bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Table 4 from Targeting the ATF6-Mediated ER Stress Response and Autophagy Blocks Integrin-Driven Prostate Cancer Progression
Authors: Macke Amanda J. , Pachikov Artem N. , Divita Taylor E. , Morris Mary E. , LaGrange Chad A. , Holzapfel Melissa S. , Kubyshkin Anatoly V. , Zyablitskaya Evgeniya Y. , Makalish Tatiana P. , Eremenko Sergey N. , Qiu Haowen , Riethoven Jean-Jack M. , Hemstreet George P. , Petrosyan Armen
Published: September 2023

Supplementary Table 4. The Chi-squared and Fisher's Exact tests of metastases in the group of mice with orthotopic tumor.
Supplementary Table 3 from Targeting the ATF6-Mediated ER Stress Response and Autophagy Blocks Integrin-Driven Prostate Cancer Progression
Authors: Macke Amanda J. , Pachikov Artem N. , Divita Taylor E. , Morris Mary E. , LaGrange Chad A. , Holzapfel Melissa S. , Kubyshkin Anatoly V. , Zyablitskaya Evgeniya Y. , Makalish Tatiana P. , Eremenko Sergey N. , Qiu Haowen , Riethoven Jean-Jack M. , Hemstreet George P. , Petrosyan Armen
Published: September 2023

Supplementary Table 3. The detailed information about orthotopic surgery, tumor sizes, and metastases.
Supplementary Table 2 from Targeting the ATF6-Mediated ER Stress Response and Autophagy Blocks Integrin-Driven Prostate Cancer Progression
Authors: Macke Amanda J. , Pachikov Artem N. , Divita Taylor E. , Morris Mary E. , LaGrange Chad A. , Holzapfel Melissa S. , Kubyshkin Anatoly V. , Zyablitskaya Evgeniya Y. , Makalish Tatiana P. , Eremenko Sergey N. , Qiu Haowen , Riethoven Jean-Jack M. , Hemstreet George P. , Petrosyan Armen
Published: September 2023

Supplementary Table 2. Combinations of siRNAs and shRNAs used for knockdown experiments.
Supplementary Table 1 from Targeting the ATF6-Mediated ER Stress Response and Autophagy Blocks Integrin-Driven Prostate Cancer Progression
Authors: Macke Amanda J. , Pachikov Artem N. , Divita Taylor E. , Morris Mary E. , LaGrange Chad A. , Holzapfel Melissa S. , Kubyshkin Anatoly V. , Zyablitskaya Evgeniya Y. , Makalish Tatiana P. , Eremenko Sergey N. , Qiu Haowen , Riethoven Jean-Jack M. , Hemstreet George P. , Petrosyan Armen
Published: September 2023

Supplementary Table 1. Combinations of Abs used for IHC experiments.
Supplementary Methods and Materials from Targeting the ATF6-Mediated ER Stress Response and Autophagy Blocks Integrin-Driven Prostate Cancer Progression
Authors: Macke Amanda J. , Pachikov Artem N. , Divita Taylor E. , Morris Mary E. , LaGrange Chad A. , Holzapfel Melissa S. , Kubyshkin Anatoly V. , Zyablitskaya Evgeniya Y. , Makalish Tatiana P. , Eremenko Sergey N. , Qiu Haowen , Riethoven Jean-Jack M. , Hemstreet George P. , Petrosyan Armen
Published: September 2023

Supplementary Methods and Materials
Supplementary Figure 4 from Targeting the ATF6-Mediated ER Stress Response and Autophagy Blocks Integrin-Driven Prostate Cancer Progression
Authors: Macke Amanda J. , Pachikov Artem N. , Divita Taylor E. , Morris Mary E. , LaGrange Chad A. , Holzapfel Melissa S. , Kubyshkin Anatoly V. , Zyablitskaya Evgeniya Y. , Makalish Tatiana P. , Eremenko Sergey N. , Qiu Haowen , Riethoven Jean-Jack M. , Hemstreet George P. , Petrosyan Armen
Published: September 2023

Figure S4. (A) Representative images of Golgi in DU145 cells treated with 60 µM HCQ for 72 h and stained by GM130 (green); bars, 20 µm. (B) Quantification of Golgi spots per cell in samples from A. Unpaired t test; **p<0.01, mean ± SD; n represents a number of cells counted. (C) Representative images of Golgi in DU145 cells treated with control or ATF6α siRNAs and stained by GM130 (green); bars, 20 µm. (D) Quantification of Golgi spots per cell in samples from C. Unpaired t test; ***p<0.001, mean ± SD; n represents number of cells counted. (E) ATF6 W-B of the lysates of DU145 cells transfected with control or ATF6α siRNAs; β-actin is a loading control. (F) Representative images of Golgi in PC-3 cells treated with control or ATG5 siRNAs and stained by GM130 (green); bars, 20 µm. (G) Quantification of Golgi spots per cell in samples from F. Unpaired t test; ****p<0.0001, mean ± SD; n represents number of cells counted. (H) ATG5 W-B of the lysates of PC-3 cells transfected with control or ATG5 siRNAs; γ-tubulin is a loading control. (I) Representative images of Golgi in DU145 cells treated with control or ATG5 siRNAs and stained by GM130 (green); bars, 20 µm. (J) Quantification of Golgi spots per cell in samples from I. Unpaired t test; ****p<0.0001, mean ± SD; n represents number of cells counted. (K) ATG5 W-B of the lysates of DU145 cells transfected with control or ATG5 siRNAs; γ-tubulin is a loading control. (L) Representative images of Golgi in PC-3 cells treated with Bafilomycin A1 (10 µM for 72 h) or appropriate amount of DMSO and stained by GM130 (green); bars, 20 µm. (M) Quantification of Golgi spots per cell in samples from L. Unpaired t test; ****p<0.0001, mean ± SD; n represents number of cells counted. (N-R) GRASP65 (N), GM130 (O), Giantin (P), Golgin-245 (Q), and TGN46 (R) W-Bs of the lysates of PC-3 cells treated with HCQ; β-actin is a loading control. All data presented are representative of at least three independent experiments.
Supplementary Figure 2 from Targeting the ATF6-Mediated ER Stress Response and Autophagy Blocks Integrin-Driven Prostate Cancer Progression
Authors: Macke Amanda J. , Pachikov Artem N. , Divita Taylor E. , Morris Mary E. , LaGrange Chad A. , Holzapfel Melissa S. , Kubyshkin Anatoly V. , Zyablitskaya Evgeniya Y. , Makalish Tatiana P. , Eremenko Sergey N. , Qiu Haowen , Riethoven Jean-Jack M. , Hemstreet George P. , Petrosyan Armen
Published: September 2023

Figure S2. (A) Representative images of triple IHC staining of Integrin αvβ5 (green), Gal-3 (red), and E-cadherin (brown) in the normal prostate and tumor tissues from PCa patients with different grades. Deconvoluted images of Integrin αvβ5 are shown on the right; bars, 100 µm. (B) Quantification of Integrin αvβ5 H-score at PM from samples in A. Dunn Test (1964) Kruskal-Wallis multiple comparisons, p-adjusted using Benjamini-Hochberg; ****p<0.0001 and ***p<0.001, median ± SD. (C) Quantification of Integrin αvβ5 and Gal-3 colocalization at PM in normal prostate and PCa, grades 2-5. Kruskal-Wallis test; ***p<0.001, mean ± SD.
Supplementary Figure 1 from Targeting the ATF6-Mediated ER Stress Response and Autophagy Blocks Integrin-Driven Prostate Cancer Progression
Authors: Macke Amanda J. , Pachikov Artem N. , Divita Taylor E. , Morris Mary E. , LaGrange Chad A. , Holzapfel Melissa S. , Kubyshkin Anatoly V. , Zyablitskaya Evgeniya Y. , Makalish Tatiana P. , Eremenko Sergey N. , Qiu Haowen , Riethoven Jean-Jack M. , Hemstreet George P. , Petrosyan Armen
Published: September 2023

