bluuebunny/crossref_metadata_2025 huggingface dataset:
Exploring Compassionate Care Patterns Among Nurses and Its Associations With Resilience: Multilevel Contextual Effects Modeling
Authors: Mousazadeh Noushin , Babaieasl Faezeh , Rezapour Maysam , Hakimi Hamideh
Published: February 2025

Background: Compassionate care and resilience play crucial roles in enhancing care quality. Understanding compassionate care patterns in the nursing population and their relationship with resilience can improve knowledge of these concepts.

Objective: To investigate compassionate care patterns among Iranian nurses and their associations with resilience at individual and contextual levels.

Method: This cross‐sectional study used Persian versions of the 28‐item Compassionate Care Questionnaire (CCQ) and Connor–Davidson Resilience Scale (CD‐RISC). 478 Iranian nurses from 19 wards across 16 hospitals in northern Iran participated between February and September 2023. Latent profile analysis (LPA) was performed on compassionate care dimensions. Multilevel logistic regression modeling explored associations between resilience dimensions and compassionate care profiles, adjusting for control variables at individual and contextual levels.

Results: LPA revealed two distinct compassionate care profiles: “Low Compassionate Care” (16.3%) and “High Compassionate Care” (83.7%). After adjusting for control variables, personal competence (OR = 1.09, 95% CI: 1.02–1.15), positive acceptance (OR = 1.23, 95% CI: 1.06–1.44), and spirituality (OR = 1.17, 95% CI: 1.01–1.38) were associated with higher odds of inclusion in the “High Compassionate Care” profile. The empty model showed that 6.5% of compassionate care patterns were explained at the ward level. After adding predictors at individual and ward levels, explained variances were reduced to 1.5% and < 0.01%, respectively.

Conclusions and Implication: This study offers insights into compassionate care among nurses, showing that few exhibited “Low Compassionate Care.” Higher resilience was positively linked to elevated compassionate care levels. Policymakers, managers, and educators can leverage these findings to enhance nursing management and support systems by prioritizing resilience‐building strategies, ultimately improving patient care quality.
Table S3 from Chromatin Helicase CHD6 Establishes Proinflammatory Enhancers and Is a Synthetic Lethal Target in FH-Deficient Renal Cell Carcinoma
Authors: Jin Juan , Luo Jun , Jin Xiaodong , Lim Kiat Shenq , He Yang , Ding Jiawei , Shen Yan , Hou Yuchen , Liu Hanqing , Zhu Xiaoyu , Zhao Jing , Zhou Wenjie , Huang Hai , Gao Yi , Xiao Jun , He Hongchao , Li Qunyi , Liu Lianxin , Chen Li , He Qiang , Zhang Chuanjie
Published: February 2025

Characteristics of patients whose tumors were used for PDOs or PDXs experiments, Related to Figure 4&7.
Supplementary Figure 6 from Chromatin Helicase CHD6 Establishes Proinflammatory Enhancers and Is a Synthetic Lethal Target in FH-Deficient Renal Cell Carcinoma
Authors: Jin Juan , Luo Jun , Jin Xiaodong , Lim Kiat Shenq , He Yang , Ding Jiawei , Shen Yan , Hou Yuchen , Liu Hanqing , Zhu Xiaoyu , Zhao Jing , Zhou Wenjie , Huang Hai , Gao Yi , Xiao Jun , He Hongchao , Li Qunyi , Liu Lianxin , Chen Li , He Qiang , Zhang Chuanjie
Published: February 2025

Supplementary Figure 6. In vitro and in vivo assessment of AU-15330 efficacy against FH-deficient RCC in multiple preclinical models, related to Figure 7. A. Dose-response curves and IC50 of FH-intact or FH-deficient cells treated with AU-15330. B. Dose-response curves of UOK-262 cells treated with AU-15330, AU-15139, or AU-16235. C-D. Mouse weight changes measurements (C) (n = 5) and complete blood counts (D) performed on vehicle control and AU-15330 treated mice as in Fig. 7A. E. Representative HE graphs showing the morphology of critical organs in mice treated with an increased amount of AU-15330. F. Representative graphs showing AU-15330 efficacy against FH-mutated RCC organoids with CHD6 depletion. Scale bar: 200 μm. G. Changes in tumour volumes of the subcutaneous PDX models receiving daily i.v. with vehicle or AU-15330 for 8 weeks (n = 8 mice per group). H. BIL signals (left) and quantification (right) of lung metastatic nodes in mice derived from indicated groups. P values were calculated using the two-tailed Student’s t-test (D), 2-way ANOVA followed by Tukey’s multiple comparisons test (F, H). *p < 0.05, **p < 0.01, and ***p < 0.001. ns, no significance.
Supplementary Figure 3 from Chromatin Helicase CHD6 Establishes Proinflammatory Enhancers and Is a Synthetic Lethal Target in FH-Deficient Renal Cell Carcinoma
Authors: Jin Juan , Luo Jun , Jin Xiaodong , Lim Kiat Shenq , He Yang , Ding Jiawei , Shen Yan , Hou Yuchen , Liu Hanqing , Zhu Xiaoyu , Zhao Jing , Zhou Wenjie , Huang Hai , Gao Yi , Xiao Jun , He Hongchao , Li Qunyi , Liu Lianxin , Chen Li , He Qiang , Zhang Chuanjie
Published: February 2025

Supplementary Figure 3. CHD6 is essential for FH-deficient RCC cells, related to Figure 4. A-B. MTT analysis of FH-WT PRCC (A) or canonical ccRCC (B) cells with or without CHD6-KD. C. Competition-based assay to measure the effect of CHD4 shRNA on the growth of UOK-262 cells (n = 3 per time point). CHD4-KD cells were identified by coexpression of green fluorescent protein (GFP) (LMN vector). The percentage of GFP+ cells was thus tracked over 12 days and normalized to GFP percentage on day 2. D. Quantified BIL signals of orthotopic (FH-intact Caki-2) renal tumors with or without CHD6 ablation. E. Serum VEGF concentrations in treated BALC/c nude mice from indicated groups were compared. F. Ki-67 (IHC) and TUNEL (IF) staining from xenografts derived from FH-KD and FH/CHD6-KD Caki-2 cells, and the quantitative results are shown in the right panel. Scale bar, 20 μm. G. Kaplan-Meier survival curve analysis of mice from Figure 4F. H. Schematic graph showing the zebrafish tumour xenograft model construction at each time point. I. Quantified tumour sizes derived from indicated cells implanted in the zebrafish embryos. J. Quantitation of organoid sizes from human FH-WT or FM-RCC samples with or without CHD6 depletion. P values were calculated using 2-way ANOVA followed by Tukey’s multiple comparisons tests (A, B), 2-tailed Student’s t-test (C-F, I-J), and log-rank test (G). *p < 0.05, **p < 0.01, and ***p < 0.001. ns, no significance.
Supplementary Figure 2 from Chromatin Helicase CHD6 Establishes Proinflammatory Enhancers and Is a Synthetic Lethal Target in FH-Deficient Renal Cell Carcinoma
Authors: Jin Juan , Luo Jun , Jin Xiaodong , Lim Kiat Shenq , He Yang , Ding Jiawei , Shen Yan , Hou Yuchen , Liu Hanqing , Zhu Xiaoyu , Zhao Jing , Zhou Wenjie , Huang Hai , Gao Yi , Xiao Jun , He Hongchao , Li Qunyi , Liu Lianxin , Chen Li , He Qiang , Zhang Chuanjie
Published: February 2025

