bluuebunny/crossref_metadata_2025 huggingface dataset:
Data from Identification and Targeting of the Developmental Blockade in Extranodal Natural Killer/T-cell Lymphoma
Authors: Mundy-Bosse Bethany L. , Weigel Christoph , Wu Yue-Zhong , Abdelbaky Salma , Youssef Youssef , Casas Susana Beceiro , Polley Nicholas , Ernst Gabrielle , Young Karen A. , McConnell Kathleen K. , Nalin Ansel P. , Wu Kevin G. , Broughton Megan , Lordo Matthew R. , Altynova Ekaterina , Hegewisch-Solloa Everardo , Enriquez-Vera Daniel Y. , Dueñas Daniela , Barrionuevo Carlos , Yu Shan-Chi , Saleem Atif , Suarez Carlos J. , Briercheck Edward L. , Molina-Kirsch Hernan , Loughran Thomas P. , Weichenhan Dieter , Plass Christoph , Reneau John C. , Mace Emily M. , Gamboa Fabiola Valvert , Weinstock David M. , Natkunam Yasodha , Caligiuri Michael A. , Mishra Anjali , Porcu Pierluigi , Baiocchi Robert A. , Brammer Jonathan E. , Freud Aharon G. , Oakes Christopher C.
Published: April 2023

Abstract
Extranodal natural killer/T-cell lymphoma (ENKTL) is an aggressive, rare lymphoma of natural killer (NK) cell origin with poor clinical outcomes. Here we used phenotypic and molecular profiling, including epigenetic analyses, to investigate how ENKTL ontogeny relates to normal NK-cell development. We demonstrate that neoplastic NK cells are stably, but reversibly, arrested at earlier stages of NK-cell maturation. Genes downregulated in the most epigenetic immature tumors were associated with polycomb silencing along with genomic gain and overexpression of EZH2. ENKTL cells exhibited genome-wide DNA hypermethylation. Tumor-specific DNA methylation gains were associated with polycomb-marked regions, involving extensive gene silencing and loss of transcription factor binding. To investigate therapeutic targeting, we treated novel patient-derived xenograft (PDX) models of ENKTL with the DNA hypomethylating agent, 5-azacytidine. Treatment led to reexpression of NK-cell developmental genes, phenotypic NK-cell differentiation, and prolongation of survival. These studies lay the foundation for epigenetic-directed therapy in ENKTL.
Significance:
Through epigenetic and transcriptomic analyses of ENKTL, a rare, aggressive malignancy, along with normal NK-cell developmental intermediates, we identified that extreme DNA hypermethylation targets genes required for NK-cell development. Disrupting this epigenetic blockade in novel PDX models led to ENKTL differentiation and improved survival.

This article is highlighted in the In This Issue feature, p. 85
Data from Perspectives on the Risk-Stratified Treatment of Multiple Myeloma
Authors: Davies Faith E. , Pawlyn Charlotte , Usmani Saad Z. , San-Miguel Jesus F. , Einsele Hermann , Boyle Eileen M. , Corre Jill , Auclair Daniel , Cho Hearn Jay , Lonial Sagar , Sonneveld Pieter , Stewart A. Keith , Bergsagel P. Leif , Kaiser Martin F. , Weisel Katja , Keats Jonathan J. , Mikhael Joseph R. , Morgan Kathryn E. , Ghobrial Irene M. , Orlowski Robert Z. , Landgren C. Ola , Gay Francesca , Caers Joseph , Chng Wee Joo , Chari Ajai , Walker Brian A. , Kumar Shaji K. , Costa Luciano J. , Anderson Kenneth C. , Morgan Gareth J.
Published: April 2023

Summary:
The multiple myeloma treatment landscape has changed dramatically. This change, paralleled by an increase in scientific knowledge, has resulted in significant improvement in survival. However, heterogeneity remains in clinical outcomes, with a proportion of patients not benefiting from current approaches and continuing to have a poor prognosis. A significant proportion of the variability in outcome can be predicted on the basis of clinical and biochemical parameters and tumor-acquired genetic variants, allowing for risk stratification and a more personalized approach to therapy. This article discusses the principles that can enable the rational and effective development of therapeutic approaches for high-risk multiple myeloma.
Data from Blockade or Deletion of IFNγ Reduces Macrophage Activation without Compromising CAR T-cell Function in Hematologic Malignancies
Authors: Bailey Stefanie R. , Vatsa Sonika , Larson Rebecca C. , Bouffard Amanda A. , Scarfò Irene , Kann Michael C. , Berger Trisha R. , Leick Mark B. , Wehrli Marc , Schmidts Andrea , Silva Harrison , Lindell Kevin A. , Demato Ashley , Gallagher Kathleen M.E. , Frigault Matthew J. , Maus Marcela V.
Published: April 2023

Abstract
Chimeric antigen receptor (CAR) T cells induce impressive responses in patients with hematologic malignancies but can also trigger cytokine release syndrome (CRS), a systemic toxicity caused by activated CAR T cells and innate immune cells. Although IFNγ production serves as a potency assay for CAR T cells, its biologic role in conferring responses in hematologic malignancies is not established. Here we show that pharmacologic blockade or genetic knockout of IFNγ reduced immune checkpoint protein expression with no detrimental effect on antitumor efficacy against hematologic malignancies in vitro or in vivo. Furthermore, IFNγ blockade reduced macrophage activation to a greater extent than currently used cytokine antagonists in immune cells from healthy donors and serum from patients with CAR T-cell–treated lymphoma who developed CRS. Collectively, these data show that IFNγ is not required for CAR T-cell efficacy against hematologic malignancies, and blocking IFNγ could simultaneously mitigate cytokine-related toxicities while preserving persistence and antitumor efficacy.
Significance:
Blocking IFNγ in CAR T cells does not impair their cytotoxicity against hematologic tumor cells and paradoxically enhances their proliferation and reduces macrophage-mediated cytokines and chemokines associated with CRS. These findings suggest that IFNγ blockade may improve CAR T-cell function while reducing treatment-related toxicity in hematologic malignancies.

See interview with Stefanie R. Bailey, PhD, recipient of the 2023 Blood Cancer Discovery Award for Outstanding Journal Article: https://vimeo.com/847433865

See related content by McNerney et al., p. 90 (17).

