BACKGROUND:To better understand HIV and cardiovascular disease (CVD) effects on brain white matter during HIV infection, advanced diffusion imaging and comprehensive predictor analyses are essential. SETTING:Prospective observational cohort study. METHOD:84 virally suppressed people with HIV infection (PWH) and 48 uninfected controls underwent T1-weighted, FLAIR, and diffusion MRI at baseline and 24 months later (75 PWH and 40 controls). White Matter Hyperintensity (WMH) volumes were derived from structural scans. Fixel-based analysis tract-based metrics included fibre density (FD), fibre cross-section (FC) and fibre density and cross-section (FDC). RESULTS:Relative to controls, mixed models showed significant reductions (p<.05 - p<.01) of FC, and lower FDC to a lesser extent, in multiple long cortical association tracts, and within striatal- and thalamic-frontoparietal connections in PWH at both time points. Higher CVD risk was associated with reduced FC in the arcuate fasciculus and FDC in the cingulate gyrus (p<.05). In PWH, more severe cognitive impairment and longer duration of HIV disease was associated with worse FDC across multiple tracts (p<.03 - p<.001). Lower baseline CD4 counts was associated with lower FD in the frontal association tracts (p<.05 - p<.005). Higher WMH volume was associated with higher CVD risk (periventricular p<.001, deep p<.03), but not HIV status. CONCLUSIONS:Major brain white matter tracts are impacted by HIV status, HIV duration, cognitive impairment, baseline CD4, and CVD risk to a lesser extent, despite equal WMH burden between infection groups. Our study provides further evidence of active immuno-vascular underpinning of HIV neuropathogenesis on fine white matter structure despite controlled HIV.

Abstract Despite sustained viral suppression with effective antiretroviral therapy (ART), impaired neuroaxonal integrity persist in a subset of people with HIV-1 (PWH). We investigated whether interferon (IFN)-inducible APOBEC3-associated mutational signatures, reflected by premature stop codons (PSCs), and reservoir-associated drug resistance mutations (RS-DRMs) within transcriptionally active HIV-1 reservoirs influence neuroaxonal integrity in fully virally suppressed individuals. Peripheral CD4⁺ T cells from individuals with undetectable plasma HIV-1 RNA (n = 27) were analyzed for long HIV-1 gag/pol transcripts (>4.2 kb), and frontal white matter (FWM) neuroaxonal integrity was assessed using proton magnetic resonance spectroscopy (¹H-MRS) measurement of N-acetylaspartate (NAA). Short HIV-1 RNA transcripts, reflecting promoter-associated transcriptional activity, were detected in all participants and were associated with reduced NAA levels in FWM, consistent with a relationship between ongoing reservoir activity and impaired neuroaxonal integrity despite virological suppression. Long gag/pol transcripts (>4.2 kb) were detected in 78% of participants and exhibited marked heterogeneity in APOBEC3-associated PSC burden. PSC-containing long transcripts were associated with higher NAA, whereas long transcripts lacking such inactivating mutations were associated with reduced NAA, suggesting that APOBEC3-associated restriction of viral translational competence may contribute to differences in the downstream neurobiological effects of transcriptionally active reservoir states. RA-DRMs were detected in 43% of participants, including triple-class resistance consistent with archived treatment exposure over more than a decade. Matching gag/pol sequences from reactivated virions confirmed latent reservoir origin; however, RS-DRMs showed no independent association with neuroaxonal outcomes. Across systemic inflammatory markers, vascular risk factors, cerebrospinal fluid immune activation measures, and clinical neurocognitive outcomes (including HAND status), no consistent associations with NAA were observed. Overall, reduced neuroaxonal integrity in the FWM was associated with the interplay between short HIV-1 RNA transcriptional activity and APOBEC3-edited translational states of long HIV-1 RNA transcripts within peripheral reservoirs, suggesting that interferon-inducible APOBEC3-associated mutational signatures may reflect biologically distinct reservoir states that correspond to neurobiological effects during suppressive antiretroviral therapy. Graphical Abstract Interferon-Inducible APOBEC3-Associated Premature Stop Codon Signatures in HIV-1 Reservoirs and Preservation of Neuroaxonal Integrity Highlights Short HIV-1 RNA transcription within peripheral CD4⁺ T-cell reservoirs was associated with reduced frontal white matter N-acetylaspartate during suppressive ART. Long HIV-1 gag/pol RNA transcripts exhibited marked heterogeneity in interferon-inducible APOBEC3-associated G-to-A hypermutation, including premature stop codon signatures. Archived reservoir-associated drug resistance mutations were identified within transcriptionally active long HIV-1 reservoir-derived RNA during suppressive ART. Reduced neuroaxonal integrity was associated with the interplay between short HIV-1 transcriptional activity and interferon-inducible APOBEC3-associated editing of long HIV-1 transcripts with reduced predicted translational competence.

