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Links from GEO DataSets

Items: 20

1.

Impact of molecular subtypes in muscle-invasive bladder cancer on predicting response and survival outcome to neoadjuvant chemotherapy: results from a multi-institutional validation study

(Submitter supplied) Four different molecular classifications of muscle-invasive bladder cancer (MIBC) based on gene expression have been proposed. With the ultimate goal of utilizing these molecular subtypes for personalized treatment, we investigated their significance in the context of neoadjuvant cisplatin-based chemotherapy (NAC).
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL22995
305 Samples
Download data: CEL
Series
Accession:
GSE87304
ID:
200087304
2.

Impact of Immune and Stromal Infiltration on Outcomes Following Bladder-Sparing Trimodality Therapy for Muscle-Invasive Bladder Cancer

(Submitter supplied) Background: Bladder-sparing trimodality therapy (TMT) is an alternative to radical cystectomy (RC) for muscle-invasive bladder cancer (MIBC), and biomarkers to inform therapy selection are needed. Objective: To evaluate immune and stromal signatures in MIBC treated with TMT.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL22995
136 Samples
Download data: CEL
Series
Accession:
GSE128701
ID:
200128701
3.

MVAC treated tumors

(Submitter supplied) validation of the survival outcomes from MVAC-Avastin treated tumors
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL14951
49 Samples
Download data: TXT
Series
Accession:
GSE70691
ID:
200070691
4.

a phase 2 trial of DDMVAC and bevacizumab in urothelial cancer

(Submitter supplied) A prognostic gene expression signature in chemotherapy-naïve bladder cancer is predictive of clinical outcomes from neoadjuvant chemotherapy
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL14951
61 Samples
Download data: TXT
Series
Accession:
GSE69795
ID:
200069795
5.

Differential neoadjuvant chemotherapy response in urothelial carcinoma molecular subtypes

(Submitter supplied) For patients with muscle-invasive bladder cancer, there are no biomarkers in clinical use that can identify patients that are sensitive or resistant to neoadjuvant chemotherapy. This study investigates how molecular subtypes impact pathological response and survival in 149 patients receiving preoperative cis-platin based chemotherapy by tumor classification using transcriptomic profiling and a 13-marker immunostaining panel. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL6244
149 Samples
Download data: CEL, TXT
Series
Accession:
GSE169455
ID:
200169455
6.

Molecular characterizaion of neuroendocrine-like bladder cancer

(Submitter supplied) Neuroendocrine bladder cancer is an aggressive variant of bladder cancer with significant metastatic potential and high risk of mortality. Diagnosis of these tumors is currently dependent on morphological criteria and staining for neuroendocrine markers. Using machine learning and multiple validation cohorts in different clinical settings, we developed a model that identifies tumors with transcriptomic profiles consistent with NE bladder cancers with an absence of NE features by morphological criteria. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL22995
256 Samples
Download data: CEL
Series
Accession:
GSE128702
ID:
200128702
7.

Divergent biological response to neoadjuvant chemotherapy in muscle-invasive bladder cancer

(Submitter supplied) Despite cisplatin-based neoadjuvant chemotherapy (NAC) 60% of patients with muscle-invasive bladder cancer still have residual invasive disease at radical cystectomy (RC). The NAC-induced biological alterations in these cisplatin-resistant tumors remain largely unstudied. We analyzed gene expression from 133 patients with residual invasive disease after cisplatin-based NAC. H&E and immunohistochemistry were used to confirm tissue sampling and gene expression analysis. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL22995
133 Samples
Download data: CEL
Series
Accession:
GSE124305
ID:
200124305
8.

Pre-clinical and clinical studies on the role of RBM3 in muscle-invasive bladder cancer: longitudinal expression, transcriptome-level effects and modulation of chemosensitivity

(Submitter supplied) Background: The response to neoadjuvant cisplatin-based chemotherapy (NAC) in muscle-invasive bladder cancer (MIBC) is impaired in up to 50% of patients due to chemoresistance, with no predictive biomarkers in clinical use. RNA-binding motif protein 3 (RBM3) has emerged as a putative modulator of chemotherapy response but has a hitherto unrecognized role in MIBC. Methods: Tumour-specific RBM3 protein expression was assessed via immunohistochemistry in paired transurethral resection of the bladder (TURB) specimens, cystectomy specimens and lymph node metastases from 145 patients. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
6 Samples
Download data: TXT
9.

