bluuebunny/crossref_metadata_2025 huggingface dataset:
Table S1 from Delta-Like Ligand–Notch1 Signaling Is Selectively Modulated by HPV16 E6 to Promote Squamous Cell Proliferation and Correlates with Cervical Cancer Prognosis
Authors: Khelil Maryam , Griffin Heather , Bleeker Maaike C.G. , Steenbergen Renske D.M. , Zheng Ke , Saunders-Wood Taylor , Samuels Sanne , Rotman Jossie , Vos Wim , van den Akker Brendy E. , de Menezes Renée X. , Kenter Gemma G. , Doorbar John , Jordanova Ekaterina S.
Published: April 2023

Clinicopathological characteristics of molecular cervical cancer subgroups (TCGA)
Figure S2 from Delta-Like Ligand–Notch1 Signaling Is Selectively Modulated by HPV16 E6 to Promote Squamous Cell Proliferation and Correlates with Cervical Cancer Prognosis
Authors: Khelil Maryam , Griffin Heather , Bleeker Maaike C.G. , Steenbergen Renske D.M. , Zheng Ke , Saunders-Wood Taylor , Samuels Sanne , Rotman Jossie , Vos Wim , van den Akker Brendy E. , de Menezes Renée X. , Kenter Gemma G. , Doorbar John , Jordanova Ekaterina S.
Published: April 2023

Immunostaining of DLL4 and N1ICD in NIKS monolayers and/or organotypic rafts.
Supplementary Table S1 from Lipidomic Profiling of Clinical Prostate Cancer Reveals Targetable Alterations in Membrane Lipid Composition
Authors: Butler Lisa M. , Mah Chui Yan , Machiels Jelle , Vincent Andrew D. , Irani Swati , Mutuku Shadrack M. , Spotbeen Xander , Bagadi Muralidhararao , Waltregny David , Moldovan Max , Dehairs Jonas , Vanderhoydonc Frank , Bloch Katarzyna , Das Rajdeep , Stahl Jurgen , Kench James G. , Gevaert Thomas , Derua Rita , Waelkens Etienne , Nassar Zeyad D. , Selth Luke A. , Trim Paul J. , Snel Marten F. , Lynn David J. , Tilley Wayne D. , Horvath Lisa G. , Centenera Margaret M. , Swinnen Johannes V.
Published: April 2023

Patient and sample clinical characteristics
Supplementary Figures S1-S6 from Lipidomic Profiling of Clinical Prostate Cancer Reveals Targetable Alterations in Membrane Lipid Composition
Authors: Butler Lisa M. , Mah Chui Yan , Machiels Jelle , Vincent Andrew D. , Irani Swati , Mutuku Shadrack M. , Spotbeen Xander , Bagadi Muralidhararao , Waltregny David , Moldovan Max , Dehairs Jonas , Vanderhoydonc Frank , Bloch Katarzyna , Das Rajdeep , Stahl Jurgen , Kench James G. , Gevaert Thomas , Derua Rita , Waelkens Etienne , Nassar Zeyad D. , Selth Luke A. , Trim Paul J. , Snel Marten F. , Lynn David J. , Tilley Wayne D. , Horvath Lisa G. , Centenera Margaret M. , Swinnen Johannes V.
Published: April 2023

Supplementary Figures S1-S6
Tables S2 from Multilevel Regulation of β-Catenin Activity by SETD2 Suppresses the Transition from Polycystic Kidney Disease to Clear Cell Renal Cell Carcinoma
Authors: Rao Hanyu , Li Xiaoxue , Liu Min , Liu Jing , Feng Wenxin , Tang Huayuan , Xu Jin , Gao Wei-Qiang , Li Li
Published: April 2023

The information of the ChIP-seq peaks.
Supplementary Figures, Table, and File Captions from Premalignant Oligodendrocyte Precursor Cells Stall in a Heterogeneous State of Replication Stress Prior to Gliomagenesis
Authors: Sutcliffe Matthew D. , Galvao Rui P. , Wang Lixin , Kim Jungeun , Rosenfeld Lauren K. , Singh Shambhavi , Zong Hui , Janes Kevin A.
Published: April 2023

Supplementary Figures S1-S15, Supplementary Table S1, and captions for Supplementary Files S1-S3.
Figure S1 from Multilevel Regulation of β-Catenin Activity by SETD2 Suppresses the Transition from Polycystic Kidney Disease to Clear Cell Renal Cell Carcinoma
Authors: Rao Hanyu , Li Xiaoxue , Liu Min , Liu Jing , Feng Wenxin , Tang Huayuan , Xu Jin , Gao Wei-Qiang , Li Li
Published: April 2023

Delete SETD2 and overexpress c-MYC in tubular epithelial cells using a transgenic Ksp1.3/Cre mouse line.
Supplementary Tables 1-2 from Endothelial Reprogramming Stimulated by Oncostatin M Promotes Inflammation and Tumorigenesis in VHL-Deficient Kidney Tissue
Authors: Nguyen-Tran Hieu-Huy , Nguyen Thi-Ngoc , Chen Chen-Yun , Hsu Tien
Published: April 2023

Supplementary Tables
Supplementary Data from ELOVL5 Is a Critical and Targetable Fatty Acid Elongase in Prostate Cancer
Authors: Centenera Margaret M. , Scott Julia S. , Machiels Jelle , Nassar Zeyad D. , Miller Deanna C. , Zinonos Irene , Dehairs Jonas , Burvenich Ingrid J.G. , Zadra Giorgia , Chetta Paolo M. , Bango Clyde , Evergren Emma , Ryan Natalie K. , Gillis Joanna L. , Mah Chui Yan , Tieu Terence , Hanson Adrienne R. , Carelli Ryan , Bloch Katarzyna , Panagopoulos Vasilios , Waelkens Etienne , Derua Rita , Williams Elizabeth D. , Evdokiou Andreas , Cifuentes-Rius Anna , Voelcker Nicolas H. , Mills Ian G. , Tilley Wayne D. , Scott Andrew M. , Loda Massimo , Selth Luke A. , Swinnen Johannes V. , Butler Lisa M.
Published: April 2023

Supplementary figures 1-9 and legends.
Figures S1-S8 from Endothelial Reprogramming Stimulated by Oncostatin M Promotes Inflammation and Tumorigenesis in VHL-Deficient Kidney Tissue
Authors: Nguyen-Tran Hieu-Huy , Nguyen Thi-Ngoc , Chen Chen-Yun , Hsu Tien
Published: April 2023

Supplementary Figures
Table S8 from Single-Cell RNA Sequencing Reveals the Cellular Origin and Evolution of Breast Cancer in BRCA1 Mutation Carriers
Authors: Hu Li , Su Liming , Cheng Hainan , Mo Chunling , Ouyang Tao , Li Jinfeng , Wang Tianfeng , Fan Zhaoqing , Fan Tie , Lin Benyao , Zhang Jianguang , Xie Yuntao
Published: April 2023

Table S8. Somatic mutations detected in the tumor tissues from the four BRCA1 mutation carriers by whole-exome sequencing.
Supplementary Table 1 from Targeting Notch Inhibitors to the Myeloma Bone Marrow Niche Decreases Tumor Growth and Bone Destruction without Gut Toxicity
Authors: Sabol Hayley M. , Ferrari Adam J. , Adhikari Manish , Amorim Tânia , McAndrews Kevin , Anderson Judith , Vigolo Michele , Lehal Rajwinder , Cregor Meloney , Khan Sharmin , Cuevas Pedro L. , Helms Jill A. , Kurihara Noriyoshi , Srinivasan Venkat , Ebetino Frank H. , Boeckman Robert K. , Roodman G. David , Bellido Teresita , Delgado-Calle Jesus
Published: April 2023

