SNPMiner Trials by Shray Alag


SNPMiner Trials: Clinical Trial Report


Report for Clinical Trial NCT02743468

Developed by Shray Alag, 2019.
SNP Clinical Trial Gene

Cytochrome P450 Epoxygenase Pathway Regulation of Macrophage Function

Background: Respiratory diseases affect more than 1 billion people worldwide. They are a growing public health concern. The lungs are constantly exposed to environmental factors such as dust, fumes, microbes, and pollutants. But much is still not known about how these pollutants lead to respiratory illnesses. Researchers want to collect samples from lungs and blood to see how genetics and environmental pollutants affect cellular responses or functioning. Objectives: To study how cytochrome P450 epoxygenase pathway enzymes affect macrophage function in the lungs and inflammatory responses. Eligibility: Adults ages 18 65 who can have a bronchoscopy. Design: All study visits will take place at the NIEHS Clinical Research Unit in Research Triangle Park, NC. At study visit 1, participants will be screened with medical history and physical exam. They will have blood and urine tests. They will take tests that measure their lung function. They will answer questionnaires. Before the visit, they will be given a list of medicines they cannot take. They also must not have caffeine on the day of their visit. The visit will last about 3 hours. At study visit 2, participants will give blood samples. They will undergo bronchoscopy. For this, they will get an intravenous line in a vein to get sedatives. Their airways will be numbed. Cells will be collected from their lungs. They will fast for 8 hours before the visit. They must have someone else drive them home from the visit. The visit will last about 3-4 hours. Participants will get a follow-up phone call about 1 day after study visit 2.

NCT02743468 Polymorphism Lung Inflammation
MeSH: Inflammation Pneumonia
HPO: Pneumonia


Primary Outcomes

Description: The primary outcome measure will evaluate macrophage phagocytosis of fluorescein isothiocyanate (FITC)-labeled beads and bacteria (Streptococcus pneumoniae) in an ex vivo assay, comparing alveolar macrophages from groups of individuals with and without EPHX2 and CYP2J2 polymorphisms of interest.

Measure: The primary outcome measure will evaluate macrophage phagocytosis of fluorescein isothiocyanate (FITC)-labeled beads and bacteria (Streptococcus pneumoniae) in an ex vivo assay.

Time: Cross-sectional

Secondary Outcomes

Description: Macrophage phagocytosis of FITC-labeled beads and bacteria (S. pneumoniae) in an ex vivo assay, comparing peripheral blood monocyte derived macrophages from groups of individuals with and without EPHX2 and CYP2J2 polymorphisms of interest

Measure: A - Macrophage phagocytosis of FITC-labeled beads and bacteria (S.pneumoniae) in an ex vivo assay.

Time: Cross-sectional

Description: Ex vivo gene expression of inflammatory receptors [e.g., toll-like receptor (TLR) 2 and peptidoglycan recognition protein (PGLYRP) 1] and cytokines [e.g., interleukin (IL) -1beta, IL-6, and tumor necrosis factor (TNF)-alpha] in stimulated macrophages (alveolar and peripheral blood monocytederived)

Measure: B - Ex vivo gene expression of inflammatory receptors [e.g., toll-like receptor (TLR) 2 and peptidoglycan recognition protein (PGLYRP) 1] and cytokines [e.g., interleukin (IL) -1beta, IL-6, and tumor necrosis factor (TNF)-alpha]

Time: Cross-sectional

Description: Assessment of the lower airway microbiome from BAL fluid

Measure: C - Assessment of the lower airway microbiome from BAL fluid

Time: Cross-sectional

Description: Eicosanoid [EET and dihydroxyeicosatrienoic acids (DHET)] and cytokine (e.g., IL- 1beta, IL-6, and TNF-alpha) levels in serum and BAL

Measure: D - Eicosanoid [EET and dihydroxyeicosatrienoic acids (DHET)] and cytokine (e.g., IL-1beta, IL-6, and TNF-alpha) levels in serum and BAL

Time: Cross-sectional

Description: Differences in effect of functional polymorphisms on macrophage function, comparing interferon (IFN)- gamma-derived (M1) versusIL-4-derived (M2) macrophages

Measure: E - Differences in effect of functional polymorphisms on macrophage function, comparing interferon (IFN)-gammaderived (M1) versus IL-4-derived (M2) macrophages

