Biology subjects

Lee, S.

Publications and source records attributed to Lee, S..

At least 325 records · Page 18Linked to original sources

bioRxiv2024

Inactivation of a non-canonical gp130 signaling arm attenuates chronic systemic inflammation and multimorbidity induced by a high-fat diet.

Interleukin-6 (IL-6) is a major pro-inflammatory cytokine for which the levels in plasma demonstrate a robust correlation with age and body mass index (BMI) as part of the senescence-associated secretory phenotype. IL-6 cytokines also play a crucial role in metabolic homeostasis and regenerative processes, primarily via the canonical STAT3 pathway. Thus, selective modulation of IL-6 signaling may offer a unique opportunity for therapeutic interventions. Recently, we discovered that a non-canonical signaling pathway downstream of tyrosine (Y) 814 within the intracellular domain of gp130, the IL-6 co-receptor, is responsible for the recruitment and activation of SRC family of kinases (SFK). Mice with constitutive genetic inactivation of gp130 Y814 (F814 mice) show accelerated resolution of inflammatory response and superior regenerative outcomes in skin wound healing and posttraumatic models of osteoarthritis. The current study was designed to explore if selective genetic or pharmacological inhibition of the non-canonical gp130-Y814/SFK signaling reduces systemic chronic inflammation and multimorbidity in a high-fat diet (HFD)-induced model of accelerated aging. F814 mice showed significantly reduced inflammatory response to HFD in adipose and liver tissue, with significantly reduced levels of systemic inflammation compared to wild type mice. F814 mice were also protected from HFD-induced bone loss and cartilage degeneration. Pharmacological inhibition of gp130-Y814/SFK in mice on HFD mirrored the effects observed in F814 mice on HFD; furthermore, this pharmacological treatment also demonstrated a marked increase in physical activity levels and protective effects against inflammation-associated suppression of neurogenesis in the brain tissue compared to the control group. These findings suggest that selective inhibition of SFK signaling downstream of gp130 receptor represents a promising strategy to alleviate systemic chronic inflammation. Increased degenerative changes and tissue senescence are inevitable in obese and aged organisms, but we demonstrated that the systemic response and inflammation-associated multi-morbidity can be therapeutically mitigated.

cell biology↗

bioRxiv2024

The Evolutionary Origins and Ancestral Features of Septins

Septins are a family of membrane-associated cytoskeletal GTPases that play crucial roles in various cellular processes, such as cell division, phagocytosis, and organelle fission. Despite their importance, the evolutionary origins and ancestral function of septins remain unclear. In opisthokonts, septins form five distinct groups of orthologs, with subunits from multiple groups assembling into heteropolymers, thus supporting their diverse molecular functions. Recent studies have revealed that septins are also conserved in algae and protists, indicating an ancient origin from the last eukaryotic common ancestor. However, the phylogenetic relationships among septins across eukaryotes remained unclear. Here, we expanded the list of non-opisthokont septins, including previously unrecognized septins from rhodophyte red algae and glaucophyte algae. Constructing a rooted phylogenetic tree of 254 total septins, we observed a bifurcation between the major non-opisthokont and opisthokont septin clades. Within the non-opisthokont septins, we identified three major subclades: Group 6 representing chlorophyte green algae (6A mostly for species with single septins, 6B for species with multiple septins), Group 7 representing algae in chlorophytes, heterokonts, haptophytes, chrysophytes, and rhodophytes, and Group 8 representing ciliates. Glaucophyte and some ciliate septins formed orphan lineages in-between all other septins and the outgroup. Combining ancestral-sequence reconstruction and AlphaFold predictions, we tracked the structural evolution of septins across eukaryotes. In the GTPase domain, we identified a conserved GAP-like arginine finger within the G-interface of at least one septin in most algal and ciliate species. This residue is required for homodimerization of the single Chlamydomonas septin, and its loss coincided with septin duplication events in various lineages. The loss of the arginine finger is often accompanied by the emergence of the 0 helix, a known NC-interface interaction motif, potentially signifying the diversification of septin-septin interaction mechanisms from homo-dimerization to hetero-oligomerization. Lastly, we found amphipathic helices in all septin groups, suggesting that curvature-sensing is an ancestral trait of septin proteins. Coiled-coil domains were also broadly distributed, while transmembrane domains were found in some septins in Group 6A and 7. In summary, this study advances our understanding of septin distribution and phylogenetic groupings, shedding light on their ancestral features, potential function, and early evolution.

