bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Table 1 from Distinct Subtypes of Gastric Cancer Defined by Molecular Characterization Include Novel Mutational Signatures with Prognostic Capability
Authors: Li Xiangchun , Wu William K.K. , Xing Rui , Wong Sunny H. , Liu Yuexin , Fang Xiaodong , Zhang Yanlin , Wang Mengyao , Wang Jiaqian , Li Lin , Zhou Yong , Tang Senwei , Peng Shaoliang , Qiu Kunlong , Chen Longyun , Chen Kexin , Yang Huanming , Zhang Wei , Chan Matthew T.V. , Lu Youyong , Sung Joseph J.Y. , Yu Jun
Published: March 2023

Supplementary Table 1: Published publications and cohorts
Supplementary Dataset 3 from Distinct Subtypes of Gastric Cancer Defined by Molecular Characterization Include Novel Mutational Signatures with Prognostic Capability
Authors: Li Xiangchun , Wu William K.K. , Xing Rui , Wong Sunny H. , Liu Yuexin , Fang Xiaodong , Zhang Yanlin , Wang Mengyao , Wang Jiaqian , Li Lin , Zhou Yong , Tang Senwei , Peng Shaoliang , Qiu Kunlong , Chen Longyun , Chen Kexin , Yang Huanming , Zhang Wei , Chan Matthew T.V. , Lu Youyong , Sung Joseph J.Y. , Yu Jun
Published: March 2023

Frequent mutations of newly identified SMGs across multiple human cancer types.
Supplementary Figures S1-S14 from TG2 and NF-κB Signaling Coordinates the Survival of Mantle Cell Lymphoma Cells via IL6-Mediated Autophagy
Authors: Zhang Han , Chen Zheng , Miranda Roberto N. , Medeiros L. Jeffrey , McCarty Nami
Published: March 2023

TG2 exon 1 was selected for a site for sgRNA-mediated silencing via a LentiCRISPR system (S1); Apoptotic evaluation of SP53 and Jeko cells with TG2KO using FACS analysis (S2); IL-8 mRNA levels were measured by qRT-PCR in MCL cells with TG2KO or TG2OE. The controls were mock-transfected cells (S3); TG2 contributes to chemotherapy resistance in MCL (S4); Jeko MCL cells with GFP+ p50KD or p65KD were imaged under microscopy (S5); IL-6 addition increases MCL cell viability against chemotherapeutic drugs (S6); TG2 and IL-6 mediates the increased colony-formation ability of MCL cells in MethoCult medium (S7); ATG5 exon 2 was selected for a site for sgRNA mediated silencing via LentiCRISPR system (S8); ATG5KO cells show reduced proliferation rate and increased apoptosis (S9); TG2 signaling regulates autophagy (S10); Upregulated autophagy is responsible for the chemotherapy resistance, which caused by TG2 overexpression in MCL (S11); TG2 overexpression leads to resistance to mTOR inhibitor in MCL (S12); The detection of mRNA levels of IL-6, IL-6 receptor, and IL-6 signal transducer (S13); CD19+ B cells were isolated from apheresis blood / bone marrow of the MCL patients or peripheral blood from healthy donors (S14).
Supplementary Material and Method Details from Novel Protein Disulfide Isomerase Inhibitor with Anticancer Activity in Multiple Myeloma
Authors: Vatolin Sergei , Phillips James G. , Jha Babal K. , Govindgari Shravya , Hu Jennifer , Grabowski Dale , Parker Yvonne , Lindner Daniel J. , Zhong Fei , Distelhorst Clark W. , Smith Mitchell R. , Cotta Claudiu , Xu Yan , Chilakala Sujatha , Kuang Rebecca R. , Tall Samantha , Reu Frederic J.
Published: March 2023

Reagent and chemical library screening details, liver homogenate preparation, CCF642 animal treatment formulation, chemical synthesis schemes, details of proteomic analysis, PDI activity assay and PDI mutant primer sequences
Supplementary Figures S2-4 from Novel Protein Disulfide Isomerase Inhibitor with Anticancer Activity in Multiple Myeloma
Authors: Vatolin Sergei , Phillips James G. , Jha Babal K. , Govindgari Shravya , Hu Jennifer , Grabowski Dale , Parker Yvonne , Lindner Daniel J. , Zhong Fei , Distelhorst Clark W. , Smith Mitchell R. , Cotta Claudiu , Xu Yan , Chilakala Sujatha , Kuang Rebecca R. , Tall Samantha , Reu Frederic J.
Published: March 2023

S2: Inactivation of bortezomib by liver homogenate; S3: CCF642 effect on survival of normal bone marrow, myeloid neoplasia, myeloma and lymphoma cells; S4: Biotin-stained Western blot after treatment of MM1.S cells with B-CCF642
Supplementary Figure S1 from Novel Protein Disulfide Isomerase Inhibitor with Anticancer Activity in Multiple Myeloma
Authors: Vatolin Sergei , Phillips James G. , Jha Babal K. , Govindgari Shravya , Hu Jennifer , Grabowski Dale , Parker Yvonne , Lindner Daniel J. , Zhong Fei , Distelhorst Clark W. , Smith Mitchell R. , Cotta Claudiu , Xu Yan , Chilakala Sujatha , Kuang Rebecca R. , Tall Samantha , Reu Frederic J.
Published: March 2023

Structure, H-NMR and HRMS of CCF642, B-CCF642 and CCF642-COOH
Supplemental Table S1 from Osteogenic Potential of Mesenchymal Stromal Cells Contributes to Primary Myelofibrosis
Authors: Martinaud Christophe , Desterke Christophe , Konopacki Johanna , Pieri Lisa , Torossian Frédéric , Golub Rachel , Schmutz Sandrine , Anginot Adrienne , Guerton Bernadette , Rochet Nathalie , Albanese Patricia , Henault Emilie , Pierre-Louis Olivier , Souraud Jean-Baptiste , de Revel Thierry , Dupriez Brigitte , Ianotto Jean-Christophe , Bourgeade Marie-Françoise , Vannucchi Alessandro M. , Lataillade Jean-Jacques , Le Bousse-Kerdilès Marie-Caroline
Published: March 2023

Primers used for RQ-PCR.
Supplementary Figure Legend, Supplementary Materials and Methods, Supplmentary Figures 1-9 from Small RNAs Recruit Chromatin-Modifying Enzymes MMSET and Tip60 to Reconfigure Damaged DNA upon Double-Strand Break and Facilitate Repair
Authors: Wang Qinhong , Goldstein Michael
Published: March 2023

