GSE144521

RNA profiles in serum and urine extracellular vesicles of patients with cholangiocarcinoma mimicking tumor expression: novel liquid biopsy approach

Whole-study status Not suitable

Dataset does not meet the current suitability threshold.

Whole-study downloads — these do not apply your sample requirements.

Selected cohort requirements

Samples meeting selected requirements: 0 cases / 0 controls

View matching samples

Patient pairs verified in indexed sample metadata: 0

A case/control comparison meeting these requirements is not confirmed.

Counts describe samples, not independent patients. Pair verification uses explicit subject identifiers in indexed sample metadata. Zero verified pairs does not establish that the study is unpaired; reported matched-normal design alone is insufficient.

Source
GEO
Assay
microarray
Organism
Homo sapiens
Whole-study samples
96 samples
Specimen
Biofluid
Reported/interpreted study design
Patient biofluid vs healthy control Design classification does not establish patient pairs.
Comparison type
Tumor vs normal
Contributors
Lapitz A, Arbelaiz A, Lavin JL, O'Rourke CJ, La Casta A, Ibarra C, Jimeno JP, Santos-Laso A, Krawczyk M, Perugorria MJ, Jimenez-Agüero R, Sanchez-Campos A, Riaño I, Gonzalez E, Lammert F, Marzioni M, Macias RI, Marin JJ, Karlsen TH, Bujanda L, Falcon-Perez J, Andersen JB, Aransay AM, Rodrigues PM, Banales JM
Contact name
Ana Maria Aransay
Submission date
2020-01-30
Last update
2020-05-18
Organization
CIC bioGUNE
Department
Genome Analysis Platform
Public date
2020-05-18
Experiment types
Expression profiling by array
Platforms
GPL14951 Illumina HumanHT-12 WG-DASL V4.0 R2 expression beadchip
Series type
Series
SubSeries
Not available
BioProject
PRJNA603909

Summary

Cholangiocarcinoma (CCA) represents a heterogeneous group of biliary cancers with poor prognosis. Although the aetiology is generally unknown, factors like Primary Sclerosing Cholangitis (PSC) predispose to its development. Simultaneously, around 80% of patients with PSC have concomitant Ulcerative Colitis (UC). As there are no specific and sensitive biomarkers for the non-invasive diagnosis of CCA, we aimed to analyse the RNA content of serum and urine extracellular vesicles (EVs) to find accurate biomarkers of CCA that could be reflecting tumor behaviour. The transcriptomic analysis of these EVs showed a differential profile of RNAs in patients with CCA compared to healthy individuals or patients with other diseases (PSC and UC), presenting some RNAs high diagnostic values to distinguish patients with CCA. Moreover, the differential abundance of several RNAs in serum and/or urine EVs correlated with the deregulated expression of those transcripts in CCA tissue compared to surrounding liver (TCGA and Copenhagen cohorts), in tumor (EGI1, TFK1) and normal cholangiocyte (NHC) cell lines as well as in EVs secreted by those cell lines; pinpointing the potential involvement of those RNAs not only as liquid biopsy biomarkers but also as potential mediators of CCA pathogenesis.

Overall design

Total RNA obtained from normal (NHC) and tumoral (EGI1 and TFK1) cholangiocyte cell lines and from extracellular vesicles (EVs) isolated from serum, urine and cholangiocyte cell line supernatant

Source Evidence

4 sources
Source Contribution Status
GEO

Original dataset metadata, sample metadata, source links, and GEO data availability flags.

Sample records
96 GSM samples
 Primary source
recount3

Planned trusted source for processed count availability.

 No match found
Expression Atlas

Planned source for curated expression experiment links.

 No match found
PubMed

Primary GEO citations and related PubMed articles that mention this dataset.

1 linked publication 1 DOI

Primary publication

  1. Patients with Cholangiocarcinoma Present Specific RNA Profiles in Serum and Urine Extracellular Vesicles Mirroring the Tumor Expression: Novel Liquid Biopsy Biomarkers for Disease Diagnosis. Cells, 2020
Available

Metadata Quality Components

Persisted metadata quality

100 pts
Clarity
100%
Weight
100 pts

Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Rule-based grouping found both case and control samples. Disease clarity: Disease or condition metadata normalized. Tissue clarity: Anatomical source metadata normalized. Treatment clarity: No unclear treatment split detected in the sample metadata. Replicate clarity: No pooled sample or technical replicate flags detected. Data availability clarity: Dataset-level processed or raw data availability is explicit.

