bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplemental Information from Predictive Gene Signatures Determine Tumor Sensitivity to MDM2 Inhibition
Authors: Ishizawa Jo , Nakamaru Kenji , Seki Takahiko , Tazaki Koichi , Kojima Kensuke , Chachad Dhruv , Zhao Ran , Heese Lauren , Ma Wencai , Ma Man Chun John , DiNardo Courtney , Pierce Sherry , Patel Keyur P. , Tse Archie , Davis R. Eric , Rao Arvind , Andreeff Michael
Published: March 2023

Supplemental Methods Table S1. Growth inhibition by DS-3032b and nutlin-3a in tumor cell lines with different p53 status. Table S2. Percent tumor growth inhibition (%TGI ) values at day 20 in SJSA-1 xenograft mice treated with DS-3032a. Table S3. GI50 values of cancer cell lines treated with DS-3032b. Table S4. Clinical information of the 41 samples Table S5. Confusion matrix of predicted and actual sensitivity of primary AML cells to DS-3032b according to TP53 mutation status. Table S6. The cut-off values used for definining sensitivity/resistance to each drug in the different phases of the signature development and validation process. Table S7. Prediction of sensitivity by 175-gene signature scoring and actual results in patient-derived xenograft models of various tumors treated with DS-3032a. Table S8. Confusion matrix of predicted and actual sensitivity of primary AML cells to DS-3032b using previously reported 4-gene signatures. Table S9. The top-ranked p53-inducible genes in the 175-gene signature. Table S10. Cancer type and TP53 mutational frequency. Table S11. Referenced 32 genes. Figure S1. Effects of DS-3032b as an MDM2 inhibitor in vitro and in vivo. Figure S2. Effects of MDM2 inhibitors (DS-3032b, DS-5272 and nutlin-3a) in OncoPanel cell lines. Figure S3. Prediction of sensitivity of tumor cells to MDM2 inhibition using the 175 gene signature.
Supplemental File 3 from Predictive Gene Signatures Determine Tumor Sensitivity to MDM2 Inhibition
Authors: Ishizawa Jo , Nakamaru Kenji , Seki Takahiko , Tazaki Koichi , Kojima Kensuke , Chachad Dhruv , Zhao Ran , Heese Lauren , Ma Wencai , Ma Man Chun John , DiNardo Courtney , Pierce Sherry , Patel Keyur P. , Tse Archie , Davis R. Eric , Rao Arvind , Andreeff Michael
Published: March 2023

List of sensitive or resistance signature genes.
Figure S2 from Mutational Mechanisms That Activate Wnt Signaling and Predict Outcomes in Colorectal Cancer Patients
Authors: Hankey William , McIlhatton Michael A. , Ebede Kenechi , Kennedy Brian , Hancioglu Baris , Zhang Jie , Brock Guy N. , Huang Kun , Groden Joanna
Published: March 2023

Genes of interest were selected by the binding of chromatin-associated APC to genomic regions encoding their human orthologs.
Supplemental File 2 from Predictive Gene Signatures Determine Tumor Sensitivity to MDM2 Inhibition
Authors: Ishizawa Jo , Nakamaru Kenji , Seki Takahiko , Tazaki Koichi , Kojima Kensuke , Chachad Dhruv , Zhao Ran , Heese Lauren , Ma Wencai , Ma Man Chun John , DiNardo Courtney , Pierce Sherry , Patel Keyur P. , Tse Archie , Davis R. Eric , Rao Arvind , Andreeff Michael
Published: March 2023

Detailed results in apoptosis assay of primary AML cells treated with DS-3032b.
Figure S1 from Mutational Mechanisms That Activate Wnt Signaling and Predict Outcomes in Colorectal Cancer Patients
Authors: Hankey William , McIlhatton Michael A. , Ebede Kenechi , Kennedy Brian , Hancioglu Baris , Zhang Jie , Brock Guy N. , Huang Kun , Groden Joanna
Published: March 2023

Unique transcriptional changes identified in adenomas from ApcMin/+ mice by RNA-seq are validated by qPCR in an independent group of mouse tissues.
Table S1 from Inhibition of Translesion DNA Synthesis as a Novel Therapeutic Strategy to Treat Brain Cancer
Authors: Choi Jung-Suk , Kim Casey Seol , Berdis Anthony
Published: March 2023

Summary of kinetic parameters for the incorporation of 5-NITP and dATP opposite an abasic site by high fidelity (pol delta and pol epsilon) and specialized (pol eta and pol iota) DNA polymerases.
Figure S7 from Inhibition of Translesion DNA Synthesis as a Novel Therapeutic Strategy to Treat Brain Cancer
Authors: Choi Jung-Suk , Kim Casey Seol , Berdis Anthony
Published: March 2023

Model for translesion DNA synthesis (panel A). Model for the potentiation of tempozolomide by 5-NIdR in which the nucleoside triphosphate (5-NITP) inhibits the replication of damaged DNA (panel B).
Supplemental Information from Selective mTORC2 Inhibitor Therapeutically Blocks Breast Cancer Cell Growth and Survival
Authors: Werfel Thomas A. , Wang Shan , Jackson Meredith A. , Kavanaugh Taylor E. , Joly Meghan Morrison , Lee Linus H. , Hicks Donna J. , Sanchez Violeta , Ericsson Paula Gonzalez , Kilchrist Kameron V. , Dimobi Somtochukwu C. , Sarett Samantha M. , Brantley-Sieders Dana M. , Cook Rebecca S. , Duvall Craig L.
Published: March 2023

Supplemental Figures S1-9 Supplemental Figure S1 - Table of Oligos Supplemental Figures S2-5 - Scheme of chemical synthesis and characterization of polymers Supplemental Figure S6 - Basic in vitro characterization of si-NPs Supplemental Figure S7 - TCGA-curated survival curves Supplemental Figures S8-9 - Toxicology data
Figure S5 from Inhibition of Translesion DNA Synthesis as a Novel Therapeutic Strategy to Treat Brain Cancer
Authors: Choi Jung-Suk , Kim Casey Seol , Berdis Anthony
Published: March 2023

Gel electrophoresis data showing that 5-NITP does not inhibit normal DNA synthesis catalyzed by high fidelity and specialized DNA polymerases.
Figure S4 from Inhibition of Translesion DNA Synthesis as a Novel Therapeutic Strategy to Treat Brain Cancer
Authors: Choi Jung-Suk , Kim Casey Seol , Berdis Anthony
Published: March 2023

Chain-termination capabilities of 5-NITP against high fidelity (pol epsilon) and specialized (pol iota) DNA polymerases.
Supplementary Tables from Integrated Molecular Characterization of the Lethal Pediatric Cancer Pancreatoblastoma
Authors: Isobe Tomoya , Seki Masafumi , Yoshida Kenichi , Sekiguchi Masahiro , Shiozawa Yusuke , Shiraishi Yuichi , Kimura Shunsuke , Yoshida Misa , Inoue Yoshikage , Yokoyama Akira , Kakiuchi Nobuyuki , Suzuki Hiromichi , Kataoka Keisuke , Sato Yusuke , Kawai Tomoko , Chiba Kenichi , Tanaka Hiroko , Shimamura Teppei , Kato Motohiro , Iguchi Akihiro , Hama Asahito , Taguchi Tomoaki , Akiyama Masaharu , Fujimura Junya , Inoue Akiko , Ito Tsuyoshi , Deguchi Takao , Kiyotani Chikako , Iehara Tomoko , Hosoi Hajime , Oka Akira , Sanada Masashi , Tanaka Yukichi , Hata Kenichiro , Miyano Satoru , Ogawa Seishi , Takita Junko
Published: March 2023

