bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Table S2 from NSD1 Inactivation and SETD2 Mutation Drive a Convergence toward Loss of Function of H3K36 Writers in Clear Cell Renal Cell Carcinomas
Authors: Su Xiaoping , Zhang Jianping , Mouawad Roger , Compérat Eva , Rouprêt Morgan , Allanic Frederick , Parra Jérôme , Bitker Marc-Olivier , Thompson Erika J. , Gowrishankar Banumathy , Houldsworth Jane , Weinstein John N. , Tost Jorg , Broom Bradley M. , Khayat David , Spano Jean-Philippe , Tannir Nizar M. , Malouf Gabriel G.
Published: April 2023

List of 369 probe sets defining the C-CIMP (CpG island methylator phenotype) in ccRCCs, including mean beta-values of those in C-CIMP (cluster 3) versus no-CIMP (cluster 2). Expression values as well as fold-changes of gene expression of those genes are also reported.
Figure S1 from Genomic Status of MET Potentiates Sensitivity to MET and MEK Inhibition in NF1-Related Malignant Peripheral Nerve Sheath Tumors
Authors: Peacock Jacqueline D. , Pridgeon Matthew G. , Tovar Elizabeth A. , Essenburg Curt J. , Bowman Megan , Madaj Zachary , Koeman Julie , Boguslawski Elissa A. , Grit Jamie , Dodd Rebecca D. , Khachaturov Vadim , Cardona Diana M. , Chen Mark , Kirsch David G. , Maina Flavio , Dono Rosanna , Winn Mary E. , Graveel Carrie R. , Steensma Matthew R.
Published: April 2023

Histological and MET copy number changes during MPNST progression.
Figure S1 from TRPM2 Mediates Neutrophil Killing of Disseminated Tumor Cells
Authors: Gershkovitz Maya , Caspi Yaki , Fainsod-Levi Tanya , Katz Ben , Michaeli Janna , Khawaled Saleh , Lev Shaya , Polyansky Lola , Shaul Merav E. , Sionov Ronit V. , Cohen-Daniel Leonor , Aqeilan Rami I. , Shaul Yoav D. , Mori Yasuo , Karni Rotem , Fridlender Zvi G. , Binshtok Alexander M. , Granot Zvi
Published: April 2023

Supplemental Figure S1. BAPTA protects tumor cells from H2O2 induced cell death. A. Extent of H2O2 (25 μM) cytotoxicity time course in 4T1 B. Annexin-V/PI analysis of vehicle and H2O2 treated (25 μM) 4T1 cells following overnight incubation. C. Effect of BAPTA-AM (5μM) on viability of 4T07, MC38, LLC, FARN and AT3 cells. D. Effect of BAPTA-AM (5μM) on neutrophil cytotoxicity in 4T07, MC38, LLC, FARN and AT3 cells. **p<0.01.
Supplementary Figures from Whole-Genome Sequencing Reveals Elevated Tumor Mutational Burden and Initiating Driver Mutations in African Men with Treatment-Naïve, High-Risk Prostate Cancer
Authors: Jaratlerdsiri Weerachai , Chan Eva K.F. , Gong Tingting , Petersen Desiree C. , Kalsbeek Anton M.F. , Venter Philip A. , Stricker Phillip D. , Bornman M.S. Riana , Hayes Vanessa M.
Published: April 2023

Supplementary Fig. S1 Transition and transversion rates of somatic SNVs observed among six SAPCS patients. Ti and Tv indicate transitional and transversional changes, respectively. Supplementary Fig. S2 Genomic rearrangements between African and European cohorts. A, Those observed for deletions (DEL), inter-chromosomal translocations (CTX), inversions (INV) and tandem duplications (DUP). B, Those observed for the four following types of large deletions: chromosomal deletions (CD), exon losses (EL), splice acceptor variant (SA), and splice donor variant (SD). Supplementary Fig. S3 Complex genomic rearrangements. A, Circos plots depicting coordinated chained events of chromoplexy in SAPCS (n = 1/6) and APCRCEUR (n = 5/9). Somatic copy number gains (red) and losses (blue) are depicted in the inner ring, while chromoplexic events between chromosomes are linked with blue lines and rearrangements not assigned to a chained event are depicted as gray lines within the plot. B, Maximal chromothriptic scores observed among tumor-matched blood pairs of SAPCS and APCRCEUR cohorts. Tumors with a ShatterProof score over 0.39 are defined as having chromothriptic characteristics; two from the APCRC are 0.43 and 0.44, which are higher than scores from their matched blood. Supplementary Fig. S4 Recurrent somatic aberrations within SAPCS, compared to AAPC (African American), TCGA, and COSMIC prostate cancer datasets. Genes or chromosome regions affected are shown next to oncoplots, with the total number of mutations within SAPCS tumors in the rightmost column. Note that a multiple hit accounts for more than one count. Abbreviations include: TFBS, transcription factor binding site; DHS, DNase I hypersensitive site; and CN, copy number. Supplementary Fig. S5 Unsupervised hierarchical clustering of SCNA segmented data observed within this study and the Memorial Sloan Kettering Cancer Center cohort (MSKCC; n = 157 primary tumors). Selected genomic regions indicative of copy number subtypes are labeled. Each column represents a genomic region. Ward's clustering with the Manhattan distance metric was applied to cluster the rows (patients) with consensus clustering. PGA, percentage of genome alteration. Supplementary Fig. S6 Model of prostate carcinogenesis among patients of African ancestry. Tajima's D statistic per chromosome of somatic SNVs present in each clone or subclone across six study participants was computed and averaged using VCFtools (Danecek et al, 2011). Abbreviations: AR, androgen receptor; PI3K, phosphoinositide 3-kinase; WNT, canonical wingless-type MMTV integration site family.
Figure S7 from Spliceosome Mutations Induce R Loop-Associated Sensitivity to ATR Inhibition in Myelodysplastic Syndromes
Authors: Nguyen Hai Dang , Leong Wan Yee , Li Weiling , Reddy Pavankumar N.G. , Sullivan Jack D. , Walter Matthew J. , Zou Lee , Graubert Timothy A.
Published: April 2023

Immunofluorescence staining of gH2AX DNA damage marker in human CD34+ hematopoietic progenitor cells.
Figure S5 from Spliceosome Mutations Induce R Loop-Associated Sensitivity to ATR Inhibition in Myelodysplastic Syndromes
Authors: Nguyen Hai Dang , Leong Wan Yee , Li Weiling , Reddy Pavankumar N.G. , Sullivan Jack D. , Walter Matthew J. , Zou Lee , Graubert Timothy A.
Published: April 2023

RNA splicing perturbation in cells confers sensitivity to ATR inhibitors.
Figure S3 from Reduced Expression of PROX1 Transitions Glioblastoma Cells into a Mesenchymal Gene Expression Subtype
Authors: Goudarzi Kaveh M. , Espinoza Jaime A. , Guo Min , Bartek Jiri , Nistér Monica , Lindström Mikael S. , Hägerstrand Daniel
Published: April 2023

