bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figures from Fusion Kinases Identified by Genomic Analyses of Sporadic Microsatellite Instability–High Colorectal Cancers
Authors: Sato Kazuhito , Kawazu Masahito , Yamamoto Yoko , Ueno Toshihide , Kojima Shinya , Nagae Genta , Abe Hiroyuki , Soda Manabu , Oga Takafumi , Kohsaka Shinji , Sai Eirin , Yamashita Yoshihiro , Iinuma Hisae , Fukayama Masashi , Aburatani Hiroyuki , Watanabe Toshiaki , Mano Hiroyuki
Published: April 2023

Supplementary Figures S1-S10: Supplementary Figure S1: Clustering of microsatellite instability-high colorectal cancers with promoter DNA methylation analysis. Supplementary Figure S2: Methylation status of CpG dinucleotides in each patient, as assessed by bisulphite sequencing. Supplementary Figure S3: Allele-specific copy number status of mismatch repair genes. Supplementary Figure S4: Summary of mutations in microsatellite instability-high colorectal tumours. Supplementary Figure S5: Transforming capacities of oncogenes detected in this study. Supplementary Figure S6: Sanger sequences of genomic fusion points. Supplementary Figure S7: Confirmation of somatic fusion by identification of genomic breakpoints. Supplementary Figure S8: Effects of kinase inhibitor therapy in in vivo mouse model. Supplementary Figure S9: Establishment of cost-effective fusion kinase detection. Supplementary Figure S10: Survival curves among patients with microsatellite instability-high colorectal cancers harbouring each mutation were estimated by the Kaplan-Meier method and compared using Bonferroni-adjusted log-rank tests.
Supplementary Data from 4-1BB Agonism Averts TIL Exhaustion and Licenses PD-1 Blockade in Glioblastoma and Other Intracranial Cancers
Authors: Woroniecka Karolina I. , Rhodin Kristen E. , Dechant Cosette , Cui Xiuyu , Chongsathidkiet Pakawat , Wilkinson Daniel , Waibl-Polania Jessica , Sanchez-Perez Luis , Fecci Peter E.
Published: April 2023

Table S1 and S2
Table S2 from Disease Monitoring Using Post-induction Circulating Tumor DNA Analysis Following First-Line Therapy in Patients with Metastatic Colorectal Cancer
Authors: Max Ma Xiaoju , Bendell Johanna C. , Hurwitz Herbert I. , Ju Christine , Lee John J. , Lovejoy Alex , Mancao Christoph , Nicholas Alan , Price Richard , Sommer Nicolas , Tikoo Nalin , Yao Lijing , Yaung Stephanie J. , Palma John F.
Published: April 2023

Supplementary Table 2
Table S1 from Disease Monitoring Using Post-induction Circulating Tumor DNA Analysis Following First-Line Therapy in Patients with Metastatic Colorectal Cancer
Authors: Max Ma Xiaoju , Bendell Johanna C. , Hurwitz Herbert I. , Ju Christine , Lee John J. , Lovejoy Alex , Mancao Christoph , Nicholas Alan , Price Richard , Sommer Nicolas , Tikoo Nalin , Yao Lijing , Yaung Stephanie J. , Palma John F.
Published: April 2023

Supplementary Table 1
Figure S6CD from Disease Monitoring Using Post-induction Circulating Tumor DNA Analysis Following First-Line Therapy in Patients with Metastatic Colorectal Cancer
Authors: Max Ma Xiaoju , Bendell Johanna C. , Hurwitz Herbert I. , Ju Christine , Lee John J. , Lovejoy Alex , Mancao Christoph , Nicholas Alan , Price Richard , Sommer Nicolas , Tikoo Nalin , Yao Lijing , Yaung Stephanie J. , Palma John F.
Published: April 2023

Supplementary Figure
Supplementary Data from The Genomic Landscape of Merkel Cell Carcinoma and Clinicogenomic Biomarkers of Response to Immune Checkpoint Inhibitor Therapy
Authors: Knepper Todd C. , Montesion Meagan , Russell Jeffery S. , Sokol Ethan S. , Frampton Garrett M. , Miller Vincent A. , Albacker Lee A. , McLeod Howard L. , Eroglu Zeynep , Khushalani Nikhil I. , Sondak Vernon K. , Messina Jane L. , Schell Michael J. , DeCaprio James A. , Tsai Kenneth Y. , Brohl Andrew S.
Published: April 2023

Table S1
Figure S4 from Disease Monitoring Using Post-induction Circulating Tumor DNA Analysis Following First-Line Therapy in Patients with Metastatic Colorectal Cancer
Authors: Max Ma Xiaoju , Bendell Johanna C. , Hurwitz Herbert I. , Ju Christine , Lee John J. , Lovejoy Alex , Mancao Christoph , Nicholas Alan , Price Richard , Sommer Nicolas , Tikoo Nalin , Yao Lijing , Yaung Stephanie J. , Palma John F.
Published: April 2023

Supplementary Figure
Figure S3 from Disease Monitoring Using Post-induction Circulating Tumor DNA Analysis Following First-Line Therapy in Patients with Metastatic Colorectal Cancer
Authors: Max Ma Xiaoju , Bendell Johanna C. , Hurwitz Herbert I. , Ju Christine , Lee John J. , Lovejoy Alex , Mancao Christoph , Nicholas Alan , Price Richard , Sommer Nicolas , Tikoo Nalin , Yao Lijing , Yaung Stephanie J. , Palma John F.
Published: April 2023

Supplementary Figure
Supplementary Data from The Genomic Landscape of Merkel Cell Carcinoma and Clinicogenomic Biomarkers of Response to Immune Checkpoint Inhibitor Therapy
Authors: Knepper Todd C. , Montesion Meagan , Russell Jeffery S. , Sokol Ethan S. , Frampton Garrett M. , Miller Vincent A. , Albacker Lee A. , McLeod Howard L. , Eroglu Zeynep , Khushalani Nikhil I. , Sondak Vernon K. , Messina Jane L. , Schell Michael J. , DeCaprio James A. , Tsai Kenneth Y. , Brohl Andrew S.
Published: April 2023

Table S2
Figure S12 from Disease Monitoring Using Post-induction Circulating Tumor DNA Analysis Following First-Line Therapy in Patients with Metastatic Colorectal Cancer
Authors: Max Ma Xiaoju , Bendell Johanna C. , Hurwitz Herbert I. , Ju Christine , Lee John J. , Lovejoy Alex , Mancao Christoph , Nicholas Alan , Price Richard , Sommer Nicolas , Tikoo Nalin , Yao Lijing , Yaung Stephanie J. , Palma John F.
Published: April 2023

Supplementary Figure
Supplementary Data from The Genomic Landscape of Merkel Cell Carcinoma and Clinicogenomic Biomarkers of Response to Immune Checkpoint Inhibitor Therapy
Authors: Knepper Todd C. , Montesion Meagan , Russell Jeffery S. , Sokol Ethan S. , Frampton Garrett M. , Miller Vincent A. , Albacker Lee A. , McLeod Howard L. , Eroglu Zeynep , Khushalani Nikhil I. , Sondak Vernon K. , Messina Jane L. , Schell Michael J. , DeCaprio James A. , Tsai Kenneth Y. , Brohl Andrew S.
Published: April 2023

