Utilisation of Waste Sludge from Drinking Water Treatment as a Filler Material in Hot Mix Asphalt

This research investigated the suitability of using sludge from the treatment of drinking water in hot mix asphalt (HMA) as a filler material. The storage and environmental impact of sludge is an enormous problem, especially for countries with large populations. Two different types of sludges, ferric chloride (FC) and aluminium sulphate (AS), were used as a filler material in HMA. The Hamburg Wheel Tracking (HWT) test, which correlates with rutting, and the Indirect Tensile Strength (ITS) test, which indicates the moisture sensitivity of HMA, were carried out at the optimum bitumen content of the mixes to investigate the usability of sludge in HMA. The test results indicate the usability of FC and AS in HMA compared to the reference mixes. However, the AS type of sludge has better rutting resistance than the FC type. Although the results support the usability of both sludges in HMA, it should be noted that the increased cost of the mix containing sludges due to the combustion process and the increased bitumen content during application should be considered.

Increased expression of CD70 in relapsed acute myeloid leukemia after hypomethylating agents

Acute myeloid leukemia (AML) is the most common acute leukemia in adults. While induction chemotherapy leads to remission in most patients, a significant number will experience relapse. Therefore, there is a need for novel therapies that can improve remission rates in patients with relapsed and refractory AML. CD70 is the natural ligand for CD27 (a member of the TNF superfamily) and appears to be a promising therapeutic target. Consequently, there is considerable interest in developing chimeric antigen receptor (CAR) T-cell therapy products that can specifically target CD70 in various neoplasms, including AML. In this study, we employed routine diagnostic techniques, such as immunohistochemistry and flow cytometry, to investigate the expression of CD70 in bone marrow samples from treatment-naïve and relapsed AML patients after hypomethylating agents (HMA). Also, we evaluated the impact of HMA on CD70 expression and examined CD70 expression in various leukemic cell subsets and normal hematopoietic progenitors.

Efficacy and safety of an HDACi- and HMA-based protocol in adults with acute myeloid leukemia of intermediate- and adverse-risk categories: a retrospective study

OBJECTIVE

Anthracyclines and cytarabine have comprised standard induction therapy for acute myeloid leukemia (AML) for decades. Low overall survival of AML is due to non-remission or relapse after remission. Hypomethylating agent (HMA) decitabine combined with low-dose chemotherapy or other targeted agents has shown promising effect for AML in clinical trials, especially in t(8;21) acute myeloid leukemia. We previously investigated histone deacetylase inhibitor (HDACi) chidamide could regulate Wnt/β-catenin signaling pathway in leukemia cell lines.

METHODS

Adult patients with de novo or relapsed/refractory AML who were treated with chidamide and decitabine in combination with chemotherapy (chidamide group, n = 23) or only decitabine combination with chemotherapy (decitabine group, n = 17) were analyzed.

RESULTS

Chidamide group represented higher complete response rate (82.6% and 52.9%, p = 0.0430, vs. decitabine group), progression-free survival and overall survival rates (p = 0.0088 and p = 0.0139, respectively), especially for patients with de novo AML. Hematological toxicity and infections were the most common adverse events (AEs) in both groups, and they were manageable by supportive treatments.

CONCLUSIONS

This HDACi- and HMA-based protocol is an effective and tolerable therapy for patients with AML. The comprehensive mechanism and effects of chidamide in combination with decitabine are worth to be further explored in AML.

A Genome-Wide Identification and Comparative Analysis of the Heavy-Metal-Associated Gene Family in Cucurbitaceae Species and Their Role in Cucurbita pepo under Arsenic Stress

The heavy-metal-associated (HMA) proteins are a class of PB1-type ATPases related to the intracellular transport and detoxification of metals. However, due to a lack of information regarding the HMA gene family in the Cucurbitaceae family, a comprehensive genome-wide analysis of the HMA family was performed in ten Cucurbitaceae species: Citrullus amarus, Citrullus colocynthis, Citrullus lanatus, Citrullus mucosospermus, Cucumis melo, Cucumis sativus, Cucurbita maxima, Cucurbita moschata, Cucurbita pepo, and Legenaria siceraria. We identified 103 Cucurbit HMA proteins with various members, ranging from 8 (Legenaria siceraria) to 14 (Cucurbita pepo) across species. The phylogenetic and structural analysis confirmed that the Cucurbitaceae HMA protein family could be further classified into two major clades: Zn/Co/Cd/Pb and Cu/Ag. The GO-annotation-based subcellular localization analysis predicted that all HMA gene family members were localized on membranes. Moreover, the analysis of conserved motifs and gene structure (intron/exon) revealed the functional divergence between clades. The interspecies microsynteny analysis demonstrated that maximum orthologous genes were found between species of the Citrullus genera. Finally, nine candidate HMA genes were selected, and their expression analysis was carried out via qRT-PCR in root, leaf, flower, and fruit tissues of C. pepo under arsenic stress. The expression pattern of the CpeHMA genes showed a distinct pattern of expression in root and shoot tissues, with a remarkable expression of CpeHMA6 and CpeHMA3 genes from the Cu/Ag clade. Overall, this study provides insights into the functional analysis of the HMA gene family in Cucurbitaceae species and lays down the basic knowledge to explore the role and mechanism of the HMA gene family to cope with arsenic stress conditions.