Analysis Readiness

Ready after review
94% DE readiness

Contrast completeness

25/25 pts

Both case and control groups are present in the proposed grouping.

Minimum group size

20/20 pts

Each contrast group has at least 2 samples.

Processed data availability

20/20 pts

Processed data is marked available in the GEO index.

Sample decision clarity

12/15 pts

All non-excluded samples are assigned; excluded samples should still be confirmed.

Blocking warnings

7/10 pts

Warnings are present, but none are critical blockers.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

No readiness blockers detected.

Next Steps

  • Verify the proposed sample assignments and case-versus-control comparison against the GEO metadata before using them in DESeq2 or another differential-expression tool.
  • Confirm processed count files and sample identifiers match the exported metadata.

Analysis Preparation Checklist

4/6 ready

Group labels reviewed

Needs review

Siftome proposed case and control labels, but no reviewer confirmation is stored yet.

Open the sample grouping CSV and confirm group labels before analysis.

Minimum sample count met

Ready

Both groups meet the minimum of 2 samples.

Confirm whether the cohort is large enough for the intended statistical analysis.

Processed counts available

Ready

Processed data availability is marked true in the GEO index.

Verify that downloaded processed files contain usable count or expression identifiers.

Ambiguous samples handled

Ready

No review-needed or unassigned samples are present in the proposed grouping.

Review the grouping table for biologically meaningful differences that the automated checks may not detect.

Exclusion decisions recorded

Needs review

16 samples have hard exclusion flags in the proposed grouping.

Confirm excluded samples and preserve the reason in the analysis handoff.

Source traceability preserved

Ready

The dataset and sample accessions can be traced back to GEO.

Keep GEO accessions with exported metadata.

Bioinformatician Review

Bioinformatician review required

Ask a bioinformatician to review grouping, count availability, exclusions, and design before DE.

Assay context may require expert handling before DESeq2-style analysis.

Why This Is Ranked Here

Tumor vs normal
Not suitable Dataset does not meet the current suitability threshold.

Applied Review Decisions

No active review decisions affect this ranking.

Derived Classifications

  • Assay differs from search intent Microarray Search intent expects bulk RNA-seq. Assay came from Normalization rules.
  • Disease context Other non-gastrointestinal cancer, ulcerative colitis Disease context came from Normalization rules.
  • Likely case group Ulcerative colitis 66 samples
  • Likely control group Healthy control 14 samples

Intent Interpretation

  • Downgrade or exclusion reason Downgraded for tissue search because it is a biofluid cohort. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

  • Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 0%.
  • Interpreted disease metadata: Other non-gastrointestinal cancer, Ulcerative colitis.
  • Processed data is available for downstream review.
  • External evidence: PubMed links 1 publication; 1 DOI available: PMID 32183400.
  • Publication context: Patients with Cholangiocarcinoma Present Specific RNA Profiles in Serum and Urine Extracellular Vesicles Mirroring the Tumor Expression: Novel Liquid Biopsy Biomarkers for Disease Diagnosis.. Cells, 2020. PMID 32183400. DOI 10.3390/cells9030721.

Cautions

  • Downgraded for tissue search because it is a biofluid cohort.
  • Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
  • Excluded sample type flags reduce suitability.
  • Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
  • Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
  • Excluded model-system sample markers reduce suitability.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

