Anti-colon Cancer Effects of Dendrobium officinale Kimura & Migo Revealed by Network Pharmacology Integrated With Molecular Docking and Metabolomics Studies

Objective

The present study aimed to investigate the potential mechanism of Dendrobium officinale (D. officinale) on colorectal cancer and the relevant targets in the pathway using a network pharmacological approach.

Methods

(1) We identified the major bioactive components of D. officinale by UPLC-ESI-MS/MS and established the in-house library by using the literature mining method. (2) Target prediction was performed by SwissADME and SwissTargetPrediction. (3) A protein–protein interaction (PPI) network and component–target–pathway network (C-T-P network) were constructed. (4) The GO pathways and the KEGG pathway enrichment analysis were carried out by the Metascape database. (5) Molecular docking was performed by AutoDock software. (6) A series of experimental assays including cell proliferation, cell invasion and migration, and TUNEL staining in CRC were performed in CRC cell lines (HT-29, Lovo, SW-620, and HCT-116) to confirm the inhibitory effects of D. officinale.

Results

(1) In total, 396 candidate active components of D. officinale were identified by UPLC-ESI-MS/MS and selected from the database. (2) From OMIM, GeneCards, DrugBank, and TTD databases, 1,666 gene symbols related to CRC were gathered, and (3) 34 overlapping gene symbols related to CRC and drugs were obtained. (4) These results suggested that the anti-CRC components of D. officinale were mainly apigenin, naringenin, caffeic acid, γ-linolenic acid, α-linolenic acid, cis-10-heptadecenoic acid, etc., and the core targets of action were mainly ESR1, EGFR, PTGS2, MMP9, MMP2, PPARG, etc. (5) The proliferation of muscle cells, the regulation of inflammatory response, the response of cells to organic cyclic compounds, and the apoptotic signaling pathway might serve as principal pathways for CRC treatment. (6) The reliability of some important active components and targets was further validated by molecular docking. The molecular docking analysis suggested an important role of apigenin, naringenin, PTGS2, and MMP9 in delivering the pharmacological activity of D. officinale against CRC. (7) These results of the evaluation experiment in vitro suggested that D. officinale had a strong inhibitory effect on CRC cell lines, and it exerted anti-CRC activity by activating CRC cell apoptosis and inhibiting CRC cell migration and invasion.

Conclusion

This study may provide valuable insights into exploring the mechanism of action of D. officinale against CRC.

Autonomous Bionanorobots via a Cage-Shaped Silsesquioxane Vehicle for In Vivo Heavy Metal Detoxification

Nanorobots hold great promise for integrated drug delivery systems that are responsive to molecular triggers. Herein, we successfully developed an automatic smart bionanorobot that has transport capability and recognizes and removes zinc ions from poisoned cells based on nanoscale polyhedral oligomeric silsesquioxane molecules. This intelligent bionanorobot can easily move inside and outside the cell and find zinc ions owing to its highly selective recognition to zinc ions and high cell permeability, especially the well-combined high penetration and strong binding energy. More importantly, it was also found that this intelligent bionanorobot can restore round HeLa cells to a normal fusiform cell morphology following high-concentration zinc treatment and does not interfere with cell proliferation and division. It was also shown by in vivo experiments that the bionanorobot can inhibit persistent enlargement of the liver caused by zinc ion poisoning.

Rhubarb free anthraquinones improved mice nonalcoholic fatty liver disease by inhibiting NLRP3 inflammasome

Background

Nonalcoholic fatty liver disease (NAFLD) is one of the most common chronic liver diseases and has become a huge public health issue worldwide. Inhibition of nucleotide oligomerization domain-like receptors containing pyrin domain 3 (NLRP3) inflammasome is a potential therapeutic strategy for NAFLD. Currently, there are no drugs targeting NLRP3 inflammasome for clinical treatment of NAFLD. In this study, we explored the efficacy and mechanism of rhubarb free anthraquinones (RFAs) in treating NAFLD by inhibiting NLRP3 inflammasome.

Methods

First, NLRP3 inflammasome was established in mouse bone marrow-derived macrophages (BMDMs), Kuffer cells and primary hepatocytes stimulated by lipopolysaccharide (LPS) and inflammasome inducers to evaluate the effect of RFAs on inhibiting NLRP3 inflammasome and explore the possible mechanism. Further, Mice NAFLD were established by methionine and choline deficiency diet (MCD) to verify the effect of RFAs on ameliorating NAFLD by inhibiting NLRP3 inflammasome.

Results

Our results demonstrated that RFAs including rhein/diacerein, emodin, aloe emodin and 1,8-dihydroxyanthraquinone inhibited interleukin-1 beta (IL-1β) but had no effect on tumor necrosis factor-alpha (TNF-α). Similar results were also showed in mouse primary hepatocytes and Kuffer cells. RFAs inhibited cleavage of caspase-1, formation of apoptosis-associated speck-like protein containing a CARD (ASC) speck, and the combination between NLRP3 and ASC. Moreover, RFAs improved liver function, serum inflammation, histopathological inflammation score and liver fibrosis.

Conclusions

RFAs including rhein/diacerein, emodin, aloe emodin and 1,8-dihydroxyanthraquinone ameliorated NAFLD by inhibiting NLRP3 inflammasome. RFAs might be a potential therapeutic agent for NAFLD.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s12967-022-03495-4.

Diacerein/rhein as NLRP3 blockers used in treating osteoarthritis clinically.

RFAs including rhein/diacerein are main components of Rhubarb contained in yinchenhao decoction.

RFAs inhibited the transcription and assembly of NLRP3 inflammasome.

RFAs, Rhubarb and yinchenhao decoction improved NAFLD probably by inhibiting NLRP3 inflammasome.

RFAs are the potential NLRP3 inflammasome blockers for treating NAFLD clinically.

Ethnicity evaluation of ferric pyrophosphate citrate among Asian and Non-Asian populations: a population pharmacokinetics analysis

Purpose

To evaluate the potential ethnic differences of ferric pyrophosphate citrate (FPC, Triferic) in healthy subjects and patients with hemodialysis-dependent stage 5 chronic kidney disease (CKD-5HD) and identify covariates that may influence pharmacokinetics (PK) of FPC.

Methods

Data were collected from 2 Asian and 4 non-Asian clinical studies involving healthy subjects and CKD-5HD patients. Three population PK models were developed: M1 for intravenous (IV) administration of FPC in healthy subjects; M2 for dialysate administration of FPC in CKD-5HD patients; M3 for pre-dialyzer administration of FPC in CKD-5HD patients. All the models were fitted to concentration versus time data of FPC using the nonlinear mixed effect approach with the NONMEM^® program. All statistical analyses were performed using SAS version 9.4.

Results

In total, 26 Asians and 65 non-Asians were included in the final model analysis database. Forty healthy subjects were administered FPC via intravenous (IV) route and 51 patients with CKD-5HD via dialysate (N = 50) and pre-dialyzer blood circuit administration (N = 51). The PK parameters of FPC IV were similar. The population PK model showed good parameter precision and reliability as shown by model evaluation, and no relevant influence of ethnicity on PK parameters was observed. In healthy subjects, the maximum observed plasma concentration (C_max) and area under the plasma concentration–time curve (AUC) decreased with increase in lean body mass (LBM) and the average serum total iron at 6 h before the baseline period (Fe_av), whereas, in both patient populations, C_max and AUC decreased with increase in LBM and decrease in Fe_baseline. Other factors such as gender, age, Fe_av, and ethnicity had no influence on PK exposures in patients. The influence of LBM on PK exposures in patients was smaller than that in healthy subjects (ratio of AUC_0-24 for the 5th [68 kg] and 95th [45 kg] patient’s LBM was almost 1). The influence of Fe_av and LBM on PK exposures was < 50%.

Conclusion

The population pharmacokinetics model successfully described the PK parameters of FPC in healthy subjects and CKD-5HD patients and were comparable between Asian and non-Asian populations.

Supplementary information

The online version contains supplementary material available at 10.1007/s00228-022-03328-9.

