bluuebunny/crossref_metadata_2025 huggingface dataset:
Data 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

Abstract
Prostate cancer (PCa) progression to the lethal metastatic castration-resistant phenotype (mCRPC) is driven by αv integrins and is associated with Golgi disorganization and activation of the ATF6 branch of unfolded protein response (UPR). Overexpression of integrins requires N-acetylglucosaminyltransferase-V (MGAT5)-mediated glycosylation and subsequent cluster formation with Galectin-3 (Gal-3). However, the mechanism underlying this altered glycosylation is missing. For the first time, using HALO analysis of immunohistochemistry, we found a strong association of Integrin αv and Gal-3 at the plasma membrane (PM) in primary PCa and mCRPC samples. We discovered that MGAT5 activation is caused by Golgi fragmentation and mislocalization of its competitor, N-acetylglucosaminyltransferase-III, MGAT3, from Golgi to the endoplasmic reticulum (ER). This was validated in an ethanol-induced model of ER stress, where alcohol treatment in androgen-refractory PC-3 and DU145 cells or alcohol consumption in PCa patient samples aggravates Golgi scattering, activates MGAT5, and enhances integrin expression at PM. This explains known link between alcohol consumption and PCa mortality. ATF6 depletion significantly blocks UPR and reduces the number of Golgi fragments in both PC-3 and DU145 cells. Inhibition of autophagy by hydroxychloroquine (HCQ) restores compact Golgi, rescues MGAT3 intra-Golgi localization, blocks glycan modification via MGAT5, and abrogates delivery of Gal-3 to the cell surface. Importantly, the loss of Gal-3 leads to reduced integrins at PM and their accelerated internalization. ATF6 depletion and HCQ treatment synergistically decrease Integrin αv and Gal-3 expression and temper orthotopic tumor growth and metastasis.

Implications: Combined ablation of ATF6 and autophagy can serve as new mCRPC therapeutic.
Data from Continuous administration of anti-VEGFA antibody upregulates PAI-1 secretion from ovarian cancer cells via miR-143-3p downregulation
Authors: Yagi Taro , Sawada Kenjiro , Miyamoto Mayuko , Shimizu Aasa , Oui Yukako , Toda Aska , Nakamura Koji , Kinose Yasuto , Kodama Michiko , Hashimoto Kae , Kimura Tadashi
Published: September 2024

Abstract
Although bevacizumab (BEV) plays a key role in ovarian cancer (OC) treatment, BEV resistance is often observed in clinical settings. This study aimed to identify the genes responsible for BEV resistance. C57BL/6 mice inoculated with ID-8 murine OC cells were treated with anti-VEGFA antibody or IgG (control) twice weekly for four weeks. The mice were sacrificed, then, RNA was extracted from the disseminated tumors. qRT-PCR assays were performed to identify angiogenesis-related genes and miRNAs that were altered by anti-VEGFA treatment. SERPINE1/PAI-1 was found to be upregulated during BEV treatment. Therefore, we focused on miRNAs to elucidate the mechanism underlying the upregulation of PAI-1 during BEV treatment. Kaplan–Meier plotter analysis revealed that higher expression levels of SERPINE1/PAI-1 were associated with poor prognoses among BEV-treated patients, suggesting that SERPINE1/PAI may be involved in the acquisition of BEV resistance. miRNA microarray analysis followed by in silico and functional assays revealed that miR-143-3p targeted SERPINE1 and negatively regulated PAI-1 expression. The transfection of miR-143-3p suppressed PAI-1 secretion from OC cells and inhibited in vitro angiogenesis in HUVECs. Next, miR-143-3p-overexpressing ES2 cells were intraperitoneally injected into BALB/c nude mice. ES2-miR-143-3p cells downregulated PAI-1 production, attenuated angiogenesis, and significantly inhibited intraperitoneal tumor growth following treatment with anti-VEGFA antibody. Continuous anti-VEGFA treatment downregulated miR-143-3p expression, which upregulated PAI-1 and activated an alternative angiogenic pathway in OC. In conclusion, the substitution of this miRNA during BEV treatment may help overcome BEV resistance, and this may be used as a novel treatment strategy in clinical settings. Implications: Continuous administration of VEGFA antibody upregulates SERPINE1/PAI1 expression via the downregulation of miR-143-3p, which contributes to acquiring bevacizumab resistance in ovarian cancer.
Data from Oncostatin-M and OSM-Receptor feed-forward activation of MAPK induces separable stem-like and mesenchymal programs
Authors: Polak Kelsey L. , Tamagno Ilaria , Parameswaran Neetha , Smigiel Jacob , Chan E. Ricky , Yuan Xueer , Rios Brenda , Jackson Mark W.
Published: September 2024

Abstract
Patients diagnosed with Pancreatic Ductal Adenocarcinoma (PDAC) frequently present with advanced metastatic disease and exhibit a poor response to therapy, resulting in poor outcomes. The tumor microenvironment cytokine Oncostatin-M (OSM) initiates PDAC plasticity, inducing the reprogramming to a stem-like/mesenchymal state, which enhances metastasis and therapy resistance. Using a panel of PDAC cells driven through epithelial-mesenchymal transition (EMT) by OSM or the transcription factors ZEB1 or SNAI1, we find that OSM uniquely induces tumor-initiation and gemcitabine resistance independently of its ability to induce a CD44HI/mesenchymal phenotype. In contrast, while ZEB1 and SNAI1 induce a CD44HI/mesenchymal phenotype and migration comparable to OSM, they are unable to promote tumor-initiation or robust gemcitabine resistance. Transcriptomic analysis identified that OSM-mediated stemness requires MAPK activation and sustained, feed-forward transcription of OSMR. MEK and ERK inhibitors prevented OSM-driven transcription of select target genes and stem-like/mesenchymal reprogramming, resulting in reduced tumor growth and re-sensitization to gemcitabine. We propose that the unique properties of OSMR, which hyperactivates MAPK signaling when compared to other IL-6 family receptors, make it an attractive therapeutic target, and that disrupting the OSM-OSMR-MAPK feed-forward loop may be a novel way to therapeutically target the stem-like behaviors common to aggressive PDAC.