cell biology↗

bioRxiv2024

Phospholipase C β4 promotes RANKL-dependent osteoclastogenesis by interacting with MKK3 and p38 MAPK

Phospholipase C beta (PLC{beta}) exerts diverse biological processes, including inflammatory responses and neurogenesis; however, its role in bone cell function is largely unknown. Among the PLC{beta} isoforms ({beta}1-{beta}4), we found that PLC{beta}4 was most highly upregulated during osteoclastogenesis. In this study, we used global knockout and osteoclast lineage-specific PLC{beta}4 conditional knockout (LysM-PLC{beta}4-/-) mice and demonstrated that PLC{beta}4 is a crucial regulator of receptor activator of nuclear factor {kappa}B ligand (RANKL)-induced osteoclast differentiation. Deletion of PLC{beta}4, both globally and in the osteoclast lineage, resulted in a significant reduction in osteoclast formation and the downregulation of osteoclast marker genes. Importantly, LysM-PLC{beta}4-/- male mice exhibited greater bone mass and a lower number of osteoclasts in vivo than their wild-type littermates, without altering osteoblast function. Mechanistically, we found that PLC{beta}4 forms a complex with p38 mitogen-activated protein kinase (MAPK) and MAPK kinase 3 (MKK3) in response to RANKL, thereby modulating p38 activation. An immunofluorescence assay further confirmed the colocalization of PLC{beta}4 with p38 after RANKL exposure. Moreover, p38 activation rescued the impaired osteoclast formation and restored the reduced p38 phosphorylation due to PLC{beta}4 deficiency. Thus, our findings reveal that PLC{beta}4 controls osteoclastogenesis via the RANKL-dependent MKK3-p38 MAPK pathway, and PLC{beta}4 may be a potential therapeutic candidate for bone diseases such as osteoporosis.

cell biology↗

bioRxiv2024

Septo-hypothalamic regulation of binge-like alcohol consumption by the nociceptin system.

High intensity alcohol drinking during binge episodes overwhelmingly contributes to the socioeconomic burden created by Alcohol Use Disorders (AUD). Novel interventions are needed to add to the current therapeutic toolkit and nociceptin receptor (NOP) antagonists have shown promise in reducing heavy drinking days in patients with an AUD. However, an endogenous locus of nociceptin peptide and discrete sites of NOP action underlying this effect remains understudied. Here we show that the lateral septum (LS), a region contributing to binge drinking, is enriched in neurons expressing mRNA coding for the nociceptin peptide (Pnoc). Pnoc-expressing neurons of the LS (LSPnoc) are tuned to stimuli associated with negative valence and display increased excitability during withdrawal from binge-like alcohol drinking. LSPnoc activation was found to have aversive qualities and also potentiates binge-like drinking behavior, suggesting a convergence of circuitry that promotes aversion and drives alcohol consumption. Viral mediated tracing and functional assessment of LSPnoc projection fields revealed GABAergic synapses locally within the LS, and downstream within the lateral hypothalamus (LH) and supramammillary nucleus (SuM). Genetic deletion of NOP from the LS attenuated binge-like alcohol intake in male mice while NOP deletion from the LH and SuM decrease alcohol intake in females. Together, these findings are the first to demonstrate an endogenous population of nociceptin-expressing neurons that contributes to alcohol consumption and identifies sex-dependent modulation of alcohol drinking by NOP.

neuroscience↗

bioRxiv2024

Dimeric R25CPTH(1-34) Activates the Parathyroid Hormone-1 Receptor in vitro and Stimulates Bone Formation in Osteoporotic Female Mice