Mitotic perturbation is a key mechanism of action of decitabine in myeloid tumor treatment

Decitabine (DAC) is clinically used to treat myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). Our genome-wide CRISPR-dCas9 activation screen using MDS-derived AML cells indicates that mitotic regulation is critical for DAC resistance. DAC strongly induces abnormal mitosis (abscission failure or tripolar mitosis) in human myeloid tumors at clinical concentrations, especially in those with TP53 mutations or antecedent hematological disorders. This DAC-induced mitotic disruption and apoptosis are significantly attenuated in DNMT1-depleted cells. In contrast, overexpression of Dnmt1, but not the catalytically inactive mutant, enhances DAC-induced mitotic defects in myeloid tumors. We also demonstrate that DAC-induced mitotic disruption is enhanced by pharmacological inhibition of the ATR-CLSPN-CHK1 pathway. These data challenge the current assumption that DAC inhibits leukemogenesis through DNMT1 inhibition and subsequent DNA hypomethylation and highlight the potent activity of DAC to disrupt mitosis through aberrant DNMT1-DNA covalent bonds.

Organosilicon Compounds in Hot-Melt Adhesive Technologies

Hot-melt adhesives (HMAs) are thermoplastic materials that can bond various substrates by solidifying rapidly upon cooling from the molten state, and their modification with organosilicon compounds can result in crosslinking behavior, characteristic of gels. Organosilicon compounds are hybrid molecules that have both inorganic and organic components and can enhance the properties and performance of HMAs. The gel aspect of HMA with and without organosilicon modifiers can be considered in organosilicon-modified systems, the modifiers are often either sol-gel condensation products or their mechanism of action on the adherent surface can be considered of sol-gel type. The purpose of this manuscript is to present the current state of the art on the formulation, characterization, and application of HMAs and optimize their performance with organosilicon compounds for application in various industries such as automotive, construction, and photovoltaics. This review covers articles published within the period of 2018-2022. The article is divided into sections, in which information about hot-melt adhesives is described at the beginning. The following part of the presented review focuses on the composition of hot-melt adhesives, which takes into account the use of organosilicon compounds. The last part of this review outlines the future trends in hot-melt adhesives.

CRISPR-Cas9-Based Functional Analysis in Amphibians: Xenopus laevis, Xenopus tropicalis, and Pleurodeles waltl

Amphibians have made many fundamental contributions to our knowledge, from basic biology to biomedical research on human diseases. Current genome editing tools based on the CRISPR-Cas system enable us to perform gene functional analysis in vivo, even in non-model organisms. We introduce here a highly efficient and easy protocol for gene knockout, which can be used in three different amphibians seamlessly: Xenopus laevis, Xenopus tropicalis, and Pleurodeles waltl. As it utilizes Cas9 ribonucleoprotein complex (RNP) for injection, this cloning-free method enables researchers to obtain founder embryos with a nearly complete knockout phenotype within a week. To evaluate somatic mutation rate and its correlation to the phenotype of a Cas9 RNP-injected embryo (crispant), we also present accurate and cost-effective genotyping methods using pooled amplicon-sequencing and a user-friendly web-based tool.

Antifungal activity of 6-substituted amiloride and hexamethylene amiloride (HMA) analogs

Fungal infections have become an increasing threat as a result of growing numbers of susceptible hosts and diminishing effectiveness of antifungal drugs due to multi-drug resistance. This reality underscores the need to develop novel drugs with unique mechanisms of action. We recently identified 5-(N,N-hexamethylene)amiloride (HMA), an inhibitor of human Na⁺/H⁺ exchanger isoform 1, as a promising scaffold for antifungal drug development. In this work, we carried out susceptibility testing of 45 6-substituted HMA and amiloride analogs against a panel of pathogenic fungi. A series of 6-(2-benzofuran)amiloride and HMA analogs that showed up to a 16-fold increase in activity against Cryptococcus neoformans were identified. Hits from these series showed broad-spectrum activity against both basidiomycete and ascomycete fungal pathogens, including multidrug-resistant clinical isolates.

Evaluating Rutting Resistance of Rejuvenated Recycled Hot-Mix Asphalt Mixtures Using Different Types of Recycling Agents

Growing environmental pollution worldwide is mostly caused by the accumulation of different types of liquid and solid wastes. Therefore, policies in developed countries seek to support the concept of waste recycling due to its significant impact on the environmental footprint. Hot-mix asphalt mixtures (HMA) with reclaimed asphalt pavement (RAP) have shown great performance under rutting. However, incorporating a high percentage of RAP (>25%) is a challenging issue due to the increased stiffness of the resulting mixture. The stiffness problem is resolved by employing different types of commercial and noncommercial rejuvenators. In this study, three types of noncommercial rejuvenators (waste cooking oil (WCO), waste engine oil (WEO), and date seed oil (DSO)) were used, in addition to one type of commercial rejuvenator. Three percentages of RAP (20%, 40%, and 60%) were utilized. Mixing proportions for the noncommercial additives were set as 0−10% for mixtures with 20% RAP, 12.5−17.5% for mixtures with 40% RAP, and 17.5−20% for mixtures with 60% RAP. In addition, mixing proportions for the commercial additive were set as 0.5−1.0% for mixtures with 20% RAP, 1.0−1.5% for mixtures with 40% RAP, and 1.5−2.0% for mixtures with 60% RAP. The rutting performance of the generated mixtures was indicated first by using the rutting index (G*/sin δ) for the combined binders and then evaluated using the Hamburg wheel-track test. The results showed that the rejuvenated mixtures with the commercial additive at 20 and 60% RAP performed well compared to the control mixture, whereas the rejuvenated ones at 40% RAP performed well with noncommercial additives in comparison to the control mixture. Furthermore, the optimum percentages for each type of the used additives were obtained, depending on their respective performance, as 10%, 12.5%, and 17.5% of WCO, 10%, 12.5−17.5%, and 17.5% of WEO, <10%, 12.5%, and 17.5% of DSO, and 0.5−1.0%, 1.0%, and 1.5−2.0% of the commercial rejuvenator, corresponding to the three adopted percentages of RAP.

