bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figure S12 from Dissecting the Mechanisms Underlying the Cytokine Release Syndrome (CRS) Mediated by T-Cell Bispecific Antibodies
Authors: Leclercq-Cohen Gabrielle , Steinhoff Nathalie , Albertí Servera Llucia , Nassiri Sina , Danilin Sabrina , Piccione Emily , Yángüez Emilio , Hüsser Tamara , Herter Sylvia , Schmeing Stephan , Gerber Petra , Schwalie Petra , Sam Johannes , Briner Stefanie , Jenni Sylvia , Bianchi Roberta , Biehl Marlene , Cremasco Floriana , Apostolopoulou Katerina , Haegel Hélène , Klein Christian , Umaña Pablo , Bacac Marina
Published: November 2023

Supplementary Figure S12. Individual tumor growth curves for each treatment group. OCI-Ly18 (DLBCL)-bearing humanized NSG mice were pre-treated with 30 mg/kg Gazyva (Gpt, grey arrow) and treated weekly with escalating doses of CD20-TCB (0.5 mg/kg, 1 mg/kg, 2 mg/kg, red arrows). Adalimumab (25 mg/kg, orange arrow, TNF-α blockade) and tocilizumab (10 mg/kg, green arrow, IL-6R blockade) were given 1 day and 1 hour before the first CD20-TCB infusion. Dexamethasone (1 mg/kg, blue arrow) was given 1 hour prior each therapy. Anakinra (10 mg/kg, purple arrow, IL-1R blockade) and the NLRP3 inhibitor (20 mg/kg, light blue arrow) were administered 1 hour before, 4 hrs and 24 hrs after the first CD20-TCB infusion as well as 1 hr before and 4 hrs after the second CD20-TCB treatment. Individual tumor growth curves for each treatment group.
Supplementary Figure S3 from Exercise Training Reduces the Inflammatory Response and Promotes Intestinal Mucosa-Associated Immunity in Lynch Syndrome
Authors: Deng Nan , Reyes-Uribe Laura , Fahrmann Johannes F. , Thoman Whittney S. , Munsell Mark F. , Dennison Jennifer B. , Murage Eunice , Wu Ranran , Hawk Ernest T. , Thirumurthi Selvi , Lynch Patrick M. , Dieli-Conwright Christina M. , Lazar Alexander J. , Jindal Sonali , Chu Khoi , Chelvanambi Manoj , Basen-Engquist Karen , Li Yisheng , Wargo Jennifer A. , McAllister Florencia , Allison James P. , Sharma Padmanee , Sinha Krishna M. , Hanash Samir , Gilchrist Susan C. , Vilar Eduardo
Published: November 2023

Figure S3. (A) Average time that study participants wore the Fitbit throughout the study; (B) Resting heart rate
in study participants at baseline; (C) Average total minutes of exercise at heart rate 70-85% of PHR; (D) Average total minutes of exercise at heart rate >85% of PHR. (***, P ≤0.001; ****, P≤0.0001).
Supplementary Table S2 from Regorafenib plus Vincristine and Irinotecan in Pediatric Patients with Recurrent/Refractory Solid Tumors: An Innovative Therapy for Children with Cancer Study
Authors: Casanova Michela , Bautista Francisco , Campbell-Hewson Quentin , Makin Guy , Marshall Lynley V. , Verschuur Arnauld C. , Cañete Nieto Adela , Corradini Nadège , Ploeger Bart A. , Brennan Barbara J. , Mueller Udo , Zebger-Gong Hong , Chung John W. , Geoerger Birgit
Published: November 2023

Table of AEs potentially related to regorafenib
Supplementary Table S3 from Clinical and Molecular Features of Long-term Response to Immune Checkpoint Inhibitors in Patients with Advanced Non–Small Cell Lung Cancer
Authors: Thummalapalli Rohit , Ricciuti Biagio , Bandlamudi Chaitanya , Muldoon Daniel , Rizvi Hira , Elkrief Arielle , Luo Jia , Alessi Joao V. , Pecci Federica , Lamberti Giuseppe , Di Federico Alessandro , Hong Lingzhi , Zhang Jianjun , Heymach John V. , Gibbons Don L. , Plodkowski Andrew J. , Ravichandran Vignesh , Donoghue Mark T.A. , Vanderbilt Chad , Ladanyi Marc , Rudin Charles M. , Kris Mark G. , Riely Gregory J. , Chaft Jamie E. , Hellmann Matthew D. , Vokes Natalie I. , Awad Mark M. , Schoenfeld Adam J.
Published: November 2023

Frequencies of alterations in individual genes among squamous and non-squamous patient groups.
Supplementary Figure S2 from Regorafenib plus Vincristine and Irinotecan in Pediatric Patients with Recurrent/Refractory Solid Tumors: An Innovative Therapy for Children with Cancer Study
Authors: Casanova Michela , Bautista Francisco , Campbell-Hewson Quentin , Makin Guy , Marshall Lynley V. , Verschuur Arnauld C. , Cañete Nieto Adela , Corradini Nadège , Ploeger Bart A. , Brennan Barbara J. , Mueller Udo , Zebger-Gong Hong , Chung John W. , Geoerger Birgit
Published: November 2023

Patient scans showing progressive reduction of tumor size in a patient with metastatic alveolar rhabdomyosarcoma.
Supplementary Data S2 from Regorafenib plus Vincristine and Irinotecan in Pediatric Patients with Recurrent/Refractory Solid Tumors: An Innovative Therapy for Children with Cancer Study
Authors: Casanova Michela , Bautista Francisco , Campbell-Hewson Quentin , Makin Guy , Marshall Lynley V. , Verschuur Arnauld C. , Cañete Nieto Adela , Corradini Nadège , Ploeger Bart A. , Brennan Barbara J. , Mueller Udo , Zebger-Gong Hong , Chung John W. , Geoerger Birgit
Published: November 2023

Supplementary results
Supplementary Figure S5 from Clinical and Molecular Features of Long-term Response to Immune Checkpoint Inhibitors in Patients with Advanced Non–Small Cell Lung Cancer
Authors: Thummalapalli Rohit , Ricciuti Biagio , Bandlamudi Chaitanya , Muldoon Daniel , Rizvi Hira , Elkrief Arielle , Luo Jia , Alessi Joao V. , Pecci Federica , Lamberti Giuseppe , Di Federico Alessandro , Hong Lingzhi , Zhang Jianjun , Heymach John V. , Gibbons Don L. , Plodkowski Andrew J. , Ravichandran Vignesh , Donoghue Mark T.A. , Vanderbilt Chad , Ladanyi Marc , Rudin Charles M. , Kris Mark G. , Riely Gregory J. , Chaft Jamie E. , Hellmann Matthew D. , Vokes Natalie I. , Awad Mark M. , Schoenfeld Adam J.
Published: November 2023