This article is highlighted in the In This Issue feature, p. 85
Data from Changes in Bone Marrow Tumor and Immune Cells Correlate with Durability of Remissions Following BCMA CAR T Therapy in Myeloma
Authors: Dhodapkar Kavita M. , Cohen Adam D. , Kaushal Akhilesh , Garfall Alfred L. , Manalo Renee Julia , Carr Allison R. , McCachren Samuel S. , Stadtmauer Edward A. , Lacey Simon F. , Melenhorst J. Joseph , June Carl H. , Milone Michael C. , Dhodapkar Madhav V.
Published: April 2023

Abstract
Chimeric antigen-receptor (CAR) T cells lead to high response rates in myeloma, but most patients experience recurrent disease. We combined several high-dimensional approaches to study tumor/immune cells in the tumor microenvironment (TME) of myeloma patients pre– and post–B-cell maturation antigen (BCMA)-specific CAR T therapy. Lower diversity of pretherapy T-cell receptor (TCR) repertoire, presence of hyperexpanded clones with exhaustion phenotype, and BAFF+PD-L1+ myeloid cells in the marrow correlated with shorter progression-free survival (PFS) following CAR T therapy. In contrast, longer PFS was associated with an increased proportion of CLEC9A+ dendritic cells (DC), CD27+TCF1+ T cells with diverse T-cell receptors, and emergence of T cells expressing marrow-residence genes. Residual tumor cells at initial response express stemlike genes, and tumor recurrence was associated with the emergence of new dominant clones. These data illustrate a dynamic interplay between endogenous T, CAR T, myeloid/DC, and tumor compartments that affects the durability of response following CAR T therapy in myeloma.
Significance:
There is an unmet need to identify determinants of durable responses following BCMA CAR T therapy of myeloma. High-dimensional analysis of the TME was performed to identify features of immune and tumor cells that correlate with survival and suggest several strategies to improve outcomes following CAR T therapy.

See related commentary by Graham and Maus, p. 478.

This article is highlighted in the In This Issue feature, p. 476
Data from Follicular Lymphoma Microenvironment Characteristics Associated with Tumor Cell Mutations and MHC Class II Expression
Authors: Han Guangchun , Deng Qing , Marques-Piubelli Mario L. , Dai Enyu , Dang Minghao , Ma Man Chun John , Li Xubin , Yang Haopeng , Henderson Jared , Kudryashova Olga , Meerson Mark , Isaev Sergey , Kotlov Nikita , Nomie Krystle J. , Bagaev Alexander , Parra Edwin R. , Solis Soto Luisa M. , Parmar Simrit , Hagemeister Fredrick B. , Ahmed Sairah , Iyer Swaminathan P. , Samaniego Felipe , Steiner Raphael , Fayad Luis , Lee Hun , Fowler Nathan H. , Flowers Christopher R. , Strati Paolo , Westin Jason R. , Neelapu Sattva S. , Nastoupil Loretta J. , Vega Francisco , Wang Linghua , Green Michael R.
Published: April 2023

Abstract
Follicular lymphoma (FL) is a B-cell malignancy with a complex tumor microenvironment that is rich in nonmalignant immune cells. We applied single-cell RNA sequencing to characterize the diverse tumor and immune cell populations of FL and identified major phenotypic subsets of FL T cells, including a cytotoxic CD4 T-cell population. We characterized four major FL subtypes with differential representation or relative depletion of distinct T-cell subsets. By integrating exome sequencing, we observed that somatic mutations are associated with, but not definitive for, reduced MHC expression on FL cells. In turn, expression of MHCII genes by FL cells was associated with significant differences in the proportions and targetable immunophenotypic characteristics of T cells. This provides a classification framework of the FL microenvironment in association with FL genotypes and MHC expression, and informs different potential immunotherapeutic strategies based upon tumor cell MHCII expression.
Significance:
We have characterized the FL-infiltrating T cells, identified cytotoxic CD4 T cells as an important component that is associated with tumor cell–intrinsic characteristics, and identified sets of targetable immune checkpoints on T cells that differed from FLs with normal versus low MHC expression.

See related commentary by Melnick, p. 374.

This article is highlighted in the In This Issue feature, p. 369
Supplementary Data S5 from Multiple germline events contribute to cancer development in patients with Li-Fraumeni syndrome
Authors: Subasri Vallijah , Light Nicholas , Kanwar Nisha , Brzezinski Jack , Luo Ping , Hansford Jordan R , Cairney Elizabeth , Portwine Carol , Elser Christine , Finlay Jonathan L. , Nichols Kim E. , Alon Noa , Brunga Ledia , Anson Jo , Kohlmann Wendy , de Andrade Kelvin C. , Khincha Payal P. , Savage Sharon A. , Schiffman Joshua D , Weksberg Rosanna , Pugh Trevor J. , Villani Anita , Shlien Adam , Goldenberg Anna , Malkin David
Published: April 2023

LFS Variants
Supplementary Data S1 from Multiple germline events contribute to cancer development in patients with Li-Fraumeni syndrome
Authors: Subasri Vallijah , Light Nicholas , Kanwar Nisha , Brzezinski Jack , Luo Ping , Hansford Jordan R , Cairney Elizabeth , Portwine Carol , Elser Christine , Finlay Jonathan L. , Nichols Kim E. , Alon Noa , Brunga Ledia , Anson Jo , Kohlmann Wendy , de Andrade Kelvin C. , Khincha Payal P. , Savage Sharon A. , Schiffman Joshua D , Weksberg Rosanna , Pugh Trevor J. , Villani Anita , Shlien Adam , Goldenberg Anna , Malkin David
Published: April 2023

LFS Cohort
Supplementary Figure 2 from Resolving the Heterogeneous Tumor-Centric Cellular Neighborhood through Multiplexed, Spatial Paracrine Interactions in the Setting of Immune Checkpoint Blockade
Authors: Maus Rachel L.G. , Leontovich Alexey A. , Moore Raymond M. , Becher Laura , Nevala Wendy K. , Flotte Thomas J. , Guo Ruifeng , Schimke Jill M. , Dicke Betty A. , Yan Yiyi , Markovic Svetomir N.
Published: April 2023

Virtual H&E images for whole excisional lymph node biopsies from each clinical case
Supplement 9 from The Vaginal Microbiome is Associated with Endometrial Cancer Grade and Histology
Authors: Hakimjavadi Hesamedin , George Sophia H. , Taub Michael , Dodds Leah V. , Sanchez-Covarrubias Alex P. , Huang Marilyn , Pearson J. Matt , Slomovitz Brian M. , Kobetz Erin N. , Gharaibeh Raad , Sowamber Ramlogan , Pinto Andre , Chamala Srikar , Schlumbrecht Matthew P.
Published: April 2023

Biomarker discovery by histology
Supplement 7 from The Vaginal Microbiome is Associated with Endometrial Cancer Grade and Histology
Authors: Hakimjavadi Hesamedin , George Sophia H. , Taub Michael , Dodds Leah V. , Sanchez-Covarrubias Alex P. , Huang Marilyn , Pearson J. Matt , Slomovitz Brian M. , Kobetz Erin N. , Gharaibeh Raad , Sowamber Ramlogan , Pinto Andre , Chamala Srikar , Schlumbrecht Matthew P.
Published: April 2023

Heatmap of abundance values
Supplement 4 from The Vaginal Microbiome is Associated with Endometrial Cancer Grade and Histology
Authors: Hakimjavadi Hesamedin , George Sophia H. , Taub Michael , Dodds Leah V. , Sanchez-Covarrubias Alex P. , Huang Marilyn , Pearson J. Matt , Slomovitz Brian M. , Kobetz Erin N. , Gharaibeh Raad , Sowamber Ramlogan , Pinto Andre , Chamala Srikar , Schlumbrecht Matthew P.
Published: April 2023

