bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary figure 1 from High-Fat Diet-Induced Complement Activation Mediates Intestinal Inflammation and Neoplasia, Independent of Obesity
Authors: Doerner Stephanie K. , Reis Edimara S. , Leung Elaine S. , Ko Justine S. , Heaney Jason D. , Berger Nathan A. , Lambris John D. , Nadeau Joseph H.
Published: April 2023

S1. White blood cell counts.
Supplemental Figure S3 from Detection of Tumor Suppressor Genes in Cancer Development by a Novel shRNA-Based Method
Authors: von Burstin Johannes , Diersch Sandra , Schneider Günter , Reichert Maximilian , Rustgi Anil K. , Schmid Roland M.
Published: April 2023

Supplemental Figure S3: shRNA mediated silencing of p16Ink4a or Trp53 leads to decreased survival. Kaplan-Meier survival analysis shows a significant decrease in survival of animals that were injected with Kras-shRNAp16Ink4a-PDCs (median survival 109 days, p=0.04) or Kras-shRNA-Trp53-PDCs (median survival 125.5 days, p=0.038)
Supplementary Figures Legend from Treatment Efficacy and Resistance Mechanisms Using the Second-Generation ALK Inhibitor AP26113 in Human NPM-ALK–Positive Anaplastic Large Cell Lymphoma
Authors: Ceccon M. , Mologni L. , Giudici G. , Piazza R. , Pirola A. , Fontana D. , Gambacorti-Passerini C.
Published: April 2023

Supplementary Figures Legend.
Supplementary Figure from Treatment Efficacy and Resistance Mechanisms Using the Second-Generation ALK Inhibitor AP26113 in Human NPM-ALK–Positive Anaplastic Large Cell Lymphoma
Authors: Ceccon M. , Mologni L. , Giudici G. , Piazza R. , Pirola A. , Fontana D. , Gambacorti-Passerini C.
Published: April 2023

Supplementary Figure 4. Characterization of Ba/F3 NPM-ALK model. Chromatograms showing the desired mutations are shown: 4472T>G (F1174V); 4544C>T (L1198F), alone or in the double mutant cell line; 4316C>G (L1122V); 4538C>A (L1196M) in the single or double mutant; 4569C>G(S1206C); 4367C>T (P1139S); 4559G>A (D1203N) in combination with L1196M. Sites of mutagenesis are highlighted by the asterisk.
Supplementary Figure 7B from Treatment Efficacy and Resistance Mechanisms Using the Second-Generation ALK Inhibitor AP26113 in Human NPM-ALK–Positive Anaplastic Large Cell Lymphoma
Authors: Ceccon M. , Mologni L. , Giudici G. , Piazza R. , Pirola A. , Fontana D. , Gambacorti-Passerini C.
Published: April 2023

Supplementary Figure 7B. Histograms with error bars summarize the densitometric analysis of western blot panels shown in figure 3
Figure S3 from Estrogen Drives Cellular Transformation and Mutagenesis in Cells Expressing the Breast Cancer–Associated R438W DNA Polymerase Lambda Protein
Authors: Nemec Antonia A. , Bush Korie B. , Towle-Weicksel Jamie B. , Taylor B. Frazier , Schulz Vincent , Weidhaas Joanne B. , Tuck David P. , Sweasy Joann B.
Published: April 2023

R438W Pol lambda induces cellular transformation in the absence of estrogen.
Figure S7: Location of metastases formed with PF-562,271 treatment. from FAK Expression, Not Kinase Activity, Is a Key Mediator of Thyroid Tumorigenesis and Protumorigenic Processes
Authors: Kessler Brittelle E. , Sharma Vibha , Zhou Qiong , Jing Xia , Pike Laura A. , Kerege Anna A. , Sams Sharon B. , Schweppe Rebecca E.
Published: April 2023

Bioluminescence images were taken of anatomic structures ex vivo upon dissection. Positive or negative bioluminescent signal from each location was recorded for each mouse. The number of metastases to the bone for each treatment group was quantified. Results shown are number of metastases per mouse per treatment group {plus minus} SD.
Supplementary figure legends from MELK and EZH2 Cooperate to Regulate Medulloblastoma Cancer Stem-like Cell Proliferation and Differentiation
Authors: Liu Hailong , Sun Qianwen , Sun Youliang , Zhang Junping , Yuan Hongyu , Pang Shuhuan , Qi Xueling , Wang Haoran , Zhang Mingshan , Zhang Hongwei , Yu Chunjiang , Gu Chunyu
Published: April 2023

supplementary figure legends.
Figure S7 from G-Protein-Coupled Estrogen Receptor 1 Promotes Gender Disparities in Hepatocellular Carcinoma via Modulation of SIN1 and mTOR Complex 2 Activity
Authors: Feng Guanying , Cai Jingshu , Huang Yunchuanxiang , Zhu Xianjun , Gong Bo , Yang Zhenglin , Yan Chunhong , Hu Zhuowei , Yang Lu , Wang Ziyan
Published: April 2023

Figure S7 demonstates that gender difference of HCC is seen in mouse and human.
Supplementary Figure 2 from MELK and EZH2 Cooperate to Regulate Medulloblastoma Cancer Stem-like Cell Proliferation and Differentiation
Authors: Liu Hailong , Sun Qianwen , Sun Youliang , Zhang Junping , Yuan Hongyu , Pang Shuhuan , Qi Xueling , Wang Haoran , Zhang Mingshan , Zhang Hongwei , Yu Chunjiang , Gu Chunyu
Published: April 2023

H.E. staining for the intracranial xenograft derived from the MB25550 CSCs.
Supplementary Table 4 from PARP1 Trapping by PARP Inhibitors Drives Cytotoxicity in Both Cancer Cells and Healthy Bone Marrow
Authors: Hopkins Todd A. , Ainsworth William B. , Ellis Paul A. , Donawho Cherrie K. , DiGiammarino Enrico L. , Panchal Sanjay C. , Abraham Vivek C. , Algire Mikkel A. , Shi Yan , Olson Amanda M. , Johnson Eric F. , Wilsbacher Julie L. , Maag David
Published: April 2023

Bone Marrow IC50s broken into cell type.
Supplementary Table 3 from PARP1 Trapping by PARP Inhibitors Drives Cytotoxicity in Both Cancer Cells and Healthy Bone Marrow
Authors: Hopkins Todd A. , Ainsworth William B. , Ellis Paul A. , Donawho Cherrie K. , DiGiammarino Enrico L. , Panchal Sanjay C. , Abraham Vivek C. , Algire Mikkel A. , Shi Yan , Olson Amanda M. , Johnson Eric F. , Wilsbacher Julie L. , Maag David
Published: April 2023

IC50 values of PARPi vs BM-CFU and BM-PAR
Supplementary Table 2 from PARP1 Trapping by PARP Inhibitors Drives Cytotoxicity in Both Cancer Cells and Healthy Bone Marrow
Authors: Hopkins Todd A. , Ainsworth William B. , Ellis Paul A. , Donawho Cherrie K. , DiGiammarino Enrico L. , Panchal Sanjay C. , Abraham Vivek C. , Algire Mikkel A. , Shi Yan , Olson Amanda M. , Johnson Eric F. , Wilsbacher Julie L. , Maag David
Published: April 2023