Genomic landscape of myelodysplastic/myeloproliferative neoplasm can predict response to hypomethylating agent therapy

There are currently no known predictors of myelodysplastic syndrome (MDS)/myeloproliferative overlap neoplasm (MPN) patients' response to hypomethylating agents (HMA). Forty-three patients with MDS/MPN who were treated with HMA during chronic phase and had next-generation sequencing using the established 63-genes panel were identified. Complete and partial remission and marrow response were assessed based on the MDS/MPN International Working Group response criteria. On univariate analysis, younger age, higher number of mutations, and mutations in SETBP1, RUNX1, or EZH2 were associated with no response. Multivariable analysis for modeling response were conducted via least absolute shrinkage and selection operator logistic regression approach, and showed that mutations in SETBP1, RUNX1, or EZH2 predict lack of HMA response. While limited by sample size, our findings suggest that genomic landscape can potentially identify MDS/MPN patients with lower likelihood of response to HMA.

Advances in Genes-Encoding Transporters for Cadmium Uptake, Translocation, and Accumulation in Plants

Cadmium (Cd) is a heavy metal that is highly toxic for plants, animals, and human beings. A better understanding of the mechanisms involved in Cd accumulation in plants is beneficial for developing strategies for either the remediation of Cd-polluted soils using hyperaccumulator plants or preventing excess Cd accumulation in the edible parts of crops and vegetables. As a ubiquitous heavy metal, the transport of Cd in plant cells is suggested to be mediated by transporters for essential elements such as Ca, Zn, K, and Mn. Identification of the genes encoding Cd transporters is important for understanding the mechanisms underlying Cd uptake, translocation, and accumulation in either crop or hyperaccumulator plants. Recent studies have shown that the transporters that mediate the uptake, transport, and accumulation of Cd in plants mainly include members of the natural resistance-associated macrophage protein (Nramp), heavy metal-transporting ATPase (HMA), zinc and iron regulated transporter protein (ZIP), ATP-binding cassette (ABC), and yellow stripe-like (YSL) families. Here, we review the latest advances in the research of these Cd transporters and lay the foundation for a systematic understanding underlying the molecular mechanisms of Cd uptake, transport, and accumulation in plants.

A Comprehensive Review of Indel Detection Methods for Identification of Zebrafish Knockout Mutants Generated by Genome-Editing Nucleases

The use of zebrafish in functional genomics and disease modeling has become popular due to the ease of targeted mutagenesis with genome editing nucleases, i.e., zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas9). These nucleases, specifically CRISPR/Cas9, are routinely used to generate gene knockout mutants by causing a double stranded break at the desired site in the target gene and selecting for frameshift insertions or deletions (indels) caused by the errors during the repair process. Thus, a variety of methods have been developed to identify fish with indels during the process of mutant generation and phenotypic analysis. These methods range from PCR and gel-based low-throughput methods to high-throughput methods requiring specific reagents and/or equipment. Here, we provide a comprehensive review of currently used indel detection methods in zebrafish. By discussing the molecular basis for each method as well as their pros and cons, we hope that this review will serve as a comprehensive resource for zebrafish researchers, allowing them to choose the most appropriate method depending upon their budget, access to required equipment and the throughput needs of the projects.

Genome-wide identification and characterization of the heavy metal ATPase (HMA) gene family in Medicago truncatula under copper stress

In nature, the normal growth, development, and quality of plants are significantly affected by many abiotic stresses, such as drought, salinity, low temperature, and heavy metals. Among heavy metals, copper is an essential element for plant growth and development but also has a toxic effect on plants when its concentration is excessive. Therefore, plants have evolved a complex regulatory network to regulate the balance of copper ions in cells. Heavy metal ATPases (HMAs), which transport heavy metals to intracellular compartments or detoxify heavy metals present at excessive concentrations, have been extensively studied in model plant species. However, no comprehensive and systematic surveys of members of the HMA gene family have been conducted in the model legume species Medicago truncatula. Here, nine putative MtHMAs were identified in the M. truncatula genome. These MtHMAs were phylogenetically divided into two distinct groups. The members in each group had a relatively conserved gene structure and motif composition. The number of introns in the MtHMAs varied from 5 to 16, with the majority of these genes containing 8 introns. The expression patterns showed that MtHMAs exhibit preferential or distinct expression patterns among different tissues. Finally, the expression patterns of the members of this gene family were verified in the leaves and roots of plants under Cu stress. Our findings will be valuable for the functional investigation and application of members of this gene family in M. truncatula and other related legume species.

Hypomethylating Agents (HMAs) as Salvage Therapy in Relapsed or Refractory AML: An Italian Multicentric Retrospective Study

Data on the use of azacytidine and decitabine as salvage therapy for acute myeloid leukemia are limited. We retrospectively reviewed clinical records of 100 patients treated with hypomethylating agents (HMA) as salvage therapy in nine Italian institutions. A total of 24% of patients obtained a response to HMA (CR, PR, or CRi), while 26% showed a stable disease (SD); 50% of patients experienced progressive disease. Median OS was 6.5 months. OS in patients with de novo AML was 6.1 months, while OS in patients with secondary AML (sAML) was 12.3 months (p = 0.037). Median OS after HMA in patients with SD as best response to HMA was similar to median OS in patients with response to HMA (10.6 months vs. 13 months). On multivariate analysis, OS difference between patients who obtained a response versus patients who did not was significant (p = 0.0037). OS difference in sAML was significantly better than in de novo AML (p < 0.00001). HMA showed a remarkable efficacy in terms of response rate and OS in a subgroup of patients (sAMLs), historically characterized by a poor outcome. Therefore, 5Azacitidine and decitabine may represent a good clinical option in a selected patient population with relapsed or refractory AML, unsuitable for allo-HSCT.

