bluuebunny/crossref_metadata_2025 huggingface dataset:
supplemental Figure legends from Long Noncoding RNA GCASPC, a Target of miR-17-3p, Negatively Regulates Pyruvate Carboxylase–Dependent Cell Proliferation in Gallbladder Cancer
Authors: Ma Ming-zhe , Zhang Yan , Weng Ming-zhe , Wang Shou-hua , Hu Ye , Hou Zhao-yuan , Qin Yi-yu , Gong Wei , Zhang Yong-Jie , Kong Xiang , Wang Jian-dong , Quan Zhi-wei
Published: April 2023

supplemental Figure 1-12. Expression levels of 10 lncRNAs by qRT-PCR in 15 GBC tissues and paired non-tumor tissues (Figure 1). Expression levels of 8 mRNAs by qRT-PCR in 15 GBC tissues and paired non-tumor tissues (Figure 2). Molecular characteristics of GCASPC (Figure 3). Nucleotide sequence of the full-length human GCASPC gene (Figure 4). GCASPC has no coding capability (Figure 5). The expression level of GCASPC in gallbladder cancer cells (Figure 6). Manipulation of GCASPC expression level (Figure 7). Anti-proliferative activity of GCASPC (Figure 8). GCASPC acts in trans (Figure 9). The effect of GCASPC on the protein, activity and mRNA levels of PC (Figure 10). GCASPC destabilizes PC protein (Figure 11). GCASPC directly binds to miR-17-3p (Figure 12).
Supplementary Figures and Tables from Inhibition of Mitochondrial Matrix Chaperones and Antiapoptotic Bcl-2 Family Proteins Empower Antitumor Therapeutic Responses
Authors: Karpel-Massler Georg , Ishida Chiaki Tsuge , Bianchetti Elena , Shu Chang , Perez-Lorenzo Rolando , Horst Basil , Banu Matei , Roth Kevin A. , Bruce Jeffrey N. , Canoll Peter , Altieri Dario C. , Siegelin Markus D.
Published: April 2023

Suppl. fig. 1: Patient derived-xenograft cells are susceptible to the combination treatment of Gamitrinib and clinically validated BH3-mimetics; Suppl. fig. 2: Transgenically-derived murine glioblastoma cells are susceptible to the combination treatment of Gamitrinib and clinically validated BH3-mimetics; Suppl. fig. 3: Carcinoma cells of different origin are sensitive to the combination treatment of Gamitrinib and clinically validated BH3-mimetics Suppl. fig. 4: The combination treatment of either broad or selective BH3-mimetics with mitochondrial matrix chaperone inhibitors elicits enhanced apoptosis Suppl. fig. 5: The combination treatment of selective BH3-mimetics, ABT199, WEHI-539, A-1210477 with Gamitrinib-TPP elicits enhanced apoptosis Suppl. fig. 6: Selective BH3-mimetics elicit enhanced loss of mitochondrial membrane potential in the presence of Gamitrinib-TPP in a cell-type dependent manner Suppl. fig. 7: The pan-BH3-mimetic GX15-070 and Gamitrinib induce enhanced apoptotic cell death in glioblastoma cells Suppl. fig. 8: Gamitrinib elicits an endoplasmic reticulum stress signature at the level of transcription. Suppl. fig. 9: Knockdown of Usp9X and Mcl-1 is sufficient to sensitize melanoma and glioblastoma cells to the cytotoxic effects of ABT263 Suppl. fig. 10: Suppression of Noxa counteracts Gamitrinib-mediated suppression of Usp9X and Mcl-1 Suppl. fig. 11: Organ toxicity analysis of mice treated with ABT263 and G-TPP Suppl. fig. 12: The combination treatment of Gamitrinib-TPP and ABT263 leads to a reduction in tumor growth in an orthotopic model of triple-receptor negative breast cancer Table S1: Consolidated representation of qualitative combined anti-proliferative effects of G-TPP (G) and ABT263 (A) or GX15-070 (GX) on different cancer cells. Table S2: ABT263 or GX15-070 treatment yields a synergistic antiproliferative effect on U251, GBM6 and GBM39 glioma cells in the presence of G-TPP. Table S3: Consolidated representation of qualitative combined anti-proliferative effects of G-TPP and ABT263 on WC62, MeWo and COLO 829 malignant melanoma cells. Table S4: Consolidated representation of qualitative combined anti-proliferative effects of G-TPP and the selective Bcl-xL inhibitor WEHI-539, the selective Bcl-2 inhibitor ABT199 and the selective Mcl-1 inhibitor A1210477 on U87MG, LN229 and T98G established glioblastoma cells as well as GBM6 primary cultured glioblastoma cells
Table S1 from The Damaging Effect of Passenger Mutations on Cancer Progression
Authors: McFarland Christopher D. , Yaglom Julia A. , Wojtkowiak Jonathan W. , Scott Jacob G. , Morse David L. , Sherman Michael Y. , Mirny Leonid A.
Published: April 2023

Table S1 - Summary of Mutagenized MCF-10A cell lines in this study
S-Figure-1 from Gemcitabine and Chk1 Inhibitor AZD7762 Synergistically Suppress the Growth of Lkb1-Deficient Lung Adenocarcinoma
Authors: Liu Yan , Li Yuyang , Wang Xiaoen , Liu Feiyang , Gao Peng , Quinn Max M. , Li Fei , Merlino Ashley A. , Benes Cyril , Liu Qingsong , Gray Nathanael S. , Wong Kwok-Kin
Published: April 2023

Lkb1-null and shRNA library synthetic lethal genetic screen identified Chek1 as a putative candidate
Supplementary Tables S1 and S2 from Characterization of MK-4166, a Clinical Agonistic Antibody That Targets Human GITR and Inhibits the Generation and Suppressive Effects of T Regulatory Cells
Authors: Sukumar Selvakumar , Wilson Douglas C. , Yu Ying , Wong Jerelyn , Naravula Saraswathi , Ermakov Grigori , Riener Romina , Bhagwat Bhagyashree , Necheva Antoaneta S. , Grein Jeff , Churakova Tatyana , Mangadu Ruban , Georgiev Peter , Manfra Denise , Pinheiro Elaine M. , Sriram Venkataraman , Bailey Wendy J. , Herzyk Danuta , McClanahan Terrill K. , Willingham Aarron , Beebe Amy M. , Sadekova Svetlana
Published: April 2023

Supplementary tables listing the affinities and bioactivities of MK-4166 and DTA-1.
Supplementary Methods from Characterization of MK-4166, a Clinical Agonistic Antibody That Targets Human GITR and Inhibits the Generation and Suppressive Effects of T Regulatory Cells
Authors: Sukumar Selvakumar , Wilson Douglas C. , Yu Ying , Wong Jerelyn , Naravula Saraswathi , Ermakov Grigori , Riener Romina , Bhagwat Bhagyashree , Necheva Antoaneta S. , Grein Jeff , Churakova Tatyana , Mangadu Ruban , Georgiev Peter , Manfra Denise , Pinheiro Elaine M. , Sriram Venkataraman , Bailey Wendy J. , Herzyk Danuta , McClanahan Terrill K. , Willingham Aarron , Beebe Amy M. , Sadekova Svetlana
Published: April 2023

