Macrophage polarization in the tumor microenvironment: Emerging roles and therapeutic potentials.

The tumor microenvironment (TME) is a combination of tumor cells and indigenous host stroma, which consists of tumor-infiltrating immune cells, endothelial cells, fibroblasts, pericytes, and non-cellular elements. Tumor-associated macrophages (TAMs) represent the major tumor-infiltrating immune cell type and are generally polarized into two functionally contradictory subtypes, namely classical activated M1 macrophages and alternatively activated M2 macrophages. Macrophage polarization refers to how macrophages are activated at a given time and space. The interplay between the TME and macrophage polarization can influence tumor initiation and progression, making TAM a potential target for cancer therapy. Here, we review the latest investigations on factors orchestrating macrophage polarization in the TME, how macrophage polarization affects tumor progression, and the perspectives in modulating macrophage polarization for cancer immunotherapy.

Extraction and Imputation of Eastern Cooperative Oncology Group Performance Status From Unstructured Oncology Notes Using Language Models.

PURPOSE: Eastern Cooperative Oncology Group (ECOG) performance status (PS) is a key clinical variable for cancer treatment and research, but it is usually only recorded in unstructured form in the electronic health record. We investigated whether natural language processing (NLP) models can impute ECOG PS using unstructured note text. MATERIALS AND METHODS: Medical oncology notes were identified from all patients with cancer at our center from 1997 to 2023 and divided at the patient level into training (approximately 80%), tuning/validation (approximately 10%), and test (approximately 10%) sets. Regular expressions were used to extract explicitly documented PS. Extracted PS labels were used to train NLP models to impute ECOG PS (0-1 v 2-4) from the remainder of the notes (with regular expression-extracted PS documentation removed). We assessed associations between imputed PS and overall survival (OS). RESULTS: ECOG PS was extracted using regular expressions from 495,862 notes, corresponding to 79,698 patients. A Transformer-based Longformer model imputed PS with high discrimination (test set area under the receiver operating characteristic curve 0.95, area under the precision-recall curve 0.73). Imputed poor PS was associated with worse OS, including among notes with no explicit documentation of PS detected (OS hazard ratio, 11.9; 95% CI, 11.1 to 12.8). CONCLUSION: NLP models can be used to impute performance status from unstructured oncologist notes at scale. This may aid the annotation of oncology data sets for clinical outcomes research and cancer care delivery.

Gastrointestinal bleeding risk factors in type A aortic dissection post-aortic arch replacement.

Background: Gastrointestinal bleeding (GIB) is a notable complication in patients diagnosed with aortic dissection (AD). We evaluated the outcomes and identified the risk factors associated with GIB in patients with AD. Methods: A retrospective case-control study was conducted on patients diagnosed with type A aortic dissection (TAAD) who underwent total aortic arch replacement (TAAR) at our institution from July 2021 to July 2023. Comprehensive clinical data, laboratory findings, and imaging results were meticulously gathered and analyzed to identify potential risk factors linked to GIB in this patient cohort. Results: Of the 198 AD patients who underwent TAAR, 38 (19.2%) developed postoperative GIB (GIB group), with a median interval of 7 days between surgery and bleeding onset. The GIB group exhibited significantly higher mortality (26.3% vs. 3.1%, P<0.001), prolonged intensive care unit (ICU) stay {15 [interquartile range (IQR), 8-25] vs. 7 (IQR, 5-12) days, P<0.001}, and extended duration of ventilation [168 (IQR, 120-372) vs. 71 (IQR, 34-148) hours, P<0.001] compared to the control group (n=160, 80.8%). Logistic regression analysis identified age >54 years [odds ratio (OR): 3.529], intraoperative red blood cell (RBC) transfusion >600 mL (OR: 3.865), and concomitant celiac trunk and superior mesenteric artery (SMA) hypoperfusion (OR: 15.974) as independent risk factors for GIB in AD patients. Conclusions: GIB subsequent to TAAR in AD patients is linked to adverse prognosis. Factors such as advanced age, extensive intraoperative transfusion, and gastrointestinal (GI) perfusion abnormalities may heighten the risk of GIB in this patient population.

