bluuebunny/crossref_metadata_2025 huggingface dataset:
Figure S1-S7 from AMPK–Akt Double-Negative Feedback Loop in Breast Cancer Cells Regulates Their Adaptation to Matrix Deprivation
Authors: Saha Manipa , Kumar Saurav , Bukhari Shoiab , Balaji Sai A. , Kumar Prashant , Hindupur Sravanth K. , Rangarajan Annapoorni
Published: March 2023

File contains supplementary figures
Supplemental Figures and Legends from Multikinase Inhibitor CT-707 Targets Liver Cancer by Interrupting the Hypoxia-Activated IGF-1R–YAP Axis
Authors: Zhu Hong , Wang Dan-Dan , Yuan Tao , Yan Fang-Jie , Zeng Chen-Ming , Dai Xiao-Yang , Chen Zi-bo , Chen Ying , Zhou Tianyi , Fan Guang-Han , Ying Meidan , Cao Ji , Luo Peihua , Liu Xi-Jie , Hu Yuandong , Peng Yong , He Qiaojun , Yang Bo
Published: March 2023

Supp Figure 1. The treatment of CT-707 reduced the protein level of CTGF under hypoxia. Supp Figure 2. CT-707 elicited apoptotic cell death but not cell cycle arrest under hypoxia. Supp Figure 3. The protein level of HIF-1α under hypoxia was not influenced by YAP depletion by siRNA. Supp Figure 4. FAK inhibition was not required for the hypoxic activity of CT-707. Supp Figure 5. The semi-quantitative analyses using density measurements on the protein levels displayed in Figure 5. Supp Figure 6. The correlation of FAK, IGF-1R and YAP target genes expression with the overall survival days of liver cancer patients. Supp Figure 7. The in vivo activities of CT-707 on HepG2-, Bel-7402-xenograft and H22-allograft models. Supp Figure 8. PF-562271 treatment caused death of HepG2-xenografted nude mice but imposed less activity than CT-707.
Supplementary Data from A Novel l-Asparaginase with low l-Glutaminase Coactivity Is Highly Efficacious against Both T- and B-cell Acute Lymphoblastic Leukemias In Vivo
Authors: Nguyen Hien Anh , Su Ying , Zhang Jenny Y. , Antanasijevic Aleksandar , Caffrey Michael , Schalk Amanda M. , Liu Li , Rondelli Damiano , Oh Annie , Mahmud Dolores L. , Bosland Maarten C. , Kajdacsy-Balla Andre , Peirs Sofie , Lammens Tim , Mondelaers Veerle , De Moerloose Barbara , Goossens Steven , Schlicht Michael J. , Kabirov Kasim K. , Lyubimov Alexander V. , Merrill Bradley J. , Saunthararajah Yogen , Van Vlierberghe Pieter , Lavie Arnon
Published: March 2023

Supplementary methods Supplementary Text: Wolinella succinogenes as a low L-glutaminase L-asparaginase Supplementary Figures: â€¢ Fig. S1. In vivo imaging showing that the L-glutaminase-diminished ErA-63Q and ErA-DM variants eliminate T-ALL LOUCY cells as effectively as the high L-glutaminase ErA-WT. â€¢ Fig. S2: In vivo imaging showing that the low L-glutaminase ErA-DM variant eliminates B-ALL SUP-B15 cells as effectively as the high L-glutaminase ErA-WT. â€¢ Fig. S3. In vivo imaging showing that the ultra-low L-glutaminase ErA-TM variant eliminates T-ALL LOUCY cells as effectively as the high L-glutaminase ErA-WT. â€¢ Fig. S4. In vitro sensitivity of two human ALL cell lines to L-asparaginases. â€¢ Fig. S5: Calibration between the in vivo imaging flux intensity and the measured %huCD45+ levels in peripheral blood (PB). â€¢ Fig. S6. In vivo imaging with signal-to-color range adjusted. â€¢ Fig. S7. Correlation between L-glutaminase activity and the reduction in mice activity. â€¢ Fig. S8. Correlation between L-glutaminase activity of the ErA variants and mice weight loss. â€¢ Fig. S9. ASNS qPCR data for the LOUCY cell line and 5 ALL patient samples. Data. Biostatistics on BLI and weight data.
Supplementary Tables from miR-508 Defines the Stem-like/Mesenchymal Subtype in Colorectal Cancer
Authors: Yan Ting-Ting , Ren Lin-Lin , Shen Chao-Qin , Wang Zhen-Hua , Yu Ya-Nan , Liang Qian , Tang Jia-Yin , Chen Ying-Xuan , Sun Dan-Feng , Zgodzinski Witold , Majewski Marek , Radwan Piotr , Kryczek Ilona , Zhong Ming , Chen Jinxian , Liu Qiang , Zou Weiping , Chen Hao-Yan , Hong Jie , Fang Jing-Yuan
Published: March 2023

This file contains supplementary tables 1-7 and the main information was described as follows. Table S1. All primers for real time PCR assay. Table S2. Differentially expressed genes between mesenchymal subtype and other non stem-like. Table S3. microRNA in stem-like/EMT CRC patients. Table S4. Full list of the predicted targets for the four key miRNAs. Table S5. Clinical information of 90 cases CRC patients (Renji cohort 1). Table S6. Clinical information of 100 cases CRC patients (Renji cohort 2). Table S7. Clinical information of 128 cases CRC patients (European cohort).
Supplementary Figures from miR-508 Defines the Stem-like/Mesenchymal Subtype in Colorectal Cancer
Authors: Yan Ting-Ting , Ren Lin-Lin , Shen Chao-Qin , Wang Zhen-Hua , Yu Ya-Nan , Liang Qian , Tang Jia-Yin , Chen Ying-Xuan , Sun Dan-Feng , Zgodzinski Witold , Majewski Marek , Radwan Piotr , Kryczek Ilona , Zhong Ming , Chen Jinxian , Liu Qiang , Zou Weiping , Chen Hao-Yan , Hong Jie , Fang Jing-Yuan
Published: March 2023

This file contains supplementary figures 1-7 and the main information was described as follows. Fig. S1. Differential microRNA and mRNA profiles in the stem-like/EMT subtype of CRC in TCGA. Fig. S2. Role of miR-506 family in the control of the stem-like/EMT subtype of CRC. Fig. S3. Target genes and role of miR-508 in CRC stem/EMT-signal activation. Fig. S4. Associations of miR-508 expression with the stem-like/EMT and stromal genes in CRC. Fig. S5. Involvement of miR-508 in the regulation of TGFβ-mediated EMT in CRC. Fig. S6. Association between miR-508 and survival in CRC. Fig. S7. Involvement of hypoxia and AK000053 lncRNA in the downregulation of miR-508 and the miR-508-mediated target gene in CRC.
Table S4 from eIF5A-PEAK1 Signaling Regulates YAP1/TAZ Protein Expression and Pancreatic Cancer Cell Growth
Authors: Strnadel Jan , Choi Sunkyu , Fujimura Ken , Wang Huawei , Zhang Wei , Wyse Meghan , Wright Tracy , Gross Emilie , Peinado Carlos , Park Hyun Woo , Bui Jack , Kelber Jonathan , Bouvet Michael , Guan Kun-Liang , Klemke Richard L.
Published: March 2023