Supplementary Figure Legends, Figure S1 Dicer- and Drosha-dependent diRNAs are essential for HR repair, Figure S2 Dicer or Drosha is required for the recruitment of MMSET and Tip60 to the DSB, Figure S3 Chemically synthesized oligo-RNAs restored the accumulation of MMSET, Tip60, H4K20me2, 3 and H4K16 Ac at the DSB, Figure S4 Chemically synthesized oligo-RNAs rescued the accumulation of AGO2 at the DSB in Dicer- or Drosha-depleted U2OS cells, Figure S5 Phosphorylation of MMSET at serine 102 site and Tip60 at Tyrosine 44 site enhance the interaction of AGO2 with MMSET and Tip60 after IR (5Gy) exposure, Figure S6 diRNAs bind to AGO2/MMSET/Tip60 complex. A-C, DR-GFP/U2OS cells transfected with indicated siRNA for two days were further transfected with infected with pCBA-β vector expressing I-SecI for another one day, Figure S7 Chemically synthesized oligo-RNAs rescued the accumulation of Rad51 and BRCA1 at the DSB, Figure S8 MMST or Tip60 is essential for chromatin relaxation and the recruitment of Rad51 and BRCA1 to the DSB, Figure S9 Dicer or Drosha has no effect on DNA end resection, Supplementary Materials and Methods,
Supplementary table 1 from A Preclinical Model of Chronic Alcohol Consumption Reveals Increased Metastatic Seeding of Colon Cancer Cells in the Liver
Authors: Im Hwi-Jin , Kim Hyeong-Geug , Lee Jin-Seok , Kim Hyo-Seon , Cho Jung-Hyo , Jo Il-Joo , Park Sung-Joo , Son Chang-Gue
Published: March 2023

Serum biochemistry data and hepatic lipid profiles
Supplemental Figure 2 Brain tumor in adult Drosophila reduces lifespan and causes motor defect. from Drosophila Brat and Human Ortholog TRIM3 Maintain Stem Cell Equilibrium and Suppress Brain Tumorigenesis by Attenuating Notch Nuclear Transport
Authors: Mukherjee Subhas , Tucker-Burden Carol , Zhang Changming , Moberg Kenneth , Read Renee , Hadjipanayis Costas , Brat Daniel J.
Published: March 2023

(A) Kaplan-Meyer survival analysis of adult female Drosophila shows that brat-RNAi leads to a reduction in mean life expectancy as compared to controls. (B) Adult flies with brain tumor also have reduced negative geotaxis, a test of motor function. (C,D,E,F) PH3 staining in whole brain shows the adult brat-RNAi brain with actively dividing cells, whereas normal brain does not contain dividing cells. N = 20. P<0.0001. (G, H) Low magnification image of control and brat-RNAi brain. Repo-GFP shows significantly higher number tumor-like cells (marked with Tub-cherry) expressing the glial marker Repo in brat-RNAi brain. (I,J) Higher magnification image of brat-RNAi brain showing cells that do not express Tub-cherry, but that show Miranda expression. bratIR is brat-RNAi. Scale bar: 150 um for (C-F), 100 um for (G,H), 10um for (I,J).
Supplementary Tables 1-9 from Exome-Scale Discovery of Hotspot Mutation Regions in Human Cancer Using 3D Protein Structure
Authors: Tokheim Collin , Bhattacharya Rohit , Niknafs Noushin , Gygax Derek M. , Kim Rick , Ryan Michael , Masica David L. , Karchin Rachel
Published: March 2023

Table S1: Hotspot regions identified by 3D HotMAPS and overlap with 1D HotMAPS algorithm. Table S2: Tumor-type specific hotspot regions identified by 3D HotMAPS, overlap with 1D HotMAPS, and charactersitic features with naïve bayes score. Table S3: Sample and coverage information for missense mutations mapping onto protein structures or models. Table S4: Genes with HotMAPS regions identified in TCGA tumor types without previous literature support. Table S5: Hotspot regions identified by the 1D algorithm only utilizing primary sequence. Table S6: Tumor-type specifc hotspot regions identified by the 1D algorithm only utilizing primary sequence. Table S7: Residues in 3D HotMAPS regions that overlap with UniProtKB annotations. Table S8: Contigency table of hotspot residues at protein-protein interfaces versus other mutated residues. Table S9: Blacklisted residues that have ambiguous mappings caused by tBLASTn.
Supplemental Figure 1 Brat protein expression is reduced in inscuteable driven brat RNAi neuroblasts at larval and adult stages. from Drosophila Brat and Human Ortholog TRIM3 Maintain Stem Cell Equilibrium and Suppress Brain Tumorigenesis by Attenuating Notch Nuclear Transport
Authors: Mukherjee Subhas , Tucker-Burden Carol , Zhang Changming , Moberg Kenneth , Read Renee , Hadjipanayis Costas , Brat Daniel J.
Published: March 2023

(A-H) Panels showing 3rd Inster larval brain. (A-D) Brain of normal larva expressing Brat protein. (E-H) Brain of brat-RNAi expressing larva showing reduced Brat protein. Scale bar: 10um. (I-X) Panels showing 5days old adult brain. (I-L and Q-T) Brain of control adult expressing Brat protein. (M-P and U-X) Brain of brat-RNAi expressing adults showing reduced Brat protein. Scare bar: (I-P) 100um and (Q-X) 10um. bratIR is brat-RNAi.
Figure S6 from Nkx2.8 Inhibits Epithelial–Mesenchymal Transition in Bladder Urothelial Carcinoma via Transcriptional Repression of Twist1
Authors: Yu Chunping , Liu Zhuowei , Chen Qiuhong , Li Yonghong , Jiang Lijuan , Zhang Zhiling , Zhou Fangjian
Published: March 2023

Typical pictures of orthotopic xenograft bladder cancer model with 5637/Nkx2.8 RNAi and 5637/Nkx2.8 RNAi/Twist1 RNAi cells
Figure S7 from RASSF1A Directly Antagonizes RhoA Activity through the Assembly of a Smurf1-Mediated Destruction Complex to Suppress Tumorigenesis
Authors: Lee Min-Goo , Jeong Seong-In , Ko Kyung-Phil , Park Soon-Ki , Ryu Byung-Kyu , Kim Ick-Young , Kim Jeong-Kook , Chi Sung-Gil
Published: March 2023

Figure S7. Representative examples of RASSF1A and RhoA immunostaining in primary and metastasized breast tumors and adjacent normal tissues.
Figure S2 from Myc Expression Drives Aberrant Lipid Metabolism in Lung Cancer
Authors: Hall Zoe , Ament Zsuzsanna , Wilson Catherine H. , Burkhart Deborah L. , Ashmore Tom , Koulman Albert , Littlewood Trevor , Evan Gerard I. , Griffin Julian L.
Published: March 2023

Relative abundances of free fatty acids, phosphatidylglycerols and phosphatidylinositols in tumour compared to normal lung tissue.
Figure S2 from RASSF1A Directly Antagonizes RhoA Activity through the Assembly of a Smurf1-Mediated Destruction Complex to Suppress Tumorigenesis
Authors: Lee Min-Goo , Jeong Seong-In , Ko Kyung-Phil , Park Soon-Ki , Ryu Byung-Kyu , Kim Ick-Young , Kim Jeong-Kook , Chi Sung-Gil
Published: March 2023

Figure S2. RASSF1A interacts with RhoA. A, No interaction between RASSF1A and active Ras proteins. HeLa cells were transfected with HA-tagged H-Ras-G14V, K-Ras-G14V, or N-Ras-Q61R. Immunoprecipitation and immunoblots were performed as indicated. B, Characterization of RASSF1A-binding region of RhoA. C, No RhoA inhibition activity of RASSF1A-R269F. Cells transfected with WT or mutant (R269F) RASSF1A were treated with EGF (10 ng/ml) for 6 h. D, Construction of exon 2Î³-deleted RASSF1C mutant (Î”2Î³). E, IP assay showing RhoA interaction with RASSF1C-Î”2Î³ but not with WT-RASSF1C.
Supplemental Informaiton from Cyclin A1 and P450 Aromatase Promote Metastatic Homing and Growth of Stem-like Prostate Cancer Cells in the Bone Marrow
Authors: Miftakhova Regina , Hedblom Andreas , Semenas Julius , Robinson Brian , Simoulis Athanasios , Malm Johan , Rizvanov Albert , Heery David M. , Mongan Nigel P. , Maitland Norman J. , Allegrucci Cinzia , Persson Jenny L.
Published: March 2023