This file contains supplementary methods that describe the antibodies used, the generation and characterization of MK-4166, various cell-based assays, and the evaluation of toxicity in cynomolgus monkeys.
Table S5. from Posttranscriptional Upregulation of IDH1 by HuR Establishes a Powerful Survival Phenotype in Pancreatic Cancer Cells
Authors: Zarei Mahsa , Lal Shruti , Parker Seth J. , Nevler Avinoam , Vaziri-Gohar Ali , Dukleska Katerina , Mambelli-Lisboa Nicole C. , Moffat Cynthia , Blanco Fernando F. , Chand Saswati N. , Jimbo Masaya , Cozzitorto Joseph A. , Jiang Wei , Yeo Charles J. , Londin Eric R. , Seifert Erin L. , Metallo Christian M. , Brody Jonathan R. , Winter Jordan M.
Published: April 2023

Table S5: Results of RNA sequencing in PDA cell lines (HS-766T and MiaPaCa2) with each modulated by CRISPR/Cas9 to delete HuR expression.
Supplementary Table S3 from Castration Resistance in Prostate Cancer Is Mediated by the Kinase NEK6
Authors: Choudhury Atish D. , Schinzel Anna C. , Cotter Maura B. , Lis Rosina T. , Labella Katherine , Lock Ying Jie , Izzo Francesca , Guney Isil , Bowden Michaela , Li Yvonne Y. , Patel Jinal , Hartman Emily , Carr Steven A. , Schenone Monica , Jaffe Jacob D. , Kantoff Philip W. , Hammerman Peter S. , Hahn William C.
Published: April 2023

GO terms for NEK6 upregulated genes Day 5 after castration (filtered for >10 GeneHits).
Supplementary Figures S1-S6 from Castration Resistance in Prostate Cancer Is Mediated by the Kinase NEK6
Authors: Choudhury Atish D. , Schinzel Anna C. , Cotter Maura B. , Lis Rosina T. , Labella Katherine , Lock Ying Jie , Izzo Francesca , Guney Isil , Bowden Michaela , Li Yvonne Y. , Patel Jinal , Hartman Emily , Carr Steven A. , Schenone Monica , Jaffe Jacob D. , Kantoff Philip W. , Hammerman Peter S. , Hahn William C.
Published: April 2023

Androgen-independent tumor formation mediated by NEK6 requires its kinase activity and is not affected by AR silencing (S1); Immunohistochemistry of NEK6 in LHSR-AR xenografts and in human primary prostate cancers (S2); NEK6 does not increase androgen receptor transcriptional activity in LNCaP cells or LHSR-AR cells in vitro (S3); NEK6 overexpression does not increase levels of nuclear beta-catenin in vivo, nor phosphorylation of putative substrates p70S6K and STAT3 (S4); NEK6 overexpression does not lead to promotion of cell cycle progression or antagonism of the p53 pathway in LHSR-AR cells (S5); NEK6 overexpression leads to increased expression of keratin 13 after castration in vivo (S6).
Supplementary Figure Legends from Castration Resistance in Prostate Cancer Is Mediated by the Kinase NEK6
Authors: Choudhury Atish D. , Schinzel Anna C. , Cotter Maura B. , Lis Rosina T. , Labella Katherine , Lock Ying Jie , Izzo Francesca , Guney Isil , Bowden Michaela , Li Yvonne Y. , Patel Jinal , Hartman Emily , Carr Steven A. , Schenone Monica , Jaffe Jacob D. , Kantoff Philip W. , Hammerman Peter S. , Hahn William C.
Published: April 2023

Legend for Supplemental Figures S1-S6.
supplemental figure s1 from Epstein–Barr Virus-Induced VEGF and GM-CSF Drive Nasopharyngeal Carcinoma Metastasis via Recruitment and Activation of Macrophages
Authors: Huang Di , Song Shi-Jian , Wu Zi-Zhao , Wu Wei , Cui Xiu-Ying , Chen Jia-Ning , Zeng Mu-Sheng , Su Shi-Cheng
Published: April 2023

Figure S1 related to Figure 1. TAM infiltration and their CCL18 expression are correlated with EBV infection and poor survival in NPC patients.
Figure S3 from Nicotinic Acid Phosphoribosyltransferase Regulates Cancer Cell Metabolism, Susceptibility to NAMPT Inhibitors, and DNA Repair
Authors: Piacente Francesco , Caffa Irene , Ravera Silvia , Sociali Giovanna , Passalacqua Mario , Vellone Valerio G. , Becherini Pamela , Reverberi Daniele , Monacelli Fiammetta , Ballestrero Alberto , Odetti Patrizio , Cagnetta Antonia , Cea Michele , Nahimana Aimable , Duchosal Michel , Bruzzone Santina , Nencioni Alessio
Published: April 2023

Figure S3 shows that NAPRT silencing sensitizes pancreatic and ovarian cancer cells to FK866.
Table S3 from Competition between DNA Methylation, Nucleotide Synthesis, and Antioxidation in Cancer versus Normal Tissues
Authors: Cao Sha , Zhu Xiwen , Zhang Chi , Qian Hong , Schuttler Heinz-Bernd , Gong Jianping , Xu Ying
Published: April 2023

Detailed rate functions for each reaction.
Figures S1, S2 from Competition between DNA Methylation, Nucleotide Synthesis, and Antioxidation in Cancer versus Normal Tissues
Authors: Cao Sha , Zhu Xiwen , Zhang Chi , Qian Hong , Schuttler Heinz-Bernd , Gong Jianping , Xu Ying
Published: April 2023

Figure S1: DNA methylation levels comparisons between tumor and normal tissues; Figure S2: Differential expressions of involved genes.
Supplemental Figure 1 from KLF6 Suppresses Metastasis of Clear Cell Renal Cell Carcinoma via Transcriptional Repression of E2F1
Authors: Gao Yu , Li Hongzhao , Ma Xin , Fan Yang , Ni Dong , Zhang Yu , Huang Qingbo , Liu Kan , Li Xintao , Wang Lei , Gu Liangyou , Yao Yuanxin , Ai Qing , Du Qingshan , Song Erlin , Zhang Xu
Published: April 2023

CpG island of the KLF6 locus was predicted in plot and the primers were designed.
Supplementary Figure S2. from Cancer-Associated Fibroblasts Share Characteristics and Protumorigenic Activity with Mesenchymal Stromal Cells
Authors: Borriello Lucia , Nakata Rie , Sheard Michael A. , Fernandez G. Esteban , Sposto Richard , Malvar Jemily , Blavier Laurence , Shimada Hiroyuki , Asgharzadeh Shahab , Seeger Robert C. , DeClerck Yves A.
Published: April 2023

CAF isolated from patients with NB share characteristics with MSC.
Supplementary Figures S1 through S28 from Early Effector T Lymphocytes Coexpress Multiple Inhibitory Receptors in Primary Non–Small Cell Lung Cancer
Authors: Tassi Elena , Grazia Giulia , Vegetti Claudia , Bersani Ilaria , Bertolini Giulia , Molla Alessandra , Baldassari Paola , Andriani Francesca , Roz Luca , Sozzi Gabriella , Pastorino Ugo , Mortarini Roberta , Anichini Andrea
Published: April 2023

