bluuebunny/crossref_metadata_2025 huggingface dataset:
High Mechanical Conditioning by Tumor Extracellular Matrix Stiffness Is a Predictive Biomarker for Antifibrotic Therapy in HER2-Negative Breast Cancer
Authors: Quintela-Fandino Miguel , Bermejo Begoña , Zamora Esther , Moreno Fernando , García-Saenz José Ángel , Pernas Sonia , Martínez-Jañez Noelia , Jiménez Desirée , Adrover Encarna , de Andrés Raquel , Mourón Silvana , Bueno Maria J. , Manso Luis , Viñas Gemma , Alba Emilio , Llombart-Cussac Antonio , Cortés Javier , Tebar Cristina , Roe Denise J. , Grant Adam , Watson Adam , Colomer Ramon , Mouneimne Ghassan
Published: September 2024

Purpose:

Tumor progression has been linked to stiffening of the extracellular matrix caused by fibrosis. Cancer cells can be mechanically conditioned by stiff extracellular matrix, exhibiting a 1,004-gene signature [mechanical conditioning (MeCo) score]. Nintedanib has demonstrated antifibrotic activity in idiopathic pulmonary fibrosis. This study explores nintedanib’s antifibrotic effect on breast cancer outcomes.

Experimental Design:

We present long-term follow-up and analysis of a neoadjuvant randomized phase II trial in early HER2-negative breast cancer. Patients (N = 130) underwent a baseline biopsy and received 12 paclitaxel courses alone (control arm) or in combination with nintedanib (experimental arm). The tumor MeCo score was determined by RNA sequencing. The primary aim was to assess nintedanib’s impact on event-free survival based on MeCo scores.

Results:

Follow-up data were retrieved from 111 patients; 75 baseline and 24 post-run-in phase samples were sequenced. After median follow-up of 9.67 years, median event-free survival was not statistically different between arms (P = 0.37). However, in the control arm, high- versus low-MeCo patients had a statistically higher relapse risk: HR = 0.21; P = 0.0075. This risk was corrected by nintedanib in the experimental arm: HR = 0.37; P = 0.16. Nintedanib demonstrated pharmacodynamic engagement, reducing the MeCo score by 25% during the run-in phase (P < 0.01). Patients with low MeCo after run-in had the best long-term prognosis (HR = 0.087; P = 0.03).

Conclusions:

High MeCo is predictive of poor outcomes in HER2-negative early breast cancer, although this risk can be mitigated by nintedanib, which is able to specifically reduce MeCo.
Fig. S6 from Small molecule mediated stabilization of PP2A modulates the Homologous Recombination pathway and potentiates DNA damage-induced cell death.
Authors: Avelar Rita A. , Armstrong Amy J. , Carvette Gracie , Gupta Riya , Puleo Noah , Colina Jose A. , Joseph Peronne , Sobeck Alexander M. , O'Connor Caitlin M. , Raines Brynne , Gandhi Agharnan , Dziubinski Michele L. , Ma Daniel S. , Resnick Kimberly , Singh Sareena , Zanotti Kristine , Nagel Christa , Waggoner Steven , Thomas Dafydd G. , Skala Stephanie L. , Zhang Junran , Narla Goutham , DiFeo Analisa
Published: September 2024

Fig. S6
Supplementary Figure S1 from Pharmacokinetic/Pharmacodynamic Analysis of Savolitinib Plus Osimertinib in an EGFR-Mutation Positive, MET-Amplified Non-Small Cell Lung Cancer Model
Authors: Jones Rhys D.O. , Petersson Klas , Tabatabai Areya , Bao Larry , Tomkinson Helen , Schuller Alwin G.
Published: September 2024

Supplementary Figure S1
Supplementary Figure 5 from Novel arginase inhibitor, AZD0011, demonstrates immune cell stimulation and anti-tumor efficacy with diverse combination partners
Authors: Doshi Aatman S. , Cantin Susan , Hernandez Marylens , Srinivasan Srimathi , Tentarelli Sharon , Griffin Matthew , Wang Yanjun , Pop-Damkov Petar , Prickett Laura B. , Kankkonen Cecilia , Shen Minhui , San Martin Maryann , Wu Song , Castaldi M Paola , Ghadially Hormas , Varnes Jeffrey , Gales Sonya , Henry David , Hoover Clare , Mele Deanna A. , Simpson Iain , Gangl Eric T. , Mlynarski Scott N. , Finlay M. Raymond V. , Drew Lisa , Fawell Stephen E. , Shao Wenlin , Schuller Alwin G.
Published: September 2024

Supplementary Figure 5
Figure S5 from Loss of LGR5 through therapy-induced downregulation or gene ablation is associated with resistance and enhanced MET-STAT3 signaling in colorectal cancer cells
Authors: Posey Tressie A. , Jacob Joan , Parkhurst Ashlyn , Subramanian Shraddha , Francisco Liezl E. , Liang Zhengdong , Carmon Kendra S.
Published: September 2024

shows LGR5 expression and cytotoxicity of irinotecan, stattic, and anti-LGR5 ADCs in PDO model
Supplementary Figures 2 - 14 from Arginase 1/2 inhibitor OATD-02: from discovery to first-in-man setup in cancer immunotherapy
Authors: Borek Bartlomiej , Nowicka Julita , Gzik Anna , Dziegielewski Marek , Jedrzejczak Karol , Brzezinska Joanna , Grzybowski Marcin , Stanczak Paulina , Pomper Paulina , Zagozdzon Agnieszka , Rejczak Tomasz , Matyszewski Krzysztof , Golebiowski Adam , Olczak Jacek , Lisiecki Kamil , Tyszkiewicz Magdalena , Kania Magdalena , Piasecka Sylwia , Cabaj Anna , Dera Paulina , Mulewski Krzysztof , Chrzanowski Jacek , Kusmirek Damian , Sobolewska Elzbieta , Magdycz Marta , Mucha Lukasz , Masnyk Marek , Golab Jakub , Nowotny Marcin , Nowak Elzbieta , Napiorkowska-Gromadzka Agnieszka , Pikul Stanislaw , Jazwiec Radoslaw , Dzwonek Karolina , Dobrzanski Pawel , Meyring Michael , Skowronek Krzysztof , Iwanowski Piotr , Zaslona Zbigniew , Blaszczyk Roman
Published: September 2024

Supplementary Figures 2 - 14 (Synthesis schemes).
Supplementary Figures 1-5 from Identification of a First-in-Class Small Molecule Inhibitor of the eIF4E-RBM38 Complex that Enhances wild-type p53 Protein Translation for Tumor Growth Suppression
Authors: Lucchesi Christopher A. , Zhang Jin , Gao Mingchun , Shaw Jared , Chen Xinbin
Published: September 2024

Supplementary Figures 1-5
Figure S1 from Antitumor Immune Mechanisms of the Anti-Complement Factor H Antibody GT103
Authors: Bushey Ryan T. , Saxena Ruchi , Campa Michael J. , Gottlin Elizabeth B. , He You-Wen , Patz Edward F.
Published: September 2024

Immunofluorescence of 33 human lung tumor samples
on a microarray probed with GT103.
Supplementary Table 2 from BET inhibition sensitizes immunologically-cold Rb-deficient prostate cancer to immune checkpoint blockade
Authors: Olson Brian M. , Chaudagar Kiranj , Bao Riyue , Saha Sweta Sharma. , Hong Christina , Li Marguerite , Rameshbabu Srikrishnan , Chen Raymond , Thomas Alison , Patnaik Akash
Published: September 2024