Normalized Fields

168 fields

Sample Group Preview

showing 80 of 96 preview rows Show Hide
Study totals: Case 66 | Control 14 | Unassigned 0 | Excluded 16 | Ambiguous 0 showing 80 of 96 preview rows
Group Role Accession Title Source / characteristics Reason
Ulcerative colitis Case GSM4289955 S_UC_10 Serum Evs Disease: Ulcerative Colitis Explicit sample label case marker detected.
Ulcerative colitis Case GSM4289956 S_UC_11 Serum Evs Disease: Ulcerative Colitis Explicit sample label case marker detected.
Ulcerative colitis Case GSM4289957 S_UC_12 Serum Evs Disease: Ulcerative Colitis Explicit sample label case marker detected.
Ulcerative colitis Case GSM4289958 S_UC_13 Serum Evs Disease: Ulcerative Colitis Explicit sample label case marker detected.
Ulcerative colitis Case GSM4289959 S_UC_14 Serum Evs Disease: Ulcerative Colitis Explicit sample label case marker detected.
Ulcerative colitis Case GSM4289960 S_UC_15 Serum Evs Disease: Ulcerative Colitis Explicit sample label case marker detected.
Ulcerative colitis Case GSM4289961 S_UC_17 Serum Evs Disease: Ulcerative Colitis Explicit sample label case marker detected.
Ulcerative colitis Case GSM4289962 S_UC_18 Serum Evs Disease: Ulcerative Colitis Explicit sample label case marker detected.
Other non-gastrointestinal cancer Case GSM4289963 S_CCA_19 Serum Evs Disease: Cholangiocarcinoma Case marker detected.
Other non-gastrointestinal cancer Case GSM4289964 S_CCA_20 Serum Evs Disease: Cholangiocarcinoma Case marker detected.
Other non-gastrointestinal cancer Case GSM4289965 S_CCA_21 Serum Evs Disease: Cholangiocarcinoma Case marker detected.
Other non-gastrointestinal cancer Case GSM4289966 S_CCA_22 Serum Evs Disease: Cholangiocarcinoma Case marker detected.
Other non-gastrointestinal cancer Case GSM4289967 S_CCA_23 Serum Evs Disease: Cholangiocarcinoma Case marker detected.
Other non-gastrointestinal cancer Case GSM4289968 S_CCA_24 Serum Evs Disease: Cholangiocarcinoma Case marker detected.
Other non-gastrointestinal cancer Case GSM4289969 S_CCA_25 Serum Evs Disease: Cholangiocarcinoma Case marker detected.
Other non-gastrointestinal cancer Case GSM4289970 S_CCA_26 Serum Evs Disease: Cholangiocarcinoma Case marker detected.
Other non-gastrointestinal cancer Case GSM4289971 S_CCA_27 Serum Evs Disease: Cholangiocarcinoma Case marker detected.
Other non-gastrointestinal cancer Case GSM4289972 S_CCA_28 Serum Evs Disease: Cholangiocarcinoma Case marker detected.
Other non-gastrointestinal cancer Case GSM4289973 S_CCA_29 Serum Evs Disease: Cholangiocarcinoma Case marker detected.
Other non-gastrointestinal cancer Case GSM4289974 S_CCA_30 Serum Evs Disease: Cholangiocarcinoma Case marker detected.
Ulcerative colitis Case GSM4289980 O_UC_36 Urine EVs Disease: Ulcerative Colitis Explicit sample label case marker detected.
Ulcerative colitis Case GSM4289981 O_UC_38 Urine EVs Disease: Ulcerative Colitis Explicit sample label case marker detected.
Ulcerative colitis Case GSM4289982 O_UC_39 Urine EVs Disease: Ulcerative Colitis Explicit sample label case marker detected.
Ulcerative colitis Case GSM4289983 O_UC_40 Urine EVs Disease: Ulcerative Colitis Explicit sample label case marker detected.
Ulcerative colitis Case GSM4289984 O_UC_41 Urine EVs Disease: Ulcerative Colitis Explicit sample label case marker detected.
Ulcerative colitis Case GSM4289985 O_UC_42 Urine EVs Disease: Ulcerative Colitis Explicit sample label case marker detected.
Ulcerative colitis Case GSM4289986 O_UC_43 Urine EVs Disease: Ulcerative Colitis Explicit sample label case marker detected.
Ulcerative colitis Case GSM4289987 O_UC_44 Urine EVs Disease: Ulcerative Colitis Explicit sample label case marker detected.