Supplementary Tables S1-S13. Supplementary Table S1. Clinical information and the summary of experiments performed on each sample. Supplementary Table S2. List of genes and regions captured for targeted deep sequencing. Supplementary Table S3. dbSNP ID list for which target baits were designed. Supplementary Table S4. Non-silent mutations detected in a validation cohort by targeted deep sequencing. Supplementary Table S5. Validated non-silent somatic mutations by PCR-based deep sequencing. Supplementary Table S6. Validated silent/non-silent somatic mutations used for clonal analysis of multiple samples from PBL001. Supplementary Table S7. Significantly hypo-/hyper-methylated gene sets in PBL compared to normal pancreas. Supplementary Table S8. Fusion genes detected by whole transcriptome sequencing in PBL. Supplementary Table S9. Genes with a significant differential expression between PBL and normal pancreatic samples. Supplementary Table S10. Significant gene set enrichment in comparison between PBL and normal pancreas. Supplementary Table S11. List of differentially expressed genes in each gene cluster identified by hierarchical clustering. Supplementary Table S12. Top 20 significantly enriched pathways in each gene cluster. Supplementary Table S13. Gene coefficients of PC1 and PC2.
Supplementary Figures from Integrated Molecular Characterization of the Lethal Pediatric Cancer Pancreatoblastoma
Authors: Isobe Tomoya , Seki Masafumi , Yoshida Kenichi , Sekiguchi Masahiro , Shiozawa Yusuke , Shiraishi Yuichi , Kimura Shunsuke , Yoshida Misa , Inoue Yoshikage , Yokoyama Akira , Kakiuchi Nobuyuki , Suzuki Hiromichi , Kataoka Keisuke , Sato Yusuke , Kawai Tomoko , Chiba Kenichi , Tanaka Hiroko , Shimamura Teppei , Kato Motohiro , Iguchi Akihiro , Hama Asahito , Taguchi Tomoaki , Akiyama Masaharu , Fujimura Junya , Inoue Akiko , Ito Tsuyoshi , Deguchi Takao , Kiyotani Chikako , Iehara Tomoko , Hosoi Hajime , Oka Akira , Sanada Masashi , Tanaka Yukichi , Hata Kenichiro , Miyano Satoru , Ogawa Seishi , Takita Junko
Published: March 2023

Supplementary Figures S1-S10. Supplementary Figure S1. Depths and coverages of targeted deep sequencing. Supplementary Figure S2. Sequencing coverages and numbers of mutations detected by WES. Supplementary Figure S3. Tumor subclonal populations in multiple samples from PBL001 estimated by PyClone. Supplementary Figure S4. Mutational signatures of primary and metastatic PBL. Supplementary Figure S5. SNP array-based copy number analysis of PBL. Supplementary Figure S6. Targeted deep sequencing based allele-specific copy number analysis of chromosome 11. Supplementary Figure S7. Bisulfite Sanger sequencing of ICR1 on chromosome 11p15.5. Supplementary Figure S8. Relative expression levels of IGF2 in CN-LOH-negative samples. Supplementary Figure S9. Aberrant activation of Wnt signaling pathway in PBL009. Supplementary Figure S10. Global DNA methylation profile of PBL.
Supplementary Methods from Hypercholesterolemia Increases Colorectal Cancer Incidence by Reducing Production of NKT and γδ T Cells from Hematopoietic Stem Cells
Authors: Tie Guodong , Yan Jinglian , Khair Lyne , Messina Julia A. , Deng April , Kang Joonsoo , Fazzio Thomas , Messina Louis M.
Published: March 2023

supplementary methods
Supplementary Figures and Table from Hypercholesterolemia Increases Colorectal Cancer Incidence by Reducing Production of NKT and γδ T Cells from Hematopoietic Stem Cells
Authors: Tie Guodong , Yan Jinglian , Khair Lyne , Messina Julia A. , Deng April , Kang Joonsoo , Fazzio Thomas , Messina Louis M.
Published: March 2023

This file contains 9 supplemental figures and one supplemental table in which we show that WT recipient mice reconstituted with HSCs from hypercholesterolemic ApoE-/- mice have normal serum cholesterol levels and white blood cell counts (S1); Hypercholesterolemia reduces the frequency and alters specific subsets and maturation of NKT and gammadelta T cells in the thymus (S2); Hypercholesterolemia-induced oxidant stress in HSCs strongly correlates with the incidence of AOM-induced colorectal neoplasia (S3); The frequency of T cell intermediate populations in thymus and cellular components related to cancer immunosurveillance in peripheral blood and colon of WT and Tet-/- mice (S4); The expression of Tet1 determines the differentiation of HSCs towards NKT and gammadelta T cells in vitro (S5); The expression of miRNA in HSCs from hypercholesterolemic mice (S6); That In HSCs, Tet1 overexpression reduces the expression of the key regulatory genes in their differentiation of NKT and gammadeltaT cells (S7); That Tet1 regulates H3K4me3 modification of the key regulatory genes in the differentiation of HSCs towards NKT and gammadeltaT cells in vitro (S8); That oxLDL impairs the differentiation of human HSCs towards NKT and gammadelta T cells in vitro (S9); and the genes related to the differentiation of NKT and gammadelta T cells (Supplemental Table 1).
Supplementary Figures from Spatial Heterogeneity and Evolutionary Dynamics Modulate Time to Recurrence in Continuous and Adaptive Cancer Therapies
Authors: Gallaher Jill A. , Enriquez-Navas Pedro M. , Luddy Kimberly A. , Gatenby Robert A. , Anderson Alexander R.A.
Published: March 2023

This file contains all supplementary figures, which show further details on the model setup and behavior. This includes separated time to recurrence plots and results from additional migration speeds and metastatic compositions.
Table S1 from Inhibin Is a Novel Paracrine Factor for Tumor Angiogenesis and Metastasis
Authors: Singh Priyanka , Jenkins Laura M. , Horst Ben , Alers Victoria , Pradhan Shrikant , Kaur Prabhjot , Srivastava Tapasya , Hempel Nadine , Győrffy Balázs , Broude Eugenia V. , Lee Nam Y. , Mythreye Karthikeyan
Published: March 2023

Quantification of parameters in the ovarian tissue array
Movie 4 from Spatial Heterogeneity and Evolutionary Dynamics Modulate Time to Recurrence in Continuous and Adaptive Cancer Therapies
Authors: Gallaher Jill A. , Enriquez-Navas Pedro M. , Luddy Kimberly A. , Gatenby Robert A. , Anderson Alexander R.A.
Published: March 2023

