Phenotypic Changes Research Articles

Identifying novel clinical phenotypes of acute respiratory distress syndrome using trajectories of daily fluid balance: a secondary analysis of randomized controlled trials

BackgroundPreviously identified phenotypes of acute respiratory distress syndrome (ARDS) could not reveal the dynamic change of phenotypes over time. We aimed to identify novel clinical phenotypes in ARDS using trajectories of fluid balance, to test whether phenotypes respond differently to different treatment, and to develop a simplified model for phenotype identification.MethodsFACTT (conservative vs liberal fluid management) trial was classified as a development cohort, joint latent class mixed models (JLCMMs) were employed to identify trajectories of fluid balance. Heterogeneity of treatment effect (HTE) for fluid management strategy across phenotypes was investigated. We also constructed a parsimonious probabilistic model using baseline data to predict the fluid trajectories in the development cohort. The trajectory groups and the probabilistic model were externally validated in EDEN (initial trophic vs full enteral feeding) trial.ResultsUsing JLCMM, we identified two trajectory groups in the development cohort: Class 1 (n = 758, 76.4% of the cohort) had an early positive fluid balance, but achieved negative fluid balance rapidly, and Class 2 (n = 234, 24.6% of the cohort) was characterized by persistent positive fluid balance. Compared to Class 1 patients, patients in Class 2 had significantly higher 60-day mortality (53.5% vs. 17.8%, p < 0.001), and fewer ventilator-free days (0 vs. 20, p < 0.001). A significant HTE between phenotypes and fluid management strategies was observed in the FACTT. An 8-variables model was derived for phenotype assignment.ConclusionsWe identified and validated two novel clinical trajectories for ARDS patients, with both prognostic and predictive enrichment. The trajectories of ARDS can be identified with simple classifier models.

The Specific ROCK2 Inhibitor KD025 Alleviates Glycolysis through Modulating STAT3-, CSTA- and S1PR3-Linked Signaling in Human Trabecular Meshwork Cells

To investigate the biological significance of Rho-associated coiled-coil-containing protein kinase (ROCK) 2 in the human trabecular meshwork (HTM), changes in both metabolic phenotype and gene expression patterns against a specific ROCK2 inhibitor KD025 were assessed in planar-cultured HTM cells. A seahorse real-time ATP rate assay revealed that administration of KD025 significantly suppressed glycolytic ATP production rate and increased mitochondrial ATP production rate in HTM cells. RNA sequencing analysis revealed that 380 down-regulated and 602 up-regulated differentially expressed genes (DEGs) were identified in HTM cells treated with KD025 compared with those that were untreated. Gene ontology analysis revealed that DEGs were more frequently related to the plasma membrane, extracellular components and integral cellular components among cellular components, and related to signaling receptor binding and activity and protein heterodimerization activity among molecular functions. Ingenuity Pathway Analysis (IPA) revealed that the detected DEGs were associated with basic cellular biological and physiological properties, including cellular movement, development, growth, proliferation, signaling and interaction, all of which are associated with cellular metabolism. Furthermore, the upstream regulator analysis and causal network analysis estimated IL-6, STAT3, CSTA and S1PR3 as possible regulators. Current findings herein indicate that ROCK2 mediates the IL-6/STAT3-, CSTA- and S1PR3-linked signaling related to basic biological activities such as glycolysis in HTM cells.

Targeted Drug Therapy for Senescent Cells Alleviates Unilateral Ureteral Obstruction-Induced Renal Injury in Rats

Hydronephrosis resulting from unilateral ureteral obstruction (UUO) is a common cause of renal injury, often progressing to late-stage renal fibrosis or even potential renal failure. Renal injury and repair processes are accompanied by changes in cellular senescence phenotypes. However, the mechanism is poorly understood. The purpose of this study is to clarify the changes in senescence phenotype at different time points in renal disease caused by UUO and to further investigate whether eliminating senescent cells using the anti-senescence drug ABT263 could attenuate UUO-induced renal disease. Specifically, renal tissues were collected from established UUO rat models on days 1, 2, 7, and 14. The extent of renal tissue injury and fibrosis in rats was assessed using histological examination, serum creatinine, and blood urea nitrogen levels. The apoptotic and proliferative capacities of renal tissues and phenotypic changes in cellular senescence were evaluated. After the intervention of the anti-senescence drug ABT263, the cellular senescence as well as tissue damage changes were re-assessed. We found that before the drug intervention, the UUO rats showed significantly declined renal function, accompanied by renal tubular injury, increased inflammatory response, and oxidative stress, alongside aggravated cellular senescence. Meanwhile, after the treatment with ABT263, the rats had a significantly lower number of senescent cells, attenuated renal tubular injury and apoptosis, enhanced proliferation, reduced oxidative stress and inflammation, improved renal function, and markedly inhibited fibrosis. This suggests that the use of the anti-senescence drug ABT263 to eliminate senescent cells can effectively attenuate UUO-induced renal injury. This highlights the critical role of cellular senescence in the transformation of acute injury into chronic fibrosis.