Microbial alpha diversities
Supplement 2 from The Vaginal Microbiome is Associated with Endometrial Cancer Grade and Histology
Authors: Hakimjavadi Hesamedin , George Sophia H. , Taub Michael , Dodds Leah V. , Sanchez-Covarrubias Alex P. , Huang Marilyn , Pearson J. Matt , Slomovitz Brian M. , Kobetz Erin N. , Gharaibeh Raad , Sowamber Ramlogan , Pinto Andre , Chamala Srikar , Schlumbrecht Matthew P.
Published: April 2023

Analysis of Confounders
Supplemental Table 6 from Race-associated Molecular Changes in Gynecologic Malignancies
Authors: Asare Amma , Yao Hui , Lara Olivia D. , Wang Ying , Zhang Lin , Sood Anil K.
Published: April 2023

Differentially methylated probes analyzed by tumor site
Supplemental Table 2 from Race-associated Molecular Changes in Gynecologic Malignancies
Authors: Asare Amma , Yao Hui , Lara Olivia D. , Wang Ying , Zhang Lin , Sood Anil K.
Published: April 2023

Differentially expressed transcripts in individual tumor types
Table S1 from Targeting the Ezrin Adaptor Protein Sensitizes Metastatic Breast Cancer Cells to Chemotherapy and Reduces Neoadjuvant Therapy–induced Metastasis
Authors: Hoskin Victoria , Ghaffari Abdi , Laight Brian J. , SenGupta Sandip , Madarnas Yolanda , Nicol Christopher J.B. , Elliott Bruce E. , Varma Sonal , Greer Peter A.
Published: April 2023

Common gene mutations or amplifications found in the BC cell line panel
Figure S2 from Targeting the Ezrin Adaptor Protein Sensitizes Metastatic Breast Cancer Cells to Chemotherapy and Reduces Neoadjuvant Therapy–induced Metastasis
Authors: Hoskin Victoria , Ghaffari Abdi , Laight Brian J. , SenGupta Sandip , Madarnas Yolanda , Nicol Christopher J.B. , Elliott Bruce E. , Varma Sonal , Greer Peter A.
Published: April 2023

Quantitation of exogenous Radixin and Moesin levels or knockdown by siRNA
Supplemental Figure S1 from BRCA1-Associated RING Domain-1 (BARD1) Loss and GBP1 Expression Enhance Sensitivity to DNA Damage in Ewing Sarcoma
Authors: Maurer Lisa M. , Daley Jessica D. , Mukherjee Elina , Venier Rosemarie E. , Julian Claire M. , Bailey Nathanael G. , Jacobs Michelle F. , Kumar-Sinha Chandan , Raphael Haley , Periyapatna Nivitha , Weiss Kurt , Janeway Katherine A. , Mody Rajen , Lucas Peter C. , McAllister-Lucas Linda M. , Bailey Kelly M.
Published: April 2023

Additional protein/mRNA expression data (corresponding to Figure 2).
Supplementary Tables 1-3 from A Genome-Wide Gene-Based Gene–Environment Interaction Study of Breast Cancer in More than 90,000 Women
Authors: Wang Xiaoliang , Chen Hongjie , Kapoor Pooja Middha , Su Yu-Ru , Bolla Manjeet K. , Dennis Joe , Dunning Alison M. , Lush Michael , Wang Qin , Michailidou Kyriaki , Pharoah Paul D.P. , Hopper John L. , Southey Melissa C. , Koutros Stella , Freeman Laura E. Beane , Stone Jennifer , Rennert Gad , Shibli Rana , Murphy Rachel A. , Aronson Kristan , Guénel Pascal , Truong Thérèse , Teras Lauren R. , Hodge James M. , Canzian Federico , Kaaks Rudolf , Brenner Hermann , Arndt Volker , Hoppe Reiner , Lo Wing-Yee , Behrens Sabine , Mannermaa Arto , Kosma Veli-Matti , Jung Audrey , Becher Heiko , Giles Graham G. , Haiman Christopher A. , Maskarinec Gertraud , Scott Christopher , Winham Stacey , Simard Jacques , Goldberg Mark S. , Zheng Wei , Long Jirong , Troester Melissa A. , Love Michael I. , Peng Cheng , Tamimi Rulla , Eliassen Heather , García-Closas Montserrat , Figueroa Jonine , Ahearn Thomas , Yang Rose , Evans D. Gareth , Howell Anthony , Hall Per , Czene Kamila , Wolk Alicja , Sandler Dale P. , Taylor Jack A. , Swerdlow Anthony J. , Orr Nick , Lacey James V. , Wang Sophia , Olsson Håkan , Easton Douglas F. , Milne Roger L. , Hsu Li , Kraft Peter , Chang-Claude Jenny , Lindström Sara
Published: April 2023

Supplementary Table 1. Sample Size of each participated study, by case-control status and genotype platform. Supplementary Table 2. Association between fourteen environmental factors and the risk of breast cancer. Supplementary Table 3. Interactions between genes and fourteen environmental factors.
Supplementary Figure 1 from A Genome-Wide Gene-Based Gene–Environment Interaction Study of Breast Cancer in More than 90,000 Women
Authors: Wang Xiaoliang , Chen Hongjie , Kapoor Pooja Middha , Su Yu-Ru , Bolla Manjeet K. , Dennis Joe , Dunning Alison M. , Lush Michael , Wang Qin , Michailidou Kyriaki , Pharoah Paul D.P. , Hopper John L. , Southey Melissa C. , Koutros Stella , Freeman Laura E. Beane , Stone Jennifer , Rennert Gad , Shibli Rana , Murphy Rachel A. , Aronson Kristan , Guénel Pascal , Truong Thérèse , Teras Lauren R. , Hodge James M. , Canzian Federico , Kaaks Rudolf , Brenner Hermann , Arndt Volker , Hoppe Reiner , Lo Wing-Yee , Behrens Sabine , Mannermaa Arto , Kosma Veli-Matti , Jung Audrey , Becher Heiko , Giles Graham G. , Haiman Christopher A. , Maskarinec Gertraud , Scott Christopher , Winham Stacey , Simard Jacques , Goldberg Mark S. , Zheng Wei , Long Jirong , Troester Melissa A. , Love Michael I. , Peng Cheng , Tamimi Rulla , Eliassen Heather , García-Closas Montserrat , Figueroa Jonine , Ahearn Thomas , Yang Rose , Evans D. Gareth , Howell Anthony , Hall Per , Czene Kamila , Wolk Alicja , Sandler Dale P. , Taylor Jack A. , Swerdlow Anthony J. , Orr Nick , Lacey James V. , Wang Sophia , Olsson Håkan , Easton Douglas F. , Milne Roger L. , Hsu Li , Kraft Peter , Chang-Claude Jenny , Lindström Sara
Published: April 2023

Quantile-Quantile plot (Q-Q plot) of the aMiSTi p-values for each set of the GxE interactions.
Supplemental Figures 1-4, Tables 1-3 from Enhanced Costimulatory Signaling Improves CAR T-cell Effector Responses in CLL
Authors: Collins McKensie A. , Jung In-Young , Zhao Ziran , Apodaca Kimberly , Kong Weimin , Lundh Stefan , Fraietta Joseph A. , Kater Arnon P. , Sun Clare , Wiestner Adrian , Melenhorst J. Joseph
Published: April 2023

