bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Table S7 from SPOP Mutations Target STING1 Signaling in Prostate Cancer and Create Therapeutic Vulnerabilities to PARP Inhibitor–Induced Growth Suppression
Authors: Geng Chuandong , Zhang Man-Chao , Manyam Ganiraju C. , Vykoukal Jody V. , Fahrmann Johannes F. , Peng Shan , Wu Cheng , Park Sanghee , Kondraganti Shakuntala , Wang Daoqi , Robinson Brian D. , Loda Massimo , Barbieri Christopher E. , Yap Timothy A. , Corn Paul G. , Hanash Samir , Broom Bradley M. , Pilié Patrick G. , Thompson Timothy C.
Published: November 2023

Supplementary Table S7. Quantification of each protein-specific band normalized to vinculin (RM-1-BM–derived models, Fig. 2C).
Supplementary Table S6 from SPOP Mutations Target STING1 Signaling in Prostate Cancer and Create Therapeutic Vulnerabilities to PARP Inhibitor–Induced Growth Suppression
Authors: Geng Chuandong , Zhang Man-Chao , Manyam Ganiraju C. , Vykoukal Jody V. , Fahrmann Johannes F. , Peng Shan , Wu Cheng , Park Sanghee , Kondraganti Shakuntala , Wang Daoqi , Robinson Brian D. , Loda Massimo , Barbieri Christopher E. , Yap Timothy A. , Corn Paul G. , Hanash Samir , Broom Bradley M. , Pilié Patrick G. , Thompson Timothy C.
Published: November 2023

Supplementary Table S6. Quantification of each protein-specific band normalized to vinculin (C4-2b-derived models, Fig. 2B).
Supplementary Table S11 from SPOP Mutations Target STING1 Signaling in Prostate Cancer and Create Therapeutic Vulnerabilities to PARP Inhibitor–Induced Growth Suppression
Authors: Geng Chuandong , Zhang Man-Chao , Manyam Ganiraju C. , Vykoukal Jody V. , Fahrmann Johannes F. , Peng Shan , Wu Cheng , Park Sanghee , Kondraganti Shakuntala , Wang Daoqi , Robinson Brian D. , Loda Massimo , Barbieri Christopher E. , Yap Timothy A. , Corn Paul G. , Hanash Samir , Broom Bradley M. , Pilié Patrick G. , Thompson Timothy C.
Published: November 2023

Supplemental Table S11. Quantification of each protein-specific band normalized to vinculin (C4-2b–derived models, Fig. 4E).
Table S2 from Cotargeting Phosphoinositide 3-Kinase and Focal Adhesion Kinase Pathways Inhibits Proliferation of NF2 Schwannoma Cells
Authors: Hardin Haley M. , Dinh Christine T. , Huegel Julianne , Petrilli Alejandra M. , Bracho Olena , Allaf Abdulrahman M. , Karajannis Matthias A. , Griswold Anthony J. , Ivan Michael E. , Morcos Jacques , Gultekin Sakir H. , Telischi Fred F. , Liu Xue Zhong , Fernandez-Valle Cristina
Published: November 2023

Supplemental Table 2. Selectivity Score of Top Three Drug Combinations for Merlin-deficient Over Isogenic Normal Human Schwann Cells.
Figure S2 from Cotargeting Phosphoinositide 3-Kinase and Focal Adhesion Kinase Pathways Inhibits Proliferation of NF2 Schwannoma Cells
Authors: Hardin Haley M. , Dinh Christine T. , Huegel Julianne , Petrilli Alejandra M. , Bracho Olena , Allaf Abdulrahman M. , Karajannis Matthias A. , Griswold Anthony J. , Ivan Michael E. , Morcos Jacques , Gultekin Sakir H. , Telischi Fred F. , Liu Xue Zhong , Fernandez-Valle Cristina
Published: November 2023

Supplemental Figure 2. Neither omipalisib nor dasatinib produce significant apoptosis.
Figure S1 from Cotargeting Phosphoinositide 3-Kinase and Focal Adhesion Kinase Pathways Inhibits Proliferation of NF2 Schwannoma Cells
Authors: Hardin Haley M. , Dinh Christine T. , Huegel Julianne , Petrilli Alejandra M. , Bracho Olena , Allaf Abdulrahman M. , Karajannis Matthias A. , Griswold Anthony J. , Ivan Michael E. , Morcos Jacques , Gultekin Sakir H. , Telischi Fred F. , Liu Xue Zhong , Fernandez-Valle Cristina
Published: November 2023

Supplemental Figure 1. HS01 western blots for dasatinib target and necroptosis markers.
Supplementary Figures from Targeting Aggressive B-cell Lymphomas through Pharmacological Activation of the Mitochondrial Protease OMA1
Authors: Schwarzer Adrian , Oliveira Matheus , Kleppa Marc-Jens , Slattery Scott D. , Anantha Andy , Cooper Alan , Hannink Mark , Schambach Axel , Dörrie Anneke , Kotlyarov Alexey , Gaestel Matthias , Hembrough Todd , Levine Jedd , Luther Michael , Stocum Michael , Stiles Linsey , Weinstock David M. , Liesa Marc , Kostura Matthew J.
Published: November 2023

Supplementary Figures and Methods
Figure S2 from Use of Payload Binding Selectivity Enhancers to Improve Therapeutic Index of Maytansinoid–Antibody–Drug Conjugates
Authors: Nguyen Toan D. , Bordeau Brandon M. , Balthasar Joseph P.
Published: November 2023

Anti-CD123 mAb binding data
Table S1 from Targeted Investigational Oncology Agents in the NCI-60: A Phenotypic Systems–based Resource
Authors: Morris Joel , Kunkel Mark W. , White Stephen L. , Wishka Donn G. , Lopez Omar D. , Bowles Lori , Sellers Brady Penny , Ramsey Patricia , Grams Julie , Rohrer Tiffany , Martin Karen , Dexheimer Thomas S. , Coussens Nathan P. , Evans David , Risbood Prabhakar , Sonkin Dmitriy , Williams John D. , Polley Eric C. , Collins Jerry M. , Doroshow James H. , Teicher Beverly A.
Published: November 2023

Table of GI50 data
Supplementary Table S5 from Combination Therapies to Improve the Efficacy of Immunotherapy in Triple-negative Breast Cancer
Authors: Alečković Maša , Li Zheqi , Zhou Ningxuan , Qiu Xintao , Lulseged Bethlehem , Foidart Pierre , Huang Xiao-Yun , Garza Kodie , Shu Shaokun , Kesten Nikolas , Li Rong , Lim Klothilda , Garrido-Castro Ana C. , Guerriero Jennifer L. , Qi Jun , Long Henry W. , Polyak Kornelia
Published: November 2023

