bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figures from TET2-Dependent Hydroxymethylome Plasticity Reduces Melanoma Initiation and Progression
Authors: Bonvin Elise , Radaelli Enrico , Bizet Martin , Luciani Flavie , Calonne Emilie , Putmans Pascale , Nittner David , Singh Nitesh Kumar , Santagostino Sara Francesca , Petit Valérie , Larue Lionel , Marine Jean Christophe , Fuks François
Published: April 2023

Histological examination of samples, mC measurement by Mass Spec, survival curves showing the effect of p16Ink4 deletion, qPCR of hmC-related enzymes and melanoma related genes, hmedIP-pcr confirmation of hmedIP-seq, list of primers
Suppl Table S3 from TET2-Dependent Hydroxymethylome Plasticity Reduces Melanoma Initiation and Progression
Authors: Bonvin Elise , Radaelli Enrico , Bizet Martin , Luciani Flavie , Calonne Emilie , Putmans Pascale , Nittner David , Singh Nitesh Kumar , Santagostino Sara Francesca , Petit Valérie , Larue Lionel , Marine Jean Christophe , Fuks François
Published: April 2023

DhmR and gene expression tet-/- related to Fig3
Supplementary data and tables from Acidification of Tumor at Stromal Boundaries Drives Transcriptome Alterations Associated with Aggressive Phenotypes
Authors: Rohani Nazanin , Hao Liangliang , Alexis Maria S. , Joughin Brian A. , Krismer Konstantin , Moufarrej Mira N. , Soltis Anthony R. , Lauffenburger Douglas A. , Yaffe Michael B. , Burge Christopher B. , Bhatia Sangeeta N. , Gertler Frank B.
Published: April 2023

Supplementary methods contains additional methods section on RNA sequencing , bioinformatics analysis and cell culture Table S1 lists all antibodies and manufacturer names Table S2 lists all primers used for RT-qPCR Table S3 shows motif hits results derived from spectrum motif analysis in human MDAMB231 and 4t1 differentially expressed genes.
Legend of supplementary data from TET2-Dependent Hydroxymethylome Plasticity Reduces Melanoma Initiation and Progression
Authors: Bonvin Elise , Radaelli Enrico , Bizet Martin , Luciani Flavie , Calonne Emilie , Putmans Pascale , Nittner David , Singh Nitesh Kumar , Santagostino Sara Francesca , Petit Valérie , Larue Lionel , Marine Jean Christophe , Fuks François
Published: April 2023

Description of supplementary tables and figures
Figure S6 from Acidification of Tumor at Stromal Boundaries Drives Transcriptome Alterations Associated with Aggressive Phenotypes
Authors: Rohani Nazanin , Hao Liangliang , Alexis Maria S. , Joughin Brian A. , Krismer Konstantin , Moufarrej Mira N. , Soltis Anthony R. , Lauffenburger Douglas A. , Yaffe Michael B. , Burge Christopher B. , Bhatia Sangeeta N. , Gertler Frank B.
Published: April 2023

Figures S6 shows a. in vivo validation of pH- induced transcriptomic events b. spatial correlation between HDAC2 expression and acidic areas in tumor.
Figure S5 from Acidification of Tumor at Stromal Boundaries Drives Transcriptome Alterations Associated with Aggressive Phenotypes
Authors: Rohani Nazanin , Hao Liangliang , Alexis Maria S. , Joughin Brian A. , Krismer Konstantin , Moufarrej Mira N. , Soltis Anthony R. , Lauffenburger Douglas A. , Yaffe Michael B. , Burge Christopher B. , Bhatia Sangeeta N. , Gertler Frank B.
Published: April 2023

Figure S5 shows a.The effect of short term or long term exposure to low pH on the induction of candidate splicing events.b. cell growth during time spent in low pH versus normal pH condition.c. lactate to glucose ratio under hypoxia and metformin conditions with or without Hepes. d. Effect of increase in histone acetylation on candidate splicing events
Figure S4 from Acidification of Tumor at Stromal Boundaries Drives Transcriptome Alterations Associated with Aggressive Phenotypes
Authors: Rohani Nazanin , Hao Liangliang , Alexis Maria S. , Joughin Brian A. , Krismer Konstantin , Moufarrej Mira N. , Soltis Anthony R. , Lauffenburger Douglas A. , Yaffe Michael B. , Burge Christopher B. , Bhatia Sangeeta N. , Gertler Frank B.
Published: April 2023

Figure S4 shows the effect of low pH on different types of splicing event and validation of candidate splicing events
Supplementary Data from Nutrient Stress–Dysregulated Antisense lncRNA GLS-AS Impairs GLS-Mediated Metabolism and Represses Pancreatic Cancer Progression
Authors: Deng Shi-Jiang , Chen Heng-Yu , Zeng Zhu , Deng Shichang , Zhu Shuai , Ye Zeng , He Chi , Liu Ming-Liang , Huang Kang , Zhong Jian-Xin , Xu Feng-Yu , Li Qiang , Liu Yang , Wang Chunyou , Zhao Gang
Published: April 2023

Supplementary Figure S1. Downregulation of GLS-AS facilitates pancreatic cancer proliferation and invasion. Supplementary Figure S2. Downregulation of GLS-AS apparently increased the GLS expression. Supplementary Figure S3. GLS-AS exert its biological function mainly through GLS. Supplementary Figure S4. The transcriptional activity of GLS promoter is not affected by GLS-AS. Supplementary Figure S5. GLS-AS inhibits GLS expression by ADAR1/Dicer-dependent RNA silencing in PANC-1 cells. Supplementary Figure S6. GLS-AS inhibits GLS expression via ADAR1/Dicer-dependent RNA silencing in BxPC-3 cells. Supplementary Figure S7. GLS-AS inhibits GLS expression by ADAR1/Dicer-dependent RNA silencing in BxPC-3 cells. Supplementary Figure S8. Schematic diagram of RNA pulldown by MS2-GST. Supplementary Figure S9. ADAR1 and Dicer are not significantly varied in pancreatic cancer cells under glucose or glutamine deprivation. Supplementary Figure S10. Downregulation of GLS-AS in pancreatic cancer might attributed to energy stress through Myc-depending regulation. Supplementary Figure S11. GLS and GLS-AS level does not affect Myc mRNA expression in pancreatic cancer cells. Supplementary Figure S12. GLS-AS is conversely correlated with Myc and GLS expression in pancreatic cancer. Supplementary Figure S13. GLS-AS suppresses pancreatic cancer cell growth, invasion and migration in vitro. Supplementary Figure S14. GLS-AS inhibits the progression of the pancreatic cancer in vivo proven with PANC-1 cells. Supplementary Figure S15. GLS-AS inhibits the progression of the pancreatic cancer in vivo proven with BxPC-3 cells.
Supplementary Data from Nutrient Stress–Dysregulated Antisense lncRNA GLS-AS Impairs GLS-Mediated Metabolism and Represses Pancreatic Cancer Progression
Authors: Deng Shi-Jiang , Chen Heng-Yu , Zeng Zhu , Deng Shichang , Zhu Shuai , Ye Zeng , He Chi , Liu Ming-Liang , Huang Kang , Zhong Jian-Xin , Xu Feng-Yu , Li Qiang , Liu Yang , Wang Chunyou , Zhao Gang
Published: April 2023