Comparing CT, AT1, and AT2 treatment schedules for a heterogeneous resistant tumor initialized by a normal distribution with a mean sensitivity s=60% and standard deviation Ïƒs=25%.
Movie 3 from Spatial Heterogeneity and Evolutionary Dynamics Modulate Time to Recurrence in Continuous and Adaptive Cancer Therapies
Authors: Gallaher Jill A. , Enriquez-Navas Pedro M. , Luddy Kimberly A. , Gatenby Robert A. , Anderson Alexander R.A.
Published: March 2023

Comparing CT, AT1, and AT2 treatment schedules for a homogeneous resistant tumor initialized by a normal distribution with a mean sensitivity s=60% and standard deviation Ïƒs=5%.
Figure S8 from Inhibin Is a Novel Paracrine Factor for Tumor Angiogenesis and Metastasis
Authors: Singh Priyanka , Jenkins Laura M. , Horst Ben , Alers Victoria , Pradhan Shrikant , Kaur Prabhjot , Srivastava Tapasya , Hempel Nadine , Győrffy Balázs , Broude Eugenia V. , Lee Nam Y. , Mythreye Karthikeyan
Published: March 2023

: Representative western blot of lysates from 6 hr serum starved HMEC-1 cells incubated with 10ng/ml Activin up to 40 min, followed by immunoblotting of lysates as indicated. Quantitation from two independent biological trials is presented (right graphs).
Movie 2 from Spatial Heterogeneity and Evolutionary Dynamics Modulate Time to Recurrence in Continuous and Adaptive Cancer Therapies
Authors: Gallaher Jill A. , Enriquez-Navas Pedro M. , Luddy Kimberly A. , Gatenby Robert A. , Anderson Alexander R.A.
Published: March 2023

Comparing CT, AT1, and AT2 treatment schedules for a heterogeneous sensitive tumor initialized by a normal distribution with a mean sensitivity s=100% and standard deviation Ïƒs=25%.
Figure S7 from Inhibin Is a Novel Paracrine Factor for Tumor Angiogenesis and Metastasis
Authors: Singh Priyanka , Jenkins Laura M. , Horst Ben , Alers Victoria , Pradhan Shrikant , Kaur Prabhjot , Srivastava Tapasya , Hempel Nadine , Győrffy Balázs , Broude Eugenia V. , Lee Nam Y. , Mythreye Karthikeyan
Published: March 2023

(i) qRT-PCR analysis for mRNA expression of type I receptors ALK1-7 in endothelial (HMEC-1) and epithelial (SKOV3) cells. (ii) Tube formation of HMEC-1 cells in the presence of Inhibin A alone or with 5mM Dorsomorphin (DM) and SB431542 (SB). Number of meshes quantified as described in Methods. n.s. = not significant.
Movie 1 from Spatial Heterogeneity and Evolutionary Dynamics Modulate Time to Recurrence in Continuous and Adaptive Cancer Therapies
Authors: Gallaher Jill A. , Enriquez-Navas Pedro M. , Luddy Kimberly A. , Gatenby Robert A. , Anderson Alexander R.A.
Published: March 2023

Comparing CT, AT1, and AT2 treatment schedules for a homogeneous sensitive tumor initialized by a normal distribution with a mean sensitivity s=100% and standard deviation Ïƒs=5%.
hTERT-/low and hTERThigh PCa cell division modes from WNT/β-Catenin Directs Self-Renewal Symmetric Cell Division of hTERThigh Prostate Cancer Stem Cells
Authors: Zhang Kai , Guo Yanjing , Wang Xue , Zhao Huifang , Ji Zhongzhong , Cheng Chaping , Li Li , Fang Yuxiang , Xu Dawei , Zhu Helen He , Gao Wei-Qiang
Published: March 2023

hTERT-/low and hTERThigh PCa cell division modes from WNT/β-Catenin Directs Self-Renewal Symmetric Cell Division of hTERThigh Prostate Cancer Stem Cells
Figure S2 from Inhibin Is a Novel Paracrine Factor for Tumor Angiogenesis and Metastasis
Authors: Singh Priyanka , Jenkins Laura M. , Horst Ben , Alers Victoria , Pradhan Shrikant , Kaur Prabhjot , Srivastava Tapasya , Hempel Nadine , Győrffy Balázs , Broude Eugenia V. , Lee Nam Y. , Mythreye Karthikeyan
Published: March 2023

(i) (Left) qRT PCR analysis of of INHA mRNA with a second shRNA (shINHA2) to INHA (shINHA2) in endothelial cells compared to shControl2 (Methods) followed by (Middle) tube formation of HMEC-1 cells. (Right) Number of meshes represents an average of 3 fields, quantified as described in Methods. ***P<0.01 (ii-iii) Tube formation of HMEC-1 cells using conditioned media from (ii) shControl SKOV3 cancer cells in the absence (IgG only) and presence of anti-Inhibin α antibody (10 µg/ml, monoclonal #sc365439, Santa Cruz) or shINHA conditioned media (iii) or conditioned media from M41 OVCA cells in the presence of IgG or anti-Inhibin α antibody. Quantitation of meshes as described in Methods. ***P<0.01.
Figure S1 from Inhibin Is a Novel Paracrine Factor for Tumor Angiogenesis and Metastasis
Authors: Singh Priyanka , Jenkins Laura M. , Horst Ben , Alers Victoria , Pradhan Shrikant , Kaur Prabhjot , Srivastava Tapasya , Hempel Nadine , Győrffy Balázs , Broude Eugenia V. , Lee Nam Y. , Mythreye Karthikeyan
Published: March 2023

(i) Sample images of immunohistochemistry (IHC) using IgG or anti-Inhibina antibody on the same ovarian tumor. (ii) Zoomed in images of regions IHC Fig 1A (Human Ovary Cancer Tissue Microarray, Protein Biotechnologies) of either normal tissue or different ovarian cancer subtypes with Inhibina staining. (iii) Additional examples of CD31 staining with corresponding Inhibina levels in the same cores from tissue array immunolabeled with anti-Inhibina or anti-CD31 antibody. (iv) ELISA for total Inhibin (Inhibina, InhibinA/B) of the CM from indicated cancer cells. Corresponding mRNA values in Fig 1E.
Supplementary Fig 8 working model from WNT/β-Catenin Directs Self-Renewal Symmetric Cell Division of hTERThigh Prostate Cancer Stem Cells
Authors: Zhang Kai , Guo Yanjing , Wang Xue , Zhao Huifang , Ji Zhongzhong , Cheng Chaping , Li Li , Fang Yuxiang , Xu Dawei , Zhu Helen He , Gao Wei-Qiang
Published: March 2023

Supplementary Fig 8 working model: Schematic model of hTERThigh PCSCs cell division modes modulated by WNT/beta-catenin
Supplemental Table 2 from Attenuated TRAF3 Fosters Activation of Alternative NF-κB and Reduced Expression of Antiviral Interferon, TP53, and RB to Promote HPV-Positive Head and Neck Cancers
Authors: Zhang Jialing , Chen Tony , Yang Xinping , Cheng Hui , Späth Stephan S. , Clavijo Paul E. , Chen Jianhong , Silvin Christopher , Issaeva Natalia , Su Xiulan , Yarbrough Wendell G. , Annunziata Christina M. , Chen Zhong , Van Waes Carter
Published: March 2023