This file contains 28 Supplementary Figures dealing with: frequency of T cell subsets in tumor and non neoplastic lung tissue (S1), activation and naive to memory profile of T cells at tumor site (S2), functional competence of T cells at tumor site (S3), frequency of PD-1+ T cells in tumor according to clinical stage and patients' survival according to PD-1+ T cell frequency in tumor (S4), Ki-67 vs eomes profile of PD-1+ T cells (S5), expression of Eomes in distinct T cell subsets at tumor site (S6), PD-1 modulation and IFN-g production in PD-1(lo) and PD-1(Hi) T cell subsets (S7), functional competence of T cell subsets according to IRs profile (S8), immunohistochemistry for CD8+FOXP3+ T cells at tumor site (S9-S12), immune profile by immunohistochemistry of lesions containing high frequency of CD8+FOXP3+ T cells (S13-S23), frequency of CD8+FOXP3+ cells at tumor site according to clinical parameters (S24), relationship of CD8+FOXP3+ cells with clinical stage and patients' survival (S25), maturation profile of CD8+FOXP3+ cells (S26), IRs expression and competence for differentiation of CD8+FOXP3+ cells (S27), co-expression of activation/proliferation markers in different T cell subsets at tumor site (S28)
Table S1and Table S2 from Tumor-Associated Macrophages Promote Malignant Progression of Breast Phyllodes Tumors by Inducing Myofibroblast Differentiation
Authors: Nie Yan , Chen Jianing , Huang Di , Yao Yandan , Chen Jiewen , Ding Lin , Zeng Jiayi , Su Shicheng , Chao Xue , Su Fengxi , Yao Herui , Hu Hai , Song Erwei
Published: April 2023

Table S1described correlations of CCL18 expressing with clinicopathological status in 268 cases of patients with breast PTs; Table S2 described Multivariate Cox proportional hazard analysis of LRFS in 268 patients with breast PTs
Figure S4 from Immune-Related Gene Expression Profiling After PD-1 Blockade in Non–Small Cell Lung Carcinoma, Head and Neck Squamous Cell Carcinoma, and Melanoma
Authors: Prat Aleix , Navarro Alejandro , Paré Laia , Reguart Noemí , Galván Patricia , Pascual Tomás , Martínez Alex , Nuciforo Paolo , Comerma Laura , Alos Llucia , Pardo Nuria , Cedrés Susana , Fan Cheng , Parker Joel S. , Gaba Lydia , Victoria Iván , Viñolas Nuria , Vivancos Ana , Arance Ana , Felip Enriqueta
Published: April 2023

Correlation between gene expression (y-axis) and tumor PDL1 IHC (x-axis).
Figure S6 from Tumor-Associated Macrophages Promote Malignant Progression of Breast Phyllodes Tumors by Inducing Myofibroblast Differentiation
Authors: Nie Yan , Chen Jianing , Huang Di , Yao Yandan , Chen Jiewen , Ding Lin , Zeng Jiayi , Su Shicheng , Chao Xue , Su Fengxi , Yao Herui , Hu Hai , Song Erwei
Published: April 2023

M-CSF and the aggressive PT cells activate the peritoneal macrophages to M2 macrophages in nude mice.
Figure S4 from Glucose Catabolism in Liver Tumors Induced by c-MYC Can Be Sustained by Various PKM1/PKM2 Ratios and Pyruvate Kinase Activities
Authors: Méndez-Lucas Andrés , Li Xiaolei , Hu Junjie , Che Li , Song Xinhua , Jia Jiaoyuan , Wang Jingxiao , Xie Chencheng , Driscoll Paul C. , Tschaharganeh Darjus F. , Calvisi Diego F. , Yuneva Mariia , Chen Xin
Published: April 2023

Study design
Figure S3 from Glucose Catabolism in Liver Tumors Induced by c-MYC Can Be Sustained by Various PKM1/PKM2 Ratios and Pyruvate Kinase Activities
Authors: Méndez-Lucas Andrés , Li Xiaolei , Hu Junjie , Che Li , Song Xinhua , Jia Jiaoyuan , Wang Jingxiao , Xie Chencheng , Driscoll Paul C. , Tschaharganeh Darjus F. , Calvisi Diego F. , Yuneva Mariia , Chen Xin
Published: April 2023

shPKM.1 and shPKM.2 efficiently silenced PKM1 and PKM2 expression in cells
Supplemental Figure from Trastuzumab Increases HER2 Uptake and Cross-Presentation by Dendritic Cells
Authors: Gall Victor A. , Philips Anne V. , Qiao Na , Clise-Dwyer Karen , Perakis Alexander A. , Zhang Mao , Clifton Guy T. , Sukhumalchandra Pariya , Ma Qing , Reddy Sangeetha M. , Yu Dihua , Molldrem Jeffrey J. , Peoples George E. , Alatrash Gheath , Mittendorf Elizabeth A.
Published: April 2023

SKBR3 breast cancer cells shed HER2 after treatment with chemotherapy or irradiation.
Supplementary Methods and Figure Legends from Systematic Drug Screening Identifies Tractable Targeted Combination Therapies in Triple-Negative Breast Cancer
Authors: Wali Vikram B. , Langdon Casey G. , Held Matthew A. , Platt James T. , Patwardhan Gauri A. , Safonov Anton , Aktas Bilge , Pusztai Lajos , Stern David F. , Hatzis Christos
Published: April 2023

Revised Supplementary Methods and Legends
Supplemental Table S1 from Next-Generation Sequencing in the Clinical Setting Clarifies Patient Characteristics and Potential Actionability
Authors: Bieg-Bourne Cheyennedra C. , Millis Sherri Z. , Piccioni David E. , Fanta Paul T. , Goldberg Michael E. , Chmielecki Juliann , Parker Barbara A. , Kurzrock Razelle
Published: April 2023

Supplemental Table S1 displays the Foundation Medicine 236 gene panel.
Figures S1-S4 from Loss of Igf2 Gene Imprinting in Murine Prostate Promotes Widespread Neoplastic Growth
Authors: Damaschke Nathan A. , Yang Bing , Bhusari Sachin , Avilla Mele , Zhong Weixiong , Blute Michael L. , Huang Wei , Jarrard David F.
Published: April 2023

This contains supplementary figures 1-4. Figure S1 displays H19 mRNA expression quantification and bodyweight measurements of additional phenotypes in the study. The data relates to Figure 1. Figure S2 contains additional IHC measurements for experimental mice for p-ERK and p-AKT. Figure S2 also contains apoptosis quantification data by TUNEL assay. These data relate to Figure 4 of the main text. Figure S2 also conatains mRNA expression measurements of proliferation related genes, related to Figure 5. Figure S3 conatains characterization data of Insulin receptor isoform expression and Igf1-receptor expression in experimental mouse prostates. Figure S4 contains additional data pertaining to human prostate IHC for IGF2, pERK, and pAKT expression, including correlation of these markers in prostate cancer and the average levels in various prostate tissue pathologies. This figure is related to Figure 5 of the main text.
Legends to Supplementary Figures from CD73 Promotes Resistance to HER2/ErbB2 Antibody Therapy
Authors: Turcotte Martin , Allard David , Mittal Deepak , Bareche Yacine , Buisseret Laurence , José Vinu , Pommey Sandra , Delisle Vincent , Loi Sherene , Joensuu Heikki , Kellokumpu-Lehtinen Pirkko-Liisa , Sotiriou Christos , Smyth Mark J. , Stagg John
Published: April 2023

