bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Video 2 from In Vivo Tomographic Imaging of Deep-Seated Cancer Using Fluorescence Lifetime Contrast
Authors: Rice William L. , Shcherbakova Daria M. , Verkhusha Vladislav V. , Kumar Anand T.N.
Published: March 2023

Tomographic reconstruction of localized MTLn3-iRFP720 yield distribution in the mouse brain registered with X-Ray CT scan of the mouse head.
Supplementary Figure S3 from TWIST1-Induced miR-424 Reversibly Drives Mesenchymal Programming while Inhibiting Tumor Initiation
Authors: Drasin David J. , Guarnieri Anna L. , Neelakantan Deepika , Kim Jihye , Cabrera Joshua H. , Wang Chu-An , Zaberezhnyy Vadym , Gasparini Pierluigi , Cascione Luciano , Huebner Kay , Tan Aik-Choon , Ford Heide L.
Published: March 2023

Supplementary Figure S3 MiR-424 increases classical EMT phenotypes while decreasing TIC phenotypes. Stable miR-424 expressing MCF12A cells displaying: (A) distance migrated over 8 hours; (B) cell cycle analysis, by BrdU/PI staining; (C) adhesion to fibronectin-coated wells; and (D) ALDH1 activity quantification. SEM shown, n{greater than or equal to}3. #p<0.1, *p<0.05, ***p<0.001, two-tailed unpaired t-test.
Supplementary Figure S2 from TWIST1-Induced miR-424 Reversibly Drives Mesenchymal Programming while Inhibiting Tumor Initiation
Authors: Drasin David J. , Guarnieri Anna L. , Neelakantan Deepika , Kim Jihye , Cabrera Joshua H. , Wang Chu-An , Zaberezhnyy Vadym , Gasparini Pierluigi , Cascione Luciano , Huebner Kay , Tan Aik-Choon , Ford Heide L.
Published: March 2023

Supplementary Figure S2 MiR-424 drives an intermediate EMT that does not repress epithelial programming. (A) Phase contrast images of SUM149PT cells stably expressing miR-424 and (B) miR-200c levels, by qPCR. MCF12A cells stably expressing miR-424 examined for (C) N-cadherin protein, (D) morphology and (E) miR-424 levels and (F) EMT markers, by qPCR. HMLE cells stably expressing miR-424 examined for (G) morphology, (H) miR-424 levels and (I) EMT markers, by qPCR, and (J) N-cadherin protein. SEM shown, n{greater than or equal to}3. *p<0.05, **p<0.01, ***p<0.001, two-tailed unpaired t-test. Bar-100 ÃŽÂ¼m.
Supplementary Figure S1 from TWIST1-Induced miR-424 Reversibly Drives Mesenchymal Programming while Inhibiting Tumor Initiation
Authors: Drasin David J. , Guarnieri Anna L. , Neelakantan Deepika , Kim Jihye , Cabrera Joshua H. , Wang Chu-An , Zaberezhnyy Vadym , Gasparini Pierluigi , Cascione Luciano , Huebner Kay , Tan Aik-Choon , Ford Heide L.
Published: March 2023

Supplementary Figure S1 SNAI1 induces mesenchymal genes prior to repression of epithelial genes, concomitant with miR-424 upregulation. (A) Phase contrast images of HMLE Empty Vector and HMLE SNAI1-inducible cells after 4 and 12 days of SNAI1 induction. Bar-100 ÃŽÂ¼m. Epithelial and mesenchymal markers, by qPCR, after (B) 4 and (C) 12 days of SNAI1 induction, two-tailed unpaired t-test. (D) Mature and (E) primary miR-424 levels, by qPCR, after 4 days of SNAI1 induction, two-way ANOVA, Bonferroni multiple comparison post-test. SEM shown, representative images/graphs of n{greater than or equal to}3. #p<0.1, *p<0.05, **p<0.01, ***p<0.001.
Supplementary Methods from Heterochromatin Protein HP1γ Promotes Colorectal Cancer Progression and Is Regulated by miR-30a
Authors: Liu Ming , Huang Feifei , Zhang Dan , Ju Junyi , Wu Xiao-Bin , Wang Ying , Wang Yadong , Wu Yupeng , Nie Min , Li Zhuchen , Ma Chi , Chen Xi , Zhou Jin-Yong , Tan Renxiang , Yang Bo-Lin , Zen Ke , Zhang Chen-Yu , Chen Yu-Gen , Zhao Quan
Published: March 2023

Description of additional methods and procedures used in the study.
Supplementary Figure S2 from Heterochromatin Protein HP1γ Promotes Colorectal Cancer Progression and Is Regulated by miR-30a
Authors: Liu Ming , Huang Feifei , Zhang Dan , Ju Junyi , Wu Xiao-Bin , Wang Ying , Wang Yadong , Wu Yupeng , Nie Min , Li Zhuchen , Ma Chi , Chen Xi , Zhou Jin-Yong , Tan Renxiang , Yang Bo-Lin , Zen Ke , Zhang Chen-Yu , Chen Yu-Gen , Zhao Quan
Published: March 2023

Effects of miR-30a on cell cycle and apoptosis.
Supplemental Table S5 from RSPO2 Enhances Canonical Wnt Signaling to Confer Stemness-Associated Traits to Susceptible Pancreatic Cancer Cells
Authors: Ilmer Matthias , Boiles Alejandro Recio , Regel Ivonne , Yokoi Kenji , Michalski Christoph W. , Wistuba Ignacio I. , Rodriguez Jaime , Alt Eckhard , Vykoukal Jody
Published: March 2023

Supplemental Table S5. Evaluation of RSpo2 protein expression in tumor microarrays.
Supplementary Figure Legends from Interferon Regulatory Factor-1 Signaling Regulates the Switch between Autophagy and Apoptosis to Determine Breast Cancer Cell Fate
Authors: Schwartz-Roberts Jessica L. , Cook Katherine L. , Chen Chun , Shajahan-Haq Ayesha N. , Axelrod Margaret , Wärri Anni , Riggins Rebecca B. , Jin Lu , Haddad Bassem R. , Kallakury Bhaskar V. , Baumann William T. , Clarke Robert
Published: March 2023

Supplementary figure legends
Supplementary Figure 4 from Interferon Regulatory Factor-1 Signaling Regulates the Switch between Autophagy and Apoptosis to Determine Breast Cancer Cell Fate
Authors: Schwartz-Roberts Jessica L. , Cook Katherine L. , Chen Chun , Shajahan-Haq Ayesha N. , Axelrod Margaret , Wärri Anni , Riggins Rebecca B. , Jin Lu , Haddad Bassem R. , Kallakury Bhaskar V. , Baumann William T. , Clarke Robert
Published: March 2023

Knockdown of IRF1 alters BECN1 and IGF1R/mTOR expression.
Supplemental Methods from RSPO2 Enhances Canonical Wnt Signaling to Confer Stemness-Associated Traits to Susceptible Pancreatic Cancer Cells
Authors: Ilmer Matthias , Boiles Alejandro Recio , Regel Ivonne , Yokoi Kenji , Michalski Christoph W. , Wistuba Ignacio I. , Rodriguez Jaime , Alt Eckhard , Vykoukal Jody
Published: March 2023

