bluuebunny/crossref_metadata_2025 huggingface dataset:
Data from Inhibition of the MNK1/2–eIF4E Axis Augments Palbociclib-Mediated Antitumor Activity in Melanoma and Breast Cancer
Authors: Prabhu Sathyen A. , Moussa Omar , Gonçalves Christophe , LaPierre Judith H. , Chou Hsiang , Huang Fan , Richard Vincent R. , Ferruzo Pault Y. M. , Guettler Elizabeth M. , Soria-Bretones Isabel , Kirby Laura , Gagnon Natascha , Su Jie , Silvester Jennifer , Krisna Sai Sakktee , Rose April A. N. , Sheppard Karen E. , Cescon David W. , Mallette Frédérick A. , Zahedi Rene P. , Borchers Christoph H. , del Rincon Sonia V. , Miller Wilson H.
Published: April 2023

Abstract
Aberrant cell-cycle progression is characteristic of melanoma, and CDK4/6 inhibitors, such as palbociclib, are currently being tested for efficacy in this disease. Despite the promising nature of CDK4/6 inhibitors, their use as single agents in melanoma has shown limited clinical benefit. Herein, we discovered that treatment of tumor cells with palbociclib induces the phosphorylation of the mRNA translation initiation factor eIF4E. When phosphorylated, eIF4E specifically engenders the translation of mRNAs that code for proteins involved in cell survival. We hypothesized that cancer cells treated with palbociclib use upregulated phosphorylated eIF4E (phospho-eIF4E) to escape the antitumor benefits of this drug. Indeed, we found that pharmacologic or genetic disruption of MNK1/2 activity, the only known kinases for eIF4E, enhanced the ability of palbociclib to decrease clonogenic outgrowth. Moreover, a quantitative proteomics analysis of melanoma cells treated with combined MNK1/2 and CDK4/6 inhibitors showed downregulation of proteins with critical roles in cell-cycle progression and mitosis, including AURKB, TPX2, and survivin. We also observed that palbociclib-resistant breast cancer cells have higher basal levels of phospho-eIF4E, and that treatment with MNK1/2 inhibitors sensitized these palbociclib-resistant cells to CDK4/6 inhibition. In vivo we demonstrate that the combination of MNK1/2 and CDK4/6 inhibition significantly increases the overall survival of mice compared with either monotherapy. Overall, our data support MNK1/2 inhibitors as promising drugs to potentiate the antineoplastic effects of palbociclib and overcome therapy-resistant disease.
Supplementary Tables 1-4 from Multi-substrate Metabolic Tracing Reveals Marked Heterogeneity and Dependency on Fatty Acid Metabolism in Human Prostate Cancer
Authors: Fidelito Gio , De Souza David P. , Niranjan Birunthi , De Nardo William , Keerthikumar Shivakumar , Brown Kristin , Taylor Renea A. , Watt Matthew J.
Published: April 2023

Supplementary Table 1: Correlation coefficients and P values of metabolic rates and ssGSEA score. Supplementary Table 2: Correlation coefficients and P values of metabolic rates and genetic mutations. Supplementary Table 3: Correlation coefficients and P values of metabolic rates and copy number changes. Supplementary Table 4: Correlation coefficients and P values of metabolic rates and patient pre-treatments.
Supplementary Table 1 from Targeting ULK1 Decreases IFNγ-Mediated Resistance to Immune Checkpoint Inhibitors
Authors: Fenton Sarah E. , Zannikou Markella , Ilut Liliana , Fischietti Mariafausta , Ji Chunni , Oku Chidera V. , Horvath Curt M. , Le Poole I. Caroline , Bosenberg Marcus , Bartom Elizabeth T. , Kocherginsky Masha , Platanias Leonidas C. , Saleiro Diana
Published: April 2023

List of the putative ULK1 interactor proteins identified by mass spectrometry analysis in A375 cells
Supplementary Figures and Supplementary Materials and Methods with References from Targeting ULK1 Decreases IFNγ-Mediated Resistance to Immune Checkpoint Inhibitors
Authors: Fenton Sarah E. , Zannikou Markella , Ilut Liliana , Fischietti Mariafausta , Ji Chunni , Oku Chidera V. , Horvath Curt M. , Le Poole I. Caroline , Bosenberg Marcus , Bartom Elizabeth T. , Kocherginsky Masha , Platanias Leonidas C. , Saleiro Diana
Published: April 2023

S1. Overexpression of ULK1 in melanoma cells has minor effects on transcription of IFNγ-induced immunostimulatory genes.S2. Effects of gene targeted inhibition of ULK1 in transcription of IFNγ-induced immunostimulatory genes in melanoma cells.S3. Effects of drug-targeted inhibition of ULK1 in transcription of IFNγ-induced immunostimulatory genes in melanoma cells.S4. Effects of siRNA-mediated knockdown of ULK1 on IFNγ-inducedSTAT1 phosphorylation.S5. Identification of putative cytoplasmic and nuclear ULK1 binding partners in melanoma cells upon IFNγ stimulation by mass spectrometry analysis.S6. Pharmacological inhibition of ULK1 enhances the anti-tumor effects of anti-PD-1 therapy in YUMMER1.7 mouse melanoma in vivo model.S7. Tumor infiltrating CD8+ T cells and TAMCs in vehicle-isotype-treated mice.S8. Tumor infiltrating CD8+ T cells and TAMCs in ULK inhibitor-treated mice.S9. Tumor infiltrating CD8+ T cells and TAMCs in anti-PD-1-treated mice.S10. Tumor infiltrating CD8+ T cells and TAMCs in ULKi plus anti-PD-1-treated mice.S11. Tumor infiltrating CD4+ T cells and Tregs in vehicle-isotype-treated mice.S12. Tumor infiltrating CD4+ T cells and Tregs in ULK inhibitor-treated mice.S13. Tumor infiltrating CD4+ T cells and Tregs in anti-PD-1treated mice.S14. Tumor infiltrating CD4+ T cells and Tregs in ULKi plus anti-PD-1-treated mice.S15. Tumor infiltrating CD8+ T cells and TAMCs in control, ULKi and/or anti-PD-1-treated mice.S16. Tumor infiltrating CD4+ T cells and Tregs in control, ULKi and/or anti-PD-1-treated mice.S17. Gating strategy for flow cytometric immunophenotyping of mouse melanoma tumors.
Supplementary Figure Legends from Evolutionary Characteristics and Immunologic Divergence of Lung and Brain Metastasis Lesions in NSCLC
Authors: Xie Tongji , Liu Zhenghao , Li Yan , Wang Shouzheng , Zhai Yixin , Teng Fei , Hao Xuezhi , Wang Yan , Wang Hongyu , Zhang Xin , Wu Xi , Ying Jianming , Li Junling , Zhang Ye , Deng Yuefei , Xing Puyuan
Published: April 2023

