Biology subjects

Tran, P. T.

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

8 recordsLinked to original sources

bioRxiv2025

CDK8 remodels the tumor microenvironment to resist the therapeutic efficacy of targeted KRASG12D inhibition in pancreatic ductal adenocarcinoma

Mutations in KRAS are a dominant driver of pancreatic ductal adenocarcinoma (PDAC), with over 40% of PDAC patients presenting with KRASG12D mutations. The recent development of small molecule inhibitors targeting KRASG12D has enabled targeting of mutant KRAS signaling and suppression of PDAC; however, the contribution of the tumor microenvironment (TME) to the sustained therapeutic efficacy of KRASG12D inhibition and mechanism/s of resistance to KRASG12D suppression remain to be elucidated. Here, we employed spatial transcriptomics, single cell RNA sequencing, and CODEX-based spatial proteomics to evaluate cancer cell intrinsic and extrinsic responses to KRASG12D inhibition with MRTX1133. While KRASG12D inhibition initially increases CD11c+ cells with impactful T cell infiltration within proximity to cancer cells, long-term treatment with MRTX1133 resulted in reversal of the immune responses leading to KRASG12D therapy resistance promoted by CDK8, a multiprotein mediator complex associated kinase. CDK8 imparts resistance in part through induction of downstream CXCL2 chemokine secretion, inhibition of FAS expression, and remodeling of the TME to promote immune evasion. Targeting CDK8 by itself and in combination with CTLA-4 immunotherapy overcomes resistance to KRASG12D inhibition with prolonged survival with translational implications.

cancer biology↗

bioRxiv2025

PP6 phosphatase and Elongator contribute to kinesin 5-dependent spindle assembly by controlling microtubule regulator levels

Eukaryotic chromosome segregation relies on the assembly of a bipolar machinery based on microtubules (MTs), named the mitotic spindle. Formation of the mitotic spindle follows a force balance mechanism that ensures the proper capture and separation of sister chromatids. Many proteins have been involved in the establishment of this force balance, although kinesin 5 is well recognized as the major outward pushing force generator, since its inactivation results in monopolar, non-functional spindles. In order to find additional players in the force balance mechanism, we have performed a suppressor screen using a conditional allele of the fission yeast kinesin 5 ortholog Cut7. This screen identified that the lack of the PP6 phosphatase partially suppresses cut7 phenotypes, at least by defective translation of MT regulators, impacting on the force balance mechanism. Additionally, our data show that the Elongator complex, a target regulated by PP6 involved in tRNA modification, also ensures the force balance, albeit to a lesser extent. Importantly, this complex has been recently involved in direct MT polymerization in metazoans, a role probably not shared by its fission yeast counterpart. AUTHOR SUMMARYThe mitotic spindle is a cellular machine made of microtubules, which become arranged in a bipolar manner to capture and segregate chromosomes into the daughter cells during cell division. Spindle bipolarization relies on a force balance mechanism established by the function of many proteins, among which, the essential kinesin 5 is the major outward force generator. To discover novel proteins involved in the force balance, we have screened for suppressors of the kinesin 5 ortholog of fission yeast Cut7. Among the hits of the screen, we found that the lack of PP6 phosphatase components allow cut7 mutants form a bipolar spindle. Our results show that this suppression is, as least in part, mediated by the inactivation of Elongator, a complex that modifies tRNAs to facilitate the translation of specific mRNAs. Our results show that PP6 and Elongator participate in the efficient production of microtubule regulators that contribute to the proper generation of the force balance for spindle assembly.

cell biology↗

bioRxiv2022

Arabidopsis LSH10 transcription factor interacts with the co-repressor histone deubiquitinase OTLD1 to recruit it to the target promoters

Histone ubiquitylation/deubiquitylation plays a major role in the epigenetic regulation of gene expression. In plants, OTLD1, a member of the ovarian tumor (OTU) deubiquitinase family, deubiquitylates monoubiquitylated histone 2B and represses the expression of genes involved in growth, cell expansion, and hormone signaling. Like many other histone-modifying enzymes, OTLD1 lacks the intrinsic ability to bind DNA. How OTLD1, as well as most other known plant histone deubiquitinases, is recruited specifically to the promoters of its target genes remains unknown. Here, we show that Arabidopsis transcription factor LSH10, a member of the ALOG protein family, interacts with OTLD1 in living plant cells. Loss-of-function LSH10 mutations relieve the OTLD1-promoted transcriptional repression of the target genes, resulting in their elevated expression, whereas recovery of the LSH10 function results in down-regulated transcription of the same genes. We then show that LSH10 associates directly with the target gene chromatin as well as with the specific DNA sequence motifs in the promoter regions of the target genes. Furthermore, in the absence of LSH10, the degree of H2B monoubiquitylation in the target promoter chromatin increases. Hence, our data suggest that OTLD1-LSH10 acts as a co-repressor complex, in which LSH1 recruits OTLD1 to the target gene promoters, potentially representing a general mechanism for recruitment of plant histone deubiquitinases to the target chromatin.

plant biology↗

bioRxiv2022

Single-nucleus chromatin accessibility identifies a critical role for TWIST1 in idiopathic pulmonary fibrosis myofibroblast activity

