bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Table 4 from Telomerase upregulation induces progression of mouse BrafV600E-driven thyroid cancers and triggers non-telomeric effects
Authors: Landa Inigo , Thornton Caitlin EM , Xu Bin , Haase Jacob , Krishnamoorthy Gnana P. , Hao Jingzhu , Knauf Jeffrey A. , Herbert Zachary T. , Martínez Paula , Blasco Maria A. , Ghossein Ronald , Fagin James A.
Published: September 2024

Differentially expressed genes from RNAseq data when comparing BrafV600E vs. BrafV600E+K5-Tert tumors from 20-week animals.
Supplementary Figure 2 from Telomerase upregulation induces progression of mouse BrafV600E-driven thyroid cancers and triggers non-telomeric effects
Authors: Landa Inigo , Thornton Caitlin EM , Xu Bin , Haase Jacob , Krishnamoorthy Gnana P. , Hao Jingzhu , Knauf Jeffrey A. , Herbert Zachary T. , Martínez Paula , Blasco Maria A. , Ghossein Ronald , Fagin James A.
Published: September 2024

Additional features of Braf and Braf+Tert murine tumors.
Supplementary Figure 2 from FBXO24 suppresses breast cancer tumorigenesis by targeting LSD1 for Ubiquitination
Authors: Dong Bo , Song Xiang , Wang Xinzhao , Dai Tao , Wang Jianlin , Yu Zhiyong , Deng Jiong , Evers B. Mark , Wu Yadi
Published: September 2024

FBXO24 degrades LSD1.
Supplementary Figure 1 from FBXO24 suppresses breast cancer tumorigenesis by targeting LSD1 for Ubiquitination
Authors: Dong Bo , Song Xiang , Wang Xinzhao , Dai Tao , Wang Jianlin , Yu Zhiyong , Deng Jiong , Evers B. Mark , Wu Yadi
Published: September 2024

FBXO24 regulates LSD1 at protein levels.
Table S1 from Competing engagement of β-arrestin isoforms balances IGF1R/p53 signaling and controls melanoma cell chemotherapeutic responsiveness
Authors: Cismas Sonia , Pasca Sylvya , Crudden Caitrin , Troccoli Drakensjo Iara , Suleymanova Naida , Zhang Simin , Gebhard Benjamin , Song Dawei , Neo Shiyong , Shibano Takashi , Smith Terry J. , Calin George A. , Girnita Ada , Girnita Leonard
Published: September 2024

Table S1. Cell lines used in this study.
Supplementary Figure 3 from Competing engagement of β-arrestin isoforms balances IGF1R/p53 signaling and controls melanoma cell chemotherapeutic responsiveness
Authors: Cismas Sonia , Pasca Sylvya , Crudden Caitrin , Troccoli Drakensjo Iara , Suleymanova Naida , Zhang Simin , Gebhard Benjamin , Song Dawei , Neo Shiyong , Shibano Takashi , Smith Terry J. , Calin George A. , Girnita Ada , Girnita Leonard
Published: September 2024

Specificity of β-arrestin1/2 siRNA effectson MDM2 localization.
Data from UBE2C-mediated autophagy inhibition via ubiquitination of SIRT1 contributes to endometrial cancer progression
Authors: Zhao Rong , Liu Yan , Wang Ziwei , Zhang Jun , Zhang Wei , Zhou Xing , Tsedendorj Sevjid , Enkhtur Amarsanaa , Feng Dilu , Wang Hongbo
Published: September 2024

Abstract
Recent studies have shown that autophagy plays an important role in gynecological tumours, and ubiquitin modification of autophagy regulatory components is essential to regulate autophagic. In this study, we found that UBE2C affects endometrial cancer cell apoptosis and proliferation by inhibiting autophagy. Electron microscopy observation of cell ultrastructure and experimental biochemical analysis showed that EC cells with UBE2C expression knocked down display typical autophagic characteristics. Cells were cotreated with the autophagy pharmacological inhibitors chloroquine and/or bafilomycin A1, and mRFP-GFP-LC3 assays were performed to monitor autophagic flux and determine whether UBE2C suppresses the autophagy program. Investigation of the corresponding mechanism by which UBE2C inhibits autophagy revealed that UBE2C induces K48-linked SIRT1 ubiquitination and promotes ubiquitination-dependent degradation of SIRT1, subsequently reducing H4K16 deacetylation levels and epigenetically inhibiting the expression of autophagy-related genes. The results of CCK-8, Hoechst staining, and immunofluorescence assays further indicated that deletion of the autophagy-related gene BECN1 significantly attenuates UBE2C knockdown-induced cell apoptosis. Moreover, overexpression of UBE2C promoted tumor growth in the xenograft mice model. While, the introduction of rapamycin, an agonist of autophagy, successfully reversed tumor growth and apoptosis inhibition mediated by UBE2C overexpression in vitro and in vivo. Taken together, our results suggested that UBE2C-mediated ubiquitination and degradation of SIRT1 contribute to the malignant progression of endometrial cancer through epigenetic inhibition of autophagy.
Implications: Our study highlights the tumorigenic role and regulatory mechanism of UBE2C in EC; UBE2C inhibits EC cell apoptosis through autophagy-related mechanisms and our findings provide new insights into the treatment of endometrial cancer.
Data from Desmoglein 2 Functions As A Receptor for Fatty Acid Binding Protein 4 in Breast Cancer Epithelial Cells
Authors: Chen Dongmei , Wirth Keith M. , Kizy Scott , Muretta Joseph M. , Markowski Todd W. , Yong Peter , Sheka Adam , Abdelwahab Hisham , Hertzel Ann V. , Ikramuddin Sayeed , Yamamoto Masato , Bernlohr David A.
Published: September 2024