Supplementary Table 1
Supplementary Data from HDAC5 Loss Impairs RB Repression of Pro-Oncogenic Genes and Confers CDK4/6 Inhibitor Resistance in Cancer
Authors: Zhou Yingke , Jin Xin , Ma Jian , Ding Donglin , Huang Zhenlin , Sheng Haoyue , Yan Yuqian , Pan Yunqian , Wei Ting , Wang Liguo , Wu Heshui , Huang Haojie
Published: April 2023

The file includes: â€¢ Supplementary Materials and Methods â€¢ Supplementary References â€¢ Supplementary Table S1. Sequence of gene specific shRNAs â€¢ Supplementary Table S2. Sequence of primers for RT-qPCR and ChIP-qPCR â€¢ Supplementary Table S3. Information of antibodies â€¢ Supplementary Table S4. Information of chemicals â€¢ Supplementary Table S5. Information of cell lines and recombinant DNA â€¢ Supplementary Table S6. QC metrics of RNA-seq data â€¢ Supplementary Table S7. Basic characteristics of ChIP-seq data â€¢ Supplementary Table S8. Top 20 enriched pathways identified by GSEA analysis â€¢ Supplementary Fig. S1. Expression of HDAC family members in the TCGA PRAD database and the effect of HDAC4 and HDAC5 dual inhibitor on PCa cell sensitivity to Palbociclib â€¢ Supplementary Fig. S2. The effect of HDAC5 deficiency on breast cancer cell sensitivity to Palbociclib â€¢ Supplementary Fig. S3. CDK4/6 phosphorylation of RB on S249/T252 impedes RB-N interaction with HDAC5 â€¢ Supplementary Fig. S4. CDK2 phosphorylation of RB on T821 dampens RB-C interaction with HDAC5 â€¢ Supplementary Fig. S5. HDAC5 is essential for Palbociclib-induced deacetylation on H3K27 â€¢ Supplementary Fig. S6. RB-HDAC5 regulate H3K27-ac in an E2F1 dependent manner
Table S2 from SHP2-Mediated Inhibition of DNA Repair Contributes to cGAS–STING Activation and Chemotherapeutic Sensitivity in Colon Cancer
Authors: Wei Bin , Xu Lingyan , Guo Wenjie , Wang Yuanyuan , Wu Jingjing , Li Xiaofei , Cai Xiaomin , Hu Jinbo , Wang Meijing , Xu Qiang , Liu Wen , Gu Yanhong
Published: April 2023

SHP2 interacting proteins pulled down by SHP2 IP/mass spectrometry from HCT-116 cell line exposure CPT-11.
Table S1 from SHP2-Mediated Inhibition of DNA Repair Contributes to cGAS–STING Activation and Chemotherapeutic Sensitivity in Colon Cancer
Authors: Wei Bin , Xu Lingyan , Guo Wenjie , Wang Yuanyuan , Wu Jingjing , Li Xiaofei , Cai Xiaomin , Hu Jinbo , Wang Meijing , Xu Qiang , Liu Wen , Gu Yanhong
Published: April 2023

Primers used for qPCR.
Supplementary Data from Ferroptosis Inducers Are a Novel Therapeutic Approach for Advanced Prostate Cancer
Authors: Ghoochani Ali , Hsu En-Chi , Aslan Merve , Rice Meghan A. , Nguyen Holly M. , Brooks James D. , Corey Eva , Paulmurugan Ramasamy , Stoyanova Tanya
Published: April 2023

Supplementary Figures and Supplementary Figure Legends 1-4
Supplementary Table S2 from AMBRA1 Promotes TGFβ Signaling via Nonproteolytic Polyubiquitylation of Smad4
Authors: Liu Jinquan , Yuan Bo , Cao Jin , Luo Hongjie , Gu Shuchen , Zhang Mengdi , Ding Ran , Zhang Long , Zhou Fangfang , Hung Mien-Chie , Xu Pinglong , Lin Xia , Jin Jianping , Feng Xin-Hua
Published: April 2023

Table S2-RT-qPCR primers used in this study
Supplementary movie 3 from Serine-Threonine Kinase TAO3-Mediated Trafficking of Endosomes Containing the Invadopodia Scaffold TKS5α Promotes Cancer Invasion and Tumor Growth
Authors: Iizuka Shinji , Quintavalle Manuela , Navarro Jose C. , Gribbin Kyle P. , Ardecky Robert J. , Abelman Matthew M. , Ma Chen-Ting , Sergienko Eduard , Zeng Fu-Yue , Pass Ian , Thomas George V. , McWeeney Shannon K. , Hassig Christian A. , Pinkerton Anthony B. , Courtneidge Sara A.
Published: April 2023

Effect of SBI-581 on Rab11 vesicle trafficking
Supplementary Figure S2 from AMBRA1 Promotes TGFβ Signaling via Nonproteolytic Polyubiquitylation of Smad4
Authors: Liu Jinquan , Yuan Bo , Cao Jin , Luo Hongjie , Gu Shuchen , Zhang Mengdi , Ding Ran , Zhang Long , Zhou Fangfang , Hung Mien-Chie , Xu Pinglong , Lin Xia , Jin Jianping , Feng Xin-Hua
Published: April 2023

AMBRA1 promotes TGF-β signaling dependent of its ubiquitin ligase activity.
Supplementary Figure S1 from AMBRA1 Promotes TGFβ Signaling via Nonproteolytic Polyubiquitylation of Smad4
Authors: Liu Jinquan , Yuan Bo , Cao Jin , Luo Hongjie , Gu Shuchen , Zhang Mengdi , Ding Ran , Zhang Long , Zhou Fangfang , Hung Mien-Chie , Xu Pinglong , Lin Xia , Jin Jianping , Feng Xin-Hua
Published: April 2023

Identification of AMBRA1 as a positive regulator of TGF-β signaling.
Supplementary Data File S7 from Targeting the HuR Oncogenic Role with a New Class of Cytoplasmic Dimerization Inhibitors
Authors: Filippova Natalia , Yang Xiuhua , Ananthan Subramaniam , Calano Jennifer , Pathak Vibha , Bratton Larry , Vekariya Rakesh H. , Zhang Sixue , Ofori Edward , Hayward Emily N. , Namkoong David , Crossman David K. , Crowley Michael R. , King Peter H. , Mobley James , Nabors Louis B.
Published: April 2023

File (individual enrichment gene plots) provides enrichment gene plots at a high resolution for a summary of the gene ontology enrichment analysis illustrated in Fig. 6.
Supplementary Data File S6 from Targeting the HuR Oncogenic Role with a New Class of Cytoplasmic Dimerization Inhibitors
Authors: Filippova Natalia , Yang Xiuhua , Ananthan Subramaniam , Calano Jennifer , Pathak Vibha , Bratton Larry , Vekariya Rakesh H. , Zhang Sixue , Ofori Edward , Hayward Emily N. , Namkoong David , Crossman David K. , Crowley Michael R. , King Peter H. , Mobley James , Nabors Louis B.
Published: April 2023

File (tmp-LBN-Report_PH-DMPK-UAB-19-001_SRI-42127 _Mouse IP Plasma Brain PK) provides pharmacokinetic data for Fig. S14.
Supplementary Table from Autocrine GMCSF Signaling Contributes to Growth of HER2+ Breast Leptomeningeal Carcinomatosis
Authors: Ansari Khairul I. , Bhan Arunoday , Saotome Mika , Tyagi Antariksh , De Kumar Bony , Chen Clara , Takaku Motoki , Jandial Rahul
Published: April 2023

