Biology subjects

Kim, Y. S.

Publications and source records attributed to Kim, Y. S..

At least 19 recordsLinked to original sources

bioRxiv2026

Dynamic Schlafen 11 (SLFN11) expression revealed by single-cell RNA sequencing of clonal human cancer cells

Schlafen 11 (SLFN11) is a key determinant of sensitivity to DNA-damaging therapies in multiple cancers including leukemia, Ewing sarcoma, head and neck cancers, mesothelioma and small cell lung cancer (SCLC). Here, utilizing immunofluorescence microscopy and single-cell RNA sequencing we characterized SLFN11 expression across eight different human cancer cell lines and found cell-to-cell heterogenous expression both at the protein and RNA levels. Gene set enrichment and pathway analyses show that SLFN11 is coexpressed with a distinct stress-response state and enhanced genome maintenance programs while being inversely correlated with protein translation pathways. Publicly available single-cell RNA-sequencing datasets of human SCLC tumors confirmed the heterogeneous distribution of SLFN11 expression and confirmed its association with replication-related transcriptional programs. These findings indicate that heterogeneous SLFN11 expression reflects dynamic regulation at the single-cell level. They also underscore the limitations of bulk proteomic and transcriptome profiling and point to a potential reservoir of intrinsic chemotherapy resistance.

cancer biology↗

bioRxiv2026

Cascaded Nano-ring Dialyzer for Continuous Regenerative Peritoneal Dialysis

End-stage kidney disease (ESKD) requires lifelong kidney replacement therapy, yet conventional hemodialysis and peritoneal dialysis remain limited by intermittent treatment, restricted mobility, and repeated dialysate exchange. Here, we developed a continuous regenerative peritoneal dialysis platform based on a nano-ring-assisted nanoelectrokinetic dialyzer for portable artificial kidney applications. We first identified key geometric and electrokinetic parameters governing the removal performance of nano-ring meshes, including mesh dimension, nano-ring coating thickness, the number of cascaded nano-rings, and the relative orientation between fluid flow and the applied electric field. We then developed a single nano-ring dialyzer operating at 1.33 mL/min and scaled the treatment capacity to approximately 10 mL min/min through parallel integration of multiple modules. In a canine model, the closed-loop system achieved approximately 10 % reduction in circulating uremic toxin levels during continuous treatment. We further improved the biocompatibility of the regenerated dialysate by integrating plate-type electrodes, activated carbon, bicarbonate buffering, and UV-C treatment. In an unanesthetized canine model, the improved system sustained continuous toxin removal for 4 h while major hepatic and inflammatory markers remained within recoverable ranges. These results demonstrate that cascaded nano-ring enables continuous dialysate regeneration with scalable throughput, reduced dependence on fresh dialysate, and in vivo control of uremic toxins, providing a technological foundation for portable or wearable regenerative peritoneal dialysis systems.

bioengineering↗

bioRxiv2026

TR-107, a novel mitochondrial ClpP agonist, induces robust antitumor activity against preclinical models of adrenocortical carcinoma