Supplemental Materials and Methods and figure text for supplemental figures
Supplemental Figure Legends from JPO2/CDCA7L and LEDGF/p75 Are Novel Mediators of PI3K/AKT Signaling and Aggressive Phenotypes in Medulloblastoma
Authors: Chan Tiffany Sin Yu , Hawkins Cynthia , Krieger Jonathan R. , McGlade C. Jane , Huang Annie
Published: March 2023

Supplemental Figure Legends 1-8
Suppl. Figure 5 from HSP70 Inhibition Limits FAK-Dependent Invasion and Enhances the Response to Melanoma Treatment with BRAF Inhibitors
Authors: Budina-Kolomets Anna , Webster Marie R. , Leu Julia I-Ju , Jennis Matthew , Krepler Clemens , Guerrini Anastasia , Kossenkov Andrew V. , Xu Wei , Karakousis Giorgos , Schuchter Lynn , Amaravadi Ravi K. , Wu Hong , Yin Xiangfan , Liu Qin , Lu Yiling , Mills Gordon B. , Xu Xiaowei , George Donna L. , Weeraratna Ashani T. , Murphy Maureen E.
Published: March 2023

Impact of PET-16 on melanoma in vivo A. Cell viability analysis of B16-F10 cell line treated with DMSO or the indicated doses of PES-Cl or PET-16 for 72 hours.
Suppl. Figure 3 from HSP70 Inhibition Limits FAK-Dependent Invasion and Enhances the Response to Melanoma Treatment with BRAF Inhibitors
Authors: Budina-Kolomets Anna , Webster Marie R. , Leu Julia I-Ju , Jennis Matthew , Krepler Clemens , Guerrini Anastasia , Kossenkov Andrew V. , Xu Wei , Karakousis Giorgos , Schuchter Lynn , Amaravadi Ravi K. , Wu Hong , Yin Xiangfan , Liu Qin , Lu Yiling , Mills Gordon B. , Xu Xiaowei , George Donna L. , Weeraratna Ashani T. , Murphy Maureen E.
Published: March 2023

RPPA Analysis of Melanoma cell lines treated with PET-16 WM793 and 1205Lu cells were treated with DMSO or with the indicated concentrations of PET-16 for 24 hours and then subjected to RPPA analysis.
Supplemental Figure 1 from IL17 Functions through the Novel REG3β–JAK2–STAT3 Inflammatory Pathway to Promote the Transition from Chronic Pancreatitis to Pancreatic Cancer
Authors: Loncle Celine , Bonjoch Laia , Folch-Puy Emma , Lopez-Millan Maria Belen , Lac Sophie , Molejon Maria Inés , Chuluyan Eduardo , Cordelier Pierre , Dubus Pierre , Lomberk Gwen , Urrutia Raul , Closa Daniel , Iovanna Juan L.
Published: March 2023

Schematic representation of the IL-17A and REG3β signaling pathway and PDAC development.
Supplementary Table 9 from MCAM and LAMA4 Are Highly Enriched in Tumor Blood Vessels of Renal Cell Carcinoma and Predict Patient Outcome
Authors: Wragg Joseph W. , Finnity Jonathan P. , Anderson Jane A. , Ferguson Henry J.M. , Porfiri Emilio , Bhatt Rupesh I. , Murray Paul G. , Heath Victoria L. , Bicknell Roy
Published: March 2023

Supplementary Table 9: Key clinical data for clear cell RCC cohort 2 showing overall survival (OS)
Supplementary Figures 1-5 from Ras Signaling Is a Key Determinant for Metastatic Dissemination and Poor Survival of Luminal Breast Cancer Patients
Authors: Wright Katherine L. , Adams Jessica R. , Liu Jeff C. , Loch Amanda J. , Wong Ruth G. , Jo Christine E.B. , Beck Lauren A. , Santhanam Divya R. , Weiss Laura , Mei Xue , Lane Timothy F. , Koralov Sergei B. , Done Susan J. , Woodgett James R. , Zacksenhaus Eldad , Hu Pingzhao , Egan Sean E.
Published: March 2023

Supplementary Figures 1-5. Supplementary Fig. 1. Kaplan-Meier overall survival curves and cause of death data for control and experimental female mice. Supplementary Fig. 2. Mammary pathology analysis and estrogen receptor α staining for experimental mice. Supplementary Fig. 3. Activation of Stat3 and Mapk signaling in mouse mammary tumors. Supplementary Fig. 4. Ras pathway activation is associated with relapse and survival of breast cancer patients independent of PI3K and Stat3 pathway activation. Supplementary Fig. 5. PI3K pathway activation is associated with relapse of patients with Basal-like breast cancer.
Supplementary Table 8 from MCAM and LAMA4 Are Highly Enriched in Tumor Blood Vessels of Renal Cell Carcinoma and Predict Patient Outcome
Authors: Wragg Joseph W. , Finnity Jonathan P. , Anderson Jane A. , Ferguson Henry J.M. , Porfiri Emilio , Bhatt Rupesh I. , Murray Paul G. , Heath Victoria L. , Bicknell Roy
Published: March 2023

Supplementary Table 8: Key clinical data for clear cell RCC cohort 1, showing overall survival (OS)
Supplemental Figure Legends from Molecular Pathology of Patient Tumors, Patient-Derived Xenografts, and Cancer Cell Lines
Authors: Guo Sheng , Qian Wubin , Cai Jie , Zhang Likun , Wery Jean-Pierre , Li Qi-Xiang
Published: March 2023

Supplemental Figure Legends
Supplementary Figures 1 through 13 from Cdk5 Directly Targets Nuclear p21CIP1 and Promotes Cancer Cell Growth
Authors: Huang Pao-Hsuan , Chen Mei-Chih , Peng Yu-Ting , Kao Wei-Hsiang , Chang Chih-Hsiang , Wang Yun-Chi , Lai Chih-Ho , Hsieh Jer-Tsong , Wang Jo-Hsin , Lee Yueh-Tsung , Lin Eugene , Yue Chia-Herng , Wang Hsin-Yi , You Shuen-Chi , Lin Ho
Published: March 2023