Supplementary Table 2. The sequences of PCR primers.
Supplementary Figure S7. The absence of STING (or p53 or p21) leads to increase in BUB1 and MAD2L1 expression. from STING Promotes Homeostasis via Regulation of Cell Proliferation and Chromosomal Stability
Authors: Ranoa Diana Rose E. , Widau Ryan C. , Mallon Stephen , Parekh Akash D. , Nicolae Claudia M. , Huang Xiaona , Bolt Michael J. , Arina Ainhoa , Parry Renate , Kron Stephen J. , Moldovan George-Lucian , Khodarev Nikolai N. , Weichselbaum Ralph R.
Published: April 2023

(A-C) BrdU/PI cell cycle profile of MEFs (A), p53-/- HCT116 (B), and CDKN1A-depleted HCT116 cells (C) at 24 hours post-IR. Flow cytometry was used to measure the percent cell population in G1, S, and G2/M phase of single cells stained with FITC-conjugated anti-BrdU (y-axis) and PI (x-axis). (D-F) Western analyses of lysates from WT and STING-/- immortalized MEFs (D), p53-negative HCT116 (E), and siCDKN1A HCT116 (F) probed for mitotic proteins BUB1 and MAD2L1 at 48 hours post-exposure to increasing IR doses. Quantified bands are shown below each of their respective Western blot panels. (G) ChIP analyses reveal that in the absence of either p21 or STING, E2F4 does not bind to the promoter region of BUB1 and MAD2L1 in HCT116 tumor cells. Data are representative of at least two experiments. P-values were determined using unpaired Student's t-test. Error bars are SEM. *P < 0.05, **P < 0.01, ***P < 0.005.
Supplementary Figure S2. STING-dependent regulation of proliferation is associated with perturbations of cell cycle. from STING Promotes Homeostasis via Regulation of Cell Proliferation and Chromosomal Stability
Authors: Ranoa Diana Rose E. , Widau Ryan C. , Mallon Stephen , Parekh Akash D. , Nicolae Claudia M. , Huang Xiaona , Bolt Michael J. , Arina Ainhoa , Parry Renate , Kron Stephen J. , Moldovan George-Lucian , Khodarev Nikolai N. , Weichselbaum Ralph R.
Published: April 2023

Cell cycle profile of pulse EdU-labeled (A) and chase EdU-labeled (B) WT and STING-/- MEFs at different time points post-IR treatment. Flow cytometry was used to measure the percent cell population in G1, S, and G2/M phase of single cells stained with AlexaFluor 647-conjugated anti-EdU (y-axis) and PI (x-axis).
Supplementary Figure S1. shRNA constructs targeting STING have varying effects on different tumor cell lines. from STING Promotes Homeostasis via Regulation of Cell Proliferation and Chromosomal Stability
Authors: Ranoa Diana Rose E. , Widau Ryan C. , Mallon Stephen , Parekh Akash D. , Nicolae Claudia M. , Huang Xiaona , Bolt Michael J. , Arina Ainhoa , Parry Renate , Kron Stephen J. , Moldovan George-Lucian , Khodarev Nikolai N. , Weichselbaum Ralph R.
Published: April 2023

Western blot analysis of multiple stable D54 (A), HCT116 (B), and MC-38 (C) cell lines expressing short hairpin RNAs targeting STING or scrambled control (SHCOO2). Quantified bands are shown below each of their respective Western blot panels.
Supplementary Data 6 from Inhibition of NF-κB–Dependent Signaling Enhances Sensitivity and Overcomes Resistance to BET Inhibition in Uveal Melanoma
Authors: Ambrosini Grazia , Do Catherine , Tycko Benjamin , Realubit Ronald B. , Karan Charles , Musi Elgilda , Carvajal Richard D. , Chua Vivian , Aplin Andrew E. , Schwartz Gary K.
Published: April 2023

Synergistic effects of the NF-kB inhibitor QNZ in combination with PLX51107 in the BETi-resistant UM cells
Table S1 from Spatiotemporal Regulation of ΔNp63 by TGFβ-Regulated miRNAs Is Essential for Cancer Metastasis
Authors: Bui Ngoc H.B. , Napoli Marco , Davis Andrew John , Abbas Hussein A. , Rajapakshe Kimal , Coarfa Cristian , Flores Elsa R.
Published: April 2023

Table S1. List of pathways enriched in Ã¢Ë†â€ Np63-induced and -repressed gene signatures.
Supplementary Data 3 from Inhibition of NF-κB–Dependent Signaling Enhances Sensitivity and Overcomes Resistance to BET Inhibition in Uveal Melanoma
Authors: Ambrosini Grazia , Do Catherine , Tycko Benjamin , Realubit Ronald B. , Karan Charles , Musi Elgilda , Carvajal Richard D. , Chua Vivian , Aplin Andrew E. , Schwartz Gary K.
Published: April 2023

The NF-kB inhibitor PDTC has synergistic activity with the BET inhibitor PLX51107
Table S4 : custom gene set signatures from Loss of Apc Rapidly Impairs DNA Methylation Programs and Cell Fate Decisions in Lgr5+ Intestinal Stem Cells
Authors: Bruschi Marco , Garnier Laure , Cleroux Elouan , Giordano Alicia , Dumas Michael , Bardet Anaïs F. , Kergrohen Thomas , Quesada Stanislas , Cesses Pierre , Weber Michael , Gerbe François , Jay Philippe
Published: April 2023

This file contains user-defined GSEA signatures related to ISC, transit-amplifying and differentiated cell lineages used in this study.
Figure S1 from Spatiotemporal Regulation of ΔNp63 by TGFβ-Regulated miRNAs Is Essential for Cancer Metastasis
Authors: Bui Ngoc H.B. , Napoli Marco , Davis Andrew John , Abbas Hussein A. , Rajapakshe Kimal , Coarfa Cristian , Flores Elsa R.
Published: April 2023

Figure S1. ÃŽâ€�Np63 promotes breast cancer cell growth in vivo
Supplementary Methods and Data from Intratumoral Genetic and Functional Heterogeneity in Pediatric Glioblastoma
Authors: Hoffman Mary , Gillmor Aaron H. , Kunz Daniel J. , Johnston Michael J. , Nikolic Ana , Narta Kiran , Zarrei Mehdi , King Jennifer , Ellestad Katrina , Dang Ngoc Ha , Cavalli Florence M.G. , Kushida Michelle M. , Coutinho Fiona J. , Zhu Yuankun , Luu Betty , Ma Yussanne , Mungall Andrew J. , Moore Richard , Marra Marco A. , Taylor Michael D. , Pugh Trevor J. , Dirks Peter B. , Strother Douglas , Lafay-Cousin Lucie , Resnick Adam C. , Scherer Stephen , Senger Donna L. , Simons Benjamin D. , Chan Jennifer A. , Morrissy A. Sorana , Gallo Marco
Published: April 2023