Kaplan-Meier curves of (A) overall survival (OS) and (B) progression-free survival (PFS) among patients with complete response (CR) in the combined cohort.
Supplementary Figure S4 from Clinical and Molecular Features of Long-term Response to Immune Checkpoint Inhibitors in Patients with Advanced Non–Small Cell Lung Cancer
Authors: Thummalapalli Rohit , Ricciuti Biagio , Bandlamudi Chaitanya , Muldoon Daniel , Rizvi Hira , Elkrief Arielle , Luo Jia , Alessi Joao V. , Pecci Federica , Lamberti Giuseppe , Di Federico Alessandro , Hong Lingzhi , Zhang Jianjun , Heymach John V. , Gibbons Don L. , Plodkowski Andrew J. , Ravichandran Vignesh , Donoghue Mark T.A. , Vanderbilt Chad , Ladanyi Marc , Rudin Charles M. , Kris Mark G. , Riely Gregory J. , Chaft Jamie E. , Hellmann Matthew D. , Vokes Natalie I. , Awad Mark M. , Schoenfeld Adam J.
Published: November 2023

Time on treatment among patients with long-term response (LTR).
Supplementary Figure S3 from Clinical and Molecular Features of Long-term Response to Immune Checkpoint Inhibitors in Patients with Advanced Non–Small Cell Lung Cancer
Authors: Thummalapalli Rohit , Ricciuti Biagio , Bandlamudi Chaitanya , Muldoon Daniel , Rizvi Hira , Elkrief Arielle , Luo Jia , Alessi Joao V. , Pecci Federica , Lamberti Giuseppe , Di Federico Alessandro , Hong Lingzhi , Zhang Jianjun , Heymach John V. , Gibbons Don L. , Plodkowski Andrew J. , Ravichandran Vignesh , Donoghue Mark T.A. , Vanderbilt Chad , Ladanyi Marc , Rudin Charles M. , Kris Mark G. , Riely Gregory J. , Chaft Jamie E. , Hellmann Matthew D. , Vokes Natalie I. , Awad Mark M. , Schoenfeld Adam J.
Published: November 2023

Kaplan-Meier curves of overall survival of patients with long-term response (LTR), short-term response (STR), and progressive disease (PD) from individual sites.
Supplementary Figure S15 from Clinical and Molecular Features of Long-term Response to Immune Checkpoint Inhibitors in Patients with Advanced Non–Small Cell Lung Cancer
Authors: Thummalapalli Rohit , Ricciuti Biagio , Bandlamudi Chaitanya , Muldoon Daniel , Rizvi Hira , Elkrief Arielle , Luo Jia , Alessi Joao V. , Pecci Federica , Lamberti Giuseppe , Di Federico Alessandro , Hong Lingzhi , Zhang Jianjun , Heymach John V. , Gibbons Don L. , Plodkowski Andrew J. , Ravichandran Vignesh , Donoghue Mark T.A. , Vanderbilt Chad , Ladanyi Marc , Rudin Charles M. , Kris Mark G. , Riely Gregory J. , Chaft Jamie E. , Hellmann Matthew D. , Vokes Natalie I. , Awad Mark M. , Schoenfeld Adam J.
Published: November 2023

Fraction of subclonal non-synonymous mutations among patients with long-term response (LTR), short-term response (STR), and progressive disease (PD).
Supplementary Figure S14 from Clinical and Molecular Features of Long-term Response to Immune Checkpoint Inhibitors in Patients with Advanced Non–Small Cell Lung Cancer
Authors: Thummalapalli Rohit , Ricciuti Biagio , Bandlamudi Chaitanya , Muldoon Daniel , Rizvi Hira , Elkrief Arielle , Luo Jia , Alessi Joao V. , Pecci Federica , Lamberti Giuseppe , Di Federico Alessandro , Hong Lingzhi , Zhang Jianjun , Heymach John V. , Gibbons Don L. , Plodkowski Andrew J. , Ravichandran Vignesh , Donoghue Mark T.A. , Vanderbilt Chad , Ladanyi Marc , Rudin Charles M. , Kris Mark G. , Riely Gregory J. , Chaft Jamie E. , Hellmann Matthew D. , Vokes Natalie I. , Awad Mark M. , Schoenfeld Adam J.
Published: November 2023

Whole exome sequencing (WES) features of patients with long-term response (LTR), short-term response (STR), and progressive disease (PD).
Supplementary Figure S2 from ATM-Inhibitor AZD1390 Is a Radiosensitizer for Breast Cancer CNS Metastasis
Authors: Tew Ben Yi , Kalfa Alex J. , Yang Zeyi , Hurth Kyle M. , Simon Thomas , Abnoosian Eric , Durant Stephen T. , Hamerlik Petra , Salhia Bodour
Published: November 2023

Supplemental Figure 2. Gene set enrichment analysis (GSEA) of progression versus stable tumors
Supplementary Figure S11 from Clinical and Molecular Features of Long-term Response to Immune Checkpoint Inhibitors in Patients with Advanced Non–Small Cell Lung Cancer
Authors: Thummalapalli Rohit , Ricciuti Biagio , Bandlamudi Chaitanya , Muldoon Daniel , Rizvi Hira , Elkrief Arielle , Luo Jia , Alessi Joao V. , Pecci Federica , Lamberti Giuseppe , Di Federico Alessandro , Hong Lingzhi , Zhang Jianjun , Heymach John V. , Gibbons Don L. , Plodkowski Andrew J. , Ravichandran Vignesh , Donoghue Mark T.A. , Vanderbilt Chad , Ladanyi Marc , Rudin Charles M. , Kris Mark G. , Riely Gregory J. , Chaft Jamie E. , Hellmann Matthew D. , Vokes Natalie I. , Awad Mark M. , Schoenfeld Adam J.
Published: November 2023

Genomic features of patients with long-term response (LTR) compared to short term response (STR), non-LTR, and progressive disease (PD) among patients with TMB z-score < 0.
Clinical Trial Protocol S1 from Phase I Results of Bromodomain and Extra-Terminal Inhibitor PLX51107 in Combination with Azacitidine in Patients with Relapsed/Refractory Myeloid Malignancies
Authors: Senapati Jayastu , Fiskus Warren C. , Daver Naval , Wilson Nathaniel R. , Ravandi Farhad , Garcia-Manero Guillermo , Kadia Tapan , DiNardo Courtney D. , Jabbour Elias , Burger Jan , Short Nicholas J. , Alvarado Yesid , Jain Nitin , Masarova Lucia , Issa Ghayas C. , Qiao Wei , Khoury Joseph D. , Pierce Sherry , Miller Darla , Sasaki Koji , Konopleva Marina , Bhalla Kapil N. , Borthakur Gautam , Pemmaraju Naveen
Published: November 2023

Clinical Trial Protocol
Supplementary Table S3 from SPOP Mutations Target STING1 Signaling in Prostate Cancer and Create Therapeutic Vulnerabilities to PARP Inhibitor–Induced Growth Suppression
Authors: Geng Chuandong , Zhang Man-Chao , Manyam Ganiraju C. , Vykoukal Jody V. , Fahrmann Johannes F. , Peng Shan , Wu Cheng , Park Sanghee , Kondraganti Shakuntala , Wang Daoqi , Robinson Brian D. , Loda Massimo , Barbieri Christopher E. , Yap Timothy A. , Corn Paul G. , Hanash Samir , Broom Bradley M. , Pilié Patrick G. , Thompson Timothy C.
Published: November 2023