Abstract Despite suppressive antiretroviral therapy (ART), people with HIV (PWH) remain at increased risk of cardiovascular disease (CVD), likely driven, at least in part, by persistent immune activation and vascular inflammation. Mechanistic pathways may include ongoing low-level HIV transcription within immune cells, particularly peripheral blood mononuclear cells (PBMCs), which may contribute to chronic inflammatory signaling. Persistent viral transcription and inflammatory signaling may also be associated with an interferon-responsive cellular environment conducive to APOBEC3 activation and mutational editing of viral transcripts. APOBEC3 enzymes, which are interferon (IFN)-inducible cytidine deaminases, generate characteristic premature stop codons (PSCs) within retroviral genomes and may reflect interferon-associated inflammatory states relevant to vascular pathology. We investigated whether APOBEC3-associated PSC signatures and reservoir-associated drug resistance mutations (RA-DRMs) in viral reservoirs, as markers of persistent reservoir transcriptional activity, are associated with vascular inflammation in ART-suppressed individuals. PBMCs from ART-suppressed PWH (n=36) were analyzed for long HIV-1 gag/pol transcripts (>4.2 kb) and PSCs as a surrogate marker of APOBEC3 activity, with RA-DRMs assessed by Oxford Nanopore sequencing. Arterial inflammation was quantified using PET imaging of the aorta and carotid arteries. Additionally, an exploratory panel of >60 cardiometabolic, clinical, and inflammatory biomarkers was profiled to identify host immune signatures associated with reservoir PSC burden, with focused analyses on circulating inflammatory biomarkers sCD14, sCD163, and IP-10. Long HIV-1 transcripts were detected in 67% (24/36) despite ART. Higher PSC frequency within these transcripts was significantly associated with increased aortic inflammation, but not carotid inflammation, in univariable analysis (β = 0.00834, p = 0.013). RA-DRMs were detected in 50% (12/24), including triple-class resistance, but were not associated with vascular inflammation or soluble biomarkers. In multivariable models, PSCs remained independently associated with aortic inflammation after adjustment for sCD14 and sCD163 (β = 0.0075, p = 0.023), and remained the only significant predictor when IP-10 was included (β = 0.0073, p = 0.036). These findings suggest that APOBEC3-associated PSC signatures in long HIV transcripts identify transcriptionally active HIV reservoir states associated with aortic inflammation during suppressive ART. Rather than reflecting ongoing mutational accumulation or direct pathogenic effects of PSCs themselves, these signatures may serve as biomarkers of an interferon-associated inflammatory reservoir state related to cardiovascular risk. Graphical Abstract Highlights: Interferon-inducible APOBEC3-associated PSC signatures in HIV reservoirs and vascular inflammation APOBEC3-associated premature stop codon (PSC) signatures were identified in transcriptionally active HIV reservoir-derived RNA despite suppressive ART. Higher PSC burden was significantly associated with increased aortic vascular inflammation measured by FDG-PET. Reservoir-associated drug resistance mutations (RA-DRMs) showed no association with arterial inflammation. PSC burden remained independently associated with aortic vascular inflammation in multivariable analyses. PSC-enriched reservoir states were associated with inflammatory biomarker patterns consistent with monocyte–macrophage activation and vascular immune activation. These findings are consistent with an interferon-inducible APOBEC3-edited reservoir state associated with persistent arterial inflammation during suppressive ART. APOBEC3-associated mutational signatures may represent a candidate biomarker of vascular inflammation and cardiovascular risk in people with HIV.

