Identification and Validation of a Prognostic Prediction Model in Diffuse Large B-Cell Lymphoma

Artificial intelligence-based prognostic model accurately predicts the survival of patients with diffuse large B-cell lymphomas: analysis of a large cohort in China

BACKGROUND

Diffuse large B-cell lymphomas (DLBCLs) display high molecular heterogeneity, but the International Prognostic Index (IPI) considers only clinical indicators and has not been updated to include molecular data. Therefore, we developed a widely applicable novel scoring system with molecular indicators screened by artificial intelligence (AI) that achieves accurate prognostic stratification and promotes individualized treatments.

METHODS

We retrospectively enrolled a cohort of 401 patients with DLBCL from our hospital, covering the period from January 2015 to January 2019. We included 22 variables in our analysis and assigned them weights using the random survival forest method to establish a new predictive model combining bidirectional long-short term memory (Bi-LSTM) and logistic hazard techniques. We compared the predictive performance of our "molecular-contained prognostic model" (McPM) and the IPI. In addition, we developed a simplified version of the McPM (sMcPM) to enhance its practical applicability in clinical settings. We also demonstrated the improved risk stratification capabilities of the sMcPM.

RESULTS

Our McPM showed superior predictive accuracy, as indicated by its high C-index and low integrated Brier score (IBS), for both overall survival (OS) and progression-free survival (PFS). The overall performance of the McPM was also better than that of the IPI based on receiver operating characteristic (ROC) curve fitting. We selected five key indicators, including extranodal involvement sites, lactate dehydrogenase (LDH), MYC gene status, absolute monocyte count (AMC), and platelet count (PLT) to establish the sMcPM, which is more suitable for clinical applications. The sMcPM showed similar OS results (P < 0.0001 for both) to the IPI and significantly better PFS stratification results (P < 0.0001 for sMcPM vs. P = 0.44 for IPI).

CONCLUSIONS

Our new McPM, including both clinical and molecular variables, showed superior overall stratification performance to the IPI, rendering it more suitable for the molecular era. Moreover, our sMcPM may become a widely used and effective stratification tool to guide individual precision treatments and drive new drug development.

Should we use nomograms for risk predictions in diffuse large B cell lymphoma patients? A systematic review

Models based on risk stratification are increasingly reported for Diffuse large B cell lymphoma (DLBCL). Due to a rising interest in nomograms for cancer patients, we aimed to review and critically appraise prognostic models based on nomograms in DLBCL patients. A literature search in PubMed/Embase identified 59 articles that proposed prognostic models for DLBCL by combining parameters of interest (e.g., clinical, laboratory, immunohistochemical, and genetic) between January 2000 and 2024. Of them, 40 studies proposed different gene expression signatures and incorporated them into nomogram-based prognostic models. Although most studies assessed discrimination and calibration when developing the model, many lacked external validation. Current nomogram-based models for DLBCL are mainly developed from publicly available databases, lack external validation, and have no applicability in clinical practice. However, they may be helpful in individual patient counseling, although careful considerations should be made regarding model development due to possible limitations when choosing nomograms for prognostication.

Genetic and transcriptomic analyses of diffuse large B-cell lymphoma patients with poor outcomes within two years of diagnosis

Despite the improvements in clinical outcomes for DLBCL, a significant proportion of patients still face challenges with refractory/relapsed (R/R) disease after receiving first-line R-CHOP treatment. To further elucidate the underlying mechanism of R/R disease and to develop methods for identifying patients at risk of early disease progression, we integrated clinical, genetic and transcriptomic data derived from 2805 R-CHOP-treated patients from seven independent cohorts. Among these, 887 patients exhibited R/R disease within two years (poor outcome), and 1918 patients remained in remission at two years (good outcome). Our analysis identified four preferentially mutated genes (TP53, MYD88, SPEN, MYC) in the untreated (diagnostic) tumor samples from patients with poor outcomes. Furthermore, transcriptomic analysis revealed a distinct gene expression pattern linked to poor outcomes, affecting pathways involved in cell adhesion/migration, T-cell activation/regulation, PI3K, and NF-κB signaling. Moreover, we developed and validated a 24-gene expression score as an independent prognostic predictor for treatment outcomes. This score also demonstrated efficacy in further stratifying high-risk patients when integrated with existing genetic or cell-of-origin subtypes, including the unclassified cases in these models. Finally, based on these findings, we developed an online analysis tool ( https://lymphprog.serve.scilifelab.se/app/lymphprog ) that can be used for prognostic prediction for DLBCL patients.

SurvIAE: Survival prediction with Interpretable Autoencoders from Diffuse Large B-Cells Lymphoma gene expression data

BACKGROUND

In Diffuse Large B-Cell Lymphoma (DLBCL), several methodologies are emerging to derive novel biomarkers to be incorporated in the risk assessment. We realized a pipeline that relies on autoencoders (AE) and Explainable Artificial Intelligence (XAI) to stratify prognosis and derive a gene-based signature.

