Transcriptional Elements Research Articles

The role and mechanism of hepatocyte nuclear factor 1β in the occurrence and development of different human tumors: A pan-cancer analysis.

Carcinomatosis is one of the leading threats to human public fitness. HNF1B is a critical transcription element in vertebrate proliferation and oncogenesis, which has been shown to play roles in reactive oxygen species (ROS) metabolism. Our previous results have identified HNF1B as a tumor suppressor that could inhibit the malignant progression of prostate cancer. Yet there is no pan-carcinomatosis analysis of HNF1B, which could help us better understand common and unique underlying mechanisms in mankind knubs to enhance novel and competent treatment. Here, in our research, we evaluated the utterance pattern and explored the function of HNF1B in 33 knub categories using the data from the Cancer Genome Atlas Program (TCGA), Gene Expression Omnibus (GEO), and CLNICAL PROTEOMICTUMOR ANALYSIS CONSORTIUM (CPTAC) dataset. We found different HNF1B roles in various cancer types. HNF1B was upregulated in CHOL, STAD, KIRP, and THCA, and was downregulated in GBM, KICH, COAD, KIRC, LUSC, SARC, PAAD, and TGCT. Prognostic analyses indicated that higher HNF1B displayed better illness outcomes in BLCA, READ, and PRAD, while poorer outcomes in LUSC and THYM. HNF1B mutation was most frequent in endometrial cancer but was not associated with disease prognosis. It was discovered that HNF1B utterance relevant to endothelial cell penetration status in BLCA, ESCA, LUAD, LUSC, and TGCT, and carcinomatosis-associated fibroblast infiltration was observed in ESCA, KIRC, LIHC, and TGCT. Moreover, functional enrichment analysis disclosed that metabolism-related functions were implicated in the function of HNF1B. Taken together, our pan- carcinomatosis analysis showed the complicated roles of HNF1B in a variety of carcinomatoses, being able to improve the extensive comprehension of HNF1B's role in tumorigenesis.

Novel protocol for isolation and transient transformation of Rhodes grass (Chloris gayana) protoplasts

Abstract Rhodes grass (Chloris gayana) is a warm-season C4 grass currently grown as a forage in some tropical regions, with anticipated future application in areas affected by climate change. However, there are few resources available for this grass, with few genomic resources and only one established transformation system, thus limiting the application of biotechnology methods for its improvement. Protoplast transformation can be used as a time- and resource-efficient way to examine gene pathways and functions of transcriptional elements via proteomics and transcriptomics, and to validate gene constructs. The aim of this work was therefore to establish the first Rhodes grass leaf mesophyll protoplast isolation and transient transformation protocol. A range of protoplast isolation factors were examined, including enzyme quantity and vacuum infiltration time. Up to 4.13 × 106 protoplasts were isolated per gram of fresh weight with an average 94.8% viability from an overnight digestion protocol with 4% (w/v) cellulase R10, 0.8% (w/v) Macerozyme R10, and no vacuum infiltration. Transformation conditions were optimized via Taguchi’s orthogonal array, which compared combinations of three levels each of green fluorescent protein (GFP) plasmid DNA quantity, polyethylene glycol (PEG) concentration, and transformation time. A transient transformation efficiency of up to 27.88% was observed by GFP expression. DNA quantity was identified to be the only factor from those tested effecting transformation efficiency (p < 0.001) in a linear way. Work here represents the first report for Rhodes grass protoplast isolation and transformation, which could facilitate genome editing and transcriptome and proteome studies.

Temporal transcriptional profiling of host cells infected by a veterinary alphaherpesvirus using nanopore sequencing

In our research, we performed temporal transcriptomic profiling of host cells infected with Equid alphaherpesvirus 1 (EHV-1) by utilizing direct cDNA sequencing based on nanopore MinION technology. The sequencing reads were harnessed for transcript quantification at various time points. Viral infection-induced differential gene expression was identified through the edgeR package. The identified genes were segmented into six groups based on their kinetic characteristics. The initial three clusters encompass immediate-early response genes, typically transcription factors and elements of antiviral signaling pathways. These genes were either upregulated (cluster 1) or downregulated (clusters 2 and 3) during the early infection phase. The remaining three clusters include late response genes. In these categories, it is challenging to determine whether changes in gene expression are directly connected to the viral infection or merely side effects of the infection. A study of gene associations using the STRINGDB software revealed several gene networks that might be directly impacted by the virus. We also explored whether gene co-expression could be a result of their collective regulation by upstream transcription factors using the Gene Regulatory Network database. Finally, our differential transcript usage (DTU) analysis identified a number of genes that exhibited altered proportions of transcript isoforms in comparison to non-infected cells. Thus, our analysis revealed that EHV-1 infection not only alters host gene expression but also leads to differential use of transcript isoforms, particularly splice variants.