Figure S1. (A) Representative images of triple IHC staining of Integrin αvβ3 (green), Gal-3 (red), and E-cadherin (brown) in normal prostate and tumor tissues from PCa patients with different grades. Deconvoluted images of Integrin αvβ3 are shown on the right; bars, 50 µm. (B) Quantification of Integrin αvβ3 H-score at PM from samples in A. Dunn Test (1964) Kruskal-Wallis multiple comparisons, p-adjusted using Benjamini-Hochberg; ****p<0.0001 and *p<0.05, median ± SD. (C) Quantification of Integrin αvβ3 and Gal-3 colocalization at PM in normal prostate and PCa with grades 2-5. Kruskal-Wallis test; *p<0.05, mean ± SD.
Movie S2 from Targeting the ATF6-Mediated ER Stress Response and Autophagy Blocks Integrin-Driven Prostate Cancer Progression
Authors: Macke Amanda J. , Pachikov Artem N. , Divita Taylor E. , Morris Mary E. , LaGrange Chad A. , Holzapfel Melissa S. , Kubyshkin Anatoly V. , Zyablitskaya Evgeniya Y. , Makalish Tatiana P. , Eremenko Sergey N. , Qiu Haowen , Riethoven Jean-Jack M. , Hemstreet George P. , Petrosyan Armen
Published: September 2023

PC-3 cell treated with HCQ, stained for Golgi (GRASP65, green) and MGAT3 (red). Surfaces were reconstructed by Imaris.
Supplementary Fig S3 from Chromatin-Associated SIN3B Protects Cancer Cells from Genotoxic Stress-Induced Apoptosis and Dictates DNA Damage Repair Pathway Choice
Authors: Morales-Valencia Jorge , Petit Coralie , Calderon Alexander , Saini Siddharth , David Gregory
Published: September 2023

Cell cycle effect on DNA damage-induced apoptosis
Supplementary Table S4 from Single-Cell Evolutionary Analysis Reveals Drivers of Plasticity and Mediators of Chemoresistance in Small Cell Lung Cancer
Authors: Wollenzien Hannah , Afeworki Tecleab Yohannes , Szczepaniak-Sloane Robert , Restaino Anthony , Kareta Michael S.
Published: September 2023

Differential gene expression across NCI-H209 and NCI-H82 cluster (related to Figure 4)
Supplementary Table S3 from Single-Cell Evolutionary Analysis Reveals Drivers of Plasticity and Mediators of Chemoresistance in Small Cell Lung Cancer
Authors: Wollenzien Hannah , Afeworki Tecleab Yohannes , Szczepaniak-Sloane Robert , Restaino Anthony , Kareta Michael S.
Published: September 2023

Gene module membership and expression of module 5 (related to Figure 1g)
Table S1 from Fibronectin Contributes to a BRAF Inhibitor–driven Invasive Phenotype in Thyroid Cancer through EGR1, Which Can Be Blocked by Inhibition of ERK1/2
Authors: Hicks Hannah M. , Pozdeyev Nikita , Sams Sharon B. , Pugazhenthi Umarani , Bales Elise S. , Hofmann Marie-Claude , McKenna Logan R. , Schweppe Rebecca E.
Published: September 2023

Table S1. Thyroid cancer cell lines and their sensitivity/resistance to BRAFi.
Supplementary Table S1 from Single-Cell Evolutionary Analysis Reveals Drivers of Plasticity and Mediators of Chemoresistance in Small Cell Lung Cancer
Authors: Wollenzien Hannah , Afeworki Tecleab Yohannes , Szczepaniak-Sloane Robert , Restaino Anthony , Kareta Michael S.
Published: September 2023

Description of samples in the autochthonous study
Figure S8 from Fibronectin Contributes to a BRAF Inhibitor–driven Invasive Phenotype in Thyroid Cancer through EGR1, Which Can Be Blocked by Inhibition of ERK1/2
Authors: Hicks Hannah M. , Pozdeyev Nikita , Sams Sharon B. , Pugazhenthi Umarani , Bales Elise S. , Hofmann Marie-Claude , McKenna Logan R. , Schweppe Rebecca E.
Published: September 2023

Figure S8. The effects of EGR1 depletion on signaling responses to BRAF inhibition and invasion.
Supplementary Figure S9 from Single-Cell Evolutionary Analysis Reveals Drivers of Plasticity and Mediators of Chemoresistance in Small Cell Lung Cancer
Authors: Wollenzien Hannah , Afeworki Tecleab Yohannes , Szczepaniak-Sloane Robert , Restaino Anthony , Kareta Michael S.
Published: September 2023

In silico removal and characterization of isolation of murine cells.
Figure S6 from Fibronectin Contributes to a BRAF Inhibitor–driven Invasive Phenotype in Thyroid Cancer through EGR1, Which Can Be Blocked by Inhibition of ERK1/2
Authors: Hicks Hannah M. , Pozdeyev Nikita , Sams Sharon B. , Pugazhenthi Umarani , Bales Elise S. , Hofmann Marie-Claude , McKenna Logan R. , Schweppe Rebecca E.
Published: September 2023

Figure S6. The ERK1/2 inhibitors SCH772984 and Ulixertinib have similar effects on cell viability in vitro.
Figure S4 from Fibronectin Contributes to a BRAF Inhibitor–driven Invasive Phenotype in Thyroid Cancer through EGR1, Which Can Be Blocked by Inhibition of ERK1/2
Authors: Hicks Hannah M. , Pozdeyev Nikita , Sams Sharon B. , Pugazhenthi Umarani , Bales Elise S. , Hofmann Marie-Claude , McKenna Logan R. , Schweppe Rebecca E.
Published: September 2023

Figure S4. The effects of fibronectin depletion on growth and signaling responses to BRAF inhibition.
Supplementary Figure S4 from Single-Cell Evolutionary Analysis Reveals Drivers of Plasticity and Mediators of Chemoresistance in Small Cell Lung Cancer
Authors: Wollenzien Hannah , Afeworki Tecleab Yohannes , Szczepaniak-Sloane Robert , Restaino Anthony , Kareta Michael S.
Published: September 2023

Gene counts and filtering.
Supplementary Figure S3 from Single-Cell Evolutionary Analysis Reveals Drivers of Plasticity and Mediators of Chemoresistance in Small Cell Lung Cancer
Authors: Wollenzien Hannah , Afeworki Tecleab Yohannes , Szczepaniak-Sloane Robert , Restaino Anthony , Kareta Michael S.
Published: September 2023

SCLC Subtype-specific marker expression from the RPR2-Cas9 mouse model.
Supplementary Figure S2 from Single-Cell Evolutionary Analysis Reveals Drivers of Plasticity and Mediators of Chemoresistance in Small Cell Lung Cancer
Authors: Wollenzien Hannah , Afeworki Tecleab Yohannes , Szczepaniak-Sloane Robert , Restaino Anthony , Kareta Michael S.
Published: September 2023

