bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Table S4 from Molecular and Pathologic Characterization of YAP1-Expressing Small Cell Lung Cancer Cell Lines Leads to Reclassification as SMARCA4-Deficient Malignancies
Authors: Ng Jin , Cai Ling , Girard Luc , Prall Owen W.J. , Rajan Neeha , Khoo Christine , Batrouney Ahida , Byrne David J. , Boyd Danielle K. , Kersbergen Ariena J. , Christie Michael , Minna John D. , Burr Marian L. , Sutherland Kate D.
Published: May 2024

Comparison of sequencing data between CCLE and UTSW.
Supplementary Tables S1-8 from Selective CDK7 Inhibition Suppresses Cell Cycle Progression and MYC Signaling While Enhancing Apoptosis in Therapy-resistant Estrogen Receptor–positive Breast Cancer
Authors: Guarducci Cristina , Nardone Agostina , Russo Douglas , Nagy Zsuzsanna , Heraud Capucine , Grinshpun Albert , Zhang Qi , Freelander Allegra , Leventhal Mathew Joseph , Feit Avery , Cohen Feit Gabriella , Feiglin Ariel , Liu Weihan , Hermida-Prado Francisco , Kesten Nikolas , Ma Wen , De Angelis Carmine , Morlando Antonio , O'Donnell Madison , Naumenko Sergey , Huang Shixia , Nguyen Quang-Dé , Huang Ying , Malorni Luca , Bergholz Johann S. , Zhao Jean J. , Fraenkel Ernest , Lim Elgene , Schiff Rachel , Shapiro Geoffrey I. , Jeselsohn Rinath
Published: May 2024

Table S1: IC50 data; Table S2: RPPA normalized raw data; Table S3: Differentially expressed analysis in all RNA-seq data; Table S4: Summary of statistical analysis results cell cycle; Table S5: Mutational landscape of the PDX1415 and PDX1526; Table S6: Focal copy number variations of the PDX1415 and PDX1526 models; Table S7: Beta score of the CRISPR/CAS9 KO screening; Table S8: Antibodies
Supplementary Figure S6 from Molecular and Pathologic Characterization of YAP1-Expressing Small Cell Lung Cancer Cell Lines Leads to Reclassification as SMARCA4-Deficient Malignancies
Authors: Ng Jin , Cai Ling , Girard Luc , Prall Owen W.J. , Rajan Neeha , Khoo Christine , Batrouney Ahida , Byrne David J. , Boyd Danielle K. , Kersbergen Ariena J. , Christie Michael , Minna John D. , Burr Marian L. , Sutherland Kate D.
Published: May 2024

mRNA expression of SMARCA4-UT associated genes and YAP1 IHC.
Supplementary Figure S3 from Molecular and Pathologic Characterization of YAP1-Expressing Small Cell Lung Cancer Cell Lines Leads to Reclassification as SMARCA4-Deficient Malignancies
Authors: Ng Jin , Cai Ling , Girard Luc , Prall Owen W.J. , Rajan Neeha , Khoo Christine , Batrouney Ahida , Byrne David J. , Boyd Danielle K. , Kersbergen Ariena J. , Christie Michael , Minna John D. , Burr Marian L. , Sutherland Kate D.
Published: May 2024

SCLC-specific markers are weak/lost in SMARCA4-deficient SCLC-Y cell lines.
Supplementary Figure S5 from Selective CDK7 Inhibition Suppresses Cell Cycle Progression and MYC Signaling While Enhancing Apoptosis in Therapy-resistant Estrogen Receptor–positive Breast Cancer
Authors: Guarducci Cristina , Nardone Agostina , Russo Douglas , Nagy Zsuzsanna , Heraud Capucine , Grinshpun Albert , Zhang Qi , Freelander Allegra , Leventhal Mathew Joseph , Feit Avery , Cohen Feit Gabriella , Feiglin Ariel , Liu Weihan , Hermida-Prado Francisco , Kesten Nikolas , Ma Wen , De Angelis Carmine , Morlando Antonio , O'Donnell Madison , Naumenko Sergey , Huang Shixia , Nguyen Quang-Dé , Huang Ying , Malorni Luca , Bergholz Johann S. , Zhao Jean J. , Fraenkel Ernest , Lim Elgene , Schiff Rachel , Shapiro Geoffrey I. , Jeselsohn Rinath
Published: May 2024

The combination of SY-1365 and fulvestrant inhibits proliferation and CDK7 targets in PDX1415-WT.
Supplementary Figure S1 from Selective CDK7 Inhibition Suppresses Cell Cycle Progression and MYC Signaling While Enhancing Apoptosis in Therapy-resistant Estrogen Receptor–positive Breast Cancer
Authors: Guarducci Cristina , Nardone Agostina , Russo Douglas , Nagy Zsuzsanna , Heraud Capucine , Grinshpun Albert , Zhang Qi , Freelander Allegra , Leventhal Mathew Joseph , Feit Avery , Cohen Feit Gabriella , Feiglin Ariel , Liu Weihan , Hermida-Prado Francisco , Kesten Nikolas , Ma Wen , De Angelis Carmine , Morlando Antonio , O'Donnell Madison , Naumenko Sergey , Huang Shixia , Nguyen Quang-Dé , Huang Ying , Malorni Luca , Bergholz Johann S. , Zhao Jean J. , Fraenkel Ernest , Lim Elgene , Schiff Rachel , Shapiro Geoffrey I. , Jeselsohn Rinath
Published: May 2024

On-target effect of SY-1365 and modulation of WT/DOX-Y537S mutant MCF7 cells gene expression after SY-1365 treatment over time.
Supplementary Figure S5 from Radiotherapy Enhances Metastasis Through Immune Suppression by Inducing PD-L1 and MDSC in Distal Sites
Authors: Hou Yuzhu , Yang Kaiting , Wang Liangliang , Wang Jiaai , Huang Xiaona , Piffkó András , Luo Sean Z. , Yu Xinshuang , Rao Enyu , Martinez Carlos , Bugno Jason , Mack Matthias , Vokes Everett E. , Pitroda Sean P. , Chmura Steven J. , Weichselbaum Ralph R. , Liang Hua Laura
Published: May 2024

Supplementary figure 5. IFNb concentration not increased in distal tissues. PD-L1 induction in
G-MDSCs is mediated by IFN-I signaling
Supplementary Table S2 from Systemic Biological Mechanisms of Neurocognitive Dysfunction in Long-Term Survivors of Childhood Hodgkin Lymphoma
Authors: Williams AnnaLynn M. , Liu Wei , Ehrhardt Matthew J. , Mirzaei Salehabadi Sedigheh , Panoskaltsis-Mortari Angela , Phillips Nicholas S. , Mulrooney Daniel A. , Flerlage Jamie E. , Yasui Yutaka , Srivastava Deokumar , Robison Leslie L. , Hudson Melissa M. , Ness Kirsten K. , Sabin Noah D. , Krull Kevin R.
Published: May 2024

