bluuebunny/crossref_metadata_2025 huggingface dataset:
Data from Topoisomerase 1 Inhibition in MYC-Driven Cancer Promotes Aberrant R-Loop Accumulation to Induce Synthetic Lethality
Authors: Lin Peter , Lourenco Corey , Cruickshank Jennifer , Palomero Luis , van Leeuwen Jenna E. , Tong Amy H. Y. , Chan Katherine , El Ghamrasni Samah , Pujana Miquel Angel , Cescon David W. , Moffat Jason , Penn Linda Z.
Published: December 2023

Abstract
MYC is a central regulator of gene transcription and is frequently dysregulated in human cancers. As targeting MYC directly is challenging, an alternative strategy is to identify specific proteins or processes required for MYC to function as a potent cancer driver that can be targeted to result in synthetic lethality. To identify potential targets in MYC-driven cancers, we performed a genome-wide CRISPR knockout screen using an isogenic pair of breast cancer cell lines in which MYC dysregulation is the switch from benign to transformed tumor growth. Proteins that regulate R-loops were identified as a potential class of synthetic lethal targets. Dysregulated MYC elevated global transcription and coincident R-loop accumulation. Topoisomerase 1 (TOP1), a regulator of R-loops by DNA topology, was validated to be a vulnerability in cells with high MYC activity. Genetic knockdown of TOP1 in MYC-transformed cells resulted in reduced colony formation compared with control cells, demonstrating synthetic lethality. Overexpression of RNaseH1, a riboendonuclease that specifically degrades R-loops, rescued the reduction in clonogenicity induced by TOP1 deficiency, demonstrating that this vulnerability is driven by aberrant R-loop accumulation. Genetic and pharmacologic TOP1 inhibition selectively reduced the fitness of MYC-transformed tumors in vivo. Finally, drug response to TOP1 inhibitors (i.e., topotecan) significantly correlated with MYC levels and activity across panels of breast cancer cell lines and patient-derived organoids. Together, these results highlight TOP1 as a promising target for MYC-driven cancers.
Significance:
CRISPR screening reveals topoisomerase 1 as an immediately actionable vulnerability in cancers harboring MYC as a driver oncoprotein that can be targeted with clinically approved inhibitors.
Supplementary Table S1 from A Pilot Study Omitting Radiation in the Treatment of Children with Newly Diagnosed Wnt-Activated Medulloblastoma
Authors: Cohen Kenneth J. , Munjapara Vasu , Aguilera Dolly , Castellino Robert C. , Stapleton Stacie L. , Landi Daniel , Ashley David M. , Rodriguez Fausto J. , Hawkins Cynthia , Yang Edward , London Wendy , Chi Susan , Bandopadhayay Pratiti
Published: December 2023

Detailed mutations
Supplementary Table S3 from Safety and Efficacy of Tucatinib, Letrozole, and Palbociclib in Patients with Previously Treated HR+/HER2+ Breast Cancer
Authors: Shagisultanova Elena , Gradishar William , Brown-Glaberman Ursa , Chalasani Pavani , Brenner Andrew J. , Stopeck Alison , Parris Hannah , Gao Dexiang , McSpadden Tessa , Mayordomo Jose , Diamond Jennifer R. , Kabos Peter , Borges Virginia F.
Published: December 2023

Characteristics of CNS cohort
Supplementary Table S1 from A Phase I Expansion Cohort Study Evaluating the Safety and Efficacy of the CHK1 Inhibitor LY2880070 with Low-dose Gemcitabine in Patients with Metastatic Pancreatic Adenocarcinoma
Authors: Huffman Brandon M. , Feng Hanrong , Parmar Kalindi , Wang Junning , Kapner Kevin S. , Kochupurakkal Bose , Martignetti David B. , Sadatrezaei Golbahar , Abrams Thomas A. , Biller Leah H. , Giannakis Marios , Ng Kimmie , Patel Anuj K. , Perez Kimberly J. , Singh Harshabad , Rubinson Douglas A. , Schlechter Benjamin L. , Andrews Elizabeth , Hannigan Alison M. , Dunwell Stanley , Getchell Zoe , Raghavan Srivatsan , Wolpin Brian M. , Fortier Caroline , D'Andrea Alan D. , Aguirre Andrew J. , Shapiro Geoffrey I. , Cleary James M.
Published: December 2023

Overall Representativeness
Supplementary Fig. S2 from Safety and Efficacy of Tucatinib, Letrozole, and Palbociclib in Patients with Previously Treated HR+/HER2+ Breast Cancer
Authors: Shagisultanova Elena , Gradishar William , Brown-Glaberman Ursa , Chalasani Pavani , Brenner Andrew J. , Stopeck Alison , Parris Hannah , Gao Dexiang , McSpadden Tessa , Mayordomo Jose , Diamond Jennifer R. , Kabos Peter , Borges Virginia F.
Published: December 2023

Grade 3 and 4 AEs - palbociclib 125mg vs 75mg
Supplementary Table S4 from A PERK-Specific Inhibitor Blocks Metastatic Progression by Limiting Integrated Stress Response–Dependent Survival of Quiescent Cancer Cells
Authors: Calvo Veronica , Zheng Wei , Adam-Artigues Anna , Staschke Kirk A. , Huang Xin , Cheung Julie F. , Nobre Ana Rita , Fujisawa Sho , Liu David , Fumagalli Maria , Surguladze David , Stokes Michael E. , Nowacek Ari , Mulvihill Mark , Farias Eduardo F. , Aguirre-Ghiso Julio A.
Published: December 2023

Supplementary Table 4: KINOMEscan™ Selectivity Score for HC4, HC19, HC28 and GSK157 at concentrations of 0.1, 1.0 and 10 mM across 468 Kinases
Supplementary Figure S3 from A PERK-Specific Inhibitor Blocks Metastatic Progression by Limiting Integrated Stress Response–Dependent Survival of Quiescent Cancer Cells
Authors: Calvo Veronica , Zheng Wei , Adam-Artigues Anna , Staschke Kirk A. , Huang Xin , Cheung Julie F. , Nobre Ana Rita , Fujisawa Sho , Liu David , Fumagalli Maria , Surguladze David , Stokes Michael E. , Nowacek Ari , Mulvihill Mark , Farias Eduardo F. , Aguirre-Ghiso Julio A.
Published: December 2023

Supplementary Figure S3. (a) Representative images of carmine staining of whole mount FVB normal mammary gland compared to vehicle- andHC4-treated MMTV-HER2 mammary gland whole mount. Scale bar 2 mm.(b) Examples of the mammary gland histological structures quantified.Scale bar 3 mm. Number of normal branches in the mammary gland ductal tree of non-tumor bearing healthy mice treated with vehicle (N=14) orHC4 (N=10). P by Mann-Whitney test. (c) The panels show representative images of histological sections showing at low magnification (top row 100µm scale bar) the indicated ductal and early lesion structures; the lower row showed higher magnification (25 µm scale bars) these structures. Theseimages were used as a key to classify per animal the effects of control or HC4 treatments.
Supplementary Figure S2 from A PERK-Specific Inhibitor Blocks Metastatic Progression by Limiting Integrated Stress Response–Dependent Survival of Quiescent Cancer Cells
Authors: Calvo Veronica , Zheng Wei , Adam-Artigues Anna , Staschke Kirk A. , Huang Xin , Cheung Julie F. , Nobre Ana Rita , Fujisawa Sho , Liu David , Fumagalli Maria , Surguladze David , Stokes Michael E. , Nowacek Ari , Mulvihill Mark , Farias Eduardo F. , Aguirre-Ghiso Julio A.
Published: December 2023