Supplemental Figure 1: An overview of study design choices. Supplemental Figure 2: IL-2 Supplementation Enhances the APC phenotype of CLL cells. Supplemental Figure 3: Exogenous Co-stimulation Improves Second-generation CAR T cell Activation. Supplemental Figure 4: aCLL Stimulation Shows Inconsistent Cytokine Production After a 6hr Incubation. Supplemental Table 1: Full Antibody List. Supplemental Table 2: CLL Donor List. Supplemental Table 3: Full list of adjusted P-values from Holm-Sidak multiple comparisons.
Supplementary Table S3 from Drug–gene Interaction Screens Coupled to Tumor Data Analyses Identify the Most Clinically Relevant Cancer Vulnerabilities Driving Sensitivity to PARP Inhibition
Authors: Jamal Kunzah , Galbiati Alessandro , Armenia Joshua , Illuzzi Giuditta , Hall James , Bentouati Sabrina , Barrell Daniel , Ahdesmäki Miika , O'Connor Mark J. , Leo Elisabetta , Forment Josep V.
Published: April 2023

Breakdown of biallelic losses (as percentages of total number of samples analysed) detected for each of the 110 confidence genes identified through CRISPR screens in all the tumour types analysed.
Supplementary Table S2 from Drug–gene Interaction Screens Coupled to Tumor Data Analyses Identify the Most Clinically Relevant Cancer Vulnerabilities Driving Sensitivity to PARP Inhibition
Authors: Jamal Kunzah , Galbiati Alessandro , Armenia Joshua , Illuzzi Giuditta , Hall James , Bentouati Sabrina , Barrell Daniel , Ahdesmäki Miika , O'Connor Mark J. , Leo Elisabetta , Forment Josep V.
Published: April 2023

List of 110 confidence genes from CRISPR-Cas9 loss-of-function screens.
Supplementary Tables 1-6 from Uterine Lavage Identifies Cancer Mutations and Increased TP53 Somatic Mutation Burden in Individuals with Ovarian Cancer
Authors: Ghezelayagh Talayeh S. , Kohrn Brendan F. , Fredrickson Jeanne , Manhardt Enna , Radke Marc R. , Katz Ronit , Gray Heidi J. , Urban Renata R. , Pennington Kathryn P. , Liao John B. , Doll Kemi M. , Simons Elise J. , Burzawa Jennifer K. , Goff Barbara A. , Speiser Paul , Swisher Elizabeth M. , Norquist Barbara M. , Risques Rosa Ana
Published: April 2023

Table S1. Clinical patient information

Table S2. Duplex Sequencing gene targets

Table S3. Custom probes for hotspots

Table S4. Mutation Frequency and Mutation Burden by patient and gene

Table S5. Codons most frequently mutated in ovarian cancers

Table S6. List of coding mutations by patient and gene
Supplementary File 2 (statistical analyses) from NetrinG1+ Cancer-Associated Fibroblasts Generate Unique Extracellular Vesicles that Support the Survival of Pancreatic Cancer Cells Under Nutritional Stress
Authors: Raghavan Kristopher S. , Francescone Ralph , Franco-Barraza Janusz , Gardiner Jaye C. , Vendramini-Costa Débora B. , Luong Tiffany , Pourmandi Narges , Andren Anthony , Kurimchak Alison , Ogier Charline , Campbell Paul M. , Duncan James S. , Lyssiotis Costas A. , Languino Lucia R. , Cukierman Edna
Published: April 2023

Spread sheet including a single tab per Figure panel conveying each graph's statistical analyses. Note that tabs are named accordingly. The tabs include the comprehensive statistical analyses that were performed for each experiment in which statistical significance was given. Each tab contains the full statistical output for its labeled experiment. The statistical test performed for each experiment is identified within the corresponding tab. Statistical tests were carried out using the software, Prism, version 7.05.
Supplementary Tables S1-S17 from Interrogation of T Cell–enriched Tumors Reveals Prognostic and Immunotherapeutic Implications of Polyamine Metabolism
Authors: Harbison R. Alex , Pandey Rajeev , Considine Michael , Leone Robert D. , Murray-Stewart Tracy , Erbe Rossin , Mandal Raj , Burns Mark , Casero Robert A. , Seiwert Tanguy , Fakhry Carole , Pardoll Drew , Fertig Elana , Powell Jonathan D.
Published: April 2023

Supplementary Tables
Supplemental Figures S1-S10 from Interrogation of T Cell–enriched Tumors Reveals Prognostic and Immunotherapeutic Implications of Polyamine Metabolism
Authors: Harbison R. Alex , Pandey Rajeev , Considine Michael , Leone Robert D. , Murray-Stewart Tracy , Erbe Rossin , Mandal Raj , Burns Mark , Casero Robert A. , Seiwert Tanguy , Fakhry Carole , Pardoll Drew , Fertig Elana , Powell Jonathan D.
Published: April 2023

Supplemental Figures S1-10
Figure S3 from A Phase I Study of Pelabresib (CPI-0610), a Small-Molecule Inhibitor of BET Proteins, in Patients with Relapsed or Refractory Lymphoma
Authors: Blum Kristie A. , Supko Jeffrey G. , Maris Michael B. , Flinn Ian W. , Goy Andre , Younes Anas , Bobba Suresh , Senderowicz Adrian M. , Efuni Sergey , Rippley Ronda , Colak Gozde , Trojer Patrick , Abramson Jeremy S.
Published: April 2023

PK/PD Analysis of the Relationship Between Maximum Relative Change in Gene Expression and Pelabresib Exposure Metrics.
Table S2 from Bintrafusp Alfa, an Anti-PD-L1:TGFβ Trap Fusion Protein, in Patients with ctDNA-positive, Liver-limited Metastatic Colorectal Cancer
Authors: Morris Van K. , Overman Michael J. , Lam Michael , Parseghian Christine M. , Johnson Benny , Dasari Arvind , Raghav Kanwal , Kee Bryan K. , Huey Ryan , Wolff Robert A. , Shen John Paul , Li June , Zorrilla Isabel , Tzeng Ching-Wei D. , Tran Cao Hop S. , Chun Yun Shin , Newhook Timothy E. , Vauthey Nicolas , Duose Dzifa , Luthra Raja , Haymaker Cara , Kopetz Scott
Published: April 2023

Supplemental Table S2
Supplementary Figure 6 from Remodeling of the Tumor Microenvironment Through PAK4 Inhibition Sensitizes Tumors to Immune Checkpoint Blockade
Authors: Abril-Rodriguez Gabriel , Torrejon Davis Y. , Karin Daniel , Campbell Katie M. , Medina Egmidio , Saco Justin D. , Galvez Mildred , Champhekar Ameya S. , Perez-Garcilazo Ivan , Baselga-Carretero Ignacio , Singh Jas , Comin-Anduix Begoña , Puig-Saus Cristina , Ribas Antoni
Published: April 2023

Supplementary Figure 6: Spatial colocalization of CD8 and CD31 positive cells.
Supplementary Figure 5 from Remodeling of the Tumor Microenvironment Through PAK4 Inhibition Sensitizes Tumors to Immune Checkpoint Blockade
Authors: Abril-Rodriguez Gabriel , Torrejon Davis Y. , Karin Daniel , Campbell Katie M. , Medina Egmidio , Saco Justin D. , Galvez Mildred , Champhekar Ameya S. , Perez-Garcilazo Ivan , Baselga-Carretero Ignacio , Singh Jas , Comin-Anduix Begoña , Puig-Saus Cristina , Ribas Antoni
Published: April 2023