Table S3
Supplementary Data from The Genomic Landscape of Merkel Cell Carcinoma and Clinicogenomic Biomarkers of Response to Immune Checkpoint Inhibitor Therapy
Authors: Knepper Todd C. , Montesion Meagan , Russell Jeffery S. , Sokol Ethan S. , Frampton Garrett M. , Miller Vincent A. , Albacker Lee A. , McLeod Howard L. , Eroglu Zeynep , Khushalani Nikhil I. , Sondak Vernon K. , Messina Jane L. , Schell Michael J. , DeCaprio James A. , Tsai Kenneth Y. , Brohl Andrew S.
Published: April 2023

Table S4
Figure S1 from Disease Monitoring Using Post-induction Circulating Tumor DNA Analysis Following First-Line Therapy in Patients with Metastatic Colorectal Cancer
Authors: Max Ma Xiaoju , Bendell Johanna C. , Hurwitz Herbert I. , Ju Christine , Lee John J. , Lovejoy Alex , Mancao Christoph , Nicholas Alan , Price Richard , Sommer Nicolas , Tikoo Nalin , Yao Lijing , Yaung Stephanie J. , Palma John F.
Published: April 2023

Supplementary Figure
Table S3 from Stratifin Inhibits SCFFBW7 Formation and Blocks Ubiquitination of Oncoproteins during the Course of Lung Adenocarcinogenesis
Authors: Shiba-Ishii Aya , Hong Jeongmin , Hirokawa Takatsugu , Kim Yunjung , Nakagawa Tomoki , Sakashita Shingo , Sakamoto Noriaki , Kozuma Yukinori , Sato Yukio , Noguchi Masayuki
Published: April 2023

Table S3
Supplementary Data from Whole-Slide Image Analysis Reveals Quantitative Landscape of Tumor–Immune Microenvironment in Colorectal Cancers
Authors: Yoo Seung-Yeon , Park Hye Eun , Kim Jung Ho , Wen Xianyu , Jeong Seorin , Cho Nam-Yun , Gwon Hwang Gwan , Kim Kwangsoo , Lee Hye Seung , Jeong Seung-Yong , Park Kyu Joo , Han Sae-Won , Kim Tae-You , Bae Jeong Mo , Kang Gyeong Hoon
Published: April 2023

Supplementary data
Table S2 from Stratifin Inhibits SCFFBW7 Formation and Blocks Ubiquitination of Oncoproteins during the Course of Lung Adenocarcinogenesis
Authors: Shiba-Ishii Aya , Hong Jeongmin , Hirokawa Takatsugu , Kim Yunjung , Nakagawa Tomoki , Sakashita Shingo , Sakamoto Noriaki , Kozuma Yukinori , Sato Yukio , Noguchi Masayuki
Published: April 2023

Table S2
Table S1 from Stratifin Inhibits SCFFBW7 Formation and Blocks Ubiquitination of Oncoproteins during the Course of Lung Adenocarcinogenesis
Authors: Shiba-Ishii Aya , Hong Jeongmin , Hirokawa Takatsugu , Kim Yunjung , Nakagawa Tomoki , Sakashita Shingo , Sakamoto Noriaki , Kozuma Yukinori , Sato Yukio , Noguchi Masayuki
Published: April 2023

Table S1
Figure S1-7 from Stratifin Inhibits SCFFBW7 Formation and Blocks Ubiquitination of Oncoproteins during the Course of Lung Adenocarcinogenesis
Authors: Shiba-Ishii Aya , Hong Jeongmin , Hirokawa Takatsugu , Kim Yunjung , Nakagawa Tomoki , Sakashita Shingo , Sakamoto Noriaki , Kozuma Yukinori , Sato Yukio , Noguchi Masayuki
Published: April 2023

Figure S1-7
Supplementary Figure S6 from PARP Inhibition Enhances Radiotherapy of SMAD4-Deficient Human Head and Neck Squamous Cell Carcinomas in Experimental Models
Authors: Hernandez Ariel L. , Young Christian D. , Bian Li , Weigel Kelsey , Nolan Kyle , Frederick Barbara , Han Gangwen , He Guanting , Devon Trahan G. , Rudolph Michael C. , Jones Kenneth L. , Oweida Ayman J. , Karam Sana D. , Raben David , Wang Xiao-Jing
Published: April 2023

Supplementary Figure S6 demonstrates the influence of SMAD4 status on DNA damage response to RT + olaparib
Supplementary Figure S5 from PARP Inhibition Enhances Radiotherapy of SMAD4-Deficient Human Head and Neck Squamous Cell Carcinomas in Experimental Models
Authors: Hernandez Ariel L. , Young Christian D. , Bian Li , Weigel Kelsey , Nolan Kyle , Frederick Barbara , Han Gangwen , He Guanting , Devon Trahan G. , Rudolph Michael C. , Jones Kenneth L. , Oweida Ayman J. , Karam Sana D. , Raben David , Wang Xiao-Jing
Published: April 2023

Supplementary Figure S5 demonstrates the influence of SMAD4 status on proliferation (with and without treatment)
Supplementary Figure S4 from PARP Inhibition Enhances Radiotherapy of SMAD4-Deficient Human Head and Neck Squamous Cell Carcinomas in Experimental Models
Authors: Hernandez Ariel L. , Young Christian D. , Bian Li , Weigel Kelsey , Nolan Kyle , Frederick Barbara , Han Gangwen , He Guanting , Devon Trahan G. , Rudolph Michael C. , Jones Kenneth L. , Oweida Ayman J. , Karam Sana D. , Raben David , Wang Xiao-Jing
Published: April 2023

Supplementary Figure S4 demonstrates the influence of SMAD4 expression in CAL27 xenograft growth
Supplementary Figure S3 from PARP Inhibition Enhances Radiotherapy of SMAD4-Deficient Human Head and Neck Squamous Cell Carcinomas in Experimental Models
Authors: Hernandez Ariel L. , Young Christian D. , Bian Li , Weigel Kelsey , Nolan Kyle , Frederick Barbara , Han Gangwen , He Guanting , Devon Trahan G. , Rudolph Michael C. , Jones Kenneth L. , Oweida Ayman J. , Karam Sana D. , Raben David , Wang Xiao-Jing
Published: April 2023

Supplementary Figure S3 demonstrates doxycyline-dependent modulation of SMAD4
Figure A3 from Rindopepimut with Bevacizumab for Patients with Relapsed EGFRvIII-Expressing Glioblastoma (ReACT): Results of a Double-Blind Randomized Phase II Trial
Authors: Reardon David A. , Desjardins Annick , Vredenburgh James J. , O'Rourke Donald M. , Tran David D. , Fink Karen L. , Nabors Louis B. , Li Gordon , Bota Daniela A. , Lukas Rimas V. , Ashby Lynn S. , Duic J. Paul , Mrugala Maciej M. , Cruickshank Scott , Vitale Laura , He Yi , Green Jennifer A. , Yellin Michael J. , Turner Christopher D. , Keler Tibor , Davis Thomas A. , Sampson John H.
Published: April 2023

