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Results for “mechanical phenotyping”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Characterizing cellular mechanical phenotypes with mechano-node-pore sensing

The mechanical properties of cells change with their differentiation, chronological age, and malignant progression. Consequently, these properties may be useful label-free biomarkers of various functional or clinically relevant cell states. Here, we demonstrate mechano-node-pore sensing (mechano-NPS), a multi-parametric single-cell-analysis method that utilizes a four-terminal measurement of the current across a microfluidic channel to quantify simultaneously cell diameter, resistance to compressive deformation, transverse deformation under constant strain, and recovery time after deformation. We define a new parameter, the whole-cell deformability index (wCDI), which provides a quantitative mechanical metric of the resistance to compressive deformation that can be used to discriminate among different cell types. The wCDI and the transverse deformation under constant strain show malignant MCF-7 and A549 cell lines are mechanically distinct from non-malignant, MCF-10A and BEAS-2B cell lines, and distinguishes between cells treated or untreated with cytoskeleton-perturbing small molecules. We categorize cell recovery time, ΔTr, as instantaneous (ΔTr ~ 0 ms), transient (ΔTr≤40 ms), or prolonged (ΔTr440 ms), and show that the composition of recovery types, which is a consequence of changes in cytoskeletal organization, correlates with cellular transformation. Through the wCDI and cell-recovery time, mechano-NPS discriminates between sub-lineages of normal primary human mammary epithelial cells with accuracy comparable to flow cytometry, but without antibody labeling. Mechano-NPS identifies mechanical phenotypes that distinguishes lineage, chronological age, and stage of malignant progression in human epithelial cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Metamaterials for Mechanically Directing Cell Phenotype

Recently, abundant research has begun to reveal how microscale surface topography can influence a wide range of cell phenotypes in vitro, such as cell mobility, cell size and cell viability (Flemming et al. 1999, Nikkhah et al. 2012, Wang et al. 2016). However, while these studies shed some light on cell interactions with 2D surfaces of different length scales, cells in vivo experience their surroundings in 3D. Therefore, investigations into cell interactions with varying 3D microstructures are needed to gain biologically relevant insight into how microarchitecture and feature size influences cell behavior. Understanding this relationship between 3D microstructure and cell behavior will have a huge impact on tissue engineering and mechanobiology. Until now, the ability to fabricate complex 3D microstructures for cell behavior studies has been limited. This study harnessed LLNL’s Projection Micro-Stereolithography (PμSL) capability to probe the effects of micron-scale changes in 3D architecture on cell phenotype. Furthermore, our studies explored the application of external forces—such as cyclic loading and flow-induced shear stress—to cell-seeded 3D microstructures to further examine cell behavior.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Adaptive Phenotypic Plasticity Stabilizes Evolution in Fluctuating Environments

Fluctuating environmental conditions are ubiquitous in natural systems, and populations have evolved various strategies to cope with such fluctuations. The particular mechanisms that evolve profoundly influence subsequent evolutionary dynamics. One such mechanism is phenotypic plasticity, which is the ability of a single genotype to produce alternate phenotypes in an environmentally dependent context. Here, we use digital organisms (self-replicating computer programs) to investigate how adaptive phenotypic plasticity alters evolutionary dynamics and influences evolutionary outcomes in cyclically changing environments. Specifically, we examined the evolutionary histories of both plastic populations and non-plastic populations to ask: (1) Does adaptive plasticity promote or constrain evolutionary change? (2) Are plastic populations better able to evolve and then maintain novel traits? And (3), how does adaptive plasticity affect the potential for maladaptive alleles to accumulate in evolving genomes? We find that populations with adaptive phenotypic plasticity undergo less evolutionary change than non-plastic populations, which must rely on genetic variation from de novo mutations to continuously readapt to environmental fluctuations. Indeed, the non-plastic populations undergo more frequent selective sweeps and accumulate many more genetic changes. We find that the repeated selective sweeps in non-plastic populations drive the loss of beneficial traits and accumulation of maladaptive alleles, whereas phenotypic plasticity can stabilize populations against environmental fluctuations. This stabilization allows plastic populations to more easily retain novel adaptive traits than their non-plastic counterparts. In general, the evolution of adaptive phenotypic plasticity shifted evolutionary dynamics to be more similar to that of populations evolving in a static environment than to non-plastic populations evolving in an identical fluctuating environment. All natural environments subject populations to some form of change; our findings suggest that the stabilizing effect of phenotypic plasticity plays an important role in subsequent adaptive evolution.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

