bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Fig.S6 from Preclinical Evaluation of 9MW2821, a Site-Specific Monomethyl Auristatin E-based Antibody-Drug Conjugate for treatment of Nectin-4-expressing Cancers
Authors: Zhou Wei , Fang Peng , Yu Dongan , Ren Hongyuan , You Meng , Yin Long , Mei Fei , Zhu Huikai , Wang Zhenzhen , Xu Hui , Cao Yuxia , Sun Xiaowei , Xu Xiaohong , Bi Jianjun , Wang Jin , Ma Lanping , Wang Xin , Chen Lin , Zhang Yongliang , Cen Xiaowei , Zhu Xi , Lou Liguang , Liu Datao , Tan Xiaoding , Yang Jinliang , Meng Tao , Shen Jingkang
Published: September 2024

Binding affinity based on enzyme-linked immunosorbent assay.
Supplementary Figure S2 from Schlafen 11 (SLFN11) kills cancer cells undergoing unscheduled re-replication
Authors: Murai Junko , Ceribelli Michele , Fu Haiqing , Redon Christophe E. , Jo Ukhyun , Murai Yasuhisa , Aladjem Mirit I. , Thomas Craig J. , Pommier Yves
Published: September 2024

Figure S2
Supplementary Data from Discovery and Preclinical Characterization of XMT-1660, an Optimized B7-H4-Targeted Antibody-Drug Conjugate for the Treatment of Cancer
Authors: Toader Dorin , Fessler Shawn P. , Collins Scott D. , Conlon Patrick R. , Bollu Reddy , Catcott Kalli C. , Chin Chen-Ni , Dirksen Anouk , Du Bingfan , Duvall Jeremy R. , Higgins Stacy , Kozytska Mariya V. , Bellovoda Kamela , Faircloth Chelsey , Lee David , Li Fu , Qin Liuliang , Routhier Caitlin , Shaw Pamela , Stevenson Cheri A. , Wang Jason , Wongthida Phonphimon , Ter-Ovanesyan Elena , Ditty Elizabeth , Bradley Stephen P. , Xu Ling , Yin Mao , Yurkovetskiy Aleksandr V. , Mosher Rebecca , Damelin Marc , Lowinger Timothy B.
Published: September 2024

Supplementary Materials
Supplementary Figure 5 from AMT-562, a novel HER3-targeting antibody drug conjugate, demonstrates a potential to broaden therapeutic opportunities for HER3-expressing tumors
Authors: Weng Weining , Meng Tao , Pu Junyi , Ma Linjie , Shen Yi , Wang Zhaohui , Pan Rong , Wang Mingqiao , Chen Caiwei , Wang Lijun , Zhang Jianjian , Zhou Biao , Shao Siyuan , Qian Yu , Liu Shu-Hui , Hu Wenhao , Meng Xun
Published: September 2024

Pathology of AMT-562 in comparison with AMT-562-T1000.
Supplementary Figure 14 from AMT-562, a novel HER3-targeting antibody drug conjugate, demonstrates a potential to broaden therapeutic opportunities for HER3-expressing tumors
Authors: Weng Weining , Meng Tao , Pu Junyi , Ma Linjie , Shen Yi , Wang Zhaohui , Pan Rong , Wang Mingqiao , Chen Caiwei , Wang Lijun , Zhang Jianjian , Zhou Biao , Shao Siyuan , Qian Yu , Liu Shu-Hui , Hu Wenhao , Meng Xun
Published: September 2024

AMT-562 overcome U3-1402 resistance in lung cancer models.
Supplementary Figure 12 from AMT-562, a novel HER3-targeting antibody drug conjugate, demonstrates a potential to broaden therapeutic opportunities for HER3-expressing tumors
Authors: Weng Weining , Meng Tao , Pu Junyi , Ma Linjie , Shen Yi , Wang Zhaohui , Pan Rong , Wang Mingqiao , Chen Caiwei , Wang Lijun , Zhang Jianjian , Zhou Biao , Shao Siyuan , Qian Yu , Liu Shu-Hui , Hu Wenhao , Meng Xun
Published: September 2024

AMT-562 is more effective as single agent or in combination therapy for colorectal cancer.
Supplementary Figure S4 from A Carbonic Anhydrase IX/SLC1A5 axis regulates glutamine metabolism dependent ferroptosis in hypoxic tumor cells
Authors: Venkateswaran Geetha , McDonald Paul C. , Chafe Shawn C. , Brown Wells S. , Gerbec Zachary J. , Awrey Shannon J. , Parker Seth J. , Dedhar Shoukat
Published: September 2024

Supplementary Figure S4 shows that the combined loss of CAIX activity and the GSH synthesis axis of Gln metabolism increases cytotoxicity of hypoxic cancer cells.
Figure S13 from Intratumoral interleukin-15 improves efficacy of near-infrared photoimmunotherapy
Authors: Fukushima Hiroshi , Furusawa Aki , Kato Takuya , Wakiyama Hiroaki , Takao Seiichiro , Okuyama Shuhei , Choyke Peter L. , Kobayashi Hisataka
Published: September 2024

Supplementary Fig. S13. Expressions of CD8+ T, NK, and NKT cells in untreated left tumors after CD44-targeted NIR-PIT using a bilateral tumor mouse model (R: hIL-15-MC38 tumor, L: MC38 tumor).
Supplementary Figure S3 from Efficacy and safety of glycosphingolipid SSEA-4 targeting CAR-T cells
in an ovarian carcinoma model
Authors: Monzo Hector J. , Kalander Kerttu , Hyytiäinen Marko M. , Elbasani Endrit , Wall Johanna , Moyano-Galceran Lidia , Tanjore Ramanathan Jayendrakishore , Jukonen Joonas J.J. , Laakkonen Pirjo , Ristimäki Ari , Carlson Joseph W. , Lehti Kaisa , Salehi Sahar , Puolakkainen Pauli , Haglund Caj , Seppänen Hanna , Leppä Sirpa , Ojala Päivi M.
Published: September 2024

Supplementary Figure S3. IFN measurement and organ BLI of the short-term in vivo study. A. IFN quantification by ELISA in post-mortem mouse blood plasma. B. Representative BLI images of isolated organs from mice treated with PBS, NT-T, and CAR-T cells at the indicated T cell doses after 32 days. C. Organ BLI quantification. N=3 for control. N=5 for all groups, except N=2 for NT-T 1M, N=3 for CAR-T 1M, and N=4 NT-T 2M. Mean ± SD. One-way ANOVA with Tukey’s multiple comparison tests. (A) ***p=0.0005, ****p=0.0001. (C) *p=0.04, **p≤0.001 to PBS group. Not significant, n.s., differences were attributed to p≥0.05. (M=1x106).
Supplementary Figure S1 from Efficacy and safety of glycosphingolipid SSEA-4 targeting CAR-T cells
in an ovarian carcinoma model
Authors: Monzo Hector J. , Kalander Kerttu , Hyytiäinen Marko M. , Elbasani Endrit , Wall Johanna , Moyano-Galceran Lidia , Tanjore Ramanathan Jayendrakishore , Jukonen Joonas J.J. , Laakkonen Pirjo , Ristimäki Ari , Carlson Joseph W. , Lehti Kaisa , Salehi Sahar , Puolakkainen Pauli , Haglund Caj , Seppänen Hanna , Leppä Sirpa , Ojala Päivi M.
Published: September 2024

