.
Immune profiles have been associated with bladder cancer outcomes and may have clinical applications for prognosis. However, associations of detailed immune cell subtypes with patient outcomes remain underexplored and may contribute crucial prognostic information for better managing bladder cancer recurrence and survival. Bladder cancer case peripheral blood DNA methylation was measured using the Illumina HumanMethylationEPIC array. Extended cell-type deconvolution quantified 12 immune cell-type proportions, including memory, naïve T and B cells, and granulocyte subtypes. DNA methylation clocks determined biological age. Cox proportional hazards models tested associations of immune cell profiles and age acceleration with bladder cancer outcomes. The partDSA algorithm discriminated 10-year overall survival groups from clinical variables and immune cell profiles, and a semi-supervised recursively partitioned mixture model (SS-RPMM) with DNA methylation data was applied to identify a classifier for 10-year overall survival. Higher CD8T memory cell proportions were associated with better overall survival [HR = 0.95, 95% confidence interval (CI) = 0.93-0.98], while higher neutrophil-to-lymphocyte ratio (HR = 1.36, 95% CI = 1.23-1.50), CD8T naïve (HR = 1.21, 95% CI = 1.04-1.41), neutrophil (HR = 1.04, 95% CI = 1.03-1.06) proportions, and age acceleration (HR = 1.06, 95% CI = 1.03-1.08) were associated with worse overall survival in patient with bladder cancer. partDSA and SS-RPMM classified five groups of subjects with significant differences in overall survival. We identified associations between immune cell subtypes and age acceleration with bladder cancer outcomes. The findings of this study suggest that bladder cancer outcomes are associated with specific methylation-derived immune cell-type proportions and age acceleration, and these factors could be potential prognostic biomarkers.
Author Seigne, John D.
Koestler, Devin C.
Andrew, Angeline S.
Kelsey, Karl T.
Christensen, Brock C.
Molinaro, Annette M.
Karagas, Margaret R.
Chen, Ji-Qing
Salas, Lucas A.
Wiencke, John K.
AuthorAffiliation 4 Department of Neurology, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire
6 Departments of Epidemiology and Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island
7 Departments of Molecular and Systems Biology, and Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire
3 Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, Kansas
1 Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire
5 Department of Surgery, Section of Urology, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire
2 Department of Neurological Surgery, University of California San Francisco, San Francisco, California
AuthorAffiliation_xml – name: 3 Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, Kansas
– name: 1 Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire
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– name: 2 Department of Neurological Surgery, University of California San Francisco, San Francisco, California
– name: 6 Departments of Epidemiology and Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island
– name: 4 Department of Neurology, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire
– name: 7 Departments of Molecular and Systems Biology, and Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire
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Snippet Immune profiles have been associated with bladder cancer outcomes and may have clinical applications for prognosis. However, associations of detailed immune...
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SubjectTerms DNA Methylation
Humans
Lymphocytes
Neoplasm Recurrence, Local - genetics
Prognosis
Proportional Hazards Models
Urinary Bladder Neoplasms
Title Genome-Scale Methylation Analysis Identifies Immune Profiles and Age Acceleration Associations with Bladder Cancer Outcomes
URI https://www.ncbi.nlm.nih.gov/pubmed/37527159
https://www.proquest.com/docview/2845107729
https://pubmed.ncbi.nlm.nih.gov/PMC10543967
https://escholarship.org/uc/item/3xb3r5dv
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