AbstractAdrenocortical carcinoma (ACC) is a rare and highly aggressive endocrine malignancy originating from the adrenal cortex with limited effective treatment options. The underlying pathophysiology of ACC is uniquely characterized by abnormal steroid production and increased metabolic activity, highlighting the critical role of mitochondria in adrenal steroid hormone biosynthesis and tumor metabolism. In this study, we investigated the therapeutic potential of TR-107, a novel and highly selective small-molecule agonist targeting the mitochondrial protease ClpP. Pharmacologic hyperactivation of ClpP disrupts mitochondrial proteostasis and bioenergetics and has shown promising antitumor activity in various preclinical models. Our results demonstrated that TR-107 induces potent dose-dependent cytotoxic effects at nanomolar concentrations in ACC cell lines NCI-H295R and mACC3 as well as short-term ACC patient-derived organoid (PDO) models, markedly reducing cell viability and confluency in vitro. Metabolic analyses revealed that TR-107 significantly impaired oxygen consumption, indicating a disruption of oxidative phosphorylation and substantial attenuation of basal cellular respiration. Mechanistic studies showed dose-dependent increases in reactive oxygen species (ROS) levels and upregulation of proteins involved in mediating the ferroptotic rheostat. Pharmacokinetic assessment uncovered that TR-107 was not a substrate of the ABCB1 (MDR1/P-glycoprotein) efflux transporter, suggesting potential to overcome common multidrug resistance mechanisms. Given the importance of IGF-2 signaling in ACC, we further explored the combinatorial effects of TR-107 with IGF-1 receptor (IGF-1R) inhibitors and discovered that co-treatment produced synergistic reductions in cell viability across NCI-H295R, mACC3, and ACC PDOs. Collectively, these findings support the potential of mitochondrial ClpP hyperactivation as a promising therapeutic strategy for ACC and demonstrate that TR-107 exhibits significant antitumor activity as a monotherapy or in combination with IGF-1R inhibitors. These findings provide a strong rationale for advancing ClpP agonists into clinical development for the management of ACC.

cancer biology↗

bioRxiv2026

Patient-Derived Liver Cancer Organoids Reflect Tumor Biology and Their Growth Phenotype Correlates with Clinical Outcomes

Liver cancer remains a major global health burden with high mortality and limited treatment response prediction tools. Patient-derived cancer organoids have emerged as promising preclinical models that recapitulate tumor heterogeneity; however, the biological significance of morphological diversity within established organoids remains poorly characterized in hepatocellular carcinoma (HCC). In this exploratory study, we investigated whether distinct organoid growth phenotypes reflect underlying tumor biology and correlate with clinical outcomes. We established liver cancer organoids from resected tumor tissues of 27 patients and analyzed their clinical, histological, and genomic characteristics. Organoids were classified morphologically into cystic and solid types. Whole exome sequencing (WES) was conducted on six matched tumor-organoid pairs to assess genomic fidelity. Associations between organoid establishment, growth characteristics, and clinical parameters were statistically evaluated. Progression-free survival (PFS) was analyzed using the Kaplan-Meier method and univariate Cox proportional hazards regression. Organoids were successfully established in 13 of 27 cases (48.1%). Solid-type organoids were significantly associated with shorter PFS compared to cystic types (HR = 13.91; p = 0.0039, log-rank test). Organoid establishment was more frequent in older patients (>70 years), those with HBV infection, and tumors with positive {beta}-catenin expression. WES analysis demonstrated high concordance in somatic mutation profiles and variant allele frequency distributions between tissues and corresponding organoids. In univariate Cox regression, organoid growth pattern (solid vs. cystic) showed a significant association with PFS within this exploratory cohort (p = 0.0207). Patient-derived liver cancer organoids preserved the genomic and histopathological features of the original tumors. Notably, solid morphology was associated with shorter PFS, suggesting that organoid growth phenotype may serve as a supplementary indicator of tumor biological behavior in HCC. Given the modest cohort size and the absence of multivariate analysis, these preliminary findings should be interpreted with caution and warrant further large-scale validation.

cancer biology↗

bioRxiv2026

Vagal dopaminergic afferents link interoception to trigeminal pain modulation

The vagus nerve conveys interoceptive information, yet how specific vagal sensory afferents regulate pain remains unclear. Here, we tested whether vagus nerve stimulation (VNS) modulates temporomandibular disorder (TMD)-related pain. In a mouse model of TMD, auricular VNS (aVNS) attenuated temporomandibular joint (TMJ) pain behaviors and suppressed sensitization of trigeminal nociceptors. We identified a subset of vagal sensory afferents with dopaminergic features that was sufficient to mediate these effects, as selective activation of these afferents recapitulated the analgesic actions of aVNS. These findings highlight an underappreciated peripheral interoceptive pathway and provide a mechanistic framework for targeted neuromodulation in chronic craniofacial pain.