Implications: Small molecule MAPK inhibitors may effectively target the OSM/OSMR-axis that leads to EMT and tumor initiating properties that promote aggressive PDAC.
Data from TRIM50 inhibits gastric cancer progression by regulating the ubiquitination and nuclear translocation of JUP
Authors: Hu Jiajia , Huang Runjie , Liang Chengcai , Wang Yingnan , Wang Min , Chen Yanxing , Wu Chenyi , Zhang Jinling , Liu Zekun , Zhao Qi , Liu Zexian , Wang Feng , Yuan Shuqiang
Published: September 2024

Abstract
Gastric cancer (GC) is one of the most frequent cancers in the world. Emerging clinical data show that ubiquitination system disruptions are likely involved in carcinoma genesis and progression. However, the precise role of ubiquitin (Ub)-mediated control of oncogene products or tumor suppressors in GC is unknown. Tripartite motif-containing 50 (TRIM50), an E3 ligase, was discovered by high-output screening of ubiquitination-related genes in tissues from GC patients to be among the ubiquitination-related enzymes whose expression was most downregulated in GC. With two different databases, we verified that TRIM50 expression was lower in tumor tissues relative to normal tissues. TRIM50 also suppressed GC cell growth and migration in vitro and in vivo. JUP, a transcription factor, was identified as a new TRIM50 ubiquitination target by mass spectrometry and coimmunoprecipitation experiments. TRIM50 increases JUP K63-linked polyubiquitination mostly at the K57 site. We discovered that the K57 site is critical for JUP nuclear translocation by prediction with the iNuLoC website and further studies. Furthermore, ubiquitination of the K57 site limits JUP nuclear translocation, consequently inhibiting the MYC signaling pathway. These findings identify TRIM50 as a novel coordinator in GC cells, providing a potential target for the development of new GC treatment strategies.
Implications: TRIM50 regulates GC tumor progression, and this study suggests TRIM50 as a new cancer target.
Data 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

Abstract
PIK3CA is the second most mutated gene in cancer leading to aberrant PI3K/AKT/mTOR signaling and increased translation, proliferation, and survival. Some 4-25% of gastric cancers display activating PIK3CA mutations including 80% of EBV-associated GCs. Small molecules including pan-PI3K and dual PI3K/mTOR inhibitors have shown moderate success clinically, due to broad on-target/off-tissue effects. Thus, isoform specific and mutant selective inhibitors have been of significant interest. However, drug resistance is a problem and has affected success of new drugs. There has been a concerted effort to define mechanisms of resistance and identify potent combinations in many tumor types, though gastric cancer is comparatively understudied. In this study we identified modulators of the response to the PI3K-alpha-specific inhibitor, BYL719, in PIK3CA mutant GCs. We found that loss of NEDD9 or inhibition of BCL-XL conferred hyper-sensitivity to BYL719, through increased cell cycle arrest and cell death, respectively. Additionally, we discovered that loss of CBFB conferred resistance to BYL719. CBFB loss led to up-regulation of the protein kinase PIM1, which can phosphorylate and activate several overlapping downstream substrates as AKT thereby maintaining pathway activity in the presence of PI3K-alpha inhibition. The addition of a pan-PIM inhibitor re-sensitized resistant cells to BYL719. Our data provide clear mechanistic insights into PI3K-alpha inhibitor response in PIK3CA mutant gastric tumors and can inform future work as mutant selective inhibitors are in development for diverse tumor types.

Implications: Loss of either NEDD9 or BCL-XL confers hyper-sensitivity to PI3K-alpha inhibition while loss of CBFB confers resistance through a CBFB/PIM1 signaling axis.
Supplementary Fig. S1 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 Fig. S1: Nelipepimut-S (NPS)-specific cytotoxic T lymphocyte (CTL) responses in patients receiving NeuVax with corresponding HER2 changes
Supplemental Table S2 from Cost-Effectiveness of p16/Ki-67 Dual-Stained Cytology Reflex Following Co-Testing with hrHPV Genotyping for Cervical Cancer Screening
Authors: Harper Diane M. , Anderson Rye J. , Baker Ed , Yu Tiffany M.
Published: September 2024

Supplemental Table S2 shows the distribution of patient attributes in the prevalent US population of women eligible for cervical cancer screening
Supplemental Figure S2 from Cost-Effectiveness of p16/Ki-67 Dual-Stained Cytology Reflex Following Co-Testing with hrHPV Genotyping for Cervical Cancer Screening
Authors: Harper Diane M. , Anderson Rye J. , Baker Ed , Yu Tiffany M.
Published: September 2024

Supplemental Figure S2 shows the proportion of the PSA simulations that were cost-effective at varying willingness-to-pay thresholds
Supplemental Figure S1 from Cost-Effectiveness of p16/Ki-67 Dual-Stained Cytology Reflex Following Co-Testing with hrHPV Genotyping for Cervical Cancer Screening
Authors: Harper Diane M. , Anderson Rye J. , Baker Ed , Yu Tiffany M.
Published: September 2024

Supplemental Figure S1 shows tornado diagrams of range of results observed in the one-way sensitivity analyses
Supplementary Table 9 from Associations between physical activity and incidence of cancer among overweight adults in Korea: Results from the Health Examinees-G study
Authors: Choi Jaesung , Park JooYong , Kim Ji-Eun , Lee Miyoung , Kang Daehee , Shin Aesun , Choi Ji-Yeob
Published: September 2024

Supplementary Table 9 shows the association of physical activity with gastric cancer incidence
Supplementary Table 2 from Associations between physical activity and incidence of cancer among overweight adults in Korea: Results from the Health Examinees-G study
Authors: Choi Jaesung , Park JooYong , Kim Ji-Eun , Lee Miyoung , Kang Daehee , Shin Aesun , Choi Ji-Yeob
Published: September 2024

Supplementary Table 2 shows the association of physical activity with overall cancer incidence after excluding those diagnosed with cancer within the first 2 years of follow-up
Supplementary Table S1 from EXAMINING THE BARRIERS AND OPPORTUNITIES FOR HUMAN PAPILLOMAVIRUS VACCINE DELIVERY IN CANCER CARE SETTINGS: A MIXED-METHODS STUDY
Authors: Garcia Melany A. , Schlecht Nicolas F. , Rokitka Denise A. , Attwood Kristopher M. , Rodriguez Elisa M.
Published: September 2024