List of oligonucleotides
Supplementary Figure 2 from BET inhibition sensitizes immunologically-cold Rb-deficient prostate cancer to immune checkpoint blockade
Authors: Olson Brian M. , Chaudagar Kiranj , Bao Riyue , Saha Sweta Sharma. , Hong Christina , Li Marguerite , Rameshbabu Srikrishnan , Chen Raymond , Thomas Alison , Patnaik Akash
Published: September 2024

Decreased Rb1 expression correlates with predicted decreased immune infiltration across multiple disease histologies.
Supplementary Figure 1 from BET inhibition sensitizes immunologically-cold Rb-deficient prostate cancer to immune checkpoint blockade
Authors: Olson Brian M. , Chaudagar Kiranj , Bao Riyue , Saha Sweta Sharma. , Hong Christina , Li Marguerite , Rameshbabu Srikrishnan , Chen Raymond , Thomas Alison , Patnaik Akash
Published: September 2024

Enrichment of Rb1 or CDKN2A loss in non-T cell-inflamed primary prostate cancer and across multiple primary tumor histologies
Supplementary Table1 from Activating an Adaptive Immune Response with a Telomerase-mediated Telomere Targeting Therapeutic in Hepatocellular Carcinoma
Authors: Mender Ilgen , Siteni Silvia , Barron Summer , Flusche Ann Marie , Kubota Naoto , Yu Chunhua , Cornelius Crystal , Tedone Enzo , Maziveyi Mazvita , Grichuk Anthony , Venkateswaran Niranjan , Conacci Sorrell Maralice , Hoshida Yujin , Kang Rui , Tang Daolin , Gryaznov Sergei , Shay Jerry W.
Published: September 2024

Supplementary Table1
Figure S1-S5 and Table S1 from Activating an Adaptive Immune Response with a Telomerase-mediated Telomere Targeting Therapeutic in Hepatocellular Carcinoma
Authors: Mender Ilgen , Siteni Silvia , Barron Summer , Flusche Ann Marie , Kubota Naoto , Yu Chunhua , Cornelius Crystal , Tedone Enzo , Maziveyi Mazvita , Grichuk Anthony , Venkateswaran Niranjan , Conacci Sorrell Maralice , Hoshida Yujin , Kang Rui , Tang Daolin , Gryaznov Sergei , Shay Jerry W.
Published: September 2024

Supplementary Figure Legends
Supplementary Data from Selective inhibition of ATM-dependent double-strand break repair and checkpoint control synergistically enhances the efficacy of ATR inhibitors
Authors: Turchick Audrey , Zimmermann Astrid , Chiu Li-Ya , Dahmen Heike , Elenbaas Brian , Zenke Frank T. , Blaukat Andree , Vassilev Lyubomir T.
Published: September 2024

Supplementary figures
Supplementary Table S2 from Efficacy and Imaging Enabled Pharmacodynamic Profiling of KRAS G12C Inhibitors in Xenograft and Genetically Engineered Mouse Models of Cancer
Authors: Lee Catherine , Jiang Ziyue Karen , Planken Simon , Manzuk Lisa K. , Ortiz Roberto , Hall Michael , Noorbehesht Kavon , Ram Sripad , Affolter Timothy , Troche Gabriel E. , Ihle Nathan T. , Johnson Theodore , Ahn Youngwook , Kraus Manfred , Giddabasappa Anand
Published: September 2024

Summarized G12C KP survival data from long-term treatment with Compound A
Supplementary Table S9 from Preclinical Evaluation of 9MW2821, a Site-Specific Monomethyl Auristatin E-based Antibody-Drug Conjugate for treatment of Nectin-4-expressing Cancers
Authors: Zhou Wei , Fang Peng , Yu Dongan , Ren Hongyuan , You Meng , Yin Long , Mei Fei , Zhu Huikai , Wang Zhenzhen , Xu Hui , Cao Yuxia , Sun Xiaowei , Xu Xiaohong , Bi Jianjun , Wang Jin , Ma Lanping , Wang Xin , Chen Lin , Zhang Yongliang , Cen Xiaowei , Zhu Xi , Lou Liguang , Liu Datao , Tan Xiaoding , Yang Jinliang , Meng Tao , Shen Jingkang
Published: September 2024

Antibody-dependent cell-mediated cytotoxicities of MW282 mAb, 9MW2821, and enfortumab vedotin
Supplementary Table S7 from Preclinical Evaluation of 9MW2821, a Site-Specific Monomethyl Auristatin E-based Antibody-Drug Conjugate for treatment of Nectin-4-expressing Cancers
Authors: Zhou Wei , Fang Peng , Yu Dongan , Ren Hongyuan , You Meng , Yin Long , Mei Fei , Zhu Huikai , Wang Zhenzhen , Xu Hui , Cao Yuxia , Sun Xiaowei , Xu Xiaohong , Bi Jianjun , Wang Jin , Ma Lanping , Wang Xin , Chen Lin , Zhang Yongliang , Cen Xiaowei , Zhu Xi , Lou Liguang , Liu Datao , Tan Xiaoding , Yang Jinliang , Meng Tao , Shen Jingkang
Published: September 2024

Binding affinity of MW282 mAb, 9MW2821, and enfortumab vedotin based on enzyme linked immunosorbent assay
Supplementary Fig.S9 from Preclinical Evaluation of 9MW2821, a Site-Specific Monomethyl Auristatin E-based Antibody-Drug Conjugate for treatment of Nectin-4-expressing Cancers
Authors: Zhou Wei , Fang Peng , Yu Dongan , Ren Hongyuan , You Meng , Yin Long , Mei Fei , Zhu Huikai , Wang Zhenzhen , Xu Hui , Cao Yuxia , Sun Xiaowei , Xu Xiaohong , Bi Jianjun , Wang Jin , Ma Lanping , Wang Xin , Chen Lin , Zhang Yongliang , Cen Xiaowei , Zhu Xi , Lou Liguang , Liu Datao , Tan Xiaoding , Yang Jinliang , Meng Tao , Shen Jingkang
Published: September 2024

Affinity of 9MW2821 and enfortumab vedotin (EV) to recombinant human Fcγ and FcRn receptors based on surface plasmon resonance measurements.
Figure S2 from Bromo- and Extra-Terminal Domain Inhibitors Induce Mitochondrial Stress in Pancreatic Ductal Adenocarcinoma
Authors: Rana Manjul , Kansal Rita G. , Bisunke Bijay , Fang Jie , Shibata David , Bajwa Amandeep , Yang Jun , Glazer Evan S.
Published: September 2024

Figure s2
Supplementary Figure 4 from AMT-562, a novel HER3-targeting antibody drug conjugate, demonstrates a potential to broaden therapeutic opportunities for HER3-expressing tumors
Authors: Weng Weining , Meng Tao , Pu Junyi , Ma Linjie , Shen Yi , Wang Zhaohui , Pan Rong , Wang Mingqiao , Chen Caiwei , Wang Lijun , Zhang Jianjian , Zhou Biao , Shao Siyuan , Qian Yu , Liu Shu-Hui , Hu Wenhao , Meng Xun
Published: September 2024

