bluuebunny/crossref_metadata_2025 huggingface dataset:
Table S8 from ZFTA–RELA Dictates Oncogenic Transcriptional Programs to Drive Aggressive Supratentorial Ependymoma
Authors: Arabzade Amir , Zhao Yanhua , Varadharajan Srinidhi , Chen Hsiao-Chi , Jessa Selin , Rivas Bryan , Stuckert Austin J. , Solis Minerva , Kardian Alisha , Tlais Dana , Golbourn Brian J. , Stanton Ann-Catherine J. , Chan Yuen San , Olson Calla , Karlin Kristen L. , Kong Kathleen , Kupp Robert , Hu Baoli , Injac Sarah G. , Ngo Madeline , Wang Peter R. , De León Luz A. , Sahm Felix , Kawauchi Daisuke , Pfister Stefan M. , Lin Charles Y. , Hodges H. Courtney , Singh Irtisha , Westbrook Thomas F. , Chintagumpala Murali M. , Blaney Susan M. , Parsons Donald W. , Pajtler Kristian W. , Agnihotri Sameer , Gilbertson Richard J. , Yi Joanna , Jabado Nada , Kleinman Claudia L. , Bertrand Kelsey C. , Deneen Benjamin , Mack Stephen C.
Published: April 2023

CRCs detected in mouse IUE ZRfus1 driven ependymoma
Table S6 from ZFTA–RELA Dictates Oncogenic Transcriptional Programs to Drive Aggressive Supratentorial Ependymoma
Authors: Arabzade Amir , Zhao Yanhua , Varadharajan Srinidhi , Chen Hsiao-Chi , Jessa Selin , Rivas Bryan , Stuckert Austin J. , Solis Minerva , Kardian Alisha , Tlais Dana , Golbourn Brian J. , Stanton Ann-Catherine J. , Chan Yuen San , Olson Calla , Karlin Kristen L. , Kong Kathleen , Kupp Robert , Hu Baoli , Injac Sarah G. , Ngo Madeline , Wang Peter R. , De León Luz A. , Sahm Felix , Kawauchi Daisuke , Pfister Stefan M. , Lin Charles Y. , Hodges H. Courtney , Singh Irtisha , Westbrook Thomas F. , Chintagumpala Murali M. , Blaney Susan M. , Parsons Donald W. , Pajtler Kristian W. , Agnihotri Sameer , Gilbertson Richard J. , Yi Joanna , Jabado Nada , Kleinman Claudia L. , Bertrand Kelsey C. , Deneen Benjamin , Mack Stephen C.
Published: April 2023

DNA motifs detected and shared with mouse embryonic fibroblasts treated with TNF-alpha
Table S5 from ZFTA–RELA Dictates Oncogenic Transcriptional Programs to Drive Aggressive Supratentorial Ependymoma
Authors: Arabzade Amir , Zhao Yanhua , Varadharajan Srinidhi , Chen Hsiao-Chi , Jessa Selin , Rivas Bryan , Stuckert Austin J. , Solis Minerva , Kardian Alisha , Tlais Dana , Golbourn Brian J. , Stanton Ann-Catherine J. , Chan Yuen San , Olson Calla , Karlin Kristen L. , Kong Kathleen , Kupp Robert , Hu Baoli , Injac Sarah G. , Ngo Madeline , Wang Peter R. , De León Luz A. , Sahm Felix , Kawauchi Daisuke , Pfister Stefan M. , Lin Charles Y. , Hodges H. Courtney , Singh Irtisha , Westbrook Thomas F. , Chintagumpala Murali M. , Blaney Susan M. , Parsons Donald W. , Pajtler Kristian W. , Agnihotri Sameer , Gilbertson Richard J. , Yi Joanna , Jabado Nada , Kleinman Claudia L. , Bertrand Kelsey C. , Deneen Benjamin , Mack Stephen C.
Published: April 2023

DNA motifs detected specifically in mouse IUE ZRfus1 tumors
Table S4 from ZFTA–RELA Dictates Oncogenic Transcriptional Programs to Drive Aggressive Supratentorial Ependymoma
Authors: Arabzade Amir , Zhao Yanhua , Varadharajan Srinidhi , Chen Hsiao-Chi , Jessa Selin , Rivas Bryan , Stuckert Austin J. , Solis Minerva , Kardian Alisha , Tlais Dana , Golbourn Brian J. , Stanton Ann-Catherine J. , Chan Yuen San , Olson Calla , Karlin Kristen L. , Kong Kathleen , Kupp Robert , Hu Baoli , Injac Sarah G. , Ngo Madeline , Wang Peter R. , De León Luz A. , Sahm Felix , Kawauchi Daisuke , Pfister Stefan M. , Lin Charles Y. , Hodges H. Courtney , Singh Irtisha , Westbrook Thomas F. , Chintagumpala Murali M. , Blaney Susan M. , Parsons Donald W. , Pajtler Kristian W. , Agnihotri Sameer , Gilbertson Richard J. , Yi Joanna , Jabado Nada , Kleinman Claudia L. , Bertrand Kelsey C. , Deneen Benjamin , Mack Stephen C.
Published: April 2023

Differentially expressed genes Between non-targeting control and Rela KO in IUE ZRfus1 model
Table S3 from ZFTA–RELA Dictates Oncogenic Transcriptional Programs to Drive Aggressive Supratentorial Ependymoma
Authors: Arabzade Amir , Zhao Yanhua , Varadharajan Srinidhi , Chen Hsiao-Chi , Jessa Selin , Rivas Bryan , Stuckert Austin J. , Solis Minerva , Kardian Alisha , Tlais Dana , Golbourn Brian J. , Stanton Ann-Catherine J. , Chan Yuen San , Olson Calla , Karlin Kristen L. , Kong Kathleen , Kupp Robert , Hu Baoli , Injac Sarah G. , Ngo Madeline , Wang Peter R. , De León Luz A. , Sahm Felix , Kawauchi Daisuke , Pfister Stefan M. , Lin Charles Y. , Hodges H. Courtney , Singh Irtisha , Westbrook Thomas F. , Chintagumpala Murali M. , Blaney Susan M. , Parsons Donald W. , Pajtler Kristian W. , Agnihotri Sameer , Gilbertson Richard J. , Yi Joanna , Jabado Nada , Kleinman Claudia L. , Bertrand Kelsey C. , Deneen Benjamin , Mack Stephen C.
Published: April 2023

HA-ZRfus1 bound and over-expressed genes compared to mouse normal brain
Table S2 from ZFTA–RELA Dictates Oncogenic Transcriptional Programs to Drive Aggressive Supratentorial Ependymoma
Authors: Arabzade Amir , Zhao Yanhua , Varadharajan Srinidhi , Chen Hsiao-Chi , Jessa Selin , Rivas Bryan , Stuckert Austin J. , Solis Minerva , Kardian Alisha , Tlais Dana , Golbourn Brian J. , Stanton Ann-Catherine J. , Chan Yuen San , Olson Calla , Karlin Kristen L. , Kong Kathleen , Kupp Robert , Hu Baoli , Injac Sarah G. , Ngo Madeline , Wang Peter R. , De León Luz A. , Sahm Felix , Kawauchi Daisuke , Pfister Stefan M. , Lin Charles Y. , Hodges H. Courtney , Singh Irtisha , Westbrook Thomas F. , Chintagumpala Murali M. , Blaney Susan M. , Parsons Donald W. , Pajtler Kristian W. , Agnihotri Sameer , Gilbertson Richard J. , Yi Joanna , Jabado Nada , Kleinman Claudia L. , Bertrand Kelsey C. , Deneen Benjamin , Mack Stephen C.
Published: April 2023