Supplementary Figure S1. SSEA-4 staining specificity and LDH cytotoxicity assay. A. SSEA-4 immunohistochemistry in paraffin-embedded gastric cancer tumor microarrays. B. Upper panel sections were treated with standard xylene/ethanol series used in paraffin embedded section treatment, whereas lower panel samples were untreated. C. Consecutive sections of fresh frozen pancreatic cancer patient samples were stained with anti-SSEA-4 antibody. The staining was blocked with SSEA-4 hexaose (middle panel) or SSEA-3 (right panel). D. Representative immunofluorescence micrographs of SSEA-4 (red) in OVCAR-4 cells (high expression) and Caov-3 cells (no expression). Nucleus (blue; Hoechst 33342). N=3. E. LDH assay to measure toxicity of anti-SSEA-4 CAR-T cells on SSEA-4 positive OVCAR-4 cells and SSEA-4 negative Caov-3 cells as a control (N=2). LDH assay was performed after 72 hours of CAR/NT-T cell treatment. ****p=0.0001, ***p=0.0002 and **p=0.0025.
Supplementary Data S1. from Efficacy and safety of glycosphingolipid SSEA-4 targeting CAR-T cells
in an ovarian carcinoma model
Authors: Monzo Hector J. , Kalander Kerttu , Hyytiäinen Marko M. , Elbasani Endrit , Wall Johanna , Moyano-Galceran Lidia , Tanjore Ramanathan Jayendrakishore , Jukonen Joonas J.J. , Laakkonen Pirjo , Ristimäki Ari , Carlson Joseph W. , Lehti Kaisa , Salehi Sahar , Puolakkainen Pauli , Haglund Caj , Seppänen Hanna , Leppä Sirpa , Ojala Päivi M.
Published: September 2024

Supplementary Data S1. Pathology Report of the long-term survival study. Post-mortem lung, intestine and kidney tissue samples collected and analyzed by Histowiz.
Figure S5 from Use of Payload Binding Selectivity Enhancers to Improve Therapeutic Index of Maytansinoid-Antibody-Drug Conjugates
Authors: Nguyen Toan Duc. , Bordeau Brandon M. , Balthasar Joseph P.
Published: September 2024

Weight loss induced by administration of 7E7 DM4-ADC to mice
Figure S4 from Use of Payload Binding Selectivity Enhancers to Improve Therapeutic Index of Maytansinoid-Antibody-Drug Conjugates
Authors: Nguyen Toan Duc. , Bordeau Brandon M. , Balthasar Joseph P.
Published: September 2024

DM4-ADC cytotoxicity data
Supplementary Figure S3 from Interferon Gamma Induces Higher Neutrophil Extracellular Traps Leading to Tumor-Killing Activity in Microsatellite Stable Colorectal Cancer
Authors: Teng Hao-Wei , Wang Tean-Ya , Lin Chun-Chi , Tong Zhen-Jie , Cheng Hsiao-Wei , Wang Hsiang-Tsui
Published: September 2024

Supplementary Figure 3 shows the effect of NET in the co-culture system of dHL60 with MSI-H or MSS CRC cells.
Data from First-in-Human Study of AZD5153, A Small Molecule Inhibitor of Bromodomain Protein 4, in Patients with Relapsed/Refractory Malignant Solid Tumors and Lymphoma
Authors: Hamilton Erika P. , Wang Judy S. , Oza Amit M. , Patel Manish R. , Ulahannan Susanna V. , Bauer Todd , Karlix Janet L. , Zeron-Medina Jorge , Fabbri Giulia , Marco-Casanova Paola , Moorthy Ganesh , Hattersley Maureen M. , Littlewood Gillian M. , Mitchell Patrick D. , Saeh Jamal . , Pouliot Gayle P. , Moore Kathleen N.
Published: September 2024

Abstract
AZD5153, a reversible, bivalent inhibitor of the bromodomain and extraterminal family protein BRD4, has preclinical activity in multiple tumors. This first-in-human, phase 1 study investigated AZD5153 alone or with olaparib in patients with relapsed/refractory solid tumors or lymphoma. Adults with relapsed tumors intolerant of, or refractory to, prior therapies received escalating doses of oral AZD5153 once-daily (QD) or twice-daily (BID) continuously (21-day cycles), or AZD5153 QD/BID continuously or intermittently plus olaparib 300 mg BID, until disease progression or unacceptable toxicity. Between June 30, 2017 and April 19, 2021, 34 patients received monotherapy and 15 received combination therapy. Dose-limiting toxicities were thrombocytopenia/platelet count decreased (n = 4/n = 2) and diarrhea (n = 1). The recommended phase 2 doses (RP2Ds) were AZD5153 30 mg QD or 15 mg BID (monotherapy) and 10 mg QD (intermittent schedule) with olaparib. With AZD5153 monotherapy, common treatment-emergent adverse events (TEAEs) included fatigue (38.2%), thrombocytopenia, and diarrhea (each 32.4%); common grade ≥ 3 TEAEs were thrombocytopenia (14.7%) and anemia (8.8%). With the combination, common TEAEs included nausea (66.7%) and fatigue (53.3%); the most common grade ≥ 3 TEAE was thrombocytopenia (26.7%). AZD5153 had dose-dependent pharmacokinetics, with minimal accumulation, and demonstrated dose-dependent modulation of peripheral biomarkers, including upregulation of HEXIM1. One patient with metastatic pancreatic cancer receiving combination treatment had a partial response lasting 4.2 months. These results show AZD5153 was tolerable as monotherapy and in combination at the RP2Ds; common toxicities were fatigue, hematologic AEs, and gastrointestinal AEs. Strong evidence of peripheral target engagement was observed.
Figure S1 from Interdependence of SS18-SSX-driven YAP1 and β-catenin activation in synovial sarcoma
Authors: Isfort Ilka , Berthold Ruth , Heinst Lorena , Wardelmann Eva , Larsson Olle , Trautmann Marcel , Hartmann Wolfgang
Published: September 2024

Figure S1 shows that the SS18-SSX fusion protein regulates TEAD- and TCF-mediated transcriptional activity, both being important for SySa cell viability.
Figure S7 from UBE2C-mediated autophagy inhibition via ubiquitination of SIRT1 contributes to endometrial cancer progression
Authors: Zhao Rong , Liu Yan , Wang Ziwei , Zhang Jun , Zhang Wei , Zhou Xing , Tsedendorj Sevjid , Enkhtur Amarsanaa , Feng Dilu , Wang Hongbo
Published: September 2024

Figure S7
Figure S1 from UBE2C-mediated autophagy inhibition via ubiquitination of SIRT1 contributes to endometrial cancer progression
Authors: Zhao Rong , Liu Yan , Wang Ziwei , Zhang Jun , Zhang Wei , Zhou Xing , Tsedendorj Sevjid , Enkhtur Amarsanaa , Feng Dilu , Wang Hongbo
Published: September 2024