Identification of novel binding partners for PROX1 protein
Supplementary Figure S7 from Amplification of Glyceronephosphate O-Acyltransferase and Recruitment of USP30 Stabilize DRP1 to Promote Hepatocarcinogenesis
Authors: Gu Li , Zhu Yahui , Lin Xi , Li Yajun , Cui Kaisa , Prochownik Edward V. , Li Youjun
Published: April 2023

Supplementary Figure S7 shows that GNPAT expression in HCC cells without GNPAT amplification is transcriptionally regulated by the complex composed of Myc and KDM1A.
Supplementary Information from Recurrent RARB Translocations in Acute Promyelocytic Leukemia Lacking RARA Translocation
Authors: Osumi Tomoo , Tsujimoto Shin-ichi , Tamura Moe , Uchiyama Meri , Nakabayashi Kazuhiko , Okamura Kohji , Yoshida Masanori , Tomizawa Daisuke , Watanabe Akihiro , Takahashi Hiroyuki , Hori Tsukasa , Yamamoto Shohei , Hamamoto Kazuko , Migita Masahiro , Ogata-Kawata Hiroko , Uchiyama Toru , Kizawa Hiroe , Ueno-Yokohata Hitomi , Shirai Ryota , Seki Masafumi , Ohki Kentaro , Takita Junko , Inukai Takeshi , Ogawa Seishi , Kitamura Toshio , Matsumoto Kimikazu , Hata Kenichiro , Kiyokawa Nobutaka , Goyama Susumu , Kato Motohiro
Published: April 2023

Supplementary Methods: IRB approval, Genomic analysis, Identification of translocations and determination of their breakpoints, Plasmids Construct, Cell line and reagent, Co-immunoprecipotation and immunoblotting analysis, Luciferase assay, Retrovirus production and transduction, FCM and Morphologic analysis, Human CB cell culture, and Colony replating assay. Supplementary Tables: Table 1. Clinical characteristics of RARA translocation negative APL cases. Table 2. BAC clones for FISH used in this study. Table 3. Primer sequences. Table 4. Somatic mutations observed in RARA-negative APL cases. Supplementary Figures: Figure 1. Morphologic feature and FISH analyisis for RARB translocations. Figure 2. Event-free survival of RARA-negative APL. Figure 3. Determination of TBL1XR1 mutated allele by allele-specific PCR. Figure 4. Constructs of TBL1XR1-RARB and other RARA fusions. Figure 5. Morphologic change in U937. Figure 6. Colony replating assay with mouse bone marrow. Figure 7. Colony replating assay with human cord blood.
Movie S3 from Emerin Deregulation Links Nuclear Shape Instability to Metastatic Potential
Authors: Reis-Sobreiro Mariana , Chen Jie-Fu , Novitskaya Tatiana , You Sungyong , Morley Samantha , Steadman Kenneth , Gill Navjot Kaur , Eskaros Adel , Rotinen Mirja , Chu Chia-Yi , Chung Leland W.K. , Tanaka Hisashi , Yang Wei , Knudsen Beatrice S. , Tseng Hsian-Rong , Rowat Amy C. , Posadas Edwin M. , Zijlstra Andries , Di Vizio Dolores , Freeman Michael R.
Published: April 2023

DU145 DIAPH3-depleted cells shed EV. Time-lapse analysis of DU145 DIAPH3-depleted cells treated with EGF and IL6 (exacerbates amoeboid features (13)) and stained with CellMask Orange. The cells were recorded over a period of 135s.
Figure S6 from Mammary Precancerous Stem and Non-Stem Cells Evolve into Cancers of Distinct Subtypes
Authors: Bu Wen , Liu Zhenyu , Jiang Weiyu , Nagi Chandandeep , Huang Shixia , Edwards Dean P. , Jo Eunji , Mo Qianxing , Creighton Chad J. , Hilsenbeck Susan G. , Leavitt Andrew D. , Lewis Michael T. , Wong Stephen T. C. , Li Yi
Published: April 2023

Wnt1 gene expression in KRT6A+ and WAP+ cells in MMTV-Wnt1 precancerous mammary glands.
Table S10, Table S11 from Transcriptomic Differences between Primary Colorectal Adenocarcinomas and Distant Metastases Reveal Metastatic Colorectal Cancer Subtypes
Authors: Kamal Yasmin , Schmit Stephanie L. , Hoehn Hannah J. , Amos Christopher I. , Frost H. Robert
Published: April 2023

Table S10. Gene overlap between the REACTOME_INFLUENZA_VIRAL_RNA_TRANSCRIPTION_AND_REPLICATION pathway and selected other pathways in the C2 collection. Table S11. Gene overlap between the HALLMARK_MYOGENESIS and HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION pathways.
Supplementary Data File 4 from Integrative Pharmacogenomics Analysis of Patient-Derived Xenografts
Authors: Mer Arvind S. , Ba-Alawi Wail , Smirnov Petr , Wang Yi X. , Brew Ben , Ortmann Janosch , Tsao Ming-Sound , Cescon David W. , Goldenberg Anna , Haibe-Kains Benjamin
Published: April 2023

Pathway stability in PDXs across passages for Reactome pathway sets.
Table 1 from Poly (ADP) Ribose Glycohydrolase Can Be Effectively Targeted in Pancreatic Cancer
Authors: Jain Aditi , Agostini Lebaron C. , McCarthy Grace A. , Chand Saswati N. , Ramirez AnnJosette , Nevler Avinoam , Cozzitorto Joseph , Schultz Christopher W. , Lowder Cinthya Yabar , Smith Kate M. , Waddell Ian D. , Raitses-Gurevich Maria , Stossel Chani , Gorman Yulia Glick , Atias Dikla , Yeo Charles J. , Winter Jordan M. , Olive Kenneth P. , Golan Talia , Pishvaian Michael J. , Ogilvie Donald , James Dominic I. , Jordan Allan M. , Brody Jonathan R.
Published: April 2023

Supplementary Table 1 describes BRCA and KRAS status of PDX models and IC50 of PDDX-001 and olaparib in PDAC/PDX lines
Figure S6 from Poly (ADP) Ribose Glycohydrolase Can Be Effectively Targeted in Pancreatic Cancer
Authors: Jain Aditi , Agostini Lebaron C. , McCarthy Grace A. , Chand Saswati N. , Ramirez AnnJosette , Nevler Avinoam , Cozzitorto Joseph , Schultz Christopher W. , Lowder Cinthya Yabar , Smith Kate M. , Waddell Ian D. , Raitses-Gurevich Maria , Stossel Chani , Gorman Yulia Glick , Atias Dikla , Yeo Charles J. , Winter Jordan M. , Olive Kenneth P. , Golan Talia , Pishvaian Michael J. , Ogilvie Donald , James Dominic I. , Jordan Allan M. , Brody Jonathan R.
Published: April 2023

Supplementary Figure S6 describes cleaved caspase 3 expression and quantitation of H2AX foci in MIA PaCa-2 after combination of PDDX-001 and oxaliplatin.
Figure S6: PMTRIP FISH-PLA can quantify COX-2-TIAR interactions in lung tissue. from Quantification and Localization of Protein–RNA Interactions in Patient-Derived Archival Tumor Tissue
Authors: Blanchard Emmeline L. , Argyropoulou Danae , Zurla Chiara , Bhosle Sushma M. , Vanover Daryll , Santangelo Philip J.
Published: April 2023

