http://hdl.handle.net/10453/35220 2026-04-29T16:18:17Z http://hdl.handle.net/10453/194664 Title: Noninvasive Assessment of Urinary Exfoliated Proximal Tubule Cell Multispectral Autofluorescence May Differentiate between Causes of Kidney Transplant Dysfunction. Authors: Wu, HHL; Lang, Y; Handley, S; Knab, A; Agha, A; Tian, Y; Bhargava, A; Goldys, EM; Pollock, CA; Saad, S Abstract: KEY POINTS: There is an unmet critical need currently for a noninvasive approach to accurately diagnose the cause of kidney transplant complications. Cell multispectral autofluorescence signals have demonstrated to be highly biologically informative, reflecting cell and tissue metabolic status. Urinary exfoliated proximal tubule cell multispectral autofluorescence could potentially be used to differentiate between causes of transplant graft dysfunction. BACKGROUND: Complications relating to delayed or deteriorating graft function following kidney transplantation are common. There is no validated method apart from transplant kidney biopsy which can accurately identify between the histopathologic causes of graft dysfunction. Considering an unmet critical need for a noninvasive approach to reliably diagnose kidney transplant complications, this work proposes a novel methodology based on the assessment of exfoliated proximal tubule cells (PTCs) extracted from urine of kidney transplant recipients by using their multispectral autofluorescence features. METHODS: Three groups of ten patients who have undergone clinically indicated transplant kidney biopsy and was subsequently diagnosed with either acute tubular necrosis (ATN), graft rejection or non–rejection-associated interstitial fibrosis, and tubular atrophy (IFTA) took part in this study. Exfoliated PTCs from urine collected before transplant biopsy were extracted using a validated immunomagnetic separation method based on anti-CD13 and anti-sodium-glucose co-transport 2 antibodies. Imaging was performed on a custom-made multispectral autofluorescence microscopy and camera system. Multispectral autofluorescence images of PTCs were quantitatively analyzed by using optimized small sets of features to prevent overfitting. Binary classification was performed by a random forest classifier and the AutoGluon machine learning software. The results were validated by five-fold cross-validation. RESULTS: For random forest classification, features were selected using entropy-based feature selection, resulting in area under the curve values of 0.92 (ATN versus graft rejection), 0.86 (ATN versus IFTA), and 0.62 (graft rejection versus IFTA) respectively. The AutoGluon classifier optimisation for the same features resulted in area under the curve values of 0.95 (ATN versus graft rejection), 0.92 (ATN versus IFTA), and 0.91 (graft rejection versus IFTA). CONCLUSIONS: Our results demonstrate a proof-of-concept that measurement of autofluorescent features from urinary exfoliated PTCs multispectral autofluorescence could differentiate between patient groups with ATN, graft rejection, and IFTA in kidney transplant recipients to an excellent degree of accuracy using AutoGluon classifier optimisation. 2025-11-01T00:00:00Z http://hdl.handle.net/10453/194662 Title: Urinary proteomic profiling to identify early biomarkers of non-diabetic chronic kidney disease. Authors: Wu, HHL; Parthiban, NK; Zenaidee, MA; Pang, I; Wu, Y; Ahn, SB; Walker, RJ; Pollock, CA; Saad, S 2025-11-01T00:00:00Z http://hdl.handle.net/10453/194661 Title: Defective HIV-1 DNA pol sequences are not associated with HIV-1 DNA levels and drive most APOBEC-context drug resistance mutations. Authors: Alidjinou, EK; Coulon, P; Tetart, M; Guigon, A; Diarra, A; Aissi, E; Bazus, H; Derdour, V; Meybeck, A; Viget, N; Hober, D; Bocket, L; Robineau, O Abstract: INTRODUCTION: The specificity of HIV-1 DNA genotypic resistance tests (GRTs) is hampered by the detection of the APOBEC-context drug resistance mutations (AC DRMs), usually harboured by replication-incompetent proviruses. We sought factors associated with defective sequences in the HIV-1 pol region. In addition, AC DRMs and their link with defective sequences were investigated. METHODS: We included ART-treated patients with viral suppression or plasma viral load (VL) lower than 200 copies/mL, who underwent HIV-1 DNA genotyping, with successful sequencing of protease (PR), reverse transcriptase (RT) and integrase (IN) regions. Sequencing was performed using either the Sanger method or the Sentosa® NGS approach with a 20% cut-off. All hypermutated sequences and/or those containing at least one stop codon were considered defective. RESULTS: A total of 613 HIV-1 DNA GRTs were analysed. Defective sequences were identified for 186 samples (30.3%) including 65 PR sequences, 92 RT sequences and 65 IN sequences. No association, including HIV-1 DNA levels, was found with the detection of defective pol sequences. A total of 226 AC DRMs were recorded in all sequences. Most of these mutations (78%) were harboured by defective sequences. AC DRMs did not emerge in the plasma viral population, and likely do not impact the virological response to ART. CONCLUSIONS: Defectives pol sequences were not associated with HIV-1 DNA levels and harboured most of the AC DRMs. Such mutations likely have no clinical impact, and should not be reported in routine practice. Consensus guidelines for reporting HIV-1 DNA GRTs are needed, especially for the assessment and management of AC DRMs. 2025-04-02T00:00:00Z http://hdl.handle.net/10453/194309 Title: SCFA biotherapy delays diabetes in humanized gnotobiotic mice by remodeling mucosal homeostasis and metabolome. Authors: Tillett, BJ; Dwiyanto, J; Secombe, KR; George, T; Zhang, V; Anderson, D; Duggan, E; Giri, R; Loo, D; Stoll, T; Morrison, M; Begun, J; Hill, MM; Gurzov, EN; Bell, KJ; Saad, S; Barlow, CK; Creek, DJ; Chong, CW; Mariño, E; Hamilton-Williams, EE Abstract: Type 1 diabetes (T1D) is linked to an altered gut microbiota characterized by reduced short-chain fatty acid (SCFA) production. Oral delivery of a SCFA-yielding biotherapy in adults with T1D was followed by increased SCFAs, altered gut microbiota and immunoregulation, as well as delaying diabetes in preclinical models. Here, we show that SCFA-biotherapy in humans is accompanied by remodeling of the gut proteome and mucosal immune homeostasis. Metabolomics showed arginine, glutamate, nucleotide and tryptophan metabolism were enriched following the SCFA-biotherapy, and found metabolites that correlated with glycemic control. Fecal microbiota transfer demonstrated that the microbiota of SCFA-responders delayed diabetes progression in humanized gnotobiotic mice. The protected mice increased similar metabolite pathways to the humans including producing aryl-hydrocarbon receptor ligands and reducing inflammatory mucosal immunity and increasing IgA production in the gut. These data demonstrate that a potent SCFA immunomodulator promotes multiple beneficial pathways and supports targeting the microbiota as an approach against T1D. Trial registration: Australia New Zealand Clinical Trials Registry ACTRN12618001391268. 2025-03-25T00:00:00Z