93 gene signature that characterizes ZFTA-Rela mouse and human tumors.
Table S1 from ZFTA–RELA Dictates Oncogenic Transcriptional Programs to Drive Aggressive Supratentorial Ependymoma
Authors: Arabzade Amir , Zhao Yanhua , Varadharajan Srinidhi , Chen Hsiao-Chi , Jessa Selin , Rivas Bryan , Stuckert Austin J. , Solis Minerva , Kardian Alisha , Tlais Dana , Golbourn Brian J. , Stanton Ann-Catherine J. , Chan Yuen San , Olson Calla , Karlin Kristen L. , Kong Kathleen , Kupp Robert , Hu Baoli , Injac Sarah G. , Ngo Madeline , Wang Peter R. , De León Luz A. , Sahm Felix , Kawauchi Daisuke , Pfister Stefan M. , Lin Charles Y. , Hodges H. Courtney , Singh Irtisha , Westbrook Thomas F. , Chintagumpala Murali M. , Blaney Susan M. , Parsons Donald W. , Pajtler Kristian W. , Agnihotri Sameer , Gilbertson Richard J. , Yi Joanna , Jabado Nada , Kleinman Claudia L. , Bertrand Kelsey C. , Deneen Benjamin , Mack Stephen C.
Published: April 2023

Differential gene expression between mouse IUE:ZRfus1 and mouse normal brain
Figure S4 from ZFTA–RELA Dictates Oncogenic Transcriptional Programs to Drive Aggressive Supratentorial Ependymoma
Authors: Arabzade Amir , Zhao Yanhua , Varadharajan Srinidhi , Chen Hsiao-Chi , Jessa Selin , Rivas Bryan , Stuckert Austin J. , Solis Minerva , Kardian Alisha , Tlais Dana , Golbourn Brian J. , Stanton Ann-Catherine J. , Chan Yuen San , Olson Calla , Karlin Kristen L. , Kong Kathleen , Kupp Robert , Hu Baoli , Injac Sarah G. , Ngo Madeline , Wang Peter R. , De León Luz A. , Sahm Felix , Kawauchi Daisuke , Pfister Stefan M. , Lin Charles Y. , Hodges H. Courtney , Singh Irtisha , Westbrook Thomas F. , Chintagumpala Murali M. , Blaney Susan M. , Parsons Donald W. , Pajtler Kristian W. , Agnihotri Sameer , Gilbertson Richard J. , Yi Joanna , Jabado Nada , Kleinman Claudia L. , Bertrand Kelsey C. , Deneen Benjamin , Mack Stephen C.
Published: April 2023

Figure S4 to show supporting data of DNA motif finding in ZRfus specific binding sites.
Figure S3 from ZFTA–RELA Dictates Oncogenic Transcriptional Programs to Drive Aggressive Supratentorial Ependymoma
Authors: Arabzade Amir , Zhao Yanhua , Varadharajan Srinidhi , Chen Hsiao-Chi , Jessa Selin , Rivas Bryan , Stuckert Austin J. , Solis Minerva , Kardian Alisha , Tlais Dana , Golbourn Brian J. , Stanton Ann-Catherine J. , Chan Yuen San , Olson Calla , Karlin Kristen L. , Kong Kathleen , Kupp Robert , Hu Baoli , Injac Sarah G. , Ngo Madeline , Wang Peter R. , De León Luz A. , Sahm Felix , Kawauchi Daisuke , Pfister Stefan M. , Lin Charles Y. , Hodges H. Courtney , Singh Irtisha , Westbrook Thomas F. , Chintagumpala Murali M. , Blaney Susan M. , Parsons Donald W. , Pajtler Kristian W. , Agnihotri Sameer , Gilbertson Richard J. , Yi Joanna , Jabado Nada , Kleinman Claudia L. , Bertrand Kelsey C. , Deneen Benjamin , Mack Stephen C.
Published: April 2023

Figure S3 demonstrating transcriptional alterations as a result of ZRfus loss of function
Figure S2 from ZFTA–RELA Dictates Oncogenic Transcriptional Programs to Drive Aggressive Supratentorial Ependymoma
Authors: Arabzade Amir , Zhao Yanhua , Varadharajan Srinidhi , Chen Hsiao-Chi , Jessa Selin , Rivas Bryan , Stuckert Austin J. , Solis Minerva , Kardian Alisha , Tlais Dana , Golbourn Brian J. , Stanton Ann-Catherine J. , Chan Yuen San , Olson Calla , Karlin Kristen L. , Kong Kathleen , Kupp Robert , Hu Baoli , Injac Sarah G. , Ngo Madeline , Wang Peter R. , De León Luz A. , Sahm Felix , Kawauchi Daisuke , Pfister Stefan M. , Lin Charles Y. , Hodges H. Courtney , Singh Irtisha , Westbrook Thomas F. , Chintagumpala Murali M. , Blaney Susan M. , Parsons Donald W. , Pajtler Kristian W. , Agnihotri Sameer , Gilbertson Richard J. , Yi Joanna , Jabado Nada , Kleinman Claudia L. , Bertrand Kelsey C. , Deneen Benjamin , Mack Stephen C.
Published: April 2023

Figure S2 supporting expression and localization of ZRfus in the mouse IUE model.
Figure S1 from ZFTA–RELA Dictates Oncogenic Transcriptional Programs to Drive Aggressive Supratentorial Ependymoma
Authors: Arabzade Amir , Zhao Yanhua , Varadharajan Srinidhi , Chen Hsiao-Chi , Jessa Selin , Rivas Bryan , Stuckert Austin J. , Solis Minerva , Kardian Alisha , Tlais Dana , Golbourn Brian J. , Stanton Ann-Catherine J. , Chan Yuen San , Olson Calla , Karlin Kristen L. , Kong Kathleen , Kupp Robert , Hu Baoli , Injac Sarah G. , Ngo Madeline , Wang Peter R. , De León Luz A. , Sahm Felix , Kawauchi Daisuke , Pfister Stefan M. , Lin Charles Y. , Hodges H. Courtney , Singh Irtisha , Westbrook Thomas F. , Chintagumpala Murali M. , Blaney Susan M. , Parsons Donald W. , Pajtler Kristian W. , Agnihotri Sameer , Gilbertson Richard J. , Yi Joanna , Jabado Nada , Kleinman Claudia L. , Bertrand Kelsey C. , Deneen Benjamin , Mack Stephen C.
Published: April 2023

Figure S1 to show differential genes expressed in ZRfus tumors vs normal brain.
Supplementary Table 1 from Werner Helicase Is a Synthetic-Lethal Vulnerability in Mismatch Repair–Deficient Colorectal Cancer Refractory to Targeted Therapies, Chemotherapy, and Immunotherapy
Authors: Picco Gabriele , Cattaneo Chiara M. , van Vliet Esmée J. , Crisafulli Giovanni , Rospo Giuseppe , Consonni Sarah , Vieira Sara F. , Rodríguez Iñigo Sánchez , Cancelliere Carlotta , Banerjee Ruby , Schipper Luuk J. , Oddo Daniele , Dijkstra Krijn K. , Cinatl Jindrich , Michaelis Martin , Yang Fengtang , Di Nicolantonio Federica , Sartore-Bianchi Andrea , Siena Salvatore , Arena Sabrina , Voest Emile E. , Bardelli Alberto , Garnett Mathew J.
Published: April 2023

