Journal: Cell Genomics

Article Title: Detection of heterogeneous resistance mechanisms to tyrosine kinase inhibitors from cell-free DNA

doi: 10.1016/j.xgen.2025.100987

Figure Lengend Snippet: Study design for patient cohorts and genomic analyses (A) Initial study criteria with study design based on sample availability and treatment timing. After whole-exome sequencing, PhylogicNDT and SignatureAnalyzer were used to identify clones and compare mutational signatures, respectively. Functional mutations were characterized based on existing evidence previously published or annotated in genomic databases, such as COSMIC, ClinVar, and OncoKB. (B) Signaling pathway landscape for paired-cohort participants ( n = 26) organized by time on tyrosine kinase treatment (days by sampled TKI) and acquired ( n = 8) or intrinsic ( n = 18) resistance. Known mechanisms in ERBB2 and PIK3CA are highlighted. Signaling pathways are depicted in decreasing frequency per number of mutations for the entire cohort of paired participants. Arrows indicate the subclonal trajectory as either growing, stable, or shrinking. The TP53 and ESR1+ regulator pathways were significantly mutated ( q < 0.05; MutSig, Fisher’s method). Stacked bar charts indicate relative contributions of mutational signatures identified by SignatureAnalyzer to the mutational spectrum of each participant. (C) Pathway-level comparison of mutation frequency between four cohorts: intrinsic ( n = 18), acquired ( n = 8), pre-TKI ( n = 55), and post-TKI ( n = 30). Pathways were included if they possessed at least one mutation. There were no significant differences in pathway-level mutation frequency between cohorts (Fisher’s exact test).

Article Snippet: The remainder of our genomic analysis relied on whole exome sequencing (WES) data generated by the Broad Institute Genomics Platform.

Techniques: Sequencing, Clone Assay, Functional Assay, Protein-Protein interactions, Comparison, Mutagenesis

Journal: Cell Reports Medicine

Article Title: Tumor immune microenvironment delineates progression trajectories of distinct nasopharyngeal carcinoma phenotypes

doi: 10.1016/j.xcrm.2025.102143

Figure Lengend Snippet: Clinical characteristics and germline variants associated with NPC subtypes ( n = 303 [L], 201 [A], 246 [D], and 244 [AD]) (A) Representative MRI scans of each NPC subtype (red, bulky tumor; blue, small tumor). (B) CONSORT diagram of patient selection for the NCCS cohort. (C) Association of NPC subtypes with OS and DFS. (D) Manhattan plot showing p values of germline variants associated with L, A, D, or AD subtype relative to healthy controls. Points above dashed line ( p = 8.9 × 10 −7 ) are significant variants post-Bonferroni adjustment. (E) Variants significantly associated with NPC subtypes identified in both the comparison against healthy controls and the comparison against all controls. (F and G) Tumor expression of FADS1 and DFS in A-subtype patients with CC vs. TC genotype of rs72643557 , respectively. The boxplots represent the IQR, with the horizontal line indicating the median. Mann-Whitney U test and log-rank test was used to compare between CC vs. TC in (F) and (G), respectively. Abbreviations: NPC, nasopharyngeal carcinoma; CONSORT, Consolidated Standards of Reporting Trials; QC, quality control; OS, overall survival; DFS, disease-free survival; L, limited; A, ascending; D, descending; AD, ascending-descending.

Article Snippet: NCCS NPC PLINK processed germline WES data , This study , Mendeley Data: https://data.mendeley.com/datasets/87cwzd56kh/1.

