DOI: 10.5061/dryad.pzgmsbcxh
title: CALERIE trial molecular data summary: DNA methylation, mRNA, smRNA for blood, adipose, and muscle

description: Caloric restriction (CR) slows biological aging and prolongs healthy
 lifespan in model organisms. Findings from the CALERIE randomized,
 controlled trial of long-term CR in healthy, non-obese humans
 (NCT00427193) broadly support a similar pattern of effects in humans. To
 expand our understanding of the molecular pathways and biological
 processes underpinning CR effects in humans, we generated a series of
 genomic datasets from stored biospecimens collected from n=218
 participants during the trial. These data constitute the first genomic
 data resource for a randomized controlled trial of an intervention
 targeting the biology of aging. Datasets include whole-genome SNP
 genotypes, and three-timepoint-longitudinal DNA methylation, mRNA, and
 small RNA datasets generated from blood, skeletal muscle, and adipose
 tissue samples (total sample n=2327). The CALERIE Genomic Data Resource
 described in this article is available from the Aging Research Biobank.
 This multi-tissue, multi-omic, longitudinal data resource has great
 potential to advance translational geroscience.
description: CALERIE Phase 2 was a multi-center, randomized controlled trial
 conducted at three clinical centers in the United States8
 (ClinicalTrials.gov Identifier: NCT00427193). It aimed to evaluate the
 time-course effects of 25% CR (that is, intake 25% below the individual’s
 baseline level) over a 2-yr period in healthy adults (men aged 21–50 yr,
 premenopausal women aged 21–47 yr) with BMI in the normal weight or
 slightly overweight range (BMI 22.0–27.9 kg m−2). The study protocol was
 approved by Institutional Review Boards at three clinical centers
 (Washington University School of Medicine, St Louis, MO, USA; Pennington
 Biomedical Research Center, Baton Rouge, LA, USA; Tufts University,
 Boston, MA, USA) and the coordinating center at Duke University (Durham,
 NC, USA). All study participants provided written informed consent.
 Nongenomic data were obtained from the CALERIE Biorepository
 (https://calerie.duke.edu/apply-samples-and-data-analysis). Oversight of
 our study was performed by the Institutional Review Board of Columbia
 University Irving Medical Center AAAS2948. Extending
 CALERIE phase I in both scale and duration, CALERIE recruited a total of
 220 subjects and assigned them in a 2:1 allocation to a CR treatment group
 or ad libitum (AL) control arm. Subjects were randomly assigned to CR or
 AL groups stratified on study site, sex, and body mass index. Participants
 in the CR group were assigned to a protocol designed to result in a 25%
 reduction in caloric intake relative to estimated energy requirements at
 enrollment. CR participants received an intensive behavioral intervention
 that included individual and group sessions, a meal provision phase,
 digital assistants to monitor caloric intake, and training in portion
 estimation and other nutrition and behavioral topics. Adherence was
 assessed using measures of energy expenditure using the doubly-labeled
 water method as well as expected changes in body composition. The duration
 of the study for both CR and AL participants was 2 years.
 Throughout the 2-year study duration, starting at baseline prior
 to randomization and recurring at months 1, 3, 6, 9, 12, 18, and 24,
 participants were evaluated for a range of pre-specified anthropometric,
 psychological, behavioral, and physiological outcomes. Blood samples were
 collected every six months. At baseline, 12-months, and 24-months, whole
 blood and samples were collected and banked. In addition, a subset of
 participants agreed to biopsies of adipose and muscle tissue at baseline,
 12-months, and 24-months. From these samples, SNP-based genotypes, DNA
 methylation, mRNA, and small RNAs were assayed. Here, we describe these
 datasets and provide an overview of this data resource (Fig. 1).
 More details about the CALERIE trial, including study protocols
 and ongoing and published research, are available at
 https://calerie.duke.edu. Data can be accessed through the Aging Research
 Biobank (https://agingresearchbiobank.nia.nih.gov/studies/calerie/). Data
 use is restricted to non-commercial use in studies to determine factors
 that affect age-related conditions. Biospecimens are available, but
 limited to research on the effects that caloric restriction may have on
 aging and aging-related diseases. Applications for data access include a
 brief summary of the research question and intended analysis and proof of
 IRB approval for the project.
