bluuebunny/crossref_metadata_2025 huggingface dataset:
Data from EXAMINING THE BARRIERS AND OPPORTUNITIES FOR HUMAN PAPILLOMAVIRUS VACCINE DELIVERY IN CANCER CARE SETTINGS: A MIXED-METHODS STUDY
Authors: Garcia Melany A. , Schlecht Nicolas F. , Rokitka Denise A. , Attwood Kristopher M. , Rodriguez Elisa M.
Published: September 2024

Abstract
While pediatric, adolescent, and young adult (PAYA) cancer survivors are at increased risks for secondary cancers, their HPV vaccine uptake rates are poor. Therefore, we conducted a mixed-methods study to identify the barriers and opportunities for HPV vaccine delivery among PAYA cancer care providers. We distributed a semi-structured questionnaire to a professional organization comprised of PAYA oncology and hematology healthcare providers between April-July 2022. Questionnaire measures included demographic and practice characteristics, HPV vaccine knowledge, willingness, barriers, opportunities, and roles for HPV vaccine delivery. Descriptive characteristics were generated for quantitative data, and content analysis was used to identify themes. A total of 49 providers responded to our survey. A majority were female (68%) and non-Hispanic white (74%). Approximately 76% were oncology or hematology physicians, and most worked in a cancer center or children’s hospital (86%). Over half (63%) had been practicing for >15 years, and a majority saw patients ages 11-17. Although less than half reported discussing HPV vaccination with their patients, 69% were willing to become involved in HPV vaccine delivery. The most frequently reported barriers identified in our content analysis were related to system-level factors. Furthermore, providers identified opportunities within cancer prevention education, transitions in care, and at the system-level. Although barriers to HPV vaccination persist in cancer care, most providers perceived there to be opportunities to become involved in HPV vaccine delivery. Identifying strategies for PAYA oncology and hematology healthcare providers to adopt a stronger role in HPV vaccination remains a significant opportunity for future implementation research.
Supplemental Figure S9 from Reprogramming Cancer into Antigen Presenting Cells as a Novel Immunotherapy
Authors: Linde Miles H. , Fan Amy C. , Kohnke Thomas , Trotman-Grant Aaron C. , Gurev Sarah F. , Phan Paul , Zhao Feifei , Haddock Naomi L. , Nuno Kevin A. , Gars Eric J. , Stafford Melissa , Marshall Payton L. , Dove Christopher G. , Linde Ian L. , Landberg Niklas , Miller Lindsay P. , Majzner Robbie G. , Zhang Tian Yi. , Majeti Ravindra
Published: September 2024

Primary B-ALL TR-APCs can be generated via exogenous
cytokine stimulation
Supplemental Figure S2 from Reprogramming Cancer into Antigen Presenting Cells as a Novel Immunotherapy
Authors: Linde Miles H. , Fan Amy C. , Kohnke Thomas , Trotman-Grant Aaron C. , Gurev Sarah F. , Phan Paul , Zhao Feifei , Haddock Naomi L. , Nuno Kevin A. , Gars Eric J. , Stafford Melissa , Marshall Payton L. , Dove Christopher G. , Linde Ian L. , Landberg Niklas , Miller Lindsay P. , Majzner Robbie G. , Zhang Tian Yi. , Majeti Ravindra
Published: September 2024

In vivo TR-APC induction results in no observable off-target toxicity
Supplementary Figures S1-S10 from p38MAPKa stromal reprogramming sensitizes metastatic breast cancer to immunotherapy
Authors: Faget Douglas V. , Luo Xianmin , Inkman Matthew J. , Ren Qihao , Su Xinming , Ding Kai , Waters Michael R. , Raut Ganesh Kumar , Pandey Gaurav , Dodhiawala Paarth B. , Ramalho-Oliveira Renata , Ye Jiayu , Cole Thomas , Murali Bhavna , Zheleznyak Alexander , Shokeen Monica , Weiss Kurt R. , Monahan Joseph B. , DeSelm Carl J. , Lee Adrian V. , Oesterreich Steffi , Weilbaecher Katherine N. , Zhang Jin , DeNardo David G. , Stewart Sheila A.
Published: September 2024

Contains supplemental figures and legends
Table S3 from Abatacept/Ruxolitinib and Screening for Concomitant Respiratory Muscle Failure to Mitigate Fatality of Immune-Checkpoint Inhibitor Myocarditis
Authors: Salem Joe-Elie , Bretagne Marie , Abbar Baptiste , LEONARD-LOUIS Sarah , Ederhy Stephane , REDHEUIL Alban , BOUSSOUAR Samia , NGUYEN Lee S. , PROCUREUR Adrien , STEIN Frederic , FENIOUX Charlotte , DEVOS Perrine , GOUGIS Paul , DRES Martin , DEMOULE Alexandre , Psimaras Dimitri , LENGLET Timothee , MAISONOBE Thierry , PINETON DE CHAMBRUN Marc , HEKIMIAN Guillaume , STRAUS Christian , GONZALEZ-BERMEJO Jesus , Klatzmann David , RIGOLET Aude , GUILLAUME-JUGNOT Perrine , CHAMPTIAUX Nicolas , BENVENISTE Olivier , WEISS Nicolas , SAHEB Samir , ROUVIER Philippe , PLU Isabelle , GANDJBAKHCH Estelle , KERNEIS Mathieu , HAMMOUDI Nadjib , ZAHR Noel , LLONTOP Claudia , MORELOT-PANZINI Capucine , Lehmann Lorenz , Qin Juan , Moslehi Javid J. , ROSENZWAJG Michelle , SIMILOWSKI Thomas , Allenbach Yves
Published: September 2024

Framework for the evaluation of global respiratory muscles and diaphragm function
Supplementary Fig. S8 from Addressing Tumor Heterogeneity by Sensitizing Resistant Cancer Cells to T cell-secreted Cytokines
Authors: Ito Yoshinaga , Pan Deng , Zhang Wubing , Zhang Xixi , Juan Tiffany Y. , Pyrdol Jason W. , Kyrysyuk Oleksandr , Doench John G. , Liu X. Shirley , Wucherpfennig Kai W.
Published: September 2024

Supplementary Fig. S8 shows CD8 T cell-dependent control of tumors containing a B2m-/- population with inactivated Rnf31 and Atg5 genes.
Supplementary Fig. S6 from Addressing Tumor Heterogeneity by Sensitizing Resistant Cancer Cells to T cell-secreted Cytokines
Authors: Ito Yoshinaga , Pan Deng , Zhang Wubing , Zhang Xixi , Juan Tiffany Y. , Pyrdol Jason W. , Kyrysyuk Oleksandr , Doench John G. , Liu X. Shirley , Wucherpfennig Kai W.
Published: September 2024

Supplementary Fig. S6 shows functional links between autophagy and cytokine signaling
pathways.
Supplementary Fig. S10 from Addressing Tumor Heterogeneity by Sensitizing Resistant Cancer Cells to T cell-secreted Cytokines
Authors: Ito Yoshinaga , Pan Deng , Zhang Wubing , Zhang Xixi , Juan Tiffany Y. , Pyrdol Jason W. , Kyrysyuk Oleksandr , Doench John G. , Liu X. Shirley , Wucherpfennig Kai W.
Published: September 2024

