bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figure S18 from Integrated genomic and transcriptomic analysis improves disease classification and risk stratification of MDS with ring sideroblasts.
Authors: Todisco Gabriele , Creignou Maria , Bernard Elsa , Björklund Ann-Charlotte , Moura Pedro Luis. , Tesi Bianca , Mortera Blanco Teresa , Sander Birgitta , Jansson Monika , Walldin Gunilla , Barbosa Indira , Reinsbach Susanne E. , Hofman Isabel Juliana. , Nilsson Christer , Yoshizato Tetsuichi , Dimitriou Marios , Chang David , Olafsdottir Svanhildur , Venckute Larsson Sigita , Tobiasson Magnus , Malcovati Luca , Woll Petter , Jacobsen Sten-Eirik W. , Papaemmanuil Elli , Hellström-Lindberg Eva
Published: September 2024

Distribution of estimated MEP proportion according to bone marrow blast percentage. P-value for each pairwise comparison is reported in the upper part of the plot.
Figure S1 from A Phase 2 Study of Durvalumab for Bacillus Calmette-Guerin (BCG) Unresponsive Urothelial Carcinoma In Situ of the Bladder
Authors: Li Roger , Sexton Wade J. , Dhillon Jasreman , Berglund Anders , Naidu Shreyas , Borjas Gustavo , Rose Kyle , Kim Youngchul , Wang Xuefeng , Conejo-Garcia Jose R. , Jain Rohit K. , Poch Michael A. , Spiess Philippe E. , Pow-Sang Julio , Gilbert Scott M. , Zhang Jingsong
Published: September 2024

12-CK Score from RNA Sequencing
Teee vs Treg Clusters DEGs DS3 from A Population of Tumor-Infiltrating CD4+ T-cells Co-expressing CD38 and CD39 is Associated with Checkpoint Inhibitor Resistance
Authors: Mitra Ankita , Thompson Brian , Strange Ann , Amato Carol M. , Vassallo Melinda , Dolgalev Igor , Hester-McCullough Jonathan , Muramatsu Tomoaki , Kimono Diana , Puranik Amrutesh S. , Weber Jeffrey S. , Woods David
Published: September 2024

Teee vs Treg Clusters DEGs
Supplementary Figure 1 from Phase I trial of the multi-kinase inhibitor cabozantinib, a CYP3A4 substrate, plus CYP3A4 interacting antiretroviral therapy in people living HIV and cancer (AMC087)
Authors: Haigentz Missak , Lee Jeannette Y. , Chiao Elizabeth Y. , Aboulafia David M. , Ratner Lee , Ambinder Richard F. , Baiocchi Robert A. , Mitsuyasu Ronald T. , Wachsman William , Sparano Joseph A. , Rudek Michelle A.
Published: September 2024

Supplementary Figure 1. Average and standard deviation concentration–time profile of cabozantinib at steady-state on a semi-log plot for stratum A (A), stratum B (B), and stratum C (C). Doses are noted in the figures.
Supplementary Table S5 from Comprehensive analysis of tumor microenvironment reveals prognostic ceRNA network related to immune infiltration in sarcoma
Authors: Leng Dongliang , Yang Ziyi , Sun Heng , Song Chengcheng , Huang Chen , Ip Ka U. , Chen Guokai , Deng Chu-Xia , Zhang Xiaohua Douglas. , Zhao Qi
Published: September 2024

Supplementary Table S5. DE genes in C2 (High) compared with C3 (Moderate).
Supplementary Table S3 from Comprehensive analysis of tumor microenvironment reveals prognostic ceRNA network related to immune infiltration in sarcoma
Authors: Leng Dongliang , Yang Ziyi , Sun Heng , Song Chengcheng , Huang Chen , Ip Ka U. , Chen Guokai , Deng Chu-Xia , Zhang Xiaohua Douglas. , Zhao Qi
Published: September 2024

Supplementary Table S3. DE genes in C2 (High) compared with C1 (Low) subtype.
Supplementary Table S14 from Comprehensive analysis of tumor microenvironment reveals prognostic ceRNA network related to immune infiltration in sarcoma
Authors: Leng Dongliang , Yang Ziyi , Sun Heng , Song Chengcheng , Huang Chen , Ip Ka U. , Chen Guokai , Deng Chu-Xia , Zhang Xiaohua Douglas. , Zhao Qi
Published: September 2024

Supplementary Table S14. Top 30 hub genes in the PPI network.
Supplementary Figure S3 from Comprehensive analysis of tumor microenvironment reveals prognostic ceRNA network related to immune infiltration in sarcoma
Authors: Leng Dongliang , Yang Ziyi , Sun Heng , Song Chengcheng , Huang Chen , Ip Ka U. , Chen Guokai , Deng Chu-Xia , Zhang Xiaohua Douglas. , Zhao Qi
Published: September 2024

Supplementary Figure S3. Characterization of subtypes of SARC.
Supplementary Figure S2 from Comprehensive analysis of tumor microenvironment reveals prognostic ceRNA network related to immune infiltration in sarcoma
Authors: Leng Dongliang , Yang Ziyi , Sun Heng , Song Chengcheng , Huang Chen , Ip Ka U. , Chen Guokai , Deng Chu-Xia , Zhang Xiaohua Douglas. , Zhao Qi
Published: September 2024

Supplementary Figure S2. Validation of subtypes of SARC using Consensus clustering analysis.
Supplementary Figure S1 from Comprehensive analysis of tumor microenvironment reveals prognostic ceRNA network related to immune infiltration in sarcoma
Authors: Leng Dongliang , Yang Ziyi , Sun Heng , Song Chengcheng , Huang Chen , Ip Ka U. , Chen Guokai , Deng Chu-Xia , Zhang Xiaohua Douglas. , Zhao Qi
Published: September 2024

Supplementary Figure S1. Classification and validation of subtypes of SARC.
Supplementary Methods S1 from Axicabtagene Ciloleucel in Combination With the 4-1BB Agonist Utomilumab in Patients With Relapsed/Refractory Large B-Cell Lymphoma: Phase 1 Results From ZUMA-11
Authors: Jain Michael D. , Miklos David B. , Jacobson Caron A. , Timmerman John M. , Sun Jennifer , Nater Jenny , Fang Xiang , Patel Ankit , Davis Madison , Heeke Darren , Trinh Tan , Mattie Mike , Neumann Frank , Kim Jenny J. , To Christina , Filosto Simone , Reshef Ran
Published: September 2024

