bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary table s5 from Predicting the Grade of Dysplasia of Pancreatic Cystic Neoplasms Using Cyst Fluid DNA Methylation Markers
Authors: Hata Tatsuo , Dal Molin Marco , Hong Seung-Mo , Tamura Koji , Suenaga Masaya , Yu Jun , Sedogawa Hiraku , Weiss Matthew J. , Wolfgang Christopher L. , Lennon Anne Marie , Hruban Ralph H. , Goggins Michael G.
Published: April 2023

Supplementary Table S5. Comparison of Methylated marker levels between IPMN and MCN cyst type classification with matched histologic grade.
Supplemental Table 5 from Detection of Therapeutically Targetable Driver and Resistance Mutations in Lung Cancer Patients by Next-Generation Sequencing of Cell-Free Circulating Tumor DNA
Authors: Thompson Jeffrey C. , Yee Stephanie S. , Troxel Andrea B. , Savitch Samantha L. , Fan Ryan , Balli David , Lieberman David B. , Morrissette Jennifer D. , Evans Tracey L. , Bauml Joshua , Aggarwal Charu , Kosteva John A. , Alley Evan , Ciunci Christine , Cohen Roger B. , Bagley Stephen , Stonehouse-Lee Susan , Sherry Victoria E. , Gilbert Elizabeth , Langer Corey , Vachani Anil , Carpenter Erica L.
Published: April 2023

Available therapies and clinical trials
Supplementary Figure legends from Predicting the Grade of Dysplasia of Pancreatic Cystic Neoplasms Using Cyst Fluid DNA Methylation Markers
Authors: Hata Tatsuo , Dal Molin Marco , Hong Seung-Mo , Tamura Koji , Suenaga Masaya , Yu Jun , Sedogawa Hiraku , Weiss Matthew J. , Wolfgang Christopher L. , Lennon Anne Marie , Hruban Ralph H. , Goggins Michael G.
Published: April 2023

Supplementary Figure legends
Supplemental Figures and Tables from A Phase I Study of Topotecan, Carboplatin and the PARP Inhibitor Veliparib in Acute Leukemias, Aggressive Myeloproliferative Neoplasms, and Chronic Myelomonocytic Leukemia
Authors: Pratz Keith W. , Rudek Michelle A. , Gojo Ivana , Litzow Mark R. , McDevitt Michael A. , Ji Jiuping , Karnitz Larry M. , Herman James G. , Kinders Robert J. , Smith B. Douglas , Gore Steven D. , Carraway Hetty E. , Showel Margaret M. , Gladstone Douglas E. , Levis Mark J. , Tsai Hua-Ling , Rosner Gary , Chen Alice , Kaufmann Scott H. , Karp Judith E.
Published: April 2023

Supplemental Figure S1. A, pretreatment bone marrow samples were treated diluent (-) with 10 μM melphalan (+) for 6 h and analyzed by immmunoblotting for FANCD2, ubiquitinated FANCD2 (Ub-FANCD2) and, as a loading control, heat shock protein 90 (HSP90). Supplemental Figure S2. A, Aliquots of whole cell lysates containing 5 x 106 pretreatment marrow mononuclear cells from the indicated patients were subjected to SDS-PAGE and blotting for the indicated antigens (lanes 5-12). Supplemental Figure S3. A, PAR suppression in PBMCs at various veliparib dose levels as a function of times during therapy. B, PAR suppression in PBMCs at 2 hours post dosing on day 1 and its relationship to clinical response. C, PAR suppression as assessed in bone marrow aspirates. Supplemental Table S1. MPN-Associated Leukemia Characteristics Supplemental Table S2 Accumulation of γH2AX in Viable Peripheral Blood CD34+ Cells Following Veliparib Administration at 80 mg Twice Daily Relative to Pretreatment (Day 0) Levels of DNA Damage
London et al_Supplementary Methods from KTN0158, a Humanized Anti-KIT Monoclonal Antibody, Demonstrates Biologic Activity against both Normal and Malignant Canine Mast Cells
Authors: London Cheryl A. , Gardner Heather L. , Rippy Sarah , Post Gerald , La Perle Krista , Crew Linda , Lopresti-Morrow Lori , Garton Andrew J. , McMahon Gerald , LaVallee Theresa M. , Gedrich Richard
Published: April 2023

Supplementary Methods
Figure S1 from KTN0158, a Humanized Anti-KIT Monoclonal Antibody, Demonstrates Biologic Activity against both Normal and Malignant Canine Mast Cells
Authors: London Cheryl A. , Gardner Heather L. , Rippy Sarah , Post Gerald , La Perle Krista , Crew Linda , Lopresti-Morrow Lori , Garton Andrew J. , McMahon Gerald , LaVallee Theresa M. , Gedrich Richard
Published: April 2023

Serum KTN0158 concentration over time
Supplementary Table 2 from Increases in Absolute Lymphocytes and Circulating CD4+ and CD8+ T Cells Are Associated with Positive Clinical Outcome of Melanoma Patients Treated with Ipilimumab
Authors: Martens Alexander , Wistuba-Hamprecht Kilian , Yuan Jianda , Postow Michael A. , Wong Phillip , Capone Mariaelena , Madonna Gabriele , Khammari Amir , Schilling Bastian , Sucker Antje , Schadendorf Dirk , Martus Peter , Dreno Brigitte , Ascierto Paolo A. , Wolchok Jedd D. , Pawelec Graham , Garbe Claus , Weide Benjamin
Published: April 2023

Impact of cell frequencies or counts on OS at single time points. Absolute (Abs.), Baseline (BL), median survival time (MST), myeloid-derived suppressor cells (MDSCs), regulatory T cells (Tregs), Relative (Rel.). *Early defines a second time-point, ranging from 2-8 weeks after start (BL) of ipilimumab. #Delayed defines a third time-point, ranging from 8-14 weeks after start (BL) of ipilimumab.
Supplemental Figure 3 from PARP Inhibitor Activity Correlates with SLFN11 Expression and Demonstrates Synergy with Temozolomide in Small Cell Lung Cancer
Authors: Lok Benjamin H. , Gardner Eric E. , Schneeberger Valentina E. , Ni Andy , Desmeules Patrice , Rekhtman Natasha , de Stanchina Elisa , Teicher Beverly A. , Riaz Nadeem , Powell Simon N. , Poirier John T. , Rudin Charles M.
Published: April 2023

Loss of SLFN11 confers resistance to PARP inhibition in SCLC doxcycline inducible construct against SLFN11 or Renilla luciferase with and without doxycycline exposure.
Supplemental Figure 1 from PARP Inhibitor Activity Correlates with SLFN11 Expression and Demonstrates Synergy with Temozolomide in Small Cell Lung Cancer
Authors: Lok Benjamin H. , Gardner Eric E. , Schneeberger Valentina E. , Ni Andy , Desmeules Patrice , Rekhtman Natasha , de Stanchina Elisa , Teicher Beverly A. , Riaz Nadeem , Powell Simon N. , Poirier John T. , Rudin Charles M.
Published: April 2023

