bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figure S6 G-K from Drugging MYCN Oncogenic Signaling through the MYCN-PA2G4 Binding Interface
Authors: Koach Jessica , Holien Jessica K. , Massudi Hassina , Carter Daniel R. , Ciampa Olivia C. , Herath Mika , Lim Taylor , Seneviratne Janith A. , Milazzo Giorgio , Murray Jayne E. , McCarroll Joshua A. , Liu Bing , Mayoh Chelsea , Keenan Bryce , Stevenson Brendan W. , Gorman Michael A. , Bell Jessica L. , Doughty Larissa , Hüttelmaier Stefan , Oberthuer Andre , Fischer Matthias , Gifford Andrew J. , Liu Tao , Zhang Xiaoling , Zhu Shizhen , Gustafson W. Clay , Haber Michelle , Norris Murray D. , Fletcher Jamie I. , Perini Giovanni , Parker Michael W. , Cheung Belamy B. , Marshall Glenn M.
Published: April 2023

Supplementary Figure S6 G-K G, Overall patient survival using Kaplan-Meier survival probability plots from the Cologne data set (http://r2.amc.nl) for PA2G4 mRNA expression subdivided around the median PA2G4 expression level among 477 neuroblastoma patients. H, Kaplan-Meier plot for event-free survival of 649 neuroblastoma patients from the kocak dataset (R2 microarray analysis and visualization platform, http://r2.amc.nl) I, Real-time PCR mRNA expression of PA2G4 among 40 neuroblastoma patient tumors treated at Sydney Children's Hospital, subdivided by MYCN amplification status. J, Multivariate event-free survival analysis using cox regression modelling. The p-values were obtained from the cox-regression analysis. K, Incidence of PA2G4 amplification among a range of different human cancer types within The Cancer Genome Atlas (TCGA). Results were generated using cBioportal for Cancer Genomics (https://cancergenome.nih.gov/). NEPC, neuroendocrine prostate cancer; CS, carcinosarcoma.
Figure S2 from SLC43A3 Is a Biomarker of Sensitivity to the Telomeric DNA Damage Mediator 6-Thio-2′-Deoxyguanosine
Authors: Mender Ilgen , Batten Kimberly , Peyton Michael , Vemula Aishwarya , Cornelius Crystal , Girard Luc , Gao Boning , Minna John D. , Shay Jerry W.
Published: April 2023

Supplementary Data 2
Figure S1 from SLC43A3 Is a Biomarker of Sensitivity to the Telomeric DNA Damage Mediator 6-Thio-2′-Deoxyguanosine
Authors: Mender Ilgen , Batten Kimberly , Peyton Michael , Vemula Aishwarya , Cornelius Crystal , Girard Luc , Gao Boning , Minna John D. , Shay Jerry W.
Published: April 2023

Supplementary Data 1
Supplementary Figure S5 F-H from Drugging MYCN Oncogenic Signaling through the MYCN-PA2G4 Binding Interface
Authors: Koach Jessica , Holien Jessica K. , Massudi Hassina , Carter Daniel R. , Ciampa Olivia C. , Herath Mika , Lim Taylor , Seneviratne Janith A. , Milazzo Giorgio , Murray Jayne E. , McCarroll Joshua A. , Liu Bing , Mayoh Chelsea , Keenan Bryce , Stevenson Brendan W. , Gorman Michael A. , Bell Jessica L. , Doughty Larissa , Hüttelmaier Stefan , Oberthuer Andre , Fischer Matthias , Gifford Andrew J. , Liu Tao , Zhang Xiaoling , Zhu Shizhen , Gustafson W. Clay , Haber Michelle , Norris Murray D. , Fletcher Jamie I. , Perini Giovanni , Parker Michael W. , Cheung Belamy B. , Marshall Glenn M.
Published: April 2023

Supplementary Figure S5 F-H F), at 72 hours post-transfection of EV or a PA2G4 expression vector. G, Cell viability measured by the Alamar Blue assay and immunoblot analyses using an antibody identifying MYC-tagged PA2G4-p42 protein expression in Kelly and SH-SY5Y cells transfected with EV or the MYC-tagged PA2G4-p42 expression vector at 48 and 72 hours post-transfection. Vinculin was used as loading control. H, Colony formation in vitro by Kelly and SH-SY5Y cells following transfection with either EV or MYC-tagged PA2G4-p42.
Supplementary Figure S5 A-E from Drugging MYCN Oncogenic Signaling through the MYCN-PA2G4 Binding Interface
Authors: Koach Jessica , Holien Jessica K. , Massudi Hassina , Carter Daniel R. , Ciampa Olivia C. , Herath Mika , Lim Taylor , Seneviratne Janith A. , Milazzo Giorgio , Murray Jayne E. , McCarroll Joshua A. , Liu Bing , Mayoh Chelsea , Keenan Bryce , Stevenson Brendan W. , Gorman Michael A. , Bell Jessica L. , Doughty Larissa , Hüttelmaier Stefan , Oberthuer Andre , Fischer Matthias , Gifford Andrew J. , Liu Tao , Zhang Xiaoling , Zhu Shizhen , Gustafson W. Clay , Haber Michelle , Norris Murray D. , Fletcher Jamie I. , Perini Giovanni , Parker Michael W. , Cheung Belamy B. , Marshall Glenn M.
Published: April 2023

Supplementary Figure S5. PA2G4 expression enhances the malignant neuroblastoma phenotype in vitro. A, Neurite formation in SH-SY5Y and BE(2)-C cells transfected with PA2G4 siRNA and then treated with 2 µM 13-cis-retinoic acid. B, Immunoblots assessing PA2G4-p48 and PA2G4-p42 protein expression levels using an anti-PA2G4 antibody against whole cell protein lysates from a panel of neuroblastoma and non-malignant myofibroblast cell lines. C, Immunoblots assessing the effect of PA2G4-p48 knockdown on PA2G4 and MYCN protein levels in BE(2)-C and CHP-134 cells. D, Immunoblots confirming transfection of PA2G4-p48 siRNA and MYCN expression plasmid DNA for 72 hours. E and F Cell proliferation measured by BrdU incorporation (E), and, cell viability measured by the Alamar Blue assay.
Supplementary Figure S4 A-E from Drugging MYCN Oncogenic Signaling through the MYCN-PA2G4 Binding Interface
Authors: Koach Jessica , Holien Jessica K. , Massudi Hassina , Carter Daniel R. , Ciampa Olivia C. , Herath Mika , Lim Taylor , Seneviratne Janith A. , Milazzo Giorgio , Murray Jayne E. , McCarroll Joshua A. , Liu Bing , Mayoh Chelsea , Keenan Bryce , Stevenson Brendan W. , Gorman Michael A. , Bell Jessica L. , Doughty Larissa , Hüttelmaier Stefan , Oberthuer Andre , Fischer Matthias , Gifford Andrew J. , Liu Tao , Zhang Xiaoling , Zhu Shizhen , Gustafson W. Clay , Haber Michelle , Norris Murray D. , Fletcher Jamie I. , Perini Giovanni , Parker Michael W. , Cheung Belamy B. , Marshall Glenn M.
Published: April 2023