Supplementary Table S3. Complete listing of antibodies used for immunoblotting (IB) and immunostaining analysis (Fig. 6C, 6D and Extended Data Fig. 5, 6). Vendor and catalog numbers are included in the list.
Supplementary Table S2 from SPOP Mutations Target STING1 Signaling in Prostate Cancer and Create Therapeutic Vulnerabilities to PARP Inhibitor–Induced Growth Suppression
Authors: Geng Chuandong , Zhang Man-Chao , Manyam Ganiraju C. , Vykoukal Jody V. , Fahrmann Johannes F. , Peng Shan , Wu Cheng , Park Sanghee , Kondraganti Shakuntala , Wang Daoqi , Robinson Brian D. , Loda Massimo , Barbieri Christopher E. , Yap Timothy A. , Corn Paul G. , Hanash Samir , Broom Bradley M. , Pilié Patrick G. , Thompson Timothy C.
Published: November 2023

Supplementary Table S2. Listing of protein features differentially expressed in Dox-inducible SPOPmut (F102C and F133V) C4-2b prostate cancer cells compared to C4-2b vector control shown in Fig. 2A upper panel
Supplementary Table S13 from SPOP Mutations Target STING1 Signaling in Prostate Cancer and Create Therapeutic Vulnerabilities to PARP Inhibitor–Induced Growth Suppression
Authors: Geng Chuandong , Zhang Man-Chao , Manyam Ganiraju C. , Vykoukal Jody V. , Fahrmann Johannes F. , Peng Shan , Wu Cheng , Park Sanghee , Kondraganti Shakuntala , Wang Daoqi , Robinson Brian D. , Loda Massimo , Barbieri Christopher E. , Yap Timothy A. , Corn Paul G. , Hanash Samir , Broom Bradley M. , Pilié Patrick G. , Thompson Timothy C.
Published: November 2023

Supplementary Table S13. Quantification of each protein-specific band normalized to vinculin (macrophage cells (RAW264.7) mono- or cocultured with RM-1-BM EV or SPOPmut models under treatment with OLA, Fig. 5E).
Supplementary Table S1 from SPOP Mutations Target STING1 Signaling in Prostate Cancer and Create Therapeutic Vulnerabilities to PARP Inhibitor–Induced Growth Suppression
Authors: Geng Chuandong , Zhang Man-Chao , Manyam Ganiraju C. , Vykoukal Jody V. , Fahrmann Johannes F. , Peng Shan , Wu Cheng , Park Sanghee , Kondraganti Shakuntala , Wang Daoqi , Robinson Brian D. , Loda Massimo , Barbieri Christopher E. , Yap Timothy A. , Corn Paul G. , Hanash Samir , Broom Bradley M. , Pilié Patrick G. , Thompson Timothy C.
Published: November 2023

Supplementary Table S1. Selected genesets annotated comprised of non-canonical STING-NF-κB and canonical STING signaling genes used in Fig. 1A, B, D
Supplementary Figure S8 from SPOP Mutations Target STING1 Signaling in Prostate Cancer and Create Therapeutic Vulnerabilities to PARP Inhibitor–Induced Growth Suppression
Authors: Geng Chuandong , Zhang Man-Chao , Manyam Ganiraju C. , Vykoukal Jody V. , Fahrmann Johannes F. , Peng Shan , Wu Cheng , Park Sanghee , Kondraganti Shakuntala , Wang Daoqi , Robinson Brian D. , Loda Massimo , Barbieri Christopher E. , Yap Timothy A. , Corn Paul G. , Hanash Samir , Broom Bradley M. , Pilié Patrick G. , Thompson Timothy C.
Published: November 2023

Supplementary Fig. S8. Original unedited IB images for representative Western blots experiments (n-2) used in Figure 3D
Supplementary Figure S18 from SPOP Mutations Target STING1 Signaling in Prostate Cancer and Create Therapeutic Vulnerabilities to PARP Inhibitor–Induced Growth Suppression
Authors: Geng Chuandong , Zhang Man-Chao , Manyam Ganiraju C. , Vykoukal Jody V. , Fahrmann Johannes F. , Peng Shan , Wu Cheng , Park Sanghee , Kondraganti Shakuntala , Wang Daoqi , Robinson Brian D. , Loda Massimo , Barbieri Christopher E. , Yap Timothy A. , Corn Paul G. , Hanash Samir , Broom Bradley M. , Pilié Patrick G. , Thompson Timothy C.
Published: November 2023

Supplementary Fig. S18. Original unedited IB images for representative Western blots experiments (n-2) used in Figure 5E.
Supplementary Figure S12 from SPOP Mutations Target STING1 Signaling in Prostate Cancer and Create Therapeutic Vulnerabilities to PARP Inhibitor–Induced Growth Suppression
Authors: Geng Chuandong , Zhang Man-Chao , Manyam Ganiraju C. , Vykoukal Jody V. , Fahrmann Johannes F. , Peng Shan , Wu Cheng , Park Sanghee , Kondraganti Shakuntala , Wang Daoqi , Robinson Brian D. , Loda Massimo , Barbieri Christopher E. , Yap Timothy A. , Corn Paul G. , Hanash Samir , Broom Bradley M. , Pilié Patrick G. , Thompson Timothy C.
Published: November 2023

Supplementary Fig. S12. Suppression of STING1 protein levels following siSTING transfection compared to siNC.
Supplementary Figure S11 from SPOP Mutations Target STING1 Signaling in Prostate Cancer and Create Therapeutic Vulnerabilities to PARP Inhibitor–Induced Growth Suppression
Authors: Geng Chuandong , Zhang Man-Chao , Manyam Ganiraju C. , Vykoukal Jody V. , Fahrmann Johannes F. , Peng Shan , Wu Cheng , Park Sanghee , Kondraganti Shakuntala , Wang Daoqi , Robinson Brian D. , Loda Massimo , Barbieri Christopher E. , Yap Timothy A. , Corn Paul G. , Hanash Samir , Broom Bradley M. , Pilié Patrick G. , Thompson Timothy C.
Published: November 2023

Supplementary Fig. S11. Original unedited IB images for representative Western blots experiments (n-2) used in Figure 3F.
Supplementary Figure S1 from SPOP Mutations Target STING1 Signaling in Prostate Cancer and Create Therapeutic Vulnerabilities to PARP Inhibitor–Induced Growth Suppression
Authors: Geng Chuandong , Zhang Man-Chao , Manyam Ganiraju C. , Vykoukal Jody V. , Fahrmann Johannes F. , Peng Shan , Wu Cheng , Park Sanghee , Kondraganti Shakuntala , Wang Daoqi , Robinson Brian D. , Loda Massimo , Barbieri Christopher E. , Yap Timothy A. , Corn Paul G. , Hanash Samir , Broom Bradley M. , Pilié Patrick G. , Thompson Timothy C.
Published: November 2023

