bluuebunny/crossref_metadata_2025 huggingface dataset:
Table S8 from Characterizing evolutionary dynamics reveals strategies to exhaust the spectrum of subclonal resistance in EGFR-mutant lung cancer
Authors: Müller Nina , Lorenz Carina , Ostendorp Jenny , Heisel Felix S. , Friese Ulrich P. , Cartolano Maria , Plenker Dennis , Tumbrink Hannah L. , Heimsoeth Alena , Baedeker Philipp , Ortiz-Cuaran Sandra , Weiss Jonathan , Büttner Reinhard , Peifer Martin , Thomas Roman K. , Sos Martin L. , Berg Johannes , Brägelmann Johannes
Published: September 2024

Suppl. Table S8, candidates from CRISPR activation screen
Table S7 from Characterizing evolutionary dynamics reveals strategies to exhaust the spectrum of subclonal resistance in EGFR-mutant lung cancer
Authors: Müller Nina , Lorenz Carina , Ostendorp Jenny , Heisel Felix S. , Friese Ulrich P. , Cartolano Maria , Plenker Dennis , Tumbrink Hannah L. , Heimsoeth Alena , Baedeker Philipp , Ortiz-Cuaran Sandra , Weiss Jonathan , Büttner Reinhard , Peifer Martin , Thomas Roman K. , Sos Martin L. , Berg Johannes , Brägelmann Johannes
Published: September 2024

Suppl. Table S7, differentially expressed genes
Supplementary Data from Characterizing evolutionary dynamics reveals strategies to exhaust the spectrum of subclonal resistance in EGFR-mutant lung cancer
Authors: Müller Nina , Lorenz Carina , Ostendorp Jenny , Heisel Felix S. , Friese Ulrich P. , Cartolano Maria , Plenker Dennis , Tumbrink Hannah L. , Heimsoeth Alena , Baedeker Philipp , Ortiz-Cuaran Sandra , Weiss Jonathan , Büttner Reinhard , Peifer Martin , Thomas Roman K. , Sos Martin L. , Berg Johannes , Brägelmann Johannes
Published: September 2024

Supplementary Methods, Figures and Tables
Supplementary Figure 8. from The genomic and epigenomic landscape of double-negative metastatic prostate cancer
Authors: Lundberg Arian , Zhang Meng , Aggarwal Rahul , Li Haolong , Zhang Li , Foye Adam , Sjöström Martin , Chou Jonathan , Chang Kevin , Moreno-Rodriguez Thaidy , Shrestha Raunak , Baskin Avi , Zhu Xiaolin , Weinstein Alana S. , Younger Noah , Alumkal Joshi J. , Beer Tomasz M. , Chi Kim N. , Evans Christopher P. , Gleave Martin , Lara Primo N. , Reiter Rob E. , Rettig Matthew B. , Witte Owen N. , Wyatt Alexander W. , Feng Felix Y. , Small Eric J. , Quigley David A.
Published: September 2024

Gene expression level of Krüppel-like factor (KLF) family among the five mCRPC subtypes
Supplementary Figure 6. from The genomic and epigenomic landscape of double-negative metastatic prostate cancer
Authors: Lundberg Arian , Zhang Meng , Aggarwal Rahul , Li Haolong , Zhang Li , Foye Adam , Sjöström Martin , Chou Jonathan , Chang Kevin , Moreno-Rodriguez Thaidy , Shrestha Raunak , Baskin Avi , Zhu Xiaolin , Weinstein Alana S. , Younger Noah , Alumkal Joshi J. , Beer Tomasz M. , Chi Kim N. , Evans Christopher P. , Gleave Martin , Lara Primo N. , Reiter Rob E. , Rettig Matthew B. , Witte Owen N. , Wyatt Alexander W. , Feng Felix Y. , Small Eric J. , Quigley David A.
Published: September 2024

Gene expression level of CHD7 among the mCRPC tumors of Beltran et al. cohort
Supplementary Data from Syk inhibition reprograms tumor-associated macrophages and overcomes gemcitabine-induced immunosuppression in pancreatic ductal adenocarcinoma
Authors: Rohila Deepak , Park In Hwan , Pham Timothy V. , Weitz Jonathan , Hurtado de Mendoza Tatiana , Madheswaran Suresh , Ishfaq Mehreen , Beaman Cooper , Tapia Elisabette , Sun Siming , Patel Jay , Tamayo Pablo , Lowy Andrew M. , Joshi Shweta
Published: September 2024

Supplementary methods and Legends to supplementary figures
Supplementary Data from Syk inhibition reprograms tumor-associated macrophages and overcomes gemcitabine-induced immunosuppression in pancreatic ductal adenocarcinoma
Authors: Rohila Deepak , Park In Hwan , Pham Timothy V. , Weitz Jonathan , Hurtado de Mendoza Tatiana , Madheswaran Suresh , Ishfaq Mehreen , Beaman Cooper , Tapia Elisabette , Sun Siming , Patel Jay , Tamayo Pablo , Lowy Andrew M. , Joshi Shweta
Published: September 2024

Supplementary table
Supplementary Materials and Methods from PTEN loss confers resistance to anti-PD-1 therapy in non-small cell lung cancer by increasing tumor infiltration of regulatory T cells
Authors: Exposito Francisco , Redrado Miriam , Houry Maeva , Hastings Katherine , Molero-Abraham Magdalena , Lozano Teresa , Solórzano José Luis. , Sanz-Ortega Julian , Adradas Vera , Amat Ramon , Redin Esther , Leon Sergio , Legarra Naroa , Garcia Javier , Serrano Diego , Valencia Karmele , Robles-Oteiza Camila , Foggetti Giorgia , Otegui Nerea , Felip Enriqueta , Lasarte Juan J. , Paz-Ares Luis , Zugazagoitia Jon , Politi Katerina , Montuenga Luis , Calvo Alfonso
Published: September 2024

Supplementary Materials and Methods
Supplementary Figure 3 from PTEN loss confers resistance to anti-PD-1 therapy in non-small cell lung cancer by increasing tumor infiltration of regulatory T cells
Authors: Exposito Francisco , Redrado Miriam , Houry Maeva , Hastings Katherine , Molero-Abraham Magdalena , Lozano Teresa , Solórzano José Luis. , Sanz-Ortega Julian , Adradas Vera , Amat Ramon , Redin Esther , Leon Sergio , Legarra Naroa , Garcia Javier , Serrano Diego , Valencia Karmele , Robles-Oteiza Camila , Foggetti Giorgia , Otegui Nerea , Felip Enriqueta , Lasarte Juan J. , Paz-Ares Luis , Zugazagoitia Jon , Politi Katerina , Montuenga Luis , Calvo Alfonso
Published: September 2024

