bluuebunny/crossref_metadata_2025 huggingface dataset:
Figure S1 from GADD45β Loss Ablates Innate Immunosuppression in Cancer
Authors: Verzella Daniela , Bennett Jason , Fischietti Mariafausta , Thotakura Anil K. , Recordati Camilla , Pasqualini Fabio , Capece Daria , Vecchiotti Davide , D'Andrea Daniel , Di Francesco Barbara , De Maglie Marcella , Begalli Federica , Tornatore Laura , Papa Salvatore , Lawrence Toby , Forbes Stuart J. , Sica Antonio , Alesse Edoardo , Zazzeroni Francesca , Franzoso Guido
Published: April 2023

Reduced DEN-induced HCC Development in 129/SvJxC57BL/6J Gadd45b-/- Mice
Supplementary Data from Inflammasome Adaptor ASC Suppresses Apoptosis of Gastric Cancer Cells by an IL18-Mediated Inflammation-Independent Mechanism
Authors: Deswaerte Virginie , Nguyen Paul , West Alison , Browning Alison F. , Yu Liang , Ruwanpura Saleela M. , Balic Jesse , Livis Thaleia , Girard Charlotte , Preaudet Adele , Oshima Hiroko , Fung Ka Yee , Tye Hazel , Najdovska Meri , Ernst Matthias , Oshima Masanobu , Gabay Cem , Putoczki Tracy , Jenkins Brendan J.
Published: April 2023

The content of this file containing Supplementary Figures (and a Supplementary Table) provides additional (and essential) data supporting our conclusions that the ASC inflammasome/caspase-1/IL-18 axis promotes gastric tumorigenesis.
The mTORC1 pathway in Cul3/p53 ko cells from Inducing Differentiation of Premalignant Hepatic Cells as a Novel Therapeutic Strategy in Hepatocarcinoma
Authors: Wolf Benita , Krieg Kathrin , Falk Christine , Breuhahn Kai , Keppeler Hildegard , Biedermann Tilo , Schmid Evi , Warmann Steven , Fuchs Joerg , Vetter Silvia , Thiele Dennis , Nieser Maike , Avci-Adali Meltem , Skokowa Yulia , Schöls Ludger , Hauser Stefan , Ringelhan Marc , Yevsa Tetyana , Heikenwalder Mathias , Kossatz-Boehlert Uta
Published: April 2023

Supplemental Figure 3 data file
Supplemental Material and Methods from Inducing Differentiation of Premalignant Hepatic Cells as a Novel Therapeutic Strategy in Hepatocarcinoma
Authors: Wolf Benita , Krieg Kathrin , Falk Christine , Breuhahn Kai , Keppeler Hildegard , Biedermann Tilo , Schmid Evi , Warmann Steven , Fuchs Joerg , Vetter Silvia , Thiele Dennis , Nieser Maike , Avci-Adali Meltem , Skokowa Yulia , Schöls Ludger , Hauser Stefan , Ringelhan Marc , Yevsa Tetyana , Heikenwalder Mathias , Kossatz-Boehlert Uta
Published: April 2023

detailed information to material and Methods
Supplmentary Figures S1- S2 and Tables S1- S7 from Improved Survival of HER2+ Breast Cancer Patients Treated with Trastuzumab and Chemotherapy Is Associated with Host Antibody Immunity against the HER2 Intracellular Domain
Authors: Knutson Keith L. , Clynes Raphael , Shreeder Barath , Yeramian Patrick , Kemp Kathleen P. , Ballman Karla , Tenner Kathleen S. , Erskine Courtney L. , Norton Nadine , Northfelt Donald , Tan Winston , Calfa Carmen , Pegram Mark , Mittendorf Elizabeth A. , Perez Edith A.
Published: April 2023

Supplementary Figure S1 describes the pre-existing antibody responses to tumor antigens in patients with surgically resected HER2+ breast cancer. Supplementary Figure S2 compares the proportion of either the metastatic or adjuvant patients that respond to therapy with increased antibody responses. Table S1 shows the demographic information for the patients in this study. Table S2 compares the levels of antibodies to tumor antigens and TT in metastatic patients and healthy controls. Table S3 compares the mean pre- and post-treatment antibody levels to all of the tumor antigens and TT in the patients with metastatic disease. Table S4 describes correlations of the antibody responses to the type of chemotherapy received in the metastatic patients. Table S5 shows the results of a cox univariate analysis correlating PFS and antibody responses. Table S6 shows the results of a cox univariate analysis correlating OS and antibody responses. Table S7 compares the mean pre- and post-treatment antibody levels to all of the tumor antigens and TT in patients with surgically-resected disease.
Effects of single or combinational doxorubicin treatment in Cul3/p53 ko cells from Inducing Differentiation of Premalignant Hepatic Cells as a Novel Therapeutic Strategy in Hepatocarcinoma
Authors: Wolf Benita , Krieg Kathrin , Falk Christine , Breuhahn Kai , Keppeler Hildegard , Biedermann Tilo , Schmid Evi , Warmann Steven , Fuchs Joerg , Vetter Silvia , Thiele Dennis , Nieser Maike , Avci-Adali Meltem , Skokowa Yulia , Schöls Ludger , Hauser Stefan , Ringelhan Marc , Yevsa Tetyana , Heikenwalder Mathias , Kossatz-Boehlert Uta
Published: April 2023

Supplemental Figure 4 data file
Characterization of CD34+ and CD34- cells from Inducing Differentiation of Premalignant Hepatic Cells as a Novel Therapeutic Strategy in Hepatocarcinoma
Authors: Wolf Benita , Krieg Kathrin , Falk Christine , Breuhahn Kai , Keppeler Hildegard , Biedermann Tilo , Schmid Evi , Warmann Steven , Fuchs Joerg , Vetter Silvia , Thiele Dennis , Nieser Maike , Avci-Adali Meltem , Skokowa Yulia , Schöls Ludger , Hauser Stefan , Ringelhan Marc , Yevsa Tetyana , Heikenwalder Mathias , Kossatz-Boehlert Uta
Published: April 2023

Supplemental Figure 1 data file
Supplementary Table S2 from Chromatin-Remodeling Complex SWI/SNF Controls Multidrug Resistance by Transcriptionally Regulating the Drug Efflux Pump ABCB1
Authors: Dubey Ramin , Lebensohn Andres M. , Bahrami-Nejad Zahra , Marceau Caleb , Champion Magali , Gevaert Olivier , Sikic Branimir I. , Carette Jan E. , Rohatgi Rajat
Published: April 2023

Table showing sequences of sites complementary to the gRNAs (Red) and mutations (Blue) in the clonal cell lines used in the study.
Supplementary Figures Legends from Transcriptional Induction of Periostin by a Sulfatase 2–TGFβ1–SMAD Signaling Axis Mediates Tumor Angiogenesis in Hepatocellular Carcinoma
Authors: Chen Gang , Nakamura Ikuo , Dhanasekaran Renumathy , Iguchi Eriko , Tolosa Ezequiel J. , Romecin Paola A. , Vera Renzo E. , Almada Luciana L. , Miamen Alexander G. , Chaiteerakij Roongruedee , Zhou Mengtao , Asiedu Michael K. , Moser Catherine D. , Han Shaoshan , Hu Chunling , Banini Bubu A. , Oseini Abdul M. , Chen Yichun , Fang Yong , Yang Dongye , Shaleh Hassan M. , Wang Shaoqing , Wu Dehai , Song Tao , Lee Ju-Seog , Thorgeirsson Snorri S. , Chevet Eric , Shah Vijay H. , Fernandez-Zapico Martin E. , Roberts Lewis R.
Published: April 2023

