|J Pathol Inform 2019,
Multi-field-of-view deep learning model predicts nonsmall cell lung cancer programmed death-ligand 1 status from whole-slide hematoxylin and eosin images
Lingdao Sha1, Boleslaw L Osinski1, Irvin Y Ho1, Timothy L Tan2, Caleb Willis1, Hannah Weiss3, Nike Beaubier1, Brett M Mahon1, Tim J Taxter1, Stephen S F Yip1
1 Tempus Labs, Inc, Chicago, IL, USA
2 Tempus Labs, Inc; Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
3 Tempus Labs, Inc; Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
|Date of Submission||26-Apr-2019|
|Date of Acceptance||06-Jun-2019|
|Date of Web Publication||23-Jul-2019|
Dr. Stephen S F Yip
Tempus Labs, Inc., 600 West Chicago Ave. Ste 510, Chicago, IL 60608
Source of Support: None, Conflict of Interest: None
| Abstract|| |
Background: Tumor programmed death-ligand 1 (PD-L1) status is useful in determining which patients may benefit from programmed death-1 (PD-1)/PD-L1 inhibitors. However, little is known about the association between PD-L1 status and tumor histopathological patterns. Using deep learning, we predicted PD-L1 status from hematoxylin and eosin (H and E) whole-slide images (WSIs) of nonsmall cell lung cancer (NSCLC) tumor samples. Materials and Methods: One hundred and thirty NSCLC patients were randomly assigned to training (n = 48) or test (n = 82) cohorts. A pair of H and E and PD-L1-immunostained WSIs was obtained for each patient. A pathologist annotated PD-L1 positive and negative tumor regions on the training samples using immunostained WSIs for reference. From the H and E WSIs, over 145,000 training tiles were generated and used to train a multi-field-of-view deep learning model with a residual neural network backbone. Results: The trained model accurately predicted tumor PD-L1 status on the held-out test cohort of H and E WSIs, which was balanced for PD-L1 status (area under the receiver operating characteristic curve [AUC] =0.80, P << 0.01). The model remained effective over a range of PD-L1 cutoff thresholds (AUC = 0.67–0.81, P ≤ 0.01) and when different proportions of the labels were randomly shuffled to simulate interpathologist disagreement (AUC = 0.63–0.77, P ≤ 0.03). Conclusions: A robust deep learning model was developed to predict tumor PD-L1 status from H and E WSIs in NSCLC. These results suggest that PD-L1 expression is correlated with the morphological features of the tumor microenvironment.
Keywords: Artificial intelligence, deep learning, digital pathology, lung cancer
|How to cite this article:|
Sha L, Osinski BL, Ho IY, Tan TL, Willis C, Weiss H, Beaubier N, Mahon BM, Taxter TJ, Yip SS. Multi-field-of-view deep learning model predicts nonsmall cell lung cancer programmed death-ligand 1 status from whole-slide hematoxylin and eosin images. J Pathol Inform 2019;10:24
|How to cite this URL:|
Sha L, Osinski BL, Ho IY, Tan TL, Willis C, Weiss H, Beaubier N, Mahon BM, Taxter TJ, Yip SS. Multi-field-of-view deep learning model predicts nonsmall cell lung cancer programmed death-ligand 1 status from whole-slide hematoxylin and eosin images. J Pathol Inform [serial online] 2019 [cited 2021 May 8];10:24. Available from: https://www.jpathinformatics.org/text.asp?2019/10/1/24/263339
| Introduction|| |
Nonsmall cell lung cancer (NSCLC) is the most common type of lung cancer, affecting over 1.5 million people worldwide. The disease often responds poorly to standard of care chemoradiotherapy and has a high incidence of recurrence, resulting in low 5-year survival rates.,, Advances in immunology showed that NSCLC frequently elevates the expression of programmed death-ligand 1 (PD-L1) to bind to programmed death-1 (PD-1) expressed on the surface of T-cells., PD-1 and PD-L1 binding deactivates T-cell antitumor responses, enabling NSCLC to evade targeting by the immune system. The discovery of the interplay between tumor progression and immune response has led to the development and regulatory approval of PD-1/PD-L1 checkpoint blockade immunotherapies such as nivolumab and pembrolizumab.,, Anti-PD-1 and anti-PD-L1 antibodies restore antitumor immune response by disrupting the interaction between PD-1 and PD-L1. Notably, PD-L1-positive NSCLC patients treated with these checkpoint inhibitors achieve durable tumor regression and improved survival.,,,,
As the role of immunotherapy in oncology expands, it is useful to accurately assess tumor PD-L1 status to identify patients who may benefit from PD-1/PD-L1 checkpoint blockade immunotherapy. Immunohistochemistry (IHC) staining of tumor tissues acquired from biopsy or surgical specimens is commonly employed to assess PD-L1 status.,, However, IHC staining can be limited by insufficient tissue samples, and in some settings, a lack of resources.,
Hematoxylin and eosin (H and E ) staining is fundamental to analyzing tissue morphological features for malignancy diagnosis, including NSCLC., Furthermore, H and E slides may capture tissue visual characteristics that are associated with PD-L1 status. For example, Velcheti et al. and McLaughlin et al. both observed that PD-L1 positive NSCLC tended to have higher levels of tumor-infiltrating lymphocytes (TILs)., However, quantification of TILs using H and E slides is laborious and affected by interobserver variability., Moreover, TILs may be inadequate to fully describe the complexity of the tumor microenvironment and its relationship with PD-L1 status.
