bluuebunny/crossref_metadata_2025 huggingface dataset:
Table S2 from Single-Cell Discovery and Multiomic Characterization of Therapeutic Targets in Multiple Myeloma
Authors: Yao Lijun , Wang Julia T. , Jayasinghe Reyka G. , O'Neal Julie , Tsai Chia-Feng , Rettig Michael P. , Song Yizhe , Liu Ruiyang , Zhao Yanyan , Ibrahim Omar M. , Fiala Mark A. , Fortier Julie M. , Chen Siqi , Gehrs Leah , Rodrigues Fernanda Martins , Wendl Michael C. , Kohnen Daniel , Shinkle Andrew , Cao Song , Foltz Steven M. , Zhou Daniel Cui , Storrs Erik , Wyczalkowski Matthew A. , Mani Smrithi , Goldsmith Scott R. , Zhu Ying , Hamilton Mark , Liu Tao , Chen Feng , Vij Ravi , Ding Li , DiPersio John F.
Published: April 2023

Novelty description of candidate tumor markers. Each gene is ranked according to existing literature and/or clinical trials investigating its role in multiple myeloma. Representative studies are listed.
Suppl video 3 from Neutrophil Conversion to a Tumor-Killing Phenotype Underpins Effective Microbial Therapy
Authors: Yam Andrew O. , Bailey Jacqueline , Lin Francis , Jakovija Arnolda , Youlten Scott E. , Counoupas Claudio , Gunzer Matthias , Bald Tobias , Woodruff Trent M. , Triccas James A. , Goldstein Leonard D. , Gallego-Ortega David , Grey Shane T. , Chtanova Tatyana
Published: April 2023

Neutrophils engage in multiple interactions with LLC tumor cells following microbial bioparticle treatment.
Table S1 from Single-Cell Discovery and Multiomic Characterization of Therapeutic Targets in Multiple Myeloma
Authors: Yao Lijun , Wang Julia T. , Jayasinghe Reyka G. , O'Neal Julie , Tsai Chia-Feng , Rettig Michael P. , Song Yizhe , Liu Ruiyang , Zhao Yanyan , Ibrahim Omar M. , Fiala Mark A. , Fortier Julie M. , Chen Siqi , Gehrs Leah , Rodrigues Fernanda Martins , Wendl Michael C. , Kohnen Daniel , Shinkle Andrew , Cao Song , Foltz Steven M. , Zhou Daniel Cui , Storrs Erik , Wyczalkowski Matthew A. , Mani Smrithi , Goldsmith Scott R. , Zhu Ying , Hamilton Mark , Liu Tao , Chen Feng , Vij Ravi , Ding Li , DiPersio John F.
Published: April 2023

Clinical information of patients in scRNA-seq discovery cohort, flow cytometry validation cohort and proteomics validation cohort, including age, gender, race, ISS stage, time to disease progression (TTPD). Disease stage for WashU cohort 1.
Suppl video 2 from Neutrophil Conversion to a Tumor-Killing Phenotype Underpins Effective Microbial Therapy
Authors: Yam Andrew O. , Bailey Jacqueline , Lin Francis , Jakovija Arnolda , Youlten Scott E. , Counoupas Claudio , Gunzer Matthias , Bald Tobias , Woodruff Trent M. , Triccas James A. , Goldstein Leonard D. , Gallego-Ortega David , Grey Shane T. , Chtanova Tatyana
Published: April 2023

Neutrophil interactions with LLC cells in unmanipulated and treated tumors.
Supplementary Figures from Single-Cell Discovery and Multiomic Characterization of Therapeutic Targets in Multiple Myeloma
Authors: Yao Lijun , Wang Julia T. , Jayasinghe Reyka G. , O'Neal Julie , Tsai Chia-Feng , Rettig Michael P. , Song Yizhe , Liu Ruiyang , Zhao Yanyan , Ibrahim Omar M. , Fiala Mark A. , Fortier Julie M. , Chen Siqi , Gehrs Leah , Rodrigues Fernanda Martins , Wendl Michael C. , Kohnen Daniel , Shinkle Andrew , Cao Song , Foltz Steven M. , Zhou Daniel Cui , Storrs Erik , Wyczalkowski Matthew A. , Mani Smrithi , Goldsmith Scott R. , Zhu Ying , Hamilton Mark , Liu Tao , Chen Feng , Vij Ravi , Ding Li , DiPersio John F.
Published: April 2023

supplementary figures
Supplementary Data from AKT Blocks SIK1-Mediated Repression of STAT3 to Promote Breast Tumorigenesis
Authors: Sun Zicheng , Jiang Qiwei , Gao Bing , Zhang Xiaomei , Bu Lang , Wang Lei , Lin Ying , Xie Wei , Li Jie , Guo Jianping
Published: April 2023

Including supplementary figure S1-9
Supplementary Figure S1 from Germline Cancer Gene Expression Quantitative Trait Loci Are Associated with Local and Global Tumor Mutations
Authors: Liu Yuxi , Gusev Alexander , Kraft Peter
Published: April 2023

Supplementary Figure S1
Table S7 from TONSL Is an Immortalizing Oncogene and a Therapeutic Target in Breast Cancer
Authors: Khatpe Aditi S. , Dirks Rebecca , Bhat-Nakshatri Poornima , Mang Henry , Batic Katie , Swiezy Sarah , Olson Jacob , Rao Xi , Wang Yue , Tanaka Hiromi , Liu Sheng , Wan Jun , Chen Duojiao , Liu Yunlong , Fang Fang , Althouse Sandra , Hulsey Emily , Granatir Maggie M. , Addison Rebekah , Temm Constance J. , Sandusky George , Lee-Gosselin Audrey , Nephew Kenneth , Miller Kathy D. , Nakshatri Harikrishna
Published: April 2023

Table S7: Univariable analysis of other tumor markers for overall and progression-free survival
Figure S1-9 from Dysregulation of Mitochondrial Translation Caused by CBFB Deficiency Cooperates with Mutant PIK3CA and Is a Vulnerability in Breast Cancer
Authors: Malik Navdeep , Kim Young-Im , Yan Hualong , Tseng Yu-Chou , du Bois Wendy , Ayaz Gamze , Tran Andy D. , Vera-Ramirez Laura , Yang Howard , Michalowski Aleksandra M. , Kruhlak Michael , Lee Maxwell , Hunter Kent W. , Huang Jing
Published: April 2023

This file contains supplementary figure 1-9.
Table S5 from TONSL Is an Immortalizing Oncogene and a Therapeutic Target in Breast Cancer
Authors: Khatpe Aditi S. , Dirks Rebecca , Bhat-Nakshatri Poornima , Mang Henry , Batic Katie , Swiezy Sarah , Olson Jacob , Rao Xi , Wang Yue , Tanaka Hiromi , Liu Sheng , Wan Jun , Chen Duojiao , Liu Yunlong , Fang Fang , Althouse Sandra , Hulsey Emily , Granatir Maggie M. , Addison Rebekah , Temm Constance J. , Sandusky George , Lee-Gosselin Audrey , Nephew Kenneth , Miller Kathy D. , Nakshatri Harikrishna
Published: April 2023

