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Original Research ARTICLE

Front. Oncol., 13 March 2020 | https://doi.org/10.3389/fonc.2020.00272

Inferring Personalized and Race-Specific Causal Effects of Genomic Aberrations on Gleason Scores: A Deep Latent Variable Model

  • 1Department of Computer Science, Xavier University of Louisiana, New Orleans, LA, United States
  • 2Department of Genetics, LSU Health Sciences Center New Orleans, New Orleans, LA, United States
  • 3Bioinformatics Core of Xavier RCMI Center for Cancer Research, Xavier University of Louisiana, New Orleans, LA, United States

Extensive research has examined socioeconomic factors influencing prostate cancer (PCa) disparities. However, to what extent molecular and genetic mechanisms may also contribute to these inequalities still remains elusive. Although various in vitro, in vivo, and population studies have originated to address this issue, they are often very costly and time-consuming by nature. In this work, we attempt to explore this problem by a preliminary study, where a joint deep latent variable model (DLVM) is proposed to in silico quantify the personalized and race-specific effects that a genomic aberration may exert on the Gleason Score (GS) of each individual PCa patient. The core of the proposed model is a deep variational autoencoder (VAE) framework, which follows the causal structure of inference with proxies. Extensive experimental results on The Cancer Genome Atlas (TCGA) 270 European-American (EA) and 43 African-American (AA) PCa patients demonstrate that ERG fusions, somatic mutations in SPOP and ATM, and copy number alterations (CNAs) in ERG are the statistically significant genomic factors across all low-, intermediate-, and high-grade PCa that may explain the disparities between these two groups. Moreover, compared to a state-of-the-art deep inference method, our proposed method achieves much higher precision in causal effect inference in terms of the impact of a studied genomic aberration on GS. Further validation on an independent set and the assessment of the genomic-risk scores along with corresponding confidence intervals not only validate our results but also provide valuable insight to the observed racial disparity between these two groups regarding PCa metastasis. The pinpointed significant genomic factors may shed light on the molecular mechanism of cancer disparities in PCa and warrant further investigation.

Introduction

Prostate cancer (PCa) is the most commonly diagnosed non-skin cancer and the second leading cause of cancer mortality in American men (1). In the US, an estimated 164,690 new cases and 29,430 deaths occurred in 2018 (1). Compared with European-American (EA) men, African American (AA) men experience a 60% higher incidence rate and a 2.4 times higher mortality rate of PCa (1). Moreover, AA men are diagnosed at an earlier age with higher Gleason Scores (GSs) and prostate-specific antigen (PSA) levels (2, 3) and are more likely to have aggressive diseases than men of other ethnic groups.

There are many factors that influence racial disparities in PCa, and a number of socioeconomic, cultural, and environmental factors have been identified (48). For example, unequal access to health care, diet, age, lifestyle, and family history strongly affect the race-specific PCa incidence and mortality rates. Other factors, such as poverty, lack of education, stigma, and type and aggressiveness of treatment have also been suggested as potential contributors to the disparity (9, 10). However, many studies have reported that the inequity remains even after those socioeconomic and treatment differences are adjusted (11). Ever-increasing evidence, on the other hand, suggests that a number of intrinsic molecular determinants specific to malignant cells, including genetic and/or genomic aberrations, must partially account for the observed health disparities (12, 13). For example, Edward et al. (14) reported that BRCA2 mutation is a potential risk factor associated with PCa incidences. Scott et al. (15) showed a much higher rate of cytochrome c oxidase subunit I (COI) mutation present in AA individuals, indicating its importance in racial disparity for PCa.

Compared to other cancer types, PCa is characterized by extraordinary genetic and genomic complexities (16, 17). Multiple studies have identified recurrent somatic mutations, copy number alterations (CNAs), and oncogenic structural DNA rearrangements in primary PCa (1823). These include point mutations in SPOP, FOXA1, and TP53; CNAs involving MYC, RB1, PTEN, and CHD1; and ERG fusions, among other biologically relevant genes. Although certain gene mutations have been reported to be of importance in racial disparity for PCa (14, 15), the personalized and race-specific causal effects of other molecular aberrations on PCa aggressiveness (i.e., GS) have not yet been quantitatively realized, especially given large amounts of multiple clinical and high-throughput omics data.