Association of Molecular Subtypes with Pathologic Response, PFS and OS in a Phase II Study of Coexpression Extrapolation (COXEN) with Neoadjuvant Chemotherapy (NAC) for Localized, Muscle-Invasive Bladder Cancer (SWOG S1314; NCT02177695)

(Submitter supplied) Investigation of RNA-based molecular subtypes as additional predictive biomarkers for neoadjuvant chemotherapy response, progression-free survival and survival in patients treated in S1314.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL570
189 Samples
Download data: CEL
Series
Accession:
GSE244266
ID:
200244266
10.

Cell-free DNA methylation as a predictive biomarker of response to neoadjuvant chemotherapy for patients with muscle invasive bladder cancer in SWOG S1314

(Submitter supplied) cfDNA methylation analysis to predict cisplatin treatment response in bladder cancer
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL21145
137 Samples
Download data: IDAT, TXT
Series
Accession:
GSE193208
ID:
200193208
11.

Gene expression Classification of Colon Cancer defines six molecular subtypes with distinct clinical, molecular and survival characteristics

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Genome variation profiling by genome tiling array; Expression profiling by array
Platforms:
GPL16070 GPL570
1048 Samples
Download data: CEL, GPR
Series
Accession:
GSE40967
ID:
200040967
12.

Gene expression Classification of Colon Cancer defines six molecular subtypes with distinct clinical, molecular and survival characteristics [CGH]

(Submitter supplied) From a clinical and molecular perspective, colon cancer (CC) is a heterogeneous disease but to date no classification based on high-density transcriptome data has been established. The aim of this study was to build up a robust molecular classification of mRNA expression profiles (Affymetrix U133Plus2) of a large series of 443 CC and to validate it on an independent serie of 123 CC and 906 public dataset. We identified and validated six molecular subtypes in this large cohort as a combination of multiple molecular processes that complement current disease stratification based on clinicopathological variables and molecular markers. more...
Organism:
Homo sapiens
Type:
Genome variation profiling by genome tiling array
Platform:
GPL16070
463 Samples
Download data: GPR, TXT
Series
Accession:
GSE40966
ID:
200040966
13.

Gene expression Classification of Colon Cancer defines six molecular subtypes with distinct clinical, molecular and survival characteristics [Expression]

(Submitter supplied) From a clinical and molecular perspective, colon cancer (CC) is a heterogeneous disease but to date no classification based on high-density transcriptome data has been established. The aim of this study was to build up a robust molecular classification of mRNA expression profiles (Affymetrix U133Plus2) of a large series of 443 CC and 19 non-tumoral colorectal mucosas, and to validate it on an independent serie of 123 CC and 906 public dataset. We identified and validated six molecular subtypes in this large cohort as a combination of multiple molecular processes that complement current disease stratification based on clinicopathological variables and molecular markers. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL570
585 Samples
Download data: CEL
Series
Accession:
GSE39582
ID:
200039582
14.

Development and validation of a NanoString BASE47 bladder cancer gene classifier

(Submitter supplied) Purpose: We sought to develop and evaluate a diagnostic classifier of UC subtype with the goal of accurate classification from clinically available specimens. Methods: Tumor samples from 52 patients with high-grade UC were profiled for BASE47 genes concurrently by RNAseq as well as NanoString. After design and technical validation of a BASE47 NanoString probeset, results from the RNAseq and NanoString were used to translate diagnostic criteria to the Nanostring platform. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
52 Samples
Download data: TXT
15.

