bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Table S3 from Association and prediction utilizing craniocaudal and mediolateral oblique view digital mammography and long-term breast cancer risk
Authors: Chen Simin , Tamimi Rulla M. , Colditz Graham A. , Jiang Shu
Published: September 2024

Supplementary Table S3: Hazards ratio for association between baseline risk factors and breast cancer risk among postmenopausal women using Full-VPD only.
Supplementary Table S1 from Association and prediction utilizing craniocaudal and mediolateral oblique view digital mammography and long-term breast cancer risk
Authors: Chen Simin , Tamimi Rulla M. , Colditz Graham A. , Jiang Shu
Published: September 2024

Supplementary Table S1: Hazards ratio for association between baseline risk factors and breast cancer risk among postmenopausal women using CC-VPD only.
Supplementary Figure S6 from Association and prediction utilizing craniocaudal and mediolateral oblique view digital mammography and long-term breast cancer risk
Authors: Chen Simin , Tamimi Rulla M. , Colditz Graham A. , Jiang Shu
Published: September 2024

Supplementary Figure S6: The proportional hazards assumption is deemed reasonable by checking the Schoenfeld residuals plot for MLO-VPD.
Supplementary Figure S2 from Association and prediction utilizing craniocaudal and mediolateral oblique view digital mammography and long-term breast cancer risk
Authors: Chen Simin , Tamimi Rulla M. , Colditz Graham A. , Jiang Shu
Published: September 2024

Supplementary Figure S2: Pearson correlation between our algorithm and Volpara shows strong positive linear relationship of 0.81.
Supplementary Table 2 from PRIMARY PREVENTION AND INTERCEPTION STUDIES IN RAS-MUTATED TUMOR MODELS EMPLOYING SMALL MOLECULES OR VACCINES
Authors: Dragnev Konstantin H. , Lubet Ronald A. , Miller Mark Steven. , Sei Shizuko , Fox Jennifer T. , You Ming
Published: September 2024

Supplementary Table 2 shows efficacy of multiple agents in MNU-induced (HRAS mutant) ER+ breast cancer in rat models.
Supplementary Table 1 from PRIMARY PREVENTION AND INTERCEPTION STUDIES IN RAS-MUTATED TUMOR MODELS EMPLOYING SMALL MOLECULES OR VACCINES
Authors: Dragnev Konstantin H. , Lubet Ronald A. , Miller Mark Steven. , Sei Shizuko , Fox Jennifer T. , You Ming
Published: September 2024

Supplementary Table 1 shows description of classes and specific agents active in RAS mutated rodent tumors.
Table S6 from Analysis of several common APOBEC-type mutations in bladder tumors suggests links to viral infection
Authors: Rao Nina , Starrett Gabriel J. , Piaskowski Mary L. , Butler Kelly E. , Golubeva Yelena , Yan Wusheng , Lawrence Scott M. , Dean Michael , Garcia-Closas Montserrat , Baris Dalsu , Johnson Alison , Schwenn Molly , Malats Nuria , Real Francisco X. , Kogevinas Manolis , Rothman Nathaniel , Silverman Debra T. , Dyrskjøt Lars , Buck Christopher B. , Koutros Stella , Prokunina-Olsson Ludmila
Published: September 2024

Table S6: Frequencies of APOBEC-type FGFR3 and PIK3CA mutations in relation to tumor viral status
Table S5 from Analysis of several common APOBEC-type mutations in bladder tumors suggests links to viral infection
Authors: Rao Nina , Starrett Gabriel J. , Piaskowski Mary L. , Butler Kelly E. , Golubeva Yelena , Yan Wusheng , Lawrence Scott M. , Dean Michael , Garcia-Closas Montserrat , Baris Dalsu , Johnson Alison , Schwenn Molly , Malats Nuria , Real Francisco X. , Kogevinas Manolis , Rothman Nathaniel , Silverman Debra T. , Dyrskjøt Lars , Buck Christopher B. , Koutros Stella , Prokunina-Olsson Ludmila
Published: September 2024