Supplementary Figure 6: PMTRIP FISH-PLA can quantify COX-2-TIAR interactions in lung tissue. A) 20 nM of V5 tagged PMTRIPs targeting COX-2 mRNA were delivered as FISH probes to colon cancer samples. PLA (green) was performed between the V5 tag and TIAR. 20x cropped image is indicated by the white box. Extended focus images are shown, with a 1 mm scale bar for full tissue. B) Extended focus images of FISH-PLA (green) controls are shown. Scale bar is 1 mm. C) Extended focus cropped images of full tissues in (A) are indicated by white boxes. Scale bars are 100 μm. D) Extended focus image of cancer tissue FISH-PLA at 63x is also shown. Scale bars for (D) are 10 μm. E) Extended focus cropped images of full tissues in (B) are indicated by white boxes. Extended focus images of tissue FISH-PLA at 63x are also shown. COX-2 FISH shown in red. Scale bars are 100 μm for 20x and 10 μm for 63x images. F) Quantification of PLA signal in (A,B). Statistics were performed with a one-way ANOVA with a Tukey's multiple comparisons test, where n=3 and * p < 0.015 and ** p < 0.0077. Standard deviations are shown in red.
Supplementary Figure S6. Ionizing radiation induces micronuclei formation in both WT and STING-/- MEFs. from STING Promotes Homeostasis via Regulation of Cell Proliferation and Chromosomal Stability
Authors: Ranoa Diana Rose E. , Widau Ryan C. , Mallon Stephen , Parekh Akash D. , Nicolae Claudia M. , Huang Xiaona , Bolt Michael J. , Arina Ainhoa , Parry Renate , Kron Stephen J. , Moldovan George-Lucian , Khodarev Nikolai N. , Weichselbaum Ralph R.
Published: April 2023

WT and STING-/- MEFs examined by cytokinesis-block micronucleus (CBMN) assay by treatment with IR, then cytochalasin at 24 hours and then fixed and stained for DNA and mitochondrial/cytoplasmic compartments using Draq5 and MitoTracker Red at 48 hours. Scale bar, 10 µm.
Table S3 from Spatiotemporal Regulation of ΔNp63 by TGFβ-Regulated miRNAs Is Essential for Cancer Metastasis
Authors: Bui Ngoc H.B. , Napoli Marco , Davis Andrew John , Abbas Hussein A. , Rajapakshe Kimal , Coarfa Cristian , Flores Elsa R.
Published: April 2023

Table S3. List of 64 TGFÃŽÂ²-induced microRNAs that are predicted to have binding sites to 3'UTR of p63 by miRWalk algorithm.
Table S5 : lists of differentially methylated regions in Lgr5-GFP+ cells from Loss of Apc Rapidly Impairs DNA Methylation Programs and Cell Fate Decisions in Lgr5+ Intestinal Stem Cells
Authors: Bruschi Marco , Garnier Laure , Cleroux Elouan , Giordano Alicia , Dumas Michael , Bardet Anaïs F. , Kergrohen Thomas , Quesada Stanislas , Cesses Pierre , Weber Michael , Gerbe François , Jay Philippe
Published: April 2023

This file contains the lists of DMR found by RRBS in FACS-sorted ApcHET- and ApcKO-Lgr5-GFP cells.
Supplementary Data and methods from Loss of Apc Rapidly Impairs DNA Methylation Programs and Cell Fate Decisions in Lgr5+ Intestinal Stem Cells
Authors: Bruschi Marco , Garnier Laure , Cleroux Elouan , Giordano Alicia , Dumas Michael , Bardet Anaïs F. , Kergrohen Thomas , Quesada Stanislas , Cesses Pierre , Weber Michael , Gerbe François , Jay Philippe
Published: April 2023

This file contains supplementary data figures and methods. Supplementary figure S1 shows accumulation of Lgr5+-GFP+ ISCs following Apc inactivation. Supplementary figure S2 describes the aberrant gene expression program triggered by the loss of Apc function in Lgr5+ ISCs and their immediate progenitor daughter cells Supplementary figure S3 identifies the focal alterations in DNA methylation that are produced upon Apc loss of function in GFP+ cells. Supplementary figure S4 demonstrates that de novo DNA methylation critically contributes to homeostatic rupture upon Apc loss. Supplementary figure S5 shows the role of the Alk-pSmad1/5/8 axis in the responsiveness to BMP signalling in ApcKO miniguts.
Figure S4 from Nicotinamide Phosphoribosyltransferase Acts as a Metabolic Gate for Mobilization of Myeloid-Derived Suppressor Cells
Authors: Travelli Cristina , Consonni Francesca Maria , Sangaletti Sabina , Storto Mariangela , Morlacchi Sara , Grolla Ambra A. , Galli Ubaldina , Tron Gian Cesare , Portararo Paola , Rimassa Lorenza , Pressiani Tiziana , Mazzone Massimiliano , Trovato Rosalinda , Ugel Stefano , Bronte Vincenzo , Tripodo Claudio , Colombo Mario P. , Genazzani Armando A. , Sica Antonio
Published: April 2023

NAMPT controls the suppressive activity of M-MDSCs
Figure S2 from Nicotinamide Phosphoribosyltransferase Acts as a Metabolic Gate for Mobilization of Myeloid-Derived Suppressor Cells
Authors: Travelli Cristina , Consonni Francesca Maria , Sangaletti Sabina , Storto Mariangela , Morlacchi Sara , Grolla Ambra A. , Galli Ubaldina , Tron Gian Cesare , Portararo Paola , Rimassa Lorenza , Pressiani Tiziana , Mazzone Massimiliano , Trovato Rosalinda , Ugel Stefano , Bronte Vincenzo , Tripodo Claudio , Colombo Mario P. , Genazzani Armando A. , Sica Antonio
Published: April 2023

NAMPT levels in conditional-deficient mice
Supplementary Data from Cytochrome c Deficiency Confers Apoptosome and Mitochondrial Dysfunction in African-American Men with Prostate Cancer
Authors: Kumar Rahul , Bhat Tariq A. , Walsh Elise M. , Chaudhary Ajay K. , O'Malley Jordan , Rhim Johng S. , Wang Jianmin , Morrison Carl D. , Attwood Kristopher , Bshara Wiam , Mohler James L. , Yadav Neelu , Chandra Dhyan
Published: April 2023

Supplementary Materials and Methods with detailed experimental procedures. Supplemental Table 1 shows the list of antibodies. Supplemental Table 2 shows the list of shRNAs and their sequences. Supplemental Table 3 shows the list of siRNAs and their sources.
Supplementary Data from Cytochrome c Deficiency Confers Apoptosome and Mitochondrial Dysfunction in African-American Men with Prostate Cancer
Authors: Kumar Rahul , Bhat Tariq A. , Walsh Elise M. , Chaudhary Ajay K. , O'Malley Jordan , Rhim Johng S. , Wang Jianmin , Morrison Carl D. , Attwood Kristopher , Bshara Wiam , Mohler James L. , Yadav Neelu , Chandra Dhyan
Published: April 2023