Supplementary Fig. S1. “Immunome” analysis of SPOPmut and SPOPwt from Beltran CRPC cohort using a compendium of publicly available data from purified immune subsets
Data from MGMT Promoter Methylation Predicts Overall Survival after Chemotherapy for 1p/19q-Codeleted Gliomas
Authors: Kinslow Connor J. , Rae Ali I. , Taparra Kekoa , Kumar Prashanth , Siegelin Markus D. , Grinband Jack , Gill Brian J.A. , McKhann Guy M. , Sisti Michael B. , Bruce Jeffrey N. , Canoll Peter D. , Iwamoto Fabio M. , Horowitz David P. , Kachnic Lisa A. , Neugut Alfred I. , Yu James B. , Cheng Simon K. , Wang Tony J.C.
Published: November 2023

AbstractPurpose:
While MGMT promoter methylation (mMGMT) is predictive of response to alkylating chemotherapy and guides treatment decisions in glioblastoma, its role in grade 2 and 3 glioma remains unclear. Recent data suggest that mMGMT is prognostic of progression-free survival in 1p/19q-codeleted oligodendrogliomas, but an effect on overall survival (OS) has not been demonstrated.
Experimental Design:
We identified patients with newly diagnosed 1p/19q-codeleted gliomas and known MGMT promoter status in the National Cancer Database from 2010 to 2019. Multivariable Cox proportional hazards regression modeling was used to assess the effect of mMGMT on OS after adjusting for age, sex, race, comorbidity, grade, extent of resection, chemotherapy, and radiotherapy.
Results:
We identified 1,297 eligible patients, 938 (72.3%) of whom received chemotherapy in their initial course of treatment. The MGMT promoter was methylated in 1,009 (77.8%) patients. Unmethylated MGMT (uMGMT) was associated with worse survival compared with mMGMT [70% {95% confidence interval (CI), 64%–77%} vs. 81% (95% CI, 78%–85%); P < 0.001; adjusted HR (aHR), 2.35 (95% CI, 1.77–3.14)]. uMGMT was associated with worse survival in patients who received chemotherapy [63% (95% CI, 55–73%) vs. 80% (95% CI, 76%–84%); P < 0.001; aHR, 2.61 (95% CI, 1.89–3.60)] but not in patients who did not receive chemotherapy [P = 0.38; HR, 1.31 (95% CI, 0.71–2.42)]. Similar results were observed regardless of World Health Organization grade and after single- or multiagent chemotherapy.
Conclusions:
Our study demonstrates an association between mMGMT and OS in 1p/19q-codeleted gliomas. MGMT promoter status should be considered as a stratification factor in future clinical trials of 1p/19q-codeleted gliomas that use OS as an endpoint.
Data from Phase I Results of Bromodomain and Extra-Terminal Inhibitor PLX51107 in Combination with Azacitidine in Patients with Relapsed/Refractory Myeloid Malignancies
Authors: Senapati Jayastu , Fiskus Warren C. , Daver Naval , Wilson Nathaniel R. , Ravandi Farhad , Garcia-Manero Guillermo , Kadia Tapan , DiNardo Courtney D. , Jabbour Elias , Burger Jan , Short Nicholas J. , Alvarado Yesid , Jain Nitin , Masarova Lucia , Issa Ghayas C. , Qiao Wei , Khoury Joseph D. , Pierce Sherry , Miller Darla , Sasaki Koji , Konopleva Marina , Bhalla Kapil N. , Borthakur Gautam , Pemmaraju Naveen
Published: November 2023

AbstractPurpose:
Treatment outcomes in patients with relapsed/refractory (R/R) myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) remains dismal. On the basis of both extensive preclinical data and emerging clinical data, treatment with bromodomain and extra-terminal domain inhibitors (BETi) is a potential approach for patients with high-risk myeloid malignancies.
Patients and Methods:
We conducted a phase I trial to study the safety and efficacy of PLX51107 (BETi) and azacitidine combination therapy in patients with R/R AML and high-risk (HR) MDS and studied mechanisms of resistance to the combination therapy.
Results:
Thirty-seven patients with HR R/R MDS (n = 4) and R/R AML (n = 33) were treated. Sixteen patients (43%) had MECOM gene rearrangement and 7 other patients had TP53 mutation. Median prior number of therapies was three (range 1–9); 97% had received prior hypomethylating agent and 84% prior venetoclax. Overall response rate was 8/37 (22%): complete remission with incomplete platelet recovery (n = 1); morphologic leukemia-free state (n = 2); hematologic improvement (n = 5). The most common nonhematologic toxicities were febrile neutropenia and pneumonia in 12 (32%) patients each; 6 patients (17%) had severe hyperbilirubinemia. RNA-sequencing analysis of mononuclear cells harvested on treatment (day 3) versus pretreatment showed significant changes in mRNA expressions in responders: downregulation of MYC, BCL2, IL7R, and CDK6 and upregulation of HEXIM1, CD93, DCXR, and CDKN1A. Immunoblot analyses confirmed reduction in protein levels of c-Myc, CDK6, BCL2, and BCL-xL, and induction of BRD4 and HEXIM1 protein levels in responders.
Conclusions:
In a heavily pretreated patient cohort with R/R MDS and AML, PLX51107+ azacitidine was well-tolerated and resulted in modest clinical benefit.
Western Blot Raw Images and Quantification from Cotargeting Phosphoinositide 3-Kinase and Focal Adhesion Kinase Pathways Inhibits Proliferation of NF2 Schwannoma Cells
Authors: Hardin Haley M. , Dinh Christine T. , Huegel Julianne , Petrilli Alejandra M. , Bracho Olena , Allaf Abdulrahman M. , Karajannis Matthias A. , Griswold Anthony J. , Ivan Michael E. , Morcos Jacques , Gultekin Sakir H. , Telischi Fred F. , Liu Xue Zhong , Fernandez-Valle Cristina
Published: November 2023

Western Blot Raw Images and Quantification
Table S4 from Cotargeting Phosphoinositide 3-Kinase and Focal Adhesion Kinase Pathways Inhibits Proliferation of NF2 Schwannoma Cells
Authors: Hardin Haley M. , Dinh Christine T. , Huegel Julianne , Petrilli Alejandra M. , Bracho Olena , Allaf Abdulrahman M. , Karajannis Matthias A. , Griswold Anthony J. , Ivan Michael E. , Morcos Jacques , Gultekin Sakir H. , Telischi Fred F. , Liu Xue Zhong , Fernandez-Valle Cristina
Published: November 2023

Supplemental Table 4. NF2 mutation status of VS tumors.
Table S3 from Cotargeting Phosphoinositide 3-Kinase and Focal Adhesion Kinase Pathways Inhibits Proliferation of NF2 Schwannoma Cells
Authors: Hardin Haley M. , Dinh Christine T. , Huegel Julianne , Petrilli Alejandra M. , Bracho Olena , Allaf Abdulrahman M. , Karajannis Matthias A. , Griswold Anthony J. , Ivan Michael E. , Morcos Jacques , Gultekin Sakir H. , Telischi Fred F. , Liu Xue Zhong , Fernandez-Valle Cristina
Published: November 2023