Table S5: Associations between driver mutations in BC and common risk factors
Table S3 from Analysis of several common APOBEC-type mutations in bladder tumors suggests links to viral infection
Authors: Rao Nina , Starrett Gabriel J. , Piaskowski Mary L. , Butler Kelly E. , Golubeva Yelena , Yan Wusheng , Lawrence Scott M. , Dean Michael , Garcia-Closas Montserrat , Baris Dalsu , Johnson Alison , Schwenn Molly , Malats Nuria , Real Francisco X. , Kogevinas Manolis , Rothman Nathaniel , Silverman Debra T. , Dyrskjøt Lars , Buck Christopher B. , Koutros Stella , Prokunina-Olsson Ludmila
Published: September 2024

Table S3: Positivity of virus transcript detection in bladder tumors from UROMOL
Figure S1 from Analysis of several common APOBEC-type mutations in bladder tumors suggests links to viral infection
Authors: Rao Nina , Starrett Gabriel J. , Piaskowski Mary L. , Butler Kelly E. , Golubeva Yelena , Yan Wusheng , Lawrence Scott M. , Dean Michael , Garcia-Closas Montserrat , Baris Dalsu , Johnson Alison , Schwenn Molly , Malats Nuria , Real Francisco X. , Kogevinas Manolis , Rothman Nathaniel , Silverman Debra T. , Dyrskjøt Lars , Buck Christopher B. , Koutros Stella , Prokunina-Olsson Ludmila
Published: September 2024

Figure S1: Molecular characterization of BKPyV in NMIBC tumors and HBLAK cells
Data from Precision cut lung slices as a preclinical model for non-small cell lung cancer chemoprevention
Authors: Sompel Kayla , Smith Alex J. , Hauer Caroline , Elango Alamelu P. , Clambey Eric T. , Keith Robert L. , Tennis Meredith A.
Published: September 2024

Abstract
Lung cancer chemoprevention is critical to addressing cancer burden in high-risk populations. Chemoprevention clinical trials rely on data from pre-clinical models however, in vivo studies have high financial, technical, and staffing requirements. Precision cut lung slices (PCLS) provide an ex vivo model that maintains the structure and function of native tissues. This model can be used for mechanistic investigations and drug screenings and reduces the number of animals and time required to test hypotheses compared to in vivo studies. We tested use of PCLS for chemoprevention studies, demonstrating recapitulation of in vivo models. Treatment of PCLS with the PPARγ agonizing chemoprevention agent iloprost produced similar effects on gene expression and downstream signaling as in vivo models. This occurred in both wildtype tissue and in Frizzled 9 knockout tissue, a transmembrane receptor required for iloprost’s preventive activity. We explored new areas of iloprost mechanisms by measuring immune and inflammation markers in PCLS tissue and media, and immune cell presence with immunofluorescence. To demonstrate potential for drug screening, we treated PCLS with additional lung cancer chemoprevention agents and confirmed activity markers in culture. PCLS offers an intermediate step for chemoprevention research between in vitro and in vivo models that can facilitate drug screening prior to in vivo studies and support mechanistic studies with more relevant tissue environments and functions than in vitro models.
Data from Reallocating Cervical Cancer Preventive Service Spending from Low to High-Value Clinical Scenarios
Authors: Rockwell Michelle S. , Armbruster Shannon D. , Capucao Jillian C. , Russell Kyle B. , Rockwell John A. , Perkins Karen E. , Huffstetler Alison N. , Mafi John N. , Fendrick A Mark.
Published: September 2024