Supplementary Figure 3
Supplementary Data 1 from Targeting KDM2A Enhances T Cell Infiltration in NSD1-Deficient Head and Neck Squamous Cell Carcinoma
Authors: Chen Chen , Shin June Ho. , Fang Zhuoqing , Brennan Kevin , Horowitz Nina B. , Pfaff Kathleen L. , Welsh Emma L. , Rodig Scott J. , Gevaert Olivier , Gozani Or , Uppaluri Ravindra , Sunwoo John B.
Published: September 2024

qRT-PCR-raw data_organized
Supplementary Data from N6-methyladenosine modification of FZR1 mRNA promotes gemcitabine resistance in pancreatic cancer
Authors: Su Jiachun , Li Rui , Chen Ziming , Liu Shaoqiu , Zhao Hongzhe , Deng Shuang , Zeng Lingxing , Xu Zilan , Zhao Sihan , Zhou Yifan , Li Mei , He Xiaowei , Liu Ji , Xue Chunling , Bai Ruihong , Zhuang Lisha , Zhou Quanbo , Zhang Shaoping , Chen Rufu , Huang Xudong , Lin Dongxin , Zheng Jian , Zhang Jialiang
Published: September 2024

Proteins identified in RNA pulldown and mass spectrometry analysis with FZR1[m6A] or FZR1[A].
Supplementary tables from Hypoxia-responsive lncRNA AC115619 encodes a micropeptide that suppresses m6A modifications and hepatocellular carcinoma progression
Authors: Zhang Qiangnu , Wei Teng , Yan Lesen , Zhu Siqi , Jin Wen , Bai Yu , Zeng Yuandi , Zhang Xiaofei , Yin Zexin , Yang Jilin , Zhang Wenjian , Wu Meilong , Zhang Yusen , Liu Liping
Published: September 2024

Information on the details of the materials involved in this study
Supplementary figures from Hypoxia-responsive lncRNA AC115619 encodes a micropeptide that suppresses m6A modifications and hepatocellular carcinoma progression
Authors: Zhang Qiangnu , Wei Teng , Yan Lesen , Zhu Siqi , Jin Wen , Bai Yu , Zeng Yuandi , Zhang Xiaofei , Yin Zexin , Yang Jilin , Zhang Wenjian , Wu Meilong , Zhang Yusen , Liu Liping
Published: September 2024

Supplementary figures with legends
Table S1 from CD36 drives metastasis and relapse in acute myeloid leukemia
Authors: Farge Thomas , Nakhle Jean , Lagarde Damien , Cognet Guillaume , Polley Nathaniel , Castellano Remy , Nicolau Marie-Laure , Bosc Claudie , Sabatier Marie , Sahal Ambrine , Saland Estelle , Jeanson Yannick , Guiraud Nathan , Boet Emeline , Bergoglio Camille , Gotanègre Mathilde , Mouchel Pierre-Luc , Stuani Lucille , Larrue Clement , Sallese Marie , De Mas Véronique , Moro Cédric , Dray Cedric , Collette Yves , Raymond-Letron Isabelle , Ader Isabelle , Recher Christian , Sarry Jean-Emmanuel , Cabon Florence , Vergez Francois , Carriere Audrey
Published: September 2024

Human antibodies for flow cytometry analyses (TUH cohort)
Supplementary Data from CD36 drives metastasis and relapse in acute myeloid leukemia
Authors: Farge Thomas , Nakhle Jean , Lagarde Damien , Cognet Guillaume , Polley Nathaniel , Castellano Remy , Nicolau Marie-Laure , Bosc Claudie , Sabatier Marie , Sahal Ambrine , Saland Estelle , Jeanson Yannick , Guiraud Nathan , Boet Emeline , Bergoglio Camille , Gotanègre Mathilde , Mouchel Pierre-Luc , Stuani Lucille , Larrue Clement , Sallese Marie , De Mas Véronique , Moro Cédric , Dray Cedric , Collette Yves , Raymond-Letron Isabelle , Ader Isabelle , Recher Christian , Sarry Jean-Emmanuel , Cabon Florence , Vergez Francois , Carriere Audrey
Published: September 2024

Supplemental Text
Supplementary Data from CD36 drives metastasis and relapse in acute myeloid leukemia
Authors: Farge Thomas , Nakhle Jean , Lagarde Damien , Cognet Guillaume , Polley Nathaniel , Castellano Remy , Nicolau Marie-Laure , Bosc Claudie , Sabatier Marie , Sahal Ambrine , Saland Estelle , Jeanson Yannick , Guiraud Nathan , Boet Emeline , Bergoglio Camille , Gotanègre Mathilde , Mouchel Pierre-Luc , Stuani Lucille , Larrue Clement , Sallese Marie , De Mas Véronique , Moro Cédric , Dray Cedric , Collette Yves , Raymond-Letron Isabelle , Ader Isabelle , Recher Christian , Sarry Jean-Emmanuel , Cabon Florence , Vergez Francois , Carriere Audrey
Published: September 2024

Figure S2
Table S3 from Mesenchymal-like tumor cells and myofibroblastic cancer-associated fibroblasts are associated with progression and immunotherapy response of clear-cell renal cell carcinoma
Authors: Davidson Guillaume , Helleux Alexandra , Vano Yann A. , Lindner Véronique , Fattori Antonin , Cerciat Marie , Elaidi Reza Thierry. , Verkarre Virginie , Sun Cheng-Ming , Chevreau Christine , Bennamoun Mostefa , Lang Hervé , Tricard Thibault , Fridman Wolf Herman. , Sautes-Fridman Catherine , Su Xiaoping , Plassard Damien , Keime Celine , Thibault-Carpentier Christelle , Barthélémy Philippe , Oudard Stéphane Marie. , Davidson Irwin , Malouf Gabriel G.
Published: September 2024

Deconvolution of cell types in TCGA-KIRC cohort.
Table S2 from Activation of the cGAS/STING axis in genome-damaged hematopoietic cells does not impact blood cell formation or leukemogenesis
Authors: Dressel Nicole , Natusch Loreen , Munz Clara M. , Costas Ramon Santiago , Morcos Mina N.F. , Loff Anja , Hiller Björn , Haase Christa , Schulze Livia , Müller Patrick , Lesche Mathias , Dahl Andreas , Luksch Hella , Roesen-Wolff Angela , Roers Axel , Behrendt Rayk , Gerbaulet Alexander
Published: September 2024

Oligo nucleotide sequences
Supplementary figures S1-S5 from Tipifarnib potentiates the antitumor effects of PI3Kα inhibition in PIK3CA- and HRAS-dysregulated HNSCC via convergent inhibition of mTOR activity
Authors: Smith Alison E. , Chan Stacia , Wang Zhiyong , McCloskey Asako , Reilly Quinn , Wang Jayden Z. , Patel Hetika Vora. , Koshizuka Keiichi , Soifer Harris S. , Kessler Linda , Dayoub Ashley , Villaflor Victoria , Adkins Douglas R. , Bruce Justine Y. , Ho Alan L. , Perez Cesar A. , Hanna Glenn J. , Gasco Hernandez Amaya , Saunders Andrew , Dale Stephen , Gutkind J. Silvio , Burrows Francis , Malik Shivani
Published: September 2024

Supplementary figures related to figures 1-5.
Supplementary Data from A non-conserved histidine residue on KRAS drives paralog selectivity of the KRASG12D inhibitor MRTX1133
Authors: Keats Miles , Han John J.W. , Lee Yeon-Hwa , Lee Chih-Shia , Luo Ji
Published: September 2024