Table S5: Description of the patients and characteristics of their tumors (n=597)
Table S4 from TONSL Is an Immortalizing Oncogene and a Therapeutic Target in Breast Cancer
Authors: Khatpe Aditi S. , Dirks Rebecca , Bhat-Nakshatri Poornima , Mang Henry , Batic Katie , Swiezy Sarah , Olson Jacob , Rao Xi , Wang Yue , Tanaka Hiromi , Liu Sheng , Wan Jun , Chen Duojiao , Liu Yunlong , Fang Fang , Althouse Sandra , Hulsey Emily , Granatir Maggie M. , Addison Rebekah , Temm Constance J. , Sandusky George , Lee-Gosselin Audrey , Nephew Kenneth , Miller Kathy D. , Nakshatri Harikrishna
Published: April 2023

Table S4: Breast cancers with TONSL amplification selectively overexpress genes associated with E2F targets, G2/M checkpoint, mitotic spindle and mTORC1 pathways.
Supplementry Table 3: REACTOME Gene Set Enrichment Analysis results from Spatially Resolved Transcriptomics Deconvolutes Prognostic Histological Subgroups in Patients with Colorectal Cancer and Synchronous Liver Metastases
Authors: Wood Colin S. , Pennel Kathryn A.F. , Leslie Holly , Legrini Assya , Cameron Andrew J. , Melissourgou-Syka Lydia , Quinn Jean A. , van Wyk Hester C. , Hay Jennifer , Roseweir Antonia K. , Nixon Colin , Roxburgh Campbell S.D. , McMillan Donald C. , Biankin Andrew V. , Sansom Owen J. , Horgan Paul G. , Edwards Joanne , Steele Colin W. , Jamieson Nigel B.
Published: April 2023

Gene Set Enrichment Analysis results obtained by interrogating ranked list of differentially expressed KM high vs KM low genes against the REACTOME curated gene set database using ClusterProfiler package
Supplementary Table 4: SpatialDecon derived immune cell counts from Spatially Resolved Transcriptomics Deconvolutes Prognostic Histological Subgroups in Patients with Colorectal Cancer and Synchronous Liver Metastases
Authors: Wood Colin S. , Pennel Kathryn A.F. , Leslie Holly , Legrini Assya , Cameron Andrew J. , Melissourgou-Syka Lydia , Quinn Jean A. , van Wyk Hester C. , Hay Jennifer , Roseweir Antonia K. , Nixon Colin , Roxburgh Campbell S.D. , McMillan Donald C. , Biankin Andrew V. , Sansom Owen J. , Horgan Paul G. , Edwards Joanne , Steele Colin W. , Jamieson Nigel B.
Published: April 2023

SpatialDecon derived immune cell counts aggregated by Region, KM grade and KRAS status with pairwise comparison between groups. Mann-Whitney test used to determine statistical significance between groups
Supplementary Methods from Spatially Resolved Transcriptomics Deconvolutes Prognostic Histological Subgroups in Patients with Colorectal Cancer and Synchronous Liver Metastases
Authors: Wood Colin S. , Pennel Kathryn A.F. , Leslie Holly , Legrini Assya , Cameron Andrew J. , Melissourgou-Syka Lydia , Quinn Jean A. , van Wyk Hester C. , Hay Jennifer , Roseweir Antonia K. , Nixon Colin , Roxburgh Campbell S.D. , McMillan Donald C. , Biankin Andrew V. , Sansom Owen J. , Horgan Paul G. , Edwards Joanne , Steele Colin W. , Jamieson Nigel B.
Published: April 2023

Supplementary details regarding methods and materials
Table S13 from TONSL Is an Immortalizing Oncogene and a Therapeutic Target in Breast Cancer
Authors: Khatpe Aditi S. , Dirks Rebecca , Bhat-Nakshatri Poornima , Mang Henry , Batic Katie , Swiezy Sarah , Olson Jacob , Rao Xi , Wang Yue , Tanaka Hiromi , Liu Sheng , Wan Jun , Chen Duojiao , Liu Yunlong , Fang Fang , Althouse Sandra , Hulsey Emily , Granatir Maggie M. , Addison Rebekah , Temm Constance J. , Sandusky George , Lee-Gosselin Audrey , Nephew Kenneth , Miller Kathy D. , Nakshatri Harikrishna
Published: April 2023

Table S13: Enrichment of binding sites for NF-kB and p53 in chromatin regions that become accessible or closed, respectively, upon TONSL overexpression. Genes names and chromatin positions are indicated.
Supplementary Data from Active Remodeling of Capillary Endothelium via Cancer Cell–Derived MMP9 Promotes Metastatic Brain Colonization
Authors: Karreman Matthia A. , Bauer Alexander T. , Solecki Gergely , Berghoff Anna S. , Mayer Chanté D. , Frey Katharina , Hebach Nils , Feinauer Manuel J. , Schieber Nicole L. , Tehranian Cedric , Mercier Luc , Singhal Mahak , Venkataramani Varun , Schubert Marc C. , Hinze Daniel , Hölzel Michael , Helfrich Iris , Schadendorf Dirk , Schneider Stefan W. , Westphal Dana , Augustin Hellmut G. , Goetz Jacky G. , Schwab Yannick , Wick Wolfgang , Winkler Frank
Published: April 2023

Supplementary Figures and Figure legends, Supplementary Video legends and supplementary materials and methods
Supplementary Data from TONSL Is an Immortalizing Oncogene and a Therapeutic Target in Breast Cancer
Authors: Khatpe Aditi S. , Dirks Rebecca , Bhat-Nakshatri Poornima , Mang Henry , Batic Katie , Swiezy Sarah , Olson Jacob , Rao Xi , Wang Yue , Tanaka Hiromi , Liu Sheng , Wan Jun , Chen Duojiao , Liu Yunlong , Fang Fang , Althouse Sandra , Hulsey Emily , Granatir Maggie M. , Addison Rebekah , Temm Constance J. , Sandusky George , Lee-Gosselin Audrey , Nephew Kenneth , Miller Kathy D. , Nakshatri Harikrishna
Published: April 2023

Contains additional materials and methods and supplementary figures
Supplementary Data from Active Remodeling of Capillary Endothelium via Cancer Cell–Derived MMP9 Promotes Metastatic Brain Colonization
Authors: Karreman Matthia A. , Bauer Alexander T. , Solecki Gergely , Berghoff Anna S. , Mayer Chanté D. , Frey Katharina , Hebach Nils , Feinauer Manuel J. , Schieber Nicole L. , Tehranian Cedric , Mercier Luc , Singhal Mahak , Venkataramani Varun , Schubert Marc C. , Hinze Daniel , Hölzel Michael , Helfrich Iris , Schadendorf Dirk , Schneider Stefan W. , Westphal Dana , Augustin Hellmut G. , Goetz Jacky G. , Schwab Yannick , Wick Wolfgang , Winkler Frank
Published: April 2023

