bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Table 1 from Disease Characteristics and Prognostic Implications of Cell-Surface FLT3 Receptor (CD135) Expression in Pediatric Acute Myeloid Leukemia: A Report from the Children's Oncology Group
Authors: Tarlock Katherine , Alonzo Todd A. , Loken Michael R. , Gerbing Robert B. , Ries Rhonda E. , Aplenc Richard , Sung Lillian , Raimondi Susana C. , Hirsch Betsy A. , Kahwash Samir B. , McKenney Amy , Kolb E. Anders , Gamis Alan S. , Meshinchi Soheil
Published: April 2023

Supplementary Table 1. Clinical and biologic characteristics of patients with CD135 expression included in the analysis compared to patients treated on AAML0531 without CD135 expression data.
Figure S1 from Amplification of 1q32.1 Refines the Molecular Classification of Endometrial Carcinoma
Authors: Depreeuw Jeroen , Stelloo Ellen , Osse Elisabeth M. , Creutzberg Carien L. , Nout Remi A. , Moisse Matthieu , Garcia-Dios Diego A. , Dewaele Michael , Willekens Karen , Marine Jean-Christophe , Matias-Guiu Xavier , Amant Frédéric , Lambrechts Diether , Bosse Tjalling
Published: April 2023

Consensus clustering of significant amplified and deleted regions for all samples.
Supplemental Information from Correlation between Ferumoxytol Uptake in Tumor Lesions by MRI and Response to Nanoliposomal Irinotecan in Patients with Advanced Solid Tumors: A Pilot Study
Authors: Ramanathan Ramesh K. , Korn Ronald L. , Raghunand Natarajan , Sachdev Jasgit C. , Newbold Ronald G. , Jameson Gayle , Fetterly Gerald J. , Prey Joshua , Klinz Stephan G. , Kim Jaeyeon , Cain Jason , Hendriks Bart S. , Drummond Daryl C. , Bayever Eliel , Fitzgerald Jonathan B.
Published: April 2023

Includes additional detail concerning methods
Figure S6 from Correlation between Ferumoxytol Uptake in Tumor Lesions by MRI and Response to Nanoliposomal Irinotecan in Patients with Advanced Solid Tumors: A Pilot Study
Authors: Ramanathan Ramesh K. , Korn Ronald L. , Raghunand Natarajan , Sachdev Jasgit C. , Newbold Ronald G. , Jameson Gayle , Fetterly Gerald J. , Prey Joshua , Klinz Stephan G. , Kim Jaeyeon , Cain Jason , Hendriks Bart S. , Drummond Daryl C. , Bayever Eliel , Fitzgerald Jonathan B.
Published: April 2023

ROC analysis of FMX lesion response. Receiver operating characteristics for lesion classification according to best lesion size reduction, either as overall lesion shrinkage or partial response criteria, had an AUC {greater than or equal to}0.8 for early FMX measurements at 1 hour (A) or 24 hours (B).
Figure S5 from Correlation between Ferumoxytol Uptake in Tumor Lesions by MRI and Response to Nanoliposomal Irinotecan in Patients with Advanced Solid Tumors: A Pilot Study
Authors: Ramanathan Ramesh K. , Korn Ronald L. , Raghunand Natarajan , Sachdev Jasgit C. , Newbold Ronald G. , Jameson Gayle , Fetterly Gerald J. , Prey Joshua , Klinz Stephan G. , Kim Jaeyeon , Cain Jason , Hendriks Bart S. , Drummond Daryl C. , Bayever Eliel , Fitzgerald Jonathan B.
Published: April 2023

Correlation between the average irinotecan concentration of the biopsied lesion of that patient and the patient's time on treatment. Biopsy samples were obtained 72 hours after nal-IRI infusion. Time on treatment is measured from the date of first nal-IRI dose to the treatment termination date.
Supplementary Table 2, online only. Immune recovery after allo-stem cell transplantation from Immunomodulatory Effect of Vitamin D after Allogeneic Stem Cell Transplantation: Results of a Prospective Multicenter Clinical Trial
Authors: Caballero-Velázquez Teresa , Montero Isabel , Sánchez-Guijo Fermín , Parody Rocío , Saldaña Raquel , Valcarcel David , López-Godino Oriana , Ferra i Coll Christelle , Cuesta Marian , Carrillo-Vico Antonio , Sánchez-Abarca Luis I. , López-Corral Lucía , Márquez-Malaver Francisco J. , Pérez-Simón José A.
Published: April 2023

Immune recovery after allo-stem cell transplantation. Mean and standard error of the mean (SEM)of different subpobpopulation of immune system are summarized in this table.
Supplementary Table 1. Toxicity. from Immunomodulatory Effect of Vitamin D after Allogeneic Stem Cell Transplantation: Results of a Prospective Multicenter Clinical Trial
Authors: Caballero-Velázquez Teresa , Montero Isabel , Sánchez-Guijo Fermín , Parody Rocío , Saldaña Raquel , Valcarcel David , López-Godino Oriana , Ferra i Coll Christelle , Cuesta Marian , Carrillo-Vico Antonio , Sánchez-Abarca Luis I. , López-Corral Lucía , Márquez-Malaver Francisco J. , Pérez-Simón José A.
Published: April 2023

Toxicities according to the criteria by National Cancer Institute are described in this table.
Figure S2 from Correlation between Ferumoxytol Uptake in Tumor Lesions by MRI and Response to Nanoliposomal Irinotecan in Patients with Advanced Solid Tumors: A Pilot Study
Authors: Ramanathan Ramesh K. , Korn Ronald L. , Raghunand Natarajan , Sachdev Jasgit C. , Newbold Ronald G. , Jameson Gayle , Fetterly Gerald J. , Prey Joshua , Klinz Stephan G. , Kim Jaeyeon , Cain Jason , Hendriks Bart S. , Drummond Daryl C. , Bayever Eliel , Fitzgerald Jonathan B.
Published: April 2023

Example patient (patient 009) with widespread hepatic metastasis who demonstrated a treatment response following therapy. (A) Selected axial images from FMX-MRI acquired from the FSPGR Fat-Sat breath-hold images (TE = 13.2 milliseconds). The lesion outlined by the red box highlights one of the target lesions that underwent biopsy analysis and subsequent response assessment by RECIST v1.1. The values above each of the axial images are the estimated iron concentrations. (B) Axial contrast-enhanced CT images demonstrating tumor shrinkage (red boxes with reduction in lesion size by 67.3% at cycle 8).
Figures S1-S6; Table S1-S5 from Elevation of TP53 Autoantibody Before CA125 in Preclinical Invasive Epithelial Ovarian Cancer
Authors: Yang Wei-Lei , Gentry-Maharaj Aleksandra , Simmons Archana , Ryan Andy , Fourkala Evangelia Ourania , Lu Zhen , Baggerly Keith A. , Zhao Yang , Lu Karen H. , Bowtell David , Jacobs Ian , Skates Steven J. , He Wei-Wu , Menon Usha , Bast Robert C.
Published: April 2023