Characterization of cell types isolated from the autochthonous scRNA-seq data.
Supplementary Figure S14 from Single-Cell Evolutionary Analysis Reveals Drivers of Plasticity and Mediators of Chemoresistance in Small Cell Lung Cancer
Authors: Wollenzien Hannah , Afeworki Tecleab Yohannes , Szczepaniak-Sloane Robert , Restaino Anthony , Kareta Michael S.
Published: September 2023

Validation of GAGE2A and PAGE5 shRNAs and overexpression vectors.
Supplementary Figure S13 from Single-Cell Evolutionary Analysis Reveals Drivers of Plasticity and Mediators of Chemoresistance in Small Cell Lung Cancer
Authors: Wollenzien Hannah , Afeworki Tecleab Yohannes , Szczepaniak-Sloane Robert , Restaino Anthony , Kareta Michael S.
Published: September 2023

Determining effective concentrations for treatment of SCLC cell lines with cisplatin and etoposide.
Supplementary Figure S12 from Single-Cell Evolutionary Analysis Reveals Drivers of Plasticity and Mediators of Chemoresistance in Small Cell Lung Cancer
Authors: Wollenzien Hannah , Afeworki Tecleab Yohannes , Szczepaniak-Sloane Robert , Restaino Anthony , Kareta Michael S.
Published: September 2023

GAGE2A and PAGE5 upregulation upon treatment of cisplatin and etoposide.
Supplementary Figure S11 from Single-Cell Evolutionary Analysis Reveals Drivers of Plasticity and Mediators of Chemoresistance in Small Cell Lung Cancer
Authors: Wollenzien Hannah , Afeworki Tecleab Yohannes , Szczepaniak-Sloane Robert , Restaino Anthony , Kareta Michael S.
Published: September 2023

Similarity analysis to determine subclonal relationships.
Supplementary Figure 5 from Targeting c-Jun Is a Potential Therapy for Luminal Breast Cancer Bone Metastasis
Authors: Han Yuxuan , Katayama Shota , Futakuchi Mitsuru , Nakamichi Kazuya , Wakabayashi Yutaro , Sakamoto Mai , Nakayama Jun , Semba Kentaro
Published: September 2023

Clinical prognosis of c-Jun-regulated gene signatures.
Supplementary Figure 3 from Targeting c-Jun Is a Potential Therapy for Luminal Breast Cancer Bone Metastasis
Authors: Han Yuxuan , Katayama Shota , Futakuchi Mitsuru , Nakamichi Kazuya , Wakabayashi Yutaro , Sakamoto Mai , Nakayama Jun , Semba Kentaro
Published: September 2023

c-Jun expression is heterogeneous in BM section.
Supplementary Table S4 from Identification of a ΔNp63-Dependent Basal-Like A Subtype-Specific Transcribed Enhancer Program (B-STEP) in Aggressive Pancreatic Ductal Adenocarcinoma
Authors: Wang Xin , Kutschat Ana P. , Aggrey-Fynn Joana , Hamdan Feda H. , Graham Rondell P. , Wixom Alexander Q. , Souto Yara , Ladigan-Badura Swetlana , Yonkus Jennifer A. , Abdelrahman Amro M. , Alva-Ruiz Roberto , Gaedcke Jochen , Ströbel Philipp , Kosinsky Robyn Laura , Wegwitz Florian , Hermann Patrick , Truty Mark J. , Siveke Jens T. , Hahn Stephan A. , Hessmann Elisabeth , Johnsen Steven A. , Najafova Zeynab
Published: September 2023

Supplementary Table S4 contains L3.6pl TP63-dependent enhancer regions.
Supplementary Table S3 from Identification of a ΔNp63-Dependent Basal-Like A Subtype-Specific Transcribed Enhancer Program (B-STEP) in Aggressive Pancreatic Ductal Adenocarcinoma
Authors: Wang Xin , Kutschat Ana P. , Aggrey-Fynn Joana , Hamdan Feda H. , Graham Rondell P. , Wixom Alexander Q. , Souto Yara , Ladigan-Badura Swetlana , Yonkus Jennifer A. , Abdelrahman Amro M. , Alva-Ruiz Roberto , Gaedcke Jochen , Ströbel Philipp , Kosinsky Robyn Laura , Wegwitz Florian , Hermann Patrick , Truty Mark J. , Siveke Jens T. , Hahn Stephan A. , Hessmann Elisabeth , Johnsen Steven A. , Najafova Zeynab
Published: September 2023

Supplementary Table S3 contains list of genes associated with Gö4Pdx4 super enhancers overlapping TP63.
Supplementary Table S2 from Identification of a ΔNp63-Dependent Basal-Like A Subtype-Specific Transcribed Enhancer Program (B-STEP) in Aggressive Pancreatic Ductal Adenocarcinoma
Authors: Wang Xin , Kutschat Ana P. , Aggrey-Fynn Joana , Hamdan Feda H. , Graham Rondell P. , Wixom Alexander Q. , Souto Yara , Ladigan-Badura Swetlana , Yonkus Jennifer A. , Abdelrahman Amro M. , Alva-Ruiz Roberto , Gaedcke Jochen , Ströbel Philipp , Kosinsky Robyn Laura , Wegwitz Florian , Hermann Patrick , Truty Mark J. , Siveke Jens T. , Hahn Stephan A. , Hessmann Elisabeth , Johnsen Steven A. , Najafova Zeynab
Published: September 2023

Supplementary Table S2 contains GöPdx4 super enhancers regions overlapping TP63
Supplementary Table S1 from Identification of a ΔNp63-Dependent Basal-Like A Subtype-Specific Transcribed Enhancer Program (B-STEP) in Aggressive Pancreatic Ductal Adenocarcinoma
Authors: Wang Xin , Kutschat Ana P. , Aggrey-Fynn Joana , Hamdan Feda H. , Graham Rondell P. , Wixom Alexander Q. , Souto Yara , Ladigan-Badura Swetlana , Yonkus Jennifer A. , Abdelrahman Amro M. , Alva-Ruiz Roberto , Gaedcke Jochen , Ströbel Philipp , Kosinsky Robyn Laura , Wegwitz Florian , Hermann Patrick , Truty Mark J. , Siveke Jens T. , Hahn Stephan A. , Hessmann Elisabeth , Johnsen Steven A. , Najafova Zeynab
Published: September 2023

Supplementary Table S1 contains list of crRNAs used in the study.
Supplementary Methods from Identification of a ΔNp63-Dependent Basal-Like A Subtype-Specific Transcribed Enhancer Program (B-STEP) in Aggressive Pancreatic Ductal Adenocarcinoma
Authors: Wang Xin , Kutschat Ana P. , Aggrey-Fynn Joana , Hamdan Feda H. , Graham Rondell P. , Wixom Alexander Q. , Souto Yara , Ladigan-Badura Swetlana , Yonkus Jennifer A. , Abdelrahman Amro M. , Alva-Ruiz Roberto , Gaedcke Jochen , Ströbel Philipp , Kosinsky Robyn Laura , Wegwitz Florian , Hermann Patrick , Truty Mark J. , Siveke Jens T. , Hahn Stephan A. , Hessmann Elisabeth , Johnsen Steven A. , Najafova Zeynab
Published: September 2023