Pharmacokinetics and Safety of Ferric Pyrophosphate Citrate in Chinese Subjects with and without Hemodialysis-Dependent Stage 5 Chronic Kidney Disease

BACKGROUND AND OBJECTIVE

Anemia caused by iron depletion is common in patients with hemodialysis-dependent stage 5 chronic kidney disease (CKD-5HD) patients. To maintain the iron levels, external administration of iron is essential. Ferric pyrophosphate citrate (FPC) is a novel, water-soluble complex iron salt. The present study was conducted to evaluate the pharmacokinetic (PK) parameters and safety of FPC in adult healthy Chinese subjects and patients with CKD-5HD.

METHODS

Two open-label, single-center studies were conducted in healthy subjects and patients with CKD-5HD. Healthy subjects received a single intravenous dose of 6.5 mg FPC solution, while CKD-5HD patients were randomized to two different sequences of FPC administration at two sequential hemodialysis (HD) treatments (dose 1 and dose 2). Patients received 27.2 mg of FPC at a dialysate concentration of 95 μg/L for 4 h or a single 6.5 mg dose of FPC administered intravenously via the pre-dialyzer blood circuit. The primary objective was to determine the PK parameters of total serum iron (Fetot), while the secondary objective was the safety of the FPC solution. PK parameters were calculated using Phoenix WinNonlin 8.1 and other parameters were analyzed using SAS 9.4 software. Comparison between HD dose 2 and HD dose 1 was performed using the Wilcoxon rank-sum test and analysis of variance (ANOVA).

RESULTS

A total of 14 healthy subjects with a mean age of 30.8 ± 5.92 years and 12 HD patients with a mean age of 54.3 ± 16.47 years were included. In healthy subjects, the peak serum concentration was reached at the end of infusion of FPC, with an adjusted mean maximum concentration (Cmax,) of 33.46 ± 4.83 μmol/L at a mean time to reach Cmax (Tmax) of 4.09 ± 0.19 h. In patients with CKD-5HD, the adjusted mean Cmax of HD dose 2 was 25.37 ± 4.30 μmol/L at a Tmax, of 3.09 ± 0.32 h, whereas the Cmax, of HD dose 1 was 24.59 ± 4.77 μmol/L at a Tmax, of 3.96 ± 0.26 h. The Fetot concentration-time curves were observed to be similar for both administration methods (HD doses 1 and 2), while the PK parameters differed significantly for Tmax (p = 0.001; baseline correction) and area under the concentration-time curve from time zero to time t (AUCt) [p = 0.031 for cycle variance; without baseline correction] between HD doses 1 and 2. The geometric mean ratios (HD dose 1/HD dose 2) for Cmax and AUCt were within the 85-125% range (Cmax 96.56%; AUCt 96.07%). A total of three and two incidences of adverse events were reported in healthy subjects and patients with CKD-5HD, respectively.

CONCLUSION

FPC showed a good PK and safety profile and hence can be used as maintenance therapy for patients with CKD-5HD by choosing a better method of administration based on clinical feasibility and requirement.

CLINICAL TRIAL REGISTRATION

CTR20181113 and CTR20181119.

Safety and pharmacokinetic profile of pretomanid in healthy Chinese adults: Results of a phase I single dose escalation study

We investigated the safety, tolerability and pharmacokinetic (PK) profile of pretomanid (formerly PA-824) in healthy Chinese volunteers. This was a single-center, double-blind, placebo-controlled, phase I dose escalation study, in which healthy volunteers were consecutively allocated to increasing pretomanid dose groups (50, 100, 200, 400, 600, 800, or 1000 mg) and randomized to receive pretomanid or matching placebo. The primary objective was to evaluate the safety, tolerability and PK profile of pretomanid. In total, 306 volunteers were screened, and 60 were assigned to treatment (pretomanid: n = 46, placebo: n = 14) of whom 83.3% were male, age ranged from 19 to 39 years and BMI ranged from 19.2 to 25.9 kg/m². At least one adverse event (AE) was reported by 67.4% of subjects assigned to pretomanid and 50.0% of those who received placebo, there were no serious AEs or AEs leading to withdrawal. Drug-related events that occurred in ≥5% of participants assigned to pretomanid were proteinuria (26.1%), insignificant microscopic hematuria (15.2%), conjugated hyperbilirubinemia (6.5%), hyperbilirubinemia (6.5%) and elevated uric acid (6.5%). No relationship between pretomanid dose and AEs was observed. In the PK analysis (n = 46), maximum pretomanid plasma concentration was reached in a median of 4 h in all dose groups except 800 mg (12 h) and the plasma half-life ranged from 20.2 to 25.2 h. No dose proportionality was observed for maximum plasma concentration, or area under the plasma concentration curve. In conclusion, single pretomanid doses from 50 to 1000 mg were well tolerated in healthy Chinese participants and the PK profile was generally consistent with findings in non-Chinese populations.

Design and development of novel fluorescence sensing material for exosome recognition

Exosomes are extracellular vesicles with relatively specific expression of CD63 transmembrane protein. In this study, We designed and constructed a multisite-targeting polymer which has both fluorescence and targeting recognition. It can bond to the hydrophilic group of CD63 by connecting with hydrogen. The chemical structure and the ability to combine with CD63 of fluorescent monomer and polymer were characterized and confirmed by FTIR and 1H NMR. MTT assay was performed to detect the cytotoxicity and biocompatibility of this polymer. Then we found the cell viability was 80.64% and the hemolysis rate of erythrocyte was only 0.101% even at F concentration of 20 µM. In vitro, the proposed polymer showed better ability to enter cells after linking exosomes via CD63; in vivo, it showed the ability to bind stably to exosomes and target tumor implants.

Novel Lysosome-Targeting Fluorescence Off-On Photosensitizer for Near-Infrared Hypoxia Imaging and Photodynamic Therapy In Vitro and In Vivo

Photodynamic therapy (PDT) has emerged as a new antitumor modality. Hypoxia, a vital characteristic of solid tumors, can be explored to stimulate the fluorescence response of photosensitizers (PSs). Considering the characteristics of PDT, the targeting of organelles employing PS would enhance antitumor effects. A new multifunctional cyanine-based PS (CLN) comprising morpholine and nitrobenzene groups was prepared and characterized. It generated fluorescence in the near-infrared (NIR) region in the presence of sodium dithionite (Na₂S₂O₄) and nitroreductase (NTR). The response mechanism of CLN was well investigated, thus revealing that its obtained reduction product was CLNH. The obtained fluorescence and singlet oxygen quantum yield of CLNH were 8.65% and 1.60%, respectively. Additionally, the selective experiment for substrates indicated that CLN exhibited a selective response to NTR. Thus, CLN fluorescence could be selectively switched on and its fluorescence intensity increased, following a prolonged stay in hypoxic cells. Furthermore, fluorescence colocalization demonstrated that CLN could effectively target lysosomes. CLN could generate reactive oxygen species and kill tumor cells (IC50 for 4T1 cells was 7.4 μM under a hypoxic condition), following its response to NTR. NIR imaging and targeted PDT were finally applied in vivo.

Large-scale chromatin reorganization reactivates placenta-specific genes that drive cellular aging

Nuclear deformation, a hallmark frequently observed in senescent cells, is presumed to be associated with the erosion of chromatin organization at the nuclear periphery. However, how such gradual changes in higher-order genome organization impinge on local epigenetic modifications to drive cellular mechanisms of aging has remained enigmatic. Here, through large-scale epigenomic analyses of isogenic young, senescent, and progeroid human mesenchymal progenitor cells (hMPCs), we delineate a hierarchy of integrated structural state changes that manifest as heterochromatin loss in repressive compartments, euchromatin weakening in active compartments, switching in interfacing topological compartments, and increasing epigenetic entropy. We found that the epigenetic de-repression unlocks the expression of pregnancy-specific beta-1 glycoprotein (PSG) genes that exacerbate hMPC aging and serve as potential aging biomarkers. Our analyses provide a rich resource for uncovering the principles of epigenomic landscape organization and its changes in cellular aging and for identifying aging drivers and intervention targets with a genome-topology-based mechanism.

A study of the inclusion complex formed between cucurbit[8]uril and isonicotinic acid

The complexation between cucurbit[8]uril, Q[8], and isonicotinic acid has been studied using 1H NMR spectroscopy, UV–Vis absorption spectroscopy, Raman spectroscopy and single crystal X-ray diffraction. The results revealed that the 2:1 inclusion complex (4-PA)2@Q[8]·25H2O is formed, with two guests simultaneously encapsulated in the hydrophobic cavity; the mean planes of the guests are 3.535 Å apart.