Clinical parameters comparison of AMT-562 and AMT-562-T1000 in cynomolgus monkey.
Supplementary File 1 from Vincristine Enhances the Efficacy of MEK Inhibitors in Preclinical Models of KRAS-mutant Colorectal Cancer
Authors: Ghosh Susmita , Fan Fan , Powell Reid T. , Roszik Jason , Park Yongsung , Stephan Clifford , Sebastian Manu , Tan Lin , Sorokin Alexey V. , Lorenzi Philip L. , Kopetz Scott , Ellis Lee M. , Bhattacharya Rajat
Published: September 2024

HTS data showing efficacy of different compounds as single agents.
Supplementary Fig.S8 from MTX-13, a novel PTK7-directed antibody-drug conjugate with widened therapeutic index shows sustained tumor regressions for a broader spectrum of PTK7-positive tumors
Authors: Kong Chao , Pu Junyi , Zhao Qianqian , Weng Weining , Ma Linjie , Qian Yu , Hu Wenhao , Meng Xun , Meng Tao
Published: September 2024

Supplementary Fig.S8 shows MTX-13 prevents metastasis in vivo in an orthotopic colon cancer xenograft model
Supplementary Fig.S2 from MTX-13, a novel PTK7-directed antibody-drug conjugate with widened therapeutic index shows sustained tumor regressions for a broader spectrum of PTK7-positive tumors
Authors: Kong Chao , Pu Junyi , Zhao Qianqian , Weng Weining , Ma Linjie , Qian Yu , Hu Wenhao , Meng Xun , Meng Tao
Published: September 2024

Supplementary Fig.S2 shows PTK7 expression in normal human tissues surveyed by mAb13
Figure S1 from T cell-intrinsic immunomodulatory effects of TAK-981 (subasumstat), a SUMO-activating enzyme inhibitor, in chronic lymphocytic leukemia
Authors: Lam Vi , Roleder Carly , Liu Tingting , Bruss Nur , Best Scott , Wang Xiaoguang , Phillips Tycel , Shouse Geoffrey , Berger Allison J. , Alinari Lapo , Wang Lili , Siddiqi Tanya , Pennock Nathan D. , Danilov Alexey V.
Published: September 2024

Figure S1 shows CD3+ T cells were pre-treated with TAK-981 at the indicated doses for 1 h, followed by TCR stimulation and quantification of western blots of figure 1
Supplementary File 1 from Safety and Tolerability of a Novel Anti-HER2 Antibody-Drug Conjugate (PF-06804103) in Patients With HER2-Expressing Solid Tumors: A Phase 1 Dose Escalation Study
Authors: Meric-Bernstam Funda , Calvo Emiliano , Lee Keun Seok , Moreno Victor , Park Yeon Hee , Rha Sun Young , Chalasani Pavani , Zhong Wei , Zhou Li , Pirie-Shepherd Steven , Leung Abraham CF. , Curigliano Giuseppe
Published: September 2024

Supplementary File 1 shows the Methods and Results for Part 1B
Supplementary Figure S3 from Safety and Tolerability of a Novel Anti-HER2 Antibody-Drug Conjugate (PF-06804103) in Patients With HER2-Expressing Solid Tumors: A Phase 1 Dose Escalation Study
Authors: Meric-Bernstam Funda , Calvo Emiliano , Lee Keun Seok , Moreno Victor , Park Yeon Hee , Rha Sun Young , Chalasani Pavani , Zhong Wei , Zhou Li , Pirie-Shepherd Steven , Leung Abraham CF. , Curigliano Giuseppe
Published: September 2024

Supplementary Figure S3 shows the time to and duration of response in patients with confirmed CR or PR (the mITT population)
Table S7 from Pan-cancer pharmacogenomic analysis of patient-derived tumor cells utilizing clinically relevant drug exposures
Authors: Chang Stephen H. , Ice Ryan J. , Chen Michelle , Sidorov Maxim , Woo Rinette W.L. , Rodriguez-Brotons Aida , Jian Damon , Kim Han Kyul , Kim Angela , Stone David E. , Nazarian Ari , Oh Alyssia , Tranah Gregory J. , Nosrati Mehdi , de Semir David , Dar Altaf A. , Desprez Pierre-Yves , Kashani-Sabet Mohammed , Soroceanu Liliana , McAllister Sean D.
Published: September 2024

Supplementary Table 7 gene_importance_t0.1_limit4_ew
Supplementary Figure Legends from Pan-cancer pharmacogenomic analysis of patient-derived tumor cells utilizing clinically relevant drug exposures
Authors: Chang Stephen H. , Ice Ryan J. , Chen Michelle , Sidorov Maxim , Woo Rinette W.L. , Rodriguez-Brotons Aida , Jian Damon , Kim Han Kyul , Kim Angela , Stone David E. , Nazarian Ari , Oh Alyssia , Tranah Gregory J. , Nosrati Mehdi , de Semir David , Dar Altaf A. , Desprez Pierre-Yves , Kashani-Sabet Mohammed , Soroceanu Liliana , McAllister Sean D.
Published: September 2024

Text of Supplementary Figure Legends
Supplementary Data Figure S3 from Pan-cancer pharmacogenomic analysis of patient-derived tumor cells utilizing clinically relevant drug exposures
Authors: Chang Stephen H. , Ice Ryan J. , Chen Michelle , Sidorov Maxim , Woo Rinette W.L. , Rodriguez-Brotons Aida , Jian Damon , Kim Han Kyul , Kim Angela , Stone David E. , Nazarian Ari , Oh Alyssia , Tranah Gregory J. , Nosrati Mehdi , de Semir David , Dar Altaf A. , Desprez Pierre-Yves , Kashani-Sabet Mohammed , Soroceanu Liliana , McAllister Sean D.
Published: September 2024

Figure S3
Figure S1, Figure S2, Figure S3, Figure S4, Figure S5, Figure S6, Table S1 from Upregulation of Somatostatin Receptor Type 2 Improves 177Lu-DOTATATE Therapy in Receptor-Deficient Pancreatic Neuroendocrine Tumor Model
Authors: Sharma Rupali , Earla Bhargav , Baidoo Kwamena E. , Zeiger Martha A. , Madigan James P. , Escorcia Freddy E. , Sadowski Samira M.
Published: September 2024

Supplementary Figures and Tables with Legend
Supplementary Data Legends from Co-targeting Phosphoinositide 3-Kinase and Focal Adhesion Kinase Pathways Inhibits Proliferation of NF2 Schwannoma Cells
Authors: Hardin Haley M. , Dinh Christine T. , Huegel Julianne , Petrilli Alejandra M. , Bracho Olena , Allaf Abdulrahman , Karajannis Matthias A. , Griswold Anthony J. , Ivan Michael E. , Morcos Jacques , Gultekin Sakir H. , Telischi Fred F. , Liu Xue Zhong , Fernandez-Valle Cristina
Published: September 2024

Table and Figure Legends for Supplementary Data
Supplementary Figure S4 from Interferon Gamma Induces Higher Neutrophil Extracellular Traps Leading to Tumor-Killing Activity in Microsatellite Stable Colorectal Cancer
Authors: Teng Hao-Wei , Wang Tean-Ya , Lin Chun-Chi , Tong Zhen-Jie , Cheng Hsiao-Wei , Wang Hsiang-Tsui
Published: September 2024