Supplemental Figures S1-S7, Supplemental Tables S1-S7. Methods and Figures S1-S8; Tables S1-S7. SF1: Heterozygous TP53 deletion in the germline and tumor of patient 1 and expression timelines of DSE. SF2: Mutational signatures in pGBM samples. SF3: Deletions at immune-modulatory loci and their effect on gene expression. SF4: Dynamics of germlines SVs during tumor evolution. SF5: Copy number assays using TaqMan probes confirm the deletion at the ATRX locus. SF6: Genetic heterogeneity at the ATRX locus. SF7: Distribution of allelic frequencies and clonal sizes in pGBM samples. ST1: Calgary pediatric GBM cohort. ST2: Therapeutic approach taken for each pediatric GBM patient in the Calgary cohort. ST3: Toronto pediatric GBM cohort used for WGS with linked reads and bulk RNA-seq. ST4: Features of each sample analyzed by whole-genome sequencing with linked reads. ST5: Genes mutated in diagnostic pGBM samples in more than one patient. ST6: Genes mutated in follow-up resections in more than one patient. ST7: Results of the fits of the first incomplete moment and the negative binomial like distribution to the samples.
Supplemental Table S2 from Spleen Tyrosine Kinase–Mediated Autophagy Is Required for Epithelial–Mesenchymal Plasticity and Metastasis in Breast Cancer
Authors: Shinde Aparna , Hardy Shana D. , Kim Dongwook , Akhand Saeed Salehin , Jolly Mohit Kumar , Wang Wen-Hung , Anderson Joshua C. , Khodadadi Ryan B. , Brown Wells S. , George Jason T. , Liu Sheng , Wan Jun , Levine Herbert , Willey Christopher D. , Krusemark Casey J. , Geahlen Robert L. , Wendt Michael K.
Published: April 2023

The table lists the phosphorylation values for the array of peptides containing tyrosine or serine/threonine phosphorylation sites. This array was used to compare lysates from HME2 parental cells, TGF-beta-induced EMT and lapatinib-induced EMT.
Supplemental Figures from Combined Menin and EGFR Inhibitors Synergize to Suppress Colorectal Cancer via EGFR-Independent and Calcium-Mediated Repression of SKP2 Transcription
Authors: Katona Bryson W. , Glynn Rebecca A. , Paulosky Kayla E. , Feng Zijie , Davis Caroline I. , Ma Jian , Berry Corbett T. , Szigety Katherine M. , Matkar Smita , Liu Yuanyuan , Wang Haoren , Wu Yuan , He Xin , Freedman Bruce D. , Brady Donita C. , Hua Xianxin
Published: April 2023

Supplemental Figure S1: Menin inhibition has minimal effects on cell growth in colon cancer cells. Supplemental Figure S2: Inhibition of menin selectively sensitizes colon cancer cells to iEGFRs. Supplemental Figure S3: BAPTA rescues cells from the combination of gefitinib plus MI-2-2. Supplemental Figure S4: SERCA2 over-expression rescues cells from thapsigargin but not gefitinib. Supplemental Figure S5: Gefitinib induced CRC suppression is mediated by activation of IP3R3. Supplemental Figure S6: Menin inhibition, gefitinib, and TG all decrease SKP2 levels. Supplemental Figure S7: Regulation of SKP2 transcription by menin and intracellular calcium levels.
Supplementary Data from Retrodifferentiation of Human Tumor Hepatocytes to Stem Cells Leads to Metabolic Reprogramming and Chemoresistance
Authors: Fekir Karim , Dubois-Pot-Schneider Hélène , Désert Romain , Daniel Yoann , Glaise Denise , Rauch Claudine , Morel Fabrice , Fromenty Bernard , Musso Orlando , Cabillic Florian , Corlu Anne
Published: April 2023

Supplemental Table 4 shows the results of a Connectivity Map analysis identifying some molecules that are likely to reverse the gene expression profile induced during HepaRG spherogenesis.
Supplementary Figure S4 from Suppression of LIM Kinase 1 and LIM Kinase 2 Limits Glioblastoma Invasion
Authors: Chen Joseph , Ananthanarayanan Badriprasad , Springer Kelsey S. , Wolf Kayla J. , Sheyman Sharon M. , Tran Vivien D. , Kumar Sanjay
Published: April 2023

LIMK1 and LIMK2 is enriched within the tumor in NT animals but diminished in LIMK1/2 KD tumors.
Supplementary Data from Targeting Novel Sodium Iodide Symporter Interactors ADP-Ribosylation Factor 4 and Valosin-Containing Protein Enhances Radioiodine Uptake
Authors: Fletcher Alice , Read Martin L. , Thornton Caitlin E.M. , Larner Dean P. , Poole Vikki L. , Brookes Katie , Nieto Hannah R. , Alshahrani Mohammed , Thompson Rebecca J. , Lavery Gareth G. , Landa Iñigo , Fagin James A. , Campbell Moray J. , Boelaert Kristien , Turnell Andrew S. , Smith Vicki E. , McCabe Christopher J.
Published: April 2023

Fletcher A et al Supplementary Information
Supplementary Data from CD38-Driven Mitochondrial Trafficking Promotes Bioenergetic Plasticity in Multiple Myeloma
Authors: Marlein Christopher R. , Piddock Rachel E. , Mistry Jayna J. , Zaitseva Lyubov , Hellmich Charlotte , Horton Rebecca H. , Zhou Zhigang , Auger Martin J. , Bowles Kristian M. , Rushworth Stuart A.
Published: April 2023

Supplementary figures. Supplementary Fig 1A shows mitochondrial function in BMSC compared to MM cells. Supplementary Fig 1B shows mitochondrial respiration of MM cells cultured with succinate compared to control. Supplementary Fig 2A shows percent of MM cell engraftment in NSG mice. Supplementary Fig 2B shows percent sorted human cells from NSG bone marrow. Supplementary Fig 3A shows quantification of in vitro mitochondrial transfer from BMSC to MM cells. Supplementary Fig 3B shows detection of mtDNA in control and rho0 BMSC. Supplementary Fig 4 shows detection of mitochondrial transfer from BMSC to MM in various culture conditions. Supplementary Fig 5A-C shows quantification of TNT formation between MM cells and BMSC. Supplementary Fig 6 shows TNT anchor points located on BMSC after coculture with MM cell lines. Supplementary Fig 7 shows TNT anchor points located on BMSC after direct coculture with MM cells. Supplementary Fig 8 shows CD38 protein expression in CD38 shRNA targeted cells. Supplementary Fig 9 shows percent engraftment of control KD and CD38 KD MM1S-luc cells in NSG mice.
Supplemental Tables from An Interactive Resource to Probe Genetic Diversity and Estimated Ancestry in Cancer Cell Lines
Authors: Dutil Julie , Chen Zhihua , Monteiro Alvaro N. , Teer Jamie K. , Eschrich Steven A.
Published: April 2023

