bluuebunny/crossref_metadata_2025 huggingface dataset:
Data from Whole-Genome DNA Methylation Profiling of Intrahepatic Cholangiocarcinoma Reveals Prognostic Subtypes with Distinct Biological Drivers
Authors: Liao Haotian , Chen Xing , Wang Haichuan , Lin Youpei , Chen Lu , Yuan Kefei , Liao Mingheng , Jiang Hanyu , Peng Jiajie , Wu Zhenru , Huang Jiwei , Li Jiaxin , Zeng Yong
Published: June 2024

Abstract
Intrahepatic cholangiocarcinoma (iCCA) is the second most prevalent primary liver cancer. Although the genetic characterization of iCCA has led to targeted therapies for treating tumors with FGFR2 alterations and IDH1/2 mutations, only a limited number of patients can benefit from these strategies. Epigenomic profiles have emerged as potential diagnostic and prognostic biomarkers for improving the treatment of cancers. In this study, we conducted whole-genome bisulfite sequencing on 331 iCCAs integrated with genetic, transcriptomic, and proteomic analyses, demonstrating the existence of four DNA methylation subtypes of iCCAs (S1–S4) that exhibited unique postoperative clinical outcomes. The S1 group was an IDH1/2 mutation–specific subtype with moderate survival. The S2 subtype was characterized by the lowest methylation level and the highest mutational burden among the four subtypes and displayed upregulation of a gene-expression pattern associated with cell cycle/DNA replication. The S3 group was distinguished by high interpatient heterogeneity of tumor immunity, a gene-expression pattern associated with carbohydrate metabolism, and an enrichment of KRAS alterations. Patients with the S2 and S3 subtypes had the shortest survival among the four subtypes. Tumors in the S4 subtype, which had the best prognosis, showed global methylation levels comparable to normal controls, increased FGFR2 fusions/BAP1 mutations, and the highest copy-number variant burdens. Further integrative and functional analyses identified GBP4 demethylation, which is highly prevalent in the S2 and S3 groups, as an epigenetic oncogenic factor that regulates iCCA proliferation, migration, and invasion. Together, this study identifies prognostic methylome alterations and epigenetic drivers in iCCA.
Significance:
Characterization of the DNA methylome of intrahepatic cholangiocarcinoma integrated with genomic, transcriptomic, and proteomic analyses uncovers molecular mechanisms affected by genome-wide DNA methylation alterations, providing a resource for identifying potential therapeutic targets.
Data from ACSL4-Mediated Membrane Phospholipid Remodeling Induces Integrin β1 Activation to Facilitate Triple-Negative Breast Cancer Metastasis
Authors: Qiu Yuxiang , Wang Xing , Sun Yan , Jin Ting , Tang Rui , Zhou Xinyue , Xu Ming , Gan Yubi , Wang Rui , Luo Haojun , Liu Manran , Tang Xi
Published: June 2024

Abstract
Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer and has a poor prognosis and a high propensity to metastasize. Lipid metabolism has emerged as a critical regulator of tumor progression and metastasis in other cancer types. Characterization of the lipid metabolic features of TNBC could provide important insights into the drivers of TNBC metastasis. Here, we showed that metastatic TNBC tumors harbor more unsaturated phospholipids, especially long-chain polyunsaturated fatty acids, at the sn-2 position of phosphatidylcholine and phosphatidylethanolamine compared with primary tumors. Metastatic TNBC tumors upregulated ACSL4, a long-chain polyunsaturated acyl-CoA synthetase that drives the preferential incorporation of polyunsaturated fatty acids into phospholipids, resulting in the alteration of membrane phospholipid composition and properties. Moreover, ACSL4-mediated phospholipid remodeling of the cell membrane induced lipid-raft localization and activation of integrin β1 in a CD47-dependent manner, which led to downstream focal adhesion kinase phosphorylation that promoted metastasis. Importantly, pharmacologic inhibition of ACSL4 suppressed tumor growth and metastasis and increased chemosensitivity in TNBC models in vivo. These findings indicate that ACSL4-mediated phospholipid remodeling enables TNBC metastasis and can be inhibited as a potential strategy to improve the efficacy of chemotherapy in TNBC.
Significance:
ACSL4 upregulation in triple-negative breast cancer alters cell membrane phospholipid composition to increase integrin β1 activation and drive metastasis, indicating that targeting ACSL4 could potentially block metastasis and improve patient outcomes.
Data from A Subpopulation of Luminal Progenitors Secretes Pleiotrophin to Promote Angiogenesis and Metastasis in Inflammatory Breast Cancer
Authors: Zhang Mengmeng , Zhou Kaiwen , Wang Zilin , Liu Ting , Stevens Laura E. , Lynce Filipa , Chen Wendy Y. , Peng Sui , Xie Yubin , Zhai Duanyang , Chen Qianjun , Shi Yawei , Shi Huijuan , Yuan Zhongyu , Li Xiaoping , Xu Juan , Cai Zhenhai , Guo Jianping , Shao Nan , Lin Ying
Published: June 2024

Abstract
Inflammatory breast cancer (IBC) is a highly aggressive subtype of breast cancer characterized by rapidly arising diffuse erythema and edema. Genomic studies have not identified consistent alterations and mechanisms that differentiate IBC from non-IBC tumors, suggesting that the microenvironment could be a potential driver of IBC phenotypes. Here, using single-cell RNA sequencing, multiplex staining, and serum analysis in patients with IBC, we identified enrichment of a subgroup of luminal progenitor (LP) cells containing high expression of the neurotropic cytokine pleiotrophin (PTN) in IBC tumors. PTN secreted by the LP cells promoted angiogenesis by directly interacting with the NRP1 receptor on endothelial tip cells located in both IBC tumors and the affected skin. NRP1 activation in tip cells led to recruitment of immature perivascular cells in the affected skin of IBC, which are correlated with increased angiogenesis and IBC metastasis. Together, these findings reveal a role for cross-talk between LPs, endothelial tip cells, and immature perivascular cells via PTN–NRP1 axis in the pathogenesis of IBC, which could lead to improved strategies for treating IBC.
Significance:
Nonmalignant luminal progenitor cells expressing pleiotrophin promote angiogenesis by activating NRP1 and induce a prometastatic tumor microenvironment in inflammatory breast cancer, providing potential therapeutic targets for this aggressive breast cancer subtype.
Supplementary Table S2 from Discovery of a Long Half-Life AURKA Inhibitor to Treat MYC-Amplified Solid Tumors as a Monotherapy and in Combination with Everolimus
Authors: Chang Chun-Ping , Yeh Teng-Kuang , Chen Chiung-Tong , Wang Wan-Ping , Chen Yen-Ting , Tsai Chia-Hua , Chen Yan-Fu , Ke Yi-Yu , Wang Jing-Ya , Chen Ching-Ping , Hsieh Tsung-Chih , Wu Mine-Hsine , Huang Chen-Lung , Chen Ya-Ping , Zhuang Hong , Chi Ya-Hui
Published: June 2024

List of KEGG pathway analyses of the 227 DEGs.
Supplementary Table S1 from Discovery of a Long Half-Life AURKA Inhibitor to Treat MYC-Amplified Solid Tumors as a Monotherapy and in Combination with Everolimus
Authors: Chang Chun-Ping , Yeh Teng-Kuang , Chen Chiung-Tong , Wang Wan-Ping , Chen Yen-Ting , Tsai Chia-Hua , Chen Yan-Fu , Ke Yi-Yu , Wang Jing-Ya , Chen Ching-Ping , Hsieh Tsung-Chih , Wu Mine-Hsine , Huang Chen-Lung , Chen Ya-Ping , Zhuang Hong , Chi Ya-Hui
Published: June 2024