Supplementary Figures - Figure S1 shows CC expression in AA and CA PCa cells. Figure S2 shows cell death and DEVDase activity in AA and CA PCa cells in response to docetaxel treatment. Figure S3 shows effect of CC knockdown on docetaxel-induced apoptotic cell death, caspase-3 and PARP cleavage in CA PCa cells; and mtDNA content in AA and CA PCa cells. Figure S4 shows levels of Nrf1, c-Myc, NF-κB, and PGC-1α in AA and CA PCa cells; and shows cell death, DEVDase activity, and CC expression in response to docetaxel treatment in the presence of c-Myc and NF-κB inhibitors in AA PCa cells. Figure S5 shows effect of Nrf1 knockdown on DEVDase activity in response to docetaxel treatment in the presence of c-Myc and NF-κB inhibitors or AKT activator in AA PCa cells. Figure S6 shows effect of genetic inhibition of c-Myc, NF-κB and PTEN on CC expression and DEVDase activity after docetaxel treatment in AA PCa cells. Figure S7 shows levels of p-Drp1S616 and p-Drp1S637 in primary prostate tumor (PT) and matching non-tumor (MN) tissue samples from AA and CA PCa patients. Figure S8 shows effect of Drp1 knockdown on docetaxel-induced DEVDase activity and apoptosis in CA PCa cells. Figure S9 shows knockdown of Drp1 and CC in AA PCa cells and its effect on DEVDase activity in response to docetaxel treatment in the presence of c-Myc and NF-κB inhibitors or AKT activator. Figure S10 shows expression levels of oxidative phosphorylation (OXPHOS) complexes III, IV and V in primary prostate tumor (PT) and matching non-tumor (MN) tissue samples from AA and CA PCa patients. Figure S11 shows levels of LDHA in primary prostate tumor (PT) and matching non-tumor (MN) tissue samples from AA and CA PCa patients.
Supplementary Data from Retrodifferentiation of Human Tumor Hepatocytes to Stem Cells Leads to Metabolic Reprogramming and Chemoresistance
Authors: Fekir Karim , Dubois-Pot-Schneider Hélène , Désert Romain , Daniel Yoann , Glaise Denise , Rauch Claudine , Morel Fabrice , Fromenty Bernard , Musso Orlando , Cabillic Florian , Corlu Anne
Published: April 2023

Supporting Materials and Methods
Supplementary Figure 2 from CoA Synthase (COASY) Mediates Radiation Resistance via PI3K Signaling in Rectal Cancer
Authors: Ferrandon Sylvain , DeVecchio Jennifer , Duraes Leonardo , Chouhan Hanumant , Karagkounis Georgios , Davenport Jacqueline , Orloff Matthew , Liska David , Kalady Matthew F.
Published: April 2023

Evaluation of COASY expression predictive power
Supplementary Table 3 from Hispanic/Latino Patients with Gastric Adenocarcinoma Have Distinct Molecular Profiles Including a High Rate of Germline CDH1 Variants
Authors: Wang Sam C. , Yeu Yunku , Hammer Suntrea T.G. , Xiao Shu , Zhu Min , Hong Changjin , Clemenceau Jean R. , Yoon Lynn Y. , Nassour Ibrahim , Shen Jeanne , Agarwal Deepak , Reznik Scott I. , Mansour John C. , Yopp Adam C. , Zhu Hao , Hwang Tae Hyun , Porembka Matthew R.
Published: April 2023

Supplementary Table 3
Supplementary Figure 1 from A miRNA Expression Signature in Breast Tumor Tissue Is Associated with Risk of Distant Metastasis
Authors: Rohan Thomas E. , Wang Tao , Weinmann Sheila , Wang Yihong , Lin Juan , Ginsberg Mindy , Loudig Olivier
Published: April 2023

Supplementary Figure 1 shows Sample distribution in sequencing libraries
Supplementary Table 2 from Hispanic/Latino Patients with Gastric Adenocarcinoma Have Distinct Molecular Profiles Including a High Rate of Germline CDH1 Variants
Authors: Wang Sam C. , Yeu Yunku , Hammer Suntrea T.G. , Xiao Shu , Zhu Min , Hong Changjin , Clemenceau Jean R. , Yoon Lynn Y. , Nassour Ibrahim , Shen Jeanne , Agarwal Deepak , Reznik Scott I. , Mansour John C. , Yopp Adam C. , Zhu Hao , Hwang Tae Hyun , Porembka Matthew R.
Published: April 2023

Supplementary Table 2
Supplementary Data from The Interaction of Platelets with Colorectal Cancer Cells Inhibits Tumor Growth but Promotes Metastasis
Authors: Plantureux Léa , Mège Diane , Crescence Lydie , Carminita Estelle , Robert Stéphane , Cointe Sylvie , Brouilly Nicolas , Ezzedine Walid , Dignat-George Françoise , Dubois Christophe , Panicot-Dubois Laurence
Published: April 2023

supplementary figures 1 to 3: SF1 represents the aggregation of Colorectal cancer cells; SF2 concerns the expression of Cadherin 6 by colorectal cancer cell lines. SF3 depicts the involvement of Cadherin 6 in the interaction between platelets and colorectal cancer cells in static conditions. SF4 is a diagram summarizing the results described in this paper.
Supplementary Data from Therapy-Induced Senescence Drives Bone Loss
Authors: Yao Zhangting , Murali Bhavna , Ren Qihao , Luo Xianmin , Faget Douglas V. , Cole Tom , Ricci Biancamaria , Thotala Dinesh , Monahan Joseph , van Deursen Jan M. , Baker Darren , Faccio Roberta , Schwarz Julie K. , Stewart Sheila A.
Published: April 2023

Supplemental Figures
Figure S5 from CXCR4 in Tumor Epithelial Cells Mediates Desmoplastic Reaction in Pancreatic Ductal Adenocarcinoma
Authors: Morita Toshihiro , Kodama Yuzo , Shiokawa Masahiro , Kuriyama Katsutoshi , Marui Saiko , Kuwada Takeshi , Sogabe Yuko , Matsumori Tomoaki , Kakiuchi Nobuyuki , Tomono Teruko , Mima Atsushi , Ueda Tatsuki , Tsuda Motoyuki , Yamauchi Yuki , Nishikawa Yoshihiro , Sakuma Yojiro , Ota Yuji , Maruno Takahisa , Uza Norimitsu , Nagasawa Takashi , Chiba Tsutomu , Seno Hiroshi
Published: April 2023

Myofibroblasts secrete Cola 1a1 and Cxcl12 in tumor environment.
Supplementary Figure S7 from BACH1 Promotes Pancreatic Cancer Metastasis by Repressing Epithelial Genes and Enhancing Epithelial–Mesenchymal Transition
Authors: Sato Masaki , Matsumoto Mitsuyo , Saiki Yuriko , Alam Mahabub , Nishizawa Hironari , Rokugo Masahiro , Brydun Andrey , Yamada Shinji , Kaneko Mika K. , Funayama Ryo , Ito Mamoru , Kato Yukinari , Nakayama Keiko , Unno Michiaki , Igarashi Kazuhiko
Published: April 2023