Supplementary Figure S4. Characterization of the PA2G4-MYCN protein-protein interface. A, BE(2)-C cells were transiently transfected with EV, wildtype PA2G4 or 6 different PA2G4 point mutants for 48 hours, then treated with 100 µg/µl Cycloheximide (CHX) for up to 60 minutes, followed by immunoblot analysis for MYCN protein half-life. B, Differential Scanning Fluorimetry (DSF) showed both the seven amino acid (DHKALST, aa248-254) and large peptide (GGDHKALSTGEDTL, aa246-259) MYCN oligopeptides, along with the MYCN oligopeptide shown not to bind via SPR (DHAALAT) changed the melting temperature of the PA2G4 protein, relative to baseline (i.e. 0mM), in a dose-response manner. Shown are the means of 3 independent experiments {plus minus} SEM. C, An example of the raw data for DHKALST, with the shift to the left correlating to an increase in concentration. D, Raw SPR data for PA2G4 triple mutant (R271A, R272A and S47A) and single mutants (S47A and R272A). Also, raw SPR data for MYCN oligopeptide mutants (DHAALST, DHAALAT and DHKALAT). For the mutants and triple mutations, no binding was observed, thus analysis could not be conducted and is not shown. E, Root Mead Squared Deviation (RMSD) of the peptide over the time of the simulation. After the first 100 frames the peptide is relatively stable. Analysis was only conducted after this time.
Supplementary Figure 6 from CTGF Mediates Tumor–Stroma Interactions between Hepatoma Cells and Hepatic Stellate Cells to Accelerate HCC Progression
Authors: Makino Yuki , Hikita Hayato , Kodama Takahiro , Shigekawa Minoru , Yamada Ryoko , Sakamori Ryotaro , Eguchi Hidetoshi , Morii Eiichi , Yokoi Hideki , Mukoyama Masashi , Hiroshi Suemizu , Tatsumi Tomohide , Takehara Tetsuo
Published: April 2023

Supplementary Fig. 6. Protein expression of p-STAT-3 in liver cancer is decreased by the hepatocyte-specific CTGF knockout in KrasG12D mice. Protein expression of p-STAT-3 in liver tumors in KrasG12D CTGF+/+, KrasG12D CTGF+/- and KrasG12D CTGF-/- mice at 8 months of age.
Supplementary Figure S2A-C from Drugging MYCN Oncogenic Signaling through the MYCN-PA2G4 Binding Interface
Authors: Koach Jessica , Holien Jessica K. , Massudi Hassina , Carter Daniel R. , Ciampa Olivia C. , Herath Mika , Lim Taylor , Seneviratne Janith A. , Milazzo Giorgio , Murray Jayne E. , McCarroll Joshua A. , Liu Bing , Mayoh Chelsea , Keenan Bryce , Stevenson Brendan W. , Gorman Michael A. , Bell Jessica L. , Doughty Larissa , Hüttelmaier Stefan , Oberthuer Andre , Fischer Matthias , Gifford Andrew J. , Liu Tao , Zhang Xiaoling , Zhu Shizhen , Gustafson W. Clay , Haber Michelle , Norris Murray D. , Fletcher Jamie I. , Perini Giovanni , Parker Michael W. , Cheung Belamy B. , Marshall Glenn M.
Published: April 2023

Supplementary Figure S2. PA2G4 increases MYCN protein stability. A and B, Representative immunoblots from cycloheximide (CHX) chase assays measuring the half-life of MYCN protein after PA2G4 knockdown (A) or overexpression (B) in BE(2)-C and Kelly cells for 48 hours. Cells were then treated with 100 µg/µl CHX for up to 60 minutes followed by immunoblotting. C, Co-IP of total protein from BE(2)-C cells using IgG, anti-MYCN, anti-PA2G4 antibodies, followed by immunoblotting with anti-MYCN, anti-PA2G4, anti-AURKA, anti-Fbxw7 or anti-vinculin antibodies.
Supplementary Figure 5 from CTGF Mediates Tumor–Stroma Interactions between Hepatoma Cells and Hepatic Stellate Cells to Accelerate HCC Progression
Authors: Makino Yuki , Hikita Hayato , Kodama Takahiro , Shigekawa Minoru , Yamada Ryoko , Sakamori Ryotaro , Eguchi Hidetoshi , Morii Eiichi , Yokoi Hideki , Mukoyama Masashi , Hiroshi Suemizu , Tatsumi Tomohide , Takehara Tetsuo
Published: April 2023

Supplementary Fig. 5. Inhibition of IL-6-STAT-3 pathway attenuates the growth-promoting effect by the co-existence of LX-2 cells. For co-culture experiments, HepG2 cells were co-cultured with the same number of LX-2 cells using Transwell. Total protein was collected 24 hours after the start of incubation. Cell growth was evaluated by a WST-8 assay at the indicated time points (N = 4). (A) Protein expression and growth of HepG2 cells co-cultured with LX-2 cells with or without 1.0 μg/mL anti-IL-6 neutralizing antibody treatment. (B) Protein expression and growth of HepG2 cells transfected with STAT-3 siRNA or control siRNA under monoculture or co-cultured with LX-2 cells. HepG2 cells were re-plated 72 hours after siRNA transfection and incubated under monoculture or co-culture with LX-2 cells. Plots with whiskers indicate mean values {plus minus} standard deviations. *p < 0.05 vs the control.
Supplementary Figure S1 F-I from Drugging MYCN Oncogenic Signaling through the MYCN-PA2G4 Binding Interface
Authors: Koach Jessica , Holien Jessica K. , Massudi Hassina , Carter Daniel R. , Ciampa Olivia C. , Herath Mika , Lim Taylor , Seneviratne Janith A. , Milazzo Giorgio , Murray Jayne E. , McCarroll Joshua A. , Liu Bing , Mayoh Chelsea , Keenan Bryce , Stevenson Brendan W. , Gorman Michael A. , Bell Jessica L. , Doughty Larissa , Hüttelmaier Stefan , Oberthuer Andre , Fischer Matthias , Gifford Andrew J. , Liu Tao , Zhang Xiaoling , Zhu Shizhen , Gustafson W. Clay , Haber Michelle , Norris Murray D. , Fletcher Jamie I. , Perini Giovanni , Parker Michael W. , Cheung Belamy B. , Marshall Glenn M.
Published: April 2023

Supplementary Figure S1. F, Confocal microscopy of SHEP Tet21N cells using anti-PA2G4 (red) and anti-MYCN (green) antibodies. G, Immunoblot analysis of cytoplasmic and nuclear fractions from BE(2)-C and Kelly human neuroblastoma cell lines with antibodies recognizing PA2G4 and MYCN, or GAPDH and topoisomerase as loading controls. H, Confocal microscopy of neuroblastoma (BE(2)-C and Kelly) cells using anti-PA2G4 (red) and anti-MYCN (green) antibodies. Alexafluor 555 anti-rabbit (to detect PA2G4) and Alexafluor 488 anti-mouse (to detect MYCN) were used as the secondary antibodies. I, Real-time PCR mRNA expression of MYCN and PA2G4 in ganglia from homozygote TH-MYCN+/+ mice, compared to wild type littermate control mice, obtained at different postnatal age (weeks).
Supplementary Figure 1 from CTGF Mediates Tumor–Stroma Interactions between Hepatoma Cells and Hepatic Stellate Cells to Accelerate HCC Progression
Authors: Makino Yuki , Hikita Hayato , Kodama Takahiro , Shigekawa Minoru , Yamada Ryoko , Sakamori Ryotaro , Eguchi Hidetoshi , Morii Eiichi , Yokoi Hideki , Mukoyama Masashi , Hiroshi Suemizu , Tatsumi Tomohide , Takehara Tetsuo
Published: April 2023