Supplementary Fig. S10 shows pharmacological sensitization to T cell cytokines in vitro and in vivo.
Supplementary Table S6 from (R)-2-hydroxyglutarate inhibits KDM5 histone lysine demethylases to drive transformation in IDH-mutant cancers
Authors: Gunn Kathryn , Myllykoski Matti , Cao John Z. , Ahmed Manna , Huang Bofu , Rouaisnel Betty , Diplas Bill H. , Levitt Michael M. , Looper Ryan , Doench John G. , Ligon Keith L. , Kornblum Harley I. , McBrayer Samuel K. , Yan Hai , Duy Cihangir , Godley Lucy A. , Koivunen Peppi , Losman Julie-Aurore
Published: September 2024

Supplementary Table S6 shows the mutational profiles of the primary AML patient samples subjected to H3K4me3 ChIP-seq.
Supplementary Table S5 from (R)-2-hydroxyglutarate inhibits KDM5 histone lysine demethylases to drive transformation in IDH-mutant cancers
Authors: Gunn Kathryn , Myllykoski Matti , Cao John Z. , Ahmed Manna , Huang Bofu , Rouaisnel Betty , Diplas Bill H. , Levitt Michael M. , Looper Ryan , Doench John G. , Ligon Keith L. , Kornblum Harley I. , McBrayer Samuel K. , Yan Hai , Duy Cihangir , Godley Lucy A. , Koivunen Peppi , Losman Julie-Aurore
Published: September 2024

Supplementary Table S5 shows the rank order list of genes targeted by sgRNAs enriched in the custom minipool CRISPR/Cas9 knockout screens.
Supplementary Table S4 from (R)-2-hydroxyglutarate inhibits KDM5 histone lysine demethylases to drive transformation in IDH-mutant cancers
Authors: Gunn Kathryn , Myllykoski Matti , Cao John Z. , Ahmed Manna , Huang Bofu , Rouaisnel Betty , Diplas Bill H. , Levitt Michael M. , Looper Ryan , Doench John G. , Ligon Keith L. , Kornblum Harley I. , McBrayer Samuel K. , Yan Hai , Duy Cihangir , Godley Lucy A. , Koivunen Peppi , Losman Julie-Aurore
Published: September 2024

Supplementary Table S4 shows the list of custom minipool sgRNA target genes.
Supplementary Table S10 from (R)-2-hydroxyglutarate inhibits KDM5 histone lysine demethylases to drive transformation in IDH-mutant cancers
Authors: Gunn Kathryn , Myllykoski Matti , Cao John Z. , Ahmed Manna , Huang Bofu , Rouaisnel Betty , Diplas Bill H. , Levitt Michael M. , Looper Ryan , Doench John G. , Ligon Keith L. , Kornblum Harley I. , McBrayer Samuel K. , Yan Hai , Duy Cihangir , Godley Lucy A. , Koivunen Peppi , Losman Julie-Aurore
Published: September 2024

Supplementary Table S10 shows the gene set enrichment analysis gene set that corresponds to Figure S6B.
Supplementary Table S1 from (R)-2-hydroxyglutarate inhibits KDM5 histone lysine demethylases to drive transformation in IDH-mutant cancers
Authors: Gunn Kathryn , Myllykoski Matti , Cao John Z. , Ahmed Manna , Huang Bofu , Rouaisnel Betty , Diplas Bill H. , Levitt Michael M. , Looper Ryan , Doench John G. , Ligon Keith L. , Kornblum Harley I. , McBrayer Samuel K. , Yan Hai , Duy Cihangir , Godley Lucy A. , Koivunen Peppi , Losman Julie-Aurore
Published: September 2024

Supplementary Table S1 shows the frequencies of TET2 and IDH mutations in clonal myeloid disorders.
Supplementary Figure S8 from (R)-2-hydroxyglutarate inhibits KDM5 histone lysine demethylases to drive transformation in IDH-mutant cancers
Authors: Gunn Kathryn , Myllykoski Matti , Cao John Z. , Ahmed Manna , Huang Bofu , Rouaisnel Betty , Diplas Bill H. , Levitt Michael M. , Looper Ryan , Doench John G. , Ligon Keith L. , Kornblum Harley I. , McBrayer Samuel K. , Yan Hai , Duy Cihangir , Godley Lucy A. , Koivunen Peppi , Losman Julie-Aurore
Published: September 2024

Characterization of isogenic IHA cell lines.
Supplementary Data: list of figures and tables from (R)-2-hydroxyglutarate inhibits KDM5 histone lysine demethylases to drive transformation in IDH-mutant cancers
Authors: Gunn Kathryn , Myllykoski Matti , Cao John Z. , Ahmed Manna , Huang Bofu , Rouaisnel Betty , Diplas Bill H. , Levitt Michael M. , Looper Ryan , Doench John G. , Ligon Keith L. , Kornblum Harley I. , McBrayer Samuel K. , Yan Hai , Duy Cihangir , Godley Lucy A. , Koivunen Peppi , Losman Julie-Aurore
Published: September 2024

List of supplementary figures and tables.
Supplementary Figure 7 from Combinatorial BCL-2 family expression in Acute Myeloid Leukemia Stem Cells predicts clinical response to Azacitidine/Venetoclax
Authors: Waclawiczek Alexander , Leppa Aino-Maija , Renders Simon , Stumpf Karolin , Reyneri Cecilia , Betz Barbara , Janssen Maike , Shahswar Rabia , Donato Elisa , Karpova Darja , Thiel Vera , Unglaub Julia M. , Grabowski Susanna , Gryzik Stefanie , Vierbaum Lisa , Schlenk Richard F. , Rollig Christoph , Hundemer Michael , Pabst Caroline , Heuser Michael , Raffel Simon , Muller-Tidow Carsten , Sauer Tim , Trumpp Andreas
Published: September 2024

MAC-Score predict response within mutational subgroups
Supplementary Figure 4 from Combinatorial BCL-2 family expression in Acute Myeloid Leukemia Stem Cells predicts clinical response to Azacitidine/Venetoclax
Authors: Waclawiczek Alexander , Leppa Aino-Maija , Renders Simon , Stumpf Karolin , Reyneri Cecilia , Betz Barbara , Janssen Maike , Shahswar Rabia , Donato Elisa , Karpova Darja , Thiel Vera , Unglaub Julia M. , Grabowski Susanna , Gryzik Stefanie , Vierbaum Lisa , Schlenk Richard F. , Rollig Christoph , Hundemer Michael , Pabst Caroline , Heuser Michael , Raffel Simon , Muller-Tidow Carsten , Sauer Tim , Trumpp Andreas
Published: September 2024

Subpopulation specific Bcl-2 family levels and response to HMA/Venetoclax
Supplementary Figure 1 from Combinatorial BCL-2 family expression in Acute Myeloid Leukemia Stem Cells predicts clinical response to Azacitidine/Venetoclax
Authors: Waclawiczek Alexander , Leppa Aino-Maija , Renders Simon , Stumpf Karolin , Reyneri Cecilia , Betz Barbara , Janssen Maike , Shahswar Rabia , Donato Elisa , Karpova Darja , Thiel Vera , Unglaub Julia M. , Grabowski Susanna , Gryzik Stefanie , Vierbaum Lisa , Schlenk Richard F. , Rollig Christoph , Hundemer Michael , Pabst Caroline , Heuser Michael , Raffel Simon , Muller-Tidow Carsten , Sauer Tim , Trumpp Andreas
Published: September 2024