Supplemental tables for the manuscript (S1-S8) List of supplemental tables Table S1 Common cell lines panels for cancer research. Table S2 Cell line annotations. Table S3 Number of cancer cell lines included in each panel, grouped by tissue of origin. Table S4 Cell lines pairs demonstrating excess genetic concordance. Table S5 Admixture proportions (%) for each cell line in relation with the average for 1000 Genomes reference superpopulations. Table S6 Genetic ancestral origin of cancer cell lines in the complete dataset and in cell lines grouped by membership to CCLE, COSMIC and NCI60 panels. Table S7 Genetic ancestral origin of cancer cell lines in the complete dataset and in cell lines grouped by cancer tissue of origin. Table S8 Thousand Genomes Population Abbreviations.
Supplemental Material and Methods from An Interactive Resource to Probe Genetic Diversity and Estimated Ancestry in Cancer Cell Lines
Authors: Dutil Julie , Chen Zhihua , Monteiro Alvaro N. , Teer Jamie K. , Eschrich Steven A.
Published: April 2023

Supplemental Methods descriptions and supplemental references supporting this additional text.
Figure S1 from The Frequency of Ras Mutations in Cancer
Authors: Prior Ian A. , Hood Fiona E. , Hartley James L.
Published: April 2023

Genetic alterations in the RTK/Ras network across cancer types. TCGA data was collated based on 85 RTK/RAS-relevant genes listed in Supplementary Table 1b. Amplification/deletion represents at least a +2/-2 change in copy number.
Supplementary Figure 1 from EBF1-Mediated Upregulation of Ribosome Assembly Factor PNO1 Contributes to Cancer Progression by Negatively Regulating the p53 Signaling Pathway
Authors: Shen Aling , Chen Youqin , Liu Liya , Huang Yue , Chen Hongwei , Qi Fei , Lin Jiumao , Shen Zhiqing , Wu Xiangyan , Wu Meizhu , Li Qiongyu , Qiu Liman , Yu Na , Sferra Thomas J. , Peng Jun
Published: April 2023

Figure S1 shows that the expression levels of endogenous PNO1 in cultured CRC cell lines are relatively higher than that of differentiated Caco2 cells, and PNO1 knockdown reduces cell viability and survival of CRC cells.
Supplementary Data Figures S1-7 and Tables S1-7 from Loss of FOXP3 and TSC1 Accelerates Prostate Cancer Progression through Synergistic Transcriptional and Posttranslational Regulation of c-MYC
Authors: Wu Lianpin , Yi Baozhu , Wei Shi , Rao Dapeng , He Youhua , Naik Gurudatta , Bae Sejong , Liu Xiaoguang M. , Yang Wei-Hsiung , Sonpavde Guru , Liu Runhua , Wang Lizhong
Published: April 2023

Supplementary Figure S1: Loss of nuclear FOXP3 accompanying gene defects in human primary prostate cancers; Supplementary Figure S2: Diagram of the floxed Foxp3 and Tsc1 loci and the position of the primers; Supplementary Figure S3: Tumor development and progression in mouse prostate of single, double, and triple mutant mice; Supplementary Figure S4: Targeted deletion of c-Myc in the mouse prostate; Supplementary Figure S5: Relative mRNA levels of the c-Myc gene in micro-dissected prostate epithelial cells; Supplementary Figure S6: Representative H&E staining of anterior lobes of mouse prostate in the mice; Supplementary Figure S7: Public datasets-based analysis of genetic alterations for FOXP3, TSC1, AKT1 and FOXP1 loci in prostate adenocarcinoma; Supplementary Table S1: Specific primary antibodies used in this study; Supplementary Table S2: The clinicopathological characteristics of patients with prostate cancer; Supplementary Table S3: The clinicopathological characteristics of patients with prostate cancer; Supplementary Table S4: Primer and siRNA sequence used in this study; Supplementary Table S5: Characterization of genetic mouse models of prostate cancer; Supplementary Table S6: Association between protein expressions of FOXP3, TSC1, and c-MYC in prostate cancer; Supplementary Table S7: Association between protein expressions of FOXP3, TSC1, and c-MYC in prostate cancer.
Figure S5 from GARP Dampens Cancer Immunity by Sustaining Function and Accumulation of Regulatory T Cells in the Colon
Authors: Salem Mohammad , Wallace Caroline , Velegraki Maria , Li Anqi , Ansa-Addo Ephraim , Metelli Alessandra , Kwon Hyunwoo , Riesenberg Brian , Wu Bill , Zhang Yongliang , Guglietta Silvia , Sun Shaoli , Liu Bei , Li Zihai
Published: April 2023

Lack of GARP Expression by Foxp3+ Treg Cells Does Not Affect the Growth of Subcutaneously Injected MC38 Colon Cancer
Supplementary figures 7 and 8 from An Orally Active Galectin-3 Antagonist Inhibits Lung Adenocarcinoma Growth and Augments Response to PD-L1 Blockade
Authors: Vuong Lynda , Kouverianou Eleni , Rooney Claire M. , McHugh Brian J. , Howie Sarah E.M. , Gregory Christopher D. , Forbes Stuart J. , Henderson Neil C. , Zetterberg Fredrik R. , Nilsson Ulf J. , Leffler Hakon , Ford Paul , Pedersen Anders , Gravelle Lise , Tantawi Susan , Schambye Hans , Sethi Tariq , MacKinnon Alison C.
Published: April 2023

Figure S7 Flow cytometric analysis of bone marrow from WT or galectin-3-/- mice. Figure S8 GB1107 and anti-PD-L1 therapy is associated with reduced intra-tumor galectin-3 and increased CD8+ T cell infiltration.
Supplementary Methods from Collagen Remodeling in the Hypoxic Tumor-Mesothelial Niche Promotes Ovarian Cancer Metastasis
Authors: Natarajan Suchitra , Foreman Kaitlyn M. , Soriano Michaela I. , Rossen Ninna S. , Shehade Hussein , Fregoso Daniel R. , Eggold Joshua T. , Krishnan Venkatesh , Dorigo Oliver , Krieg Adam J. , Heilshorn Sarah C. , Sinha Subarna , Fuh Katherine C. , Rankin Erinn B.
Published: April 2023

Document contains detailed procedures of materials and methods.
Supplementary Figures and Legends from Collagen Remodeling in the Hypoxic Tumor-Mesothelial Niche Promotes Ovarian Cancer Metastasis
Authors: Natarajan Suchitra , Foreman Kaitlyn M. , Soriano Michaela I. , Rossen Ninna S. , Shehade Hussein , Fregoso Daniel R. , Eggold Joshua T. , Krishnan Venkatesh , Dorigo Oliver , Krieg Adam J. , Heilshorn Sarah C. , Sinha Subarna , Fuh Katherine C. , Rankin Erinn B.
Published: April 2023

