Transcript Levels Research Articles

Changes in growth, lanthanide binding, and gene expression in Pseudomonas alloputida KT2440 in response to light and heavy lanthanides.

Pseudomonas alloputida KT2440 is a ubiquitous, soil-dwelling bacterium that metabolizes recalcitrant and volatile carbon sources. The latter is utilized by two redundant, Ca- and lanthanide (Ln)-dependent, pyrroloquinoline quinone-dependent alcohol dehydrogenases (PQQ ADH), PedE and PedH, whose expression is regulated by Ln availability. P. alloputida KT2440 is the best-studied non-methylotroph in the context of Ln-utilization. Combined with microfluidic cultivation and single-cell elemental analysis, we studied the impact of light and heavy Ln on transcriptome-wide gene expression when growing P. alloputida KT2440 with 2-phenylethanol as the carbon and energy source. Light Ln (La, Ce, and Nd) and a mixture of light and heavy Ln (La, Ce, Nd, Dy, Ho, Er, and Yb) had a positive effect on growth, whereas supplementation with heavy Ln (Dy, Ho, Er, and Yb) exerted fitness costs. These were likely a consequence of mismetallation and non-utilizable Ln interfering with Ln sensing and signaling. The measured amounts of cell-associated Ln varied between elements. Gene expression analysis suggested that the Ln sensing and signaling machinery, the two-component system PedS2R2 and PedH, responds differently to (non-)utilizable Ln. We expanded our understanding of the lanthanide (Ln) switch in P. alloputida KT2440, demonstrating that it adjusts the levels of pedE and pedH transcripts based on the availability of Ln. We propose that the usability of Ln influences the bacterium's response to different Ln elements.IMPORTANCEThe Ln switch, the inverse regulation of Ca- and Ln-dependent PQQ ADH in response to Ln availability in organisms featuring both, is central to our understanding of Ln utilization. Although the preference of bacteria for light Ln is well known, the effect of different Ln, light and heavy, on growth and gene expression has rarely been studied. We provide evidence for a fine-tuning mechanism of Ca- and Ln-dependent PQQ ADH in P. alloputida KT2440 on the transcriptome level. The response to (non-)utilizable Ln differs depending on the element. Ln commonly co-occur in nature. Our findings underline that Ln-utilizing microbes must be able to discriminate between Ln to use them effectively. Considering the prevalence of Ln-dependent proteins in many microbial taxa, more work addressing Ln sensing and signaling is needed. Ln availability likely necessitates different adaptations regarding Ln utilization.

Growth hormone is involved in GATA1 gene expression via STAT5B in human erythroleukemia and monocytic cell lines

GATAs are a family of transcription factors consisting of six members. Particularly, GATA1 and GATA2 have been reported to promote the development of erythrocytes, megakaryocytes, eosinophils, and mast cells. However, little information is available on the extracellular ligands that promote GATA1 expression. We evaluated whether growth hormone (GH) is an extracellular stimulator that participates in the signal transduction of GATAs, focusing on GATA1 expression in hematopoietic cell lineages. We used a reporter assay, RT-PCR, real-time quantitative PCR, and western blotting to evaluate GH-induced expression of GATA1 and GATA2 in the human erythroleukemic cell line K562 and the non-erythroid cell line U937. GATA1 expression in these hematopoietic cell lines increased at the transcriptional and protein levels in the presence of GH, and was inhibited by a STAT5 specific inhibitor. Cells transfected with activated STAT5B showed increased expression of GATA1. We identified functional STAT5B consensus sequences as binding site-158 bp from the transcription starting site in the GATA1 promoter region. These results suggest that GH directly induces GATA1 expression via GHR/JAK/STAT5 and is related to hematopoietic cell proliferation.

The Drosophila maternal-effect gene abnormal oocyte (ao) does not repress histone gene expression.