Abstract
Timely follow-up care after an abnormal cervical cancer screening test result is critical to the prevention and early diagnosis of cervical cancer. The current inadequate and inequitable delivery of these potentially life-saving services is attributed to several factors, including patient out-of-pocket costs. Waiving of consumer cost-sharing for follow-up testing (e.g., colposcopy and related cervical services) is likely to improve access and uptake, especially among underserved populations. One approach to defray the incremental costs of providing more generous coverage for follow-up testing is reducing expenditures on ‘low value’ cervical cancer screening services. To explore the potential fiscal implications of a policy that redirects cervical cancer screening resources from potentially low to high-value clinical scenarios, we analyzed 2019 claims from the Virginia All-Payer Claims Database to quantify: 1) total spending on low-value cervical cancer screening and 2) out-of-pocket costs associated with colposcopy and related cervical services among commercially-insured Virginians. In a cohort of 1,806,921 female patients (aged 48.1 + 24.8 years), 295,193 claims for cervical cancer screening were reported, 100,567 (34.0%) of which were determined to be low-value ($4,394,361 total; $4,172,777 for payers and $221,584 out-of-pocket [$2/patient]). Claims for 52,369 colposcopy and related cervical services were reported ($40,994,016 total; $33,457,518 for payers and $7,536,498 out-of-pocket [$144/patient]). These findings suggest that reallocating savings incurred from unnecessary spending to fund more generous coverage of necessary follow-up care is a feasible approach to enhancing cervical cancer prevention equity and outcomes.
Data from Associations between physical activity and incidence of cancer among overweight adults in Korea: Results from the Health Examinees-G study
Authors: Choi Jaesung , Park JooYong , Kim Ji-Eun , Lee Miyoung , Kang Daehee , Shin Aesun , Choi Ji-Yeob
Published: September 2024

Abstract
Although the protective effects of physical activity against several cancers are well established, evidence is inconsistent concerning Asian populations. Therefore, we assessed the association between the characteristics of physical activity and overall and type-specific cancer incidence in Koreans and examined the differences in association according to obesity status. Using prospective data from 112,108 participants in the Health Examinees study-G from 2004 to 2013, we evaluated the association between leisure-time physical activity (LTPA) and the incidence of overall and type-specific cancers using the Cox proportional hazards model. Self-reported LTPA participation, duration per week, intensity, type, and diversity were assessed. The incidence of overall and type-specific cancers, including colorectal, gastric, lung, breast, and prostate cancer and 13 obesity-related cancers, was identified using the Korea Central Cancer Registry from 1999 to 2018. Analyses were also stratified according to obesity status. In overweight males, participation in vigorous LTPA (hazard ratio [HR]: 0.84, 95% confidence interval [CI]: 0.72–0.97) and walking (HR: 0.84, 95% CI: 0.72–0.98) were associated with a lower risk of cancer overall. Regarding cancer types, climbing was marginally associated with a lower risk of colorectal cancer in overweight males (HR: 0.61, 95% CI: 0.37–1.00). In normal-weight females, although there was an increased risk in those performing recreational activities, this risk was attenuated when those diagnosed with thyroid cancer were excluded. In the analysis for 13 obesity-related cancers, consistent associations were found. These findings suggest the need for greater public awareness regarding physical activity among overweight individuals within the Asian population.
Supplementary Figure S1-S11 and Table S1 from Splicing Factor SRSF1 Promotes Pancreatitis and KRASG12D-Mediated Pancreatic Cancer
Authors: Wan Ledong , Lin Kuang-Ting , Rahman Mohammad Alinoor. , Ishigami Yuma , Wang Zhikai , Jensen Mads A. , Wilkinson John E. , Park Youngkyu , Tuveson David A. , Krainer Adrian R.
Published: September 2024

Figure S1. Elevated SRSF1 induces pancreatitis and is associated with its duration. Figure S2. Elevated SRSF1 predicts poor PDAC clinical prognosis and is associated with PDAC progression. Figure S3. SRSF1 accelerates KRASG12D-mediated PDAC tumorigenesis. Figure S4. SRSF1 loss delays KRASG12D-mediated PDAC initiation. Figure S5. Opposite patterns of pathway enrichment by KRASG12D mutation versus SRSF1 upregulation. Figure S6. Recombination and activation of KrasG12D allele in pancreas cells from KC mice. Figure S7. KSC and KPSC mice exhibit a hyper-activated MAPK pathway, suppression of which diminished SRSF1-induced pancreatitis. Figure S8. Decreased SRSF1 expression perturbs MAPK signaling. Figure S9. MYC promotes SRSF1 expression in PDAC. Figure S10. SRSF1 regulates IL1R1 alternative splicing and expression. Figure S11. Knockout of Il1r1 rescues SRSF1-induced pancreatitis. Table S1. Oligonucleotides for PCR and short hairpin RNAs.
Supplemental Figure S8 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