Homologous recombination deficiency genomic scar assays do not predict sensitivity to PARP inhibitors in SCLC cell lines.
Supplementary Figure 3 from Increases in Absolute Lymphocytes and Circulating CD4+ and CD8+ T Cells Are Associated with Positive Clinical Outcome of Melanoma Patients Treated with Ipilimumab
Authors: Martens Alexander , Wistuba-Hamprecht Kilian , Yuan Jianda , Postow Michael A. , Wong Phillip , Capone Mariaelena , Madonna Gabriele , Khammari Amir , Schilling Bastian , Sucker Antje , Schadendorf Dirk , Martus Peter , Dreno Brigitte , Ascierto Paolo A. , Wolchok Jedd D. , Pawelec Graham , Garbe Claus , Weide Benjamin
Published: April 2023

Increases of CD4+, CD8+ and CD3- cell counts according to changes in ALC and overall survival according to changes of CD4+, CD8+ and CD3- cell counts. Absolute lymphocyte counts (ALC). *Early defines changes between baseline (BL) and a second time-point, ranging from 2-8 weeks after start of ipilimumab. #Delayed defines changes between BL and a third time-point, ranging from 8-14 weeks after start of ipilimumab. The percentage of patients identified with an increase in absolute numbers of CD4+, CD8+ T cells or CD3- lymphocytes was defined within patients showing an early increase or decrease in ALC (A). Kaplan-Meier analysis of overall survival according to early and delayed changes (increase vs. decrease) of absolute CD4+ T cells (B, E), CD8+ T cells (C, F) and CD3- lymphocytes (D, G) observed during ipilimumab treatment. Censoring is indicated by vertical lines; p-values were calculated by log rank statistics.
Supplementary Figure 2 from Increases in Absolute Lymphocytes and Circulating CD4+ and CD8+ T Cells Are Associated with Positive Clinical Outcome of Melanoma Patients Treated with Ipilimumab
Authors: Martens Alexander , Wistuba-Hamprecht Kilian , Yuan Jianda , Postow Michael A. , Wong Phillip , Capone Mariaelena , Madonna Gabriele , Khammari Amir , Schilling Bastian , Sucker Antje , Schadendorf Dirk , Martus Peter , Dreno Brigitte , Ascierto Paolo A. , Wolchok Jedd D. , Pawelec Graham , Garbe Claus , Weide Benjamin
Published: April 2023

Individual early changes in absolute lymphocyte counts and delayed changes in frequencies of CD4+ and CD8+ T cells in different outcome groups. Individual early changes of absolute lymphocyte counts (ALC; A-C), and delayed changes in frequencies of CD4+ (D-F) and CD8+ (G-I) T cells during ipilimumab are presented for patients who were assigned to three prognostic groups differing in survival after start of ipilimumab (A, D, G - left: {less than or equal to}6 months; A, D, G - middle: 7-18 months; A, D, G - right: >18 months). Patients censored at 18 months of less were excluded (A, D, G). Individual early changes in ALC, delayed changes in % of CD4+ and CD8+ are presented in patients who experienced progressive disease (B, E, H - left) or clinical benefit (complete response or partial response or stable disease; B, E, H - right) and in non-responders (stable or progressive disease; C, F, I - left) or in responders (complete or partial response; C, F, I - right) according to immune related response criteria (irRC). Changes were analyzed separately for all groups using Wilcoxon matched pairs tests. The p-value is presented in case of a significant change or strong trend within the respective group.
Supplemental Fig.1-4;Supplemental Tables 1-3; Suipplemental Methods from Molecular and Clinical Effects of Notch Inhibition in Glioma Patients: A Phase 0/I Trial
Authors: Xu Ran , Shimizu Fumiko , Hovinga Koos , Beal Kathryn , Karimi Sasan , Droms Leif , Peck Kyung K. , Gutin Philip , Iorgulescu J. Bryan , Kaley Thomas , DeAngelis Lisa , Pentsova Elena , Nolan Craig , Grommes Christian , Chan Timothy , Bobrow Dylan , Hormigo Adilia , Cross Justin R. , Wu Nian , Takebe Naoko , Panageas Katherine , Ivy Percy , Supko Jeffrey G. , Tabar Viviane , Omuro Antonio
Published: April 2023

Supp. Fig.1. CONSORT Flow Diagram Supp. Fig.2. MRI Perfusion Parameters Supp. Fig. 3. Immunohistochemistry Supp. Fig. 4. Gene Expression Profile Supp. Table 1. Adverse Events Supp. Table 2. Pharmacokinetic Data Supp. Table 3. Molar Drug Levels Supplemental Methods
Supplementary Table 2 from Age and Gender Associations of Virus Positivity in Merkel Cell Carcinoma Characterized Using a Novel RNA In Situ Hybridization Assay
Authors: Wang Lisha , Harms Paul W. , Palanisamy Nallasivam , Carskadon Shannon , Cao Xuhong , Siddiqui Javed , Patel Rajiv M. , Zelenka-Wang Sylvia , Durham Alison B. , Fullen Douglas R. , Harms Kelly L. , Su Fengyun , Shukla Sudhanshu , Mehra Rohit , Chinnaiyan Arul M.
Published: April 2023

ISH product scores.
Supplementary Table 1 from Age and Gender Associations of Virus Positivity in Merkel Cell Carcinoma Characterized Using a Novel RNA In Situ Hybridization Assay
Authors: Wang Lisha , Harms Paul W. , Palanisamy Nallasivam , Carskadon Shannon , Cao Xuhong , Siddiqui Javed , Patel Rajiv M. , Zelenka-Wang Sylvia , Durham Alison B. , Fullen Douglas R. , Harms Kelly L. , Su Fengyun , Shukla Sudhanshu , Mehra Rohit , Chinnaiyan Arul M.
Published: April 2023

Case details.
Figure S5 from Genetic and Methylation-Induced Loss of miR-181a2/181b2 within chr9q33.3 Facilitates Tumor Growth of Cervical Cancer through the PIK3R3/Akt/FoxO Signaling Pathway
Authors: Mei Qian , Li Xiang , Zhang Kang , Wu Zhiqiang , Li Xiaolei , Meng Yuanguang , Guo Mingzhou , Luo Guangbin , Fu Xiaobing , Han Weidong
Published: April 2023

Figure S5. The relationship between miR-181a2/181b2, p-Akt, p-FoxO1 and p-JNK levels
Supplemental Figure Legends from Age and Gender Associations of Virus Positivity in Merkel Cell Carcinoma Characterized Using a Novel RNA In Situ Hybridization Assay
Authors: Wang Lisha , Harms Paul W. , Palanisamy Nallasivam , Carskadon Shannon , Cao Xuhong , Siddiqui Javed , Patel Rajiv M. , Zelenka-Wang Sylvia , Durham Alison B. , Fullen Douglas R. , Harms Kelly L. , Su Fengyun , Shukla Sudhanshu , Mehra Rohit , Chinnaiyan Arul M.
Published: April 2023