neuroscience↗

bioRxiv2025

Evidence for age-related vulnerability in dopamine-glutamate projections to the lateral entorhinal cortex

The lateral entorhinal cortex (LEC) supports novelty detection and episodic memory and is selectively vulnerable to aging. Dopamine signals novelty in LEC, but how aging alters this input is unclear. Using intersectional viral strategies to distinguish ventral tegmental area (VTA) dopamine neurons with or without glutamate co-release, we find that co-releasing neurons are a minority ([~]30%) in the VTA, yet provide [~]93% of the dopaminergic projections to LEC. In aged mice, dopamine-glutamate labeling in VTA and LEC decreases [~]80%, whereas pan-dopaminergic labeling of LEC axons remains, consistent with functional silencing rather than degeneration. In LEC dopaminergic axons, dopamine synthesis is reduced while glutamate vesicular packaging is relatively spared. Optogenetic stimulation combined with a dopamine sensor reveals diminished dopamine release at high frequencies, when synthesis demand is greatest. These findings identify selective vulnerability of dopamine-glutamate neurons as a cell- and circuit-specific mechanism that weakens dopamine signaling within memory circuits.

neuroscience↗

bioRxiv2025

Progressive Loss of Astrocytic AIBP Expression during Alzheimer's Disease Pathology

Astrocytes and microglia play crucial roles in mediating neuroinflammation during Alzheimers disease (AD) progression. ApoA-I binding protein (APOA1BP, also known as AIBP/NAXE) attenuates neuroinflammation by blocking amyloid {beta}-induced TLR4 inflammaraft formation and oxidative stress. Apoa1bp knockout in APP/PS1 mice exacerbates microgliosis, increases amyloid plaque burden, neuronal cell loss, and reduces survival at 6 months. Although APOA1BP mRNA is ubiquitously expressed in humans, its cell-type-specific distribution in the brain remains unclear. To examine AIBP protein expression in the human brain, we performed immunohistochemistry on hippocampal sections from postmortem brain specimens from subjects aged 75-96 of both sexes. Using GFAP and IBA1 to label astrocytes and microglia, respectively, we found that AIBP protein was highly expressed in astrocytes, but not in microglia. Stratification of subjects by Braak stage (I-II, III-IV, V-VI) revealed a progressive decline in astrocytic AIBP expression with advancing AD pathology. Meta-analysis of RNA-seq profiling indicated enriched Apoa1bp expression in adult mouse astrocytes. Systemic Apoa1bp knockout in the APP/PS1 mouse exacerbated astrogliosis. These findings demonstrate that AIBP is predominantly expressed in astrocytes and its expression declines with AD progression, suggesting a potential role for AIBP in astrocyte-mediated neuroprotection and AD pathogenesis.

neuroscience↗

bioRxiv2025

Multiscale 3D whole joint cellular and molecular mapping dissects the relationship between structure and pain

Understanding musculoskeletal joints from a 3D multiscale perspective, from molecular to anatomical levels, is essential for resolving the confounding relationships between structure and pain, elucidating the intricate mechanisms regulating joint health and diseases, and developing new treatment strategies. Here, we introduce a musculoskeletal joint immunostaining and clearing (MUSIC) method specifically designed to overcome key challenges of immunostaining and optical clearing of intact joints. Coupled with large-field light sheet microscopy, our approach enables 3D high-resolution, microscale neurovascular mapping within the context of whole-joint anatomy without the need for image coregistration across various joints, including temporomandibular joints, knees, and spines, and multiple species, including mouse, rat, and pig. Our findings reveal 3D heterogeneous distributions of neurovascular networks and previously uncharacterized neurovascular pathways within joints. Using the proteoglycan 4 knockout (Prg4-/-) mouse model of joint degeneration, we identified significant alterations in joint-wide neurovascular architecture, highlighting neurovascular changes along degenerative processes. Furthermore, in a traumatic joint injury mouse model, we observed long-lasting pain behavior and a time-course 3D neurovascular remodeling preceding detectable joint morphological change, bridging microscale alterations with potential pain mechanisms. This platform offers a powerful tool for multiscale 3D analysis, enabling new insights into joint pathophysiology and intricate interplay among joint tissues.