TR-APC induction in solid tumor models attenuates tumor growth kinetics and prolongs survival
Table S2 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 Table S2: ## Raw count matrix of mini-pool CRISPR screens. ## Normalized gene scores in mini-pool screens.
Supplementary Fig. S2 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. S2 shows efficiency of gene editing in tumor cell lines for co-dependency screen.
Supplementary Table 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

Supplementary Table S8 shows the pathway analysis of the expression data from Supplementary Table S7.
Supplementary Figure 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

Prolonged exposure to MLL inhibitor VTP50469 does not affect the proliferation of TF-1 cells grown under cytokine-rich conditions.
Supplementary Figures S1-S24 from Integrative pan-cancer genomic and transcriptomic analyses of refractory metastatic cancer
Authors: Pradat Yoann , Viot Julien , Yurchenko Andrey A. , Gunbin Konstantin , Cerbone Luigi , Deloger Marc , Grisay Guillaume , Verlingue Loic , Scott Veronique , Padioleau Ismael , Panunzi Leonardo , Michiels Stefan , Hollebecque Antoine , Jules-Clement Gerome , Mezquita Laura , Laine Antoine , Loriot Yohann , Besse Benjamin , Friboulet Luc , Andre Fabrice , Cournede Paul-Henry , Gautheret Daniel , Nikolaev Sergey I.
Published: September 2024

These figures provide complementary information for the figures presented in the main text and illustrations of the methods section.
Supplementary Figure 5 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 time on HMA/Venetoclax
Supplementary Figure 3 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

Bcl-2 family gene expression in LSCs predicts in vitro response to HMA/VEN
Supplementary Figure 2 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

Transcriptomic and functional characterization of LSC-like cells
Supplementary Table S1 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

Differentially expressed pathways comparing transcriptomes in KRAS-TP53 co-altered (n=23) and KRAS-altered/TP53WT (n=5) derived from Cancer Cell Line Encyclopedia
Supplementary Materials 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

Supplementary Methods
Supplementary Figures with legends
Supplementary Tables S2, S4, S5-7
Supplementary Table S5 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 details of mutations identified in WGS of E-GM samples.
Supplementary Table S4 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 results of pairwise differential expression analysis between E-GM and gastric tissues and Atrophic gastritis and gastric tissue.
Supplementary Table S2 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 each cluster of cells.
Table 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

Genes comprising the TCF7 regulon, the type I IFN signature, and the EGR2 Co-expression signatures. Gene names and symbols are listed.
Figure S7 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

Gene expression and pathway enrichment analysis of CD4+ T cell clusters. (A) Heatmap showing differentially expressed genes between AAVS1 and EGR2 knockout (KO) CD4+ T-cells. (B-D) Top differentially regulated pathways in CD4+ EGR2 KO compared to AAVS1 KO CAR T-cells. Pathways were explored using: B, GO biological process. C, NCI-Nature Pathway Interaction Database 2015. D, ARCHS4 transcription factor (TF) co-expression.
Figure S4 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

Marker gene expression in CAR T-cell clusters. A, Uniform manifold approximation and projection (UMAP) plot of AAVS1 and EGR2 knockout (KO) CAR T-cell samples is shown. B, UMAP plots showing expression levels of CD4 and CD8. C, Violin plot depicting expression of cluster-defining markers in CD4+ T-cells. D, Differentially expressed genes in IL7R+ versus CTLA4+ CD4+ T-cells. E, Violin plots showing expression levels of cluster-defining markers in CD8+ T-cells. F, Heatmap displaying differentially expressed genes between CD8+ cell clusters. G, Cell cycle scores mapped on UMAP plots.
Supplementary Figure 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 Figure S5 demonstrate the significance of our liver score in predicting outcomes of BC and PDAC patients
Supplementary Table S5 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 - overall survival
Supplementary Figure S8 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) Survival outcomes in patients with additional RAS co-alterations (KRAS amplification, other KRAS, NRAS and/or HRAS somatic mutations) in the KSCWT population; B) outcomes according to AKT1/PIK3CA/MTOR/TSC1/2/PTEN co-mutation status for all patients evaluable for these co-alterations; survival outcomes according to ALK, ROS1, NTRK1-3 co-mutation status in C) all mutation-evaluable patients, and D) limiting the analysis to the KSC WT population.
Supplementary Figure S3 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