Techniques: Selection, Comparison, Expressing, MANN-WHITNEY, Control

Journal: Cell Reports Medicine

Article Title: Tumor immune microenvironment delineates progression trajectories of distinct nasopharyngeal carcinoma phenotypes

doi: 10.1016/j.xcrm.2025.102143

Figure Lengend Snippet: Analysis of TIME in NPC subtypes using whole slide imaging ( n = 39 [L], 35 [A], 33 [D], and 48 [AD]) (A) Workflow of spatial analyses leading to immune classification based on spatial distribution and density of immune-rich tiles within the WSI of the tumor. (B) Proportion of immune-rich tiles in WSIs for the four subtypes. (C) Mean tumor-immune tile distances in WSIs for the four subtypes. (D) Distribution of the three immune classes in WSIs for the four subtypes. (E) Association of immune classes with DFS for both NCCS and JXCH cohorts. No hazard ratio was computed for JXCH cohort due to absence of DFS events in the immune-dense class. Log-rank test was used to compare between immune classes. The boxplots represent the IQR, with the horizontal line indicating the median. Mann-Whitney U test was used to compare between NPC subtypes unless otherwise indicated. Abbreviations: WSIs, whole-slide images; DFS, disease-free survival.

Article Snippet: NCCS NPC PLINK processed germline WES data , This study , Mendeley Data: https://data.mendeley.com/datasets/87cwzd56kh/1.

Techniques: Imaging, MANN-WHITNEY

Journal: Cell Reports Medicine

Article Title: Tumor immune microenvironment delineates progression trajectories of distinct nasopharyngeal carcinoma phenotypes

doi: 10.1016/j.xcrm.2025.102143

Figure Lengend Snippet: Clinical characteristics and germline variants associated with NPC subtypes ( n = 303 [L], 201 [A], 246 [D], and 244 [AD]) (A) Representative MRI scans of each NPC subtype (red, bulky tumor; blue, small tumor). (B) CONSORT diagram of patient selection for the NCCS cohort. (C) Association of NPC subtypes with OS and DFS. (D) Manhattan plot showing p values of germline variants associated with L, A, D, or AD subtype relative to healthy controls. Points above dashed line ( p = 8.9 × 10 −7 ) are significant variants post-Bonferroni adjustment. (E) Variants significantly associated with NPC subtypes identified in both the comparison against healthy controls and the comparison against all controls. (F and G) Tumor expression of FADS1 and DFS in A-subtype patients with CC vs. TC genotype of rs72643557 , respectively. The boxplots represent the IQR, with the horizontal line indicating the median. Mann-Whitney U test and log-rank test was used to compare between CC vs. TC in (F) and (G), respectively. Abbreviations: NPC, nasopharyngeal carcinoma; CONSORT, Consolidated Standards of Reporting Trials; QC, quality control; OS, overall survival; DFS, disease-free survival; L, limited; A, ascending; D, descending; AD, ascending-descending.

Article Snippet: NCCS NPC processed somatic WES data , This study , Mendeley Data: https://data.mendeley.com/datasets/87cwzd56kh/1.

Techniques: Selection, Comparison, Expressing, MANN-WHITNEY, Control

Journal: Cell Reports Medicine

Article Title: Tumor immune microenvironment delineates progression trajectories of distinct nasopharyngeal carcinoma phenotypes

doi: 10.1016/j.xcrm.2025.102143

Figure Lengend Snippet: Analysis of TIME in NPC subtypes using whole slide imaging ( n = 39 [L], 35 [A], 33 [D], and 48 [AD]) (A) Workflow of spatial analyses leading to immune classification based on spatial distribution and density of immune-rich tiles within the WSI of the tumor. (B) Proportion of immune-rich tiles in WSIs for the four subtypes. (C) Mean tumor-immune tile distances in WSIs for the four subtypes. (D) Distribution of the three immune classes in WSIs for the four subtypes. (E) Association of immune classes with DFS for both NCCS and JXCH cohorts. No hazard ratio was computed for JXCH cohort due to absence of DFS events in the immune-dense class. Log-rank test was used to compare between immune classes. The boxplots represent the IQR, with the horizontal line indicating the median. Mann-Whitney U test was used to compare between NPC subtypes unless otherwise indicated. Abbreviations: WSIs, whole-slide images; DFS, disease-free survival.

Article Snippet: NCCS NPC processed somatic WES data , This study , Mendeley Data: https://data.mendeley.com/datasets/87cwzd56kh/1.

Techniques: Imaging, MANN-WHITNEY