SUPPLEMENTARY METHODS
Supplementary Figure S7 from Axicabtagene Ciloleucel in Combination With the 4-1BB Agonist Utomilumab in Patients With Relapsed/Refractory Large B-Cell Lymphoma: Phase 1 Results From ZUMA-11
Authors: Jain Michael D. , Miklos David B. , Jacobson Caron A. , Timmerman John M. , Sun Jennifer , Nater Jenny , Fang Xiang , Patel Ankit , Davis Madison , Heeke Darren , Trinh Tan , Mattie Mike , Neumann Frank , Kim Jenny J. , To Christina , Filosto Simone , Reshef Ran
Published: September 2024

Serum IFNγ, IL-10, and IL-2 AUC0–28 (ng/mL)
Tables 2 from Tumor microenvironment modifications induced by afatinib in squamous cell carcinoma of the head and neck - a window-of-opportunity study (EORTC90111-24111)
Authors: Beyaert Simon P. , Loriot Axelle E. , Huyghe Nicolas D. , Goebbels Rose M. , Mendola Antonella , Govaerts Anne-Sophie , Fortpied Catherine , Baldin Pamela , Licitra Lisa F. , Lalami Yassine , Clement Paul M. , Machiels Jean-Pascal H. , Schmitz Sandra
Published: September 2024

Lists of differentially expressed genes in RNA-seq analyses of bulk biopsies
Supplementary Table S12 from Single-cell RNA analysis reveals cell-intrinsic functions of CAR-T cells correlating with response in a phase II study of lymphoma patients
Authors: Sarén Tina , Ramachandran Mohanraj , Gammelgård Gustav , Lövgren Tanja , Mirabello Claudio , Björklund Åsa K. , Wikström Kristina , Hashemi Jamileh , Freyhult Eva , Ahlström Håkan , Amini Rose-Marie , Hagberg Hans , Loskog Angelica , Enblad Gunilla , Essand Magnus
Published: September 2024

List of antibodies and dyes used for functionality flow cytometry assays
Supplementary Figure S5 from Single-cell RNA analysis reveals cell-intrinsic functions of CAR-T cells correlating with response in a phase II study of lymphoma patients
Authors: Sarén Tina , Ramachandran Mohanraj , Gammelgård Gustav , Lövgren Tanja , Mirabello Claudio , Björklund Åsa K. , Wikström Kristina , Hashemi Jamileh , Freyhult Eva , Ahlström Håkan , Amini Rose-Marie , Hagberg Hans , Loskog Angelica , Enblad Gunilla , Essand Magnus
Published: September 2024

Supplementary Figure S5. Clinical response could not be predicted from CAR-T expansion invivo, transduction efficiency or CD8/CD4 ratio of the CAR-T product
Supplementary Methods S1 from Neoantigen targetability in progressive advanced melanoma
Authors: van den Bulk Jitske , Verdegaal Els M.E. , van der Ploeg Manon , Visser Marten , Nunes Joana B. , de Ru Arnoud H. , Tjokrodirijo Rayman T.N. , Ijsselsteijn Marieke E. , Janssen Natasja I. , van der Breggen Ruud , de Bruin Linda , de Kok Pita , Janssen George M.C. , Ruano Dina , Kapiteijn Ellen H.W. , van veelen Peter A. , de Miranda Noel F.C.C. , van der Burg Sjoerd H.
Published: September 2024

More detailed information on: 1) Immune-fluorescent staining, 2) Mass spectrometry, 3) MLTC and TIL cultures.
Supplementary Figure S3 from Neoantigen targetability in progressive advanced melanoma
Authors: van den Bulk Jitske , Verdegaal Els M.E. , van der Ploeg Manon , Visser Marten , Nunes Joana B. , de Ru Arnoud H. , Tjokrodirijo Rayman T.N. , Ijsselsteijn Marieke E. , Janssen Natasja I. , van der Breggen Ruud , de Bruin Linda , de Kok Pita , Janssen George M.C. , Ruano Dina , Kapiteijn Ellen H.W. , van veelen Peter A. , de Miranda Noel F.C.C. , van der Burg Sjoerd H.
Published: September 2024

T cell recognition of melanoma cell lines derived from early and later metastatic lesions.
Supplementary Figure S2 from Neoantigen targetability in progressive advanced melanoma
Authors: van den Bulk Jitske , Verdegaal Els M.E. , van der Ploeg Manon , Visser Marten , Nunes Joana B. , de Ru Arnoud H. , Tjokrodirijo Rayman T.N. , Ijsselsteijn Marieke E. , Janssen Natasja I. , van der Breggen Ruud , de Bruin Linda , de Kok Pita , Janssen George M.C. , Ruano Dina , Kapiteijn Ellen H.W. , van veelen Peter A. , de Miranda Noel F.C.C. , van der Burg Sjoerd H.
Published: September 2024

HLA class I and II expression on melanoma cell lines derived from early and later metastatic
lesions.
Supplemental Figure S1 from Depth of radiographic response (DpR) and time to tumor regrowth (TTG) predicts overall survival following anti-VEGF therapy in recurrent glioblastoma
Authors: Ellingson Benjamin M. , Hagiwara Akifumi , Morris Connor J. , Cho Nicholas S. , Oshima Sonoko , Sanvito Francesco , Oughourlian Talia C. , Telesca Donatello , Raymond Catalina , Abrey Lauren E. , Garcia Josep , Aftab Dana T. , Hessel Colin , Rachmilewitz Minei Tamar , Harats Dror , Nathanson David A. , Wen Patrick Y. , Cloughesy Timothy F.
Published: September 2024

Supplemental Figure S1
Supplementary Tables 1-3 from Efficacy and safety of stereotactic body radiotherapy combined with Camrelizumab and Apatinib in hepatocellular carcinoma patients with portal vein tumor thrombus
Authors: Hu Yue , Zhou Min , Tang Jing , Li Shuang , Liu Hongli , Hu Jianli , Ma Hong , Liu Junli , Qin Tingting , Yu Xiongjie , Chen Yongshun , Peng Jin , Zou Yanmei , Zhang Tao , Xue Jun
Published: September 2024

