bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Data Figure 2 from Preexisting Commensal Dysbiosis Is a Host-Intrinsic Regulator of Tissue Inflammation and Tumor Cell Dissemination in Hormone Receptor–Positive Breast Cancer
Authors: Buchta Rosean Claire , Bostic Raegan R. , Ferey Joshua C.M. , Feng Tzu-Yu , Azar Francesca N. , Tung Kenneth S. , Dozmorov Mikhail G. , Smirnova Ekaterina , Bos Paula D. , Rutkowski Melanie R.
Published: March 2023

Commensal dysbiosis does not induce histopathology (A, B - image examples) or mammary gland metabolism (D) as compared to fecal metabolism as a positive control (C)
Supplemental Tables 1,2,3 from LINC00261 Is an Epigenetically Regulated Tumor Suppressor Essential for Activation of the DNA Damage Response
Authors: Shahabi Shandy , Kumaran Vishaly , Castillo Jonathan , Cong Zhengmin , Nandagopal Gopika , Mullen Daniel J. , Alvarado Alexander , Correa Michele Ramos , Saizan Autumn , Goel Riya , Bhat Amrita , Lynch Sean K. , Zhou Beiyun , Borok Zea , Marconett Crystal N.
Published: March 2023

Supplemental Table T1. List of Primers for LINC00261 detection and cloning. Supplemental Table T2. Differentially expressed lncRNAs in LUAD versus primary AEC. Supplemental Table T3. Differentially expressed genes in H522-CMV-LINC00261 vs CMV-NEO control cells.
Figure S7 from LINC00261 Is an Epigenetically Regulated Tumor Suppressor Essential for Activation of the DNA Damage Response
Authors: Shahabi Shandy , Kumaran Vishaly , Castillo Jonathan , Cong Zhengmin , Nandagopal Gopika , Mullen Daniel J. , Alvarado Alexander , Correa Michele Ramos , Saizan Autumn , Goel Riya , Bhat Amrita , Lynch Sean K. , Zhou Beiyun , Borok Zea , Marconett Crystal N.
Published: March 2023

Figure S7. TCGA LUAD methylation at the FOXA2 locus. A. Individual CpGs are denoted by their Illumina 450K designation. Scale = 0 (no methylation) to 1 (complete methylation). Hg19-based coordinates for each probe are listed below the cg ascension number. Distance from FOXA2 transcript variant 1 Transcription Start Site (TSS) is also shown. "+" is downstream of TSS (within the gene), "-" is upstream of TSS. B. Luciferase assay for activity of FOXA2 promoter in the presence or absence of in vitro SssI methylation. Data is normalized to CpGLess empty vector values from appropriate treatment group. A paired t-test was performed on N=3 biological replicates, each performed in technical triplicate.
Figure S6 from LINC00261 Is an Epigenetically Regulated Tumor Suppressor Essential for Activation of the DNA Damage Response
Authors: Shahabi Shandy , Kumaran Vishaly , Castillo Jonathan , Cong Zhengmin , Nandagopal Gopika , Mullen Daniel J. , Alvarado Alexander , Correa Michele Ramos , Saizan Autumn , Goel Riya , Bhat Amrita , Lynch Sean K. , Zhou Beiyun , Borok Zea , Marconett Crystal N.
Published: March 2023

Figure S6. TCGA LUAD methylation at the LINC00261 locus. A. Individual CpGs are denoted by their Illumina 450K designation. Scale = 0 (no methylation) to 1 (complete methylation). Hg19-based coordinates for each probe are listed below the cg ascension number. Distance from the LINC00261 Transcription Start Site (TSS) is also shown. "+" is downstream of TSS (within the gene), "-" is upstream of TSS. B. RNA expression levels of DNMT enzymes in normal human alveolar epithelial cells (AEC) and available 16 LUAD cancer cell lines (LUAD). Dashed line denotes RPKM cutoff of 3, the commonly accepted cutoff for baseline expression. ** = p value 0.0076, unpaired T Test. N=3 for AEC, 16 for LUAD.
Figure S5 from LINC00261 Is an Epigenetically Regulated Tumor Suppressor Essential for Activation of the DNA Damage Response
Authors: Shahabi Shandy , Kumaran Vishaly , Castillo Jonathan , Cong Zhengmin , Nandagopal Gopika , Mullen Daniel J. , Alvarado Alexander , Correa Michele Ramos , Saizan Autumn , Goel Riya , Bhat Amrita , Lynch Sean K. , Zhou Beiyun , Borok Zea , Marconett Crystal N.
Published: March 2023

Figure S5. Gene expression analysis of LINC00261 co-regulated genes. A. Overlap between H522 differentially expressed genes. Blue circle = Differentially expressed genes in H522 RNAseq. Purple circle = genes co-expressed with LINC00261 in TCGA LUAD (TANRIC). B. DNA damage signaling cascade with genes differentially expressed in A549 shScrambled vs. A549-shLINC00261 (LINC00261 knock down). Pink = upregulated in shLINC00261 samples, green = downregulated. C. Western blotting for additional DDR pathway members in the presence of CMV-LINC00261 or CMV-NEO controls, as indicated. Loading controls were HSP90 or actin, as indicated. Representative blots of three independent experiments shown.
Supplementary Video S2_NME1_H118F from Metastasis Suppressors NME1 and NME2 Promote Dynamin 2 Oligomerization and Regulate Tumor Cell Endocytosis, Motility, and Metastasis
Authors: Khan Imran , Gril Brunilde , Steeg Patricia S.
Published: March 2023

Endocytosis of pHrodo Red-EGF in NME1_H118F (mutant) expressing cells
Supplementary Video S1_Vector from Metastasis Suppressors NME1 and NME2 Promote Dynamin 2 Oligomerization and Regulate Tumor Cell Endocytosis, Motility, and Metastasis
Authors: Khan Imran , Gril Brunilde , Steeg Patricia S.
Published: March 2023

Endocytosis of pHrodo Red-EGF in vector expressing cells
Figure S2 from LINC00261 Is an Epigenetically Regulated Tumor Suppressor Essential for Activation of the DNA Damage Response
Authors: Shahabi Shandy , Kumaran Vishaly , Castillo Jonathan , Cong Zhengmin , Nandagopal Gopika , Mullen Daniel J. , Alvarado Alexander , Correa Michele Ramos , Saizan Autumn , Goel Riya , Bhat Amrita , Lynch Sean K. , Zhou Beiyun , Borok Zea , Marconett Crystal N.
Published: March 2023

Figure S2. Further analysis of LINC00261 expression in multiple cancer types. A. Stratification of LINC00261 expression from TCGA LUSC samples based on stage at diagnosis. B. Upper panel: Overall survival of patients stratified by expression level of LINC00261 derived from Breast Invasive Carcinoma (BRCA) microarray data in KMplot, stratified by upper quartile. Red = high LINC00261 expression, Black = low LINC00261 expression. Lower panel: Survival in liver hepatocellular adenocarcinoma (LIHC) stratified by LINC00261 expression in the OncoLnc database (46) FDR-corrected Cox regression p value = 5.97E-02. Blue = high LINC00261 expression, red = low LINC00261 expression. C. Expression of LINC00261 in TCGA LUAD samples, stratified by smoking history.
Supplementary Figures from Metastasis Suppressors NME1 and NME2 Promote Dynamin 2 Oligomerization and Regulate Tumor Cell Endocytosis, Motility, and Metastasis
Authors: Khan Imran , Gril Brunilde , Steeg Patricia S.
Published: March 2023