Supplementary Table from Autocrine GMCSF Signaling Contributes to Growth of HER2+ Breast Leptomeningeal Carcinomatosis
Supplementary Figure from Autocrine GMCSF Signaling Contributes to Growth of HER2+ Breast Leptomeningeal Carcinomatosis
Authors: Ansari Khairul I. , Bhan Arunoday , Saotome Mika , Tyagi Antariksh , De Kumar Bony , Chen Clara , Takaku Motoki , Jandial Rahul
Published: April 2023

Supplementary Figure from Autocrine GMCSF Signaling Contributes to Growth of HER2+ Breast Leptomeningeal Carcinomatosis
Supplementary Figure S7 from α1-Acid Glycoprotein Enhances the Immunosuppressive and Protumor Functions of Tumor-Associated Macrophages
Authors: Matsusaka Kotaro , Fujiwara Yukio , Pan Cheng , Esumi Shigeyuki , Saito Yoichi , Bi Jing , Nakamura Yuka , Mukunoki Ayumi , Takeo Toru , Nakagata Naomi , Yoshii Daiki , Fukuda Ryo , Nagasaki Taisei , Tanaka Ryusei , Komori Hisakazu , Maeda Hitoshi , Watanabe Hiroshi , Tamada Koji , Komohara Yoshihiro , Maruyama Toru
Published: April 2023

Effect of macrophage depletion on tumor development in AGP-treated tumor-bearing mouse model. AGP (2 mg/mouse) was administered to LM8 bearing C3H HeN mice treated with clodronate liposome to deplete macrophages, followed by the determination of subcutaneous tumor weights (A) (n=10 mice per group). Iba-1-positive cells in LM8 subcutaneous tumor tissues were evaluated by immunostaining (B). Statistical differences between groups were calculated by non-repeated-measures ANOVA.
Supplementary Data from Light at Night and Risk of Pancreatic Cancer in the NIH-AARP Diet and Health Study
Authors: Xiao Qian , Jones Rena R. , James Peter , Stolzenberg-Solomon Rachael Z.
Published: April 2023

Suppl Tables
Figure S7 from Metabolic Enzyme DLST Promotes Tumor Aggression and Reveals a Vulnerability to OXPHOS Inhibition in High-Risk Neuroblastoma
Authors: Anderson Nicole M. , Qin Xiaodan , Finan Jennifer M. , Lam Andrew , Athoe Jacob , Missiaen Rindert , Skuli Nicolas , Kennedy Annie , Saini Amandeep S. , Tao Ting , Zhu Shizhen , Nissim Itzhak , Look A. Thomas , Qing Guoliang , Simon M. Celeste , Feng Hui
Published: April 2023

Sup. Figure 7
Figure S4 from Metabolic Enzyme DLST Promotes Tumor Aggression and Reveals a Vulnerability to OXPHOS Inhibition in High-Risk Neuroblastoma
Authors: Anderson Nicole M. , Qin Xiaodan , Finan Jennifer M. , Lam Andrew , Athoe Jacob , Missiaen Rindert , Skuli Nicolas , Kennedy Annie , Saini Amandeep S. , Tao Ting , Zhu Shizhen , Nissim Itzhak , Look A. Thomas , Qing Guoliang , Simon M. Celeste , Feng Hui
Published: April 2023

Sup. Figure 4
Figure S3 from Metabolic Enzyme DLST Promotes Tumor Aggression and Reveals a Vulnerability to OXPHOS Inhibition in High-Risk Neuroblastoma
Authors: Anderson Nicole M. , Qin Xiaodan , Finan Jennifer M. , Lam Andrew , Athoe Jacob , Missiaen Rindert , Skuli Nicolas , Kennedy Annie , Saini Amandeep S. , Tao Ting , Zhu Shizhen , Nissim Itzhak , Look A. Thomas , Qing Guoliang , Simon M. Celeste , Feng Hui
Published: April 2023

Sup. Figure 3
Figure S4 from Targeting c-Myc to Overcome Acquired Resistance of EGFR Mutant NSCLC Cells to the Third-Generation EGFR Tyrosine Kinase Inhibitor, Osimertinib
Authors: Zhu Lei , Chen Zhen , Zang Hongjing , Fan Songqing , Gu Jiajia , Zhang Guojing , Sun Kevin D.-Y. , Wang Qiming , He Yong , Owonikoko Taofeek K. , Ramalingam Suresh S. , Sun Shi-Yong
Published: April 2023

Mouse body weight changes in tumors exposed to osimertinib.
Figure S3 from Targeting c-Myc to Overcome Acquired Resistance of EGFR Mutant NSCLC Cells to the Third-Generation EGFR Tyrosine Kinase Inhibitor, Osimertinib
Authors: Zhu Lei , Chen Zhen , Zang Hongjing , Fan Songqing , Gu Jiajia , Zhang Guojing , Sun Kevin D.-Y. , Wang Qiming , He Yong , Owonikoko Taofeek K. , Ramalingam Suresh S. , Sun Shi-Yong
Published: April 2023

c-Myc knockdown augments oeimertinib-induced apoptosis in HCC827/AR cells.
Supplementary Data from The Transcription Factor SLUG Uncouples Pancreatic Cancer Progression from the RAF–MEK1/2–ERK1/2 Pathway
Authors: Bilal Faiz , Arenas Enrique J. , Pedersen Kim , Martínez-Sabadell Alex , Nabet Behnam , Guruceaga Elizabeth , Vicent Silvestre , Tabernero Josep , Macarulla Teresa , Arribas Joaquín
Published: April 2023

Supplementary Figures
Supplementary Data from Targeting Epigenetic and Posttranscriptional Gene Regulation by PSF Impairs Hormone Therapy–Refractory Cancer Growth
Authors: Takayama Ken-ichi , Honma Teruki , Suzuki Takashi , Kondoh Yasumitsu , Osada Hiroyuki , Suzuki Yutaka , Yoshida Minoru , Inoue Satoshi
Published: April 2023

Supplementary Methods, Tables, and Figures
Supplementary Movie 2 from Loss-of-Function Mutations in TRAF7 and KLF4 Cooperatively Activate RAS-Like GTPase Signaling and Promote Meningioma Development
Authors: Najm Paul , Zhao Peihua , Steklov Mikhail , Sewduth Raj Nayan , Baietti Maria Francesca , Pandolfi Silvia , Criem Nathan , Lechat Benoit , Maia Teresa Mendes , Van Haver Delphi , Corthout Nikky , Eyckerman Sven , Impens Francis , Sablina Anna A.
Published: April 2023

Supplementary Movie 2
Supplementary table 6 from Inhibition of Jumonji Histone Demethylases Selectively Suppresses HER2+ Breast Leptomeningeal Carcinomatosis Growth via Inhibition of GMCSF Expression
Authors: Bhan Arunoday , Ansari Khairul I. , Chen Mike Y. , Jandial Rahul
Published: April 2023

Supplementary table 6 Quantification of Cytokine array based immunoblots
Supplementary table 5 from Inhibition of Jumonji Histone Demethylases Selectively Suppresses HER2+ Breast Leptomeningeal Carcinomatosis Growth via Inhibition of GMCSF Expression
Authors: Bhan Arunoday , Ansari Khairul I. , Chen Mike Y. , Jandial Rahul
Published: April 2023