Graphical abstract

Biomimetic Organic-Inorganic Hybrid Membranes for Removal of Fluoride Ions

Carbon nanofibers (CaNFs) exhibit promising applications in the fields of environmental science and nanotechnology, and self-assembled peptide nanofibers (PNFs) are useful for the biomimetic synthesis of organic-inorganic hybrid nanomaterials and the fabrication of functional hybrid membranes for the removal of various pollutants from water. In this work, we report the biomimetic synthesis of hybrid nanomaterials by the interweaving of CaNFs and PNFs. Using the biomimetic mineralization properties of PNFs, ZrO₂ nanoparticles were synthesized along the nanofiber surface, and then functional nanohybrid porous membranes were prepared by the vacuum filtration technology. For the fabrication of membranes, the amount of PNFs and ZrO₂ precursors in the hybrid membrane were optimized. The designed organic-inorganic hybrid membranes exhibited high removal performance for fluorine ion (F⁻) from water, and the removal efficiency of the fabricated membranes towards F⁻ ion-containing aqueous solution with a concentration of 50–100 mg/L reached more than 80%. In addition, the nanofiltration membranes revealed good adsorption capacity for F⁻ ions. It is expected that the strategies shown in this study will be beneficial for the design, biomimetic synthesis, and fabrication of nanoporous membranes for economic, rapid, and efficient water purification.

Two-Dimensional Material-Based Electrochemical Sensors/Biosensors for Food Safety and Biomolecular Detection

Two-dimensional materials (2DMs) exhibited great potential for applications in materials science, energy storage, environmental science, biomedicine, sensors/biosensors, and others due to their unique physical, chemical, and biological properties. In this review, we present recent advances in the fabrication of 2DM-based electrochemical sensors and biosensors for applications in food safety and biomolecular detection that are related to human health. For this aim, firstly, we introduced the bottom-up and top-down synthesis methods of various 2DMs, such as graphene, transition metal oxides, transition metal dichalcogenides, MXenes, and several other graphene-like materials, and then we demonstrated the structure and surface chemistry of these 2DMs, which play a crucial role in the functionalization of 2DMs and subsequent composition with other nanoscale building blocks such as nanoparticles, biomolecules, and polymers. Then, the 2DM-based electrochemical sensors/biosensors for the detection of nitrite, heavy metal ions, antibiotics, and pesticides in foods and drinks are introduced. Meanwhile, the 2DM-based sensors for the determination and monitoring of key small molecules that are related to diseases and human health are presented and commented on. We believe that this review will be helpful for promoting 2DMs to construct novel electronic sensors and nanodevices for food safety and health monitoring.

Management of granulomatous lobular mastitis: an international multidisciplinary consensus (2021 edition)

Granulomatous lobular mastitis (GLM) is a rare and chronic benign inflammatory disease of the breast. Difficulties exist in the management of GLM for many front-line surgeons and medical specialists who care for patients with inflammatory disorders of the breast. This consensus is summarized to establish evidence-based recommendations for the management of GLM. Literature was reviewed using PubMed from January 1, 1971 to July 31, 2020. Sixty-six international experienced multidisciplinary experts from 11 countries or regions were invited to review the evidence. Levels of evidence were determined using the American College of Physicians grading system, and recommendations were discussed until consensus. Experts discussed and concluded 30 recommendations on historical definitions, etiology and predisposing factors, diagnosis criteria, treatment, clinical stages, relapse and recurrence of GLM. GLM was recommended as a widely accepted definition. In addition, this consensus introduced a new clinical stages and management algorithm for GLM to provide individual treatment strategies. In conclusion, diagnosis of GLM depends on a combination of history, clinical manifestations, imaging examinations, laboratory examinations and pathology. The approach to treatment of GLM should be applied according to the different clinical stage of GLM. This evidence-based consensus would be valuable to assist front-line surgeons and medical specialists in the optimal management of GLM.

The Combination of Two-Dimensional Nanomaterials with Metal Oxide Nanoparticles for Gas Sensors: A Review

Metal oxide nanoparticles have been widely utilized for the fabrication of functional gas sensors to determine various flammable, explosive, toxic, and harmful gases due to their advantages of low cost, fast response, and high sensitivity. However, metal oxide-based gas sensors reveal the shortcomings of high operating temperature, high power requirement, and low selectivity, which limited their rapid development in the fabrication of high-performance gas sensors. The combination of metal oxides with two-dimensional (2D) nanomaterials to construct a heterostructure can hybridize the advantages of each other and overcome their respective shortcomings, thereby improving the sensing performance of the fabricated gas sensors. In this review, we present recent advances in the fabrication of metal oxide-, 2D nanomaterials-, as well as 2D material/metal oxide composite-based gas sensors with highly sensitive and selective functions. To achieve this aim, we firstly introduce the working principles of various gas sensors, and then discuss the factors that could affect the sensitivity of gas sensors. After that, a lot of cases on the fabrication of gas sensors by using metal oxides, 2D materials, and 2D material/metal oxide composites are demonstrated. Finally, we summarize the current development and discuss potential research directions in this promising topic. We believe in this work is helpful for the readers in multidiscipline research fields like materials science, nanotechnology, chemical engineering, environmental science, and other related aspects.

An enhancer variant at 16q22.1 predisposes to hepatocellular carcinoma via regulating PRMT7 expression

Most cancer causal variants are found in gene regulatory elements, e.g., enhancers. However, enhancer variants predisposing to hepatocellular carcinoma (HCC) remain unreported. Here we conduct a genome-wide survey of HCC-susceptible enhancer variants through a three-stage association study in 11,958 individuals and identify rs73613962 (T > G) within the intronic region of PRMT7 at 16q22.1 as a susceptibility locus of HCC (OR = 1.41, P = 6.02 × 10^-10). An enhancer dual-luciferase assay indicates that the rs73613962-harboring region has allele-specific enhancer activity. CRISPR-Cas9/dCas9 experiments further support the enhancer activity of this region to regulate PRMT7 expression. Mechanistically, transcription factor HNF4A binds to this enhancer region, with preference to the risk allele G, to promote PRMT7 expression. PRMT7 upregulation contributes to in vitro, in vivo, and clinical HCC-associated phenotypes, possibly by affecting the p53 signaling pathway. This concept of HCC pathogenesis may open a promising window for HCC prevention/treatment.

a Versatile Schiff Base Chemosensor for the Determination of Trace Co2+, Ni2+, Cu2+, and Zn2+ in the Water and Its Bioimaging Applications

In this work, a simple and versatile Schiff base chemosensor (L) was developed for the detection of four adjacent row 4 metal ions (Co²⁺, Ni²⁺, Cu²⁺, and Zn²⁺) through colorimetric or fluorescent analyses. L could recognize the target ions in solutions containing a wide range of other cations and anions. The recognition mechanisms were verified with a Job's plot, HR-MS assays, and ¹H NMR titration experiments. Then, L was employed to develop colorimetric test strips and TLC plates for Co²⁺. Meanwhile, L was capable of quantitatively measuring the amount of target ions in tap water and river water samples. Notably, L was used for imaging Zn²⁺ in HepG2 cells, zebrafish, and tumor-bearing mice, which demonstrated its potential biological applications. Therefore, L can probably serve as a versatile tool for the detection of the target metal ions in environmental and biological applications.

Recent advances in the hybridization of cellulose and carbon nanomaterials: Interactions, structural design, functional tailoring, and applications

Due to the good biocompatibility and flexibility of cellulose and the excellent optical, electronic, as well as mechanical properties of carbon nanomaterials (CNMs), cellulose/CNM hybrid materials have been widely synthesized and used in energy storage, sensors, adsorption, biomedicine, and many other fields. In this review, we present recent advances (2016-current) in the design, structural design, functional tailoring and various applications of cellulose/CNM hybrid materials. For this aim, first the interactions between cellulose and CNMs for promoting the formation of cellulose/CNM materials are analyzed, and then the hybridization between cellulose with various CNMs for tailoring the structures and functions of hybrid materials is introduced. Further, abundant applications of cellulose/CNM hybrid materials in various fields are presented and discussed. This comprehensive review will be helpful for readers to understand the functional design and facile synthesis of cellulose-based nanocomposites, and to promote the high-performance utilization and sustainability of biomass materials in the future.