Clinical RP2D concentrations for PARP inhibitors.
Supplementary Table 1 from PARP1 Trapping by PARP Inhibitors Drives Cytotoxicity in Both Cancer Cells and Healthy Bone Marrow
Authors: Hopkins Todd A. , Ainsworth William B. , Ellis Paul A. , Donawho Cherrie K. , DiGiammarino Enrico L. , Panchal Sanjay C. , Abraham Vivek C. , Algire Mikkel A. , Shi Yan , Olson Amanda M. , Johnson Eric F. , Wilsbacher Julie L. , Maag David
Published: April 2023

IC50s (nM) for inhibition of enzyme activity for PARP family members
Supplemental Materials and Methods and Figure Legends from Targeting RRM2 and Mutant BRAF Is a Novel Combinatorial Strategy for Melanoma
Authors: Fatkhutdinov Nail , Sproesser Katrin , Krepler Clemens , Liu Qin , Brafford Patricia A. , Herlyn Meenhard , Aird Katherine M. , Zhang Rugang
Published: April 2023

Supplemental Materials and Methods and Figure Legends from Targeting RRM2 and Mutant BRAF Is a Novel Combinatorial Strategy for Melanoma
Supplemental Figure S4 from Targeting RRM2 and Mutant BRAF Is a Novel Combinatorial Strategy for Melanoma
Authors: Fatkhutdinov Nail , Sproesser Katrin , Krepler Clemens , Liu Qin , Brafford Patricia A. , Herlyn Meenhard , Aird Katherine M. , Zhang Rugang
Published: April 2023

Figure S4. The combination of knockdown of RRM2 and mutant BRAF inhibition in a patient derived xenograft inhibits melanoma tumor growth.
Supplementary Table S6 from The ERG-Regulated LINC00920 Promotes Prostate Cancer Cell Survival via the 14-3-3ϵ–FOXO Pathway
Authors: Angeles Arlou Kristina , Heckmann Doreen , Flosdorf Niclas , Duensing Stefan , Sültmann Holger
Published: April 2023

Proteins interacting with LINC00920 as identified by ChIRP-MS.
Supplemental Figure S2 from Disruption of Proline Synthesis in Melanoma Inhibits Protein Production Mediated by the GCN2 Pathway
Authors: Kardos Gregory R. , Wastyk Hannah C. , Robertson Gavin P.
Published: April 2023

Supplemental Figure S2. Cell line melanoma tumor progression model shows levels of intracellular metabolites in each cell line.
Supplemental Figure S1 from Disruption of Proline Synthesis in Melanoma Inhibits Protein Production Mediated by the GCN2 Pathway
Authors: Kardos Gregory R. , Wastyk Hannah C. , Robertson Gavin P.
Published: April 2023

Supplemental Figure S1. ALDH18A1 identification in a siRNA screen.
Figure S2 from R-spondin2 Suppresses the Progression of Hepatocellular Carcinoma via MAPK Signaling Pathway
Authors: Zheng Chang , Zhou Fan , Shi Liang Liang , Xu Gui Fang , Zhang Bin , Wang Lei , Zhuge Yuzheng , Zou Xiao Ping , Wang Yi
Published: April 2023

Figure S2. Proliferation and apoptosis of cells cultured with recombinant cytokine R-spondin2. (A) Total apoptosis of these HCC cell lines were not significantly affected when cultured with 50 ng/ml recombinant cytokine R-spondin2 for 48h. (B) Total apoptosis of Huh-7 and HCCL-M3 cells cultured with higher concentrations recombinant cytokine R-spondin2 (200, 400 ng/ml) and only 200 ng/ml recombinant cytokine R-spondin2 showed promoting effect in Huh-7. (C) Cell proliferation abilities were not significantly affected by recombinant cytokine R-spondin1, 2, 3 in these six HCC cell lines (50, 100, 200 ng/ml), as shown by CCK-8 assay. Three individual experiment results are presented as mean {plus minus} SD. *P < 0.05 vs control.
Supplemental Table 6 from Genomic Integration of High-Risk HPV Alters Gene Expression in Oropharyngeal Squamous Cell Carcinoma
Authors: Walline Heather M. , Komarck Christine M. , McHugh Jonathan B. , Bellile Emily L. , Brenner J. Chad , Prince Mark E. , McKean Erin L. , Chepeha Douglas B. , Wolf Gregory T. , Worden Francis P. , Bradford Carol R. , Carey Thomas E.
Published: April 2023

Supplemental Table 6. Summary of genomic aberrations to identified genes with integrated HPV. The Oncomine database was used to assess genomic aberrations in all publicly available HNSCC next generation sequencing data sets including (1, 2) 1. Agrawal N, Frederick MJ, Pickering CR, Bettegowda C, Chang K, Li RJ, Fakhry C, Xie TX, Zhang J, Wang J, Zhang N, El-Naggar AK, Jasser SA, Weinstein JN, Trevino L, Drummond JA, Muzny DM, Wu Y, Wood LD, Hruban RH, Westra WH, Koch WM, Califano JA, Gibbs RA, Sidransky D, Vogelstein B, Velculescu VE, Papadopoulos N, Wheeler DA, Kinzler KW, Myers JN. Exome sequencing of head and neck squamous cell carcinoma reveals inactivating mutations in NOTCH1. Science. 2011;333(6046):1154-7. doi: 10.1126/science.1206923. PubMed PMID: 21798897; PMCID: PMC3162986. 2. Stransky N, Egloff AM, Tward AD, Kostic AD, Cibulskis K, Sivachenko A, Kryukov GV, Lawrence MS, Sougnez C, McKenna A, Shefler E, Ramos AH, Stojanov P, Carter SL, Voet D, Cortes ML, Auclair D, Berger MF, Saksena G, Guiducci C, Onofrio RC, Parkin M, Romkes M, Weissfeld JL, Seethala RR, Wang L, Rangel-Escareno C, Fernandez-Lopez JC, Hidalgo-Miranda A, Melendez-Zajgla J, Winckler W, Ardlie K, Gabriel SB, Meyerson M, Lander ES, Getz G, Golub TR, Garraway LA, Grandis JR. The mutational landscape of head and neck squamous cell carcinoma. Science. 2011;333(6046):1157-60. doi: 10.1126/science.1208130. PubMed PMID: 21798893; PMCID: PMC3415217.
Supplementary Movie 2 from Relocation of CLIC1 Promotes Tumor Cell Invasion and Colonization of Fibrin
Authors: Gurski Lisa A. , Knowles Lynn M. , Basse Per H. , Maranchie Jodi K. , Watkins Simon C. , Pilch Jan
Published: April 2023

Live cell imaging of fibrin-embedded shCLIC1 786-O cells.
Supplementary Figure S1 from Tumor Suppressor Activity of Klotho in Breast Cancer Is Revealed by Structure–Function Analysis
Authors: Ligumsky Hagai , Rubinek Tami , Merenbakh-Lamin Keren , Yeheskel Adva , Sertchook Rotem , Shahmoon Shiri , Aviel-Ronen Sarit , Wolf Ido
Published: April 2023

Klotho wild type, truncated and mutated secretion analysis.
Supplemental Table S8 from Inhibition of S-Adenosylmethionine-Dependent Methyltransferase Attenuates TGFβ1-Induced EMT and Metastasis in Pancreatic Cancer: Putative Roles of miR-663a and miR-4787-5p
Authors: Mody Hardik R. , Hung Sau Wai , AlSaggar Mohammad , Griffin Jazmine , Govindarajan Rajgopal
Published: April 2023