ROS-dependent S-palmitoylation activates cleaved and intact gasdermin D.

Gasdermin D (GSDMD) is the common effector for cytokine secretion and pyroptosis downstream of inflammasome activation and was previously shown to form large transmembrane pores after cleavage by inflammatory caspases to generate the GSDMD N-terminal domain (GSDMD-NT)1-10. Here we report that GSDMD Cys191 is S-palmitoylated and that palmitoylation is required for pore formation. S-palmitoylation, which does not affect GSDMD cleavage, is augmented by mitochondria-generated reactive oxygen species (ROS). Cleavage-deficient GSDMD (D275A) is also palmitoylated after inflammasome stimulation or treatment with ROS activators and causes pyroptosis, although less efficiently than palmitoylated GSDMD-NT. Palmitoylated, but not unpalmitoylated, full-length GSDMD induces liposome leakage and forms a pore similar in structure to GSDMD-NT pores shown by cryogenic electron microscopy. ZDHHC5 and ZDHHC9 are the major palmitoyltransferases that mediate GSDMD palmitoylation, and their expression is upregulated by inflammasome activation and ROS. The other human gasdermins are also palmitoylated at their N termini. These data challenge the concept that cleavage is the only trigger for GSDMD activation. They suggest that reversible palmitoylation is a checkpoint for pore formation by both GSDMD-NT and intact GSDMD that functions as a general switch for the activation of this pore-forming family.

Progesterone-mediated remodeling of the maternal-fetal interface by a PGRMC1-dependent mechanism.

Implantation and maintenance of pregnancy involve intricate immunological processes that enable the developing fetus to coexist with the maternal immune system. Progesterone, a critical hormone during pregnancy, is known to promote immune tolerance and prevent preterm labor. However, the mechanism by which progesterone mediates these effects remains unclear. In this study, we investigated the role of the non-classical progesterone receptor membrane component 1 (PGRMC1) in progesterone signaling at the maternal-fetal interface. Using JEG3 cells, a trophoblast model cell line, we observed that progesterone stimulation increased the expression of human leukocyte antigen-C (HLA-C) and HLA-G, key molecules involved in immune tolerance. We also found that progesterone upregulated the expression of the transcription factor ELF3, which is known to regulate trophoblast-specific HLA-C expression. Interestingly, JEG3 cells lacked expression of classical progesterone receptors (PRs) but exhibited high expression of PGRMC1, a finding we confirmed in primary trophoblasts by mining sc-RNA seq data from human placenta. To investigate the role of PGRMC1 in progesterone signaling, we used CRISPR/Cas9 technology to knockout PGRMC1 in JEG3 cells. PGRMC1-deficient cells showed a diminished response to progesterone stimulation. Furthermore, we found that the progesterone antagonist RU486 inhibited ELF3 expression in a PGRMC1-dependent manner, suggesting that RU486 acts as a progesterone antagonist by competing for receptor binding. Additionally, we found that RU486 inhibited cell invasion, an important process for successful pregnancy, and this inhibitory effect was dependent on PGRMC1. Our findings highlight the crucial role of PGRMC1 in mediating the immunoregulatory effects of progesterone at the maternal-fetal interface.

Genome-Wide Association Study of the Reproductive Traits of the Dazu Black Goat (Capra hircus) Using Whole-Genome Resequencing.

Reproductive traits are the basic economic traits of goats and important indicators in goat breeding. In this study, Dazu black goats (DBGs; n = 150), an important Chinese local goat breed with excellent reproductive performance, were used to screen for important variation loci and genes of reproductive traits. Through genome-wide association studies (GWAS), 18 SNPs were found to be associated with kidding traits (average litter size, average litter size in the first three parity, and average litter size in the first six parity), and 10 SNPs were associated with udder traits (udder depth, teat diameter, teat length, and supernumerary teat). After gene annotation of the associated SNPs and in combination with relevant references, the candidate genes, namely ATP1A1, LRRC4C, SPCS2, XRRA1, CELF4, NTM, TMEM45B, ATE1, and FGFR2, were associated with udder traits, while the ENSCHIG00000017110, SLC9A8, GLRB, GRIA2, GASK1B, and ENSCHIG00000026285 genes were associated with litter size. These SNPs and candidate genes can provide useful biological information for improvement of the reproductive traits of goats.

