A primary challenge in single-cell RNA sequencing (scRNA-seq) studies comes from the massive amount of data and the excess noise level. To address this challenge, we introduce an analysis framework, ...named single-cell Decomposition using Hierarchical Autoencoder (scDHA), that reliably extracts representative information of each cell. The scDHA pipeline consists of two core modules. The first module is a non-negative kernel autoencoder able to remove genes or components that have insignificant contributions to the part-based representation of the data. The second module is a stacked Bayesian autoencoder that projects the data onto a low-dimensional space (compressed). To diminish the tendency to overfit of neural networks, we repeatedly perturb the compressed space to learn a more generalized representation of the data. In an extensive analysis, we demonstrate that scDHA outperforms state-of-the-art techniques in many research sub-fields of scRNA-seq analysis, including cell segregation through unsupervised learning, visualization of transcriptome landscape, cell classification, and pseudo-time inference.
Fibroblast pathology in inflammatory diseases Wei, Kevin; Nguyen, Hung N; Brenner, Michael B
The Journal of clinical investigation,
10/2021, Letnik:
131, Številka:
20
Journal Article
Recenzirano
Odprti dostop
Fibroblasts are important cells for the support of homeostatic tissue function. In inflammatory diseases such as rheumatoid arthritis and inflammatory bowel disease, fibroblasts take on different ...roles (a) as inflammatory cells themselves and (b) in recruiting leukocytes, driving angiogenesis, and enabling chronic inflammation in tissues. Recent advances in single-cell profiling techniques have transformed the ability to examine fibroblast states and populations in inflamed tissues, providing evidence of previously underappreciated heterogeneity and disease-associated fibroblast populations. These studies challenge the preconceived notion that fibroblasts are homogeneous and provide new insights into the role of fibroblasts in inflammatory pathology. In addition, new molecular insights into the mechanisms of fibroblast activation reveal powerful cell-intrinsic amplification loops that synergize with primary fibroblast stimuli to result in striking responses. In this Review, we focus on recent developments in our understanding of fibroblast heterogeneity and fibroblast pathology across tissues and diseases in rheumatoid arthritis and inflammatory bowel diseases. We highlight new approaches to, and applications of, single-cell profiling techniques and what they teach us about fibroblast biology. Finally, we address how these insights could lead to the development of novel therapeutic approaches to targeting fibroblasts in disease.
Three new lanthanide-based metal–organic frameworks (Ln-MOFs), namely MOF-590, -591, and -592 constructed from a tetratopic linker, benzoimidephenanthroline tetracarboxylic acid (H4BIPA-TC), were ...synthesized under solvothermal conditions and fully characterized. All of the new MOFs exhibit three-dimensional frameworks, which adopt unprecedented topologies in MOF field. Gas adsorption measurements of MOF-591 and -592 revealed good adsorption of CO2 (low pressure, at room temperature) and moderate CO2 selectivity over N2 and CH4. Consequently, breakthrough experiments illustrated the separation of CO2 from binary mixture of CO2 and N2 with the use of MOF-592. Accordingly, MOF-592 revealed the selective CO2 capture effectively without any loss in performance after three cycles. Moreover, MOF-590, -591, and -592 showed to be catalytically active in the oxidative carboxylation of styrene and CO2 for a one-pot synthesis of styrene carbonate under mild conditions (1 atm CO2, 80 °C, and without solvent). Among the new materials, MOF-590 revealed a remarkable efficiency with exceptional conversion (96%), selectivity (95%), and yield (91%).