List of the 227 differential express genes (DEGs) in the tumor xenografts treated with DBPR728 for 24 hr vs mock and 48 hr vs mock.
Supplementary Figure 3 from Patient-Derived Tumor Xenograft Study with CDK4/6 Inhibitor Plus AKT Inhibitor for the Management of Metastatic Castration-Resistant Prostate Cancer
Authors: Kase Adam M. , Gleba Justyna , Miller James L. , Miller Erin , Petit Joachim , Barrett Michael T. , Zhou Yumei , Parent Ephraim E. , Cai Hancheng , Knight Joshua A. , Orme Jacob , Reynolds Jordan , Durham William F. , Metz Thomas M. , Meurice Nathalie , Edenfield Brandy , Alasonyalilar Demirer Aylin , Bilgili Ahmet , Hickman Peyton G. , Pawlush Matthew L. , Marlow Laura , Wickland Daniel P. , Tan Winston , Copland John A.
Published: June 2024

Supplementary Figure 3
Supplementary Methods from A Novel Dual ATM/DNA-PK Inhibitor, XRD-0394, Potently Radiosensitizes and Potentiates PARP and Topoisomerase I Inhibitors
Authors: Gilmer Tona M. , Lai Chun-Hsiang , Guo Kexiao , Deland Katherine , Ashcraft Kathleen A. , Stewart Amy E. , Wang Yaode , Fu Jianmin , Wood Kris C. , Kirsch David G. , Kastan Michael B.
Published: June 2024

Kinase Assays and synthesis of XRD-0394
Figure S6 from A Novel Dual ATM/DNA-PK Inhibitor, XRD-0394, Potently Radiosensitizes and Potentiates PARP and Topoisomerase I Inhibitors
Authors: Gilmer Tona M. , Lai Chun-Hsiang , Guo Kexiao , Deland Katherine , Ashcraft Kathleen A. , Stewart Amy E. , Wang Yaode , Fu Jianmin , Wood Kris C. , Kirsch David G. , Kastan Michael B.
Published: June 2024

in vivo efficacy with radiation
Supplemental Table S1 from Mitochondrial and Cytosolic One-Carbon Metabolism Is a Targetable Metabolic Vulnerability in Cisplatin-Resistant Ovarian Cancer
Authors: Wallace-Povirk Adrianne , O'Connor Carrie , Dekhne Aamod S. , Bao Xun , Nayeen Md. Junayed , Schneider Mathew , Katinas Jade M. , Wong-Roushar Jennifer , Kim Seongho , Polin Lisa , Li Jing , Back Jessica B. , Dann Charles E. , Gangjee Aleem , Hou Zhanjun , Matherly Larry H.
Published: June 2024

This table shows information of ovarian cancer tissue cDNA array for real-time RT-PCR.
Supplemental Tables from 89Zr-ImmunoPET for the Specific Detection of EMP2-Positive Tumors
Authors: Chan Ann M. , Olafsen Tove , Tsui Jessica , Salazar Felix B. , Aguirre Brian , Zettlitz Kirstin A. , Condro Michael , Wu Anna M. , Braun Jonathan , Gordon Lynn K. , Ashki Negin , Whitelegge Julian , Xu Shili , Ikotun Oluwatayo , Lee Jason Thanh , Wadehra Madhuri
Published: June 2024

Supplemental Tables
Figure S5 from Proton FLASH Radiotherapy Ameliorates Radiation-induced Salivary Gland Dysfunction and Oral Mucositis and Increases Survival in a Mouse Model of Head and Neck Cancer
Authors: Chowdhury Priyanka , Velalopoulou Anastasia , Verginadis Ioannis I. , Morcos George , Loo Phoebe E. , Kim Michele M. , Motlagh Seyyedeh Azar Oliaei , Shoniyozov Khayrullo , Diffenderfer Eric S. , Ocampo Emilio A. , Putt Mary , Assenmacher Charles-Antoine , Radaelli Enrico , Lu Jiawei , Qin Ling , Liu Hengxi , Leli Nektaria Maria , Girdhani Swati , Denef Nicolas , Vander Stappen Francois , Cengel Keith A. , Busch Theresa M. , Metz James M. , Dong Lei , Lin Alexander , Koumenis Constantinos
Published: June 2024

Detection of oral mucositis as observed after staining with 1% Toluidine Blue.
Figure S4 from Proton FLASH Radiotherapy Ameliorates Radiation-induced Salivary Gland Dysfunction and Oral Mucositis and Increases Survival in a Mouse Model of Head and Neck Cancer
Authors: Chowdhury Priyanka , Velalopoulou Anastasia , Verginadis Ioannis I. , Morcos George , Loo Phoebe E. , Kim Michele M. , Motlagh Seyyedeh Azar Oliaei , Shoniyozov Khayrullo , Diffenderfer Eric S. , Ocampo Emilio A. , Putt Mary , Assenmacher Charles-Antoine , Radaelli Enrico , Lu Jiawei , Qin Ling , Liu Hengxi , Leli Nektaria Maria , Girdhani Swati , Denef Nicolas , Vander Stappen Francois , Cengel Keith A. , Busch Theresa M. , Metz James M. , Dong Lei , Lin Alexander , Koumenis Constantinos
Published: June 2024

Histopathological analysis of submandibular gland tissues post-28 days of irradiation with S-PRT/F-PRT.
Supplementary Table 5 from Thio-2 Inhibits Key Signaling Pathways Required for the Development and Progression of Castration-resistant Prostate Cancer
Authors: Neeb Antje , Figueiredo Ines , Bogdan Denisa , Cato Laura , Stober Jutta , Jiménez-Vacas Juan M. , Gourain Victor , Lee Irene I. , Seeger Rebecca , Muhle-Goll Claudia , Gurel Bora , Welti Jonathan , Nava Rodrigues Daniel , Rekowski Jan , Qiu Xintao , Jiang Yija , Di Micco Patrizio , Mateos Borja , Bielskutė Stasė , Riisnaes Ruth , Ferreira Ana , Miranda Susana , Crespo Mateus , Buroni Lorenzo , Ning Jian , Carreira Suzanne , Bräse Stefan , Jung Nicole , Gräßle Simone , Swain Amanda , Salvatella Xavier , Plymate Stephen R. , Al-Lazikani Bissan , Long Henry W. , Yuan Wei , Brown Myles , Cato Andrew C.B. , de Bono Johann S. , Sharp Adam
Published: June 2024

Cell lines.
Supplementary Figure 3 from Thio-2 Inhibits Key Signaling Pathways Required for the Development and Progression of Castration-resistant Prostate Cancer
Authors: Neeb Antje , Figueiredo Ines , Bogdan Denisa , Cato Laura , Stober Jutta , Jiménez-Vacas Juan M. , Gourain Victor , Lee Irene I. , Seeger Rebecca , Muhle-Goll Claudia , Gurel Bora , Welti Jonathan , Nava Rodrigues Daniel , Rekowski Jan , Qiu Xintao , Jiang Yija , Di Micco Patrizio , Mateos Borja , Bielskutė Stasė , Riisnaes Ruth , Ferreira Ana , Miranda Susana , Crespo Mateus , Buroni Lorenzo , Ning Jian , Carreira Suzanne , Bräse Stefan , Jung Nicole , Gräßle Simone , Swain Amanda , Salvatella Xavier , Plymate Stephen R. , Al-Lazikani Bissan , Long Henry W. , Yuan Wei , Brown Myles , Cato Andrew C.B. , de Bono Johann S. , Sharp Adam
Published: June 2024