SF1: Two model systems of NME mediated motility suppression; SF2: NME overexpression has reduced surface receptors and pHrodo® Red-EGF staining predominantly merged with early endosomes (Rab5); SF3: NME failed to suppress motility in the presence of dynamin inhibitors; SF4: DNM2 depletion has no effect on NME1 NDPK activity and histidine auto-phosphorylation but causes motility reversal; SF5: NME mutants fail to induce tumor cell endocytosis (TfR and EGFR); SF6: NME mutants fail to inhibit EGFR signaling, despite co-immunoprecipitation; SF7: No detectable phosphotransfer between NME1 and DNM2.
Figure S7 from Genetic Ablation of the Cystine Transporter xCT in PDAC Cells Inhibits mTORC1, Growth, Survival, and Tumor Formation via Nutrient and Oxidative Stresses
Authors: Daher Boutaina , Parks Scott K. , Durivault Jerome , Cormerais Yann , Baidarjad Hanane , Tambutte Eric , Pouysségur Jacques , Vučetić Milica
Published: March 2023

Cell viability
Figure S6 from Genetic Ablation of the Cystine Transporter xCT in PDAC Cells Inhibits mTORC1, Growth, Survival, and Tumor Formation via Nutrient and Oxidative Stresses
Authors: Daher Boutaina , Parks Scott K. , Durivault Jerome , Cormerais Yann , Baidarjad Hanane , Tambutte Eric , Pouysségur Jacques , Vučetić Milica
Published: March 2023

Western blot & Bodipy
Targeting the High Mobility Group Box 3 protein sensitizes chemoresistant ovarian cancer cells to cisplatin from Targeting the High-Mobility Group Box 3 Protein Sensitizes Chemoresistant Ovarian Cancer Cells to Cisplatin
Authors: Mukherjee Anirban , Huynh Van , Gaines Kailee , Reh Wade Alan , Vasquez Karen M.
Published: March 2023

The Supplementary Materials include figures, which show siRNA-mediated depletion of HMGB1, HMGB2 and HMGB3 proteins in U2OS cells (Supplementary Figure 1), expression levels of HMGB3 in human ovarian cancer cells (Supplementary Figure 2), LD50 values determined from cisplatin treatment of the A2780 and the A2780/CP70 cells via MTT assays (Supplementary Figure 3), and a luciferase assay to demonstrate transcriptional repression by HMGB3 (Supplementary Figure 4). In addition, there are 3 tables showing the siRNA sequences and the primer sequences used to measure gene expression levels and used for ChIP assays.
Figure S2 from Genetic Ablation of the Cystine Transporter xCT in PDAC Cells Inhibits mTORC1, Growth, Survival, and Tumor Formation via Nutrient and Oxidative Stresses
Authors: Daher Boutaina , Parks Scott K. , Durivault Jerome , Cormerais Yann , Baidarjad Hanane , Tambutte Eric , Pouysségur Jacques , Vučetić Milica
Published: March 2023

Bodipy and Cell morphology
Supplementary Data from Upregulation of Scavenger Receptor B1 Is Required for Steroidogenic and Nonsteroidogenic Cholesterol Metabolism in Prostate Cancer
Authors: Gordon Jacob A. , Noble Jake W. , Midha Ankur , Derakhshan Fatemeh , Wang Gang , Adomat Hans H. , Tomlinson Guns Emma S. , Lin Yen-Yi , Ren Shancheng , Collins Collin C. , Nelson Peter S. , Morrissey Colm , Wasan Kishor M. , Cox Michael E.
Published: March 2023

Supplementary information describing methods for cell culture, HDL assay,qPCR and western blotting analysis, steroid analysis and BLT-1 pharmacokinetic analysis. Supplemental statistical analysis of IHC samples and results of in vivo profiling of BLT-1
Video S3 from Contact-Dependent Killing by Cytotoxic T Lymphocytes Is Insufficient for EL4 Tumor Regression In Vivo
Authors: Beck Richard J. , Slagter Maarten , Beltman Joost B.
Published: March 2023

Supplemental Video 3
Video S1 from Contact-Dependent Killing by Cytotoxic T Lymphocytes Is Insufficient for EL4 Tumor Regression In Vivo
Authors: Beck Richard J. , Slagter Maarten , Beltman Joost B.
Published: March 2023

Supplemental Video
Supplementary Figure5 from Temozolomide Induces Senescence and Repression of DNA Repair Pathways in Glioblastoma Cells via Activation of ATR–CHK1, p21, and NF-κB
Authors: Aasland Dorthe , Götzinger Laura , Hauck Laura , Berte Nancy , Meyer Jessica , Effenberger Melanie , Schneider Simon , Reuber Emelie E. , Roos Wynand P. , Tomicic Maja T. , Kaina Bernd , Christmann Markus
Published: March 2023

Impact of NfkB on senescence and mRNA expression of IL6, IL8, c-IAP2, BclXL, XIAP and Survivin.
Supplementary Figure3 from Temozolomide Induces Senescence and Repression of DNA Repair Pathways in Glioblastoma Cells via Activation of ATR–CHK1, p21, and NF-κB
Authors: Aasland Dorthe , Götzinger Laura , Hauck Laura , Berte Nancy , Meyer Jessica , Effenberger Melanie , Schneider Simon , Reuber Emelie E. , Roos Wynand P. , Tomicic Maja T. , Kaina Bernd , Christmann Markus
Published: March 2023

Impact of CHK1 on the G2/M arrest and senescence
Supplementary Materials and Methods from Role of Chromatin Damage and Chromatin Trapping of FACT in Mediating the Anticancer Cytotoxicity of DNA-Binding Small-Molecule Drugs
Authors: Nesher Elimelech , Safina Alfiya , Aljahdali Ieman , Portwood Scott , Wang Eunice S. , Koman Igor , Wang Jianmin , Gurova Katerina V.
Published: March 2023

File contains the list of all chemicals, reagents, antibodies and cells used with sources and catalogue numbers, as well as detailed description of all methods, mentioned in the in the main text, including cytotoxicity assays, imaging, cell-free experiments nascent RNA-seq, ChIP-seq. Includes Supplementary Table 1.
Supplementary Table 1b from miR-450a Acts as a Tumor Suppressor in Ovarian Cancer by Regulating Energy Metabolism
Authors: Muys Bruna Rodrigues , Sousa Josane F. , Plaça Jessica Rodrigues , de Araújo Luíza Ferreira , Sarshad Aishe A. , Anastasakis Dimitrios G. , Wang Xiantao , Li Xiao Ling , de Molfetta Greice Andreotti , Ramão Anelisa , Lal Ashish , Vidal Daniel Onofre , Hafner Markus , Silva Wilson A.
Published: March 2023

Supplementary Table 1. List of potential total miRNA and miR-450a only binding sites from A2780 cell line and expressing miR-450a
Supplementary Table S8 from tRNA Fragments Show Intertwining with mRNAs of Specific Repeat Content and Have Links to Disparities
Authors: Telonis Aristeidis G. , Loher Phillipe , Magee Rogan , Pliatsika Venetia , Londin Eric , Kirino Yohei , Rigoutsos Isidore
Published: March 2023