Associations between clinical, demographic, and treatment exposures and serum biomarkers among survivors of Hodgkin lymphoma.
Supplementary Material 1 from Phase I/II Study of Combined BCL-xL and MEK Inhibition with Navitoclax and Trametinib in KRAS or NRAS Mutant Advanced Solid Tumors
Authors: Corcoran Ryan B. , Do Khanh T. , Kim Jeong E. , Cleary James M. , Parikh Aparna R. , Yeku Oladapo O. , Xiong Niya , Weekes Colin D. , Veneris Jennifer , Ahronian Leanne G. , Mauri Gianluca , Tian Jun , Norden Bryanna L. , Michel Alexa G. , Van Seventer Emily E. , Siravegna Giulia , Camphausen Kyle , Chi Gary , Fetter Isobel J. , Brugge Joan S. , Chen Helen , Takebe Naoko , Penson Richard T. , Juric Dejan , Flaherty Keith T. , Sullivan Ryan J. , Clark Jeffrey W. , Heist Rebecca S. , Matulonis Ursula A. , Liu Joyce F. , Shapiro Geoffrey I.
Published: May 2024

Supplementary Table S1, Supplementary Table S2, Supplementary Figure S1
Supplementary Figure 2 from Optimizing Cervical Target Volume in Patients with Nasopharyngeal Cancer Based On Nodal Drainage Distance
Authors: Liu Yang , Yan Wenbin , Hu Chaosu , Huang Xiaodong , Wang Kai , Qu Yuan , Chen Xuesong , Wu Runye , Zhang Ye , Zhang Jianghu , Luo Jingwei , Li Yexiong , Wang Jingbo , Yi Junlin
Published: May 2024

The number and percentage of caudally located LNs included in each maximum diameter (MD) range.
Supplementary Table S4 from Improved Risk-Stratification Scheme for Mismatch-Repair Proficient Stage II Colorectal Cancers Using the Digital Pathology Biomarker QuantCRC
Authors: Wu Christina , Pai Reetesh K. , Kosiorek Heidi , Banerjee Imon , Pfeiffer Ashlyn , Hagen Catherine E. , Hartley Christopher P. , Graham Rondell P. , Sonbol Mohamad B. , Bekaii-Saab Tanios , Xie Hao , Sinicrope Frank A. , Patel Bhavik , Westerling-Bui Thomas , Shivji Sameer , Conner James , Swallow Carol , Savage Paul , Cyr David P. , Kirsch Richard , Pai Rish K.
Published: May 2024

Supplementary Table S4. Clinical and Pathologic features in patients that were concordant or discordant in the ASCO and QuantCRC-Integrated schemes.
Supplementary Table S5 from Improved Innate Immune Function in Patients with Chronic Lymphocytic Leukemia Treated with Targeted Therapy in Clinical Trials
Authors: Svanberg Teglgaard Rebecca , Marquart Hanne Vibeke , Hartling Hans Jakob , Bay Jakob Thaning , da Cunha-Bang Caspar , Brieghel Christian , Faitová Tereza , Enggaard Lisbeth , Kater Arnon P. , Levin Mark-David , Kersting Sabina , Ostrowski Sisse Rye , Niemann Carsten U.
Published: May 2024

Supplementary Table S5. Baseline patient- and disease related characteristics for patients with or without history of infections.
Supplemental Table 4 from Broad Next-Generation Integrated Sequencing of Myelofibrosis Identifies Disease-Specific and Age-Related Genomic Alterations
Authors: Kandarpa Malathi , Robinson Dan , Wu Yi-Mi , Qin Tingting , Pettit Kristen , Li Qing , Luker Gary , Sartor Maureen , Chinnaiyan Arul , Talpaz Moshe
Published: May 2024

Supplemental Table 4. Subject identifiers and designated disease
Supplementary Figure S4 from Improved Innate Immune Function in Patients with Chronic Lymphocytic Leukemia Treated with Targeted Therapy in Clinical Trials
Authors: Svanberg Teglgaard Rebecca , Marquart Hanne Vibeke , Hartling Hans Jakob , Bay Jakob Thaning , da Cunha-Bang Caspar , Brieghel Christian , Faitová Tereza , Enggaard Lisbeth , Kater Arnon P. , Levin Mark-David , Kersting Sabina , Ostrowski Sisse Rye , Niemann Carsten U.
Published: May 2024

Supplementary Figure S4. Changes in immune cell activation marker expression during targeted treatment.
Supplemental Table 2 from Broad Next-Generation Integrated Sequencing of Myelofibrosis Identifies Disease-Specific and Age-Related Genomic Alterations
Authors: Kandarpa Malathi , Robinson Dan , Wu Yi-Mi , Qin Tingting , Pettit Kristen , Li Qing , Luker Gary , Sartor Maureen , Chinnaiyan Arul , Talpaz Moshe
Published: May 2024

Supplemental Table 2. Gene Variants in MF
Supplemental Figure 7 from Broad Next-Generation Integrated Sequencing of Myelofibrosis Identifies Disease-Specific and Age-Related Genomic Alterations
Authors: Kandarpa Malathi , Robinson Dan , Wu Yi-Mi , Qin Tingting , Pettit Kristen , Li Qing , Luker Gary , Sartor Maureen , Chinnaiyan Arul , Talpaz Moshe
Published: May 2024

Supplemental Figure 7. Differential gene expression in MF with Spleen size >7 cm vs <7 cm. Panel A is a heatmap of the differentially expressed genes, 554 genes upregulated in MF with large spleen and 303 genes downregulated. Panel B is Volcano plot showing log fold change and p value of the genes depicted in A. Panel C shows RNA enrichment analysis shows GO pathways that are down regulated (green) and upregulated (red) in MF with spleen enlargement.
Supplementary Tables 1 from Improvements in Posttransplant Outcomes Over Two Decades in Older Patients with Acute Myeloid Leukemia in the EBMT ALWP Study
Authors: Bazarbachi Ali , Labopin Myriam , Moukalled Nour , Kröger Nicolaus , Rautenberg Christina , Schetelig Johannes , Finke Jürgen , Blau Igor Wolfgang , Blaise Didier , Stelljes Matthias , Eder Matthias , Platzbecker Uwe , Dreger Peter , Bethge Wolfgang , Tischer Johanna , Burns David , Sengeloev Henrik , Brissot Eolia , Giebel Sebastian , Nagler Arnon , Ciceri Fabio , Mohty Mohamad
Published: May 2024

Univariate and multivariate analysis for subgroup with active disease
Supplemental Figure 5 from Broad Next-Generation Integrated Sequencing of Myelofibrosis Identifies Disease-Specific and Age-Related Genomic Alterations
Authors: Kandarpa Malathi , Robinson Dan , Wu Yi-Mi , Qin Tingting , Pettit Kristen , Li Qing , Luker Gary , Sartor Maureen , Chinnaiyan Arul , Talpaz Moshe
Published: May 2024