Figure S1. Cdk5 activity is correspondent to itself protein level and type. Figure S2. The analysis of Cdk5 and p21CIP1protein levels in the specimens of breast cancer patients. Figure S3. Representative images of immunohistochemicalstaining. Figure S4. Inhibition of proteasome activity by lactacystinrestores Cdk5-triggered p21CIP1protein decrease. Figure S5. The proteasome inhibitors, MG132 and Lactacystin, do not influence the trends of p21CIP1mRNA levels regulated by different statuses of Cdk5 activation. Figure S6. The efficiency test of different clones of shCdk5and shCdk2 in cancer cells and the knockdown efficiency of shCdk2in xenograft tumors. Figure S7. The nuclear levels of p21CIP1protein were increased by Cdk5 knockdown. Figure S8. The protein levels of Cdk5 and p21CIP1transient transfections in MCF-7 cells for the reference of Figure 5B. Figure S9. Nuclear S130A p21CIP1is resistant to Cdk5-induced degradation. Figure S10. Cdk5-induced p21CIP1degradation is ubiquitination-independent. Figure S11. Cdk5 enables to decrease p21 protein with or without Aktinhibition. Figure S12. Cdk5 activity is not essential to its protein interaction with p21CIP1. Figure S13. Nuclear S130A p21CIP1is tightly interacted with Cdk5 in nucleus.
Supplemental figure 3 from CCR2 Influences T Regulatory Cell Migration to Tumors and Serves as a Biomarker of Cyclophosphamide Sensitivity
Authors: Loyher Pierre-Louis , Rochefort Juliette , Baudesson de Chanville Camille , Hamon Pauline , Lescaille Géraldine , Bertolus Chloé , Guillot-Delost Maude , Krummel Matthew F. , Lemoine François M. , Combadière Christophe , Boissonnas Alexandre
Published: March 2023

CCL2-AF647 staning allows specific characterization of CCR2 receptor expression on Tregs
Supplemental figure 1 from CCR2 Influences T Regulatory Cell Migration to Tumors and Serves as a Biomarker of Cyclophosphamide Sensitivity
Authors: Loyher Pierre-Louis , Rochefort Juliette , Baudesson de Chanville Camille , Hamon Pauline , Lescaille Géraldine , Bertolus Chloé , Guillot-Delost Maude , Krummel Matthew F. , Lemoine François M. , Combadière Christophe , Boissonnas Alexandre
Published: March 2023

Tregs fail to migrate to the tumor in Ccr2-/- mice but accumulate in the dLN
Supplementary Materials and Methods from Kv1.3 Channels Mark Functionally Competent CD8+ Tumor-Infiltrating Lymphocytes in Head and Neck Cancer
Authors: Chimote Ameet A. , Hajdu Peter , Sfyris Alexandros M. , Gleich Brittany N. , Wise-Draper Trisha , Casper Keith A. , Conforti Laura
Published: March 2023

Methods for Supplementary Figure S6
Supplementary Figure S6 from Kv1.3 Channels Mark Functionally Competent CD8+ Tumor-Infiltrating Lymphocytes in Head and Neck Cancer
Authors: Chimote Ameet A. , Hajdu Peter , Sfyris Alexandros M. , Gleich Brittany N. , Wise-Draper Trisha , Casper Keith A. , Conforti Laura
Published: March 2023

CD3+ cell infiltration into HNC tumors
Supplementary Figure S5 from Kv1.3 Channels Mark Functionally Competent CD8+ Tumor-Infiltrating Lymphocytes in Head and Neck Cancer
Authors: Chimote Ameet A. , Hajdu Peter , Sfyris Alexandros M. , Gleich Brittany N. , Wise-Draper Trisha , Casper Keith A. , Conforti Laura
Published: March 2023

Viability and phenotyping of freshly isolated TILs isolated from a HNC patient
Supplementary Figure S4 from Kv1.3 Channels Mark Functionally Competent CD8+ Tumor-Infiltrating Lymphocytes in Head and Neck Cancer
Authors: Chimote Ameet A. , Hajdu Peter , Sfyris Alexandros M. , Gleich Brittany N. , Wise-Draper Trisha , Casper Keith A. , Conforti Laura
Published: March 2023

Quantitation of Kv1.3 protein expression in CD8+ TIL
Supplementary Table S1 from Pharmacological Inhibition of Centrosome Clustering by Slingshot-Mediated Cofilin Activation and Actin Cortex Destabilization
Authors: Konotop Gleb , Bausch Elena , Nagai Tomoaki , Turchinovich Andrey , Becker Natalia , Benner Axel , Boutros Michael , Mizuno Kensaku , Krämer Alwin , Raab Marc Steffen
Published: March 2023

Screen result. For each library and concentration, compounds are divided into two groups, according to readout significance (black, P < 0.05; grey P > 0.05) and sorted from highest to lowest CCI index. Compounds highlighted in bold represent a CCI index higher than 0.3, indicating that viability of cells with CA was significantly affected in comparison to cells with normal centrosome content (by approx. 20%). Relative overall viability of each drug-treated cell population in comparison to the corresponding DMSO-treated population (maximum viability = 1) is indicated by rel.Control or rel.Tet. Compounds that eradicated both cell populations, giving a false positive result are highlighted in red (i.e. Crizotinib).
Supplementary Figure S2 from Kv1.3 Channels Mark Functionally Competent CD8+ Tumor-Infiltrating Lymphocytes in Head and Neck Cancer
Authors: Chimote Ameet A. , Hajdu Peter , Sfyris Alexandros M. , Gleich Brittany N. , Wise-Draper Trisha , Casper Keith A. , Conforti Laura
Published: March 2023

Assessment of background staining for non-conjugated antibodies
Supplementary Table S2 from Glucose Metabolism Reprogrammed by Overexpression of IKKϵ Promotes Pancreatic Tumor Growth
Authors: Zubair Haseeb , Azim Shafquat , Srivastava Sanjeev Kumar , Ahmad Aamir , Bhardwaj Arun , Khan Mohammad Aslam , Patel Girijesh Kumar , Arora Sumit , Carter James Elliot , Singh Seema , Singh Ajay Pratap
Published: March 2023

Population doubling time of IKKepsilon-silenced cell lines and their respective controls in hours.
SI Table 1 from TLR Adaptor Protein MYD88 Mediates Sensitivity to HDAC Inhibitors via a Cytokine-Dependent Mechanism
Authors: New Maria , Sheikh Semira , Bekheet Mina , Olzscha Heidi , Thezenas Marie-Laetitia , Care Matthew A. , Fotheringham Susan , Tooze Reuben M. , Kessler Benedikt , La Thangue Nicholas B.
Published: March 2023

Supplemental figures 1-5 legends
SI Figure 1 from TLR Adaptor Protein MYD88 Mediates Sensitivity to HDAC Inhibitors via a Cytokine-Dependent Mechanism
Authors: New Maria , Sheikh Semira , Bekheet Mina , Olzscha Heidi , Thezenas Marie-Laetitia , Care Matthew A. , Fotheringham Susan , Tooze Reuben M. , Kessler Benedikt , La Thangue Nicholas B.
Published: March 2023

MYD88 expression and IL-6 sensitises cells to HDAC inhibition
Supplementary Table S2 from Ovarian Cancer Chemoresistance Relies on the Stem Cell Reprogramming Factor PBX1
Authors: Jung Jin-Gyoung , Shih Ie-Ming , Park Joon Tae , Gerry Emily , Kim Tae Hoen , Ayhan Ayse , Handschuh Karen , Davidson Ben , Fader Amanda N. , Selleri Licia , Wang Tian-Li
Published: March 2023

Enriched IPA pathways inferred from PBX1-ChIP target genes.
Supplementary Data from Ovarian Cancer Chemoresistance Relies on the Stem Cell Reprogramming Factor PBX1
Authors: Jung Jin-Gyoung , Shih Ie-Ming , Park Joon Tae , Gerry Emily , Kim Tae Hoen , Ayhan Ayse , Handschuh Karen , Davidson Ben , Fader Amanda N. , Selleri Licia , Wang Tian-Li
Published: March 2023