Supplemental Methods. Description of additional methods and procedures used in the study.
Supplementary Figure S6 from CD271 Expression on Patient Melanoma Cells Is Unstable and Unlinked to Tumorigenicity
Authors: Boyle Samantha E. , Fedele Clare G. , Corbin Vincent , Wybacz Elisha , Szeto Pacman , Lewin Jeremy , Young Richard J. , Wong Annie , Fuller Robert , Spillane John , Speakman David , Donahoe Simon , Pohl Miklos , Gyorki David , Henderson Michael A. , Johnstone Ricky W. , Papenfuss Anthony T. , Shackleton Mark
Published: March 2023

Marker expression patterns in PDX tumors grown from CD271- and CD271+ cells.
Video 3 from Impact of Metabolic Heterogeneity on Tumor Growth, Invasion, and Treatment Outcomes
Authors: Robertson-Tessi Mark , Gillies Robert J. , Gatenby Robert A. , Anderson Alexander R.A.
Published: March 2023

Video 3: Anti-angiogenic therapy. Simulation of anti-angiogenic therapy
Video 1 from Impact of Metabolic Heterogeneity on Tumor Growth, Invasion, and Treatment Outcomes
Authors: Robertson-Tessi Mark , Gillies Robert J. , Gatenby Robert A. , Anderson Alexander R.A.
Published: March 2023

Video 1: Tumor growth. Simulation of untreated tumor growth
Supplementary Methods, Figures 1 - 9 from AIP1 Expression in Tumor Niche Suppresses Tumor Progression and Metastasis
Authors: Ji Weidong , Li Yonghao , He Yun , Yin Mingzhu , Zhou Huanjiao Jenny , Boggon Titus J. , Zhang Haifeng , Min Wang
Published: March 2023

Supplementary Figure S1-S9 - qRT-PCR for AIP1 expression in vascular EC but not in TAMs (S1); Examination of tumor growth and metastasis of orthotopic breast cancer model in AIP1-deficient mice (S2); Elucidation of potential steps prior to extravasation regulated by AIP1 during tumor metastasis (S3); Examination of tumor lymphangiogenesis in AIP1-deficient mice (S4); Measurement of gene expression of pre-niche markers at the lung of AIP1-deficient mice (S5); Effects of VEGFR2 inhibitors on tumor angiogenesis, pre-metastatic niche formation and tumor metastasis (S6); Measurement of tumor cell EMT in AIP1-deficient environment (S7); Examination of AIP1-VEGFR2 signaling in tumor cell EMT program (S8); Measurement of EC proliferation and EC apoptosis in primary tumor and lung tissue of AIP1-deficient mice (S9).
Supplementary Table 1 from Correlation between Density of CD8+ T-cell Infiltrate in Microsatellite Unstable Colorectal Cancers and Frameshift Mutations: A Rationale for Personalized Immunotherapy
Authors: Maby Pauline , Tougeron David , Hamieh Mohamad , Mlecnik Bernhard , Kora Hafid , Bindea Gabriela , Angell Helen K. , Fredriksen Tessa , Elie Nicolas , Fauquembergue Emilie , Drouet Aurélie , Leprince Jérôme , Benichou Jacques , Mauillon Jacques , Le Pessot Florence , Sesboüé Richard , Tuech Jean-Jacques , Sabourin Jean-Christophe , Michel Pierre , Frébourg Thierry , Galon Jérôme , Latouche Jean-Baptiste
Published: March 2023

Frequency of frameshift mutations within target genes and proportion of tumors harboring these mutations in all malignant cells.
Supplementary Figures S1-S9 from M-CSF and GM-CSF Receptor Signaling Differentially Regulate Monocyte Maturation and Macrophage Polarization in the Tumor Microenvironment
Authors: Van Overmeire Eva , Stijlemans Benoît , Heymann Felix , Keirsse Jiri , Morias Yannick , Elkrim Yvon , Brys Lea , Abels Chloé , Lahmar Qods , Ergen Can , Vereecke Lars , Tacke Frank , De Baetselier Patrick , Van Ginderachter Jo A. , Laoui Damya
Published: March 2023

Effects of α-M-CSFR Ab treatment on Ly6Chi monocyte function (S1); Effect of M-CSFR blockade on the survival of Ly6Chi monocytes and TAM (S2); Effect of M-CSFR blockade on Ly6Chi monocyte percentages in peripheral blood, spleen and bone marrow (S3); Absolute numbers of myeloid cell subsets in tumors from isotype or α-M-CSFR Ab-treated animals (S4); Production of M-CSF, IL-34 and GM-CSF by 3LL-R tumors (S5); Effect of M-CSFR blockade on monocyte differentiation in TS/A breast carcinoma tumors (S6); M-CSFR-mediated regulation of gene expression is IL-4Rα- independent (S7); Mixed Leukocyte Reaction (MLR) by TAM subsets from isotype or α-M-CSFR Ab treated animals (S8); M-CSFR blockade enhanced the M1-like MHC-IIhi TAM gene signature independently of GM-CSFR signaling (S9).
Supplementary Figure Legend from Correlation between Density of CD8+ T-cell Infiltrate in Microsatellite Unstable Colorectal Cancers and Frameshift Mutations: A Rationale for Personalized Immunotherapy
Authors: Maby Pauline , Tougeron David , Hamieh Mohamad , Mlecnik Bernhard , Kora Hafid , Bindea Gabriela , Angell Helen K. , Fredriksen Tessa , Elie Nicolas , Fauquembergue Emilie , Drouet Aurélie , Leprince Jérôme , Benichou Jacques , Mauillon Jacques , Le Pessot Florence , Sesboüé Richard , Tuech Jean-Jacques , Sabourin Jean-Christophe , Michel Pierre , Frébourg Thierry , Galon Jérôme , Latouche Jean-Baptiste
Published: March 2023

Supplementary Figure Legend
Supplemental Figures 1-10, Supplemental Tables 1-6, Supplemental Materials and Methods. from ATDC/TRIM29 Drives Invasive Bladder Cancer Formation through miRNA-Mediated and Epigenetic Mechanisms
Authors: Palmbos Phillip L. , Wang Lidong , Yang Huibin , Wang Yin , Leflein Jacob , Ahmet McKenzie L. , Wilkinson John E. , Kumar-Sinha Chandan , Ney Gina M. , Tomlins Scott A. , Daignault Stephanie , Kunju Lakshmi. P. , Wu Xue-Ru , Lotan Yair , Liebert Monica , Ljungman Mats E. , Simeone Diane M.
Published: March 2023

