Supplementary data for Xu QW, Zhao W, Wang Y, Sartor MA, Han DM, Deng JX, Ponnala R, Yang JY, Zhang QY, Liao GQ, Qu YM, Li L, Liu FF, Zhao HM, Lan F, Yin YH, Chen WF, Zhang Y, Wang XS, An integrated genome-wide approach to discover tumor specific antigens as potential immunological and clinical targets in cancer. Cancer Research. 2012 doi: 10.1158/0008-5472.CAN-12-1656. [Abstract]

 
Putative tumor specific antigens in multiple tumor entities can be downloaded from here.
Putative overexpressed antigens in multiple tumor entities can be downloaded from here.

The principle of HEPA analysis

      Tumor specific antigen genes are pivotal targets in the management of human cancers. By analysis of gene expression profiles for eight well-established tumor specific antigen genes widely accepted as clinical targets，we observed that these proto-type tumor-specific antigen genes usually exhibit distinctive heterogeneous expression profiles (Figure 1).

    


Figure 1. The heterogenous gene expression profiles of 8 prototype tumor specific antigens widely adopted as clinical targets. Gene expression profiles are analyzed using publicly available Affymetrix U133 plus 2.0 microarray datasets for 34 normal tissues from human body index dataset and 28 cancer types (see Data Source). The expression values are median-centered and scaled to a median absolute deviation of 1, and then depicted by grey color scales. Each of the antigens shows a typical heterogeneous expression pattern.
     

    This observation lays the foundation to discover tumor specific genes as immunological and clinical targets by gene expression profile analysis. Toward this end, we developed a novel analysis called the Heterogeneous Expression Profile Analysis (HEPA), incorporating the key expression features of clinically adopted TSA genes (Figure 2).

 


Figure 2. The principle and algorithm of HEPA analysis.  A. The heterogeneous expression profile of MAGEA3, a canonical cancer-testis antigen gene, across a compendium of gene expression datasets from multiple tumor entities and a spectrum of normal tissues. Individual samples from normal or malignant tissues are sorted in descending order based on gene expression signals to reveal the marked over-expression of MAGEA3 in a small subset of tumor or normal samples (outliers). B. The algorithms of HEPA analysis. Microarray gene expression data from j normal somatic tissue types and cancer type k are shown in the heat-map. Data were processed as described in Methods, resulting in a final HEPA score which accentuates heterogeneously expressed genes in cancers. C.  The rationale of using the adjusted upper quartile mean (Mean{P75~P95}), to highlight heterogeneously expressed genes in cancer. The upper plot shows the expression of Genes X and Y with the same average expression level in transitional cell carcinoma. The “mean” function fails to discriminate Gene Y with distinct over-expression in a subset of samples. The middle plot shows that the 85 percentile function fails to highlight Gene Y over-expressed in less than 15% of TCC. The lower plot shows the expression of Genes X and Y with the same upper quartile mean (UQM). UQM fails to discriminate gene X with a biased max expression signal.  

 

The Source Data for Heterogeneous Expression Profile Analysis
GEO ID Primary site Tissues types (n) Samples (n)
GSE7307 Normal tissues from multiple sites 34 291
GSE2109 Cancer tissues from multiple tumor entities 28 1800
GSE6764 Tumor tissues from hepatocellular carcinoma 1 35
GSE6338 Tumor tissues from lymphoma 1 40
GSE7127 Cell lines from melanoma 1 63







Note: for most cancer types, GSE7307 and GSE2109 are sufficient for analysis. The other three datasets can be excluded from the analysis unless liver cancer, lymphoma or melanoma are concerned.

        Gene expression values were extracted with the MAS5 algorithm and were scaled to a reference sample, using a house-keeping gene probe set provided by Affymetrix. These normalized expression signals are directly applied to HEPA analysis, which represent “absolute expression level” as apposed to “relative expression level” in mean- or median-centered data.