Novel mechanism for scavenging of hypochlorite involving a periplasmic methionine-rich peptide and methionine sulfoxide reductase

Reactive chlorine species (RCS) defense mechanisms are important for bacterial fitness in diverse environments. In addition to the anthropogenic use of RCS in the form of bleach, these compounds are also produced naturally through photochemical reactions of natural organic matter and in vivo by the mammalian immune system in response to invading microorganisms. To gain insight into bacterial RCS defense mechanisms, we investigated Azospira suillum strain PS, which produces periplasmic RCS as an intermediate of perchlorate respiration. Our studies identified an RCS response involving an RCS stress-sensing sigma/anti-sigma factor system (SigF/NrsF), a soluble hypochlorite-scavenging methionine-rich periplasmic protein (MrpX), and a putative periplasmic methionine sulfoxide reductase (YedY1). We investigated the underlying mechanism by phenotypic characterization of appropriate gene deletions, chemogenomic profiling of barcoded transposon pools, transcriptome sequencing, and biochemical assessment of methionine oxidation. Our results demonstrated that SigF was specifically activated by RCS and initiated the transcription of a small regulon centering around yedY1 and mrpX. A yedY1 paralog ( yedY2 ) was found to have a similar fitness to yedY1 despite not being regulated by SigF. Markerless deletions of yedY2 confirmed its synergy with the SigF regulon. MrpX was strongly induced and rapidly oxidized by RCS, especially hypochlorite. Our results suggest a mechanism involving hypochlorite scavenging by sacrificial oxidation of the MrpX in the periplasm. Reduced MrpX is regenerated by the YedY methionine sulfoxide reductase activity. The phylogenomic distribution of this system revealed conservation in several Proteobacteria of clinical importance, including uropathogenic Escherichia coli and Brucella spp., implying a putative role in immune response evasion in vivo . In addition, bacteria are often stressed in the environment by reactive chlorine species (RCS) of either anthropogenic or natural origin, but little is known of the defense mechanisms they have evolved. Using a microorganism that generates RCS internally as part of its respiratory process allowed us to uncover a novel defense mechanism based on RCS scavenging by reductive reaction with a sacrificial methionine-rich peptide and redox recycling through a methionine sulfoxide reductase. As a result, this system is conserved in a broad diversity of organisms, including some of clinical importance, invoking a possible important role in innate immune system evasion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Phylogenetically Driven Sequencing of Extremely Halophilic Archaea Reveals Strategies for Static and Dynamic Osmo-response

Organisms across the tree of life use a variety of mechanisms to respond to stress-inducing fluctuations in osmotic conditions. Cellular response mechanisms and phenotypes associated with osmoadaptation also play important roles in bacterial virulence, human health, agricultural production and many other biological systems. To improve understanding of osmoadaptive strategies, we have generated 59 high-quality draft genomes for the haloarchaea (a euryarchaeal clade whose members thrive in hypersaline environments and routinely experience drastic changes in environmental salinity) and analyzed these new genomes in combination with those from 21 previously sequenced haloarchaeal isolates. We propose a generalized model for haloarchaeal management of cytoplasmic osmolarity in response to osmotic shifts, where potassium accumulation and sodium expulsion during osmotic upshock are accomplished via secondary transport using the proton gradient as an energy source, and potassium loss during downshock is via a combination of secondary transport and non-specific ion loss through mechanosensitive channels. We also propose new mechanisms for magnesium and chloride accumulation. We describe the expansion and differentiation of haloarchaeal general transcription factor families, including two novel expansions of the TATA-binding protein family, and discuss their potential for enabling rapid adaptation to environmental fluxes. We challenge a recent high-profile proposal regarding the evolutionary origins of the haloarchaea by showing that inclusion of additional genomes significantly reduces support for a proposed large-scale horizontal gene transfer into the ancestral haloarchaeon from the bacterial domain. The combination of broad (17 genera) and deep (≥5 species in four genera) sampling of a phenotypically unified clade has enabled us to uncover both highly conserved and specialized features of osmoadaptation. Finally, we demonstrate the broad utility of such datasets, for metagenomics, improvements to automated gene annotation and investigations of evolutionary processes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Secure biosystems design in Saccharomyces cerevisiae establishes effective biocontainment strategies and mechanisms of escape