Co-occurence of TRAF3 and NF-kappaB pathway alterations
Supplementary Fig 5 related to Fig 5 from WNT/β-Catenin Directs Self-Renewal Symmetric Cell Division of hTERThigh Prostate Cancer Stem Cells
Authors: Zhang Kai , Guo Yanjing , Wang Xue , Zhao Huifang , Ji Zhongzhong , Cheng Chaping , Li Li , Fang Yuxiang , Xu Dawei , Zhu Helen He , Gao Wei-Qiang
Published: March 2023

Supplementary Fig 5 related to Fig 5: The Effects of WNT ligands and WNT inhibitors on SCD I, SCD II and ACD ratio of hTERThigh LNCaP cells
Supplementary Fig 4 related to Fig 4 from WNT/β-Catenin Directs Self-Renewal Symmetric Cell Division of hTERThigh Prostate Cancer Stem Cells
Authors: Zhang Kai , Guo Yanjing , Wang Xue , Zhao Huifang , Ji Zhongzhong , Cheng Chaping , Li Li , Fang Yuxiang , Xu Dawei , Zhu Helen He , Gao Wei-Qiang
Published: March 2023

Supplementary Fig 4 related to Fig 4: hTERThigh PCa cells exhibit three distinct cell division modes in a Numb-dsRed segregation context
Supplementary Figure S1, S2, S3, S4, S5 and S6. Supplementary Tables S1 and S2. from VEGFR2–Mediated Reprogramming of Mitochondrial Metabolism Regulates the Sensitivity of Acute Myeloid Leukemia to Chemotherapy
Authors: Nóbrega-Pereira Sandrina , Caiado Francisco , Carvalho Tânia , Matias Inês , Graça Gonçalo , Gonçalves Luís G. , Silva-Santos Bruno , Norell Haakan , Dias Sérgio
Published: March 2023

Supplementary Material and Methods. Supplementary Fig. S1. Additional characterization of in vivo chemotherapy treatment of human AML xenotransplanted mice and metabolic characterization of chemotherapy exposed human AML cells. Supplementary Fig. S2. Chemotherapy treated AML cells exhibited enhanced VEGFR- 2 expression. Supplementary Fig. S3. VEGFR-2 signaling regulates mitochondrial homeostasis and oxidative stress in AML. Supplementary Fig. S4. Regulation of PGC-1α by VEGFR-2 signaling underlies the chemotherapy-sensitization provided by VEGFR-2 inhibition in AML. Supplementary Fig. S5. Kaplan-Meier Curve for AML patients. Supplementary Fig. S6. Uncropped Western blot membranes. Supplementary Table S1. 1H-NMR metabolite assignments. Supplementary Table S2. List of primers used for measurements of gene expression levels and mtDNA content by quantitative Real-Time PCR.
Supplementary Fig 2 related to Fig 2 from WNT/β-Catenin Directs Self-Renewal Symmetric Cell Division of hTERThigh Prostate Cancer Stem Cells
Authors: Zhang Kai , Guo Yanjing , Wang Xue , Zhao Huifang , Ji Zhongzhong , Cheng Chaping , Li Li , Fang Yuxiang , Xu Dawei , Zhu Helen He , Gao Wei-Qiang
Published: March 2023

Supplementary Fig 2 related to Fig 2: hTERT promotes xenograft tumor growth and EMT of PCa cells
Figure S4 from Kindlin-1 Promotes Pulmonary Breast Cancer Metastasis
Authors: Sarvi Sana , Patel Hitesh , Li Jun , Dodd Georgia L. , Creedon Helen , Muir Morwenna , Ward Jocelyn , Dawson John C. , Lee Martin , Culley Jayne , Salter Donald M. , Sims Andrew H. , Byron Adam , Brunton Valerie G.
Published: March 2023

Figure S4 shows supporting data that Kindlin-1 reduces integrin activation and lung colonization
Table S1 from A Large-Scale, Exome-Wide Association Study of Han Chinese Women Identifies Three Novel Loci Predisposing to Breast Cancer
Authors: Zhang Bo , Chen Men-Yun , Shen Yu-Jun , Zhuo Xian-Bo , Gao Ping , Zhou Fu-Sheng , Liang Bo , Zu Jun , Zhang Qin , Suleman Sufyan , Xu Yi-Hui , Xu Min-Gui , Xu Jin-Kai , Liu Chen-Cheng , Giannareas Nikolaos , Xia Ji-Han , Zhao Yuan , Huang Zhong-Lian , Yang Zhen , Cheng Huai-Dong , Li Na , Hong Yan-Yan , Li Wei , Zhang Min-Jun , Yu Ke-Da , Li Guoliang , Sun Meng-Hong , Chen Zhen-Dong , Wei Gong-Hong , Shao Zhi-Min
Published: March 2023

Associations of selected SNPs in the screening and the replication stages.
Figure S3 from Kindlin-1 Promotes Pulmonary Breast Cancer Metastasis
Authors: Sarvi Sana , Patel Hitesh , Li Jun , Dodd Georgia L. , Creedon Helen , Muir Morwenna , Ward Jocelyn , Dawson John C. , Lee Martin , Culley Jayne , Salter Donald M. , Sims Andrew H. , Byron Adam , Brunton Valerie G.
Published: March 2023

Figure S3 shows generation of Kindlin-1 deficient Met-1 cells
Table S3 from ERα-Mediated Nuclear Sequestration of RSK2 Is Required for ER+ Breast Cancer Tumorigenesis
Authors: Ludwik Katarzyna A. , McDonald Oliver G. , Brenin David R. , Lannigan Deborah A.
Published: March 2023

Analysis of ER+ and ER- clustering on invasive ductal carcinoma samples using different gene sets
Supplementary Materials and Methods from Kinome-Wide RNA Interference Screen Reveals a Role for PDK1 in Acquired Resistance to CDK4/6 Inhibition in ER-Positive Breast Cancer
Authors: Jansen Valerie M. , Bhola Neil E. , Bauer Joshua A. , Formisano Luigi , Lee Kyung-Min , Hutchinson Katherine E. , Witkiewicz Agnieszka K. , Moore Preston D. , Estrada Mónica Valéria , Sánchez Violeta , Ericsson Paula G. , Sanders Melinda E. , Pohlmann Paula R. , Pishvaian Michael J. , Riddle David A. , Dugger Teresa C. , Wei Wenyi , Knudsen Erik S. , Arteaga Carlos L.
Published: March 2023

Supplementary Materials and Methods and Figure Legends for Supplementary Figures S1-6
Table S1 from ERα-Mediated Nuclear Sequestration of RSK2 Is Required for ER+ Breast Cancer Tumorigenesis
Authors: Ludwik Katarzyna A. , McDonald Oliver G. , Brenin David R. , Lannigan Deborah A.
Published: March 2023

Patient histopathological information
Supplementary Figures 1-11 from STAT3/PIAS3 Levels Serve as “Early Signature” Genes in the Development of High-Grade Serous Carcinoma from the Fallopian Tube
Authors: Saini Uksha , Suarez Adrian A. , Naidu Shan , Wallbillich John J. , Bixel Kristin , Wanner Ross A. , Bice Jason , Kladney Raleigh D. , Lester Jenny , Karlan Beth Y. , Goodfellow Paul J. , Cohn David E. , Selvendiran Karuppaiyah
Published: March 2023