Technological advances have enabled the digitization of histopathology H and E and IHC slides into high-resolution whole-slide images (WSIs), providing opportunities to develop computer vision tools for a wide range of clinical applications.,, Recently, deep learning applications to pathology images have shown tremendous promise in predicting treatment outcomes, disease subtypes,, lymph node status,, and genetic characteristics,, in various malignancies. Deep learning is a subset of machine learning wherein models are built with a number of discrete neural node layers, imitating the structure of the human brain. These models learn to recognize complex visual features from WSIs by iteratively updating the weighting of each neural node based on the training examples. To our knowledge, deep learning has never been applied to predicting PD-L1 status from H and E imaging features in NSCLC patients.
Here, we hypothesized that morphological changes to the NSCLC microenvironment associated with elevated PD-L1 expression can be recognized by deep learning. Our results may aid the further development of H and E -based imaging biomarkers that complement clinical IHC testing for tumor PD-L1 status.
| Materials and Methods|| |
The tissue samples and patient-related health information used in the study that is described in the manuscript were deidentified. All digital images and clinical data related to the tumor tissues were also anonymized.
Programmed death-ligand 1 immunohistochemistry assay
A total of 130 deidentified, archival formalin-fixed, paraffin-embedded (FFPE) tumor tissues (1 tissue sample/patient) from NSCLC patients were used in this study. All the FFPE blocks were processed, reviewed, and stored in a College of American Pathologists (CAP) accredited and Clinical Laboratory Improvement Amendments (CLIA) certified laboratory (Tempus Labs Chicago, IL, USA).
Each FFPE block was cut into 4 μm-thick serial sections for H and E and IHC stains. H and E staining was performed on the Leica Autostainer XL staining platform. The sections were stained with H and E and anti-PD-L1 (clone 22c3, pharmDx Kit Dako) using an automated staining system (BOND-III: Leica Microsystems). IHC slides were stained with anti-PD-L1 22C3 monoclonal mouse primary antibody using the Bond Polymer Refine detection system on a Leica Microsystems BOND-III with positive and negative cell line run controls.
Assessment of programmed death-ligand 1 expression
The level of PD-L1 expression, referred to as tumor PD-L1 score or tumor proportion score, was defined as the number of partially or completely stained tumor cells at any intensity divided by the total number of tumor cells. In accordance with the Food and Drug Administration (FDA) documents, a tumor tissue was considered to have a PD-L1 positive (PD-L1+) status if its expression level was >1%., Tumor tissue with a PD-L1 expression level ≤1% was considered PD-L1 negative (PD-L1−). One of three CAP-CLIA certified laboratory pathologists (N.B., B.M., or T.J.T.) reviewed IHC-stained slides and scored the level of PD-L1 expression.