Supplementary Figure 1. The TMB distribution of all primary and metastases samples. The total TMB (defined as the number of nonsynonymous mutations) in each group.Supplementary Table 1. The basic clinical information of all patients.
Figure S1 from Evolutionary Characteristics and Immunologic Divergence of Lung and Brain Metastasis Lesions in NSCLC
Authors: Xie Tongji , Liu Zhenghao , Li Yan , Wang Shouzheng , Zhai Yixin , Teng Fei , Hao Xuezhi , Wang Yan , Wang Hongyu , Zhang Xin , Wu Xi , Ying Jianming , Li Junling , Zhang Ye , Deng Yuefei , Xing Puyuan
Published: April 2023

The TMB distribution of all primary and metastases samples. The total TMB (defined as the number of nonsynonymous mutations) in each group.
Supplementary Tables 1-5 from Malignant Progression of an Ancestral Bone Marrow Clone Harboring a CIC-NUTM2A Fusion in Isolated Myeloid Sarcoma
Authors: Kamens Jennifer L. , Dang Jinjun , Shaw Timothy I. , Gout Alexander M. , Newman Scott , Hagiwara Kohei , Smith Amelia M.R. , Obermayer Alyssa N. , Aldridge Sarah , Ma Jing , Zhang Yang , Wu Gang , Leventaki Vasiliki , Santiago Teresa , Raimondi Susana , Nakitandwe Joy , Pappo Alberto , Li Chunliang , Zhang Jinghui , Gruber Tanja A.
Published: April 2023

Supplementary Table 1. Validated Tier 1-3 Mutation CallsSupplementary Table 2. Genes Upregulated in CIC-NUTM2ASupplementary Table 3. CIC-NUTM2A Gene Set Enrichment Analysis in Pediatric Hematologic MalignanciesSupplementary Table 4. ssGSEA for Top Scoring Signaling Pathways in the Clinical DatasetSupplementary Table 5. CRISPR Screen Day 2 vs. Day 17
Supplementary Figures 1-7 from Malignant Progression of an Ancestral Bone Marrow Clone Harboring a CIC-NUTM2A Fusion in Isolated Myeloid Sarcoma
Authors: Kamens Jennifer L. , Dang Jinjun , Shaw Timothy I. , Gout Alexander M. , Newman Scott , Hagiwara Kohei , Smith Amelia M.R. , Obermayer Alyssa N. , Aldridge Sarah , Ma Jing , Zhang Yang , Wu Gang , Leventaki Vasiliki , Santiago Teresa , Raimondi Susana , Nakitandwe Joy , Pappo Alberto , Li Chunliang , Zhang Jinghui , Gruber Tanja A.
Published: April 2023

Supplementary Methods and FiguresSupplementary Figure 1. A newborn with isolated myeloid sarcoma.Supplementary Figure 2. Myeloid Sarcoma Histology.Supplementary Figure 3. Bone Marrow.Supplementary Figure 4. Genes Upregulated in CIC-NUTM2A.Supplementary Figure 5. Differential Serial Re-plating Capacity of NUT Family Members.Supplementary Figure 6. Gene Expression Analysis of CIC-NUTM2A Signature.Supplementary Figure 7. Receptor Tyrosine Kinase Signaling.
Supplementary Table S4 from A Human Genome-Wide RNAi Screen Reveals Diverse Modulators that Mediate IRE1α–XBP1 Activation
Authors: Yang Zhifen , Zhang Jing , Jiang Dadi , Khatri Purvesh , Solow-Cordero David E. , Toesca Diego A.S. , Koumenis Constantinos , Denko Nicholas C. , Giaccia Amato J. , Le Quynh-Thu , Koong Albert C.
Published: April 2023

Summary of Screening Validation.
Supplementary Table S3 from A Human Genome-Wide RNAi Screen Reveals Diverse Modulators that Mediate IRE1α–XBP1 Activation
Authors: Yang Zhifen , Zhang Jing , Jiang Dadi , Khatri Purvesh , Solow-Cordero David E. , Toesca Diego A.S. , Koumenis Constantinos , Denko Nicholas C. , Giaccia Amato J. , Le Quynh-Thu , Koong Albert C.
Published: April 2023

Table representing the effects of the four individual siRNAs tested during secondary screen (deconvolution).
Supplementary Figure 4 from Small-Molecule Sigma1 Modulator Induces Autophagic Degradation of PD-L1
Authors: Maher Christina M. , Thomas Jeffrey D. , Haas Derick A. , Longen Charles G. , Oyer Halley M. , Tong Jane Y. , Kim Felix J.
Published: April 2023

Subcellular fractionation.
Supplementary Figure 2 from Small-Molecule Sigma1 Modulator Induces Autophagic Degradation of PD-L1
Authors: Maher Christina M. , Thomas Jeffrey D. , Haas Derick A. , Longen Charles G. , Oyer Halley M. , Tong Jane Y. , Kim Felix J.
Published: April 2023

Multiple Sigma1 shRNA and absence of general protein level changes - evidence of selective actions.
Supplementary Figure 1 from Small-Molecule Sigma1 Modulator Induces Autophagic Degradation of PD-L1
Authors: Maher Christina M. , Thomas Jeffrey D. , Haas Derick A. , Longen Charles G. , Oyer Halley M. , Tong Jane Y. , Kim Felix J.
Published: April 2023

Isopycnic fractionation.
Supplementary Tables from Circular RNA ciRS-7 Maintains Metastatic Phenotypes as a ceRNA of miR-1299 to Target MMPs
Authors: Sang Meixiang , Meng Lingjiao , Liu Sihua , Ding Pingan , Chang Sheng , Ju Yingchao , Liu Fei , Gu Lina , Lian Yishui , Geng Cuizhi
Published: April 2023

Supplementary Table S1. The primer, siRNA and miRNA sequences Supplementary Table S2. Clinicopathological feathers of 164 cases of breast cancer patients and the expression of ciRS-7 and miR-1299
Supplementary Figure S1 from A Human Genome-Wide RNAi Screen Reveals Diverse Modulators that Mediate IRE1α–XBP1 Activation
Authors: Yang Zhifen , Zhang Jing , Jiang Dadi , Khatri Purvesh , Solow-Cordero David E. , Toesca Diego A.S. , Koumenis Constantinos , Denko Nicholas C. , Giaccia Amato J. , Le Quynh-Thu , Koong Albert C.
Published: April 2023

Data analysis for genome-wide RNAi screen.
Supplementary Figures 1-7 from Targeting RNA Polymerase I with Hernandonine Inhibits Ribosomal RNA Synthesis and Tumor Cell Growth
Authors: Chen Yen-Ting , Chen Jih-Jung , Wang Hsiang-Tsui
Published: April 2023

S1. Hernandonine induces higher cytotoxicity and cellular apoptosis in HeLa and SAS cells. S2. Hernadonine induces rRNA polymerase I degradation, rRNA transcription, nucleolar cap and nucleolar disintegration in OECM-1. S3. Hernandonine induces p53-dependent and independent nucleolar stress pathways in HCT116 and OECM-1 cells. S4. Hernandonine induces expression of PUMA, but decreases expression of BCL-2 in HeLa and SAS cells. S5. Hernandonine induces nucleolar cap. S6. Hernandonine induces different cell fates in normal and cancer cells after recovery of treatment. S7. Higher dosage of hernandonine induces cellular apoptosis in NOK and Beas-2B cells.
Supplementary Tables from Serine Threonine Kinase 17A Maintains the Epithelial State in Colorectal Cancer Cells
Authors: Short Sarah P. , Thompson Joshua J. , Bilotta Anthony J. , Chen Xi , Revetta Frank L. , Washington M. Kay , Williams Christopher S.
Published: April 2023

