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At least 19 records

NF-κB and neutrophil extracellular traps cooperate to promote breast cancer progression and metastasis

Highlights: • Cancer cells–derived factors, such as IL-8 and G-CSF, induce NETs formation via PAD4 and NF-κB. • NETs increase the interaction of NEMO with IKKα/β and enhance NF-κB activation. • Blockade of NETs using PAD4 inhibitor decreases NF-κB and tumor metastasis. • Selective inhibition of NF-κB reduces NETs formation and tumor growth and metastasis. Aberrant NF-κB activation and neutrophil extracellular traps (NETs) are associated with breast cancer progression. How NF-κB and NETs modulate each other in breast cancer development remains unclear. Here, we found that NETs induced by phorbol 12-myristate 13-acetate promote breast cancer cell progression. In turn, cancer cells–derived factors, such as IL-8 and granulocyte colony-stimulating factor, stimulate neutrophils to form NETs. Mechanistically, NETs increased the interaction of NF-κB essential modifier (NEMO) with IκB kinase (IKK)α/β and enhanced NF-κB activation. We then employed a cell-permeable peptide corresponding to the NEMO-binding domain (NBD) of IKKα/β, termed NBD peptide, which disrupts NETs-mediated NEMO interaction with IKKα/β and abolished NF-κB activation in vitro. NBD peptide also reduced IL-8 level and NETs formation, and suppressed primary tumor growth and/or lung metastasis in human breast cancer mouse xenograft models and mouse spontaneous breast cancer model. Blockade of NET formation using a peptidylarginine deiminase 4 (PAD4) pharmacologic inhibitor decreased NF-κB activation and tumor metastasis. Collectively, these data suggest that NF-κB associates with NETs to form a positive loop facilitating breast tumor progression and metastasis, and that selective inhibition of NF-κB and PAD4-dependent NETs provides an effective therapeutic approach for treating breast cancer.

60 APPLIED LIFE SCIENCES↗

Continuous NF-κB pathway inhibition promotes expansion of human phenotypical hematopoietic stem/progenitor cells through metabolism regulation

Highlights: • Small molecular inhibition of NF-κB pathway efficiently expands human HSPCs. • NF-κB inhibition with TPCA-1 improves the self-renewal potential and biological function maintenance of expanded CD34{sup +} cells. • NF-κB pathway inhibition reprograms metabolism and enhances glycolysis. • Continuous NF-κB inhibition is required in the culture process to facilitate primitive HSC maintenance. Hematopoietic stem/progenitor cells (HSPCs) ex vivo expansion is critical in facilitating their widespread clinical application. NF-κB pathway is implicated in the energy homeostasis and metabolic adaptation. To explore the effect of NF-κB pathway on the ex vivo HSPC expansion and metabolism, the 50 nM–1 μM inhibitor of NF-κB pathway TPCA-1 was used to expand cord blood derived CD34{sup +} cells in serum-free culture. The expansion folds, function, mitochondrial profile and metabolism of HSPCs were determined. After 10 days of culture with 100 nM TPCA-1, the expansion of total cells CD34{sup +}CD38{sup −} cells and CD34{sup +}CD38{sup −}CD45RA{sup −}CD90{sup +}CD49f{sup +} cells were significantly increased compared to the cytokine priming alone. Notably, TPCA-1 treatment generated ~ 2-fold greater percentage of CD34{sup +}EPCR{sup +} and CD34{sup +}CD38{sup −}CD45RA{sup −}CD90{sup +}CD49f{sup +} cells compared to cytokine only conditions. Moreover, TPCA-1 expanded CD34{sup +} cells displayed enhanced serial colonies forming potential and secondary expansion capability. NF-κB inhibition increased the expression of self-renewal related genes, while downregulated the expression of mitochondrial biogenesis regulator (Pgc1α) and mitochondrial chaperones and proteases (ClpP, Hsp10, Hsp60). Mitochondrial mass and membrane potential were markedly decreased with TPCA-1 treatment, leading to the reduced mitochondrial reactive oxygen species (ROS) level in HSPCs. NF-κB inhibition displayed augmented glycolysis rate with compromising mitochondrial metabolism. This study demonstrated that NF-κB pathway inhibition improved glycolysis and limited ROS production that promoted the ex vivo expansion and maintenance of functional HSPCs.