Genomic location of gained ATAC sites.
Supplementary Table S4 from Combination Therapies to Improve the Efficacy of Immunotherapy in Triple-negative Breast Cancer
Authors: Alečković Maša , Li Zheqi , Zhou Ningxuan , Qiu Xintao , Lulseged Bethlehem , Foidart Pierre , Huang Xiao-Yun , Garza Kodie , Shu Shaokun , Kesten Nikolas , Li Rong , Lim Klothilda , Garrido-Castro Ana C. , Guerriero Jennifer L. , Qi Jun , Long Henry W. , Polyak Kornelia
Published: November 2023

Genes differentially expressed in CD45+ leukocytes.
Supplementary Table S2 from Combination Therapies to Improve the Efficacy of Immunotherapy in Triple-negative Breast Cancer
Authors: Alečković Maša , Li Zheqi , Zhou Ningxuan , Qiu Xintao , Lulseged Bethlehem , Foidart Pierre , Huang Xiao-Yun , Garza Kodie , Shu Shaokun , Kesten Nikolas , Li Rong , Lim Klothilda , Garrido-Castro Ana C. , Guerriero Jennifer L. , Qi Jun , Long Henry W. , Polyak Kornelia
Published: November 2023

Immune cell quantification by FACS.
Supplementary Fig. S4 from Combination Therapies to Improve the Efficacy of Immunotherapy in Triple-negative Breast Cancer
Authors: Alečković Maša , Li Zheqi , Zhou Ningxuan , Qiu Xintao , Lulseged Bethlehem , Foidart Pierre , Huang Xiao-Yun , Garza Kodie , Shu Shaokun , Kesten Nikolas , Li Rong , Lim Klothilda , Garrido-Castro Ana C. , Guerriero Jennifer L. , Qi Jun , Long Henry W. , Polyak Kornelia
Published: November 2023

Supplementary Fig. S4 shows additional RNA-seq data analyses.
Supplementary Fig. S2 from Combination Therapies to Improve the Efficacy of Immunotherapy in Triple-negative Breast Cancer
Authors: Alečković Maša , Li Zheqi , Zhou Ningxuan , Qiu Xintao , Lulseged Bethlehem , Foidart Pierre , Huang Xiao-Yun , Garza Kodie , Shu Shaokun , Kesten Nikolas , Li Rong , Lim Klothilda , Garrido-Castro Ana C. , Guerriero Jennifer L. , Qi Jun , Long Henry W. , Polyak Kornelia
Published: November 2023

Supplementary Fig. S2 shows the long-term effects of combination treatment in the EMT-6 mammary tumor model.
Supplementary Figure S7 from Efficacy and Safety of Glycosphingolipid SSEA-4 Targeting CAR-T Cells in an Ovarian Carcinoma Model
Authors: Monzo Hector J. , Kalander Kerttu , Hyytiäinen Marko M. , Elbasani Endrit , Wall Johanna , Moyano-Galceran Lidia , Tanjore Ramanathan Jayendrakishore , Jukonen Joonas , Laakkonen Pirjo , Ristimäki Ari , Carlson Joseph W. , Lehti Kaisa , Salehi Sahar , Puolakkainen Pauli , Haglund Caj , Seppänen Hanna , Leppä Sirpa , Ojala Päivi M.
Published: November 2023

Supplementary Figure S7. T cell detection in mouse tissues after the long-term survival study. Indicated tissues were stained with HOECHST 33342 for nuclei (blue), anti-EGFR to detect CAR-T cells (middle panel; green) and anti-CD3 for T cells (right panel, white). Left panel shows a merged image of all three channels. Arrows highlight CAR-T and CD3 positive cells, while arrowheads highlight erythrocytes with an intense background staining.
Supplementary Figure S5 from Efficacy and Safety of Glycosphingolipid SSEA-4 Targeting CAR-T Cells in an Ovarian Carcinoma Model
Authors: Monzo Hector J. , Kalander Kerttu , Hyytiäinen Marko M. , Elbasani Endrit , Wall Johanna , Moyano-Galceran Lidia , Tanjore Ramanathan Jayendrakishore , Jukonen Joonas , Laakkonen Pirjo , Ristimäki Ari , Carlson Joseph W. , Lehti Kaisa , Salehi Sahar , Puolakkainen Pauli , Haglund Caj , Seppänen Hanna , Leppä Sirpa , Ojala Päivi M.
Published: November 2023

Supplementary Figure S5. Weight monitoring during the long-term in vivo study. Mice treated with 2M CAR-T dose showed pronounced weight loss and health deterioration at earlier time points than mice treated with 1M CAR-T dose. PBS, tumor-free CAR/NT-T 1M, and NT-T groups did not show weight loss and remained healthy during the duration of the experiment. Unless otherwise indicated, mice groups are tumor-bearing. (M=1x106).
Supplementary Figure S4 from Efficacy and Safety of Glycosphingolipid SSEA-4 Targeting CAR-T Cells in an Ovarian Carcinoma Model
Authors: Monzo Hector J. , Kalander Kerttu , Hyytiäinen Marko M. , Elbasani Endrit , Wall Johanna , Moyano-Galceran Lidia , Tanjore Ramanathan Jayendrakishore , Jukonen Joonas , Laakkonen Pirjo , Ristimäki Ari , Carlson Joseph W. , Lehti Kaisa , Salehi Sahar , Puolakkainen Pauli , Haglund Caj , Seppänen Hanna , Leppä Sirpa , Ojala Päivi M.
Published: November 2023

Supplementary Figure S4. Anti-tumor response and survival in the long-term in vivo study. A. Treatment groups and used T cell doses. B. Representative BLI images of mice treated with PBS, 1M, and 2M NT or CAR-T cells doses at the indicated time points (days; d). (M=1x106). *Asterisks indicate mice sacrificed due to toxicities.
Supplementary Figure S3 from Efficacy and Safety of Glycosphingolipid SSEA-4 Targeting CAR-T Cells in an Ovarian Carcinoma Model
Authors: Monzo Hector J. , Kalander Kerttu , Hyytiäinen Marko M. , Elbasani Endrit , Wall Johanna , Moyano-Galceran Lidia , Tanjore Ramanathan Jayendrakishore , Jukonen Joonas , Laakkonen Pirjo , Ristimäki Ari , Carlson Joseph W. , Lehti Kaisa , Salehi Sahar , Puolakkainen Pauli , Haglund Caj , Seppänen Hanna , Leppä Sirpa , Ojala Päivi M.
Published: November 2023

Supplementary Figure S3. IFN measurement and organ BLI of the short-term in vivo study. A. IFN quantification by ELISA in post-mortem mouse blood plasma. B. Representative BLI images of isolated organs from mice treated with PBS, NT-T, and CAR-T cells at the indicated T cell doses after 32 days. C. Organ BLI quantification. N=3 for control. N=5 for all groups, except N=2 for NT-T 1M, N=3 for CAR-T 1M, and N=4 NT-T 2M. Mean ± SD. One-way ANOVA with Tukey’s multiple comparison tests. (A) ***p=0.0005, ****p=0.0001. (C) *p=0.04, **p≤0.001 to PBS group. Not significant, n.s., differences were attributed to p≥0.05. (M=1x106).
Supplementary Figure S1 from Efficacy and Safety of Glycosphingolipid SSEA-4 Targeting CAR-T Cells in an Ovarian Carcinoma Model
Authors: Monzo Hector J. , Kalander Kerttu , Hyytiäinen Marko M. , Elbasani Endrit , Wall Johanna , Moyano-Galceran Lidia , Tanjore Ramanathan Jayendrakishore , Jukonen Joonas , Laakkonen Pirjo , Ristimäki Ari , Carlson Joseph W. , Lehti Kaisa , Salehi Sahar , Puolakkainen Pauli , Haglund Caj , Seppänen Hanna , Leppä Sirpa , Ojala Päivi M.
Published: November 2023