Figure S1
Table S1 from USP10 regulates ZEB1 ubiquitination and protein stability to inhibit ZEB1-mediated colorectal cancer metastasis
Authors: Sun Lei , Yu Jia , Guinney Justin , Qin Bo , Sinicrope Frank A.
Published: September 2024

Deubiquitinases identified from the Biogrid database that may potentially interact with ZEB1.
Supplemental Figure 1 from USP10 regulates ZEB1 ubiquitination and protein stability to inhibit ZEB1-mediated colorectal cancer metastasis
Authors: Sun Lei , Yu Jia , Guinney Justin , Qin Bo , Sinicrope Frank A.
Published: September 2024

Schematic Model. Constitutive activation of the RAS/RAS/MEK/ERK axis phosphorylates the deubiquitinase USP10 at serine 236, and this phosphorylation induces the dissociation of USP10 from ZEB1 resulting in stabilization of ZEB1.
Supplementary Figures 1 - 12, Supplementary Tables 1-5 from BLEACH&STAIN 15-marker multiplexed imaging in 3098 human carcinomas reveals 6 major PD-L1-driven immune phenotypes with distinct spatial orchestration
Authors: Bady Elena , Moeller Katharina , Mandelkow Tim , Raedler Jonas B. , Yang Cheng , Ebner Julia , Lurati Magalie C.J. , Simon Ronald , Vettorazzi Eik , Buescheck Franziska , Luebke Andreas M. , Dum David , Menz Anne , Sauter Guido , Hoeflmayer Doris , Weidemann Soeren , Fraune Christoph , Uhlig Ria , Bernreuther Christian , Jacobsen Frank , Clauditz Till S. , Wilczak Waldemar , Burandt Eike , Steurer Stefan , Minner Sarah , Lennartz Maximilian , Blessin Niclas C.
Published: September 2024

Figure S1a: Representative images of the BLEACH&STAIN 15+1 staining.
Figure S1b: BLEACH&STAIN 15+1 validation.
Figure S2: Deep learning framework for automated cell type identification.
Figure S3: Performance of a Deep Learning-based framework for cell type identification compared to manual set thresholds.
Figure S4: Comparison between BLEACH&STAIN and manual PD-L1 assessment.
Figure S5: Immune phenotype identification.
Figure S6: Association between the immune phenotypes and the individual immune cell parameters.
Figure S7: Representative image of the 6 major immune phenotypes of Figure 2
Figure S8a: Association between PD-L1 phenotypes and clinico-histopathological parameters.
Figure S8b: Distribution of six PD-L1 phenotypes across 44 carcinoma entities.
Figure S9: Spatial orchestration of immune cells across the PD-L1 immune phenotypes.
Figure S10: Representative image of the spatial orchestration shown in Figure 3
Figure S11: Composition of immune cells across the three PD-L1 phenotypes
Figure S12: Prognosis analysis of spatial immune parameters in breast cancer for overall 5-years survival after surgery.

Table S1: TMA cohort of the PD-L1 15+1 study.
Table S2: List of the used antibodies, antigen retrieval (AR), dilutions, and Opal dyes for multiplex fluorescence immunohistochemistry.
Table S3: List of 132 immune cell (sub)population.
Table S4: Associations between spatial parameters and PD-L1 phenotypes were independent from the used threshold.
Table S5: Immune landscape of 3098 human carcinoma samples.
Supplementary Table 2 from Disruption of the MYC Super-Enhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia
Authors: Yashar William M. , Curtiss Brittany M. , Coleman Daniel J. , VanCampen Jake , Kong Garth , Macaraeg Jommel , Estabrook Joseph , Demir Emek , Long Nicola , Bottomly Daniel , McWeeney Shannon K. , Tyner Jeffrey W. , Druker Brian J. , Maxson Julia E. , Braun Theodore P.
Published: September 2024

Transcription Factor Enrichment Analysis of MOLM13 Bulk RNA-Seq (24 Hours After Drug Treatment)
Supplementary Table 16 from Disruption of the MYC Super-Enhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia
Authors: Yashar William M. , Curtiss Brittany M. , Coleman Daniel J. , VanCampen Jake , Kong Garth , Macaraeg Jommel , Estabrook Joseph , Demir Emek , Long Nicola , Bottomly Daniel , McWeeney Shannon K. , Tyner Jeffrey W. , Druker Brian J. , Maxson Julia E. , Braun Theodore P.
Published: September 2024

Transcription Factor Enrichment Analysis of Primary AML Bulk RNA-Seq (24 Hours After Drug Treatment)
Supplementary Table 10 from Disruption of the MYC Super-Enhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia
Authors: Yashar William M. , Curtiss Brittany M. , Coleman Daniel J. , VanCampen Jake , Kong Garth , Macaraeg Jommel , Estabrook Joseph , Demir Emek , Long Nicola , Bottomly Daniel , McWeeney Shannon K. , Tyner Jeffrey W. , Druker Brian J. , Maxson Julia E. , Braun Theodore P.
Published: September 2024

Correlation of Regulon Enrichment Signatures with MYC Gene Expression in Primary AML
Supplementary Fig. 7 from Disruption of the MYC Super-Enhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia
Authors: Yashar William M. , Curtiss Brittany M. , Coleman Daniel J. , VanCampen Jake , Kong Garth , Macaraeg Jommel , Estabrook Joseph , Demir Emek , Long Nicola , Bottomly Daniel , McWeeney Shannon K. , Tyner Jeffrey W. , Druker Brian J. , Maxson Julia E. , Braun Theodore P.
Published: September 2024

GFI1 knockdown weakens the effects of dual FLT3/LSD1 inhibition.
Supplementary Fig. 6 from Disruption of the MYC Super-Enhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia
Authors: Yashar William M. , Curtiss Brittany M. , Coleman Daniel J. , VanCampen Jake , Kong Garth , Macaraeg Jommel , Estabrook Joseph , Demir Emek , Long Nicola , Bottomly Daniel , McWeeney Shannon K. , Tyner Jeffrey W. , Druker Brian J. , Maxson Julia E. , Braun Theodore P.
Published: September 2024

Stat5 over-expression diminishes the efficacy of combined FLT3/LSD1 inhibition.
Supplementary Fig. 5 from Disruption of the MYC Super-Enhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia
Authors: Yashar William M. , Curtiss Brittany M. , Coleman Daniel J. , VanCampen Jake , Kong Garth , Macaraeg Jommel , Estabrook Joseph , Demir Emek , Long Nicola , Bottomly Daniel , McWeeney Shannon K. , Tyner Jeffrey W. , Druker Brian J. , Maxson Julia E. , Braun Theodore P.
Published: September 2024

STAT5 and MYC play a key role in the response to FLT3/LSD1 inhibition.
Supplementary Fig. 4 from Disruption of the MYC Super-Enhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia
Authors: Yashar William M. , Curtiss Brittany M. , Coleman Daniel J. , VanCampen Jake , Kong Garth , Macaraeg Jommel , Estabrook Joseph , Demir Emek , Long Nicola , Bottomly Daniel , McWeeney Shannon K. , Tyner Jeffrey W. , Druker Brian J. , Maxson Julia E. , Braun Theodore P.
Published: September 2024