Supplementary Figure 5: PAK4 deletion increases CXCL10 expression in vivo.
Supplementary Figure 2 from Remodeling of the Tumor Microenvironment Through PAK4 Inhibition Sensitizes Tumors to Immune Checkpoint Blockade
Authors: Abril-Rodriguez Gabriel , Torrejon Davis Y. , Karin Daniel , Campbell Katie M. , Medina Egmidio , Saco Justin D. , Galvez Mildred , Champhekar Ameya S. , Perez-Garcilazo Ivan , Baselga-Carretero Ignacio , Singh Jas , Comin-Anduix Begoña , Puig-Saus Cristina , Ribas Antoni
Published: April 2023

Supplementary Figure 2: PAK4 deletion does not affect CCL21 secretion.
Supplementary Materials and Methods1 from Loss of Vascular Endothelial Glutaminase Inhibits Tumor Growth and Metastasis, and Increases Sensitivity to Chemotherapy
Authors: Ngwa Verra M. , Edwards Deanna N. , Hwang Yoonha , Karno Breelyn , Wang Xiaoyong , Yan Chi , Richmond Ann , Brantley-Sieders Dana M. , Chen Jin
Published: April 2023

This is additional Supplementary Materials and Methods including tables.
Supplementary Fig. S6 from Loss of Vascular Endothelial Glutaminase Inhibits Tumor Growth and Metastasis, and Increases Sensitivity to Chemotherapy
Authors: Ngwa Verra M. , Edwards Deanna N. , Hwang Yoonha , Karno Breelyn , Wang Xiaoyong , Yan Chi , Richmond Ann , Brantley-Sieders Dana M. , Chen Jin
Published: April 2023

This figure shows volcano plots of differentially expressed genes in GLSECKO versus WT endothelial cell, differentially enriched pathways up and down, Gene set enrichment analysis, -log FPKM of Gls, Gls2, angiogenic genes, qRT-PCR of leptin and angiogenic genes in GLSECKO versus WT.
Supplementary Fig. S2 from Loss of Vascular Endothelial Glutaminase Inhibits Tumor Growth and Metastasis, and Increases Sensitivity to Chemotherapy
Authors: Ngwa Verra M. , Edwards Deanna N. , Hwang Yoonha , Karno Breelyn , Wang Xiaoyong , Yan Chi , Richmond Ann , Brantley-Sieders Dana M. , Chen Jin
Published: April 2023

This figure shows immunofluorescence images and quantification of CD31 and α-SMA in mammary gland, kidney, Lung and Liver tissues from non-tumor bearing mice after they were treated with tamoxifen.
Supplementary Figure 6 from Protein Kinase C Alpha is a Central Node for Tumorigenic Transcriptional Networks in Human Prostate Cancer
Authors: Cooke Mariana , Zhang Xuyao , Zhang Suli , Eruslanov Evgeniy , Lal Priti , Daniel Reba E. , Feldman Michael D. , Abba Martin C. , Kazanietz Marcelo G.
Published: April 2023

Reduced production of cytokines in PC3 cells subjected to PKCalpha RNAi depletion. IL-8 and GRO were measured in conditioned medium of PC3 cells by ELISA.
Table S1 from The MDM2 Inhibitor Navtemadlin Arrests Mouse Melanoma Growth In Vivo and Potentiates Radiotherapy
Authors: Ingelshed Katrine , Spiegelberg Diana , Kannan Pavitra , Påvénius Linnéa , Hacheney Jessica , Jiang Long , Eisinger Silke , Lianoudaki Danai , Lama Dilraj , Castillo Francisca , Bosdotter Cecilia , Kretzschmar Warren W. , Al-Radi Omayma , Fritz Nicolas , Villablanca Eduardo J. , Karlsson Mikael C. I. , Wermeling Fredrik , Nestor Marika , Lane David P. , Sedimbi Saikiran K.
Published: April 2023

Proteomics data.
Figure S7 from The MDM2 Inhibitor Navtemadlin Arrests Mouse Melanoma Growth In Vivo and Potentiates Radiotherapy
Authors: Ingelshed Katrine , Spiegelberg Diana , Kannan Pavitra , Påvénius Linnéa , Hacheney Jessica , Jiang Long , Eisinger Silke , Lianoudaki Danai , Lama Dilraj , Castillo Francisca , Bosdotter Cecilia , Kretzschmar Warren W. , Al-Radi Omayma , Fritz Nicolas , Villablanca Eduardo J. , Karlsson Mikael C. I. , Wermeling Fredrik , Nestor Marika , Lane David P. , Sedimbi Saikiran K.
Published: April 2023

Navtemadlin treatment does not affect tumor infiltrating myeloid cells.
Figure S2 from The MDM2 Inhibitor Navtemadlin Arrests Mouse Melanoma Growth In Vivo and Potentiates Radiotherapy
Authors: Ingelshed Katrine , Spiegelberg Diana , Kannan Pavitra , Påvénius Linnéa , Hacheney Jessica , Jiang Long , Eisinger Silke , Lianoudaki Danai , Lama Dilraj , Castillo Francisca , Bosdotter Cecilia , Kretzschmar Warren W. , Al-Radi Omayma , Fritz Nicolas , Villablanca Eduardo J. , Karlsson Mikael C. I. , Wermeling Fredrik , Nestor Marika , Lane David P. , Sedimbi Saikiran K.
Published: April 2023

Incucyte images.
Supplementary Tables 1-10 from Whole-exome Sequencing of Nigerian Prostate Tumors from the Prostate Cancer Transatlantic Consortium (CaPTC) Reveals DNA Repair Genes Associated with African Ancestry
Authors: White Jason A. , Kaninjing Ernest T. , Adeniji Kayode A. , Jibrin Paul , Obafunwa John O. , Ogo Chidiebere N. , Mohammed Faruk , Popoola Ademola , Fatiregun Omolara A. , Oluwole Olabode P. , Karanam Balasubramanyam , Elhussin Isra , Ambs Stefan , Tang Wei , Davis Melissa , Polak Paz , Campbell Moray J. , Brignole Kathryn R. , Rotimi Solomon O. , Dean-Colomb Windy , Odedina Folake T. , Martin Damali N. , Yates Clayton
Published: April 2023

Supplementary Table 1. Known Germline Variants. Supplementary Table 2. Germline Variants. Supplementary Table 3. Known Somatic Variants. Supplementary Table 4. Somatic Vars in NG Normal. Supplementary Table 5. NG WES QC Metrics. Supplementary Table 6. NG Cohort Description. Supplementary Table 7. TCGA Cohort Description. Supplementary Table 8. AA Germ Var Frequency. Supplementary Table 9. Somatic Variants. Supplementary Table 10. NG Somatic ClueGo Results.
Supplementary Figures 1-7, Table 1 from The Wnt Pathway Inhibitor RXC004 Blocks Tumor Growth and Reverses Immune Evasion in Wnt Ligand–dependent Cancer Models
Authors: Phillips Caroline , Bhamra Inder , Eagle Catherine , Flanagan Eimear , Armer Richard , Jones Clifford D. , Bingham Matilda , Calcraft Peter , Edmenson Cook Alicia , Thompson Ben , Woodcock Simon A.
Published: April 2023

