bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Movies 7-9 from Combined Analysis of Antigen Presentation and T-cell Recognition Reveals Restricted Immune Responses in Melanoma
Authors: Kalaora Shelly , Wolf Yochai , Feferman Tali , Barnea Eilon , Greenstein Erez , Reshef Dan , Tirosh Itay , Reuben Alexandre , Patkar Sushant , Levy Ronen , Quinkhardt Juliane , Omokoko Tana , Qutob Nouar , Golani Ofra , Zhang Jianhua , Mao Xizeng , Song Xingzhi , Bernatchez Chantale , Haymaker Cara , Forget Marie-Andrée , Creasy Caitlin , Greenberg Polina , Carter Brett W. , Cooper Zachary A. , Rosenberg Steven A. , Lotem Michal , Sahin Ugur , Shakhar Guy , Ruppin Eytan , Wargo Jennifer A. , Friedman Nir , Admon Arie , Samuels Yardena
Published: April 2023

2P microscopy movies of in vivo experiments
Table S2 from Ex Vivo Profiling of PD-1 Blockade Using Organotypic Tumor Spheroids
Authors: Jenkins Russell W. , Aref Amir R. , Lizotte Patrick H. , Ivanova Elena , Stinson Susanna , Zhou Chensheng W. , Bowden Michaela , Deng Jiehui , Liu Hongye , Miao Diana , He Meng Xiao , Walker William , Zhang Gao , Tian Tian , Cheng Chaoran , Wei Zhi , Palakurthi Sangeetha , Bittinger Mark , Vitzthum Hans , Kim Jong Wook , Merlino Ashley , Quinn Max , Venkataramani Chandrasekar , Kaplan Joshua A. , Portell Andrew , Gokhale Prafulla C. , Phillips Bart , Smart Alicia , Rotem Asaf , Jones Robert E. , Keogh Lauren , Anguiano Maria , Stapleton Lance , Jia Zhiheng , Barzily-Rokni Michal , Cañadas Israel , Thai Tran C. , Hammond Marc R. , Vlahos Raven , Wang Eric S. , Zhang Hua , Li Shuai , Hanna Glenn J. , Huang Wei , Hoang Mai P. , Piris Adriano , Eliane Jean-Pierre , Stemmer-Rachamimov Anat O. , Cameron Lisa , Su Mei-Ju , Shah Parin , Izar Benjamin , Thakuria Manisha , LeBoeuf Nicole R. , Rabinowits Guilherme , Gunda Viswanath , Parangi Sareh , Cleary James M. , Miller Brian C. , Kitajima Shunsuke , Thummalapalli Rohit , Miao Benchun , Barbie Thanh U. , Sivathanu Vivek , Wong Joshua , Richards William G. , Bueno Raphael , Yoon Charles H. , Miret Juan , Herlyn Meenhard , Garraway Levi A. , Van Allen Eliezer M. , Freeman Gordon J. , Kirschmeier Paul T. , Lorch Jochen H. , Ott Patrick A. , Hodi F. Stephen , Flaherty Keith T. , Kamm Roger D. , Boland Genevieve M. , Wong Kwok-Kin , Dornan David , Paweletz Cloud Peter , Barbie David A.
Published: April 2023

In vitro kinase inhibitory activity of Compound 1
Supplementary Movies 4-6 from Combined Analysis of Antigen Presentation and T-cell Recognition Reveals Restricted Immune Responses in Melanoma
Authors: Kalaora Shelly , Wolf Yochai , Feferman Tali , Barnea Eilon , Greenstein Erez , Reshef Dan , Tirosh Itay , Reuben Alexandre , Patkar Sushant , Levy Ronen , Quinkhardt Juliane , Omokoko Tana , Qutob Nouar , Golani Ofra , Zhang Jianhua , Mao Xizeng , Song Xingzhi , Bernatchez Chantale , Haymaker Cara , Forget Marie-Andrée , Creasy Caitlin , Greenberg Polina , Carter Brett W. , Cooper Zachary A. , Rosenberg Steven A. , Lotem Michal , Sahin Ugur , Shakhar Guy , Ruppin Eytan , Wargo Jennifer A. , Friedman Nir , Admon Arie , Samuels Yardena
Published: April 2023

In vitro killing assay movies. Co-culture of 12T melanoma cells with irrelevant 108TILs
Supplementary Data from Ex Vivo Profiling of PD-1 Blockade Using Organotypic Tumor Spheroids
Authors: Jenkins Russell W. , Aref Amir R. , Lizotte Patrick H. , Ivanova Elena , Stinson Susanna , Zhou Chensheng W. , Bowden Michaela , Deng Jiehui , Liu Hongye , Miao Diana , He Meng Xiao , Walker William , Zhang Gao , Tian Tian , Cheng Chaoran , Wei Zhi , Palakurthi Sangeetha , Bittinger Mark , Vitzthum Hans , Kim Jong Wook , Merlino Ashley , Quinn Max , Venkataramani Chandrasekar , Kaplan Joshua A. , Portell Andrew , Gokhale Prafulla C. , Phillips Bart , Smart Alicia , Rotem Asaf , Jones Robert E. , Keogh Lauren , Anguiano Maria , Stapleton Lance , Jia Zhiheng , Barzily-Rokni Michal , Cañadas Israel , Thai Tran C. , Hammond Marc R. , Vlahos Raven , Wang Eric S. , Zhang Hua , Li Shuai , Hanna Glenn J. , Huang Wei , Hoang Mai P. , Piris Adriano , Eliane Jean-Pierre , Stemmer-Rachamimov Anat O. , Cameron Lisa , Su Mei-Ju , Shah Parin , Izar Benjamin , Thakuria Manisha , LeBoeuf Nicole R. , Rabinowits Guilherme , Gunda Viswanath , Parangi Sareh , Cleary James M. , Miller Brian C. , Kitajima Shunsuke , Thummalapalli Rohit , Miao Benchun , Barbie Thanh U. , Sivathanu Vivek , Wong Joshua , Richards William G. , Bueno Raphael , Yoon Charles H. , Miret Juan , Herlyn Meenhard , Garraway Levi A. , Van Allen Eliezer M. , Freeman Gordon J. , Kirschmeier Paul T. , Lorch Jochen H. , Ott Patrick A. , Hodi F. Stephen , Flaherty Keith T. , Kamm Roger D. , Boland Genevieve M. , Wong Kwok-Kin , Dornan David , Paweletz Cloud Peter , Barbie David A.
Published: April 2023

Supplementary Figure Legends and Figures
Supp. Movie 3 from Ex Vivo Profiling of PD-1 Blockade Using Organotypic Tumor Spheroids
Authors: Jenkins Russell W. , Aref Amir R. , Lizotte Patrick H. , Ivanova Elena , Stinson Susanna , Zhou Chensheng W. , Bowden Michaela , Deng Jiehui , Liu Hongye , Miao Diana , He Meng Xiao , Walker William , Zhang Gao , Tian Tian , Cheng Chaoran , Wei Zhi , Palakurthi Sangeetha , Bittinger Mark , Vitzthum Hans , Kim Jong Wook , Merlino Ashley , Quinn Max , Venkataramani Chandrasekar , Kaplan Joshua A. , Portell Andrew , Gokhale Prafulla C. , Phillips Bart , Smart Alicia , Rotem Asaf , Jones Robert E. , Keogh Lauren , Anguiano Maria , Stapleton Lance , Jia Zhiheng , Barzily-Rokni Michal , Cañadas Israel , Thai Tran C. , Hammond Marc R. , Vlahos Raven , Wang Eric S. , Zhang Hua , Li Shuai , Hanna Glenn J. , Huang Wei , Hoang Mai P. , Piris Adriano , Eliane Jean-Pierre , Stemmer-Rachamimov Anat O. , Cameron Lisa , Su Mei-Ju , Shah Parin , Izar Benjamin , Thakuria Manisha , LeBoeuf Nicole R. , Rabinowits Guilherme , Gunda Viswanath , Parangi Sareh , Cleary James M. , Miller Brian C. , Kitajima Shunsuke , Thummalapalli Rohit , Miao Benchun , Barbie Thanh U. , Sivathanu Vivek , Wong Joshua , Richards William G. , Bueno Raphael , Yoon Charles H. , Miret Juan , Herlyn Meenhard , Garraway Levi A. , Van Allen Eliezer M. , Freeman Gordon J. , Kirschmeier Paul T. , Lorch Jochen H. , Ott Patrick A. , Hodi F. Stephen , Flaherty Keith T. , Kamm Roger D. , Boland Genevieve M. , Wong Kwok-Kin , Dornan David , Paweletz Cloud Peter , Barbie David A.
Published: April 2023