Human-derived fecal microbiota transplantation alleviates social deficits of the BTBR mouse model of autism through a potential mechanism involving vitamin B6 metabolism.

Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental condition characterized by social communication deficiencies and stereotypic behaviors influenced by hereditary and/or environmental risk factors. There are currently no approved medications for treating the core symptoms of ASD. Human fecal microbiota transplantation (FMT) has emerged as a potential intervention to improve autistic symptoms, but the underlying mechanisms are not fully understood. In this study, we evaluated the effects of human-derived FMT on behavioral and multi-omics profiles of the BTBR mice, an established model for ASD. FMT effectively alleviated the social deficits in the BTBR mice and normalized their distinct plasma metabolic profile, notably reducing the elevated long-chain acylcarnitines. Integrative analysis linked these phenotypic changes to specific Bacteroides species and vitamin B6 metabolism. Indeed, vitamin B6 supplementation improved the social behaviors in BTBR mice. Collectively, these findings shed new light on the interplay between FMT and vitamin B6 metabolism and revealed a potential mechanism underlying the therapeutic role of FMT in ASD.IMPORTANCEAccumulating evidence supports the beneficial effects of human fecal microbiota transplantation (FMT) on symptoms associated with autism spectrum disorder (ASD). However, the precise mechanism by which FMT induces a shift in the microbiota and leads to symptom improvement remains incompletely understood. This study integrated data from colon-content metagenomics, colon-content metabolomics, and plasma metabolomics to investigate the effects of FMT treatment on the BTBR mouse model for ASD. The analysis linked the amelioration of social deficits following FMT treatment to the restoration of mitochondrial function and the modulation of vitamin B6 metabolism. Bacterial species and compounds with beneficial roles in vitamin B6 metabolism and mitochondrial function may further contribute to improving FMT products and designing novel therapies for ASD treatment.

Cordycepin Triphosphate as a Potential Modulator of Cellular Plasticity in Cancer via cAMP-Dependent Pathways: An In Silico Approach

Cordycepin, or 3′-deoxyadenosine, is an adenosine analog with a broad spectrum of biological activity. The key structural difference between cordycepin and adenosine lies in the absence of a hydroxyl group at the 3′ position of the ribose ring. Upon administration, cordycepin can undergo an enzymatic transformation in specific tissues, forming cordycepin triphosphate. In this study, we conducted a comprehensive analysis of the structural features of cordycepin and its derivatives, contrasting them with endogenous purine-based metabolites using chemoinformatics and bioinformatics tools in addition to molecular dynamics simulations. We tested the hypothesis that cordycepin triphosphate could bind to the active site of the adenylate cyclase enzyme. The outcomes of our molecular dynamics simulations revealed scores that are comparable to, and superior to, those of adenosine triphosphate (ATP), the endogenous ligand. This interaction could reduce the production of cyclic adenosine monophosphate (cAMP) by acting as a pseudo-ATP that lacks a hydroxyl group at the 3′ position, essential to carry out nucleotide cyclization. We discuss the implications in the context of the plasticity of cancer and other cells within the tumor microenvironment, such as cancer-associated fibroblast, endothelial, and immune cells. This interaction could awaken antitumor immunity by preventing phenotypic changes in the immune cells driven by sustained cAMP signaling. The last could be an unreported molecular mechanism that helps to explain more details about cordycepin’s mechanism of action.

Tea green leafhopper infestations affect tea plant growth by altering the synthesis of brassinolide.