Legends for Supp Figures
Supplementary Table S1 from Chromatin-Remodeling Complex SWI/SNF Controls Multidrug Resistance by Transcriptionally Regulating the Drug Efflux Pump ABCB1
Authors: Dubey Ramin , Lebensohn Andres M. , Bahrami-Nejad Zahra , Marceau Caleb , Champion Magali , Gevaert Olivier , Sikic Branimir I. , Carette Jan E. , Rohatgi Rajat
Published: April 2023

Top 35 hits from the doxorubicin screen based on a False Discovery Rate corrected p-value threshold of 0.01.
Supplementary Figures 1-5 from Transcriptional Induction of Periostin by a Sulfatase 2–TGFβ1–SMAD Signaling Axis Mediates Tumor Angiogenesis in Hepatocellular Carcinoma
Authors: Chen Gang , Nakamura Ikuo , Dhanasekaran Renumathy , Iguchi Eriko , Tolosa Ezequiel J. , Romecin Paola A. , Vera Renzo E. , Almada Luciana L. , Miamen Alexander G. , Chaiteerakij Roongruedee , Zhou Mengtao , Asiedu Michael K. , Moser Catherine D. , Han Shaoshan , Hu Chunling , Banini Bubu A. , Oseini Abdul M. , Chen Yichun , Fang Yong , Yang Dongye , Shaleh Hassan M. , Wang Shaoqing , Wu Dehai , Song Tao , Lee Ju-Seog , Thorgeirsson Snorri S. , Chevet Eric , Shah Vijay H. , Fernandez-Zapico Martin E. , Roberts Lewis R.
Published: April 2023

Supplementary Figure 1 Schematic representation of experimental design for HCC carcinogenesis in mice. Supplementary Figure 2 Loss of Sulf2 impairs tumor growth and incidence in DEN-model of HCC carcinogenesis. Supplementary Figure 3 Conditioned media from SULF2-transfected HCC cells promotes endothelial cells viability and adhesion. Supplementary Figure 4 In silico analysis of HCC-angiogenic factors. Supplementary Figure 5 Expression of POSTN in Sulf2 knockout or wild type animals.
Supplementary Methods and References from Chromatin-Remodeling Complex SWI/SNF Controls Multidrug Resistance by Transcriptionally Regulating the Drug Efflux Pump ABCB1
Authors: Dubey Ramin , Lebensohn Andres M. , Bahrami-Nejad Zahra , Marceau Caleb , Champion Magali , Gevaert Olivier , Sikic Branimir I. , Carette Jan E. , Rohatgi Rajat
Published: April 2023

Description of additional methods and procedures used in the study. Also includes Supplementary References.
Supplementary Table 3- from Systematic Analysis of AU-Rich Element Expression in Cancer Reveals Common Functional Clusters Regulated by Key RNA-Binding Proteins
Authors: Hitti Edward , Bakheet Tala , Al-Souhibani Norah , Moghrabi Walid , Al-Yahya Suhad , Al-Ghamdi Maha , Al-Saif Maher , Shoukri Mohamed M. , Lánczky András , Grépin Renaud , Győrffy Balázs , Pagès Gilles , Khabar Khalid S.A.
Published: April 2023

Correlation data of the mRNA levels for TTP, HuR, TTP/HuR ratio with ARE- and non-ARE mRNA expression.
Supplementary Movie 1 from NOTCH Signaling Regulates Asymmetric Cell Fate of Fast- and Slow-Cycling Colon Cancer–Initiating Cells
Authors: Srinivasan Tara , Walters Jewell , Bu Pengcheng , Than Elaine Bich , Tung Kuei-Ling , Chen Kai-Yuan , Panarelli Nicole , Milsom Jeff , Augenlicht Leonard , Lipkin Steven M. , Shen Xiling
Published: April 2023

3D reconstruction of LGR5+/BMI1+ CCIC-1 asymmetric daughter cell pair
Supplementary Table 1 from Systematic Analysis of AU-Rich Element Expression in Cancer Reveals Common Functional Clusters Regulated by Key RNA-Binding Proteins
Authors: Hitti Edward , Bakheet Tala , Al-Souhibani Norah , Moghrabi Walid , Al-Yahya Suhad , Al-Ghamdi Maha , Al-Saif Maher , Shoukri Mohamed M. , Lánczky András , Grépin Renaud , Győrffy Balázs , Pagès Gilles , Khabar Khalid S.A.
Published: April 2023

Details of Patients' gene expression datasets.
Supplementary Figures from Systematic Analysis of AU-Rich Element Expression in Cancer Reveals Common Functional Clusters Regulated by Key RNA-Binding Proteins
Authors: Hitti Edward , Bakheet Tala , Al-Souhibani Norah , Moghrabi Walid , Al-Yahya Suhad , Al-Ghamdi Maha , Al-Saif Maher , Shoukri Mohamed M. , Lánczky András , Grépin Renaud , Győrffy Balázs , Pagès Gilles , Khabar Khalid S.A.
Published: April 2023

Supplementary Figures comprising Fig.S1: HuR kb polyadenylation variants in Glioblastoma and lung adenocarcinoma; Fig. S2: Correlations of TTP and HuR with cancer ARE-mRNAs; Fig. S3: Normal versus cancer mRNA intensity levels of the mitotic ARE-gene cluster members. Fig. S4: Negative correlation between the 11 members of the ARE-mitotic genes cluster and the TTP/HuR ratio; and Fig. S5 Kaplan Meier survival analysis for expression level of the mitotic ARE-mRNA cluster
Supplementary Figure 5 from NRF2 Induction Supporting Breast Cancer Cell Survival Is Enabled by Oxidative Stress–Induced DPP3–KEAP1 Interaction
Authors: Lu Kevin , Alcivar Allen L. , Ma Jianglin , Foo Tzeh Keong , Zywea Susan , Mahdi Amar , Huo Yanying , Kensler Thomas W. , Gatza Michael L. , Xia Bing
Published: April 2023

Effect of mutating individual cysteine residues of DPP3 on its interaction with KEAP1.
Supplementary materials and methods from Identification of a Natural Killer Cell Receptor Allele That Prolongs Survival of Cytomegalovirus-Positive Glioblastoma Patients
Authors: Dominguez–Valentin Mev , Gras Navarro Andrea , Rahman Aminur Mohummad , Kumar Surendra , Retière Christèle , Ulvestad Elling , Kristensen Vessela , Lund-Johansen Morten , Lie Benedicte Alexandra , Enger Per Øyvind , Njølstad Gro , Kristoffersen Einar , Lie Stein Atle , Chekenya Martha
Published: April 2023