The abnormal oocyte (ao) gene of Drosophila melanogaster is a maternal-effect lethal gene previously identified as encoding a transcriptional regulator of core histones. However, background genetic mutations in existing ao mutant strains could compromise their utility in manipulating histone levels. To distinguish the true ao phenotype from background effects, we created two new ao reagents: a CRISPR/Cas9-mediated knockout of the ao allele for genetic and molecular analyses and an epitope-tagged ao allele for cytological experiments. Using these reagents, we confirm previous findings that ao exhibits maternal-effect lethality, which can be rescued by either a decrease in the histone gene copy number or by Y chromosome heterochromatin. We also confirm that the Ao protein localizes to the histone locus bodies in ovaries. Our data also suggest that ao genetically interacts with the histone genes and heterochromatin, as previously suggested. However, contrary to prior findings, we find that ao does not repress core histone transcript levels. Thus, the molecular basis for ao-associated maternal-effect lethality remains unknown.

Effects of propolis extract administration on immune parameters, faecal consistency scores, and growth performance of Holstein-Friesian calves.

The purpose of the study was to investigate the effect of Ethanolic Extract of Propolis (EEP) administration on immune parameters, faecal consistency scores, growth performance, and feed efficiency of Holstein Friesian calves. A total of 24 calves were divided into two different groups, control (n = 12) and EEP (n = 12). Both groups consisted of 6 male and 6 female calves. The calves were fed milk amounting to 10% of their birth weight each day until they reached 60days of age. Additionally, they were given starter feed and dry hay once a day. Calves assigned to the EEP group received 4ml of EEP daily. Use of EEP increased (P < 0.05) the serum IgG and IgM levels at 2months of age compared to the control group. EEP also showed efficacy (P < 0.01) in reducing faecal consistency in calves throughout the study. The levels of IL-1β, IL-6, TNF-α and NF-κB expression in calves treated with EEP were lower (P < 0.05) throughout the EEP application period. On the other hand, IGF-1 mRNA transcript levels were (P < 0.01) higher in EEP group calves than in the control group. Furthermore, EEP-fed calves consumed less dry matter for 1kg of live weight gain during the weaning-4months (P < 0.01) and birth-4months (P < 0.05) periods. These results indicate that EEP supplementation, through its immunostimulatory effects, plays a crucial role in the control of neonatal calf diarrhoea. Growth and development as well as IGF-1, which stimulates growth in almost all somatic cells, was also significantly increased by EEP supplementation. The combined effect of the rich bioactive compounds found in EEP appears to have a significant impact on health and well-being, resulting in improved early life performance in dairy calves.

Reference gene considerations for toxicological assessment of the flame retardant triphenyl phosphate in an in vitro fish embryonic model.

The reliability of relative quantification RT-qPCR depends upon the gene of interest being normalized to one or more reference genes, with the assumption that the chosen reference genes do not experience altered expression with experimental conditions. The correct choice of stable reference genes is critical when investigating alterations to gene transcript levels following exposure to endocrine and metabolic disrupting chemicals, such as the flame retardant triphenyl phosphate (TPhP). This study assessed the stability of eight reference genes following TPhP exposure in embryonic cells derived from rainbow trout (Oncorhynchus mykiss). The genes β-actin (actb) and 18s rRNA (18s) were stable, while glyceraldehyde-3-phosphate dehydrogenase (gapdh) relative expression was found to be increased. gapdh is a popular reference gene and has been previously used in the literature for investigating TPhP exposure in teleost fish models. We discuss the implications of gapdh upregulation in the context of TPhP as a metabolic disrupting chemical. Furthermore, we quantified the expression of the tumor suppressor gene p53 following TPhP exposure in relation to different reference genes to use as an example to report on how discrepancies in findings might arise depending on the stability of the chosen reference gene.