Dual FLT3/LSD1 inhibition suppresses MYC expression and activity.
Supplementary Fig. 2 from Disruption of the MYC Super-Enhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia
Authors: Yashar William M. , Curtiss Brittany M. , Coleman Daniel J. , VanCampen Jake , Kong Garth , Macaraeg Jommel , Estabrook Joseph , Demir Emek , Long Nicola , Bottomly Daniel , McWeeney Shannon K. , Tyner Jeffrey W. , Druker Brian J. , Maxson Julia E. , Braun Theodore P.
Published: September 2024

Efficacy of dual FLT3/LSD1 inhibition in MOLM13 cells.
Supplementary Fig. 12 from Disruption of the MYC Super-Enhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia
Authors: Yashar William M. , Curtiss Brittany M. , Coleman Daniel J. , VanCampen Jake , Kong Garth , Macaraeg Jommel , Estabrook Joseph , Demir Emek , Long Nicola , Bottomly Daniel , McWeeney Shannon K. , Tyner Jeffrey W. , Druker Brian J. , Maxson Julia E. , Braun Theodore P.
Published: September 2024

Dual FLT3/LSD1 inhibition disrupts LSC clonogenicity.
Supplementary Fig. 1 from Disruption of the MYC Super-Enhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia
Authors: Yashar William M. , Curtiss Brittany M. , Coleman Daniel J. , VanCampen Jake , Kong Garth , Macaraeg Jommel , Estabrook Joseph , Demir Emek , Long Nicola , Bottomly Daniel , McWeeney Shannon K. , Tyner Jeffrey W. , Druker Brian J. , Maxson Julia E. , Braun Theodore P.
Published: September 2024

Drug synergy between FLT3 and LSD1 inhibitors in FLT3-ITD and FLT3-wildtype cell lines.
Supplementary Table 3 from EIF4A3 acts on the PI3K-AKT-ERK1/2-P70S6K pathway through FLOT1 to influence the development of lung adenocarcinoma
Authors: Yu Wenhao , Liang Jinghui , Fang Tao , Jiang Jin , Zhao Renchang , Li Rongyang , Han Jingyi , Tian Hui
Published: September 2024

Correlation between EIF4A3 expression and clinicopathological characteristics in LUAD
Supplementary Figure 3 from Tumor-derived CCL5 recruits cancer-associated fibroblasts and promotes tumor cell proliferation in esophageal squamous cell carcinoma
Authors: Dunbar Karen J. , Karakasheva Tatiana A. , Tang Qiaosi , Efe Gizem , Lin Eric W. , Harris Michael , Sahu Varun , Sachdeva Uma M. , Hu Jianhua , Klein-Szanto Andres J. , Henick Brian , Diehl J. Alan , Nakagawa Hiroshi , Rustgi Anil K.
Published: September 2024

ERK1/2 signaling pathway in CCL5 knockout cells.
Supplementary Figure 1 from Tumor-derived CCL5 recruits cancer-associated fibroblasts and promotes tumor cell proliferation in esophageal squamous cell carcinoma
Authors: Dunbar Karen J. , Karakasheva Tatiana A. , Tang Qiaosi , Efe Gizem , Lin Eric W. , Harris Michael , Sahu Varun , Sachdeva Uma M. , Hu Jianhua , Klein-Szanto Andres J. , Henick Brian , Diehl J. Alan , Nakagawa Hiroshi , Rustgi Anil K.
Published: September 2024

Confirmation of CCL5 knockout clones.
Supplementary Figure S1, S2, S3 from MACdb: A curated knowledgebase for metabolic associations across human cancers
Authors: Sun Yanling , Zheng Xinchang , Wang Guoliang , Wang Yibo , Chen Xiaoning , Sun Jiani , Xiong Zhuang , Zhang Sisi , Wang Tianyi , Fan Zhuojing , Bu Congfan , Bao Yiming , Zhao Wenming
Published: September 2024

Supplementary Figure S1, S2, S3
Supplementary Figure 2 from Truncation of GalNAc-type O-glycans suppresses CD44-mediated osteoclastogenesis and bone metastasis in breast cancer
Authors: Lin Neng-Yu , Lee Jian-Jr , Chen Syue-Ting , Lin Jung-An , Lin Chia-Hsuan , Lin Hsuan-Yu , Su Yong-Han , Chen Cheng-Chang , Lin Mei-Chun , Kuo Ching-Ying , Haung Min-Chuan
Published: September 2024

Construction of multiple mutations at O-glycosites in the stem region of CD44.
Supplementary Figure 1 from Critical role of 6-phosphogluconate dehydrogenase in TAp73-mediated cancer cell proliferation
Authors: Qiao Rui , Wei Mengmeng , Chen Hui , Zhang Xianhong , Zhang Jie , Gao Liyang , Ma Haijun , Wang Yujiong , Li Le
Published: September 2024

S1. TAp73 activates the expression of 6PGD
Figure S7 from Dynamic intestinal stem cell plasticity and lineage remodeling by a nutritional environment relevant to human risk for tumorigenesis
Authors: Choi Jiahn , Zhang Xusheng , Li Wenge , Houston Michele , Peregrina Karina , Dubin Robert , Ye Kenny , Augenlicht Leonard
Published: September 2024

The western diet causes chronic pro-tumorigenic inflammation.
Figure S4 from Dynamic intestinal stem cell plasticity and lineage remodeling by a nutritional environment relevant to human risk for tumorigenesis
Authors: Choi Jiahn , Zhang Xusheng , Li Wenge , Houston Michele , Peregrina Karina , Dubin Robert , Ye Kenny , Augenlicht Leonard
Published: September 2024

Targeted knockout of Ppargc1a in Lgr5hi cells was confirmed, and trajectory analyses of dietary and genetic alterations confirmed by marker expression.
Figure S1 from Dynamic intestinal stem cell plasticity and lineage remodeling by a nutritional environment relevant to human risk for tumorigenesis
Authors: Choi Jiahn , Zhang Xusheng , Li Wenge , Houston Michele , Peregrina Karina , Dubin Robert , Ye Kenny , Augenlicht Leonard
Published: September 2024

The western diet extensively reprograms Lgr5hi stem cells that expands with time and is reversible. This includes the TCA cycle and Oxphos pathways
Supplementary Figure S7 from Overlaid transcriptome and proteome analyses identify mitotic kinesins as important targets of arylsulfonamide-mediated RBM39 degradation
Authors: Coomar Seemon , Mota Pedro , Penson Alexander , Schwaller Juerg , Abdel-Wahab Omar , Gillingham Dennis
Published: September 2024

Supplementary Figure S7
Figure S7 from A comparative study of neuroendocrine heterogeneity in small cell lung cancer and neuroblastoma
Authors: Cai Ling , DeBerardinis Ralph J. , Xie Yang , Minna John D. , Xiao Guanghua
Published: September 2024