To fill this gap, we propose a joint deep latent variable model, named DLVM, to integratedly estimate the personalized and race-specific causal effects that a genomic aberration may exert or not exert on a patient's GS. The core of DLVM is a deep variational autoencoder (VAE) framework, which follows the causal structure of inference with proxies. By deep learning multi-observational data of patients, DLVM is able to integrate the potential influence of immeasurable confounders or latent variables (e.g., interactions among interested genes) in its inferences. Exploratory studies on The Cancer Genome Atlas (TCGA) PCa tumor samples demonstrate that DLVM can pinpoint genomic aberrations that may be of significance for racial disparities in PCa. Moreover, compared to another state-of-the-art deep inference method, DLVM achieves much higher precision in causal inferences. Further validation on an independent set and the assessment of the estimated genomic-risk scores not only mutually validate the results but also elucidate the observed racial disparity between these two groups regarding PCa metastasis.

Materials and Methods

Data and Studied Genomic Aberrations

We downloaded the multi-omics TCGA “Prostate Adenocarcinoma” (PRAD) dataset from cBioPortal1. The original dataset contains 270 EAs, 43 AAs, 8 Asians, and 179 patients whose race/ethnicity information is unavailable. To the best of our knowledge, the TCGA PRAD cohort is the only publicly available PCa dataset with the self-reported race/ethnicity information and matched multilevel genomic and clinical data. Those matched data, especially the clinical features, mutation profiles, and gene expression values, are essential for DLVM modeling. As such, we conducted the initial modeling on the primary set of 270 EA and 43 AA patients. Moreover, an independent validation was performed on the corresponding data of 166 patients (i.e., 144 EAs and 22 AAs) whose racial information is imputed by a published deep learning method (see Race/Ethnicity Imputation). The details of sources of data and the utilized features for model training are presented in Supplementary Text S1. Figure 1 illustrates the patient distributions with respect to varied grades of GS in the primary and validation datasets, where the high-risk/aggressive PCa is defined as GS ≥ 8, intermediate-risk PCa is defined as GS = 7, and low-risk/non-aggressive PCa is defined as GS ≤ 6 (24).

FIGURE 1
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Figure 1. Patient distributions with respect to race and varied grades of Gleason scores in the primary and validation data, respectively.

In this work, without further specifications, the studied genomic aberrations include ERG fusions; somatic mutations in SPOP, TP53, FOXA1, ATM, BRCA2, and PTEN; germline mutations in BRCA1 and BRCA2; and CNAs in LCP1, ERG, PTEN, and FOXA1. We choose these aberrations because they are the most frequent genomic alterations as summarized by cBioPortal1. Nevertheless, the potential values of these aberrations in PCa racial disparities are largely unknown. It is worth noting that when a specific genomic aberration is treated as the intervention variable, its gene expression values are excluded from the continuous variables to do the inferences.

Race/Ethnicity Imputation

To obtain the unknown race or ethnicity of the 179 patients in the validation data, we utilized a deep imputation method similar to RIDDLE (25) to train a predictive model on the primary data with known racial information. Specifically, a multilayer perceptron (MLP) network that contains an input layer with 112 nodes (i.e., each node corresponds to a feature as described in Supplementary Text S1), two hidden layers with 512 Parametric Rectified Linear Unit (PReLU) nodes, and a softmax output layer with three nodes (i.e., each corresponds to EA, AA, and Asian) is designed to impute the racial information. Out of the 179 patients, 144, 22, and 13 patients are predicted to be EAs, AAs, and Asians, respectively (Figure 1).

Method and Implementation of Deep Latent Variable Model

To learn the personalized causal effect of an event or intervention on a certain outcome, one has to know the true or factual outcomes with and without the intervention. However, in reality, one can only observe one of the outcomes and the other has to be reconstructed and inferred (Table 1). To infer the unknown outcome from observational data, confounders, i.e., the factors that affect the intervention, its outcomes and the observed noisy variables, need to be carefully handled. In our study, the intervention is an interested genomic aberration, the outcome is the GS of an individual AA or EA patient, and the observed noisy variables are the patients' multi-omics and clinical data. As PCa disparity is a multifactorial construct, it is reasonable to assume that multiple confounders, observed and latent, affect the way that a genomic aberration impacts a patient's GS. Specifically, an example of observed confounders is gene expression data, and examples of latent confounders include the crosstalk/interactions among genes or unseen influences between genotypes and clinical features. As a result, we propose a joint DLVM to tackle this problem.