BACH1 high expression is correlated with poor prognosis. Details are described in methods and legends file (Supplementary_methods_and_legends).
Supplementary Figure S4 from BACH1 Promotes Pancreatic Cancer Metastasis by Repressing Epithelial Genes and Enhancing Epithelial–Mesenchymal Transition
Authors: Sato Masaki , Matsumoto Mitsuyo , Saiki Yuriko , Alam Mahabub , Nishizawa Hironari , Rokugo Masahiro , Brydun Andrey , Yamada Shinji , Kaneko Mika K. , Funayama Ryo , Ito Mamoru , Kato Yukinari , Nakayama Keiko , Unno Michiaki , Igarashi Kazuhiko
Published: April 2023

Immunofluorescence staining of BACH1 and E-cadherin in AsPC-1/sgBACH1 cells and the expression amounts of BACH1 in pancreatic cancer cell line models used. Details are described in methods and legends file (Supplementary_methods_and_legends).
Figures S3 and S4 from The MEK5–ERK5 Kinase Axis Controls Lipid Metabolism in Small-Cell Lung Cancer
Authors: Cristea Sandra , Coles Garry L. , Hornburg Daniel , Gershkovitz Maya , Arand Julia , Cao Siqi , Sen Triparna , Williamson Stuart C. , Kim Jun W. , Drainas Alexandros P. , He Andrew , Cam Laurent Le , Byers Lauren Averett , Snyder Michael P. , Contrepois Kévin , Sage Julien
Published: April 2023

Related to Figure 3: Transcriptomic changes upon reduction of the MEK5-ERK5 axis in SCLC cells
Supplementary Movie 2 from An Engineered Tumor-on-a-Chip Device with Breast Cancer–Immune Cell Interactions for Assessing T-cell Recruitment
Authors: Aung Aereas , Kumar Vardhman , Theprungsirikul Jomkuan , Davey Shruti K. , Varghese Shyni
Published: April 2023

Supplementary Movie 2
Supplementary Data from Hypoxia Induces Transcriptional and Translational Downregulation of the Type I IFN Pathway in Multiple Cancer Cell Types
Authors: Miar Ana , Arnaiz Esther , Bridges Esther , Beedie Shaunna , Cribbs Adam P. , Downes Damien J. , Beagrie Robert A. , Rehwinkel Jan , Harris Adrian L.
Published: April 2023

supplementary figures and materials
Supplementary Data from Mass Spectrometry Imaging Enables Discrimination of Renal Oncocytoma from Renal Cell Cancer Subtypes and Normal Kidney Tissues
Authors: Zhang Jialing , Li Shirley Q. , Lin John Q. , Yu Wendong , Eberlin Livia S.
Published: April 2023

Supplementary Figures and Supplementary Figure legends. Supplementary Fig. 1.- Tandem mass spectrum of m/z 810.527 and the tentative assignment, Supplementary Fig. 2.- Tandem mass spectrum of m/z 723.478 and the tentative assignment, Supplementary Fig. 3.- Comparison of mass spectra of kidney cortex tissue sections from normal patient, Supplementary Fig. 4.- Comparison of mass spectra from normal patients which contain both cortex and medulla, Supplementary Fig. 5.- PCA analysis of normal kidney tissues containing both cortex and medulla and the biplot, Supplementary Fig. 6.- The graphical summary from PCA of cortex and medulla tissue for six selected ions, Supplementary Fig. 7.- Tandem mass spectrum of m/z 887.557 and the tentative assignment, Supplementary Fig. 8.- Tentative peak assignment for m/z 215.032, Supplementary Fig. 9.- Tandem mass spectrum of m/z 175.025 and the tentative assignment, Supplementary Fig. 10.- Tandem mass spectrum of m/z 885.547 and the tentative assignment, Supplementary Fig. 11.- Tandem mass spectrum of m/z 773.532 and the tentative assignment, Supplementary Fig. 12.- Tandem mass spectrum of m/z 766.538 and the tentative assignment, Supplementary Fig. 13.- Tandem mass spectrum of m/z 1035.772 and the tentative assignment, Supplementary Fig. 14.- Tandem mass spectrum of m/z 737.490 and the tentative assignment, Supplementary Fig. 15.- Tandem mass spectrum of m/z 464.314, m/z 697.482, and m/z 842.589 and the tentative assignment, Supplementary Fig. 16.- Tandem mass spectrum of m/z 306.077 and the tentative assignment, Supplementary Fig. 17.- Tandem mass spectrum of m/z 712.485 and the tentative assignment, Supplementary Fig. 18.- Mass spectrometric profile from normal kidney tissue at mass range from m/z 723 to m/z 728, Supplementary Fig. 19.- PCA analysis of averaged mass spectra of ROchRCC tissues and ccRCCppRCC tissues and the biplot. Supplementary Tables. Supplementary Table 1. m/z values selected by the lasso as important for characterizing normal kidney, RO and RCC, Supplementary Table 2. m/z values selected by the lasso as important for characterizing RO and chRCC, Supplementary Table 3. CL and PE related species selected by the lasso for characterizing RO and chRCC, Supplementary Table 4. m/z values selected by the lasso as important for characterizing three renal cancer subtypes (ccRCC, chRCC, and ppRCC), Supplementary Table 5. The top loading plots of PC1 and PC2 for PCA of cortex and medulla in normal kidney tissue, Supplementary Table 6. The top loading plots of PC1 and PC2 for PCA of ROchRCC vs ppRCCccRCC. Supplementary Data Supplementary Results, Supplementary Methods, Supplementary Discussion
Table S1 from Human Epidermal Growth Factor Receptor 2–Positive Breast Cancer Is Associated with Indigenous American Ancestry in Latin American Women
Authors: Marker Katie M. , Zavala Valentina A. , Vidaurre Tatiana , Lott Paul C. , Vásquez Jeannie Navarro , Casavilca-Zambrano Sandro , Calderón Mónica , Abugattas Julio E. , Gómez Henry L. , Fuentes Hugo A. , Picoaga Ruddy Liendo , Cotrina Jose M. , Neciosup Silvia P. , Castañeda Carlos A. , Morante Zaida , Valencia Fernando , Torres Javier , Echeverry Magdalena , Bohórquez Mabel E. , Polanco-Echeverry Guadalupe , Estrada-Florez Ana P. , Serrano-Gómez Silvia J. , Carmona-Valencia Jenny A. , Alvarado-Cabrero Isabel , Sanabria-Salas María Carolina , Velez Alejandro , Donado Jorge , Song Sikai , Cherry Daniel , Tamayo Lizeth I. , Huntsman Scott , Hu Donglei , Ruiz-Cordero Roberto , Balassanian Ronald , Ziv Elad , Zabaleta Jovanny , Carvajal-Carmona Luis , Fejerman Laura
Published: April 2023

Association between ER/PR/HER2 defined groups and European genetic ancestry (for every 10% increase)
Supplementary Data from Futibatinib Is a Novel Irreversible FGFR 1–4 Inhibitor That Shows Selective Antitumor Activity against FGFR-Deregulated Tumors
Authors: Sootome Hiroshi , Fujita Hidenori , Ito Kenjiro , Ochiiwa Hiroaki , Fujioka Yayoi , Ito Kimihiro , Miura Akihiro , Sagara Takeshi , Ito Satoru , Ohsawa Hirokazu , Otsuki Sachie , Funabashi Kaoru , Yashiro Masakazu , Matsuo Kenichi , Yonekura Kazuhiko , Hirai Hiroshi
Published: April 2023