Supplementary Table S1 presents the findings from our survey questionnaire pertaining to HPV infection and vaccine knowledge among PAYA cancer care providers.
Supplementary Table S3 from Progressive spreading of DNA methylation in the GSTP1 promoter CpG island across transitions from precursors to invasive prostate cancer
Authors: Gupta Harshath , Inoue Hitoshi , Nakai Yasutomo , Nakayama Masashi , Jones Tracy , Hicks Jessica L. , Kumar Balasubramanian , Gurel Meltem , Nelson William G. , De Marzo Angelo M. , Yegnasubramanian Srinivasan
Published: September 2024

Supplementary Table S3 shows the phased methylation of the GSTP1 promoter region across 908 alleles, or clones, classified by density of methylation.
Supplementary Table S2 from Progressive spreading of DNA methylation in the GSTP1 promoter CpG island across transitions from precursors to invasive prostate cancer
Authors: Gupta Harshath , Inoue Hitoshi , Nakai Yasutomo , Nakayama Masashi , Jones Tracy , Hicks Jessica L. , Kumar Balasubramanian , Gurel Meltem , Nelson William G. , De Marzo Angelo M. , Yegnasubramanian Srinivasan
Published: September 2024

Supplementary Table S2 shows the phased methylation of the GSTP1 promoter region across 102 lesions classified by density of methylation.
Supplementary Figure S1 from Progressive spreading of DNA methylation in the GSTP1 promoter CpG island across transitions from precursors to invasive prostate cancer
Authors: Gupta Harshath , Inoue Hitoshi , Nakai Yasutomo , Nakayama Masashi , Jones Tracy , Hicks Jessica L. , Kumar Balasubramanian , Gurel Meltem , Nelson William G. , De Marzo Angelo M. , Yegnasubramanian Srinivasan
Published: September 2024

Supplementary Figure S1 shows the phased methylation by allele of the GSTP1 promoter region classified by density of methylation.
Supplementary Figure S7 from Association and prediction utilizing craniocaudal and mediolateral oblique view digital mammography and long-term breast cancer risk
Authors: Chen Simin , Tamimi Rulla M. , Colditz Graham A. , Jiang Shu
Published: September 2024

Supplementary Figure S7: The proportional hazards assumption is deemed reasonable by checking the Schoenfeld residuals plot for Full-VPD.
Supplementary Figure S4 from Association and prediction utilizing craniocaudal and mediolateral oblique view digital mammography and long-term breast cancer risk
Authors: Chen Simin , Tamimi Rulla M. , Colditz Graham A. , Jiang Shu
Published: September 2024

Supplementary Figure S4: The linearity assumption is checked with Martingale residual plots.
Supplementary Figure S3 from Association and prediction utilizing craniocaudal and mediolateral oblique view digital mammography and long-term breast cancer risk
Authors: Chen Simin , Tamimi Rulla M. , Colditz Graham A. , Jiang Shu
Published: September 2024

Supplementary Figure S3: Pearson correlation separated by view and case control status.
Supplementary Table 1 from Rates of intervention and cancer detection on initial versus subsequent whole body MRI screening in Li-Fraumeni Syndrome
Authors: Kagami Laura AT. , Du Yun K. , Fernandes Conrad J. , Le Anh N. , Good Madeline , Duvall Melani M. , Baldino Sarah E. , Powers Jacquelyn , Zelley Kristin , States Lisa J. , Mathew Manoj C. , Katona Bryson W. , MacFarland Suzanne P. , Maxwell Kara N.
Published: September 2024

Supplementary Table 1 shows non-malignant findings identified on WBMRI screening in our patient cohort with corresponding patient IDs to cancer diagnoses identified on WBMRI screening.
Table S4 from Analysis of several common APOBEC-type mutations in bladder tumors suggests links to viral infection
Authors: Rao Nina , Starrett Gabriel J. , Piaskowski Mary L. , Butler Kelly E. , Golubeva Yelena , Yan Wusheng , Lawrence Scott M. , Dean Michael , Garcia-Closas Montserrat , Baris Dalsu , Johnson Alison , Schwenn Molly , Malats Nuria , Real Francisco X. , Kogevinas Manolis , Rothman Nathaniel , Silverman Debra T. , Dyrskjøt Lars , Buck Christopher B. , Koutros Stella , Prokunina-Olsson Ludmila
Published: September 2024

Table S4: Top recurrent mutations in FGFR3 and PIK3CA within NMIBC (1,573 patients) and MIBC (1,243 patients)
Supplemental Table 1 from Reprogramming Cancer into Antigen Presenting Cells as a Novel Immunotherapy
Authors: Linde Miles H. , Fan Amy C. , Kohnke Thomas , Trotman-Grant Aaron C. , Gurev Sarah F. , Phan Paul , Zhao Feifei , Haddock Naomi L. , Nuno Kevin A. , Gars Eric J. , Stafford Melissa , Marshall Payton L. , Dove Christopher G. , Linde Ian L. , Landberg Niklas , Miller Lindsay P. , Majzner Robbie G. , Zhang Tian Yi. , Majeti Ravindra
Published: September 2024

Summary of clinical features of primary B-ALL specimens
Supplemental Figure S7 from Reprogramming Cancer into Antigen Presenting Cells as a Novel Immunotherapy
Authors: Linde Miles H. , Fan Amy C. , Kohnke Thomas , Trotman-Grant Aaron C. , Gurev Sarah F. , Phan Paul , Zhao Feifei , Haddock Naomi L. , Nuno Kevin A. , Gars Eric J. , Stafford Melissa , Marshall Payton L. , Dove Christopher G. , Linde Ian L. , Landberg Niklas , Miller Lindsay P. , Majzner Robbie G. , Zhang Tian Yi. , Majeti Ravindra
Published: September 2024

Benchmarking antigen presentation by TR-APCs
Supplemental Figure S6 from Reprogramming Cancer into Antigen Presenting Cells as a Novel Immunotherapy
Authors: Linde Miles H. , Fan Amy C. , Kohnke Thomas , Trotman-Grant Aaron C. , Gurev Sarah F. , Phan Paul , Zhao Feifei , Haddock Naomi L. , Nuno Kevin A. , Gars Eric J. , Stafford Melissa , Marshall Payton L. , Dove Christopher G. , Linde Ian L. , Landberg Niklas , Miller Lindsay P. , Majzner Robbie G. , Zhang Tian Yi. , Majeti Ravindra
Published: September 2024

