Ömer H. Yilmaz

Genetic dissection of DNA damage response pathways reveals divergent modulation of PD-1 blockade response in colorectal cancer

This study identifies DDR gene alterations that modulate PD-1 blockade response in MSS colorectal cancer, showing that some defects enhance immunotherapy while others reduce benefit.

Pancreatic cancer-associated organ dysfunction promotes muscle autophagy and contributes to peripheral tissue wasting

This study shows pancreatic cancer disrupts normal pancreatic function, leading to systemic nutrient depletion and muscle wasting, with autophagy in muscle playing a key role in nutrient redistribution to support tumor growth.

Chronic metabolic stress drives developmental programs and loss of tissue functions in non-transformed liver that mirror tumor states and stratify survival

The paper shows chronic metabolic stress in liver cells drives developmental programs and functional loss, mirroring tumor states and predicting poor cancer survival.

Polyamines sustain epithelial regeneration in aged intestines by modulating protein homeostasis

This study identifies polyamines as key regulators of epithelial regeneration in aged intestines, showing they enhance protein homeostasis and restore regenerative capacity through dietary manipulation.

Programmable conjugative CRISPR interference targeting genotoxin in the gut

This paper develops a CRISPRi system to suppress colibactin production in pks E. coli, reducing DNA damage and tumorigenesis in mice.

The Wnt/APC destruction complex targets SREBP2 in a β-catenin-independent pathway to control cholesterol metabolism

This study identifies SREBP2 as a direct APC-AXIN1 substrate degraded via a β-catenin-independent pathway, regulating cholesterol metabolism and providing a target for APC-mutant colorectal cancer.

Leveraging WNT Hyperactivation to Kill Colorectal Cancer While Rejuvenating Healthy Intestine.

This paper identifies a therapeutic strategy using WNT hyperactivation to kill colorectal cancer cells while rejuvenating healthy intestinal tissue.

Dietary cysteine enhances intestinal stemness via CD8+ T cell-derived IL-22

This study shows that dietary cysteine improves intestinal stem cell repair through IL-22 from CD8+ T cells.

PPARγ downregulation in colonic CD8+ T cells results in epithelial barrier disruption in people with HIV on antiretroviral therapy

This study shows that PPARγ downregulation in colonic CD8+ T cells of people with HIV on ART leads to epithelial barrier disruption by promoting lipid uptake and apoptosis.

Sideroflexins enable mitochondrial transport and metabolism of neutral amino acids

The paper identifies sideroflexins as mitochondrial transporters for neutral amino acids and shows functional overlap among paralogues.

Dietary lipids, not ketone body metabolites, influence intestinal tumorigenesis in a ketogenic diet

This study shows that dietary lipids, not ketone body metabolites, drive intestinal tumorigenesis in ketogenic diets, highlighting the role of fatty acid oxidation.

Genetically encoded fluorescent reporter for polyamines

This paper introduces a genetically encoded fluorescent reporter for real-time measurement of polyamine levels in single cells and identifies a link between mitochondrial respiration and polyamine import in Parkinson's disease.

Clonal memory of colitis accumulates and promotes tumor growth

The paper shows that colitis leaves an epigenetic memory in colonic stem cells that promotes tumor growth by enhancing regenerative gene programs and AP-1 activity.

Intestinal stem cells enhance local mucosal immunity through apoptotic body phagocytosis

This study shows that intestinal stem cells (ISCs) enhance local mucosal immunity by engulfing apoptotic bodies, which leads to increased T cell activity through TNF signaling.

Optimizing single-cell RNA sequencing methods for human colon biopsies: droplet-based vs. picowell-based platforms

This study compares droplet-based and picowell-based single-cell RNA sequencing platforms for human colon biopsies, finding differences in cell recovery, typeability, and gene expression consistency.