60 APPLIED LIFE SCIENCES↗

Discrepancies between Theory and Experiment in Determining the Ionization Energy of NF 3

High-accuracy ab initio thermochemical predictions for the ionization energy of NF 3 , the barrier height (to inversion) of NF 3 + , and the dissociative ionization threshold of NF 3 to NF 2 + + F are presented and incorporated into Active Thermochemical Tables. The adiabatic ionization energy of the first ionization band of NF 3 , calculated at 12.647 ± 0.010 eV, is at odds with previous experimental interpretations by nearly 0.36 eV due to unfavorable Franck-Condon factors associated with this transition. The barrier (to inversion) height is calculated to be about 0.6 eV lower in energy than the prior interpretation, which instigates a discussion of the supposed vibrational structure of the first ionization band of NF 3 . Updated assignments of the photoelectron spectrum are proposed, and the loss in vibrational spacing on the high-energy side of the experimental ionization band is discussed. Rudimentary anharmonic Franck-Condon simulations qualitatively reproduce the broad spectral features observed in experiment.

Active Thermochemical Tables↗

BST-2/Tetherin is involved in BAFF-enhanced proliferation and survival via canonical NF-κB signaling in neoplastic B-lymphoid cells

Highlights: • BST-2 doze dependently responded to BAFF in neoplastic B cells. • BST-2 inhibition defected the proliferation and survival of neoplastic B cells. • BST-2 facilitated BAFF-induced NF-κB signaling in neoplastic B-lymphoid cells. • BAFF-induced NF-κB signaling is required for the proliferation and survival of neoplastic B cells. The development of Sjögren's syndrome (SS) is accompanied by B cell hyperproliferation and mutation. Our previous study identified aberrant expression of BST-2 (also known as Tetherin/CD317) in B cells from either the peripheral blood or infiltrated salivary glands. However, the roles of BST-2 in the regulation of B cell activation remain unknown. In this study, we identified that BST-2 can respond to BAFF simulation but not to other B cell simulators in neoplastic B cell lines. A CCK-8 assay, an EdU assay and Annexin V/PI staining indicated that BST-2 inhibition attenuated BAFF-enhanced proliferation and survival in both Raji cells and Daudi cells. Screening of BAFF-related signaling in neoplastic B-lymphoid cells indicated that BST-2 was involved in the regulation of NF-κB signaling upon BAFF simulation. However, inhibition of NF-κB by JSH-23 significantly reduced the proliferation and survival of Raji and Daudi cells under both normal and BAFF-simulated conditions. Collectively, our results indicate that BST-2/Tetherin is a BAFF-responsive membrane factor involved in the regulation of NF-κB signaling, thereby assisting in the proliferation and survival of neoplastic B-lymphoid cells. Our study provides a potential molecular mechanism underlying aberrant overactivation of B cells upon SS development.

60 APPLIED LIFE SCIENCES↗

X-ray Crystallographic Study of Preferred Spacing by the NF-κB p50 Homodimer on κB DNA

Though originally characterized as an inactive or transcriptionally repressive factor, the NF-κB p50 homodimer has become appreciated as a physiologically relevant driver of specific target gene expression. By virtue of its low affinity for cytoplasmic IκB protein inhibitors, p50 accumulates in the nucleus of resting cells, where it is a binding target for the transcriptional co-activator IκBζ. In this study, we employed X-ray crystallography to analyze the structure of the p50 homodimer on κB DNA from the promoters of human interleukin-6 (IL-6) and neutrophil-gelatinase-associated lipocalin (NGAL) genes, both of which respond to IκBζ. The NF-κB p50 homodimer binds 11-bp on IL-6 κB DNA, while, on NGAL κB DNA, the spacing is 12-bp. This begs the question: what DNA binding mode is preferred by NF-κB p50 homodimer? To address this, we engineered a “Test” κB-like DNA containing the core sequence 5'-GGGGAATTCCCC-3' and determined its X-ray crystal structure in complex with p50. This revealed that, when presented with multiple options, NF-κB p50 homodimer prefers to bind 11-bp, which necessarily imposes asymmetry on the complex despite the symmetry inherent in both the protein and its target DNA, and that the p50 dimerization domain can contact DNA via distinct modes.

