Thi Ly - Academia.edu (original) (raw)

Papers by Thi Ly

Additional file 1: Figure S1. Multiple sequence alignment of TMEM67 sequences across species show... more Additional file 1: Figure S1. Multiple sequence alignment of TMEM67 sequences across species showing that the nucleotide c.313-3 T variant is well conserved throughout evolution (red box).

BMC Medical Genetics, 2020

Background Joubert syndrome is a genetically heterogeneous autosomal recessive ciliopathy charact... more Background Joubert syndrome is a genetically heterogeneous autosomal recessive ciliopathy characterized by the combination of hypoplasia/aplasia of the cerebellar vermis, thickened and elongated superior cerebellar peduncles and a deep interpeduncular fossa, known as “molar tooth sign” associated with hypotonia, respiratory control disturbances and abnormal eye movements. To date, pathogenic variants in over 35 genes are known to cause autosomal recessive Joubert Syndrome, while one gene is associated with X-linked recessive inheritance. Case presentation We describe here a non-consanguineous Vietnamese family with Joubert syndrome, a fetus and 10-year-old developmentally delayed boy. Ultrasonography showed ventriculomegaly at 26 + 6 weeks of gestation in the fetus. The 10-year-old-boy was diagnosed with cerebral palsy of unknown origin. Clinical physical examination at the age of 10, he showed clinical features of Joubert syndrome including typical facial dysmorphism, ataxia, sever...

Nature Structural Biology, 2002

The 7-methyl guanosine cap structure of RNA is essential for key aspects of RNA processing, inclu... more The 7-methyl guanosine cap structure of RNA is essential for key aspects of RNA processing, including pre-mRNA splicing, 3&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39; end formation, U snRNA transport, nonsense-mediated decay and translation. Two cap-binding proteins mediate these effects: cytosolic eIF-4E and nuclear cap-binding protein complex (CBC). The latter consists of a CBP20 subunit, which binds the cap, and a CBP80 subunit, which ensures high-affinity cap binding. Here we report the 2.1 A resolution structure of human CBC with the cap analog m7GpppG, as well as the structure of unliganded CBC. Comparisons between these structures indicate that the cap induces substantial conformational changes within the N-terminal loop of CBP20, enabling Tyr 20 to join Tyr 43 in pi-pi stacking interactions with the methylated guanosine base. CBP80 stabilizes the movement of the N-terminal loop of CBP20 and locks the CBC into a high affinity cap-binding state. The structure for the CBC bound to m7GpppG highlights interesting similarities and differences between CBC and eIF-4E, and provides insights into the regulatory mechanisms used by growth factors and other extracellular stimuli to influence the cap-binding state of the CBC.

BMC biology, Jan 7, 2005

Compartmentalization is a key feature of eukaryotic cells, but its evolution remains poorly under... more Compartmentalization is a key feature of eukaryotic cells, but its evolution remains poorly understood. GTPases are the oldest enzymes that use nucleotides as substrates and they participate in a wide range of cellular processes. Therefore, they are ideal tools for comparative genomic studies aimed at understanding how aspects of biological complexity such as cellular compartmentalization evolved. We describe the identification and characterization of a unique family of circularly permuted GTPases represented by the human orthologue of yeast Lsg1p. We placed the members of this family in the phylogenetic context of the YlqF Related GTPase (YRG) family, which are present in Eukarya, Bacteria and Archea and include the stem cell regulator Nucleostemin. To extend the computational analysis, we showed that hLsg1 is an essential GTPase predominantly located in the endoplasmic reticulum and, in some cells, in Cajal bodies in the nucleus. Comparison of localization and siRNA datasets sugge...

