bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figures from Huwe1 Sustains Normal Ovarian Epithelial Cell Transformation and Tumor Growth through the Histone H1.3-H19 Cascade
Authors: Yang Dong , Sun Bin , Zhang Xiaohong , Cheng Daomei , Yu Xiaoping , Yan Lanzhen , Li Lei , An Sanqi , Jiang Hua , Lasorella Anna , Iavarone Antonio , Zhang Shu , Zou Fangdong , Zhao Xudong
Published: March 2023

Supplementary Fig. 1 The genetic status of the KRAS, MYC and TP53 genes in ovarian cancer.Supplementary Fig. 2 CK8 staining in cultured mouse ovarian surface epithelial cells.Supplementary Fig. 3 Detection of Huwe1 knockout in MOSE cells.Supplementary Fig. 4 Huwe1 knockout inhibits cell proliferation.Supplementary Fig. 5 Deleting Huwe1 does not promote apoptosis in MOSE-Huwe1L/L-CreER cells.Supplementary Fig. 6 CK8 staining in tumors formed by MOSE-Huwe1L/L-CreER cells.Supplementary Fig. 7 RNAseq analysis of MOSE-Huwe1L/L-CreER and MOSE-Huwe1L/L-Cre cells.Supplementary Fig. 8 The knockdown efficiency of the H19 shRNA in MOSE-Huwe1L/L-CreER cells.Supplementary Fig. 9 The knockdown efficiency of the H1.3 shRNA in MOSE-Huwe1L/L-CreER and MOSE-Huwe1L/L-Cre cells. Supplementary Fig. 10 The knockdown efficiency of HUWE1 shRNA in SKOV-3 cells.Supplementary Fig. 11 Reduced HUWE1 expression inhibited proliferation in SKOV-3 cells.Supplementary Fig. 12 Staining for Ki67 and HUWE1 in tumors formed by SKOV-3/teton-shHUWE1 cells.Supplementary Fig. 13 HUWE1 binds to and ubiquitinates H1.3 in SKOV-3 cells.
Supplementary figure S6 from Differential PI3Kδ Signaling in CD4+ T-cell Subsets Enables Selective Targeting of T Regulatory Cells to Enhance Cancer Immunotherapy
Authors: Ahmad Shamim , Abu-Eid Rasha , Shrimali Rajeev , Webb Mason , Verma Vivek , Doroodchi Atbin , Berrong Zuzana , Samara Raed , Rodriguez Paulo C. , Mkrtichyan Mikayel , Khleif Samir N.
Published: March 2023

Continuous inhibition of PI3KÎ' sustained the reduced number of Tregs in vivo and has no effect on Tconvs.
Vehicle Treated Mouse Video from Granzyme B PET Imaging as a Predictive Biomarker of Immunotherapy Response
Authors: Larimer Benjamin M. , Wehrenberg-Klee Eric , Dubois Frank , Mehta Anila , Kalomeris Taylor , Flaherty Keith , Boland Genevieve , Mahmood Umar
Published: March 2023

Rotating Maximum Intensity Projection Video of Vehicle Treated Mouse
Supplementary figure S4 from Differential PI3Kδ Signaling in CD4+ T-cell Subsets Enables Selective Targeting of T Regulatory Cells to Enhance Cancer Immunotherapy
Authors: Ahmad Shamim , Abu-Eid Rasha , Shrimali Rajeev , Webb Mason , Verma Vivek , Doroodchi Atbin , Berrong Zuzana , Samara Raed , Rodriguez Paulo C. , Mkrtichyan Mikayel , Khleif Samir N.
Published: March 2023

Inhibition of PI3KÎ' selectively blocked the activation of Akt (T308)
Supplementary Materials from Granzyme B PET Imaging as a Predictive Biomarker of Immunotherapy Response
Authors: Larimer Benjamin M. , Wehrenberg-Klee Eric , Dubois Frank , Mehta Anila , Kalomeris Taylor , Flaherty Keith , Boland Genevieve , Mahmood Umar
Published: March 2023

This file contains supplementary figures pertaining to granzyme B heterogeneity, immunohistochemical and immunofluorescent analyses, peptide biodistribution and dynamic PET analysis.
Supplementary Figure Legends from Differential PI3Kδ Signaling in CD4+ T-cell Subsets Enables Selective Targeting of T Regulatory Cells to Enhance Cancer Immunotherapy
Authors: Ahmad Shamim , Abu-Eid Rasha , Shrimali Rajeev , Webb Mason , Verma Vivek , Doroodchi Atbin , Berrong Zuzana , Samara Raed , Rodriguez Paulo C. , Mkrtichyan Mikayel , Khleif Samir N.
Published: March 2023

Legends for supplemental figures.
Supplementary Data from Distinct Angiogenic Changes during Carcinogenesis Defined by Novel Label-Free Dark-Field Imaging in a Hamster Cheek Pouch Model
Authors: Hu Fangyao , Martin Hannah , Martinez Amy , Everitt Jeffrey , Erkanli Alaattin , Lee Walter T. , Dewhirst Mark , Ramanujam Nimmi
Published: March 2023

Supplementary Figure S1: Algorithm for segmenting the vasculature. Supplementary Figure S2: Algorithm for splitting the vessel masks by diameter. Supplementary Table S1: Breakdown of AUC data using individual parameters and their combinations. Supplementary Figure S3: Quantification of additional vascular parameters. Supplementary Figure S4: Future applications using Pocket microscope
Supplementary Table S7 from Systematic Pan-Cancer Analysis Reveals Immune Cell Interactions in the Tumor Microenvironment
Authors: Varn Frederick S. , Wang Yue , Mullins David W. , Fiering Steven , Cheng Chao
Published: March 2023

Cox proportional hazard model meta-z-scores for PRECOG cancer types.
Supplementary Table S4 from Systematic Pan-Cancer Analysis Reveals Immune Cell Interactions in the Tumor Microenvironment
Authors: Varn Frederick S. , Wang Yue , Mullins David W. , Fiering Steven , Cheng Chao
Published: March 2023

Flow cytometry correlations.
Supplementary Table S3 from Systematic Pan-Cancer Analysis Reveals Immune Cell Interactions in the Tumor Microenvironment
Authors: Varn Frederick S. , Wang Yue , Mullins David W. , Fiering Steven , Cheng Chao
Published: March 2023

ImmGen weights and TCGA infiltration scores.
Supplementary Table S2 from Systematic Pan-Cancer Analysis Reveals Immune Cell Interactions in the Tumor Microenvironment
Authors: Varn Frederick S. , Wang Yue , Mullins David W. , Fiering Steven , Cheng Chao
Published: March 2023

PRECOG sample sizes by cancer type.
Materials and Methods from miR-519d Promotes Melanoma Progression by Downregulating EphA4
Authors: Hua Kuo-Tai , Hong Jin-Bong , Sheen Yi-Shuan , Huang Hsin-Yi , Huang Yi-Ling , Chen Jau-Shiuh , Liao Yi-Hua
Published: March 2023

Materials and Methods
Supplementary Table S1 from Systematic Pan-Cancer Analysis Reveals Immune Cell Interactions in the Tumor Microenvironment
Authors: Varn Frederick S. , Wang Yue , Mullins David W. , Fiering Steven , Cheng Chao
Published: March 2023

TCGA sample sizes and abbreviations.
Figure S5 from miR-519d Promotes Melanoma Progression by Downregulating EphA4
Authors: Hua Kuo-Tai , Hong Jin-Bong , Sheen Yi-Shuan , Huang Hsin-Yi , Huang Yi-Ling , Chen Jau-Shiuh , Liao Yi-Hua
Published: March 2023

