bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Materials and Methods, Figures S1 - S2, Tables S1 - S4 from Proximal Aberrant Crypt Foci Associate with Synchronous Neoplasia and Are Primed for Neoplastic Progression
Authors: Drew David A. , Mo Allen , Grady James J. , Stevens Richard G. , Levine Joel B. , Brenner Bruce M. , Anderson Joseph C. , Forouhar Faripour , O'Brien Michael J. , Devers Thomas J. , Rosenberg Daniel W.
Published: April 2023

Supplementary Figure S1. Endoscopic counts of aberrant crypt foci (ACF) by colonic location stratified by the presence of at least one proximal ACF. Supplementary Figure S2. Polyp counts according to the presence of at least one histologically confirmed proximal ACF. Supplementary Table S1. Histologic Distribution of Biopsied Aberrant Crypt Foci. Supplementary Table S2. Polyp Location and Histology Distribution in Study Population. Supplementary Table S3. Synchronous polyps within subjects with a confirmed proximal ACF mutation. Supplementary Table S4. Synchronous polyps within subjects without an ACF mutation.
Supplementary Figure S4 from Runx2 Suppression by miR-342 and miR-363 Inhibits Multiple Myeloma Progression
Authors: Gowda Pramod S. , Wildman Benjamin J. , Trotter Timothy N. , Xu Xiaoxuan , Hao Xiaoxiao , Hassan Mohammad Q. , Yang Yang
Published: April 2023

Runx2 knockdown by shRNA and miRNAs in 5TGM1 cells suppress PD-L1 mRNA levels.
Supplementary Figures and Tables from TFE3 Xp11.2 Translocation Renal Cell Carcinoma Mouse Model Reveals Novel Therapeutic Targets and Identifies GPNMB as a Diagnostic Marker for Human Disease
Authors: Baba Masaya , Furuya Mitsuko , Motoshima Takanobu , Lang Martin , Funasaki Shintaro , Ma Wenjuan , Sun Hong-Wei , Hasumi Hisashi , Huang Ying , Kato Ikuma , Kadomatsu Tsuyoshi , Satou Yorifumi , Morris Nicole , Karim Baktiar O. , Ileva Lilia , Kalen Joseph D. , Wilan Krisna Luh Ade , Hasumi Yukiko , Sugiyama Aiko , Kurahashi Ryoma , Nishimoto Koshiro , Oyama Masafumi , Nagashima Yoji , Kuroda Naoto , Araki Kimi , Eto Masatoshi , Yao Masahiro , Kamba Tomomi , Suda Toshio , Oike Yuichi , Schmidt Laura S. , Linehan W. Marston
Published: April 2023

Supplemental Figure S1. Representative images of TFE3 immunohistochemistry of renal papillae and renal pelvis (a, b), ureters (c, d), and bladders (e, f) from a 10-month-old PRCC-TFE3; KSP-Cre- (a, c, e) mouse and a PRCC-TFE3; KSP-Cre+ (b, d, f) mouse. S2, S3, S4, S5. Supplemental Table S1. (a) List of top 50 significantly upregulated (q-value < 0.05, fold change > 2) genes in kidneys from 4 month old PRCC-TFE3; KSP-Cre+ mice. (b) List of significantly downregulated (q-value < 0.05, fold change < 1/2) genes in kidneys from 4 month old PRCC-TFE3; KSP-Cre+ mice. Supplemental Table S2 (a) List of top 50 significantly upregulated (q-value < 0.05, fold change > 2) genes in kidneys from 7 month old PRCC-TFE3; KSP-Cre+ mice. (b) List of top 50 significantly downregulated (q-value < 0.05, fold change < 1/2) genes in kidneys from 7 month old PRCC-TFE3; KSP-Cre+ mice. Supplemental Fig. S2 Gene Set Enrichment Analysis (GSEA) of microarray data from 4 month old PRCC-TFE3; KSP-Cre+ mouse kidneys (n=4) vs 4 month old PRCC-TFE3; KSP-Cre- mouse kidneys (n=4) (a, b, c, g, h, i) and 7 month old PRCC-TFE3;KSP-Cre+ mouse kidneys (n=4) vs 7 month old PRCC-TFE3; KSP-Cre- mouse kidneys (n=3) (d, e, f, j, k, l). Supplemental Table S3 List of commonly upregulated genes in PRCC-TFE3; KSP-Cre+ mouse kidneys (4 month old and 7 month old) and TFEB overexpressed mouse kidneys (P0 and P14, Calcagni et al. Supplemental Fig. S3 Gene Set Enrichment Analysis (GSEA) of microarray data from 4 month old PRCC-TFE3; KSP-Cre+ mouse kidneys (n=4) vs 4 month old PRCC-TFE3; KSP-Cre- mouse kidneys (n=4) (a) and 7 month old PRCC-TFE3;KSP-Cre+ mouse kidneys (n=4) vs 7 month old PRCC-TFE3; KSP-Cre- mouse kidneys (n=3) (b). Marginal (a) and significant (b) enrichment of genes associated with KRAS activation in kidneys from PRCC-TFE3; KSP-Cre+ mice. Supplemental Fig. S4. The immunohistochemical staining of Tfe3 (a), Gpnmb (b), and Ret (c) on PRCC-TFE3;KSP-Cre- kidneys and PRCC-TFE3;KSP-Cre+ kidneys was semiquantified and scored as (-), (1+) and (2+). Supplemental Fig. S5. Volcano plot of gene expression changes for 4 month-old (a) and 7 month-old (b) PRCC-TFE3; KSP-Cre- kidneys and PRCC-TFE3; KSP-Cre+ kidneys.
Supplementary Figure S3 from Runx2 Suppression by miR-342 and miR-363 Inhibits Multiple Myeloma Progression
Authors: Gowda Pramod S. , Wildman Benjamin J. , Trotter Timothy N. , Xu Xiaoxuan , Hao Xiaoxiao , Hassan Mohammad Q. , Yang Yang
Published: April 2023

Assessment of the number of PD-1+ and Tim-3+ CD8+ T cells from a population of gated CD3+ CD8+ T cells and of the number of IFN-γ+ CD3+ T cells from total CD3+ T cells.
Supplementary Figure 5 from LINC00152 Promotes Invasion through a 3′-Hairpin Structure and Associates with Prognosis in Glioblastoma
Authors: Reon Brian J. , Takao Real Karia Bruno , Kiran Manjari , Dutta Anindya
Published: April 2023