Supplementary discussion, supplementary tables and figures.
Supplementary Data from SENP1 decreases RNF168 phase separation to promote DNA damage repair and drug resistance in colon cancer
Authors: Wei Min , Huang Xinping , Liao Liming , Tian Yonglu , Zheng Xiaofeng
Published: September 2024

Figures S1-S6
Supplementary Data from SENP1 decreases RNF168 phase separation to promote DNA damage repair and drug resistance in colon cancer
Authors: Wei Min , Huang Xinping , Liao Liming , Tian Yonglu , Zheng Xiaofeng
Published: September 2024

Supplementary video 2
Supplementary Table 1 from ESRRB inhibits the TGF-β signaling pathway to drive cell proliferation in cervical cancer
Authors: Li Qin-Shu , Zheng Peng-Sheng
Published: September 2024

Semi‒quantitative statistical table of ESRRB staining in NC, HSIL and CC
Figure S3 from ESRRB inhibits the TGF-β signaling pathway to drive cell proliferation in cervical cancer
Authors: Li Qin-Shu , Zheng Peng-Sheng
Published: September 2024

Fig. S3 describes the wide field diagram of ICC
Figure S2 from ESRRB inhibits the TGF-β signaling pathway to drive cell proliferation in cervical cancer
Authors: Li Qin-Shu , Zheng Peng-Sheng
Published: September 2024

Fig. S2 describes RNA sequencing results; Expression of cell-cycle markers in xenograft.
Table S5 from Crosstalk between myeloid and B cells shapes the distinct microenvironments of primary and secondary liver cancer
Authors: Chen Zhihang , Zhang Guopei , Ren Xiaoxue , Yao Zhijia , Zhou Qian , Ren Xuxin , Chen Shuling , Xu Lixia , Sun Kaiyu , Zeng Qianwen , Kuang Ming , Kuang Dong-Ming , Peng Sui
Published: September 2024

Table S5
Table S2 from Crosstalk between myeloid and B cells shapes the distinct microenvironments of primary and secondary liver cancer
Authors: Chen Zhihang , Zhang Guopei , Ren Xiaoxue , Yao Zhijia , Zhou Qian , Ren Xuxin , Chen Shuling , Xu Lixia , Sun Kaiyu , Zeng Qianwen , Kuang Ming , Kuang Dong-Ming , Peng Sui
Published: September 2024

Table S2
Figure S9 from Crosstalk between myeloid and B cells shapes the distinct microenvironments of primary and secondary liver cancer
Authors: Chen Zhihang , Zhang Guopei , Ren Xiaoxue , Yao Zhijia , Zhou Qian , Ren Xuxin , Chen Shuling , Xu Lixia , Sun Kaiyu , Zeng Qianwen , Kuang Ming , Kuang Dong-Ming , Peng Sui
Published: September 2024

Figure S9
Figure S6 from Crosstalk between myeloid and B cells shapes the distinct microenvironments of primary and secondary liver cancer
Authors: Chen Zhihang , Zhang Guopei , Ren Xiaoxue , Yao Zhijia , Zhou Qian , Ren Xuxin , Chen Shuling , Xu Lixia , Sun Kaiyu , Zeng Qianwen , Kuang Ming , Kuang Dong-Ming , Peng Sui
Published: September 2024

Figure S6
Figure S2 from Crosstalk between myeloid and B cells shapes the distinct microenvironments of primary and secondary liver cancer
Authors: Chen Zhihang , Zhang Guopei , Ren Xiaoxue , Yao Zhijia , Zhou Qian , Ren Xuxin , Chen Shuling , Xu Lixia , Sun Kaiyu , Zeng Qianwen , Kuang Ming , Kuang Dong-Ming , Peng Sui
Published: September 2024

Figure S2
Supplementary Data from Mutant KRAS mediates circARFGEF2 biogenesis to promote lymphatic metastasis of pancreatic ductal adenocarcinoma
Authors: Kong Yao , Luo Yuming , Zheng Shangyou , Yang Jiabin , Zhang Dingwen , Zhao Yue , Zheng Hanhao , An Mingjie , Lin Yan , Ai Le , Diao Xiarao , Lin Qing , Chen Changhao , Chen Rufu
Published: September 2024

Figure S1-S10, Table S1-S5 and Supplementary methods
Table S7 from CD25high Effector Regulatory T Cells Hamper Responses to PD-1 Blockade in Triple-Negative Breast Cancer
Authors: Fattori Stéphane , Le Roy Aude , Houacine Jemila , Robert Lucie , Abes Riad , Gorvel Laurent , Granjeaud Samuel , Rouvière Marie-Sarah , Ben Amara Amira , Boucherit Nicolas , Tarpin Carole , Pakradouni Jihane , Charafe-Jauffret Emmanuelle , Houvenaeghel Gilles , Lambaudie Eric , Bertucci Francois , Rochigneux Philippe , Gonçalves Anthony , Foussat Arnaud , Chrétien Anne-Sophie , Olive Daniel
Published: September 2024

Percentage of immune cell types in primary TNBC, related to Figure 2
Table S2 from CD25high Effector Regulatory T Cells Hamper Responses to PD-1 Blockade in Triple-Negative Breast Cancer
Authors: Fattori Stéphane , Le Roy Aude , Houacine Jemila , Robert Lucie , Abes Riad , Gorvel Laurent , Granjeaud Samuel , Rouvière Marie-Sarah , Ben Amara Amira , Boucherit Nicolas , Tarpin Carole , Pakradouni Jihane , Charafe-Jauffret Emmanuelle , Houvenaeghel Gilles , Lambaudie Eric , Bertucci Francois , Rochigneux Philippe , Gonçalves Anthony , Foussat Arnaud , Chrétien Anne-Sophie , Olive Daniel
Published: September 2024

T cell and NK cell subpopulations gene features, related to Figure 1
Supplementary Table 1 from Abemaciclib is effective in palbociclib-resistant hormone receptor-positive metastatic breast cancers
Authors: Navarro-Yepes Juliana , Kettner Nicole M. , Rao Xiayu , Bishop Cassandra Santaella. , Bui Tuyen N. , Wingate Hannah F. , Singareeka Raghavendra Akshara , Wang Yan , Wang Jing , Sahin Aysegul A. , Meric-Bernstam Funda , Hunt Kelly K. , Damodaran Senthil , Tripathy Debu , Keyomarsi Khandan
Published: September 2024

This file contains Supplementary Table 1, pertaining to the proteomic classification of RPPA antibodies
Table S1 from Intratumoral Microbiota Composition Regulates Chemoimmunotherapy Response in Esophageal Squamous Cell Carcinoma
Authors: Wu Hong , Leng Xuefeng , Liu Qianshi , Mao Tianqin , Jiang Tao , Liu Yiqiang , Li Feifei , Cao Chenhui , Fan Jun , Chen Liang , Chen Yaqi , Yao Quan , Lu Shun , Liang Renchuan , Hu Lanlin , Liu Mingxin , Wan Yejian , Li Zhaoshen , Peng Jun , Luo Qiyu , Zhou Hang , Yin Jun , Xu Ke , Lan Mei , Peng Xinhao , Lan Haitao , Li Gang , Han Yongtao , Zhang Xia , Xiao Zhi-Xiong Jim. , Lang Jinyi , Wang Guihua , Xu Chuan
Published: September 2024