Supplemental Table 1. qRT-PCR and mutagenesis primer sequences. Supplemental Table 2. Clinical features of human tumors from which organoid lines were derived. Supplemental Table 3. Components of complete human organoid media.
Supplementary Table 2 from The Pioneering Role of GATA2 in Androgen Receptor Variant Regulation Is Controlled by Bromodomain and Extraterminal Proteins in Castrate-Resistant Prostate Cancer
Authors: Chaytor Lewis , Simcock Matthew , Nakjang Sirintra , Heath Richard , Walker Laura , Robson Craig , Jones Dominic , Gaughan Luke
Published: April 2023

qPCR primers
Supplementary Data, Supplementary Figures S1-S9 from The Pioneering Role of GATA2 in Androgen Receptor Variant Regulation Is Controlled by Bromodomain and Extraterminal Proteins in Castrate-Resistant Prostate Cancer
Authors: Chaytor Lewis , Simcock Matthew , Nakjang Sirintra , Heath Richard , Walker Laura , Robson Craig , Jones Dominic , Gaughan Luke
Published: April 2023

S1: GATA2 depletion down-regulates AR-V target genes S2: Chromatin occupancy of AR-Vs is not perturbed by GATA2 depletion S3: Overlapping GATA2 and AR-V transcriptomes S4: Gene ontology of GATA2 and AR-V transcriptomes S5: Assessing GATA2 and BET protein interplay in prostate cancer cell lines S6: Global cistromic analysis of GATA2 S7: Overlapping cistromes of GATA2 and BET family members S8: Assessing overlap of GATA2 and BET protein-regulated transcriptomes S9: GATA2 regulates splicing activity in prostate cancer cells
Table S2 from Identification of Genes Regulating Breast Cancer Dormancy in 3D Bone Endosteal Niche Cultures
Authors: McGrath Julie , Panzica Louis , Ransom Ryan , Withers Henry G. , Gelman Irwin H.
Published: April 2023

pGIPZ Lentiviral shRNAmir-GFP Human shRNA clones
Supplemental Legend from Identification of Genes Regulating Breast Cancer Dormancy in 3D Bone Endosteal Niche Cultures
Authors: McGrath Julie , Panzica Louis , Ransom Ryan , Withers Henry G. , Gelman Irwin H.
Published: April 2023

S1. shRNA normalization controls
Figure S6 from Dual TGFβ/BMP Pathway Inhibition Enables Expansion and Characterization of Multiple Epithelial Cell Types of the Normal and Cancerous Breast
Authors: Prasad Mayuri , Kumar Brijesh , Bhat-Nakshatri Poornima , Anjanappa Manjushree , Sandusky George , Miller Kathy D. , Storniolo Anna Maria , Nakshatri Harikrishna
Published: April 2023

Properties of cells grown from ascites fluids of ovarian cancer patients and a liver metastasis of pancreatic cancer
Figure S1 from Identification of Genes Regulating Breast Cancer Dormancy in 3D Bone Endosteal Niche Cultures
Authors: McGrath Julie , Panzica Louis , Ransom Ryan , Withers Henry G. , Gelman Irwin H.
Published: April 2023

shRNA normalization controls
Figure S4 from Dual TGFβ/BMP Pathway Inhibition Enables Expansion and Characterization of Multiple Epithelial Cell Types of the Normal and Cancerous Breast
Authors: Prasad Mayuri , Kumar Brijesh , Bhat-Nakshatri Poornima , Anjanappa Manjushree , Sandusky George , Miller Kathy D. , Storniolo Anna Maria , Nakshatri Harikrishna
Published: April 2023

Properties of breast cells derived from women carrying breast cancer protective alleles and with tumors
Figure S3 from Dual TGFβ/BMP Pathway Inhibition Enables Expansion and Characterization of Multiple Epithelial Cell Types of the Normal and Cancerous Breast
Authors: Prasad Mayuri , Kumar Brijesh , Bhat-Nakshatri Poornima , Anjanappa Manjushree , Sandusky George , Miller Kathy D. , Storniolo Anna Maria , Nakshatri Harikrishna
Published: April 2023

Properties of breast epithelial cells generated from BRCA1 and BRCA2 mutant carriers.
Supplementary Table 5 from BORIS Expression in Ovarian Cancer Precursor Cells Alters the CTCF Cistrome and Enhances Invasiveness through GALNT14
Authors: Hillman Joanna C. , Pugacheva Elena M. , Barger Carter J. , Sribenja Sirinapa , Rosario Spencer , Albahrani Mustafa , Truskinovsky Alexander M. , Stablewski Aimee , Liu Song , Loukinov Dmitri I. , Zentner Gabriel E. , Lobanenkov Victor V. , Karpf Adam R. , Higgins Michael J.
Published: April 2023

BORIS vs. GALNT14 mRNA expression correlations in TCGA data
Supplementary Data from Establishment and Characterization of Four Novel Thyroid Cancer Cell Lines and PDX Models Expressing the RET/PTC1 Rearrangement, BRAFV600E, or RASQ61R as Drivers
Authors: Schweppe Rebecca E. , Pozdeyev Nikita , Pike Laura A. , Korch Christopher , Zhou Qiong , Sams Sharon B. , Sharma Vibha , Pugazhenthi Umarani , Raeburn Christopher , Albuja-Cruz Maria B. , Reigan Philip , LaBarbera Daniel V. , Landa Iñigo , Knauf Jeffrey A. , Fagin James A. , Haugen Bryan R.
Published: April 2023

Kinase inhibitor sensitivity of the CUTC cell lines.
Figure S1 from Establishment and Characterization of Four Novel Thyroid Cancer Cell Lines and PDX Models Expressing the RET/PTC1 Rearrangement, BRAFV600E, or RASQ61R as Drivers
Authors: Schweppe Rebecca E. , Pozdeyev Nikita , Pike Laura A. , Korch Christopher , Zhou Qiong , Sams Sharon B. , Sharma Vibha , Pugazhenthi Umarani , Raeburn Christopher , Albuja-Cruz Maria B. , Reigan Philip , LaBarbera Daniel V. , Landa Iñigo , Knauf Jeffrey A. , Fagin James A. , Haugen Bryan R.
Published: April 2023

Electropherograms of the CUTC5, CUTC48, CUTC60 and CUTC61 cell line, PDX, and patient samples.
Supplementary Figures 1 - 5 from ONC201 Targets AR and AR-V7 Signaling, Reduces PSA, and Synergizes with Everolimus in Prostate Cancer
Authors: Lev Avital , Lulla Amriti R. , Ross Brian C. , Ralff Marie D. , Makhov Petr B. , Dicker David T. , El-Deiry Wafik S.
Published: April 2023