Tea green leafhoppers are insects widely distributed in major tea-growing areas. At present, less attention has been paid to the study on effect of tea green leafhopper infestation on tea growth phenotype. In this study, tea green leafhoppers were used to treat tea branches in laboratory and co-treated with brassinolide (BL), the highest bioactivity of brassinosteroids (BRs), in tea garden. The results showed that the expression of genes related to BRs synthesis was inhibited and BL content was reduced in tea shoots after infestation by tea green leafhoppers. In addition, area of each leaf position, length and diameter of internodes, and the biomass of the tender shoots of tea plant were decreased after infestation by tea green leafhoppers. The number of trichomes, leaf thickness, palisade tissue thickness and cuticle thickness of tea shoots were increased after tea green leafhoppers infestation. BL spraying could partially recover the phenotypic changes of tea branches caused by tea green leafhoppers infestation. Further studies showed that tea green leafhoppers infestation may regulate the expression of CsDWF4 (a key gene for BL synthesis) through transcription factors CsFP1 and CsTCP1a, which finally affect the BL content. Moreover, BL was applied to inhibit the tea green leafhoppers infestation on tea shoots. In conclusion, our study revealed the effect of plant hormone BL-mediated tea green leafhoppers infestation on the growth phenotype of tea plants.

Single molecule delivery into living cells

Controlled manipulation of cultured cells by delivery of exogenous macromolecules is a cornerstone of experimental biology. Here we describe a platform that uses nanopipettes to deliver defined numbers of macromolecules into cultured cell lines and primary cells at single molecule resolution. In the nanoinjection platform, the nanopipette is used as both a scanning ion conductance microscope (SICM) probe and an injection probe. The SICM is used to position the nanopipette above the cell surface before the nanopipette is inserted into the cell into a defined location and to a predefined depth. We demonstrate that the nanoinjection platform enables the quantitative delivery of DNA, globular proteins, and protein fibrils into cells with single molecule resolution and that delivery results in a phenotypic change in the cell that depends on the identity of the molecules introduced. Using experiments and computational modeling, we also show that macromolecular crowding in the cell increases the signal-to-noise ratio for the detection of translocation events, thus the cell itself enhances the detection of the molecules delivered.

#1699 The role of interleukin 12 cytokine family in autosomal dominant polycystic kidney disease physiopathology

Abstract Background and Aims Autosomal dominant polycystic kidney disease (ADPKD) is an inherited, complex disease, characterized by cysts formation and phenotypic changes. ADPKD physiopathology is under research, the role of proinflammatory chemokines responsible for perpetuating the cycle of chronic inflammation leading to kidney damage being intensively studied. We aimed to explore the individualized contribution of IL-12 interleukin family members in ADPKD physiopathology. Method We developed a prospective, case control study, in Carol Davila Clinical Hospital of Nephrology, including a group of 66 ADPKD subjects (56.1 years old, men:women 35:32), and a group of 40 healthy subjects, similar as sex, mean age. ADPKD diagnosis was based on familial history, clinical exam and CT or MRI scan. We excluded from the study subjects that presented cysts in other organs except the kidney, with eGFR&amp;lt;60 mL/min/1.73 mp, with history of hematuria, cysts infection, urinary tract infection, renal lithiasis, with unstable blood pressure in the last 6 months. Laboratory tests: serum levels of monomers IL-12 p40 and IL-20 p35 and heterodimers IL-12 p70, IL-23, IL 35, assessed by ELISA method. Statistical analysis. All the results were analyzed using IBM SPSS Statistics 2015 and were presented as average value ± standard deviation. p &amp;lt; 0.05 was considered with statistical significance. Results In ADPKD patients, we detected altered production of IL-12 cytokine, with low production of IL-12 p35 and IL-35, respectively high production of IL-12 p70, IL-23 and IL-12 p40 versus control. IL-12 p35 and IL-35 had statistically significant lower levels in ADPKD patients with eGFR&amp;lt;90 ml/min/1.73 mp, when compared with ADPKD patients with eGFR&amp;gt;90 ml/min/1.73 mp (Table 1). IL-12 p70, IL-23 and IL-12 p40 had statistically significant higher levels in ADPKD patients with eGFR&amp;lt;90 ml/min/1.73 mp, when compared with ADPKD patients with eGFR&amp;gt;90 ml/min/1.73 mp (Table 1). IL-12p70, IL-23 and IL-12 p40 had a negative significant correlation with eGFR, while IL-12p35 and IL-35 had a positive significant correlation with eGFR. Though, IL-12p35 and IL-35 serum levels correlated negatively with IL-12p70, IL-23 and IL-12 p40 serum levels in ADPKD patients. Conclusion The results of the present study suggest that ADPKD is a cellular source of IL-12 family, cytokines produced by antigenic stimulation. IL-12 family programming is abnormal in ADPKD patients. We detected synergic and divergent action of IL-12 cytokine family members, relevant for ADPKD physiopathology.