Supplementary Table 1
Supplementary Figure 5 from Werner Helicase Is a Synthetic-Lethal Vulnerability in Mismatch Repair–Deficient Colorectal Cancer Refractory to Targeted Therapies, Chemotherapy, and Immunotherapy
Authors: Picco Gabriele , Cattaneo Chiara M. , van Vliet Esmée J. , Crisafulli Giovanni , Rospo Giuseppe , Consonni Sarah , Vieira Sara F. , Rodríguez Iñigo Sánchez , Cancelliere Carlotta , Banerjee Ruby , Schipper Luuk J. , Oddo Daniele , Dijkstra Krijn K. , Cinatl Jindrich , Michaelis Martin , Yang Fengtang , Di Nicolantonio Federica , Sartore-Bianchi Andrea , Siena Salvatore , Arena Sabrina , Voest Emile E. , Bardelli Alberto , Garnett Mathew J.
Published: April 2023

Supplementary Figure 5
Supplementary Figure 4 from Werner Helicase Is a Synthetic-Lethal Vulnerability in Mismatch Repair–Deficient Colorectal Cancer Refractory to Targeted Therapies, Chemotherapy, and Immunotherapy
Authors: Picco Gabriele , Cattaneo Chiara M. , van Vliet Esmée J. , Crisafulli Giovanni , Rospo Giuseppe , Consonni Sarah , Vieira Sara F. , Rodríguez Iñigo Sánchez , Cancelliere Carlotta , Banerjee Ruby , Schipper Luuk J. , Oddo Daniele , Dijkstra Krijn K. , Cinatl Jindrich , Michaelis Martin , Yang Fengtang , Di Nicolantonio Federica , Sartore-Bianchi Andrea , Siena Salvatore , Arena Sabrina , Voest Emile E. , Bardelli Alberto , Garnett Mathew J.
Published: April 2023

Supplementary Figure 4
Supplementary Figure 3 from Werner Helicase Is a Synthetic-Lethal Vulnerability in Mismatch Repair–Deficient Colorectal Cancer Refractory to Targeted Therapies, Chemotherapy, and Immunotherapy
Authors: Picco Gabriele , Cattaneo Chiara M. , van Vliet Esmée J. , Crisafulli Giovanni , Rospo Giuseppe , Consonni Sarah , Vieira Sara F. , Rodríguez Iñigo Sánchez , Cancelliere Carlotta , Banerjee Ruby , Schipper Luuk J. , Oddo Daniele , Dijkstra Krijn K. , Cinatl Jindrich , Michaelis Martin , Yang Fengtang , Di Nicolantonio Federica , Sartore-Bianchi Andrea , Siena Salvatore , Arena Sabrina , Voest Emile E. , Bardelli Alberto , Garnett Mathew J.
Published: April 2023

Supplementary Figure 3
Supplementary Figure 1 from Werner Helicase Is a Synthetic-Lethal Vulnerability in Mismatch Repair–Deficient Colorectal Cancer Refractory to Targeted Therapies, Chemotherapy, and Immunotherapy
Authors: Picco Gabriele , Cattaneo Chiara M. , van Vliet Esmée J. , Crisafulli Giovanni , Rospo Giuseppe , Consonni Sarah , Vieira Sara F. , Rodríguez Iñigo Sánchez , Cancelliere Carlotta , Banerjee Ruby , Schipper Luuk J. , Oddo Daniele , Dijkstra Krijn K. , Cinatl Jindrich , Michaelis Martin , Yang Fengtang , Di Nicolantonio Federica , Sartore-Bianchi Andrea , Siena Salvatore , Arena Sabrina , Voest Emile E. , Bardelli Alberto , Garnett Mathew J.
Published: April 2023

Supplementary Figure 1
Cell Model Network-UK from Werner Helicase Is a Synthetic-Lethal Vulnerability in Mismatch Repair–Deficient Colorectal Cancer Refractory to Targeted Therapies, Chemotherapy, and Immunotherapy
Authors: Picco Gabriele , Cattaneo Chiara M. , van Vliet Esmée J. , Crisafulli Giovanni , Rospo Giuseppe , Consonni Sarah , Vieira Sara F. , Rodríguez Iñigo Sánchez , Cancelliere Carlotta , Banerjee Ruby , Schipper Luuk J. , Oddo Daniele , Dijkstra Krijn K. , Cinatl Jindrich , Michaelis Martin , Yang Fengtang , Di Nicolantonio Federica , Sartore-Bianchi Andrea , Siena Salvatore , Arena Sabrina , Voest Emile E. , Bardelli Alberto , Garnett Mathew J.
Published: April 2023

The Cell Model Network-UK group author list
Supplementary Table S1 from Simultaneous Inhibition of LSD1 and TGFβ Enables Eradication of Poorly Immunogenic Tumors with Anti–PD-1 Treatment
Authors: Sheng Wanqiang , Liu Yi , Chakraborty Damayanti , Debo Brian , Shi Yang
Published: April 2023

GO enrichment of upregulated genes in Lsd1 KO versus scramble B16 tumor cells
Supplementary Tables from Resolving the Spatial and Cellular Architecture of Lung Adenocarcinoma by Multiregion Single-Cell Sequencing
Authors: Sinjab Ansam , Han Guangchun , Treekitkarnmongkol Warapen , Hara Kieko , Brennan Patrick M. , Dang Minghao , Hao Dapeng , Wang Ruiping , Dai Enyu , Dejima Hitoshi , Zhang Jiexin , Bogatenkova Elena , Sanchez-Espiridion Beatriz , Chang Kyle , Little Danielle R. , Bazzi Samer , Tran Linh M. , Krysan Kostyantyn , Behrens Carmen , Duose Dzifa Y. , Parra Edwin R. , Raso Maria Gabriela , Solis Luisa M. , Fukuoka Junya , Zhang Jianjun , Sepesi Boris , Cascone Tina , Byers Lauren Averett , Gibbons Don L. , Chen Jichao , Moghaddam Seyed Javad , Ostrin Edwin J. , Rosen Daniel , Heymach John V. , Scheet Paul , Dubinett Steven M. , Fujimoto Junya , Wistuba Ignacio I. , Stevenson Christopher S. , Spira Avrum , Wang Linghua , Kadara Humam
Published: April 2023

Supplementary Tables
Supplementary Fig S9 from Resolving the Spatial and Cellular Architecture of Lung Adenocarcinoma by Multiregion Single-Cell Sequencing
Authors: Sinjab Ansam , Han Guangchun , Treekitkarnmongkol Warapen , Hara Kieko , Brennan Patrick M. , Dang Minghao , Hao Dapeng , Wang Ruiping , Dai Enyu , Dejima Hitoshi , Zhang Jiexin , Bogatenkova Elena , Sanchez-Espiridion Beatriz , Chang Kyle , Little Danielle R. , Bazzi Samer , Tran Linh M. , Krysan Kostyantyn , Behrens Carmen , Duose Dzifa Y. , Parra Edwin R. , Raso Maria Gabriela , Solis Luisa M. , Fukuoka Junya , Zhang Jianjun , Sepesi Boris , Cascone Tina , Byers Lauren Averett , Gibbons Don L. , Chen Jichao , Moghaddam Seyed Javad , Ostrin Edwin J. , Rosen Daniel , Heymach John V. , Scheet Paul , Dubinett Steven M. , Fujimoto Junya , Wistuba Ignacio I. , Stevenson Christopher S. , Spira Avrum , Wang Linghua , Kadara Humam
Published: April 2023