PURPOSE OF REVIEW:To discuss neurocognition measurement in view of current controversies in HIV-associated neurocognitive disorders (HAND). RECENT FINDINGS:The HAND criteria have been criticised for several reasons with some proposing alternative criteria and terminology, HIV-associated brain injury (HABI). The following concerns have been raised: the legacy effect from past ineffective therapy is not included, the adoption of an asymptomatic neurocognitive impairment (ANI) stage, including liberal neuropsychological test cut-offs overestimate neurocognitive impairment (NCI), and that NCI with viral suppression is still related to HIV rather than the effect of either legacy and/or comorbidities. However, the legacy effect cannot be easily identified, the HAND criteria have been inappropriately used, and there is increasing evidence that low level HIV replication is important in virally suppressed HAND, though likely mitigated in some by resilience factors. Potential solutions to addressing these within the HAND framework will be proposed. SUMMARY:The HAND framework is still useful but it must be put in clinical context. ANI should be considered a research category pending further clarification of its clinical utility. Further work is needed to identify and quantify the legacy effect/ongoing NCI, as well as the nature of resilience.

PURPOSE OF REVIEW:The neuropathogenesis of acute HIV leads to rapid central nervous system (CNS) involvement, characterized by early viral entry, immune activation, and the formation of viral reservoirs. Despite effective antiretroviral therapy (ART), these reservoirs persist, drive neuroinflammation and injury and lead to HIV-associated neurodegenerative disorders (HAND). This review provides an updated synthesis of the mechanisms in acute HIV neuropathogenesis, biomarkers of CNS injury and emerging therapeutic approaches. A deeper understanding of these mechanisms is critical for addressing persistent HAND in ART-treated individuals. RECENT FINDINGS:Growing evidence now supports the principal role of infected CD4 + T cells in mediating HIV neuroinvasion alongside monocytes, resulting in seeding in perivascular macrophages, pericytes, and adjacent microglia and astrocytes. These reservoirs contribute to ongoing transcriptional activity and viral persistence despite antiretroviral therapy. Neuroinflammation, driven by activated microglia, astrocytes, inflammasomes, and neurotoxic viral proteins, disrupts neuronal homeostasis. Emerging therapies, including latency-reversing agents and transcription inhibitors, show promise in reducing neuroinflammation and reservoir activity. SUMMARY:Understanding the mechanisms of HIV neuropathogenesis and reservoir persistence has significant implications for developing targeted therapies to mitigate HAND. Strategies to eliminate CNS reservoirs and reduce neuroinflammation should be prioritized to improve long-term cognitive outcomes in people with HIV.

Prevalence and incidence of HIV among people aged 50 years and older continue to rise worldwide, generating increasing awareness among care providers, scientists, and the HIV community about the importance of brain health in older adults with HIV. Many age-related factors that adversely affect brain health can occur earlier and more often among people with HIV, including epigenetic ageing, chronic medical conditions (eg, cardiovascular disease), and age-related syndromes (eg, frailty). Extensive dialogue between HIV community leaders, health-care providers, and scientists has led to the development of a multidimensional response strategy to protect and enhance brain health in people ageing with HIV that spans across public health, clinical spaces, and research spaces. This response strategy was informed by integrated ageing care frameworks and is centred on prevention, early detection, and management of brain health issues associated with HIV (eg, neurocognitive disorders), with specific considerations for low-resource or middle-resource countries. A collaborative, international, and data-informed update of the diagnostic criteria for HIV-associated neurocognitive disorders is a cornerstone of the proposed response strategy. The proposed response strategy includes a dynamic, international, online knowledge hub that will provide a crucial community resource for emerging evidence on the brain health of people ageing with HIV.