Supplementary figures, tables and materials & methods Supplementary Figure 1. Schematic presentation of steps in immunoassay development, validation and studies for screening TP53 autoantibody in human serum samples. Supplementary Figure 2. Identifying a common cut-off value for TP53 autoantibody immunoassay. Supplementary Table 1. Characteristics of patients with invasive epithelial ovarian/tubal/peritoneal cancer in MDACC-NROSS set Supplementary Table 2. Characteristics of patients with invasive epithelial ovarian/tubal/peritoneal cancer in AOCS set Supplementary Table 3. Characteristics of patients with invasive epithelial ovarian/tubal/peritoneal cancer by stage and primary site in the UKCTOCS study Supplementary Figure 3. Examples of longitudinal analysis of CA125 and TP53 autoantibody titers in pre-diagnostic serial serum samples from ovarian cancer patients in the UKCTOCS Study. Supplementary Figure 4. ROC curve analysis for TP53 autoantibody and CA125 biomarkers in UKCTOCS trial. Supplementary Figure 5. Comparison of TP53 autoantibody titers between cancer cases with TP53 wild-type and mutant genes in the AOCS biobanking study. Supplementary Figure 6. The list of TP53 mutant protein candidates for preliminary screening of autoantibody against specific TP53 mutant proteins. Supplementary Table 4. Summary of specific TP53 mutant autoantibody titers of individual cancer patients with corresponding TP53 protein mutations in the AOCS biobanking study Supplementary Table 5. Summary of multiplex immunoassay results for screening TP53 mutant-specific autoantibody using samples from the AOCS biobanking study.
Supplementary Figures 1_9 from PI3K Pathway Inhibition Achieves Potent Antitumor Activity in Melanoma Brain Metastases In Vitro and In Vivo
Authors: Niessner Heike , Schmitz Jennifer , Tabatabai Ghazaleh , Schmid Andreas M. , Calaminus Carsten , Sinnberg Tobias , Weide Benjamin , Eigentler Thomas K. , Garbe Claus , Schittek Birgit , Quintanilla-Fend Leticia , Bender Benjamin , Mai Marion , Praetorius Christian , Beissert Stefan , Schackert Gabriele , Muders Michael H. , Meinhardt Matthias , Baretton Gustavo B. , Dummer Reinhard , Flaherty Keith , Pichler Bernd J. , Kulms Dagmar , Westphal Dana , Meier Friedegund
Published: April 2023

Figure S1: The PI3K inhibitor buparlisib inhibits AKT phosphorylation and cell growth and induces cell cycle arrest and apoptosis in BRAF-mutant metastatic melanoma cell lines Figure S2: The PI3K inhibitor buparlisib inhibits AKT phosphorylation and cell growth and induces cell cycle arrest and apoptosis in NRAS-mutant metastatic melanoma cell lines Figure S3: Investigating the effects of buparlisib when combined with a MEK or BRAF inhibitor Figure S4: The PI3K inhibitor buparlisib inhibits cell growth in short-term brain melanoma cell lines Figure S5: Fibroblasts are resistant to the PI3K inhibitor buparlisib Figure S6: Buparlisib inhibits exponential growth pattern of brain metastasis in nude mice Figure S7: Histological sections of the brain melanoma tumors provide evidence of hemorrhages, necrosis and tumor regression Figure S8: Buparlisib downregulates pAKT and inhibits proliferation but does not induce apoptosis in brain metastases of nude mice Figure S9: Buparlisib downregulates PLEKHA5 in brain metastases of nude mice
Supplementary Figure 4 from Unique and Novel Urinary Metabolomic Features in Malignant versus Benign Adrenal Neoplasms
Authors: Patel Dhaval , Thompson Matthew D. , Manna Soumen K. , Krausz Kristopher W. , Zhang Lisa , Nilubol Naris , Gonzalez Frank J. , Kebebew Electron
Published: April 2023

(A) MS-MS confirmation of identity of creatine riboside in comparison to commercial available and synthesized standards. (B) MS-MS confirmation of identity of L-tryptophan in comparison to commercial available and synthesized standards. (C) MS-MS confirmation of identity of Nε, Nε, Nε-trimethyllysine in comparison to commercial available and synthesized standards. (D) MS-MS confirmation of identity of 3-methylhistidine in comparison to commercial available and synthesized standards.
Supplementary table from A Novel Compound ARN-3236 Inhibits Salt-Inducible Kinase 2 and Sensitizes Ovarian Cancer Cell Lines and Xenografts to Paclitaxel
Authors: Zhou Jinhua , Alfraidi Albandri , Zhang Shu , Santiago-O'Farrill Janice M. , Yerramreddy Reddy Venkata Krishna , Alsaadi Abdulkhaliq , Ahmed Ahmed A. , Yang Hailing , Liu Jinsong , Mao Weiqun , Wang Yan , Takemori Hiroshi , Vankayalapati Hariprasad , Lu Zhen , Bast Robert C.
Published: April 2023

Supplementary Table 1
Supplementary data from A Novel Compound ARN-3236 Inhibits Salt-Inducible Kinase 2 and Sensitizes Ovarian Cancer Cell Lines and Xenografts to Paclitaxel
Authors: Zhou Jinhua , Alfraidi Albandri , Zhang Shu , Santiago-O'Farrill Janice M. , Yerramreddy Reddy Venkata Krishna , Alsaadi Abdulkhaliq , Ahmed Ahmed A. , Yang Hailing , Liu Jinsong , Mao Weiqun , Wang Yan , Takemori Hiroshi , Vankayalapati Hariprasad , Lu Zhen , Bast Robert C.
Published: April 2023