Supplementary Fig S9 and legend
Supplementary Fig S21-S24 from Resolving the Spatial and Cellular Architecture of Lung Adenocarcinoma by Multiregion Single-Cell Sequencing
Authors: Sinjab Ansam , Han Guangchun , Treekitkarnmongkol Warapen , Hara Kieko , Brennan Patrick M. , Dang Minghao , Hao Dapeng , Wang Ruiping , Dai Enyu , Dejima Hitoshi , Zhang Jiexin , Bogatenkova Elena , Sanchez-Espiridion Beatriz , Chang Kyle , Little Danielle R. , Bazzi Samer , Tran Linh M. , Krysan Kostyantyn , Behrens Carmen , Duose Dzifa Y. , Parra Edwin R. , Raso Maria Gabriela , Solis Luisa M. , Fukuoka Junya , Zhang Jianjun , Sepesi Boris , Cascone Tina , Byers Lauren Averett , Gibbons Don L. , Chen Jichao , Moghaddam Seyed Javad , Ostrin Edwin J. , Rosen Daniel , Heymach John V. , Scheet Paul , Dubinett Steven M. , Fujimoto Junya , Wistuba Ignacio I. , Stevenson Christopher S. , Spira Avrum , Wang Linghua , Kadara Humam
Published: April 2023

Supplementary Figures S21-S24 and figure legends
Supplementary Fig S10-S20 from Resolving the Spatial and Cellular Architecture of Lung Adenocarcinoma by Multiregion Single-Cell Sequencing
Authors: Sinjab Ansam , Han Guangchun , Treekitkarnmongkol Warapen , Hara Kieko , Brennan Patrick M. , Dang Minghao , Hao Dapeng , Wang Ruiping , Dai Enyu , Dejima Hitoshi , Zhang Jiexin , Bogatenkova Elena , Sanchez-Espiridion Beatriz , Chang Kyle , Little Danielle R. , Bazzi Samer , Tran Linh M. , Krysan Kostyantyn , Behrens Carmen , Duose Dzifa Y. , Parra Edwin R. , Raso Maria Gabriela , Solis Luisa M. , Fukuoka Junya , Zhang Jianjun , Sepesi Boris , Cascone Tina , Byers Lauren Averett , Gibbons Don L. , Chen Jichao , Moghaddam Seyed Javad , Ostrin Edwin J. , Rosen Daniel , Heymach John V. , Scheet Paul , Dubinett Steven M. , Fujimoto Junya , Wistuba Ignacio I. , Stevenson Christopher S. , Spira Avrum , Wang Linghua , Kadara Humam
Published: April 2023

Supplementary Figures S10-S20 and figure legends
Supplementary Fig S1-S7 from Resolving the Spatial and Cellular Architecture of Lung Adenocarcinoma by Multiregion Single-Cell Sequencing
Authors: Sinjab Ansam , Han Guangchun , Treekitkarnmongkol Warapen , Hara Kieko , Brennan Patrick M. , Dang Minghao , Hao Dapeng , Wang Ruiping , Dai Enyu , Dejima Hitoshi , Zhang Jiexin , Bogatenkova Elena , Sanchez-Espiridion Beatriz , Chang Kyle , Little Danielle R. , Bazzi Samer , Tran Linh M. , Krysan Kostyantyn , Behrens Carmen , Duose Dzifa Y. , Parra Edwin R. , Raso Maria Gabriela , Solis Luisa M. , Fukuoka Junya , Zhang Jianjun , Sepesi Boris , Cascone Tina , Byers Lauren Averett , Gibbons Don L. , Chen Jichao , Moghaddam Seyed Javad , Ostrin Edwin J. , Rosen Daniel , Heymach John V. , Scheet Paul , Dubinett Steven M. , Fujimoto Junya , Wistuba Ignacio I. , Stevenson Christopher S. , Spira Avrum , Wang Linghua , Kadara Humam
Published: April 2023

Supplementary Figures S1-S7 and figure legends
Table S5 from CARM1 Inhibition Enables Immunotherapy of Resistant Tumors by Dual Action on Tumor Cells and T Cells
Authors: Kumar Sushil , Zeng Zexian , Bagati Archis , Tay Rong En , Sanz Lionel A. , Hartono Stella R. , Ito Yoshinaga , Abderazzaq Fieda , Hatchi Elodie , Jiang Peng , Cartwright Adam N.R. , Olawoyin Olamide , Mathewson Nathan D. , Pyrdol Jason W. , Li Mamie Z. , Doench John G. , Booker Matthew A. , Tolstorukov Michael Y. , Elledge Stephen J. , Chédin Frédéric , Liu X. Shirley , Wucherpfennig Kai W.
Published: April 2023

Genes in CARM1-KO signature
Table S3 from CARM1 Inhibition Enables Immunotherapy of Resistant Tumors by Dual Action on Tumor Cells and T Cells
Authors: Kumar Sushil , Zeng Zexian , Bagati Archis , Tay Rong En , Sanz Lionel A. , Hartono Stella R. , Ito Yoshinaga , Abderazzaq Fieda , Hatchi Elodie , Jiang Peng , Cartwright Adam N.R. , Olawoyin Olamide , Mathewson Nathan D. , Pyrdol Jason W. , Li Mamie Z. , Doench John G. , Booker Matthew A. , Tolstorukov Michael Y. , Elledge Stephen J. , Chédin Frédéric , Liu X. Shirley , Wucherpfennig Kai W.
Published: April 2023

RNA-seq of Carm1 KO tumor cells
Table S1 from CARM1 Inhibition Enables Immunotherapy of Resistant Tumors by Dual Action on Tumor Cells and T Cells
Authors: Kumar Sushil , Zeng Zexian , Bagati Archis , Tay Rong En , Sanz Lionel A. , Hartono Stella R. , Ito Yoshinaga , Abderazzaq Fieda , Hatchi Elodie , Jiang Peng , Cartwright Adam N.R. , Olawoyin Olamide , Mathewson Nathan D. , Pyrdol Jason W. , Li Mamie Z. , Doench John G. , Booker Matthew A. , Tolstorukov Michael Y. , Elledge Stephen J. , Chédin Frédéric , Liu X. Shirley , Wucherpfennig Kai W.
Published: April 2023

CRISPR screen in tumor-infiltrating T cells
Table S3 from Cancer Cells Retrace a Stepwise Differentiation Program during Malignant Progression
Authors: Saghafinia Sadegh , Homicsko Krisztian , Di Domenico Annunziata , Wullschleger Stephan , Perren Aurel , Marinoni Ilaria , Ciriello Giovanni , Michael Iacovos P. , Hanahan Douglas
Published: April 2023

Supplementary Table S3
Table S2 from Cancer Cells Retrace a Stepwise Differentiation Program during Malignant Progression
Authors: Saghafinia Sadegh , Homicsko Krisztian , Di Domenico Annunziata , Wullschleger Stephan , Perren Aurel , Marinoni Ilaria , Ciriello Giovanni , Michael Iacovos P. , Hanahan Douglas
Published: April 2023

Supplementary Table S2
Figure S7 from Cancer Cells Retrace a Stepwise Differentiation Program during Malignant Progression
Authors: Saghafinia Sadegh , Homicsko Krisztian , Di Domenico Annunziata , Wullschleger Stephan , Perren Aurel , Marinoni Ilaria , Ciriello Giovanni , Michael Iacovos P. , Hanahan Douglas
Published: April 2023

Supplementary Figure S7
Figure S6 from Cancer Cells Retrace a Stepwise Differentiation Program during Malignant Progression
Authors: Saghafinia Sadegh , Homicsko Krisztian , Di Domenico Annunziata , Wullschleger Stephan , Perren Aurel , Marinoni Ilaria , Ciriello Giovanni , Michael Iacovos P. , Hanahan Douglas
Published: April 2023