Correlation of PEAK1 mRNA expression with YAP1, TEAD1, and CTGF in human cancers
Table S3 from eIF5A-PEAK1 Signaling Regulates YAP1/TAZ Protein Expression and Pancreatic Cancer Cell Growth
Authors: Strnadel Jan , Choi Sunkyu , Fujimura Ken , Wang Huawei , Zhang Wei , Wyse Meghan , Wright Tracy , Gross Emilie , Peinado Carlos , Park Hyun Woo , Bui Jack , Kelber Jonathan , Bouvet Michael , Guan Kun-Liang , Klemke Richard L.
Published: March 2023

List of PEAK1 regulated proteins involved in cytoskeleton organization
Table S2 from eIF5A-PEAK1 Signaling Regulates YAP1/TAZ Protein Expression and Pancreatic Cancer Cell Growth
Authors: Strnadel Jan , Choi Sunkyu , Fujimura Ken , Wang Huawei , Zhang Wei , Wyse Meghan , Wright Tracy , Gross Emilie , Peinado Carlos , Park Hyun Woo , Bui Jack , Kelber Jonathan , Bouvet Michael , Guan Kun-Liang , Klemke Richard L.
Published: March 2023

List of PEAK1 regulated proteins involved in translation
Supplementary figures and methods from Oncolytic Adenoviral Delivery of an EGFR-Targeting T-cell Engager Improves Antitumor Efficacy
Authors: Fajardo Carlos Alberto , Guedan Sonia , Rojas Luis Alfonso , Moreno Rafael , Arias-Badia Marcel , de Sostoa Jana , June Carl H. , Alemany Ramon
Published: March 2023

Supplementary figures 1-6 and supplementary methods. S1, EGFR and CD3 profiles of the cell lines used in the study; S2, cBiTE antibodies are expressed from ICO15K-cBiTE-infected cells and specifically bind to target cells; S3, Characterization of adenovirus infection in A431 cells; S4. Preactivated T cells produce proinflammatory cytokines and show higher killing capacities than naïve T cells when engaged by the cBiTE; S5, Luciferase- and GFP-expressing T cells retain their proliferative capacities in vitro; S6, Immunohistological detection of adenovirus and cBiTE in tumor samples.
Table S1 from eIF5A-PEAK1 Signaling Regulates YAP1/TAZ Protein Expression and Pancreatic Cancer Cell Growth
Authors: Strnadel Jan , Choi Sunkyu , Fujimura Ken , Wang Huawei , Zhang Wei , Wyse Meghan , Wright Tracy , Gross Emilie , Peinado Carlos , Park Hyun Woo , Bui Jack , Kelber Jonathan , Bouvet Michael , Guan Kun-Liang , Klemke Richard L.
Published: March 2023

Complete list of proteins identified in PEAK1-depleted PDAC cells by LC/MS/MS
Figure S4 from eIF5A-PEAK1 Signaling Regulates YAP1/TAZ Protein Expression and Pancreatic Cancer Cell Growth
Authors: Strnadel Jan , Choi Sunkyu , Fujimura Ken , Wang Huawei , Zhang Wei , Wyse Meghan , Wright Tracy , Gross Emilie , Peinado Carlos , Park Hyun Woo , Bui Jack , Kelber Jonathan , Bouvet Michael , Guan Kun-Liang , Klemke Richard L.
Published: March 2023

Western blots showing PEAk1 and YAP1 depletion in PDAC cells treated with two independent shRNAs
Figure S3A from eIF5A-PEAK1 Signaling Regulates YAP1/TAZ Protein Expression and Pancreatic Cancer Cell Growth
Authors: Strnadel Jan , Choi Sunkyu , Fujimura Ken , Wang Huawei , Zhang Wei , Wyse Meghan , Wright Tracy , Gross Emilie , Peinado Carlos , Park Hyun Woo , Bui Jack , Kelber Jonathan , Bouvet Michael , Guan Kun-Liang , Klemke Richard L.
Published: March 2023

Informatics analyses of cytoskeleton proteins altered in PEAK1-depleted PDAC cells
Figure S2B from eIF5A-PEAK1 Signaling Regulates YAP1/TAZ Protein Expression and Pancreatic Cancer Cell Growth
Authors: Strnadel Jan , Choi Sunkyu , Fujimura Ken , Wang Huawei , Zhang Wei , Wyse Meghan , Wright Tracy , Gross Emilie , Peinado Carlos , Park Hyun Woo , Bui Jack , Kelber Jonathan , Bouvet Michael , Guan Kun-Liang , Klemke Richard L.
Published: March 2023

Informatics analyses of translation proteins altered in PEAK1-depleted PDAC cells
Suppl Figures 1, 2, 3, 4, 5, 6 and legends from PPARδ Elicits Ligand-Independent Repression of Trefoil Factor Family to Limit Prostate Cancer Growth
Authors: Martín-Martín Natalia , Zabala-Letona Amaia , Fernández-Ruiz Sonia , Arreal Leire , Camacho Laura , Castillo-Martin Mireia , Cortazar Ana R. , Torrano Verónica , Astobiza Ianire , Zúñiga-García Patricia , Ugalde-Olano Aitziber , Loizaga-Iriarte Ana , Unda Miguel , Valcárcel-Jiménez Lorea , Arruabarrena-Aristorena Amaia , Piva Marco , Sánchez-Mosquera Pilar , Aransay Ana M. , Gomez-Muñoz Antonio , Barrio Rosa , Sutherland James D. , Carracedo Arkaitz
Published: March 2023

Suppl Figures 1, 2, 3, 4, 5, 6
Figure S2A from eIF5A-PEAK1 Signaling Regulates YAP1/TAZ Protein Expression and Pancreatic Cancer Cell Growth
Authors: Strnadel Jan , Choi Sunkyu , Fujimura Ken , Wang Huawei , Zhang Wei , Wyse Meghan , Wright Tracy , Gross Emilie , Peinado Carlos , Park Hyun Woo , Bui Jack , Kelber Jonathan , Bouvet Michael , Guan Kun-Liang , Klemke Richard L.
Published: March 2023

Informatics analyses of translation proteins altered in PEAK1-depleted PDAC cells
Figure S1-S8 from Tamoxifen Resistance in Breast Cancer Is Regulated by the EZH2–ERα–GREB1 Transcriptional Axis
Authors: Wu Yanming , Zhang Zhao , Cenciarini Mauro E. , Proietti Cecilia J. , Amasino Matias , Hong Tao , Yang Mei , Liao Yiji , Chiang Huai-Chin , Kaklamani Virginia G. , Jeselsohn Rinath , Vadlamudi Ratna K. , Huang Tim Hui-Ming , Li Rong , De Angelis Carmine , Fu Xiaoyong , Elizalde Patricia V. , Schiff Rachel , Brown Myles , Xu Kexin
Published: March 2023

This file contains eight supplementary figures depicting the experiments validated in different cell lines and cohorts, as well as the results supportive to the main text.
Supplementary Table 8 from Mapping the HLA Ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation
Authors: Löffler Markus W. , Kowalewski Daniel J. , Backert Linus , Bernhardt Jörg , Adam Patrick , Schuster Heiko , Dengler Florian , Backes Daniel , Kopp Hans-Georg , Beckert Stefan , Wagner Silvia , Königsrainer Ingmar , Kohlbacher Oliver , Kanz Lothar , Königsrainer Alfred , Rammensee Hans-Georg , Stevanović Stefan , Haen Sebastian P.
Published: March 2023

