A double-stranded RNA binding protein enhances drought resistance via protein phase separation in rice

Drought stress significantly impacts global rice production, highlighting the critical need to understand the genetic basis of drought resistance in rice. Here, through a genome-wide association study, we reveal that natural variations in DROUGHT RESISTANCE GENE 9 (DRG9), encoding a double-stranded RNA (dsRNA) binding protein, contribute to drought resistance. Under drought stress, DRG9 condenses into stress granules (SGs) through liquid-liquid phase separation via a crucial α-helix. DRG9 recruits the mRNAs of OsNCED4, a key gene for the biosynthesis of abscisic acid, into SGs and protects them from degradation. In drought-resistant DRG9 allele, natural variations in the coding region, causing an amino acid substitution (G267F) within the zinc finger domain, increase DRG9's binding ability to OsNCED4 mRNA and enhance drought resistance. Introgression of the drought-resistant DRG9 allele into the elite rice Huanghuazhan significantly improves its drought resistance. Thus, our study underscores the role of a dsRNA-binding protein in drought resistance and its promising value in breeding drought-resistant rice.

Prenatal Diagnosis of Esophageal Atresia - Performance and Consequences

BACKGROUND

Prenatal diagnosis of congenital malformations is considered favorable. Esophageal atresia (EA) is prenatally detected in 10-40% of patients. The aims of our study were to assess factors influencing the prenatal detection rate and to study the outcome in EA patients with and without prenatal diagnosis.

METHOD

We included 136 patients in two time periods, group 1 (1996-2002, n = 68) and group 2 (2014-2020, n = 68). We registered clinical variables; prenatal signs, perinatal and postnatal outcome from the electronic patient record.

RESULTS

Twenty-five patients (18%) had a prenatal diagnosis of EA, significantly more during 2014-2020 (28%), than during 1996-2002 (9%). Patients with EA type A or B and with associated anomalies had increased likelihood of prenatal diagnosis, odds ratio (OR) 9.00 (1.99-40.69) and 3.53 (1.24-10.06), respectively. Among the 25 patients with prenatal diagnosis all had polyhydramnios and 16 had small/absent stomach. Prenatally diagnosed patients arrived significantly earlier at the surgical unit (median 2 h (2 h-1 days) vs 21 h (2 h-1275 days)), had more delayed primary anastomosis (OR 8.80 (2.68-28.92)) and anastomotic stricture (OR 3.11 (1.20-8.04)), longer length of stay (median 62 days (11-212 days) vs 20 days (2-270 days)) and longer time on ventilator (median 5 days (1-25 days) vs 1.5 days (0.5-33 days)) compared to patients without prenatal diagnosis. In multivariate analysis prenatal diagnosis predicts length of stay.

CONCLUSION

Prenatally diagnosed EA patients have more; type A and B malformations, associated anomalies and neonatal morbidity. Consequences of the assumed benefits of prenatal diagnosis; opportunity of early arrival to surgical care and prenatal counselling, must be further studied.

The association between mammographic density and breast cancer molecular subtypes: a systematic review and meta-analysis

AIM

To conduct a systematic review and meta-analysis to evaluate the whether high mammographic density (MD) is differentially associated with all subtypes of breast cancer.

MATERIALS AND METHODS

The PubMed, Cochrane Library, and Embase databases were searched systematically in October 2022 to include all studies that investigated the association between MD and breast cancer subtype. Aggregate data of 17,193 breast cancer cases from 23 studies were selected, including five cohort/case-control and 18 case-only studies. The relative risk (RR) of MD were combined using random/fixed effects models for case-control studies, and for case-only studies, relative risk ratios (RRRs) were a combination of luminal A, luminal B, and HER2-positive versus triple-negative tumours.

RESULTS

Women in the highest density category in case-control/cohort studies had a 2.24-fold (95% confidence interval [CI] 1.53, 3.28), 1.81-fold (95% CI 1.15, 2.85), 1.44-fold (95% CI 1.14, 1.81), and 1.59-fold (95% CI 0.89, 2.85) higher risk of triple-negative, HER-2 (human epidermal growth factor receptor 2) positive, luminal A, and luminal B breast cancer compared to women in the lowest density category. RRRs for breast tumours being luminal A, luminal B, and HER-2 positive versus triple-negative in case-only studies were 1.62 (95% CI 1.14, 2.31), 1.81 (95% CI 1.22, 2.71) and 2.58 (95% CI 1.63, 4.08), respectively, for BIRADS 4 versus BIRADS 1.

CONCLUSION

The evidence indicates MD is a potent risk factor for the majority of breast cancer subtypes to different degrees. Increased MD is more strongly linked to HER-2-positive cancers compared to other breast cancer subtypes. The application of MD as a subtype-specific risk marker may facilitate the creation of personalised risk prediction models and screening procedures.

Serine protease NAL1 exerts pleiotropic functions through degradation of TOPLESS-related corepressor in rice

NARROW LEAF 1 (NAL1) is a breeding-valuable pleiotropic gene that affects multiple agronomic traits in rice, although the molecular mechanism is largely unclear. Here, we report that NAL1 is a serine protease and displays a novel hexameric structure consisting of two ATP-mediated doughnut-shaped trimeric complexes. Moreover, we identified TOPLESS-related corepressor OsTPR2 involved in multiple growth and development processes as the substrate of NAL1. We found that NAL1 degraded OsTPR2, thus modulating the expression of downstream genes related to hormone signalling pathways, eventually achieving its pleiotropic physiological function. An elite allele, NAL1A, which may have originated from wild rice, could increase grain yield. Furthermore, the NAL1 homologues in different crops have a similar pleiotropic function to NAL1. Our study uncovers a NAL1-OsTPR2 regulatory module and provides gene resources for the design of high-yield crops.

Improvement in Neisseria gonorrhoeae culture rates by bedside inoculation and incubation at a clinic for sexually transmitted infections

BACKGROUND

Culture of Neisseria gonorrhoeae is essential for surveillance of complete antimicrobial susceptibility profiles. In 2014, the culture success rate of N. gonorrhoeae from samples taken at the clinic for sexually transmitted infections (STI clinic), Oslo University Hospital, Norway, was only 20%. The present study aimed to improve gonococcal culture rates using bedside inoculation of patient samples on gonococcal agar plates and incubation at the STI clinic.