Legends to Supplementary Figures
Supplemental Figure 4 from Sigma1 Targeting to Suppress Aberrant Androgen Receptor Signaling in Prostate Cancer
Authors: Thomas Jeffrey D. , Longen Charles G. , Oyer Halley M. , Chen Nan , Maher Christina M. , Salvino Joseph M. , Kania Blase , Anderson Kelsey N. , Ostrander William F. , Knudsen Karen E. , Kim Felix J.
Published: April 2023

Nuclear hormone receptors that are not eliminated by small molecule Sigma1 inhibitor (IPAG).
Supplemental Figure S2 from Bone-Induced Expression of Integrin β3 Enables Targeted Nanotherapy of Breast Cancer Metastases
Authors: Ross Michael H. , Esser Alison K. , Fox Gregory C. , Schmieder Anne H. , Yang Xiaoxia , Hu Grace , Pan Dipanjan , Su Xinming , Xu Yalin , Novack Deborah V. , Walsh Thomas , Colditz Graham A. , Lukaszewicz Gabriel H. , Cordell Elizabeth , Novack Joshua , Fitzpatrick James A. J. , Waning David L. , Mohammad Khalid S. , Guise Theresa A. , Lanza Gregory M. , Weilbaecher Katherine N.
Published: April 2023

Integrin subunit mRNA expression by breast cancer cells grown in vitro
Supplementary Figure S4. HuR regulates PARG protein expression and function and not of other PAR removing enzymes from Posttranscriptional Regulation of PARG mRNA by HuR Facilitates DNA Repair and Resistance to PARP Inhibitors
Authors: Chand Saswati N. , Zarei Mahsa , Schiewer Matthew J. , Kamath Akshay R. , Romeo Carmella , Lal Shruti , Cozzitorto Joseph A. , Nevler Avinoam , Scolaro Laura , Londin Eric , Jiang Wei , Meisner-Kober Nicole , Pishvaian Michael J. , Knudsen Karen E. , Yeo Charles J. , Pascal John M. , Winter Jordan M. , Brody Jonathan R.
Published: April 2023

HuR silencing results in downregulation of PARG expression, which prevents efficient removal of PAR polymers with or without PARPi stress. Expression and function of other PAR removing enzymes is not affected with HuR silencing.
Viewing SNP in IGV from Variant Review with the Integrative Genomics Viewer
Authors: Robinson James T. , Thorvaldsdóttir Helga , Wenger Aaron M. , Zehir Ahmet , Mesirov Jill P.
Published: April 2023

Video 1. Annotated screencast of using IGV.
Figure S1 from A Convolutional Neural Network Uses Microscopic Images to Differentiate between Mouse and Human Cell Lines and Their Radioresistant Clones
Authors: Toratani Masayasu , Konno Masamitsu , Asai Ayumu , Koseki Jun , Kawamoto Koichi , Tamari Keisuke , Li Zhihao , Sakai Daisuke , Kudo Toshihiro , Satoh Taroh , Sato Katsutoshi , Motooka Daisuke , Okuzaki Daisuke , Doki Yuichiro , Mori Masaki , Ogawa Kazuhiko , Ishii Hideshi
Published: April 2023

Figure S1
Supplementary Methods from Gemcitabine-Induced TIMP1 Attenuates Therapy Response and Promotes Tumor Growth and Liver Metastasis in Pancreatic Cancer
Authors: D'Costa Zenobia , Jones Keaton , Azad Abul , van Stiphout Ruud , Lim Su Y. , Gomes Ana L. , Kinchesh Paul , Smart Sean C. , Gillies McKenna W. , Buffa Francesca M. , Sansom Owen J. , Muschel Ruth J. , O'Neill Eric , Fokas Emmanouil
Published: April 2023

Supplementary Methods including MRI imaging, immunofluorescence, Western blot, flow
Video 2 from Optical Coherence Tomography Detects Necrotic Regions and Volumetrically Quantifies Multicellular Tumor Spheroids
Authors: Huang Yongyang , Wang Shunqiang , Guo Qiongyu , Kessel Sarah , Rubinoff Ian , Chan Leo Li-Ying , Li Peter , Liu Yaling , Qiu Jean , Zhou Chao
Published: April 2023

3D rendering of a HCT 116 tumor spheroid over 21 days.
Figure S2 from Downregulation of Membrane Trafficking Proteins and Lactate Conditioning Determine Loss of Dendritic Cell Function in Lung Cancer
Authors: Caronni Nicoletta , Simoncello Francesca , Stafetta Francesca , Guarnaccia Corrado , Ruiz-Moreno Juan Sebastian , Opitz Bastian , Galli Thierry , Proux-Gillardeaux Veronique , Benvenuti Federica
Published: April 2023

TCM-induced suppression of DC innate functions is not dependent on inflammatory pathways or anti-inflammatory cytokines
Supplementary video 3 from A Novel Small-Molecule Inhibitor of MRCK Prevents Radiation-Driven Invasion in Glioblastoma
Authors: Birch Joanna L. , Strathdee Karen , Gilmour Lesley , Vallatos Antoine , McDonald Laura , Kouzeli Ariadni , Vasan Richa , Qaisi Abdulrahman Hussain , Croft Daniel R. , Crighton Diane , Gill Kathryn , Gray Christopher H. , Konczal Jennifer , Mezna Mokdad , McArthur Duncan , Schüttelkopf Alexander W. , McConnell Patricia , Sime Mairi , Holmes William M. , Bower Justin , McKinnon Heather J. , Drysdale Martin , Olson Michael F. , Chalmers Anthony J.
Published: April 2023

Subconfluent migration assay in the presence of DMSO
Supplementary Figures S1-S8 from Comprehensive Phenotypic Characterization of Human Invasive Lobular Carcinoma Cell Lines in 2D and 3D Cultures
Authors: Tasdemir Nilgun , Bossart Emily A. , Li Zheqi , Zhu Li , Sikora Matthew J. , Levine Kevin M. , Jacobsen Britta M. , Tseng George C. , Davidson Nancy E. , Oesterreich Steffi
Published: April 2023