A novel series of two zirconium- and one indium-based metal–organic frameworks (MOFs), namely, MOF-892, MOF-893, and MOF-894, constructed from the hexatopic linker, ...1′,2′,3′,4′,5′,6′-hexakis(4-carboxyphenyl)benzene, were synthesized and fully characterized. MOF-892 and MOF-893 are two new exemplars of materials with topologies previously unseen in the important family of zirconium MOFs. MOF-892, MOF-893, and MOF-894 exhibit efficient heterogeneous catalytic activity for the cycloaddition of CO2, resulting in a cyclic organic carbonate formation with high conversion, selectivity, and yield under mild conditions (1 atm CO2, 80 °C, and solvent-free). Because of the structural features provided by their building units, MOF-892 and MOF-893 are replete with accessible Lewis and Brønsted acid sites located at the metal clusters and the non-coordinating carboxylic groups of the linkers, respectively, which is found to promote the catalytic CO2 cycloaddition reaction. As a proof-of-concept, MOF-892 exhibits high catalytic activity in the one-pot synthesis of styrene carbonate from styrene and CO2 without preliminary synthesis and isolation of styrene oxide.
With over 1 million incidence cases and more than 780,000 deaths in 2018, gastric cancer (GC) was ranked as the 5th most common cancer and the 3rd leading cause of cancer deaths worldwide. Though ...several biomarkers, including carcinoembryonic antigen (CEA), cancer antigen 19-9 (CA19-9), and cancer antigen 72-4 (CA72-4), have been identified, their diagnostic accuracies were modest. Circulating tumor cells (CTCs), cells derived from tumors and present in body fluids, have recently emerged as promising biomarkers, diagnostically and prognostically, of cancers, including GC. In this review, we present the landscape of CTCs from migration, to the presence in circulation, biologic properties, and morphologic heterogeneities. We evaluated clinical implications of CTCs in GC patients, including diagnosis, prognosis, and therapeutic management, as well as their application in immunotherapy. On the one hand, major challenges in using CTCs in GC were analyzed, from the differences of cut-off values of CTC positivity, to techniques used for sampling, storage conditions, and CTC molecular markers, as well as the unavailability of relevant enrichment and detection techniques. On the other hand, we discussed future perspectives of using CTCs in GC management and research, including the use of circulating tumor microembolies; of CTC checkpoint blockade in immunotherapy; and of organoid models. Despite the fact that there are remaining challenges in techniques, CTCs have potential as novel biomarkers and/or a non-invasive method for diagnostics, prognostics, and treatment monitoring of GC, particularly in the era of precision medicine.
This work studies the Pb(II) removal onto bentonite clay modified by hexadecyl trimethyl ammonium bromide (HDTMA). Characterizations of the unmodified and modified materials were performed by using ...XRD, SEM, TG-DSC, FT-IR, and BET surface area analyses. Factors influencing the uptake of Pb(II) from aqueous solution, such as pHsolution, ion strength, uptake time, adsorbent dosage, and initial Pb(II) concentration, were examined. The obtained results showed that bentonite clay was successfully modified by HDTMA, resulting in an increase in its surface area by about 70 %. The Pb(II) adsorption onto modified bentonite clay reached equilibrium at pH = 5.0 after 120 min. Studies within the isotherm and kinetic models demonstrated that the adsorption followed the Sips isotherm and pseudo-second-order kinetic models. The maximum monolayer adsorption capacity calculated from the Langmuir model at 30 °C was 25.8 mg/g, which is much higher than that obtained for the unmodified sample (18.9 mg/g). The FT-IR and TG-DSC analyses indicated that the formation of inner-sphere complexes plays a fundamental role in the mechanism of Pb(II) uptake onto HDTMA-bentonite clay. This mechanism of Pb(II) adsorption was further investigated, for the first time, by using the positron annihilation lifetime (PAL) and electron momentum (EMD) measurements. The PAL and EMD analyses indicated that the existence of Al and Si mono-vacancies in the HDTMA-bentonite should have essential contributions to the adsorption mechanism. In particular, we found a very interesting mechanism that the Pb(II) adsorption should occur inside the interlayer spaces of the HDTMA-bentonite.