Supplementary Figure 2. FH deficiency accumulates CHD6 via inactivating Keap1, related to Figure 2&3. A. WB and co-IP analysis indicating no interactions between VHL and CHD6 proteins in WCLs of ACHN cells. B. WB analysis (left) and RT-qPCR (right) indicated the CHD6 protein or mRNA levels in control and VHL-depleted RCC cells. C. Schematic illustration of Keap1 deletion mutants. The binding capacity of Keap1 to CHD6 is indicated with the symbol. D. Western blots showing in vitro ubiquitination assays conducted by incubating the reconstituted Keap1–CUL3–RBX1 E3 ubiquitin ligase complex with E1 and E2 enzymes, ubiquitin and GST-CHD6 at 30 °C for 2 h. E. Aligning ETGE motif sequence in CHD6 and other known Keap1 substrates. F. Western blots of WCLs and co-IP samples of anti-FLAG antibody from ACHN cells transfected with the indicated plasmids and treated with 20 µM MG132 for 8 h. G. Western blots of WCLs from ACHN cells transfected with the indicated plasmids. H. Cells infected with indicated plasmids for 48 h and then treated with 50 μg/mL cycloheximide (CHX) and harvested at different time points. Quantified data were shown. I. Western blot showing the products of in vivo ubiquitination assays from ACHN cells infected with lentivirus expressing FH-specific shRNA or control for 48 h. RT-qPCR analysis (right) showing the Keap1 mRNA levels in indicated samples. J. Western blot showing the products of in vivo ubiquitination assays from UOK-262 cells with or without FH overexpression. RT-qPCR analysis (right) indicating the Keap1 mRNA levels. K. Chemical reaction process showing the generation of D2-DMF. DMAD, dimethyl acetylenedicarboxylate; PPh3, triphenylphosphine; D2O, heavy water (2H2O); THF, tetrahydrofuran. L. FH-WT cells were treated with increased DMF, and fumarate levels were detected. M. WB analysis showing Keap1 expressions in cells treated with or without DMF. N. Decreased fumarate levels were detected in control and FH-overexpressing UOK-262, Caki-2 (D238 H), and Caki-2 (E378K) cells. C1 and C2 indicate the different clones. O. Western blotting assays and Co-IP analysis showing the Keap1-CHD6 interactions in UOK-262 cells. P values were calculated using a two-tailed unpaired t-test (B, I, J, L, N). *p < 0.05, **p < 0.01, and ***p < 0.001. ns, no significance.
Supplementary Dataset 5 from Energy Stress–Induced circEPB41(2) Promotes Lipogenesis in Hepatocellular Carcinoma
Authors: Yang Yang , Luo Jingjing , Wang Zhongyu , Liu Kaiyue , Feng Keyi , Wang Fang , Mei Yide
Published: February 2025

Overlapping Genes with Decreased H3K9ac Deposition and Down-regulated Expression upon circEPB41(2) Knockdown
Supplementary Table S8 from PTBP1 Lactylation Promotes Glioma Stem Cell Maintenance through PFKFB4-Driven Glycolysis
Authors: Zhou Zijian , Yin Xianyong , Sun Hao , Lu Jiaze , Li Yuming , Fan Yang , Lv Peiwen , Han Min , Wu Jing , Li Shengjie , Liu Zihao , Zhao Hongbo , Sun Haohan , Fan Hao , Wang Shan , Xin Tao
Published: February 2025

Supplementary Table S8. Upregulated proteins in HGG (high-grade glioma) vs LGG (low-grade glioma) in CPTAC database (study ID: PDC000180)
Supplementary Table S2 from PTBP1 Lactylation Promotes Glioma Stem Cell Maintenance through PFKFB4-Driven Glycolysis
Authors: Zhou Zijian , Yin Xianyong , Sun Hao , Lu Jiaze , Li Yuming , Fan Yang , Lv Peiwen , Han Min , Wu Jing , Li Shengjie , Liu Zihao , Zhao Hongbo , Sun Haohan , Fan Hao , Wang Shan , Xin Tao
Published: February 2025

Supplementary Table S2. Clinical characteristics for specimens in this study
Supplementary Figures and notes from PTBP1 Lactylation Promotes Glioma Stem Cell Maintenance through PFKFB4-Driven Glycolysis
Authors: Zhou Zijian , Yin Xianyong , Sun Hao , Lu Jiaze , Li Yuming , Fan Yang , Lv Peiwen , Han Min , Wu Jing , Li Shengjie , Liu Zihao , Zhao Hongbo , Sun Haohan , Fan Hao , Wang Shan , Xin Tao
Published: February 2025

This file includes: Supplementary Figures. S1 to S37 Supplementary Note S1
Supplementary Tables 1-11 from Plasma Cell–Free DNA Chromatin Immunoprecipitation Profiling Depicts Phenotypic and Clinical Heterogeneity in Advanced Prostate Cancer
Authors: Sipola Joonatan , Munzur Aslı D. , Kwan Edmond M. , Seo Clara C.Y. , Hauk Benjamin J. , Parekh Karan , Liao Yi Jou (Ruby) , Bernales Cecily Q. , Donnellan Gráinne , Bloise Ingrid , Fung Emily , Ng Sarah W.S. , Wang Gang , Vandekerkhove Gillian , Nykter Matti , Annala Matti , Maurice-Dror Corinne , Chi Kim N. , Herberts Cameron , Wyatt Alexander W. , Takeda David Y.
Published: February 2025

Supplementary Tables 1-11
Supplementary Data Table 2 from A Potent, Selective, Small-Molecule Inhibitor of DHX9 Abrogates Proliferation of Microsatellite Instable Cancers with Deficient Mismatch Repair
Authors: Castro Jennifer , Daniels Matthew H. , Brennan David , Johnston Brian , Gotur Deepali , Lee Young-Tae , Knockenhauer Kevin E. , Lu Chuang , Wu Jie , Nayak Sunaina , Collins Cindy , Bansal Rishabh , Buker Shane M. , Case April , Liu Julie , Yao Shihua , Sparling Brian A. , Sickmier E. Allen , Silver Serena J. , Blakemore Stephen J. , Boriack-Sjodin P. Ann , Duncan Kenneth W. , Ribich Scott , Copeland Robert A.
Published: February 2025

Supplementary Data Table 2
Supplemental Table 4 from Imlunestrant Is an Oral, Brain-Penetrant Selective Estrogen Receptor Degrader with Potent Antitumor Activity in ESR1 Wild-Type and Mutant Breast Cancer
Authors: Bhagwat Shripad V. , Mur Cecilia , Vandekopple Matthew , Zhao Baohui , Shen Weihua , Marugán Carlos , Capen Andrew , Kindler Lisa , Stephens Jennifer R. , Huber Lysiane , Castanares Mark A. , Garcia-Tapia David , Cohen Jeff D. , Bastian Jolie , Mattioni Brian , Yuen Eunice , Baker Thomas K. , Rodriguez Cruz Vivian , Fei Dongling , Manro Jason R. , Pulliam Nicholas , Dowless Michele S. , Ortiz Ruiz Maria Jesus , Yu Chunping , Puca Loredana , Klippel Anke , Bacchion Francesca , Ismail-Khan Roohi , Rodrik-Outmezguine Vanessa , Peng Sheng-Bin , Lallena María Jose , Gong Xueqian , de Dios Alfonso
Published: February 2025