Supplementary Figure 1: Effect of RXC004 on gene expression, caspase activity and cell growth in colorectal and pancreatic cancer cell lines in vitro. Supplementary Figure 2: RXC004 effects on gene expression in in vivo xenograft tumor models. Supplementary Figure 3: Pharmacokinetic/pharmacodynamic (PK/PD) analysis of RXC004 in SNU-1411/NOD-SCID mice. Supplementary Figure 4: Dose-dependent effects of RXC004 on tumor markers, intestinal Ki67 and bodyweight. Supplementary Figure 5: Effect of RXC004 with or without anti-PD-1 on body weight and survival in in vivo models. Supplementary Figure 6: Dose-dependent effects of RXC004 alone or in combination with anti-CTLA-4 in B16F10/C57BL/6 syngeneic model. Supplementary Figure 7: In vitro PBMC co-culture additional cytokines and monocultures. Supplementary Table 1: In vivo exposure data for RXC004.
Supplementary Table S2 from Mitochondrial Matrix Protease ClpP Agonists Inhibit Cancer Stem Cell Function in Breast Cancer Cells by Disrupting Mitochondrial Homeostasis
Authors: Greer Yoshimi Endo , Hernandez Lidia , Fennell Emily M.J. , Kundu Manjari , Voeller Donna , Chari Raj , Gilbert Samuel F. , Gilbert Thomas S.K. , Ratnayake Shashikala , Tang Binwu , Hafner Markus , Chen Qingrong , Meerzaman Daoud , Iwanowicz Edwin , Annunziata Christina M. , Graves Lee M. , Lipkowitz Stanley
Published: April 2023

RNAseq raw data (3 replicates for each time point 0, 6, 12, 24h ONC201 treatment)
Supplementary Figure S1 from ZL-1211 Exhibits Robust Antitumor Activity by Enhancing ADCC and Activating NK Cell–mediated Inflammation in CLDN18.2-High and -Low Expressing Gastric Cancer Models
Authors: Konno Hiroyasu , Lin Tracey , Wu Renyi , Dai Xinchuan , Li Shou , Wang Grace , Chen Min , Li Wenying , Wang Lina , Sun Bee-Chun , Luo Zhen , Huang Tom , Chen Yuping , Zhang John , Ye Qiuping , Bellovin David , Wan Bing , Kang Lishan , Szeto Christopher , Hsu Karl , Kabbarah Omar
Published: April 2023

Supplementary Figure 1 shows characterization of ZL-1211.
Supporting Information S3 from An Informatics Bridge to Improve the Design and Efficiency of Phase I Clinical Trials for Anticancer Drug Combinations
Authors: Wang Lei , Wei Lai , Zhang Shijun , Cheng Lijun , Shendre Aditi , Carson Williams , Chen James L. , Owen Dwight , Gregory Megan , Li Lang
Published: April 2023

Supporting Information S3 provides original study design of two case studies.
Supplementary Table 1 from Mavorixafor, an Orally Bioavailable CXCR4 Antagonist, Increases Immune Cell Infiltration and Inflammatory Status of Tumor Microenvironment in Patients with Melanoma
Authors: Andtbacka Robert H.I. , Wang Yan , Pierce Robert H. , Campbell Jean S. , Yushak Melinda , Milhem Mohammed , Ross Merrick , Niland Katie , Arbeit Robert D. , Parasuraman Sudha , Bickley Kris , Yeung Cecilia CS , Aicher Lauri D. , Smythe Kimberly S. , Gan Lu
Published: April 2023

Antibody panels used for mIF analyses.
Supplementary Data S2 from On the Choice of Longitudinal Models for the Analysis of Antitumor Efficacy in Mouse Clinical Trials of Patient-derived Xenograft Models
Authors: Savel Hélène , Barbier Sandrine , Proust-Lima Cécile , Rondeau Virginie , Thiébaut Rodolphe , Meyer-Losic Florence , Richert Laura
Published: April 2023

Details on statistical modeling strategy.
Fig. S6 from Targeting Lymphoma-associated Macrophage Expansion via CSF1R/JAK Inhibition is a Therapeutic Vulnerability in Peripheral T-cell Lymphomas
Authors: Gao Xin , Kady Nermin , Wang Chenguang , Abdelrahman Suhaib , Gann Peter , Sverdlov Maria , Wolfe Ashley , Brown Noah , Reneau John , Robida Aaron M. , Murga-Zamalloa Carlos , Wilcox Ryan A.
Published: April 2023

Fig. S6: GSEA in LAM
Table TS4 from A Phase I Trial of VEGF-A Inhibition Combined with PD-L1 Blockade for Recurrent Glioblastoma
Authors: Chiu Daniel , Qi Jingjing , Thin Tin Htwe , Garcia-Barros Monica , Lee Brian , Hahn Mary , Mandeli John , Belani Puneet , Nael Kambiz , Rashidipour Omid , Ghatan Saadi , Hadjipanayis Constantinos G. , Yong Raymund L. , Germano Isabelle M. , Brody Rachel , Tsankova Nadejda M. , Gnjatic Sacha , Kim-Schulze Seunghee , Hormigo Adília
Published: April 2023

One-way ANOVA analysis comparing expression of cytokines between Avelumab treated and Avelumab combined with Bevacizumab
Fig. S3 from Targeting Lymphoma-associated Macrophage Expansion via CSF1R/JAK Inhibition is a Therapeutic Vulnerability in Peripheral T-cell Lymphomas
Authors: Gao Xin , Kady Nermin , Wang Chenguang , Abdelrahman Suhaib , Gann Peter , Sverdlov Maria , Wolfe Ashley , Brown Noah , Reneau John , Robida Aaron M. , Murga-Zamalloa Carlos , Wilcox Ryan A.
Published: April 2023

PTCL induced myelopoiesis.
Table TS1 from A Phase I Trial of VEGF-A Inhibition Combined with PD-L1 Blockade for Recurrent Glioblastoma
Authors: Chiu Daniel , Qi Jingjing , Thin Tin Htwe , Garcia-Barros Monica , Lee Brian , Hahn Mary , Mandeli John , Belani Puneet , Nael Kambiz , Rashidipour Omid , Ghatan Saadi , Hadjipanayis Constantinos G. , Yong Raymund L. , Germano Isabelle M. , Brody Rachel , Tsankova Nadejda M. , Gnjatic Sacha , Kim-Schulze Seunghee , Hormigo Adília
Published: April 2023

Table S1. Representativeness of Study Participants
Suppl Fig FS3 from A Phase I Trial of VEGF-A Inhibition Combined with PD-L1 Blockade for Recurrent Glioblastoma
Authors: Chiu Daniel , Qi Jingjing , Thin Tin Htwe , Garcia-Barros Monica , Lee Brian , Hahn Mary , Mandeli John , Belani Puneet , Nael Kambiz , Rashidipour Omid , Ghatan Saadi , Hadjipanayis Constantinos G. , Yong Raymund L. , Germano Isabelle M. , Brody Rachel , Tsankova Nadejda M. , Gnjatic Sacha , Kim-Schulze Seunghee , Hormigo Adília
Published: April 2023