Mouse organ hematoxylin and eosin, and BAG-1 immunohistochemistry, in BAG-1 knockout mice.
Supplementary Figure S7 from Structural Basis for Multivalent MUC16 Recognition and Robust Anti-Pancreatic Cancer Activity of Humanized Antibody AR9.6
Authors: Aguilar Eric N. , Sagar Satish , Murray Brandy R. , Rajesh Christabelle , Lei Eric K. , Michaud Sarah A. , Goodlett David R. , Caffrey Thomas C. , Grandgenett Paul M. , Swanson Benjamin , Brooks Teresa M. , Black Adrian R. , van Faassen Henk , Hussack Greg , Henry Kevin A. , Hollingsworth Michael A. , Brooks Cory L. , Radhakrishnan Prakash
Published: June 2024

Figure S7. huAR9.6 mediates tumor burden reduction by targeting the MUC16-ErbB signaling axis and the apoptotic cascade. (A) IHC for pErbB3 (Y1289), pErbB2 (Y1248), pErbB1 (Y1173) and pAKT (S473) in subcutaneous tumor tissues obtained from mice treated with vehicle (PBS) and huAR9.6 (500 µg/25 g bodyweight, i.p.). Histoscore quantification of (B) pErbB3, (C) pErbB2, (D) pErbB1 and (E) pAKT staining. (F) IHC for pErbB3 (Y1289), pErbB2 (Y1248), pAKT (S473) in patient-derived organoids treated with vehicle (PBS), isotype control huIgG and huAR9.6 (40 µg/mL for 24 h). (G) IHC for cleaved caspase 3 in subcutaneous tumor tissues obtained from mice treated with vehicle (PBS) and huAR9.6 (500 µg/25 g bodyweight, i.p.) (n=5). (H) Histoscore quantification of cleaved caspase 3. Scale bar 50 µm. Mean ± SD, p < 0.05 was considered as statistically significant using the Student’s t-test.
Supplementary Figure 2 from ATPase Copper Transporting Beta (ATP7B) Is a Novel Target for Improving the Therapeutic Efficacy of Docetaxel by Disulfiram/Copper in Human Prostate Cancer
Authors: Song Liankun , Nguyen Vyvyan , Xie Jun , Jia Shang , Chang Christopher J. , Uchio Edward , Zi Xiaolin
Published: June 2024

The effect of docetaxel on the growth of DU145 parental cells after control siRNA or ATP7B siRNA transfections.
Data from A Novel Dual ATM/DNA-PK Inhibitor, XRD-0394, Potently Radiosensitizes and Potentiates PARP and Topoisomerase I Inhibitors
Authors: Gilmer Tona M. , Lai Chun-Hsiang , Guo Kexiao , Deland Katherine , Ashcraft Kathleen A. , Stewart Amy E. , Wang Yaode , Fu Jianmin , Wood Kris C. , Kirsch David G. , Kastan Michael B.
Published: June 2024

Abstract
A majority of patients with cancer receive radiotherapy as part of their treatment regimens whether using external beam therapy or locally-delivered radioisotopes. While often effective, some tumors are inadequately controlled with radiation and radiotherapy has significant short-term and long-term toxicities for cancer survivors. Insights into molecular mechanisms involved in cellular responses to DNA breaks introduced by radiation or other cancer therapies have been gained in recent years and approaches to manipulate these responses to enhance tumor cell killing or reduce normal tissue toxicity are of great interest. Here, we report the identification and initial characterization of XRD-0394, a potent and specific dual inhibitor of two DNA damage response kinases, ATM and DNA-PKcs. This orally bioavailable molecule demonstrates significantly enhanced tumor cell kill in the setting of therapeutic ionizing irradiation in vitro and in vivo. XRD-0394 also potentiates the effectiveness of topoisomerase I inhibitors in vitro. In addition, in cells lacking BRCA1/2 XRD-0394 shows single-agent activity and synergy in combination with PARP inhibitors. A phase Ia clinical trial (NCT05002140) with XRD-0394 in combination with radiotherapy has completed. These results provide a rationale for future clinical trials with XRD-0394 in combination with radiotherapy, PARP inhibitors, and targeted delivery of topoisomerase I inhibitors.
Supplementary Table 1 from FATP5 Is Indispensable for the Growth of Intrahepatic Cholangiocarcinoma
Authors: Shihadih Diyala , Wang Xue , Zushin Peter-James H. , Khodakivskyi Pavlo , Park Hyo Min , Tso Emily , Shiblak Jena , Misic Angela , Louie Sharon M. , Ward Catherine , Hellerstein Marc , Nomura Daniel K. , Goun Elena , Urigo Francesco , Calvisi Diego F. , Chen Xin , Stahl Andreas
Published: June 2024

The comprehensive information about all detected lipids
Supplementary Table S3 from Serotonin Receptor HTR2B Facilitates Colorectal Cancer Metastasis via CREB1–ZEB1 Axis–Mediated Epithelial–Mesenchymal Transition
Authors: Li Tao , Wei Lei , Zhang Xin , Fu Bin , Zhou Yunjiang , Yang Mengdi , Cao Mengran , Chen Yaxin , Tan Yingying , Shi Yongwei , Wu Leyin , Xuan Chenyuan , Du Qianming , Hu Rong
Published: June 2024

This file contains Supplementary Table S3.
Supplementary Table S2 from Serotonin Receptor HTR2B Facilitates Colorectal Cancer Metastasis via CREB1–ZEB1 Axis–Mediated Epithelial–Mesenchymal Transition
Authors: Li Tao , Wei Lei , Zhang Xin , Fu Bin , Zhou Yunjiang , Yang Mengdi , Cao Mengran , Chen Yaxin , Tan Yingying , Shi Yongwei , Wu Leyin , Xuan Chenyuan , Du Qianming , Hu Rong
Published: June 2024

This file contains Supplementary Table S2.
Supplementary Figure S17 from Serotonin Receptor HTR2B Facilitates Colorectal Cancer Metastasis via CREB1–ZEB1 Axis–Mediated Epithelial–Mesenchymal Transition
Authors: Li Tao , Wei Lei , Zhang Xin , Fu Bin , Zhou Yunjiang , Yang Mengdi , Cao Mengran , Chen Yaxin , Tan Yingying , Shi Yongwei , Wu Leyin , Xuan Chenyuan , Du Qianming , Hu Rong
Published: June 2024

This file contains Supplementary Figure S17 and its legend.
Supplementary Figure S16 from Serotonin Receptor HTR2B Facilitates Colorectal Cancer Metastasis via CREB1–ZEB1 Axis–Mediated Epithelial–Mesenchymal Transition
Authors: Li Tao , Wei Lei , Zhang Xin , Fu Bin , Zhou Yunjiang , Yang Mengdi , Cao Mengran , Chen Yaxin , Tan Yingying , Shi Yongwei , Wu Leyin , Xuan Chenyuan , Du Qianming , Hu Rong
Published: June 2024