Including Supplementary Figures and Methods
Supplemental Table S1 from Ovarian Cancer Chemoresistance Relies on the Stem Cell Reprogramming Factor PBX1
Authors: Jung Jin-Gyoung , Shih Ie-Ming , Park Joon Tae , Gerry Emily , Kim Tae Hoen , Ayhan Ayse , Handschuh Karen , Davidson Ben , Fader Amanda N. , Selleri Licia , Wang Tian-Li
Published: March 2023

Gene promoters identified by PBX1 ChIP-on-chip.
Supplementary Table S3 from Molecular Evolution Patterns in Metastatic Lymph Nodes Reflect the Differential Treatment Response of Advanced Primary Lung Cancer
Authors: Um Sang-Won , Joung Je-Gun , Lee Hyun , Kim Hojoong , Kim Kyu-Tae , Park Jinha , Hayes D. Neil , Park Woong-Yang
Published: March 2023

Table S3. The list of samples used in whole-exome and RNA sequencing from advanced lung cancer patients
Table S3 from Spatial Proximity to Fibroblasts Impacts Molecular Features and Therapeutic Sensitivity of Breast Cancer Cells Influencing Clinical Outcomes
Authors: Marusyk Andriy , Tabassum Doris P. , Janiszewska Michalina , Place Andrew E. , Trinh Anne , Rozhok Andrii I. , Pyne Saumyadipta , Guerriero Jennifer L. , Shu Shaokun , Ekram Muhammad , Ishkin Alexander , Cahill Daniel P. , Nikolsky Yuri , Chan Timothy A. , Rimawi Mothaffar F. , Hilsenbeck Susan , Schiff Rachel , Osborne Kent C. , Letai Antony , Polyak Kornelia
Published: March 2023

List of differentially present metabolites. The table lists fold change value of metabolites differentially detected in CAF co-cultures compared to separately cultured cells in at least one of the cell lines. Bold font indicates statistically significant (p<0.05, pairwise t-test) changes.
Supplementary Figure S5 from Molecular Evolution Patterns in Metastatic Lymph Nodes Reflect the Differential Treatment Response of Advanced Primary Lung Cancer
Authors: Um Sang-Won , Joung Je-Gun , Lee Hyun , Kim Hojoong , Kim Kyu-Tae , Park Jinha , Hayes D. Neil , Park Woong-Yang
Published: March 2023

Figure S5. The measurement representing early vs. late metastasis. (A) The percentage of trunk/non-trunk mutations for six cases. (B) The expression levels of AKT2 gene as a potential early event in tumorigenesis.
Supplementary Figure S4 from Molecular Evolution Patterns in Metastatic Lymph Nodes Reflect the Differential Treatment Response of Advanced Primary Lung Cancer
Authors: Um Sang-Won , Joung Je-Gun , Lee Hyun , Kim Hojoong , Kim Kyu-Tae , Park Jinha , Hayes D. Neil , Park Woong-Yang
Published: March 2023

Figure S4. The genomic and transcriptomic pattern of TH6 case. (A) The mutation heatmap. (B) The scatter plot shows the similarity of gene expression profiles between nodes (using 15,842 genes with at least > 5 reads) by measuring Pearson's correlation coefficient (r). (C) The density plot of cancer cell fraction (CCF) between the primary and the lymph node. (D) The gene expression pattern of genes belonging to SQCCs, PI(3)K/RTK/RAS signaling. Gene expression values in lymph nodes were mapped on the distribution of gene expression in TCGA SQCCs (n=495), represented by the boxplot. AKT2 and RASA1 show significant clinical outcome difference in the gene expression of TCGA SQCCs patients; *P < 0.05.
Supplementary Table S1 from LncRNA HOXA11-AS Promotes Proliferation and Invasion of Gastric Cancer by Scaffolding the Chromatin Modification Factors PRC2, LSD1, and DNMT1
Authors: Sun Ming , Nie Fengqi , Wang Yunfei , Zhang Zhihong , Hou Jiakai , He Dandan , Xie Min , Xu Lin , De Wei , Wang Zhaoxia , Wang Jun
Published: March 2023

The patients clinical data, primer, siRNA and shRNA sequences, TCGA and GEO analysis results.
Supplementary Figure S6 from LncRNA HOXA11-AS Promotes Proliferation and Invasion of Gastric Cancer by Scaffolding the Chromatin Modification Factors PRC2, LSD1, and DNMT1
Authors: Sun Ming , Nie Fengqi , Wang Yunfei , Zhang Zhihong , Hou Jiakai , He Dandan , Xie Min , Xu Lin , De Wei , Wang Zhaoxia , Wang Jun
Published: March 2023

Analysis of PRSS8 and KLF2 expression levels in GC tissues.
Supplementary Figure S5 from LncRNA HOXA11-AS Promotes Proliferation and Invasion of Gastric Cancer by Scaffolding the Chromatin Modification Factors PRC2, LSD1, and DNMT1
Authors: Sun Ming , Nie Fengqi , Wang Yunfei , Zhang Zhihong , Hou Jiakai , He Dandan , Xie Min , Xu Lin , De Wei , Wang Zhaoxia , Wang Jun
Published: March 2023

The KLF2 and PRSS8 are key underlying targets of HOXA11-AS in GC cells.
Supplementary Figure S3 from LncRNA HOXA11-AS Promotes Proliferation and Invasion of Gastric Cancer by Scaffolding the Chromatin Modification Factors PRC2, LSD1, and DNMT1
Authors: Sun Ming , Nie Fengqi , Wang Yunfei , Zhang Zhihong , Hou Jiakai , He Dandan , Xie Min , Xu Lin , De Wei , Wang Zhaoxia , Wang Jun
Published: March 2023

HOXA11-AS promotes GC cells proliferation, migration and invasion.
Supplementary Figure 3 from JNK Pathway Activation Modulates Acquired Resistance to EGFR/HER2–Targeted Therapies
Authors: Manole Simin , Richards Edward J. , Meyer Aaron S.
Published: March 2023

Parameter outputs of regression model in Figure 3C.
Supplementary Figure 2 from JNK Pathway Activation Modulates Acquired Resistance to EGFR/HER2–Targeted Therapies
Authors: Manole Simin , Richards Edward J. , Meyer Aaron S.
Published: March 2023

Validation of RTK overexpression.
Supplementary Figure S1 from LncRNA HOXA11-AS Promotes Proliferation and Invasion of Gastric Cancer by Scaffolding the Chromatin Modification Factors PRC2, LSD1, and DNMT1
Authors: Sun Ming , Nie Fengqi , Wang Yunfei , Zhang Zhihong , Hou Jiakai , He Dandan , Xie Min , Xu Lin , De Wei , Wang Zhaoxia , Wang Jun
Published: March 2023

The HOXA11-AS and five other lncRNAs expression levels in GC and other cancers tissues.
Supplementary Figure 1 from JNK Pathway Activation Modulates Acquired Resistance to EGFR/HER2–Targeted Therapies
Authors: Manole Simin , Richards Edward J. , Meyer Aaron S.
Published: March 2023

Mismatched RTK capacity and pathway dependency fail to provide bypass resistance.
Supplementary Figure Legends from LncRNA HOXA11-AS Promotes Proliferation and Invasion of Gastric Cancer by Scaffolding the Chromatin Modification Factors PRC2, LSD1, and DNMT1
Authors: Sun Ming , Nie Fengqi , Wang Yunfei , Zhang Zhihong , Hou Jiakai , He Dandan , Xie Min , Xu Lin , De Wei , Wang Zhaoxia , Wang Jun
Published: March 2023