Table S8. Bioinformatic predictions of DZNep-induced miRNAs to target players in the TGF-beta signaling pathway (TGF-beta1
Supplemental Table S1 from Inhibition of S-Adenosylmethionine-Dependent Methyltransferase Attenuates TGFβ1-Induced EMT and Metastasis in Pancreatic Cancer: Putative Roles of miR-663a and miR-4787-5p
Authors: Mody Hardik R. , Hung Sau Wai , AlSaggar Mohammad , Griffin Jazmine , Govindarajan Rajgopal
Published: April 2023

S1: Clinical and histological characterization of human pancreatic tumor tissue sample.
Supplementary Data from AKT1E17K Activates Focal Adhesion Kinase and Promotes Melanoma Brain Metastasis
Authors: Kircher David A. , Trombetti Kirby A. , Silvis Mark R. , Parkman Gennie L. , Fischer Grant M. , Angel Stephanie N. , Stehn Christopher M. , Strain Sean C. , Grossmann Allie H. , Duffy Keith L. , Boucher Kenneth M. , McMahon Martin , Davies Michael A. , Mendoza Michelle C. , VanBrocklin Matthew W. , Holmen Sheri L.
Published: April 2023

Supplementary Materials and Methods
Supplementary Figure S4 from Integration of Downstream Signals of Insulin-like Growth Factor-1 Receptor by Endoplasmic Reticulum Stress for Estrogen-Induced Growth or Apoptosis in Breast Cancer Cells
Authors: Fan Ping , Cunliffe Heather E. , Maximov Philipp Y. , Agboke Fadeke A. , McDaniel Russell E. , Zou Xiaojun , Ramos Pilar , Russell Megan L. , Jordan V. Craig
Published: April 2023

(A) MCF-7:5C cells were treated with vehicle (0.1% EtOH; con) or E2 (10-9 mol/L) for 72 hours. Cells were harvested in TRIzol. IGF-1RÎ² was quantitated by real-time RT-PCR. p<0.001, ** compared with control. (B) MCF-7:5C cells were treated with vehicle (0.1% DMSO; con) or AG1024 (5Ã—10-6 mol/L) for 48 hours. Total-IGF-1RÎ² and p-IGF-1RÎ² were examined by Western blot.
Figure S1 from AKT1E17K Activates Focal Adhesion Kinase and Promotes Melanoma Brain Metastasis
Authors: Kircher David A. , Trombetti Kirby A. , Silvis Mark R. , Parkman Gennie L. , Fischer Grant M. , Angel Stephanie N. , Stehn Christopher M. , Strain Sean C. , Grossmann Allie H. , Duffy Keith L. , Boucher Kenneth M. , McMahon Martin , Davies Michael A. , Mendoza Michelle C. , VanBrocklin Matthew W. , Holmen Sheri L.
Published: April 2023

Supplementary Figure 1. RCAS mutant AKT viruses infect TVA+ melanoma cells.
Supplementary Figure Legends from Integration of Downstream Signals of Insulin-like Growth Factor-1 Receptor by Endoplasmic Reticulum Stress for Estrogen-Induced Growth or Apoptosis in Breast Cancer Cells
Authors: Fan Ping , Cunliffe Heather E. , Maximov Philipp Y. , Agboke Fadeke A. , McDaniel Russell E. , Zou Xiaojun , Ramos Pilar , Russell Megan L. , Jordan V. Craig
Published: April 2023

Legends of supplementary Figures
Supplementary Figure from Cdc42 Mediates Cancer Cell Chemotaxis in Perineural Invasion
Authors: Chernichenko Natalya , Omelchenko Tatiana , Deborde Sylvie , Bakst Richard L. , He Shizhi , Chen Chun-Hao , Gusain Laxmi , Vakiani Efsevia , Katabi Nora , Hall Alan , Wong Richard J.
Published: April 2023

Supplementary Figure
Supplemental Table S1 from HDAC6 Deacetylates HMGN2 to Regulate Stat5a Activity and Breast Cancer Growth
Authors: Medler Terry R. , Craig Justin M. , Fiorillo Alyson A. , Feeney Yvonne B. , Harrell J. Chuck , Clevenger Charles V.
Published: April 2023

Supplemental Table S1. Primers used for mutagenesis.
Supp. Fig. 5 from SOCS3 Modulates the Response to Enzalutamide and Is Regulated by Androgen Receptor Signaling and CpG Methylation in Prostate Cancer Cells
Authors: Handle Florian , Erb Holger H.H. , Luef Birgit , Hoefer Julia , Dietrich Dimo , Parson Walther , Kristiansen Glen , Santer Frédéric R. , Culig Zoran
Published: April 2023

SOCS3 is not regulated on post-transcriptional level by R1881. A luciferase reporter vector containing the coding sequence (CDS) and the 3'UTR of SOCS3 in the untranslated region after the luciferase stop codon was transfected into LNCaP cells. Treatment with 1 nM R1881 did not influence the reported expression, whereas, as a positive control, co-transfection with a shRNA targeting SOCS3 reduced the luciferase activity by more than 50 %. The firefly luc2 luciferase activity was normalized to a co-transfected renilla luciferase control vector.
Figure S1 from Kinase-Dependent and -Independent Roles for PTK6 in Colon Cancer
Authors: Mathur Priya S. , Gierut Jessica J. , Guzman Grace , Xie Hui , Xicola Rosa M. , Llor Xavier , Chastkofsky Michael I. , Perekatt Ansu O. , Tyner Angela L.
Published: April 2023

Supplemental Figure; Additional PTK6 localization and expression data
Figure S3 from CD71+ Population Enriched by HPV-E6 Protein Promotes Cancer Aggressiveness and Radioresistance in Cervical Cancer Cells
Authors: Leung Thomas Ho-Yin , Tang Hermit Wai-Man , Siu Michelle Kwan-Yee , Chan David Wai , Chan Karen Kar-Loen , Cheung Annie Nga-Yin , Ngan Hextan Yuen-Sheung
Published: April 2023

The mutations in R28 were validated by sequencing analysis.
Supplemental Tables S1-2, Figures S1-2 from Breast Cancer–Specific miR Signature Unique to Extracellular Vesicles Includes “microRNA-like” tRNA Fragments
Authors: Guzman Nicole , Agarwal Kitty , Asthagiri Dilip , Yu Lianbo , Saji Motoyasu , Ringel Matthew D. , Paulaitis Michael E.
Published: April 2023

Supplemental Tables S1-2, Figures S1-2. Table S1. NanoString nCounterTM assay measurements of miRNA copy numbers/cell detected in MCF7 and MCF10A cells at 72 hrs of serum deprivation and in EVs derived from MCF7 and MCF10A cells over 72 hrs of serum deprivation. Table S2. qRT-PCR assay measurements of miRNA copy numbers/cell detected in MCF7 and MCF10A cells at 72 hrs of serum deprivation and in EVs secreted from MCF7 and MCF10A cells over 72 hrs of serum deprivation. Figure S1. Total cellular RNA concentration (top panel) and changes in miR-21 expression levels (middle panel) and changes in miR-1274a and miR-1274b expression levels (bottom panel) for MCF10A cells (open symbols) and MCF7 cells (filled symbols) as a function of time in response to serum deprivation at 0 hrs. Figure S2. Sequence alignments for miRNA pairs depicting positions that share identical nucleotides.
Supplemental Figure 1 from PRAS40 Phosphorylation Correlates with Insulin-Like Growth Factor-1 Receptor-Induced Resistance to Epidermal Growth Factor Receptor Inhibition in Head and Neck Cancer Cells
Authors: Dougherty Michael I. , Lehman Christine E. , Spencer Adam , Mendez Rolando E. , David Abel P. , Taniguchi Linnea E. , Wulfkuhle Julie , Petricoin Emanuel F. , Gioeli Daniel , Jameson Mark J.
Published: April 2023