Supplemental Figure Legends
SFigure S3 from Age and Gender Associations of Virus Positivity in Merkel Cell Carcinoma Characterized Using a Novel RNA In Situ Hybridization Assay
Authors: Wang Lisha , Harms Paul W. , Palanisamy Nallasivam , Carskadon Shannon , Cao Xuhong , Siddiqui Javed , Patel Rajiv M. , Zelenka-Wang Sylvia , Durham Alison B. , Fullen Douglas R. , Harms Kelly L. , Su Fengyun , Shukla Sudhanshu , Mehra Rohit , Chinnaiyan Arul M.
Published: April 2023

(A) Percentage of positive cells in MCPyV-positive tumors by RNA-ISH (n=42). (B) Photomicrograph of MCC/25 (Patient 12) with positive MCPyV RNA-ISH. The tumor (lymph node metastasis) was composed of a focal area of tumor cells surrounded by lymphocytes (green arrow). Tumor cells stain positively (red arrows) with punctate brown staining (400X magnification). (C) Comparison of percentage of positive cells by RNA-ISH and LTAg copy number by qPCR.
Figure S3 from Genetic and Methylation-Induced Loss of miR-181a2/181b2 within chr9q33.3 Facilitates Tumor Growth of Cervical Cancer through the PIK3R3/Akt/FoxO Signaling Pathway
Authors: Mei Qian , Li Xiang , Zhang Kang , Wu Zhiqiang , Li Xiaolei , Meng Yuanguang , Guo Mingzhou , Luo Guangbin , Fu Xiaobing , Han Weidong
Published: April 2023

Figure S3. miR-181a2/181b2 did not exhibit significant effect on migration, invasion, and EMT of cervical cancer cells
SFigure S2 from Age and Gender Associations of Virus Positivity in Merkel Cell Carcinoma Characterized Using a Novel RNA In Situ Hybridization Assay
Authors: Wang Lisha , Harms Paul W. , Palanisamy Nallasivam , Carskadon Shannon , Cao Xuhong , Siddiqui Javed , Patel Rajiv M. , Zelenka-Wang Sylvia , Durham Alison B. , Fullen Douglas R. , Harms Kelly L. , Su Fengyun , Shukla Sudhanshu , Mehra Rohit , Chinnaiyan Arul M.
Published: April 2023

Read depth histograms across the Merkel cell polyomavirus (MCPyV) genome for two Merkel cell carcinoma (MCC) tumors.
Figure S2 from Genetic and Methylation-Induced Loss of miR-181a2/181b2 within chr9q33.3 Facilitates Tumor Growth of Cervical Cancer through the PIK3R3/Akt/FoxO Signaling Pathway
Authors: Mei Qian , Li Xiang , Zhang Kang , Wu Zhiqiang , Li Xiaolei , Meng Yuanguang , Guo Mingzhou , Luo Guangbin , Fu Xiaobing , Han Weidong
Published: April 2023

Figure S2. miR-181a/181b function as tumor suppressors in cervical cancer in vitro
SFigure S1 from Age and Gender Associations of Virus Positivity in Merkel Cell Carcinoma Characterized Using a Novel RNA In Situ Hybridization Assay
Authors: Wang Lisha , Harms Paul W. , Palanisamy Nallasivam , Carskadon Shannon , Cao Xuhong , Siddiqui Javed , Patel Rajiv M. , Zelenka-Wang Sylvia , Durham Alison B. , Fullen Douglas R. , Harms Kelly L. , Su Fengyun , Shukla Sudhanshu , Mehra Rohit , Chinnaiyan Arul M.
Published: April 2023

Representative microphotographs of samples showing different MCPyV RNA in situ hybridization (RNA-ISH) intensity (400X magnification)
Figure S3 from Age and Gender Associations of Virus Positivity in Merkel Cell Carcinoma Characterized Using a Novel RNA In Situ Hybridization Assay
Authors: Wang Lisha , Harms Paul W. , Palanisamy Nallasivam , Carskadon Shannon , Cao Xuhong , Siddiqui Javed , Patel Rajiv M. , Zelenka-Wang Sylvia , Durham Alison B. , Fullen Douglas R. , Harms Kelly L. , Su Fengyun , Shukla Sudhanshu , Mehra Rohit , Chinnaiyan Arul M.
Published: April 2023

(A) Percentage of positive cells in MCPyV-positive tumors by RNA-ISH (n=42). (B) Photomicrograph of MCC/25 (Patient 12) with positive MCPyV RNA-ISH. The tumor (lymph node metastasis) was composed of a focal area of tumor cells surrounded by lymphocytes (green arrow). Tumor cells stain positively (red arrows) with punctate brown staining (400X magnification). (C) Comparison of percentage of positive cells by RNA-ISH and LTAg copy number by qPCR.
Supplemental Figures 1-5 from A CK1α Activator Penetrates the Brain and Shows Efficacy Against Drug-resistant Metastatic Medulloblastoma
Authors: Rodriguez-Blanco Jezabel , Li Bin , Long Jun , Shen Chen , Yang Fan , Orton Darren , Collins Sara , Kasahara Noriyuki , Ayad Nagi G. , McCrea Heather J. , Roussel Martine F. , Weiss William A. , Capobianco Anthony J. , Robbins David J.
Published: April 2023

Supplemental Figures 1-5 with corresponding legends
Supplementary Figure Legends from Strategic Therapeutic Targeting to Overcome Venetoclax Resistance in Aggressive B-cell Lymphomas
Authors: Pham Lan V. , Huang Shengjian , Zhang Hui , Zhang Jun , Bell Taylor , Zhou Shouhao , Pogue Elizabeth , Ding Zhiyong , Lam Laura , Westin Jason , Davis R. Eric , Young Ken H. , Medeiros L. Jeffrey , Ford Richard J. , Nomie Krystle , Zhang Leo , Wang Michael
Published: April 2023

Supplementary Figure Legends
Figure S4 from Strategic Therapeutic Targeting to Overcome Venetoclax Resistance in Aggressive B-cell Lymphomas
Authors: Pham Lan V. , Huang Shengjian , Zhang Hui , Zhang Jun , Bell Taylor , Zhou Shouhao , Pogue Elizabeth , Ding Zhiyong , Lam Laura , Westin Jason , Davis R. Eric , Young Ken H. , Medeiros L. Jeffrey , Ford Richard J. , Nomie Krystle , Zhang Leo , Wang Michael
Published: April 2023

Representative heatmap showing the up and downregulated proteins in the Mino parental (Mino-P) vs. Mino-venetoclax resistant (Mino-VR) cell lines.
Supplemental Table S1 from Biochemical and Epigenetic Insights into L-2-Hydroxyglutarate, a Potential Therapeutic Target in Renal Cancer
Authors: Shelar Sandeep , Shim Eun-Hee , Brinkley Garrett J. , Kundu Anirban , Carobbio Francesca , Poston Tyler , Tan Jubilee , Parekh Vishwas , Benson Daniel , Crossman David K. , Buckhaults Phillip J. , Rakheja Dinesh , Kirkman Richard , Sato Yusuke , Ogawa Seishi , Dutta Shilpa , Velu Sadanandan E. , Emberley Ethan , Pan Alison , Chen Jason , Huang Tony , Absher Devin , Becker Anja , Kunick Conrad , Sudarshan Sunil
Published: April 2023