Supplementary Figure 4 shows the effects of IFNgamma on the formation of NETs in PMNs from HD and the impact on MSS CRC cell fates.
Supplementary Methods from Activation of Hepatocyte Growth Factor/MET Signaling as a Mechanism of Acquired Resistance to a Novel YAP1/TEAD Small Molecule Inhibitor
Authors: Moure Casey J. , Vara Brandon , Cheng Mangeng M. , Sondey Christopher , Muise Eric , Park Eunsil , Vela Ramirez Julia Eulalia , Su Dan , D’Souza Shanti , Yan Qingyun , Yeung Charles S. , Zhang Minjia , Mansueto My Sam , Linn Doug , Buchanan Mark , Foti Robert , DiMauro Erin , Long Brian , Simov Vladimir , Barry Evan R.
Published: September 2024

Supplementary/extended materials and methods
Figure S5 from Interdependence of SS18-SSX-driven YAP1 and β-catenin activation in synovial sarcoma
Authors: Isfort Ilka , Berthold Ruth , Heinst Lorena , Wardelmann Eva , Larsson Olle , Trautmann Marcel , Hartmann Wolfgang
Published: September 2024

Figure S5 shows that there is no
interdependency between YAP1/TAZ and β-catenin activation in control cell lines.
Figure S2 from Interdependence of SS18-SSX-driven YAP1 and β-catenin activation in synovial sarcoma
Authors: Isfort Ilka , Berthold Ruth , Heinst Lorena , Wardelmann Eva , Larsson Olle , Trautmann Marcel , Hartmann Wolfgang
Published: September 2024

Figure S2 shows that inhibition of YAP1, TAZ or β-catenin via siRNA-mediated knockdown or inhibitor treatment reduces each other's transcriptional activity.
Figure S4 from UBE2C-mediated autophagy inhibition via ubiquitination of SIRT1 contributes to endometrial cancer progression
Authors: Zhao Rong , Liu Yan , Wang Ziwei , Zhang Jun , Zhang Wei , Zhou Xing , Tsedendorj Sevjid , Enkhtur Amarsanaa , Feng Dilu , Wang Hongbo
Published: September 2024

Figure S4
Figure S3 from UBE2C-mediated autophagy inhibition via ubiquitination of SIRT1 contributes to endometrial cancer progression
Authors: Zhao Rong , Liu Yan , Wang Ziwei , Zhang Jun , Zhang Wei , Zhou Xing , Tsedendorj Sevjid , Enkhtur Amarsanaa , Feng Dilu , Wang Hongbo
Published: September 2024

Figure S3
Table S2 from USP10 regulates ZEB1 ubiquitination and protein stability to inhibit ZEB1-mediated colorectal cancer metastasis
Authors: Sun Lei , Yu Jia , Guinney Justin , Qin Bo , Sinicrope Frank A.
Published: September 2024

Human colon cancer cohorts with tumors subjected to comprehensive gene expression profiling for determination of consensus molecular subtypes (CMS)[33].
Supplementary Table 11 from Disruption of the MYC Super-Enhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia
Authors: Yashar William M. , Curtiss Brittany M. , Coleman Daniel J. , VanCampen Jake , Kong Garth , Macaraeg Jommel , Estabrook Joseph , Demir Emek , Long Nicola , Bottomly Daniel , McWeeney Shannon K. , Tyner Jeffrey W. , Druker Brian J. , Maxson Julia E. , Braun Theodore P.
Published: September 2024

Super-Enhancer-Type Analysis of STAT5 ChIP-Seq Peaks (24 Hours After Drug Treatment).
Supplementary Fig. 9 from Disruption of the MYC Super-Enhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia
Authors: Yashar William M. , Curtiss Brittany M. , Coleman Daniel J. , VanCampen Jake , Kong Garth , Macaraeg Jommel , Estabrook Joseph , Demir Emek , Long Nicola , Bottomly Daniel , McWeeney Shannon K. , Tyner Jeffrey W. , Druker Brian J. , Maxson Julia E. , Braun Theodore P.
Published: September 2024

SPI1 knockdown does not disrupt dual FLT3/LSD1 inhibition synergy.
Supplementary Fig. 8 from Disruption of the MYC Super-Enhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia
Authors: Yashar William M. , Curtiss Brittany M. , Coleman Daniel J. , VanCampen Jake , Kong Garth , Macaraeg Jommel , Estabrook Joseph , Demir Emek , Long Nicola , Bottomly Daniel , McWeeney Shannon K. , Tyner Jeffrey W. , Druker Brian J. , Maxson Julia E. , Braun Theodore P.
Published: September 2024

Combined FLT3/LSD1 inhibition does not substantially alter myeloid differentiation.
Supplementary Table 2 from EIF4A3 acts on the PI3K-AKT-ERK1/2-P70S6K pathway through FLOT1 to influence the development of lung adenocarcinoma
Authors: Yu Wenhao , Liang Jinghui , Fang Tao , Jiang Jin , Zhao Renchang , Li Rongyang , Han Jingyi , Tian Hui
Published: September 2024

Information of antibodies
Supplementary Methods from MACdb: A curated knowledgebase for metabolic associations across human cancers
Authors: Sun Yanling , Zheng Xinchang , Wang Guoliang , Wang Yibo , Chen Xiaoning , Sun Jiani , Xiong Zhuang , Zhang Sisi , Wang Tianyi , Fan Zhuojing , Bu Congfan , Bao Yiming , Zhao Wenming
Published: September 2024

Supplementary Methods
Supplementary Figure 3 from Truncation of GalNAc-type O-glycans suppresses CD44-mediated osteoclastogenesis and bone metastasis in breast cancer
Authors: Lin Neng-Yu , Lee Jian-Jr , Chen Syue-Ting , Lin Jung-An , Lin Chia-Hsuan , Lin Hsuan-Yu , Su Yong-Han , Chen Cheng-Chang , Lin Mei-Chun , Kuo Ching-Ying , Haung Min-Chuan
Published: September 2024

Effects of CD44 O-glycans on tumor sphere formation in breast cancer cells.
Supplementary Figure 1 from Truncation of GalNAc-type O-glycans suppresses CD44-mediated osteoclastogenesis and bone metastasis in breast cancer
Authors: Lin Neng-Yu , Lee Jian-Jr , Chen Syue-Ting , Lin Jung-An , Lin Chia-Hsuan , Lin Hsuan-Yu , Su Yong-Han , Chen Cheng-Chang , Lin Mei-Chun , Kuo Ching-Ying , Haung Min-Chuan
Published: September 2024

C1GALT1 knockdown in breast cancer cells did not cause significant changes in CD44 mRNA levels.
Supplementary Figure Legends 1-7 from Dynamic intestinal stem cell plasticity and lineage remodeling by a nutritional environment relevant to human risk for tumorigenesis
Authors: Choi Jiahn , Zhang Xusheng , Li Wenge , Houston Michele , Peregrina Karina , Dubin Robert , Ye Kenny , Augenlicht Leonard
Published: September 2024

S1. The western diet extensively reprograms Lgr5hi stem cells that expands with time and is reversible. This includes the TCA cycle and Oxphos pathways.
S2. The western diet elevates and suppresses multiple pathways by 3 months, most persisting to 12 months, and reversible by switching to control diet.
S3. The western diet suppresses expression of a large number of genes encoding subunits of each of the 5 complexes of mitochondrial electron transport.
S4. Mouse genotyping identified presence of the wild-type, or heterozygous or homozygous conditionally targeted Ppargc1a allele.
S5. Rapid dietary cross-over experiment of Fig 3.
S6. scRNAseq analysis of Bmi1+ derived cells.
S7. Inflammatory response to NWD1.
Supplementary Figure S4 from Overlaid transcriptome and proteome analyses identify mitotic kinesins as important targets of arylsulfonamide-mediated RBM39 degradation
Authors: Coomar Seemon , Mota Pedro , Penson Alexander , Schwaller Juerg , Abdel-Wahab Omar , Gillingham Dennis
Published: September 2024