Survival outcomes according to KEAP1 (A), SMARCA4 (B), and CDKN2A (C) co-mutation status in Cohorts A and B.
Supplementary Figure S1 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

Clinical outcomes in Cohorts A (left) and B (right). A) progression-free survival; B) overall survival.
Supplementary Table S14 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 S14: PUFA/MUFA ratios in phospholipids
Supplementary Table S11 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 S11
Table S7 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

Current list of cancer cell lines with available drug perturbation RNASeq profiles, which together comprise the PanACEA resource.
Table S1 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

Summary of enrollment for the N of 1 trial to date, including numbers by cancer type, the attempt to develop a PDX, establishment of PDX, RNASeq/VIPER profiling of PDX when established, and completion of drug testing.
Supplementary Figures Part 2 from Analysis of donor pancreata defines the transcriptomic signature and microenvironment of early neoplastic lesions.
Authors: Carpenter Eileen S. , Elhossiny Ahmed M. , Kadiyala Padma , Li Jay , McGue Jake , Griffith Brian D. , Zhang Yaqing , Edwards Jacob , Nelson Sarah , Lima Fatima , Donahue Katelyn L. , Du Wenting , Bischoff Allison C. , Alomari Danyah , Watkoske Hannah R. , Mattea Michael , The Stephanie , Espinoza Carlos E. , Barrett Meredith , Sonnenday Christopher J. , Olden Nicholas , Chen Chin-Tung , Peterson Nicole , Gunchick Valerie , Sahai Vaibhav , Rao Arvind , Bednar Filip , Shi Jiaqi , Frankel Timothy L. , Pasca di Magliano Marina
Published: September 2024

Supplementary Figures 11-14 and associated legends.
Supplementary Figures Part 1 from Analysis of donor pancreata defines the transcriptomic signature and microenvironment of early neoplastic lesions.
Authors: Carpenter Eileen S. , Elhossiny Ahmed M. , Kadiyala Padma , Li Jay , McGue Jake , Griffith Brian D. , Zhang Yaqing , Edwards Jacob , Nelson Sarah , Lima Fatima , Donahue Katelyn L. , Du Wenting , Bischoff Allison C. , Alomari Danyah , Watkoske Hannah R. , Mattea Michael , The Stephanie , Espinoza Carlos E. , Barrett Meredith , Sonnenday Christopher J. , Olden Nicholas , Chen Chin-Tung , Peterson Nicole , Gunchick Valerie , Sahai Vaibhav , Rao Arvind , Bednar Filip , Shi Jiaqi , Frankel Timothy L. , Pasca di Magliano Marina
Published: September 2024

Supplementary Figures 1-10 and associated legends
Supplementary Figures S1-S22 from Integrative analysis of a large real-world cohort of small cell lung cancer identifies distinct genetic subtypes and insights into histological transformation
Authors: Sivakumar Smruthy , Moore Jay A. , Montesion Meagan , Sharaf Radwa , Lin Douglas I. , Colon Caterina I. , Fleischmann Zoe , Ebot Ericka M. , Newberg Justin Y. , Mills Jennifer M. , Hegde Priti S. , Pan Quintin , Dowlati Afshin , Frampton Garrett M. , Sage Julien , Lovly Christine M.
Published: September 2024

