Biology subjects

Wan, J. C.

Publications and source records attributed to Wan, J. C..

5 recordsLinked to original sources

bioRxiv2023

DFNA5-mediated pyroptosis is a driver for venetoclax and azacytidine synergy in myeloid leukemia

Acute myeloid leukemia (AML) remains the deadliest adult leukemia with dismal clinical outcomes. Since 2020, a combination of BCL-2 inhibitor (venetoclax, VEN) with hypomethylating agent (azacytidine/decitabine, AZA/DAC) has become a new standard of care in elderly or unfit AML patients. However, the underlying mechanism of synergy between venetoclax and azacytidine combination is not well understood. While apoptosis is regarded as the primary mode of cell death mechanism caused by the venetoclax and azacytidine combination, we provide novel evidence for pyroptosis as additional cell death mechanisms in response to venetoclax and azacytidine combination therapy. We found that long-term treatment with azacytidine caused hypomethylation and significant upregulation in DFNA5/GSDME, pore forming Gasdermin family gene that is otherwise silent in myeloid leukemia. We found that azacytidine mediates N-terminal pore-forming DFNA5 cleavage, membrane rupture, and subsequent pyroptosis of DFNA5 overexpressing cells in response to venetoclax and azacytidine. Deletion of DFNA5 reduced total cell viability, where DFNA5 KO cells exclusively underwent apoptosis while DFNA5 OE cells showed increased propidium iodide uptake, a marker for membrane rupture. Overall, our study establishes DFNA5 as an important mediator of venetoclax and azacytidine-induced cell death via non-apoptotic mechanisms.

cancer biology↗

bioRxiv2020

Global RNA sequencing reveals enhanced photosynthetic activity and auxin response in Brassica napus treated with Pseudomonas chlororaphis PA23

Plant growth promoting bacteria (PGPB) are a growing subset of agricultural adjuncts which can be used to increase crop yield and plant productivity. Although substantial research has been conducted on the metabolites and active molecules secreted by PGPBs, relatively little is known about their effects on the global transcriptome of the host plant. The present study was carried out to investigate changes in the gene expression landscape of early vegetative Brassica napus following treatment with Pseudomonas chlororaphis PA23. This PGPB was isolated from the soybean rhizosphere and has been extensively studied as a biocontrol agent. However, little is known about its effects on plant growth and development. Using a combination of RNA-sequencing and physiological analyses, we identified increased abundance of mRNA transcripts associated with photosynthesis and phytohormone response. Phenotypically we observed increased photosynthetic rates and larger root and shoot systems in B. napus following P. chlororaphis PA23 treatment. Lastly, we identified auxin production by P. chlororaphis PA23 which likely contributes to changes in gene expression and the observed phenotypic differences in root and shoot structures. Together, the results of our study suggest that PA23 is a potent plant growth promoting agent with the potential for field applications as an agricultural adjunct.

plant biology↗

bioRxiv2019

Comprehensive characterisation of cell-free tumour DNA in plasma and urine of patients with renal tumours

Cell-free tumour-derived DNA (ctDNA) allows non-invasive monitoring of cancers but its utility in renal cell cancer (RCC) has not been established. Here, untargeted and targeted sequencing methods, applied to two independent cohorts of renal tumour patients (n=90), were used to determine ctDNA content in plasma and urine. Our data revealed lower plasma ctDNA levels in RCC relative to other cancers, with untargeted detection of [~]33%. A sensitive personalised approach, applied to plasma and urine from select patients improved detection to [~]50%, including in patients with early-stage and even benign lesions.\n\nA machine-learning based model predicted detection, potentially offering a means of triaging samples for personalised analysis. In addition, with limited data we observed that plasma, and for the first time, urine ctDNA may better represent tumour heterogeneity than tissue biopsy. Furthermore, longitudinal sampling of >200 plasma samples revealed that ctDNA can track disease course. Additional datasets will be required to validate these findings.\n\nOverall, our data highlight RCC as a ctDNA-low malignancy, but indicate potential clinical utility provided improvement in detection approaches.\n\nOne sentence summaryComplementary sequencing methods show that cell-free tumour DNA levels are low in renal cancer though, via various strategies, may still be informative.

cancer biology↗

bioRxiv2019

High-sensitivity monitoring of ctDNA by patient-specific sequencing panels and integration of variant reads

Circulating tumor-derived DNA (ctDNA) can be used to monitor cancer dynamics noninvasively. Patients with small tumors have few copies of ctDNA in plasma, resulting in limited sensitivity to detect low-volume or residual disease. We show that sampling limitations can be overcome and sensitivity for ctDNA detection can be improved by massively parallel sequencing when hundreds to thousands of mutations are identified by tumor genotyping. We describe the INtegration of VAriant Reads (INVAR) analysis pipeline, which combines patient-specific mutation lists with both custom error-suppression methods and signal enrichment based on biological features of ctDNA. In this framework, the sensitivity can be estimated independently for each sample based on the number of informative reads, which is the product of the number of mutations analyzed and the average depth of unique sequencing reads. We applied INVAR to deep sequencing data generated by custom hybrid-capture panels, and showed that when ~106 informative reads were obtained INVAR allowed detection of tumor-derived DNA fractions to parts per million (ppm). In serial samples from patients with advanced melanoma on treatment, we detected ctDNA when imaging confirmed tumor volume of ~1cm3. In patients with resected early-stage melanoma, ctDNA was detected in 40% of patients who later relapsed, with higher rates of detection when more informative reads were obtained. We further demonstrated that INVAR can be generalized and allows improved detection of ctDNA from whole-exome and low-depth whole-genome sequencing data.

cancer biology↗

bioRxiv2019

Detection of ctDNA from dried blood spots after DNA size selection

Recent advances in the research and clinical applications of circulating tumour DNA (ctDNA) is limited by practical considerations of sample collection. Whole genome sequencing (WGS) is increasingly used for analysis of ctDNA, identifying copy-number alterations, fragment size patterns, and other genomic features. We hypothesised that low-depth WGS data may be generated from minute amounts of cell-free DNA, and that fragment-size selection may be effective to remove contaminating genomic DNA (gDNA) from small volumes of blood. There are practical advantages to using dried blood spots as these are easier to collect, facilitate serial sampling, and support novel study designs in prospective human studies, animal models and expand the utilisation of archival samples by the removal of gDNA in small volumes. We therefore developed a protocol for the isolation and analysis of cell-free DNA from dried blood spots. Analysing a dried blood spot of 50L frozen whole blood from a patient with melanoma, we identified ctDNA based on tumour-specific somatic copy-number alterations, and found a fragment size profile similar to that observed in plasma DNA processed by traditional methods. We extended this approach to detect tumour-derived cell-free DNA in a dried blood spot from a mouse xenograft model and were able to identify ctDNA from the originally grafted ascites. Together, our data suggests that ctDNA can be detected and monitored in dried blood spots. This will enable new approaches for sample collection from patients and in vivo models.

cancer biology↗