Statistics over-represented peptides HLA class II
Table S7 from Genomic and Epigenomic Signatures in Ovarian Cancer Associated with Resensitization to Platinum Drugs
Authors: Fang Fang , Cardenas Horacio , Huang Hao , Jiang Guanglong , Perkins Susan M. , Zhang Chi , Keer Harold N. , Liu Yunlong , Nephew Kenneth P. , Matei Daniela
Published: March 2023

Table S7. 165 cancer and 218 stromal markers
Table S4, S5, S6 from Genomic and Epigenomic Signatures in Ovarian Cancer Associated with Resensitization to Platinum Drugs
Authors: Fang Fang , Cardenas Horacio , Huang Hao , Jiang Guanglong , Perkins Susan M. , Zhang Chi , Keer Harold N. , Liu Yunlong , Nephew Kenneth P. , Matei Daniela
Published: March 2023

Table S4. 1155 genes associated with PFS Table S5. 203 guadecitabine deM genes associated with PFS Table S6. 293 guadecitabine upregulated genes associated with PFS
Supplementary Figures 1-6 from Mapping the HLA Ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation
Authors: Löffler Markus W. , Kowalewski Daniel J. , Backert Linus , Bernhardt Jörg , Adam Patrick , Schuster Heiko , Dengler Florian , Backes Daniel , Kopp Hans-Georg , Beckert Stefan , Wagner Silvia , Königsrainer Ingmar , Kohlbacher Oliver , Kanz Lothar , Königsrainer Alfred , Rammensee Hans-Georg , Stevanović Stefan , Haen Sebastian P.
Published: March 2023

Complete supplementary figures containing: Suppl. Fig. 1: HLA-coverage (Caucasian); Suppl. Fig. 2: Maximum attainable quantities of source proteins; Suppl. Fig. 3: Comparsion with complete benign dataset; Suppl. Fig. 4: Legend PANTHER analysis; Suppl. Fig. 5: Legend KEGG analysis; Suppl. Fig. 6: Representation analysis HLA class II
Table S3 from Genomic and Epigenomic Signatures in Ovarian Cancer Associated with Resensitization to Platinum Drugs
Authors: Fang Fang , Cardenas Horacio , Huang Hao , Jiang Guanglong , Perkins Susan M. , Zhang Chi , Keer Harold N. , Liu Yunlong , Nephew Kenneth P. , Matei Daniela
Published: March 2023

Table S3. 77 integrated genes
Supplementary-Tables from A Subpopulation of Stromal Cells Controls Cancer Cell Homing to the Bone Marrow
Authors: Rossnagl Stephanie , Ghura Hiba , Groth Christopher , Altrock Eva , Jakob Franz , Schott Sarah , Wimberger Pauline , Link Theresa , Kuhlmann Jan Dominik , Stenzl Arnulf , Hennenlotter Jörg , Todenhöfer Tilmann , Rojewski Markus , Bieback Karen , Nakchbandi Inaam A.
Published: March 2023

Supplementary-Table 1A. The markers for murine mesenchymal stromal cells were selected based on literature. Supplementary-Table 1B. Model summary of stepwise multiple-regression analysis of the relation of the selected murine MSC markers and homing of tumor cells; *p<0.05; ***p<0.001 (n=48). Supplementary-Table 2A. The markers for human mesenchymal stromal cells were selected based on literature. Supplementary-Table 2B. Model summary of stepwise or enter multiple-regression analysis of proposed human MSC markers and cytokeratin staining in bone marrow aspirates from patients with prostate (PC: n=36) and breast cancer (BC: n=60); *p<0.05, **p<0.01, ***p<0.001. Supplementary-Table 3A. Clinical characteristics of prostate cancer patients (n=36) at the time of diagnosis. Numbers (percentages) of affected patients are provided. Supplementary-Table 3B. Clinical characteristics of breast cancer patients (n=60) at the time of surgery. The cohort was followed for a median of 21.4 months (Range 1.9-40.0 months). T: tumor size; N: nodal status; HR: hazard ratio; CI: confidence interval; ref.: reference. Significant p-values are bolded.
Supplementary Figure Legends from A Subpopulation of Stromal Cells Controls Cancer Cell Homing to the Bone Marrow
Authors: Rossnagl Stephanie , Ghura Hiba , Groth Christopher , Altrock Eva , Jakob Franz , Schott Sarah , Wimberger Pauline , Link Theresa , Kuhlmann Jan Dominik , Stenzl Arnulf , Hennenlotter Jörg , Todenhöfer Tilmann , Rojewski Markus , Bieback Karen , Nakchbandi Inaam A.
Published: March 2023

Supplementary-Figure 1. Tumor cell infiltration of other organs after PTH/ZA treatment. Evaluation of blood vessel numbers and binding of cancer cells to vascular cells after PTH/ZA treatment. PTH/ZA treatment does not affect colony forming units of hematopoietic populations. Supplementary-Figure 2. Characterization of the affected stromal population after PTH/ZA treatment. Supplementary-Figure 3. Correlations between MSCs, CFU-f and homing. Apoptosis after PTH/ZA treatment. Supplementary-Figure 4. Absolute numbers of HSPCs and MSCs after G-CSF and G-CSF PTH/ZA treatment and in Mx 1fl/fl knockout mice. Expression of MSC markers on low-passage human MSCs. Supplementary-Figure 5. Flow cytometry of MSC markers in human bone marrow biopsies.
Supplementary File 3 from Distinct TP63 Isoform-Driven Transcriptional Signatures Predict Tumor Progression and Clinical Outcomes
Authors: Abbas Hussein A. , Bui Ngoc Hoang Bao , Rajapakshe Kimal , Wong Justin , Gunaratne Preethi , Tsai Kenneth Y. , Coarfa Cristian , Flores Elsa R.
Published: March 2023

Components of tumor development TAp63 (3.1) and Î"Np63 (3.2) signatures used in this study. Pathways enriched in TAp63 (3.3) and Î"Np63 (3.4) tumor development signatures.
Figure S4 from A Subpopulation of Stromal Cells Controls Cancer Cell Homing to the Bone Marrow
Authors: Rossnagl Stephanie , Ghura Hiba , Groth Christopher , Altrock Eva , Jakob Franz , Schott Sarah , Wimberger Pauline , Link Theresa , Kuhlmann Jan Dominik , Stenzl Arnulf , Hennenlotter Jörg , Todenhöfer Tilmann , Rojewski Markus , Bieback Karen , Nakchbandi Inaam A.
Published: March 2023