Role of STAT3 in high-grade serous carcinoma
Supplementary Information from Interleukin-27 Exerts Its Antitumor Effects by Promoting Differentiation of Hematopoietic Stem Cells to M1 Macrophages
Authors: Chiba Yukino , Mizoguchi Izuru , Furusawa Junichi , Hasegawa Hideaki , Ohashi Mio , Xu Mingli , Owaki Toshiyuki , Yoshimoto Takayuki
Published: March 2023

This file contains Supplemental Table 1, Supplementary Figure Legends, and Supplementary Figures. Supplemental Table 1 shows primers used in this study. Supplementary Figure Legends describe the legend for each supplementary figure. Figure S1 shows the gating strategy in flow cytometry analysis. Figure S2 shows that IL-27 augments the infiltration of CD11b+ myeloid cells into MC38 tumor. Figure S3 shows that IL-27 promotes the differentiation into M1 macrophages in MC38 tumor-bearing mice. Figure S4 shows that IL-27 much less but significantly augments the infiltration of M1 macrophages into B16F10 tumor when the tumor size in B16F10-IL-27 tumor-bearing mice reaches the similar tumor size to that in control tumor-bearing mice. Figure S5 shows that IL-27 inhibits the differentiation into immunosuppressive macrophages in MC38 tumor-bearing mice. Figure S6 shows the therapeutic potential of the CD11b+ myeloid cells purified from tumors of B16F10-IL-27 tumor-bearing mice on pre-existing tumor model. Figure S7 shows that IL-27-induced MC38 tumor-infiltrating myeloid cells exert direct antitumor effects by killing tumor through NO. Figure S8 shows that the enhanced mRNA expression of immune checkpoint molecules and TGF-β1 in CD11b+ myeloid cells in IL-27-expressing tumor-bearing mice.
Supplementary Figures S1-S9 and List of Supplementary Tables from Adaptive and Reversible Resistance to Kras Inhibition in Pancreatic Cancer Cells
Authors: Chen Pan-Yu , Muzumdar Mandar Deepak , Dorans Kimberly Judith , Robbins Rebecca , Bhutkar Arjun , del Rosario Amanda , Mertins Philipp , Qiao Jana , Schafer Anette Claudia , Gertler Frank , Carr Steven , Jacks Tyler
Published: March 2023

Figures showing on-target effects of Kras knockdown in murine and human PDAC cells in vitro and in vivo, Gpr56 knockdown, SILAC and iTRAQ workflow and additional proteomics data, pharmacological inhibition of Src and FAK, and genetic inhibition of FAK.
Supplemental Information from hPCL3s Promotes Hepatocellular Carcinoma Metastasis by Activating β-Catenin Signaling
Authors: Cai Zhen , Qian Zhen-Yu , Jiang Hao , Ma Ning , Li Zhi , Liu Li-Yu , Ren Xin-Xin , Shang Yu-Rong , Wang Jing-Jing , Li Jing-Jing , Liu Dong-Ping , Zhang Xiu-Ping , Feng Dan , Ni Qian-Zhi , Feng Yuan-Yuan , Li Nan , Zhou Xiao-Yan , Wang Xiang , Bao Ying , Zhang Xue-Li , Deng Yue-Zhen , Xie Dong
Published: March 2023

The supplementary infomation containing Figure legends, five supplemental figures and 3 supplemental tables. Figure S1 The higher expression of hPCL3s correlated with the poor survival of HCC patients. Figure S2 hPCL3s did not promote the tumorigenesis in vivo. Figure S3 The effects of hPCL3s on the growth of Hep3B, Huh7 and PVTT cells in a 48-hour time window were evaluated using MTT assay. Figure S4 Screening the signal pathways affected by hPCL3s. Figure S5 The AAV delivered Flag-hPCL3s was dominantly expressed in the liver. Table S1 Primer sequences. Table S2 The correlation between the expression of hPCL3s and clinical feature (Tissue array 2). Table S3 Microarray data.
Table S3 from XIAP Regulation by MNK Links MAPK and NFκB Signaling to Determine an Aggressive Breast Cancer Phenotype
Authors: Evans Myron K. , Brown Michael C. , Geradts Joseph , Bao Xuhui , Robinson Timothy J. , Jolly Mohit Kumar , Vermeulen Peter B. , Palmer Gregory M. , Gromeier Matthias , Levine Herbert , Morse Michael A. , Van Laere Steven J. , Devi Gayathri R.
Published: March 2023

Gene expression profiles identified 933 differentially expressed genes between control and wtXIAP tumors
Supplemental Movie 5: Interstitial convection and Gd-DTPA enhancement with time in an LS174T tumor from Investigating Low-Velocity Fluid Flow in Tumors with Convection-MRI
Authors: Walker-Samuel Simon , Roberts Thomas A. , Ramasawmy Rajiv , Burrell Jake S. , Johnson Sean Peter , Siow Bernard M. , Richardson Simon , Gonçalves Miguel R. , Pendse Douglas , Robinson Simon P. , Pedley R. Barbara , Lythgoe Mark F.
Published: March 2023

Supplemental Movie 5: Interstitial convection, measured using EVAC-MRI and animated using a particle simulation (left), compared with MRI signal enhancement with time, following injection with a contrast agent (Gd-DTPA), in an LS174T tumour.
Supplemental Movie 4: Interstitial convection and vascular perfusion in an SW1222 tumor from Investigating Low-Velocity Fluid Flow in Tumors with Convection-MRI
Authors: Walker-Samuel Simon , Roberts Thomas A. , Ramasawmy Rajiv , Burrell Jake S. , Johnson Sean Peter , Siow Bernard M. , Richardson Simon , Gonçalves Miguel R. , Pendse Douglas , Robinson Simon P. , Pedley R. Barbara , Lythgoe Mark F.
Published: March 2023

Supplemental Movie 4: Animated EVAC streamlines (grey lines), showing the path taken by interstitial fluid, overlaid on vascular perfusion measurements (colour scale, measured in vivo using arterial spin labelling) and the location of blood vessels (yellow structures, measured ex vivo using micro-CT). The data were acquired in an SW1222 colorectal carcinoma tumour xenograft.
Supplemental Movie 1: Convection-MRI sequence from Investigating Low-Velocity Fluid Flow in Tumors with Convection-MRI
Authors: Walker-Samuel Simon , Roberts Thomas A. , Ramasawmy Rajiv , Burrell Jake S. , Johnson Sean Peter , Siow Bernard M. , Richardson Simon , Gonçalves Miguel R. , Pendse Douglas , Robinson Simon P. , Pedley R. Barbara , Lythgoe Mark F.
Published: March 2023