Enhancing human ACE2 expression in mouse models to improve COVID-19 research.

Mice are one of the most common biological models for laboratory use. However, wild-type mice are not susceptible to COVID-19 infection due to the low affinity of mouse ACE2, the entry protein for SARS-CoV-2. Although mice with human ACE2 (hACE2) driven by Ace2 promoter reflect its tissue specificity, these animals exhibit low ACE2 expression, potentially limiting their fidelity in mimicking COVID-19 manifestations and their utility in viral studies. Here, we created and compared hACE2 mouse models generated with different strategies. Our findings show that distinct β-globin insertion within hACE2 cassette significantly influences its expression, with downstream placement enhancing transcription. Moreover, optimizing hACE2 codons (opt-hACE2) improves translation efficiency in multiple tissues. Notably, opt-hACE2 mice displayed more active immune responses and severe COVID-19 phenotypes following SARS-CoV-2 challenge compared to other models. Our study demonstrates the dual regulatory role of β-globin element in transgene transcription and suggests that opt-hACE2 mice might serve as valuable tools for SARS-CoV-2 research.

Specific SOX10 enhancer elements modulate phenotype plasticity and drug resistance in melanoma.

Recent studies indicate that the development of drug resistance and increased invasiveness in melanoma is largely driven by transcriptional plasticity rather than canonical coding mutations. Understanding the mechanisms behind cell identity shifts in oncogenic transformation and cancer progression is crucial for advancing our understanding of melanoma and other aggressive cancers. While distinct melanoma phenotypic states have been well characterized, the processes and transcriptional controls that enable cells to shift between these states remain largely unknown. In this study, we initially leverage the well-established zebrafish melanoma model as a high-throughput system to dissect and analyze transcriptional control elements that are hijacked by melanoma. We identify key characteristics of these elements, making them translatable to human enhancer identification despite the lack of direct sequence conservation. Building on our identification of a zebrafish sox10 enhancer necessary for melanoma initiation, we extend these findings to human melanoma, identifying two human upstream enhancer elements that are critical for full SOX10 expression. Stable biallelic deletion of these enhancers using CRISPR-Cas9 induces a distinct phenotype shift across multiple human melanoma cell lines from a melanocytic phenotype towards an undifferentiated phenotype and is also characterized by an increase in drug resistance that mirrors clinical data including an upregulation of NTRK1, a tyrosine kinase, and potential therapeutic target. These results provide new insights into the transcriptional regulation of SOX10 in human melanoma and underscore the role of individual enhancer elements and potentially NTRK1 in driving melanoma phenotype plasticity and drug resistance. Our work lays the groundwork for future gene-based and combination kinase-inhibitor therapies targeting SOX10 regulation and NTRK1 as a potential avenue for enhancing the efficacy of current melanoma treatments.

Spatial multiomic landscape of the human placenta at molecular resolution.

Successful pregnancy relies directly on the placenta's complex, dynamic, gene-regulatory networks. Disruption of this vast collection of intercellular and intracellular programs leads to pregnancy complications and developmental defects. In the present study, we generated a comprehensive, spatially resolved, multimodal cell census elucidating the molecular architecture of the first trimester human placenta. We utilized paired single-nucleus (sn)ATAC (assay for transposase accessible chromatin) sequencing and RNA sequencing (RNA-seq), spatial snATAC-seq and RNA-seq, and in situ sequencing and hybridization mapping of transcriptomes at molecular resolution to spatially reconstruct the joint epigenomic and transcriptomic regulatory landscape. Paired analyses unraveled intricate tumor-like gene expression and transcription factor motif programs potentially sustaining the placenta in a hostile uterine environment; further investigation of gene-linked cis-regulatory elements revealed heightened regulatory complexity that may govern trophoblast differentiation and placental disease risk. Complementary spatial mapping techniques decoded these programs within the placental villous core and extravillous trophoblast cell column architecture while simultaneously revealing niche-establishing transcriptional elements and cell-cell communication. Finally, we computationally imputed genome-wide, multiomic single-cell profiles and spatially characterized the placental chromatin accessibility landscape. This spatially resolved, single-cell multiomic framework of the first trimester human placenta serves as a blueprint for future studies on early placental development and pregnancy.

