Summary of Study ST001306

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000887. The data can be accessed directly via it's Project DOI: 10.21228/M81M59 This work is supported by NIH grant, U2C- DK119886.

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Study IDST001306
Study TitleBiomolecular analyses of hypospadias according to severity
Study SummaryHypospadias, characterized by the displacement of the opening of the urethra at any point in the medial-ventral side of the penis, is classified upon severity as mild (Type I) and severe (Type II and Type III) hypospadias. Hypospadias’ etiology is idiopathic in the majority of cases, and underlying causes seem of multifactorial origin. Studies regarding genetic variants support this notion. It is unknown whether downstream gene products fit this profile. This study evaluated the metabolome of hypospadias by using the emerging technology of metabolomics in the search for distinct cellular processes associated with hypospadias’ etiology according to the severity of this congenital urogenital condition. Foreskin samples were collected during urethroplasty from boys with Type I, II, and III hypospadias or undergoing elective circumcision (N=28) between 5 to 28 months of age. Samples were processed and submitted to gas chromatography-mass spectrometry (GC/MS). MetaboloAnalyst (http://www.metaboanalyst.ca/) online platform was used for bioinformatic analyses. The metabolome of Type II and Type III hypospadias patients differs from the metabolome of Type I hypospadias and control patients. Thirty-five metabolites were identified by GC/MS. Of those, 14 metabolites, amino acids, were found in significantly low concentrations in Type II and Type III hypospadias in comparison to Type I hypospadias and controls. Amino acids comprised asparagine, aspartate, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, and tyrosine. The difference observed in the metabolome between severe and mild hypospadias supports previous research work of plausible severity-dependent etiologies for hypospadias. The observed downregulation of specific amino acids in severe hypospadias provides alternative routes for future research aiming to identify disrupted networks and pathways while considering the severity of hypospadias.
Institute
University of Puerto Rico, Medical Sciences Campus
DepartmentAnatomy & Neurobiology
Last NamePiñeyro-Ruiz
First NameCoriness
AddressUniversity of Puerto Rico, Medical Sciences Campus, Department of Anatomy & Neurobiology, Main Building, 5th Floor, Room A-521 PO BOX 365067 San Juan, PR 00936-5067
Emailcoriness.pineyro@upr.edu
Phone7877582525
Submit Date2020-01-17
Num Groups4
Total Subjects28
Num Males28
Raw Data AvailableYes
Raw Data File Type(s)gqd
Analysis Type DetailGC-MS
Release Date2020-03-03
Release Version1
Coriness Piñeyro-Ruiz Coriness Piñeyro-Ruiz
https://dx.doi.org/10.21228/M81M59
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000887
Project DOI:doi: 10.21228/M81M59
Project Title:Biomolecular analyses of hypospadias according to severity
Project Summary:Hypospadias, characterized by the displacement of the opening of the urethra at any point in the medial-ventral side of the penis, is classified upon severity as mild (Type I) and severe (Type II and Type III) hypospadias. Hypospadias’ etiology is idiopathic in the majority of cases, and underlying causes seem of multifactorial origin. Studies regarding genetic variants support this notion. It is unknown whether downstream gene products fit this profile. This study evaluated the metabolome of hypospadias by using the emerging technology of metabolomics in the search for distinct cellular processes associated with hypospadias’ etiology according to the severity of this congenital urogenital condition. Foreskin samples were collected during urethroplasty from boys with Type I, II, and III hypospadias or undergoing elective circumcision (N=28) between 5 to 28 months of age. Samples were processed and submitted to gas chromatography-mass spectrometry (GC/MS). MetaboloAnalyst (http://www.metaboanalyst.ca/) online platform was used for bioinformatic analyses. The metabolome of Type II and Type III hypospadias patients differs from the metabolome of Type I hypospadias and control patients. Thirty-five metabolites were identified by GC/MS. Of those, 14 metabolites, amino acids, were found in significantly low concentrations in Type II and Type III hypospadias in comparison to Type I hypospadias and controls. Amino acids comprised asparagine, aspartate, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, and tyrosine. The difference observed in the metabolome between severe and mild hypospadias supports previous research work of plausible severity-dependent etiologies for hypospadias. The observed downregulation of specific amino acids in severe hypospadias provides alternative routes for future research aiming to identify disrupted networks and pathways while considering the severity of hypospadias.
Institute:University of Puerto Rico, Medical Sciences Campus
Department:Anatomy & Neurobiology
Last Name:Piñeyro-Ruiz
First Name:Coriness
Address:University of Puerto Rico, Medical Sciences Campus, Department of Anatomy & Neurobiology, Main Building, 5th Floor, Room A-521 PO BOX 365067 San Juan, PR 00936-5067
Email:coriness.pineyro@upr.edu
Phone:7877582525 ext. 1506
Funding Source:MBRS-RISE (R25GM061838); CCRHD-NIMHD RCMI (U54M007600); NIGMS-INBRE-PR NIH (5P20GM103475-16); NIMHD & NIAID (2U54MD007587)