TABLE 1
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Table 1. Different scenarios of causal effect inferences: Ideal-World vs. Real-World vs. Model-Inference [e.g., deep latent variable model (DLVM)].

Without loss of generality, we assume that the true intervention is t = 1 and the true outcome is y(1) for a certain patient (e.g., the n-th patient in Table 1). Figure 2 demonstrates the underlying inference mechanism of DLVM. In DLVM, y denotes the outcome (e.g., GS of a patient); t represents the intervention (e.g., a specific genomic aberration); x1 and x2, respectively, denote the observed discrete and continuous noisy multi-omics and clinical variables; z1 and z2, respectively, denote the discrete and continuous latent confounders, and Z represents the joint latent confounder. We assume that the joint distribution p(Z, z1, z2, x1, x2, t, y) of the latent confounders and the observed data can be approximately reconstructed from the observations (x1, x2, t, y). As indicated by blue and red, respectively (Figure 2), there are two processes in DLVM: reconstruction of the true outcome [i.e., ŷ(1)] and estimation of the unknown outcome [i.e., ŷ(0)]. More specifically, in both processes, we first parameterize the discrete prior distribution p(z1) as a Bernoulli distribution and the continuous prior distribution p(z2) as a Gaussian distribution. Then, the conditional distributions p(x1|z1), p(x2|z2), and p(Z|z1, z2) can be obtained via deep decoders or encoders of the VAEs (27). After that, we use the graphical representation to compute p(Z, t, y) = p(Z)p(t|Z)p(y|t, Z), whereby the overall joint distribution can be estimated by p(Z, z1, z2, x1, x2, t, y) = p(z1)p(z2)p(x1|z1)p(x2|z2)p(Z|z1, z2)p(t|Z)p(y|t, Z)(Please refer to the detailed discussion in Supplementary Text S2). Finally, given the assumed true intervention t = 1, reconstruction of the true outcome [i.e., ŷ(1)] and estimation of the unknown outcome [i.e., ŷ(0)] can be achieved by using the estimated joint distribution p(Z, z1, z2, x1, x2, t, y). In this way, for the outcome of a certain patient (i.e., GS in our case), the reconstruction precision and individual causal effect (ICE) can be computed by |ŷ(1) − y(1)| and y(1) − ŷ(0), respectively.

FIGURE 2
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Figure 2. The graphical representation of the proposed deep latent variable model (DLVM) with two processes for reconstruction of the true outcome (in blue) and estimation of the unknown outcome (in red), respectively. Please see detailed descriptions in Method and Implementation of Deep Latent Variable Model.

In summary, using VAEs as its core inference technique, DLVM is able to derive the complex non-linear relationships between (x1, x2) and (Z, z1, z2, t, y) and approximately reconstruct p(Z, z1, z2, x1, x2, t, y). This capability allows DLVM to further infer the unknown outcome given an counterfactual/hypothetical intervention (e.g., t = 0) (via the deep encoder) and approximate the true outcome given a truthful/factual intervention (e.g., t = 1) (by the deep decoder). The details of DLVM modeling, inference, and optimization (with theoretical proofs) are presented in Supplementary Text S2. From a technical perspective, DLVM is a variant of causal effect inference methods with latent variable modeling capability. The interested readers can refer to Kingma and Welling (26), Box and Tiao (27), Goodfellow et al. (28), Lee et al. (29), Louizos et al. (30), and Yoon et al. (31) for reviews of related work.

In this study, we prototype DLVM by two deep VAEs with three hidden layers for discrete and continuous latent variables. Each of the first two hidden layers contains 300 neurons, and there are 100 neurons in the third one. We adopt the sigmoid activation function in each hidden layer and the softmax function in the output layer. The dimensions of the latent confounders Z, z1 and z2 are set as 50, 160, and 160, respectively. The DNN is trained using the gradient descent algorithm with up to 300 epochs, a batch size of 10, a learning rate of 1e−5, and a decay rate of 1e−5. ADAM (32) is used as the optimizer, and all model parameters are determined via a preliminary validation process. DLVM is implemented by modifying the source code of CEVAE2 with the utilization of additional Python packages, such as numpy, sklearn, tensorflow, and PyTorch.

