Biology subjects

Qin, N.

Publications and source records attributed to Qin, N..

8 recordsLinked to original sources

bioRxiv2026

CCR2 is a potential biomarker and therapeutic target in Group 3 medulloblastoma

Background: Medulloblastoma (MB) is the most common malignant pediatric brain tumor, classified into four molecular subgroups: WNT, SHH, Group 3, and Group 4. Among these, Group 3 MB displays the worst prognosis with highest rates of dissemination and the worst survival outcomes. While current therapies control the primary tumor, metastatic disease remains largely incurable underscoring the need for novel therapeutic options. The CCL2/CCR2 axis is a well establish metastases driver in systemic tumors through the promotion of angiogenesis and cell migration. Recently, this axis has been implicated in MB pathogenesis and dissemination, particularly in Group 3 tumors. Therefore, we hypothesize that CCR2 represents a therapeutically actionable driver in aggressive MB. Methods: The clinical relevance of CCR2 in MB was assessed using publicly available gene expression data from two independent datasets. CCR2 expression was further evaluated by immunohistochemistry on paired primary and recurrent/metastatic tumor samples to validate these findings. Functional studies using ONS76 and UW228 MB cells with CCR2 overexpression evaluated proliferation, migration and CCR2 downstream signaling. Orthotopic xenograft mouse models assessed CCR2 effect on tumor invasion, dissemination, and survival. An in-silico drug screening identified potential CCR2 antagonists that were tested in vitro and in vivo. Results: Gene expression data analysis across 1094 MB primary samples correlated high CCR2 expression with dissemination and reduced survival in Group 3 MB patients. In an independent MB patient cohort, CCR2 protein levels were increased in recurrent/metastatic tumors compared with paired primary tumors. CCR2 overexpression in vitro promoted cancer cell proliferation and migration. CCR2-driven MB mouse xenografts, exhibited an aggressive disease phenotype and decreased survival, resembling Group 3 tumors. CCR2 targeting with Cenicriviroc suppressed CCR2-mediated signaling and showed therapeutic efficacy against established MB tumors in vivo. Conclusions: CCR2 identifies aggressive Group 3 MB and represents a promising actionable target for therapy.

cancer biology↗

bioRxiv2025

Transcriptome and metabolome analyses reveal novel genetic targets for L-tryptophan overproduction in Corynebacterium glutamicum

Corynebacterium glutamicum is a promising microbial chassis for the industrial production of L-tryptophan, which has exhibited increasing demand due to its diverse applications and high market value. In previous work, we developed an L-tryptophan-overproducing C. glutamicum strain TR26 through multiple rounds of rational metabolic engineering. Here, comparative transcriptome and metabolome analyses were conducted between TR26 and its progenitor strain MB001 to reveal the underlying mechanisms and potential bottlenecks for L-tryptophan production in TR26. Furthermore, by systematically down- and up-regulating differentially expressed genes of interest, two novel genetic targets, glnK and sugR, were identified as being associated with L-tryptophan synthesis. Specifically, the repression of glnK and overexpression of sugR in strain TR26 increased the titer of L-tryptophan by 6.7% and 20.9%, respectively. Gene transcription profiling and intracellular metabolite analysis further suggested that the observed improvements in L-tryptophan synthesis could be attributed to optimized nitrogen transport and metabolism, efficient reallocation of cellular resources and enhanced supply of phosphoenolpyruvate (PEP). This study advances our understanding of the regulation mechanisms governing L-tryptophan synthesis in C. glutamicum and provides valuable insights for further optimization of industrial cell factories.

synthetic biology↗

bioRxiv2025

Acute chromatin decompaction stiffens the nucleus as revealed by nanopillar-induced nuclear deformation in cells