The kynurenine pathway (KP) is the canonical route by which tryptophan is metabolised, almost all of which occurs in the liver, with significant expression of its enzymes also known in the kidney. We generated two novel mouse models for inducible global knockout of midpoint KP enzyme kynurenine-3-monooxygenase (KMO) and endpoint enzyme quinolinate phosphoribosyltransferase (QPRT; converts known neurotoxic KP metabolite Quinolinic acid to nicotinamide adenine dinucleotide (NAD) precursor via the de novo synthesis pathway). The KP is dysregulated in many renal and hepatic disorders, but as an essential step prior to use in disease studies, we set out to characterise their basal KP metabolome and investigate any changes to their overall phenotype in the liver and kidney, free of exogenous inflammatory stimuli. Both enzyme knockouts caused rapid alterations in accumulation of blood metabolite levels upstream of the affected enzyme, although downstream metabolite concentrations were surprisingly unaffected. KMO knockout elevated kynurenine, kynurenic acid and anthranilic acid, while QPRT knockout elevated quinolinic acid. Regardless of these significant metabolic alterations, histological examination of liver and kidney tissues, standard clinical blood chemistry and gross animal observations indicated no evidence of pathological changes in both the renal and hepatic systems. Our findings suggest that in a timeframe of 1-5 weeks and without evoked inflammation, robust homeostatic mechanisms can accommodate substantial fluctuations in KP metabolite concentrations in knockout mice without affecting renal or hepatic structure or function.

Integrase strand transfer inhibitors (INSTIs) are the cornerstone of modern antiretroviral therapy (ART), achieving durable plasma HIV-1 suppression in most people living with HIV (PLWH). Previous comparisons of INSTI- and non-INSTI-based regimens have largely focused on HIV reservoir proviral assessments- typically total HIV DNA -without assessing reservoir activity. In this first functional comparison, we measured cell-associated (CA) short HIV-1 RNA transcripts, a marker of active transcription, alongside HIV-1 DNA in white blood cells from 92 virally suppressed individuals on INSTI-based (n = 73) or non-INSTI-based (n = 19) ART. CA short RNA transcripts were detected in all participants and HIV-1 DNA in 99 %, despite undetectable plasma viremia in >93 %. Individuals with prior "blips" - defined as a maximum of two episodes with 20-200 copies/mL plasma HIV-1 RNA over more than two years - had significantly higher CA RNA and HIV DNA than non-blip participants, confirming our previous findings. However, reservoir size and transcriptional activity did not differ significantly between INSTI and non-INSTI groups. These findings indicate that while INSTIs effectively block new integration events, they do not suppress ongoing transcription from the latent reservoir. Therapeutic strategies directly targeting HIV transcription should therefore be prioritized in cure-oriented research for PLWH on long-term suppressive ART.

Progranulin (PGRN), a glycoprotein secreted by microglia and neurons, regulates lysosomal function, neuroinflammation, and has neurotrophic effects. Variants in the granulin gene ( GRN ) that cause a reduction of PGRN in plasma and cerebrospinal fluid (CSF) are associated with an increased risk of Alzheimer’s disease (AD). The sortilin receptor (SORT1) on neurons and microglia regulates PGRN degradation. GSK4527226 (AL101) is a human monoclonal immunoglobulin G1 antibody that inhibits SORT1 and increases extracellular PGRN levels in plasma and CSF. In Phase I studies, GSK4527226 was well tolerated with an acceptable safety profile in healthy volunteers, and showed dose-dependent PGRN elevation in plasma and CSF (Ward et al. CTAD 2021; Germani et al. ACCP 2023). PROGRESS-AD is a phase 2, parallel group, randomized, double-blind, global study which aims to evaluate the efficacy and safety of GSK4527226 versus placebo in patients with early AD (N = 282) (EU CT: 2023-505083-11-00; NCT06079190). Eligible patients are in the Alzheimer’s continuum, with amyloid positivity and clinical severity consistent with mild cognitive impairment or mild dementia, as defined by the 2018 National Institute on Aging and Alzheimer’s Association Research Framework ( Figure ). Patients (aged 50-85 years) will be randomized to receive intravenous GSK4527226 (dose 1), GSK4527226 (dose 2), or placebo for 76 weeks, followed by a 12-week safety follow-up period ( Figure ). Randomization will be stratified by APOE4 status, AD stage and participation in the CSF sub-study. The primary endpoint is change from baseline (CFB) in the Clinical Dementia Rating-Sum of Boxes (CDR-SB) score across Weeks 52, 64, and 76. Key secondary endpoints include CFB in the iADRS, ADAS-Cog14, ADCS-iADL component of ADCS-ADL-MCI, and ADCOMS. Safety endpoints include incidence of treatment-emergent adverse events. Key exploratory endpoints include effect of GSK4527226 on pharmacodynamic and disease biomarkers, and pharmacokinetics of GSK4527226. The primary analysis will use a proportional MMRM (Wang, 2022) under a Bayesian framework with a non-informative prior distributions. Three sub-studies will be conducted to assess the effects of GSK4527226 on amyloid PET, tau PET, and CSF biomarkers. N/A. This study of the anti-sortilin antibody, GSK4527226, will comprehensively evaluate its efficacy, safety and effects on pathogenesis in early AD.