Figure S1: The omental metastatic microenvironment is hypoxic (suppl. to Fig. 1); Figure S2: Hypoxia preferentially upregulates the expression of enzymes involved in collagen biogenesis and mechanical stability in mesothelial cells (suppl. to Fig. 3); Figure S3: LOX is highly expressed by both tumor cells and mesothelial cells upon hypoxia (suppl. to Fig. 5); Figure S4: LOX expression by both the tumor and mesothelial cells enhances collagen remodeling and invasion (suppl. to Fig. 6); Figure S5: LOX inhibition with B-aminopropionitrile (BAPN) does not affect body weight in mice (suppl. to Fig. 7)
Endothelial cell qPCR array from Platelet-Specific PDGFB Ablation Impairs Tumor Vessel Integrity and Promotes Metastasis
Authors: Zhang Yanyu , Cedervall Jessica , Hamidi Anahita , Herre Melanie , Viitaniemi Kati , D'Amico Gabriela , Miao Zuoxiu , Unnithan Ragaseema Valsala Madhavan , Vaccaro Alessandra , van Hooren Luuk , Georganaki Maria , Thulin Åsa , Qiao Qi , Andrae Johanna , Siegbahn Agneta , Heldin Carl-Henrik , Alitalo Kari , Betsholtz Christer , Dimberg Anna , Olsson Anna-Karin
Published: April 2023

Data from endothelial cell qPCR array.
Supplementary Figure 4 from CoA Synthase (COASY) Mediates Radiation Resistance via PI3K Signaling in Rectal Cancer
Authors: Ferrandon Sylvain , DeVecchio Jennifer , Duraes Leonardo , Chouhan Hanumant , Karagkounis Georgios , Davenport Jacqueline , Orloff Matthew , Liska David , Kalady Matthew F.
Published: April 2023

COASY protein expression is not modified by irradiation
Supplementary Figure 1 from CoA Synthase (COASY) Mediates Radiation Resistance via PI3K Signaling in Rectal Cancer
Authors: Ferrandon Sylvain , DeVecchio Jennifer , Duraes Leonardo , Chouhan Hanumant , Karagkounis Georgios , Davenport Jacqueline , Orloff Matthew , Liska David , Kalady Matthew F.
Published: April 2023

COASY is overexpressed in multiple cancer types compared to normal tissue.
Supplementary figures from HIF2-Induced Long Noncoding RNA RAB11B-AS1 Promotes Hypoxia-Mediated Angiogenesis and Breast Cancer Metastasis
Authors: Niu Yanling , Bao Lei , Chen Yan , Wang Chenliang , Luo Maowu , Zhang Bo , Zhou Mi , Wang Jennifer E. , Fang Yisheng V. , Kumar Ashwani , Xing Chao , Wang Yingfei , Luo Weibo
Published: April 2023

Fig. S1-6. Supplementary Fig. S1. The nucleotide sequence of RAB11B-AS1 identified by 5'- and 3'- RACE in human MDA-MB-231 cells. The RAB11B-AS1 sequence from 5'- and 3'-RACE is shown in orange and the mutated nucleotides are marked in blue as compared with the reference sequence in the GenBank (NR_038237.1), which is shown in black. The nucleotide sequence of RAB11B-AS1 has been deposited in the GenBank with the accession number MK855053. Supplementary Fig. S2. Validation of HIF-2a protein levels in overexpressed and knockout cells. Supplementary Fig. S3. RAB11B-AS1 increases breast cancer cell migration and invasion in vitro. Supplementary Fig. S4. RAB11B-AS1 has no effect on caspase-3-dependent cell death in tumors. Supplementary Fig. S5. RAB11B-AS1 increases hypoxia-induced expression of angiogenic factors in breast cancer cells. Supplementary Fig. S6. RAB11B-AS1 fails to regulate HIF transcriptional activity.
Supplementary Figures and legends from Targeting the E3 Ubiquitin Ligase PJA1 Enhances Tumor-Suppressing TGFβ Signaling
Authors: Chen Jian , Mitra Abhisek , Li Shulin , Song Shumei , Nguyen Bao-Ngoc , Chen Jiun-Sheng , Shin Ji-Hyun , Gough Nancy R. , Lin Paul , Obias Vincent , He Aiwu Ruth , Yao Zhixing , Malta Tathiane M. , Noushmehr Houtan , Latham Patricia S. , Su Xiaoping , Rashid Asif , Mishra Bibhuti , Wu Ray-Chang , Mishra Lopa
Published: April 2023

Supplementary Figures and legends
Supplementary Data from HDAC6 Plays a Noncanonical Role in the Regulation of Antitumor Immune Responses, Dissemination, and Invasiveness of Breast Cancer
Authors: Banik Debarati , Noonepalle Satish , Hadley Melissa , Palmer Erica , Gracia-Hernandez Maria , Zevallos-Delgado Christian , Manhas Namratta , Simonyan Hayk , Young Colin N. , Popratiloff Anastas , Chiappinelli Katherine B. , Fernandes Rohan , Sotomayor Eduardo M. , Villagra Alejandro
Published: April 2023

Supplementary methods and tables
Fig Supp 7 from HDAC6 Plays a Noncanonical Role in the Regulation of Antitumor Immune Responses, Dissemination, and Invasiveness of Breast Cancer
Authors: Banik Debarati , Noonepalle Satish , Hadley Melissa , Palmer Erica , Gracia-Hernandez Maria , Zevallos-Delgado Christian , Manhas Namratta , Simonyan Hayk , Young Colin N. , Popratiloff Anastas , Chiappinelli Katherine B. , Fernandes Rohan , Sotomayor Eduardo M. , Villagra Alejandro
Published: April 2023

Fig Supp 7
Fig Supp 2 from HDAC6 Plays a Noncanonical Role in the Regulation of Antitumor Immune Responses, Dissemination, and Invasiveness of Breast Cancer
Authors: Banik Debarati , Noonepalle Satish , Hadley Melissa , Palmer Erica , Gracia-Hernandez Maria , Zevallos-Delgado Christian , Manhas Namratta , Simonyan Hayk , Young Colin N. , Popratiloff Anastas , Chiappinelli Katherine B. , Fernandes Rohan , Sotomayor Eduardo M. , Villagra Alejandro
Published: April 2023

Fig Supp 2
Fig Supp 1 from HDAC6 Plays a Noncanonical Role in the Regulation of Antitumor Immune Responses, Dissemination, and Invasiveness of Breast Cancer
Authors: Banik Debarati , Noonepalle Satish , Hadley Melissa , Palmer Erica , Gracia-Hernandez Maria , Zevallos-Delgado Christian , Manhas Namratta , Simonyan Hayk , Young Colin N. , Popratiloff Anastas , Chiappinelli Katherine B. , Fernandes Rohan , Sotomayor Eduardo M. , Villagra Alejandro
Published: April 2023