A total of 130 H and E and their corresponding PD-L1 IHC slides were scanned and digitized at a resolution of 0.25 μm/pixel (40× magnification) using a Philips Ultra Fast Scanner (Philips, Eindhoven, The Netherlands). The images were initially acquired in the iSyntax format and then converted to the tagged image format file (TIFF) format using Philips' proprietary algorithm. Eighty-two of these WSIs were randomly chosen as an independent test cohort. To ensure a balanced test cohort (i.e., 41 PD-L1+ and 41 PD-L1−), these slides were equally sampled from tumor PD-L1+ and PD-L1− cases [Table 1]. The remaining 48 were used as a training cohort to train our deep learning architecture [Figure 1]a and [Figure 1]b.
|Figure 1: (a) Network architecture: Our deep learning framework consists of a fully convolutional ResNet-18 that processes a large field of view, along with two additional branches that process small field of views. The ResNet-18 backbone contains multiple shortcut connections. The dotted lines indicate shortcut connections where feature maps are also downsampled by 2. The small field-of-view branches emerge after the second convolutional block. The feature maps of the small field-of-view branches are downsampled by 8 to match the dimensions of the ResNet-18 feature map. These feature maps are concatenated before passing through a softmax output to produce a programmed death-ligand 1 staining probability map. (b) Model training: matching areas on Immunohistochemistry and H and E slides were annotated. The annotated regions of the H and E image were tiled into overlapping tiles (466 × 466 pixels) with a stride of 32 pixels, producing our training data. The multi-field-of-view ResNet-18 model was then trained using a cross-entropy loss function. The yellow square in the model schematic depicts the central region that is cropped for the small field of views. (c) Model inference: each image was divided into large nonoverlapping 4096 × 4096 input windows (blue dashed lines). Each large window was passed through the trained model. Because the model is fully convolutional, each tile within the large input window was processed in parallel, producing a 128 × 128 × 3 probability cube (the last dimension represents three classes). The resulting probability cubes were slotted into place and assembled to generate a probability map of the whole image. The class with the maximum probability was assigned to each tile|
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Training example generation
In the training cohort, PD-L1+ and PD-L1− tumor regions of IHC slides were manually annotated by a pathologist (T.L.T.). Annotations were made using the publicly-available digital pathology software QuPath. Then, using the IHC annotations as a reference, matching areas on the corresponding H and E slides were annotated [Figure 1]b. In total, three classes (i.e., tumor PD-L1+, tumor PD-L1−, and other) were annotated on the H and E slides. Nontumor regions on the H and E slides, such as stroma, necrosis, and normal epithelium, were annotated as a single “other” class.
The annotated regions were tiled into overlapping tiles (466 × 466 pixels) with a stride of 32 pixels at 10× magnification (1 pixel = 1 μm). Only tiles whose center fell within the annotated regions were kept. The tile size was chosen to provide spatial context to the network, while the stride was chosen to increase sampling density and the number of training examples. This procedure produced 107,854 PD-L1+ and 57,837 PD-L1− tiles.
Deep learning architecture
Our deep learning architecture is composed of three major components: (1) a fully convolutional residual neural network (ResNet) backbone that processes a large 466 × 466 field of view (FOV), (2) two branches that process 32 × 32 small FOVs, and (3) concatenation of small and large FOV features for multi-FOV classification [Figure 1].
We chose ResNet because it overcomes the accuracy degradation challenges traditionally suffered by “very deep” neural networks (i.e., neural networks with more than 16 convolutional layers)., ResNet consists of a stack of convolutional layers interleaved with “shortcut connections” which skip intermediate layers [Figure 1]a. These connections use earlier layers as a reference point to guide deeper layers to learn the residual between layer outputs rather than learning an identity mapping between layers. This innovation improves convergence speed and stability during training and allows deeper networks to perform better than their shallower counterparts.
The backbone of our model consisted of an 18-layer version of ResNet (ResNet-18) with some modifications. The ResNet-18 backbone was converted into a fully convolutional network (FCN) by removing the global average pooling layer and eliminating zero padding in downsampled layers. This enables the output of a two-dimensional probability map rather than a one-dimensional probability vector [Figure 1]c. The tile size (466 × 466 pixels) is over twice the tile size of a standard ResNet, providing our model with a larger FOV that allows it to learn surrounding morphological features.
The model includes two additional branches with receptive fields restricted to a small FOV (32 × 32 pixels) in the center of the second convolutional feature map [Figure 1]b. One branch passes a copy of the small FOV through a convolutional filter, while the other branch is a standard shortcut connection with downsampling. The features produced by these additional branches are concatenated to the features from the main backbone just before the model outputs are converted into probabilities in the softmax layer. In this way, the model combines information from multiple FOVs, much like a pathologist relies on various zoom levels when diagnosing slides; our implementation ensures that the central region of each tile contributes more to classification than the tile edges, resulting in a more accurate classification map across the entire WSI.