Supplementary materials and methods. Detailed bioinformatics analysis methods (softwares commands and parameters) used to analyse in silicon TCGA and OKG exam sequencing data.
Supplementary Table S1 from High-Order Drug Combinations Are Required to Effectively Kill Colorectal Cancer Cells
Authors: Horn Thomas , Ferretti Stéphane , Ebel Nicolas , Tam Angela , Ho Samuel , Harbinski Fred , Farsidjani Ali , Zubrowski Matthew , Sellers William R. , Schlegel Robert , Porter Dale , Morris Erick , Wuerthner Jens , Jeay Sébastien , Greshock Joel , Halilovic Ensar , Garraway Levi A. , Caponigro Giordano , Lehár Joseph
Published: April 2023

Cell lines used in this study.
Supplementary Methods and References from High-Order Drug Combinations Are Required to Effectively Kill Colorectal Cancer Cells
Authors: Horn Thomas , Ferretti Stéphane , Ebel Nicolas , Tam Angela , Ho Samuel , Harbinski Fred , Farsidjani Ali , Zubrowski Matthew , Sellers William R. , Schlegel Robert , Porter Dale , Morris Erick , Wuerthner Jens , Jeay Sébastien , Greshock Joel , Halilovic Ensar , Garraway Levi A. , Caponigro Giordano , Lehár Joseph
Published: April 2023

Description of additional methods and procedures used in the study. Also includes Supplementary References.
Supplementary Figures from BRCA2 Hypomorphic Missense Variants Confer Moderate Risks of Breast Cancer
Authors: Shimelis Hermela , Mesman Romy L.S. , Von Nicolai Catharina , Ehlen Asa , Guidugli Lucia , Martin Charlotte , Calléja Fabienne M.G.R. , Meeks Huong , Hallberg Emily , Hinton Jamie , Lilyquist Jenna , Hu Chunling , Aalfs Cora M. , Aittomäki Kristiina , Andrulis Irene , Anton-Culver Hoda , Arndt Volker , Beckmann Matthias W. , Benitez Javier , Bogdanova Natalia V. , Bojesen Stig E. , Bolla Manjeet K. , Borresen-Dale Anne-Lise , Brauch Hiltrud , Brennan Paul , Brenner Hermann , Broeks Annegien , Brouwers Barbara , Brüning Thomas , Burwinkel Barbara , Chang-Claude Jenny , Chenevix-Trench Georgia , Cheng Ching-Yu , Choi Ji-Yeob , Collée J. Margriet , Cox Angela , Cross Simon S. , Czene Kamila , Darabi Hatef , Dennis Joe , Dörk Thilo , dos-Santos-Silva Isabel , Dunning Alison M. , Fasching Peter A. , Figueroa Jonine , Flyger Henrik , García-Closas Montserrat , Giles Graham G. , Glendon Gord , Guénel Pascal , Haiman Christopher A. , Hall Per , Hamann Ute , Hartman Mikael , Hogervorst Frans B. , Hollestelle Antoinette , Hopper John L. , Ito Hidemi , Jakubowska Anna , Kang Daehee , Kosma Veli-Matti , Kristensen Vessela , Lai Kah-Nyin , Lambrechts Diether , Marchand Loic Le , Li Jingmei , Lindblom Annika , Lophatananon Artitaya , Lubinski Jan , Machackova Eva , Mannermaa Arto , Margolin Sara , Marme Frederik , Matsuo Keitaro , Miao Hui , Michailidou Kyriaki , Milne Roger L. , Muir Kenneth , Neuhausen Susan L. , Nevanlinna Heli , Olson Janet E. , Olswold Curtis , Oosterwijk Jan J.C. , Osorio Ana , Peterlongo Paolo , Peto Julian , Pharoah Paul D.P. , Pylkäs Katri , Radice Paolo , Rashid Muhammad Usman , Rhenius Valerie , Rudolph Anja , Sangrajrang Suleeporn , Sawyer Elinor J. , Schmidt Marjanka K. , Schoemaker Minouk J. , Seynaeve Caroline , Shah Mitul , Shen Chen-Yang , Shrubsole Martha , Shu Xiao-Ou , Slager Susan , Southey Melissa C. , Stram Daniel O. , Swerdlow Anthony , Teo Soo H. , Tomlinson Ian , Torres Diana , Truong Thérèse , van Asperen Christi J. , van der Kolk Lizet E. , Wang Qin , Winqvist Robert , Wu Anna H. , Yu Jyh-Cherng , Zheng Wei , Zheng Ying , Leary Jennifer , Walker Logan , Foretova Lenka , Fostira Florentia , Claes Kathleen B.M. , Varesco Liliana , Moghadasi Setareh , Easton Douglas F. , Spurdle Amanda , Devilee Peter , Vrieling Harry , Monteiro Alvaro N.A. , Goldgar David E. , Carreira Aura , Vreeswijk Maaike P.G. , Couch Fergus J.
Published: April 2023

Figure S1: BCRA2 p.Y3035S Pedigrees. Figure S2: Western blot of ectopically expressed full-length wildtype and mutant hBRCA2 protein in VC8 DR-GFP cells subjected to HDR assay. Figure S3: Purification of wildtype and mutant BRCA2 from human cells. Figure S4: Position of BRCA2 DNA binding domain (DBD) variants on a ribbon diagram of the murine DBD crystal structure.
Supplementary Tables from Preclinical Evidence That 3′-Deoxy-3′-[18F]Fluorothymidine PET Can Visualize Recovery of Hematopoiesis after Gemcitabine Chemotherapy
Authors: Schelhaas Sonja , Held Annelena , Bäumer Nicole , Viel Thomas , Hermann Sven , Müller-Tidow Carsten , Jacobs Andreas H.
Published: April 2023

Supplementary Table S1. Mean values [plus minus] standard deviations of different PET quantification approaches and number of samples analyzed. Supplementary Table S2. Mean values [plus minus] standard deviations of the figures presented in the results section and number of samples analyzed. Supplementary Table S3. Mean values [plus minus] standard deviation of peripheral blood counts measured at various time points after gemcitabine administration.
Supplementary Figure S5. Acute impact of EO771 breast cancer exosomes on immune microenvironment in the bone marrow. from The Biodistribution and Immune Suppressive Effects of Breast Cancer–Derived Exosomes
Authors: Wen Shu Wen , Sceneay Jaclyn , Lima Luize Goncalves , Wong Christina S.F. , Becker Melanie , Krumeich Sophie , Lobb Richard J. , Castillo Vanessa , Wong Ke Ni , Ellis Sarah , Parker Belinda S. , Möller Andreas
Published: April 2023

C57BL/6 mice received a single intravenous injection of EO771-derived exosomes (50 µg/mouse; 4E11 particles), or liposomes. Immune composition changes in the bone marrow was assessed 24-hours later by flow cytometry. Frequency of (A) myeloid cells (CD11b+), (B) dendritic cells (DC; CD11C+/MHCII+), (C) macrophages (mø; CD11b+/F4/80+), (D) Natural Killer cells (NK; NK1.1+/CD3-), (E) CD4 T-cells (CD3+/CD8+), and (F) CD8 T-cells (CD3+/CD8+). Results are presented as mean {plus minus} s.e.m. (n=5 animals/group) and analyzed by 2-tailed Mann-Whitney nonparametric U-tests, and Holm-Sidak multiple testing correction method.
Supplementary Figure S4. Acute impact of EO771 breast cancer exosomes on immune microenvironment in the lung. from The Biodistribution and Immune Suppressive Effects of Breast Cancer–Derived Exosomes
Authors: Wen Shu Wen , Sceneay Jaclyn , Lima Luize Goncalves , Wong Christina S.F. , Becker Melanie , Krumeich Sophie , Lobb Richard J. , Castillo Vanessa , Wong Ke Ni , Ellis Sarah , Parker Belinda S. , Möller Andreas
Published: April 2023