Supplementary Tables 1-3
Supplementary Data Tables S1-S5 from Diagnostic Performance of a Tumor Marker Gene Test to Personalize Serum CA19-9 Reference Ranges
Authors: Dbouk Mohamad , Abe Toshiya , Koi Chiho , Ando Yohei , Saba Helena , Abou Diwan Elizabeth , Macgregor-Das Anne , Blackford Amanda L. , Mocci Evelina , Beierl Katie , Dbouk Ali , He Jin , Burkhart Richard , Lennon Anne Marie , Sokoll Lori , Canto Marcia Irene. , Eshleman James R. , Goggins Michael
Published: September 2024

Supplementary tables
Supplementary Table S9 from SPOP mutations target STING1 signaling in prostate cancer and create therapeutic vulnerabilities to PARP inhibitor–induced growth suppression
Authors: Geng Chuandong , Zhang Man-Chao , Manyam Ganiraju C. , Vykoukal Jody V. , Fahrmann Johannes F. , Peng Shan , Wu Cheng , Park Sanghee , Kondraganti Shakuntala , Wang Daoqi , Robinson Brian D. , Loda Massimo , Barbieri Christopher E. , Yap Timothy A. , Corn Paul G. , Hanash Samir , Broom Bradley M. , Pilie Patrick G. , Thompson Timothy C.
Published: September 2024

Supplementary Table S9. Quantification of each protein-specific band normalized to vinculin (Dox-inducible C4-2b–derived models, Fig. 4D, upper panel).
Supplementary Table S5 from SPOP mutations target STING1 signaling in prostate cancer and create therapeutic vulnerabilities to PARP inhibitor–induced growth suppression
Authors: Geng Chuandong , Zhang Man-Chao , Manyam Ganiraju C. , Vykoukal Jody V. , Fahrmann Johannes F. , Peng Shan , Wu Cheng , Park Sanghee , Kondraganti Shakuntala , Wang Daoqi , Robinson Brian D. , Loda Massimo , Barbieri Christopher E. , Yap Timothy A. , Corn Paul G. , Hanash Samir , Broom Bradley M. , Pilie Patrick G. , Thompson Timothy C.
Published: September 2024

Supplementary Table S5. Complete listing and details of siRNA targeting sequences used for gene knockdown in Fig. 4A and Extended Data Fig. 3.
Supplementary Figure S17 from SPOP mutations target STING1 signaling in prostate cancer and create therapeutic vulnerabilities to PARP inhibitor–induced growth suppression
Authors: Geng Chuandong , Zhang Man-Chao , Manyam Ganiraju C. , Vykoukal Jody V. , Fahrmann Johannes F. , Peng Shan , Wu Cheng , Park Sanghee , Kondraganti Shakuntala , Wang Daoqi , Robinson Brian D. , Loda Massimo , Barbieri Christopher E. , Yap Timothy A. , Corn Paul G. , Hanash Samir , Broom Bradley M. , Pilie Patrick G. , Thompson Timothy C.
Published: September 2024

Supplementary Fig. S17. Original unedited IB images for representative Western blots experiments (n-2) used in Figure 4E right panels (RM-1-BM-EV/ SPOPmuts).
Supplementary Figure S12 from SPOP mutations target STING1 signaling in prostate cancer and create therapeutic vulnerabilities to PARP inhibitor–induced growth suppression
Authors: Geng Chuandong , Zhang Man-Chao , Manyam Ganiraju C. , Vykoukal Jody V. , Fahrmann Johannes F. , Peng Shan , Wu Cheng , Park Sanghee , Kondraganti Shakuntala , Wang Daoqi , Robinson Brian D. , Loda Massimo , Barbieri Christopher E. , Yap Timothy A. , Corn Paul G. , Hanash Samir , Broom Bradley M. , Pilie Patrick G. , Thompson Timothy C.
Published: September 2024

Supplementary Fig. S12. Suppression of STING1 protein levels following siSTING transfection compared to siNC.
Supplementary Figure S1 from SPOP mutations target STING1 signaling in prostate cancer and create therapeutic vulnerabilities to PARP inhibitor–induced growth suppression
Authors: Geng Chuandong , Zhang Man-Chao , Manyam Ganiraju C. , Vykoukal Jody V. , Fahrmann Johannes F. , Peng Shan , Wu Cheng , Park Sanghee , Kondraganti Shakuntala , Wang Daoqi , Robinson Brian D. , Loda Massimo , Barbieri Christopher E. , Yap Timothy A. , Corn Paul G. , Hanash Samir , Broom Bradley M. , Pilie Patrick G. , Thompson Timothy C.
Published: September 2024

Supplementary Fig. S1. “Immunome” analysis of SPOPmut and SPOPwt from Beltran CRPC cohort using a compendium of publicly available data from purified immune subsets
Data from Impact of Frontline Ivosidenib on Volumetric Growth Patterns in Isocitrate Dehydrogenase–mutant Astrocytic and Oligodendroglial Tumors
Authors: Kamson David Olayinka , Puri Sushant , Sang Yingying , Shi Meihui Jessica , Blair Lindsay , Blakeley Jaishri O. , Laterra John
Published: September 2024