Quantitatively characterize the response of the hybrid grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂) under elevated temperature stress

Global warming may affect the health of marine species. However, the collected information on quantitative assessment of response in fish under elevated temperature is poorly defined. The present study aimed to quantitatively evaluate the effects of the hybrid grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂) under elevated temperature (33 °C and 36 °C, ET1 and ET2) stress for 14 days. As endpoints, we examined changes in body growth, hemato-immunological parameters, liver oxidative stress markers, as well as changes of the stomach digestive enzymes. Compared to the control, the body weight was significantly decreased in ET2 group for 14 d exposure, and a remarkable change of differential leukocyte counts of the fish was observed in ET1 group at 3 d and in ET2 group at 14 d. The respiratory burst activity of the hybrid grouper leukocytes markedly decreased in the treatment groups after 14-d exposure. Overall, the antioxidant enzyme activities and transcriptional levels of superoxide dismutase (SOD), catalase (CAT), glutathione reductase (GR), and glutathione peroxidase (GSH-PX) were markedly inhibited in the liver for 3-d and 14-d exposure. The expression levels of nf-κb mRNA were significantly inhibited while the expression levels of atp2b1 mRNA were significantly induced after 14-d exposure. The activities of pepsin and lipase in the stomach were significantly reduced. In addition, an innovative hazard classification system (ET-HCS) was developed to quantitatively characterize the stress response of the fish following elevated temperature treatments. The stress level of ET2 group for 14-d exposure was ranked as level IV (high stress), and the other treatments were ranked as level II (low stress). Taken together, the findings of this study further extend our understanding of quantitative assessment of response in fish under high-temperature stress, which provides valuable information for improving countermeasures of mariculture industry.

Cocktail effects of clothianidin and imidacloprid in zebrafish embryonic development, with high and low concentrations of mixtures.

There is growing concern that sprayed neonicotinoid pesticides (neonics) persist in mixed forms in the environmental soil and water systems, and these concerns stem from reports of increase in both the detection frequency and concentration of these pollutants. To confirm the toxic effects of neonics, we conducted toxicity tests on two neonics, clothianidin (CLO) and imidacloprid (IMD), in embryos of zebrafish. Toxicity tests were performed with two different types of mixtures: potential mixture compounds and realistic mixture compounds. Potential mixtures of CLO and IMD exhibited synergistic effects, in a dose-dependent manner, in zebrafish embryonic toxicity. Realistic mixture toxicity tests that are reflecting the toxic effects of mixture in the aquatic environment were conducted with zebrafish embryos. The toxicity of the CLO and IMD mixture at environmentally-relevant concentrations was confirmed by the alteration of the transcriptional levels of target genes, such as cell damage linked to oxidative stress response and thyroid hormone synthesis related to zebrafish embryonic development. Consequently, the findings of this study can be considered a strategy for examining mixture toxicity in the range of detected environmental concentrations. In particular, our results will be useful in explaining the mode of toxic action of chemical mixtures following short-term exposure. Finally, the toxicity information of CLO and IMD mixtures will be applied for the agricultural environment, as a part of chemical regulation guideline for the use and production of pesticides.

Niosomes containing enciprazine hydrochloride have been shown to efficiently inhibit the proliferation and induce apoptosis in colorectal cancer cells

Colorectal cancer (CRC), currently the second most widespread cancer globally, exhibits a higher incidence in young individuals. Advancements have been made in developing anti-colorectal cancer drugs, including cytotoxic chemicals, in the past few decades. There is a need for new and innovative medications to overcome the current challenges in cancer treatment. Recent research examined the efficacy of innovative formulations in the prevention of colorectal cancer. In this study, we evaluated the efficacy of a niosome formulation loaded with Enciprazine hydrochloride (Nio-USAN). We assessed the anti-colorectal cancer characteristics of Nio-USAN by employing several techniques including CCK-8, invasion test, MTT test, flow cytometry, and cell cycle assessment. Quantitative real-time PCR was utilized to assess the transcription of genes linked to apoptosis. The F1-Nio-USAN and F2-Nio-USAN have average sizes of 200 and 500 nm, respectively. The entrapment effectiveness (EE%) of the F1-Nio-USAN and F2-Nio-USAN was measured to be 85.32 ± 0.27 % and 87.12 ± 0.35 %, respectively. The F1-Nio-USAN group exhibited the following percentages of HT-29 cell states: 43 % early apoptosis, 21 % late apoptosis, 7 % necrotic, and 29 % viable. The levels of transcription for cas8, Bid, BAX, cas9, and cas3 were significantly elevated in the treatment groups as compared to the PBS control group (P < 0.001). In addition, the treatment group exhibited significantly reduced levels of BCL2 gene transcription compared to the PBS control group (P < 0.01). These results suggest that it may be possible to improve the efficacy of USAN formulations in combating cancer by utilizing noisome encapsulation.