C57BL/6 mice received a single intravenous injection of EO771-derived exosomes (50 µg/mouse; 4E11 particles) or liposomes. Immune composition changes in the lung was assessed 24-hours later by flow cytometry. Frequency of (A) myeloid cells (CD11b+), (B) dendritic cells (DC; CD11C+/MHCII+), (C) macrophages (mø; CD11b+/F4/80+), (D) Natural Killer cells (NK; NK1.1+/CD3-), (E) CD4 T-cells (CD3+/CD8+), and (F) CD8 T-cells (CD3+/CD8+). Results are presented as mean {plus minus} s.e.m. (n=5 animals/group) and analyzed by 2-tailed Mann-Whitney U-tests, and Holm-Sidak multiple testing correction method; *: p<0.05, **: p<0.01.
Supplementary Figure S3. Uptake of 4T1- and 67NR-derived exosomes by immune cell lineages. from The Biodistribution and Immune Suppressive Effects of Breast Cancer–Derived Exosomes
Authors: Wen Shu Wen , Sceneay Jaclyn , Lima Luize Goncalves , Wong Christina S.F. , Becker Melanie , Krumeich Sophie , Lobb Richard J. , Castillo Vanessa , Wong Ke Ni , Ellis Sarah , Parker Belinda S. , Möller Andreas
Published: April 2023

BALB/C mice received a single intravenous injection of DiD-labeled 4T1- or 67NR-derived exosomes (20 µg; 1.2E11 particles). Liposomes injected at equivalent particle numbers served as control. Assessment of exosome uptake by immune cell lineages in the bone marrow (BM), spleen and lung was carried out 24-hours later by flow cytometry. (A) Representative flow cytometric plots (left) and quantification (right) of distinct DiD+ population within CD45+ cells. (B-G) Frequency of DiD+ subpopulation within (B) myeloid cells (CD11b+), (C) CD11b+/Gr1+ MDSCs, (D) dendritic cells (CD11C+/MHCII+), (E) macrophages (mø; CD11b+/F4/80+), (F) CD8 T-cells (CD3+/CD8+) and (G) CD4 T-cells (CD3+/CD4+). Results are presented as mean {plus minus} s.e.m. (n=5-7/group) as analyzed by ANOVA; *: p<0.01 compared to liposome control, #: p<0.01 compared to 67NR DiD-exosomes.
Supplementary Tables S1-S4 from The BRCA1-Δ11q Alternative Splice Isoform Bypasses Germline Mutations and Promotes Therapeutic Resistance to PARP Inhibition and Cisplatin
Authors: Wang Yifan , Bernhardy Andrea J. , Cruz Cristina , Krais John J. , Nacson Joseph , Nicolas Emmanuelle , Peri Suraj , van der Gulden Hanneke , van der Heijden Ingrid , O'Brien Shane W. , Zhang Yong , Harrell Maribel I. , Johnson Shawn F. , Candido Dos Reis Francisco J. , Pharoah Paul D. P. , Karlan Beth , Gourley Charlie , Lambrechts Diether , Chenevix-Trench Georgia , Olsson Håkan , Benitez Javier J. , Greene Mark H. , Gore Martin , Nussbaum Robert , Sadetzki Siegal , Gayther Simon A. , Kjaer Susanne K. , D'Andrea Alan D. , Shapiro Geoffrey I. , Wiest David L. , Connolly Denise C. , Daly Mary B. , Swisher Elizabeth M. , Bouwman Peter , Jonkers Jos , Balmaña Judith , Serra Violeta , Johnson Neil
Published: April 2023

RNA-seq analyses of global exon splicing events (S1); Cell line therapy sensitivities (S2); Hazard ratios for survival of patients with serous ovarian carcinomas associated with BRCA1 mutation, age at diagnosis and stage (S3); Characteristics of studies included in survival analysis from Fig. 5A (S4).
Supplementary Figure Legends from The Biodistribution and Immune Suppressive Effects of Breast Cancer–Derived Exosomes
Authors: Wen Shu Wen , Sceneay Jaclyn , Lima Luize Goncalves , Wong Christina S.F. , Becker Melanie , Krumeich Sophie , Lobb Richard J. , Castillo Vanessa , Wong Ke Ni , Ellis Sarah , Parker Belinda S. , Möller Andreas
Published: April 2023

Supplementary Figure Legends
Supplementary Figure S4 from The BRCA1-Δ11q Alternative Splice Isoform Bypasses Germline Mutations and Promotes Therapeutic Resistance to PARP Inhibition and Cisplatin
Authors: Wang Yifan , Bernhardy Andrea J. , Cruz Cristina , Krais John J. , Nacson Joseph , Nicolas Emmanuelle , Peri Suraj , van der Gulden Hanneke , van der Heijden Ingrid , O'Brien Shane W. , Zhang Yong , Harrell Maribel I. , Johnson Shawn F. , Candido Dos Reis Francisco J. , Pharoah Paul D. P. , Karlan Beth , Gourley Charlie , Lambrechts Diether , Chenevix-Trench Georgia , Olsson Håkan , Benitez Javier J. , Greene Mark H. , Gore Martin , Nussbaum Robert , Sadetzki Siegal , Gayther Simon A. , Kjaer Susanne K. , D'Andrea Alan D. , Shapiro Geoffrey I. , Wiest David L. , Connolly Denise C. , Daly Mary B. , Swisher Elizabeth M. , Bouwman Peter , Jonkers Jos , Balmaña Judith , Serra Violeta , Johnson Neil
Published: April 2023

CRISPR/Cas9 editing of SUM149PT cells.
Supplementary methods from Epigenetic Switch between SOX2 and SOX9 Regulates Cancer Cell Plasticity
Authors: Lin Sheng-Chieh , Chou Yu-Ting , Jiang Shih Sheng , Chang Junn-Liang , Chung Chih-Hung , Kao Yu-Rung , Chang I-Shou , Wu Cheng-Wen
Published: April 2023

This file contains technical details of experimental methods used in this study: 1. Colony formation assay; 2. Matrigel invasion assay; 3. Live cell migration assay; 4. Flow cytometry analysis; 5. Immunostaining; 6. ChIP-qPCR; 7. Cell proliferation assay; 8. Animal experiment.
Supplementary Figure 1 from MNX1 Is Oncogenically Upregulated in African-American Prostate Cancer
Authors: Zhang Li , Wang Jianghua , Wang Yongquan , Zhang Yiqun , Castro Patricia , Shao Longjiang , Sreekumar Arun , Putluri Nagireddy , Guha Nilanjan , Deepak Saligrama , Padmanaban Arunkumar , Creighton Chad J. , Ittmann Michael
Published: April 2023

