Comprehensive in-silico analysis of deleterious SNPs in APOC2 and APOA5 and their differential expression in cancer and cardiovascular diseases conditions.

Genetic variations in APOC2 and APOA5 genes involve activating lipoprotein lipase (LPL), responsible for the hydrolysis of triglycerides (TG) in blood and whose impaired functions affect the TG metabolism and are associated with metabolic diseases. In this study, we investigate the biological significance of genetic variations at the DNA sequence and structural level using various computational tools. Subsequently, 8 (APOC2) and 17 (APOA5) non-synonymous SNPs (nsSNPs) were identified as high-confidence deleterious SNPs based on the effects of the mutations on protein conservation, stability, and solvent accessibility. Furthermore, based on our docking results, the interaction of native and mutant forms of the corresponding proteins with LPL depicts differences in root mean square deviation (RMSD), and binding affinities suggest that these mutations may affect their function. Furthermore, in vivo, and in vitro studies have shown that differential expression of these genes in disease conditions due to the influence of nsSNPs abundance may be associated with promoting the development of cancer and cardiovascular diseases. Preliminary screening using computational methods can be a helpful start in understanding the effects of mutations in APOC2 and APOA5 on lipid metabolism; however, further wet-lab experiments would further strengthen the conclusions drawn from the computational study.

Elevated signature of a gene module coexpressed with CDC20 marks genomic instability in glioma.

Genomic instability (GI) drives tumor heterogeneity and promotes tumor progression and therapy resistance. However, causative factors underlying GI and means for clinical detection of GI in glioma are inadequately identified. We describe here that elevated expression of a gene module coexpressed with CDC20 (CDC20-M), the activator of the anaphase-promoting complex in the cell cycle, marks GI in glioma. The CDC20-M, containing 139 members involved in cell proliferation, DNA damage response, and chromosome segregation, was found to be consistently coexpressed in glioma transcriptomes. The coexpression of these genes was conserved across multiple species and organ systems, particularly in human neural stem and progenitor cells. CDC20-M expression was not correlated with the morphological subtypes, nor with the recently defined molecular subtypes of glioma. CDC20-M signature was an independent and robust predictor for poorer prognosis in over 1,000 patients from four large databases. Elevated CDC20-M signature enabled the identification of individual glioma samples with severe chromosome instability and mutation burden and of primary glioma cell lines with extensive mitotic errors leading to chromosome mis-segregation. AURKA, a core member of CDC20-M, was amplified in one-third of CDC20-M-high gliomas with gene-dosage-dependent expression. MLN8237, a Food and Drug Administration-approved AURKA inhibitor, selectively killed temozolomide-resistant primary glioma cells in vitro and prolonged the survival of a patient-derived xenograft mouse model with a high-CDC20-M signature. Our findings suggest that application of the CDC20-M signature may permit more selective use of adjuvant therapies for glioma patients and that dysregulated CDC20-M members may provide a therapeutic vulnerability in glioma.

Widely Targeted Metabolomics Analysis of Soybean and Chickpea and Their Different Advantages and New Functional Compounds for Diabetes.

Soybean is widely used as a kind of bean for daily consumption. Chickpea is increasingly utilised because of its good healthcare function. At present, using chickpeas could have better results than soybeans in some areas. Previous studies of the two legumes focused on certain components and failed to fully reveal the differences between the two legumes. Thus, understanding the comprehensive similarities and differences between the two legumes is necessary to apply and develop these legumes effectively. In this study, we performed a UPLC-ESI-MS/MS-based widely targeted metabolomics analysis on two legumes. A total of 776 metabolites (including primary metabolites and secondary metabolites) were detected, which were divided into more than a dozen broad categories. The differential analysis of these metabolites showed that there were 480 metabolites with significant differences in relative contents between the two legumes. Compared with soybean, the expression of 374 metabolites of chickpea was down-regulated and that of 106 metabolites was up-regulated. The metabolic pathway analysis showed significant differences in the flavonoids biosynthesis, phenylpropanoid biosynthesis, linoleic acid metabolism and alkaloid biosynthesis between the two legumes. The advantages and applicability of the two kinds of legumes were confirmed through the analysis of anti-diabetic components. Moreover, some novel compounds (with contents higher than that of soybean) with hypoglycaemic activity were found in chickpea. This study provides an important reference for the in-depth study and comparative application of soybean and chickpea.

