Transcription Factor Gene Expression Research Articles

Yeast One-Hybrid Screening for Regulators of IbWD40 in Purple-Fleshed Sweet Potato (Ipomoea batatas [L] Lam.).

The transcription regulator IbWD40 is known to be involved in anthocyanin biosynthesis in purple-flesh sweet potato (Ipomoea batatas). However, little is known about the upstream transcription regulators on the promoter of IbWD40. Yeast one-hybrid screening was performed on the storage roots of purple-fleshed sweet potato to identity upstream transcription regulators on the promoter of IbWD40. Luciferase reporter assays and Yeast one-hybrid assays were used to verify these upstream binding proteins interacted with the promoter. Real-time PCR was used to analyze the gene expression of upstream transcription regulators, transcription factors, and structural genes involved in anthocyanin biosynthesis in different root stages of purple-fleshed and white-fleshed sweet potato. IbERF1, IbERF10, IbEBF2, IbPDC, IbPGP19, IbUR5GT, IbDRM, IbPPA and IbERF73 were identified as candidate binding proteins for the promoter of IbWD40. Furthermore, IbERF1, IbERF10 and IbERF73 were identified as upstream transcription regulators on the promoter of IbWD40 involved in anthocyanin biosynthesis. IbERF1, IbERF10 and IbERF73 were identified as transcription regulators on the promoter of IbWD40, which is involved in the regulation of anthocyanin biosynthesis in purple-fleshed sweet potato.

Curcumin's spice-infused therapeutic promise: disease severity alleviation in a mouse model of multiple sclerosis via modulation of immune responses.

Multiple sclerosis (MS) is an autoimmune central nervous system (CNS) disorder indicated by demyelination, chronic inflammation, and neuronal destruction. Regional demyelination, inflammation responses, scar development, and various axonal damage are pathological characteristics of MS. Curcumin is a hydrophobic polyphenol extracted from the rhizome of the turmeric plant. In addition to anti-inflammatory effects, beneficial therapeutic effects such as antioxidant, anti-cancer and nerve protection have also been seen from this compound. The purpose of the current investigation was to provide light on the potential benefits of Curcumin in treating experimental autoimmune encephalomyelitis (EAE), the animal model of MS. in Female C57BL/6 mice were used to induce EAE through myelin oligodendroglial glycoprotein (MOG). Curcumin doses of 100 and 200mg/kg were administered orally in the treatment groups starting on the first day of EAE induction. Brains and splenocytes were extracted from euthanized animals on day 25 following EAE induction. Demyelination and leukocyte infiltration, proliferation, cytokine, and gene expression profiles were assessed. Our findings demonstrate that both low and high doses of Curcumin decreased the progression of EAE. Histological analyses revealed low infiltration of leukocytes into the CNS. Curcumin therapy enhanced Th2 and Treg cell secretion of IL-4, IL-10, and TGF-β although considerably decreasing IFN-γ and TNF-α. Curcumin-induced Th2 and Treg cell cytokine production and transcription factor gene expression (IL-13, GATA3, STAT6 and IL-35, CTLA4, Foxp3) and anti-inflammatory cytokines (IL-27, IL-33). Overall, these findings provide additional evidence that Curcumin can slow disease development and alleviate symptoms in EAE through stimulating Treg and Th2 cell polarization. They support Curcumin's potential therapeutic role in MS.