Objective:To discover microRNA (miRNA)-RNA transcript interactions dysregulated in brains from persons with HIV-associated neurocognitive disorder (HAND), we investigated RNA expression using machine learning tools.Design:Brain-derived host RNA transcript and miRNA expression was examined from persons with or without HAND using bioinformatics platforms.Methods:By combining next generation sequencing, droplet digital (dd)PCR quantitation of HIV-1 genomes, with bioinformatics and statistical tools, we investigated differential RNA expression in frontal cortex from persons without HIV [HIV(-)], with HIV without brain disease [HIV(+)], with HAND, or HAND with encephalitis (HIVE).Results:Expression levels for 147 transcripts and 43 miRNAs showed a minimum four-fold difference between clinical groups with a predominance of antiviral (type I interferon) signaling-related, neural cell maintenance-related, and neurodevelopmental disorder-related genes that was validated by gene ontology and molecular pathway inferences. Scale of signal-to-noise ratio (SSNR) and biweight midcorrelation (bicor) analyses identified 14 miRNAs and 45 RNA transcripts, which were highly correlated and differentially expressed (P <= 0.05). Machine learning applications compared regression models predicated on HIV-1 DNA, or RNA viral quantities that disclosed miR-4683 and miR-154-5p were dominant variables associated with differential expression of host RNAs. These miRNAs were also associated with antiviral-related, cell maintenance-related, and neurodevelopmental disorder-related genes.Conclusion:Antiviral as well as neurodevelopmental disorder-related pathways in brain were associated with HAND, based on correlated RNA transcripts and miRNAs. Integrated molecular methods with machine learning offer insights into disease mechanisms, underpinning brain-related biotypes among persons with HIV that could direct clinical care.

Objective: To discover microRNA (miRNA)-RNA transcript interactions dysregulated in brains from persons with HIV-associated neurocognitive disorder (HAND), we investigated RNA expression using machine learning tools. Design: Brain-derived host RNA transcript and miRNA expression was examined from persons with or without HAND using bioinformatics platforms. Methods: By combining next generation sequencing, droplet digital (dd)PCR quantitation of HIV-1 genomes, with bioinformatics and statistical tools, we investigated differential RNA expression in frontal cortex from persons without HIV (HIV[-]), with HIV without brain disease (HIV[+]), with HIV-associated neurocognitive disorder (HAND), or HAND with encephalitis (HIVE). Results: Expression levels for 147 transcripts and 43 miRNAs showed a minimum 4-fold difference between clinical groups with a predominance of antiviral (Type I interferon) signaling-, neural cell maintenance-, and neurodevelopmental disorder-related genes that was validated by gene ontology and molecular pathway inferences. Scale of signal-to-noise ratio (SSNR) and biweight midcorrelation (bicor) analyses identified 14 miRNAs and 45 RNA transcripts, which were highly correlated and differentially expressed (p ≤ 0.05). Machine learning applications compared regression models predicated on HIV-1 DNA, or RNA viral quantities that disclosed miR-4683 and miR-154-5p were dominant variables associated with differential expression of host RNAs. These miRNAs were also associated with antiviral-, cell maintenance-, and neurodevelopmental disorder-related genes. Conclusions: Antiviral as well as neurodevelopmental disorder-related pathways in brain were associated with HAND, based on correlated RNA transcripts and miRNAs. Integrated molecular methods with machine learning offer insights into disease mechanisms, underpinning brain-related biotypes among persons with HIV that could direct clinical care.