This file contains Supplementary Figure S16 and its legend.
Supplementary Figure S12 from Serotonin Receptor HTR2B Facilitates Colorectal Cancer Metastasis via CREB1–ZEB1 Axis–Mediated Epithelial–Mesenchymal Transition
Authors: Li Tao , Wei Lei , Zhang Xin , Fu Bin , Zhou Yunjiang , Yang Mengdi , Cao Mengran , Chen Yaxin , Tan Yingying , Shi Yongwei , Wu Leyin , Xuan Chenyuan , Du Qianming , Hu Rong
Published: June 2024

This file contains Supplementary Figure S12 and its legend.
Supplementary Figure S11 from Serotonin Receptor HTR2B Facilitates Colorectal Cancer Metastasis via CREB1–ZEB1 Axis–Mediated Epithelial–Mesenchymal Transition
Authors: Li Tao , Wei Lei , Zhang Xin , Fu Bin , Zhou Yunjiang , Yang Mengdi , Cao Mengran , Chen Yaxin , Tan Yingying , Shi Yongwei , Wu Leyin , Xuan Chenyuan , Du Qianming , Hu Rong
Published: June 2024

This file contains Supplementary Figure S11 and its legend.
Supplementary Table S3 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis
Authors: Meuser Elena , Chang Kyle , Walters Angharad , Hurley Joanna J. , West Hannah D. , Perry Iain , Mort Matthew , Reyes-Uribe Laura , Truscott Rebekah , Jones Nicholas , Lawrence Rachel , Jenkins Gareth , Giles Peter , Dolwani Sunil , Al-Sarireh Bilal , Hawkes Neil , Short Emma , Williams Geraint T. , Taggart Melissa W. , Luetchford Kim , Lynch Patrick M. , Terlouw Diantha , Nielsen Maartje , Walton Sarah-Jane , Latchford Andrew , Clark Susan K. , Sampson Julian R. , Vilar Eduardo , Thomas Laura E.
Published: June 2024

Summary statistics for all FAP and MAP patient-derived intestinal samples analysed in this study. Data sets are from two centres, Cardiff University (CU) and MD Anderson Cancer Center (MDACC). Statistically significant P-values < 0.05 are in bold.
Supplementary Table 5 from Surgical Tumor Resection Deregulates Hallmarks of Cancer in Resected Tissue and the Surrounding Microenvironment
Authors: Chaubal Rohan , Gardi Nilesh , Joshi Shalaka , Pantvaidya Gouri , Kadam Rasika , Vanmali Vaibhav , Hawaldar Rohini , Talker Elizabeth , Chitra Jaya , Gera Poonam , Bhatia Dimple , Kalkar Prajakta , Gurav Mamta , Shetty Omshree , Desai Sangeeta , Krishnan Neeraja M. , Nair Nita , Parmar Vani , Dutt Amit , Panda Binay , Gupta Sudeep , Badwe Rajendra
Published: June 2024

Supplementary Table 5 shows the GO terms for 85 significantly de-regulated genes common to the individual patient time-series analysis and replicative analysis in Breast Cancer Patients.
Supplementary Table 11 from Surgical Tumor Resection Deregulates Hallmarks of Cancer in Resected Tissue and the Surrounding Microenvironment
Authors: Chaubal Rohan , Gardi Nilesh , Joshi Shalaka , Pantvaidya Gouri , Kadam Rasika , Vanmali Vaibhav , Hawaldar Rohini , Talker Elizabeth , Chitra Jaya , Gera Poonam , Bhatia Dimple , Kalkar Prajakta , Gurav Mamta , Shetty Omshree , Desai Sangeeta , Krishnan Neeraja M. , Nair Nita , Parmar Vani , Dutt Amit , Panda Binay , Gupta Sudeep , Badwe Rajendra
Published: June 2024

Supplementary Table 11 shows Overlap of genes de-regulated from our study with genes known to be de-regulated due to hypoxia in literature.
Supplementary Materials and Methods from Surgical Tumor Resection Deregulates Hallmarks of Cancer in Resected Tissue and the Surrounding Microenvironment
Authors: Chaubal Rohan , Gardi Nilesh , Joshi Shalaka , Pantvaidya Gouri , Kadam Rasika , Vanmali Vaibhav , Hawaldar Rohini , Talker Elizabeth , Chitra Jaya , Gera Poonam , Bhatia Dimple , Kalkar Prajakta , Gurav Mamta , Shetty Omshree , Desai Sangeeta , Krishnan Neeraja M. , Nair Nita , Parmar Vani , Dutt Amit , Panda Binay , Gupta Sudeep , Badwe Rajendra
Published: June 2024

Supplementary Materials and Methods
Supplementary Figure 3 from Surgical Tumor Resection Deregulates Hallmarks of Cancer in Resected Tissue and the Surrounding Microenvironment
Authors: Chaubal Rohan , Gardi Nilesh , Joshi Shalaka , Pantvaidya Gouri , Kadam Rasika , Vanmali Vaibhav , Hawaldar Rohini , Talker Elizabeth , Chitra Jaya , Gera Poonam , Bhatia Dimple , Kalkar Prajakta , Gurav Mamta , Shetty Omshree , Desai Sangeeta , Krishnan Neeraja M. , Nair Nita , Parmar Vani , Dutt Amit , Panda Binay , Gupta Sudeep , Badwe Rajendra
Published: June 2024

Supplementary Figure 3 summarises differential genes identified via class comparisons AvB, BvC and AvC in replicate analysis of breast cancer RNA-Seq data.
Data from FATP5 Is Indispensable for the Growth of Intrahepatic Cholangiocarcinoma
Authors: Shihadih Diyala , Wang Xue , Zushin Peter-James H. , Khodakivskyi Pavlo , Park Hyo Min , Tso Emily , Shiblak Jena , Misic Angela , Louie Sharon M. , Ward Catherine , Hellerstein Marc , Nomura Daniel K. , Goun Elena , Urigo Francesco , Calvisi Diego F. , Chen Xin , Stahl Andreas
Published: June 2024

Abstract
Altered lipid metabolism is a common hallmark of various cancers, including intrahepatic cholangiocarcinoma (ICC), a highly lethal carcinoma that lacks effective treatment options. To elucidate the lipid metabolism changes in ICC, we coupled the expression of the firefly luciferase gene (FFL) to AKT1 (AKT-FFL) via an IRES linker, and then hydrodynamically injected mice with AKT-FFL and Notch1 intracellular cytoplasmic domain (NICD) to establish a luciferase-positive ICC model. This model not only enabled us to monitor and quantify tumor growth by injecting the mice with luciferin, but also allowed us to assess the fatty acid uptake rate by injecting the mice with free fatty acid luciferin (FFA-Luc). The ICC model exhibited robust uptake of exogenous fatty acids compared with the HCC model induced by AKT-FFL/ neuroblastoma Ras (Ras). Lipidomics analysis showed a dramatically higher level of fatty acid in ICC, further supporting the increased fatty acids uptake. Mechanistic studies identified FATP5 as the predominant mediator of fatty acid uptake required for ICC growth using Fatp5 knockout mice and AAV-based shRNA silencing of Fatp5. Our study discovered a novel therapeutic target for the treatment of ICC and shed light on the contributions of lipid metabolism to ICC development.
Implications:
This study provides the first in vivo evidence that FATP5 is a potential therapeutic target for treating ICC.
Data from Systematic Characterization of p53-Regulated Long Noncoding RNAs across Human Cancers Reveals Remarkable Heterogeneity among Different Tumor Types
Authors: Regunath Kausik , Fomin Vitalay , Liu Zhaoqi , Wang Pingzhang , Hoque Mainul , Tian Bin , Rabadan Raul , Prives Carol
Published: June 2024

