Biology subjects

Iwatani, Y.

Publications and source records attributed to Iwatani, Y..

7 recordsLinked to original sources

bioRxiv2026

Transcriptionally Active HIV Reservoirs Enriched for Interferon-Inducible APOBEC3-Related Mutational Signatures Associate with Arterial Inflammation

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 ({beta} = 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 ({beta} = 0.0075, p = 0.023), and remained the only significant predictor when IP-10 was included ({beta} = 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 O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=76 SRC="FIGDIR/small/729898v1_ufig1.gif" ALT="Figure 1"> View larger version (13K): org.highwire.dtl.DTLVardef@531cb9org.highwire.dtl.DTLVardef@82c53corg.highwire.dtl.DTLVardef@16318aaorg.highwire.dtl.DTLVardef@e87e22_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights: Interferon-inducible APOBEC3-associated PSC signatures in HIV reservoirs and vascular inflammationO_LIAPOBEC3-associated premature stop codon (PSC) signatures were identified in transcriptionally active HIV reservoir-derived RNA despite suppressive ART. C_LIO_LIHigher PSC burden was significantly associated with increased aortic vascular inflammation measured by FDG-PET. C_LIO_LIReservoir-associated drug resistance mutations (RA-DRMs) showed no association with arterial inflammation. C_LIO_LIPSC burden remained independently associated with aortic vascular inflammation in multivariable analyses. C_LIO_LIPSC-enriched reservoir states were associated with inflammatory biomarker patterns consistent with monocyte-macrophage activation and vascular immune activation. C_LIO_LIThese findings are consistent with an interferon-inducible APOBEC3-edited reservoir state associated with persistent arterial inflammation during suppressive ART. C_LIO_LIAPOBEC3-associated mutational signatures may represent a candidate biomarker of vascular inflammation and cardiovascular risk in people with HIV. C_LI

molecular biology↗

bioRxiv2026

Transcriptionally Active HIV Reservoirs Enriched for Interferon-Inducible APOBEC3-Related Mutational Signatures Associate with Reduced Neuroaxonal Integrity

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 ({superscript 1}H-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 AbstractInterferon-Inducible APOBEC3-Associated Premature Stop Codon Signatures in HIV-1 Reservoirs and Preservation of Neuroaxonal Integrity O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=88 SRC="FIGDIR/small/729658v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@19c98d8org.highwire.dtl.DTLVardef@1f6c627org.highwire.dtl.DTLVardef@4b33a7org.highwire.dtl.DTLVardef@12c4a54_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIShort HIV-1 RNA transcription within peripheral CD4 T-cell reservoirs was associated with reduced frontal white matter N-acetylaspartate during suppressive ART. C_LIO_LILong HIV-1 gag/pol RNA transcripts exhibited marked heterogeneity in interferon-inducible APOBEC3-associated G-to-A hypermutation, including premature stop codon signatures. C_LIO_LIArchived reservoir-associated drug resistance mutations were identified within transcriptionally active long HIV-1 reservoir-derived RNA during suppressive ART. C_LIO_LIReduced 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. C_LI

molecular biology↗

bioRxiv2025

Lenacapavir binding to immature Gag triggers the emergence of giant HIV-1 virions

Lenacapavir (LEN), a potent capsid inhibitor, suppresses reverse transcription and nuclear import by disrupting capsid core formation in human immunodeficiency virus type 1 (HIV-1). However, its effect on the late-stage viral assembly remains unclear. Although p24 ELISA suggested that LEN inhibited HIV-1, both RT-dPCR and Vpr-HiBiT assays indicated no reduction in the viral output. This discrepancy was attributed to LEN-induced epitope masking of p24, which was reversed by altered sample processing. Furthermore, LEN induced numerous abnormal, discrete clusters of Gag at the plasma membrane. Mass photometry and transmission electron microscopy revealed heterogeneous viral-like particles (LENiVLPs; diameter >200 nm), containing both Gag and Env proteins. Although LENiVLPs retained membrane fusion capability, they were non-infectious owing to post-entry defects. Thus, LEN binds to the precursor Gag and promotes aberrant particle formation, offering novel insights that could guide the development of next-generation LEN-based therapeutics targeting the late stages of the viral life cycle.

microbiology↗

bioRxiv2023

Pulsation waves along the Ciona heart tube reverse by bimodal rhythms expressed by a remote pair of pacemakers

