Biology subjects

Chen, M.-S.

Publications and source records attributed to Chen, M.-S..

6 recordsLinked to original sources

bioRxiv2026

Chromosome-scale genome of the woody oilseed crop sacha inchi elucidates the molecular basis of alpha-linolenic acid biosynthesis and triacylglycerol accumulation in seeds

Sacha inchi (Plukenetia volubilis L.) is an emerging woody oilseed crop prized for its high alpha-linolenic acid (ALA) content. Despite its nutritional and economic value, the lack of high-quality genomic resources has hindered genetic improvement and the elucidation of its unique polyunsaturated fatty acid and lipid biosynthetic pathways. In this study, we report a high-quality, chromosome-scale genome assembly of sacha inchi with a total length of 710.62 Mb, integrated from Illumina, PacBio, and chromosome conformation capture (Hi-C) technology. The genome harbors 37,570 protein-coding genes, and 379.86 Mb (53.45%) of repetitive sequences. Phylogenomic analysis reveals that sacha inchi diverged from its closest relative Ricinus communis, [~] approximately 36.2 million years ago. Comparative genomics indicates that sacha inchi experienced only ancient whole genome duplication events. To elucidate the mechanisms governing ALA biosynthesis and triacylglycerol (TAG) accumulation in sacha inchi seeds, we performed temporal transcriptome profiling across six seed development stages. Our findings demonstrate that high TAG content is primarily driven by the sustained expression of biosynthetic genes and low activity of degradation genes during mid-to-late seed development. Notably, while genes encoding stearoyl-ACP desaturases (SADs) maintain the precursor pool, the expression of genes encoding fatty-acid desaturase 2 (FAD2) and fatty-acid desaturase 3 (FAD3) is positively correlated with the final accumulation of C18:2 and C18:3 fatty acids. We also identified lncRNAs as potential epigenetic regulators of these key pathways. This high-quality genome provides a critical foundation for elucidating the molecular mechanisms of seed growth and development in sacha inchi.

genomics↗

bioRxiv2022

Aldo-Keto Reductase Family 1 Member A1 (AKR1A1) Deficiency Exacerbates Alcohol-Induced Hepatic Oxidative Stress, Inflammation, Steatosis, and Fibrosis

BackgroundAlcohol-associated liver disease (ALD) covers a wide range of hepatic lesions that depend on the amount and duration of alcohol consumption, from early and reversible conditions to hepatic steatosis and severe lesions, including steatohepatitis and alcoholic fibrosis, to irreversible cirrhosis. AKR1A1, an aldo-keto reductase family member, participates in the detoxification of alcohol-derived acetaldehyde, but its role in ALD remains unclear. In this study, we studied the role of AKR1A1 in the development of ALD using Akr1a1-/- knockout mice and palmitic acid/oleic acid (P/O) plus ethanol-treated AML12 hepatocyte cells. MethodsLevels of AKR1A1 were measured in mice fed with the Lieber-DeCarli diet containing 5% alcohol (alcohol-fed, AF) or control liquid diet (pair-fed, PF). The effects of AKR1A1 on the liver function, inflammation, oxidative stress, lipid accumulation, and fibrosis were assessed in AF-induced Akr1a1-/- and ICR control mice. ResultsData showed that AF-Akr1a1-/- mice exhibited an exacerbation of liver injury and increased gene and protein levels of inflammatory mediators, oxidative stress, lipid accumulation, and fibrosis, whilst decreased expression of antioxidant enzymes in their livers than the AF-ICR mice. Therefore, loss of AKR1A1 can activate 4-HNE/p53 signaling to modulate ROS and antioxidant balance, increase lipid peroxidation, fatty acid synthesis and lipid droplet formation, reduced fatty acid {beta}-oxidation, and elevated proinflammatory and fibrotic mediator, eventually exacerbate the ALD. In in vitro study, we further demonstrated that knockdown of Akrlal aggravated the effects of alcohol plus P/O-induced oxidative stress and steatosis, LPS-stimulated inflammation, and TGF-{beta}1-induced fibrosis in AML12 hepatocyte cells. Conclusionour results revealed that AKR1A1 exerts protective effects on alcohol-induced liver injury, steatosis, and fibrosis, possibly by regulating the 4-HNE-p53 signaling pathway.

pathology↗

bioRxiv2021

Chromosome-level genome assembly of the horned-gall aphid, Schlechtendalia chinensis (Hemiptera: Aphididae: Erisomatinae)

The horned gall aphid Schlechtendalia chinensis, is an economically important insect that induces galls valuable for medicinal and chemical industries. S. chinensis manipulates its host plant to form well-organized horned galls during feeding. So far, more than twenty aphid genomes have been reported; however, all of those are derived from free-living aphids. Here we generated a high-quality genome assembly of S. chinensis, representing the first genome sequence of a galling aphid. The final genome assembly was 280.43 Mb, with 97% of the assembled sequences anchored into thirteen chromosomes. S. chinensis presents the smallest aphid genome size among available aphid genomes to date. The contig and scaffold N50 values were 3.39 Mb and 20.58 Mb, respectively. The assembly included 96.4% of conserved arthropod and 97.8% of conserved Hemiptera single-copy orthologous genes based on BUSCO analysis. A total of 13,437 protein-coding genes were predicted. Phylogenomic analysis showed that S. chinensis formed a single clade between the Eriosoma lanigerum clade and the Aphidini+Macrosiphini aphid clades. In addition, salivary proteins were found to be differentially expressed when S. chinensis underwent host alternation, indicating their potential roles in gall formation and plant defense suppression. A total of 36 cytochrome P450 genes were identified in S. chinensis, considerably fewer compared to other aphids, probably due to its small host plant range. The high-quality S. chinensis genome assembly and annotation provide an essential genetic background for future studies to reveal the mechanism of gall formation and to explore the interaction between aphids and their host plants.