Abstract
The p53 tumor suppressor protein, a sequence-specific DNA binding transcription factor, regulates the expression of a large number of genes, in response to various forms of cellular stress. Although the protein coding target genes of p53 have been well studied, less is known about its role in regulating long noncoding genes and their functional relevance to cancer. Here we report the genome-wide identification of a large set (>1,000) of long noncoding RNAs (lncRNA), which are putative p53 targets in a colon cancer cell line and in human patient datasets from five different common types of cancer. These lncRNAs have not been annotated by other studies of normal unstressed systems. In the colon cancer cell line, a high proportion of these lncRNAs are uniquely induced by different chemotherapeutic agents that activate p53, whereas others are induced by more than one agent tested. Further, subsets of these lncRNAs independently predict overall and disease-free survival of patients across the five different common cancer types. Interestingly, both genetic alterations and patient survival associated with different lncRNAs are unique to each cancer tested, indicating extraordinary tissue-specific variability in the p53 noncoding response. The newly identified noncoding p53 target genes have allowed us to construct a classifier for tumor diagnosis and prognosis.
Implications:
Our results not only identify myriad p53-regulated long noncoding (lncRNA), they also reveal marked drug-induced, as well as tissue- and tumor-specific heterogeneity in these putative p53 targets and our findings have enabled the construction of robust classifiers for diagnosis and prognosis.
Supplementary Table 2 from Low-Carbohydrate Diet Score and Risk of Hepatocellular Carcinoma: Findings from a Prospective Cohort Study
Authors: Pham Yen Thi-Hai , Jin Aizhen , Wang Renwei , Behari Jaideep , Koh Woon-Puay , Yuan Jian-Min , Luu Hung N.
Published: June 2024

Supplementary Table 2. Baseline characteristics of participants according to quartiles of overall, animal-based, and plant-based low-carbohydrate diet scores: The Singapore Chinese Health Study, 1993-2015
Table S9 from Circulating miRNA Signature Predicts Cancer Incidence in Lynch Syndrome—A Pilot Study
Authors: Sievänen Tero , Jokela Tiina , Hyvärinen Matti , Korhonen Tia-Marje , Pylvänäinen Kirsi , Mecklin Jukka-Pekka , Karvanen Juha , Sillanpää Elina , Seppälä Toni T. , Laakkonen Eija K.
Published: June 2024

Table S9: Model fits in the full CRC sample. b = regression coefficient; HR = hazard ratio; 95% CI = 95% confidence interval; P- value = P-value significant at <0.05 level; Full model C-index = Harrel’s concordance (C) index. N = 101 of whom 9 developed CRC during the surveillance.
Table S8 from Circulating miRNA Signature Predicts Cancer Incidence in Lynch Syndrome—A Pilot Study
Authors: Sievänen Tero , Jokela Tiina , Hyvärinen Matti , Korhonen Tia-Marje , Pylvänäinen Kirsi , Mecklin Jukka-Pekka , Karvanen Juha , Sillanpää Elina , Seppälä Toni T. , Laakkonen Eija K.
Published: June 2024

Table S8: 5-fold cross-validated MLH1 c-miR risk sum score model.
Table S6 from Circulating miRNA Signature Predicts Cancer Incidence in Lynch Syndrome—A Pilot Study
Authors: Sievänen Tero , Jokela Tiina , Hyvärinen Matti , Korhonen Tia-Marje , Pylvänäinen Kirsi , Mecklin Jukka-Pekka , Karvanen Juha , Sillanpää Elina , Seppälä Toni T. , Laakkonen Eija K.
Published: June 2024

Table S6: Model fits in the full MLH1 sample. b = regression coefficient; HR = hazard ratio; 95% CI = 95% confidence interval; P-value = P-value significant at <0.05 level; Full model C-index = Harrel’s concordance (C) index. N = 74 of whom 14 developed cancers during the surveillance.
Table S11 from Circulating miRNA Signature Predicts Cancer Incidence in Lynch Syndrome—A Pilot Study
Authors: Sievänen Tero , Jokela Tiina , Hyvärinen Matti , Korhonen Tia-Marje , Pylvänäinen Kirsi , Mecklin Jukka-Pekka , Karvanen Juha , Sillanpää Elina , Seppälä Toni T. , Laakkonen Eija K.
Published: June 2024

Table S11: 5-fold cross-validated CRC c-miR risk sum score model.
Supplementary Table S8 from Translational and Therapeutic Evaluation of RAS-GTP Inhibition by RMC-6236 in RAS-Driven Cancers
Authors: Jiang Jingjing , Jiang Lingyan , Maldonato Benjamin J. , Wang Yingyun , Holderfield Matthew , Aronchik Ida , Winters Ian P. , Salman Zeena , Blaj Cristina , Menard Marie , Brodbeck Jens , Chen Zhe , Wei Xing , Rosen Michael J. , Gindin Yevgeniy , Lee Bianca J. , Evans James W. , Chang Stephanie , Wang Zhican , Seamon Kyle J. , Parsons Dylan , Cregg James , Marquez Abby , Tomlinson Aidan C.A. , Yano Jason K. , Knox John E. , Quintana Elsa , Aguirre Andrew J. , Arbour Kathryn C. , Reed Abby , Gustafson W. Clay , Gill Adrian L. , Koltun Elena S. , Wildes David , Smith Jacqueline A.M. , Wang Zhengping , Singh Mallika
Published: June 2024

Supplementary Table S8 shows all parameter estimates for PK/Efficacy and PK/PD modeling.
Supplementary Table S2 from Efficacy and Safety of Adagrasib plus Cetuximab in Patients with KRASG12C-Mutated Metastatic Colorectal Cancer
Authors: Yaeger Rona , Uboha Nataliya V. , Pelster Meredith S. , Bekaii-Saab Tanios S. , Barve Minal , Saltzman Joel , Sabari Joshua K. , Peguero Julio A. , Paulson Andrew Scott , Jänne Pasi A. , Cruz-Correa Marcia , Anderes Kenna , Velastegui Karen , Yan Xiaohong , Der-Torossian Hirak , Klempner Samuel J. , Kopetz Scott E.
Published: June 2024

Table S2. Demographics and baseline characteristics of patients with KRASG12C-mutated unresectable or metastatic CRC receiving adagrasib monotherapy.
Supplementary Figure S1 from Efficacy and Safety of Adagrasib plus Cetuximab in Patients with KRASG12C-Mutated Metastatic Colorectal Cancer
Authors: Yaeger Rona , Uboha Nataliya V. , Pelster Meredith S. , Bekaii-Saab Tanios S. , Barve Minal , Saltzman Joel , Sabari Joshua K. , Peguero Julio A. , Paulson Andrew Scott , Jänne Pasi A. , Cruz-Correa Marcia , Anderes Kenna , Velastegui Karen , Yan Xiaohong , Der-Torossian Hirak , Klempner Samuel J. , Kopetz Scott E.
Published: June 2024