Supplemental Movie 1: Schematic movie illustrating the physical principles underpinning the convection-MRI sequence
Supplementary Table S3 from Utility of Single-Cell Genomics in Diagnostic Evaluation of Prostate Cancer
Authors: Alexander Joan , Kendall Jude , McIndoo Jean , Rodgers Linda , Aboukhalil Robert , Levy Dan , Stepansky Asya , Sun Guoli , Chobardjiev Lubomir , Riggs Michael , Cox Hilary , Hakker Inessa , Nowak Dawid G. , Laze Juliana , Llukani Elton , Srivastava Abhishek , Gruschow Siobhan , Yadav Shalini S. , Robinson Brian , Atwal Gurinder , Trotman Lloyd C. , Lepor Herbert , Hicks James , Wigler Michael , Krasnitz Alexander
Published: March 2023

A zipped file archive containing Supplementary Table 3 as an Excel spreadsheet and a subfolder with graphic images pointed to by the hyperlinks in the spreadsheet.
Supplemental Figure 3 from Investigating Low-Velocity Fluid Flow in Tumors with Convection-MRI
Authors: Walker-Samuel Simon , Roberts Thomas A. , Ramasawmy Rajiv , Burrell Jake S. , Johnson Sean Peter , Siow Bernard M. , Richardson Simon , Gonçalves Miguel R. , Pendse Douglas , Robinson Simon P. , Pedley R. Barbara , Lythgoe Mark F.
Published: March 2023

High-resolution copy of Figure 6b. Fluid flow measured in vivo with convectionMRI is shown as grey streamlines and perfusion is shown as a colorscale. The location of blood vessels is represented by yellow volume renderings, acquired using ex vivo microvascular casting and imaged with micro-CT.
Supplementary Table S1 from Utility of Single-Cell Genomics in Diagnostic Evaluation of Prostate Cancer
Authors: Alexander Joan , Kendall Jude , McIndoo Jean , Rodgers Linda , Aboukhalil Robert , Levy Dan , Stepansky Asya , Sun Guoli , Chobardjiev Lubomir , Riggs Michael , Cox Hilary , Hakker Inessa , Nowak Dawid G. , Laze Juliana , Llukani Elton , Srivastava Abhishek , Gruschow Siobhan , Yadav Shalini S. , Robinson Brian , Atwal Gurinder , Trotman Lloyd C. , Lepor Herbert , Hicks James , Wigler Michael , Krasnitz Alexander
Published: March 2023

A zipped file archive containing Supplementary Table 1 as an Excel spreadsheet and a subfolder with graphic images pointed to by the hyperlinks in the spreadsheet.
Figure S1-9 from Multiregional Sequencing Reveals Genomic Alterations and Clonal Dynamics in Primary Malignant Melanoma of the Esophagus
Authors: Li Jingjing , Yan Shi , Liu Zhen , Zhou Yong , Pan Yaqi , Yuan WenQin , Liu Mengfei , Tan Qin , Tian Geng , Dong Bin , Cai Hong , Wu Nan , Ke Yang
Published: March 2023

Figure S1: Geographic distribution of multiregional samples obtained from the dissection of esophagectomy PMME specimens. Figure S2: Hematoxylin and eosin-stained (H&E) and immunostained sections of spatial samples in PMME. Figure S3: Comparison of variant allele frequency between members in each tumor clade. Figure S4: BAF (B allele frequencies) profiles and LogR values across the genome of PMME. Figure S5: CCF distribution in each spatial samples. Figure S6: Metastastic subclones containing pathogenic mutations of ARHGAP26 and PIK3CA, and arm level chromosome deletion in Chr13 experienced subclonal expansion in metastasis sites. Figure S7: Composite copy number profiles for primary melanoma (n=78) and metastasis melanoma (n=283) with gains in red and losses in blue. Figure S8: Venn diagram of nonsynonymous mutations between ME1, N3 and primary tumor clone. Figure S9: Determine threshold for detecting copy number alterations in ME1 and N3.
Figure S7 from Type I IFN Receptor Signaling Controls IL7-Dependent Accumulation and Activity of Protumoral IL17A-Producing γδT Cells in Breast Cancer
Authors: Patin Emmanuel C. , Soulard Daphnée , Fleury Sébastien , Hassane Maya , Dombrowicz David , Faveeuw Christelle , Trottein François , Paget Christophe
Published: March 2023

Early IL-7 depletion reduces accumulation of IL-17A+ CD3bright gamma/delta T cells in 4T1.2 breast cancer model
Table S6D from Membrane-Depolarizing Channel Blockers Induce Selective Glioma Cell Death by Impairing Nutrient Transport and Unfolded Protein/Amino Acid Responses
Authors: Niklasson Mia , Maddalo Gianluca , Sramkova Zuzana , Mutlu Ercan , Wee Shimei , Sekyrova Petra , Schmidt Linnéa , Fritz Nicolas , Dehnisch Ivar , Kyriatzis Gregorios , Krafcikova Michaela , Carson Brittany B. , Feenstra Jennifer M. , Marinescu Voichita D. , Segerman Anna , Haraldsson Martin , Gustavsson Anna-Lena , Hammarström Lars G.J. , Jenmalm Jensen Annika , Uhrbom Lene , Altelaar A.F. Maarten , Linnarsson Sten , Uhlén Per , Trantirek Lukas , Vincent C. Theresa , Nelander Sven , Enger Per Øyvind , Andäng Michael
Published: March 2023

RNA sequencing data mibefradil vs control (DMSO)
Figure S5 from Type I IFN Receptor Signaling Controls IL7-Dependent Accumulation and Activity of Protumoral IL17A-Producing γδT Cells in Breast Cancer
Authors: Patin Emmanuel C. , Soulard Daphnée , Fleury Sébastien , Hassane Maya , Dombrowicz David , Faveeuw Christelle , Trottein François , Paget Christophe
Published: March 2023

Type I IFN signalling does not impact on non-CD3bright gamma/delta T cells
Figure S4 from Type I IFN Receptor Signaling Controls IL7-Dependent Accumulation and Activity of Protumoral IL17A-Producing γδT Cells in Breast Cancer
Authors: Patin Emmanuel C. , Soulard Daphnée , Fleury Sébastien , Hassane Maya , Dombrowicz David , Faveeuw Christelle , Trottein François , Paget Christophe
Published: March 2023

Type I IFN signalling blockade does not enhance the frequency of IL-17A+ NKT and conventional CD4 T cells
Figure S1 from Type I IFN Receptor Signaling Controls IL7-Dependent Accumulation and Activity of Protumoral IL17A-Producing γδT Cells in Breast Cancer
Authors: Patin Emmanuel C. , Soulard Daphnée , Fleury Sébastien , Hassane Maya , Dombrowicz David , Faveeuw Christelle , Trottein François , Paget Christophe
Published: March 2023

IL-17A promotes tumor growth of breast cancer in BALB/c mice
Table S5 from Genes Predisposed to DNA Hypermethylation during Acquired Resistance to Chemotherapy Are Identified in Ovarian Tumors by Bivalent Chromatin Domains at Initial Diagnosis
Authors: Curry Edward , Zeller Constanze , Masrour Nahal , Patten Darren K. , Gallon John , Wilhelm-Benartzi Charlotte S. , Ghaem-Maghami Sadaf , Bowtell David D. , Brown Robert
Published: March 2023