5154 Regulation Of T2D Genes In Human Adipocytes

Abstract Disclosure: Q. Zhang: None. Type 2 diabetes (T2D) is a chronic disease that affects 415 million people around the world and was the fourth leading cause of death (2015). Insulin resistance (IR), one of the major pathophysiological mechanisms that characterize T2D, is defined as the state in which cells, tissues, or organisms no longer respond appropriately to endogenous or exogenous insulin. We have generated detailed transcriptomes and chromatin state maps from the isolated adipocytes of insulin sensitive (IS) and insulin resistant (IR) human subjects. Mapping IR/IS differentially enriched H3K27ac peaks onto T2D GWAS SNPs suggested several loci as noncoding regulatory elements (REs) of human IR. We focused on the IRS1 gene, a known T2D related locus that encodes a critical protein in the insulin signaling cascade. We developed a CRISPRi-based assay that enabled us to determine which noncoding regulatory elements are required for normal IRS1 expression in human adipocytes. Our data indicate that many IR/IS differentially regulated H3K27ac peaks are critical regulatory elements for IRS1 transcription, although we did not observe that peaks that were increased in the IS state had a larger effect, as predicted. Overall, we have developed a CRISPRi-based screening system for noncoding elements in human adipocytes, which can be deployed to study many different loci related to metabolic disease. Presentation: 6/2/2024

Constructing the dynamic transcriptional regulatory networks to identify phenotype-specific transcription regulators.

The transcriptional regulatory network (TRN) is a graph framework that helps understand the complex transcriptional regulation mechanisms in the transcription process. Identifying the phenotype-specific transcription regulators is vital to reveal the functional roles of transcription elements in associating the specific phenotypes. Although many methods have been developed towards detecting the phenotype-specific transcription elements based on the static TRN in the past decade, most of them are not satisfactory for elucidating the phenotype-related functional roles of transcription regulators in multiple levels, as the dynamic characteristics of transcription regulators are usually ignored in static models. In this study, we introduce a novel framework called DTGN to identify the phenotype-specific transcription factors (TFs) and pathways by constructing dynamic TRNs. We first design a graph autoencoder model to integrate the phenotype-oriented time-series gene expression data and static TRN to learn the temporal representations of genes. Then, based on the learned temporal representations of genes, we develop a statistical method to construct a series of dynamic TRNs associated with the development of specific phenotypes. Finally, we identify the phenotype-specific TFs and pathways from the constructed dynamic TRNs. Results from multiple phenotypic datasets show that the proposed DTGN framework outperforms most existing methods in identifying phenotype-specific TFs and pathways. Our framework offers a new approach to exploring the functional roles of transcription regulators that associate with specific phenotypes in a dynamic model.

Androgens contribute to sex bias of autoimmunity in mice by T cell-intrinsic regulation of Ptpn22 phosphatase expression

Autoimmune diseases such as systemic lupus erythematosus (SLE) display a strong female bias. Although sex hormones have been associated with protecting males from autoimmunity, the molecular mechanisms are incompletely understood. Here we report that androgen receptor (AR) expressed in T cells regulates genes involved in T cell activation directly, or indirectly via controlling other transcription factors. T cell-specific deletion of AR in mice leads to T cell activation and enhanced autoimmunity in male mice. Mechanistically, Ptpn22, a phosphatase and negative regulator of T cell receptor signaling, is downregulated in AR-deficient T cells. Moreover, a conserved androgen-response element is found in the regulatory region of Ptpn22 gene, and the mutation of this transcription element in non-obese diabetic mice increases the incidence of spontaneous and inducible diabetes in male mice. Lastly, Ptpn22 deficiency increases the disease severity of male mice in a mouse model of SLE. Our results thus implicate AR-regulated genes such as PTPN22 as potential therapeutic targets for autoimmune diseases.