Glutathione dynamics is a potential diagnostic and therapeutic trait determining the neoadjuvant chemotherapy response to bladder cancer

(Submitter supplied) Radical cystectomy with preoperative cisplatin-based neoadjuvant chemotherapy (NAC) is a current standard care for muscle-invasive bladder cancers (MIBCs). However, the response rate remains relatively low, and current clinico-pathologic and molecular classifications are inadequate to prospectively stratify MBIC patients regarding the NAC response. Here, we showed that dysregulation in glutathione (GSH) pathway is fundamental for the NAC resistance of MBICs. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
39 Samples
Download data: TXT
Series
Accession:
GSE212810
ID:
200212810
16.

Naturally-occurring canine invasive urothelial carcinoma harbors luminal and basal transcriptional subtypes found in human muscle invasive bladder cancer 

(Submitter supplied) RNA-seq was used to identify basal and luminal subtypes in canine bladder cancer. In addition to larger gene-sets, a smaller panel of genes was developed to stratify canine samples into either basal or luminal subtype prospectively. Immune signature patterns were queried in basal and luminal subtypes.
Organism:
Canis lupus familiaris
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24229
33 Samples
Download data: TXT
Series
Accession:
GSE110661
ID:
200110661
17.

A new epithelial cell subpopulation predicts response to surgery, chemotherapy, and immunotherapy in bladder cancer

(Submitter supplied) The advent of neoadjuvant chemotherapy (NAC) prior to surgery and immune checkpoint therapy (ICT) have revolutionized bladder cancer management1-7. However, stratification of patients that would benefit most from these modalities remains a major clinical challenge. Here, we combine single nuclei RNA sequencing with spatial transcriptomics and single cell resolution spatial proteomic analysis of human bladder cancer to identify a novel epithelial subpopulation with therapeutic response prediction ability. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24676
4 Samples
Download data: H5AD, JPG
Series
Accession:
GSE171351
ID:
200171351
18.

A new epithelial cell subpopulation predicts response to surgery, chemotherapy, and immunotherapy in bladder cancer

(Submitter supplied) The advent of neoadjuvant chemotherapy (NAC) prior to surgery and immune checkpoint therapy (ICT) have revolutionized bladder cancer management1-7. However, stratification of patients that would benefit most from these modalities remains a major clinical challenge. Here, we combine single nuclei RNA sequencing with spatial transcriptomics and single cell resolution spatial proteomic analysis of human bladder cancer to identify a novel epithelial subpopulation with therapeutic response prediction ability. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24676
30 Samples
Download data: CSV, H5AD
Series
Accession:
GSE169379
ID:
200169379
19.

Tumor immune dysfunction and exclusion subtypes in bladder cancer and pan-cancer: a novel molecular subtyping strategy and immunotherapeutic prediction model

(Submitter supplied) Molecular subtyping is expected to enable bladder cancer (BC) precise treatment. However, reliable subtyping strategies for clinical application remains defective and controversial. Given the significance of tumor immune dysfunction and exclusion (TIDE) in tumor immune escape and immunotherapy, we aimed to develop a novel TIDE-based subtyping method to facilitate personalized management. Transcriptome data of BC was used to evaluate the heterogeneity and the status of TIDE patterns. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24676
51 Samples
Download data: TXT
Series
Accession:
GSE248167
ID:
200248167
20.

Immune Signatures and Tumor Biomarkers from Whole Transcriptome Sequencing Predict Outcome in Recurrent Resectable Stage III and IV Melanoma when Evaluated Following Treatment with Hu14.18-IL2

(Submitter supplied) We analyzed whole transcriptome sequencing in tumors from 23 patients with stage III or IV melanoma from a pilot trial of the anti-GD2 immunocytokine, hu14.18-IL2, in melanoma patients at high risk for recurrence to identify predictive immune and/or tumor biomarkers. Patients with advanced resectable melanoma were randomized to receive the first of 3 monthly-courses of hu14.18-IL2 immunotherapy either before (Group A) or after (Group B) complete surgical resection of all known disease. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
23 Samples
Download data: TXT
Series
Accession:
GSE133713
ID:
200133713
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