Chromatin architecture is critical in determining nuclear mechanics. Most studies focus on the mechanical rigidity conferred by chromatin compaction from densely packed heterochromatin, but less is known on how transient changes in chromatin decompaction state impinge on nucleus stiffness. Here, we used an array of vertically aligned nanopillars to study nuclear deformability in situ after chromatin decompaction in cells. The nucleus significantly stiffened within 4 hours of chromatin decompaction but softened at longer timescales. This acute nucleus stiffening was predominantly underlied by an increase in nucleus volume, nuclear import and partially enhanced by lamin protein recruitment to the nuclear periphery. The coupling between nucleus stiffening and acute chromatin decompaction was observed in cancer cell lines with lower malignancy (e.g. MCF7, PEO1, A549) but weakened in those with higher metastatic potential (e.g. MDA-MB-231, HEYA8, HT1080), which was found to be associated with the capacity to efficiently compact heterochromatin into foci that sustains nucleus deformability required for confined migration. Our work signals how a rapid chromatin remodeling is a physiologically relevant pathway to modulate nucleus mechanics and cell migration behavior. STATEMENT OF SIGNIFICANCEMany cell processes such as wound healing, immune activation and DNA damage repair require a decompact and accessible chromatin structure. Whether such short-term remodeling of the chromatin impacts nucleus mechanics and function is poorly defined. Using nanopillars that allow interrogation of nucleus rigidity within intact cells, we showed that contrary to conventional knowledge the nucleus becomes less deformable and more rigid when chromatin is acutely decompacted due to enhanced nuclear import and swelling of the nucleus. In cancer cells, the coupling of transient chromatin decompaction to nucleus rigidity is weakened and appears to be countered by heterochromatin formation and compaction. We demonstrate here how short-term chromatin remodeling can impact nucleus and cellular properties in a time-dependent and non-genetic manner.

bioengineering↗

bioRxiv2024

Linker histone H1-0 is a specific mediator of the repressive ETV6::RUNX1 transcriptional landscape

ETV6::RUNX1 is the most common oncogenic fusion in pediatric B cell precursor acute lymphoblastic leukemia (BCP-ALL). It induces a clinically silent preleukemic state that requires secondary mutations for progression to leukemia. However, the molecular mechanisms contributing to the characteristic quiescence of ETV6::RUNX1+ preleukemic cells remain elusive. Here, we detect factors involved in the preleukemic state by generating human induced pluripotent stem cell (hiPSC) models using CRISPR/Cas9 gene editing. We identified upregulation of linker histone H1-0 in our preleukemic models, which was preserved upon hematopoietic differentiation and transformation to BCP-ALL. ETV6::RUNX1 induces H1-0 promoter activity whereas depletion of H1-0 specifically inhibited ETV6::RUNX1 signature genes, indicating its role as a key mediator of the ETV6::RUNX1 transcriptome. Single-cell gene expression analysis revealed high H1-0 levels in quiescent cells during hematopoiesis and inverse correlation with transcriptional activity. Pharmacologically, H1-0 protein levels correspond to susceptibility of BCP-ALL towards histone deacetylase inhibitors (HDACi). Altogether, our study provides novel insights into ETV6::RUNX1-induced quiescence and suggests that further investigation into combinatorial treatment of BCP-ALL using the H1-0- inducing HDACi Quisinostat may be worthwhile.

cancer biology↗

bioRxiv2024

Transpirational water loss from flowers is low but unregulated

Flowers play a critical role in reproduction for most of the flowering plants, and maintaining flowers throughout their lifespan can require substantial resources, such as carbon and water. Increases in temperature and aridity due to climate change are shifting the atmospheric conditions experienced by flowers, potentially altering the costs of floral maintenance. However, little is known about floral physiology and the capacity of flowers to regulate water loss. Because many flowers have few, if any, stomata, flowers may not be able to curtail water loss when the atmospheric demand for water vapor is high. Here, we tested whether the surface conductance of of flower petals, tepals, and showy bracts responds dynamically to changes in the vapor pressure gradient driving water loss. We measure the responses of flower surface conductance (gs) to step changes in the vapor pressure gradient on nine species. Across species, gs was low among all species, and there was little, if any, response in gs to step changes in humidity. The lack of response in gs resulted in linear responses of transpirational water loss to variation in vapor pressure deficit. These results suggest that unusually hot, dry conditions could elevate water loss from flowers, leading to premature wilting and senescence, thereby shortening floral longevity.

