Biology subjects

Mak, T. W.

Publications and source records attributed to Mak, T. W..

5 recordsLinked to original sources

bioRxiv2024

Identification of KIFC1 as a putative vulnerability in lung cancers with centrosome amplification

Centrosome amplification (CA), an abnormal increase in the number of centrosomes in the cell, is a recurrent phenomenon in lung and other malignancies. Although CA contributes to tumor development and progression by promoting genomic instability (GIN), it also induces mitotic stress that jeopardizes cellular integrity. The presence of extra centrosomes leads to the formation of multipolar mitotic spindles prone to causing lethal chromosome segregation errors during cell division. To sustain the benefits of CA, malignant cells are dependent on adaptive mechanisms to mitigate its detrimental consequences, and these mechanisms represent therapeutic vulnerabilities. We aimed to discover genetic dependencies associated with CA in lung cancer. Combining a CRISPR/Cas9 functional genomics screen with analyses of tumor genomic data, we identified the motor protein KIFC1 as a putative vulnerability specifically in lung cancers with CA. KIFC1 expression was positively correlated with CA in lung adenocarcinoma (LUAD) cell lines and with a gene expression signature predictive of CA in LUAD tumor tissues. High KIFC1 expression was associated with worse patient outcomes, smoking history, and indicators of GIN. KIFC1 loss-of-function sensitized LUAD cells to potentiation of CA and sensitization was associated with a diminished ability of KIFC1-depleted cells to cluster extra centrosomes into pseudo-bipolar mitotic spindles. Our work suggests that KIFC1 inhibition represents a novel approach for potentiating GIN to lethal levels in LC with CA by forcing cells to divide with multipolar spindles, rationalizing the clinical development of KIFC1 inhibitors and further studies to investigate its therapeutic potential.

cancer biology↗

bioRxiv2022

Inhibition of CHK2 dependent DNA damage response suppresses Zika virus infection through a STING dependent mechanism

Zika virus (ZIKV) is a mosquito-borne flavivirus that causes neurological disorders and microcephaly. Recent research has shown that ZIKV causes cell cycle arrest and DNA damage response in neuronal progenitor cells that potentially leads to congenital neurodevelopmental defects. However, the specific role of regulators that control DNA damage response to ZIKV infection and the related mechanisms remain largely unknown. Here through both in vitro and in vivo studies, we observe that ZIKV induces DNA damage response in both human cell line and mouse embryo. When CHK2 dependent DNA damage response pathway is inhibited by a small molecule inhibitor or genetic deletion, ZIKV production is reduced and the embryonic developmental defects are rescued. Furthermore, we demonstrate that in ZIKV infected Chk2-/- mice, the reduced viral load correlates with elevated antiviral innate immune response which is found to be dependent on the STING signaling pathway. Collectively, our study reveals a specific role of CHK2 for ZIKV infection and pathogenesis, demonstrating a mechanism that inhibition of the CHK2 axis suppresses ZIKV infection through the STING-dependent antiviral pathway, thus providing a new therapeutic strategy against ZIKV. These findings also suggest the intriguing possibility that ZIKV evolved to orchestrate DNA damage response factors to create a beneficial environment for its infection in the host cells.

immunology↗

bioRxiv2021

De Novo Pyrimidine Synthesis is a Targetable Vulnerability in IDH Mutant Glioma

Mutations affecting isocitrate dehydrogenase (IDH) enzymes are prevalent in glioma, leukemia, and other cancers. Although mutant IDH inhibitors are effective against leukemia, they appear less active in aggressive glioma, underscoring the need for alternative treatment strategies. Through a chemical synthetic lethality screen, we discovered that IDH1 mutant glioma cells are hypersensitive to drugs targeting enzymes in the de novo pyrimidine nucleotide synthesis pathway, including dihydroorotate dehydrogenase (DHODH). We developed a genetically engineered mouse model of mutant IDH1-driven astrocytoma and used it and multiple patient-derived models to show that the brain-penetrant DHODH inhibitor BAY 2402234 displays monotherapy efficacy against IDH mutant gliomas. Mechanistically, this vulnerability selectively applies to de novo pyrimidine, but not purine, synthesis because glioma cells engage disparate programs to produce these nucleotide species and because IDH oncogenes increase DNA damage upon nucleotide pool imbalance. Our work outlines a tumor-selective, biomarker-guided therapeutic strategy that is poised for clinical translation.