Supplementary Movie 1
Supplementary Table S1 from G-Quadruplex Structures Are Key Modulators of Somatic Structural Variants in Cancers
Authors: Zhang Rongxin , Shu Huiling , Wang Yuqi , Tao Tiantong , Tu Jing , Wang Cheng , Mergny Jean-Louis , Sun Xiao
Published: April 2023

in vivo G-quadruplex data used in this study
Supplementary Data from Active Remodeling of Capillary Endothelium via Cancer Cell–Derived MMP9 Promotes Metastatic Brain Colonization
Authors: Karreman Matthia A. , Bauer Alexander T. , Solecki Gergely , Berghoff Anna S. , Mayer Chanté D. , Frey Katharina , Hebach Nils , Feinauer Manuel J. , Schieber Nicole L. , Tehranian Cedric , Mercier Luc , Singhal Mahak , Venkataramani Varun , Schubert Marc C. , Hinze Daniel , Hölzel Michael , Helfrich Iris , Schadendorf Dirk , Schneider Stefan W. , Westphal Dana , Augustin Hellmut G. , Goetz Jacky G. , Schwab Yannick , Wick Wolfgang , Winkler Frank
Published: April 2023

Supplementary Movie 2
Supplementary Data from Active Remodeling of Capillary Endothelium via Cancer Cell–Derived MMP9 Promotes Metastatic Brain Colonization
Authors: Karreman Matthia A. , Bauer Alexander T. , Solecki Gergely , Berghoff Anna S. , Mayer Chanté D. , Frey Katharina , Hebach Nils , Feinauer Manuel J. , Schieber Nicole L. , Tehranian Cedric , Mercier Luc , Singhal Mahak , Venkataramani Varun , Schubert Marc C. , Hinze Daniel , Hölzel Michael , Helfrich Iris , Schadendorf Dirk , Schneider Stefan W. , Westphal Dana , Augustin Hellmut G. , Goetz Jacky G. , Schwab Yannick , Wick Wolfgang , Winkler Frank
Published: April 2023

Supplementary Movie 3
Supplementary Data from Active Remodeling of Capillary Endothelium via Cancer Cell–Derived MMP9 Promotes Metastatic Brain Colonization
Authors: Karreman Matthia A. , Bauer Alexander T. , Solecki Gergely , Berghoff Anna S. , Mayer Chanté D. , Frey Katharina , Hebach Nils , Feinauer Manuel J. , Schieber Nicole L. , Tehranian Cedric , Mercier Luc , Singhal Mahak , Venkataramani Varun , Schubert Marc C. , Hinze Daniel , Hölzel Michael , Helfrich Iris , Schadendorf Dirk , Schneider Stefan W. , Westphal Dana , Augustin Hellmut G. , Goetz Jacky G. , Schwab Yannick , Wick Wolfgang , Winkler Frank
Published: April 2023

Supplementary Movie 4
Supplementary Data from Active Remodeling of Capillary Endothelium via Cancer Cell–Derived MMP9 Promotes Metastatic Brain Colonization
Authors: Karreman Matthia A. , Bauer Alexander T. , Solecki Gergely , Berghoff Anna S. , Mayer Chanté D. , Frey Katharina , Hebach Nils , Feinauer Manuel J. , Schieber Nicole L. , Tehranian Cedric , Mercier Luc , Singhal Mahak , Venkataramani Varun , Schubert Marc C. , Hinze Daniel , Hölzel Michael , Helfrich Iris , Schadendorf Dirk , Schneider Stefan W. , Westphal Dana , Augustin Hellmut G. , Goetz Jacky G. , Schwab Yannick , Wick Wolfgang , Winkler Frank
Published: April 2023

Supplementary Movie 6
Data from Fructose Metabolism in Tumor Endothelial Cells Promotes Angiogenesis by Activating AMPK Signaling and Mitochondrial Respiration
Authors: Fang Jian-Hong , Chen Jie-Ying , Zheng Jia-Lin , Zeng Hui-Xian , Chen Jun-Guang , Wu Chen-Hui , Cai Jia-Li , Wang Zhi-Yong , Zhuang Shi-Mei
Published: April 2023

Abstract
Angiogenesis is vital for tumor growth and metastasis. Emerging evidence suggests that metabolic reprogramming in endothelial cells (EC) may affect angiogenesis. Here, we showed that multiple regulators in the fructose metabolism pathway, especially fructose transporter SLC2A5 and fructose-metabolizing enzyme ketohexokinase (KHK), were upregulated in tumor endothelial cells from hepatocellular carcinoma (HCC). In mouse models with hepatoma xenografts or with Myc/sgp53-induced liver cancer, dietary fructose enhanced tumor angiogenesis, tumor growth, and metastasis, which could be attenuated by treatment with an inhibitor of SLC2A5. Furthermore, vessel growth was substantially increased in fructose-containing Matrigel compared with PBS-Matrigel. Inhibiting fructose metabolism in EC cells in vivo using EC-targeted nanoparticles loaded with siRNA against KHK significantly abolished fructose-induced tumor angiogenesis. Fructose treatment promoted the proliferation, migration, and tube formation of ECs and stimulated mitochondrial respiration and ATP production. Elevated fructose metabolism activated AMPK to fuel mitochondrial respiration, resulting in enhanced EC migration. Fructose metabolism was increased under hypoxic conditions as a result of HIF1α-mediated upregulation of multiple genes in the fructose metabolism pathway. These findings highlight the significance of fructose metabolism in ECs for promoting tumor angiogenesis. Restricting fructose intake or targeting fructose metabolism is a potential strategy to reduce angiogenesis and suppress tumor growth.
Significance:
Fructose metabolism in endothelial cells fuels mitochondrial respiration to stimulate tumor angiogenesis, revealing fructose metabolism as a therapeutic target and fructose restriction as a dietary intervention for treating cancer.
Data from Single-Cell Discovery and Multiomic Characterization of Therapeutic Targets in Multiple Myeloma
Authors: Yao Lijun , Wang Julia T. , Jayasinghe Reyka G. , O'Neal Julie , Tsai Chia-Feng , Rettig Michael P. , Song Yizhe , Liu Ruiyang , Zhao Yanyan , Ibrahim Omar M. , Fiala Mark A. , Fortier Julie M. , Chen Siqi , Gehrs Leah , Rodrigues Fernanda Martins , Wendl Michael C. , Kohnen Daniel , Shinkle Andrew , Cao Song , Foltz Steven M. , Zhou Daniel Cui , Storrs Erik , Wyczalkowski Matthew A. , Mani Smrithi , Goldsmith Scott R. , Zhu Ying , Hamilton Mark , Liu Tao , Chen Feng , Vij Ravi , Ding Li , DiPersio John F.
Published: April 2023

