Biology subjects

Semenza, E. R.

Publications and source records attributed to Semenza, E. R..

5 recordsLinked to original sources

bioRxiv2026

Disruption of lamina-associated genome organization activates neuronal gene programs in H3.3K27M DIPG

Diffuse intrinsic pontine glioma (DIPG) is a fatal pediatric brain tumor frequently driven by a histone H3 mutation that substitutes lysine 27 with methionine (H3K27M). While H3K27M is known to cause a global depletion of the repressive histone mark H3K27me3, how this epigenetic disruption contributes to oncogenic transcriptional reprogramming remains incompletely understood. Here, we show that H3.3K27M DIPG cells exhibit widespread disruption of lamina-associated domain (LAD) organization across primary tumors and patient-derived cell lines. H3.3K27M was enriched at genomic regions that lost lamina association, which acquired increased H3K27ac and showed activation of neuronal and oncogenic gene programs. Notably, LAD loss was more strongly associated with transcriptional activation than H3K27me3 depletion, linking altered LAD organization to the transcriptional consequences of H3.3K27M. Finally, expression of H3.3K27M in human embryonic stem cell-derived neural precursor cells (NPCs) was sufficient to induce LAD remodeling, predominantly through loss of lamina association, leading to activation of neuronal gene programs. Together, these findings identify disruption of lamina-associated genome architecture as a key mechanism by which the H3.3K27M oncohistone drives oncogenic transcriptional reprogramming in DIPG.

genomics↗

bioRxiv2024

Spatial 3D genome organization controls the activity of bivalent chromatin during human neurogenesis

The nuclear genome is spatially organized into a three-dimensional (3D) architecture by physical association of large chromosomal domains with subnuclear compartments including the nuclear lamina at the radial periphery and nuclear speckles within the nucleoplasm1-5. However, how spatial genome architecture regulates human brain development has been overlooked owing to technical limitations. Here, we generate high-resolution maps of genomic interactions with the lamina and speckles in cells of the neurogenic lineage isolated from midgestational human cortex, uncovering an intimate association between subnuclear genome compartmentalization, chromatin state and transcription. During cortical neurogenesis, spatial genome organization is extensively remodeled, relocating hundreds of neuronal genes from the lamina to speckles including key neurodevelopmental genes bivalent for H3K27me3 and H3K4me3. At the lamina, bivalent genes have exceptionally low expression, and relocation to speckles enhances resolution of bivalent chromatin to H3K4me3 and increases transcription >7-fold. We further demonstrate that proximity to the nuclear periphery - not the presence of H3K27me3 - is the dominant factor in maintaining the lowly expressed, poised state of bivalent genes embedded in the lamina. In addition to uncovering a critical role of subnuclear genome compartmentalization in neurogenic transcriptional regulation, our results establish a new paradigm in which knowing the spatial location of a gene is necessary to understanding its epigenomic regulation.

neuroscience↗

bioRxiv2021

D-cysteine is an endogenous regulator of neural progenitor cell dynamics in the mammalian brain

D-amino acids are increasingly recognized as important signaling molecules in the mammalian central nervous system. However, the D-stereoisomer of the amino acid with the fastest in vitro spontaneous racemization rate, cysteine, has not been examined in mammals. Using chiral high-performance liquid chromatography and an stereospecific luciferase assay, we identify endogenous D-cysteine in the mammalian brain. We identify serine racemase (SR), which generates the NMDA glutamate receptor co-agonist D-serine, as a candidate biosynthetic enzyme for D-cysteine. Levels of D-cysteine are enriched over twentyfold in the embryonic mouse brain compared to the adult. D-cysteine reduces the proliferation of cultured mouse embryonic neural progenitor cells (NPCs) by approximately 50%, effects not shared with D-serine or L-cysteine. The antiproliferative effect of D-cysteine is mediated by the transcription factors FoxO1 and FoxO3a. The selective influence of D-cysteine on NPC proliferation is reflected in overgrowth and aberrant lamination of the cerebral cortex in neonatal SR knockout mice. Finally, we perform an unbiased screen for D-cysteine-binding proteins in NPCs by immunoprecipitation with a D-cysteine-specific antibody followed by mass spectrometry. This approach identifies myristoylated alanine-rich C-kinase substrate (MARCKS) as a putative D-cysteine-binding protein. Together, these results establish endogenous mammalian D-cysteine and implicate it as a physiologic regulator of NPC homeostasis in the developing brain.

neuroscience↗

bioRxiv2020

Biliverdin reductase bridges focal adhesion kinase to Src to modulate synaptic signaling

Synapses are complex bridges that connect discrete neurons into vast networks that send, receive, and encode diverse forms of information. However, they must remain dynamic in order to adapt to changing inputs. Here, we report that the enzyme biliverdin reductase (BVR) physically links together key molecules in focal adhesion signaling at the synapse. In challenging mice with a battery of neurocognitive tasks, we first discover that BVR null (BVR-/-) mice exhibit profound deficits in learning and memory. We uncover that these deficits may be explained by a loss of focal adhesion signaling that is both transcriptionally and biochemically disrupted in BVR-/- hippocampi. We learn that BVR mediates focal adhesion signaling by physically bridging the initiatory kinases FAK/Pyk2 to the effector kinase Src. Activated Src normally promotes synaptic plasticity by phosphorylating the N-methyl-D-aspartate (NMDA) receptor, but FAK/Pyk2 are unable to bind and stimulate Src without BVR. Src itself is a molecular hub upon which many signaling pathways converge in order to stimulate NMDA neurotransmission, positioning BVR at a prominent intersection of synaptic signaling.

neuroscience↗

bioRxiv2020

Cocaine receptor identified as BASP1

Cocaine is a behavioral stimulant with substantial abuse potential related to its positively rewarding actions 1,2. Cocaine inhibits the reuptake inactivation of neurotransmitters such as dopamine, serotonin, and norepinephrine at high nanomolar to low micromolar concentrations 2. There is evidence for substantially more potent influences of cocaine. For instance, Calligaro and Eldefrawi reported binding of [3H]cocaine to brain membranes with a dissociation constant of about 16 nM 3. At 10 nM concentration, cocaine elicits environmental place conditioning in planarians 4. Furthermore, 1nM cocaine enhances dopamine D2 receptor agonist-mediated signaling 5. Inhibition of amine reuptake by cocaine is substantially less potent than some of these high affinity actions. Thus, evidence for a specific, high affinity receptor for cocaine that mediates its behavioral actions has been lacking. We now report high affinity binding of cocaine to the membrane-associated brain acid soluble protein-1 (BASP1) with a Kd of 7 nM. Knocking down BASP1 in the striatum inhibits [3H]cocaine binding to striatal synaptosomes. Depletion of BASP1 in the nucleus accumbens diminishes locomotor stimulation, acquisition, and expression of locomotor sensitization to cocaine. Our findings indicate that BASP1 is a pharmacologically relevant receptor for cocaine and a putative therapeutic target for psychostimulant addiction.

pharmacology and toxicology↗