Osteoporosis, characterized by reduced bone density and strength, increases fracture risk, pain, and limits mobility. Established therapies of Parathyroid hormone (PTH) analogs effectively promote bone formation and reduce fractures in severe osteoporosis, but their use is limited by potential adverse effects. In the pursuit of safer osteoporosis treatments, we investigated R25CPTH, a PTH variant wherein the native arginine at position 25 is substituted by cysteine. These studies were prompted by our finding of high bone mineral density in a hypoparathyroidism patient with the R25C homozygous mutation, and we explored its effects on PTH type-1 receptor (PTH1R) signaling in cells and bone metabolism in mice. Our findings indicate that R25CPTH(1-84) forms dimers both intracellularly and extracellularly, and the synthetic dimeric peptide, R25CPTH(1-34), exhibits altered activity in PTH1R-mediated cAMP response. Upon a single injection in mice, dimeric R25CPTH(1-34) induced acute calcemic and phosphaturic responses comparable to PTH(1-34). Furthermore, repeated daily injections increased calvarial bone thickness in intact mice and improved trabecular and cortical bone parameters in ovariectomized (OVX) mice, akin to PTH(1-34). The overall results reveal a capacity of a dimeric PTH peptide ligand to activate the PTH1R in vitro and in vivo as PTH, suggesting a potential path of therapeutic PTH analog development.

genomics↗

bioRxiv2024

Self-organization of embryonic stem cells into a reproducible embryo model through epigenome editing

Embryonic stem cells (ESCs) can self-organize in vitro into developmental patterns with spatial organization and molecular similarity to that of early embryonic stages. This self-organization of ESCs requires transmission of signaling cues, via addition of small molecule chemicals or recombinant proteins, to induce distinct embryonic cellular fates and subsequent assembly into structures that can mimic aspects of early embryonic development. During natural embryonic development, different embryonic cell types co-develop together, where each cell type expresses specific fate-inducing transcription factors through activation of non-coding regulatory elements and interactions with neighboring cells. However, previous studies have not fully explored the possibility of engineering endogenous regulatory elements to shape self-organization of ESCs into spatially-ordered embryo models. Here, we hypothesized that cell-intrinsic activation of a minimum number of such endogenous regulatory elements is sufficient to self-organize ESCs into early embryonic models. Our results show that CRISPR-based activation (CRISPRa) of only two endogenous regulatory elements in the genome of pluripotent stem cells is sufficient to generate embryonic patterns that show spatial and molecular resemblance to that of pre-gastrulation mouse embryonic development. Quantitative single-cell live fluorescent imaging showed that the emergence of spatially-ordered embryonic patterns happens through the intrinsic induction of cell fate that leads to an orchestrated collective cellular motion. Based on these results, we propose a straightforward approach to efficiently form 3D embryo models through intrinsic CRISPRa-based epigenome editing and independent of external signaling cues. CRISPRa-Programmed Embryo Models (CPEMs) show highly consistent composition of major embryonic cell types that are spatially-organized, with nearly 80% of the structures forming an embryonic cavity. Single cell transcriptomics confirmed the presence of main embryonic cell types in CPEMs with transcriptional similarity to pre-gastrulation mouse embryos and revealed novel signaling communication links between different embryonic cell types. Our findings offer a programmable embryo model and demonstrate that minimum intrinsic epigenome editing is sufficient to self-organize ESCs into highly consistent pre-gastrulation embryo models

developmental biology↗

bioRxiv2024

Ultraviolet B acts as a dietary restriction mimetic by targeting mitochondrial bioenergetics.

Ultraviolet (UV) light is a common environmental stimulus, and UV exposure confers health benefits, with cellular targets still unclear. Here, we show that ultraviolet B (UVB) exposure alters mitochondrial bioenergetics in C. elegans and human skin fibroblasts triggering loss of membrane potential, mitochondrial fission and calcium release. This initial stress is followed by a recovery process relying on mitochondrial biogenesis and fusion, which prevents lasting mitochondrial damage. Strikingly, the transient decline of ATP synthesis caused by UVB-induced mitochondrial changes triggers a swift metabolic re-wiring response that resembles effects of dietary restriction (DR) at the organismal and molecular levels. Both recovery from UVB and DR-mimetic UVB effects require mitochondrial fusion, and we found that dysfunction of fusion during aging abrogates UVB benefits and sensitizes old nematodes to UVB toxicity. Finally, UVB irradiation of the skin was effective in inducing organismal fasting-like phenomena in proof-of-concept tests in young mice. We thus uncovered a novel evolutionary conserved cellular mechanism connecting UV light and metabolism. Our findings illuminate potential DR-mimetic properties of UVB and explain late life-specific UVB intolerance.