Supplementary Fig. 1. CTGF is mainly derived from tumor cells in liver tumors. (A) Immunohistochemistry for AFP and CTGF in serial sections of human HCC tissues. (B) Double immunofluorescence staining for CTGF and α-SMA in human HCC tissues. (C) Immunohistochemistry for AFP and CTGF in serial sections of liver tumors from 8-month-old KrasG12D mice. (D) Double immunofluorescence staining for CTGF and α-SMA in 9-month-old KrasG12D mice. Arrowheads of the same color indicate the identical cells in serial sections (A and C).
Supplemental Table S3. from Ablation of the Brca1–Palb2 Interaction Phenocopies Fanconi Anemia in Mice
Authors: Park Dongju , Bergin Stephen M. , Jones Dan , Ru Peng , Koivisto Christopher S. , Jeon Young-Jun , Sizemore Gina M. , Kladney Raleigh D. , Hadjis Ashley , Shakya Reena , Ludwig Thomas
Published: April 2023

Notch1 mutations detected by exome sequencing from Brca1L1363P/ L1363P; p53-/- thymic tumor
Supplemental Table S2. from Ablation of the Brca1–Palb2 Interaction Phenocopies Fanconi Anemia in Mice
Authors: Park Dongju , Bergin Stephen M. , Jones Dan , Ru Peng , Koivisto Christopher S. , Jeon Young-Jun , Sizemore Gina M. , Kladney Raleigh D. , Hadjis Ashley , Shakya Reena , Ludwig Thomas
Published: April 2023

Notch1 mutations detected by exome sequencing from Brca1L1363P/ L1363P; p53+/- thymic tumor
Supplemental Table S1. from Ablation of the Brca1–Palb2 Interaction Phenocopies Fanconi Anemia in Mice
Authors: Park Dongju , Bergin Stephen M. , Jones Dan , Ru Peng , Koivisto Christopher S. , Jeon Young-Jun , Sizemore Gina M. , Kladney Raleigh D. , Hadjis Ashley , Shakya Reena , Ludwig Thomas
Published: April 2023

Notch1 mutations detected by exome sequencing from Brca1L1363P/ L1363P; p53+/+ thymic tumor
Supplementary Figures from The Pathognomonic FOXL2 C134W Mutation Alters DNA-Binding Specificity
Authors: Carles Annaïck , Trigo-Gonzalez Genny , Cao Qi , Cheng S.-W. Grace , Moksa Michelle , Bilenky Misha , Huntsman David G. , Morin Gregg B. , Hirst Martin
Published: April 2023

File containing supplemental figures and legends
Figure S3 from Ablation of the Brca1–Palb2 Interaction Phenocopies Fanconi Anemia in Mice
Authors: Park Dongju , Bergin Stephen M. , Jones Dan , Ru Peng , Koivisto Christopher S. , Jeon Young-Jun , Sizemore Gina M. , Kladney Raleigh D. , Hadjis Ashley , Shakya Reena , Ludwig Thomas
Published: April 2023

T cell population analysis in Brca1L1363P/L1363P thymus
Figure S1 from Ablation of the Brca1–Palb2 Interaction Phenocopies Fanconi Anemia in Mice
Authors: Park Dongju , Bergin Stephen M. , Jones Dan , Ru Peng , Koivisto Christopher S. , Jeon Young-Jun , Sizemore Gina M. , Kladney Raleigh D. , Hadjis Ashley , Shakya Reena , Ludwig Thomas
Published: April 2023

Generation of the Brca1 L1363P knock-in mice
Supplementary Data from Chromosomal Instability and mTORC1 Activation through PTEN Loss Contribute to Proteotoxic Stress in Ovarian Carcinoma
Authors: Chui M. Herman , Doodnauth Sasha A. , Erdmann Natalie , Tiedemann Rodger E. , Sircoulomb Fabrice , Drapkin Ronny , Shaw Patricia , Rottapel Robert
Published: April 2023

Supplementary Figure S1. Chromosome missegregation in FTSECs by pharmacologic inhibition of Mps1 and CENP-E (relates to Figures 1 and 2); Supplementary Figure S2. Comparisons of monolayer versus spheroid cultures of ovarian cancer cells (relates to Figure 4); Supplementary Figure S3. Marker expression in ovarian cancer cell cultures (relates to Figure 4); Supplementary Figure S4. mTORC1 activation potentiates aneuploidy-associated UPR induction, while suppression of mTORC1 by rapamycin causes mild cytostatic effects (relates to Figure 5); Supplementary Figure S5. mTORC1 activation sensitizes to bortezomib in ovarian cancer cells (relates to Figure 5); Supplementary Figure S6. PTEN loss sensitizes to bortezomib in TOV1946 xenografts (relates to Figure 6); Supplementary Table S1. List of primary antibodies; and Supplementary Methods.
Supplementary Table from Accumulation of Molecular Aberrations Distinctive to Hepatocellular Carcinoma Progression
Authors: Midorikawa Yutaka , Yamamoto Shogo , Tatsuno Kenji , Renard-Guillet Claire , Tsuji Shingo , Hayashi Akimasa , Ueda Hiroki , Fukuda Shiro , Fujita Takanori , Katoh Hiroto , Ishikawa Shumpei , Covington Kyle R. , Creighton Chad J. , Sugitani Masahiko , Wheeler David A. , Shibata Tatsuhiro , Nagae Genta , Takayama Tadatoshi , Aburatani Hiroyuki
Published: April 2023

Table S1 shows Clinical features. Table S2 shows Patient/sample information and NGS statistics. Table S3 shows Methylation status of CpG sites of WNT targets with CTNNB1 mutation. Table S4 shows Chromosomal aberrations.
Supplementary Figure from Accumulation of Molecular Aberrations Distinctive to Hepatocellular Carcinoma Progression
Authors: Midorikawa Yutaka , Yamamoto Shogo , Tatsuno Kenji , Renard-Guillet Claire , Tsuji Shingo , Hayashi Akimasa , Ueda Hiroki , Fukuda Shiro , Fujita Takanori , Katoh Hiroto , Ishikawa Shumpei , Covington Kyle R. , Creighton Chad J. , Sugitani Masahiko , Wheeler David A. , Shibata Tatsuhiro , Nagae Genta , Takayama Tadatoshi , Aburatani Hiroyuki
Published: April 2023