TR-APC induction results in inflammatory rewiring of the tumor
microenvironment.
Supplemental Figure S4 from Reprogramming Cancer into Antigen Presenting Cells as a Novel Immunotherapy
Authors: Linde Miles H. , Fan Amy C. , Kohnke Thomas , Trotman-Grant Aaron C. , Gurev Sarah F. , Phan Paul , Zhao Feifei , Haddock Naomi L. , Nuno Kevin A. , Gars Eric J. , Stafford Melissa , Marshall Payton L. , Dove Christopher G. , Linde Ian L. , Landberg Niklas , Miller Lindsay P. , Majzner Robbie G. , Zhang Tian Yi. , Majeti Ravindra
Published: September 2024

In vitro re-exposure of T cells from surviving mice demonstrates TR-APC-mediated generation of tumor-specific memory.
Supplemental Figure S10 from Reprogramming Cancer into Antigen Presenting Cells as a Novel Immunotherapy
Authors: Linde Miles H. , Fan Amy C. , Kohnke Thomas , Trotman-Grant Aaron C. , Gurev Sarah F. , Phan Paul , Zhao Feifei , Haddock Naomi L. , Nuno Kevin A. , Gars Eric J. , Stafford Melissa , Marshall Payton L. , Dove Christopher G. , Linde Ian L. , Landberg Niklas , Miller Lindsay P. , Majzner Robbie G. , Zhang Tian Yi. , Majeti Ravindra
Published: September 2024

Primary B-ALL-derived TR-APCs activate T cells in an MHC-restricted manner according to the inflammatory milieu
Supplemental Figure S1 from Reprogramming Cancer into Antigen Presenting Cells as a Novel Immunotherapy
Authors: Linde Miles H. , Fan Amy C. , Kohnke Thomas , Trotman-Grant Aaron C. , Gurev Sarah F. , Phan Paul , Zhao Feifei , Haddock Naomi L. , Nuno Kevin A. , Gars Eric J. , Stafford Melissa , Marshall Payton L. , Dove Christopher G. , Linde Ian L. , Landberg Niklas , Miller Lindsay P. , Majzner Robbie G. , Zhang Tian Yi. , Majeti Ravindra
Published: September 2024

In vivo doxycycline administration results in significant TR-APC
induction throughout tumors
Supplementary Table S1 from p38MAPKa stromal reprogramming sensitizes metastatic breast cancer to immunotherapy
Authors: Faget Douglas V. , Luo Xianmin , Inkman Matthew J. , Ren Qihao , Su Xinming , Ding Kai , Waters Michael R. , Raut Ganesh Kumar , Pandey Gaurav , Dodhiawala Paarth B. , Ramalho-Oliveira Renata , Ye Jiayu , Cole Thomas , Murali Bhavna , Zheleznyak Alexander , Shokeen Monica , Weiss Kurt R. , Monahan Joseph B. , DeSelm Carl J. , Lee Adrian V. , Oesterreich Steffi , Weilbaecher Katherine N. , Zhang Jin , DeNardo David G. , Stewart Sheila A.
Published: September 2024

Table containing all of our reagents
Table S6 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

Treatment modalities and reported adverse events by quartile of period of inclusion.
Table 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

Definitions used for adjudication and grading of the different evaluated events
Table S2 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

Diagnostic work-up for suspected ICI-myocarditis and evaluation of severity criteria
Table S1 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

Diagnostic certainty criteria for ICI-myocarditis
Figure S11 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

Analysis of survival outcomes and EGR2 gene expression in CD19 CAR T-cell products. The figure presents the P values and hazard ratio of different EGR2 molecular marker stratification points in relation to A, overall survival and B, event-free survival The black arrows indicate the stratification points used in the study. C, EGR2-targeted gene expression scores in CD19 CAR T-cell products from responders and non-responders in pediatric ALL. D, Summary of how EGR2 regulates resistance to CAR T-cell therapy through the type I IFN pathway.
Supplementary Figure S2 from Early infiltration of innate immune cells to the liver depletes HNF4a and promotes extra-hepatic carcinogenesis
Authors: Goldman Omer , Adler Lital N. , Hajaj Emma , Croese Tommaso , Darzi Naama , Galai Sivan , Tishler Hila , Ariav Yarden , Lavie Dor , Fellus-Alyagor Liat , Oren Roni , Kuznetsov Yuri , David Eyal , Jaschek Rami , Stossel Chani , Singer Oded , Malitsky Sergey , Barak Renana , Seger Rony , Erez Neta , Amit Ido , Tanay Amos , Saada Ann , Golan Talia , Rubinek Tamar , Sang Lee Joo , Ben-Shachar Shay , Wolf Ido , Erez Ayelet
Published: September 2024

Supplementary Figure S2 demonstrates the infiltration of mature innate immune cells to the liver during breast carcinogenesis
Supplementary Tables S1-S8 from Late-stage metastatic melanoma emerges through a diversity of evolutionary pathways
Authors: Spain Lavinia , Coulton Alexander , Lobon Irene , Rowan Andrew , Schnidrig Desiree , Shepherd Scott T.C. , Shum Benjamin , Byrne Fiona , Goicoechea Maria , Piperni Elisa , Au Lewis , Edmonds Kim , Carlyle Eleanor , Hunter Nikki , Renn Alexandra , Messiou Christina , Hughes Peta , Nobbs Jaime , Foijer Floris , van den Bos Hilda , Wardenaar Rene , Spierings Diana C.J. , Spencer Charlotte , Schmitt Andreas M. , Tippu Zayd , Lingard Karla , Grostate Lauren , Peat Kema , Kelly Kayleigh , Sarker Sarah , Vaughan Sarah , Mangwende Mary , Terry Lauren , Kelly Denise , Biano Jennifer , Murra Aida , Korteweg Justine , Lewis Charlotte , OFlaherty Molly , Cattin Anne-Laure , Emmerich Max , Gerard Camille L. , Pallikonda Husayn Ahmed. , Lynch Joanna , Mason Robert , Rogiers Aljosja , Xu Hang , Huebner Ariana , McGranahan Nicholas , Al Bakir Maise , Murai Jun , Naceur-Lombardelli Cristina , Borg Elaine , Mitchison Miriam , Moore David A. , Falzon Mary , Proctor Ian , Stamp Gordon W H. , Nye Emma L. , Young Kate , Furness Andrew J.S. , Pickering Lisa , Stewart Ruby , Mahadeva Ula , Green Anna , Larkin James , Litchfield Kevin , Swanton Charles , Jamal-Hanjani Mariam , Turajlic Samra
Published: September 2024