Supplementary table 5 DepMap based Cell lines screen
Supplementary Figures 1-7 from Loss-of-Function Mutations in TRAF7 and KLF4 Cooperatively Activate RAS-Like GTPase Signaling and Promote Meningioma Development
Authors: Najm Paul , Zhao Peihua , Steklov Mikhail , Sewduth Raj Nayan , Baietti Maria Francesca , Pandolfi Silvia , Criem Nathan , Lechat Benoit , Maia Teresa Mendes , Van Haver Delphi , Corthout Nikky , Eyckerman Sven , Impens Francis , Sablina Anna A.
Published: April 2023

Supplementary Figures 1-7
Supplementary table 4 from Inhibition of Jumonji Histone Demethylases Selectively Suppresses HER2+ Breast Leptomeningeal Carcinomatosis Growth via Inhibition of GMCSF Expression
Authors: Bhan Arunoday , Ansari Khairul I. , Chen Mike Y. , Jandial Rahul
Published: April 2023

Supplementary table 4 Tumorsphere based chemical screen
Supplementary Data from Inhibition of Jumonji Histone Demethylases Selectively Suppresses HER2+ Breast Leptomeningeal Carcinomatosis Growth via Inhibition of GMCSF Expression
Authors: Bhan Arunoday , Ansari Khairul I. , Chen Mike Y. , Jandial Rahul
Published: April 2023

Supplemental data file 1-14
Supplementary Data from Loss-of-Function Mutations in TRAF7 and KLF4 Cooperatively Activate RAS-Like GTPase Signaling and Promote Meningioma Development
Authors: Najm Paul , Zhao Peihua , Steklov Mikhail , Sewduth Raj Nayan , Baietti Maria Francesca , Pandolfi Silvia , Criem Nathan , Lechat Benoit , Maia Teresa Mendes , Van Haver Delphi , Corthout Nikky , Eyckerman Sven , Impens Francis , Sablina Anna A.
Published: April 2023

Supplementary Material and Methods
Supplementary Table S1 from Genetic Variation and Recurrent Haplotypes on Chromosome 6q23-25 Risk Locus in Familial Lung Cancer
Authors: Musolf Anthony M. , Simpson Claire L. , Moiz Bilal A. , Pikielny Claudio W. , Middlebrooks Candace D. , Mandal Diptasri , de Andrade Mariza , Cole Michael D. , Gaba Colette , Yang Ping , You Ming , Li Yafang , Kupert Elena Y. , Anderson Marshall W. , Schwartz Ann G. , Pinney Susan M. , Amos Christopher I. , Bailey-Wilson Joan E.
Published: April 2023

Details about data set
Supplementary Figure S4 from Genetic Variation and Recurrent Haplotypes on Chromosome 6q23-25 Risk Locus in Familial Lung Cancer
Authors: Musolf Anthony M. , Simpson Claire L. , Moiz Bilal A. , Pikielny Claudio W. , Middlebrooks Candace D. , Mandal Diptasri , de Andrade Mariza , Cole Michael D. , Gaba Colette , Yang Ping , You Ming , Li Yafang , Kupert Elena Y. , Anderson Marshall W. , Schwartz Ann G. , Pinney Susan M. , Amos Christopher I. , Bailey-Wilson Joan E.
Published: April 2023

Supplementary Figure S4: Segregation of potential causal variants in MAP3K4 in families 42 and 44. In both pedigrees, gray symbols represent non-affected individuals (coded as missing in the analysis) and black symbol represent affected individuals. The diagonal slash through the symbol represents a deceased individual and brackets around an individual's ID represents individuals who were sequenced. A) Family 42 pedigree with the two letters underneath the individual ID represents the individual's genotype at rs140997681 (major allele = A, minor allele = G) B) Family 44 pedigree with the two letters underneath the individual ID represents the individual's genotype at rs62435519 (major allele = G, minor allele = C)
Supplementary Figure S3 from Genetic Variation and Recurrent Haplotypes on Chromosome 6q23-25 Risk Locus in Familial Lung Cancer
Authors: Musolf Anthony M. , Simpson Claire L. , Moiz Bilal A. , Pikielny Claudio W. , Middlebrooks Candace D. , Mandal Diptasri , de Andrade Mariza , Cole Michael D. , Gaba Colette , Yang Ping , You Ming , Li Yafang , Kupert Elena Y. , Anderson Marshall W. , Schwartz Ann G. , Pinney Susan M. , Amos Christopher I. , Bailey-Wilson Joan E.
Published: April 2023

Supplementary Figure S3: Segregation of potential causal variants in ARID1B in families 47 and 59. In both pedigrees, gray symbols represent non-affected individuals (coded as missing in the analysis) and black symbol represent affected individuals. The diagonal slash through the symbol represents a deceased individual and brackets around an individual's ID represents individuals who were sequenced. A) Family 47 pedigree with the first two letters underneath the individual ID represents the individual's genotype at rs564982701 (major allele = T, minor allele = C) and the second two letters underneath the individual ID represents the individual's genotype at rs150018283 (major allele = T, minor allele = A). B) Family 59 pedigree with the two letters underneath the individual ID represents the individual's genotype at rs187390535 (major allele = C, minor allele = G)
Supplementary Figure S2 from Genetic Variation and Recurrent Haplotypes on Chromosome 6q23-25 Risk Locus in Familial Lung Cancer
Authors: Musolf Anthony M. , Simpson Claire L. , Moiz Bilal A. , Pikielny Claudio W. , Middlebrooks Candace D. , Mandal Diptasri , de Andrade Mariza , Cole Michael D. , Gaba Colette , Yang Ping , You Ming , Li Yafang , Kupert Elena Y. , Anderson Marshall W. , Schwartz Ann G. , Pinney Susan M. , Amos Christopher I. , Bailey-Wilson Joan E.
Published: April 2023

Supplementary Figure S2: HLOD and LOD Scores across all nine families, family 102 only and family 12 only. A) The HLOD scores across all nine families for the targeted 6q region. B) The family specific LOD scores for family 102. C) The family specific LOD scores for family 12. For family 12, variants were filtered to MAF < 0.01 for noncoding variants and to MAF < 0.03 for coding variants. For all panels, line represents genome-wide suggestive, defined as HLOD {greater than or equal to} 1.9 by Lander and Kruglyak.
Supplementary Table from Inhibition of Granulocytic Myeloid-Derived Suppressor Cells Overcomes Resistance to Immune Checkpoint Inhibition in LKB1-Deficient Non–Small Cell Lung Cancer
Authors: Li Rui , Salehi-Rad Ramin , Crosson William , Momcilovic Milica , Lim Raymond J. , Ong Stephanie L. , Huang Zi Ling , Zhang Tianhao , Abascal Jensen , Dumitras Camelia , Jing Zhe , Park Stacy J. , Krysan Kostyantyn , Shackelford David B. , Tran Linh M. , Liu Bin , Dubinett Steven M.
Published: April 2023

Gene-Specific Primers and Flow Antibodies
Supplementary Figures from Inhibition of Granulocytic Myeloid-Derived Suppressor Cells Overcomes Resistance to Immune Checkpoint Inhibition in LKB1-Deficient Non–Small Cell Lung Cancer
Authors: Li Rui , Salehi-Rad Ramin , Crosson William , Momcilovic Milica , Lim Raymond J. , Ong Stephanie L. , Huang Zi Ling , Zhang Tianhao , Abascal Jensen , Dumitras Camelia , Jing Zhe , Park Stacy J. , Krysan Kostyantyn , Shackelford David B. , Tran Linh M. , Liu Bin , Dubinett Steven M.
Published: April 2023