Supplementary Figure S2. (a) Normalized area of single macro-metastases in lung in vehicle (N=22) and HC4-treated animals (N=15). P by MannWhitney test. (b) 2.5x105 HNSCC T-Hep3 cells as single cell suspensions were injected via tail vein in Balb/c nu/nu mice and 24 h after injectionanimals were treated with vehicle or HC4 (50 mg/kg) for 10 days. Frequency of T-HEp3 DCCs in the lung detected via a human specific anti-vimentinantibody was scored. 5 lung sections/animal ± s.d (N=5 per group). Scale bar, 10 µm. P by Mann-Whitney test. (c) Balb/c syngeneic EMT6 micewere treated with HC4 at 10 mg/kg for 17 days. Metastatic lesions were detected by H&E staining and quantified in 5 lung section/animal. P byMann-Whitney test. (d) Quantification of circulating tumor cells/ml blood by HER2 staining of cytospins (N=4 per group) P by Mann-Whitney test. (e)Percentage P-Rb+ micro-metastasis per lung section/animal in vehicle (N=4) and HC4-treated animals (N=6). Scale bar, 25 µm. P by Student’s ttest. (f) Number of D-Hep3 cells per nodule in vehicle and HC4-treated (20 µM, 6 days) CAM tumors (N=6 per group) (left); quantification andrepresentative images of D-HEp3 CAM tumors stained for cleaved caspase-3 (green), vimentin (red), and DAPI (blue) (right). Approximately 1000cells per group were assessed, p by Mann-Whitney test. Scale bars, 25 μm. (g) Mice were injected with MMTV-HER2 cells from primary tumorlesions via the tail vein, allowed them to expand into established metastatic lesions for 3 weeks and treated with vehicle or HC4 (50 mg/kg) for 2weeks. Micro-metastasis were detected by H&E or IF (HER2 detection) staining and quantified in 5 lung section/animal ±s.d (N=8 per group). P byMann-Whitney test
Supplementary Figure S1 from A PERK-Specific Inhibitor Blocks Metastatic Progression by Limiting Integrated Stress Response–Dependent Survival of Quiescent Cancer Cells
Authors: Calvo Veronica , Zheng Wei , Adam-Artigues Anna , Staschke Kirk A. , Huang Xin , Cheung Julie F. , Nobre Ana Rita , Fujisawa Sho , Liu David , Fumagalli Maria , Surguladze David , Stokes Michael E. , Nowacek Ari , Mulvihill Mark , Farias Eduardo F. , Aguirre-Ghiso Julio A.
Published: December 2023

Supplementary Figure S1. (a) MCF10A cells were treated with DMSO, thapsigargin (0.2 µM) alone or in combination with PERK inhibitors (2 µM)for 24 h and assayed for GADD34 expression by RT-qPCR. N = 3 wells per group (left graph). E0771 cells were treated with DMSO, thapsigargin(0.1 µM) alone or in combination with PERK inhibitors (2 µM) for 16 h and assayed for GADD34 expression by RT-qPCR. N = 3 wells per group (rightgraph) ****, p <0.0001 by t-test. (b) Flow diagram of the steps followed for single cell gene expression analysis with C1 and Biomark HD Fluidigm. Atotal of 255 DCCs and 90 primary tumor (PT) cells were analyzed. (c) List of the genes analyzed by high-throughput qPCR. (d) (upper) Immunoblotshowing the inhibition of PERK phosphorylation (T982) by the PERK inhibitor HC4 (2 µM) in MCF10A-HER2 cells plated on low attachment platesand incubated with inhibitor for 24 h. (lower) Immunoblot showing inhibition of PERK phosphorylation by treatment with increasing doses of HC4,HC19, HC28 and GSK2656157 for 4 h upon incubation with ER stress inducer tunicamycin in HEK293 cells. (e) The PERK inhibitor HC4 sensitizesto low dose ER stress-induced cell death in vitro. HC4 dose-response viability curve (Cell Titer Blue, CTB) in MCF10A-HER2 cells, in the absence (-)or in the presence of stress (low dose thapsigargin, Tg 2 nM) after 48 h. Dashed line indicates IC50 (≈ 9 nM). (f) MCF10A-Fv2E-PERK cells in 2Dculture were treated daily with 2 nM AP20187 (AP), HC4 2 µM and combination and assayed for cell death (left) or protein expression (right) after 24h. (g) In vivo pharmacokinetic profile of HC4 in mouse plasma. Dashed lines indicate the different biochemical, cellular and in vitro viability IC50s. (h)Effect of HC4 on body weight in female BALB/c mice (7–8-week-old) females treated twice per day (BID) with HC4 at indicated concentrations. (i)Effect of HC4 on total bone marrow cells (in two lower limbs) in MMTV-HER2 females treated for 2 weeks (N=5 per group) (left graph); effect of HC4on total white blood cells in MMTV-HER2 females treated for 2 weeks (N=11 per group) (middle graph)
Supplementary Table S4 from The Clinical Implications of Reversions in Patients with Advanced Pancreatic Cancer and Pathogenic Variants in BRCA1, BRCA2, or PALB2 after Progression on Rucaparib
Authors: Brown Timothy J. , Yablonovitch Arielle , Till Jacob E. , Yen Jennifer , Kiedrowski Lesli A. , Hood Ryan , O'Hara Mark H. , Teitelbaum Ursina , Karasic Thomas B. , Schneider Charles , Carpenter Erica L. , Nathanson Katherine , Domchek Susan M. , Reiss Kim A.
Published: December 2023

ROC and Test Characteristics from VAF Analysis with Binary Outcome of 12-month OS
Supplementary Table S3 from The Clinical Implications of Reversions in Patients with Advanced Pancreatic Cancer and Pathogenic Variants in BRCA1, BRCA2, or PALB2 after Progression on Rucaparib
Authors: Brown Timothy J. , Yablonovitch Arielle , Till Jacob E. , Yen Jennifer , Kiedrowski Lesli A. , Hood Ryan , O'Hara Mark H. , Teitelbaum Ursina , Karasic Thomas B. , Schneider Charles , Carpenter Erica L. , Nathanson Katherine , Domchek Susan M. , Reiss Kim A.
Published: December 2023

Patient-Level Data for Patients with Reversion Mutations
Supplementary Table S1 from The Clinical Implications of Reversions in Patients with Advanced Pancreatic Cancer and Pathogenic Variants in BRCA1, BRCA2, or PALB2 after Progression on Rucaparib
Authors: Brown Timothy J. , Yablonovitch Arielle , Till Jacob E. , Yen Jennifer , Kiedrowski Lesli A. , Hood Ryan , O'Hara Mark H. , Teitelbaum Ursina , Karasic Thomas B. , Schneider Charles , Carpenter Erica L. , Nathanson Katherine , Domchek Susan M. , Reiss Kim A.
Published: December 2023