Device loading, media addition, media extraction
Supplementary Figures 1-17 from Combined Analysis of Antigen Presentation and T-cell Recognition Reveals Restricted Immune Responses in Melanoma
Authors: Kalaora Shelly , Wolf Yochai , Feferman Tali , Barnea Eilon , Greenstein Erez , Reshef Dan , Tirosh Itay , Reuben Alexandre , Patkar Sushant , Levy Ronen , Quinkhardt Juliane , Omokoko Tana , Qutob Nouar , Golani Ofra , Zhang Jianhua , Mao Xizeng , Song Xingzhi , Bernatchez Chantale , Haymaker Cara , Forget Marie-Andrée , Creasy Caitlin , Greenberg Polina , Carter Brett W. , Cooper Zachary A. , Rosenberg Steven A. , Lotem Michal , Sahin Ugur , Shakhar Guy , Ruppin Eytan , Wargo Jennifer A. , Friedman Nir , Admon Arie , Samuels Yardena
Published: April 2023

Supplementary Figures 1-17
Supplementary Figure S1 from Circulating Cell-Free DNA to Guide Prostate Cancer Treatment with PARP Inhibition
Authors: Goodall Jane , Mateo Joaquin , Yuan Wei , Mossop Helen , Porta Nuria , Miranda Susana , Perez-Lopez Raquel , Dolling David , Robinson Dan R. , Sandhu Shahneen , Fowler Gemma , Ebbs Berni , Flohr Penny , Seed George , Rodrigues Daniel Nava , Boysen Gunther , Bertan Claudia , Atkin Mark , Clarke Matthew , Crespo Mateus , Figueiredo Ines , Riisnaes Ruth , Sumanasuriya Semini , Rescigno Pasquale , Zafeiriou Zafeiris , Sharp Adam , Tunariu Nina , Bianchini Diletta , Gillman Alexa , Lord Christopher J. , Hall Emma , Chinnaiyan Arul M. , Carreira Suzanne , de Bono Johann S.
Published: April 2023

Consort diagram describing samples disposition in the study.
Supplemental Table S1 from Circulating Cell-Free DNA to Guide Prostate Cancer Treatment with PARP Inhibition
Authors: Goodall Jane , Mateo Joaquin , Yuan Wei , Mossop Helen , Porta Nuria , Miranda Susana , Perez-Lopez Raquel , Dolling David , Robinson Dan R. , Sandhu Shahneen , Fowler Gemma , Ebbs Berni , Flohr Penny , Seed George , Rodrigues Daniel Nava , Boysen Gunther , Bertan Claudia , Atkin Mark , Clarke Matthew , Crespo Mateus , Figueiredo Ines , Riisnaes Ruth , Sumanasuriya Semini , Rescigno Pasquale , Zafeiriou Zafeiris , Sharp Adam , Tunariu Nina , Bianchini Diletta , Gillman Alexa , Lord Christopher J. , Hall Emma , Chinnaiyan Arul M. , Carreira Suzanne , de Bono Johann S.
Published: April 2023

Summary of tumor (baseline) and cfDNA (baseline and progression) mutations detected by WES for a patient who responded to Olaparib. New events in TP53 and TSC2 were detected at progression.
Supplementary Data from CDK4/6 Inhibition Augments Antitumor Immunity by Enhancing T-cell Activation
Authors: Deng Jiehui , Wang Eric S. , Jenkins Russell W. , Li Shuai , Dries Ruben , Yates Kathleen , Chhabra Sandeep , Huang Wei , Liu Hongye , Aref Amir R. , Ivanova Elena , Paweletz Cloud P. , Bowden Michaela , Zhou Chensheng W. , Herter-Sprie Grit S. , Sorrentino Jessica A. , Bisi John E. , Lizotte Patrick H. , Merlino Ashley A. , Quinn Max M. , Bufe Lauren E. , Yang Annan , Zhang Yanxi , Zhang Hua , Gao Peng , Chen Ting , Cavanaugh Megan E. , Rode Amanda J. , Haines Eric , Roberts Patrick J. , Strum Jay C. , Richards William G. , Lorch Jochen H. , Parangi Sareh , Gunda Viswanath , Boland Genevieve M. , Bueno Raphael , Palakurthi Sangeetha , Freeman Gordon J. , Ritz Jerome , Haining W. Nicholas , Sharpless Norman E. , Arthanari Haribabu , Shapiro Geoffrey I. , Barbie David A. , Gray Nathanael S. , Wong Kwok-Kin
Published: April 2023

Figure S1. Characterization of cells and CDK4/6 inhibitors; Figure S2. CDK6 phosphorylates serine residues of the regulatory domain of NFAT4 (NFATc3); Figure S3. Analysis of lung tumor immune infiltrates after CDK4/6 inhibition from KrasG12D (Kras), KrasG12DLkb1 (KL) or KrasG12DTrp53fl/fl (KP) mice; Figure S4. T cell proliferation and cytokine/chemokine profiling of KrasG12DTrp53fl/fl GEMM mice; Figure S5. Tumor antigen experienced T cells are more sensitive to CDK4/6 inhibition; Figure S6. Short-term CDK4/6 inhibition alters the cell cycle status of tumor infiltrating T cells; Figure S7. CDK4/6 inhibition induces changes in the expression of activation and suppression marker genes in tumor-infiltrating T cells; Figure S8. Combination treatment of CDK4/6 inhibitor and anti-PD-1 antibody elicits anti-tumor immunity; Figure S9. Combination treatment of CDK4/6 inhibitor and anti-PD-1 antibody on established tumor; Figure S10. Effect of TCR stimulation and CDK4/6 inhibition on phosphorylation of NFkB; Supplementary Table S1; Supplmentary Table S2; Supplementary Table S3: Selected genes reported to be regulated by NFAT
Supplementary Table S1 from Loss of RasGAP Tumor Suppressors Underlies the Aggressive Nature of Luminal B Breast Cancers
Authors: Olsen Sarah Naomi , Wronski Ania , Castaño Zafira , Dake Benjamin , Malone Clare , De Raedt Thomas , Enos Miriam , DeRose Yoko S. , Zhou Wenhui , Guerra Stephanie , Loda Massimo , Welm Alana , Partridge Ann H. , McAllister Sandra S. , Kuperwasser Charlotte , Cichowski Karen
Published: April 2023

Various Annotations of ER+ Breast Cancer Cell Lines.
Supplementary Figure S3 from Loss of RasGAP Tumor Suppressors Underlies the Aggressive Nature of Luminal B Breast Cancers
Authors: Olsen Sarah Naomi , Wronski Ania , Castaño Zafira , Dake Benjamin , Malone Clare , De Raedt Thomas , Enos Miriam , DeRose Yoko S. , Zhou Wenhui , Guerra Stephanie , Loda Massimo , Welm Alana , Partridge Ann H. , McAllister Sandra S. , Kuperwasser Charlotte , Cichowski Karen
Published: April 2023