Supplementary Figure S1. SSEA-4 staining specificity and LDH cytotoxicity assay. A. SSEA-4 immunohistochemistry in paraffin-embedded gastric cancer tumor microarrays. B. Upper panel sections were treated with standard xylene/ethanol series used in paraffin embedded section treatment, whereas lower panel samples were untreated. C. Consecutive sections of fresh frozen pancreatic cancer patient samples were stained with anti-SSEA-4 antibody. The staining was blocked with SSEA-4 hexaose (middle panel) or SSEA-3 (right panel). D. Representative immunofluorescence micrographs of SSEA-4 (red) in OVCAR-4 cells (high expression) and Caov-3 cells (no expression). Nucleus (blue; Hoechst 33342). N=3. E. LDH assay to measure toxicity of anti-SSEA-4 CAR-T cells on SSEA-4 positive OVCAR-4 cells and SSEA-4 negative Caov-3 cells as a control (N=2). LDH assay was performed after 72 hours of CAR/NT-T cell treatment. ****p=0.0001, ***p=0.0002 and **p=0.0025.
Supplementary Figure Legends from Efficacy and Safety of Glycosphingolipid SSEA-4 Targeting CAR-T Cells in an Ovarian Carcinoma Model
Authors: Monzo Hector J. , Kalander Kerttu , Hyytiäinen Marko M. , Elbasani Endrit , Wall Johanna , Moyano-Galceran Lidia , Tanjore Ramanathan Jayendrakishore , Jukonen Joonas , Laakkonen Pirjo , Ristimäki Ari , Carlson Joseph W. , Lehti Kaisa , Salehi Sahar , Puolakkainen Pauli , Haglund Caj , Seppänen Hanna , Leppä Sirpa , Ojala Päivi M.
Published: November 2023

Supplementary Figure legends
Data from Cotargeting Phosphoinositide 3-Kinase and Focal Adhesion Kinase Pathways Inhibits Proliferation of NF2 Schwannoma Cells
Authors: Hardin Haley M. , Dinh Christine T. , Huegel Julianne , Petrilli Alejandra M. , Bracho Olena , Allaf Abdulrahman M. , Karajannis Matthias A. , Griswold Anthony J. , Ivan Michael E. , Morcos Jacques , Gultekin Sakir H. , Telischi Fred F. , Liu Xue Zhong , Fernandez-Valle Cristina
Published: November 2023

Abstract
Neurofibromatosis Type 2 (NF2) is a tumor predisposition syndrome caused by germline inactivating mutations in the NF2 gene encoding the merlin tumor suppressor. Patients develop multiple benign tumor types in the nervous system including bilateral vestibular schwannomas (VS). Standard treatments include surgery and radiation therapy, which may lead to loss of hearing, impaired facial nerve function, and other complications. Kinase inhibitor monotherapies have been evaluated clinically for NF2 patients with limited success, and more effective nonsurgical therapies are urgently needed. Schwannoma model cells treated with PI3K inhibitors upregulate activity of the focal adhesion kinase (FAK) family as a compensatory survival pathway. We screened combinations of 13 clinically relevant PI3K and FAK inhibitors using human isogenic normal and merlin-deficient Schwann cell lines. The most efficacious combination was PI3K/mTOR inhibitor omipalisib with SRC/FAK inhibitor dasatinib. Sub-GI50 doses of the single drugs blocked phosphorylation of their major target proteins. The combination was superior to either single agent in promoting a G1 cell-cycle arrest and produced a 44% decrease in tumor growth over a 2-week period in a pilot orthotopic allograft model. Evaluation of single and combination drugs in six human primary VS cell models revealed the combination was superior to the monotherapies in 3 of 6 VS samples, highlighting inter-tumor variability between patients consistent with observations from clinical trials with other molecular targeted agents. Dasatinib alone performed as well as the combination in the remaining three samples. Preclinically validated combination therapies hold promise for NF2 patients and warrants further study in clinical trials.
Supplementary Data File S2 from USP1 Expression Driven by EWS::FLI1 Transcription Factor Stabilizes Survivin and Mitigates Replication Stress in Ewing Sarcoma
Authors: Mallard Halle J. , Wan Shibiao , Nidhi Prakriti , Hanscom-Trofy Yvan D. , Mohapatra Bhopal , Woods Nicholas T. , Lopez-Guerrero Jose Antonio , Llombart-Bosch Antonio , Machado Isidro , Scotlandi Katia , Kreiling Natasha F. , Perry Megan C. , Mirza Sameer , Coulter Donald W. , Band Vimla , Band Hamid , Ghosal Gargi
Published: November 2023

Analysis of TMT-MS data; Page 2: DAVID pathway analysis of differentially expressed proteins identified by TMT-MS.
Figure S5 from USP1 Expression Driven by EWS::FLI1 Transcription Factor Stabilizes Survivin and Mitigates Replication Stress in Ewing Sarcoma
Authors: Mallard Halle J. , Wan Shibiao , Nidhi Prakriti , Hanscom-Trofy Yvan D. , Mohapatra Bhopal , Woods Nicholas T. , Lopez-Guerrero Jose Antonio , Llombart-Bosch Antonio , Machado Isidro , Scotlandi Katia , Kreiling Natasha F. , Perry Megan C. , Mirza Sameer , Coulter Donald W. , Band Vimla , Band Hamid , Ghosal Gargi
Published: November 2023

Figure S5 shows EWS cells are sensitive to doxorubicin and etoposide treatment.
Supplementary Figure 1 from A Novel Role of Prostate-Specific Membrane Antigen in Telomere Stability in Prostate Cancer Cells
Authors: Reddy Vidyavathi , Hwang Clara , Reddy G. Prem-Veer , Kim Sahn-Ho
Published: November 2023

Supplementary Figure 1
Supplementary Figure 1 Legend from A Novel Role of Prostate-Specific Membrane Antigen in Telomere Stability in Prostate Cancer Cells
Authors: Reddy Vidyavathi , Hwang Clara , Reddy G. Prem-Veer , Kim Sahn-Ho
Published: November 2023

Lack of AR expression is not the cause for telomere DNA damage in PC-3 cells.
Table S7 from CBF-Beta Mitigates PI3K-Alpha–Specific Inhibitor Killing through PIM1 in PIK3CA-Mutant Gastric Cancer
Authors: Stanland Lyla J. , Ang Hazel X. , Hoj Jacob P. , Chu Yunqiang , Tan Patrick , Wood Kris C. , Luftig Micah A.
Published: November 2023