Supplementary Figure S4
Supplementary Data from Overlaid transcriptome and proteome analyses identify mitotic kinesins as important targets of arylsulfonamide-mediated RBM39 degradation
Authors: Coomar Seemon , Mota Pedro , Penson Alexander , Schwaller Juerg , Abdel-Wahab Omar , Gillingham Dennis
Published: September 2024

TMT Proteomics Datasets
Supplementary Data Table 2 from Overlaid transcriptome and proteome analyses identify mitotic kinesins as important targets of arylsulfonamide-mediated RBM39 degradation
Authors: Coomar Seemon , Mota Pedro , Penson Alexander , Schwaller Juerg , Abdel-Wahab Omar , Gillingham Dennis
Published: September 2024

Supplementary Data Table 2
Figure S4 from A comparative study of neuroendocrine heterogeneity in small cell lung cancer and neuroblastoma
Authors: Cai Ling , DeBerardinis Ralph J. , Xie Yang , Minna John D. , Xiao Guanghua
Published: September 2024

SCLC vs. NBL concordance of NE score association with omics, drug sensitivity, and dependency data.
Figure S3 from A comparative study of neuroendocrine heterogeneity in small cell lung cancer and neuroblastoma
Authors: Cai Ling , DeBerardinis Ralph J. , Xie Yang , Minna John D. , Xiao Guanghua
Published: September 2024

Controlling for MYCN amplification status increases the statistical significance of NE score vs. MYCN expression association.
Supplementary Table 3 from Absence of either Ripk3 or Mlkl reduces incidence of hepatocellular carcinoma independent of liver fibrosis
Authors: Mohammed Sabira , Thadathil Nidheesh , Ohene-Marfo Phoebe , Tran Albert L. , Van Der Veldt Michael , Georgescu Constantin , Oh Sangphil , Nicklas Evan H. , Wang Dawei , Haritha Nair Hariprasad , Luo Wenyi , Janknecht Ralf , Miller Benjamin F. , Wren Jonathan D. , Freeman Willard M. , Deepa Sathyaseelan S.
Published: September 2024

List of primers used for quantitative real time PCR
Fig. S2 from Absence of either Ripk3 or Mlkl reduces incidence of hepatocellular carcinoma independent of liver fibrosis
Authors: Mohammed Sabira , Thadathil Nidheesh , Ohene-Marfo Phoebe , Tran Albert L. , Van Der Veldt Michael , Georgescu Constantin , Oh Sangphil , Nicklas Evan H. , Wang Dawei , Haritha Nair Hariprasad , Luo Wenyi , Janknecht Ralf , Miller Benjamin F. , Wren Jonathan D. , Freeman Willard M. , Deepa Sathyaseelan S.
Published: September 2024

Figure S2 shows body weight changes, liver weight changes, Transcript levels of Il1b and H&E staining for showing KC population
Figure S5 from Fibronectin contributes to a BRAF inhibitor-driven invasive phenotype in thyroid cancer through EGR1, which can be blocked by inhibition of ERK1/2.
Authors: Hicks Hannah M. , Pozdeyev Nikita , Sams Sharon B. , Pugazhenthi Umarani , Bales Elise S. , Hofmann Marie-Claude , McKenna Logan R. , Schweppe Rebecca E.
Published: September 2024

Figure S5. ERK Score correlates with Tumor Stage and ATA Risk Group in thyroid cancer.
Figure S3 from Fibronectin contributes to a BRAF inhibitor-driven invasive phenotype in thyroid cancer through EGR1, which can be blocked by inhibition of ERK1/2.
Authors: Hicks Hannah M. , Pozdeyev Nikita , Sams Sharon B. , Pugazhenthi Umarani , Bales Elise S. , Hofmann Marie-Claude , McKenna Logan R. , Schweppe Rebecca E.
Published: September 2024

Figure S3. Sensitivity to BRAF inhibition does not correlate with fibronectin, α5β1 integrin, c-MET, or FAK/Src levels. BRAF inhibition increases fibronectin expression and secretion, which is blocked by ERK1/2 inhibition.
Figure S2 from Fibronectin contributes to a BRAF inhibitor-driven invasive phenotype in thyroid cancer through EGR1, which can be blocked by inhibition of ERK1/2.
Authors: Hicks Hannah M. , Pozdeyev Nikita , Sams Sharon B. , Pugazhenthi Umarani , Bales Elise S. , Hofmann Marie-Claude , McKenna Logan R. , Schweppe Rebecca E.
Published: September 2024

Figure S2. BRAF inhibition increases fibronectin expression and secretion, which is blocked by ERK1/2 inhibition.
Figure S1 from Fibronectin contributes to a BRAF inhibitor-driven invasive phenotype in thyroid cancer through EGR1, which can be blocked by inhibition of ERK1/2.
Authors: Hicks Hannah M. , Pozdeyev Nikita , Sams Sharon B. , Pugazhenthi Umarani , Bales Elise S. , Hofmann Marie-Claude , McKenna Logan R. , Schweppe Rebecca E.
Published: September 2024

Figure S1. BRAF-V600E-mutated thyroid cancer cells lines exhibit varying levels of migration and baseline invasiveness.
SupplementaryTable S7 from Single-Cell Evolutionary Analysis Reveals Drivers of Plasticity and Mediators of Chemoresistance in Small Cell Lung Cancer
Authors: Wollenzien Hannah , Tecleab Yohannes Afeworki A. , Szczepaniak-Sloane Robert , Restaino Anthony , Kareta Michael S.
Published: September 2024

Normalized CTA expression from NCI-H209 cell, xenografts, and chemo-treated xenografts (related to Figure 5f)
Supplementary Figure S7 from Single-Cell Evolutionary Analysis Reveals Drivers of Plasticity and Mediators of Chemoresistance in Small Cell Lung Cancer
Authors: Wollenzien Hannah , Tecleab Yohannes Afeworki A. , Szczepaniak-Sloane Robert , Restaino Anthony , Kareta Michael S.
Published: September 2024

Determination of LBC counts by PCR error correction.
Supplementary Figure S11 from Single-Cell Evolutionary Analysis Reveals Drivers of Plasticity and Mediators of Chemoresistance in Small Cell Lung Cancer
Authors: Wollenzien Hannah , Tecleab Yohannes Afeworki A. , Szczepaniak-Sloane Robert , Restaino Anthony , Kareta Michael S.
Published: September 2024

Similarity analysis to determine subclonal relationships.
Supplementary Table S3 from Identification of a ΔNp63-Dependent Basal-Like A Subtype-Specific Transcribed Enhancer Program (B-STEP) in Aggressive Pancreatic Ductal Adenocarcinoma
Authors: Wang Xin , Kutschat Ana P. , Aggrey-Fynn Joana , Hamdan Feda H. , Graham Rondell P. , Wixom Alexander Q. , Souto Yara , Ladigan-Badura Swetlana , Yonkus Jennifer A. , Abdelrahman Amro M. , Alva-Ruiz Roberto , Gaedcke Jochen , Strobel Philipp , Kosinsky Robyn Laura , Wegwitz Florian , Hermann Patrick , Truty Mark J. , Siveke Jens T. , Hahn Stephan A. , Hessmann Elisabeth , Johnsen Steven A. , Najafova Zeynab
Published: September 2024