Supplemental Figure 5. RNAseq gene expression of select genes. Expression values for differentially expressed genes in both CD34 cell population and mononuclear cell compartment from MF and ET/PV/PrePMF cohorts. Mean and SEM is plotted of the RPKM values for each data set are plotted. ADGRL4 and DNASE1L3 are downregulated in MF and PLEKGH4B, HSPG2, MAMDC2 an DPYSL3 are upregulated in MF. Fold change and P value for the differentially expressed genes are summarized in the table.
Supplementary Video S9 from Mesothelin CAR T Cells Secreting Anti-FAP/Anti-CD3 Molecules Efficiently Target Pancreatic Adenocarcinoma and its Stroma
Authors: Wehrli Marc , Guinn Samantha , Birocchi Filippo , Kuo Adam , Sun Yi , Larson Rebecca C. , Almazan Antonio J. , Scarfò Irene , Bouffard Amanda A. , Bailey Stefanie R. , Anekal Praju Vikas , Montero Llopis Paula , Nieman Linda T. , Song Yuhui , Xu Katherine H. , Berger Trisha R. , Kann Michael C. , Leick Mark B. , Silva Harrison , Salas-Benito Diego , Kienka Tamina , Grauwet Korneel , Armstrong Todd D. , Zhang Rui , Zhu Qingfeng , Fu Juan , Schmidts Andrea , Korell Felix , Jan Max , Choi Bryan D. , Liss Andrew S. , Boland Genevieve M. , Ting David T. , Burkhart Richard A. , Jenkins Russell W. , Zheng Lei , Jaffee Elizabeth M. , Zimmerman Jacquelyn W. , Maus Marcela V.
Published: May 2024

Supplementary Video S9. UTD T cells on AsPC1 + CAF
Supplementary Methods 1 from Mesothelin CAR T Cells Secreting Anti-FAP/Anti-CD3 Molecules Efficiently Target Pancreatic Adenocarcinoma and its Stroma
Authors: Wehrli Marc , Guinn Samantha , Birocchi Filippo , Kuo Adam , Sun Yi , Larson Rebecca C. , Almazan Antonio J. , Scarfò Irene , Bouffard Amanda A. , Bailey Stefanie R. , Anekal Praju Vikas , Montero Llopis Paula , Nieman Linda T. , Song Yuhui , Xu Katherine H. , Berger Trisha R. , Kann Michael C. , Leick Mark B. , Silva Harrison , Salas-Benito Diego , Kienka Tamina , Grauwet Korneel , Armstrong Todd D. , Zhang Rui , Zhu Qingfeng , Fu Juan , Schmidts Andrea , Korell Felix , Jan Max , Choi Bryan D. , Liss Andrew S. , Boland Genevieve M. , Ting David T. , Burkhart Richard A. , Jenkins Russell W. , Zheng Lei , Jaffee Elizabeth M. , Zimmerman Jacquelyn W. , Maus Marcela V.
Published: May 2024

Supplementary Methods
Supplementary Figure S1 from FDG PET/CT Imaging 1 Week after a Single Dose of Pembrolizumab Predicts Treatment Response in Patients with Advanced Melanoma
Authors: Anderson Thomas M. , Chang Bryan H. , Huang Alexander C. , Xu Xiaowei , Yoon Daniel , Shang Catherine G. , Mick Rosemarie , Schubert Erin , McGettigan Suzanne , Kreider Kristin , Xu Wei , Wherry E. John , Schuchter Lynn M. , Amaravadi Ravi K. , Mitchell Tara C. , Farwell Michael D.
Published: May 2024

Supplementary Figure S1. Analysis of Ki67+ CD8 T cells in peripheral blood.
Data from Targeting Dendritic Cell Dysfunction to Circumvent Anti-PD1 Resistance in Head and Neck Cancer
Authors: Saito Shin , Kono Michihisa , Nguyen Hoang C.B. , Egloff Ann Marie , Messier Cameron , Lizotte Patrick , Paweletz Cloud , Adkins Douglas , Uppaluri Ravindra
Published: May 2024

AbstractPurpose:
Neoadjuvant anti-PD1 (aPD1) therapies are being explored in surgically resectable head and neck squamous cell carcinoma (HNSCC). Encouraging responses have been observed, but further insights into the mechanisms underlying resistance and approaches to improve responses are needed.
Experimental Design:
We integrated data from syngeneic mouse oral carcinoma (MOC) models and neoadjuvant pembrolizumab HNSCC patient tumor RNA-sequencing data to explore the mechanism of aPD1 resistance. Tumors and tumor-draining lymph nodes (DLN) from MOC models were analyzed for antigen-specific priming. CCL5 expression was enforced in an aPD1-resistant model.
Results:
An aPD1-resistant mouse model showed poor priming in the tumor DLN due to type 1 conventional dendritic cell (cDC1) dysfunction, which correlated with exhausted and poorly responsive antigen-specific T cells. Tumor microenvironment analysis also showed decreased cDC1 in aPD1-resistant tumors compared with sensitive tumors. Following neoadjuvant aPD1 therapy, pathologic responses in patients also positively correlated with baseline transcriptomic cDC1 signatures. In an aPD1-resistant model, intratumoral cDC1 vaccine was sufficient to restore aPD1 response by enhancing T-cell infiltration and increasing antigen-specific responses with improved tumor control. Mechanistically, CCL5 expression significantly correlated with neoadjuvant aPD1 response and enforced expression of CCL5 in an aPD1-resistant model, enhanced cDC1 tumor infiltration, restored antigen-specific responses, and recovered sensitivity to aPD1 treatment.
Conclusions:
These data highlight the contribution of tumor-infiltrating cDC1 in HNSCC aPD1 response and approaches to enhance cDC1 infiltration and function that may circumvent aPD1 resistance in patients with HNSCC.
Data from Breast Cancer Index and Prediction of Extended Aromatase Inhibitor Therapy Benefit in Hormone Receptor-Positive Breast Cancer from the NRG Oncology/NSABP B-42 Trial
Authors: Mamounas Eleftherios P. , Bandos Hanna , Rastogi Priya , Zhang Yi , Treuner Kai , Lucas Peter C. , Geyer Charles E. , Fehrenbacher Louis , Chia Stephen K. , Brufsky Adam M. , Walshe Janice M. , Soori Gamini S. , Dakhil Shaker , Paik Soonmyung , Swain Sandra M. , Sgroi Dennis C. , Schnabel Catherine A. , Wolmark Norman
Published: May 2024