Abstract
Multiple myeloma (MM) is a highly refractory hematologic cancer. Targeted immunotherapy has shown promise in MM but remains hindered by the challenge of identifying specific yet broadly representative tumor markers. We analyzed 53 bone marrow (BM) aspirates from 41 MM patients using an unbiased, high-throughput pipeline for therapeutic target discovery via single-cell transcriptomic profiling, yielding 38 MM marker genes encoding cell-surface proteins and 15 encoding intracellular proteins. Of these, 20 candidate genes were highlighted that are not yet under clinical study, 11 of which were previously uncharacterized as therapeutic targets. The findings were cross-validated using bulk RNA sequencing, flow cytometry, and proteomic mass spectrometry of MM cell lines and patient BM, demonstrating high overall concordance across data types. Independent discovery using bulk RNA sequencing reiterated top candidates, further affirming the ability of single-cell transcriptomics to accurately capture marker expression despite limitations in sample size or sequencing depth. Target dynamics and heterogeneity were further examined using both transcriptomic and immuno-imaging methods. In summary, this study presents a robust and broadly applicable strategy for identifying tumor markers to better inform the development of targeted cancer therapy.
Significance:
Single-cell transcriptomic profiling and multiomic cross-validation to uncover therapeutic targets identifies 38 myeloma marker genes, including 11 transcribing surface proteins with previously uncharacterized potential for targeted antitumor therapy.
Data from Neutrophil Conversion to a Tumor-Killing Phenotype Underpins Effective Microbial Therapy
Authors: Yam Andrew O. , Bailey Jacqueline , Lin Francis , Jakovija Arnolda , Youlten Scott E. , Counoupas Claudio , Gunzer Matthias , Bald Tobias , Woodruff Trent M. , Triccas James A. , Goldstein Leonard D. , Gallego-Ortega David , Grey Shane T. , Chtanova Tatyana
Published: April 2023

Abstract
The inflammatory microenvironment of solid tumors creates a protumorigenic milieu that resembles chronic inflammation akin to a subverted wound healing response. Here, we investigated the effect of converting the tumor microenvironment from a chronically inflamed state to one of acute microbial inflammation by injecting microbial bioparticles directly into tumors. Intratumoral microbial bioparticle injection led to rapid and dramatic changes in the tumor immune composition, the most striking of which was a substantial increase in the presence of activated neutrophils. In situ photoconversion and intravital microscopy indicated that tumor neutrophils transiently switched from sessile producers of VEGF to highly motile neutrophils that clustered to make neutrophil-rich domains in the tumor. The neutrophil clusters remodeled tumor tissue and repressed tumor growth. Single-cell transcriptional analysis of microbe-stimulated neutrophils showed a profound shift in gene expression towards heightened activation and antimicrobial effector function. Microbe-activated neutrophils also upregulated chemokines known to regulate neutrophil and CD8+ T-cell recruitment. Microbial therapy also boosted CD8+ T-cell function and enhanced the therapeutic benefit of checkpoint inhibitor therapy in tumor-bearing mice and provided protection in a model of tumor recurrence. These data indicate that one of the major effector mechanisms of microbial therapy is the conversion of tumor neutrophils from a wound healing to an acutely activated cytotoxic phenotype, highlighting a rationale for broader deployment of microbial therapy in the treatment of solid cancers.
Significance:
Intratumoral injection of microbial bioparticles stimulates neutrophil antitumor functions, suggesting pathways for optimizing efficacy of microbial therapies and paving the way for their broader utilization in the clinic.
Data from G-Quadruplex Structures Are Key Modulators of Somatic Structural Variants in Cancers
Authors: Zhang Rongxin , Shu Huiling , Wang Yuqi , Tao Tiantong , Tu Jing , Wang Cheng , Mergny Jean-Louis , Sun Xiao
Published: April 2023

Abstract
G-quadruplexes (G4) are noncanonical secondary genome structures. Aberrant formation of G4s can impair genome integrity. Investigation of the relationship between G4s and somatic structural variants (SV) in cancers could provide a better understanding of the role of G4 formation in cancer development and progression. In this study, we combined bioinformatic approaches and multiomics data to investigate the connection between G4s and the somatic SVs. Somatic SV breakpoints were significantly enriched in G4 regions, regardless of SV subtypes. This enrichment was only observed in regions demonstrated to form G4s in cells (“active quadruplexes”), rather than in regions with a sequence compatible with G4 formation but without confirmed G4 formation (“potential quadruplexes”). Several genomic features affected the connection between G4s and SVs, with the enrichment being notably strengthened at the boundary of topologically associated domains. Somatic breakpoints were also preferentially associated with G4 regions with earlier replication timing and open chromatin status. In patients with cancer with homologous recombination repair defects, G4s and somatic breakpoints were substantially more strongly associated. Machine learning models were constructed that showed that G4 propensity is a potent feature for predicting the density of SV breakpoints. Altogether, these findings suggest that the G4 structures play a critical role in modulating the production of somatic SVs in cancers.
Significance:
G-quadruplex structure formation constitutes a critical step in the production of somatic structural variants in cancers, suggesting G-quadruplex structures as potential targets for future cancer prevention and treatment strategies.
Caffeine Supplementation and FOXM1 Inhibition Enhance the Antitumor Effect of Statins in Neuroblastoma
Authors: Tran Gia-Buu , Ding Jane , Ye Bingwei , Liu Mengling , Yu Yajie , Zha Yunhong , Dong Zheng , Liu Kebin , Sudarshan Sunil , Ding Han-Fei
Published: April 2023

High-risk neuroblastoma exhibits transcriptional activation of the mevalonate pathway that produces cholesterol and nonsterol isoprenoids. A better understanding of how this metabolic reprogramming contributes to neuroblastoma development could help identify potential prevention and treatment strategies. Here, we report that both the cholesterol and nonsterol geranylgeranyl-pyrophosphate branches of the mevalonate pathway are critical to sustain neuroblastoma cell growth. Blocking the mevalonate pathway by simvastatin, a cholesterol-lowering drug, impeded neuroblastoma growth in neuroblastoma cell line xenograft, patient-derived xenograft (PDX), and TH-MYCN transgenic mouse models. Transcriptional profiling revealed that the mevalonate pathway was required to maintain the FOXM1-mediated transcriptional program that drives mitosis. High FOXM1 expression contributed to statin resistance and led to a therapeutic vulnerability to the combination of simvastatin and FOXM1 inhibition. Furthermore, caffeine synergized with simvastatin to inhibit the growth of neuroblastoma cells and PDX tumors by blocking statin-induced feedback activation of the mevalonate pathway. This function of caffeine depended on its activity as an adenosine receptor antagonist, and the A2A adenosine receptor antagonist istradefylline, an add-on drug for Parkinson's disease, could recapitulate the synergistic effect of caffeine with simvastatin. This study reveals that the FOXM1-mediated mitotic program is a molecular statin target in cancer and identifies classes of agents for maximizing the therapeutic efficacy of statins, with implications for treatment of high-risk neuroblastoma.

Significance:

Caffeine treatment and FOXM1 inhibition can both enhance the antitumor effect of statins by blocking the molecular and metabolic processes that confer statin resistance, indicating potential combination therapeutic strategies for neuroblastoma.