Venetoclax-based combinations for the treatment of newly diagnosed acute myeloid leukemia

Elderly and/or unfit patients with acute myeloid leukemia have historically been challenging to manage as they were ineligible for what was considered standard of care treatment with induction chemotherapy. The emergence of venetoclax with hypomethylating agents or low-dose cytarabine has substantially improved outcomes in the frontline setting with manageable toxicity. However, this regimen can be challenging to deliver given its differences from standard intensive chemotherapy. In this review, we summarize the landmark trials that established venetoclax-based combinations as a new standard of care for patients with acute myeloid leukemia not suitable for intense chemotherapy, provide practical clinical pearls for managing patients on these therapies, and offer a brief overview of modifications to these regimens under development to improve their efficacy and/or applicability.

The Antifungal Activity of HMA, an Amiloride Analog and Inhibitor of Na+/H+ Exchangers

One path toward identifying effective and easily accessible antifungals is to repurpose commonly used drugs. Amiloride, a widely used diuretic, inhibits different isoforms of Na⁺/H⁺ exchangers, Na⁺ channels, and Na⁺/Ca²⁺ exchangers. Here, we found that amiloride had poor antifungal activity against isolates of Cryptococcus prompting the examination of the amiloride analog, HMA [5-(N,N-hexamethylene)amiloride]. HMA possesses strong activity against Na⁺/H⁺ exchangers (NHEs) and little K⁺-associated toxicity since HMA has only minimal inhibitory effects toward epithelial sodium channels (ENaC), the diuretic and antikaliuretic target of amiloride. Although HMA produced a robust dose-dependent growth inhibition of several fungal isolates, susceptibility assays revealed modest MICs against isolates of Cryptococcus. A checkerboard dilution strategy resulted in fractional inhibitory concentrations (FIC) < 0.5, suggesting that HMA displays synergy with several antifungal azole drugs including posaconazole, voriconazole, and ketoconazole. Itraconazole and ravuconazole showed moderate synergy with HMA across all tested fungal isolates. In combination with HMA, ravuconazole had MICs of 0.004-0.008 μg/ml, a ∼16-fold reduction compared to MICs of ravuconazole when used alone and significantly more effective than the overall MIC₉₀ (0.25 μg/ml) reported for ravuconazole against 541 clinical isolates of Cryptococcus neoformans. In combination with azole drugs, MICs of HMA ranged from 3.2 μM (1 μg/ml) to 26 μM (16 μg/ml), HMA was not cytotoxic at concentrations ≤ 8 μg/ml, but MICs were above the reported HMA K_i of 0.013-2.4 μM for various Na⁺/H⁺ exchangers. Our results suggest that HMA has limited potential as a monotherapy and may have additional targets in fungal/yeast cells since strains lacking NHEs remained sensitive to HMA. We determined that the hydrophobic substituent at the 5-amino group of HMA is likely responsible for the observed antifungal activity and synergy with several azoles since derivatives with bulky polar substitutions showed no activity against Cryptococcus, indicating that other 5-substituted HMA derivatives could possess stronger antifungal activity. Moreover, substitution of other positions around the pyrazine core of HMA has not been investigated but could reveal new leads for antifungal drug development.

Current and emerging strategies for management of myelodysplastic syndromes

Myelodysplastic syndromes (MDS) are characterized by ineffective hematopoiesis with varying degrees of dysplasia and peripheral cytopenias. MDS are driven by structural chromosomal alterations and somatic mutations in neoplastic myeloid cells, which are supported by a tumorigenic and a proinflammatory marrow microenvironment. Current treatment strategies for lower-risk MDS focus on improving quality of life and cytopenias, while prolonging survival and delaying disease progression is the focus for higher-risk MDS. Several promising drugs are in the horizon, including the hypoxia-inducible factor stabilizer roxadustat, telomerase inhibitor imetelstat, oral hypomethylating agents (CC-486), TP53 modulators (APR-246 and ALRN-6924), and the anti-CD47 antibody magrolimab. Targeted therapies approved for acute myeloid leukemia treatment, such as isocitrate dehdyrogenase inhibitors and venetoclax, are also being studied for use in MDS. In this review, we provide a brief overview of pathogenesis and current treatment strategies in MDS followed by a discussion of newer agents that are under clinical investigation.

Genome-wide identification of ATP binding cassette (ABC) transporter and heavy metal associated (HMA) gene families in flax (Linum usitatissimum L.)

Background

The recent release of the reference genome sequence assembly of flax, a self-pollinated crop with 15 chromosome pairs, into chromosome-scale pseudomolecules enables the characterization of gene families. The ABC transporter and HMA gene families are important in the control of cadmium (Cd) accumulation in crops. To date, the genome-wide analysis of these two gene families has been successfully conducted in some plant species, but no systematic evolutionary analysis is available for the flax genome.