AbstractPurpose:
BCI (H/I) has been shown to predict extended endocrine therapy (EET) benefit. We examined BCI (H/I) for EET benefit prediction in NSABP B-42, which evaluated extended letrozole therapy (ELT) in patients with hormone receptor-positive breast cancer after 5 years of ET.
Experimental Design:
A stratified Cox model was used to analyze RFI as the primary endpoint, with DR, BCFI, and DFS as secondary endpoints. Because of a nonproportional effect of ELT on DR, time-dependent analyses were performed.
Results:
The translational cohort included 2,178 patients (45% BCI (H/I)-High, 55% BCI (H/I)-Low). ELT showed an absolute 10-year RFI benefit of 1.6% (P = 0.10), resulting in an underpowered primary analysis (50% power). ELT benefit and BCI (H/I) did not show a significant interaction for RFI (BCI (H/I)-Low: 10 years absolute benefit 1.1% [HR, 0.70; 95% confidence interval (CI), 0.43–1.12; P = 0.13]; BCI (H/I)-High: 2.4% [HR, 0.83; 95% CI, 0.55–1.26; P = 0.38]; Pinteraction = 0.56). Time-dependent DR analysis showed that after 4 years, BCI (H/I)-High patients had significant ELT benefit (HR = 0.29; 95% CI, 0.12–0.69; P < 0.01), whereas BCI (H/I)-Low patients were less likely to benefit (HR, 0.68; 95% CI, 0.33–1.39; P = 0.29; Pinteraction = 0.14). Prediction of ELT benefit by BCI (H/I) was more apparent in the HER2- subset after 4 years (ELT-by-BCI (H/I) Pinteraction = 0.04).
Conclusions:
BCI (H/I)-High versus BCI (H/I)-Low did not show a statistically significant difference in ELT benefit for the primary endpoint (RFI). However, in time-dependent DR analysis, BCI (H/I)-High patients experienced statistically significant benefit from ELT after 4 years, whereas (H/I)-Low patients did not. Because BCI (H/I) has been validated as a predictive marker of EET benefit in other trials, additional follow-up may enable further characterization of BCI's predictive ability.
Data from Belzutifan for von Hippel–Lindau Disease: Pancreatic Lesion Population of the Phase 2 LITESPARK-004 Study
Authors: Else Tobias , Jonasch Eric , Iliopoulos Othon , Beckermann Kathryn E. , Narayan Vivek , Maughan Benjamin L. , Oudard Stephane , Maranchie Jodi K. , Iversen Ane B. , Goldberg Cynthia M. , Fu Wei , Perini Rodolfo F. , Liu Yanfang , Linehan W. Marston , Srinivasan Ramaprasad
Published: May 2024

AbstractPurpose:
Primary analysis of the ongoing, single-arm, phase 2 LITESPARK-004 study (NCT03401788) showed clinically meaningful antitumor activity in von Hippel–Lindau (VHL) disease–associated renal cell carcinoma (RCC) and other neoplasms with belzutifan treatment. We describe results of belzutifan treatment for VHL disease–associated pancreatic lesions [pancreatic neuroendocrine tumors (pNET) and serous cystadenomas].
Patients and Methods:
Adults with VHL diagnosis based on germline VHL alteration, ≥1 measurable RCC tumor, no renal tumor >3 cm or other VHL neoplasm requiring immediate surgery, Eastern Cooperative Oncology Group performance status of 0 or 1, and no prior systemic anticancer treatment received belzutifan 120 mg once daily. End points included objective response rate (ORR), duration of response (DOR), progression-free survival (PFS), and linear growth rate (LGR) in all pancreatic lesions and pNETs per RECIST version 1.1 by independent review committee, and safety.
Results:
All 61 enrolled patients (100%) had ≥1 pancreatic lesion and 22 (36%) had ≥1 pNET measurable at baseline. Median follow-up was 37.8 months (range, 36.1–46.1). ORR was 84% [51/61; 17 complete responses (CR)] in pancreatic lesions and 91% (20/22; 7 CRs) in pNETs. Median DOR and median PFS were not reached in pancreatic lesions or pNETs. After starting treatment, median LGR for pNETs was –4.2 mm per year (range, –7.9 to –0.8). Eleven patients (18%) had ≥1 grade 3 treatment-related adverse event (AE). No grade 4 or 5 treatment-related AEs occurred.
Conclusions:
Belzutifan continued to show robust activity and manageable safety in VHL disease–associated pNETs.
Data from Systemic Biological Mechanisms of Neurocognitive Dysfunction in Long-Term Survivors of Childhood Hodgkin Lymphoma
Authors: Williams AnnaLynn M. , Liu Wei , Ehrhardt Matthew J. , Mirzaei Salehabadi Sedigheh , Panoskaltsis-Mortari Angela , Phillips Nicholas S. , Mulrooney Daniel A. , Flerlage Jamie E. , Yasui Yutaka , Srivastava Deokumar , Robison Leslie L. , Hudson Melissa M. , Ness Kirsten K. , Sabin Noah D. , Krull Kevin R.
Published: May 2024

AbstractPurpose:
Hodgkin lymphoma (HL) survivors experience neurocognitive impairment despite receiving no central nervous system–directed therapy, though little is known about the underlying mechanisms.
Experimental Design:
HL survivors (n = 197) and age-, sex- and race/ethnicity frequency-matched community controls (n = 199) underwent standardized neurocognitive testing, and serum collection. Luminex multiplex or ELISA assays measured markers of inflammation and oxidative stress. Linear regression models compared biomarker concentrations between survivors and controls and with neurocognitive outcomes, adjusting for age, sex, race, body mass index, anti-inflammatory medication, and recent infections.
Results:
HL survivors [mean (SD) current age 36 (8) years, 22 (8) years after diagnosis] demonstrated higher concentrations of interleukin-6 (IL6), high-sensitivity c-reactive protein (hs-CRP), oxidized low-density lipoprotein, and glutathione peroxidase (GPx), compared with controls (P’s < 0.001). Among survivors, higher concentrations of IL6 were associated with worse visuomotor processing speed (P = 0.046). hs-CRP ≥3 mg/L was associated with worse attention, processing speed, memory, and executive function (P’s < 0.05). Higher concentrations of malondialdehyde were associated with worse focused attention and visual processing speed (P’s < 0.05). Homocysteine was associated with worse short-term recall (P = 0.008). None of these associations were statistically significant among controls. Among survivors, hs-CRP partially mediated associations between cardiovascular or endocrine conditions and visual processing speed, whereas IL6 partially mediated associations between pulmonary conditions and visuomotor processing speed.
Conclusions:
Neurocognitive function in long-term survivors of HL appears to be associated with inflammation and oxidative stress, both representing potential targets for future intervention trials.
Supplementary Figure S9 from Jak2V617F Reversible Activation Shows Its Essential Requirement in Myeloproliferative Neoplasms
Authors: Dunbar Andrew J. , Bowman Robert L. , Park Young C. , O'Connor Kavi , Izzo Franco , Myers Robert M. , Karzai Abdul , Zaroogian Zachary , Kim Won Jun , Fernández-Maestre Inés , Waarts Michael R. , Nazir Abbas , Xiao Wenbin , Codilupi Tamara , Brodsky Max , Farina Mirko , Cai Louise , Cai Sheng F. , Wang Benjamin , An Wenbin , Yang Julie L. , Mowla Shoron , Eisman Shira E. , Hanasoge Somasundara Amritha Varshini , Glass Jacob L. , Mishra Tanmay , Houston Remie , Guzzardi Emily , Martinez Benitez Anthony R. , Viny Aaron D. , Koche Richard P. , Meyer Sara C. , Landau Dan A. , Levine Ross L.
Published: May 2024

