Pharmacokinetic and oral bioavailability study of schaftoside in rats.

A simple and sensitive LC-tandem mass spectrometry method was established and validated for the determination of schaftoside in rat plasma. After prepared by protein precipitation with acetonitrile, schaftoside and internal standard were separated on a Waters HSS T3 column using acetonitrile containing 0.1% formic acid and 0.1% formic acid in water as the mobile phase by gradient elution. The method showed excellent linearity over the range of 0.5-500 ng/mL with acceptable intra- and inter-day precision, accuracy, matrix effect, and recovery. The stability assay indicated that schaftoside was stable during the sample acquisition, preparation, and storage. The method was applied to a pharmacokinetic study of schaftoside in rats. The result suggested that after intravenous administration at a dose of 1 mg/kg, schaftoside was quickly eliminated from the plasma with an elimination half-life of 0.58 h. After oral administration at doses of 5, 10, and 20 mg/kg, schaftoside was quickly absorbed into the plasma and reached the peak concentration (Cmax) of 45.1-104.99 ng/mL at 0.67-1.17 h. The increase of exposure (area under the curve) was linear with the increase of dose. The oral bioavailability was 0.42%-0.71% in the range of 5-20 mg/kg.

Haplotype-resolved karyotype construction from Hi-C data using refLinker.

Chromosomal aberrations are prevalent in cancer genomes, yet it remains challenging to resolve the long-range structure of rearranged chromosomes. A key problem is to determine the chromosomal origin of rearranged genomic segments, which requires chromosome-length haplotype information. Here we describe refLinker, a new computational method for whole-chromosome haplotype inference using external reference panels and Hi-C. We show that refLinker ensures consistent long-range phasing accuracy in both diploid human genomes and aneuploid cancers, including regions with loss-of-heterozygosity and high-level focal amplification. We further demonstrate the feasibility of complex genome reconstruction using haplotype-specific Hi-C contacts, revealing new karyotype features in two widely studied cancer cell lines. Together, these findings provide a new framework for the complete resolution of long-range chromosome structure in complex genomes and highlight the unique advantages of Hi-C data for reconstructing cancer genomes with chromosome-scale continuity.

Gooderoside A from Anoectochilus elatus attenuates acute and chronic pains by inhibiting NO/cGMP and IRAK4/IRAK1/TAK1 signaling pathways.

ETHNOPHARMACOLOGICAL RELEVANCE: Anoectochilus elatus Lindl. was traditionally used for pain treatment and Gooderoside A (GA) was regarded as its principal constituent. AIM OF THE STUDY: To investigate whether GA can be responsible for the antinociceptive activity of A. elatus and explore its underlying mechanism. MATERIALS AND METHODS: Acetic acid-induced abdominal writhing and tail flick tests were employed to evaluate the antinociceptive activity of ethanolic extract of A. elatus (EEA) and GA. Formalin test was used to ascertain the antinociceptive pattern of GA. Entobarbital sodium induced sleep test was adopted to exclude its hypnotic effect, while open-field test was performed to rule out its motor impairment effect. Chronic constriction injury (CCI)-induced neuropathic pain in rats was developed to evaluate its efficacy on neuropathic pain, and BV-2 cells were used to explore the underlying mechanism. RESULTS: EEA and GA, significantly inhibited chemical and thermal nociception. GA suppressed nociception in formalin test in both phase I and II, whereas methylene blue and L-NAME partially reversed its efficacy. GA located inner and slightly blocked sodium channel current, and did not show any hypnotic effect or motor impairment effect. Crucially, GA markedly attenuated chronic neuropathic pain in rats, inhibited the phosphorylation of IRAK4, IRAK1 and TAK1, and suppressed MAPKs pathway in BV-2 cells. CONCLUSION: GA relieved acute and chronic pains in vivo. The mechanism of action involves the blocking of NO/cGMP and IRAK4/IRAK1/TAK1 pathways. These results suggested GA may be a promising candidate for antinociceptive drug development.

Genomic signatures of past and present chromosomal instability in Barrett's esophagus and early esophageal adenocarcinoma.