Supplementary Figure 1 related to Figure 2. (A) In vitro kinetic curve of SIK2 kinase activity in the presence of ARN-3236. The reaction mixture contained SIK2 recombinant protein (15 nM), ATP (10 μM), and substrate peptide (TORC2 aa162-179) (1 μM). (B-J) Indicated cells were treated same as in Figure 1B, Cell viability was tested Supplementary Figure 2 related to Figure 3. (A-H) Different cell lines were plated at density of 8000/well in 96-well plate, then sequentially treated with ARN-3236 (IC30 of each cell line) or DMSO for 24 hr and with increasing concentration of paclitaxel for another 72 hr. Cell viability was measured with an SRB assay. Supplementary Figure 3 related to Figure 4. (A) A2780 cells were transfected with the indicated siRNA or treated with DMSO or ARN-3236 (1 μM). The average nuclear centrosome distance and the percentage of cells with NCU was calculated and plotted. (B, C) OVCAR8 and A2780 cells were treated as in Figure 4B. Bar plots represent the mean {plus minus} s.d. of the percentage of cells at different stage of mitosis (left plot) and the mean prometaphase/metaphase ratio {plus minus} s.d (right plot). Supplementary Figure 4 related to Figure 5. (A) OC316 and OVCAR8 ovarian cancer cells were treated as in Figure 5A, fixed, stained with PI, and subjected to cell cycle analysis. (B) OC316 and OVCAR8 ovarian cancer cells were treated as in Figure 5B, the representative percentage of apoptotic cells is shown. Supplementary Figure 5 related to Figure 6. (A) The expression of 272 proteins was measured using a reverse phase protein array after treatment of SKOv3 ovarian cancer cells with 2 μM of ARN-3236 for 48 hrs. The log2 (fold change) of each protein were plotted. (B) OC316, A2780 and OVCAR8 ovarian cancer cell lines were treated with ARN-3236 for 48 hrs, cell lysates were collected and analyzed by western blot for AKT-pS473, AKT-pT308, AKT and survivn, GAPDH was used as a loading control. (C) Western analysis of phosphorylation of AKT and survivin was performed using three vehicle and ARN-3236 treated tumor cell lysates.
Supplementary Tables S1-S9 from Mutational Heterogeneity in APC and KRAS Arises at the Crypt Level and Leads to Polyclonality in Early Colorectal Tumorigenesis
Authors: Gausachs Mireia , Borras Ester , Chang Kyle , Gonzalez Sara , Azuara Daniel , Delgado Amador Axel , Lopez-Doriga Adriana , San Lucas F. Anthony , Sanjuan Xavier , Paules Maria J. , Taggart Melissa W. , Davies Gareth E. , Ehli Erik A. , Fowler Jerry , Moreno Victor , Pineda Marta , You Y. Nancy , Lynch Patrick M. , Lazaro Conxi , Navin Nicholas E. , Scheet Paul A. , Hawk Ernest T. , Capella Gabriel , Vilar Eduardo
Published: April 2023

Table S1. Summary of adenomas with multiple APC and KRAS somatic hits identified by next-generation sequencing. Table S2. Clinical and pathologic characteristics of patients analyzed in this manuscript. Table S3. Analysis of APC, KRAS and 5q loss using AmpliSeq and SNP array TableS4. Number of normal mucosa, adenomas, tumors and crypts analyzed per case. NM; normal mucosa. Table S5. Analytical sensibility of Light Cycler® 480 (Roche) and dynamic array (Fluidigm) to detect KRAS mutations. Table S6. In silico of the APC somatic hits observed by next-generaiton sequencing that were labelled as VUS. B, benign; N, neutral; D, damaging; P, Probably damaging. Table S7. APC analysis of adenomas and carcinomas in bulk biopsies and isolated crypts. The analysis of adjancent normal mucosa was not performed. Table S8. KRAS genotyping results of adenomas and carcinomas by digital and dynamic array (Fluidigm) in bulk biopsies and isolated crypts Table S9. Primers and probes used in this manuscript.
Supplementary Materials and Methods from Mutational Heterogeneity in APC and KRAS Arises at the Crypt Level and Leads to Polyclonality in Early Colorectal Tumorigenesis
Authors: Gausachs Mireia , Borras Ester , Chang Kyle , Gonzalez Sara , Azuara Daniel , Delgado Amador Axel , Lopez-Doriga Adriana , San Lucas F. Anthony , Sanjuan Xavier , Paules Maria J. , Taggart Melissa W. , Davies Gareth E. , Ehli Erik A. , Fowler Jerry , Moreno Victor , Pineda Marta , You Y. Nancy , Lynch Patrick M. , Lazaro Conxi , Navin Nicholas E. , Scheet Paul A. , Hawk Ernest T. , Capella Gabriel , Vilar Eduardo
Published: April 2023

Supplementary Materials and Methods (Includes reference to Table S9 and Figures S11-15)
Supplementary Table 1 from High BCR–ABL/GUSIS Levels at Diagnosis of Chronic Phase CML Are Associated with Unfavorable Responses to Standard-Dose Imatinib
Authors: Vigneri Paolo , Stagno Fabio , Stella Stefania , Cupri Alessandra , Forte Stefano , Massimino Michele , Antolino Agostino , Siragusa Sergio , Mannina Donato , Impera Stefana Stella , Musolino Caterina , Malato Alessandra , Mineo Giuseppe , Tomaselli Carmela , Murgano Pamela , Musso Maurizio , Morabito Fortunato , Molica Stefano , Martino Bruno , Manzella Livia , Müller Martin C. , Hochhaus Andreas , Raimondo Francesco Di
Published: April 2023

Supplementary Table 1. Patient Characteristics (N = 272)
Supplementary Table S1 from Cyst Fluid Telomerase Activity Predicts the Histologic Grade of Cystic Neoplasms of the Pancreas
Authors: Hata Tatsuo , Dal Molin Marco , Suenaga Masaya , Yu Jun , Pittman Meredith , Weiss Matthew , Canto Marcia I. , Wolfgang Christopher , Lennon Anne Marie , Hruban Ralph H. , Goggins Michael
Published: April 2023

Supplementary Table S1. Characteristics of all patients in the discovery and validation sets.
Supplementary Table 3 from Antitumor Effect of Programmed Death-1 (PD-1) Blockade in Humanized the NOG-MHC Double Knockout Mouse
Authors: Ashizawa Tadashi , Iizuka Akira , Nonomura Chizu , Kondou Ryota , Maeda Chie , Miyata Haruo , Sugino Takashi , Mitsuya Koichi , Hayashi Nakamasa , Nakasu Yoko , Maruyama Kouji , Yamaguchi Ken , Katano Ikumi , Ito Mamoru , Akiyama Yasuto
Published: April 2023

Flow cytometry analysis of TIL from control or anti-PD-1 antibody-treated SCC-3 tumors.
Supplementary Fig. 3 from Antitumor Effect of Programmed Death-1 (PD-1) Blockade in Humanized the NOG-MHC Double Knockout Mouse
Authors: Ashizawa Tadashi , Iizuka Akira , Nonomura Chizu , Kondou Ryota , Maeda Chie , Miyata Haruo , Sugino Takashi , Mitsuya Koichi , Hayashi Nakamasa , Nakasu Yoko , Maruyama Kouji , Yamaguchi Ken , Katano Ikumi , Ito Mamoru , Akiyama Yasuto
Published: April 2023