Phenotypic characterization and Jak2V617F oncogenic dependency in the setting of concomitant Tet2 loss
Supplementary Figure S5 from Jak2V617F Reversible Activation Shows Its Essential Requirement in Myeloproliferative Neoplasms
Authors: Dunbar Andrew J. , Bowman Robert L. , Park Young C. , O'Connor Kavi , Izzo Franco , Myers Robert M. , Karzai Abdul , Zaroogian Zachary , Kim Won Jun , Fernández-Maestre Inés , Waarts Michael R. , Nazir Abbas , Xiao Wenbin , Codilupi Tamara , Brodsky Max , Farina Mirko , Cai Louise , Cai Sheng F. , Wang Benjamin , An Wenbin , Yang Julie L. , Mowla Shoron , Eisman Shira E. , Hanasoge Somasundara Amritha Varshini , Glass Jacob L. , Mishra Tanmay , Houston Remie , Guzzardi Emily , Martinez Benitez Anthony R. , Viny Aaron D. , Koche Richard P. , Meyer Sara C. , Landau Dan A. , Levine Ross L.
Published: May 2024

Effects of Jak2V617F deletion on MPN stem cell fitness and disease transplantability
Table S5 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Authors: An Minae , Mehta Arnav , Min Byung Hoon , Heo You Jeong , Wright Samuel J. , Parikh Milan , Bi Lynn , Lee Hyuk , Kim Tae Jun , Lee Song-Yi , Moon Jeonghyeon , Park Ryan J. , Strickland Matthew R. , Park Woong-Yang , Kang Won Ki , Kim Kyoung-Mee , Kim Seung Tae , Klempner Samuel J. , Lee Jeeyun
Published: May 2024

Significant covarying programs
Table S2 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Authors: An Minae , Mehta Arnav , Min Byung Hoon , Heo You Jeong , Wright Samuel J. , Parikh Milan , Bi Lynn , Lee Hyuk , Kim Tae Jun , Lee Song-Yi , Moon Jeonghyeon , Park Ryan J. , Strickland Matthew R. , Park Woong-Yang , Kang Won Ki , Kim Kyoung-Mee , Kim Seung Tae , Klempner Samuel J. , Lee Jeeyun
Published: May 2024

Adverse events on single arm sequential CAPOX and pembrolizumab in advanced gastric cancer.
Figure S8 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Authors: An Minae , Mehta Arnav , Min Byung Hoon , Heo You Jeong , Wright Samuel J. , Parikh Milan , Bi Lynn , Lee Hyuk , Kim Tae Jun , Lee Song-Yi , Moon Jeonghyeon , Park Ryan J. , Strickland Matthew R. , Park Woong-Yang , Kang Won Ki , Kim Kyoung-Mee , Kim Seung Tae , Klempner Samuel J. , Lee Jeeyun
Published: May 2024

Figure S8. Copy number profiles of all epithelial cells from each patient’s samples inferred using inferCNV.
Figure S6 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Authors: An Minae , Mehta Arnav , Min Byung Hoon , Heo You Jeong , Wright Samuel J. , Parikh Milan , Bi Lynn , Lee Hyuk , Kim Tae Jun , Lee Song-Yi , Moon Jeonghyeon , Park Ryan J. , Strickland Matthew R. , Park Woong-Yang , Kang Won Ki , Kim Kyoung-Mee , Kim Seung Tae , Klempner Samuel J. , Lee Jeeyun
Published: May 2024

Figure S6. (A) UMAP embedding of single cell transcriptomes obtained from all
samples in this trial. Labeled are canonical cell types separated by tumor v.s.
normal tissue, and by timepoint. (B) Heatmap and (C) UMAP embeddings showing
marker gene expression for broad cell types in (A). (D) Broad cell type composition
per sample across tumor and normal tissue. (E) Cell type proportions from scSeq
data by timepoint in tumor and normal tissue excluding HER2+ patients. (F) Cell
type proportions from scSeq data by timepoint and TCGA classification excluding
HER2+ patients.
Figure S23 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Authors: An Minae , Mehta Arnav , Min Byung Hoon , Heo You Jeong , Wright Samuel J. , Parikh Milan , Bi Lynn , Lee Hyuk , Kim Tae Jun , Lee Song-Yi , Moon Jeonghyeon , Park Ryan J. , Strickland Matthew R. , Park Woong-Yang , Kang Won Ki , Kim Kyoung-Mee , Kim Seung Tae , Klempner Samuel J. , Lee Jeeyun
Published: May 2024

Figure S23. Heatmaps showing the number of significant inferred ligandreceptor
interactions between major cell types using CellPhoneDB on
scRNAseq data in (A) normal, (B) baseline tumor, (C) post-chemotherapy (FU1)
tumor and (D) post-immunotherapy (FU2) tumor samples.
Figure S17 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Authors: An Minae , Mehta Arnav , Min Byung Hoon , Heo You Jeong , Wright Samuel J. , Parikh Milan , Bi Lynn , Lee Hyuk , Kim Tae Jun , Lee Song-Yi , Moon Jeonghyeon , Park Ryan J. , Strickland Matthew R. , Park Woong-Yang , Kang Won Ki , Kim Kyoung-Mee , Kim Seung Tae , Klempner Samuel J. , Lee Jeeyun
Published: May 2024

Figure S17. Heatmap showing pairwise correlation of gene program activities
across all patient samples post-immunotherapy (FU2) using the 90th percentile
of patient-level program activity in epithelial, myeloid, T, NK and stromal cells.
Hierarchical clustering was performed to identify clusters of co-varying proteins.
Figure S16 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Authors: An Minae , Mehta Arnav , Min Byung Hoon , Heo You Jeong , Wright Samuel J. , Parikh Milan , Bi Lynn , Lee Hyuk , Kim Tae Jun , Lee Song-Yi , Moon Jeonghyeon , Park Ryan J. , Strickland Matthew R. , Park Woong-Yang , Kang Won Ki , Kim Kyoung-Mee , Kim Seung Tae , Klempner Samuel J. , Lee Jeeyun
Published: May 2024

Figure S16. Heatmap showing pairwise correlation of gene program activities
across all patient samples post-chemotherapy (FU1) using the 90th percentile of
patient-level program activity in epithelial, myeloid, T, NK and stromal cells.
Hierarchical clustering was performed to identify clusters of co-varying proteins.
Figure S14 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Authors: An Minae , Mehta Arnav , Min Byung Hoon , Heo You Jeong , Wright Samuel J. , Parikh Milan , Bi Lynn , Lee Hyuk , Kim Tae Jun , Lee Song-Yi , Moon Jeonghyeon , Park Ryan J. , Strickland Matthew R. , Park Woong-Yang , Kang Won Ki , Kim Kyoung-Mee , Kim Seung Tae , Klempner Samuel J. , Lee Jeeyun
Published: May 2024

Figure S14. cNMF was performed on epithelial cells at baseline. Shown is the
mean usage of each cNMF gene program in the epithelial cells of fast and slow
progressing patients.
Figure S13 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Authors: An Minae , Mehta Arnav , Min Byung Hoon , Heo You Jeong , Wright Samuel J. , Parikh Milan , Bi Lynn , Lee Hyuk , Kim Tae Jun , Lee Song-Yi , Moon Jeonghyeon , Park Ryan J. , Strickland Matthew R. , Park Woong-Yang , Kang Won Ki , Kim Kyoung-Mee , Kim Seung Tae , Klempner Samuel J. , Lee Jeeyun
Published: May 2024