59 BASIC BIOLOGICAL SCIENCES↗

NF-κB Blockade by NEMO Binding Domain Peptide Ameliorates Inflammation and Neurobehavioral Sequelae After Cranial Radiation Therapy in Juvenile Mice

Cranial radiation therapy (CRT) is a common treatment for pediatric brain tumor patients. However, side effects include significant neurobehavioral dysfunction in survivors. This dysfunction may in part be caused by inflammation, including increased production of tumor necrosis factor alpha (TNFα) and its receptor TNFR1, which can activate the nuclear factor kappa light-chain enhancer of activated B cells (NF-κB). The TNFα blockade abrogates this inflammatory response, although it presents immunologic risks. Thus, modulation of pathway subsets may be preferable. Here, we test whether inhibition of NF-κB activation using an NF-κB essential modulator binding domain (NBD) peptide mitigates CRT-induced neuroinflammation and improves behavioral outcomes.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

NF-κB activation in retinal microglia is involved in the inflammatory and neovascularization signaling in laser-induced choroidal neovascularization in mice

Highlights: • IMD0354 treatment reduced the microglia infiltration, fluorescein leakage and size of the laser CNV spots. • IKK2 inhibition suppressed phospho-IκBα, VEGF-A, and COX-2 in the Laser CNV mouse eyes. • IMD-0354 treated eyes demonstrated reduced microglial migration to the laser injury site. • In vitro, IKK2 inhibition reduced NF-κB activation, COX-2, Actin-F presence, and the microglia cells' migration capacity. To evaluate Nuclear Factor NF-κB (NF-κB) signaling on microglia activation, migration, and angiogenesis in laser-induced choroidal neovascularization (CNV).

60 APPLIED LIFE SCIENCES↗

AGTR1 blocker attenuates activation of Tenon's capsule fibroblasts after glaucoma filtration surgery via the NF-κB signaling pathway

Activation of Tenon's capsule fibroblasts limits the success rate of glaucoma filtration surgery (GFS), the most efficacious therapy for patients with glaucoma. Angiotensin type 1 receptor (AGTR1) is involved in tissues remodeling and fibrogenesis. However, whether AGTR1 is involved in the progress of fibrogenesis after GFS is not fully elucidated. The aim of this study was to investigate the role of an AGTR1 in scar formation after GFS and the potential anti-fibrosis effect of AGTR1 blocker. AGTR1 expression level was increased in subconjunctival tissues in a rat model of GFS and transforming growth factor-beta 2 (TGF-β2)-induced human Tenon's capsule fibroblasts (HTFs). AGTR1 blocker treatment suppressed TGF-β2-induced HTF migration and α-smooth muscle actin (α-SMA) and fibronectin (FN) expression. AGTR1 blocker treatment also attenuated collagen deposition and α-SMA and FN expression in subconjunctival tissues of the rat model after GFS. Moreover, AGTR1 blocker decreased TGF-β2-induced P65 phosphorylation, P65 nuclear translocation, and nuclear factor kappa B (NF-κB) luciferase activity. Additionally, BAY 11–7082 (an NF-κB inhibitor) significantly suppressed HTF fibrosis. In conclusion, our results indicate that AGTR1 is involved in scar formation after GFS. The AGTR1 blocker attenuates subconjunctival fibrosis after GFS by inhibiting the NF-κB signaling pathway. These findings indicate that targeting AGTR1 is a potential approach to attenuate fibrosis after GFS.

60 APPLIED LIFE SCIENCES↗

Structural and biochemical analyses of the nuclear IκBζ protein in complex with the NF-κB p50 homodimer

As part of the efforts to understand nuclear IκB function in NF-κB-dependent gene expression, we report an X-ray crystal structure of the IκBζ ankyrin repeat domain in complex with the dimerization domain of the NF-κB p50 homodimer. IκBζ possesses an N-terminal α helix that conveys domain folding stability. Affinity and specificity of the complex depend on a small portion of p50 at the nuclear localization signal. The model suggests that only one p50 subunit supports binding with IκBζ, and biochemical experiments confirm that IκBζ associates with DNA-bound NF-κB p50:RelA heterodimers. Comparisons of IκBζ:p50 and p50:κB DNA complex crystallographic models indicate that structural rearrangement is necessary for ternary complex formation of IκBζ and p50 with DNA.