The CTCF/LncRNA‐PACERR complex recruits E1A binding protein p300 to induce pro‐tumour macrophages in pancreatic ductal adenocarcinoma via directly regulating PTGS2 expression

Background

Tumour‐associated macrophages (TAMs) play an important role in promoting the progression of pancreatic ductal adenocarcinoma (PDAC). Here, we aimed to study the epigenetic mechanisms in regulating pro‐tumour M2‐polarised TAMs in the PDAC tumour microenvironment.

Methods

This study was conducted based on ex vivo TAMs isolated from PDAC tissues and in vitro THP1‐derived TAM model. RNA‐sequencing (RNA‐seq), assay for transposase‐accessible chromatin with sequencing and chromatin immunoprecipitation sequencing were performed to investigate gene expression, chromatin accessibility, transcription factor binding sites and histone modifications. Gene knockdown in THP1‐derived TAMs was performed with lentivirus, and the impact of THP1‐derived TAMs on invasion and metastasis ability of PDAC cells were investigated with in vitro and in vivo functional assays. RNA‐chromatin interaction was analysed by chromatin isolation through RNA purification with sequencing. RNA‐protein interaction was studied by RNA immunoprecipitation and RNA pull‐down.

Results

Our data showed that the transcription factor CTCF (CCCTC‐binding factor) was highly expressed in TAMs and predicted to be significantly enriched in hyper‐accessible chromatin regions when compared to monocytes. High infiltration of CTCF⁺ TAMs was significantly associated with poor prognosis in PDAC patients. Knockdown of CTCF in THP1‐derived TAMs led to the down‐regulation of specific markers for M2‐polarised TAMs, including CD206 and CD163. When THP1‐derived TAMs with CTCF knockdown, they showed a decreased ability of invasion and metastasis. Further integrative analysis of multi‐omics data revealed that prostaglandin‐endoperoxide synthase 2 (PTGS2) and PTGS2 antisense NF‐κB1 complex‐mediated expression regulator RNA (PACERR) were critical downstream targets of CTCF and positively correlated with each other, which are closely situated on a chromosome. Knockdown of PACERR exhibited a similar phenotype as observed in CTCF knockdown THP1‐derived TAMs. Moreover, PACERR could directly bind to CTCF and recruit histone acetyltransferase E1A binding protein p300 to the promoter regions of PACERR and PTGS2, thereby enhancing histone acetylation and gene transcription, promoting the M2 polarization of TAMs in PDAC.

Conclusions

Our study demonstrated a novel epigenetic regulation mechanism of promoting pro‐tumour M2‐polarised TAMs in the PDAC tumour microenvironment.

A new toad species of the genus Brachytarsophrys Tian & Hu, 1983 (Anura, Megophryidae) from Guizhou Province, China

Background

The toads of the genus Brachytarsophrys Tian & Hu, 1983 are distributed in southern China, Myanmar, Vietnam, Laos and northern Thailand. Seven species of the genus have been recognised, of which five of them are known from China so far.

New information

Brachytarsophrysqiannanensis sp. nov., a new species of the short-legged toad genus is here described from southern Guizhou Province, China. Diagnostic characters of the new species are illustrated and comparisons with its congeners are provided. Its validity is also affirmed by its distinct mitochondrial gene sequence divergence with all congeners and its monophyly recovered in the mitochondrial gene-based phylogenetic analyses.

Changes in the phenotype and function of mucosal-associated invariant T cells in neutrophilic asthma

Asthma is a chronic heterogeneous inflammatory disease. Most neutrophilic asthma (NA) cases are severe asthma involving many inflammatory cells and mediators, although the specific pathogenesis is not clear. Mucosal-associated invariant T (MAIT) cells as innate-like T lymphocytes play an important role in the immune response in asthma by producing cytokines. In this study, we evaluated the phenotype and function of circulating MAIT cells in patients with NA and inflammatory-related cytokines in plasma and induced sputum supernatants using flow cytometry. The results showed that the frequency of circulating MAIT cells in asthma patients, particularly NA patients, decreased significantly, and CD8⁺ MAIT and MAIT Temra cells also decreased significantly. Increased expression of CD69 and PD-1 on MAIT cells indicated excessive activation and depletion, leading to the decrease in MAIT cells. Levels of IL-17A and TNF-α secreted by MAIT cells of NA patients increased, whereas IFN-γ levels decreased, indicating that MAIT cells in NA are biased to the Th17 subtype. MAIT cells were also negatively correlated with clinical parameters, indicating that these cells are related to asthma severity. Pro-inflammatory cytokines in plasma and sputum supernatant increased to varying degrees, whereas IL-10 declined, corresponding with asthma severity. We speculate that increased IL-17A and TNF-α synergistically stimulated respiratory epithelial cells to secrete IL-6 and IL-8, thereby recruiting neutrophils to inflammatory sites and aggravating asthma symptoms. Therefore, MAIT cells could serve as a potential therapeutic target in NA immunity, thus providing a new strategy for the treatment of asthma.

Two-dimensional material-based functional aerogels for treating hazards in the environment: synthesis, functional tailoring, applications, and sustainability analysis

Environmental pollution is a global problem that endangers human health and ecological balance. As a new type of functional material, two-dimensional material (2DM)-based aerogel is one of the most promising candidates for pollutant detection and environmental remediation. The porous, network-like, interconnected three-dimensional (3D) structure of 2DM-based aerogels can not only preserve the characteristics of the original 2DMs, but also bring many distinct physical and chemical properties to offer abundant active sites for adsorbing and combining pollutants, thereby facilitating highly efficient monitoring and treatment of hazardous pollutants. In this review, the synthesis methods of 2DM aerogels and their broad environmental applications, including various sensors, adsorbents, and photocatalysts for the detection and treatment of pollutants, are summarized and discussed. In addition, the sustainability of 2DM aerogels compared to other water purification materials, such as activated carbon, 2DMs, and other aerogels are analyzed by the Sustainability Footprint method. According to the characteristics of different 2DMs, special focuses and perspectives are given on the adsorption properties of graphene, MXene, and boron nitride aerogels, as well as the sensing and photocatalytic properties of transition metal dichalcogenide/oxide and carbon nitride aerogels. This comprehensive work introduces the synthesis, modification, and functional tailoring strategies of different 2DM aerogels, as well as their unique characteristics of adsorption, photocatalysis, and recovery, which will be useful for the readers in various fields of materials science, nanotechnology, environmental science, bioanalysis, and others.

Tailoring Peptide Self-Assembly and Formation of 2D Nanoribbons on Mica and HOPG Surface

Studying the interactions between biomolecules and material interfaces play a crucial role in the designing and synthesizing of functional bionanomaterials with tailored structure and function. Previously, a lot of studies were performed on the self-assembly of peptides in solution through internal and external stimulations, which mediated the creation of peptide nanostructures from zero-dimension to three-dimension. In this study, we demonstrate the self-assembly behavior of the GNNQQNY peptide on the surface of mica and highly oriented pyrolytic graphite through tailoring the self-assembly conditions. Various factors, such as the type of dissolvent, peptide concentration, pH value, and evaporation period on the formation of peptide nanofibers and nanoribbons with single- and bi-directional arrays are investigated. It is found that the creation of peptide nanoribbons on both mica and HOPG can be achieved effectively through adjusting and optimizing the experimental parameters. Based on the obtained results, the self-assembly and formation mechanisms of peptide nanoribbons on both material interfaces are discussed. It is expected that the findings obtained in this study will inspire the design of motif-specific peptides with high binding affinity towards materials and mediate the green synthesis of peptide-based bionanomaterials with unique function and application potential.

Encapsulation of l-valine, d-leucine and d-methionine by cucurbit[8]uril

The binding interactions of cucurbit[8]uril (Q[8]) with l-valine, d-leucine, and d-methionine, both in aqueous solution and solid state, have been studied by 1H NMR spectroscopy and X-ray crystallography.

Host-guest inclusion complexes formed between a symmetrical tetrasubstituted cucurbit[6]uril and glycine

Herein, we have investigated the host-guest inclusion complexes formed on interaction of the symmetric tetramethyl-substituted cucurbit[6]uril (TMeQ[6]) with glycine (Gly) under different conditions. The interactions have been studied both in...