LINC00152 full length and deletion mutants. A) Predicted secondary structures of LINC00152 deletion mutants. M2 and M3 lack the protein bound stem-loop. M8 is highlighted by the boxed area (nucleotides 280-401). On the other hand, M4 through M8 contain the protein bound stem-loop (highlighted by the boxed area). B) Schematics of LINC00152 siRNA and primers relative to LINC00152 sequence.
Supplementary information from Stemness Is Enhanced in Gastric Cancer by a SET/PP2A/E2F1 Axis
Authors: Enjoji Shuhei , Yabe Ryotaro , Tsuji Shunya , Yoshimura Kazuhiro , Kawasaki Hideyoshi , Sakurai Masashi , Sakai Yusuke , Takenouchi Hiroko , Yoshino Shigefumi , Hazama Shoichi , Nagano Hiroaki , Oshima Hiroko , Oshima Masanobu , Vitek Michael P. , Matsuura Tetsuya , Hippo Yoshitaka , Usui Tatsuya , Ohama Takashi , Sato Koichi
Published: April 2023

This file contains detailed material and methods, and supplemental data related with Fig. 1g, Fig. 2a, b, Fig. 3c, d, Fig. 4a, b, c, Fig. 5c
Supplementary Figure 2 from SPHK1 Is a Novel Target of Metformin in Ovarian Cancer
Authors: Hart Peter C. , Chiyoda Tatsuyuki , Liu Xiaojing , Weigert Melanie , Curtis Marion , Chiang Chun-Yi , Loth Rachel , Lastra Ricardo , McGregor Stephanie M. , Locasale Jason W. , Lengyel Ernst , Romero Iris L.
Published: April 2023

Analysis of SPHK1 expression in multiple OvCa cell lines.
Video from Interactions with Muscle Cells Boost Fusion, Stemness, and Drug Resistance of Prostate Cancer Cells
Authors: Uygur Berna , Leikina Evgenia , Melikov Kamran , Villasmil Rafael , Verma Santosh K. , Vary Calvin P.H. , Chernomordik Leonid V.
Published: April 2023

Video 1. hMYO-induced fusion of PC3 cells. A mix of PC3 cells expressing and not expressing GFP were co-plated with hMYO on 35 mm ibiTreat μ-dishes (ibidi, Germany) and co-incubated for 48h before imaging. Time on the video denotes time from the start of the movie. GFP signal is shown in green and DNA dye signal is shown in red.
Figure S2 from Antisecretory Factor–Mediated Inhibition of Cell Volume Dynamics Produces Antitumor Activity in Glioblastoma
Authors: Ilkhanizadeh Shirin , Sabelström Hanna , Miroshnikova Yekaterina A. , Frantz Aaron , Zhu Wen , Idilli Aurora , Lakins Jon N. , Schmidt Christin , Quigley David A. , Fenster Trenten , Yuan Edith , Trzeciak Jacqueline R. , Saxena Supna , Lindberg Olle R. , Mouw Janna K. , Burdick Jason A. , Magnitsky Sergey , Berger Mitchel S. , Phillips Joanna J. , Arosio Daniele , Sun Dandan , Weaver Valerie M. , Weiss William A. , Persson Anders I.
Published: April 2023

Fig. S2. Interstitial fluid pressure (IFP) pressure sensors do not increase reactive gliosis or microglia activation during tumor progression. (A, B) GFAP+ reactive astrocytes (DAB; brown) and (C, D) Iba1+ tumor-associated macrophages (DAB; brown) in progressing GBM43 tumors in the absence or presence of IFP sensor. Nuclei are counterstained with hematoxylin (blue). Scale bar: 40 μm.
Supplementary Figure S1 - Figure S7Data from β8 Integrin Mediates Pancreatic Cancer Cell Radiochemoresistance
Authors: Jin Sha , Lee Wei-Chun , Aust Daniela , Pilarsky Christian , Cordes Nils
Published: April 2023

Supplementary Figure 1. Flowchart of high throughout screen (3D HTesiRNAS) in 3D PDAC organoids. Supplementary Figure 2. β8 integrin expression in cell fractions. Supplementary Figure 3. β8 integrin knockdown also radiosensitizes 2D PDAC cell cultures. Supplementary Figure 4. Co-immunofluorescence staining of β8 integrin with GM130, mitotracker, αV integrin, APPL2 and Caveolin. Supplementary Figure 5. Impact of αV integrin expression on survival of patients with PDAC. Supplementary Figure 6. Cytotoxicity of Gemcitabine, chloroquine, colchicine and paclitaxel in BxPC cells. Supplementary Figure 7. β8 integrin and LC3B double staining upon β8 integrin knockdown. Supplementary Table 1. Data of high-throughput esiRNA knockdown screen of 117 focal adhesion proteins in 3D PDAC cell culture. RLUC was the control. Supplementary Table 2. Classification of proteins of the β8 integrin interactome based on raw data of sequential immunoprecipitation-mass spectrometry using PANTHER database
Supplementary Tables S1 - S5 from Imprecision and DNA Break Repair Biased towards Incompatible End Joining in Leukemia
Authors: Gassner Franz Josef , Schubert Maria , Rebhandl Stefan , Spandl Karina , Zaborsky Nadja , Catakovic Kemal , Blaimer Stephanie , Hebenstreit Daniel , Greil Richard , Geisberger Roland
Published: April 2023

Supplementary table S1. Patient information. Supplementary table S2. Plasmid assay data for all inter- and intramolecular junctions in CLL and B cells. Supplementary table S3. Plasmid assay data for the most frequent intramolecular junctions in CLL and B cells. Supplementary table S4. Plasmid assay data for the most frequent inter- and intramolecular junctions in CLL and B cells including sequences. Supplementary table S5. Number of reads from plasmid assays corresponding to amplicons amplified by forward and reverse primer pairs.
Supplementary Data from β8 Integrin Mediates Pancreatic Cancer Cell Radiochemoresistance
Authors: Jin Sha , Lee Wei-Chun , Aust Daniela , Pilarsky Christian , Cordes Nils
Published: April 2023

Supplementary Figure Legends, Supplementary Table S1 and S2
Supplementary Figure S4 from Imprecision and DNA Break Repair Biased towards Incompatible End Joining in Leukemia
Authors: Gassner Franz Josef , Schubert Maria , Rebhandl Stefan , Spandl Karina , Zaborsky Nadja , Catakovic Kemal , Blaimer Stephanie , Hebenstreit Daniel , Greil Richard , Geisberger Roland
Published: April 2023

Realtime RT-PCR on Lig1, XRCC1 and PARP1 on cDNA from CLL cells, B cells and Mec1 cells. Transcript levels are shown as relative abundance, normalized to the respective mean in B cells.
Table S2 from Precision Oncology beyond Targeted Therapy: Combining Omics Data with Machine Learning Matches the Majority of Cancer Cells to Effective Therapeutics
Authors: Ding Michael Q. , Chen Lujia , Cooper Gregory F. , Young Jonathan D. , Lu Xinghua
Published: April 2023

A list of non-FDA approved medications tested in the GDSC study.
Tabel S4 from Precision Oncology beyond Targeted Therapy: Combining Omics Data with Machine Learning Matches the Majority of Cancer Cells to Effective Therapeutics
Authors: Ding Michael Q. , Chen Lujia , Cooper Gregory F. , Young Jonathan D. , Lu Xinghua
Published: April 2023