Legend for Supplementary Figures S1-S6.
Supplementary Methods and References from Splenic Marginal Zone Granulocytes Acquire an Accentuated Neutrophil B-Cell Helper Phenotype in Chronic Lymphocytic Leukemia
Authors: Gätjen Marcel , Brand Franziska , Grau Michael , Gerlach Kerstin , Kettritz Ralph , Westermann Jörg , Anagnostopoulos Ioannis , Lenz Peter , Lenz Georg , Höpken Uta E. , Rehm Armin
Published: March 2023

Description of additional methods and procedures used in the study. Also includes Supplementary References.
Supplementary Figure S6 from Splenic Marginal Zone Granulocytes Acquire an Accentuated Neutrophil B-Cell Helper Phenotype in Chronic Lymphocytic Leukemia
Authors: Gätjen Marcel , Brand Franziska , Grau Michael , Gerlach Kerstin , Kettritz Ralph , Westermann Jörg , Anagnostopoulos Ioannis , Lenz Peter , Lenz Georg , Höpken Uta E. , Rehm Armin
Published: March 2023

The extracellular matrix protein TGFBi is stronger expressed in tumor-bearing Eμ-Tcl1 mice.
Table S1 from Signal-Oriented Pathway Analyses Reveal a Signaling Complex as a Synthetic Lethal Target for p53 Mutations
Authors: Lu Songjian , Cai Chunhui , Yan Gonghong , Zhou Zhuan , Wan Yong , Chen Vicky , Chen Lujia , Cooper Gregory F. , Obeid Lina M. , Hannun Yusuf A. , Lee Adrian V. , Lu Xinghua
Published: March 2023

An MS Excel file listing Response Modules
Supplementary Figure S4 from Splenic Marginal Zone Granulocytes Acquire an Accentuated Neutrophil B-Cell Helper Phenotype in Chronic Lymphocytic Leukemia
Authors: Gätjen Marcel , Brand Franziska , Grau Michael , Gerlach Kerstin , Kettritz Ralph , Westermann Jörg , Anagnostopoulos Ioannis , Lenz Peter , Lenz Georg , Höpken Uta E. , Rehm Armin
Published: March 2023

Neutrophil depletion does not affect the pro-inflammatory cytokine milieu in Eμ-Tcl1 leukemia B cells.
Tabel S2 from Signal-Oriented Pathway Analyses Reveal a Signaling Complex as a Synthetic Lethal Target for p53 Mutations
Authors: Lu Songjian , Cai Chunhui , Yan Gonghong , Zhou Zhuan , Wan Yong , Chen Vicky , Chen Lujia , Cooper Gregory F. , Obeid Lina M. , Hannun Yusuf A. , Lee Adrian V. , Lu Xinghua
Published: March 2023

An MS Excel file containing the response modules that are highly informative of patient outcome.
Supplementary Figure S3 from Splenic Marginal Zone Granulocytes Acquire an Accentuated Neutrophil B-Cell Helper Phenotype in Chronic Lymphocytic Leukemia
Authors: Gätjen Marcel , Brand Franziska , Grau Michael , Gerlach Kerstin , Kettritz Ralph , Westermann Jörg , Anagnostopoulos Ioannis , Lenz Peter , Lenz Georg , Höpken Uta E. , Rehm Armin
Published: March 2023

Neutrophil localization in human SMZL and benign spleen tissues.
Supplementary figures from CIC-DUX4 Induces Small Round Cell Sarcomas Distinct from Ewing Sarcoma
Authors: Yoshimoto Toyoki , Tanaka Miwa , Homme Mizuki , Yamazaki Yukari , Takazawa Yutaka , Antonescu Cristina R. , Nakamura Takuro
Published: March 2023

Supplementary data including supplementary figures 1-4 and legends
Supplemental Table S4 from CIC-DUX4 Induces Small Round Cell Sarcomas Distinct from Ewing Sarcoma
Authors: Yoshimoto Toyoki , Tanaka Miwa , Homme Mizuki , Yamazaki Yukari , Takazawa Yutaka , Antonescu Cristina R. , Nakamura Takuro
Published: March 2023

Downregulated genes in eMCs expressing CIC-DUX4 vs eMCs with an empty vector
Supplemental Table S3 from CIC-DUX4 Induces Small Round Cell Sarcomas Distinct from Ewing Sarcoma
Authors: Yoshimoto Toyoki , Tanaka Miwa , Homme Mizuki , Yamazaki Yukari , Takazawa Yutaka , Antonescu Cristina R. , Nakamura Takuro
Published: March 2023

Unregulated genes in eMCs expressing CIC-DUX4 vs eMCs with an empty vector
Supplementary Materials and Methods from Pyruvate Kinase Inhibits Proliferation during Postnatal Cerebellar Neurogenesis and Suppresses Medulloblastoma Formation
Authors: Tech Katherine , Tikunov Andrey P. , Farooq Hamza , Morrissy A. Sorana , Meidinger Jessica , Fish Taylor , Green Sarah C. , Liu Hedi , Li Yisu , Mungall Andrew J. , Moore Richard A. , Ma Yussanne , Jones Steven J.M. , Marra Marco A. , Vander Heiden Matthew G. , Taylor Michael D. , Macdonald Jeffrey M. , Gershon Timothy R.
Published: March 2023

Supplementary Materials and Methods, including NMR, LC-MS and RNA-seq methods
Supplementary Figure Legends from Androgen and Estrogen Receptors in Breast Cancer Coregulate Human UDP-Glucuronosyltransferases 2B15 and 2B17
Authors: Hu Dong G. , Selth Luke A. , Tarulli Gerard A. , Meech Robyn , Wijayakumara Dhilushi , Chanawong Apichaya , Russell Roslin , Caldas Carlos , Robinson Jessica L.L. , Carroll Jason S. , Tilley Wayne D. , Mackenzie Peter I. , Hickey Theresa E.
Published: March 2023

Word Document with legends for supplementary figures
Supplementary Figure S5 from The p53/p21 Complex Regulates Cancer Cell Invasion and Apoptosis by Targeting Bcl-2 Family Proteins
Authors: Kim Eun Mi , Jung Chan-Hun , Kim Jongdoo , Hwang Sang-Gu , Park Jong Kuk , Um Hong-Duck
Published: March 2023

p53-p21 cooperation in HCT116 cells in vivo
Supplementary Table 2 from IGFBP2 Activates the NF-κB Pathway to Drive Epithelial–Mesenchymal Transition and Invasive Character in Pancreatic Ductal Adenocarcinoma
Authors: Gao Song , Sun Yan , Zhang Xuebin , Hu Limei , Liu Yuexin , Chua Corrine Yingxuan , Phillips Lynette M. , Ren He , Fleming Jason B. , Wang Huamin , Chiao Paul J. , Hao Jihui , Zhang Wei
Published: March 2023