Statistical analysis of iFN-γ-based CTL assay and NK cell assay.
SUPPLEMENTAL FIGURES AND TABLES from Bevacizumab May Differentially Improve Ovarian Cancer Outcome in Patients with Proliferative and Mesenchymal Molecular Subtypes
Authors: Kommoss Stefan , Winterhoff Boris , Oberg Ann L. , Konecny Gottfried E. , Wang Chen , Riska Shaun M. , Fan Jian-Bing , Maurer Matthew J. , April Craig , Shridhar Viji , Kommoss Friedrich , du Bois Andreas , Hilpert Felix , Mahner Sven , Baumann Klaus , Schroeder Willibald , Burges Alexander , Canzler Ulrich , Chien Jeremy , Embleton Andrew C. , Parmar Mahesh , Kaplan Richard , Perren Timothy , Hartmann Lynn C. , Goode Ellen L. , Dowdy Sean C. , Pfisterer Jacobus
Published: April 2023

Appendix 1: Additional Methods for Subtype Assignment Figure S1. Consistency check between published supervised classification vs. novel unsupervised clustering in TCGA Figure S2. Subclasses were computed by applying a consensus NMF clustering method which confirmed the presence of four stable clusters. Consensus matrices and sample correlation matrices are shown for k=2 to k=8 using the 1500 probe sets based on genes described by TCGA. Figure S3. Kaplan Meier analysis of progression free and overall survival for bevacizumab vs. standard treatment. Panel A: total study population. Panel B: patients at high risk for progression (suboptimally cytoreduced stage III and all stage IV patients) Supplemental Table 1. Results of progression-free survival restricted mean
Supplemental Figure 2 from Exposure–Response Analysis of Alvocidib (Flavopiridol) Treatment by Bolus or Hybrid Administration in Newly Diagnosed or Relapsed/Refractory Acute Leukemia Patients
Authors: LaCerte Carl , Ivaturi Vijay , Gobburu Joga , Greer Jacqueline M. , Doyle L. Austin , Wright John J. , Karp Judith E. , Rudek Michelle A.
Published: April 2023

Observed versus Predicted Flavopiridol Concentrations: Total Individual (A), Unbound Individual (B), Total Population (C), or Unbound Population (D).
Supplementary Data from Prognostic Utility of a New mRNA Expression Signature of Gleason Score
Authors: Sinnott Jennifer A. , Peisch Sam F. , Tyekucheva Svitlana , Gerke Travis , Lis Rosina , Rider Jennifer R. , Fiorentino Michelangelo , Stampfer Meir J. , Mucci Lorelei A. , Loda Massimo , Penney Kathryn L.
Published: April 2023

Supplementary Table 1. Comparison of signature gene expression in normal, Gleason score {less than or equal to}6, and Gleason score {greater than or equal to}8 using t-tests with p-values calculated using the bootstrap to account for the matching between some tumor and normal samples.
Supplemental Figure Legends from Hypermutated Circulating Tumor DNA: Correlation with Response to Checkpoint Inhibitor–Based Immunotherapy
Authors: Khagi Yulian , Goodman Aaron M. , Daniels Gregory A. , Patel Sandip P. , Sacco Assuntina G. , Randall James M. , Bazhenova Lyudmila A. , Kurzrock Razelle
Published: April 2023

Supplemental Figure Legends
Supplemental Figures 1-6 from Blocking Indolamine-2,3-Dioxygenase Rebound Immune Suppression Boosts Antitumor Effects of Radio-Immunotherapy in Murine Models and Spontaneous Canine Malignancies
Authors: Monjazeb Arta M. , Kent Michael S. , Grossenbacher Steven K. , Mall Christine , Zamora Anthony E. , Mirsoian Annie , Chen Mingyi , Kol Amir , Shiao Stephen L. , Reddy Abhinav , Perks Julian R. , T.N. Culp William , Sparger Ellen E. , Canter Robert J. , Sckisel Gail D. , Murphy William J.
Published: April 2023

Supplemental Figure 1: Schema and background data for the canine clinical trial; Supplemental Figure 2: flow cytometry based immunophenotyping of peripheral and tumor draining lymph nodes; Supplemental Figure 3: Flow cytometric assessment of Treg levels at day 21; Supplemental Figure 4: Intratumoral IL-6 levels; Supplemental Figure 5: CD8+ T-cell dependent effects of RT + CpG + 1MT; Supplemental Figure 6: Intratumoral DC activation
Table S1 from A Pilot Study of Stereotactic Body Radiation Therapy Combined with Cytoreductive Nephrectomy for Metastatic Renal Cell Carcinoma
Authors: Singh Anurag K. , Winslow Timothy B. , Kermany Mohammad Habiby , Goritz Vincent , Heit Lilia , Miller Austin , Hoffend Nicholas C. , Stein Leighton C. , Kumaraswamy Lalith K. , Warren Graham W. , Bshara Wiam , Odunsi Kunle , Matsuzaki Junko , Abrams Scott I. , Schwaab Thomas , Muhitch Jason B.
Published: April 2023

Supplementary table S1 shows the characteristics of flow and immunohistochemistry patient control cohorts.
Experimental workflow from A Case-Matched Gender Comparison Transcriptomic Screen Identifies eIF4E and eIF5 as Potential Prognostic Markers in Male Breast Cancer
Authors: Humphries Matthew P. , Sundara Rajan Sreekumar , Droop Alastair , Suleman Charlotte A.B. , Carbone Carmine , Nilsson Cecilia , Honarpisheh Hedieh , Cserni Gabor , Dent Jo , Fulford Laura , Jordan Lee B. , Jones J. Louise , Kanthan Rani , Litwiniuk Maria , Di Benedetto Anna , Mottolese Marcella , Provenzano Elena , Shousha Sami , Stephens Mark , Walker Rosemary A. , Kulka Janina , Ellis Ian O. , Jeffery Margaret , Thygesen Helene H. , Cappelletti Vera , Daidone Maria G. , Hedenfalk Ingrid A. , Fjällskog Marie-Louise , Melisi Davide , Stead Lucy F. , Shaaban Abeer M. , Speirs Valerie
Published: April 2023

Details of the male breast cancer samples used at different stages of the experimental workflow
Supplementary Figure Legend from Autologous Heat Shock Protein Peptide Vaccination for Newly Diagnosed Glioblastoma: Impact of Peripheral PD-L1 Expression on Response to Therapy
Authors: Bloch Orin , Lim Michael , Sughrue Michael E. , Komotar Ricardo J. , Abrahams John M. , O'Rourke Donald M. , D'Ambrosio Anthony , Bruce Jeffrey N. , Parsa Andrew T.
Published: April 2023

Figure Legend
Figure S1 from Genome-wide DNA Methylation Analysis Reveals GABBR2 as a Novel Epigenetic Target for EGFR 19 Deletion Lung Adenocarcinoma with Induction Erlotinib Treatment
Authors: Niu Xiaomin , Liu Fatao , Zhou Yi , Zhou Zhen , Zhou Daizhan , Wang Ting , Li Ziming , Ye Xiangyun , Yu Yongfeng , Weng Xiaoling , Zhang Hong , Ye Junyi , Liao Meilin , Liu Yun , Chen Zhiwei , Lu Shun
Published: April 2023