Supplemental Figure 1: The signaling impact of IGF1R activation in sensitive vs. resistant cell lines. Lysates from 6 HNSCC cell lines were assessed by reverse phase protein array (RPPA) to determine protein changes following treatment with desIGF1 (NT+IGF), each single EGFR-TKI (Erl = erlotinib, Gef = gefitinib, or Lap = lapatinib), or the combination of EGFR-TKI and desIGF1 (Erl+IGF, Gef+IGF, or Lap+IGF). Representative heat maps depict changes among the 157 epitopes in each of the 6 cell lines assessed by RPPA. Heat map representing changes upon treatment with (A) gefitinib, (B) erlotinib and (C) lapatinib. Asterisks represent significant changes with p<0.05 as compared to untreated.
Supplementary Figure S3 from Combined Src/EGFR Inhibition Targets STAT3 Signaling and Induces Stromal Remodeling to Improve Survival in Pancreatic Cancer
Authors: Dosch Austin R. , Dai Xizi , Reyzer Michelle L. , Mehra Siddharth , Srinivasan Supriya , Willobee Brent A. , Kwon Deukwoo , Kashikar Nilesh , Caprioli Richard , Merchant Nipun B. , Nagathihalli Nagaraj S.
Published: April 2023

Weight of PKT mice during treatment regimen.
Supplementary Figure S1 from Combined Src/EGFR Inhibition Targets STAT3 Signaling and Induces Stromal Remodeling to Improve Survival in Pancreatic Cancer
Authors: Dosch Austin R. , Dai Xizi , Reyzer Michelle L. , Mehra Siddharth , Srinivasan Supriya , Willobee Brent A. , Kwon Deukwoo , Kashikar Nilesh , Caprioli Richard , Merchant Nipun B. , Nagathihalli Nagaraj S.
Published: April 2023

Combined Src and EGFR inhibition decreases collagen I content in PANC1 orthotopic xenograft models of PDAC.
Supplementary Figure S1 from A YAP/TAZ-Regulated Molecular Signature Is Associated with Oral Squamous Cell Carcinoma
Authors: Hiemer Samantha E. , Zhang Liye , Kartha Vinay K. , Packer Trevor S. , Almershed Munirah , Noonan Vikki , Kukuruzinska Maria , Bais Manish V. , Monti Stefano , Varelas Xaralabos
Published: April 2023

Supplementary Figure S1. Additional images showing that nuclear YAP accumulates in oral tissues with epithelial hyperplasia and dysplasia histopathology.
Supplementary Figure 4 from p53–Pirh2 Complex Promotes Twist1 Degradation and Inhibits EMT
Authors: Yang-Hartwich Yang , Tedja Roslyn , Roberts Cai M. , Goodner-Bingham Jamie , Cardenas Carlos , Gurea Marta , Sumi Natalia J. , Alvero Ayesha B. , Glackin Carlotta A. , Mor Gil
Published: April 2023

Expression of p53-associated E3 ligase in cancer cell lines. (A) RNA expression of MDM2, Pirh2, and E6-AP1, and TOPORS assessed by QPCR in R182 (p53high/Twist-) and Tara R182 (p53low/Twist+) cells. GADPH was used as reference gene. (B) Protein expression of Pirh2 assessed by Western blot. Î²-actin was used as loading control.
Supplementary Figure 3 from p53–Pirh2 Complex Promotes Twist1 Degradation and Inhibits EMT
Authors: Yang-Hartwich Yang , Tedja Roslyn , Roberts Cai M. , Goodner-Bingham Jamie , Cardenas Carlos , Gurea Marta , Sumi Natalia J. , Alvero Ayesha B. , Glackin Carlotta A. , Mor Gil
Published: April 2023

Mdm2 does not interact with Twist1. (A) Mdm2 and Twist1 were transfected in HEK293T. Western blot was used to detected the effect of Mdm2 on Twist1 protein level. (B) Mdm2 was immunoprecipitated in HEK293T cells that were transfected with Mdm2 and Twist1 plasmids. p53 was detected in the IP product by western blot. Twist1 was not detected in the IP product.
Supplemental File 2 from Molecular Portrait of Hypoxia in Breast Cancer: A Prognostic Signature and Novel HIF-Regulated Genes
Authors: Ye I. Chae , Fertig Elana J. , DiGiacomo Josh W. , Considine Michael , Godet Inês , Gilkes Daniele M.
Published: April 2023

Source code and searchable database
Supplementary Data 5 from miR-122-5p Expression and Secretion in Melanoma Cells Is Amplified by the LPAR3 SH3–Binding Domain to Regulate Wnt1
Authors: Byrnes Charnel C. , Jia Wei , Alshamrani Ali A. , Kuppa Sudeepti S. , Murph Mandi M.
Published: April 2023

Supplementary Figure 5. miR-122-5p abundance fluctuates in heart tissue, resultant from LPAR3 expression. Tissues were collected from knock-out mice lacking the first exon of the LPAR3 and their wild-type siblings and assessed for miR-122-5p and LPAR3. Heart tissue samples exhibited statistically lower miR-122-5p levels when compared to wild-type mice (*p<0.05). No significant differences were detected in liver and kidney tissue samples.
Supplementary Data 3C from miR-122-5p Expression and Secretion in Melanoma Cells Is Amplified by the LPAR3 SH3–Binding Domain to Regulate Wnt1
Authors: Byrnes Charnel C. , Jia Wei , Alshamrani Ali A. , Kuppa Sudeepti S. , Murph Mandi M.
Published: April 2023

Supplementary Figure 3. Microfluidics visualization of nanoparticles from LPAR3. The movies illustrate the difference between the smaller/almost indiscernible white dots, which are exosome nanoparticles, secreted by cells expressing LPAR3-wt versus the larger particles, likely multi-vesicular bodies, but not exosomes.
Figure S5 from Tumor Progression Is Mediated by Thymosin-β4 through a TGFβ/MRTF Signaling Axis
Authors: Morita Tsuyoshi , Hayashi Ken'ichiro
Published: April 2023

Figure S5 shows survival analysis of human cancer patients.
Supplementary Figure S3 from Global Increase of p16INK4a in APC-Deficient Mouse Liver Drives Clonal Growth of p16INK4a-Negative Tumors
Authors: Ueberham Elke , Glöckner Pia , Göhler Claudia , Straub Beate K. , Teupser Daniel , Schönig Kai , Braeuning Albert , Höhn Anne Kathrin , Jerchow Boris , Birchmeier Walter , Gaunitz Frank , Arendt Thomas , Sansom Owen , Gebhardt Rolf , Ueberham Uwe
Published: April 2023