Supplementary Figure S1. Changes from baseline in sum of target lesion diameters over time for patients continuing treatment after progression, either with adagrasib plus cetuximab (n = 38), adagrasib only (n = 10), or cetuximab only (n = 1). Only patients with available post-progression scans are included in the plot (n = 33 for adagrasib plus cetuximab; n = 1 for adagrasib only).
Supplementary Table S1 from Translational and Therapeutic Evaluation of RAS-GTP Inhibition by RMC-6236 in RAS-Driven Cancers
Authors: Jiang Jingjing , Jiang Lingyan , Maldonato Benjamin J. , Wang Yingyun , Holderfield Matthew , Aronchik Ida , Winters Ian P. , Salman Zeena , Blaj Cristina , Menard Marie , Brodbeck Jens , Chen Zhe , Wei Xing , Rosen Michael J. , Gindin Yevgeniy , Lee Bianca J. , Evans James W. , Chang Stephanie , Wang Zhican , Seamon Kyle J. , Parsons Dylan , Cregg James , Marquez Abby , Tomlinson Aidan C.A. , Yano Jason K. , Knox John E. , Quintana Elsa , Aguirre Andrew J. , Arbour Kathryn C. , Reed Abby , Gustafson W. Clay , Gill Adrian L. , Koltun Elena S. , Wildes David , Smith Jacqueline A.M. , Wang Zhengping , Singh Mallika
Published: June 2024

Supplementary Table S1 shows information on the PRISM cell set comprised of 845 cell lines representing more than 45 lineages.
Supplementary Tables S1-S12 from The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy
Authors: Martin Michael V. , Aguilar-Rosas Salvador , Franke Katka , Pieterse Mark , Langelaar Jamie van , Schreurs Renée , Bijlsma Maarten F. , Besselink Marc G. , Koster Jan , Timens Wim , Khasraw Mustafa , Ashley David M. , Keir Stephen T. , Ottensmeier Christian H. , King Emma V. , Verheij Joanne , Waasdorp Cynthia , Valk Peter J.M. , Engels Sem A.G. , Oostenbach Ellen , van Dinter Jip T. , Hofman Damon A. , Mok Juk Yee , van Esch Wim J.E. , Wilmink Hanneke , Monkhorst Kim , Verheul Henk M.W. , Poel Dennis , Hiltermann T. Jeroen N. , Kempen Léon C.L.T. van , Groen Harry J.M. , Aerts Joachim G.J.V. , Heesch Sebastiaan van , Löwenberg Bob , Plasterk Ronald , Kloosterman Wigard P.
Published: June 2024

Combined spreadsheet with Supplementary Tables S1 - S12
Figure S9 from The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy
Authors: Martin Michael V. , Aguilar-Rosas Salvador , Franke Katka , Pieterse Mark , Langelaar Jamie van , Schreurs Renée , Bijlsma Maarten F. , Besselink Marc G. , Koster Jan , Timens Wim , Khasraw Mustafa , Ashley David M. , Keir Stephen T. , Ottensmeier Christian H. , King Emma V. , Verheij Joanne , Waasdorp Cynthia , Valk Peter J.M. , Engels Sem A.G. , Oostenbach Ellen , van Dinter Jip T. , Hofman Damon A. , Mok Juk Yee , van Esch Wim J.E. , Wilmink Hanneke , Monkhorst Kim , Verheul Henk M.W. , Poel Dennis , Hiltermann T. Jeroen N. , Kempen Léon C.L.T. van , Groen Harry J.M. , Aerts Joachim G.J.V. , Heesch Sebastiaan van , Löwenberg Bob , Plasterk Ronald , Kloosterman Wigard P.
Published: June 2024

Figure S9: Results of NOP identification using simulated sequencing data.
Supplementary Figure S6 from An IRF2-Expressing Oncolytic Virus Changes the Susceptibility of Tumor Cells to Antitumor T Cells and Promotes Tumor Clearance
Authors: Shao Lulu , Srivastava Rashmi , Delgoffe Greg M. , Thorne Stephen H. , Sarkar Saumendra N.
Published: June 2024

Supplementary Figure S6 with legend
Figure S15 from The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy
Authors: Martin Michael V. , Aguilar-Rosas Salvador , Franke Katka , Pieterse Mark , Langelaar Jamie van , Schreurs Renée , Bijlsma Maarten F. , Besselink Marc G. , Koster Jan , Timens Wim , Khasraw Mustafa , Ashley David M. , Keir Stephen T. , Ottensmeier Christian H. , King Emma V. , Verheij Joanne , Waasdorp Cynthia , Valk Peter J.M. , Engels Sem A.G. , Oostenbach Ellen , van Dinter Jip T. , Hofman Damon A. , Mok Juk Yee , van Esch Wim J.E. , Wilmink Hanneke , Monkhorst Kim , Verheul Henk M.W. , Poel Dennis , Hiltermann T. Jeroen N. , Kempen Léon C.L.T. van , Groen Harry J.M. , Aerts Joachim G.J.V. , Heesch Sebastiaan van , Löwenberg Bob , Plasterk Ronald , Kloosterman Wigard P.
Published: June 2024

Figure S15: Tetramer gating strategy.
Supplementary Methods from Unleashing Natural IL18 Activity Using an Anti-IL18BP Blocker Induces Potent Immune Stimulation and Antitumor Effects
Authors: Menachem Assaf , Alteber Zoya , Cojocaru Gady , Fridman Kfir Tal , Blat Dan , Leiderman Olga , Galperin Moran , Sever Lital , Cohen Nadav , Cohen Keren , Granit Roy Z. , Vols Sandra , Frenkel Masha , Soffer Liron , Meyer Karin , Menachem Keren , Galon Tilleman Hadas , Morein Dina , Borukhov Itamar , Toporik Amir , Perpinial Shahor Michal , Tatirovsky Evgeny , Mizrachi Aviram , Levy-Barda Adva , Sadot Eran , Strenov Yulia , Eitan Ram , Jakobson-Setton Ariella , Yanichkin Natalia , Ferre Pierre , Ophir Eran
Published: June 2024

Supplementary Methods
Supplementary Table S1 from Preclinical Evaluation of Off-The-Shelf PD-L1+ Human Natural Killer Cells Secreting IL15 to Treat Non–Small Cell Lung Cancer
Authors: Lu Ting , Ma Rui , Mansour Anthony G. , Bustillos Christian , Li Zhiyao , Li Zhenlong , Ma Shoubao , Teng Kun-Yu , Chen Hanyu , Zhang Jianying , Villalona-Calero Miguel A. , Caligiuri Michael A. , Yu Jianhua
Published: June 2024

Supplementary Table S1
Supplementary Figure S5 from Preclinical Evaluation of Off-The-Shelf PD-L1+ Human Natural Killer Cells Secreting IL15 to Treat Non–Small Cell Lung Cancer
Authors: Lu Ting , Ma Rui , Mansour Anthony G. , Bustillos Christian , Li Zhiyao , Li Zhenlong , Ma Shoubao , Teng Kun-Yu , Chen Hanyu , Zhang Jianying , Villalona-Calero Miguel A. , Caligiuri Michael A. , Yu Jianhua
Published: June 2024