METHODS

This prospective quality improvement study was conducted by the STI clinic and the Department of Microbiology at Oslo University Hospital from May 2016 - October 2017. When culture of N. gonorrhoeae was clinically indicated, we introduced a parallel 'bedside culture' at the STI clinic and compared results with the standard culture at the microbiology department. Samples were taken from urethra, anorectum, pharynx and cervix. Culture rates were compared across symptomatic and asymptomatic anatomical sites.

RESULTS

From 596 gonococcal-positive PCR samples, bedside culture had a significantly higher success rate of 57% compared to 41% with standard culture (p < 0.05). Overall, culture rate from symptomatic sites was 91% v. 45% from asymptomatic sites. The culture rates from different anatomical sites were as follows: urethra 93%, anorectum 64%, pharynx 28% and cervix 70%. Bedside culture significantly (p < 0.05) improved the culture rates for symptomatic urethral and asymptomatic pharyngeal samples.

CONCLUSIONS

Where feasible, bedside inoculation on gonococcal agar plates and incubation of samples from patients with gonorrhoea is recommended. This will improve the culture diagnostics and provide additional gonococcal isolates for antimicrobial resistance surveillance.

Flower Development in Arabidopsis

Like in other angiosperms, the development of flowers in Arabidopsis starts right after the floral transition, when the shoot apical meristem (SAM) stops producing leaves and makes flowers instead. On the flanks of the SAM emerge the flower meristems (FM) that will soon differentiate into the four main floral organs, sepals, petals, stamens, and pistil, stereotypically arranged in concentric whorls. Each phase of flower development-floral transition, floral bud initiation, and floral organ development-is under the control of specific gene networks. In this chapter, we describe these different phases and the gene regulatory networks involved, from the floral transition to the floral termination.

Identification of Plant Transcription Factor DNA-Binding Sites Using seq-DAP-seq

The identification of genome-wide transcription factor binding sites (TFBS) is a critical step in deciphering gene and transcriptional regulatory networks. However, determining the genome-wide binding of specific TFs or TF complexes remains a technical challenge. DNA affinity purification sequencing (DAP-seq) and modifications such as sequential DAP-seq (seq-DAP-seq) are robust in vitro methods for mapping individual TF or TF complex binding sites in a genome-wide manner. DAP-seq protocols use a genomic DNA (gDNA) library from any target organism with or without amplification, allowing the determination of TF binding on naked or endogenously modified DNA, respectively. As a first step, the gDNA is fragmented to ~200 bp, end-repaired, and sequencing adaptors are added. This gDNA library can be used directly or an amplification step may be performed to remove DNA modifications such as cytosine methylation. DNA libraries are then incubated with an affinity-tagged TF or TF- complex immobilized on magnetic beads. The TF or TF complex of interest is generally produced using recombinant protein expression and purified prior to DNA affinity purification. After incubation of the DNA library with the immobilized TF of interest, multiple wash steps are performed to reduce non-specific DNA binding and the TF-DNA complexes eluted. The eluted DNA is PCR-amplified and sequenced using next-generation sequencing. The resulting sequence reads are mapped to the corresponding reference genome, identifying direct potential bound regions and binding sites of the TF or TF complex of interest. Predictive TFBS models are generated from the bound regions using downstream bioinformatics analysis pipelines. Here, we present a detailed protocol outlining the steps required for seq-DAP-seq of a heterooligomeric TF complex (Fig. 1) and briefly describe the downstream bioinformatics pipeline used to develop a robust TFBS model from sequencing data generated from a DAP-seq experiment.

Advances in physiological mechanisms of selenium to improve heavy metal stress tolerance in plants

Selenium (Se) is a metalloid mineral nutrient for human and animal health. Plants are the main foodstuff source of the Se intake of humans. For plants, the addition of an appropriate amount of Se could promotes growth and development, and improves the tolerance to environmental stress, especially stress from some of heavy metals (HM) stress, such as cadmium (Cd) and mercury (Hg). This paper mainly reviews and summarizes the physiological mechanism of Se in enhancing HM stress tolerance in plants. The antagonistic effect of Se on HM is a comprehensive effect that includes many physiological mechanisms. Se can promote the removal of excessive reactive oxygen species and reduce the oxidative damage of plant cells under HM elements stress. Se participates in the regulation of the transportation and distribution of HM ions in plants, and alleviates the damage caused by of HM stress. Moreover, Se combine with HM elements to form Se-HM complexes and promote the production of phytochelatins (PCs), thereby reducing the accumulation of HM ions in plants. Overall, Se plays an important role in plant response to HM stress, but current studies mainly focus on physiological mechanism, and further in-depth study on the molecular mechanism is essential to confirm the participation of Se in plant response to environmental stress. This review helps to comprehensively understand the physiological mechanism of Se in plant tolerance against to HM stress of plants, and provides important theoretical support for the practical application of Se in environmental remediation and agricultural development.

[Mapping Regulatory Elements within 5' and 3' UTRs of SIGLEC15 with a Use of Reporter System]

Siglec-15 is an immune suppressor with broad upregulation on various cancer types and has emerged as a potential target for cancer immunotherapy. However, it remains unclear how SIGLEC15 expression is controlled in normal or cancer cells. In this work, we utilized reporter assays to evaluate the impact of the 5' UTR and the 3' UTR of SIGLEC15 mRNA on gene expression. We found that the 3' UTR dramatically reduced reporter protein production, whereas the 5' UTR showed modest inhibitory effect. Quantification of steady-state mRNA revealed the good coupling of protein amount and mRNA abundance that was associated with the 3' UTR. In contrast, the 5' UTR had little effect on mRNA abundance compared with the empty control. By measuring mRNA half-life, we showed that the 3' UTR markedly promoted mRNA degradation. Testing shortened 3' UTR fragments demonstrated five out of the six having notable inhibitory effect, with the one spanning 993-1317 had the most robust activity. More interestingly, the 993-1317 region contains a predicted 43-nt stem-loop structure that showed apparent inhibitory activity in four cell lines tested. These results suggested that the 3' UTR inhibited reporter gene expression by accelerating mRNA decay possibly via multiple cis-regulatory elements, but the 5' UTR repressed gene expression by inhibiting translation. Thus, our findings provided a clue to the molecular mechanism underlying the regulation of SIGLEC15 expression.

