GeneMiner: A tool for extracting phylogenetic markers from next-generation sequencing data.

The advancement of next-generation sequencing (NGS) technologies has been revolutionary for the field of evolutionary biology. This technology has led to an abundance of available genomes and transcriptomes for researchers to mine. Specifically, researchers can mine for various types of molecular markers that are vital for phylogenetic, evolutionary and ecological studies. Numerous tools have been developed to extract these molecular markers from NGS data. However, due to an insufficient number of well-annotated reference genomes for non-model organisms, it remains challenging to obtain these markers accurately and efficiently. Here, we present GeneMiner, an improved and expanded version of our previous tool, Easy353. GeneMiner combines the reference-guided de Bruijn graph assembly with seed self-discovery and greedy extension. Additionally, it includes a verification step using a parameter-bootstrap method to reduce the pitfalls associated with using a relatively distant reference. Our results, using both experimental and simulation data, showed GeneMiner can accurately acquire phylogenetic molecular markers for plants using transcriptomic, genomic and other NGS data. GeneMiner is designed to be user-friendly, fast and memory-efficient. Further, it is compatible with Linux, Windows and macOS. All source codes are publicly available on GitHub (https://github.com/sculab/GeneMiner) and Gitee (https://gitee.com/sculab/GeneMiner) for easy accessibility and transparency.

Easy353: A Tool to Get Angiosperms353 Genes for Phylogenomic Research.

The Angiosperms353 gene set (AGS) consists of a set of 353 universal low-copy nuclear genes that were selected by examining more than 600 angiosperm species. These genes can be used for phylogenetic studies and population genetics at multiple taxonomic scales. However, current pipelines are not able to recover Angiosperms353 genes efficiently and accurately from high-throughput sequences. Here, we developed Easy353, a reference-guided assembly tool to recover the AGS from high-throughput sequencing (HTS) data (including genome skimming, RNA-seq, and target enrichment). Easy353 is an open-source user-friendly assembler for diverse types of high-throughput data. It has a graphical user interface and a command-line interface that is compatible with all widely-used computer systems. Evaluations, based on both simulated and empirical data, suggest that Easy353 yields low rates of assembly errors.

HDAC3 Silencing Enhances Acute B Lymphoblastic Leukaemia Cells Sensitivity to MG-132 by Inhibiting the JAK/Signal Transducer and Activator of Transcription 3 Signaling Pathway.

PURPOSE: HDAC3, which is associated with smurf2, has been shown to be associated with poor prognosis in B-ALL. This study examined the efficacy of targeting HDAC3 combined with MG-132 as a possible therapeutic strategy for B-ALL patients. METHODS: Real-time PCR and western blot were used to measure the expression of smurf2 and HDAC3 from B-ALL patients bone marrow samples. Sup-B15 and CCRF-SB cells were treated with MG-132, small interfering RNA of smurf2 or HDAC3. A plasmid designed to up-regulate smurf2 expression was transfected into B-ALL cells. Flow cytometry and western blot were used to measure variation due to these treatments in terms of apoptosis and cell cycle arrest. RESULTS: Expression of Smurf2 and HDAC3 mRNA were inversely related in B-ALL patients. Up-regulation of smurf2 or MG-132 influenced HDAC3, further inhibiting the JAK/signal transducer and activator of transcription 3 (STAT3) signal pathway and inducing apoptosis in B-ALL cells. When we treated Sup-B15 and CCRF-SB cells with siHDAC3 and MG-132 for 24 h, silencing HDAC3 enhanced the apoptosis rate induced by MG-132 in B-ALL cells and further inhibited the JAK/STAT3 pathway. Furthermore, MG-132 was observed to cause G2/M phase arrest in B-ALL cells and inhibited the JAK/STAT3 pathway, leading to apoptosis. CONCLUSIONS: Silencing of HDAC3 enhanced the sensitivity of B-ALL cells to MG-132. The combination of targeting HDAC3 and MG-132 may provide a new avenue for clinical treatment of acute B lymphocytic leukaemia and improve the poor survival of leukaemia patients.

Overexpression of heme oxygenase-1 in microenvironment mediates vincristine resistance of B-cell acute lymphoblastic leukemia by promoting vascular endothelial growth factor secretion.