Algorithms for Heterogeneous Expression Profile Analysis

 

A. Parameters of HEPA analysis

 

To evaluate the expression silence profile of candidate antigens in normal tissues, we first need to specify the expression silence threshold (φ) indicating the maximum noise signals from nonexpressing genes, and the immunogenicity constant (κ) representing the estimated threshold of expression signals below which the gene products would presumably not be able to educate the developing immune system for central tolerance specific to these antigens (Figure 3). This was done through analyzing 91 reported TSAs compiled from publications1-3. The expression silence threshold (φ) was set according to the 95th percentile of the median expression levels of these TSAs across 34 normal tissues except the immunoprivileged organ testis, placenta, and ovary. The 95th percentile was chosen to avoid misrepresentation by the technical outliers of microarray hybridization.

   

 

where {agm}j is the expression signal of antigen m in tissue j.

The immunogenicity constant (k) represents the maximum expression level that is normally “overlooked” by the immune systems. Practically, it was estimated with the upper 95th percentile of the median deviated expression level of known tumor antigens (Figure 3). The immunoprivileged organs were excluded from the analysis because antigens expressed there are usually not accessible to developing lymphocytes so that their immunogenicity should be well preserved. The 95th percentile, as opposed to the greatest values, also avoids the possible misrepresentation by technical outliers.

 

 (m and j: antigen m in tissue j)

  

where {agm}j is the expression signal of antigen m in tissue j. MAD is median absolute deviation.

 

 

Figure 3. The algorithm for determining the expression silence signal φ and the immunogenicity constant κ. The microarray gene expression data from normal tissues 1,…,j for antigens 1,…,m are shown in the upper heat map. The median expression signal Median {agm}j and median deviated expression signal Median {agm}j +MAD {agm}j from j tissues are aligned descendingly and the P95 values are designated as φ or κ, respectively. The detailed algorithms are discussed in the methods section.

 

 

B. Depreciatory Penalty

 

The Depreciatory Penalty (DP) score is calculated on the basis of expression signals across healthy somatic tissues. As the expression signals less than φ are considered as noise signals, and should not affect the DP score, the gene expression signals were transformed by subtractingφfrom each expression value and setting the negative values to zero. The transformed values were further divided by (κ-φ) to underscore the magnification of these values against the expression value presumably not recognizable by immune systems (Figure 2b). Let

 

  

where xi is the expression signal of ith sample in tissue type j, yj are tissue j specific ratio.

The depreciatory penalty was then estimated from the weighted power sum of tissue-specific ratios yj across all normal tissues:

   

                                                   (1)

  

Where ωj is weight of tissue type j, n is the total number of normal tissue types. The power r penalizes the expression signals in somatic tissues. By testing the enrichment of the 8 prototype tumor antigens in top-scoring genes (Figure 4) with Kolmogorov-Smirnov statistics, the optimal range of power r was found to be between 1 and 1.5 (1 ≤ r ≤ 1.5). The exact value should be set according to research purposes. A higher value directs findings towards antigens with more restrictive expression in somatic tissues, whereas a lower one tends to predict over-expressed antigens. In this study, we used r =1.2 for the calculation of the HEPA score to reveal the genes with substantial expression in tumor tissues while retaining a strict expression-silence in normal tissues.

 



Figure 4. Determination of the optimal range of power r in the calculation of Depreciatory Penalty. The Kolmogorov-Smirnov (K-S) test was performed to benchmark the performance of max HEPA score in prioritizing the eight established TSAs from the genome, with different power r ranging from linear to square. A range of power r from 1 to 1.5 generates most favorable prioritization results.

 

To determine the tissue weights (ωj), the tissues were first empirically ranked according to their consequences in autoimmune toxicity and surgical resectability (Table 1), and the weights were then calculated using Analytic Hierarchy Process (AHP, Thomas L. Saaty, 1970).