S. Table 1: List of PEACE Consortium members.
S. Table 2: Sample database used for the study for Panel, Exome and RNASeq samples.
S. Table 3: Overview of lines of treatment given to each patient.
S. Table 4: Lesions and patients included in the lesion-level response to ICI analysis.
S. Table 5: Hallmark genesets significantly upregulated in normal tissue vs tumor tissue. Table shows p-values for tissue type, purity; T value for tissue type, purity; q-value for tissue type, purity (FDR corrected).
S. Table 6: Hallmark genesets significantly upregulated in tumor tissue vs normal tissue. Table shows p-values for tissue type, purity; T value for tissue type, purity; q-value for tissue type, purity (FDR corrected).
S. Table 7: Genes included in the target panel.
S. Table 8: Tree topology comparisons between manually constructed trees and pairtree-constructed trees.
Supplementary Table S5 from Mitophagy promotes resistance to BH3 mimetics in acute myeloid leukemia
Authors: Glytsou Christina , Chen Xufeng , Zacharioudakis Emmanouil , Al-Santli Wafa , Zhou Hua , Nadorp Bettina , Lee Soobeom , Lasry Audrey , Sun Zhengxi , Papaioannou Dimitrios , Cammer Michael , Wang Kun , Zal Tomasz , Zal Malgorzata Anna. , Carter Bing Z. , Ishizawa Jo , Tibes Raoul , Tsirigos Aristotelis , Andreeff Michael , Gavathiotis Evripidis , Aifantis Iannis
Published: September 2024

Supplementary Table S5 shows sgRNA, primers, shRNA sequences used in this study.
Supplementary Table S4 from Mitophagy promotes resistance to BH3 mimetics in acute myeloid leukemia
Authors: Glytsou Christina , Chen Xufeng , Zacharioudakis Emmanouil , Al-Santli Wafa , Zhou Hua , Nadorp Bettina , Lee Soobeom , Lasry Audrey , Sun Zhengxi , Papaioannou Dimitrios , Cammer Michael , Wang Kun , Zal Tomasz , Zal Malgorzata Anna. , Carter Bing Z. , Ishizawa Jo , Tibes Raoul , Tsirigos Aristotelis , Andreeff Michael , Gavathiotis Evripidis , Aifantis Iannis
Published: September 2024

Supplementary Table S4 shows autophagy related genes and their ranking in NMF analysis of scRNAseq data.
Supplementary Methods from Mitophagy promotes resistance to BH3 mimetics in acute myeloid leukemia
Authors: Glytsou Christina , Chen Xufeng , Zacharioudakis Emmanouil , Al-Santli Wafa , Zhou Hua , Nadorp Bettina , Lee Soobeom , Lasry Audrey , Sun Zhengxi , Papaioannou Dimitrios , Cammer Michael , Wang Kun , Zal Tomasz , Zal Malgorzata Anna. , Carter Bing Z. , Ishizawa Jo , Tibes Raoul , Tsirigos Aristotelis , Andreeff Michael , Gavathiotis Evripidis , Aifantis Iannis
Published: September 2024

Supplementary Methods, Tables, and References
Supplementary Table S2 from Co-mutations and KRAS G12C inhibitor efficacy in advanced NSCLC
Authors: Negrao Marcelo V. , Araujo Haniel A. , Lamberti Giuseppe , Cooper Alissa J. , Akhave Neal S. , Zhou Teng , Delasos Lukas , Hicks J Kevin. , Aldea Mihaela , Minuti Gabriele , Hines Jacobi , Aredo Jacqueline V. , Dennis Michael J. , Chakrabarti Turja , Scott Susan C. , Bironzo Paolo , Scheffler Matthias , Christopoulos Petros , Stenzinger Albrecht , Riess Jonathan W. , Kim So Yeon , Goldberg Sarah B. , Li Mingjia , Wang Qi , Qing Yun , Ni Ying , Do Minh Truong , Lee Richard , Ricciuti Biagio , Alessi Joao Victor. , Wang Jing , Resuli Blerina , Landi Lorenza , Tseng Shu-Chi , Nishino Mizuki , Digumarthy Subba R. , Rinsurongkawong Waree , Rinsurongkawong Vadeerat , Vaporciyan Ara A , Blumenschein George R. , Zhang Jianjun , Owen Dwight H. , Blakely Collin M. , Mountzios Giannis , Shu Catherine A. , Bestvina Christine M. , Garassino Marina Chiara. , Marrone Kristen A. , Gray Jhanelle E. , Patel Sandip Pravin. , Cummings Amy L. , Wakelee Heather A. , Wolf Juergen , Scagliotti Giorgio Vittorio. , Cappuzzo Federico , Barlesi Fabrice , Patil Pradnya D. , Drusbosky Leylah , Gibbons Don L. , Meric-Bernstam Funda , Lee J. Jack , Heymach John V. , Hong David S. , Heist Rebecca S. , Awad Mark M. , Skoulidis Ferdinandos
Published: September 2024

Baseline Patient Characteristics – Cohort A
Supplementary Table S8 from C/EBPa confers dependence to fatty acid anabolic pathways and vulnerability to lipid oxidative stress-induced ferroptosis in FLT3-mutant leukemia
Authors: Sabatier Marie , Birsen Rudy , Lauture Laura , Mouche Sarah , Angelino Paolo , Dehairs Jonas , Goupille Lea , Boussaid Ismael , Heiblig Mael , Boet Emeline , Sahal Ambrine , Saland Estelle , Santos Juliana C. , Armengol Marc , Fernandez-Serrano Miranda , Farge Thomas , Cognet Guillaume , Simonetta Federico , Pignon Corentin , Graffeuil Antoine , Mazzotti Celine , Avet-Loiseau Herve , Delos Oceane , Bertrand-Michel Justine , Chedru Amelie , Dembitz Vilma , Gallipoli Paolo , Anstee Natasha S. , Loo Sun , Wei Andrew H. , Carroll Martin , Goubard Armelle , Castellano Remy , Collette Yves , Vergez Francois , Mansat-De Mas Veronique , Bertoli Sarah , Tavitian Suzanne , Picard Muriel , Recher Christian , Bourges-Abella Nathalie , Granat Fanny , Kosmider Olivier , Sujobert Pierre , Colsch Benoit , Joffre Carine , Stuani Lucille , Swinnen Johannes V. , Guillou Herve , Roue Gael , Hakim Nawad , Dejean Anne S. , Tsantoulis Petros , Larrue Clement , Bouscary Didier , Tamburini Jerome , Sarry Jean-Emmanuel
Published: September 2024