Fig Supp 1
Supplementary Materials and Methods from Thermal Proteome Profiling Identifies Oxidative-Dependent Inhibition of the Transcription of Major Oncogenes as a New Therapeutic Mechanism for Select Anticancer Compounds
Authors: Peuget Sylvain , Zhu Jiawei , Sanz Gema , Singh Madhurendra , Gaetani Massimiliano , Chen Xinsong , Shi Yao , Saei Amir Ata , Visnes Torkild , Lindström Mikael S. , Rihani Ali , Moyano-Galceran Lidia , Carlson Joseph W. , Hjerpe Elisabet , Joneborg Ulrika , Lehti Kaisa , Hartman Johan , Helleday Thomas , Zubarev Roman , Selivanova Galina
Published: April 2023

Supplementary Materials and Methods
Supplementary Materials and Methods from Pyrvinium Pamoate Induces Death of Triple-Negative Breast Cancer Stem–Like Cells and Reduces Metastases through Effects on Lipid Anabolism
Authors: Dattilo Rosanna , Mottini Carla , Camera Emanuela , Lamolinara Alessia , Auslander Noam , Doglioni Ginevra , Muscolini Michela , Tang Wei , Planque Melanie , Ercolani Cristiana , Buglioni Simonetta , Manni Isabella , Trisciuoglio Daniela , Boe Alessandra , Grande Sveva , Luciani Anna Maria , Iezzi Manuela , Ciliberto Gennaro , Ambs Stefan , De Maria Ruggero , Fendt Sarah-Maria , Ruppin Eytan , Cardone Luca
Published: April 2023

This file includes additional cellular and molecular methods, plus computational and metabolomics methods.
Supplementary Data from Pyrvinium Pamoate Induces Death of Triple-Negative Breast Cancer Stem–Like Cells and Reduces Metastases through Effects on Lipid Anabolism
Authors: Dattilo Rosanna , Mottini Carla , Camera Emanuela , Lamolinara Alessia , Auslander Noam , Doglioni Ginevra , Muscolini Michela , Tang Wei , Planque Melanie , Ercolani Cristiana , Buglioni Simonetta , Manni Isabella , Trisciuoglio Daniela , Boe Alessandra , Grande Sveva , Luciani Anna Maria , Iezzi Manuela , Ciliberto Gennaro , Ambs Stefan , De Maria Ruggero , Fendt Sarah-Maria , Ruppin Eytan , Cardone Luca
Published: April 2023

The File contains legends relative to 14 supplementary figures
Supplementary Tables from Cross-talk between SOX2 and TGFβ Signaling Regulates EGFR–TKI Tolerance and Lung Cancer Dissemination
Authors: Kuo Ming-Han , Lee An-Chun , Hsiao Shih-Hsin , Lin Sey-En , Chiu Yu-Fan , Yang Li-Hao , Yu Chia-Cherng , Chiou Shih-Hwa , Huang Hsien-Neng , Ko Jen-Chung , Chou Yu-Ting
Published: April 2023

Supplementary Table S1-S6
Supplementary Materials and Methods from Cross-talk between SOX2 and TGFβ Signaling Regulates EGFR–TKI Tolerance and Lung Cancer Dissemination
Authors: Kuo Ming-Han , Lee An-Chun , Hsiao Shih-Hsin , Lin Sey-En , Chiu Yu-Fan , Yang Li-Hao , Yu Chia-Cherng , Chiou Shih-Hwa , Huang Hsien-Neng , Ko Jen-Chung , Chou Yu-Ting
Published: April 2023

Supplementary Materials and Methods
Figure S7 from Loss of a Negative Feedback Loop between IRF8 and AR Promotes Prostate Cancer Growth and Enzalutamide Resistance
Authors: Wu Hongxi , You Linjun , Li Yan , Zhao Zhili , Shi Guangjiang , Chen Zhen , Wang Zhuo , Li Xianjing , Du Shijia , Ye Wanli , Gao Xiaofang , Duan Jingjing , Cheng Yan , Tao Weiyan , Bian Jinsong , Zhou Jin-Rong , Zhu Qingyi , Yang Yong
Published: April 2023

IFNα enhances ENZ sensitivity targeting the AR/IRF8 axis.
Figure S4 from Dual Oxidase-Induced Sustained Generation of Hydrogen Peroxide Contributes to Pharmacologic Ascorbate-Induced Cytotoxicity
Authors: Gibson Adrienne R. , O'Leary Brianne R. , Du Juan , Sarsour Ehab H. , Kalen Amanda L. , Wagner Brett A. , Stolwijk Jeffrey M. , Falls-Hubert Kelly C. , Alexander Matthew S. , Carroll Rory S. , Spitz Douglas R. , Buettner Garry R. , Goswami Prabhat C. , Cullen Joseph J.
Published: April 2023

Ascorbate-2-phosphate treatment does not induce sustained DUOX expression.
Figure S2 from Dual Oxidase-Induced Sustained Generation of Hydrogen Peroxide Contributes to Pharmacologic Ascorbate-Induced Cytotoxicity
Authors: Gibson Adrienne R. , O'Leary Brianne R. , Du Juan , Sarsour Ehab H. , Kalen Amanda L. , Wagner Brett A. , Stolwijk Jeffrey M. , Falls-Hubert Kelly C. , Alexander Matthew S. , Carroll Rory S. , Spitz Douglas R. , Buettner Garry R. , Goswami Prabhat C. , Cullen Joseph J.
Published: April 2023

Increased DUOX1 and DUOX2 expression is reversed by catalase.
Figure S4 from Loss of a Negative Feedback Loop between IRF8 and AR Promotes Prostate Cancer Growth and Enzalutamide Resistance
Authors: Wu Hongxi , You Linjun , Li Yan , Zhao Zhili , Shi Guangjiang , Chen Zhen , Wang Zhuo , Li Xianjing , Du Shijia , Ye Wanli , Gao Xiaofang , Duan Jingjing , Cheng Yan , Tao Weiyan , Bian Jinsong , Zhou Jin-Rong , Zhu Qingyi , Yang Yong
Published: April 2023

Figure S4. IRF8 reduces AR protein levels and activity.
Figure S2 from Loss of a Negative Feedback Loop between IRF8 and AR Promotes Prostate Cancer Growth and Enzalutamide Resistance
Authors: Wu Hongxi , You Linjun , Li Yan , Zhao Zhili , Shi Guangjiang , Chen Zhen , Wang Zhuo , Li Xianjing , Du Shijia , Ye Wanli , Gao Xiaofang , Duan Jingjing , Cheng Yan , Tao Weiyan , Bian Jinsong , Zhou Jin-Rong , Zhu Qingyi , Yang Yong
Published: April 2023

IRF8 expression is regulated by the androgen-AR pathway.
Supplementary Tables from Metabolic Reprogramming in Cancer Is Induced to Increase Proton Production
Authors: Sun Huiyan , Zhou Yi , Skaro Michael Francis , Wu Yiran , Qu Zexing , Mao Fenglou , Zhao Suwen , Xu Ying
Published: April 2023