Abstract
Fatty acid binding protein 4 (FABP4) is a secreted adipokine linked to obesity and progression of a variety of cancers. Obesity increases extracellular FABP4 (eFABP4) levels in animal models and in obese breast cancer patients compared to lean healthy controls. Using MCF-7 and T47D breast cancer epithelial cells, we show herein that eFABP4 stimulates cellular proliferation in a time and concentration dependent manner while the non-fatty acid-binding mutant, R126Q, failed to potentiate growth. When E0771 murine breast cancer cells were injected into mice, FABP4 null animals exhibited delayed tumor growth and enhanced survival compared to injections into control C57Bl/6J animals. eFABP4 treatment of MCF-7 cells resulted in a significant increase in phosphorylation of extracellular signal-regulated kinase 1/2 (pERK), transcriptional activation of nuclear factor E2-related factor 2 (NRF2) and corresponding gene targets ALDH1A1, CYP1A1, HMOX1, SOD1 and decreased oxidative stress, while R126Q treatment did not show any effects. Proximity-labeling employing an APEX2-FABP4 fusion protein revealed several proteins functioning in desmosomes as eFABP4 receptor candidates including desmoglein, desmocollin, junction plankoglobin, desomoplankin and cytokeratins. AlphaFold modeling predicted an interaction between eFABP4, and the extracellular cadherin repeats of DSG2 and pull-down and immunoprecipitation assays confirmed complex formation that was potentiated by oleic acid. Silencing of Desmoglein 2 in MCF-7 cells attenuated eFABP4 effects on cellular proliferation, pERK levels, and ALDH1A1 expression compared to controls.
Implications: These results suggest desmosomal proteins, and in particular Desmoglein 2, may function as receptors of eFABP4 and provide new insight into the development and progression of obesity-associated cancers.
Data from Overlaid transcriptome and proteome analyses identify mitotic kinesins as important targets of arylsulfonamide-mediated RBM39 degradation
Authors: Coomar Seemon , Mota Pedro , Penson Alexander , Schwaller Juerg , Abdel-Wahab Omar , Gillingham Dennis
Published: September 2024

Abstract
Certain arylsulfonamides (ArSulfs) induce an interaction between the E3 ligase substrate adaptor DCAF15 and the critical splicing factor RBM39, ultimately causing its degradation. However, degradation of a splicing factor introduces complex pleiotropic effects that are difficult to untangle, since, aside from direct protein degradation, downstream transcriptional effects also influence the proteome. By overlaying transcriptional data and proteome datasets, we distinguish transcriptional from direct degradation effects, pinpointing those proteins most impacted by splicing changes. Using our workflow, we identify and validate the upregulation of the argininie-and-serine rich protein (RSRP1) and the downregulation of the key kinesin motor proteins KIF20A and KIF20B due to altered splicing in the absence of RBM39. We further show that kinesin downregulation is connected to the multinucleation phenotype observed upon RBM39 depletion by ArSulfs. Our approach should be helpful in the assessment of potential cancer drug candidates which target splicing factors.

Implications: Our approach provides a workflow for identifying and studying the most strongly modulated proteins when splicing is altered; the work also uncovers a splicing-based approach toward pharmacological targeting of mitotic kinesins.
Data from Podoplanin drives amoeboid invasion in canine and human mucosal melanoma
Authors: Shinada Masahiro , Kato Daiki , Motegi Tomoki , Tsuboi Masaya , Ikeda Namiko , Aoki Susumu , Iguchi Takaaki , Li Toshio , Kodera Yuka , Ota Ryosuke , Hashimoto Yuko , Takahashi Yosuke , Chambers James , Uchida Kazuyuki , Kato Yukinari , Nishimura Ryohei , Nakagawa Takayuki
Published: September 2024

Abstract
Mucosal melanoma metastasizes at an early stage of the disease in human and dog. We revealed that overexpression of podoplanin (PDPN) in tumor invasion fronts (IFs) was related to poor prognosis of dogs with mucosal melanoma. Moreover, PDPN expressed in canine mucosal melanoma cells promotes proliferation and aggressive amoeboid invasion by activating Rho-associated kinase (ROCK)-myosin light chain 2 (MLC2) signaling. PDPN-ROCK-MLC2 signaling plays a role in cell cycle arrest and cellular senescence escape as a mechanism for regulating proliferation. PDPN induces amoeboid invasion in the IFs of mouse xenografted tumor tissues, similar to canine mucosal melanoma clinical samples. We further identified that PDPN expression was related to poor prognosis of human patients with mucosal melanoma, and human mucosal melanoma with PDPN high expression enriched gene signatures related to amoeboid invasion, similar to canine mucosal melanoma. Overall, we propose that PDPN promotes canine and human mucosal melanoma metastasis by inducing aggressive amoeboid invasion and naturally occurring canine mucosal melanoma can be a novel research model for PDPN expressing human mucosal melanoma.
Implications: PDPN could be a new therapeutic target to restrict the metastatic dissemination of canine and human mucosal melanoma.
Supplementary Figure S2 from Simple Prediction Model for Colorectal Serrated Polyps: Development and External Validation Study in US Prospective Cohorts
Authors: Lyu Zhangyan , Hang Dong , He Xiaosheng , Wu Kana , Cao Yin , Rosner Bernard , Chan Andrew T. , Ogino Shuji , Li Ni , Dai Min , Giovannucci Edward L. , Song Mingyang
Published: September 2024

Supplementary Figure S2: The calibration plot of the simple risk prediction model for high-risk serrated polyps (SPs) across deciles of predicted risk, in women and men.
Supplementary Table S2 from Validation of an abridged breast cancer risk prediction model for the general population
Authors: Spaeth Erika L. , Dite Gillian S. , Hopper John L. , Allman Richard
Published: September 2024

Supplementary Table S2 shows the study eligibility criteria
Supplementary Table S2 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

Supplementary Table S2 lists antibody information for immunofluorescence in Figure 5.
Data from Validation of an abridged breast cancer risk prediction model for the general population
Authors: Spaeth Erika L. , Dite Gillian S. , Hopper John L. , Allman Richard
Published: September 2024