#2144 Expression profile induced by TGF-β1 in senescent human peritoneal mesothelial cells is less pronounced than in young cells

Abstract Background and Aims Transforming growth factor β1 (TGF-β1) is a recognized driver of both mesothelial-to-mesenchymal transition (MMT) and cellular senescence observed in vitro in human peritoneal mesothelial cells (HPMCs), and have a significant role in adverse peritoneal remodelling of patients treated with peritoneal dialysis (PD). We have previously shown that senescent HPMCs spontaneously acquire some phenotypic features of MMT which in young HPMCs are induced by TGF-β1. At the same time, senescent HPMCs appeared to be less responsive to TGF-β. It is not clear what determines which pathway is activated by TGF-β1. Here, we aimed to extend previous observations and used electron microscopy, transcriptomics, and proteomics to identify differences between young and senescent cells in their responsiveness to TGF-β. Method Replicative senescence of omentum-derived HPMCs isolated from 4 separate donors was induced by serial passages until cells ceased to grow and expressed senescence-associated β-galactosidase. Serum-starved young and senescent cells were treated in parallel with 1 ng/mL of TGF-β1 for 72 hours. Fixed cells were analyzed with a Jeol transmission electron microscope at 80 kV (Jeol, Tokyo, Japan). Cell lysates were analysed for global gene and protein expression using an integrated transcriptomic (Array-based) and proteomic (LC/MS-based) approach. Results Exposure to TGF-β1 led to phenotypic changes consistent with MMT in young, but not in senescent HPMCs (Fig. 1A). The omics analyses revealed that the response to TGF-β1 was associated with 89 genes being differentially expressed (55 down- and 34 up-upregulated) in young HPMCs and with 13 genes (5 down- and 8 up-regulated) in senescent HPMCs (Fig. 1B). In addition, TGF-β1 changed the expression of 131 proteins in young HPMCs (72 down- and 59 up-regulated) and 232 proteins in senescent HPMCs (127 down- and 105 up-regulated) (Fig. 1C). The responses to TGF-β identified at both the transcriptome and protein levels (Fig. 1D) and present in both young and senescent HPMCs included TGFBI (TGF-β-induced) and ITGB3 (β3 integrin), which were upregulated, and UPK1B (uroplakin 1B) and SEMA3B (semaphorin 3B), which were downregulated. Changes in response to TGF-β seen at the RNA and protein level included also VCAN (versican), ITGA11 (integrin α11), FN1 (fibronectin 1), CCNYL1 (Cyclin Y-like 1) and MYOZ2 (myozenin 2), however, these were observed only in young cells. A decrease in KLK7 (Kallikrein 7) gene expression after exposure to TGF-β was seen both in young and senescent HPMCs, with a decrease in KLK7 protein detected only in senescent cells. Finally, exposure to TGF-β led to an increase in THBS1 (thrombospondin 1) expression in young cells and at the protein level in senescent cells. Conclusion In conclusion, the profound morphological changes seen in senescent HPMCs are not significantly exacerbated by TGFβ. Likewise, changes in global gene and protein profiles in response to TGF-β appear to be less pronounced in senescent cells. Among the genes and proteins affected by TGF-β, those involved in angiogenesis and fibrosis deserve further attention as they may contribute to adverse peritoneal remodelling in PD patients.

#2641 MiR-200b induces ZEB1 mediated upregulation of Matriptase and affects expression of podocin

Abstract Background and Aims Diabetic kidney disease (DKD) is the leading cause of chronic kidney disease and a predominant reason for renal failure. Evidence from previous research indicates that abnormal expression of microRNAs (miRs) links closely to the occurrence and progression of DKD. Methods Expression of miRs in urine samples from DKD patients and in cultured renal cells stressed with transforming growth factor beta 1 (TGF-β1) was evaluated by TaqMan assay. The emerging miR of interest and its downstream targets were analyzed in human renal sections, in cultured human podocytes and in zebrafish. Results Cell free urine screening showed increased abundance of miR-200b in samples from patients with DKD when compared to healthy controls. In situ hybridization confirmed expression of miR-200b in kidney specimens from DKD patients, but was not detected in healthy renal parenchyma. Transcriptome profiling of cultured human podocytes overexpressing miR-200b identified this miR as a regulator of the ZEB1 mediated matriptase (ST14)/ podocin pathway and found TGF- β1 stress to be upstream activators of miR-200b expression in these cells. Immunofluorescence analysis of kidney sections from DKD patients showed increased expression of ST14 and decreased expression of podocin when compared to healthy controls. Furthermore, injection of a miR-200b mimic in zebrafish larvae caused an upregulation of ST14 and was accompanied by phenotypic changes such as edema, proteinuria and podocyte effacement. Conclusion Our results show that miR-200b is expressed in glomeruli and found at elevated levels in urine of DKD patients. Overexpression of miR-200b in cultured podocytes and in zebrafish induces upregulation of matriptase, a serine protease previously shown to cleave podocin. The observed increase in matriptase and decrease in podocin levels in glomeruli from DKD patients, together with the effect of a miR-200b mimic on proteinuria and ultrastructure of the pronephros in zebrafish positions miR-200b as a key regulator that modulates matriptase overactivation in DKD and warrants further studies.