Chromogenic multiplex expression analysis of different biomarkers in formalin-fixed paraffin-embedded tissue of 34364, 34368, 34369, 34370, and 34371 tumors and quantitative analysis using Halo® Image Analysis Platform
Suppl Fig FS2 from A Phase I Trial of VEGF-A Inhibition Combined with PD-L1 Blockade for Recurrent Glioblastoma
Authors: Chiu Daniel , Qi Jingjing , Thin Tin Htwe , Garcia-Barros Monica , Lee Brian , Hahn Mary , Mandeli John , Belani Puneet , Nael Kambiz , Rashidipour Omid , Ghatan Saadi , Hadjipanayis Constantinos G. , Yong Raymund L. , Germano Isabelle M. , Brody Rachel , Tsankova Nadejda M. , Gnjatic Sacha , Kim-Schulze Seunghee , Hormigo Adília
Published: April 2023

Chromogenic multiplex expression analysis of different biomarkers in formalin-fixed paraffin-embedded tissue of a patient's tumor when diagnosed with glioblastoma (34369), before treated with LITT (34370) and after treatment with LITT and avelumab (34371) and quantitative analysis using Halo® Image Analysis Platform.
Supplementary Figure S7 from Targeting Tumor Angiogenesis with the Selective VEGFR-3 Inhibitor EVT801 in Combination with Cancer Immunotherapy
Authors: Paillasse Michael R. , Esquerré Michael , Bertrand Florie A. , Poussereau-Pomié Céline , Pichery Mélanie , Visentin Virgile , Gueguen-Dorbes Geneviève , Gaujarengues Florence , Barron Pauline , Badet Gaelle , Briaux Anne , Ancey Pierre-Benoit , Sibrac David , Erdociain Eric , Özcelik Dennis , Meneyrol Jérôme , Martin Valérie , Gomez-Brouchet Anne , Selves Janik , Rochaix Philippe , Battistella Maxime , Lebbé Céleste , Delord Jean-Pierre , Dol-Gleizes Frédérique , Bono Françoise , Blanc Isabelle , Alam Antoine , Hunneyball Ian , Whittaker Mark , Fons Pierre
Published: April 2023

Supplementary Figure S7 shows that EVT801 decreases immunosuppressive cell infiltration in VEGFR3-positive BNL hepatoma tumors
Figure S3 from Structures of Cancer Antigen Mesothelin and Its Complexes with Therapeutic Antibodies
Authors: Zhan Jingyu , Lin Dong , Watson Nathan , Esser Lothar , Tang Wai Kwan , Zhang Alex , Liu Xiufen , Hassan Raffit , Gleinich Anne , Shajahan Asif , Azadi Parastoo , Pastan Ira , Xia Di
Published: April 2023

Mapping epitopes of monoclonal antibodies to the structure of MSLN.
Figure S1 from Structures of Cancer Antigen Mesothelin and Its Complexes with Therapeutic Antibodies
Authors: Zhan Jingyu , Lin Dong , Watson Nathan , Esser Lothar , Tang Wai Kwan , Zhang Alex , Liu Xiufen , Hassan Raffit , Gleinich Anne , Shajahan Asif , Azadi Parastoo , Pastan Ira , Xia Di
Published: April 2023

Arrangement of MSLN molecules in the crystal.
Supplementary Data from Circulating IgA Antibodies Against Fusobacterium nucleatum Amyloid Adhesin FadA are a Potential Biomarker for Colorectal Neoplasia
Authors: Baik Jung Eun , Li Li , Shah Manish A. , Freedberg Daniel E. , Jin Zhezhen , Wang Timothy C. , Han Yiping W.
Published: April 2023

Supplementary Data from Circulating IgA Antibodies Against Fusobacterium nucleatum Amyloid Adhesin FadA are a Potential Biomarker for Colorectal Neoplasia
Figure S8 from Nanoparticle STING Agonist Reprograms the Bone Marrow to an Antitumor Phenotype and Protects Against Bone Destruction
Authors: Florian David C. , Bennett Natalie E. , Odziomek Mateusz , Baljon Jessalyn J. , Wehbe Mohamed , Merkel Alyssa R. , Fischer Melissa A. , Savona Michael R. , Rhoades Julie A. , Guelcher Scott A. , Wilson John T.
Published: April 2023

Supplementary Figure 8: Concentration of FOXP3+ cells in healthy STING NP-treated BM over time.
Figure S6 from Nanoparticle STING Agonist Reprograms the Bone Marrow to an Antitumor Phenotype and Protects Against Bone Destruction
Authors: Florian David C. , Bennett Natalie E. , Odziomek Mateusz , Baljon Jessalyn J. , Wehbe Mohamed , Merkel Alyssa R. , Fischer Melissa A. , Savona Michael R. , Rhoades Julie A. , Guelcher Scott A. , Wilson John T.
Published: April 2023

Supplementary Figure 6: Concentration of CD11B+ cells in healthy STING NP-treated BM over time.
Figure S2 from Nanoparticle STING Agonist Reprograms the Bone Marrow to an Antitumor Phenotype and Protects Against Bone Destruction
Authors: Florian David C. , Bennett Natalie E. , Odziomek Mateusz , Baljon Jessalyn J. , Wehbe Mohamed , Merkel Alyssa R. , Fischer Melissa A. , Savona Michael R. , Rhoades Julie A. , Guelcher Scott A. , Wilson John T.
Published: April 2023

Supplementary Figure 2: Gating scheme for T cell activation flow panel.
Figure S1 from Nanoparticle STING Agonist Reprograms the Bone Marrow to an Antitumor Phenotype and Protects Against Bone Destruction
Authors: Florian David C. , Bennett Natalie E. , Odziomek Mateusz , Baljon Jessalyn J. , Wehbe Mohamed , Merkel Alyssa R. , Fischer Melissa A. , Savona Michael R. , Rhoades Julie A. , Guelcher Scott A. , Wilson John T.
Published: April 2023

Supplementary Figure 1: Gating scheme for myeloid flow panel.
Supplementary Table 2 from The Splicing Factor PTBP1 Represses TP63 γ Isoform Production in Squamous Cell Carcinoma
Authors: Taylor William , Deschamps Stéphane , Reboutier David , Paillard Luc , Méreau Agnès , Audic Yann
Published: April 2023

Results of the dunnet's tests presented in the figures
Supplementary Table 1 from The Splicing Factor PTBP1 Represses TP63 γ Isoform Production in Squamous Cell Carcinoma
Authors: Taylor William , Deschamps Stéphane , Reboutier David , Paillard Luc , Méreau Agnès , Audic Yann
Published: April 2023

Reagents table
Supplementary Figure 8 from The Splicing Factor PTBP1 Represses TP63 γ Isoform Production in Squamous Cell Carcinoma
Authors: Taylor William , Deschamps Stéphane , Reboutier David , Paillard Luc , Méreau Agnès , Audic Yann
Published: April 2023

endogenous TP63 regulation is unaffected in HaCaT cell lines expressing minigenes
Supplementary Data SD1 from Small-molecule PTPN2 Inhibitors Sensitize Resistant Melanoma to Anti-PD-1 Immunotherapy
Authors: Zhu Zhouting , Tang Rachel , Huff Sarah , Kummetha Indrasena Reddy , Wang Lingling , Li Na , Rana Tariq M.
Published: April 2023

Compounds design, synthesis, and characterization
Table S1. Calculated physicochemical properties of Ptpn2 inhibitors.