Chemoresistance often causes treatment failure of B-cell acute lymphoblastic leukemia (B-ALL). However, the mechanism remains unclear at present. Herein, overexpression of heme oxygenase-1 (HO-1) was found in the bone marrow stromal cells (BMSCs) from B-ALL patients developing resistance to vincristine (VCR), a chemotherapeutic agent. Two B-ALL cell lines Super B15 and CCRF-SB were cocultured with BMSCs transfected with lentivirus to regulate the expression of HO-1. Silencing HO-1 expression in BMSCs increased the apoptotic rates of B-ALL cell lines induced by VCR, whereas upregulating HO-1 expression reduced the rate. Cell cycle can be arrested in the G2/M phase by VCR. In contrast, B-ALL cells were arrested in the G0/G1 phase due to HO-1 overexpression in BMSCs, which avoided damage from the G2/M phase. Vascular endothelial growth factor (VEGF) in BMSCs, as a key factor in the microenvironment-associated chemoresistance, was also positively coexpressed with HO-1. VEGF secretion was markedly increased in BMSCs with HO-1 upregulation but decreased in BMSCs with HO-1 silencing. B-ALL cell lines became resistant to VCR when cultured with VEGF recombinant protein, so VEGF secretion induced by HO-1 expression may promote the VCR resistance of B-ALL cells. As to the molecular mechanism, the PI3K/AKT pathway mediated regulation of VEGF by HO-1. In conclusion, this study clarifies a mechanism by which B-ALL is induced to resist VCR through HO-1 overexpression in BMSCs, and provides a novel strategy for overcoming VCR resistance in clinical practice.

Histone deacetylase inhibitor LMK-235-mediated HO-1 expression induces apoptosis in multiple myeloma cells via the JNK/AP-1 signaling pathway.

AIMS: Histone deacetylase inhibitors (HDACis) are promising anticancer drugs that open new areas of epigenetic drug discovery. Multiple myeloma (MM) is a malignant tumor of the blood system that is difficult to cure and often relapses. Here, we investigated the in vitro effects of a novel HDACi, LMK-235, on MM cells, and explored the underlying mechanisms. MAIN METHODS: Real-time PCR and western blot were used to measure the expression of HDAC4 and HO-1 in MM cells treated with LMK-235. si-RNA was used to transfect MM cells. Hemin or ZnPP was combined to regulate heme oxygenase-1 (HO-1), and a pathway inhibitor was added to measure changes in the JNK/AP-1 signaling pathway. Apoptosis and proliferation were assessed by flow cytometry and CCK-8 assay, respectively. KEY FINDINGS: We found that LMK-235, a selective inhibitor of class IIA HDAC4/5, induced apoptosis of MM cells by downregulating HO-1 that is closely related to HDAC4. LMK-235 increased phosphorylation of JNK and c -Jun in MM cells. Downregulation of HO-1 expression in combination with LMK-235 expression further activated phosphorylation of JNK and c-Jun and induced apoptosis in MM cells. When the JNK inhibitor SP600125 was used in combination, the apoptosis phenomenon was reversed. However, when HO-1 was upregulated, LMK-235-mediated phosphorylation of JNK and c-Jun was inhibited, and apoptosis of MM cells began to decrease. SIGNIFICANCE: These data suggest that LMK-235 has potent anti-myeloma activity through regulation of HO-1-induced apoptosis via the JNK/AP-1 pathway. This provides a new concept for the treatment of multiple myeloma.

Up-regulation of HO-1 promotes resistance of B-cell acute lymphocytic leukemia cells to HDAC4/5 inhibitor LMK-235 via the Smad7 pathway.

PURPOSE: HDAC4/5 and Smad7 are potential therapeutic targets for the onset and progression of B-cell acute lymphocytic leukemia (B-ALL) and indices for clinical prognosis. In contrast, HO-1 (heat shock protein 32) plays a key role in protecting tumor cells from apoptosis. METHODS: HDAC4/5, HO-1 and Smad7 expressions in 34 newly diagnosed B-ALL cases were detected by real-time PCR and Western blot. Lentivirus and small interference RNA were used to transfect B-ALL cells. The expression of Smad7 was detected after treatment with LMK-235 or Hemin and ZnPP. Apoptosis and proliferation were evaluated by flow cytometry, CCK-8 assay and Western blot. RESULTS: HDAC4/5 was overexpressed in B-ALL patients with high HO-1 levels. Increasing the concentration of HDAC4/5 inhibitor LMK-235 induced the decrease of Smad7 and HO-1 expressions and the apoptosis of B-ALL cells by suppressing the phosphorylation of AKT (Protein kinase B). Up-regulating HO-1 alleviated the decrease of Smad7 expression and enhanced B-ALL resistance to LMK-235 by activating p-AKT which reduced the apoptosis of B-ALL cells and influenced the survival of leukemia patients. Silencing Smad7 also augmented the apoptosis rate of B-ALL cells by suppressing p-AKT. CONCLUSION: HO-1 played a key role in protecting tumor cells from apoptosis, and HDAC4/5 were related with the apoptosis of B-ALL cells. LMK-235 may be able to improve the poor survival of leukemia patients.

