Journal: iScience

Article Title: ExIR enables prioritizing driver and biomarker genes from omics data in a reference free manner

doi: 10.1016/j.isci.2026.116303

Figure Lengend Snippet: Differential immunoreactivity of known and novel ExIR-predicted LUAD biomarkers between normal and cancer samples (A–E) Immunohistochemical (IHC) data from the Human Protein Atlas database in LUAD and normal lung tissue for top five known LUAD biomarkers. (A) SFTPC–ExIR rank #1, LUAD (negative intensity; patient ID: 1847) and normal pneumocytes (quantity: 75%–25%; strong intensity; patient ID: 2268). (B) SPP1—ExIR rank #117, LUAD (quantity: >75%; moderate intensity; patient ID: 537) and normal pneumocytes (not detected; patient ID: 2268). (C) CBLC—ExIR rank #140, LUAD (quantity: >75%; moderate intensity; patient ID: 1847) and normal pneumocytes (not detected; patient ID: 2417). (D) MDK—ExIR rank #247, LUAD (quantity: 75%–25%; strong intensity; patient ID: 1847) and normal pneumocytes (not detected; patient ID: 2222). (E) MRC1 – ExIR rank #471, LUAD (undetected; patient ID: 1932) and normal macrophages (quantity: 75%–25%; strong intensity; patient ID: 2208). (F–I) IHC data of top five ExIR-predicted LUAD biomarkers (excluding SFTPC rank #1 already in a). (F) AGER – ExIR rank #2, LUAD (not detected; patient ID: 3144) and normal pneumocytes (quantity: >75%; strong intensity; patient ID: 4840). (G) EMP2 – ExIR rank #3, LUAD (not detected; patient ID: 1847) and normal pneumocytes (quantity: >75%; strong intensity; patient ID: 2101). (H) CAV1 – ExIR rank #4, LUAD (not detected; patient ID: 1249) and normal pneumocytes (quantity: >75%; strong intensity; patient ID: 2208). i, RTKN2 – ExIR rank 5, LUAD (not detected; patient ID: 3003) and normal pneumocytes (quantity: <25%; moderate intensity; patient ID: 2268).(J–N) IHC data of top six ExIR-predicted LUAD up-regulated biomarkers (excluding FAM83A rank #2, for which no IHC data was available). (J) PYCR1 – ExIR rank #1, LUAD (quantity: >75%; moderate intensity; patient ID: 2777) and normal pneumocytes (not detected; patient ID: 2208). (K) TOP2A – ExIR rank #3, LUAD (quantity: 75%–25%; strong intensity; patient ID: 3003) and normal pneumocytes (quantity: 75%–25%; weak intensity; patient ID: 2101). (L) MMP11 – ExIR rank #4, LUAD (quantity: >75%; weak intensity; patient ID: 1847) and normal pneumocytes (not detected; patient ID: 2438). (M) TEDC2– ExIR rank 5, LUAD (quantity: 75%–25%; moderate intensity; patient ID: 4208) and normal pneumocytes (not detected; patient ID: 1470). (N) IQGAP3– ExIR rank 6, LUAD (quantity: >75%; strong intensity; patient ID: 3048) and normal pneumocytes (not detected; patient ID: 1470). Per the Human Protein Atlas database usage guidelines, the link to the immunostaining images of all of the selected proteins in normal pneumocytes and LUAD samples are included as hyperlinks within the figure legend. Ab: antibody; LUAD: lung adenocarcinoma.

Article Snippet: Additionally, immunohistochemical data for the specific lung adenocarcinoma (LUAD) subtype analyzed were available from the Human Protein Atlas.

Techniques: Immunohistochemical staining, Immunostaining

Journal: iScience

Article Title: ExIR enables prioritizing driver and biomarker genes from omics data in a reference free manner

