TY  - JOUR
A1  - Marquardt, André
A1  - Solimando, Antonio Giovanni
A1  - Kerscher, Alexander
A1  - Bittrich, Max
A1  - Kalogirou, Charis
A1  - Kübler, Hubert
A1  - Rosenwald, Andreas
A1  - Bargou, Ralf
A1  - Kollmannsberger, Philip
A1  - Schilling, Bastian
A1  - Meierjohann, Svenja
A1  - Krebs, Markus
T1  - Subgroup-Independent Mapping of Renal Cell Carcinoma — Machine Learning Reveals Prognostic Mitochondrial Gene Signature Beyond Histopathologic Boundaries
JF  - Frontiers in Oncology
N2  - Background: Renal cell carcinoma (RCC) is divided into three major histopathologic groups—clear cell (ccRCC), papillary (pRCC) and chromophobe RCC (chRCC). We performed a comprehensive re-analysis of publicly available RCC datasets from the TCGA (The Cancer Genome Atlas) database, thereby combining samples from all three subgroups, for an exploratory transcriptome profiling of RCC subgroups.
Materials and Methods: We used FPKM (fragments per kilobase per million) files derived from the ccRCC, pRCC and chRCC cohorts of the TCGA database, representing transcriptomic data of 891 patients. Using principal component analysis, we visualized datasets as t-SNE plot for cluster detection. Clusters were characterized by machine learning, resulting gene signatures were validated by correlation analyses in the TCGA dataset and three external datasets (ICGC RECA-EU, CPTAC-3-Kidney, and GSE157256).
Results: Many RCC samples co-clustered according to histopathology. However, a substantial number of samples clustered independently from histopathologic origin (mixed subgroup)—demonstrating divergence between histopathology and transcriptomic data. Further analyses of mixed subgroup via machine learning revealed a predominant mitochondrial gene signature—a trait previously known for chRCC—across all histopathologic subgroups. Additionally, ccRCC samples from mixed subgroup presented an inverse correlation of mitochondrial and angiogenesis-related genes in the TCGA and in three external validation cohorts. Moreover, mixed subgroup affiliation was associated with a highly significant shorter overall survival for patients with ccRCC—and a highly significant longer overall survival for chRCC patients.
Conclusions: Pan-RCC clustering according to RNA-sequencing data revealed a distinct histology-independent subgroup characterized by strengthened mitochondrial and weakened angiogenesis-related gene signatures. Moreover, affiliation to mixed subgroup went along with a significantly shorter overall survival for ccRCC and a longer overall survival for chRCC patients. Further research could offer a therapy stratification by specifically addressing the mitochondrial metabolism of such tumors and its microenvironment.
KW  - kidney cancer
KW  - pan-RCC
KW  - machine learning
KW  - mitochondrial DNA
KW  - mtDNA
KW  - mTOR
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-232107
SN  - 2234-943X
VL  - 11
ER  - 
TY  - JOUR
A1  - Jessen, Christina
A1  - Kreß, Julia K. C.
A1  - Baluapuri, Apoorva
A1  - Hufnagel, Anita
A1  - Schmitz, Werner
A1  - Kneitz, Susanne
A1  - Roth, Sabine
A1  - Marquardt, André
A1  - Appenzeller, Silke
A1  - Ade, Casten P.
A1  - Glutsch, Valerie
A1  - Wobser, Marion
A1  - Friedmann-Angeli, José Pedro
A1  - Mosteo, Laura
A1  - Goding, Colin R.
A1  - Schilling, Bastian
A1  - Geissinger, Eva
A1  - Wolf, Elmar
A1  - Meierjohann, Svenja
T1  - The transcription factor NRF2 enhances melanoma malignancy by blocking differentiation and inducing COX2 expression
JF  - Oncogene
N2  - The transcription factor NRF2 is the major mediator of oxidative stress responses and is closely connected to therapy resistance in tumors harboring activating mutations in the NRF2 pathway. In melanoma, such mutations are rare, and it is unclear to what extent melanomas rely on NRF2. Here we show that NRF2 suppresses the activity of the melanocyte lineage marker MITF in melanoma, thereby reducing the expression of pigmentation markers. Intriguingly, we furthermore identified NRF2 as key regulator of immune-modulating genes, linking oxidative stress with the induction of cyclooxygenase 2 (COX2) in an ATF4-dependent manner. COX2 is critical for the secretion of prostaglandin E2 and was strongly induced by H\(_2\)O\(_2\) or TNFα only in presence of NRF2. Induction of MITF and depletion of COX2 and PGE2 were also observed in NRF2-deleted melanoma cells in vivo. Furthermore, genes corresponding to the innate immune response such as RSAD2 and IFIH1 were strongly elevated in absence of NRF2 and coincided with immune evasion parameters in human melanoma datasets. Even in vitro, NRF2 activation or prostaglandin E2 supplementation blunted the induction of the innate immune response in melanoma cells. Transcriptome analyses from lung adenocarcinomas indicate that the observed link between NRF2 and the innate immune response is not restricted to melanoma.
KW  - NRF2
KW  - melanoma malignancy
KW  - COX2 expression
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-235064
SN  - 0950-9232
VL  - 39
ER  -