The widespread application of recombinant DNA and synthetic biology approaches for microbial metabolic engineering pursuits has motivated the development of biocontainment strategies, targeting safe and secure deployment of genetically modified microorganisms (GMMs). However, the design rules and mechanistic drivers governing biocontainment efficacy, as well as impacts of biocontainment upon microbial fitness, remain to be comprehensively evaluated, hindering predictive design and application of these strategies. We have developed a platform for high-resolution analysis of a transactivated kill switch in laboratory and industrial strains of Saccharomyces cerevisiae to assess modes of biocontainment escape and establish design rules for development of kill switch systems in diverse microbes. A camphor-regulated, RelE toxin system was systematically deployed to assess the impacts of differential kill switch copy number and ploidy in laboratory vs industrial strains. CRISPR-mediated integration of the biocontainment system at various loci revealed rapid escape events driven, in part, by mutations to both the Cam-transactivator (cam-TA) and RelE toxin. Genetic engineering enabled recapitulation of escape phenotypes, confirming mechanisms of escape and establishing structure-function relationships in the cam-TA system. Interestingly, genomic resequencing of escape mutants also revealed a series of off-target mutations, implicating additional modes of kill switch escape. Multi-copy integration of the kill switch system mitigated these effects by orders of magnitude, without compromising the biosynthetic capacity of the microbes, but proved insufficient to establish sustained biocontainment. The resultant data define a series of key design rules for next-generation biocontainment strategies and add to a growing foundational knowledge base targeting establishment of secure biosystems designs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Limited Support for Thyroid Hormone or Corticosterone Related Gene Expression as a Proximate Mechanism of Incubation Temperature-Dependent Phenotypes in Birds

The conditions that animals experience during early development can have profound consequences for health and fitness. In birds, one of the most important aspects of development is egg incubation temperature. A small decrease in average temperature leads to various impacts on offspring phenotype, such as smaller body sizes, slower growth rates, and less efficient metabolic activity. Little is known, however, about the proximate mechanisms underlying these incubation temperature-induced phenotypic changes. Two important hormones which could play a proximate role are thyroid hormone and corticosterone, which mobilize stored energy reserves and coordinate the normal growth of tissues, particularly in the brain. Previous research shows that circulating blood concentrations of both hormones are influenced by incubation temperature, but the mechanism by which incubation temperature may lead to these changes is unknown. We hypothesized that incubation temperature induces changes in thyroid hormone and corticosterone regulation, leading to changes in expression of hormone-sensitive genes in the brain. To test this, we incubated wood duck (Aix sponsa) eggs at three different temperatures within the natural range (35.0, 35.8, and 37.0°C). We measured mRNA expression of thyroid hormone-related neuroendocrine endpoints (deiodinase 2/3, thyroid hormone receptor α/β, neural regeneration related protein, and Krueppel-like factor 9) in newly hatched ducklings and corticosterone-related neuroendocrine endpoints (mineralocorticoid receptor, glucocorticoid receptor, cholecystokinin, and brain-derived neurotrophic factor) in 15 day-old ducklings using qPCR on brain tissue from the hippocampus and hypothalamus. Contrary to our predictions, we found that mRNA expression of thyroid hormone-related endpoints in both brain areas were largely unaffected by incubation temperature, although there was a trend for an inverse relationship between mRNA expression and incubation temperature for several genes in the hypothalamus. We also found that mineralocorticoid receptor mRNA expression in the hypothalamus was lower in ducklings incubated at the low relative to the high temperatures. This study is the first to evaluate the effects of incubation temperature on mRNA expression of neuroendocrine endpoints in the developing avian brain and suggests that these particular endpoints may be largely resistant to changes in incubation temperature. Thus, further research into the proximate mechanisms for incubation temperature-induced developmental plasticity is needed.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Genome resources for three modern cotton lines guide future breeding efforts