Table S1 shows clinical characteristics of esophageal squamous cell carcinoma (ESCC) patients who underwent upfront surgery.
Figure S6 from Intratumoral Microbiota Composition Regulates Chemoimmunotherapy Response in Esophageal Squamous Cell Carcinoma
Authors: Wu Hong , Leng Xuefeng , Liu Qianshi , Mao Tianqin , Jiang Tao , Liu Yiqiang , Li Feifei , Cao Chenhui , Fan Jun , Chen Liang , Chen Yaqi , Yao Quan , Lu Shun , Liang Renchuan , Hu Lanlin , Liu Mingxin , Wan Yejian , Li Zhaoshen , Peng Jun , Luo Qiyu , Zhou Hang , Yin Jun , Xu Ke , Lan Mei , Peng Xinhao , Lan Haitao , Li Gang , Han Yongtao , Zhang Xia , Xiao Zhi-Xiong Jim. , Lang Jinyi , Wang Guihua , Xu Chuan
Published: September 2024

Figure S6 shows immune cell clusters and signatures revealed by single-cell RNA sequencing in patients with ESCC.
Figure S1 from Intratumoral Microbiota Composition Regulates Chemoimmunotherapy Response in Esophageal Squamous Cell Carcinoma
Authors: Wu Hong , Leng Xuefeng , Liu Qianshi , Mao Tianqin , Jiang Tao , Liu Yiqiang , Li Feifei , Cao Chenhui , Fan Jun , Chen Liang , Chen Yaqi , Yao Quan , Lu Shun , Liang Renchuan , Hu Lanlin , Liu Mingxin , Wan Yejian , Li Zhaoshen , Peng Jun , Luo Qiyu , Zhou Hang , Yin Jun , Xu Ke , Lan Mei , Peng Xinhao , Lan Haitao , Li Gang , Han Yongtao , Zhang Xia , Xiao Zhi-Xiong Jim. , Lang Jinyi , Wang Guihua , Xu Chuan
Published: September 2024

Figure S1 shows detection of intra-tumoral microbiota in the ESCC tissues.
Supplementary Tables S2-13 from Endocrine therapy synergizes with SMAC mimetics to potentiate antigen presentation and tumor regression in hormone receptor-positive breast cancer
Authors: Hermida-Prado Francisco , Xie Yingtian , Sherman Shira , Nagy Zsuzsanna , Russo Douglas , Akhshi Tara , Chu Zhengtao , Feit Avery , Campisi Marco , Chen Minyue , Nardone Agostina , Guarducci Cristina , Lim Klothilda , Font-Tello Alba , Lee Irene , García-Pedrero Juana , Canadas Israel , Agudo Judith , Huang Ying , Sella Tal , Jin Qingchun , Tayob Nabihah , Mittendorf Elizabeth A. , Tolaney Sara M. , Qiu Xintao , Long Henry , Symmans William F. , Lin Jia-Ren , Santagata Sandro , Bedrosian Isabelle , Yardley Denise A. , Mayer Ingrid A. , Richardson Edward T. , Oliveira Giacomo , Wu Catherine J. , Schuster Eugene F. , Dowsett Mitch , Welm Alana L. , Barbie David , Metzger Otto , Jeselsohn Rinath
Published: September 2024

Supplementary Tables S2-13
Supplementary Fig. S7 from Endocrine therapy synergizes with SMAC mimetics to potentiate antigen presentation and tumor regression in hormone receptor-positive breast cancer
Authors: Hermida-Prado Francisco , Xie Yingtian , Sherman Shira , Nagy Zsuzsanna , Russo Douglas , Akhshi Tara , Chu Zhengtao , Feit Avery , Campisi Marco , Chen Minyue , Nardone Agostina , Guarducci Cristina , Lim Klothilda , Font-Tello Alba , Lee Irene , García-Pedrero Juana , Canadas Israel , Agudo Judith , Huang Ying , Sella Tal , Jin Qingchun , Tayob Nabihah , Mittendorf Elizabeth A. , Tolaney Sara M. , Qiu Xintao , Long Henry , Symmans William F. , Lin Jia-Ren , Santagata Sandro , Bedrosian Isabelle , Yardley Denise A. , Mayer Ingrid A. , Richardson Edward T. , Oliveira Giacomo , Wu Catherine J. , Schuster Eugene F. , Dowsett Mitch , Welm Alana L. , Barbie David , Metzger Otto , Jeselsohn Rinath
Published: September 2024

Supplementary Fig. S7. Impact of treatment with fulvestrant, birinapant, and their combination on a PDX model of HR+ breast cancer.
Supplementary Fig. S3 from Endocrine therapy synergizes with SMAC mimetics to potentiate antigen presentation and tumor regression in hormone receptor-positive breast cancer
Authors: Hermida-Prado Francisco , Xie Yingtian , Sherman Shira , Nagy Zsuzsanna , Russo Douglas , Akhshi Tara , Chu Zhengtao , Feit Avery , Campisi Marco , Chen Minyue , Nardone Agostina , Guarducci Cristina , Lim Klothilda , Font-Tello Alba , Lee Irene , García-Pedrero Juana , Canadas Israel , Agudo Judith , Huang Ying , Sella Tal , Jin Qingchun , Tayob Nabihah , Mittendorf Elizabeth A. , Tolaney Sara M. , Qiu Xintao , Long Henry , Symmans William F. , Lin Jia-Ren , Santagata Sandro , Bedrosian Isabelle , Yardley Denise A. , Mayer Ingrid A. , Richardson Edward T. , Oliveira Giacomo , Wu Catherine J. , Schuster Eugene F. , Dowsett Mitch , Welm Alana L. , Barbie David , Metzger Otto , Jeselsohn Rinath
Published: September 2024

Supplementary Fig. S3. Summary of protein expression changes after 24 weeks of endocrine treatment (ET) and/or Palbociclib (palbo) treatment.
Table S6 from LncRNA AGPG confers endocrine resistance in breast cancer by promoting E2F1 activity
Authors: Yu Shiyi , Wang Ying , Gong Xue , Fan Zhehao , Wang Zheng , Liang Zhengyan , Wu Rui , Cao Binjie , Wang Ning , Bi Caili , Lv Dan , Sun Haibo
Published: September 2024

Table S6
Table S5 from LncRNA AGPG confers endocrine resistance in breast cancer by promoting E2F1 activity
Authors: Yu Shiyi , Wang Ying , Gong Xue , Fan Zhehao , Wang Zheng , Liang Zhengyan , Wu Rui , Cao Binjie , Wang Ning , Bi Caili , Lv Dan , Sun Haibo
Published: September 2024

Table S5
Table S3 from LncRNA AGPG confers endocrine resistance in breast cancer by promoting E2F1 activity
Authors: Yu Shiyi , Wang Ying , Gong Xue , Fan Zhehao , Wang Zheng , Liang Zhengyan , Wu Rui , Cao Binjie , Wang Ning , Bi Caili , Lv Dan , Sun Haibo
Published: September 2024

Table S3
Table S1 from LncRNA AGPG confers endocrine resistance in breast cancer by promoting E2F1 activity
Authors: Yu Shiyi , Wang Ying , Gong Xue , Fan Zhehao , Wang Zheng , Liang Zhengyan , Wu Rui , Cao Binjie , Wang Ning , Bi Caili , Lv Dan , Sun Haibo
Published: September 2024