Figure A3 from Rindopepimut with Bevacizumab for Patients with Relapsed EGFRvIII-Expressing Glioblastoma (ReACT): Results of a Double-Blind Randomized Phase II Trial
Supplementary Figure S1 from PARP Inhibition Enhances Radiotherapy of SMAD4-Deficient Human Head and Neck Squamous Cell Carcinomas in Experimental Models
Authors: Hernandez Ariel L. , Young Christian D. , Bian Li , Weigel Kelsey , Nolan Kyle , Frederick Barbara , Han Gangwen , He Guanting , Devon Trahan G. , Rudolph Michael C. , Jones Kenneth L. , Oweida Ayman J. , Karam Sana D. , Raben David , Wang Xiao-Jing
Published: April 2023

Supplementary Figure S1 demonstrates the correlation between SMAD4 levels and FANC/BRCA family genes (in TCGA analyses)
Supplementary Table S4 from Validation of the OncoMasTR Risk Score in Estrogen Receptor–Positive/HER2-Negative Patients: A TransATAC study
Authors: Buus Richard , Sestak Ivana , Barron Stephen , Loughman Tony , Fender Bozena , Ruiz Cesar Lopez , Dynoodt Peter , Wang Chan-Ju Angel , O'Leary Des , Gallagher William M. , Dowsett Mitch , Cuzick Jack
Published: April 2023

Clinical characteristics of patients in the present study and those where RS data was available but were not assessed in the present study
Supplementary Table S2 from Validation of the OncoMasTR Risk Score in Estrogen Receptor–Positive/HER2-Negative Patients: A TransATAC study
Authors: Buus Richard , Sestak Ivana , Barron Stephen , Loughman Tony , Fender Bozena , Ruiz Cesar Lopez , Dynoodt Peter , Wang Chan-Ju Angel , O'Leary Des , Gallagher William M. , Dowsett Mitch , Cuzick Jack
Published: April 2023

Added prognostic information to NPI. Likelihood (Ï‡Â²) for distant recurrence for all prognostic scores in all patients and subgroups. DR, distant recurrence; OMm, OncoMasTR Molecular Score; OMclin2, OncoMasTR Risk Score; NPI, Nottingham Prognostic Index.
Supplementary Table 1 from Somatic Epigenetic Silencing of RIPK3 Inactivates Necroptosis and Contributes to Chemoresistance in Malignant Mesothelioma
Authors: Tan Yinfei , Sementino Eleonora , Cheung Mitchell , Peri Suraj , Menges Craig W. , Kukuyan Anna-Mariya , Zhang Ting , Khazak Vladimir , Fox Lauren A. , Ross Eric A. , Ramanathan Suresh , Jhanwar Suresh C. , Flores Raja M. , Balachandran Siddharth , Testa Joseph R.
Published: April 2023

Patient background information for 27 primary pleural malignant mesothelioma (MM) samples used in this investigation.
Supplementary Figure 9A from Somatic Epigenetic Silencing of RIPK3 Inactivates Necroptosis and Contributes to Chemoresistance in Malignant Mesothelioma
Authors: Tan Yinfei , Sementino Eleonora , Cheung Mitchell , Peri Suraj , Menges Craig W. , Kukuyan Anna-Mariya , Zhang Ting , Khazak Vladimir , Fox Lauren A. , Ross Eric A. , Ramanathan Suresh , Jhanwar Suresh C. , Flores Raja M. , Balachandran Siddharth , Testa Joseph R.
Published: April 2023

Drug sensitivity differences between 12 RIPK3-negative and 3 RIPK3-positive human MM cell lines as assessed by MTS assay. Treatment of MM cell lines with three different doses of cisplatin. First three bars in each bar graph represent viability of RIPK3-positive (+) MM cell lines, M49, M29 and M217, respectively. The bars shown to the right in each graph represent the viability of each of the 12 RIPK3-negative (-) MM lines. All drug treatments were for 72 h.
Figure S5 from A Noninvasive Blood-based Combinatorial Proteomic Biomarker Assay to Detect Breast Cancer in Women over age 50 with BI-RADS 3, 4, or 5 Assessment
Authors: Henderson Meredith C. , Silver Michael , Tran Quynh , Letsios Elias E. , Mulpuri Rao , Reese David E. , Lourenco Ana P. , LaBaer Joshua , Anderson Karen S. , Alpers Josie , Costantini Carrie , Rohatgi Nitin , Ali Haythem , Baker Karen , Northfelt Donald W. , Ghosh Karthik , Grobmyer Stephen R. , Polen Winnie , Wolf Judith K.
Published: April 2023

Figure S5: Individual ROC curves for Videssa Breast model training and validation. Curves shown correspond to those in Fig. 2.
Supplementary Figure 7C, D from Somatic Epigenetic Silencing of RIPK3 Inactivates Necroptosis and Contributes to Chemoresistance in Malignant Mesothelioma
Authors: Tan Yinfei , Sementino Eleonora , Cheung Mitchell , Peri Suraj , Menges Craig W. , Kukuyan Anna-Mariya , Zhang Ting , Khazak Vladimir , Fox Lauren A. , Ross Eric A. , Ramanathan Suresh , Jhanwar Suresh C. , Flores Raja M. , Balachandran Siddharth , Testa Joseph R.
Published: April 2023

Expression of RIPK3 induced activation of MLKL and cell death, which was rescued by treatment with GSK'872. Transduction of M12 cells (C) and M22 cells (D) with lentivirus expressing shMLKL or shGFP and then selected for 72 h with puromycin. Stable cells expressing shMLKL or shGFP were then infected with WPI or WPI expressing RIPK3. Immunoblotting and cell viability were performed after 48 h to detect the activation of MLKL. Expression of RIPK3 induced necroptosis, which was rescued by MLKL knockdown.
Figure S1 from A Noninvasive Blood-based Combinatorial Proteomic Biomarker Assay to Detect Breast Cancer in Women over age 50 with BI-RADS 3, 4, or 5 Assessment
Authors: Henderson Meredith C. , Silver Michael , Tran Quynh , Letsios Elias E. , Mulpuri Rao , Reese David E. , Lourenco Ana P. , LaBaer Joshua , Anderson Karen S. , Alpers Josie , Costantini Carrie , Rohatgi Nitin , Ali Haythem , Baker Karen , Northfelt Donald W. , Ghosh Karthik , Grobmyer Stephen R. , Polen Winnie , Wolf Judith K.
Published: April 2023

Figure S1: Breakdown of imaging modalities used to enroll subjects in Provista-002. Some subjects underwent multiple imaging procedures prior to enrollment, these are noted in side boxes for screening mammogram and diagnostic mammogram.
Supplementary Figure 2 from Somatic Epigenetic Silencing of RIPK3 Inactivates Necroptosis and Contributes to Chemoresistance in Malignant Mesothelioma
Authors: Tan Yinfei , Sementino Eleonora , Cheung Mitchell , Peri Suraj , Menges Craig W. , Kukuyan Anna-Mariya , Zhang Ting , Khazak Vladimir , Fox Lauren A. , Ross Eric A. , Ramanathan Suresh , Jhanwar Suresh C. , Flores Raja M. , Balachandran Siddharth , Testa Joseph R.
Published: April 2023