Ulcerative colitis Case GSM4289988 O_UC_45 Urine EVs Disease: Ulcerative Colitis Explicit sample label case marker detected.
Primary sclerosing cholangitis Case GSM4289989 O_PSC_46 Urine EVs Disease: Primary Sclerosing Cholangitis Explicit characteristic comparison arm detected.
Primary sclerosing cholangitis Case GSM4289990 O_PSC_48 Urine EVs Disease: Primary Sclerosing Cholangitis Explicit characteristic comparison arm detected.
Primary sclerosing cholangitis Case GSM4289991 O_PSC_49 Urine EVs Disease: Primary Sclerosing Cholangitis Explicit characteristic comparison arm detected.
Primary sclerosing cholangitis Case GSM4289992 O_PSC_50 Urine EVs Disease: Primary Sclerosing Cholangitis Explicit characteristic comparison arm detected.
Ulcerative colitis Case GSM4289993 O_PSC_51 Urine EVs Disease: Ulcerative Colitis Case marker detected.
Primary sclerosing cholangitis Case GSM4289994 O_PSC_52 Urine EVs Disease: Primary Sclerosing Cholangitis Explicit characteristic comparison arm detected.
Other non-gastrointestinal cancer Case GSM4289995 O_CCA_51 Urine EVs Disease: Cholangiocarcinoma Case marker detected.
Other non-gastrointestinal cancer Case GSM4289996 O_CCA_52 Urine EVs Disease: Cholangiocarcinoma Case marker detected.
Other non-gastrointestinal cancer Case GSM4289997 O_CCA_55 Urine EVs Disease: Cholangiocarcinoma Case marker detected.
Other non-gastrointestinal cancer Case GSM4289998 O_CCA_56 Urine EVs Disease: Cholangiocarcinoma Case marker detected.
Other non-gastrointestinal cancer Case GSM4289999 O_CCA_57 Urine EVs Disease: Cholangiocarcinoma Case marker detected.
Other non-gastrointestinal cancer Case GSM4290000 O_CCA_58 Urine EVs Disease: Cholangiocarcinoma Case marker detected.
Other non-gastrointestinal cancer Case GSM4290001 O_CCA_59 Urine EVs Disease: Cholangiocarcinoma Case marker detected.
Other non-gastrointestinal cancer Case GSM4290002 O_CCA_60 Urine EVs Disease: Cholangiocarcinoma Case marker detected.
Other non-gastrointestinal cancer Case GSM4290003 O_CCA_61 Urine EVs Disease: Cholangiocarcinoma Case marker detected.
Other non-gastrointestinal cancer Case GSM4290004 O_CCA_63 Urine EVs Disease: Cholangiocarcinoma Case marker detected.
Other non-gastrointestinal cancer Case GSM4290005 O_CCA_65 Urine EVs Disease: Cholangiocarcinoma Case marker detected.
Other non-gastrointestinal cancer Case GSM4290006 O_CCA_66 Urine EVs Disease: Cholangiocarcinoma Case marker detected.
Other non-gastrointestinal cancer Case GSM4290007 O_CCA_67 Urine EVs Disease: Cholangiocarcinoma Case marker detected.
Other non-gastrointestinal cancer Case GSM4290008 O_CCA_69 Urine EVs Disease: Cholangiocarcinoma Case marker detected.
Other non-gastrointestinal cancer Case GSM4290009 O_CCA_70 Urine EVs Disease: Cholangiocarcinoma Case marker detected.
16 additional case samples are hidden from this preview.
Healthy control Control GSM4289946 S_ctrl_1 Serum Evs Disease: Healthy Sample-local control marker detected.
Healthy control Control GSM4289947 S_ctrl_2 Serum Evs Disease: Healthy Sample-local control marker detected.
Healthy control Control GSM4289948 S_ctrl_3 Serum Evs Disease: Healthy Sample-local control marker detected.
Healthy control Control GSM4289949 S_ctrl_4 Serum Evs Disease: Healthy Sample-local control marker detected.
Healthy control Control GSM4289950 S_ctrl_5 Serum Evs Disease: Healthy Sample-local control marker detected.
Healthy control Control GSM4289951 S_ctrl_6 Serum Evs Disease: Healthy Sample-local control marker detected.
Healthy control Control GSM4289952 S_ctrl_7 Serum Evs Disease: Healthy Sample-local control marker detected.