Suppl. Figure 5. Immunohistochemical analysis of EphA4 in representative benign or malignant melanocytic lesions. A, Strong staining was observed in pancreatic ductal adenocarcinoma (PDAC) cells, which acted as the positive control of EphA4 staining. B and C, Absent EphA4 immunostaining in normal human skin (B, Ã-400) and acquired intradermal melanocytic nevus (C, Ã-200). D, Strong immunoreactivity was found in the radial growth phase of primary cutaneous melanoma and the immunointensity was decreased in the vertical growth tumor parts in the dermis. E, Bar graph summary of the grading of EphA4 immunoreactivity in 28 pairs of primary cutaneous melanoma and metastatic tumors from the same patient. The result is similar to the total recruited cases as shown in Fig. 7E.
Supplementary Software S2 from Systematic Pan-Cancer Analysis Reveals Immune Cell Interactions in the Tumor Microenvironment
Authors: Varn Frederick S. , Wang Yue , Mullins David W. , Fiering Steven , Cheng Chao
Published: March 2023

R source code for the BASE algorithm.
Supplementary Software S1 from Systematic Pan-Cancer Analysis Reveals Immune Cell Interactions in the Tumor Microenvironment
Authors: Varn Frederick S. , Wang Yue , Mullins David W. , Fiering Steven , Cheng Chao
Published: March 2023

R source code for calculating immune cell specificity gene weights.
Figure S1 from miR-519d Promotes Melanoma Progression by Downregulating EphA4
Authors: Hua Kuo-Tai , Hong Jin-Bong , Sheen Yi-Shuan , Huang Hsin-Yi , Huang Yi-Ling , Chen Jau-Shiuh , Liao Yi-Hua
Published: March 2023

Suppl. Figure 1. Loss of E-cadherin expression in A2058 melanoma cells. MCF7 breast cancer cell line was used as a positive control.
Supplemental Table 2 from Cancer Stem Cells Regulate Cancer-Associated Fibroblasts via Activation of Hedgehog Signaling in Mammary Gland Tumors
Authors: Valenti Giovanni , Quinn Hazel M. , Heynen Guus J.J.E. , Lan Linxiang , Holland Jane D. , Vogel Regina , Wulf-Goldenberg Annika , Birchmeier Walter
Published: March 2023

List of CAF ligand - CSC receptor interactions
Supplemental Figures 1 to 7 from Cancer Stem Cells Regulate Cancer-Associated Fibroblasts via Activation of Hedgehog Signaling in Mammary Gland Tumors
Authors: Valenti Giovanni , Quinn Hazel M. , Heynen Guus J.J.E. , Lan Linxiang , Holland Jane D. , Vogel Regina , Wulf-Goldenberg Annika , Birchmeier Walter
Published: March 2023

Supplementary Figure 1. CAFs are generated in the stroma of Wnt-Met mammary gland tumors Supplementary Figure 2. CD140b+CD90+ cells isolated from Wnt-Met mammary gland tumors exhibit CAF features. Supplementary Figure 3. CAFs promote mammosphere formation and enhance the capacity of CSCs to form invasive 3D structures in Wnt-Met mammary gland tumors Supplementary Figure 4. CAFs from Wnt-Met mammary gland tumors display activation of Hedgehog signaling Supplementary Figure 5. Hedgehog signaling regulates CAFs in Wnt-Met mammary gland tumors Supplementary Figure 6. Therapeutic treatment of Wnt-Met mice with a Hedgehog pathway inhibitor depletes tumor stroma and prevents CSC expansion Supplementary Figure 7. Hedgehog signaling regulates the production of CAF ligands involved in the regulation of CSCs in Wnt-Met mammary gland tumors
supplemental table from YAP/TAZ-Mediated Upregulation of GAB2 Leads to Increased Sensitivity to Growth Factor–Induced Activation of the PI3K Pathway
Authors: Wang Chao , Gu Chao , Jeong Kang Jin , Zhang Dong , Guo Wei , Lu Yiling , Ju Zhenlin , Panupinthu Nattapon , Yang Ji Yeon , Gagea Mihai (Mike) , Ng Patrick Kwok Shing , Zhang Fan , Mills Gordon B.
Published: March 2023

Multivariate Cox Proportional Hazard modeling of survival. Cox modeling of the main and interaction effects of pYAP and ageï¼Œ grade and stage.
Supplementary Figure S4 from CXCL-8/IL8 Produced by Diffuse Large B-cell Lymphomas Recruits Neutrophils Expressing a Proliferation-Inducing Ligand APRIL
Authors: Manfroi Benoit , McKee Thomas , Mayol Jean Francois , Tabruyn Sebastien , Moret Sebastien , Villiers Christian , Righini Christian , Dyer Martin , Callanan Mary , Schneider Pascal , Tzankov Alexandar , Matthes Thomas , Sturm Nathalie , Huard Bertrand
Published: March 2023

Healthy B-cells are CXCL-8 negative.
supplemental figure legend from YAP/TAZ-Mediated Upregulation of GAB2 Leads to Increased Sensitivity to Growth Factor–Induced Activation of the PI3K Pathway
Authors: Wang Chao , Gu Chao , Jeong Kang Jin , Zhang Dong , Guo Wei , Lu Yiling , Ju Zhenlin , Panupinthu Nattapon , Yang Ji Yeon , Gagea Mihai (Mike) , Ng Patrick Kwok Shing , Zhang Fan , Mills Gordon B.
Published: March 2023

supplemental figure legend
Supplementary Figure S3 from CXCL-8/IL8 Produced by Diffuse Large B-cell Lymphomas Recruits Neutrophils Expressing a Proliferation-Inducing Ligand APRIL
Authors: Manfroi Benoit , McKee Thomas , Mayol Jean Francois , Tabruyn Sebastien , Moret Sebastien , Villiers Christian , Righini Christian , Dyer Martin , Callanan Mary , Schneider Pascal , Tzankov Alexandar , Matthes Thomas , Sturm Nathalie , Huard Bertrand
Published: March 2023

CXCL-8+ neutrophils are present in DLBCL necrotic tumors.
Supplementary Figure S1 from CXCL-8/IL8 Produced by Diffuse Large B-cell Lymphomas Recruits Neutrophils Expressing a Proliferation-Inducing Ligand APRIL
Authors: Manfroi Benoit , McKee Thomas , Mayol Jean Francois , Tabruyn Sebastien , Moret Sebastien , Villiers Christian , Righini Christian , Dyer Martin , Callanan Mary , Schneider Pascal , Tzankov Alexandar , Matthes Thomas , Sturm Nathalie , Huard Bertrand
Published: March 2023

CXCL-8 is the unique neutrophil chemokine detectable in DLBCL biopsies.
Supplemental figure 3 from YAP/TAZ-Mediated Upregulation of GAB2 Leads to Increased Sensitivity to Growth Factor–Induced Activation of the PI3K Pathway
Authors: Wang Chao , Gu Chao , Jeong Kang Jin , Zhang Dong , Guo Wei , Lu Yiling , Ju Zhenlin , Panupinthu Nattapon , Yang Ji Yeon , Gagea Mihai (Mike) , Ng Patrick Kwok Shing , Zhang Fan , Mills Gordon B.
Published: March 2023