This table reports L2HGDH mRNA expression as a function of 14q Status
Table S2 from Therapeutic Immune Modulation against Solid Cancers with Intratumoral Poly-ICLC: A Pilot Trial
Authors: Kyi Chrisann , Roudko Vladimir , Sabado Rachel , Saenger Yvonne , Loging William , Mandeli John , Thin Tin Htwe , Lehrer Deborah , Donovan Michael , Posner Marshall , Misiukiewicz Krzysztof , Greenbaum Benjamin , Salazar Andres , Friedlander Philip , Bhardwaj Nina
Published: April 2023

Supplemental Table 2. List of genes, forming gene signature sets shown at Figure 6.
Figure S4 from Therapeutic Immune Modulation against Solid Cancers with Intratumoral Poly-ICLC: A Pilot Trial
Authors: Kyi Chrisann , Roudko Vladimir , Sabado Rachel , Saenger Yvonne , Loging William , Mandeli John , Thin Tin Htwe , Lehrer Deborah , Donovan Michael , Posner Marshall , Misiukiewicz Krzysztof , Greenbaum Benjamin , Salazar Andres , Friedlander Philip , Bhardwaj Nina
Published: April 2023

Supplemental Figure 4. Selected Broad Institute C7 immune geneset enrichments (FDR < 0,25). Gene names of enriched genesets are publicly available online at MSigDB: http://software.broadinstitute.org/gsea/msigdb/index.jsp.
Supplementary Table S3. OncoPlus Gene List and Identified Variants from B-Cell Lymphoma Patient-Derived Xenograft Models Enable Drug Discovery and Are a Platform for Personalized Therapy
Authors: Zhang Leo , Nomie Krystle , Zhang Hui , Bell Taylor , Pham Lan , Kadri Sabah , Segal Jeremy , Li Shaoying , Zhou Shouhao , Santos David , Richard Shawana , Sharma Shruti , Chen Wendy , Oriabure Onyekachukwu , Liu Yang , Huang Shengjian , Guo Hui , Chen Zhihong , Tao Wenjing , Li Carrie , Wang Jack , Fang Bingliang , Wang Jacqueline , Li Lei , Badillo Maria , Ahmed Makhdum , Thirumurthi Selvi , Huang Steven Y. , Shao Yiping , Lam Laura , Yi Qing , Wang Y. Lynn , Wang Michael
Published: April 2023

Supplementary Table S3. OncoPlus Gene List and Identified Variants
Supplementary Table S2. The RPPA antibody list from B-Cell Lymphoma Patient-Derived Xenograft Models Enable Drug Discovery and Are a Platform for Personalized Therapy
Authors: Zhang Leo , Nomie Krystle , Zhang Hui , Bell Taylor , Pham Lan , Kadri Sabah , Segal Jeremy , Li Shaoying , Zhou Shouhao , Santos David , Richard Shawana , Sharma Shruti , Chen Wendy , Oriabure Onyekachukwu , Liu Yang , Huang Shengjian , Guo Hui , Chen Zhihong , Tao Wenjing , Li Carrie , Wang Jack , Fang Bingliang , Wang Jacqueline , Li Lei , Badillo Maria , Ahmed Makhdum , Thirumurthi Selvi , Huang Steven Y. , Shao Yiping , Lam Laura , Yi Qing , Wang Y. Lynn , Wang Michael
Published: April 2023

Supplementary Table S2. The RPPA antibody list
Figure from Fibrotic Response to Neoadjuvant Therapy Predicts Survival in Pancreatic Cancer and Is Measurable with Collagen-Targeted Molecular MRI
Authors: Erstad Derek J. , Sojoodi Mozhdeh , Taylor Martin S. , Jordan Veronica Clavijo , Farrar Christian T. , Axtell Andrea L. , Rotile Nicholas J. , Jones Chloe , Graham-O'Regan Katherine A. , Ferreira Diego S. , Michelakos Theodoros , Kontos Filippos , Chawla Akhil , Li Shen , Ghoshal Sarani , Chen Yin-Ching Iris , Arora Gunisha , Humblet Valerie , Deshpande Vikram , Qadan Motaz , Bardeesy Nabeel , Ferrone Cristina R. , Lanuti Michael , Tanabe Kenneth K. , Caravan Peter , Fuchs Bryan C.
Published: April 2023

Supplementary figures
Supplementary Tables from Pooled Clustering of High-Grade Serous Ovarian Cancer Gene Expression Leads to Novel Consensus Subtypes Associated with Survival and Surgical Outcomes
Authors: Wang Chen , Armasu Sebastian M. , Kalli Kimberly R. , Maurer Matthew J. , Heinzen Ethan P. , Keeney Gary L. , Cliby William A. , Oberg Ann L. , Kaufmann Scott H. , Goode Ellen L.
Published: April 2023

Supplementary Table 1. Key clinical characteristics of public cohort with respect to individual 14 studies Supplementary Table 2. Key clinical characteristics of Mayo Clinic HGSOC cohort Supplementary Table 3. Expression centroids of five de novo subtypes Supplementary Table 4. Expression centroids of four Tothill's HGSOC subtypes (C1/C2/C4/C5) Supplementary Table 5. Cross-tab between de novo subtypes and two other subtyping systems in public cohort Supplementary Table 6. The differential expression analysis results between s1.MES and rest de novo subtypes in public cohort Supplementary Table 7. The differential expression analysis results between s2.IMM and rest de novo subtypes in public cohort Supplementary Table 8. The differential expression analysis results between s3.RPO and rest de novo subtypes in public cohort Supplementary Table 9. The differential expression analysis results between s4.DIF and rest de novo subtypes in public cohort Supplementary Table 10. The differential expression analysis results between s5.ANM and rest de novo subtypes in public cohort Supplementary Table 11. Distribution tables of HGSOC molecular subtypes vs. surgical outcomes (optimal- and sub-optimal debulking) in Public and Mayo Clinic cohorts Supplementary Table 12. Previously reported debulking-predictive genes and their differential expressions related to s1.MES subtype in HGSOC public cases Supplementary Table 13. Enriched pathways (q-value <=0.1) for s1.MES vs. rest de novo subtypes comparisons Supplementary Table 14. Enriched pathways (q-value <=0.1) for s2.IMM vs. rest de novo subtypes comparisons Supplementary Table 15. Enriched pathways (q-value <=0.1) for s3.PRO vs. rest de novo subtypes comparisons Supplementary Table 16. Enriched pathways (q-value <=0.1) for s4.DIF vs. rest de novo subtypes comparisons Supplementary Table 17. Enriched pathways (q-value <=0.1) for s5.ANM vs. rest de novo subtypes comparisons Supplementary Table 18. Distributions of BRCAness status versus de novo subtypes for TCGA cases with mutation and methylation calls: "mBRCA" indicates cases with germline or somatic deleterious mutations in BRCA1/2; "meth.BRCA1" indicates cases with BRCA1 promoter methylation; "wtBRCA" indicates cases without known BRCA1/2 mutations or promoter methylations.
Supplementary Figure S4. Carfilzomib overcomes primary ibrutinib resistance in vivo from B-Cell Lymphoma Patient-Derived Xenograft Models Enable Drug Discovery and Are a Platform for Personalized Therapy
Authors: Zhang Leo , Nomie Krystle , Zhang Hui , Bell Taylor , Pham Lan , Kadri Sabah , Segal Jeremy , Li Shaoying , Zhou Shouhao , Santos David , Richard Shawana , Sharma Shruti , Chen Wendy , Oriabure Onyekachukwu , Liu Yang , Huang Shengjian , Guo Hui , Chen Zhihong , Tao Wenjing , Li Carrie , Wang Jack , Fang Bingliang , Wang Jacqueline , Li Lei , Badillo Maria , Ahmed Makhdum , Thirumurthi Selvi , Huang Steven Y. , Shao Yiping , Lam Laura , Yi Qing , Wang Y. Lynn , Wang Michael
Published: April 2023