Cell line sensitivity and additional patient data
Supplementary Figure 6 from Combinatorial BCL-2 family expression in Acute Myeloid Leukemia Stem Cells predicts clinical response to Azacitidine/Venetoclax
Authors: Waclawiczek Alexander , Leppa Aino-Maija , Renders Simon , Stumpf Karolin , Reyneri Cecilia , Betz Barbara , Janssen Maike , Shahswar Rabia , Donato Elisa , Karpova Darja , Thiel Vera , Unglaub Julia M. , Grabowski Susanna , Gryzik Stefanie , Vierbaum Lisa , Schlenk Richard F. , Rollig Christoph , Hundemer Michael , Pabst Caroline , Heuser Michael , Raffel Simon , Muller-Tidow Carsten , Sauer Tim , Trumpp Andreas
Published: September 2024

Comparison of MAC-Score and BH-3 profiling based response prediction
Supplementary Table S3 from Cell-autonomous Cxcl1 sustains tolerogenic circuitries and stromal inflammation via neutrophil-derived TNF in pancreatic cancer
Authors: Bianchi Anna , De Castro Silva Iago , Deshpande Nilesh U. , Singh Samara , Mehra Siddharth , Garrido Vanessa T. , Guo Xinyu , Nivelo Luis A. , Kolonias Despina S. , Saigh Shannon J. , Wieder Eric , Rafie Christine I. , Dosch Austin R. , Zhou Zhiqun , Umland Oliver , Amirian Haleh , Ogobuiro Ifeanyichukwu C. , Zhang Jian , Ban Yuguang , Shiau Carina , Nagathihalli Nagaraj S. , Montgomery Elizabeth A. , Hwang William L. , Brambilla Roberta , Komanduri Krishna , Villarino Alejandro V. , Toska Eneda , Stanger Ben Z. , Gabrilovich Dmitry I. , Merchant Nipun B. , Datta Jashodeep
Published: September 2024

Co-occupied and unique target genes shared between Creb and RNApol-II in chromatin immunoprecipitation and sequencing (ChIP-seq) experiments performed in murine Kras-Trp53 cooperative KPC pancreatic cancer cells
Supplementary Table S6 from Single-cell RNA sequencing unifies developmental programs of Esophageal and Gastric Intestinal Metaplasia.
Authors: Nowicki-Osuch Karol , Zhuang Lizhe , Cheung Tik Shing , Black Emily L. , Masque-Soler Neus , Devonshire Ginny , Redmond Aisling M. , Freeman Adam , di Pietro Massimilliano , Pilonis Nastazja , Januszewicz Wladyslaw , O'Donovan Maria , Tavare Simon , Shields Jacqueline D. , Fitzgerald Rebecca C.
Published: September 2024

This table contains marker genes identified in the pairwise comparison of clusters identified in fibroblast population
Supplementary Table S3 from Single-cell RNA sequencing unifies developmental programs of Esophageal and Gastric Intestinal Metaplasia.
Authors: Nowicki-Osuch Karol , Zhuang Lizhe , Cheung Tik Shing , Black Emily L. , Masque-Soler Neus , Devonshire Ginny , Redmond Aisling M. , Freeman Adam , di Pietro Massimilliano , Pilonis Nastazja , Januszewicz Wladyslaw , O'Donovan Maria , Tavare Simon , Shields Jacqueline D. , Fitzgerald Rebecca C.
Published: September 2024

This table contains marker genes identified in the pairwise comparison of clusters defined as columnar cells.
Supplementary Table S1 from Single-cell RNA sequencing unifies developmental programs of Esophageal and Gastric Intestinal Metaplasia.
Authors: Nowicki-Osuch Karol , Zhuang Lizhe , Cheung Tik Shing , Black Emily L. , Masque-Soler Neus , Devonshire Ginny , Redmond Aisling M. , Freeman Adam , di Pietro Massimilliano , Pilonis Nastazja , Januszewicz Wladyslaw , O'Donovan Maria , Tavare Simon , Shields Jacqueline D. , Fitzgerald Rebecca C.
Published: September 2024

This file contains details of individual samples (including clinical data) used in the sutdy
Supplementary Tables S1-S15 from Tracing founder mutations in circulating and tissue-resident follicular lymphoma precursors
Authors: Schroers-Martin Joseph G. , Soo Joanne , Brisou Gabriel , Scherer Florian , Kurtz David M. , Sworder Brian J. , Khodadoust Michael S. , Jin Michael C. , Bru Agnes , Liu Chih Long , Stehr Henning , Vineis Paolo , Natkunam Yasodha , Teras Lauren R. , Song Joo Y. , Nadel Bertrand , Diehn Maximilian , Roulland Sandrine , Alizadeh Ash A.
Published: September 2024

Supplementary Table S1. Patient and control clinical characteristics
Supplementary Table S2. Sequencing metrics for FL cases & controls
Supplementary Table S3. Identified mutations in EPIC FL pre-diagnostic samples
Supplementary Table S4. Identified mutations in control samples
Supplementary Table S5. Statistical significance for detection in prediagnostic samples with paired tumor biopsy
Supplementary Table S6. Identified mutations in FL tumors with detection in paired prediagnostic samples
Supplementary Table S7. Paired tumor cohort histology & sample characteristics
Supplementary Table S8. Identified mutations in paired biopsy samples
Supplementary Table S9. Clonal VDJ rearrangements in paired biopsies
Supplementary Table S10. Concordance analysis of paired biopsy samples
Supplementary Table S11. Patient characteristics, marrow and sorting studies
Supplementary Table S12. DNA and sequencing metrics for marrow and sorting studies
Supplementary Table S13. Monoclonal antibodies and manufacturers
Supplementary Table S14. Mutations detected in marrow and sorting studies
Supplementary Table S15. Genes fully or partially covered in lymphoma-focused CAPP-Seq selector
Figure S2 from Type I Interferon Signaling via the EGR2 Transcriptional Regulator Potentiates CAR T cell-intrinsic Dysfunction
Authors: Jung In-Young , Bartoszek Robert L. , Rech Andrew J. , Collins Sierra M. , Ooi Soon-Keat , Williams Erik F. , Hopkins Caitlin R. , Narayan Vivek , Haas Naomi B. , Frey Noelle V. , Hexner Elizabeth O. , Siegel Donald L. , Plesa Gabriela , Porter David L. , Cantu Adrian , Everett John K. , Guedan Sonia , Berger Shelley L. , Bushman Frederic D. , Herbst Friederike , Fraietta Joseph A.
Published: September 2024

Impact of EGR2 knockout on CD8+/CD4+ ratio and Th2 cytokine production in the setting of chronic tumor antigen stimulation. A, Comparison of CD8+/CD4+ ratio in control and EGR2 knockout (KO) CAR T-cells after chronic CAR stimulation. B, Th2 cytokine production by control and EGR2 KO CAR T-cells after 24 hours of CAR stimulation (Mann-Whitney test, n = 4). All experiments were performed using T-cells from three independent healthy donors. Panel B is representative data from one donor. *P < 0.05, **P < 0.01, ***P < 0.001, ns: not significant.
Figure S10 from Type I Interferon Signaling via the EGR2 Transcriptional Regulator Potentiates CAR T cell-intrinsic Dysfunction
Authors: Jung In-Young , Bartoszek Robert L. , Rech Andrew J. , Collins Sierra M. , Ooi Soon-Keat , Williams Erik F. , Hopkins Caitlin R. , Narayan Vivek , Haas Naomi B. , Frey Noelle V. , Hexner Elizabeth O. , Siegel Donald L. , Plesa Gabriela , Porter David L. , Cantu Adrian , Everett John K. , Guedan Sonia , Berger Shelley L. , Bushman Frederic D. , Herbst Friederike , Fraietta Joseph A.
Published: September 2024