Unraveling the role of MADS transcription factor complexes in apple tree dormancy

A group of MADS transcription factors (TFs) are believed to control temperature-mediated bud dormancy. These TFs, called DORMANCY-ASSOCIATED MADS-BOX (DAM), are encoded by genes similar to SHORT VEGETATIVE PHASE (SVP) from Arabidopsis. MADS proteins form transcriptional complexes whose combinatory composition defines their molecular function. However, how MADS multimeric complexes control the dormancy cycle in trees is unclear. Apple MdDAM and other dormancy-related MADS proteins form complexes with MdSVPa, which is essential for the ability of transcriptional complexes to bind to DNA. Sequential DNA-affinity purification sequencing (seq-DAP-seq) was performed to identify the genome-wide binding sites of apple MADS TF complexes. Target genes associated with the binding sites were identified by combining seq-DAP-seq data with transcriptomics datasets obtained using a glucocorticoid receptor fusion system, and RNA-seq data related to apple dormancy. We describe a gene regulatory network (GRN) formed by MdSVPa-containing complexes, which regulate the dormancy cycle in response to environmental cues and hormonal signaling pathways. Additionally, novel molecular evidence regarding the evolutionary functional segregation between DAM and SVP proteins in the Rosaceae is presented. MdSVPa sequentially forms complexes with the MADS TFs that predominate at each dormancy phase, altering its DNA-binding specificity and, therefore, the transcriptional regulation of its target genes.

The PKM2 activator TEPP-46 attenuates MCD feeding-induced nonalcoholic steatohepatitis by inhibiting the activation of Kupffer cells

OBJECTIVE

The present study aimed to investigate the effect and molecular mechanism of the PKM2 small molecule agonist TEPP-46 on the development of methionine choline-deficient (MCD) diet-induced nonalcoholic steatohepatitis (NASH) in mice.

MATERIALS AND METHODS

In this study, C57BL/6 mice were fed an MCD diet for 15 days to establish a NASH model. The protein expression levels of pyruvate kinase M2 (PKM2), PKM1, hypoxia-inducible factor-1α (HIF-1α) and NLRP3 in liver Kupffer cells (KCs) were measured by Western blotting. Immunofluorescence analysis was used to analyze the nuclear translocation of PKM2 in KCs, and the levels of IL-1β and TNF-α in mouse serum and the cell polarization indexes were determined. The MCD diet-fed mice were injected with 30 mg/kg of TEPP-46 intraperitoneally every 5 days. After 15 days, the liver tissue and peripheral blood were collected for analysis.

RESULTS

We found the NASH model was successfully established after the mice were fed an MCD diet for 15 days. MCD feeding promoted the expression of the PKM2 monomer/dimer and inhibited the expression of the PKM2 tetramer in KCs. Immunofluorescence analysis further confirmed that MCD feeding inhibited the nuclear translocation of PKM2. Besides, MCD feeding promoted the expression of HIF-1α and NLRP3 in KCs, promoted M1 KCs polarization and inhibited M2 KCs polarization. Intraperitoneal injection 30 mg/kg of TEPP-46 significantly inhibited the development of MCD diet-induced NASH, alleviated the pathological changes in the liver, improved liver function, promoted the expression of the PKM2 tetramer in KCs, and inhibited the expression of HIF-1α and NLRP3.

CONCLUSIONS

This study demonstrated that TEPP-46, a small molecule agonist of PKM2, may inhibit the nuclear translocation of PKM2 and the activation of KCs by promoting the expression of PKM2 tetramers in KCs, thus inhibiting the development of MCD diet-induced NASH in mice.

The LEAFY floral regulator displays pioneer transcription factor properties

Pioneer transcription factors (TFs) are a special category of TFs with the capacity to bind to closed chromatin regions in which DNA is wrapped around histones and may be highly methylated. Subsequently, pioneer TFs are able to modify the chromatin state to initiate gene expression. In plants, LEAFY (LFY) is a master floral regulator and has been suggested to act as a pioneer TF in Arabidopsis. Here, we demonstrate that LFY is able to bind both methylated and non-methylated DNA using a combination of in vitro genome-wide binding experiments and structural modeling. Comparisons between regions bound by LFY in vivo and chromatin accessibility data suggest that a subset of LFY bound regions is occupied by nucleosomes. We confirm that LFY is able to bind nucleosomal DNA in vitro using reconstituted nucleosomes. Finally, we show that constitutive LFY expression in seedling tissues is sufficient to induce chromatin accessibility in the LFY direct target genes APETALA1 and AGAMOUS. Taken together, our study suggests that LFY possesses key pioneer TF features that contribute to launching the floral gene expression program.

Genome-wide binding of SEPALLATA3 and AGAMOUS complexes determined by sequential DNA-affinity purification sequencing

The MADS transcription factors (TF), SEPALLATA3 (SEP3) and AGAMOUS (AG) are required for floral organ identity and floral meristem determinacy. While dimerization is obligatory for DNA binding, SEP3 and SEP3–AG also form tetrameric complexes. How homo and hetero-dimerization and tetramerization of MADS TFs affect genome-wide DNA-binding and gene regulation is not known. Using sequential DNA affinity purification sequencing (seq-DAP-seq), we determined genome-wide binding of SEP3 homomeric and SEP3–AG heteromeric complexes, including SEP3^Δtet-AG, a complex with a SEP3 splice variant, SEP3^Δtet, which is largely dimeric and SEP3–AG tetramer. SEP3 and SEP3–AG share numerous bound regions, however each complex bound unique sites, demonstrating that protein identity plays a role in DNA-binding. SEP3–AG and SEP3^Δtet-AG share a similar genome-wide binding pattern; however the tetrameric form could access new sites and demonstrated a global increase in DNA-binding affinity. Tetramerization exhibited significant cooperative binding with preferential distances between two sites, allowing efficient binding to regions that are poorly recognized by dimeric SEP3^Δtet-AG. By intersecting seq-DAP-seq with ChIP-seq and expression data, we identified unique target genes bound either in SEP3–AG seq-DAP-seq or in SEP3/AG ChIP-seq. Seq-DAP-seq is a versatile genome-wide technique and complements in vivo methods to identify putative direct regulatory targets.