Efficacy of RCI001 as a Therapeutic Candidate in a Primary Sjögren Syndrome Mouse Model.

The aim of this study was to investigate the efficacy of RCI001 (RCI) in a mouse model of primary Sjögren syndrome. Eight 12-week-old NOD.B10-H2b mice were used in this study. All experimental animals were randomly divided into phosphate-buffered saline (PBS) and RCI groups in NOD.B10-H2b mice. The eyes of mice were topically treated with PBS or RCI twice a day for a week. Ocular surface staining (OSS) and tear secretion were compared between before and after treatment. The transcript levels of inflammatory cytokines and nicotinamide adenine dinucleotide phosphate oxidase (NOX) in the conjunctiva and cornea (CC) and lacrimal gland were assayed. In addition, immunofluorescence staining of the conjunctiva was assessed. The RCI group showed significant clinical improvement in OSS and tear secretion after 1 week of treatment compared with the baseline (both P < 0.001) and showed better improvement in OSS and tear secretion than the PBS group after 1 week of treatment (both P < 0.05). The levels of IL-1β and IL-17 in CC and IL-6 in the lacrimal gland were also significantly reduced in the RCI group compared with the PBS group (each P < 0.05). Transcript levels of NOX2 and NOX4 were also significantly reduced in CC of the RCI group compared with those of the PBS group (P < 0.05). The RCI group also resulted in lower conjunctival expression of oxidative stress markers (4-hydroxy-2-nonenal, hexanoyl-lysine, and NOX4) than the PBS group. Topical RCI001 demonstrated excellent therapeutic efficacy in a mouse model of primary Sjögren syndrome by inhibiting inflammation and oxidative stress.

Proteasome inhibition enhances the anti-leukemic efficacy of chimeric antigen receptor (CAR) expressing NK cells against acute myeloid leukemia

BackgroundRelapsed and refractory acute myeloid leukemia (AML) carries a dismal prognosis. CAR T cells have shown limited efficacy in AML, partially due to dysfunctional autologous T cells and the extended time for generation of patient specific CAR T cells. Allogeneic NK cell therapy is a promising alternative, but strategies to enhance efficacy and persistence may be necessary. Proteasome inhibitors (PI) induce changes in the surface proteome which may render malignant cells more vulnerable to NK mediated cytotoxicity. Here, we investigated the potential benefit of combining PIs with CAR-expressing allogeneic NK cells against AML.MethodsWe established the IC50 concentrations for Bortezomib and Carfilzomib against several AML cell lines. Surface expression of class-I HLA molecules and stress-associated proteins upon treatment with proteasome inhibitors was determined by multiparameter flow cytometry. Using functional in vitro assays, we explored the therapeutic synergy between pre-treatment with PIs and the anti-leukemic efficacy of NK cells with or without expression of AML-specific CAR constructs against AML cell lines and primary patient samples. Also, we investigated the tolerability and efficacy of a single PI application strategy followed by (CAR-) NK cell infusion in two different murine xenograft models of AML.ResultsAML cell lines and primary AML patient samples were susceptible to Bortezomib and Carfilzomib mediated cytotoxicity. Conditioned resistance to Azacitidine/Venetoclax did not confer primary resistance to PIs. Treating AML cells with PIs reduced the surface expression of class-I HLA molecules on AML cells in a time-and-dose dependent manner. Stress-associated proteins were upregulated on the transcriptional level and on the cell surface. NK cell mediated killing of AML cells was enhanced in a synergistic manner. PI pre-treatment increased effector-target cell conjugate formation and Interferon-γ secretion, resulting in enhanced NK cell activity against AML cell lines and primary samples in vitro. Expression of CD33- and CD70-specific CARs further improved the antileukemic efficacy. In vivo, Bortezomib pre-treatment followed by CAR-NK cell infusion reduced AML growth, leading to prolonged overall survival.ConclusionsPIs enhance the anti-leukemic efficacy of CAR-expressing allogeneic NK cells against AML in vitro and in vivo, warranting further exploration of this combinatorial treatment within early phase clinical trials.