Correlation of tumor IGFBP2 expression with clinicopathologic characteristics of 80 patients with PDAC
Supplementary Table 1 from IGFBP2 Activates the NF-κB Pathway to Drive Epithelial–Mesenchymal Transition and Invasive Character in Pancreatic Ductal Adenocarcinoma
Authors: Gao Song , Sun Yan , Zhang Xuebin , Hu Limei , Liu Yuexin , Chua Corrine Yingxuan , Phillips Lynette M. , Ren He , Fleming Jason B. , Wang Huamin , Chiao Paul J. , Hao Jihui , Zhang Wei
Published: March 2023

Antibodies, siRNAs, and primers used in this study
SUPPLEMENTARY figure 7 from IGFBP2 Activates the NF-κB Pathway to Drive Epithelial–Mesenchymal Transition and Invasive Character in Pancreatic Ductal Adenocarcinoma
Authors: Gao Song , Sun Yan , Zhang Xuebin , Hu Limei , Liu Yuexin , Chua Corrine Yingxuan , Phillips Lynette M. , Ren He , Fleming Jason B. , Wang Huamin , Chiao Paul J. , Hao Jihui , Zhang Wei
Published: March 2023

Expression of IGFBP1, IGFBP3, IGFBP4, and IGFBP5 in tumors from PDAC patients and relationship of IGFBP3 and IGFBP5 expression to patient survival.
Supplementary Figure S1 from The p53/p21 Complex Regulates Cancer Cell Invasion and Apoptosis by Targeting Bcl-2 Family Proteins
Authors: Kim Eun Mi , Jung Chan-Hun , Kim Jongdoo , Hwang Sang-Gu , Park Jong Kuk , Um Hong-Duck
Published: March 2023

p53-p21 cooperation for H2O2-induced apoptosis
Supplementary Fig. 6 from APOBEC3A and APOBEC3B Activities Render Cancer Cells Susceptible to ATR Inhibition
Authors: Buisson Rémi , Lawrence Michael S. , Benes Cyril H. , Zou Lee
Published: March 2023

This figure provides additional information on the induction of AP sites at replication forks in ATRi-treated A3A expressing cells. It is supplementary to the main figure 6.
Supplementary Fig. 4 from APOBEC3A and APOBEC3B Activities Render Cancer Cells Susceptible to ATR Inhibition
Authors: Buisson Rémi , Lawrence Michael S. , Benes Cyril H. , Zou Lee
Published: March 2023

This figure contains data concerning the regulation of the ATRi-induced DNA damage in A3A expressing cells. It is supplementary to the main figure 4.
Supplementary Methods from MAPK Signaling and Inflammation Link Melanoma Phenotype Switching to Induction of CD73 during Immunotherapy
Authors: Reinhardt Julia , Landsberg Jennifer , Schmid-Burgk Jonathan L. , Ramis Bartomeu Bibiloni , Bald Tobias , Glodde Nicole , Lopez-Ramos Dorys , Young Arabella , Ngiow Shin Foong , Nettersheim Daniel , Schorle Hubert , Quast Thomas , Kolanus Waldemar , Schadendorf Dirk , Long Georgina V. , Madore Jason , Scolyer Richard A. , Ribas Antoni , Smyth Mark J. , Tumeh Paul C. , Tüting Thomas , Hölzel Michael
Published: March 2023

This file contains updated supplemental methods
Supplementary Fig. 2 from APOBEC3A and APOBEC3B Activities Render Cancer Cells Susceptible to ATR Inhibition
Authors: Buisson Rémi , Lawrence Michael S. , Benes Cyril H. , Zou Lee
Published: March 2023

This files contains the data showing the depletion of endogenous APOBEC3A/B. It is supplementary to the main figure 2.
Supplementary Figure 1 to 7 from MAPK Signaling and Inflammation Link Melanoma Phenotype Switching to Induction of CD73 during Immunotherapy
Authors: Reinhardt Julia , Landsberg Jennifer , Schmid-Burgk Jonathan L. , Ramis Bartomeu Bibiloni , Bald Tobias , Glodde Nicole , Lopez-Ramos Dorys , Young Arabella , Ngiow Shin Foong , Nettersheim Daniel , Schorle Hubert , Quast Thomas , Kolanus Waldemar , Schadendorf Dirk , Long Georgina V. , Madore Jason , Scolyer Richard A. , Ribas Antoni , Smyth Mark J. , Tumeh Paul C. , Tüting Thomas , Hölzel Michael
Published: March 2023

Supplemental Figure S1. Validation of anti-CD73 antibody used for IHC and analysis of cutaneous melanoma metastases. Supplemental Figure S2. Next-generation sequencing based analysis of bisulfite conversion to assess CpG island methylation in the NT5E (CD73) promoter region. Supplemental Figure S3. c-Jun and FOSL1 protein expression in MaMel melanoma cell lines. Supplemental Figure S4. Functional role of AP-1 sites in the NT5E (CD73) genomic region for the induction of CD73 by c-Jun. Supplemental Figure S5. IHC analysis of CD73 expression by melanoma cells in mouse ACT relapse melanomas. Supplemental Figure S6. Comparison of the 'proliferative' melanoma phenotype gene set with the cell proliferation associated E2F and MYC gene sets. Supplemental Figure S7. Graphical abstract of CD73 expression in melanoma phenotype switching.
Supplementary Fig. 1 from APOBEC3A and APOBEC3B Activities Render Cancer Cells Susceptible to ATR Inhibition
Authors: Buisson Rémi , Lawrence Michael S. , Benes Cyril H. , Zou Lee
Published: March 2023

This file contains the data showing expression of APOBEC3A/B in cancer cell lines and activity of APOPBEC3A/B in cancer cell lines. It is linked to the main figure 1.
Table S5 from Therapeutic Effects of XPO1 Inhibition in Thymic Epithelial Tumors
Authors: Conforti Fabio , Zhang Xu , Rao Guanhua , De Pas Tommaso , Yonemori Yoko , Rodriguez Jose Antonio , McCutcheon Justine N. , Rahhal Raneen , Alberobello Anna T. , Wang Yisong , Zhang Yu-Wen , Guha Udayan , Giaccone Giuseppe
Published: March 2023

Affected pathways
Table S3 from Therapeutic Effects of XPO1 Inhibition in Thymic Epithelial Tumors
Authors: Conforti Fabio , Zhang Xu , Rao Guanhua , De Pas Tommaso , Yonemori Yoko , Rodriguez Jose Antonio , McCutcheon Justine N. , Rahhal Raneen , Alberobello Anna T. , Wang Yisong , Zhang Yu-Wen , Guha Udayan , Giaccone Giuseppe
Published: March 2023

Affected Networks
Table S2 from Therapeutic Effects of XPO1 Inhibition in Thymic Epithelial Tumors
Authors: Conforti Fabio , Zhang Xu , Rao Guanhua , De Pas Tommaso , Yonemori Yoko , Rodriguez Jose Antonio , McCutcheon Justine N. , Rahhal Raneen , Alberobello Anna T. , Wang Yisong , Zhang Yu-Wen , Guha Udayan , Giaccone Giuseppe
Published: March 2023

Cytoplasmic proteins
Supplementary tables from Targeting a Single Alternative Polyadenylation Site Coordinately Blocks Expression of Androgen Receptor mRNA Splice Variants in Prostate Cancer
Authors: Van Etten Jamie L. , Nyquist Michael , Li Yingming , Yang Rendong , Ho Yeung , Johnson Rachel , Ondigi Olivia , Voytas Daniel F. , Henzler Christine , Dehm Scott M.
Published: March 2023