Despite viral suppression with antiretroviral therapy (ART), people with HIV (PWH) continue to exhibit brain pathology, and ~20% of individuals develop HIV-associated neurocognitive disorders. However, the state of cellular activation in the brain of virally suppressed (VS) PWH and the impact of local viral reservoirs on cellular activation are unclear. Using multiplex immunofluorescence imaging, here, we demonstrate that the frontal cortex brain tissue from both non-virally suppressed (nVS; n=17) and VS PWH (n=18) have higher frequencies of astrocytes and myeloid cells expressing interferon-inducible Mx-1 and proinflammatory TNFα relative to HIV-seronegative individuals (p<0.05 for all). The frequency of TGF-β1+ cells were also elevated in the brain tissue from both nVS and VS PWH, which may support active immunoregulatory responses despite ART. Importantly, the frequency of Mx1+ myeloid cells correlated with levels of total HIV DNA and intact and 5' defective HIV proviral DNA (p<0.05 for all) in the brain of VS PWH. These findings demonstrate that cell activation persists in the brain of VS PWH and is associated with HIV DNA in the brain, which may contribute to neuropathology.

The glymphatic system, a waste clearance pathway, has been implicated in several neurological conditions associated with neuroinflammation. COVID-19 associated neurocognitive impairment, part of the post-acute sequelae of SARS-CoV-2 infection (PASC), is strongly associated with neuroinflammation and disrupted blood-brain barrier (BBB). Several studies have implicated a synergistic interaction between the glymphatic system dysfunction and BBB disruption. In this proof-of-concept study, we investigated the role of the MRI metric diffusion along the perivascular spaces DTI (DTI-ALPS) in patients with PASC and correlated this with the BBB capillary permeability metric- K trans derived from Dynamic contrast enhanced (DCE) perfusion. 14 subjects with PASC who had persisting symptoms of anosmia, ageusia, fatigue, and cognitive impairment (CI) and ten healthy age and sex matched controls were recruited. All PASC subjects underwent routine and advanced MR brain imaging at two time points, (3 months +/- 2 weeks) after initial infection - referred as Time Point 1 (TP-1) - and 10 repeated the MRI scan 12 months (+/- 2 weeks) later - referred as Time Point 2 (TP-2), while the controls had MR imaging done only at TP-1. All had mild neurocognitive impairment. In the final analysis we included those who had DTI study at both time points (n-10). MR imaging included DCE perfusion and DTI in addition to anatomical imaging. Given the small size of the sample and nonnormality of data in the descriptive analyses, nonparametric analyses were used for group comparisons. A two-sample Wilcoxon rank sum test was used to show the differences in DTI-ALPS between the patients and controls in the predefined regions of interest. Spearman’s correlation coefficient (rho) was used to assess the correlation between DTI-ALPS index with K trans. There was significant reduction in the DTI-ALPS index between the patients and controls in the left hemisphere (z = 2.04, p < 0.04). However, there was no significant change over time in the index. There was a strong inverse correlation between the central white matter K trans and DTI-ALPS index (rho = 0.66, p < 0.03). Our study indicates that disordered para vascular drainage, a marker for glymphatic system and BBB damage may contribute to neurocognitive impairment (NCI) among patients with PASC. The DTI-ALPS index, which does not require contrast injection, has the potential to serve as a non-invasive biomarker.