Association analysis of polymorphisms at GLRB, GRIA2, and GASK1B genes with reproductive traits in Dazu Black Goats.

Reproductive traits are essential economic traits in goats. This study aimed to analyze the relationship between single nucleotide polymorphisms (SNPs) within the genes of GLRB, GRIA2, and GASK1B, and reproductive traits (kidding traits and placental traits) in goats. We used the resequencing data of 150 Dazu Black Goats to perform correlation analysis with the average litter size. We screened thirteen SNPs loci in introns and then used the Sanger method to genotype the remaining 150 Dazu Black Goats. The results showed that a total of six SNPs were screened. Three SNPs related to litter size and live litter size (g.28985790T > G, g.28986352A > G, and g.28987976A > G); one SNP related to total cotyledon area (g.29203243G > A); two SNPs related to placental efficiency (g.30189055G > A and g.30193974C > T); one SNP associated with cotyledon support efficiency (g.30193974C > T). The qPCR results showed that GLRB, GRIA2, and GASK1B were all highly expressed in the udder, kidney, uterus, and ovary. It indicated that these three candidate genes might affect the reproductive traits, which could be used as candidate markers for reproductive traits in Dazu Black Goats. Moreover, association studies on a large scale are still needed to figure out what effect these SNPs have on reproductive traits.

Machine learning approach identified clusters for patients with low cardiac output syndrome and outcomes after cardiac surgery.

Background: Low cardiac output syndrome (LCOS) is the most serious physiological abnormality with high mortality for patients after cardiac surgery. This study aimed to explore the multidimensional data of clinical features and outcomes to provide individualized care for patients with LCOS. Methods: The electronic medical information of the intensive care units (ICUs) was extracted from a tertiary hospital in South China. We included patients who were diagnosed with LCOS in the ICU database. We used the consensus clustering approach based on patient characteristics, laboratory data, and vital signs to identify LCOS subgroups. The consensus clustering method involves subsampling from a set of items, such as microarrays, and determines to cluster of specified cluster counts (k). The primary clinical outcome was in-hospital mortality and was compared between the clusters. Results: A total of 1,205 patients were included and divided into three clusters. Cluster 1 (n = 443) was defined as the low-risk group [in-hospital mortality =10.1%, odds ratio (OR) = 1]. Cluster 2 (n = 396) was defined as the medium-risk group [in-hospital mortality =25.0%, OR = 2.96 (95% CI = 1.97-4.46)]. Cluster 3 (n = 366) was defined as the high-risk group [in-hospital mortality =39.2%, OR = 5.75 (95% CI = 3.9-8.5)]. Conclusion: Patients with LCOS after cardiac surgery could be divided into three clusters and had different outcomes.

The ZFP541-KCTD19 complex is essential for pachytene progression by activating meiotic genes during mouse spermatogenesis.

Meiosis is essential for fertility in sexually reproducing species and this sophisticated process has been extensively studied. Notwithstanding these efforts, key factors involved in meiosis have not been fully characterized. In this study, we investigate the regulatory roles of zinc finger protein 541 (ZFP541) and its interacting protein potassium channel tetramerization domain containing 19 (KCTD19) in spermatogenesis. ZFP541 is expressed from leptotene to the round spermatid stage, while the expression of KCTD19 is initiated in pachytene. Depletion of Zfp541 or Kctd19 leads to infertility in male mice and delays progression from early to mid/late pachynema. In addition, Zfp541-/- spermatocytes show abnormal programmed DNA double-strand break repair, impaired crossover formation and resolution, and asynapsis of the XY chromosomes. ZFP541 interacts with KCTD19, histone deacetylase 1/2 (HDAC1/2), and deoxynucleotidyl transferase terminal-interacting protein 1 (DNTTIP1). Moreover, ZFP541 binds to and activates the expression of genes involved in meiosis and post-meiosis including Kctd19; in turn, KCTD19 promotes the transcriptional activation activity of ZFP541. Taken together, our studies reveal that the ZFP541/KCTD19 signaling complex, acting as a key transcription regulator, plays an indispensable role in male fertility by regulating pachytene progression.