Our model was implemented using PyTorch and trained on an NVIDIA Tesla V100 GPU by stochastic gradient descent with a batch size of 100. The ResNet-18 backbone was initialized with pretrained ImageNet weights. Image augmentations, including random crop, random rotation, random flip, and color jitter, were performed batchwise during training. Batch normalization, where each layer is independently normalized by subtracting the mean and dividing by the standard deviation (SD) of each training batch, was also implemented to accelerate training, improve network stability, and reduce overfitting. We used a cross-entropy loss function with the Adam optimizer and an initial learning rate of 0.001, which was decreased by 50% at epochs 3, 5, 7, and 9. Twenty percentage of training tiles were randomly reserved for a validation set to monitor validation accuracy during training. The model was trained with 10 epochs, at which point validation loss no longer decreased.
Inference on unseen WSIs was performed in three stages: (1) division of the image into large input windows consisting of many overlapping tiles, (2) simultaneous classification of all tiles within each input window using the trained fully-convolutional deep learning model, and (3) Computation of model score by aggregating tile classifications.
Since the tiles are 466 × 466 pixels large with a stride of only 32 pixels, they overlap significantly. While this overlap ensures that the resulting WSI classification map is smooth, it also represents a substantial potential for computational redundancy, as the convolutional features computed for overlapping regions will be identical. A single WSI can be over 5GB, with ≥1010 pixels and hundreds of thousands of tiles. To reduce this redundant computation, we took advantage of the fully convolutional nature of our model [Figure 1]c. Instead of using 466 × 466 pixel tiles as the model input, we used much larger 4096 × 4096 pixels input windows. The FCN treats the large input window as an array of tiles and computes their features simultaneously. Consequently, many of the convolutional features computed for a single tile are reused for neighboring tiles, enabling efficient computation.
Processing all tiles in this fashion produces a 2D probability map of the three classes (i.e., tumor PD-L1+, tumor PD-L1−, and other) for each tile in the image. The class with the highest probability is assigned to each tile. The model score is then calculated as the ratio of the number of predicted tumor PD-L1+ tiles to the total number of predicted tumor tiles (both tumor PD-L1+ and tumor PD-L1−). The model score ranged from 0% to 100%, where 0% implies no tumor tiles are predicted to be PD-L1+ and 100% implies all tumor tiles are predicted to be PD-L1+.
Statistical analysis with an independent test cohort
Two analyses were performed to evaluate prediction of PD-L1 status based on H and E images alone. Both analyses were performed on the 82 “unseen” test cases that were held out from the model during training. In the first analysis, we assessed whether the average model score of the predicted PD-L1+ group was significantly greater than the PD-L1− group using the Welch's t-test (considered significant if Pt-test< 0.05). Average model score was defined as the score averaged over all patients within the group. For example, in the PD-L1+ group, the average model score was equal to the sum of each patient's model score divided by 42 (i.e., the total number of patients in the PD-L1+ group).
Second, the area under the receiver operating characteristic curve (AUC) was employed to quantify the power of the deep learning model score in predicting tumor PD-L1 status. A permutation test was implemented to assess if AUC was significantly different from random chance. In the permutation test, all PD-L1 labels of the test cohort were randomized 3000 times. A new AUC (AUCnew) was computed each time the label was randomized. AUC was considered to be significantly different from random if AUCnew ≥AUC <5% of the time (i.e., Ppermutation <0.05). We reported Ppermutation<<0.01 if none of the AUCnew ≥AUC.
Both analyses were also performed independently on adenocarcinoma and squamous cell carcinoma (SCC) cases.
The robustness of our model was examined by testing the impact of different PD-L1 positivity cutoffs and shuffled PD-L1 statuses.
Programmed death-ligand 1 cutoff variation
The effect of changing the PD-L1 positivity cutoff on model predictions was investigated. For example, if the PD-L1 expression cutoff was set to 15%, a tumor tissue was only considered to be PD-L1+ if over 15% of the tumor cells were stained. The default cutoff in the test cohort was chosen to be 1% as aforementioned. Here, the cutoff was varied from 5% to 50% in increments of 5% and the AUC was computed for each cutoff.
