Natalie Shih
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View article: DTC-Flow: a flow cytometry-based detection platform for characterizing bone marrow disseminated tumor cells in breast cancer
DTC-Flow: a flow cytometry-based detection platform for characterizing bone marrow disseminated tumor cells in breast cancer Open
The presence of bone marrow (BM) disseminated tumor cells (DTCbm) identifies early-stage breast cancer patients at increased risk of recurrence and poorer overall survival. However, limitations in detecting DTCbm by standard immunohistoche…
View article: Intratumoral preservation of the stem-like malignant cell proportion in glioblastoma, prognostic impact, and its radiomethylomic signatures
Intratumoral preservation of the stem-like malignant cell proportion in glioblastoma, prognostic impact, and its radiomethylomic signatures Open
Background Glioblastoma (GBM) exhibits significant intratumoral heterogeneity. However, the presence and extent of intratumoral heterogeneity of stem-like and differentiated cell components based on methylation profiles remain poorly under…
View article: Supplementary Table S7 from Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma
Supplementary Table S7 from Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma Open
WTA probe details
View article: Supplementary Table S8 from Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma
Supplementary Table S8 from Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma Open
This SupplementaryTable S8 is the normalized count matrix File for GeoMx data for the manuscript: Kader, Lin, Hug and colleagues titled "Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian T…
View article: Supplementary Figures 1 to 29 from Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma
Supplementary Figures 1 to 29 from Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma Open
Supplementary Figures provide additional evidence of IFN signaling pathway activation and heterogeneity during HGSOC progression.
View article: Supplementary Methods from Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma
Supplementary Methods from Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma Open
Supplementary methods describe details of CyCIF as well as GeoMx ROI collection and QC process
View article: Supplementary Table S2 from Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma
Supplementary Table S2 from Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma Open
GeoMx ROI annotations
View article: Supplementary Table S4 from Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma
Supplementary Table S4 from Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma Open
CyCIF antibody panels with RRIDs
View article: Supplementary Table S6 from Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma
Supplementary Table S6 from Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma Open
stat summary
View article: Supplementary Table S11 from Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma
Supplementary Table S11 from Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma Open
reactome pathway outcome-stroma: FT/Fim.I vs p53.I
View article: Supplementary Video from Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma
Supplementary Video from Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma Open
Supplementary Video shows MN rupture in 3D
View article: Supplementary Table S3 from Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma
Supplementary Table S3 from Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma Open
published gene set used in this study
View article: Supplementary Table S5 from Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma
Supplementary Table S5 from Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma Open
data summary
View article: Supplementary Table S9 from Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma
Supplementary Table S9 from Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma Open
segment and probe properties post QC (GeoMx)
View article: Data from Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma
Data from Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma Open
High-grade serous ovarian cancer (HGSOC) originates from fallopian tube (FT) precursors. However, the molecular changes that occur as precancerous lesions progress to HGSOC are not well understood. To address this, we integrated high-plex …
View article: Supplementary Table S10 from Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma
Supplementary Table S10 from Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma Open
reactome pathway outcome-epithelial: FT/Fim.I vs p53.I
View article: Supplementary Table S1 from Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma
Supplementary Table S1 from Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma Open
cohort description
View article: Impact of BRCA mutations, age, surgical indication, and hormone status on the molecular phenotype of the human Fallopian tube
Impact of BRCA mutations, age, surgical indication, and hormone status on the molecular phenotype of the human Fallopian tube Open
The human Fallopian tube (FT) is an important organ in the female reproductive system and has been implicated as a site of origin for pelvic serous cancers, including high-grade serous tubo-ovarian carcinoma (HGSC). We have generated compr…
View article: Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma
Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma Open
High-grade serous ovarian cancer (HGSOC) originates from fallopian tube (FT) precursors. However, the molecular changes that occur as precancerous lesions progress to HGSOC are not well understood. To address this, we integrated high-plex …
View article: Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma
Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma Open
High-Grade Serous Ovarian Cancer (HGSOC) originates from fallopian tube (FT) precursors. However, the molecular changes that occur as precancerous lesions progress to HGSOC are not well understood. To address this, we integrated high-plex …
View article: Exploiting the CD200-CD200R immune checkpoint axis in multiple myeloma to enhance CAR T-cell therapy
Exploiting the CD200-CD200R immune checkpoint axis in multiple myeloma to enhance CAR T-cell therapy Open
Patients with multiple myeloma (MM) treated with B-cell maturation antigen (BCMA)-specific chimeric antigen receptor (CAR) T cells usually relapse with BCMA+ disease, indicative of CAR T-cell suppression. CD200 is an immune checkpoint that…
View article: Prognostic correlations with the microbiome of breast cancer subtypes
Prognostic correlations with the microbiome of breast cancer subtypes Open
Alterations to the natural microbiome are linked to different diseases, and the presence or absence of specific microbes is directly related to disease outcomes. We performed a comprehensive analysis with unique cohorts of the four subtype…
View article: Computer extracted gland features from H&E predicts prostate cancer recurrence comparably to a genomic companion diagnostic test: a large multi-site study
Computer extracted gland features from H&E predicts prostate cancer recurrence comparably to a genomic companion diagnostic test: a large multi-site study Open
Existing tools for post-radical prostatectomy (RP) prostate cancer biochemical recurrence (BCR) prognosis rely on human pathologist-derived parameters such as tumor grade, with the resulting inter-reviewer variability. Genomic companion di…
View article: Metadata record for the manuscript: Computer extracted gland features from H&E predicts prostate cancer recurrence comparably to a genomic companion diagnostic test: a large multi-site study
Metadata record for the manuscript: Computer extracted gland features from H&E predicts prostate cancer recurrence comparably to a genomic companion diagnostic test: a large multi-site study Open
Summary This metadata record provides details of the data supporting the claims of the related manuscript: “Computer extracted gland features from H&E; predicts prostate cancer recurrence comparably to a genomic companion diagnostic test: …
View article: Genomic landscape of metastatic breast cancer identifies preferentially dysregulated pathways and targets
Genomic landscape of metastatic breast cancer identifies preferentially dysregulated pathways and targets Open
Nearly all breast cancer deaths result from metastatic disease. Despite this, the genomic events that drive metastatic recurrence are poorly understood. We performed whole-exome and shallow whole-genome sequencing to identify genes and pat…
View article: PD52-02 COMPUTER-EXTRACTED FEATURES OF GLAND MORPHOLOGY FROM DIGITAL TISSUE IMAGES IS COMPARABLE TO DECIPHER FOR PROGNOSIS OF BIOCHEMICAL RECURRENCE RISK POST-SURGERY
PD52-02 COMPUTER-EXTRACTED FEATURES OF GLAND MORPHOLOGY FROM DIGITAL TISSUE IMAGES IS COMPARABLE TO DECIPHER FOR PROGNOSIS OF BIOCHEMICAL RECURRENCE RISK POST-SURGERY Open
You have accessJournal of UrologyProstate Cancer: Markers II (PD52)1 Apr 2020PD52-02 COMPUTER-EXTRACTED FEATURES OF GLAND MORPHOLOGY FROM DIGITAL TISSUE IMAGES IS COMPARABLE TO DECIPHER FOR PROGNOSIS OF BIOCHEMICAL RECURRENCE RISK POST-SUR…