Biology subjects

Pang, A.

Publications and source records attributed to Pang, A..

10 recordsLinked to original sources

bioRxiv2026

Genetic characterisation and aggressiveness of the Fusarium oxysporum Species Complex in tomato plants and irrigation water from Australian processing fields

Fusarium oxysporum Species Complex (FOSC) includes important soilborne pathogens of a range of crops worldwide. In Victoria (VIC) and New South Wales (NSW), Australia, FOSC has been identified as the cause of stunting and poor growth in processing tomato fields, resulting in significant yield losses. A total of 40 FOSC isolates were obtained from symptomatic tomato plants, irrigation water samples and culture collections, which were confirmed to be FOSC by multi-gene phylogenetic analyses based on four genomic loci: beta tubulin, calmodulin, the second largest subunit of nuclear RNA polymerase II, and translation elongation factor one-alpha. There was a high level of genetic diversity among isolates, with multiple phylogenetic lineages detected. Glasshouse bioassays demonstrated that all isolates were pathogenic to processing tomato, resulting in significant reductions in plant growth, with above ground height reduced by 11 to 26% and root dry weight by 44 to 83% compared with the control (p < 0.05). Although aggressiveness varied among isolates, growth reduction occurred irrespective of their phylogenetic placement. Moreover, the shared genetic background of isolates from irrigation water and plant samples highlights the role of irrigation water as a potential source of inoculum in Fusarium epidemics, underscoring its significance for disease management in Australian processing tomato systems.

plant biology↗

bioRxiv2026

Cell fusion reprograms tumor cells and promotes RUNX1-mediated invasion and dissemination in colorectal cancer

Metastasis remains the primary cause of cancer-related morbidity and mortality, despite significant advances in targeted therapies. Although metastatic dissemination requires tumor cells to escape the primary lesion and colonize distant organs, the mechanisms by which primary tumor cells gain metastatic competence remain poorly understood. Increasing evidence demonstrates that fusion of tumor (i.e., neoplastic) and immune (e.g., macrophages) cells generate a distinct population of tumor-immune hybrid cells with enhanced functional ability to migrate and disseminate into peripheral blood. Herein, our study investigates tumor-macrophage hybrid cells, an underexplored population of disseminated tumor cells, and their inherent heterogeneity and acquisition of molecular mechanisms underlying their dissemination as metastatic effectors in colorectal cancer (CRC). Through hybrid cell phenotyping utilizing integrative single-cell RNA sequencing (scRNA-seq), cyclic immunofluorescence (cyCIF) and functional assays with an in vitro model of CRC hybrid cells, we identify Runt-related transcription factor 1 (Runx1) as a central regulator of hybrid cell motility and invasion. Runx1 depletion in hybrid cells suppressed functional protease expression, chemotactic activity and extracellular matrix (ECM) invasion. Furthermore, pharmacologic inhibition of RUNX1 in an in vivo model reduced hybrid tumor growth and dissemination into peripheral blood, key attributes of metastatic spread of disease. In patients with CRC, RUNX1+ hybrid cells were identified in both primary tumor and peripheral blood, where circulating hybrid cells (CHCs) exhibited enriched migratory and epithelial-to-mesenchymal transition (EMT) phenotypes. Taken together, these findings reveal a mechanistic role for RUNX1 in driving invasive behavior of tumor-immune hybrids and highlight disseminated CHCs as an under-recognized contributor to metastatic spread and a promising noninvasive biomarker for tumor progression.

cancer biology↗

bioRxiv2025

Ethological profiling of pain and analgesia in a mouse model of complex regional pain syndrome.

Complex regional pain syndrome (CRPS) is a form of chronic post-injury pain affecting the extremities. The mouse tibial fracture- cast model was developed to enable preclinical study of CRPS mechanisms and guide condition-specific drug development. Given the inherent limitations of reflex pain measures in mice, we sought to characterize pain-like behaviors in this model more holistically. We evaluated spontaneous and evoked pain and naturalistic behaviors after tibial fracture-cast injury in male mice in neutral and aversive environments using LabGym. Here, we report a unique ethological signature of pain in injured mice characterized by reflexive allodynia, thermal hyperalgesia, frequent grooming and reduced rearing in neutral and aversive environments, and decreased paw withdrawal and increased paw licking in an aversive environment. As proof-of-concept, we also leveraged this holistic behavioral evaluation for drug screening by characterizing the peripheral versus central effects of targeting alpha-2 receptors (2-AR) in the tibial fracture-cast model. We evaluated the impact of systemic delivery of dexmedetomidine (DEX), a selective 2-AR agonist, with or without antagonists, on holistic behavioral metrics in injured male mice. We found that DEX reduced mechanical allodynia primarily via central 2-ARs. DEX also decreased motion metrics, grooming and rearing in an open field, and distinctly affected the quality and quantity of grooming in an aversive environment, and this effect was not suppressed by systemic 2-AR antagonists. Ultimately, this study holistically captures pain-related behaviors and provides a detailed characterization of the relative contributions of peripheral and central 2-ARs to alpha2-mediated analgesia in male mice after tibial fracture-cast injury.