This file contains the results on the enriched pathways in the correlations of mitochondrial tRFs with mRNAs.
Supplementary Table S7 from tRNA Fragments Show Intertwining with mRNAs of Specific Repeat Content and Have Links to Disparities
Authors: Telonis Aristeidis G. , Loher Phillipe , Magee Rogan , Pliatsika Venetia , Londin Eric , Kirino Yohei , Rigoutsos Isidore
Published: March 2023

This file contains the results on the enriched pathways in the correlations of nuclear tRFs with mRNAs.
Supplementary Figure 1 from miR-450a Acts as a Tumor Suppressor in Ovarian Cancer by Regulating Energy Metabolism
Authors: Muys Bruna Rodrigues , Sousa Josane F. , Plaça Jessica Rodrigues , de Araújo Luíza Ferreira , Sarshad Aishe A. , Anastasakis Dimitrios G. , Wang Xiantao , Li Xiao Ling , de Molfetta Greice Andreotti , Ramão Anelisa , Lal Ashish , Vidal Daniel Onofre , Hafner Markus , Silva Wilson A.
Published: March 2023

Supplementary Figure 1. miR-450a overexpression and effects in SKOV-3 ovarian cancer cell line.
Supplementary Table S5 from tRNA Fragments Show Intertwining with mRNAs of Specific Repeat Content and Have Links to Disparities
Authors: Telonis Aristeidis G. , Loher Phillipe , Magee Rogan , Pliatsika Venetia , Londin Eric , Kirino Yohei , Rigoutsos Isidore
Published: March 2023

This file contains the significant correlations of mitochondrial tRFs with mRNAs.
Supplementary Figures from tRNA Fragments Show Intertwining with mRNAs of Specific Repeat Content and Have Links to Disparities
Authors: Telonis Aristeidis G. , Loher Phillipe , Magee Rogan , Pliatsika Venetia , Londin Eric , Kirino Yohei , Rigoutsos Isidore
Published: March 2023

This file contains the results on tRNA modification analyses, cleavage patterns and the associations with mRNAs.
Supplementary Table S2 from Psychologic Distress Is Associated with Cancer-Specific Mortality among Patients with Cervical Cancer
Authors: Lu Donghao , Andrae Bengt , Valdimarsdóttir Unnur , Sundström Karin , Fall Katja , Sparén Pär , Fang Fang
Published: March 2023

Associations of psychological distress with mortality risks, by the timing of the occurrence of distress.
Supplementary Data from T-cell–Secreted TNFα Induces Emergency Myelopoiesis and Myeloid-Derived Suppressor Cell Differentiation in Cancer
Authors: Al Sayed Mohamad F. , Amrein Michael A. , Bührer Elias D. , Huguenin Anne-Laure , Radpour Ramin , Riether Carsten , Ochsenbein Adrian F.
Published: March 2023

Table S1: suppl. cell cycle analysis to Fig 3; Table S2: suppl. BrDU and AnnexinV analysis to Fig 3; Table S3: suppl. analysis of the compositions of HSPC compartments to Fig 4; Figure S1: suppl. to Fig 1; Figure S2: suppl. to Fig 4; Figure S3: suppl. to Fig 6; Figure S4: suppl. to Fig 7
Supplementary Figure S2 from Psychologic Distress Is Associated with Cancer-Specific Mortality among Patients with Cervical Cancer
Authors: Lu Donghao , Andrae Bengt , Valdimarsdóttir Unnur , Sundström Karin , Fall Katja , Sparén Pär , Fang Fang
Published: March 2023

Association of psychological distress with the risk of overall mortality.
Supplementary Figure S1 from Psychologic Distress Is Associated with Cancer-Specific Mortality among Patients with Cervical Cancer
Authors: Lu Donghao , Andrae Bengt , Valdimarsdóttir Unnur , Sundström Karin , Fall Katja , Sparén Pär , Fang Fang
Published: March 2023

Association of psychological distress with the risk of cancer-specific mortality, by excluding deaths coded as unspecified uterine cancer.
Supplementary table 1 from SF3B2-Mediated RNA Splicing Drives Human Prostate Cancer Progression
Authors: Kawamura Norihiko , Nimura Keisuke , Saga Kotaro , Ishibashi Airi , Kitamura Koji , Nagano Hiromichi , Yoshikawa Yusuke , Ishida Kyoso , Nonomura Norio , Arisawa Mitsuhiro , Luo Jun , Kaneda Yasufumi
Published: March 2023

A list of primers used for PCR and gRNA
Supplemental Table 4 from Inactivation of Bap1 Cooperates with Losses of Nf2 and Cdkn2a to Drive the Development of Pleural Malignant Mesothelioma in Conditional Mouse Models
Authors: Kukuyan Anna-Mariya , Sementino Eleonora , Kadariya Yuwaraj , Menges Craig W. , Cheung Mitchell , Tan Yinfei , Cai Kathy Q. , Slifker Michael J. , Peri Suraj , Klein-Szanto Andres J. , Rauscher Frank J. , Testa Joseph R.
Published: March 2023

Top 199 gene sets differentially affected (FDRa < 0.25) in human MMs from TCGA data set with TKO versus DKO status using GSEA applied to MSigDB gene sets.
Supplementary Data from SF3B2-Mediated RNA Splicing Drives Human Prostate Cancer Progression
Authors: Kawamura Norihiko , Nimura Keisuke , Saga Kotaro , Ishibashi Airi , Kitamura Koji , Nagano Hiromichi , Yoshikawa Yusuke , Ishida Kyoso , Nonomura Norio , Arisawa Mitsuhiro , Luo Jun , Kaneda Yasufumi
Published: March 2023

Supplementary Figures 1-8. (1) Figure S1 shows Identification of SF3B2 as a splicing modulating factor associated with AR-V7 expression. (2) Figure S2 shows FACS analysis of gRNA against each candidate gene-transfected AR-V7-GFP cell population. (3) Figure S3 shows Kaplan-Meier curves of overall survival in cancer patients with SF3B2 high or low expression divided by the median. (4) Figure S4 shows Validation of RNAseq and SF3B2 PAR-CLIP. (5) Figure S5 shows Effects of SF3B2 depletion on splicing and gene expression. (6) Figure S6 shows Construction of SF3B2-stably expressed and AR-V7-knock out 22Rv1 and LNCaP95 cells. (7) Figure S7 shows Effects of SF3B2 stably expression on splicing and gene expression. (8) Figure S8 shows Pladienolide B represses SF3B2-addicted tumor growth and AR-V7 expression.
Supplementary Materials and Methods from LOXL2 Upregulates Phosphorylation of Ezrin to Promote Cytoskeletal Reorganization and Tumor Cell Invasion
Authors: Zhan Xiu-Hui , Jiao Ji-Wei , Zhang Hai-Feng , Xu Xiu-E , He Jian-Zhong , Li Run-Liu , Zou Hai-Ying , Wu Zhi-Yong , Wang Shao-Hong , Wu Jian-Yi , Liao Lian-Di , Wang Juan-Juan , Cheng Yin-Wei , Zhang Kai , Neufeld Gera , Xu Li-Yan , Li En-Min
Published: March 2023