Supplemental Figure 1. ATDC mRNA expression in normal littermate (N) or CAG-ATDC transgenic bladders Supplemental Figure 2. Bladder urothelial lesions in CAG-ATDC transgenic line A of 8-12 months of age. Supplemental Figure 3. ATDC mRNA levels in CAG-ATDC tumors (T) are similar to human bladder cancers (UC9 and UC14) and ~20 fold higher than normal mouse (N) or human urothelial cell (TRTHU) expression. Mean{plus minus}SE, n = 3 for each column, * p < 0.05 compared to N. Supplemental Figure 4. ATDC immunostaining in two representative human invasive urothelial carcinomas demonstrates predominantly cytoplasmic staining (A) in most samples with rare tumors showing nuclear localization (B). Supplemental Figure 5. ATDC overexpression drives invasion in UC10 bladder cancer cell line. Supplemental Figure 6. PTEN immunostaining in three representative images of normal mouse bladder, CAG-ATDC mouse bladder or CAG-ATDC mouse tumor specimens demonstrating decreased PTEN expression in ATDC transgene expressing tissues Supplemental Figure 7. PTEN Quantitative methylation specific PCR. Supplemental Figure 8. Knockdown of ATDC results in reduction in DNMT3A, but not DNMT1 or DNMT3B in UC14 cell line as measured by immunoblot. Supplemental Figure 9. ATDC overexpression up-regulates DNMT3A, Ã´â‚¬Â�â€¦-catenin and c-MYC mRNA expression and suppresses expression of PTEN. Supplemental Figure 10. Knockdown of MYC increases miR-29A and B1 in bladder cancer cell lines. Supplemental Table 1. Summary of bladder urothelial lesions in CAG-ATDC mouse line A. Supplemental Table 2. ATDC is significantly over-expressed in human bladder cancer. Supplemental Table 3. Genes up-regulated in all three CAG-ATDC invasive bladder tumors. Supplemental Table 4. Genes up-regulated in CAG-ATDC bladder cancers show significant overlap with the top 5-10% of overexpressed genes in bladder cancer in the Oncomine database. Supplemental Table 5. Molecular concepts showing enrichment with expression signature of genes over-expressed in CAG-ATDC bladder cancers through Oncomine analysis. Supplemental Table 6. ATDC and DNMT3A IHC Expression Correlation.
Supplementary Figure Legends from RAGE Mediates S100A7-Induced Breast Cancer Growth and Metastasis by Modulating the Tumor Microenvironment
Authors: Nasser Mohd W. , Wani Nissar Ahmad , Ahirwar Dinesh K. , Powell Catherine A. , Ravi Janani , Elbaz Mohamad , Zhao Helong , Padilla Laura , Zhang Xiaoli , Shilo Konstantin , Ostrowski Michael , Shapiro Charles , Carson William E. , Ganju Ramesh K.
Published: March 2023

Supplementary Figure Legends
Supplementary Movie 1 from Urokinase Exerts Antimetastatic Effects by Dissociating Clusters of Circulating Tumor Cells
Authors: Choi Jin Woo , Kim Jun Ki , Yang Yun Jung , Kim Pilhan , Yoon Kwon-Ha , Yun Seok Hyun
Published: March 2023

For Fig 3C
Supplementary Figure Legends: from Adoptive Transfer of CD8+ T Cells Generated from Induced Pluripotent Stem Cells Triggers Regressions of Large Tumors Along with Immunological Memory
Authors: Saito Hidehito , Okita Keisuke , Chang Alfred E. , Ito Fumito
Published: March 2023

Phenotypic analysis of Pmel-1 splenocytes, thymocytes, ESCs (R1), and Pmel-1 iPSCs cultured on OP9 followed by OP9-DL1.
Supplemental Figure S4 from Targeted Deletion of p53 in Lgr5-Expressing Intestinal Stem Cells Promotes Colon Tumorigenesis in a Preclinical Model of Colitis-Associated Cancer
Authors: Davidson Laurie A. , Callaway Evelyn S. , Kim Eunjoo , Weeks Brad R. , Fan Yang-Yi , Allred Clinton D. , Chapkin Robert S.
Published: March 2023

Timeline for the AOM tumor study.
Supplementary Figure 2 from Tumor-Derived Osteopontin Reprograms Normal Mammary Fibroblasts to Promote Inflammation and Tumor Growth in Breast Cancer
Authors: Sharon Yoray , Raz Yael , Cohen Noam , Ben-Shmuel Amir , Schwartz Hila , Geiger Tamar , Erez Neta
Published: March 2023

Figure S2: CD44 expression is up regulated in CAFs and in activated NMFs.
Supplemental Table S2 from A Novel Bispecific Antibody Targeting EGFR and cMet Is Effective against EGFR Inhibitor–Resistant Lung Tumors
Authors: Moores Sheri L. , Chiu Mark L. , Bushey Barbara S. , Chevalier Kristen , Luistro Leopoldo , Dorn Keri , Brezski Randall J. , Haytko Peter , Kelly Thomas , Wu Sheng-Jiun , Martin Pauline L. , Neijssen Joost , Parren Paul W.H.I. , Schuurman Janine , Attar Ricardo M. , Laquerre Sylvie , Lorenzi Matthew V. , Anderson G. Mark
Published: March 2023

Antibody-Dependent Cellular Cytotoxicity Activity Profile of JNJ-61186372 in Human Lung Cancer Cell Lines
Supplementary Figures S1-S6 from Cytidine Deaminase Axis Modulated by miR-484 Differentially Regulates Cell Proliferation and Chemoresistance in Breast Cancer
Authors: Ye Fu-Gui , Song Chuan-Gui , Cao Zhi-Gang , Xia Chen , Chen Dan-Na , Chen Li , Li Shan , Qiao Feng , Ling Hong , Yao Ling , Hu Xin , Shao Zhi-Ming
Published: March 2023

Supplementary Figures S1-S6: qPCR analysis of selected genes was performed in MDA-231-Gem and parental MDA-231 cells (S1); qPCR analysis of 7 genes in the gemcitabine metabolism pathway was performed in MDA-231-Gem and parental MDA-231 cells (S2); The expression of miR-339-5p, miR-484 and miR-345-5p was assessed by miRNA qPCR in MDA-231-Gem cells compared to MDA-231 cells (S3); Constructing an mRNA-miRNA network associated with the gemcitabine metabolism pathway (S4); Patient cohorts for IHC analysis (S5); Patient cohort for mRNA and miRNA expression analyses (S6).
Supplementary Figure Legends from Acute Tissue Injury Activates Satellite Cells and Promotes Sarcoma Formation via the HGF/c-MET Signaling Pathway
Authors: Van Mater David , Añó Leonor , Blum Jordan M. , Webster Micah T. , Huang WeiQiao , Williams Nerissa , Ma Yan , Cardona Diana M. , Fan Chen-Ming , Kirsch David G.
Published: March 2023

Supplementary Figure Legends. Legends for Supplementary Figures S1-S3.
Supplementary Table 1 and Supplementary Figures 1 through 4 from Tumor-Specific Effector CD8+ T Cells That Can Establish Immunological Memory in Humans after Adoptive Transfer Are Marked by Expression of IL7 Receptor and c-myc
Authors: Chandran Smita S. , Paria Biman C. , Srivastava Abhishek K. , Rothermel Luke D. , Stephens Daniel J. , Kammula Udai S.
Published: March 2023

Supplementary Table and Figures Supplementary Table 1: Differentially expressed genes between persisting and non-persisting clones. Supplementary Figure 1: % IL-7R expressing cells in the infusion bag correlates with persistence of CD8+ effector clones. Supplementary Figure 2: Representative phenotypic profiling of IL7R+ and IL7R- subsets found within infused effector clones. Supplementary Figure 3: IL-7R expression correlates with c-myc mRNA expression in CD8+ effector clones. Supplementary Figure 4: IL-7R expression correlates with induced pSTAT5 expression in CD8+ effector clones.
Supplemental Figure 3 from CSF1 Receptor Targeting in Prostate Cancer Reverses Macrophage-Mediated Resistance to Androgen Blockade Therapy
Authors: Escamilla Jemima , Schokrpur Shiruyeh , Liu Connie , Priceman Saul J. , Moughon Diana , Jiang Ziyue , Pouliot Frederic , Magyar Clara , Sung James L. , Xu Jingying , Deng Gang , West Brian L. , Bollag Gideon , Fradet Yves , Lacombe Louis , Jung Michael E. , Huang Jiaoti , Wu Lily
Published: March 2023