Supplementary Figure 1. UPR genes in DU145 cells. Supplementary Figure 2. ONC201 does not inhibit translocation of AR-GFP to the nucleus upon DHT treatment and does not induce AR degradation. Supplementary Figure 3. ONC201 partly synergizes with docetaxol. Supplementary Figure 4. ONC201 partly synergizes with crizotinib. Supplementary Figure 5. Biweekly measurements of mouse weights after the indicated treatments in different prostate cancer xenograft models.
Supplemental Figure Legends 1-9 from BORIS Expression in Ovarian Cancer Precursor Cells Alters the CTCF Cistrome and Enhances Invasiveness through GALNT14
Authors: Hillman Joanna C. , Pugacheva Elena M. , Barger Carter J. , Sribenja Sirinapa , Rosario Spencer , Albahrani Mustafa , Truskinovsky Alexander M. , Stablewski Aimee , Liu Song , Loukinov Dmitri I. , Zentner Gabriel E. , Lobanenkov Victor V. , Karpf Adam R. , Higgins Michael J.
Published: April 2023

Figure S1. CSIOVDB Disease State Analysis. Figure S2. CSIOVDB histology and tumor grade analysis. Figure S3. Survival of ovarian cancer patients in CSIOVDB cohort with respect the ratio of BORIS/CTCF expression. Figure S4. Survival of ovarian cancer patients in TCGA cohort with respect to BORIS expression and the ratio of BORIS/CTCF expression. Figure S5. Survival of ovarian cancer patients in CSIOVDB cohort (high grade serous only) with respect to BORIS expression. Figure S6. Cellular morphology and proliferation analyses of FT282-EV and FT282-BORIS cells. Figure S7. Expression of BORIS in FT282 cells alters CTCF occupancy. Figure S8. Representative genome browser shots of CTCF and BORIS ChIP-seq tracks and RNA-seq tracks for FT282-EV and FT282-BORIS cells. Figure S9. Survival of ovarian cancer patients in CSIOVDB cohort with respect the (A) CHSY3 and (B) SERPINB2 expression.
Supplementary Figure Legends from ONC201 Targets AR and AR-V7 Signaling, Reduces PSA, and Synergizes with Everolimus in Prostate Cancer
Authors: Lev Avital , Lulla Amriti R. , Ross Brian C. , Ralff Marie D. , Makhov Petr B. , Dicker David T. , El-Deiry Wafik S.
Published: April 2023

Supplementary Figure 1. UPR genes in DU145 cells. Supplementary Figure 2. ONC201 does not inhibit translocation of AR-GFP to the nucleus upon DHT treatment and does not induce AR degradation. Supplementary Figure 3. ONC201 partly synergizes with docetaxol. Supplementary Figure 4. ONC201 partly synergizes with crizotinib. Supplementary Figure 5. Biweekly measurements of mouse weights after the indicated treatments in different prostate cancer xenograft models.
Supplemental Figures and Tables from CRISPR Knockout of the HuR Gene Causes a Xenograft Lethal Phenotype
Authors: Lal Shruti , Cheung Edwin C. , Zarei Mahsa , Preet Ranjan , Chand Saswati N. , Mambelli-Lisboa Nicole C. , Romeo Carmella , Stout Matthew C. , Londin Eric , Goetz Austin , Lowder Cinthya Y. , Nevler Avinoam , Yeo Charles J. , Campbell Paul M. , Winter Jordan M. , Dixon Dan A. , Brody Jonathan R.
Published: April 2023

Figure S1: HuR inhibition was successfully achieved by CRISPR/cas9 system. Figure S2: HuR inhibition sensitizes cells to drugs. Figure S3: PDA xenografts with HuR inhibition failed to form tumors. Table S1: Lists the three guide RNAs used to generate CRISPR knockout of HuR in MIA PaCa-2 and Hs 766T cell lines. Table S2: Lists the primers used to detect the mutation created by all three guide RNAs in CRISPR knockout of HuR MIA PaCa-2 and Hs 766T cell lines. Table S3: Lists the clones along with their genotypes obtained for all three guide RNAs.
Table S2 from Multifunctional APJ Pathway Promotes Ovarian Cancer Progression and Metastasis
Authors: Neelakantan Deepika , Dogra Samrita , Devapatla Bharat , Jaiprasart Pharavee , Mukashyaka Marie Claire , Janknecht Ralf , Dwivedi Shailendra Kumar Dhar , Bhattacharya Resham , Husain Sanam , Ding Kai , Woo Sukyung
Published: April 2023

Antibody dilutions used for Western blot and Immunohistochemical analyses.
Table S1 from Multifunctional APJ Pathway Promotes Ovarian Cancer Progression and Metastasis
Authors: Neelakantan Deepika , Dogra Samrita , Devapatla Bharat , Jaiprasart Pharavee , Mukashyaka Marie Claire , Janknecht Ralf , Dwivedi Shailendra Kumar Dhar , Bhattacharya Resham , Husain Sanam , Ding Kai , Woo Sukyung
Published: April 2023

Primer sequences for qRT-PCR.
Supplementary Table S3 from TP53 Mutation by CRISPR System Enhances the Malignant Potential of Colon Cancer
Authors: Watanabe Sho , Tsuchiya Kiichiro , Nishimura Ryu , Shirasaki Tomoaki , Katsukura Nobuhiro , Hibiya Shuji , Okamoto Ryuichi , Nakamura Tetsuya , Watanabe Mamoru
Published: April 2023

Common set of downregulated genes in both TP53 mutant cell lines compared with TP53WT cells
Figure S6 from Multifunctional APJ Pathway Promotes Ovarian Cancer Progression and Metastasis
Authors: Neelakantan Deepika , Dogra Samrita , Devapatla Bharat , Jaiprasart Pharavee , Mukashyaka Marie Claire , Janknecht Ralf , Dwivedi Shailendra Kumar Dhar , Bhattacharya Resham , Husain Sanam , Ding Kai , Woo Sukyung
Published: April 2023

Increased APJ expression in vivo has no significant effect on tumor volume or mouse weights in OvCa mouse models.
Supplementary Figure S4 from TP53 Mutation by CRISPR System Enhances the Malignant Potential of Colon Cancer
Authors: Watanabe Sho , Tsuchiya Kiichiro , Nishimura Ryu , Shirasaki Tomoaki , Katsukura Nobuhiro , Hibiya Shuji , Okamoto Ryuichi , Nakamura Tetsuya , Watanabe Mamoru
Published: April 2023

CRISPR-mediated mutagenesis of TP53 in HCT-116 cells
Figure S2 from Multifunctional APJ Pathway Promotes Ovarian Cancer Progression and Metastasis
Authors: Neelakantan Deepika , Dogra Samrita , Devapatla Bharat , Jaiprasart Pharavee , Mukashyaka Marie Claire , Janknecht Ralf , Dwivedi Shailendra Kumar Dhar , Bhattacharya Resham , Husain Sanam , Ding Kai , Woo Sukyung
Published: April 2023

APJ specifically increases proliferation in OvCa cells.
Supplementary Figure S2 from TP53 Mutation by CRISPR System Enhances the Malignant Potential of Colon Cancer
Authors: Watanabe Sho , Tsuchiya Kiichiro , Nishimura Ryu , Shirasaki Tomoaki , Katsukura Nobuhiro , Hibiya Shuji , Okamoto Ryuichi , Nakamura Tetsuya , Watanabe Mamoru
Published: April 2023

