Biology subjects

Dou, L.

Publications and source records attributed to Dou, L..

3 recordsLinked to original sources

bioRxiv2025

Deciphering of single-cell chromatin accessibility and transcriptome reveals the discrepancy for ex vivo human erythropoiesis

BackgroundErythroid cells can be generated from hematopoietic stem and progenitor cells (HSPC) derived from various sources; however, few studies decode ex vivo human erythropoiesis for the discrepancies at single-cell multi-omics resolution and uncover the underlying restraints for erythrocyte regeneration. ResultsWe deciphered ex vivo human erythropoiesis at two differentiation states from three sources at single-cell chromatin accessibility and transcriptomes level. We identified detrimental myeloid differentiation tendencies during early differentiation. These tendencies were linked to low glutamine activity in cord blood- and iPSC-derived erythropoiesis. The erythroid progenitor differentiation is restricted by cell cycle and hypoxia signaling deficiencies, which are pronounced in the iPSC-derived erythropoiesis. We delineated the erythroid differentiation trajectory of various ex vivo erythropoiesis systems, and revealed a distinct roadmap from HSC to orthochromatic erythroblast with unprecedented resolution. The integrative analysis of single-cell chromatin accessibility and transcriptome across developmental stages uncovered a dynamic coordination, and highlighted the pivotal role of chromatin accessibility and associated enhancers in regulating ex vivo erythropoiesis. Cell-cell communications in the ex vivo erythropoiesis system were not as well established as those in the BM, suggesting that modulating cell-cell communication signals in distinct ex vivo erythropoiesis system may facilitate erythrocyte regeneration. ConclusionsThis study comprehensively characterized the discrepancies and constraints in ex vivo human erythropoiesis at single-cell multi-omics resolution, offering novel strategies to overcome these constraints. These insights are critical for advancing functional erythrocyte generation and have significant implications for clinical applications.

developmental biology↗

bioRxiv2024

Targeting the 3D genome by anthracyclines for chemotherapeutic effects

The chromatin is folded into three-dimensional (3D) structures, and aberrant 3D chromatin folding has been implicated in cancer. We performed ATAC-seq and TOP2A ChIP-seq to assess the potential effects of various anthracycline drugs on the chromatin architecture. We found that specific anthracycline variants selectively disrupt chromatin looping anchors by interfering with CTCF binding, suggesting an additional therapeutic mechanism of anthracycline drugs targeting the 3D genome. Hi-C experiments in K562 cells treated with anthracycline drugs revealed widespread disruption of 3D chromatin organization, including altered long-range regulation at the Myc locus. Furthermore, AML patients treated with anthracycline drugs exhibited changes in chromatin structures near possible looping anchors, which were associated with distinct clinical outcomes. Together, our findings indicate that anthracycline drugs function as potent and selective epigenomic modulators, with the capacity to further target the 3D genome to exert anticancer effects, highlighting their potential for personalized therapy in tumors with aberrant 3D chromatin architecture. SignificanceChromatin structure plays a crucial role in regulating gene expression and maintaining cellular function. Aberrant chromatin 3D organization is a common feature in cancer. In this study, we investigate how anthracycline chemotherapy affects chromatin architecture using state-of-the-art genomic profiling techniques, including ATAC-seq, TOP2A ChIP-seq, CTCF ChIP-seq, and Hi-C. We show that certain anthracycline variants disrupt chromatin looping by interfering with CTCF binding, thereby altering the spatial genome organization. This disruption leads to changes in the regulation of associated genes, as exemplified by the Myc locus, and is associated with distinct clinical outcomes in AML patients. These findings highlight the potential of anthracycline drugs as therapeutics that target both the epigenome and 3D chromatin architecture, a promising strategy in personalized therapy.

cancer biology↗

bioRxiv2024

Engineered Migrasomes: A Robust, Thermally Stable Vaccination Platform

The increasing ability of pathogens and tumor cells to evade immune detection underscores the urgent need for novel vaccine platforms leveraging diverse biological mechanisms. Additionally, logistical challenges associated with cold-chain transportation significantly limit vaccine accessibility, especially in resource-limited regions. Recently, we identified migrasomes, specialized organelles generated during cell migration, which are inherently stable and enriched with immune-modulating molecules. To address the low yield of natural migrasomes, we engineered migrasome-like vesicles (eMigrasomes) using hypotonic shock combined with cytoskeletal disruption to enhance vesicle formation. The biogenesis of eMigrasomes relies on the core migrasome machinery, faithfully recapitulating the biophysical attributes of native migrasomes while significantly improving production efficiency. We demonstrate that eMigrasomes loaded with a model antigen elicit potent antibody responses and maintain structural integrity and immunogenic potential at room temperature. Furthermore, eMigrasomes displaying the SARS-CoV-2 Spike protein induce robust humoral immune responses, providing effective protection against viral infection. Our findings highlight the potential of utilizing migrasome biology and hypotonic shock-driven vesicle generation as an innovative, stable, and broadly accessible vaccine platform.

cell biology↗