neuroscience↗

bioRxiv2024

Discovery of a single-subunit oligosaccharyltransferase that enables glycosylation of full-length IgG antibodies in Escherichia coli

Human immunoglobulin G (IgG) antibodies are one of the most important classes of biotherapeutic agents and undergo glycosylation at the conserved N297 site in the CH2 domain, which is critical for IgG Fc effector functions and anti-inflammatory activity. Hence, technologies for producing authentically glycosylated IgGs are in high demand. While attempts to engineer Escherichia coli for this purpose have been described, they have met limited success due in part to the lack of available oligosaccharyltransferase (OST) enzymes that can install N-linked glycans within the QYNST sequon of the IgG CH2 domain. Here, we identified a previously uncharacterized single-subunit OST (ssOST) from the bacterium Desulfovibrio marinus that exhibited greatly relaxed substrate specificity and, as a result, was able to catalyze glycosylation of native CH2 domains in the context of both a hinge-Fc fragment and a full-length IgG. Although the attached glycans were bacterial in origin, conversion to a homogeneous, asialo complex-type G2 N-glycan at the QYNST sequon of the E. coli-derived hinge-Fc was achieved via chemoenzymatic glycan remodeling. Importantly, the resulting G2-hinge-Fc exhibited strong binding to human Fc{gamma}RIIIa (CD16a), one of the most potent receptors for eliciting antibody-dependent cellular cytotoxicity (ADCC). Taken together, the discovery of a unique ssOST from D. marinus provides previously unavailable biocatalytic capabilities to the bacterial glycoprotein engineering toolbox and opens the door to using E. coli for the production and glycoengineering of human IgGs and fragments derived thereof.

synthetic biology↗

bioRxiv2024

Macropinocytosis mediates resistance to loss of glutamine transport in triple-negative breast cancer

Triple-negative breast cancer (TNBC) relies on glutamine uptake by the transporter ASCT2 to sustain their unique glutamine metabolism and growth. Despite previous data showing cell growth inhibition after ASCT2 knockdown, ASCT2 CRISPR knockout was well-tolerated by breast cancer cell lines. Despite the loss of a glutamine transporter and low rate of glutamine uptake, intracellular glutamine steady state levels were higher in ASCT2 knockout compared to control TNBC cells. Proteomics data revealed upregulation of macropinocytosis, reduction in glutamine efflux and glutamine synthesis in ASCT2 knockout cells. Loss of ASCT2 in TNBC cell line HCC1806 induced a 5-10-fold increase in macropinocytosis across 5 separate ASCT2 knockout clones, compared to a modest 2-fold increase in the shRNA ASCT2 knockdown. By comparison, ASCT2 knockout impaired cell proliferation in a non-macropinocytic breast cancer cell line, HCC1569. These data suggest that macropinocytosis provides a novel resistance mechanism to strategies targeting glutamine uptake alone. Despite this adaptation, TNBC cells continue to rely on glutamine metabolism for their growth, which suggests therapeutic targeting may need to focus on downstream glutamine metabolism pathways.

cancer biology↗

bioRxiv2024

The effect of the size of gold nanoparticle contrast agents on CT imaging of the gastrointestinal tract and inflammatory bowel disease

Ulcerative colitis (UC) is a chronic inflammatory bowel disease (IBD). CT imaging with contrast agents is commonly used for visualizing the gastrointestinal (GI) tract in UC patients. CT is a common imaging modality for evaluating IBD, especially in patients with acute abdominal pain presenting to emergency departments. CTs major limitation lies in its lack of specificity for imaging UC, as the commonly used agents are not well-suited for inflamed areas. Recent studies gastrointestinal tract (GIT) in UC. Further systemic research is needed to explore novel contrast agents that can specifically image disease processes in this disease setting.

bioengineering↗

bioRxiv2023

Single-cell T cell receptor sequencing of paired tissue and blood samples reveals clonal expansion of CD8+ effector T cells in patients with calcific aortic valve disease