CRISPR-mediated mutagenesis of TP53 in HCT-116 cells
Supplementary Materials and Methods, Figures S1 - S8 from Periprostatic Adipose Tissue Favors Prostate Cancer Cell Invasion in an Obesity-Dependent Manner: Role of Oxidative Stress
Authors: Laurent Victor , Toulet Aurélie , Attané Camille , Milhas Delphine , Dauvillier Stéphanie , Zaidi Falek , Clement Emily , Cinato Mathieu , Le Gonidec Sophie , Guérard Adrien , Lehuédé Camille , Garandeau David , Nieto Laurence , Renaud-Gabardos Edith , Prats Anne-Catherine , Valet Philippe , Malavaud Bernard , Muller Catherine
Published: April 2023

Supplementary Figure S1. Coculture with preadipocytes has no effect on cancer cell invasion and coculture with mature adipocytes has no effect on prostate cancer cell number. Supplementary Figure S2. Adrenergic receptors do not control adipocyte lipolysis in response to tumor cell secretions. Supplementary Figure S3. The metabolic remodeling towards uncoupled FAO observed in cocultivated cells is not involved in the increase in prostate cancer invasion induced by adipocytes. Supplementary Figure S4. ROS positively regulate prostate cancer cells invasion. Supplementary Figure S5. 10mM NAC and 10μM DPI do not affect PC3 viability. Supplementary Figure S6. Coculture and palmitate stimulate tumor invasion through NOX in Du-145 cells. Supplementary Figure S7. NOX5 invalidation leads to a strong decrease in cell survival.
Supplementary Figures, Tables and Materials and Methods from RAIN Is a Novel Enhancer-Associated lncRNA That Controls RUNX2 Expression and Promotes Breast and Thyroid Cancer
Authors: Rossi Teresa , Pistoni Mariaelena , Sancisi Valentina , Gobbi Giulia , Torricelli Federica , Donati Benedetta , Ribisi Salvatore , Gugnoni Mila , Ciarrocchi Alessia
Published: April 2023

S1. Schematic representation of the central hypervariable region of RAIN S2. qRT-PCR analysis of SUPT3H expression in the indicated cell lines. S3. qRT-PCR analysis of RUNX2 and RAIN expression in TPC1 cells treated with 1 μM JQ1 or mock (DMSO). S4. Schematic representation of the distribution of the biotin 3'-end TEG probes on the 3'-end long RAIN region used for ChIRP. S5. ChIP analysis of RUNX2 ENHs (ENH3, ENH10, ENH11 and ENH13) with anti-WDR5. S6. Scratch wound healing assay in TPC1 and MDA-MB231 cells transfected with l-RAIN or scramble oligos in presence of mitomycin C. S7. MA plot. S8. RUNX2-RAIN neighboring genes.
Supplementary Table 7 from Sophoridine Inhibits Human Colorectal Cancer Progression via Targeting MAPKAPK2
Authors: Wang Rui , Liu Hongwei , Shao Yingying , Wang Kailong , Yin Shuangshuang , Qiu Yuling , Wu Honghua , Liu Erwei , Wang Tao , Gao Xiumei , Yu Haiyang
Published: April 2023

Cancer-associated genes were retrieved from the disGeNET database
Supplementary Table 6 from Sophoridine Inhibits Human Colorectal Cancer Progression via Targeting MAPKAPK2
Authors: Wang Rui , Liu Hongwei , Shao Yingying , Wang Kailong , Yin Shuangshuang , Qiu Yuling , Wu Honghua , Liu Erwei , Wang Tao , Gao Xiumei , Yu Haiyang
Published: April 2023

Pharmacophore candidates identified by pharmMapper
Supplementary Figures 1-6 from Prostate Tumor Cell–Derived IL1β Induces an Inflammatory Phenotype in Bone Marrow Adipocytes and Reduces Sensitivity to Docetaxel via Lipolysis-Dependent Mechanisms
Authors: Herroon Mackenzie K. , Diedrich Jonathan D. , Rajagurubandara Erandi , Martin Carly , Maddipati Krishna R. , Kim Seongho , Heath Elisabeth I. , Granneman James , Podgorski Izabela
Published: April 2023

Figure S1: Production of eicosanoid species in tumor cell-adipocyte Transwell co-cultures and experimental bone tumors Figure S2. Bone marrow adipocyte numbers are increased in mice treated with Rosiglitazone (ROSI) and in genetically obese ob/ob mice. Figure S3. MCP-1 expression is induced in bone marrow adipocytes interacting with prostate tumor cells in vivo and in vitro. Figure S4. HFD and Rosiglitazone do not have significant effect on COX-2, mPGES and MCP-1 levels in subcutaneous tumors. Figure S5. IL-1b expression in experimental ARCaP(M) tumors and bone metastasis tissues from PCa patients. Figure S6. Tumor-induced adipocyte expression of mPGES and MCP-1 is sensitive to inhibition by IL-1RA.
Figure S4 (A,B) from Dual Targeting of EGFR and IGF1R in the TNFAIP8 Knockdown Non–Small Cell Lung Cancer Cells
Authors: Day Timothy F. , Kallakury Bhaskar V.S. , Ross Jeffrey S. , Voronel Olga , Vaidya Shantashri , Sheehan Christine E. , Kasid Usha N.
Published: April 2023

EGFR localization to early endosomes
Supplementary Data from Sophoridine Inhibits Human Colorectal Cancer Progression via Targeting MAPKAPK2
Authors: Wang Rui , Liu Hongwei , Shao Yingying , Wang Kailong , Yin Shuangshuang , Qiu Yuling , Wu Honghua , Liu Erwei , Wang Tao , Gao Xiumei , Yu Haiyang
Published: April 2023

Supplementary Figure 1. The pharmacokinetics and cytotoxic effects of Sophoridine. Supplementary Figure 2. Sophoridine inhibited MAPKAPK2 activity and the docking interaction of p38-MAPKAPK2. Supplementary Figure 3. Sophoridine promotes the apoptotic and autophagic capacities and cell cycle arrest via MAPKAPK2 inactivation. Supplementary Figure 4. Full scans of western-blot data shown in Figure 1. Supplementary Figure 5. Full scans of western-blot data shown in Figure 2. Supplementary Figure 6. Full scans of western-blot data shown in Figure 4. Supplementary Figure 7. Full scans of western-blot data shown in Figure 5.
Figure S1 from Dual Targeting of EGFR and IGF1R in the TNFAIP8 Knockdown Non–Small Cell Lung Cancer Cells
Authors: Day Timothy F. , Kallakury Bhaskar V.S. , Ross Jeffrey S. , Voronel Olga , Vaidya Shantashri , Sheehan Christine E. , Kasid Usha N.
Published: April 2023

TNFAIP8 knockdown inhibits cell migration
Figure S1-S3, Table S1-S3 from Adipose-Derived VEGF–mTOR Signaling Promotes Endometrial Hyperplasia and Cancer: Implications for Obese Women
Authors: Sahoo Subhransu S. , Lombard Janine M. , Ius Yvette , O'Sullivan Rachel , Wood Lisa G. , Nahar Pravin , Jaaback Kenneth , Tanwar Pradeep S.
Published: April 2023