This file contains supplementary tables Table S1: Repeat variable dinucleotide (RVD) modules used to create tAR2 left and right TALENs, Table S2: Mean per-base read coverage and copy number of the AR gene for 22Rv1 sub-lines, Table S3: Confirmation of 22Rv1 genetic background in undup1, undup3 sub-lines.
Supplementary figures and figure legends from Targeting a Single Alternative Polyadenylation Site Coordinately Blocks Expression of Androgen Receptor mRNA Splice Variants in Prostate Cancer
Authors: Van Etten Jamie L. , Nyquist Michael , Li Yingming , Yang Rendong , Ho Yeung , Johnson Rachel , Ondigi Olivia , Voytas Daniel F. , Henzler Christine , Dehm Scott M.
Published: March 2023

This file contains supplementary figures S1-S10 and corresponding figure legends. Figure S1: TALEN activity and genetic correction of 22Rv1 sub-lines. Figure S2: 5' and 3' breakpoint sequence junctions of 22Rv1 undup1-3 sub-lines. Figure S3: AR subcellular localization in 22Rv1-undup3 cell line. Figure S4: AR target gene expression panel in 22Rv1 and gene corrected sublines. Figure S5: Knockdown of splicing factors U2AF2, SRSF1, and PTBP1. Figure S6: Blockade of the AR CE3 PAS blocks AR-V expression in LNCaP and VCaP cells. Figure S7: Knockdown of CE3 in 22Rv1 and VCaP cells. Figure S8: Mutual exclusivity matrix depicting co-occurrence of alterations in the core CPSF complex. Figure S9: Confirmation of CPSF complex gene knockdown. Figure S10: Knockdown of CPSF1 in LNCaP95 cells.
Figure S2 from Therapeutic Effects of XPO1 Inhibition in Thymic Epithelial Tumors
Authors: Conforti Fabio , Zhang Xu , Rao Guanhua , De Pas Tommaso , Yonemori Yoko , Rodriguez Jose Antonio , McCutcheon Justine N. , Rahhal Raneen , Alberobello Anna T. , Wang Yisong , Zhang Yu-Wen , Guha Udayan , Giaccone Giuseppe
Published: March 2023

Effects of XPO1 knockdown on NF-κB and cell proliferation
Supplementary Materials and Methods from Targeting a Single Alternative Polyadenylation Site Coordinately Blocks Expression of Androgen Receptor mRNA Splice Variants in Prostate Cancer
Authors: Van Etten Jamie L. , Nyquist Michael , Li Yingming , Yang Rendong , Ho Yeung , Johnson Rachel , Ondigi Olivia , Voytas Daniel F. , Henzler Christine , Dehm Scott M.
Published: March 2023

This file contains supplementary materials and methods including qPCR primer sequences, 2C subcellular fractionation, and additional details for RNA-Seq analyses.
Figure S1 from Therapeutic Effects of XPO1 Inhibition in Thymic Epithelial Tumors
Authors: Conforti Fabio , Zhang Xu , Rao Guanhua , De Pas Tommaso , Yonemori Yoko , Rodriguez Jose Antonio , McCutcheon Justine N. , Rahhal Raneen , Alberobello Anna T. , Wang Yisong , Zhang Yu-Wen , Guha Udayan , Giaccone Giuseppe
Published: March 2023

Immunofluorescence staining of XPO1, p53 and NK-κB
Table S2 from Methods of Academic Course Planning for Cancer Biology PhD Students to Enhance Knowledge of Clinical Oncology
Authors: Mattes Malcolm D. , Swart Elizabeth , Markwell Steven M. , Wen Sijin , Vona-Davis Linda C.
Published: March 2023

Survey questions for students
Supplementary Figure Legends from Therapeutic Rationale to Target Highly Expressed CDK7 Conferring Poor Outcomes in Triple-Negative Breast Cancer
Authors: Li Bo , Ni Chonghaile Triona , Fan Yue , Madden Stephen F. , Klinger Rut , O'Connor Aisling E. , Walsh Louise , O'Hurley Gillian , Mallya Udupi Girish , Joseph Jesuchristopher , Tarrant Finbarr , Conroy Emer , Gaber Alexander , Chin Suet-Feung , Bardwell Helen A. , Provenzano Elena , Crown John , Dubois Thierry , Linn Sabine , Jirstrom Karin , Caldas Carlos , O'Connor Darran P. , Gallagher William M.
Published: March 2023

Supplementary Figure Legends
Supplementary Materials & Methods, Figures S1-S5, Table S1 from Smurf2-Mediated Stabilization of DNA Topoisomerase IIα Controls Genomic Integrity
Authors: Emanuelli Andrea , Borroni Aurora P. , Apel-Sarid Liat , Shah Pooja A. , Ayyathan Dhanoop Manikoth , Koganti Praveen , Levy-Cohen Gal , Blank Michael
Published: March 2023

This file contains supplementary Materials and Methods, five supplementary figures and one supplementary table pertinent to the submitted manuscript, as follows: Figure S1 shows that Smurf2 interacts with Topo IIα through the nuclear volume. Figure S2 shows expression levels of Topo IIα in different mouse tissues derived from Smurf2KO and control animals. The figure also demonstrates that decreased cellular levels of Topo IIα in Smurf2-knockdown cells are independent on cell fixation. Figure S3 shows cell cycle distribution of Smurf2- and Topo IIα-depleted cells vs. controls. Figure S4 demonstrates that stability of Topo IIα is regulated through the proteasomal degradation pathway and is under control of Smurf2. Figure S5 shows cell fractionation analysis of Smurf2 and Topo IIα knockdown cells; Top1 enzymatic activities in Smurf2 knockdown cells; Topo IIα expression pattern and chromosome dynamics in Smurf2-depleted and Topo IIα-reconstituted cells; DNA decatenation assay in these cells, as well as sensitivity of Smurf2KO MEFs to etoposide treatment. Supplementary Table S1 shows calculated number of tissue samples in which a direct correlation between Smurf2 and Topo IIα intensity and percentage of positive cells was observed.
Figure S5 from Therapeutic Rationale to Target Highly Expressed CDK7 Conferring Poor Outcomes in Triple-Negative Breast Cancer
Authors: Li Bo , Ni Chonghaile Triona , Fan Yue , Madden Stephen F. , Klinger Rut , O'Connor Aisling E. , Walsh Louise , O'Hurley Gillian , Mallya Udupi Girish , Joseph Jesuchristopher , Tarrant Finbarr , Conroy Emer , Gaber Alexander , Chin Suet-Feung , Bardwell Helen A. , Provenzano Elena , Crown John , Dubois Thierry , Linn Sabine , Jirstrom Karin , Caldas Carlos , O'Connor Darran P. , Gallagher William M.
Published: March 2023

Combination treatment with THZ1 and ABT-263 shows synergistic effects in TNBC cells
Table S1 from Micronuclei Frequency in Tumors Is a Predictive Biomarker for Genetic Instability and Sensitivity to the DNA Repair Inhibitor AsiDNA
Authors: Jdey Wael , Thierry Sylvain , Popova Tatiana , Stern Marc-Henri , Dutreix Marie
Published: March 2023

Micronuclei assessement in Breast Cancer patients'' biopsies. MN, Micronuclei; BC, Breast Cancer; C: canalar; L: lobular.