Figure S1: Patterns of tumor mutational burden across different ancestry groups.
Figure S2: Spectrum of TP53 and RB1 mutations in SCLC.
Figure S3: Gene alteration landscape detected from targeted sequencing of liquid biopsies.
Figure S4: Chromosomal loss events are frequent in SCLC and are preferentially enriched for tumor suppressor genes.
Figure S5: Hematoxylin & Eosin (H&E) staining for some representative SCLC tumors with rare genomic alterations.
Figure S6: Gene alterations detected in SMARCA4-altered SCLC.
Figure S7: SCLC tumors exhibit recurrent gene rearrangements with therapeutic potential.
Figure S8: Trends of overall survival across different ancestry groups and stage in the clinical cohort.
Figure S9: Examination of tumor purity and tumor mutational burden (TMB).
Figure S10: Liver and Brain SCLC metastases are enriched for chromosomal arm-level gains compared to lung-biopsied SCLC tumors.
Figure S11: SCLC tumors present with unique co-occurring and mutual exclusive patterns of gene alterations.
Figure S12: SCLC tumors with wild-type TP53 and/or RB1 have a low tumor mutational burden.
Figure S13: SCLC tumors with wild-type TP53 and/or RB1 present with specific gene alterations.
Figure S14: A smoking-associated mutational signature is rare in TP53/RB1 WT SCLC tumors.
Figure S15: TP53 and RB1 alterations are less frequent in never smokers.
Figure S16: Patterns of overall survival based on TP53 and RB1 alteration status.
Figure S17: TP53 and RB1 mutations are more frequent in older patients with SCLC.
Figure S18: Gene alterations detected in HPV-positive SCLC.
Figure S19: Examination of HPV subtypes and prevalence in TP53/RB1 mutant and wild-type SCLC tumors.
Figure S20: EGFR-mutant SCLC tumors exhibit unique mutational signature profiles.
Figure S21: No overall survival differences based on EGFR mutation status in SCLC.
Figure S22: Putative transformed SCLC tumors from EGFR-mutant NSCLC are enriched for EGFR exon 19 deletions.
Table S5 from An African-specific variant of TP53 reveals PADI4 as a regulator of p53-mediated tumor suppression
Authors: Indeglia Alexandra , Leung Jessica C. , Miller Sven A. , Leu Julia I-Ju , Dougherty James F. , Clarke Nicole L. , Kirven Nicole A. , Shao Chunlei , Ke Lei , Lovell Scott , Barnoud Thibaut , Lu David Y. , Lin Cindy , Kannan Toshitha , Battaile Kevin P. , Yang Tyler Hong Loong. , Batista Oliva Isabela , Claiborne Daniel T. , Vogel Peter , Liu Lijun , Liu Qin , Nefedova Yulia , Cassel Joel , Auslander Noam , Kossenkov Andrew V. , Karanicolas John , Murphy Maureen E.
Published: September 2024

Secondary Validations of top drug hits from HCT116 WT vs Y107H clones.
Table S1 from An African-specific variant of TP53 reveals PADI4 as a regulator of p53-mediated tumor suppression
Authors: Indeglia Alexandra , Leung Jessica C. , Miller Sven A. , Leu Julia I-Ju , Dougherty James F. , Clarke Nicole L. , Kirven Nicole A. , Shao Chunlei , Ke Lei , Lovell Scott , Barnoud Thibaut , Lu David Y. , Lin Cindy , Kannan Toshitha , Battaile Kevin P. , Yang Tyler Hong Loong. , Batista Oliva Isabela , Claiborne Daniel T. , Vogel Peter , Liu Lijun , Liu Qin , Nefedova Yulia , Cassel Joel , Auslander Noam , Kossenkov Andrew V. , Karanicolas John , Murphy Maureen E.
Published: September 2024

RNA-seq of top genes identified in Y107H vs WT LCLs, related to Figure 2.
Supplementary Tables S1-S12 from Targeting N-linked Glycosylation for the Therapy of Aggressive Lymphomas
Authors: Scheich Sebastian , Chen Jiji , Liu Jiamin , Schnutgen Frank , Enssle Julius C. , Ceribelli Michele , Thomas Craig J. , Choi Jaewoo , Morris Vivian , Hsiao Tony , Nguyen Hang , Wang Boya , Bolomsky Arnold , Phelan James D. , Corcoran Sean , Urlaub Henning , Young Ryan M. , Haupl Bjorn , Wright George W. , Huang Da Wei , Ji Yanlong , Yu Xin , Xu Weihong , Yang Yandan , Zhao Hong , Muppidi Jagan , Pan Kuan-Ting , Oellerich Thomas , Staudt Louis M.
Published: September 2024