Fig. S1. In vitro characterization of pre-adipocytes and adipocytes. Fig. S2. Histological analysis of ovaries and oviducts of obese and control mice. Fig. S3. Foxa2, a marker of endometrial glands, staining in the uteri of obese and control mice. Table S1. A list of proteins that are differentially expressed between pre-adipocytes and adipocytes-derived conditioned media. Table S2. The outcome of breeding trials in obese and control mice. Table S3. Human endometrial cancer patient information
Supplemental Figure 4 from Centriole Overduplication is the Predominant Mechanism Leading to Centrosome Amplification in Melanoma
Authors: Denu Ryan A. , Shabbir Maria , Nihal Minakshi , Singh Chandra K. , Longley B. Jack , Burkard Mark E. , Ahmad Nihal
Published: April 2023

Validation of PLK4 antibody in cell lines.
Supplemental Figure 3 from Centriole Overduplication is the Predominant Mechanism Leading to Centrosome Amplification in Melanoma
Authors: Denu Ryan A. , Shabbir Maria , Nihal Minakshi , Singh Chandra K. , Longley B. Jack , Burkard Mark E. , Ahmad Nihal
Published: April 2023

Testing of four different PLK4 antibodies.
Supplemental Figure 1 from Centriole Overduplication is the Predominant Mechanism Leading to Centrosome Amplification in Melanoma
Authors: Denu Ryan A. , Shabbir Maria , Nihal Minakshi , Singh Chandra K. , Longley B. Jack , Burkard Mark E. , Ahmad Nihal
Published: April 2023

Validation of CEP170 staining in overduplication- versus cell doubling-induced centrosome amplification.
Supplementary Tables S1-S2, Supplementary Figures S1-S5 from PDCD4 Is an Androgen-Repressed Tumor Suppressor that Regulates Prostate Cancer Growth and Castration Resistance
Authors: Zennami Kenji , Choi Su Mi , Liao Ross , Li Ying , Dinalankara Wikum , Marchionni Luigi , Rafiqi Fatema H. , Kurozumi Akira , Hatano Koji , Lupold Shawn E.
Published: April 2023

Supplementary Table S1: siRNA and shRNA Vectors Supplementary Table S2: The sequence of primers used in this study Supplementary Figure S1. miR-21 suppresses PDCD4 expression in normal prostate epithelial cells. Supplementary Figure S2. Androgen signaling and miR-21 suppresses PDCD4 mRNA expression. Supplementary Figure S3. Transient PDCD4 over-expression and PDCD4 knockdown. Supplementary Figure S4. Transient PDCD4-overexpression induces apoptosis of LAPC4, but not LNCaP, cells. Supplementary Figure S5. PDCD4 expression regulates cell proliferation and apoptosis.
Supplementary Figures 1-3, Tables 1-3 from LSD1 Inhibition Attenuates Tumor Growth by Disrupting PLK1 Mitotic Pathway
Authors: Dalvi Priya S. , Macheleidt Iris F. , Lim So-Young , Meemboor Sonja , Müller Marion , Eischeid-Scholz Hannah , Schaefer Stephan C. , Buettner Reinhard , Klein Sebastian , Odenthal Margarete
Published: April 2023

S1: LSD1 inhibition reduces cell viability and migration capacities. S2: Multivariate analysis shows no significant expression differences for the studied genes in between untreated A549 and cisplatin treated A549 cells. S3: IHC staining shows colocalization of LSD1 and PLK1 in LUAD. Table S1: Cell line information Table S2: Primer sequences used for qPCR Table S3: Antibodies used for western blotting and IF
Supplementary Data and Methods from Identification of De Novo Enhancers Activated by TGFβ to Drive Expression of CDKN2A and B in HeLa Cells
Authors: Liu Yen-Ting , Xu Lin , Bennett Lynda , Hooks Jared C. , Liu Jing , Zhou Qinbo , Liem Priscilla , Zheng Yanbin , Skapek Stephen X.
Published: April 2023

Supplementary Table S1. Sequences of siRNAs, sgRNAs and primers for regular PCR, qRT-PCR and ChIP-qPCR Figure S1. Global analysis of ARF regulation from The Cancer Genome Atlas (TCGA). Figure S2. The status of DNA methylation at promoter regions of CDKN2A/B from DNA methylation data in ENCODE. Figure S3. Induction of ARF by TGFbeta in HeLa cells but not other cervical cancer cell lines. Figure S4. Transcriptional regulation of ARF by TGFbeta in HeLa cells. Figure S5. ARF induction by TGFbeta requires SMAD, p38MAPK and SP1. Figure S6. Deletion of CAD risk interval reflects the long-range gene regulation in Chr4Î"70kb/Î"70kb MEFs. Figure S7. CDKN2A/B expression in response to TGFbetaï�¢ induction in HeLaÎ"20kb-PD cells.
Supplemental Material, Figures 1, 2 and 3 from Spindle Assembly Disruption and Cancer Cell Apoptosis with a CLTC-Binding Compound
Authors: Bond Michael J. , Bleiler Marina , Harrison Lauren E. , Scocchera Eric W. , Nakanishi Masako , G-Dayanan Narendran , Keshipeddy Santosh , Rosenberg Daniel W. , Wright Dennis L. , Giardina Charles
Published: April 2023

S1: Results from AK306 testing on the NCI60 cancer cell line panel. Testing was done by the National Institutes of Health Developmental Therapeutics Program. S2: AK3-BODIPY arrests YAMC cells in mitosis at 600 and 800 nM. YAMCs were treated with compound overnight and then assayed for mitotic arrest by staining for phospho-histone H3. S3: Tumor-bearing ApcÃŽâ€�14/+ mice were treated with five injections of AK306 (30 mg/kg) over the course of three days. Animals were sacrificed and tissue analyzed for PCNA staining (A) and phospho-histone H3 staining (B). Representative staining images are shown in the right panels, with quantified staining shown in the left panels.
Supp. Figure 5 from Targeted AKT Inhibition in Prostate Cancer Cells and Spheroids Reduces Aerobic Glycolysis and Generation of Hyperpolarized [1-13C] Lactate
Authors: Tee Sui Seng , Suster Izabela , Truong Steven , Jeong Sangmoo , Eskandari Roozbeh , DiGialleonardo Valentina , Alvarez Julio A. , Aldeborgh Hannah N. , Keshari Kayvan R.
Published: April 2023

Hyperpolarized MRS of sodium alginate thread cultures. (A) Bright-field image of an alginate thread in culture and (B) H&E stain of the same thread and (C) another cross-section stained with Ki-67. (D) Representative images of an alginate thread cultured in a rotating plate over a period of 4 days and stained with Ki67 All scale bars represent 500 μm. (E) Thread cultures wound on a custom-printed 3D insert, directly deposited into a 5mm NMR tube metabolizes hyperpolarized [1-13C] pyruvate to lactate after injection of 1mM hyperpolarized pyruvate (F). Quantification of integrals of the lactate and pyruvate hydrate peaks over time (G).
Supp. Figure 4 from Targeted AKT Inhibition in Prostate Cancer Cells and Spheroids Reduces Aerobic Glycolysis and Generation of Hyperpolarized [1-13C] Lactate
Authors: Tee Sui Seng , Suster Izabela , Truong Steven , Jeong Sangmoo , Eskandari Roozbeh , DiGialleonardo Valentina , Alvarez Julio A. , Aldeborgh Hannah N. , Keshari Kayvan R.
Published: April 2023