Genome-Wide Association Study of Body Conformation Traits by Whole Genome Sequencing in Dazu Black Goats.

Identifying associations between genetic markers and economic traits has practical benefits for the meat goat industry. To better understand the genomic regions and biological pathways contributing to body conformation traits of meat goats, a genome-wide association study was performed using Dazu black goats (DBGs), a Chinese indigenous goat breed. In particular, 150 DBGs were genotyped by whole-genome sequencing, and six body conformation traits, including body height (BH), body length (BL), cannon circumference (CC), chest depth (CD), chest width (CW), and heart girth (HG), were examined. In total, 53 potential SNPs were associated with these body conformation traits. A bioinformatics analysis was performed to evaluate the genes located close to the significant SNPs. Finally, 42 candidate genes (e.g., PSTPIP2, C7orf57, CCL19, FGF9, SGCG, FIGN, and SIPA1L) were identified as components of the genetic architecture underlying body conformation traits. Our results provide useful biological information for the improvement of growth performance and have practical applications for genomic selection in goats.

Screening Candidate Genes Regulating Placental Development from Trophoblast Transcriptome at Early Pregnancy in Dazu Black Goats (Capra hircus).

This study explored the trophoblast transcriptome to understand potential functional genes involved in early placental development in goats and their enriched signaling pathways. Trophoblast samples were collected from nine Dazu Black goats on days 20, 25, and 30 of pregnancy (D20, D25, and D30). As the pregnancy progressed, the morphology and histological structures showed significant growth, adhesion, and angiogenesis. A total of 23,253 commonly expressed genes (CEGs) and 4439 differently expressed genes (DEGs) were detected by RNA sequencing. The common highly expressed genes (ChEGs) (the top 100 CEGs) with the highest FPKM percentage (29.9%) of all CEGs were annotated to the ribosome pathway and maintain pregnancy. DEGs were abundant in D30 vs. D20 (3715 DEGs). Besides, the DEGs were associated with the inhibition of oxidative phosphorylation and activation of PI3K-Akt, focal adhesion, ECM-receptor interaction, Rap1, and CAM signaling pathways. The RAP1 may be a central pathway since it coordinates with others to regulate the cell proliferation, invasion, migration, and fusion of trophoblasts. qRT-PCR and Western blot analysis confirmed the transcriptional expression in IGF1, VEGFC, RAPGEF3, PIK3CA, AKT3, ITGB3, ITGA11, SPP1, NOS1, and ATP6V0B genes and protein levels in VEGF, RAPGEF3, and Akt. This is the first study of transcriptome profiling in goat placenta and provides diverse genetic resources for further research on placenta development.

Simultaneous removal of Cd (II), Ni (II), and Pb (II) from water by a submerged macrophyte pondweed (Potamogeton malaianus).

The current work investigated the potential of submerged macrophyte pondweed (Potamogeton malaianus) in treating cadmium, nickel, and lead-contaminated water through phytoremediation. The adsorption for the three metal ions occurred rapidly within 2 h and attained dynamic equilibrium in no more than 72 h. The removal efficiencies of Cd (II), Ni (II), and Pb (II) were high, passing 94% in both single- and multi-metal systems. The kinetic adsorption curves of Cd (II), Ni (II), and Pb (II) were fitted well by both pseudo-first-order and pseudo-second-order kinetics (R2 = 0.9875-0.9995). The equilibrium adsorption capacities of Cd (II), Ni (II), and Pb (II) for P. malaianus were 6.29-6.97 mg kg-1 . In plants, the higher concentration of each metal ions was accumulated in leaves (12.44-38.15 mg kg-1 ) than in roots (10.32-26.10 mg kg-1 ). The chlorophyll contents increased from 0.69 to 0.89-1.00 mg g-1 under the treatment of Cd (II), Ni (II), and Pb (II), whereas the chlorophyll a/b ratio was kept constant. There was no significant difference between single- and multi-metal systems. FT-IR spectra showed that COH and C═N might be involved in the adsorption of Cd (II), Ni (II), and Pb (II). This study demonstrated that P. malaianus could be a suitable submerged macrophyte for the simultaneous removal of Cd (II), Ni (II), and Pb (II) from water.