Chemical Synthesis of a Full-Length G-Protein-Coupled Receptor ß2-Adrenergic Receptor with Defined Modification Patterns at the C-Terminus.

The ß2-adrenergic receptor (ß2AR) is a G-protein-coupled receptor (GPCR) that responds to the hormone adrenaline and is an important drug target in the context of respiratory diseases, including asthma. ß2AR function can be regulated by post-translational modifications such as phosphorylation and ubiquitination at the C-terminus, but access to the full-length ß2AR with well-defined and homogeneous modification patterns critical for biochemical and biophysical studies remains challenging. Here, we report a practical synthesis of differentially modified, full-length ß2AR based on a combined native chemical ligation (NCL) and sortase ligation strategy. An array of homogeneous samples of full-length ß2ARs with distinct modification patterns, including a full-length ß2AR bearing both monoubiquitination and octaphosphorylation modifications, were successfully prepared for the first time. Using these homogeneously modified full-length ß2AR receptors, we found that different phosphorylation patterns mediate different interactions with ß-arrestin1 as reflected in different agonist binding affinities. Our experiments also indicated that ubiquitination can further modulate interactions between ß2AR and ß-arrestin1. Access to full-length ß2AR with well-defined and homogeneous modification patterns at the C-terminus opens a door to further in-depth mechanistic studies into the structure and dynamics of ß2AR complexes with downstream transducer proteins, including G proteins, arrestins, and GPCR kinases.

Phosphorus recovery from urine using cooling water system effluent as a precipitant.

Phosphorus (P) recovery from wastewater has been recognized as a critical technology for solving the sustainable supply of this indispensable and non - renewable natural resource. In this study, the cost - free magnesium and calcium sources of using the cooling water system effluent (CWSE) in two thermal power plants were proposed (Z - CWSE and G - CWSE) and the P recovery performance from source - separated urine was investigated. About 90% P recovery efficiency was achieved from the hydrolyzed urine when Z - CWSE and G - CWSE were added at the Ca: Mg: P molar ratios of 3.1 : 4.0: 1 and 3.6 : 3.4: 1, respectively. More than 95% P recovery performance was obtained from the fresh urine as the initial pH of the CWSE - FU mixtures was adjusted to over 9.5 and 10.0, respectively. The precipitates obtained contain 10.84-17.04% Ca, 6.22-9.58% P, 0.75-3.76% Mg and 0.13-0.23% N. XRD analysis confirmed the presence of struvite in the precipitates. The reuse of precipitates is secure due to extremely low contents of heavy metals. The feasibility of using CWSEs as the flushing water in urinals and toilets was assessed. Besides, we proposed CWSEs could be invoked as precipitants in various wastewaters as long as it contains considerable phosphate, e.g. P concentration more than 100 mg/L and 50 mg/L for Z - CWSE and G - CWSE, respectively.

MCL1 gene co-expression module stratifies multiple myeloma and predicts response to proteasome inhibitor-based therapy.

Multiple myeloma (MM) is the second most common hematologic cancer, characterized by abnormal accumulation of plasma cells in the bone marrow. The extensive biological and clinical heterogeneity of MM hinders effective treatment and etiology research. Several molecular classification systems of prognostic impact have been proposed, but they do not predict the response to treatment nor do they correlate to plasma cell development pathways. Here we describe the classification of MM into two distinct subtypes based on the expression levels of a gene module coexpressed with MCL1 (MCL1-M), a regulator of plasma cell survival. The classification system enabled prediction of the prognosis and the response to bortezomib-based therapy. Moreover, the two MM subtypes were associated with two different plasma cell differentiation pathways (enrichment of a preplasmablast signature versus aberrant expression of B cell genes). 1q gain, harboring 63 of the 87 MCL1-M members including MCL1, was found in about 80% of the MM with upregulated MCL1-M expression. Clonal analysis showed that 1q gain tended to occur as an early clonal event. Members of MCL1-M captured both MM cell-intrinsically acting signals and the signals regulating the interaction between MM cells with bone marrow microenvironment. MCL1-M members were co-expressed in mouse germinal center B cells. Together, these findings indicate that MCL1-M may play previously inadequately recognized, initiating role in the pathogenesis of MM. Our findings suggest that MCL1-M signature-based molecular clustering of MM constitutes a solid framework toward understanding the etiology of this disease and establishing personalized care. Article Summary: A pathogenic mechanism-guided molecular classification would facilitate treatment decision and etiology research of multiple myeloma. On the basis of the expression levels of a gene module coexpressed with MCL1, we have established a classification scheme assigning multiple myeloma into two subtypes with distinct prognosis, treatment responses and pathogenic backgrounds.