bioengineering↗

bioRxiv2025

Neuroligin-3 interaction with CSPG4 regulates normal and malignant glial precursors through PIEZO1

Glioma pathophysiology is robustly regulated by interactions with neurons. Key to these interactions is the role of neuroligin-3 (NLGN3), a synaptic adhesion molecule shed in response to neuronal activity1-5 that functions as a paracrine factor crucial for glioma growth. Here, we elucidate the mechanistic pathway whereby shed NLGN3 interacts with glioma and their normal glial counterpart. NLGN3 interacts with Chondroitin Sulfate Proteoglycan 4 (CSPG4) on both glioma and healthy oligodendrocyte precursor cells (OPCs)6-9, facilitating CSPG4 shedding by ADAM10. NLGN3-CSPG4 interactions and consequent shedding alter membrane tension, thereby activating PIEZO1 mechanosensitive channels and causing membrane depolarization. The NLGN3-CSPG4-PIEZO1 axis maintains OPCs in an undifferentiated, stem-like state and promotes glioma proliferation, underscoring important functional roles for the NLGN3-CSPG4-PIEZO1 axis in both healthy and malignant glial precursors.

neuroscience↗

bioRxiv2025

Two parallel lineage-committed progenitors contribute to the developing brain

The hindbrain is a life-sustaining brain region. In one model, a common neural progenitor generates all brain regions. Here our studies of mouse embryos and human pluripotent stem cells (hPSCs) support a different model: two parallel brain progenitors emerge simultaneously during gastrulation, anterior neural ectoderm (forebrain/midbrain progenitor) and posterior neural ectoderm (hindbrain progenitor). Not only are they lineage-committed to respectively form forebrain/midbrain vs. hindbrain in vitro, but they also have diverging chromatin landscapes foreshadowing future forebrain/midbrain vs. hindbrain identities. Leveraging these differences, we differentiated hPSCs into hindbrain rhombomere 5/6-specific motor neurons, hitherto difficult to generate in vitro. We postulate the brain is a composite organ emanating from two lineage-restricted progenitors; these dual progenitors may be evolutionarily conserved across 550 million years from hemichordates to mammals.

developmental biology↗

bioRxiv2025

Coevolutionary cycling in allele frequencies and the evolution of virulence

Coevolutionary cycling in allele frequencies due to negative frequency-dependent selection--sometimes referred to as Red Queen Dynamics--is a key potential outcome of host-parasite coevolution. While many theoretical studies have focused on understanding the consequences of coevolutionary cycling for the evolution of sex and recombination, little is known about the impact of coevolutionary cycling on the evolution of other life history traits. It is therefore currently unknown how coevolutionary cycling in allele frequencies affects the evolution of key disease characteristics, such as virulence. Here, we combine population genetic and quantitative genetic approaches to theoretically determine the impacts of coevolutionary cycling in allele frequencies on the evolution of virulence in a free-living parasite. By varying the level of genetic specificity required for infection while controlling for the average infection rate, we induce coevolutionary cycles and examine their effects on virulence evolution. We show that coevolutionary cycling does indeed have a strong impact on virulence evolution, with more specific infection genetics and higher allelic diversity generally driving larger and more rapid cycles in allele frequencies, leading to selection for higher virulence. Our research provides new fundamental insights into the relationship between coevolutionary cycling and the evolution of virulence.

evolutionary biology↗

bioRxiv2024

Identification of DLK1, a Notch ligand, as an immunotherapeutic target and regulator of tumor cell plasticity and chemoresistance in adrenocortical carcinoma