GenoMine: a CRISPR-Cas9-based kill switch for biocontainment of Pseudomonas putida.

Synthetic genetic circuits have revolutionised our capacity to control cell viability by conferring microorganisms with programmable functionalities to limit survival to specific environmental conditions. Here, we present the GenoMine safeguard, a CRISPR-Cas9-based kill switch for the biotechnological workhorse Pseudomonas putida that employs repetitive genomic elements as cleavage targets to unleash a highly genotoxic response. To regulate the system's activation, we tested various circuit-based mechanisms including the digitalised version of an inducible expression system that operates at the transcriptional level and different options of post-transcriptional riboregulators. All of them were applied not only to directly control Cas9 and its lethal effects, but also to modulate the expression of two of its inhibitors: the AcrIIA4 anti-CRISPR protein and the transcriptional repressor TetR. Either upon direct induction of the endonuclease or under non-induced conditions of its inhibitors, the presence of Cas9 suppressed cell survival which could be exploited beyond biocontainment in situations where further CRISPR genome editing is undesirable.

Targeted Metabolites and Transcriptome Analysis Uncover the Putative Role of Auxin in Floral Sex Determination in Litchi chinensis Sonn.

Litchi exhibits a large number of flowers, many flowering batches, and an inconsistent ratio of male and female flowers, frequently leading to a low fruit-setting rate. Floral sexual differentiation is a crucial phase in perennial trees to ensure optimal fruit production. However, the mechanism behind floral differentiation remains unclear. The objective of the study was to identify the role of auxin in floral differentiation at the transcriptional level. The results showed that the ratio of female flowers treated with naphthalene acetic acid (NAA) was significantly lower than that of the control stage (M0/F0). The levels of endogenous auxin and auxin metabolites were measured in male and female flowers at different stages of development. It was found that the levels of IAA, IAA-Glu, IAA-Asp, and IAA-Ala were significantly higher in male flowers compared to female flowers. Next-generation sequencing and modeling were employed to perform an in-depth transcriptome analysis on all flower buds in litchi 'Feizixiao' cultivars (Litchi chinensis Sonn.). Plant hormones were found to exert a significant impact on the litchi flowering process and flower proliferation. Specifically, a majority of differentially expressed genes (DEGs) related to the auxin pathway were noticeably increased during male flower bud differentiation. The current findings will enhance our comprehension of the process and control mechanism of litchi floral sexual differentiation. It also offers a theoretical foundation for implementing strategies to regulate flowering and enhance fruit production in litchi cultivation.

RALF22 is a key modulator of the root hair growth responses to fungal ethylene emissions in Arabidopsis.

In Arabidopsis (Arabidopsis thaliana (L.) Heynh), exposure to volatile compounds (VCs) emitted by Penicillium aurantiogriseum promotes root hair (RH) proliferation and hyper-elongation through mechanisms involving ethylene, auxin and photosynthesis signaling. In addition, this treatment enhances the levels of the small signalling peptide RAPID ALKALINIZATION FACTOR 22 (RALF22). Here we used genetics to address the role of RALF22 in fungal VC-promoted RH growth and to identify the bioactive fungal VC. We found that RHs of ralf22 and feronia (fer-4) plants impaired in the expression of RALF22 and its receptor FERONIA, respectively, responded weakly to fungal VCs. Unlike in WT roots, fungal VC exposure did not enhance RALF22 transcript levels in roots of fer-4 and ethylene- and auxin- insensitive mutants. In ralf22 and fer-4 roots, this treatment did not enhance the levels of ERS2 transcripts encoding one member of the ethylene receptor family and those of some RH-related genes. RHs of ers2-1 and the rsl2rsl4 double mutants impaired in the expression of ERS2 and the ethylene- and auxin-responsive ROOT HAIR DEFECTIVE 6-LIKE 2 and 4 transcription factors, respectively, weakly responded to fungal VCs. Moreover, roots of plants defective in photosynthetic responsiveness to VCs exhibited weak RALF22 expression and RH growth responses to fungal VCs. VCs of ΔefeA strains of P. aurantiogriseum cultures impaired in ethylene synthesis weakly promoted RH proliferation and elongation in exposed plants. We conclude that RALF22 simultaneously functions as a transcriptionally regulated signaling molecule that participates in the ethylene, auxin and photosynthesis signaling-mediated RH growth response to fungal ethylene emissions and regulation of ethylene perception in RHs.