Unusual progression of polycythemia vera

The case of a male patient with newly diagnosed polycythemia vera showing rare and unusually rapid progression with phenotypic change towards chronic myelomonocytic leukemia is presented. The case report illustrates remarkably rapid disease progression including a structural change in usually indolent polycythemia vera and highlights the prognostic relevance of enhanced molecular genetic testing.

In vitro induction of tetraploids and their phenotypic and transcriptome analysis in Glehnia littoralis

BackgroundGlehnia littoralis is a medicinal and edible plant species having commercial value and has several hundred years of cultivation history. Polyploid breeding is one of the most important and fastest ways to generate novel varieties. To obtain tetraploids of G. littoralis in vitro, colchicine treatment was given to the seeds and then were screened based on morphology, flow cytometry, and root tip pressing assays. Furthermore, transcriptome analysis was performed to identity the differentially expressed genes associated with phenotypic changes in tetraploid G. littoralis.ResultsThe results showed that 0.05% (w/v) colchicine treatment for 48 h was effective in inducing tetraploids in G. littoralis. The tetraploid G. littoralis (2n = 4x = 44) was superior in leaf area, leaf thickness, petiole diameter, SPAD value (Chl SPAD), stomatal size, epidermal tissues thickness, palisade tissues thickness, and spongy tissues thickness to the diploid ones, while the stomatal density of tetraploids was significantly lower. Transcriptome sequencing revealed, a total of 1336 differentially expressed genes (DEGs) between tetraploids and diploids. Chromosome doubling may lead to DNA content change and gene dosage effect, which directly affects changes in quantitative traits, with changes such as increased chlorophyll content, larger stomata and thicker tissue of leaves. Several up-regulated DEGs were found related to growth and development in tetraploid G. littoralis such as CKI, PPDK, hisD and MDP1. KEGG pathway enrichment analyses showed that most of DEGs were enriched in metabolic pathways.ConclusionsThis is the first report of the successful induction of tetraploids in G. littoralis. The information presented in this study facilitate breeding programs and molecular breeding of G. littoralis varieties.

Energy deprivation affects nitrogen assimilation and fatty acid biosynthesis leading to leaf chlorosis under waterlogging stress in the endangered Abies koreana.

Energy deprivation triggers various physiological, biochemical and molecular changes in plants under abiotic stress. We investigated the oxidative damages in the high altitude grown conifer Abies koreana exposed to waterlogging stress. Our experimental results showed that waterlogging stress led to leaf chlorosis, 35days after treatment (DAT). A significant decrease in leaf fresh weight, chlorophyll, and sugar content supported this phenotypic change. Biochemical analysis showed a significant increase in leaf proline, lipid peroxidase and DPPH free radical content of waterlogged plants. To elucidate the molecular mechanisms, we conducted RNA-sequencing and de novo assembly. Using RNA-Seq analysis approach and filtering (P<0.05 and FDR<0.001), we obtained 134 unigenes upregulated and 574 unigenes downregulated. GO and KEGG pathway analysis, placed the obtained differentially expressed unigenes (DEGs) in α-linoleic pathway, fatty acid degradation, glycosis, glycolipid metabolism and oligosaccharide biosynthesis process. Mapping of unigenes with Arabidopsis using BLASTn tool, showed several critical genes in photosynthesis and carbon metabolism downregulated. Following this, we found the repression of multiple nitrogen (N) assimilation and nucleotide biosynthesis genes including purine metabolism. In addition, waterlogging stress reduced the levels of polyunsaturated fatty acids with a concomitant increase only in myristic acid. Together, our results indicate that the prolonged snowmelt may cause inability of Abies koreana seedlings to lead the photosynthesis normally, due to the lack of root intercellular oxygen and emphasizes a detrimental effect on the N metabolic pathway, compromising this endangered tree's ability to be fully functional under waterlogging stress.