Supplemental Figures S1-S6
Supplemental Figure 6 from PPARα Agonist Fenofibrate Enhances Cancer Vaccine Efficacy
Authors: Chekaoui Arezki , Ertl Hildegund C.J.
Published: April 2023

The cartoon describes the experimental set-up used to generate the results shown in Figures 4B and 6. Mice were challenged with tumor cells. Three days later they were vaccinated with AdC68-gDMelapoly. Fenofibrate or diluent treatment was started 5 days later and continued daily till day 27. Mice were euthanized ~ 24 hours later to perform the analyses.
Supplementary Data from Epstein–Barr Virus Induces Adipocyte Dedifferentiation to Modulate the Tumor Microenvironment
Authors: Liu Shu-Chen , Tsang Ngan-Ming , Lee Po-Ju , Sui Yun-Hua , Huang Chen-Han , Liu Tzu-Tung
Published: April 2023

Supplementary Figures, Tables, and Methods
Supplemental Figure 1 from PPARα Agonist Fenofibrate Enhances Cancer Vaccine Efficacy
Authors: Chekaoui Arezki , Ertl Hildegund C.J.
Published: April 2023

The cartoon describes the experimental set-up used to generate the results shown in Figure 1. Groups of mice were injected with B16BrafV600E cells. Starting 6 or 8 days later mice were treated daily for 3 weeks with fenofibrate (FF) or diluent. Tumor sizes were recorded over time.
Supplementary Data from Mesenchymal Stem Cell–Secreted Extracellular Vesicles Instruct Stepwise Dedifferentiation of Breast Cancer Cells into Dormancy at the Bone Marrow Perivascular Region
Authors: Sandiford Oleta A. , Donnelly Robert J. , El-Far Markos H. , Burgmeyer Lisa M. , Sinha Garima , Pamarthi Sri Harika , Sherman Lauren S. , Ferrer Alejandra I. , DeVore Dariana E. , Patel Shyam A. , Naaldijk Yahaira , Alonso Sara , Barak Pradeep , Bryan Margarette , Ponzio Nicholas M. , Narayanan Ramaswamy , Etchegaray Jean-Pierre , Kumar Rakesh , Rameshwar Pranela
Published: April 2023

Methods, Supplemental Figs 1-7
Table S1-S5, Figure S1-S12 from Upregulation of FGF9 in Lung Adenocarcinoma Transdifferentiation to Small Cell Lung Cancer
Authors: Ishioka Kota , Yasuda Hiroyuki , Hamamoto Junko , Terai Hideki , Emoto Katsura , Kim Tae-Jung , Hirose Shigemichi , Kamatani Takashi , Mimaki Sachiyo , Arai Daisuke , Ohgino Keiko , Tani Tetsuo , Masuzawa Keita , Manabe Tadashi , Shinozaki Taro , Mitsuishi Akifumi , Ebisudani Toshiki , Fukushima Takahiro , Ozaki Mari , Ikemura Shinnosuke , Kawada Ichiro , Naoki Katsuhiko , Nakamura Morio , Ohtsuka Takashi , Asamura Hisao , Tsuchihara Katsuya , Hayashi Yuichiro , Hegab Ahmed E. , Kobayashi Susumu S. , Kohno Takashi , Watanabe Hideo , Ornitz David M. , Betsuyaku Tomoko , Soejima Kenzo , Fukunaga Koichi
Published: April 2023

Supplementary Table S1. Mutation signature analysis. Supplementary Table S2. Baseline characteristics of the transdifferentiated SCLC patients included in this study. Supplementary Table S3. Intensity of EGFR and Ki67 staining in lung cancer tissues obtained from the indicated patients. Supplementary Table S4. Baseline characteristics of the primary SCLC patients included in this study. Supplementary Table S5. Genetic alterations of the indicated lung cancer cell lines. Supplementary Figure S1. FGF9 immunohistochemistry staining in lung cancer cell lines. Supplementary Figure S2. List of the mutated genes before and after transdifferentiation. Supplementary Figure S3. Gene ontology term analysis in the context of upregulated (A) and downregulated (B) genes. Supplementary Figure S4. Computed tomography images of the patients (Case2-4) during the course of gefitinib therapy. Supplementary Figure S5. EGFR, Ki67 and FGFR1 immunohistochemistry staining of tissues from Cases #5 and #6. Supplementary Figure S6. mRNA expression levels of FGF family genes in lung cancer cell lines. Supplementary Figure S7. Expression of FGF9 and FGF2 in human NSCLC and SCLC cells. Supplementary Figure S8. Functional evaluations of FGF9 in human SCLC cell lines. Supplementary Figure S9. Tumor volumes after MLE12-EGFR transplantation. Supplementary Figure S10. Expression levels of Fgfr family genes in MLE12-FGF9 cells in vitro and in vivo. Supplementary Figure S11. Characteristics of lung adenocarcinoma cell lines. Supplementary Figure S12. In vivo evaluations of FGF9 in H2087 and H2110 cells.
Supplementary Table 2 from Cancer-Associated Fibroblasts Promote Aggressive Gastric Cancer Phenotypes via Heat Shock Factor 1–Mediated Secretion of Extracellular Vesicles
Authors: Grunberg Nil , Pevsner-Fischer Meirav , Goshen-Lago Tal , Diment Judith , Stein Yaniv , Lavon Hagar , Mayer Shimrit , Levi-Galibov Oshrat , Friedman Gil , Ofir-Birin Yifat , Syu Li-Jyun , Migliore Cristina , Shimoni Eyal , Stemmer Salomon M. , Brenner Baruch , Dlugosz Andrzej A. , Lyden David , Regev-Rudzki Neta , Ben-Aharon Irit , Scherz-Shouval Ruth
Published: April 2023

Distances of patient samples in PCA analysis
Supplementary Table 11 from Cancer-Associated Fibroblasts Promote Aggressive Gastric Cancer Phenotypes via Heat Shock Factor 1–Mediated Secretion of Extracellular Vesicles
Authors: Grunberg Nil , Pevsner-Fischer Meirav , Goshen-Lago Tal , Diment Judith , Stein Yaniv , Lavon Hagar , Mayer Shimrit , Levi-Galibov Oshrat , Friedman Gil , Ofir-Birin Yifat , Syu Li-Jyun , Migliore Cristina , Shimoni Eyal , Stemmer Salomon M. , Brenner Baruch , Dlugosz Andrzej A. , Lyden David , Regev-Rudzki Neta , Ben-Aharon Irit , Scherz-Shouval Ruth
Published: April 2023

Patient data and expression levels of genes from the mCAF_up_sig and mCAF_down_sig of triple-transgenic gastric cancer mice
Figure S3 from An AIB1 Isoform Alters Enhancer Access and Enables Progression of Early-Stage Triple-Negative Breast Cancer
Authors: Sharif Ghada M. , Campbell Moray J. , Nasir Apsra , Sengupta Surojeet , Graham Garrett T. , Kushner Max H. , Kietzman William B. , Schmidt Marcel O. , Pearson Gray W. , Loudig Olivier , Fineberg Susan , Wellstein Anton , Riegel Anna T.
Published: April 2023