Genomic-Risk Scores Obtained via Deep Latent Variable Model Estimation

As DLVM is able to estimate the GS for each patient assuming that an interested genomic aberration does occur (i.e., t = 1), we also compute the genomic risk scores (GRSs) based on the DLVM's estimates so that the impacts of these genomic aberrations can also be interpreted at the population level regarding PCa metastasis. Specifically, based on the obtained GSs from DLVM, a genomic risk assessment model as documented in Mahal et al. (24) and Spratt et al. (33) is first used to compute the GRSs, and then, we compare these aberration-specific GRSs between AAs and EAs by a two-sided (α = 0.05) statistical t-test. The implementations are performed with R 3.6.0 (R package: EBPRS). It is worth noting that the output GRSs are continuous between 0 and 1, with higher scores indicating a greater risk of PCa metastasis.

Measurement Metrics and Experimental Design

To quantitatively assess to what extent a studied genomic aberration may affect the GS of each individual patient, we train DLVM with the GS as the outcome (i.e., y) and each genomic aberration as a binary intervention variable (i.e., t = 1 or 0). Let yi(0) and yi(1) be the true outcomes of the ith patient when t = 0 and t = 1 and ŷi(0) and ŷi(1) be the outcomes estimated by DLVM, the individual causal effect (ICE) for the i-th patient can be measured by ŷi(1) − yi(0) (if the studied aberration does not occur, i.e., t = 0) or yi(1) − ŷi(0) (if the studied aberration occurs, i.e., t = 1). The population causal effect for a racial group can be estimated by the average ICE (AICE), which is defined as: AICE=i{i|t=0}(y^i(1)-yi(0))2+i{i|t=1}(yi(1)- y^i(0))2n, where n is the number of samples in a group. We use root mean square error (RMSE) defined as follows to measure the precision of the causal inference process: RMSE=i{i|t=0}(y^i(0)-yi(0))2+i{i|t=1}(y^i(1)-yi(1) )2n.

In the experiments, we report the average AICE and RMSE over 10 replications of 3-fold cross validations on each racial group. In each fold, ~47, 20, and 33% of the samples in a racial group are used for model training, validation, and testing purposes. This experimental design ensures that all the samples are used for model performance assessment, i.e., calculations of AICE and RMSE.

Experimental Results

Inference Precision Comparison to a Benchmark Method on the Primary Data

To demonstrate the inference precision of DLVM, we first compare it with one of the state-of-the-art inference methods [i.e., causal effect VAE (CEVAE) (30)] w.r.t. the RMSE metric using the primary data. As shown by Figure 3 and Supplementary Table S1, for each racial group, DLVM consistently achieves lower RMSEs than CEVAE in causal effect inferences over all studied genomic aberrations with p < 0.0001. Compared to CEVAE, the overall average reductions in inference RMSEs achieved by DLVM on AAs and EAs are 19.03 and 22.98%, respectively. Specifically, in terms of ERG fusions, the average RMSEs of DLVM on AAs and EAs are 8.54 and 27.02% lower than those of CEVAE. With respect to the studied somatic mutations, the average RMSEs of DLVM on AAs and EAs are 21.03 and 19.01% lower than those of CEVAE. As to the germline mutations (or CNAs), the average RMSEs of DLVM on AAs and EAs are 14.26 and 28.70% (or 21.03 and 25.06%) lower than those of CEVAE. These results indicate that, compared to CEVAE, DLVM is more precise and reliable in inferring the race-specific causal effects that a genomic aberration may pose on GS.

FIGURE 3
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Figure 3. Inference precision comparisons measured by root mean square errors (RMSEs): deep latent variable model (DLVM) vs. causal effect variational autoencoder (CEVAE) on African Americans (AAs) and European-Americans (EAs) in the primary data. CNAs, copy number alterations.

Identifying Race-Specific Genomic Aberrations via Average Individual Causal Effects on the Primary Data

To determine potential genomic aberrations of significance for racial disparities in PCa aggressiveness, we compare the race-specific AICEs of the studied genomic aberrations for low-grade (GS ≤ 6), intermediate-grade (GS = 7), and high-grade (GS ≥ 8) EA and AA patients on the primary data. It is worth noting that AICE can assess the population causal effect of a genomic aberration with respect to different GSs. In addition to AICE, DLVM is able to estimate the ICE for each patient (see Materials and Methods).

