bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Table 5 from Elimusertib has Antitumor Activity in Preclinical Patient-Derived Pediatric Solid Tumor Models
Authors: Pusch Fabian F. , Dorado García Heathcliff , Xu Robin , Gürgen Dennis , Bei Yi , Brückner Lotte , Röefzaad Claudia , von Stebut Jennifer , Bardinet Victor , Chamorro Gonzalez Rocío , Eggert Angelika , Schulte Johannes H. , Hundsdörfer Patrick , Seifert Georg , Haase Kerstin , Schäfer Beat W. , Wachtel Marco , Kühl Anja A. , Ortiz Michael V. , Wengner Antje M. , Scheer Monika , Henssen Anton G.
Published: April 2024

Supplementary Table 5 lists the quantifications of IHC markers in EWS and OS PDX.
Supplementary Figure 9 from Elimusertib has Antitumor Activity in Preclinical Patient-Derived Pediatric Solid Tumor Models
Authors: Pusch Fabian F. , Dorado García Heathcliff , Xu Robin , Gürgen Dennis , Bei Yi , Brückner Lotte , Röefzaad Claudia , von Stebut Jennifer , Bardinet Victor , Chamorro Gonzalez Rocío , Eggert Angelika , Schulte Johannes H. , Hundsdörfer Patrick , Seifert Georg , Haase Kerstin , Schäfer Beat W. , Wachtel Marco , Kühl Anja A. , Ortiz Michael V. , Wengner Antje M. , Scheer Monika , Henssen Anton G.
Published: April 2024

Supplementary Figure 9 shows the IHC markers tested in OS, ARMS and ERMS PDXs.
Supplementary Figure 6 from Elimusertib has Antitumor Activity in Preclinical Patient-Derived Pediatric Solid Tumor Models
Authors: Pusch Fabian F. , Dorado García Heathcliff , Xu Robin , Gürgen Dennis , Bei Yi , Brückner Lotte , Röefzaad Claudia , von Stebut Jennifer , Bardinet Victor , Chamorro Gonzalez Rocío , Eggert Angelika , Schulte Johannes H. , Hundsdörfer Patrick , Seifert Georg , Haase Kerstin , Schäfer Beat W. , Wachtel Marco , Kühl Anja A. , Ortiz Michael V. , Wengner Antje M. , Scheer Monika , Henssen Anton G.
Published: April 2024

Supplementary Figure 6 displays the body weight curves of all PDX-bearing mice over the course of treatment.
Supplementary Figure 2 from Elimusertib has Antitumor Activity in Preclinical Patient-Derived Pediatric Solid Tumor Models
Authors: Pusch Fabian F. , Dorado García Heathcliff , Xu Robin , Gürgen Dennis , Bei Yi , Brückner Lotte , Röefzaad Claudia , von Stebut Jennifer , Bardinet Victor , Chamorro Gonzalez Rocío , Eggert Angelika , Schulte Johannes H. , Hundsdörfer Patrick , Seifert Georg , Haase Kerstin , Schäfer Beat W. , Wachtel Marco , Kühl Anja A. , Ortiz Michael V. , Wengner Antje M. , Scheer Monika , Henssen Anton G.
Published: April 2024

Supplementary Figure 2 demonstrates an increase of sub-G1 fragments upon elimusertib treatment as measured using FACS.
Supplementary Figure 13 from Elimusertib has Antitumor Activity in Preclinical Patient-Derived Pediatric Solid Tumor Models
Authors: Pusch Fabian F. , Dorado García Heathcliff , Xu Robin , Gürgen Dennis , Bei Yi , Brückner Lotte , Röefzaad Claudia , von Stebut Jennifer , Bardinet Victor , Chamorro Gonzalez Rocío , Eggert Angelika , Schulte Johannes H. , Hundsdörfer Patrick , Seifert Georg , Haase Kerstin , Schäfer Beat W. , Wachtel Marco , Kühl Anja A. , Ortiz Michael V. , Wengner Antje M. , Scheer Monika , Henssen Anton G.
Published: April 2024

Supplementary Figure 13 depicts the correlation of baseline IHC marker expression to treatment response.
Supplementary Figure 10 from Elimusertib has Antitumor Activity in Preclinical Patient-Derived Pediatric Solid Tumor Models
Authors: Pusch Fabian F. , Dorado García Heathcliff , Xu Robin , Gürgen Dennis , Bei Yi , Brückner Lotte , Röefzaad Claudia , von Stebut Jennifer , Bardinet Victor , Chamorro Gonzalez Rocío , Eggert Angelika , Schulte Johannes H. , Hundsdörfer Patrick , Seifert Georg , Haase Kerstin , Schäfer Beat W. , Wachtel Marco , Kühl Anja A. , Ortiz Michael V. , Wengner Antje M. , Scheer Monika , Henssen Anton G.
Published: April 2024

Supplementary Figure 10 shows the IHC markers tested in MNA and NMNA NB PDXs.
Supplementary Figure 1 from Elimusertib has Antitumor Activity in Preclinical Patient-Derived Pediatric Solid Tumor Models
Authors: Pusch Fabian F. , Dorado García Heathcliff , Xu Robin , Gürgen Dennis , Bei Yi , Brückner Lotte , Röefzaad Claudia , von Stebut Jennifer , Bardinet Victor , Chamorro Gonzalez Rocío , Eggert Angelika , Schulte Johannes H. , Hundsdörfer Patrick , Seifert Georg , Haase Kerstin , Schäfer Beat W. , Wachtel Marco , Kühl Anja A. , Ortiz Michael V. , Wengner Antje M. , Scheer Monika , Henssen Anton G.
Published: April 2024

Supplementary Figure 1 shows cell viability assays of various pediatric cancer cell lines.
Supplementary Figure S8 from Combination Therapy with EGFR Tyrosine Kinase Inhibitors and TEAD Inhibitor Increases Tumor Suppression Effects in EGFR Mutation–positive Lung Cancer
Authors: Ogimoto Tatsuya , Ozasa Hiroaki , Tsuji Takahiro , Funazo Tomoko , Yamazoe Masatoshi , Hashimoto Kentaro , Yoshida Hiroshi , Hosoya Kazutaka , Ajimizu Hitomi , Nomizo Takashi , Yoshida Hironori , Hamaji Masatsugu , Menju Toshi , Yoshizawa Akihiko , Date Hiroshi , Hirai Toyohiro
Published: April 2024

Supplementary Figure S8 shows the cell growth assay of KTOR27 cells treated with afatinib with TEAD1 knockdown.
Supplementary Figure S7 from Combination Therapy with EGFR Tyrosine Kinase Inhibitors and TEAD Inhibitor Increases Tumor Suppression Effects in EGFR Mutation–positive Lung Cancer
Authors: Ogimoto Tatsuya , Ozasa Hiroaki , Tsuji Takahiro , Funazo Tomoko , Yamazoe Masatoshi , Hashimoto Kentaro , Yoshida Hiroshi , Hosoya Kazutaka , Ajimizu Hitomi , Nomizo Takashi , Yoshida Hironori , Hamaji Masatsugu , Menju Toshi , Yoshizawa Akihiko , Date Hiroshi , Hirai Toyohiro
Published: April 2024