Programmed death-ligand 1 label shuffle
To simulate the effect of pathologist variability, 5%–30% of the PD-L1 status labels in the test cohort were randomly shuffled in increments of 5%. Each shuffle was repeated 3000 times. The AUC was calculated for each repetition, and the permutation test assessed whether the average AUC (over 3000 repetitions) was significant.
| Results|| |
This study assessed the ability of our deep learning model to predict PD-L1 status from H and E images in 82 independent test cases. Most patients (>70%) in the test cohort had adenocarcinoma and were former/current smokers [Table 1]. Approximately half of the patients were female. Of all patients, 54% (44/82) and 38% (31/82) were overall Stage I/II and Stage III/IV, respectively. However, stage information was unavailable for 8% (7/82) patients. The test cohort was perfectly balanced, consisting of 50% (41/82) PD-L1+ and 50% (41/82) PD-L1− cases to prevent bias in our model evaluation.
The test WSIs ranged in size from 500MB to 5GB and measured 10,000–200,000 pixels in each dimension. The average computation time to generate a PD-L1 probability map was 40 s (7.9–66 s) on an AWS EC2 p3.2× large instance (NVIDIA V100, Intel Xeon E5-2686).
For PD-L1+ slides, the location of tissue regions with high predicted PD-L1+ probability typically corresponded to the location of observed PD-L1 IHC expression [Figure 2]a, [Figure 2]b, [Figure 2]c. For PD-L1− slides, most of the slide area was usually predicted to be tumor PD-L1− or other, with only a few sparse areas predicted to be tumor PD-L1+ [Figure 2]d, [Figure 2]e, [Figure 2]f. For all NSCLC test cases, the average deep learning model score for PD-L1+ WSIs (26% ±24%) was significantly greater than that for PD-L1− WSIs (6.5%±9.7%) with Pt-test = 4.01 × 10− 7. As observed in [Figure 3], the model score significantly separated PD-L1+ samples from PD-L1− samples. The deep learning model significantly predicted PD-L1 status in all test cases with an AUC of 0.80 (Ppermutation<<0.01).
|Figure 2: Top row: representative positive case (a) H and E whole-slide image, (b) probability map overlaid on H and E, and (c) programmed death-ligand 1 immunohistochemistry stain. Bottom row: representative negative case (d) H and E whole-slide image, (e) probability map overlaid on H and E, and (f) programmed death-ligand 1 immunohistochemistry stain. The color bar indicates the predicted probability of the tumor programmed death-ligand 1 + class. The outline marked in A and B is a laboratory remnant and unrelated to the model|
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|Figure 3: Test cohort results. Top row: Box plots depicting how tumor programmed death-ligand 1 statuses are separated by deep learning model score in (a) all nonsmall cell lung cancer, (b) lung adenocarcinoma, (c) lung squamous cell carcinoma. Bottom row: Receiver operating characteristic curve for (d) all nonsmall cell lung cancer, (e) adenocarcinoma, and (f) squamous cell carcinoma. The horizontal line indicates median|
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The analysis was also performed independently for the two NSCLC subtypes, lung adenocarcinoma and lung SCC. The model scores were greater for PD-L1+ than PD-L1− cases in both subtypes [Figure 3]b, [Figure 3]c. The model score was observed to significantly discriminate PD-L1+ adenocarcinomas from PD-L1− adenocarcinomas (average model score = 28% ±25% vs. 5.3% ±7.5%) with Pt-test = 1.6 × 10− 6 and AUC = 0.83 (Ppermutation<<0.01). On the other hand, PD-L1+ SCC and PD-L1− SCC were not significantly discriminated by the model score in SCC (Pt-test= 0.32, AUC = 0.64, Ppermutation = 0.18). The average model score was 23% ±27% and 10% ±14% for PD-L1+ SCC and PD-L1− SCC, respectively.
Programmed death-ligand 1 cutoff variation
The impact of the PD-L1 positivity cutoff on the robustness of our model's predictive power was investigated. The AUCs varied moderately between 0.81 and 0.67 (Ppermutation ≤ 0.01) as the cutoff threshold used to determine positive PD-L1 status increased from 5% to 50% [Figure 4]a. Notably, the model score significantly separated PD-L1+ samples from PD-L1− samples for all cutoffs with Pt-test ≤ 0.03.