GAB2 mediates the effects of siYAP/TAZ on the PI3K/AKT pathway
Supporting Information for CTC clusters in early lung cancer from Poor Prognosis Indicated by Venous Circulating Tumor Cell Clusters in Early-Stage Lung Cancers
Authors: Murlidhar Vasudha , Reddy Rishindra M. , Fouladdel Shamileh , Zhao Lili , Ishikawa Martin K. , Grabauskiene Svetlana , Zhang Zhuo , Lin Jules , Chang Andrew C. , Carrott Philip , Lynch William R. , Orringer Mark B. , Kumar-Sinha Chandan , Palanisamy Nallasivam , Beer David G. , Wicha Max S. , Ramnath Nithya , Azizi Ebrahim , Nagrath Sunitha
Published: March 2023

Supporting information showing CTC enumeration and gene expression profiling data for CTC clusters from early stage lung cancer.
Supplemental figure 1 from YAP/TAZ-Mediated Upregulation of GAB2 Leads to Increased Sensitivity to Growth Factor–Induced Activation of the PI3K Pathway
Authors: Wang Chao , Gu Chao , Jeong Kang Jin , Zhang Dong , Guo Wei , Lu Yiling , Ju Zhenlin , Panupinthu Nattapon , Yang Ji Yeon , Gagea Mihai (Mike) , Ng Patrick Kwok Shing , Zhang Fan , Mills Gordon B.
Published: March 2023

siYAP/TAZ inhibits PI3K/AKT pathway activation
Supplementary figure 1 from Bone Metastasis of Prostate Cancer Can Be Therapeutically Targeted at the TBX2–WNT Signaling Axis
Authors: Nandana Srinivas , Tripathi Manisha , Duan Peng , Chu Chia-Yi , Mishra Rajeev , Liu Chunyan , Jin Renjie , Yamashita Hironobu , Zayzafoon Majd , Bhowmick Neil A. , Zhau Haiyen E. , Matusik Robert J. , Chung Leland W.K.
Published: March 2023

Plot showing relative protein expression of TBX2 and WNT3A in human PCa cell lines
Supplementary Materials and Methods from Bone Metastasis of Prostate Cancer Can Be Therapeutically Targeted at the TBX2–WNT Signaling Axis
Authors: Nandana Srinivas , Tripathi Manisha , Duan Peng , Chu Chia-Yi , Mishra Rajeev , Liu Chunyan , Jin Renjie , Yamashita Hironobu , Zayzafoon Majd , Bhowmick Neil A. , Zhau Haiyen E. , Matusik Robert J. , Chung Leland W.K.
Published: March 2023

Supplementary Materials and Methods
Supplementary Table 1 and Supplementary Figures 1 through 7 from Tumor-Associated Neutrophils and Macrophages Promote Gender Disparity in Hepatocellular Carcinoma in Zebrafish
Authors: Yan Chuan , Yang Qiqi , Gong Zhiyuan
Published: March 2023

Supplementary Table S1. Sequences of RT-qPCR primers; Supplementary Figure S1. Representative images for differential responses of neutrophils/macrophages in male and female zebrafish during krasV12-induced carcinogenesis; Supplementary Figure S2. Comparison of gene expression between wild type male and female zebrafish (3 months old) in FACS-isolated neutrophils, macrophages and hepatocytes. Supplementary Figure S3. Manipulation of neutrophil and macrophage differentiation in 6-dpf zebrafish larvae; Supplementary Figure S4. Representative images for differential production of cortisol and induction of Tgfb1 expression by cortisol in krasV12 expressing livers between genders; Supplementary Figure S5. Effect of cortisol on neutrophil and macrophage number in zebrafish larvae; Supplementary Figure S6. Effects of cortisol on TAN and TAM infiltration in krasV12-expressing livers; Supplementary Figure S7. Schematics of possible mechanism of cortisol involved gender disparity in liver tumorigenesis.
Supplementary Figure 4 from Bone Metastasis of Prostate Cancer Can Be Therapeutically Targeted at the TBX2–WNT Signaling Axis
Authors: Nandana Srinivas , Tripathi Manisha , Duan Peng , Chu Chia-Yi , Mishra Rajeev , Liu Chunyan , Jin Renjie , Yamashita Hironobu , Zayzafoon Majd , Bhowmick Neil A. , Zhau Haiyen E. , Matusik Robert J. , Chung Leland W.K.
Published: March 2023

Micro-CT images of mouse tibiae injected with ARCaPM-TBX2 and ARCaPM-Neo cells
Supplementary Table S1 from Anti-Folate Receptor-α IgE but not IgG Recruits Macrophages to Attack Tumors via TNFα/MCP-1 Signaling
Authors: Josephs Debra H. , Bax Heather J. , Dodev Tihomir , Georgouli Mirella , Nakamura Mano , Pellizzari Giulia , Saul Louise , Karagiannis Panagiotis , Cheung Anthony , Herraiz Cecilia , Ilieva Kristina M. , Correa Isabel , Fittall Matthew , Crescioli Silvia , Gazinska Patrycja , Woodman Natalie , Mele Silvia , Chiaruttini Giulia , Gilbert Amy E. , Koers Alexander , Bracher Marguerite , Selkirk Christopher , Lentfer Heike , Barton Claire , Lever Elliott , Muirhead Gareth , Tsoka Sophia , Canevari Silvana , Figini Mariangela , Montes Ana , Downes Noel , Dombrowicz David , Corrigan Christopher J. , Beavil Andrew J. , Nestle Frank O. , Jones Paul S. , Gould Hannah J. , Sanz-Moreno Victoria , Blower Philip J. , Spicer James F. , Karagiannis Sophia N.
Published: March 2023

Table of Patient Characteristics
Supplementary Figure 2 from Bone Metastasis of Prostate Cancer Can Be Therapeutically Targeted at the TBX2–WNT Signaling Axis
Authors: Nandana Srinivas , Tripathi Manisha , Duan Peng , Chu Chia-Yi , Mishra Rajeev , Liu Chunyan , Jin Renjie , Yamashita Hironobu , Zayzafoon Majd , Bhowmick Neil A. , Zhau Haiyen E. , Matusik Robert J. , Chung Leland W.K.
Published: March 2023

Quantitative Real-Time RT-PCR and Invasion assay of LNCaP-TBX2 and LNCaP-Neo cells
Suplplementary Figure Legend from Bone Metastasis of Prostate Cancer Can Be Therapeutically Targeted at the TBX2–WNT Signaling Axis
Authors: Nandana Srinivas , Tripathi Manisha , Duan Peng , Chu Chia-Yi , Mishra Rajeev , Liu Chunyan , Jin Renjie , Yamashita Hironobu , Zayzafoon Majd , Bhowmick Neil A. , Zhau Haiyen E. , Matusik Robert J. , Chung Leland W.K.
Published: March 2023

Legend to Supplementary Figures
Supplementary Figure S3 from Anti-Folate Receptor-α IgE but not IgG Recruits Macrophages to Attack Tumors via TNFα/MCP-1 Signaling
Authors: Josephs Debra H. , Bax Heather J. , Dodev Tihomir , Georgouli Mirella , Nakamura Mano , Pellizzari Giulia , Saul Louise , Karagiannis Panagiotis , Cheung Anthony , Herraiz Cecilia , Ilieva Kristina M. , Correa Isabel , Fittall Matthew , Crescioli Silvia , Gazinska Patrycja , Woodman Natalie , Mele Silvia , Chiaruttini Giulia , Gilbert Amy E. , Koers Alexander , Bracher Marguerite , Selkirk Christopher , Lentfer Heike , Barton Claire , Lever Elliott , Muirhead Gareth , Tsoka Sophia , Canevari Silvana , Figini Mariangela , Montes Ana , Downes Noel , Dombrowicz David , Corrigan Christopher J. , Beavil Andrew J. , Nestle Frank O. , Jones Paul S. , Gould Hannah J. , Sanz-Moreno Victoria , Blower Philip J. , Spicer James F. , Karagiannis Sophia N.
Published: March 2023