Representativeness of Study Participants
Supplementary Table S2 from OvaPrint—A Cell-free DNA Methylation Liquid Biopsy for the Risk Assessment of High-grade Serous Ovarian Cancer
Authors: Buckley David N. , Lewinger Juan Pablo , Gooden Gerald , Spillman Monique , Neuman Monica , Guo X. Mona , Tew Ben Yi , Miller Heather , Khetan Varun U. , Shulman Lee P. , Roman Lynda , Salhia Bodour
Published: December 2023

Table S2: Tissue source for samples used in RRBS.
Table summarizes the source of each tissue sample with totals annotated in the final row and final column.
Supplementary Table S1 from OvaPrint—A Cell-free DNA Methylation Liquid Biopsy for the Risk Assessment of High-grade Serous Ovarian Cancer
Authors: Buckley David N. , Lewinger Juan Pablo , Gooden Gerald , Spillman Monique , Neuman Monica , Guo X. Mona , Tew Ben Yi , Miller Heather , Khetan Varun U. , Shulman Lee P. , Roman Lynda , Salhia Bodour
Published: December 2023

Table S1: Sample summary.
Table summarizes demographic information for tissue (A) and cfDNA (B) samples presented. Rows represent histological subtypes. B is subdivided into benign and malignant categories. Each table is annotated with mean age and age range. Sample counts by race and stage are also shown with totals annotated at the bottom of each table.
Supplementary Table 7 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: December 2023

Supplemental Table 7. Clinical information and CD73 IHC score for patient tumor tissue microarray.
Supplementary Figure S3 from OvaPrint—A Cell-free DNA Methylation Liquid Biopsy for the Risk Assessment of High-grade Serous Ovarian Cancer
Authors: Buckley David N. , Lewinger Juan Pablo , Gooden Gerald , Spillman Monique , Neuman Monica , Guo X. Mona , Tew Ben Yi , Miller Heather , Khetan Varun U. , Shulman Lee P. , Roman Lynda , Salhia Bodour
Published: December 2023

Figure S3: Reproducibility of OvaPrint™ assay
Supplementary Table 4 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: December 2023

Supplemental Table 4. Top 200 markers of NT5E+ cells (by fold change vs. NT5E- cells) from nine EwS cell lines by single cell sequencing.
Supplemental Figure S6 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: December 2023

Supplemental Figure S6. Intertumoral heterogeneity of CD73+ tumor cells and ECM deposition in patient biopsies. Related to Figure 6.
Supplementary Table S2 from Genomic Tumor Correlates of Clinical Outcomes Following Organ-Sparing Chemoradiation Therapy for Bladder Cancer
Authors: Kamran Sophia C. , Zhou Yuzhen , Otani Keisuke , Drumm Michael , Otani Yukako , Wu Shulin , Wu Chin-Lee , Feldman Adam S. , Wszolek Matthew , Lee Richard J. , Saylor Philip J. , Lennerz Jochen , Van Allen Eliezer , Willers Henning , Hong Theodore S. , Liu Yang , Davicioni Elai , Gibb Ewan A. , Shipley William U. , Mouw Kent W. , Efstathiou Jason A. , Miyamoto David T.
Published: December 2023

Association of Alliance/RETAIN Trial DDR Genes with Clinical Outcomes following TMT
Supplemental Figure S3 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: December 2023

Supplemental Figure S3. Spatial heterogeneity of CD73+ tumor cells and ECM deposition in additional xenograft and PDX-derived models. Related to Figure 3.
Supplementary Table S1 from Genomic Tumor Correlates of Clinical Outcomes Following Organ-Sparing Chemoradiation Therapy for Bladder Cancer
Authors: Kamran Sophia C. , Zhou Yuzhen , Otani Keisuke , Drumm Michael , Otani Yukako , Wu Shulin , Wu Chin-Lee , Feldman Adam S. , Wszolek Matthew , Lee Richard J. , Saylor Philip J. , Lennerz Jochen , Van Allen Eliezer , Willers Henning , Hong Theodore S. , Liu Yang , Davicioni Elai , Gibb Ewan A. , Shipley William U. , Mouw Kent W. , Efstathiou Jason A. , Miyamoto David T.
Published: December 2023

Whole exome sequencing metrics for bladder tumor samples
Supplementary Figure S9 from Genomic Tumor Correlates of Clinical Outcomes Following Organ-Sparing Chemoradiation Therapy for Bladder Cancer
Authors: Kamran Sophia C. , Zhou Yuzhen , Otani Keisuke , Drumm Michael , Otani Yukako , Wu Shulin , Wu Chin-Lee , Feldman Adam S. , Wszolek Matthew , Lee Richard J. , Saylor Philip J. , Lennerz Jochen , Van Allen Eliezer , Willers Henning , Hong Theodore S. , Liu Yang , Davicioni Elai , Gibb Ewan A. , Shipley William U. , Mouw Kent W. , Efstathiou Jason A. , Miyamoto David T.
Published: December 2023

Association of select DNA Damage Response (DDR) genes and Overall Survival in the TCGA cohort.
Supplementary Figure S8 from Genomic Tumor Correlates of Clinical Outcomes Following Organ-Sparing Chemoradiation Therapy for Bladder Cancer
Authors: Kamran Sophia C. , Zhou Yuzhen , Otani Keisuke , Drumm Michael , Otani Yukako , Wu Shulin , Wu Chin-Lee , Feldman Adam S. , Wszolek Matthew , Lee Richard J. , Saylor Philip J. , Lennerz Jochen , Van Allen Eliezer , Willers Henning , Hong Theodore S. , Liu Yang , Davicioni Elai , Gibb Ewan A. , Shipley William U. , Mouw Kent W. , Efstathiou Jason A. , Miyamoto David T.
Published: December 2023

Tumor Mutational Burden between Patients with Favorable (F) versus
Unfavorable (UF) mBI-EFS Outcomes following TMT.
Supplementary Figure S6 from Genomic Tumor Correlates of Clinical Outcomes Following Organ-Sparing Chemoradiation Therapy for Bladder Cancer
Authors: Kamran Sophia C. , Zhou Yuzhen , Otani Keisuke , Drumm Michael , Otani Yukako , Wu Shulin , Wu Chin-Lee , Feldman Adam S. , Wszolek Matthew , Lee Richard J. , Saylor Philip J. , Lennerz Jochen , Van Allen Eliezer , Willers Henning , Hong Theodore S. , Liu Yang , Davicioni Elai , Gibb Ewan A. , Shipley William U. , Mouw Kent W. , Efstathiou Jason A. , Miyamoto David T.
Published: December 2023

Association of gene signature scores and TP53-mutated tumors.
Supplementary Table S3 from Zoledronic Acid Add-on Therapy for Standard-Risk Ewing Sarcoma Patients in the Ewing 2008R1 Trial
Authors: Koch Raphael , Haveman Lianne , Ladenstein Ruth , Brichard Benedicte , Jürgens Heribert , Cyprova Sona , van den Berg Henk , Hassenpflug Wolf , Raciborska Anna , Ek Torben , Baumhoer Daniel , Egerer Gerlinde , Kager Leo , Renard Marleen , Hauser Peter , Burdach Stefan , Bovee Judith V.M.G. , Hong Angela M. , Reichardt Peter , Kruseova Jarmila , Streitbürger Arne , Kühne Thomas , Kessler Torsten , Bernkopf Marie , Butterfaß-Bahloul Trude , Dhooge Catharina , Bauer Sebastian , Kiss János , Paulussen Michael , Bonar Fiona , Ranft Andreas , Timmermann Beate , Rascon Jelena , Vieth Volker , Kanerva Jukka , Faldum Andreas , Hartmann Wolfgang , Hjorth Lars , Bhadri Vivek A. , Metzler Markus , Gelderblom Hans , Dirksen Uta
Published: December 2023