DMW - Deutsche Medizinische Wochenschrift, 2008

The Journal of General and Applied Microbiology, 1990

Cocultures of three Listeria species, L. monocytogenes, L, seeligeri, and L. innocua with Acantha... more Cocultures of three Listeria species, L. monocytogenes, L, seeligeri, and L. innocua with Acanthamoeba castellanii, and Tetrahymena pyriformis, respectively, were investigated. The Listeria were ingested intracellularly by the protozoans. However, they were not killed, on the contrary, they survived. The two hemolytic Listeria species, i.e. L. monocytogenes and L. seeligeri ruptured their host cells completely after a few days and became free. Subsequently, they died. On the other hand, the apathogenic L. innocua partially lysed the protozoans and coexisted intracellularly as well as extracellularly for some weeks. Additionally, cocultures of L. monocytogenes, Escherichia coli, Salmonella typhimurium, and A. castellanii, T. pyriformis, respectively, were studied. The results showed that both protozoans possess similar distinct preferences for the Salmonella and Listeria, but E. coli was not desirable `prey.' Ingested S. typhimurium were killed but L. monocytogenes survived. The observed phenomena provide a special insight regarding L. monocytogenes infection in man and animals in respect to the different behaviour patterns of the three Listeria species investigated.

Proceedings of the National Academy of Sciences, 2006

Opposing cellular responses are typically regulated by distinct sets of genes. However, tissue tr... more Opposing cellular responses are typically regulated by distinct sets of genes. However, tissue transglutaminase (TGase) provides an interesting example of a single gene product that has been implicated both in affording protection against cellular insults as well as in promoting cell death. Here, we shed some light on how these conflicting activities might be manifested by demonstrating that alternative transcripts of TGase differentially affect cell viability. We show that although the full-length TGase protein affords strong protection against cell death signals, a shorter version of TGase that is truncated at the 3′ end, and thus called TGase-short (TGase-S), is cytotoxic. The apoptotic activity of TGase-S is not dependent on its transamidation activity because the mutation of a cysteine residue that is essential for catalyzing this reaction does not compromise the ability of TGase-S to induce cell death. Intriguingly, TGase-S undergoes inappropriate oligomer formation in cells b...

Nature Cell Biology, 2006

Cool-1 (cloned-out of library 1) has a key role in regulating epidermal growth factor receptor (E... more Cool-1 (cloned-out of library 1) has a key role in regulating epidermal growth factor receptor (EGFR) degradation. Here, we show that Cool-1 performs this function by functioning as both an upstream activator and downstream target for Cdc42. EGFdependent phosphorylation of Cool-1 enables it to act as a nucleotide exchange factor for Cdc42 and to form a complex with the E3 ligase Cbl, thus regulating Cbl-catalysed EGFR degradation. The EGF-dependent phosphorylation is normally transient; however, Cool-1 phosphorylation is sustained in cells expressing v-Src and is essential for cellular transformation, as well as for v-Src-induced tumour formation in mice. These findings demonstrate that the regulated phosphorylation of Cool-1 is necessary to maintain the balance between normal signalling by EGFR and Src versus aberrant growth and transformation. Overexpression or hyperactivation of EGFR has been linked to the progression of a variety of human tumours, including different forms of breast, lung and brain cancers 1-3. Thus, it is important that EGFcoupled signalling is carefully regulated. Ubiquitination targets EGFRs for degradation that is catalysed by the Casitas B-lymphoma (Cbl) proteins 4,5. When the ubiquitin ligase activity of Cbl is compromised, the balance between EGFR recycling to the cell surface and degradation in the lysosome is disrupted, resulting in receptor accumulation and excessive mitogenic signalling 4,6. Several studies have suggested that Cbl is also required for receptor endocytosis 5,7-9 , either through its ability to catalyse ubiquitination 5,10 or by linking receptors to the CIN85-endophilin complex 11. Cbl-catalysed ubiquitination of EGFRs is negatively regulated by the GTPase Cdc42 (ref. 12). This is not due to a direct interaction between Cdc42 and Cbl, but instead is mediated by Cool-1 (also known as β-Pix, β-Pak-interactive exchange factor). Members of the Cool family of proteins contain tandem diffuse B-cell lymphoma (Dbl) and pleckstrinhomology domains 13-15 and have been assumed to function as guanine nucleotide exchange factors (GEFs) 16,17. We have previously shown that the specific GEF activity exhibited by Cool-2 (also known as α-Pix) was dependent on whether it existed as a dimer (Rac-GEF) or a monomer (Rac-or Cdc42-GEF) 18,19. However, although Cool-1 contains a unique sequence (called T1) that prevents it from exhibiting constitutive GEF activity, it is able to bind activated Cdc42 as well as Cbl (refs 12, 20, 21). Expression of the constitutively active Cdc42 F28L mutant in NIH3T3 cells led to the formation of Cdc42-Cool-1-Cbl complexes and the persistent sequestration of Cbl, resulting in EGFR accumulation and cellular transformation 12. Although these findings provided insights into how Cdc42 influences EGFR degradation, a number of questions remained. For example, it was not known how Cdc42 is activated in an EGF-dependent manner so that it binds to Cool-1 and sequesters Cbl away from EGFRs, or how these interactions are regulated and what the consequences are when this regulation is lost. Here, we show that Cool-1 is phosphorylated in an EGF-dependent manner, enabling it to act both as an upstream activator and a downstream target of Cdc42. The EGF-dependent phosphorylation of Cool-1 is transient, whereas phosphorylation is sustained when Cool-1 is ectopically expressed together with v-Src. Overexpression of Cool-1 augments v-Src-induced transformation, whereas expression of phosphorylation-defective Cool-1, as well as knockdowns of Cool-1 by RNA interference (RNAi), strongly inhibit transformation. These findings highlight a previously unappreciated role for the phosphorylation of Cool-1 as an essential regulatory event, both for normal EGFR-coupled signalling and for cellular transformation by v-Src. RESULTS Cdc42-Cool-1 interactions are necessary for normal EGFRcoupled signalling We previously showed that the constitutively active Cdc42 F28L mutant caused cellular transformation by inhibiting EGFR-Cbl interactions and altering EGFR homeostasis 12. This implied that the EGF-dependent interactions between Cdc42, Cool-1 and Cbl are important for maintaining the proper balance between EGFR signalling and degradation. Thus, disabling either Cdc42 or Cool-1 function should compromise normal mitogenic signalling through the EGFR. Inhibiting the actions of endogenous Cdc42 by expressing a dominant-negative