Gating strategy used in the characterization of tumor-infiltrating macrophages by flow cytometry
Supplementary Tables from Gastric Cancer Cell Proliferation and Survival Is Enabled by a Cyclophilin B/STAT3/miR-520d-5p Signaling Feedback Loop
Authors: Li Ting , Guo Hanqing , Zhao Xiaodi , Jin Jiang , Zhang Lifeng , Li Hong , Lu Yuanyuan , Nie Yongzhan , Wu Kaichun , Shi Yongquan , Fan Daiming
Published: March 2023

Supplementary Tables
Supplementary Figure S1 from Anti-Folate Receptor-α IgE but not IgG Recruits Macrophages to Attack Tumors via TNFα/MCP-1 Signaling
Authors: Josephs Debra H. , Bax Heather J. , Dodev Tihomir , Georgouli Mirella , Nakamura Mano , Pellizzari Giulia , Saul Louise , Karagiannis Panagiotis , Cheung Anthony , Herraiz Cecilia , Ilieva Kristina M. , Correa Isabel , Fittall Matthew , Crescioli Silvia , Gazinska Patrycja , Woodman Natalie , Mele Silvia , Chiaruttini Giulia , Gilbert Amy E. , Koers Alexander , Bracher Marguerite , Selkirk Christopher , Lentfer Heike , Barton Claire , Lever Elliott , Muirhead Gareth , Tsoka Sophia , Canevari Silvana , Figini Mariangela , Montes Ana , Downes Noel , Dombrowicz David , Corrigan Christopher J. , Beavil Andrew J. , Nestle Frank O. , Jones Paul S. , Gould Hannah J. , Sanz-Moreno Victoria , Blower Philip J. , Spicer James F. , Karagiannis Sophia N.
Published: March 2023

Demarcation of tumor islets and immune cell infiltrates in rat lung sections
Figure S9 from Gastric Cancer Cell Proliferation and Survival Is Enabled by a Cyclophilin B/STAT3/miR-520d-5p Signaling Feedback Loop
Authors: Li Ting , Guo Hanqing , Zhao Xiaodi , Jin Jiang , Zhang Lifeng , Li Hong , Lu Yuanyuan , Nie Yongzhan , Wu Kaichun , Shi Yongquan , Fan Daiming
Published: March 2023

Knockdown of miR-520d-5p through independent antagomiR promoted GC growth.
Supplemental Figure 7 from Mitochondrial Genomic Backgrounds Affect Nuclear DNA Methylation and Gene Expression
Authors: Vivian Carolyn J. , Brinker Amanda E. , Graw Stefan , Koestler Devin C. , Legendre Christophe , Gooden Gerald C. , Salhia Bodour , Welch Danny R.
Published: March 2023

Supplemental Figure 7. Apoptosis Analysis. Annexin V-FITC/propidium iodide (PI) staining assay were used to measure apoptosis in MEFs harvested from the following strains: FF, FC, BB, FB, CC, CH, HH, HC (as described in Table 1). Apoptotic cells were detected by flow cytometry and analyzed using FACS Diva.
Supplemental Figure 6 from Mitochondrial Genomic Backgrounds Affect Nuclear DNA Methylation and Gene Expression
Authors: Vivian Carolyn J. , Brinker Amanda E. , Graw Stefan , Koestler Devin C. , Legendre Christophe , Gooden Gerald C. , Salhia Bodour , Welch Danny R.
Published: March 2023

Supplemental Figure 6. Cell Cycle Analysis. Cell cycle analysis using propidium iodide (PI) staining was performed on mouse embryo fibroblasts (MEFs) harvested from the following strains: FF, FC, BB, FB, CC, CH, HH, HC (as described in Table 1). Cell cycle was performed by flow cytometry and analyzed using FACS Diva.
Supplemental Figure 5 from Mitochondrial Genomic Backgrounds Affect Nuclear DNA Methylation and Gene Expression
Authors: Vivian Carolyn J. , Brinker Amanda E. , Graw Stefan , Koestler Devin C. , Legendre Christophe , Gooden Gerald C. , Salhia Bodour , Welch Danny R.
Published: March 2023

Supplemental Figure 5. Litter sizes and gender distribution. Female to male ratios with the average litter size and total number of mice used for each strain. For the female to male ratio the average litter size was calculated from over 20 litters generated. The number of females and males from each litter were counted.
Figure S5 from Gastric Cancer Cell Proliferation and Survival Is Enabled by a Cyclophilin B/STAT3/miR-520d-5p Signaling Feedback Loop
Authors: Li Ting , Guo Hanqing , Zhao Xiaodi , Jin Jiang , Zhang Lifeng , Li Hong , Lu Yuanyuan , Nie Yongzhan , Wu Kaichun , Shi Yongquan , Fan Daiming
Published: March 2023

STAT3 directly suppressed miR-520d-5p expression in SGC7901 cells.
Supplemental Figure 4 from Mitochondrial Genomic Backgrounds Affect Nuclear DNA Methylation and Gene Expression
Authors: Vivian Carolyn J. , Brinker Amanda E. , Graw Stefan , Koestler Devin C. , Legendre Christophe , Gooden Gerald C. , Salhia Bodour , Welch Danny R.
Published: March 2023

Supplemental Figure 4. Life Span. Life span of the MNX strains was measured in days and compared to the vendor information (Jackson Laboratories for C57Bl/6 and FVB/NJ mice and Envigo Laboratories for C3H/HeN mice). N= 15 for the females. N=5 for the males.
Figure S4 from Gastric Cancer Cell Proliferation and Survival Is Enabled by a Cyclophilin B/STAT3/miR-520d-5p Signaling Feedback Loop
Authors: Li Ting , Guo Hanqing , Zhao Xiaodi , Jin Jiang , Zhang Lifeng , Li Hong , Lu Yuanyuan , Nie Yongzhan , Wu Kaichun , Shi Yongquan , Fan Daiming
Published: March 2023

miR-520d-5p rescued tumor growth promotion induced by CypB-wt-UTR.
Figure S3 from Gastric Cancer Cell Proliferation and Survival Is Enabled by a Cyclophilin B/STAT3/miR-520d-5p Signaling Feedback Loop
Authors: Li Ting , Guo Hanqing , Zhao Xiaodi , Jin Jiang , Zhang Lifeng , Li Hong , Lu Yuanyuan , Nie Yongzhan , Wu Kaichun , Shi Yongquan , Fan Daiming
Published: March 2023

miR-520d-5p inhibit GC cell growth in BGC823 and SGC7901 cells.
Supplemental Figure 1 from Mitochondrial Genomic Backgrounds Affect Nuclear DNA Methylation and Gene Expression
Authors: Vivian Carolyn J. , Brinker Amanda E. , Graw Stefan , Koestler Devin C. , Legendre Christophe , Gooden Gerald C. , Salhia Bodour , Welch Danny R.
Published: March 2023