Table S1
Supplementary information from LncRNA AGPG confers endocrine resistance in breast cancer by promoting E2F1 activity
Authors: Yu Shiyi , Wang Ying , Gong Xue , Fan Zhehao , Wang Zheng , Liang Zhengyan , Wu Rui , Cao Binjie , Wang Ning , Bi Caili , Lv Dan , Sun Haibo
Published: September 2024

Figure legends for supplementary figures
Figure S3 from LncRNA AGPG confers endocrine resistance in breast cancer by promoting E2F1 activity
Authors: Yu Shiyi , Wang Ying , Gong Xue , Fan Zhehao , Wang Zheng , Liang Zhengyan , Wu Rui , Cao Binjie , Wang Ning , Bi Caili , Lv Dan , Sun Haibo
Published: September 2024

Figure S3
Figure S2 from LncRNA AGPG confers endocrine resistance in breast cancer by promoting E2F1 activity
Authors: Yu Shiyi , Wang Ying , Gong Xue , Fan Zhehao , Wang Zheng , Liang Zhengyan , Wu Rui , Cao Binjie , Wang Ning , Bi Caili , Lv Dan , Sun Haibo
Published: September 2024

Figure S2
Supplementary Table S1 from Histone methyltransferase NSD2 activates PKCα to drive metabolic reprogramming and lenalidomide resistance in multiple myeloma
Authors: Chong Phyllis S.Y. , Chooi Jing-Yuan , Lim Julia S.L. , Leow Aaron C.Y. , Toh Sabrina Hui Min. , Azaman Irfan , Koh Mun Yee , Teoh Phaik Ju , Tan Tuan Zea , Chung Tae-Hoon , Chng Wee Joo
Published: September 2024

Supplementary Table S1
Supplementary Figure S5 from Radiation therapy-induced neurocognitive impairment is driven by heightened apoptotic priming in early life and prevented by blocking BAX
Authors: Singh Rumani , Yu Stacey , Osman Marwa , Inde Zintis , Fraser Cameron , Cleveland Abigail H. , Almanzar Nicole , Lim Chuan Bian , Joshi Gaurav N. , Spetz Johan , Qin Xingping , Toprani Sneh M. , Nagel Zachary , Hocking Matthew C. , Cormack Robert A. , Yock Torunn I. , Miller Jeffrey W. , Yuan Zhi-Min , Gershon Timothy , Sarosiek Kristopher A.
Published: September 2024

Supplementary Figure S5
Supplementary Table S5 from Single-cell characterization of pulmonary nodules implicates suppression of immunosurveillance across early stages of lung adenocarcinoma
Authors: Yanagawa Jane , Tran Linh M. , Salehi-Rad Ramin , Lim Raymond J. , Dumitras Camelia , Fung Eileen , Wallace William D. , Prosper Ashley E. , Fishbein Gregory , Shea Conor , Hong Rui , Kahangi Bitta , Deng John J. , Gower Adam C. , Liu Bin , Campbell Joshua D. , Mazzilli Sarah A. , Beane Jennifer E. , Kadara Humam , Lenburg Marc E. , Spira Avrum E. , Aberle Denise R. , Krysan Kostyantyn , Dubinett Steven M.
Published: September 2024

DEGs between subsolid and nLung AT2 cells
Supplementary Table S3 from Single-cell characterization of pulmonary nodules implicates suppression of immunosurveillance across early stages of lung adenocarcinoma
Authors: Yanagawa Jane , Tran Linh M. , Salehi-Rad Ramin , Lim Raymond J. , Dumitras Camelia , Fung Eileen , Wallace William D. , Prosper Ashley E. , Fishbein Gregory , Shea Conor , Hong Rui , Kahangi Bitta , Deng John J. , Gower Adam C. , Liu Bin , Campbell Joshua D. , Mazzilli Sarah A. , Beane Jennifer E. , Kadara Humam , Lenburg Marc E. , Spira Avrum E. , Aberle Denise R. , Krysan Kostyantyn , Dubinett Steven M.
Published: September 2024

Summary of immune and non-immune cell clusters based on quality control metrics
Supplementary Fig. 4 from Spatial profiling of circular RNAs in cancer reveals high expression in muscle and stromal cells
Authors: García-Rodríguez Juan L. , Korsgaard Ulrik , Ahmadov Ulvi , Jarlstad Olesen Morten T. , Dietrich Kim-Gwendolyn , Hansen Emma B. , Vissing Stine M. , Ulhøi Benedicte P. , Dyrskjøt Lars , Sørensen Karina D. , Kjems Jørgen , Hager Henrik , Kristensen Lasse S.
Published: September 2024

circRNAs expression patterns from tissue sub-compartments compared to colon cancer cell lines.
Nanostring normalized counts for circAbParts, circABR, circAKAP12, circCCDC66, circRBM23, circSLC8A1, circSPECC1,
circTNFRSF21, circZNF609, circCAMSAP1 and circXPO1 in each of the sub-compartments for each patient and compared to
4 different colon cancer cell lines.
Supplementary Figures from Bi-allelic Dicer1 mutations in the gynecologic tract of mice drive lineage-specific development of DICER1 syndrome-associated cancer
Authors: Wang Yemin , Chen Shary Yuting , Ta Monica , Senz Janine , Tao Lan Valerie. , Thornton Shelby , Tamvada Nirupama , Yang Winnie , Moscovitz Yana , Li Eunice , Guo Jingjie , Shen Cindy , Douglas J. Maxwell , El-Naggar Amal M. , Kommoss Felix K. F. , Underhill T. Michael , Singh Naveena , Gilks C. Blake , Morin Gregg B. , Huntsman David G.
Published: September 2024

Supplementary Fig. S1-S11
Figure S5 from Targeting the immunoglobulin IGSF9 enhances anti-tumor T cell activity and sensitivity to anti-PD-1 immunotherapy
Authors: Liu Yifan , Wang Hongying , Zhao Xinyu , Zhang Jiashen , Zhao Zhiling , Lian Xia , Zhang Juan , Kong Feng , Hu Tao , Wang Ting , Li Xiaohua , Wang Lei , Wang Dapeng , Li Chunling , Luan Huiwen , Liu Xiaoli , Wang Chunyan , Jiang Yun , Li Xiaomin , Li Fangmin , Ji Shuhao , Wang Yaopeng , Li Zunling
Published: September 2024

IGSF9 itself did not affect tumor cell proliferation.
Figure S1 from Targeting the immunoglobulin IGSF9 enhances anti-tumor T cell activity and sensitivity to anti-PD-1 immunotherapy
Authors: Liu Yifan , Wang Hongying , Zhao Xinyu , Zhang Jiashen , Zhao Zhiling , Lian Xia , Zhang Juan , Kong Feng , Hu Tao , Wang Ting , Li Xiaohua , Wang Lei , Wang Dapeng , Li Chunling , Luan Huiwen , Liu Xiaoli , Wang Chunyan , Jiang Yun , Li Xiaomin , Li Fangmin , Ji Shuhao , Wang Yaopeng , Li Zunling
Published: September 2024