Treatment details of patients with major protocol deviation who were excluded from the per protocol collective (N=48)
Supplementary Statistics S1 from Zoledronic Acid Add-on Therapy for Standard-Risk Ewing Sarcoma Patients in the Ewing 2008R1 Trial
Authors: Koch Raphael , Haveman Lianne , Ladenstein Ruth , Brichard Benedicte , Jürgens Heribert , Cyprova Sona , van den Berg Henk , Hassenpflug Wolf , Raciborska Anna , Ek Torben , Baumhoer Daniel , Egerer Gerlinde , Kager Leo , Renard Marleen , Hauser Peter , Burdach Stefan , Bovee Judith V.M.G. , Hong Angela M. , Reichardt Peter , Kruseova Jarmila , Streitbürger Arne , Kühne Thomas , Kessler Torsten , Bernkopf Marie , Butterfaß-Bahloul Trude , Dhooge Catharina , Bauer Sebastian , Kiss János , Paulussen Michael , Bonar Fiona , Ranft Andreas , Timmermann Beate , Rascon Jelena , Vieth Volker , Kanerva Jukka , Faldum Andreas , Hartmann Wolfgang , Hjorth Lars , Bhadri Vivek A. , Metzler Markus , Gelderblom Hans , Dirksen Uta
Published: December 2023

Details of statistical adaptive design and primary confirmatory analysis
Supplementary Figure S14 from Genomic Tumor Correlates of Clinical Outcomes Following Organ-Sparing Chemoradiation Therapy for Bladder Cancer
Authors: Kamran Sophia C. , Zhou Yuzhen , Otani Keisuke , Drumm Michael , Otani Yukako , Wu Shulin , Wu Chin-Lee , Feldman Adam S. , Wszolek Matthew , Lee Richard J. , Saylor Philip J. , Lennerz Jochen , Van Allen Eliezer , Willers Henning , Hong Theodore S. , Liu Yang , Davicioni Elai , Gibb Ewan A. , Shipley William U. , Mouw Kent W. , Efstathiou Jason A. , Miyamoto David T.
Published: December 2023

Hallmark DNA repair signature score by ERCC2 mutation status.
Supplementary Figure S1 from Zoledronic Acid Add-on Therapy for Standard-Risk Ewing Sarcoma Patients in the Ewing 2008R1 Trial
Authors: Koch Raphael , Haveman Lianne , Ladenstein Ruth , Brichard Benedicte , Jürgens Heribert , Cyprova Sona , van den Berg Henk , Hassenpflug Wolf , Raciborska Anna , Ek Torben , Baumhoer Daniel , Egerer Gerlinde , Kager Leo , Renard Marleen , Hauser Peter , Burdach Stefan , Bovee Judith V.M.G. , Hong Angela M. , Reichardt Peter , Kruseova Jarmila , Streitbürger Arne , Kühne Thomas , Kessler Torsten , Bernkopf Marie , Butterfaß-Bahloul Trude , Dhooge Catharina , Bauer Sebastian , Kiss János , Paulussen Michael , Bonar Fiona , Ranft Andreas , Timmermann Beate , Rascon Jelena , Vieth Volker , Kanerva Jukka , Faldum Andreas , Hartmann Wolfgang , Hjorth Lars , Bhadri Vivek A. , Metzler Markus , Gelderblom Hans , Dirksen Uta
Published: December 2023

Ewing 2008 Treatment Schema R1
Supplementary Figure S11 from Genomic Tumor Correlates of Clinical Outcomes Following Organ-Sparing Chemoradiation Therapy for Bladder Cancer
Authors: Kamran Sophia C. , Zhou Yuzhen , Otani Keisuke , Drumm Michael , Otani Yukako , Wu Shulin , Wu Chin-Lee , Feldman Adam S. , Wszolek Matthew , Lee Richard J. , Saylor Philip J. , Lennerz Jochen , Van Allen Eliezer , Willers Henning , Hong Theodore S. , Liu Yang , Davicioni Elai , Gibb Ewan A. , Shipley William U. , Mouw Kent W. , Efstathiou Jason A. , Miyamoto David T.
Published: December 2023

Distribution of ERCC2 mutations present in TCGA Bladder.
Supplementary Data S2 from Zoledronic Acid Add-on Therapy for Standard-Risk Ewing Sarcoma Patients in the Ewing 2008R1 Trial
Authors: Koch Raphael , Haveman Lianne , Ladenstein Ruth , Brichard Benedicte , Jürgens Heribert , Cyprova Sona , van den Berg Henk , Hassenpflug Wolf , Raciborska Anna , Ek Torben , Baumhoer Daniel , Egerer Gerlinde , Kager Leo , Renard Marleen , Hauser Peter , Burdach Stefan , Bovee Judith V.M.G. , Hong Angela M. , Reichardt Peter , Kruseova Jarmila , Streitbürger Arne , Kühne Thomas , Kessler Torsten , Bernkopf Marie , Butterfaß-Bahloul Trude , Dhooge Catharina , Bauer Sebastian , Kiss János , Paulussen Michael , Bonar Fiona , Ranft Andreas , Timmermann Beate , Rascon Jelena , Vieth Volker , Kanerva Jukka , Faldum Andreas , Hartmann Wolfgang , Hjorth Lars , Bhadri Vivek A. , Metzler Markus , Gelderblom Hans , Dirksen Uta
Published: December 2023

Criteria for the definition of the per protocol set
Supplementary Figure S10 from Genomic Tumor Correlates of Clinical Outcomes Following Organ-Sparing Chemoradiation Therapy for Bladder Cancer
Authors: Kamran Sophia C. , Zhou Yuzhen , Otani Keisuke , Drumm Michael , Otani Yukako , Wu Shulin , Wu Chin-Lee , Feldman Adam S. , Wszolek Matthew , Lee Richard J. , Saylor Philip J. , Lennerz Jochen , Van Allen Eliezer , Willers Henning , Hong Theodore S. , Liu Yang , Davicioni Elai , Gibb Ewan A. , Shipley William U. , Mouw Kent W. , Efstathiou Jason A. , Miyamoto David T.
Published: December 2023