Table S1. Brunello library sgRNA normalized read counts of IRF4 sorted CRISPR screens. Table S2. Segregation score of IRF4 sorted CRISPR screens. Table S3. Glycoproteomics in STT3A or STT3B KO cells. Table S4. Brunello sgRNA Library Normalized Read Counts of CRISPR screens. Table S5. CRISPR screen score of essentiality screens. Table S6. Glycoproteomics after NGI-1 treatment. Table S7.HBL1 and TMD8 Phosphotyrosone Phosphoproteome (pYome). Table S8. TMD8 CD79A-BioID. Table S9. HBL1 CD22 BioID. Table S10. Brunello library sgRNA normalized read counts of NGI-1 drug modified screen (TMD8). Table S11. CRISPR screen score of NGI-1 drug modifier screen. Table S12. TMD8 Drug screen Excess HSA.
Supplementary Table S2 from Distinct assemblies of heterodimeric cytokine receptors govern stemness programs in leukemia
Authors: Kan Winnie L. , Dhagat Urmi , Kaufmann Kerstin B. , Hercus Timothy R. , Nero Tracy L. , Zeng Andy GX. , Toubia John , Barry Emma F. , Broughton Sophie E. , Gomez Guillermo A. , Benard Brooks A. , Dottore Mara , Cheung Tung Shing Karen S. , Boutzen Helena , Samaraweera Saumya E. , Simpson Kaylene J. , Jin Liqing , Goodall Gregory J. , Begley C. Glenn , Thomas Daniel , Ekert Paul G. , Tvorogov Denis , D'Andrea Richard J. , Dick John E. , Parker Michael W. , Lopez Angel F.
Published: September 2024

Summary of the key interactions in the IL-3R ternary complex in the IL-3R ternary complex crystal structure.
Figure S4 from Distinct assemblies of heterodimeric cytokine receptors govern stemness programs in leukemia
Authors: Kan Winnie L. , Dhagat Urmi , Kaufmann Kerstin B. , Hercus Timothy R. , Nero Tracy L. , Zeng Andy GX. , Toubia John , Barry Emma F. , Broughton Sophie E. , Gomez Guillermo A. , Benard Brooks A. , Dottore Mara , Cheung Tung Shing Karen S. , Boutzen Helena , Samaraweera Saumya E. , Simpson Kaylene J. , Jin Liqing , Goodall Gregory J. , Begley C. Glenn , Thomas Daniel , Ekert Paul G. , Tvorogov Denis , D'Andrea Richard J. , Dick John E. , Parker Michael W. , Lopez Angel F.
Published: September 2024

The IL-3R dodecamer activates STAT1 to induce cell differentiation.
Figure S1 from Distinct assemblies of heterodimeric cytokine receptors govern stemness programs in leukemia
Authors: Kan Winnie L. , Dhagat Urmi , Kaufmann Kerstin B. , Hercus Timothy R. , Nero Tracy L. , Zeng Andy GX. , Toubia John , Barry Emma F. , Broughton Sophie E. , Gomez Guillermo A. , Benard Brooks A. , Dottore Mara , Cheung Tung Shing Karen S. , Boutzen Helena , Samaraweera Saumya E. , Simpson Kaylene J. , Jin Liqing , Goodall Gregory J. , Begley C. Glenn , Thomas Daniel , Ekert Paul G. , Tvorogov Denis , D'Andrea Richard J. , Dick John E. , Parker Michael W. , Lopez Angel F.
Published: September 2024

IL3Rα/βc transcript and protein expression ratio in AML patient samples.
Supplementary Data Tables from A Novel Autologous CAR-T Therapy, YTB323, with Preserved T-Cell Stemness Shows Enhanced CAR T-Cell Efficacy in Preclinical and Early Clinical Development
Authors: Dickinson Michael J. , Barba Pere , Jager Ulrich , Shah Nirav N. , Blaise Didier , Briones Javier , Shune Leyla , Boissel Nicolas , Bondanza Attilio , Mariconti Luisa , Marchal Anne-Laure , Quinn David S. , Yang Jennifer , Price Andrew , Sohoni Akash , Treanor Louise M. , Orlando Elena J. , Mataraza Jennifer , Davis Jaclyn , Lu Darlene , Zhu Xu , Engels Boris , Moutouh-de Parseval Laure , Brogdon Jennifer L. , Moschetta Michele , Flinn Ian W.
Published: September 2024