Identification of a specific APOE transcript and functional elements associated with Alzheimer’s disease

BackgroundThe APOE gene is the strongest genetic risk factor for late-onset Alzheimer’s Disease (LOAD). However, the gene regulatory mechanisms at this locus remain incompletely characterized.MethodsTo identify novel AD-linked functional elements within the APOE locus, we integrated SNP variants with multi-omics data from human postmortem brains including 2,179 RNA-seq samples from 3 brain regions and two ancestries (European and African), 667 DNA methylation samples, and ChIP-seq samples. Additionally, we plotted the expression trajectory of APOE transcripts in human brains during development.ResultsWe identified an AD-linked APOE transcript (jxn1.2.2) particularly observed in the dorsolateral prefrontal cortex (DLPFC). The APOE jxn1.2.2 transcript is associated with brain neuropathological features, cognitive impairment, and the presence of the APOE4 allele in DLPFC. We prioritized two independent functional SNPs (rs157580 and rs439401) significantly associated with jxn1.2.2 transcript abundance and DNA methylation levels. These SNPs are located within active chromatin regions and affect brain-related transcription factor-binding affinities. The two SNPs shared effects on the jxn1.2.2 transcript between European and African ethnic groups.ConclusionThe novel APOE functional elements provide potential therapeutic targets with mechanistic insight into the disease etiology.

Quantitative analysis of cis-regulatory elements in transcription with KAS-ATAC-seq

Cis-regulatory elements (CREs) are pivotal in orchestrating gene expression throughout diverse biological systems. Accurate identification and in-depth characterization of functional CREs are crucial for decoding gene regulation networks during cellular processes. In this study, we develop Kethoxal-Assisted Single-stranded DNA Assay for Transposase-Accessible Chromatin with Sequencing (KAS-ATAC-seq) to quantitatively analyze the transcriptional activity of CREs. A main advantage of KAS-ATAC-seq lies in its precise measurement of ssDNA levels within both proximal and distal ATAC-seq peaks, enabling the identification of transcriptional regulatory sequences. This feature is particularly adept at defining Single-Stranded Transcribing Enhancers (SSTEs). SSTEs are highly enriched with nascent RNAs and specific transcription factors (TFs) binding sites that define cellular identity. Moreover, KAS-ATAC-seq provides a detailed characterization and functional implications of various SSTE subtypes. Our analysis of CREs during mouse neural differentiation demonstrates that KAS-ATAC-seq can effectively identify immediate-early activated CREs in response to retinoic acid (RA) treatment. Our findings indicate that KAS-ATAC-seq provides more precise annotation of functional CREs in transcription. Future applications of KAS-ATAC-seq would help elucidate the intricate dynamics of gene regulation in diverse biological processes.

A modular toolkit for environmental Rhodococcus, Gordonia, and Nocardia enables complex metabolic manipulation.

Soil-dwelling Actinomycetes are a diverse and ubiquitous component of the global microbiome but largely lack genetic tools comparable to those available in model species such as Escherichia coli or Pseudomonas putida, posing a fundamental barrier to their characterization and utilization as hosts for biotechnology. To address this, we have developed a modular plasmid assembly framework, along with a series of genetic control elements for the previously genetically intractable Gram-positive environmental isolate Rhodococcus ruber C208, and demonstrate conserved functionality in 11 additional environmental isolates of Rhodococcus, Nocardia, and Gordonia. This toolkit encompasses five Mycobacteriale origins of replication, five broad-host-range antibiotic resistance markers, transcriptional and translational control elements, fluorescent reporters, a tetracycline-inducible system, and a counter-selectable marker. We use this toolkit to interrogate the carotenoid biosynthesis pathway in Rhodococcus erythropolis N9T-4, a weakly carotenogenic environmental isolate and engineer higher pathway flux toward the keto-carotenoid canthaxanthin. This work establishes several new genetic tools for environmental Mycobacteriales and provides a synthetic biology framework to support the design of complex genetic circuits in these species.IMPORTANCESoil-dwelling Actinomycetes, particularly the Mycobacteriales, include both diverse new hosts for sustainable biomanufacturing and emerging opportunistic pathogens. Rhodococcus, Gordonia, and Nocardia are three abundant genera with particularly flexible metabolisms and untapped potential for natural product discovery. Among these, Rhodococcus ruber C208 was shown to degrade polyethylene; Gordonia paraffinivorans can assimilate carbon from solid hydrocarbons; and Nocardia neocaledoniensis (and many other Nocardia spp.) possesses dual isoprenoid biosynthesis pathways. Many species accumulate high levels of carotenoid pigments, indicative of highly active isoprenoid biosynthesis pathways which may be harnessed for fermentation of terpenes and other commodity isoprenoids. Modular genetic toolkits have proven valuable for both fundamental and applied research in model organisms, but such tools are lacking for most Actinomycetes. Our suite of genetic tools and DNA assembly framework were developed for broad functionality and to facilitate rapid prototyping of genetic constructs in these organisms.