From Figure 4 and Supplementary Figure S1, we have the following observations. First, for low-grade patients, AICEs of AAs are statistically significantly higher than those of EAs over most of the studied genomic aberrations, including ERG fusions, somatic mutations in SPOP, FOXA1 and BRCA2, BRCA2 and BRCA1 germline mutations, and CNAs in ERG and FOXA1. The AICE of EAs is statistically significantly higher than that of AAs only on somatic mutations in ATM. There is no statistically significant difference in AICEs of AAs and EAs for TP53 and PTEN mutations as well as LCP1 and PTEN CNAs. Second, regarding intermediate-grade patients, AICEs of EAs are statistically significantly higher than those of AAs on ERG fusions, somatic mutations in SPOP, PTEN, ATM and TP53, BRCA2 germline mutation, and CNAs in LCP1, ERG, and PTEN. There is no statistically significant difference in AICEs of AAs and EAs for FOXA1 and BRCA2 mutations, BRCA1 germline mutation, and FOXA1 CNAs. Third, for high-grade patients, AICEs of AAs are statistically significantly higher than those of EAs on BRCA2 germline mutation, BRCA2 and FOXA1 somatic mutations, and CNAs in FOXA1; while AICEs of EAs are statistically significantly higher than those of AAs on ERG fusions, somatic mutations in SPOP, PTEN, ATM, and TP53 and CNAs in ERG and LCP1. There is no statistically significant difference in AICEs of AAs and EAs for BRCA1 germline mutation and CNAs in PTEN. The results for each grade of PCa patients suggest that: (1) Those identified significant genomic aberrations could be important molecular determinants of the racial disparity in the corresponding grade of tumors; and (2) For patients within the same grade category, each of those aberrations may pose a larger impact on AAs (or EAs) than EAs (or AAs) depending on which racial group of a higher AICE. Lastly, AICEs are statistically significantly differentiated between AAs and EAs across all three grades of GS with respect to ERG fusions, somatic mutations in SPOP and ATM, BRCA2 germline mutation, and CNAs in ERG compared to other genomic aberrations. The details of all estimated race-specific AICEs and related statistics for different grades of GS are summarized in Supplementary Table S2.

FIGURE 4
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Figure 4. Box plots of six genomic-aberration specific average individual causal effects (AICEs) of African Americans (AAs) and European-Americans (EAs) in the primary data for different grades of Gleason Score (GS). The paired t-test with the significance level α = 0.05 is utilized for hypothesis testing, where the null hypothesis is “H = 0: genomic aberration-specific AICEs are not differentiated over racial groups” and the alternative hypothesis is “H = 1: genomic aberration-specific AICEs are differentiated over racial groups.” CI, confidence interval.

Genomic Risk Score-Based Assessment on the Primary Data

To further explore the impacts of the studied genomic aberrations at the population level regarding PCa metastasis, we report the genomic aberration-specific GRSs of EAs and AAs in the primary data w.r.t. different grades of GS in Figure 5, Supplementary Figure S2, and Supplementary Table S3. In fact, as shown by Supplementary Table S4, the race-specific GRS patterns that the genomic aberrations impact patients' GSs are quite similar to the race-specific patterns observed for AICEs. Please see the implications of such a similarity in the Discussion section.

FIGURE 5
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Figure 5. Box plots of six genomic aberration-specific genomic risk scores (GRSs) of African Americans (AAs) and European Americans (EAs) in the primary data for different grades of Gleason Score (GS). The paired t-test with the significance level α = 0.05 is utilized for hypothesis testing, where the null hypothesis is “H = 0: genomic aberration-specific GRSs are not differentiated over racial groups” and the alternative hypothesis is “H = 1: genomic aberration-specific GRSs are differentiated over racial groups.” CI, confidence interval.