Immunohistochemical depiction of p16INK4a in situ.
Supplemental Figure 1 from Genomic cfDNA Analysis of Aqueous Humor in Retinoblastoma Predicts Eye Salvage: The Surrogate Tumor Biopsy for Retinoblastoma
Authors: Berry Jesse L. , Xu Liya , Kooi Irsan , Murphree A. Linn , Prabakar Rishvanth K. , Reid Mark , Stachelek Kevin , Le Bao Han A. , Welter Lisa , Reiser Bibiana J. , Chévez-Barrios Patricia , Jubran Rima , Lee Thomas C. , Kim Jonathan W. , Kuhn Peter , Cobrinik David , Hicks James
Published: April 2023

Supplemental Figure 1, online only: a positive correlation was seen between the age at diagnosis and genomic instability which is defined as the overall size of the copy number variation found in the initial AH samples (p=<0.0001, R2=0.658). For the 3 bilateral patients, only 1 eye was included in the analysis, for a total of 26 eyes.
Supplementary Figure Legends S1-S5 from Global Increase of p16INK4a in APC-Deficient Mouse Liver Drives Clonal Growth of p16INK4a-Negative Tumors
Authors: Ueberham Elke , Glöckner Pia , Göhler Claudia , Straub Beate K. , Teupser Daniel , Schönig Kai , Braeuning Albert , Höhn Anne Kathrin , Jerchow Boris , Birchmeier Walter , Gaunitz Frank , Arendt Thomas , Sansom Owen , Gebhardt Rolf , Ueberham Uwe
Published: April 2023

Supplementary Figure legends
Supplementary Figure S1-S8 from Targeting the MIF/CXCR7/AKT Signaling Pathway in Castration-Resistant Prostate Cancer
Authors: Rafiei Shahrzad , Gui Bin , Wu Jiaxin , Liu X. Shirley , Kibel Adam S. , Jia Li
Published: April 2023

Supplementary Figures
Supplementary Tables and Figures from Comparative Genomics Reveals Shared Mutational Landscape in Canine Hemangiosarcoma and Human Angiosarcoma
Authors: Megquier Kate , Turner-Maier Jason , Swofford Ross , Kim Jong-Hyuk , Sarver Aaron L. , Wang Chao , Sakthikumar Sharadha , Johnson Jeremy , Koltookian Michele , Lewellen Mitzi , Scott Milcah C. , Schulte Ashley J. , Borst Luke , Tonomura Noriko , Alfoldi Jessica , Painter Corrie , Thomas Rachael , Karlsson Elinor K. , Breen Matthew , Modiano Jaime F. , Elvers Ingegerd , Lindblad-Toh Kerstin
Published: April 2023

Table S1. Canine cohort metadata Table S2. Canine library preparation, amplification, and complexity Table S3. COSMIC Cancer Gene Census genes Table S4. Summary of canine RNA-seq data Table S5. RNA-seq validation Table S6. RNA-seq survey Table S7. Enrichment of protein domains in hemangiosarcoma and angiosarcoma Table S8. Canine somatic copy number aberrations by oaCGH Table S9. Comparison of top SCNAs in human Angiosarcoma Project data with canine oaCGH data Figure S1 - Canine exome sequencing workflow Figure S2 - Canine SMGs called in normal vs. overamplified libraries Figure S3 - Mutational landscape of entire canine cohort Figure S4 - Mutational landscape: FFPE vs Frozen Figure S5 - Mutational landscape: Canine Tumor Location Figure S6 - FFPE vs Frozen exome SCNA data clustering
Supplementary Data from Proinflammatory Macrophages Promote Multiple Myeloma Resistance to Bortezomib Therapy
Authors: Beyar-Katz Ofrat , Magidey Ksenia , Reiner-Benaim Anat , Barak Noga , Avivi Irit , Cohen Yael , Timaner Michael , Avraham Shimrit , Hayun Michal , Lavi Noa , Bersudsky Marina , Voronov Elena , Apte Ron N. , Shaked Yuval
Published: April 2023

Figure S1. Bone marrow-derived macrophages enrich MM TICs. Figure S2. IL-1β promotes MM-TIC enrichment. Figure S3. Reduced survival in MM patients with high levels of M1 pro-inflammatory macrophages and TICs. Table S1: Patient characteristics and treatment description Table S2. Panel of antibodies and isotype conjugates used in CyTOF.
Supplementary Figure 6 from Adaptation to HIF1α Deletion in Hypoxic Cancer Cells by Upregulation of GLUT14 and Creatine Metabolism
Authors: Valli Alessandro , Morotti Matteo , Zois Christos E. , Albers Patrick K. , Soga Tomoyoshi , Feldinger Katharina , Fischer Roman , Frejno Martin , McIntyre Alan , Bridges Esther , Haider Syed , Buffa Francesca M. , Baban Dilair , Rodriguez Miguel , Yanes Oscar , Whittington Hannah J. , Lake Hannah A. , Zervou Sevasti , Lygate Craig A. , Kessler Benedikt M. , Harris Adrian L.
Published: April 2023

S6. Phosphocreatine/Creatine ratio per cell in WTN, KON, WTH, and KOH.
Supplementary Figure S1 from The Aged Microenvironment Influences the Tumorigenic Potential of Malignant Prostate Epithelial Cells
Authors: Bianchi-Frias Daniella , Damodarasamy Mamatha , Hernandez Susana A. , Gil da Costa Rui M. , Vakar-Lopez Funda , Coleman Ilsa M. , Reed May J. , Nelson Peter S.
Published: April 2023

Macrophage IHC
Supplementary Figure 3 from Adaptation to HIF1α Deletion in Hypoxic Cancer Cells by Upregulation of GLUT14 and Creatine Metabolism
Authors: Valli Alessandro , Morotti Matteo , Zois Christos E. , Albers Patrick K. , Soga Tomoyoshi , Feldinger Katharina , Fischer Roman , Frejno Martin , McIntyre Alan , Bridges Esther , Haider Syed , Buffa Francesca M. , Baban Dilair , Rodriguez Miguel , Yanes Oscar , Whittington Hannah J. , Lake Hannah A. , Zervou Sevasti , Lygate Craig A. , Kessler Benedikt M. , Harris Adrian L.
Published: April 2023

S3. HIF1α and hypoxia-dependent effects on transcription and protein levels.
p16 promoter DNA methylation and expression in response to decitabine treatment from Histone H3.3K27M Represses p16 to Accelerate Gliomagenesis in a Murine Model of DIPG
Authors: Cordero Francisco J. , Huang Zhiqing , Grenier Carole , He Xingyao , Hu Guo , McLendon Roger E. , Murphy Susan K. , Hashizume Rintaro , Becher Oren J.
Published: April 2023

Percent DNA methylation and p16 expression changes with or without DNA methytransferase inhibition.
Supplemental Figure legends from Histone H3.3K27M Represses p16 to Accelerate Gliomagenesis in a Murine Model of DIPG
Authors: Cordero Francisco J. , Huang Zhiqing , Grenier Carole , He Xingyao , Hu Guo , McLendon Roger E. , Murphy Susan K. , Hashizume Rintaro , Becher Oren J.
Published: April 2023