Supplementary Table S1. Bridging chemotherapies by ATC class and preferred term (safety set); Supplementary Table S2. Lymphodepleting chemotherapies (safety set); Supplementary Table S3. Cytokine release syndrome following YTB323 infusion; Supplementary Table S4. Neurological adverse reactions following YTB323 infusion; Supplementary Table S5. Summary of cellular kinetic parameters in peripheral blood by flow cytometry for YTB323 at DL1 and DL2; Supplementary Table S6. Summary of cellular kinetic parameters in peripheral blood by flow cytometry and qPCR for YTB323 at DL1 and DL2.
Supplementary Data Figures from A Novel Autologous CAR-T Therapy, YTB323, with Preserved T-Cell Stemness Shows Enhanced CAR T-Cell Efficacy in Preclinical and Early Clinical Development
Authors: Dickinson Michael J. , Barba Pere , Jager Ulrich , Shah Nirav N. , Blaise Didier , Briones Javier , Shune Leyla , Boissel Nicolas , Bondanza Attilio , Mariconti Luisa , Marchal Anne-Laure , Quinn David S. , Yang Jennifer , Price Andrew , Sohoni Akash , Treanor Louise M. , Orlando Elena J. , Mataraza Jennifer , Davis Jaclyn , Lu Darlene , Zhu Xu , Engels Boris , Moutouh-de Parseval Laure , Brogdon Jennifer L. , Moschetta Michele , Flinn Ian W.
Published: September 2024

Supplementary Fig. S1. Preclinical evaluation and characterization of YTB323 and CTL*019 for Donor 2 and 3; Supplementary Fig. S2. Differential gene expression of CTL*019 cells versus YTB323 cells (preclinical); Supplementary Fig. S3. Preclinical validation of YTB323; Supplementary Fig. S4. Dose-dependent expansion (Cmax and AUC0-21d) of YTB323 and CTL*019 in NSG mice with NALM6; Supplementary Fig. S5. CD4:CD8 ratio comparison of leukapheresis and cell products of YTB323 and tisagenlecleucel; Supplementary Fig. S6. Stemness and memory differentiation gene signatures are retained or enriched for in YTB323 final product; Supplementary Fig. S7. Differential gene expression of tisagenlecleucel versus YTB323 final product; Supplementary Fig. S8. Naive/TSCM cells and a naive stem-like gene signature correlate with higher expansion and a better response; Supplementary Fig. S9. T-cell subset and checkpoint inhibitor analysis by flow cytometry on PBMCs collected post-YTB323 infusion; Supplementary Fig. S10. Pre-clinical T-cell gating strategies.
Supplementary Table S1 from FH variant pathogenicity promotes purine salvage pathway dependence in kidney cancer
Authors: Wilde Blake R. , Chakraborty Nishma , Matulionis Nedas , Hernandez Stephanie , Ueno Daiki , Gee Michayla E. , Esplin Edward D. , Ouyang Karen , Nykamp Keith , Shuch Brian , Christofk Heather R.
Published: September 2024

Supplementary Table S1: FH variants with population frequencies, interpretations of pathogenicity, catalytic efficiencies, and multimerization states
Supplementary Table 2 from The MDM2–p53 antagonist BI 907828 in patients with advanced or metastatic solid tumors: results of a phase Ia, first-in-human, dose-escalation study
Authors: LoRusso Patricia , Yamamoto Noboru , Patel Manish R. , Laurie Scott A. , Bauer Todd M. , Geng Junxian , Davenport Teffany , Teufel Michael , Li Jian , Lahmar Mehdi , Gounder Mrinal M.
Published: September 2024

Most common any-cause adverse events by highest CTCAE grade with BI 907828 monotherapy
Supplementary Table 1 from The MDM2–p53 antagonist BI 907828 in patients with advanced or metastatic solid tumors: results of a phase Ia, first-in-human, dose-escalation study
Authors: LoRusso Patricia , Yamamoto Noboru , Patel Manish R. , Laurie Scott A. , Bauer Todd M. , Geng Junxian , Davenport Teffany , Teufel Michael , Li Jian , Lahmar Mehdi , Gounder Mrinal M.
Published: September 2024

Study representativeness table