CFD simulation of the aeration process and baffle influence in a full-scale commercial flat sheet module.

The goal of the present paper is to investigate the aeration process and the enhanced effect of baffles in a full-scale commercial membrane bioreactor (MBR) system configured with a flat sheet (FS) membrane module. Through a computational fluid dynamics (CFD) simulation, two aerated FS membrane modules for full-scale applications with 26 membrane sheets were simulated. The numerical results indicate that the presence of baffles and the distances between the baffle and the outmost membrane sheet have a minor influence on the area-weighted shear stress for full-scale MBRs. In addition, bubble size and the bottom distance between the aerator and membrane bottom do not affect the average shear stress of full-scale FS membrane modules much. However, an increase in air flow rate has a significant effect on the area-weighted shear stress. A large FS membrane module is recommended, as it could achieve the same cleaning effect as the small one with a lower specific aeration demand for membranes.

Dual Recognition of H3K4me3 and DNA by the ISWI Component ARID5 Regulates the Floral Transition in Arabidopsis.

Chromatin remodeling and histone modifications are important for development and floral transition in plants. However, it is largely unknown whether and how these two epigenetic regulators coordinately regulate the important biological processes. Here, we identified three types of Imitation Switch (ISWI) chromatin-remodeling complexes in Arabidopsis (Arabidopsis thaliana). We found that AT-RICH INTERACTING DOMAIN5 (ARID5), a subunit of a plant-specific ISWI complex, can regulate development and floral transition. The ARID-PHD dual domain cassette of ARID5 recognizes both the H3K4me3 histone mark and AT-rich DNA. We determined the ternary complex structure of the ARID5 ARID-PHD cassette with an H3K4me3 peptide and an AT-containing DNA. The H3K4me3 peptide is combinatorially recognized by the PHD and ARID domains, while the DNA is specifically recognized by the ARID domain. Both PHD and ARID domains are necessary for the association of ARID5 with chromatin. The results suggest that the dual recognition of AT-rich DNA and H3K4me3 by the ARID5 ARID-PHD cassette may facilitate the association of the ISWI complex with specific chromatin regions to regulate development and floral transition.

FHA2 is a plant-specific ISWI subunit responsible for stamen development and plant fertility.

Imitation Switch (ISWI) chromatin remodelers are known to function in diverse multi-subunit complexes in yeast and animals. However, the constitution and function of ISWI complexes in Arabidopsis thaliana remain unclear. In this study, we identified forkhead-associated domain 2 (FHA2) as a plant-specific subunit of an ISWI chromatin-remodeling complex in Arabidopsis. By in vivo and in vitro analyses, we demonstrated that FHA2 directly binds to RLT1 and RLT2, two redundant subunits of the ISWI complex in Arabidopsis. The stamen filament is shorter in the fha2 and rlt1/2 mutants than in the wild type, whereas their pistil lengths are comparable. The shorter filament, which is due to reduced cell size, results in insufficient pollination and reduced fertility. The rlt1/2 mutant shows an early-flowering phenotype, whereas the phenotype is not shared by the fha2 mutant. Consistent with the functional specificity of FHA2, our RNA-seq analysis indicated that the fha2 mutant affects a subset of RLT1/2-regulated genes that does not include genes involved in the regulation of flowering time. This study demonstrates that FHA2 functions as a previously uncharacterized subunit of the Arabidopsis ISWI complex and is exclusively involved in regulating stamen development and plant fertility.

The role of submerged macrophytes in phytoremediation of arsenic from contaminated water: A case study on Vallisneria natans (Lour.) Hara.