A prion-like domain in ELF3 functions as a thermosensor in Arabidopsis

Temperature controls plant growth and development, and climate change has already altered the phenology of wild plants and crops¹. However, the mechanisms by which plants sense temperature are not well understood. The evening complex is a major signalling hub and a core component of the plant circadian clock^2,3. The evening complex acts as a temperature-responsive transcriptional repressor, providing rhythmicity and temperature responsiveness to growth through unknown mechanisms^2,4-6. The evening complex consists of EARLY FLOWERING 3 (ELF3)^4,7, a large scaffold protein and key component of temperature sensing; ELF4, a small α-helical protein; and LUX ARRYTHMO (LUX), a DNA-binding protein required to recruit the evening complex to transcriptional targets. ELF3 contains a polyglutamine (polyQ) repeat^8-10, embedded within a predicted prion domain (PrD). Here we find that the length of the polyQ repeat correlates with thermal responsiveness. We show that ELF3 proteins in plants from hotter climates, with no detectable PrD, are active at high temperatures, and lack thermal responsiveness. The temperature sensitivity of ELF3 is also modulated by the levels of ELF4, indicating that ELF4 can stabilize the function of ELF3. In both Arabidopsis and a heterologous system, ELF3 fused with green fluorescent protein forms speckles within minutes in response to higher temperatures, in a PrD-dependent manner. A purified fragment encompassing the ELF3 PrD reversibly forms liquid droplets in response to increasing temperatures in vitro, indicating that these properties reflect a direct biophysical response conferred by the PrD. The ability of temperature to rapidly shift ELF3 between active and inactive states via phase transition represents a previously unknown thermosensory mechanism.

Evaluating Inoculation Methods to Infect Sugar Beet with Fusarium oxysporum f. betae and F. secorum

Minnesota and North Dakota combined contain 55% of the sugar beet production area in the United States, contributing to 49% of the nation's sugar beet production in 2018. Fusarium diseases caused by Fusarium oxysporum f. betae and F. secorum on sugar beet can cause significant reduction in both root yield and sucrose concentration and purity. The objective of this research was to identify an alternative artificial inoculation method to induce Fusarium diseases on sugar beet leaves and roots caused by both Fusarium spp. in greenhouse conditions to better aid in research efforts. We tested four inoculation methods, including barley to seed, barley to root, drenching, and cutting. and compared them with the conventional root-dipping inoculation method. The inoculation method of placing Fusarium-colonized barley seed close to sugar beet seed (barley to seed) caused levels of symptom severities on both leaves and roots similar to the root-dipping method. Because the traditional root-dipping method involves a laborious transplant process, use of infected barley seed as inoculum may serve as an alternative method in the evaluation of host resistance and pathogen virulence among Fusarium diseases by Fusarium spp. on sugar beet at the seed or seedling stage.

Contrasted evolutionary trajectories of plant transcription factors

Because of their prominent roles in plant development, transcription factors (TF) play central roles as drivers of innovation in the evolution of the green lineage (viridiplantae). The advent of massive sequencing combined with comparative genetics/genomics allows a rigorous investigation of how TF families have contributed to plant diversification from charophyte algae to bryophytes to angiosperms. Here, we review recent progress on TF family reconstruction and the identification of distantly related TFs present throughout the evolutionary timeline from algae to angiosperms. These data provide examples of contrasting evolutionary trajectories of TF families and illustrate how conserved TFs adopt diverse roles over the course of evolution.

Unwinding BRAHMA Functions in Plants

The ATP-dependent Switch/Sucrose non-fermenting (SWI/SNF) chromatin remodeling complex (CRC) regulates the transcription of many genes by destabilizing interactions between DNA and histones. In plants, BRAHMA (BRM), one of the two catalytic ATPase subunits of the complex, is the closest homolog of the yeast and animal SWI2/SNF2 ATPases. We summarize here the advances describing the roles of BRM in plant development as well as its recently reported chromatin-independent role in pri-miRNA processing in vitro and in vivo. We also enlighten the roles of plant-specific partners that physically interact with BRM. Three main types of partners can be distinguished: (i) DNA-binding proteins such as transcription factors which mostly cooperate with BRM in developmental processes, (ii) enzymes such as kinases or proteasome-related proteins that use BRM as substrate and are often involved in response to abiotic stress, and (iii) an RNA-binding protein which is involved with BRM in chromatin-independent pri-miRNA processing. This overview contributes to the understanding of the central position occupied by BRM within regulatory networks controlling fundamental biological processes in plants.

Structural Basis for Plant MADS Transcription Factor Oligomerization

MADS transcription factors (TFs) are DNA binding proteins found in almost all eukaryotes that play essential roles in diverse biological processes. While present in animals and fungi as a small TF family, the family has dramatically expanded in plants over the course of evolution, with the model flowering plant, Arabidopsis thaliana, possessing over 100 type I and type II MADS TFs. All MADS TFs contain a core and highly conserved DNA binding domain called the MADS or M domain. Plant MADS TFs have diversified this domain with plant-specific auxiliary domains. Plant type I MADS TFs have a highly diverse and largely unstructured Carboxy-terminal (C domain), whereas type II MADS have added oligomerization domains, called Intervening (I domain) and Keratin-like (K domain), in addition to the C domain. In this mini review, we describe the overall structure of the type II "MIKC" type MADS TFs in plants, with a focus on the K domain, a critical oligomerization module. We summarize the determining factors for oligomerization and provide mechanistic insights on how secondary structural elements are required for oligomerization capability and specificity. Using MADS TFs that are involved in flower organ specification as an example, we provide case studies and homology modeling of MADS TFs complex formation. Finally, we highlight outstanding questions in the field.

Building Transcription Factor Binding Site Models to Understand Gene Regulation in Plants

Transcription factors (TFs) are key cellular components that control gene expression. They recognize specific DNA sequences, the TF binding sites (TFBSs), and thus are targeted to specific regions of the genome where they can recruit transcriptional co-factors and/or chromatin regulators to fine-tune spatiotemporal gene regulation. Therefore, the identification of TFBSs in genomic sequences and their subsequent quantitative modeling is of crucial importance for understanding and predicting gene expression. Here, we review how TFBSs can be determined experimentally, how the TFBS models can be constructed in silico, and how they can be optimized by taking into account features such as position interdependence within TFBSs, DNA shape, and/or by introducing state-of-the-art computational algorithms such as deep learning methods. In addition, we discuss the integration of context variables into the TFBS modeling, including nucleosome positioning, chromatin states, methylation patterns, 3D genome architectures, and TF cooperative binding, in order to better predict TF binding under cellular contexts. Finally, we explore the possibilities of combining the optimized TFBS model with technological advances, such as targeted TFBS perturbation by CRISPR, to better understand gene regulation, evolution, and plant diversity.