Comparison of Patient Eligibility based on select DNA Damage Response (DDR) gene mutations for the Alliance A031701, RETAIN-BLADDER Trials and by mBI-EFS Favorable/Unfavorable Outcomes following TMT.
Supplementary Data S1 from Zoledronic Acid Add-on Therapy for Standard-Risk Ewing Sarcoma Patients in the Ewing 2008R1 Trial
Authors: Koch Raphael , Haveman Lianne , Ladenstein Ruth , Brichard Benedicte , Jürgens Heribert , Cyprova Sona , van den Berg Henk , Hassenpflug Wolf , Raciborska Anna , Ek Torben , Baumhoer Daniel , Egerer Gerlinde , Kager Leo , Renard Marleen , Hauser Peter , Burdach Stefan , Bovee Judith V.M.G. , Hong Angela M. , Reichardt Peter , Kruseova Jarmila , Streitbürger Arne , Kühne Thomas , Kessler Torsten , Bernkopf Marie , Butterfaß-Bahloul Trude , Dhooge Catharina , Bauer Sebastian , Kiss János , Paulussen Michael , Bonar Fiona , Ranft Andreas , Timmermann Beate , Rascon Jelena , Vieth Volker , Kanerva Jukka , Faldum Andreas , Hartmann Wolfgang , Hjorth Lars , Bhadri Vivek A. , Metzler Markus , Gelderblom Hans , Dirksen Uta
Published: December 2023

Key amendments
Supplementary Table S8 from Safety and Efficacy of NY-ESO-1 Antigen-Specific T-Cell Receptor Gene-Transduced T Lymphocytes in Patients with Synovial Sarcoma: A Phase I/II Clinical Trial
Authors: Kawai Akira , Ishihara Mikiya , Nakamura Tomoki , Kitano Shigehisa , Iwata Shintaro , Takada Kohichi , Emori Makoto , Kato Koji , Endo Makoto , Matsumoto Yoshihiro , Kakunaga Shigeki , Sato Eiichi , Miyahara Yoshihiro , Morino Kunihiko , Tanaka Shinya , Takahashi Shuichi , Matsuo Fujio , Matsumine Akihiko , Kageyama Shinichi , Ueda Takafumi
Published: December 2023

Summary of lymphocyte test values
Supplementary Table S5 from Comprehensive Single-Cell Immune Profiling Defines the Patient Multiple Myeloma Microenvironment Following Oncolytic Virus Therapy in a Phase Ib Trial
Authors: Nawrocki Steffan T. , Olea Julian , Villa Celi Claudia , Dadrastoussi Homa , Wu Kaijin , Tsao-Wei Denice , Colombo Anthony , Coffey Matt , Fernandez Hernandez Eduardo , Chen Xuelian , Nuovo Gerard J. , Carew Jennifer S. , Mohrbacher Ann F. , Fields Paul , Kuhn Peter , Siddiqi Imran , Merchant Akil , Kelly Kevin R.
Published: December 2023

Supplementary Table 5. Distance from tumor cell to immune cell for each patient (Figure 5E)
Supplementary Table S3 from Comprehensive Single-Cell Immune Profiling Defines the Patient Multiple Myeloma Microenvironment Following Oncolytic Virus Therapy in a Phase Ib Trial
Authors: Nawrocki Steffan T. , Olea Julian , Villa Celi Claudia , Dadrastoussi Homa , Wu Kaijin , Tsao-Wei Denice , Colombo Anthony , Coffey Matt , Fernandez Hernandez Eduardo , Chen Xuelian , Nuovo Gerard J. , Carew Jennifer S. , Mohrbacher Ann F. , Fields Paul , Kuhn Peter , Siddiqi Imran , Merchant Akil , Kelly Kevin R.
Published: December 2023

Supplementary Table 3. Toxicity summary excluding toxicities defined as unrelated to either bortezomib or pelareorep
Supplementary Table S2 from Comprehensive Single-Cell Immune Profiling Defines the Patient Multiple Myeloma Microenvironment Following Oncolytic Virus Therapy in a Phase Ib Trial
Authors: Nawrocki Steffan T. , Olea Julian , Villa Celi Claudia , Dadrastoussi Homa , Wu Kaijin , Tsao-Wei Denice , Colombo Anthony , Coffey Matt , Fernandez Hernandez Eduardo , Chen Xuelian , Nuovo Gerard J. , Carew Jennifer S. , Mohrbacher Ann F. , Fields Paul , Kuhn Peter , Siddiqi Imran , Merchant Akil , Kelly Kevin R.
Published: December 2023

Supplementary Table 2: Representativeness of Study Participants
Supplementary Table S3 from Safety and Efficacy of NY-ESO-1 Antigen-Specific T-Cell Receptor Gene-Transduced T Lymphocytes in Patients with Synovial Sarcoma: A Phase I/II Clinical Trial
Authors: Kawai Akira , Ishihara Mikiya , Nakamura Tomoki , Kitano Shigehisa , Iwata Shintaro , Takada Kohichi , Emori Makoto , Kato Koji , Endo Makoto , Matsumoto Yoshihiro , Kakunaga Shigeki , Sato Eiichi , Miyahara Yoshihiro , Morino Kunihiko , Tanaka Shinya , Takahashi Shuichi , Matsuo Fujio , Matsumine Akihiko , Kageyama Shinichi , Ueda Takafumi
Published: December 2023

Criteria of cytokine release syndrome severity
Supplementary Methods S1 from Comprehensive Single-Cell Immune Profiling Defines the Patient Multiple Myeloma Microenvironment Following Oncolytic Virus Therapy in a Phase Ib Trial
Authors: Nawrocki Steffan T. , Olea Julian , Villa Celi Claudia , Dadrastoussi Homa , Wu Kaijin , Tsao-Wei Denice , Colombo Anthony , Coffey Matt , Fernandez Hernandez Eduardo , Chen Xuelian , Nuovo Gerard J. , Carew Jennifer S. , Mohrbacher Ann F. , Fields Paul , Kuhn Peter , Siddiqi Imran , Merchant Akil , Kelly Kevin R.
Published: December 2023

Supplementary Methods
Supplementary Table S2 from Safety and Efficacy of NY-ESO-1 Antigen-Specific T-Cell Receptor Gene-Transduced T Lymphocytes in Patients with Synovial Sarcoma: A Phase I/II Clinical Trial
Authors: Kawai Akira , Ishihara Mikiya , Nakamura Tomoki , Kitano Shigehisa , Iwata Shintaro , Takada Kohichi , Emori Makoto , Kato Koji , Endo Makoto , Matsumoto Yoshihiro , Kakunaga Shigeki , Sato Eiichi , Miyahara Yoshihiro , Morino Kunihiko , Tanaka Shinya , Takahashi Shuichi , Matsuo Fujio , Matsumine Akihiko , Kageyama Shinichi , Ueda Takafumi
Published: December 2023

List of the exclusion criteria
Supplementary Figure S4 from Comprehensive Single-Cell Immune Profiling Defines the Patient Multiple Myeloma Microenvironment Following Oncolytic Virus Therapy in a Phase Ib Trial
Authors: Nawrocki Steffan T. , Olea Julian , Villa Celi Claudia , Dadrastoussi Homa , Wu Kaijin , Tsao-Wei Denice , Colombo Anthony , Coffey Matt , Fernandez Hernandez Eduardo , Chen Xuelian , Nuovo Gerard J. , Carew Jennifer S. , Mohrbacher Ann F. , Fields Paul , Kuhn Peter , Siddiqi Imran , Merchant Akil , Kelly Kevin R.
Published: December 2023