Human malignant mesothelioma (MM) cell lines frequently show down regulated expression of RIPK3 protein. Western blotting illustrating RIPK3 protein expression in 20 human MM cell lines. Normal mesothelial cell line NM311A was used as a control.
Supplementary Figure 1A from Somatic Epigenetic Silencing of RIPK3 Inactivates Necroptosis and Contributes to Chemoresistance in Malignant Mesothelioma
Authors: Tan Yinfei , Sementino Eleonora , Cheung Mitchell , Peri Suraj , Menges Craig W. , Kukuyan Anna-Mariya , Zhang Ting , Khazak Vladimir , Fox Lauren A. , Ross Eric A. , Ramanathan Suresh , Jhanwar Suresh C. , Flores Raja M. , Balachandran Siddharth , Testa Joseph R.
Published: April 2023

Efficiency of infection of MM cell lines infected with a pWPI lentivirus that expresses GFP marker alone (pWPI, control) or with a pWPI lentivirus that expresses both GFP and either RIPK3 WT or RIPK3-KD. Representative images indicate efficiency of infection of RIPK3-negative MM cell lines M12 and MSTO211H. Photographs of GFP fluorescence and combined GFP plus brightfield were taken 24 h after the initiation of infection. Note that most cells infected with pWPI-RIPK3 WT were floating, dead cells.
Supplementary Figure 10 from Somatic Epigenetic Silencing of RIPK3 Inactivates Necroptosis and Contributes to Chemoresistance in Malignant Mesothelioma
Authors: Tan Yinfei , Sementino Eleonora , Cheung Mitchell , Peri Suraj , Menges Craig W. , Kukuyan Anna-Mariya , Zhang Ting , Khazak Vladimir , Fox Lauren A. , Ross Eric A. , Ramanathan Suresh , Jhanwar Suresh C. , Flores Raja M. , Balachandran Siddharth , Testa Joseph R.
Published: April 2023

Expression levels of MLKL, CASP8 and FADD were not significantly correlated with MM patient survival. Data are from TCGA dataset of 87 primary pleural MM patients. A, C and E, Box plots of mRNA expression of MLKL, CASP8 and FADD where each X-axis shows quartile-based mRNA expression categories, and each Y-axis indicates the log-transformed RSEM mRNA expression values. In box plots, color code orange indicates high gene expression, and blue indicates low expression. B, D and F, Kaplan-Meier curves indicating OS of MM patients based on mRNA expression of MLKL, CASP8 and FADD, with MM patients having low expression of each gene shown with blue line and MM patients with high levels of expression of each of gene shown with an orange line.
Supplemental Figure 4 from Somatic Epigenetic Silencing of RIPK3 Inactivates Necroptosis and Contributes to Chemoresistance in Malignant Mesothelioma
Authors: Tan Yinfei , Sementino Eleonora , Cheung Mitchell , Peri Suraj , Menges Craig W. , Kukuyan Anna-Mariya , Zhang Ting , Khazak Vladimir , Fox Lauren A. , Ross Eric A. , Ramanathan Suresh , Jhanwar Suresh C. , Flores Raja M. , Balachandran Siddharth , Testa Joseph R.
Published: April 2023

Treatment of MM cells with the DNA demethylase 5-aza-2'-deoxycytidine (5-Aza) results in restoration of RIPK3 expression. MM cells lacking RIPK3 protein expression (RIPK3-negative) were treated with 30 µM of 5-Aza for 4 days. Semi-quantitative RT-PCR analysis was performed to analyze RIPK3 transcript levels in the RIPK3-negative cell lines.
Figure from Somatic Epigenetic Silencing of RIPK3 Inactivates Necroptosis and Contributes to Chemoresistance in Malignant Mesothelioma
Authors: Tan Yinfei , Sementino Eleonora , Cheung Mitchell , Peri Suraj , Menges Craig W. , Kukuyan Anna-Mariya , Zhang Ting , Khazak Vladimir , Fox Lauren A. , Ross Eric A. , Ramanathan Suresh , Jhanwar Suresh C. , Flores Raja M. , Balachandran Siddharth , Testa Joseph R.
Published: April 2023

Restoration of RIPK3 expression triggers necroptosis in RIPK3-negative MM cells. A, Lentivirus expressing RIPK3-WT, RIPK3-KD, or empty vector only was used to transduce RIPK3-negative MM cells at MOI=5. Flow cytometry analysis of MM cells stained with AnnexinV and PI. B, Bar graphs depicting percentages of early apoptotic (AnnexinV only), later apoptotic (AnnexinV+PI), and necrotic (PI only) populations.
Supplementary Tables from Molecular Subtype Not Immune Response Drives Outcomes in Endometrial Carcinoma
Authors: Talhouk Aline , Derocher Heather , Schmidt Pascal , Leung Samuel , Milne Katy , Gilks C. Blake , Anglesio Michael S. , Nelson Brad H. , McAlpine Jessica N.
Published: April 2023

Supplementary Tables S1-S6
Table S13 from Significance of BRCA2 and RB1 Co-loss in Aggressive Prostate Cancer Progression
Authors: Chakraborty Goutam , Armenia Joshua , Mazzu Ying Z. , Nandakumar Subhiksha , Stopsack Konrad H. , Atiq Mohammad O. , Komura Kazumasa , Jehane Lina , Hirani Rahim , Chadalavada Kalyani , Yoshikawa Yuki , Khan Nabeela A. , Chen Yu , Abida Wassim , Mucci Lorelei A. , Lee Gwo-Shu Mary , Nanjangud Gouri J. , Kantoff Philip W.
Published: April 2023

Supplementary Table S13
Table S12 from Significance of BRCA2 and RB1 Co-loss in Aggressive Prostate Cancer Progression
Authors: Chakraborty Goutam , Armenia Joshua , Mazzu Ying Z. , Nandakumar Subhiksha , Stopsack Konrad H. , Atiq Mohammad O. , Komura Kazumasa , Jehane Lina , Hirani Rahim , Chadalavada Kalyani , Yoshikawa Yuki , Khan Nabeela A. , Chen Yu , Abida Wassim , Mucci Lorelei A. , Lee Gwo-Shu Mary , Nanjangud Gouri J. , Kantoff Philip W.
Published: April 2023

Supplementary Table S12
Supplementary Data from Significance of BRCA2 and RB1 Co-loss in Aggressive Prostate Cancer Progression
Authors: Chakraborty Goutam , Armenia Joshua , Mazzu Ying Z. , Nandakumar Subhiksha , Stopsack Konrad H. , Atiq Mohammad O. , Komura Kazumasa , Jehane Lina , Hirani Rahim , Chadalavada Kalyani , Yoshikawa Yuki , Khan Nabeela A. , Chen Yu , Abida Wassim , Mucci Lorelei A. , Lee Gwo-Shu Mary , Nanjangud Gouri J. , Kantoff Philip W.
Published: April 2023

â€¢ Figure legends S1 to S6. â€¢ Tables S1 and S4, part of Table S8, and Tables S9, S10, and S11.
Supplementary Infomation from CKAP4, a DKK1 Receptor, Is a Biomarker in Exosomes Derived from Pancreatic Cancer and a Molecular Target for Therapy
Authors: Kimura Hirokazu , Yamamoto Hideki , Harada Takeshi , Fumoto Katsumi , Osugi Yoshihito , Sada Ryota , Maehara Natsumi , Hikita Hayato , Mori Soichiro , Eguchi Hidetoshi , Ikawa Masahito , Takehara Tetsuo , Kikuchi Akira
Published: April 2023

