added gut microbiome publication

bib/references.bib

@@ -3611,4 +3611,20 @@ @article{robrahn_2022
 sciwheel-projects = {Thesis},
 abstract = {The hypoxia-inducible transcription factor 1 ({HIF}-1) has been shown to enhance microbial killing and to ameliorate the course of bacterial infections. While the impact of {HIF}-1 on inflammatory diseases of the gut has been studied intensively, its function in bacterial infections of the gastrointestinal tract remains largely elusive. With the help of a publicly available gene expression data set, we could infer significant activation of {HIF}-1 after oral infection of mice with Salmonella Typhimurium. Immunohistochemistry and western blot analysis confirmed marked {HIF}-1\alpha protein stabilization, especially in the intestinal epithelium. This prompted us to analyze conditional Hif1a-deficient mice to examine cell type-specific functions of {HIF}-1 in this model. Our results demonstrate enhanced non-canonical induction of {HIF}-1 activity upon Salmonella infection in the intestinal epithelium as well as in macrophages. Surprisingly, Hif1a deletion in intestinal epithelial cells did not impact on inflammatory gene expression, bacterial spread or disease outcome. In contrast, Hif1a deletion in myeloid cells enhanced intestinal Cxcl2 expression and reduced the cecal Salmonella load. In vitro, {HIF}-1\alpha-deficient macrophages showed an overall impaired transcription of {mRNA} encoding pro-inflammatory factors, however, intracellular survival of Salmonella was not impacted by {HIF}-1\alpha deficiency.}
 }
+@article{schneider_2022,
+title = {Imbalanced gut microbiota fuels hepatocellular carcinoma development by shaping the hepatic inflammatory microenvironment},
+author = {Schneider, Kai Markus and Mohs, Antje and Gui, Wenfang and Galvez, Eric J. C. and Candels, Lena Susanna and Hoenicke, Lisa and Muthukumarasamy, Uthayakumar and Holland, Christian H. and Elfers, Carsten and Kilic, Konrad and Schneider, Carolin Victoria and Schierwagen, Robert and Strnad, Pavel and Wirtz, Theresa H. and Marschall, Hanns-Ulrich and Latz, Eicke and Lelouvier, Benjamin and Saez-Rodriguez, Julio and de Vos, Willem and Strowig, Till and Trebicka, Jonel and Trautwein, Christian},
+pages = {3964},
+url = {https://www.nature.com/articles/s41467-022-31312-5},
+year = {2022},
+month = {dec},
+urldate = {2022-07-08},
+journal = {Nature Communications},
+volume = {13},
+number = {1},
+issn = {2041-1723},
+doi = {10.1038/s41467-022-31312-5},
+sciwheel-projects = {Thesis},
+abstract = {Hepatocellular carcinoma ({HCC}) is a leading cause of cancer-related deaths worldwide, and therapeutic options for advanced {HCC} are limited. Here, we observe that intestinal dysbiosis affects antitumor immune surveillance and drives liver disease progression towards cancer. Dysbiotic microbiota, as seen in Nlrp6−/− mice, induces a Toll-like receptor 4 dependent expansion of hepatic monocytic myeloid-derived suppressor cells ({mMDSC}) and suppression of T-cell abundance. This phenotype is transmissible via fecal microbiota transfer and reversible upon antibiotic treatment, pointing to the high plasticity of the tumor microenvironment. While loss of Akkermansia muciniphila correlates with {mMDSC} abundance, its reintroduction restores intestinal barrier function and strongly reduces liver inflammation and fibrosis. Cirrhosis patients display increased bacterial abundance in hepatic tissue, which induces pronounced transcriptional changes, including activation of fibro-inflammatory pathways as well as circuits mediating cancer immunosuppression. This study demonstrates that gut microbiota closely shapes the hepatic inflammatory microenvironment opening approaches for cancer prevention and therapy.}
+}
 

prelims/preface.Rmd

@@ -86,13 +86,12 @@ Taus P, Dugourd A, **Holland CH**, RO Ramirez Flores, Saez-Rodriguez J.
 from omics data". _Bioinformatics Advances._ [-@badiaimompel_2022]. DOI: 
 [10.1093/bioadv/vbac016](https://doi.org/10.1093/bioadv/vbac016).
 
-11. Schneider KM^\*^, Mohs A^\*^, Gui W, Galvez EJC, Candels LS, Hoenicke L, 
-Muthukumarasamy U, **Holland CH**, Elfers C, Kilic K, Schneider CV, Strnad P, 
-Wirtz TH, Marschall HU, Latz E, Lelouvier B, Saez-Rodriguez J, de Vos W, 
-Strowig T, Trebicka J, Trautwein C. "Imbalanced gut microbiota fuels HCC 
-development by shaping the hepatic inflammatory microenvironment." 
-_Under review at Nature Communications_. 2022. 
-DOI: [xxx](xxx).
+11. Schneider KM^\*^, Mohs A^\*^, Gui W, Gálvez EJC, Candels LS, Hoenicke L, 
+Muthukumarasamy U, **Holland CH**, Elfers C, Kilic K, Schneider CV, Schierwagen R, 
+Strnad P, Wirtz TH, Marschall HU, Latz E, Lelouvier B, Saez-Rodriguez J, 
+de Vos W, Strowig T, Trebicka J and Trautwein C. "Imbalanced gut microbiota 
+fuels hepatocellular carcinoma development by shaping the hepatic inflammatory 
+microenvironment." _Nature Communications_. [-@schneider_2022]. DOI: [10.1038/s41467-022-31312-5](https://doi.org/10.1038/s41467-022-31312-5).
 
 ^\*^_Shared first authorship_ 
 ^#^_Shared senior authorship_