Supplementary Figure S7 shows the relative expression of TEAD1 and CTGF in KTOR27 cells treated with afatinib with TEAD1 knockdown.
Supplementary Figure S11 from Combination Therapy with EGFR Tyrosine Kinase Inhibitors and TEAD Inhibitor Increases Tumor Suppression Effects in EGFR Mutation–positive Lung Cancer
Authors: Ogimoto Tatsuya , Ozasa Hiroaki , Tsuji Takahiro , Funazo Tomoko , Yamazoe Masatoshi , Hashimoto Kentaro , Yoshida Hiroshi , Hosoya Kazutaka , Ajimizu Hitomi , Nomizo Takashi , Yoshida Hironori , Hamaji Masatsugu , Menju Toshi , Yoshizawa Akihiko , Date Hiroshi , Hirai Toyohiro
Published: April 2024

Supplementary Figure S11 shows immunofluorescent staining of H1975 cells treated with osimertinib.
Supplementary Figure S10 from Combination Therapy with EGFR Tyrosine Kinase Inhibitors and TEAD Inhibitor Increases Tumor Suppression Effects in EGFR Mutation–positive Lung Cancer
Authors: Ogimoto Tatsuya , Ozasa Hiroaki , Tsuji Takahiro , Funazo Tomoko , Yamazoe Masatoshi , Hashimoto Kentaro , Yoshida Hiroshi , Hosoya Kazutaka , Ajimizu Hitomi , Nomizo Takashi , Yoshida Hironori , Hamaji Masatsugu , Menju Toshi , Yoshizawa Akihiko , Date Hiroshi , Hirai Toyohiro
Published: April 2024

Supplementary Figure S10 shows cell viability assays of H1975 cells treated with osimertinib and VT104.
Supplementary Data from ADCT-602, a Novel PBD Dimer–containing Antibody–Drug Conjugate for Treating CD22-positive Hematologic Malignancies
Authors: Zammarchi Francesca , Havenith Karin E. , Sachini Nikoleta , Janghra Narinder , Chivers Simon , Idusogie Esohe , Gaudio Eugenio , Tarantelli Chiara , Bertelli Francois , Santos Kathleen , Tyrer Peter , Corbett Simon , Spriano Filippo , Golino Gaetanina , Cascione Luciano , Bertoni Francesco , Hartley John A. , van Berkel Patrick H.
Published: April 2024

Supplementary Tables
Figure S9 from ADCT-602, a Novel PBD Dimer–containing Antibody–Drug Conjugate for Treating CD22-positive Hematologic Malignancies
Authors: Zammarchi Francesca , Havenith Karin E. , Sachini Nikoleta , Janghra Narinder , Chivers Simon , Idusogie Esohe , Gaudio Eugenio , Tarantelli Chiara , Bertelli Francois , Santos Kathleen , Tyrer Peter , Corbett Simon , Spriano Filippo , Golino Gaetanina , Cascione Luciano , Bertoni Francesco , Hartley John A. , van Berkel Patrick H.
Published: April 2024

Supplementary Fig. S9. In vitro cytotoxicity of B12-C220-SG3249 following pretreatment with chidamide for 7 days (Ramos, TMD8, and SU-DHL-4 cell lines).
Supplementary Figure 9 from Oncogenic Cells of Renal Embryonic Lineage Sensitive to the Small-Molecule Inhibitor QC6352 Display Depletion of KDM4 Levels and Disruption of Ribosome Biogenesis
Authors: Pichavaram Prahalathan , Jablonowski Carolyn M. , Fang Jie , Fleming Andrew M. , Gil Hyea Jin , Boghossian Andrew S. , Rees Matthew G. , Ronan Melissa M. , Roth Jennifer A. , Morton Christopher L. , Zambetti Gerard P. , Davidoff Andrew M. , Yang Jun , Murphy Andrew J.
Published: April 2024

QC6352 treatment (25nM x 72 hours) causes increased nuclear expression of H3K9me3 in WiT49 and HEK293 cells.
Supplementary Figure 6 from Oncogenic Cells of Renal Embryonic Lineage Sensitive to the Small-Molecule Inhibitor QC6352 Display Depletion of KDM4 Levels and Disruption of Ribosome Biogenesis
Authors: Pichavaram Prahalathan , Jablonowski Carolyn M. , Fang Jie , Fleming Andrew M. , Gil Hyea Jin , Boghossian Andrew S. , Rees Matthew G. , Ronan Melissa M. , Roth Jennifer A. , Morton Christopher L. , Zambetti Gerard P. , Davidoff Andrew M. , Yang Jun , Murphy Andrew J.
Published: April 2024

PRISM gene set analysis. (A) PRISM multiplexed cell line profiling RNA expression and compound sensitivity correlation analysis from 931 cancer cell lines was utilized to determine genes with basal RNA expression that correlated with QC6352 sensitivity. Analysis of the top 100 genes with basal expression levels associated with QC6352 sensitivity using the Enrichr database demonstrated that 9 of the top 10 pathways identified on gene set analysis were associated with the ribosome. (B) Tabular view of the top 10 gene sets. (C) Individual ribosomal protein genes comprising the gene sets from A and B that were among the top 100 genes in the PRISM analysis.
Figure S3 from ADCT-602, a Novel PBD Dimer–containing Antibody–Drug Conjugate for Treating CD22-positive Hematologic Malignancies
Authors: Zammarchi Francesca , Havenith Karin E. , Sachini Nikoleta , Janghra Narinder , Chivers Simon , Idusogie Esohe , Gaudio Eugenio , Tarantelli Chiara , Bertelli Francois , Santos Kathleen , Tyrer Peter , Corbett Simon , Spriano Filippo , Golino Gaetanina , Cascione Luciano , Bertoni Francesco , Hartley John A. , van Berkel Patrick H.
Published: April 2024

Supplementary Fig. S3. Confocal microscopy images of Ramos cells treated with B12-C220-SG3249 and stained for nuclei (blue), LAMP-1 (red), and human IgG antibody (green).
Supplementary Figure 16 from Oncogenic Cells of Renal Embryonic Lineage Sensitive to the Small-Molecule Inhibitor QC6352 Display Depletion of KDM4 Levels and Disruption of Ribosome Biogenesis
Authors: Pichavaram Prahalathan , Jablonowski Carolyn M. , Fang Jie , Fleming Andrew M. , Gil Hyea Jin , Boghossian Andrew S. , Rees Matthew G. , Ronan Melissa M. , Roth Jennifer A. , Morton Christopher L. , Zambetti Gerard P. , Davidoff Andrew M. , Yang Jun , Murphy Andrew J.
Published: April 2024

