Biology subjects

Amin, K.

Publications and source records attributed to Amin, K..

5 recordsLinked to original sources

bioRxiv2026

Optineurin Deficiency Collapses the Host Endolysosomal Network and Impairs Xenophagy to Accelerate Mycobacterium tuberculosis Growth

Selective autophagy is a host defense mechanism against Mycobacterium tuberculosis (Mtb) that restricts bacterial growth by targeting ubiquitin-coated bacilli for lysosomal degradation via autophagy receptors. Optineurin is a selective autophagy receptor that targets pathogens and modulates immune signaling; however, its precise structural mechanism during Mtb infection remains poorly defined. Here, we show that while Optineurin deficiency spares the global host transcriptomic response to infection, it collapses the host endolysosomal network, reducing LAMP1+ and LysoTracker+ reserves by half. Multi-dose bafilomycin A1 flux assays demonstrated that this structural depletion selectively blocks the dynamic, directional trafficking and functional delivery of autophagosomes to the pathogen, significantly reducing Mtb-DQ-BSA colocalization. Genetic complementation restored bacterial restriction in a manner dependent on three phosphosites (Ser187, Ser530, and the uncharacterized Ser556). In the context of reduced autophagic containment and increased Mtb replication, Optineurin deficiency accelerated necrotic-like host cell death. In vivo, Optineurin deficiency enhanced bacterial replication and impaired the Type I interferon response during acute Mtb infection but did not affect long-term survival. Together, these findings identify Optineurin as a critical regulator of autophagic flux, host cell death, and Type I interferon responses that limit early Mtb pathogenesis.

microbiology↗

bioRxiv2025

SIRT4 positively regulates autophagy via ULK1, but independently of HDAC6 and OPA1

The sirtuin SIRT4 has been implicated in the control of autophagy and mitochondrial quality control via mitophagy, but the regulatory role of SIRT4 in autophagy/mitophagy induced by different stressors is unclear. Here, we show that cells expressing SIRT4(H161Y), a catalytically inactive, dominant-negative mutant of SIRT4, fail to upregulate LC3B-II and show a reduced autophagic flux upon treatment with different inducers of mitophagy/autophagy, i.e., CoCl2-triggered pseudohypoxia, CCCP/oligomycin-mediated respiratory chain inhibition, or rapamycin treatment. Interestingly, SIRT4(H161Y) expression (i) upregulated protein levels of HDAC6, which is involved in mitochondrial trafficking and autophagosome-lysosome fusion, and (ii) inhibited the conversion of OPA1-L to OPA1-S, which is associated with increased mitochondrial fusion and decreased mitophagy. Both HDAC6 and OPA1 are SIRT4 interactors. However, pharmacological inhibition of neither HDAC6 via Tubacin nor OPA1 via MYLS22 restored the stress-induced upregulation of LC3B-II levels upon autophagy/mitophagy treatment of SIRT4(H161Y)-expressing cells. Remarkably, inhibition of autophagosome-lysosome fusion and thus disruption of late autophagic flux by BafA1 treatment also failed to restore LC3B-II levels upon autophagy/mitophagy treatment, suggesting an inhibitory effect of SIRT4(H161Y) on the initiation/early phase of autophagy. Consistent with this idea, we show that SIRT4(H161Y) promoted the phosphorylation of ULK1 at S638 and S758 (mTORC1 targets), both of which mediate an important inhibitory regulation of autophagy initiation. Thus, our data suggest a positive regulatory function of SIRT4, presumably via modulation of AMPK/mTORC1 signaling, in the ULK1-dependent early regulation/initiation of stress-induced autophagic flux.

biochemistry↗

bioRxiv2024

Dynamic Regulation Of The Chromatin Environment By ASH1L Modulates Human Neuronal Structure And Function