PEA1 and PEA2 Cell Line Gene Expression. Table of genomic co-ordinates for candidate genes and mapped RNA-seq reads for each gene, in each of 3 independent RNA extractions from the cell lines PEA1 and PEA2.
Table S2 from Membrane-Depolarizing Channel Blockers Induce Selective Glioma Cell Death by Impairing Nutrient Transport and Unfolded Protein/Amino Acid Responses
Authors: Niklasson Mia , Maddalo Gianluca , Sramkova Zuzana , Mutlu Ercan , Wee Shimei , Sekyrova Petra , Schmidt Linnéa , Fritz Nicolas , Dehnisch Ivar , Kyriatzis Gregorios , Krafcikova Michaela , Carson Brittany B. , Feenstra Jennifer M. , Marinescu Voichita D. , Segerman Anna , Haraldsson Martin , Gustavsson Anna-Lena , Hammarström Lars G.J. , Jenmalm Jensen Annika , Uhrbom Lene , Altelaar A.F. Maarten , Linnarsson Sten , Uhlén Per , Trantirek Lukas , Vincent C. Theresa , Nelander Sven , Enger Per Øyvind , Andäng Michael
Published: March 2023

Secondary screen data
Table S4 from Genes Predisposed to DNA Hypermethylation during Acquired Resistance to Chemotherapy Are Identified in Ovarian Tumors by Bivalent Chromatin Domains at Initial Diagnosis
Authors: Curry Edward , Zeller Constanze , Masrour Nahal , Patten Darren K. , Gallon John , Wilhelm-Benartzi Charlotte S. , Ghaem-Maghami Sadaf , Bowtell David D. , Brown Robert
Published: March 2023

Gene Ontology Enrichments. Table of Gene Ontology Biological Process terms enriched in the set of bivalently-marked and relapse-hypermethylated genes from this study.
Figure S4 from Membrane-Depolarizing Channel Blockers Induce Selective Glioma Cell Death by Impairing Nutrient Transport and Unfolded Protein/Amino Acid Responses
Authors: Niklasson Mia , Maddalo Gianluca , Sramkova Zuzana , Mutlu Ercan , Wee Shimei , Sekyrova Petra , Schmidt Linnéa , Fritz Nicolas , Dehnisch Ivar , Kyriatzis Gregorios , Krafcikova Michaela , Carson Brittany B. , Feenstra Jennifer M. , Marinescu Voichita D. , Segerman Anna , Haraldsson Martin , Gustavsson Anna-Lena , Hammarström Lars G.J. , Jenmalm Jensen Annika , Uhrbom Lene , Altelaar A.F. Maarten , Linnarsson Sten , Uhlén Per , Trantirek Lukas , Vincent C. Theresa , Nelander Sven , Enger Per Øyvind , Andäng Michael
Published: March 2023

Cell death analysis
Table S1 from Genes Predisposed to DNA Hypermethylation during Acquired Resistance to Chemotherapy Are Identified in Ovarian Tumors by Bivalent Chromatin Domains at Initial Diagnosis
Authors: Curry Edward , Zeller Constanze , Masrour Nahal , Patten Darren K. , Gallon John , Wilhelm-Benartzi Charlotte S. , Ghaem-Maghami Sadaf , Bowtell David D. , Brown Robert
Published: March 2023

Tables of primer sequences used for PCR of ChIP-enriched DNA and for pyrosequencing of bisulphite-treated DNA
Supplementary Information from Genes Predisposed to DNA Hypermethylation during Acquired Resistance to Chemotherapy Are Identified in Ovarian Tumors by Bivalent Chromatin Domains at Initial Diagnosis
Authors: Curry Edward , Zeller Constanze , Masrour Nahal , Patten Darren K. , Gallon John , Wilhelm-Benartzi Charlotte S. , Ghaem-Maghami Sadaf , Bowtell David D. , Brown Robert
Published: March 2023

Data showing greater than expected overlap of H3K4me3 and H3K27me3 marks in gene promoters and how variable ChIP-seq library complexity impacts upon discovery of bivalent domains
Figure S3 from Membrane-Depolarizing Channel Blockers Induce Selective Glioma Cell Death by Impairing Nutrient Transport and Unfolded Protein/Amino Acid Responses
Authors: Niklasson Mia , Maddalo Gianluca , Sramkova Zuzana , Mutlu Ercan , Wee Shimei , Sekyrova Petra , Schmidt Linnéa , Fritz Nicolas , Dehnisch Ivar , Kyriatzis Gregorios , Krafcikova Michaela , Carson Brittany B. , Feenstra Jennifer M. , Marinescu Voichita D. , Segerman Anna , Haraldsson Martin , Gustavsson Anna-Lena , Hammarström Lars G.J. , Jenmalm Jensen Annika , Uhrbom Lene , Altelaar A.F. Maarten , Linnarsson Sten , Uhlén Per , Trantirek Lukas , Vincent C. Theresa , Nelander Sven , Enger Per Øyvind , Andäng Michael
Published: March 2023

Proteomics analysis
Supplementary Figure S1, S2 and S3 from Genes Predisposed to DNA Hypermethylation during Acquired Resistance to Chemotherapy Are Identified in Ovarian Tumors by Bivalent Chromatin Domains at Initial Diagnosis
Authors: Curry Edward , Zeller Constanze , Masrour Nahal , Patten Darren K. , Gallon John , Wilhelm-Benartzi Charlotte S. , Ghaem-Maghami Sadaf , Bowtell David D. , Brown Robert
Published: March 2023

Supplementary Figure S1 - DNA Methylation Change in Relapse Cancer Cells Relative to Primary Tumours Supplementary Figure S2 - Average Promoter Methylation of Bivalent Genes in Ovarian Tumours Supplementary Figure S3 - Change in DNA Methylation and Gene Expression for Candidate Pathways
Figure S2 from Membrane-Depolarizing Channel Blockers Induce Selective Glioma Cell Death by Impairing Nutrient Transport and Unfolded Protein/Amino Acid Responses
Authors: Niklasson Mia , Maddalo Gianluca , Sramkova Zuzana , Mutlu Ercan , Wee Shimei , Sekyrova Petra , Schmidt Linnéa , Fritz Nicolas , Dehnisch Ivar , Kyriatzis Gregorios , Krafcikova Michaela , Carson Brittany B. , Feenstra Jennifer M. , Marinescu Voichita D. , Segerman Anna , Haraldsson Martin , Gustavsson Anna-Lena , Hammarström Lars G.J. , Jenmalm Jensen Annika , Uhrbom Lene , Altelaar A.F. Maarten , Linnarsson Sten , Uhlén Per , Trantirek Lukas , Vincent C. Theresa , Nelander Sven , Enger Per Øyvind , Andäng Michael
Published: March 2023

VGCC channel identification
Supplemetary Figure S3 from Perioperative, Spatiotemporally Coordinated Activation of T and NK Cells Prevents Recurrence of Pancreatic Cancer
Authors: Brooks Jennifer , Fleischmann-Mundt Bettina , Woller Norman , Niemann Julia , Ribback Silvia , Peters Kristin , Demir Ihsan Ekin , Armbrecht Nina , Ceyhan Guralp O. , Manns Michael P. , Wirth Thomas C. , Kubicka Stefan , Bernhardt Gunter , Smyth Mark J. , Calvisi Diego F. , Gürlevik Engin , Kühnel Florian
Published: March 2023