Comparing NE score-associated features between SCLC and other cancer types.
Fig. S4 from Absence of either Ripk3 or Mlkl reduces incidence of hepatocellular carcinoma independent of liver fibrosis
Authors: Mohammed Sabira , Thadathil Nidheesh , Ohene-Marfo Phoebe , Tran Albert L. , Van Der Veldt Michael , Georgescu Constantin , Oh Sangphil , Nicklas Evan H. , Wang Dawei , Haritha Nair Hariprasad , Luo Wenyi , Janknecht Ralf , Miller Benjamin F. , Wren Jonathan D. , Freeman Willard M. , Deepa Sathyaseelan S.
Published: September 2024

Fig S4 shows transcript levels of Col1a1, western blots for Desmin, a-SMA and b-tubulin, Transcript levels of TGFb
Supplementary Table S5 from Single-Cell Evolutionary Analysis Reveals Drivers of Plasticity and Mediators of Chemoresistance in Small Cell Lung Cancer
Authors: Wollenzien Hannah , Tecleab Yohannes Afeworki A. , Szczepaniak-Sloane Robert , Restaino Anthony , Kareta Michael S.
Published: September 2024

Normalized gene expression across NCI-H209 subclones (related to Figure 4)
Supplementary Figure S6 from Single-Cell Evolutionary Analysis Reveals Drivers of Plasticity and Mediators of Chemoresistance in Small Cell Lung Cancer
Authors: Wollenzien Hannah , Tecleab Yohannes Afeworki A. , Szczepaniak-Sloane Robert , Restaino Anthony , Kareta Michael S.
Published: September 2024

Expression and validation of AP-1 family genes in late tumor development.
Supplementary Figure S2 from Single-Cell Evolutionary Analysis Reveals Drivers of Plasticity and Mediators of Chemoresistance in Small Cell Lung Cancer
Authors: Wollenzien Hannah , Tecleab Yohannes Afeworki A. , Szczepaniak-Sloane Robert , Restaino Anthony , Kareta Michael S.
Published: September 2024

Characterization of cell types isolated from the autochthonous scRNA-seq data.
Supplementary Figure S13 from Single-Cell Evolutionary Analysis Reveals Drivers of Plasticity and Mediators of Chemoresistance in Small Cell Lung Cancer
Authors: Wollenzien Hannah , Tecleab Yohannes Afeworki A. , Szczepaniak-Sloane Robert , Restaino Anthony , Kareta Michael S.
Published: September 2024

Determining effective concentrations for treatment of SCLC cell lines with cisplatin and etoposide.
Supplementary Table S5 from Identification of a ΔNp63-Dependent Basal-Like A Subtype-Specific Transcribed Enhancer Program (B-STEP) in Aggressive Pancreatic Ductal Adenocarcinoma
Authors: Wang Xin , Kutschat Ana P. , Aggrey-Fynn Joana , Hamdan Feda H. , Graham Rondell P. , Wixom Alexander Q. , Souto Yara , Ladigan-Badura Swetlana , Yonkus Jennifer A. , Abdelrahman Amro M. , Alva-Ruiz Roberto , Gaedcke Jochen , Strobel Philipp , Kosinsky Robyn Laura , Wegwitz Florian , Hermann Patrick , Truty Mark J. , Siveke Jens T. , Hahn Stephan A. , Hessmann Elisabeth , Johnsen Steven A. , Najafova Zeynab
Published: September 2024

Supplementary Table S5 contains list of genes associated with L3.6pl TP63 dependent
enhancers.
Supplementary Figure 7 from Targeting c-Jun is a potential therapy for luminal breast cancer bone metastasis
Authors: Han Yuxuan , Katayama Shota , Futakuchi Mitsuru , Nakamichi Kazuya , Wakabayashi Yutaro , Sakamoto Mai , Nakayama Jun , Semba Kentaro
Published: September 2024

Evaluation of JNK-IN-8 inhibition of MCF7-BM cells.
Supplementary Figure 2 from Targeting c-Jun is a potential therapy for luminal breast cancer bone metastasis
Authors: Han Yuxuan , Katayama Shota , Futakuchi Mitsuru , Nakamichi Kazuya , Wakabayashi Yutaro , Sakamoto Mai , Nakayama Jun , Semba Kentaro
Published: September 2024

TAM67 suppressed osteolytic bone metastasis of MCF7-BM02 cells.
Supplementary Methods and Materials from Targeting the ATF6-mediated ER stress response and autophagy blocks integrin-driven prostate cancer progression
Authors: Macke Amanda J. , Pachikov Artem N. , Divita Taylor E. , Morris Mary E. , LaGrange Chad A. , Holzapfel Melissa S. , Kubyshkin Anatoly V. , Zyablitskaya Evgeniya Y. , Makalish Tatiana P. , Eremenko Sergey N. , Qiu Haowen , Riethoven Jean-Jack M. , Hemstreet George P. , Petrosyan Armen
Published: September 2024

Supplementary Methods and Materials
Fig S1 from HCK promotes high-grade serous ovarian cancer tumorigenesis through CD44 and NOTCH3 signaling
Authors: Khella Christen A. , Franciosa Lucyann , Rodriguez-Rodriguez Lorna , Rajkarnikar Resha , Mythreye Karthikeyan , Gatza Michael L.
Published: September 2024

Distribution of clinical features associated with poor and good prognostic HGSOC patient samples in the TCGA U133A dataset.
Supplemental Table 3 from Allele-specific gene regulation, phenotypes, and therapeutic vulnerabilities in estrogen receptor alpha mutant endometrial cancer
Authors: Blanchard Zannel , Rush Craig M. , Arnesen Spencer , Vahrenkamp Jeffery M. , Rodriguez Adriana C. , Jarboe Elke A. , Brown Callie , Chang Matthew E.K. , Flory Mark R. , Mohammed Hisham , Modzelewska Katarzyna , Lum David H. , Gertz Jason
Published: September 2024

Differentially expressed genes from in vivo RNA-seq experiments
Supplemental Figure 7 from Allele-specific gene regulation, phenotypes, and therapeutic vulnerabilities in estrogen receptor alpha mutant endometrial cancer
Authors: Blanchard Zannel , Rush Craig M. , Arnesen Spencer , Vahrenkamp Jeffery M. , Rodriguez Adriana C. , Jarboe Elke A. , Brown Callie , Chang Matthew E.K. , Flory Mark R. , Mohammed Hisham , Modzelewska Katarzyna , Lum David H. , Gertz Jason
Published: September 2024

In vivo exploration of novel therapeutic targets in ER active and mutant endometrial cancer
Supplementary Table 4 from Hierarchical phosphorylation of HOXB13 by mTOR dictates its activity and oncogenic function in prostate cancer
Authors: Chen Yonghong , Dufour Catherine R. , Han Lingwei , Li Ting , Xia Hui , Giguere Vincent
Published: September 2024