Supplemental Figure 1. Validation of Methyl-Seq and RNA-Seq. Several hypo-/hyper-methylated and down-/up-regulated genes were selected for validation using methylation specific primers (64) or quantitative PCR, respectively. Graphs depict fold-change between MNX strains and corresponding wild-type mice are shown to the left. All gene expression data were normalized to beta actin. Each bar combines pools A and B and the experiments were performed in triplicate. Error bars represent standard error. Representative gels showing unmethylated (U) and methylated (M) DNA are shown. The table summarizes specific genes tested and whether the RNA-or Methyl-Seq data were and were not validated.
Figure S1 from Gastric Cancer Cell Proliferation and Survival Is Enabled by a Cyclophilin B/STAT3/miR-520d-5p Signaling Feedback Loop
Authors: Li Ting , Guo Hanqing , Zhao Xiaodi , Jin Jiang , Zhang Lifeng , Li Hong , Lu Yuanyuan , Nie Yongzhan , Wu Kaichun , Shi Yongquan , Fan Daiming
Published: March 2023

Receiver operating characteristic analysis for the serum CypB, CEA and CA-199.
Supplementary Table S2andS3 from H3B-6527 Is a Potent and Selective Inhibitor of FGFR4 in FGF19-Driven Hepatocellular Carcinoma
Authors: Joshi Jaya Julie , Coffey Heather , Corcoran Erik , Tsai Jennifer , Huang Chia-Ling , Ichikawa Kana , Prajapati Sudeep , Hao Ming-Hong , Bailey Suzanna , Wu Jeremy , Rimkunas Victoria , Karr Craig , Subramanian Vanitha , Kumar Pavan , MacKenzie Crystal , Hurley Raelene , Satoh Takashi , Yu Kun , Park Eunice , Rioux Nathalie , Kim Amy , Lai Weidong G. , Yu Lihua , Zhu Ping , Buonamici Silvia , Larsen Nicholas , Fekkes Peter , Wang John , Warmuth Markus , Reynolds Dominic J. , Smith Peter G. , Selvaraj Anand
Published: March 2023

H3B-6527 response in 40 HCC cell lines and 625 cell lines.
Supplementary Table S1 from H3B-6527 Is a Potent and Selective Inhibitor of FGFR4 in FGF19-Driven Hepatocellular Carcinoma
Authors: Joshi Jaya Julie , Coffey Heather , Corcoran Erik , Tsai Jennifer , Huang Chia-Ling , Ichikawa Kana , Prajapati Sudeep , Hao Ming-Hong , Bailey Suzanna , Wu Jeremy , Rimkunas Victoria , Karr Craig , Subramanian Vanitha , Kumar Pavan , MacKenzie Crystal , Hurley Raelene , Satoh Takashi , Yu Kun , Park Eunice , Rioux Nathalie , Kim Amy , Lai Weidong G. , Yu Lihua , Zhu Ping , Buonamici Silvia , Larsen Nicholas , Fekkes Peter , Wang John , Warmuth Markus , Reynolds Dominic J. , Smith Peter G. , Selvaraj Anand
Published: March 2023

Crystallographic Data collection and Refinement Statistics.
Supplemental Figure 6 from Armed Oncolytic Adenovirus–Expressing PD-L1 Mini-Body Enhances Antitumor Effects of Chimeric Antigen Receptor T Cells in Solid Tumors
Authors: Tanoue Kiyonori , Rosewell Shaw Amanda , Watanabe Norihiro , Porter Caroline , Rana Bhakti , Gottschalk Stephen , Brenner Malcolm , Suzuki Masataka
Published: March 2023

Systemic treatment of PD-L1 IgG reduces the amount of human T-cells in mice at 24 hrs post-injection.
Supplementary Figure S7 from H3B-6527 Is a Potent and Selective Inhibitor of FGFR4 in FGF19-Driven Hepatocellular Carcinoma
Authors: Joshi Jaya Julie , Coffey Heather , Corcoran Erik , Tsai Jennifer , Huang Chia-Ling , Ichikawa Kana , Prajapati Sudeep , Hao Ming-Hong , Bailey Suzanna , Wu Jeremy , Rimkunas Victoria , Karr Craig , Subramanian Vanitha , Kumar Pavan , MacKenzie Crystal , Hurley Raelene , Satoh Takashi , Yu Kun , Park Eunice , Rioux Nathalie , Kim Amy , Lai Weidong G. , Yu Lihua , Zhu Ping , Buonamici Silvia , Larsen Nicholas , Fekkes Peter , Wang John , Warmuth Markus , Reynolds Dominic J. , Smith Peter G. , Selvaraj Anand
Published: March 2023

RNA-seq analysis of TCGA HCC samples.
Supplemental Figure 4 from Armed Oncolytic Adenovirus–Expressing PD-L1 Mini-Body Enhances Antitumor Effects of Chimeric Antigen Receptor T Cells in Solid Tumors
Authors: Tanoue Kiyonori , Rosewell Shaw Amanda , Watanabe Norihiro , Porter Caroline , Rana Bhakti , Gottschalk Stephen , Brenner Malcolm , Suzuki Masataka
Published: March 2023

Co-infection of Onc.Ad with HDPD-L1 increased PD-L1 mini-body in vitro, but PD-L1 mini-body was undetectable in the serum of mice.
Supplemental Figure 2 from Armed Oncolytic Adenovirus–Expressing PD-L1 Mini-Body Enhances Antitumor Effects of Chimeric Antigen Receptor T Cells in Solid Tumors
Authors: Tanoue Kiyonori , Rosewell Shaw Amanda , Watanabe Norihiro , Porter Caroline , Rana Bhakti , Gottschalk Stephen , Brenner Malcolm , Suzuki Masataka
Published: March 2023

PD-L1 mini-body induces dose-dependent IFNb secretion and T-cell proliferation similar to anti-PD-L1 IgG in MLR.
Supplementary Figure S3andS4 from H3B-6527 Is a Potent and Selective Inhibitor of FGFR4 in FGF19-Driven Hepatocellular Carcinoma
Authors: Joshi Jaya Julie , Coffey Heather , Corcoran Erik , Tsai Jennifer , Huang Chia-Ling , Ichikawa Kana , Prajapati Sudeep , Hao Ming-Hong , Bailey Suzanna , Wu Jeremy , Rimkunas Victoria , Karr Craig , Subramanian Vanitha , Kumar Pavan , MacKenzie Crystal , Hurley Raelene , Satoh Takashi , Yu Kun , Park Eunice , Rioux Nathalie , Kim Amy , Lai Weidong G. , Yu Lihua , Zhu Ping , Buonamici Silvia , Larsen Nicholas , Fekkes Peter , Wang John , Warmuth Markus , Reynolds Dominic J. , Smith Peter G. , Selvaraj Anand
Published: March 2023

H3B-6527 efficacy studies in 30 PDX models show that 10 models are responsive
Supplementary Figure S2 from H3B-6527 Is a Potent and Selective Inhibitor of FGFR4 in FGF19-Driven Hepatocellular Carcinoma
Authors: Joshi Jaya Julie , Coffey Heather , Corcoran Erik , Tsai Jennifer , Huang Chia-Ling , Ichikawa Kana , Prajapati Sudeep , Hao Ming-Hong , Bailey Suzanna , Wu Jeremy , Rimkunas Victoria , Karr Craig , Subramanian Vanitha , Kumar Pavan , MacKenzie Crystal , Hurley Raelene , Satoh Takashi , Yu Kun , Park Eunice , Rioux Nathalie , Kim Amy , Lai Weidong G. , Yu Lihua , Zhu Ping , Buonamici Silvia , Larsen Nicholas , Fekkes Peter , Wang John , Warmuth Markus , Reynolds Dominic J. , Smith Peter G. , Selvaraj Anand
Published: March 2023