Supplementary Figure 1. Localization of MNX1 mRNA in prostate cancer tissues. MNX1 mRNA was detected using RNAScope detection technology with brown dots represent mRNA signals. A, B. Strong expression of MNX1 mRNA in prostate cancer cells (arrowheads). Minimal expression was seen in benign epithelium (double arrow). No expression was seen in stromal tissues. C, D. Weak expression of MNX1 mRNA in prostate cancer cells (arrowheads).
Supplementary Figures 1 through 6 from SMYD3-Mediated H2A.Z.1 Methylation Promotes Cell Cycle and Cancer Proliferation
Authors: Tsai Cheng-Hui , Chen Yun-Ju , Yu Chia-Jung , Tzeng Shiou-Ru , Wu I-Chen , Kuo Wen-Hung , Lin Ming-Chieh , Chan Nei-Li , Wu Kou-Juey , Teng Shu-Chun
Published: April 2023

Fig. S1. Representative mass spectrometry data of methylated H2A.Z. Fig. S2. Methylation activity of SMYD3 on histones in the context of nucleosome and evaluation of the H2A.ZK101me2 antibody. Fig. S3. Dimethylation of H2A.Z is critical for its protein interaction. Fig. S4. Dimethylation of H2A.Z is critical for promoting cell growth. Fig. S5. Genes affected by SMYD3 knockdown and H2A.ZK101Q expression. Fig. S6. Cyclin A1 is one of the downstream targets co-regulated by SMYD3 and H2A.ZK101me2.
Supplementary Table 5 from A Transcriptional Signature Identifies LKB1 Functional Status as a Novel Determinant of MEK Sensitivity in Lung Adenocarcinoma
Authors: Kaufman Jacob M. , Yamada Tadaaki , Park Kyungho , Timmers Cynthia D. , Amann Joseph M. , Carbone David P.
Published: April 2023

Gene expression data for resected lung adenocarcinomas and cell lines
Supplementary Figures S1-S4 from A Transcriptional Signature Identifies LKB1 Functional Status as a Novel Determinant of MEK Sensitivity in Lung Adenocarcinoma
Authors: Kaufman Jacob M. , Yamada Tadaaki , Park Kyungho , Timmers Cynthia D. , Amann Joseph M. , Carbone David P.
Published: April 2023

Supporting information including gene correlation matrix for LKB1 loss signature genes and additional drug sensitivity analyses.
Supplementary Materials and Methods from IDH2 Mutations Define a Unique Subtype of Breast Cancer with Altered Nuclear Polarity
Authors: Chiang Sarah , Weigelt Britta , Wen Huei-Chi , Pareja Fresia , Raghavendra Ashwini , Martelotto Luciano G. , Burke Kathleen A. , Basili Thais , Li Anqi , Geyer Felipe C. , Piscuoglio Salvatore , Ng Charlotte K.Y. , Jungbluth Achim A. , Balss Jörg , Pusch Stefan , Baker Gabrielle M. , Cole Kimberly S. , von Deimling Andreas , Batten Julie M. , Marotti Jonathan D. , Soh Hwei-Choo , McCalip Benjamin L. , Serrano Jonathan , Lim Raymond S. , Siziopikou Kalliopi P. , Lu Song , Liu Xiaolong , Hammour Tarek , Brogi Edi , Snuderl Matija , Iafrate A. John , Reis-Filho Jorge S. , Schnitt Stuart J.
Published: April 2023

Document containing methods on whole exome and targeted massively parallel sequencing analysis, 2-hydroxyglutarate (2HG) assay of cell lines, methylation profiling, and supplementary references.
Supplementary Figures from Tie2 Expression on Macrophages Is Required for Blood Vessel Reconstruction and Tumor Relapse after Chemotherapy
Authors: Chen Lin , Li Jie , Wang Fei , Dai Chengliang , Wu Fan , Liu Xiaoman , Li Taotao , Glauben Rainer , Zhang Yi , Nie Guangjun , He Yulong , Qin Zhihai
Published: April 2023

Relapse of transplanted MCA205 tumors after chemotherapy.Blood vessels were less covered by pericytes during tumor relapse. FACS analysis of Tie2+CD11b+ cells in DOX-treated tumor and peripheral blood.Generation and genotyping of Tie2 conditional knockout mice.CD11b+Ly6C+ MDSC accumulated in tumor microenvironment after chemotherapy.DOX induced higher level of hypoxia in tumor microenvironment.DOX did not directly induce Tie2 expression on CD11b+Ly6C+ MDSC in vitro.No Tie2+EGFP+ cells in spleen and blood of DOX-treated mice.Identification of Tie2 expression on transfected macrophages.Tie2 sustains the viability of macrophages in stressed condition.Tie2 gene deletion in CD11b+Ly6C+ MDSC did not impair their viability in spleens. Schematic diagram of tumor blood vessel reconstruction after chemotherapy.
Supplementary Figures 1 through 5 from Agonistic CD40 mAb-Driven IL12 Reverses Resistance to Anti-PD1 in a T-cell–Rich Tumor
Authors: Ngiow Shin Foong , Young Arabella , Blake Stephen J. , Hill Geoffrey R. , Yagita Hideo , Teng Michele W. L. , Korman Alan J. , Smyth Mark J.
Published: April 2023

Supplementary Figure 1: Anti-CTLA4 reduces intratumor T cell PD1. Supplementary Figure 2: Anti-CD40 lowers intratumor T cell PD1 in a dose-dependent manner. Supplementary Figure 3. Induction of T cell PD1 expression correlates with the absence of synergistic effect of anti-CD40 and anti-PD1 mAbs. Supplementary Figure 4. Anti-CD40 effects on intratumor T cell immune receptor expression. Supplementary Figure 5. IL-12 modulates CD8+ T cell PD1 expression.
Supplemental figures 1-7 from Cell Adhesion Molecule CD166 Drives Malignant Progression and Osteolytic Disease in Multiple Myeloma
Authors: Xu Linlin , Mohammad Khalid S. , Wu Hao , Crean Colin , Poteat Bradley , Cheng Yinghua , Cardoso Angelo A. , Machal Christophe , Hanenberg Helmut , Abonour Rafat , Kacena Melissa A. , Chirgwin John , Suvannasankha Attaya , Srour Edward F.
Published: April 2023

S1: Distribution of CD166 mRNA expression across 30 multiple myeloma and 22 breast cancer cell lines were analyzed; S2: The percentage of CD166+ cells within H929 cells from BM-homed cells were examined flow cytometrically; S3: Data are representative of 2 separate experiments (mean{plus minus}SEM, N = 6mice/group/experiment, each assayed individually); S5: Data represent 3 separate experiments done in triplicates for each group and are expressed as mean{plus minus} SEM, *P<0.05; S6: 2 out 5 left tibiae from mock control group showed detectable GFP+ MM cell; S7: Expression of MCSF was detected by quantitative PCR relative to GAPDH.
Supplemental figure legend from Cell Adhesion Molecule CD166 Drives Malignant Progression and Osteolytic Disease in Multiple Myeloma
Authors: Xu Linlin , Mohammad Khalid S. , Wu Hao , Crean Colin , Poteat Bradley , Cheng Yinghua , Cardoso Angelo A. , Machal Christophe , Hanenberg Helmut , Abonour Rafat , Kacena Melissa A. , Chirgwin John , Suvannasankha Attaya , Srour Edward F.
Published: April 2023