Specifically, for low-grade patients, we also find that: (1) GRSs of AAs are statistically significantly higher than those of EAs on ERG fusions, somatic mutations in SPOP, FOXA1 and BRCA2, BRCA2 and BRCA1 germline mutations, and CNAs in ERG and FOXA1; (2) The GRS of EAs is statistically significantly higher than that of AAs only on somatic mutations in ATM; and (3) There is no statistically significant difference in GRSs of AAs and EAs for TP53 and PTEN mutations as well as LCP1 and PTEN CNAs. As to intermediate-grade patients, GRSs of EAs are also statistically significantly higher than those of AAs on ERG fusions, somatic mutations in SPOP, PTEN, ATM, and TP53, BRCA2 germline mutations, and CNAs in LCP1, ERG, and PTEN. There is no statistically significant difference in GRSs of AAs and EAs for BRCA2 mutations, BRCA1 germline mutations, and FOXA1 CNAs. Compared to the AICE patterns of this grade category, one difference is that the GRS of AAs is statistically significantly higher than that of EAs on somatic mutations in FOXA1. For high-grade patients, GRSs of AAs are statistically significantly higher than those of EAs on BRCA2 and FOXA1 somatic mutations and CNAs in FOXA1, while GRSs of EAs are statistically significantly higher than those of AAs on EGR fusions, somatic mutations in SPOP, PTEN, ATM, and TP53, and CNAs in ERG and LCP1. There is no statistically significant difference in GRSs of AAs and EAs for BRCA1 and BRCA2 germline mutations and CNAs in PTEN. Across all three grades of GS, GRSs are statistically significantly differentiated between AAs and EAs with respect to ERG fusions, somatic mutations in SPOP, FOXA1, and ATM, and CNAs in ERG compared to other genomic aberrations.

Validation of the Identified Race-Specific Genomic Aberrations

We further test our proposed method on the validation data containing 144 EAs and 22 AAs, where patients' racial information is inferred using the deep imputation method (25). Similarly, we compare the race-specific AICEs of the studied genomic aberrations for low-grade (GS ≤ 6), intermediate-grade (GS = 7), and high-grade (GS ≥ 8) EA and AA patients.

From Figure 6 and Supplementary Figure S3, we have the following observations. First, for low-grade patients, AICEs of AAs are statistically significantly higher than those of EAs on ERG fusions, somatic mutations in SPOP, FOXA1 and BRCA2, BRCA2 and BRCA1 germline mutations, and CNAs in ERG and FOXA1. AICEs of EAs are statistically significantly higher than those of AAs only on somatic mutations in ATM. There is no statistically significant difference in AICEs of AAs and EAs for TP53 and PTEN somatic mutations as well as LCP1 and PTEN CNAs. Second, regarding intermediate-grade patients, AICEs of EAs are statistically significantly higher than those of AAs on somatic mutations in TP53, ATM, and PTEN, BRCA2 germline mutation, and CNAs in LCP1, ERG, and PTEN. There is no statistically significant difference in AICEs of AAs and EAs for nearly one third of the studied genomic aberrations, i.e., somatic mutations in SPOP and FOXA1, BRCA1 germline mutations, and CNAs in FOXA1. Lastly, for high-grade patients, AICEs of EAs are statistically significantly higher than those of AAs on ERG fusions, SPOP, TP53, ATM, and PTEN somatic mutations, and CNAs in LCP1, ERG, and FOXA1, while AICEs of AAs are statistically significantly higher than those of EAs on somatic mutations in FOXA1 and BRCA2 and BRCA2 germline mutation. There is no statistically significant difference in AICEs of AAs and EAs for BRCA1 germline mutation and CNAs in PTEN. The details of all estimated race-specific AICEs and related statistics for different grades of GS using the validation data are summarized in Supplementary Table S5.

FIGURE 6
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Figure 6. Box plots of six genomic aberration-specific average individual causal effects (AICEs) of African Americans (AAs) and European Americans (EAs) in the validation data for different grades of Gleason Score (GS). The paired t-test with the significance level α = 0.05 is utilized for hypothesis testing, where the null hypothesis is “H = 0: genomic aberration-specific AICEs are not differentiated over racial groups” and the alternative hypothesis is “H = 1: genomic aberration-specific AICEs are differentiated over racial groups.” CI, confidence interval.