LGR5 Modulates Differentiated Phenotypes of Chondrocytes Through PI3K/AKT Signaling Pathway.

Tissue engineering is increasingly viewed as a promising avenue for functional cartilage reconstruction. However, chondrocyte dedifferentiation during in vitro culture remains an obstacle for clinical translation of tissue engineered cartilage. Re-differentiated induction have been employed to induce dedifferentiated chondrocytes back to their original phenotype. Regrettably, these strategies have been proven to be only moderately effective. To explore underlying mechanism, RNA transcriptome sequencing was conducted on primary chondrocytes (P0), dedifferentiated chondrocytes (P5), and redifferentiated chondrocytes (redifferentiation-induction of P5, P5.R). Based on multiple bioinformatics analysis, LGR5 was identified as a target gene. Subsequently, stable cell lines with LGR5 knocking-down and overexpression were established using P0 chondrocytes. The phenotypic changes in P1 and P5 chondrocytes with either LGR5 knockdown or overexpression were assessed to ascertain the potential influence of LGR5 dysregulation on chondrocyte phenotypes. Regulatory mechanism was then investigated using bioinformatic analysis, protein-protein docking, immunofluorescence co-localization and immunoprecipitation. The current study found that dysregulation of LGR5 can significantly impact the dedifferentiated phenotypes of chondrocytes (P5). Upregulation of LGR5 appears to activate the PI3K/AKT signal via increasing the phosphorylation levels of AKT (p-AKT1). Moreover, the increase of p-AKT1 may stabilize β-catenin and enhance the intensity of Wnt/β-catenin signal, and help to restore the dedifferentated phenotype of chondrocytes. LGR5 can modulate the phenotypes of chondrocytes in P5 passage through PI3K/AKT signaling pathway.

Epithelial-to-mesenchymal transition and NF-kB pathways are promoted by a mutant form of DDB2, unable to bind PCNA, in UV-damaged human cells

BackgroundDNA-Damaged Binding protein 2 (DDB2) is a protein involved in the early step of Nucleotide Excision Repair. Recently, it has been reported that DDB2 is involved in epithelial-to-mesenchymal transition (EMT), key process in tumour invasiveness and metastasis formation. However, its role is not completely known.MethodsBoyden chamber and cell adhesion assays, and ICELLigence analysis were performed to detect HEK293 adhesion and invasion. Western blotting and gelatine zymography techniques were employed to assess the EMT protein levels and MMP enzymatic activity. Immunofluorescence analysis and pull-down assays facilitated the detection of NF-kB sub-cellular localization and interaction.ResultsWe have previously demonstrated that the loss of DDB2-PCNA binding favours genome instability, and increases cell proliferation and motility. Here, we have investigated the phenotypic and molecular EMT-like changes after UV DNA damage, in HEK293 clones stably expressing DDB2Wt protein or a mutant form unable to interact with PCNA (DDB2PCNA−), as well as in HeLa cells transiently expressing the same DDB2 constructs. Cells expressing DDB2PCNA− showed morphological modifications along with a reduced expression of E-cadherin, an increased activity of MMP-9 and an improved ability to migrate, in concomitance with a significant upregulation of EMT-associated Transcription Factors (TFs), whose expression has been reported to favour tumour invasion. We observed a higher expression of c-Myc oncogene, NF-kB, both regulating cell proliferation and metastatic process, as well as ZEB1, a TF significantly associated with tumorigenic potential and cell migratory ability. Interestingly, a novel interaction of DDB2 with NF-kB was detected and found to be increased in cells expressing the DDB2PCNA−, suggesting a direct modulation of NF-kB by DDB2.ConclusionThese results highlight the role of DDB2-PCNA interaction in counteracting EMT since DDB2PCNA− protein induces in HEK293 transformed cells a gain of function contributing to the acquisition of a more aggressive phenotype.