Supplementary Figure S5
Supplemental Figure 1 from Unleashing Natural IL18 Activity Using an Anti-IL18BP Blocker Induces Potent Immune Stimulation and Antitumor Effects
Authors: Menachem Assaf , Alteber Zoya , Cojocaru Gady , Fridman Kfir Tal , Blat Dan , Leiderman Olga , Galperin Moran , Sever Lital , Cohen Nadav , Cohen Keren , Granit Roy Z. , Vols Sandra , Frenkel Masha , Soffer Liron , Meyer Karin , Menachem Keren , Galon Tilleman Hadas , Morein Dina , Borukhov Itamar , Toporik Amir , Perpinial Shahor Michal , Tatirovsky Evgeny , Mizrachi Aviram , Levy-Barda Adva , Sadot Eran , Strenov Yulia , Eitan Ram , Jakobson-Setton Ariella , Yanichkin Natalia , Ferre Pierre , Ophir Eran
Published: June 2024

Supplemental Figure S1. IL-18BP is a potential soluble immune checkpoint in cancer.
Supplementary Figure S4 from Preclinical Evaluation of Off-The-Shelf PD-L1+ Human Natural Killer Cells Secreting IL15 to Treat Non–Small Cell Lung Cancer
Authors: Lu Ting , Ma Rui , Mansour Anthony G. , Bustillos Christian , Li Zhiyao , Li Zhenlong , Ma Shoubao , Teng Kun-Yu , Chen Hanyu , Zhang Jianying , Villalona-Calero Miguel A. , Caligiuri Michael A. , Yu Jianhua
Published: June 2024

Supplementary Figure S4
Supplementary Figure S1 from Preclinical Evaluation of Off-The-Shelf PD-L1+ Human Natural Killer Cells Secreting IL15 to Treat Non–Small Cell Lung Cancer
Authors: Lu Ting , Ma Rui , Mansour Anthony G. , Bustillos Christian , Li Zhiyao , Li Zhenlong , Ma Shoubao , Teng Kun-Yu , Chen Hanyu , Zhang Jianying , Villalona-Calero Miguel A. , Caligiuri Michael A. , Yu Jianhua
Published: June 2024

Supplementary Figure S1
Supplementary Figure 6 from Intratumoral TREX1 Induction Promotes Immune Evasion by Limiting Type I IFN
Authors: Toufektchan Eléonore , Dananberg Alexandra , Striepen Josefine , Hickling James H. , Shim Abraham , Chen Yanyang , Nichols Ashley , Duran Paez Mercedes A. , Mohr Lisa , Bakhoum Samuel F. , Maciejowski John
Published: June 2024

Characterization of intratumoral immune cell infiltration.
Supplementary Figure 10 from Intratumoral TREX1 Induction Promotes Immune Evasion by Limiting Type I IFN
Authors: Toufektchan Eléonore , Dananberg Alexandra , Striepen Josefine , Hickling James H. , Shim Abraham , Chen Yanyang , Nichols Ashley , Duran Paez Mercedes A. , Mohr Lisa , Bakhoum Samuel F. , Maciejowski John
Published: June 2024

Characterization of Irf3 KOs and individual growth curves of tumors following disruption of IFN signaling.
Supplementary Table 2 from The Exonuclease TREX1 Constitutes an Innate Immune Checkpoint Limiting cGAS/STING-Mediated Antitumor Immunity
Authors: Lim Junghyun , Rodriguez Ryan , Williams Katherine , Silva John , Gutierrez Alan G. , Tyler Paul , Baharom Faezzah , Sun Tao , Lin Eva , Martin Scott , Kayser Brandon D. , Johnston Robert J. , Mellman Ira , Delamarre Lélia , West Nathaniel R. , Müller Sören , Qu Yan , Heger Klaus
Published: June 2024

Top 30 genes contributing to tNMFs1-10 (related to Figure 4 and Supplementary Figure 6)
Supplementary Figure 4 from The Exonuclease TREX1 Constitutes an Innate Immune Checkpoint Limiting cGAS/STING-Mediated Antitumor Immunity
Authors: Lim Junghyun , Rodriguez Ryan , Williams Katherine , Silva John , Gutierrez Alan G. , Tyler Paul , Baharom Faezzah , Sun Tao , Lin Eva , Martin Scott , Kayser Brandon D. , Johnston Robert J. , Mellman Ira , Delamarre Lélia , West Nathaniel R. , Müller Sören , Qu Yan , Heger Klaus
Published: June 2024

Supplementary Figure 4. Single-cell RNA sequencing workflow and ISG expression across immune cells in the tumor microenvironment
Supplementary Figure 3 from The Exonuclease TREX1 Constitutes an Innate Immune Checkpoint Limiting cGAS/STING-Mediated Antitumor Immunity
Authors: Lim Junghyun , Rodriguez Ryan , Williams Katherine , Silva John , Gutierrez Alan G. , Tyler Paul , Baharom Faezzah , Sun Tao , Lin Eva , Martin Scott , Kayser Brandon D. , Johnston Robert J. , Mellman Ira , Delamarre Lélia , West Nathaniel R. , Müller Sören , Qu Yan , Heger Klaus
Published: June 2024

Supplementary Figure 3. Assessment of TREX1’s catalytic activity and cGAS dependency.
Supplementary Figure 2 from The Exonuclease TREX1 Constitutes an Innate Immune Checkpoint Limiting cGAS/STING-Mediated Antitumor Immunity
Authors: Lim Junghyun , Rodriguez Ryan , Williams Katherine , Silva John , Gutierrez Alan G. , Tyler Paul , Baharom Faezzah , Sun Tao , Lin Eva , Martin Scott , Kayser Brandon D. , Johnston Robert J. , Mellman Ira , Delamarre Lélia , West Nathaniel R. , Müller Sören , Qu Yan , Heger Klaus
Published: June 2024

Supplementary Figure 2. Tumor-intrinsic TREX1 loss impairs CT26 tumor growth in immunocompetent mice in a cGAS dependent manner.
Supplementary Figure 1 from The Exonuclease TREX1 Constitutes an Innate Immune Checkpoint Limiting cGAS/STING-Mediated Antitumor Immunity
Authors: Lim Junghyun , Rodriguez Ryan , Williams Katherine , Silva John , Gutierrez Alan G. , Tyler Paul , Baharom Faezzah , Sun Tao , Lin Eva , Martin Scott , Kayser Brandon D. , Johnston Robert J. , Mellman Ira , Delamarre Lélia , West Nathaniel R. , Müller Sören , Qu Yan , Heger Klaus
Published: June 2024

Supplementary Figure 1. TREX1 limits an ISG response in CT26 and STING-expressing MC38 cells.
Supplementary File 1 from Randomized Phase II Study Evaluating the Addition of Pembrolizumab to Radium-223 in Metastatic Castration-resistant Prostate Cancer
Authors: Choudhury Atish D. , Kwak Lucia , Cheung Alexander , Allaire Kathryn M. , Marquez Jaqueline , Yang David D. , Tripathi Abhishek , Kilar Jacqueline M. , Flynn Meredith , Maynard Brianna , Reichel Rebecca , Pace Amanda F. , Chen Brandon K. , Van Allen Eliezer M. , Kilbridge Kerry , Wei Xiao X. , McGregor Bradley A. , Pomerantz Mark M. , Bhatt Rupal S. , Sweeney Christopher J. , Bubley Glenn J. , Jacene Heather A. , Taplin Mary-Ellen , Huang Franklin W. , Harshman Lauren C. , Fong Lawrence
Published: June 2024