A) Representative images of hematoxylin and eosin (H&E) staining of MCFDCIS, MCFDCIS-Î"4 and mixed (4:1 respectively) tumors that were injected in the mammary fat pad of SCID/Beige mice after two or five weeks. MCFDCIS-Î"4 tumors were not collected at two weeks due to small tumor size. Scale bar=50Î¼m. B) Growth of subcutaneous tumors of DCIS or DCIS-Î"4-hy in athymic nude mice. n=5. **p<0.01. H&E tumor histology at 3 weeks. Scale bar = 50Î¼m. C) Quantification of P63 and Luciferase (unique to DCIS) co-localization in mixed tumors at 2 and 5 weeks. ROI= 2007x1500um. **p<0.01. D) Representative images and quantification of p63 and CD44 IHC on tumors from S3B. **p<0.01, ***p<0.001. Scale bar = 50Î¼m. E) Bioluminescence images showing lung metastases at 2-3 months. Signal is detected from parental DCIS that harbor the luciferase construct. DCIS-Î"4 cells are luciferase negative. F) qPCR of genomic DNA from the lungs of mice harboring mix tumors. Primers are specific to either the unique region on AIB1 gene that was created by CRISPR editing (CRISPR) or human intronic DNA as a control (Intronic). Mouse intronic DNA was used for normalization. G) Bioluminescence images and graph showing tumor recurrence rate after DCIS or Mix primary tumor removal when they reached an area of ~80mm2. Two million cells were injected in the MFP of SCID mice. H) qPCR of human genomic DNA for either the unique region on AIB1 gene that was created by CRISPR editing (CRISPR) or human intronic DNA as a control (Intronic). MCFDCIS and MCFDCIS-Î"4 cell lines were used as reference points for MCFDCIS and Mix tumors (MCFDCIS and MCFDCIS-Î"4).
Table S1 from Gut Microbiota–Derived Short-Chain Fatty Acids Promote Prostate Cancer Growth via IGF1 Signaling
Authors: Matsushita Makoto , Fujita Kazutoshi , Hayashi Takuji , Kayama Hisako , Motooka Daisuke , Hase Hiroaki , Jingushi Kentaro , Yamamichi Gaku , Yumiba Satoru , Tomiyama Eisuke , Koh Yoko , Hayashi Yujiro , Nakano Kosuke , Wang Cong , Ishizuya Yu , Kato Taigo , Hatano Koji , Kawashima Atsunari , Ujike Takeshi , Uemura Motohide , Imamura Ryoichi , Rodriguez Pena Maria D.C. , Gordetsky Jennifer B. , Netto George J. , Tsujikawa Kazutake , Nakamura Shota , Takeda Kiyoshi , Nonomura Norio
Published: April 2023

Composition and energy values of control diet and high-fat diet
Supplementary Methods from Gut Microbiota–Derived Short-Chain Fatty Acids Promote Prostate Cancer Growth via IGF1 Signaling
Authors: Matsushita Makoto , Fujita Kazutoshi , Hayashi Takuji , Kayama Hisako , Motooka Daisuke , Hase Hiroaki , Jingushi Kentaro , Yamamichi Gaku , Yumiba Satoru , Tomiyama Eisuke , Koh Yoko , Hayashi Yujiro , Nakano Kosuke , Wang Cong , Ishizuya Yu , Kato Taigo , Hatano Koji , Kawashima Atsunari , Ujike Takeshi , Uemura Motohide , Imamura Ryoichi , Rodriguez Pena Maria D.C. , Gordetsky Jennifer B. , Netto George J. , Tsujikawa Kazutake , Nakamura Shota , Takeda Kiyoshi , Nonomura Norio
Published: April 2023

Method details
Supplementary File S4 from Pan-Cancer Drivers Are Recurrent Transcriptional Regulatory Heterogeneities in Early-Stage Luminal Breast Cancer
Authors: Singh Shambhavi , Sutcliffe Matthew D. , Repich Kathy , Atkins Kristen A. , Harvey Jennifer A. , Janes Kevin A.
Published: April 2023

Summary of differentially expressed genes based on a comparison of pool-and-split controls for each UVABC case compared to aggregated scRNA-seq data of breast epithelia from three reduction mammoplasties. Shared transcripts that were predicted to be differentially abundant in all five UVABC cases are assembled in the last worksheet. Each transcript reports the log2 fold change (log2FoldChange) and adjusted p value (padj).
Supplementary File S3 from Pan-Cancer Drivers Are Recurrent Transcriptional Regulatory Heterogeneities in Early-Stage Luminal Breast Cancer
Authors: Singh Shambhavi , Sutcliffe Matthew D. , Repich Kathy , Atkins Kristen A. , Harvey Jennifer A. , Janes Kevin A.
Published: April 2023

Summary of candidate heterogeneities identified from stochastic profiling by 10cRNA-seq and organized by UVABC case. RHEGs recurring in at-least three UVABC cases are assembled (Sheet 6) along with RHEGs not detected by scRNA-seq (Sheet 7). For each candidate, the log2 fold change (log2FoldChange) and adjusted p value (padj) are reported when the candidate was reliably detected in the aggregated scRNA-seq data of breast epithelia from three reduction mammoplasties.
Supplementary File S1 from Pan-Cancer Drivers Are Recurrent Transcriptional Regulatory Heterogeneities in Early-Stage Luminal Breast Cancer
Authors: Singh Shambhavi , Sutcliffe Matthew D. , Repich Kathy , Atkins Kristen A. , Harvey Jennifer A. , Janes Kevin A.
Published: April 2023

Summary of somatic mutations organized by mutation type, gene, and UVABC case. Luminal breast cancer driver genes are highlighted.
Supplementary Table S5-11 from M6A Demethylase ALKBH5 Regulates PD-L1 Expression and Tumor Immunoenvironment in Intrahepatic Cholangiocarcinoma
Authors: Qiu Xinyao , Yang Shuai , Wang Shan , Wu Jianmin , Zheng Bo , Wang Kaiting , Shen Siyun , Jeong Seogsong , Li Zhixuan , Zhu Yanjing , Wu Tong , Wu Xuan , Wu Rui , Liu Weiwei , Wang Hong-Yang , Chen Lei
Published: April 2023

Supplementary Table S5. RNA-seq: Significant DEGs (differentially expressed genes) with log|foldchange| > 1 and p-value <0.05. Supplementary Table S6. m6A-seq: RBE- shALKBH5 peaks related genes. Supplementary Table S7. m6A-seq: RBE- shCtrl peaks related genes. Supplementary Table S8. m6A-seq: RBE-shALKBH5 unique peaks related genes. Supplementary Table S9. m6A-seq: RBE-shCtrl unique peaks related genes. Supplementary Table S10. m6A-seq: common differential peaks related genes Supplementary Table S11. RNA-seq: log2normalized_count.
Supplementary Movie from In Vivo Imaging of Methionine Aminopeptidase II for Prostate Cancer Risk Stratification
Authors: Xie Jinghang , Rice Meghan A. , Chen Zixin , Cheng Yunfeng , Hsu En-Chi , Chen Min , Song Guosheng , Cui Liyang , Zhou Kaixiang , Castillo Jessa B. , Zhang Chiyuan A. , Shen Bin , Chin Frederick T. , Kunder Christian A. , Brooks James D. , Stoyanova Tanya , Rao Jianghong
Published: April 2023

Movie of super-resolution imaging of assembled probes in a single cell.
Supplementary Data from GPR15 Facilitates Recruitment of Regulatory T Cells to Promote Colorectal Cancer
Authors: Adamczyk Alexandra , Pastille Eva , Kehrmann Jan , Vu Vivian P. , Geffers Robert , Wasmer Marie-Hélène , Kasper Stefan , Schuler Martin , Lange Christian M. , Muggli Beat , Rau Tilman T. , Klein Diana , Hansen Wiebke , Krebs Philippe , Buer Jan , Westendorf Astrid M.
Published: April 2023