Supplementary Figure 4. Increased immune cell activity observed by imaging mass cytometry (IMC)
Supplementary Table S1 from Safety and Efficacy of NY-ESO-1 Antigen-Specific T-Cell Receptor Gene-Transduced T Lymphocytes in Patients with Synovial Sarcoma: A Phase I/II Clinical Trial
Authors: Kawai Akira , Ishihara Mikiya , Nakamura Tomoki , Kitano Shigehisa , Iwata Shintaro , Takada Kohichi , Emori Makoto , Kato Koji , Endo Makoto , Matsumoto Yoshihiro , Kakunaga Shigeki , Sato Eiichi , Miyahara Yoshihiro , Morino Kunihiko , Tanaka Shinya , Takahashi Shuichi , Matsuo Fujio , Matsumine Akihiko , Kageyama Shinichi , Ueda Takafumi
Published: December 2023

List of the inclusion criteria
Supplementary Figure S3 from Comprehensive Single-Cell Immune Profiling Defines the Patient Multiple Myeloma Microenvironment Following Oncolytic Virus Therapy in a Phase Ib Trial
Authors: Nawrocki Steffan T. , Olea Julian , Villa Celi Claudia , Dadrastoussi Homa , Wu Kaijin , Tsao-Wei Denice , Colombo Anthony , Coffey Matt , Fernandez Hernandez Eduardo , Chen Xuelian , Nuovo Gerard J. , Carew Jennifer S. , Mohrbacher Ann F. , Fields Paul , Kuhn Peter , Siddiqi Imran , Merchant Akil , Kelly Kevin R.
Published: December 2023

Supplementary Figure 3. Imaging mass cytometry (IMC) staining overview
Supplementary Table S7 from SNP of Aromatase Predict Long-term Survival and Aromatase Inhibitor Toxicity in Patients with Early Breast Cancer: A Biomarker Analysis of the GIM4 and GIM5 Trials
Authors: Conte Benedetta , Boni Luca , Bisagni Giancarlo , Durando Antonio , Sanna Giovanni , Gori Stefania , Garrone Ornella , Tamberi Stefano , De Placido Sabino , Schettini Francesco , Pazzola Antonio , Ponzone Riccardo , Montemurro Filippo , Lunardi Gianluigi , Notaro Rosario , De Angioletti Maria , Turletti Anna , Mansutti Mauro , Puglisi Fabio , Frassoldati Antonio , Porpiglia Mauro , Fabi Alessandra , Generali Daniele , Scognamiglio Giovanni , Rossi Maura , Brasó-Maristany Fara , Prat Aleix , Cardinali Barbara , Piccioli Patrizia , Serra Martina , Lastraioli Sonia , Bighin Claudia , Poggio Francesca , Lambertini Matteo , Del Mastro Lucia
Published: December 2023

Patients’ characteristics SNP rs727479
Supplementary Table S3 from Phase II Trial of Nivolumab in Metastatic Rare Cancer with dMMR or MSI-H and Relation with Immune Phenotypic Analysis (the ROCK Trial)
Authors: Okuma Hitomi S. , Watanabe Keisuke , Tsuchihashi Kenji , Machida Ryunosuke , Sadachi Ryo , Hirakawa Akihiro , Ariyama Hiroshi , Kanai Masashi , Kamikura Masahisa , Anjo Kenta , Hiramitsu Akari , Sekine Shigeki , Okita Natsuko , Mano Hiroyuki , Nishikawa Hiroyoshi , Nakamura Kenichi , Yonemori Kan
Published: December 2023

Supplementary Table S3: Subgroup analysis of the response rate
Supplementary Table S2 from Phase II Trial of Nivolumab in Metastatic Rare Cancer with dMMR or MSI-H and Relation with Immune Phenotypic Analysis (the ROCK Trial)
Authors: Okuma Hitomi S. , Watanabe Keisuke , Tsuchihashi Kenji , Machida Ryunosuke , Sadachi Ryo , Hirakawa Akihiro , Ariyama Hiroshi , Kanai Masashi , Kamikura Masahisa , Anjo Kenta , Hiramitsu Akari , Sekine Shigeki , Okita Natsuko , Mano Hiroyuki , Nishikawa Hiroyoshi , Nakamura Kenichi , Yonemori Kan
Published: December 2023

Supplementary Table 2: Response rate assessed by independent central review.
Supplementary Table S2 from SNP of Aromatase Predict Long-term Survival and Aromatase Inhibitor Toxicity in Patients with Early Breast Cancer: A Biomarker Analysis of the GIM4 and GIM5 Trials
Authors: Conte Benedetta , Boni Luca , Bisagni Giancarlo , Durando Antonio , Sanna Giovanni , Gori Stefania , Garrone Ornella , Tamberi Stefano , De Placido Sabino , Schettini Francesco , Pazzola Antonio , Ponzone Riccardo , Montemurro Filippo , Lunardi Gianluigi , Notaro Rosario , De Angioletti Maria , Turletti Anna , Mansutti Mauro , Puglisi Fabio , Frassoldati Antonio , Porpiglia Mauro , Fabi Alessandra , Generali Daniele , Scognamiglio Giovanni , Rossi Maura , Brasó-Maristany Fara , Prat Aleix , Cardinali Barbara , Piccioli Patrizia , Serra Martina , Lastraioli Sonia , Bighin Claudia , Poggio Francesca , Lambertini Matteo , Del Mastro Lucia
Published: December 2023

Patients’ characteristics main and SNPs cohorts GIM4
Supplementary Table S15 from SNP of Aromatase Predict Long-term Survival and Aromatase Inhibitor Toxicity in Patients with Early Breast Cancer: A Biomarker Analysis of the GIM4 and GIM5 Trials
Authors: Conte Benedetta , Boni Luca , Bisagni Giancarlo , Durando Antonio , Sanna Giovanni , Gori Stefania , Garrone Ornella , Tamberi Stefano , De Placido Sabino , Schettini Francesco , Pazzola Antonio , Ponzone Riccardo , Montemurro Filippo , Lunardi Gianluigi , Notaro Rosario , De Angioletti Maria , Turletti Anna , Mansutti Mauro , Puglisi Fabio , Frassoldati Antonio , Porpiglia Mauro , Fabi Alessandra , Generali Daniele , Scognamiglio Giovanni , Rossi Maura , Brasó-Maristany Fara , Prat Aleix , Cardinali Barbara , Piccioli Patrizia , Serra Martina , Lastraioli Sonia , Bighin Claudia , Poggio Francesca , Lambertini Matteo , Del Mastro Lucia
Published: December 2023

Univariate analyses for sekeltal and cardiovascular events- alternative definition
Supplementary Figure S2 from Phase II Trial of Nivolumab in Metastatic Rare Cancer with dMMR or MSI-H and Relation with Immune Phenotypic Analysis (the ROCK Trial)
Authors: Okuma Hitomi S. , Watanabe Keisuke , Tsuchihashi Kenji , Machida Ryunosuke , Sadachi Ryo , Hirakawa Akihiro , Ariyama Hiroshi , Kanai Masashi , Kamikura Masahisa , Anjo Kenta , Hiramitsu Akari , Sekine Shigeki , Okita Natsuko , Mano Hiroyuki , Nishikawa Hiroyoshi , Nakamura Kenichi , Yonemori Kan
Published: December 2023