Appendix
Supplementary Video 5 from Diagnostic Accuracy of Quantitative Micro-Elastography for Margin Assessment in Breast-Conserving Surgery
Authors: Kennedy Kelsey M. , Zilkens Renate , Allen Wes M. , Foo Ken Y. , Fang Qi , Chin Lixin , Sanderson Rowan W. , Anstie James , Wijesinghe Philip , Curatolo Andrea , Tan Hsern Ern I. , Morin Narelle , Kunjuraman Bindu , Yeomans Chris , Chin Synn Lynn , DeJong Helen , Giles Katharine , Dessauvagie Benjamin F. , Latham Bruce , Saunders Christobel M. , Kennedy Brendan F.
Published: April 2023

OCT and QME of ductal carcinoma in situ
Supplementary Figure 5 from Rb and p53-Deficient Myxofibrosarcoma and Undifferentiated Pleomorphic Sarcoma Require Skp2 for Survival
Authors: Li George Z. , Okada Tomoyo , Kim Young-Mi , Agaram Narasimhan P. , Sanchez-Vega Francisco , Shen Yawei , Tsubokawa Norifumi , Rios Jordan , Martin Axel S. , Dickson Mark A. , Qin Li-Xuan , Socci Nicholas D. , Singer Samuel
Published: April 2023

The Skp2-specific inhibitor C1 is cytotoxic to 8000s cells and increases their expression of p21 and p27
Table S4 from Heritability of Mammographic Breast Density, Density Change, Microcalcifications, and Masses
Authors: Holowko Natalie , Eriksson Mikael , Kuja-Halkola Ralf , Azam Shadi , He Wei , Hall Per , Czene Kamila
Published: April 2023

Univariate ACE estimates among women who did not develop breast cancer during follow-up
Supplementary Figure 6 from Beclin 1 Promotes Endosome Recruitment of Hepatocyte Growth Factor Tyrosine Kinase Substrate to Suppress Tumor Proliferation
Authors: Matthew-Onabanjo Asia N. , Janusis Jenny , Mercado-Matos Jose , Carlisle Anne E. , Kim Dohoon , Levine Fayola , Cruz-Gordillo Peter , Richards Ryan , Lee Michael J. , Shaw Leslie M.
Published: April 2023

This Figure show analysis of shATG5 tumors.
Supplementary Figures 1-11, Table 1, method and references from Acquired Resistance to HER2-Targeted Therapies Creates Vulnerability to ATP Synthase Inhibition
Authors: Gale Molly , Li Yao , Cao Jian , Liu Zongzhi Z. , Holmbeck Marissa A. , Zhang Meiling , Lang Sabine M. , Wu Lizhen , Do Carmo Mariana , Gupta Swati , Aoshima Keisuke , DiGiovanna Michael P. , Stern David F. , Rimm David L. , Shadel Gerald S. , Chen Xiang , Yan Qin
Published: April 2023

Supplementary Figure 1: Generation and characterization of resistant cell pools. Supplementary Figure 2: Copy number assessment of receptor tyrosine kinases in resistant cell pools. Supplementary Figure 3: Trastuzumab resistance is reversible. Supplementary Figure 4: Drug resistant cells are more sensitive to OXPHOS inhibitors than parental cells. Supplementary Figure 5: Drug resistant cells have similar mitochondrial DNA copy numbers and ATP levels as the parental cells. Supplementary Figure 6: Glycolysis in parental BT474 versus trastuzumab resistant cells. Supplementary Figure 7: ATP synthase gene expression in BT474, SKBR3 cells and their derived trastuzumab-resistant cells. Supplementary Figure 8: Cumulative survival of breast cancer (all, basal, luminal) patients with patients divided in half by ATP5B (left) or ATP5A1 (right) mRNA level. Supplementary Figure 9: ATP5B protein expression correlation with survival in HER2+, trastuzumab treated patients from HeCOG 10/05. Supplementary Figure 10: ATP5B is required for the maintenance of resistance. Supplementary Figure 11: BT-TR2 tumor morphology and proliferation. Supplementary Table 1: Sequences of primers and plasmid inserts. Supplementary Methods Supplementary References
Supplementary text from Therapeutic Targeting of the Secreted Lysophospholipase D Autotaxin Suppresses Tuberous Sclerosis Complex-Associated Tumorigenesis
Authors: Feng You , Mischler William J. , Gurung Ashish C. , Kavanagh Taylor R. , Androsov Grigoriy , Sadow Peter M. , Herbert Zachary T. , Priolo Carmen
Published: April 2023

Supplementary Methods and Supplementary Figure legends
Supplementary Figure 3 from Therapeutic Targeting of the Secreted Lysophospholipase D Autotaxin Suppresses Tuberous Sclerosis Complex-Associated Tumorigenesis
Authors: Feng You , Mischler William J. , Gurung Ashish C. , Kavanagh Taylor R. , Androsov Grigoriy , Sadow Peter M. , Herbert Zachary T. , Priolo Carmen
Published: April 2023

Impact of LPA and S1P on the transcriptome and proliferation of human TSC2-deficient cells treated with GLPG1690
Supplementary Data from Combined MEK and PI3K/p110β Inhibition as a Novel Targeted Therapy for Malignant Mesothelioma Displaying Sarcomatoid Features
Authors: Marqués Miriam , Tranchant Robin , Risa-Ebrí Blanca , Suárez-Solís María L. , Fernández Luis C. , Carrillo-de-Santa-Pau Enrique , del Pozo Natalia , Martínez de Villarreal Jaime , Meiller Clément , Allory Yves , Blum Yuna , Pirker Christine , Hegedus Balazs , Barry Simon T. , Carnero Amancio , Berger Walter , Jean Didier , Real Francisco X.
Published: April 2023