Cell Biology↗

NF-κB perturbation reveals unique immunomodulatory functions in Prx1 + fibroblasts that promote development of atopic dermatitis

Skin is composed of diverse cell populations that cooperatively maintain homeostasis. Up-regulation of the nuclear factor κB (NF-κB) pathway may lead to the development of chronic inflammatory disorders of the skin, but its role during the early events remains unclear. Here, through analysis of single-cell RNA sequencing data via iterative random forest leave one out prediction, an explainable artificial intelligence method, we identified an immunoregulatory role for a unique paired related homeobox-1 (Prx1) + fibroblast subpopulation. Disruption of Ikkb–NF-κB under homeostatic conditions in these fibroblasts paradoxically induced skin inflammation due to the overexpression of C-C motif chemokine ligand 11 (CCL11; or eotaxin-1) characterized by eosinophil infiltration and a subsequent T H 2 immune response. Because the inflammatory phenotype resembled that seen in human atopic dermatitis (AD), we examined human AD skin samples and found that human AD fibroblasts also overexpressed CCL11 and that perturbation of Ikkb–NF-κB in primary human dermal fibroblasts up-regulated CCL11. Monoclonal antibody treatment against CCL11 was effective in reducing the eosinophilia and T H 2 inflammation in a mouse model. Together, the murine model and human AD specimens point to dysregulated Prx1 + fibroblasts as a previously unrecognized etiologic factor that may contribute to the pathogenesis of AD and suggest that targeting CCL11 may be a way to treat AD-like skin lesions.

60 APPLIED LIFE SCIENCES↗

Materials Data on SnH4(NF)2 by Materials Project

SnH4(NF)2 crystallizes in the monoclinic C2/m space group. The structure is one-dimensional and consists of two SnH4(NF)2 ribbons oriented in the (0, 1, 0) direction. Sn4+ is bonded to four equivalent N3- and two equivalent F1- atoms to form edge-sharing SnN4F2 octahedra. All Sn–N bond lengths are 2.18 Å. Both Sn–F bond lengths are 2.05 Å. N3- is bonded in a distorted water-like geometry to two equivalent Sn4+ and two H1+ atoms. There is one shorter (1.02 Å) and one longer (1.03 Å) N–H bond length. There are two inequivalent H1+ sites. In the first H1+ site, H1+ is bonded in a single-bond geometry to one N3- atom. In the second H1+ site, H1+ is bonded in a single-bond geometry to one N3- atom. F1- is bonded in a single-bond geometry to one Sn4+ atom.

36 MATERIALS SCIENCE↗

Materials Data on InH5(NF)2 by Materials Project

InH5(NF)2 crystallizes in the monoclinic P2_1/c space group. The structure is two-dimensional and consists of one InH5(NF)2 sheet oriented in the (-1, 0, 2) direction. In3+ is bonded to three N3- and three F1- atoms to form a mixture of distorted corner and edge-sharing InN3F3 octahedra. The corner-sharing octahedral tilt angles are 59°. There are a spread of In–N bond distances ranging from 2.20–2.26 Å. There are a spread of In–F bond distances ranging from 2.14–2.26 Å. There are two inequivalent N3- sites. In the first N3- site, N3- is bonded in a distorted water-like geometry to two equivalent In3+ and two H1+ atoms. Both N–H bond lengths are 1.03 Å. In the second N3- site, N3- is bonded in a distorted trigonal non-coplanar geometry to one In3+ and three H1+ atoms. All N–H bond lengths are 1.03 Å. There are five inequivalent H1+ sites. In the first H1+ site, H1+ is bonded in a single-bond geometry to one N3- atom. In the second H1+ site, H1+ is bonded in a single-bond geometry to one N3- atom. In the third H1+ site, H1+ is bonded in a single-bond geometry to one N3- atom. In the fourth H1+ site, H1+ is bonded in a single-bond geometry to one N3- atom. In the fifth H1+ site, H1+ is bonded in a single-bond geometry to one N3- atom. There are two inequivalent F1- sites. In the first F1- site, F1- is bonded in a water-like geometry to two equivalent In3+ atoms. In the second F1- site, F1- is bonded in a single-bond geometry to one In3+ atom.