Time: Cross-sectional

Time Perspective: Cross-Sectional

Cohort


There are 2 SNPs

SNPs


1 K55R

- INCLUSION CRITERIA: 1. Age 18 to 65 years, inclusive (males and females) 2. Able to travel to the NIEHS CRU for required study visits 3. Able to present a valid government-issued form of identification for entry to the NIEHS campus 4. Able to fast for 8 hours prior to the visit where bronchoscopy occurs 5. Has a responsible party who is willing and able to attend Visit 2 and drive the participant away from the CRU after completion of Visit 2, if the participant elects to undergo conscious sedation 6. Genotype information available for relevant CYP2J2 and EPHX2 polymorphisms, which indicates: - Wild type with respect to EPHX2 K55R, EPHX2 R287Q, and CYP2J2*7; or - Homozygous for EPHX2 K55R (wild type for the other SNPs); or - Homozygous for EPHX2 R287Q (wild type for the other SNPs); or - Homozygous for CYP2J2*7 (wild type for the other SNPs) EXCLUSION CRITERIA: 1. --- K55R ---

- INCLUSION CRITERIA: 1. Age 18 to 65 years, inclusive (males and females) 2. Able to travel to the NIEHS CRU for required study visits 3. Able to present a valid government-issued form of identification for entry to the NIEHS campus 4. Able to fast for 8 hours prior to the visit where bronchoscopy occurs 5. Has a responsible party who is willing and able to attend Visit 2 and drive the participant away from the CRU after completion of Visit 2, if the participant elects to undergo conscious sedation 6. Genotype information available for relevant CYP2J2 and EPHX2 polymorphisms, which indicates: - Wild type with respect to EPHX2 K55R, EPHX2 R287Q, and CYP2J2*7; or - Homozygous for EPHX2 K55R (wild type for the other SNPs); or - Homozygous for EPHX2 R287Q (wild type for the other SNPs); or - Homozygous for CYP2J2*7 (wild type for the other SNPs) EXCLUSION CRITERIA: 1. --- K55R --- --- R287Q --- --- K55R ---

EXCL 4. Any food or fluids for 8 hours prior to the bronchoscopy - INCLUSION CRITERIA: 1. Age 18 to 65 years, inclusive (males and females) 2. Able to travel to the NIEHS CRU for required study visits 3. Able to present a valid government-issued form of identification for entry to the NIEHS campus 4. Able to fast for 8 hours prior to the visit where bronchoscopy occurs 5. Has a responsible party who is willing and able to attend Visit 2 and drive the participant away from the CRU after completion of Visit 2, if the participant elects to undergo conscious sedation 6. Genotype information available for relevant CYP2J2 and EPHX2 polymorphisms, which indicates: - Wild type with respect to EPHX2 K55R, EPHX2 R287Q, and CYP2J2*7; or - Homozygous for EPHX2 K55R (wild type for the other SNPs); or - Homozygous for EPHX2 R287Q (wild type for the other SNPs); or - Homozygous for CYP2J2*7 (wild type for the other SNPs) EXCLUSION CRITERIA: 1. --- K55R ---

EXCL 4. Any food or fluids for 8 hours prior to the bronchoscopy - INCLUSION CRITERIA: 1. Age 18 to 65 years, inclusive (males and females) 2. Able to travel to the NIEHS CRU for required study visits 3. Able to present a valid government-issued form of identification for entry to the NIEHS campus 4. Able to fast for 8 hours prior to the visit where bronchoscopy occurs 5. Has a responsible party who is willing and able to attend Visit 2 and drive the participant away from the CRU after completion of Visit 2, if the participant elects to undergo conscious sedation 6. Genotype information available for relevant CYP2J2 and EPHX2 polymorphisms, which indicates: - Wild type with respect to EPHX2 K55R, EPHX2 R287Q, and CYP2J2*7; or - Homozygous for EPHX2 K55R (wild type for the other SNPs); or - Homozygous for EPHX2 R287Q (wild type for the other SNPs); or - Homozygous for CYP2J2*7 (wild type for the other SNPs) EXCLUSION CRITERIA: 1. --- K55R --- --- R287Q --- --- K55R ---


2 R287Q

- INCLUSION CRITERIA: 1. Age 18 to 65 years, inclusive (males and females) 2. Able to travel to the NIEHS CRU for required study visits 3. Able to present a valid government-issued form of identification for entry to the NIEHS campus 4. Able to fast for 8 hours prior to the visit where bronchoscopy occurs 5. Has a responsible party who is willing and able to attend Visit 2 and drive the participant away from the CRU after completion of Visit 2, if the participant elects to undergo conscious sedation 6. Genotype information available for relevant CYP2J2 and EPHX2 polymorphisms, which indicates: - Wild type with respect to EPHX2 K55R, EPHX2 R287Q, and CYP2J2*7; or - Homozygous for EPHX2 K55R (wild type for the other SNPs); or - Homozygous for EPHX2 R287Q (wild type for the other SNPs); or - Homozygous for CYP2J2*7 (wild type for the other SNPs) EXCLUSION CRITERIA: 1. --- K55R --- --- R287Q ---