See related commentary by Stouth et al., p. 2091
TONSL Is an Immortalizing Oncogene and a Therapeutic Target in Breast Cancer
Authors: Khatpe Aditi S. , Dirks Rebecca , Bhat-Nakshatri Poornima , Mang Henry , Batic Katie , Swiezy Sarah , Olson Jacob , Rao Xi , Wang Yue , Tanaka Hiromi , Liu Sheng , Wan Jun , Chen Duojiao , Liu Yunlong , Fang Fang , Althouse Sandra , Hulsey Emily , Granatir Maggie M. , Addison Rebekah , Temm Constance J. , Sandusky George , Lee-Gosselin Audrey , Nephew Kenneth , Miller Kathy D. , Nakshatri Harikrishna
Published: April 2023

Study of genomic aberrations leading to immortalization of epithelial cells has been technically challenging due to the lack of isogenic models. To address this, we used healthy primary breast luminal epithelial cells of different genetic ancestry and their hTERT-immortalized counterparts to identify transcriptomic changes associated with immortalization. Elevated expression of TONSL (Tonsoku-like, DNA repair protein) was identified as one of the earliest events during immortalization. TONSL, which is located on chromosome 8q24.3, was found to be amplified in approximately 20% of breast cancers. TONSL alone immortalized primary breast epithelial cells and increased telomerase activity, but overexpression was insufficient for neoplastic transformation. However, TONSL-immortalized primary cells overexpressing defined oncogenes generated estrogen receptor–positive adenocarcinomas in mice. Analysis of a breast tumor microarray with approximately 600 tumors revealed poor overall and progression-free survival of patients with TONSL-overexpressing tumors. TONSL increased chromatin accessibility to pro-oncogenic transcription factors, including NF-κB and limited access to the tumor-suppressor p53. TONSL overexpression resulted in significant changes in the expression of genes associated with DNA repair hubs, including upregulation of several genes in the homologous recombination (HR) and Fanconi anemia pathways. Consistent with these results, TONSL-overexpressing primary cells exhibited upregulated DNA repair via HR. Moreover, TONSL was essential for growth of TONSL-amplified breast cancer cell lines in vivo, and these cells were sensitive to TONSL–FACT complex inhibitor CBL0137. Together, these findings identify TONSL as a regulator of epithelial cell immortalization to facilitate cancer initiation and as a target for breast cancer therapy.

Significance:

The chr.8q24.3 amplicon-resident gene TONSL is upregulated during the initial steps of tumorigenesis to support neoplastic transformation by increasing DNA repair and represents a potential therapeutic target for treating breast cancer.
BRCAness, Homologous Recombination Deficiencies, and Synthetic Lethality
Authors: Murai Junko , Pommier Yves
Published: April 2023

The concept of “BRCAness” was first described in 2004 to define the situation in which a homologous recombination repair (HRR) defect in a tumor relates to and phenocopies BRCA1 or BRCA2 loss-of-function mutations. Soon after the discovery of synthetic lethality of PARP1/2 inhibitors in BRCA1- or BRCA2-deficient cells, McCabe and colleagues extended the concept of BRCAness to homologous recombination deficiency (HRD) by studying the sensitivity of cancer cells to PARP inhibitors. They genetically revealed that deficiency in HR-related genes (RAD51, RAD54, DSS1, and RPA1), DNA damage signaling genes (ATR, ATM, CHK1, CHK2, and NBS1), or Fanconi anemia–related genes (FANCD2, FANCA, and FANCC) conferred sensitivity to PARP inhibitors. Thus, cells acquire BRCAness either by genetic inactivation of the BRCA or HRD genes. Here, we briefly review how genomic profiling can identify BRCAness and deficiencies in HRD genes and the current difficulty to apply BRCAness/HRD in the clinic. We also discuss how BRCAness relates to HRD and the utility of evaluating BRCAness/HRD to select therapies with PARP inhibitors (olaparib, rucaparib, niraparib, talazoparib, pamiparib, fuzuloparib), topoisomerase I (TOP1) inhibitors (irinotecan, topotecan, and tumor-targeted TOP1 inhibitors), and platinum derivatives (cisplatin and carboplatin).

See related article by McCabe and colleagues, Cancer Res 2006;66:8109–15.
Supplementary Figure from Systemic Levels of Estrogens and PGE2 Synthesis in Relation to Postmenopausal Breast Cancer Risk
Authors: Kim Sangmi , Campbell Jeff , Yoo Wonsuk , Taylor Jack A. , Sandler Dale P.
Published: April 2023

Supplementary Figure from Systemic Levels of Estrogens and PGE2 Synthesis in Relation to Postmenopausal Breast Cancer Risk
Data from Systemic Levels of Estrogens and PGE2 Synthesis in Relation to Postmenopausal Breast Cancer Risk
Authors: Kim Sangmi , Campbell Jeff , Yoo Wonsuk , Taylor Jack A. , Sandler Dale P.
Published: April 2023

AbstractBackground:
Prostaglandin E2 (PGE2) induces aromatase expression in adipose tissue, leading to increased estrogen production that may promote the development and progression of breast cancer. However, few studies have simultaneously investigated systemic levels of PGE2 and estrogen in relation to postmenopausal breast cancer risk.
Methods:
Here, we determined urinary estrogen metabolites (EM) using mass spectrometry in a case–cohort study (295 incident breast cancer cases and 294 subcohort members), and using linear regression estimated the effect of urinary levels of a major PGE2 metabolite (PGE-M) on EMs. HRs for the risk of developing breast cancer in relation to PGE-M and EMs were compared between Cox regression models with and without mutual adjustment.
Results:
PGE-M was a significant predictor of estrone (E1), but not estradiol (E2) levels in multivariable analysis. Elevated E2 levels were associated with an increased risk of developing breast cancer [HRQ5vs.Q1, 1.54; 95% confidence interval (CI), 1.01–2.35], and this association remained unchanged after adjustment for PGE-M (HRQ5vs.Q1, 1.52; 95% CI, 0.99–2.33). Similarly, elevated levels of PGE-M were associated with increased risk of developing breast cancer (HRQ4vs.Q1, 2.01; 95% CI, 1.01–4.29), and this association was only nominally changed after consideration of E1 or E2 levels.
Conclusions:
Urinary levels of PGE-M and estrogens were independently associated with future risk of developing breast cancer among these postmenopausal women.
Impact:
Increased breast cancer risk associated with PGE-M might not be fully explained by the estrogens–breast cancer association alone but also by additional effects related to inflammation. Cancer Epidemiol Biomarkers Prev; 26(3); 383–8. ©2016 AACR.
Supplementary Table S4 from Phase I Study of the Liposomal Formulation of Eribulin (E7389-LF): Results from the Advanced Gastric Cancer Expansion Cohort
Authors: Shitara Kohei , Hirao Motohiro , Iwasa Satoru , Oshima Takashi , Komatsu Yoshito , Kawazoe Akihito , Sato Yasuyoshi , Hamakawa Takuya , Yonemori Kan , Machida Nozomu , Yuki Satoshi , Suzuki Takuya , Okumura Shiori , Takase Takao , Semba Taro , Zimmermann Bob , Teng Angela , Yamaguchi Kensei
Published: April 2023

Supplementary Table S4 provides a summary of biomarker changes in this gastric cancer cohort.
Table S4 from MEK Inhibition Synergizes with TYK2 Inhibitors in NF1-Associated Malignant Peripheral Nerve Sheath Tumors
Authors: Borcherding Dana C. , Amin Neha V. , He Kevin , Zhang Xiaochun , Lyu Yang , Dehner Carina , Bhatia Himanshi , Gothra Angad , Daud Layla , Ruminski Peter , Pratilas Christine A. , Pollard Kai , Sundby Taylor , Widemann Brigitte C. , Hirbe Angela C.
Published: April 2023