Legends describing all supplemental figures.
Table S2 from T-Cell Deletion of MyD88 Connects IL17 and IκBζ to RAS Oncogenesis
Authors: Cataisson Christophe , Salcedo Rosalba , Michalowski Aleksandra M. , Klosterman Mary , Naik Shruti , Li Luowei , Pan Michelle J. , Sweet Amalia , Chen Jin-Qiu , Kostecka Laurie G. , Karwan Megan , Smith Loretta , Dai Ren-Ming , Stewart C. Andrew , Lyakh Lyudmila , Hsieh Wang-Ting , Khan Asra , Yang Howard , Lee Maxwell , Trinchieri Giorgio , Yuspa Stuart H.
Published: April 2023

Supplemental table 2: List of genes from RNA profiling, the expression of which is significantly affected (by at least 1.5-fold change and FDR <10%) by IL-17 in RAS-keratinocytes.
EZH2 inhibitors are not effective against H3.3K27M tumor cells from Histone H3.3K27M Represses p16 to Accelerate Gliomagenesis in a Murine Model of DIPG
Authors: Cordero Francisco J. , Huang Zhiqing , Grenier Carole , He Xingyao , Hu Guo , McLendon Roger E. , Murphy Susan K. , Hashizume Rintaro , Becher Oren J.
Published: April 2023

A. Positive (Hoxa11) and negative (actin) promoter control loci for H3K27me3 ChIP-qPCR. B. H3K27me3 ChIP-qPCR analysis of murine tumor cells on downstream p16 exon 1α and exon 2. C. Histone extraction western blot of H3.3K27M-GFP and H3.3WT-GFP expressing murine tumor lines treated with 1μM EPZ-6438 for 7 days. D. H3K4me3 ChIP-qPCR analyzing the p16 promoter region with or without 7 day GSK343 treatment (p= 0.035 by paired t-test) E. 21 day treatment with EZH2 inhibitor GSK343 followed by qPCR for p16 expression (p=0.036) F. BrdU incorporation on H3.3K27M-GFP and H3.3WT-GFP expressing murine tumor lines with EZH2 inhibitors GSK343 (p= 0.012), EPZ-6438, and GSK126 (p= 0.002) treatments incubated for 72hrs.
Supplementary Table S2 from Estrogen-Induced Apoptosis in Breast Cancers Is Phenocopied by Blocking Dephosphorylation of Eukaryotic Initiation Factor 2 Alpha (eIF2α) Protein
Authors: Sengupta Surojeet , Sevigny Catherine M. , Bhattacharya Poulomi , Jordan V. Craig , Clarke Robert
Published: April 2023

Details of Primary antibody sources
Supplementary Figure S6 from Estrogen-Induced Apoptosis in Breast Cancers Is Phenocopied by Blocking Dephosphorylation of Eukaryotic Initiation Factor 2 Alpha (eIF2α) Protein
Authors: Sengupta Surojeet , Sevigny Catherine M. , Bhattacharya Poulomi , Jordan V. Craig , Clarke Robert
Published: April 2023

Effect of salubrinal on MCF10A cells
Supplementary Figure S4 from Estrogen-Induced Apoptosis in Breast Cancers Is Phenocopied by Blocking Dephosphorylation of Eukaryotic Initiation Factor 2 Alpha (eIF2α) Protein
Authors: Sengupta Surojeet , Sevigny Catherine M. , Bhattacharya Poulomi , Jordan V. Craig , Clarke Robert
Published: April 2023

Similar Regulation of additional UPR genes by estrogen and salubrinal in MCF7:5C cells.
Supplemental Legends from Alectinib Resistance in ALK-Rearranged Lung Cancer by Dual Salvage Signaling in a Clinically Paired Resistance Model
Authors: Tsuji Takahiro , Ozasa Hiroaki , Aoki Wataru , Aburaya Shunsuke , Funazo Tomoko , Furugaki Koh , Yoshimura Yasushi , Ajimizu Hitomi , Okutani Ryoko , Yasuda Yuto , Nomizo Takashi , Uemasu Kiyoshi , Hasegawa Koichi , Yoshida Hironori , Yagi Yoshitaka , Nagai Hiroki , Sakamori Yuichi , Ueda Mitsuyoshi , Hirai Toyohiro , Kim Young Hak
Published: April 2023

Fig. S1. Supplementary data for Fig. 1 Fig. S2. Supplementary drug sensitivity data to ALK inhibitors in KTOR1 and KTOR1-RE. Fig. S3. Supplementary results of the phosphoproteome analysis Fig. S4. Saracatinib sensitized KTOR1-RE cells to crizotinib Fig. S5. Combined knockdown of MET and SRC inhibited proliferation and induces apoptosis Fig. S6. Supplementary data for Fig. 6 Table S1. Primer sequences for direct sequence of ALK exons Table S2. Primer sequences for detection and sequence of EML4-ALK rearrangement Table S3. Primer sequences for qRT-PCR
Supplementary Figure, Figure Legends, Tables and Material and Methods from The Codon 72 TP53 Polymorphism Contributes to TSC Tumorigenesis through the Notch–Nodal Axis
Authors: Cho Jun-Hung , Patel Bhaumik , Bonala Santosh , Mansouri Hossein , Manne Sasikanth , Vadrevu Surya Kumari , Ghouse Shanawaz , Kung Che-Pei , Murphy Maureen E. , Astrinidis Aristotelis , Henske Elizabeth P. , Kwiatkowski David J. , Markiewski Maciej M. , Karbowniczek Magdalena
Published: April 2023

S1. Expression of hamartin and p53 in mice. S2. CRISPR-Cas9 mediated editing of TP53 codon 72 in angiomyolipoma cells and the impact of R72 on Notch/Nodal axis. S3. Overexpression of Nodal in LAM. S4. Overexpression of Nodal in TSC-associated renal tumors. S5. R72 increases migration of angiomyolipoma cells. Supplementary Table S1. The frequency of TP53 codon 72 germline polymorphism in TSC and LAM patients. Supplementary Table S2. The frequency of TP53 R72 codon polymorphism in TSC and sporadic angiomyolipoma and TSC-associated RCC. Supplementary Table S3. The number of experimental mice used in study.
Supplemental Figures 1-7 from B-cell Receptor Signaling Regulates Metabolism in Chronic Lymphocytic Leukemia
Authors: Vangapandu Hima V. , Havranek Ondrej , Ayres Mary L. , Kaipparettu Benny Abraham , Balakrishnan Kumudha , Wierda William G. , Keating Michael J. , Davis R. Eric , Stellrecht Christine M. , Gandhi Varsha
Published: April 2023

Supplemental Figure 1. Graphical representation of extracellular flux stress profiles from a CLL patient. Supplemental Figure 2. Sorting BCR knockout cells from Cas9 transfected JeKo-1 cells. Supplemental Figure 3. Sorting PIK3CD knockout cells from Cas9 transfected JeKo-1 cells. Supplemental Figure 4. CLL OCR correlation with CD38 expression and age. Supplemental Figure 5. Effect of PI3K inhibitor (IPI-145 or duvelisib) on CLL metabolism. Supplemental Figure 6. Influence of duvelisib (IPI-145) treatment on nutrient uptake mitochondrial biology and functionalities in CLL lymphocytes. Supplemental Figure 7. Effect of AKT inhibitor (MK-2206) on CLL metabolism.
Tables S1-3 and Figures S1-4 from TAS6417/CLN-081 Is a Pan-Mutation–Selective EGFR Tyrosine Kinase Inhibitor with a Broad Spectrum of Preclinical Activity against Clinically Relevant EGFR Mutations
Authors: Udagawa Hibiki , Hasako Shinichi , Ohashi Akihiro , Fujioka Rumi , Hakozaki Yumi , Shibuya Mikiko , Abe Naomi , Komori Toshiharu , Haruma Tomonori , Terasaka Miki , Fujita Ryoto , Hashimoto Akihiro , Funabashi Kaoru , Yasuda Hiroyuki , Miyadera Kazutaka , Goto Koichi , Costa Daniel B. , Kobayashi Susumu S.
Published: April 2023