Figure S1 shows Histological findings of stepwise hepatocarcinogenesis and somatic substitution patterns. Figure S2 shows Activation of WNT targets. Figure S3 shows Homozygous deletion in 4q and 16q. Figure S4 shows Circos plot and transcription of the 5' portion of fusion genes that included TERT sequences. Figure S5 shows Upregulation mechanisms of TERT gene. Figure S6 shows Classification of HCC samples based on the methylation data.
Table S5 from Chromothripsis in Human Breast Cancer
Authors: Bolkestein Michiel , Wong John K.L. , Thewes Verena , Körber Verena , Hlevnjak Mario , Elgaafary Shaymaa , Schulze Markus , Kommoss Felix K.F. , Sinn Hans-Peter , Anzeneder Tobias , Hirsch Steffen , Devens Frauke , Schröter Petra , Höfer Thomas , Schneeweiss Andreas , Lichter Peter , Zapatka Marc , Ernst Aurélie
Published: April 2023

Recurrent fusion genes and parameters of the regression analysis
Table S4 from Chromothripsis in Human Breast Cancer
Authors: Bolkestein Michiel , Wong John K.L. , Thewes Verena , Körber Verena , Hlevnjak Mario , Elgaafary Shaymaa , Schulze Markus , Kommoss Felix K.F. , Sinn Hans-Peter , Anzeneder Tobias , Hirsch Steffen , Devens Frauke , Schröter Petra , Höfer Thomas , Schneeweiss Andreas , Lichter Peter , Zapatka Marc , Ernst Aurélie
Published: April 2023

Chromosome regions with significant differences in copy-number gains and losses between cases with and without chromothripsis
Table S2 from Chromothripsis in Human Breast Cancer
Authors: Bolkestein Michiel , Wong John K.L. , Thewes Verena , Körber Verena , Hlevnjak Mario , Elgaafary Shaymaa , Schulze Markus , Kommoss Felix K.F. , Sinn Hans-Peter , Anzeneder Tobias , Hirsch Steffen , Devens Frauke , Schröter Petra , Höfer Thomas , Schneeweiss Andreas , Lichter Peter , Zapatka Marc , Ernst Aurélie
Published: April 2023

Chromothripsis scoring by visual and algorithm-based approaches
Figure S1 from HDAC6 Inhibition Synergizes with Anti-PD-L1 Therapy in ARID1A-Inactivated Ovarian Cancer
Authors: Fukumoto Takeshi , Fatkhutdinov Nail , Zundell Joseph A. , Tcyganov Evgenii N. , Nacarelli Timothy , Karakashev Sergey , Wu Shuai , Liu Qin , Gabrilovich Dmitry I. , Zhang Rugang
Published: April 2023

Figure S1 shows ARID1A localizes to the promoter region of the PD-L1 encoding CD274 gene.
Supplementary Data from CD122-Selective IL2 Complexes Reduce Immunosuppression, Promote Treg Fragility, and Sensitize Tumor Response to PD-L1 Blockade
Authors: Drerup Justin M. , Deng Yilun , Pandeswara Sri Lakshmi , Padrón Álvaro S. , Reyes Ryan M. , Zhang Xinyue , Mendez Jenny , Liu Aijie , Clark Curtis A. , Chen Wanjiao , Conejo-Garcia José R. , Hurez Vincent , Gupta Harshita , Curiel Tyler J.
Published: April 2023

Supplementary figures 1-10. Figure S1. IL-2c increases conventional CD4 T cell in ascites three weeks after final IL-2c, but does not affect ascites Treg and effector T cell numbers at one week after final IL-2c administration. Figure S2. IL-2c treatment increases CD8+ central and effector memory T cells in the ascites, and central memory T cells in TDLN. Fig S3. Additional Treg phenotype in ascites and TDLN after IL-2c treatment. Fig S4. IL-2c directly inhibits Treg suppression specifically in the tumor microenvironment. Fig S5. IL-2 signaling is not impaired in TDLN after IL-2c treatment. Figure S6. Specific Treg depletion is highly effective against ID8agg. Figure S7. αCD25 attenuates IL-2c-induced tumor rejection and T cell function in ID8agg OC. Figure S8. IL-2c promotes intratumoral T cell infiltration. Figure S9. IL-2c reduces intratumoral Treg activation and functional molecules in B16 melanoma. Figure S10. IL-2c increases TIGIT+LAG-3+PD-1+ CD8+ T cells in B16 tumors.
Supplementary Methods from FGFR1 Is Critical for RBL2 Loss–Driven Tumor Development and Requires PLCG1 Activation for Continued Growth of Small Cell Lung Cancer
Authors: Kim Kee-Beom , Kim Youngchul , Rivard Christopher J. , Kim Dong-Wook , Park Kwon-Sik
Published: April 2023

Sequences of guid RNAs, shRNAs, oligo nucleotides for cloning, List of antibodies, Methods of immunohistochemistry for RBL2, FGFR1, and PLCG1 on tumor microarrays
Supplementary Fig 4 from FGFR1 Is Critical for RBL2 Loss–Driven Tumor Development and Requires PLCG1 Activation for Continued Growth of Small Cell Lung Cancer
Authors: Kim Kee-Beom , Kim Youngchul , Rivard Christopher J. , Kim Dong-Wook , Park Kwon-Sik
Published: April 2023

RT-qPCR for Fgfr1 mRNA normalized to Gapdh (n=3 replicates per group). Fgfr1 transcript levels are higher in subcutaneous tumors generated from preSCs with mutant Rbl2, Crebbp, or Ep300 than control or Col22a1 mutant preSCs.
Supplementary Fig 2 from FGFR1 Is Critical for RBL2 Loss–Driven Tumor Development and Requires PLCG1 Activation for Continued Growth of Small Cell Lung Cancer
Authors: Kim Kee-Beom , Kim Youngchul , Rivard Christopher J. , Kim Dong-Wook , Park Kwon-Sik
Published: April 2023

Immunoblot for FGFR1 in primary cells derived from lung tumors. FGFR1 expression in primary cells from a tumor developed in Fgfr1lox/lox Rb1/Trp53/Rbl2 mouse (cohort #1) is reduced but readily detected, suggesting incomplete recombination of Fgfr1 lox alleles. GAPDH verifies equal loading of total proteins.
Supplementary Data 3 from FGFR1 Is Critical for RBL2 Loss–Driven Tumor Development and Requires PLCG1 Activation for Continued Growth of Small Cell Lung Cancer
Authors: Kim Kee-Beom , Kim Youngchul , Rivard Christopher J. , Kim Dong-Wook , Park Kwon-Sik
Published: April 2023

Results of IHC on SCLC lines-derived xenograft TMA and resected primary SCLC TMA, and IHC protocols.
Supplementary Data Figures S1-S14 from State-Transition Analysis of Time-Sequential Gene Expression Identifies Critical Points That Predict Development of Acute Myeloid Leukemia
Authors: Rockne Russell C. , Branciamore Sergio , Qi Jing , Frankhouser David E. , O'Meally Denis , Hua Wei-Kai , Cook Guerry , Carnahan Emily , Zhang Lianjun , Marom Ayelet , Wu Herman , Maestrini Davide , Wu Xiwei , Yuan Yate-Ching , Liu Zheng , Wang Leo D. , Forman Stephen , Carlesso Nadia , Kuo Ya-Huei , Marcucci Guido
Published: April 2023