Let {s1, s2, …, sn} be the ranks of normal tissues, then

The weight for tissue j can be calculated as follows,

The weights calculated from AHP tend to exaggerate the difference of top ranked tissues, thus adjustments were made to balance the weights of the top three tissues, the heart, kidney and lung, as autoimmune response against any of these organs will be life-threatening. In situations where the tissue is dispensable or even resectable in the course of cancer therapy, the weight was set to zero. To nominate differentiation antigens from specific cancers, including melanoma, prostate and gastrocolonic cancer, the weights of the normal tissues from which the tumor arises were also set to zero.

 

Table 1. The weights for normal adult somatic tissues for the calculation of Depreciatory Penalty score.

 

Rank Normal Tissues Weight Rank Normal Tissues Weight Rank Normal Tissues Weight
1 heart 0.169 13 spinal cord 0.02 25 uterus 0.004
2 kidney 0.159 14 pancreas 0.019 26 adipose 0
3 lung 0.149 15 nerve 0.017 27 breast 0
4 brain 0.065 16 vessels 0.016 28 fetal 0
5 cerebellum 0.052 17 airtube 0.015 29 ovary 0
6 liver 0.043 18 small intestine 0.014 30 placenta 0
7 muscle 0.037 19 skin 0.011 31 soft tissue 0
8 bone marrow 0.032 20 thyroid 0.011 32 testis 0
9 thymus 0.029 21 stomach 0.007 33 urethra 0
10 lymphnode 0.026 22 colon 0.007 34 vagina 0
11 spleen 0.024 23 esophagus 0.006
12 adrenal 0.022 24 prostate 0.005
 

C. Beneficial Bonus, BB

 

The beneficial bonus is a signal measure of increased beneficial outliers in specific cancer k. The scoring function for the beneficial bonus takes the log 2 ratio of the adjusted upper quartile mean .  was calculated by averaging the expression signals from P75 to P95, representing the mean biological outlier expression signal. The log 2 transformed  features the marked over-expression of candidate genes in a subset of tumors while preserving a similar scale with DP (Figure 2b). Let

  

 

Then the Beneficial Bonus of cancer type k is given as

  

                                                     (2)

 

D. HEPA score

 

The depreciatory penalty score was then subtracted from the beneficial bonus score, which was designated as the HEPA score.

  

                           (3)

        The cut-off for a meaningful HEPA score is determined based on optimal detection of known TSAs. In our compendia of datasets, a cut-off of 6 is found to be the highest cut-off offering optimal detection of known TSAs (Figure 5). In addition, a HEPA score >8 is empirically considered as high and >10 as very high.

 


Figure 5. Determining the cut-off for a meaningful HEPA score based on optimal detection of known TSAs. The detection rate of known TSAs is determined with different cut-offs of HEPA score ranging from 1 to 15. A cut-off of 6 is found to be the highest cut-off offering optimal detection of known TSAs and clinically important TSAs. The detection rates will significantly drop with a cut-off higher than 6. In addition, a HEPA score >8 is empirically considered as high and >10 as very high. All prototype tumor antigens have a HEPA score >10. Known TSAs and clinically important TSAs used in this analysis are listed in Supplementary Table 3.

     

        The HEPA analysis ranks the putative antigens by taking the individual HEPA scores for different cancer types. By calculating cancer type specific HEPA scores, distinct cancer datasets can be compared with the normal tissue dataset, while minimizing the deleterious batch effects among datasets. Each gene may be represented by multiple probes, and a subset of these may generate distinct expression profiles from the others, either due to cross-hybridization or representing the specific exon not expressed in cancers. To address this issue, we used the best representative probe generating the greatest HEPA score sum for each gene. Then the candidate antigens are ranked by the max HEPA scores to evaluate their potential clinical value and immunogenicity. To prioritize candidates in specific tumor entities, the putative TSA genes with consensus coding sequences were ranked by their HEPA score in each cancer type, and then lead candidates are subjected to a manual inspection of expression profiles.