doi: 10.1016/j.isci.2026.116303

Figure Lengend Snippet: Differential immunoreactivity of known and novel ExIR-predicted LUAD biomarkers between normal and cancer samples (A–E) Immunohistochemical (IHC) data from the Human Protein Atlas database in LUAD and normal lung tissue for top five known LUAD biomarkers. (A) SFTPC–ExIR rank #1, LUAD (negative intensity; patient ID: 1847) and normal pneumocytes (quantity: 75%–25%; strong intensity; patient ID: 2268). (B) SPP1—ExIR rank #117, LUAD (quantity: >75%; moderate intensity; patient ID: 537) and normal pneumocytes (not detected; patient ID: 2268). (C) CBLC—ExIR rank #140, LUAD (quantity: >75%; moderate intensity; patient ID: 1847) and normal pneumocytes (not detected; patient ID: 2417). (D) MDK—ExIR rank #247, LUAD (quantity: 75%–25%; strong intensity; patient ID: 1847) and normal pneumocytes (not detected; patient ID: 2222). (E) MRC1 – ExIR rank #471, LUAD (undetected; patient ID: 1932) and normal macrophages (quantity: 75%–25%; strong intensity; patient ID: 2208). (F–I) IHC data of top five ExIR-predicted LUAD biomarkers (excluding SFTPC rank #1 already in a). (F) AGER – ExIR rank #2, LUAD (not detected; patient ID: 3144) and normal pneumocytes (quantity: >75%; strong intensity; patient ID: 4840). (G) EMP2 – ExIR rank #3, LUAD (not detected; patient ID: 1847) and normal pneumocytes (quantity: >75%; strong intensity; patient ID: 2101). (H) CAV1 – ExIR rank #4, LUAD (not detected; patient ID: 1249) and normal pneumocytes (quantity: >75%; strong intensity; patient ID: 2208). i, RTKN2 – ExIR rank 5, LUAD (not detected; patient ID: 3003) and normal pneumocytes (quantity: <25%; moderate intensity; patient ID: 2268).(J–N) IHC data of top six ExIR-predicted LUAD up-regulated biomarkers (excluding FAM83A rank #2, for which no IHC data was available). (J) PYCR1 – ExIR rank #1, LUAD (quantity: >75%; moderate intensity; patient ID: 2777) and normal pneumocytes (not detected; patient ID: 2208). (K) TOP2A – ExIR rank #3, LUAD (quantity: 75%–25%; strong intensity; patient ID: 3003) and normal pneumocytes (quantity: 75%–25%; weak intensity; patient ID: 2101). (L) MMP11 – ExIR rank #4, LUAD (quantity: >75%; weak intensity; patient ID: 1847) and normal pneumocytes (not detected; patient ID: 2438). (M) TEDC2– ExIR rank 5, LUAD (quantity: 75%–25%; moderate intensity; patient ID: 4208) and normal pneumocytes (not detected; patient ID: 1470). (N) IQGAP3– ExIR rank 6, LUAD (quantity: >75%; strong intensity; patient ID: 3048) and normal pneumocytes (not detected; patient ID: 1470). Per the Human Protein Atlas database usage guidelines, the link to the immunostaining images of all of the selected proteins in normal pneumocytes and LUAD samples are included as hyperlinks within the figure legend. Ab: antibody; LUAD: lung adenocarcinoma.

Article Snippet: Figure 4 Differential immunoreactivity of known and novel ExIR-predicted LUAD biomarkers between normal and cancer samples (A–E) Immunohistochemical (IHC) data from the Human Protein Atlas database in LUAD and normal lung tissue for top five known LUAD biomarkers. (A) SFTPC–ExIR rank #1, LUAD (negative intensity; patient ID: 1847) and normal pneumocytes (quantity: 75%–25%; strong intensity; patient ID: 2268). (B) SPP1—ExIR rank #117, LUAD (quantity: >75%; moderate intensity; patient ID: 537) and normal pneumocytes (not detected; patient ID: 2268). (C) CBLC—ExIR rank #140, LUAD (quantity: >75%; moderate intensity; patient ID: 1847) and normal pneumocytes (not detected; patient ID: 2417). (D) MDK—ExIR rank #247, LUAD (quantity: 75%–25%; strong intensity; patient ID: 1847) and normal pneumocytes (not detected; patient ID: 2222). (E) MRC1 – ExIR rank #471, LUAD (undetected; patient ID: 1932) and normal macrophages (quantity: 75%–25%; strong intensity; patient ID: 2208). (F–I) IHC data of top five ExIR-predicted LUAD biomarkers (excluding SFTPC rank #1 already in a). (F) AGER – ExIR rank #2, LUAD (not detected; patient ID: 3144) and normal pneumocytes (quantity: >75%; strong intensity; patient ID: 4840). (G) EMP2 – ExIR rank #3, LUAD (not detected; patient ID: 1847) and normal pneumocytes (quantity: >75%; strong intensity; patient ID: 2101). (H) CAV1 – ExIR rank #4, LUAD (not detected; patient ID: 1249) and normal pneumocytes (quantity: >75%; strong intensity; patient ID: 2208). i, RTKN2 – ExIR rank 5, LUAD (not detected; patient ID: 3003) and normal pneumocytes (quantity: <25%; moderate intensity; patient ID: 2268). (J–N) IHC data of top six ExIR-predicted LUAD up-regulated biomarkers (excluding FAM83A rank #2, for which no IHC data was available). (J) PYCR1 – ExIR rank #1, LUAD (quantity: >75%; moderate intensity; patient ID: 2777) and normal pneumocytes (not detected; patient ID: 2208). (K) TOP2A – ExIR rank #3, LUAD (quantity: 75%–25%; strong intensity; patient ID: 3003) and normal pneumocytes (quantity: 75%–25%; weak intensity; patient ID: 2101). (L) MMP11 – ExIR rank #4, LUAD (quantity: >75%; weak intensity; patient ID: 1847) and normal pneumocytes (not detected; patient ID: 2438). (M) TEDC2– ExIR rank 5, LUAD (quantity: 75%–25%; moderate intensity; patient ID: 4208) and normal pneumocytes (not detected; patient ID: 1470). (N) IQGAP3– ExIR rank 6, LUAD (quantity: >75%; strong intensity; patient ID: 3048) and normal pneumocytes (not detected; patient ID: 1470).