Supplementary Table S3 contains list of genes associated with Gö4Pdx4 super enhancers overlapping TP63.
Supplementary Figure S3 from Identification of a ΔNp63-Dependent Basal-Like A Subtype-Specific Transcribed Enhancer Program (B-STEP) in Aggressive Pancreatic Ductal Adenocarcinoma
Authors: Wang Xin , Kutschat Ana P. , Aggrey-Fynn Joana , Hamdan Feda H. , Graham Rondell P. , Wixom Alexander Q. , Souto Yara , Ladigan-Badura Swetlana , Yonkus Jennifer A. , Abdelrahman Amro M. , Alva-Ruiz Roberto , Gaedcke Jochen , Strobel Philipp , Kosinsky Robyn Laura , Wegwitz Florian , Hermann Patrick , Truty Mark J. , Siveke Jens T. , Hahn Stephan A. , Hessmann Elisabeth , Johnsen Steven A. , Najafova Zeynab
Published: September 2024

Verification of P63-dependence and B-STEP enhancer-gene regulations.
Supplementary Figure 5 from Targeting c-Jun is a potential therapy for luminal breast cancer bone metastasis
Authors: Han Yuxuan , Katayama Shota , Futakuchi Mitsuru , Nakamichi Kazuya , Wakabayashi Yutaro , Sakamoto Mai , Nakayama Jun , Semba Kentaro
Published: September 2024

Clinical prognosis of c-Jun-regulated gene signatures.
Supplementary Figure 6 from Oncostatin-M and OSM-Receptor feed-forward activation of MAPK induces separable stem-like and mesenchymal programs
Authors: Polak Kelsey L. , Tamagno Ilaria , Parameswaran Neetha , Smigiel Jacob , Chan E. Ricky , Yuan Xueer , Rios Brenda , Jackson Mark W.
Published: September 2024

S6. Generation and analysis of SMAD3 knock-out cells.
Supplementary Figure 5 from Oncostatin-M and OSM-Receptor feed-forward activation of MAPK induces separable stem-like and mesenchymal programs
Authors: Polak Kelsey L. , Tamagno Ilaria , Parameswaran Neetha , Smigiel Jacob , Chan E. Ricky , Yuan Xueer , Rios Brenda , Jackson Mark W.
Published: September 2024

S5. MEK inhibitors block OSM-driven conversion to a CD44HI/mesenchymal state.
Supplementary Movies Description from Targeting the ATF6-mediated ER stress response and autophagy blocks integrin-driven prostate cancer progression
Authors: Macke Amanda J. , Pachikov Artem N. , Divita Taylor E. , Morris Mary E. , LaGrange Chad A. , Holzapfel Melissa S. , Kubyshkin Anatoly V. , Zyablitskaya Evgeniya Y. , Makalish Tatiana P. , Eremenko Sergey N. , Qiu Haowen , Riethoven Jean-Jack M. , Hemstreet George P. , Petrosyan Armen
Published: September 2024

Supplemental Movie 1
PC-3 cell treated with water, stained for Golgi (GRASP65, green) and MGAT3 (red). Surfaces were reconstructed by Imaris.
Supplemental Movie 2
PC-3 cell treated with HCQ, stained for Golgi (GRASP65, green) and MGAT3 (red). Surfaces were reconstructed by Imaris.
Supplemental Movie 3
PC-3 cell treated with water, stained for Integrin αv (red), Gal-3 (green), EEA1 (magenta). Areas of 3-color colocalization are highlighted with white. Surfaces were reconstructed by Imaris.
Supplemental Movie 4
PC-3 cell treated with HCQ, stained for Integrin αv (red), Gal-3 (green), EEA1 (magenta). Areas of 3-color colocalization are highlighted with white. Surfaces were reconstructed by Imaris.
Supplementary Figure 5 from Continuous administration of anti-VEGFA antibody upregulates PAI-1 secretion from ovarian cancer cells via miR-143-3p downregulation
Authors: Yagi Taro , Sawada Kenjiro , Miyamoto Mayuko , Shimizu Aasa , Oui Yukako , Toda Aska , Nakamura Koji , Kinose Yasuto , Kodama Michiko , Hashimoto Kae , Kimura Tadashi
Published: September 2024

Supplementary Figure 5 shows thatVEGF induces in vitro tube formation in HUVECs at a concentration of ≥ 3 ng/ml, whereas treatment with 100 µg/ml anti-VEGFA antibody attenuates the effects of VEGF.
Supplementary Figure 4 from Continuous administration of anti-VEGFA antibody upregulates PAI-1 secretion from ovarian cancer cells via miR-143-3p downregulation
Authors: Yagi Taro , Sawada Kenjiro , Miyamoto Mayuko , Shimizu Aasa , Oui Yukako , Toda Aska , Nakamura Koji , Kinose Yasuto , Kodama Michiko , Hashimoto Kae , Kimura Tadashi
Published: September 2024

Supplementary Figure 4 shows that the knockdown of VEGFA significantly inhibited the expression level of miR-143-3p, followed by the upregulation of PAI secretion from OC cells.
Table S2 from HCK promotes high-grade serous ovarian cancer tumorigenesis through CD44 and NOTCH3 signaling
Authors: Khella Christen A. , Franciosa Lucyann , Rodriguez-Rodriguez Lorna , Rajkarnikar Resha , Mythreye Karthikeyan , Gatza Michael L.
Published: September 2024

CAOV3 RPPA data summary
Supplementary Table 1 from LncRNA-encoded Micropeptide ACLY‍-‍BP drives lipid deposition and cell proliferation in Clear Cell Renal Cell Carcinoma via maintenance of ACLY acetylation
Authors: Zhang Shenghua , Zhang Zheng , Liu Xiaolong , Deng Yibin , Zheng Jian , Deng Jieqiong , Wang Yirong , Guo Binbin , Li Fanrong , Chen Xiaoyue , Pan Yacheng , Wang Jieyu , Lu Jiachun , Wu Siqi , Guo Qiang , Zhou Yifeng
Published: September 2024

Primary clinical and histological characteristics of 67 study patients
Supplementary Figure 2 from LncRNA-encoded Micropeptide ACLY‍-‍BP drives lipid deposition and cell proliferation in Clear Cell Renal Cell Carcinoma via maintenance of ACLY acetylation
Authors: Zhang Shenghua , Zhang Zheng , Liu Xiaolong , Deng Yibin , Zheng Jian , Deng Jieqiong , Wang Yirong , Guo Binbin , Li Fanrong , Chen Xiaoyue , Pan Yacheng , Wang Jieyu , Lu Jiachun , Wu Siqi , Guo Qiang , Zhou Yifeng
Published: September 2024

Related to Figure 2
Supplementary Figure 4 from Hierarchical phosphorylation of HOXB13 by mTOR dictates its activity and oncogenic function in prostate cancer
Authors: Chen Yonghong , Dufour Catherine R. , Han Lingwei , Li Ting , Xia Hui , Giguere Vincent
Published: September 2024