Drug sensitivity enrichment in specific tissue types
Supplementary Figures S1 - S4 from Overt Increase of Oxidative Stress and DNA Damage in Murine and Human Colitis and Colitis-Associated Neoplasia
Authors: Frick Adrian , Khare Vineeta , Paul Gregor , Lang Michaela , Ferk Franziska , Knasmüller Siegfried , Beer Andrea , Oberhuber Georg , Gasche Christoph
Published: April 2023

Supplementary Figure 1: Tumor burden and inflammation in IL-10 KO mice. Supplementary Figure 2: LOH, MSI and CIMP in IL-10 KO mice. Supplementary Figure 3: DNA damage and apoptosis in IL-10KO mice. Supplementary Figure 4: Nrf2 is increased in IL-10 KO small and large intestinal organoids.
Table S2 from High Prevalence of a Hotspot of Noncoding Somatic Mutations in Intron 6 of GPR126 in Bladder Cancer
Authors: Garinet Simon , Pignot Géraldine , Vacher Sophie , Le Goux Constance , Schnitzler Anne , Chemlali Walid , Sirab Nanor , Barry Delongchamps Nicolas , Zerbib Marc , Sibony Mathilde , Allory Yves , Damotte Diane , Bieche Ivan
Published: April 2023

Relationship between GPR126 transcript level and standard clinical pathological and biological parameters in NMIBC
Table S3 from Differential Regulation of LET-7 by LIN28B Isoform–Specific Functions
Authors: Mizuno Rei , Chatterji Priya , Andres Sarah , Hamilton Kathryn , Simon Lauren , Foley Shawn W. , Jeganathan Arjun , Gregory Brian D. , Madison Blair , Rustgi Anil K.
Published: April 2023

shRNA
Supplementary Data 3 from Prostate Cancer in World Trade Center Responders Demonstrates Evidence of an Inflammatory Cascade
Authors: Gong Yixuan , Wang Li , Yu Haocheng , Alpert Naomi , Cohen Mitchell D. , Prophete Colette , Horton Lori , Sisco Maureen , Park Sung-Hyun , Lee Hyun-Wook , Zelikoff Judith , Chen Lung-Chi , Hashim Dana , Suarez-Farinas Mayte , Donovan Michael J. , Aaronson Stuart A. , Galsky Matthew , Zhu Jun , Taioli Emanuela , Oh William K.
Published: April 2023

Differentially expressed genes in rat prostates exposed to WTC dusts
Supplementary Tables 1-15 from Frequent ESR1 and CDK Pathway Copy-Number Alterations in Metastatic Breast Cancer
Authors: Basudan Ahmed , Priedigkeit Nolan , Hartmaier Ryan J. , Sokol Ethan S. , Bahreini Amir , Watters Rebecca J. , Boisen Michelle M. , Bhargava Rohit , Weiss Kurt R. , Karsten Maria M. , Denkert Carsten , Blohmer Jens-Uwe , Leone Jose P. , Hamilton Ronald L. , Brufsky Adam M. , Elishaev Esther , Lucas Peter C. , Lee Adrian V. , Oesterreich Steffi
Published: April 2023

Table S1. Clinicopathological characteristics and sample distribution by site Table S2. Primers/probes design for ddPCR (ESR1, EIF2C, AP3P1) Table S3. Raw nanoString counts Table S4. Normalized copy number calls (ER+ samples) Table S5. Normalized copy number calls (ER- samples) Table S6. DdPCR analysis of cell lines Table S7. NanoString raw counts (cell lines) Table S8. NanoString copy number calls (cell lines) Table S9. Nanostring log2 normalized counts (cell lines) Table S10. ESR1 CN amplifications by site in ER- samples Table S11. Multiple Fisher exact comparisons Table S12. ESR1 5`-3` copy number imbalance Table S13. Correlation matrix of ESR1 copy number calls by the different exons and mRNA expression Table S14. Normalized copy number calls for other genes (ER+ samples) Table S15. Normalized copy number calls other genes (ER- samples)
Supplementary Figure S2 from PTEN Regulates Nonhomologous End Joining By Epigenetic Induction of NHEJ1/XLF
Authors: Sulkowski Parker L. , Scanlon Susan E. , Oeck Sebastian , Glazer Peter M.
Published: April 2023

Additional DNA Repair Data with PTEN-Complemented Cells
Figure S2 from EGFRvIII–Stat5 Signaling Enhances Glioblastoma Cell Migration and Survival
Authors: Roos Alison , Dhruv Harshil D. , Peng Sen , Inge Landon J. , Tuncali Serdar , Pineda Michael , Millard Nghia , Mayo Zachary , Eschbacher Jennifer M. , Loftus Joseph C. , Winkles Jeffrey A. , Tran Nhan L.
Published: April 2023

Specificity of siRNAs targeting Stat isoforms in GBM cells
Figure S1 from EGFRvIII–Stat5 Signaling Enhances Glioblastoma Cell Migration and Survival
Authors: Roos Alison , Dhruv Harshil D. , Peng Sen , Inge Landon J. , Tuncali Serdar , Pineda Michael , Millard Nghia , Mayo Zachary , Eschbacher Jennifer M. , Loftus Joseph C. , Winkles Jeffrey A. , Tran Nhan L.
Published: April 2023

Confirmation of Stat activation and mRNA expression of Fn14 in GBM cells
Supplementary Figure 7 from Ovarian Tumor Cell Expression of Claudin-4 Reduces Apoptotic Response to Paclitaxel
Authors: Breed Christopher , Hicks Douglas A. , Webb Patricia G. , Galimanis Carly E. , Bitler Benjamin G. , Behbakht Kian , Baumgartner Heidi K.
Published: April 2023

Apoptotic response to paclitaxel with claudin-4 overexpression.
Supplementary Figure 5 from Ovarian Tumor Cell Expression of Claudin-4 Reduces Apoptotic Response to Paclitaxel
Authors: Breed Christopher , Hicks Douglas A. , Webb Patricia G. , Galimanis Carly E. , Bitler Benjamin G. , Behbakht Kian , Baumgartner Heidi K.
Published: April 2023

Images of apoptotic response (loss of claudin-4 expression).
Table S2 from BRD4 Regulates Metastatic Potential of Castration-Resistant Prostate Cancer through AHNAK
Authors: Shafran Jordan S. , Andrieu Guillaume P. , Györffy Balázs , Denis Gerald V.
Published: April 2023

SU2C repository gene expression data.
Figure S4 from BRD4 Regulates Metastatic Potential of Castration-Resistant Prostate Cancer through AHNAK
Authors: Shafran Jordan S. , Andrieu Guillaume P. , Györffy Balázs , Denis Gerald V.
Published: April 2023