AAV-mediated gene delivery to the cardiac conduction system

Abstract Funding Acknowledgements Type of funding sources: Public grant(s) – National budget only. Main funding source(s): NWO open technology program Biopace #18485 Background Gene therapy for cardiac arrhythmias has so far mostly focused on modifying the arrhythmogenic substrate in working myocardium or on creating biological pacemakers with viral vectors that did not selectively target the cardiac conduction system (CCS). As a result, CCS targeting by viral vectors is a relatively unexplored area. Aim In the current project, we explored the basic requirements for CCS targeting using adeno-associated virus (AAV) vectors. Methods Regular AAV9 and AAV-Myo4A capsid-pseudotyped AAV2 vectors (hereafter called AAV2/9 and AAV2/Myo4A vectors, respectively) expressing enhanced green fluorescent protein (eGFP) from a CMV or TNNT2 promoter, respectively, and an AAV2/9 vector expressing eGFP from a human GJA5 regulatory element were systemically injected in mice. After 4 weeks, hearts were harvested, fixed with paraformaldehyde and stained for TNNT2, eGFP, HCN4 and DNA to determine CCS transduction. Results Transduction of the sinoatrial and atrioventricular (AV) node using AAV2/9 vectors was very poor, while transduction was visible in the atrioventricular (i.e. His) bundle and working myocardium. In contrast, the transduction rate of the AV node and bundle using AAV2/Myo4A vectors were similar to that of the working myocardium. The human GJA5 regulatory element was able to restrict eGFP expression by AAV2/9 vectors to the AV bundle in 2/3 animals but the transduction efficiency was low. A third animal showed no transduction of any tissue, either indicative of the low transduction efficiency or of a failed injection. Conclusion This study not only provides proof-of-principle for CCS-targeted gene therapy but also shows that CCS transduction can be improved through AAV capsid engineering and be restricted to (parts of) the CCS by using specific transcriptional control elements.

Discovery of an efficacious KDM5B PROTAC degrader GT-653 up-regulating IFN response genes in prostate cancer

Epigenetic alterations promote cancer development by regulating the expression of various oncogenes and anti-oncogenes. Histone methylation modification represents a pivotal area in epigenetic research and numerous publications have demonstrated that aberrant histone methylation is highly correlated with tumorigenesis and development. As a key histone demethylase, lysine-specific demethylase 5B (KDM5B) demethylates lysine 4 of histone 3 (H3K4) and serves as a transcriptional repressor of certain tumor suppressor genes. Meanwhile, KDM5B inhibits STING-induced intrinsic immune response of tumor cells or recruits SETDB1 through non-enzymatic function to silence reverse transcription elements to promote immune escape. The conventional small molecule inhibitors can only inhibit the enzymatic function of KDM5B with no effect on the non-enzymatic function. In the article, we present the development of the first series of KDM5B degraders based on CPI-455 to inhibit the non-enzymatic function. Among them, GT-653 showed optimal KDM5B degradation efficiency in a ubiquitin proteasome-dependent manner. GT-653 efficiently reduced KDM5B protein levels without affecting KDM5B transcription. Interestingly, GT-653 increased H3K4me3 levels and activated the type-I interferon signaling pathway in 22RV1 cells without significant phenotypic response on cell proliferation.

Discovery of Highly Potent and Efficient CBP/p300 Degraders with Strong In Vivo Antitumor Activity.