Human Umbilical Cord Mesenchymal Stem Cells Alleviate Myocardial Endothelial-Mesenchymal Transition in a Rat Dilated Cardiomyopathy Model

BACKGROUND

Human umbilical cord-derived mesenchymal stem cells (HuMSCs) have been shown to suppress cardiac fibrosis; however, the underlying mechanisms are not fully understood. Recent studies have shown that endothelial-mesenchymal transition (EndMT) plays a crucial part in myocardial fibrosis. In the present study, we investigated the suppressive role of HuMSCs in cardiac fibrosis and related mechanisms in a rat dilated cardiomyopathy (DCM) model.

METHODS

Male Lewis rats were randomly divided into 3 groups. Rats without any treatment served as a negative control group, while the DCM rats, which were generated by immunization with porcine myosin, were divided into 2 groups: a HuMSC group, in which HuMSCs (1 × 10⁶ cells/rat) were injected intravenously, and a vehicle group, in which rats were injected with volume-matched solution containing no HuMSCs. Histologic and immunofluorescent measurements were used to evaluate the effects of HuMSCs on cardiac fibrosis and EndMT.

RESULTS

We observed a significant increase in myocardial fibrosis, and elevated EndMT in rats of the vehicle group were observed compared with those in the negative control group along with the increased activity of transforming growth factor (TGF)-β1/extracellular signal-regulated kinase (ERK) 1/2 signaling. Treatment with HuMSCs repressed the increase in myocardial fibrosis and EndMT observed in DCM rats, which correlated with decreased activity of TGF-β1/ERK1/2 signaling.

CONCLUSION

The HuMSCs attenuated cardiac fibrosis at least partly through the inhibition of TGF-β/ERK-induced EndMT.

Differential expression profile of hepatic circular RNAs in chronic hepatitis B

CircRNAs exert gene regulatory effects by sequestering target microRNAs (miRNAs) and play a vital role in the onset and development of disease. Until recently, little has been known about the expression, regulation and biological function of circRNAs in both health and chronic hepatitis B (CHB).To identify hepatic circRNAs associated with CHB, we performed RNA sequencing using liver biopsies from untreated CHB patients and controls. We then established a bioinformatics pipeline for identification of CHB-associated circRNAs and in silico analysis of the circRNA-miRNA-mRNA pathways. We used quantitative reverse transcription polymerase chain reaction (qRT-PCR) to confirm these results. The profiles of hepatic circRNA expression were significantly different in CHB compared with controls, with a total of 99 dysregulated circRNAs identified to be correlated with CHB. Computational analysis of the circRNA-miRNA-mRNA pathways revealed a large number of miRNAs (665), which were putatively targeted by the differentially expressed hepatic circRNAs. Interestingly, four of the predicted CHB-related circRNA-miRNA-mRNA pathways were found to be involved in the pathogenesis of HBV infection and progression of HBV-associated liver disease. Among these pathways, regression analysis of gene expression revealed a strong positive correlation between hsa_circ_0000650 and TGFβ2 and a negative correlation between hsa_circ_0000650 and miR-6873-3p, which hinted that hsa_circ_0000650 interacted with TGFβ2 mediated by miR-6873-3p. This study firstly demonstrates that patients with CHB present different profiles of hepatic circRNAs and circRNA/miRNA interactions. Thus, circRNAs have promise as novel mechanisms underlying the pathogenesis and progression of CHB.

Systematic review and meta-analysis: Development of hepatocellular carcinoma in chronic hepatitis B patients with hepatitis e antigen seroconversion

Hepatitis B e antigen (HBeAg) seroconversion is considered to have significantly favourable clinical outcomes for patients with chronic hepatitis B (CHB). However, inconsistent study results suggest that hepatocellular carcinoma (HCC) still occurs in patients with HBeAg seroconversion. We performed a systematic review and meta-analysis to determine the incidence of HCC in patients with CHB after HBeAg seroconversion. Web of Science, PubMed and Embase databases were searched through January 2017. The incidence of HCC in CHB patients after HBeAg seroconversion was pooled using a random-effects model or fix-effects model. Sixteen studies were finally included, involving 4910 patients with HBeAg seroconversion. The overall pooled proportion suggested that 3.33% (95% confidence interval (CI): 2.28%-4.58%) of patients with CHB develop HCC despite HBeAg seroconversion. In patients with HBeAg seroconversion without cirrhosis, the pooled proportion of HCC development was 0.94% (95% CI: 0.15%-2.4%). Moreover, patients with cirrhosis, active hepatitis, or aged greater than 40 years at the time of HBeAg seroconversion were at significantly higher risk for HCC development. HBeAg seroconversion was significantly associated with a reduced risk of HCC compared with persistently positive HBeAg (RR = 0.58, 95% CI: 0.35-0.97, P = .04). Despite the reduced risk with HBeAg seroconversion, HCC can still occur in a proportion of patients with CHB after HBeAg seroconversion. Long-term monitoring is needed for patients with established cirrhosis, active hepatitis or those older than 40 years at the time of HBeAg seroconversion.

Pioneer Factors in Animals and Plants-Colonizing Chromatin for Gene Regulation

Unlike most transcription factors (TF), pioneer TFs have a specialized role in binding closed regions of chromatin and initiating the subsequent opening of these regions. Thus, pioneer TFs are key factors in gene regulation with critical roles in developmental transitions, including organ biogenesis, tissue development, and cellular differentiation. These developmental events involve some major reprogramming of gene expression patterns, specifically the opening and closing of distinct chromatin regions. Here, we discuss how pioneer TFs are identified using biochemical and genome-wide techniques. What is known about pioneer TFs from animals and plants is reviewed, with a focus on the strategies used by pioneer factors in different organisms. Finally, the different molecular mechanisms pioneer factors used are discussed, highlighting the roles that tertiary and quaternary structures play in nucleosome-compatible DNA-binding.