Differing responses of osteogenic cell lines to β-glycerophosphate

Ascorbic acid (Asc), dexamethasone (Dex) and β-glycerophosphate (β-Gly) are commonly used to promote osteogenic behaviour by osteoblasts in vitro. According to the literature, several osteosarcoma cells lines appear to respond differently to the latter with regards to proliferation kinetics and osteogenic gene transcription. Unsurprisingly, these differences lead to contrasting data between publications that necessitate preliminary studies to confirm the phenotype of the chosen osteosarcoma cell line in the presence of Asc, Dex and β-Gly. The present study exposed Saos-2 cells to different combinations of Asc, Dex and β-Gly for 14 days and compared the response with immortalised human mesenchymal stromal/stem cells (MSCs). Cell numbers, cytotoxicity, mineralised matrix deposition and cell proliferation were analysed to assess osteoblast-like behaviour in the presence of Asc, Dex and β-Gly. Additionally, gene expression of runt-related transcription factor 2 (RUNX2); osteocalcin (OCN); alkaline phosphatase (ALP); phosphate regulating endopeptidase homolog X-linked (PHEX); marker of proliferation MKI67 and proliferating cell nuclear antigen (PCNA) was performed every two days during the 14-day cultures. It was found that proliferation of Saos-2 cells was significantly decreased by the presence of β-Gly which contrasted with hMSCs where no change was observed. Furthermore, unlike hMSCs, Saos-2 cells demonstrated an upregulated expression of late osteoblastic markers, OCN and PHEX that suggested β-Gly could affect later stages of osteogenic differentiation. In summary, it is important to consider that β-Gly significantly affects key cell processes of Saos-2 when using it as an osteoblast-like cell model.

SnRK2.10 kinase differentially modulates expression of hub WRKY transcription factors genes under salinity and oxidative stress in Arabidopsis thaliana.

In nature, all living organisms must continuously sense their surroundings and react to the occurring changes. In the cell, the information about these changes is transmitted to all cellular compartments, including the nucleus, by multiple phosphorylation cascades. Sucrose Non-Fermenting 1 Related Protein Kinases (SnRK2s) are plant-specific enzymes widely distributed across the plant kingdom and key players controlling abscisic acid (ABA)-dependent and ABA-independent signaling pathways in the plant response to osmotic stress and salinity. The main deleterious effects of salinity comprise water deficiency stress, disturbances in ion balance, and the accompanying appearance of oxidative stress. The reactive oxygen species (ROS) generated at the early stages of salt stress are involved in triggering intracellular signaling required for the fast stress response and modulation of gene expression. Here we established in Arabidopsis thaliana that salt stress or induction of ROS accumulation by treatment of plants with H2O2 or methyl viologen (MV) induces the expression of several genes encoding transcription factors (TFs) from the WRKY DNA-Binding Protein (WRKY) family. Their induction by salinity was dependent on SnRK2.10, an ABA non-activated kinase, as it was strongly reduced in snrk2.10 mutants. The effect of ROS was clearly dependent on their source. Following the H2O2 treatment, SnRK2.10 was activated in wild-type (wt) plants and the induction of the WRKY TFs expression was only moderate and was enhanced in snrk2.10 lines. In contrast, MV did not activate SnRK2.10 and the WRKY induction was very strong and was similar in wt and snrk2.10 plants. A bioinformatic analysis indicated that the WRKY33, WRKY40, WRKY46, and WRKY75 transcription factors have a similar target range comprising numerous stress-responsive protein kinases. Our results indicate that the stress-related functioning of SnRK2.10 is fine-tuned by the source and intracellular distribution of ROS and the co-occurrence of other stress factors.

Genome-wide characterization, evolutionary analysis, and expression pattern analysis of the trihelix transcription factor family and gene expression analysis under MeJA treatment in Panax ginseng

Panax ginseng is a well-known medicinal plant with several pharmacological uses in China. The trihelix family transcription factors, also known as GT factors, can be involved in the regulation of growth and developmental processes in plants. There have been no in-depth reports or systematic studies about the trihelix transcription factor in ginseng. In this study, the structure, chromosomal localization, gene duplication, phylogeny, functional differentiation, expression patterns and coexpression interactions of trihelix transcripts were analysed using bioinformatics methods based on the ginseng transcriptome database. Thirty-two trihelix transcription factor genes were identified in ginseng, and these genes were alternatively spliced to obtain 218 transcripts. These transcripts were unevenly distributed on different chromosomes of ginseng, and phylogenetic analysis classified the PgGT transcripts into five subgroups. Gene Ontology (GO) analysis classified PgGT transcripts into eight functional subclasses, indicating that they are functionally diverse. The expression pattern analysis of 218 PgGT transcripts revealed that their expression was tissue-specific and spatiotemporally-specific in 14 different tissues of 4-year-old ginseng, 4 different ages of ginseng roots, and 42 farmers’ cultivars of 4-year-old ginseng roots. Despite the differences in the expression patterns of these transcripts, coexpression network analysis revealed that these transcripts could be expressed synergistically in ginseng. In addition, two randomly selected PgGT transcripts in each of the five different subfamilies were subjected to methyl jasmonate treatment at different times, and PgGT was able to respond to the regulation of methy1 jasmonate. These results provide a theoretical basis and gene resources for an in-depth study of the function of trihelix genes in other plants.