Results

Here we describe the ABC transporter and HMA gene families in flax to provide a comprehensive overview of its evolution and some support towards the functional annotation of its members. The 198 ABC transporter and 12 HMA genes identified in the flax genome were classified into eight ABC transporter and four HMA subfamilies based on their phylogenetic analysis and domains’ composition. Nine of these genes, i.e., LuABCC9, LuABCC10, LuABCG58, LuABCG59, LuABCG71, LuABCG72, LuABCG73, LuHMA3, and LuHMA4, were orthologous with the Cd associated genes in Arabidopsis, rice and maize. Ten motifs were identified from all ABC transporter and HMA genes. Also, several motifs were conserved among genes of similar length, but each subfamily each had their own motif structures. Both the ABC transporter and HMA gene families were highly conserved among subfamilies of flax and with those of Arabidopsis. While four types of gene duplication were observed at different frequencies, whole-genome or segmental duplications were the most frequent with 162 genes, followed by 29 dispersed, 14 tandem and 4 proximal duplications, suggesting that segmental duplications contributed the most to the expansion of both gene families in flax. The rates of non-synonymous to synonymous (Ka/Ks) mutations of paired duplicated genes were for the most part lower than one, indicative of a predominant purifying selection. Only five pairs of genes clearly exhibited positive selection with a Ka/Ks ratio greater than one. Gene ontology analyses suggested that most flax ABC transporter and HMA genes had a role in ATP binding, transport, catalytic activity, ATPase activity, and metal ion binding. The RNA-Seq analysis of eight different organs demonstrated diversified expression profiling patterns of the genes and revealed their functional or sub-functional conservation and neo-functionalization.

Conclusion

Characterization of the ABC transporter and HMA gene families will help in the functional analysis of candidate genes in flax and other crop species.

The genome-wide impact of cadmium on microRNA and mRNA expression in contrasting Cd responsive wheat genotypes

BACKGROUND

Heavy metal ATPases (HMAs) are responsible for Cd translocation and play a primary role in Cd detoxification in various plant species. However, the characteristics of HMAs and the regulatory mechanisms between HMAs and microRNAs in wheat (Triticum aestivum L) remain unknown.

RESULTS

By comparative microRNA and transcriptome analysis, a total three known and 19 novel differentially expressed microRNAs (DEMs) and 1561 differentially expressed genes (DEGs) were found in L17 after Cd treatment. In H17, by contrast, 12 known and 57 novel DEMs, and only 297 Cd-induced DEGs were found. Functional enrichments of DEMs and DEGs indicate how genotype-specific biological processes responded to Cd stress. Processes found to be involved in microRNAs-associated Cd response include: ubiquitin mediated proteolysis, tyrosine metabolism, and carbon fixation pathways and thiamine metabolism. For the mRNA response, categories including terpenoid backbone biosynthesis and phenylalanine metabolism, and photosynthesis - antenna proteins and ABC transporters were enriched. Moreover, we identified 32 TaHMA genes in wheat. Phylogenetic trees, chromosomal locations, conserved motifs and expression levels in different tissues and roots under Cd stress are presented. Finally, we infer a microRNA-TaHMAs expression network, indicating that miRNAs can regulate TaHMAs.

CONCLUSION

Our findings suggest that microRNAs play important role in wheat under Cd stress through regulation of targets such as TaHMA2;1. Identification of these targets will be useful for screening and breeding low-Cd accumulation wheat lines.

RBC transfusion independence among lower risk MDS patients receiving hypomethylating agents: a population-level analysis

Most patients with lower risk myelodysplastic syndromes (LR-MDS) become red blood cell (RBC) transfusion dependent at some time during their disease course. Hypomethylating agents (HMAs) are frequently used in this setting; however, reported rates of in RBC transfusion independence (TI) achieved with HMA therapy vary significantly between studies. Here we study the real-life clinical effectiveness of HMA in inducing RBC TI in anemic LR-MDS patients using the Surveillance, Epidemiology and End Results (SEER)-Medicare database. We find that approximately 40% of LR-MDS patients who were receiving RBC transfusions and 33% who were dependent on RBC transfusions at HMA initiation ultimately achieved TI. The receipt of ≥3 transfusions in the 8-week period before HMA initiation was significantly associated with lower odds of achieving TI. Our study provides important population level estimates of clinical effectiveness of HMAs in LR-MDS.

Beyond the Edge of Hypomethylating Agents: Novel Combination Strategies for Older Adults with Advanced MDS and AML

Higher-risk myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) of the elderly exhibit several commonalities, including first line treatment with hypomethylating agents (HMA) like azacitidine (AZA) or decitabine (DAC). Until today, response to treatment occurs in less than 50 percent of patients, and is often short-lived. Moreover, patients failing HMA have a dismal prognosis. Current developments include combinations of HMA with novel drugs targeting epigenetic or immunomodulatory pathways. Other efforts focus on the prevention of resistance to HMA using checkpoint inhibitors to enhance immune attack. This review focuses on recent advances in the field of HMA-based front-line therapies in elderly patients with myeloid diseases.