EGR2 knockout enhances the long-term potency and memory function of CAR T-cells in vivo. A, Schematic of the tumor rechallenge experiments. B, Tumor growth after the first (left) and second (right) NALM6 challenges (Mann-Whitney test, n = 10). C, Mouse survival after high-dose second tumor challenge (Log-rank test). D, Tumor growth inhibition in a prostate cancer model using PSMA-targeting CAR T-cells with EGR2 or AAVS1 knockout (KO) compared to control CD19 CAR T-cells (19BBz). The tumor growth was monitored over time using caliper-based measurements in NSG mice (n = 8).
Figure S1 from Type I Interferon Signaling via the EGR2 Transcriptional Regulator Potentiates CAR T cell-intrinsic Dysfunction
Authors: Jung In-Young , Bartoszek Robert L. , Rech Andrew J. , Collins Sierra M. , Ooi Soon-Keat , Williams Erik F. , Hopkins Caitlin R. , Narayan Vivek , Haas Naomi B. , Frey Noelle V. , Hexner Elizabeth O. , Siegel Donald L. , Plesa Gabriela , Porter David L. , Cantu Adrian , Everett John K. , Guedan Sonia , Berger Shelley L. , Bushman Frederic D. , Herbst Friederike , Fraietta Joseph A.
Published: September 2024

Analysis of EGR2 and type I IFN pathway regulation in CAR T-cells. (A-C) ATAC-seq tracks of genes associated with dysfunction, type I IFN signaling, and memory differentiation are shown, with differentially accessible regions indicated. D, Heatmap showing expression of exhaustion genes in tonically signaling GD2 and functional CD19 naïve CD8+ CAR-T cells (GSE136891). E, Comparison of EGR2 and type I IFN gene signature scores in central memory CD8+ T-cells expressing a tonically signaling GD2 CAR and control CD19 CAR. CAR T-cells were generated using T-cells from a healthy donor (GSE136891). F, Top transcription factor co-expression signatures overexpressed in CD19 CAR T-cell products of CLL complete responders. G, Comparison of EGR2 and type I IFN signature scores in unstimulated CD19 CAR T-cell products from CLL patients (CR: complete response, PRTD: very good partial response, PR: conventional partial response, NR: no response). H, Comparison of type I IFN and EGR2 module scores in PSMA CAR T-cells from lymphodepleted prostate cancer patients, and their association with in vivo CAR T-cell proliferation and PSA decline.
Supplementary Table S5 from Early infiltration of innate immune cells to the liver depletes HNF4a and promotes extra-hepatic carcinogenesis
Authors: Goldman Omer , Adler Lital N. , Hajaj Emma , Croese Tommaso , Darzi Naama , Galai Sivan , Tishler Hila , Ariav Yarden , Lavie Dor , Fellus-Alyagor Liat , Oren Roni , Kuznetsov Yuri , David Eyal , Jaschek Rami , Stossel Chani , Singer Oded , Malitsky Sergey , Barak Renana , Seger Rony , Erez Neta , Amit Ido , Tanay Amos , Saada Ann , Golan Talia , Rubinek Tamar , Sang Lee Joo , Ben-Shachar Shay , Wolf Ido , Erez Ayelet
Published: September 2024

Supplementary Table S5 lists the antibodies used for CyTOF
Supplementary Table S3 from Early infiltration of innate immune cells to the liver depletes HNF4a and promotes extra-hepatic carcinogenesis
Authors: Goldman Omer , Adler Lital N. , Hajaj Emma , Croese Tommaso , Darzi Naama , Galai Sivan , Tishler Hila , Ariav Yarden , Lavie Dor , Fellus-Alyagor Liat , Oren Roni , Kuznetsov Yuri , David Eyal , Jaschek Rami , Stossel Chani , Singer Oded , Malitsky Sergey , Barak Renana , Seger Rony , Erez Neta , Amit Ido , Tanay Amos , Saada Ann , Golan Talia , Rubinek Tamar , Sang Lee Joo , Ben-Shachar Shay , Wolf Ido , Erez Ayelet
Published: September 2024

Supplementary Table S3 lists the primers used for qPCR
Supplementary Table S2 from Early infiltration of innate immune cells to the liver depletes HNF4a and promotes extra-hepatic carcinogenesis
Authors: Goldman Omer , Adler Lital N. , Hajaj Emma , Croese Tommaso , Darzi Naama , Galai Sivan , Tishler Hila , Ariav Yarden , Lavie Dor , Fellus-Alyagor Liat , Oren Roni , Kuznetsov Yuri , David Eyal , Jaschek Rami , Stossel Chani , Singer Oded , Malitsky Sergey , Barak Renana , Seger Rony , Erez Neta , Amit Ido , Tanay Amos , Saada Ann , Golan Talia , Rubinek Tamar , Sang Lee Joo , Ben-Shachar Shay , Wolf Ido , Erez Ayelet
Published: September 2024

Supplementary Table S2 lists the antibodies used for western blots
Supplementary Table S1 from Early infiltration of innate immune cells to the liver depletes HNF4a and promotes extra-hepatic carcinogenesis
Authors: Goldman Omer , Adler Lital N. , Hajaj Emma , Croese Tommaso , Darzi Naama , Galai Sivan , Tishler Hila , Ariav Yarden , Lavie Dor , Fellus-Alyagor Liat , Oren Roni , Kuznetsov Yuri , David Eyal , Jaschek Rami , Stossel Chani , Singer Oded , Malitsky Sergey , Barak Renana , Seger Rony , Erez Neta , Amit Ido , Tanay Amos , Saada Ann , Golan Talia , Rubinek Tamar , Sang Lee Joo , Ben-Shachar Shay , Wolf Ido , Erez Ayelet
Published: September 2024

Supplementary Table S1 details clinical data of PDAC patients
Supplementary Figure S1 from Early infiltration of innate immune cells to the liver depletes HNF4a and promotes extra-hepatic carcinogenesis
Authors: Goldman Omer , Adler Lital N. , Hajaj Emma , Croese Tommaso , Darzi Naama , Galai Sivan , Tishler Hila , Ariav Yarden , Lavie Dor , Fellus-Alyagor Liat , Oren Roni , Kuznetsov Yuri , David Eyal , Jaschek Rami , Stossel Chani , Singer Oded , Malitsky Sergey , Barak Renana , Seger Rony , Erez Neta , Amit Ido , Tanay Amos , Saada Ann , Golan Talia , Rubinek Tamar , Sang Lee Joo , Ben-Shachar Shay , Wolf Ido , Erez Ayelet
Published: September 2024

Supplementary Figure S1 demonstrates global metabolic changes in liver metabolism during early BC carcinogenesis
Supplementary Extended Data 1 from Early infiltration of innate immune cells to the liver depletes HNF4a and promotes extra-hepatic carcinogenesis
Authors: Goldman Omer , Adler Lital N. , Hajaj Emma , Croese Tommaso , Darzi Naama , Galai Sivan , Tishler Hila , Ariav Yarden , Lavie Dor , Fellus-Alyagor Liat , Oren Roni , Kuznetsov Yuri , David Eyal , Jaschek Rami , Stossel Chani , Singer Oded , Malitsky Sergey , Barak Renana , Seger Rony , Erez Neta , Amit Ido , Tanay Amos , Saada Ann , Golan Talia , Rubinek Tamar , Sang Lee Joo , Ben-Shachar Shay , Wolf Ido , Erez Ayelet
Published: September 2024