cell biology↗

bioRxiv2024

Human immunodeficiency virus-1 induces and targets host genomic R-loops for viral genome integration

Although HIV-1 integration sites favor active transcription units in the human genome, high-resolution analysis of individual HIV-1 integration sites has shown that the virus can integrate into a variety of host genomic locations, including non-genic regions. The invisible infection by HIV-1 integrating into non-genic regions, challenging the traditional understanding of HIV-1 integration site selection, is more problematic because they are selected for preservation in the host genome during prolonged antiretroviral therapies. Here, we showed that HIV-1 integrates its viral genome into the vicinity of R-loops, a genomic structure composed of DNA- RNA hybrids. VSV-G-pseudotyped HIV-1 infection initiates the formation of R-loops in both genic and non-genic regions of the host genome and preferentially integrates into R-loop-rich regions. Using a HeLa cell model that can independently control transcriptional activity and R-loop formation, we demonstrated that the exogenous formation of R-loops directs HIV-1 integration-targeting sites. We also found that HIV-1 integrase proteins physically bind to the host genomic R-loops. These findings provide novel insights into the mechanisms underlying retroviral integration and the new strategies for antiretroviral therapy against HIV-1 latent infection.

molecular biology↗

bioRxiv2024

Immunogenicity and safety of a live-attenuated SARS-CoV-2 vaccine candidate based on multiple attenuation mechanisms

mRNA vaccines against SARS-CoV-2 were rapidly developed and effective during the pandemic. However, some limitations remain to be resolved, such as the short-lived induced immune response and certain adverse effects. Therefore, there is an urgent need to develop new vaccines that address these issues. While live-attenuated vaccines are a highly effective modality, they pose a risk of adverse effects, including virulence reversion. In the current study, we constructed a live-attenuated vaccine candidate, BK2102, combining naturally occurring virulence-attenuating mutations in the NSP14, NSP1, spike and ORF7-8 coding regions. Intranasal inoculation with BK2102 induced humoral and cellular immune responses in Syrian hamsters without apparent tissue damage in the lungs, leading to protection against a SARS-CoV-2 D614G and an Omicron BA.5 strains. The neutralizing antibodies induced by BK2102 persisted for up to 364 days, which indicated that they confer long-term protection against infection. Furthermore, we confirmed the safety of BK2102 using transgenic (Tg) mice expressing human ACE2 (hACE2), that are highly susceptible to SARS-CoV-2. BK2102 did not kill the Tg mice, even when virus was administered at a dose of 106 plaque-forming units (PFU), while 102 PFU of the D614G strain or an attenuated strain lacking the furin cleavage site (FCS) of the spike was sufficient to kill mice. These results suggest that BK2102 is a promising live-vaccine candidate strain that confers long-term protection without significant virulence.

microbiology↗

bioRxiv2024

Nanogap Solid-State Single-Molecule Detection at Mars, Europa, and Microgravity Conditions

Solid-state nanogap systems are an emerging technology for in-situ life detection due to their single-molecule resolution of a wide range of biomolecules, including amino acids and informational polymers, at the parts per billion to trillion level. By targeting the abundance distributions of organic molecules, this technology is a candidate for detecting ancient and extant life and discriminating between biotic and abiotic organics on future planetary missions to Mars and icy moons such as Enceladus and Europa. A benchtop system developed at Osaka University has a proven ability to detect and discriminate among single amino acids, RNA, and DNA using nanogap chips. The Electronic Life-detection Instrument for Enceladus/Europa (ELIE) prototype was subsequently developed to make this technology viable for space instrumentation through the simplification of electronics, reduction of size and weight, and automation of gap formation. Initial ground testing using a manually formed nanogap with the first ELIE prototype detected the amino acid L-proline. However, this manual adjustment approach posed limitations in maintaining a consistent gap size. To address this challenge, we integrated an automated piezo actuator to enable real-time gap control, permitting single-molecule identification of a target amino acid, L-proline, under reduced gravity (g), including Mars (g = 0.378), Europa or Lunar (g = 0.166), and microgravity conditions (g = 0.03-0.06), as validated through parabolic flight testing. Power supply noise and experimental constraints of the experiment design limited data collection to short segments of good-quality data. Nevertheless, the subsequent analysis of detected events within these segments revealed a consistent system performance and a controlled gap size across the different accelerations. This finding highlights the systems resilience to physical vibrations. Future goals are to progress the instrument towards technology readiness level 4 with further reductions of size and mass, lower noise, and additional system automation. With further development, ELIE has the potential to be an autonomous and sensitive single-molecule detection instrument for deployment throughout the solar system.