Supplementary-Figure 4 Absolute numbers of HSPCs and MSCs after G-CSF and G-CSF+PTH/ZA treatment and in Mx 1fl/fl knockout mice (A) The absolute number of HSPCs per femur was lower after treatment with G-CSF, whereas the number of MSCs was higher, n=12/14 in 3 experiments. (B) Addition of PTH/ZA to G-CSF did not affect HSPCs further, but reduced the absolute number of MSCs, n=14/14 in 3 experiments. (C) Conditional deletion of integrin 1 (Mx 1fl/fl) in the bone marrow had no effect on HSPCs, but led to increased absolute numbers of MSCs, n=6/9 in 2 experiments. Expression of MSC markers on low-passage human MSCs (D) In order to evaluate potential MSC markers, adherent human bone marrow cells (passages 0 or 1) were dissociated from the plates and stained for flow cytometry analysis. Shown is a graph summarizing the findings. In addition, in each panel the unstained control is shown on the left and the bone marrow staining on the right (E). The cells were 79% positive for CD31, 91% positive for CD44, 22% positive for CD56, 95% positive for CD73, 59% positive for CD140b, 61% positive for CD144, 72% positive for CD146, 87% positive for CD271, 87% positive for CD349, 90% positive for FAP, 90% positive for MSCA1, and 92% positive for Stro1; n=4 different aspirates.
Supplementary File 1 from Distinct TP63 Isoform-Driven Transcriptional Signatures Predict Tumor Progression and Clinical Outcomes
Authors: Abbas Hussein A. , Bui Ngoc Hoang Bao , Rajapakshe Kimal , Wong Justin , Gunaratne Preethi , Tsai Kenneth Y. , Coarfa Cristian , Flores Elsa R.
Published: March 2023

TAp63-/- versus wildtype keratinocytes signature analysis
Figure S2 from A Subpopulation of Stromal Cells Controls Cancer Cell Homing to the Bone Marrow
Authors: Rossnagl Stephanie , Ghura Hiba , Groth Christopher , Altrock Eva , Jakob Franz , Schott Sarah , Wimberger Pauline , Link Theresa , Kuhlmann Jan Dominik , Stenzl Arnulf , Hennenlotter Jörg , Todenhöfer Tilmann , Rojewski Markus , Bieback Karen , Nakchbandi Inaam A.
Published: March 2023

Supplementary-Figure 2 Characterization of the affected stromal population after PTH/ZA treatment (A-B) Using flow cytometry, potential markers of mesenchymal stromal cells were evaluated in bone marrow of PTH/ZA-treated mice. Gating was applied after the exclusion of hematopoietic and erythroid cells (CD45- Ter119-). (B) PTH/ZA diminished the size of populations expressing the following surface markers: Sca1+, CD29+, CD31+, CD44-, αSMA+, leptin receptor+, and CD146+; n=15/15 in 3 experiments.
Supplementary Tables from Acetylation within the N- and C-Terminal Domains of Src Regulates Distinct Roles of STAT3-Mediated Tumorigenesis
Authors: Huang Chao , Zhang Zhe , Chen Lihan , Lee Hank W. , Ayrapetov Marina K. , Zhao Ting C. , Hao Yimei , Gao Jinsong , Yang Chunzhang , Mehta Gautam U. , Zhuang Zhengping , Zhang Xiaoren , Hu Guohong , Chin Y. Eugene
Published: March 2023

Predicted and mass spectrometry identified Src posttranslational modification residues
Figure S1 from A Subpopulation of Stromal Cells Controls Cancer Cell Homing to the Bone Marrow
Authors: Rossnagl Stephanie , Ghura Hiba , Groth Christopher , Altrock Eva , Jakob Franz , Schott Sarah , Wimberger Pauline , Link Theresa , Kuhlmann Jan Dominik , Stenzl Arnulf , Hennenlotter Jörg , Todenhöfer Tilmann , Rojewski Markus , Bieback Karen , Nakchbandi Inaam A.
Published: March 2023

Supplementary-Figure 1 Tumor cell infiltration of other organs after PTH/ZA treatment (A) The combined treatment with PTH/ZA does not affect the homing of MDA tumor cells to other organs; n=14/15 in 2 experiments. Evaluation of blood vessel numbers and binding of cancer cells to vascular cells after PTH/ZA treatment (B) PTH/ZA did not affect blood vessel numbers in the treated mice. Proximal tibiae from 4 mice/group were evaluated and the number of blood vessels adjusted to the evaluated area. (C) Binding of cancer cells to immune cells (CD45+) or vascular cells (CD31 or PLVAP) was not affected by treatment with PTH/ZA, n=13/11. Bone marrow from control and treated mice that received cancer cells 24 hours prior to bone marrow isolation was subjected to addition of magnetic beads precoated with CD45 antibody and carefully removed. Addition of either CD31 or PLVAP antibody coated beads followed and beads were used for DNA isolation and evaluation of cancer cell presence. The amount of cancer cell specific DNA was corrected to murine -actin. PTH/ZA treatment does not affect colony forming units of hematopoietic populations (D) There were no changes in various progenitor colonies when bone marrow from treated mice was cultured in vitro for 2 weeks in specialized media, stained with crystal violet and counted; n=6/6/6/6 in 3 experiments. CFU-GEMM is shown in Fig. 1C. Examples of the various colonies are shown below the graphs (light microscopy, 40x).
Figure S7 from Acetylation within the N- and C-Terminal Domains of Src Regulates Distinct Roles of STAT3-Mediated Tumorigenesis
Authors: Huang Chao , Zhang Zhe , Chen Lihan , Lee Hank W. , Ayrapetov Marina K. , Zhao Ting C. , Hao Yimei , Gao Jinsong , Yang Chunzhang , Mehta Gautam U. , Zhuang Zhengping , Zhang Xiaoren , Hu Guohong , Chin Y. Eugene
Published: March 2023

Expression of acetyl-Src and phospho-Stat3 in cancer tissues
Figure S6 from Acetylation within the N- and C-Terminal Domains of Src Regulates Distinct Roles of STAT3-Mediated Tumorigenesis
Authors: Huang Chao , Zhang Zhe , Chen Lihan , Lee Hank W. , Ayrapetov Marina K. , Zhao Ting C. , Hao Yimei , Gao Jinsong , Yang Chunzhang , Mehta Gautam U. , Zhuang Zhengping , Zhang Xiaoren , Hu Guohong , Chin Y. Eugene
Published: March 2023

Src acetylation regulates STAT3 Y705 phosphorylation and colony formation.
Figure S5 from Acetylation within the N- and C-Terminal Domains of Src Regulates Distinct Roles of STAT3-Mediated Tumorigenesis
Authors: Huang Chao , Zhang Zhe , Chen Lihan , Lee Hank W. , Ayrapetov Marina K. , Zhao Ting C. , Hao Yimei , Gao Jinsong , Yang Chunzhang , Mehta Gautam U. , Zhuang Zhengping , Zhang Xiaoren , Hu Guohong , Chin Y. Eugene
Published: March 2023

Validation of various phospho-Stat3 antibodies
Video V2 from PanIN Neuroendocrine Cells Promote Tumorigenesis via Neuronal Cross-talk
Authors: Sinha Smrita , Fu Ya-Yuan , Grimont Adrien , Ketcham Maren , Lafaro Kelly , Saglimbeni Joseph A. , Askan Gokce , Bailey Jennifer M. , Melchor Jerry P. , Zhong Yi , Joo Min Geol , Grbovic-Huezo Olivera , Yang In-Hong , Basturk Olca , Baker Lindsey , Park Young , Kurtz Robert C. , Tuveson David , Leach Steven D. , Pasricha Pankaj J.
Published: March 2023