Supplementary Figure S6
Figure S5 from Cancer Cells Retrace a Stepwise Differentiation Program during Malignant Progression
Authors: Saghafinia Sadegh , Homicsko Krisztian , Di Domenico Annunziata , Wullschleger Stephan , Perren Aurel , Marinoni Ilaria , Ciriello Giovanni , Michael Iacovos P. , Hanahan Douglas
Published: April 2023

Supplementary Figure S5
Figure S3 from Cancer Cells Retrace a Stepwise Differentiation Program during Malignant Progression
Authors: Saghafinia Sadegh , Homicsko Krisztian , Di Domenico Annunziata , Wullschleger Stephan , Perren Aurel , Marinoni Ilaria , Ciriello Giovanni , Michael Iacovos P. , Hanahan Douglas
Published: April 2023

Supplementary Figure S3
Figure S2 from Cancer Cells Retrace a Stepwise Differentiation Program during Malignant Progression
Authors: Saghafinia Sadegh , Homicsko Krisztian , Di Domenico Annunziata , Wullschleger Stephan , Perren Aurel , Marinoni Ilaria , Ciriello Giovanni , Michael Iacovos P. , Hanahan Douglas
Published: April 2023

Supplementary Figure S2
Supplementary Data from Discovery and Features of an Alkylating Signature in Colorectal Cancer
Authors: Gurjao Carino , Zhong Rong , Haruki Koichiro , Li Yvonne Y. , Spurr Liam F. , Lee-Six Henry , Reardon Brendan , Ugai Tomotaka , Zhang Xuehong , Cherniack Andrew D. , Song Mingyang , Van Allen Eliezer M. , Meyerhardt Jeffrey A. , Nowak Jonathan A. , Giovannucci Edward L. , Fuchs Charles S. , Wu Kana , Ogino Shuji , Giannakis Marios
Published: April 2023

Tables S1 S5
Supplementary Figures S1-S12 from Mutant NPM1 Directly Regulates Oncogenic Transcription in Acute Myeloid Leukemia
Authors: Uckelmann Hannah J. , Haarer Elena L. , Takeda Reina , Wong Eric M. , Hatton Charlie , Marinaccio Christian , Perner Florian , Rajput Masooma , Antonissen Noa J.C. , Wen Yanhe , Yang Lu , Brunetti Lorenzo , Chen Chun-Wei , Armstrong Scott A.
Published: April 2023

Supplementary Figure 1. NPM1c degradation leads to differentiation of OCI-AML3 cells.Supplementary Figure 2. NPM1c chromatin targets identified in OCI-AML3-NPM1c-FKBP12 cells and validated by targeted degradation.Supplementary Figure 3. Motif analysis reveals developmental transcription factor binding sites at NPM1c bound regions.Supplementary Figure 4. NPM1c chromatin targets are highly expressed in patient samples of NPM1c AML.Supplementary Figure 5. NPM1c degradation has rapid effects on transcription at it target genes.Supplementary Figure 6. Transcriptional machinery is lost from NPM1c targets after 1 hour of NPM1c degradation.Supplementary Figure 7. CRIPSR domain scan reveals specific dependency of NPM1 mutant cells on the
AS2 region.Supplementary Figure 8. The AS2 region affects NPM1c localization in 293T and OCI-AML3 cells.Supplementary Figure 9. Selinexor treatment disrupts NPM1c chromatin binding.Supplementary Figure 10. NPM1c cooperates with MLL1 to drive oncogenic gene expression.Supplementary Figure 11. NPM1c is selectively lost from chromatin in response to Menin inhibitor treatment.Supplementary Figure 12. Menin-MLL inhibition leads to selective loss of NPM1c target gene expression.
Figure S8 from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha
Authors: Sahu Avinash , Wang Xiaoman , Munson Phillip , Klomp Jan P.G. , Wang Xiaoqing , Gu Shengqing Stan , Han Ya , Qian Gege , Nicol Phillip , Zeng Zexian , Wang Chenfei , Tokheim Collin , Zhang Wubing , Fu Jingxin , Wang Jin , Nair Nishanth Ulhas , Rens Joost A.P. , Bourajjaj Meriem , Jansen Bas , Leenders Inge , Lemmers Jaap , Musters Mark , van Zanten Sanne , van Zelst Laura , Worthington Jenny , Liu Jun S. , Juric Dejan , Meyer Clifford A. , Oubrie Arthur , Liu X. Shirley , Fisher David E. , Flaherty Keith T.
Published: April 2023

The effect of ESRRA inhibition on tumor microenvironments at single-cell resolutions.
Figure S5 from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha
Authors: Sahu Avinash , Wang Xiaoman , Munson Phillip , Klomp Jan P.G. , Wang Xiaoqing , Gu Shengqing Stan , Han Ya , Qian Gege , Nicol Phillip , Zeng Zexian , Wang Chenfei , Tokheim Collin , Zhang Wubing , Fu Jingxin , Wang Jin , Nair Nishanth Ulhas , Rens Joost A.P. , Bourajjaj Meriem , Jansen Bas , Leenders Inge , Lemmers Jaap , Musters Mark , van Zanten Sanne , van Zelst Laura , Worthington Jenny , Liu Jun S. , Juric Dejan , Meyer Clifford A. , Oubrie Arthur , Liu X. Shirley , Fisher David E. , Flaherty Keith T.
Published: April 2023

Robust in vivo antitumor elimination by ESRRA inhibition.
Figure S3 from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha
Authors: Sahu Avinash , Wang Xiaoman , Munson Phillip , Klomp Jan P.G. , Wang Xiaoqing , Gu Shengqing Stan , Han Ya , Qian Gege , Nicol Phillip , Zeng Zexian , Wang Chenfei , Tokheim Collin , Zhang Wubing , Fu Jingxin , Wang Jin , Nair Nishanth Ulhas , Rens Joost A.P. , Bourajjaj Meriem , Jansen Bas , Leenders Inge , Lemmers Jaap , Musters Mark , van Zanten Sanne , van Zelst Laura , Worthington Jenny , Liu Jun S. , Juric Dejan , Meyer Clifford A. , Oubrie Arthur , Liu X. Shirley , Fisher David E. , Flaherty Keith T.
Published: April 2023

ESRRA inhibition is associated with immune infiltrations and proinflammatory signaling in patient tumors.
Figure S15 from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha
Authors: Sahu Avinash , Wang Xiaoman , Munson Phillip , Klomp Jan P.G. , Wang Xiaoqing , Gu Shengqing Stan , Han Ya , Qian Gege , Nicol Phillip , Zeng Zexian , Wang Chenfei , Tokheim Collin , Zhang Wubing , Fu Jingxin , Wang Jin , Nair Nishanth Ulhas , Rens Joost A.P. , Bourajjaj Meriem , Jansen Bas , Leenders Inge , Lemmers Jaap , Musters Mark , van Zanten Sanne , van Zelst Laura , Worthington Jenny , Liu Jun S. , Juric Dejan , Meyer Clifford A. , Oubrie Arthur , Liu X. Shirley , Fisher David E. , Flaherty Keith T.
Published: April 2023

Evaluation of scRNA-BipotentR (BipotentR without bulk-tumor sub-module).
Figure S13 from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha
Authors: Sahu Avinash , Wang Xiaoman , Munson Phillip , Klomp Jan P.G. , Wang Xiaoqing , Gu Shengqing Stan , Han Ya , Qian Gege , Nicol Phillip , Zeng Zexian , Wang Chenfei , Tokheim Collin , Zhang Wubing , Fu Jingxin , Wang Jin , Nair Nishanth Ulhas , Rens Joost A.P. , Bourajjaj Meriem , Jansen Bas , Leenders Inge , Lemmers Jaap , Musters Mark , van Zanten Sanne , van Zelst Laura , Worthington Jenny , Liu Jun S. , Juric Dejan , Meyer Clifford A. , Oubrie Arthur , Liu X. Shirley , Fisher David E. , Flaherty Keith T.
Published: April 2023