Supplemental Table 3. Efficacy of Drug Combinations in Additional Cell Lines.
Supplementary Table S5 from Targeting Aggressive B-cell Lymphomas through Pharmacological Activation of the Mitochondrial Protease OMA1
Authors: Schwarzer Adrian , Oliveira Matheus , Kleppa Marc-Jens , Slattery Scott D. , Anantha Andy , Cooper Alan , Hannink Mark , Schambach Axel , Dörrie Anneke , Kotlyarov Alexey , Gaestel Matthias , Hembrough Todd , Levine Jedd , Luther Michael , Stocum Michael , Stiles Linsey , Weinstock David M. , Liesa Marc , Kostura Matthew J.
Published: November 2023

Spearmans Rank correlation of gene expression with response to compound in the cell line screening data.
Supplementary Data Legends from Cotargeting Phosphoinositide 3-Kinase and Focal Adhesion Kinase Pathways Inhibits Proliferation of NF2 Schwannoma Cells
Authors: Hardin Haley M. , Dinh Christine T. , Huegel Julianne , Petrilli Alejandra M. , Bracho Olena , Allaf Abdulrahman M. , Karajannis Matthias A. , Griswold Anthony J. , Ivan Michael E. , Morcos Jacques , Gultekin Sakir H. , Telischi Fred F. , Liu Xue Zhong , Fernandez-Valle Cristina
Published: November 2023

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

Supplemental table 2: CD123 cell expression data
Figure S5 from Use of Payload Binding Selectivity Enhancers to Improve Therapeutic Index of Maytansinoid–Antibody–Drug Conjugates
Authors: Nguyen Toan D. , Bordeau Brandon M. , Balthasar Joseph P.
Published: November 2023

Weight loss induced by administration of 7E7 DM4-ADC to mice
Figure S3 from Use of Payload Binding Selectivity Enhancers to Improve Therapeutic Index of Maytansinoid–Antibody–Drug Conjugates
Authors: Nguyen Toan D. , Bordeau Brandon M. , Balthasar Joseph P.
Published: November 2023

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

Analytical Data
Supplementary Fig. S3 from Combination Therapies to Improve the Efficacy of Immunotherapy in Triple-negative Breast Cancer
Authors: Alečković Maša , Li Zheqi , Zhou Ningxuan , Qiu Xintao , Lulseged Bethlehem , Foidart Pierre , Huang Xiao-Yun , Garza Kodie , Shu Shaokun , Kesten Nikolas , Li Rong , Lim Klothilda , Garrido-Castro Ana C. , Guerriero Jennifer L. , Qi Jun , Long Henry W. , Polyak Kornelia
Published: November 2023

Supplementary Fig. S3 shows analyses of tumor cell immune cell composition.
Supplementary Fig. S1 from Combination Therapies to Improve the Efficacy of Immunotherapy in Triple-negative Breast Cancer
Authors: Alečković Maša , Li Zheqi , Zhou Ningxuan , Qiu Xintao , Lulseged Bethlehem , Foidart Pierre , Huang Xiao-Yun , Garza Kodie , Shu Shaokun , Kesten Nikolas , Li Rong , Lim Klothilda , Garrido-Castro Ana C. , Guerriero Jennifer L. , Qi Jun , Long Henry W. , Polyak Kornelia
Published: November 2023

Supplementary Fig. S1 shows the effect of combination treatment on mice and tumors.
Supplementary Fig. S3 from Preclinical Development of Brain Permeable ERβ Agonist for the Treatment of Glioblastoma
Authors: Pratap Uday P. , Tidwell Michael , Balinda Henriette U. , Clanton Nicholas A. , Yang Xue , Viswanadhapalli Suryavathi , Sareddy Gangadhara R. , Liang Dong , Xie Huan , Chen Yidong , Lai Zhao , Tekmal Rajeshwar R. , McHardy Stanton F. , Brenner Andrew J. , Vadlamudi Ratna K.
Published: November 2023

Supplementary Fig.S3 shows efficacy of CIDD-0149897 combination therapy.
Figure S2 from USP1 Expression Driven by EWS::FLI1 Transcription Factor Stabilizes Survivin and Mitigates Replication Stress in Ewing Sarcoma
Authors: Mallard Halle J. , Wan Shibiao , Nidhi Prakriti , Hanscom-Trofy Yvan D. , Mohapatra Bhopal , Woods Nicholas T. , Lopez-Guerrero Jose Antonio , Llombart-Bosch Antonio , Machado Isidro , Scotlandi Katia , Kreiling Natasha F. , Perry Megan C. , Mirza Sameer , Coulter Donald W. , Band Vimla , Band Hamid , Ghosal Gargi
Published: November 2023

Figure S2 shows USP1 knockdown or inhibition decreases cell growth.
Table S9 from CBF-Beta Mitigates PI3K-Alpha–Specific Inhibitor Killing through PIM1 in PIK3CA-Mutant Gastric Cancer
Authors: Stanland Lyla J. , Ang Hazel X. , Hoj Jacob P. , Chu Yunqiang , Tan Patrick , Wood Kris C. , Luftig Micah A.
Published: November 2023

Quantification of Human Phospho-Proteome Array
Supplementary Figure Legends 1-7 from CBF-Beta Mitigates PI3K-Alpha–Specific Inhibitor Killing through PIM1 in PIK3CA-Mutant Gastric Cancer
Authors: Stanland Lyla J. , Ang Hazel X. , Hoj Jacob P. , Chu Yunqiang , Tan Patrick , Wood Kris C. , Luftig Micah A.
Published: November 2023

S1. BYL719 and DMSO beta scores
S2. Ribbon plots of non-gastric cancer cell lines included in screen.
S3. Dasatinib renders AGS cells hyper-sensitive to BYL719
S4. Loss of BCL-XL induces cell death in BYL719 treated MKN1
S5. BCL-XL inhibitor A-1331852 is the only inhibitor capable of increasing BYL719-induced cell death and inhibiting cell growth.
S6. CBFB binding co-factor RUNX1 is down-regulated at protein and mRNA level in BYL719 resistant clones.
S7. Pan-PIM inhibition or PIM1 KO re-sensitizes CBFB KO and resistant clones to BYL719.
Figure S7 from CBF-Beta Mitigates PI3K-Alpha–Specific Inhibitor Killing through PIM1 in PIK3CA-Mutant Gastric Cancer
Authors: Stanland Lyla J. , Ang Hazel X. , Hoj Jacob P. , Chu Yunqiang , Tan Patrick , Wood Kris C. , Luftig Micah A.
Published: November 2023

Figure S7 shows loss of PIM1 re-sensitizes resistant cells to BYL719
Figure S4 from CBF-Beta Mitigates PI3K-Alpha–Specific Inhibitor Killing through PIM1 in PIK3CA-Mutant Gastric Cancer
Authors: Stanland Lyla J. , Ang Hazel X. , Hoj Jacob P. , Chu Yunqiang , Tan Patrick , Wood Kris C. , Luftig Micah A.
Published: November 2023