The transcriptional coactivator cAMP response element binding protein (CREB)-binding protein (CBP) and its homologue p300 have emerged as attractive therapeutic targets for human cancers such as acute myeloid leukemia (AML). Herein, we report the design, synthesis, and biological evaluation of a series of cereblon (CRBN)-recruiting CBP/p300 proteolysis targeting chimeras (PROTACs) based on the inhibitor CCS1477. The representative compounds 14g (XYD190) and 14h (XYD198) potently inhibited the growth of AML cells with low nanomolar IC50 values and effectively degraded CBP and p300 proteins in a concentration- and time-dependent manner. Mechanistic studies confirmed that 14g and 14h can selectively bind to CBP/p300 bromodomains and induce CBP and p300 degradation in bromodomain family proteins in a CRBN- and proteasome-dependent manner. 14g and 14h displayed remarkable antitumor efficacy in the MV4;11 xenograft model (TGI = 88% and 93%, respectively). Our findings demonstrated that 14g and 14h are useful lead compounds and deserve further optimization and activity evaluation for the treatment of human cancers.

Avian leukosis virus usurps the cellular SERBP1 protein to enhance its transcription and promote productive infections in avian cells

Avian leukosis virus subgroup K (ALV-K) is composed of newly emerging isolates, which cluster separately from the well-characterized subgroups A, B, C, D, E, and J in sequence analysis, and exhibits a specific host range and a unique pattern of superinfection interference. Avian leukosis virus subgroup K replicate more slowly in avian cells than other ALV strains, leading to escaped detection during ALV eradication, but the underlying mechanism are largely unknown. In our previous study, we have reported that JS11C1 and most of other suspected ALV-K strains possessed unique mutations in the U3 region. Here, we selected 5 mutations in some important transcriptional regulation elements to explore the possible factor contributing for the lower activity of LTR, including CA-TG mutation in the CAAT box, 21 nt deletion in the CAAT box, A-G and A-T mutations in the CArG boxes, 11 nt insertion in the PRE boxes, and C-T mutation in the TATA box. On the basis of infectious clone of JS11C1, we demonstrated that the 11 nt fragment in the PRE boxes was associated with the transcription activity of LTR, the enhancer ability of U3, and the replication capacity of the virus. Notably, we determined the differential U3-protein interaction profile of ALVs and found that the 11 nt fragment specifically binds to cellular SERPINE1 mRNA binding protein 1 (SERBP1) to increase the LTR activity and enhance virus replication. Collectively, these findings reveal that a 11 nt fragment in the U3 gene contributed to its binding ability to the cellular SERBP1 to enhance its transcription and the infectious virus productions in avian cells. This study highlighted the vital role of host factor in retrovirus replication and thus provides a new perspective to elucidate the interaction between retrovirus and its host and a molecular basis to develop efficient strategies against retroviruses.

The immunoglobulin heavy chain super enhancer controls class switch recombination in developing B cells

Class switch recombination (CSR) plays an important role in adaptive immune response by enabling mature B cells to replace the initial IgM by another antibody class (IgG, IgE or IgA). CSR is preceded by transcription of the IgH constant genes and is controlled by the super-enhancer 3′ regulatory region (3′RR) in an activation-specific manner. The 3’RR is composed of four enhancers (hs3a, hs1-2, hs3b and hs4). In mature B cells, 3’RR activity correlates with transcription of its enhancers. CSR can also occur in primary developing B cells though at low frequency, but in contrast to mature B cells, the transcriptional elements that regulate the process in developing B cells are ill-known. In particular, the role of the 3’RR in the control of constant genes’ transcription and CSR has not been addressed. Here, by using a mouse line devoid of the 3’RR and a culture system that highly enriches in pro-B cells, we show that the 3’RR activity is indeed required for switch transcription and CSR, though its effect varies in an isotype-specific manner and correlates with transcription of hs4 enhancer only.

Unveiling Innovative Approaches to Mitigate Metals/Metalloids Toxicity for Sustainable Agriculture.