Immunotherapeutic targeting of cell surface proteins is an increasingly effective cancer therapy. However, given the limited number of current targets, the identification of new surface proteins, particularly those with biological importance, is critical. Here, we uncover delta-like non-canonical Notch ligand 1 (DLK1) as a cell surface protein with limited normal tissue expression and high expression in multiple refractory adult metastatic cancers including small cell lung cancer (SCLC) and adrenocortical carcinoma (ACC), a rare cancer with few effective therapies. In ACC, ADCT-701, a DLK1 targeting antibody-drug conjugate (ADC), shows potent in vitro activity among established cell lines and a new cohort of patient-derived organoids as well as robust in vivo anti-tumor responses in cell line-derived and patient-derived xenografts. However, ADCT-701 efficacy is overall limited in ACC due to high expression and activity of the drug efflux protein ABCB1 (MDR1, P-glycoprotein). In contrast, ADCT-701 is extremely potent and induces complete responses in DLK1+ ACC and SCLC in vivo models with low or no ABCB1 expression. Genetic deletion of DLK1 in ACC dramatically downregulates ABCB1 and increases ADC payload and chemotherapy sensitivity through NOTCH1-mediated adrenocortical de-differentiation. Single cell RNA-seq of ACC metastatic tumors reveals significantly decreased adrenocortical differentiation in DLK low or negative cells compared to DLK1 positive cells. This works identifies DLK1 as a novel immunotherapeutic target that regulates tumor cell plasticity and chemoresistance in ACC. Our data support targeting DLK1 with an ADC in ACC and neuroendocrine neoplasms in an active first-in-human phase I clinical trial (NCT06041516).

cancer biology↗

bioRxiv2024

Cholinergic Neuronal Activity Promotes Diffuse Midline Glioma Growth through Muscarinic Signaling

Neuronal activity promotes the proliferation of healthy oligodendrocyte precursor cells (OPC) and their malignant counterparts, gliomas. Many gliomas arise from and closely resemble oligodendroglial lineage precursors, including diffuse midline glioma (DMG), a cancer affecting midline structures such as the thalamus, brainstem and spinal cord. In DMG, glutamatergic and GABAergic neuronal activity promotes progression through both paracrine signaling and through bona-fide neuron-to-glioma synapses. However, the putative roles of other neuronal subpopulations - especially neuromodulatory neurons located in the brainstem that project to long-range target sites in midline anatomical locations where DMGs arise - remain largely unexplored. Here, we demonstrate that the activity of cholinergic midbrain neurons modulates both healthy OPC and malignant DMG proliferation in a circuit-specific manner at sites of long-range cholinergic projections. Optogenetic stimulation of the cholinergic pedunculopontine nucleus (PPN) promotes glioma growth in pons, while stimulation of the laterodorsal tegmentum nucleus (LDT) facilitates proliferation in thalamus, consistent with the predominant projection patterns of each cholinergic midbrain nucleus. Reciprocal signaling was evident, as increased activity of cholinergic neurons in the PPN and LDT was observed in pontine DMG-bearing mice. In co-culture, hiPSC-derived cholinergic neurons form neuron-to-glioma networks with DMG cells and robustly promote proliferation. Single-cell RNA sequencing analyses revealed prominent expression of the muscarinic receptor genes CHRM1 and CHRM3 in primary patient DMG samples, particularly enriched in the OPC-like tumor subpopulation. Acetylcholine, the neurotransmitter cholinergic neurons release, exerts a direct effect on DMG tumor cells, promoting increased proliferation and invasion through muscarinic receptors. Pharmacological blockade of M1 and M3 acetylcholine receptors abolished the activity-regulated increase in DMG proliferation in cholinergic neuron-glioma co-culture and in vivo. Taken together, these findings demonstrate that midbrain cholinergic neuron long-range projections to midline structures promote activity-dependent DMG growth through M1 and M3 cholinergic receptors, mirroring a parallel proliferative effect on healthy OPCs. HIGHLIGHTSO_LIActivity of midbrain cholinergic neuron long-range projections increases proliferation of both healthy oligodendrocyte precursor cells (OPC) and malignant diffuse midline glioma (DMG) cells. C_LIO_LIOptogenetic stimulation of cholinergic midbrain nuclei promotes growth in thalamic and pontine glioma in a circuit-dependent manner. C_LIO_LIReciprocally, DMG cells increase cholinergic neuronal activity in cholinergic midbrain nuclei. C_LIO_LIThe muscarinic receptors CHRM1 and CHRM3 are identified as therapeutic targets in DMG. C_LI

