Biology subjects

Coussens, A. K.

Publications and source records attributed to Coussens, A. K..

6 recordsLinked to original sources

bioRxiv2026

A mixer tap mechanism in Mycobacterium tuberculosis regulates a critical metabolic node in response to nutrient availability

Mycobacterium tuberculosis persists within the host by exploiting metabolic flexibility underpinned by the tricarboxylic acid (TCA) cycle-glyoxylate shunt junction, where isocitrate dehydrogenase (ICD) and isocitrate lyase (ICL) compete to direct carbon flux between energy production and carbon conservation. Yet, how nutrient availability regulates flux partitioning at this junction is unknown. We show that among the four gatekeeping isoforms of isocitrate lyase (ICL1/2) and isocitrate dehydrogenase (ICD1/2), only icl1 transcription substantially responds to carbon substrate switching. Systematic metabolite screening revealed that pyruvate, oxaloacetate, and glyoxylate are novel allosteric activators of ICD2, while concurrently inhibiting ICL1/2 at their physiological concentrations. To resolve how these regulatory layers integrate, we developed an experimental 1H NMR-based flux assay that combines recombinant enzymes with metabolomics-informed metabolite conditions to quantify flux partitioning under defined states. This systems-level framework reveals that flux partitioning emerges from coordinated balancing of enzyme abundance and protein-metabolite effector combinations that shift in a time-dependent, nutrient-responsive manner. This dynamic, multi-layered regulatory framework, analogous to a mixer-tap mechanism, offers new strategies for therapeutic disruption of M. tuberculosis metabolism.

biochemistry↗

bioRxiv2025

Digital PCR detection of Mycobacterium tuberculosis and HIV-1 co-localization in spinal tuberculosis biopsies

BackgroundMycobacterium tuberculosis (Mtb) and HIV-1 co-infection in tissues is suggested to favour reciprocal replication, infection and reservoir expansion. Yet, confirmation of this detrimental synergism in diseased tissues is limited. MethodsIn this prospective study of 25 adults investigated for spinal tuberculosis (STB) in South Africa (13 (52%) people living with HIV-1 (PLWH), on antiretroviral treatment) 25 open surgery or CT-guided biopsies were collected and portioned into 93 segments. Extracted DNA was analysed by droplet digital PCR (ddPCR) to detect and quantify Mtb complex (MTBC) (rpoB, IS6110), HIV-1 (pol, gag) and Human (RPP30) gene copies. ddPCR sensitivity for Mtb was validated against Xpert-Ultra and culture. Total biopsy and intra-biopsy variation in pathogen DNA abundance, co-detection, and relationships to human cellularity, HIV status, and peripheral viral load (VL) evaluated. ResultsddPCR detected MTBC DNA in biopsies from 10/10 (100%) culture-confirmed STB, 5/6 (83%) Xpert Ultra-confirmed STB and 4/9 (44%) diagnosed Not STB (all 4 with previous pulmonary TB). Detected MTBC ranged from 8-59,144 rpoB copies/biopsy. RpoB copies/million human cells were higher in biopsies from PLWH (p=0.0096) and positively correlated with matched-segment HIV-1 pol copies/million cells (r=0.40; p=0.0003), but not VL. HIV-1 DNA was detected in all PLWH biopsies, four with undetectable VL. HIV-1 pol copies/million cells were higher in segments with MTBC DNA co-detected (p=0.011) and also correlated with VL (r=0.91; p=0.0003). ConclusionsReciprocal relationships exists between Mtb and HIV-1 abundance in spinal tissue. Findings support investigating TB-HIV co-infected tissue segments to characterise how the immune microenvironment impacts HIV-1/Mtb reservoir persistence and/or expansion.

molecular biology↗

bioRxiv2023

Voltage-gated T-type calcium channel blockers reduce apoptotic body-mediated SARS-CoV-2 cell-to-cell spread and subsequent cytokine storm