The results proved that the whole-genome DNA methylation sequencing results were accurate and reliable from different aspects.
Full Description of Figure 4 from Found in Translation: Maximizing the Clinical Relevance of Nonclinical Oncology Studies
Authors: Spilker Mary E. , Chen Xiaoying , Visswanathan Ravi , Vage Chandra , Yamazaki Shinji , Li Gang , Lucas Judy , Bradshaw-Pierce Erica L. , Vicini Paolo
Published: April 2023

Full Description with references for the data included in Figure 4.
Supplementary Material S3 from How to Deal with Interval-Censored Data Practically while Assessing the Progression-Free Survival: A Step-by-Step Guide Using SAS and R Software
Authors: Dugué Audrey Emmanuelle , Pulido Marina , Chabaud Sylvie , Belin Lisa , Gal Jocelyn
Published: April 2023

R INPUT AND OUTPUT
Supplementary Tables S1, S2 from Endothelial Nitric Oxide Synthase Traffic Inducer (NOSTRIN) is a Negative Regulator of Disease Aggressiveness in Pancreatic Cancer
Authors: Wang Jian , Yang Shouhui , He Peijun , Schetter Aaron J. , Gaedcke Jochen , Ghadimi B. Michael , Ried Thomas , Yfantis Harris G. , Lee Dong H. , Gaida Matthias M. , Hanna Nader , Alexander H. Richard , Hussain S. Perwez
Published: April 2023

Table S1: Clinical characteristics of long and short survival groups of PDAC patients in test cohort. Table S2: Clinical Characteristics of test and validation cohorts.
Figure S6 from Exome Analysis Reveals Genomic Markers Associated with Better Efficacy of Nivolumab in Lung Cancer Patients
Authors: Richard Corentin , Fumet Jean-David , Chevrier Sandy , Derangère Valentin , Ledys Fanny , Lagrange Aurélie , Favier Laure , Coudert Bruno , Arnould Laurent , Truntzer Caroline , Boidot Romain , Ghiringhelli François
Published: April 2023

Figure S6 Figure S6. (A) Barplot showing the number of patients with at least one mutation in the MAPK, PI3K/AKT, or WNT pathways. (B-C) Kaplan-Meier estimates for progression-free survival (PFS) (B) and overall survival (OS) (C); patients were stratified according to the presence (activated; in blue) or absence (wild-type; in red) of somatic mutations in genes involved in the MAPK/PI3K/AKT pathways. (D) Kaplan-Meier estimates for PFS; patients were stratified according to the presence (activated; in blue) or absence (wild-type; in red) of mutations in genes involved in the WNT pathway. (E) Cumulative barplot showing the number of patients with mutations in the HR, NER, BER, POL, MMR, and NHEJ pathways: somatic mutations are in black, germline mutations are in white. (F) Boxplots representing the tumour mutational burden (TMB) per Mb for patients with altered genes involved in DNA repair pathways (altered; grey) or without altered genes in DNA repair pathways (wild-type; black), respectively. (G-H) Kaplan-Meier estimates for OS; patients were stratified according to the presence of somatic mutations (G) and pooled somatic and constitutional mutations (H) in genes involved in DNA repair pathways: wild-type (in red) and altered (in blue). (I) Kaplan-Meier estimates for OS; patients were stratified according to the DNA repair pathway state: single hit (only one mutation; in red) or double hit (in blue), which is at least two mutations or one mutation and one loss of heterozygosity. Only patients with at least one mutation in the DNA repair pathway were retained in this analysis. *: p < 0.05; **: p < 0.01; ***: p < 0.001; ****: p < 0.0001; ns: not significant.
Supplementary Legends from Vulvar Squamous Cell Carcinoma (VSCC) as Two Diseases: HPV Status Identifies Distinct Mutational Profiles Including Oncogenic Fibroblast Growth Factor Receptor 3
Authors: Weberpals Johanne I. , Lo Bryan , Duciaume Marc M. , Spaans Johanna N. , Clancy Aisling A. , Dimitroulakos Jim , Goss Glenwood D. , Sekhon Harman S.
Published: April 2023

Supplementary Figure and Table legends
Figure S2 from Vulvar Squamous Cell Carcinoma (VSCC) as Two Diseases: HPV Status Identifies Distinct Mutational Profiles Including Oncogenic Fibroblast Growth Factor Receptor 3
Authors: Weberpals Johanne I. , Lo Bryan , Duciaume Marc M. , Spaans Johanna N. , Clancy Aisling A. , Dimitroulakos Jim , Goss Glenwood D. , Sekhon Harman S.
Published: April 2023

Univariate analysis of HPV status and clinical data
Supplemental video S3 from Dasatinib Reversibly Disrupts Endothelial Vascular Integrity by Increasing Non-Muscle Myosin II Contractility in a ROCK-Dependent Manner
Authors: Kreutzman Anna , Colom-Fernández Beatriz , Jiménez Ana Marcos , Ilander Mette , Cuesta-Mateos Carlos , Pérez-García Yaiza , Arévalo Cristina Delgado , Brück Oscar , Hakanen Henna , Saarela Jani , Ortega-Carrión Alvaro , de Rosendo Ana , Juanes-García Alba , Steegmann Juan Luis , Mustjoki Satu , Vicente-Manzanares Miguel , Muñoz-Calleja Cecilia
Published: April 2023

Wound healing in control conditions.
Figure S1 from Vulvar Squamous Cell Carcinoma (VSCC) as Two Diseases: HPV Status Identifies Distinct Mutational Profiles Including Oncogenic Fibroblast Growth Factor Receptor 3
Authors: Weberpals Johanne I. , Lo Bryan , Duciaume Marc M. , Spaans Johanna N. , Clancy Aisling A. , Dimitroulakos Jim , Goss Glenwood D. , Sekhon Harman S.
Published: April 2023

Summary of variants with corresponding allele frequencies including COSMIC reference
Supplementary table 8 from Transcription Factor Myeloid Zinc-Finger 1 Suppresses Human Gastric Carcinogenesis by Interacting with Metallothionein 2A
Authors: Lin Shuye , Wang Xiaoyue , Pan Yuanming , Tian Rongmeng , Lin Bonan , Jiang Guosheng , Chen Keqiang , He Yuqi , Zhang Lulu , Zhai Wanli , Jin Peng , Yang Lang , Li Guoqiang , Wu Yun , Hu Jiang , Gong Wanghua , Chang Zhijie , Sheng Jian-qiu , Lu Youyong , Wang Ji Ming , Huang Jiaqiang
Published: April 2023