neuroscience↗

bioRxiv2024

Cyclic Electromagnetic DNA Simulation (CEDS) can enhance the Functions of Anticancer miR-26a-5p and miR-126-5p in RAW 264.7 cells

Since cyclic electromagnetic DNA simulation (CEDS) was found to increase the hybridization potential of double-stranded DNA (dsDNA) and affect the functions of plasmid DNA (1), in this study, Dodecagonal CEDS was applied to RAW 264.7 cells to target anticancer miRNAs, miR-26a-5p and miR-126-5p, at 20-25 Gauss for 20 min during cell culture, followed by cytological observation, quantitative polymerase chain reaction (qPCR), and immunoprecipitation-based high-performance liquid chromatography (IP-HPLC). Both of miR-26a-5p*-CEDS and miR-126-5p*-CEDS induced significant decrease in cell number, and strong immunoreaction of c-caspase 3 in the remaining cells compared to oncogenic miR-21-5p*-CEDS and untreated control. In qPCR results, miR-26a-5p*-CEDS and miR-126-5p*-CEDS markedly increased the expression of target primary and mature miRNAs. IP-HPLC analysis showed that both miR-26a-5p*-CEDS and miR-126-5p*-CEDS induced potent anticancer effect on RAW 264.7 cells by suppressing RAS signaling, proliferation-growth-cytodifferentiation signaling axis, and angiogenesis-survival-oncogenesis-chronic inflammation axis compared to the untreated control and the positive control performed with non-specific poly-A 12A*-CEDS. MiR-26a-5p*-CEDS increased miRNA biogenesis and ER stress signaling more than miR-126-5p*-CEDS, while miR-126-5p*-CEDS increased NFkB signaling-immunity-apoptosis signaling axis more than miR-26a-5p*-CEDS. Therefore, it is proposed that the sequential treatment of miR-26a-5p*-CEDS and miR-126-5p*-CEDS may give a synergistic anticancer effect on RAW 264.7 cells. It is postulated that CEDS using a miRNA sequence can stimulate hybridization between miRNA and target mRNA and also increase the expression of target miRNA, and subsequently decrease the expression of miRNA target proteins, resulting in the alteration of protein signaling pathways in cells.

molecular biology↗

bioRxiv2024

Cyclic Electromagnetic DNA Simulation (CEDS) targeting Telomere Repeat Sequence can enhance Anticancer Effect, while CEDS targeting Canonical E-box Sequence induce Oncogenic Effect in Cells

Cyclic electromagnetic DNA simulation (CEDS) was used in the previous study (1) to stimulate the base pair polarities of oligo-dsDNAs, plasmid DNAs, and miRNAs. This study applied dodecagonal CEDS to target telomere repeat sequence (TTAGGG*-CEDS), canonical E-box sequence (CACGTG*-CEDS) in genomic DNA of RAW 264.7 cells and KB cells. During cell culture, CEDS was performed at 20-25 Gauss for 20 min, and followed by cytological observation and immunoprecipitation high-performance liquid chromatography (IP-HPLC) using 350 antisera. KB cells treated with TTAGGG*-CEDS showed a significant decrease in cell density and metachromasia in toluidine blue staining compared to untreated control, while only a slight decrease in cell density and metachromasia was observed by telomere mutation sequence, TTTGGG*-CEDS. Conversely, CACGTG*-CEDS induced almost no change in cell density, cell number, metachromasia in toluidine blue staining compared to random sequence*-CEDS (2(ACGT)*-CEDS) and untreated control. IP-HPLC results showed that TTAGGG*-CEDS induced a potent anticancer effect by downregulating RAS, oncogenesis, and telomere signaling, and activating NFkB signaling-p53-and FAS-mediated apoptosis-innate and cellular immunity signaling axis compared to untreated control and positive control performed with nonspecific poly-A 12A*-CEDS. In contrast, CACGTG*-CEDS exhibited a significant oncogenic effect by enhancing of RAS and NFkB signaling and resulting oncogenesis-glycolysis-chronic inflammation signaling axis. Therefore, it is suggested that CEDS is able to target DNA motif sequences in genomic DNA, and that TTAGGG*-CEDS and CACGTG*-CEDS are favorable candidates to regulate important genes involved in oncogenesis, inflammation, apoptosis, etc.