Immunoprecipitation of KDM4A-C in WiT49 and HEK293 cells. Reciprocal immunoprecipitation experiments compared to Figure 6 were performed using antibodies against KDM4A, B, C. Elutions of each protein with subsequent western blot for KDM4 A, B, C demonstrate adequate pulldown of KDM4A, B, or C. Immunoprecipitation for KDM4A, B, or C followed by western blot for ubiquitin supports a direct interaction between KDM4A and KDM4C in (A) WiT49 and (B) HEK293 cells. QC6352 may have increased the association between KDM4A and ubiquitin in WiT49 cells.
Supplementary Figure 15 from Oncogenic Cells of Renal Embryonic Lineage Sensitive to the Small-Molecule Inhibitor QC6352 Display Depletion of KDM4 Levels and Disruption of Ribosome Biogenesis
Authors: Pichavaram Prahalathan , Jablonowski Carolyn M. , Fang Jie , Fleming Andrew M. , Gil Hyea Jin , Boghossian Andrew S. , Rees Matthew G. , Ronan Melissa M. , Roth Jennifer A. , Morton Christopher L. , Zambetti Gerard P. , Davidoff Andrew M. , Yang Jun , Murphy Andrew J.
Published: April 2024

RNA-seq of QC6352-treated WiT49 and HEK293 cells (25nM x 72 hours) did not demonstrate a change in KDM4 A, B, or C transcript levels.
Figure S6 from Glucocorticoid Receptor (GR) Activation Is Associated with Increased cAMP/PKA Signaling in Castration-Resistant Prostate Cancer
Authors: Bennett Lynda , Jaiswal Praveen Kumar , Harkless Ryan V. , Long Tiha M. , Gao Ning , Vandenburg Brianna , Selman Phillip , Durdana Ishrat , Lastra Ricardo R. , Vander Griend Donald , Adelaiye-Ogala Remi , Szmulewitz Russell Z. , Conzen Suzanne D.
Published: April 2024

Overlap of GR DEGs from Arora et al. and the present study
Supplementary Figure 12 from Oncogenic Cells of Renal Embryonic Lineage Sensitive to the Small-Molecule Inhibitor QC6352 Display Depletion of KDM4 Levels and Disruption of Ribosome Biogenesis
Authors: Pichavaram Prahalathan , Jablonowski Carolyn M. , Fang Jie , Fleming Andrew M. , Gil Hyea Jin , Boghossian Andrew S. , Rees Matthew G. , Ronan Melissa M. , Roth Jennifer A. , Morton Christopher L. , Zambetti Gerard P. , Davidoff Andrew M. , Yang Jun , Murphy Andrew J.
Published: April 2024

(A) SiRNA-mediated knockdown of KDM4A reflected the phenotype seen with QC6352 treatment in WiT49 and HEK293 cells by increasing the proportion of cells in the S-phase. Of note, SiRNA-mediated knockdown of KDM4A (but not KDM4B or KDM4C) induced aneuploidy in WiT49 and HEK293 cells (green and yellow peaks).( B) Comet assay (quantitation shown in manuscript Figure 5) demonstrated DNA damage (tails shown with white arrows) in WiT49 and HEK293 cells in response to siKDM4A. Doxorubicin (10nM) is shown as a positive control.
Supplementary Figure 10 from Oncogenic Cells of Renal Embryonic Lineage Sensitive to the Small-Molecule Inhibitor QC6352 Display Depletion of KDM4 Levels and Disruption of Ribosome Biogenesis
Authors: Pichavaram Prahalathan , Jablonowski Carolyn M. , Fang Jie , Fleming Andrew M. , Gil Hyea Jin , Boghossian Andrew S. , Rees Matthew G. , Ronan Melissa M. , Roth Jennifer A. , Morton Christopher L. , Zambetti Gerard P. , Davidoff Andrew M. , Yang Jun , Murphy Andrew J.
Published: April 2024

Transmission electron microscopy demonstrates that 25 nM QC6352 treatment for 72 hours caused a structural change resulting in less compact nucleoli WiT49 and HEK293 cells. More compact nucleoli with dense/compact fibrillar centers are known to be more active. Nuclear membranes indicated with black arrows and nucleoli are labeled.
Figure S3 from Glucocorticoid Receptor (GR) Activation Is Associated with Increased cAMP/PKA Signaling in Castration-Resistant Prostate Cancer
Authors: Bennett Lynda , Jaiswal Praveen Kumar , Harkless Ryan V. , Long Tiha M. , Gao Ning , Vandenburg Brianna , Selman Phillip , Durdana Ishrat , Lastra Ricardo R. , Vander Griend Donald , Adelaiye-Ogala Remi , Szmulewitz Russell Z. , Conzen Suzanne D.
Published: April 2024

Western blot of PKIB in LAPC4 and CWR-22Rv1 cells
Supplementary Data File 3 from Oncogenic Cells of Renal Embryonic Lineage Sensitive to the Small-Molecule Inhibitor QC6352 Display Depletion of KDM4 Levels and Disruption of Ribosome Biogenesis
Authors: Pichavaram Prahalathan , Jablonowski Carolyn M. , Fang Jie , Fleming Andrew M. , Gil Hyea Jin , Boghossian Andrew S. , Rees Matthew G. , Ronan Melissa M. , Roth Jennifer A. , Morton Christopher L. , Zambetti Gerard P. , Davidoff Andrew M. , Yang Jun , Murphy Andrew J.
Published: April 2024

RNA-seq gene set enrichment analysis for siRNA KDM4 A, B, C, A-C, and non-targeting control in HEK293 cells
Figure S1 from Glucocorticoid Receptor (GR) Activation Is Associated with Increased cAMP/PKA Signaling in Castration-Resistant Prostate Cancer
Authors: Bennett Lynda , Jaiswal Praveen Kumar , Harkless Ryan V. , Long Tiha M. , Gao Ning , Vandenburg Brianna , Selman Phillip , Durdana Ishrat , Lastra Ricardo R. , Vander Griend Donald , Adelaiye-Ogala Remi , Szmulewitz Russell Z. , Conzen Suzanne D.
Published: April 2024

GR-mediated cAMP signaling pathway-related genes with co-treatment of SGRMs
Supplementary Table S4 from Cereblon-based Bifunctional Degrader of SOS1, BTX-6654, Targets Multiple KRAS Mutations and Inhibits Tumor Growth
Authors: Begovich Kyle , Schoolmeesters Angela , Rajapakse Navin , Martinez-Terroba Elena , Kumar Maneesh , Shakya Arvind , Lai Chon , Greene Steven , Whitefield Brandon , Okano Akinori , Mali Venkat , Huang Shenlin , Chourasia Aparajita H. , Fung Leah
Published: April 2024

Supplementary Table S4 displays the IC50 values for BTX-6654 and BTX-7312 from all 3D proliferation assays examined in this study
Supplementary Methods from Cereblon-based Bifunctional Degrader of SOS1, BTX-6654, Targets Multiple KRAS Mutations and Inhibits Tumor Growth
Authors: Begovich Kyle , Schoolmeesters Angela , Rajapakse Navin , Martinez-Terroba Elena , Kumar Maneesh , Shakya Arvind , Lai Chon , Greene Steven , Whitefield Brandon , Okano Akinori , Mali Venkat , Huang Shenlin , Chourasia Aparajita H. , Fung Leah
Published: April 2024