Supplementary Materials and Methods
Supplementary Figures from LOXL2 Upregulates Phosphorylation of Ezrin to Promote Cytoskeletal Reorganization and Tumor Cell Invasion
Authors: Zhan Xiu-Hui , Jiao Ji-Wei , Zhang Hai-Feng , Xu Xiu-E , He Jian-Zhong , Li Run-Liu , Zou Hai-Ying , Wu Zhi-Yong , Wang Shao-Hong , Wu Jian-Yi , Liao Lian-Di , Wang Juan-Juan , Cheng Yin-Wei , Zhang Kai , Neufeld Gera , Xu Li-Yan , Li En-Min
Published: March 2023

Supplementary Figure S1-S9. Figure S1. Specificity of antibody directed against the L2Δ13 splice form of LOXL2 in histological analysis. Figure S2. LOXL2 and L2Δ13 promote ESCC cell migration and invasion. Figure S3. Histological analysis of tumors and popliteal lymph nodes derived from the xenografts. Figure S4. LOXL2 and L2Δ13 interact with actin-binding proteins ezrin, fascin, HSPB1 and TMOD3. Figure S5. Co-localizations of L2Δ13 with four cytoskeletal binding proteins in ESCC cells. Figure S6. Kaplan-Meier curves and log-rank tests of fascin, HSPB1 and TMOD3 for overall survival and disease-free survival in ESCC patients. Figure S7. Molecular models of LOXL2/L2Δ13 and its actin-binding interacting partners predict poor prognosis in ESCC patients. Figure S8. LOXL2 is an oncogenic modulator in the activation of ezrin via phosphorylating ezrin at T567. Figure S9. LOXL2 modulates PKC-stimulated ezrin-T567 phosphorylation in ESCC cells.
Supplementary Figure S2 from Disruption of the Scaffolding Function of mLST8 Selectively Inhibits mTORC2 Assembly and Function and Suppresses mTORC2-Dependent Tumor Growth In Vivo
Authors: Hwang Yoonha , Kim Laura C. , Song Wenqiang , Edwards Deanna N. , Cook Rebecca S. , Chen Jin
Published: March 2023

Disruption of mTOR-mLST8 binding specifically inhibits mTORC2 activity
Supplementary Figure S1 from Disruption of the Scaffolding Function of mLST8 Selectively Inhibits mTORC2 Assembly and Function and Suppresses mTORC2-Dependent Tumor Growth In Vivo
Authors: Hwang Yoonha , Kim Laura C. , Song Wenqiang , Edwards Deanna N. , Cook Rebecca S. , Chen Jin
Published: March 2023

mLST8 is required for mTORC2 activity in cancer cells
Supplementary Figure Legends from LOXL2 Upregulates Phosphorylation of Ezrin to Promote Cytoskeletal Reorganization and Tumor Cell Invasion
Authors: Zhan Xiu-Hui , Jiao Ji-Wei , Zhang Hai-Feng , Xu Xiu-E , He Jian-Zhong , Li Run-Liu , Zou Hai-Ying , Wu Zhi-Yong , Wang Shao-Hong , Wu Jian-Yi , Liao Lian-Di , Wang Juan-Juan , Cheng Yin-Wei , Zhang Kai , Neufeld Gera , Xu Li-Yan , Li En-Min
Published: March 2023

Supplementary Figure Legends
Supplementary Data from Targeting the Temporal Dynamics of Hypoxia-Induced Tumor-Secreted Factors Halts Tumor Migration
Authors: Singh Manjulata , Tian Xiao-Jun , Donnenberg Vera S. , Watson Alan M. , Zhang JingYu , Stabile Laura P. , Watkins Simon C. , Xing Jianhua , Sant Shilpa
Published: March 2023

Supplementary Information includes supplemental experimental procedures, description of gene regulatory network, two tables, eight figures and a supplementary video. Supplementary Table S1. List of primers used Supplementary Table S2. Parameters used in the ODEs Supplementary Figure S1: Large T47D microtumors exhibit collective migration, hypoxia and aggressive phenotype. Supplementary video showing migration of a microtumor Supplementary Figure S2: Treatment of 150 and 600μm microtumors with conditioned media of 150μm microtumors (150/CM). Supplementary Figure S3: Morphology and multi-parameter flow cytometry on breast cancer metastatic pleural effusion cells. Supplementary Figure S4: Large microtumors of patient-derived primary cancer cells and xenograft cells showed migratory behavior. Supplementary Figure S5: Integrated regulatory network of tumor secretome factors and signaling molecules involved in microtumor migration. Supplementary Figure S6: HIF-1α inhibition at later time points does not inhibit migration of 600μm microtumors. Supplementary Figure S7: Effect of MMP inhibitor treatment on the collective migration of large microtumors of T47D cell line and patient-derived metastatic breast cancer (mBC) cells. Supplementary Figure S8: Effect of Anti-sE-CAD antibody treatment on the collective migration of large microtumors of T47D cells and patient-derived metastatic breast cancer (mBC) cells.
Supplementary Data from APE1 Upregulates MMP-14 via Redox-Sensitive ARF6-Mediated Recycling to Promote Cell Invasion of Esophageal Adenocarcinoma
Authors: Lu Heng , Bhat Ajaz A. , Peng Dunfa , Chen Zheng , Zhu Shoumin , Hong Jun , Maacha Selma , Yan Jin , Robbins David J. , Washington M. Kay , Belkhiri Abbes , El-Rifai Wael
Published: March 2023

Supplementary Methods
Supplementary Figure legend from M2 Macrophage-Derived Exosomes Promote Cell Migration and Invasion in Colon Cancer
Authors: Lan Jingqin , Sun Li , Xu Feng , Liu Lu , Hu Fuqing , Song Da , Hou Zhenlin , Wu Wei , Luo Xuelai , Wang Jing , Yuan Xianglin , Hu Junbo , Wang Guihua
Published: March 2023

Supplementary Figure legend
Figure S1 from Poly (ADP) Ribose Glycohydrolase Can Be Effectively Targeted in Pancreatic Cancer
Authors: Jain Aditi , Agostini Lebaron C. , McCarthy Grace A. , Chand Saswati N. , Ramirez AnnJosette , Nevler Avinoam , Cozzitorto Joseph , Schultz Christopher W. , Lowder Cinthya Yabar , Smith Kate M. , Waddell Ian D. , Raitses-Gurevich Maria , Stossel Chani , Gorman Yulia Glick , Atias Dikla , Yeo Charles J. , Winter Jordan M. , Olive Kenneth P. , Golan Talia , Pishvaian Michael J. , Ogilvie Donald , James Dominic I. , Jordan Allan M. , Brody Jonathan R.
Published: March 2023

Supplementary Figure S1 describes mRNA and protein expression of PARG in shPARG models and in vitro sensitivity to oxaliplatin.
Figure S1, Figure S2, Figure S3, Figure S4, Figure S5, Figure S6, Figure S7, Table S1, Table S2, Table S3, Table S4 from Single-Cell Transcriptome Analyses Reveal Endothelial Cell Heterogeneity in Tumors and Changes following Antiangiogenic Treatment
Authors: Zhao Qi , Eichten Alexandra , Parveen Asma , Adler Christina , Huang Ying , Wang Wei , Ding Yueming , Adler Alexander , Nevins Thomas , Ni Min , Wei Yi , Thurston Gavin
Published: March 2023