Supplementary Data
Table S3 from GLUT1 Expression in Tumor-Associated Neutrophils Promotes Lung Cancer Growth and Resistance to Radiotherapy
Authors: Ancey Pierre-Benoit , Contat Caroline , Boivin Gael , Sabatino Silvia , Pascual Justine , Zangger Nadine , Perentes Jean Yannis , Peters Solange , Abel E. Dale , Kirsch David G. , Rathmell Jeffrey C. , Vozenin Marie-Catherine , Meylan Etienne
Published: April 2023

Significant differentially expressed Hallmarks upregulated in TANs versus HLNs.
Supplementary Data from Inhibition of the FACT Complex Targets Aberrant Hedgehog Signaling and Overcomes Resistance to Smoothened Antagonists
Authors: Mo Jialin , Liu Fang , Sun Xi , Huang Hongting , Tan Kezhe , Zhao Xiaojing , Li Rui , Jiang Wenyan , Sui Yi , Chen Xiaosong , Shen Kunwei , Zhang Liye , Ma Jie , Zhao Kewen , Tang Yujie
Published: April 2023

Supplementary Figs. S1 to S9 Supplementary table legends
Supplementary Data from Inhibition of the FACT Complex Targets Aberrant Hedgehog Signaling and Overcomes Resistance to Smoothened Antagonists
Authors: Mo Jialin , Liu Fang , Sun Xi , Huang Hongting , Tan Kezhe , Zhao Xiaojing , Li Rui , Jiang Wenyan , Sui Yi , Chen Xiaosong , Shen Kunwei , Zhang Liye , Ma Jie , Zhao Kewen , Tang Yujie
Published: April 2023

Supplementary Table S1_Mouse_ sgRNA library_Sequences
Supplementary Data from Inhibition of the FACT Complex Targets Aberrant Hedgehog Signaling and Overcomes Resistance to Smoothened Antagonists
Authors: Mo Jialin , Liu Fang , Sun Xi , Huang Hongting , Tan Kezhe , Zhao Xiaojing , Li Rui , Jiang Wenyan , Sui Yi , Chen Xiaosong , Shen Kunwei , Zhang Liye , Ma Jie , Zhao Kewen , Tang Yujie
Published: April 2023

Supplementary Table S4_shRNA and sgRNA oligonucleotides
Supplementary Figure from Phosphoinositide-Binding Protein TIPE1 Promotes Alternative Activation of Macrophages and Tumor Progression via PIP3/Akt/TGFβ Axis
Authors: Cheng Yang , Bai Fuxiang , Ren Xiaolei , Sun Renhui , Guo Xiaowei , Liu Wen , Wang Bo , Yang Yongheng , Zhang Xiaolu , Xu Yong , Li Chunyang , Yang Xiaoyun , Gao Lifen , Ma Chunhong , Li Xueen , Liang Xiaohong
Published: April 2023

Supplementary Figure from Phosphoinositide-Binding Protein TIPE1 Promotes Alternative Activation of Macrophages and Tumor Progression via PIP3/Akt/TGFβ Axis
Figure S7 from Nuclear Receptor Coactivator NCOA3 Regulates UV Radiation–Induced DNA Damage and Melanoma Susceptibility
Authors: de Semir David , Bezrookove Vladimir , Nosrati Mehdi , Dar Altaf A. , Miller James R. , Leong Stanley P. , Kim Kevin B. , Liao Wilson , Soroceanu Liliana , McAllister Sean , Debs Robert J. , Schadendorf Dirk , Leachman Sancy A. , Cleaver James E. , Kashani-Sabet Mohammed
Published: April 2023

Supplementary Figure 7
Supplementary Data from Neuroblastoma Formation Requires Unconventional CD4 T Cells and Arginase-1–Dependent Myeloid Cells
Authors: Van de Velde Lee-Ann , Allen E. Kaitlynn , Crawford Jeremy Chase , Wilson Taylor L. , Guy Clifford S. , Russier Marion , Zeitler Leonie , Bahrami Armita , Finkelstein David , Pelletier Stephane , Schultz-Cherry Stacey , Thomas Paul G. , Murray Peter J.
Published: April 2023

Supplemental text
Supplementary Data from Neuroblastoma Formation Requires Unconventional CD4 T Cells and Arginase-1–Dependent Myeloid Cells
Authors: Van de Velde Lee-Ann , Allen E. Kaitlynn , Crawford Jeremy Chase , Wilson Taylor L. , Guy Clifford S. , Russier Marion , Zeitler Leonie , Bahrami Armita , Finkelstein David , Pelletier Stephane , Schultz-Cherry Stacey , Thomas Paul G. , Murray Peter J.
Published: April 2023

Table S4
Supplementary File 4 from BRAF Inhibitors Reprogram Cancer-Associated Fibroblasts to Drive Matrix Remodeling and Therapeutic Escape in Melanoma
Authors: Liu Tianyi , Zhou Linli , Xiao Yao , Andl Thomas , Zhang Yuhang
Published: April 2023

Supplementary File 4
POSTN sequence and primers for ChIP assay
Supplementary File 1 from BRAF Inhibitors Reprogram Cancer-Associated Fibroblasts to Drive Matrix Remodeling and Therapeutic Escape in Melanoma
Authors: Liu Tianyi , Zhou Linli , Xiao Yao , Andl Thomas , Zhang Yuhang
Published: April 2023

Supplementary File 1
Supplementary tables and figures
Supplementary Table from Immune Infiltrate and Tumor Microenvironment Transcriptional Programs Stratify Pediatric Osteosarcoma into Prognostic Groups at Diagnosis
Authors: Marchais Antonin , Marques da Costa Maria Eugenia , Job Bastien , Abbas Rachid , Drubay Damien , Piperno-Neumann Sophie , Fromigué Olivia , Gomez-Brouchet Anne , Redini Françoise , Droit Robin , Lervat Cyril , Entz-Werle Natacha , Pacquement Hélène , Devoldere Catherine , Cupissol Didier , Bodet Damien , Gandemer Virginie , Berger Marc , Marec-Berard Perrine , Jimenez Marta , Vassal Gilles , Geoerger Birgit , Brugières Laurence , Gaspar Nathalie
Published: April 2023

Supplementary Table from Immune Infiltrate and Tumor Microenvironment Transcriptional Programs Stratify Pediatric Osteosarcoma into Prognostic Groups at Diagnosis
Table S9 from Alterations in the Global Proteome and Phosphoproteome in Third Generation EGFR TKI Resistance Reveal Drug Targets to Circumvent Resistance
Authors: Zhang Xu , Maity Tapan K. , Ross Karen E. , Qi Yue , Cultraro Constance M. , Bahta Meriam , Pitts Stephanie , Keswani Meghana , Gao Shaojian , Nguyen Khoa Dang P. , Cowart Julie , Kirkali Fatos , Wu Cathy , Guha Udayan
Published: April 2023

Table S9
Table S6 from Alterations in the Global Proteome and Phosphoproteome in Third Generation EGFR TKI Resistance Reveal Drug Targets to Circumvent Resistance
Authors: Zhang Xu , Maity Tapan K. , Ross Karen E. , Qi Yue , Cultraro Constance M. , Bahta Meriam , Pitts Stephanie , Keswani Meghana , Gao Shaojian , Nguyen Khoa Dang P. , Cowart Julie , Kirkali Fatos , Wu Cathy , Guha Udayan
Published: April 2023