Cotton ( Gossypium hirsutum L.) is the key renewable fibre crop worldwide, yet its yield and fibre quality show high variability due to genotype-specific traits and complex interactions among cultivars, management practices and environmental factors. Modern breeding practices may limit future yield gains due to a narrow founding gene pool. Precision breeding and biotechnological approaches offer potential solutions, contingent on accurate cultivar-specific data. Here we address this need by generating high-quality reference genomes for three modern cotton cultivars (‘UGA230’, ‘UA48’ and ‘CSX8308’) and updating the ‘TM-1’ cotton genetic standard reference. Despite hypothesized genetic uniformity, considerable sequence and structural variation was observed among the four genomes, which overlap with ancient and ongoing genomic introgressions from ‘Pima’ cotton, gene regulatory mechanisms and phenotypic trait divergence. Differentially expressed genes across fibre development correlate with fibre production, potentially contributing to the distinctive fibre quality traits observed in modern cotton cultivars. These genomes and comparative analyses provide a valuable foundation for future genetic endeavours to enhance global cotton yield and sustainability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment

Abstract Shimia strain SK013 is an aerobic, Gram-negative, rod shaped alphaproteobacterium affiliated with the Roseobacter group within the family Rhodobacteraceae . The strain was isolated from surface sediment (0–1 cm) of the Skagerrak at 114 m below sea level. The 4,049,808 bp genome of Shimia str. SK013 comprises 3,981 protein-coding genes and 47 RNA genes. It contains one chromosome and no extrachromosomal elements. The genome analysis revealed the presence of genes for a dimethylsulfoniopropionate lyase, demethylase and the trimethylamine methyltransferase ( mttB ) as well as genes for nitrate, nitrite and dimethyl sulfoxide reduction. This indicates that Shimia str. SK013 is able to switch from aerobic to anaerobic metabolism and thus is capable of aerobic and anaerobic sulfur cycling at the seafloor. Among the ability to convert other sulfur compounds it has the genetic capacity to produce climatically active dimethyl sulfide. Growth on glutamate as a sole carbon source results in formation of cell-connecting filaments, a putative phenotypic adaptation of the surface-associated strain to the environmental conditions at the seafloor. Genome analysis revealed the presence of a flagellum ( fla 1) and a type IV pilus biogenesis, which is speculated to be a prerequisite for biofilm formation. This is also related to genes responsible for signalling such as N-acyl homoserine lactones, as well as quip-genes responsible for quorum quenching and antibiotic biosynthesis. Pairwise similarities of 16S rRNA genes (98.56 % sequence similarity to the next relative S. haliotis ) and the in silico DNA-DNA hybridization (21.20 % sequence similarity to S. haliotis ) indicated Shimia str. SK013 to be considered as a new species. The genome analysis of Shimia str. SK013 offered first insights into specific physiological and phenotypic adaptation mechanisms of Roseobacter- affiliated bacteria to the benthic environment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Predictive Radiation Oncology – A New NCI–DOE Scientific Space and Community