Bright field and fluorescent live imaging of NK1-Rlow (red) and NK1-Rhi/GFP (yellow) cells plated together in organoid culture.
Figure S4 from Acetylation within the N- and C-Terminal Domains of Src Regulates Distinct Roles of STAT3-Mediated Tumorigenesis
Authors: Huang Chao , Zhang Zhe , Chen Lihan , Lee Hank W. , Ayrapetov Marina K. , Zhao Ting C. , Hao Yimei , Gao Jinsong , Yang Chunzhang , Mehta Gautam U. , Zhuang Zhengping , Zhang Xiaoren , Hu Guohong , Chin Y. Eugene
Published: March 2023

Src plasma membrane association and dissociation under different conditions
Video V1 from PanIN Neuroendocrine Cells Promote Tumorigenesis via Neuronal Cross-talk
Authors: Sinha Smrita , Fu Ya-Yuan , Grimont Adrien , Ketcham Maren , Lafaro Kelly , Saglimbeni Joseph A. , Askan Gokce , Bailey Jennifer M. , Melchor Jerry P. , Zhong Yi , Joo Min Geol , Grbovic-Huezo Olivera , Yang In-Hong , Basturk Olca , Baker Lindsey , Park Young , Kurtz Robert C. , Tuveson David , Leach Steven D. , Pasricha Pankaj J.
Published: March 2023

3D animation showing innervation of a PanIN lesion.
Figure S2 from Acetylation within the N- and C-Terminal Domains of Src Regulates Distinct Roles of STAT3-Mediated Tumorigenesis
Authors: Huang Chao , Zhang Zhe , Chen Lihan , Lee Hank W. , Ayrapetov Marina K. , Zhao Ting C. , Hao Yimei , Gao Jinsong , Yang Chunzhang , Mehta Gautam U. , Zhuang Zhengping , Zhang Xiaoren , Hu Guohong , Chin Y. Eugene
Published: March 2023

Validation of various acetyl-Src antibodies
Supplemental Table S1 from PanIN Neuroendocrine Cells Promote Tumorigenesis via Neuronal Cross-talk
Authors: Sinha Smrita , Fu Ya-Yuan , Grimont Adrien , Ketcham Maren , Lafaro Kelly , Saglimbeni Joseph A. , Askan Gokce , Bailey Jennifer M. , Melchor Jerry P. , Zhong Yi , Joo Min Geol , Grbovic-Huezo Olivera , Yang In-Hong , Basturk Olca , Baker Lindsey , Park Young , Kurtz Robert C. , Tuveson David , Leach Steven D. , Pasricha Pankaj J.
Published: March 2023

List of target genes and their respective primer sequences used in qPCR analyses.
Supplemental Figures from PanIN Neuroendocrine Cells Promote Tumorigenesis via Neuronal Cross-talk
Authors: Sinha Smrita , Fu Ya-Yuan , Grimont Adrien , Ketcham Maren , Lafaro Kelly , Saglimbeni Joseph A. , Askan Gokce , Bailey Jennifer M. , Melchor Jerry P. , Zhong Yi , Joo Min Geol , Grbovic-Huezo Olivera , Yang In-Hong , Basturk Olca , Baker Lindsey , Park Young , Kurtz Robert C. , Tuveson David , Leach Steven D. , Pasricha Pankaj J.
Published: March 2023

Figure S1 (Supports Figures 1 and 3) Co-culture of DRG neurons with cell and organoid lines. Figure S2 (Supports Figure 6) Histopathologic techniques for PanIN quantification and tumor identification. Figure S3 (Supports Figure 4) FACS sorting of PanIN neuroendocrine cells and expansion in organoid culture. Figure S4 (Supports Figure 1) Innervation of wild type pancreas and PanIN-free acinar tissue and axon recruitment by PDAC cell lines. Figure S5 (Supports Figure 2) Mouse and human PanINs contain NK1-R+ cells. Figure S6 (Supports Figure 2) Human duodenal enteroendocrine cells express the NK1-R. Figure S7 (Supports Figure 3) PanIN organoids express CgA and neuronal conditioned media increases PanIN organoid proliferation. Figure S8 (Supports Figure 4) Neuroendocrine cells exert trophic influences in vitro. Figure S9 (Supports Figure 6) Quantifications in control and denervated mice. Figure S10 (Supports Figure 6) Quantification of p-Stat3 in vivo. Figure S11 (Supports Figure 6) Quantification of NK1-R+ cells. Table S1. qPCR primer sequences. Video V1 (Supports Figure 1). Video V2 (Supports Figure 4).
Figure S1 from Acetylation within the N- and C-Terminal Domains of Src Regulates Distinct Roles of STAT3-Mediated Tumorigenesis
Authors: Huang Chao , Zhang Zhe , Chen Lihan , Lee Hank W. , Ayrapetov Marina K. , Zhao Ting C. , Hao Yimei , Gao Jinsong , Yang Chunzhang , Mehta Gautam U. , Zhuang Zhengping , Zhang Xiaoren , Hu Guohong , Chin Y. Eugene
Published: March 2023

Interaction between Src and CBP
Supplemental Table 6 from Comparative Transcriptome Analysis Quantifies Immune Cell Transcript Levels, Metastatic Progression, and Survival in Osteosarcoma
Authors: Scott Milcah C. , Temiz Nuri A. , Sarver Anne E. , LaRue Rebecca S. , Rathe Susan K. , Varshney Jyotika , Wolf Natalie K. , Moriarity Branden S. , O'Brien Timothy D. , Spector Logan G. , Largaespada David A. , Modiano Jaime F. , Subramanian Subbaya , Sarver Aaron L.
Published: March 2023

Supplemental Table 6. Gene Cluster Expression Summary Scores. Tab 1 Human GCESS values Tab 2 Mouse GCESS values Tab 3 Dog GCESS values Tab 4 GSE212257 GCESS values
Supplemental Data Table 2 from Coactivation of Estrogen Receptor and IKKβ Induces a Dormant Metastatic Phenotype in ER-Positive Breast Cancer
Authors: El-Shennawy Lamiaa , Dubrovskyi Oleksii , Kastrati Irida , Danes Jeanne M. , Zhang Yiqun , Whiteley Herbert E. , Creighton Chad J. , Frasor Jonna
Published: March 2023

This file contains significantly enriched MSigDB gene sets from pathway analysis of the six gene regulatory patterns found in figure 6.
Supplemental Table 5 from Comparative Transcriptome Analysis Quantifies Immune Cell Transcript Levels, Metastatic Progression, and Survival in Osteosarcoma
Authors: Scott Milcah C. , Temiz Nuri A. , Sarver Anne E. , LaRue Rebecca S. , Rathe Susan K. , Varshney Jyotika , Wolf Natalie K. , Moriarity Branden S. , O'Brien Timothy D. , Spector Logan G. , Largaespada David A. , Modiano Jaime F. , Subramanian Subbaya , Sarver Aaron L.
Published: March 2023

Supplemental Table 5. IPA enrichment analyses of recurrent human gene clusters.
Supplemental Table 4 from Comparative Transcriptome Analysis Quantifies Immune Cell Transcript Levels, Metastatic Progression, and Survival in Osteosarcoma
Authors: Scott Milcah C. , Temiz Nuri A. , Sarver Anne E. , LaRue Rebecca S. , Rathe Susan K. , Varshney Jyotika , Wolf Natalie K. , Moriarity Branden S. , O'Brien Timothy D. , Spector Logan G. , Largaespada David A. , Modiano Jaime F. , Subramanian Subbaya , Sarver Aaron L.
Published: March 2023