Kaplan–Meier plots showing progression-free survival and overall survival differences for patients receiving anti-PD1 between the low-risk and high-risk groups defined by the median value of deepBTAS.
Figure S12 from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha
Authors: Sahu Avinash , Wang Xiaoman , Munson Phillip , Klomp Jan P.G. , Wang Xiaoqing , Gu Shengqing Stan , Han Ya , Qian Gege , Nicol Phillip , Zeng Zexian , Wang Chenfei , Tokheim Collin , Zhang Wubing , Fu Jingxin , Wang Jin , Nair Nishanth Ulhas , Rens Joost A.P. , Bourajjaj Meriem , Jansen Bas , Leenders Inge , Lemmers Jaap , Musters Mark , van Zanten Sanne , van Zelst Laura , Worthington Jenny , Liu Jun S. , Juric Dejan , Meyer Clifford A. , Oubrie Arthur , Liu X. Shirley , Fisher David E. , Flaherty Keith T.
Published: April 2023

deepBTAS improve the performance of current ICB biomarkers.
Data from Intratumoral Heterogeneity and Clonal Evolution Induced by HPV Integration
Authors: Akagi Keiko , Symer David E. , Mahmoud Medhat , Jiang Bo , Goodwin Sara , Wangsa Darawalee , Li Zhengke , Xiao Weihong , Dan Dunn Joe , Ried Thomas , Coombes Kevin R. , Sedlazeck Fritz J. , Gillison Maura L.
Published: April 2023

Abstract
The human papillomavirus (HPV) genome is integrated into host DNA in most HPV-positive cancers, but the consequences for chromosomal integrity are unknown. Continuous long-read sequencing of oropharyngeal cancers and cancer cell lines identified a previously undescribed form of structural variation, “heterocateny,” characterized by diverse, interrelated, and repetitive patterns of concatemerized virus and host DNA segments within a cancer. Unique breakpoints shared across structural variants facilitated stepwise reconstruction of their evolution from a common molecular ancestor. This analysis revealed that virus and virus–host concatemers are unstable and, upon insertion into and excision from chromosomes, facilitate capture, amplification, and recombination of host DNA and chromosomal rearrangements. Evidence of heterocateny was detected in extrachromosomal and intrachromosomal DNA. These findings indicate that heterocateny is driven by the dynamic, aberrant replication and recombination of an oncogenic DNA virus, thereby extending known consequences of HPV integration to include promotion of intratumoral heterogeneity and clonal evolution.
Significance:
Long-read sequencing of HPV-positive cancers revealed “heterocateny,” a previously unreported form of genomic structural variation characterized by heterogeneous, interrelated, and repetitive genomic rearrangements within a tumor. Heterocateny is driven by unstable concatemerized HPV genomes, which facilitate capture, rearrangement, and amplification of host DNA, and promotes intratumoral heterogeneity and clonal evolution.

See related commentary by McBride and White, p. 814.

This article is highlighted in the In This Issue feature, p. 799
Supplementary table S2 from Cross-Talk between Myeloid-Derived Suppressor Cells and Mast Cells Mediates Tumor-Specific Immunosuppression in Prostate Cancer
Authors: Jachetti Elena , Cancila Valeria , Rigoni Alice , Bongiovanni Lucia , Cappetti Barbara , Belmonte Beatrice , Enriquez Claudia , Casalini Patrizia , Ostano Paola , Frossi Barbara , Sangaletti Sabina , Chiodoni Claudia , Chiorino Giovanna , Pucillo Carlo E. , Tripodo Claudio , Colombo Mario P.
Published: April 2023

The file contains the lists of MC and MDSC related genes
Supplementary data from Cross-Talk between Myeloid-Derived Suppressor Cells and Mast Cells Mediates Tumor-Specific Immunosuppression in Prostate Cancer
Authors: Jachetti Elena , Cancila Valeria , Rigoni Alice , Bongiovanni Lucia , Cappetti Barbara , Belmonte Beatrice , Enriquez Claudia , Casalini Patrizia , Ostano Paola , Frossi Barbara , Sangaletti Sabina , Chiodoni Claudia , Chiorino Giovanna , Pucillo Carlo E. , Tripodo Claudio , Colombo Mario P.
Published: April 2023

Supplementary Figure 1. Representative plots illustrating analysis of tumor-specific CD8+ T cell response in TRAMP and KitWsh-TRAMP mice. Supplementary Figure 2. CD8+T cells from PDLN and prostates of KitWsh-TRAMP mice are responsive. Supplementary Figure 3. Quantification of MCs or T cells after reconstitution of depletion, respectively. Supplementary Figure 4. Flow cytometry identification of T cells in spleen and prostate of TRAMP and KitWsh-TRAMP mice. Supplementary Figure 5. Flow cytometry identification of myeloid cells in spleen and prostate of TRAMP and KitWsh-TRAMP mice. Supplementary Figure 6. MCs and PMN-MDSC can interact via CD40L-CD40 in TRAMP mice. Supplementary Figure 7. Wild type and CD40L-/- BMMC are equally functional, but CD8+T cells from PDLN and prostates of KitWsh-TRAMP mice reconstituted with BMMC CD40L-/- are still responsive. Supplementary Figure 8. MCs, CD40L and CD33 co-localize in human tumor prostate cancer samples. Supplementary Figure 9. Correlation between MC-genes and MDSC-activity genes in human prostate cancer data sets. Supplementary Figure 10. MC/PMN-MDSC signatures outperform random signatures of the same length.
Table S1 from Treg Depletion Licenses T Cell–Driven HEV Neogenesis and Promotes Tumor Destruction
Authors: Colbeck Emily J. , Jones Emma , Hindley James P. , Smart Kathryn , Schulz Ralph , Browne Molly , Cutting Scott , Williams Anwen , Parry Lee , Godkin Andrew , Ware Carl F. , Ager Ann , Gallimore Awen
Published: April 2023

Table S1
Supplementary Figure 2 from GITR Pathway Activation Abrogates Tumor Immune Suppression through Loss of Regulatory T-cell Lineage Stability
Authors: Schaer David A. , Budhu Sadna , Liu Cailian , Bryson Campbell , Malandro Nicole , Cohen Adam , Zhong Hong , Yang Xia , Houghton Alan N. , Merghoub Taha , Wolchok Jedd D.
Published: April 2023

PDF file - 84K, Percentage of CD4+Foxp3+ Tregs in IgG vs DTA-1 treated tumors
Supplementary Table 1 from NY-ESO-1 Expression in Meningioma Suggests a Rationale for New Immunotherapeutic Approaches
Authors: Baia Gilson S. , Caballero Otavia L. , Ho Janelle S.Y. , Zhao Qi , Cohen Tzeela , Binder Zev A. , Salmasi Vafi , Gallia Gary L. , Quinones-Hinojosa Alfredo , Olivi Alessandro , Brem Henry , Burger Peter , Strausberg Robert L. , Simpson Andrew J.G. , Eberhart Charles G. , Riggins Gregory J.
Published: April 2023

XLSX file - 45K, Primer Sequences for PCR Amplification of Cancer/Testis Genes.
Table S1 from Baseline Cytokine Profiles of Tuberculin-Specific CD4+ T Cells in Non–Muscle-Invasive Bladder Cancer May Predict Outcomes of BCG Immunotherapy
Authors: Jallad Samer , Thomas Philip , Newport Melanie J. , Kern Florian
Published: April 2023