Figure S1. Details of animal model and fusion gene CM, Figure S2. Ex vivo flow cytometry analysis of bone marrow, Figure S3. Details of principal component analysis, Figure S4. Comparison of state-space construction with different dimension reduction methods, Figure S5. Hierarchical clustering of time-series RNA-seq data and relation to state-space, Figure S6. Details of critical point estimation, construction of quasi-potential, and state-space dynamics, Figure S7. Correlation of state-space geometry with Kit and CM gene expression. Sensitivity of state-space geometry to inclusion of Kit and CM, Figure S8. Volcano plots of critical-point based differential gene expression analysis, Figure S9. Heatmaps of selected GO pathways in early, transition, persistent, and leukemic events, Figure S10. Computation of eigengene angle in state-space, Figure S11. Details of principal component analysis of validation cohorts and state-space dynamics, Figure S12. Mean-squared displacement analysis of particle trajectories in state-space and calibration of Fokker-Planck diffusion coefficient with training cohort, Figure S13. Sensitivity analysis of state-space construction to sample and normalization thresholds, Figure S14. Bootstrap cross validation of state-space construction.
Supplementary Data 1 from FGFR1 Is Critical for RBL2 Loss–Driven Tumor Development and Requires PLCG1 Activation for Continued Growth of Small Cell Lung Cancer
Authors: Kim Kee-Beom , Kim Youngchul , Rivard Christopher J. , Kim Dong-Wook , Park Kwon-Sik
Published: April 2023

List of differentially expressed genes between control and FGFR1-expressing preSC
Supplementary Data from ATF3 Coordinates Antitumor Synergy between Epigenetic Drugs and Protein Disulfide Isomerase Inhibitors
Authors: Duncan Ravyn M. , Reyes Leticia , Moats Katelyn , Robinson Reeder M. , Murphy Sara A. , Kaur Balveen , Stessman Holly A.F. , Dolloff Nathan G.
Published: April 2023

The supplementary figures provide data supporting the combination drug screening process that uncovered synergy between PDI and HDAC inhibitors, and further supplements the findings in the main figures demonstrating the genomic, biochemical, and cellular characterization of the molecular mechanisms responsible for that synergy.
Supplementary Figure S5 from Replication Stress Drives Constitutive Activation of the DNA Damage Response and Radioresistance in Glioblastoma Stem-like Cells
Authors: Carruthers Ross D. , Ahmed Shafiq U. , Ramachandran Shaliny , Strathdee Karen , Kurian Kathreena M. , Hedley Ann , Gomez-Roman Natividad , Kalna Gabriela , Neilson Mathew , Gilmour Lesley , Stevenson Katrina H. , Hammond Ester M. , Chalmers Anthony J.
Published: April 2023

Supplementary Figure S5 shows additional immunofluorescent staining images and quantification in human GBM samples
Supplementary Figure S3 from Replication Stress Drives Constitutive Activation of the DNA Damage Response and Radioresistance in Glioblastoma Stem-like Cells
Authors: Carruthers Ross D. , Ahmed Shafiq U. , Ramachandran Shaliny , Strathdee Karen , Kurian Kathreena M. , Hedley Ann , Gomez-Roman Natividad , Kalna Gabriela , Neilson Mathew , Gilmour Lesley , Stevenson Katrina H. , Hammond Ester M. , Chalmers Anthony J.
Published: April 2023

Supplementary Figure S3 shows additional immunofluorescent staining and conventional IHC in GBM intracranial xenografts.
Supplementary Data from ERINA Is an Estrogen-Responsive LncRNA That Drives Breast Cancer through the E2F1/RB1 Pathway
Authors: Fang Zihui , Wang Yue , Wang Zehua , Xu Meishu , Ren Songrong , Yang Da , Hong Mei , Xie Wen
Published: April 2023

Supplementary Figures 1-5. Supplementary Figure 1. ERINA is a nuclear lncRNA that affects the survival and cell proliferation marker of ER-positive breast cancer patients. Supplementary Figure 2. ERINA knockdown and overexpression efficiency and the morphology change of knockdown cells. Supplementary Figure 3. RNA sequencing analysis showed the number of up-regulated genes and downregulated genes in T47D cells. Supplementary Figure 4. GSEA analysis revealed ERINA played a crucial role in RB1-involved pathway. Supplementary Figure 5. ChIP-seq analysis reveals the binding of RNA polymerase II within the promoter region of ERINA. (A) Alignment of RNA polymerase II ChIP-seq in MCF7 cells. The binding peak and genomic locus are shown.
Supplementary Figure Legend from Oncogenic ERG Represses PI3K Signaling through Downregulation of IRS2
Authors: Mao Ninghui , Gao Dong , Hu Wenhuo , Gadal Sunyana , Hieronymus Haley , Wang Shangqian , Lee Young Sun , Sullivan Patrick , Zhang Zeda , Choi Danielle , Rosen Neal , Sawyers Charles L. , Gopalan Anuradha , Chen Yu , Carver Brett S.
Published: April 2023

Figure Legend for supplementary figures
Supplementary Data from Circulating Proteoglycan Endocan Mediates EGFR-Driven Progression of Non–Small Cell Lung Cancer
Authors: Yang Yi-Chieh , Pan Ke-Fan , Lee Wei-Jiunn , Chang Jer-Hwa , Tan Peng , Gu Chia-Chi , Chang Wei-Min , Yang Shun-Fa , Hsiao Michael , Hua Kuo-Tai , Chien Ming-Hsien
Published: April 2023

SUPPLEMENTARY INFORMATION Supplementary material and methods, Table S1, and Figure S1-S7 - This file contains Supplementary material and methods; Table S1. The Cox univariate and multivariate analyses of endocan and clinicopathological factors in overall survival of patients in NSCLC patients.; Supplementary Figure S1. The clinical value of endocan in lung adenocarcinoma.; Supplementary Figure S2. Correlation of endocan and EGFR expression in lung cancer patients.; Supplementary Figure S3. Endocan enhances EGFâ€�induced activation of EGFR in a concentration-dependent manner.; Supplementary Figure S4. The JAK/STAT3 and ERK/ELK signaling regulates endocan promoter activity.; Supplementary Figure S5. The interaction of endocan and EGF/EGFR complex.; Supplementary Figure S6. Endocan peptide treatment inhibits the PC9 tumor growth in vivo.; Supplementary Figure S7. Endocan peptide treatment suppresses the activation of EGFR harboring L858R/T790M/C797S triple mutations.
Supplementary Data from Nudix Hydrolase NUDT16 Regulates 53BP1 Protein by Reversing 53BP1 ADP-Ribosylation
Authors: Zhang Fan , Lou Lihong , Peng Bo , Song Xiaotian , Reizes Ofer , Almasan Alexandru , Gong Zihua
Published: April 2023

Supplementary Data from Nudix Hydrolase NUDT16 Regulates 53BP1 Protein by Reversing 53BP1 ADP-Ribosylation
Supplementary Figures from Comprehensive Analysis of Radiomic Datasets by RadAR
Authors: Benelli Matteo , Barucci Andrea , Zoppetti Nicola , Calusi Silvia , Redapi Laura , Della Gala Giuseppe , Piffer Stefano , Bernardi Luca , Fusi Franco , Pallotta Stefania
Published: April 2023