Supplementary table
Supplementary table 5 from Transcription Factor Myeloid Zinc-Finger 1 Suppresses Human Gastric Carcinogenesis by Interacting with Metallothionein 2A
Authors: Lin Shuye , Wang Xiaoyue , Pan Yuanming , Tian Rongmeng , Lin Bonan , Jiang Guosheng , Chen Keqiang , He Yuqi , Zhang Lulu , Zhai Wanli , Jin Peng , Yang Lang , Li Guoqiang , Wu Yun , Hu Jiang , Gong Wanghua , Chang Zhijie , Sheng Jian-qiu , Lu Youyong , Wang Ji Ming , Huang Jiaqiang
Published: April 2023

Supplementary table
Supplemental Table 2 from CD103 and Intratumoral Immune Response in Breast Cancer
Authors: Wang Zhi-Qiang , Milne Katy , Derocher Heather , Webb John R. , Nelson Brad H. , Watson Peter H.
Published: April 2023

Supplemental Table 2. Association of CD103 TIL and other markers of intra-tumoral immune response.
Supplementary Data from Targeting an Autocrine Regulatory Loop in Cancer Stem-like Cells Impairs the Progression and Chemotherapy Resistance of Bladder Cancer
Authors: Wang Kai-Jian , Wang Chao , Dai Li-He , Yang Jun , Huang Hai , Ma Xiao-Jing , Zhou Zhe , Yang Ze-Yu , Xu Wei-Dong , Hua Mei-Mian , Lu Xin , Zeng Shu-Xiong , Wang Hui-Qing , Zhang Zhen-Sheng , Cheng Yan-Qiong , Liu Dan , Tian Qin-Qin , Sun Ying-Hao , Xu Chuan-Liang
Published: April 2023

Supplementary Figures and Figure Legends
Supplementary Figures from Homeobox B9 Mediates Resistance to Anti-VEGF Therapy in Colorectal Cancer Patients
Authors: Carbone Carmine , Piro Geny , Simionato Francesca , Ligorio Francesca , Cremolini Chiara , Loupakis Fotios , Alì Greta , Rossini Daniele , Merz Valeria , Santoro Raffaela , Zecchetto Camilla , Zanotto Marco , Di Nicolantonio Federica , Bardelli Alberto , Fontanini Gabriella , Tortora Giampaolo , Melisi Davide
Published: April 2023

Figure S1. HOXB9 expression and activation correlate with aggressiveness of pancreatic cancer cells. Figure S2. HOXB9-silencing in bevacizumab-resistant pancreatic cancer cells reduces mRNA expression levels of pro-inflammatory factors and proliferation. Figure S3. HOXB9 oligonucleotide decoy treatment reduces FGBR pancreatic cancer cell migration. Figure S4. HOXB9-silencing in bevacizumab-resistant pancreatic cancer cells reduces infiltration by CD11b+ proangiogenic myeloid cells. Figure S5. HOXB9 expression and activation correlate with aggressiveness of colorectal cancer cells. Figure S6. CD11b+ proangiogenic myeloid cells infiltration in colorectal tumors. Figure S7. HOXB9-silencing in MDST8 cancer cells reduces mRNA expression levels of pro-inflammatory factors and proliferation. Figure S8. HOXB9 oligonucleotide decoy treatment reduces MDST8 cancer cell migration. Figure S9. HOXB9-silencing in bevacizumab-resistant MDST8 cancer cells reduces infiltration by CD11b+ proangiogenic myeloid cells.
Supplementary Data from Evaluation of Salivary Exosomal Chimeric GOLM1-NAA35 RNA as a Potential Biomarker in Esophageal Carcinoma
Authors: Lin Yusheng , Dong Hongmei , Deng Weilun , Lin Wan , Li Kai , Xiong Xiao , Guo Yi , Zhou Fuyou , Ma Changchun , Chen Yuping , Ren Hongzheng , Yang Haijun , Dai Ningtao , Ma Lang , Meltzer Stephen J. , Yeung Sai-Ching J. , Zhang Hao
Published: April 2023

Supplementary information including supplementary methods, supplementary figures and tables
Raw data 2 from Evaluation of Salivary Exosomal Chimeric GOLM1-NAA35 RNA as a Potential Biomarker in Esophageal Carcinoma
Authors: Lin Yusheng , Dong Hongmei , Deng Weilun , Lin Wan , Li Kai , Xiong Xiao , Guo Yi , Zhou Fuyou , Ma Changchun , Chen Yuping , Ren Hongzheng , Yang Haijun , Dai Ningtao , Ma Lang , Meltzer Stephen J. , Yeung Sai-Ching J. , Zhang Hao
Published: April 2023

Raw data 2-Supplementary Zip including supplementary tables with the qRT-PCR data from the patient cohorts with the amplification profile data (training cohort)
Supplemental Table 4 from A Combination CDK4/6 and IGF1R Inhibitor Strategy for Ewing Sarcoma
Authors: Guenther Lillian M. , Dharia Neekesh V. , Ross Linda , Conway Amy , Robichaud Amanda L. , Catlett Jerrel L. , Wechsler Caroline S. , Frank Elizabeth S. , Goodale Amy , Church Alanna J. , Tseng Yuen-Yi , Guha Rajarshi , McKnight Crystal G. , Janeway Katherine A. , Boehm Jesse S. , Mora Jaume , Davis Mindy I. , Alexe Gabriela , Piccioni Federica , Stegmaier Kimberly
Published: April 2023

Related to Figure 3
Supplemental Table 3 from A Combination CDK4/6 and IGF1R Inhibitor Strategy for Ewing Sarcoma
Authors: Guenther Lillian M. , Dharia Neekesh V. , Ross Linda , Conway Amy , Robichaud Amanda L. , Catlett Jerrel L. , Wechsler Caroline S. , Frank Elizabeth S. , Goodale Amy , Church Alanna J. , Tseng Yuen-Yi , Guha Rajarshi , McKnight Crystal G. , Janeway Katherine A. , Boehm Jesse S. , Mora Jaume , Davis Mindy I. , Alexe Gabriela , Piccioni Federica , Stegmaier Kimberly
Published: April 2023

Related to Figure 2
supplemental information from Lymphotoxin-β Interacts with Methylated EGFR to Mediate Acquired Resistance to Cetuximab in Head and Neck Cancer
Authors: Hsu Dennis Shin-Shian , Hwang Wei-Lun , Yuh Chiou-Hwa , Chu Chen-Hsi , Ho Yang-Hui , Chen Pon-Bo , Lin Han-Syuan , Lin Hua-Kuo , Wu Shih-Pei , Lin Chih-Yi , Hsu Wen-Hao , Lan Hsin-Yi , Wang Hsiao-Jung , Tai Shyh-Kuan , Hung Mien-Chie , Yang Muh-Hwa
Published: April 2023

Includes legends to 5 supplementary figures, supplementary methods, and supplementary references
Supplemental Figures from Decreased Suppression and Increased Phosphorylated STAT3 in Regulatory T Cells are Associated with Benefit from Adjuvant PD-1 Blockade in Resected Metastatic Melanoma
Authors: Woods David M. , Ramakrishnan Rupal , Laino Andressa S. , Berglund Anders , Walton Kelly , Betts Brian C. , Weber Jeffrey S.
Published: April 2023