Table S6
Supplementary Figure from Immune Infiltrate and Tumor Microenvironment Transcriptional Programs Stratify Pediatric Osteosarcoma into Prognostic Groups at Diagnosis
Authors: Marchais Antonin , Marques da Costa Maria Eugenia , Job Bastien , Abbas Rachid , Drubay Damien , Piperno-Neumann Sophie , Fromigué Olivia , Gomez-Brouchet Anne , Redini Françoise , Droit Robin , Lervat Cyril , Entz-Werle Natacha , Pacquement Hélène , Devoldere Catherine , Cupissol Didier , Bodet Damien , Gandemer Virginie , Berger Marc , Marec-Berard Perrine , Jimenez Marta , Vassal Gilles , Geoerger Birgit , Brugières Laurence , Gaspar Nathalie
Published: April 2023

Supplementary Figure from Immune Infiltrate and Tumor Microenvironment Transcriptional Programs Stratify Pediatric Osteosarcoma into Prognostic Groups at Diagnosis
Combined Supplementary Data from Oncostatin M Receptor–Targeted Antibodies Suppress STAT3 Signaling and Inhibit Ovarian Cancer Growth
Authors: Geethadevi Anjali , Nair Ajay , Parashar Deepak , Ku Zhiqiang , Xiong Wei , Deng Hui , Li Yongsheng , George Jasmine , McAllister Donna M. , Sun Yunguang , Kadamberi Ishaque P. , Gupta Prachi , Dwinell Michael B. , Bradley William H. , Rader Janet S. , Rui Hallgeir , Schwabe Robert F. , Zhang Ningyan , Pradeep Sunila , An Zhiqiang , Chaluvally-Raghavan Pradeep
Published: April 2023

Combined Supplementary Figures, Supplementary Tables, Legends and Key Resource Tables
Supplementary Data from A BRCA1 Coiled-Coil Domain Variant Disrupting PALB2 Interaction Promotes the Development of Mammary Tumors and Confers a Targetable Defect in Homologous Recombination Repair
Authors: Pulver Emilia M. , Mukherjee Chirantani , van de Kamp Gerarda , Roobol Stefan J. , Rother Magdalena B. , van der Gulden Hanneke , de Bruijn Roebi , Lattanzio Maria Valeria , van der Burg Eline , Drenth Anne Paulien , Verkaik Nicole S. , Hahn Kerstin , Klarenbeek Sjoerd , de Korte-Grimmerink Renske , van de Ven Marieke , Pritchard Colin E.J. , Huijbers Ivo J. , Xia Bing , van Gent Dik C. , Essers Jeroen , van Attikum Haico , Ray Chaudhuri Arnab , Bouwman Peter , Jonkers Jos
Published: April 2023

Included are the supplementary methods, tables, and figures.
Supplementary Table 4 from Estrogen Receptor β-Mediated Inhibition of Actin-Based Cell Migration Suppresses Metastasis of Inflammatory Breast Cancer
Authors: Thomas Christoforos , Karagounis Ilias V. , Srivastava Ratnesh K. , Vrettos Nicholas , Nikolos Fotis , Francois Noëlle , Huang Menggui , Gong Siliang , Long Qi , Kumar Sushil , Koumenis Constantinos , Krishnamurthy Savitri , Ueno Naoto T. , Chakrabarti Rumela , Maity Amit
Published: April 2023

Table with patient characteristics
Supplementary Table3 from SLFN11 Inactivation Induces Proteotoxic Stress and Sensitizes Cancer Cells to Ubiquitin Activating Enzyme Inhibitor TAK-243
Authors: Murai Yasuhisa , Jo Ukhyun , Murai Junko , Jenkins Lisa M. , Huang Shar-Yin N. , Chakka Sirisha , Chen Lu , Cheng Ken , Fukuda Shinsaku , Takebe Naoko , Pommier Yves
Published: April 2023

Results of RNAi screening
Supplementary Table1 from SLFN11 Inactivation Induces Proteotoxic Stress and Sensitizes Cancer Cells to Ubiquitin Activating Enzyme Inhibitor TAK-243
Authors: Murai Yasuhisa , Jo Ukhyun , Murai Junko , Jenkins Lisa M. , Huang Shar-Yin N. , Chakka Sirisha , Chen Lu , Cheng Ken , Fukuda Shinsaku , Takebe Naoko , Pommier Yves
Published: April 2023

List of reagents and resources
Supplementary Figures S1-S5 from SLFN11 Inactivation Induces Proteotoxic Stress and Sensitizes Cancer Cells to Ubiquitin Activating Enzyme Inhibitor TAK-243
Authors: Murai Yasuhisa , Jo Ukhyun , Murai Junko , Jenkins Lisa M. , Huang Shar-Yin N. , Chakka Sirisha , Chen Lu , Cheng Ken , Fukuda Shinsaku , Takebe Naoko , Pommier Yves
Published: April 2023

FigureS1(A) Cell viability to TAK-243 in our drug screening. (B) SLFN11-KO cell lines in Li-7 by Western blotting. (C) CPT cytotoxicity in Li-7 SLFN11-WT and -KO cell lines. (D) The intensity of colony forming. (E) Cellular apoptosis by flow cytometry (F) Cleaved-PARP and cleaved-Caspase 3 by Western blotting. FigureS2(A, B) EdU incorporation in DU145 treated by TAK-243 for 24h or 48h. (C, D) Fork elongation speed. The length of red or green-colored part. FigureS3 (A) DNA damage response (DDR) proteins after long-term TAK-243 treatment. (B) CHK1 activation by CPT is reduced by the ATR inhibitor. FigureS4(A) UPR Activation by TAK-243 in CCRF-CEM cells. (B, C) UPR Activation by long-term TAK-243 treatment in DU145 and DMS114. (D) Accumulation of short-lived proteins. (E-F) Cell viability with p97 inhibitors in DU145. (G-H) Ubiquitin conjugates in CCRF-CEM with TAK-243 (1 hour). (I-J) Ubiquitin conjugates changes in DU145 cells with TAK-243(24 hours). FigureS5 (A-C) Newly synthesized protein detection by L-HPG in Li-7. Representative image and quantitation (D) Gene ontology (GO) analysis of molecular network associated with SLFN11. (E-F) Validation of SLFN11 interactions with the indicated translation initiation (EIF3B and EIF3L) and protein folding (CCT2) factors. (G) Relative cell viability with gene depletion of the TRiC/CCT chaperonin complex in RNAi screening. (H) Cell viability after transfection with siCCT2.
Supplementary Table 2 from E2F1 and E2F2-Mediated Repression of CPT2 Establishes a Lipid-Rich Tumor-Promoting Environment
Authors: González-Romero Francisco , Mestre Daniela , Aurrekoetxea Igor , O'Rourke Colm J. , Andersen Jesper B. , Woodhoo Ashwin , Tamayo-Caro Miguel , Varela-Rey Marta , Palomo-Irigoyen Marta , Gómez-Santos Beatriz , de Urturi Diego Sáenz , Núñez-García Maitane , García-Rodríguez Juan L. , Fernández-Ares Larraitz , Buqué Xabier , Iglesias-Ara Ainhoa , Bernales Irantzu , De Juan Virginia Gutierrez , Delgado Teresa C. , Goikoetxea-Usandizaga Naroa , Lee Richard , Bhanot Sanjay , Delgado Igotz , Perugorria Maria J. , Errazti Gaizka , Mosteiro Lorena , Gaztambide Sonia , Martinez de la Piscina Idoia , Iruzubieta Paula , Crespo Javier , Banales Jesus M. , Martínez-Chantar Maria L. , Castaño Luis , Zubiaga Ana M. , Aspichueta Patricia
Published: April 2023

Supplementary table 2