Supplementary Table S4
Table S3 from MEK Inhibition Synergizes with TYK2 Inhibitors in NF1-Associated Malignant Peripheral Nerve Sheath Tumors
Authors: Borcherding Dana C. , Amin Neha V. , He Kevin , Zhang Xiaochun , Lyu Yang , Dehner Carina , Bhatia Himanshi , Gothra Angad , Daud Layla , Ruminski Peter , Pratilas Christine A. , Pollard Kai , Sundby Taylor , Widemann Brigitte C. , Hirbe Angela C.
Published: April 2023

Supplementary Table S3
Table S1 from MEK Inhibition Synergizes with TYK2 Inhibitors in NF1-Associated Malignant Peripheral Nerve Sheath Tumors
Authors: Borcherding Dana C. , Amin Neha V. , He Kevin , Zhang Xiaochun , Lyu Yang , Dehner Carina , Bhatia Himanshi , Gothra Angad , Daud Layla , Ruminski Peter , Pratilas Christine A. , Pollard Kai , Sundby Taylor , Widemann Brigitte C. , Hirbe Angela C.
Published: April 2023

Supplementary Table S1
Supplementary Figure S5 from Phase I Study of the Liposomal Formulation of Eribulin (E7389-LF): Results from the Advanced Gastric Cancer Expansion Cohort
Authors: Shitara Kohei , Hirao Motohiro , Iwasa Satoru , Oshima Takashi , Komatsu Yoshito , Kawazoe Akihito , Sato Yasuyoshi , Hamakawa Takuya , Yonemori Kan , Machida Nozomu , Yuki Satoshi , Suzuki Takuya , Okumura Shiori , Takase Takao , Semba Taro , Zimmermann Bob , Teng Angela , Yamaguchi Kensei
Published: April 2023

Supplementary Figure S5 shows pharmacodynamic changes in biomarkers over time (A) and changes by best overall response (B) in all study 114 cohorts.
Figure S9 from MEK Inhibition Synergizes with TYK2 Inhibitors in NF1-Associated Malignant Peripheral Nerve Sheath Tumors
Authors: Borcherding Dana C. , Amin Neha V. , He Kevin , Zhang Xiaochun , Lyu Yang , Dehner Carina , Bhatia Himanshi , Gothra Angad , Daud Layla , Ruminski Peter , Pratilas Christine A. , Pollard Kai , Sundby Taylor , Widemann Brigitte C. , Hirbe Angela C.
Published: April 2023

Supplemental Fig.S9. Synergy of TYK2 and MEK inhibitors in MPNST-724 cells.
Figure S7 from MEK Inhibition Synergizes with TYK2 Inhibitors in NF1-Associated Malignant Peripheral Nerve Sheath Tumors
Authors: Borcherding Dana C. , Amin Neha V. , He Kevin , Zhang Xiaochun , Lyu Yang , Dehner Carina , Bhatia Himanshi , Gothra Angad , Daud Layla , Ruminski Peter , Pratilas Christine A. , Pollard Kai , Sundby Taylor , Widemann Brigitte C. , Hirbe Angela C.
Published: April 2023

Supplemental Fig.S7. The TYK2 inhibitor, WU-76, reduces activation of STAT3 while stimulating activation of ERK1/2 in MPNST cells.
Supplementary Figure S2 from Phase I Study of the Liposomal Formulation of Eribulin (E7389-LF): Results from the Advanced Gastric Cancer Expansion Cohort
Authors: Shitara Kohei , Hirao Motohiro , Iwasa Satoru , Oshima Takashi , Komatsu Yoshito , Kawazoe Akihito , Sato Yasuyoshi , Hamakawa Takuya , Yonemori Kan , Machida Nozomu , Yuki Satoshi , Suzuki Takuya , Okumura Shiori , Takase Takao , Semba Taro , Zimmermann Bob , Teng Angela , Yamaguchi Kensei
Published: April 2023

Supplementary Figure S2 is a swimmer plot of patients’ treatment durations.
Figure S4 from MEK Inhibition Synergizes with TYK2 Inhibitors in NF1-Associated Malignant Peripheral Nerve Sheath Tumors
Authors: Borcherding Dana C. , Amin Neha V. , He Kevin , Zhang Xiaochun , Lyu Yang , Dehner Carina , Bhatia Himanshi , Gothra Angad , Daud Layla , Ruminski Peter , Pratilas Christine A. , Pollard Kai , Sundby Taylor , Widemann Brigitte C. , Hirbe Angela C.
Published: April 2023

Supplemental Fig.S4. TYK2 knockout decreases proliferation of MPNST-724 cells.
Figure S1 from MEK Inhibition Synergizes with TYK2 Inhibitors in NF1-Associated Malignant Peripheral Nerve Sheath Tumors
Authors: Borcherding Dana C. , Amin Neha V. , He Kevin , Zhang Xiaochun , Lyu Yang , Dehner Carina , Bhatia Himanshi , Gothra Angad , Daud Layla , Ruminski Peter , Pratilas Christine A. , Pollard Kai , Sundby Taylor , Widemann Brigitte C. , Hirbe Angela C.
Published: April 2023

Supplemental Fig.S1. Inhibition of TYK2 induces apoptosis in MPNST cell-lines
Supplementary Data TS1 from Membranous NECTIN-4 Expression Frequently Decreases during Metastatic Spread of Urothelial Carcinoma and Is Associated with Enfortumab Vedotin Resistance
Authors: Klümper Niklas , Ralser Damian J. , Ellinger Jörg , Roghmann Florian , Albrecht Julia , Below Eduard , Alajati Abdullah , Sikic Danijel , Breyer Johannes , Bolenz Christian , Zengerling Friedemann , Erben Philipp , Schwamborn Kristina , Wirtz Ralph M. , Horn Thomas , Nagy Dora , Toma Marieta , Kristiansen Glen , Büttner Thomas , Hahn Oliver , Grünwald Viktor , Darr Christopher , Erne Eva , Rausch Steffen , Bedke Jens , Schlack Katrin , Abbas Mahmoud , Zschäbitz Stefanie , Schwab Constantin , Mustea Alexander , Adam Patrick , Manseck Andreas , Wullich Bernd , Ritter Manuel , Hartmann Arndt , Gschwend Jürgen , Weichert Wilko , Erlmeier Franziska , Hölzel Michael , Eckstein Markus
Published: April 2023

Supplementary Table 1. Clinico-pathological characteristics of the UC progression PRIM-MET study cohort. BRA=brain metastasis; HEP=hepatic metastasis; LYM=non-locoregionary lymph node metastasis; OSS=bone metastasis; OTH= metastasis at other locations including soft tissue; PER=peritoneal metastasis; PUL=pulmonary metastasis.
Table S6 from Genomic and Transcriptomic Characteristics of Metastatic Thyroid Cancers with Exceptional Responses to Radioactive Iodine Therapy
Authors: Boucai Laura , Saqcena Mahesh , Kuo Fengshen , Grewal Ravinder K. , Socci Nicholas , Knauf Jeffrey A. , Krishnamoorthy Gnana P. , Ryder Mabel , Ho Alan L. , Ghossein Ronald A. , Morris Luc G.T. , Seshan Venkatraman , Fagin James A.
Published: April 2023