Figure S1. Human ILC cell lines do not form robust mammospheres. Figure S2. p120 and E-cadherin co-immunofluorescence staining in ILC and IDC cells. Figure S3. Human ILC cell lines do not form robust mammospheres. Figure S4. Higher Collagen deposition in human ILC versus IDC tumors. Figure S5. Adhesion of human ILC and IDC cell lines to different ECM proteins. Figure S6. Overexpression of PIK3CA mutants and PTEN knockdown in MDA-MB-134 cells activate downstream PI3K/Akt signaling but do not enhance cell migration. Figure S7. Human ILC cell lines do not exhibit substantial invasion of non-crosslinked Collagen I in transwell Boyden chamber assays. Figure S8. Differentially expressed genes between human ILC and IDC cell lines and tumors.
Supplementary figure legends from A Novel Small-Molecule Inhibitor of MRCK Prevents Radiation-Driven Invasion in Glioblastoma
Authors: Birch Joanna L. , Strathdee Karen , Gilmour Lesley , Vallatos Antoine , McDonald Laura , Kouzeli Ariadni , Vasan Richa , Qaisi Abdulrahman Hussain , Croft Daniel R. , Crighton Diane , Gill Kathryn , Gray Christopher H. , Konczal Jennifer , Mezna Mokdad , McArthur Duncan , Schüttelkopf Alexander W. , McConnell Patricia , Sime Mairi , Holmes William M. , Bower Justin , McKinnon Heather J. , Drysdale Martin , Olson Michael F. , Chalmers Anthony J.
Published: April 2023

Supplemental figure legends
Suppl Table 2 from CANCERTOOL: A Visualization and Representation Interface to Exploit Cancer Datasets
Authors: Cortazar Ana R. , Torrano Veronica , Martín-Martín Natalia , Caro-Maldonado Alfredo , Camacho Laura , Hermanova Ivana , Guruceaga Elizabeth , Lorenzo-Martín Luis F. , Caloto Ruben , Gomis Roger R. , Apaolaza Iñigo , Quesada Victor , Trka Jan , Gomez-Muñoz Antonio , Vincent Silvestre , Bustelo Xose R. , Planes Francisco J. , Aransay Ana M. , Carracedo Arkaitz
Published: April 2023

Suppl Table 2
Supplementary Tables (word) from Whole-Genome Sequencing Reveals Elevated Tumor Mutational Burden and Initiating Driver Mutations in African Men with Treatment-Naïve, High-Risk Prostate Cancer
Authors: Jaratlerdsiri Weerachai , Chan Eva K.F. , Gong Tingting , Petersen Desiree C. , Kalsbeek Anton M.F. , Venter Philip A. , Stricker Phillip D. , Bornman M.S. Riana , Hayes Vanessa M.
Published: April 2023

Supplementary Tables as a word document including: Supplementary Table S1. Clinical presentation, sequencing statistics and genomic variation. Supplementary Table S2. Mitochondrial DNA genotypes and their frequency across six African patients between McCrow et al. (2016) and this study. Supplementary Table S3. Sequencing library statistics for tumor and blood samples. Supplementary Table S4. Total number and impact of small somatic variations in primary prostate cancer from African men. Supplementary Table S8. Prostate cancer risk alleles observed within the SAPCS cohort. Supplementary Table S12. Transposable elements and other repeats observed within acquired duplication events of UP2133. Supplementary Table S13. Genes impacted by a single chromoplexic event in UP2133 tumor.
Video 2 from Long Noncoding RNA CRYBG3 Blocks Cytokinesis by Directly Binding G-Actin
Authors: Pei Hailong , Hu Wentao , Guo Ziyang , Chen Huaiyuan , Ma Ji , Mao Weidong , Li Bingyan , Wang Aiqing , Wan Jianmei , Zhang Jian , Nie Jing , Zhou Guangming , Hei Tom K.
Published: April 2023

Using a live cell imaging system showed cytokinesis and cell movement after overexpress of LNC CRYBG3.
Supplemental Figure S7 from Therapeutically Active RIG-I Agonist Induces Immunogenic Tumor Cell Killing in Breast Cancers
Authors: Elion David L. , Jacobson Max E. , Hicks Donna J. , Rahman Bushra , Sanchez Violeta , Gonzales-Ericsson Paula I. , Fedorova Olga , Pyle Anna M. , Wilson John T. , Cook Rebecca S.
Published: April 2023

Cells were transfected, and after 16 h, total RNA was assessed by RT-qPCR to measure expression of the indicated gene.. Each point represents the average of three experimental replicates, N = 3. Midlines are average {plus minus} S.D. Student's T-test.
Supplemental Figure S5 from Therapeutically Active RIG-I Agonist Induces Immunogenic Tumor Cell Killing in Breast Cancers
Authors: Elion David L. , Jacobson Max E. , Hicks Donna J. , Rahman Bushra , Sanchez Violeta , Gonzales-Ericsson Paula I. , Fedorova Olga , Pyle Anna M. , Wilson John T. , Cook Rebecca S.
Published: April 2023

Immunohistochemistry was used to measure CD45, F4,80, CD4, and CD8 in tumors harvested at day 5. Representative Images are shown. N = 5
Supplemental Figure S1 from Therapeutically Active RIG-I Agonist Induces Immunogenic Tumor Cell Killing in Breast Cancers
Authors: Elion David L. , Jacobson Max E. , Hicks Donna J. , Rahman Bushra , Sanchez Violeta , Gonzales-Ericsson Paula I. , Fedorova Olga , Pyle Anna M. , Wilson John T. , Cook Rebecca S.
Published: April 2023

A. METABRIC-curated clinical dataset of invasive breast cancers (N = 817, Ref. here) was assessed for samples harboring genomic loss (solid blue boxes) or mRNA down-regulation (defined as < -2 S.D. from the mean DDX58 expression among the entire dataset, and shown in blue outline). B. A lollipop graph was used to show the relative positioning of DDX58 missense mutations found in a TCGA-curated clinical dataset of invasive breast tumors (N = 817). No recurrent mutations were identified.
Figure S2 from Plk1-Mediated Phosphorylation of TSC1 Enhances the Efficacy of Rapamycin
Authors: Li Zhiguo , Kong Yifan , Song Longzhen , Luo Qian , Liu Jinghui , Shao Chen , Hou Xianzeng , Liu Xiaoqi
Published: April 2023

TSC1 hyper-phosphorylation is dependent on Cdk1 and Plk1
Figure S4 from YAP1-Mediated Suppression of USP31 Enhances NFκB Activity to Promote Sarcomagenesis
Authors: Ye Shuai , Lawlor Matthew A. , Rivera-Reyes Adrian , Egolf Shaun , Chor Susan , Pak Koreana , Ciotti Gabrielle E. , Lee Avery C. , Marino Gloria E. , Shah Jennifer , Niedzwicki David , Weber Kristy , Park Paul M.C. , Alam Md. Zahidul , Grazioli Alison , Haldar Malay , Xu Mousheng , Perry Jennifer A. , Qi Jun , Eisinger-Mathason T.S. Karin
Published: April 2023

The role of myc in UPS and the effects of SAHA/JQ1 on YAP1 levels in sarcoma cell lines
Figure S1 from YAP1-Mediated Suppression of USP31 Enhances NFκB Activity to Promote Sarcomagenesis
Authors: Ye Shuai , Lawlor Matthew A. , Rivera-Reyes Adrian , Egolf Shaun , Chor Susan , Pak Koreana , Ciotti Gabrielle E. , Lee Avery C. , Marino Gloria E. , Shah Jennifer , Niedzwicki David , Weber Kristy , Park Paul M.C. , Alam Md. Zahidul , Grazioli Alison , Haldar Malay , Xu Mousheng , Perry Jennifer A. , Qi Jun , Eisinger-Mathason T.S. Karin
Published: April 2023