AbstractPurpose:
Isocitrate dehydrogenase (IDH)-mutant gliomas are usually treated with radiotherapy and chemotherapy, which increases the risk for neurocognitive sequelae during patients’ most productive years. We report our experience using off-label first-in-class mutant IDH1 inhibitor ivosidenib and its impact on tumor volume in IDH-mutant gliomas.
Experimental Design:
We retrospectively analyzed patients ages ≥18 years with radiation/chemotherapy-naïve, mutant IDH1, nonenhancing, radiographically active, grade 2/3 gliomas, and ≥2 pretreatment and ≥2 on-treatment ivosidenib MRIs. T2/FLAIR-based tumor volumes, growth rates, and progression-free survival (PFS) were analyzed. log-linear mixed-effect modeling of growth curves adjusted for grade, histology, and age was performed.
Results:
We analyzed 116 MRIs of 12 patients [10 males, median age 46 years (range: 26–60)]: 8 astrocytomas (50% grade 3) and 4 grade 2 oligodendrogliomas. Median on-drug follow-up was 13.2 months [interquartile range (IQR): 9.7–22.2]. Tolerability was 100%. A total of 50% of patients experienced ≥20% tumor volume reduction on-treatment and absolute growth rate was lower during treatment (−1.2 ± 10.6 cc/year) than before treatment (8.0 ± 7.7 cc/year; P ≤ 0.05). log-linear models in the Stable group (n = 9) showed significant growth before treatment (53%/year; P = 0.013), and volume reduction (−34%/year; P = 0.037) after 5 months on treatment. After treatment, volume curves were significantly lower than before treatment (after/before treatment ratio 0.5; P < 0.01). Median time-to-best response was 11.2 (IQR: 1.7–33.4) months, and 16.8 (IQR: 2.6–33.5) months in patients on drug for ≥1 year. PFS at 9 months was 75%.
Conclusions:
Ivosidenib was well tolerated and induced a high volumetric response rate. Responders had significant reduction in tumor growth rates and volume reductions observed after a 5-month delay. Thus, ivosidenib appears useful to control tumor growth and delay more toxic therapies in IDH-mutant nonenhancing indolently growing gliomas.

See related commentary by Lukas and Horbinski, p. 4709
Data from Trackable Intratumor Microdosing and Spatial Profiling Provide Early Insights into Activity of Investigational Agents in the Intact Tumor Microenvironment
Authors: Derry Jonathan M.J. , Burns Connor , Frazier Jason P. , Beirne Emily , Grenley Marc , DuFort Christopher C. , Killingbeck Emily , Leon Michael , Williams Claire , Gregory Mark , Houlton Jeffrey , Clayburgh Daniel , Swiecicki Paul , Huszar Dennis , Berger Allison , Klinghoffer Richard A.
Published: September 2024

Abstract
Purpose: Cancer drug development is currently limited by a paradigm of preclinical evaluation that does not adequately recapitulate the complexity of the intact human tumor microenvironment (TME). To overcome this, we combined trackable intratumor microdosing (CIVOTM) with spatial biology readouts to directly assess drug effects in patient tumors in situ. Patients and Methods: In a first-of-its-kind Phase 0 clinical trial, we explored the effects of an investigational stage SUMOylation Activating Enzyme (SAE) inhibitor, subasumstat (TAK-981) in 12 patients with head and neck carcinoma (HNC). Patients scheduled for tumor resection received percutaneous intratumor injections of subasumstat and vehicle control 1 to 4 days prior to surgery, resulting in spatially localized and graded regions of drug exposure (~1000-2000 microns in diameter). Drug-exposed (n=214) and unexposed regions (n=140) were compared by GeoMx Digital Spatial Profiler, with evaluation at single cell resolution in a subset of these by CosMx Spatial Molecular Imager. Results: Localized regions of subasumstat exposure revealed SUMO pathway inhibition, elevation of Type I interferon (IFN-I) response, and inhibition of cell cycle across all tumor samples. Single cell analysis by CosMx demonstrated cell cycle inhibition specific to the tumor epithelium, and IFN pathway induction commensurate with a TME shift from immune-suppressive to immune-permissive. Conclusions: Pairing CIVO with spatial profiling enabled detailed investigation of response to subasumstat across a diverse sampling of native and intact TMEs. We demonstrate that drug mechanism of action can be directly evaluated in a spatially precise manner in the most translationally relevant setting: an in situ human tumor.
Data from Estrogen therapy induces receptor-dependent DNA damage enhanced by PARP inhibition in ER+ breast cancer
Authors: Traphagen Nicole A. , Schwartz Gary N. , Tau Steven , Roberts Alyssa M. , Jiang Amanda , Hosford Sarah R. , Marotti Jonathan D. , Goen Abigail E. , Romo Bianca A. , Johnson Anneka L. , Duffy Emily-Claire K. , Demidenko Eugene , Heverly Paul , Mosesson Yaron , Soucy Shannon M. , Kolling Fred , Miller Todd W.
Published: September 2024

Abstract
Purpose: Clinical evidence indicates that treatment with estrogens elicits anti-cancer effects in ~30% of patients with advanced endocrine-resistant estrogen receptor alpha (ER)-positive breast cancer. Despite the proven efficacy of estrogen therapy, its mechanism of action is unclear and this treatment remains under-utilized. Mechanistic understanding may offer strategies to enhance therapeutic efficacy. Experimental Design: We performed genome-wide CRISPR/Cas9 screening and transcriptomic profiling in long-term estrogen-deprived (LTED) ER+ breast cancer cells to identify pathways required for therapeutic response to the estrogen 17b-estradiol (E2). We validated findings in cell lines, patient-derived xenografts (PDXs), and patient samples, and developed a novel combination treatment through testing in cell lines and PDX models. Results: Cells treated with E2 exhibited replication-dependent markers of DNA damage and the DNA damage response prior to apoptosis. Such DNA damage was partially driven by the formation of DNA:RNA hybrids (R-loops). Pharmacological suppression of the DNA damage response via poly(ADP-ribose) polymerase (PARP) inhibition with olaparib enhanced E2-induced DNA damage. PARP inhibition synergized with E2 to suppress growth and prevent tumor recurrence in BRCA1/2-mutant and BRCA1/2-wild-type cell line and PDX models. Conclusions: E2-induced ER activity drives DNA damage and growth inhibition in endocrine-resistant breast cancer cells. Inhibition of the DNA damage response using drugs such as PARP inhibitors can enhance therapeutic response to E2. These findings warrant clinical exploration of the combination of E2 with DNA damage response inhibitors in advanced ER+ breast cancer, and suggest that PARP inhibitors may synergize with therapeutics that exacerbate transcriptional stress.
Data from A prognostic model based on residual cancer burden and tumor-infiltrating lymphocytes on residual disease after neoadjuvant therapy in HER2+ breast cancer
Authors: Miglietta Federica , Ragazzi Moira , Fernandes Bethania , Griguolo Gaia , Massa Davide , Girardi Fabio , Bottosso Michele , Bisagni Alessandra , Zarrilli Giovanni , Porra Francesca , Iannaccone Daniela , Dore Leocadia , Gaudio Mariangela , Santandrea Giacomo , Fassan Matteo , Lo Mele Marcello , De Sanctis Rita , Zambelli Alberto , Bisagni Giancarlo , Guarneri Valentina , Dieci Maria Vittoria
Published: September 2024