Supplementary Figures 1-5. Supplementary Figure 1. Box plots showing the distribution of the top 4 radiomic features resulting from differential analysis of Dead vs Alive patients in the Lung1 datasets. Supplementary Figure 2. Box plots showing the distribution of the top 4 radiomic features resulting from differential analysis of Dead vs Alive patients in the Lung1 datasets. Values were scaled by min-max procedure. Supplementary Figure 3. Box plot of the distribution of the feature "Maximum" between alive and dead patients in Lung1 dataset using original (left) and normalized (right) values. The p-value of the difference of feature levels between alive and dead patients was estimated by Wilcoxon-Mann-Whitney test and adjusted by Benjamini-Hochberg procedure (False Discovery Rate, FDR). Supplementary Figure 4. Box plots showing the distribution of the top 2 radiomic features resulting from differential analysis of patients in the Lung1 datasets across disease stages. Values were quantilenormalized. Supplementary Figure 5. Heat map of radiomic profiles of n=388 patients from the Lung1 dataset.
Supplementary Data from Pharmacokinetic Profiles Determine Optimal Combination Treatment Schedules in Computational Models of Drug Resistance
Authors: Irurzun-Arana Itziar , McDonald Thomas O. , Trocóniz Iñaki F. , Michor Franziska
Published: April 2023

Supplemental data for the main manuscript. Contains equation description of the main features of the framework, description of the pharmacokinetic models and parameter estimates used for the simulations of the treatment effects, additional model fitting results and synergy/antagornism assesments, analysis of different dosing schedules and four different demos of the R package.
Figure S4 from Microenvironmental Cues Determine Tumor Cell Susceptibility to Neutrophil Cytotoxicity
Authors: Gershkovitz Maya , Fainsod-Levi Tanya , Khawaled Saleh , Shaul Merav E. , Sionov Ronit V. , Cohen-Daniel Leonor , Aqeilan Rami I. , Shaul Yoav D. , Fridlender Zvi G. , Granot Zvi
Published: April 2023

Supplemental Figure S4. EMT increases TRPM2 expression and renders cells susceptible to neutrophil cytotoxicity. A. Representative images showing control and Snail overexpressing 4T1 cells. B. Snail expression in control and Snail overexpressing 4T1 cells. C. qPCR analysis of TRPM2, Vimentin (Vim.) and E-Cadherin (E-Cad.) expression in control and Snail overexpressing 4T1 cells. D. Extent of neutrophil cytotoxicity in co-culture with 4T1 control cells (Cont.) or 4T1 cells induced to undergo EMT by Snail overexpression (Snail). E. Representative images showing HMLE cells before (HMLE) and after prolonged treatment with 10 ng/ml TGFÎ² to induce EMT. F. qPCR analysis of TRPM2, Vimentin (Vim.) and E-Cadherin (E-Cad.) in control and TGFÎ²â^'treated HMLE cells. G. Extent of neutrophil cytotoxicity in co-culture with control (Cont.) or TGFÎ²-pretreated HMLE cells that have undergone EMT. H. Representative images showing control and Twist overexpressing HMLE cells. I. Twist expression in control and Twist overexpressing HMLE cells. J. qPCR analysis of TRPM2, Vimentin (Vim.) and E-Cadherin (E-Cad.) expression in control and Twist overexpressing HMLE cells. K. Extent of neutrophil cytotoxicity in co-culture with HMLE control cells (Cont.) or HMLE cells induced to undergo EMT by Twist overexpression (Twist). *p<0.05, **p<0.01.
Video S4 from ΔNp63-Regulated Epithelial-to-Mesenchymal Transition State Heterogeneity Confers a Leader–Follower Relationship That Drives Collective Invasion
Authors: Westcott Jill M. , Camacho Sharon , Nasir Apsra , Huysman Molly E. , Rahhal Raneen , Dang Tuyen T. , Riegel Anna T. , Brekken Rolf A. , Pearson Gray W.
Published: April 2023

Live imaging of SUM159O cells embedded in ECM containing fluorescent microbeads (blue) showing ECM reorganization through bead movement.
Video S3 from ΔNp63-Regulated Epithelial-to-Mesenchymal Transition State Heterogeneity Confers a Leader–Follower Relationship That Drives Collective Invasion
Authors: Westcott Jill M. , Camacho Sharon , Nasir Apsra , Huysman Molly E. , Rahhal Raneen , Dang Tuyen T. , Riegel Anna T. , Brekken Rolf A. , Pearson Gray W.
Published: April 2023

Live imaging of SUM159T cells embedded in ECM containing fluorescent microbeads (blue) showing ECM reorganization through bead movement.
Supplementary Tables S1-S2 from MRI Distinguishes Tumor Hypoxia Levels of Different Prognostic and Biological Significance in Cervical Cancer
Authors: Hillestad Tiril , Hompland Tord , Fjeldbo Christina S. , Skingen Vilde E. , Salberg Unn Beate , Aarnes Eva-Katrine , Nilsen Anja , Lund Kjersti V. , Evensen Tina S. , Kristensen Gunnar B. , Stokke Trond , Lyng Heidi
Published: April 2023

Characteristics of the cervical cancer patient cohort (S1). Hallmarks associated with MRI-based hypoxia levels in cervical cancer (S2)
Supplementary Method S1 from MRI Distinguishes Tumor Hypoxia Levels of Different Prognostic and Biological Significance in Cervical Cancer
Authors: Hillestad Tiril , Hompland Tord , Fjeldbo Christina S. , Skingen Vilde E. , Salberg Unn Beate , Aarnes Eva-Katrine , Nilsen Anja , Lund Kjersti V. , Evensen Tina S. , Kristensen Gunnar B. , Stokke Trond , Lyng Heidi
Published: April 2023

DCE-MRI and digital histopathology
Video S1 from ΔNp63-Regulated Epithelial-to-Mesenchymal Transition State Heterogeneity Confers a Leader–Follower Relationship That Drives Collective Invasion
Authors: Westcott Jill M. , Camacho Sharon , Nasir Apsra , Huysman Molly E. , Rahhal Raneen , Dang Tuyen T. , Riegel Anna T. , Brekken Rolf A. , Pearson Gray W.
Published: April 2023

Live imaging of clustered spheroids containing SUM159T-dox:Î"Np63 cells {plus minus} doxycycline (H2B:GFP, green, nuclei) showing cell motility.
Supplementary Figures S1-S9 from MRI Distinguishes Tumor Hypoxia Levels of Different Prognostic and Biological Significance in Cervical Cancer
Authors: Hillestad Tiril , Hompland Tord , Fjeldbo Christina S. , Skingen Vilde E. , Salberg Unn Beate , Aarnes Eva-Katrine , Nilsen Anja , Lund Kjersti V. , Evensen Tina S. , Kristensen Gunnar B. , Stokke Trond , Lyng Heidi
Published: April 2023

Comparison of MRI with histology, construction of hypoxia images, and hypoxia levels in patients
Supplementary Data from ΔNp63-Regulated Epithelial-to-Mesenchymal Transition State Heterogeneity Confers a Leader–Follower Relationship That Drives Collective Invasion
Authors: Westcott Jill M. , Camacho Sharon , Nasir Apsra , Huysman Molly E. , Rahhal Raneen , Dang Tuyen T. , Riegel Anna T. , Brekken Rolf A. , Pearson Gray W.
Published: April 2023