DAB2IP Expression in a Panel of MMTVNeu/RASAL2-/- Tumors.
Supplementary Figure S2 from Loss of RasGAP Tumor Suppressors Underlies the Aggressive Nature of Luminal B Breast Cancers
Authors: Olsen Sarah Naomi , Wronski Ania , Castaño Zafira , Dake Benjamin , Malone Clare , De Raedt Thomas , Enos Miriam , DeRose Yoko S. , Zhou Wenhui , Guerra Stephanie , Loda Massimo , Welm Alana , Partridge Ann H. , McAllister Sandra S. , Kuperwasser Charlotte , Cichowski Karen
Published: April 2023

RASAL2 Expression/Promoter Methylation Analysis and Behavior of Various Breast Cancer Cell Lines.
Supplementary Figure Legends from Loss of RasGAP Tumor Suppressors Underlies the Aggressive Nature of Luminal B Breast Cancers
Authors: Olsen Sarah Naomi , Wronski Ania , Castaño Zafira , Dake Benjamin , Malone Clare , De Raedt Thomas , Enos Miriam , DeRose Yoko S. , Zhou Wenhui , Guerra Stephanie , Loda Massimo , Welm Alana , Partridge Ann H. , McAllister Sandra S. , Kuperwasser Charlotte , Cichowski Karen
Published: April 2023

Supplementary Figure Legends
Supplementary Figure 8 from Cabozantinib Eradicates Advanced Murine Prostate Cancer by Activating Antitumor Innate Immunity
Authors: Patnaik Akash , Swanson Kenneth D. , Csizmadia Eva , Solanki Aniruddh , Landon-Brace Natalie , Gehring Marina P. , Helenius Katja , Olson Brian M. , Pyzer Athalia R. , Wang Lily C. , Elemento Olivier , Novak Jesse , Thornley Thomas B. , Asara John M. , Montaser Laleh , Timmons Joshua J. , Morgan Todd M. , Wang Yugang , Levantini Elena , Clohessy John G. , Kelly Kathleen , Pandolfi Pier Paolo , Rosenblatt Jacalyn M. , Avigan David E. , Ye Huihui , Karp Jeffrey M. , Signoretti Sabina , Balk Steven P. , Cantley Lewis C.
Published: April 2023

Dexamethasone attenuates the tumor clearance elicited by cabozantinib.
Supplementary Figure 7 from Cabozantinib Eradicates Advanced Murine Prostate Cancer by Activating Antitumor Innate Immunity
Authors: Patnaik Akash , Swanson Kenneth D. , Csizmadia Eva , Solanki Aniruddh , Landon-Brace Natalie , Gehring Marina P. , Helenius Katja , Olson Brian M. , Pyzer Athalia R. , Wang Lily C. , Elemento Olivier , Novak Jesse , Thornley Thomas B. , Asara John M. , Montaser Laleh , Timmons Joshua J. , Morgan Todd M. , Wang Yugang , Levantini Elena , Clohessy John G. , Kelly Kathleen , Pandolfi Pier Paolo , Rosenblatt Jacalyn M. , Avigan David E. , Ye Huihui , Karp Jeffrey M. , Signoretti Sabina , Balk Steven P. , Cantley Lewis C.
Published: April 2023

Blockade of neutrophil chemotaxis/infiltration rescues cabozantinib-induced tumor regression.
Supplementary Figure 5 from Cabozantinib Eradicates Advanced Murine Prostate Cancer by Activating Antitumor Innate Immunity
Authors: Patnaik Akash , Swanson Kenneth D. , Csizmadia Eva , Solanki Aniruddh , Landon-Brace Natalie , Gehring Marina P. , Helenius Katja , Olson Brian M. , Pyzer Athalia R. , Wang Lily C. , Elemento Olivier , Novak Jesse , Thornley Thomas B. , Asara John M. , Montaser Laleh , Timmons Joshua J. , Morgan Todd M. , Wang Yugang , Levantini Elena , Clohessy John G. , Kelly Kathleen , Pandolfi Pier Paolo , Rosenblatt Jacalyn M. , Avigan David E. , Ye Huihui , Karp Jeffrey M. , Signoretti Sabina , Balk Steven P. , Cantley Lewis C.
Published: April 2023

Increased myeloid CD86-expressing APCs following cabozantinib treatment.
Supplementary Figure 4 from Cabozantinib Eradicates Advanced Murine Prostate Cancer by Activating Antitumor Innate Immunity
Authors: Patnaik Akash , Swanson Kenneth D. , Csizmadia Eva , Solanki Aniruddh , Landon-Brace Natalie , Gehring Marina P. , Helenius Katja , Olson Brian M. , Pyzer Athalia R. , Wang Lily C. , Elemento Olivier , Novak Jesse , Thornley Thomas B. , Asara John M. , Montaser Laleh , Timmons Joshua J. , Morgan Todd M. , Wang Yugang , Levantini Elena , Clohessy John G. , Kelly Kathleen , Pandolfi Pier Paolo , Rosenblatt Jacalyn M. , Avigan David E. , Ye Huihui , Karp Jeffrey M. , Signoretti Sabina , Balk Steven P. , Cantley Lewis C.
Published: April 2023

Increased CXCL12 within tumor cells by RNA in situ hybridization following cabozantinib treatment.
Supplementary Figure 3 from Cabozantinib Eradicates Advanced Murine Prostate Cancer by Activating Antitumor Innate Immunity
Authors: Patnaik Akash , Swanson Kenneth D. , Csizmadia Eva , Solanki Aniruddh , Landon-Brace Natalie , Gehring Marina P. , Helenius Katja , Olson Brian M. , Pyzer Athalia R. , Wang Lily C. , Elemento Olivier , Novak Jesse , Thornley Thomas B. , Asara John M. , Montaser Laleh , Timmons Joshua J. , Morgan Todd M. , Wang Yugang , Levantini Elena , Clohessy John G. , Kelly Kathleen , Pandolfi Pier Paolo , Rosenblatt Jacalyn M. , Avigan David E. , Ye Huihui , Karp Jeffrey M. , Signoretti Sabina , Balk Steven P. , Cantley Lewis C.
Published: April 2023

Cabozantinib-mediated granulocytic infiltration within tumors.
Supplementary Figure 2 from Cabozantinib Eradicates Advanced Murine Prostate Cancer by Activating Antitumor Innate Immunity
Authors: Patnaik Akash , Swanson Kenneth D. , Csizmadia Eva , Solanki Aniruddh , Landon-Brace Natalie , Gehring Marina P. , Helenius Katja , Olson Brian M. , Pyzer Athalia R. , Wang Lily C. , Elemento Olivier , Novak Jesse , Thornley Thomas B. , Asara John M. , Montaser Laleh , Timmons Joshua J. , Morgan Todd M. , Wang Yugang , Levantini Elena , Clohessy John G. , Kelly Kathleen , Pandolfi Pier Paolo , Rosenblatt Jacalyn M. , Avigan David E. , Ye Huihui , Karp Jeffrey M. , Signoretti Sabina , Balk Steven P. , Cantley Lewis C.
Published: April 2023

Cabozantinib and PF-04217903 both abolish c-MET phosphorylation in vivo.
Supplementary Figure 1 from Cabozantinib Eradicates Advanced Murine Prostate Cancer by Activating Antitumor Innate Immunity
Authors: Patnaik Akash , Swanson Kenneth D. , Csizmadia Eva , Solanki Aniruddh , Landon-Brace Natalie , Gehring Marina P. , Helenius Katja , Olson Brian M. , Pyzer Athalia R. , Wang Lily C. , Elemento Olivier , Novak Jesse , Thornley Thomas B. , Asara John M. , Montaser Laleh , Timmons Joshua J. , Morgan Todd M. , Wang Yugang , Levantini Elena , Clohessy John G. , Kelly Kathleen , Pandolfi Pier Paolo , Rosenblatt Jacalyn M. , Avigan David E. , Ye Huihui , Karp Jeffrey M. , Signoretti Sabina , Balk Steven P. , Cantley Lewis C.
Published: April 2023