AHNAK knockdown inhibits DU 145 cell invasion and AHNAK overexpression rescues cell migration in BRD4-depleted cells
Supplementary Figure S3 from The Transcription Factor AP4 Promotes Oncogenic Phenotypes and Cisplatin Resistance by Regulating LAPTM4B Expression
Authors: Wang Lu , Meng Yue , Xu Jian-Jun , Zhang Qing-Yun
Published: April 2023

Supplementary Figure S3 shows that knockdown of AP4 by three siRNAs decreased LAPTM4B protein levels in MCF7 and MDA-MB-231 cells.
Supplementary Methods and Figures 1 - 6 from A Bispecific Antibody Targeting the αv and α5β1 Integrins Induces Integrin Degradation in Prostate Cancer Cells and Is Superior to Monospecific Antibodies
Authors: Joshi Raghav , Ren Wenying , Mathew Paul
Published: April 2023

Supplementary Methods and Figures 1 - 6
Supplementary Tables from AR Expression in Breast Cancer CTCs Associates with Bone Metastases
Authors: Aceto Nicola , Bardia Aditya , Wittner Ben S. , Donaldson Maria C. , O'Keefe Ryan , Engstrom Amanda , Bersani Francesca , Zheng Yu , Comaills Valentine , Niederhoffer Kira , Zhu Huili , Mackenzie Olivia , Shioda Toshi , Sgroi Dennis , Kapur Ravi , Ting David T. , Moy Beverly , Ramaswamy Sridhar , Toner Mehmet , Haber Daniel A. , Maheswaran Shyamala
Published: April 2023

Supplementary Table S1: Patients and clinical information. Supplementary Table S2: Genes used to determine the AR signature.
Supplementary Figure S5 from Hyperphosphorylation of CDH1 in Glioblastoma Cancer Stem Cells Attenuates APC/CCDH1 Activity and Pharmacologic Inhibition of APC/CCDH1/CDC20 Compromises Viability
Authors: De Kuntal , Grubb Treg M. , Zalenski Abigail A. , Pfaff Kayla E. , Pal Debjani , Majumder Shubhra , Summers Matthew K. , Venere Monica
Published: April 2023

Representative confluence NSTC images collected by the IncuCyte Zoom
Supplementary Data from A LHFPL3-AS1/miR-580-3p/STAT3 Feedback Loop Promotes the Malignancy in Melanoma via Activation of JAK2/STAT3 Signaling
Authors: Peng Qian , Liu Linbo , Pei Hui , Zhang Jianwen , Chen Minjing , Zhai Xiaomei
Published: April 2023

Figure S1. Overexpression of LHFPL3-AS1 facilitated malignant behaviors in HEMa-LP cells. Figure S2. LHFPL3-AS1 positively regulated STAT3 expression. Figure S3. Upregulated LHFPL3-AS1 rescued the functional impacts of elevated miR-580-3p in melanoma cells. Figure S4. Cucurbitacin I-inhibited JAK/STAT3 pathway counteracted the influences of LHFPL3-AS1 upregulation or miR-580-3p inhibition on the behaviors of melanoma cells. Figure S5. LHFPL3-AS1 aggravated in vivo tumorigenesis in melanoma via targeting miR-580-3p/STAT3 signaling. Supplementary file 1. The promoter sequence for LHFPL3-AS1 was obtained after searching UCSC database.
Figure S1, Figure S2, Figure S3 from Kinetics of Nuclear Uptake and Site-Specific DNA Cleavage during CRISPR-Directed Gene Editing in Solid Tumor Cells
Authors: Banas Kelly , Rivera-Torres Natalia , Bialk Pawel , Yoo Byung-Chun , Kmiec Eric B.
Published: April 2023

Figure S1. Fluorescence compensation of mock transfected, GFP- and ATTO 550-fluorescing cells. Figure S2. Representative images used for time course analysis. Figure S3. In vitro cleavage reaction of wildtype and R34G-mutated NRF2 amplicons with varying concentrations of the R34G RNP.
Supplementary Figure 2 from Anti–miR-21 Suppresses Hepatocellular Carcinoma Growth via Broad Transcriptional Network Deregulation
Authors: Wagenaar Timothy R. , Zabludoff Sonya , Ahn Sung-Min , Allerson Charles , Arlt Heike , Baffa Raffaele , Cao Hui , Davis Scott , Garcia-Echeverria Carlos , Gaur Rajula , Huang Shih-Min A. , Jiang Lan , Kim Deokhoon , Metz-Weidmann Christiane , Pavlicek Adam , Pollard Jack , Reeves Jason , Rocnik Jennifer L. , Scheidler Sabine , Shi Chaomei , Sun Fangxian , Tolstykh Tatiana , Weber William , Winter Christopher , Yu Eunsil , Yu Qunyan , Zheng Gang , Wiederschain Dmitri
Published: April 2023

Supplementary Figure 2. Anti-miR-21 treatment causes limited caspase 3/7 activation in non-transformed cell lines. Caspase 3/7 activation after treatment of SKHep1, IMR-90, and WI-38 cells with MM control or anti-miR-21 for 72 hours. (Mean, {plus minus} SEM, n=3).
Supplementary Figures S1 - S8 from Bayesian Modeling Identifies PLAG1 as a Key Regulator of Proliferation and Survival in Rhabdomyosarcoma Cells
Authors: Zheng Yanbin , Xu Lin , Hassan Mohammed , Zhou Xiaoyun , Zhou Qinbo , Rakheja Dinesh , Skapek Stephen X.
Published: April 2023

S1. Confirmation of knockdown of PLAG1 in RMS cells. S2. Knockdown of PLAG1 increases cleaved PARP1 expression in RD-like cells. S3. Knockdown of PLAG1 with another siRNA (#2) also impairs cell accumulation and induces apoptosis in RMS cells. S4. Knockdown of PLAG1 decreases IGF2 expression in RH30 cells. S5. Exogenous IGF2 decreases the sub-G1 cell population triggered by PLAG1 knockdown. S6. Addition of IGF2 partially restores attenuated AKT phosphorylation induced by PLAG1 knockdown in RH30 cells. S7. Ectopic expression of PLAG1 induces IGF2 and activates IGF1R in RH30 cells. S8. BMS754807 inhibits IGF1R phosphorylation in RD cells.
Table S1 from Transcriptome-wide Landscape of Pre-mRNA Alternative Splicing Associated with Metastatic Colonization
Authors: Lu Zhi-xiang , Huang Qin , Park Juw Won , Shen Shihao , Lin Lan , Tokheim Collin J. , Henry Michael D. , Xing Yi
Published: April 2023