The progression of precancerous lesions to malignancy is often accompanied by increasing complexity of chromosomal alterations but how these alterations arise is poorly understood. Here we perform haplotype-specific analysis of chromosomal copy-number evolution in the progression of Barrett's esophagus (BE) to esophageal adenocarcinoma (EAC) on multiregional whole-genome sequencing data of BE with dysplasia and microscopic EAC foci. We identify distinct patterns of copy-number evolution indicating multigenerational chromosomal instability that is initiated by cell division errors but propagated only after p53 loss. While abnormal mitosis, including whole-genome duplication, underlies chromosomal copy-number changes, segmental alterations display signatures of successive breakage-fusion-bridge cycles and chromothripsis of unstable dicentric chromosomes. Our analysis elucidates how multigenerational chromosomal instability generates copy-number variation in BE cells, precipitates complex alterations including DNA amplifications, and promotes their independent clonal expansion and transformation. In particular, we suggest sloping copy-number variation as a signature of ongoing chromosomal instability that precedes copy-number complexity. These findings suggest copy-number heterogeneity in advanced cancers originates from chromosomal instability in precancerous cells and such instability may be identified from the presence of sloping copy-number variation in bulk sequencing data.

A genetic basis for cancer sex differences revealed in Xp11 translocation renal cell carcinoma.

Xp11 translocation renal cell carcinoma (tRCC) is a female-predominant kidney cancer driven by translocations between the TFE3 gene on chromosome Xp11.2 and partner genes located on either chrX or on autosomes. The rearrangement processes that underlie TFE3 fusions, and whether they are linked to the female sex bias of this cancer, are largely unexplored. Moreover, whether oncogenic TFE3 fusions arise from both the active and inactive X chromosomes in females remains unknown. Here we address these questions by haplotype-specific analyses of whole-genome sequences of 29 tRCC samples from 15 patients and by re-analysis of 145 published tRCC whole-exome sequences. We show that TFE3 fusions universally arise as reciprocal translocations with minimal DNA loss or insertion at paired break ends. Strikingly, we observe a near exact 2:1 female:male ratio in TFE3 fusions arising via X:autosomal translocation (but not via X inversion), which accounts for the female predominance of tRCC. This 2:1 ratio is at least partially attributable to oncogenic fusions involving the inactive X chromosome and is accompanied by partial re-activation of silenced chrX genes on the rearranged chromosome. Our results highlight how somatic alterations involving the X chromosome place unique constraints on tumor initiation and exemplify how genetic rearrangements of the sex chromosomes can underlie cancer sex differences.

Heritable transcriptional defects from aberrations of nuclear architecture.

Transcriptional heterogeneity due to plasticity of the epigenetic state of chromatin contributes to tumour evolution, metastasis and drug resistance1-3. However, the mechanisms that cause this epigenetic variation are incompletely understood. Here we identify micronuclei and chromosome bridges, aberrations in the nucleus common in cancer4,5, as sources of heritable transcriptional suppression. Using a combination of approaches, including long-term live-cell imaging and same-cell single-cell RNA sequencing (Look-Seq2), we identified reductions in gene expression in chromosomes from micronuclei. With heterogeneous penetrance, these changes in gene expression can be heritable even after the chromosome from the micronucleus has been re-incorporated into a normal daughter cell nucleus. Concomitantly, micronuclear chromosomes acquire aberrant epigenetic chromatin marks. These defects may persist as variably reduced chromatin accessibility and reduced gene expression after clonal expansion from single cells. Persistent transcriptional repression is strongly associated with, and may be explained by, markedly long-lived DNA damage. Epigenetic alterations in transcription may therefore be inherently coupled to chromosomal instability and aberrations in nuclear architecture.

Simultaneous determination of abrine, hypaphorine, schaftoside and soyasaponin Bb in rat plasma by UPLC-MS/MS and its application to a pharmacokinetic study after oral administration of Abrus cantoniensis Hance extract.