Histone deacetylase inhibitor BG45-mediated HO-1 expression induces apoptosis of multiple myeloma cells by the JAK2/STAT3 pathway.

Multiple myeloma (MM) is a hematological malignancy that is characterized by the clonal expansion of plasma cells in the bone marrow. Histone deacetylases (HDACs) represent a new type of molecular targeted therapy for different types of cancers and promising targets for myeloma therapy. We showed that HDAC3 mRNA and protein levels of CD138 mononuclear cells from MM patients were higher than those in healthy donors. Therefore, we investigated the effects of a novel class I HDAC inhibitor BG45 on MM cells in vitro. BG45 downmodulated heme oxygenase 1 (HO-1) when class I HDACs decreased in MM cells. HO-1 is a target for the treatment of MM. Moreover, BG45 induced hyperacetylation of histone H3 and inhibited the growth, especially the apoptosis of MM cell lines. Treatment with BG45 induced apoptosis by downregulating bcl-2 and Bcl-xl, upregulating Bax and other antiapoptotic proteins and activating poly(ADP-ribose)polymerase, and decreasing protein levels of p-JAK2 and p-STAT3. These effects were partly blocked by HO-1. Correspondingly, BG45 led to an accumulation in the G0/G1 phase, accompanied by decreased levels of CDK4 and phospho-retinoblastoma protein, an increased level of p21, and a moderately reduced level of CDK2. Clinical use of single agents was limited because of toxic side effects and drug resistance. However, combining BG45 with lenalidomide exerted synergistic effects. In conclusion, we verified the potent antimyeloma activity of this novel HDAC inhibitor and that the combination of BG45 and lenalidomide is a new method for MM treatment. Thus, BG45 may be applicable to the treatment of MM and other hematological malignancies.

Electronic binding energy and thermal relaxation of Li and LiNa atomic alloying clusters.

We examined the effects of atomic hetero- and under-coordination on the relaxation of the interatomic bonding and electronic binding energy of Li and LiNa cluster alloying using a combination of the bond-order-length-strength correlation and density functional theory calculations. We found that bond nature alteration by heterocoordination, bond relaxation by thermal excitation and atomic coordination contribute intrinsically to the core-level energy shifts with resolution of the binding energy at the atomic sites of terrace edges, facets, and bulk of the LiNa alloy nanoclusters. Our strategies may simplify the complexity of core electron binding energies in analyzing the experimental data of the irregularly coordinating atoms.

Skin Bond Electron Relaxation Dynamics of Germanium Manipulated by Interactions with H2 , O2 , H2 O, H2 O2 , HF, and Au.

Although germanium performs amazingly well at sites surrounding hetero-coordinated impurities and under-coordinated defects or skins with unusual properties, having important impact on electronic and optical devices, understanding the behavior of the local bonds and electrons at such sites remains a great challenge. Here we show that a combination of density functional theory calculations, zone-resolved X-ray photoelectron spectroscopy, and bond order length strength correlation mechanism has enabled us to clarify the physical origin of the Ge 3d core-level shift for the under-coordinated (111) and (100) skin with and without hetero-coordinated H2 , O2 , H2 O, H2 O2 , HF impurities. The Ge 3d level shifts from 27.579 (for an isolated atom) by 1.381 to 28.960 eV upon bulk formation. Atomic under-coordination shifts the binding energy further to 29.823 eV for the (001) and to 29.713 eV for the (111) monolayer skin. Addition of O2 , HF, H2 O, H2 O2 and Au impurities results in quantum entrapment by different amounts, but H adsorption leads to polarization.

Atomistic bond relaxation, energy entrapment, and electron polarization of the RbN and CsN clusters (N ≤ 58).

We systematically examined the effect of atomic undercoordination on the performance of bonds and electrons of Rb and Cs atomic clusters and their solid skins using a combination of photoelectron spectrometric analysis and density functional theory calculations. Results show that atomic coordination number reduction shortens the bonds by up to 30% for the Rb13 and Cs13 clusters, which densifies the local electrons and entraps their binding energies. Consistency between predictions and observations revealed that the Rb 4p level shifts from 13.654 eV for an isolated atom to a bulk value of 14.940 eV and the Cs 5p level shifts from 10.284 to 11.830 eV upon bulk formation. Such core-electron densification and entrapment polarize the valence charge from the inner to the outermost layer of skins, which perturbs the local Hamiltonian and hence dictates the unusual behavior of the Rb and Cs solid skins and nanocrystals.