Figure S4 shows loss of BCL-XL and BYL719 treatment in additional gastric cancer cell line
Figure S1 from CBF-Beta Mitigates PI3K-Alpha–Specific Inhibitor Killing through PIM1 in PIK3CA-Mutant Gastric Cancer
Authors: Stanland Lyla J. , Ang Hazel X. , Hoj Jacob P. , Chu Yunqiang , Tan Patrick , Wood Kris C. , Luftig Micah A.
Published: November 2023

Figure S1 shows BYL719 and DMSO beta scores calculated by the MAGeCK analysis pipeline
Supplementary Table 1 from Exon Junction Complex Mediates the Cap-Independent Translation of Circular RNA
Authors: Lin Hui-Hsuan , Chang Chiu-Yuan , Huang Yi-Ren , Shen Che-Hung , Wu Yu-Chen , Chang Kai-Li , Lee Yueh-Chun , Lin Ya-Chi , Ting Wen-Chien , Chien Han-Ju , Zheng Yi-Feng , Lai Chien-Chen , Hsiao Kuei-Yang
Published: November 2023

Sequences
Table S4 from Stromal DDR2 Promotes Ovarian Cancer Metastasis through Regulation of Metabolism and Secretion of Extracellular Matrix Proteins
Authors: Schab Angela M. , Greenwade Molly M. , Stock Elizabeth , Lomonosova Elena , Cho Kevin , Grither Whitney R. , Noia Hollie , Wilke Daniel , Mullen Mary M. , Hagemann Andrea R. , Hagemann Ian S. , Thaker Premal H. , Kuroki Lindsay M. , McCourt Carolyn K. , Khabele Dineo , Powell Matthew A. , Mutch David G. , Zhao Peinan , Shriver Leah P. , Patti Gary J. , Longmore Gregory D. , Fuh Katherine C.
Published: November 2023

Metabolism pathways
Table S3 from Stromal DDR2 Promotes Ovarian Cancer Metastasis through Regulation of Metabolism and Secretion of Extracellular Matrix Proteins
Authors: Schab Angela M. , Greenwade Molly M. , Stock Elizabeth , Lomonosova Elena , Cho Kevin , Grither Whitney R. , Noia Hollie , Wilke Daniel , Mullen Mary M. , Hagemann Andrea R. , Hagemann Ian S. , Thaker Premal H. , Kuroki Lindsay M. , McCourt Carolyn K. , Khabele Dineo , Powell Matthew A. , Mutch David G. , Zhao Peinan , Shriver Leah P. , Patti Gary J. , Longmore Gregory D. , Fuh Katherine C.
Published: November 2023

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

Patient cohort
Figure S3 from Stromal DDR2 Promotes Ovarian Cancer Metastasis through Regulation of Metabolism and Secretion of Extracellular Matrix Proteins
Authors: Schab Angela M. , Greenwade Molly M. , Stock Elizabeth , Lomonosova Elena , Cho Kevin , Grither Whitney R. , Noia Hollie , Wilke Daniel , Mullen Mary M. , Hagemann Andrea R. , Hagemann Ian S. , Thaker Premal H. , Kuroki Lindsay M. , McCourt Carolyn K. , Khabele Dineo , Powell Matthew A. , Mutch David G. , Zhao Peinan , Shriver Leah P. , Patti Gary J. , Longmore Gregory D. , Fuh Katherine C.
Published: November 2023

Stromal cell expression of DDR2 is critical for migration of ovarian cancer cells, related to Figure 4
Figure S1 from Stromal DDR2 Promotes Ovarian Cancer Metastasis through Regulation of Metabolism and Secretion of Extracellular Matrix Proteins
Authors: Schab Angela M. , Greenwade Molly M. , Stock Elizabeth , Lomonosova Elena , Cho Kevin , Grither Whitney R. , Noia Hollie , Wilke Daniel , Mullen Mary M. , Hagemann Andrea R. , Hagemann Ian S. , Thaker Premal H. , Kuroki Lindsay M. , McCourt Carolyn K. , Khabele Dineo , Powell Matthew A. , Mutch David G. , Zhao Peinan , Shriver Leah P. , Patti Gary J. , Longmore Gregory D. , Fuh Katherine C.
Published: November 2023

Mouse ovarian cancer cell line ID8Trp53-/-Brca2-/- express DDR2. Related to Figure 2
Supplementary Table 7 from Telomerase Upregulation Induces Progression of Mouse BrafV600E-Driven Thyroid Cancers and Triggers Nontelomeric Effects
Authors: Landa Iñigo , Thornton Caitlin E.M. , Xu Bin , Haase Jacob , Krishnamoorthy Gnana P. , Hao Jingzhu , Knauf Jeffrey A. , Herbert Zachary T. , Martínez Paula , Blasco María A. , Ghossein Ronald , Fagin James A.
Published: November 2023

Full list of significantly upregulated terms (q-value<0.05) in BrafV600E+K5-Tert tumors, compared to BrafV600E, from 20-week animals, employing the GSEA (gene set enrichment analysis) hallmarks of cancer database on RNAseq data.
Supplementary Table 5 from Telomerase Upregulation Induces Progression of Mouse BrafV600E-Driven Thyroid Cancers and Triggers Nontelomeric Effects
Authors: Landa Iñigo , Thornton Caitlin E.M. , Xu Bin , Haase Jacob , Krishnamoorthy Gnana P. , Hao Jingzhu , Knauf Jeffrey A. , Herbert Zachary T. , Martínez Paula , Blasco María A. , Ghossein Ronald , Fagin James A.
Published: November 2023

Full list of KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis “up terms” for the BrafV600E vs. BrafV600E+K5-Tert comparison.
Supplementary Table 4 from Telomerase Upregulation Induces Progression of Mouse BrafV600E-Driven Thyroid Cancers and Triggers Nontelomeric Effects
Authors: Landa Iñigo , Thornton Caitlin E.M. , Xu Bin , Haase Jacob , Krishnamoorthy Gnana P. , Hao Jingzhu , Knauf Jeffrey A. , Herbert Zachary T. , Martínez Paula , Blasco María A. , Ghossein Ronald , Fagin James A.
Published: November 2023

Differentially expressed genes from RNAseq data when comparing BrafV600E vs. BrafV600E+K5-Tert tumors from 20-week animals.
Table 3 from Polymorphisms in Cyclooxygenase, Lipoxygenase, and TP53 Genes Predict Colorectal Polyp Risk Reduction by Aspirin in the seAFOod Polyp Prevention Trial
Authors: Davies John R. , Mell Tracey , Fuller Harriett , Harland Mark , Saleh Rasha N.M. , Race Amanda D. , Rees Colin J. , Brown Louise C. , Loadman Paul M. , Downing Amy , Minihane Anne Marie , Williams Elizabeth A. , Hull Mark A.
Published: November 2023