Supplementary Extended Data 1 describes the FACS gating startegy
Supplementary Table S3 from Mitophagy promotes resistance to BH3 mimetics in acute myeloid leukemia
Authors: Glytsou Christina , Chen Xufeng , Zacharioudakis Emmanouil , Al-Santli Wafa , Zhou Hua , Nadorp Bettina , Lee Soobeom , Lasry Audrey , Sun Zhengxi , Papaioannou Dimitrios , Cammer Michael , Wang Kun , Zal Tomasz , Zal Malgorzata Anna. , Carter Bing Z. , Ishizawa Jo , Tibes Raoul , Tsirigos Aristotelis , Andreeff Michael , Gavathiotis Evripidis , Aifantis Iannis
Published: September 2024

Supplementary Table S3 shows the information of the AML patient samples used in this study.
Supplementary Table S2 from Mitophagy promotes resistance to BH3 mimetics in acute myeloid leukemia
Authors: Glytsou Christina , Chen Xufeng , Zacharioudakis Emmanouil , Al-Santli Wafa , Zhou Hua , Nadorp Bettina , Lee Soobeom , Lasry Audrey , Sun Zhengxi , Papaioannou Dimitrios , Cammer Michael , Wang Kun , Zal Tomasz , Zal Malgorzata Anna. , Carter Bing Z. , Ishizawa Jo , Tibes Raoul , Tsirigos Aristotelis , Andreeff Michael , Gavathiotis Evripidis , Aifantis Iannis
Published: September 2024

Supplementary Table S2 shows the correlation score of MFN2 expression with the ex vivo drug response (IC50, BeatAML data).
Supplementary Table S1 from Mitophagy promotes resistance to BH3 mimetics in acute myeloid leukemia
Authors: Glytsou Christina , Chen Xufeng , Zacharioudakis Emmanouil , Al-Santli Wafa , Zhou Hua , Nadorp Bettina , Lee Soobeom , Lasry Audrey , Sun Zhengxi , Papaioannou Dimitrios , Cammer Michael , Wang Kun , Zal Tomasz , Zal Malgorzata Anna. , Carter Bing Z. , Ishizawa Jo , Tibes Raoul , Tsirigos Aristotelis , Andreeff Michael , Gavathiotis Evripidis , Aifantis Iannis
Published: September 2024

Supplementary Table 1 shows the results of our CRISPRi screens.
Supplementary Figures 1-7 from Mitophagy promotes resistance to BH3 mimetics in acute myeloid leukemia
Authors: Glytsou Christina , Chen Xufeng , Zacharioudakis Emmanouil , Al-Santli Wafa , Zhou Hua , Nadorp Bettina , Lee Soobeom , Lasry Audrey , Sun Zhengxi , Papaioannou Dimitrios , Cammer Michael , Wang Kun , Zal Tomasz , Zal Malgorzata Anna. , Carter Bing Z. , Ishizawa Jo , Tibes Raoul , Tsirigos Aristotelis , Andreeff Michael , Gavathiotis Evripidis , Aifantis Iannis
Published: September 2024

Supplemental Figure S1 shows the integration of CRISPR/Cas9 loss-of-function screens to identify dependencies and liabilities in BH3-mimetics treatments.

Supplemental Figure S2 demonstrates that increased mitochondria-ER interactions contribute to BH3-mimetics resistance.

Supplemental Figure S3 shows that mitophagy affects the responsiveness of AML cells to BH3-mimetics.

Supplemental Figure S4 reveals that enhanced autophagic clearance of mitochondria as a mechanism of resistance to BH3-mimetics in AML.

Supplemental Figure S5 exhibits the synergism between BH3-mimetics and macroautophagy inhibition in human AML.

Supplemental Figure S6 shows that deletion of MFN2 or MARCH5 sensitizes AML cells to BH3-mimetics.

Supplemental Figure S7 displays that targeting of MFN2 or MARCH5 impairs the process of mitophagy.
Supplementary Table S6 from Co-mutations and KRAS G12C inhibitor efficacy in advanced NSCLC
Authors: Negrao Marcelo V. , Araujo Haniel A. , Lamberti Giuseppe , Cooper Alissa J. , Akhave Neal S. , Zhou Teng , Delasos Lukas , Hicks J Kevin. , Aldea Mihaela , Minuti Gabriele , Hines Jacobi , Aredo Jacqueline V. , Dennis Michael J. , Chakrabarti Turja , Scott Susan C. , Bironzo Paolo , Scheffler Matthias , Christopoulos Petros , Stenzinger Albrecht , Riess Jonathan W. , Kim So Yeon , Goldberg Sarah B. , Li Mingjia , Wang Qi , Qing Yun , Ni Ying , Do Minh Truong , Lee Richard , Ricciuti Biagio , Alessi Joao Victor. , Wang Jing , Resuli Blerina , Landi Lorenza , Tseng Shu-Chi , Nishino Mizuki , Digumarthy Subba R. , Rinsurongkawong Waree , Rinsurongkawong Vadeerat , Vaporciyan Ara A , Blumenschein George R. , Zhang Jianjun , Owen Dwight H. , Blakely Collin M. , Mountzios Giannis , Shu Catherine A. , Bestvina Christine M. , Garassino Marina Chiara. , Marrone Kristen A. , Gray Jhanelle E. , Patel Sandip Pravin. , Cummings Amy L. , Wakelee Heather A. , Wolf Juergen , Scagliotti Giorgio Vittorio. , Cappuzzo Federico , Barlesi Fabrice , Patil Pradnya D. , Drusbosky Leylah , Gibbons Don L. , Meric-Bernstam Funda , Lee J. Jack , Heymach John V. , Hong David S. , Heist Rebecca S. , Awad Mark M. , Skoulidis Ferdinandos
Published: September 2024

List of major molecular profiling platforms included in the cohort
Supplementary Table S4 from Co-mutations and KRAS G12C inhibitor efficacy in advanced NSCLC
Authors: Negrao Marcelo V. , Araujo Haniel A. , Lamberti Giuseppe , Cooper Alissa J. , Akhave Neal S. , Zhou Teng , Delasos Lukas , Hicks J Kevin. , Aldea Mihaela , Minuti Gabriele , Hines Jacobi , Aredo Jacqueline V. , Dennis Michael J. , Chakrabarti Turja , Scott Susan C. , Bironzo Paolo , Scheffler Matthias , Christopoulos Petros , Stenzinger Albrecht , Riess Jonathan W. , Kim So Yeon , Goldberg Sarah B. , Li Mingjia , Wang Qi , Qing Yun , Ni Ying , Do Minh Truong , Lee Richard , Ricciuti Biagio , Alessi Joao Victor. , Wang Jing , Resuli Blerina , Landi Lorenza , Tseng Shu-Chi , Nishino Mizuki , Digumarthy Subba R. , Rinsurongkawong Waree , Rinsurongkawong Vadeerat , Vaporciyan Ara A , Blumenschein George R. , Zhang Jianjun , Owen Dwight H. , Blakely Collin M. , Mountzios Giannis , Shu Catherine A. , Bestvina Christine M. , Garassino Marina Chiara. , Marrone Kristen A. , Gray Jhanelle E. , Patel Sandip Pravin. , Cummings Amy L. , Wakelee Heather A. , Wolf Juergen , Scagliotti Giorgio Vittorio. , Cappuzzo Federico , Barlesi Fabrice , Patil Pradnya D. , Drusbosky Leylah , Gibbons Don L. , Meric-Bernstam Funda , Lee J. Jack , Heymach John V. , Hong David S. , Heist Rebecca S. , Awad Mark M. , Skoulidis Ferdinandos
Published: September 2024