Statistical analysis of imlunestrant and fulvestrant efficacy alone and in combination with abemaciclib, alpelisib, and everolimus in ESR1-wild type and mutant xenograft and PDX breast cancer models
Supplemental Table 3 from Imlunestrant Is an Oral, Brain-Penetrant Selective Estrogen Receptor Degrader with Potent Antitumor Activity in ESR1 Wild-Type and Mutant Breast Cancer
Authors: Bhagwat Shripad V. , Mur Cecilia , Vandekopple Matthew , Zhao Baohui , Shen Weihua , Marugán Carlos , Capen Andrew , Kindler Lisa , Stephens Jennifer R. , Huber Lysiane , Castanares Mark A. , Garcia-Tapia David , Cohen Jeff D. , Bastian Jolie , Mattioni Brian , Yuen Eunice , Baker Thomas K. , Rodriguez Cruz Vivian , Fei Dongling , Manro Jason R. , Pulliam Nicholas , Dowless Michele S. , Ortiz Ruiz Maria Jesus , Yu Chunping , Puca Loredana , Klippel Anke , Bacchion Francesca , Ismail-Khan Roohi , Rodrik-Outmezguine Vanessa , Peng Sheng-Bin , Lallena María Jose , Gong Xueqian , de Dios Alfonso
Published: February 2025

In vivo imlunestrant efficacy alone and in combination with abemaciclib, alpelisib, and everolimus in CDX breast cancer models.
Supplemental Figure 2 from Imlunestrant Is an Oral, Brain-Penetrant Selective Estrogen Receptor Degrader with Potent Antitumor Activity in ESR1 Wild-Type and Mutant Breast Cancer
Authors: Bhagwat Shripad V. , Mur Cecilia , Vandekopple Matthew , Zhao Baohui , Shen Weihua , Marugán Carlos , Capen Andrew , Kindler Lisa , Stephens Jennifer R. , Huber Lysiane , Castanares Mark A. , Garcia-Tapia David , Cohen Jeff D. , Bastian Jolie , Mattioni Brian , Yuen Eunice , Baker Thomas K. , Rodriguez Cruz Vivian , Fei Dongling , Manro Jason R. , Pulliam Nicholas , Dowless Michele S. , Ortiz Ruiz Maria Jesus , Yu Chunping , Puca Loredana , Klippel Anke , Bacchion Francesca , Ismail-Khan Roohi , Rodrik-Outmezguine Vanessa , Peng Sheng-Bin , Lallena María Jose , Gong Xueqian , de Dios Alfonso
Published: February 2025

Imlunestrant PK/PD and uterotrophic activity.
Supplementary Data Figure 4 from A Potent, Selective, Small-Molecule Inhibitor of DHX9 Abrogates Proliferation of Microsatellite Instable Cancers with Deficient Mismatch Repair
Authors: Castro Jennifer , Daniels Matthew H. , Brennan David , Johnston Brian , Gotur Deepali , Lee Young-Tae , Knockenhauer Kevin E. , Lu Chuang , Wu Jie , Nayak Sunaina , Collins Cindy , Bansal Rishabh , Buker Shane M. , Case April , Liu Julie , Yao Shihua , Sparling Brian A. , Sickmier E. Allen , Silver Serena J. , Blakemore Stephen J. , Boriack-Sjodin P. Ann , Duncan Kenneth W. , Ribich Scott , Copeland Robert A.
Published: February 2025

Supplementary Data Figure 4
Supplementary text from HBV Remodels PP2A Complexes to Rewire Kinase Signaling in Hepatocellular Carcinoma
Authors: Turnham Rigney E. , Pitea Adriana , Jang Gwendolyn M. , Xu Zhong , Lim Huat Chye , Choi Alex L. , Von Dollen John , Levin Rebecca S. , Webber James T. , McCarthy Elizabeth , Hu Junjie , Li Xiaolei , Che Li , Singh Ananya , Yoon Alex , Chan Gary K.L. , Kelley Robin K. , Swaney Danielle L. , Zhang Wei , Bandyopadhyay Sourav , Theis Fabian J. , Eckhardt Manon , Chen Xin , Shokat Kevan M. , Ideker Trey , Krogan Nevan J. , Gordan John D.
Published: February 2025

Supplementary methods and figure legends
Figure S1 from HBV Remodels PP2A Complexes to Rewire Kinase Signaling in Hepatocellular Carcinoma
Authors: Turnham Rigney E. , Pitea Adriana , Jang Gwendolyn M. , Xu Zhong , Lim Huat Chye , Choi Alex L. , Von Dollen John , Levin Rebecca S. , Webber James T. , McCarthy Elizabeth , Hu Junjie , Li Xiaolei , Che Li , Singh Ananya , Yoon Alex , Chan Gary K.L. , Kelley Robin K. , Swaney Danielle L. , Zhang Wei , Bandyopadhyay Sourav , Theis Fabian J. , Eckhardt Manon , Chen Xin , Shokat Kevan M. , Ideker Trey , Krogan Nevan J. , Gordan John D.
Published: February 2025

Supplementary Figure 1
Figure S9 from Breast Cancer Subtype–Specific Organotropism Is Dictated by FOXF2-Regulated Metastatic Dormancy and Recovery
Authors: Jiang Wen-Jing , Zhou Tian-Hao , Huang Huan-Jing , Li Lin-Sen , Tan Hao , Zhang Rui , Wang Qing-Shan , Feng Yu-Mei
Published: February 2025

Supplementary Figure 9
Figure S5 from Breast Cancer Subtype–Specific Organotropism Is Dictated by FOXF2-Regulated Metastatic Dormancy and Recovery
Authors: Jiang Wen-Jing , Zhou Tian-Hao , Huang Huan-Jing , Li Lin-Sen , Tan Hao , Zhang Rui , Wang Qing-Shan , Feng Yu-Mei
Published: February 2025

Supplementary Figure 5
Figure S4 from Breast Cancer Subtype–Specific Organotropism Is Dictated by FOXF2-Regulated Metastatic Dormancy and Recovery
Authors: Jiang Wen-Jing , Zhou Tian-Hao , Huang Huan-Jing , Li Lin-Sen , Tan Hao , Zhang Rui , Wang Qing-Shan , Feng Yu-Mei
Published: February 2025

Supplementary Figure 4
Figure S2 from Breast Cancer Subtype–Specific Organotropism Is Dictated by FOXF2-Regulated Metastatic Dormancy and Recovery
Authors: Jiang Wen-Jing , Zhou Tian-Hao , Huang Huan-Jing , Li Lin-Sen , Tan Hao , Zhang Rui , Wang Qing-Shan , Feng Yu-Mei
Published: February 2025

Supplementary Figure 2
Figure S12 from Breast Cancer Subtype–Specific Organotropism Is Dictated by FOXF2-Regulated Metastatic Dormancy and Recovery
Authors: Jiang Wen-Jing , Zhou Tian-Hao , Huang Huan-Jing , Li Lin-Sen , Tan Hao , Zhang Rui , Wang Qing-Shan , Feng Yu-Mei
Published: February 2025

Supplementary Figure 12
Figure S10 from Breast Cancer Subtype–Specific Organotropism Is Dictated by FOXF2-Regulated Metastatic Dormancy and Recovery
Authors: Jiang Wen-Jing , Zhou Tian-Hao , Huang Huan-Jing , Li Lin-Sen , Tan Hao , Zhang Rui , Wang Qing-Shan , Feng Yu-Mei
Published: February 2025