A simple and sensitive liquid chromatography tandem mass spectrometry method was established and validated for the quantitative determination of abrine, hypaphorine, schaftoside and soyasaponin Bb in rat plasma. After preparation by protein precipitation with acetonitrile, the analytes and internal standard were separated on a Waters CORTECS T3 column using acetonitrile containing 0.1% formic acid and 0.1% formic acid in water as mobile phase by gradient elution in 2 min. The method showed excellent linearity over the range of 5-500 ng/ml with acceptable intra- and inter-day precision, accuracy, matrix effect and recovery. The stability assay indicated that the four analytes were stable during the analysis process. The method was applied to a pharmacokinetic study of Abrus cantoniensis Hance in rats. The result suggested that after oral administration, the four analytes were quickly absorbed into the plasma. The dose-normalized exposure of hypaphorine was the highest with a long elimination half-life (t1/2 9.83 h), followed by abrine and schaftoside with t1/2 values of 1.07 and 1.15 h. The dose normalized exposure of soyasaponin Bb was the lowest, which is possibily due to the high polarity and poor permeability. This study provides a basis for elucidating the material foundation of A. cantoniensis Hance.

Total lignans from Vitex negundo seeds attenuate osteoarthritis and their main component vitedoin A alleviates osteoclast differentiation by suppressing ERK/NFATc1 signaling.

The seeds of Vitex negundo have been used for inflammation-related disease treatment in traditional medicine. This study focused on the anti-osteoarthritis (OA) effects of the total lignans of V. negundo seeds (TOV) in monosodium iodoacetate-induced osteoarthritis rats and its pharmacokinetic properties, as well as the effects and potential mechanism of its main components VN1 (6-hydroxy-4-(4-hydroxy-3-methoxy-phenyl)-3-hydro-xymethyl-7-methoxy-3,4-dihydro-2-naphthaldehydeb) and VN2 (vitedoin A) on receptor activator of NF-κB ligand (RANKL)-induced osteoclast differentiation in bone marrow macrophages (BMMs). TOV significantly attenuated osteoarthritis, leading to an increase in pain thresholds, improvement of knee articular cartilages and chondrocytes loss, and decreased total joint scores and serum levels of TNF-α, interleukin-1ß (IL-1ß), and prostaglandin E2 (PGE2) in osteoarthritis rats. The half-time (T1/2 ) was 2.82 h and 1.33 h, and the bioavailability was 15.34%-21.89% and 16.29%-22.11%, for VN1 and VN2, respectively. VN2, rather than VN1, remarkably inhibited tartrate-resistant acid phosphatase (TRAP) activity, reduced the number of TRAP-positive multinuclear cells, diminished the formation of actin ring, and decreased mRNA levels of cathepsin K (CTSK), TRAP, nuclear factor of activated T cell 1 (NFATc1), and osteoclast-associated receptor, as well as downregulated protein levels of p-ERK (phosphorylated extracellular signal-regulated kinase), TRAP, CTSK and NFATc1 in BMMs. These findings suggest TOV has promising therapeutic potential for OA treatment and VN2, in particular, attenuates osteoclast differentiation by suppressing ERK/NFATc1 signaling and actin ring, mainly accounting for the anti-OA efficacy of TOV.

A comparison review of Hehuan flowers and Hehuan bark on the traditional applications, phytochemistry and pharmacological effects.