Techniques: Immunohistochemical staining, Immunostaining

Journal: PeerJ

Article Title: ERO1A as a novel biomarker for risk stratification and immunotherapeutic guidance in early-stage lung adenocarcinoma

doi: 10.7717/peerj.21347

Figure Lengend Snippet: (A) Pan-cancer analysis of ERO1A expression between tumor and normal (or primary and metastatic) tissues from the TIMER database. (B) ERO1A expression in LUAD and normal tissues based on TCGA and GTEx data (GEPIA). *** P < 0.001; unpaired Student’s t-test. (C) Representative immunohistochemical (IHC) staining images of ERO1A in normal and LUAD tissues from the Human Protein Atlas (HPA) database. (D) ERO1A protein expression in normal lung tissues and LUAD tissues based on the HPA database. (E, F) Survival analysis (GEPIA) of ERO1A expression in TCGA-LUAD: (E) overall survival (OS, P < 0.001), (F) disease-free survival (DFS, P = 0.018). (G) ERO1A mRNA expression in TCGA-esLUAD tumors ( n = 233) vs normal tissues ( n = 32). *** P < 0.001; unpaired t-test. (H) Receiver operating characteristic (ROC) curve evaluating the performance of ERO1A expression in discriminating tumor from normal tissue (AUC = 0.988). (I, J) Kaplan-Meier survival analysis in TCGA-esLUAD based on ERO1A expression: (I) OS ( P = 0.007), (J) relapse-free survival (RFS, P = 0.004); log-rank test. (K, L) Time-dependent ROC (tROC) curves predicting (K) OS and (L) RFS at 1, 2, and 3 years in the TCGA-esLUAD cohort. (M) Kaplan-Meier analysis of OS in the GSE72094 esLUAD cohort stratified by ERO1A expression. *** P < 0.001; log-rank test. (N) ERO1A expression between alive ( n = 144) and deceased ( n = 77) patients in the GSE72094 esLUAD cohort. *** P < 0.001; unpaired t-test. (O) Representative images of ERO1A IHC staining in our institutional cohort of esLUAD tissue sections ( n = 90); right panel shows a magnified view of the region indicated by the box. Scale bar: 200 μm. (P) DFS analysis based on ERO1A high/low expression groups defined by IHC H-Score from our cohort. P = 0.002, log-rank test. (Q) Comparison of ERO1A H-Score between patients with ( n = 8) and without ( n = 82) DFS events. P = 0.008; Mann-Whitney U test. Abbreviations: esLUAD, early-stage lung adenocarcinoma; TIMER, tumor immune estimation resource; LUAD, lung adenocarcinoma; TCGA, the cancer genome atlas; GTEx, genotype-tissue expression; GEPIA, gene expression profiling interactive analysis; IHC, immunohistochemistry; HPA, human protein atlas; OS, overall survival; DFS, disease-free survival; ROC, receiver operating characteristic; AUC, area under the curve; RFS, relapse-free survival; tROC, time-dependent receiver operating characteristic; H-score, histochemistry score. *** P < 0.001; ** P < 0.01; * P < 0.05; ns, not significant.

Article Snippet: Immunohistochemistry (IHC) data from the Human Protein Atlas further revealed that normal lung parenchyma was almost devoid of ERO1A protein, whereas virtually all LUAD specimens exhibited positive staining with intensities ranging from weak to strong, resulting in a significantly higher overall protein level than normal controls ( , ; with quantitative data shown in ).

Techniques: Expressing, Immunohistochemical staining, Immunohistochemistry, Comparison, MANN-WHITNEY, Gene Expression