Cytokine Gene Expression Profiles during HIV and Helminth Coinfection in Underprivileged Peri-Urban South African Adults.

Intestinal helminth parasites are potent stimulators of T helper type 2 (Th2) and regulatory Th3 anti-inflammatory immune responses, while human immunodeficiency virus (HIV) infections are activators of predominantly T helper type 1(Th1) pro-inflammatory responses. Studies investigating the immune profiles of individuals coinfected with helminths and HIV are scarce. Although it is well known that helminths cause a type 2 immune response during the chronic stage of infection that is characterised by Th2 cell differentiation, eosinophil recruitment, and alternative macrophage activation, the immune mechanisms that regulate tissue damage at the time of parasite invasion are poorly understood. The aim of the study was to determine the cytokine gene expression profiles during HIV and helminth coinfection in underprivileged South African adults living in a peri-urban area with poor sanitary conditions and a lack of clean water supply. Study participants (n = 164) were subdivided into uninfected controls, HIV-infected, helminth-infected, and HIV and helminth-coinfected groups. The Kato-Katz and Mini Parasep techniques and Ascaris lumbricoides-specific Immunoglobulin E (IgE) and Immunoglobulin G4 (IgG4) levels were used to detect helminth infections. Participants' HIV status was determined using two HIV1/2 antibody test kits. RNA was isolated from white blood cells for cytokine (Th1-, Th2-, and Th17-related) and transcription factor gene expression profiling using real-time PCR. Multivariate regression data were adjusted for age, gender, BMI, antiretroviral treatment (ART), and nutritional supplement intake. The HIV and helminth-coinfected group had significantly higher tumour necrosis factor alpha (TNF-α) (adjusted β = 0.53, p = 0.036), interleukin 2 (IL-2) (adjusted β = 6.48, p = 0.008), and interleukin 17 (IL-17) (adjusted β = 1.16, p = 0.001) levels and lower GATA binding protein 3 (GATA3) levels (adjusted β = -0.77, p = 0.018) compared to the uninfected controls. No statistical significance was noted for Th2-related cytokines. The coinfected group had higher proinflammatory Th1- and Th17-related cytokine gene expression profiles compared to the uninfected controls. The findings suggest that pro-inflammatory responses are elevated during coinfection, which supports the hypothesis that helminths have a deleterious effect on HIV immune responses.

Lipid accumulation and gene expression changes induced by tributyltin exposure in primary hepatocytes of lined seahorse (Hippocampus erectus)

Tributyltin (TBT), an antifouling biocide frequently detected in aquatic systems, is generally considered to be an environmental obesogen. However, alterations in lipid metabolism in aquatic animals that are exposed to TBT are scarcely known. This study examined the effects of in vitro exposure to TBT on hepatic lipid homeostasis in the lined seahorse (Hippocampus erectus). Primary seahorse hepatocyte cultures were established for the first time. TBT exposure (100 and 500 nM for 24 h) significantly promoted lipid accumulation in seahorse hepatocytes and drastically reduced the number of active intracellular lysosomes. Furthermore, exposure to TBT significantly upregulated the gene expression of lipogenic enzymes and transcription factors but downregulated that of genes involved in the catabolism of lipid droplets in seahorse hepatocytes. These results indicate that TBT disrupts hepatic lipid homeostasis by simultaneously promoting lipid synthesis and inhibiting lipid droplet breakdown in seahorses. The present study extends our understanding of the utilization of primary hepatocytes from marine animals for toxicological research, and the molecular evidence of the effects of TBT on hepatic lipid homeostasis in teleost fishes.