Supplementary Methods describes the synthesis of compounds used in this study
Supplementary Table S5 from Neutrophil Elastase Remodels Mammary Tumors to Facilitate Lung Metastasis
Authors: Lulla Amriti R. , Akli Said , Karakas Cansu , Caruso Joseph A. , Warma Lucas D. , Fowlkes Natalie W. , Rao Xiayu , Wang Jing , Hunt Kelly K. , Watowich Stephanie S. , Keyomarsi Khandan
Published: April 2024

Sequences for forward (FWD) and reverse (REV) primers used in qRT-PCR assays
Supplementary Table S4 from Neutrophil Elastase Remodels Mammary Tumors to Facilitate Lung Metastasis
Authors: Lulla Amriti R. , Akli Said , Karakas Cansu , Caruso Joseph A. , Warma Lucas D. , Fowlkes Natalie W. , Rao Xiayu , Wang Jing , Hunt Kelly K. , Watowich Stephanie S. , Keyomarsi Khandan
Published: April 2024

List of antibodies used in all the flow cytometric analysis
Supplementary Table S1 from Neutrophil Elastase Remodels Mammary Tumors to Facilitate Lung Metastasis
Authors: Lulla Amriti R. , Akli Said , Karakas Cansu , Caruso Joseph A. , Warma Lucas D. , Fowlkes Natalie W. , Rao Xiayu , Wang Jing , Hunt Kelly K. , Watowich Stephanie S. , Keyomarsi Khandan
Published: April 2024

Comparison of Clinical and Pathological Characteristics of Breast Cancer Patients as a Function of Tumor Associated Neutrophils (TAN) status
Supplementary Data 1 from Neutrophil Elastase Remodels Mammary Tumors to Facilitate Lung Metastasis
Authors: Lulla Amriti R. , Akli Said , Karakas Cansu , Caruso Joseph A. , Warma Lucas D. , Fowlkes Natalie W. , Rao Xiayu , Wang Jing , Hunt Kelly K. , Watowich Stephanie S. , Keyomarsi Khandan
Published: April 2024

The file contains NMR spectrometry, LC-MS and HPLC analyses was performed to confirm the purity of and the metabolites profile of AZD9668
Figure S9 from Neutrophil Elastase Remodels Mammary Tumors to Facilitate Lung Metastasis
Authors: Lulla Amriti R. , Akli Said , Karakas Cansu , Caruso Joseph A. , Warma Lucas D. , Fowlkes Natalie W. , Rao Xiayu , Wang Jing , Hunt Kelly K. , Watowich Stephanie S. , Keyomarsi Khandan
Published: April 2024

Supplementary Figure S9: Human TNBC cell lines MDA-MB-231 and MDA-MB-468 were injected in the T4 mammary fat pad of 12 week old nude mice. When tumors reached size of 100mm3, mice were randomized in Vehicle and AZD9668 100mg/kg groups. Mice were then treated daily B.I.D until the endpoint of Vehicle tumors reaching 2000mm3. (A, B) Tumor growth curves of mice treated with either Vehicle or AZD9668 100mg/kg in the MDA-MB-231 and MDA- MB-468 models respectively. Endpoint tumors harvested were subject to BrdU staining. (C, D) Representative images BrdU staining and (E, F) their corresponding quantitation in the MDA- MB-231 and MDA-MB-468 models respectively. (G) Spontaneous tumors isolated from PyMT NE+/+ were implanted in FVB NE+/+ mice. When tumors reached a measurable size of 30- 50mm3, mice were randomized into Vehicle and AZD9668 100mg/kg group and treated B.I.D until 400-500mm3. Tumor growth curves, as a function of time are shown.
Figure S6 from Neutrophil Elastase Remodels Mammary Tumors to Facilitate Lung Metastasis
Authors: Lulla Amriti R. , Akli Said , Karakas Cansu , Caruso Joseph A. , Warma Lucas D. , Fowlkes Natalie W. , Rao Xiayu , Wang Jing , Hunt Kelly K. , Watowich Stephanie S. , Keyomarsi Khandan
Published: April 2024

Supplementary Figure S6: (A) Fraction of immune vs. non-immune (primarily epithelial) cells from PyMT tumors used for RNA-seq. A small fraction of tumor tissues was isolated for this QC analysis, including CD45 fraction as presented in this figure. (B) Of the top 32 genes shown in Figure 3B, NE-specific genes were identified by performing qRT-PCR analysis in 10-week old PyMT NE+/+ (N=5) and PyMT NE-/- (N=4) pre-metastatic, malignant mammary tissues. 12 genes shown here were significantly different as a function of NE status. (C) Quantification of the total percentage of fibroblasts (CD140+ve cells) isolated from each genotype is indicated.
Supplemental Table S8 from The Methyltransferases METTL7A and METTL7B Confer Resistance to Thiol-Based Histone Deacetylase Inhibitors
Authors: Robey Robert W. , Fitzsimmons Christina M. , Guiblet Wilfried M. , Frye William J.E. , González Dalmasy José M. , Wang Li , Russell Drake A. , Huff Lyn M. , Perciaccante Andrew J. , Ali-Rahmani Fatima , Lipsey Crystal C. , Wade Heidi M. , Mitchell Allison V. , Maligireddy Siddhardha S. , Terrero David , Butcher Donna , Edmondson Elijah F. , Jenkins Lisa M. , Nikitina Tatiana , Zhurkin Victor B. , Tiwari Amit K. , Piscopio Anthony D. , Totah Rheem A. , Bates Susan E. , Arda H. Efsun , Gottesman Michael M. , Batista Pedro J.
Published: April 2024

Supplemental Table S8 contains information about METTL7A and METTL7B in T-cell lymphoma tissue microarray samples
Supplemental Table S5 from The Methyltransferases METTL7A and METTL7B Confer Resistance to Thiol-Based Histone Deacetylase Inhibitors
Authors: Robey Robert W. , Fitzsimmons Christina M. , Guiblet Wilfried M. , Frye William J.E. , González Dalmasy José M. , Wang Li , Russell Drake A. , Huff Lyn M. , Perciaccante Andrew J. , Ali-Rahmani Fatima , Lipsey Crystal C. , Wade Heidi M. , Mitchell Allison V. , Maligireddy Siddhardha S. , Terrero David , Butcher Donna , Edmondson Elijah F. , Jenkins Lisa M. , Nikitina Tatiana , Zhurkin Victor B. , Tiwari Amit K. , Piscopio Anthony D. , Totah Rheem A. , Bates Susan E. , Arda H. Efsun , Gottesman Michael M. , Batista Pedro J.
Published: April 2024

Supplemental Table S5 contains information about the cross-resistance profile of the MCF7, MCF7 DpVp300, and METTL7A knockout clones
Supplemental Table S3 from The Methyltransferases METTL7A and METTL7B Confer Resistance to Thiol-Based Histone Deacetylase Inhibitors
Authors: Robey Robert W. , Fitzsimmons Christina M. , Guiblet Wilfried M. , Frye William J.E. , González Dalmasy José M. , Wang Li , Russell Drake A. , Huff Lyn M. , Perciaccante Andrew J. , Ali-Rahmani Fatima , Lipsey Crystal C. , Wade Heidi M. , Mitchell Allison V. , Maligireddy Siddhardha S. , Terrero David , Butcher Donna , Edmondson Elijah F. , Jenkins Lisa M. , Nikitina Tatiana , Zhurkin Victor B. , Tiwari Amit K. , Piscopio Anthony D. , Totah Rheem A. , Bates Susan E. , Arda H. Efsun , Gottesman Michael M. , Batista Pedro J.
Published: April 2024