QPCR primers
Table S5 from CBF-Beta Mitigates PI3K-Alpha–Specific Inhibitor Killing through PIM1 in PIK3CA-Mutant Gastric Cancer
Authors: Stanland Lyla J. , Ang Hazel X. , Hoj Jacob P. , Chu Yunqiang , Tan Patrick , Wood Kris C. , Luftig Micah A.
Published: November 2023

Genes present in each of the 8 clusters
Table S3 from CBF-Beta Mitigates PI3K-Alpha–Specific Inhibitor Killing through PIM1 in PIK3CA-Mutant Gastric Cancer
Authors: Stanland Lyla J. , Ang Hazel X. , Hoj Jacob P. , Chu Yunqiang , Tan Patrick , Wood Kris C. , Luftig Micah A.
Published: November 2023

Beta scores generated for DMSO and BYL719 treated populations using MAGeCK analysis pipeline
Figure S6 from CBF-Beta Mitigates PI3K-Alpha–Specific Inhibitor Killing through PIM1 in PIK3CA-Mutant Gastric Cancer
Authors: Stanland Lyla J. , Ang Hazel X. , Hoj Jacob P. , Chu Yunqiang , Tan Patrick , Wood Kris C. , Luftig Micah A.
Published: November 2023

Figure S6 shows down-regulation of RUNX1 in BYL719 resistant cells
Figure S2 from CBF-Beta Mitigates PI3K-Alpha–Specific Inhibitor Killing through PIM1 in PIK3CA-Mutant Gastric Cancer
Authors: Stanland Lyla J. , Ang Hazel X. , Hoj Jacob P. , Chu Yunqiang , Tan Patrick , Wood Kris C. , Luftig Micah A.
Published: November 2023

Figure S2 shows ribbon plots generated for non-gastric cancer cell lines included in the screen
Supplementary Table 2 from Podoplanin Drives Amoeboid Invasion in Canine and Human Mucosal Melanoma
Authors: Shinada Masahiro , Kato Daiki , Motegi Tomoki , Tsuboi Masaya , Ikeda Namiko , Aoki Susumu , Iguchi Takaaki , Li Toshio , Kodera Yuka , Ota Ryosuke , Hashimoto Yuko , Takahashi Yosuke , Chambers James , Uchida Kazuyuki , Kato Yukinari , Nishimura Ryohei , Nakagawa Takayuki
Published: November 2023

Univariate survival analysis of dogs with mucosal melanoma.
Supplementary Materials and Methods from Podoplanin Drives Amoeboid Invasion in Canine and Human Mucosal Melanoma
Authors: Shinada Masahiro , Kato Daiki , Motegi Tomoki , Tsuboi Masaya , Ikeda Namiko , Aoki Susumu , Iguchi Takaaki , Li Toshio , Kodera Yuka , Ota Ryosuke , Hashimoto Yuko , Takahashi Yosuke , Chambers James , Uchida Kazuyuki , Kato Yukinari , Nishimura Ryohei , Nakagawa Takayuki
Published: November 2023

Supplementary Materials and Methods
Supplementary Figure Legends from Podoplanin Drives Amoeboid Invasion in Canine and Human Mucosal Melanoma
Authors: Shinada Masahiro , Kato Daiki , Motegi Tomoki , Tsuboi Masaya , Ikeda Namiko , Aoki Susumu , Iguchi Takaaki , Li Toshio , Kodera Yuka , Ota Ryosuke , Hashimoto Yuko , Takahashi Yosuke , Chambers James , Uchida Kazuyuki , Kato Yukinari , Nishimura Ryohei , Nakagawa Takayuki
Published: November 2023

Supplementary Figure Legends 1-12
Supplementary Figure 8 from Podoplanin Drives Amoeboid Invasion in Canine and Human Mucosal Melanoma
Authors: Shinada Masahiro , Kato Daiki , Motegi Tomoki , Tsuboi Masaya , Ikeda Namiko , Aoki Susumu , Iguchi Takaaki , Li Toshio , Kodera Yuka , Ota Ryosuke , Hashimoto Yuko , Takahashi Yosuke , Chambers James , Uchida Kazuyuki , Kato Yukinari , Nishimura Ryohei , Nakagawa Takayuki
Published: November 2023

PDPN promotes tumor growth and amoeboid invasion in vivo.
Table S1 from Stromal DDR2 Promotes Ovarian Cancer Metastasis through Regulation of Metabolism and Secretion of Extracellular Matrix Proteins
Authors: Schab Angela M. , Greenwade Molly M. , Stock Elizabeth , Lomonosova Elena , Cho Kevin , Grither Whitney R. , Noia Hollie , Wilke Daniel , Mullen Mary M. , Hagemann Andrea R. , Hagemann Ian S. , Thaker Premal H. , Kuroki Lindsay M. , McCourt Carolyn K. , Khabele Dineo , Powell Matthew A. , Mutch David G. , Zhao Peinan , Shriver Leah P. , Patti Gary J. , Longmore Gregory D. , Fuh Katherine C.
Published: November 2023

Primer Sequences
Supplementary Figure 6 from Podoplanin Drives Amoeboid Invasion in Canine and Human Mucosal Melanoma
Authors: Shinada Masahiro , Kato Daiki , Motegi Tomoki , Tsuboi Masaya , Ikeda Namiko , Aoki Susumu , Iguchi Takaaki , Li Toshio , Kodera Yuka , Ota Ryosuke , Hashimoto Yuko , Takahashi Yosuke , Chambers James , Uchida Kazuyuki , Kato Yukinari , Nishimura Ryohei , Nakagawa Takayuki
Published: November 2023

ROCK inhibition suppresses features of amoeboid invasion.
Figure S6 from Stromal DDR2 Promotes Ovarian Cancer Metastasis through Regulation of Metabolism and Secretion of Extracellular Matrix Proteins
Authors: Schab Angela M. , Greenwade Molly M. , Stock Elizabeth , Lomonosova Elena , Cho Kevin , Grither Whitney R. , Noia Hollie , Wilke Daniel , Mullen Mary M. , Hagemann Andrea R. , Hagemann Ian S. , Thaker Premal H. , Kuroki Lindsay M. , McCourt Carolyn K. , Khabele Dineo , Powell Matthew A. , Mutch David G. , Zhao Peinan , Shriver Leah P. , Patti Gary J. , Longmore Gregory D. , Fuh Katherine C.
Published: November 2023

Tumor LOXL2 and DDR2 expression correlates with survival
Supplementary Figure 4 from Podoplanin Drives Amoeboid Invasion in Canine and Human Mucosal Melanoma
Authors: Shinada Masahiro , Kato Daiki , Motegi Tomoki , Tsuboi Masaya , Ikeda Namiko , Aoki Susumu , Iguchi Takaaki , Li Toshio , Kodera Yuka , Ota Ryosuke , Hashimoto Yuko , Takahashi Yosuke , Chambers James , Uchida Kazuyuki , Kato Yukinari , Nishimura Ryohei , Nakagawa Takayuki
Published: November 2023