Supplementary Figure 10
Table S7 from Mapping of the T-cell Landscape of Biliary Tract Cancer Unravels Anatomic Subtype-Specific Heterogeneity
Authors: Nie Jianhua , Zhang Shuyuan , Guo Ying , Liu Caiqi , Shi Jiaqi , Wu Haotian , Na Ruisi , Liang Yingjian , Yu Shan , Quan Fei , Liu Kun , Li Mingwei , Zhou Meng , Zhao Ying , Li Xuehan , Luo Shengnan , Zhang Qian , Wang Guangyu , Zhang Yanqiao , Yao Yuanfei , Xiao Yun , Tai Sheng , Zheng Tongsen
Published: February 2025

Differentially expressed genes in ICC, ECC and GBC, respectively.
Figure S1 from Breast Cancer Subtype–Specific Organotropism Is Dictated by FOXF2-Regulated Metastatic Dormancy and Recovery
Authors: Jiang Wen-Jing , Zhou Tian-Hao , Huang Huan-Jing , Li Lin-Sen , Tan Hao , Zhang Rui , Wang Qing-Shan , Feng Yu-Mei
Published: February 2025

Supplementary Figure 1
Table S4 from Mapping of the T-cell Landscape of Biliary Tract Cancer Unravels Anatomic Subtype-Specific Heterogeneity
Authors: Nie Jianhua , Zhang Shuyuan , Guo Ying , Liu Caiqi , Shi Jiaqi , Wu Haotian , Na Ruisi , Liang Yingjian , Yu Shan , Quan Fei , Liu Kun , Li Mingwei , Zhou Meng , Zhao Ying , Li Xuehan , Luo Shengnan , Zhang Qian , Wang Guangyu , Zhang Yanqiao , Yao Yuanfei , Xiao Yun , Tai Sheng , Zheng Tongsen
Published: February 2025

Antibodies used in human sample.
Table S1 from Mapping of the T-cell Landscape of Biliary Tract Cancer Unravels Anatomic Subtype-Specific Heterogeneity
Authors: Nie Jianhua , Zhang Shuyuan , Guo Ying , Liu Caiqi , Shi Jiaqi , Wu Haotian , Na Ruisi , Liang Yingjian , Yu Shan , Quan Fei , Liu Kun , Li Mingwei , Zhou Meng , Zhao Ying , Li Xuehan , Luo Shengnan , Zhang Qian , Wang Guangyu , Zhang Yanqiao , Yao Yuanfei , Xiao Yun , Tai Sheng , Zheng Tongsen
Published: February 2025

Clinical characteristics of each sample used in scRNA-seq and scTCR-seq study.
Figure S11 from Mapping of the T-cell Landscape of Biliary Tract Cancer Unravels Anatomic Subtype-Specific Heterogeneity
Authors: Nie Jianhua , Zhang Shuyuan , Guo Ying , Liu Caiqi , Shi Jiaqi , Wu Haotian , Na Ruisi , Liang Yingjian , Yu Shan , Quan Fei , Liu Kun , Li Mingwei , Zhou Meng , Zhao Ying , Li Xuehan , Luo Shengnan , Zhang Qian , Wang Guangyu , Zhang Yanqiao , Yao Yuanfei , Xiao Yun , Tai Sheng , Zheng Tongsen
Published: February 2025

LGALS1 was highly expressed in ICC and associated with immunosuppression of Tregs.
Table S5 from Mapping of the T-cell Landscape of Biliary Tract Cancer Unravels Anatomic Subtype-Specific Heterogeneity
Authors: Nie Jianhua , Zhang Shuyuan , Guo Ying , Liu Caiqi , Shi Jiaqi , Wu Haotian , Na Ruisi , Liang Yingjian , Yu Shan , Quan Fei , Liu Kun , Li Mingwei , Zhou Meng , Zhao Ying , Li Xuehan , Luo Shengnan , Zhang Qian , Wang Guangyu , Zhang Yanqiao , Yao Yuanfei , Xiao Yun , Tai Sheng , Zheng Tongsen
Published: February 2025

Antibodies and primers used in mouse sample.
Supplementary Data from Mapping of the T-cell Landscape of Biliary Tract Cancer Unravels Anatomic Subtype-Specific Heterogeneity
Authors: Nie Jianhua , Zhang Shuyuan , Guo Ying , Liu Caiqi , Shi Jiaqi , Wu Haotian , Na Ruisi , Liang Yingjian , Yu Shan , Quan Fei , Liu Kun , Li Mingwei , Zhou Meng , Zhao Ying , Li Xuehan , Luo Shengnan , Zhang Qian , Wang Guangyu , Zhang Yanqiao , Yao Yuanfei , Xiao Yun , Tai Sheng , Zheng Tongsen
Published: February 2025

Supplementary Materials
Figure S7 from Mapping of the T-cell Landscape of Biliary Tract Cancer Unravels Anatomic Subtype-Specific Heterogeneity
Authors: Nie Jianhua , Zhang Shuyuan , Guo Ying , Liu Caiqi , Shi Jiaqi , Wu Haotian , Na Ruisi , Liang Yingjian , Yu Shan , Quan Fei , Liu Kun , Li Mingwei , Zhou Meng , Zhao Ying , Li Xuehan , Luo Shengnan , Zhang Qian , Wang Guangyu , Zhang Yanqiao , Yao Yuanfei , Xiao Yun , Tai Sheng , Zheng Tongsen
Published: February 2025

The TCR diversity and clonal expansion differences of TIL-T among different anatomical subtypes of BTC.
Figure S12 from Mapping of the T-cell Landscape of Biliary Tract Cancer Unravels Anatomic Subtype-Specific Heterogeneity
Authors: Nie Jianhua , Zhang Shuyuan , Guo Ying , Liu Caiqi , Shi Jiaqi , Wu Haotian , Na Ruisi , Liang Yingjian , Yu Shan , Quan Fei , Liu Kun , Li Mingwei , Zhou Meng , Zhao Ying , Li Xuehan , Luo Shengnan , Zhang Qian , Wang Guangyu , Zhang Yanqiao , Yao Yuanfei , Xiao Yun , Tai Sheng , Zheng Tongsen
Published: February 2025

OTX008 treatment altered the landscape of T cells in tumor and spleen within ICC mouse model.
Figure S10 from Mapping of the T-cell Landscape of Biliary Tract Cancer Unravels Anatomic Subtype-Specific Heterogeneity
Authors: Nie Jianhua , Zhang Shuyuan , Guo Ying , Liu Caiqi , Shi Jiaqi , Wu Haotian , Na Ruisi , Liang Yingjian , Yu Shan , Quan Fei , Liu Kun , Li Mingwei , Zhou Meng , Zhao Ying , Li Xuehan , Luo Shengnan , Zhang Qian , Wang Guangyu , Zhang Yanqiao , Yao Yuanfei , Xiao Yun , Tai Sheng , Zheng Tongsen
Published: February 2025

The CXCL13+ T cells are associated with the maturation of TLS in ECC.
Data from Mapping of the T-cell Landscape of Biliary Tract Cancer Unravels Anatomic Subtype-Specific Heterogeneity
Authors: Nie Jianhua , Zhang Shuyuan , Guo Ying , Liu Caiqi , Shi Jiaqi , Wu Haotian , Na Ruisi , Liang Yingjian , Yu Shan , Quan Fei , Liu Kun , Li Mingwei , Zhou Meng , Zhao Ying , Li Xuehan , Luo Shengnan , Zhang Qian , Wang Guangyu , Zhang Yanqiao , Yao Yuanfei , Xiao Yun , Tai Sheng , Zheng Tongsen
Published: February 2025