Stem cells are ubiquitously found in various tissues and organs in the body, and underpin the body’s ability to repair itself following injury or disease initiation, though repair can sometimes be compromised. Understanding how stem cells are produced, and functional signaling systems between different niches is critical to understanding the potential use of stem cells in regenerative medicine. In this context, this review considers kynurenine pathway (KP) metabolism in multipotent adult progenitor cells, embryonic, haematopoietic, neural, cancer, cardiac and induced pluripotent stem cells, endothelial progenitor cells, and mesenchymal stromal cells. The KP is the major enzymatic pathway for sequentially catabolising the essential amino acid tryptophan (TRP), resulting in key metabolites including kynurenine, kynurenic acid, and quinolinic acid (QUIN). QUIN metabolism transitions into the adjoining de novo pathway for nicotinamide adenine dinucleotide (NAD) production, a critical cofactor in many fundamental cellular biochemical pathways. How stem cells uptake and utilise TRP varies between different species and stem cell types, because of their expression of transporters and responses to inflammatory cytokines. Several KP metabolites are physiologically active, with either beneficial or detrimental outcomes, and evidence of this is presented relating to several stem cell types, which is important as they may exert a significant impact on surrounding differentiated cells, particularly if they metabolise or secrete metabolites differently. Interferon-gamma (IFN-γ) in mesenchymal stromal cells, for instance, highly upregulates rate-limiting enzyme indoleamine-2,3-dioxygenase (IDO-1), initiating TRP depletion and production of metabolites including kynurenine/kynurenic acid, known agonists of the Aryl hydrocarbon receptor (AhR) transcription factor. AhR transcriptionally regulates an immunosuppressive phenotype, making them attractive for regenerative therapy. We also draw attention to important gaps in knowledge for future studies, which will underpin future application for stem cell-based cellular therapies or optimising drugs which can modulate the KP in innate stem cell populations, for disease treatment.

ABSTRACTLongitudinal studies that continuously generate data enable the capture of temporal variations in experimentally observed parameters, facilitating the interpretation of results in a time-aware manner. We propose IL-VIS (Incrementally Learned Visualizer), a new machine learning pipeline that incrementally learns and visualizes a progression trajectory representing the longitudinal changes in longitudinal studies. At each sampling time point in an experiment, IL-VIS generates a snapshot of the longitudinal process on the data observed thus far, a new feature that is beyond the reach of classical static models. We first verify the utility and correctness of IL-VIS using simulated data, for which the true progression trajectories are known. We find that it accurately captures and visualizes the trends and (dis)similarities between high-dimensional progression trajectories. We then apply IL-VIS to longitudinal Multi-Electrode Array data from brain cortical organoids when exposed to different levels of Quinolinic Acid, a metabolite contributing to many neuroinflammatory diseases including Alzheimer’s disease, and its blocking antibody. We uncover valuable insights into the organoids’ electrophysiological maturation and response patterns over time under these conditions.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the highly contagious respiratory disease Corona Virus Disease 2019 (COVID-19) that may lead to various neurological and psychological disorders that can be acute, lasting days to weeks or months and possibly longer. The latter is known as long-COVID or more recently post-acute sequelae of COVID (PASC). During acute COVID-19 infection, a strong inflammatory response, known as the cytokine storm, occurs in some patients. The levels of interferon‐γ (IFN‐γ), interferon-β (IFN-β), interleukin-6 (IL-6) and tumour necrosis factor-alpha (TNF-α) are particularly increased. These cytokines are known to activate the enzyme indoleamine 2,3-dioxygenase 1 (IDO-1), catalysing the first step of tryptophan (Trp) catabolism through the kynurenine pathway (KP) leading to the production of several neurotoxic and immunosuppressive metabolites. There is already data showing elevation in KP metabolites both acutely and in PASC, especially regarding cognitive impairment. Thus, it is likely that KP involvement is significant in SARS-CoV-2 pathogenesis especially neurologically.