Abstract
Purpose: We aim to evaluate the prognostic significance of tumor-infiltrating lymphocyte on residual disease (RD-TIL) in HER2+ breast cancer (BC) patients who failed to achieve pathologic-complete response (pCR) after anti-HER2+chemotherapy (CT)-based neoadjuvant treatment (NAT). We assessed the feasibility of combining the prognostic information provided by residual cancer burden (RCB) and RD-TILs into a composite score (RCB+TILs). Experimental Design: HER2+ BC patients treated with CT+anti-HER2-based NAT at three institutions were retrospectively included. RCB and TILs levels were evaluated on hematoxylin and eosin-stained slides from surgical samples according to available recommendations. Overall survival (OS) was used as an outcome measure. Results: 295 patients were included, of whom 195 had RD. RCB was significantly associated with OS. Higher RD-TILs were significantly associated with poorer OS as compared to lower RD-TILs (15% cutoff). In multivariate analysis, both RCB and RD-TIL maintained their independent prognostic value. A combined score, RCB+TIL, was calculated from the estimated coefficient of RD-TILs and the RCB index in a bivariate logistic model for OS. The RCB+TIL score was significantly associated with OS. The C-index for OS of the RCB+TIL score was numerically higher than that of RCB and significantly higher than that of RD-TILs. Conclusions: We have reported an independent prognostic impact of RD-TILs after anti-HER2+CT NAT, which might underlie an imbalance of the RD microenvironment towards immunosuppressive features. We provided a new composite prognostic score based on RCB+TIL, which was significantly associated with OS and proved to be more informative than the isolated evaluation of RCB and RD-TILs.
Data from Cancer-associated fibroblast-like tumor cells remodel the Ewing sarcoma tumor microenvironment
Authors: Wrenn Emma D. , Apfelbaum April A. , Rudzinski Erin R. , Deng Xuemei , Jiang Wei , Sud Sudha , Van Noord Raelene A. , Newman Erika A. , Garcia Nicolas M. , Miyaki Aya , Hoglund Virginia J. , Bhise Shruti S. , Kanaan Sami B. , Waltner Olivia G. , Furlan Scott N. , Lawlor Elizabeth R.
Published: September 2024

Abstract
Purpose: Despite limited genetic and histologic heterogeneity, Ewing sarcoma (EwS) tumor cells are transcriptionally heterogeneous and display varying degrees of mesenchymal lineage specification in vitro. In this study, we investigated if and how transcriptional heterogeneity of EwS cells contributes to heterogeneity of tumor phenotypes in vivo. Experimental Design: Single cell proteogenomic-sequencing of EwS cell lines was performed and integrated with patient tumor transcriptomic data. Cell subpopulations were isolated by FACS for assessment of gene expression and phenotype. Digital spatial profiling and human whole transcriptome analysis interrogated transcriptomic heterogeneity in EwS xenografts. Tumor cell subpopulations and matrix protein deposition were evaluated in xenografts and patient tumors using multiplex immunofluorescence staining. Results: We identified CD73 as a biomarker of highly mesenchymal EwS cell subpopulations in tumor models and patient biopsies. CD73+ tumor cells displayed distinct transcriptional and phenotypic properties, including selective upregulation of genes that are repressed by EWS::FLI1, and increased migratory potential. CD73+ cells were distinguished in vitro and in vivo by increased expression of matrisomal genes and abundant deposition of extracellular matrix (ECM) proteins. In epithelial-derived malignancies, ECM is largely deposited by cancer-associated fibroblasts (CAFs) and we thus labeled CD73+ EwS cells, CAF-like tumor cells. Marked heterogeneity of CD73+ EwS cell frequency and distribution were detected in tumors in situ, and CAF-like tumor cells and associated ECM were observed in peri-necrotic regions and invasive foci. Conclusions: EwS tumor cells can adopt CAF-like properties and these distinct cell subpopulations contribute to tumor heterogeneity by remodeling the tumor microenvironment.
Data from A Phase II Trial of the CD40 Agonist Sotigalimab (APX005M) in Combination with Nivolumab in Subjects with Metastatic Melanoma with Disease Progression on Anti-PD-1
Authors: Weiss Sarah A. , Sznol Mario , Shaheen Montaser , Berciano-Guerrero Miguel-Angel , Muñoz-Couselo Eva , Rodríguez-Abreu Delvys , Boni Valentina , Schuchter Lynn M. , Gonzalez Cao Maria , Arance Fernandez Ana , Wei Wei , Ganti Apar Kishor , Hauke Ralph J. , Berrocal Alfonso , Iannotti Nicholas O. , Hsu Frank J. , Kluger Harriet M.
Published: September 2024

Abstract
Purpose: Disease progression during or after anti-PD-1-based treatment is common in advanced melanoma. Sotigalimab is a CD40 agonist antibody with unique epitope specificity and Fc-receptor binding profile optimized for activation of CD40-expressing antigen presenting cells. Preclinical data indicated that CD40 agonists combined with anti-PD1 could overcome resistance to anti-PD-1. Methods: We conducted a multi-center, open-label, phase II trial to evaluate the combination of sotigalimab 0.3mg/kg and nivolumab 360mg q3wk in patients with advanced melanoma following confirmed disease progression on anti-PD-1. The primary objective was to determine the objective response rate (ORR). Results: Thirty-eight subjects were enrolled and evaluable for safety. Thirty-three were evaluable for activity. Five confirmed partial responses (PR) were observed for an ORR of 15%. Two PRs are ongoing at 45.9+ and 26+ months while the other 3 responders relapsed at 41.1, 18.7, and 18.4 months. Median duration of response was at least 26 months. Two additional patients had stable disease for > 6 months. Thirty-four patients (89%) experienced at least one adverse event (AE) and 13% experienced a grade 3 AE related to sotigalimab. The most common AEs were pyrexia, chills, nausea, fatigue, pruritus, elevated liver function, rash, vomiting, headache, arthralgia, asthenia, myalgia, and diarrhea. There were no treatment-related SAEs, deaths, or discontinuation of sotigalimab due to AEs. Conclusions: Sotigalimab plus nivolumab had a favorable safety profile consistent with the toxicity profiles of each agent. The combination resulted in durable and prolonged responses in a subset of patients with anti-PD-1-resistant melanoma, warranting further evaluation in this setting.
Table S3 from Small molecule mediated stabilization of PP2A modulates the Homologous Recombination pathway and potentiates DNA damage-induced cell death.
Authors: Avelar Rita A. , Armstrong Amy J. , Carvette Gracie , Gupta Riya , Puleo Noah , Colina Jose A. , Joseph Peronne , Sobeck Alexander M. , O'Connor Caitlin M. , Raines Brynne , Gandhi Agharnan , Dziubinski Michele L. , Ma Daniel S. , Resnick Kimberly , Singh Sareena , Zanotti Kristine , Nagel Christa , Waggoner Steven , Thomas Dafydd G. , Skala Stephanie L. , Zhang Junran , Narla Goutham , DiFeo Analisa
Published: September 2024