Loss of PDPN leads to cell cycle arrest and cellular senescence.
Supplementary Figure 12 from Podoplanin Drives Amoeboid Invasion in Canine and Human Mucosal Melanoma
Authors: Shinada Masahiro , Kato Daiki , Motegi Tomoki , Tsuboi Masaya , Ikeda Namiko , Aoki Susumu , Iguchi Takaaki , Li Toshio , Kodera Yuka , Ota Ryosuke , Hashimoto Yuko , Takahashi Yosuke , Chambers James , Uchida Kazuyuki , Kato Yukinari , Nishimura Ryohei , Nakagawa Takayuki
Published: November 2023

Human mucosal melanomas with PDPN high expression demonstrate enrichment of gene signatures associated with amoeboid invasion.
Supplementary Figure 11 from Podoplanin Drives Amoeboid Invasion in Canine and Human Mucosal Melanoma
Authors: Shinada Masahiro , Kato Daiki , Motegi Tomoki , Tsuboi Masaya , Ikeda Namiko , Aoki Susumu , Iguchi Takaaki , Li Toshio , Kodera Yuka , Ota Ryosuke , Hashimoto Yuko , Takahashi Yosuke , Chambers James , Uchida Kazuyuki , Kato Yukinari , Nishimura Ryohei , Nakagawa Takayuki
Published: November 2023

Canine mucosal melanomas with PDPN high expression demonstrate enrichment of gene signatures associated with amoeboid invasion.
Figure S2 from Stromal DDR2 Promotes Ovarian Cancer Metastasis through Regulation of Metabolism and Secretion of Extracellular Matrix Proteins
Authors: Schab Angela M. , Greenwade Molly M. , Stock Elizabeth , Lomonosova Elena , Cho Kevin , Grither Whitney R. , Noia Hollie , Wilke Daniel , Mullen Mary M. , Hagemann Andrea R. , Hagemann Ian S. , Thaker Premal H. , Kuroki Lindsay M. , McCourt Carolyn K. , Khabele Dineo , Powell Matthew A. , Mutch David G. , Zhao Peinan , Shriver Leah P. , Patti Gary J. , Longmore Gregory D. , Fuh Katherine C.
Published: November 2023

Stromal cell expression of DDR2 is critical for clearance, related to Figure 3
Supplementary Figure 1 from Podoplanin Drives Amoeboid Invasion in Canine and Human Mucosal Melanoma
Authors: Shinada Masahiro , Kato Daiki , Motegi Tomoki , Tsuboi Masaya , Ikeda Namiko , Aoki Susumu , Iguchi Takaaki , Li Toshio , Kodera Yuka , Ota Ryosuke , Hashimoto Yuko , Takahashi Yosuke , Chambers James , Uchida Kazuyuki , Kato Yukinari , Nishimura Ryohei , Nakagawa Takayuki
Published: November 2023

PDPN overexpression in the invasion fronts (IFs) is associated with poor prognosis of dogs with mucosal melanoma.
Supplementary Table and Figure Legends from Telomerase Upregulation Induces Progression of Mouse BrafV600E-Driven Thyroid Cancers and Triggers Nontelomeric Effects
Authors: Landa Iñigo , Thornton Caitlin E.M. , Xu Bin , Haase Jacob , Krishnamoorthy Gnana P. , Hao Jingzhu , Knauf Jeffrey A. , Herbert Zachary T. , Martínez Paula , Blasco María A. , Ghossein Ronald , Fagin James A.
Published: November 2023

Supplementary TableS 1-7 and Figure Legends 1-5
Supplementary Table 3 from Telomerase Upregulation Induces Progression of Mouse BrafV600E-Driven Thyroid Cancers and Triggers Nontelomeric Effects
Authors: Landa Iñigo , Thornton Caitlin E.M. , Xu Bin , Haase Jacob , Krishnamoorthy Gnana P. , Hao Jingzhu , Knauf Jeffrey A. , Herbert Zachary T. , Martínez Paula , Blasco María A. , Ghossein Ronald , Fagin James A.
Published: November 2023

Differentially expressed genes from RNAseq data
Supplementary Table 2 from Telomerase Upregulation Induces Progression of Mouse BrafV600E-Driven Thyroid Cancers and Triggers Nontelomeric Effects
Authors: Landa Iñigo , Thornton Caitlin E.M. , Xu Bin , Haase Jacob , Krishnamoorthy Gnana P. , Hao Jingzhu , Knauf Jeffrey A. , Herbert Zachary T. , Martínez Paula , Blasco María A. , Ghossein Ronald , Fagin James A.
Published: November 2023

CRISPRESSO sequencing results
Supplementary Table 1 from Telomerase Upregulation Induces Progression of Mouse BrafV600E-Driven Thyroid Cancers and Triggers Nontelomeric Effects
Authors: Landa Iñigo , Thornton Caitlin E.M. , Xu Bin , Haase Jacob , Krishnamoorthy Gnana P. , Hao Jingzhu , Knauf Jeffrey A. , Herbert Zachary T. , Martínez Paula , Blasco María A. , Ghossein Ronald , Fagin James A.
Published: November 2023

List of primers used for quantitative PCR.
Supplementary Figure 4 from Telomerase Upregulation Induces Progression of Mouse BrafV600E-Driven Thyroid Cancers and Triggers Nontelomeric Effects
Authors: Landa Iñigo , Thornton Caitlin E.M. , Xu Bin , Haase Jacob , Krishnamoorthy Gnana P. , Hao Jingzhu , Knauf Jeffrey A. , Herbert Zachary T. , Martínez Paula , Blasco María A. , Ghossein Ronald , Fagin James A.
Published: November 2023

Additional analyses of RNA sequencing data from mouse tumors with telomerase upregulation.
Supplementary Figure 3 from Telomerase Upregulation Induces Progression of Mouse BrafV600E-Driven Thyroid Cancers and Triggers Nontelomeric Effects
Authors: Landa Iñigo , Thornton Caitlin E.M. , Xu Bin , Haase Jacob , Krishnamoorthy Gnana P. , Hao Jingzhu , Knauf Jeffrey A. , Herbert Zachary T. , Martínez Paula , Blasco María A. , Ghossein Ronald , Fagin James A.
Published: November 2023

Additional insights from RNAscope analysis and telomere length evaluation. A-L. Analysis of intratumoral heterogeneity of Tert transcription via RNAscope.
Supplementary Figure 2 from Telomerase Upregulation Induces Progression of Mouse BrafV600E-Driven Thyroid Cancers and Triggers Nontelomeric Effects
Authors: Landa Iñigo , Thornton Caitlin E.M. , Xu Bin , Haase Jacob , Krishnamoorthy Gnana P. , Hao Jingzhu , Knauf Jeffrey A. , Herbert Zachary T. , Martínez Paula , Blasco María A. , Ghossein Ronald , Fagin James A.
Published: November 2023