Genotyping of CRISPR/Cas9 Genome Edited Xenopus tropicalis

The targeted nuclease revolution (ZFN, TALEN, and CRISPR/Cas9) has led to a myriad of reports describing genotyping methodologies for genome edited founders (F0-crispants) and their offspring (F1). As such, choosing a specific genotyping methodology for your Xenopus CRISPR/Cas9 experiments can be challenging. In this chapter we will discuss, with emphasis on Xenopus tropicalis (X. tropicalis), different methods for assessing genome editing efficiencies within F0 CRISPR/Cas9 founders and for identification of their hetero-, compound hetero-, and homozygous mutant F1 offspring. For F0 crispants, we will provide the protocols and the respective (dis)advantages of genotyping with heteroduplex mobility assay (HMA), subclone Sanger sequencing, and sequence trace decomposition. Furthermore, we provide a previously unpublished pipe-line for rapid genotyping of F1 offspring-high resolution melting analysis (HRMA) and sequence trace decomposition-procured from breeding with F0 crispants. As such, we report here the current state-of-the-art cost- and time-effective approaches to perform genotyping of CRISPR/Cas9 experiments for the Xenopus tropicalis researcher.

The effects of endophytic bacterium SaMR12 on Sedum alfredii Hance metal ion uptake and the expression of three transporter family genes after cadmium exposure

A hydroponic experiment was conducted to investigate the effects of an endophytic bacterium SaMR12 on Sedum alfredii Hance metal ion accumulation, chlorophyll concentration, and the expression of three metal transporter families, zinc-regulated transporters, iron-regulated transporter-like protein (ZIP); natural resistance-associated macrophage protein; and heavy metal ATPase (HMA) at different Cd treatment levels. The results showed that at relatively low Cd conditions (≤25 μM), SaMR12 demonstrated a 19.5-27.5% increase in Fe, a 46.7-90.7% increase in Zn, and a 7.9-43.7% increase in Cu content in the shoot and elevated expression of SaIRT1, SaZIP3, SaHMA2, and SaNramp3 in the shoot and SaZIP1, SaHMA2, SaNramp1, and SaNramp3 in the root. At high Cd conditions (100 and 400 μM), SaMR12 demonstrated a 16.4-18.5% increase in leaf chlorophyll concentration, a 18.9-23.2% increase in Fe, and a 15.4-17.5% increase in Mg content in the shoot and elevated expression of SaZIP3, SaNramp6, SaHMA2, and SaHMA3 in the shoot and SaZIP3, SaNarmp1, SaNarmp3, and SaNarmp6 in the root. These results indicated that SaMR12 can elevate essential metal ion uptake and regulate the expression of transport genes to promote plant growth and enhance Cd tolerance and uptake to improve Cd accumulation up to 118-130%.

Molecular features of the cytotoxicity of an NHE inhibitor: Evidence of mitochondrial alterations, ROS overproduction and DNA damage

BACKGROUND

NH exchangers (NHEs) play a crucial role in regulating intra/extracellular pH, which is altered in cancer cells, and are therefore suitable targets to alter cancer cell metabolism in order to inhibit cell survival and proliferation. Among NHE inhibitors, amiloride family members are commonly used in clinical practice as diuretics; we focused on the amiloride HMA, reporting a net cytotoxic effect on a panel of human cancer cell lines; now we aim to provide new insights into the molecular events leading to cell death by HMA.

METHODS

Colon cancer cell lines were treated with HMA and analysed with: morphological and cellular assays for cell viability and death, and autophagy; biochemical approaches to evaluate mitochondrial function and ROS production; in situ detection of DNA damage; molecular tools to silence crucial autophagy/necroptosis factors.

RESULTS

HMA affects cellular morphology, alters mitochondrial structure and function, causes an increase in ROS, which is detrimental to DNA integrity, stimulates poly(ADP-ribose) synthesis, activates RIPK3-dependent death and triggers autophagy, which is unable to rescue cell survival. These features are hot points of an intricate network of processes, including necroptosis and autophagy, regulating the homeostasis between survival and death.

CONCLUSION

Our results allow the identification of multiple events leading to cell death in cancer cells treated with HMA. The here-defined intricate network activated by HMA could be instrumental to selectively target the key players of each pathway in the attempt to improve the global response to HMA. Our data could be the starting point for developing a newly designed targeted therapy.

A clinical-molecular update on azanucleoside-based therapy for the treatment of hematologic cancers

The azanucleosides azacitidine and decitabine are currently used for the treatment of acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS) in patients not only eligible for intensive chemotherapy but are also being explored in other hematologic and solid cancers. Based on their capacity to interfere with the DNA methylation machinery, these drugs are also referred to as hypomethylating agents (HMAs). As DNA methylation contributes to epigenetic regulation, azanucleosides are further considered to be among the first true “epigenetic drugs” that have reached clinical application. However, intriguing new evidence suggests that DNA hypomethylation is not the only mechanism of action for these drugs. This review summarizes the experience from more than 10 years of clinical practice with azanucleosides and discusses their molecular actions, including several not related to DNA methylation. A particular focus is placed on possible causes of primary and acquired resistances to azanucleoside treatment. We highlight current limitations for the success and durability of azanucleoside-based therapy and illustrate that a better understanding of the molecular determinants of drug response holds great potential to overcome resistance.

Genome-wide characterization of soybean P 1B -ATPases gene family provides functional implications in cadmium responses

BACKGROUND

The P1B-ATPase subfamily is an important group involved in transporting heavy metals and has been extensively studied in model plants, such as Arabidopsis thaliana and Oryza sativa. Emerging evidence indicates that one homolog in Glycine max is also involved in cadmium (Cd) stress, but the gene family has not been fully investigated in soybean.