HDAC1 regulates the chromatin landscape to control transcriptional dependencies in chronic lymphocytic leukemia.

Chronic lymphocytic leukemia (CLL) is a quiescent B-cell malignancy that depends on transcriptional dysregulation for survival. The histone deacetylases are transcriptional regulators whose role within the regulatory chromatin and consequence on the CLL transcriptome is poorly characterized. Here, we profiled and integrated the genome-wide occupancy of HDAC1, BRD4, H3K27Ac, and H3K9Ac signals with chromatin accessibility, Pol2 occupancy, and target expression signatures in CLL cells. We identified that when HDAC1 was recruited within super-enhancers (SEs) marked by acetylated H3K27 and BRD4, it functioned as a transcriptional activator that drove the de novo expression of select genes to facilitate survival and progression in CLL. Targeting HDACs reduced BRD4 and Pol2 engagement to downregulate the transcript and proteins levels of specific oncogenic driver genes in CLL such as BLK, a key mediator of the B-cell receptor pathway, core transcription factors such as PAX5 and IKZF3, and the antiapoptotic gene, BCL2. Concurrently, HDAC1, when recruited in the absence of SEs, repressed target gene expression. HDAC inhibition reversed silencing of a defined set of protein-coding and noncoding RNA genes. We focused on a specific set of microRNA genes and showed that their upregulation was inversely correlated with the expression of CLL-specific survival, transcription factor, and signaling genes. Our findings identify that the transcriptional activator and repressor functions of HDACs cooperate within the same tumor to establish the transcriptional dependencies essential for survival in CLL.

Targeted deletion of grape retrotransposon associated with fruit skin color via CRISPR/Cas9 in Vitis labrascana 'Shine Muscat'.

Transposition of transposable elements affect expression levels, splicing and epigenetic status, and function of genes located in, or near, the inserted/excised locus. For example, in grape, presence of the Gret1 retrotransposon in the promoter region of the VvMYBA1a allele at the VvMYBA1 locus suppress the expression of the VvMYBA1 transcription factor gene for the anthocyanin biosynthesis and this transposon insertion is responsible for the green berry skin color of Vitis labrascana, 'Shine Muscat', a major grape cultivar in Japan. To prove that transposons in grape genome can be removed by genome editing, we focused on Gret1 in the VvMYBA1a allele as a target of CRISPR/Cas9 mediated transposon removal. PCR amplification and sequencing detected Gret1 eliminated cells in 19 of 45 transgenic plants. Although we have not yet confirmed any effects on grape berry skin color, we were successful in demonstrating that cleaving the long terminal repeat (LTR) present at both ends of Gret1 can efficiently eliminate the transposon.

Combining nano-curcumin with catechin improves COVID-19-infected patient's inflammatory conditions

AimsA hyperinflammatory condition is brought on by the development of Coronavirus disease 2019 (COVID-19), which is characterized by an elevation of T helper (Th) 17 cells, high levels of pro-inflammatory cytokines, and a depletion of regulatory T (Treg) cells. MethodsIn this research, we examined the effect of nano-curcumin and catechin on the TCD4+, TCD8+, Th17, and Treg cells and their associated factors in COVID-19 patients. For this purpose, 160 (50 patients excluded during the study) COVID-19 patients were divided into four groups: placebo, nano-curcumin, catechin, and nano-curcumin + catechin. The frequency of TCD4+, TCD8+, Th17, and Treg cells, the gene expression of transcription factors (STAT3, RORt, and FoxP3) relevant to Th17 and Treg, as well as the serum levels of cytokines (IL-6, IL17, IL1-b, IL-10, and TGF-), were all evaluated intra- and inter-group, before and after treatment, in all groups. ResultsOur study showed that TCD4 + and TCD8 + cells were significantly higher in the nano-curcumin + catechin group compared to the control group, whereas Th17 was lower than the initial value. Furthermore, compared to the placebo-received group, cytokines and transcription factors associated with Th17 were significantly lower in the nano-curcumin + catechin group. Additionally, combined therapy increased Treg cells and transcription factors compared to the placebo group. ConclusionOverall, our results show that combining nano-curcumin with catechin has a more notable impact on the enhancement of TCD4+, TCD8+, and Treg cells, as well as a decrease in Th17 cells and their mediators, suggesting a promising combination therapy in reducing the inflammatory conditions of COVID-19 infected patients.