The impact of CSF-1/CSF1R blockade is not tumor-intrinsic.
Figure S7 from ERAP1 Regulates Natural Killer Cell Function by Controlling the Engagement of Inhibitory Receptors
Authors: Cifaldi Loredana , Romania Paolo , Falco Michela , Lorenzi Silvia , Meazza Raffaella , Petrini Stefania , Andreani Marco , Pende Daniela , Locatelli Franco , Fruci Doriana
Published: March 2023

Supplementary Figure S7 shows distribution of HLA-B supertypes expressed by LCLs clustered in three groups based on MHC class I-fold changes
Figure S2 from ERAP1 Regulates Natural Killer Cell Function by Controlling the Engagement of Inhibitory Receptors
Authors: Cifaldi Loredana , Romania Paolo , Falco Michela , Lorenzi Silvia , Meazza Raffaella , Petrini Stefania , Andreani Marco , Pende Daniela , Locatelli Franco , Fruci Doriana
Published: March 2023

Supplementary Figure S2 shows the gating scheme for analysis of CD107a on human NK cells cultured with medium or K562 cells.
Supplementary Table 1 - 5 from PARD3 Inactivation in Lung Squamous Cell Carcinomas Impairs STAT3 and Promotes Malignant Invasion
Authors: Bonastre Ester , Verdura Sara , Zondervan Ilse , Facchinetti Federica , Lantuejoul Sylvie , Chiara Maria Dolores , Rodrigo Juan Pablo , Carretero Julian , Condom Enric , Vidal Agustin , Sidransky David , Villanueva Alberto , Roz Luca , Brambilla Elisabeth , Savola Suvi , Sanchez-Cespedes Montse
Published: March 2023

Table S1. List of lung cancer cell lines and histopathological type used to determine the status of the PARD3. Table S2. List of primers used for cloning, PCR and Sanger sequencing of PARD3. Table S3. List of single nucleotide polymorphisms (SNPs) and variants of unknown biological significance identified in lung cancer cell lines and lung primary tumors tested. Table S4. Clinical and pathological parameters of the NSCLC patients and tumors included in the PARD3 gene alterations screening. Table S5. List of genes selected from those genes that fulfilled the criteria: i) adjusted p<0.05; ii) at least 1.5-fold induction or repression in the wild type- H157tr-wtPAR3 (dox+) relative to H157tr (dox+).
Supplementary Methods from PARD3 Inactivation in Lung Squamous Cell Carcinomas Impairs STAT3 and Promotes Malignant Invasion
Authors: Bonastre Ester , Verdura Sara , Zondervan Ilse , Facchinetti Federica , Lantuejoul Sylvie , Chiara Maria Dolores , Rodrigo Juan Pablo , Carretero Julian , Condom Enric , Vidal Agustin , Sidransky David , Villanueva Alberto , Roz Luca , Brambilla Elisabeth , Savola Suvi , Sanchez-Cespedes Montse
Published: March 2023

Supplementary Materials and Methods
Supplementary figure legends from Enhanced Histone Deacetylase Activity in Malignant Melanoma Provokes RAD51 and FANCD2-Triggered Drug Resistance
Authors: Krumm Andrea , Barckhausen Christina , Kücük Pelin , Tomaszowski Karl-Heinz , Loquai Carmen , Fahrer Jörg , Krämer Oliver Holger , Kaina Bernd , Roos Wynand Paul
Published: March 2023

Legends for Table S1, Table S2, Figore S1, Figure S2 and Figure S3
Supplementary Methods and References from Genomic Profiling of Penile Squamous Cell Carcinoma Reveals New Opportunities for Targeted Therapy
Authors: McDaniel Andrew S. , Hovelson Daniel H. , Cani Andi K. , Liu Chia-Jen , Zhai Yali , Zhang Yajia , Weizer Alon Z. , Mehra Rohit , Feng Felix Y. , Alva Ajjai S. , Morgan Todd M. , Montgomery Jeffrey S. , Siddiqui Javed , Sadis Seth , Bandla Santhoshi , Williams Paul D. , Cho Kathleen R. , Rhodes Daniel R. , Tomlins Scott A.
Published: March 2023

Description of additional methods and procedures used in the study. Also includes Supplementary References.
Supplementary Figures S1-S5 from Genomic Profiling of Penile Squamous Cell Carcinoma Reveals New Opportunities for Targeted Therapy
Authors: McDaniel Andrew S. , Hovelson Daniel H. , Cani Andi K. , Liu Chia-Jen , Zhai Yali , Zhang Yajia , Weizer Alon Z. , Mehra Rohit , Feng Felix Y. , Alva Ajjai S. , Morgan Todd M. , Montgomery Jeffrey S. , Siddiqui Javed , Sadis Seth , Bandla Santhoshi , Williams Paul D. , Cho Kathleen R. , Rhodes Daniel R. , Tomlins Scott A.
Published: March 2023

Sanger sequencing validation of next generation sequencing (NGS) variant calls ; Alternative view of integrative molecular profiling heatmap ; p16 expression via immunohistochemistry ; Kaplan-Meier analysis of histologic subtypes of PeSCCA ; Comparison of prioritized molecular alterations in penile (PN) squamous cell carcinomas (SCCA) compared to other SCCAs .
Supplementary Table S3 from miR-634 Activates the Mitochondrial Apoptosis Pathway and Enhances Chemotherapy-Induced Cytotoxicity
Authors: Fujiwara Naoto , Inoue Jun , Kawano Tatsuyuki , Tanimoto Kousuke , Kozaki Ken-ichi , Inazawa Johji
Published: March 2023

Supplementary Table S3. List of anti-apoptosis-, mitochondria-, and lysosome-related genes among the predicted target genes of miR-634.
Supplementary Figures S1-S7 from miR-634 Activates the Mitochondrial Apoptosis Pathway and Enhances Chemotherapy-Induced Cytotoxicity
Authors: Fujiwara Naoto , Inoue Jun , Kawano Tatsuyuki , Tanimoto Kousuke , Kozaki Ken-ichi , Inazawa Johji
Published: March 2023

Supplementary Figures S1-S7. Effect of miR-634 overexpression in normal fibroblasts and LCLs (S1); Effect of NRF2 inhibition by specific siRNA transfection (S2); Simultaneous down-regulation of target genes by 7 siRNAs (S3); Expression analysis of miR-634 and target proteins in normal fibroblasts and LCLs (S4); Establishment of CDDP-resistant ESCC cell line and expression analysis of miR-634 and target proteins (S5); Changes in body weights of 6 mice in PBS group (S6); Expression analysis of miR-634 in ESCC samples (S7).
Supplementary Figure Legend from Diverse Targets of β-Catenin during the Epithelial–Mesenchymal Transition Define Cancer Stem Cells and Predict Disease Relapse
Authors: Chang Yi-Wen , Su Ying-Jhen , Hsiao Michael , Wei Kuo-Chen , Lin Wei-Hsin , Liang Chi-Jung , Chen Shin-Cheh , Lee Jia-Lin
Published: March 2023