Healthy control Control GSM4289953 S_ctrl_8 Serum Evs Disease: Healthy Sample-local control marker detected.
Healthy control Control GSM4289954 S_ctrl_9 Serum Evs Disease: Healthy Sample-local control marker detected.
Healthy control Control GSM4289975 OCtrl_31 Urine EVs Disease: Healthy Sample-local control marker detected.
Healthy control Control GSM4289976 OCtrl_32 Urine EVs Disease: Healthy Sample-local control marker detected.
Healthy control Control GSM4289977 OCtrl_33 Urine EVs Disease: Healthy Sample-local control marker detected.
Healthy control Control GSM4289978 OCtrl_34 Urine EVs Disease: Healthy Sample-local control marker detected.
Healthy control Control GSM4289979 OCtrl_35 Urine EVs Disease: Healthy Sample-local control marker detected.
Excluded: Cell line Excluded GSM4290026 EV_NHC Cell line-derived Evs Disease: Normal cholangiocyte; Cell line: NHC cell line: Normalized exclusion flag detected: cell line.
Excluded: Cell line Excluded GSM4290027 EV_H69 Cell line-derived Evs Disease: Immortalized cholangiocyte; Cell line: H69 cell line: Normalized exclusion flag detected: cell line.
Excluded: Cell line Excluded GSM4290028 EV_EGI1 Cell line-derived Evs Disease: Tumor cholangiocyte; Cell line: EGI1 cell line: Normalized exclusion flag detected: cell line.
Excluded: Cell line Excluded GSM4290029 EV_TFK1 Cell line-derived Evs Disease: Tumor cholangiocyte; Cell line: TFK1 cell line: Normalized exclusion flag detected: cell line.
Excluded: Cell line Excluded GSM4290030 NHCWCE_1 Cell line Disease: Normal cholangiocyte; Cell line: NHC cell line: Normalized exclusion flag detected: cell line.
Excluded: Cell line Excluded GSM4290031 NHCWCE_2 Cell line Disease: Normal cholangiocyte; Cell line: NHC cell line: Normalized exclusion flag detected: cell line.
Excluded: Cell line Excluded GSM4290032 NHCWCE_3 Cell line Disease: Normal cholangiocyte; Cell line: NHC cell line: Normalized exclusion flag detected: cell line.
Excluded: Cell line Excluded GSM4290033 H69WCE_1 Cell line Disease: Immortalized cholangiocyte; Cell line: H69 cell line: Normalized exclusion flag detected: cell line.
Excluded: Cell line Excluded GSM4290034 H69WCE_2 Cell line Disease: Immortalized cholangiocyte; Cell line: H69 cell line: Normalized exclusion flag detected: cell line.
Excluded: Cell line Excluded GSM4290035 H69WCE_3 Cell line Disease: Immortalized cholangiocyte; Cell line: H69 cell line: Normalized exclusion flag detected: cell line.
Excluded: Cell line Excluded GSM4290036 EGIWCE_1 Cell line Disease: Tumor cholangiocyte; Cell line: EGI1 cell line: Normalized exclusion flag detected: cell line.
Excluded: Cell line Excluded GSM4290037 EGIWCE_2 Cell line Disease: Tumor cholangiocyte; Cell line: EGI1 cell line: Normalized exclusion flag detected: cell line.
Excluded: Cell line Excluded GSM4290038 EGIWCE_3 Cell line Disease: Tumor cholangiocyte; Cell line: EGI1 cell line: Normalized exclusion flag detected: cell line.
Excluded: Cell line Excluded GSM4290039 TFKWCE_1 Cell line Disease: Tumor cholangiocyte; Cell line: TFK1 cell line: Normalized exclusion flag detected: cell line.
Excluded: Cell line Excluded GSM4290040 TFKWCE_2 Cell line Disease: Tumor cholangiocyte; Cell line: TFK1 cell line: Normalized exclusion flag detected: cell line.
Excluded: Cell line Excluded GSM4290041 TFKWCE_3 Cell line Disease: Tumor cholangiocyte; Cell line: TFK1 cell line: Normalized exclusion flag detected: cell line.

Use as Discovery Cohort

External Validation Finder

Carry Siftome's disease, organism, specimen, assay, data type, and accession into a validation project. Uncertain fields remain Unknown.