Table S3
Fig. S7 from Small molecule mediated stabilization of PP2A modulates the Homologous Recombination pathway and potentiates DNA damage-induced cell death.
Authors: Avelar Rita A. , Armstrong Amy J. , Carvette Gracie , Gupta Riya , Puleo Noah , Colina Jose A. , Joseph Peronne , Sobeck Alexander M. , O'Connor Caitlin M. , Raines Brynne , Gandhi Agharnan , Dziubinski Michele L. , Ma Daniel S. , Resnick Kimberly , Singh Sareena , Zanotti Kristine , Nagel Christa , Waggoner Steven , Thomas Dafydd G. , Skala Stephanie L. , Zhang Junran , Narla Goutham , DiFeo Analisa
Published: September 2024

Fig. S7
Fig. S4 from Small molecule mediated stabilization of PP2A modulates the Homologous Recombination pathway and potentiates DNA damage-induced cell death.
Authors: Avelar Rita A. , Armstrong Amy J. , Carvette Gracie , Gupta Riya , Puleo Noah , Colina Jose A. , Joseph Peronne , Sobeck Alexander M. , O'Connor Caitlin M. , Raines Brynne , Gandhi Agharnan , Dziubinski Michele L. , Ma Daniel S. , Resnick Kimberly , Singh Sareena , Zanotti Kristine , Nagel Christa , Waggoner Steven , Thomas Dafydd G. , Skala Stephanie L. , Zhang Junran , Narla Goutham , DiFeo Analisa
Published: September 2024

Fig. S4
Fig. S3 from Small molecule mediated stabilization of PP2A modulates the Homologous Recombination pathway and potentiates DNA damage-induced cell death.
Authors: Avelar Rita A. , Armstrong Amy J. , Carvette Gracie , Gupta Riya , Puleo Noah , Colina Jose A. , Joseph Peronne , Sobeck Alexander M. , O'Connor Caitlin M. , Raines Brynne , Gandhi Agharnan , Dziubinski Michele L. , Ma Daniel S. , Resnick Kimberly , Singh Sareena , Zanotti Kristine , Nagel Christa , Waggoner Steven , Thomas Dafydd G. , Skala Stephanie L. , Zhang Junran , Narla Goutham , DiFeo Analisa
Published: September 2024

Fig. S3
Supplementary Table S3 from Pharmacokinetic/Pharmacodynamic Analysis of Savolitinib Plus Osimertinib in an EGFR-Mutation Positive, MET-Amplified Non-Small Cell Lung Cancer Model
Authors: Jones Rhys D.O. , Petersson Klas , Tabatabai Areya , Bao Larry , Tomkinson Helen , Schuller Alwin G.
Published: September 2024

Supplementary Table S3
Supplementary Figure S2 from Pharmacokinetic/Pharmacodynamic Analysis of Savolitinib Plus Osimertinib in an EGFR-Mutation Positive, MET-Amplified Non-Small Cell Lung Cancer Model
Authors: Jones Rhys D.O. , Petersson Klas , Tabatabai Areya , Bao Larry , Tomkinson Helen , Schuller Alwin G.
Published: September 2024

Supplementary Figure S2
Figure S2 from Loss of LGR5 through therapy-induced downregulation or gene ablation is associated with resistance and enhanced MET-STAT3 signaling in colorectal cancer cells
Authors: Posey Tressie A. , Jacob Joan , Parkhurst Ashlyn , Subramanian Shraddha , Francisco Liezl E. , Liang Zhengdong , Carmon Kendra S.
Published: September 2024

shows inhibitors of IL6/Gp130 and EGFR do not attenuate STAT3 activation in LGR5 KD/KO CRC cells, LGR5 KD in DLD-1 cells increases MET-STAT3 activation, and the effects of MET and STAT3 inhibitors at different time-points
Supplementary Materials and Methods from Arginase 1/2 inhibitor OATD-02: from discovery to first-in-man setup in cancer immunotherapy
Authors: Borek Bartlomiej , Nowicka Julita , Gzik Anna , Dziegielewski Marek , Jedrzejczak Karol , Brzezinska Joanna , Grzybowski Marcin , Stanczak Paulina , Pomper Paulina , Zagozdzon Agnieszka , Rejczak Tomasz , Matyszewski Krzysztof , Golebiowski Adam , Olczak Jacek , Lisiecki Kamil , Tyszkiewicz Magdalena , Kania Magdalena , Piasecka Sylwia , Cabaj Anna , Dera Paulina , Mulewski Krzysztof , Chrzanowski Jacek , Kusmirek Damian , Sobolewska Elzbieta , Magdycz Marta , Mucha Lukasz , Masnyk Marek , Golab Jakub , Nowotny Marcin , Nowak Elzbieta , Napiorkowska-Gromadzka Agnieszka , Pikul Stanislaw , Jazwiec Radoslaw , Dzwonek Karolina , Dobrzanski Pawel , Meyring Michael , Skowronek Krzysztof , Iwanowski Piotr , Zaslona Zbigniew , Blaszczyk Roman
Published: September 2024