Abstract
Accurate breast cancer risk prediction could improve risk-reduction paradigms if thoughtfully employed in clinical practice. Identification of at-risk women is the first step in tailoring risk screening and risk-reduction protocols to women’s needs. Using the UK Biobank, we validated a simple risk model to predict breast cancer risk in the general population. Our simple breast cancer risk (BRISK) model integrates a combination of impactful breast cancer-associated risk factors including extended family history and polygenic risk allowing for the removal of moderate factors currently found in comprehensive traditional models. Using two versions of BRISK, differing by 77-SNP versus 313-SNP polygenic risk score integration, we found improved discrimination and risk categorization of both BRISK models compared to one of the most well-known models, the Breast Cancer Risk Assessment Tool (BRCAT). Over a five-year period, at-risk women classified ≥3% 5-year risk by BRISK had a 1.829 (95% CI = 1.710, 1.956) times increased incidence of breast cancer compared to the population, which was higher than the 1.413 (95% CI = 1.217 to 1.640) times increased incidence for women classified ≥3% by BCRAT.
Table S1 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 S1: # Raw count of the genome-wide CRISPR screen for identifying T cell-mediated tumor killing in B2m-deficient cells. # MAGeCK results (Gene summary) for the genome-wide CRISPR screen from the B2m-deficient cells. # Gene log2FC in CRISPR screens from B2m-WT cells and B2m-KO cells. ## Common regulators of T cell mediated tumor killing in both B2m-WT and B2m-KO cells
Supplementary Fig. S9 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. S9 shows enhanced IFNg and TNFa expression by T cells and NK cells in
Rnf31/Atg5-dKO tumors.
Supplementary Fig. S5 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. S5 shows association of Atg5-KO and Rnf31/Atg5-dKO signatures with
patient survival.
Supplementary Fig. S11 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. S11 shows pharmacological sensitization of human melanoma cell line to T
cell cytokines.
Supplementary Table S9 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 S9 shows the gene set enrichment analysis gene set that corresponds to Figure S6A.
Supplementary Table S7 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 S7 shows the gene set enrichment analysis gene set that corresponds to Figure 4E.
Supplementary Table S2 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 S2 shows the quantification of (R)-2HG in TF-1 cells.
Supplementary Table S11 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 S11 shows the characteristics of the primary glioma patient samples.
Supplementary Figure S9: 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

Genomic regions marked by increased trimethyl-H3K4 are enriched in IDH1-mutant glioma MCTS lines when compared to IDH1-wild-type MCTS lines.
Supplementary Figure S7 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

5mC levels in primary AML and primary glioma samples and in MCTS lines.
Supplementary Figure S6 from (R)-2-hydroxyglutarate inhibits KDM5 histone lysine demethylases to drive transformation in IDH-mutant cancers
Authors: Gunn Kathryn , Myllykoski Matti , Cao John Z. , Ahmed Manna , Huang Bofu , Rouaisnel Betty , Diplas Bill H. , Levitt Michael M. , Looper Ryan , Doench John G. , Ligon Keith L. , Kornblum Harley I. , McBrayer Samuel K. , Yan Hai , Duy Cihangir , Godley Lucy A. , Koivunen Peppi , Losman Julie-Aurore
Published: September 2024

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

Characterization of KDM5A mutants.
Supplementary Figure S3 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

Trimethyl-H3K4 is not enriched upon knock-down of TET2 in TF-1 cells.
Supplementary Tables 1-7 from Combinatorial BCL-2 family expression in Acute Myeloid Leukemia Stem Cells predicts clinical response to Azacitidine/Venetoclax
Authors: Waclawiczek Alexander , Leppa Aino-Maija , Renders Simon , Stumpf Karolin , Reyneri Cecilia , Betz Barbara , Janssen Maike , Shahswar Rabia , Donato Elisa , Karpova Darja , Thiel Vera , Unglaub Julia M. , Grabowski Susanna , Gryzik Stefanie , Vierbaum Lisa , Schlenk Richard F. , Rollig Christoph , Hundemer Michael , Pabst Caroline , Heuser Michael , Raffel Simon , Muller-Tidow Carsten , Sauer Tim , Trumpp Andreas
Published: September 2024

7 Tables showing: molecular and clinical patient data, cell line info, antibody panels and overview of assays used
Table S5 from Spatial Transcriptomics of Intraductal Papillary Mucinous Neoplasms of The Pancreas Identifies NKX6-2 as a Driver of Gastric Differentiation and Indolent Biological Potential
Authors: Sans Marta , Makino Yuki , Min Jimin , Rajapakshe Kimal I. , Yip-Schneider Michele , Schmidt C. Max , Hurd Mark W. , Burks Jared K. , Gomez Javier A. , Thege Fredrik I. , Fahrmann Johannes F. , Wolff Robert A. , Kim Michael P. , Guerrero Paola A. , Maitra Anirban
Published: September 2024

Differentially expressed genes between LG and HGPDAC juxtalesional spots.
Table S4 from Spatial Transcriptomics of Intraductal Papillary Mucinous Neoplasms of The Pancreas Identifies NKX6-2 as a Driver of Gastric Differentiation and Indolent Biological Potential
Authors: Sans Marta , Makino Yuki , Min Jimin , Rajapakshe Kimal I. , Yip-Schneider Michele , Schmidt C. Max , Hurd Mark W. , Burks Jared K. , Gomez Javier A. , Thege Fredrik I. , Fahrmann Johannes F. , Wolff Robert A. , Kim Michael P. , Guerrero Paola A. , Maitra Anirban
Published: September 2024

Differentially expressed genes between LG and HGPDAC epilesional spots.
Table S24 from Spatial Transcriptomics of Intraductal Papillary Mucinous Neoplasms of The Pancreas Identifies NKX6-2 as a Driver of Gastric Differentiation and Indolent Biological Potential
Authors: Sans Marta , Makino Yuki , Min Jimin , Rajapakshe Kimal I. , Yip-Schneider Michele , Schmidt C. Max , Hurd Mark W. , Burks Jared K. , Gomez Javier A. , Thege Fredrik I. , Fahrmann Johannes F. , Wolff Robert A. , Kim Michael P. , Guerrero Paola A. , Maitra Anirban
Published: September 2024

Protein panel used for the COMET protocol for cyclic immunofluorescent staining.
Table S14 from Spatial Transcriptomics of Intraductal Papillary Mucinous Neoplasms of The Pancreas Identifies NKX6-2 as a Driver of Gastric Differentiation and Indolent Biological Potential
Authors: Sans Marta , Makino Yuki , Min Jimin , Rajapakshe Kimal I. , Yip-Schneider Michele , Schmidt C. Max , Hurd Mark W. , Burks Jared K. , Gomez Javier A. , Thege Fredrik I. , Fahrmann Johannes F. , Wolff Robert A. , Kim Michael P. , Guerrero Paola A. , Maitra Anirban
Published: September 2024