This file contains Supplementary Material and Methods. Supplementary Table S1 summarizes the antibodies used for IHC and WB; Supplementary Table S2 shows the primers and the shRNAs sequences used; Supplementary Table S3 shows the Selumetinib and AZD8186 concentration ranges used for in vitro experiments; Supplementary Table S4. Summary of patient and tumor characteristics corresponding to the TMA from each institution; Supplementary Table S5. Drug sensitivity values for Selumetinib/AZD8186 responder cells. Supplementary Figure S1. Histology of the metastases of Pten;Trp53-null mouse tumors. Representative H&E staining of kidney, spleen and pancreas metastases of Pten;Trp53-null tumors. Scale bar 200µm (right panels) and 50µm (left panels). Supplementary Figure S2. Signaling analysis of Pten;Trp53-null and Pik3ca*;Trp53-null mouse tumors. Supplementary Figure S3. Characterization of cell lines derived from Pten;Trp53-null and Pik3ca*;Trp53-null tumors. Supplementary Figure S4. Effect of MEK and p110b inhibitors on signaling in Pten;Trp53-null and Pik3ca*;Trp53-null cells. Supplementary Figure S5. A fraction of Selumetinib/AZD8186 treated mice had no macroscopically detectable tumors at autopsy. Supplementary Figure S6. Analysis of synergy between Selumetinib and AZD8186 in the extended panel of primary human PMM cells. Supplementary Figure S7. Comparison of the response of human Pl-MM cultures to the Selumetinib/AZD8186 combination compared to cisplatin. Viability of primary human PMM cells after 72h exposure to serial dilutions of cisplatin or constant ratio combination of Selumetinib/AZD8186. Compound concentration range: 0.025-20µM for Selumetinib and AZD8186 and 1.25-40 µM for cisplatin. The combination ratios for Selumetinib and AZD8186 in each specific culture are specified in Supplementary table S3. Mean+ SEM (n=2-3).
Supplementary Figure 1 from The Fire Within: NF-κB Involvement in Non–Small Cell Lung Cancer
Authors: Dimitrakopoulos Foteinos-Ioannis D. , Kottorou Anastasia E. , Kalofonou Melpomeni , Kalofonos Haralabos P.
Published: April 2023

Supplementary Figure S1. Hallmarks of lung cancer influenced by NF-κB activity.
Figure S3 from Remission of Spontaneous Canine Tumors after Systemic Cellular Viroimmunotherapy
Authors: Cejalvo Teresa , Perisé-Barrios Ana Judith , del Portillo Isabel , Laborda Eduardo , Rodriguez-Milla Miguel A. , Cubillo Isabel , Vázquez Fernando , Sardón David , Ramirez Manuel , Alemany Ramon , del Castillo Noemí , García-Castro Javier
Published: April 2023

Hyaluronic acid detection on canine biopsies
Supplementary Tables from Physical Activity Does Not Lower the Risk of Lung Cancer
Authors: Baumeister Sebastian-Edgar , Leitzmann Michael F. , Bahls Martin , Meisinger Christa , Amos Christopher I. , Hung Rayjean J. , Teumer Alexander , Baurecht Hansjörg
Published: April 2023

Supplementary Tables 1-14
Figure S4 from SMAD4 Suppresses WNT-Driven Dedifferentiation and Oncogenesis in the Differentiated Gut Epithelium
Authors: Perekatt Ansu O. , Shah Pooja P. , Cheung Shannon , Jariwala Nidhi , Wu Alex , Gandhi Vishal , Kumar Namit , Feng Qiang , Patel Neeket , Chen Lei , Joshi Shilpy , Zhou Anbo , Taketo M. Mark , Xing Jinchuan , White Eileen , Gao Nan , Gatza Michael L. , Verzi Michael P.
Published: April 2023

Differentiated lineages within the ectopic crypts
Supplementary Figure 3 from CTGF Mediates Tumor–Stroma Interactions between Hepatoma Cells and Hepatic Stellate Cells to Accelerate HCC Progression
Authors: Makino Yuki , Hikita Hayato , Kodama Takahiro , Shigekawa Minoru , Yamada Ryoko , Sakamori Ryotaro , Eguchi Hidetoshi , Morii Eiichi , Yokoi Hideki , Mukoyama Masashi , Hiroshi Suemizu , Tatsumi Tomohide , Takehara Tetsuo
Published: April 2023

Supplementary Fig. 3. CTGF expression and secretion levels in hepatoma cells. CTGF mRNA and protein expression and concentration in the culture supernatant of hepatoma cell lines (A) and parental, mock-transfected, and CTGF-overexpressing PLC/PRF/5 cells (B). Cell lysates and culture supernatants were collected 72 hours after plating (N = 4-6 per group). In bar graphs, bars and top whiskers represent mean values and standard deviations, respectively. *p < 0.05 vs. PLC/PRF/5 cells.
Supplementary Figure 2 from CTGF Mediates Tumor–Stroma Interactions between Hepatoma Cells and Hepatic Stellate Cells to Accelerate HCC Progression
Authors: Makino Yuki , Hikita Hayato , Kodama Takahiro , Shigekawa Minoru , Yamada Ryoko , Sakamori Ryotaro , Eguchi Hidetoshi , Morii Eiichi , Yokoi Hideki , Mukoyama Masashi , Hiroshi Suemizu , Tatsumi Tomohide , Takehara Tetsuo
Published: April 2023

Supplementary Fig. 2. CTGF expression is regulated through the Ras/Mek/Erk pathway. (A-D) CTGF expression in liver cancer cell lines was evaluated after activation or inhibition of the Ras signaling pathway (N = 4 per group). Expression levels of CTGF and phosphorylated Erk and Akt and CTGF concentration in culture supernatants at the indicated time point after treatment with 100 ng/mL EGF in Kras wild-type Huh7 cells (A). Cells were serum-starved for 12 hours before the addition of EGF. Gene and protein expression of Ras and CTGF 72 hours after transfection of Kras siRNAs (#1 and #2) or control siRNA into Kras mutant-type HepG2 cells (B). Protein expression of p-Akt and p-Erk 3 hours after the addition of LY294002 (a PI3K inhibitor), U0126 (a Mek inhibitor) or FR180204 (an Erk inhibitor) at indicated doses (C). CTGF gene expression and cell viability in HepG2 cells 6 hours after the addition of inhibitors at indicated doses (D). Cell viability was evaluated using a WST-8 assay (N = 4 per group). (E) Correlation between the CTGF gene expression levels and single-sample gene set enrichment analysis (ssGSEA) enrichment scores of the Ras/Mek/Erk pathway in 220 samples of non-tumorous liver tissues. In bar graphs, bars and top whiskers represent mean values and standard deviations, respectively. *p < 0.05 vs. the control.
Supplementary Data from A Biophysical Model Uncovers the Size Distribution of Migrating Cell Clusters across Cancer Types
Authors: Bocci Federico , Kumar Jolly Mohit , Onuchic José Nelson
Published: April 2023

The first part of the supplementary information provides details on the derivation of the model. The second part provides supplementary figures.
Table S6 from Chromothripsis in Human Breast Cancer
Authors: Bolkestein Michiel , Wong John K.L. , Thewes Verena , Körber Verena , Hlevnjak Mario , Elgaafary Shaymaa , Schulze Markus , Kommoss Felix K.F. , Sinn Hans-Peter , Anzeneder Tobias , Hirsch Steffen , Devens Frauke , Schröter Petra , Höfer Thomas , Schneeweiss Andreas , Lichter Peter , Zapatka Marc , Ernst Aurélie
Published: April 2023

Differentially expressed genes between cases with and without chromothripsis
Supplementary Methods from Chromothripsis in Human Breast Cancer
Authors: Bolkestein Michiel , Wong John K.L. , Thewes Verena , Körber Verena , Hlevnjak Mario , Elgaafary Shaymaa , Schulze Markus , Kommoss Felix K.F. , Sinn Hans-Peter , Anzeneder Tobias , Hirsch Steffen , Devens Frauke , Schröter Petra , Höfer Thomas , Schneeweiss Andreas , Lichter Peter , Zapatka Marc , Ernst Aurélie
Published: April 2023