molecular biology↗

bioRxiv2024

Cyclic Electromagnetic DNA Simulation (CEDS) influences the functions of Long Oligo-dsDNAs and Plasmid DNAs

Hydrogen bonding magnetic resonance-based cyclic electromagnetic DNA simulation (CEDS) was proposed to play a role in regulating the function of target short oligo-dsDNA in the previous study, as the decagonal CEDS was found to induce the hybridization and conformational changes of target short oligo-dsDNA in a sequence-specific manner. This study applied dodecagonal CEDS on 24 bps oligo-dsDNAs and plasmid DNAs. CEDS can affect 24 bps oligo-dsDNAs intercalated by ethidium bromide (EtBr) or condensed by spermidine by stimulating them to partially remove EtBr or spermidine, respectively, depending on CEDS time. When the multiple cloning site of pBluescript was digested with eight restriction endonucleases (RE) under CEDS separately, all RE digests were enhanced depending on CEDS time compared to the negative and positive controls both in EtBr intercalated electrophoresis and HPLC analysis. In vitro RNA transcription from human VEGFA, vWF or elafin cDNA subcloned into pBluescript DNA was increased by CEDS using each promoter sequence depending on CEDS time compared to negative and positive controls. In addition, the productions of green fluorescent protein (GFP) and {beta}-galactosidase were enhanced by CEDS using each promoter sequence from pE-GFP-1 and pBluescript, respectively. In the survival assay using E. coli transfected with pBluescript containing ampicillin resistance gene, the number of surviving E. coli was increased by CEDS using a T3 promoter sequence compared to the control during two days of culture, while it was decreased by CEDS using a T7 promoter, non-specific 12A, 6(TA), or mutation-2 (GG18,19CC) T3 promoter sequence. Therefore, it is suggested that dodecagonal CEDS can target 24 bps oligo-dsDNAs and promoter sequences of plasmid DNAs in a sequence-specific manner and influence their functions.

molecular biology↗

bioRxiv2024

Hydrogen Bonding Magnetic Resonance (HBMR)-based Cyclic Electromagnetic DNA Simulation (CEDS) can affect DNA Hybridization and Conformation

The proton magnetic resonance is commonly used in MRI machines with a strong magnetic field of over 1 T, while this study hypothesized that a weak magnetic field below 0.01 T can induce the proton magnetic resonance in hydrogen bonds of double-stranded DNA (dsDNA). This study found the hydrogen bonding magnetic resonance (HBMR) in dsDNA can modulate the conformations and functions of dsDNAs (1). Decagonal or dodecagonal cyclic electromagnetic DNA simulation (CEDS) was designed to target three-dimensional structures of randomly oriented dsDNAs with about 25% efficiency. This study found that the most effective magnetic exposure times for inducing an electric potential in A-T and G-C base pairs were 280 and 480 msec, respectively. Decagonal CEDS using a target sequence at 20-25 Gauss for 30 min was able to induce sequence-specific hybridization of target short oligo-dsDNAs in 0.005M NaCl solution and their unique conformation in 0.1M NaCl solution. There was a tendency that Pyu oligo-dsDNAs showed more hybridization and unique conformational changes by CEDS using a target sequence than Puy oligo-dsDNAs. This CEDS effect on Pyu ds6(2C2A) increased with CEDS time up to 90 min and gradually decreased to about half (51.8%) of the increase at 240 min resting time. CEDS influenced the oligo-dsDNAs to increase their infrared (IR) absorbance at approximately 3700-2800 cm-1 band compared to the positive and negative controls, which was more dominant in Pyu oligo-dsDNAs than in Puy oligo-dsDNAs. Therefore, it is postulated that HBMR-based CEDS using a weak magnetic field can increase the hybridization potential of oligo-dsDNAs and subsequently lead to unique DNA conformation required for the initiation of various DNA functions. Therefore, it is suggested that decagonal CEDS play a role in regulating the function of target short oligo-dsDNA.