Tables S1-S25: Average TPMs of genes in corresponding pathways in 14 cancer types. Transcripts per million (TPM) are considered more comparable between samples than raw counts or FPKM. Table S26: A summary of the net protons/CO2 consumed or produced by different RMs. Table S27: Linear regression result for the estimated level of cytosolic Fenton reactions against all the RMs, where the numerical value in each cell is a p-value representing the level of contribution of the relevant RM to the R2 value of the regression model for the relevant cancer type; a 1.0 indicates that the relevant RM is not used in the regression model. All cells with a p-value < 0.05 is highlighted. Table S28: published data on inhibition of key enzymes in RMs studied here. Table S29: Identified serum small molecule biomarkers reported in the literature, along with their pKa value.
Supplementary Table S2 from Telomere Maintenance Mechanisms Define Clinical Outcome in High-Risk Neuroblastoma
Authors: Koneru Balakrishna , Lopez Gonzalo , Farooqi Ahsan , Conkrite Karina L. , Nguyen Thinh H. , Macha Shawn J. , Modi Apexa , Rokita Jo Lynne , Urias Eduardo , Hindle Ashly , Davidson Heather , Mccoy Kristyn , Nance Jonas , Yazdani Vanda , Irwin Meredith S. , Yang Shengping , Wheeler David A. , Maris John M. , Diskin Sharon J. , Reynolds C. Patrick
Published: April 2023

Supplementary Table S2
Supplementary Figure S3 from NOX4 Inhibition Potentiates Immunotherapy by Overcoming Cancer-Associated Fibroblast-Mediated CD8 T-cell Exclusion from Tumors
Authors: Ford Kirsty , Hanley Christopher J. , Mellone Massimiliano , Szyndralewiez Cedric , Heitz Freddy , Wiesel Philippe , Wood Oliver , Machado Maria , Lopez Maria-Antoinette , Ganesan Anusha-Preethi , Wang Chuan , Chakravarthy Ankur , Fenton Tim R. , King Emma V. , Vijayanand Pandurangan , Ottensmeier Christian H. , Al-Shamkhani Aymen , Savelyeva Natalia , Thomas Gareth J.
Published: April 2023

Supplementary Figure S3
Supplementary Figure S2 from NOX4 Inhibition Potentiates Immunotherapy by Overcoming Cancer-Associated Fibroblast-Mediated CD8 T-cell Exclusion from Tumors
Authors: Ford Kirsty , Hanley Christopher J. , Mellone Massimiliano , Szyndralewiez Cedric , Heitz Freddy , Wiesel Philippe , Wood Oliver , Machado Maria , Lopez Maria-Antoinette , Ganesan Anusha-Preethi , Wang Chuan , Chakravarthy Ankur , Fenton Tim R. , King Emma V. , Vijayanand Pandurangan , Ottensmeier Christian H. , Al-Shamkhani Aymen , Savelyeva Natalia , Thomas Gareth J.
Published: April 2023

Supplementary Figure S2
Supplementary Figure S1 from NOX4 Inhibition Potentiates Immunotherapy by Overcoming Cancer-Associated Fibroblast-Mediated CD8 T-cell Exclusion from Tumors
Authors: Ford Kirsty , Hanley Christopher J. , Mellone Massimiliano , Szyndralewiez Cedric , Heitz Freddy , Wiesel Philippe , Wood Oliver , Machado Maria , Lopez Maria-Antoinette , Ganesan Anusha-Preethi , Wang Chuan , Chakravarthy Ankur , Fenton Tim R. , King Emma V. , Vijayanand Pandurangan , Ottensmeier Christian H. , Al-Shamkhani Aymen , Savelyeva Natalia , Thomas Gareth J.
Published: April 2023

Supplementary Figure S1
Supplementary Figure S1-S8 from The NOTCH–FOXM1 Axis Plays a Key Role in Mitochondrial Biogenesis in the Induction of Human Stem Cell Memory–like CAR-T Cells
Authors: Kondo Taisuke , Ando Makoto , Nagai Nao , Tomisato Wataru , Srirat Tanakorn , Liu Binbin , Mise-Omata Setsuko , Ikeda Mari , Chikuma Shunsuke , Nishimasu Hiroshi , Nureki Osamu , Ohmura Mitsuyo , Hayakawa Noriyo , Hishiki Takako , Uchibori Ryosuke , Ozawa Keiya , Yoshimura Akihiko
Published: April 2023

Supplementary Figure S1. Metabolic analysis before or after the OP9-hDLL1 co-culture. Supplementary Figure S2. Metformin disrupts iTSCM induction Supplementary Figure S3. Anti-CD19 CAR-iTSCM cells possess superior antitumor ability in B-ALL models. Supplementary Figure S4. The effects of Notch intracellular domain(NICD) overexpression on T cell phenotypes. Supplementary Figure S5. NICDÎ"ANK-overexpression does not induce iTSCM cells Supplementary Figure S6. The regulation of FOXM1 expression by NICD or FOXM1 knockout. Supplementary Figure S7. FOXM1â^†N-overexpression induces iTSCM formation Supplementary Figure S8. NICD- and FOXM1-overexpressed TSCM-like cells are close to iTSCM cells induced by OP9-hDLL1 cells.
Supplementary Table S1 from Genome-Wide CRISPR-Cas9 Screen Reveals Selective Vulnerability of ATRX-Mutant Cancers to WEE1 Inhibition
Authors: Liang Junbo , Zhao Hong , Diplas Bill H. , Liu Song , Liu Jianmei , Wang Dingding , Lu Yan , Zhu Qing , Wu Jiayu , Wang Wenjia , Yan Hai , Zeng Yi-Xin , Wang Xiaoyue , Jiao Yuchen
Published: April 2023

Supplementary Table S1. lists all the candidate genes identified from the ATRX synthetic lethal CRISPR-Cas9 screen.
Table S1 from Murine Oviductal High-Grade Serous Carcinomas Mirror the Genomic Alterations, Gene Expression Profiles, and Immune Microenvironment of Their Human Counterparts
Authors: McCool Kevin W. , Freeman Zachary T. , Zhai Yali , Wu Rong , Hu Kevin , Liu Chia-Jen , Tomlins Scott A. , Fearon Eric R. , Magnuson Brian , Kuick Rork , Cho Kathleen R.
Published: April 2023

Supplementary Table 1. Somatic mutations acquired by tumors arising in BPRN mice
Supplementary Methods from Murine Oviductal High-Grade Serous Carcinomas Mirror the Genomic Alterations, Gene Expression Profiles, and Immune Microenvironment of Their Human Counterparts
Authors: McCool Kevin W. , Freeman Zachary T. , Zhai Yali , Wu Rong , Hu Kevin , Liu Chia-Jen , Tomlins Scott A. , Fearon Eric R. , Magnuson Brian , Kuick Rork , Cho Kathleen R.
Published: April 2023

Supplementary Methods
Supplementary Figure S8 from Murine Oviductal High-Grade Serous Carcinomas Mirror the Genomic Alterations, Gene Expression Profiles, and Immune Microenvironment of Their Human Counterparts
Authors: McCool Kevin W. , Freeman Zachary T. , Zhai Yali , Wu Rong , Hu Kevin , Liu Chia-Jen , Tomlins Scott A. , Fearon Eric R. , Magnuson Brian , Kuick Rork , Cho Kathleen R.
Published: April 2023