Acidity suppresses CD8 + T-cell function by perturbing IL-2, mTORC1, and c-Myc signaling.

CD8 + T cells have critical roles in tumor control, but a range of factors in their microenvironment such as low pH can suppress their function. Here, we demonstrate that acidity restricts T-cell expansion mainly through impairing IL-2 responsiveness, lowers cytokine secretion upon re-activation, and reduces the cytolytic capacity of CD8 + T cells expressing low-affinity TCR. We further find decreased mTORC1 signaling activity and c-Myc levels at low pH. Mechanistically, nuclear/cytoplasmic acidification is linked to mTORC1 suppression in a Rheb-, Akt/TSC2/PRAS40-, GATOR1- and Lkb1/AMPK-independent manner, while c-Myc levels drop due to both decreased transcription and higher levels of proteasome-mediated degradation. In addition, lower intracellular levels of glutamine, glutamate, and aspartate, as well as elevated proline levels are observed with no apparent impact on mTORC1 signaling or c-Myc levels. Overall, we suggest that, due to the broad impact of acidity on CD8 + T cells, multiple interventions will be required to restore T-cell function unless intracellular pH is effectively controlled.

Lipoprotein metabolism mediates hematopoietic stem cell responses under acute anemic conditions

Hematopoietic stem cells (HSCs) react to various stress conditions. However, it is unclear whether and how HSCs respond to severe anemia. Here, we demonstrate that upon induction of acute anemia, HSCs rapidly proliferate and enhance their erythroid differentiation potential. In severe anemia, lipoprotein profiles largely change and the concentration of ApoE increases. In HSCs, transcription levels of lipid metabolism-related genes, such as very low-density lipoprotein receptor (Vldlr), are upregulated. Stimulation of HSCs with ApoE enhances their erythroid potential, whereas HSCs in Apoe knockout mice do not respond to anemia induction. VldlrhighHSCs show higher erythroid potential, which is enhanced after acute anemia induction. VldlrhighHSCs are epigenetically distinct because of their low chromatin accessibility, and more chromatin regions are closed upon acute anemia induction. Chromatin regions closed upon acute anemia induction are mainly binding sites of Erg. Inhibition of Erg enhanced the erythroid differentiation potential of HSCs. Our findings indicate that lipoprotein metabolism plays an important role in HSC regulation under severe anemic conditions.

Transcriptional changes impact hepatic proteome in autophagy-impaired liver.

Hepatic proteomes are intricately controlled through biosynthesis, extracellular secretion, and intrahepatic degradation. Autophagy governs lysosome-mediated intrahepatic degradation and the hepatic proteome. When autophagy is impaired, it leads to the accumulation of intrahepatic proteins, causing proteinopathy. This study investigates whether autophagy can modulate the hepatic proteome non-degradatively. Utilizing conditional, inducible, and hepatotoxin models of hepatic autophagy impairment, we assessed the overall hepatic proteome expression using Coomassie brilliant blue (CBB) staining and liquid chromatography-tandem mass spectrometry (LC/MS). We pinpointed and confirmed four specific hepatic proteins-Cps1, Ahcy, Ca3, and Gstm1-that were selectively modified in autophagy-deficient livers. Expression of Cps1, Ahcy, and Ca3 were significantly reduced, while Gstm1 expression increased in livers with autophagy impairment. Interestingly, these changes in hepatic protein levels were not due to defective autophagic degradation but were associated with alterations in mRNA transcript levels. Moreover, as a result of autophagic dysfunction, sustained activation of the nuclear erythroid-derived 2-like 2 (Nrf2) transcription factor, transcriptionally regulated the mRNA levels of these proteins. Our findings indicate that autophagy can influence hepatic proteins not solely via traditional degradative routes but also through non-degradative transcriptional processes by modulating Nrf2.