Pre-existing chromatin accessibility of switchable repressive compartment delineates cell plasticity

Cell plasticity endows differentiated cells with competence to be reprogrammed to other lineages. Although extrinsic factors driving cell-identity conversion have been extensively characterized, it remains elusive which intrinsic epigenetic attributes, including high-order chromatin organization, delineate cell plasticity. By analysing the transcription-factor-induced transdifferentiation from fibroblasts to hepatocytes, we uncovered contiguous compartment-switchable regions (CSRs) as a unique chromatin unit. Specifically, compartment B-to-A CSRs, enriched with hepatic genes, possessed a mosaic status of inactive chromatin and pre-existing and continuous accessibility in fibroblasts. Pre-existing accessibility enhanced the binding of inducible factor Foxa3, which triggered epigenetic activation and chromatin interaction as well as hepatic gene expression. Notably, these changes were restrained within B-to-A CSR boundaries that were defined by CTCF occupancy. Moreover, such chromatin organization and mosaic status were detectable in different cell types and involved in multiple reprogramming processes, suggesting an intrinsic chromatin attribute in understanding cell plasticity.

Identification of hub genes and construction of an mRNA-miRNA-lncRNA network of gastric carcinoma using integrated bioinformatics analysis

Background

Gastric carcinoma (GC) is one of the most common cancer globally. Despite its worldwide decline in incidence and mortality over the past decades, gastric cancer still has a poor prognosis. However, the key regulators driving this process and their exact mechanisms have not been thoroughly studied. This study aimed to identify hub genes to improve the prognostic prediction of GC and construct a messenger RNA-microRNA-long non-coding RNA(mRNA-miRNA-lncRNA) regulatory network.

Methods

The GSE66229 dataset, from the Gene Expression Omnibus (GEO) database, and The Cancer Genome Atlas (TCGA) database were used for the bioinformatic analysis. Differential gene expression analysis methods and Weighted Gene Co-expression Network Analysis (WGCNA) were used to identify a common set of differentially co-expressed genes in GC. The genes were validated using samples from TCGA database and further validation using the online tools GEPIA database and Kaplan-Meier(KM) plotter database. Gene set enrichment analysis(GSEA) was used to identify hub genes related to signaling pathways in GC. The RNAInter database and Cytoscape software were used to construct an mRNA-miRNA-lncRNA network.

Results

A total of 12 genes were identified as the common set of differentially co-expressed genes in GC. After verification of these genes, 3 hub genes, namely CTHRC1, FNDC1, and INHBA, were found to be upregulated in tumor and associated with poor GC patient survival. In addition, an mRNA-miRNA-lncRNA regulatory network was established, which included 12 lncRNAs, 5 miRNAs, and the 3 hub genes.

Conclusions

In summary, the identification of these hub genes and the establishment of the mRNA-miRNA-lncRNA regulatory network provide new insights into the underlying mechanisms of gastric carcinogenesis. In addition, the identified hub genes, CTHRC1, FNDC1, and INHBA, may serve as novel prognostic biomarkers and therapeutic targets.

Recent Advances in Bunyavirus Reverse Genetics Research: Systems Development, Applications, and Future Perspectives

Bunyaviruses are members of the Bunyavirales order, which is the largest group of RNA viruses, comprising 12 families, including a large group of emerging and re-emerging viruses. These viruses can infect a wide variety of species worldwide, such as arthropods, protozoans, plants, animals, and humans, and pose substantial threats to the public. In view of the fact that a better understanding of the life cycle of a highly pathogenic virus is often a precondition for developing vaccines and antivirals, it is urgent to develop powerful tools to unravel the molecular basis of the pathogenesis. However, biosafety level −3 or even −4 containment laboratory is considered as a necessary condition for working with a number of bunyaviruses, which has hampered various studies. Reverse genetics systems, including minigenome (MG), infectious virus-like particle (iVLP), and infectious full-length clone (IFLC) systems, are capable of recapitulating some or all steps of the viral replication cycle; among these, the MG and iVLP systems have been very convenient and effective tools, allowing researchers to manipulate the genome segments of pathogenic viruses at lower biocontainment to investigate the viral genome transcription, replication, virus entry, and budding. The IFLC system is generally developed based on the MG or iVLP systems, which have facilitated the generation of recombinant infectious viruses. The MG, iVLP, and IFLC systems have been successfully developed for some important bunyaviruses and have been widely employed as powerful tools to investigate the viral replication cycle, virus–host interactions, virus pathogenesis, and virus evolutionary process. The majority of bunyaviruses is generally enveloped negative-strand RNA viruses with two to six genome segments, of which the viruses with bipartite and tripartite genome segments have mostly been characterized. This review aimed to summarize current knowledge on reverse genetic studies of representative bunyaviruses causing severe diseases in humans and animals, which will contribute to the better understanding of the bunyavirus replication cycle and provide some hints for developing designed antivirals.

Effects of Different Molecular Weight Polysaccharides From Dendrobium officinale Kimura & Migo on Human Colorectal Cancer and Transcriptome Analysis of Differentially Expressed Genes

We investigated the antitumor effects of four fractions of Dendrobium officinale Kimura & Migo (D. officinale) polysaccharides with different molecular weights (Mw), Astragalus membranaceus polysaccharides (APS) and Lentinus edodes polysaccharides (LNT) on colorectal cancer (CRC) using a zebrafish xenograft model. Transcriptome sequencing was performed to further explore the possible antitumor mechanisms of D. officinale polysaccharides. Fractions of D. officinale polysaccharides, LNT, and APS could significantly inhibit the growth of HT-29 cells in a zebrafish xenograft model. One fraction of D. officinale polysaccharides called DOPW-1 (Mw of 389.98 kDa) exhibited the strongest tumor inhibition. Compared with the control group, RNA-seq revealed that the DOPW-1–treated experimental group had 119 differentially expressed genes (DEGs), of which 45 had upregulated expression and 74 had downregulated expression. Analyses using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes suggested that the pathway “apoptosis-multiple species” was the most significantly enriched. Our data indicated that 1) fractions of D. officinale polysaccharides of Mw 389.98 kDa were most suitable against CRC; 2) DOPW-1 could be developed into a clinical agent against CRC; and 3) an apoptosis pathway is important for DOPW-1 to inhibit the proliferation of HT-29 cells.

Stimulus-responsive nanomaterials under physical regulation for biomedical applications

Cancer is a growing threat to human beings. Traditional treatments for malignant tumors usually involve invasive means to healthy human tissues, such as surgical treatment and chemotherapy. In recent years the use of specific stimulus-responsive materials in combination with some non-contact, non-invasive stimuli can lead to better efficacy and has become an important area of research. It promises to develop personalized treatment systems for four types of physical stimuli: light, ultrasound, magnetic field, and temperature. Nanomaterials that are responsive to these stimuli can be used to enhance drug delivery, cancer treatment, and tissue engineering. This paper reviews the principles of the stimuli mentioned above, their effects on materials, and how they work with nanomaterials. For this aim, we focus on specific applications in controlled drug release, cancer therapy, tissue engineering, and virus detection, with particular reference to recent photothermal, photodynamic, sonodynamic, magnetothermal, radiation, and other types of therapies. It is instructive for the future development of stimulus-responsive nanomaterials for these aspects.

Lung cancer cells expressing a shortened CDK16 3'UTR escape senescence through impaired miR-485-5p targeting

Inducing senescence in cancer cells is an emerging strategy for cancer therapy. The dysregulation and mutation of genes encoding cyclin‐dependent kinases (CDKs) have been implicated in various human cancers. However, whether CDK can induce cancer cell senescence remains poorly understood. We observed that CDK16 expression was high in multiple cancer types, including lung cancer, whereas various replicative senescence models displayed low CDK16 expression. CDK16 knockdown caused senescence‐associated phenotypes in lung cancer cell lines. Interestingly, the CDK16 3′ UTR was shortened in cancer and lengthened in senescence models, which was regulated by alternative polyadenylation (APA). The longer 3′UTR [using the distal polyA (pA) site] generated less protein than the shorter one (using the proximal pA site). Since microRNAs (miRNAs) usually bind to the 3′UTR of target genes to suppress their expression, we investigated whether miRNAs targeting the region between the shortened and longer 3′UTR are responsible for the reduced expression. We found that miR‐485‐5p targeted the 3′UTR between the distal and proximal pA site and caused senescence‐associated phenotypes by reducing protein production from the longer CDK16 transcript. Of note, CDK16 knockdown led to a reduced expression of MYC proto‐oncogene, bHLH transcription factor (MYC) and CD274 molecule (PD‐L1), which in turn enhanced the tumor‐suppressive effects of senescent cancer cells. The present study discovered that CDK16, whose expression is under the regulation of APA and miR‐485‐5p, is a potential target for prosenescence therapy for lung cancer.