Table S8: Multimodal analysis of shCEBPA versus shCTL MOLM14 cell line
Supplementary Table S7 from C/EBPa confers dependence to fatty acid anabolic pathways and vulnerability to lipid oxidative stress-induced ferroptosis in FLT3-mutant leukemia
Authors: Sabatier Marie , Birsen Rudy , Lauture Laura , Mouche Sarah , Angelino Paolo , Dehairs Jonas , Goupille Lea , Boussaid Ismael , Heiblig Mael , Boet Emeline , Sahal Ambrine , Saland Estelle , Santos Juliana C. , Armengol Marc , Fernandez-Serrano Miranda , Farge Thomas , Cognet Guillaume , Simonetta Federico , Pignon Corentin , Graffeuil Antoine , Mazzotti Celine , Avet-Loiseau Herve , Delos Oceane , Bertrand-Michel Justine , Chedru Amelie , Dembitz Vilma , Gallipoli Paolo , Anstee Natasha S. , Loo Sun , Wei Andrew H. , Carroll Martin , Goubard Armelle , Castellano Remy , Collette Yves , Vergez Francois , Mansat-De Mas Veronique , Bertoli Sarah , Tavitian Suzanne , Picard Muriel , Recher Christian , Bourges-Abella Nathalie , Granat Fanny , Kosmider Olivier , Sujobert Pierre , Colsch Benoit , Joffre Carine , Stuani Lucille , Swinnen Johannes V. , Guillou Herve , Roue Gael , Hakim Nawad , Dejean Anne S. , Tsantoulis Petros , Larrue Clement , Bouscary Didier , Tamburini Jerome , Sarry Jean-Emmanuel
Published: September 2024

Table S7: Transcriptomics analysis of shCEBPA#2 versus shCTL
Supplementary Table S4 from C/EBPa confers dependence to fatty acid anabolic pathways and vulnerability to lipid oxidative stress-induced ferroptosis in FLT3-mutant leukemia
Authors: Sabatier Marie , Birsen Rudy , Lauture Laura , Mouche Sarah , Angelino Paolo , Dehairs Jonas , Goupille Lea , Boussaid Ismael , Heiblig Mael , Boet Emeline , Sahal Ambrine , Saland Estelle , Santos Juliana C. , Armengol Marc , Fernandez-Serrano Miranda , Farge Thomas , Cognet Guillaume , Simonetta Federico , Pignon Corentin , Graffeuil Antoine , Mazzotti Celine , Avet-Loiseau Herve , Delos Oceane , Bertrand-Michel Justine , Chedru Amelie , Dembitz Vilma , Gallipoli Paolo , Anstee Natasha S. , Loo Sun , Wei Andrew H. , Carroll Martin , Goubard Armelle , Castellano Remy , Collette Yves , Vergez Francois , Mansat-De Mas Veronique , Bertoli Sarah , Tavitian Suzanne , Picard Muriel , Recher Christian , Bourges-Abella Nathalie , Granat Fanny , Kosmider Olivier , Sujobert Pierre , Colsch Benoit , Joffre Carine , Stuani Lucille , Swinnen Johannes V. , Guillou Herve , Roue Gael , Hakim Nawad , Dejean Anne S. , Tsantoulis Petros , Larrue Clement , Bouscary Didier , Tamburini Jerome , Sarry Jean-Emmanuel
Published: September 2024

Table S4: GSEA results in FLT3-ITD PDX AML cells ex vivo-treated with QUIZ or Veh.
Supplementary Table S15 from C/EBPa confers dependence to fatty acid anabolic pathways and vulnerability to lipid oxidative stress-induced ferroptosis in FLT3-mutant leukemia
Authors: Sabatier Marie , Birsen Rudy , Lauture Laura , Mouche Sarah , Angelino Paolo , Dehairs Jonas , Goupille Lea , Boussaid Ismael , Heiblig Mael , Boet Emeline , Sahal Ambrine , Saland Estelle , Santos Juliana C. , Armengol Marc , Fernandez-Serrano Miranda , Farge Thomas , Cognet Guillaume , Simonetta Federico , Pignon Corentin , Graffeuil Antoine , Mazzotti Celine , Avet-Loiseau Herve , Delos Oceane , Bertrand-Michel Justine , Chedru Amelie , Dembitz Vilma , Gallipoli Paolo , Anstee Natasha S. , Loo Sun , Wei Andrew H. , Carroll Martin , Goubard Armelle , Castellano Remy , Collette Yves , Vergez Francois , Mansat-De Mas Veronique , Bertoli Sarah , Tavitian Suzanne , Picard Muriel , Recher Christian , Bourges-Abella Nathalie , Granat Fanny , Kosmider Olivier , Sujobert Pierre , Colsch Benoit , Joffre Carine , Stuani Lucille , Swinnen Johannes V. , Guillou Herve , Roue Gael , Hakim Nawad , Dejean Anne S. , Tsantoulis Petros , Larrue Clement , Bouscary Didier , Tamburini Jerome , Sarry Jean-Emmanuel
Published: September 2024