IGSF9 expression was detected in tumor tissue arrays by immunohistochemistry.
Supplementary Tables from The IGF2BP3-COPS7B axis facilitates mRNA translation to drive colorectal cancer progression
Authors: Tang Jing , Wang Shuoshuo , Weng Mingjiao , Guo Qingyu , Ren Lili , He Yan , Cui Zihan , Cong Mingqi , Qin Minglu , Yu Jia , Su Rui , Li Xiaobo
Published: September 2024

Supplementary Tables
Supplementary Table 1 - Gene Expression from Parkin deficiency suppresses antigen presentation to promote tumor immune evasion and immunotherapy resistance
Authors: Perales-Linares Renzo , Leli Nektaria Maria , Mohei Hesham , Beghi Silvia , Rivera Osvaldo D. , Kostopoulos Nektarios , Giglio Andrea , George Subin S. , Uribe-Herranz Mireia , Costabile Francesca , Pierini Stefano , Pustylnikov Sergei , Skoufos Giorgos , Barash Yoseph , Hatzigeorgiou Artemis G. , Koumenis Constantinos , Maity Amit , Lotze Michael T. , Facciabene Andrea
Published: September 2024

Gene Expression-RNAseq. Summary gene expression data of the individual tumors included in Fig. 5a-c.
Tables S10-S12 from Integrative genomic analyses identify lncRNA regulatory networks across pediatric leukemias and solid tumors
Authors: Modi Apexa , Lopez Gonzalo , Conkrite Karina L. , Su Chun , Leung Tsz Ching , Ramanan Sathvik , Manduchi Elisabetta , Johnson Matthew E. , Cheung Daphne , Gadd Samantha , Zhang Jinghui , Smith Malcolm A. , Guidry Auvil Jaime M. , Meshinchi Soheil , Perlman Elizabeth J. , Hunger Stephen P. , Maris John M. , Wells Andrew D. , Grant Struan F.A. , Diskin Sharon J.
Published: September 2024

Table S10: Statistics for input and output variables of lncMod analysis (xls file), Table S11: Significantly dysregulated lncMod triplets, Table S12: lncRNA TF associations ranked by # target genes
Supplementary Information from Integrative genomic analyses identify lncRNA regulatory networks across pediatric leukemias and solid tumors
Authors: Modi Apexa , Lopez Gonzalo , Conkrite Karina L. , Su Chun , Leung Tsz Ching , Ramanan Sathvik , Manduchi Elisabetta , Johnson Matthew E. , Cheung Daphne , Gadd Samantha , Zhang Jinghui , Smith Malcolm A. , Guidry Auvil Jaime M. , Meshinchi Soheil , Perlman Elizabeth J. , Hunger Stephen P. , Maris John M. , Wells Andrew D. , Grant Struan F.A. , Diskin Sharon J.
Published: September 2024

Supplementary Methods, Index for Tables S1-S17, Index for Figures S1-S8
Figure S7 from Integrative genomic analyses identify lncRNA regulatory networks across pediatric leukemias and solid tumors
Authors: Modi Apexa , Lopez Gonzalo , Conkrite Karina L. , Su Chun , Leung Tsz Ching , Ramanan Sathvik , Manduchi Elisabetta , Johnson Matthew E. , Cheung Daphne , Gadd Samantha , Zhang Jinghui , Smith Malcolm A. , Guidry Auvil Jaime M. , Meshinchi Soheil , Perlman Elizabeth J. , Hunger Stephen P. , Maris John M. , Wells Andrew D. , Grant Struan F.A. , Diskin Sharon J.
Published: September 2024

Figure S7: Validation of TBX2-AS1 expression in NBL cell lines and impact on NBL cell growth
Figure S4 from Integrative genomic analyses identify lncRNA regulatory networks across pediatric leukemias and solid tumors
Authors: Modi Apexa , Lopez Gonzalo , Conkrite Karina L. , Su Chun , Leung Tsz Ching , Ramanan Sathvik , Manduchi Elisabetta , Johnson Matthew E. , Cheung Daphne , Gadd Samantha , Zhang Jinghui , Smith Malcolm A. , Guidry Auvil Jaime M. , Meshinchi Soheil , Perlman Elizabeth J. , Hunger Stephen P. , Maris John M. , Wells Andrew D. , Grant Struan F.A. , Diskin Sharon J.
Published: September 2024

Figure S4: Structural variants impact lncRNAs in pediatric cancers
Supplementary Information from Prostate Cancer Risk Stratification via Nondestructive 3D Pathology with Deep Learning–Assisted Gland Analysis
Authors: Xie Weisi , Reder Nicholas P. , Koyuncu Can , Leo Patrick , Hawley Sarah , Huang Hongyi , Mao Chenyi , Postupna Nadia , Kang Soyoung , Serafin Robert , Gao Gan , Han Qinghua , Bishop Kevin W. , Barner Lindsey A. , Fu Pingfu , Wright Jonathan L. , Keene C. Dirk , Vaughan Joshua C. , Janowczyk Andrew , Glaser Adam K. , Madabhushi Anant , True Lawrence D. , Liu Jonathan T.C.
Published: September 2024

Supplementary methods, notes, figures, tables, video captions, and references
Data from circFNDC3B accelerates vasculature formation and metastasis in oral squamous cell carcinoma
Authors: Li Xiang , Wang Chenxing , Zhang Hang , Li Yangjie , Hou Deqiang , Liu Dingshan , Xu Rongyao , Cheng Jie , Liu Lai-Kui , Fu Yu , Ye Jinhai , Jiang Hongbing
Published: September 2024

Abstract
Emerging evidence has demonstrated that circular RNAs (circRNAs) are involved in cancer metastasis. Further elucidation of the role of circRNAs in oral squamous cell carcinoma (OSCC) could provide insights into mechanisms driving metastasis and potential therapeutic targets. Here, we identify a circRNA, circFNDC3B, that is significantly upregulated in OSCC and is positively associated with lymph node (LN) metastasis. In vitro and in vivo functional assays showed that circFNDC3B accelerated the migration and invasion of OSCC cells and the tube-forming capacity of human umbilical vein endothelial cells (HUVEC) and human lymphatic endothelial cells (HLEC). Mechanistically, circFNDC3B regulated ubiquitylation of the RNA-binding protein FUS and the deubiquitylation of HIF1A through the E3 ligase MDM2 to promote VEGFA transcription, thereby enhancing angiogenesis. Meanwhile, circFNDC3B sequestered miR-181c-5p to upregulate SERPINE1 and PROX1, which drove epithelial-mesenchymal transition (EMT) or partial-EMT (p-EMT) in OSCC cells and promoted lymphangiogenesis to accelerate lymph node metastasis. Overall, these findings uncovered the mechanistic role of circFNDC3B in orchestrating cancer cell metastatic properties and vasculature formation, suggesting circFNDC3B could be a potential target to reduce OSCC metastasis.
Data from Enhancer co-amplification and hijacking promote oncogene expression in liposarcoma
Authors: Liu Tingting , Wang Juan , Yang Hongbo , Jin Qiushi , Wang Xiaotao , Fu Yihao , Luan Yu , Wang Qixuan , Youngblood Mark W. , Lu Xinyan , Casadei Lucia , Pollock Raphael , Yue Feng
Published: September 2024