LnCAP cells were grown on coverslips, fixed and permeabilized for detection of Glut-1 coupled to Alexa488. Scale bar = 100 μm
Supp. Fig 1-6 and Supp. Materials from USP11 Enhances TGFβ-Induced Epithelial–Mesenchymal Plasticity and Human Breast Cancer Metastasis
Authors: Garcia Daniel A. , Baek Christina , Estrada M. Valeria , Tysl Tiffani , Bennett Eric J. , Yang Jing , Chang John T.
Published: April 2023

Supp. Fig. 1. High USP11 expression correlates with decreased survival in breast cancer patients. Supp. Fig. 2. Validation of retroviral overexpression and shRNA knockdown of select DUBs. Supp. Fig. 3. USP11 regulates self-renewal in normal human epithelial cells. Supp. Fig. 4. USP11 is upregulated in human breast cancer cell lines. Supp. Fig. 5. SUM159 transwell migration is TGF-beta-dependent. Supp. Fig. 6. USP11 regulates TGF-beta induced expression of EMT markers in human breast cancer cell lines.
Supplementary Table 2 from Combined AURKA and H3K9 Methyltransferase Targeting Inhibits Cell Growth By Inducing Mitotic Catastrophe
Authors: Mathison Angela , Salmonson Ann , Missfeldt Mckenna , Bintz Jennifer , Williams Monique , Kossak Sarah , Nair Asha , de Assuncao Thiago M. , Christensen Trace , Buttar Navtej , Iovanna Juan , Huebert Robert , Lomberk Gwen
Published: April 2023

IC50 values for PDAC cell lines.
Table S6 from Molecular Correlates of Metastasis by Systematic Pan-Cancer Analysis Across The Cancer Genome Atlas
Authors: Chen Fengju , Zhang Yiqun , Varambally Sooryanarayana , Creighton Chad J.
Published: April 2023

For each cancer type, top metastasis-associated DNA methylation CpG Island features, selected using Pearson's correlation (logit-transformed values) with Storey and Tibshirini estimate of False Discovery Rate (FDR) of <10%. Differential mRNA statistics (metastasis versus primary) corresponding to the associated genes are also included.
Supplementary Table 1 from Combined AURKA and H3K9 Methyltransferase Targeting Inhibits Cell Growth By Inducing Mitotic Catastrophe
Authors: Mathison Angela , Salmonson Ann , Missfeldt Mckenna , Bintz Jennifer , Williams Monique , Kossak Sarah , Nair Asha , de Assuncao Thiago M. , Christensen Trace , Buttar Navtej , Iovanna Juan , Huebert Robert , Lomberk Gwen
Published: April 2023

List of Antibodies.
Table S4 from Molecular Correlates of Metastasis by Systematic Pan-Cancer Analysis Across The Cancer Genome Atlas
Authors: Chen Fengju , Zhang Yiqun , Varambally Sooryanarayana , Creighton Chad J.
Published: April 2023

Gene Ontology (GO) term associations for the top metastasis-associated genes for each cancer type.
Supplementary face from Satellite RNA Increases DNA Damage and Accelerates Tumor Formation in Mouse Models of Pancreatic Cancer
Authors: Kishikawa Takahiro , Otsuka Motoyuki , Suzuki Tatsunori , Seimiya Takahiro , Sekiba Kazuma , Ishibashi Rei , Tanaka Eri , Ohno Motoko , Yamagami Mari , Koike Kazuhiko
Published: April 2023

Supplementary face
Supplementary Information from Molecular Correlates of Metastasis by Systematic Pan-Cancer Analysis Across The Cancer Genome Atlas
Authors: Chen Fengju , Zhang Yiqun , Varambally Sooryanarayana , Creighton Chad J.
Published: April 2023

Supplementary Figures and Description of Data Files
Figure S1 from Satellite RNA Increases DNA Damage and Accelerates Tumor Formation in Mouse Models of Pancreatic Cancer
Authors: Kishikawa Takahiro , Otsuka Motoyuki , Suzuki Tatsunori , Seimiya Takahiro , Sekiba Kazuma , Ishibashi Rei , Tanaka Eri , Ohno Motoko , Yamagami Mari , Koike Kazuhiko
Published: April 2023

Phenotype of MajSAT RNA-expressing mice.
Supplementary Data from Targeting of SGK1 by miR-576-3p Inhibits Lung Adenocarcinoma Migration and Invasion
Authors: Greenawalt Evan J. , Edmonds Mick D. , Jain Neha , Adams Clare M. , Mitra Ramkrishna , Eischen Christine M.
Published: April 2023

Table S1. Clinicopathologic features of patient samples Table S2. Clinicopathologic features of matched stage I samples Supplemental Figure 1. miR-576-3p expression is downregulated in late stage lung adenocarcinoma. Supplemental Figure 2. miR-576 overexpression in lung adenocarcinoma cells does not affect proliferation. Supplemental Figure 3. miR-576-3p inhibits migration and invasion of lung adenocarcinoma cells. Supplemental Figure 4. Pharmacological SGK inhibition prevents downstream target phosphorylation and cell migration and invasion.
Table S3 from HPV Integration in HNSCC Correlates with Survival Outcomes, Immune Response Signatures, and Candidate Drivers
Authors: Koneva Lada A. , Zhang Yanxiao , Virani Shama , Hall Pelle B. , McHugh Jonathan B. , Chepeha Douglas B. , Wolf Gregory T. , Carey Thomas E. , Rozek Laura S. , Sartor Maureen A.
Published: April 2023

Network statistics for network constructed from 89 genes with/near integration events.
Table S2 from HPV Integration in HNSCC Correlates with Survival Outcomes, Immune Response Signatures, and Candidate Drivers
Authors: Koneva Lada A. , Zhang Yanxiao , Virani Shama , Hall Pelle B. , McHugh Jonathan B. , Chepeha Douglas B. , Wolf Gregory T. , Carey Thomas E. , Rozek Laura S. , Sartor Maureen A.
Published: April 2023

HPV gene expression levels in the 84 HNSCC tumors.
Supplemental Materials and Methods; Supplementary Tables 5-14; Supplementary Figures 1-3. from HPV Integration in HNSCC Correlates with Survival Outcomes, Immune Response Signatures, and Candidate Drivers
Authors: Koneva Lada A. , Zhang Yanxiao , Virani Shama , Hall Pelle B. , McHugh Jonathan B. , Chepeha Douglas B. , Wolf Gregory T. , Carey Thomas E. , Rozek Laura S. , Sartor Maureen A.
Published: April 2023