PT8 was clinically primary ibrutinib resistant. PT8-MCL PDX was generated and passaged. G3 mice were treated with vehicle control, IBN, and CFZ (P < 0.01, CFZ versus vehicle control or IBN, n = 5).
Supplementary Index from Pooled Clustering of High-Grade Serous Ovarian Cancer Gene Expression Leads to Novel Consensus Subtypes Associated with Survival and Surgical Outcomes
Authors: Wang Chen , Armasu Sebastian M. , Kalli Kimberly R. , Maurer Matthew J. , Heinzen Ethan P. , Keeney Gary L. , Cliby William A. , Oberg Ann L. , Kaufmann Scott H. , Goode Ellen L.
Published: April 2023

Additional materials.
Supplementary Figure S2. Characterization of the B-cell lymphoma PDX models from B-Cell Lymphoma Patient-Derived Xenograft Models Enable Drug Discovery and Are a Platform for Personalized Therapy
Authors: Zhang Leo , Nomie Krystle , Zhang Hui , Bell Taylor , Pham Lan , Kadri Sabah , Segal Jeremy , Li Shaoying , Zhou Shouhao , Santos David , Richard Shawana , Sharma Shruti , Chen Wendy , Oriabure Onyekachukwu , Liu Yang , Huang Shengjian , Guo Hui , Chen Zhihong , Tao Wenjing , Li Carrie , Wang Jack , Fang Bingliang , Wang Jacqueline , Li Lei , Badillo Maria , Ahmed Makhdum , Thirumurthi Selvi , Huang Steven Y. , Shao Yiping , Lam Laura , Yi Qing , Wang Y. Lynn , Wang Michael
Published: April 2023

Representative tumor mass and histology of tumor series passages of PT1 MCL and PT2 Burkitt's lymphoma (BL). B-C, PDX tumors invaded the mouse spleen and formed splenomegaly. D, Patient abdomen PET/CT images of PT1 and PT5 showed splenomegaly (left panel). Autopsy of PT1 G3 NSG mouse and PT5 G1 SCID-hu mouse also showed splenomegaly (middle panel), and H&E staining of mouse spleens in PDXs indicated extensive lymphoma involvement (right panel).
Supplementary Figure S1. Schematic representation and establishment of the B-cell lymphoma PDX models from B-Cell Lymphoma Patient-Derived Xenograft Models Enable Drug Discovery and Are a Platform for Personalized Therapy
Authors: Zhang Leo , Nomie Krystle , Zhang Hui , Bell Taylor , Pham Lan , Kadri Sabah , Segal Jeremy , Li Shaoying , Zhou Shouhao , Santos David , Richard Shawana , Sharma Shruti , Chen Wendy , Oriabure Onyekachukwu , Liu Yang , Huang Shengjian , Guo Hui , Chen Zhihong , Tao Wenjing , Li Carrie , Wang Jack , Fang Bingliang , Wang Jacqueline , Li Lei , Badillo Maria , Ahmed Makhdum , Thirumurthi Selvi , Huang Steven Y. , Shao Yiping , Lam Laura , Yi Qing , Wang Y. Lynn , Wang Michael
Published: April 2023

A, Schematic describing the primary B-cell lymphoma PDX SCID/NSG-hu mouse model. Six-to 8-week-old male NSG or CB-17 SCID mice were implanted with human fetal bone. Approximately 4 to 6 weeks following bone implantation, one injection of 5 Ã- 106 patient tumor cells were administered directly into the human fetal bone chip as the first generation (G1). The levels of circulating human Î²2M in mouse serum were used to monitor tumor engraftment and growth in G1 mice. Once tumor burden was detected, the pieces of tumor with bone chip were subcutaneously transplanted into NSG mice as the second generation (G2). After G2, the consistent growths of tumor in NSG mice were acquired. Single-agent targeted therapy, drug-resistant treatment, or combination therapy, were administered in the indicated generations. B, Human Î²2M reflected the tumor burdens of 16 B-cell lymphomas in PDX-G1 mice. After 3-4 weeks of tumor inoculation, mouse sera were collected from the peripheral blood of tail vein, and the level of human Î²2M was determined by ELISA.
Supplementary Table 1 from An Expression Signature as an Aid to the Histologic Classification of Non–Small Cell Lung Cancer
Authors: Girard Luc , Rodriguez-Canales Jaime , Behrens Carmen , Thompson Debrah M. , Botros Ihab W. , Tang Hao , Xie Yang , Rekhtman Natasha , Travis William D. , Wistuba Ignacio I. , Minna John D. , Gazdar Adi F.
Published: April 2023

Gene Lists for the ADC-SCC and Tumor-Nonmalignant Signatures
Supplementary Tables from SNP rs16906252C>T Is an Expression and Methylation Quantitative Trait Locus Associated with an Increased Risk of Developing MGMT-Methylated Colorectal Cancer
Authors: Kuroiwa-Trzmielina Joice , Wang Fan , Rapkins Robert W. , Ward Robyn L. , Buchanan Daniel D. , Win Aung Ko , Clendenning Mark , Rosty Christophe , Southey Melissa C. , Winship Ingrid M. , Hopper John L. , Jenkins Mark A. , Olivier Jake , Hawkins Nicholas J. , Hitchins Megan P.
Published: April 2023