Joint reconstruction of rest/stress myocardial perfusion SPECT

Myocardial perfusion imaging (MPI) using rest/stress single photon emission computed tomography (SPECT) allows non-invasive assessment of reversible cardiac perfusion defects. Conventionally, reversible defects are identified using a difference image, called reversible map, obtained by subtracting the stress image from the rest image after registration and normalization of the two images. The identification of reversible defects using the conventional subtraction method is however limited by noise. We propose to jointly reconstruct rest and stress projection data to directly obtain the reversible map in a single reconstruction framework to improve the detectability of reversible defects. To evaluate the performance of the proposed method, we performed phantom studies to mimic reversible defects with different levels of severity and doses. As compared to the conventional subtraction method, the joint method yielded reversible maps with much lower noise and improved defect detectability. At a normal clinical dose level, the joint method improved the signal to noise ratio (SNR) of defect contrast in reversible maps from 13.2 to 66.4, 9.7 to 35.0, 6.1 to 13.2, and 3.1 to 6.5, for defect to normal myocardium concentration ratios of 0%, 25%, 50%, and 75%, respectively. The SNRs obtained using the joint method were improved from 6.1 to 13.2, 3.9 to 9.4, 3.0 to 8.0, and 2.1 to 7.1, for 100%, 75%, 50%, and 25% of the normal clinical dose as compared to the conventional subtraction method. To access clinical feasibility, we applied the joint method to a rest/stress SPECT MPI patient study. The joint method yielded a reversible map with much lower noise, translating into a much higher defect detectability as compared to the conventional subtraction method. Our results indicate that the joint method has the potential to improve radiologists' performance for assessing defects in rest/stress SPECT MPI. In addition, the joint method can be used to reduce dose or imaging time.

Tim-3 exacerbates kidney ischaemia/reperfusion injury through the TLR-4/NF-κB signalling pathway and an NLR-C4 inflammasome activation

T cell immunoglobulin domain and mucin domain-containing molecule-3 (Tim-3), a member of the immunoglobulin superfamily, has been shown to play a crucial role in host adaptive immunity and tolerance. However, its role in kidney ischaemia-reperfusion injury (IRI) remains unknown. In this study, we investigated the role and mechanism of Tim-3 signalling after kidney IRI. In an established murine model of kidney IRI, we found that Tim-3 expression is enhanced on monocytes/macrophages. Anti-Tim-3 antibody RMT3-23 ameliorates biochemical and histological kidney injury, reduces apoptosis and decreases macrophage infiltration and cytokine production in ischaemic kidneys. Cell culture experiments also demonstrated that the role of Tim-3 in IRI-induced macrophage activation leads to the secretion of proinflammatory cytokines and chemokines. In addition, Toll-like receptor (TLR)-4 and Nod-like receptor (NLR) family CARD domain-containing protein 4 (NLR-C4) expression were enhanced after kidney IRI and decreased significantly by RMT3-23. Tim-3 not only promotes TLR-mediated nuclear factor kappa B (NF-κB) activation and cytokine and chemokine release, but also participates in NLR-C4 inflammasome activation. Taken together, our data confirm that Tim-3 signalling enhances injury after kidney IRI and demonstrated that Tim-3 is involved in regulating TLR-4/NF-κB signalling and NLR-C4 inflammasome activation, which provide evidence that Tim-3 signalling is critical for kidney IRI and may provide a new means to ameliorate kidney tissue immune responses in the clinics.

Abstract P2-08-03: An essential role of GRB7 in promoting the growth of therapy resistant HER-2 positive human breast cancer cells in culture and animal models

Background- GRB7 gene encodes a multi-domain signal transduction molecule and is part of the core of the HER-2 amplicon. GRB7 is commonly co-amplified and over-expressed with HER-2 in human breast cancer. Earlier studies found a functional role of GRB7 in breast cancer. The role of GRB7 in HER-2 positive human breast cancer resistant to HER-2 targeted therapy remains unexplored however.

Materials and Methods- HCC-1954, 21MT1 and JimT1 are human HER-2 positive breast cancer cell lines that are resistant to trastuzumab and lapatinib treatment. Transient knock down of GRB7 protein expression was achieved with siRNA transfection and stable knock down with lentiviral vector mediated shRNA over-expression. Cell lines transfected with non-targeting siRNA or shRNA serve as negative controls. Knock down of GRB7 protein expression is verified by Western blotting. The growth of human breast cancer cell lines after GRB7 knock down in vitro is measured with the CellTiter Glo assay as well as the Incucyte live cell imaging. Activation status of specific signaling pathways was examined with phospho-specific antibody by immune-blotting and immune-precipitation. To assess the growth promoting function of GRB7 in human breast cancer cell lines in vivo, polyclonal HCC-1954, 21MT1 and JimT1 cells, with GRB7 knock down or their corresponding negative control, were orthotopically injected into the mammary fat pads of female immune-deficient NSG mice. The growth rates of these tumors, measured serially with caliper, and final tumor weights were compared between GRB7 knock down and the negative control. The proliferation rate and apoptosis of these tumors were studied with ki-67 staining and Tunel assay.The effects of GRB7 knock down on signaling were investigated with a proteome profiler receptor tyrosine kinase kit (R&D). The role of signaling molecules differentially activated in the growth of breast cancer cells by GRB7 knock down was examined utilizing siRNA mediated knock down, and antibody and small molecule inhibitors.

Results- GRB7 knock down decreased the growth of HCC-1954, 21MT1 and JimT1 cells in vitro and the growth of tumor xenograft these cells formed in animal models. When assayed by ki67 staining and Tunel assay, the mechanism of reduced tumor xenograft growth appeared to be distinct. Reduced proliferation and increased apoptosis were seen in 21MT1 cells, while reduced proliferation was seen in HCC-1954 cells and increased apoptosis in JimT1 cells. Protein profiling found that tyrosine phosphorylation of candidate signaling molecules was reduced with GRB7 knock down in JimT1 cells. Immuno-blotting and immuno-precipitation experiments were performed to evaluate these effects in other cell lines. The effect of targeting these molecules in breast cancer cell growth by siRNA and inhibitors is being examined.

Discussion- GRB7 has essential growth promoting function in therapy resistant HER-2 positive human breast cancer cells. GRB7 knock down has pleiotropic effects on signaling in various cellular contexts. The potential of targeting GRB7 signaling in treating therapy resistant HER-2 positive breast cancer merits further study.