Urine cytokines before and after BCG induction therapy
Figure S3 from Baseline Cytokine Profiles of Tuberculin-Specific CD4+ T Cells in Non–Muscle-Invasive Bladder Cancer May Predict Outcomes of BCG Immunotherapy
Authors: Jallad Samer , Thomas Philip , Newport Melanie J. , Kern Florian
Published: April 2023

Recurrence free survival and effect of BCG-inducible IL2 secretion
Figure S2 from Baseline Cytokine Profiles of Tuberculin-Specific CD4+ T Cells in Non–Muscle-Invasive Bladder Cancer May Predict Outcomes of BCG Immunotherapy
Authors: Jallad Samer , Thomas Philip , Newport Melanie J. , Kern Florian
Published: April 2023

Flow-cytometry gating strategy
Figure S1 from Baseline Cytokine Profiles of Tuberculin-Specific CD4+ T Cells in Non–Muscle-Invasive Bladder Cancer May Predict Outcomes of BCG Immunotherapy
Authors: Jallad Samer , Thomas Philip , Newport Melanie J. , Kern Florian
Published: April 2023

Study time line
Supplementary Figure 2 from T Cells Specific for an Unconventional Natural Antigen Fail to Recognize Leukemic Cells
Authors: Pont Margot J. , Oostvogels Rimke , van Bergen Cornelis A.M. , van der Meijden Edith D. , Honders Maria W. , Bliss Sophie , Jongsma Marlieke L.M. , Lokhorst Henk M. , Falkenburg J.H. Frederik , Mutis Tuna , Griffioen Marieke , Spaapen Robbert M.
Published: April 2023

Supplementary Figure 2. The generation of the LB-TTK-1D peptide is proteasome-dependent. LB-TTK-1D antigen positive EBV-LCLs were treated with increasing concentrations of the proteasome inhibitor bortezomib for 48h, washed and exposed to LB-TTK-1D-specific T cells (clone 10-5). T cell-produced IFN-γ was determined in the supernatant of the cultures by ELISA. Depicted are OD450 values.
Supplementary Figure 1 from T Cells Specific for an Unconventional Natural Antigen Fail to Recognize Leukemic Cells
Authors: Pont Margot J. , Oostvogels Rimke , van Bergen Cornelis A.M. , van der Meijden Edith D. , Honders Maria W. , Bliss Sophie , Jongsma Marlieke L.M. , Lokhorst Henk M. , Falkenburg J.H. Frederik , Mutis Tuna , Griffioen Marieke , Spaapen Robbert M.
Published: April 2023

Supplementary Figure 1. The LB-TTK-1D-specific (clone 10-5) and USP11-specific T cell clones have a similar affinity for their cognate peptide. Synthetic peptides RLHDGRVFV (peptideTTK) or FTWEGLYNV (peptideUSP11) were loaded on T2 cells in a serial dilution. The depicted T cell clones were stimulated using these target cells followed by determination of IFN-γ secretion in the supernatant (ELISA). Calculated EC50 values are depicted.
Supplementary Figure 1 from High-Throughput Stability Screening of Neoantigen/HLA Complexes Improves Immunogenicity Predictions
Authors: Blaha Dylan T. , Anderson Scott D. , Yoakum Daniel M. , Hager Marlies V. , Zha Yuanyuan , Gajewski Thomas F. , Kranz David M.
Published: April 2023

Sample analysis of DSF data
Supplementary Data from High-Throughput Stability Screening of Neoantigen/HLA Complexes Improves Immunogenicity Predictions
Authors: Blaha Dylan T. , Anderson Scott D. , Yoakum Daniel M. , Hager Marlies V. , Zha Yuanyuan , Gajewski Thomas F. , Kranz David M.
Published: April 2023

Supplementary Tables
Supplementary Figures 1 - 3 from Regression of Metastatic Merkel Cell Carcinoma Following Transfer of Polyomavirus-Specific T Cells and Therapies Capable of Reinducing HLA Class-I
Authors: Chapuis Aude G. , Afanasiev Olga K. , Iyer Jayasri G. , Paulson Kelly G. , Parvathaneni Upendra , Hwang Joo Ha , Lai Ivy , Roberts Ilana M. , Sloan Heather L. , Bhatia Shailender , Shibuya Kendall C. , Gooley Ted , Desmarais Cindy , Koelle David M. , Yee Cassian , Nghiem Paul
Published: April 2023

PDF file - 738K, Supplementary Fig. S1: Detection of MCPyV-specific CD8 T cells among tumor infiltrating lymphocytes (TIL) from the primary MCC tumor (left) and PBMC (right). Cells were stained with A24/MCPyV.LT.92-101 tetramer and CD8. Supplementary Fig. S2: A) Cell products destined for infusions 1, 2 and 3 bound the MCPyV LT-Ag92-101 peptide-HLA tetramer. B) Products secreted IFNγ (left) and lysed MCPyV LT-Ag92-101 -pulsed FUJI (A24+ cell line) and autologous PBMC pulsed with 10?g/ml peptide (right). The product used for infusion 1 is shown and is representative. Supplementary Fig. S3: Assessment of CD25hiCD127loCD4+ T-cells in PBMC collected at baseline (137 days and immediately prior to the first treatment) and at indicated timepoints after treatments. Gray bars on x-axis indicate the timing of each treatment as detailed in Figure 1.
Supplementary materials and methods, figures and legends from Protumor Steering of Cancer Inflammation by p50 NF-κB Enhances Colorectal Cancer Progression
Authors: Porta Chiara , Ippolito Alessandro , Consonni Francesca Maria , Carraro Lorenzo , Celesti Giuseppe , Correale Carmen , Grizzi Fabio , Pasqualini Fabio , Tartari Silvia , Rinaldi Maurizio , Bianchi Paolo , Balzac Fiorella , Vetrano Stefania , Turco Emilia , Hirsch Emilio , Laghi Luigi , Sica Antonio
Published: April 2023

S1: Analysis of p50 NF-κB ablation in myeloid cells (p50Fl/Fl; Lyz2Cre mice) and enterocytes (p50Fl/Fl; VillinCre mice). S2: Analysis of inflammatory gene expression at different phases of colitisassociated CRC (CAC) development. S3: Lack of p50 NF-κB exacerbates DSS-induced colitis. S4: Genetic ablation of p50 unleashes anti-tumor M1-polarized activation of TAMs. S5: Lack of p50 shapes gut associated immune populations in AOM/DSS treated. S6: Lack of p50 selectively impairs lamina propria monocytes/macrophages accumulation in steady state conditions. mice. S7: Wt and p50-/- mice show similar levels of proliferative colonic cancer cells. S8: Nuclear accumulation of p50 in TAM at the inner tumor tissue does not correlate with CRC patients' outcome.
Supplementary Figure 3 from Intravenous Injection of MVA Virus Targets CD8+ Lymphocytes to Tumors to Control Tumor Growth upon Combinatorial Treatment with a TLR9 Agonist
Authors: Fend Laetitia , Gatard-Scheikl Tanja , Kintz Jacqueline , Gantzer Murielle , Schaedler Emmanuelle , Rittner Karola , Cochin Sandrine , Fournel Sylvie , Préville Xavier
Published: April 2023