Supplementary Figure 4. Androgen response dependency on HOXB13 phosphorylation.
Supplementary Figure 1 from Podoplanin drives amoeboid invasion in canine and human mucosal melanoma
Authors: Shinada Masahiro , Kato Daiki , Motegi Tomoki , Tsuboi Masaya , Ikeda Namiko , Aoki Susumu , Iguchi Takaaki , Li Toshio , Kodera Yuka , Ota Ryosuke , Hashimoto Yuko , Takahashi Yosuke , Chambers James , Uchida Kazuyuki , Kato Yukinari , Nishimura Ryohei , Nakagawa Takayuki
Published: September 2024

PDPN overexpression in the invasion fronts (IFs) is associated with poor prognosis of dogs with mucosal melanoma.
Supplementary Table 5 from Telomerase upregulation induces progression of mouse BrafV600E-driven thyroid cancers and triggers non-telomeric effects
Authors: Landa Inigo , Thornton Caitlin EM , Xu Bin , Haase Jacob , Krishnamoorthy Gnana P. , Hao Jingzhu , Knauf Jeffrey A. , Herbert Zachary T. , Martínez Paula , Blasco Maria A. , Ghossein Ronald , Fagin James A.
Published: September 2024

Full list of KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis “up terms” for the BrafV600E vs. BrafV600E+K5-Tert comparison.
Supplementary Table 2 from Telomerase upregulation induces progression of mouse BrafV600E-driven thyroid cancers and triggers non-telomeric effects
Authors: Landa Inigo , Thornton Caitlin EM , Xu Bin , Haase Jacob , Krishnamoorthy Gnana P. , Hao Jingzhu , Knauf Jeffrey A. , Herbert Zachary T. , Martínez Paula , Blasco Maria A. , Ghossein Ronald , Fagin James A.
Published: September 2024

CRISPRESSO sequencing results
Supplementary Figure 4 from Telomerase upregulation induces progression of mouse BrafV600E-driven thyroid cancers and triggers non-telomeric effects
Authors: Landa Inigo , Thornton Caitlin EM , Xu Bin , Haase Jacob , Krishnamoorthy Gnana P. , Hao Jingzhu , Knauf Jeffrey A. , Herbert Zachary T. , Martínez Paula , Blasco Maria A. , Ghossein Ronald , Fagin James A.
Published: September 2024

Additional analyses of RNA sequencing data from mouse tumors with telomerase upregulation.
Supplementary Data File S3 from USP1 expression driven by EWS::FLI1 transcription factor stabilizes Survivin and mitigates replication stress in Ewing sarcoma
Authors: Mallard Halle J. , Wan Shibiao , Nidhi Prakriti , Hanscom-Trofy Yvan D. , Mohapatra Bhopal , Woods Nicholas T. , Lopez-Guerrero Jose Antonio , Llombart-Bosch Antonio , Machado Isidro , Scotlandi Katia , Kreiling Natasha F. , Perry Megan C. , Mirza Sameer , Coulter Donald W. , Band Vimla , Band Hamid , Ghosal Gargi
Published: September 2024

Page 1: RT-qPCR primers used for DUB array; Page 2: Primers used for ChIP-qPCR analysis; Page 3: shRNA sequences used for EWS::FLI1 and USP1 knockdown cell line generation; Page 4: gRNA sequences used for USP1 knockout cell line generation; Page 5: List of working dilutions for antibodies used in this study; Page 6: List of reagents, with product information and RRIDs, used in this study; Page 7: List of biological resources, with product information and RRIDs, used in this study
Table S8 from CBF-beta mitigates PI3K-alpha-specific inhibitor killing through PIM1 in PIK3CA mutant gastric cancer
Authors: Stanland Lyla J. , Ang Hazel X. , Hoj Jacob P. , Chu Yunqiang , Tan Patrick , Wood Kris C. , Luftig Micah A.
Published: September 2024

Antibody dilutions for primary and secondary antibodies used
Table S6 from CBF-beta mitigates PI3K-alpha-specific inhibitor killing through PIM1 in PIK3CA mutant gastric cancer
Authors: Stanland Lyla J. , Ang Hazel X. , Hoj Jacob P. , Chu Yunqiang , Tan Patrick , Wood Kris C. , Luftig Micah A.
Published: September 2024

Sequences of guide RNAs used to generate genetic knockouts
Table S2 from CBF-beta mitigates PI3K-alpha-specific inhibitor killing through PIM1 in PIK3CA mutant gastric cancer
Authors: Stanland Lyla J. , Ang Hazel X. , Hoj Jacob P. , Chu Yunqiang , Tan Patrick , Wood Kris C. , Luftig Micah A.
Published: September 2024

Raw read counts for each guide RNA in screen
Supplementary Figure 3 from FBXO24 suppresses breast cancer tumorigenesis by targeting LSD1 for Ubiquitination
Authors: Dong Bo , Song Xiang , Wang Xinzhao , Dai Tao , Wang Jianlin , Yu Zhiyong , Deng Jiong , Evers B. Mark , Wu Yadi
Published: September 2024

FBXO24 blocks tumor migration and invasion.
Supplementary Figures S1-S17 from Dynamic glycoprotein hyposialylation promotes chemotherapy evasion and metastatic seeding of quiescent circulating tumor cell clusters in breast cancer
Authors: Dashzeveg Nurmaa K. , Jia Yuzhi , Zhang Youbin , Gerratana Lorenzo , Patel Priyam , Shajahan Asif , Dandar Tsogbadrakh , Ramos Erika K. , Almubarak Hannah F. , Adorno-Cruz Valery , Taftaf Rokana , Schuster Emma J. , Scholten David , Sokolowski Michael T. , Reduzzi Carolina , El-Shennawy Lamiaa , Hoffmann Andrew D. , Manai Maroua , Zhang Qiang , D'Amico Paolo , Azadi Parastoo , Colley Karen J. , Platanias Leonidas C. , Shah Ami N. , Gradishar William J. , Cristofanilli Massimo , Muller William A. , Cobb Brian A. , Liu Huiping
Published: September 2024

Supplementary Figure S1-S17 show the methods of CTC analysis and CTC-associated survival (S1); glycosylation profiles of patient CTCs (S2); phenotypic effects of neuraminidase treatment and CD44 depletion on tumor clustering and sialylation (S3); N-glycomic analysis of α2,6-SA peaks in WT and ST6KO cells (S4); Depletion of ST6GAL1 or ST3GAL1 promotes clustering and chemo-evasion (S5); ST6GAL1 expression and cell sensitivity to therapeutics (paclitaxel, doxorubicine and palbociclib) (S6); he altered gene pathways in ST6GAL1-KO cells (S7); ST6GAL1 is associated with cell growth and patient survival (S8); dynamic glycosylation profile in PDXs and breast tumors (S9); ST6GAL1 suppresses metastatic seeding (S10); Counts and Ki67 expression of CTCs and DTCs in situ (S11); depletion of ST6GAL1 promotes transendothelial migration and seeding (S12); α2,6-sialylation of CD44 by ST6GAL1 (S13); ST6GAL1 substrates regulate cluster formation via altered binding affinity (S14); the down-regulation of ST6GAL1 substrates inhibits metastatic seeding (S15); anti-PODXL inhibits tumor cell cluster formation and metastatic seeding (S16); and anti-PODXL effects on CTCs and seeding of PDX-M1 (S17).
Supplementary Excel S1 from Dynamic glycoprotein hyposialylation promotes chemotherapy evasion and metastatic seeding of quiescent circulating tumor cell clusters in breast cancer
Authors: Dashzeveg Nurmaa K. , Jia Yuzhi , Zhang Youbin , Gerratana Lorenzo , Patel Priyam , Shajahan Asif , Dandar Tsogbadrakh , Ramos Erika K. , Almubarak Hannah F. , Adorno-Cruz Valery , Taftaf Rokana , Schuster Emma J. , Scholten David , Sokolowski Michael T. , Reduzzi Carolina , El-Shennawy Lamiaa , Hoffmann Andrew D. , Manai Maroua , Zhang Qiang , D'Amico Paolo , Azadi Parastoo , Colley Karen J. , Platanias Leonidas C. , Shah Ami N. , Gradishar William J. , Cristofanilli Massimo , Muller William A. , Cobb Brian A. , Liu Huiping
Published: September 2024