Figure S13. Boxplots showing usage of epithelial cNMF programs in epithelial
cells of fast and slow progressors (A) post-chemotherapy (FU1) and (B) postimmunotherapy
(FU2).
Supplementary figure S1 from TREX1 Inactivation Unleashes Cancer Cell STING–Interferon Signaling and Promotes Antitumor Immunity
Authors: Tani Tetsuo , Mathsyaraja Haritha , Campisi Marco , Li Ze-Hua , Haratani Koji , Fahey Caroline G. , Ota Keiichi , Mahadevan Navin R. , Shi Yingxiao , Saito Shin , Mizuno Kei , Thai Tran C. , Sasaki Nobunari , Homme Mizuki , Yusuf Choudhury Fabliha B. , Kashishian Adam , Panchal Jipsa , Wang Min , Wolf Benjamin J. , Barbie Thanh U. , Paweletz Cloud P. , Gokhale Prafulla C. , Liu David , Uppaluri Ravindra , Kitajima Shunsuke , Cain Jennifer , Barbie David A.
Published: May 2024

Supplementary figureS1 shows the figures related to Figure 1.
Supplementary Table S1 from TREX1 Inactivation Unleashes Cancer Cell STING–Interferon Signaling and Promotes Antitumor Immunity
Authors: Tani Tetsuo , Mathsyaraja Haritha , Campisi Marco , Li Ze-Hua , Haratani Koji , Fahey Caroline G. , Ota Keiichi , Mahadevan Navin R. , Shi Yingxiao , Saito Shin , Mizuno Kei , Thai Tran C. , Sasaki Nobunari , Homme Mizuki , Yusuf Choudhury Fabliha B. , Kashishian Adam , Panchal Jipsa , Wang Min , Wolf Benjamin J. , Barbie Thanh U. , Paweletz Cloud P. , Gokhale Prafulla C. , Liu David , Uppaluri Ravindra , Kitajima Shunsuke , Cain Jennifer , Barbie David A.
Published: May 2024

Sup. Table S1 shows sequence for qRT-PCR primers and sgRNAs
Supplementary Table S6 from Pan-Cancer Comparative and Integrative Analyses of Driver Alterations Using Japanese and International Genomic Databases
Authors: Horie Sara , Saito Yuki , Kogure Yasunori , Mizuno Kota , Ito Yuta , Tabata Mariko , Kanai Takanori , Murakami Koichi , Koya Junji , Kataoka Keisuke
Published: May 2024

Details of clinically actionable alterations with OncoKB evidence level 1
Supplementary Table 5 from Long-term Multimodal Recording Reveals Epigenetic Adaptation Routes in Dormant Breast Cancer Cells
Authors: Rosano Dalia , Sofyali Emre , Dhiman Heena , Ghirardi Chiara , Ivanoiu Diana , Heide Timon , Vingiani Andrea , Bertolotti Alessia , Pruneri Giancarlo , Canale Eleonora , Dewhurst Hannah F. , Saha Debjani , Slaven Neil , Barozzi Iros , Li Tong , Zemlyanskiy Grigory , Phillips Henry , James Chela , Győrffy Balázs , Lynn Claire , Cresswell George D. , Rehman Farah , Noberini Roberta , Bonaldi Tiziana , Sottoriva Andrea , Magnani Luca
Published: May 2024

Differentially expressed genes for MCF7: AI (-E2) latency and dormancy samples Vs POT; awakening Vs Dormancy samples
Supplementary Table 4 from Long-term Multimodal Recording Reveals Epigenetic Adaptation Routes in Dormant Breast Cancer Cells
Authors: Rosano Dalia , Sofyali Emre , Dhiman Heena , Ghirardi Chiara , Ivanoiu Diana , Heide Timon , Vingiani Andrea , Bertolotti Alessia , Pruneri Giancarlo , Canale Eleonora , Dewhurst Hannah F. , Saha Debjani , Slaven Neil , Barozzi Iros , Li Tong , Zemlyanskiy Grigory , Phillips Henry , James Chela , Győrffy Balázs , Lynn Claire , Cresswell George D. , Rehman Farah , Noberini Roberta , Bonaldi Tiziana , Sottoriva Andrea , Magnani Luca
Published: May 2024

Differentially expressed genes for MCF7 Untreated samples Vs POT
Supplementary Table 3 from Long-term Multimodal Recording Reveals Epigenetic Adaptation Routes in Dormant Breast Cancer Cells
Authors: Rosano Dalia , Sofyali Emre , Dhiman Heena , Ghirardi Chiara , Ivanoiu Diana , Heide Timon , Vingiani Andrea , Bertolotti Alessia , Pruneri Giancarlo , Canale Eleonora , Dewhurst Hannah F. , Saha Debjani , Slaven Neil , Barozzi Iros , Li Tong , Zemlyanskiy Grigory , Phillips Henry , James Chela , Győrffy Balázs , Lynn Claire , Cresswell George D. , Rehman Farah , Noberini Roberta , Bonaldi Tiziana , Sottoriva Andrea , Magnani Luca
Published: May 2024

GeoMx data
Supplementary Figure S6 from Acquired Cross-Resistance in Small Cell Lung Cancer due to Extrachromosomal DNA Amplification of MYC Paralogs
Authors: Pal Choudhuri Shreoshi , Girard Luc , Lim Jun Yi Stanley , Wise Jillian F. , Freitas Braeden , Yang Di , Wong Edmond , Hamilton Seth , Chien Victor D. , Kim Yoon Jung , Gilbreath Collin , Zhong Jun , Phat Sarah , Myers David T. , Christensen Camilla L. , Mazloom-Farsibaf Hanieh , Stanzione Marcello , Wong Kwok-Kin , Hung Yin P. , Farago Anna F. , Meador Catherine B. , Dyson Nicholas J. , Lawrence Michael S. , Wu Sihan , Drapkin Benjamin J.
Published: May 2024

Levels of ecMYC in untreated and treated MGH1518-3A xenografts
Supplementary Figure S3 from Long-term Multimodal Recording Reveals Epigenetic Adaptation Routes in Dormant Breast Cancer Cells
Authors: Rosano Dalia , Sofyali Emre , Dhiman Heena , Ghirardi Chiara , Ivanoiu Diana , Heide Timon , Vingiani Andrea , Bertolotti Alessia , Pruneri Giancarlo , Canale Eleonora , Dewhurst Hannah F. , Saha Debjani , Slaven Neil , Barozzi Iros , Li Tong , Zemlyanskiy Grigory , Phillips Henry , James Chela , Győrffy Balázs , Lynn Claire , Cresswell George D. , Rehman Farah , Noberini Roberta , Bonaldi Tiziana , Sottoriva Andrea , Magnani Luca
Published: May 2024

Genomic profiling of patients (rare cohort treated with long-term ET until progression)
Supplementary Figure S14 from Acquired Cross-Resistance in Small Cell Lung Cancer due to Extrachromosomal DNA Amplification of MYC Paralogs
Authors: Pal Choudhuri Shreoshi , Girard Luc , Lim Jun Yi Stanley , Wise Jillian F. , Freitas Braeden , Yang Di , Wong Edmond , Hamilton Seth , Chien Victor D. , Kim Yoon Jung , Gilbreath Collin , Zhong Jun , Phat Sarah , Myers David T. , Christensen Camilla L. , Mazloom-Farsibaf Hanieh , Stanzione Marcello , Wong Kwok-Kin , Hung Yin P. , Farago Anna F. , Meador Catherine B. , Dyson Nicholas J. , Lawrence Michael S. , Wu Sihan , Drapkin Benjamin J.
Published: May 2024