Hydrolysis of polyaluminum chloride prior to coagulation: Effects on coagulation behavior and implications for improving coagulation performance.

The effects of polyaluminum chloride (PACl) hydrolysis prior to coagulation on both the coagulation zone and coagulation performance of a kaolin suspension were investigated by a novel jar test named the "reversed coagulation test". The tests showed that PACl hydrolysis prior to coagulation decreased the performance of charge neutralization coagulation in the case of short-time slow mixing (10min; G=15sec-1) and increased the optimal dosage for charge neutralization and sweep coagulation. Moreover, the hydrolysis time had insignificant effects on the size and zeta potential of PACl precipitates and the residual turbidity of the raw water. However, PACl hydrolysis prior to coagulation and the size of PACl precipitates had a negligible effect on the performance of sweep coagulation. The results imply that, in practice, preparing a PACl solution with deionized water, rather than tap water or the outlet water from a wastewater treatment unit, can significantly save PACl consumption and improve the performance of charge neutralization coagulation, while preparing the PACl solution with tap or outlet water would not affect the performance of sweep coagulation. In addition, the optimal rapid mixing intensity appears to be determined by a balance between the degree of coagulant hydrolysis before contacting the primary particles and the average size of flocs in the rapid mixing period. These results provide new insights into the role of PACl hydrolysis and will be useful for improving coagulation efficiency.

Synthesis of Spiro-lactams and Polysubstituted Pyrroles via Ceric Ammonium Nitrate-Mediated Oxidative Cyclization of N-Furan-2-ylmethyl-ß-Enaminones.

Spiro-lactams and polysubstituted pyrroles were synthesized by reactions of furfurylamines with ynones followed by oxidation. Specifically, the protocol involved in situ generation of N-furan-2-ylmethyl-ß-enaminones and their subsequent oxidation by ceric ammonium nitrate (6 equiv for spiro-lactam formation, 3 equiv for pyrrole formation). This useful dearomatizing oxidation, which likely proceeds via a free-radical pathway, can be expected to extend the synthetic applications of furan and pyrrole derivatives.

Retention in treated wastewater affects survival and deposition of Staphylococcus aureus and Escherichia coli in sand columns.

The fate and transport of pathogenic bacteria from wastewater treatment facilities in the Earth's subsurface have attracted extensive concern over recent decades, while the impact of treated-wastewater chemistry on bacterial viability and transport behavior remains unclear. The influence of retention time in effluent from a full-scale municipal wastewater treatment plant on the survival and deposition of Staphylococcus aureus and Escherichia coli strains in sand columns was investigated in this paper. In comparison to the bacteria cultivated in nutrient-rich growth media, retention in treated wastewater significantly reduced the viability of all strains. Bacterial surface properties, e.g., zeta potential, hydrophobicity, and surface charges, varied dramatically in treated wastewater, though no universal trend was found for different strains. Retention in treated wastewater effluent resulted in changes in bacterial deposition in sand columns. Longer retention periods in treated wastewater decreased bacterial deposition rates for the strains evaluated and elevated the transport potential in sand columns. We suggest that the wastewater quality should be taken into account in estimating the fate of pathogenic bacteria discharged from wastewater treatment facilities and the risks they pose in the aquatic environment.

Influence of Adhesion Force on icaA and cidA Gene Expression and Production of Matrix Components in Staphylococcus aureus Biofilms.