description: # CALERIE trial molecular data summary: DNA methylation, mRNA, smRNA for
 blood, adipose, and muscle
 [https://doi.org/10.5061/dryad.pzgmsbcxh](https://doi.org/10.5061/dryad.pzgmsbcxh) ## Description of the data and file structure **Principle Investigator Contact Information** Name: Calen Patrick Ryan, PhD Institution: Columbia Aging Center Geroscience Computational Core, Columbia University Email: [cpr2139@cumc.columbia.edu](mailto:cpr2139@cumc.columbia.edu) **Alternate Contact Information** Name: Daniel W. Belsky, PhD Institution: Department of Epidemiology, Columbia Aging Center Geroscience Computational Core, Columbia University Email: [db3275@cumc.columbia.edu](mailto:db3275@cumc.columbia.edu) ### Funding This research utilized the FlowSorted.BloodExtended.EPIC software packages developed at Dartmouth College which are governed by the licensing terms provided by Dartmouth Technology Transfer ([https://github.com/immunomethylomics/FlowSorted.BloodExtended.EPIC/blob/main/SoftwareLicense.FlowSorted.BloodExtended.EPIC%20to%20sign.pdf](https://github.com/immunomethylomics/FlowSorted.BloodExtended.EPIC/blob/main/SoftwareLicense.FlowSorted.BloodExtended.EPIC%20to%20sign.pdf)). Figures 1 and 2 and Extended Figures 1 and 2 include images created in BioRender in the Columbia Aging Center Geroscience Computational Core (2024) [https://biorender.com/t12h125](https://biorender.com/t12h125). CALERIE is a registered trademark. The authors confirm all summary data in this repository can be published under a CC0 license waiver. #### Recommended Citation CP Ryan, DL Corcoran, N Banskota, C Eckstein Indik, A Floratos, R Friedman, MS Kobor, VB Kraus, WE Kraus, JL MacIsaac, MC Orenduff, CF Pieper, JP White, L Ferrucci, S Horvath, KM Huffman, DW Belsky. (2024) CALERIE trial molecular data summary: DNA methylation, mRNA, smRNA for blood, adipose, and muscle. Dryad Data Repository. https://doi.org/10.5061/dryad.pzgmsbcxh ### Description of the data and file structure This contains two main folders: Data and Code. Data contains summary data (not raw data) for each dataset. Code contains code used to process data or create summaries and figures in the paper. #### Files and Folders ##### Data/DNAm Contains all DNA methylation summary files. ###### blood\_dnam\_summary Blood_DNAm_all_baseline_probes.csv Blood_DNAm_all_12_month_probes.csv Blood_DNAm_all_24_month_probes.csv Blood_DNAm_all_samples_probes.csv These files contain a list of probes with complete data for samples at baseline only, samples at 12-month follow-up only, samples at 24-month follow-up only, or all samples at all timepoints in the study, respectively. Blood_DNAm_all_baseline_summary.csv Blood_DNAm_all_12_month_summary.csv Blood_DNAm_all_24_month_summary.csv Blood_DNAm_all_samples_summary.csv These files contain a list of probes, where each row corresponds to each probe, and columns are for the number of samples missing that probe, the mean, standard deviation, median, minimum, and maximum beta values. ###### muscle\_dnam\_summary Muscle_DNAm_all_baseline_probes.csv Muscle_DNAm_all_12_month_probes.csv Muscle_DNAm_all_24_month_probes.csv Muscle_DNAm_all_samples_probes.csv These files contain a list of probes with complete data for samples at baseline only, samples at 12-month follow-up only, samples at 24-month follow-up only, or all samples at all time points in the study, respectively. Muscle_DNAm_all_baseline_summary.csv Muscle_DNAm_all_12_month_summary.csv Muscle_DNAm_all_24_month_summary.csv Muscle_DNAm_all_samples_summary.csv These files contain a list of probes, where each row corresponds to each probe, and columns are for the number of samples missing that probe, the mean, standard deviation, median, minimum, and maximum beta values. ###### adipose\_dnam\_summary Adipose_DNAm_all_baseline_probes.csv Adipose_DNAm_all_12_month_probes.csv Adipose_DNAm_all_24_month_probes.csv Adipose_DNAm_all_samples_probes.csv These files contain a list of probes with complete data for samples at baseline only, samples at 12-month follow-up only, samples at 24-month follow-up only, or all samples at all time points in the study, respectively. Adipose_DNAm_all_baseline_summary.csv Adipose_DNAm_all_12_month_summary.csv Adipose_DNAm_all_24_month_summary.csv Adipose_DNAm_all_samples_summary.csv These files contain a list of probes, where each row corresponds to each probe, and columns are for the number of samples missing that probe, the mean, standard deviation, median, minimum, and maximum beta values. ##### Data/mRNA Contains all mRNA summary files. ###### muscle\_rna\_summary Muscle_mRNA_all_baseline_summary.csv Muscle_mRNA_all_12_month_summary.csv Muscle_mRNA_all_24_month_summary.csv Muscle_mRNA_all_samples_summary.csv These files contain a list of transcripts, where each row corresponds to each transcript, and columns are for the number of samples missing that probe, the mean, standard deviation, median, minimum, and maximum beta values. Transcripts