Due to anthropogenic activities, environmental pollution of heavy metals/metalloids (HMs) has increased and received growing attention in recent decades. Plants growing in HM-contaminated soils have slower growth and development, resulting in lower agricultural yield. Exposure to HMs leads to the generation of free radicals (oxidative stress), which alters plant morpho-physiological and biochemical pathways at the cellular and tissue levels. Plants have evolved complex defense mechanisms to avoid or tolerate the toxic effects of HMs, including HMs absorption and accumulation in cell organelles, immobilization by forming complexes with organic chelates, extraction via numerous transporters, ion channels, signaling cascades, and transcription elements, among others. Nonetheless, these internal defensive mechanisms are insufficient to overcome HMs toxicity. Therefore, unveiling HMs adaptation and tolerance mechanisms is necessary for sustainable agriculture. Recent breakthroughs in cutting-edge approaches such as phytohormone and gasotransmitters application, nanotechnology, omics, and genetic engineering tools have identified molecular regulators linked to HMs tolerance, which may be applied to generate HMs-tolerant future plants. This review summarizes numerous systems that plants have adapted to resist HMs toxicity, such as physiological, biochemical, and molecular responses. Diverse adaptation strategies have also been comprehensively presented to advance plant resilience to HMs toxicity that could enable sustainable agricultural production.

Treatment of infantile-onset Pompe disease in a rat model with muscle-directed AAV gene therapy

ObjectivePompe disease (PD) is caused by deficiency of the lysosomal enzyme acid α-glucosidase (GAA), leading to progressive glycogen accumulation and severe myopathy with progressive muscle weakness. In the Infantile-Onset PD (IOPD), death generally occurs <1 year of age. There is no cure for IOPD. Mouse models of PD do not completely reproduce human IOPD severity. Our main objective was to generate the first IOPD rat model to assess an innovative muscle-directed adeno-associated viral (AAV) vector-mediated gene therapy. MethodsPD rats were generated by CRISPR/Cas9 technology. The novel highly myotropic bioengineered capsid AAVMYO3 and an optimized muscle-specific promoter in conjunction with a transcriptional cis-regulatory element were used to achieve robust Gaa expression in the entire muscular system. Several metabolic, molecular, histopathological, and functional parameters were measured. ResultsPD rats showed early-onset widespread glycogen accumulation, hepato- and cardiomegaly, decreased body and tissue weight, severe impaired muscle function and decreased survival, closely resembling human IOPD. Treatment with AAVMYO3-Gaa vectors resulted in widespread expression of Gaa in muscle throughout the body, normalizing glycogen storage pathology, restoring muscle mass and strength, counteracting cardiomegaly and normalizing survival rate. ConclusionsThis gene therapy holds great potential to treat glycogen metabolism alterations in IOPD. Moreover, the AAV-mediated approach may be exploited for other inherited muscle diseases, which also are limited by the inefficient widespread delivery of therapeutic transgenes throughout the muscular system.

CDH2-microRNA Axis Provides Insights into Sustained Breast Cancer Dormancy in the Bone Marrow Niche

Despite long-term remission of breast cancer (BC), cancer resurgence remains a clinical issue. This issue is mostly due to BC cells (BCCs) being able to survive in dormancy for decades. This is particularly relevant to the bone marrow (BM) where the dormant BCCs survive as cancer stem cells (CSCs). The BM niche maintains BCCs in dormancy, and also mediates dedifferentiation of BCCs to CSCs. Since dormancy can occur at any time during the disease, including decades before clinical diagnosis, it is important to understand how these cells survive to allow for the development of safe treatments. Dormant BCCs establish gap junctional intercellular communication (GJIC) with BM niche such as fibroblasts and mesenchymal stem cells (MSCs). GJIC requires connexin 43 (Cx43) but cannot be a safe target since this connexin is also important for hematopoietic function. This study focused on N-cadherin (CDH2) because it facilitates Cx43-mediated GJIC between BCCs and BM niche cells. We found Cx43 and CDH2 mutually regulated their gene expression. Cloning of the 5′ regulatory regions of CDH2 unraveled DNA sequences as possible elements of repressor and activator transcription. We identified potential transcription factors (TFs) that could regulate CDH2 and showed how miRNAs that could cross GJIC might be responsible for regulating the TFs. The axis developed by CDH2 and miRNAs provide insights into how CDH2 is maintained at low level to sustain BC dormancy. The findings, together with previous findings, provide avenues for therapeutic intervention to safely reverse and target dormant BCCs in the BM niche.