Significant Tumor Shrinkage following cabozantinib treatment.
Supplementary Figures 1 through 7 from Discovery and Optimization of HKT288, a Cadherin-6–Targeting ADC for the Treatment of Ovarian and Renal Cancers
Authors: Bialucha Carl U. , Collins Scott D. , Li Xiao , Saxena Parmita , Zhang Xiamei , Dürr Clemens , Lafont Bruno , Prieur Pierric , Shim Yeonju , Mosher Rebecca , Lee David , Ostrom Lance , Hu Tiancen , Bilic Sanela , Rajlic Ivana Liric , Capka Vladimir , Jiang Wei , Wagner Joel P. , Elliott GiNell , Veloso Artur , Piel Jessica C. , Flaherty Meghan M. , Mansfield Keith G. , Meseck Emily K. , Rubic-Schneider Tina , London Anne Serdakowski , Tschantz William R. , Kurz Markus , Nguyen Duc , Bourret Aaron , Meyer Matthew J. , Faris Jason E. , Janatpour Mary J. , Chan Vivien W. , Yoder Nicholas C. , Catcott Kalli C. , McShea Molly A. , Sun Xiuxia , Gao Hui , Williams Juliet , Hofmann Francesco , Engelman Jeffrey A. , Ettenberg Seth A. , Sellers William R. , Lees Emma
Published: April 2023

Supplementary Figure 1. Schematic of high-content imaging-based internalization assay. Supplementary Figure 2. OVCAR3 xenografts were grown subcutaneously in NSG mice and treated with a single i.v. dose of 10 mg/kg control IgG1 or CDH6-targeting antibodies conjugated to SMCC-DM1. Supplementary Figure 3. Tumors of the PDX model HOVX2263 were grown subcutaneously in female nude mice randomized into groups of equal mean tumor volume and treated every two weeks with a 5 mg/kg i.v. dose of either IgG1-SPDB-DM4, or CDH6-targeting antibodies conjugated to SPDB-DM4. Supplementary Figure 4. Interaction analysis of anti-CDH6 antibody and CDH6 ECD protein. Supplementary Figure 5. Unenrolled NSG mice bearing OVCAR3 tumors from a separate efficacy study were allowed to grow to ~600 mm3 before being treated with either IgG1-SPDB-DM4 or CDH6-SPDB-DM4 at 8.5 mg/kg i.v. on day 34 post implant and re-dosed as indicated by arrows. Supplementary Figure 6. Representative CDH6 IHC images of the OVCAR3 subcutaneous xenograft grown in NSG mice (A), OVCAR3Luc intraperitoneal xenograft grown in SCID beige mice (B), HOVX2263 ovarian PDX subcutaneous xenograft grown in female nude mice (C), and HOVX4863 ovarian PDX subcutaneous xenograft grown in female nude mice (D). Supplementary Figure 7. (A) Correlation plot of response to HKT288 by best average response vs. CDH6 RNA expression. (B) Waterfall plot of percent best average response to CDH6-sulfoSPDB-DM4 treatment in PCT.
Supplementary Methods from AG-221, a First-in-Class Therapy Targeting Acute Myeloid Leukemia Harboring Oncogenic IDH2 Mutations
Authors: Yen Katharine , Travins Jeremy , Wang Fang , David Muriel D. , Artin Erin , Straley Kimberly , Padyana Anil , Gross Stefan , DeLaBarre Byron , Tobin Erica , Chen Yue , Nagaraja Raj , Choe Sung , Jin Lei , Konteatis Zenon , Cianchetta Giovanni , Saunders Jeffrey O. , Salituro Francesco G. , Quivoron Cyril , Opolon Paule , Bawa Olivia , Saada Véronique , Paci Angelo , Broutin Sophie , Bernard Olivier A. , de Botton Stéphane , Marteyn Benoît S. , Pilichowska Monika , Xu YingXia , Fang Cheng , Jiang Fan , Wei Wentao , Jin Shengfang , Silverman Lee , Liu Wei , Yang Hua , Dang Lenny , Dorsch Marion , Penard-Lacronique Virginie , Biller Scott A. , Su Shin-San Michael
Published: April 2023

Supplementary Methods
Supplementary Figures 1 - 11 from AG-221, a First-in-Class Therapy Targeting Acute Myeloid Leukemia Harboring Oncogenic IDH2 Mutations
Authors: Yen Katharine , Travins Jeremy , Wang Fang , David Muriel D. , Artin Erin , Straley Kimberly , Padyana Anil , Gross Stefan , DeLaBarre Byron , Tobin Erica , Chen Yue , Nagaraja Raj , Choe Sung , Jin Lei , Konteatis Zenon , Cianchetta Giovanni , Saunders Jeffrey O. , Salituro Francesco G. , Quivoron Cyril , Opolon Paule , Bawa Olivia , Saada Véronique , Paci Angelo , Broutin Sophie , Bernard Olivier A. , de Botton Stéphane , Marteyn Benoît S. , Pilichowska Monika , Xu YingXia , Fang Cheng , Jiang Fan , Wei Wentao , Jin Shengfang , Silverman Lee , Liu Wei , Yang Hua , Dang Lenny , Dorsch Marion , Penard-Lacronique Virginie , Biller Scott A. , Su Shin-San Michael
Published: April 2023

Supplementary Figure 1. Synthesis and pharmacokinetic characterization of AG-221. Supplementary Figure 2. Biochemical attributes of AG-221. Supplementary Figure 3. Biochemistry of AG-221 with respect to substrate and cofactor. Supplementary Figure 4. TF-1 IDH2R140Q cells treated with AG-221. Supplementary Figure 5. AG-221 can reverse the block in EPO-induced differentiation caused by the expression of IDH2R140Q in the TF-1 erythroleukemia cell line. Supplementary Figure 6. Pharmacokinetics/pharmacodynamics of AG-221 in IDH2R140Qmutant U87MG xenograft tumor-bearing mice. Supplementary Figure 7. AG-221 does not affect intrinsic hematological parameters or body weight. Supplementary Figure 8. AG-221 strongly reduces the number of human IDH2R140Q blasts in the liver and spleen in AML-1, AML-2, and AML-3. Supplementary Figure 9. Flow cytometry analyses of bone marrow-derived hCD45+ cells in primary human AML xenograft models. Supplementary Figure 10. Affinity of the IDH2R140Q homodimer for NADPH. Supplementary Figure 11. Electron density map diagrams for bound ligands for IDH2R140Q co-complex structures determined by X-ray crystallography.
Supplementary table and figure legends from SHP2 Inhibition Prevents Adaptive Resistance to MEK Inhibitors in Multiple Cancer Models
Authors: Fedele Carmine , Ran Hao , Diskin Brian , Wei Wei , Jen Jayu , Geer Mitchell J. , Araki Kiyomi , Ozerdem Ugur , Simeone Diane M. , Miller George , Neel Benjamin G. , Tang Kwan Ho
Published: April 2023

Supplementary table and figure legends
Supplementary Method from SHP2 Inhibition Prevents Adaptive Resistance to MEK Inhibitors in Multiple Cancer Models
Authors: Fedele Carmine , Ran Hao , Diskin Brian , Wei Wei , Jen Jayu , Geer Mitchell J. , Araki Kiyomi , Ozerdem Ugur , Simeone Diane M. , Miller George , Neel Benjamin G. , Tang Kwan Ho
Published: April 2023