Table of gene set enrichments for individual comparisons.
Supplementary Table 1 from Brief Report: Combination of Osimertinib and Dacomitinib to Mitigate Primary and Acquired Resistance in EGFR-Mutant Lung Adenocarcinomas
Authors: Elkrief Arielle , Makhnin Alex , Moses Khadeja A. , Ahn Linda S. , Preeshagul Isabel R. , Iqbal Afsheen N. , Hayes Sara A. , Plodkowski Andrew J. , Paik Paul K. , Ladanyi Marc , Kris Mark G. , Riely Gregory J. , Michor Franziska , Yu Helena A.
Published: April 2023

Supplemental Table 1
Supplemental Figure 4 from Brief Report: Combination of Osimertinib and Dacomitinib to Mitigate Primary and Acquired Resistance in EGFR-Mutant Lung Adenocarcinomas
Authors: Elkrief Arielle , Makhnin Alex , Moses Khadeja A. , Ahn Linda S. , Preeshagul Isabel R. , Iqbal Afsheen N. , Hayes Sara A. , Plodkowski Andrew J. , Paik Paul K. , Ladanyi Marc , Kris Mark G. , Riely Gregory J. , Michor Franziska , Yu Helena A.
Published: April 2023

Supplemental Figure 4. A. Median progression-free survival and B. Overall survival for patients enrolled in the acquired resistance study
Table S4 from Genomic and Transcriptomic Characteristics of Metastatic Thyroid Cancers with Exceptional Responses to Radioactive Iodine Therapy
Authors: Boucai Laura , Saqcena Mahesh , Kuo Fengshen , Grewal Ravinder K. , Socci Nicholas , Knauf Jeffrey A. , Krishnamoorthy Gnana P. , Ryder Mabel , Ho Alan L. , Ghossein Ronald A. , Morris Luc G.T. , Seshan Venkatraman , Fagin James A.
Published: April 2023

Gene lists for computing the eTDS and BRS scores.
Table S3 from Genomic and Transcriptomic Characteristics of Metastatic Thyroid Cancers with Exceptional Responses to Radioactive Iodine Therapy
Authors: Boucai Laura , Saqcena Mahesh , Kuo Fengshen , Grewal Ravinder K. , Socci Nicholas , Knauf Jeffrey A. , Krishnamoorthy Gnana P. , Ryder Mabel , Ho Alan L. , Ghossein Ronald A. , Morris Luc G.T. , Seshan Venkatraman , Fagin James A.
Published: April 2023

Chromosomal and cytogenetic locations of 505 genes in the MSK-IMPACT panel.
Table S2 from Genomic and Transcriptomic Characteristics of Metastatic Thyroid Cancers with Exceptional Responses to Radioactive Iodine Therapy
Authors: Boucai Laura , Saqcena Mahesh , Kuo Fengshen , Grewal Ravinder K. , Socci Nicholas , Knauf Jeffrey A. , Krishnamoorthy Gnana P. , Ryder Mabel , Ho Alan L. , Ghossein Ronald A. , Morris Luc G.T. , Seshan Venkatraman , Fagin James A.
Published: April 2023

Somatic mutations identified by WES, nonsilent and null mutations identified by MutSigCV in WES, MSK-IMPACT gene list, and the list of genes used for Oncoprint.
Figure S4 from Genomic and Transcriptomic Characteristics of Metastatic Thyroid Cancers with Exceptional Responses to Radioactive Iodine Therapy
Authors: Boucai Laura , Saqcena Mahesh , Kuo Fengshen , Grewal Ravinder K. , Socci Nicholas , Knauf Jeffrey A. , Krishnamoorthy Gnana P. , Ryder Mabel , Ho Alan L. , Ghossein Ronald A. , Morris Luc G.T. , Seshan Venkatraman , Fagin James A.
Published: April 2023

Supplementary Figure S4.
Supplemental Figure S6 from [18F]FluorThanatrace ([18F]FTT) PET Imaging of PARP-Inhibitor Drug-Target Engagement as a Biomarker of Response in Ovarian Cancer, a Pilot Study
Authors: Pantel Austin R. , Gitto Sarah B. , Makvandi Mehran , Kim Hyoung , Medvedv Sergey , Weeks Joanna K. , Torigian Drew A. , Hsieh Chia-Ju , Ferman Benjamin , Latif Nawar A. , Tanyi Janos L. , Martin Lainie P. , Lanzo Shannon M. , Liu Fang , Cao Quy , Mills Gordon B. , Doot Robert K. , Mankoff David A. , Mach Robert H. , Lin Lilie L. , Simpkins Fiona
Published: April 2023

18F]FTT-PET on subject previously treated with PARPi.
Supplementary Data 1 from Phase I Study and Cell-Free DNA Analysis of T-DM1 and Metronomic Temozolomide for Secondary Prevention of HER2-Positive Breast Cancer Brain Metastases
Authors: Jenkins Sarah , Zhang Wei , Steinberg Seth M. , Nousome Darryl , Houston Nicole , Wu Xiaolin , Armstrong Terri S. , Burton Eric , Smart Dee Dee , Shah Ritu , Peer Cody J. , Mozarsky Brett , Arisa Oluwatobi , Figg William D. , Mendoza Tito R. , Vera Elizabeth , Brastianos Priscilla , Carter Scott , Gilbert Mark R. , Anders Carey K. , Connolly Roisín M. , Tweed Carol , Smith Karen L. , Khan Imran , Lipkowitz Stanley , Steeg Patricia S. , Zimmer Alexandra S.
Published: April 2023

Supplemental Methods
Supplemental Figure S2 from [18F]FluorThanatrace ([18F]FTT) PET Imaging of PARP-Inhibitor Drug-Target Engagement as a Biomarker of Response in Ovarian Cancer, a Pilot Study
Authors: Pantel Austin R. , Gitto Sarah B. , Makvandi Mehran , Kim Hyoung , Medvedv Sergey , Weeks Joanna K. , Torigian Drew A. , Hsieh Chia-Ju , Ferman Benjamin , Latif Nawar A. , Tanyi Janos L. , Martin Lainie P. , Lanzo Shannon M. , Liu Fang , Cao Quy , Mills Gordon B. , Doot Robert K. , Mankoff David A. , Mach Robert H. , Lin Lilie L. , Simpkins Fiona
Published: April 2023

Time between [18F]FTT imaging scans did not significantly impact SUV measurements.
Supplemental Figure S1 from [18F]FluorThanatrace ([18F]FTT) PET Imaging of PARP-Inhibitor Drug-Target Engagement as a Biomarker of Response in Ovarian Cancer, a Pilot Study
Authors: Pantel Austin R. , Gitto Sarah B. , Makvandi Mehran , Kim Hyoung , Medvedv Sergey , Weeks Joanna K. , Torigian Drew A. , Hsieh Chia-Ju , Ferman Benjamin , Latif Nawar A. , Tanyi Janos L. , Martin Lainie P. , Lanzo Shannon M. , Liu Fang , Cao Quy , Mills Gordon B. , Doot Robert K. , Mankoff David A. , Mach Robert H. , Lin Lilie L. , Simpkins Fiona
Published: April 2023