Table S1. Primer sequences used in this study
Figure S1 from Transcriptome-wide Landscape of Pre-mRNA Alternative Splicing Associated with Metastatic Colonization
Authors: Lu Zhi-xiang , Huang Qin , Park Juw Won , Shen Shihao , Lin Lan , Tokheim Collin J. , Henry Michael D. , Xing Yi
Published: April 2023

Figure S1. The effects of EMT-relevant transcription factors on NOVA1 protein expression
Data Supplement from The lncRNA PCAT29 Inhibits Oncogenic Phenotypes in Prostate Cancer
Authors: Malik Rohit , Patel Lalit , Prensner John R. , Shi Yang , Iyer Matthew K. , Subramaniyan Shruthi , Carley Alexander , Niknafs Yashar S. , Sahu Anirban , Han Sumin , Ma Teng , Liu Meilan , Asangani Irfan A. , Jing Xiaojun , Cao Xuhong , Dhanasekaran Saravana M. , Robinson Dan R. , Feng Felix Y. , Chinnaiyan Arul M.
Published: April 2023

Supplementary Figure 4. Overlap of positive and negative correlations.
Supplementary Figure 5 from Salt-Inducible Kinase 2 Regulates Mitotic Progression and Transcription in Prostate Cancer
Authors: Bon Hélène , Wadhwa Karan , Schreiner Alexander , Osborne Michelle , Carroll Thomas , Ramos-Montoya Antonio , Ross-Adams Helen , Visser Matthieu , Hoffmann Ralf , Ahmed Ahmed Ashour , Neal David E. , Mills Ian G.
Published: April 2023

Supplementary Figure 5. Validation of SIK2, TORC1, TORC2 and TORC3 antibodies by Western-Blot.
Supplemental Figure 2 from RSK Promotes Prostate Cancer Progression in Bone through ING3, CKAP2, and PTK6-Mediated Cell Survival
Authors: Yu Guoyu , Lee Yu-Chen , Cheng Chien-Jui , Wu Chuan-Fen , Song Jian H. , Gallick Gary E. , Yu-Lee Li-Yuan , Kuang Jian , Lin Sue-Hwa
Published: April 2023

X-ray analysis the effects of RSK1 and RSK2 on PC3-mm2-induced bone changes.
Supplemental Figure 1 from RSK Promotes Prostate Cancer Progression in Bone through ING3, CKAP2, and PTK6-Mediated Cell Survival
Authors: Yu Guoyu , Lee Yu-Chen , Cheng Chien-Jui , Wu Chuan-Fen , Song Jian H. , Gallick Gary E. , Yu-Lee Li-Yuan , Kuang Jian , Lin Sue-Hwa
Published: April 2023

Expression of pRSK(T359/S363) in human bone metastasis PCa specimens.
Supplementary Figures from Radiation Attenuates Prostate Tumor Antiviral Responses to Vesicular Stomatitis Virus Containing IFNβ, Resulting in Pronounced Antitumor Systemic Immune Responses
Authors: Udayakumar Thirupandiyur S. , Betancourt Dillon M. , Ahmad Anis , Tao Wensi , Totiger Tulasigeri M. , Patel Mausam , Marples Brian , Barber Glen , Pollack Alan
Published: April 2023

Supplementary Figures 1-3
Supplemental Figure 2. from lincRNA-RoR and miR-145 Regulate Invasion in Triple-Negative Breast Cancer via Targeting ARF6
Authors: Eades Gabriel , Wolfson Benjamin , Zhang Yongshu , Li Qinglin , Yao Yuan , Zhou Qun
Published: April 2023

Supplemental Figure 2. miR-145 overexpression impacts tumor cell invasion but not tumor cell proliferation in TNBC cell lines. A, Ki67 staining of MDA-MB-231 cells transfected with control or miR-145 overexpression vectors. B, MTT assay for HS578T cells transfected with control or miR-145 expression vectors. C, Transwell invasion assay for HS578T control and HS578T overexpressing miR-145.
Supplementary Figure S1 from Systemic Ablation of MMP-9 Triggers Invasive Growth and Metastasis of Pancreatic Cancer via Deregulation of IL6 Expression in the Bone Marrow
Authors: Grünwald Barbara , Vandooren Jennifer , Gerg Michael , Ahomaa Kaarin , Hunger Annique , Berchtold Sonja , Akbareian Sophia , Schaten Susanne , Knolle Percy , Edwards Dylan R. , Opdenakker Ghislain , Krüger Achim
Published: April 2023

MMP2 in KPC mice.
Supplementary Figure 3 from Augmented HR Repair Mediates Acquired Temozolomide Resistance in Glioblastoma
Authors: Gil del Alcazar Carlos Rodrigo , Todorova Pavlina Krasimirova , Habib Amyn A. , Mukherjee Bipasha , Burma Sandeep
Published: April 2023

Supplemental Figure 3. A-B. U251 cells and their TMZ-treated counterparts (U251-T12) were A) pulsed with 10 μM TMZ for 48 hours, or B) treated with 1 Gy of IR, fixed at the indicated time points post-treatment, immunofluorescence-stained for 53BP1 foci, and imaged at 40X magnification. Representative images are shown. Rates of repair of TMZ-induced DSBs were determined by scoring 53BP1 foci. Average number of 53BP1 foci per nucleus (y-axis) is plotted against the corresponding time post-treatment (x-axis). Error bars, S.E.M. ****, p< 0.0001. C. Sensitivities of U251 and U251-T12 cells to IR were assessed by colony formation assays. The fraction of surviving colonies (y-axis) is plotted against the corresponding TMZ dose (x-axis). Error bars, S.D.
Supplementary Figure 1 from Augmented HR Repair Mediates Acquired Temozolomide Resistance in Glioblastoma
Authors: Gil del Alcazar Carlos Rodrigo , Todorova Pavlina Krasimirova , Habib Amyn A. , Mukherjee Bipasha , Burma Sandeep
Published: April 2023

Supplemental Figure 1. A. Survival of GBM9 tumor-bearing, untreated or TMZ-treated mice was recorded and represented in a Kaplan-Meier plot. *, p=0.0253 (untreated vs. TMZ treated). B. Primary (483 and 484, in black) and recurrent (419 and 481, in green) cultures were treated with 10 Gy of IR, and cell cycle distribution was assessed by single-parameter flow cytometry after propidium iodide staining for DNA content (x-axis). Please note that all lines are capable of G2 arrest in response to ionizing radiation. C. Primary and recurrent cultures were either mock-irradiated (M) or treated with 10 Gy of ionizing radiation (IR), and harvested after 30 minutes. Whole cell lysates of irradiated cultures were probed for CHK1 and CHK2 phosphorylation by Western blotting with phospho-specific antibodies. Please note activation of CHK1 and CHK2 in both primary and recurrent cultures.
Data Supplement from The Lipid Kinase PI4KIIIβ Is Highly Expressed in Breast Tumors and Activates Akt in Cooperation with Rab11a
Authors: Morrow Anne A. , Alipour Mohsen Amir , Bridges Dave , Yao Zemin , Saltiel Alan R. , Lee Jonathan M.
Published: April 2023