Abstract
Liposarcoma (LPS) is the most common soft-tissue sarcoma in adults with two major subtypes, well differentiated and dedifferentiated. Both subtypes are characterized with the pathognomonic giant ring or marker chromosomes that harbor high copy-numbers of known oncogenes. Here, we reported a comprehensive molecular characterization of both tumor and normal tissues from the same LPS patients, including whole genome sequencing (WGS), transcriptome, enhancer landscape, and genome-wide 3D genome structure by Hi-C. Tumor-specific transcripts and regulatory elements were identified, and enhancer co-amplification and hijacking events were discovered as novel mechanisms upregulating oncogenes such as MDM2, CDK4 and HMGA2. Combining Hi-C, optical mapping, nanopore long reads and WGS data partially resolved complex structural variations and reconstructed the local genome and the giant chromosome. Overall, this study provides a comprehensive resource for LPS research and offers insights into how altered enhancers and the 3D genome contribute to gene dysregulation in cancer.
Data from Cancer-associated fibroblast-derived miR-146a-5p generates a niche that promotes bladder cancer stemness and chemoresistance
Authors: Zhuang Junlong , Shen Lan , Li Meiqian , Sun Jingya , Hao Jiange , Li Jiaxuan , Zhu Zhen , Ge Shuning , Zhang Dianzheng , Guo Hongqian , Huang Ruimin , Yan Jun
Published: September 2024

Abstract
Cancer stem-like cells (CSCs) play pivotal roles in both chemoresistance and recurrence of many cancer types, including urothelial bladder cancer (UBC). In addition to intrinsic signaling pathways, extracellular cues from the tumor microenvironment (TME) are indispensable for the maintenance of CSCs. To better understand the mechanisms involved in TME-mediated generation and support of UBC CSCs, we focused on the role of cancer-associated fibroblasts (CAFs) in this study. Overexpression of miR-146a-5p in CAFs promoted CAF-to-UBC cell interactions, cancer stemness, and chemoresistance to treatment with gemcitabine and cisplatin. Mechanistically, miR-146-5p upregulated SVEP1 in CAFs by enhancing the recruitment of transcriptional factor YY1. Meanwhile, by targeting the 3’UTR of mRNAs of ARID1A and PRKAA2 (also known as AMPKα2) in UBC cells, CAF-secreted miR-146a-5p promoted cancer stemness and chemoresistance. Downregulation of ARID1A resulted in the inhibition of SOCS1 and subsequent STAT3 activation, and downregulated PRKAA2 led to the activation of mTOR signaling. Elevated levels of exosomal miR-146a-5p in the serum of UBC patients were correlated with both tumor stage and relapse risk. These findings altogether indicate that CAF-derived miR-146a-5p can promote stemness and enhance chemoresistance in UBC. Exosomal miR-146a-5p may be a biomarker of UBC recurrence and a potential therapeutic target.
Data from BCA101 is a Tumor-Targeted Bifunctional Fusion Antibody that Simultaneously Inhibits EGFR and TGF-β Signalling to Durably Suppress Tumor Growth
Authors: Boreddy Srinivas Reddy , Nair Reshmi , Pandey Prashant Kumar. , Kuriakose Anshu , Marigowda Shivakumar Bhadravathi. , Dey Chaitali , Banerjee Arindam , Kulkarni Hanumant , Sagar Milind , Krishn Shiv Ram , Rao Shruthi , A R Madhukara , Tiwari Vinita , Alke Bhavna , MV Prashantha Kumara , Shri Meena , Dhamne Chaitrali , Patel Sonal , Sharma Pinky , Periyasamy Sankar , Bhatnagar Jaya , Kuriakose Moni Abraham. , Reddy Ram Bhupal , Suresh Amritha , Sreenivas Suma , Govindappa Nagaraja , Moole Praveen Reddy. , Bughani Usha , Tan Seng-Lai , Nair Pradip
Published: September 2024

Abstract
The EGFR and TGF-β signalling pathways are important mediators of tumorigenesis, and crosstalk between them contributes to cancer progression and drug resistance. Therapies capable of simultaneously targeting EGFR and TGF-β could help improve patient outcomes across various cancer types. Here, we developed BCA101, an anti-EGFR IgG1 monoclonal antibody linked to an extracellular domain of human TGF-βRII. The TGF-β “trap” fused to the light chain in BCA101 did not sterically interfere with its ability to bind EGFR, inhibit cell proliferation, or mediate antibody-dependent cellular cytotoxicity. Functional neutralization of TGF-β by BCA101 was demonstrated by several in vitro assays. BCA101 increased production of proinflammatory cytokines and key markers associated with T and NK cell activation, while suppressing VEGF secretion. Additionally, BCA101 inhibited differentiation of naïve CD4+ T cells to inducible T-regulatory (iTreg) cells more strongly than the anti-EGFR antibody cetuximab. BCA101 localized to tumor tissues in xenograft mouse models with comparable kinetics to cetuximab, both having better tumor tissue retention over TGF-β “trap”. TGF-β in tumors was neutralized by approximately 90% in animals dosed with 10 mg/kg of BCA101 compared to 54% in animals dosed with equimolar TGF-βRII-Fc. In patient-derived xenograft mouse models of head and neck squamous cell carcinoma, BCA101 showed durable response post dose cessation. The combination of BCA101 and anti-PD1 antibody improved tumor inhibition in both B16-hEGFR expressing syngeneic mouse models and in humanized HuNOG-EXL mice bearing human PC-3 xenografts. Together, these results support the clinical development of BCA101 as a monotherapy and in combination with immune checkpoint therapy.
Data from ZDHHC2-mediated AGK palmitoylation activates AKT/mTOR signaling to reduce sunitinib sensitivity in renal cell carcinoma
Authors: Sun Yan , Zhu Liang , Liu Pian , Zhang Huan , Guo Feng , Jin Xin
Published: September 2024

Abstract
Tyrosine kinase inhibitors (TKIs) that can suppress the VEGF signaling pathway and angiogenesis have been developed to impede the progression of malignant tumors and have been approved as first-line targeted agents for clear cell renal cell carcinoma (ccRCC). Dysregulation of lipid metabolism is a major driver of TKI resistance in renal cancer. In this study, we showed that the palmitoyl acyltransferase ZDHHC2 is abnormally upregulated in tissues and cell lines resistant to TKIs, such as sunitinib. Upregulation of ZDHHC2 contributed to sunitinib resistance in cells and mice, and ZDHHC2 regulated angiogenesis and cell proliferation in ccRCC. Mechanistically, ZDHHC2 mediated AGK S-palmitoylation to promote translocation of AGK into the plasma membrane and activation of the PI3K-AKT-mTOR signaling pathway in ccRCC, which modulated sunitinib sensitivity. In conclusion, these results identify a ZDHHC2-AGK signaling axis and suggest that ZDHHC2 is a targetable candidate for improving the anti-tumor efficacy of sunitinib in ccRCC.
Data from PTEN loss confers resistance to anti-PD-1 therapy in non-small cell lung cancer by increasing tumor infiltration of regulatory T cells
Authors: Exposito Francisco , Redrado Miriam , Houry Maeva , Hastings Katherine , Molero-Abraham Magdalena , Lozano Teresa , Solórzano José Luis. , Sanz-Ortega Julian , Adradas Vera , Amat Ramon , Redin Esther , Leon Sergio , Legarra Naroa , Garcia Javier , Serrano Diego , Valencia Karmele , Robles-Oteiza Camila , Foggetti Giorgia , Otegui Nerea , Felip Enriqueta , Lasarte Juan J. , Paz-Ares Luis , Zugazagoitia Jon , Politi Katerina , Montuenga Luis , Calvo Alfonso
Published: September 2024