SARS-CoV-2 typically utilises host angiotensin-converting enzyme 2 (ACE2) as a cellular surface receptor and host serine protease TMPRSS2 for the proteolytic activation of viral spike protein enabling viral entry. Although macrophages express low levels of ACE2, they are often found positive for SARS-CoV-2 in autopsied lungs from COVID-19 patients. As viral-induced macrophage inflammation and overwhelming cytokine release are key immunopathological events that drives exacerbated tissue damage in severe COVID-19 patients, insights into the entry of SARS-CoV-2 into macrophages are therefore critical to understand COVID-19 pathogenesis and devise novel COVID-19 therapies. Mounting evidence suggest that COVID-19 pathogenesis is associated with apoptosis, a type of programmed cell death that often leads to the release of numerous large extracellular vesicles (EVs) called apoptotic bodies (ApoBDs). Here, we showed that ApoBDs derived from SARS-CoV-2-infected cells carry viral antigens and infectious virions. Human monocyte-derived macrophages readily efferocytosed SARS-CoV-2-induced ApoBDs, resulting in SARS-CoV-2 entry and pro-inflammatory responses. To target this novel ApoBD-mediated viral entry process, we screened for ApoBD formation inhibitors and discovered that T-type voltage-gated calcium channel (T-channel) blockers can inhibit SARS-CoV-2-induced ApoBD formation. Mechanistically, T-channel blockers impaired the extracellular calcium influxes required for ApoBD biogenesis. Importantly, blockade of ApoBD formation by T-channel blockers were able to limit viral dissemination and virus-induced macrophage inflammation in vitro and in a pre-clinical mouse model of severe COVID-19. Our discovery of the ApoBD-efferocytosis-mediated viral entry reveals a novel route for SARS-CoV-2 infection and cytokine storm induction, expanding our understanding of COVID-19 pathogenesis and offering new therapeutic avenues for infectious diseases.

cell biology↗

bioRxiv2023

Altered neutrophil extracellular traps in response to Mycobacterium tuberculosis in persons living with HIV with no previous TB and negative TST and IGRA

Persons living with HIV (PLWH) have an increased risk for tuberculosis (TB). After prolonged and repeated exposure, some PLWH never develop TB and test persistently negative in tests of immune sensitization tuberculin skin test (TST) and interferon gamma release assays (IGRA) for Mycobacterium tuberculosis (Mtb). This group has been identified and defined as HIV+ persistently TB, tuberculin and IGRA negative (HITTIN). To investigate potential innate mechanisms unique to individuals with the HITTIN phenotype we compared their neutrophil Mtb infection response to that of PLWH, with no TB history, but who test persistently IGRA positive, and tuberculin positive (HIT). Neutrophil samples from 17 HITTIN (PMNHITTIN) and 11 HIT (PMNHIT) were isolated and infected with Mtb H37Rv for 1h and 6h. RNA was extracted and used for RNAseq analysis. At 1h of Mtb infection, PMNHITTIN displayed 151 significantly upregulated and 40 significantly downregulated differentially expressed genes (DEGs) and PMNHIT 98 significantly upregulated and 11 significantly downregulated DEGs. At the 6h timepoint, PMNHITTIN displayed 3106 significantly upregulated and 3548 significantly downregulated DEGs while PMNHIT had 3816 significantly up- and 3794 significantly downregulated DEGs. There was no significant differential transcriptional response at 1h between infected PMNHITTIN and PMNHIT. However, when contrasting the log2FC 6h infection response to Mtb from PMNHITTIN against PMNHIT, 2285 genes showed significant differential response between the two groups. Apoptosis and NETosis were key pathways linked to the enrichment of genes in PMNHITTIN when contrasted to PMNHIT after 6h infection with Mtb. Fluorescence microscopy revealed relatively lower neutrophil extracellular trap formation and cell loss in PMNHITTIN compared to PMNHIT, showing that PMNHITTIN have a distinct response to Mtb.

genetics↗

bioRxiv2022

Quantifying spatial dynamics and regulators of Mycobacterium tuberculosis phagocytosis by primary human macrophages using microfabricated patterns