Supplemental Figures with Legends
Supplementary Figure Legends from A Phase I/Ib Study of Enzalutamide Alone and in Combination with Endocrine Therapies in Women with Advanced Breast Cancer
Authors: Schwartzberg Lee S. , Yardley Denise A. , Elias Anthony D. , Patel Manish , LoRusso Patricia , Burris Howard A. , Gucalp Ayca , Peterson Amy C. , Blaney Martha E. , Steinberg Joyce L. , Gibbons Jacqueline A. , Traina Tiffany A.
Published: April 2023

Supplementary figure legends
Legends to supplementary figures from MET-Oncogenic and JAK2-Inactivating Alterations Are Independent Factors That Affect Regulation of PD-L1 Expression in Lung Cancer
Authors: Saigi Maria , Alburquerque-Bejar Juan J. , Mc Leer-Florin Anne , Pereira Carolina , Pros Eva , Romero Octavio A. , Baixeras Nuria , Esteve-Codina Anna , Nadal Ernest , Brambilla Elisabeth , Sanchez-Cespedes Montse
Published: April 2023

Legends to supplementary figures from 1 to 4
Figure S1 from Capecitabine Efficacy Is Correlated with TYMP and RB1 Expression in PDX Established from Triple-Negative Breast Cancers
Authors: Marangoni Elisabetta , Laurent Cécile , Coussy Florence , El-Botty Rania , Château-Joubert Sophie , Servely Jean-Luc , de Plater Ludmilla , Assayag Franck , Dahmani Ahmed , Montaudon Elodie , Nemati Fariba , Fleury Justine , Vacher Sophie , Gentien David , Rapinat Audrey , Foidart Pierre , Sounni Nor Eddine , Noel Agnès , Vincent-Salomon Anne , Lae Marick , Decaudin Didier , Roman-Roman Sergio , Bièche Ivan , Piccart Martine , Reyal Fabien
Published: April 2023

A) Disease histories of individual patients. Time 0 corresponds to surgery, and each line of chemotherapy is shown. Primary tumors are distinguished from residual disease. B) Circle distribution of vital status, lymphovascular invasion and metastatic status, according to type of tumor (primary or residual), showing that a large proportion of the patients with residual disease died from their cancer, with most of these patients presenting LVI and metastases. By contrast, 50% of the patients for whom PDXs were derived from primary tumors died from their disease, with metastasis noted in a large proportion. However, the proportion of these patients with LVI was similar amongst the patient still alive and those who died. C) Distribution of the the sites at which the first metastasis was detected.
Supplementary Table S5. from Phase II Study of Taselisib (GDC-0032) in Combination with Fulvestrant in Patients with HER2-Negative, Hormone Receptor–Positive Advanced Breast Cancer
Authors: Dickler Maura N. , Saura Cristina , Richards Donald A. , Krop Ian E. , Cervantes Andrés , Bedard Philippe L. , Patel Manish R. , Pusztai Lajos , Oliveira Mafalda , Cardenas Alison K. , Cui Na , Wilson Timothy R. , Stout Thomas J. , Wei Michael C. , Hsu Jerry Y. , Baselga José
Published: April 2023

Clinical activity in patients with and without measurable disease at baseline
Supplementary Table S2. from Phase II Study of Taselisib (GDC-0032) in Combination with Fulvestrant in Patients with HER2-Negative, Hormone Receptor–Positive Advanced Breast Cancer
Authors: Dickler Maura N. , Saura Cristina , Richards Donald A. , Krop Ian E. , Cervantes Andrés , Bedard Philippe L. , Patel Manish R. , Pusztai Lajos , Oliveira Mafalda , Cardenas Alison K. , Cui Na , Wilson Timothy R. , Stout Thomas J. , Wei Michael C. , Hsu Jerry Y. , Baselga José
Published: April 2023

Serious adverse events (SAEs) regardless of attribution in the safety population
Supplementary Figure S2: PCA Map of Small (circle) and Large (triangle) tumors from Genomic Heterogeneity and the Small Renal Mass
Authors: Ueno Daiki , Xie Zuoquan , Boeke Marta , Syed Jamil , Nguyen Kevin A. , McGillivray Patrick , Adeniran Adebowale , Humphrey Peter , Dancik Garrett M. , Kluger Yuval , Liu Zongzhi , Kluger Harriet , Shuch Brian
Published: April 2023

PCA map showed within-sample variation in a) ccA/ccB gene set and b) CCP gene set. Each color of dot represents individual tumor. Small tumors were indicated as round dot. Large tumors were indicated as triangular dot.
Supplementary Methods from Pan-Cancer Molecular Classes Transcending Tumor Lineage Across 32 Cancer Types, Multiple Data Platforms, and over 10,000 Cases
Authors: Chen Fengju , Zhang Yiqun , Gibbons Don L. , Deneen Benjamin , Kwiatkowski David J. , Ittmann Michael , Creighton Chad J.
Published: April 2023

Supplementary Methods, some additional details from main Methods, as well as Methods involving the Supplementary Figures.
Supplementary Figures 1-12 from Pan-Cancer Molecular Classes Transcending Tumor Lineage Across 32 Cancer Types, Multiple Data Platforms, and over 10,000 Cases
Authors: Chen Fengju , Zhang Yiqun , Gibbons Don L. , Deneen Benjamin , Kwiatkowski David J. , Ittmann Michael , Creighton Chad J.
Published: April 2023

Supplementary Figure 1. Schematic of the various analyses performed in this study (with associated main and supplementary figures) and their relation to results provided in the supplementary data files; Supplementary Figure 2. Multiplatform-based molecular classification of cancers representing 32 major types; Supplementary Figure 3, related to Supplementary Figure 2. DNA copy alteration patterns associated with the multiplatform-based molecular subtypes of Supplementary Figure 1; Supplementary Figure 4, related to Supplementary Figure 2. Multiplatform-based molecular classification of cancers using k-means clustering method; Supplementary Figure 5, related to Figure 1. Additional molecular features characterizing the pan-cancer molecular subclasses; Supplementary Figure 7, related to Figure 1. Enriched gene categories associated with pan-cancer molecular classes. Supplementary Figure 6, related to Figure 1. Associations of pan-cancer molecular classes with TCGA sample batches; Supplementary Figure 8. Somatic mutations and associated pathways across pan-cancer molecular classes; Supplementary Figure 9, related to Supplementary Figure 8. Somatic alteration patterns across pan-cancer molecular classes and cancer types; Supplementary Figure 10, related to Supplementary Figure 8. Somatic alteration patterns across pan-cancer molecular classes and cancer types, with considerations for cancer type and mutation rate; Supplementary Figure 11, related to Supplementary Figure 8. Somatic alteration patterns across pan-cancer molecular classes and cancer types, with considerations for tumor purity and sequencing coverage; Supplementary Figure 12, related to Figure 2. Other associations relevant to pan-cancer genomic classes associated with mesenchymal features.
Supplemental Table 8 from Acquired FGFR and FGF Alterations Confer Resistance to Estrogen Receptor (ER) Targeted Therapy in ER+ Metastatic Breast Cancer
Authors: Mao Pingping , Cohen Ofir , Kowalski Kailey J. , Kusiel Justin G. , Buendia-Buendia Jorge E. , Cuoco Michael S. , Exman Pedro , Wander Seth A. , Waks Adrienne G. , Nayar Utthara , Chung Jon , Freeman Samuel , Rozenblatt-Rosen Orit , Miller Vincent A. , Piccioni Federica , Root David E. , Regev Aviv , Winer Eric P. , Lin Nancy U. , Wagle Nikhil
Published: April 2023