Supplemental figure legend
Supplemental Table 1 from Cell Adhesion Molecule CD166 Drives Malignant Progression and Osteolytic Disease in Multiple Myeloma
Authors: Xu Linlin , Mohammad Khalid S. , Wu Hao , Crean Colin , Poteat Bradley , Cheng Yinghua , Cardoso Angelo A. , Machal Christophe , Hanenberg Helmut , Abonour Rafat , Kacena Melissa A. , Chirgwin John , Suvannasankha Attaya , Srour Edward F.
Published: April 2023

Supplemental table 1
Figure S5 from INT6/EIF3E Controls the RNF8-Dependent Ubiquitylation Pathway and Facilitates DNA Double-Strand Break Repair in Human Cells
Authors: Morris Christelle , Tomimatsu Nozomi , Burma Sandeep , Jalinot Pierre
Published: April 2023

S5 illustrates the defect of BRCA2 recruitment to DNA damage foci in INT6-silenced cells
Figure S2 from INT6/EIF3E Controls the RNF8-Dependent Ubiquitylation Pathway and Facilitates DNA Double-Strand Break Repair in Human Cells
Authors: Morris Christelle , Tomimatsu Nozomi , Burma Sandeep , Jalinot Pierre
Published: April 2023

S2 shows the HR defect in cells treated with different anti-INT6 siRNAs
Supplementary Tables 1 through 3 from CBX4 Suppresses Metastasis via Recruitment of HDAC3 to the Runx2 Promoter in Colorectal Carcinoma
Authors: Wang Xin , Li Liping , Wu Yuanzhong , Zhang Ruhua , Zhang Meifang , Liao Dan , Wang Gang , Qin Ge , Xu Rui-hua , Kang Tiebang
Published: April 2023

Table S1 is the correlation between CBX4 expression and Runx2 expression of CRC patients, Table S2 is correlation between CBX4 expression and clinicopathologic characteristics of CRC patients, and Table S3 is univariate and multivariate analysis for overall survival.
Supplementary Materials and Methods from CBX4 Suppresses Metastasis via Recruitment of HDAC3 to the Runx2 Promoter in Colorectal Carcinoma
Authors: Wang Xin , Li Liping , Wu Yuanzhong , Zhang Ruhua , Zhang Meifang , Liao Dan , Wang Gang , Qin Ge , Xu Rui-hua , Kang Tiebang
Published: April 2023

Addtional information on shRNA sequences, qRT-PCR primers, promoter cloning primers, antibodies and ChIP-qPCR primers used in this study.
Supplemental table 1 from Dietary Emulsifier–Induced Low-Grade Inflammation Promotes Colon Carcinogenesis
Authors: Viennois Emilie , Merlin Didier , Gewirtz Andrew T. , Chassaing Benoit
Published: April 2023

Oligonucleotides used in this study.
Supplemental figure legends from Dietary Emulsifier–Induced Low-Grade Inflammation Promotes Colon Carcinogenesis
Authors: Viennois Emilie , Merlin Didier , Gewirtz Andrew T. , Chassaing Benoit
Published: April 2023

Legends for the supplemental figures 1-11, that provide supplemental experimental data on how dietary emulsifiers can promote colon carcinogenesis.
Figure S5: Effect of androgen deprivation on EMP in xenografts from Disrupting Androgen Receptor Signaling Induces Snail-Mediated Epithelial–Mesenchymal Plasticity in Prostate Cancer
Authors: Miao Lu , Yang Lin , Li Rui , Rodrigues Daniel N. , Crespo Mateus , Hsieh Jer-Tsong , Tilley Wayne D. , de Bono Johann , Selth Luke A. , Raj Ganesh V.
Published: April 2023

10 million C4-2 cells were injected subcutaneously into two locations into 8 nude mice. 4 mice (8 tumors) were subject to surgical castration, and the other 4 mice were left intact. Six days after surgery, the mice were sacrificed and the tumors were subjected to H&E (B) and IHC evaluation for E-Cadherin and Fibronectin (C).
Supplemental Figure 3 from Transcription Factor ZBP-89 Drives a Feedforward Loop of β-Catenin Expression in Colorectal Cancer
Authors: Essien Bryan E. , Sundaresan Sinju , Ocadiz-Ruiz Ramon , Chavis Aaron , Tsao Amy C. , Tessier Arthur J. , Hayes Michael M. , Photenhauer Amanda , Saqui-Salces Milena , Kang Anthony J. , Shah Yatrik M. , Győrffy Balazs , Merchant Juanita L.
Published: April 2023

Complementation of ZNF148 reduced viability by S33Y using MTT
Supplemental Figure 1 from Transcription Factor ZBP-89 Drives a Feedforward Loop of β-Catenin Expression in Colorectal Cancer
Authors: Essien Bryan E. , Sundaresan Sinju , Ocadiz-Ruiz Ramon , Chavis Aaron , Tsao Amy C. , Tessier Arthur J. , Hayes Michael M. , Photenhauer Amanda , Saqui-Salces Milena , Kang Anthony J. , Shah Yatrik M. , Győrffy Balazs , Merchant Juanita L.
Published: April 2023

ZBP-89 Probe Sets:BFCOL1 and BERF1
Supplemental Data from Transcription Factor ZBP-89 Drives a Feedforward Loop of β-Catenin Expression in Colorectal Cancer
Authors: Essien Bryan E. , Sundaresan Sinju , Ocadiz-Ruiz Ramon , Chavis Aaron , Tsao Amy C. , Tessier Arthur J. , Hayes Michael M. , Photenhauer Amanda , Saqui-Salces Milena , Kang Anthony J. , Shah Yatrik M. , Győrffy Balazs , Merchant Juanita L.
Published: April 2023

Supplemental Methods, Figure Legends and References for Supplemental Methods
Supplementary figure legends from IKBKE Is a Substrate of EGFR and a Therapeutic Target in Non–Small Cell Lung Cancer with Activating Mutations of EGFR
Authors: Challa Sridevi , Guo Jian-Ping , Ding Xiaowen , Xu Cheng-Xiong , Li Yajuan , Kim Donghwa , Smith Matthew A. , Cress Douglas W. , Coppola Domenico , Haura Eric B. , Cheng Jin Q.
Published: April 2023

Figure legends for supplementary figures
Supplemental Figure 8 from IKBKE Is a Substrate of EGFR and a Therapeutic Target in Non–Small Cell Lung Cancer with Activating Mutations of EGFR
Authors: Challa Sridevi , Guo Jian-Ping , Ding Xiaowen , Xu Cheng-Xiong , Li Yajuan , Kim Donghwa , Smith Matthew A. , Cress Douglas W. , Coppola Domenico , Haura Eric B. , Cheng Jin Q.
Published: April 2023

Effects of inhibitor of IKBKE and MEK on HCC827 xenograft growth.
Supplemental Figure 7 from IKBKE Is a Substrate of EGFR and a Therapeutic Target in Non–Small Cell Lung Cancer with Activating Mutations of EGFR
Authors: Challa Sridevi , Guo Jian-Ping , Ding Xiaowen , Xu Cheng-Xiong , Li Yajuan , Kim Donghwa , Smith Matthew A. , Cress Douglas W. , Coppola Domenico , Haura Eric B. , Cheng Jin Q.
Published: April 2023