cancer biology↗

bioRxiv2019

DJ-1 (Park7) affects the gut microbiome, metabolites, and development of Innate Lymphoid Cells (ILCs)

The proper communication between gut and brain is pivotal for maintenance of health and dysregulation of the gut-brain axis can lead to several clinical disorders. Also, in Parkinsons disease (PD) 85% of all patients experienced constipation long before showing any signs of motor phenotypes. For differential diagnosis and when it comes to preventive treatment there is an urgent need for the identification of biomarkers indicating early disease stages long before the disease phenotype manifests. DJ-1 is a chaperon protein involved in the protection against PD and genetic mutations in this protein have been shown to cause familial PD. However, how the deficiency of DJ-1 modifies the PD risk remains incompletely understood. In the present study we provide evidence that DJ-1 is implicated in shaping the gut microbiome including their metabolite production or innate immune cells (ILCs) development. We revealed that in 4 months old mice genetic deficiency of DJ-1 leads to significantly decrease in several bacterial genera and significantly increase in two specific genera, namely Alistipes and Rikenella. DJ-1 deficient mice have a higher production of calprotectin/MCP-1 inflammatory protein - a known protein involved in colonic inflammation - and significantly higher expression of glial fibrillary acidic protein (GFAP) than control littermates. Expression of a-Synuclein, a key protein in Lewy bodies, in the colon was not significantly different between genotypes. Metabolic profiles of feces extracts analysed by H1-NMR spectroscopy showed increased short chain fatty acids (SCFAs) and decreased amino acid levels, suggesting a general switch from protein towards fibre degrading strains in DJ-1 deficient mice. We observed that Malonate - which is known to influence the immune system - has significantly higher concentrations in DJ-1 deficient mice. Moreover, DJ-1 deficient mice have high levels of the phenol derivate 3-(3-Hydroxyphenyl) propanoic acid (3-HPPA) which is a breakdown product of aromatic substrates like tyrosine, phenylalanine and polyphenols. DJ-1 deficient mice also showed significantly reduced percentage of ILCs. Thus, our data suggests that absence of DJ-1 leads to increase in gut inflammatory bacteria composition, deregulated metabolites and dysregulated innate immunity which could be a key factor in the initiation of PD disease in the gut, and potentially also in brain during disease progression.

immunology↗

bioRxiv2017

Gene isoforms as expression-based biomarkers predictive of drug response in vitro

BackgroundOne of the main challenges in precision medicine is the identification of molecular features associated to drug response to provide clinicians with tools to select the best therapy for each individual cancer patient. The recent adoption of next-generation sequencing technologies enables accurate profiling of not only gene expression but also alternatively-spliced transcripts in large-scale pharmacogenomic studies. Given that altered mRNA splicing has been shown to be prominent in cancers, linking this feature to drug response will open new avenues of research in biomarker discovery.\n\nMethodsTo address the lack of reproducibility of drug sensitivity measurements across studies, we developed a meta-analytical framework combining the pharmacological data generated within the Cancer Cell Line Encyclopedia (CCLE) and the Genomics of Drug Sensitivity in Cancer (GDSC). Predictive models are fitted with CCLE RNA-seq data as predictor variables, controlled for tissue type, and combined GDSC and CCLE drug sensitivity values as dependent variables.\n\nResultsWe first validated the biomarkers identified from GDSC and CCLE using an existing pharmacogenomic dataset of 70 breast cancer cell lines. We further selected four drugs with the most promising biomarkers to test whether their predictive value is robust to change in pharmacological assay. We successfully validated 10 isoform-based biomarkers predictive of drug response in breast cancer, including TGFA-001 for the MEK tyrosine kinase inhibitor (TKI) AZD6244, DUOX-001 for the EGFR inhibitor erlotinib, and CPEB4-001 transcript expression associated with lack of sensitivity to paclitaxel.\n\nConclusionThe results of our meta-analysis of pharmacogenomic data suggest that isoforms represent a rich resource for biomarkers predictive of response to chemo- and targeted therapies. Our study also showed that the validation rate for this type of biomarkers is low (<50%) for most drugs, supporting the requirements for independent datasets to identify reproducible predictors of response to anticancer drugs.

bioinformatics↗