Additional features of Braf and Braf+Tert murine tumors.
Supplementary Figure 1 from Polymorphisms in Cyclooxygenase, Lipoxygenase, and TP53 Genes Predict Colorectal Polyp Risk Reduction by Aspirin in the seAFOod Polyp Prevention Trial
Authors: Davies John R. , Mell Tracey , Fuller Harriett , Harland Mark , Saleh Rasha N.M. , Race Amanda D. , Rees Colin J. , Brown Louise C. , Loadman Paul M. , Downing Amy , Minihane Anne Marie , Williams Elizabeth A. , Hull Mark A.
Published: November 2023

Supplementary Figure 1 shows the distribution of individual total (combined adenomatous and serrated polyp) colorectal polyp counts according to seAFOod trial treatment allocation by factorial margins and PTGS SNP genotypes.
Supplemental Figure 1 from Methylated DNA Markers for Sporadic Colorectal and Endometrial Cancer Are Strongly Associated with Lynch Syndrome Cancers
Authors: Bramblet Rachel M. , Bakkum-Gamez Jamie N. , Slettedahl Seth W. , Foote Patrick H. , Taylor William R. , Berger Calise K. , Gysbers Brianna J. , Arndt Jacquelyn , Chen Longwen , Doering Karen A. , Burger Kelli N. , Mahoney Douglas W. , Sherman Mark E. , Kisiel John B. , Samadder N. Jewel
Published: November 2023

Supplemental Figure 1: Distributions of all methylated DNA markers tested for colorectal cancers and controls, stratified by Lynch syndrome. Log10 strand counts are adjusted based on the level of the control gene, ACTB, in all controls (SPOR-CRC-CTRL and LS-CRC-CTRL). P-value provided to show statistical significance of difference of medians between CASE and CTRL samples within SPOR and LS subgroups.
Supplementary Table S4 from Dynamic Risk Prediction of Treatment Discontinuation Using Patient-Reported Outcomes Data in the Phase III NSABP B-35 Trial
Authors: Calsavara Vinicius F. , Henry Norah L. , Hays Ron D. , Kim Sungjin , Luu Michael , Diniz Márcio A. , Gresham Gillian , Cecchini Reena S. , Yothers Greg , Ganz Patricia A. , Rogatko André , Tighiouart Mourad
Published: November 2023

Supplementary Table S4 presents the optimal risk thresholds (c) and estimates of diagnostic measures such as sensitivity, specificity, and accuracy, along with their corresponding 95% confidence intervals. These values are derived from the PCCox and PCCox BLUP models based on treatment, as applied in the validation cohort.
Supplementary Table S3 from Dynamic Risk Prediction of Treatment Discontinuation Using Patient-Reported Outcomes Data in the Phase III NSABP B-35 Trial
Authors: Calsavara Vinicius F. , Henry Norah L. , Hays Ron D. , Kim Sungjin , Luu Michael , Diniz Márcio A. , Gresham Gillian , Cecchini Reena S. , Yothers Greg , Ganz Patricia A. , Rogatko André , Tighiouart Mourad
Published: November 2023

Supplementary Table S3 provides information about the number of patients with missing adverse events at each timepoint for tamoxifen treatment.
Supplementary Table S2 from Dynamic Risk Prediction of Treatment Discontinuation Using Patient-Reported Outcomes Data in the Phase III NSABP B-35 Trial
Authors: Calsavara Vinicius F. , Henry Norah L. , Hays Ron D. , Kim Sungjin , Luu Michael , Diniz Márcio A. , Gresham Gillian , Cecchini Reena S. , Yothers Greg , Ganz Patricia A. , Rogatko André , Tighiouart Mourad
Published: November 2023

Supplementary Table S2 provides information about the number of patients with missing adverse events at each timepoint for anastrozole treatment.
Supplementary Methods S1 from Dynamic Risk Prediction of Treatment Discontinuation Using Patient-Reported Outcomes Data in the Phase III NSABP B-35 Trial
Authors: Calsavara Vinicius F. , Henry Norah L. , Hays Ron D. , Kim Sungjin , Luu Michael , Diniz Márcio A. , Gresham Gillian , Cecchini Reena S. , Yothers Greg , Ganz Patricia A. , Rogatko André , Tighiouart Mourad
Published: November 2023

Supplementary Methods S1 provides a comprehensive statistical description of the two applied predictive survival models (PC Cox model and PC Cox BLUP model).
Supplementary Figure S4 from Dynamic Risk Prediction of Treatment Discontinuation Using Patient-Reported Outcomes Data in the Phase III NSABP B-35 Trial
Authors: Calsavara Vinicius F. , Henry Norah L. , Hays Ron D. , Kim Sungjin , Luu Michael , Diniz Márcio A. , Gresham Gillian , Cecchini Reena S. , Yothers Greg , Ganz Patricia A. , Rogatko André , Tighiouart Mourad
Published: November 2023

Supplementary Figure S4 illustrates the estimated time-dependent ROC curves using the PCCox and PCCox BLUP models in the validation cohort for anastrozole treatment. The area under the ROC curve (AUC) and its corresponding 95% confidence interval for the four sets of s and tau are embedded within the plots.
Supplementary Figure S2 from Dynamic Risk Prediction of Treatment Discontinuation Using Patient-Reported Outcomes Data in the Phase III NSABP B-35 Trial
Authors: Calsavara Vinicius F. , Henry Norah L. , Hays Ron D. , Kim Sungjin , Luu Michael , Diniz Márcio A. , Gresham Gillian , Cecchini Reena S. , Yothers Greg , Ganz Patricia A. , Rogatko André , Tighiouart Mourad
Published: November 2023

Supplementary Figure S2 shows the estimated discontinuation curves by training dataset and validation cohort for the anastrozole-treated patients.
Data from Methylated DNA Markers for Sporadic Colorectal and Endometrial Cancer Are Strongly Associated with Lynch Syndrome Cancers
Authors: Bramblet Rachel M. , Bakkum-Gamez Jamie N. , Slettedahl Seth W. , Foote Patrick H. , Taylor William R. , Berger Calise K. , Gysbers Brianna J. , Arndt Jacquelyn , Chen Longwen , Doering Karen A. , Burger Kelli N. , Mahoney Douglas W. , Sherman Mark E. , Kisiel John B. , Samadder N. Jewel
Published: November 2023

Abstract
Lynch syndrome (LS) markedly increases risks of colorectal and endometrial cancers. Early detection biomarkers for LS cancers could reduce the needs for invasive screening and surgical prophylaxis.

To validate a panel of methylated DNA markers (MDM) previously identified in sporadic colorectal cancer and endometrial cancer for discrimination of these cancers in LS.

In a case–control design, previously identified MDMs for the detection of colorectal cancer and endometrial cancer were assayed by qMSP on tissue-extracted DNA. Results were normalized to ACTB values within each sample. Least absolute shrinkage and selection operator models to classify colorectal cancer and endometrial cancer were trained on sporadic cases and controls and then applied to classify colorectal cancer and endometrial cancer, in those with LS, and cross-validated.