biophysics↗

bioRxiv2024

Optogenetic fMRI reveals therapeutic circuits of subthalamic nucleus deep brain stimulation

While deep brain stimulation (DBS) is widely employed for managing motor symptoms in Parkinsons disease (PD), its exact circuit mechanisms remain controversial. To identify the neural targets affected by therapeutic DBS in PD, we analyzed DBS-evoked whole brain activity in female hemi-parkinsonian rats using function magnetic resonance imaging (fMRI). We delivered subthalamic nucleus (STN) DBS at various stimulation pulse repetition rates using optogenetics, allowing unbiased examinations of cell-type specific STN feed-forward neural activity. Unilateral STN optogenetic stimulation elicited pulse repetition rate-dependent alterations of blood-oxygenation-level-dependent (BOLD) signals in SNr (substantia nigra pars reticulata), GP (globus pallidus), and CPu (caudate putamen). Notably, these manipulations effectively ameliorated pathological circling behavior in animals expressing the kinetically faster Chronos opsin, but not in animals expressing ChR2. Furthermore, mediation analysis revealed that the pulse repetition rate-dependent behavioral rescue was significantly mediated by optogenetically induced activity changes in GP and CPu, but not in SNr. This suggests that the activation of GP and CPu are critically involved in the therapeutic mechanisms of STN DBS.

neuroscience↗

bioRxiv2024

Pathologic α-Synuclein-NOD2 Interaction and RIPK2 Activation Drives Microglia-Induced Neuroinflammation in Parkinson's Disease

Pathological aggregation of -Synuclein (-Syn) and neuroinflammation are closely linked to Parkinsons disease (PD). However, the specific regulators of the neuroinflammation caused by pathological -syn remain obscure. In this study, we show that NOD2/RIPK2 signaling is a crucial regulator of neuroinflammation in PD. Pathological -syn binds to NOD2, causing self-oligomerization and complex formation with RIPK2, leading to RIPK2 ubiquitination and activation of MAPK and NF-kB. Notably, this NOD2/RIPK2 signaling is particularly active in microglia of human PD brains and the -Syn preformed fibril (-Syn PFF) mouse model. Depleting NOD2 or RIPK2 reduces neuroinflammation and protects against dopamine neuron degeneration in a pathologic -Syn mouse model by blocking the formation of neurotoxic reactive astrocytes caused by microglia activation. The discovery of NOD2/RIPK2 signaling as a key regulator of neuroinflammation in PD provides a new understanding of -Syn-driven neuroinflammation and neurodegeneration in PD and a potential new therapeutic strategy. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/580982v2_ufig1.gif" ALT="Figure 1"> View larger version (74K): org.highwire.dtl.DTLVardef@10c010aorg.highwire.dtl.DTLVardef@1183b23org.highwire.dtl.DTLVardef@1d289dborg.highwire.dtl.DTLVardef@158b6ef_HPS_FORMAT_FIGEXP M_FIG C_FIG In briefPathological -Synuclein (-Syn) binds to the microglial NOD2 protein, which in turn triggers NOD2/RIPK2 complex and RIPK2 phosphorylation/ubiquitination. This process activates the NF-kB/MAPK pathways, ultimately leading to neurotoxic reactive astrocyte-induced dopaminergic neurodegeneration. Depletion of RIPK2 (RIPK2 KO) or NOD2 (NOD2) protects dopamine neurons in a mouse model of Parkinsons disease (PD). These findings provide insights into -Syn-driven neuroinflammation and offer potential therapeutic strategies for PD. HighlightsNOD2/RIPK2 signaling is identified as a crucial regulator of neuroinflammation in PD. NOD2/RIPK2 signaling is highly active in microglia in human PD brains and -Syn PFF mouse models. Pathological -Syn binds to NOD2, triggering self-oligomerization and RIPK2 complex formation, leading to MAPK and NF-kB activation Genetic depletion of NOD2 or RIPK2 reduces neuroinflammation and protects dopamine neurons by blocking the formation of neurotoxic reactive astrocytes.