In addition, as shown by Supplementary Table S6, the race-specific AICE patterns obtained on the primary data are quite similar to those obtained on the validation data. Among 39 comparisons with respect to 13 genomic aberrations and three grades, there are only three differences. They are somatic mutations in SPOP and BRCA2 for intermediate-grade patients and CNAs in FOXA1 for high-grade patients. Over 92% consistency rate between race-specific AICE patterns obtained on the primary and independent validation data further demonstrates the efficacy and robust capability of DLVM in causal inference.

Discussion

Remarkable racial disparities have been reported in PCa incidence and mortality rates. In spite of these recognitions, precise mechanisms underlying these prevailing racial disparities remain poorly understood. Although socioeconomic factors play critical roles in such health disparities, increasing efforts have begun to explore molecular mechanisms in tumor biology and ancestry-related aspects that may be attributed to the observed PCa health disparities. However, most of these efforts are confined to expensive and time-consuming in vitro, in vivo, and population studies, where non-omics features and high-throughput multi-omics data cannot be well-integrated to infer potential race-specific causal biological determinants in an efficient and cost-effective manner.

To our knowledge, this is the first study to apply the machine learning approach (i.e., deep learning) to integratedly examine the personalized and race-specific causal effects that molecular aberrations may pose on classic PCa phenotypic risk factors (i.e., GS) via multi-omics and non-omics data. For 13 well-known molecular aberrations in PCa biology, we computationally explore their potentials as biological determinants of racial disparities in PCa via a novel DLVM and multiple population-level evaluation metrics (i.e., RMSEs, AICEs, and GRSs). By scrutinizing the TCGA PCa patients in different grades of GS and over all grades, we report race-specific AICEs, GRSs, related statistics, as well as the studied genomic aberrations that could contribute to PCa racial disparities. Some of the findings are consistent with what has been reported in the literature, which validates the results to a certain extent. For example, we find that for low-grade PCa, both AICEs and GRSs of AAs are statistically significantly higher than those of EAs over most of the studied genomic aberrations (i.e., ERG fusions, somatic mutations in SPOP, BRCA2, and FOXA1, germline mutations in BRCA2 and BRCA1, and CNAs in ERG and FOXA1). This indicates that AAs with low-grade PCa may suffer from higher tumor burdens and risks. As such, special care in addition to active surveillance should be given to AA men as they are more likely to die from low-grade PCa (34). This perception is consistent with the latest recommendations made by Mahal et al. (25, 35), National Cancer Institute (34), and Tsivian et al. (36).

Moreover, it is worth noting that the race-specific GRS patterns that the genomic aberrations affect patients' GSs highly resemble the race-specific patterns observed for AICEs. There are only two differences when these two sets of patterns are compared with respect to different grades of GS. One is that for intermediate-grade patients, AAs' GRS is statistically significantly higher than EAs' GRS on somatic mutations in FOXA1, while there is no statistically significant difference in AICEs of the two groups for the same aberration. The other is that for high-grade patients, AAs' AICE is statistically significantly higher than EAs' AICE on BRCA2 germline mutations, while there is no statistically significant difference in GRSs of the two groups for this alternation. Such a high similarity between these two result sets not only provides mutual verification but also indicates that the genomic aberrations directly identified as race-specific causal factors for PCa aggressiveness may also offer insights to PCa metastasis. We further compare the results obtained from AICEs and GRSs across patients in all three grades. We find that four shared genomic aberrations, ERG fusions, somatic mutations in SPOP and ATM, and CNAs in ERG, are the statistically significant genomic factors that may contribute to the disparities between these two groups. Some of these findings are largely consistent to the ethnic differences observed for ERG gene fusions and SPOP mutation (37, 38).

Compared to previous research, our study also leads to some new findings. For example, we find that: (1) for intermediate- and high-grade PCa, most of the studied aberrations (i.e., ERG fusions, somatic mutations in SPOP, TP53, ATM, and PTEN, CNAs in LCP1 and ERG) affect EAs more than AAs and (2) somatic mutations in ATM consistently impact EAs more over all three grades. In contrast to prior studies (11, 39), we do observe that somatic mutations in TP53 impacts intermediate- and high-grade patients, which is especially true for EAs. Part of this observation is consistent to the reported critical role of TP53 mutations in PCa tumor progression and metastasis (40, 41), which suggests that this gene might serve as a marker of disease aggressiveness and progression for PCa. All of these findings depict a small part of a complex picture of causal relations between race and tumor burden across the spectrum of PCa. Further efforts are warranted to validate the results and to enhance the capacity of the proposed deep model.

