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nature research | reporting summary

October 2018

Outcomes Primary Outcome Measures :

1. Disease-free Survival (DFS) [ Time Frame: 3 years ]
   The DFS hazard rate and 95% confidence interval will be reported. At this time, event time distributions for disease-free survival
   in the two arms will be estimated with the method of Kaplan and Meier and compared using a stratified Cox-proportional
   hazards model (stratified for stage IA vs IB) with a two-sided alpha of 10%.
   Secondary Outcome Measures :


2. Factors That Predict Clinical Outcome in Patients Treated With Combination Epigenetic Therapy in Terms of Epigenomic Data
   Generated From the Illumina Platform [ Time Frame: Up to 2 years ]
   The study was terminated early due to poor accrual since the requirement of clinic administration of the 5AZA daily and post-
   operative patients not wanting 6 months of treatment. For this reason, 13 pts were enrolled and data was not analyzed, for
   which we are unable to make any conclusions or report results.


3. Median Disease-free Survival [ Time Frame: Up to 5 years ]
   Determined by the method determined by Kaplan and Meier. Estimated with 95% confidence intervals. Cox proportional hazard
   modeling will be used for multivariate analysis.


4. Number of Relapses and Deaths Per Total Time of Follow-up Comparing Patients With N2 Lymph Nodes in Terms of
   Methylated and Unmethylated [ Time Frame: Up to 5 years ]
   Kaplan Meier curves will be used.


5. Overall Survival [ Time Frame: Up to 5 years ]
   Determined by the method determined by Kaplan and Meier. Estimated with 95% confidence intervals. Cox proportional hazard
   modeling will be used for multivariate analysis.


6. Presence of Methylation Patterns [ Time Frame: Up to 2 years ]
   McNemar's test will be used to compare the change in methylation after treatment in sputum.


7. Toxicities Graded According to the National Cancer Institute Common Terminology Criteria for Adverse Events (NCI CTCAE)
   v4.0 [ Time Frame: Up to 5 years ]
   Simple descriptive statistics will be utilized to display the data.

Flow Cytometry

Plots

Confirm that:

The axis labels state the marker and fluorochrome used (e.g. CD4-FITC).

The axis scales are clearly visible. Include numbers along axes only for bottom left plot of group (a 'group' is an analysis of identical markers).

All plots are contour plots with outliers or pseudocolor plots.

A numerical value for number of cells or percentage (with statistics) is provided.

Methodology

Sample preparation See methods

Instrument Cell were recorded on an LSR II Flow Cytometer (BD Biosciences), or on a MoFlo XDP Cell Sorter (BECKMAN COULTER)

Software Data were analyzed using FlowJo v10.0.0 software, or Summit 5.4 software.

Cell population abundance For sorting experiments, the cell were subsequently analyzed by FACS and >98% purity was achieved.

Gating strategy Following routine gating strategy.

Tick this box to confirm that a figure exemplifying the gating strategy is provided in the Supplementary Information.