Supplemental Table 4. Gene lists identified in the clustering. Tab 1 Genes in Human clusters (n=7), mouse clusters (n=11), dog clusters (n=5), GSE212257 (n=14) Tab 2 Overlap counts of RNASEQ cluster lists. Tab 3 Overlap of human cluster 1 and human cluster 8 with LM22 signature
Supplemental Table 3 from Comparative Transcriptome Analysis Quantifies Immune Cell Transcript Levels, Metastatic Progression, and Survival in Osteosarcoma
Authors: Scott Milcah C. , Temiz Nuri A. , Sarver Anne E. , LaRue Rebecca S. , Rathe Susan K. , Varshney Jyotika , Wolf Natalie K. , Moriarity Branden S. , O'Brien Timothy D. , Spector Logan G. , Largaespada David A. , Modiano Jaime F. , Subramanian Subbaya , Sarver Aaron L.
Published: March 2023

Read Counts, mapping percentage and expressed gene count for all RNAseq samples. Tab 1 Human Tab 2 Dog Tab 3 Mouse
Supplemental Information on model formulation, data analysis and experimental evidence from Modeling the Genetic Regulation of Cancer Metabolism: Interplay between Glycolysis and Oxidative Phosphorylation
Authors: Yu Linglin , Lu Mingyang , Jia Dongya , Ma Jianpeng , Ben-Jacob Eshel , Levine Herbert , Kaipparettu Benny Abraham , Onuchic José N.
Published: March 2023

The supplemental information includes detailed descriptions about the mathematical models for the core AMPK:HIF-1:ROS circuit, the regulation of metabolism by MYC, c-SRC and RAS and the evaluation of different metabolic therapeutic strategies, all the parameters used in the modeling and the parameter sensitivity analysis, detailed procedures to generate the AMPK and HIF-1 signatures and to quantify the activity of MYC, c-SRC and AKT and the experimental evidence on the core AMPK:HIF-1:ROS regulatory circuit and different metabolic therapies.
Supplementary data 2 from MBD2 Ablation Impairs Lymphopoiesis and Impedes Progression and Maintenance of T-ALL
Authors: Zhou Mi , Zhou Kuangguo , Cheng Ling , Chen Xing , Wang Jue , Wang Xiao-Min , Zhang Yingchi , Yu Qilin , Zhang Shu , Wang Di , Huang Liang , Huang Mei , Ma Ding , Cheng Tao , Wang Cong-Yi , Yuan Weiping , Zhou Jianfeng
Published: March 2023

This file contains sequence validation of Î²-catenin in lentiviral expression vector.
Supplemental Table S3 from MBD2 Ablation Impairs Lymphopoiesis and Impedes Progression and Maintenance of T-ALL
Authors: Zhou Mi , Zhou Kuangguo , Cheng Ling , Chen Xing , Wang Jue , Wang Xiao-Min , Zhang Yingchi , Yu Qilin , Zhang Shu , Wang Di , Huang Liang , Huang Mei , Ma Ding , Cheng Tao , Wang Cong-Yi , Yuan Weiping , Zhou Jianfeng
Published: March 2023

This table shows Wnt-Specific gene set list from KEGG.
Supplemental information from YAP1 and COX2 Coordinately Regulate Urothelial Cancer Stem-like Cells
Authors: Ooki Akira , Del Carmen Rodriguez Pena Maria , Marchionni Luigi , Dinalankara Wikum , Begum Asma , Hahn Noah M. , VandenBussche Christopher J. , Rasheed Zeshaan A. , Mao Shifeng , Netto George J. , Sidransky David , Hoque Mohammad O.
Published: March 2023

Supplemental information includes Supplemental Figure S1. The characterization of SOX2 as an oncogene in bladder cancer, Supplemental Figure S2. Stem cell-related molecules associated with SOX2 expression, Supplemental Figure S3. CD24+/CD133+ as a potential marker for SOX2-expressing CSCs, Supplemental Figure S4. COX2/PGE2 signaling pathway in regulating SOX2, Supplemental Figure S5. The association of PGE2 expression with apoptosis in YAP1-LV or YAP1-sh cells, Supplemental Figure S6. Correlation among SOX2, YAP1, and COX2 expression in human UCB samples, Supplemental Figure S7. CSC expansion following CDDP treatment suppressed by combination treatment with verteporfin and celecoxib, Supplemental Figure S8. The EGFR-regulated YAP1 expression via PI3K signaling in basal-type UCB, and Supplementary Materials and Methods.
Supplementary data from Distinct Interactions of EBP1 Isoforms with FBXW7 Elicits Different Functions in Cancer
Authors: Wang Yuli , Zhang Pengju , Wang Yunshan , Zhan Panpan , Liu Chunyan , Mao Jian-Hua , Wei Guangwei
Published: March 2023

This part contains supplementary figure legends and supplementary Table 1.
Figure S2 from RSK Regulates PFK-2 Activity to Promote Metabolic Rewiring in Melanoma
Authors: Houles Thibault , Gravel Simon-Pierre , Lavoie Geneviève , Shin Sejeong , Savall Mathilde , Méant Antoine , Grondin Benoit , Gaboury Louis , Yoon Sang-Oh , St-Pierre Julie , Roux Philippe P.
Published: March 2023

RSK Inhibition in Melanoma Cells do not Affect Glycolytic Enzyme mRNA.
Supplementary Figures from Distinct Interactions of EBP1 Isoforms with FBXW7 Elicits Different Functions in Cancer
Authors: Wang Yuli , Zhang Pengju , Wang Yunshan , Zhan Panpan , Liu Chunyan , Mao Jian-Hua , Wei Guangwei
Published: March 2023

This part describes further supportive information for the distinctive interactions of EBP1 isoforms with FBXW7 including the data to describe that FBXW7-mediated ubiquitination and degradation of EBP1 P48 in a GSK3β-dependent manner and to illustrate that FBXW7 binds to P48 through its WD domain and P48 S44 is crucial for its interaction with FBXW7.
Figure S1 from RSK Regulates PFK-2 Activity to Promote Metabolic Rewiring in Melanoma
Authors: Houles Thibault , Gravel Simon-Pierre , Lavoie Geneviève , Shin Sejeong , Savall Mathilde , Méant Antoine , Grondin Benoit , Gaboury Louis , Yoon Sang-Oh , St-Pierre Julie , Roux Philippe P.
Published: March 2023

RSK Inhibition in Melanoma Cells do not Affect Amino Acid Levels.
Supplementary Figure 3 from Radioresistant Cervical Cancers Are Sensitive to Inhibition of Glycolysis and Redox Metabolism
Authors: Rashmi Ramachandran , Huang Xiaojing , Floberg John M. , Elhammali Adnan E. , McCormick Michael L. , Patti Gary J. , Spitz Douglas R. , Schwarz Julie K.
Published: March 2023