Precise regulation of the chromatin environment through post-translational histone modification modulates transcription and controls brain development. Not surprisingly, mutations in a large number of histone-modifying enzymes underlie complex brain disorders. In particular, the histone methyltransferase ASH1L modifies histone marks linked to transcriptional activation and has been implicated in multiple neuropsychiatric disorders. However, the mechanisms underlying the pathobiology of ASH1L-asociated disease remain underexplored. We generated human isogenic stem cells with a mutation in ASH1Ls catalytic domain. We find that ASH1L dysfunction results in reduced neurite outgrowth, which correlates with alterations in the chromatin profile of activating and repressive histone marks, as well as the dysregulation of gene programs important for neuronal structure and function implicated in neuropsychiatric disease. We also identified a novel regulatory node implicating both the SP and Kruppel-like families of transcription factors and ASH1L relevant to human neuronal development. Finally, we rescue cellular defects linked to ASH1L dysfunction by leveraging two independent epigenetic mechanisms that promote transcriptional activation. In summary, we identified an ASH1L-driven epigenetic and transcriptional axis essential for human brain development and complex brain disorders that provide insights into future therapeutic strategies for ASH1L-related disorders.

neuroscience↗

bioRxiv2023

Developing a safe 15-hour preservation protocol of donor kidneys using normothermic machine perfusion

IntroductionO_ST_ABSBackgroundC_ST_ABSNormothermic machine perfusion (NMP) offers a superior alternative to existing hypothermic preservation strategies but is currently limited to 1-3 hours. Extending the time a kidney can be sustained using this technology could electivise transplantation, and enable physiological assessments of renal function. We aimed to develop a protocol that allows the safe preservation of donor kidneys for 12 hours using this technique. MethodsPorcine kidneys (n=20) were retrieved and flushed with 1L preservation solution before being stored on ice. Following a cold ischaemic time of 3.5 hours, kidneys were placed onto a NMP circuit and perfused for 12 hours. Renal haemodynamics, biochemistry and urine output were recorded and analysed. At the end of perfusion, kidneys were scored based on the clinical assessment score and their suitability for transplant determined. Biopsies were collected at the end for histological assessment. ResultsAll kidneys were successfully perfused with immediate recordable renal blood flow (RBF). RBF continually improved over the course of the perfusions, peaking at 12 hours, and negatively correlated with intra-renal resistance. Perfusate sodium concentrations remained stable and within physiological parameters. Sodium bicarbonate increased over time with a corresponding decrease in lactate concentrations, demonstrating active renal gluconeogenesis and Cori cycle processes. Urine production began immediately in all kidneys and was sustained throughout, indicating active renal function. Under the clinical perfusion assessment score, all kidneys received a score of 1 and would be considered suitable for transplantation. Histological assessment revealed kidneys were injury free with REMUZZI scores of 0 in all samples. ConclusionWe have developed an NMP protocol that safely preserves donor kidneys for over 15 hours. Successful perfusion was achieved with stable haemodynamics, blood-perfusate biochemistry, and maintained urine output. Importantly, kidneys remained in optimal health, with no evidence of injury. This protocol may enable the electivisation of transplantation, while reducing ischaemic injury associated with static cold storage.

physiology↗

bioRxiv2023

Polysulfide Nanoparticles Ameliorate Ischaemia Reperfusion Injury in Renal Transplantation and Improve Kidney Function Post-Transplantation

Ischemia-reperfusion injury (IRI) is a significant complication in kidney transplantation, often affecting the viability and function of organs. Normothermic machine perfusion (NMP) is a technique used to improve the condition of organs prior to transplantation. In this study, we show that incorporating antioxidant poly(propylene sulfide) nanoparticles (PPS-NPs) during cold-storage and NMP significantly enhances its efficacy in reducing IRI upon porcine kidney transplantation. We found that by scavenging reactive oxygen species, PPS-NPs reduced oxidative stress and inflammation that occurs during ischemia-reperfusion with oxidized DNA reduced 5.3x and both TNF- and complement activation approximately halved. Our studies show that this approach led to significantly improved hemodynamics, better renal function, and tissue health compared to NMP alone. The results suggest that incorporating PPS-NPs into transplantation protocols may expand the pool of kidneys suitable for transplantation and enhance overall transplantation success rates. The broader impact of this work could extend to other organ transplants, suggesting a wider application for nanoantioxidant technologies in organ preservation.

synthetic biology↗