- INCLUSION CRITERIA: 1. Age 18 to 65 years, inclusive (males and females) 2. Able to travel to the NIEHS CRU for required study visits 3. Able to present a valid government-issued form of identification for entry to the NIEHS campus 4. Able to fast for 8 hours prior to the visit where bronchoscopy occurs 5. Has a responsible party who is willing and able to attend Visit 2 and drive the participant away from the CRU after completion of Visit 2, if the participant elects to undergo conscious sedation 6. Genotype information available for relevant CYP2J2 and EPHX2 polymorphisms, which indicates: - Wild type with respect to EPHX2 K55R, EPHX2 R287Q, and CYP2J2*7; or - Homozygous for EPHX2 K55R (wild type for the other SNPs); or - Homozygous for EPHX2 R287Q (wild type for the other SNPs); or - Homozygous for CYP2J2*7 (wild type for the other SNPs) EXCLUSION CRITERIA: 1. --- K55R --- --- R287Q --- --- K55R --- --- R287Q ---

EXCL 4. Any food or fluids for 8 hours prior to the bronchoscopy - INCLUSION CRITERIA: 1. Age 18 to 65 years, inclusive (males and females) 2. Able to travel to the NIEHS CRU for required study visits 3. Able to present a valid government-issued form of identification for entry to the NIEHS campus 4. Able to fast for 8 hours prior to the visit where bronchoscopy occurs 5. Has a responsible party who is willing and able to attend Visit 2 and drive the participant away from the CRU after completion of Visit 2, if the participant elects to undergo conscious sedation 6. Genotype information available for relevant CYP2J2 and EPHX2 polymorphisms, which indicates: - Wild type with respect to EPHX2 K55R, EPHX2 R287Q, and CYP2J2*7; or - Homozygous for EPHX2 K55R (wild type for the other SNPs); or - Homozygous for EPHX2 R287Q (wild type for the other SNPs); or - Homozygous for CYP2J2*7 (wild type for the other SNPs) EXCLUSION CRITERIA: 1. --- K55R --- --- R287Q ---

EXCL 4. Any food or fluids for 8 hours prior to the bronchoscopy - INCLUSION CRITERIA: 1. Age 18 to 65 years, inclusive (males and females) 2. Able to travel to the NIEHS CRU for required study visits 3. Able to present a valid government-issued form of identification for entry to the NIEHS campus 4. Able to fast for 8 hours prior to the visit where bronchoscopy occurs 5. Has a responsible party who is willing and able to attend Visit 2 and drive the participant away from the CRU after completion of Visit 2, if the participant elects to undergo conscious sedation 6. Genotype information available for relevant CYP2J2 and EPHX2 polymorphisms, which indicates: - Wild type with respect to EPHX2 K55R, EPHX2 R287Q, and CYP2J2*7; or - Homozygous for EPHX2 K55R (wild type for the other SNPs); or - Homozygous for EPHX2 R287Q (wild type for the other SNPs); or - Homozygous for CYP2J2*7 (wild type for the other SNPs) EXCLUSION CRITERIA: 1. --- K55R --- --- R287Q --- --- K55R --- --- R287Q ---



HPO Nodes


HPO:
Pneumonia
Genes 117
CYBB NHLRC1 PIGN SLC25A24 CACNA1C RAG1 RAG2 EPM2A COL11A2 FMO3 SAMD9 RNF168 WAS OFD1 USB1 TNFSF12 SFTPC DOCK8 ORC6 SGCG POLA1 SLC35C1 CCDC114 NADK2 ACP5 GNPTAB CFTR NCF1 DDR2 ACTA1 KIAA0586 GAS8 SLC35A1 PEPD BLNK IRF8 CD55 GBA TCIRG1 CASP8 SRP54 NBN NCF2 CHD7 TNFRSF11A NSMCE3 ADA CR2 SELENON SP110 TERT ZAP70 GFI1 LEP ZBTB24 CFB RYR1 STAT3 TBC1D24 RNU4ATAC WDR19 IFNGR1 UNC119 JAK3 RMRP DNAI1 LIG4 TIMM8A KMT2D PANK2 ICOS SFTPA2 RNF125 ALMS1 CD19 MS4A1 EGFR DCLRE1C MTHFD1 TK2 CXCR4 NFIX IGHM KCNJ6 NFKB1 BTK IL21R NFKB2 SETBP1 TNFRSF13C ELANE TNFRSF13B SMARCD2 PRKCD CD79B CD81 CARD11 LTBP3 IGLL1 TAF1 LRBA PLG PLOD1 IL2RG CSPP1 KDM6A NIPBL CFAP410 AFF4 NOTCH3 IL7R MASP2 PNP DNMT3B PMM2 CYBA FOXP3