Richard P. Koche

This paper shows that timed WNT pulses can specify distinct neural domains in human pluripotent stem cells, enabling the generation of specific neuron and progenitor types.

This study develops a method to detect minimal residual disease in neuroblastoma using ecDNA breakpoints, achieving high sensitivity and specificity in bone marrow samples.

Loss of extracellular matrix-integrin signaling switches off YAP/TEAD and lets prostate adenocarcinoma organoids turn neuroendocrine; LATS inhibition reverses it, and combined YAP, NOTCH and AR inhibition fully reprograms them.

The paper identifies transient squamous-state excursions in cancer cells as a source of APOBEC3A mutagenesis, linking it to lineage-state plasticity rather than persistent inflammation.

The paper identifies a TIP60 coactivator switch in neuroendocrine prostate cancer, revealing a therapeutic target for MYC-driven diseases.

This study shows that mitochondrial ATP production, induced by D-α-hydroxybutyrate, promotes T cell differentiation and function by regulating chromatin accessibility and gene expression.

This study shows that TET2 and TP53 mutations work together to promote leukemic transformation by altering inflammatory responses and chemotherapy tolerance in hematopoietic stem cells.

This study shows p53 enables lipid headgroup recycling during senescence by increasing phosphoethanolamine supply through autophagy and lysosomal catabolism, revealing a metabolic vulnerability in p53-activated cells.

This study shows adult Nestin+ cerebellar astroglia have limited regenerative potential compared to neonatal cells, with ATAC-seq revealing developmental gene silencing as a key factor.

This study shows that metastatic site influences the function of driver genes like SMAD4 in pancreatic cancer, with organ-specific epigenetic states affecting tumor growth.

This study identifies SP5 and SP8 as transcription factors that drive primary cilia formation through genetic and transcriptomic analyses in mouse embryos.

This study shows mechanical confinement drives phenotype switching in melanoma via chromatin remodeling mediated by HMGB2.

The paper identifies L1CAM-driven planar cell polarity signaling as a mechanism promoting SOX2+ metastatic progenitors in lung adenocarcinoma.

This study shows that loss of MHC Class II in BRAF-mutant anaplastic thyroid cancers leads to resistance to MAPK inhibitors by reducing CD4+ T-cell activation.

This study shows that reactive oxygen species (ROS) increase in the neonatal cerebellum after injury, and reducing ROS impairs regenerative processes.

This paper introduces a proximity-tagging method called PCP to map chromatin architecture in yeast, revealing nucleosome organization and long-range interactions.

The paper shows that TAD hierarchy restricts LTR activation, and its loss in cancer allows LTRs to act as alternative promoters, driving oncogene activation and transcriptional diversity.

The paper identifies a sequential transcriptional cascade in the thalamo-cortical circuit that enables memory stabilization over time.

This study shows that ecDNA mis-segregation leads to micronuclei formation, reduced oncogene transcription, and improved patient survival in neuroblastoma.

This study shows that cohesin mutations alter chromatin accessibility, enhancing FLI1-Menin interaction and promoting leukemogenesis through therapeutic vulnerabilities.

The paper identifies genetic variants that influence DNA methylation stability and imprint deregulation in naive pluripotent stem cells across different mouse strains.

This study identifies a nucleosome switch that primes Hepatitis B Virus infection by driving X gene transcription and shows that CBL137 inhibits this process.

The paper shows that ecDNA inheritance is ensured through mitotic transcription and chromosomal tethering via BRD4 and PVT1, preventing cytosolic mis-segregation and chromosomal integration.

This study identifies a pathogenic subpopulation of glioma-associated macrophages (mGAMs) linked to glioma progression through GRN analysis and functional validation.

This study shows aging reduces lung stem cell function and suppresses lung cancer by inducing iron deficiency through the NUPR1-lipocalin-2 pathway.

This study identifies RXR signaling as a mediator of lipid metabolism in leptomeningeal metastatic cancer cells, revealing a potential therapeutic target.

This study identifies TET2-mutant clonal hematopoiesis in thyroid cancer microenvironments and shows that TGFβ signaling from these macrophages mediates resistance to BRAF/MEK inhibition, with TGFβ inhibition restoring sensitivity.

This paper shows that mutant IDH disrupts p53 target gene regulation by altering chromatin states, disabling tumor suppression, and that this effect can be reversed with IDH inhibition.

This paper establishes a pluripotent stem cell platform using genetically diverse mouse lines to study the impact of natural genetic variation on development and gene regulation.

Chromatin regulators including EZH2, EHMT1/2, and DOT1L establish an epigenetic barrier in human neural progenitors that poises maturation genes and sets the protracted pace of cortical neuron maturation.