Citation Format: Luoh S-W, Wagoner W, Lai X, Hu Z, Chin K, Ramsey B. An essential role of GRB7 in promoting the growth of therapy resistant HER-2 positive human breast cancer cells in culture and animal models [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-08-03.

Characterization and transplantation of enteric neural crest cells from human induced pluripotent stem cells

The enteric nervous system (ENS) is recognized as a second brain because of its complexity and its largely autonomic control of bowel function. Recent progress in studying the interactions between the ENS and the central nervous system (CNS) has implicated alterations of the gut/brain axis as a possible mechanism in the pathophysiology of autism spectrum disorders (ASDs), Parkinson's disease (PD) and other human CNS disorders, whereas the underlying mechanisms are largely unknown because of the lack of good model systems. Human induced pluripotent stem cells (hiPSCs) have the ability to proliferate indefinitely and differentiate into cells of all three germ layers, thus making iPSCs an ideal source of cells for disease modelling and cell therapy. Here, hiPSCs were induced to differentiate into neural crest stem cells (NCSCs) efficiently. When co-cultured with smooth muscle layers of ganglionic gut tissue, the NCSCs differentiated into different subtypes of mature enteric-like neurons expressing nitric oxide synthase (nNOS), vasoactive intestinal polypeptide (VIP), choline acetyltransferase (ChAT) or calretinin with typical electrophysiological characteristics of functional neurons. Furthermore, when they were transplanted into aneural or aganglionic chick, mouse or human gut tissues in ovo, in vitro or in vivo, hiPSC-derived NCSCs showed extensive migration and neural differentiation capacity, generating neurons and glial cells that expressed phenotypic markers characteristic of the enteric nervous system. Our results indicate that enteric NCSCs derived from hiPSCs supply a powerful tool for studying the pathogenesis of gastrointestinal disorders and brain/gut dysfunction and represent a potentially ideal cell source for enteric neural transplantation treatments.

A protective role for FADD dominant negative (FADD-DN) mutant in trinitrochlorobenzene (TNCB)-induced murine contact hypersensitivity reactions

BACKGROUND

Fas-associated protein with death domain (FADD) is a classic adaptor protein in apoptosis. Increasing evidence has shown that FADD is also implicated in T-cell development, activation and proliferation. The role of FADD in inflammatory disorders remains largely unexplored.

AIM

To assess the role of FADD in inflammatory disorders.

METHODS

We established an experimental model of contact hypersensitivity (CHS) by using 2,4,6-trinitrochlorobenzene (TNCB) on transgenic mice expressing a dominant negative mutant of FADD (FADD-DN), RESULTS: CHS responses were clearly attenuated in FADD-DN mice compared with control mice. In the retroauricular lymph nodes, the ratio of CD8+ T cells was also decreased.

CONCLUSION

FADD-DN appears to play a protective role in TNCB-induced CHS reactions.

[Association between behavioral problems and gastrointestinal disorders among children with autism spectrum disorder]

Objective: To investigate the relationship between gastrointestinal disorders (GID) and core symptoms or behavioral problems among the children with autism spectrum disorder (ASD) . Method: Totally 328 children with ASD and 202 normal controls were enrolled in this cross-sectional study from August 2013 to October 2016. The information about the gastrointestinal disorders, behavioral and emotional problems was collected by using questionnaires. Childhood Autism Rating Scale (CARS), Autism Behavior Checklist (ABC) were used to assess the core symptoms of the children with ASD. Neurodevelopmental status was evaluated with Gesell Developmental Scale (GDS). These variables were analyzed by using student's t-test and chi-square test. Result: The prevalence of GID was significantly higher in the children with ASD than in the normally developing children (49.4% (162/328) vs.25.7% (52/202), χ(2)=29.039, P=0.000), especially the symptoms of constipation (33.2% (109/328) vs. 13.9% (28/202)), diarrhea (9.5%(31/328) vs. 1.5% (3/202)), nausea and vomiting (9.5% (31/328) vs. 3.5% (7/202)), and foul defecation (16.5% (54/328) vs. 5.0% (10/202)) (all P<0.05). Among the ASD children, the prevalence of GID was similar between male and female (46.7% (133/285) vs. 46.5%(20/43), χ(2)=0.006, P=0.938), as well as among all age groups (χ(2)=1.907, P=0.862). There was no significant difference in scores of GDS in the ASD children with or without GID (all P>0.05). Compared with ASD children without GID (n=166), the ASD children with GID (n=162) got higher scores in the "Body and Object Use" of ABC scale ( (16.4±9.3) vs. (12.3±6.7) scores, t=2.258, P=0.028), and had more emotional problems (63.6% (103/162) vs. 49.4% (82/166), χ(2)=6.707, P=0.010). Moreover, the score of behavior problems questionnaire was higher in the ASD children with GID ( (35.3±16.8) vs. (16.1±13.6) scores, t=5.748, P=0.000). Conclusion: Children with ASD have higher risk of GID than the normal developing children. While the stereotyped behaviors, problem behaviors and emotional problems are severer in the ASD children with GID. Hence, it is important to provide comprehensive treatment and management for these groups of children.

Structure and Function of Human Tyrosinase and Tyrosinase-Related Proteins

Melanin is the main pigment responsible for the color of human skin, hair and eye. Its biosynthesis requires three melanogenic enzymes, tyrosinase (TYR), and the tyrosinase-related proteins TYRP1 and TYRP2. The difficulty of isolating pure and homogeneous proteins from endogenous sources has hampered their study, and resulted in many contradictory findings regarding their physiological functions. In this review, we summarize recent advances on the structure and function of TYR and TYRPs by virtue of the crystal structure of human TYRP1, which is the first available structure of a mammalian melanogenic enzyme. This structure, combined with tyrosinase structures from other lower eukaryotes and mutagenesis studies of key active site residues, sheds light on the mechanism of TYR and TYRPs. Furthermore, a TYRP1-based homology model of TYR provides a high-quality platform to map and analyze albinism-related mutations, as well as the design of specific antimelanogenic compounds. Finally, we provide perspectives for future structure/function studies of TYR and TYRPs.