Genes included in the GIP signature with their corresponding GSEA gene sets and enrichment scores.
Table S12 from Spatial Transcriptomics of Intraductal Papillary Mucinous Neoplasms of The Pancreas Identifies NKX6-2 as a Driver of Gastric Differentiation and Indolent Biological Potential
Authors: Sans Marta , Makino Yuki , Min Jimin , Rajapakshe Kimal I. , Yip-Schneider Michele , Schmidt C. Max , Hurd Mark W. , Burks Jared K. , Gomez Javier A. , Thege Fredrik I. , Fahrmann Johannes F. , Wolff Robert A. , Kim Michael P. , Guerrero Paola A. , Maitra Anirban
Published: September 2024

Differentially expressed genes between NKX6-2 "high", "mid", and "low" spots.
Supplementary Table S6 from Clinical activity and exploratory resistance mechanism of milademetan, an MDM2 inhibitor, in intimal sarcoma with MDM2 amplification: an open-label phase 1b/2 study
Authors: Koyama Takafumi , Shimizu Toshio , Kojima Yuki , Sudo Kazuki , Okuma Hitomi Sumiyoshi. , Shimoi Tatsunori , Ichikawa Hitoshi , Kohsaka Shinji , Sadachi Ryo , Hirakawa Akihiro , Yoshida Akihiko , Ando Reiko Makihara. , Ueno Toshihide , Yanagaki Mitsuru , Matsui Naoko , Nakamura Kenichi , Yamamoto Noboru , Yonemori Kan
Published: September 2024

Targeted sequencing analysis of cell-free DNA samples
Supplementary Table S2 from Clinical activity and exploratory resistance mechanism of milademetan, an MDM2 inhibitor, in intimal sarcoma with MDM2 amplification: an open-label phase 1b/2 study
Authors: Koyama Takafumi , Shimizu Toshio , Kojima Yuki , Sudo Kazuki , Okuma Hitomi Sumiyoshi. , Shimoi Tatsunori , Ichikawa Hitoshi , Kohsaka Shinji , Sadachi Ryo , Hirakawa Akihiro , Yoshida Akihiko , Ando Reiko Makihara. , Ueno Toshihide , Yanagaki Mitsuru , Matsui Naoko , Nakamura Kenichi , Yamamoto Noboru , Yonemori Kan
Published: September 2024

Patient characteristics
Supplementary Table S7 from An inflammatory checkpoint generated by IL1RN splicing offers therapeutic opportunity for KRAS mutant intrahepatic cholangiocarcinoma
Authors: Zhang Mao , Huang Yingying , Pan Jiaomeng , Sang Chen , Lin Youpei , Dong Liangqing , Shen Xia , Wu Yingcheng , Song Guohe , Ji Shuyi , Liu Fen , Wang Mengcheng , Zheng Yuyan , Zhang Sirui , Wang Zefeng , Ren Jianke , Gao Daming , Zhou Jian , Fan Jia , Wei Wu , Lin Jian , Gao Qiang
Published: September 2024

Supplementary Table S7. Patient information.
Supplementary Table S5 from An inflammatory checkpoint generated by IL1RN splicing offers therapeutic opportunity for KRAS mutant intrahepatic cholangiocarcinoma
Authors: Zhang Mao , Huang Yingying , Pan Jiaomeng , Sang Chen , Lin Youpei , Dong Liangqing , Shen Xia , Wu Yingcheng , Song Guohe , Ji Shuyi , Liu Fen , Wang Mengcheng , Zheng Yuyan , Zhang Sirui , Wang Zefeng , Ren Jianke , Gao Daming , Zhou Jian , Fan Jia , Wei Wu , Lin Jian , Gao Qiang
Published: September 2024

Supplementary Table S5. Top 200 genes for each T cell cluster obtained by wilcox test with the rank_genes_groups function in Scanpy.
Supplementary Figures S1-9 from An inflammatory checkpoint generated by IL1RN splicing offers therapeutic opportunity for KRAS mutant intrahepatic cholangiocarcinoma
Authors: Zhang Mao , Huang Yingying , Pan Jiaomeng , Sang Chen , Lin Youpei , Dong Liangqing , Shen Xia , Wu Yingcheng , Song Guohe , Ji Shuyi , Liu Fen , Wang Mengcheng , Zheng Yuyan , Zhang Sirui , Wang Zefeng , Ren Jianke , Gao Daming , Zhou Jian , Fan Jia , Wei Wu , Lin Jian , Gao Qiang
Published: September 2024

Supplementary Figure S1. Determination of AS index in iCCA.
Supplementary Figure S2. Validation of distinct immune features in iCCA.
Supplementary Figure S3. Detection of KRAS mutation associated indicators.
Supplementary Figure S4. Exploration of the molecular mechanisms of IL1RN201/203 in iCCA.
Supplementary Figure S5. Comparison between KRAS mutant (YAK) or KRASWT (YA) iCCA mice and functional validation of IL1RN-201/203.
Supplementary Figure S6. Definition, validation and functional exploration of neutrophil clusters.
Supplementary Figure S7. Effects of T cells, especially GZMB+ CD8+ T cells, on IL1RN-201/203 efficacy.
Supplementary Figure S8. The roles of anti-PD1 Ab in KRASWT iCCA mice and anti-PD1 Ab plus anakinra in KRAS mutant iCCA mice.
Supplementary Figure S9. Immunologic features of cancer patients with or without KRAS mutation.
Tables S4-S5 from Inhibition of METTL3 results in a cell-intrinsic interferon response that enhances
anti-tumour immunity
Authors: Guirguis Andrew A. , Ofir-Rosenfeld Yaara , Knezevic Kathy , Blackaby Wesley , Hardick David , Chan Yih-Chih , Motazedian Ali , Gillespie Andrea , Vassiliadis Dane , Lam Enid YN. , Tran Kevin , Andrews Byron , Harbour Michael E. , Vasiliauskaite Lina , Saunders Claire J. , Tsagkogeorga Georgia , Azevedo Aleksandra , Obacz Joanna , Pilka Ewa S. , Carkill Marie , MacPherson Laura , Wainwright Elanor N. , Liddicoat Brian , Blyth Benjamin J. , Albertella Mark R. , Rausch Oliver , Dawson Mark A.
Published: September 2024