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•Bentonite clay was modified by HDTMA to enhance the Pb(II) removal.•The Langmuir monolayer adsorption capacity of HDTMA-modified bentonite was 25.8 mg/g.•The mechanisms of Pb(II) adsorption were studied via different analytical methods.•The formation of inner-sphere complexes played a major mechanism in the Pb(II) uptake.
In this study, the biosorption mechanisms of methylene blue (MB) and Cr(
iii
) onto pomelo peel collected from our local fruits are investigated by combining experimental analysis with
ab initio
...simulations. Factors that affect the adsorption such as pH, adsorption time, adsorbent dosage and initial adsorbate concentration, are fully considered. Five isotherm models-Langmuir, Freundlich, Sips, Temkin, and Dubinin-Radushkevich-are employed to estimate the capacity of pomelo peel adsorption, whereas four kinetic models-pseudo-first-order, pseudo-second-order, Elovich and intra-diffusion models-are also used to investigate the mechanisms of the uptake of MB and Cr(
iii
) onto the pomelo fruit peel. The maximum biosorption capacities calculated from the Langmuir models for MB and Cr(
iii
) at 303 K are, 218.5 mg g
−1
and 11.3 mg g
−1
, respectively. In particular, by combining, for the first time, the experimental FT-IR spectra with those obtained from
ab initio
calculations, we are able to demonstrate that the primary adsorption mechanisms of the uptake of MB onto pomelo fruit peel are electrostatic attraction and hydrogen-bond formations, whereas the adsorption mechanisms for Cr(
iii
) are electrostatic attraction and n-d interactions.
In this study, the biosorption mechanisms of methylene blue (MB) and Cr(
iii
) onto pomelo peel collected from our local fruits are investigated by combining experimental analysis with
ab initio
simulations.
Fibroblasts are major contributors to and regulators of inflammation and dominant producers of interleukin-6 (IL-6) in inflammatory diseases like rheumatoid arthritis. Yet, compared to leukocytes, ...the regulation of inflammatory pathways in fibroblasts is largely unknown. Here, we report that analyses of genes coordinately upregulated with IL-6 pointed to STAT4 and leukemia inhibitory factor (LIF) as potentially linked. Gene silencing revealed that STAT4 was required for IL-6 transcription. STAT4 was recruited to the IL-6 promoter after fibroblast activation, and LIF receptor (LIFR) and STAT4 formed a molecular complex that, together with JAK1 and TYK2 kinases, controlled STAT4 activation. Importantly, a positive feedback loop involving autocrine LIF, LIFR, and STAT4 drove sustained IL-6 transcription. Besides IL-6, this autorine loop also drove the production of other key inflammatory factors including IL-8, granulocyte-colony stimulating factor (G-CSF), IL-33, IL-11, IL-1α, and IL-1β. These findings define the transcriptional regulation of fibroblast-mediated inflammation as distinct from leukocytes.
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•During inflammation, human fibroblasts upregulate LIF and STAT4•LIF acts in an autocrine manner via LIF receptor to promote STAT4 activation•Activated STAT4 together with NF-κB/p65-p52 and C/EBPβ enhances IL-6 transcription•LIFR/STAT4 circuit also regulates IL-8, G-CSF, IL-33, IL-11, IL-1α, and IL-1β
Growing evidence implicates fibroblasts as inflammatory cells in sites of peripheral inflammation. Nguyen and colleagues demonstrate that regulation of IL-6 along with a set of other inflammatory cytokines and chemokines is regulated by a positive feedback loop involving LIF, LIF receptor, and STAT4 that selectively operates in fibroblasts.