Journal of Cell Science, 2008

Although cells migrate in a constrained 3D environment in vivo, in-vitro studies have mainly focu... more Although cells migrate in a constrained 3D environment in vivo, in-vitro studies have mainly focused on the analysis of cells moving on 2D substrates. Under such conditions, the Golgi complex is always located towards the leading edge of the cell, suggesting that it is involved in the directional movement. However, several lines of evidence indicate that this location can vary depending on the cell type, the environment or the developmental processes. We have used micro contact printing (μCP) to study the migration of cells that have a geometrically constrained shape within a polarized phenotype. Cells migrating on micropatterned lines of fibronectin are polarized and migrate in the same direction. Under such conditions, the Golgi complex and the centrosome are located behind the nucleus. In addition, the Golgi complex is often displaced several micrometres away from the nucleus. Finally, we used the zebrafish lateral line primordium as an in-vivo model of cells migrating in a const...

Journal of Biological Chemistry, 2009

Although the small GTPase Ran is best known for its roles in nucleocytoplasmic transport, mitotic... more Although the small GTPase Ran is best known for its roles in nucleocytoplasmic transport, mitotic spindle assembly, and nuclear envelope formation, recent studies have demonstrated the overexpression of Ran in multiple tumor types and that its expression is correlated with a poor patient prognosis, providing evidence for the importance of this GTPase in cell growth regulation. Here we show that Ran is subject to growth factor regulation by demonstrating that it is activated in a serum-dependent manner in human breast cancer cells and, in particular, in response to heregulin, a growth factor that activates the Neu/ ErbB2 tyrosine kinase. The heregulin-dependent activation of Ran requires mTOR (mammalian target of rapamycin) and stimulates the capped RNA binding capability of the cap-binding complex in the nucleus, thus influencing gene expression at the level of mRNA processing. We further demonstrate that the excessive activation of Ran has important consequences for cell growth by showing that a novel, activated Ran mutant is sufficient to transform NIH-3T3 cells in an mTOR-and epidermal growth factor receptor-dependent manner and that Ran-transformed cells form tumors in mice.