Primer + shRNA + Taqman probe sequences
Figure S6 from Inhibition of METTL3 results in a cell-intrinsic interferon response that enhances
anti-tumour immunity
Authors: Guirguis Andrew A. , Ofir-Rosenfeld Yaara , Knezevic Kathy , Blackaby Wesley , Hardick David , Chan Yih-Chih , Motazedian Ali , Gillespie Andrea , Vassiliadis Dane , Lam Enid YN. , Tran Kevin , Andrews Byron , Harbour Michael E. , Vasiliauskaite Lina , Saunders Claire J. , Tsagkogeorga Georgia , Azevedo Aleksandra , Obacz Joanna , Pilka Ewa S. , Carkill Marie , MacPherson Laura , Wainwright Elanor N. , Liddicoat Brian , Blyth Benjamin J. , Albertella Mark R. , Rausch Oliver , Dawson Mark A.
Published: September 2024

PDL1 expression + STM3006 pharmacokinetic studies
Data 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

Abstract
Oncogenic mutations in isocitrate dehydrogenase (IDH)-1 and -2 occur in a wide range of cancers, including acute myeloid leukemia (AML) and glioma. Mutant IDH enzymes convert 2-oxoglutarate (2OG) to (R)-2-hydroxyglutarate ((R)-2HG)), an oncometabolite that is hypothesized to promote cellular transformation by dysregulating 2OG-dependent enzymes. The only (R)-2HG target that has been convincingly shown to contribute to transformation by mutant IDH is the myeloid tumor suppressor TET2. However, there is ample evidence to suggest that (R)-2HG has other functionally relevant targets in IDH-mutant cancers. Here, we show that (R)-2HG inhibits KDM5 histone lysine demethylases and that this inhibition contributes to cellular transformation in IDH-mutant AML and IDH-mutant glioma. These studies provide the first evidence of a functional link between dysregulation of histone lysine methylation and transformation in IDH-mutant cancers.
Data from Resistance to selective FGFR inhibitors in FGFR-driven urothelial cancer
Authors: Facchinetti Francesco , Hollebecque Antoine , Braye Floriane , Vasseur Damien , Pradat Yoann , Bahleda Rastislav , Pobel Cedric , Bigot Ludovic , Deas Olivier , Florez Arango Juan David , Guaitoli Giorgia , Mizuta Hayato , Combarel David , Tselikas Lambros , Michiels Stefan , Nikolaev Sergey I. , Scoazec Jean-Yves , Ponce-Aix Santiago , Besse Benjamin , Olaussen Ken A. , Loriot Yohann , Friboulet Luc
Published: September 2024

Abstract
Several FGFR inhibitors are approved or in clinical development for the treatment of FGFR-driven urothelial cancer, and molecular mechanisms of resistance leading to patient relapses have not been fully explored. We identified 21 FGFR-driven urothelial cancer patients treated with selective FGFR inhibitors and analyzed post-progression tissue and/or circulating tumor DNA (ctDNA). We detected single mutations in the FGFR tyrosine kinase domain in seven (33%) patients (FGFR3 N540K, V553L/M, V555L/M, E587Q; FGFR2 L551F) and multiple mutations in one (5%) case (FGFR3 N540K, V555L, L608V). Using Ba/F3 cells, we defined their spectrum of resistance/sensitivity to multiple selective FGFR inhibitors. Eleven (52%) patients harbored alterations in the PI3K-mTOR pathway (n = 5 TSC1/2, n = 5 PIK3CA, n = 1 NF2, n = 1 PTEN). In patient-derived models, erdafitinib was synergic with pictilisib in the presence of PIK3CA E545K, while erdafitinib-gefitinib combination was able to overcome bypass resistance mediated by EGFR activation.
Data from Colorectal cancer organoid-stroma biobank allows subtype-specific assessment of individualized therapy responses
Authors: Farin Henner F. , Mosa Mohammed H. , Ndreshkjana Benardina , Grebbin Britta M. , Ritter Birgit , Menche Constantin , Kennel Kilian B. , Ziegler Paul K. , Szabo Lili , Bollrath Julia , Rieder Dietmar , Michels Birgitta E. , Kress Alena , Bozlar Muge , Darvishi Tahmineh , Stier Sara , Kur Ivan-Maximiliano , Bankov Katrin , Kesselring Rebecca , Fichtner-Feigl Stefan , Brune Bernhard , Goetze Thorsten O. , Al-Batran Salah-Eddin , Brandts Christian H. , Bechstein Wolf O. , Wild Peter J. , Weigert Andreas , Muller Susanne , Knapp Stefan , Trajanoski Zlatko , Greten Florian R.
Published: September 2024

Abstract
In colorectal cancers (CRC) the tumor microenvironment plays a key role for prognosis and therapy efficacy. Patient-derived tumor organoids (PDTOs) show enormous potential for preclinical testing, however, cultured tumor cells lose important characteristics including the ‘consensus molecular subtypes’ (CMS). To better reflect the cellular heterogeneity, we established the CRC organoid-stroma biobank of matched PDTOs and cancer-associated fibroblasts (CAFs) from 30 patients. Context-specific phenotyping showed that xenotransplantation or co-culture with CAFs improves the transcriptomic fidelity and instructs subtype-specific stromal gene expression. Furthermore, functional profiling in co-culture exposed CMS4-specific therapeutic resistance to Gefitinib and SN-38 and prognostic expression signatures. Chemogenomic library screening identified patient- and therapy-dependent mechanisms of stromal resistance including MET as common target. Our results demonstrate that CRC phenotypes are encrypted in the cancer epithelium in a plastic fashion that strongly depends on the context. Consequently, CAFs are essential for faithful representation of molecular subtypes and therapy responses ex vivo.
Supplementary Figure 1 from MYC induces immunotherapy and interferon-γ resistance through downregulation of JAK2
Authors: Markovits Ettai , Harush Ortal , Baruch Erez N. , Shulman Eldad D. , Debby Assaf , Itzhaki Orit , Anafi Liat , Danilevsky Artem , Shomron Noam , Ben-Betzalel Guy , Asher Nethanel , Shapira-Frommer Ronnie , Schachter Jacob , Barshack Iris , Geiger Tamar , Elkon Ran , Besser Michal J. , Markel Gal
Published: September 2024