Supplemental patient information from tissue microarray and additional quantitations.
Supplementary data from Modulation of Macropinocytosis-Mediated Internalization Decreases Ocular Toxicity of Antibody–Drug Conjugates
Authors: Zhao Hui , Atkinson John , Gulesserian Sara , Zeng Zhilan , Nater Jenny , Ou Jimmy , Yang Peng , Morrison Karen , Coleman Jeffrey , Malik Faisal , Challita-Eid Pia , Karki Sher , Aviña Hector , Hubert René , Capo Linnette , Snyder Josh , Moon Sung-Ju , Luethy Roland , Mendelsohn Brian A. , Stover David R. , Doñate Fernando
Published: April 2023

Supplemental tables 1-5: Table 1: Characteristics of peptide modified ADCs tested and IC50 in the HCEC and KU812 assays. Table 2: Characteristics. of PEG modified ADCs tested and data in the HCEC and KU812 assays. Table 3: Characteristics of mutated ADCs tested in the HCEC and KU812 cytotoxicity assays. Table 4: Pharmacokinetic parameters in mice and rabbits. ADC and Tab. Table 5: Body gain weight of rabbits treated with AGS-16C3F and other ADCs. Supplemental Materials and Methods Summplemental Figure Legends Supplemental figures 1-4: Fig S1: Lack of ENPP3 expression in corneas from humans and cynomolgus monkeys. Fig S2: Characterization of human corneal epithelial cells (HCEC). Fig S3: Target expression in HCEC and normal corneal epithelial cells by microarray analysis. Fig S4: Binding of AGS-16C3F to primary cells. References
Figure S5 from Semaphorin 7A Promotes Macrophage-Mediated Lymphatic Remodeling during Postpartum Mammary Gland Involution and in Breast Cancer
Authors: Elder Alan M. , Tamburini Beth A.J. , Crump Lyndsey S. , Black Sarah A. , Wessells Veronica M. , Schedin Pepper J. , Borges Virginia F. , Lyons Traci R.
Published: April 2023

Additional information regarding SEMA7A, CD68, and PDPN expression levels in normal vs cancer
Table S2 from Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism
Authors: Lopes-Ramos Camila M. , Kuijjer Marieke L. , Ogino Shuji , Fuchs Charles S. , DeMeo Dawn L. , Glass Kimberly , Quackenbush John
Published: April 2023

Pathways differentially targeted between male and female colon cancer regulatory networks in the discovery and validation datasets.
Figure S2 from Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism
Authors: Lopes-Ramos Camila M. , Kuijjer Marieke L. , Ogino Shuji , Fuchs Charles S. , DeMeo Dawn L. , Glass Kimberly , Quackenbush John
Published: April 2023

Overall survival analysis based on chemotherapy treatment.
Table S2 from The Canonical Wnt Pathway Drives Macropinocytosis in Cancer
Authors: Redelman-Sidi Gil , Binyamin Anna , Gaeta Isabella , Palm Wilhelm , Thompson Craig B. , Romesser Paul B. , Lowe Scott W. , Bagul Mukta , Doench John G. , Root David E. , Glickman Michael S.
Published: April 2023

Table S2: A Whole-genome shRNA screen for inhibitors of macropinocytosis
Supplementary Data from CBP Modulates Sensitivity to Dasatinib in Pre-BCR+ Acute Lymphoblastic Leukemia
Authors: Duque-Afonso Jesús , Lin Chiou-Hong , Han Kyuho , Morgens David W. , Jeng Edwin E. , Weng Ziming , Jeong Johan , Wong Stephen Hon Kit , Zhu Li , Wei Michael C. , Chae Hee-Don , Schrappe Martin , Cario Gunnar , Duyster Justus , Xiao Xiangshu , Sakamoto Kathleen M. , Bassik Michael C. , Cleary Michael L.
Published: April 2023

Unbiased shRNA library screening and global transcriptome analyses reveal mechanisms that modulate dasatinib sensitivity and suggest therapeutic strategies to improve outcome of patients with acute lymphoblastic leukemia.
Supplementary Figures 6-8 from Extracorporeal Photochemotherapy Drives Monocyte-to-Dendritic Cell Maturation to Induce Anticancer Immunity
Authors: Ventura Alessandra , Vassall Aaron , Robinson Eve , Filler Renata , Hanlon Douglas , Meeth Katrina , Ezaldein Harib , Girardi Michael , Sobolev Olga , Bosenberg Marcus W. , Edelson Richard L.
Published: April 2023

Additional data for Figures 4, 5, and 6, respectively, showing representative tumor growth volumes, for review and publication
Supplementary Data from PHF5A Epigenetically Inhibits Apoptosis to Promote Breast Cancer Progression
Authors: Zheng Yi-Zi , Xue Meng-Zhu , Shen Hong-Jie , Li Xiao-Guang , Ma Ding , Gong Yue , Liu Yi-Rong , Qiao Feng , Xie Hong-Yan , Lian Bi , Sun Wei-Li , Zhao Hai-Yun , Yao Ling , Zuo Wen-Jia , Li Da-Qiang , Wang Peng , Hu Xin , Shao Zhi-Ming
Published: April 2023

Fig. S1. RNA-seq based RBP Library construction and CRISPR screen reveals RBP hits related to tumor growth and metastasis. Fig. S2. PHF5A is frequently up-regulated in breast cancer, associated with poor clinical outcome, and essential for cancer cell proliferation and migration. Fig. S3. PHF5A associates with the U2 snRNP complex and regulates complex stability. Fig. S4. PHF5A globally regulates splicing. Fig. S5. The PHD-like domain in PHF5A is required for its association with Histone H3. Fig. S6 PHF5A regulates FASTK splicing to antagonize apoptotic signaling in breast cancer cells. Table S1. Clinicopathologic Variables in 40 Cases of TNBC Patients. Table S2. Primers Used in RT-PCR and qPCR Analyses. Table S3. Gene List of a Census of 1,542 Manually Curated RBPs and 159 Library Contained RBPs. Table S4. sgRNA Sequence of Genes in RBP library. Table S5. RIGER Ranking of Screen Hits. Table S6. Correlation between Clinicopathologic Variables and Expression of PHF5A in 373 Cases of Breast Cancer. Table S7. Univariate and Multivariate Analysis of DFS. Table S8. Univariate and Multivariate Analysis of DFS in TNBC Subgroup.
Figure S2 from Loss of MED12 Induces Tumor Dormancy in Human Epithelial Ovarian Cancer via Downregulation of EGFR
Authors: Luo Xiao-Lin , Deng Cheng-Cheng , Su Xiao-Dong , Wang Fang , Chen Zhen , Wu Xing-Ping , Liang Shao-Bo , Liu Ji-Hong , Fu Li-Wu
Published: April 2023

Dormancy induced by MED12 KO is involved in down-regulating EGFR.
Figure S2 from Pharmacologic Ascorbate Reduces Radiation-Induced Normal Tissue Toxicity and Enhances Tumor Radiosensitization in Pancreatic Cancer
Authors: Alexander Matthew S. , Wilkes Justin G. , Schroeder Samuel R. , Buettner Garry R. , Wagner Brett A. , Du Juan , Gibson-Corley Katherine , O’Leary Brianne R. , Spitz Douglas R. , Buatti John M. , Berg Daniel J. , Bodeker Kellie L. , Vollstedt Sandy , Brown Heather A. , Allen Bryan G. , Cullen Joseph J.
Published: April 2023