The file contains additional supplementary methods
Supplementary Figure S3 from Identification of a ΔNp63-Dependent Basal-Like A Subtype-Specific Transcribed Enhancer Program (B-STEP) in Aggressive Pancreatic Ductal Adenocarcinoma
Authors: Wang Xin , Kutschat Ana P. , Aggrey-Fynn Joana , Hamdan Feda H. , Graham Rondell P. , Wixom Alexander Q. , Souto Yara , Ladigan-Badura Swetlana , Yonkus Jennifer A. , Abdelrahman Amro M. , Alva-Ruiz Roberto , Gaedcke Jochen , Ströbel Philipp , Kosinsky Robyn Laura , Wegwitz Florian , Hermann Patrick , Truty Mark J. , Siveke Jens T. , Hahn Stephan A. , Hessmann Elisabeth , Johnsen Steven A. , Najafova Zeynab
Published: September 2023

Verification of P63-dependence and B-STEP enhancer-gene regulations.
Supplementary Figure S2 from Identification of a ΔNp63-Dependent Basal-Like A Subtype-Specific Transcribed Enhancer Program (B-STEP) in Aggressive Pancreatic Ductal Adenocarcinoma
Authors: Wang Xin , Kutschat Ana P. , Aggrey-Fynn Joana , Hamdan Feda H. , Graham Rondell P. , Wixom Alexander Q. , Souto Yara , Ladigan-Badura Swetlana , Yonkus Jennifer A. , Abdelrahman Amro M. , Alva-Ruiz Roberto , Gaedcke Jochen , Ströbel Philipp , Kosinsky Robyn Laura , Wegwitz Florian , Hermann Patrick , Truty Mark J. , Siveke Jens T. , Hahn Stephan A. , Hessmann Elisabeth , Johnsen Steven A. , Najafova Zeynab
Published: September 2023

Defining the specificity and P63-dependence of B-STEP
Supplementary Table 3 from Absence of Either Ripk3 or Mlkl Reduces Incidence of Hepatocellular Carcinoma Independent of Liver Fibrosis
Authors: Mohammed Sabira , Thadathil Nidheesh , Ohene-Marfo Phoebe , Tran Albert L. , Van Der Veldt Michael , Georgescu Constantin , Oh Sangphil , Nicklas Evan H. , Wang Dawei , Haritha Nair Hariprasad , Luo Wenyi , Janknecht Ralf , Miller Benjamin F. , Wren Jonathan D. , Freeman Willard M. , Deepa Sathyaseelan S.
Published: September 2023

List of primers used for quantitative real time PCR
Supplementary Table 2 from Absence of Either Ripk3 or Mlkl Reduces Incidence of Hepatocellular Carcinoma Independent of Liver Fibrosis
Authors: Mohammed Sabira , Thadathil Nidheesh , Ohene-Marfo Phoebe , Tran Albert L. , Van Der Veldt Michael , Georgescu Constantin , Oh Sangphil , Nicklas Evan H. , Wang Dawei , Haritha Nair Hariprasad , Luo Wenyi , Janknecht Ralf , Miller Benjamin F. , Wren Jonathan D. , Freeman Willard M. , Deepa Sathyaseelan S.
Published: September 2023

List of significantly altered transcripts from RNA Seq analysis
Supplementary Data Legends from Absence of Either Ripk3 or Mlkl Reduces Incidence of Hepatocellular Carcinoma Independent of Liver Fibrosis
Authors: Mohammed Sabira , Thadathil Nidheesh , Ohene-Marfo Phoebe , Tran Albert L. , Van Der Veldt Michael , Georgescu Constantin , Oh Sangphil , Nicklas Evan H. , Wang Dawei , Haritha Nair Hariprasad , Luo Wenyi , Janknecht Ralf , Miller Benjamin F. , Wren Jonathan D. , Freeman Willard M. , Deepa Sathyaseelan S.
Published: September 2023

Supplementary Figures 1 -7 and Supplementary Tables 1 - 3 legends
Fig. S1 from Absence of Either Ripk3 or Mlkl Reduces Incidence of Hepatocellular Carcinoma Independent of Liver Fibrosis
Authors: Mohammed Sabira , Thadathil Nidheesh , Ohene-Marfo Phoebe , Tran Albert L. , Van Der Veldt Michael , Georgescu Constantin , Oh Sangphil , Nicklas Evan H. , Wang Dawei , Haritha Nair Hariprasad , Luo Wenyi , Janknecht Ralf , Miller Benjamin F. , Wren Jonathan D. , Freeman Willard M. , Deepa Sathyaseelan S.
Published: September 2023

Figure S1 shows the experimental plan of the study, IHC staining for Ripk3, Transcript levels of Mlkl and Ripk3, Western blots for Cleaved and Total Caspase 3
Supplementary Figure 5 from Oncostatin-M and OSM-Receptor Feed-Forward Activation of MAPK Induces Separable Stem-like and Mesenchymal Programs
Authors: Polak Kelsey L. , Tamagno Ilaria , Parameswaran Neetha , Smigiel Jacob , Chan E. Ricky , Yuan Xueer , Rios Brenda , Jackson Mark W.
Published: September 2023

S5. MEK inhibitors block OSM-driven conversion to a CD44HI/mesenchymal state.
Supplementary Figure 4 from Oncostatin-M and OSM-Receptor Feed-Forward Activation of MAPK Induces Separable Stem-like and Mesenchymal Programs
Authors: Polak Kelsey L. , Tamagno Ilaria , Parameswaran Neetha , Smigiel Jacob , Chan E. Ricky , Yuan Xueer , Rios Brenda , Jackson Mark W.
Published: September 2023

S4. OSM-expressing cells are distinct from CD44HI/mesenchymal cells created by EMT transcription factors.
Supplementary Figure 2 from Oncostatin-M and OSM-Receptor Feed-Forward Activation of MAPK Induces Separable Stem-like and Mesenchymal Programs
Authors: Polak Kelsey L. , Tamagno Ilaria , Parameswaran Neetha , Smigiel Jacob , Chan E. Ricky , Yuan Xueer , Rios Brenda , Jackson Mark W.
Published: September 2023

S2. Kaplan Meier comparison of IL-6 family member receptors.
Supplementary Table S6 from Association and Prediction Utilizing Craniocaudal and Mediolateral Oblique View Digital Mammography and Long-Term Breast Cancer Risk
Authors: Chen Simin , Tamimi Rulla M. , Colditz Graham A. , Jiang Shu
Published: September 2023

Supplementary Table S6: Hazards ratio of association among premenopausal women for baseline risk factors and breast cancer risk utilizing FULL-VPD
Supplementary Table S5 from Association and Prediction Utilizing Craniocaudal and Mediolateral Oblique View Digital Mammography and Long-Term Breast Cancer Risk
Authors: Chen Simin , Tamimi Rulla M. , Colditz Graham A. , Jiang Shu
Published: September 2023

Supplementary Table S5: Hazards ratio (95% Confidence Interval) for association inure-menopausal women between baseline risk factors and breast cancer risk utilizing MLOL-VPD
Supplementary Figure S6 from Association and Prediction Utilizing Craniocaudal and Mediolateral Oblique View Digital Mammography and Long-Term Breast Cancer Risk
Authors: Chen Simin , Tamimi Rulla M. , Colditz Graham A. , Jiang Shu
Published: September 2023