The majority of human infections are caused by biofilms. The biofilm mode of growth enhances the pathogenicity of Staphylococcus spp. considerably, because once they adhere, staphylococci embed themselves in a protective, self-produced matrix of extracellular polymeric substances (EPSs). The aim of this study was to investigate the influence of forces of staphylococcal adhesion to different biomaterials on icaA (which regulates the production of EPS matrix components) and cidA (which is associated with cell lysis and extracellular DNA [eDNA] release) gene expression in Staphylococcus aureus biofilms. Experiments were performed with S. aureus ATCC 12600 and its isogenic mutant, S. aureus ATCC 12600 Δpbp4, deficient in peptidoglycan cross-linking. Deletion of pbp4 was associated with greater cell wall deformability, while it did not affect the planktonic growth rate, biofilm formation, cell surface hydrophobicity, or zeta potential of the strains. The adhesion forces of S. aureus ATCC 12600 were the strongest on polyethylene (4.9 ± 0.5 nN), intermediate on polymethylmethacrylate (3.1 ± 0.7 nN), and the weakest on stainless steel (1.3 ± 0.2 nN). The production of poly-N-acetylglucosamine, eDNA presence, and expression of icaA genes decreased with increasing adhesion forces. However, no relation between adhesion forces and cidA expression was observed. The adhesion forces of the isogenic mutant S. aureus ATCC 12600 Δpbp4 (deficient in peptidoglycan cross-linking) were much weaker than those of the parent strain and did not show any correlation with the production of poly-N-acetylglucosamine, eDNA presence, or expression of the icaA and cidA genes. This suggests that adhesion forces modulate the production of the matrix molecule poly-N-acetylglucosamine, eDNA presence, and icaA gene expression by inducing nanoscale cell wall deformation, with cross-linked peptidoglycan layers playing a pivotal role in this adhesion force sensing.

Residence-time dependent cell wall deformation of different Staphylococcus aureus strains on gold measured using surface-enhanced-fluorescence.

Bacterial adhesion to surfaces is accompanied by cell wall deformation that may extend to the lipid membrane with an impact on the antimicrobial susceptibility of the organisms. Nanoscale cell wall deformation upon adhesion is difficult to measure, except for Δpbp4 mutants, deficient in peptidoglycan cross-linking. This work explores surface enhanced fluorescence to measure the cell wall deformation of Staphylococci adhering on gold surfaces. Adhesion-related fluorescence enhancement depends on the distance of the bacteria from the surface and the residence-time of the adhering bacteria. A model is forwarded based on the adhesion-related fluorescence enhancement of green-fluorescent microspheres, through which the distance to the surface and cell wall deformation of adhering bacteria can be calculated from their residence-time dependent adhesion-related fluorescence enhancement. The distances between adhering bacteria and a surface, including compression of their extracellular polymeric substance (EPS)-layer, decrease up to 60 min after adhesion, followed by cell wall deformation. Cell wall deformation is independent of the integrity of the EPS-layer and proceeds fastest for a Δpbp4 strain.

Current Status of Vaccines for Porcine Reproductive and Respiratory Syndrome: Interferon Response, Immunological Overview, and Future Prospects.

Porcine reproductive and respiratory syndrome (PRRS) remains a formidable challenge for the global pig industry. Caused by PRRS virus (PRRSV), this disease primarily affects porcine reproductive and respiratory systems, undermining effective host interferon and other immune responses, resulting in vaccine ineffectiveness. In the absence of specific antiviral treatments for PRRSV, vaccines play a crucial role in managing the disease. The current market features a range of vaccine technologies, including live, inactivated, subunit, DNA, and vector vaccines, but only modified live virus (MLV) and killed virus (KV) vaccines are commercially available for PRRS control. Live vaccines are promoted for their enhanced protective effectiveness, although their ability to provide cross-protection is modest. On the other hand, inactivated vaccines are emphasized for their safety profile but are limited in their protective efficacy. This review updates the current knowledge on PRRS vaccines' interactions with the host interferon system, and other immunological aspects, to assess their current status and evaluate advents in PRRSV vaccine development. It presents the strengths and weaknesses of both live attenuated and inactivated vaccines in the prevention and management of PRRS, aiming to inspire the development of innovative strategies and technologies for the next generation of PRRS vaccines.

Perfluorobutanoic acid triggers metabolic and transcriptional reprogramming in wheat seedlings.