Abstract
Immunotherapy resistance in non-small cell lung cancer (NSCLC) may be mediated by an immunosuppressive microenvironment, which can be shaped by the mutational landscape of the tumor. Here, we observed genetic alterations in the PTEN/PI3K/AKT/mTOR pathway and/or loss of PTEN expression in >25% NSCLC patients, with higher frequency in lung squamous carcinomas (LUSCs). Patients with PTEN-low tumors had higher levels of PD-L1 and PD-L2 and showed worse progression-free survival when treated with immunotherapy. Development of a Pten-null LUSC mouse model revealed that tumors with PTEN loss were refractory to anti-PD-1, highly metastatic and fibrotic, and secreted TGF-β/CXCL10 to promote conversion of CD4+ lymphocytes into regulatory T cells (Tregs). Human and mouse PTEN-low tumors were enriched in Tregs and expressed higher levels of immunosuppressive genes. Importantly, treatment of mice bearing Pten-null tumors with TLR agonists and anti-TGF-β antibody aimed to alter this immunosuppressive microenvironment led to tumor rejection and immunological memory in 100% of mice. These results demonstrate that lack of PTEN causes immunotherapy resistance in LUSC by establishing an immunosuppressive tumor microenvironment that can be reversed therapeutically.
Data from PP2Ac Deficiency Enhances Tumor Immunogenicity by Activating STING-Type I Interferon Signaling in Glioblastoma
Authors: Mondal Isha , Das Oishika , Sun Raymond , Gao Jian , Yu Bohyeon , Diaz Aaron , Behnan Jinan , Dubey Abhishek , Meng Zhipeng , Eskandar Emad , Xu Beisi , Lu Rongze Olivia. , Ho Winson S.
Published: September 2024

Abstract
Glioblastoma (GBM) is an immunologically “cold” tumor that does not respond to current immunotherapy. Here, we demonstrate a fundamental role for the α-isoform of the catalytic subunit of protein phosphatase-2A (PP2Ac) in regulating glioma immunogenicity. Genetic ablation of PP2Ac in glioma cells enhanced double stranded DNA (dsDNA) production and cGAS-type I interferon (IFN) signaling, MHC-I expression, and tumor mutational burden. In co-culture experiments, PP2Ac deficiency in glioma cells promoted dendritic cell (DC) cross presentation and clonal expansion of CD8+ T cells. In vivo, PP2Ac depletion sensitized tumors to immune checkpoint blockade and radiotherapy treatment. Single cell analysis demonstrated that PP2Ac deficiency increased CD8+ T cell, NK cell, and DC accumulation and reduced immunosuppressive tumor associated macrophages. Furthermore, loss of PP2Ac increased IFN signaling in myeloid and tumor cells and reduced expression of a tumor gene signature associated with worse patient survival in TCGA. Collectively, this study establishes a novel role for PP2Ac in inhibiting dsDNA-cGAS-STING signaling to suppress anti-tumor immunity in glioma.
Data from Supraphysiological Androgens Promote the Tumor Suppressive Activity of the Androgen Receptor Through cMYC Repression and Recruitment of the DREAM Complex
Authors: Nyquist Michael D. , Coleman Ilsa M. , Lucas Jared M. , Li Dapei , Hanratty Brian , Meade Hannah , Mostaghel Elahe A. , Plymate Stephen R. , Corey Eva , Haffner Michael C. , Nelson Peter S.
Published: September 2024

Abstract
The androgen receptor (AR) pathway regulates key cell survival programs in prostate epithelium. The AR represents a near-universal driver and therapeutic vulnerability in metastatic prostate cancer, and targeting AR has a remarkable therapeutic index. Though most approaches directed toward AR focus on inhibiting AR signaling, laboratory and now clinical data have shown that high dose, supraphysiological androgen treatment (SPA) results in growth repression and improved outcomes in subsets of prostate cancer patients. A better understanding of the mechanisms contributing to SPA response and resistance could help guide patient selection and combination therapies to improve efficacy. To characterize SPA signaling, we integrated metrics of gene expression changes induced by SPA together with cistrome data and protein-interactomes. These analyses indicated that the Dimerization partner, RB-like, E2F and Multi-vulval class B (DREAM) complex mediates growth repression and downregulation of E2F targets in response to SPA. Notably, prostate cancers with complete genomic loss of RB1 responded to SPA treatment whereas loss of DREAM complex components such as RBL1/2 promoted resistance. Overexpression of MYC resulted in complete resistance to SPA and attenuated the SPA/AR-mediated repression of E2F target genes. These findings support a model of SPA-mediated growth repression that relies on the negative regulation of MYC by AR leading to repression of E2F1 signaling via the DREAM complex. The integrity of MYC signaling and DREAM complex assembly may consequently serve as determinants of SPA responses and as pathways mediating SPA resistance.
Data from Nanoparticle-based combination therapy enhances fulvestrant efficacy and overcomes tumor resistance in ER-positive breast cancer
Authors: Li Bozhao , Qi Feilong , Zhu Fei , Lu Zefang , Wang Meiqi , Chu Tianjiao , Wu Suying , Wei Jingyan , Song Zhenchuan , Sukumar Saraswati , Zhang Cheng , Xu Jiangfei , Li Suping , Nie Guangjun
Published: September 2024

Abstract
Nanoparticles (NPs) spanning diverse materials and properties have the potential to encapsulate and protect a wide range of therapeutic cargos to increase bioavailability, prevent undesired degradation, and mitigate toxicity. Fulvestrant, a selective estrogen receptor degrader (SERD), is commonly used for treating estrogen receptor (ER)-positive breast cancer patients, but its broad and continual application is limited by poor solubility, invasive muscle administration, and drug resistance. Here, we developed an active targeting motif-modified, intravenously injectable, hydrophilic NP that encapsulates fulvestrant to facilitate its delivery via the bloodstream to tumors, improving bioavailability and systemic tolerability. Additionally, the NP was co-loaded with abemaciclib, an inhibitor of cyclin-dependent kinases 4 and 6 (CDK4/6), to prevent the development of drug resistance associated with long-term fulvestrant treatment. Targeting peptide modifications on the NP surface assisted in the site-specific release of the drugs to ensure specific toxicity in the tumor tissues and spare normal tissue. The NP formulation (PPFA-cRGD) exhibited efficient tumor cell killing in both in vitro organoid models and in vivo orthotopic ER-positive breast cancer models without apparent adverse effects, as verified in mouse and Bama miniature pig models. This NP-based therapeutic provides an opportunity for continual and extensive clinical application of fulvestrant, thus indicating its promise as a treatment option for patients with ER-positive breast cancer.