plant biology↗

bioRxiv2022

UBE2C promotes leptomeningeal dissemination and is a therapeutic target in brain metastatic disease

Despite current improvements in systemic cancer treatment, brain metastases (BM) remain incurable, and there is an unmet clinical need for effective targeted therapies. Here, we sought common molecular events in brain metastatic disease. RNA sequencing of thirty human BM identified the upregulation of UBE2C, a gene that ensures the correct transition from metaphase to anaphase, across different primary tumor origins. Tissue microarray analysis of an independent BM patient cohort revealed that high expression of UBE2C was associated with decreased survival. UBE2C-driven orthotopic mouse models developed extensive leptomeningeal dissemination, likely due to increased migration and invasion. Early cancer treatment with dactolisib (dual PI3K/mTOR inhibitor) prevented the development of UBE2C-induced leptomeningeal metastases. Our findings reveal UBE2C as a key player in the development of metastatic brain disease and highlight PI3K/mTOR inhibition as a promising anticancer therapy to prevent late-stage metastatic brain cancer.

cancer biology↗

bioRxiv2020

Generalizability of "GWAS hits" in clinical populations: Lessons from childhood cancer survivors

With mounting interest in translating GWAS hits from large meta-analyses (meta-GWAS) in diverse clinical settings, evaluating their generalizability in target populations is crucial. Here we consider long-term survivors of childhood cancers from the St. Jude Lifetime Cohort Study and show the limited generalizability of 1,376 robust SNP associations reported in the general population across 12 complex anthropometric and cardiometabolic phenotypes (N=2,231; observed-to-expected replication ratio=0.68, P=2.4x10-9). An examination of five comparable phenotypes in a second independent cohort of survivors from the Childhood Cancer Survivor Study corroborated the overall limited generalizability of meta-GWAS hits to survivors (N=4,212, observed-to-expected replication ratio=0.53, P=1.1x10-16). Meta-GWAS hits were less likely to be replicated in survivors exposed to cancer therapies associated with phenotype risk. Examination of complementary DNA methylation data in a subset of survivors revealed that treatment-related methylation patterns at genomic sites linked to meta-GWAS hits may disrupt established genetic signals in survivors.

genetics↗

bioRxiv2019

Meiosis related cancer-testis genes correlate with tumor aneuploidy and immune infiltration in 21 cancer types

The meiosis stage of spermatogenesis and the aneuploidy generation in tumorigenesis are highly linked. Cancer-testis genes (CT genes) were specifically expressed in testis and cancers and may serve as the molecular basis of the shared features between spermatogenesis and tumorigenesis. In the present study, we integrated multi-omics data from bulk samples and cell lines, and single cell RNA-Seq data from testis and two tumors to systematically investigate the association between CT genes and aneuploidy. After ranking genes according to their association with aneuploidy level, we found that CT genes, especially CT genes specifically expressed in meiosis, showed a consistently positive correlation with aneuploidy and homologous recombination deficiency (HRD) level. Similar results were also found in the CT non-coding genes. Then, we constructed a regulatory network based on the single cell RNA-seq data and revealed that the gain of accelerator transcriptional factors (TFs) E2F7 and E2F8 and the loss of the stabilizer TFs RFX2 and NFYA aberrantly activated CT genes in the cancers and were associated with the increase of HRD level. Finally, we found that the association between CT genes and cytotoxic infiltrating lymphocytes can be influenced by the HRD level. In sum, our results revealed the evidence of pseudomeiotic functions of CT genes in the aneuploidy generation process in the cancer cells. The results may help illuminate the origin of aneuploidy in cancers and guide future immunotherapy targeting CT antigens.

genomics↗