Supplemental Table S3 contains information from high-throughput sequencing
Table S1 from Development of a Novel DNA Mono-alkylator Platform for Antibody–Drug Conjugates
Authors: Thomas Joshua D. , Yurkovetskiy Aleksandr V. , Yin Mao , Bodyak Natalya D. , Tang Shuyi , Protopopova Marina , Kelleher Eugene , Jones Brian , Yang Liping , Custar Daniel , Catcott Kalli C. , Demady Damon R. , Collins Scott D. , Xu Ling , Bu Charlie , Qin LiuLiang , Ter-Ovanesyan Elena , Damelin Marc , Toader Dorin , Lowinger Timothy B.
Published: April 2024

Extinction coefficient used to determine DAR for ADCs
Supplemental Table S1 from The Methyltransferases METTL7A and METTL7B Confer Resistance to Thiol-Based Histone Deacetylase Inhibitors
Authors: Robey Robert W. , Fitzsimmons Christina M. , Guiblet Wilfried M. , Frye William J.E. , González Dalmasy José M. , Wang Li , Russell Drake A. , Huff Lyn M. , Perciaccante Andrew J. , Ali-Rahmani Fatima , Lipsey Crystal C. , Wade Heidi M. , Mitchell Allison V. , Maligireddy Siddhardha S. , Terrero David , Butcher Donna , Edmondson Elijah F. , Jenkins Lisa M. , Nikitina Tatiana , Zhurkin Victor B. , Tiwari Amit K. , Piscopio Anthony D. , Totah Rheem A. , Bates Susan E. , Arda H. Efsun , Gottesman Michael M. , Batista Pedro J.
Published: April 2024

Supplemental Table S1 contains information about the chemical structures of the HDACi
Figure S4 from The Methyltransferases METTL7A and METTL7B Confer Resistance to Thiol-Based Histone Deacetylase Inhibitors
Authors: Robey Robert W. , Fitzsimmons Christina M. , Guiblet Wilfried M. , Frye William J.E. , González Dalmasy José M. , Wang Li , Russell Drake A. , Huff Lyn M. , Perciaccante Andrew J. , Ali-Rahmani Fatima , Lipsey Crystal C. , Wade Heidi M. , Mitchell Allison V. , Maligireddy Siddhardha S. , Terrero David , Butcher Donna , Edmondson Elijah F. , Jenkins Lisa M. , Nikitina Tatiana , Zhurkin Victor B. , Tiwari Amit K. , Piscopio Anthony D. , Totah Rheem A. , Bates Susan E. , Arda H. Efsun , Gottesman Michael M. , Batista Pedro J.
Published: April 2024

Figure S4 contains cytotoxicity assay and immunoblot data from the MCF7 and MCF7 DpVp300 cell lines showing that expression of METTL7A confers resistance.
Supplementary Figure 1 from RETRACTED: Minocycline Targets the NF-κB Nexus through Suppression of TGF-β1-TAK1-IκB Signaling in Ovarian Cancer
Authors: Ataie-Kachoie Parvin , Badar Samina , Morris David L. , Pourgholami Mohammad H.
Published: April 2024

PDF file - 1416K, Minocycline ablated TAK-1-induced activation of NF-кB.
Supplementary Table 1 from Identification of Colorectal Cancer Cell Stemness from Single-Cell RNA Sequencing
Authors: Lin Kangyu , Chowdhury Saikat , Zeineddine Mohammad A. , Zeineddine Fadl A. , Hornstein Nicholas J. , Villarreal Oscar E. , Maru Dipen M. , Haymaker Cara L. , Vauthey Jean-Nicolas , Chang George J. , Bogatenkova Elena , Menter David , Kopetz Scott , Shen John Paul
Published: April 2024

The clinical information of the patients in this study.
Supplementary Tables 1-3 from Peritoneal Microenvironment Promotes Appendiceal Adenocarcinoma Growth: A Multi-omics Approach Using Patient-Derived Xenografts
Authors: Pattalachinti Vinay K. , Ito Ichiaki , Chowdhury Saikat , Yousef Abdelrahman , Gu Yue , Gunes Betul Beyza , Salle Emma R. , Taggart Melissa W. , Fournier Keith , Fowlkes Natalie W. , Shen John Paul
Published: April 2024

Table S1: Tumor and PDX information (left) and the number of samples collected for each of the analyses (right). “Initial Implant Site” indicates where passages were run prior to the current experiments with the tumor. “Implant Site” indicates where the tumors were implanted to generate the data for this manuscript.
Table S2: Table of antibodies used for immunohistochemistry (IHC). M, mouse; R, rabbit; Hu, human; Mk, monkey; NHP, non-human primates.
Table S3: Differentially expressed genes from comparing the peritoneal PDX vs. flank PDX tumor transcriptomes. LFC>0 indicates relative upregulation in peritoneal PDXs.
Figure S6 from Mass Spectrometry–Based Proteomics Identifies Serpin B9 as a Key Protein in Promoting Bone Metastases in Lung Cancer
Authors: Huang Yufeng , Gong Ming , Chen Hongmin , Deng Chuangzhong , Zhu Xiaojun , Lin Jiaming , Huang Anfei , Xu Yanyang , Tai Yi , Song Guohui , Xu Huaiyuan , Hu Jinxin , Feng Huixiong , Tang Qinglian , Lu Jinchang , Wang Jin
Published: April 2024

Representative flow cytometry dot plots and quantitative analyses of immune subpopulations across the two groups in BM by CA injection.
(A)TAMs(CD45+CD11b+F4/80+Ly6C-Ly6G-), (B)MDSCs(CD45+CD11b+Gr1+CD3-) , (C)Tregs(CD4+CD25+FOXP3+), (D)Tem cells(CD8+CD44+CD62L-), (E)CD8+GrB+T cells, (F)CD8+IFN-γ+T cells, (G)CD8+TNF-α+T cells, (H)CD8+KLRG-1+T cells, (I)CD8+CD57+T cells, (J)CD8+ PD-1+T cells, (K)CD8+LAG-3+T cells and (L)CD8+TIGIT+T cells.
Figure S5 from Mass Spectrometry–Based Proteomics Identifies Serpin B9 as a Key Protein in Promoting Bone Metastases in Lung Cancer
Authors: Huang Yufeng , Gong Ming , Chen Hongmin , Deng Chuangzhong , Zhu Xiaojun , Lin Jiaming , Huang Anfei , Xu Yanyang , Tai Yi , Song Guohui , Xu Huaiyuan , Hu Jinxin , Feng Huixiong , Tang Qinglian , Lu Jinchang , Wang Jin
Published: April 2024