Calcific aortic valve disease (CAVD) is a complex cardiovascular pathology, culminating in aortic stenosis, heart failure and premature mortality, with no comprehensive treatment strategy, except valve replacement. While T cells have been identified within the valve, their contribution to pathogenesis remains unclear. To elucidate the heterogenous phenotype of the immune populations present within patients with CAVD, deep phenotypic screens of paired valve and peripheral blood cells were conducted via flow cytometry (n=20) and immunohistochemistry (n=10). Following identification of a significant population of memory T cells; specifically, CD8+ T cells within the valve, single cell RNA sequencing and paired single T cell receptor sequencing was conducted on a further 4 patients on CD45+ CD3+, CD4+ or CD8+ T cells. Through unsupervised clustering, 7 T cell populations were identified within the blood and 10 identified within the valve. Tissue resident memory (TRM) T cells were detected for the first time within the valve, exhibiting a highly cytotoxic, activated, and terminally differentiated phenotype. This pan-pro-inflammatory signal was differentially identified in T cells originating from the valve, and not observed in the blood, indicative of an adaptive, local not-systemic inflammatory signature in CAVD patients. T cell receptor analysis identified hyperexpanded clones within the CD8+ T cell central memory (TCM) population, with TRM cells comprising the majority of large and medium clonal expansion within the entire T cell population. Clonal interaction network analysis demonstrated the greatest proportion of clones originating from CD8+ T cell effector memory (TEM) and CD4+ naive / TCM populations and ending in the CD8+ TRM and CD8+ TCM clusters, suggesting a clonal expansion and predicted trajectory of T cells towards a tissue resident, cytotoxic environment within the valve. CDR3 epitope predictive analysis identified 7 potential epitope targets, of which GALNT4 and CR1L have previously been implicated in a cardiovascular context as mediators of inflammation. Taken together, the data identified T cell sub-populations within the context of CAVD and further predicted possible epitopes responsible for the clonal expansion of the valvular T cells, which may be important for propagating inflammation in CAVD.

immunology↗

bioRxiv2021

Chromosome-level genome assembly of the functionally extinct northern white rhinoceros (Ceratotherium simum cottoni).

The northern white rhinoceros (NWR; Ceratotherium simum cottoni) is functionally extinct, with only two females remaining alive. Efforts to rescue the NWR have inspired the exploration of unconventional conservation methods, including the generation of artificial gametes from induced pluripotent stem cells and somatic cell nuclear transfer. To enable the technologies required for these approaches, we used complementary sequencing and mapping methods to generate a NWR chromosome-level reference genome that meets or exceeds the metrics proposed by the Vertebrate Genome Project. It represents 40 autosomes, an X and a partially-resolved Y chromosome, and the mitochondrial genome. We compared the NWR reference genome to the southern white rhinoceros (SWR) population that has been physically separated from the NWR for tens of thousands of years. Using short-read data from the SWR and optical mapping, we found that the two populations are very similar on both the chromosome level and mitochondrial genome level. The results of this study are encouraging for the efforts underway to rescue the NWR.

genomics↗

bioRxiv2020

Inhibition of guanosine monophosphate synthetase (GMPS) blocks glutamine metabolism and prostate cancer growth in vitro and in vivo

Cancer cells increase their uptake of nutrients and metabolize them to provide the necessary building blocks for new cancer cells. Glutamine is a critical nutrient in cancer, however its contribution to purine metabolism in prostate cancer has not previously been determined. Guanosine monophosphate synthetase (GMPS) acts in the de novo purine biosynthesis pathway, utilizing a glutamine amide to synthesize the guanine nucleotide and replenish the purine pool in proliferative cancer cells. This study demonstrates that GMPS mRNA expression correlates with Gleason score in prostate cancer samples, while high GMPS expression was associated with decreased rates of overall and disease/progression-free survival. Pharmacological inhibition or knockdown of GMPS significantly decreased cell growth in both LNCaP and PC-3 prostate cancer cells. GMPS knockdown was rescued by addition of extracellular guanosine to the media, suggesting a direct effect on nucleotide synthesis. We utilized 15N-(amide)-glutamine and U-13C5-glutamine metabolomics to dissect the pathways involved, and intriguingly, despite similar growth inhibition by GMPS knockdown, we show unique metabolic effects across each cell line. PC-3 cells showed a build-up of purine precursors, as well as activation of purine salvage pathways highlighted by significant increases in guanine, adenosine, inosine and cytosine. Both cell lines exhibited increased levels of pyrimidines and prioritized TCA cycle in distinct ways to produce increased aspartate, another important purine precursor. Using a PC-3 xenograft mouse model, tumor growth was also significantly decreased after GMPS knockdown. These data further highlight the importance of glutamine metabolism for prostate cancer cell growth and provide support for GMPS as a new therapeutic target in prostate cancer.

cancer biology↗

bioRxiv2019

Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation

We present high quality, phased genome assemblies representative of taurine and indicine cattle, subspecies that differ markedly in productivity-related traits and environmental adaptation. We report a new haplotype-aware scaffolding and polishing pipeline using contigs generated by the trio binning method to produce haplotype-resolved, chromosome-level genome assemblies of Angus (taurine) and Brahman (indicine) cattle breeds. These assemblies were used to identify structural and copy number variants that differentiate the subspecies and we found variant detection was sensitive to the specific reference genome chosen. Six gene families with immune related functions are expanded in the indicine lineage. Assembly of the genomes of both subspecies from a single individual enabled transcripts to be phased to detect allele-specific expression, and to study genome-wide selective sweeps. An indicus-specific extra copy of fatty acid desaturase is under positive selection and may contribute to indicine adaptation to heat and drought.

genomics↗