genomics↗

bioRxiv2018

Gfi1-expressing Paneth cells revert to stem cells following intestinal injury

BackgroundAimChemotherapy drugs harm rapidly dividing normal healthy cells such as those lining the gastrointestinal tract, causing morbidity and mortality that complicates medical treatment modalities. Growth Factor-Independent 1 (GFI1) is a zinc finger transcriptional repressor implicated in the differentiation of secretory precursors into Paneth and goblet cells in the intestinal epithelium. We hypothesize that stimulating the reversion of Gfi1+ secretory cells into stem cells will improve intestinal epithelial regeneration and mitigate injury.\n\nMethodsGfi1 reporter mice (Gfi1cre/+; ROSA26 LSL-YFP) were treated with Doxorubicin, radiation, anti-CD3 antibody, and rotavirus to induce intestinal injury. Mice and intestinal organoids (enteroids) were used to investigate cellular repair mechanisms following injury.\n\nResultsUnder homeostatic conditions, Gfi1-lineage cells are Paneth and goblet cells, which were non-proliferative and not part of the stem cell pool. After injury, Gfi1+ secretory cells can re-enter the cell cycle and give rise to all cell lineages of the intestinal epithelium including stem cells. Reversion of Gfi1-lineage cells was observed in other injury model systems, including irradiation and anti-CD3 treatment, but not in ISC-sparing rotavirus infection. Our results also demonstrated that PI3kinase/AKT activation improved cell survival, and elevated WNT signaling increased the efficiency of Gfi1+ cell reversion upon injury.\n\nConclusionsThese findings indicate that Gfi1+ secretory cells display plasticity and reacquire stemness following severe damage. Moreover, PI3kinase/AKT and WNT are key regulators involved in injury-induced regeneration. Our studies identified potential therapeutic intervention strategies to mitigate the adverse effects of chemotherapy-induced damage to normal tissues and improve the overall effectiveness of cancer chemotherapy.

cell biology↗

bioRxiv2018

Growth Factor Independent 1 is a tumor suppressor gene in colorectal cancer

Colorectal cancer (CRC) is the third most common cancer and the third leading cause of cancer death in the United States, causing about 50,000 deaths each year. Growth Factor-Independent 1 (GFI1) is a critical zinc finger transcriptional repressor responsible for controlling secretory cell differentiation in the small intestine and colon. GFI1 plays a significant role in the development of human malignancies, including leukemia, lung cancer and prostate cancer. However, the role of GFI1 in CRC progression is largely unknown. Our results demonstrate that RNA and protein expression of GFI1 are reduced in advanced stages of non-mucinous CRC. Subcutaneous tumor models demonstrated that the re-expression of GFI1 in 4 different human CRC cell lines inhibits tumor growth by 25-60%. To further investigate the role of Gfi1 in de novo colorectal tumorigenesis, we developed transgenic mice harboring a deletion of Gfi1 in the distal intestine driven by the CDX2cre (Gfi1F/F; CDX2cre/+) and crossed them with ApcMin/+ mice (ApcMin/+; Gfi1F/F; CDX2cre/+). Loss of Gfi1 significantly increased the total number of colorectal adenomas compared to littermate controls with an APC mutation alone. Furthermore, we found that compound (ApcMin/+; Gfi1F/F; CDX2cre/+) mice develop both adenomas as well as carcinoid-like tumors expressing the neuroendocrine marker chromogranin A, a feature that has not been previously described in APC-mutant tumors in mice. Collectively, these results demonstrate that Gfi1 deficiency promotes colorectal tumorigenesis, and suggest that loss of Gfi1 may promote formation of carcinoid cancers of the large intestines.\n\nSignificanceThese findings reveal that GFI1 functions as a tumor suppressor gene in colorectal tumorigenesis.

cancer biology↗

bioRxiv2018

Variation and diversification of the microbiome of Schlechtendalia chinensis on two alternate host plants

Schlechtendalia chinensis, a gall-inducing aphid, has two host plants in its life cycle. Its wintering host is a moss (typically Plagiomnium maximoviczii) and its main host is Rhus chinensis (Sumac), on which it forms galls during the summer.. This study investigated bacteria associated with S. chinensis living on the two different host plants by sequencing 16S rRNAs. A total of 183 Operational Taxonomic Units (OTUs) from 50 genera were identified from aphids living on moss, whereas 182 OTUs from 49 genera were found from aphids living in Sumac galls. The most abundant bacterial genus among identified OTUs from aphids feeding on both hosts was Buchnera. Despite similar numbers of OTUs, the composition of bacterial taxa showed significant differences between aphids living on moss and those living on R. chinensis. Specifically, there were 12 OTUs from 5 genera (family) unique to aphids living on moss, and 11 OTUs from 4 genera (family) unique to aphids feeding in galls on R. Chinensis. Principal Coordinate Analysis (PCoA) also revealed that bacteria from moss-residing aphids clustered differently from aphids collected from galls. Our results provid a foundation for future analyses on the roles of symbiotic bacteria in plant - aphid interactions in general, and how gall-specific symbionts differ in this respect.

microbiology↗