RESULTS

Here, we identified 20 heavy metal ATPase (HMA) family members in the soybean genome, presented as 10 paralogous pairs, which is significantly greater than the number in Arabidopsis or rice, and was likely caused by the latest whole genome duplication event in soybean. A phylogenetic analysis divided the 20 members into six groups, each having conserved or divergent gene structures and protein motif patterns. The integration of RNA-sequencing and qRT-PCR data from multiple tissues provided an overall expression pattern for the HMA family in soybean. Further comparisons of expression patterns and the single nucleotide polymorphism distribution between paralogous pairs suggested functional conservation and the divergence of HMA genes during soybean evolution. Finally, analyses of the HMAs expressed in response to Cd stress provided evidence on how plants manage Cd tolerance, at least in the two contrasting soybean genotypes examined.

CONCLUSIONS

The genome-wide identification, chromosomal distribution, gene structures, and evolutionary and expression analyses of the 20 HMA genes in soybean provide an overall insight into their potential involvement in Cd responses. These results will facilitate further research on the HMA gene family, and their conserved and divergent biological functions in soybean.

Detection of Multiple Genome Modifications Induced by the CRISPR/Cas9 System

The recent remarkable innovation of an RNA-guided nuclease system, the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) system, enables us the modification of specific genomic loci in various model animals including zebrafish. With this system, multiple guide RNAs simultaneously injected with the Cas9 nuclease into zebrafish embryos cause multiple genome modifications at different genomic loci with high efficiency; therefore, a simple method to detect individual mutations at distinct loci is desired. In this chapter, we describe a procedure for inducing multiple CRISPR/Cas9-mediated genome modifications in zebrafish and a convenient method to detect CRISPR/Cas9-induced insertion and/or deletion (indel) mutations using a heteroduplex mobility assay (HMA).

Genotypic variations in the dynamics of metal concentrations in poplar leaves: a field study with a perspective on phytoremediation

Poplar is commonly used for phytoremediation of metal polluted soils. However, the high concentrations of trace elements present in leaves may return to soil upon leaf abscission. To investigate the mechanisms controlling leaf metal content, metal concentrations and expression levels of genes involved in metal transport were monitored at different developmental stages on leaves from different poplar genotypes growing on a contaminated field. Large differences in leaf metal concentrations were observed among genotypes. Whereas Mg was remobilized during senescence, Zn and Cd accumulation continued until leaf abscission in all genotypes. A positive correlation between Natural Resistance Associated Macrophage Protein 1 (NRAMP1) expression levels and Zn bio-concentration factors was observed. Principal component analyses of metal concentrations and gene expression levels clearly discriminated poplar genotypes. This study highlights a general absence of trace element remobilization from poplar leaves despite genotype specificities in the control of leaf metal homeostasis.

HPLC separation of human serum albumin isoforms based on their isoelectric points

Human serum albumin (HSA) is the most abundant protein in plasma. Cys34, the only free Cys residue, is the predominant plasma thiol and a relevant sacrificial antioxidant. Both in vivo circulating HSA and pharmaceutical preparations are heterogeneous with respect to the oxidation state of Cys34. In this work, we developed an external pH gradient chromatofocusing procedure that allows the analysis of the oxidation status of HSA in human plasma and biopharmaceutical products based on the different apparent isoelectric points and chemical properties of the redox isoforms. Specifically, reduced-mercury blocked HSA (HSA-SHg(+)), HSA with Cys34 oxidized to sulfenic acid (HSA-SOH) and HSA oxidized to sulfinate anion (HSA-SO2(-)) can be separated with resolutions of 1.4 and 3.1 (first and last pair) and hence quantified and purified. In addition, an N-terminally degraded isoform (HSA3-585) in different redox states can be resolved as well. Confirmation of the identity of the chromatofocusing isolated isoforms was achieved by high resolution whole protein MS. It is proposed that the chromatofocusing procedure can be used to produce more exact and complete descriptions of the redox status of HSA in vivo and in vitro. Finally, the scalability capabilities of the chromatofocusing procedure allow for the preparation of highly pure standards of several redox isoforms of HSA.

Oxidative albumin damage in chronic liver failure: relation to albumin binding capacity, liver dysfunction and survival

BACKGROUND & AIMS

Impaired binding function of albumin has been demonstrated in end-stage liver disease. This and other functional disturbances of albumin may be related to oxidative stress which is believed to play an important role in the pathogenesis of liver failure as well as sepsis. The aim of the present study was to relate oxidative modification of albumin to loss of albumin binding function in advanced chronic liver failure and in sepsis.

METHODS

Patients with decompensated cirrhosis or sepsis and healthy controls were investigated. Three fractions of albumin were separated by chromatography according to the redox state of cysteine-34: non-oxidized human mercaptalbumin, reversibly oxidized human non-mercaptalbumin-1, and irreversibly oxidized human non-mercaptalbumin-2 (HNA2). Binding properties of albumin site II were measured using dansylsarcosine as a ligand.

RESULTS

Both in cirrhotic and septic patients, fractions of oxidized albumin were increased and binding capacity for dansylsarcosine was decreased. Mass spectroscopy confirmed specific oxidation of cysteine-34. In cirrhotic patients, dansylsarcosine binding correlated strongly with liver function parameters and moderately with HNA2. Baseline levels of HNA2 accurately predicted 30-day and 90-day survival in cirrhotic patients and this was confirmed in an external validation cohort.

CONCLUSIONS

Our results suggest that oxidative damage impairs binding properties of albumin. In advanced liver disease, reduced binding capacity of albumin site II is mainly related to impaired liver function. The plasma level of HNA2 is closely related to survival and may represent a novel biomarker for liver failure.