Supplementary Figure Legend from Diverse Targets of β-Catenin during the Epithelial–Mesenchymal Transition Define Cancer Stem Cells and Predict Disease Relapse
Supplementary Table S2 from Pulsed High-Intensity Focused Ultrasound Enhances Delivery of Doxorubicin in a Preclinical Model of Pancreatic Cancer
Authors: Li Tong , Wang Yak-Nam , Khokhlova Tatiana D. , D'Andrea Samantha , Starr Frank , Chen Hong , McCune Jeannine S. , Risler Linda J. , Mashadi-Hossein Afshin , Hingorani Sunil R. , Chang Amy , Hwang Joo Ha
Published: March 2023

Supplementary Table S2. Estimated regression coefficients from equation 2.
Supplementary Dataset S2 from The miR-146b-3p/PAX8/NIS Regulatory Circuit Modulates the Differentiation Phenotype and Function of Thyroid Cells during Carcinogenesis
Authors: Riesco-Eizaguirre Garcilaso , Wert-Lamas León , Perales-Patón Javier , Sastre-Perona Ana , Fernández Lara P. , Santisteban Pilar
Published: March 2023

Most abundantly deregulated miRs in normal thyroid and PTC corresponding to 80 % of the reads.
Supplementary Materials and Methods from Pulsed High-Intensity Focused Ultrasound Enhances Delivery of Doxorubicin in a Preclinical Model of Pancreatic Cancer
Authors: Li Tong , Wang Yak-Nam , Khokhlova Tatiana D. , D'Andrea Samantha , Starr Frank , Chen Hong , McCune Jeannine S. , Risler Linda J. , Mashadi-Hossein Afshin , Hingorani Sunil R. , Chang Amy , Hwang Joo Ha
Published: March 2023

Supplementary Materials and Methods. Description of additional methods and procedures used in the study.
Supplementary Tables S1-S2, Figures S1-S9, and Methods from Crosstalk between KIT and FGFR3 Promotes Gastrointestinal Stromal Tumor Cell Growth and Drug Resistance
Authors: Javidi-Sharifi Nathalie , Traer Elie , Martinez Jacqueline , Gupta Anu , Taguchi Takehiro , Dunlap Jennifer , Heinrich Michael C. , Corless Christopher L. , Rubin Brian P. , Druker Brian J. , Tyner Jeffrey W.
Published: March 2023

Supplementary Tables S1-S2, Figures S1-S9, and Methods Table S1: Raw siRNA screening results Figure S1: Response of GIST cell lines to the KIT inhibitor, imatinib Figure S2: Testing of individual FGFR3 siRNA duplexes for efficacy of reducing GIST T1 and GIST 10R cell viability Figure S3: Potential degradation product of FGFR3 upon inhibition with a small-molecule inhibitor Figure S4: FGF1 restores KIT phosphorylation and rescues GIST cells from imatinib inhibition Figure S5: SCF rescues GIST cells from FGFR inhibition Figure S6: FGFR expression levels after siRNA knockdown Figure S7: Combination of B-RAF inhibitor with imatinib is synergistic for GIST 10R cells Figure S8: FGF2 expression levels after siRNA knockdown Figure S9: Illustration of patient tissue analysis using the Aperio ScanScope CS Slide Scanner Supplemental Materials and Methods
Supplementary Figure Legends from Pulsed High-Intensity Focused Ultrasound Enhances Delivery of Doxorubicin in a Preclinical Model of Pancreatic Cancer
Authors: Li Tong , Wang Yak-Nam , Khokhlova Tatiana D. , D'Andrea Samantha , Starr Frank , Chen Hong , McCune Jeannine S. , Risler Linda J. , Mashadi-Hossein Afshin , Hingorani Sunil R. , Chang Amy , Hwang Joo Ha
Published: March 2023

Supplementary Figure Legends. Legends for Supplementary Figures S1-S2.
Supplementary Figure Legends-Unmarked from Modification of Helicobacter pylori Peptidoglycan Enhances NOD1 Activation and Promotes Cancer of the Stomach
Authors: Suarez Giovanni , Romero-Gallo Judith , Piazuelo M. Blanca , Wang Ge , Maier Robert J. , Forsberg Lennart S. , Azadi Parastoo , Gomez Martin A. , Correa Pelayo , Peek Richard M.
Published: March 2023

Supplementary Figure Legends
Supplementary Figure 3 from Modification of Helicobacter pylori Peptidoglycan Enhances NOD1 Activation and Promotes Cancer of the Stomach
Authors: Suarez Giovanni , Romero-Gallo Judith , Piazuelo M. Blanca , Wang Ge , Maier Robert J. , Forsberg Lennart S. , Azadi Parastoo , Gomez Martin A. , Correa Pelayo , Peek Richard M.
Published: March 2023

Supplemental Figure 3. Cell viability as determined by MTT assays of HEK293 cells transfected with empty vector (Control) or a NOD1-expression construct (pUNO1-hNOD1, Invivogen). Cells were challenged with C12-iE-DAP, PMA, or wild type H. pylori strain 7.13 at MOIs of 10 and 50 for 4 hours. Data are represented as mean{plus minus}SEM from 2 independent experiments.
Logical model from A Modeling Approach to Explain Mutually Exclusive and Co-Occurring Genetic Alterations in Bladder Tumorigenesis
Authors: Remy Elisabeth , Rebouissou Sandra , Chaouiya Claudine , Zinovyev Andrei , Radvanyi François , Calzone Laurence
Published: March 2023

Logical model - Model files in SBML qual format and in GINsim format can be found at: http://www.ginsim.org/node/188.
Supplementary Methods, Results and Figures 1 to 5 from A Central Role for Heme Iron in Colon Carcinogenesis Associated with Red Meat Intake
Authors: Bastide Nadia M. , Chenni Fatima , Audebert Marc , Santarelli Raphaelle L. , Taché Sylviane , Naud Nathalie , Baradat Maryse , Jouanin Isabelle , Surya Reggie , Hobbs Ditte A. , Kuhnle Gunter G. , Raymond-Letron Isabelle , Gueraud Françoise , Corpet Denis E. , Pierre Fabrice H.F.
Published: March 2023

Supplementary Methods, Results, and Figures 1 to 5. Supplementary Figure 1: Flowchart of Bastide et al. Supplementary Figure 2. The consequences of the loss of Apc function in an intestinal cellular model derived from C57BL/6J mice. Supplementary Figure 3. A diet with 1% hemoglobin results in increased heme in rat fecal water and in increased urinary biomarkers in rats. Supplementary Figure 4. The dose-dependent cytotoxic effects of HNE, MDA, and HHE on Apc +/+ cells (grey line) and Apc -/+ cells (black line) after 24 h of exposure. Supplementary Figure 5. The effect of a hemoglobin diet on intestinal tumorigenesis in Min mice and modulation of a urinary biomarker linked to intestinal tumorigenesis.
Supplemental Table S9 from The Distinctive Mutational Spectra of Polyomavirus-Negative Merkel Cell Carcinoma
Authors: Harms Paul William , Vats Pankaj , Verhaegen Monique Elise , Robinson Dan R. , Wu Yi-Mi , Dhanasekaran Saravana Mohan , Palanisamy Nallasivam , Siddiqui Javed , Cao Xuhong , Su Fengyun , Wang Rui , Xiao Hong , Kunju Lakshmi P. , Mehra Rohit , Tomlins Scott A. , Fullen Douglas Randall , Bichakjian Christopher Keram , Johnson Timothy M. , Dlugosz Andrzej Antoni , Chinnaiyan Arul M.
Published: March 2023