Figure S1, Heart endothelial cell subpopulations. Figure S2, Expression of selected genes that could distinguish EC subpopulations in heart. Figure S3, Composition of COLO205 tumor stromal cells. Figure S4, Subpopulations of tumor endothelial cells. Figure S5, Gene ontology annotation and pathway enrichment analyses on differentially. expressed genes between anti-angiogenic drug vs. hFc treatment in tip-like cells. Figure S6, Subpopulations in COLO205-derived TAFs. Figure S7, Subpopulations in heart-derived stromal fibroblasts. Table S1, Top 90 genes by ANOVA test p value that have distinctive expression pattern among heart endothelial cell subpopulations. Table S2, Top 30 genes that have distinctive expression pattern in heart EC subpopulations. Table S3, Comparison between overlapping endothelial subpopulation markers identified in heart and tumor tissue. Table S4, Changes of tumor endothelial cells expressing cell cycle genes following anti-angiogenic treatment.
Supplementary Data from Targeting BCR-ABL1 in Chronic Myeloid Leukemia by PROTAC-Mediated Targeted Protein Degradation
Authors: Burslem George M. , Schultz Anna Reister , Bondeson Daniel P. , Eide Christopher A. , Savage Stevens Samantha L. , Druker Brian J. , Crews Craig M.
Published: March 2023

Table S1 - Reverse phase protein array data for K562 cells treated with GMB-475 or GMB-651.
Figure S7 from Remodeling the Tumor Microenvironment Sensitizes Breast Tumors to Anti-Programmed Death-Ligand 1 Immunotherapy
Authors: Clift Renee , Souratha Jennifer , Garrovillo Sheryl A. , Zimmerman Susan , Blouw Barbara
Published: March 2023

Pegvorhyaluronidase alfa effect on density of T-cells and NK cells and proportion of Gr1+ myeloid-derived suppressor cells in EMT-6 orthotopic breast tumors
Figure S6 from Remodeling the Tumor Microenvironment Sensitizes Breast Tumors to Anti-Programmed Death-Ligand 1 Immunotherapy
Authors: Clift Renee , Souratha Jennifer , Garrovillo Sheryl A. , Zimmerman Susan , Blouw Barbara
Published: March 2023

Pegvorhyaluronidase alfa in combination with anti-PD-L1 effect on density of T-cells and NK cells and the proportion of Gr1+ myeloid-derived suppressor cells in EMT-6 orthotopic breast tumors
Figure S5 from Genetic Variants of VEGFA and FLT4 Are Determinants of Survival in Renal Cell Carcinoma Patients Treated with Sorafenib
Authors: Crona Daniel J. , Skol Andrew D. , Leppänen Veli-Matti , Glubb Dylan M. , Etheridge Amy S. , Hilliard Eleanor , Peña Carol E. , Peterson Yuri K. , Klauber-DeMore Nancy , Alitalo Kari K. , Innocenti Federico
Published: March 2023

Effects of VEGFA rs58159269 (T>C) on endothelial cell proliferation in sunitinib.
Supplementary Material and Methods from Multiparametric MRI and Coregistered Histology Identify Tumor Habitats in Breast Cancer Mouse Models
Authors: Jardim-Perassi Bruna V. , Huang Suning , Dominguez-Viqueira William , Poleszczuk Jan , Budzevich Mikalai M. , Abdalah Mahmoud A. , Pillai Smitha R. , Ruiz Epifanio , Bui Marilyn M. , Zuccari Debora A.P.C. , Gillies Robert J. , Martinez Gary V.
Published: March 2023

Supplementary Material and Methods
Figure S2 from Arming Tumor-Associated Macrophages to Reverse Epithelial Cancer Progression
Authors: Wettersten Hiromi I. , Weis Sara M. , Pathria Paulina , Von Schalscha Tami , Minami Toshiyuki , Varner Judith A. , Cheresh David A.
Published: March 2023

Enlarged images showing immunohistochemistry for integrin beta3 and macrophage markers for multiple tumor types.
Supplementary Video1 from Volumetric Optoacoustic Imaging Unveils High-Resolution Patterns of Acute and Cyclic Hypoxia in a Murine Model of Breast Cancer
Authors: Ron Avihai , Deán-Ben Xosé Luís , Gottschalk Sven , Razansky Daniel
Published: March 2023

A time-lapse video of the Local sO2 responses in single voxels to an oxygen challenge
Supplementary Figures S1-S10 from TLR Signaling Is Activated in Lymph Node–Resident CLL Cells and Is Only Partially Inhibited by Ibrutinib
Authors: Dadashian Eman L. , McAuley Erin M. , Liu Delong , Shaffer Arthur L. , Young Ryan M. , Iyer Jessica R. , Kruhlak Michael J. , Staudt Louis M. , Wiestner Adrian , Herman Sarah E. M.
Published: March 2023

Supplementary Figure S1: Dose response experiments with the IRAK1/4 inhibitor (IRAKi) in CLL cells. Supplementary Figure S2: TLR signaling is active in lymph node-resident CLL cells. Supplementary Figure S3: Flow Cytometry gating strategy. Supplementary Figure S4: Early activation of STAT3 leads to early production of serum IL-10. Supplementary Figure S5: TLR signaling induces similar levels of IRAK1 degradation and STAT signaling in vitro with CpG stimulation in primary CLL PBMCs. Supplementary Figure S6: Upstream IRAK1 degradation and downstream phosphorylation of STAT3 and IκBα are inversely related. Supplementary Figure S7: CpG induced TLR signaling promotes cell survival and activates CLL cells in vitro. Supplementary Figure S8: Inhibiting induced TLR activation downregulates expression of activation markers and prevents the survival advantage in CLL cells. Supplementary Figure S9: αIgM stimulation induces activation of BCR pathway signaling. Supplementary Figure S10: Ibrutinib inhibits both BCR and TLR signaling in activated CLL cells harvested from the lymph node.
Supplementary Figure Legends from TLR Signaling Is Activated in Lymph Node–Resident CLL Cells and Is Only Partially Inhibited by Ibrutinib
Authors: Dadashian Eman L. , McAuley Erin M. , Liu Delong , Shaffer Arthur L. , Young Ryan M. , Iyer Jessica R. , Kruhlak Michael J. , Staudt Louis M. , Wiestner Adrian , Herman Sarah E. M.
Published: March 2023

Supplementary Figure Legends S1-S10
Figure S1 from Use of a Single CAR T Cell and Several Bispecific Adapters Facilitates Eradication of Multiple Antigenically Different Solid Tumors
Authors: Lee Yong Gu , Marks Isaac , Srinivasarao Madduri , Kanduluru Ananda Kumar , Mahalingam Sakkarapalayam M. , Liu Xin , Chu Haiyan , Low Philip S.
Published: March 2023

Design and characterization of anti-FITC CAR T cell and CAMs
Supplementary Table 3 from Molecular Profiling Establishes Genetic Features Predictive of the Efficacy of the p110β Inhibitor KIN-193
Authors: Sethi Isha , Cai Zhenying , Roberts Thomas M. , Yuan Guo-Cheng
Published: March 2023