Arsenic contamination of water is a global concern due to its heavy threat to human health. In this study, the submerged macrophyte Vallisneria natans (Lour.) Hara was used to remove environmentally relevant concentrations of arsenic in the binary As(III)/As(V) system. The concentrations of total arsenic (tAs) and As(III) in water dropped rapidly within 3 days, while As(V) first increased slightly within 3 days and then gradually decreased. About 1.2% dimethylarsinate (DMA) was detected at the 14th day of treatment. These findings indicated that As(III) could be oxidized to As(V) and methylated to DMA in water with V. natans. In relation to V. natans, both tAs and As(V) were much higher in roots compared to leaves. Arsenate was the predominant species (≥ 95.65 ±â€¯0.10%) in roots, and As(III) was only found at the 14th day (3.45-6.96 mg kg-1). In leaves, As(III) significantly increased (P < 0.05) as the treatment duration increased. The proportions of As(V) (27.99-40.03%) were lower than those of As(III) and arsenobetaine (AsB) was detected (0.52-1.87 mg kg-1) after 7 d. The results of arsenic speciation demonstrated that the transformation of arsenic species in V. natans included As(V) reduction and As(III) methylation to AsB. There were a decrease in chlorophyll content, and an increase in MDA level and antioxidant enzymes (SOD, CAT, and POD) activities. The MDA level was much higher in leaves than roots, whereas the activities of SOD, CAT, and POD were the opposite, suggesting their possible role in arsenic resistance and detoxification. Our results indicate the potential of V. natans in phytoremediation of arsenic-contaminated water.

Roles of Phosphoric Acid in Biochar Formation: Synchronously Improving Carbon Retention and Sorption Capacity.

Pretreatment of biomass with phosphoric acid (HPO) for biochar production was expected to improve carbon (C) retention, porosity structure, and the sorption ability of biochar. This study investigated the interaction of phosphorus with the C structure to elucidate the mechanisms by which HPO simultaneously captured C and created micropores. Sawdust was soaked in diluted HPO and dried for pyrolytic biochar generation at 350, 500, and 650°C. Results showed that HPO pretreatment resulted in 70 to 80% of biomass C retention in biochar, compared with only about 50% remaining without pretreatment. The specific surface area and total pore volume of the HPO-pretreated biochar were 930 m g and 0.558 cm g, respectively, compared with <51.0 m g and 0.046 cm g in the untreated biochar. The volume of micropores (<10 nm) increased from 59.0% to 78.4-81.9%. The presence of HPO shifted the decomposition temperature to a lower value and decreased the energy required for biomass decomposition. Micropore formation was via the insertion of P-O-P into the C lattice, leading to swelling and amplification of amorphous form and lattice defect of the C structure, as evidenced by Raman spectrum and small-angle X-ray scattering analysis. The crosslinking of P-O-P and C bonds resulted in greater biomass C retention in biochar. This biochar-phosphorus composite had a much higher sorption ability for Pb than the unmodified biochar, which was possibly dominated by phosphate precipitation and surface adsorption. This study provided a simple method to improve biochar properties and explored the multiple benefits of HPO in biomass pyrolysis.

Postzygotic single-nucleotide mosaicisms in whole-genome sequences of clinically unremarkable individuals.

Postzygotic single-nucleotide mutations (pSNMs) have been studied in cancer and a few other overgrowth human disorders at whole-genome scale and found to play critical roles. However, in clinically unremarkable individuals, pSNMs have never been identified at whole-genome scale largely due to technical difficulties and lack of matched control tissue samples, and thus the genome-wide characteristics of pSNMs remain unknown. We developed a new Bayesian-based mosaic genotyper and a series of effective error filters, using which we were able to identify 17 SNM sites from ~80× whole-genome sequencing of peripheral blood DNAs from three clinically unremarkable adults. The pSNMs were thoroughly validated using pyrosequencing, Sanger sequencing of individual cloned fragments, and multiplex ligation-dependent probe amplification. The mutant allele fraction ranged from 5%-31%. We found that C→T and C→A were the predominant types of postzygotic mutations, similar to the somatic mutation profile in tumor tissues. Simulation data showed that the overall mutation rate was an order of magnitude lower than that in cancer. We detected varied allele fractions of the pSNMs among multiple samples obtained from the same individuals, including blood, saliva, hair follicle, buccal mucosa, urine, and semen samples, indicating that pSNMs could affect multiple sources of somatic cells as well as germ cells. Two of the adults have children who were diagnosed with Dravet syndrome. We identified two non-synonymous pSNMs in SCN1A, a causal gene for Dravet syndrome, from these two unrelated adults and found that the mutant alleles were transmitted to their children, highlighting the clinical importance of detecting pSNMs in genetic counseling.