With a widely attended virtual kickoff event on January 29, 2021, the National Cancer Institute (NCI) and the Department of Energy (DOE) launched a series of 4 interactive, interdisciplinary workshops—and a final concluding “World Café” on March 29, 2021—focused on advancing computational approaches for predictive oncology in the clinical and research domains of radiation oncology. These events reflect 3,870 human hours of virtual engagement with representation from 8 DOE national laboratories and the Frederick National Laboratory for Cancer Research (FNL), 4 research institutes, 5 cancer centers, 17 medical schools and teaching hospitals, 5 companies, 5 federal agencies, 3 research centers, and 27 universities. Here we summarize the workshops by first describing the background for the workshops. Participants identified twelve key questions—and collaborative parallel ideas—as the focus of work going forward to advance the field. These were then used to define short-term and longer-term “Blue Sky” goals. In addition, the group determined key success factors for predictive oncology in the context of radiation oncology, if not the future of all of medicine. These are: cross-discipline collaboration, targeted talent development, development of mechanistic mathematical and computational models and tools, and access to high-quality multiscale data that bridges mechanisms to phenotype. The workshop participants reported feeling energized and highly motivated to pursue next steps together to address the unmet needs in radiation oncology specifically and in cancer research generally and that NCI and DOE project goals align at the convergence of radiation therapy and advanced computing.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2016

Next Generation Protein Interactomes for Plant Systems Biology and Biomass Feedstock Research

Biofuel crop cultivation is a necessary step in heading towards a sustainable future, making their genomic studies a priority. While technology platforms that currently exist for studying non-model crop species, like switch-grass or sorghum, have yielded large quantities of genomic and expression data, still a large gap exists between molecular mechanism and phenotype. The aspect of molecular activity at the level of protein-protein interactions has recently begun to bridge this gap, providing a more global perspective. Interactome analysis has defined more specific functional roles of proteins based on their interaction partners, neighborhoods, and other network features, making it possible to distinguish unique modules of immune response to different plant pathogens(Jiang, Dong, and Zhang 2016). As we work towards cultivating heartier biofuel crops, interactome data will lead to uncovering crop-specific defense and development networks. However, the collection of protein interaction data has been limited to expensive, time-consuming, hard-to-scale assays that mostly require cloned ORF collections. For these reasons, we have successfully developed a highly scalable, economical, and sensitive yeast two-hybrid assay, ProCREate, that can be universally applied to generate proteome-wide primary interactome data. ProCREate enables en masse pooling and massively paralleled sequencing for the identification of interacting proteins by exploiting Cre-lox recombination. ProCREate can be used to screen ORF/cDNA libraries from feedstock plant tissues. The interactome data generated will yield deeper insight into many molecular processes and pathways that can be used to guide improvement of feedstock productivity and sustainability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Identifying intragenic functional modules of genomic variations associated with cancer phenotypes by learning representation of association networks

Background Genome-wide Association Studies (GWAS) aims to uncover the link between genomic variation and phenotype. They have been actively applied in cancer biology to investigate associations between variations and cancer phenotypes, such as susceptibility to certain types of cancer and predisposed responsiveness to specific treatments. Since GWAS primarily focuses on finding associations between individual genomic variations and cancer phenotypes, there are limitations in understanding the mechanisms by which cancer phenotypes are cooperatively affected by more than one genomic variation. Results This paper proposes a network representation learning approach to learn associations among genomic variations using a prostate cancer cohort. The learned associations are encoded into representations that can be used to identify functional modules of genomic variations within genes associated with early- and late-onset prostate cancer. The proposed method was applied to a prostate cancer cohort provided by the Veterans Administration’s Million Veteran Program to identify candidates for functional modules associated with early-onset prostate cancer. The cohort included 33,159 prostate cancer patients, 3181 early-onset patients, and 29,978 late-onset patients. The reproducibility of the proposed approach clearly showed that the proposed approach can improve the model performance in terms of robustness. Conclusions To our knowledge, this is the first attempt to use a network representation learning approach to learn associations among genomic variations within genes. Associations learned in this way can lead to an understanding of the underlying mechanisms of how genomic variations cooperatively affect each cancer phenotype. This method can reveal unknown knowledge in the field of cancer biology and can be utilized to design more advanced cancer-targeted therapies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Truncated dystrophin ameliorates the dystrophic phenotype of mdx mice by reducing sarcolipin-mediated SERCA inhibition