Table S15: Relative quantification by lipid class
Supplementary Table S13 from C/EBPa confers dependence to fatty acid anabolic pathways and vulnerability to lipid oxidative stress-induced ferroptosis in FLT3-mutant leukemia
Authors: Sabatier Marie , Birsen Rudy , Lauture Laura , Mouche Sarah , Angelino Paolo , Dehairs Jonas , Goupille Lea , Boussaid Ismael , Heiblig Mael , Boet Emeline , Sahal Ambrine , Saland Estelle , Santos Juliana C. , Armengol Marc , Fernandez-Serrano Miranda , Farge Thomas , Cognet Guillaume , Simonetta Federico , Pignon Corentin , Graffeuil Antoine , Mazzotti Celine , Avet-Loiseau Herve , Delos Oceane , Bertrand-Michel Justine , Chedru Amelie , Dembitz Vilma , Gallipoli Paolo , Anstee Natasha S. , Loo Sun , Wei Andrew H. , Carroll Martin , Goubard Armelle , Castellano Remy , Collette Yves , Vergez Francois , Mansat-De Mas Veronique , Bertoli Sarah , Tavitian Suzanne , Picard Muriel , Recher Christian , Bourges-Abella Nathalie , Granat Fanny , Kosmider Olivier , Sujobert Pierre , Colsch Benoit , Joffre Carine , Stuani Lucille , Swinnen Johannes V. , Guillou Herve , Roue Gael , Hakim Nawad , Dejean Anne S. , Tsantoulis Petros , Larrue Clement , Bouscary Didier , Tamburini Jerome , Sarry Jean-Emmanuel
Published: September 2024

Table S13: lipidomic results by lipid species in dox-inducible and constitutives shRNAs and siRNA CTL/CEBPA, empty vector/CEBPA-OE and vehicle/QUIZ conditions in MOLM-14 cells
Supplementary Table S12 from C/EBPa confers dependence to fatty acid anabolic pathways and vulnerability to lipid oxidative stress-induced ferroptosis in FLT3-mutant leukemia
Authors: Sabatier Marie , Birsen Rudy , Lauture Laura , Mouche Sarah , Angelino Paolo , Dehairs Jonas , Goupille Lea , Boussaid Ismael , Heiblig Mael , Boet Emeline , Sahal Ambrine , Saland Estelle , Santos Juliana C. , Armengol Marc , Fernandez-Serrano Miranda , Farge Thomas , Cognet Guillaume , Simonetta Federico , Pignon Corentin , Graffeuil Antoine , Mazzotti Celine , Avet-Loiseau Herve , Delos Oceane , Bertrand-Michel Justine , Chedru Amelie , Dembitz Vilma , Gallipoli Paolo , Anstee Natasha S. , Loo Sun , Wei Andrew H. , Carroll Martin , Goubard Armelle , Castellano Remy , Collette Yves , Vergez Francois , Mansat-De Mas Veronique , Bertoli Sarah , Tavitian Suzanne , Picard Muriel , Recher Christian , Bourges-Abella Nathalie , Granat Fanny , Kosmider Olivier , Sujobert Pierre , Colsch Benoit , Joffre Carine , Stuani Lucille , Swinnen Johannes V. , Guillou Herve , Roue Gael , Hakim Nawad , Dejean Anne S. , Tsantoulis Petros , Larrue Clement , Bouscary Didier , Tamburini Jerome , Sarry Jean-Emmanuel
Published: September 2024

Table S12: gene signatures used to analyze RNA-seq data from patients with AML before/after GILT
Supplementary Table S10 from C/EBPa confers dependence to fatty acid anabolic pathways and vulnerability to lipid oxidative stress-induced ferroptosis in FLT3-mutant leukemia
Authors: Sabatier Marie , Birsen Rudy , Lauture Laura , Mouche Sarah , Angelino Paolo , Dehairs Jonas , Goupille Lea , Boussaid Ismael , Heiblig Mael , Boet Emeline , Sahal Ambrine , Saland Estelle , Santos Juliana C. , Armengol Marc , Fernandez-Serrano Miranda , Farge Thomas , Cognet Guillaume , Simonetta Federico , Pignon Corentin , Graffeuil Antoine , Mazzotti Celine , Avet-Loiseau Herve , Delos Oceane , Bertrand-Michel Justine , Chedru Amelie , Dembitz Vilma , Gallipoli Paolo , Anstee Natasha S. , Loo Sun , Wei Andrew H. , Carroll Martin , Goubard Armelle , Castellano Remy , Collette Yves , Vergez Francois , Mansat-De Mas Veronique , Bertoli Sarah , Tavitian Suzanne , Picard Muriel , Recher Christian , Bourges-Abella Nathalie , Granat Fanny , Kosmider Olivier , Sujobert Pierre , Colsch Benoit , Joffre Carine , Stuani Lucille , Swinnen Johannes V. , Guillou Herve , Roue Gael , Hakim Nawad , Dejean Anne S. , Tsantoulis Petros , Larrue Clement , Bouscary Didier , Tamburini Jerome , Sarry Jean-Emmanuel
Published: September 2024

Table S10: EnrichR analysis of CEBPA_UP signature
Supplementary Table S1 from C/EBPa confers dependence to fatty acid anabolic pathways and vulnerability to lipid oxidative stress-induced ferroptosis in FLT3-mutant leukemia
Authors: Sabatier Marie , Birsen Rudy , Lauture Laura , Mouche Sarah , Angelino Paolo , Dehairs Jonas , Goupille Lea , Boussaid Ismael , Heiblig Mael , Boet Emeline , Sahal Ambrine , Saland Estelle , Santos Juliana C. , Armengol Marc , Fernandez-Serrano Miranda , Farge Thomas , Cognet Guillaume , Simonetta Federico , Pignon Corentin , Graffeuil Antoine , Mazzotti Celine , Avet-Loiseau Herve , Delos Oceane , Bertrand-Michel Justine , Chedru Amelie , Dembitz Vilma , Gallipoli Paolo , Anstee Natasha S. , Loo Sun , Wei Andrew H. , Carroll Martin , Goubard Armelle , Castellano Remy , Collette Yves , Vergez Francois , Mansat-De Mas Veronique , Bertoli Sarah , Tavitian Suzanne , Picard Muriel , Recher Christian , Bourges-Abella Nathalie , Granat Fanny , Kosmider Olivier , Sujobert Pierre , Colsch Benoit , Joffre Carine , Stuani Lucille , Swinnen Johannes V. , Guillou Herve , Roue Gael , Hakim Nawad , Dejean Anne S. , Tsantoulis Petros , Larrue Clement , Bouscary Didier , Tamburini Jerome , Sarry Jean-Emmanuel
Published: September 2024