Supplementary Tables S1-S8
Supplementary Document S1 from MRI Distinguishes Tumor Hypoxia Levels of Different Prognostic and Biological Significance in Cervical Cancer
Authors: Hillestad Tiril , Hompland Tord , Fjeldbo Christina S. , Skingen Vilde E. , Salberg Unn Beate , Aarnes Eva-Katrine , Nilsen Anja , Lund Kjersti V. , Evensen Tina S. , Kristensen Gunnar B. , Stokke Trond , Lyng Heidi
Published: April 2023

Validation of algorithm for assessing hypoxia levels in patient tumors
Supplementary Data from Plasma Gelsolin Inhibits CD8+ T-cell Function and Regulates Glutathione Production to Confer Chemoresistance in Ovarian Cancer
Authors: Asare-Werehene Meshach , Communal Laudine , Carmona Euridice , Han Youngjin , Song Yong Sang , Burger Dylan , Mes-Masson Anne-Marie , Tsang Benjamin K.
Published: April 2023

This file contains supplementary figures and tables with their legends.
Supplementary Figure S7 from Blocking Angiopoietin-2 Promotes Vascular Damage and Growth Inhibition in Mouse Tumors Treated with Small Doses of Radiation
Authors: Kallio Pauliina , Jokinen Elina , Högström Jenny , Das Suvendu , Heino Sarika , Lähde Marianne , Brodkin Jefim , Korhonen Emilia A. , Alitalo Kari
Published: April 2023

Supplementary Figure S7
Supplementary Data from Neutrophil Extracellular Traps Drive Mitochondrial Homeostasis in Tumors to Augment Growth
Authors: Yazdani Hamza O. , Roy Eva , Comerci Alexander J. , van der Windt Dirk J. , Zhang Hongji , Huang Hai , Loughran Patricia , Shiva Sruti , Geller David A. , Bartlett David L. , Tsung Allan , Sheng Tai , Simmons Richard L. , Tohme Samer
Published: April 2023

Supplementary Figure 1: Contains result showing 1) PCR analysis of the hypoxic cancer cells showed an elevated mRNA expression of neutrophil attractant chemokines 2) Increased in neutrophil cell migration in the presence of cancer hypoxic media 3) Increased levels of HMGB1 in both mice and human hypoxic cancer cell lines; Supplementary Figure 2: Contains result showing 1) Immunofluorescence imagining of TOM20 in the tumor tissue of mice treated with DNAse and NEi. 2) Decreased in mitochondrial DNA assay and ATP levels in DNAse/NEI treated mice. 3) Western blot analysis of mitochondrial biogenesis associated genes (PGC-1α, NRF1 and TFAM) showed decreased expression in NET depleted tumors. 4) Increased in the number of mitochondria in NET treated MC38 cells observed by TME. 5) Increased in the staining of neutrophil elastase in human CRLM tissue. 6) Immunofluorescence imaging indicated release of NE during NET formation: Supplementary Figure 3: Contains result showing 1 and 2) Protein expression for PGC-1a, NRF1, TFAM and phosphorylated p38 were observed in a control and TLR4 siRNA transfected cells. 3) Increased mitochondrial masss observed in cancer cell treated with rNE or NETs observed by Mitotracker staining. 4 and 5) Flowcytometry and MTT analysis showed an increase in the proliferation of cancer cells after treating with either NETs or rNE; Supplementary Figure 4: Schematic diagrams of the proposed role of NETs in the tumor growth.; Supplementary Material and Methods
Supplementary Data from Inhibition of Rspo-Lgr4 Facilitates Checkpoint Blockade Therapy by Switching Macrophage Polarization
Authors: Tan Binghe , Shi Xiujuan , Zhang Jie , Qin Juliang , Zhang Na , Ren Hua , Qian Min , Siwko Stefan , Carmon Kendra , Liu Qingyun , Han Honghui , Du Bing , Liu Mingyao
Published: April 2023

This file contains the characterization of M2 (Supplementary Fig.S1) and M1 (Supplementary Fig.S2) type polarization in both Lgr4 knockdown and overexpression cells; the expression and immune regulation of Lgr4 in tumor tissues (Supplementary Fig.S3); the toxicity of LGR4 ECD, Rspo1 antibody and BLZ945 on tumor cells and macrophages (Supplementary Fig.S4); the immune regulation of Rspo/Lgr4 blockade in B16F10 melanoma mouse model (Supplementary Fig.S5).
Supplementary Data from Multiomic Analysis of Subtype Evolution and Heterogeneity in High-Grade Serous Ovarian Carcinoma
Authors: Geistlinger Ludwig , Oh Sehyun , Ramos Marcel , Schiffer Lucas , LaRue Rebecca S. , Henzler Christine M. , Munro Sarah A. , Daughters Claire , Nelson Andrew C. , Winterhoff Boris J. , Chang Zenas , Talukdar Shobhana , Shetty Mihir , Mullany Sally A. , Morgan Martin , Parmigiani Giovanni , Birrer Michael J. , Qin Li-Xuan , Riester Markus , Starr Timothy K. , Waldron Levi
Published: April 2023

Supplementary Materials & Methods. Supplemental Tables 1-3 and Supplemental Figures 1-19.
Figure S1 from Obesity/Type 2 Diabetes-Associated Liver Tumors Are Sensitive to Cyclin D1 Deficiency
Authors: Luo Chi , Liang Jiaxin , Sharabi Kfir , Hatting Maximilian , Perry Elizabeth A. , Tavares Clint D.J. , Goyal Lipika , Srivastava Amitabh , Bilodeau Marc , Zhu Andrew X. , Sicinski Piotr , Puigserver Pere
Published: April 2023

Gene expression profiles of liver or HCC derived from lean and obese/diabetic mice.
Supplementary Data from The Synthetic Small Molecule FL3 Combats Intestinal Tumorigenesis via Axin1-Mediated Inhibition of Wnt/β-Catenin Signaling
Authors: Jackson Dakota N. , Alula Kibrom M. , Delgado-Deida Yaritza , Tabti Redouane , Turner Kevin , Wang Xuan , Venuprasad K. , Souza Rhonda F. , Désaubry Laurent , Theiss Arianne L.
Published: April 2023

FL3 induces RKO and SW48 cell death
Supplementary Methods and Materials from Chemotherapy-Induced Upregulation of Small Extracellular Vesicle-Associated PTX3 Accelerates Breast Cancer Metastasis
Authors: Wills Carson A. , Liu Xiaoming , Chen Longgui , Zhao Yuanjun , Dower Christopher M. , Sundstrom Jeffrey , Wang Hong-Gang
Published: April 2023

Supplementary Methods and Materials
Figure S6 from Chemotherapy-Induced Upregulation of Small Extracellular Vesicle-Associated PTX3 Accelerates Breast Cancer Metastasis
Authors: Wills Carson A. , Liu Xiaoming , Chen Longgui , Zhao Yuanjun , Dower Christopher M. , Sundstrom Jeffrey , Wang Hong-Gang
Published: April 2023