Supplementary File 1
Supplemental Figure 6 from Randomized Phase II Study Evaluating the Addition of Pembrolizumab to Radium-223 in Metastatic Castration-resistant Prostate Cancer
Authors: Choudhury Atish D. , Kwak Lucia , Cheung Alexander , Allaire Kathryn M. , Marquez Jaqueline , Yang David D. , Tripathi Abhishek , Kilar Jacqueline M. , Flynn Meredith , Maynard Brianna , Reichel Rebecca , Pace Amanda F. , Chen Brandon K. , Van Allen Eliezer M. , Kilbridge Kerry , Wei Xiao X. , McGregor Bradley A. , Pomerantz Mark M. , Bhatt Rupal S. , Sweeney Christopher J. , Bubley Glenn J. , Jacene Heather A. , Taplin Mary-Ellen , Huang Franklin W. , Harshman Lauren C. , Fong Lawrence
Published: June 2024

Kaplan-Meier estimates of time to treatment failure (TTF), radiographic progression-free survival (rPFS), and overall survival (OS) by A. CD4+FoxP3- (effector) proportion increase vs. decrease from baseline to 8-week biopsy. B. CD8+ increase vs. decrease. C. CD8+ / CD4+FoxP3+ (Treg) ratio increase vs. decrease. N.B. Patients were event-free for 2 months as they need to have on treatment biopsy at week 8 of treatment.
Supplemental Figure 1 from Randomized Phase II Study Evaluating the Addition of Pembrolizumab to Radium-223 in Metastatic Castration-resistant Prostate Cancer
Authors: Choudhury Atish D. , Kwak Lucia , Cheung Alexander , Allaire Kathryn M. , Marquez Jaqueline , Yang David D. , Tripathi Abhishek , Kilar Jacqueline M. , Flynn Meredith , Maynard Brianna , Reichel Rebecca , Pace Amanda F. , Chen Brandon K. , Van Allen Eliezer M. , Kilbridge Kerry , Wei Xiao X. , McGregor Bradley A. , Pomerantz Mark M. , Bhatt Rupal S. , Sweeney Christopher J. , Bubley Glenn J. , Jacene Heather A. , Taplin Mary-Ellen , Huang Franklin W. , Harshman Lauren C. , Fong Lawrence
Published: June 2024

Radium-223 was administered as 55 kBq/kg q4weeks and pembrolizumab as 200 mg q3weeks. Biopsies were performed pre-treatment and after 8 weeks of treatment.
Figure S7 from Engineering CD3/CD137 Dual Specificity into a DLL3-Targeted T-Cell Engager Enhances T-Cell Infiltration and Efficacy against Small-Cell Lung Cancer
Authors: Mikami Hirofumi , Feng Shu , Matsuda Yutaka , Ishii Shinya , Naoi Sotaro , Azuma Yumiko , Nagano Hiroaki , Asanuma Kentaro , Kayukawa Yoko , Tsunenari Toshiaki , Kamikawaji Shogo , Iwabuchi Ryutaro , Shinozuka Junko , Yamazaki Masaki , Kuroi Haruka , Ho Samantha Shu Wen , Gan Siok Wan , Chichili Priyanka , Pang Chai Ling , Yeo Chiew Ying , Shimizu Shun , Hironiwa Naoka , Kinoshita Yasuko , Shimizu Yuichiro , Sakamoto Akihisa , Muraoka Masaru , Takahashi Noriyuki , Kawa Tatsuya , Shiraiwa Hirotake , Mimoto Futa , Kashima Kenji , Kamata-Sakurai Mika , Ishikawa Shumpei , Aburatani Hiroyuki , Kitazawa Takehisa , Igawa Tomoyuki
Published: June 2024

Supplementary Figure S7. DLL3 expression of SCLC xenograft models.
Figure S5 from Engineering CD3/CD137 Dual Specificity into a DLL3-Targeted T-Cell Engager Enhances T-Cell Infiltration and Efficacy against Small-Cell Lung Cancer
Authors: Mikami Hirofumi , Feng Shu , Matsuda Yutaka , Ishii Shinya , Naoi Sotaro , Azuma Yumiko , Nagano Hiroaki , Asanuma Kentaro , Kayukawa Yoko , Tsunenari Toshiaki , Kamikawaji Shogo , Iwabuchi Ryutaro , Shinozuka Junko , Yamazaki Masaki , Kuroi Haruka , Ho Samantha Shu Wen , Gan Siok Wan , Chichili Priyanka , Pang Chai Ling , Yeo Chiew Ying , Shimizu Shun , Hironiwa Naoka , Kinoshita Yasuko , Shimizu Yuichiro , Sakamoto Akihisa , Muraoka Masaru , Takahashi Noriyuki , Kawa Tatsuya , Shiraiwa Hirotake , Mimoto Futa , Kashima Kenji , Kamata-Sakurai Mika , Ishikawa Shumpei , Aburatani Hiroyuki , Kitazawa Takehisa , Igawa Tomoyuki
Published: June 2024

Supplementary Figure S5. DLL3 trispecific induces cytotoxicity against non-SCLC tumors.
Figure S3 from Engineering CD3/CD137 Dual Specificity into a DLL3-Targeted T-Cell Engager Enhances T-Cell Infiltration and Efficacy against Small-Cell Lung Cancer
Authors: Mikami Hirofumi , Feng Shu , Matsuda Yutaka , Ishii Shinya , Naoi Sotaro , Azuma Yumiko , Nagano Hiroaki , Asanuma Kentaro , Kayukawa Yoko , Tsunenari Toshiaki , Kamikawaji Shogo , Iwabuchi Ryutaro , Shinozuka Junko , Yamazaki Masaki , Kuroi Haruka , Ho Samantha Shu Wen , Gan Siok Wan , Chichili Priyanka , Pang Chai Ling , Yeo Chiew Ying , Shimizu Shun , Hironiwa Naoka , Kinoshita Yasuko , Shimizu Yuichiro , Sakamoto Akihisa , Muraoka Masaru , Takahashi Noriyuki , Kawa Tatsuya , Shiraiwa Hirotake , Mimoto Futa , Kashima Kenji , Kamata-Sakurai Mika , Ishikawa Shumpei , Aburatani Hiroyuki , Kitazawa Takehisa , Igawa Tomoyuki
Published: June 2024

Supplementary Figure S3. Binding of DLL3 trispecific to FcγRs, C1q, and FcRn. (
Figure S1 from Engineering CD3/CD137 Dual Specificity into a DLL3-Targeted T-Cell Engager Enhances T-Cell Infiltration and Efficacy against Small-Cell Lung Cancer
Authors: Mikami Hirofumi , Feng Shu , Matsuda Yutaka , Ishii Shinya , Naoi Sotaro , Azuma Yumiko , Nagano Hiroaki , Asanuma Kentaro , Kayukawa Yoko , Tsunenari Toshiaki , Kamikawaji Shogo , Iwabuchi Ryutaro , Shinozuka Junko , Yamazaki Masaki , Kuroi Haruka , Ho Samantha Shu Wen , Gan Siok Wan , Chichili Priyanka , Pang Chai Ling , Yeo Chiew Ying , Shimizu Shun , Hironiwa Naoka , Kinoshita Yasuko , Shimizu Yuichiro , Sakamoto Akihisa , Muraoka Masaru , Takahashi Noriyuki , Kawa Tatsuya , Shiraiwa Hirotake , Mimoto Futa , Kashima Kenji , Kamata-Sakurai Mika , Ishikawa Shumpei , Aburatani Hiroyuki , Kitazawa Takehisa , Igawa Tomoyuki
Published: June 2024

Supplementary Figure S1. The composition of the antibodies