Supplementary Figure S6: The proportional hazards assumption is deemed reasonable by checking the Schoenfeld residuals plot for MLO-VPD.
Supplementary Figure S4 from Association and Prediction Utilizing Craniocaudal and Mediolateral Oblique View Digital Mammography and Long-Term Breast Cancer Risk
Authors: Chen Simin , Tamimi Rulla M. , Colditz Graham A. , Jiang Shu
Published: September 2023

Supplementary Figure S4: The linearity assumption is checked with Martingale residual plots.
Supplementary Figure S1 from Association and Prediction Utilizing Craniocaudal and Mediolateral Oblique View Digital Mammography and Long-Term Breast Cancer Risk
Authors: Chen Simin , Tamimi Rulla M. , Colditz Graham A. , Jiang Shu
Published: September 2023

Supplementary Figure S1: Cohort recruit and follow up chart.
Supplementary Figures from Aerobic Exercise Alters the Melanoma Microenvironment and Modulates ERK5 S496 Phosphorylation
Authors: Savage Hannah , Pareek Sumedha , Lee Jonghae , Ballarò Riccardo , Conterno Minussi Darlan , Hayek Karma , Sadullozoda Mumina , Lochmann Brooke S. , McQuade Jennifer L. , LaVoy Emily C. , Marmonti Enrica , Patel Hetal , Wang Guangyu , Imanishi Masaki , Kotla Sivareddy , Abe Jun-ichi , Schadler Keri
Published: September 2023

Supplementary Figures S1-S8
Supplementary Table S2 from AXL Inhibition Improves the Antitumor Activity of Chimeric Antigen Receptor T Cells
Authors: Sakemura R. Leo , Hefazi Mehrdad , Cox Michelle J. , Siegler Elizabeth L. , Sinha Sutapa , Hansen Michael J. , Stewart Carli M. , Feigin Jennifer M. , Manriquez Roman Claudia , Schick Kendall J. , Can Ismail , Tapper Erin E. , Horvei Paulina , Adada Mohamad M. , Bezerra Evandro D. , Kankeu Fonkoua Lionel Aurelien , Ruff Michael W. , Forsman Cynthia L. , Nevala Wendy K. , Boysen Justin C. , Tschumper Renee C. , Grand Cory L. , Kuchimanchi Kameswara R. , Mouritsen Lars , Foulks Jason M. , Warner Steven L. , Call Timothy G. , Parikh Sameer A. , Ding Wei , Kay Neil E. , Kenderian Saad S.
Published: September 2023

Supplementary Table S2
Supplementary Table S1 from AXL Inhibition Improves the Antitumor Activity of Chimeric Antigen Receptor T Cells
Authors: Sakemura R. Leo , Hefazi Mehrdad , Cox Michelle J. , Siegler Elizabeth L. , Sinha Sutapa , Hansen Michael J. , Stewart Carli M. , Feigin Jennifer M. , Manriquez Roman Claudia , Schick Kendall J. , Can Ismail , Tapper Erin E. , Horvei Paulina , Adada Mohamad M. , Bezerra Evandro D. , Kankeu Fonkoua Lionel Aurelien , Ruff Michael W. , Forsman Cynthia L. , Nevala Wendy K. , Boysen Justin C. , Tschumper Renee C. , Grand Cory L. , Kuchimanchi Kameswara R. , Mouritsen Lars , Foulks Jason M. , Warner Steven L. , Call Timothy G. , Parikh Sameer A. , Ding Wei , Kay Neil E. , Kenderian Saad S.
Published: September 2023

Supplementary Table S1
Supplementary Tables from A Bispecific γδ T-cell Engager Targeting EGFR Activates a Potent Vγ9Vδ2 T cell–Mediated Immune Response against EGFR-Expressing Tumors
Authors: King Lisa A. , Toffoli Elisa C. , Veth Myrthe , Iglesias-Guimarais Victoria , Slot Manon C. , Amsen Derk , van de Ven Rieneke , Derks Sarah , Fransen Marieke F. , Tuynman Jurriaan B. , Riedl Thilo , Roovers Rob C. , Adang Anton E.P. , Ruben Jurjen M. , Parren Paul W.H.I. , de Gruijl Tanja D. , van der Vliet Hans J.
Published: September 2023

Supplementary tables 1-6
Supplementary Figures from A Bispecific γδ T-cell Engager Targeting EGFR Activates a Potent Vγ9Vδ2 T cell–Mediated Immune Response against EGFR-Expressing Tumors
Authors: King Lisa A. , Toffoli Elisa C. , Veth Myrthe , Iglesias-Guimarais Victoria , Slot Manon C. , Amsen Derk , van de Ven Rieneke , Derks Sarah , Fransen Marieke F. , Tuynman Jurriaan B. , Riedl Thilo , Roovers Rob C. , Adang Anton E.P. , Ruben Jurjen M. , Parren Paul W.H.I. , de Gruijl Tanja D. , van der Vliet Hans J.
Published: September 2023

Figures S1-9
Supplementary Table 1 from Enhancing CAR T-cell Therapy Using Fab-Based Constitutively Heterodimeric Cytokine Receptors
Authors: Righi Matteo , Gannon Isaac , Robson Matthew , Srivastava Saket , Kokalaki Evangelia , Grothier Thomas , Nannini Francesco , Allen Christopher , Bai Yuchen V. , Sillibourne James , Cordoba Shaun , Thomas Simon , Pule Martin
Published: September 2023

Supplementary Table 1: Key Resources
Supplementary Data Legends from HER2Δ16 Engages ENPP1 to Promote an Immune-Cold Microenvironment in Breast Cancer
Authors: Attalla Sherif Samer , Boucher Jonathan , Proud Hailey , Taifour Tarek , Zuo Dongmei , Sanguin-Gendreau Virginie , Ling Chen , Johnson Gabriella , Li Vincent , Luo Robin B. , Kuasne Hellen , Papavasiliou Vasilios , Walsh Logan A. , Barok Mark , Joensuu Heikki , Park Morag , Roux Philippe P. , Muller William J.
Published: September 2023

Legends for Supp. Figures S1-20
Data from Aerobic Exercise Alters the Melanoma Microenvironment and Modulates ERK5 S496 Phosphorylation
Authors: Savage Hannah , Pareek Sumedha , Lee Jonghae , Ballarò Riccardo , Conterno Minussi Darlan , Hayek Karma , Sadullozoda Mumina , Lochmann Brooke S. , McQuade Jennifer L. , LaVoy Emily C. , Marmonti Enrica , Patel Hetal , Wang Guangyu , Imanishi Masaki , Kotla Sivareddy , Abe Jun-ichi , Schadler Keri
Published: September 2023

Abstract
Exercise changes the tumor microenvironment by remodeling blood vessels and increasing infiltration by cytotoxic immune cells. The mechanisms driving these changes remain unclear. Herein, we demonstrate that exercise normalizes tumor vasculature and upregulates endothelial expression of VCAM1 in YUMMER 1.7 and B16F10 murine models of melanoma but differentially regulates tumor growth, hypoxia, and the immune response. We found that exercise suppressed tumor growth and increased CD8+ T-cell infiltration in YUMMER but not in B16F10 tumors. Single-cell RNA sequencing and flow cytometry revealed exercise modulated the number and phenotype of tumor-infiltrating CD8+ T cells and myeloid cells. Specifically, exercise caused a phenotypic shift in the tumor-associated macrophage population and increased the expression of MHC class II transcripts. We further demonstrated that ERK5 S496A knock-in mice, which are phosphorylation deficient at the S496 residue, “mimicked” the exercise effect when unexercised, yet when exercised, these mice displayed a reversal in the effect of exercise on tumor growth and macrophage polarization compared with wild-type mice. Taken together, our results reveal tumor-specific differences in the immune response to exercise and show that ERK5 signaling via the S496 residue plays a crucial role in exercise-induced tumor microenvironment changes.