Immunohistochemical analysis of E-Cadherin expression
Supplementary Figure S5 from Perioperative, Spatiotemporally Coordinated Activation of T and NK Cells Prevents Recurrence of Pancreatic Cancer
Authors: Brooks Jennifer , Fleischmann-Mundt Bettina , Woller Norman , Niemann Julia , Ribback Silvia , Peters Kristin , Demir Ihsan Ekin , Armbrecht Nina , Ceyhan Guralp O. , Manns Michael P. , Wirth Thomas C. , Kubicka Stefan , Bernhardt Gunter , Smyth Mark J. , Calvisi Diego F. , Gürlevik Engin , Kühnel Florian
Published: March 2023

NK cell cytotoxicity assay
Supplemental Data from E6 Protein Expressed by High-Risk HPV Activates Super-Enhancers of the EGFR and c-MET Oncogenes by Destabilizing the Histone Demethylase KDM5C
Authors: Chen Xiaohua , Loo Jun Xian , Shi Xin , Xiong Wenjun , Guo Yong , Ke Haiqiang , Yang Mingkun , Jiang Yanping , Xia Siyu , Zhao Min , Zhong Shan , He Chunjiang , Fu Li , Li Feng
Published: March 2023

Supplementary Figures - Supplementary Figures S1-9. Supplementary Figure S1. Mutual co-immunoprecipitation of HPV16 E6 and KDM5C; Supplementary Figure S2. HPV16 E6 attenuates the KDM5C protein level and KDM5C mRNA quantification; Supplementary Figure S3. HPV16 E6 destabilizes KDM5C and alters the global H3K4 methylation; Supplementary Figure S4. KDM5C does not visibly alters HPV 16E6, HPV 16E7 mRNA and protein levels; Supplementary Figure S5. KDM5C knock out increases tumorigenicity in mice xenograft assay; Supplementary Figure S6. H3K27Ac recruitment to chromatin in the parental cells was examined by the genomic analysis of ChIP-seq signals. ; Supplementary Figure S7. Normalized ChIP-seq signal for H3K27Ac across the EGFR gene and c-MET gene. Supplementary Figure S8. Normalized H3K4me1 levels at KDM5C-bound super enhancers in CaSki-vector and CaSki-KDM5C cells. Supplementary Figure S9. HPV 16E6 depletion leads to EGFR and c-MET super-enhancer inhibition. Supplementary Methods - Description of additional experimental methods including Transfection, siRNA and MG132 treatment, Antibodies, Co-immunoprecipitation and ubiquitination assays, Immunofluorescence Microscopy, Maltose Binding Protein (MBP) Pull-down Assay, Chromatin immunoprecipitation (ChIP)-PCR and ChIP-Seq, Cell Invasion Assay, Real Time Cell Proliferation Assay, Wound healing Assay, Trypsin Digestion and Mass spectrometry analysis Supplementary Tables - Supplementary Tables S1-2. Supplementary Table S1. List of qPCR primers used in this study. Table S2. List of DNA oligonucleotides used in this study.
Supplementary Figure S2 from Perioperative, Spatiotemporally Coordinated Activation of T and NK Cells Prevents Recurrence of Pancreatic Cancer
Authors: Brooks Jennifer , Fleischmann-Mundt Bettina , Woller Norman , Niemann Julia , Ribback Silvia , Peters Kristin , Demir Ihsan Ekin , Armbrecht Nina , Ceyhan Guralp O. , Manns Michael P. , Wirth Thomas C. , Kubicka Stefan , Bernhardt Gunter , Smyth Mark J. , Calvisi Diego F. , Gürlevik Engin , Kühnel Florian
Published: March 2023

Analysis of of activation markers on CD8 T cells after neoadjuvant treatment.
Supplementary Figure S1 from Perioperative, Spatiotemporally Coordinated Activation of T and NK Cells Prevents Recurrence of Pancreatic Cancer
Authors: Brooks Jennifer , Fleischmann-Mundt Bettina , Woller Norman , Niemann Julia , Ribback Silvia , Peters Kristin , Demir Ihsan Ekin , Armbrecht Nina , Ceyhan Guralp O. , Manns Michael P. , Wirth Thomas C. , Kubicka Stefan , Bernhardt Gunter , Smyth Mark J. , Calvisi Diego F. , Gürlevik Engin , Kühnel Florian
Published: March 2023

Analysis of CD8+ CD90.2+ cells in immune cell populations isolated from primary tumors after neoadjuvant treatment.
Figure Legends for Supplementary Figures from Perioperative, Spatiotemporally Coordinated Activation of T and NK Cells Prevents Recurrence of Pancreatic Cancer
Authors: Brooks Jennifer , Fleischmann-Mundt Bettina , Woller Norman , Niemann Julia , Ribback Silvia , Peters Kristin , Demir Ihsan Ekin , Armbrecht Nina , Ceyhan Guralp O. , Manns Michael P. , Wirth Thomas C. , Kubicka Stefan , Bernhardt Gunter , Smyth Mark J. , Calvisi Diego F. , Gürlevik Engin , Kühnel Florian
Published: March 2023

Figure Legends for Figure S1-S5
Supplementary MATLAB file from Combination Therapy and the Evolution of Resistance: The Theoretical Merits of Synergism and Antagonism in Cancer
Authors: Saputra Elysia C. , Huang Lu , Chen Yihui , Tucker-Kellogg Lisa
Published: March 2023

MATLAB code for running the published simulations.
Supplemental Data from Evidence for Kaposi Sarcoma Originating from Mesenchymal Stem Cell through KSHV-induced Mesenchymal-to-Endothelial Transition
Authors: Li Yuqing , Zhong Canrong , Liu Dawei , Yu Wenjing , Chen Weikang , Wang Yan , Shi Songtao , Yuan Yan
Published: March 2023

Fig. S1. Infectivity of KSHV in PDLSCs, GMSCs and DPSCs. Fig. S2. Persistent KSHV infection in PDLSCs. Fig. S3. Long-term cultured KSHV-infected PDLSCs preserve the potential of tubulogenesis and invasiveness. Fig. S4. Expression of oral MSC-specific and endothelial markers in mock- and KSHV-infected MSCs in mouse kidney capsule implant. Fig. S5. Gene expression profiling analysis of KSHV-infected oral MSCs. Fig. S6. Top 20 significantly enriched Gene Ontology (GO) categories of molecular function and biological process in KSHV-infected PDLSC. Fig. S7. Recalculation of the average linkage distance between KS and each cell group from published data. Fig. S8. Relationship of KSHV-infected MSC and an MEndT model (induced hAMSC) in gene expression profile. Table S1. Common DEGs in KSHV-PDLSC vs. PDLSC and KS signature Table S2. Consistently regulated genes between KSHV-PDLSC vs. PDLSC and MEndT hAMSC vs. hAMSC. Table S3. Common DEGs in KSHV-HDMEC vs. HDMEC and KS signature. Table S4. Common DEGs in KSHV-HMVEC vs. HMVEC and KS signature. Table S5. Common DEGs in KSHV-LEC vs. LEC and KS signature. Table S6. Common DEGs in KSHV-BEC vs. BEC and KS signature.