Multivariable analysis - progression-free survival
Supplementary Figure S9 from Co-mutations and KRAS G12C inhibitor efficacy in advanced NSCLC
Authors: Negrao Marcelo V. , Araujo Haniel A. , Lamberti Giuseppe , Cooper Alissa J. , Akhave Neal S. , Zhou Teng , Delasos Lukas , Hicks J Kevin. , Aldea Mihaela , Minuti Gabriele , Hines Jacobi , Aredo Jacqueline V. , Dennis Michael J. , Chakrabarti Turja , Scott Susan C. , Bironzo Paolo , Scheffler Matthias , Christopoulos Petros , Stenzinger Albrecht , Riess Jonathan W. , Kim So Yeon , Goldberg Sarah B. , Li Mingjia , Wang Qi , Qing Yun , Ni Ying , Do Minh Truong , Lee Richard , Ricciuti Biagio , Alessi Joao Victor. , Wang Jing , Resuli Blerina , Landi Lorenza , Tseng Shu-Chi , Nishino Mizuki , Digumarthy Subba R. , Rinsurongkawong Waree , Rinsurongkawong Vadeerat , Vaporciyan Ara A , Blumenschein George R. , Zhang Jianjun , Owen Dwight H. , Blakely Collin M. , Mountzios Giannis , Shu Catherine A. , Bestvina Christine M. , Garassino Marina Chiara. , Marrone Kristen A. , Gray Jhanelle E. , Patel Sandip Pravin. , Cummings Amy L. , Wakelee Heather A. , Wolf Juergen , Scagliotti Giorgio Vittorio. , Cappuzzo Federico , Barlesi Fabrice , Patil Pradnya D. , Drusbosky Leylah , Gibbons Don L. , Meric-Bernstam Funda , Lee J. Jack , Heymach John V. , Hong David S. , Heist Rebecca S. , Awad Mark M. , Skoulidis Ferdinandos
Published: September 2024

A) Venn diagram depicting co-mutation overlap between KEAP1, SMARCA4, and CDKN2A – KSC genes; survival outcomes according to co-mutation overlap in any of the KSC genes - PFS (B) and OS (C). Only patients whose tumor was profiled with a NGS panel providing coverage for all 3 genes were included in this analysis.
Supplementary Figure S6 from Co-mutations and KRAS G12C inhibitor efficacy in advanced NSCLC
Authors: Negrao Marcelo V. , Araujo Haniel A. , Lamberti Giuseppe , Cooper Alissa J. , Akhave Neal S. , Zhou Teng , Delasos Lukas , Hicks J Kevin. , Aldea Mihaela , Minuti Gabriele , Hines Jacobi , Aredo Jacqueline V. , Dennis Michael J. , Chakrabarti Turja , Scott Susan C. , Bironzo Paolo , Scheffler Matthias , Christopoulos Petros , Stenzinger Albrecht , Riess Jonathan W. , Kim So Yeon , Goldberg Sarah B. , Li Mingjia , Wang Qi , Qing Yun , Ni Ying , Do Minh Truong , Lee Richard , Ricciuti Biagio , Alessi Joao Victor. , Wang Jing , Resuli Blerina , Landi Lorenza , Tseng Shu-Chi , Nishino Mizuki , Digumarthy Subba R. , Rinsurongkawong Waree , Rinsurongkawong Vadeerat , Vaporciyan Ara A , Blumenschein George R. , Zhang Jianjun , Owen Dwight H. , Blakely Collin M. , Mountzios Giannis , Shu Catherine A. , Bestvina Christine M. , Garassino Marina Chiara. , Marrone Kristen A. , Gray Jhanelle E. , Patel Sandip Pravin. , Cummings Amy L. , Wakelee Heather A. , Wolf Juergen , Scagliotti Giorgio Vittorio. , Cappuzzo Federico , Barlesi Fabrice , Patil Pradnya D. , Drusbosky Leylah , Gibbons Don L. , Meric-Bernstam Funda , Lee J. Jack , Heymach John V. , Hong David S. , Heist Rebecca S. , Awad Mark M. , Skoulidis Ferdinandos
Published: September 2024

Progression-free survival (left) and overall survival (right) according to TP53 co-mutation status in A) overall cohort, B) cohort A, and C) cohort B.
Supplementary Table S9 from C/EBPa confers dependence to fatty acid anabolic pathways and vulnerability to lipid oxidative stress-induced ferroptosis in FLT3-mutant leukemia
Authors: Sabatier Marie , Birsen Rudy , Lauture Laura , Mouche Sarah , Angelino Paolo , Dehairs Jonas , Goupille Lea , Boussaid Ismael , Heiblig Mael , Boet Emeline , Sahal Ambrine , Saland Estelle , Santos Juliana C. , Armengol Marc , Fernandez-Serrano Miranda , Farge Thomas , Cognet Guillaume , Simonetta Federico , Pignon Corentin , Graffeuil Antoine , Mazzotti Celine , Avet-Loiseau Herve , Delos Oceane , Bertrand-Michel Justine , Chedru Amelie , Dembitz Vilma , Gallipoli Paolo , Anstee Natasha S. , Loo Sun , Wei Andrew H. , Carroll Martin , Goubard Armelle , Castellano Remy , Collette Yves , Vergez Francois , Mansat-De Mas Veronique , Bertoli Sarah , Tavitian Suzanne , Picard Muriel , Recher Christian , Bourges-Abella Nathalie , Granat Fanny , Kosmider Olivier , Sujobert Pierre , Colsch Benoit , Joffre Carine , Stuani Lucille , Swinnen Johannes V. , Guillou Herve , Roue Gael , Hakim Nawad , Dejean Anne S. , Tsantoulis Petros , Larrue Clement , Bouscary Didier , Tamburini Jerome , Sarry Jean-Emmanuel
Published: September 2024

Table S9: CEBPA_UP signature
Supplementary Table S5 from C/EBPa confers dependence to fatty acid anabolic pathways and vulnerability to lipid oxidative stress-induced ferroptosis in FLT3-mutant leukemia
Authors: Sabatier Marie , Birsen Rudy , Lauture Laura , Mouche Sarah , Angelino Paolo , Dehairs Jonas , Goupille Lea , Boussaid Ismael , Heiblig Mael , Boet Emeline , Sahal Ambrine , Saland Estelle , Santos Juliana C. , Armengol Marc , Fernandez-Serrano Miranda , Farge Thomas , Cognet Guillaume , Simonetta Federico , Pignon Corentin , Graffeuil Antoine , Mazzotti Celine , Avet-Loiseau Herve , Delos Oceane , Bertrand-Michel Justine , Chedru Amelie , Dembitz Vilma , Gallipoli Paolo , Anstee Natasha S. , Loo Sun , Wei Andrew H. , Carroll Martin , Goubard Armelle , Castellano Remy , Collette Yves , Vergez Francois , Mansat-De Mas Veronique , Bertoli Sarah , Tavitian Suzanne , Picard Muriel , Recher Christian , Bourges-Abella Nathalie , Granat Fanny , Kosmider Olivier , Sujobert Pierre , Colsch Benoit , Joffre Carine , Stuani Lucille , Swinnen Johannes V. , Guillou Herve , Roue Gael , Hakim Nawad , Dejean Anne S. , Tsantoulis Petros , Larrue Clement , Bouscary Didier , Tamburini Jerome , Sarry Jean-Emmanuel
Published: September 2024