Supplementary Methods
Supplementary Figure 4 from Chromothripsis in Human Breast Cancer
Authors: Bolkestein Michiel , Wong John K.L. , Thewes Verena , Körber Verena , Hlevnjak Mario , Elgaafary Shaymaa , Schulze Markus , Kommoss Felix K.F. , Sinn Hans-Peter , Anzeneder Tobias , Hirsch Steffen , Devens Frauke , Schröter Petra , Höfer Thomas , Schneeweiss Andreas , Lichter Peter , Zapatka Marc , Ernst Aurélie
Published: April 2023

Unsupervised clustering analyses of RNAseq data for ER+, HER- liver metastases of the CATCH cohort (a) and luminal tumors from the DKFZ-HIPO17 cohort (b)
Supplementary Figure 3 from Chromothripsis in Human Breast Cancer
Authors: Bolkestein Michiel , Wong John K.L. , Thewes Verena , Körber Verena , Hlevnjak Mario , Elgaafary Shaymaa , Schulze Markus , Kommoss Felix K.F. , Sinn Hans-Peter , Anzeneder Tobias , Hirsch Steffen , Devens Frauke , Schröter Petra , Höfer Thomas , Schneeweiss Andreas , Lichter Peter , Zapatka Marc , Ernst Aurélie
Published: April 2023

Fusion genes in tumors with and without chromothripsis
Supplementary Figure 2 from Chromothripsis in Human Breast Cancer
Authors: Bolkestein Michiel , Wong John K.L. , Thewes Verena , Körber Verena , Hlevnjak Mario , Elgaafary Shaymaa , Schulze Markus , Kommoss Felix K.F. , Sinn Hans-Peter , Anzeneder Tobias , Hirsch Steffen , Devens Frauke , Schröter Petra , Höfer Thomas , Schneeweiss Andreas , Lichter Peter , Zapatka Marc , Ernst Aurélie
Published: April 2023

Copy-number differences between cases with and without chromothripsis in the CATCH cohort
Supplementary Figure 1 from Chromothripsis in Human Breast Cancer
Authors: Bolkestein Michiel , Wong John K.L. , Thewes Verena , Körber Verena , Hlevnjak Mario , Elgaafary Shaymaa , Schulze Markus , Kommoss Felix K.F. , Sinn Hans-Peter , Anzeneder Tobias , Hirsch Steffen , Devens Frauke , Schröter Petra , Höfer Thomas , Schneeweiss Andreas , Lichter Peter , Zapatka Marc , Ernst Aurélie
Published: April 2023

Overall chromothripsis prevalence (DKFZ-HIPO17, WES), link with clinical outcome and chromothripsis â€©occurrence per chromosome for each breast cancer subtype
Supplementary Methods from State-Transition Analysis of Time-Sequential Gene Expression Identifies Critical Points That Predict Development of Acute Myeloid Leukemia
Authors: Rockne Russell C. , Branciamore Sergio , Qi Jing , Frankhouser David E. , O'Meally Denis , Hua Wei-Kai , Cook Guerry , Carnahan Emily , Zhang Lianjun , Marom Ayelet , Wu Herman , Maestrini Davide , Wu Xiwei , Yuan Yate-Ching , Liu Zheng , Wang Leo D. , Forman Stephen , Carlesso Nadia , Kuo Ya-Huei , Marcucci Guido
Published: April 2023

In this supplement we provide additional data and methods to support our results. In particular, we show: details of our mouse model of AML; demonstrate the robustness of our state-space construction to normalization methods and gene selection criteria; compare dimension reduction methods; show bootstrap cross-validation of our predictions; compare hierarchical clustering with our state-space approach; and finally, provide full lists of differentially expressed genes and gene ontology (GO) term enrichment.
Supplementary Fig 1 from FGFR1 Is Critical for RBL2 Loss–Driven Tumor Development and Requires PLCG1 Activation for Continued Growth of Small Cell Lung Cancer
Authors: Kim Kee-Beom , Kim Youngchul , Rivard Christopher J. , Kim Dong-Wook , Park Kwon-Sik
Published: April 2023

A. Immunoblot for FGFR1, phosphorylated-FGFR1 (Tyr653/654), RBL2, phosphorylated-RBL2 (Ser672), E2F1, and E2F4 among human SCLC lines. ACTB blot verifies equal loading of total proteins. Arrows indicate specific bands. B. A hypothetical model of mechanisms regulating FGFR1 transcription. E2F1-driven FGFR1 transcription is suppressed by RBL2-E2F4 repressor complex. In the event of RBL2 loss or phosphorylation, E2F4 loses its ability to repress FGFR1, and E2F1 activates FGFR1 transcription.
Supplementary figure and table legends from Replication Stress Drives Constitutive Activation of the DNA Damage Response and Radioresistance in Glioblastoma Stem-like Cells
Authors: Carruthers Ross D. , Ahmed Shafiq U. , Ramachandran Shaliny , Strathdee Karen , Kurian Kathreena M. , Hedley Ann , Gomez-Roman Natividad , Kalna Gabriela , Neilson Mathew , Gilmour Lesley , Stevenson Katrina H. , Hammond Ester M. , Chalmers Anthony J.
Published: April 2023

Legends for supplementary figures and tables
Supplementary Data from ATF3 Coordinates Antitumor Synergy between Epigenetic Drugs and Protein Disulfide Isomerase Inhibitors
Authors: Duncan Ravyn M. , Reyes Leticia , Moats Katelyn , Robinson Reeder M. , Murphy Sara A. , Kaur Balveen , Stessman Holly A.F. , Dolloff Nathan G.
Published: April 2023

The supplementary tables provide a list of antibodies, plasmids, and primer sets that were used throughout the study. They also include gene transcripts from RNA-Seq analysis that show the genomic pathways altered by the combination of PDI and HDAC inhibitors, as well as ATF3-dependent gene transcripts.
Supplementary Data from Spatial Density and Distribution of Tumor-Associated Macrophages Predict Survival in Non–Small Cell Lung Carcinoma
Authors: Zheng Xiang , Weigert Andreas , Reu Simone , Guenther Stefan , Mansouri Siavash , Bassaly Birgit , Gattenlöhner Stefan , Grimminger Friedrich , Savai Pullamsetti Soni , Seeger Werner , Winter Hauke , Savai Rajkumar
Published: April 2023

Supplementary Data with figures
Supplementary Data from ERINA Is an Estrogen-Responsive LncRNA That Drives Breast Cancer through the E2F1/RB1 Pathway
Authors: Fang Zihui , Wang Yue , Wang Zehua , Xu Meishu , Ren Songrong , Yang Da , Hong Mei , Xie Wen
Published: April 2023

Supplementary Tables 1-3. Supplementary Table 1. shRNA sequences used. Supplementary Table 2. Primers sequences. Supplemental Table 3. Antibodies used
Supplementary Data from Comprehensive Analysis of Radiomic Datasets by RadAR
Authors: Benelli Matteo , Barucci Andrea , Zoppetti Nicola , Calusi Silvia , Redapi Laura , Della Gala Giuseppe , Piffer Stefano , Bernardi Luca , Fusi Franco , Pallotta Stefania
Published: April 2023

RadaR tutorial