Abstract
Biliary tract cancer (BTC), encompassing diseases such as intrahepatic (ICC), extrahepatic cholangiocarcinoma (ECC), and gallbladder cancer, is not only increasing but also poses a significant and urgent health threat due to its high malignancy. Genomic differences point to the possibility that these subtypes represent distinct diseases. Elucidation of the specific distribution of T-cell subsets, critical to cancer immunity, across these diseases could provide better insights into the unique biology of BTC subtypes and help identify potential precision medicine strategies. To address this, we conducted single-cell RNA sequencing and T-cell receptor sequencing on CD3+ T cells from 36 samples from 16 patients with BTC across all subtypes and analyzed 355 pathologic slides to examine the spatial distribution of T cells and tertiary lymphoid structures. Compared with ICC and gallbladder cancer, ECC possessed a unique immune profile characterized by T-cell exhaustion, elevated CXCL13 expression in CD4+ T helper–like and CD8+CXCL13+ exhausted T cells, more mature tertiary lymphoid structures, and fewer desert immunophenotypes. Conversely, ICC displayed an inflamed immunophenotype with an enrichment of IFN-related pathways and high expression of LGALS1 in activated regulatory T cells, associated with immunosuppression. Inhibition of LGALS1 reduced tumor growth and regulatory T-cell prevalence in ICC mouse models. Overall, this study unveils T-cell diversity across BTC subtypes at the single-cell and spatial level that could open paths for tailored immunotherapies.

Significance: Single-cell and spatial analyses detailed the T-cell characteristics specific to anatomic subtypes of biliary tract cancer, identifying unique immunologic features that could potentially be harnessed to improve patient outcomes.
Supplementary Table S4 from HMGA2 Expression Predicts Subtype, Survival, and Treatment Outcome in Pancreatic Ductal Adenocarcinoma
Authors: Yamamoto Naomi , Dobersch Stephanie , Loveless Ian , Samraj Annie N. , Jang Gun Ho , Haraguchi Miki , Kang Liang-I. , Ruzinova Marianna B. , Vij Kiran R. , Mudd Jacqueline L. , Walsh Thomas , Safyan Rachael A. , Chiorean Elena Gabriela , Hingorani Sunil R. , Bolton Nathan M. , Li Li , Fields Ryan C. , DeNardo David G. , Notta Faiyaz , Crawford Howard C. , Steele Nina G. , Kugel Sita
Published: February 2025

Supplementary Table S4. Chemotherapy Regimens.
Supplementary Table S3 from HMGA2 Expression Predicts Subtype, Survival, and Treatment Outcome in Pancreatic Ductal Adenocarcinoma
Authors: Yamamoto Naomi , Dobersch Stephanie , Loveless Ian , Samraj Annie N. , Jang Gun Ho , Haraguchi Miki , Kang Liang-I. , Ruzinova Marianna B. , Vij Kiran R. , Mudd Jacqueline L. , Walsh Thomas , Safyan Rachael A. , Chiorean Elena Gabriela , Hingorani Sunil R. , Bolton Nathan M. , Li Li , Fields Ryan C. , DeNardo David G. , Notta Faiyaz , Crawford Howard C. , Steele Nina G. , Kugel Sita
Published: February 2025

Supplementary Table S3. HMGA2 vs GATA6 Differential Genes.
Supplementary Figure S6 from HMGA2 Expression Predicts Subtype, Survival, and Treatment Outcome in Pancreatic Ductal Adenocarcinoma
Authors: Yamamoto Naomi , Dobersch Stephanie , Loveless Ian , Samraj Annie N. , Jang Gun Ho , Haraguchi Miki , Kang Liang-I. , Ruzinova Marianna B. , Vij Kiran R. , Mudd Jacqueline L. , Walsh Thomas , Safyan Rachael A. , Chiorean Elena Gabriela , Hingorani Sunil R. , Bolton Nathan M. , Li Li , Fields Ryan C. , DeNardo David G. , Notta Faiyaz , Crawford Howard C. , Steele Nina G. , Kugel Sita
Published: February 2025

Supplementary Figure S6. GATA6 expression predicts chemotherapy response to GnP but not mFFX. A) GATA6low metastatic tumors have significantly worse overall survival when treated with combination GnP first-line chemotherapy. B) GATA6 status does not predict overall survival when patients receive first line mFFX chemotherapy.
Supplementary Figure S3 from HMGA2 Expression Predicts Subtype, Survival, and Treatment Outcome in Pancreatic Ductal Adenocarcinoma
Authors: Yamamoto Naomi , Dobersch Stephanie , Loveless Ian , Samraj Annie N. , Jang Gun Ho , Haraguchi Miki , Kang Liang-I. , Ruzinova Marianna B. , Vij Kiran R. , Mudd Jacqueline L. , Walsh Thomas , Safyan Rachael A. , Chiorean Elena Gabriela , Hingorani Sunil R. , Bolton Nathan M. , Li Li , Fields Ryan C. , DeNardo David G. , Notta Faiyaz , Crawford Howard C. , Steele Nina G. , Kugel Sita
Published: February 2025

Supplementary Figure S3. Consort Diagram and Mixed Populations. A) Consort diagram of analyzed samples. For survival analyses, all patients with intact cores (n = 491) were assessed. For treatment response analyses, patients were further subdivided by type of chemotherapy received, and neoadjuvant-treated samples were considered separately (n = 51). B) Mixed (HMGA2+ GATA6+) and double negative (HMGA2- GATA6-) populations show intermediate survival between basal and classical tumors.
Supplementary Figure S1 from HMGA2 Expression Predicts Subtype, Survival, and Treatment Outcome in Pancreatic Ductal Adenocarcinoma
Authors: Yamamoto Naomi , Dobersch Stephanie , Loveless Ian , Samraj Annie N. , Jang Gun Ho , Haraguchi Miki , Kang Liang-I. , Ruzinova Marianna B. , Vij Kiran R. , Mudd Jacqueline L. , Walsh Thomas , Safyan Rachael A. , Chiorean Elena Gabriela , Hingorani Sunil R. , Bolton Nathan M. , Li Li , Fields Ryan C. , DeNardo David G. , Notta Faiyaz , Crawford Howard C. , Steele Nina G. , Kugel Sita
Published: February 2025

Supplementary Figure S1. Example images of IHC of FFPE samples. A) HMGA2 positive glands. B) GATA6 positive glands. Scale bars = 50 μm.
Supplementary Table S4 from The Prostaglandin EP4 Antagonist Vorbipiprant Combined with PD-1 Blockade for Refractory Microsatellite-Stable Metastatic Colorectal Cancer: A Phase Ib/IIa Trial
Authors: Pietrantonio Filippo , Morano Federica , Niger Monica , Ghelardi Filippo , Chiodoni Claudia , Palazzo Michele , Nichetti Federico , Manca Paolo , Cristarella Eleonora , Doldi Valentina , Zaffaroni Nadia , Sabella Giovanna , Brambilla Nadia , Benincasa Elena , Giacovelli Giampaolo , Vitalini Cristina , Girolami Federica , Rovati Lucio C.
Published: February 2025

Supplementary Table S4. Logistic regression analysis results of immunecell phenotypes enrichment scores as predictors of treatment response.
Supplementary Table S2 from The Prostaglandin EP4 Antagonist Vorbipiprant Combined with PD-1 Blockade for Refractory Microsatellite-Stable Metastatic Colorectal Cancer: A Phase Ib/IIa Trial
Authors: Pietrantonio Filippo , Morano Federica , Niger Monica , Ghelardi Filippo , Chiodoni Claudia , Palazzo Michele , Nichetti Federico , Manca Paolo , Cristarella Eleonora , Doldi Valentina , Zaffaroni Nadia , Sabella Giovanna , Brambilla Nadia , Benincasa Elena , Giacovelli Giampaolo , Vitalini Cristina , Girolami Federica , Rovati Lucio C.
Published: February 2025