Supplemental Methods, References, and Figure Legends.
Supplementary Figures from CKAP4, a DKK1 Receptor, Is a Biomarker in Exosomes Derived from Pancreatic Cancer and a Molecular Target for Therapy
Authors: Kimura Hirokazu , Yamamoto Hideki , Harada Takeshi , Fumoto Katsumi , Osugi Yoshihito , Sada Ryota , Maehara Natsumi , Hikita Hayato , Mori Soichiro , Eguchi Hidetoshi , Ikawa Masahito , Takehara Tetsuo , Kikuchi Akira
Published: April 2023

Secretion of CKAP4 with SEVs (Figure S1). Generation of CKAP4 KO mice (Figure S2). Determination of epitopes of anti-CKAP4 mAbs (Figure S3). Development of ELISA for the detection of human serum CKAP4 (Figure S4). Detection of human serum CKAP4 by the ELISA (Figure S5). Characterization of anti-CKAP4 mAbs (Figure S6). Inhibition of xenograft tumor formation by anti-CKAP4 mAbs (Figure S7).
Figure S3 from Significance of BRCA2 and RB1 Co-loss in Aggressive Prostate Cancer Progression
Authors: Chakraborty Goutam , Armenia Joshua , Mazzu Ying Z. , Nandakumar Subhiksha , Stopsack Konrad H. , Atiq Mohammad O. , Komura Kazumasa , Jehane Lina , Hirani Rahim , Chadalavada Kalyani , Yoshikawa Yuki , Khan Nabeela A. , Chen Yu , Abida Wassim , Mucci Lorelei A. , Lee Gwo-Shu Mary , Nanjangud Gouri J. , Kantoff Philip W.
Published: April 2023

Supplementary Figure S3
Supplementary Data from Design and Evaluation of an External Control Arm Using Prior Clinical Trials and Real-World Data
Authors: Ventz Steffen , Lai Albert , Cloughesy Timothy F. , Wen Patrick Y. , Trippa Lorenzo , Alexander Brian M.
Published: April 2023

Statistical Details and Supplementary Figures/Tables
Figure S1 from Significance of BRCA2 and RB1 Co-loss in Aggressive Prostate Cancer Progression
Authors: Chakraborty Goutam , Armenia Joshua , Mazzu Ying Z. , Nandakumar Subhiksha , Stopsack Konrad H. , Atiq Mohammad O. , Komura Kazumasa , Jehane Lina , Hirani Rahim , Chadalavada Kalyani , Yoshikawa Yuki , Khan Nabeela A. , Chen Yu , Abida Wassim , Mucci Lorelei A. , Lee Gwo-Shu Mary , Nanjangud Gouri J. , Kantoff Philip W.
Published: April 2023

Supplementary Figure S1
Supplemental data from Racial Differences in the Association Between Luminal Master Regulator Gene Expression Levels and Breast Cancer Survival
Authors: Byun Jung S. , Singhal Sandeep K. , Park Samson , Yi Dae Ik , Yan Tingfen , Caban Ambar , Jones Alana , Mukhopadhyay Partha , Gil Sara M. , Hewitt Stephen M. , Newman Lisa , Davis Melissa B. , Jenkins Brittany D. , Sepulveda Jorge L. , De Siervi Adriana , Nápoles Anna María , Vohra Nasreen A. , Gardner Kevin
Published: April 2023

Supplemental data
Supplemental Table 3 from Racial Differences in the Association Between Luminal Master Regulator Gene Expression Levels and Breast Cancer Survival
Authors: Byun Jung S. , Singhal Sandeep K. , Park Samson , Yi Dae Ik , Yan Tingfen , Caban Ambar , Jones Alana , Mukhopadhyay Partha , Gil Sara M. , Hewitt Stephen M. , Newman Lisa , Davis Melissa B. , Jenkins Brittany D. , Sepulveda Jorge L. , De Siervi Adriana , Nápoles Anna María , Vohra Nasreen A. , Gardner Kevin
Published: April 2023

Supplemental Table 3 Race and Survival Predictor Regulon Gene Enrichment Ontology Processes
Supplemental Table 2 from Racial Differences in the Association Between Luminal Master Regulator Gene Expression Levels and Breast Cancer Survival
Authors: Byun Jung S. , Singhal Sandeep K. , Park Samson , Yi Dae Ik , Yan Tingfen , Caban Ambar , Jones Alana , Mukhopadhyay Partha , Gil Sara M. , Hewitt Stephen M. , Newman Lisa , Davis Melissa B. , Jenkins Brittany D. , Sepulveda Jorge L. , De Siervi Adriana , Nápoles Anna María , Vohra Nasreen A. , Gardner Kevin
Published: April 2023

Supplemental Table 2 Race and 3-year Survival Regulon RFS
Supplemental Table 1 from Racial Differences in the Association Between Luminal Master Regulator Gene Expression Levels and Breast Cancer Survival
Authors: Byun Jung S. , Singhal Sandeep K. , Park Samson , Yi Dae Ik , Yan Tingfen , Caban Ambar , Jones Alana , Mukhopadhyay Partha , Gil Sara M. , Hewitt Stephen M. , Newman Lisa , Davis Melissa B. , Jenkins Brittany D. , Sepulveda Jorge L. , De Siervi Adriana , Nápoles Anna María , Vohra Nasreen A. , Gardner Kevin
Published: April 2023

Supplemental Table 1 Survival and Race Predictor Regulon Gene Descriptions & Regulons
Supplemental Figure 5 from Racial Differences in the Association Between Luminal Master Regulator Gene Expression Levels and Breast Cancer Survival
Authors: Byun Jung S. , Singhal Sandeep K. , Park Samson , Yi Dae Ik , Yan Tingfen , Caban Ambar , Jones Alana , Mukhopadhyay Partha , Gil Sara M. , Hewitt Stephen M. , Newman Lisa , Davis Melissa B. , Jenkins Brittany D. , Sepulveda Jorge L. , De Siervi Adriana , Nápoles Anna María , Vohra Nasreen A. , Gardner Kevin
Published: April 2023

Supplemental Figure 5 Overall breast cancer survival based on median income of county of diagnosis in European American (EA) (A) compared to African American (AA) patients (B). CI, confidence interval.
Supplemental Figure 4 from Racial Differences in the Association Between Luminal Master Regulator Gene Expression Levels and Breast Cancer Survival
Authors: Byun Jung S. , Singhal Sandeep K. , Park Samson , Yi Dae Ik , Yan Tingfen , Caban Ambar , Jones Alana , Mukhopadhyay Partha , Gil Sara M. , Hewitt Stephen M. , Newman Lisa , Davis Melissa B. , Jenkins Brittany D. , Sepulveda Jorge L. , De Siervi Adriana , Nápoles Anna María , Vohra Nasreen A. , Gardner Kevin
Published: April 2023

Supplemental Figure 4 Quantitative correlation of biomarker expression stratified by race.
Supplemental Figure 3 from Racial Differences in the Association Between Luminal Master Regulator Gene Expression Levels and Breast Cancer Survival
Authors: Byun Jung S. , Singhal Sandeep K. , Park Samson , Yi Dae Ik , Yan Tingfen , Caban Ambar , Jones Alana , Mukhopadhyay Partha , Gil Sara M. , Hewitt Stephen M. , Newman Lisa , Davis Melissa B. , Jenkins Brittany D. , Sepulveda Jorge L. , De Siervi Adriana , Nápoles Anna María , Vohra Nasreen A. , Gardner Kevin
Published: April 2023