36 MATERIALS SCIENCE↗

Materials Data on GaH5(NF)2 by Materials Project

GaH5(NF)2 crystallizes in the monoclinic C2/m space group. The structure is two-dimensional and consists of two GaH5(NF)2 sheets oriented in the (1, 0, 0) direction. there are two inequivalent Ga3+ sites. In the first Ga3+ site, Ga3+ is bonded to two equivalent N3- and four equivalent F1- atoms to form corner-sharing GaN2F4 octahedra. The corner-sharing octahedral tilt angles are 45°. Both Ga–N bond lengths are 1.85 Å. All Ga–F bond lengths are 2.19 Å. In the second Ga3+ site, Ga3+ is bonded to two equivalent N3- and four equivalent F1- atoms to form corner-sharing GaN2F4 octahedra. The corner-sharing octahedral tilt angles are 45°. Both Ga–N bond lengths are 2.01 Å. All Ga–F bond lengths are 1.99 Å. There are two inequivalent N3- sites. In the first N3- site, N3- is bonded in a distorted trigonal planar geometry to one Ga3+ and two H1+ atoms. Both N–H bond lengths are 1.01 Å. In the second N3- site, N3- is bonded in a distorted trigonal non-coplanar geometry to one Ga3+ and three H1+ atoms. There is one shorter (1.02 Å) and two longer (1.03 Å) N–H bond length. There are four inequivalent H1+ sites. In the first H1+ site, H1+ is bonded in a single-bond geometry to one N3- atom. In the second H1+ site, H1+ is bonded in a single-bond geometry to one N3- atom. In the third H1+ site, H1+ is bonded in a single-bond geometry to one N3- atom. In the fourth H1+ site, H1+ is bonded in a single-bond geometry to one N3- atom. F1- is bonded in a distorted bent 150 degrees geometry to two Ga3+ atoms.

36 MATERIALS SCIENCE↗

Materials Data on FeH9(NF)3 by Materials Project

FeH9(NF)3 is Hg_xSn-like structured and crystallizes in the monoclinic P2_1/c space group. The structure is zero-dimensional and consists of four FeH9(NF)3 clusters. Fe3+ is bonded in an octahedral geometry to three N3- and three F1- atoms. There are one shorter (2.15 Å) and two longer (2.16 Å) Fe–N bond lengths. There is two shorter (1.95 Å) and one longer (1.96 Å) Fe–F bond length. There are three inequivalent N3- sites. In the first N3- site, N3- is bonded in a distorted trigonal non-coplanar geometry to one Fe3+ and three H1+ atoms. All N–H bond lengths are 1.03 Å. In the second N3- site, N3- is bonded in a distorted trigonal non-coplanar geometry to one Fe3+ and three H1+ atoms. All N–H bond lengths are 1.03 Å. In the third N3- site, N3- is bonded in a distorted trigonal non-coplanar geometry to one Fe3+ and three H1+ atoms. All N–H bond lengths are 1.03 Å. There are nine inequivalent H1+ sites. In the first H1+ site, H1+ is bonded in a single-bond geometry to one N3- atom. In the second H1+ site, H1+ is bonded in a single-bond geometry to one N3- atom. In the third H1+ site, H1+ is bonded in a single-bond geometry to one N3- atom. In the fourth H1+ site, H1+ is bonded in a single-bond geometry to one N3- atom. In the fifth H1+ site, H1+ is bonded in a single-bond geometry to one N3- atom. In the sixth H1+ site, H1+ is bonded in a single-bond geometry to one N3- atom. In the seventh H1+ site, H1+ is bonded in a single-bond geometry to one N3- atom. In the eighth H1+ site, H1+ is bonded in a single-bond geometry to one N3- atom. In the ninth H1+ site, H1+ is bonded in a single-bond geometry to one N3- atom. There are three inequivalent F1- sites. In the first F1- site, F1- is bonded in a single-bond geometry to one Fe3+ atom. In the second F1- site, F1- is bonded in a single-bond geometry to one Fe3+ atom. In the third F1- site, F1- is bonded in a single-bond geometry to one Fe3+ atom.