Foundation Medicine cohort
Supplemental Table 7 from Acquired FGFR and FGF Alterations Confer Resistance to Estrogen Receptor (ER) Targeted Therapy in ER+ Metastatic Breast Cancer
Authors: Mao Pingping , Cohen Ofir , Kowalski Kailey J. , Kusiel Justin G. , Buendia-Buendia Jorge E. , Cuoco Michael S. , Exman Pedro , Wander Seth A. , Waks Adrienne G. , Nayar Utthara , Chung Jon , Freeman Samuel , Rozenblatt-Rosen Orit , Miller Vincent A. , Piccioni Federica , Root David E. , Regev Aviv , Winer Eric P. , Lin Nancy U. , Wagle Nikhil
Published: April 2023

clinicopathologic info
Supplemental Table 6 from Acquired FGFR and FGF Alterations Confer Resistance to Estrogen Receptor (ER) Targeted Therapy in ER+ Metastatic Breast Cancer
Authors: Mao Pingping , Cohen Ofir , Kowalski Kailey J. , Kusiel Justin G. , Buendia-Buendia Jorge E. , Cuoco Michael S. , Exman Pedro , Wander Seth A. , Waks Adrienne G. , Nayar Utthara , Chung Jon , Freeman Samuel , Rozenblatt-Rosen Orit , Miller Vincent A. , Piccioni Federica , Root David E. , Regev Aviv , Winer Eric P. , Lin Nancy U. , Wagle Nikhil
Published: April 2023

Evolutionary status data
Supplemental Table 5 from Acquired FGFR and FGF Alterations Confer Resistance to Estrogen Receptor (ER) Targeted Therapy in ER+ Metastatic Breast Cancer
Authors: Mao Pingping , Cohen Ofir , Kowalski Kailey J. , Kusiel Justin G. , Buendia-Buendia Jorge E. , Cuoco Michael S. , Exman Pedro , Wander Seth A. , Waks Adrienne G. , Nayar Utthara , Chung Jon , Freeman Samuel , Rozenblatt-Rosen Orit , Miller Vincent A. , Piccioni Federica , Root David E. , Regev Aviv , Winer Eric P. , Lin Nancy U. , Wagle Nikhil
Published: April 2023

Complete exome data
Data from NGALR Is Overexpressed and Regulated by Hypomethylation in Esophageal Squamous Cell Carcinoma
Authors: Cui Lei , Xu Li-Yan , Shen Zhong-Ying , Tao Qian , Gao Shu-Ying , Lv Zhuo , Du Ze-Peng , Fang Wang-Kai , Li En-Min
Published: April 2023

Abstract
Purpose: Neutrophil gelatinase-associated lipocalin receptor (NGALR) mRNA level is reduced in isolated chronic myelogenous leukemia blasts but up-regulated in esophageal squamous cell carcinoma (ESCC). The mechanism of NGALR regulation is unknown. Here, we show the expression pattern of NGALR and examine the aberrant methylation of its gene in ESCC and esophageal carcinoma cell lines.

Experimental Design: The expression pattern of NGALR was analyzed by immunohistochemistry in 59 ESCCs and compared with noncancerous tissues. The DNA methylation status was investigated by methylation-specific PCR and by bisulfite genomic sequencing in esophageal carcinoma cell lines and surgically resected samples. Methylated cell lines were treated with a methylation inhibitor to restore NGALR expression.

Results: The expression of NGALR in ESCC was significantly higher in tumor cell membrane and cytoplasm than in normal esophageal epithelium (P < 0.01). Methylated alleles were detected in three NGALR-nonexpressing cell lines but were not detected in three NGALR-expressing cell lines. Treatment of methylated cell lines with 5-aza-2′-deoxycytidine, a methylation inhibitor, restored NGALR expression. In surgically resected samples, 31 of 77 (40.3%) primary esophageal carcinomas and 46 of 77 (59.7%) paired normal tissues contained methylated NGALR alleles (P < 0.05).

Conclusions: Our results suggest that NGALR hypomethylation contributes to its expression in esophageal carcinomas and that this overexpression may play a role in the pathogenesis of esophageal carcinomas.
Data from Effective CpG Immunotherapy of Breast Carcinoma Prevents but Fails to Eradicate Established Brain Metastasis
Authors: Xiong Zhengming , Gharagozlou Soheila , Vengco Isabelita , Chen Wei , Ohlfest John R.
Published: April 2023

Abstract
Purpose: Breast cancer patients with brain metastasis have a dismal prognosis. We determined the ability of immunostimulatory CpG oligodeoxynucleotides (ODN) to treat or prevent brain metastasis in a mouse model.

Experimental Design: Mice bearing orthotopic breast carcinoma with or without concurrent i.c. tumors were treated by injections of CpG ODN at the primary tumor. Immunologic memory was tested by tumor rechallenge and immune responses were assessed by flow cytometry, delayed-type hypersensitivity, and CTL assays.

Results: Orthotopic tumors regressed in treated mice regardless of whether concurrent i.c. disease was present. In mice bearing only orthotopic tumors, CpG ODN rendered 50% tumor-free and they rejected tumor rechallenge in breast and brain. In mice with concurrent i.c. disease, there was no difference in brain tumor growth compared with saline controls, despite regression of the primary tumor. Flow cytometry revealed that treated mice that died from i.c. disease exhibited a significant increase in brain-infiltrating T and natural killer cells relative to saline controls. CTLs from these mice were able to kill tumor in vitro and extend survival of naive mice bearing less-established brain tumors by adoptive transfer.

Conclusions: The lack of survival benefit in mice with appreciable brain metastasis was not explained by a deficit in lymphocyte trafficking or function because CTLs from these mice killed tumor and inhibited microscopic brain metastasis by adoptive transfer. These results indicate that CpG ODN might be beneficial as a preventative adjuvant to initial therapy preceding brain metastasis or to inhibit progression of microscopic brain metastases.