Identification of Induced Chemical Mutants for Improving Yield and its Attributing Traits in Wheat (Triticum aestivum L.) against Changing Climate

Background: The enhancement of genetic traits in any crop relies on the existing variability within that particular crop. Through hybridization and traditional breeding methods, the variability within wheat crops has been nearly exhausted. Consequently, mutation breeding emerges as the sole viable and promising approach to introduce new variability for further improvements. Methods: An experiment was conducted during the Rabi seasons of 2020-21 (M1 generation) and 2021-22 (M2 generation) at the Crop Research Centre, Department of Genetics and Plant Breeding, ITM University Gwalior. The experiment assessed the impact of five different concentrations of Sodium Azide (0.02%, 0.03%, 0.04%, 0.05%, and 0.1%) and Hydroxyl Amine (0.2%, 0.3%, 0.4%, 0.5% and 0.6%), in addition to a control, on the wheat varieties MP-3382 and RVW-4106. It employed a randomized block design with three replications. Result: The findings revealed that Sodium Azide and Hydroxyl Amine, the most effective dosages were observed to be 0.1per cent and 0.4 per cent, respectively, in inducing genetic and phenotypic changes in seed quality parameters. Specifically, for the flag leaf area characteristic, the most effective concentrations were 0.03 per cent Sodium Azide and 0.4 percent Hydroxyl Amine. Plant height exhibited the greatest variability at 0.03 per cent Sodium Azide, 0.5 per cent Hydroxyl Amine and 0.1 percent Sodium Azide. A dosage of 0.5 per cent Hydroxyl Amine was found to be most effective in altering spike length. In terms of days to 50 per cent flowering, 0.05 per cent Sodium Azide was identified as the most effective dosage. From the study of traits in both the M1 and M2 generations, 12 mutants were confirmed, with seven validated for variety MP-3382 and five for variety RVW-4106.

Robust differential expression testing for single-cell CRISPR screens at low multiplicity of infection.

Single-cell CRISPR screens (perturb-seq) link genetic perturbations to phenotypic changes in individual cells. The most fundamental task in perturb-seq analysis is to test for association between a perturbation and a count outcome, such as gene expression. We conduct the first-ever comprehensive benchmarking study of association testing methods for low multiplicity-of-infection (MOI) perturb-seq data, finding that existing methods produce excess false positives. We conduct an extensive empirical investigation of the data, identifying three core analysis challenges: sparsity, confounding, and model misspecification. Finally, we develop an association testing method - SCEPTRE low-MOI - that resolves these analysis challenges and demonstrates improved calibration and power.

Phenotypic changes of γδ T cells in Plasmodium falciparum placental malaria and pregnancy outcomes in women at delivery in Cameroon

IntroductionDepending on the microenvironment, γδ T cells may assume characteristics similar to those of Th1, Th2, Th17, regulatory T cells or antigen presenting cells. Despite the wide documentation of the effect of Th1/Th2 balance on pregnancy associated malaria and outcomes, there are no reports on the relationship between γδ T cell phenotype change and Placental Malaria (PM) with pregnancy outcomes. This study sought to investigate the involvement of γδ T cells and its subsets in placental Plasmodium falciparum malaria.MethodsIn a case-control study conducted in Yaoundé, Cameroon from March 2022 to May 2023, peripheral, placental and cord blood samples were collected from 50 women at delivery (29 PM negative: PM- and 21 PM positive: PM+; as diagnosed by light microscopy). Hemoglobin levels were measured using hemoglobinometer. PBMCs, IVBMCs and CBMCs were isolated using histopaque-1077 and used to characterize total γδ T cell populations and subsets (Vδ1+, Vδ2+, Vδ1-Vδ2-) by flow cytometry.ResultsPlacental Plasmodium falciparum infection was associated with significant increase in the frequency of total γδ T cells in IVBMC and of the Vδ1+ subset in PBMC and IVBMC, but decreased frequency of the Vδ2+ subset in PBMC and IVBMC. The expression of the activation marker: HLA-DR, and the exhaustion markers (PD1 and TIM3) within total γδ T cells and subsets were significantly up-regulated in PM+ compared to PM- group. The frequency of total γδ T cells in IVBMC, TIM-3 expression within total γδ T cells and subsets in IVBMC, as well as HLA-DR expression within total γδ T cells and Vδ2+ subset in IVBMC were negatively associated with maternal hemoglobin levels. Furthermore, the frequency of total γδ T cells in PBMC and PD1 expression within the Vδ2+ subset in CBMC were negatively associated with birth weight contrary to the frequency of Vδ1-Vδ2- subset in PBMC and HLA-DR expression within the Vδ2+ subset in IVBMC which positively associated with maternal hemoglobin level and birth weight, respectively.ConclusionThe data indicate up-regulation of activated and exhausted γδ T cells in Plasmodium falciparum placental malaria, with effects on pregnancy outcomes including maternal hemoglobin level and birth weight.