Supplementary Table 4. Source data.
Supplementary Table 2 from Podoplanin drives amoeboid invasion in canine and human mucosal melanoma
Authors: Shinada Masahiro , Kato Daiki , Motegi Tomoki , Tsuboi Masaya , Ikeda Namiko , Aoki Susumu , Iguchi Takaaki , Li Toshio , Kodera Yuka , Ota Ryosuke , Hashimoto Yuko , Takahashi Yosuke , Chambers James , Uchida Kazuyuki , Kato Yukinari , Nishimura Ryohei , Nakagawa Takayuki
Published: September 2024

Univariate survival analysis of dogs with mucosal melanoma.
Supplementary Materials and Methods from Podoplanin drives amoeboid invasion in canine and human mucosal melanoma
Authors: Shinada Masahiro , Kato Daiki , Motegi Tomoki , Tsuboi Masaya , Ikeda Namiko , Aoki Susumu , Iguchi Takaaki , Li Toshio , Kodera Yuka , Ota Ryosuke , Hashimoto Yuko , Takahashi Yosuke , Chambers James , Uchida Kazuyuki , Kato Yukinari , Nishimura Ryohei , Nakagawa Takayuki
Published: September 2024

Supplementary Materials and Methods
Supplementary Figure Legends from Podoplanin drives amoeboid invasion in canine and human mucosal melanoma
Authors: Shinada Masahiro , Kato Daiki , Motegi Tomoki , Tsuboi Masaya , Ikeda Namiko , Aoki Susumu , Iguchi Takaaki , Li Toshio , Kodera Yuka , Ota Ryosuke , Hashimoto Yuko , Takahashi Yosuke , Chambers James , Uchida Kazuyuki , Kato Yukinari , Nishimura Ryohei , Nakagawa Takayuki
Published: September 2024

Supplementary Figure Legends 1-12
Supplementary Figure 9 from Podoplanin drives amoeboid invasion in canine and human mucosal melanoma
Authors: Shinada Masahiro , Kato Daiki , Motegi Tomoki , Tsuboi Masaya , Ikeda Namiko , Aoki Susumu , Iguchi Takaaki , Li Toshio , Kodera Yuka , Ota Ryosuke , Hashimoto Yuko , Takahashi Yosuke , Chambers James , Uchida Kazuyuki , Kato Yukinari , Nishimura Ryohei , Nakagawa Takayuki
Published: September 2024

PDPN promotes distant colonization.
Supplementary Figure 3 from Podoplanin drives amoeboid invasion in canine and human mucosal melanoma
Authors: Shinada Masahiro , Kato Daiki , Motegi Tomoki , Tsuboi Masaya , Ikeda Namiko , Aoki Susumu , Iguchi Takaaki , Li Toshio , Kodera Yuka , Ota Ryosuke , Hashimoto Yuko , Takahashi Yosuke , Chambers James , Uchida Kazuyuki , Kato Yukinari , Nishimura Ryohei , Nakagawa Takayuki
Published: September 2024

PDPN regulates features of amoeboid invasion via the ROCK-MLC2 signaling.
Supplementary Figure 11 from Podoplanin drives amoeboid invasion in canine and human mucosal melanoma
Authors: Shinada Masahiro , Kato Daiki , Motegi Tomoki , Tsuboi Masaya , Ikeda Namiko , Aoki Susumu , Iguchi Takaaki , Li Toshio , Kodera Yuka , Ota Ryosuke , Hashimoto Yuko , Takahashi Yosuke , Chambers James , Uchida Kazuyuki , Kato Yukinari , Nishimura Ryohei , Nakagawa Takayuki
Published: September 2024

Canine mucosal melanomas with PDPN high expression demonstrate enrichment of gene signatures associated with amoeboid invasion.
Figure S3 from USP1 expression driven by EWS::FLI1 transcription factor stabilizes Survivin and mitigates replication stress in Ewing sarcoma
Authors: Mallard Halle J. , Wan Shibiao , Nidhi Prakriti , Hanscom-Trofy Yvan D. , Mohapatra Bhopal , Woods Nicholas T. , Lopez-Guerrero Jose Antonio , Llombart-Bosch Antonio , Machado Isidro , Scotlandi Katia , Kreiling Natasha F. , Perry Megan C. , Mirza Sameer , Coulter Donald W. , Band Vimla , Band Hamid , Ghosal Gargi
Published: September 2024

Figure S3 shows USP1 knockdown or inhibition induces apoptotic cell death.
Table S7 from CBF-beta mitigates PI3K-alpha-specific inhibitor killing through PIM1 in PIK3CA mutant gastric cancer
Authors: Stanland Lyla J. , Ang Hazel X. , Hoj Jacob P. , Chu Yunqiang , Tan Patrick , Wood Kris C. , Luftig Micah A.
Published: September 2024

QPCR primers
Table S1 from CBF-beta mitigates PI3K-alpha-specific inhibitor killing through PIM1 in PIK3CA mutant gastric cancer
Authors: Stanland Lyla J. , Ang Hazel X. , Hoj Jacob P. , Chu Yunqiang , Tan Patrick , Wood Kris C. , Luftig Micah A.
Published: September 2024

Genes included in the CRISPR screening library
Supplementary Materials and Methods from Exon junction complex mediates the cap-independent translation of circular RNA
Authors: Lin Hui-Hsuan , Chang Chiu-Yuan , Huang Yi-Ren , Shen Che-Hung , Wu Yu-Chen , Chang Kai-Li , Lee Yueh-Chun , Lin Ya-Chi , Ting Wen-Chien , Chien Han-Ju , Zheng Yi-Feng , Lai Chien-Chen , Hsiao Kuei-Yang
Published: September 2024

Supplementary Materials and Methods
Table S4 from FBXO24 suppresses breast cancer tumorigenesis by targeting LSD1 for Ubiquitination
Authors: Dong Bo , Song Xiang , Wang Xinzhao , Dai Tao , Wang Jianlin , Yu Zhiyong , Deng Jiong , Evers B. Mark , Wu Yadi
Published: September 2024

Supplemental table 4. Tumor samples with Lymph node metastases of breast cancer.
Supplementary Figure 6 from FBXO24 suppresses breast cancer tumorigenesis by targeting LSD1 for Ubiquitination
Authors: Dong Bo , Song Xiang , Wang Xinzhao , Dai Tao , Wang Jianlin , Yu Zhiyong , Deng Jiong , Evers B. Mark , Wu Yadi
Published: September 2024

FBXO24 expression is associated with a good prognosis.
Supplementary Figure 5 from Competing engagement of β-arrestin isoforms balances IGF1R/p53 signaling and controls melanoma cell chemotherapeutic responsiveness
Authors: Cismas Sonia , Pasca Sylvya , Crudden Caitrin , Troccoli Drakensjo Iara , Suleymanova Naida , Zhang Simin , Gebhard Benjamin , Song Dawei , Neo Shiyong , Shibano Takashi , Smith Terry J. , Calin George A. , Girnita Ada , Girnita Leonard
Published: September 2024

