Relating the gut metagenome and metatranscriptome to immunotherapy responses in melanoma patients.

Relating the gut metagenome and metatranscriptome to immunotherapy responses in melanoma patients.

Publication date: Oct 09, 2019

Recent evidence suggests that immunotherapy efficacy in melanoma is modulated by gut microbiota. Few studies have examined this phenomenon in humans, and none have incorporated metatranscriptomics, important for determining expression of metagenomic functions in the microbial community.

In melanoma patients undergoing immunotherapy, gut microbiome was characterized in pre-treatment stool using 16S rRNA gene and shotgun metagenome sequencing (n = 27). Transcriptional expression of metagenomic pathways was confirmed with metatranscriptome sequencing in a subset of 17. We examined associations of taxa and metagenomic pathways with progression-free survival (PFS) using 500 cD7 10-fold cross-validated elastic-net penalized Cox regression.

Higher microbial community richness was associated with longer PFS in 16S and shotgun data (p 

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Peters, B.A., Wilson, M., Moran, U., Pavlick, A., Izsak, A., Wechter, T., Weber, J.S., , Osman, and Ahn, J. Relating the gut metagenome and metatranscriptome to immunotherapy responses in melanoma patients. 24420. 2019 Genome Med (11):1.

Concepts Keywords
16S RRNA Immunotherapy efficacy melanoma
Cox Regression Immunotherapy
Cross Branches of biology
Gut Microbiota Microbiology
Immunotherapy Environmental microbiology
Melanoma Bacteriology
Metagenome Genomics
Metagenomic Metatranscriptomics
Metatranscriptomics Microbiota
Microbiome Human microbiota
Sequencing Metagenomics
Shotgun Gut flora
Taxa 16S ribosomal RNA

Semantics

Type Source Name
gene UNIPROT KCTD11
gene UNIPROT REN
drug DRUGBANK Lactic Acid
disease DOID Cancer
gene UNIPROT UBXN11
gene UNIPROT SOAT1
gene UNIPROT EAF2
drug DRUGBANK (S)-Des-Me-Ampa
pathway BSID Metabolic pathways
gene UNIPROT APPL1
gene UNIPROT PROC
disease MESH recurrence
gene UNIPROT CXCL2
drug DRUGBANK Ipilimumab
gene UNIPROT EXOG
gene UNIPROT BRAF
gene UNIPROT SIL1
gene UNIPROT PHB2
gene UNIPROT OCA2
drug DRUGBANK Proline
disease MESH **p
gene UNIPROT YME1L1
gene UNIPROT MAL
gene UNIPROT MRTFA
gene UNIPROT TIRAP
gene UNIPROT CD8A
disease MESH men
drug DRUGBANK Pectin
drug DRUGBANK Amino acids
disease DOID colitis
disease MESH colitis
gene UNIPROT RHO
disease MESH inflammation
drug DRUGBANK Folic Acid
drug DRUGBANK Hexocyclium
drug DRUGBANK Pembrolizumab
drug DRUGBANK Nivolumab
drug DRUGBANK Enterococcus faecium
gene UNIPROT RELA
drug DRUGBANK Hyaluronic acid
disease MESH tumors
gene UNIPROT MENT
drug DRUGBANK Trestolone
pathway BSID Isoleucine Biosynthesis
gene UNIPROT KLK6
pathway BSID Pectin degradation
drug DRUGBANK Rhamnose
drug DRUGBANK Phosphate ion
drug DRUGBANK Pyridoxal
drug DRUGBANK Pantothenic acid
drug DRUGBANK L-Isoleucine
gene UNIPROT MET
gene UNIPROT SLTM
drug DRUGBANK Methionine
gene UNIPROT DEPP1
gene UNIPROT GOPC
drug DRUGBANK Coenzyme M
gene UNIPROT MEA1
drug DRUGBANK Cysteamine
drug DRUGBANK Ademetionine
gene UNIPROT FBLN5
gene UNIPROT TNFRSF11A
gene UNIPROT ABCC8
disease MESH community
disease MESH metastases
gene UNIPROT PLXNA3
drug DRUGBANK Stavudine
gene UNIPROT SAGE1
gene UNIPROT PREP
gene UNIPROT PITRM1
gene UNIPROT DYNLL1
drug DRUGBANK Pirenzepine
gene UNIPROT BPNT1
gene UNIPROT PIP
drug DRUGBANK Amlodipine
drug DRUGBANK Water
gene UNIPROT KIT
disease MESH diagnosis
gene UNIPROT MS4A2
gene UNIPROT SCN8A
disease MESH death
gene UNIPROT NFKBIZ
gene UNIPROT TUBE1
gene UNIPROT EGR3
drug DRUGBANK Indoleacetic acid
gene UNIPROT TBPL1
pathway BSID Immune System
gene UNIPROT LARGE1
drug DRUGBANK Guanosine
gene UNIPROT CPOX
gene UNIPROT ELK3
gene UNIPROT EPHB1
gene UNIPROT SLC6A2
pathway BSID Melanoma
disease DOID melanoma
disease MESH melanoma

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