Supplementary Table 1. Statistical comparisons between the methylation status of the MGMT promoter within colorectal carcinoma (CRC) and clinicopathological features, molecular features of tumors, and rs16906252C>T genotype in cases from the Sydney CRC series. Supplementary Table 2. Statistical comparisons of the methylation status of the MGMT promoter within the colorectal carcinoma (CRC) of cases from the Australasian Colorectal Cancer Family Registry (ACCFR). Supplementary Table 3. Performance of the rs16906252C>T genotype in predicting the MGMT methylation status of the primary CRC of cases from the Sydney and Australasian colon cancer family registry (ACCFR) CRC series. Supplementary Table 4. MGMT methylation in normal tissues of a subset of colorectal cancer cases and healthy controls is associated with the rs16906252C>T variant. Supplementary Table 5. Performance of the rs16906252C>T genotype and presence of lowlevel MGMT methylation in normal tissues of CRC cases in predicting the MGMT methylation status of the primary CRC in a subset of 62 cases from the Sydney CRC series.
Supplementary Methods from SNP rs16906252C>T Is an Expression and Methylation Quantitative Trait Locus Associated with an Increased Risk of Developing MGMT-Methylated Colorectal Cancer
Authors: Kuroiwa-Trzmielina Joice , Wang Fan , Rapkins Robert W. , Ward Robyn L. , Buchanan Daniel D. , Win Aung Ko , Clendenning Mark , Rosty Christophe , Southey Melissa C. , Winship Ingrid M. , Hopper John L. , Jenkins Mark A. , Olivier Jake , Hawkins Nicholas J. , Hitchins Megan P.
Published: April 2023

Supplementary methods providing additional technical detail for methods that is relevant only to those who wish to repeat them exactly
Supplemental Figures from Cytokines Produced by Dendritic Cells Administered Intratumorally Correlate with Clinical Outcome in Patients with Diverse Cancers
Authors: Subbiah Vivek , Murthy Ravi , Hong David S. , Prins Robert M. , Hosing Chitra , Hendricks Kyle , Kolli Deepthi , Noffsinger Lori , Brown Robert , McGuire Mary , Fu Siquing , Piha-Paul Sarina , Naing Aung , Conley Anthony P. , Benjamin Robert S. , Kaur Indreshpal , Bosch Marnix L.
Published: April 2023

Supplemental Figures S1-S2
Supplemental Table 1. from Use of Expansion Cohorts in Phase I Trials and Probability of Success in Phase II for 381 Anticancer Drugs
Authors: Bugano Diogo D.G. , Hess Kenneth , Jardim Denis L.F. , Zer Alona , Meric-Bernstam Funda , Siu Lillian L. , Razak Albiruni R.A. , Hong David S.
Published: April 2023

Drugs Approved by the U.S. Food and Drug Administration by April 30, 2014, That Were Included in the Analysis
Figure S5 from Screening of Conditionally Reprogrammed Patient-Derived Carcinoma Cells Identifies ERCC3–MYC Interactions as a Target in Pancreatic Cancer
Authors: Beglyarova Natalya , Banina Eugenia , Zhou Yan , Mukhamadeeva Ramilia , Andrianov Grigorii , Bobrov Egor , Lysenko Elena , Skobeleva Natalya , Gabitova Linara , Restifo Diana , Pressman Max , Serebriiskii Ilya G. , Hoffman John P. , Paz Keren , Behrens Diana , Khazak Vladimir , Jablonski Sandra A. , Golemis Erica A. , Weiner Louis M. , Astsaturov Igor
Published: April 2023

Supplemental Figure 5. Quantified protein expression in PDAC 001 cells.
Figure S4 from Screening of Conditionally Reprogrammed Patient-Derived Carcinoma Cells Identifies ERCC3–MYC Interactions as a Target in Pancreatic Cancer
Authors: Beglyarova Natalya , Banina Eugenia , Zhou Yan , Mukhamadeeva Ramilia , Andrianov Grigorii , Bobrov Egor , Lysenko Elena , Skobeleva Natalya , Gabitova Linara , Restifo Diana , Pressman Max , Serebriiskii Ilya G. , Hoffman John P. , Paz Keren , Behrens Diana , Khazak Vladimir , Jablonski Sandra A. , Golemis Erica A. , Weiner Louis M. , Astsaturov Igor
Published: April 2023

Supplemental Figure 4. mRNA abundance in triptolide-treated PDAC 001 cells
Figure S3 from Screening of Conditionally Reprogrammed Patient-Derived Carcinoma Cells Identifies ERCC3–MYC Interactions as a Target in Pancreatic Cancer
Authors: Beglyarova Natalya , Banina Eugenia , Zhou Yan , Mukhamadeeva Ramilia , Andrianov Grigorii , Bobrov Egor , Lysenko Elena , Skobeleva Natalya , Gabitova Linara , Restifo Diana , Pressman Max , Serebriiskii Ilya G. , Hoffman John P. , Paz Keren , Behrens Diana , Khazak Vladimir , Jablonski Sandra A. , Golemis Erica A. , Weiner Louis M. , Astsaturov Igor
Published: April 2023

Supplemental Figure 3. Testing screen hits in patient-derived xenografts.
Suppl Fig. 1 from Patient-derived Interstitial Fluids and Predisposition to Aggressive Sporadic Breast Cancer through Collagen Remodeling and Inactivation of p53
Authors: Kenny Timothy C. , Schmidt Hank , Adelson Kerin , Hoshida Yujin , Koh Anna P. , Shah Nagma , Mandeli John , Ting Jess , Germain Doris
Published: April 2023

Supplementary Figure 1: Invasion inducing capacity of low and high score PSF is not species specific. Invasion assays were performed on a murine HER2 mammary carcinoma cell line derived from inducible MMTV-rtTA/TetO/NeuNT mice using 8 different PSF samples (High, n = 4; Low, n = 4) (scale bar = 100μm).
Figure S2 from Screening of Conditionally Reprogrammed Patient-Derived Carcinoma Cells Identifies ERCC3–MYC Interactions as a Target in Pancreatic Cancer
Authors: Beglyarova Natalya , Banina Eugenia , Zhou Yan , Mukhamadeeva Ramilia , Andrianov Grigorii , Bobrov Egor , Lysenko Elena , Skobeleva Natalya , Gabitova Linara , Restifo Diana , Pressman Max , Serebriiskii Ilya G. , Hoffman John P. , Paz Keren , Behrens Diana , Khazak Vladimir , Jablonski Sandra A. , Golemis Erica A. , Weiner Louis M. , Astsaturov Igor
Published: April 2023

Supplemental Figure 2. Rapid derivation of PDAC cells in culture.
Table S1, Table S2, Table S3 from Functional Ex Vivo Assay Reveals Homologous Recombination Deficiency in Breast Cancer Beyond BRCA Gene Defects
Authors: Meijer Titia G. , Verkaik Nicole S. , Sieuwerts Anieta M. , van Riet Job , Naipal Kishan A.T. , van Deurzen Carolien H.M. , den Bakker Michael A. , Sleddens Hein F.B.M. , Dubbink Hendrikus-Jan , den Toom T. Dorine , Dinjens Winand N.M. , Lips Esther , Nederlof Petra M. , Smid Marcel , van de Werken Harmen J.G. , Kanaar Roland , Martens John W.M. , Jager Agnes , van Gent Dik C.
Published: April 2023