See related Spotlight by Betof Warner, p. 1158
Table S3 from HTLV-1 bZIP Factor-Induced Reprogramming of Lactate Metabolism and Epigenetic Status Promote Leukemic Cell Expansion
Authors: Toyoda Kosuke , Yasunaga Jun-ichirou , Shichijo Takafumi , Arima Yuichiro , Tsujita Kenichi , Tanaka Azusa , Salah Tarig , Zhang Wenyi , Hussein Osama , Sonoda Miyu , Watanabe Miho , Kurita Daisuke , Nakashima Kazutaka , Yamada Kyohei , Miyoshi Hiroaki , Ohshima Koichi , Matsuoka Masao
Published: September 2023

Oligonucleotides used in this study.
Figure S5 from HTLV-1 bZIP Factor-Induced Reprogramming of Lactate Metabolism and Epigenetic Status Promote Leukemic Cell Expansion
Authors: Toyoda Kosuke , Yasunaga Jun-ichirou , Shichijo Takafumi , Arima Yuichiro , Tsujita Kenichi , Tanaka Azusa , Salah Tarig , Zhang Wenyi , Hussein Osama , Sonoda Miyu , Watanabe Miho , Kurita Daisuke , Nakashima Kazutaka , Yamada Kyohei , Miyoshi Hiroaki , Ohshima Koichi , Matsuoka Masao
Published: September 2023

Transcriptional regulation of SLC16A1 and SLC16A3 by TAp73, and mRNA expression levels of MCT-coding genes among various cancers.
Figure S4 from HTLV-1 bZIP Factor-Induced Reprogramming of Lactate Metabolism and Epigenetic Status Promote Leukemic Cell Expansion
Authors: Toyoda Kosuke , Yasunaga Jun-ichirou , Shichijo Takafumi , Arima Yuichiro , Tsujita Kenichi , Tanaka Azusa , Salah Tarig , Zhang Wenyi , Hussein Osama , Sonoda Miyu , Watanabe Miho , Kurita Daisuke , Nakashima Kazutaka , Yamada Kyohei , Miyoshi Hiroaki , Ohshima Koichi , Matsuoka Masao
Published: September 2023

TAp73 significance in HBZ pathogenesis and its effect on cellular metabolism.
Figure S2 from HTLV-1 bZIP Factor-Induced Reprogramming of Lactate Metabolism and Epigenetic Status Promote Leukemic Cell Expansion
Authors: Toyoda Kosuke , Yasunaga Jun-ichirou , Shichijo Takafumi , Arima Yuichiro , Tsujita Kenichi , Tanaka Azusa , Salah Tarig , Zhang Wenyi , Hussein Osama , Sonoda Miyu , Watanabe Miho , Kurita Daisuke , Nakashima Kazutaka , Yamada Kyohei , Miyoshi Hiroaki , Ohshima Koichi , Matsuoka Masao
Published: September 2023

HBZ protein alters epigenetic regulation of TAp73 by EZH2.
Figure S1 from HTLV-1 bZIP Factor-Induced Reprogramming of Lactate Metabolism and Epigenetic Status Promote Leukemic Cell Expansion
Authors: Toyoda Kosuke , Yasunaga Jun-ichirou , Shichijo Takafumi , Arima Yuichiro , Tsujita Kenichi , Tanaka Azusa , Salah Tarig , Zhang Wenyi , Hussein Osama , Sonoda Miyu , Watanabe Miho , Kurita Daisuke , Nakashima Kazutaka , Yamada Kyohei , Miyoshi Hiroaki , Ohshima Koichi , Matsuoka Masao
Published: September 2023

Transcriptional regulation by HBZ protein and RNA and the status of TP73 expression.
Table S6 from A Single-Cell Taxonomy Predicts Inflammatory Niche Remodeling to Drive Tissue Failure and Outcome in Human AML
Authors: Chen Lanpeng , Pronk Eline , van Dijk Claire , Bian Yujie , Feyen Jacqueline , van Tienhoven Tim , Yildirim Meltem , Pisterzi Paola , de Jong Madelon M.E. , Bastidas Alejandro , Hoogenboezem Remco M. , Wevers Chiel , Bindels Eric M. , Löwenberg Bob , Cupedo Tom , Sanders Mathijs A. , Raaijmakers Marc H.G.P.
Published: September 2023

Supplementary Table 6. Differentially expressed genes in BMSCs from AML vs. BMSCs from NBM (purified BMSC RNAseq)
Table S5 from A Single-Cell Taxonomy Predicts Inflammatory Niche Remodeling to Drive Tissue Failure and Outcome in Human AML
Authors: Chen Lanpeng , Pronk Eline , van Dijk Claire , Bian Yujie , Feyen Jacqueline , van Tienhoven Tim , Yildirim Meltem , Pisterzi Paola , de Jong Madelon M.E. , Bastidas Alejandro , Hoogenboezem Remco M. , Wevers Chiel , Bindels Eric M. , Löwenberg Bob , Cupedo Tom , Sanders Mathijs A. , Raaijmakers Marc H.G.P.
Published: September 2023

Table S5 Differentially expressed genes in residual normal/pre-leukemic HSCs in AML vs. HSCs from NBM (scRNAseq)
Table S4 from A Single-Cell Taxonomy Predicts Inflammatory Niche Remodeling to Drive Tissue Failure and Outcome in Human AML
Authors: Chen Lanpeng , Pronk Eline , van Dijk Claire , Bian Yujie , Feyen Jacqueline , van Tienhoven Tim , Yildirim Meltem , Pisterzi Paola , de Jong Madelon M.E. , Bastidas Alejandro , Hoogenboezem Remco M. , Wevers Chiel , Bindels Eric M. , Löwenberg Bob , Cupedo Tom , Sanders Mathijs A. , Raaijmakers Marc H.G.P.
Published: September 2023

Table S4 Differentially expressed genes and transcriptional programs (GSEA Hallmark) in BMSCs from AML vs. BMSCs from NBM (scRNAseq)
Table S3 from A Single-Cell Taxonomy Predicts Inflammatory Niche Remodeling to Drive Tissue Failure and Outcome in Human AML
Authors: Chen Lanpeng , Pronk Eline , van Dijk Claire , Bian Yujie , Feyen Jacqueline , van Tienhoven Tim , Yildirim Meltem , Pisterzi Paola , de Jong Madelon M.E. , Bastidas Alejandro , Hoogenboezem Remco M. , Wevers Chiel , Bindels Eric M. , Löwenberg Bob , Cupedo Tom , Sanders Mathijs A. , Raaijmakers Marc H.G.P.
Published: September 2023