Effect of catalase over expression in the clonogenic survival of 2-DG, BSO and AUR treated cells. (A-B) Cells were seeded and transduced with Ad CAT and Ad empty viruses and CFA was done as described in the materials and methods section. (C) CaSki cells were treated with 20mM 2-DG, 1mM BSO and 100nM AUR for 24h along with or without CQ (60μM) and cell viability was determined by Alamar Blue. Statistical Analysis: (A) *p < 0.05 Ad-empty vs Ad-CAT BSO (B) p < 0.07 Ad-empty vs Ad-CAT for DG, BSO and BA. (C) ***DBA vs DBA+CQ, p<0.05, N=3.
supplemental tables and figures from Scavenger Receptor A1 Prevents Metastasis of Non–Small Cell Lung Cancer via Suppression of Macrophage Serum Amyloid A1
Authors: Zhang Yan , Wei Yongyue , Jiang Bin , Chen Lili , Bai Hui , Zhu Xudong , Li Xiaoyu , Zhang Hanwen , Yang Qing , Ma Junqing , Xu Yong , Ben Jingjing , Christiani David C. , Chen Qi
Published: March 2023

table S1-3,population data;Fig S1,SR-A1 deficiency exacerbates LLC metastasis;Fig S2, signal pathways in LLC cells;Fig S3,macrophage migration assay;Fig S4,qRT-PCR data.
Supplementary Figure 2 from Radioresistant Cervical Cancers Are Sensitive to Inhibition of Glycolysis and Redox Metabolism
Authors: Rashmi Ramachandran , Huang Xiaojing , Floberg John M. , Elhammali Adnan E. , McCormick Michael L. , Patti Gary J. , Spitz Douglas R. , Schwarz Julie K.
Published: March 2023

Role of anti-oxidant NAC on 2-DG, BSO and AUR induced cell viability. (A-B) Cells were seeded and treated with 2-DG and BSO for 24h followed by 5hrs of 10mM NAC with replacement of 2-DG, BSO and AUR for another 24h. Cell viability was determined by Alamar blue. Statistical Analysis: (A) BA vs NAC+BA, p<0.05, N=3 (B) BA vs NAC+BA and DBA vs NAC+DBA, p<0.05, N=3.
supplemental methods from Scavenger Receptor A1 Prevents Metastasis of Non–Small Cell Lung Cancer via Suppression of Macrophage Serum Amyloid A1
Authors: Zhang Yan , Wei Yongyue , Jiang Bin , Chen Lili , Bai Hui , Zhu Xudong , Li Xiaoyu , Zhang Hanwen , Yang Qing , Ma Junqing , Xu Yong , Ben Jingjing , Christiani David C. , Chen Qi
Published: March 2023

methods in detail
Supplementary Figure Legends from Combined PET Imaging of the Inflammatory Tumor Microenvironment Identifies Margins of Unique Radiotracer Uptake
Authors: Zinnhardt Bastian , Pigeon Hayet , Thézé Benoit , Viel Thomas , Wachsmuth Lydia , Fricke Inga B. , Schelhaas Sonja , Honold Lisa , Schwegmann Katrin , Wagner Stefan , Faust Andreas , Faber Cornelius , Kuhlmann Michael T. , Hermann Sven , Schäfers Michael , Winkeler Alexandra , Jacobs Andreas H.
Published: March 2023

Supplementary Figure Legends 1-5
Suppl. Fig. 5: Assessment of intra-rater reproducibility of the volumetric relation of [18F]DPA-714 and [18F]FET. from Combined PET Imaging of the Inflammatory Tumor Microenvironment Identifies Margins of Unique Radiotracer Uptake
Authors: Zinnhardt Bastian , Pigeon Hayet , Thézé Benoit , Viel Thomas , Wachsmuth Lydia , Fricke Inga B. , Schelhaas Sonja , Honold Lisa , Schwegmann Katrin , Wagner Stefan , Faust Andreas , Faber Cornelius , Kuhlmann Michael T. , Hermann Sven , Schäfers Michael , Winkeler Alexandra , Jacobs Andreas H.
Published: March 2023

An exemplary subset of n=6 mice were randomly assessed for intra-rater reproducibility. (A-E) [18F]DPA-714 and [18F]FET images were on two consecutive days repeatedly co-registered. Volumetry was performed twice (coreg 2 and coreg 3) and compared to the data reported in the main text (coreg 1). Dotted lines represent the overall mean for all n=20 animals reported in the main text. No significant changes for all parameters, except for the "percentage of [18F]DPA-714 only" between coreg 1 and 3, was found over the three different time points of co-registration.
Suppl. Fig. 4: Influence of imaging sequence. from Combined PET Imaging of the Inflammatory Tumor Microenvironment Identifies Margins of Unique Radiotracer Uptake
Authors: Zinnhardt Bastian , Pigeon Hayet , Thézé Benoit , Viel Thomas , Wachsmuth Lydia , Fricke Inga B. , Schelhaas Sonja , Honold Lisa , Schwegmann Katrin , Wagner Stefan , Faust Andreas , Faber Cornelius , Kuhlmann Michael T. , Hermann Sven , Schäfers Michael , Winkeler Alexandra , Jacobs Andreas H.
Published: March 2023

(A) T/B ratios, (B-D) tracer volumes, (E-J) areas of unique tracer uptake and overlapping regions. No significant effect on volumetric data was observed based on the order of imaging experiments.
Suppl. Fig. 3: Illustration of the applied thresholding. from Combined PET Imaging of the Inflammatory Tumor Microenvironment Identifies Margins of Unique Radiotracer Uptake
Authors: Zinnhardt Bastian , Pigeon Hayet , Thézé Benoit , Viel Thomas , Wachsmuth Lydia , Fricke Inga B. , Schelhaas Sonja , Honold Lisa , Schwegmann Katrin , Wagner Stefan , Faust Andreas , Faber Cornelius , Kuhlmann Michael T. , Hermann Sven , Schäfers Michael , Winkeler Alexandra , Jacobs Andreas H.
Published: March 2023

(A) An elliptical VOI (yellow) was drawn in the striatum. (B) Another elliptical VOI (green) was placed over the affected hemisphere. (C) After application of a thresholding based on the control VOI. The same original VOIs (left and middle) were used for all animals for individual thresholding.
Supplementary Figure S6 from Myeloid Cells That Impair Immunotherapy Are Restored in Melanomas with Acquired Resistance to BRAF Inhibitors
Authors: Steinberg Shannon M. , Shabaneh Tamer B. , Zhang Peisheng , Martyanov Viktor , Li Zhenghui , Malik Brian T. , Wood Tamara A. , Boni Andrea , Molodtsov Aleksey , Angeles Christina V. , Curiel Tyler J. , Whitfield Michael L. , Turk Mary Jo
Published: March 2023

Tumor growth in mice treated with BRAFi +/- MDSC depletion.
Suppl. Fig. 2: Workflow of imaging data co-registration. from Combined PET Imaging of the Inflammatory Tumor Microenvironment Identifies Margins of Unique Radiotracer Uptake
Authors: Zinnhardt Bastian , Pigeon Hayet , Thézé Benoit , Viel Thomas , Wachsmuth Lydia , Fricke Inga B. , Schelhaas Sonja , Honold Lisa , Schwegmann Katrin , Wagner Stefan , Faust Andreas , Faber Cornelius , Kuhlmann Michael T. , Hermann Sven , Schäfers Michael , Winkeler Alexandra , Jacobs Andreas H.
Published: March 2023