Antifungal mechanisms of the antagonistic bacterium Bacillus mojavensis UTF-33 and its potential as a new biopesticide.

Biological control has gradually become the dominant means of controlling fungal disease over recent years. In this study, an endophytic strain of UTF-33 was isolated from acid mold (Rumex acetosa L.) leaves. Based on 16S rDNA gene sequence comparison, and biochemical and physiological characteristics, this strain was formally identified as Bacillus mojavensis. Bacillus mojavensis UTF-33 was sensitive to most of the antibiotics tested except neomycin. Moreover, the filtrate fermentation solution of Bacillus mojavensis UTF-33 had a significant inhibitory effect on the growth of rice blast and was used in field evaluation tests, which reduced the infestation of rice blast effectively. Rice treated with filtrate fermentation broth exhibited multiple defense mechanisms in response, including the enhanced expression of disease process-related genes and transcription factor genes, and significantly upregulated the gene expression of titin, salicylic acid pathway-related genes, and H2O2 accumulation, in plants; this may directly or indirectly act as an antagonist to pathogenic infestation. Further analysis revealed that the n-butanol crude extract of Bacillus mojavensis UTF-33 could retard or even inhibit conidial germination and prevent the formation of adherent cells both in vitro and in vivo. In addition, the amplification of functional genes for biocontrol using specific primers showed that Bacillus mojavensis UTF-33 expresses genes that can direct the synthesis of bioA, bmyB, fenB, ituD, srfAA and other substances; this information can help us to determine the extraction direction and purification method for inhibitory substances at a later stage. In conclusion, this is the first study to identify Bacillus mojavensis as a potential agent for the control of rice diseases; this strain, and its bioactive substances, have the potential to be developed as biopesticides.

The Self-assembling peptide P11-4 influences viability and osteogenic differentiation of stem cells of the apical papilla (SCAP)

ObjectiveTo analyze the effect of P11–4 self-assembly peptide on cell viability and osteogenic capacity of SCAPs through mineral deposition and gene expression of osteogenic markers. MethodsSCAPs were seeded in contact with P11–4 (10 µg/ml, 100 µg/ml and 1 mg/ml) solution. Cell viability was evaluated using a colorimetric assay MTT: 3-(4,5-dimethyl-thiazolyl-2)-2,5- diphenyltetrazolium bromide) in an experimental time of 24, 48 and 72 h (n = 7). Mineral deposition and quantification provided by the cells was tested using the Alizarin Red staining and Cetylpyridinium Chloride (CPC), respectively, after 30 days (n = 4). Gene expression of Runt-related transcription factor 2 (RUNX2), Alkaline phosphatase (ALP) and Osteocalcin (OCN) was quantified using quantitative polymerase chain reaction (RT-qPCR), at 3 and 7 days with Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) as the housekeeping gene, and relative gene expression was measured using the ΔΔCq method. Data were analyzed using Kruskall-Wallis followed by multiple comparisons, and T-test for gene expression with α=0.05. ResultsAll tested concentrations (10 µg/ml, 100 µg/ml and 1 mg/ml) were not cytotoxic at time 24 and 48 h. After 72 h, a slight decrease in cell viability was observed for the lowest concentration (10 µg/ml). The concentration of 100 µg/ml P11–4 showed the highest mineral deposition. However, qPCR analysis of P11–4 (10 µg/ml) showed upregulation of RUNX2 and OCN at 3 days, with downregulation of ALP at 3 and 7d ConclusionP11–4 did not affect cell viability, induced mineral deposition in SCAPs, and upregulated the expression of RUNX2 and OCN genes at 3 days, while downregulating ALP expression at 3 and 7 days. Clinical significanceBased on the results obtained in this study it can be stated that self-assembling peptide P11–4 is a potential candidate to induce mineralization on dental stem cells for regenerative purposes and also for a clinical use as a capping agent without compromising the cells health.