RNA-seq analysis of 24 CCLE HCC cell lines.
Supplementary Figure S1 from H3B-6527 Is a Potent and Selective Inhibitor of FGFR4 in FGF19-Driven Hepatocellular Carcinoma
Authors: Joshi Jaya Julie , Coffey Heather , Corcoran Erik , Tsai Jennifer , Huang Chia-Ling , Ichikawa Kana , Prajapati Sudeep , Hao Ming-Hong , Bailey Suzanna , Wu Jeremy , Rimkunas Victoria , Karr Craig , Subramanian Vanitha , Kumar Pavan , MacKenzie Crystal , Hurley Raelene , Satoh Takashi , Yu Kun , Park Eunice , Rioux Nathalie , Kim Amy , Lai Weidong G. , Yu Lihua , Zhu Ping , Buonamici Silvia , Larsen Nicholas , Fekkes Peter , Wang John , Warmuth Markus , Reynolds Dominic J. , Smith Peter G. , Selvaraj Anand
Published: March 2023

H3B-6527 effects in a HCC cell line Hep3B orthotopic xenografts in female nude mice.
Table S1. List of genes amplified in tumors from E3 Ubiquitin Ligase UBR5 Drives the Growth and Metastasis of Triple-Negative Breast Cancer
Authors: Liao Liqiu , Song Mei , Li Xin , Tang Lili , Zhang Tuo , Zhang Lixing , Pan Yihang , Chouchane Lotfi , Ma Xiaojing
Published: March 2023

This list contains all genes amplified 2-fold or more in tumors.
Supplemental Figures and Legends from E3 Ubiquitin Ligase UBR5 Drives the Growth and Metastasis of Triple-Negative Breast Cancer
Authors: Liao Liqiu , Song Mei , Li Xin , Tang Lili , Zhang Tuo , Zhang Lixing , Pan Yihang , Chouchane Lotfi , Ma Xiaojing
Published: March 2023

This file contains supplemental data figures for many experimental controls and statistical analysis relevant to the manuscript.
Supplementary Figure S3 from CYP27A1 Loss Dysregulates Cholesterol Homeostasis in Prostate Cancer
Authors: Alfaqih Mahmoud A. , Nelson Erik R. , Liu Wen , Safi Rachid , Jasper Jeffery S. , Macias Everardo , Geradts Joseph , Thompson J. Will , Dubois Laura G. , Freeman Michael R. , Chang Ching-yi , Chi Jen-Tsan , McDonnell Donald P. , Freedland Stephen J.
Published: March 2023

overexpression does not lead to 1,25-dihydroxyvitamin D3 production in prostate cancer cells
Supplementary Figure S2 from CYP27A1 Loss Dysregulates Cholesterol Homeostasis in Prostate Cancer
Authors: Alfaqih Mahmoud A. , Nelson Erik R. , Liu Wen , Safi Rachid , Jasper Jeffery S. , Macias Everardo , Geradts Joseph , Thompson J. Will , Dubois Laura G. , Freeman Michael R. , Chang Ching-yi , Chi Jen-Tsan , McDonnell Donald P. , Freedland Stephen J.
Published: March 2023

Evaluation of CYP27A1 expression in PC cells
Supplementary Figure S1 from CYP27A1 Loss Dysregulates Cholesterol Homeostasis in Prostate Cancer
Authors: Alfaqih Mahmoud A. , Nelson Erik R. , Liu Wen , Safi Rachid , Jasper Jeffery S. , Macias Everardo , Geradts Joseph , Thompson J. Will , Dubois Laura G. , Freeman Michael R. , Chang Ching-yi , Chi Jen-Tsan , McDonnell Donald P. , Freedland Stephen J.
Published: March 2023

LDL enhances PC cell growth and assessment of CYP27A1 expression levels in different stages of PC
Supplementary tables 1 and 2 from Mass Spectrometry–Based Proteomics Reveals Potential Roles of NEK9 and MAP2K4 in Resistance to PI3K Inhibition in Triple-Negative Breast Cancers
Authors: Mundt Filip , Rajput Sandeep , Li Shunqiang , Ruggles Kelly V. , Mooradian Arshag D. , Mertins Philipp , Gillette Michael A. , Krug Karsten , Guo Zhanfang , Hoog Jeremy , Erdmann-Gilmore Petra , Primeau Tina , Huang Shixia , Edwards Dean P. , Wang Xiaowei , Wang Xuya , Kawaler Emily , Mani D.R. , Clauser Karl R. , Gao Feng , Luo Jingqin , Davies Sherri R. , Johnson Gary L. , Huang Kuan-lin , Yoon Christopher J. , Ding Li , Fenyö David , Ellis Matthew J. , Townsend R. Reid , Held Jason M. , Carr Steven A. , Ma Cynthia X.
Published: March 2023

Supplementary tables 1 and 2; Clinical information about the patients that the PDX models were established from and pathways that are regulated in the sensitive tumors after buparlisib treatment, respectively.
Supplementary File 5 from Mass Spectrometry–Based Proteomics Reveals Potential Roles of NEK9 and MAP2K4 in Resistance to PI3K Inhibition in Triple-Negative Breast Cancers
Authors: Mundt Filip , Rajput Sandeep , Li Shunqiang , Ruggles Kelly V. , Mooradian Arshag D. , Mertins Philipp , Gillette Michael A. , Krug Karsten , Guo Zhanfang , Hoog Jeremy , Erdmann-Gilmore Petra , Primeau Tina , Huang Shixia , Edwards Dean P. , Wang Xiaowei , Wang Xuya , Kawaler Emily , Mani D.R. , Clauser Karl R. , Gao Feng , Luo Jingqin , Davies Sherri R. , Johnson Gary L. , Huang Kuan-lin , Yoon Christopher J. , Ding Li , Fenyö David , Ellis Matthew J. , Townsend R. Reid , Held Jason M. , Carr Steven A. , Ma Cynthia X.
Published: March 2023

Response markers (pathways)
Supplementary methods from JAM-C Identifies Src Family Kinase-Activated Leukemia-Initiating Cells and Predicts Poor Prognosis in Acute Myeloid Leukemia
Authors: De Grandis Maria , Bardin Florence , Fauriat Cyril , Zemmour Christophe , El-Kaoutari Abdessamad , Sergé Arnauld , Granjeaud Samuel , Pouyet Laurent , Montersino Camille , Chretien Anne-Sophie , Mozziconacci Marie-Joelle , Castellano Remy , Bidaut Ghislain , Boher Jean-Marie , Collette Yves , Mancini Stéphane J.C. , Vey Norbert , Aurrand-Lions Michel
Published: March 2023

Supplementary methods describing flow-cytometry, cumulative relapse incidence calculation and mass spectrometry.
Supplementary Tables from JAM-C Identifies Src Family Kinase-Activated Leukemia-Initiating Cells and Predicts Poor Prognosis in Acute Myeloid Leukemia
Authors: De Grandis Maria , Bardin Florence , Fauriat Cyril , Zemmour Christophe , El-Kaoutari Abdessamad , Sergé Arnauld , Granjeaud Samuel , Pouyet Laurent , Montersino Camille , Chretien Anne-Sophie , Mozziconacci Marie-Joelle , Castellano Remy , Bidaut Ghislain , Boher Jean-Marie , Collette Yves , Mancini Stéphane J.C. , Vey Norbert , Aurrand-Lions Michel
Published: March 2023