Supplementary Figure 2
Figure S1 from Circular RNA hsa_circ_0014130 Inhibits Apoptosis in Non–Small Cell Lung Cancer by Sponging miR-136-5p and Upregulating BCL2
Authors: Geng Ying , Bao Yongxia , Deng Lili , Su Dongju , Zheng Hongyan , Zhang Wei
Published: April 2023

Supplementary Figure 1 Predicted downstream miRNAs.
Figure S1 from Gas1 Inhibits Metastatic and Metabolic Phenotypes in Colorectal Carcinoma
Authors: Li Qingguo , Qin Yi , Wei Ping , Lian Peng , Li Yaqi , Xu Ye , Li Xinxiang , Li Dawei , Cai Sanjun
Published: April 2023

Endogenous expression level of Gas1 in six colon cancer cells demonstrated by Western blot (A) and RT-PCR (B).
Supplemental Figure Legends. from Distinct Transcriptional Changes and Epithelial–Stromal Interactions Are Altered in Early-Stage Colon Cancer Development
Authors: Mo Allen , Jackson Stephen , Varma Kamini , Carpino Alan , Giardina Charles , Devers Thomas J. , Rosenberg Daniel W.
Published: April 2023

Figure legend for figure S1.
Supplementary Figure 1 from Targeting MPS1 Enhances Radiosensitization of Human Glioblastoma by Modulating DNA Repair Proteins
Authors: Maachani Uday Bhanu , Kramp Tamalee , Hanson Ryan , Zhao Shuping , Celiku Orieta , Shankavaram Uma , Colombo Riccardo , Caplen Natasha J. , Camphausen Kevin , Tandle Anita
Published: April 2023

Supplementary Figure 1: Inhibition of MPS1 activity compromises the viability of GBM tumor cells.
Table S1 from Aquaporin-9, Mediated by IGF2, Suppresses Liver Cancer Stem Cell Properties via Augmenting ROS/β-Catenin/FOXO3a Signaling
Authors: Zheng Xi , Li Chuanfei , Yu Keqi , Shi Shasha , Chen Hongyu , Qian Yanzhi , Mei Zhechuan
Published: April 2023

Table S1 shows the primer sequences for RT-qPCR.
Figure S4 from DNA Replication Stress Induced by Trifluridine Determines Tumor Cell Fate According to p53 Status
Authors: Kataoka Yuki , Iimori Makoto , Fujisawa Ryo , Morikawa-Ichinose Tomomi , Niimi Shinichiro , Wakasa Takeshi , Saeki Hiroshi , Oki Eiji , Miura Daisuke , Tsurimoto Toshiki , Maehara Yoshihiko , Kitao Hiroyuki
Published: April 2023

Data related to Fig. 4.
Supplementary Methods, Figures 1 - 3, Tables 1 - 3 from EZH2 Represses Target Genes through H3K27-Dependent and H3K27-Independent Mechanisms in Hepatocellular Carcinoma
Authors: Gao Shu-Bin , Zheng Qi-Fan , Xu Bin , Pan Chang-Bao , Li Kang-Li , Zhao Yue , Zheng Qi-Lin , Lin Xiao , Xue Li-Xiang , Jin Guang-Hui
Published: April 2023

PDF file - 484K, S1. The efficiency of EZH2 and SUZ12 silencing by shRNA. S2. EZH2 repress TP53 expression in HCC cells. S3. PcG regulated P53 expression through H3K27me3 in an independent manner. Supplemental Table 1. The list of antibodies used in the study. Supplemental Table 2. The list of primers used in the study. Supplemental Table 3. The list of top 200 genes differentially regulated by PcG.
Supplementary Table 2 from Evolution of Dermatofibrosarcoma Protuberans to DFSP-Derived Fibrosarcoma: An Event Marked by Epithelial–Mesenchymal Transition–like Process and 22q Loss
Authors: Stacchiotti Silvia , Astolfi Annalisa , Gronchi Alessandro , Fontana Andrea , Pantaleo Maria A. , Negri Tiziana , Brenca Monica , Tazzari Marcella , Urbini Milena , Indio Valentina , Colombo Chiara , Radaelli Stefano , Brich Silvia , Dei Tos Angelo P. , Casali Paolo G. , Castelli Chiara , Dagrada Gian Paolo , Pilotti Silvana , Maestro Roberta
Published: April 2023

Top 50 upregulated and downregulated genes in FS-DFSP vs DFSP and pathway analyses.
Supplementary Fig. S3 from Hepatitis B Virus X Protein Induces RHAMM-Dependent Motility in Hepatocellular Carcinoma Cells via PI3K–Akt–Oct-1 Signaling
Authors: Liu Yu-Chin , Lu Li-Feng , Li Chia-Jung , Sun Nian-Kang , Guo Jing-You , Huang Ya-Hui , Yeh Chau-Ting , Chao Chuck C.-K.
Published: April 2023

The validation of HBx, Oct-1, and RHAMM expression on xenografts by IHC.
Supplementary Fig. S2 from Hepatitis B Virus X Protein Induces RHAMM-Dependent Motility in Hepatocellular Carcinoma Cells via PI3K–Akt–Oct-1 Signaling
Authors: Liu Yu-Chin , Lu Li-Feng , Li Chia-Jung , Sun Nian-Kang , Guo Jing-You , Huang Ya-Hui , Yeh Chau-Ting , Chao Chuck C.-K.
Published: April 2023

The investigation of HBx and RHAMM regulation on cell motility via Transwell assay.
Supplementary Video 1 from CD44 Regulates Formation of Spheroids and Controls Organ-Specific Metastatic Colonization in Epithelial Ovarian Carcinoma
Authors: Sacks Suarez Joelle , Gurler Main Hilal , Muralidhar Goda G. , Elfituri Osama , Xu Hao-Liang , Kajdacsy-Balla Andre A. , Barbolina Maria V.
Published: April 2023

Adhesion of CD44-/- cells to solid supports.
Figure S6 from CD44 Regulates Formation of Spheroids and Controls Organ-Specific Metastatic Colonization in Epithelial Ovarian Carcinoma
Authors: Sacks Suarez Joelle , Gurler Main Hilal , Muralidhar Goda G. , Elfituri Osama , Xu Hao-Liang , Kajdacsy-Balla Andre A. , Barbolina Maria V.
Published: April 2023