Table S1: Transcriptome analysis of FLT3-ITD cell lines after FLT3 inhbition
Supplementary Table 5 from A Compendium of Syngeneic, Transplantable Pediatric High-Grade Glioma Models Reveals Subtype-Specific Therapeutic Vulnerabilities
Authors: McNicholas Michael , De Cola Antonella , Bashardanesh Zahedeh , Foss Amelia , Lloyd Cameron B. , Hebert Steven , Faury Damien , Andrade Augusto Faria. , Jabado Nada , Kleinman Claudia L. , Pathania Manav
Published: September 2024

Cell type ontologies derived from snRNA-seq data.
Supplementary Tables 1-3, 7-9 from A Compendium of Syngeneic, Transplantable Pediatric High-Grade Glioma Models Reveals Subtype-Specific Therapeutic Vulnerabilities
Authors: McNicholas Michael , De Cola Antonella , Bashardanesh Zahedeh , Foss Amelia , Lloyd Cameron B. , Hebert Steven , Faury Damien , Andrade Augusto Faria. , Jabado Nada , Kleinman Claudia L. , Pathania Manav
Published: September 2024

Tables describing statistical analyses, median survivals, IC50 values calculated from cell viability assays, primer sequences and antibodies.
Supplementary Table 6 from A Compendium of Syngeneic, Transplantable Pediatric High-Grade Glioma Models Reveals Subtype-Specific Therapeutic Vulnerabilities
Authors: McNicholas Michael , De Cola Antonella , Bashardanesh Zahedeh , Foss Amelia , Lloyd Cameron B. , Hebert Steven , Faury Damien , Andrade Augusto Faria. , Jabado Nada , Kleinman Claudia L. , Pathania Manav
Published: September 2024

ssGEA signatures derived from snRNA-seq data.
Supplementary Figures S1-S16 from Sex-biased T cell exhaustion drives differential immune responses in glioblastoma
Authors: Lee Juyeun , Nicosia Michael , Hong Ellen S. , Silver Daniel J. , Li Cathy , Bayik Defne , Watson Dionysios C. , Lauko Adam , Kay Kristen E. , Wang Sabrina Z. , Johnson Sadie , McGraw Mary , Grabowski Matthew M. , Kish Danielle D. , Desai Amar B. , Goodman Wendy A. , Cameron Scott J. , Okada Hideho , Valujskikh Anna , Fairchild Robert L. , Ahluwalia Manmeet S. , Lathia Justin D.
Published: September 2024

Supplementary Fig. S1. Immune cell-dependent survival differences between males and females in murine glioblastoma models.
Supplementary Fig. S2. Mouse syngeneic GBM cell lines do not contain a Y chromosome.
Supplementary Fig. S3. Frequencies of tumor-infiltrating immune cells in SB28 model.
Supplementary Fig. S4. Sex difference in survival in SB28-OVA model and GL261 model.
Supplementary Fig. S5. No sex difference in T cells was observed at an earlier time point.
Supplementary Fig. S6. Male T cells are more exhausted in the GL261 model.
Supplementary Fig. S7. Phenotype of T cells in the periphery does not replicate the sex differences shown in tumor-infiltrating T cells.
Supplementary Fig. S8. Frequencies of exhausted T cell subsets.
Supplementary Fig. S9. PD1 blockade enhanced immune responses
Supplementary Fig. S10. No significant difference in the immune cell composition of bone marrow chimera mice before tumor implantation.
Supplementary Fig. S11. Male and female CD8+ T cells in mixed bone marrow chimera model.
Supplementary Fig. S12. Phenotyping tumor-infiltrating CD8+ T cell from GBM patient tumors.
Supplementary Fig. S13. scRNA-seq analysis of tumor-infiltrating CD8+ T cells from GBM patients.
Supplementary Fig. S14. mRNA expression level of transcription factors in human in vitro exhausted T cells.
Supplementary Fig. S15. Expression level of X chromosome inactivation (XCI) genes in exhausted T cells.
Supplementary Fig. S16. Inhibition of UTX abrogates sex differences in T cell exhaustion.
Supplementary Table S8 from Clinical activity and exploratory resistance mechanism of milademetan, an MDM2 inhibitor, in intimal sarcoma with MDM2 amplification: an open-label phase 1b/2 study
Authors: Koyama Takafumi , Shimizu Toshio , Kojima Yuki , Sudo Kazuki , Okuma Hitomi Sumiyoshi. , Shimoi Tatsunori , Ichikawa Hitoshi , Kohsaka Shinji , Sadachi Ryo , Hirakawa Akihiro , Yoshida Akihiko , Ando Reiko Makihara. , Ueno Toshihide , Yanagaki Mitsuru , Matsui Naoko , Nakamura Kenichi , Yamamoto Noboru , Yonemori Kan
Published: September 2024

Eligibility and exclusion criteria
Supplementary Figure S5 from Clinical activity and exploratory resistance mechanism of milademetan, an MDM2 inhibitor, in intimal sarcoma with MDM2 amplification: an open-label phase 1b/2 study
Authors: Koyama Takafumi , Shimizu Toshio , Kojima Yuki , Sudo Kazuki , Okuma Hitomi Sumiyoshi. , Shimoi Tatsunori , Ichikawa Hitoshi , Kohsaka Shinji , Sadachi Ryo , Hirakawa Akihiro , Yoshida Akihiko , Ando Reiko Makihara. , Ueno Toshihide , Yanagaki Mitsuru , Matsui Naoko , Nakamura Kenichi , Yamamoto Noboru , Yonemori Kan
Published: September 2024

Correlation between the MDM2 copy number and tumor shrinkage
Supplementary Figure 3 from Resistance to selective FGFR inhibitors in FGFR-driven urothelial cancer
Authors: Facchinetti Francesco , Hollebecque Antoine , Braye Floriane , Vasseur Damien , Pradat Yoann , Bahleda Rastislav , Pobel Cedric , Bigot Ludovic , Deas Olivier , Florez Arango Juan David , Guaitoli Giorgia , Mizuta Hayato , Combarel David , Tselikas Lambros , Michiels Stefan , Nikolaev Sergey I. , Scoazec Jean-Yves , Ponce-Aix Santiago , Besse Benjamin , Olaussen Ken A. , Loriot Yohann , Friboulet Luc
Published: September 2024

Acquisition of mutations in PI3K/TSC1 pathway at progression to FGFR inhibitors.