5 PTEN WT cell-lines from CCLE that are predicted to be resistant to KIN-193. Columns 1-6 give information on the prediction status of the cell-lines using MIA-RNMI and MIA-Eqwt models. Columns 7-9 give information on experimental validations based on published datasets.
Supplementary Table 2 from Molecular Profiling Establishes Genetic Features Predictive of the Efficacy of the p110β Inhibitor KIN-193
Authors: Sethi Isha , Cai Zhenying , Roberts Thomas M. , Yuan Guo-Cheng
Published: March 2023

PTEN null resistant cell-lines that have a mutation in PIK3CB or PIK3R1. Columns 1:3 give information about cell-line and columns 4:8 give details about the mutation.
Supplementary Data from Multiregion Sequencing Reveals the Genetic Heterogeneity and Evolutionary History of Osteosarcoma and Matched Pulmonary Metastases
Authors: Wang Di , Niu Xiaohui , Wang Zhijie , Song Cheng-Li , Huang Zhen , Chen Ke-Neng , Duan Jianchun , Bai Hua , Xu Jiachen , Zhao Jun , Wang Yu , Zhuo Minglei , Xie X. Sunney , Kang Xiaozheng , Tian Yanhua , Cai Liangliang , Han Jie-Fei , An Tongtong , Sun Yu , Gao Shugeng , Ying Jianming , Wang Luhua , He Jie , Wang Jie
Published: March 2023

Supplementary Table S2's patient detail information
Supplementary Data from Multiregion Sequencing Reveals the Genetic Heterogeneity and Evolutionary History of Osteosarcoma and Matched Pulmonary Metastases
Authors: Wang Di , Niu Xiaohui , Wang Zhijie , Song Cheng-Li , Huang Zhen , Chen Ke-Neng , Duan Jianchun , Bai Hua , Xu Jiachen , Zhao Jun , Wang Yu , Zhuo Minglei , Xie X. Sunney , Kang Xiaozheng , Tian Yanhua , Cai Liangliang , Han Jie-Fei , An Tongtong , Sun Yu , Gao Shugeng , Ying Jianming , Wang Luhua , He Jie , Wang Jie
Published: March 2023

Supplementary Table S2's detail information of germline mutations in each patient
Supplementary Information from ATP-Competitive Inhibitors Midostaurin and Avapritinib Have Distinct Resistance Profiles in Exon 17–Mutant KIT
Authors: Apsel Winger Beth , Cortopassi Wilian A. , Garrido Ruiz Diego , Ding Lucky , Jang Kibeom , Leyte-Vidal Ariel , Zhang Na , Esteve-Puig Rosaura , Jacobson Matthew P. , Shah Neil P.
Published: March 2023

This document contains supplementary methods, tables, figures and references for the manuscript "ATP-competitive inhibitors midostaurin and avapritinib have distinct resistance profiles in exon 17-mutant KIT".
Figure S1-4 and supplementary material and methods from SCFFBXW7/GSK3β-Mediated GFI1 Degradation Suppresses Proliferation of Gastric Cancer Cells
Authors: Kuai Xiaoling , Li Long , Chen Ran , Wang Kangjunjie , Chen Min , Cui Binghai , Zhang Yuxue , Li Junqiang , Zhu Hongwen , Zhou Hu , Huang Jianfei , Qin Jun , Wang Zhiwei , Wei Wenyi , Gao Daming
Published: March 2023

Figure S1-GFI1 promotes GC cell proliferation and suppresses GKN2 expression.Figure S2-FBXW7 governs GFI1 stability.Figure S3-GSK3β destabilizes GFI1 and negatively regulates GFI1 expression. Figure S4-Spectrum of peptide containing GFI1 S94 phosphorylation.
Supplementary Figure S6 from Deletion of Calcineurin Promotes a Protumorigenic Fibroblast Phenotype
Authors: Lieberman Allyson , Barrett Richard , Kim Jaewon , Zhang Kathy L. , Avery Diana , Monslow James , Kim Hyunsoo , Kim Bang-Jin , Puré Ellen , Ryeom Sandra
Published: March 2023

Actin staining of LLCs cultured on WT and CN-/- FDMs
Supplementary Figure S2 from Deletion of Calcineurin Promotes a Protumorigenic Fibroblast Phenotype
Authors: Lieberman Allyson , Barrett Richard , Kim Jaewon , Zhang Kathy L. , Avery Diana , Monslow James , Kim Hyunsoo , Kim Bang-Jin , Puré Ellen , Ryeom Sandra
Published: March 2023

IF confirmation of caNFATc1 expression.
Supplementary Figure S1 from Deletion of Calcineurin Promotes a Protumorigenic Fibroblast Phenotype
Authors: Lieberman Allyson , Barrett Richard , Kim Jaewon , Zhang Kathy L. , Avery Diana , Monslow James , Kim Hyunsoo , Kim Bang-Jin , Puré Ellen , Ryeom Sandra
Published: March 2023

Western blots confirming CnB/CnA deletion.
eTable from Posttraumatic Stress Disorder Is Associated with Increased Risk of Ovarian Cancer: A Prospective and Retrospective Longitudinal Cohort Study
Authors: Roberts Andrea L. , Huang Tianyi , Koenen Karestan C. , Kim Yongjoo , Kubzansky Laura D. , Tworoger Shelley S.
Published: March 2023

Traumatic events and PTSD symptoms queried
Supplementary Data from A Collaborative Analysis of Individual Participant Data from 19 Prospective Studies Assesses Circulating Vitamin D and Prostate Cancer Risk
Authors: Travis Ruth C. , Perez-Cornago Aurora , Appleby Paul N. , Albanes Demetrius , Joshu Corinne E. , Lutsey Pamela L. , Mondul Alison M. , Platz Elizabeth A. , Weinstein Stephanie J. , Layne Tracy M. , Helzlsouer Kathy J. , Visvanathan Kala , Palli Domenico , Peeters Petra H. , Bueno-de-Mesquita Bas , Trichopoulou Antonia , Gunter Marc J. , Tsilidis Konstantinos K. , Sánchez Maria-Jose , Olsen Anja , Brenner Hermann , Schöttker Ben , Perna Laura , Holleczek Bernd , Knekt Paul , Rissanen Harri , Yeap Bu B. , Flicker Leon , Almeida Osvaldo P. , Wong Yuen Yee Elizabeth , Chan June M. , Giovannucci Edward L. , Stampfer Meir J. , Ursin Giske , Gislefoss Randi E. , Bjørge Tone , Meyer Haakon E. , Blomhoff Rune , Tsugane Shoichiro , Sawada Norie , English Dallas R. , Eyles Darryl W. , Heath Alicia K. , Williamson Elizabeth J. , Manjer Jonas , Malm Johan , Almquist Martin , Marchand Loic Le , Haiman Christopher A. , Wilkens Lynne R. , Schenk Jeannette M. , Tangen Cathy M. , Black Amanda , Cook Michael B. , Huang Wen-Yi , Ziegler Regina G. , Martin Richard M. , Hamdy Freddie C. , Donovan Jenny L. , Neal David E. , Touvier Mathilde , Hercberg Serge , Galan Pilar , Deschasaux Mélanie , Key Timothy J. , Allen Naomi E.
Published: March 2023