SNP genotypes in ALOX genes and the TP53 gene that are associated with modification of the effect of aspirin on colorectal polyp number in the seAFOod polyp prevention trial.
Supplemental Figure 2 from Methylated DNA Markers for Sporadic Colorectal and Endometrial Cancer Are Strongly Associated with Lynch Syndrome Cancers
Authors: Bramblet Rachel M. , Bakkum-Gamez Jamie N. , Slettedahl Seth W. , Foote Patrick H. , Taylor William R. , Berger Calise K. , Gysbers Brianna J. , Arndt Jacquelyn , Chen Longwen , Doering Karen A. , Burger Kelli N. , Mahoney Douglas W. , Sherman Mark E. , Kisiel John B. , Samadder N. Jewel
Published: November 2023

Supplemental Figure 2: Distributions of all methylated DNA markers tested for endometrial cancers and controls, stratified by Lynch syndrome. Log10 strand counts are adjusted based on the level of the control gene, ACTB, in all controls (SPOR-EC-CTRL and LS-EC-CTRL). P-value provided to show statistical significance of difference of medians between CASE and CTRL samples within SPOR and LS subgroups.
Figure 1 from Polymorphisms in Cyclooxygenase, Lipoxygenase, and TP53 Genes Predict Colorectal Polyp Risk Reduction by Aspirin in the seAFOod Polyp Prevention Trial
Authors: Davies John R. , Mell Tracey , Fuller Harriett , Harland Mark , Saleh Rasha N.M. , Race Amanda D. , Rees Colin J. , Brown Louise C. , Loadman Paul M. , Downing Amy , Minihane Anne Marie , Williams Elizabeth A. , Hull Mark A.
Published: November 2023

seAFOod trial participants and samples contributing to the gene × treatment interaction analysis. 666 of 707 seAFOod trial participants provided at least one buffy coat sample for DNA extraction. The number of samples lost during either DNA extraction or SNP genotyping is described at each stage. The final study population consisted of 542 participants for whom SNP genotype and trial exit colonoscopy data were available. EPA, eicosapentaenoic acid; SNP, single-nucleotide polymorphism.
Supplementary Table S4 from Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer
Authors: Grillo Giacomo , Keshavarzian Tina , Linder Simon , Arlidge Christopher , Mout Lisanne , Nand Ankita , Teng Mona , Qamra Aditi , Zhou Stanley , Kron Ken J. , Murison Alex , Hawley James R. , Fraser Michael , van der Kwast Theodorus H. , Raj Ganesh V. , He Housheng Hansen , Zwart Wilbert , Lupien Mathieu
Published: November 2023

pluripotent stem cell- and tissue state-specific transposable element families
Supplementary Table S25 from Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer
Authors: Grillo Giacomo , Keshavarzian Tina , Linder Simon , Arlidge Christopher , Mout Lisanne , Nand Ankita , Teng Mona , Qamra Aditi , Zhou Stanley , Kron Ken J. , Murison Alex , Hawley James R. , Fraser Michael , van der Kwast Theodorus H. , Raj Ganesh V. , He Housheng Hansen , Zwart Wilbert , Lupien Mathieu
Published: November 2023

List of gRNA sequences used in this article
Supplementary Table S20 from Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer
Authors: Grillo Giacomo , Keshavarzian Tina , Linder Simon , Arlidge Christopher , Mout Lisanne , Nand Ankita , Teng Mona , Qamra Aditi , Zhou Stanley , Kron Ken J. , Murison Alex , Hawley James R. , Fraser Michael , van der Kwast Theodorus H. , Raj Ganesh V. , He Housheng Hansen , Zwart Wilbert , Lupien Mathieu
Published: November 2023

Top 5% transcription factor cistromes enriched at reprogrammed transposable element families (CPC-GENE reprogrammed patients)
Supplementary Table S19 from Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer
Authors: Grillo Giacomo , Keshavarzian Tina , Linder Simon , Arlidge Christopher , Mout Lisanne , Nand Ankita , Teng Mona , Qamra Aditi , Zhou Stanley , Kron Ken J. , Murison Alex , Hawley James R. , Fraser Michael , van der Kwast Theodorus H. , Raj Ganesh V. , He Housheng Hansen , Zwart Wilbert , Lupien Mathieu
Published: November 2023

Clinical information Porto patients
Supplementary Table S18 from Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer
Authors: Grillo Giacomo , Keshavarzian Tina , Linder Simon , Arlidge Christopher , Mout Lisanne , Nand Ankita , Teng Mona , Qamra Aditi , Zhou Stanley , Kron Ken J. , Murison Alex , Hawley James R. , Fraser Michael , van der Kwast Theodorus H. , Raj Ganesh V. , He Housheng Hansen , Zwart Wilbert , Lupien Mathieu
Published: November 2023

Clinical information CPC-GENE patients
Supplementary Figure S1 from SHP2: A Pleiotropic Target at the Interface of Cancer and Its Microenvironment
Authors: Sodir Nicole M. , Pathria Gaurav , Adamkewicz Joanne I. , Kelley Elizabeth H. , Sudhamsu Jawahar , Merchant Mark , Chiarle Roberto , Maddalo Danilo
Published: November 2023

Allosteric inhibitor SHP099 (1), general pharmacophore (2) and subsequent reported allosteric SHP2 inhibitors (3-6).
Table S8 from Clinical Efficacy of ONC201 in H3K27M-Mutant Diffuse Midline Gliomas Is Driven by Disruption of Integrated Metabolic and Epigenetic Pathways
Authors: Venneti Sriram , Kawakibi Abed Rahman , Ji Sunjong , Waszak Sebastian M. , Sweha Stefan R. , Mota Mateus , Pun Matthew , Deogharkar Akash , Chung Chan , Tarapore Rohinton S. , Ramage Samuel , Chi Andrew , Wen Patrick Y. , Arrillaga-Romany Isabel , Batchelor Tracy T. , Butowski Nicholas A. , Sumrall Ashley , Shonka Nicole , Harrison Rebecca A. , de Groot John , Mehta Minesh , Hall Matthew D. , Daghistani Doured , Cloughesy Timothy F. , Ellingson Benjamin M. , Beccaria Kevin , Varlet Pascale , Kim Michelle M. , Umemura Yoshie , Garton Hugh , Franson Andrea , Schwartz Jonathan , Jain Rajan , Kachman Maureen , Baum Heidi , Burant Charles F. , Mottl Sophie L. , Cartaxo Rodrigo T. , John Vishal , Messinger Dana , Qin Tingting , Peterson Erik , Sajjakulnukit Peter , Ravi Karthik , Waugh Alyssa , Walling Dustin , Ding Yujie , Xia Ziyun , Schwendeman Anna , Hawes Debra , Yang Fusheng , Judkins Alexander R. , Wahl Daniel , Lyssiotis Costas A. , de la Nava Daniel , Alonso Marta M. , Eze Augustine , Spitzer Jasper , Schmidt Susanne V. , Duchatel Ryan J. , Dun Matthew D. , Cain Jason E. , Jiang Li , Stopka Sylwia A. , Baquer Gerard , Regan Michael S. , Filbin Mariella G. , Agar Nathalie Y.R. , Zhao Lili , Kumar-Sinha Chandan , Mody Rajen , Chinnaiyan Arul , Kurokawa Ryo , Pratt Drew , Yadav Viveka N. , Grill Jacques , Kline Cassie , Mueller Sabine , Resnick Adam , Nazarian Javad , Allen Joshua E. , Odia Yazmin , Gardner Sharon L. , Koschmann Carl
Published: November 2023