|Figure 4: (a) Area under the receiver operating characteristic curve as a function of the programmed death-ligand 1 positivity cutoffs (b) area under the receiver operating characteristic curve as a function of the percentage of shuffled programmed death-ligand 1 labels|
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Programmed death-ligand 1 label shuffle
The effect of interpathologist variability on the model was simulated by shuffling PD-L1 status label. The average AUC decreased steadily from 0.77 ± 0.02 to 0.63 ± 0.05 as 5% (4/82) to 30% (25/82) of the labels were randomly shuffled [Figure 4]b. The overall SDs of the average AUC ranged from 0.02 to 0.08. All of the averaged AUCs were significant (Ppermutation ≤ 0.03).
| Discussion|| |
In this study, we developed and trained a deep learning model to recognize H and E imaging patterns for tumor PD-L1 status prediction in NSCLC. During training, our model was presented with over 145,000 examples to learn H and E image characteristics of PD-L1+ and PD-L1− tissue. The trained model reliably predicted PD-L1 status in the “unseen” test cohort (AUC = 0.80). Using ResNet18 as the backbone, our trained multi-FOV deep learning model reliably predicted PD-L1 status in the “unseen” test cohort (AUC = 0.80). Other architectures, such as ResNet 50, have been shown to outperform ResNet18 in image classification tasks. Replacing our deep learning model backbone with other existing architectures (e.g., ResNet50, Inception v3) may further improve the ability of deep learning to predict PD-L1 status in NSCLC. The effect of backbone architecture on performance needs to be further investigated.
A convolutional neural network like our model learns a series of features to classify images. These features can be subtle and imperceptible to the naked eye. This method is distinct from previous studies that sought to recognize associations between tumor PD-L1 status and specific pathologist-defined features. For example, an increased density of TILs has been associated with PD-L1+ status in multiple malignancies.,,, However, manual quantification of TILs on WSIs is subjective and time-consuming. Furthermore, the microenvironment driven by the interaction between a tumor and the immune system is highly complex, and therefore, high levels of TILs and PD-L1 expression may not always co-occur. Thus, a deep learning model that directly predicts PD-L1 status from imaging may represent a more holistic approach. Future work should investigate the relationship between TIL density and the deep learning features that are important for PD-L1 prediction.
Our deep learning model predicted PD-L1 status in lung adenocarcinoma better than in lung SCC. Model score was significantly predictive in the adenocarcinoma subtype (AUC ≈ 0.85, Ppermutation<<0.01), but not in the SCC subtype (AUC = 0.64, Ppermutation = 0.18). In SCC, the model score was higher for PD-L1+ samples than PD-L1− samples [Figure 3]c and [Figure 3]f, although the separation was not statistically significant (Pt-test> 0.05). The training cohort only contained 10 SCC cases (and 37 adenocarcinoma cases), which might been insufficient for the model to reliably identify subtle features associated with SCC PD-L1 status. A larger dataset with more SCC training examples could improve model performance.
The model performed well regardless of the specified PD-L1 positivity cutoff value. PD-L1 protein levels expressed by NSCLC tumors exist on a spectrum. There is currently no consensus on a cutoff value to define PD-L1 positivity, resulting in a wide range of PD-L1 expression level cutoffs in clinical practice and trials.,,, For example, pembrolizumab was approved by the FDA as a single agent for metastatic NSCLC patients with tumor PD-L1 ≥1% who failed platinum-based chemotherapy. However, PD-L1 expression cutoffs of ≥1%, ≥5%, and ≥10% were used in a Phase III clinical trial of NSCLC patients treated with nivolumab, which revealed that higher levels of PD-L1 expression are associated with greater efficacy of nivolumab. Due to the discrepancy in these definitions of PD-L1 positivity, we conducted a sensitivity study to evaluate the impact of varying PD-L1 cutoffs on the model's ability to predict PD-L1 status. Adjusting the PD-L1 expression cutoffs from 5% to 50% had a moderate effect on the results with an AUC of 0.81 and 0.67, respectively. Despite this effect, a permutation test showed that all the predictions performed using various cutoffs were significant. The model recognizes complex H and E morphological features associated with different levels of tumor PD-L1 expression, suggesting it can be used in applications with varying PD-L1 cutoff values.
In the present study, tumor PD-L1 status was assessed using a Dako PD-L1 22c3 IHC assay, the FDA approved companion diagnostic for pembrolizumab prescription. Other assays, including Ventana SP142, Ventana SP263, and Dako 28-8, are used as diagnostic tests for atezolizumab, durvalumab, and nivolumab, respectively.,, All IHC assays, except Ventana SP142, are concordant with the Dako 22c3 assay in assessing PD-L1 expression.,, This suggests that our model can be used to predict PD-L1 status as determined by the Dako 28-8 and Ventana SP263 IHC assays; however, further studies are needed to investigate the model's performance in predicting Ventana SP142-assessed tumor PD-L1 status.