ETHNOPHARMACOLOGICAL RELEVANCE: Albizia julibrissin Durazz is a well-known medicinal plant with the Chinese name Hehuan []. Hehuan bark and Hehuan flowers have long been recognized as traditional Chinese herbal medicine for treating anxiety, melancholy, insomnia, bruises, pulmonary abscess, fractures, carbuncle, amnesia, acute conjunctivitis, blurred vision, neonatal tetanus and stroke for thousands of years. They are recorded in Chinese Pharmacopoeia separately with different properties. Until now, new chemical constituents and pharmacological activities of Hehuan have been continuously studied and revealed. THE AIM OF THE REVIEW: This review aims to provide a comprehensive summary of traditional applications, phytochemistry, pharmacology effects, and toxicology of Hehuan bark and Hehuan flowers, and give critical assessment and point out the promising direction for further research on Hehuan. MATERIAL AND METHODS: A literature search was undertaken on Hehuan bark and Hehuan flowers by analyzing the information from scientific databases (SciFinder, Pubmed, Elsevier, Google Scholar, Web of Science, and Baidu Scholar). We also gathered the information of Hehuan from classic herbal literatures and conference papers on ethnopharmacology. RESULTS: According to Chinese and English documents, the medicinal history of Hehuan in China can be traced back to ad 25. Meanwhile, its medicinal history as a kind of herbal medicine can also be found in other Asian countries. So far about 140 compounds have been isolated from Hehuan bark and Hehuan flowers, including triterpenoids, flavonoids, lignans, phenolic acids, alkaloids, etc. Among them, flavonoids mainly exist in Hehuan flowers, while Hehuan bark contains lignans and saponins. The composition differences between the barks and flowers of Hehuan account for the different effects and applications. Modern pharmacological studies have indicated that crude extracts and pure compounds of Hehuan flowers and Hehuan bark have multiple pharmacological activities, such as antineoplastic, immunomodulatory, anti-inflammatory, anxiolytic, antidepressant, metabolic regulation, anti-insomnia, neuroprotective, hepatoprotective, sedative, and anti-osteolytic activities. CONCLUSIONS: Hehuan (Albizia julibrissin Durazz) is traditionally used to relieve depression, calm nerves, promote blood circulation and reduce swelling. Modern pharmacological studies have revealed that natural products from Hehuan bark and Hehuan flowers possess extensive pharmacological activities in treating cancer, enhancing immunity, regulating metabolism, improving mental state, etc. These properties make it great clinical application potential. Further research on natural pharmaceutical chemistry, pharmacology, toxicology, pharmacokinetics, and quality standards of Hehuan are still required to verify the efficacy and safety for future clinical applications.

Determining Complete Chromosomal Haplotypes by mLinker.

Haplotype ("haploid genotype") phase is the combination of genotypes at sites of genetic variation along a chromosome [1]. We previously demonstrated that the complete chromosomal haplotype of diploid human genomes can be determined using molecular linkage from Hi-C sequencing and linked-reads sequencing [2]. In this chapter, we present a step-by-step guide to perform this analysis using mLinker, a software package for haplotype inference.

Hsa_circ_0012919 promotes pyroptosis in CD4+T cells of systemic lupus erythematous by miR-125a-3p/GSDMD axis.

The etiology of systemic lupus erythematous (SLE) remains unclear. Pyroptosis, a new model of programmed cell death, was poorly explored in the pathogenesis of SLE. We found cell pyroptosis in CD4+T cells of SLE patients and kidneys from MRL/lpr mice by examining caspase-1 and gasdermin D (GSDMD) in by RT-PCR, Western blot, and levels of IL-1ß, IL-18 and TNF-α were detected by RT-PCR and Elisa. Expression of caspase-1 and GSDMD and levels of IL-1ß, IL-18, TNF-α decreased significantly after downregulation of hsa_circ_0012919 (p < 0.05). Inhibition of miR-125a-3p enhanced expression of caspase-1 and GSDMD (p < 0.05), and increased the release of IL-1ß, IL-18 and TNF-α (p < 0.05), thereby counteracting the effect of hsa_circ_0012919 knockdown on pyroptosis. Finally, we identified GSDMD as the target gene of miR-125a-3p. Silencing GSDMD reversed the effect of 5-aza-deoxycytidine in increasing release of IL-1ß, IL-18, TNF-α and activating caspase-1, but it could be reversed by miR-125a-3p inhibitor. In conclusion, hsa_circ_0012919 regulated the pyroptosis in the CD4+ T cells of SLE patients by miR-125a-3p/GSDMD axis.

Trichoderma species from plant and soil: An excellent resource for biosynthesis of terpenoids with versatile bioactivities.