Rescue-validation of β-arrestin imbalance effects on MDM2-dependent IGF1R expression.
Data from Allele-specific gene regulation, phenotypes, and therapeutic vulnerabilities in estrogen receptor alpha mutant endometrial cancer
Authors: Blanchard Zannel , Rush Craig M. , Arnesen Spencer , Vahrenkamp Jeffery M. , Rodriguez Adriana C. , Jarboe Elke A. , Brown Callie , Chang Matthew E.K. , Flory Mark R. , Mohammed Hisham , Modzelewska Katarzyna , Lum David H. , Gertz Jason
Published: September 2024

Abstract
Activating estrogen receptor alpha (ER) mutations are present in primary endometrial and metastatic breast cancers, promoting estrogen-independent activation of the receptor. Functional characterizations in breast cancer have established unique molecular and phenotypic consequences of the receptor, yet the impact of ER mutations in endometrial cancer has not been fully explored. In this study, we used CRISPR-Cas9 to model the clinically prevalent ER-Y537S mutation and compared results to ER-D538G to discover allele-specific differences between ER mutations in endometrial cancer. We found that constitutive activity of mutant ER resulted in changes in the expression of thousands of genes, stemming from combined alterations to ER binding and chromatin accessibility. The unique gene expression programs resulted in ER mutant cells developing increased cancer associated phenotypes, including migration, invasion, anchorage independent growth, and growth in vivo. To uncover potential treatment strategies, we identified ER associated proteins via Rapid Immunoprecipitation and Mass Spectrometry of Endogenous Proteins (RIME) and interrogated two candidates, CDK9 and NCOA3. Inhibition of these regulatory proteins resulted in decreased growth and migration, representing potential novel treatment strategies for ER mutant endometrial cancer.

Implications: This study provides insight into mutant ER activity in endometrial cancer and identifies potential therapies for women with ER mutant endometrial cancer.
Supplemental Figure 1 from Breastfeeding and Mammographic Breast Density: A Cross-sectional Study
Authors: Getz Kayla R. , Adedokun Babatunde , Xu Shuai , Toriola Adetunji T.
Published: September 2024

Supplemental Figure 1: Flowchart displaying how we arrived at the final analytic sample. Among the women recruited to the study, 127 were missing breastfeeding duration and 32 were missing values for all of the MBD measures. An additional 18 participants were missing values for one of the confounding variables; 11 women were missing age at menarche, 1 woman was missing BMI and 6 women were missing information about family history of breast cancer.
Supplemental Methods 1 from Risk Factors for Early Onset Sporadic Colorectal Cancer in Male Veterans
Authors: Imperiale Thomas F. , Myers Laura J. , Barker Barry C. , Larson Jason , Stump Timothy E. , Daggy Joanne K.
Published: September 2024

Supplemental Methods 1: Contains details pertaining to data analysis
Supplementary Table S5 from Phase II Trial of Nelipepimut-S Peptide Vaccine in Women with Ductal Carcinoma in Situ
Authors: O'Shea Anne E. , Clifton Guy T. , Qiao Na , Heckman-Stoddard Brandy M. , Wojtowicz Malgorzata , Dimond Eileen , Bedrosian Isabelle , Weber Diane , Garber Judy E. , Husband Alexander , Pastorello Ricardo , Lee J. Jack , Hernandez Mike , Liu Diane D. , Vornik Lana A. , Brown Powel H. , Alatrash Gheath , Peoples George E. , Mittendorf Elizabeth A.
Published: September 2024

Supplementary Table S5: HER2 expression in biopsy and resection specimens
Supplementary Table S3 from Phase II Trial of Nelipepimut-S Peptide Vaccine in Women with Ductal Carcinoma in Situ
Authors: O'Shea Anne E. , Clifton Guy T. , Qiao Na , Heckman-Stoddard Brandy M. , Wojtowicz Malgorzata , Dimond Eileen , Bedrosian Isabelle , Weber Diane , Garber Judy E. , Husband Alexander , Pastorello Ricardo , Lee J. Jack , Hernandez Mike , Liu Diane D. , Vornik Lana A. , Brown Powel H. , Alatrash Gheath , Peoples George E. , Mittendorf Elizabeth A.
Published: September 2024

Supplementary Table S3: Pathologic characteristics
Supplementary Table S2 from Phase II Trial of Nelipepimut-S Peptide Vaccine in Women with Ductal Carcinoma in Situ
Authors: O'Shea Anne E. , Clifton Guy T. , Qiao Na , Heckman-Stoddard Brandy M. , Wojtowicz Malgorzata , Dimond Eileen , Bedrosian Isabelle , Weber Diane , Garber Judy E. , Husband Alexander , Pastorello Ricardo , Lee J. Jack , Hernandez Mike , Liu Diane D. , Vornik Lana A. , Brown Powel H. , Alatrash Gheath , Peoples George E. , Mittendorf Elizabeth A.
Published: September 2024

Supplementary Table S2: Median changes in percentage of nelipepimut (NPS)-specific cytotoxic lymphocytes (CTL)
Data from Breastfeeding and Mammographic Breast Density: A Cross-sectional Study
Authors: Getz Kayla R. , Adedokun Babatunde , Xu Shuai , Toriola Adetunji T.
Published: September 2024

Abstract
Breastfeeding is inversely associated with breast cancer risk but the associations of breastfeeding with mammographic breast density (MBD) are not clear. We investigated the association between breastfeeding and volumetric measures of MBD (volumetric percent density (VPD), dense volume (DV) and non-dense volume (NDV)) and evaluated whether it differs by race, menopausal status, and body mass index (BMI).
The study population was comprised of 964 women (67% non-Hispanic white, 29% non-Hispanic black) who had screening mammography at Washington University School of Medicine, St. Louis, MO. VPD, DV and NDV were log10 transformed. We performed multivariable linear regression models adjusted for age, BMI, family history of breast cancer, race, and age at menarche among all participants and exclusively in parous women.
Mean age was 50.7 years. VPD was 12% lower among women who breastfed 0-6 months, (10^β=0.88, 95%CI (0.79,0.98)) compared to nulliparous women. Breastfeeding was inversely associated with DV (parous never breastfed: 10^β=0.93, 95%CI (0.83,1.04), breastfed 0-6 months: 10^β=0.91, 95%CI (0.79,1.05), breastfed 7-12 months: 10^β=0.94, 95%CI (0.81,1.10), breastfed >12 months: 10^β=0.87, 95%CI (0.78,0.98), p-trend=0.03). BMI modified the association between breastfeeding and VPD. Women who breastfed for 0-6 months and had a BMI < 25kg/m2 had lower VPD compared to nulliparous women, but among women with a BMI ≥ 25kg/m2 there was no association (p-interaction=0.04).
In this diverse study population, the association of breastfeeding with VPD appears to be modified by BMI, but not by race or menopausal status. Future research exploring the associations of breastfeeding with other mammographic features are needed.
Figure S4 from Abatacept/Ruxolitinib and Screening for Concomitant Respiratory Muscle Failure to Mitigate Fatality of Immune-Checkpoint Inhibitor Myocarditis
Authors: Salem Joe-Elie , Bretagne Marie , Abbar Baptiste , LEONARD-LOUIS Sarah , Ederhy Stephane , REDHEUIL Alban , BOUSSOUAR Samia , NGUYEN Lee S. , PROCUREUR Adrien , STEIN Frederic , FENIOUX Charlotte , DEVOS Perrine , GOUGIS Paul , DRES Martin , DEMOULE Alexandre , Psimaras Dimitri , LENGLET Timothee , MAISONOBE Thierry , PINETON DE CHAMBRUN Marc , HEKIMIAN Guillaume , STRAUS Christian , GONZALEZ-BERMEJO Jesus , Klatzmann David , RIGOLET Aude , GUILLAUME-JUGNOT Perrine , CHAMPTIAUX Nicolas , BENVENISTE Olivier , WEISS Nicolas , SAHEB Samir , ROUVIER Philippe , PLU Isabelle , GANDJBAKHCH Estelle , KERNEIS Mathieu , HAMMOUDI Nadjib , ZAHR Noel , LLONTOP Claudia , MORELOT-PANZINI Capucine , Lehmann Lorenz , Qin Juan , Moslehi Javid J. , ROSENZWAJG Michelle , SIMILOWSKI Thomas , Allenbach Yves
Published: September 2024