We identified colorectal cancer cases (23 with LS, 48 sporadic), colorectal controls (32 LS, 48 sporadic), endometrial cancer cases (30 LS, 48 sporadic), and endometrial controls (29 LS, 37 sporadic). A 3-MDM panel (LASS4, LRRC4, and PPP2R5C) classified LS-CRC from LS controls with an AUC of 0.92 (0.84–0.99); results were similar for sporadic colorectal cancer. A 6-MDM panel (SFMBT2, MPZ, CYTH2, DIDO1, chr10.4479, and EMX2OS) discriminated LS-EC from LS controls with an AUC of 0.92 (0.83–1.0); the AUC for sporadic endometrial cancer versus sporadic controls was nominally higher, 0.99 (0.96–1.0).

MDMs previously identified in sporadic endometrial cancer and colorectal cancer discriminate between endometrial cancer and benign endometrium and colorectal cancer and benign colorectum in LS. This supports the inclusion of patients with LS within future prospective clinical trials evaluating endometrial cancer and colorectal cancer MDMs and may provide a new avenue for cancer screening or surveillance in this high-risk population.
Prevention Relevance:
Lynch syndrome (LS) markedly increases risks of colorectal and endometrial cancers. Early detection biomarkers for LS cancers could reduce the needs for invasive screening and surgery. Methylated DNA markers previously identified in sporadic endometrial cancer and colorectal cancer discriminate between benign and cancer tissue in LS.
Supplementary Table S7 from Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer
Authors: Grillo Giacomo , Keshavarzian Tina , Linder Simon , Arlidge Christopher , Mout Lisanne , Nand Ankita , Teng Mona , Qamra Aditi , Zhou Stanley , Kron Ken J. , Murison Alex , Hawley James R. , Fraser Michael , van der Kwast Theodorus H. , Raj Ganesh V. , He Housheng Hansen , Zwart Wilbert , Lupien Mathieu
Published: November 2023

Top 5% transcription factor cistromes enriched at benign prostate transposable elements
Supplementary Table S6 from Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer
Authors: Grillo Giacomo , Keshavarzian Tina , Linder Simon , Arlidge Christopher , Mout Lisanne , Nand Ankita , Teng Mona , Qamra Aditi , Zhou Stanley , Kron Ken J. , Murison Alex , Hawley James R. , Fraser Michael , van der Kwast Theodorus H. , Raj Ganesh V. , He Housheng Hansen , Zwart Wilbert , Lupien Mathieu
Published: November 2023

Top 5% transcription factor cistromes enriched at pluripotent stem cell transposable elements
Supplementary Table S24 from Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer
Authors: Grillo Giacomo , Keshavarzian Tina , Linder Simon , Arlidge Christopher , Mout Lisanne , Nand Ankita , Teng Mona , Qamra Aditi , Zhou Stanley , Kron Ken J. , Murison Alex , Hawley James R. , Fraser Michael , van der Kwast Theodorus H. , Raj Ganesh V. , He Housheng Hansen , Zwart Wilbert , Lupien Mathieu
Published: November 2023

Pathwyas significantly different in all three CRISPRi 22Rv1 clones (Tigger3a vs Control)
Supplementary Table S23 from Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer
Authors: Grillo Giacomo , Keshavarzian Tina , Linder Simon , Arlidge Christopher , Mout Lisanne , Nand Ankita , Teng Mona , Qamra Aditi , Zhou Stanley , Kron Ken J. , Murison Alex , Hawley James R. , Fraser Michael , van der Kwast Theodorus H. , Raj Ganesh V. , He Housheng Hansen , Zwart Wilbert , Lupien Mathieu
Published: November 2023

Top 5% transcription factor cistromes enriched at reprogrammed transposable element families (Porto constant patients)
Supplementary Appendix from Neoadjuvant Durvalumab Alone or Combined with Novel Immuno-Oncology Agents in Resectable Lung Cancer: The Phase II NeoCOAST Platform Trial
Authors: Cascone Tina , Kar Gozde , Spicer Jonathan D. , García-Campelo Rosario , Weder Walter , Daniel Davey B. , Spigel David R. , Hussein Maen , Mazieres Julien , Oliveira Julio , Yau Edwin H. , Spira Alexander I. , Anagnostou Valsamo , Mager Raymond , Hamid Oday , Cheng Lin-Yang , Zheng Ying , Blando Jorge , Tan Tze Heng , Surace Michael , Rodriguez-Canales Jaime , Gopalakrishnan Vancheswaran , Sellman Bret R. , Grenga Italia , Soo-Hoo Yee , Kumar Rakesh , McGrath Lara , Forde Patrick M.
Published: November 2023

Additional details on safety endpoints. Supplementary tables: 1, Representativeness of study participants; 2, Efficacy summary; 3, Adverse events occurring in ≥10% of patients; 4, Treatment-related adverse events occurring in ≥5% of patients; 5, Adverse events of special or potential interest; 6, Baseline biomarker association with response. Supplementary figures: 1, Mechanism of action for each study drug; 2, Violin plots with median % residual viable tumor cells; 3, Additional immunohistochemistry biomarker to major pathological response; 4, Calculation of gene signatures associated with tertiary lymphoid structure (TLS) formation; 5, Changes in immune cell populations by deconvolution; 6, Stool microbiome richness and diversity; 7, ctDNA dynamics.
Supplementary Table S21 from Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer
Authors: Grillo Giacomo , Keshavarzian Tina , Linder Simon , Arlidge Christopher , Mout Lisanne , Nand Ankita , Teng Mona , Qamra Aditi , Zhou Stanley , Kron Ken J. , Murison Alex , Hawley James R. , Fraser Michael , van der Kwast Theodorus H. , Raj Ganesh V. , He Housheng Hansen , Zwart Wilbert , Lupien Mathieu
Published: November 2023

Top 5% transcription factor cistromes enriched at reprogrammed transposable element families (Porto reprogrammed patients)
Supplementary Video 2 from SHP2: A Pleiotropic Target at the Interface of Cancer and Its Microenvironment
Authors: Sodir Nicole M. , Pathria Gaurav , Adamkewicz Joanne I. , Kelley Elizabeth H. , Sudhamsu Jawahar , Merchant Mark , Chiarle Roberto , Maddalo Danilo
Published: November 2023

Supplementary Video 2 shows the conformational changes occurring within SHP2 upon its activation
Supplementary Figure S2 from SHP2: A Pleiotropic Target at the Interface of Cancer and Its Microenvironment
Authors: Sodir Nicole M. , Pathria Gaurav , Adamkewicz Joanne I. , Kelley Elizabeth H. , Sudhamsu Jawahar , Merchant Mark , Chiarle Roberto , Maddalo Danilo
Published: November 2023

