Biology subjects

Tran, M. T.

Publications and source records attributed to Tran, M. T..

5 recordsLinked to original sources

bioRxiv2026

Unconventional presentation of an immunodominant HLA-DR15-restricted nephritogenic proteinase 3 epitope implicated in vasculitis

Proteinase 3 (PR3) anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis is associated with HLA-DR15, implicating HLA-DR15-restricted CD4 T cell autoimmunity in the disease. However, the PR3 epitopes presented by HLA-DR15 and the autoreactive CD4 T cell responses they elicit are undefined. Using humanized hPR3.DR15+ mice, we identified PR3216-231 as an immunodominant human PR3-derived CD4 T cell epitope presented by HLA-DR15. Immunopeptidomic profiling confirmed the natural processing and HLA-DR15-restricted presentation of PR3216-231. Structural analyses of HLA-DR15-PR3216-231 complexes revealed an unconventional mode of HLA class II antigen presentation, in which a 10 amino acid peptide core occupies the 9 amino acid binding groove, causing a central kink in the bound peptide. PR3216-231-specific CD4 T cells from both hPR3.DR15+ mice and patients with PR3-ANCA-associated vasculitis exhibited convergent T cell receptor features, and patients with active vasculitis displayed a clonally expanded, PR3216-231-specific CD4 TCR repertoire. Immunization of hPR3.DR15 mice with PR3216-231 induced cell-mediated glomerulonephritis characterized by increased renal infiltration of CD4 T cells and macrophages together with segmental glomerular necrosis. These findings identify a nephritogenic PR3-derived CD4 T cell epitope presented by HLA-DR15 in ANCA-associated vasculitis and define a new extended core binding pattern, broadening our understanding of HLA class II peptide presentation.

immunology↗

bioRxiv2024

Redirecting DNA repair for efficient CRISPR-Cas-based gene targeting in tomato

The CRISPR-Cas-based gene targeting (GT) method has enabled precise modifications of genomic DNA ranging from single base to several kilobase scales through homologous recombination (HR). In plant somatic cells, canonical nonhomologous end-joining (cNHEJ) is the predominant mechanism for repairing double-stranded breaks (DSBs), thus limiting the HR-mediated GT. In this study, we implemented various approaches to shift the repair pathway preference toward HR by using a dominant-negative KU80 mutant protein (KUDN) to disrupt the initiation of cNHEJ and enhance DSB end resection through nucleases. Our results show from 1.71- to 3.55-fold improvement of the GT efficiency at the callus stage and a more remarkable, up to 9.84-fold, increase in GT efficiency at two specific tomato loci, SlHKT1;2 and SlEPSPS1, when we screened transformants obtained from the KUDN-mediated cNHEJ suppression approach. With practical levels of efficiency, this enhanced KUDN-based GT tool successfully facilitated GT at an additional locus, SlCAB13. These findings provide a promising method for more efficient and precise plant breeding in the future.

plant biology↗

bioRxiv2022

CRISPR/Cas-based precision gene replacement in plants via homologous recombination-independent approaches

Precise gene or allele replacement is a desirable technology, but implementing it in plants remains challenging. CRISPR-Cas-based approaches, such as gene targeting (GT) and prime editing (PE), have opened up new possibilities for precise gene replacement in plants. However, their editing size and efficiency still need improvement. Recently, strategies using canonical nonhomologous end-joining (cNHEJ) and microhomology-mediated end joining (MMEJ) have been considered promising alternatives for precise gene replacement in yeast and mammals. However, these approaches have not been extensively explored and applied to plants. Here, we proposed and tested a CRISPR-Cas-based tool, termed PREMJ (precision gene replacement via microhomology-mediated end joining), for precision gene replacement in plants. The PREMJ strategy employing 20-bp microhomology MMEJ donors ([~]100 bp lengths) and a canonical nonhomologous end-joining (cNHEJ) inhibitor, NU7441, produced high targeted gene replacement efficiencies, up to 1.60 {+/-} 0.14, 4.47 {+/-} 1.98, and 8.98 {+/-} 4.73 % in protoplasts of tomato, lettuce, and cabbage, respectively. Our data also revealed the critical impacts of the microhomology length and NU7441 concentration on PREMJ-based precision gene editing in plants. Although obtaining edited plants remains challenging due to inefficient protoplast regenerations and Agrobacterium-mediated delivery, PREMJ may significantly contribute to precision gene editing in plants competent to PREMJ complex delivery and plant regeneration. Key MessageWe designed and tested a method, termed PREMJ, for precise gene replacement using the CRISPR-Cas-mediated double-stranded break (DSB) formation and repairing the DSBs via microhomology-mediated end joining (MMEJ) with MMEJ donor template carrying desired base changes and microhomologies flanking the DSB ends. PREMJ showed feasibility in precise gene replacement in protoplasts of tomatoes, lettuce, and cabbage, albeit its efficacy in Agrobacterium-mediated plant transformation requires further optimization.

synthetic biology↗

bioRxiv2019

SCAND1 suppresses CDC37 gene transcription by repressing MZF1

CDC37 increases the stability of HSP90 client proteins and is essential for numerous intracellular oncogenic signaling pathways. Elevated expression of CDC37 was found in prostate cancer cells, although the regulatory mechanisms through which CDC37 expression becomes increased are unknown. Here we show both positive and negative regulation of CDC37 gene transcription by two members of the SCAN transcription factor family- MZF1 and SCAND1, respectively. Consensus DNA-binding motifs for MZF1 were abundant in the CDC37 promoter region. MZF1 became bound to these regulatory sites and trans-activated the CDC37 gene whereas MZF1 depletion decreased CDC37 transcrption and reduced tumorigenesis of prostate cancer cells. On the other hand, SCAND1, a zinc-fingerless SCAN box protein that potentially inhibits MZF1, accumulated at MZF1-binding sites in CDC37 gene, negatively regulated CDC37 gene and inhibited tumorigenesis. SCAND1 was abundantly expressed in normal prostate cells but was reduced in prostate cancer cells, suggesting a potential tumor suppressor role of SCAND1 in prostate cancer. These findings indicate that CDC37, a crucial protein in prostate cancer progression, is regulated reciprocally by MZF1 and SCAND1.

molecular biology↗

bioRxiv2019

Homology-directed repair using transient CRISPR/Cpf1-geminiviral replicon in tomato

Genome editing via the homology-directed repair (HDR) pathway in somatic plant cells is very inefficient compared to error-prone repair by nonhomologous end joining (NHEJ). Here, we increased HDR-based genome editing efficiency approximately 3-fold compared to a Cas9-based single-replicon system via the use of de novo multi-replicon systems equipped with CRISPR/LbCpf1 in tomato and obtained replicon-free but stable HDR alleles. The efficiency of CRISPR/LbCpf1-based HDR was significantly modulated by physical culture conditions such as temperature and light. Ten days of incubation at 31{degrees}C under a light/dark cycle after Agrobacterium-mediated transformation resulted in the best performance among the tested conditions. Furthermore, we developed our single-replicon system into a multi-replicon system that effectively increased HDR efficiency. Although this approach is still challenging, we showed the feasibility of HDR-based genome editing of a salt-tolerant SlHKT1;2 allele without genomic integration of antibiotic markers or any phenotypic selection. Self-pollinated offspring plants carrying the HKT1;2 HDR allele showed stable inheritance and germination tolerance in the presence of 100 mM NaCl. Our work may pave the way for transgene-free editing of alleles of interest in asexually as well as sexually reproducing plants.

molecular biology↗