Table S2. CRISPR target guide sequence to generate stable cell lines.

Table S3. The primers used for quantitative RT-PCR.

Figures S1 - S10. Analytical spectra for Ptpn2 inhibitors
Figure S4 from Small-molecule PTPN2 Inhibitors Sensitize Resistant Melanoma to Anti-PD-1 Immunotherapy
Authors: Zhu Zhouting , Tang Rachel , Huff Sarah , Kummetha Indrasena Reddy , Wang Lingling , Li Na , Rana Tariq M.
Published: April 2023

Supplementary Figure S4
Figure S1 from The Splicing Factor PTBP1 Represses TP63 γ Isoform Production in Squamous Cell Carcinoma
Authors: Taylor William , Deschamps Stéphane , Reboutier David , Paillard Luc , Méreau Agnès , Audic Yann
Published: April 2023

TP63 gene structure and annotation
Supplementary Figure S4 from The WAVE2/miR-29/Integrin-β1 Oncogenic Signaling Axis Promotes Tumor Growth and Metastasis in Triple-negative Breast Cancer
Authors: Rana Priyanka S. , Wang Wei , Markovic Vesna , Szpendyk Justin , Chan Ernest Ricky , Sossey-Alaoui Khalid
Published: April 2023

Quantification of volume of tumors derived from Control or WAVE2-KO MDA-MB-468 cells.
Supplementary Figure S2 from The WAVE2/miR-29/Integrin-β1 Oncogenic Signaling Axis Promotes Tumor Growth and Metastasis in Triple-negative Breast Cancer
Authors: Rana Priyanka S. , Wang Wei , Markovic Vesna , Szpendyk Justin , Chan Ernest Ricky , Sossey-Alaoui Khalid
Published: April 2023

Effect of loss of WAVE2 expression on tumorsphere invasion.
Supplementary Figure S11 from The WAVE2/miR-29/Integrin-β1 Oncogenic Signaling Axis Promotes Tumor Growth and Metastasis in Triple-negative Breast Cancer
Authors: Rana Priyanka S. , Wang Wei , Markovic Vesna , Szpendyk Justin , Chan Ernest Ricky , Sossey-Alaoui Khalid
Published: April 2023

Analysis of the potential role of DGCR8 in the WAVE2-mediated regulation of miR-29 in BC.
Supplementary Data File SD2 from The WAVE2/miR-29/Integrin-β1 Oncogenic Signaling Axis Promotes Tumor Growth and Metastasis in Triple-negative Breast Cancer
Authors: Rana Priyanka S. , Wang Wei , Markovic Vesna , Szpendyk Justin , Chan Ernest Ricky , Sossey-Alaoui Khalid
Published: April 2023

Raw RNA-seq Data of Control vs W2KO-MDA-MB-468 cells
Supplementary Figures S1-S17 from Inactivation of Notch4 Attenuated Pancreatic Tumorigenesis in Mice
Authors: Saeki Kiyoshi , Qiu Wanglong , Friedman Richard A. , Pan Samuel , Lu Jordan , Ichimiya Shu , Chio Iok In Christine , Shawber Carrie J. , Kitajewski Jan , Hu Jianhua , Su Gloria H.
Published: April 2023

Supplementary Figure 1. Inactivation of Notch1 had no impact on pancreatic tumorigenesis driven by oncogenic Kras in the context of p16 inactivation.

Supplementary Figure 2. Histological analyses of the pancreatic tissues of the PKC, the N1+/- PKC, and the N1fl/flPKC mice revealed no significant differences.

Supplementary Figure 3. Representative H&E from the PKC, the N1+/- PKC, and the N1fl/flPKC mice at 2 months of age (PanIN, A, C, E) and 5 months of age (PDAC, B, D, F).

Supplementary Figure 4. Comparative histological analyses of PanIN lesions in the PKC, the N1+/- PKC, and the N1fl/flPKC mice revealed no significant differences.

Supplementary Figure 5. Inactivation of Notch4 reduced the formation of high-grade PanIN, although not at a statistically significant level.

Supplementary Figure 6. Representative Notch4-ICD expression in the pancreases of PKC mice

Supplementary Figure 7. The expressions of Notch4 and Endomucin were both detected in the endothelial compartment by IHC.

Supplementary Figure 8. Slight differential Endomucin expression was detected between the KC and the N4-/- KC mice by day 21 post the caerulein treatment.

Supplementary Figure 9. Inactivation of Notch4 was associated with reduced but not significant Endomucin-positive angiogenesis at 2 months of age.

Supplementary Figure 10. Inactivation of Notch4 was associated with significant reduction of Endomucin-positive angiogenesis at 5 months of age.

Supplementary Figure 11. Inactivation of Notch4 attenuated desmoplastic reaction in the pancreases treated by Caerulein.

Supplementary Figure 12. Reduced desmoplasia was observed in N4-/- PKC mice when compared to PKC mice.

Supplementary Figure 13. Inactivation of Notch4 did not alter macrophage infiltration in the pancreases treated by Caerulein.

Supplementary Figure 14. Inactivation of Notch4 did not alter macrophage infiltration in the pancreatic tumors induced by oncogenic Kras.

Supplementary Figure 15. scRNA-Seq analysis revealed Notch4 expression in the endothelial and CK19+ normal and tumor cells in pancreatic tumorigenesis.

Supplementary Figure 16. Increased expression of the NGF gene was observed with Notch4 inactivation, but not with a statistically significant association.

Supplementary Figure 17. Notch4 RNA expression level in Panc 08.13 was the highest among candidate human PDAC cell lines.
Supplemental Table ST1 from Incorporating RNA-based Risk Scores for Genomic Instability to Predict Breast Cancer Recurrence and Immunogenicity in a Diverse Population
Authors: Hamilton Alina M. , Van Alsten Sarah C. , Gao Xiaohua , Nsonwu-Farley Joseph , Calhoun Benjamin C. , Love Michael I. , Troester Melissa A. , Hoadley Katherine A.
Published: April 2023

Supplemental table 1 displays tumor and patient characteristics by estrogen receptor status in CBCS, TCGA and METABRIC.
Table TS4 from Combination of a New Oral Demethylating Agent, OR2100, and Venetoclax for Treatment of Acute Myeloid Leukemia
Authors: Kamachi Kazuharu , Ureshino Hiroshi , Watanabe Tatsuro , Yoshida-Sakai Nao , Fukuda-Kurahashi Yuki , Kawasoe Kazunori , Hoshiko Toshimi , Yamamoto Yuta , Kurahashi Yuki , Kimura Shinya
Published: April 2023

The transcripts per million (TPM) values of six downregulated genes