Supplementary Table 1. IC50 values of Ba/F3 cells expressing common mutations in the presence or absence of the T790M to EGFR TKIs tested. Supplementary Table 2. IC50 values of Ba/F3 cells expressing uncommon mutations in the presence or absence of the T790M to EGFR TKIs tested. Supplementary Table 3. IC50 values of Ba/F3 cells expressing EGFR ins20 mutations to EGFR TKIs tested. Supplementary Figure 1. Western blot analysis showing the effects of increasing concentration of poziotinib, TAS6417, afatinib, or osimertinib, in NHEK-Neo cells. Supplementary Figure 2. TAS6417 exhibits slow-dissociation kinetics. Supplementary Figure 3. TAS6417 induces apoptosis in EGFR mutant cell lines but not in normal cells. Supplementary Figure 4. TAS6417 suppresses the growth of tumors driven by EGFR G719A+T790M.
Supplementary Figure 4 from Intron 1–Mediated Regulation of EGFR Expression in EGFR-Dependent Malignancies Is Mediated by AP-1 and BET Proteins
Authors: Jameson Nathan M. , Ma Jianhui , Benitez Jorge , Izurieta Alejandro , Han Jee Yun , Mendez Robert , Parisian Alison , Furnari Frank
Published: April 2023

Supplementary figure 4 shows the de novo motif generation and validation of AP-1 factors in ENCODE data. It also shows JunDN effects on EGFR in U87 cells.
Supplementary Figure 2 from Intron 1–Mediated Regulation of EGFR Expression in EGFR-Dependent Malignancies Is Mediated by AP-1 and BET Proteins
Authors: Jameson Nathan M. , Ma Jianhui , Benitez Jorge , Izurieta Alejandro , Han Jee Yun , Mendez Robert , Parisian Alison , Furnari Frank
Published: April 2023

Supplementary figure 2 shows the segmentation of intron 1 for luciferase reporter assays
Supplementary figures from The Landscape of Isoform Switches in Human Cancers
Authors: Vitting-Seerup Kristoffer , Sandelin Albin
Published: April 2023

Figure S1A: Extent of isoform switching across cancer types. Figure S1B: Extent of isoform switch usage in any cancer type. Figure S1C: Fraction of isoform switches with consequence. Figure S1D: Funtional enrichment analysis. Figure S1E: Global analysis of isoform fraction. Figure S2A: Extent of predicted functional consequences. Figure S2B: Background distribution of protein domain gain/loss. Figure S2C: Co-occurrence of consequences. Figure S2D: Definition of non-coding transcripts. Figure S2E: Difference in length of isoforms in an isoform switch. Figure S3A: Loss vs. gain of protein domain analysis. Figure S3B: Interaction network of genes involved in pan-cancer isoform switches. Figure S4: Figure S3B: Interaction network of genes involved in pan-cancer isoform switches. Figure S5A: Tools for identification of differential full-length isoform usage. Figure S5B: Isoform switch in insulin receptor. Figure S6A: Generation of high-qulaity data. Figure S6B: Assessment of CPAT cutoffs. Figure S6C. ORF prediction accuracy.
Supplementary Methods from Discrete Adaptive Responses to MEK Inhibitor in Subpopulations of Triple-Negative Breast Cancer
Authors: Goulet Daniel R. , Foster Joseph P. , Zawistowski Jon S. , Bevill Samantha M. , Noël Mélodie P. , Olivares-Quintero José F. , Sciaky Noah , Singh Darshan , Santos Charlene , Pattenden Samantha G. , Davis Ian J. , Johnson Gary L.
Published: April 2023

Supplementary Methods
Figure S5 from Discrete Adaptive Responses to MEK Inhibitor in Subpopulations of Triple-Negative Breast Cancer
Authors: Goulet Daniel R. , Foster Joseph P. , Zawistowski Jon S. , Bevill Samantha M. , Noël Mélodie P. , Olivares-Quintero José F. , Sciaky Noah , Singh Darshan , Santos Charlene , Pattenden Samantha G. , Davis Ian J. , Johnson Gary L.
Published: April 2023

Wild-type KRAS is Amplified in Trametinib Resistant POS Cells Following Dose Escalation.
Supplemental Tables 1 - 3 from Identification and Characterization of Oncogenic SOS1 Mutations in Lung Adenocarcinoma
Authors: Cai Diana , Choi Peter S. , Gelbard Maya , Meyerson Matthew
Published: April 2023

Table S1. Mutageneis primers Table S2. shRNA sequences Table S3. Significantly enriched gene sets for SOS1 N233Y vs. SOS1 WT from gene set enrichment analysis
Table S3 from Digital PCR-Based T-cell Quantification–Assisted Deconvolution of the Microenvironment Reveals that Activated Macrophages Drive Tumor Inflammation in Uveal Melanoma
Authors: de Lange Mark J. , Nell Rogier J. , Lalai Rajshri N. , Versluis Mieke , Jordanova Ekaterina S. , Luyten Gre P.M. , Jager Martine J. , van der Burg Sjoerd H. , Zoutman Willem H. , van Hall Thorbald , van der Velden Pieter A.
Published: April 2023

Amplicon sequences
Figure S5 from CREBBP/EP300 Bromodomain Inhibition Affects the Proliferation of AR-Positive Breast Cancer Cell Lines
Authors: Garcia-Carpizo Veronica , Ruiz-Llorente Sergio , Sarmentero Jacinto , González-Corpas Ana , Barrero Maria J.
Published: April 2023

Selection of direct target genes of CREBBP/EP300 bromodomain inhibitors in MDA-MB-453. (a) Overlap of CBP30 downregulated genes in the GSEA leading edge of the Doane's (DOANE), CBP30 downregulated genes in the GSEA leading edge of the Farmer's (FARMER) signature, genes associated with SEs and occupied by AR (AR) in MDA-MB-453. (b) Genomic tracks showing the levels of H3K27ac and AR in MDA-MB-453 surrounding selected genes. Intervals corresponding to SEs are also shown. Grey boxes show the location of the amplified genomic regions in the ChIP-qPCR experiments (c) Expression of selected genes in the indicated cell lines and treatments according to our RNA-seq data.
Table S2 from Digital PCR-Based T-cell Quantification–Assisted Deconvolution of the Microenvironment Reveals that Activated Macrophages Drive Tumor Inflammation in Uveal Melanoma
Authors: de Lange Mark J. , Nell Rogier J. , Lalai Rajshri N. , Versluis Mieke , Jordanova Ekaterina S. , Luyten Gre P.M. , Jager Martine J. , van der Burg Sjoerd H. , Zoutman Willem H. , van Hall Thorbald , van der Velden Pieter A.
Published: April 2023

