Sparassis latifolia and exercise training as complementary medicine mitigated the 5-fluorouracil potent side effects in mice with colorectal cancer: bioinformatics approaches, novel monitoring pathological metrics, screening signatures, and innovative management tactic

BACKGROUND

Prompt identification and assessment of the disease are essential for reducing the death rate associated with colorectal cancer (COL). Identifying specific causal or sensitive components, such as coding RNA (cRNA) and non-coding RNAs (ncRNAs), may greatly aid in the early detection of colorectal cancer.

METHODS

For this purpose, we gave natural chemicals obtained from Sparassis latifolia (SLPs) either alone or in conjunction with chemotherapy (5-Fluorouracil to a mouse colorectal tumor model induced by AOM-DSS. The transcription profile of non-coding RNAs (ncRNAs) and their target hub genes was evaluated using qPCR Real-Time, and ELISA techniques.

RESULTS

MSX2, MMP7, ITIH4, and COL1A2 were identified as factors in inflammation and oxidative stress, leading to the development of COL. The hub genes listed, upstream regulatory factors such as lncRNA PVT1, NEAT1, KCNQ1OT1, SNHG16, and miR-132-3p have been discovered as biomarkers for prognosis and diagnosis of COL. The SLPs and exercise, effectively decreased the size and quantity of tumors.

CONCLUSIONS

This effect may be attributed to the modulation of gene expression levels, including MSX2, MMP7, ITIH4, COL1A2, PVT1, NEAT1, KCNQ1OT1, SNHG16, and miR-132-3p. Ultimately, SLPs and exercise have the capacity to be regarded as complementing and enhancing chemotherapy treatments, owing to their efficacious components.

Transcriptome Analysis Revealed the Mechanism of Inhibition of Saprophytic Growth of Sparassis latifolia by Excessive Oxalic Acid

Sparassis latifolia, a highly valued edible fungus, is a crucial medicinal and food resource owing to its rich active ingredients and pharmacological effects. Excessive oxalic acid secreted on a pine-sawdust-dominated substrate inhibits its mycelial growth, and severely restricts the wider development of its cultivation. However, the mechanism underlying the relationship between oxalic acid and slow mycelial growth remains unclear. The present study reported the transcriptome-based response of S. latifolia induced by different oxalic acid concentrations. In total, 9206 differentially expressed genes were identified through comparisons of three groups; 4587 genes were down-regulated and 5109 were up-regulated. Transcriptome analysis revealed that excessive oxalic acid mainly down-regulates the expression of genes related to carbohydrate utilization pathways, energy metabolism, amino acid metabolism, protein synthesis metabolism, glycan biosynthesis, and signal transduction pathways. Moreover, genes encoding for wood-degrading enzymes were predominantly down-regulated in the mycelia treated with excessive oxalic acid. Taken together, the study results provide a speculative mechanism underlying the inhibition of saprophytic growth by excessive oxalic acid and a foundation for further research on the growth of S. latifolia mycelia.

Excessive Oxalic Acid Secreted by Sparassis latifolia Inhibits the Growth of Mycelia during Its Saprophytic Process

Sparassis latifolia is an edible and medicinal mushroom in Asia commercially cultivated on substrates containing pine sawdust. Its slow mycelial growth rate greatly increases the cultivation cycle. In this study, we mainly studied the role of oxalic acid (OA) secreted by S. latifolia in its saprophytic process. Our results show that crystals observed on the mycelial surface contained calcium oxalate monohydrate (COM) and calcium oxalate dihydrate (COD) according to X-ray diffraction (XRD). Vegetative mycelia secreted large amounts of OA during extended culture periods. However, high concentrations of OA decreased the mycelial growth rate significantly. Moreover, the degradation of lignocellulose was significantly inhibited under high concentrations of OA. These changes could be attributed to the significantly decreased activities of lignocellulose-degrading enzymes. In conclusion, by establishing a link between OA secretion by the mycelium and the slow growth rate of its saprophytic process, this work provides fundamental information for shortening the cultivation cycle of S. latifolia.