Supplemental Table S9. Fusion calls in Merkel cell carcinoma by transcriptome sequencing
Supplementary Fig. S7 from Combining miR-10b–Targeted Nanotherapy with Low-Dose Doxorubicin Elicits Durable Regressions of Metastatic Breast Cancer
Authors: Yoo Byunghee , Kavishwar Amol , Ross Alana , Wang Ping , Tabassum Doris P. , Polyak Kornelia , Barteneva Natalia , Petkova Victoria , Pantazopoulos Pamela , Tena Aseda , Moore Anna , Medarova Zdravka
Published: March 2023

Supplementary Fig. S7. Long-term cancer-free survival.
Supplemental Table S4 from The Distinctive Mutational Spectra of Polyomavirus-Negative Merkel Cell Carcinoma
Authors: Harms Paul William , Vats Pankaj , Verhaegen Monique Elise , Robinson Dan R. , Wu Yi-Mi , Dhanasekaran Saravana Mohan , Palanisamy Nallasivam , Siddiqui Javed , Cao Xuhong , Su Fengyun , Wang Rui , Xiao Hong , Kunju Lakshmi P. , Mehra Rohit , Tomlins Scott A. , Fullen Douglas Randall , Bichakjian Christopher Keram , Johnson Timothy M. , Dlugosz Andrzej Antoni , Chinnaiyan Arul M.
Published: March 2023

Supplemental Table S4. Copy number variations detected by exome sequencing in index cases
Supplementary Fig. S5 from Combining miR-10b–Targeted Nanotherapy with Low-Dose Doxorubicin Elicits Durable Regressions of Metastatic Breast Cancer
Authors: Yoo Byunghee , Kavishwar Amol , Ross Alana , Wang Ping , Tabassum Doris P. , Polyak Kornelia , Barteneva Natalia , Petkova Victoria , Pantazopoulos Pamela , Tena Aseda , Moore Anna , Medarova Zdravka
Published: March 2023

Supplementary Fig. S5. Histopathological analysis of the lymph nodes and lungs of the animals obtained at the endpoint of the therapeutic study.
Supplemental Table S3 from The Distinctive Mutational Spectra of Polyomavirus-Negative Merkel Cell Carcinoma
Authors: Harms Paul William , Vats Pankaj , Verhaegen Monique Elise , Robinson Dan R. , Wu Yi-Mi , Dhanasekaran Saravana Mohan , Palanisamy Nallasivam , Siddiqui Javed , Cao Xuhong , Su Fengyun , Wang Rui , Xiao Hong , Kunju Lakshmi P. , Mehra Rohit , Tomlins Scott A. , Fullen Douglas Randall , Bichakjian Christopher Keram , Johnson Timothy M. , Dlugosz Andrzej Antoni , Chinnaiyan Arul M.
Published: March 2023

Supplemental Table S3. MCPyV detection in MCC tumors by qPCR, immunohistochemistry, and transcriptome sequencing
Supplementary Fig. S3 from Combining miR-10b–Targeted Nanotherapy with Low-Dose Doxorubicin Elicits Durable Regressions of Metastatic Breast Cancer
Authors: Yoo Byunghee , Kavishwar Amol , Ross Alana , Wang Ping , Tabassum Doris P. , Polyak Kornelia , Barteneva Natalia , Petkova Victoria , Pantazopoulos Pamela , Tena Aseda , Moore Anna , Medarova Zdravka
Published: March 2023

Supplementary Fig. S3. Effect of miR-10b knock-out on the phenotype of human metastatic breast cancer cells.
Supplemental Figure S4 from The Distinctive Mutational Spectra of Polyomavirus-Negative Merkel Cell Carcinoma
Authors: Harms Paul William , Vats Pankaj , Verhaegen Monique Elise , Robinson Dan R. , Wu Yi-Mi , Dhanasekaran Saravana Mohan , Palanisamy Nallasivam , Siddiqui Javed , Cao Xuhong , Su Fengyun , Wang Rui , Xiao Hong , Kunju Lakshmi P. , Mehra Rohit , Tomlins Scott A. , Fullen Douglas Randall , Bichakjian Christopher Keram , Johnson Timothy M. , Dlugosz Andrzej Antoni , Chinnaiyan Arul M.
Published: March 2023

Supplemental Figure S4. A novel MLH1-SPATA4 gene fusion
Supplementary Fig. S1 from Combining miR-10b–Targeted Nanotherapy with Low-Dose Doxorubicin Elicits Durable Regressions of Metastatic Breast Cancer
Authors: Yoo Byunghee , Kavishwar Amol , Ross Alana , Wang Ping , Tabassum Doris P. , Polyak Kornelia , Barteneva Natalia , Petkova Victoria , Pantazopoulos Pamela , Tena Aseda , Moore Anna , Medarova Zdravka
Published: March 2023

Supplementary Fig. S1. Viability of 4T1, SUM149PT and SUM159PT breast cancer cells treated with MN-anti-miR10b and low-dose doxorubicin.
Supplemental Methods and Figure Legends from A Urokinase Receptor–Bim Signaling Axis Emerges during EGFR Inhibitor Resistance in Mutant EGFR Glioblastoma
Authors: Wykosky Jill , Hu Jingjing , Gomez German G. , Taylor Tiffany , Villa Genaro R. , Pizzo Donald , VandenBerg Scott R. , Thorne Amy Haseley , Chen Clark C. , Mischel Paul S. , Gonias Steven L. , Cavenee Webster K. , Furnari Frank B.
Published: March 2023

Supplemental Methods and Figure Legends
Supplemental Figure S1 from The Distinctive Mutational Spectra of Polyomavirus-Negative Merkel Cell Carcinoma
Authors: Harms Paul William , Vats Pankaj , Verhaegen Monique Elise , Robinson Dan R. , Wu Yi-Mi , Dhanasekaran Saravana Mohan , Palanisamy Nallasivam , Siddiqui Javed , Cao Xuhong , Su Fengyun , Wang Rui , Xiao Hong , Kunju Lakshmi P. , Mehra Rohit , Tomlins Scott A. , Fullen Douglas Randall , Bichakjian Christopher Keram , Johnson Timothy M. , Dlugosz Andrzej Antoni , Chinnaiyan Arul M.
Published: March 2023

Supplemental Figure S1. Mutational signatures of Merkel cell polyomavirus-negative Merkel cell carcinomas
Supplemental Figure S3 from A Urokinase Receptor–Bim Signaling Axis Emerges during EGFR Inhibitor Resistance in Mutant EGFR Glioblastoma
Authors: Wykosky Jill , Hu Jingjing , Gomez German G. , Taylor Tiffany , Villa Genaro R. , Pizzo Donald , VandenBerg Scott R. , Thorne Amy Haseley , Chen Clark C. , Mischel Paul S. , Gonias Steven L. , Cavenee Webster K. , Furnari Frank B.
Published: March 2023