Supplementary Table S2. Logistic regression analysis results of inflammatory gene expression signatures enrichment scores as predictors of treatment response.
Supplementary Table S3 from Complete Remissions of HER2-Positive Trastuzumab-Resistant Xenografts Using a Potent [225Ac]Ac-Labeled Anti-HER2 Antibody–Drug Radioconjugate
Authors: Pougoue Ketchemen Jessica , Njotu Fabrice Ngoh , Babeker Hanan , Monzer Alissar , Nwangele Emmanuel , Tikum Anjong Florence , Henning Nikita , Hassani Nava , Frye Sarah , Perron Randy , Byrne Chris , Didychuk Candice , Qi Qi , Bannister Laura , Doroudi Alireza , Fonge Humphrey
Published: February 2025

Supplementary Table S3: Blood chemistry panel for toxicity of [225Ac]Ac-Macropa-T-PEG6-DM1 in non-tumor bearing Balb/C mice
Supplementary Figure S8 from Complete Remissions of HER2-Positive Trastuzumab-Resistant Xenografts Using a Potent [225Ac]Ac-Labeled Anti-HER2 Antibody–Drug Radioconjugate
Authors: Pougoue Ketchemen Jessica , Njotu Fabrice Ngoh , Babeker Hanan , Monzer Alissar , Nwangele Emmanuel , Tikum Anjong Florence , Henning Nikita , Hassani Nava , Frye Sarah , Perron Randy , Byrne Chris , Didychuk Candice , Qi Qi , Bannister Laura , Doroudi Alireza , Fonge Humphrey
Published: February 2025

Supplementary Fig. S8: H&E staining of some major organs. Micrographs show no major microscopic differences between control (saline) and treatment groups. T: trastuzumab; T-PEG6-DM1: trastuzumab-PEG6-DM1; [225Ac]Ac-T-PEG6-DM1 = [225Ac]Ac-Macropa-trastuzumab-PEG6-DM1.
Supplementary Figure S4 from The Prostaglandin EP4 Antagonist Vorbipiprant Combined with PD-1 Blockade for Refractory Microsatellite-Stable Metastatic Colorectal Cancer: A Phase Ib/IIa Trial
Authors: Pietrantonio Filippo , Morano Federica , Niger Monica , Ghelardi Filippo , Chiodoni Claudia , Palazzo Michele , Nichetti Federico , Manca Paolo , Cristarella Eleonora , Doldi Valentina , Zaffaroni Nadia , Sabella Giovanna , Brambilla Nadia , Benincasa Elena , Giacovelli Giampaolo , Vitalini Cristina , Girolami Federica , Rovati Lucio C.
Published: February 2025

Supplementary Figure S4. ESTIMATE-based deconvolution analysis comparing patients with PFS< or >4 months.
Supplementary Figure S7 from Complete Remissions of HER2-Positive Trastuzumab-Resistant Xenografts Using a Potent [225Ac]Ac-Labeled Anti-HER2 Antibody–Drug Radioconjugate
Authors: Pougoue Ketchemen Jessica , Njotu Fabrice Ngoh , Babeker Hanan , Monzer Alissar , Nwangele Emmanuel , Tikum Anjong Florence , Henning Nikita , Hassani Nava , Frye Sarah , Perron Randy , Byrne Chris , Didychuk Candice , Qi Qi , Bannister Laura , Doroudi Alireza , Fonge Humphrey
Published: February 2025

Supplementary Fig. S7: In vitro stability of [225Ac]Ac-Macropa-T-PEG6-DM1 and radioligand binding assay. (A) Stability of [225Ac]Ac-Macropa-T-PEG6-DM1 was studied in human serum (HS) and PBS for up to 10-d in duplicate (n = 2). (B) Saturation binding assay was carried out in HER2-positive HCC1954 cell line in triplicate (n = 3).
Supplementary Figure S5 from Complete Remissions of HER2-Positive Trastuzumab-Resistant Xenografts Using a Potent [225Ac]Ac-Labeled Anti-HER2 Antibody–Drug Radioconjugate
Authors: Pougoue Ketchemen Jessica , Njotu Fabrice Ngoh , Babeker Hanan , Monzer Alissar , Nwangele Emmanuel , Tikum Anjong Florence , Henning Nikita , Hassani Nava , Frye Sarah , Perron Randy , Byrne Chris , Didychuk Candice , Qi Qi , Bannister Laura , Doroudi Alireza , Fonge Humphrey
Published: February 2025

Supplementary Fig. S5: Chemical structure of trastuzumab-antibody-drug radioconjugate (T-ADR). The naked trastuzumab was first conjugated with the drug linker, then with p-SCN-Macropa prior to the [225Ac]Ac-labeling.
Supplementary Table S4 from Genomic Profiling Reveals SMARCA4 Mutations Are Associated with Shorter Overall and Intracranial Progression-Free Survival in Patients with Melanoma Brain Metastases
Authors: Fischer Grant M. , Lamba Nayan , Vogelzang Jayne , Aizer Ayal , Ligon Keith L.
Published: February 2025

Supplementary Table S4. MSK-IMPACT primary tumor samples used in analyses, information on if brain metastases ever developed in patients, and survival information from the time of melanoma diagnosis.
Supplemental Table 7 from Duvelisib with Docetaxel for Patients with Anti–PD-1 Refractory, Recurrent, or Metastatic Head and Neck Squamous Cell Carcinoma
Authors: Hanna Glenn J. , Oakley L. B. , Shi R. , ONeill A. , Shin K. Y. , Scarfo N. , Sehgal K. , Dennis M. J. , Quinn N. , Jo V. Y. , Wong K. , Shvyrkova A. , Kushnarev V. , Shanthappa B. U. , Tkachuk A. , Kryukov K. , Sarachakov A. , Svekolkin V. , Lennerz J. , Waters S. , Haddad R. I.
Published: February 2025

Supplemental Table 7. Correlating pre-treatment tumor immune cell parameters with outcomes (N=18).
Supplemental Table 6 from Duvelisib with Docetaxel for Patients with Anti–PD-1 Refractory, Recurrent, or Metastatic Head and Neck Squamous Cell Carcinoma
Authors: Hanna Glenn J. , Oakley L. B. , Shi R. , ONeill A. , Shin K. Y. , Scarfo N. , Sehgal K. , Dennis M. J. , Quinn N. , Jo V. Y. , Wong K. , Shvyrkova A. , Kushnarev V. , Shanthappa B. U. , Tkachuk A. , Kryukov K. , Sarachakov A. , Svekolkin V. , Lennerz J. , Waters S. , Haddad R. I.
Published: February 2025

Supplemental Table 6. Results of multiplex immunofluorescence profiling on tumor specimens.
Supplementary Table 6 from A Phase I Study of FHD-609, a Heterobifunctional Degrader of Bromodomain-Containing Protein 9, in Patients with Advanced Synovial Sarcoma or SMARCB1-Deficient Tumors
Authors: Livingston J. Andrew , Blay Jean-Yves , Trent Jonathan , Valverde Claudia , Agulnik Mark , Gounder Mrinal , Le Cesne Axel , McKean Meredith , Wagner Michael J. , Stacchiotti Silvia , Agresta Samuel , Quintás-Cardama Alfonso , Reilly Sarah A. , Healy Kathleen , Hickman Denice , Zhao Tina , Ballesteros-Perez Alex , Khalil Alexis , Collins Michael P. , Piel Jessica , Horrigan Kim , Lefkovith Ariel , Innis Scott , Lazar Alexander J. , Cote Gregory M. , Wagner Andrew J.
Published: February 2025