Duchenne muscular dystrophy (DMD) and the less severe Becker muscular dystrophy (BMD) are due to mutations in the DMD gene. Previous reports show that in-frame deletion of exons 45–55 produces an internally shorted, but functional, dystrophin protein resulting in a very mild BMD phenotype. In order to elucidate the molecular mechanism leading to this phenotype, we generated exon 45–55 deleted dystrophin transgenic/mdx (Tg/mdx) mice. Muscular function of Tg/mdx mice was restored close to that of wild type (WT) mice but the localization of the neuronal type of nitric oxide synthase was changed from the sarcolemma to the cytosol. This led to hyper-nitrosylation of the ryanodine receptor 1 causing increased Ca{sup 2+} release from the sarcoplasmic reticulum. On the other hand, Ca{sup 2+} reuptake by the sarcoplasmic/endoplasmic reticulum Ca{sup 2+}-ATPase (SERCA) was restored to the level of WT mice, suggesting that the Ca{sup 2+} dysregulation had been compensated by SERCA activation. In line with this, expression of sarcolipin (SLN), a SERCA-inhibitory peptide, was upregulated in mdx mice, but strongly reduced in Tg/mdx mice. Furthermore, knockdown of SLN ameliorated the cytosolic Ca{sup 2+} homeostasis and the dystrophic phenotype in mdx mice. These findings suggest that SLN may be a novel target for DMD therapy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Complement 5a stimulates macrophage polarization and contributes to tumor metastases of colon cancer

Highlights: • The mechanisms regulating the TAM M2 phenotype in tumor metastases remain unclear. • C5a regulates the M2 phenotype of TAMs in tumor metastases through NF-κB signaling. • C5aR may be a novel marker for cancer prognosis and drugs targeting for management. Inflammatory cells such as macrophages can play a pro-tumorigenic role in the tumor stroma. Tumor-associated macrophages (TAMs) generally display an M2 phenotype with tumor-promoting activity; however, the mechanisms regulating the TAM phenotype remain unclear. Complement 5a (C5a) is a cytokine-like polypeptide that is generated during complement system activation and is known to promote tumor growth. Herein, we investigated the role of C5a on macrophage polarization in colon cancer metastasis in mice. We found that deficiency of the C5a receptor (C5aR) severely impairs the metastatic ability of implanted colon cancer cells. C5aR was expressed on TAMs, which exhibited an M2-like functional profile in colon cancer liver metastatic lesions. Furthermore, C5a mediated macrophage polarization and this process relied substantially on activation of the nuclear factor-kappa B (NF-κB) pathway. Finally, analysis of human colon carcinoma indicated that C5aR expression is negatively associated with tumor differentiation grade. Our results demonstrate that C5aR has a central role in regulating the M2 phenotype of TAMs, which in turn, contributes to hepatic metastasis of colon cancer through NF-κB signaling. C5a is a potential novel marker for cancer prognosis and drugs targeting complement system activation, specifically the C5aR pathway, may offer new therapeutic opportunities for colon cancer management.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Irisin reverses platelet derived growth factor-BB-induced vascular smooth muscle cells phenotype modulation through STAT3 signaling pathway

Vascular smooth muscle cells (VSMCs) phenotype modulation toward a synthetic phenotype is the main cause of cardiovascular disease. As a newly discovered myokine, Irisin is thought to be a promising candidate for the treatment of metabolic disturbances, as well as cardiovascular disease. However, no evidence has been shown for the direct effect of Irisin on VSMCs phenotype modulation and its underling mechanisms. The aim of this study was to explore the effect of Irisin on VSMCs phenotype modulation and the mechanisms involved. In the present study, it was found that Irisin restored the PDGF-BB-induced VSMCs phenotype modulation which exhibited down-regulation of smooth muscle cells (SMC) expression and up-regulation of matrix synthesis related marker expression, as well as proliferative phenotype. Moreover, our research demonstrated that Irisin further activated STAT3 signaling pathways. Finally, by applying an STAT3 inhibitor, WP1066, we revealed the roles of STAT3 in the PDGF-BB-induced VSMCs phenotype modulation when they were treated with Irisin. Taken together, these results demonstrated that Irisin may play a crucial role in regulating VSMCs phenotype modulation via the STAT3 signaling pathway. - Highlights: • Irisin prevents PDGF-BB-stimulated VSMCs dedifferentiation. • Irisin inhibits VSMCs towards a proliferative synthetic phenotype induced by PDGF-BB stimulation. • Irisin treatment further activates STAT3 in VSMCs. • The effect of Irisin on VSMCs phenotype modulation might be STAT3-dependent.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Matrix metalloproteinase-14 mediates formation of bile ducts and hepatic maturation of fetal hepatic progenitor cells