Study of response of Swiss Webster mice to light subunit of mushroom tyrosinase

The light subunit of mushroom, Agaricus bisporus, tyrosinase (LSMT), has been identified as an extrinsic component of the enzyme. Its function is unknown, but it can cross an epithelial cell layer, which suggests that it can be absorbed by the intestine. A similar capability has been demonstrated for the HA-33 component of the progenitor toxin from Clostridium botulinum, which is the closest structural homolog of LSMT. Unlike HA-33, LSMT appears to be non-immunogenic as shown by preliminary tests in Swiss Webster mice. We investigated the immunogenicity and histopathology of LSMT in mice to determine its safety in vivo. LSMT did not evoke generation of antibodies after prolonged periods of intraperitoneal administration. Histopathological observations confirmed the absence of responses in organs after twelve weekly administrations of LSMT. We found that LSMT is not toxic and is less immunogenic than the C. botulinum HA-33 protein, which supports further research and development for pharmaceutical application.

Structure of Human Tyrosinase Related Protein 1 Reveals a Binuclear Zinc Active Site Important for Melanogenesis

Tyrosinase‐related protein 1 (TYRP1) is one of three tyrosinase‐like glycoenzymes in human melanocytes that are key to the production of melanin, the compound responsible for the pigmentation of skin, eye, and hair. Difficulties with producing these enzymes in pure form have hampered the understanding of their activity and the effect of mutations that cause albinism and pigmentation disorders. Herein we show that the typical tyrosinase‐like subdomain of TYRP1 contains two zinc ions in the active site instead of copper ions as found in tyrosinases, which explains why TYRP1 does not exhibit tyrosinase redox activity. In addition, the structures reveal for the first time that the Cys‐rich subdomain, which is unique to vertebrate melanogenic proteins, has an epidermal growth factor‐like fold and is tightly associated with the tyrosinase subdomain. Our structures suggest that most albinism‐related mutations of TYRP1 affect its stability or activity.

NOVEL GENETIC FINDINGS IN A CHINESE FAMILY WITH EARLY-ONSET FEMALE-RELATED TYPE 2 DIABETES

No inheritance of early-onset female-related type 2 diabetes was reported within Chinese families. In this study, we aim to describe the inheritance pattern of type 2 diabetes in a 3-generation family and identify the gene responsible for type 2 diabetes. Genome-wide multipoint parametric linkage analysis revealed a maximum multipoint logarithm of odds (lod) score of 2.1 for a locus being associated with type 2 diabetes in this family on chromosome 20p11.2-12 between 23.5~30.8cM. Type 2 diabetes may be transmitted as an autosomal dominant trait with a high female-related penetrance in this family. Here we describe the first genetic locus for type 2 diabetes at chromosome 20p11.2-12. This region contains 8 known or predicted genes (PLCB1, PLCB4, LAMP5, PAK7, ANKEF1, SNAP25, SLX4IP, and JAG1). Gene SNAP25 which linked to energy or glucose homeostasis associated phenotypes may play a role in the development of type 2 diabetes in this family.

The evening complex coordinates environmental and endogenous signals in Arabidopsis

Plants maximize their fitness by adjusting their growth and development in response to signals such as light and temperature. The circadian clock provides a mechanism for plants to anticipate events such as sunrise and adjust their transcriptional programmes. However, the underlying mechanisms by which plants coordinate environmental signals with endogenous pathways are not fully understood. Using RNA-sequencing and chromatin immunoprecipitation sequencing experiments, we show that the evening complex (EC) of the circadian clock plays a major role in directly coordinating the expression of hundreds of key regulators of photosynthesis, the circadian clock, phytohormone signalling, growth and response to the environment. We find that the ability of the EC to bind targets genome-wide depends on temperature. In addition, co-occurrence of phytochrome B (phyB) at multiple sites where the EC is bound provides a mechanism for integrating environmental information. Hence, our results show that the EC plays a central role in coordinating endogenous and environmental signals in Arabidopsis.

Large-Scale Recombinant Expression and Purification of Human Tyrosinase Suitable for Structural Studies

Human tyrosinase (TYR) is a glycoprotein that initiates the first two reactions in the melanin biosynthesis pathway. Mutations in its encoding gene cause Oculocutaneous Albinism type I (OCA1), the most severe form of albinism, which is a group of autosomal recessive disorders characterized by reduced or absent production of melanin in skin, hair and eyes. Despite extensive structural and characterization studies of its homologues in lower eukaryotic organisms, the catalytic mechanism of human TYR and the molecular basis of OCA1 are largely unknown. In this work, we have carried out a large-scale recombinant expression of TYR that has enabled us to obtain high yields of pure and active protein, required for crystallization trials and screening of skin whitening agents, which is highly demanded in the cosmetic industry. Addition of an N-terminal honeybee melittin signal peptide for secretion of the produced protein into the (protein-free) medium, as well as a cleavable His-tag at the C-terminus, was crucial for increasing the yield of pure protein. We have successfully crystallized two TYR variants, in both glycosylated and deglycosylated forms, showing preliminary X-ray diffraction patterns at 3.5 Å resolution. Hence, we have established an expression and purification protocol suitable for the crystal structure determination of human TYR, which will give unique atomic insight into the nature and conformation of the residues that shape the substrate binding pocket that will ultimately lead to efficient compound design.

Edible bird's nest enhances antioxidant capacity and increases lifespan in Drosophila Melanogaster

In this study, we aims to investigate the effects of edible bird's nest (EBN) on anti-aging efficacy. In order to investigate lifespan and mortality rate of flies, we treated flies with various doses of EBN. Besides, fecundity, water content and food are determined and heat-stress test is conducted after flies treating with different medium. Effects of EBN on total antioxidant activity (T-AOC), super-oxide dismutase activity (SOD), catalase activity (CAT), and malondialdehyde (MDA) were examined in drosophila melanogaster. Results indicated that flies in EBN treated group illustrated significantly lower mortality rates and longer median and maximum lifespan compared to control group (P<0.05). The fecundity in EBN-treated group was increased compared to control group. SOD levels and CAT activity were significantly increased, and MDA levels decreased in EBN-treated group compared to control group (P<0.01). In conclusion, EBN can extend lifespan, decrease mortality rate and increase survival rate in heat-stress test, and which can also promote SOD and CAT activity and reduce MDA levels. EBN is able to delay drosophila melanogaster aging, attributing to the increasing antioxidant enzyme activities and decreasing content of lipid peroxidation products in drosophila melanogaster.