METHODS

AE was exploited to learn an unsupervised representation of the gene expression (GE) from three publicly available datasets, each with its own technology. Multi-layer perceptron (MLP) was used to classify prognosis from latent representation. GE data were preprocessed as normalized, scaled, and standardized. Four different AE architectures (Large, Medium, Small and Extra Small) were compared to find the most suitable for GE data. The joint AE-MLP classified patients on six different outcomes: overall survival at 12, 36, 60 months and progression-free survival (PFS) at 12, 36, 60 months. XAI techniques were used to derive a gene-based signature aimed at refining the Revised International Prognostic Index (R-IPI) risk, which was validated in a fourth independent publicly available dataset. We named our tool SurvIAE: Survival prediction with Interpretable AE.

RESULTS

From the latent space of AEs, we observed that scaled and standardized data reduced the batch effect. SurvIAE models outperformed R-IPI with Matthews Correlation Coefficient up to 0.42 vs. 0.18 for the validation-set (PFS36) and to 0.30 vs. 0.19 for the test-set (PFS60). We selected the SurvIAE-Small-PFS36 as the best model and, from its gene signature, we stratified patients in three risk groups: R-IPI Poor patients with High levels of GAB1, R-IPI Poor patients with Low levels of GAB1 or R-IPI Good/Very Good patients with Low levels of GPR132, and R-IPI Good/Very Good patients with High levels of GPR132.

CONCLUSIONS

SurvIAE showed the potential to derive a gene signature with translational purpose in DLBCL. The pipeline was made publicly available and can be reused for other pathologies.

Development and validation of nomogram prognostic model for predicting OS in patients with diffuse large B-cell lymphoma: a cohort study in China

This study comprehensively incorporates pathological parameters and novel clinical prognostic factors from the international prognostic index (IPI) to develop a nomogram prognostic model for overall survival in patients with diffuse large B-cell lymphoma (DLBCL). The aim is to facilitate personalized treatment and management strategies. This study enrolled a total of 783 cases for analysis. LASSO regression and stepwise multivariate COX regression were employed to identify significant variables and build a nomogram model. The calibration curve, receiver operating characteristic (ROC) curve, and decision curve analysis (DCA) curve were utilized to assess the model's performance and effectiveness. Additionally, the time-dependent concordance index (C-index) and time-dependent area under the ROC curve (AUC) were computed to validate the model's stability across different time points. The study utilized 8 selected clinical features as predictors to develop a nomogram model for predicting the overall survival of DLBCL patients. The model exhibited robust generalization ability with an AUC exceeding 0.7 at 1, 3, and 5 years. The calibration curve displayed evenly distributed points on both sides of the diagonal, and the slopes of the three calibration curves were close to 1 and statistically significant, indicating high prediction accuracy of the model. Furthermore, the model demonstrated valuable clinical significance and holds the potential for widespread adoption in clinical practice. The novel prognostic model developed for DLBCL patients incorporates readily accessible clinical parameters, resulting in significantly enhanced prediction accuracy and performance. Moreover, the study's use of a continuous general cohort, as opposed to clinical trials, makes it more representative of the broader lymphoma patient population, thus increasing its applicability in routine clinical care.

Identification of lactate regulation pattern on tumor immune infiltration, therapy response, and DNA methylation in diffuse large B-cell lymphoma

Background

Lactate, produced through glycolytic metabolism in the tumor microenvironment (TME), is implicated in tumorigenesis and progression in diverse cancers. However, the impact of lactate on the remodeling of the TME in diffuse large B-cell lymphoma (DLBCL) and its implications for therapy options remain unclear.

Method

A lactate-related (LAR) scoring model was constructed in DLBCL patients using bioinformatic methods. CIBERSORT, XCELL, and ssGSEA algorithms were used to determine the correlation between LAR score and immune cell infiltration. Tumor Immune Dysfunction and Exclusion (TIDE), rituximab, cyclophosphamide, adriamycin, vincristine, and prednisone (R-CHOP) cohorts, and Genomics of Drug Sensitivity in Cancer (GDSC) were utilized to predict the therapeutic response of DLBCL patients. The impact of the hub gene STAT4 on tumor biological behavior and DNA methylation was experimentally validated or accessed by the TSIDE database.

Results

The LAR scoring model was developed based on 20 prognosis-related lactate genes, which enabled the division of DLBCL patients into high- and low-risk groups based on the median LAR score. Patients with high-risk DLBCL exhibited significantly worse survival outcomes in both the training cohorts (GSE181063) and the validation cohorts (GSE10846, GSE32918, and GSE69053), as indicated by statistically significant differences (all P<0.05) and area under the curve (AUC) values exceeding 0.6. Immune analyses revealed that low-risk DLBCL patients had higher levels of immune cell infiltration and antitumor immune activation compared to high-risk DLBCL patients. Furthermore, DLBCL patients with high LAR scores were associated with a lower TIDE value and poor therapeutic efficacy of the R-CHOP regimen. GDSC analysis identified 18 drugs that exhibited significant response sensitivity in low-risk DLBCL patients. Moreover, in vitro experiments demonstrated that overexpression of the lactate key gene STAT4 could suppress proliferation and migration, induce cell cycle arrest, and promote cell apoptosis in DLBCL cells. Transcriptional expression and methylation of the STAT4 gene were found to be associated with immunomodulators and chemokines.

Conclusion

The lactate-based gene signature effectively predicts the prognosis and regulates TME in DLBCL. Our study underscores the role of lactate gene, STAT4, as an important tumor suppressor in DLBCL. Modulating STAT4 could be a promising strategy for DLBCL in clinical practice.