SUPPLEMENTARY FIGURE 6. Creation and characterization of CD44-/- clones of ES2 and SKOV-3.
SI figure legends from Extracellular ATP a New Player in Cancer Metabolism: NSCLC Cells Internalize ATP In Vitro and In Vivo Using Multiple Endocytic Mechanisms
Authors: Qian Yanrong , Wang Xuan , Li Yunsheng , Cao Yanyang , Chen Xiaozhuo
Published: April 2023

supplementary figure legends
SI Methods from Extracellular ATP a New Player in Cancer Metabolism: NSCLC Cells Internalize ATP In Vitro and In Vivo Using Multiple Endocytic Mechanisms
Authors: Qian Yanrong , Wang Xuan , Li Yunsheng , Cao Yanyang , Chen Xiaozhuo
Published: April 2023

supplementary methods
Figure S5 from Extracellular ATP a New Player in Cancer Metabolism: NSCLC Cells Internalize ATP In Vitro and In Vivo Using Multiple Endocytic Mechanisms
Authors: Qian Yanrong , Wang Xuan , Li Yunsheng , Cao Yanyang , Chen Xiaozhuo
Published: April 2023

Fig. S5. A549 tumors internalized injected HMWFD and LMWFD and the internalization was reduced by macropinocytosis inhibitor.
Data Supplement from Hypoxia Provokes Base Excision Repair Changes and a Repair-Deficient, Mutator Phenotype in Colorectal Cancer Cells
Authors: Chan Norman , Ali Mohsin , McCallum Gordon P. , Kumareswaran Ramya , Koritzinsky Marianne , Wouters Bradly G. , Wells Peter G. , Gallinger Steven , Bristow Robert G.
Published: April 2023

Supplementary Figure 1. (A) There is no effect on cell proliferation in RKO cells. (B) There is no effect on S-phase fraction in RKO and paired HCT116 cells. (C) 50-65% Clonogenic cell survival in RKO and paired HCT116 cells. (D) BER mRNA expression is unchanged in RKO cells. qRT-PCR analyses show no significant effects of prolonged hypoxia (72 h x 0.2% O2) on the mRNA levels of selected BER genes in RKO cells. Carbonic anhydrase IX (CAIX) is shown as a positive control for hypoxia.
Figure S8 from DNA Methylome Analyses Implicate Fallopian Tube Epithelia as the Origin for High-Grade Serous Ovarian Cancer
Authors: Klinkebiel David , Zhang Wa , Akers Stacey N. , Odunsi Kunle , Karpf Adam R.
Published: April 2023

TCGA 27K Pearson correlation coefficient analysis.
Supplementary Figure 4 from Systematic Screening of Promoter Regions Pinpoints Functional Cis-Regulatory Mutations in a Cutaneous Melanoma Genome
Authors: Poulos Rebecca C. , Thoms Julie A.I. , Shah Anushi , Beck Dominik , Pimanda John E. , Wong Jason W.H.
Published: April 2023

Supplementary Figure 4. NDUFB9 expression and survival in TCGA cutaneous melanoma sample cohort.
Supplemental Figure Legends from Notch Signaling Activation Is Associated with Patient Mortality and Increased FGF1-Mediated Invasion in Squamous Cell Carcinoma of the Oral Cavity
Authors: Weaver Alice N. , Burch M. Benjamin , Cooper Tiffiny S. , Della Manna Deborah L. , Wei Shi , Ojesina Akinyemi I. , Rosenthal Eben L. , Yang Eddy S.
Published: April 2023

Figure legends for supplemental figures 1-3
Supplemental Figure 3 from Notch Signaling Activation Is Associated with Patient Mortality and Increased FGF1-Mediated Invasion in Squamous Cell Carcinoma of the Oral Cavity
Authors: Weaver Alice N. , Burch M. Benjamin , Cooper Tiffiny S. , Della Manna Deborah L. , Wei Shi , Ojesina Akinyemi I. , Rosenthal Eben L. , Yang Eddy S.
Published: April 2023

Notch-mediated increases in cell migration and invasion are dependent on FGF1 expression in the FaDu cell line.
FIGURE S1 from c-MYC Generates Repair Errors via Increased Transcription of Alternative-NHEJ Factors, LIG3 and PARP1, in Tyrosine Kinase–Activated Leukemias
Authors: Muvarak Nidal , Kelley Shannon , Robert Carine , Baer Maria R. , Perrotti Danilo , Gambacorti-Passerini Carlo , Civin Curt , Scheibner Kara , Rassool Feyruz V.
Published: April 2023

FIGURE S1. SiRNA depletion of c-myc in MO7e-BCR/ABL cells studied for viability
Supplementary Figure Legends from COX-2 Elevates Oncogenic miR-526b in Breast Cancer by EP4 Activation
Authors: Majumder Mousumi , Landman Erin , Liu Ling , Hess David , Lala Peeyush K.
Published: April 2023

Supplementary Figure Legends. Description of supplementary Figures 1-4
Figure S5 from MAPK7 Regulates EMT Features and Modulates the Generation of CTCs
Authors: Javaid Sarah , Zhang Jianmin , Smolen Gromoslaw A. , Yu Min , Wittner Ben S. , Singh Anurag , Arora Kshitij S. , Madden Marissa W. , Desai Rushil , Zubrowski Matthew J. , Schott Benjamin J. , Ting David T. , Stott Shannon L. , Toner Mehmet , Maheswaran Shyamala , Shioda Toshi , Ramaswamy Sridhar , Haber Daniel A.
Published: April 2023

Figure S5. Knockdown of MAPK7, CDC7, CDC2L5 and CSNKID induces Mesenchymal-Epithelial Transition (MET).
S6 from Augmented TME O-GlcNAcylation Promotes Tumor Proliferation through the Inhibition of p38 MAPK
Authors: Moriwaki Kazumasa , Asahi Michio
Published: April 2023

Supplemental Table 3.
Supplementary Figure S2 from AMPK-Independent LKB1 Activity Is Required for Efficient Epithelial Ovarian Cancer Metastasis
Authors: Buensuceso Adrian , Ramos-Valdes Yudith , DiMattia Gabriel E. , Shepherd Trevor G.
Published: April 2023

Effect of LKB1 loss on cell clonogenicity.
Supplementary methods and figure legends from Targeting RICTOR Sensitizes SMAD4-Negative Colon Cancer to Irinotecan
Authors: Wong Chen Khuan , Lambert Arthur W. , Ozturk Sait , Papageorgis Panagiotis , Lopez Delia , Shen Ning , Sen Zaina , Abdolmaleky Hamid M. , Győrffy Balázs , Feng Hui , Thiagalingam Sam
Published: April 2023

Supplementary methods and figure legends
Supplementary Tables 1-8 from Targeting TSLP-Induced Tyrosine Kinase Signaling Pathways in CRLF2-Rearranged Ph-like ALL
Authors: Sia Keith C.S. , Zhong Ling , Mayoh Chelsea , Norris Murray D. , Haber Michelle , Marshall Glenn M. , Raftery Mark J. , Lock Richard B.
Published: April 2023