Fetal hepatic stem/progenitor cells, called hepatoblasts, play central roles in liver development; however, the molecular mechanisms regulating the phenotype of these cells have not been completely elucidated. Matrix metalloproteinase (MMP)-14 is a type I transmembrane proteinase regulating pericellular proteolysis of the extracellular matrix and is essential for the activation of several MMPs and cytokines. However, the physiological functions of MMP-14 in liver development are unknown. Here we describe a functional role for MMP-14 in hepatic and biliary differentiation of mouse hepatoblasts. MMP-14 was upregulated in cells around the portal vein in perinatal stage liver. Formation of bile duct-like structures in MMP-14–deficient livers was significantly delayed compared with wild-type livers in vivo. In vitro biliary differentiation assays showed that formation of cholangiocytic cysts derived from MMP-14–deficient hepatoblasts was completely impaired, and that overexpression of MMP-14 in hepatoblasts promoted the formation of bile duct-like cysts. In contrast, the expression of molecules associated with metabolic functions in hepatocytes, including hepatic nuclear factor 4α and tryptophan 2,3-dioxygenase, were significantly increased in MMP-14–deficient livers. Expression of the epidermal growth factor receptor and phosphorylation of mitogen-activated protein kinases were significantly upregulated in MMP-14–deficient livers. We demonstrate that MMP-14–mediated signaling in fetal hepatic progenitor cells promotes biliary luminal formation around the portal vein and negatively controls the maturation of hepatocytes. - Highlights: • Loss of MMP-14 delayed formation of bile duct-like structures in perinatal liver. • Overexpression of MMP-14 in hepatobalsts promoted the biliary formation in vitro. • Loss of MMP-14 promoted hepatocyte maturation of hepatoblasts in vivo. • MMP-14–mediated signaling regulates terminal differentiation of hepatoblasts.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Functional analysis of a conserved site mutation in the DNA end processing enzyme PNKP leading to ataxia with oculomotor apraxia type 4 in humans

Polynucleotide kinase 3'-phosphatase (PNKP), an essential DNA end-processing enzyme in mammals with 3'-phosphatase and 5'-kinase activities, plays a pivotal role in multiple DNA repair pathways. Its functional deficiency has been etiologically linked to various neurological disorders. Recent reports have shown that mutation at a conserved glutamine (Gln) in PNKP leads to late-onset ataxia with oculomotor apraxia type 4 (AOA4) in humans and embryonic lethality in pigs. However, the molecular mechanism underlying such phenotypes remains elusive. Here, we report that the enzymatic activities of the mutant versus WT PNKP are comparable; however, cells expressing mutant PNKP and peripheral blood mononuclear cells (PBMCs) of AOA4 patients showed a significant amount of DNA double-strand break accumulation and consequent activation of the DNA damage response. Further investigation revealed that the nuclear localization of mutant PNKP is severely abrogated, and the mutant proteins remain primarily in the cytoplasm. Western blot analysis of AOA4 patient-derived PBMCs also revealed the presence of mutated PNKP predominantly in the cytoplasm. To understand the molecular determinants, we identified that mutation at a conserved Gln residue impedes the interaction of PNKP with importin alpha but not with importin beta, two highly conserved proteins that mediate the import of proteins from the cytoplasm into the nucleus. Collectively, our data suggest that the absence of PNKP in the nucleus leads to constant activation of the DNA damage response due to persistent accumulation of double-strand breaks in the mutant cells, triggering death of vulnerable brain cells—a potential cause of neurodegeneration in AOA4 patients.

59 BASIC BIOLOGICAL SCIENCES↗