Supplemental Figure S3. Suppression of Akt activation in resistant clones
Supplementary Table 1, Supplementary Methods, and Supplementary Figure Legends from IL6 Blockade Reprograms the Lung Tumor Microenvironment to Limit the Development and Progression of K-ras–Mutant Lung Cancer
Authors: Caetano Mauricio S. , Zhang Huiyuan , Cumpian Amber M. , Gong Lei , Unver Nese , Ostrin Edwin J. , Daliri Soudabeh , Chang Seon Hee , Ochoa Cesar E. , Hanash Samir , Behrens Carmen , Wistuba Ignacio I. , Sternberg Cinthya , Kadara Humam , Ferreira Carlos Gil , Watowich Stephanie S. , Moghaddam Seyed Javad
Published: March 2023

Table 1. List of Q-RT-PCR primers. Supplementary methods and supplementary figure legends.
Supplementary Figure 7 from IL6 Blockade Reprograms the Lung Tumor Microenvironment to Limit the Development and Progression of K-ras–Mutant Lung Cancer
Authors: Caetano Mauricio S. , Zhang Huiyuan , Cumpian Amber M. , Gong Lei , Unver Nese , Ostrin Edwin J. , Daliri Soudabeh , Chang Seon Hee , Ochoa Cesar E. , Hanash Samir , Behrens Carmen , Wistuba Ignacio I. , Sternberg Cinthya , Kadara Humam , Ferreira Carlos Gil , Watowich Stephanie S. , Moghaddam Seyed Javad
Published: March 2023

Supplementary Figure 7. Relative expression of Scgb1 (CCSP) mRNA in lungs of CC-LR mice.
Supplementary Figure S2 from PIK3CAH1047R Accelerates and Enhances KRASG12D-Driven Lung Tumorigenesis
Authors: Green Shon , Trejo Christy L. , McMahon Martin
Published: March 2023

Ex vivo analysis of KRASG12D- versus KRASG12D/PIK3CAH1047R-driven lung tumor cell proliferation in vibratome sections.
Supplementary Figure 1 from IL6 Blockade Reprograms the Lung Tumor Microenvironment to Limit the Development and Progression of K-ras–Mutant Lung Cancer
Authors: Caetano Mauricio S. , Zhang Huiyuan , Cumpian Amber M. , Gong Lei , Unver Nese , Ostrin Edwin J. , Daliri Soudabeh , Chang Seon Hee , Ochoa Cesar E. , Hanash Samir , Behrens Carmen , Wistuba Ignacio I. , Sternberg Cinthya , Kadara Humam , Ferreira Carlos Gil , Watowich Stephanie S. , Moghaddam Seyed Javad
Published: March 2023

Supplementary Figure 1. Gating method for FACS analysis and sorting.
Supplementary Figure S4 from Noninvasive Quantification of 2-Hydroxyglutarate in Human Gliomas with IDH1 and IDH2 Mutations
Authors: Emir Uzay E. , Larkin Sarah J. , de Pennington Nick , Voets Natalie , Plaha Puneet , Stacey Richard , Al-Qahtani Khalid , Mccullagh James , Schofield Christopher J. , Clare Stuart , Jezzard Peter , Cadoux-Hudson Tom , Ansorge Olaf
Published: March 2023

Phantom experiments and density-matrix simulations of the timing of the semi-LASER sequence were performed at TE = 36 (TE1 =11 ms, TE2 = 15 ms and TE3 = 10 ms) and 110 ms (TE1 =11 ms, TE2 = 65 ms and TE3 = 34 ms).
Supplemental Table S1 from Chaperone Hsp47 Drives Malignant Growth and Invasion by Modulating an ECM Gene Network
Authors: Zhu Jieqing , Xiong Gaofeng , Fu Hanjiang , Evers B. Mark , Zhou Binhua P. , Xu Ren
Published: March 2023

Supplemental Table S1. Expression of Hsp47 and ECM protein genes is correlated in mammary cell lines.
Supplementary Figure S1 from Noninvasive Quantification of 2-Hydroxyglutarate in Human Gliomas with IDH1 and IDH2 Mutations
Authors: Emir Uzay E. , Larkin Sarah J. , de Pennington Nick , Voets Natalie , Plaha Puneet , Stacey Richard , Al-Qahtani Khalid , Mccullagh James , Schofield Christopher J. , Clare Stuart , Jezzard Peter , Cadoux-Hudson Tom , Ansorge Olaf
Published: March 2023

LCModel analysis.
Supplemental Figure S3 from Chaperone Hsp47 Drives Malignant Growth and Invasion by Modulating an ECM Gene Network
Authors: Zhu Jieqing , Xiong Gaofeng , Fu Hanjiang , Evers B. Mark , Zhou Binhua P. , Xu Ren
Published: March 2023

Supplemental Figure S3. Hsp47 expression is associated with poor prognosis and contributes to the deposition of ECM proteins in breast cancer tissue.
Supplementary Table Legend from Hepatocyte Growth Factor/cMET Pathway Activation Enhances Cancer Hallmarks in Adrenocortical Carcinoma
Authors: Phan Liem M. , Fuentes-Mattei Enrique , Wu Weixin , Velazquez-Torres Guermarie , Sircar Kanishka , Wood Christopher G. , Hai Tao , Jimenez Camilo , Cote Gilbert J. , Ozsari Levent , Hofmann Marie-Claude , Zheng Siyuan , Verhaak Roeland , Pagliaro Lance , Cortez Maria Angelica , Lee Mong-Hong , Yeung Sai-Ching J. , Habra Mouhammed Amir
Published: March 2023

Supplementary Table Legend from Hepatocyte Growth Factor/cMET Pathway Activation Enhances Cancer Hallmarks in Adrenocortical Carcinoma
Table S3. Gene Set Enrichment Analysis (GSEA) C2 gene sets. from Proteasomal Inhibition by Ixazomib Induces CHK1 and MYC-Dependent Cell Death in T-cell and Hodgkin Lymphoma
Authors: Ravi Dashnamoorthy , Beheshti Afshin , Abermil Nasséra , Passero Frank , Sharma Jaya , Coyle Michael , Kritharis Athena , Kandela Irawati , Hlatky Lynn , Sitkovsky Michail V. , Mazar Andrew , Gartenhaus Ronald B. , Evens Andrew M.
Published: March 2023

Complete list of GSEA for C2 curated gene sets in the ixazomib 25nM/24 hours versus control for Jurkat, L428, and L540 cells. Leading edge analysis with a FDR {less than or equal to} 0.05 determined significant gene sets enriched for each group. The normalized enrichment score (NES) indicates whether the gene set is up- (>0) or down-regulated (<0) for each group determined with the # of leading edge genes (appears in parenthesis).
Supplemental Methods, Tables 1-9, and Figures 1-9 from Notch1 Activation or Loss Promotes HPV-Induced Oral Tumorigenesis
Authors: Zhong Rong , Bao Riyue , Faber Pieter W. , Bindokas Vytautas P. , Bechill John , Lingen Mark W. , Spiotto Michael T.
Published: March 2023