Supplementary Table 3. Differentially expressed genes in the NBM BMSC cluster 0 vs. other BMSC clusters
Table S2 from A Single-Cell Taxonomy Predicts Inflammatory Niche Remodeling to Drive Tissue Failure and Outcome in Human AML
Authors: Chen Lanpeng , Pronk Eline , van Dijk Claire , Bian Yujie , Feyen Jacqueline , van Tienhoven Tim , Yildirim Meltem , Pisterzi Paola , de Jong Madelon M.E. , Bastidas Alejandro , Hoogenboezem Remco M. , Wevers Chiel , Bindels Eric M. , Löwenberg Bob , Cupedo Tom , Sanders Mathijs A. , Raaijmakers Marc H.G.P.
Published: September 2023

Table S2 Differentially expressed genes in the HSC (low-output) cluster 0 vs. (high-output) HSC/MPP clusters 1-4
Table S1 from A Single-Cell Taxonomy Predicts Inflammatory Niche Remodeling to Drive Tissue Failure and Outcome in Human AML
Authors: Chen Lanpeng , Pronk Eline , van Dijk Claire , Bian Yujie , Feyen Jacqueline , van Tienhoven Tim , Yildirim Meltem , Pisterzi Paola , de Jong Madelon M.E. , Bastidas Alejandro , Hoogenboezem Remco M. , Wevers Chiel , Bindels Eric M. , Löwenberg Bob , Cupedo Tom , Sanders Mathijs A. , Raaijmakers Marc H.G.P.
Published: September 2023

Table S1 patient characteristics
Supplementary Figure 1-9 from A Single-Cell Taxonomy Predicts Inflammatory Niche Remodeling to Drive Tissue Failure and Outcome in Human AML
Authors: Chen Lanpeng , Pronk Eline , van Dijk Claire , Bian Yujie , Feyen Jacqueline , van Tienhoven Tim , Yildirim Meltem , Pisterzi Paola , de Jong Madelon M.E. , Bastidas Alejandro , Hoogenboezem Remco M. , Wevers Chiel , Bindels Eric M. , Löwenberg Bob , Cupedo Tom , Sanders Mathijs A. , Raaijmakers Marc H.G.P.
Published: September 2023

Fig S1-S9
Supplementary Movie from Next-Generation JAK2 Inhibitors for the Treatment of Myeloproliferative Neoplasms: Lessons from Structure-Based Drug Discovery Approaches
Authors: Nair Pramod C. , Piehler Jacob , Tvorogov Denis , Ross David M. , Lopez Angel F. , Gotlib Jason , Thomas Daniel
Published: September 2023

JAK2-PK
Supplementary File 2 from Next-Generation JAK2 Inhibitors for the Treatment of Myeloproliferative Neoplasms: Lessons from Structure-Based Drug Discovery Approaches
Authors: Nair Pramod C. , Piehler Jacob , Tvorogov Denis , Ross David M. , Lopez Angel F. , Gotlib Jason , Thomas Daniel
Published: September 2023

JAK2-monomer-500ns.pdb. (Structure of human JAK2 monomer at 500 ns simulation).
Supplementary File 1 from Next-Generation JAK2 Inhibitors for the Treatment of Myeloproliferative Neoplasms: Lessons from Structure-Based Drug Discovery Approaches
Authors: Nair Pramod C. , Piehler Jacob , Tvorogov Denis , Ross David M. , Lopez Angel F. , Gotlib Jason , Thomas Daniel
Published: September 2023

JAK2-monomer-0ns.pdb. (Model of human JAK2 monomer used for molecular dynamics simulation).
Supplementary Figure S1 from Next-Generation JAK2 Inhibitors for the Treatment of Myeloproliferative Neoplasms: Lessons from Structure-Based Drug Discovery Approaches
Authors: Nair Pramod C. , Piehler Jacob , Tvorogov Denis , Ross David M. , Lopez Angel F. , Gotlib Jason , Thomas Daniel
Published: September 2023

Figure showing X-ray crystal structure of pseudokinase domain inhibitor
Table S5 from Time-Dependent Prognostic Value of Serological and Measurable Residual Disease Assessments after Idecabtagene Vicleucel
Authors: Paiva Bruno , Manrique Irene , Rytlewski Julie , Campbell Timothy , Kazanecki Christian C. , Martin Nathan , Anderson Larry D. , Berdeja Jesús G. , Lonial Sagar , Raje Noopur S. , Lin Yi , Moreau Philippe , San-Miguel Jesús F. , Munshi Nikhil C. , Kaiser Shari M.
Published: September 2023

number samples with inferior limit of MRD
Figure S2 from Time-Dependent Prognostic Value of Serological and Measurable Residual Disease Assessments after Idecabtagene Vicleucel
Authors: Paiva Bruno , Manrique Irene , Rytlewski Julie , Campbell Timothy , Kazanecki Christian C. , Martin Nathan , Anderson Larry D. , Berdeja Jesús G. , Lonial Sagar , Raje Noopur S. , Lin Yi , Moreau Philippe , San-Miguel Jesús F. , Munshi Nikhil C. , Kaiser Shari M.
Published: September 2023

Landmark PFS
Table S1 from Discovery and Characterization of ZL-2201, a Potent, Highly Selective, and Orally Bioavailable Small-molecule DNA-PK Inhibitor
Authors: Lal Shruti , Bhola Neil E. , Sun Bee-Chun , Chen Yuping , Huang Tom , Morton Vivian , Chen Kevin X. , Xia Shanghua , Zhang Haoyu , Parikh Nehal S. , Ye Qiuping , Veiby O. Petter , Bellovin David I. , Ji Yuhua
Published: September 2023

ZL-2201 anti-proliferative IC50s and ATM mutational and VAF status
TABLE 1 from Discovery and Characterization of ZL-2201, a Potent, Highly Selective, and Orally Bioavailable Small-molecule DNA-PK Inhibitor
Authors: Lal Shruti , Bhola Neil E. , Sun Bee-Chun , Chen Yuping , Huang Tom , Morton Vivian , Chen Kevin X. , Xia Shanghua , Zhang Haoyu , Parikh Nehal S. , Ye Qiuping , Veiby O. Petter , Bellovin David I. , Ji Yuhua
Published: September 2023

In vitro pharmacology of ZL-2201 against PIKK family members
Supplementary Methods from Discovery and Characterization of ZL-2201, a Potent, Highly Selective, and Orally Bioavailable Small-molecule DNA-PK Inhibitor
Authors: Lal Shruti , Bhola Neil E. , Sun Bee-Chun , Chen Yuping , Huang Tom , Morton Vivian , Chen Kevin X. , Xia Shanghua , Zhang Haoyu , Parikh Nehal S. , Ye Qiuping , Veiby O. Petter , Bellovin David I. , Ji Yuhua
Published: September 2023

Supplementary Methods
Figure S3 from Discovery and Characterization of ZL-2201, a Potent, Highly Selective, and Orally Bioavailable Small-molecule DNA-PK Inhibitor
Authors: Lal Shruti , Bhola Neil E. , Sun Bee-Chun , Chen Yuping , Huang Tom , Morton Vivian , Chen Kevin X. , Xia Shanghua , Zhang Haoyu , Parikh Nehal S. , Ye Qiuping , Veiby O. Petter , Bellovin David I. , Ji Yuhua
Published: September 2023