Supplementary Materials and Methods not included in the main manuscript
Supplementary Figure 15 from Arginase 1/2 inhibitor OATD-02: from discovery to first-in-man setup in cancer immunotherapy
Authors: Borek Bartlomiej , Nowicka Julita , Gzik Anna , Dziegielewski Marek , Jedrzejczak Karol , Brzezinska Joanna , Grzybowski Marcin , Stanczak Paulina , Pomper Paulina , Zagozdzon Agnieszka , Rejczak Tomasz , Matyszewski Krzysztof , Golebiowski Adam , Olczak Jacek , Lisiecki Kamil , Tyszkiewicz Magdalena , Kania Magdalena , Piasecka Sylwia , Cabaj Anna , Dera Paulina , Mulewski Krzysztof , Chrzanowski Jacek , Kusmirek Damian , Sobolewska Elzbieta , Magdycz Marta , Mucha Lukasz , Masnyk Marek , Golab Jakub , Nowotny Marcin , Nowak Elzbieta , Napiorkowska-Gromadzka Agnieszka , Pikul Stanislaw , Jazwiec Radoslaw , Dzwonek Karolina , Dobrzanski Pawel , Meyring Michael , Skowronek Krzysztof , Iwanowski Piotr , Zaslona Zbigniew , Blaszczyk Roman
Published: September 2024

Crystal structure of OATD-02 bound to hARG1
Table S2 from Antitumor Immune Mechanisms of the Anti-Complement Factor H Antibody GT103
Authors: Bushey Ryan T. , Saxena Ruchi , Campa Michael J. , Gottlin Elizabeth B. , He You-Wen , Patz Edward F.
Published: September 2024

Genes regulated by GT103 in CR2+ intratumoral B cells
Supplementary Figure 4 from BET inhibition sensitizes immunologically-cold Rb-deficient prostate cancer to immune checkpoint blockade
Authors: Olson Brian M. , Chaudagar Kiranj , Bao Riyue , Saha Sweta Sharma. , Hong Christina , Li Marguerite , Rameshbabu Srikrishnan , Chen Raymond , Thomas Alison , Patnaik Akash
Published: September 2024

Loss of Rb results in altered gene expression that promotes immune suppression as well as increased Tmem173/STING expression.
Supplementary Figure 3 from BET inhibition sensitizes immunologically-cold Rb-deficient prostate cancer to immune checkpoint blockade
Authors: Olson Brian M. , Chaudagar Kiranj , Bao Riyue , Saha Sweta Sharma. , Hong Christina , Li Marguerite , Rameshbabu Srikrishnan , Chen Raymond , Thomas Alison , Patnaik Akash
Published: September 2024

Generation and characterization of growth kinetics of Rb-deficient Myc-CaP cell line.
Supplementary Table S8 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 and kinetics based on Bio Layer Interferometry
Supplementary Figure 10 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

HER3 expression in a panel of CDX/PDX models by immunohistochemistry.
Supplementary Figure Legends from Targeting up-regulated cIAP2 in SOX10-deficient drug tolerant melanoma
Authors: Glasheen McKenna Q. , Caksa Signe , Young Amelia G. , Wilski Nicole A. , Ott Connor A. , Chervoneva Inna , Flaherty Keith T. , Herlyn Meenhard , Xu Xiaowei , Aplin Andrew E. , Capparelli Claudia
Published: September 2024

Supplementary Figure Legends and References
Supplementary Figure S6 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 S6 shows IHC staining for 4-HNE in SUM159PT tumors, demonstrating that co-targeting CAIX/XII activity and GSH synthesis increases lipid peroxidation in vivo.
Supplementary Figure S5 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 S5 shows heatmaps demonstrating that combined inhibition of CAIX activity and GCLC or RSL3 synergize to increase cytotoxicity of hypoxic cancer cells.
Supplementary material and method from S-531011, a novel anti-human CCR8 antibody, induces potent anti-tumor responses through depletion of tumor-infiltrating CCR8-expressing regulatory T cells
Authors: Nagira Yoji , Nagira Morio , Nagai Ryohei , Nogami Wataru , Hirata Michinari , Ueyama Azumi , Yoshida Tetsuya , Yoshikawa Mai , Shinonome Satomi , Yoshida Hiroshi , Haruna Miya , Miwa Hiroto , Chatani Natsumi , Ohkura Naganari , Wada Hisashi , Tanaka Hidekazu
Published: September 2024

Supplementary Information
Figure S4 from S-531011, a novel anti-human CCR8 antibody, induces potent anti-tumor responses through depletion of tumor-infiltrating CCR8-expressing regulatory T cells
Authors: Nagira Yoji , Nagira Morio , Nagai Ryohei , Nogami Wataru , Hirata Michinari , Ueyama Azumi , Yoshida Tetsuya , Yoshikawa Mai , Shinonome Satomi , Yoshida Hiroshi , Haruna Miya , Miwa Hiroto , Chatani Natsumi , Ohkura Naganari , Wada Hisashi , Tanaka Hidekazu
Published: September 2024

Binding profile of the newly created CCR8 antibody
Figure S2 from S-531011, a novel anti-human CCR8 antibody, induces potent anti-tumor responses through depletion of tumor-infiltrating CCR8-expressing regulatory T cells
Authors: Nagira Yoji , Nagira Morio , Nagai Ryohei , Nogami Wataru , Hirata Michinari , Ueyama Azumi , Yoshida Tetsuya , Yoshikawa Mai , Shinonome Satomi , Yoshida Hiroshi , Haruna Miya , Miwa Hiroto , Chatani Natsumi , Ohkura Naganari , Wada Hisashi , Tanaka Hidekazu
Published: September 2024

Generation of humanized CCR8 KI mice
Supplementary Table S3 from Safety and Tolerability of a Novel Anti-HER2 Antibody-Drug Conjugate (PF-06804103) in Patients With HER2-Expressing Solid Tumors: A Phase 1 Dose Escalation Study
Authors: Meric-Bernstam Funda , Calvo Emiliano , Lee Keun Seok , Moreno Victor , Park Yeon Hee , Rha Sun Young , Chalasani Pavani , Zhong Wei , Zhou Li , Pirie-Shepherd Steven , Leung Abraham CF. , Curigliano Giuseppe
Published: September 2024