All currently known inhibitors of SHP2 bind at the interface between the N-SH2 (beige), C-SH2 (light green) and PTP (salmon) domains, stabilizing the inactive conformation of SHP2. Shown in blue is the inhibitor SHP099, bound to SHP2, which further stabilizes the inactive conformation.
Supplementary Table S15 from Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer
Authors: Grillo Giacomo , Keshavarzian Tina , Linder Simon , Arlidge Christopher , Mout Lisanne , Nand Ankita , Teng Mona , Qamra Aditi , Zhou Stanley , Kron Ken J. , Murison Alex , Hawley James R. , Fraser Michael , van der Kwast Theodorus H. , Raj Ganesh V. , He Housheng Hansen , Zwart Wilbert , Lupien Mathieu
Published: November 2023

Differentially enriched transposable element families between intermediate and constant Porto patients
Supplementary Table S14 from Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer
Authors: Grillo Giacomo , Keshavarzian Tina , Linder Simon , Arlidge Christopher , Mout Lisanne , Nand Ankita , Teng Mona , Qamra Aditi , Zhou Stanley , Kron Ken J. , Murison Alex , Hawley James R. , Fraser Michael , van der Kwast Theodorus H. , Raj Ganesh V. , He Housheng Hansen , Zwart Wilbert , Lupien Mathieu
Published: November 2023

Differentially enriched transposable element families between reprogrammed and constant Porto patients
Supplementary Table S13 from Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer
Authors: Grillo Giacomo , Keshavarzian Tina , Linder Simon , Arlidge Christopher , Mout Lisanne , Nand Ankita , Teng Mona , Qamra Aditi , Zhou Stanley , Kron Ken J. , Murison Alex , Hawley James R. , Fraser Michael , van der Kwast Theodorus H. , Raj Ganesh V. , He Housheng Hansen , Zwart Wilbert , Lupien Mathieu
Published: November 2023

Differentially enriched transposable element families between reprogrammed and constant CPC-GENE patients
Supplementary Table S12 from Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer
Authors: Grillo Giacomo , Keshavarzian Tina , Linder Simon , Arlidge Christopher , Mout Lisanne , Nand Ankita , Teng Mona , Qamra Aditi , Zhou Stanley , Kron Ken J. , Murison Alex , Hawley James R. , Fraser Michael , van der Kwast Theodorus H. , Raj Ganesh V. , He Housheng Hansen , Zwart Wilbert , Lupien Mathieu
Published: November 2023

FOXA1 GIGGLE enrichment scores at FOXA1-bound benign prostate transposable elements
Supplementary Table S11 from Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer
Authors: Grillo Giacomo , Keshavarzian Tina , Linder Simon , Arlidge Christopher , Mout Lisanne , Nand Ankita , Teng Mona , Qamra Aditi , Zhou Stanley , Kron Ken J. , Murison Alex , Hawley James R. , Fraser Michael , van der Kwast Theodorus H. , Raj Ganesh V. , He Housheng Hansen , Zwart Wilbert , Lupien Mathieu
Published: November 2023

AR GIGGLE enrichment scores at AR-bound benign prostate transposable elements
Supplementary Table S1 from Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer
Authors: Grillo Giacomo , Keshavarzian Tina , Linder Simon , Arlidge Christopher , Mout Lisanne , Nand Ankita , Teng Mona , Qamra Aditi , Zhou Stanley , Kron Ken J. , Murison Alex , Hawley James R. , Fraser Michael , van der Kwast Theodorus H. , Raj Ganesh V. , He Housheng Hansen , Zwart Wilbert , Lupien Mathieu
Published: November 2023

ENCODE samples accession numbers used in this article
Supplementary Figure S6 from Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer
Authors: Grillo Giacomo , Keshavarzian Tina , Linder Simon , Arlidge Christopher , Mout Lisanne , Nand Ankita , Teng Mona , Qamra Aditi , Zhou Stanley , Kron Ken J. , Murison Alex , Hawley James R. , Fraser Michael , van der Kwast Theodorus H. , Raj Ganesh V. , He Housheng Hansen , Zwart Wilbert , Lupien Mathieu
Published: November 2023

This figure showcases dCas9-KRAB and H3K27ac profiling in CRISPRi 22Rv1 clones #1 and #3 nucleofected with control or Tigger3a gRNA combos (clone #2 is showcased in Figure 5)
Table S4 from Clinical Efficacy of ONC201 in H3K27M-Mutant Diffuse Midline Gliomas Is Driven by Disruption of Integrated Metabolic and Epigenetic Pathways
Authors: Venneti Sriram , Kawakibi Abed Rahman , Ji Sunjong , Waszak Sebastian M. , Sweha Stefan R. , Mota Mateus , Pun Matthew , Deogharkar Akash , Chung Chan , Tarapore Rohinton S. , Ramage Samuel , Chi Andrew , Wen Patrick Y. , Arrillaga-Romany Isabel , Batchelor Tracy T. , Butowski Nicholas A. , Sumrall Ashley , Shonka Nicole , Harrison Rebecca A. , de Groot John , Mehta Minesh , Hall Matthew D. , Daghistani Doured , Cloughesy Timothy F. , Ellingson Benjamin M. , Beccaria Kevin , Varlet Pascale , Kim Michelle M. , Umemura Yoshie , Garton Hugh , Franson Andrea , Schwartz Jonathan , Jain Rajan , Kachman Maureen , Baum Heidi , Burant Charles F. , Mottl Sophie L. , Cartaxo Rodrigo T. , John Vishal , Messinger Dana , Qin Tingting , Peterson Erik , Sajjakulnukit Peter , Ravi Karthik , Waugh Alyssa , Walling Dustin , Ding Yujie , Xia Ziyun , Schwendeman Anna , Hawes Debra , Yang Fusheng , Judkins Alexander R. , Wahl Daniel , Lyssiotis Costas A. , de la Nava Daniel , Alonso Marta M. , Eze Augustine , Spitzer Jasper , Schmidt Susanne V. , Duchatel Ryan J. , Dun Matthew D. , Cain Jason E. , Jiang Li , Stopka Sylwia A. , Baquer Gerard , Regan Michael S. , Filbin Mariella G. , Agar Nathalie Y.R. , Zhao Lili , Kumar-Sinha Chandan , Mody Rajen , Chinnaiyan Arul , Kurokawa Ryo , Pratt Drew , Yadav Viveka N. , Grill Jacques , Kline Cassie , Mueller Sabine , Resnick Adam , Nazarian Javad , Allen Joshua E. , Odia Yazmin , Gardner Sharon L. , Koschmann Carl
Published: November 2023

Summary of historical control datasets.
Supplementary Figure S2 from Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer
Authors: Grillo Giacomo , Keshavarzian Tina , Linder Simon , Arlidge Christopher , Mout Lisanne , Nand Ankita , Teng Mona , Qamra Aditi , Zhou Stanley , Kron Ken J. , Murison Alex , Hawley James R. , Fraser Michael , van der Kwast Theodorus H. , Raj Ganesh V. , He Housheng Hansen , Zwart Wilbert , Lupien Mathieu
Published: November 2023

This figure complements Figure 2 and showcases the enrichment of tranposable element families in TCGA PRAD ATAC data