Supplementary Figure S2: Disposition of Patients in the Study
Supplementary Table S14 from SNP of Aromatase Predict Long-term Survival and Aromatase Inhibitor Toxicity in Patients with Early Breast Cancer: A Biomarker Analysis of the GIM4 and GIM5 Trials
Authors: Conte Benedetta , Boni Luca , Bisagni Giancarlo , Durando Antonio , Sanna Giovanni , Gori Stefania , Garrone Ornella , Tamberi Stefano , De Placido Sabino , Schettini Francesco , Pazzola Antonio , Ponzone Riccardo , Montemurro Filippo , Lunardi Gianluigi , Notaro Rosario , De Angioletti Maria , Turletti Anna , Mansutti Mauro , Puglisi Fabio , Frassoldati Antonio , Porpiglia Mauro , Fabi Alessandra , Generali Daniele , Scognamiglio Giovanni , Rossi Maura , Brasó-Maristany Fara , Prat Aleix , Cardinali Barbara , Piccioli Patrizia , Serra Martina , Lastraioli Sonia , Bighin Claudia , Poggio Francesca , Lambertini Matteo , Del Mastro Lucia
Published: December 2023

Multivariable Fine-Gray model for cardiovascular events
Supplementary Table S11 from SNP of Aromatase Predict Long-term Survival and Aromatase Inhibitor Toxicity in Patients with Early Breast Cancer: A Biomarker Analysis of the GIM4 and GIM5 Trials
Authors: Conte Benedetta , Boni Luca , Bisagni Giancarlo , Durando Antonio , Sanna Giovanni , Gori Stefania , Garrone Ornella , Tamberi Stefano , De Placido Sabino , Schettini Francesco , Pazzola Antonio , Ponzone Riccardo , Montemurro Filippo , Lunardi Gianluigi , Notaro Rosario , De Angioletti Maria , Turletti Anna , Mansutti Mauro , Puglisi Fabio , Frassoldati Antonio , Porpiglia Mauro , Fabi Alessandra , Generali Daniele , Scognamiglio Giovanni , Rossi Maura , Brasó-Maristany Fara , Prat Aleix , Cardinali Barbara , Piccioli Patrizia , Serra Martina , Lastraioli Sonia , Bighin Claudia , Poggio Francesca , Lambertini Matteo , Del Mastro Lucia
Published: December 2023

Univariate analyses for DFS, OS and BC metastases according to SNPs-based groups
Supplementary Figure S3 from SNP of Aromatase Predict Long-term Survival and Aromatase Inhibitor Toxicity in Patients with Early Breast Cancer: A Biomarker Analysis of the GIM4 and GIM5 Trials
Authors: Conte Benedetta , Boni Luca , Bisagni Giancarlo , Durando Antonio , Sanna Giovanni , Gori Stefania , Garrone Ornella , Tamberi Stefano , De Placido Sabino , Schettini Francesco , Pazzola Antonio , Ponzone Riccardo , Montemurro Filippo , Lunardi Gianluigi , Notaro Rosario , De Angioletti Maria , Turletti Anna , Mansutti Mauro , Puglisi Fabio , Frassoldati Antonio , Porpiglia Mauro , Fabi Alessandra , Generali Daniele , Scognamiglio Giovanni , Rossi Maura , Brasó-Maristany Fara , Prat Aleix , Cardinali Barbara , Piccioli Patrizia , Serra Martina , Lastraioli Sonia , Bighin Claudia , Poggio Francesca , Lambertini Matteo , Del Mastro Lucia
Published: December 2023

Figure S3. Frequencies of different SNPs genotypes across SNPs-based prognostic groups
Supplementary Figure S2 from SNP of Aromatase Predict Long-term Survival and Aromatase Inhibitor Toxicity in Patients with Early Breast Cancer: A Biomarker Analysis of the GIM4 and GIM5 Trials
Authors: Conte Benedetta , Boni Luca , Bisagni Giancarlo , Durando Antonio , Sanna Giovanni , Gori Stefania , Garrone Ornella , Tamberi Stefano , De Placido Sabino , Schettini Francesco , Pazzola Antonio , Ponzone Riccardo , Montemurro Filippo , Lunardi Gianluigi , Notaro Rosario , De Angioletti Maria , Turletti Anna , Mansutti Mauro , Puglisi Fabio , Frassoldati Antonio , Porpiglia Mauro , Fabi Alessandra , Generali Daniele , Scognamiglio Giovanni , Rossi Maura , Brasó-Maristany Fara , Prat Aleix , Cardinali Barbara , Piccioli Patrizia , Serra Martina , Lastraioli Sonia , Bighin Claudia , Poggio Francesca , Lambertini Matteo , Del Mastro Lucia
Published: December 2023

Figure S2. Linkage disequilibrium plot (a) and haplotypes frequencies (b) of the four analyzed SNPs of CYP19 in the Caucasian population
Supplementary Figure S7 from Hyper-Dependence on NHEJ Enables Synergy between DNA-PK Inhibitors and Low-Dose Doxorubicin in Leiomyosarcoma
Authors: Marino-Enriquez Adrian , Novotny Jan Philipp , Gulhan Doga C. , Klooster Isabella , Tran Antuan V. , Kasbo Macy , Lundberg Meijun Z. , Ou Wen-Bin , Tao Derrick L. , Pilco-Janeta Daniel F. , Mao Victor Y. , Zenke Frank T. , Leeper Brittaney A. , Gokhale Prafulla C. , Cowley Glenn S. , Baker Laurence H. , Ballman Karla V. , Root David E. , Albers Joachim , Park Peter J. , George Suzanne , Fletcher Jonathan A.
Published: December 2023

Supplementary Figure S7
Computationally assisted analysis of cell culture confluence of representative cell culture images of LMS04 cultures untreated or treated with 2nM doxorubicin, 400nM peposertib, or the combination of both. Segmentation was performed with the generalist deep learning-based segmentation algorithm Cellpose v0.6 (34). Multiple segmentation runs with increasing cell size diameter parameter (30-120px) were required to capture all cells.
Supplementary Figure S1 from SNP of Aromatase Predict Long-term Survival and Aromatase Inhibitor Toxicity in Patients with Early Breast Cancer: A Biomarker Analysis of the GIM4 and GIM5 Trials
Authors: Conte Benedetta , Boni Luca , Bisagni Giancarlo , Durando Antonio , Sanna Giovanni , Gori Stefania , Garrone Ornella , Tamberi Stefano , De Placido Sabino , Schettini Francesco , Pazzola Antonio , Ponzone Riccardo , Montemurro Filippo , Lunardi Gianluigi , Notaro Rosario , De Angioletti Maria , Turletti Anna , Mansutti Mauro , Puglisi Fabio , Frassoldati Antonio , Porpiglia Mauro , Fabi Alessandra , Generali Daniele , Scognamiglio Giovanni , Rossi Maura , Brasó-Maristany Fara , Prat Aleix , Cardinali Barbara , Piccioli Patrizia , Serra Martina , Lastraioli Sonia , Bighin Claudia , Poggio Francesca , Lambertini Matteo , Del Mastro Lucia
Published: December 2023