Chemotherapy upregulates small extracellular vesicle-associated PTX3 protein expression, which has no effect on cell migration and invasion in vitro or primary tumor growth in vivo.
Table S5 from 3D Functional Genomics Screens Identify CREBBP as a Targetable Driver in Aggressive Triple-Negative Breast Cancer
Authors: Peck Barrie , Bland Philip , Mavrommati Ioanna , Muirhead Gareth , Cottom Hannah , Wai Patty T. , Maguire Sarah L. , Barker Holly E. , Morrison Eamonn , Kriplani Divya , Yu Lu , Gibson Amy , Falgari Giulia , Brennan Keith , Farnie Gillian , Buus Richard , Marlow Rebecca , Novo Daniela , Knight Eleanor , Guppy Naomi , Kolarevic Daniela , Susnjar Snezana , Milijic Natasa Medic , Naidoo Kalnisha , Gazinska Patrycja , Roxanis Ioannis , Pancholi Sunil , Martin Lesley-Ann , Holgersen Erle M. , Cheang Maggie C.U. , Noor Farzana , Postel-Vinay Sophie , Quinn Gerard , McDade Simon , Krasny Lukas , Huang Paul , Daley Frances , Wallberg Fredrik , Choudhary Jyoti S. , Haider Syed , Tutt Andrew N. , Natrajan Rachael
Published: April 2023

Enrichment analysis from TCGA RNA-seq and RPPA data comparing CREBBPaltered versus wild-type patients.
Figure S3 from Chemotherapy-Induced Upregulation of Small Extracellular Vesicle-Associated PTX3 Accelerates Breast Cancer Metastasis
Authors: Wills Carson A. , Liu Xiaoming , Chen Longgui , Zhao Yuanjun , Dower Christopher M. , Sundstrom Jeffrey , Wang Hong-Gang
Published: April 2023

DXR-EVs do not affect tumor cell migration or invasion in vitro.
Table S2 from 3D Functional Genomics Screens Identify CREBBP as a Targetable Driver in Aggressive Triple-Negative Breast Cancer
Authors: Peck Barrie , Bland Philip , Mavrommati Ioanna , Muirhead Gareth , Cottom Hannah , Wai Patty T. , Maguire Sarah L. , Barker Holly E. , Morrison Eamonn , Kriplani Divya , Yu Lu , Gibson Amy , Falgari Giulia , Brennan Keith , Farnie Gillian , Buus Richard , Marlow Rebecca , Novo Daniela , Knight Eleanor , Guppy Naomi , Kolarevic Daniela , Susnjar Snezana , Milijic Natasa Medic , Naidoo Kalnisha , Gazinska Patrycja , Roxanis Ioannis , Pancholi Sunil , Martin Lesley-Ann , Holgersen Erle M. , Cheang Maggie C.U. , Noor Farzana , Postel-Vinay Sophie , Quinn Gerard , McDade Simon , Krasny Lukas , Huang Paul , Daley Frances , Wallberg Fredrik , Choudhary Jyoti S. , Haider Syed , Tutt Andrew N. , Natrajan Rachael
Published: April 2023

High throughput spheroid screen results (z scores) in the MCF10 progression series. Gene rank for the validation screen (average z scores across cell lines).
Supplementary Methods from 3D Functional Genomics Screens Identify CREBBP as a Targetable Driver in Aggressive Triple-Negative Breast Cancer
Authors: Peck Barrie , Bland Philip , Mavrommati Ioanna , Muirhead Gareth , Cottom Hannah , Wai Patty T. , Maguire Sarah L. , Barker Holly E. , Morrison Eamonn , Kriplani Divya , Yu Lu , Gibson Amy , Falgari Giulia , Brennan Keith , Farnie Gillian , Buus Richard , Marlow Rebecca , Novo Daniela , Knight Eleanor , Guppy Naomi , Kolarevic Daniela , Susnjar Snezana , Milijic Natasa Medic , Naidoo Kalnisha , Gazinska Patrycja , Roxanis Ioannis , Pancholi Sunil , Martin Lesley-Ann , Holgersen Erle M. , Cheang Maggie C.U. , Noor Farzana , Postel-Vinay Sophie , Quinn Gerard , McDade Simon , Krasny Lukas , Huang Paul , Daley Frances , Wallberg Fredrik , Choudhary Jyoti S. , Haider Syed , Tutt Andrew N. , Natrajan Rachael
Published: April 2023

Supplementary Materials and Methods
Figure S1- S8 from 3D Functional Genomics Screens Identify CREBBP as a Targetable Driver in Aggressive Triple-Negative Breast Cancer
Authors: Peck Barrie , Bland Philip , Mavrommati Ioanna , Muirhead Gareth , Cottom Hannah , Wai Patty T. , Maguire Sarah L. , Barker Holly E. , Morrison Eamonn , Kriplani Divya , Yu Lu , Gibson Amy , Falgari Giulia , Brennan Keith , Farnie Gillian , Buus Richard , Marlow Rebecca , Novo Daniela , Knight Eleanor , Guppy Naomi , Kolarevic Daniela , Susnjar Snezana , Milijic Natasa Medic , Naidoo Kalnisha , Gazinska Patrycja , Roxanis Ioannis , Pancholi Sunil , Martin Lesley-Ann , Holgersen Erle M. , Cheang Maggie C.U. , Noor Farzana , Postel-Vinay Sophie , Quinn Gerard , McDade Simon , Krasny Lukas , Huang Paul , Daley Frances , Wallberg Fredrik , Choudhary Jyoti S. , Haider Syed , Tutt Andrew N. , Natrajan Rachael
Published: April 2023

Supplementary Figures and legends
Supplementary Data from Association of Pathologic Complete Response with Long-Term Survival Outcomes in Triple-Negative Breast Cancer: A Meta-Analysis
Authors: Huang Min , O'Shaughnessy Joyce , Zhao Jing , Haiderali Amin , Cortés Javier , Ramsey Scott D. , Briggs Andrew , Hu Peter , Karantza Vassiliki , Aktan Gursel , Qi Cynthia Z. , Gu Chenyang , Xie Jipan , Yuan Muhan , Cook John , Untch Michael , Schmid Peter , Fasching Peter A.
Published: April 2023

Supplemental Tables 1-2. Table S1. Main characteristics of trials included in the analysis. Table S2. Sensitivity analysis: Subgroup comparisons of HR for EFS and OS. Supplemental Figures 1-2. Figure S1. Study selection chart. Figure S2. Survival curves of EFS and OS derived from the meta-analysis by pCR status and adjuvant therapy use.
Supplementary Appendix from Radiomic Detection of EGFR Mutations in NSCLC
Authors: Rossi Giovanni , Barabino Emanuele , Fedeli Alessandro , Ficarra Gianluca , Coco Simona , Russo Alessandro , Adamo Vincenzo , Buemi Francesco , Zullo Lodovica , Dono Mariella , De Luca Giuseppa , Longo Luca , Dal Bello Maria Giovanna , Tagliamento Marco , Alama Angela , Cittadini Giuseppe , Pronzato Paolo , Genova Carlo
Published: April 2023

Supplementary Data