Plasma ascorbate concentrations.
Figure S2 from Targeting CCR8 Induces Protective Antitumor Immunity and Enhances Vaccine-Induced Responses in Colon Cancer
Authors: Villarreal Daniel O. , L'Huillier Andrew , Armington Susan , Mottershead Cristina , Filippova Elena V. , Coder Brandon D. , Petit Robert G. , Princiotta Michael F.
Published: April 2023

The frequency of peripheral Tregs in tumor-bearing αCCR8-treated mice and the effects of αCCR8 on ex vivo tumor CD8+ and CD4+ T cells.
Table S4 from Reduced Expression of PROX1 Transitions Glioblastoma Cells into a Mesenchymal Gene Expression Subtype
Authors: Goudarzi Kaveh M. , Espinoza Jaime A. , Guo Min , Bartek Jiri , Nistér Monica , Lindström Mikael S. , Hägerstrand Daniel
Published: April 2023

Intersect of PROX1 correlated genes from different datasets
Table S1 from Reduced Expression of PROX1 Transitions Glioblastoma Cells into a Mesenchymal Gene Expression Subtype
Authors: Goudarzi Kaveh M. , Espinoza Jaime A. , Guo Min , Bartek Jiri , Nistér Monica , Lindström Mikael S. , Hägerstrand Daniel
Published: April 2023

STR data for U-343 cell lines and subclones
Supplementary Figure Legends S1-S4 from A2AR Adenosine Signaling Suppresses Natural Killer Cell Maturation in the Tumor Microenvironment
Authors: Young Arabella , Ngiow Shin Foong , Gao Yulong , Patch Ann-Marie , Barkauskas Deborah S. , Messaoudene Meriem , Lin Gene , Coudert Jerome D. , Stannard Kimberley A. , Zitvogel Laurence , Degli-Esposti Mariapia A. , Vivier Eric , Waddell Nicola , Linden Joel , Huntington Nicholas D. , Souza-Fonseca-Guimaraes Fernando , Smyth Mark J.
Published: April 2023

Figure S1. Liver ILC1s express high levels of adenosine-related molecules. Figure S2. A2AR-deficient NK cells display enhanced competitive proliferation. Figure S3. NK cell specific deletion of the A2AR provides improved proliferative capacity. Figure S4. Tumor-infiltrating leukocytes from NK cell specific A2AR deletion.
Supplementary Table S1 from Targeting STAT5 or STAT5-Regulated Pathways Suppresses Leukemogenesis of Ph+ Acute Lymphoblastic Leukemia
Authors: Minieri Valentina , De Dominici Marco , Porazzi Patrizia , Mariani Samanta A. , Spinelli Orietta , Rambaldi Alessandro , Peterson Luke F. , Porcu Pierluigi , Nevalainen Marja T. , Calabretta Bruno
Published: April 2023

Primary human Ph+ ALL samples
Supplementary Figures from Cotargeting BCL-2 and PI3K Induces BAX-Dependent Mitochondrial Apoptosis in AML Cells
Authors: Rahmani Mohamed , Nkwocha Jewel , Hawkins Elisa , Pei Xinyan , Parker Rebecca E. , Kmieciak Maciej , Leverson Joel D. , Sampath Deepak , Ferreira-Gonzalez Andrea , Grant Steven
Published: April 2023

Supplementary Figures S1: Activity of combined treatment with venetoclax and GDC-0980 in human AML cells. Supplementary Figures S1: Synergistic interaction between venetoclax and GDC-0980 using median dose effect analysis. Supplementary Figures S3: Effects of venetoclax/GDC-0980 on PI3K/AKT/mTOR pathway activity and BCL-2 members expression. Supplementary Figure S4: Mutation analysis of primary AML specimens using targeted next-generation sequencing. Supplementary Figure S5. Combined treatment with venetoclax/GDC-0980 or taselisib exhibits potent in vivo anti-AML activity without significant toxicity Supplementary Figure S6. BIM is not required for BAX activation by venetoclax or venetoclax/GDC-0980, and Mcl-1 downregulation plays a significant functional role in venetoclax/GDC-0980 lethality. Supplementary Figure S7. Mitochondrial BAX translocation in venetoclax-resistant MV4-11 cells following combined treatment
Supplementary Tables from Amplification of Glyceronephosphate O-Acyltransferase and Recruitment of USP30 Stabilize DRP1 to Promote Hepatocarcinogenesis
Authors: Gu Li , Zhu Yahui , Lin Xi , Li Yajun , Cui Kaisa , Prochownik Edward V. , Li Youjun
Published: April 2023

Supplementary Table S1 lists antibodies used for Western blot, co-immunoprecipitation and chromatin immunoprecipitation used in this study. Supplementary Table S2 lists sequences of primers used for quantification of gene expression changes, gene cloning, chromatin immunoprecipitation, sequences used for shRNA mediated gene silence and CRISPR/Cas9 mediated knockout in this study.
Supplementary Figure legends from Emerin Deregulation Links Nuclear Shape Instability to Metastatic Potential
Authors: Reis-Sobreiro Mariana , Chen Jie-Fu , Novitskaya Tatiana , You Sungyong , Morley Samantha , Steadman Kenneth , Gill Navjot Kaur , Eskaros Adel , Rotinen Mirja , Chu Chia-Yi , Chung Leland W.K. , Tanaka Hisashi , Yang Wei , Knudsen Beatrice S. , Tseng Hsian-Rong , Rowat Amy C. , Posadas Edwin M. , Zijlstra Andries , Di Vizio Dolores , Freeman Michael R.
Published: April 2023

Emerin deregulation links nuclear shape instability to metastatic potential
Table S1, Table S2, and Supplementary Note from Analysis of Over 140,000 European Descendants Identifies Genetically Predicted Blood Protein Biomarkers Associated with Prostate Cancer Risk
Authors: Wu Lang , Shu Xiang , Bao Jiandong , Guo Xingyi , Kote-Jarai Zsofia , Haiman Christopher A. , Eeles Rosalind A. , Zheng Wei
Published: April 2023

Table S1, Table S2, and Supplementary Note, which includes PIs from the PRACTICAL, CRUK, BPC3, CAPS, PEGASUS consortia, and Funding Acknowledgements
Table S7, Table S8, Table S9 from Transcriptomic Differences between Primary Colorectal Adenocarcinomas and Distant Metastases Reveal Metastatic Colorectal Cancer Subtypes
Authors: Kamal Yasmin , Schmit Stephanie L. , Hoehn Hannah J. , Amos Christopher I. , Frost H. Robert
Published: April 2023