The environmental risks of fluorinated alternatives are of great concern with the phasing out of perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate. Here, multi-omics (i.e., metabolomics and transcriptomics) coupled with physiological and biochemical analyses were employed to investigate the stress responses of wheat seedings (Triticum aestivum L.) to perfluorobutanoic acid (PFBA), one of the short-chain per- and polyfluoroalkyl substances (PFAS) and PFOA alternatives, at environmentally relevant concentrations (0.1-100 ng/g). After 28 days of soil exposure, PFBA boosted the generation of OH and O2- in wheat seedlings, resulting in lipid peroxidation, protein perturbation and impaired photosynthesis. Non-enzymatic antioxidant defense systems (e.g., glutathione, phenolics, and vitamin C) and enzymatic antioxidant copper/zinc superoxide dismutase were strikingly activated (p < 0.05). PFBA-triggered oxidative stress induced metabolic and transcriptional reprogramming, including carbon and nitrogen metabolisms, lipid metabolisms, immune responses, signal transduction processes, and antioxidant defense-related pathways. Down-regulation of genes related to plant-pathogen interaction suggested suppression of the immune-response, offering a novel understanding on the production of reactive oxygen species in plants under the exposure to PFAS. The identified MAPK signaling pathway illuminated a novel signal transduction mechanism in plant cells in response to PFAS. These findings provide comprehensive understandings on the phytotoxicity of PFBA to wheat seedlings and new insights into the impacts of PFAS on plants.

The deleterious variants of N-acetylgalactosamine-6-sulfatase (GalN6S) enzyme trigger Morquio a syndrome by disrupting protein foldings.

Lysosomal enzymes degrade cellular macromolecules, while their inactivation causes human hereditary metabolic disorders. Mucopolysaccharidosis IVA (MPS IVA; Moquio A syndrome) is one of the lysosomal storage disorders caused by a defective Galactosamine-6-sulfatase (GalN6S) enzyme. In several populations, disease incidence is elevated due to missense mutations brought on by non-synonymous allelic variation in the GalN6S enzyme. Here, we studied the effect of non-synonymous single nucleotide polymorphism (nsSNPs) on the structural dynamics of the GalN6S enzyme and its binding with N-acetylgalactosamine (GalNAc) using all-atom molecular dynamics simulation and an essential dynamics approach. Consequently, in this study, we have identified three functionally disruptive mutations in domain-I and domain-II, that is, S80L, R90W, and S162F, which presumably contribute to post-translational modifications. The study delineated that both domains work cooperatively, and alteration in domain II (S80L, R90W) leads to conformational changes in the catalytic site in domain-I, while mutation S162F mainly provokes higher residual flexibility of domain II. These results show that these mutations impair the hydrophobic core, implying that Morquio A syndrome is caused by misfolding of the GalN6S enzyme. The results also show the instability of the GalN6S-GalNAc complex upon substitution. Overall, the structural dynamics resulting from point mutations give the molecular rationale for Moquio A syndrome and, more importantly, the Mucopolysaccharidoses (MPS) family of diseases, re-establishing MPS IVA as a protein-folding disease.Communicated by Ramaswamy H. Sarma.

Surface enhanced bacterial fluorescence and enumeration of bacterial adhesion.

The use of flow displacement systems for studying initial bacterial adhesion to surfaces is mostly confined to transparent substrata. The objective of this study was to investigate a method based on macroscopic fluorescence imaging to enumerate adhering fluorescent bacteria on non-transparent substrata, real-time and under flow. To this end, a stepwise protocol is described to quantify adhesion of green-fluorescent-protein producing Staphylococcus aureus on polished and non-polished metal and polymer surfaces accounting for surface-enhanced-fluorescence on metal surfaces, quantified by the ratio of the single cell fluorescence observed for adhering and planktonic bacteria. Enumeration of adhering fluorescent staphylococci by the proposed method is consistent with results obtained using metallurgical microscopy. An advantage however, is that the non-homogeneous surface coverage and surface roughness do not limit the applicability of the method. Moreover, the accurate quantification of surface-enhanced-fluorescence arising from adhering bacteria offers a new pathway for evaluating bacterial cell surface deformation during adhesion.

Simultaneous determination of erythromycin and its transformation products in treated erythromycin fermentation residue and amended soil.