36 MATERIALS SCIENCE↗

Materials Data on Sn(NF)2 by Materials Project

Sn(NF)2 crystallizes in the monoclinic C2/m space group. The structure is two-dimensional and consists of two Sn(NF)2 sheets oriented in the (0, 1, 0) direction. Sn4+ is bonded to four equivalent F1- atoms to form distorted edge-sharing SnF4 hexagonal bipyramids. All Sn–F bond lengths are 2.35 Å. N1- is bonded in a 2-coordinate geometry to one N1- and one F1- atom. The N–N bond length is 1.12 Å. The N–F bond length is 2.55 Å. F1- is bonded in a 3-coordinate geometry to two equivalent Sn4+ and one N1- atom.

36 MATERIALS SCIENCE↗

FOXM1-activated SIRT4 inhibits NF-κB signaling and NLRP3 inflammasome to alleviate kidney injury and podocyte pyroptosis in diabetic nephropathy

Highlights: • FOXM1 is downregulated in kidney tissues of patients with DN. • Overexpression of FOXM1 alleviates kidney injury in DN modeled mice. • Overexpression of FOXM1 reduces pyroptosis of HG-treated podocytes. • FOXM1 activates SIRT4 to inhibit the NFκB pathway and the NLRP3 inflammasome. • Downregulation of SIRT4 blocks the protective roles of FOXM1 in podocytes and mice. Forkhead box M1 (FOXM1) has been reported to play a protective role against acute kidney injury by driving tubular regeneration. This study aims to probe the function of FOXM1 in diabetic nephropathy (DN) and the molecules involved. FOXM1 was poorly expressed in DN-diseased kidney tissues. A murine model of DN was established, and podocytes cells (MPC5) were treated with high-glucose (HG) for in vitro studies. FOXM1 overexpression improved kidney function and reduced pathological changes in mice, and it increased the expression of the podocyte marker Nephrin in kidney tissues. In vitro, FOXM1 increased viability and reduced pyroptosis of the HG-treated MPC5 cells, and it elevated the expression of the podocyte marker Nephrin whereas reduced the expression of pyroptosis-related NLRP3 inflammasome and cleaved caspase 1. FOXM1 bound to the promoter of sirtuin 4 (SIRT4) to induce transcriptional activation. Downregulation of SIRT4 blocked the protective roles of FOXM1 both in vivo and in vitro. Phosphorylation of nuclear factor-kappa B (NF-κB) in HG-treated cells was suppressed by FOXM1 but restored after SIRT4 inhibition. In conclusion, this study suggested that FOXM1 transcriptionally activates SIRT4 and inhibits NF-κB signaling and the NLRP3 inflammasome to alleviate kidney injury and podocyte pyroptosis in DN.

60 APPLIED LIFE SCIENCES↗

nf-core/proteinfamilies: a scalable pipeline for the generation of protein families

The growth of metagenomics-derived amino acid sequence data has transformed our understanding of protein function, microbial diversity, and evolutionary relationships. However, the vast majority of these proteins remain functionally uncharacterized. Grouping the millions of such uncharacterized sequences with the few experimentally characterized ones allows the transfer of annotations, while the inspection of conserved residues with multiple sequence alignments can provide clues to function, even in the absence of existing functional information. To address the challenges associated with this data surge and the need to group sequences, we present a scalable, open-source, parametrizable Nextflow pipeline (nf-core/proteinfamilies) that generates nascent protein families or assigns new proteins to existing families. The computational benchmarks demonstrated that resource usage scales approximately linearly with input size, and the biological benchmarks showed that the generated protein families closely resemble manually curated families in widely used databases.

Nextflow↗

Materials Data on NF by Materials Project

NF is Wurtzite structured and crystallizes in the orthorhombic Cmc2_1 space group. The structure is zero-dimensional and consists of four monofluoroamine molecules. N1+ is bonded in a single-bond geometry to one F1- atom. The N–F bond length is 1.33 Å. F1- is bonded in a single-bond geometry to one N1+ atom.

36 MATERIALS SCIENCE↗