A novel soybean transcription factor, DREB7, regulates RD29A and SODFe gene expression in transgenic tobacco plants

A novel soybean transcription factor, DREB7, regulates RD29A and SODFe gene expression in transgenic tobacco plants

The ARF2-MYB6 module mediates auxin-regulated petal expansion in rose.

In cut rose (Rosa hybrida), the flower-opening process is closely associated with vase life. Auxin induces the expression of transcription factor genes that function in petal growth via cell expansion. However, the molecular mechanisms underlying the auxin effect during flower opening are not well understood. Here, we identified the auxin-inducible transcription factor gene RhMYB6, whose expression level is high during the early stages of flower opening. Silencing of RhMYB6 delayed flower opening by controlling petal cell expansion through down-regulation of cell expansion-related genes. Furthermore, we demonstrated that the auxin response factor RhARF2 directly interacts with the promoter of RhMYB6 and represses its transcription. Silencing of RhARF2 resulted in larger petal size and delayed petal movement. We also showed that the expression of genes related to ethylene and petal movement showed substantial differences in RhARF2-silenced petals. Our results indicate that auxin-regulated RhARF2 is a critical player that controls flower opening by governing RhMYB6 expression and mediating the crosstalk between auxin and ethylene signaling.

Characterization of ZmPMP3g function in drought tolerance of maize

The genes enconding proteins containing plasma membrane proteolipid 3 (PMP3) domain are responsive to abiotic stresses, but their functions in maize drought tolerance remain largely unknown. In this study, the transgenic maize lines overexpressing maize ZmPMP3g gene were featured by enhanced drought tolerance; increases in total root length, activities of superoxide dismutase and catalase, and leaf water content; and decreases in leaf water potential, levels of O2−·and H2O2, and malondialdehyde content under drought. Under treatments with foliar spraying with abscisic acid (ABA), drought tolerance of both transgenic line Y7-1 overexpressing ZmPMP3g and wild type Ye478 was enhanced, of which Y7-1 showed an increased endogenous ABA and decreased endogenous gibberellin (GA) 1 (significantly) and GA3 (very slightly but not significantly) and Ye478 had a relatively lower ABA and no changes in GA1 and GA3. ZmPMP3g overexpression in Y7-1 affected the expression of multiple key transcription factor genes in ABA-dependent and -independent drought signaling pathways. These results indicate that ZmPMP3g overexpression plays a role in maize drought tolerance by harmonizing ABA-GA1-GA3 homeostasis/balance, improving root growth, enhancing antioxidant capacity, maintaining membrane lipid integrity, and regulating intracellular osmotic pressure. A working model on ABA-GA-ZmPMP3g was proposed and discussed.

Metformin attenuates diabetes-induced osteopenia in rats is associated with down-regulation of the RAGE-JAK2-STAT1 signal axis.