neuroscience↗

bioRxiv2024

The sperm hook in house mice: a functional adaptation for migration and self-organised behaviour

In most murine species, spermatozoa exhibit a falciform apical hook at the head end. The function of the sperm hook is not yet clearly understood. In this study, we investigate the role of the sperm hook in the migration of spermatozoa through the female reproductive tract in Mus musculus (C57BL/6), using a deep tissue imaging custom-built two-photon microscope. Through live reproductive tract imaging, we found evidence indicating that the sperm hook aids in the attachment of spermatozoa to the epithelium and facilitates interactions between spermatozoa and the epithelium during migration in the uterus and oviduct. We also observed synchronised sperm beating, which resulted from the spontaneous unidirectional rearrangement of spermatozoa in the uterus. Based on live imaging of spermatozoa-epithelium interaction dynamics, we propose that the sperm hook plays a crucial role in successful migration through the female reproductive tract by providing anchor-like mechanical support and facilitating interactions between spermatozoa and the female reproductive tract in the house mouse.

cell biology↗

bioRxiv2024

Tissue-resident regulatory T cells exert dualistic anti-tumour and pro-repair function in the exocrine pancreas

Regulatory T cells are fundamentally important for maintaining immune homeostasis, and their potent immune-suppressive roles make them attractive immunotherapeutic targets in cancer. Recent work suggests potential functions of tissue-resident Tregs (trTregs) in tissue-repair and epithelial cell homeostasis. Here, we describe a rare population of trTreg in the exocrine pancreas. We show that these cells share common features of trTregs, including expression of the IL-33 receptor ST2 and production of the epithelial growth factor Amphiregulin, and display an oligoclonal T cell receptor repertoire. Using a mouse model of acute pancreatitis, we show that pancreatic Tregs rapidly expand upon release of IL-33 by fibroblasts. Moreover, depletion of Tregs after initiation of pancreatic injury impairs the regeneration of the exocrine parenchyma. This effect is due, in part, through a direct effect of Tregs on acinar cell proliferation. Finally, we show that transient Treg depletion in established orthotopic pancreatic tumours leads to tumour rejection yet provokes long-lasting damages to surrounding exocrine parenchyma. In all, our results demonstrate the tissue-repair capacity of pancreatic Tregs, and highlight a dualistic role of these cells in the pancreatic tumour ecosystem, with their harmful immune-suppressive function in the tumour coupled to a beneficial tissue-repair function in the surrounding tissue.

immunology↗

bioRxiv2024

Glyoxalase 1: emerging biomarker and therapeutic target in cervical cancer progression

IntroductionCervical cancer presents a significant global health challenge, disproportionately impacting underserved populations with limited access to healthcare. Early detection and effective management are vital in addressing this public health concern. This study focuses on Glyoxalase-1 (GLO1), an enzyme crucial for methylglyoxal detoxification, in the context of cervical cancer. MethodsWe assessed GLO1 expression in cervical cancer patient samples using immunohistochemistry. In vitro experiments using HeLa cell lines were conducted to evaluate the impact of GLO1 inhibition on cell viability and migration. Single-cell RNA sequencing (scRNA-seq) and gene set variation analysis were utilized to investigate GLO1s role in the metabolism of cervical cancer. Additionally, public microarray data were analyzed to determine GLO1 expression across various stages of cervical cancer. ResultsOur analysis included 58 cervical cancer patients, and showed that GLO1 is significantly upregulated in cervical cancer tissues compared to normal cervical tissues, independent of pathological findings and disease stage. In vitro experiments indicated that GLO1 downregulation decreased cell viability and migration in cervical cancer cell lines. Analyses of scRNA-seq data and public gene expression datasets corroborated the overexpression of GLO1 and its involvement in cancer metabolism, particularly glycolysis. An examination of expression data from precancerous lesions revealed a progressive increase in GLO1 expression from normal tissue to invasive cervical cancer. ConclusionsThis study highlights the critical role of GLO1 in the progression of cervical cancer, presenting it as a potential biomarker and therapeutic target. These findings contribute valuable insights towards personalized treatment approaches and augment the ongoing efforts to combat cervical cancer. Further research is necessary to comprehensively explore GLO1s potential in clinical applications. SynopsisThis study examines Glyoxalase-1 (GLO1) in cervical cancer and reveals its significant upregulation in cancerous tissues compared to normal counterparts. In vitro experiments show that downregulating GLO1 decreases cell viability and migration. Single-cell RNA sequencing and gene expression analysis substantiate GLO1s involvement in cancer metabolism, notably in glycolysis. These findings identify GLO1 as a potential biomarker and therapeutic target, offering insights for personalized treatment approaches in cervical cancer management.