Characterization of active transposable elements and their new insertions in tuber propagated greater yam (Dioscorea alata)

BackgroundGreater yam is a key staple crop grown in tropical and subtropical regions, while its asexual propagation mode had led to non-flowering mutations. How transposable elements contribute to its genetic variations is rarely analyzed. We used transcriptome and whole genome sequencing data to identify active transposable elements (TEs) and genetic variation caused by these active TEs. Our aim was to shed light on which TEs would lead to its intraspecies variation.ResultsAnnotation of de novo assembly transcripts indicated that 0.8 − 0.9% of transcripts were TE related, with LTR retrotransposons (LTR-RTs) accounted for 65% TE transcripts. A large portion of these transcripts were non-autonomous TEs, which had incomplete functional domains. The majority of mapped transcripts were distributed in genic deficient regions, with 9% of TEs overlapping with genic regions. Moreover, over 90% TE transcripts exhibited low expression levels and insufficient reads coverage to support full-length structure assembly. Subfamily analysis of Copia and Gypsy, the two LTR-RTs revealed that a small number of subfamilies contained a significantly larger number of members, which play a key role in generating TE transcript. Based on resequencing data, 15,002 L-RT insertion loci were detected for active LTR-RT members. The insertion loci of LTR-RTs were highly divergent among greater yam accessions.ConclusionsThis study showed the ongoing transcription and transpositions of TEs in greater yam, despite low transcription levels and incomplete proteins insufficient for autonomous transposition. While our research did not directly link these TEs to specific yam traits such as tuber yield and propagation mode, it lays a crucial foundation for further research on how these TE insertion polymorphisms (TIPs) might be related to variations in greater yam traits and its tuber propagation mode. Future research may explore the potential roles of TEs in trait variations, such as tuber yield and stress resistance, in greater yam.

The Role of Estrogen in Brain MicroRNAs Regulation

Brain disorders are global health issues and cause mortality and morbidity. Experimental data have shown that the rate of cognitive impairments in the reproductive age is lower in women than men, which refers to the importance of sex hormones in the brain. Estrogen as a sex hormone has a protective effect on the central nervous system (1) diseases and its role is changed by aging. Estrogenic hormonal activity affects brain function through their specific estrogen receptors to promote the expression of target gene changes at the transcriptional level. miRNAs regulate gene expression via inhibiting translational processes and have been estimated to be involved in regulating almost 30% of all protein-coding genes in mammals. Our review highlights the present knowledge about the role of estrogen-sensitive miRNAs and their efficacy in regulating brain functions and disorders.

Sex-specific molecular signature of mouse podocytes in homeostasis and in response to pharmacological challenge with rapamycin

BackgroundSex differences exist in the prevalence and progression of major glomerular diseases. Podocytes are the essential cell-type in the kidney which maintain the physiological blood-urine barrier, and pathological changes in podocyte homeostasis are critical accelerators of impairment of kidney function. However, sex-specific molecular signatures of podocytes under physiological and stress conditions remain unknown. This work aimed at identifying sexual dimorphic molecular signatures of podocytes under physiological condition and pharmacologically challenged homeostasis with mechanistic target of rapamycin (mTOR) inhibition. mTOR is a crucial regulator involved in a variety of physiological and pathological stress responses in the kidney and inhibition of this pathway may therefore serve as a general stress challenger to get fundamental insights into sex differences in podocytes.MethodsThe genomic ROSAmT/mG-NPHS2 Cre mouse model was used which allows obtaining highly pure podocyte fractions for cell-specific molecular analyses, and vehicle or pharmacologic treatment with the mTOR inhibitor rapamycin was performed for 3 weeks. Subsequently, deep RNA sequencing and proteomics were performed of the isolated podocytes to identify intrinsic sex differences. Studies were supplemented with metabolomics from kidney cortex tissues.ResultsAlthough kidney function and morphology remained normal in all experimental groups, RNA sequencing, proteomics and metabolomics revealed strong intrinsic sex differences in the expression levels of mitochondrial, translation and structural transcripts, protein abundances and regulation of metabolic pathways. Interestingly, rapamycin abolished prominent sex-specific clustering of podocyte gene expression and induced major changes only in male transcriptome. Several sex-biased transcription factors could be identified as possible upstream regulators of these sexually dimorphic responses. Concordant to transcriptomics, metabolomic changes were more prominent in males. Remarkably, high number of previously reported kidney disease genes showed intrinsic sexual dimorphism and/or different response patterns towards mTOR inhibition.ConclusionsOur results highlight remarkable intrinsic sex-differences and sex-specific response patterns towards pharmacological challenged podocyte homeostasis which might fundamentally contribute to sex differences in kidney disease susceptibilities and progression. This work provides rationale and an in-depth database for novel targets to be tested in specific kidney disease models to advance with sex-specific treatment strategies.