Osteopenia and fragile fractures are diabetes-associated complications. Many hypoglycemic drugs have effects on bone metabolism. Metformin, as is a prescribed medication for type 2 diabetes mellitus (T2DM), had been reported to have osteoprotective effects beyond its hypoglycemic effect, however the potential mechanism behind these effects remains unclear. In this study, we aimed to investigate the comprehensive effects of metformin on bone metabolism in T2DM rat model and elucidate the potential mechanism. Goto-Kakizaki spontaneous T2DM rats with significant hyperglycemia were treated with/without metformin for 20 weeks. Glucose tolerance was tested and all rats were weighed every two weeks. The osteoprotective effects of metformin in diabetic rats were determined by quantifying serum bone biomarkers, μ-CT imaging, histological staining, bone histomorphometry, and biomechanical properties analyses. Potential targets of metformin in the treatment of T2DM and osteoporosis were predicted using network pharmacology. The effects of metformin on mesenchymal stem cells (C3H10) cultured in high glucose medium were evaluated by CCK-8 assay, alkaline phosphatase (ALP) staining, qPCR and western blotting. This study demonstrated that metformin significantly attenuated osteopenia, decreased serum glucose and glycated serum protein (GSP) levels, improved bone microarchitecture, and biomechanical properties in GK rats with T2DM. Metformin significantly increased biomarkers of bone formation, and significantly decreased muscle ubiquitin C (Ubc) expression. Network pharmacology analysis found that signal transducer and activator of transcription1 (STAT1) would be a potential target of metformin for regulating bone metabolism. Metformin increased C3H10​cell viability in vitro, alleviated ALP inhibition caused by hyperglycemia, increased the osteogenic gene expression of runt-related transcription factor 2 (RUNX2), collagen type I alpha 1 (Col1a1), osteocalcin (OCN), and ALP, while suppressing RAGE and STAT1 expression. Metformin also increased the protein expression of Osterix and decreased that of RAGE, p-JAK2, and p-STAT1. Our results demonstrate that metformin attenuated osteopenia and improved bone microarchitecture in GK rats with T2DM and significantly promoted stem cell osteogenic differentiation under high glucose condition. The effects of metformin on bone metabolism are closely associated with the suppression of RAGE-JAK2-STAT1 signaling axis. Our research provides experiment evidence and potential mechanistic rationale for the use of metformin as an effective candidate for diabetes-induced osteopenia treatment.

Distinct gene expression profiles underlie morphological and etiological differences in pediatric cataracts.

Pediatric cataract is a major cause of preventable childhood blindness worldwide. Although genetic mutations or infections have been described in patients, the mechanistic basis of human cataract development remains poorly understood. Therefore, gene expression of structural, developmental, profibrotic, and transcription factors in phenotypically and etiologically distinct forms of pediatric cataracts were evaluated. This cross-sectional study included 89 pediatric cataract subjects subtyped into 1) prenatal infectious (cytomegalovirus, rubella, and combined cytomegalovirus with rubella infection), 2) prenatal non-infectious, 3) posterior capsular anomalies, 4) postnatal, 5) traumatic, and 6) secondary, and compared to clear, non-cataractous material of eyes with the subluxated lenses. Expression of lens structure-related genes (Aqp-0, HspA4/Hsp70, CrygC), transcription factors (Tdrd7, FoxE3, Maf, Pitx 3) and profibrotic genes (Tgfβ, Bmp7, αSmA, vimentin) in surgically extracted cataract lens material were studied and correlated clinically. In cataract material, the lens-related gene expression profiles were uniquely associated with phenotype/etiology of different cataracts. Postnatal cataracts showed a significantly altered FoxE3 expression. Low levels of Tdrd7 expression correlated with posterior subcapsular opacity, whereas CrygC correlated significantly with anterior capsular ruptures. The expression of Aqp0 and Maf was elevated in infectious cataracts, particularly in CMV infections, compared to other cataract subtypes. Tgfβ showed significantly low expression in various cataract subtypes, whereas vimentin had elevated gene expression in infectious and prenatal cataracts. A significant association between lens gene expression patterns in phenotypically and etiologically distinct subtypes of pediatric cataracts suggests regulatory mechanisms in cataractogenesis. The data reveal that cataract formation and presentation is a consequence of altered expression of a complex network of genes.