Example of the first severe ICI-myocarditis case treated with abatacept guided by real-time immune-monitoring assessment of CD86RO (CD86 receptor occupancy) on circulating monocytes.
Figure S3 from Abatacept/Ruxolitinib and Screening for Concomitant Respiratory Muscle Failure to Mitigate Fatality of Immune-Checkpoint Inhibitor Myocarditis
Authors: Salem Joe-Elie , Bretagne Marie , Abbar Baptiste , LEONARD-LOUIS Sarah , Ederhy Stephane , REDHEUIL Alban , BOUSSOUAR Samia , NGUYEN Lee S. , PROCUREUR Adrien , STEIN Frederic , FENIOUX Charlotte , DEVOS Perrine , GOUGIS Paul , DRES Martin , DEMOULE Alexandre , Psimaras Dimitri , LENGLET Timothee , MAISONOBE Thierry , PINETON DE CHAMBRUN Marc , HEKIMIAN Guillaume , STRAUS Christian , GONZALEZ-BERMEJO Jesus , Klatzmann David , RIGOLET Aude , GUILLAUME-JUGNOT Perrine , CHAMPTIAUX Nicolas , BENVENISTE Olivier , WEISS Nicolas , SAHEB Samir , ROUVIER Philippe , PLU Isabelle , GANDJBAKHCH Estelle , KERNEIS Mathieu , HAMMOUDI Nadjib , ZAHR Noel , LLONTOP Claudia , MORELOT-PANZINI Capucine , Lehmann Lorenz , Qin Juan , Moslehi Javid J. , ROSENZWAJG Michelle , SIMILOWSKI Thomas , Allenbach Yves
Published: September 2024

Effect of plasmapheresis on ICI circulating levels in the 10 patients receiving plasmapheresis in our cohort.
Table S3 from Type I Interferon Signaling via the EGR2 Transcriptional Regulator Potentiates CAR T cell-intrinsic Dysfunction
Authors: Jung In-Young , Bartoszek Robert L. , Rech Andrew J. , Collins Sierra M. , Ooi Soon-Keat , Williams Erik F. , Hopkins Caitlin R. , Narayan Vivek , Haas Naomi B. , Frey Noelle V. , Hexner Elizabeth O. , Siegel Donald L. , Plesa Gabriela , Porter David L. , Cantu Adrian , Everett John K. , Guedan Sonia , Berger Shelley L. , Bushman Frederic D. , Herbst Friederike , Fraietta Joseph A.
Published: September 2024

Chromatin accessibility profiles for EGR2 knockout (KO) and AAVS1 knockout (AAVS1) CD8+ CAR T-cells. The table provides information on the locus mapping, p-value, average log2 fold change, percentage of cells, adjusted p-value, transcript ID, gene name, gene ID, gene biotype, region type, closest region, query region, and distance.
Table S2 from Type I Interferon Signaling via the EGR2 Transcriptional Regulator Potentiates CAR T cell-intrinsic Dysfunction
Authors: Jung In-Young , Bartoszek Robert L. , Rech Andrew J. , Collins Sierra M. , Ooi Soon-Keat , Williams Erik F. , Hopkins Caitlin R. , Narayan Vivek , Haas Naomi B. , Frey Noelle V. , Hexner Elizabeth O. , Siegel Donald L. , Plesa Gabriela , Porter David L. , Cantu Adrian , Everett John K. , Guedan Sonia , Berger Shelley L. , Bushman Frederic D. , Herbst Friederike , Fraietta Joseph A.
Published: September 2024

Genes deferentially expressed in EGR2 compared to AAVS1 knockout CD8+ CAR T-cells. The corresponding log2 fold change values and statistical significance are provided for the listed genes.
Figure S8 from Type I Interferon Signaling via the EGR2 Transcriptional Regulator Potentiates CAR T cell-intrinsic Dysfunction
Authors: Jung In-Young , Bartoszek Robert L. , Rech Andrew J. , Collins Sierra M. , Ooi Soon-Keat , Williams Erik F. , Hopkins Caitlin R. , Narayan Vivek , Haas Naomi B. , Frey Noelle V. , Hexner Elizabeth O. , Siegel Donald L. , Plesa Gabriela , Porter David L. , Cantu Adrian , Everett John K. , Guedan Sonia , Berger Shelley L. , Bushman Frederic D. , Herbst Friederike , Fraietta Joseph A.
Published: September 2024

Comparison of Type I IFN gene expression in different CAR-T engineering approaches. (A-F) show volcano plots and a heatmap of gene expression in engineered CAR T-cells, with type I IFN genes highlighted in blue. These data represent different CAR-T engineering approaches, including: BRG1/BRM-associated factors (BAF) complex, Gata3, INO80 complex knockout (PMID35750052), BATF overexpression (PMID34282330), 4-1BB- versus CD28-based GD2 CAR activity (PMID 25939063) and 1xx CD19 CAR T-cells (GSE121226). These plots allow for a comparison of the levels of type I IFN gene expression in each of these different CAR-T engineering methods.
Figure S5 from Type I Interferon Signaling via the EGR2 Transcriptional Regulator Potentiates CAR T cell-intrinsic Dysfunction
Authors: Jung In-Young , Bartoszek Robert L. , Rech Andrew J. , Collins Sierra M. , Ooi Soon-Keat , Williams Erik F. , Hopkins Caitlin R. , Narayan Vivek , Haas Naomi B. , Frey Noelle V. , Hexner Elizabeth O. , Siegel Donald L. , Plesa Gabriela , Porter David L. , Cantu Adrian , Everett John K. , Guedan Sonia , Berger Shelley L. , Bushman Frederic D. , Herbst Friederike , Fraietta Joseph A.
Published: September 2024

Gene expression and pathway enrichment analysis of CD8+ T cell clusters. A, Heatmap showing differentially expressed genes between memory-like KLF2+ and exhausted-like MKI67+ CD8+ T-cells. Gene signature scores related to cell cycle and clinical response are indicated on the top bars. B, Top downregulated GO biological processes in EGR2 compared to AAVS1 knockout CAR T-cells.