Erythromycin fermentation residue (EFR) is a solid waste generated from the fermentation process of erythromycin A production. Some byproducts are produced during the fermentation process of erythromycin A production, and erythromycin A can also undergo hydrolysis and biodegradation reactions in the environment with the formation of transformation products. Herein, an accurate analytical method was established and validated to quantify erythromycin A, two byproducts and five hydrolysis or biodegradation products, in solid or semi-solid media of waste EFR and the amended soil. The method mainly included ultrasonic solvent extraction, solid phase extraction, and ultra-performance liquid chromatography-tandem mass spectrometry quantification. All analytes could be effectively extracted in a single process, and the recoveries ranged from 76% to 122% for different matrices. Low matrix effects and excellent precision were achieved by optimizing the mass spectrometry parameters, extraction solution, number of extractions and eluent. This method was applied to evaluate the residual analytes in EFR, treated EFR after industrial-scale hydrothermal treatment, and the subsequent soil application. Seven analytes were detected in the EFR, while six were found in the treated EFR and amended soils. The concentration of erythromycin A in EFR was 1,629 ± 100 mg/kg·TS, and the removal efficiency of hydrothermal treatment (180 °C, 60 min) was about 99.6%. Three hydrolysis products were the main residuals in treated EFR, with anhydroerythromycin A showing the highest concentration. The concentrations of the analytes in soil ranged from 2.17 ± 1.04 to 92.33 ± 20.70 µg/kg·TS, and anhydroerythromycin A contributed 65%-77% of the total concentration. Erythromycin B, a byproduct, was still detected in soil. This work provides an accurate analytical method which would be useful to evaluate the potential risk of byproducts and transformation products of erythromycin A in environment.

Hyper-thermophilic anaerobic pretreatment enhances the removal of transferable oxazolidinone and phenicol cross-resistance gene optrA in enterococci.

The extensive use of florfenicol in poultry industry results in the emergence of optrA gene, which also confers resistance to clinically important antibiotic linezolid. This study investigated the occurrence, genetic environments, and removal of optrA in enterococci in mesophilic (37 °C) and thermophilic (55 °C) anaerobic digestion systems, and a hyper-thermophilic (70 °C) anaerobic pretreatment system for chicken waste. A total of 331 enterococci were isolated and analyzed for antibiotic resistance against linezolid and florfenicol. The optrA gene was frequently detected in enterococci from chicken waste (42.7%) and effluents from mesophilic (72%) and thermophilic (56.8%) reactors, but rarely detected in the hyper-thermophilic (5.8%) effluent. Whole-genome sequencing revealed that optrA-carrying Enterococcus faecalis sequence type (ST) 368 and ST631 were the dominant clones in chicken waste, and they remained dominant in mesophilic and thermophilic effluents, respectively. The plasmid-borne IS1216E-fexA-optrA-erm(A)-IS1216E was the core genetic element for optrA in ST368, whereas chromosomal Tn554-fexA-optrA was the key one in ST631. IS1216E might play a key role in horizontal transfer of optrA due to its presence in different clones. Hyper-thermophilic pretreatment removed enterococci with plasmid-borne IS1216E-fexA-optrA-erm(A)-IS1216E. A hyper-thermophilic pretreatment is recommended for chicken waste to mitigate dissemination of optrA from animal waste to the environment.

Partial nitritation and nitrogen removal of vacuum toilet wastewater from high-speed trains in a sequential batch reactor.

Owing to the high contents of organics and nitrogen in vacuum toilet wastewater (VTW) generated from high-speed trains, onsite pretreatment is usually required before VTW can be discharged into municipal sewers. In this study, a partial nitritation process was stably established in a sequential batch reactor to efficiently utilize the organics in synthetic and real VTWs for nitrogen removal and to produce an effluent suitable for anaerobic ammonia oxidation. In spite of the high fluctuations of COD and nitrogen in VTW, the organics used for nitrogen removal stabilized at 1.97 ± 0.18 mg COD mg N-1 removed, and the effluent NO2--N/NH4+-N ratios were maintained at 1.26 ± 0.13. The removal efficiencies of nitrogen and COD were 31.8 ± 3.5% and 65.2 ± 5.3% under the volumetric loading rates of 1.14 ± 0.15 kg N m-3 d-1 and 1.03 ± 0.26 kg COD m-3 d-1 for real VTW, respectively. Microbial community analysis revealed that Nitrosomonas (0.95%-1.71%) was the dominant autotrophic ammonium-oxidizing bacterial genus, but nitrite-oxidizing bacteria, Nitrolancea, was severely inhibited, with a relative abundance less than 0.05%. The relative abundance of denitrifying bacteria increased by 7.34% when the influent was switched to real VTW. Functional profile predictions of the biomass showed that the decrease in the COD/N ratio and the switch of reactor influent from synthetic to real VTW increased the relative abundance of enzymes and modules involved in carbon and nitrogen metabolisms.