Due to some privacy and socioeconomic concerns of AA patients, most of the PCa data in the public domain belong to the European ancestry. To the best of our knowledge, the TCGA PRAD cohort is the only publicly available PCa dataset that contains a decent number of AA and EA patients with self-reported race/ethnicity as well as the matched multilevel genomic and clinical data. Those clinical and multi-omics data, especially the mutation profiles and gene expression values, are necessities for DLVM modeling. As a result, we carried out the model training on the primary data of 270 EA and 43 AA patients. Furthermore, an independent validation was performed on the corresponding data of 166 patients (including 144 EAs and 22 AAs), whose race/ethnicity was predicted by a deep imputation method (25). Over 92% consistency rate between the race-specific AICE patterns obtained on the primary and independent validation sets further demonstrates DLVM's ability in unbiasedly inferring the true causal effects between GS and an interested genomic aberration. As part of future work, we will impute PSA levels missing in the TCGA cohort using established methods so that our study can be extended to this widely used component of nearly all risk stratification methods for PCa. The co-effects of multiple alternations as the intervention will be further explored by coupling DLVM with some robust frequent pattern mining techniques (42, 43). Lastly, we will refine the proposed algorithm to take into account other variables, such as germline single-nucleotide polymorphisms (SNPs) and critical race-relevant socioeconomic and/or environmental factors in the modeling process for population-focused cancer research.

Conclusion

In this paper, we introduce the first deep learning-based approach (i.e., DLVM) to inferring the personalized and race-specific causal effects that genomic aberrations (i.e., gene fusions, somatic mutations, germline mutations, and CNAs) may exert on PCa aggressiveness (i.e., GS). As PCa disparity is a multifactorial construct, DLVM assumes that multiple confounders, observed and latent, influence the way that genomic aberrations affect a patient's GS. As such, by jointly learning multi-observational data of patients, DLVM is able to incorporate the potential influence of immeasurable confounders or latent variables (e.g., interactions among interested genes) in its inferences. Thorough empirical studies and multiple evaluation metrics on 313 TCGA primary PCa and 166 samples (i.e., 144 EAs and 22 AAs) in an independent validation set demonstrate the efficacies of DLVM in identifying significant genomic factors that may contribute to the molecular basis of PCa racial disparities. Findings obtained through this study, once further validated, will shed light on developing molecular markers of predictive and prognostic values and therapeutic targets for men of African or European descent.

Data Availability Statement

Publicly available datasets were analyzed in this study. This data can be found here: CBioPortal, Prostate Adenocarcinoma (TCGA, Cell 2015).

Author Contributions

ZC and KZ designed the experiments with help from AE and CH. ZC performed the experiments. ZC and KZ analyzed the data. KZ, ZC, AE, and CH wrote the paper. KZ conceived and supervised this study. All the authors read and approved the final manuscript.

Funding

This work was partly supported by funding from the National Institutes of Health (NIH) grants 2U54MD007595, 5P20GM103424, P01CA214091, and U19AG055373. The contents are solely the responsibility of the authors and do not necessarily represent the official views of the NIH.

Conflict of Interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Supplementary Material

The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fonc.2020.00272/full#supplementary-material

Footnotes

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Keywords: deep latent variable model, causal effect inference, prostate cancer, racial disparity, genomic aberrations, Gleason scores

Citation: Chen Z, Edwards A, Hicks C and Zhang K (2020) Inferring Personalized and Race-Specific Causal Effects of Genomic Aberrations on Gleason Scores: A Deep Latent Variable Model. Front. Oncol. 10:272. doi: 10.3389/fonc.2020.00272

Received: 20 October 2019; Accepted: 17 February 2020;
Published: 13 March 2020.

Edited by:

Guangwen Cao, Second Military Medical University, China

Reviewed by:

Ahmed Abdalla Agab Eldour, Kordofan University, South Sudan
Hong-Wei Zhang, Second Military Medical University, China
Jianhua Yin, Second Military Medical University, China

Copyright © 2020 Chen, Edwards, Hicks and Zhang. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

*Correspondence: Kun Zhang, kzhang@xula.edu