BACKGROUND: Trichoderma species are rich source of bioactive secondary metabolites. In the past decades, a series of secondary metabolites were reported from different Trichoderma fungi, among which terpenoids possessing versatile structural diversities and extensive pharmacological activities are one of the particularly important categories. AIM OF REVIEW: The review aims to summarize the terpenoids isolated from Trichoderma species regarding their structural diversities, biological activities, and promising biosynthetic potentials. KEY SCIENTIFIC CONCEPTS OF REVIEW: So far, a total of 253 terpenoids, including 202 sesquiterpenes, 48 diterpenes, 2 monoterpenes and 1 meroterpenoid, were isolated and identified from Trichoderma species between 1948 and 2022. Pharmacological investigations of Trichoderma terpenoids mainly focused on their antibacterial activities, antifungal activities, inhibitory activities on marine plankton species and cytotoxic activities, indicating that Trichoderma species are important microbial agents for drug discovery and environmentally friendly agrochemicals development. Intriguing chemistry and enzymology involved in the biosynthesis of Trichoderma terpenoids were also presented to facilitate further precise genome mining-guided novel structure discovery. Taken together, the abundance of novel skeletons, bioactivities and biosynthetic potentials presents new opportunities for drug and agrochemicals discovery, genome mining and enzymology exploration from Trichoderma species. The work will provide references for the profound study of terpenoids derived from Trichoderma, and facilitate further studies on Trichoderma species in the areas of chemistry, medicine, agriculture and microbiology.

Examining the cooperation between extrachromosomal DNA circles.

In a departure from previous findings, new results suggest that free-floating pieces of DNA which carry additional copies of cancer-driving genes do not tend to cluster or have increased transcription.

Somatic XIST activation and features of X chromosome inactivation in male human cancers.

Expression of the non-coding RNA XIST is essential for initiating X chromosome inactivation (XCI) during early development in female mammals. As the main function of XCI is to enable dosage compensation of chromosome X genes between the sexes, XCI and XIST expression are generally absent in male normal tissues, except in germ cells and in individuals with supernumerary X chromosomes. Via a systematic analysis of public sequencing data of both cancerous and normal tissues, we report that XIST is somatically activated in a subset of male human cancers across diverse lineages. Some of these cancers display hallmarks of XCI, including silencing of gene expression, reduced chromatin accessibility, and increased DNA methylation across chromosome X, suggesting that the developmentally restricted, female-specific program of XCI can be somatically accessed in male cancers.

Synthesis of harmine-nitric oxide donor derivatives as potential antitumor agents.

To further improve the anti-tumor activity of Harmine (HM), we took the hybridization approach and synthesized harmine derivatives-furoxan hybrids containing nitric oxide (NO) releasing parts by connecting NO donors with anti-tumor active fragments to harmine. Then, the synthesized compounds were evaluated for their in vitro cytotoxicity against five human cancer cell lines. Among them, compound 10 was found to have the strongest antiproliferative activity against HepG2 (IC50 = 1.79 µM). In addition, compound 10 produced high levels of NO in vitro, verifying that the release of NO was closely correlated to the antiproliferative activity. In addition, Compound 10 also showed good plasma stability. Finally, we also preliminarily investigated the acute toxicity of compound 10 in mice and assessed the absorption of compound 10 by Caco-2 cell permeability assay. In brief, the remarkable biological characteristics of the new harmine derivatives-furoxan hybrids may make them promising candidates for human cancer intervention.

Cell-free DNA for the detection of emerging treatment failure in relapsed/ refractory multiple myeloma.

Interrogation of cell-free DNA (cfDNA) represents an emerging approach to non-invasively estimate disease burden in multiple myeloma (MM). Here, we examined low-pass whole genome sequencing (LPWGS) of cfDNA for its predictive value in relapsed/ refractory MM (RRMM). We observed that cfDNA positivity, defined as ≥10% tumor fraction by LPWGS, was associated with significantly shorter progression-free survival (PFS) in an exploratory test cohort of 16 patients who were actively treated on diverse regimens. We prospectively determined the predictive value of cfDNA in 86 samples from 45 RRMM patients treated with elotuzumab, pomalidomide, bortezomib, and dexamethasone in a phase II clinical trial (NCT02718833). PFS in patients with tumor-positive and -negative cfDNA after two cycles of treatment was 1.6 and 17.6 months, respectively (HR 7.6, P < 0.0001). Multivariate hazard modelling confirmed cfDNA as independent risk factor (HR 96.6, P = 6.92e-05). While correlating with serum-free light chains and bone marrow, cfDNA additionally discriminated patients with poor PFS among those with the same response by IMWG criteria. In summary, detectability of MM-derived cfDNA, as a measure of substantial tumor burden with therapy, independently predicts poor PFS and may provide refinement for standard-of-care response parameters to identify patients with poor response to treatment earlier than is currently feasible.