O14 Monocytes and macrophages in the melanoma tumour microenvironment express Fc receptors which can be engaged with monoclonal antibodies of different isotypes

Abstract Introduction and aims Melanoma is the deadliest form of skin cancer and has an increasing worldwide incidence. It is well established that the melanoma tumour microenvironment (TME) has a large immune cell infiltrate, including a prominent monocytic compartment. Monocytic cells within the TME support melanoma growth, survival and metastasis. Contrastingly, such cells can be stimulated to promote tumour killing when engaged with monoclonal antibodies (mAbs) against cancer antigens, owing to their expression of multiple Fc receptors (FcRs). However, little is known about the monocytic subsets present within melanoma, the FcRs they express and how engaging their FcRs may influence function. Methods Flow cytometry on peripheral monocytes isolated from patients with melanoma and healthy volunteers enabled the characterization of cell surface markers. Next, publicly available single-cell RNA-Seq datasets were analysed to explore the transcriptome of melanoma-associated macrophages and these phenotypes were recapitulated in vitro. Finally, monocytes and macrophages were cocultured with melanoma cells, with or without the addition of mAbs against a melanoma antigen, in order to assess the effect of FcR crosslinking on monocyte and macrophage phenotype and function. Results Circulating monocytes in patients with melanoma feature an inhibitory phenotype, and express multiple FcRs, including Fcε and Fcγ receptors, which could be targeted with mAbs of multiple isotypes. Secondly, monocytic cells within the melanoma TME express protumour genes, including metalloproteinases and angiogenic factors. However, FcR expression suggests that tumour-promoting subsets can be targeted with mAbs. Finally, in ex vivo cocultures with melanoma cells, the FcRs of both human monocytes and macrophages are able to engage antimelanoma mAbs of multiple isotypes, inducing differential phenotype change. This is demonstrated by the upregulation of activation markers and costimulatory cell surface markers. Conclusions Together, these data suggest that tumour-promoting monocytic cells within the melanoma TME can be engaged and harnessed using different isotypes of mAbs targeting melanoma.

Adaptive attenuation of virulence in hypervirulent carbapenem-resistant Klebsiella pneumoniae.

The emergence of nosocomial infections caused by hypervirulent and carbapenem-resistant K. pneumoniae (hv-CRKP) has become a significant public health challenge. The genetic traits of virulence and resistance plasmids in hv-CRKP have been extensively studied; however, research on the adaptive evolution strategies of clinical strains inside the host was scarce. This study aimed to understand the effects of antibiotic treatment on the phenotype and genotype characteristics of hv-CRKP. We investigated the evolution of hv-CRKP strains isolated from the same patient to elucidate the transition between hospital invasion and colonization. A comparative genomics analysis was performed to identify single nucleotide polymorphisms in the rmpA promoter. Subsequent validation through RNA-seq and gene deletion confirmed that distinct rmpA promoter sequences exert control over the mucoid phenotype. Additionally, biofilm experiments, cell adhesion assays, and animal infection models were conducted to illuminate the influence of rmpA promoter diversity on virulence changes. We demonstrated that the P12T and P11T promoters of rmpA possess strong activity, which leads to the evolution of CRKP into infectious and virulent strains. Meanwhile, the specific sequence of polyT motifs in the rmpA promoter led to a decrease in the lethality of hv-CRKP and enhanced cell adhesion and colonization. To summarize, the rmpA promoter of hv-CRKP is utilized to control capsule production, thereby modifying pathogenicity to better suit the host's ecological environment.IMPORTANCEThe prevalence of hospital-acquired illness caused by hypervirulent carbapenem-resistant Klebsiella pneumoniae (hv-CRKP) is significant, leading to prolonged antibiotic treatment. However, there are few reports on the phenotypic changes of hv-CRKP in patients undergoing antibiotic treatment. We performed a comprehensive examination of the genetic evolutionary traits of hv-CRKP obtained from the same patient and observed variations in the promoter sequences of the virulence factor rmpA. The strong activity of the promoter sequences P11T and P12T enhances the consistent production of capsule polysaccharides, resulting in an invasive strain. Conversely, weak promoter activity of P9T and P10T is advantageous for exposing pili, hence improving bacterial cell attachment ability and facilitating bacterial colonization. This finding also explains the confusion of some clinical strains carrying wild-type rmpA but exhibiting a low mucoid phenotype. This adaptive alteration facilitates the dissemination of K. pneumoniae within the hospital setting.