Macrophages provide a first line of defense against invading pathogens, including the leading cause of bacterial mortality, Mycobacterium tuberculosis (Mtb). Phagocytosing extracellular organisms mediate pathogen clearance via a multitude of antimicrobial mechanisms, uniquely designed against an array of pathogens. Macrophages are able to execute different programs of activation in response to pathogenic challenge with host mediators, polarizing them to a variety of differentiation states, including the pro-inflammatory M1 and anti-inflammatory M2 states. The functional polarization of a macrophage prior to infection, thus impacts the outcome of host-pathogen interaction. One of the limitations when using in vitro differentiated human primary monocyte-derived macrophages (MDMs) is the heterogeneous nature of the mature population, which presents a challenge for quantitative characterization of various host-pathogen processes. Here, we describe an approach to minimize this heterogeneity, based on micropatterning of cells to reintroduce aspects of cellular homogeneity lost in a 2D tissue culture. Micropatterning consists of growing cells at the single cell level on microfabricated patterns, to constrain the size and shape of the cell, reducing cell-to-cell variation and mimicking the physiological spatial confinement that cells experience in tissues. We infected micropatterned GM-CSF- (M1) and M-CSF- (M2) derived human MDMs with Mtb, which allowed us to study host-pathogen interactions at a single cell level, at high resolution and in a quantitative manner, across tens to hundreds of cells in parallel. Using our approach, we were able to quantify phagocytosis of Mtb in MDMs, finding phagocytic contraction is increased by interferon-gamma stimulation, whilst contraction and bacterial uptake is decreased following silencing of phagocytosis regulator NHLRC2 or Tween80 removal of bacterial surface lipids. We also identify alterations in host organelle position within Mtb infected MDMs, as well as identifying differences in Mtb subcellular localization in relation to the microtubule organizing center (MTOC) and in line with the cellular polarity in M1 and M2 MDMs. Our approach described here can be adapted to study other host-pathogen interactions and co-infections in MDMs and can be coupled with downstream automated analytical approaches.

cell biology↗

bioRxiv2017

Viral apoptosis evasion via the MAPK pathway by use of a host long noncoding RNA

An emerging realisation of infectious disease is the high incidence of genetic instability resulting from pathogen-induced DNA lesions, often leading to classical hallmarks of cancer such as evasion of apoptosis. The Human Immunodeficiency Virus type 1 (HIV-1) induces apoptosis in CD4+ T cells but is largely non-cytopathic in macrophages, thereby leading to long-term dissemination of the pathogen specifically by these host cells. Apoptosis is triggered by double-strand breaks (DSBs), such as those induced by integrating retroviruses, and is coordinated by the p53-regulated long noncoding RNA lincRNA-p21, in a complex with its protein binding partners HuR and hnRNP-K. Here, we monitor the cellular response to infection to determine how HIV-1 induces DSBs in macrophages yet evades apoptosis in these cells. We show that the virus does so by securing the pro-survival MAP2K1/ERK2 cascade early upon entry, in a gp120-dependent manner, to orchestrate a complex dysregulation of lincRNA-p21. By sequestering HuR in the nucleus, HIV-1 enables lincRNA-p21 degradation. Simultaneously, the virus permits transcription of pro-survival genes by sequestering hnRNP-K in the cytoplasm via the MAP2K1/ERK2 pathway. Notably, this pro-survival cascade is unavailable for similar viral manipulation in CD4+ T cells. The introduction of MAP2K1, ERK2 or HDM2 inhibitors in HIV-infected macrophages results in apoptosis providing strong evidence that the viral-mediated apoptotic block can be released, specifically by restoring the nuclear interaction of lincRNA-p21 and hnRNP-K. These results reveal pathogenic control of apoptosis and DNA damage via a host long noncoding RNA, and present MAP2K1/ERK2 inhibitors as a novel therapeutic intervention strategy for HIV-1 infection in macrophages.

molecular biology↗