Supplementary methods, tables and figures
Figure S1-S7 from LKB1 and KEAP1/NRF2 Pathways Cooperatively Promote Metabolic Reprogramming with Enhanced Glutamine Dependence in KRAS-Mutant Lung Adenocarcinoma
Authors: Galan-Cobo Ana , Sitthideatphaiboon Piyada , Qu Xiao , Poteete Alissa , Pisegna Marlese A. , Tong Pan , Chen Pei-Hsuan , Boroughs Lindsey K. , Rodriguez Mirna L.M. , Zhang Winter , Parlati Francesco , Wang Jing , Gandhi Varsha , Skoulidis Ferdinandos , DeBerardinis Ralph J. , Minna John D. , Heymach John V.
Published: March 2023

Supplementary bioinformatic analysis and CB-839 effects on in vitro cell proliferation, ROS stress and metabolism.
Supplementary Data from Collagen Prolyl Hydroxylation–Dependent Metabolic Perturbation Governs Epigenetic Remodeling and Mesenchymal Transition in Pluripotent and Cancer Cells
Authors: D'Aniello Cristina , Cermola Federica , Palamidessi Andrea , Wanderlingh Luca G. , Gagliardi Miriam , Migliaccio Agnese , Varrone Francesca , Casalino Laura , Matarazzo Maria R. , De Cesare Dario , Scita Giorgio , Patriarca Eduardo J. , Minchiotti Gabriella
Published: March 2023

Supplementary data include Figure S1(Structural determinants of ESC inhibitors), Figure S2 (Validation and functional characterization of esMTi), Figure S3 (Generation and characterization of P4H deficient ESCs), Figure S4 (Budesonide activity on A549 lung tumor cells ); Figure S5 (Budesonide activity on SUM159 cells); Table S1 (The primer sequences and application); Table S2 (The Primary Antibodies and application); Table S3 (List of all ESC inhibitors), Table S4 (ESC inhibitors with anti-cancer activity and related references); Table S5 (List of esMT inhibitors), Table S6 (esMT inhibitors with anti-collagen/fibortic effects)
Table S1 from Glucocorticoid Receptor Signaling Activates TEAD4 to Promote Breast Cancer Progression
Authors: He Lingli , Yuan Liang , Sun Yang , Wang Pingyang , Zhang Hailin , Feng Xue , Wang Zuoyun , Zhang Wenxiang , Yang Chuanyu , Zeng Yi Arial , Zhao Yun , Chen Ceshi , Zhang Lei
Published: March 2023

Compounds, drugs, antibodies and primers
Figure S5 from Glucocorticoid Receptor Signaling Activates TEAD4 to Promote Breast Cancer Progression
Authors: He Lingli , Yuan Liang , Sun Yang , Wang Pingyang , Zhang Hailin , Feng Xue , Wang Zuoyun , Zhang Wenxiang , Yang Chuanyu , Zeng Yi Arial , Zhao Yun , Chen Ceshi , Zhang Lei
Published: March 2023

Supplementary Figure 5. TEAD4 shows no expression in Her2+ and ER+ breast cancer samples.
Figure S3 from Glucocorticoid Receptor Signaling Activates TEAD4 to Promote Breast Cancer Progression
Authors: He Lingli , Yuan Liang , Sun Yang , Wang Pingyang , Zhang Hailin , Feng Xue , Wang Zuoyun , Zhang Wenxiang , Yang Chuanyu , Zeng Yi Arial , Zhao Yun , Chen Ceshi , Zhang Lei
Published: March 2023

Supplementary Figure 3. Glucocorticoid receptor signaling activates TEAD4 independent of YAP/TAZ.
Figure S5 from Upregulation of PD-L1 via HMGB1-Activated IRF3 and NF-κB Contributes to UV Radiation-Induced Immune Suppression
Authors: Wang Wei , Chapman Nicole M. , Zhang Bo , Li Mingqi , Fan Meiyun , Laribee R. Nicholas , Zaidi M. Raza , Pfeffer Lawrence M. , Chi Hongbo , Wu Zhao-Hui
Published: March 2023

UVR decreased melanoma susceptibility to CTLs which required IRF3.
Figure S4 from Upregulation of PD-L1 via HMGB1-Activated IRF3 and NF-κB Contributes to UV Radiation-Induced Immune Suppression
Authors: Wang Wei , Chapman Nicole M. , Zhang Bo , Li Mingqi , Fan Meiyun , Laribee R. Nicholas , Zaidi M. Raza , Pfeffer Lawrence M. , Chi Hongbo , Wu Zhao-Hui
Published: March 2023

RAGE and IRF3 are required for PD-L1 induction by UVB.
Supplementary methods from Recycling Endosomes in Mature Epithelia Restrain Tumorigenic Signaling
Authors: D'Agostino Luca , Nie Yingchao , Goswami Sayantani , Tong Kevin , Yu Shiyan , Bandyopadhyay Sheila , Flores Juan , Zhang Xiao , Balasubramanian Iyshwarya , Joseph Ivor , Sakamori Ryotaro , Farrell Victoria , Li Qi , Yang Chung S. , Gao Bin , Ferraris Ronaldo P. , Yehia Ghassan , Bonder Edward M. , Goldenring James R. , Verzi Michael P. , Zhang Lanjing , Ip Y. Tony , Gao Nan
Published: March 2023

Detailed description of the various methods utilized in this manuscript in addition to the methods mentioned in the primary article
Supplementary Figure 6 from Recycling Endosomes in Mature Epithelia Restrain Tumorigenic Signaling
Authors: D'Agostino Luca , Nie Yingchao , Goswami Sayantani , Tong Kevin , Yu Shiyan , Bandyopadhyay Sheila , Flores Juan , Zhang Xiao , Balasubramanian Iyshwarya , Joseph Ivor , Sakamori Ryotaro , Farrell Victoria , Li Qi , Yang Chung S. , Gao Bin , Ferraris Ronaldo P. , Yehia Ghassan , Bonder Edward M. , Goldenring James R. , Verzi Michael P. , Zhang Lanjing , Ip Y. Tony , Gao Nan
Published: March 2023

RAB11A-KD cells show increased YAP signaling and proliferation.
Table S1, Figure S1-5 from IL6 Promotes a STAT3-PRL3 Feedforward Loop via SHP2 Repression in Multiple Myeloma
Authors: Chong Phyllis S.Y. , Zhou Jianbiao , Lim Julia S.L. , Hee Yan Ting , Chooi Jing-Yuan , Chung Tae-Hoon , Tan Zea Tuan , Zeng Qi , Waller Daniel D. , Sebag Michael , Chng Wee-Joo
Published: March 2023