Table S7. Pathway enrichment differences between CRC primary tumors and metastases (lung and liver) in the MCC and Consortium datasets after adjusting for age, sex, treatment exposure status, and anatomical origin in the tissue sensitive setting: Hallmark and C2 Collections. Table S8. Top 500 differentially expressed genes between CRC primary tumors and metastases (liver and lung) in the tissue sensitive setting for the MCC and Consortium datasets while adjusting for age, sex, anatomical origin, and treatment exposure status in the tissue sensitive setting. We also computed a Fischer's meta-analysis for the top 500 genes enriched in both the MCC and Consortium datasets. Table S9. Pathway enrichment differences between CRC primary tumors and metastases (liver and lung) while adjusting for microsatellite instability (MSI) status in the MCC dataset in the tissue sensitive setting: Hallmark and C2 Collections.
Supplementary Methods, Figure S1, Figure S2, Figure S3, Figure S4, Figure S5, Figure S6, Figure S7, Figure S8 from Transcriptomic Differences between Primary Colorectal Adenocarcinomas and Distant Metastases Reveal Metastatic Colorectal Cancer Subtypes
Authors: Kamal Yasmin , Schmit Stephanie L. , Hoehn Hannah J. , Amos Christopher I. , Frost H. Robert
Published: April 2023

A detailed description of the MCC and TCC Consortium Cohorts is provided, along with an extended description of the gene-level and pathway-level tissue sensitive analysis. Figure S1-S8 are also contained in this file.
Supplementary Tables from Inhibition of Thioredoxin/Thioredoxin Reductase Induces Synthetic Lethality in Lung Cancers with Compromised Glutathione Homeostasis
Authors: Yan Xiang , Zhang Xiaoshan , Wang Li , Zhang Ran , Pu Xingxiang , Wu Shuhong , Li Lei , Tong Pan , Wang Jing , Meng Qing H. , Jensen Vanessa B. , Girard Luc , Minna John D. , Roth Jack A. , Swisher Stephen G. , Heymach John V. , Fang Bingliang
Published: April 2023

Table S1 shows IC50 of auranofin in 129 lung cancer cell lines. Table S2 shows correlations of auranofin activity and gene expression levels (based 76 cell lines whose mRNA levels were available). Table S3 shows co-expressions of GSR with other genes (data obtained from cBioportal.org)
Supplementary Figure S10-19 from ROCK Inhibition Induces Terminal Adipocyte Differentiation and Suppresses Tumorigenesis in Chemoresistant Osteosarcoma Cells
Authors: Takahashi Nobuhiro , Nobusue Hiroyuki , Shimizu Takatsune , Sugihara Eiji , Yamaguchi-Iwai Sayaka , Onishi Nobuyuki , Kunitomi Haruko , Kuroda Tatsuo , Saya Hideyuki
Published: April 2023

Supplementary Fig. S10 Knockdown of either ROCK1 or ROCK2 alone induces terminal adipocyte differentiation and growth suppression of AO cells. Supplementary Fig. S11 Effect of chemical agents that induce depolymerization of the actin cytoskeleton on terminal adipocyte differentiation in AO cells. Supplementary Fig. S12 Immunohistochemical staining for MKL1 in an array of human osteosarcoma specimens. Supplementary Fig. S13 Effects of induction of a constitutively active mutant of MKL1 on the expression of MKL1 target genes in AO cells. Supplementary Fig. S14 Effects of fasudil treatment in mice injected with AO cells. Supplementary Fig. S15 Effect of fasudil treatment on terminal adipocyte differentiation in heterogeneous osteosarcoma cells. Supplementary Fig. S16 Effects of sequential treatment with doxorubicin and fasudil in heterogeneous osteosarcoma cells in vitro. Supplementary Fig. S17 Effects of sequential treatment with doxorubicin and fasudil in mice injected with heterogeneous osteosarcoma cells. Fig. S18 Osteogenic potential of AO and AX cells. Fig. S19 Effects of fasudil on the antiproliferative action of clinically administrated anticancer agents in AO cells.
Supplementary Figure Legends from ROCK Inhibition Induces Terminal Adipocyte Differentiation and Suppresses Tumorigenesis in Chemoresistant Osteosarcoma Cells
Authors: Takahashi Nobuhiro , Nobusue Hiroyuki , Shimizu Takatsune , Sugihara Eiji , Yamaguchi-Iwai Sayaka , Onishi Nobuyuki , Kunitomi Haruko , Kuroda Tatsuo , Saya Hideyuki
Published: April 2023

Supplementary Figure Legends
Supplementary Figure S1-7 from ME1 Regulates NADPH Homeostasis to Promote Gastric Cancer Growth and Metastasis
Authors: Lu Yun-Xin , Ju Huai-Qiang , Liu Ze-Xian , Chen Dong-Liang , Wang Yun , Zhao Qi , Wu Qi-Nian , Zeng Zhao-lei , Qiu Hai-Bo , Hu Pei-Shan , Wang Zhi-Qiang , Zhang Dong-Sheng , Wang Feng , Xu Rui-Hua
Published: April 2023

Supplementary Figure S1. SMAD4 and ME2 copy number are frequently altered in human malignancies. Supplementary Figure S2. ME1 maintains cell survival during glucose deprivation. Supplementary Figure S3. Effects of ME1 on epithelial mesenchymal transition in gastric cancer. Supplementary Figure S4. Simultaneous knockdown of ME1 and ME2 in HGC27 cells significantly suppressed tumor growth in vivo. Supplementary Figure S5. Immunoblots show increased ME1 and decreased ME2 expression in the tumor tissues compared with corresponding normal tissues of PDX models. Supplementary Figure S6. ETV4 regulates ME1 expression in gastric cancer. Supplementary Figure S7. Clinical significance of ETV4/ME1 axis in gastric cancer.
Supplementary Data File 2 from Integrative Pharmacogenomics Analysis of Patient-Derived Xenografts
Authors: Mer Arvind S. , Ba-Alawi Wail , Smirnov Petr , Wang Yi X. , Brew Ben , Ortmann Janosch , Tsao Ming-Sound , Cescon David W. , Goldenberg Anna , Haibe-Kains Benjamin
Published: April 2023

Intra-class correlation coefficient (ICC) values for genes across all samples and stratified by tissue type.
Figure S2 from CBP/p300 Drives the Differentiation of Regulatory T Cells through Transcriptional and Non-Transcriptional Mechanisms
Authors: Castillo Joseph , Wu Esther , Lowe Christopher , Srinivasan Shrividhya , McCord Ron , Wagle Marie-Claire , Jayakar Sangeeta , Edick Melissa Gonzalez , Eastham-Anderson Jeffrey , Liu Bonnie , Hutchinson Katherine E. , Jones Wendell , Stokes Matthew P. , Tarighat Somayeh S. , Holcomb Thomas , Glibicky Andrew , Romero F. Anthony , Magnuson Steven , Huang Shih-Min A. , Plaks Vicki , Giltnane Jennifer M. , Lackner Mark R. , Mounir Zineb
Published: April 2023

Supplementary figure 2 shows supportive naïve T cell transcriptional profiling data and additional supportive TF analyses.
Figure S2 from Remodeling the Tumor Microenvironment Sensitizes Breast Tumors to Anti-Programmed Death-Ligand 1 Immunotherapy
Authors: Clift Renee , Souratha Jennifer , Garrovillo Sheryl A. , Zimmerman Susan , Blouw Barbara
Published: April 2023

Immune cell composition in 4T1 and 4T1/HAS3 orthotopic breast tumors