Supplementary Table 6
Supplementary Table 5 from A Phase I Study of FHD-609, a Heterobifunctional Degrader of Bromodomain-Containing Protein 9, in Patients with Advanced Synovial Sarcoma or SMARCB1-Deficient Tumors
Authors: Livingston J. Andrew , Blay Jean-Yves , Trent Jonathan , Valverde Claudia , Agulnik Mark , Gounder Mrinal , Le Cesne Axel , McKean Meredith , Wagner Michael J. , Stacchiotti Silvia , Agresta Samuel , Quintás-Cardama Alfonso , Reilly Sarah A. , Healy Kathleen , Hickman Denice , Zhao Tina , Ballesteros-Perez Alex , Khalil Alexis , Collins Michael P. , Piel Jessica , Horrigan Kim , Lefkovith Ariel , Innis Scott , Lazar Alexander J. , Cote Gregory M. , Wagner Andrew J.
Published: February 2025

Supplementary Table 5
Supplemental Appendix 1 from Duvelisib with Docetaxel for Patients with Anti–PD-1 Refractory, Recurrent, or Metastatic Head and Neck Squamous Cell Carcinoma
Authors: Hanna Glenn J. , Oakley L. B. , Shi R. , ONeill A. , Shin K. Y. , Scarfo N. , Sehgal K. , Dennis M. J. , Quinn N. , Jo V. Y. , Wong K. , Shvyrkova A. , Kushnarev V. , Shanthappa B. U. , Tkachuk A. , Kryukov K. , Sarachakov A. , Svekolkin V. , Lennerz J. , Waters S. , Haddad R. I.
Published: February 2025

Supplemental Appendix 1. Study protocol.
Supplementary Table S4 from Bladder Preservation with Durvalumab plus Tremelimumab and Concurrent Radiotherapy in Patients with Localized Muscle-Invasive Bladder Cancer (IMMUNOPRESERVE): A Phase II Spanish Oncology GenitoUrinary Group Trial
Authors: Garcia-del-Muro Xavier , P. Valderrama Begoña , Medina-Colmenero Ana , Etxaniz Olatz , Gironés Sarrió Regina , Juan-Fita María José , Costa-García Marcel , Moreno Rafael , Miras Rodríguez Isabel , Ortiz Irene , Cuéllar Andrés , Ferrer Ferran , Vigués Francesc , de Haro Piedra Roberto , Candal Gomez Arturo , Villà Salvador , Pontones José Luis , Murria Yasmina , Lendínez-Cano Guillermo , Alemany Ramon
Published: February 2025

Supplementary Table 4. Pathological response rate According to PD-L1 status. PD-L1 status was assessed in 27 patients.
Supplementary Table S2 from Bladder Preservation with Durvalumab plus Tremelimumab and Concurrent Radiotherapy in Patients with Localized Muscle-Invasive Bladder Cancer (IMMUNOPRESERVE): A Phase II Spanish Oncology GenitoUrinary Group Trial
Authors: Garcia-del-Muro Xavier , P. Valderrama Begoña , Medina-Colmenero Ana , Etxaniz Olatz , Gironés Sarrió Regina , Juan-Fita María José , Costa-García Marcel , Moreno Rafael , Miras Rodríguez Isabel , Ortiz Irene , Cuéllar Andrés , Ferrer Ferran , Vigués Francesc , de Haro Piedra Roberto , Candal Gomez Arturo , Villà Salvador , Pontones José Luis , Murria Yasmina , Lendínez-Cano Guillermo , Alemany Ramon
Published: February 2025

Supplementary Table 2. Antibody panels used for PBMC samples analysis by flow cytometer.
Supplementary Data 2 from A Phase I Study of FHD-609, a Heterobifunctional Degrader of Bromodomain-Containing Protein 9, in Patients with Advanced Synovial Sarcoma or SMARCB1-Deficient Tumors
Authors: Livingston J. Andrew , Blay Jean-Yves , Trent Jonathan , Valverde Claudia , Agulnik Mark , Gounder Mrinal , Le Cesne Axel , McKean Meredith , Wagner Michael J. , Stacchiotti Silvia , Agresta Samuel , Quintás-Cardama Alfonso , Reilly Sarah A. , Healy Kathleen , Hickman Denice , Zhao Tina , Ballesteros-Perez Alex , Khalil Alexis , Collins Michael P. , Piel Jessica , Horrigan Kim , Lefkovith Ariel , Innis Scott , Lazar Alexander J. , Cote Gregory M. , Wagner Andrew J.
Published: February 2025

Supplementary Data Clinical Protocol
Supplementary Table S8 from Next-Generation Sequencing–Based MSI Scoring Predicts Benefit in Mismatch Repair–Deficient Tumors Treated with Nivolumab: Follow-up on NCI-MATCH Arm Z1D
Authors: Schoenfeld Jonathan D. , Azad Nilofer S. , Gross Jacob , Chen Li , Overman Michael J. , Kao Katrina , Jackson Latifa , Brunnquell Donna , Bu Xiangning , Coppola Christina , Guan Ping , Lee Jennifer , Sims David , Fuchs Rebecca , Weirather Jason L. , Pfaff Kathleen L. , Gunasti Lauren , Ranasinghe Srin , Hamilton Stanley R. , Wang Victoria , O’Dwyer Peter J. , Wu Catherine J. , Rodig Scott J. , Patton David R. , Harris Lyndsay
Published: February 2025

Summary of evidence evaluating potential predictive biomarkers of response to immune checkpoint blockade in patients with MSI-H non-colorectal cancer tumors
Supplementary Table S7 from Next-Generation Sequencing–Based MSI Scoring Predicts Benefit in Mismatch Repair–Deficient Tumors Treated with Nivolumab: Follow-up on NCI-MATCH Arm Z1D
Authors: Schoenfeld Jonathan D. , Azad Nilofer S. , Gross Jacob , Chen Li , Overman Michael J. , Kao Katrina , Jackson Latifa , Brunnquell Donna , Bu Xiangning , Coppola Christina , Guan Ping , Lee Jennifer , Sims David , Fuchs Rebecca , Weirather Jason L. , Pfaff Kathleen L. , Gunasti Lauren , Ranasinghe Srin , Hamilton Stanley R. , Wang Victoria , O’Dwyer Peter J. , Wu Catherine J. , Rodig Scott J. , Patton David R. , Harris Lyndsay
Published: February 2025

RNAseq Expression analysis using GSEA
Supplementary Table S5 from Next-Generation Sequencing–Based MSI Scoring Predicts Benefit in Mismatch Repair–Deficient Tumors Treated with Nivolumab: Follow-up on NCI-MATCH Arm Z1D
Authors: Schoenfeld Jonathan D. , Azad Nilofer S. , Gross Jacob , Chen Li , Overman Michael J. , Kao Katrina , Jackson Latifa , Brunnquell Donna , Bu Xiangning , Coppola Christina , Guan Ping , Lee Jennifer , Sims David , Fuchs Rebecca , Weirather Jason L. , Pfaff Kathleen L. , Gunasti Lauren , Ranasinghe Srin , Hamilton Stanley R. , Wang Victoria , O’Dwyer Peter J. , Wu Catherine J. , Rodig Scott J. , Patton David R. , Harris Lyndsay
Published: February 2025