missing in any sample were removed. ###### adipose\_rna\_summary Adipose_mRNA_all_baseline_summary.csv Adipose_mRNA_all_12_month_summary.csv Adipose_mRNA_all_24_month_summary.csv Adipose_mRNA_all_samples_summary.csv These files contain a list of transcripts, where each row corresponds to each transcript, and columns are for the number of samples missing that probe, the mean, standard deviation, median, minimum, and maximum beta values. Transcripts missing in any sample were removed. ##### Data/smallRNA Contains all smallRNA summary files. ###### Plasma Plasma_smRNA_all_baseline_summary.xlsx Plasma_smRNA_all_12_month_summary.xlsx Plasma_smRNA_all_24_month_summary.xlsx Plasma_smRNA_all_samples_summary.xlsx These files contain a list of transcripts, where each row corresponds to each transcript, and columns are for the number of samples missing that probe, the mean, standard deviation, median, minimum, and maximum beta values. Transcripts missing in any sample were removed. ###### Muscle Muscle_smRNA_all_baseline_summary.xlsx Muscle_smRNA_all_12_month_summary.xlsx Muscle_smRNA_all_24_month_summary.xlsx Muscle_smRNA_all_samples_summary.xlsx These files contain a list of transcripts, where each row corresponds to each transcript, and columns are for the number of samples missing that probe, the mean, standard deviation, median, minimum, and maximum beta values. Transcripts missing in any sample were removed. ###### Adipose Adipose_smRNA_all_baseline_summary.xlsx Adipose_smRNA_all_12_month_summary.xlsx Adipose_smRNA_all_24_month_summary.xlsx Adipose_smRNA_all_samples_summary.xlsx These files contain a list of transcripts, where each row corresponds to each transcript, and columns are for the number of samples missing that probe, the mean, standard deviation, median, minimum, and maximum beta values. Transcripts missing in any sample were removed. ## Code/Software ##### README.md Basic readme file for the GitHub with code at: [https://github.com/CPRyan/CALERIE_Genomic_Data_Resource](https://github.com/CPRyan/CALERIE_Genomic_Data_Resource) ##### Phenotypes\_by\_Tissue\_Molecular\_Datatype.R Code used to produce a simple table showing key anthropometric and demographic information on participants for each molecular dataset. ##### Sample\_Overlap\_and\_Matrix\_Clean.R Code used to determine upset plots and sample overlap matrix file provided with the paper (Figure 1C). This file allows researchers to determine, for a given sample, which molecular data types are available at which time points. #### Blood\_DNAm ##### Processing/processRawData.R Processing pipeline for blood DNAm. ##### Derived\_Variables/CALERIE\_Biorepository\_age\_scatterplot\_matrix.R Code used to produce age correlations between clocks (residualized) and between clocks and age, as shown in Figure 4. ##### Derived\_Variables/cell\_counts\_for\_biorepository.R Code used to produce cell count boxplots in Figure 5 in the paper. ##### Summary\_Tables/Blood\_Summary\_Tables.R Code used to generate blood DNAm summary tables. #### Muscle\_DNAm ##### Processing/Muscle\_Corcoran\_Pipeline.R Processing pipeline for muscle DNAm. ##### Summary\_Tables/Muscle\_Summary\_Tables.R Code used to generate muscle DNAm summary tables. #### Adipose\_DNAm ##### Processing/Adipose\_Corcoran\_Pipeline.R Processing pipeline for adipose DNAm. ##### Summary\_Tables/Muscle\_Summary\_Tables.R Code used to generate adipose DNAm summary tables. #### Muscle\_RNA ##### Muscle\_RNAseq\_Summary.R Code used to generate muscle RNA summary tables. #### Adipose\_RNA ##### Adipose\_RNAseq\_Summary.R Code used to generate adipose RNA summary tables. ##### Adipose\_RNA\_volcano.R Code used to generate volcano plots in Figure 6 from limma output (Tables S4 and S5) for 12-month and 24-month time points. ##### GSEA\_Function.R The function used in Run_GSEA_on_Adipose_RNAseq.R generates enrichment figures in Figure 6. ##### Run\_GSEA\_on\_Adipose\_RNAseq.R The code used to run GSEA is used for Figure 6 and Tables S2 and S3. ## Access Information/Data and Code Availability Other publicly accessible locations of the data: * [https://github.com/CPRyan/CALERIE_Genomic_Data_Resource](https://github.com/CPRyan/CALERIE_Genomic_Data_Resource) Processed data can be accessed through the Aging Research Biobank ([https://agingresearchbiobank.nia.nih.gov/studies/calerie/](https://agingresearchbiobank.nia.nih.gov/studies/calerie/)). Data use is restricted to non-commercial use in studies to determine factors that affect age-related conditions. Applications for data access include a brief summary of the research question and intended analysis and proof of IRB approval for the project. Original raw data may be obtained from the Belsky Lab ([cac_geroscience@cumc.columbia.edu](mailto:cac_geroscience@cumc.columbia.edu)). Code used in the production of summary data and figures are available at [https://github.com/CPRyan/CALERIE_Genomic_Data_Resource](https://github.com/CPRyan/CALERIE_Genomic_Data_Resource)