Investigating the critical characteristics of thermal runaway process for LiFePO4/graphite batteries by a ceased segmented method

Lithium-ion batteries (LIBs) are widely used as the energy carrier in our daily life. However, the higher energy density of LIBs results in poor safety performance. Thermal runaway (TR) is the critical problem which hinders the further application of LIBs. Clarifying the mechanism of TR evolution is beneficial to safer cell design and safety management. In this paper, liquid nitrogen spray is proved to be an effective way to stop the violent reaction of LIBs during the TR process. Based on extended-volume accelerating rate calorimetry, the liquid nitrogen ceasing combined with non-atmospheric exposure analysis is used to investigate the TR evolution about LiFePO₄/graphite batteries at critical temperature. Specifically, the geometrical shape, voltage, and impedance change are monitored during the TR process on the cell level. The morphologies/constitution of electrodes and separators are presented on the component level. Utilizing the gas analysis, the failure mechanism of the prismatic LiFePO₄/graphite battery is studied comprehensively.

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A comparative study on the thermal runaway evolution of LIBs

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The gas release before venting is analyzed

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The voltage shake after internal short circuit occurs is explained

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The deposition/decomposition of LiPF₆ affects the morphology of electrodes

Comprehensive characterization of somatic variants associated with intronic polyadenylation in human cancers

Somatic single nucleotide variants (SNVs) in cancer genome affect gene expression through various mechanisms depending on their genomic location. While somatic SNVs near canonical splice sites have been reported to cause abnormal splicing of cancer-related genes, whether these SNVs can affect gene expression through other mechanisms remains an open question. Here, we analyzed RNA sequencing and exome data from 4,998 cancer patients covering ten cancer types and identified 152 somatic SNVs near splice sites that were associated with abnormal intronic polyadenylation (IPA). IPA-associated somatic variants favored the localization near the donor splice sites compared to the acceptor splice sites. A proportion of SNV-associated IPA events overlapped with premature cleavage and polyadenylation events triggered by U1 small nuclear ribonucleoproteins (snRNP) inhibition. GC content, intron length and polyadenylation signal were three genomic features that differentiated between SNV-associated IPA and intron retention. Notably, IPA-associated SNVs were enriched in tumor suppressor genes (TSGs), including the well-known TSGs such as PTEN and CDH1 with recurrent SNV-associated IPA events. Minigene assay confirmed that SNVs from PTEN, CDH1, VEGFA, GRHL2, CUL3 and WWC2 could lead to IPA. This work reveals that IPA acts as a novel mechanism explaining the functional consequence of somatic SNVs in human cancer.

The thermogenic activity of adjacent adipocytes fuels the progression of ccRCC and compromises anti-tumor therapeutic efficacy

Clear cell renal cell carcinoma (ccRCC) preferentially invades into perinephric adipose tissue (PAT), a process associated with poor prognosis. However, the detailed mechanisms underlying this interaction remain elusive. Here, we describe a bi-directional communication between ccRCC cells and the PAT. We found that ccRCC cells secrete parathyroid-hormone-related protein (PTHrP) to promote the browning of PAT by PKA activation, while PAT-mediated thermogenesis results in the release of excess lactate to enhance ccRCC growth, invasion, and metastasis. Further, tyrosine kinase inhibitors (TKIs) extensively used in the treatment of ccRCC enhanced this vicious cycle of ccRCC-PAT communication by promoting the browning of PAT. However, if this cross-communication was short circuited by the pharmacological suppression of adipocyte browning via H89 or KT5720, the anti-tumor efficacy of the TKI, sunitinib, was enhanced. These results suggest that ccRCC-PAT cross-communication has important clinical relevance, and use of combined therapy holds great promise in enhancing the efficacy of TKIs.

Transcriptome study of oleanolic acid in the inhibition of breast tumor growth based on high-throughput sequencing

The function of oleanolic acid (OA) in various types of cancer has been reported frequently, especially for breast cancer. However, the regulation of breast tumor growth in response to OA treatment has not been studied in depth. Here, we first explored the effect of OA treatment on breast tumors in vitro and in vivo and then used RNA-seq technology to study the effect and molecular mechanism of OA treatment of MCF-7 cells, particularly at the level of functional genomics. The results showed that 40 μM OA treatment could significantly inhibit the proliferation and induce the apoptosis of MCF-7 cells. Through analysis of RNA sequencing data quality and differentially expressed genes (DEGs), 67 significantly downregulated genes and 260 significantly upregulated genes were identified to be involved in OA treatment of MCF-7 cells. Among these genes, 43 unique DEGs were enriched in several signaling pathways and Gene Ontology terms, such as p53 signaling pathway, TNF signaling pathway and mTOR signaling pathway. Six downregulated genes, including THBS1, EDN1, CACNG4, CCN2, AXIN2 and BMP4, as well as six upregulated genes, including ATF4, SERPINE1, SESN2, PPARGC1A, EGR1 and JAG1, were selected as target genes in response to OA treatment. The inhibitory effect of OA on breast cancer was also found in the following mouse experiments. Our study provides evidence and molecular support for the treatment of breast cancer with OA.

LncRNA DARS-AS1 aggravates the growth and metastasis of hepatocellular carcinoma via regulating the miR-3200-5p-Cytoskeleton associated protein 2 (CKAP2) axis

Accumulating signs have found that long noncoding RNAs (lncRNAs) contribute to hepatocellular carcinoma (HCC). Here, we probed the effect and mechanism of lncRNA DARS-AS1 in HCC. The profiles of DARS-AS1 and Cytoskeleton associated protein 2 (CKAP2) in 50 HCC tissues and non-tumor tissues were examined by real-time quantitative polymerase chain reaction (RT-qPCR). DARS-AS1 and CKAP2 overexpression and/or knockdown cell models were established. The proliferation, apoptosis, invasion and epithelial-mesenchymal transition (EMT) were determined. CKAP2, and focal adhesion kinase (FAK)-extracellular signal-regulated kinase (ERK) was tested by Western blot (WB). The relationship between DARS-AS1 and CKAP2 was predicted by Bioinformatics, and the dual-luciferase reporter assay was applied to verify the targeting association between miR-3200-5p and DARS-AS1 and CKAP2. DARS-AS1 was overexpressed in HCC tissues (vs. that in non-tumor tissues) and was closely correlated with the patients’ tumor stage. DARS-AS1 facilitated HCC cell proliferation and hampered apoptosis. HCC cell migration and EMT were enhanced by DARS-AS1. DARS-AS1 up-regulated CKAP2, which aggravated HCC. Further investigation illustrated that either DARS-AS1 or CKAP2 activated FAK-ERK pathway, and miR-3200-5p was competitively restrained by DARS-AS1. miR-3200-5p exerted tumor-suppressive effects in HCC and inactivated CKAP2 and FAK-ERK pathway. All in all, this study corroborates that DARS-AS1 facilitates HCC proliferation and metastasis by regulating miR-3200-5p-mediated CKAP2, which provides a potential target for HCC diagnosis and treatment.

Abbreviations: CCK-8: cell counting kit-8; CKAP2: Cytoskeleton associated protein 2; cDNA:complementary DNA; DAPI: 4ʹ,6-diamidino-2-phenylindole; DARS-AS1: DARS1 antisense RNA 1; DEPC: diethyl pyrocarbonate; DMEM-F12: Dulbecco’s minimal essential medium/Ham’s-F12; EMT: epithelial-mesenchymal transition; ERK: extracellular signal-regulated kinase; FAK: focal adhesion kinase; FBS: fetal bovine serum; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; HCC: hepatocellular carcinoma; HE: hematoxylin-eosin; IHC: Immunohistochemistry; LIHC: Liver hepatocellular carcinoma; lncRNAs: long noncoding RNAs; MIAT: lncRNA myocardial infarction-related transcripts; MT: Mutant; NC: negative control; PBS: phosphate-buffered saline; PMSF: Phenylmethylsulfonyl fluoride; PVDF: polyvinylidene difluoride; RT: room temperature; RT-qPCR: real-time quantitative polymerase chain reaction; SDS-PAGE: sodium dodecyl sulfate-polyacrylamide gel electrophoresis; SPF: specific pathogen-free; TMAP: tumor-associated microtubule-associated protein; TUNEL: TdT-mediated dUTP nick end labeling; V: volume; WT: wild type.