Our model predictions are also robust to simulated interpathologist variability. Assessments of tumor PD-L1 status can be affected by interpathologist disagreement. Ratcliffe et al. compared the agreement in NSCLC PD-L1 status assessment between a CLIA laboratory pathologist and an independent pathologist. The agreement between the two pathologists increased from moderate (75%) to excellent (96%) as the PD-L1 positivity cutoff increased from 1%–50%. To mimic the effect of interpathologist disagreement, we randomly shuffled 5%–30% of the PD-L1 labels in our test cohort. As expected, the power of our model in predicting PD-L1 status decreased as the proportion of shuffled labels increased [Figure 4]b. However, even in the case corresponding to maximum interpathologist divergence (25% shuffled samples), the model retained predictive power (AUC = 0.66, Ppermutation = 0.01).
This study has two limitations. First, our training slides were annotated by only one pathologist. It is possible that the samples may include some bias arising from interpathologist variability. Despite this possibility, the model performed well in predicting PD-L1 status from H and E WSI. The model is expected to perform equally well or better with the use of consensus annotations from multiple pathologists. Second, the successful prediction of overall PD-L1 status did not require an accurate probability prediction at every individual location on each slide. For instance, in test cases with negative PD-L1 status, the average model score was approximately 5%, while the pathologist score was <1%, indicating that the model predicted some PD-L1− tumor regions as PD-L1+. Increasing the number of training examples will improve the model's ability to identify unique features that are associated with PD-L1+ tiles. This improvement is anticipated to allow more precise prediction of local PD-L1 expression.
Prospective studies with large, independent datasets and masked tumor PD-L1 status are needed to confirm our findings. Finally, future studies will need to investigate which interpretable morphological features contribute most to our deep learning model in order to extract biological meaning. For example, our model could be extended by adding the ability to classify PD-L1 expression among TILs. While overall tumor PD-L1+ status is commonly used as a response biomarker for checkpoint inhibitor immunotherapy,, PD-L1 expression on TILs is also strongly associated with improved response to checkpoint inhibitors in various cancer types., A model that classifies tumor and lymphocyte PD-L1 status simultaneously would have broader applications for cancer patients. Furthermore, it would be an interesting future study to investigate if deep learning can uncover novel H and E and PD-L1 IHC features for enhanced prognosis and response prediction.
Our histopathological slides were prepared at a single CAP-accredited and CLIA-certified laboratory and were scanned using the same scanner. Other laboratories may follow different staining protocols, leading to color variations of the slides. Color normalization schemes, such as sparse nonnegative matrix factorization, have been used to standardized appearance of tissues slides and have shown to improve the performance of computer vision algorithms., Thus, the robustness of our deep learning model can be further improved by implementing color normalization into our deep learning model. The diagnostic performance of scanners between different vendors has not been studied. The discordance and concordance in diagnosis between glass slides and WSI acquired from various scanners were about 15% and 85%, respectively. Scanner variability is thus expected to have moderate effect on the performance of our deep learning model.
| Conclusions|| |
In this study, we developed a fast and robust deep learning model to predict tumor PD-L1 status from H and E WSIs in NSCLC. The prediction of tumor PD-L1 status was significant regardless of expression cutoff values, and the results were robust to interpathologist variability. This analysis may open new avenues to further developing an H and E image-based test to complement IHC staining for PD-L1 assessment, especially when there is insufficient tissue, and in some settings, a lack of resources for IHC staining.
The authors would like to thank Dr. Alexandria Bobe and Matthew Kase for editorial assistance. The authors would also like to express their appreciation to Erin McCarthy, Hunter Lane, Dr. Kevin White, Dr. Katie Igartua, Dr. Denise Lau, Dr. Martin Stumpe, and Dr. Rafi Pelossof for valuable comments on the manuscript.
Financial support and sponsorship
Conflicts of interest
L.S., B.L.O., I.Y.H., C.W., N.B., B.M.M., T.J.T., and S.S.F.Y. are employees and/or shareholders of Tempus Labs. H.W. is an intern at Tempus Labs. T.L.T. was compensated by Tempus Labs for his participation as a pathologist.
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