Subject:

Subject ID:SU001380
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:5-28 months
Gender:Male
Human Ethnicity:Hispanic
Human Inclusion Criteria:(1) boys diagnosed with hypospadias with no comorbidities; (2) children undergoing elective circumcision without a clinical diagnosis; (3) age must be between 0 to 28 months; (4) parents' authorization and sign inform consent
Human Exclusion Criteria:(1) being unable to understand spoken and written language in Spanish; (2) not being willing to provide authorization for collection of tissue sample during the surgical repair of hypospadias and circumcision procedure

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Condition
SA094385H42-CControl
SA094386H8-CControl
SA094387H29-CControl
SA094388H28-CControl
SA094389H15-CControl
SA094390H21-CControl
SA094391H22-CControl
SA094392H27-CControl
SA094393H32-IType I
SA094394H26-IType I
SA094395H40-IType I
SA094396H23-IType I
SA094397H3-IType I
SA094398H12-IType I
SA094399H20-IType I
SA094400H43-IIType II
SA094401H35-IIType II
SA094402H36-IIType II
SA094403H33-IIType II
SA094404H24-IIType II
SA094405H30-IIType II
SA094406H31-IIType II
SA094407H44-IIIType III
SA094408H41-IIIType III
SA094409H37-IIIType III
SA094410H14-IIIType III
SA094411H38-IIIType III
SA094412H39-IIIType III
Showing results 1 to 28 of 28

Collection:

Collection ID:CO001375
Collection Summary:Foreskin samples were collected from children undergoing urethroplasty and boys scheduled for elective circumcision at the University District Hospital, San Juan, Puerto Rico, and HIMA San Pablo Hospital, Caguas, Puerto Rico. Samples were immediately frozen in dry ice and stored at -80 °C.
Sample Type:Foreskin

Treatment:

Treatment ID:TR001395
Treatment Summary:No treatment.

Sample Preparation:

Sampleprep ID:SP001388
Sampleprep Summary:Foreskin samples are cut into small pieces with a scalpel (new) on ice. Weight 50 mg of the foreskin for each sample in 1.5 mL Eppendorf tubes. Sample homogenization and extraction of metabolites is perform adding 1 ml of chloroform/MeOH/H2O (2:5:2) to each sample. Samples are sonicated using a polytron for 15 seconds (3X) in a beaker with ice. Shake samples for 15 minutes in a nutating vortex and centrifuge at 13000 rpm for 10 minutes at 4°C. The supernatant is collected and transferred into 1.5 glass vials for drying. For evaporation, use plastic caps with hole caps. Make a little hole in the center for evaporation to take place. Evaporate samples in SpeedVac until samples are completely dried.

Combined analysis:

Analysis ID AN002175
Analysis type MS
Chromatography type GC
Chromatography system Shimadzu GCMS-QP2010 ultra
Column Shimadzu SH-Rxi-5ms (30m x 0.25mm,0.25um)
MS Type EI
MS instrument type Single quadrupole
MS instrument name Shimadzu QP2010 Ultra
Ion Mode UNSPECIFIED
Units millimolar

Chromatography:

Chromatography ID:CH001591
Instrument Name:Shimadzu GCMS-QP2010 ultra
Column Name:Shimadzu SH-Rxi-5ms (30m x 0.25mm,0.25um)
Chromatography Type:GC

MS:

MS ID:MS002023
Analysis ID:AN002175
Instrument Name:Shimadzu QP2010 Ultra
Instrument Type:Single quadrupole
MS Type:EI
MS Comments:Data was processed using GCMS Labsolution data analysis software (Shimadzu) equipped with NIST14/2014/EPA/NIH database.
Ion Mode:UNSPECIFIED
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