Supplementary Figure 1
Supplementary Tables from KRT17 promotes T-lymphocyte infiltration through the YTHDF2-CXCL10 axis in colorectal cancer
Authors: Liang Wenfeng , Liu Huashan , Zeng Ziwei , Liang Zhenxing , Xie Hao , Li Wenxin , Xiong Li , Liu Zhihang , Chen Mian , Jie Haiqing , Zheng Xiaobin , Huang Liang , Kang Liang
Published: September 2024

Materials were used in the research.
Figure S1, S2, S3, S4, S5, S6, S7, S8, S9, S10, S11 from CD69 imposes tumor-specific CD8+ T-cell fate in tumor-draining lymph nodes
Authors: Koyama-Nasu Ryo , Kimura Motoko Y. , Kiuchi Masahiro , Aoki Ami , Wang Yangsong , Mita Yukiyoshi , Hasegawa Ichita , Endo Yukihiro , Onodera Atsushi , Hirahara Kiyoshi , Motohashi Shinichiro , Nakayama Toshinori
Published: September 2024

Figure S1, S2, S3, S4, S5, S6, S7, S8, S9, S10, S11
Supplementary Table 2 from Systemic Alterations in Type-2 Conventional Dendritic Cells Leads to Impaired Tumor Immunity in Pancreatic Cancer
Authors: James C. Alston. , Baer John M. , Zuo Chong , Panni Usman Y. , Knolhoff Brett L. , Hogg Graham D. , Kingston Natalie L. , Kang Liang-I , Lander Varintra E. , Luo Jingqin , Tao Yu , Watson Mark A. , Aft Rebecca , Fields Ryan C. , Hawkins William G. , DeNardo David G.
Published: September 2024

Supplementary Table 2
Supplementary Table S5 from Immunogenetic metabolomics reveals key enzymes that modulate CAR T-cell metabolism and function
Authors: Renauer Paul , Park Jonathan J. , Bai Meizhu , Acosta Arianny , Lee Won-Ho , Lin Guang Han , Zhang Yueqi , Dai Xiaoyun , Wang Guangchuan , Errami Youssef , Wu Terence , Clark Paul , Ye Lupeng , Yang Quanjun , Chen Sidi
Published: September 2024

Supplementary Table S5
Supplementary Table 1 from Granulocyte-Macrophage Colony-Stimulating Factor (GM-CSF) Influence on Soluble and Membrane Bound ICOS in Combination with Immune Checkpoint Blockade
Authors: Li Xiaoyu , Li Jingjing , zheng Yue , Lee Sandra J. , Zhou Jun , Giobbie-Hurder Anita , Butterfield Lisa H. , Dranoff Glenn , Hodi F. Stephen.
Published: September 2024

Supplementary table 1
Supplementary Figure 5 from Granulocyte-Macrophage Colony-Stimulating Factor (GM-CSF) Influence on Soluble and Membrane Bound ICOS in Combination with Immune Checkpoint Blockade
Authors: Li Xiaoyu , Li Jingjing , zheng Yue , Lee Sandra J. , Zhou Jun , Giobbie-Hurder Anita , Butterfield Lisa H. , Dranoff Glenn , Hodi F. Stephen.
Published: September 2024

Supplementary figure 5
Supplementary Figure 1 from Granulocyte-Macrophage Colony-Stimulating Factor (GM-CSF) Influence on Soluble and Membrane Bound ICOS in Combination with Immune Checkpoint Blockade
Authors: Li Xiaoyu , Li Jingjing , zheng Yue , Lee Sandra J. , Zhou Jun , Giobbie-Hurder Anita , Butterfield Lisa H. , Dranoff Glenn , Hodi F. Stephen.
Published: September 2024

Supplementary Figure1
Supplementary Data from Circulating and intratumoral immune determinants of response to atezolizumab plus bevacizumab in patients with variant histology or sarcomatoid renal cell carcinoma
Authors: Saliby Renee Maria , El Zarif Talal , Bakouny Ziad , Shah Valisha , Xie Wanling , Flippot Ronan , Denize Thomas , Kane M. Harry , Madsen Katrine N. , Ficial Miriam , Hirsch Laure , Wei Xiao X. , Steinarter John A. , Harshman Lauren C. , Vaishampayan Ulka N. , Severgnini Mariano , McDermott David F. , Lee Gwo-Shu Mary. , Xu Wenxin , Van Allen Eliezer M. , McGregor Bradley A. , Signoretti Sabina , Choueiri Toni K. , McKay Rana R. , Braun David A.
Published: September 2024

Titles and captions of supplementary figures
Figure S7 from Circulating and intratumoral immune determinants of response to atezolizumab plus bevacizumab in patients with variant histology or sarcomatoid renal cell carcinoma
Authors: Saliby Renee Maria , El Zarif Talal , Bakouny Ziad , Shah Valisha , Xie Wanling , Flippot Ronan , Denize Thomas , Kane M. Harry , Madsen Katrine N. , Ficial Miriam , Hirsch Laure , Wei Xiao X. , Steinarter John A. , Harshman Lauren C. , Vaishampayan Ulka N. , Severgnini Mariano , McDermott David F. , Lee Gwo-Shu Mary. , Xu Wenxin , Van Allen Eliezer M. , McGregor Bradley A. , Signoretti Sabina , Choueiri Toni K. , McKay Rana R. , Braun David A.
Published: September 2024