In idiopathic pulmonary fibrosis (IPF) myofibroblasts are key effectors of fibrosis and architectural distortion by excessive deposition of extracellular matrix and their acquired contractile capacity. Single-cell RNA-sequencing has precisely defined the IPF myofibroblast transcriptome, but identifying critical transcription factor activity by this approach is imprecise. We performed and integrated snATAC-seq and scRNA-seq from human IPF and donor control explants to identify differentially accessible chromatin regions and enriched transcription factor motifs within lung cell populations. TWIST1 and other E-box transcription factor motifs were significantly enriched in IPF myofibroblasts compared to both IPF non-myogenic and control fibroblasts. TWIST1 expression was also selectively upregulated in IPF myofibroblasts. Overexpression of Twist1 in lung COL1A2-expressing fibroblasts in bleomycin-injured mice was associated with increased collagen synthesis. Our studies utilizing human multiomic single-cell analyses combined with in vivo murine disease models confirm a critical regulatory function for TWIST1 in IPF myofibroblast activity in the fibrotic lung. Understanding the global process of opening TWIST1 and other E-box TF motifs that govern myofibroblast differentiation may identify new therapeutic interventions for fibrotic pulmonary diseases.

molecular biology↗

bioRxiv2021

Microtubule rescue at midzone edges promotes overlap stability and prevents spindle collapse during anaphase B

During anaphase B, molecular motors slide interpolar microtubules to elongate the mitotic spindle, contributing to the separation of chromosomes. However, sliding of antiparallel microtubules reduces their overlap, which may lead to spindle breakage, unless microtubules grow to compensate sliding. How sliding and growth are coordinated is still poorly understood. In this study, we have used the fission yeast S. pombe to measure microtubule dynamics during anaphase B. We report that the coordination of microtubule growth and sliding relies on promoting rescues at the midzone edges. This makes microtubules stable from pole to midzone, while their distal parts including the plus ends alternate between assembly and disassembly. Consequently, the midzone keeps a constant length throughout anaphase, enabling sustained sliding without the need for a precise regulation of microtubule growth speed. Additionally, we found that in S. pombe, which undergoes closed mitosis, microtubule growth speed decreases when the nuclear membrane wraps around the spindle midzone.

cell biology↗

bioRxiv2018

HOOK3 is a scaffold for the opposite-polarity microtubule-based motors cytoplasmic dynein and KIF1C

The unidirectional and opposite-polarity microtubule-based motors, dynein and kinesin, drive long-distance intracellular cargo transport. Cellular observations support the existence of mechanisms to couple opposite polarity motors: in cells some cargos rapidly switch directions and kinesin motors can be used to localize dynein. We recently identified an interaction between the cytoplasmic dynein-1 activating adaptor HOOK3 and the kinesin-3 KIF1C. Here we show that KIF1C and dynein/dynactin can exist in a single complex scaffolded by HOOK3. Full-length HOOK3 binds to and activates dynein/dynactin motility. HOOK3 also binds to a short region in the \"tail\" of KIF1C, but unlike dynein/dynactin, this interaction does not affect the processive motility of KIF1C. HOOK3 scaffolding allows dynein to transport KIF1C towards the microtubule minus end, and KIF1C to transport dynein towards the microtubule plus end. We propose that linking dynein and kinesin motors by dynein activating adaptors may be a general mechanism to regulate bidirectional motility.

cell biology↗

bioRxiv2017

Lis1 has two opposing modes of regulating cytoplasmic dynein

Regulation is central to the functional versatility of cytoplasmic dynein, a motor involved in intracellular transport, cell division, and neurodevelopment. Previous work established that Lis1, a conserved and ubiquitous regulator of dynein, binds to its motor domain and induces a tight microtubule-binding state in dynein. The work we present here--a combination of biochemistry, single-molecule assays, cryo-electron microscopy and in vivo experiments--led to the surprising discovery that Lis1 has two opposing modes of regulating dynein, being capable of inducing both low and high affinity for the microtubule. We show that these opposing modes depend on the stoichiometry of Lis1 binding to dynein and that this stoichiometry is regulated by the nucleotide state of dyneins AAA3 domain. We present data on the in vitro and in vivo consequences of abolishing the novel Lis1-induced weak microtubule-binding state in dynein and propose a new model for the regulation of dynein by Lis1.

cell biology↗

bioRxiv2017

The Human Cytoplasmic Dynein Interactome Reveals Novel Activators Of Motility

In human cells, cytoplasmic dynein-1 is essential for long-distance transport of many cargos, including organelles, RNAs, proteins, and viruses, towards microtubule minus ends. To understand how a single motor achieves cargo specificity, we identified the human dynein interactome or \"transportome\" by attaching a promiscuous biotin ligase (\"BioID\") to seven components of the dynein machinery, including a subunit of the essential cofactor dynactin. This method reported spatial information about the large cytosolic dynein/dynactin complex in living cells. To achieve maximal motile activity and to bind its cargos, human dynein/dynactin requires \"activators\", of which only five have been described. We developed methods to identify new activators in our BioID data, and discovered that ninein and ninein-like are a new family of dynein activators. Analysis of the protein interactomes for six activators, including ninein and ninein-like, suggests that each dynein activator has multiple cargos.

cell biology↗