Biology subjects

Park, B. J.

Publications and source records attributed to Park, B. J..

4 recordsLinked to original sources

bioRxiv2025

Deciphering Tumor Microenvironment Dynamics in Tumorigenesis and Lymph Node Metastasis of Esophageal Squamous Cell Carcinoma using Single-Cell RNA Sequencing

Esophageal squamous cell carcinoma (ESCC) exhibits profound inter-tissue heterogeneity, yet how immune and stromal ecosystems diverge between primary tumors and metastatic lymph nodes remains poorly understood. Here, we generated a single-cell atlas of 344,790 cells and paired T cell receptor profiles from primary tumor mucosa, adjacent mucosa, non-metastatic lymph nodes, and metastatic lymph nodes from 18 patients with treatment-naive ESCC. We identify compartment-specific immune and stromal architectures that shape distinct antitumor responses and suppressive programs. Primary tumors were characterized by marked enrichment of regulatory T cells (TREG) and activated dendritic cells coordinated through CTLA4-associated circuits, accompanied by accelerated CD8+ T cell differentiation toward intermediate and terminal exhaustion with loss of cytotoxicity. In contrast, metastatic lymph nodes preserved substantial pools of pre-exhausted CD8+ T cells with retained effector potential and strong clonal connectivity to the primary tumor, suggesting sustained antigen-driven trafficking. However, these reinvigoration-competent populations were embedded within a niche dominated by TREM2high macrophages that delivered SPP1-dependent suppressive signals to exhausted and regulatory T cells. Stromal lineages also displayed niche-specific specialization: tumor mucosa contained chemokine-rich inflammatory fibroblasts, whereas metastatic lymph nodes upregulated extracellular matrix remodeling programs. Together, our findings demonstrate that ESCC progression is governed by anatomically distinct exhaustion trajectories, clonal behaviors, stromal states, and suppressive circuits. This framework provides mechanistic insight into why lymph node response is a key determinant of clinical outcome and highlights the need for site-tailored immunomodulation strategies that target TREG-mediated suppression in primary tumors and TREM2high macrophage programs in metastatic nodes.

cancer biology↗

bioRxiv2025

CUT&Tag Identifies Repetitive Genomic Loci that are Excluded from ChIP Assays

Determining the genomic localization of chromatin features is an essential aspect of investigating gene expression control, and ChIP-Seq has long been the gold standard technique for interrogating chromatin landscapes. Recently, the development of alternative methods, such as CUT&Tag, have provided researchers with alternative strategies that eliminate the need for chromatin purification, and allow for in situ investigation of histone modifications and chromatin bound factors. Mindful of technical differences, we set out to investigate whether distinct chromatin modifications were equally compatible with these different chromatin interrogation techniques. We found that ChIP-Seq and CUT&Tag performed similarly for modifications known to reside at gene regulatory regions, such as promoters and enhancers, but major differences were observed when we assessed enrichment over heterochromatin-associated loci. Unlike ChIP-Seq, CUT&Tag detects robust levels of H3K9me3 at a substantial number of repetitive elements, with especially high sensitivity over evolutionarily young retrotransposons. IAPEz-int elements for example, exhibited underrepresentation in mouse ChIP-Seq datasets but strong enrichment using CUT&Tag. Additionally, we identified several euchromatin-associated proteins that co-purify with repetitive loci and are similarly depleted when applying ChIP-based methods. This study reveals that our current knowledge of chromatin states across the heterochromatin portions of the mammalian genome is extensively incomplete, largely due to limitations of ChIP-Seq. We also demonstrate that newer in situ chromatin fragmentation-based techniques, such as CUT&Tag and CUT&RUN, are more suitable for studying chromatin modifications over repetitive elements and retrotransposons. HighlightsIn situ fragmentation overcomes biases produced by ChIP-Seq. Heterochromatic regions of the genome are lost to the insoluble pellet during ChIP-Seq. CUT&Tag allows for mapping chromatin features at young repetitive elements. Euchromatin-associated regulatory factors co-purify with insoluble heterochromatin.

genomics↗

bioRxiv2023

Integrator-mediated clustering of poised RNA polymerase II synchronizes histone transcription

Numerous components of the transcription machinery, including RNA polymerase II (Pol II), accumulate in high-concentration clusters at promoters. Whether these clusters assemble on demand during transcription or constitute regulatory units remains unclear. Examining the Drosophila histone locus--where histone genes are transcribed exclusively during S phase--we unexpectedly found large clusters containing non-chromatin-bound Pol II and elongation factors outside S phase. When transcription is activated during S phase, P-TEFb drives accelerated turnover of cluster components. Dispersion of clusters through depletion of the Integrator complex endonuclease module causes histone transcription to have a diminished S-phase peak and instead occur ectopically throughout the cell cycle. We propose that clusters act as gatekeeping hubs by maintaining a poised machinery pool, thereby restricting gene activation to defined temporal windows.

genetics↗

bioRxiv2023

Activity-induced gene expression in the human brain

Direct electrical stimulation (eSTIM) is widely used clinically, from neurosurgical mapping to therapeutic interventions for neurological and neuropsychiatric disorders1-10. Despite over a century of application, its molecular and cellular underpinnings remain unknown. Here, using state-of-the-art single-nuclei multiomic profiling, we map changes in cell-type-specific gene expression and chromatin accessibility in vivo in the human cortex following eSTIM of neurosurgery patients. eSTIM impacts a network of cells that extends beyond excitatory neurons to include inhibitory neurons, astrocytes, oligodendrocytes and microglia. We observed an upregulation of canonical immediate-early genes (IEGs: FOS, NPAS4, EGR4) in excitatory and inhibitory neurons and induction of cytokine-related genes CCL3 and CCL4 in microglia. The cross-species conservation of this gene signature, together with our examination of a cohort of both epilepsy and cancer patients, underscores the fundamental role of these changes in stimulation-driven plasticity while controlling for disease and environmental confounds. Our study of changes in chromatin accessibility reveals a common code that involves a cell-type specific signature of transcription factor binding motifs for members of the EGR family. By addressing these previously unexplored questions about activity-induced gene expression in vivo in the human brain, our findings challenge the long-standing neuron-centric view of eSTIM, highlighting the broader role of non-neuronal cells, including microglia, in mediating the impact of brain stimulation.

neuroscience↗