Detailed Supplementary Method
Supplementary figures and tables from The Genetic Landscape and Clonal Evolution of Breast Cancer Resistance to Palbociclib plus Fulvestrant in the PALOMA-3 Trial
Authors: O'Leary Ben , Cutts Rosalind J. , Liu Yuan , Hrebien Sarah , Huang Xin , Fenwick Kerry , André Fabrice , Loibl Sibylle , Loi Sherene , Garcia-Murillas Isaac , Cristofanilli Massimo , Huang Bartlett Cynthia , Turner Nicholas C.
Published: April 2023

Supplementary figures and tables
Supplementary Table 5 from Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma
Authors: Jusakul Apinya , Cutcutache Ioana , Yong Chern Han , Lim Jing Quan , Huang Mi Ni , Padmanabhan Nisha , Nellore Vishwa , Kongpetch Sarinya , Ng Alvin Wei Tian , Ng Ley Moy , Choo Su Pin , Myint Swe Swe , Thanan Raynoo , Nagarajan Sanjanaa , Lim Weng Khong , Ng Cedric Chuan Young , Boot Arnoud , Liu Mo , Ong Choon Kiat , Rajasegaran Vikneswari , Lie Stefanus , Lim Alvin Soon Tiong , Lim Tse Hui , Tan Jing , Loh Jia Liang , McPherson John R. , Khuntikeo Narong , Bhudhisawasdi Vajaraphongsa , Yongvanit Puangrat , Wongkham Sopit , Totoki Yasushi , Nakamura Hiromi , Arai Yasuhito , Yamasaki Satoshi , Chow Pierce Kah-Hoe , Chung Alexander Yaw Fui , Ooi London Lucien Peng Jin , Lim Kiat Hon , Dima Simona , Duda Dan G. , Popescu Irinel , Broet Philippe , Hsieh Sen-Yung , Yu Ming-Chin , Scarpa Aldo , Lai Jiaming , Luo Di-Xian , Carvalho André Lopes , Vettore André Luiz , Rhee Hyungjin , Park Young Nyun , Alexandrov Ludmil B. , Gordân Raluca , Rozen Steven G. , Shibata Tatsuhiro , Pairojkul Chawalit , Teh Bin Tean , Tan Patrick
Published: April 2023

Coverage Statistics and List of Genes for Targeted Sequencing.
Supplementary Table 4 from Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma
Authors: Jusakul Apinya , Cutcutache Ioana , Yong Chern Han , Lim Jing Quan , Huang Mi Ni , Padmanabhan Nisha , Nellore Vishwa , Kongpetch Sarinya , Ng Alvin Wei Tian , Ng Ley Moy , Choo Su Pin , Myint Swe Swe , Thanan Raynoo , Nagarajan Sanjanaa , Lim Weng Khong , Ng Cedric Chuan Young , Boot Arnoud , Liu Mo , Ong Choon Kiat , Rajasegaran Vikneswari , Lie Stefanus , Lim Alvin Soon Tiong , Lim Tse Hui , Tan Jing , Loh Jia Liang , McPherson John R. , Khuntikeo Narong , Bhudhisawasdi Vajaraphongsa , Yongvanit Puangrat , Wongkham Sopit , Totoki Yasushi , Nakamura Hiromi , Arai Yasuhito , Yamasaki Satoshi , Chow Pierce Kah-Hoe , Chung Alexander Yaw Fui , Ooi London Lucien Peng Jin , Lim Kiat Hon , Dima Simona , Duda Dan G. , Popescu Irinel , Broet Philippe , Hsieh Sen-Yung , Yu Ming-Chin , Scarpa Aldo , Lai Jiaming , Luo Di-Xian , Carvalho André Lopes , Vettore André Luiz , Rhee Hyungjin , Park Young Nyun , Alexandrov Ludmil B. , Gordân Raluca , Rozen Steven G. , Shibata Tatsuhiro , Pairojkul Chawalit , Teh Bin Tean , Tan Patrick
Published: April 2023

Structural Variations across 71 WGS CCAs.
Supplementary Table 3 from Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma
Authors: Jusakul Apinya , Cutcutache Ioana , Yong Chern Han , Lim Jing Quan , Huang Mi Ni , Padmanabhan Nisha , Nellore Vishwa , Kongpetch Sarinya , Ng Alvin Wei Tian , Ng Ley Moy , Choo Su Pin , Myint Swe Swe , Thanan Raynoo , Nagarajan Sanjanaa , Lim Weng Khong , Ng Cedric Chuan Young , Boot Arnoud , Liu Mo , Ong Choon Kiat , Rajasegaran Vikneswari , Lie Stefanus , Lim Alvin Soon Tiong , Lim Tse Hui , Tan Jing , Loh Jia Liang , McPherson John R. , Khuntikeo Narong , Bhudhisawasdi Vajaraphongsa , Yongvanit Puangrat , Wongkham Sopit , Totoki Yasushi , Nakamura Hiromi , Arai Yasuhito , Yamasaki Satoshi , Chow Pierce Kah-Hoe , Chung Alexander Yaw Fui , Ooi London Lucien Peng Jin , Lim Kiat Hon , Dima Simona , Duda Dan G. , Popescu Irinel , Broet Philippe , Hsieh Sen-Yung , Yu Ming-Chin , Scarpa Aldo , Lai Jiaming , Luo Di-Xian , Carvalho André Lopes , Vettore André Luiz , Rhee Hyungjin , Park Young Nyun , Alexandrov Ludmil B. , Gordân Raluca , Rozen Steven G. , Shibata Tatsuhiro , Pairojkul Chawalit , Teh Bin Tean , Tan Patrick
Published: April 2023

Summary of CCA Alterations.
Supplementary Table 2 from Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma
Authors: Jusakul Apinya , Cutcutache Ioana , Yong Chern Han , Lim Jing Quan , Huang Mi Ni , Padmanabhan Nisha , Nellore Vishwa , Kongpetch Sarinya , Ng Alvin Wei Tian , Ng Ley Moy , Choo Su Pin , Myint Swe Swe , Thanan Raynoo , Nagarajan Sanjanaa , Lim Weng Khong , Ng Cedric Chuan Young , Boot Arnoud , Liu Mo , Ong Choon Kiat , Rajasegaran Vikneswari , Lie Stefanus , Lim Alvin Soon Tiong , Lim Tse Hui , Tan Jing , Loh Jia Liang , McPherson John R. , Khuntikeo Narong , Bhudhisawasdi Vajaraphongsa , Yongvanit Puangrat , Wongkham Sopit , Totoki Yasushi , Nakamura Hiromi , Arai Yasuhito , Yamasaki Satoshi , Chow Pierce Kah-Hoe , Chung Alexander Yaw Fui , Ooi London Lucien Peng Jin , Lim Kiat Hon , Dima Simona , Duda Dan G. , Popescu Irinel , Broet Philippe , Hsieh Sen-Yung , Yu Ming-Chin , Scarpa Aldo , Lai Jiaming , Luo Di-Xian , Carvalho André Lopes , Vettore André Luiz , Rhee Hyungjin , Park Young Nyun , Alexandrov Ludmil B. , Gordân Raluca , Rozen Steven G. , Shibata Tatsuhiro , Pairojkul Chawalit , Teh Bin Tean , Tan Patrick
Published: April 2023