PDX models treated with PARPi therapies.
Figure S3 from Phase I Study and Cell-Free DNA Analysis of T-DM1 and Metronomic Temozolomide for Secondary Prevention of HER2-Positive Breast Cancer Brain Metastases
Authors: Jenkins Sarah , Zhang Wei , Steinberg Seth M. , Nousome Darryl , Houston Nicole , Wu Xiaolin , Armstrong Terri S. , Burton Eric , Smart Dee Dee , Shah Ritu , Peer Cody J. , Mozarsky Brett , Arisa Oluwatobi , Figg William D. , Mendoza Tito R. , Vera Elizabeth , Brastianos Priscilla , Carter Scott , Gilbert Mark R. , Anders Carey K. , Connolly Roisín M. , Tweed Carol , Smith Karen L. , Khan Imran , Lipkowitz Stanley , Steeg Patricia S. , Zimmer Alexandra S.
Published: April 2023

Supplemental Fig. 3. ERB-B-2 Status of Patients.
Figure S2 from Phase I Study and Cell-Free DNA Analysis of T-DM1 and Metronomic Temozolomide for Secondary Prevention of HER2-Positive Breast Cancer Brain Metastases
Authors: Jenkins Sarah , Zhang Wei , Steinberg Seth M. , Nousome Darryl , Houston Nicole , Wu Xiaolin , Armstrong Terri S. , Burton Eric , Smart Dee Dee , Shah Ritu , Peer Cody J. , Mozarsky Brett , Arisa Oluwatobi , Figg William D. , Mendoza Tito R. , Vera Elizabeth , Brastianos Priscilla , Carter Scott , Gilbert Mark R. , Anders Carey K. , Connolly Roisín M. , Tweed Carol , Smith Karen L. , Khan Imran , Lipkowitz Stanley , Steeg Patricia S. , Zimmer Alexandra S.
Published: April 2023

Supplemental Fig 2. Total mutation Burden by MB.
Supplementary tables 1-4 from Single-Cell Transcriptomics Reveals Immune Reconstitution in Patients with R/R T-ALL/LBL Treated with Donor-Derived CD7 CAR-T Therapy
Authors: Chen Wei , Shi Hui , Liu Zhuojun , Yang Fan , Liu Jia , Zhang Leqiang , Wu Yajin , Xia Yuanshi , Ou Yuxuan , Li Ruiting , Zhang Ting , Zhang Jiecheng , Ke Xiaoyan , Hu Kai , Yu Jian
Published: April 2023

Supplementary table 1-4
Supplementary Table S6 from Addition of Losartan to FOLFIRINOX and Chemoradiation Reduces Immunosuppression-Associated Genes, Tregs, and FOXP3+ Cancer Cells in Locally Advanced Pancreatic Cancer
Authors: Boucher Yves , Posada Jessica M. , Subudhi Sonu , Kumar Ashwin S. , Rosario Spencer R. , Gu Liqun , Kumra Heena , Mino-Kenudson Mari , Talele Nilesh P. , Duda Dan G. , Fukumura Dai , Wo Jennifer Y. , Clark Jeffrey W. , Ryan David P. , Fernandez-Del Castillo Carlos , Hong Theodore S. , Pittet Mikael J. , Jain Rakesh K.
Published: April 2023

Relationship between pathological response and circulating biomarker levels in the plasma of treated patients.
Supplementary table 7 from Single-Cell Transcriptomics Reveals Immune Reconstitution in Patients with R/R T-ALL/LBL Treated with Donor-Derived CD7 CAR-T Therapy
Authors: Chen Wei , Shi Hui , Liu Zhuojun , Yang Fan , Liu Jia , Zhang Leqiang , Wu Yajin , Xia Yuanshi , Ou Yuxuan , Li Ruiting , Zhang Ting , Zhang Jiecheng , Ke Xiaoyan , Hu Kai , Yu Jian
Published: April 2023

Supplementary table 7
Supplementary table 6 from Single-Cell Transcriptomics Reveals Immune Reconstitution in Patients with R/R T-ALL/LBL Treated with Donor-Derived CD7 CAR-T Therapy
Authors: Chen Wei , Shi Hui , Liu Zhuojun , Yang Fan , Liu Jia , Zhang Leqiang , Wu Yajin , Xia Yuanshi , Ou Yuxuan , Li Ruiting , Zhang Ting , Zhang Jiecheng , Ke Xiaoyan , Hu Kai , Yu Jian
Published: April 2023

Supplementary table 6
Supplementary Table S1 from Addition of Losartan to FOLFIRINOX and Chemoradiation Reduces Immunosuppression-Associated Genes, Tregs, and FOXP3+ Cancer Cells in Locally Advanced Pancreatic Cancer
Authors: Boucher Yves , Posada Jessica M. , Subudhi Sonu , Kumar Ashwin S. , Rosario Spencer R. , Gu Liqun , Kumra Heena , Mino-Kenudson Mari , Talele Nilesh P. , Duda Dan G. , Fukumura Dai , Wo Jennifer Y. , Clark Jeffrey W. , Ryan David P. , Fernandez-Del Castillo Carlos , Hong Theodore S. , Pittet Mikael J. , Jain Rakesh K.
Published: April 2023

Differentially expressed genes (DEG) in losartan+FFX+CRT versus FFX+CRT, losartan+FFX+CRT versus untreated, and FFX+CRT versus untreated.
Supplementary table 5 from Single-Cell Transcriptomics Reveals Immune Reconstitution in Patients with R/R T-ALL/LBL Treated with Donor-Derived CD7 CAR-T Therapy
Authors: Chen Wei , Shi Hui , Liu Zhuojun , Yang Fan , Liu Jia , Zhang Leqiang , Wu Yajin , Xia Yuanshi , Ou Yuxuan , Li Ruiting , Zhang Ting , Zhang Jiecheng , Ke Xiaoyan , Hu Kai , Yu Jian
Published: April 2023

Supplementary table 5
Supplementary Figure S7 from Addition of Losartan to FOLFIRINOX and Chemoradiation Reduces Immunosuppression-Associated Genes, Tregs, and FOXP3+ Cancer Cells in Locally Advanced Pancreatic Cancer
Authors: Boucher Yves , Posada Jessica M. , Subudhi Sonu , Kumar Ashwin S. , Rosario Spencer R. , Gu Liqun , Kumra Heena , Mino-Kenudson Mari , Talele Nilesh P. , Duda Dan G. , Fukumura Dai , Wo Jennifer Y. , Clark Jeffrey W. , Ryan David P. , Fernandez-Del Castillo Carlos , Hong Theodore S. , Pittet Mikael J. , Jain Rakesh K.
Published: April 2023

Immunofluorescence staining and quantitative analysis in PDAC lesions from losartan+FFX+CRT-treated patients.