Tumor T-cell count
Supplementary Figures 1-7 from A Ca2+-ATPase Regulates E-cadherin Biogenesis and Epithelial–Mesenchymal Transition in Breast Cancer Cells
Authors: Dang Donna K. , Makena Monish Ram , Llongueras José P. , Prasad Hari , Ko Myungjun , Bandral Manuj , Rao Rajini
Published: April 2023

S1. SPCA2 is transcriptionally linked with E-cadherin in breast cancer. S2. Selective effects of SPCA gene knockdown on protein expression. S3. SPCA1 expression in breast cancer cell lines. S4. SPCA2 alters expression of cancer stem cell gene markers. S5. Transcriptional links between EMT-associated genes and SPCA. S6. SPCA2 suppresses mesenchymal markers in multiple breast cancer cell lines. S7. SPCA2 suppresses metastasis of MDA-MB-231 cells in vivo.
Supplementary Figure S6 from Genetic and Epigenetic Characterization of Growth Hormone–Secreting Pituitary Tumors
Authors: Välimäki Niko , Schalin-Jäntti Camilla , Karppinen Atte , Paetau Anders , Kivipelto Leena , Aaltonen Lauri A. , Karhu Auli
Published: April 2023

Supplementary Figure S6 shows Ki-67- and PTTG1 immunostainings.
Supplementary Table S2 from HBx-K130M/V131I Promotes Liver Cancer in Transgenic Mice via AKT/FOXO1 Signaling Pathway and Arachidonic Acid Metabolism
Authors: Chiu Amy P. , Tschida Barbara R. , Sham Tung-Ting , Lo Lilian H. , Moriarity Branden S. , Li Xiao-Xiao , Lo Regina C. , Hinton David E. , Rowlands Dewi K. , Chan Chi-On , Mok Daniel K.W. , Largaespada David A. , Warner Nadia , Keng Vincent W.
Published: April 2023

Supplementary Table S2. KEGG canonical signaling pathways and metabolic pathways.
Supplementary Figure S3 from HBx-K130M/V131I Promotes Liver Cancer in Transgenic Mice via AKT/FOXO1 Signaling Pathway and Arachidonic Acid Metabolism
Authors: Chiu Amy P. , Tschida Barbara R. , Sham Tung-Ting , Lo Lilian H. , Moriarity Branden S. , Li Xiao-Xiao , Lo Regina C. , Hinton David E. , Rowlands Dewi K. , Chan Chi-On , Mok Daniel K.W. , Largaespada David A. , Warner Nadia , Keng Vincent W.
Published: April 2023

Supplementary Figure S3. RNA sequencing result of HBx-B Mut tumours against peripheral normal tissues.
Supplementary Figures 1-6, Supplemental Table 1 from Discovery and Characterization of Recurrent, Targetable ALK Fusions in Leiomyosarcoma
Authors: Davis Lara E. , Nusser Kevin D. , Przybyl Joanna , Pittsenbarger Janét , Hofmann Nicolle E. , Varma Sushama , Vennam Sujay , Debiec-Rychter Maria , van de Rijn Matt , Davare Monika A.
Published: April 2023

Supplementary Figure S1. ALK copy number data from TCGA-FX-A48G and TCGA-IW-A3M6 LMS visualized using IGV (Broad, MIT) Supplementary Table S1. Identification of ALK rearrangements using ChimeraScan algorithm. Supplementary Figure S2. Results from the fusion analysis pipeline run on RNA-seq data for TCGA-FX-A48G identifying KANK2-ALK Supplementary Figure S3. Results from the fusion analysis pipeline run on RNA-seq data for TCGA-IW-A3M6 identifying ACTG2-ALK Supplementary Figure S4. Confirmation of KANK2-ALK transgene expression from transformed Ba/F3 cells. Supplementary Figure S5. Dose-response inhibitor assay with ALK inhibitors with Ba/F3 parental cells in presence of IL-3 Supplementary Figure S6. Body weight of mice treated with vehicle, crizotinib or lorlatinib
Supplementary Figure 1 from Epigenetic Suppression of SERPINB1 Promotes Inflammation-Mediated Prostate Cancer Progression
Authors: Lerman Irina , Ma Xiaoting , Seger Christina , Maolake Aerken , Garcia-Hernandez Maria de la Luz , Rangel-Moreno Javier , Ackerman Jessica , Nastiuk Kent L. , Susiarjo Martha , Hammes Stephen R.
Published: April 2023

Supplementary Figure 1. SERPINB1 expression is reduced in Pten-null compared to wild type mouse prostates.
Supplementary Tables S1-S5 from The Clonal Evolution of Metastatic Osteosarcoma as Shaped by Cisplatin Treatment
Authors: Brady Samuel W. , Ma Xiaotu , Bahrami Armita , Satas Gryte , Wu Gang , Newman Scott , Rusch Michael , Putnam Daniel K. , Mulder Heather L. , Yergeau Donald A. , Edmonson Michael N. , Easton John , Alexandrov Ludmil B. , Chen Xiang , Mardis Elaine R. , Wilson Richard K. , Downing James R. , Pappo Alberto S. , Raphael Benjamin J. , Dyer Michael A. , Zhang Jinghui
Published: April 2023

Osteosarcoma clinical history and capture validation sequencing data. Supplementary Table S1. Sample and treatment information for relapsed osteosarcoma patients. Supplementary Table S2. SJOS0011101 SNVs detected by capture validation and tumor purity. Supplementary Table S3. SJOS0011105 SNVs detected by capture validation and tumor purity. Supplementary Table S4. SJOS0011107 SNVs detected by capture validation and tumor purity. Supplementary Table S5. SJOS010 SNVs detected by capture validation and tumor purity.
Supplementary Tables 1-9, 11, 13-15 from Loss of MAP3K7 Sensitizes Prostate Cancer Cells to CDK1/2 Inhibition and DNA Damage by Disrupting Homologous Recombination
Authors: Washino Satoshi , Rider Leah C. , Romero Lina , Jillson Lauren K. , Affandi Trisiani , Ohm Angela M. , Lam Elaine T. , Reyland Mary E. , Costello James C. , Cramer Scott D.
Published: April 2023

Tables s1-9, 11, 13-15. These tables provide statistical data, gene list, and results from TRAP and GSEA that support the conclusions of the manuscript and provide full disclosure of our results.
Supplementary Table 12 from Loss of MAP3K7 Sensitizes Prostate Cancer Cells to CDK1/2 Inhibition and DNA Damage by Disrupting Homologous Recombination
Authors: Washino Satoshi , Rider Leah C. , Romero Lina , Jillson Lauren K. , Affandi Trisiani , Ohm Angela M. , Lam Elaine T. , Reyland Mary E. , Costello James C. , Cramer Scott D.
Published: April 2023

Table S12 shows quantitative statistical data from the curves presented in figure 4.
Supplementary Table 10 from Loss of MAP3K7 Sensitizes Prostate Cancer Cells to CDK1/2 Inhibition and DNA Damage by Disrupting Homologous Recombination
Authors: Washino Satoshi , Rider Leah C. , Romero Lina , Jillson Lauren K. , Affandi Trisiani , Ohm Angela M. , Lam Elaine T. , Reyland Mary E. , Costello James C. , Cramer Scott D.
Published: April 2023

Table S10 shows IC50 and statistical data from several drugs tested that are presented in figure 1