Chromosome-scale assembly of the Sparassis latifolia genome obtained using long-read and Hi-C sequencing

Sparassis latifolia is a valuable edible mushroom cultivated in China. In 2018, our research group reported an incomplete and low-quality genome of S. latifolia obtained by Illumina HiSeq 2500 sequencing. These limitations in the available genome have constrained genetic and genomic studies in this mushroom resource. Herein, an updated draft genome sequence of S. latifolia was generated by Oxford Nanopore sequencing and the high-through chromosome conformation capture (Hi-C) technique. A total of 8.24 Gb of Oxford Nanopore long reads representing ∼198.08X coverage of the S. latifolia genome were generated. Subsequently, a high-quality genome of 41.41 Mb, with scaffold and contig N50 sizes of 3.31 and 1.51 Mb, respectively, was assembled. Hi-C scaffolding of the genome resulted in 12 pseudochromosomes containing 93.56% of the bases in the assembled genome. Genome annotation further revealed that 17.47% of the genome was composed of repetitive sequences. In addition, 13,103 protein-coding genes were predicted, among which 98.72% were functionally annotated. BUSCO assay results further revealed that there were 92.07% complete BUSCOs. The improved chromosome-scale assembly and genome features described here will aid further molecular elucidation of various traits, breeding of S. latifolia, and evolutionary studies with related taxa.

Alginate-Derived Elicitors Enhance β-Glucan Content and Antioxidant Activities in Culinary and Medicinal Mushroom, Sparassis latifolia

This study aimed to investigate the elicitation effects of alginate oligosaccharides extracted from brown algae (Sargassum species) on β-glucan production in cauliflower mushroom (Sparassis latifolia). Sodium alginate was refined from Sargassum fulvellum, S. fusiforme, and S. horneri, and characterized by proton nuclear magnetic resonance spectroscopy (¹H NMR), resulting mannuronic acid to guluronic acid (M/G) rationes from 0.64 to 1.38. Three oligosaccharide fractions, ethanol fraction (EF), solid fraction (SF), and liquid fraction (LF), were prepared by acid hydrolysis and analyzed by Fourier transform infrared (FT-IR) spectra and high-performance anion-exchange chromatography with a pulsed amperometric detector (HPAEC-PAD). The samples of S. fusiforme resulted in the highest hydrolysate in SF and the lowest in LF, which was consistent with its highest M/G ratio. The SF of S. fusiforme and LF of S. horneri were chosen for elicitation on S. latifolia, yielding the highest β-glucan contents of 56.01 ± 3.45% and 59.74 ± 4.49% in the stalk, respectively. Total polyphenol content (TPC) and antioxidant activities (2,2’-Azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) radical scavenging and Superoxide dismutase (SOD)-like activity) of aqueous extracts of S. latifolia were greatly stimulated by alginate elicitation. These results demonstrate that alginate oligosaccharides extracted from brown algae may be useful as an elicitor to enhance the nutritional value of mushrooms.

Integration of ATAC-Seq and RNA-Seq Identifies Key Genes in Light-Induced Primordia Formation of Sparassis latifolia

Light is an essential environmental factor for Sparassis latifolia primordia formation, but the molecular mechanism is still unclear. In this study, differential expression profiling of light-induced primordia formation (LIPF) was established by integrating the assay for transposase accessible chromatin by sequencing (ATAC-seq) and RNA-seq technology. The integrated results from the ATAC-seq and RNA-seq showed 13 down-regulated genes and 17 up-regulated genes in both the L vs. D and P vs. D groups, for both methods. According to the gene ontology (GO) annotation of these differentially expressed genes (DEGs), the top three biological process categories were cysteine biosynthetic process via cystathionine, vitamin B6 catabolic, and glycine metabolic; the top three molecular function categories were 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity, glycine binding, and pyridoxal phosphate binding; cellular component categories were significantly enriched in the glycine cleavage complex. The KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis revealed that these genes were associated with vitamin B6 metabolism; selenocompound metabolism; cysteine and methionine metabolism; glycine, serine, and threonine metabolism; and glyoxylate and dicarboxylate metabolism pathways. The expression of most of the DEGs was validated by qRT-PCR. To the best of our knowledge, this study is the first integrative analysis of ATAC-seq and RNA-seq for macro-fungi. These results provided a new perspective on the understanding of key pathways and hub genes in LIPF in S. latifolia. It will be helpful in understanding the primary environmental response, and provides new information to the existing models of primordia formation in edible and medicinal fungi.