Amlexanox synergizes with AZD6244 in EGFR-mutated HCC827 cells.
Supplementary Figure S4 from IL4 Primes the Dynamics of Breast Cancer Progression via DUSP4 Inhibition
Authors: Gaggianesi Miriam , Turdo Alice , Chinnici Aurora , Lipari Elisa , Apuzzo Tiziana , Benfante Antonina , Sperduti Isabella , Di Franco Simone , Meraviglia Serena , Lo Presti Elena , Dieli Francesco , Caputo Valentina , Militello Gabriella , Vieni Salvatore , Stassi Giorgio , Todaro Matilde
Published: April 2023

DUSP4 reduces aggressiveness of ER+ and TN cancer cells
Supplemental Figure 5 from IKBKE Is a Substrate of EGFR and a Therapeutic Target in Non–Small Cell Lung Cancer with Activating Mutations of EGFR
Authors: Challa Sridevi , Guo Jian-Ping , Ding Xiaowen , Xu Cheng-Xiong , Li Yajuan , Kim Donghwa , Smith Matthew A. , Cress Douglas W. , Coppola Domenico , Haura Eric B. , Cheng Jin Q.
Published: April 2023

Effect of EGFR phosphorylation of IKBKE-Y153/179 on EGFR-induced cell phenotype
Supplementary Figure S2 from IL4 Primes the Dynamics of Breast Cancer Progression via DUSP4 Inhibition
Authors: Gaggianesi Miriam , Turdo Alice , Chinnici Aurora , Lipari Elisa , Apuzzo Tiziana , Benfante Antonina , Sperduti Isabella , Di Franco Simone , Meraviglia Serena , Lo Presti Elena , Dieli Francesco , Caputo Valentina , Militello Gabriella , Vieni Salvatore , Stassi Giorgio , Todaro Matilde
Published: April 2023

IL-4DM blocks IL-4 pathway activation in breast cancer cells
Supplemental Figure 3 from IKBKE Is a Substrate of EGFR and a Therapeutic Target in Non–Small Cell Lung Cancer with Activating Mutations of EGFR
Authors: Challa Sridevi , Guo Jian-Ping , Ding Xiaowen , Xu Cheng-Xiong , Li Yajuan , Kim Donghwa , Smith Matthew A. , Cress Douglas W. , Coppola Domenico , Haura Eric B. , Cheng Jin Q.
Published: April 2023

Identification of IKBKE tyrosine residue(s) phosphorylated by EGFR
Supplementary Figure 9 from αvβ6 Integrin Promotes Castrate-Resistant Prostate Cancer through JNK1-Mediated Activation of Androgen Receptor
Authors: Lu Huimin , Wang Tao , Li Jing , Fedele Carmine , Liu Qin , Zhang Jianzhong , Jiang Zhong , Jain Dhanpat , Iozzo Renato V. , Violette Shelia M. , Weinreb Paul H. , Davis Roger J. , Gioeli Daniel , FitzGerald Thomas J. , Altieri Dario C. , Languino Lucia R.
Published: April 2023

Immunostaining of alphavbeta6 integrin in human prostate AdCa.
Supplementary Figure 3 from αvβ6 Integrin Promotes Castrate-Resistant Prostate Cancer through JNK1-Mediated Activation of Androgen Receptor
Authors: Lu Huimin , Wang Tao , Li Jing , Fedele Carmine , Liu Qin , Zhang Jianzhong , Jiang Zhong , Jain Dhanpat , Iozzo Renato V. , Violette Shelia M. , Weinreb Paul H. , Davis Roger J. , Gioeli Daniel , FitzGerald Thomas J. , Altieri Dario C. , Languino Lucia R.
Published: April 2023

alphavbeta6 integrin, but not alphavbeta3 integrin, promotes tumor growth.
Supplementary materials and methods from tRF/miR-1280 Suppresses Stem Cell–like Cells and Metastasis in Colorectal Cancer
Authors: Huang Bingqing , Yang Huipeng , Cheng Xixi , Wang Dan , Fu Shuyu , Shen Wencui , Zhang Qi , Zhang Lijuan , Xue Zhenyi , Li Yan , Da Yurong , Yang Qing , Li Zesong , Liu Li , Qiao Liang , Kong Ying , Yao Zhi , Zhao Peng , Li Min , Zhang Rongxin
Published: April 2023

Supplementary materials and methods
Supplementary figure 1 from Differential Effects of IL6 and Activin A in the Development of Cancer-Associated Cachexia
Authors: Chen Justin L. , Walton Kelly L. , Qian Hongwei , Colgan Timothy D. , Hagg Adam , Watt Matthew J. , Harrison Craig A. , Gregorevic Paul
Published: April 2023

Mice bearing colon-26 tumors rapidly lose lean and fat mass, together with significant wasting of muscle groups. These losses correlate with increases in the phosphorylation of the transcription factors, Stat3 and Smad3, which are activated by IL-6 and activin A, respectively. Smad3 target genes are also altered in cachectic mice.
Supplementary Materials and Methods from Tissue-Specific Signaling Networks Rewired by Major Somatic Mutations in Human Cancer Revealed by Proteome-Wide Discovery
Authors: Zhao Junfei , Cheng Feixiong , Zhao Zhongming
Published: April 2023

Supplementary material and methods
Supplementary Table S4 from Recurrent PPP2R1A Mutations in Uterine Cancer Act through a Dominant-Negative Mechanism to Promote Malignant Cell Growth
Authors: Haesen Dorien , Abbasi Asbagh Layka , Derua Rita , Hubert Antoine , Schrauwen Stefanie , Hoorne Yana , Amant Frédéric , Waelkens Etienne , Sablina Anna , Janssens Veerle
Published: April 2023

Comprehensive mass spectrometry data set for the determination of semi-quantitative mutant or WT AÎ± interactomes in HEC-1-A cells.
Supplementary Table S2 from Recurrent PPP2R1A Mutations in Uterine Cancer Act through a Dominant-Negative Mechanism to Promote Malignant Cell Growth
Authors: Haesen Dorien , Abbasi Asbagh Layka , Derua Rita , Hubert Antoine , Schrauwen Stefanie , Hoorne Yana , Amant Frédéric , Waelkens Etienne , Sablina Anna , Janssens Veerle
Published: April 2023

Oligonucleotides used for site-directed mutagenesis of AÎ± and shRNA-mediated knockdown of TIPRL1.
Supplementary Table 2: Human primer sequences used for RT-qPCR analysis from Accumulation of MDSC and Th17 Cells in Patients with Metastatic Colorectal Cancer Predicts the Efficacy of a FOLFOX–Bevacizumab Drug Treatment Regimen
Authors: Limagne Emeric , Euvrard Romain , Thibaudin Marion , Rébé Cédric , Derangère Valentin , Chevriaux Angélique , Boidot Romain , Végran Frédérique , Bonnefoy Nathalie , Vincent Julie , Bengrine-Lefevre Leila , Ladoire Sylvain , Delmas Dominique , Apetoh Lionel , Ghiringhelli François
Published: April 2023