Supplementary Table S3 shows the biomarker results
Table S1 from Pan-cancer pharmacogenomic analysis of patient-derived tumor cells utilizing clinically relevant drug exposures
Authors: Chang Stephen H. , Ice Ryan J. , Chen Michelle , Sidorov Maxim , Woo Rinette W.L. , Rodriguez-Brotons Aida , Jian Damon , Kim Han Kyul , Kim Angela , Stone David E. , Nazarian Ari , Oh Alyssia , Tranah Gregory J. , Nosrati Mehdi , de Semir David , Dar Altaf A. , Desprez Pierre-Yves , Kashani-Sabet Mohammed , Soroceanu Liliana , McAllister Sean D.
Published: September 2024

Supplementary Table 1 drug concentrations
Figure S8 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. S8. Multiplex immunohistochemistry (IHC) of hIL-15-MC38 or parental MC38 tumors four days after CD44-targeted NIR-PIT.
Figure S7 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. S7. Host tumor immunity two days after CD44-targeted NIR-PIT against hIL-15-MC38 or MC38 tumors.
Figure S1 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

Pharmacokinetic model and data
Supplementary figures and tables legends from Conditional dependency of LP-184 on prostaglandin reductase 1 is synthetic lethal in pancreatic cancers with DNA damage repair deficiencies
Authors: Restifo Diana , McDermott Joseph R. , Cvetkovic Dusica , Dos Santos Troy , Ogier Charline , Surumbayeva Aizhan , Handorf Elizabeth A. , Schimke Caleb , Ma Charlie , Cai Kathy Q. , Olszanski Anthony J. , Kathad Umesh , Bhatia Kishor , Sharma Panna , Kulkarni Aditya , Astsaturov Igor
Published: September 2024

Supplementary figure legends and Tables
Supplementary Figure S2 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 2 shows the surface marker of CD11b in dHL60 cells and analysis of NET formation in the co-culture system of dHL60 or PMNs from HD with MSI-H or MSS CRC cells.
Figure S2 from Activation of Hepatocyte Growth Factor/MET Signaling as a Mechanism of Acquired Resistance to a Novel YAP1/TEAD Small Molecule Inhibitor
Authors: Moure Casey J. , Vara Brandon , Cheng Mangeng M. , Sondey Christopher , Muise Eric , Park Eunsil , Vela Ramirez Julia Eulalia , Su Dan , D’Souza Shanti , Yan Qingyun , Yeung Charles S. , Zhang Minjia , Mansueto My Sam , Linn Doug , Buchanan Mark , Foti Robert , DiMauro Erin , Long Brian , Simov Vladimir , Barry Evan R.
Published: September 2024

In vitro RNA-Seq characterization of MRK-A.
Figure S1 from Activation of Hepatocyte Growth Factor/MET Signaling as a Mechanism of Acquired Resistance to a Novel YAP1/TEAD Small Molecule Inhibitor
Authors: Moure Casey J. , Vara Brandon , Cheng Mangeng M. , Sondey Christopher , Muise Eric , Park Eunsil , Vela Ramirez Julia Eulalia , Su Dan , D’Souza Shanti , Yan Qingyun , Yeung Charles S. , Zhang Minjia , Mansueto My Sam , Linn Doug , Buchanan Mark , Foti Robert , DiMauro Erin , Long Brian , Simov Vladimir , Barry Evan R.
Published: September 2024

In vitro characterization of MRK-A.
Supplementary Table 1 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

Table S1. Primers for qPCR
Figure S6 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 S6
Supplementary Table 1 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

Sequence of small interfering RNA
Supplementary Figure S8 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 S8
Figure S2 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

Known NBL prognostic factors consistently associate with outcome across different NBL studies but not NE scores.
Supplementary Data Legends 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

Supplementary Figures 1 -7 and Supplementary Tables 1 - 3 legends
Fig. S3 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 S3 shows flow cytometry data for CD45, gating strategy and transcript levels of CD68 and TLR4
Table S2 from Fibronectin contributes to a BRAF inhibitor-driven invasive phenotype in thyroid cancer through EGR1, which can be blocked by inhibition of ERK1/2.
Authors: Hicks Hannah M. , Pozdeyev Nikita , Sams Sharon B. , Pugazhenthi Umarani , Bales Elise S. , Hofmann Marie-Claude , McKenna Logan R. , Schweppe Rebecca E.
Published: September 2024

Table S2. NormLinear: provides normalized RPPA data in linear values.
Figure S8 from Fibronectin contributes to a BRAF inhibitor-driven invasive phenotype in thyroid cancer through EGR1, which can be blocked by inhibition of ERK1/2.
Authors: Hicks Hannah M. , Pozdeyev Nikita , Sams Sharon B. , Pugazhenthi Umarani , Bales Elise S. , Hofmann Marie-Claude , McKenna Logan R. , Schweppe Rebecca E.
Published: September 2024

Figure S8. The effects of EGR1 depletion on signaling responses to BRAF inhibition and invasion.
Figure S6 from Fibronectin contributes to a BRAF inhibitor-driven invasive phenotype in thyroid cancer through EGR1, which can be blocked by inhibition of ERK1/2.
Authors: Hicks Hannah M. , Pozdeyev Nikita , Sams Sharon B. , Pugazhenthi Umarani , Bales Elise S. , Hofmann Marie-Claude , McKenna Logan R. , Schweppe Rebecca E.
Published: September 2024

Figure S6. The ERK1/2 inhibitors SCH772984 and Ulixertinib have similar effects on cell viability in vitro.
Figure S4 from Fibronectin contributes to a BRAF inhibitor-driven invasive phenotype in thyroid cancer through EGR1, which can be blocked by inhibition of ERK1/2.
Authors: Hicks Hannah M. , Pozdeyev Nikita , Sams Sharon B. , Pugazhenthi Umarani , Bales Elise S. , Hofmann Marie-Claude , McKenna Logan R. , Schweppe Rebecca E.
Published: September 2024

Figure S4. The effects of fibronectin depletion on growth and signaling responses to BRAF inhibition.
Supplementary Figure 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

Cell cycle stage assignment of the SCLC cells from the autochthonous model.
Supplementary Figure S10 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

Graphic displaying the sample makeup of the three NCI-H209 sample arms.
Supplementary Figure 8 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

Clinical clustering of breast cancer subtypes using c-Jun-regulated gene signatures.