MYC paralog amplifications that were detected or omitted by segmented copy number analysis, and patient survival compared with ecDNA status of PDX models.
Supplementary Figure S27 from Long-term Multimodal Recording Reveals Epigenetic Adaptation Routes in Dormant Breast Cancer Cells
Authors: Rosano Dalia , Sofyali Emre , Dhiman Heena , Ghirardi Chiara , Ivanoiu Diana , Heide Timon , Vingiani Andrea , Bertolotti Alessia , Pruneri Giancarlo , Canale Eleonora , Dewhurst Hannah F. , Saha Debjani , Slaven Neil , Barozzi Iros , Li Tong , Zemlyanskiy Grigory , Phillips Henry , James Chela , Győrffy Balázs , Lynn Claire , Cresswell George D. , Rehman Farah , Noberini Roberta , Bonaldi Tiziana , Sottoriva Andrea , Magnani Luca
Published: May 2024

Stratification of BC patients using the epigenetic dormancy signature
Supplementary Figure S10 from Acquired Cross-Resistance in Small Cell Lung Cancer due to Extrachromosomal DNA Amplification of MYC Paralogs
Authors: Pal Choudhuri Shreoshi , Girard Luc , Lim Jun Yi Stanley , Wise Jillian F. , Freitas Braeden , Yang Di , Wong Edmond , Hamilton Seth , Chien Victor D. , Kim Yoon Jung , Gilbreath Collin , Zhong Jun , Phat Sarah , Myers David T. , Christensen Camilla L. , Mazloom-Farsibaf Hanieh , Stanzione Marcello , Wong Kwok-Kin , Hung Yin P. , Farago Anna F. , Meador Catherine B. , Dyson Nicholas J. , Lawrence Michael S. , Wu Sihan , Drapkin Benjamin J.
Published: May 2024

Reconstruction of ecDNAs that do not contain MYC paralogs.
Supplementary Figure S1 from Acquired Cross-Resistance in Small Cell Lung Cancer due to Extrachromosomal DNA Amplification of MYC Paralogs
Authors: Pal Choudhuri Shreoshi , Girard Luc , Lim Jun Yi Stanley , Wise Jillian F. , Freitas Braeden , Yang Di , Wong Edmond , Hamilton Seth , Chien Victor D. , Kim Yoon Jung , Gilbreath Collin , Zhong Jun , Phat Sarah , Myers David T. , Christensen Camilla L. , Mazloom-Farsibaf Hanieh , Stanzione Marcello , Wong Kwok-Kin , Hung Yin P. , Farago Anna F. , Meador Catherine B. , Dyson Nicholas J. , Lawrence Michael S. , Wu Sihan , Drapkin Benjamin J.
Published: May 2024

Calculation of delta-AUC and comparison of EC with EP in PDX models.
Supplementary Figure S22 from Long-term Multimodal Recording Reveals Epigenetic Adaptation Routes in Dormant Breast Cancer Cells
Authors: Rosano Dalia , Sofyali Emre , Dhiman Heena , Ghirardi Chiara , Ivanoiu Diana , Heide Timon , Vingiani Andrea , Bertolotti Alessia , Pruneri Giancarlo , Canale Eleonora , Dewhurst Hannah F. , Saha Debjani , Slaven Neil , Barozzi Iros , Li Tong , Zemlyanskiy Grigory , Phillips Henry , James Chela , Győrffy Balázs , Lynn Claire , Cresswell George D. , Rehman Farah , Noberini Roberta , Bonaldi Tiziana , Sottoriva Andrea , Magnani Luca
Published: May 2024

TRADITIOM LSC Cell cycle states
Table S8 from Large-scale Pan-cancer Cell Line Screening Identifies Actionable and Effective Drug Combinations
Authors: Bashi Azadeh C. , Coker Elizabeth A. , Bulusu Krishna C. , Jaaks Patricia , Crafter Claire , Lightfoot Howard , Milo Marta , McCarten Katrina , Jenkins David F. , van der Meer Dieudonne , Lynch James T. , Barthorpe Syd , Andersen Courtney L. , Barry Simon T. , Beck Alexandra , Cidado Justin , Gordon Jacob A. , Hall Caitlin , Hall James , Mali Iman , Mironenko Tatiana , Mongeon Kevin , Morris James , Richardson Laura , Smith Paul D. , Tavana Omid , Tolley Charlotte , Thomas Frances , Willis Brandon S. , Yang Wanjuan , O'Connor Mark J. , McDermott Ultan , Critchlow Susan E. , Drew Lisa , Fawell Stephen E. , Mettetal Jerome T. , Garnett Mathew J.
Published: May 2024

Supplementary Table 8 shows the top combination-cancer type pairs in solid tumors showing activity in at least 10% of tested cell lines in that specific cancer type ranked based on their activity (% responders) and disease selectivity
Supplementary Figure S14 from Long-term Multimodal Recording Reveals Epigenetic Adaptation Routes in Dormant Breast Cancer Cells
Authors: Rosano Dalia , Sofyali Emre , Dhiman Heena , Ghirardi Chiara , Ivanoiu Diana , Heide Timon , Vingiani Andrea , Bertolotti Alessia , Pruneri Giancarlo , Canale Eleonora , Dewhurst Hannah F. , Saha Debjani , Slaven Neil , Barozzi Iros , Li Tong , Zemlyanskiy Grigory , Phillips Henry , James Chela , Győrffy Balázs , Lynn Claire , Cresswell George D. , Rehman Farah , Noberini Roberta , Bonaldi Tiziana , Sottoriva Andrea , Magnani Luca
Published: May 2024

Frequencies of winner barcodes (Traditiom samples)
Table S5 from Large-scale Pan-cancer Cell Line Screening Identifies Actionable and Effective Drug Combinations
Authors: Bashi Azadeh C. , Coker Elizabeth A. , Bulusu Krishna C. , Jaaks Patricia , Crafter Claire , Lightfoot Howard , Milo Marta , McCarten Katrina , Jenkins David F. , van der Meer Dieudonne , Lynch James T. , Barthorpe Syd , Andersen Courtney L. , Barry Simon T. , Beck Alexandra , Cidado Justin , Gordon Jacob A. , Hall Caitlin , Hall James , Mali Iman , Mironenko Tatiana , Mongeon Kevin , Morris James , Richardson Laura , Smith Paul D. , Tavana Omid , Tolley Charlotte , Thomas Frances , Willis Brandon S. , Yang Wanjuan , O'Connor Mark J. , McDermott Ultan , Critchlow Susan E. , Drew Lisa , Fawell Stephen E. , Mettetal Jerome T. , Garnett Mathew J.
Published: May 2024