Leukoencephalopathy from infectious agents may have a rapid course, such as human simplex virus encephalitis; however, in many diseases, it may take months or years before diagnosis, such as in subacute sclerosing panencephalitis or Whipple disease. There are wide geographic distributions and susceptible populations, including both immunocompetent and immunodeficient patients. Many infections have high mortality rates, such as John Cunningham virus and subacute sclerosing panencephalitis, although others have effective treatments if suspected and treated early, such as herpes simplex encephalitis. This chapter will describe viral, bacterial, and protozoal infections, which predominantly cause leukoencephalopathy. We focus on the clinical presentation of these infectious agents briefly covering epidemiology and subtypes of infections. Next, we detail current pathophysiologic mechanisms causing white matter injury. Diagnostic and confirmatory tests are discussed. We cover predominantly MRI imaging features of leukoencephalopathies, and in addition, summarize the common imaging features. Additionally, we detail how imaging features may be used to narrow the differential of a leukoencephalopathy clinical presentation. Lastly, we present an outline of common treatment approaches where available.

HIV persistence in the brain is a barrier to cure, and potentially contributes to HIV-associated neurocognitive disorders. Whether HIV transcription persists in the brain despite viral suppression with antiretroviral therapy (ART) and is subject to the same blocks to transcription seen in other tissues and blood, is unclear. Here, we quantified the level of HIV transcripts in frontal cortex tissue from virally suppressed or non-virally suppressed people with HIV (PWH). HIV transcriptional profiling of frontal cortex brain tissue (and PBMCs where available) from virally suppressed (n = 11) and non-virally suppressed PWH (n = 13) was performed using digital polymerase chain reaction assays (dPCR). CD68+ myeloid cells or CD3+ T cells expressing HIV p24 protein present in frontal cortex tissue was detected using multiplex immunofluorescence imaging. Frontal cortex brain tissue from PWH had HIV TAR (n = 23/24) and Long-LTR (n = 20/24) transcripts. Completion of HIV transcription was evident in brain tissue from 12/13 non-virally suppressed PWH and from 5/11 virally suppressed PWH, with HIV p24+CD68+ cells detected in these individuals. While a block to proximal elongation was present in frontal cortex tissue from both PWH groups, this block was more extensive in virally suppressed PWH. These findings suggest that the brain is a transcriptionally active HIV reservoir in a subset of virally suppressed PWH.

BACKGROUND:HE is a neuropsychiatric complication of liver disease characterized by systemic elevation in ammonia and proinflammatory cytokines. These neurotoxins cross the blood-brain barrier and cause neuroinflammation, which can activate the kynurenine pathway (KP). This results in dysregulated production of neuroactive KP metabolites, such as quinolinic acid, which is known to cause astrocyte and neuronal death. Our aim was to compare KP activity between patients with covert HE (CHE), patients without encephalopathic cirrhosis (NHE), and healthy controls (HCs). METHODS:This was a single-center prospective cohort study conducted between 2018 and 2021 at St Vincent's Hospital, Sydney. Overall, 13 patients with CHE, 10 patients with NHE, and 12 with HC were recruited. Patients with cirrhosis were diagnosed with CHE if they scored ≤-4 on the Psychometric Hepatic Encephalopathy Score. KP metabolite levels were quantified on plasma samples via HPLC and gas chromatography/mass spectrometry. One-way Kruskal-Wallis test was used to compare the expression levels of KP enzymes. RESULTS:KP was highly activated in patients with cirrhosis, demonstrated by higher levels of activity in the rate-limiting enzymes, indoleamine 2,3-dioxygenase, and tryptophan-2,3-dioxygenase in both CHE (65.04±20.72, p=0.003) and patients with NHE (64.85±22.10, p=0.015) compared to HC (40.95±7.301). Higher quinolinic acid concentrations were demonstrated in CHE (3726 nM±3385, p<0.001) and patients with NHE (1788 nM±632.3, p=0.032) compared to HC (624 nM±457). KP activation was positively correlated with inflammatory marker C-reactive protein in patients with CHE (Rs=0.721, p≤0.01). CONCLUSIONS:KP is highly activated in patients with CHE, resulting in heightened production of neurotoxic metabolites. Dysregulation of the pathway is demonstrable in patients who do not yet show clinical signs of neurocognitive impairment. Therapeutic agents that modulate KP activity may be able to alleviate symptoms of patients with CHE.