Supplementary Table S1. Genomic characteristic of ALL PDXs including ALL subtype and key genomic alterations. Supplementary Table S2. Top 5 enriched signaling pathways from the 52 query proteins, as analysed by GO and KEGG pathway analysis platforms. Supplementary Table S3. In vitro combination effects of BMS-754807 and ponatinib. Supplementary Table S4. Differentially expressed genes between Combination and Control (FDR < 0.05). Supplementary Table S5. Differentially expressed genes between BMS-754807 and Control (FDR < 0.05). Supplementary Table S6. Differentially expressed genes between Ponatinib and Control (FDR < 0.05). Supplementary Table S7. KEGG pathway analysis of the differentially expressed genes caused by each treatment condition against control (FDR < 0.25). Supplementary Table S8. Plasma concentration of BMS-754807 and ponatinib as measured by LC-MS/MS.
Supplementary Figure 5 from Colorectal Carcinogenesis: Connecting K-RAS–Induced Transformation and CREB Activity In Vitro and In Vivo
Authors: Steven André , Heiduk Max , Recktenwald Christian V. , Hiebl Bernhard , Wickenhauser Claudia , Massa Chiara , Seliger Barbara
Published: April 2023

Supplementary Figure 5: Influence of CREB on MMP promoter activity
Supplemental Figure Legends from The Histone Demethylase Jumonji Coordinates Cellular Senescence Including Secretion of Neural Stem Cell–Attracting Cytokines
Authors: Perrigue Patrick M. , Silva Michael E. , Warden Charles D. , Feng Nathan L. , Reid Michael A. , Mota Daniel J. , Joseph Lauren P. , Tian Yangzi Isabel , Glackin Carlotta A. , Gutova Margarita , Najbauer Joseph , Aboody Karen S. , Barish Michael E.
Published: April 2023

Supplemental Figure Legends
FigureS3 from Clinical Characteristics and Exploratory Genomic Analyses of Germline BRCA1 or BRCA2 Mutations in Breast Cancer
Authors: Park Sehhoon , Lee Eunjin , Park Seri , Lee Sohee , Nam Seok Jin , Kim Seok Won , Lee Jeong Eon , Yu Jong-Han , Kim Ji-Yeon , Ahn Jin Seok , Im Young-Hyuck , Park Woong-Yang , Park Kyunghee , Park Yeon Hee
Published: April 2023

Figure S3. Mutation profile of genes with top 30 incidence rate in the study population and reference samples.
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 1. Cell selection scheme. For every resistant cell lines all selection steps are shown. Numbers represent AP26113 concentration (nanomolar) added to the medium. For each step a new cell line was established and stored frozen. Cell lines resistant to the highest drug doses were preliminarily tested for AP26113 IC50 value.
Figure S4 from Identification of Endogenous Adenomatous Polyposis Coli Interaction Partners and β-Catenin–Independent Targets by Proteomics
Authors: Popow Olesja , Paulo João A. , Tatham Michael H. , Volk Melanie S. , Rojas-Fernandez Alejandro , Loyer Nicolas , Newton Ian P. , Januschke Jens , Haigis Kevin M. , Näthke Inke
Published: April 2023

Changes in protein abundances in response to APC depletion
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 5. Differential impairment in ALK targeting on all Ba/F3 NPM-ALK mutant cell lines by all clinically relevant ALK inhibitors. All cell lines were incubated for 4 hours in the presence of increasing doses of the compound, then ALK P-Tyr 1604 was assessed by western blot. β-actin was used as loading control.
Figure S4: Proliferation of PTC and ATC orthotopic tumors is not affected by FAK inhibition in vivo. 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

IHC staining on (A) BCPAP and (B) 8505C orthotopic thyroid tumors for Ki67, a marker of cellular proliferation, was performed on sections of each tumor. The percent of Ki67 positive cells was scored. Results are % Ki67 {plus minus} SEM.
Figure S3: FAK kinase inhibition and FAK expression do not regulate thyroid cancer invasion in vitro. 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

BCPAP and 8505C cells exposed to (A) 1uM PF-573,228 for 24 hours or those expressing (B) shFAK were assessed for migration through Matrigel-coated transwell chambers. Invaded cells treated with DMSO control or those expressing scrambled control were set to 100%. Results are percent inhibition of invasion {plus minus} SEM of at least 3 experiments performed in triplicate. No significance observed by Student's t-test.
Supplementary Figure 6 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

The pathological characteristics about MB25550 showed the classic (left) and SHH (right) subgroups.
Supplementary Figure 4 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

Western blot analysis showed the elimination of MELK and EZH2 by being infected with lentivirus encoding shMELK, shEZH2 in comparison to no-target shRNA.
Supplementary Table S1, Supplementary Table S2, Supplementary Figure 1-3. from miR-106a Regulates Cell Proliferation and Autophagy by Targeting LKB1 in HPV-16–Associated Cervical Cancer
Authors: Cui Xiujie , Wang Xiao , Zhou Xiaoqing , Jia Jihui , Chen Hanxiang , Zhao Weiming
Published: April 2023

Table S1. Correlation between miR-106a and clinicopathological features and multivariate logistic regression analysis of risk factors for the high expression of miR-106a (n=91). Table S2. Oligo sequences used in the present study. Figure S1. Transfection efficiency of miR-106a inhibitor and mimics. Figure S2. miR-106a promotes cell proliferation in SiHa and HeLa cells. Figure S3. The knockdown efficiency of HPV-16 E6 and E7 in CaSki.
Supplemental Figure S3 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 S3. Knockdown of RRM2 prolongs PLX4720 treatment response after drug withdrawal.
Supplemental Figure S2 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 S2. Combinatorial inhibition of RRM2 and mutant BRAF increases DNA damage accumulation and apoptosis, which correlates with decreased expression of DNA damage repair genes.
Supplemental Figure S1 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 S1. Combinatorial inhibition of RRM2 and mutant BRAF inhibits cell proliferation to a greater extent than either treatment alone.
Supplemental Figure S3 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 S3. Ornithine, but not citrulline, supplementation partially reversed effects observed with P5CS protein knockdown.
Supplementary Table S3 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

Small interfering RNAs (siRNAs) used in this study.
Supplementary Data from Metabolic Profiling of Formalin-Fixed Paraffin-Embedded Tissues Discriminates Normal Colon from Colorectal Cancer
Authors: Arima Kota , Lau Mai Chan , Zhao Melissa , Haruki Koichiro , Kosumi Keisuke , Mima Kosuke , Gu Mancang , Väyrynen Juha P. , Twombly Tyler S. , Baba Yoshifumi , Fujiyoshi Kenji , Kishikawa Junko , Guo Chunguang , Baba Hideo , Richards William G. , Chan Andrew T. , Nishihara Reiko , Meyerhardt Jeffrey A. , Nowak Jonathan A. , Giannakis Marios , Fuchs Charles S. , Ogino Shuji
Published: April 2023

Supplementary Figure Legends