Supplemental Figure 3 Racial difference in survival in (A) Luminal A compared to (B) TNBC breast cancer. CI, confidence interval.
Supplemental Figure 1 from Racial Differences in the Association Between Luminal Master Regulator Gene Expression Levels and Breast Cancer Survival
Authors: Byun Jung S. , Singhal Sandeep K. , Park Samson , Yi Dae Ik , Yan Tingfen , Caban Ambar , Jones Alana , Mukhopadhyay Partha , Gil Sara M. , Hewitt Stephen M. , Newman Lisa , Davis Melissa B. , Jenkins Brittany D. , Sepulveda Jorge L. , De Siervi Adriana , Nápoles Anna María , Vohra Nasreen A. , Gardner Kevin
Published: April 2023

Supplemental Figure 1 Comparison of subtype distribution by ancestry in the current cohort study
Supplementary Tables from Genetic, Epigenetic, and Immunologic Profiling of MMR-Deficient Relapsed Glioblastoma
Authors: Indraccolo Stefano , Lombardi Giuseppe , Fassan Matteo , Pasqualini Lorenza , Giunco Silvia , Marcato Raffaella , Gasparini Alessandra , Candiotto Cinzia , Nalio Silvia , Fiduccia Pasquale , Fanelli Giuseppe Nicolò , Pambuku Ardi , Della Puppa Alessandro , D'Avella Domenico , Bonaldi Laura , Gardiman Marina Paola , Bertorelle Roberta , De Rossi Anita , Zagonel Vittorina
Published: April 2023

Supplementary Tables
Tables S1 - S11 from Identification of Hypermutation and Defective Mismatch Repair in ctDNA from Metastatic Prostate Cancer
Authors: Ritch Elie , Fu Simon Y.F. , Herberts Cameron , Wang Gang , Warner Evan W. , Schönlau Elena , Taavitsainen Sinja , Murtha Andrew J. , Vandekerkhove Gillian , Beja Kevin , Loktionova Yulia , Khalaf Daniel , Fazli Ladan , Kushnir Igal , Ferrario Cristiano , Hotte Sebastien , Annala Matti , Chi Kim N. , Wyatt Alexander W.
Published: April 2023

Supplementary Table 1: Somatic mutation count across all samples within meta-cohort. Counts of mutations in all ctDNA positive samples. 95th and 90th percentile are highlighted. Samples are named as a function of their relative mutation count. Supplementary Table 2: Evidence for mismatch repair deficiency by patient. See also Figure 2 Supplementary Table 3: Somatic mismatch repair gene alterations detected in patients with hypermutation. The status of key mismatch repair genes with respect to mutations and copynumber events. ClinVar version 20180603 annotations are included. *Clinvar annotation absent; **Diploid or lack of evidence for deviation from diploid ploidy; blue colour indicates the patients without MMRd etiology Supplementary Table 4: Whole exome sequencing summary statistics. Read depth and subsequent frequency calculations are based on unique read depth, post duplicate removal. Supplementary Table 5: Frequency of mutation and copy number changes in key genes. Comparison of gene and copy number frequencies in mimsatch repair cohort compared to control. P value and odds ratio generated using scipy.stats.fisher_exact verion 1.2.1 Supplementary Table 6: Somatic coding region altering mutations detected through targeted DNA sequencing (all cases in 95th percentile). Mutation annotation format with refseq protein change annotation. Supplementary Table 7: AR and other oncogene mutations detected across serial cfDNA collections. Protein changes are annotated with all refseq isoform amino acid changes. Variant allele frequency (VAF) is provided for each mutation. Supplementary Table 8: Distribution of variant allele frequencies for somatic mutations in each sample. Column D indicates the proportion of mutations in each sample that are considered subclonal. Predicted ctDNA fractions are calculated on max allele frequency of mutations in gene panel. Other columns contain descriptive statistics that summarize the central tendency, dispersion and shape of the distribution of variant allele frequencies per sample. Supplementary Table 9: CtDNA fraction by sample. The highest allele frequency mutation from each sample which does not belong to copy altered segment of the genome is used in the calculation of ctDNA fraction. Supplementary Table 10: Comparison of variant allele frequencies between tissue and ctDNA samples from patients P04 and P10. Supplementary Table 11: Clinical characteristics and PSA response to first-line AR-pathway inhibitor in the MMRd and control (MMR intact) cohort.
Figure S7 from Identification of Hypermutation and Defective Mismatch Repair in ctDNA from Metastatic Prostate Cancer
Authors: Ritch Elie , Fu Simon Y.F. , Herberts Cameron , Wang Gang , Warner Evan W. , Schönlau Elena , Taavitsainen Sinja , Murtha Andrew J. , Vandekerkhove Gillian , Beja Kevin , Loktionova Yulia , Khalaf Daniel , Fazli Ladan , Kushnir Igal , Ferrario Cristiano , Hotte Sebastien , Annala Matti , Chi Kim N. , Wyatt Alexander W.
Published: April 2023

Supplementary Figure 7. Immunohistochemical staining of MSH2, MSH6, MLH1, and PMS2.
Supplementary Data from Harnessing Androgen Receptor Pathway Activation for Targeted Alpha Particle Radioimmunotherapy of Breast Cancer
Authors: Thorek Daniel L.J. , Ku Anson T. , Mitsiades Nicholas , Veach Darren , Watson Philip A. , Metha Dipti , Strand Sven-Erik , Sharma Sai Kiran , Lewis Jason S. , Abou Diane S. , Lilja Hans G. , Larson Steven M. , McDevitt Michael R. , Ulmert David
Published: April 2023

Supplementary figure 2
Figure S4 from Identification of Hypermutation and Defective Mismatch Repair in ctDNA from Metastatic Prostate Cancer
Authors: Ritch Elie , Fu Simon Y.F. , Herberts Cameron , Wang Gang , Warner Evan W. , Schönlau Elena , Taavitsainen Sinja , Murtha Andrew J. , Vandekerkhove Gillian , Beja Kevin , Loktionova Yulia , Khalaf Daniel , Fazli Ladan , Kushnir Igal , Ferrario Cristiano , Hotte Sebastien , Annala Matti , Chi Kim N. , Wyatt Alexander W.
Published: April 2023

Supplementary Figure 4. Evidence for loss of heterozygosity across mismatch repair genes MSH2 and MSH6.
Supplemental Tables from Host IDO2 Gene Status Influences Tumor Progression and Radiotherapy Response in KRAS-Driven Sporadic Pancreatic Cancers
Authors: Nevler Avinoam , Muller Alexander J. , Sutanto-Ward Erika , DuHadaway James B. , Nagatomo Kei , Londin Eric , O'Hayer Kevin , Cozzitorto Joseph A. , Lavu Harish , Yeo Theresa P. , Curtis Mark , Villatoro Tatiana , Leiby Benjamin E. , Mandik-Nayak Laura , Winter Jordan M. , Yeo Charles J. , Prendergast George C. , Brody Jonathan R.
Published: April 2023