Expression values, Spearman’s correlation coefficient, and GSEA of genes associated with positive or negative correlation with radiographic response to ONC201 treatment.
Table S5 from Clinical Efficacy of ONC201 in H3K27M-Mutant Diffuse Midline Gliomas Is Driven by Disruption of Integrated Metabolic and Epigenetic Pathways
Authors: Venneti Sriram , Kawakibi Abed Rahman , Ji Sunjong , Waszak Sebastian M. , Sweha Stefan R. , Mota Mateus , Pun Matthew , Deogharkar Akash , Chung Chan , Tarapore Rohinton S. , Ramage Samuel , Chi Andrew , Wen Patrick Y. , Arrillaga-Romany Isabel , Batchelor Tracy T. , Butowski Nicholas A. , Sumrall Ashley , Shonka Nicole , Harrison Rebecca A. , de Groot John , Mehta Minesh , Hall Matthew D. , Daghistani Doured , Cloughesy Timothy F. , Ellingson Benjamin M. , Beccaria Kevin , Varlet Pascale , Kim Michelle M. , Umemura Yoshie , Garton Hugh , Franson Andrea , Schwartz Jonathan , Jain Rajan , Kachman Maureen , Baum Heidi , Burant Charles F. , Mottl Sophie L. , Cartaxo Rodrigo T. , John Vishal , Messinger Dana , Qin Tingting , Peterson Erik , Sajjakulnukit Peter , Ravi Karthik , Waugh Alyssa , Walling Dustin , Ding Yujie , Xia Ziyun , Schwendeman Anna , Hawes Debra , Yang Fusheng , Judkins Alexander R. , Wahl Daniel , Lyssiotis Costas A. , de la Nava Daniel , Alonso Marta M. , Eze Augustine , Spitzer Jasper , Schmidt Susanne V. , Duchatel Ryan J. , Dun Matthew D. , Cain Jason E. , Jiang Li , Stopka Sylwia A. , Baquer Gerard , Regan Michael S. , Filbin Mariella G. , Agar Nathalie Y.R. , Zhao Lili , Kumar-Sinha Chandan , Mody Rajen , Chinnaiyan Arul , Kurokawa Ryo , Pratt Drew , Yadav Viveka N. , Grill Jacques , Kline Cassie , Mueller Sabine , Resnick Adam , Nazarian Javad , Allen Joshua E. , Odia Yazmin , Gardner Sharon L. , Koschmann Carl
Published: November 2023

VST-transformed gene expression values for all samples and protein-coding genes.
Supplementary Figure S3 from Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer
Authors: Grillo Giacomo , Keshavarzian Tina , Linder Simon , Arlidge Christopher , Mout Lisanne , Nand Ankita , Teng Mona , Qamra Aditi , Zhou Stanley , Kron Ken J. , Murison Alex , Hawley James R. , Fraser Michael , van der Kwast Theodorus H. , Raj Ganesh V. , He Housheng Hansen , Zwart Wilbert , Lupien Mathieu
Published: November 2023

This figure showcases the entire molecular and clinical characterization of CPC-GENE and Porto patients' groups identified using transposable element families differentially enriched between pluripotent stem cells and benign prostate tissue states
Figure 5 from STX-478, a Mutant-Selective, Allosteric PI3Kα Inhibitor Spares Metabolic Dysfunction and Improves Therapeutic Response in PI3Kα-Mutant Xenografts
Authors: Buckbinder Leonard , St. Jean David J. , Tieu Trang , Ladd Brendon , Hilbert Brendan , Wang Weixue , Alltucker Jacob T. , Manimala Samantha , Kryukov Gregory V. , Brooijmans Natasja , Dowdell Gregory , Jonsson Philip , Huff Michael , Guzman-Perez Angel , Jackson Erica L. , Goncalves Marcus D. , Stuart Darrin D.
Published: November 2023

The efficacy of STX-478 is similar or superior to high-dose alpelisib across PI3Kα-mutant tumor xenografts while sparing insulin resistance (p.o., oral administration; q.d., daily). A, Final tumor volume percent change is represented for GP2d, Detroit 562, NCI-H1048, and HCC1954 CDX tumors. BrCa, breast cancer. B, Tumor volumes over time from PDX models (N = 3/group) harboring PI3Kα mutations in the kinase domain (ST1056: H1047R PI3Kα), kinase and helical domains (ST1799: E542K/H1065L PI3Kα), and helical domain (ST2652: E545K PI3Kα) treated with either vehicle, STX-478, or alpelisib. Statistical significance was calculated using two-way ANOVA and Dunnett multiple comparisons tests. End-of-study tumors were harvested 4 hours after the final dose, and pAKT (S473) was analyzed by Western blot. IsoSeq analysis of a tumor from model ST1799 showed that the E542K/H1065L PI3Kα mutations are in cis. AKT and pAKT (S473) were blotted separately, and a representative vinculin blot is shown.
Figure 1 from STX-478, a Mutant-Selective, Allosteric PI3Kα Inhibitor Spares Metabolic Dysfunction and Improves Therapeutic Response in PI3Kα-Mutant Xenografts
Authors: Buckbinder Leonard , St. Jean David J. , Tieu Trang , Ladd Brendon , Hilbert Brendan , Wang Weixue , Alltucker Jacob T. , Manimala Samantha , Kryukov Gregory V. , Brooijmans Natasja , Dowdell Gregory , Jonsson Philip , Huff Michael , Guzman-Perez Angel , Jackson Erica L. , Goncalves Marcus D. , Stuart Darrin D.
Published: November 2023

STX-478 binds a novel allosteric site on PI3Kα and achieves mutant selectivity through differential binding kinetics. A, The molecular structure of STX-478. B, Inhibition of enzyme activities of WT PI3Kα as well as kinase-domain and helical-domain mutant proteins by alpelisib and STX-478 showing the geometric mean and standard deviation. C, The 2.9Å X-ray structure of PI3Kα (p110 purple, p85 orange) with GDC-0077 (red spheres) bound in the ATP site and STX-478 (green spheres) bound in an allosteric site. D, Arrows indicate Cα (spheres) movements of ≥3Å between aligned H1047R (teal, Protein Data Bank 3HHM) and the STX-478–bound structure (purple). 3HHM lacks residues 941–952 for direct comparison. E, Detailed view of bound STX-478. Labeled residues significantly contribute to compound binding. F, SPR sensorgrams for STX-478 (top) and duvelisib (bottom) binding to PI3Kα H1047R–mutant protein. KD, kon, and koff values as determined by single-cycle kinetics SPR for binding to WT, H1047R-mutant, and E545K-mutant PI3Kα proteins are shown in the table below the sensorgrams.