molecular biology↗

bioRxiv2024

Cyclic Electromagnetic DNA Simulation (CEDS) can regulate the Functions of Oncogenesis-related miRNAs and DNA Motifs: Protein Signaling Pathways in RAW 264.7 Cells detected by IP-HPLC Analysis

Based on the hydrogen bonding magnetic resonance (HBMR) in double-stranded DNAs (dsDNAs) exhibiting unique base pair polarities, Cyclic Electromagnetic DNA Simulation (CEDS)1 was designed to target nine miRNAs and four protein binding site sequences, which are known to have an anti-oncogenic or oncogenic role in cells. RAW 264.7 cells were cultured and treated with CEDS at 20-25 Gauss in a 5% CO2 and 37 incubator for 20 min. Besides the cytological observation, the expressions of murine miRNAs and proteins were assessed by quantitative polymerase chain reaction (qPCR) and immunoprecipitation high-performance liquid chromatography (IP-HPLC) using 350 antisera, respectively. The results demonstrated that CEDS was found to increase the number of the corresponding mature and primary miRNAs and influenced the protein signaling in cells. For example, miR-34a-5p*-CEDS was able to downregulate 59 out of 43 target proteins (72.9%), and attenuated RAS-NFkB signaling axis, which subsequently led to the inactivation of proliferation-related signaling axis, protection-ER stress-survival signaling axis, telomere-glycolysis-fibrosis signaling axis, and FAS- and PARP-mediated apoptosis signaling axis. Conversely, miR-34a-5p*-CEDS activated the p53/Rb/E2F1-SHH/PTCH/GLI-Notch/Jagged proliferation signaling axis, epigenetic modification-RAS-p53 associated apoptosis signaling axis, and oncogenesis-senescence-innate immunity-chronic inflammation signaling axis. Among nine CEDS targeting mature miRNAs, miR-150-5p*-CEDSs exhibited a potent anti-oncogenic effect on RAW 264.7 cells, while miR-34a-5p*-, miR-181a-5p*-, miR-216a-5p*-, miR-365a-3p*-, and miR-655-3p*-CEDSs exhibited a dual effect, inducing both anti-oncogenic and oncogenic effects. Conversely, miR-155-5p*-CEDS appears to induce marked oncogenic effect, rather than anti-oncogenic effect. Among four CEDS targeting protein binding site sequences, p53 binding site sequence AGACATGCCT*-CEDS induced an oncogenic effect by upregulating proliferation, telomere, and oncogenesis signaling, while concomitantly inducing an anti-oncogenic effect by downregulating RAS and NFkB signaling and upregulating p53- and PARP-mediated apoptosis. Canonical E2Fs binding site sequence TTTC(C/G)CGC*-CEDS facilitated an oncogenic effect by enhancing RAS and NFkB signaling, resulting in the upregulation of proliferation, telomere, and senescence signaling. Consequently, it was found that CEDS using a miRNA or protein binding site sequence impacted the protein signaling in RAW 264.7 cells in a sequence-specific manner. It is therefore proposed that CEDS can target miRNAs and DNA motifs, influencing their hybridization and conformation, and subsequently regulate the protein signaling in the cells.

molecular biology↗