Supplementary Tables S1 to S8. S1 shows de novo AML patient characteristics. S2 shows JAM-C expression in monocytic AML. S3 shows multivariate Cox regression data. S4 shows genes selected for single cell gene expression study. S5 shows statistical analysis of genes used in Fig 3C. S6 shows limit dilution assay data in vitro. S7 shows limit dilution assay data in vivo. S8 shows frequencies of human and mouse cells from Fig 5E.
Supplementary Figures from JAM-C Identifies Src Family Kinase-Activated Leukemia-Initiating Cells and Predicts Poor Prognosis in Acute Myeloid Leukemia
Authors: De Grandis Maria , Bardin Florence , Fauriat Cyril , Zemmour Christophe , El-Kaoutari Abdessamad , Sergé Arnauld , Granjeaud Samuel , Pouyet Laurent , Montersino Camille , Chretien Anne-Sophie , Mozziconacci Marie-Joelle , Castellano Remy , Bidaut Ghislain , Boher Jean-Marie , Collette Yves , Mancini Stéphane J.C. , Vey Norbert , Aurrand-Lions Michel
Published: March 2023

Supplementary Figures S1 to S7. S1 shows JAM-C, CD90 and CD45RA expression in leukemic fraction. S2 shows JAM-C expression in leukemic cells and HSPCs. S3 shows JAM-C expression in cell lines and genes differentially expressed between KG1/JAM-CNeg and KG1/JAM-CPos variant cell lines. S4 shows characterization of engrafting and non-engrafting AML patient samples. S5 shows cell cycle and proliferation properties of KG1/JAM-CNeg and KG1/JAM-CPos variant cells. S6 shows signaling pathways in KG1/JAM-CNeg and KG1/JAM-CPos. S7 shows comparison of SFK phosphorylation in CD45dimCD34+ and CD45dimCD34- leukemic cells.
Supplementary File 1 from Mass Spectrometry–Based Proteomics Reveals Potential Roles of NEK9 and MAP2K4 in Resistance to PI3K Inhibition in Triple-Negative Breast Cancers
Authors: Mundt Filip , Rajput Sandeep , Li Shunqiang , Ruggles Kelly V. , Mooradian Arshag D. , Mertins Philipp , Gillette Michael A. , Krug Karsten , Guo Zhanfang , Hoog Jeremy , Erdmann-Gilmore Petra , Primeau Tina , Huang Shixia , Edwards Dean P. , Wang Xiaowei , Wang Xuya , Kawaler Emily , Mani D.R. , Clauser Karl R. , Gao Feng , Luo Jingqin , Davies Sherri R. , Johnson Gary L. , Huang Kuan-lin , Yoon Christopher J. , Ding Li , Fenyö David , Ellis Matthew J. , Townsend R. Reid , Held Jason M. , Carr Steven A. , Ma Cynthia X.
Published: March 2023

mRNA isoforms
Supplementary Figures from Mass Spectrometry–Based Proteomics Reveals Potential Roles of NEK9 and MAP2K4 in Resistance to PI3K Inhibition in Triple-Negative Breast Cancers
Authors: Mundt Filip , Rajput Sandeep , Li Shunqiang , Ruggles Kelly V. , Mooradian Arshag D. , Mertins Philipp , Gillette Michael A. , Krug Karsten , Guo Zhanfang , Hoog Jeremy , Erdmann-Gilmore Petra , Primeau Tina , Huang Shixia , Edwards Dean P. , Wang Xiaowei , Wang Xuya , Kawaler Emily , Mani D.R. , Clauser Karl R. , Gao Feng , Luo Jingqin , Davies Sherri R. , Johnson Gary L. , Huang Kuan-lin , Yoon Christopher J. , Ding Li , Fenyö David , Ellis Matthew J. , Townsend R. Reid , Held Jason M. , Carr Steven A. , Ma Cynthia X.
Published: March 2023

Supplementary Figures 1-10 supporting the study Mundt et al., "Proteomic profiling of PI3K inhibitor resistance"
Figure S3 from Hsp72 and Nek6 Cooperate to Cluster Amplified Centrosomes in Cancer Cells
Authors: Sampson Josephina , O'Regan Laura , Dyer Martin J.S. , Bayliss Richard , Fry Andrew M.
Published: March 2023

Figure S3 shows Hsp70 inhibition does not perturb mitotic progression in RPE1 cells
Figure S2 from Hsp72 and Nek6 Cooperate to Cluster Amplified Centrosomes in Cancer Cells
Authors: Sampson Josephina , O'Regan Laura , Dyer Martin J.S. , Bayliss Richard , Fry Andrew M.
Published: March 2023

Figure S2 shows Hsp70 inhibition does not block clustering of acentrosomal spindle poles.
Supplementary Table S2 from ASXL3 Is a Novel Pluripotency Factor in Human Respiratory Epithelial Cells and a Potential Therapeutic Target in Small Cell Lung Cancer
Authors: Shukla Vivek , Rao Mahadev , Zhang Hongen , Beers Jeanette , Wangsa Darawalee , Wangsa Danny , Buishand Floryne O. , Wang Yonghong , Yu Zhiya , Stevenson Holly S. , Reardon Emily S. , McLoughlin Kaitlin C. , Kaufman Andrew S. , Payabyab Eden C. , Hong Julie A. , Zhang Mary , Davis Sean , Edelman Daniel , Chen Guokai , Miettinen Markku M. , Restifo Nicholas P. , Ried Thomas , Meltzer Paul A. , Schrump David S.
Published: March 2023

DNA Methylation Pattern of PRC2 Target Genes
Supplementary Fig.1-11 from Genomic and Epigenomic Heterogeneity of Hepatocellular Carcinoma
Authors: Lin De-Chen , Mayakonda Anand , Dinh Huy Q. , Huang Pinbo , Lin Lehang , Liu Xiaoping , Ding Ling-wen , Wang Jie , Berman Benjamin P. , Song Er-Wei , Yin Dong , Koeffler H. Phillip
Published: March 2023

Files containing resutls related to genomic and methylation ITH , detailed mutational signatures, and sample pathology
Supplemental Tables S1-4 from Genomic and Epigenomic Heterogeneity of Hepatocellular Carcinoma
Authors: Lin De-Chen , Mayakonda Anand , Dinh Huy Q. , Huang Pinbo , Lin Lehang , Liu Xiaoping , Ding Ling-wen , Wang Jie , Berman Benjamin P. , Song Er-Wei , Yin Dong , Koeffler H. Phillip
Published: March 2023

Files containing sequencing details and sample information
Supplementary Figure S4 from ASXL3 Is a Novel Pluripotency Factor in Human Respiratory Epithelial Cells and a Potential Therapeutic Target in Small Cell Lung Cancer
Authors: Shukla Vivek , Rao Mahadev , Zhang Hongen , Beers Jeanette , Wangsa Darawalee , Wangsa Danny , Buishand Floryne O. , Wang Yonghong , Yu Zhiya , Stevenson Holly S. , Reardon Emily S. , McLoughlin Kaitlin C. , Kaufman Andrew S. , Payabyab Eden C. , Hong Julie A. , Zhang Mary , Davis Sean , Edelman Daniel , Chen Guokai , Miettinen Markku M. , Restifo Nicholas P. , Ried Thomas , Meltzer Paul A. , Schrump David S.
Published: March 2023

Methylation patterns of repetitive elements and PRC2 targets in teratogenic iPSCs
Supplemental Table S5 from Genomic and Epigenomic Heterogeneity of Hepatocellular Carcinoma
Authors: Lin De-Chen , Mayakonda Anand , Dinh Huy Q. , Huang Pinbo , Lin Lehang , Liu Xiaoping , Ding Ling-wen , Wang Jie , Berman Benjamin P. , Song Er-Wei , Yin Dong , Koeffler H. Phillip
Published: March 2023