Supplemental table 1: Comparison of clinicopathologic characteristics between successful tests and not successful tests. Supplemental table 2: Comparison of clinicopathologic characteristics RECAP positive/negative/intermediate tumors. Supplemental table 3: All characteristics and RECAP test outcomes per tumor
Supplemental Table 2 from Underreporting of Research Biopsies from Clinical Trials in Oncology
Authors: Parseghian Christine M. , Raghav Kanwal , Wolff Robert A. , Ensor Joe , Yao James , Ellis Lee M. , Tam Alda L. , Overman Michael J.
Published: April 2023

Factors Correlating with Research Biopsy Reporting from Published Manuscripts
Supplemental legend from Functional Ex Vivo Assay Reveals Homologous Recombination Deficiency in Breast Cancer Beyond BRCA Gene Defects
Authors: Meijer Titia G. , Verkaik Nicole S. , Sieuwerts Anieta M. , van Riet Job , Naipal Kishan A.T. , van Deurzen Carolien H.M. , den Bakker Michael A. , Sleddens Hein F.B.M. , Dubbink Hendrikus-Jan , den Toom T. Dorine , Dinjens Winand N.M. , Lips Esther , Nederlof Petra M. , Smid Marcel , van de Werken Harmen J.G. , Kanaar Roland , Martens John W.M. , Jager Agnes , van Gent Dik C.
Published: April 2023

Supplemental legend
Figure S4 from Functional Ex Vivo Assay Reveals Homologous Recombination Deficiency in Breast Cancer Beyond BRCA Gene Defects
Authors: Meijer Titia G. , Verkaik Nicole S. , Sieuwerts Anieta M. , van Riet Job , Naipal Kishan A.T. , van Deurzen Carolien H.M. , den Bakker Michael A. , Sleddens Hein F.B.M. , Dubbink Hendrikus-Jan , den Toom T. Dorine , Dinjens Winand N.M. , Lips Esther , Nederlof Petra M. , Smid Marcel , van de Werken Harmen J.G. , Kanaar Roland , Martens John W.M. , Jager Agnes , van Gent Dik C.
Published: April 2023

Microsatellite instability. Pentaplex PCR showed presence of MSI in M77 and M188.
Table S3 from Phase I Dose-Escalation and -Expansion Study of the BRAF Inhibitor Encorafenib (LGX818) in Metastatic BRAF-Mutant Melanoma
Authors: Delord Jean-Pierre , Robert Caroline , Nyakas Marta , McArthur Grant A. , Kudchakar Ragini , Mahipal Amit , Yamada Yasuhide , Sullivan Ryan , Arance Ana , Kefford Richard F. , Carlino Matteo S. , Hidalgo Manuel , Gomez-Roca Carlos , Michel Daniela , Seroutou Abdelkader , Aslanis Vassilios , Caponigro Giordano , Stuart Darrin D. , Moutouh-de Parseval Laure , Demuth Tim , Dummer Reinhard
Published: April 2023

Summary of pharmacokinetic parameters (cycle 1 day 1 [C1D1] and cycle 1 day 15 [C1D15]) by treatment group in the dose-escalation phase (QD regimen)
Figure S6 from Aberrant Lck Signal via CD28 Costimulation Augments Antigen-Specific Functionality and Tumor Control by Redirected T Cells with PD-1 Blockade in Humanized Mice
Authors: Gulati Pratiksha , Rühl Julia , Kannan Abhilash , Pircher Magdalena , Schuberth Petra , Nytko Katarzyna J. , Pruschy Martin , Sulser Simon , Haefner Mark , Jensen Shawn , Soltermann Alex , Jungraithmayr Wolfgang , Eisenring Maya , Winder Thomas , Samaras Panagiotis , Tabor Annett , Stenger Rene , Stupp Roger , Weder Walter , Renner Christoph , Münz Christian , Petrausch Ulf
Published: April 2023

Baseline level of cytokines
Figure S4 from Aberrant Lck Signal via CD28 Costimulation Augments Antigen-Specific Functionality and Tumor Control by Redirected T Cells with PD-1 Blockade in Humanized Mice
Authors: Gulati Pratiksha , Rühl Julia , Kannan Abhilash , Pircher Magdalena , Schuberth Petra , Nytko Katarzyna J. , Pruschy Martin , Sulser Simon , Haefner Mark , Jensen Shawn , Soltermann Alex , Jungraithmayr Wolfgang , Eisenring Maya , Winder Thomas , Samaras Panagiotis , Tabor Annett , Stenger Rene , Stupp Roger , Weder Walter , Renner Christoph , Münz Christian , Petrausch Ulf
Published: April 2023

Generation of humanized mice using leukapheresis or human fetal liver (HFL) derived CD34+ cells.
Figure S2 from Aberrant Lck Signal via CD28 Costimulation Augments Antigen-Specific Functionality and Tumor Control by Redirected T Cells with PD-1 Blockade in Humanized Mice
Authors: Gulati Pratiksha , Rühl Julia , Kannan Abhilash , Pircher Magdalena , Schuberth Petra , Nytko Katarzyna J. , Pruschy Martin , Sulser Simon , Haefner Mark , Jensen Shawn , Soltermann Alex , Jungraithmayr Wolfgang , Eisenring Maya , Winder Thomas , Samaras Panagiotis , Tabor Annett , Stenger Rene , Stupp Roger , Weder Walter , Renner Christoph , Münz Christian , Petrausch Ulf
Published: April 2023

Flow chart of transcriptome profiling after antigen-specific stimulation of redirected T cells with different co-stimulations
Figure S1 from Aberrant Lck Signal via CD28 Costimulation Augments Antigen-Specific Functionality and Tumor Control by Redirected T Cells with PD-1 Blockade in Humanized Mice
Authors: Gulati Pratiksha , Rühl Julia , Kannan Abhilash , Pircher Magdalena , Schuberth Petra , Nytko Katarzyna J. , Pruschy Martin , Sulser Simon , Haefner Mark , Jensen Shawn , Soltermann Alex , Jungraithmayr Wolfgang , Eisenring Maya , Winder Thomas , Samaras Panagiotis , Tabor Annett , Stenger Rene , Stupp Roger , Weder Walter , Renner Christoph , Münz Christian , Petrausch Ulf
Published: April 2023

Phenotypic and functional comparison of redirected T cells
Supplementary Table 1 from Single-Cell Profiling of Cutaneous T-Cell Lymphoma Reveals Underlying Heterogeneity Associated with Disease Progression
Authors: Borcherding Nicholas , Voigt Andrew P. , Liu Vincent , Link Brian K. , Zhang Weizhou , Jabbari Ali
Published: April 2023

Supplementary Table 1
Legend, Figure S1 from Single-Cell Profiling of Cutaneous T-Cell Lymphoma Reveals Underlying Heterogeneity Associated with Disease Progression
Authors: Borcherding Nicholas , Voigt Andrew P. , Liu Vincent , Link Brian K. , Zhang Weizhou , Jabbari Ali
Published: April 2023