cancer biology↗

bioRxiv2024

TopoQual polishes circular consensus sequencing data and accurately predicts quality scores

SummaryPacific Biosciences (PacBio) circular consensus sequencing (CCS) aka high fidelity (HiFi) technology has revolutionized modern genomics by producing long (10+kb) and highly accurate reads by sequencing circularized DNA molecules multiple times and combining them into a consensus sequence. Currently the accuracy and quality value estimation is more than sufficient for genome assembly and germline variant calling, but the estimated quality scores are not accurate enough for confident somatic variant calling on single reads. Here we introduce TopoQual, a tool utilizing partial order alignments (POA), topologically parallel bases, and deep learning to polish consensus sequences and more accurately predict base qualities. We correct ~31.9% of errors in PacBio consensus sequences and validate base qualities up to q59 which is one error in 0.9 million bases enabling accurate somatic variant calling with HiFi data. Availability and implementationThe source code and installation instructions as well as validation dataset used are freely available at https://github.com/lorewar2/TopoQual

bioinformatics↗

bioRxiv2024

Enhancing Bone Regeneration and Osseointegration using rhPTH(1-34) and Dimeric R25CPTH(1-34) in an Osteoporotic Beagle Model

IntroductionDespite continuous parathyroid hormone (PTH) exposure potentially accelerating bone resorption, intermittent PTH administration has shown anabolic effects on bone microarchitecture. This study investigates the therapeutic impacts of two PTH analogs, rhPTH(1-34) and dimeric R25CPTH(1-34) on bone regeneration and osseointegration in a postmenopausal osteoporosis animal model. MethodsTwelve female beagles, osteoporotic post-ovariectomy, underwent implant surgeries. Animals were divided into three groups: control, daily rhPTH(1-34) injection, and daily dimeric R25CPTH(1-34) injection. After 10 weeks, bone regeneration and implant osseointegration were evaluated using micro-CT, histological/histomorphometric analyses, and serum biochemical analysis. ResultsWhile the rhPTH(1-34) group demonstrated improved microarchitectural characteristics, such as BMD, BV, trabecular metrics, and osseointegration degree, the dimeric R25CPTH(1-34) group showed similarly enhanced anabolic effects around the titanium implants, albeit these were less pronounced than the rhPTH(1-34), yet significantly better than the control group. Histologic and TRAP assays revealed that both PTH analogs significantly promoted bone regeneration and remodeling, especially in artificially created bone defects. ConclusionThis study demonstrated the therapeutic effects of rhPTH(1-34) and dimeric R25CPTH(1-34) on bone regeneration and titanium osseointegration in a beagle model with osteoporosis.

pathology↗

bioRxiv2024

Focal Deletions of a Promoter Tether Activate the IRX3 Oncogene in T Cell Acute Lymphoblastic Leukemia

Oncogenes can be activated in cis through multiple mechanisms including enhancer hijacking events and noncoding mutations that create enhancers or promoters de novo. These paradigms have helped parse somatic variation of noncoding cancer genomes, thereby providing a rationale to identify noncanonical mechanisms of gene activation. Here we describe a novel mechanism of oncogene activation whereby focal copy number loss of an intronic element within the FTO gene leads to aberrant expression of IRX3, an oncogene in T cell acute lymphoblastic leukemia (T-ALL). Loss of this CTCF bound element downstream to IRX3 (+224 kb) leads to enhancer hijack of an upstream developmentally active super-enhancer of the CRNDE long noncoding RNA (-644 kb). Unexpectedly, the CRNDE super-enhancer interacts with the IRX3 promoter with no transcriptional output until it is untethered from the FTO intronic site. We propose that promoter tethering of oncogenes to inert regions of the genome is a previously unappreciated biological mechanism preventing tumorigenesis.

cancer biology↗