File containing all somatic mutations
Table S3 from PP2A Inactivation Mediated by PPP2R4 Haploinsufficiency Promotes Cancer Development
Authors: Sents Ward , Meeusen Bob , Kalev Petar , Radaelli Enrico , Sagaert Xavier , Miermans Eline , Haesen Dorien , Lambrecht Caroline , Dewerchin Mieke , Carmeliet Peter , Westermarck Jukka , Sablina Anna , Janssens Veerle
Published: March 2023

Overview of cancer-associated PPP2R4 exome mutations found in COSMIC and cBioportal cancer databases.
Table S2 from PP2A Inactivation Mediated by PPP2R4 Haploinsufficiency Promotes Cancer Development
Authors: Sents Ward , Meeusen Bob , Kalev Petar , Radaelli Enrico , Sagaert Xavier , Miermans Eline , Haesen Dorien , Lambrecht Caroline , Dewerchin Mieke , Carmeliet Peter , Westermarck Jukka , Sablina Anna , Janssens Veerle
Published: March 2023

Antibodies used in this study.
Table S1 from PP2A Inactivation Mediated by PPP2R4 Haploinsufficiency Promotes Cancer Development
Authors: Sents Ward , Meeusen Bob , Kalev Petar , Radaelli Enrico , Sagaert Xavier , Miermans Eline , Haesen Dorien , Lambrecht Caroline , Dewerchin Mieke , Carmeliet Peter , Westermarck Jukka , Sablina Anna , Janssens Veerle
Published: March 2023

Oligonucleotides used for site-directed mutagenesis of PTPA, and for genomic characterization of Ppp2r4 gene-trapped ES-cells and mice.
Supplementary Data from Glioblastoma Therapy Can Be Augmented by Targeting IDH1-Mediated NADPH Biosynthesis
Authors: Wahl Daniel R. , Dresser Joseph , Wilder-Romans Kari , Parsels Joshua D. , Zhao Shuang G. , Davis Mary , Zhao Lili , Kachman Maureen , Wernisch Stefanie , Burant Charles F. , Morgan Meredith A. , Feng Felix Y. , Speers Corey , Lyssiotis Costas A. , Lawrence Theodore S.
Published: March 2023

Supplementary Table 1: Experimental Details of Mass Spectrometry Supplemental Figure 1: Effects of IDH1 KD on radiation-induced apoptosis and autophagy. Effect of low dose radiation on expression of NADPH-producing enzymes Supplemental Figure 2: Effect of IDH1 KD on radiation induced DNA double strand break repair and homologous recombination repair Supplemental Figure 3: Cell cycle effects of IDH1 knockdown. Supplemental Figure 4: Effects of doxycycline and radiation on control i-shNT xenografts.
Supplementary methods from Biomarker-Based PET Imaging of Diffuse Intrinsic Pontine Glioma in Mouse Models
Authors: Kossatz Susanne , Carney Brandon , Schweitzer Melanie , Carlucci Giuseppe , Miloushev Vesselin Z. , Maachani Uday B. , Rajappa Prajwal , Keshari Kayvan R. , Pisapia David , Weber Wolfgang A. , Souweidane Mark M. , Reiner Thomas
Published: March 2023

More detailed description of methods mentioned in the main manuscript
Figure S1 from PP2A Inactivation Mediated by PPP2R4 Haploinsufficiency Promotes Cancer Development
Authors: Sents Ward , Meeusen Bob , Kalev Petar , Radaelli Enrico , Sagaert Xavier , Miermans Eline , Haesen Dorien , Lambrecht Caroline , Dewerchin Mieke , Carmeliet Peter , Westermarck Jukka , Sablina Anna , Janssens Veerle
Published: March 2023

Optimalisation of phosphorylase-a phosphatase activity assays in total brain lysates, using PP1 and PP2A specificity controls: time and concentration courses
Supplementary Table S2 from Biomarker Dynamics in B-cell Lymphoma: A Longitudinal Prospective Study of Plasma Samples Up to 25 Years before Diagnosis
Authors: Späth Florentin , Wibom Carl , Krop Esmeralda J.M. , Johansson Ann-Sofie , Bergdahl Ingvar A. , Vermeulen Roel , Melin Beatrice
Published: March 2023

Case-only analysis confirming steeper slopes towards diagnosis.
Supplementary Fig. 5 from Biomarker-Based PET Imaging of Diffuse Intrinsic Pontine Glioma in Mouse Models
Authors: Kossatz Susanne , Carney Brandon , Schweitzer Melanie , Carlucci Giuseppe , Miloushev Vesselin Z. , Maachani Uday B. , Rajappa Prajwal , Keshari Kayvan R. , Pisapia David , Weber Wolfgang A. , Souweidane Mark M. , Reiner Thomas
Published: March 2023

PARP1 IHC of brain areas and relevant tissues and organs of ntv-a;p53fl/fl mice.
Supplementary Table S1 from Biomarker Dynamics in B-cell Lymphoma: A Longitudinal Prospective Study of Plasma Samples Up to 25 Years before Diagnosis
Authors: Späth Florentin , Wibom Carl , Krop Esmeralda J.M. , Johansson Ann-Sofie , Bergdahl Ingvar A. , Vermeulen Roel , Melin Beatrice
Published: March 2023

Case-only analysis for linear mixed effect modeling.
Supplementary Fig. 4 from Biomarker-Based PET Imaging of Diffuse Intrinsic Pontine Glioma in Mouse Models
Authors: Kossatz Susanne , Carney Brandon , Schweitzer Melanie , Carlucci Giuseppe , Miloushev Vesselin Z. , Maachani Uday B. , Rajappa Prajwal , Keshari Kayvan R. , Pisapia David , Weber Wolfgang A. , Souweidane Mark M. , Reiner Thomas
Published: March 2023

PET/CT whole body image of [18F]PARPi 2 h p.i. Whole body PET/CT images of tumor bearing ntv-a;p53fl/fl mice. The brain tumor can clearly be distinguished from background brain signal. In the body, high uptake can be seen especially in the gut. This is due to the hepatobiliary excretion of the molecule, caused by its high lipophilicity which is necessary in order to reach the target in the cell nucleus.
Supplementary Fig. 3 from Biomarker-Based PET Imaging of Diffuse Intrinsic Pontine Glioma in Mouse Models
Authors: Kossatz Susanne , Carney Brandon , Schweitzer Melanie , Carlucci Giuseppe , Miloushev Vesselin Z. , Maachani Uday B. , Rajappa Prajwal , Keshari Kayvan R. , Pisapia David , Weber Wolfgang A. , Souweidane Mark M. , Reiner Thomas
Published: March 2023

Histological characterization of GEMM tumor model and PARPi-FL localization. (a) The GEMM model showed heterogenous morphological characteristics, representing high grade areas (with necrotic features, high cellularity, microvascular proliferation) and lower grade areas (less cellular, no necrosis). PARP1 expression was more pronounced in high grade areas compared to low grade areas and very low in normal pons. (b) Immunofluorescent characterization of high grade and low grade tumor areas and healthy brain. Tissues were stained for Ki67, CD31 and PARP1 expression. This was compared to the localization of intravenously in vivo injected PARPi-FL.
Supplementary Figure and Data from Chemosensitivity of IDH1-Mutated Gliomas Due to an Impairment in PARP1-Mediated DNA Repair
Authors: Lu Yanxin , Kwintkiewicz Jakub , Liu Yang , Tech Katherine , Frady Lauren N. , Su Yu-Ting , Bautista Wendy , Moon Seog In , MacDonald Jeffrey , Ewend Matthew G. , Gilbert Mark R. , Yang Chunzhang , Wu Jing
Published: March 2023

Supplementary figures and tables