Kinetics of Bleomycin-induced DNA-PK phosphorylation by ZL-2201
Figure S2 from Discovery and Characterization of ZL-2201, a Potent, Highly Selective, and Orally Bioavailable Small-molecule DNA-PK Inhibitor
Authors: Lal Shruti , Bhola Neil E. , Sun Bee-Chun , Chen Yuping , Huang Tom , Morton Vivian , Chen Kevin X. , Xia Shanghua , Zhang Haoyu , Parikh Nehal S. , Ye Qiuping , Veiby O. Petter , Bellovin David I. , Ji Yuhua
Published: September 2023

Cellular efficacy of ZL-2201 across cancer cell lines
FIGURE 5 from Discovery and Characterization of ZL-2201, a Potent, Highly Selective, and Orally Bioavailable Small-molecule DNA-PK Inhibitor
Authors: Lal Shruti , Bhola Neil E. , Sun Bee-Chun , Chen Yuping , Huang Tom , Morton Vivian , Chen Kevin X. , Xia Shanghua , Zhang Haoyu , Parikh Nehal S. , Ye Qiuping , Veiby O. Petter , Bellovin David I. , Ji Yuhua
Published: September 2023

Phosphoproteomic screen identifies MCM2 Ser108 phosphorylation decreased by ZL-2201. A, Simple Western showing inhibition of pDNA-PK upon treatment with PRKDC siRNA, 300 nmol/L and 3.5 μmol/L of ZL-2201 ± 10 μmol/L bleomycin used in phospho-MS screen analysis. B, The Venn diagram of phosphoproteins with ATM and DNA-PK substrate motifs decreased with bleomycin + ZL-2201 and PRKDC siRNAs at the indicated timepoints. C, Simple Western validation showing inhibition of pMCM2 (S108) upon treatment with ZL-2201 in NCI-H1703 cells. D, Simple Western showing inhibition of pMCM2 (S108) upon treatment with ZL-2201 (5 mg/kg) in NCI-H1703 tumor xenografts over the course of 2–10 hours (n = 4–5).
FIGURE 3 from Discovery and Characterization of ZL-2201, a Potent, Highly Selective, and Orally Bioavailable Small-molecule DNA-PK Inhibitor
Authors: Lal Shruti , Bhola Neil E. , Sun Bee-Chun , Chen Yuping , Huang Tom , Morton Vivian , Chen Kevin X. , Xia Shanghua , Zhang Haoyu , Parikh Nehal S. , Ye Qiuping , Veiby O. Petter , Bellovin David I. , Ji Yuhua
Published: September 2023

Phenotypic evaluation of ZL-2201 synergy with various DNA-damaging agents. A, Synergy scores of ZL-2201 in combination with various classes of antineoplastic drugs in A549 and NCI-H1703 cancer cells were analyzed after 6 days of combination treatments. The Bliss synergy score was measured using Combenefit and SynergyFinder. A synergy score of >10 is indicative of synergistic activity, <10 and >−10 are indicative of additive activity, and those below −10 are indicative of antagonism (n = 2–6). B, A549 and NCI-H1703 cells were cotreated with the increasing concentration of ZL-2201 and doxorubicin for 6 days. The synergistic activity of ZL-2201 with doxorubicin was analyzed by Combenefit. The blue color highlights the synergy. The graphs show the concentration-dependent cellular efficacy as a single agent as well as combinational treatments. One of the representative experiments is shown (n = 3). C, NCI-H1703 cells were treated with ZL-2201 (0.1, 0.3, 0.5, 1, and 3.6 μmol/L) and a low dose of doxorubicin (0.006 μmol/L) for 2 hours. Whole-cell lysates were harvested, and Simple Western was used to show the inhibition of pDNA-PK upon combination treatment of ZL-2201 with doxorubicin. D, NCI-H1703 cells were treated with ZL-2201 (0.1, 0.3, 0.5, 1 and 3.6 μmol/L) and a low dose of doxorubicin (0.006 μmol/L) for 72 hours. Single cells were harvested and stained with PI/RNAse solution. The cell-cycle distribution based on DNA content was determined by flow cytometry. E, NCI-H1703 cells were treated with ZL-2201 (0.1, 0.3, 0.5, 1, and 3.6 μmol/L) and a low dose of doxorubicin (0.006 μmol/L) for 2, 24, and 72 hours. Cells were stained with γH2AX (a DNA damage marker), and high-content imaging analysis was performed. One of the representative images of 72-hour timepoint is shown. Average yH2AX foci intensity across 16 fields/well was quantified. Blue: Hoescht; Green: γH2AX; Number of fields per image: 16.
Pencegahan COVID-19 di Panti dan Pondok melalui Pendidikan dan Perilaku Hidup yang Bersih dan Sehat
Authors: Muhammad Iqbal , Putra Ngakan , Djajalaksana Susanthy , Sari Fitri , Falyani Silvy , Yusdianto Adrian , Fahmi Kristia
Published: September 2023

Background: COVID-19 is an infectious illness that has become a global pandemic and is a major concern, particularly for children and other susceptible groups. The introduction of the viral variation that causes COVID-19 is also a hazard, particularly to youngsters, as the delta variant has infected children aged 1 to 14 years. Clean and Healthy Living Behavior (PHBS) is an effective technique for preventing the spread of COVID-19 that may be used by all segments of society, including children.

Aim: This study intends to determine the efficacy of PHBS education as a COVID-19 preventive strategy at the Malang City Orphanage.

Methods: This study method is action research with a participatory action program strategy (participatory action program) pre-test and post-test engaging the target community group, which consists of 65 orphans in orphanages. The data was acquired by questionnaires administered before and after counseling in the form of PHBS education for COVID-19 prevention, and SPSS was used to process the data.

Results: The average score of respondents' knowledge prior to counseling was 85.08 and climbed to 94.15 after counseling; these results were statistically significant with a p-value of less than 0.05.

Conclusion: There is a significant difference in the level of knowledge of PHBS as a prevention of COVID-19 before and after counseling for orphans in orphanages.
Profil Klinikopatologi Meningioma di Instalasi Patologi Anatomi RSUD Dr. Saiful Anwar Malang Periode Tahun 2016-2020
Authors: Putri Anggie Sasmita Kharisma , Diah Prabawati  , Dewi Rose Khasana , Angelina Aina
Published: September 2023

Background. The most common intracranial neoplasms worldwide is meningioma. It has been classified into three grades by World Health Organization (WHO) in which each grade has several histological variants. The prognosis of meningioma is affected by many factors including histopathological type of tumor, age, and gender.

Objective. The aim of this study is to determine the frequency of meningioma based on histopathological type, age, and gender from 2016 to 2020 in Saiful Anwar General Hospital Malang.

Methods. This study was a quantitative descriptive study and data was collected from medical records from 2016 to 2020 in Department of Anatomic Pathology, Medical Faculty, Brawijaya University, Saiful Anwar General Hospital Malang. Histopathological type of meningioma, age, and gender were acquired.

Results and Discussion. From 2016 to 2020, there were 96 eligible cases of meningioma. Ratio of men to women was 1:12.7.  Meningioma was most commonly found in age group 41­50 years old (43.75%). The most common histopathological type of meningioma was meningotheliomatous meningioma (37.5%). The average of meningioma cases was 19 per year. In this study, there was an increase in incidence rate of meningioma in 2017, and decreased in 2020. It may happen because The government has a better referral system to provide health care, thus meningioma can be detected earlier.

Conclusion. Frequency of meningioma is higher in women than men, and increases with age until 50 years, which then decreases. Meningotheliomatous meningioma is the most common histopathological type in this study.