EnrichR results of top mutant genes from MutSig2CV
Supplementary Table S3 from Smoking-Associated Carcinogen–Induced Inflammation Promotes Lung Carcinogenesis via IRAK4 Activation
Authors: Aggarwal Ritesh K. , Sidoli Simone , Wang Jingli , Sahu Srabani , Sanawar Rahul , Gupta Varun , Aluri Srinivas , Sukrithan Vineeth , Vegivinti Charan T.R. , Zavras Phaedon D. , Verma Divij , Gordon-Mitchell Shanisha , Agarwal Beamon , Verma Tanya , Starczynowski Daniel T. , Steidl Ulrich G. , Shastri Aditi , Halmos Balazs , LaFave Lindsay M. , Cheng Haiying , Verma Amit , Zou Yiyu
Published: February 2025

Supplementary Table S3. Manuscript Figure 3 data - The Excel file has data points for easy access to infer numerical values for data presented in the manuscript. Also see Data Availability Statement.
Supplementary Table S1 from Next-Generation Sequencing–Based MSI Scoring Predicts Benefit in Mismatch Repair–Deficient Tumors Treated with Nivolumab: Follow-up on NCI-MATCH Arm Z1D
Authors: Schoenfeld Jonathan D. , Azad Nilofer S. , Gross Jacob , Chen Li , Overman Michael J. , Kao Katrina , Jackson Latifa , Brunnquell Donna , Bu Xiangning , Coppola Christina , Guan Ping , Lee Jennifer , Sims David , Fuchs Rebecca , Weirather Jason L. , Pfaff Kathleen L. , Gunasti Lauren , Ranasinghe Srin , Hamilton Stanley R. , Wang Victoria , O’Dwyer Peter J. , Wu Catherine J. , Rodig Scott J. , Patton David R. , Harris Lyndsay
Published: February 2025

Baseline characteristics for patients with (in) or without (out) molecular data
Supplementary Figure S7 from Next-Generation Sequencing–Based MSI Scoring Predicts Benefit in Mismatch Repair–Deficient Tumors Treated with Nivolumab: Follow-up on NCI-MATCH Arm Z1D
Authors: Schoenfeld Jonathan D. , Azad Nilofer S. , Gross Jacob , Chen Li , Overman Michael J. , Kao Katrina , Jackson Latifa , Brunnquell Donna , Bu Xiangning , Coppola Christina , Guan Ping , Lee Jennifer , Sims David , Fuchs Rebecca , Weirather Jason L. , Pfaff Kathleen L. , Gunasti Lauren , Ranasinghe Srin , Hamilton Stanley R. , Wang Victoria , O’Dwyer Peter J. , Wu Catherine J. , Rodig Scott J. , Patton David R. , Harris Lyndsay
Published: February 2025

Differences in infiltrating immune cell populations as determined by multiplex immunofluorescence among subjects with and without clinical benefit
Supplementary Table S1 from Smoking-Associated Carcinogen–Induced Inflammation Promotes Lung Carcinogenesis via IRAK4 Activation
Authors: Aggarwal Ritesh K. , Sidoli Simone , Wang Jingli , Sahu Srabani , Sanawar Rahul , Gupta Varun , Aluri Srinivas , Sukrithan Vineeth , Vegivinti Charan T.R. , Zavras Phaedon D. , Verma Divij , Gordon-Mitchell Shanisha , Agarwal Beamon , Verma Tanya , Starczynowski Daniel T. , Steidl Ulrich G. , Shastri Aditi , Halmos Balazs , LaFave Lindsay M. , Cheng Haiying , Verma Amit , Zou Yiyu
Published: February 2025

Supplementary Table S1. Manuscript Figure 1 data - The Excel file has data points for easy access to infer numerical values for data presented in the manuscript. Also see Data Availability Statement.
Supplementary Figure S6 from Next-Generation Sequencing–Based MSI Scoring Predicts Benefit in Mismatch Repair–Deficient Tumors Treated with Nivolumab: Follow-up on NCI-MATCH Arm Z1D
Authors: Schoenfeld Jonathan D. , Azad Nilofer S. , Gross Jacob , Chen Li , Overman Michael J. , Kao Katrina , Jackson Latifa , Brunnquell Donna , Bu Xiangning , Coppola Christina , Guan Ping , Lee Jennifer , Sims David , Fuchs Rebecca , Weirather Jason L. , Pfaff Kathleen L. , Gunasti Lauren , Ranasinghe Srin , Hamilton Stanley R. , Wang Victoria , O’Dwyer Peter J. , Wu Catherine J. , Rodig Scott J. , Patton David R. , Harris Lyndsay
Published: February 2025

Gene mutation profile in the cohort with corresponding clinical benefit status, MSI score, best confirmed response and TMB score
Supplementary Figure S4 from Next-Generation Sequencing–Based MSI Scoring Predicts Benefit in Mismatch Repair–Deficient Tumors Treated with Nivolumab: Follow-up on NCI-MATCH Arm Z1D
Authors: Schoenfeld Jonathan D. , Azad Nilofer S. , Gross Jacob , Chen Li , Overman Michael J. , Kao Katrina , Jackson Latifa , Brunnquell Donna , Bu Xiangning , Coppola Christina , Guan Ping , Lee Jennifer , Sims David , Fuchs Rebecca , Weirather Jason L. , Pfaff Kathleen L. , Gunasti Lauren , Ranasinghe Srin , Hamilton Stanley R. , Wang Victoria , O’Dwyer Peter J. , Wu Catherine J. , Rodig Scott J. , Patton David R. , Harris Lyndsay
Published: February 2025

Mutations across genes by type and/or frequency
Supplementary Figure S3 from Next-Generation Sequencing–Based MSI Scoring Predicts Benefit in Mismatch Repair–Deficient Tumors Treated with Nivolumab: Follow-up on NCI-MATCH Arm Z1D
Authors: Schoenfeld Jonathan D. , Azad Nilofer S. , Gross Jacob , Chen Li , Overman Michael J. , Kao Katrina , Jackson Latifa , Brunnquell Donna , Bu Xiangning , Coppola Christina , Guan Ping , Lee Jennifer , Sims David , Fuchs Rebecca , Weirather Jason L. , Pfaff Kathleen L. , Gunasti Lauren , Ranasinghe Srin , Hamilton Stanley R. , Wang Victoria , O’Dwyer Peter J. , Wu Catherine J. , Rodig Scott J. , Patton David R. , Harris Lyndsay
Published: February 2025

Receiver operating curve demonstrating relationship between tumor mutational burden and clinical benefit
Supplementary Figure S2 from Smoking-Associated Carcinogen–Induced Inflammation Promotes Lung Carcinogenesis via IRAK4 Activation
Authors: Aggarwal Ritesh K. , Sidoli Simone , Wang Jingli , Sahu Srabani , Sanawar Rahul , Gupta Varun , Aluri Srinivas , Sukrithan Vineeth , Vegivinti Charan T.R. , Zavras Phaedon D. , Verma Divij , Gordon-Mitchell Shanisha , Agarwal Beamon , Verma Tanya , Starczynowski Daniel T. , Steidl Ulrich G. , Shastri Aditi , Halmos Balazs , LaFave Lindsay M. , Cheng Haiying , Verma Amit , Zou Yiyu
Published: February 2025

Supplementary Figure S2. Uncropped Western Blots for Figure 6A data presented in the manuscript. Also see Data Availability Statement.