List of primer used for mRNA relative expression in different myeloid subsets.
Supplementary Figure 6: mRNA relative expression of genes involved in immunosuppression from Accumulation of MDSC and Th17 Cells in Patients with Metastatic Colorectal Cancer Predicts the Efficacy of a FOLFOX–Bevacizumab Drug Treatment Regimen
Authors: Limagne Emeric , Euvrard Romain , Thibaudin Marion , Rébé Cédric , Derangère Valentin , Chevriaux Angélique , Boidot Romain , Végran Frédérique , Bonnefoy Nathalie , Vincent Julie , Bengrine-Lefevre Leila , Ladoire Sylvain , Delmas Dominique , Apetoh Lionel , Ghiringhelli François
Published: April 2023

gMDSC and mMDSC were cell sorted from four mCRC patient blood. mRNA were extracted and the expression of Entpd1, Nt5e, Pdl1, Pdl2, Indo, Arg1 and Inos was determined using RT-qPCR.
Table S2. Association of tumor fragmentation with clinico-pathological parameters. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness
Authors: Casanova Ruben , Xia Daniel , Rulle Undine , Nanni Paolo , Grossmann Jonas , Vrugt Bart , Wettstein Reto , Ballester-Ripoll Rafael , Astolfo Alberto , Weder Walter , Moch Holger , Stampanoni Marco , Beck Andrew H. , Soltermann Alex
Published: April 2023

The table shows proportions of patients among low and high TF groups (dichotomized at the median TF scores) stratified by clinical parameters. Chi-square tests and Spearman's rank correlations were used for categorical (low/high TF) and continuous TF scores respectively.
Supplementary Figure 2: MDSC gating strategy and IL-4Rα expression analysis. from Accumulation of MDSC and Th17 Cells in Patients with Metastatic Colorectal Cancer Predicts the Efficacy of a FOLFOX–Bevacizumab Drug Treatment Regimen
Authors: Limagne Emeric , Euvrard Romain , Thibaudin Marion , Rébé Cédric , Derangère Valentin , Chevriaux Angélique , Boidot Romain , Végran Frédérique , Bonnefoy Nathalie , Vincent Julie , Bengrine-Lefevre Leila , Ladoire Sylvain , Delmas Dominique , Apetoh Lionel , Ghiringhelli François
Published: April 2023

Flow cytometry gating strategy to identify MDSC subpopulations and granulocytes (1) through SCC-A, Lin- (=CD3, CD20, CD19 and CD56) CD14, CD15, CD33 and HLA-DR labeling (upper panel). For each selected population with CD14 and CD15 labelling, mMDSC (2) and gMDSC (3) were identified as HLA-DRlow/- and CD33high (lower panel). CD33 labeling for each population gated on CD14 and CD15 expression (1, 2 and 3). Representative histogram (left panel) and MFI for 3 patients (right panel) Pictures correspond to May-Grünwald Giemsa (MGG) staining of granulocytes, mMDSC and gMDSC isolated after cell sorting (upper panel). Quantification of cellular aspect (granulocytic or monocytic) after MGG staining (lower panel) Expression of IL-4Rα (CD124) in MDSC subpopulations and granulocytes. Representative histogram of CD124 expression (left panel) and MFI for 3 patients are shown (right panel).
Figure S3. Biological processes associated with TF morphotypes from TCGA mRNAseq and WS Mass Spectrometry data. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness
Authors: Casanova Ruben , Xia Daniel , Rulle Undine , Nanni Paolo , Grossmann Jonas , Vrugt Bart , Wettstein Reto , Ballester-Ripoll Rafael , Astolfo Alberto , Weder Walter , Moch Holger , Stampanoni Marco , Beck Andrew H. , Soltermann Alex
Published: April 2023

A) gene ontology network visualization of RNAs overexpressed in high (red) and low TF (blue) groups. B) bar plot showing molecular pathways associated with low (blue) and high (red) TF, at the RNA level. C) bar plot showing biological processes (BP) associated with increasing (red) and decreasing (blue) TF, at the protein level. Numbers indicate protein counts per category; asterisks* indicate BPs also enriched at the RNA Level.
Supplementary Tables from Interleukin-30 Promotes Breast Cancer Growth and Progression
Authors: Airoldi Irma , Cocco Claudia , Sorrentino Carlo , Angelucci Domenico , Di Meo Serena , Manzoli Lamberto , Esposito Silvia , Ribatti Domenico , Bertolotto Maria , Iezzi Laura , Natoli Clara , Di Carlo Emma
Published: April 2023

Supplementary Table S1. Antibodies used in immunostaining. Supplementary Table S2. Characteristics and outcomes by levels of IL-30 expression in tumor cells (primary tumor). Supplementary Table S3. Characteristics and outcomes by levels of IL-30 expression in leukocytes infiltrating the primary tumor. Supplementary Table S4. Multivariable regression models evaluating the association between cancer stage at baseline and IL-30 expression levels.
Figure S1. Frequency distributions, intra-tumor heterogeneity and inter-observer variability for TF scores. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness
Authors: Casanova Ruben , Xia Daniel , Rulle Undine , Nanni Paolo , Grossmann Jonas , Vrugt Bart , Wettstein Reto , Ballester-Ripoll Rafael , Astolfo Alberto , Weder Walter , Moch Holger , Stampanoni Marco , Beck Andrew H. , Soltermann Alex
Published: April 2023

A) Percentage distribution of computed TF scores for TMA and correlation between matching cores. B) Percentage distribution of computed TF scores for WS and correlation between matching whole sections. C) Percentage distribution of human-based TF scores for TMA and correlation between matching cores. B) Percentage distribution of human-based TF scores for WS and correlation between matching whole sections. E) Percentage distribution of human-based TF scores for TCGA images from observer 1 (Obs1) and correlations between the three observers on a subset of pictures (n=67). Dashed line indicates the median.
Supplemental Tables from Aberrant JMJD3 Expression Upregulates Slug to Promote Migration, Invasion, and Stem Cell–Like Behaviors in Hepatocellular Carcinoma
Authors: Tang Bo , Qi Guangying , Tang Fang , Yuan Shengguang , Wang Zhenran , Liang Xingsi , Li Bo , Yu Shuiping , Liu Jie , Huang Qi , Wei Yangchao , Zhai Run , Lei Biao , Yu Hongping , Tomlinson Stephen , He Songqing
Published: April 2023

Supplemental Table 1. JMJD3 staining and clinicopathologic characteristics of 285 hepatocellular carcinoma patients. Supplemental Table 2. Primer sequences used for qRT-PCR and qChIP Supplemental Table 3. List of genes significantly differentially expressed after JMJD3 overexpression (fold change {greater than or equal to}5)
Supplemental Materials and Methods from Aberrant JMJD3 Expression Upregulates Slug to Promote Migration, Invasion, and Stem Cell–Like Behaviors in Hepatocellular Carcinoma
Authors: Tang Bo , Qi Guangying , Tang Fang , Yuan Shengguang , Wang Zhenran , Liang Xingsi , Li Bo , Yu Shuiping , Liu Jie , Huang Qi , Wei Yangchao , Zhai Run , Lei Biao , Yu Hongping , Tomlinson Stephen , He Songqing
Published: April 2023

Supplemental Materials and Methods