Abstract C033: Targeting PIKfyve-driven lipid metabolism in pancreatic cancer

Abstract Pancreatic ductal adenocarcinoma (PDAC) subsists in a nutrient-deregulated microenvironment, making it particularly susceptible to treatments that interfere with cancer metabolism. For example, PDAC utilizes and is dependent on high levels of autophagy and other lysosomal processes including macropinocytosis. Although targeting these pathways has shown potential in preclinical studies, progress has been hampered by the challenge of identifying and characterizing favorable targets for drug development. In our study, we aimed to characterize PIKfyve, a lipid kinase integral to lysosomal functioning, as a novel and targetable vulnerability in PDAC. We first confirmed that PIKfyve inhibition disrupted autophagic flux and disrupted lysosomal function. Next, to understand the metabolic effects of PIKfyve inhibition in PDAC cells, we employed a metabolism-focused CRISPR screen. Through this, we identified that PIKfyve inhibition increases PDAC cells’ dependency on de novo fatty acid synthesis through genes such as FASN and ACACA. Accordingly, PIKfyve inhibition triggered an increase in SREBP1-driven transcriptional and metabolic signatures favoring de novo fatty acid synthesis through increasing expression of genes such as FASN and ACACA. Further, employing targeted lipidomics, we determined that PIKfyve inhibition triggered an SREBP1-dependent accumulation of long-chain sphingolipids and that knockout of serine palmitoyl transferase subunits SPTLC1 and SPTLC2 sensitized PDAC cells to PIKfyve inhibition. Taken together, PIKfyve inhibition disrupts PDAC lipid homeostasis such that PDAC cells upregulate de novo synthesis of sphingolipids as a compensatory mechanism, suggesting that co-targeting de novo fatty acid synthesis and PIKfyve would result in synergistic effects. Given the importance of KRAS-MAPK signaling in controlling PDAC metabolic homeostasis, we hypothesized that the KRAS-MAPK signaling pathway is a primary driver of de novo lipid synthesis, specifically enhancing FASN and ACACA levels. Utilizing chromatin immunoprecipitation sequencing, we determined that KRAS or MEK inhibition reduces MYC binding to FASN and ACACA promoters. In line with this observation, KRAS or MEK perturbation decreased FASN and ACACA transcript and protein levels, suggesting that KRAS or MEK inhibition may sensitize PDAC cells to PIKfyve inhibition. Indeed, the simultaneous targeting of PIKfyve and KRAS-MAPK resulted in the elimination of tumor burden in a syngeneic orthotopic model and tumor regression in a xenograft model of PDAC. Taken together, these studies suggest that disrupting lipid metabolism through PIKfyve inhibition induces synthetic lethality in conjunction with KRAS-MAPK-directed therapies for PDAC. Citation Format: Caleb Cheng, Jasmine P Wisniewski, Sydney Peters, Jing Hu, Rahul Mannan, Bailey Jackson, Rüya Pakkan, Pietro Morlacchi, Brian Magnuson, Tongchen He, Rupam Bhattacharyya, Yuanyuan Qiao, Costas A Lyssiotis, Arul M Chinnaiyan. Targeting PIKfyve-driven lipid metabolism in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr C033.