Gating strategy flowchart.
A: Gating strategy for immunosuppressive cells,including TAMs,MDSCs and Tregs.
B: Gating strategy for anti-tumor effector T cells,including effector memory CD8+T cells (Tem), GrB+CD8+T cells, TNF-α+CD8+ T cells and IFN-γ+CD8+ T cells.
C: Gating strategy for CTL phenotypes of senescent markers,including CD57+CD8+T cells,KLRG-1+CD8+T cells.
D: Gating strategy for CTL phenotypes of exhausted markers,including PD-1+ CD8+T cells, LAG-3+CD8+T cells and TIGIT+CD8+ T cells.
Figure S2 from Mass Spectrometry–Based Proteomics Identifies Serpin B9 as a Key Protein in Promoting Bone Metastases in Lung Cancer
Authors: Huang Yufeng , Gong Ming , Chen Hongmin , Deng Chuangzhong , Zhu Xiaojun , Lin Jiaming , Huang Anfei , Xu Yanyang , Tai Yi , Song Guohui , Xu Huaiyuan , Hu Jinxin , Feng Huixiong , Tang Qinglian , Lu Jinchang , Wang Jin
Published: April 2024

SB9 expression is associated with lung cancer bone metastasis
A. Kaplan-Meier curves with a survival period of 28 to 3650 days for overall survival analysis of the LUSC(Lung squamous cell carcinoma) patients from TCGA(The Cancer Genome Atlas Program). The red line represents the high expression group, and the blue line denotes the low expression group. Only these genes with a P value < 0.05 were considered as prognostic-related genes.
B. Functional enrichment analysis of differential proteins. Top ten biological functions closely related to differential proteins in GO analysis.
C-D. Secondary mass spectrogram of two specific peptides of SB9 protein.
E. The standard curve of ELISA assay to measure the SB9 protein in condition-media of LLC1-BM3 and LLC1-Pa.
Figure S6 from miR-217 Regulates Normal and Tumor Cell Fate Following Induction of Endoplasmic Reticulum Stress
Authors: Dey Neekkan , Koumenis Costas , Ruggero Davide , Fuchs Serge Y. , Diehl J. Alan
Published: April 2024

S6. Relative band intensities compared to actin controls for Fig 6d.
Table S1 from NRAS Mutant Dictates AHCYL1-Governed ER Calcium Homeostasis for Melanoma Tumor Growth
Authors: Cai Chufan , Tu Jiayi , Najarro Jeronimo , Zhang Rukang , Fan Hao , Zhang Freya Q. , Li Jiacheng , Xie Zhicheng , Su Rui , Dong Lei , Arellano Nicole , Ciboddo Michele , Elf Shannon E. , Gao Xue , Chen Jing , Wu Rong
Published: April 2024

Supplemental Table 1. Transcription factor scan. Transcription factors candidates for AHCYL1 transcription were generated based on reported binding response elements that can match AHCYL1 promoter region sequence.
Figure S11 from NRAS Mutant Dictates AHCYL1-Governed ER Calcium Homeostasis for Melanoma Tumor Growth
Authors: Cai Chufan , Tu Jiayi , Najarro Jeronimo , Zhang Rukang , Fan Hao , Zhang Freya Q. , Li Jiacheng , Xie Zhicheng , Su Rui , Dong Lei , Arellano Nicole , Ciboddo Michele , Elf Shannon E. , Gao Xue , Chen Jing , Wu Rong
Published: April 2024

Supplementary Figure 11. There is positive correlation between ATF2 and AHCYL1 mRNA levels in human cutaneous melanoma patients by TCGA analysis.
Figure S10 from NRAS Mutant Dictates AHCYL1-Governed ER Calcium Homeostasis for Melanoma Tumor Growth
Authors: Cai Chufan , Tu Jiayi , Najarro Jeronimo , Zhang Rukang , Fan Hao , Zhang Freya Q. , Li Jiacheng , Xie Zhicheng , Su Rui , Dong Lei , Arellano Nicole , Ciboddo Michele , Elf Shannon E. , Gao Xue , Chen Jing , Wu Rong
Published: April 2024

Supplementary Figure 10. CREB doesn’t positively regulate AHCYL1 transcription.
Supplementary Figure 1 from Semi-Supervised, Attention-Based Deep Learning for Predicting TMPRSS2:ERG Fusion Status in Prostate Cancer Using Whole Slide Images
Authors: Omar Mohamed , Xu Zhuoran , Rand Sophie B. , Alexanderani Mohammad K. , Salles Daniela C. , Valencia Itzel , Schaeffer Edward M. , Robinson Brian D. , Lotan Tamara L. , Loda Massimo , Marchionni Luigi
Published: April 2024

Supplementary Figure 1. Progression-free survival in the TCGA cohort using the cellular composition of the whole slide images. Kaplan-Meier curves showing the association between the fraction of each nuclear type and progression-free survival. The fraction of each cell type was calculated by dividing the absolute number of that cell type over the number of all cells in the whole slide. The stromal to neoplastic ratio was calculated by dividing the number of stromal cells by that of neoplastic cells in the whole slide. These fractions were then then binarized into high versus low using maximally selected log-rank statistics.
Data from Identification of Colorectal Cancer Cell Stemness from Single-Cell RNA Sequencing
Authors: Lin Kangyu , Chowdhury Saikat , Zeineddine Mohammad A. , Zeineddine Fadl A. , Hornstein Nicholas J. , Villarreal Oscar E. , Maru Dipen M. , Haymaker Cara L. , Vauthey Jean-Nicolas , Chang George J. , Bogatenkova Elena , Menter David , Kopetz Scott , Shen John Paul
Published: April 2024

Abstract
Cancer stem cells (CSC) play a critical role in metastasis, relapse, and therapy resistance in colorectal cancer. While characterization of the normal lineage of cell development in the intestine has led to the identification of many genes involved in the induction and maintenance of pluripotency, recent studies suggest significant heterogeneity in CSC populations. Moreover, while many canonical colorectal cancer CSC marker genes have been identified, the ability to use these classical markers to annotate stemness at the single-cell level is limited. In this study, we performed single-cell RNA sequencing on a cohort of 6 primary colon, 9 liver metastatic tumors, and 11 normal (nontumor) controls to identify colorectal CSCs at the single-cell level. Finding poor alignment of the 11 genes most used to identify colorectal CSC, we instead extracted a single-cell stemness signature (SCS_sig) that robustly identified “gold-standard” colorectal CSCs that expressed all marker genes. Using this SCS_sig to quantify stemness, we found that while normal epithelial cells show a bimodal distribution, indicating distinct stem and differentiated states, in tumor epithelial cells stemness is a continuum, suggesting greater plasticity in these cells. The SCS_sig score was quite variable between different tumors, reflective of the known transcriptomic heterogeneity of CRC. Notably, patients with higher SCS_sig scores had significantly shorter disease-free survival time after curative intent surgical resection, suggesting stemness is associated with relapse.
Implications:
This study reveals significant heterogeneity of expression of genes commonly used to identify colorectal CSCs, and identifies a novel stemness signature to identify these cells from scRNA-seq data.
Data from Peritoneal Microenvironment Promotes Appendiceal Adenocarcinoma Growth: A Multi-omics Approach Using Patient-Derived Xenografts
Authors: Pattalachinti Vinay K. , Ito Ichiaki , Chowdhury Saikat , Yousef Abdelrahman , Gu Yue , Gunes Betul Beyza , Salle Emma R. , Taggart Melissa W. , Fournier Keith , Fowlkes Natalie W. , Shen John Paul
Published: April 2024