Recent Advances in the Fabrication and Environmental Science Applications of Cellulose Nanofibril-Based Functional Materials

Cellulose is one of the important biomass materials in nature and has shown wide applications in various fields from materials science, biomedicine, tissue engineering, wearable devices, energy, and environmental science, as well as many others. Due to their one-dimensional nanostructure, high specific surface area, excellent biodegradability, low cost, and high sustainability, cellulose nanofibrils/nanofibers (CNFs) have been widely used for environmental science applications in the last years. In this review, we summarize the advance in the design, synthesis, and water purification applications of CNF-based functional nanomaterials. To achieve this aim, we firstly introduce the synthesis and functionalization of CNFs, which are further extended for the formation of CNF hybrid materials by combining with other functional nanoscale building blocks, such as polymers, biomolecules, nanoparticles, carbon nanotubes, and two-dimensional (2D) materials. Then, the fabrication methods of CNF-based 2D membranes/films, three-dimensional (3D) hydrogels, and 3D aerogels are presented. Regarding the environmental science applications, CNF-based nanomaterials for the removal of metal ions, anions, organic dyes, oils, and bio-contents are demonstrated and discussed in detail. Finally, the challenges and outlooks in this promising research field are discussed. It is expected that this topical review will guide and inspire the design and fabrication of CNF-based novel nanomaterials with high sustainability for practical applications.

Cancer-associated dynamics and potential regulators of intronic polyadenylation revealed by IPAFinder using standard RNA-seq data

Intronic polyadenylation (IpA) usually leads to changes in the coding region of an mRNA, and its implication in diseases has been recognized, although at its very beginning status. Conveniently and accurately identifying IpA is of great importance for further evaluating its biological significance. Here, we developed IPAFinder, a bioinformatic method for the de novo identification of intronic poly(A) sites and their dynamic changes from standard RNA-seq data. Applying IPAFinder to 256 pan-cancer tumor/normal pairs across six tumor types, we discovered 490 recurrent dynamically changed IpA events, some of which are novel and derived from cancer-associated genes such as TSC1, SPERD2, and CCND2. Furthermore, IPAFinder revealed that IpA could be regulated by factors related to splicing and m⁶A modification. In summary, IPAFinder enables the global discovery and characterization of biologically regulated IpA with standard RNA-seq data and should reveal the biological significance of IpA in various processes.

[ELF4 promotes proliferation and inhibits apoptosis of human insulinoma cells by activating Akt signaling]

OBJECTIVE

To investigate the effect of overexpression of the oncogenic transcription factor ELF4 on proliferation and apoptosis in human insulinoma cells and explore the underlying mechanism.

METHODS

A human insulinoma BON cell line with stable overexpression of ELF4 (BON-ELF4 cells) was constructed using a recombinant retrovirus vector and the expression of ELF4 protein was verified using Western blotting. MTT assay was used to assess the proliferation of BON-ELF4 cells and BON-Vector cells, and the cell apoptosis induced by treatment with epirubicin (0.1 μmol/L for 24 h) was analyzed by detecting the expressions of cleaved caspase-8, caspase-9, and PARP using Western blotting. Flow cytometry with Annexin VFITC/PI staining was performed to analyze the numbers of apoptotic BON-Vector or BON-ELF4 cells. The expressions of phosphorylated Akt and total Akt in the cells were detected using Western blotting.

RESULTS

BON-ELF4 cell line with stable overexpression of ELF4 was successfully established. ELF4 overexpression significantly promoted the proliferation (P < 0.05) and obviously suppressed epirubicin- induced apoptosis in BON cells, resulting also in significantly reduced expressions of cleaved caspase-8, caspase-9 and PARP (P < 0.05). The results of flow cytometry showed a significantly lower apoptotic rate in BON-ELF4 cells than in BON-Vector cells following epirubicin treatment (6.03% vs 22.90%). The phosphorylation levels of Akt (Thr308 and Ser473) were significantly increased (P < 0.05) while the level of total Akt remained unchanged (P>0.05) in ELF4- overexpressing cells.

CONCLUSION

ELF4 overexpression enhances the proliferation and suppresses apoptosis of insulinomas cells by activating Akt signaling.

Supramolecular peptide nano-assemblies for cancer diagnosis and therapy: from molecular design to material synthesis and function-specific applications

Peptide molecule has high bioactivity, good biocompatibility, and excellent biodegradability. In addition, it has adjustable amino acid structure and sequence, which can be flexible designed and tailored to form supramolecular nano-assemblies with specific biomimicking, recognition, and targeting properties via molecular self-assembly. These unique properties of peptide nano-assemblies made it possible for utilizing them for biomedical and tissue engineering applications. In this review, we summarize recent progress on the motif design, self-assembly synthesis, and functional tailoring of peptide nano-assemblies for both cancer diagnosis and therapy. For this aim, firstly we demonstrate the methodologies on the synthesis of various functional pure and hybrid peptide nano-assemblies, by which the structural and functional tailoring of peptide nano-assemblies are introduced and discussed in detail. Secondly, we present the applications of peptide nano-assemblies for cancer diagnosis applications, including optical and magnetic imaging as well as biosensing of cancer cells. Thirdly, the design of peptide nano-assemblies for enzyme-mediated killing, chemo-therapy, photothermal therapy, and multi-therapy of cancer cells are introduced. Finally, the challenges and perspectives in this promising topic are discussed. This work will be useful for readers to understand the methodologies on peptide design and functional tailoring for highly effective, specific, and targeted diagnosis and therapy of cancers, and at the same time it will promote the development of cancer diagnosis and therapy by linking those knowledges in biological science, nanotechnology, biomedicine, tissue engineering, and analytical science.

Recent advance in the fabrication of carbon nanofiber-based composite materials for wearable devices

Carbon nanofibers (CNFs) exhibit the advantages of high mechanical strength, good conductivity, easy production, and low cost, which have shown wide applications in the fields of materials science, nanotechnology, biomedicine, tissue engineering, sensors, wearable electronics, and other aspects. To promote the applications of CNF-based nanomaterials in wearable devices, the flexibility, electronic conductivity, thickness, weight, and bio-safety of CNF-based films/membranes are crucial. In this review, we present recent advances in the fabrication of CNF-based composite nanomaterials for flexible wearable devices. For this aim, firstly we introduce the synthesis and functionalization of CNFs, which promote the optimization of physical, chemical, and biological properties of CNFs. Then, the fabrication of two-dimensional and three-dimensional CNF-based materials are demonstrated. In addition, enhanced electric, mechanical, optical, magnetic, and biological properties of CNFs through the hybridization with other functional nanomaterials by synergistic effects are presented and discussed. Finally, wearable applications of CNF-based materials for flexible batteries, supercapacitors, strain/piezoresistive sensors, bio-signal detectors, and electromagnetic interference shielding devices are introduced and discussed in detail. We believe that this work will be beneficial for readers and researchers to understand both structural and functional tailoring of CNFs, and to design and fabricate novel CNF-based flexible and wearable devices for advanced applications.