Supplementary figure 7
Supplementary Table 2 from Enhancing CAR T-cell therapy using Fab-Based Constitutively Heterodimeric Cytokine Receptors
Authors: Righi Matteo , Gannon Isaac , Robson Mathew , Srivastava Saket , Kokalaki Evangelia , Grothier Thomas , Nannini Francesco , Allen Christopher , Bai Yuchen V. , Sillibourne James , Cordoba Shaun , Thomas Simon , Pule Martin
Published: September 2024

Supplementary Table S2. Top 50 up-regulated GSEA pathways.
Supplementary Figure S1-S26 from Enhancing CAR T-cell therapy using Fab-Based Constitutively Heterodimeric Cytokine Receptors
Authors: Righi Matteo , Gannon Isaac , Robson Mathew , Srivastava Saket , Kokalaki Evangelia , Grothier Thomas , Nannini Francesco , Allen Christopher , Bai Yuchen V. , Sillibourne James , Cordoba Shaun , Thomas Simon , Pule Martin
Published: September 2024

Supplementary Figure S1-S26
Supplementary Figures from A bispecific γδ T-cell engager targeting EGFR activates a potent Vγ9Vδ2 T cell–mediated immune response against EGFR-expressing tumors
Authors: King Lisa A. , Toffoli Elisa C. , Veth Myrthe , Iglesias-Guimarais Victoria , Slot Manon C. , Amsen Derk , van de Ven Rieneke , Derks Sarah , Fransen Marieke F. , Tuynman Jurriaan B. , Riedl Thilo , Roovers Rob C. , Adang Anton E.P. , Ruben Jurjen M. , Parren Paul W.H.I. , de Gruijl Tanja D. , van der Vliet Hans J.
Published: September 2024

Figures S1-9
Supplementary Table S1 from AXL inhibition improves the anti-tumor activity of chimeric antigen receptor T cells
Authors: Sakemura R. Leo , Hefazi Mehrdad , Cox Michelle J. , Siegler Elizabeth L. , Sinha Sutapa , Hansen Michael J. , Stewart Carli M. , Feigin Jennifer M. , Manriquez Roman Claudia , Schick Kendall J. , Can Ismail , Tapper Erin E. , Horvei Paulina , Adada Mohamad M. , Bezerra Evandro D. , Kankeu Fonkoua Lionel Aurelien. , Ruff Michael W. , Forsman Cynthia L. , Nevala Wendy K. , Boysen Justin C. , Tschumper Renee C. , Grand Cory L. , Kuchimanchi Kamesh R. , Mouritsen Lars , Foulks Jason M. , Warner Steven L. , Call Timothy G. , Parikh Sameer A. , Ding Wei , Kay Neil E. , Kenderian Saad S.
Published: September 2024

Supplementary Table S1
Supplementary Figures from AXL inhibition improves the anti-tumor activity of chimeric antigen receptor T cells
Authors: Sakemura R. Leo , Hefazi Mehrdad , Cox Michelle J. , Siegler Elizabeth L. , Sinha Sutapa , Hansen Michael J. , Stewart Carli M. , Feigin Jennifer M. , Manriquez Roman Claudia , Schick Kendall J. , Can Ismail , Tapper Erin E. , Horvei Paulina , Adada Mohamad M. , Bezerra Evandro D. , Kankeu Fonkoua Lionel Aurelien. , Ruff Michael W. , Forsman Cynthia L. , Nevala Wendy K. , Boysen Justin C. , Tschumper Renee C. , Grand Cory L. , Kuchimanchi Kamesh R. , Mouritsen Lars , Foulks Jason M. , Warner Steven L. , Call Timothy G. , Parikh Sameer A. , Ding Wei , Kay Neil E. , Kenderian Saad S.
Published: September 2024

Supplementary Figures S1-S17
Supplementary Tables from Clec4A4 Acts As A Negative Immune Checkpoint Regulator to Suppress Antitumor Immunity
Authors: Uto Tomofumi , Fukaya Tomohiro , Mitoma Shuya , Nishikawa Yotaro , Tominaga Moe , Choijookhuu Narantsog , Hishikawa Yoshitaka , Sato Katsuaki
Published: September 2024

Supplementary Tables
Supplementary Table S3 from Combinatorial immunotherapy with agonistic CD40 activates dendritic cells to express IL12 and overcomes PD-1 resistance
Authors: Krykbaeva Irina , Bridges Kate , Damsky William , Pizzurro Gabriela A. , Alexander Amanda F. , McGeary Meaghan K. , Park Koonam , Muthusamy Viswanathan , Eyles Jim , Luheshi Nadia , Turner Noel , Weiss Sarah A. , Olino Kelly , Kaech Susan M. , Kluger Harriet M. , Miller-Jensen Kathryn , Bosenberg Marcus
Published: September 2024

Supplementary Table S3
Supplementary Data from Tumor cell–intrinsic c-Myb upregulation stimulates antitumor immunity in a murine colorectal cancer model
Authors: van Gogh Merel , Glaus Garzon Jesus F. , Sahin Dilara , Knopfova Lucia , Benes Petr , Boyman Onur , Jurisica Igor , Borsig Lubor
Published: September 2024

Supplementary Figures and Tables
Supplementary Figures S1-10 from ANXA1 promotes tumor immune evasion by binding PARP1 and upregulating Stat3-induced expression of PD-L1 in multiple cancers
Authors: Xiao Ding , Zeng Ting , Zhu Wei , Yu Zheng-Zheng , Huang Wei , Yi Hong , Lu Shan-Shan , Feng Juan , Feng Xue-Ping , Wu Di , Wen Qi , Zhou Jian-Hua , Yuan Li , Zhuang Wei , Xiao Zhi-Qiang
Published: September 2024

Supplementary Figures S1-10
Data from Enhancing CAR T-cell therapy using Fab-Based Constitutively Heterodimeric Cytokine Receptors
Authors: Righi Matteo , Gannon Isaac , Robson Mathew , Srivastava Saket , Kokalaki Evangelia , Grothier Thomas , Nannini Francesco , Allen Christopher , Bai Yuchen V. , Sillibourne James , Cordoba Shaun , Thomas Simon , Pule Martin
Published: September 2024