Table S5: GSEA results in FLT3-ITD PDX AML cells in vivo-treated with GILT or Veh.
Supplementary Table S3 from C/EBPa confers dependence to fatty acid anabolic pathways and vulnerability to lipid oxidative stress-induced ferroptosis in FLT3-mutant leukemia
Authors: Sabatier Marie , Birsen Rudy , Lauture Laura , Mouche Sarah , Angelino Paolo , Dehairs Jonas , Goupille Lea , Boussaid Ismael , Heiblig Mael , Boet Emeline , Sahal Ambrine , Saland Estelle , Santos Juliana C. , Armengol Marc , Fernandez-Serrano Miranda , Farge Thomas , Cognet Guillaume , Simonetta Federico , Pignon Corentin , Graffeuil Antoine , Mazzotti Celine , Avet-Loiseau Herve , Delos Oceane , Bertrand-Michel Justine , Chedru Amelie , Dembitz Vilma , Gallipoli Paolo , Anstee Natasha S. , Loo Sun , Wei Andrew H. , Carroll Martin , Goubard Armelle , Castellano Remy , Collette Yves , Vergez Francois , Mansat-De Mas Veronique , Bertoli Sarah , Tavitian Suzanne , Picard Muriel , Recher Christian , Bourges-Abella Nathalie , Granat Fanny , Kosmider Olivier , Sujobert Pierre , Colsch Benoit , Joffre Carine , Stuani Lucille , Swinnen Johannes V. , Guillou Herve , Roue Gael , Hakim Nawad , Dejean Anne S. , Tsantoulis Petros , Larrue Clement , Bouscary Didier , Tamburini Jerome , Sarry Jean-Emmanuel
Published: September 2024

Table S3: Clinical characteristics of samples from patients with AML used in PDX assays
Supplementary Information v.2 from C/EBPa confers dependence to fatty acid anabolic pathways and vulnerability to lipid oxidative stress-induced ferroptosis in FLT3-mutant leukemia
Authors: Sabatier Marie , Birsen Rudy , Lauture Laura , Mouche Sarah , Angelino Paolo , Dehairs Jonas , Goupille Lea , Boussaid Ismael , Heiblig Mael , Boet Emeline , Sahal Ambrine , Saland Estelle , Santos Juliana C. , Armengol Marc , Fernandez-Serrano Miranda , Farge Thomas , Cognet Guillaume , Simonetta Federico , Pignon Corentin , Graffeuil Antoine , Mazzotti Celine , Avet-Loiseau Herve , Delos Oceane , Bertrand-Michel Justine , Chedru Amelie , Dembitz Vilma , Gallipoli Paolo , Anstee Natasha S. , Loo Sun , Wei Andrew H. , Carroll Martin , Goubard Armelle , Castellano Remy , Collette Yves , Vergez Francois , Mansat-De Mas Veronique , Bertoli Sarah , Tavitian Suzanne , Picard Muriel , Recher Christian , Bourges-Abella Nathalie , Granat Fanny , Kosmider Olivier , Sujobert Pierre , Colsch Benoit , Joffre Carine , Stuani Lucille , Swinnen Johannes V. , Guillou Herve , Roue Gael , Hakim Nawad , Dejean Anne S. , Tsantoulis Petros , Larrue Clement , Bouscary Didier , Tamburini Jerome , Sarry Jean-Emmanuel
Published: September 2024

Supplementary materials and methods
Supplementary Table 4 from A Compendium of Syngeneic, Transplantable Pediatric High-Grade Glioma Models Reveals Subtype-Specific Therapeutic Vulnerabilities
Authors: McNicholas Michael , De Cola Antonella , Bashardanesh Zahedeh , Foss Amelia , Lloyd Cameron B. , Hebert Steven , Faury Damien , Andrade Augusto Faria. , Jabado Nada , Kleinman Claudia L. , Pathania Manav
Published: September 2024

Quality control and filtering of snRNA-seq data.
Supplementary Figures 1-27 from A Compendium of Syngeneic, Transplantable Pediatric High-Grade Glioma Models Reveals Subtype-Specific Therapeutic Vulnerabilities
Authors: McNicholas Michael , De Cola Antonella , Bashardanesh Zahedeh , Foss Amelia , Lloyd Cameron B. , Hebert Steven , Faury Damien , Andrade Augusto Faria. , Jabado Nada , Kleinman Claudia L. , Pathania Manav
Published: September 2024

Figures describing hindbrain vs ganglionic eminence targeting strategies, each of the 16 models generated and validation that they expressed the introduced mutations, survival of GE vs CTX-electroporated embryos, and cell viability data shown in bar graph format.
Table S5 from A transcriptome-based precision oncology platform for patient-therapy alignment in a diverse set of treatment resistant malignancies
Authors: Mundi Prabhjot S. , Dela Cruz Filemon S. , Grunn Adina , Diolaiti Daniel , Mauguen Audrey , Rainey Allison R. , Guillan Kristina , Siddiquee Armaan , You Daoqi , Realubit Ronald , Karan Charles , Ortiz Michael V. , Douglass Eugene F. , Accordino Melissa , Mistretta Suzanne , Brogan Frances , Bruce Jeffrey N. , Caescu Cristina I. , Carvajal Richard D. , Crew Katherine D. , Decastro Guarionex , Heaney Mark , Henick Brian S. , Hershman Dawn L. , Hou June Y. , Iwamoto Fabio M. , Jurcic Joseph G. , Kiran Ravi P. , Kluger Michael D. , Kreisl Teri , Lamanna Nicole , Lassman Andrew B. , Lim Emerson A. , Manji Gulam A. , McKhann Guy M. , McKiernan James M. , Neugut Alfred I. , Olive Kenneth P. , Rosenblat Todd , Schwartz Gary K. , Shu Catherine A. , Sisti Michael B. , Tergas Ana , Vattakalam Reena M. , Welch Mary , Wenske Sven , Wright Jason D. , Canoll Peter , Hibshoosh Hanina , Kalinsky Kevin , Aburi Mahalaxmi , Sims Peter A. , Alvarez Mariano J. , Kung Andrew L. , Califano Andrea
Published: September 2024

Comprehensive list of clinically relevant drugs screened in cell lines (not all were available at time of study). The list is divided into three sections, including one with FDA approved antineoplastics, one with experimental antineoplastics in clinical trials, and one with non-antineoplastics and tool compounds selectively screened when demonstrating an EC50 < 2μM.
Table S20 from Spatial Transcriptomics of Intraductal Papillary Mucinous Neoplasms of The Pancreas Identifies NKX6-2 as a Driver of Gastric Differentiation and Indolent Biological Potential
Authors: Sans Marta , Makino Yuki , Min Jimin , Rajapakshe Kimal I. , Yip-Schneider Michele , Schmidt C. Max , Hurd Mark W. , Burks Jared K. , Gomez Javier A. , Thege Fredrik I. , Fahrmann Johannes F. , Wolff Robert A. , Kim Michael P. , Guerrero Paola A. , Maitra Anirban
Published: September 2024