Figure S1: CONSORT diagram of all patients included from the GIM4 and GIM5 trials
Supplementary Figure S5 from Hyper-Dependence on NHEJ Enables Synergy between DNA-PK Inhibitors and Low-Dose Doxorubicin in Leiomyosarcoma
Authors: Marino-Enriquez Adrian , Novotny Jan Philipp , Gulhan Doga C. , Klooster Isabella , Tran Antuan V. , Kasbo Macy , Lundberg Meijun Z. , Ou Wen-Bin , Tao Derrick L. , Pilco-Janeta Daniel F. , Mao Victor Y. , Zenke Frank T. , Leeper Brittaney A. , Gokhale Prafulla C. , Cowley Glenn S. , Baker Laurence H. , Ballman Karla V. , Root David E. , Albers Joachim , Park Peter J. , George Suzanne , Fletcher Jonathan A.
Published: December 2023

Supplementary Figure S5:
Biochemical effects of increasing doses of doxorubicin in LMS04 cells, starting at unconventionally low
doses.
Table S5 from Lenvatinib, Toripalimab plus FOLFOX Chemotherapy in Hepatocellular Carcinoma Patients with Extrahepatic Metastasis: A Biomolecular Exploratory, Phase II Trial (LTSC)
Authors: He MinKe , Huang YeXing , Du ZeFeng , Lai ZhiCheng , Ouyang Hanyue , Shen JingXian , Wen DongSheng , Li QiJiong , Zhang YaoJun , Wei Wei , Chen MinShan , Xu Li , Kan Anna , Shi Ming
Published: December 2023

Differential expression genes across clusters in the training cohort.
Supplementary Figure S2 from Hyper-Dependence on NHEJ Enables Synergy between DNA-PK Inhibitors and Low-Dose Doxorubicin in Leiomyosarcoma
Authors: Marino-Enriquez Adrian , Novotny Jan Philipp , Gulhan Doga C. , Klooster Isabella , Tran Antuan V. , Kasbo Macy , Lundberg Meijun Z. , Ou Wen-Bin , Tao Derrick L. , Pilco-Janeta Daniel F. , Mao Victor Y. , Zenke Frank T. , Leeper Brittaney A. , Gokhale Prafulla C. , Cowley Glenn S. , Baker Laurence H. , Ballman Karla V. , Root David E. , Albers Joachim , Park Peter J. , George Suzanne , Fletcher Jonathan A.
Published: December 2023

Supplementary Figure S2:
A. Counts of small deletions (<30kb) are compared in Sig3+ and Sig3- LMS tumors (analyzed by
OncoPanel v3 and v 3.1, n=166). B. Counts of small deletions (<30kb) are significantly higher in tumors
with deleterious alterations in POLH, POLD1, FANCM or XRCC1, all of which are implicated in DNA
double strand break repair during different phases of the cell cycle (**** = p < 0.0001; n.s.= not
significant)
Supplementary Figure S11 from Hyper-Dependence on NHEJ Enables Synergy between DNA-PK Inhibitors and Low-Dose Doxorubicin in Leiomyosarcoma
Authors: Marino-Enriquez Adrian , Novotny Jan Philipp , Gulhan Doga C. , Klooster Isabella , Tran Antuan V. , Kasbo Macy , Lundberg Meijun Z. , Ou Wen-Bin , Tao Derrick L. , Pilco-Janeta Daniel F. , Mao Victor Y. , Zenke Frank T. , Leeper Brittaney A. , Gokhale Prafulla C. , Cowley Glenn S. , Baker Laurence H. , Ballman Karla V. , Root David E. , Albers Joachim , Park Peter J. , George Suzanne , Fletcher Jonathan A.
Published: December 2023

Supplementary Figure S11:
A-G. Relative body weight change of mice in cohorts treated with low-dose doxorubicin or pegylated
liposomal doxorubicin, peposertib, and the combination of both, in the drug efficacy studies illustrated in
Figure 5 and Supplementary Figure S9. H. Experimental design and drug doses utilized
Supplementary Figure S10 from Hyper-Dependence on NHEJ Enables Synergy between DNA-PK Inhibitors and Low-Dose Doxorubicin in Leiomyosarcoma
Authors: Marino-Enriquez Adrian , Novotny Jan Philipp , Gulhan Doga C. , Klooster Isabella , Tran Antuan V. , Kasbo Macy , Lundberg Meijun Z. , Ou Wen-Bin , Tao Derrick L. , Pilco-Janeta Daniel F. , Mao Victor Y. , Zenke Frank T. , Leeper Brittaney A. , Gokhale Prafulla C. , Cowley Glenn S. , Baker Laurence H. , Ballman Karla V. , Root David E. , Albers Joachim , Park Peter J. , George Suzanne , Fletcher Jonathan A.
Published: December 2023

Supplementary Figure S10:
Effect of peposertib (100 mg/kg bid), low-dose pegylated liposomal doxorubicin (3 mg/kg qw) and
combination on additional LMS PDX. A. CTG-1182. B. CTG-1005. C. CTG-1079.
Figure S5 from Lenvatinib, Toripalimab plus FOLFOX Chemotherapy in Hepatocellular Carcinoma Patients with Extrahepatic Metastasis: A Biomolecular Exploratory, Phase II Trial (LTSC)
Authors: He MinKe , Huang YeXing , Du ZeFeng , Lai ZhiCheng , Ouyang Hanyue , Shen JingXian , Wen DongSheng , Li QiJiong , Zhang YaoJun , Wei Wei , Chen MinShan , Xu Li , Kan Anna , Shi Ming
Published: December 2023

Representative images of patient four.
Supplementary Figure S7 from CD24hiCD27+ Bregs within Metastatic Lymph Nodes Promote Multidrug Resistance in Breast Cancer
Authors: Huang Huanhuan , Yao Yao , Shen Lesang , Jiang Jingxin , Zhang Ting , Xiong Jia , Li Jiaxin , Sun Shanshan , Zheng Siwei , Jia Fang , Zhou Jun , Yu Xiuyan , Chen Wuzhen , Shen Jun , Xia Wenjie , Shao Xuan , Wang Qingqing , Huang Jian , Ni Chao
Published: December 2023

Fig. S7. CD24hiCD27+ Bregs induce drug resistance by activating NF-kB and STAT3 signalling in BC cells with effect stronger when in a direct contact.
Figure S12 from Lenvatinib, Toripalimab plus FOLFOX Chemotherapy in Hepatocellular Carcinoma Patients with Extrahepatic Metastasis: A Biomolecular Exploratory, Phase II Trial (LTSC)
Authors: He MinKe , Huang YeXing , Du ZeFeng , Lai ZhiCheng , Ouyang Hanyue , Shen JingXian , Wen DongSheng , Li QiJiong , Zhang YaoJun , Wei Wei , Chen MinShan , Xu Li , Kan Anna , Shi Ming
Published: December 2023

Integration analysis of immune-related signatures with malignant hepatocytes.
Figure S11 from Lenvatinib, Toripalimab plus FOLFOX Chemotherapy in Hepatocellular Carcinoma Patients with Extrahepatic Metastasis: A Biomolecular Exploratory, Phase II Trial (LTSC)
Authors: He MinKe , Huang YeXing , Du ZeFeng , Lai ZhiCheng , Ouyang Hanyue , Shen JingXian , Wen DongSheng , Li QiJiong , Zhang YaoJun , Wei Wei , Chen MinShan , Xu Li , Kan Anna , Shi Ming
Published: December 2023

Integration analysis of malignant hepatocytes.