Abstract
Appendiceal adenocarcinoma (AA) is unique from other gastrointestinal malignancies in that it almost exclusively metastasizes to the peritoneal cavity. However, few studies have investigated the molecular interaction of the peritoneal microenvironment and AA. Here, we use a multi-omics approach with orthotopic and flank-implanted patient-derived xenografts (PDX) to study the effect of the peritoneal microenvironment on AA. AA tumors implanted in the peritoneal microenvironment tended to grow faster and displayed greater nuclear expression of Ki-67 relative to the same tumors implanted in the flank. Comparing the tumor-specific transcriptome (excluding stromal transcription), the peritoneal microenvironment relatively upregulated genes related to proliferation, including MKI67 and EXO1. Peritoneal tumors were also enriched for proliferative gene sets, including E2F and Myc Targets. Proteomic studies found a 2.5-fold increased ratio of active-to-inactive phosphoforms of the YAP oncoprotein in peritoneal tumors, indicating downregulation of Hippo signaling.
Implications:
The peritoneal microenvironment promotes growth of appendiceal tumors and expression of proliferative pathways in PDXs.
Data from Mass Spectrometry–Based Proteomics Identifies Serpin B9 as a Key Protein in Promoting Bone Metastases in Lung Cancer
Authors: Huang Yufeng , Gong Ming , Chen Hongmin , Deng Chuangzhong , Zhu Xiaojun , Lin Jiaming , Huang Anfei , Xu Yanyang , Tai Yi , Song Guohui , Xu Huaiyuan , Hu Jinxin , Feng Huixiong , Tang Qinglian , Lu Jinchang , Wang Jin
Published: April 2024

Abstract
Bone metastasis (BM) is one of the most common complications of advanced cancer. Immunotherapy for bone metastasis of lung cancer (LCBM) is not so promising and the immune mechanisms are still unknown. Here, we utilized a model of BM by injecting cancer cells through caudal artery (CA) to screen out a highly bone metastatic derivative (LLC1-BM3) from a murine lung cancer cell line LLC1. Mass spectrometry–based proteomics was performed in LLC1-parental and LLC1-BM3 cells. Combining with prognostic survival information from patients with lung cancer, we identified serpin B9 (SB9) as a key factor in BM. Molecular characterization showed that SB9 overexpression was associated with poor prognosis and high bone metastatic burden in lung cancer. Moreover, SB9 could increase the ability of lung cancer cells to metastasize to the bone. The mechanistic studies revealed that tumor-derived SB9 promoted BM through an immune cell–dependent way by inactivating granzyme B, manifesting with the decreased infiltration of cytotoxic T cells and increased expression level of exhausted markers. A specific SB9-targeting inhibitor [1,3-benzoxazole-6-carboxylic acid (BTCA)] significantly suppressed LCBM in the CA mouse model. This study reveals that SB9 may serve as a therapeutic target and potential prognostic marker for patients with LCBM.
Implications:
SB9 as a therapeutic target for LCBM.
Supplemental Figure 1 from Identification of a Biomarker Panel from Genome-Wide Methylation to Detect Early HPV-Associated Oropharyngeal Cancer
Authors: Dickey Brittney L. , Putney Ryan M. , Schell Michael J. , Berglund Anders E. , Amelio Antonio L. , Caudell Jimmy J. , Chung Christine H. , Giuliano Anna R.
Published: April 2024

Supplemental Figure 1 shows the number of non-zero coefficients per variable that was examined in the variable selection processing for the final biomarker panel.
Supplementary Table S2 from The Effects of Black Raspberry as a Whole Food–Based Approach on Biomarkers of Oxidative Stress in Buccal Cells and Urine of Smokers
Authors: Chen Kun-Ming , Sun Yuan-Wan , Krebs Nicolle M. , Reinhart Lisa , Sun Dongxiao , Liao Jiangang , Cook Rachel , Bond Paige Elizabeth , Mallery Susan R. , El-Bayoumy Karam
Published: April 2024

Supplementary Table S2: In this study 21 smokers were included (males = 8, females = 13) and the mean age + SD was 44.3 + 11.2. The number and type of cigarettes are shown in this table.
Supplementary Table S1 from The Effects of Black Raspberry as a Whole Food–Based Approach on Biomarkers of Oxidative Stress in Buccal Cells and Urine of Smokers
Authors: Chen Kun-Ming , Sun Yuan-Wan , Krebs Nicolle M. , Reinhart Lisa , Sun Dongxiao , Liao Jiangang , Cook Rachel , Bond Paige Elizabeth , Mallery Susan R. , El-Bayoumy Karam
Published: April 2024

Supplementary Table S1: The Certificate of Analysis of the lozenge (1.3402 g) provides levels of select vitamins, inorganic elements, quercetin dihydrate, total anthocyanosides, free anthocyanidin, various chlorogenic acids and ellagic acid.
Supplementary Figure S1 from The Effects of Black Raspberry as a Whole Food–Based Approach on Biomarkers of Oxidative Stress in Buccal Cells and Urine of Smokers
Authors: Chen Kun-Ming , Sun Yuan-Wan , Krebs Nicolle M. , Reinhart Lisa , Sun Dongxiao , Liao Jiangang , Cook Rachel , Bond Paige Elizabeth , Mallery Susan R. , El-Bayoumy Karam
Published: April 2024

Supplementary Figure S1: The consumption of BRB had no effect on the urinary cotinine levels throughout the duration of the study.
Supplemental Table 2 from Differences in Serum miRNA Profiles by Race, Ethnicity, and Socioeconomic Status: Implications for Developing an Equitable Ovarian Cancer Screening Test
Authors: Alimena Stephanie , Stephenson Briana Joy K. , Webber James W. , Wollborn Laura , Sussman Chad B. , Packard Daniel George , Williams Marta , Comrie Cameron Elizabeth , Wang Joyce Y. , Markert Tahireh , Spiegel Julia , Rodriguez Carmen B. , Lightfoot Maya , Graye Amia , O'Connor Sean , Elias Kevin M.
Published: April 2024

Supplemental Table 2: Correlation between all tested socioeconomic indices and miRNA values for eight miRNA previously associated with ovarian cancer risk, among Massachusetts residents. We confined this analysis to Massachusetts residents given there were a minority of non-Massachusetts residents in the cohort, and zip code was needed to perform the correlations with various socioeconomic indices.
Data from Identification of a Biomarker Panel from Genome-Wide Methylation to Detect Early HPV-Associated Oropharyngeal Cancer
Authors: Dickey Brittney L. , Putney Ryan M. , Schell Michael J. , Berglund Anders E. , Amelio Antonio L. , Caudell Jimmy J. , Chung Christine H. , Giuliano Anna R.
Published: April 2024

Abstract
As oropharyngeal cancer (OPC) associated with human papillomavirus (HPV) increases in men, the need for a screening test to diagnose OPC early is crucial. This study agnostically identified differentially methylated CpG sites to identify additional biomarkers to improve screening for early OPC.