Supplemental Methods, Tables S5-S14, and Figures S1-S3
Figure S1 from Neoadjuvant Chemotherapy Shifts Breast Tumor Microbiota Populations to Regulate Drug Responsiveness and the Development of Metastasis
Authors: Chiba Akiko , Bawaneh Alaa , Velazquez Christine , Clear Kenysha Y.J. , Wilson Adam S. , Howard-McNatt Marissa , Levine Edward A. , Levi-Polyachenko Nicole , Yates-Alston Shaina A. , Diggle Stephen P. , Soto-Pantoja David R. , Cook Katherine L.
Published: April 2023

Obesity influences breast tumor microbiota populations. Breast tumor 16S sequencing results were stratified based upon patient body mass index (BMI). Tumor bacterial populations from non-obese patients with a BMI of 20-27 (n=9) were compared with bacterial populations from obese patients with a BMI of 31-48 (n=8). A. Relative abundance of bacterial genera in different tumor samples is visualized by bar plots. Each bar represents a single tumor and each colored box a bacterial taxon. The height of a color box represents the relative abundance of that organism within the sample. ''Other'' represents lower abundance taxa. B. Phylum level distribution in tumors from obese and non-obese patients. Primary breast tumors from obese patients have decreased proportional abundance of Comamonadaceae (C) and Ruminococcaceae (D) family level taxa. E. Obese patients' breast tumors display elevated abundance of Enterobacteriaceae_unclassified. *p<0.05 and error bars show the min to max distribution.
Supplementary Table 1 from Loss of TP63 Promotes the Metastasis of Head and Neck Squamous Cell Carcinoma by Activating MAPK and STAT3 Signaling
Authors: Lakshmanachetty Senthilnath , Balaiya Velmurugan , High Whitney A. , Koster Maranke I.
Published: April 2023

Table S1. Significantly differentially expressed genes in TP63 knockdown SCCs compared to NS shRNA SCCs.
Supplementary Figures 1-15 from Loss of TP63 Promotes the Metastasis of Head and Neck Squamous Cell Carcinoma by Activating MAPK and STAT3 Signaling
Authors: Lakshmanachetty Senthilnath , Balaiya Velmurugan , High Whitney A. , Koster Maranke I.
Published: April 2023

S1. TP63 expression is downregulated in late-stage human larynx HNSCCs. S2. Histopathological analysis of mouse tongue SCCs. S3. TP63 and KRT14 (epithelial marker) expression is lost in a subset of human HNSCC cell lines. S4. Loss of TP63 in HNSCC cell lines does not alter cell cycle distribution. S5. Loss of TP63 promotes the migration and invasion of HNSCC cell lines. S6. Loss of TP63 promotes cervical lymph node metastasis in vivo. S7. Loss of TP63 promotes cervical lymph node metastasis of CAL27 cells. S8. Loss of TP63 in HNSCCs does not alter E-cadherin localization. S9. TP63 regulated pathways in HNSCCs identified using Gene Set Enrichment analysis (GSEA). S10. Loss of TP63 in HNSCCs does not alter P-STAT3 (Tyr705) expression. S11. MAPK and P-STA3 (Ser 727) signaling is upregulated in poorly-differentiated larynx SCCs. S12. EGF treatment of HNSCC cells leads to upregulation of P-ERK1/2, P-STAT3 (Ser 727), and MMP-15 in HNSCC cells. S13. Inhibition of MAPK signaling in HNSCC cell lines by treatment with Trametinib. S14. Inhibition of MAPK signaling by Trametinib prevents the cervical lymph node metastasis of TP63 knockdown HNSCCs. S15. Inhibition of MAPK signaling by Trametinib treatment prevents the cervical lymph node metastasis of CAL27-TP63 shRNA3 HNSCCs.
Supplementary Figure S1 from Loss of Uracil DNA Glycosylase Selectively Resensitizes p53-Mutant and -Deficient Cells to 5-FdU
Authors: Yan Yan , Qing Yulan , Pink John J. , Gerson Stanton L.
Published: April 2023

Figure S1 shows the effect of irradiation on p21 induction in various cancer cells with different p53 status.
Figure S9 from FLYWCH1, a Novel Suppressor of Nuclear β-Catenin, Regulates Migration and Morphology in Colorectal Cancer
Authors: Muhammad Belal A. , Almozyan Sheema , Babaei-Jadidi Roya , Onyido Emenike K. , Saadeddin Anas , Kashfi Seyed Hossein , Spencer-Dene Bradley , Ilyas Mohammad , Lourdusamy Anbarasu , Behrens Axel , Nateri Abdolrahman S.
Published: April 2023

S9. FLYWCH1 alteration and its correlation with EMT transcription factors, ZEB1, CDH1 and EPHA4 gene expression.
Supplementary Figures 1-6 from p53 Function Is Compromised by Inhibitor 2 of Phosphatase 2A in Sonic Hedgehog Medulloblastoma
Authors: Wei Yun , Maximov Victor , Morrissy Sorana A. , Taylor Michael D. , Pallas David C. , Kenney Anna Marie
Published: April 2023

S1. Nutlin-3a treatment caused apoptosis and cell cycle arrest. S2. Whole blots of MDM2 and p-MDM2S166 in SmoA1 tumors. S3. Normalized expression levels of I2PP2A mRNA in medulloblastoma patients showed a small difference between SHH medulloblastoma samples and cerebellar controls. S4. p-MDM2 is regulated by both PP2A and p-Akt. S5. Lentivirus and retrovirus infection on SmoA1 MBCs are successful. S6. I2PP2A knockdown affected p53 targets and SHH signaling only in ONS76 cells.
Figure S7 from FLYWCH1, a Novel Suppressor of Nuclear β-Catenin, Regulates Migration and Morphology in Colorectal Cancer
Authors: Muhammad Belal A. , Almozyan Sheema , Babaei-Jadidi Roya , Onyido Emenike K. , Saadeddin Anas , Kashfi Seyed Hossein , Spencer-Dene Bradley , Ilyas Mohammad , Lourdusamy Anbarasu , Behrens Axel , Nateri Abdolrahman S.
Published: April 2023

S7. FLYWCH1 reduces wound-closure capacity of CRC cells
Figure S6 from FLYWCH1, a Novel Suppressor of Nuclear β-Catenin, Regulates Migration and Morphology in Colorectal Cancer
Authors: Muhammad Belal A. , Almozyan Sheema , Babaei-Jadidi Roya , Onyido Emenike K. , Saadeddin Anas , Kashfi Seyed Hossein , Spencer-Dene Bradley , Ilyas Mohammad , Lourdusamy Anbarasu , Behrens Axel , Nateri Abdolrahman S.
Published: April 2023

S6. FLYWCH1 mutation in human cancers and analysis of cell cycle by flow cytometry
Figure S1 from FLYWCH1, a Novel Suppressor of Nuclear β-Catenin, Regulates Migration and Morphology in Colorectal Cancer
Authors: Muhammad Belal A. , Almozyan Sheema , Babaei-Jadidi Roya , Onyido Emenike K. , Saadeddin Anas , Kashfi Seyed Hossein , Spencer-Dene Bradley , Ilyas Mohammad , Lourdusamy Anbarasu , Behrens Axel , Nateri Abdolrahman S.
Published: April 2023

S1. FLYWCH motifs within FLYWCH1 family of proteins in several mammals and protein interaction assays between FLYWCH1 and Î²-catenin