Overlap between genes differentially expressed in the NKX6-2 overexpressing and control Kras;Gnas cell line and genes differentially expressed in Nkx6-2 positive and negative spots from the Kras;Gnas ST epithelial spots.
Table S2 from Spatial Transcriptomics of Intraductal Papillary Mucinous Neoplasms of The Pancreas Identifies NKX6-2 as a Driver of Gastric Differentiation and Indolent Biological Potential
Authors: Sans Marta , Makino Yuki , Min Jimin , Rajapakshe Kimal I. , Yip-Schneider Michele , Schmidt C. Max , Hurd Mark W. , Burks Jared K. , Gomez Javier A. , Thege Fredrik I. , Fahrmann Johannes F. , Wolff Robert A. , Kim Michael P. , Guerrero Paola A. , Maitra Anirban
Published: September 2024

Gene markers per each of the scMC clusters from the IPMN dataset
Table S18 from Spatial Transcriptomics of Intraductal Papillary Mucinous Neoplasms of The Pancreas Identifies NKX6-2 as a Driver of Gastric Differentiation and Indolent Biological Potential
Authors: Sans Marta , Makino Yuki , Min Jimin , Rajapakshe Kimal I. , Yip-Schneider Michele , Schmidt C. Max , Hurd Mark W. , Burks Jared K. , Gomez Javier A. , Thege Fredrik I. , Fahrmann Johannes F. , Wolff Robert A. , Kim Michael P. , Guerrero Paola A. , Maitra Anirban
Published: September 2024

Differentially expressed genes between Nkx6-2 positive and negative spots in the Kras;Gnas ST epithelial spots.
Table S16 from Spatial Transcriptomics of Intraductal Papillary Mucinous Neoplasms of The Pancreas Identifies NKX6-2 as a Driver of Gastric Differentiation and Indolent Biological Potential
Authors: Sans Marta , Makino Yuki , Min Jimin , Rajapakshe Kimal I. , Yip-Schneider Michele , Schmidt C. Max , Hurd Mark W. , Burks Jared K. , Gomez Javier A. , Thege Fredrik I. , Fahrmann Johannes F. , Wolff Robert A. , Kim Michael P. , Guerrero Paola A. , Maitra Anirban
Published: September 2024

Top regulons in LG NKX6-2 positive and negative IPMN spots predicted with SCENIC.
Table S15 from Spatial Transcriptomics of Intraductal Papillary Mucinous Neoplasms of The Pancreas Identifies NKX6-2 as a Driver of Gastric Differentiation and Indolent Biological Potential
Authors: Sans Marta , Makino Yuki , Min Jimin , Rajapakshe Kimal I. , Yip-Schneider Michele , Schmidt C. Max , Hurd Mark W. , Burks Jared K. , Gomez Javier A. , Thege Fredrik I. , Fahrmann Johannes F. , Wolff Robert A. , Kim Michael P. , Guerrero Paola A. , Maitra Anirban
Published: September 2024

Predicted NKX6-2 targets and transcription factors associated with NKX6-2 expression evaluated by GENIE3.
Table S13 from Spatial Transcriptomics of Intraductal Papillary Mucinous Neoplasms of The Pancreas Identifies NKX6-2 as a Driver of Gastric Differentiation and Indolent Biological Potential
Authors: Sans Marta , Makino Yuki , Min Jimin , Rajapakshe Kimal I. , Yip-Schneider Michele , Schmidt C. Max , Hurd Mark W. , Burks Jared K. , Gomez Javier A. , Thege Fredrik I. , Fahrmann Johannes F. , Wolff Robert A. , Kim Michael P. , Guerrero Paola A. , Maitra Anirban
Published: September 2024

Correlation between percentage of NKX6-2 positive nuclei and GATA-6, MUC5AC, TFF1, and VIM protein expression.
Table S1 from Spatial Transcriptomics of Intraductal Papillary Mucinous Neoplasms of The Pancreas Identifies NKX6-2 as a Driver of Gastric Differentiation and Indolent Biological Potential
Authors: Sans Marta , Makino Yuki , Min Jimin , Rajapakshe Kimal I. , Yip-Schneider Michele , Schmidt C. Max , Hurd Mark W. , Burks Jared K. , Gomez Javier A. , Thege Fredrik I. , Fahrmann Johannes F. , Wolff Robert A. , Kim Michael P. , Guerrero Paola A. , Maitra Anirban
Published: September 2024

Table containing demographic and clinical patient information
Supplementary Table 6 from A novel type of monocytic leukemia stem cell revealed by the clinical use of venetoclax-based therapy
Authors: Pei Shanshan , Shelton Ian T. , Gillen Austin E. , Stevens Brett M. , Gasparetto Maura , Wang Yanan , Liu Lina , Liu Jun , Brunetti Tonya M. , Engel Krysta , Staggs Sarah , Showers William , Sheth Anagha Inguva. , Amaya Maria L. , Minhajuddin Mohammad , Winters Amanda , Patel Sweta B. , Tolison Hunter , Krug Anna E. , Young Tracy N. , Schowinsky Jeffrey , McMahon Christine M. , Smith Clayton A. , Pollyea Daniel A. , Jordan Craig T.
Published: September 2024

List of specimens used for CITE-seq analysis
Supplementary Table S5B from Clinical activity and exploratory resistance mechanism of milademetan, an MDM2 inhibitor, in intimal sarcoma with MDM2 amplification: an open-label phase 1b/2 study
Authors: Koyama Takafumi , Shimizu Toshio , Kojima Yuki , Sudo Kazuki , Okuma Hitomi Sumiyoshi. , Shimoi Tatsunori , Ichikawa Hitoshi , Kohsaka Shinji , Sadachi Ryo , Hirakawa Akihiro , Yoshida Akihiko , Ando Reiko Makihara. , Ueno Toshihide , Yanagaki Mitsuru , Matsui Naoko , Nakamura Kenichi , Yamamoto Noboru , Yonemori Kan
Published: September 2024

Whole-exome sequencing and RNA sequencing analyses of tumor tissue samples at pre-and post-treatment
Supplementary Table S4 from Clinical activity and exploratory resistance mechanism of milademetan, an MDM2 inhibitor, in intimal sarcoma with MDM2 amplification: an open-label phase 1b/2 study
Authors: Koyama Takafumi , Shimizu Toshio , Kojima Yuki , Sudo Kazuki , Okuma Hitomi Sumiyoshi. , Shimoi Tatsunori , Ichikawa Hitoshi , Kohsaka Shinji , Sadachi Ryo , Hirakawa Akihiro , Yoshida Akihiko , Ando Reiko Makihara. , Ueno Toshihide , Yanagaki Mitsuru , Matsui Naoko , Nakamura Kenichi , Yamamoto Noboru , Yonemori Kan
Published: September 2024

Progression-free survival ratio
Supplementary Table S3A-B from Clinical activity and exploratory resistance mechanism of milademetan, an MDM2 inhibitor, in intimal sarcoma with MDM2 amplification: an open-label phase 1b/2 study
Authors: Koyama Takafumi , Shimizu Toshio , Kojima Yuki , Sudo Kazuki , Okuma Hitomi Sumiyoshi. , Shimoi Tatsunori , Ichikawa Hitoshi , Kohsaka Shinji , Sadachi Ryo , Hirakawa Akihiro , Yoshida Akihiko , Ando Reiko Makihara. , Ueno Toshihide , Yanagaki Mitsuru , Matsui Naoko , Nakamura Kenichi , Yamamoto Noboru , Yonemori Kan
Published: September 2024

Pharmacokinetics