PET and CT images were co-registered using three CT-detectable, molecular sieve spheres (# 1-3) rinsed in radiotracer solution. After segmentation of spheres in the CT image (arrows), PET and CT images were superimposed by using the automated "Landmark tool" provided by the Vinci software. The "Magic tool" was applied for minor corrections of co-registrations. The resulting resliced PET image was saved for further processing. In a second step, MR and CT images were superimposed using the "Fusion- and Magic tool". For illustration MR is pseudocolored in red, while the CT was inverted in color (black). The CT contour was further superimposed to demonstrate co-registration accuracy. Selected bone structures were used as additional quality measures of image registration. The resliced CT image was saved with the new transformation matrix. In a last step, the before mentioned transformation of the CT (CTMR) was transferred to the PET, resulting in co-registration of PET/MR/CT. This workflow was repeated for every PET scan per mouse.
Supplementary Figure S4 from Myeloid Cells That Impair Immunotherapy Are Restored in Melanomas with Acquired Resistance to BRAF Inhibitors
Authors: Steinberg Shannon M. , Shabaneh Tamer B. , Zhang Peisheng , Martyanov Viktor , Li Zhenghui , Malik Brian T. , Wood Tamara A. , Boni Andrea , Molodtsov Aleksey , Angeles Christina V. , Curiel Tyler J. , Whitfield Michael L. , Turk Mary Jo
Published: March 2023

Effects of the CCR2/CCL2 axis on intratumoral MDSC populations and tumor growth.
Supplementary Information from TGFβ Promotes Genomic Instability after Loss of RUNX3
Authors: Krishnan Vaidehi , Chong Yu Lin , Tan Tuan Zea , Kulkarni Madhura , Bin Rahmat Muhammad Bakhait , Tay Lavina Sierra , Sankar Haresh , Jokhun Doorgesh S. , Ganesan Amudha , Chuang Linda Shyue Huey , Voon Dominic C. , Shivashankar GV , Thiery Jean-Paul , Ito Yoshiaki
Published: March 2023

Supplementary Methods, Legends for Supplementary Figures,Legend for Table 1 and References
Supplementary Figures 1-8 from TGFβ Promotes Genomic Instability after Loss of RUNX3
Authors: Krishnan Vaidehi , Chong Yu Lin , Tan Tuan Zea , Kulkarni Madhura , Bin Rahmat Muhammad Bakhait , Tay Lavina Sierra , Sankar Haresh , Jokhun Doorgesh S. , Ganesan Amudha , Chuang Linda Shyue Huey , Voon Dominic C. , Shivashankar GV , Thiery Jean-Paul , Ito Yoshiaki
Published: March 2023

This file contains Supplementary Figures 1-8. Fig.S1 shows Characterization of TGF-β-dependent EMT. Fig.S2 shows an analysis of endogenous DNA damage accumulation in the presence of TGF-β. Fig.S3 shows the Upregulation of NOX4 and downregulation of NRF-dependent genes upon TGF-β exposure.Fig.S4 displays that RNA-sequencing analysis unveils spontaneous EMT upon RUNX3 knockdown. Fig.S5 shows the regulation of HMOX1 expression by RUNX3. Figure.S6 shows how BACH1-KD in RUNX3-depleted cells rescues the accumulation of DNA damage. Fig.S7 displays RUNX1 depletion results in DNA damage accumulation and senescence in the presence of TGF-β. Fig.S8 shows HMOX1 depletion results in heightened ROS production and senescence in the presence of TGF-β.
Supplementary Figure S1 from Myeloid Cells That Impair Immunotherapy Are Restored in Melanomas with Acquired Resistance to BRAF Inhibitors
Authors: Steinberg Shannon M. , Shabaneh Tamer B. , Zhang Peisheng , Martyanov Viktor , Li Zhenghui , Malik Brian T. , Wood Tamara A. , Boni Andrea , Molodtsov Aleksey , Angeles Christina V. , Curiel Tyler J. , Whitfield Michael L. , Turk Mary Jo
Published: March 2023

Flow cytometry gating strategies.
Figure S4 from Tumor-Associated Fatigue in Cancer Patients Develops Independently of IL1 Signaling
Authors: Grossberg Aaron J. , Vichaya Elisabeth G. , Christian Diana L. , Molkentine Jessica M. , Vermeer Daniel W. , Gross Phillip S. , Vermeer Paola D. , Lee John H. , Dantzer Robert
Published: March 2023

This file shows burrowing behavior in tumor-bearing mice that were or were not treated with systemic IL-1ra.
Supplementary Figure S6 from LSD1 Stimulates Cancer-Associated Fibroblasts to Drive Notch3-Dependent Self-Renewal of Liver Cancer Stem–like Cells
Authors: Liu Chungang , Liu Limei , Chen Xuejiao , Cheng Jiamin , Zhang Heng , Zhang Chengcheng , Shan Juanjuan , Shen Junjie , Qian Cheng
Published: March 2023

Notch3 play an important role in LSD1 expression and protein stability.
Figure S1 from Tumor-Associated Fatigue in Cancer Patients Develops Independently of IL1 Signaling
Authors: Grossberg Aaron J. , Vichaya Elisabeth G. , Christian Diana L. , Molkentine Jessica M. , Vermeer Daniel W. , Gross Phillip S. , Vermeer Paola D. , Lee John H. , Dantzer Robert
Published: March 2023

This file contains additional inflammatory phenotyping of the mEER tumor, including serum cytokine levels and brain region-specific cytokine expression profiles.
Supplementary Figure S2 from LSD1 Stimulates Cancer-Associated Fibroblasts to Drive Notch3-Dependent Self-Renewal of Liver Cancer Stem–like Cells
Authors: Liu Chungang , Liu Limei , Chen Xuejiao , Cheng Jiamin , Zhang Heng , Zhang Chengcheng , Shan Juanjuan , Shen Junjie , Qian Cheng
Published: March 2023

Control of stem transcript factor expression by LSD1.
Figure S8 from Mutational Mechanisms That Activate Wnt Signaling and Predict Outcomes in Colorectal Cancer Patients
Authors: Hankey William , McIlhatton Michael A. , Ebede Kenechi , Kennedy Brian , Hancioglu Baris , Zhang Jie , Brock Guy N. , Huang Kun , Groden Joanna
Published: March 2023

SERPINE2 expression is stable following knockdown of endogenous APC or induction of exogenous APC at three time points examined.
Figure S7 from Mutational Mechanisms That Activate Wnt Signaling and Predict Outcomes in Colorectal Cancer Patients
Authors: Hankey William , McIlhatton Michael A. , Ebede Kenechi , Kennedy Brian , Hancioglu Baris , Zhang Jie , Brock Guy N. , Huang Kun , Groden Joanna
Published: March 2023

A predicted enhancer region 47 kb upstream of the SERPINE2 transcription start site is transcriptionally repressed rather than activated following APC silencing.
Figure S5 from Mutational Mechanisms That Activate Wnt Signaling and Predict Outcomes in Colorectal Cancer Patients
Authors: Hankey William , McIlhatton Michael A. , Ebede Kenechi , Kennedy Brian , Hancioglu Baris , Zhang Jie , Brock Guy N. , Huang Kun , Groden Joanna
Published: March 2023

Correlations between overexpression of MAP6, MSRB3 or PXDC1 in human colorectal tumors and shorter disease-free survival do not validate in the TCGA dataset.