Supplemental Methods, Tables 1-9 and Figures 1-9. Supplemental Methods: Animals; Sleeping Beauty transposon mapping; Reagents and antibodies; HPV recombination, T2/Onc excision and Hras mutation specific PCRs. Supplemental Table 1: Mouse strains used in this study. Supplemental Table 2: Primers used in the generation of insertional mutagenesis libraries. Supplemental Table 3: Common insertion sites (CIS) in DMBA and 4-NQO treated HPV-positive and HPV-negative tumors. Supplemental Table 4: Characterizations of Notch1 insertions. Supplemental Table 5: Transposon orientation and frequency for candidate genes in Figure 3B. Supplemental Table 6: Differentially expressed genes in KHR compared to KHR-N-/- and KHR-N+/- tumors. Supplemental Table 7: Differentially expressed genes in KHR-N-/- compared to KHRNICD tumors. Supplemental Table 8: Comparison of pathway analysis for KHR-N+/- and KHR-N-/- tumors compared to KR-N-/- tumors. Supplemental Table 9: Summary of GSEA Hallmark gene sets significantly enriched in KHRNICD and KHR-N-/- tumors. Supplemental Figure 1. LSL-HPV recombination, T2/Onc transposition and Ha-Ras mutations in HPV-positive and HPV-negative tumors. Supplemental Figure 2. Sleeping Beauty insertional mutagenesis accelerated tumorigenesis in 4-NQO treated HPV-positive and HPV-negative mice. Supplemental Figure 3. Tumors with activating T2/Onc insertions have higher Notch1 expression compared to tumors with inactivating T2/Onc insertions. Supplemental Figure 4. Validation of NICD expression in KHRNICD oral tumors. Supplemental Figure 5. KHRNICD oral tumors had increased Hes1 and Hey1 nuclear expression. Supplemental Figure 6. KHR and KHRNICD oral tumors had similar CK14 expression. Supplemental Figure 7. KHR and KHR-Notch1+/- and KHR-Notch1-/- oral tumors had similar CK14 expression. Supplemental Figure 8. KHR, KHR-Notch+/- and KHR-Notch-/- oral tumors have invasive components. Supplemental Figure 9. NOTCH1 somatic mutations in ALTCL, CESC and HNSC patients.
Table S1. Common upstream regulators. from Proteasomal Inhibition by Ixazomib Induces CHK1 and MYC-Dependent Cell Death in T-cell and Hodgkin Lymphoma
Authors: Ravi Dashnamoorthy , Beheshti Afshin , Abermil Nasséra , Passero Frank , Sharma Jaya , Coyle Michael , Kritharis Athena , Kandela Irawati , Hlatky Lynn , Sitkovsky Michail V. , Mazar Andrew , Gartenhaus Ronald B. , Evens Andrew M.
Published: March 2023

A. Common upstream regulators predicted to be activated or inhibited (as indicated by the activation Z-score) in the ixazomib 25nM/24 hours versus control for Jurkat, L540 and L428 cells obtained through the use of Ingenuity Pathway Analysis (IPA) software. Regulation z-score indicates the degree of inhibition (for negative values) or activation (for positive values). The third column denotes the effects that the upstream regulators have on tumor progression (reference in parenthesis). B. Common upstream regulators predicted to be activated or inhibited (as described in Table S1A), are highlighted (shaded in red) based on their functional link in "hallmarks of cancer," with literature evidences listed.
Figure S1. Quantitative RT-PCR validation of ixazomib genes. from Proteasomal Inhibition by Ixazomib Induces CHK1 and MYC-Dependent Cell Death in T-cell and Hodgkin Lymphoma
Authors: Ravi Dashnamoorthy , Beheshti Afshin , Abermil Nasséra , Passero Frank , Sharma Jaya , Coyle Michael , Kritharis Athena , Kandela Irawati , Hlatky Lynn , Sitkovsky Michail V. , Mazar Andrew , Gartenhaus Ronald B. , Evens Andrew M.
Published: March 2023

The bar graph show results (as fold-change values) from quantitative RT-PCR validation of the following genes, MYC, lysosomal - SQSTM1/p62, proteasomal function- PSMB3, PSMB5, PSMD1, PSMD2, common overlapping gene- PSAP, with RNA isolated from control and ixazomib treated Jurkat (TCL) and L540 and L428 (HL) cells, and comparison with the results from microarray experiment. The calculated the p-values (* = p < 0.05, ** = p < 0.01, and *** p < 0.001), were determined based on the fold change values between control and ixazomib treated cells.
Supplemental Video 2 from A Quantitative System for Studying Metastasis Using Transparent Zebrafish
Authors: Heilmann Silja , Ratnakumar Kajan , Langdon Erin M. , Kansler Emily R. , Kim Isabella S. , Campbell Nathaniel R. , Perry Elizabeth B. , McMahon Amy J. , Kaufman Charles K. , van Rooijen Ellen , Lee William , Iacobuzio-Donahue Christine A. , Hynes Richard O. , Zon Leonard I. , Xavier Joao B. , White Richard M.
Published: March 2023

Supplemental Video 2: Time-lapse video from 1-21 days post transplantation of ZMEL1-GFP cells into adult zebrafish showing primary growth and metastatic spread.
Supplemental Video 1 from A Quantitative System for Studying Metastasis Using Transparent Zebrafish
Authors: Heilmann Silja , Ratnakumar Kajan , Langdon Erin M. , Kansler Emily R. , Kim Isabella S. , Campbell Nathaniel R. , Perry Elizabeth B. , McMahon Amy J. , Kaufman Charles K. , van Rooijen Ellen , Lee William , Iacobuzio-Donahue Christine A. , Hynes Richard O. , Zon Leonard I. , Xavier Joao B. , White Richard M.
Published: March 2023

Supplemental Video 1: 12 hours post-transplantation of ZMEL1-GFP cells into larval zebrafish showing cells in widespread circulation
Supplemental Table 3 from A Quantitative System for Studying Metastasis Using Transparent Zebrafish
Authors: Heilmann Silja , Ratnakumar Kajan , Langdon Erin M. , Kansler Emily R. , Kim Isabella S. , Campbell Nathaniel R. , Perry Elizabeth B. , McMahon Amy J. , Kaufman Charles K. , van Rooijen Ellen , Lee William , Iacobuzio-Donahue Christine A. , Hynes Richard O. , Zon Leonard I. , Xavier Joao B. , White Richard M.
Published: March 2023

Supplemental Table 3. This Table provides all of the features initially extracted from the zebrafish images and an explanation of how each was used or not.
Supplemetary Video S5 from Snail1-Expressing Fibroblasts in the Tumor Microenvironment Display Mechanical Properties That Support Metastasis
Authors: Stanisavljevic Jelena , Loubat-Casanovas Jordina , Herrera Mercedes , Luque Tomás , Peña Raúl , Lluch Ana , Albanell Joan , Bonilla Félix , Rovira Ana , Peña Cristina , Navajas Daniel , Rojo Federico , García de Herreros Antonio , Baulida Josep
Published: March 2023

Video S5. Ela-Myc cells on 3D-ECM generated by Control MEFs.