Ryan J. Park
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View article: Differential T cell clonal dynamics underlie outcomes to frontline chemoimmunotherapy in advanced gastric cancer
Differential T cell clonal dynamics underlie outcomes to frontline chemoimmunotherapy in advanced gastric cancer Open
The addition of aPD1 to 5-FU/platinum in advanced gastric cancer (GC) yields variable responses. To understand cooperativity between chemotherapy and immunotherapy, we previously reported a phase II trial sequentially adding pembrolizumab …
View article: Multimodal blood based profiling reveals insights into mechanisms of immunotherapy resistance
Multimodal blood based profiling reveals insights into mechanisms of immunotherapy resistance Open
Many cancer patients treated with immune checkpoint blockade (ICB) do not have durable treatment responses. Circulating biomarkers have the potential to identify patients with primary resistance or early progression on therapy to alter tre…
View article: Characterization of cell states in biliary tract cancers identifies mechanisms of therapeutic resistance in a phase II trial of DKN-01/nivolumab
Characterization of cell states in biliary tract cancers identifies mechanisms of therapeutic resistance in a phase II trial of DKN-01/nivolumab Open
Biliary tract cancers demonstrate profound therapeutic resistance, and broadly effective therapies for refractory disease are lacking. We conducted a single-arm, second-line phase II trial combining DKN-01, a humanized monoclonal antibody …
View article: Bladder-preserving radiation therapy for patients with locally advanced and node-positive bladder cancer
Bladder-preserving radiation therapy for patients with locally advanced and node-positive bladder cancer Open
In this cohort with LA-MIBC treated with RT, distant failures predominate, local failures are less common, and toxicity was minimal. Survival outcomes remain encouraging for RT in this challenging patient population. Further investigation …
View article: Achieving Inclusive Healthcare through Integrating Education and Research with AI and Personalized Curricula
Achieving Inclusive Healthcare through Integrating Education and Research with AI and Personalized Curricula Open
Background: Precision medicine promises significant health benefits but faces challenges such as complex data management and analytics, interdisciplinary collaboration, and education of researchers, healthcare professionals, and participan…
View article: Table S5 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Table S5 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer Open
Significant covarying programs
View article: Figure S11 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Figure S11 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer Open
Figure S11. Mean usage of myeloid cNMF programs per myeloid cell subset at (A) baseline, (B) post-chemotherapy (FU1) and (C) post-immunotherapy (FU2). Mean usage of T cell cNMF programs per T cell cell subset at (D) baseline, (E) postchemo…
View article: Figure S8 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Figure S8 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer Open
Figure S8. Copy number profiles of all epithelial cells from each patient’s samples inferred using inferCNV.
View article: Table S8 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Table S8 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer Open
Representativeness of study participants
View article: Table S4 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Table S4 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer Open
Annotated cNMF programs
View article: Figure S2 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Figure S2 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer Open
Figure S2. (A) CoMut plot demonstrating TCGA subtype, tumor mutational burden, mutational signature enrichment and mutational profiles of key driver genes for all patient samples at baseline in the reported clinical trial. (B) PD-L1 expres…
View article: Figure S14 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Figure S14 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer Open
Figure S14. cNMF was performed on epithelial cells at baseline. Shown is the mean usage of each cNMF gene program in the epithelial cells of fast and slow progressing patients.
View article: Figure S23 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Figure S23 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer Open
Figure S23. Heatmaps showing the number of significant inferred ligandreceptor interactions between major cell types using CellPhoneDB on scRNAseq data in (A) normal, (B) baseline tumor, (C) post-chemotherapy (FU1) tumor and (D) post-immun…
View article: Figure S1 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Figure S1 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer Open
(A) Swimmers plot of patient response and duration in the described clinical trial. (B) Scatter plot showing temporal course of tumor response measured by RECIST for all patients in the reported clinical trial. (C) Progression free surviva…
View article: Figure S23 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Figure S23 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer Open
Figure S23. Heatmaps showing the number of significant inferred ligandreceptor interactions between major cell types using CellPhoneDB on scRNAseq data in (A) normal, (B) baseline tumor, (C) post-chemotherapy (FU1) tumor and (D) post-immun…
View article: Figure S24 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Figure S24 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer Open
Figure S24. (A) Immune gene expression program signature scored from bulk RNA-seq profiles across all samples separated by timepoint. (B) Immunogenic cell death signatures scored from bulk RNA-seq profiles split by fast and slow progressin…
View article: Figure S4 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Figure S4 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer Open
Figure S4. Multiplexed immunofluorescence (mIF) images of BL and FU1 samples from two patients, E17 (slow progressor) and E35 (fast progressor), staining for (A) panCK, PD-L1, CD163, CD68, CD14 and CD8, and (B) panCK, PD-L1, CD4, CD8 and G…
View article: Figure S13 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Figure S13 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer Open
Figure S13. Boxplots showing usage of epithelial cNMF programs in epithelial cells of fast and slow progressors (A) post-chemotherapy (FU1) and (B) postimmunotherapy (FU2).
View article: Table S2 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Table S2 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer Open
Adverse events on single arm sequential CAPOX and pembrolizumab in advanced gastric cancer.
View article: Figure S1 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Figure S1 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer Open
(A) Swimmers plot of patient response and duration in the described clinical trial. (B) Scatter plot showing temporal course of tumor response measured by RECIST for all patients in the reported clinical trial. (C) Progression free surviva…
View article: Table S7 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Table S7 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer Open
CellPhoneDB unique ligand receptor interactions
View article: Figure S26 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Figure S26 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer Open
Figure S26. (A) Proportion of CD8 T cells in non-responder and responder patients split by timepoint. Statistical comparisons performed using a Wilcoxon signed-rank test. (B) Multiplexed immunofluorescence (mIF) images of BL, FU1 and FU2 s…
View article: Data from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Data from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer Open
Adding anti–programmed cell death protein 1 (anti–PD-1) to 5-fluorouracil (5-FU)/platinum improves survival in some advanced gastroesophageal adenocarcinomas (GEA). To understand the effects of chemotherapy and immunotherapy, we conducted …
View article: Table S5 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Table S5 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer Open
Significant covarying programs
View article: Table S2 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Table S2 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer Open
Adverse events on single arm sequential CAPOX and pembrolizumab in advanced gastric cancer.
View article: Figure S19 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Figure S19 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer Open
Figure S19. (A) UMAP embedding of single cell transcriptomes of all macrophages obtained from all samples in this trial. Labeled are granular macrophage subsets separated by tumor v.s. normal tissue, and by timepoint. (B) UMAP embeddings s…
View article: Table S1 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Table S1 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer Open
Patient demographics
View article: Table S7 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Table S7 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer Open
CellPhoneDB unique ligand receptor interactions
View article: Table S3 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Table S3 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer Open
Detailed cell type proportions
View article: Figure S15 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Figure S15 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer Open
Figure S15. Heatmap showing pairwise correlation of gene program activities across all patient samples at baseline using the 90th percentile of patient-level program activity in epithelial, myeloid, T, NK and stromal cells. Hierarchical cl…