Alterations in CCA Clusters.
Supplementary Table 1 from Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma
Authors: Jusakul Apinya , Cutcutache Ioana , Yong Chern Han , Lim Jing Quan , Huang Mi Ni , Padmanabhan Nisha , Nellore Vishwa , Kongpetch Sarinya , Ng Alvin Wei Tian , Ng Ley Moy , Choo Su Pin , Myint Swe Swe , Thanan Raynoo , Nagarajan Sanjanaa , Lim Weng Khong , Ng Cedric Chuan Young , Boot Arnoud , Liu Mo , Ong Choon Kiat , Rajasegaran Vikneswari , Lie Stefanus , Lim Alvin Soon Tiong , Lim Tse Hui , Tan Jing , Loh Jia Liang , McPherson John R. , Khuntikeo Narong , Bhudhisawasdi Vajaraphongsa , Yongvanit Puangrat , Wongkham Sopit , Totoki Yasushi , Nakamura Hiromi , Arai Yasuhito , Yamasaki Satoshi , Chow Pierce Kah-Hoe , Chung Alexander Yaw Fui , Ooi London Lucien Peng Jin , Lim Kiat Hon , Dima Simona , Duda Dan G. , Popescu Irinel , Broet Philippe , Hsieh Sen-Yung , Yu Ming-Chin , Scarpa Aldo , Lai Jiaming , Luo Di-Xian , Carvalho André Lopes , Vettore André Luiz , Rhee Hyungjin , Park Young Nyun , Alexandrov Ludmil B. , Gordân Raluca , Rozen Steven G. , Shibata Tatsuhiro , Pairojkul Chawalit , Teh Bin Tean , Tan Patrick
Published: April 2023

Summary of Patients and Clinical Data.
Supplementary Tables and Supplementary Figures 1 through 11 from Secondary Somatic Mutations Restoring RAD51C and RAD51D Associated with Acquired Resistance to the PARP Inhibitor Rucaparib in High-Grade Ovarian Carcinoma
Authors: Kondrashova Olga , Nguyen Minh , Shield-Artin Kristy , Tinker Anna V. , Teng Nelson N.H. , Harrell Maria I. , Kuiper Michael J. , Ho Gwo-Yaw , Barker Holly , Jasin Maria , Prakash Rohit , Kass Elizabeth M. , Sullivan Meghan R. , Brunette Gregory J. , Bernstein Kara A. , Coleman Robert L. , Floquet Anne , Friedlander Michael , Kichenadasse Ganessan , O'Malley David M. , Oza Amit , Sun James , Robillard Liliane , Maloney Lara , Bowtell David , Giordano Heidi , Wakefield Matthew J. , Kaufmann Scott H. , Simmons Andrew D. , Harding Thomas C. , Raponi Mitch , McNeish Iain A. , Swisher Elizabeth M. , Lin Kevin K. , Scott Clare L.
Published: April 2023

Supplementary Tables, Figures and Video legends, Tables 2,3,5 and all Supplementary Figures. Supplementary Table 2. Confirmation of cis configuration of BRCA1 primary and secondary mutations in case 4 by colony PCR. Supplementary Table 3. IC50 (mircoM) values of the PARPi and platinum drugs in parental OVCAR8 cell line and OVCAR8 RAD51C KO clone, and the fold change in IC50 values. Supplementary Table 5. Sequences of primers used for site-directed mutagenesis. Supplementary Figure 1. Foundation Medicine NGS analysis of the 12 cases with archival tissue and/or pre-treatment and post-progression biopsies. Supplementary Figure 2. Sanger sequencing trace of the primary and secondary BRCA1 mutations in cis configuration in case 4 post-progression biopsy sample. Supplementary Figure 3. In vitro response to PARP inhibitor therapy and platinum agents in RAD51C deficient cell lines, with primary or secondary mutations in RAD51C. Supplementary Figure 4. RAD51 foci formation in geminin positive cells deficient for RAD51C, complemented with primary or secondary mutations in RAD51C. Supplementary Figure 5. Diagram of HR reporter assay. Supplementary Figure 6. RAD51C expression in MCF10A cells and in yeast. Supplementary Figure 7. Analysis of serial sections by direct PCR sequencing approach of a post-progression biopsy containing multiple secondary mutations in RAD51C. Supplementary Figure 8. Molecular Dynamics Modeling of WT RAD51D protein and RAD51D protein with secondary mutation c.770_776delinsA, p.S257_R259delinsK. Supplementary Figure 9. In vitro response to PARP inhibitor therapy and cisplatin in RAD51D deficient CHO cell line, with primary or secondary mutation in RAD51D. Supplementary Figure 10. Examination of the parental PEO4 cell line, PEO4 cells with the homozygous frameshift RAD51D mutation (c.762_763del, D254E*fs72) in the same exon as the primary mutation and PEO4 cells with the homozygous secondary RAD51D mutation (c.770_776delinsA, S257_R259delinsK). Supplementary Figure 11. Modeling of tumor clonal fractions in the post-progression biopsy sample with germline RAD51C mutation and multiple secondary mutations.
Supplementary Figures 1-6 from Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma
Authors: Jusakul Apinya , Cutcutache Ioana , Yong Chern Han , Lim Jing Quan , Huang Mi Ni , Padmanabhan Nisha , Nellore Vishwa , Kongpetch Sarinya , Ng Alvin Wei Tian , Ng Ley Moy , Choo Su Pin , Myint Swe Swe , Thanan Raynoo , Nagarajan Sanjanaa , Lim Weng Khong , Ng Cedric Chuan Young , Boot Arnoud , Liu Mo , Ong Choon Kiat , Rajasegaran Vikneswari , Lie Stefanus , Lim Alvin Soon Tiong , Lim Tse Hui , Tan Jing , Loh Jia Liang , McPherson John R. , Khuntikeo Narong , Bhudhisawasdi Vajaraphongsa , Yongvanit Puangrat , Wongkham Sopit , Totoki Yasushi , Nakamura Hiromi , Arai Yasuhito , Yamasaki Satoshi , Chow Pierce Kah-Hoe , Chung Alexander Yaw Fui , Ooi London Lucien Peng Jin , Lim Kiat Hon , Dima Simona , Duda Dan G. , Popescu Irinel , Broet Philippe , Hsieh Sen-Yung , Yu Ming-Chin , Scarpa Aldo , Lai Jiaming , Luo Di-Xian , Carvalho André Lopes , Vettore André Luiz , Rhee Hyungjin , Park Young Nyun , Alexandrov Ludmil B. , Gordân Raluca , Rozen Steven G. , Shibata Tatsuhiro , Pairojkul Chawalit , Teh Bin Tean , Tan Patrick
Published: April 2023

Supplementary Figure 1. Unsupervised Clustering on CCA samples. Supplementary Figure 2. Alterations Found in CCA Clusters. Supplementary Figure 3. MAP2K4 Homozygous Deletions and ERBB2 Amplifications. Supplementary Figure 4. Alterations Related to Structural Variations Found in CCAs. Supplementary Figure 5. FIREFLY Analysis of Pathways Systematically Dysregulated by Somatic Promoter Mutations that Alter Transcription Factor Binding. Supplementary Figure 6. Epigenetic Clusters and Mutation Signatures.
Supplemental Table 1 from Constitutive Signaling from an Engineered IL7 Receptor Promotes Durable Tumor Elimination by Tumor-Redirected T Cells
Authors: Shum Thomas , Omer Bilal , Tashiro Haruko , Kruse Robert L. , Wagner Dimitrios L. , Parikh Kathan , Yi Zhongzhen , Sauer Tim , Liu Daofeng , Parihar Robin , Castillo Paul , Liu Hao , Brenner Malcolm K. , Metelitsa Leonid S. , Gottschalk Stephen , Rooney Cliona M.
Published: April 2023