Table S1. Sequencing primers for IDO2 functional polymorphisms. Table S2. IDO2 genotype functionality definitions. A three-tier scale describes possible genotype combinations of IDO2 functional polymorphisms.
Figure S1 from Host IDO2 Gene Status Influences Tumor Progression and Radiotherapy Response in KRAS-Driven Sporadic Pancreatic Cancers
Authors: Nevler Avinoam , Muller Alexander J. , Sutanto-Ward Erika , DuHadaway James B. , Nagatomo Kei , Londin Eric , O'Hayer Kevin , Cozzitorto Joseph A. , Lavu Harish , Yeo Theresa P. , Curtis Mark , Villatoro Tatiana , Leiby Benjamin E. , Mandik-Nayak Laura , Winter Jordan M. , Yeo Charles J. , Prendergast George C. , Brody Jonathan R.
Published: April 2023

Flow cytometry graphs (black and white line and dot drawing)
Figure S1 from Identification of Hypermutation and Defective Mismatch Repair in ctDNA from Metastatic Prostate Cancer
Authors: Ritch Elie , Fu Simon Y.F. , Herberts Cameron , Wang Gang , Warner Evan W. , Schönlau Elena , Taavitsainen Sinja , Murtha Andrew J. , Vandekerkhove Gillian , Beja Kevin , Loktionova Yulia , Khalaf Daniel , Fazli Ladan , Kushnir Igal , Ferrario Cristiano , Hotte Sebastien , Annala Matti , Chi Kim N. , Wyatt Alexander W.
Published: April 2023

Supplementary Figure 1 Consort diagram of patient selection and analysis performed.
Supplementary Data from Measurement of Tumor Antioxidant Capacity and Prediction of Chemotherapy Resistance in Preclinical Models of Ovarian Cancer by Positron Emission Tomography
Authors: Greenwood Hannah E. , McCormick Patrick N. , Gendron Thibault , Glaser Matthias , Pereira Raul , Maddocks Oliver D. K. , Sander Kerstin , Zhang Tong , Koglin Norman , Lythgoe Mark F. , Årstad Erik , Hochhauser Daniel , Witney Timothy H.
Published: April 2023

Supplementary Figures 1 - 6. Fig. S1 shows the ability of PEO1, PEO4 and PEO6 cells to form colonies following cisplatin treatment; Fig. S2 demonstrates that [18F]FDG uptake in A2780 cells is unrelated to drug resistance; Fig. S3 examines the expression of key ABC transporters; Fig. S4 provides representative PET images of mice bearing A2780 WT and A2780 DoxR tumors; Fig. S5 quantifies the [18F]FSPG tumor-to-background ratio in WT and DoxR tumor-bearing mice; and Fig. S6 illustrates [18F]FSPG DoxR tumor retention after doxil treatment of mice.
Supplementary Table 3 from Alterations in the Transcriptional Programs of Myeloma Cells and the Microenvironment during Extramedullary Progression Affect Proliferation and Immune Evasion
Authors: Ryu Daeun , Kim Seok Jin , Hong Yourae , Jo Areum , Kim Nayoung , Kim Hee-Jin , Lee Hae-Ock , Kim Kihyun , Park Woong-Yang
Published: April 2023

Gene-set enrichment analysis between BM and EM
Move S3 from Measurement of Tumor Antioxidant Capacity and Prediction of Chemotherapy Resistance in Preclinical Models of Ovarian Cancer by Positron Emission Tomography
Authors: Greenwood Hannah E. , McCormick Patrick N. , Gendron Thibault , Glaser Matthias , Pereira Raul , Maddocks Oliver D. K. , Sander Kerstin , Zhang Tong , Koglin Norman , Lythgoe Mark F. , Årstad Erik , Hochhauser Daniel , Witney Timothy H.
Published: April 2023

Video 3
Supplementary Figure 4 from Alterations in the Transcriptional Programs of Myeloma Cells and the Microenvironment during Extramedullary Progression Affect Proliferation and Immune Evasion
Authors: Ryu Daeun , Kim Seok Jin , Hong Yourae , Jo Areum , Kim Nayoung , Kim Hee-Jin , Lee Hae-Ock , Kim Kihyun , Park Woong-Yang
Published: April 2023

Gene expression features of myeloma cells.
Move S2 from Measurement of Tumor Antioxidant Capacity and Prediction of Chemotherapy Resistance in Preclinical Models of Ovarian Cancer by Positron Emission Tomography
Authors: Greenwood Hannah E. , McCormick Patrick N. , Gendron Thibault , Glaser Matthias , Pereira Raul , Maddocks Oliver D. K. , Sander Kerstin , Zhang Tong , Koglin Norman , Lythgoe Mark F. , Årstad Erik , Hochhauser Daniel , Witney Timothy H.
Published: April 2023

Video 2
Supplementary Figure 2 from Alterations in the Transcriptional Programs of Myeloma Cells and the Microenvironment during Extramedullary Progression Affect Proliferation and Immune Evasion
Authors: Ryu Daeun , Kim Seok Jin , Hong Yourae , Jo Areum , Kim Nayoung , Kim Hee-Jin , Lee Hae-Ock , Kim Kihyun , Park Woong-Yang
Published: April 2023

Cytotoxic immune cells in the peripheral blood of healthy donors and multiple myeloma patients.
Figure S2 from Identification of Therapeutic Vulnerabilities in Small-cell Neuroendocrine Prostate Cancer
Authors: Corella Alexandra N. , Cabiliza Ordonio Ma Victoria Andrea , Coleman Ilsa , Lucas Jared M. , Kaipainen Arja , Nguyen Holly M. , Sondheim Daniel , Brown Lisha G. , True Lawrence D. , Lee John K. , MacPherson David , Nghiem Paul , Gulati Roman , Morrissey Colm , Corey Eva , Nelson Peter S.
Published: April 2023

Figure S2. Analyses of BCL2 family members in prostate cancer.
Supplementary Data from Altered Gene Expression along the Glycolysis–Cholesterol Synthesis Axis Is Associated with Outcome in Pancreatic Cancer
Authors: Karasinska Joanna M. , Topham James T. , Kalloger Steve E. , Jang Gun Ho , Denroche Robert E. , Culibrk Luka , Williamson Laura M. , Wong Hui-Li , Lee Michael K.C. , O'Kane Grainne M. , Moore Richard A. , Mungall Andrew J. , Moore Malcolm J. , Warren Cassia , Metcalfe Andrew , Notta Faiyaz , Knox Jennifer J. , Gallinger Steven , Laskin Janessa , Marra Marco A. , Jones Steven J.M. , Renouf Daniel J. , Schaeffer David F.
Published: April 2023

Supplemental Figures and Tables
Supplementary Table S1. Use of Grouped Termsa for Summary Tabulations of Adverse Reactions from FDA Approval: Blinatumomab for Patients with B-cell Precursor Acute Lymphoblastic Leukemia in Morphologic Remission with Minimal Residual Disease
Authors: Jen Emily Y. , Xu Qing , Schetter Aaron , Przepiorka Donna , Shen Yuan Li , Roscoe Donna , Sridhara Rajeshwari , Deisseroth Albert , Philip Reena , Farrell Ann T. , Pazdur Richard
Published: April 2023