Figure S8 shows heterogeneity of immune response to tumors arising in BPRN mice using immunohistochemical stain of select cell types.
Supplementary Figure S4. from Genome-Wide CRISPR-Cas9 Screen Reveals Selective Vulnerability of ATRX-Mutant Cancers to WEE1 Inhibition
Authors: Liang Junbo , Zhao Hong , Diplas Bill H. , Liu Song , Liu Jianmei , Wang Dingding , Lu Yan , Zhu Qing , Wu Jiayu , Wang Wenjia , Yan Hai , Zeng Yi-Xin , Wang Xiaoyue , Jiao Yuchen
Published: April 2023

Figure S4. Sensitivity to AZD1775 in ATRX WT and KO PLC/PRF/5 cells after adjusting for differences in growth rates.
Supplementary Figure S6 from Murine Oviductal High-Grade Serous Carcinomas Mirror the Genomic Alterations, Gene Expression Profiles, and Immune Microenvironment of Their Human Counterparts
Authors: McCool Kevin W. , Freeman Zachary T. , Zhai Yali , Wu Rong , Hu Kevin , Liu Chia-Jen , Tomlins Scott A. , Fearon Eric R. , Magnuson Brian , Kuick Rork , Cho Kathleen R.
Published: April 2023

Figure S6 shows correlations of estimates of 28 immune cell types between human and mouse tumor samples.
Supplementary Data from Circulating Immune Cell Composition and Cancer Risk: A Prospective Study Using Epigenetic Cell Count Measures
Authors: Le Cornet Charlotte , Schildknecht Konstantin , Rossello Chornet Araceli , Fortner Renée T. , González Maldonado Sandra , Katzke Verena A. , Kühn Tilman , Johnson Theron , Olek Sven , Kaaks Rudolf
Published: April 2023

Table S1 shows partial Spearman correlations between relative immune cell count adjusted for age at blood collection and sex within the subcohort. Table S2 shows cross-sectional associations of circulating immune cell composition and various covariates within the subcohort overall as well as separately in men and in women using Dirichlet regression. Table S3 shows partial spearman's rank correlation coefficients of relative counts of immune markers measured one and 15 years apart. Table S4 shows the hazard ratios and confidence intervals for the association between relative counts of circulating immune cell and cancer risk adjusted for age and sex as well as factors that showed cross-sectional relationships to immune composition in the Dirichlet regression. Table S5 shows the results from the sensitivity analyses which meant to exclude subjects with follow-up shorter than two years. Hazard ratios and confidence intervals are presented for the association between relative counts of circulating immune cell and cancer risk adjusted for age and sex. Figure S1 shows stacked bar chart of normalized immune cell counts across strata of baseline characteristics that were found significant in the Dirichlet regression in the sub-cohort overall, and separately in men and in women.
Figure S8 from Oxygen-Enhanced Optoacoustic Tomography Reveals the Effectiveness of Targeting Heme and Oxidative Phosphorylation at Normalizing Tumor Vascular Oxygenation
Authors: Ghosh Poorva , Guo Yihang , Ashrafi Adnin , Chen Jingyu , Dey Sanchareeka , Zhong Shigen , Liu Jie , Campbell James , Konduri Purna Chaitanya , Gerberich Jeni , Garrossian Massoud , Mason Ralph P. , Zhang Li , Liu Li
Published: April 2023

Fig. S8. HSP2 and CycT do not affect iron metabolism and hypoxia induction of HIF1ï�¡. (A) Iron stain did not detect any difference between control and treated tumor tissues. Shown are montages, 10X, and 40X images of control, HSP2 and CycT-treated tumor tissue sections stained with Iron Stain. The blue rectangles in montages, 10X images the regions shown in 10X and 40X images, respectively. Scale bar: montage, 1 mm for controls and 500 Âµm for HSP2 and CycT treated tissues; 10X, 200 Âµm, 40X 50 Âµm. (B) Representative IHC images of H1299 NSCLC tumor tissue sections and graphs showing the levels of transferrin receptor TFRC in control, HSP2, and CycT-treated tumors. (C) Representative IHC images of H1299 tumor tissue sections and graphs showing the levels of ferroportin 1, SLC40A1, in control, HSP2, and CycT-treated tumors. Shown are montages and 10X images of control, HSP2 and CycT-treated tumor tissue sections stained with DAPI or antibodies against the indicated protein. The white rectangles in DAPI images denote the regions shown in 10X images. Scale bar: montage, 1 mm (for control tumor sections) and 500 Âµm (for HSP2 and CycT treated tumor sections); 10X, 20 Âµm. Protein levels were quantified, and data are plotted as mean {plus minus} SEM. The values shown in the graphs are averages of signals quantified from three independent IHC experiments. For statistical analysis, the levels in treated tumors were compared to the levels in control tumors with a Welch 2-sample t-test. P * <0.05, ** < 0.005. (D) Representative images of cells stained with DAPI or antibodies to HIF1ï�¡. H1299 cells pretreated with no reagent, HSP2, or CycT were subjected to hypoxia for 24 hours, and then cells were subjected to immunofluorescence staining with anti-HIF1ï�¡ antibodies. HIF1ï�¡ levels were estimated by quantifying fluorescence intensities and plotted here. Normoxic cells are also shown for comparison. Scale bar: 40X, 100 Âµm. For statistical analysis, the levels in hypoxic cells were compared to the levels in normoxic cells with a Welch 2-sample t-test. P * <0.05, ** < 0.005.
Figure S7 from Oxygen-Enhanced Optoacoustic Tomography Reveals the Effectiveness of Targeting Heme and Oxidative Phosphorylation at Normalizing Tumor Vascular Oxygenation
Authors: Ghosh Poorva , Guo Yihang , Ashrafi Adnin , Chen Jingyu , Dey Sanchareeka , Zhong Shigen , Liu Jie , Campbell James , Konduri Purna Chaitanya , Gerberich Jeni , Garrossian Massoud , Mason Ralph P. , Zhang Li , Liu Li
Published: April 2023

Fig. S7. The effect of HSP2 on oxygenation of subcutaneous NSCLC A549-luc tumor xenografts after 3 weeks of treatment (same tumors as shown in Fig. S1). (A) Representative tumor images of spatial distribution of oxygen saturation [sO2 (O2)] after the oxygen challenge and the amplitude of signal change (Î"sO2) for each treatment group from breathing air to breathing 100% oxygen. The change in sO2 (Î"sO2) is calculated by subtracting the average tumor sO2 while breathing air from the average tumor sO2 while breathing oxygen. The sizes of the shown tumors were: Control: 111 mm3; HSP2: 51.9 mm3. (B & C) Quantification of sO2 (O2) and Î"sO2 for each treatment group. For statistical analysis, the levels in treated tumors were compared to the levels in control tumors with a Welch 2-sample t-test. ***, P < 0.001. Box is between 25th and 75th percentile, line at median.