Temporal and spatial stability of the EM/PM molecular subtypes in adult diffuse glioma.

Detailed characterizations of genomic alterations have not identified subtype-specific vulnerabilities in adult gliomas. Mapping gliomas into developmental programs may uncover new vulnerabilities that are not strictly related to genomic alterations. After identifying conserved gene modules co-expressed with EGFR or PDGFRA (EM or PM), we recently proposed an EM/PM classification scheme for adult gliomas in a histological subtype- and grade-independent manner. By using cohorts of bulk samples, paired primary and recurrent samples, multi-region samples from the same glioma, single-cell RNA-seq samples, and clinical samples, we here demonstrate the temporal and spatial stability of the EM and PM subtypes. The EM and PM subtypes, which progress in a subtype-specific mode, are robustly maintained in paired longitudinal samples. Elevated activities of cell proliferation, genomic instability and microenvironment, rather than subtype switching, mark recurrent gliomas. Within individual gliomas, the EM/PM subtype was preserved across regions and single cells. Malignant cells in the EM and PM gliomas were correlated to neural stem cell and oligodendrocyte progenitor cell compartment, respectively. Thus, while genetic makeup may change during progression and/or within different tumor areas, adult gliomas evolve within a neurodevelopmental framework of the EM and PM molecular subtypes. The dysregulated developmental pathways embedded in these molecular subtypes may contain subtype-specific vulnerabilities.

Stalled oligodendrocyte differentiation in IDH-mutant gliomas.

BACKGROUND: Roughly 50% of adult gliomas harbor isocitrate dehydrogenase (IDH) mutations. According to the 2021 WHO classification guideline, these gliomas are diagnosed as astrocytomas, harboring no 1p19q co-deletion, or oligodendrogliomas, harboring 1p19q co-deletion. Recent studies report that IDH-mutant gliomas share a common developmental hierarchy. However, the neural lineages and differentiation stages in IDH-mutant gliomas remain inadequately characterized. METHODS: Using bulk transcriptomes and single-cell transcriptomes, we identified genes enriched in IDH-mutant gliomas with or without 1p19q co-deletion, we also assessed the expression pattern of stage-specific signatures and key regulators of oligodendrocyte lineage differentiation. We compared the expression of oligodendrocyte lineage stage-specific markers between quiescent and proliferating malignant single cells. The gene expression profiles were validated using RNAscope analysis and myelin staining and were further substantiated using data of DNA methylation and single-cell ATAC-seq. As a control, we assessed the expression pattern of astrocyte lineage markers. RESULTS: Genes concordantly enriched in both subtypes of IDH-mutant gliomas are upregulated in oligodendrocyte progenitor cells (OPC). Signatures of early stages of oligodendrocyte lineage and key regulators of OPC specification and maintenance are enriched in all IDH-mutant gliomas. In contrast, signature of myelin-forming oligodendrocytes, myelination regulators, and myelin components are significantly down-regulated or absent in IDH-mutant gliomas. Further, single-cell transcriptomes of IDH-mutant gliomas are similar to OPC and differentiation-committed oligodendrocyte progenitors, but not to myelinating oligodendrocyte. Most IDH-mutant glioma cells are quiescent; quiescent cells and proliferating cells resemble the same differentiation stage of oligodendrocyte lineage. Mirroring the gene expression profiles along the oligodendrocyte lineage, analyses of DNA methylation and single-cell ATAC-seq data demonstrate that genes of myelination regulators and myelin components are hypermethylated and show inaccessible chromatin status, whereas regulators of OPC specification and maintenance are hypomethylated and show open chromatin status. Markers of astrocyte precursors are not enriched in IDH-mutant gliomas. CONCLUSIONS: Our studies show that despite differences in clinical manifestation and genomic alterations, all IDH-mutant gliomas resemble early stages of oligodendrocyte lineage and are stalled in oligodendrocyte differentiation due to blocked myelination program. These findings provide a framework to accommodate biological features and therapy development for IDH-mutant gliomas.