Supplementary Table 5 shows combinations with broad activity across tumor types
Table S4 from Large-scale Pan-cancer Cell Line Screening Identifies Actionable and Effective Drug Combinations
Authors: Bashi Azadeh C. , Coker Elizabeth A. , Bulusu Krishna C. , Jaaks Patricia , Crafter Claire , Lightfoot Howard , Milo Marta , McCarten Katrina , Jenkins David F. , van der Meer Dieudonne , Lynch James T. , Barthorpe Syd , Andersen Courtney L. , Barry Simon T. , Beck Alexandra , Cidado Justin , Gordon Jacob A. , Hall Caitlin , Hall James , Mali Iman , Mironenko Tatiana , Mongeon Kevin , Morris James , Richardson Laura , Smith Paul D. , Tavana Omid , Tolley Charlotte , Thomas Frances , Willis Brandon S. , Yang Wanjuan , O'Connor Mark J. , McDermott Ultan , Critchlow Susan E. , Drew Lisa , Fawell Stephen E. , Mettetal Jerome T. , Garnett Mathew J.
Published: May 2024

Supplementary Table 4 shows combination-cancer type pairs with less than 10 percent responder cell lines
Table S3 from Large-scale Pan-cancer Cell Line Screening Identifies Actionable and Effective Drug Combinations
Authors: Bashi Azadeh C. , Coker Elizabeth A. , Bulusu Krishna C. , Jaaks Patricia , Crafter Claire , Lightfoot Howard , Milo Marta , McCarten Katrina , Jenkins David F. , van der Meer Dieudonne , Lynch James T. , Barthorpe Syd , Andersen Courtney L. , Barry Simon T. , Beck Alexandra , Cidado Justin , Gordon Jacob A. , Hall Caitlin , Hall James , Mali Iman , Mironenko Tatiana , Mongeon Kevin , Morris James , Richardson Laura , Smith Paul D. , Tavana Omid , Tolley Charlotte , Thomas Frances , Willis Brandon S. , Yang Wanjuan , O'Connor Mark J. , McDermott Ultan , Critchlow Susan E. , Drew Lisa , Fawell Stephen E. , Mettetal Jerome T. , Garnett Mathew J.
Published: May 2024

Supplementary Table 3 shows combination-cancer type pairs with 10 percent or more responder cell lines
Figure 3 from Long-term Multimodal Recording Reveals Epigenetic Adaptation Routes in Dormant Breast Cancer Cells
Authors: Rosano Dalia , Sofyali Emre , Dhiman Heena , Ghirardi Chiara , Ivanoiu Diana , Heide Timon , Vingiani Andrea , Bertolotti Alessia , Pruneri Giancarlo , Canale Eleonora , Dewhurst Hannah F. , Saha Debjani , Slaven Neil , Barozzi Iros , Li Tong , Zemlyanskiy Grigory , Phillips Henry , James Chela , Győrffy Balázs , Lynn Claire , Cresswell George D. , Rehman Farah , Noberini Roberta , Bonaldi Tiziana , Sottoriva Andrea , Magnani Luca
Published: May 2024

Adaptation is driven by divergent transcriptional reprogramming. A, Tamoxifen resistance analysis of the TAM TEPs (late progression) to increasing doses of 4-OHT is depicted in the left. Growth rates of –E2 (AI) TEPs in response to treatment with different drugs: Tamoxifen (Tam, 4-OHT), fulvestrant (Fulv), CDK7 inhibitor (CDK7i), CDK4/6i (palbociclib) are depicted on the right. Representative graphs are shown as normalized confluency fold change upon 7 days of compound treatment (n = 3). B, Principal component analysis (PCA) of bulk RNA-seq expression data for all MCF7 TRADITIOM samples (POT (pretreatment), latency (time between onset of treatment and dormancy), dormancy, awakening (early progression), and TEP (late progression) of both treatment arms [TAM and –E2(AI)] and their counterpart untreated (UT) samples cultured in parallel for 170 days. C, Heat map from bulk RNA-seq data depicting a subset of TRADITIOM MCF7 dormancy signature with top 50 significantly up- and downregulated genes in TAM and –E2 (AI) treated samples during dormancy in comparison with POT (pretreatment). D, GSEA for TRADITIOM dormancy signature.
Table S13 from Large-scale Pan-cancer Cell Line Screening Identifies Actionable and Effective Drug Combinations
Authors: Bashi Azadeh C. , Coker Elizabeth A. , Bulusu Krishna C. , Jaaks Patricia , Crafter Claire , Lightfoot Howard , Milo Marta , McCarten Katrina , Jenkins David F. , van der Meer Dieudonne , Lynch James T. , Barthorpe Syd , Andersen Courtney L. , Barry Simon T. , Beck Alexandra , Cidado Justin , Gordon Jacob A. , Hall Caitlin , Hall James , Mali Iman , Mironenko Tatiana , Mongeon Kevin , Morris James , Richardson Laura , Smith Paul D. , Tavana Omid , Tolley Charlotte , Thomas Frances , Willis Brandon S. , Yang Wanjuan , O'Connor Mark J. , McDermott Ultan , Critchlow Susan E. , Drew Lisa , Fawell Stephen E. , Mettetal Jerome T. , Garnett Mathew J.
Published: May 2024

Supplementary Table 13 shows significant biomarkers and significant emergent biomarkers
Figure 6 from Large-scale Pan-cancer Cell Line Screening Identifies Actionable and Effective Drug Combinations
Authors: Bashi Azadeh C. , Coker Elizabeth A. , Bulusu Krishna C. , Jaaks Patricia , Crafter Claire , Lightfoot Howard , Milo Marta , McCarten Katrina , Jenkins David F. , van der Meer Dieudonne , Lynch James T. , Barthorpe Syd , Andersen Courtney L. , Barry Simon T. , Beck Alexandra , Cidado Justin , Gordon Jacob A. , Hall Caitlin , Hall James , Mali Iman , Mironenko Tatiana , Mongeon Kevin , Morris James , Richardson Laura , Smith Paul D. , Tavana Omid , Tolley Charlotte , Thomas Frances , Willis Brandon S. , Yang Wanjuan , O'Connor Mark J. , McDermott Ultan , Critchlow Susan E. , Drew Lisa , Fawell Stephen E. , Mettetal Jerome T. , Garnett Mathew J.
Published: May 2024

Capivasertib (AZD5363) plus AZD5991 combination activity in endometrial cell lines. A, Screening results of combo Emax versus HSA in endometrial cell lines treated with AZD5363 plus AZD5991. Cell lines with high combination activity are in red. B, Representative growth inhibition and HSA excess matrix plots in endometrial AN3CA cells. C, Matrix plot measuring apoptosis with AZD5991 and AZD5363 at indicated doses for 6 hours in AN3-CA cells. D, Matrix plots showing viability for AN3-CA cells pretreated with DMSO or QVD (caspase inhibitor) for 16 hours prior to the combination for 6 hours. E, Western blot analysis in AN3-CA cells treated with AZD5363 (1 μmol/L), AZD5991 (500 nmol/L), or in combination at indicated times. F, Matrix plots showing viability in AN3-CA cells treated with AZD5991 or venetoclax (ABT-199 -BCL2 inhibitor), AZD4320 or AZ3202 (BCL-XL inhibitors) with AZD5363 at indicated doses for 6 hours.