Abstract
Adoptive T-cell therapy aims to achieve lasting tumor clearance, requiring enhanced engraftment and survival of the immune cells. Cytokines are paramount modulators of T-cell survival and proliferation. Cytokine receptors signal via ligand-induced dimerization, and this principle has been hijacked utilizing non-native dimerization domains. A major limitation of current technologies resides in the absence of a module that recapitulates the natural cytokine receptor heterodimeric pairing. To circumvent this, we created a new engineered cytokine receptor able to constitutively recreate receptor-heterodimer utilizing the heterodimerization domain derived from the IgG1 antibody (dFab_CCR). We found that the signal delivered by the dFab_CCR-IL2 proficiently mimicked the cytokine receptor heterodimerization, with transcriptomic signatures like those obtained by activation of the native IL2 receptor. Moreover, we found that this dimerization structure was agnostic, efficiently activating signaling through four cytokine receptor families. Using a combination of in vivo and in vitro screening approaches, we characterized a library of 18 dFab_CCRs co-expressed with a clinically relevant solid tumor–specific GD2-specific CAR. Based on this characterization, we suggest that the co-expression of either the common β-chain GMCSF or the IL18 dFab_CCRs is optimal to improve CAR T-cell expansion, engraftment, and efficacy. Our results demonstrate how Fab dimerization is efficient and versatile in recapitulating a cytokine receptor heterodimerization signal. This module could be applied for the enhancement of adoptive T-cell therapies, as well as therapies based on other immune cell types. Furthermore, these results provide a choice of cytokine signal to incorporate with adoptive T-cell therapies.
Data from CCRL2 expression by specialized lung capillary endothelial cells controls NK-cell homing in lung cancer
Authors: Sozio Francesca , Schioppa Tiziana , Laffranchi Mattia , Salvi Valentina , Tamassia Nicola , Bianchetto-Aguilera Francisco M. , Tiberio Laura , Bonecchi Raffaella , Bosisio Daniela , Parmentier Marc , Bottazzi Barbara , Leone Roberto , Russo Eleonora , Bernardini Giovanni , Garofalo Stefano , Limatola Cristina , Gismondi Angela , Sciumè Giuseppe , Mantovani Alberto , Del Prete Annalisa , Sozzani Silvano
Published: September 2024

Abstract
Patterns of receptors for chemotactic factors regulate the homing of leukocytes to tissues. Here we report that the CCRL2/chemerin/CMKLR1 axis represents a selective pathway for the homing of NK cells to the lung. C-C motif Chemokine Receptor-Like 2 (CCRL2) is a non-signaling seven-transmembrane domain receptor able to control lung tumor growth. CCRL2 constitutive or conditional endothelial cell targeted ablation, or deletion of its ligand chemerin, were found to promote tumor progression in a Kras/p53Flox lung cancer cell model. This phenotype was dependent on the reduced recruitment of CD27–CD11b+ mature NK cells. Other chemotactic receptors identified in lung-infiltrating NK cells by single-cell RNA sequencing (scRNA-seq), such as Cxcr3, Cx3cr1, and S1pr5, were found to be dispensable in the regulation of NK-cell infiltration of the lung and lung tumor growth. scRNA-seq identified CCRL2 as the hallmark of general alveolar lung capillary endothelial cells. CCRL2 expression was epigenetically regulated in lung endothelium and it was upregulated by the demethylating agent 5-aza-2’-deoxycytidine (5-Aza). In vivo administration of low doses of 5-Aza induced CCRL2 upregulation, increased recruitment of NK cells, and reduced lung tumor growth. These results identify CCRL2 as an NK-cell lung homing molecule that has the potential to be exploited to promote NK cell–mediated lung immune surveillance.
Figure S1 from HTLV-1 bZIP factor-induced reprogramming of lactate metabolism and epigenetic status promote leukemic cell expansion
Authors: Toyoda Kosuke , Yasunaga Jun-ichirou , Shichijo Takafumi , Arima Yuichiro , Tsujita Kenichi , Tanaka Azusa , Salah Tarig , Zhang Wenyi , Hussein Osama , Sonoda Miyu , Watanabe Miho , Kurita Daisuke , Nakashima Kazutaka , Yamada Kyohei , Miyoshi Hiroaki , Ohshima Koichi , Matsuoka Masao
Published: September 2024

Transcriptional regulation by HBZ protein and RNA and the status of TP73 expression.
Table S3 from A SINGLE-CELL TAXONOMY PREDICTS INFLAMMATORY NICHE REMODELING TO DRIVE TISSUE FAILURE AND OUTCOME IN HUMAN AML
Authors: Chen Lanpeng , Pronk Eline , van Dijk Claire , Bian Yujie , Feyen Jacqueline , van Tienhoven Tim , Yildirim Meltem , Pisterzi Paola , De Jong Madelon M E. , Bastidas Alejandro , Hoogenboezem Remco M. , Wevers Chiel , Bindels Eric M. , Löwenberg Bob , Cupedo Tom , Sanders Mathijs A. , Raaijmakers Marc HGP.
Published: September 2024

Supplementary Table 3. Differentially expressed genes in the NBM BMSC cluster 0 vs. other BMSC clusters
Table S2 from Time-dependent prognostic value of serological and measurable residual disease assessments after idecabtagene vicleucel
Authors: Paiva Bruno , Manrique Irene , Rytlewski Julie , Campbell Timothy , Kazanecki Christian C. , Martin Nathan , Anderson Larry D. , Berdeja Jesus G. , Lonial Sagar , Raje Noopur S. , Lin Yi , Moreau Philippe , San-Miguel Jesus F. , Munshi Nikhil C. , Kaiser Shari
Published: September 2024

HR for PFS according to MRD status
Table S1 from Time-dependent prognostic value of serological and measurable residual disease assessments after idecabtagene vicleucel
Authors: Paiva Bruno , Manrique Irene , Rytlewski Julie , Campbell Timothy , Kazanecki Christian C. , Martin Nathan , Anderson Larry D. , Berdeja Jesus G. , Lonial Sagar , Raje Noopur S. , Lin Yi , Moreau Philippe , San-Miguel Jesus F. , Munshi Nikhil C. , Kaiser Shari
Published: September 2024

Patient distribution of paired results