Supplemental Table 1: Differential gene expression in GD2-CAR.C7R T-cells compared to GD2-CAR T-cells.
Supp Table 4 from Secondary Somatic Mutations Restoring RAD51C and RAD51D Associated with Acquired Resistance to the PARP Inhibitor Rucaparib in High-Grade Ovarian Carcinoma
Authors: Kondrashova Olga , Nguyen Minh , Shield-Artin Kristy , Tinker Anna V. , Teng Nelson N.H. , Harrell Maria I. , Kuiper Michael J. , Ho Gwo-Yaw , Barker Holly , Jasin Maria , Prakash Rohit , Kass Elizabeth M. , Sullivan Meghan R. , Brunette Gregory J. , Bernstein Kara A. , Coleman Robert L. , Floquet Anne , Friedlander Michael , Kichenadasse Ganessan , O'Malley David M. , Oza Amit , Sun James , Robillard Liliane , Maloney Lara , Bowtell David , Giordano Heidi , Wakefield Matthew J. , Kaufmann Scott H. , Simmons Andrew D. , Harding Thomas C. , Raponi Mitch , McNeish Iain A. , Swisher Elizabeth M. , Lin Kevin K. , Scott Clare L.
Published: April 2023

Copy number estimation by SNP array in the archival tumor tissue of the patient identified to have a germline RAD51C mutation (c.577C
Supp Table 1 from Secondary Somatic Mutations Restoring RAD51C and RAD51D Associated with Acquired Resistance to the PARP Inhibitor Rucaparib in High-Grade Ovarian Carcinoma
Authors: Kondrashova Olga , Nguyen Minh , Shield-Artin Kristy , Tinker Anna V. , Teng Nelson N.H. , Harrell Maria I. , Kuiper Michael J. , Ho Gwo-Yaw , Barker Holly , Jasin Maria , Prakash Rohit , Kass Elizabeth M. , Sullivan Meghan R. , Brunette Gregory J. , Bernstein Kara A. , Coleman Robert L. , Floquet Anne , Friedlander Michael , Kichenadasse Ganessan , O'Malley David M. , Oza Amit , Sun James , Robillard Liliane , Maloney Lara , Bowtell David , Giordano Heidi , Wakefield Matthew J. , Kaufmann Scott H. , Simmons Andrew D. , Harding Thomas C. , Raponi Mitch , McNeish Iain A. , Swisher Elizabeth M. , Lin Kevin K. , Scott Clare L.
Published: April 2023

A list of copy number alterations, rearrangements and short variants detected by Foundation Medicine NGS
Supplemental Figure 6 from Constitutive Signaling from an Engineered IL7 Receptor Promotes Durable Tumor Elimination by Tumor-Redirected T Cells
Authors: Shum Thomas , Omer Bilal , Tashiro Haruko , Kruse Robert L. , Wagner Dimitrios L. , Parikh Kathan , Yi Zhongzhen , Sauer Tim , Liu Daofeng , Parihar Robin , Castillo Paul , Liu Hao , Brenner Malcolm K. , Metelitsa Leonid S. , Gottschalk Stephen , Rooney Cliona M.
Published: April 2023

Supplementary Figure 6: Efficient retroviral transduction of T-cells with Î"34, C7R, GD2-CAR, and GD2-CAR.C7R constructs.
Supplemental Figure 4 from Constitutive Signaling from an Engineered IL7 Receptor Promotes Durable Tumor Elimination by Tumor-Redirected T Cells
Authors: Shum Thomas , Omer Bilal , Tashiro Haruko , Kruse Robert L. , Wagner Dimitrios L. , Parikh Kathan , Yi Zhongzhen , Sauer Tim , Liu Daofeng , Parihar Robin , Castillo Paul , Liu Hao , Brenner Malcolm K. , Metelitsa Leonid S. , Gottschalk Stephen , Rooney Cliona M.
Published: April 2023

Supplementary Figure 4: C7R prolongs survival of GD2-CAR T-cells but does not support autonomous cell expansion.
Supplementary Table S9 from BCL6 Antagonizes NOTCH2 to Maintain Survival of Human Follicular Lymphoma Cells
Authors: Valls Ester , Lobry Camille , Geng Huimin , Wang Ling , Cardenas Mariano , Rivas Martín , Cerchietti Leandro , Oh Philmo , Yang Shao Ning , Oswald Erin , Graham Camille W. , Jiang Yanwen , Hatzi Katerina , Agirre Xabier , Perkey Eric , Li Zhuoning , Tam Wayne , Bhatt Kamala , Leonard John P. , Zweidler-McKay Patrick A. , Maillard Ivan , Elemento Olivier , Ci Weimin , Aifantis Iannis , Melnick Ari
Published: April 2023

Supplementary Table S9. Overlap BCL6 target genes on FL and DLBCL datasets. (See Figure 1B for full FL datasets and Supplementary Figure S1F for DLBCL datasets).
Supplemental Figure 3 from Constitutive Signaling from an Engineered IL7 Receptor Promotes Durable Tumor Elimination by Tumor-Redirected T Cells
Authors: Shum Thomas , Omer Bilal , Tashiro Haruko , Kruse Robert L. , Wagner Dimitrios L. , Parikh Kathan , Yi Zhongzhen , Sauer Tim , Liu Daofeng , Parihar Robin , Castillo Paul , Liu Hao , Brenner Malcolm K. , Metelitsa Leonid S. , Gottschalk Stephen , Rooney Cliona M.
Published: April 2023

Supplementary Figure 3: C7R signaling does not change phenotypic composition of GD2-CAR T-cells during culture.
Supplemental Figure 2 from Constitutive Signaling from an Engineered IL7 Receptor Promotes Durable Tumor Elimination by Tumor-Redirected T Cells
Authors: Shum Thomas , Omer Bilal , Tashiro Haruko , Kruse Robert L. , Wagner Dimitrios L. , Parikh Kathan , Yi Zhongzhen , Sauer Tim , Liu Daofeng , Parihar Robin , Castillo Paul , Liu Hao , Brenner Malcolm K. , Metelitsa Leonid S. , Gottschalk Stephen , Rooney Cliona M.
Published: April 2023

Supplementary Figure 2: Efficient retroviral transduction of C7R and Î"34 in both CD4 and CD8 selected T-cells.
Supplementary Table S7 from BCL6 Antagonizes NOTCH2 to Maintain Survival of Human Follicular Lymphoma Cells
Authors: Valls Ester , Lobry Camille , Geng Huimin , Wang Ling , Cardenas Mariano , Rivas Martín , Cerchietti Leandro , Oh Philmo , Yang Shao Ning , Oswald Erin , Graham Camille W. , Jiang Yanwen , Hatzi Katerina , Agirre Xabier , Perkey Eric , Li Zhuoning , Tam Wayne , Bhatt Kamala , Leonard John P. , Zweidler-McKay Patrick A. , Maillard Ivan , Elemento Olivier , Ci Weimin , Aifantis Iannis , Melnick Ari
Published: April 2023

Supplementary Table S7. BCL6 target genes in GCB-DLBCL. Spearman and rho. (See Supplementary Figure S1F).
Supplementary Table S4 from BCL6 Antagonizes NOTCH2 to Maintain Survival of Human Follicular Lymphoma Cells
Authors: Valls Ester , Lobry Camille , Geng Huimin , Wang Ling , Cardenas Mariano , Rivas Martín , Cerchietti Leandro , Oh Philmo , Yang Shao Ning , Oswald Erin , Graham Camille W. , Jiang Yanwen , Hatzi Katerina , Agirre Xabier , Perkey Eric , Li Zhuoning , Tam Wayne , Bhatt Kamala , Leonard John P. , Zweidler-McKay Patrick A. , Maillard Ivan , Elemento Olivier , Ci Weimin , Aifantis Iannis , Melnick Ari
Published: April 2023