Antigen experience history directs distinct functional states of CD8+ CAR T cells during the anti-leukemia response

Abstract Chimeric antigen receptor (CAR) T cells are highly effective in treating hematologic cancers, but patients can relapse due to downregulation of the CAR-targeted antigen, leading to the hypothesis that CAR T cells require high density of target antigen to be effective. Non-engineered CD8+ memory T cells generate more rapid and robust effector T cell responses upon secondary infection, relative to their naïve counterparts, and can display higher antigen sensitivity. Our objective was to characterize the role of prior CD8+ T cell antigen experience (AgEx) in dictating functional CAR-mediated anti-tumor responses. To study the effect of T cell AgEx history on CD8+ CAR T cell (CAR8) function in vivo, we used a vaccine model to control prior T cell AgEx history, and a syngeneic adoptive transfer model with murine anti-CD19 CAR8 targeting murine leukemia engineered to express a low or high level of CD19. We analyzed CAR8 expansion and leukemia burden using flow cytometry and performed ATACseq and RNAseq at timepoints pre- and post-CAR transduction and after reinfusion of CAR8 into leukemia-bearing mice to ask whether CAR8 function was determined by the epigenetic and/or transcriptomic state of the starting cell population. We found that starting cell state dictated in vivo CAR8 effector functions, expansion, and differential chromatin accessibility in regions containing binding motifs for AP-1, Runx, Tcf and other transcription factor (TF) families. Motif chromatin accessibility and gene expression of many TFs showed distinct patterns temporally. We conclude that CAR8 maintain functional traits epigenetically imprinted in the starting cell and predict these analyses could inform methods to transcriptionally modulate CAR T cell function.

NF-κB signaling promotes SARS-CoV2 infection in human lung epithelial cells

Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), is responsible for over 660 million infections, and more than 6 million deaths worldwide. There is an increasing need for more treatment options that addresses SARS-CoV-2 infection and its replication. Innate immune pathways including interferon signaling and inflammatory NF-κB signaling are important players in regulating immune responses, these pathways are often targeted by viral pathogens to enhance viral replication, host immune evasion, and host cell survival. The respiratory tract is the major target for SARS-CoV-2; thus, we are exploring the role of innate immune signaling in regulating infection in these cells. We found that both interferon and NF-κB signaling are induced by SARS-CoV-2 infection as measured by increases in transcription factor localization and gene expression. Moreover, pharmacological inhibition of NF-κB signaling but not interferon signaling blocks SARS CoV-2 infection of these respiratory cells. We are exploring how NF-κB signaling impacts viral infection. Indeed, we found that the activity of the NF-κB pathway is independent of interferon signaling. Further mechanistic studies are underway to define the role of NF-κB in coronavirus infection and suggest that inhibitors of the NF-κB signaling pathway may be a novel pharmacological target for the treatment of SARS-CoV-2.

CRISPR/Cas9 screen of B cell differentiation pathways

Abstract To provide immunity to pathogens, naïve B cells undergo differentiation to several states such as plasma cells and memory B cells. The transcription factors and epigenetic modifiers that program a naïve B cell to adopt a cell fate have not been fully characterized. During differentiation, B cells undergo extensive changes in transcription factor networks and gene expression that are underpinned by changes in the epigenome. One such example is a transition from expression of glycolysis related genes to increased expression of genes related to oxidative phosphorylation metabolism pathways. We previously demonstrated that in vivo, naïve B cells take 8 cell divisions to reach the plasma cell terminal differentiation and that at each division, the B cells also go through a hierarchy of reprogramming before becoming plasma cells after exposure to T independent antigens. Our data also showed that at division 3–4 a second branch emerged that expressed genes associated with the memory B cell fate. In order to find genes that play a key role in committing a naïve B cell to the plasma cell or memory B cell fate, cells committed to the two branches after T independent antigen exposure were sorted and analyzed with RNA sequencing. Analysis of this data revealed 67 genes involved in transcriptional and epigenetic regulation that were significantly differentially expressed between the two branches. In order to determine the role these genes play in B cell lineage path commitment, retrovirus libraries containing gRNAs for each of the 67 genes were constructed and tested in a targeted CRISPR/Cas9 knock out screen. This study identifies mechanisms of early memory B cell fate commitment. This work was supported by NIH R01 AI123733, P01 AI125180 and T32 GM008490 to JMB