Table S1: RT-PCR primers Figure S1: mRNA and protein expression of PRL-3 in HMCLs. Figure S2. IL-6 treatment of MM cell lines. Figure S3. Cellular effects of PRL-3 knockdown in HMCLs. Figure S4. Treatment of BTZ-resistant cells with PRL-3 inhibitor I. Figure S5. CoMMpass Dataset analysis
Supplementary Figure 5 from Recycling Endosomes in Mature Epithelia Restrain Tumorigenic Signaling
Authors: D'Agostino Luca , Nie Yingchao , Goswami Sayantani , Tong Kevin , Yu Shiyan , Bandyopadhyay Sheila , Flores Juan , Zhang Xiao , Balasubramanian Iyshwarya , Joseph Ivor , Sakamori Ryotaro , Farrell Victoria , Li Qi , Yang Chung S. , Gao Bin , Ferraris Ronaldo P. , Yehia Ghassan , Bonder Edward M. , Goldenring James R. , Verzi Michael P. , Zhang Lanjing , Ip Y. Tony , Gao Nan
Published: March 2023

Rab11a-deficient intestinal tumors have high levels of Yap expression.
Supplementary Figure 4 from Recycling Endosomes in Mature Epithelia Restrain Tumorigenic Signaling
Authors: D'Agostino Luca , Nie Yingchao , Goswami Sayantani , Tong Kevin , Yu Shiyan , Bandyopadhyay Sheila , Flores Juan , Zhang Xiao , Balasubramanian Iyshwarya , Joseph Ivor , Sakamori Ryotaro , Farrell Victoria , Li Qi , Yang Chung S. , Gao Bin , Ferraris Ronaldo P. , Yehia Ghassan , Bonder Edward M. , Goldenring James R. , Verzi Michael P. , Zhang Lanjing , Ip Y. Tony , Gao Nan
Published: March 2023

Induced deletion of Rab11 causes Yap nuclear accumulation.
Supplementary Figure 3 from Recycling Endosomes in Mature Epithelia Restrain Tumorigenic Signaling
Authors: D'Agostino Luca , Nie Yingchao , Goswami Sayantani , Tong Kevin , Yu Shiyan , Bandyopadhyay Sheila , Flores Juan , Zhang Xiao , Balasubramanian Iyshwarya , Joseph Ivor , Sakamori Ryotaro , Farrell Victoria , Li Qi , Yang Chung S. , Gao Bin , Ferraris Ronaldo P. , Yehia Ghassan , Bonder Edward M. , Goldenring James R. , Verzi Michael P. , Zhang Lanjing , Ip Y. Tony , Gao Nan
Published: March 2023

RAB11 expression is reduced in tissues obtained from colon cancer patients.
Supplementary Figure 2 from Recycling Endosomes in Mature Epithelia Restrain Tumorigenic Signaling
Authors: D'Agostino Luca , Nie Yingchao , Goswami Sayantani , Tong Kevin , Yu Shiyan , Bandyopadhyay Sheila , Flores Juan , Zhang Xiao , Balasubramanian Iyshwarya , Joseph Ivor , Sakamori Ryotaro , Farrell Victoria , Li Qi , Yang Chung S. , Gao Bin , Ferraris Ronaldo P. , Yehia Ghassan , Bonder Edward M. , Goldenring James R. , Verzi Michael P. , Zhang Lanjing , Ip Y. Tony , Gao Nan
Published: March 2023

Loss of Rab11a increases intestinal tumorigenic susceptibility to carcinogen and other tumor developing mutations
Supplementary Figure 1 from Recycling Endosomes in Mature Epithelia Restrain Tumorigenic Signaling
Authors: D'Agostino Luca , Nie Yingchao , Goswami Sayantani , Tong Kevin , Yu Shiyan , Bandyopadhyay Sheila , Flores Juan , Zhang Xiao , Balasubramanian Iyshwarya , Joseph Ivor , Sakamori Ryotaro , Farrell Victoria , Li Qi , Yang Chung S. , Gao Bin , Ferraris Ronaldo P. , Yehia Ghassan , Bonder Edward M. , Goldenring James R. , Verzi Michael P. , Zhang Lanjing , Ip Y. Tony , Gao Nan
Published: March 2023

Mice with intestinal epithelium specific deletion of Rab11a develop epithelial hyperplasia and dysplasia
Supplementary Data from Identification of Novel Susceptibility Loci and Genes for Prostate Cancer Risk: A Transcriptome-Wide Association Study in Over 140,000 European Descendants
Authors: Wu Lang , Wang Jifeng , Cai Qiuyin , Cavazos Taylor B. , Emami Nima C. , Long Jirong , Shu Xiao-Ou , Lu Yingchang , Guo Xingyi , Bauer Joshua A. , Pasaniuc Bogdan , Penney Kathryn L. , Freedman Matthew L. , Kote-Jarai Zsofia , Witte John S. , Haiman Christopher A. , Eeles Rosalind A. , Zheng Wei
Published: March 2023

Supplementary file including three sup figures and 11 sup tables, and Supplementary Note including consortia PIs, Funding Acknowledgements, and references. Supplementary Figure 1. Model external performance using data from the Mayo Clinic study by the internal performance (R2) of models built using GTEx data for (A) prostate tissue models, and (B) cross tissue models. Supplementary Figure 2. Model external performance using data from the TCGA study by the internal performance (R2) of models built using GTEx data for (A) prostate tissue models, and (B) cross tissue models. Supplemental Figure 3. Validation of knockdown in (A) PC-3, (B) DU-145, and (C) LNCaP cells. Supplementary Table 1. Primer sequences Supplementary Table 2. siRNA sequences for examined protein-coding genes Supplemental Table 3. siRNA sequences for examined long non-coding RNAs Supplementary Table 4. Internal performance of prostate and cross-tissue gene expression prediction models built using GTEx data Supplementary Table 5. Forty-eight gene expression-trait associations with p > 0.05 after conditioning on reported prostate cancer risk variants for genes located at genomic loci within 500kb of previous GWAS-identified prostate cancer risk variants Supplementary Table 6. Thirty-four expression-trait associations for genes previously reported as potential target genes of GWAS-identified prostate cancer risk variants Supplementary Table 7. Full list of risk SNPs adjusted for in conditional analyses, and their distances with the associated genes Supplementary Table 8. Associations of predicted gene expression using either prostate models or Cross Tissue models with prostate cancer risk for all 137 identified genes Supplementary Table 9. Patterns of 137 identified prostate cancer risk associated genes in human cancer tissues, cell lines, and normal tissues, as well as prognostic utility in human cancers, based on The Human Protein Atlas Supplementary Table 10. Independent predicting SNPs for identified associated genes using prostate tissue models, their weight values in prostate tissue gene expression prediction models, and associations with prostate cancer risk Supplementary Table 11. Independent predicting SNPs for identified associated genes using cross tissue models, their weight values in cross tissue gene expression prediction models, and associations with prostate cancer risk
Supplementary Data from IL12 Abrogates Calcineurin-Dependent Immune Evasion during Leukemia Progression
Authors: Rabe Jennifer L. , Gardner Lori , Hunter Rae , Fonseca Jairo A. , Dougan Jodi , Gearheart Christy M. , Leibowitz Michael S. , Lee-Miller Cathy , Baturin Dmitry , Fosmire Susan P. , Zelasko Susan E. , Jones Courtney L. , Slansky Jill E. , Rupji Manali , Dwivedi Bhakti , Henry Curtis J. , Porter Christopher C.
Published: March 2023

SF1: Leukemia model SF2: Data from individual mice SF3: Flow cytometry gating strategy SF4: Immunomodulatory Molecules SF5: Cytokine arrays