DNA was extracted from oral gargles of 89 early cases and 108 frequency matched healthy controls, and processed for genome-wide methylation using the Illumina Infinium MethylationEPIC BeadChip. Selected sites were combined with our prior methylation data in the EPB41L3 gene (CpG sites 438, 427, and 425) and oral HPV16 and HPV18 status were considered as binary variables (positive/negative). Lasso regression identified CpG sites strongly associated with early OPC. ROC curves with AUC were generated. The panel was validated utilizing bootstrap resampling.

Machine learning analyses identified 14 markers that are significantly associated with early OPC, including one EPB41L3 CpG site (438) and oral HPV16 status. A final model was trained on all available samples using the discovered panel and was able to predict early OPC compared with controls with an AUC of 0.970 on the training set. In the bootstrap validation sets, the average AUC was 0.935, indicating adequate internal validity.

Our data suggest that this panel can detect OPC early, however external validation of this panel is needed. Further refinement of a panel of biomarkers to diagnose OPC earlier is urgently needed to prevent complex treatment of OPC and associated comorbidities, while reducing risk of recurrence.
Prevention Relevance:
This study identified biomarkers using genome-wide methylation to create a panel capable of discerning early oropharyngeal cancer (OPC) from those without OPC. Such a biomarker panel would be an effective tool to detect OPC early and prevent complications of treatment associated with later diagnosis.
Data from Differences in Serum miRNA Profiles by Race, Ethnicity, and Socioeconomic Status: Implications for Developing an Equitable Ovarian Cancer Screening Test
Authors: Alimena Stephanie , Stephenson Briana Joy K. , Webber James W. , Wollborn Laura , Sussman Chad B. , Packard Daniel George , Williams Marta , Comrie Cameron Elizabeth , Wang Joyce Y. , Markert Tahireh , Spiegel Julia , Rodriguez Carmen B. , Lightfoot Maya , Graye Amia , O'Connor Sean , Elias Kevin M.
Published: April 2024

Abstract
Serum miRNAs are promising biomarkers for several clinical conditions, including ovarian cancer. To inform equitable implementation of these tests, we investigated the effects of race, ethnicity, and socioeconomic status on serum miRNA profiles. Serum samples from a large institutional biobank were analyzed using a custom panel of 179 miRNA species highly expressed in human serum, measured using the Abcam Fireplex assay via flow cytometry. Data were log-transformed prior to analysis. Differences in miRNA by race and ethnicity were assessed using logistic regression. Pairwise t tests analyzed racial and ethnic differences among eight miRNAs previously associated with ovarian cancer risk. Pearson correlations determined the relationship between mean miRNA expression and the social deprivation index (SDI) for Massachusetts residents. Of 1,586 patients (76.9% white, non-Hispanic), compared with white, non-Hispanic patients, those from other racial and ethnic groups were younger (41.9 years ± 13.2 vs. 51.3 ± 15.1, P < 0.01) and had fewer comorbidities (3.5 comorbidities ± 2.7 vs. 4.6 ± 2.8, P < 0.01). On logistic regression, miRNAs predicted race and ethnicity at an AUC of 0.69 (95% confidence interval, 0.66–0.72), which remained consistent when stratified by most comorbidities. Among eight miRNAs previously associated with ovarian cancer risk, seven significantly varied by race and ethnicity (all P < 0.01). There were no significant differences in SDI for any of these eight miRNAs. miRNA expression is significantly influenced by race and ethnicity, which remained consistent after controlling for confounders. Understanding baseline differences in biomarker test characteristics prior to clinical implementation is essential to ensure instruments perform comparably across diverse populations.
Prevention Relevance:
This study aimed to understand factors affecting miRNA expression, to ensure we create equitable screening tests for ovarian cancer that perform well in diverse populations. The goal is to ensure that we are detecting ovarian cancer cases earlier (secondary prevention) in women of all races, ethnic backgrounds, and socioeconomic means.
Supplementary Table S2 from Reprogramming the Intrahepatic Cholangiocarcinoma Immune Microenvironment by Chemotherapy and CTLA-4 Blockade Enhances Anti–PD-1 Therapy
Authors: Chen Jiang , Amoozgar Zohreh , Liu Xin , Aoki Shuichi , Liu Zelong , Shin Sarah M. , Matsui Aya , Hernandez Alexei , Pu Zhangya , Halvorsen Stefan , Lei Pin-Ji , Datta Meenal , Zhu Lingling , Ruan Zhiping , Shi Lei , Staiculescu Daniel , Inoue Koetsu , Munn Lance L. , Fukumura Dai , Huang Peigen , Sassi Slim , Bardeesy Nabeel , Ho Won Jin , Jain Rakesh K. , Duda Dan G.
Published: April 2024

Supplementary Table S2: Primers for PCR.
Supplementary Fig. S9 from Reprogramming the Intrahepatic Cholangiocarcinoma Immune Microenvironment by Chemotherapy and CTLA-4 Blockade Enhances Anti–PD-1 Therapy
Authors: Chen Jiang , Amoozgar Zohreh , Liu Xin , Aoki Shuichi , Liu Zelong , Shin Sarah M. , Matsui Aya , Hernandez Alexei , Pu Zhangya , Halvorsen Stefan , Lei Pin-Ji , Datta Meenal , Zhu Lingling , Ruan Zhiping , Shi Lei , Staiculescu Daniel , Inoue Koetsu , Munn Lance L. , Fukumura Dai , Huang Peigen , Sassi Slim , Bardeesy Nabeel , Ho Won Jin , Jain Rakesh K. , Duda Dan G.
Published: April 2024

Supplementary Fig. S9: Expression levels of Cxcr3 and its ligands are increased in ICC tissues after GC/dual ICB treatment in murine 425-ICC.
Supplementary Fig. S8 from Reprogramming the Intrahepatic Cholangiocarcinoma Immune Microenvironment by Chemotherapy and CTLA-4 Blockade Enhances Anti–PD-1 Therapy
Authors: Chen Jiang , Amoozgar Zohreh , Liu Xin , Aoki Shuichi , Liu Zelong , Shin Sarah M. , Matsui Aya , Hernandez Alexei , Pu Zhangya , Halvorsen Stefan , Lei Pin-Ji , Datta Meenal , Zhu Lingling , Ruan Zhiping , Shi Lei , Staiculescu Daniel , Inoue Koetsu , Munn Lance L. , Fukumura Dai , Huang Peigen , Sassi Slim , Bardeesy Nabeel , Ho Won Jin , Jain Rakesh K. , Duda Dan G.
Published: April 2024

Supplementary Fig. S8: Bulk tissue RNA sequencing analysis of ICC after GC/dual ICB combination therapy in orthotopic murine 425-ICC model.