Grouped terms used in safety analyses
Figure S3 from Altered Gene Expression along the Glycolysis–Cholesterol Synthesis Axis Is Associated with Outcome in Pancreatic Cancer
Authors: Karasinska Joanna M. , Topham James T. , Kalloger Steve E. , Jang Gun Ho , Denroche Robert E. , Culibrk Luka , Williamson Laura M. , Wong Hui-Li , Lee Michael K.C. , O'Kane Grainne M. , Moore Richard A. , Mungall Andrew J. , Moore Malcolm J. , Warren Cassia , Metcalfe Andrew , Notta Faiyaz , Knox Jennifer J. , Gallinger Steven , Laskin Janessa , Marra Marco A. , Jones Steven J.M. , Renouf Daniel J. , Schaeffer David F.
Published: April 2023

Box plots depicting tumor content levels across the metabolic subgroups in each PDAC cohort.
Supplementary Figure S1. Study 20120148 - Hematological relapse-free survival for patients in CR1 by MRD level at baseline after at least 3 intensive chemotherapy blocks from FDA Approval: Blinatumomab for Patients with B-cell Precursor Acute Lymphoblastic Leukemia in Morphologic Remission with Minimal Residual Disease
Authors: Jen Emily Y. , Xu Qing , Schetter Aaron , Przepiorka Donna , Shen Yuan Li , Roscoe Donna , Sridhara Rajeshwari , Deisseroth Albert , Philip Reena , Farrell Ann T. , Pazdur Richard
Published: April 2023

RFS by baseline MRD level from Study 20120148
Supplementary Tables from Multi-Omics Profiling Reveals Distinct Microenvironment Characterization and Suggests Immune Escape Mechanisms of Triple-Negative Breast Cancer
Authors: Xiao Yi , Ma Ding , Zhao Shen , Suo Chen , Shi Jinxiu , Xue Meng-Zhu , Ruan Miao , Wang Hai , Zhao Jingjing , Li Qin , Wang Peng , Shi Leming , Yang Wen-Tao , Huang Wei , Hu Xin , Yu Ke-Da , Huang Shenglin , Bertucci François , Jiang Yi-Zhou , Shao Zhi-Ming
Published: April 2023

Supplementary Table 1. The compendium of microenvironment cell subtypes in triple-negative breast cancer. Supplementary Table 2. Correlation of estimated microenvironment cell numbers between our compendium and CIBERSORT or MCP-counter. Supplementary Table 3. Clinicopathological characteristics of three microenvironment phenotypes in FUSCC, METABRIC and TCGA cohort. Supplementary Table 4. Prognostic value of each cell subset by univariate Cox proportional hazards model for relapse free survival. Supplementary Table 5. The signatures of ten oncogenic pathways. Supplementary Table 6. Comparison of gene mutation frequency among clusters. Supplementary Table 7. Comparison of somatic copy number alterations among clusters. Supplementary Table 8. GO and KEGG annotation of genes in cluster-specific copy number variation peaks.
Figure S2 from A Phase I Study of Pegylated Arginine Deiminase (Pegargiminase), Cisplatin, and Pemetrexed in Argininosuccinate Synthetase 1-Deficient Recurrent High-grade Glioma
Authors: Hall Peter E. , Lewis Rachel , Syed Nelofer , Shaffer Richard , Evanson Jane , Ellis Stephen , Williams Matthew , Feng Xiaoxing , Johnston Amanda , Thomson Jim A. , Harris Fiona P. , Jena Raj , Matys Tomasz , Jefferies Sarah , Smith Kate , Wu Bor-Wen , Bomalaski John S. , Crook Timothy , O'Neill Kevin , Paraskevopoulos Dimitris , Khadeir Ramsay S. , Sheaff Michael , Pacey Simon , Plowman Piers N. , Szlosarek Peter W.
Published: April 2023

Kaplan Meier plots for PFS and OS
Table S1, Table S2; Figure S1, Figure S2, Figure S3, Figure S4, Figure S5 from Lucitanib for the Treatment of HR+/HER2− Metastatic Breast Cancer: Results from the Multicohort Phase II FINESSE Study
Authors: Hui Rina , Pearson Alex , Cortes Javier , Campbell Christine , Poirot Camille , Azim Hatem A. , Fumagalli Debora , Lambertini Matteo , Daly Fergus , Arahmani Amal , Perez-Garcia José , Aftimos Philippe , Bedard Philippe L. , Xuereb Laura , Scheepers Elsemieke D. , Vicente Malou , Goulioti Theodora , Loibl Sibylle , Loi Sherene , Pierrat Marie-Jeanne , Turner Nicholas C. , Andre Fabrice , Curigliano Giuseppe
Published: April 2023

Supplementary Table S1. Treatment dose, duration, interruption and reduction. Supplementary Table S2A. Performance of the FGF23 ELISA, Kainos Laboratories Inc., cat# CY4000. Supplementary Table S2B. Concentration range of FGF23 in serum and plasma samples. Supplementary Table S2C. ddPCR assays used for determination of FGFR1 CNV. Supplementary Figure S1. A) FINESSE study design. B) Supplementary Figure S1B. FINESSE CONSORT diagram. Supplementary Figure S2. FISH screening results for FGFR1, CCND1/11q and FGF3,4,19. All samples were screened for both FGFR1 and CCND1/11q. Only samples positive for CCND1/11q amplification were assessed for FGF3,4,19 amplification. Of these, 1 patient was not assessed for FGF3,4,19 at the request of the site. 3 patients assessed as FGF3,4,19 amplified by additional evalution criteria to those described in the Methods section, with >50% of tumour cells showing {greater than or equal to}5 gene signals/nucleus. Supplementary Figure S3. Progression-free survival by A) FGFR1 amplification status by FISH and B) FGFR1 expression by IHC. Supplementary Figure S4. Expression of endothelial FGF2 and Ki67 presented by trial cohort. Supplementary Figure S5. Progression free survival by A) endothelial FGF2 and B) endothelial Ki67 expression.
Supplementary Table and Figures from Transcriptomic and Protein Analysis of Small-cell Bladder Cancer (SCBC) Identifies Prognostic Biomarkers and DLL3 as a Relevant Therapeutic Target
Authors: Koshkin Vadim S. , Garcia Jorge A. , Reynolds Jordan , Elson Paul , Magi-Galluzzi Cristina , McKenney Jesse K. , Isse Kumiko , Bishop Evan , Saunders Laura R. , Balyimez Aysegul , Rashid Summya , Hu Ming , Stephenson Andrew J. , Fergany Amr F. , Lee Byron H. , Haber Georges-Pascal , Dowlati Afshin , Gilligan Timothy , Ornstein Moshe C. , Rini Brian I. , Abazeed Mohamed E. , Mian Omar Y. , Grivas Petros
Published: April 2023

Figure S1, Supplementary Table, Figure S2, Figure S3, Figure S4, Figure S5
Figure S4 from Unbiased Metabolic Profiling Predicts Sensitivity of High MYC-Expressing Atypical Teratoid/Rhabdoid Tumors to Glutamine Inhibition with 6-Diazo-5-Oxo-L-Norleucine
Authors: Wang Sabrina Z. , Poore Brad , Alt Jesse , Price Antoinette , Allen Sariah J. , Hanaford Allison R. , Kaur Harpreet , Orr Brent A. , Slusher Barbara S. , Eberhart Charles G. , Raabe Eric H. , Rubens Jeffrey A.
Published: April 2023

Weight of mice throguhout in vivo treatments