Supplementary Figure 3. Percentages of splenic and tumor infiltrating T lymphocytes expressing CCR1, CCR2, CCR3 or CCR5.
Figure S8 from Antibody-Neutralized Reovirus Is Effective in Oncolytic Virotherapy
Authors: Berkeley Robert A. , Steele Lynette P. , Mulder Aat A. , van den Wollenberg Diana J.M. , Kottke Timothy J. , Thompson Jill , Coffey Matthew , Hoeben Rob C. , Vile Richard G. , Melcher Alan , Ilett Elizabeth J.
Published: April 2023

Serum from mice immunized against reovirus is highly neutralizing
Figure S3 from Antibody-Neutralized Reovirus Is Effective in Oncolytic Virotherapy
Authors: Berkeley Robert A. , Steele Lynette P. , Mulder Aat A. , van den Wollenberg Diana J.M. , Kottke Timothy J. , Thompson Jill , Coffey Matthew , Hoeben Rob C. , Vile Richard G. , Melcher Alan , Ilett Elizabeth J.
Published: April 2023

UV-inactivated reovirus induces monocyte activation
Figure S1 from Antibody-Neutralized Reovirus Is Effective in Oncolytic Virotherapy
Authors: Berkeley Robert A. , Steele Lynette P. , Mulder Aat A. , van den Wollenberg Diana J.M. , Kottke Timothy J. , Thompson Jill , Coffey Matthew , Hoeben Rob C. , Vile Richard G. , Melcher Alan , Ilett Elizabeth J.
Published: April 2023

Patient-derived serum is highly neutralizing
Supplementary Figure 1 - PDF file - 42K from Microvesicle Cargo of Tumor-Associated MUC1 to Dendritic Cells Allows Cross-presentation and Specific Carbohydrate Processing
Authors: Rughetti Aurelia , Rahimi Hassan , Belleudi Francesca , Napoletano Chiara , Battisti Federico , Zizzari Ilaria G. , Antonilli Morena , Bellati Filippo , Wandall Hans H. , Benedetti Panici Pierluigi , Burchell Joy M. , Torrisi Mara R. , Nuti Marianna
Published: April 2023

Cellular distribution of HLAII-DR molecules in iDCs was visualized after 2 or 12 hours from cell harvesting and incubation at 37{degree sign}C (columns 1 and 2, respectively) by immunofluorescence staining by Apotome module employing the anti-HLA-DR MoAb L243 (red signal). Nuclei are visualized in blu DAPI staining. Magnification 60X; Bars: 10microm.
Supplemental Figure 2: Characterization of MUC1-DG75 transfectant cell line and of the MUC1-DG75-MVs. from Microvesicle Cargo of Tumor-Associated MUC1 to Dendritic Cells Allows Cross-presentation and Specific Carbohydrate Processing
Authors: Rughetti Aurelia , Rahimi Hassan , Belleudi Francesca , Napoletano Chiara , Battisti Federico , Zizzari Ilaria G. , Antonilli Morena , Bellati Filippo , Wandall Hans H. , Benedetti Panici Pierluigi , Burchell Joy M. , Torrisi Mara R. , Nuti Marianna
Published: April 2023

A, MUC1 glycoform expression of MUC1-DG75 transfectant detected by flow cytometry employing anti-MUC1 glycoform specific MoAbs. Only the ST-MUC1 glycoform, (MoAb MYE12), is expressed on the surface of transfectant cells. B, MUC1 distribution on MVs shed by MUC1-DG75 cells as detected by Immunogold staining in TEM using the anti-MUC1 MoAb Ma552. C, MUC1 detection in cell extracts and MVs of MUC1-DG75 and DG75 cell lines by Western Blot analysis employing the anti-MUC1 MoAb Ma552. The specific bands above 170kDa are present only in the MUC1-DG75 cell extract and MVs. D, ELISA of the MUC1 glycoprofile expressed by MUC1-DG75-MVs and by rST-MUC1. The ST-MUC1 is the unique MUC1 glycoepitope detected in both samples.
Supplemental Figure 1: HLAII-DR molecule accumulates at the periphery of DCs after 12 hours incubation from Microvesicle Cargo of Tumor-Associated MUC1 to Dendritic Cells Allows Cross-presentation and Specific Carbohydrate Processing
Authors: Rughetti Aurelia , Rahimi Hassan , Belleudi Francesca , Napoletano Chiara , Battisti Federico , Zizzari Ilaria G. , Antonilli Morena , Bellati Filippo , Wandall Hans H. , Benedetti Panici Pierluigi , Burchell Joy M. , Torrisi Mara R. , Nuti Marianna
Published: April 2023

Cellular distribution of HLAII-DR molecules in iDCs was visualized after 2 or 12 hours from cell harvesting and incubation at 37{degree sign}C (columns 1 and 2, respectively) by immunofluorescence staining by Apotome module employing the anti-HLA-DR MoAb L243 (red signal). Nuclei are visualized in blu DAPI staining. Magnification 60X; Bars: 10μm.
Supplementary Table and Figures from Loss of CXCR4 in Myeloid Cells Enhances Antitumor Immunity and Reduces Melanoma Growth through NK Cell and FASL Mechanisms
Authors: Yang Jinming , Kumar Amrendra , Vilgelm Anna E. , Chen Sheau-Chiann , Ayers Gregory D. , Novitskiy Sergey V. , Joyce Sebastian , Richmond Ann
Published: April 2023

Supplementary Table 1 and Figures 1-7
Figure S3 from Peripheral Blood TCR Repertoire Profiling May Facilitate Patient Stratification for Immunotherapy against Melanoma
Authors: Hogan Sabrina A. , Courtier Anaïs , Cheng Phil F. , Jaberg-Bentele Nicoletta F. , Goldinger Simone M. , Manuel Manuarii , Perez Solène , Plantier Nadia , Mouret Jean-François , Nguyen-Kim Thi Dan Linh , Raaijmakers Marieke I.G. , Kvistborg Pia , Pasqual Nicolas , Haanen John B.A.G. , Dummer Reinhard , Levesque Mitchell P.
Published: April 2023

Baseline DE50 in anti-PD1 treated patients who A) had a PFS above or under 12 months, B) survived more or less than 24 months. Dashed line = 20.4%. P value calculated with Fisher's test.
Figure S2 from Peripheral Blood TCR Repertoire Profiling May Facilitate Patient Stratification for Immunotherapy against Melanoma
Authors: Hogan Sabrina A. , Courtier Anaïs , Cheng Phil F. , Jaberg-Bentele Nicoletta F. , Goldinger Simone M. , Manuel Manuarii , Perez Solène , Plantier Nadia , Mouret Jean-François , Nguyen-Kim Thi Dan Linh , Raaijmakers Marieke I.G. , Kvistborg Pia , Pasqual Nicolas , Haanen John B.A.G. , Dummer Reinhard , Levesque Mitchell P.
Published: April 2023

Lymphocyte to leukocyte ratio in high and low ANC/ALC groups for anti-PD1 treated patients at baseline. (Wilcoxon test)
Tables S1 and S2 from Rapid Construction of Antitumor T-cell Receptor Vectors from Frozen Tumors for Engineered T-cell Therapy
Authors: Tsuji Takemasa , Yoneda Akira , Matsuzaki Junko , Miliotto Anthony , Ryan Courtney , Koya Richard C. , Odunsi Kunle
Published: April 2023

Tables S1 and S2 describe sequences of primers and TCR, respectively.
Figure S7 from Rapid Construction of Antitumor T-cell Receptor Vectors from Frozen Tumors for Engineered T-cell Therapy
Authors: Tsuji Takemasa , Yoneda Akira , Matsuzaki Junko , Miliotto Anthony , Ryan Courtney , Koya Richard C. , Odunsi Kunle
Published: April 2023

Fig. S7 describes recognition of Glycine-substituted peptides by library-derived TCR.