Enzyme-assisted Solvent Extraction of High-yield Paeonia suffruticosa Andr. Seed Oil and Fatty Acid Composition and Anti-Alzheimer's Disease Activity

Enzyme-assisted solvent extraction (EASE) of Paeonia suffruticosa Andr. seed oil (PSO) was optimized by response surface methodology (RSM). The fatty acid composition and anti-Alzheimer's disease (AD) activity of PSO were analyzed. An enzyme mixture composed of cellulase and hemicellulase (1:1, w/w) was most effective in determining the extraction yield of PSO. The ideal extraction conditions were a pH value of 5.1, an enzymolysis time of 68 min, and a temperature of 50℃. The average extraction yield of PSO was 38.2 mL/100 g, 37.4% higher than that of untreated peony seed (27.8 mL/100 g). The fatty acid composition of PSO under optimal conditions for EASE was analyzed by gas chromatography-mass spectrometry (GC-MS). The predominant unsaturated fatty acids of PSO were determined to be more than 90.00%, including n-3 α-linolenic acid (43.33%), n-6 linoleic acid (23.40%) and oleic acid (23.59%). In this experiment, the anti-AD effect of PSO was also analyzed by performing learning and memory ability tests with Drosophila. PSO retarded the decrease in climbing ability in AD Drosophila. The 1% and 5% PSO groups were significantly different from the model group (^b p < 0.05). The smell short-term memory ability test revealed the number of Drosophila in barrier and barrier-free centrifuge tubes in each group. PSO feeding improved learning and memory in AD Drosophila, with the highest number entering the barrierfree centrifuge tube. The performance index (PI) measured by the Pavlov olfactory avoidance conditioning test also demonstrated the effect of PSO on the learning and memory abilities of Drosophila. The PI of the PSO group was significantly increased compared to that of the model group. HE-stained brain tissue sections of AD Drosophila showed higher neurodegenerative changes, while PSO significantly reduced neurodegenerative damage. These results indicated that PSO can significantly improve the cognitive function of AD Drosophila and may help to prevent AD.

Two-Dimensional Material-Based Colorimetric Biosensors: A Review

Two-dimensional (2D) materials such as graphene, graphene oxide, transition metal oxide, MXene and others have shown high potential for the design and fabrication of various sensors and biosensors due to their 2D layered structure and unique properties. Compared to traditional fluorescent, electrochemical, and electrical biosensors, colorimetric biosensors exhibit several advantages including naked-eye determination, low cost, quick response, and easy fabrication. In this review, we present recent advances in the design, fabrication, and applications of 2D material-based high-performance colorimetric biosensors. Potential colorimetric sensing mechanisms and optimal material selection as well as sensor fabrication are introduced in brief. In addition, colorimetric biosensors based on different 2D materials such as graphene, transition metal dichalcogenide/oxide, MXenes, metal-organic frameworks, and metal nanoplates for the sensitive detection of DNA, proteins, viruses, small molecules, metallic ions, and others are presented and discussed in detail. This work will be helpful for readers to understand the knowledge of 2D material modification, nanozymes, and the synthesis of hybrid materials; meanwhile, it could be valuable to promote the design, fabrication, and applications of 2D material-based sensors and biosensors in quick bioanalysis and disease diagnostics.

Integrated Chromatin Accessibility and Transcriptome Landscapes of Doxorubicin-Resistant Breast Cancer Cells

BACKGROUND

Doxorubicin is one of the most effective chemotherapeutic drugs for breast cancer while its common drug resistance leads to poor patient prognosis and survival. Growing evidence indicate dynamically reorganized chromatin allows rapid access of the gene regulatory machinery to open genomic regions facilitating subsequent gene expression through direct transcription factor (TF) activation and regulatory element binding.

METHODS

To better understand the regulatory network underlying doxorubicin resistance in breast cancer cells, we explored the systematic alterations of chromatin accessibility and gene expression by the assay for transposase-accessible chromatin using sequencing (ATAC-seq) in combination with RNA sequencing, followed by integrative analysis to identify potential regulators and their targets associated with differentially accessible regions (DARs) in doxorubicin-resistant MCF7 (MCF7-DR) cells.

RESULTS

A total of 3,963 differentially expressed genes (DEGs) related to doxorubicin resistance were identified, including dramatically up-regulated MT1E, GSTP1, LDHB, significantly down-regulated TFF1, UBB, DSCAM-AS1, and histone-modifying enzyme coding genes HDAC2, EZH2, PRMT5, etc. By integrating with transcriptomic datasets, we identified 18,228 DARs in MCF7-DR cells compared to control, which were positively correlated with their nearest DEGs (r = 0.6). There were 11,686 increased chromatin-accessible regions, which were enriched in up-regulated genes related to diverse KEGG pathways, such as the cell cycle, regulation of actin cytoskeleton, signaling pathways of MAPK, PI3K/Akt and Hippo, which play essential roles in regulating cell apoptosis, proliferation, metabolism, and inflammatory responses. The 6,542 decreased chromatin-accessible regions were identified for the declined doxorubicin-associated biological processes, for instance, endocrine and insulin resistance, central carbon metabolism, signaling pathways of TGF-beta and P53. Combining data from TCGA, analyses of the DAR sequences associated with the DNA-binding motifs of significantly enriched TF families including AP-1, TEAD and FOX, indicated that the loss-function of FOXA1 might play a critical role in doxorubicin-resistant breast cancer cells (DOX-R BCCs).

CONCLUSION

These data exhibit the non-genetic landscape of chromatin accessibility and transcript levels in the DOX-R BCCs, and provide clear insights and resources for the detection of critical TFs and potential cis-regulatory elements-based putative therapeutic targets.

Independent component analysis based gene co-expression network inference (ICAnet) to decipher functional modules for better single-cell clustering and batch integration

With the tremendous increase of publicly available single-cell RNA-sequencing (scRNA-seq) datasets, bioinformatics methods based on gene co-expression network are becoming efficient tools for analyzing scRNA-seq data, improving cell type prediction accuracy and in turn facilitating biological discovery. However, the current methods are mainly based on overall co-expression correlation and overlook co-expression that exists in only a subset of cells, thus fail to discover certain rare cell types and sensitive to batch effect. Here, we developed independent component analysis-based gene co-expression network inference (ICAnet) that decomposed scRNA-seq data into a series of independent gene expression components and inferred co-expression modules, which improved cell clustering and rare cell-type discovery. ICAnet showed efficient performance for cell clustering and batch integration using scRNA-seq datasets spanning multiple cells/tissues/donors/library types. It works stably on datasets produced by different library construction strategies and with different sequencing depths and cell numbers. We demonstrated the capability of ICAnet to discover rare cell types in multiple independent scRNA-seq datasets from different sources. Importantly, the identified modules activated in acute myeloid leukemia scRNA-seq datasets have the potential to serve as new diagnostic markers. Thus, ICAnet is a competitive tool for cell clustering and biological interpretations of single-cell RNA-seq data analysis.

Sodium butyrate relieves lung ischemia-reperfusion injury by inhibiting NF-κB and JAK2/STAT3 signaling pathways

OBJECTIVE

Ischemia-reperfusion (IR) is the main cause of acute lung injury (ALI) in clinical lung transplantation, extracorporeal circulation, lung sleeve resection, trauma and cardiopulmonary resuscitation. The inflammatory response and oxidative stress following IR are factors that cause and aggravate its secondary damage. The purpose of this study was to investigate the efficacy and mechanism of sodium butyrate (NaB) on lung ischemia-reperfusion injury (LIRI).

MATERIALS AND METHODS

We used male C57BL/6 mice to construct the LIRI model and administered the mice with NaB. By examining the expression of inflammatory factors and oxidative stress-related molecules in mouse lung tissue, we investigated the effects of NaB on inflammation and oxidative stress in lung tissue after IR. In addition, the changes in the activity of the NF-κB and JAK2/STAT3 signaling pathways were also examined to determine the mechanism of NaB.

RESULTS

The expression levels of the inflammatory factors (IL-1β, IL-6 and TNF-α) in lung tissue of mice after IR were significantly increased, while NaB reduced the expression of inflammatory factors. In addition, the oxidative stress level of mouse lung tissue after IR increased significantly, showing the decrease of antioxidant molecules SOD1/2, catalase (CAT), and Peroxiredoxin 1 (Prdx1), while the intake of NaB increased the antioxidant level of mouse lung tissue. The activities of NF-κB and JAK2/STAT3 signaling pathways were significantly increased in lung tissue after IR, whereas NaB inhibited the activity of NF-κB and JAK2/STAT3 signaling pathways.

CONCLUSIONS

NaB relieves LIRI by inhibiting NF-κB and JAK2/STAT3 signaling pathways to reduce inflammation and oxidative stress levels in lung tissue of mice after IR.

H3K4 Methyltransferase Smyd3 Mediates Vascular Smooth Muscle Cell Proliferation, Migration, and Neointima Formation

[Figure: see text].