Zinc uptake and radial transport in roots of Arabidopsis thaliana: a modelling approach to understand accumulation

BACKGROUND AND AIMS

Zinc uptake in roots is believed to be mediated by ZIP (ZRT-, IRT-like proteins) transporters. Once inside the symplast, zinc is transported to the pericycle, where it exits by means of HMA (heavy metal ATPase) transporters. The combination of symplastic transport and spatial separation of influx and efflux produces a pattern in which zinc accumulates in the pericycle. Here, mathematical modelling was employed to study the importance of ZIP regulation, HMA abundance and symplastic transport in creation of the radial pattern of zinc in primary roots of Arabidopsis thaliana.

METHODS

A comprehensive one-dimensional dynamic model of radial zinc transport in roots was developed and used to conduct simulations. The model accounts for the structure of the root consisting of symplast and apoplast and includes effects of water flow, diffusion and cross-membrane transport via transporters. It also incorporates the radial geometry and varying porosity of root tissues, as well as regulation of ZIP transporters.

KEY RESULTS

Steady-state patterns were calculated for various zinc concentrations in the medium, water influx and HMA abundance. The experimentally observed zinc gradient was reproduced very well. An increase of HMA or decrease in water influx led to loss of the gradient. The dynamic behaviour for a change in medium concentration and water influx was also simulated showing short adaptation times in the range of seconds to minutes. Slowing down regulation led to oscillations in expression levels, suggesting the need for rapid regulation and existence of buffering agents.

CONCLUSIONS

The model captures the experimental findings very well and confirms the hypothesis that low abundance of HMA4 produces a radial gradient in zinc concentration. Surprisingly, transpiration was found also to be a key parameter. The model suggests that ZIP regulation takes place on a comparable timescale as symplastic transport.

Redox properties of serum albumin

BACKGROUND

Oxidative damage results in protein modification, and is observed in numerous diseases. Human serum albumin (HSA), the most abundant circulating protein in the plasma, exerts important antioxidant activities against oxidative damage.

SCOPE OF REVIEW

The present review focuses on the characterization of chemical changes in HSA that are induced by oxidative damage, their relevance to human pathology and the most recent advances in clinical applications.

MAJOR CONCLUSIONS

The antioxidant properties of HSA are largely dependent on Cys34 and its contribution to the maintenance of intravascular homeostasis, including protecting the vascular endothelium under disease conditions related to oxidative stress. Recent studies also evaluated the susceptibility of other important amino acid residues to free radicals. The findings suggest that a redox change in HSA is related to the oxidation of several amino acid residues by different oxidants. Further, Cys34 adducts, such as S-nitrosylated and S-guanylated forms also play an important role in clinical applications. On the other hand, the ratio of the oxidized form to the normal form of albumin (HMA/HNA), which is a function of the redox states of Cys34, could serve as a useful marker for evaluating systemic redox states, which would be useful for the evaluation of disease progression and therapeutic efficacy.

GENERAL SIGNIFICANCE

This review provides new insights into our current understanding of the mechanism of HSA oxidation, based on in vitro and in vivo studies. This article is part of a Special Issue entitled Serum Albumin.

Implications of a zinc uptake and transport model

While physicists regularly use mathematical equations to describe natural phenomena, mathematical modeling of biological systems is still not well established and is hampered by communication barriers between experimental and theoretical biologists. In a recent study we developed a mathematical model of zinc uptake and radial transport in Arabidopsis thaliana roots. By refraining from writing many equations in the main text and confining the derivation of formulas to a supplemental file, we attempted to reach both experimentalists and theoreticians likewise. Here, we give a short summary of our results on the accumulation pattern of zinc and the importance of transporter regulation, water flow and geometry. For a better understanding of the dynamics of adaptation to changes in external conditions, we plead for more detailed and frequent measurements. As a new aspect, we analyzed the effect of buffering. Simulations indicate that it dampens oscillations and may therefore play a key role in zinc homeostasis.

Use of the heteroduplex mobility assay and cell sorting to select genome sequences of the CCR5 gene in HEK 293T cells edited by transcription activator-like effector nucleases

Engineered nucleases such as zinc finger nucleases (ZFN) and transcription activator-like effector nucleases (TALEN) are one of the most promising tools for modifying genomes. These site-specific enzymes cause double-strand breaks that allow gene disruption or gene insertion, thereby facilitating genetic manipulation. The major problem associated with this approach is the labor-intensive procedures required to screen and confirm the cellular modification by nucleases. In this work, we produced a TALEN that targets the human CCR5 gene and developed a heteroduplex mobility assay for HEK 293T cells to select positive colonies for sequencing. This approach provides a useful tool for the quick detection and easy assessment of nuclease activity.

The role of heavy-metal ATPases, HMAs, in zinc and cadmium transport in rice

The P(1B)-type heavy metal ATPases (HMAs) are diverse in terms of tissue distribution, subcellular localization, and metal specificity. Functional studies of HMAs have shown that these transporters can be divided into two subgroups based on their metal-substrate specificity: a copper (Cu)/silver (Ag) group and a zinc (Zn)/cobalt (Co)/cadmium (Cd)/lead (Pb) group. Studies on Arabidopsis thaliana and metal hyperaccumulator plants indicate that HMAs play an important role in the translocation or detoxification of Zn and Cd in plants. Rice possesses nine HMA genes, of which OsHMA1-OsHMA3 belong to the Zn/Co/Cd/Pb subgroup. OsHMA2 plays an important role in root-to-shoot translocation of Zn and Cd, and participates in Zn and Cd transport to developing seeds in rice. OsHMA3 transports Cd and plays a role in the sequestration of Cd into vacuoles in root cells. Modification of the expression of these genes might be an effective approach for reducing the Cd concentration in rice grains.