Supplementary Table S4. p value of NOTCH2 target genes and members of its transcriptional complex that are inversely correlated to BCL6 in primary FL specimens.
Supplementary Table S3 from BCL6 Antagonizes NOTCH2 to Maintain Survival of Human Follicular Lymphoma Cells
Authors: Valls Ester , Lobry Camille , Geng Huimin , Wang Ling , Cardenas Mariano , Rivas Martín , Cerchietti Leandro , Oh Philmo , Yang Shao Ning , Oswald Erin , Graham Camille W. , Jiang Yanwen , Hatzi Katerina , Agirre Xabier , Perkey Eric , Li Zhuoning , Tam Wayne , Bhatt Kamala , Leonard John P. , Zweidler-McKay Patrick A. , Maillard Ivan , Elemento Olivier , Ci Weimin , Aifantis Iannis , Melnick Ari
Published: April 2023

Supplementary Table S3. Excel file containing the statistical analysis of the 184 FL targets with significant inverse correlation with BCL6.
Supplementary Table S2 from BCL6 Antagonizes NOTCH2 to Maintain Survival of Human Follicular Lymphoma Cells
Authors: Valls Ester , Lobry Camille , Geng Huimin , Wang Ling , Cardenas Mariano , Rivas Martín , Cerchietti Leandro , Oh Philmo , Yang Shao Ning , Oswald Erin , Graham Camille W. , Jiang Yanwen , Hatzi Katerina , Agirre Xabier , Perkey Eric , Li Zhuoning , Tam Wayne , Bhatt Kamala , Leonard John P. , Zweidler-McKay Patrick A. , Maillard Ivan , Elemento Olivier , Ci Weimin , Aifantis Iannis , Melnick Ari
Published: April 2023

Supplementary Table S2. Gene sets that are enriched among BCL6 target genes in FL samples.
Supplementary Text and Figures from Prediction of DNA Repair Inhibitor Response in Short-Term Patient-Derived Ovarian Cancer Organoids
Authors: Hill Sarah J. , Decker Brennan , Roberts Emma A. , Horowitz Neil S. , Muto Michael G. , Worley Michael J. , Feltmate Colleen M. , Nucci Marisa R. , Swisher Elizabeth M. , Nguyen Huy , Yang Chunyu , Morizane Ryuji , Kochupurakkal Bose S. , Do Khanh T. , Konstantinopoulos Panagiotis A. , Liu Joyce F. , Bonventre Joseph V. , Matulonis Ursula A. , Shapiro Geoffrey I. , Berkowitz Ross S. , Crum Christopher P. , D'Andrea Alan D.
Published: April 2023

All supplemental text and 9 supplementary figures
Supplementary Table S1 from BCL6 Antagonizes NOTCH2 to Maintain Survival of Human Follicular Lymphoma Cells
Authors: Valls Ester , Lobry Camille , Geng Huimin , Wang Ling , Cardenas Mariano , Rivas Martín , Cerchietti Leandro , Oh Philmo , Yang Shao Ning , Oswald Erin , Graham Camille W. , Jiang Yanwen , Hatzi Katerina , Agirre Xabier , Perkey Eric , Li Zhuoning , Tam Wayne , Bhatt Kamala , Leonard John P. , Zweidler-McKay Patrick A. , Maillard Ivan , Elemento Olivier , Ci Weimin , Aifantis Iannis , Melnick Ari
Published: April 2023

Supplementary Table S1. BCL6 target genes on FL patient samples ChIp-onChIP.
Supplementary Methods, Figures 1 - 8, Table 5 from BCL6 Antagonizes NOTCH2 to Maintain Survival of Human Follicular Lymphoma Cells
Authors: Valls Ester , Lobry Camille , Geng Huimin , Wang Ling , Cardenas Mariano , Rivas Martín , Cerchietti Leandro , Oh Philmo , Yang Shao Ning , Oswald Erin , Graham Camille W. , Jiang Yanwen , Hatzi Katerina , Agirre Xabier , Perkey Eric , Li Zhuoning , Tam Wayne , Bhatt Kamala , Leonard John P. , Zweidler-McKay Patrick A. , Maillard Ivan , Elemento Olivier , Ci Weimin , Aifantis Iannis , Melnick Ari
Published: April 2023

Supplementary Figure S1. BCL6 displays a specific genomic localization pattern in FL. Supplementary Figure S2. Inverse correlation between BCL6 and NOTCH2 complex genes in primary GC B-cells. Supplementary Figure S3. GC reaction is impaired in Notch2 knock-in mice. Supplementary Figure S4. GC reaction is impaired in Notch2 knock-in mice. Supplementary Figure S5. BCL6 represses NOTCH2 complex genes and Notch activity. Supplementary Figure S6. FL cells are dependent on BCL6 in a NOTCH2-dependent manner. Supplementary Figure S7. Evaluation of the in vivo potency and specificity of anti-Notch2 blockade. Supplementary Figure S8. RI-BPI suppresses FL tumors in vivo and ex vivo. Supplementary Table S5. Primers used for RT-PCR.
Supplementary Methods from Identifying and Targeting Sporadic Oncogenic Genetic Aberrations in Mouse Models of Triple-Negative Breast Cancer
Authors: Liu Hui , Murphy Charles J. , Karreth Florian A. , Emdal Kristina B. , White Forest M. , Elemento Olivier , Toker Alex , Wulf Gerburg M. , Cantley Lewis C.
Published: April 2023

Detailed method descriptions
Supplementary Figures and Legends from Identifying and Targeting Sporadic Oncogenic Genetic Aberrations in Mouse Models of Triple-Negative Breast Cancer
Authors: Liu Hui , Murphy Charles J. , Karreth Florian A. , Emdal Kristina B. , White Forest M. , Elemento Olivier , Toker Alex , Wulf Gerburg M. , Cantley Lewis C.
Published: April 2023

Supplementary figures and figure legends for S1-7
SuppTable5 from Identifying and Targeting Sporadic Oncogenic Genetic Aberrations in Mouse Models of Triple-Negative Breast Cancer
Authors: Liu Hui , Murphy Charles J. , Karreth Florian A. , Emdal Kristina B. , White Forest M. , Elemento Olivier , Toker Alex , Wulf Gerburg M. , Cantley Lewis C.
Published: April 2023

Supplementary table 5 lists potential draggable target(s) for each tumor
Supplementary Table 1 from Prediction of DNA Repair Inhibitor Response in Short-Term Patient-Derived Ovarian Cancer Organoids
Authors: Hill Sarah J. , Decker Brennan , Roberts Emma A. , Horowitz Neil S. , Muto Michael G. , Worley Michael J. , Feltmate Colleen M. , Nucci Marisa R. , Swisher Elizabeth M. , Nguyen Huy , Yang Chunyu , Morizane Ryuji , Kochupurakkal Bose S. , Do Khanh T. , Konstantinopoulos Panagiotis A. , Liu Joyce F. , Bonventre Joseph V. , Matulonis Ursula A. , Shapiro Geoffrey I. , Berkowitz Ross S. , Crum Christopher P. , D'Andrea Alan D.
Published: April 2023

Supplementary Table 1
SuppTable3 from Identifying and Targeting Sporadic Oncogenic Genetic Aberrations in Mouse Models of Triple-Negative Breast Cancer
Authors: Liu Hui , Murphy Charles J. , Karreth Florian A. , Emdal Kristina B. , White Forest M. , Elemento Olivier , Toker Alex , Wulf Gerburg M. , Cantley Lewis C.
Published: April 2023

Supplementary Table 3 lists all CNAs
SuppTable1 from Identifying and Targeting Sporadic Oncogenic Genetic Aberrations in Mouse Models of Triple-Negative Breast Cancer
Authors: Liu Hui , Murphy Charles J. , Karreth Florian A. , Emdal Kristina B. , White Forest M. , Elemento Olivier , Toker Alex , Wulf Gerburg M. , Cantley Lewis C.
Published: April 2023

Supplementary table 1 shows tumor classification