Legend, Figure S1
Supplementary figure S6 from Endoglin Expression on Cancer-Associated Fibroblasts Regulates Invasion and Stimulates Colorectal Cancer Metastasis
Authors: Paauwe Madelon , Schoonderwoerd Mark J.A. , Helderman Roxan F.C.P. , Harryvan Tom J. , Groenewoud Arwin , van Pelt Gabi W. , Bor Rosalie , Hemmer Danielle M. , Versteeg Henri H. , Snaar-Jagalska B. Ewa , Theuer Charles P. , Hardwick James C.H. , Sier Cornelis F.M. , ten Dijke Peter , Hawinkels Lukas J.A.C.
Published: April 2023

Endoglin expression by CRC cells, HT29 proliferation and in vivo data HT29 only injections
Table S1 from An Anti–CLL-1 Antibody–Drug Conjugate for the Treatment of Acute Myeloid Leukemia
Authors: Zheng Bing , Yu Shang-Fan , del Rosario Geoffrey , Leong Steven R. , Lee Genee Y. , Vij Rajesh , Chiu Cecilia , Liang Wei-Ching , Wu Yan , Chalouni Cecile , Sadowsky Jack , Clark Vanessa , Hendricks Angela , Poon Kirsten Achilles , Chu Wayne , Pillow Thomas , Schutten Melissa M. , Flygare John , Polson Andrew G.
Published: April 2023

hydroxyl radical footprinting of hu6E7.N54A
Supplementary figure S4 from Endoglin Expression on Cancer-Associated Fibroblasts Regulates Invasion and Stimulates Colorectal Cancer Metastasis
Authors: Paauwe Madelon , Schoonderwoerd Mark J.A. , Helderman Roxan F.C.P. , Harryvan Tom J. , Groenewoud Arwin , van Pelt Gabi W. , Bor Rosalie , Hemmer Danielle M. , Versteeg Henri H. , Snaar-Jagalska B. Ewa , Theuer Charles P. , Hardwick James C.H. , Sier Cornelis F.M. , ten Dijke Peter , Hawinkels Lukas J.A.C.
Published: April 2023

HEK293 invasion, BMP-9 expression by CRC cells and CAFs, invasion assays
Supplementary figure S3 from Endoglin Expression on Cancer-Associated Fibroblasts Regulates Invasion and Stimulates Colorectal Cancer Metastasis
Authors: Paauwe Madelon , Schoonderwoerd Mark J.A. , Helderman Roxan F.C.P. , Harryvan Tom J. , Groenewoud Arwin , van Pelt Gabi W. , Bor Rosalie , Hemmer Danielle M. , Versteeg Henri H. , Snaar-Jagalska B. Ewa , Theuer Charles P. , Hardwick James C.H. , Sier Cornelis F.M. , ten Dijke Peter , Hawinkels Lukas J.A.C.
Published: April 2023

Quantification of pSmad western blots and endoglin konock down in endothelial cells
Supplementary figure S2 from Endoglin Expression on Cancer-Associated Fibroblasts Regulates Invasion and Stimulates Colorectal Cancer Metastasis
Authors: Paauwe Madelon , Schoonderwoerd Mark J.A. , Helderman Roxan F.C.P. , Harryvan Tom J. , Groenewoud Arwin , van Pelt Gabi W. , Bor Rosalie , Hemmer Danielle M. , Versteeg Henri H. , Snaar-Jagalska B. Ewa , Theuer Charles P. , Hardwick James C.H. , Sier Cornelis F.M. , ten Dijke Peter , Hawinkels Lukas J.A.C.
Published: April 2023

Endoglin is not expressed on NF in vivo, CAF marker protein expression, total Smad2 and endoglin expression on mCAFs
Supplementary Tables S1-6 and S8 from Sarcomatoid Renal Cell Carcinoma Has a Distinct Molecular Pathogenesis, Driver Mutation Profile, and Transcriptional Landscape
Authors: Wang Zixing , Kim Tae Beom , Peng Bo , Karam Jose , Creighton Chad , Joon Aron , Kawakami Fumi , Trevisan Patricia , Jonasch Eric , Chow Chi-Wan , Canales Jaime Rodriguez , Tamboli Pheroze , Tannir Nizar , Wood Christopher , Monzon Federico , Baggerly Keith , Varella-Garcia Marileila , Czerniak Bogdan , Wistuba Ignacio , Mills Gordon , Shaw Kenna , Chen Ken , Sircar Kanishka
Published: April 2023

Table S1. Clinicopathologic characteristics of sarcomatoid and non-sarcomatoid RCC cases Table S2. Non-synonymous mutations in sarcomatoid RCC samples Table S3a. Significantly mutated genes in Sarcomatoid RCC Table S3b. Mutations in sarcomatoid RCC versus RCC across different subtypes, by P value (Odds Ratio) Table S4. Comparison of arm-level chromosomal losses (d) and gains (a) between sarcomatoid ccRCC versus non-sarcomatoid ccRCC across different Fuhrman grades, by P value Table S5. Fewer segmental 3p21-3p25.3 deletions in sarcomatoid ccRCC compared to non-sarcomatoid ccRCC across different Fuhrman grades, by P value Table S6. A mutation in one of TP53, PTEN, or RELN genes correlates with sarcomatoid change in clear cell RCC Table S8. Mutations in sarcomatoid RCC when assaying multiple tumor regions from the same patients
Supplementary Methods from Sarcomatoid Renal Cell Carcinoma Has a Distinct Molecular Pathogenesis, Driver Mutation Profile, and Transcriptional Landscape
Authors: Wang Zixing , Kim Tae Beom , Peng Bo , Karam Jose , Creighton Chad , Joon Aron , Kawakami Fumi , Trevisan Patricia , Jonasch Eric , Chow Chi-Wan , Canales Jaime Rodriguez , Tamboli Pheroze , Tannir Nizar , Wood Christopher , Monzon Federico , Baggerly Keith , Varella-Garcia Marileila , Czerniak Bogdan , Wistuba Ignacio , Mills Gordon , Shaw Kenna , Chen Ken , Sircar Kanishka
Published: April 2023

Supplemental Methods 1. Exome sequencing pipeline Supplemental Methods 2. RNA seq pipeline Supplemental Methods 3. DNA methylation profiling pipeline Supplemental Methods 4. Fluorescence in situ hybridization Supplemental Methods 5. TCGA samples with possible copy neutral loss of heterozygosity in 3p21 and 3p25 regions
Supplementary Tables S1-S4 from Cell Surface Notch Ligand DLL3 is a Therapeutic Target in Isocitrate Dehydrogenase–mutant Glioma
Authors: Spino Marissa , Kurz Sylvia C. , Chiriboga Luis , Serrano Jonathan , Zeck Briana , Sen Namita , Patel Seema , Shen Guomiao , Vasudevaraja Varshini , Tsirigos Aristotelis , Suryadevara Carter M. , Frenster Joshua D. , Tateishi Kensuke , Wakimoto Hiroaki , Jain Rajan , Riina Howard A. , Nicolaides Theodore P. , Sulman Erik P. , Cahill Daniel P. , Golfinos John G. , Isse Kumiko , Saunders Laura R. , Zagzag David , Placantonakis Dimitris G. , Snuderl Matija , Chi Andrew S.
Published: April 2023

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