Fibroblasts regulate tissue homeostasis, coordinate inflammatory responses, and mediate tissue damage. In rheumatoid arthritis (RA), synovial fibroblasts maintain chronic inflammation which leads to ...joint destruction. Little is known about fibroblast heterogeneity or if aberrations in fibroblast subsets relate to pathology. Here, we show functional and transcriptional differences between fibroblast subsets from human synovial tissues using bulk transcriptomics of targeted subpopulations and single-cell transcriptomics. We identify seven fibroblast subsets with distinct surface protein phenotypes, and collapse them into three subsets by integrating transcriptomic data. One fibroblast subset, characterized by the expression of proteins podoplanin, THY1 membrane glycoprotein and cadherin-11, but lacking CD34, is threefold expanded in patients with RA relative to patients with osteoarthritis. These fibroblasts localize to the perivascular zone in inflamed synovium, secrete proinflammatory cytokines, are proliferative, and have an in vitro phenotype characteristic of invasive cells. Our strategy may be used as a template to identify pathogenic stromal cellular subsets in other complex diseases.
Nanocovax is a recombinant severe acute respiratory syndrome coronavirus 2 subunit vaccine composed of full-length prefusion stabilized recombinant SARS-CoV-2 spike glycoproteins (S-2P) and aluminium ...hydroxide adjuvant.
We conducted a dose-escalation, open label trial (phase 1) and a randomized, double-blind, placebo-controlled trial (phase 2) to evaluate the safety and immunogenicity of the Nanocovax vaccine (in 25 mcg, 50 mcg, and 75 mcg doses, aluminium hydroxide adjuvanted (0·5 mg/dose) in 2-dose regime, 28 days apart (ClinicalTrials.gov number, NCT04683484). In phase 1, 60 participants received two intramuscular injection of the vaccine following dose-escalation procedure. The primary outcomes were reactogenicity and laboratory tests to evaluate the vaccine safety. In phase 2, 560 healthy adults received either vaccine doses similar in phase 1 (25 or 50 or 75 mcg S antigen in 0·5 mg aluminium per dose) or adjuvant (0·5 mg aluminium) in a ratio of 2:2:2:1. One primary outcome was the vaccine safety, including solicited adverse events for 7 day and unsolicited adverse events for 28 days after each injection as well as serious adverse event or adverse events of special interest throughout the study period. Another primary outcome was anti-S IgG antibody response (Index unit/ml). Secondary outcomes were surrogate virus neutralisation (inhibition percentage), wild-type SARS-CoV-2 neutralisation (dilution fold), and T-cell responses by intracellular staining for interferon gamma (IFNg). Anti-S IgG and neutralising antibody levels were compared with convalescent serum samples from symptomatic Covid-19 patients.
For phase 1 study, no serious adverse events were observed for all 60 participants. Most adverse events were grade 1 and disappeared shortly after injection. For phase 2 study, after randomisation, 480 participants were assigned to receive the vaccine with adjuvant, and 80 participants were assigned to receive the placebo (adjuvant only). Reactogenicity was absent or mild in the majority of participants and of short duration (mean ≤3 days). Unsolicited adverse events were mild in most participants. There were no serious adverse events related to Nanocovax. Regarding the immunogenicity, Nanocovax induced robust anti-S antibody responses. In general, there humoral responses were similar among vaccine groups which reached their peaks at day 42 and declined afterward. At day 42, IgG levels of vaccine groups were 60·48 CI95%: 51·12–71·55, 49·11 41·26–58·46, 57·18 48·4-67·5 compared to 7·10 6·32-13·92 of convalescent samples. IgG levels reported here can be converted to WHO international standard binding antibody unit (BAU/ml) by multiplying them to a conversion factor of 21·8. Neutralising antibody titre of vaccine groups at day 42 were 89·2 52·2–152·3, 80·0 50·8–125.9 and 95·1 63·1–143·6, compared to 55·1 33·4-91·0 of the convalescent group.
Up to day 90, Nanocovax was found to be safe, well tolerated, and induced robust immune responses.
This work was funded by the Coalition for Epidemic Preparedness Innovations (CEPI), the Ministry of Science and Technology of Vietnam, and Nanogen Pharmaceutical Biotechnology JSC.
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