Supplementary Excel S1 shows CTC numbers of the patients analyzed by CellSearch.
Supplementary Table S3 from Mitochondrial-encoded complex I impairment induces a targetable dependency on aerobic fermentation in Hurthle cell carcinoma of the thyroid
Authors: Frank Anderson R. , Li Vicky , Shelton Spencer D. , Kim Jiwoong , Stott Gordon M. , Neckers Leonard M. , Xie Yang , Williams Noelle S. , Mishra Prashant , McFadden David G.
Published: September 2024

Supplementary Table S3 shows the results of our genome-wide and targeted CRISPR-Cas9 screens.
Supplementary Table S1 from Mitochondrial-encoded complex I impairment induces a targetable dependency on aerobic fermentation in Hurthle cell carcinoma of the thyroid
Authors: Frank Anderson R. , Li Vicky , Shelton Spencer D. , Kim Jiwoong , Stott Gordon M. , Neckers Leonard M. , Xie Yang , Williams Noelle S. , Mishra Prashant , McFadden David G.
Published: September 2024

Supplementary Table S1 shows key mtDNA mutations identified through whole-exome sequencing and targeted mtDNA sequencing.
Supplementary_Table4 from Effectors enabling adaptation to mitochondrial complex I loss in Hurthle cell carcinoma
Authors: Gopal Raj K. , Vantaku Venkata R. , Panda Apekshya , Reimer Bryn , Rath Sneha , To Tsz-Leung , Fisch Adam S. , Cetinbas Murat , Livneh Maia , Calcaterra Michael J. , Gigliotti Benjamin J. , Pierce Kerry A. , Clish Clary B. , Dias-Santagata Dora , Sadow Peter M. , Wirth Lori J. , Daniels Gilbert H. , Sadreyev Ruslan I. , Calvo Sarah E. , Parangi Sareh , Mootha Vamsi K.
Published: September 2024

Supplementary Table4 provides the metabolomics analysis
Supplementary_Table1 from Effectors enabling adaptation to mitochondrial complex I loss in Hurthle cell carcinoma
Authors: Gopal Raj K. , Vantaku Venkata R. , Panda Apekshya , Reimer Bryn , Rath Sneha , To Tsz-Leung , Fisch Adam S. , Cetinbas Murat , Livneh Maia , Calcaterra Michael J. , Gigliotti Benjamin J. , Pierce Kerry A. , Clish Clary B. , Dias-Santagata Dora , Sadow Peter M. , Wirth Lori J. , Daniels Gilbert H. , Sadreyev Ruslan I. , Calvo Sarah E. , Parangi Sareh , Mootha Vamsi K.
Published: September 2024

Supplementary Table 1 describes the HCC clinical cohort
Supplementary Video S1 Legend from RLY-4008, the first highly selective FGFR2 inhibitor with activity across FGFR2 alterations and resistance mutations
Authors: Subbiah Vivek , Sahai Vaibhav , Maglic Dejan , Bruderek Kamil , Toure B. Barry. , Zhao Songping , Valverde Roberto , O'Hearn Patrick J. , Moustakas Demetri T. , Schonherr Heike , Gerami-Moayed Nastaran , Taylor Alexander M. , Hudson Brandi M. , Houde Damian J. , Pal Debjani , Foster Lindsey , Gunaydin Hakan , Ayaz Pelin , Sharon Dina A. , Goyal Lipika , Schram Alison M. , Kamath Suneel , Sherwin Cori Ann , Schmidt-Kittler Oleg , Jen Kai Yu , Ricard Fabien , Wolf Beni B. , Shaw David E. , Bergstrom Donald A. , Watters James , Casaletto Jessica B.
Published: September 2024

Supplementary video legend describing schematic video of P-loop dynamics
Supplementary Table S3 from RLY-4008, the first highly selective FGFR2 inhibitor with activity across FGFR2 alterations and resistance mutations
Authors: Subbiah Vivek , Sahai Vaibhav , Maglic Dejan , Bruderek Kamil , Toure B. Barry. , Zhao Songping , Valverde Roberto , O'Hearn Patrick J. , Moustakas Demetri T. , Schonherr Heike , Gerami-Moayed Nastaran , Taylor Alexander M. , Hudson Brandi M. , Houde Damian J. , Pal Debjani , Foster Lindsey , Gunaydin Hakan , Ayaz Pelin , Sharon Dina A. , Goyal Lipika , Schram Alison M. , Kamath Suneel , Sherwin Cori Ann , Schmidt-Kittler Oleg , Jen Kai Yu , Ricard Fabien , Wolf Beni B. , Shaw David E. , Bergstrom Donald A. , Watters James , Casaletto Jessica B.
Published: September 2024

Antiproliferative effect of RLY-4008 and pan-FGFRi in human tumor cell lines
Supplementary Table S2 from RLY-4008, the first highly selective FGFR2 inhibitor with activity across FGFR2 alterations and resistance mutations
Authors: Subbiah Vivek , Sahai Vaibhav , Maglic Dejan , Bruderek Kamil , Toure B. Barry. , Zhao Songping , Valverde Roberto , O'Hearn Patrick J. , Moustakas Demetri T. , Schonherr Heike , Gerami-Moayed Nastaran , Taylor Alexander M. , Hudson Brandi M. , Houde Damian J. , Pal Debjani , Foster Lindsey , Gunaydin Hakan , Ayaz Pelin , Sharon Dina A. , Goyal Lipika , Schram Alison M. , Kamath Suneel , Sherwin Cori Ann , Schmidt-Kittler Oleg , Jen Kai Yu , Ricard Fabien , Wolf Beni B. , Shaw David E. , Bergstrom Donald A. , Watters James , Casaletto Jessica B.
Published: September 2024

Biochemical inhibition of FGFR by RLY-4008 and pan-FGFRi
Supplementary Table S1 from RLY-4008, the first highly selective FGFR2 inhibitor with activity across FGFR2 alterations and resistance mutations
Authors: Subbiah Vivek , Sahai Vaibhav , Maglic Dejan , Bruderek Kamil , Toure B. Barry. , Zhao Songping , Valverde Roberto , O'Hearn Patrick J. , Moustakas Demetri T. , Schonherr Heike , Gerami-Moayed Nastaran , Taylor Alexander M. , Hudson Brandi M. , Houde Damian J. , Pal Debjani , Foster Lindsey , Gunaydin Hakan , Ayaz Pelin , Sharon Dina A. , Goyal Lipika , Schram Alison M. , Kamath Suneel , Sherwin Cori Ann , Schmidt-Kittler Oleg , Jen Kai Yu , Ricard Fabien , Wolf Beni B. , Shaw David E. , Bergstrom Donald A. , Watters James , Casaletto Jessica B.
Published: September 2024

Potency (kinact/KI) of RLY-4008 against FGFR1 and FGFR2