The heart of ascidians, marine invertebrate chordates, exhibits a tubular structure, and heartbeats propagate from one end to the other. The direction of pulsation waves intermittently reverses in the heart of ascidians and their relatives; however, the underlying mechanisms remain unclear. We herein performed a series of experiments to characterize the pacemaker systems in isolated hearts and their fragments and applied a mathematical model to examine the conditions leading to heart reversals. The isolated heart of Ciona sufficiently performed heart reversals, and experimental bisections of isolated hearts revealed that independent pacemakers resided on each side and also that their beating frequencies periodically changed as they expressed bimodal rhythms. Only fragments including 5% or shorter terminal regions of the heart tube maintained autonomous pulsation rhythms, whereas other regions did not. Our mathematical model, based on FitzHugh-Nagumo equations applied to a one-dimensional alignment of cells, demonstrated that the difference between frequencies expressed by the two independent terminal pacemakers determined the direction of propagated waves. Changes in the statuses of the terminal pacemakers between the excitatory and oscillatory modes as well as in their endogenous oscillation frequencies were sufficient to lead to heart reversals. These results suggest that the directions of pulsation waves in the Ciona heart reverse according to the changing rhythms independently expressed by remotely coupled terminal pacemakers. Summary statementPulsation waves traveling along the heart tube of the ascidian Ciona intermittently reverse because of autonomous and periodical changes in beating frequencies at a pair of terminal pacemakers.

physiology↗

bioRxiv2021

Neural mechanism of experience-dependent sensory gain control in C. elegans

Animals sensory systems adjust their responsiveness to environmental stimuli that vary greatly in their intensity. Here we report the neural mechanism of experience-dependent sensory adjustment, especially gain control, in the ASH nociceptive neurons in Caenorhabditis elegans. Using calcium imaging under gradual changes in stimulus intensity, we find that the ASH neurons of naive animals respond to concentration increases in a repulsive odor 2-nonanone regardless of the magnitude of the concentration increase. However, after preexposure to the odor, the ASH neurons exhibit significantly weak responses to a small gradual increase in odor concentration while their responses to a large gradual increase remain strong. Thus, preexposure changes the slope of stimulus-response relationships (i.e., gain control). Behavioral analysis suggests that this gain control contributes to the preexposure-dependent enhancement of odor avoidance behavior. Mathematical analysis reveals that the ASH response consists of fast and slow components, and that the fast component is specifically suppressed by preexposure. In addition, genetic analysis suggests that G protein signaling is required for the fast component. Thus, our integrative study demonstrates how prior experience dynamically modulates stimulus-response relationships in sensory neurons, eventually leading to adaptive modulation of behavior.

neuroscience↗

bioRxiv2021

An autonomous tail-beating cycle period expressed by a region-specific swimming pattern generator in the Ciona larva

Swimming locomotion in aquatic vertebrates, such as fish and tadpoles, is expressed through orchestrated operations of central pattern generators. These parallel neuronal circuits are ubiquitously distributed and mutually coupled along the spinal cord to express undulation patterns accommodated to efferent and afferent inputs. While such sets of schemes have been shown in vertebrates, the evolutionary origin of those mechanisms along the chordate phylogeny remains unclear. Ascidians, representing a sister group of vertebrates, give rise to tadpole larvae that freely swim in seawater. In this study, we tried to locate the swimming pattern generator in larvae of the ascidian Ciona by examining locomotor ability of segmented body fragments. Our experiments demonstrated necessary and sufficient pattern generator activity in a short region ([~]10% of the body length as the longest estimation) including the trunk-tail junction but excluding most of the trunk and tail with major sensory apparatuses therein. Moreover, we found that these "mid-piece" body fragments express periodic tail beating bursts with [~]20-s intervals without any exogenous stimuli. Comparisons among temporal patterns of tail beating bursts expressed by the mid-piece fragments and by whole larvae placed under different sensory conditions suggested that the presence of parts other than the critical mid-piece had effects to shorten swimming burst intervals, especially in the dark, and also to expand the variance in burst durations. We propose that Ciona larvae perform swimming as modified representations of autonomous and periodic pattern generator drives, which operate locally in the region of the trunk-tail junction. Summary statementMid-piece fragments of tadpole larvae of the ascidian Ciona, lacking most of the anterior trunk and posterior tail, autonomously and periodically express tail beating bursts.

zoology↗

bioRxiv2020

Naturally mutated spike proteins of SARS-CoV-2 variants show differential levels of cell entry

The causative agent of the coronavirus disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is steadily mutating during continuous transmission among humans. Such mutations can occur in the spike (S) protein that binds to the angiotensin-converting enzyme-2 (ACE2) receptor and is cleaved by transmembrane protease serine 2 (TMPRSS2). However, whether S mutations affect SARS-CoV-2 infectivity remains unknown. Here, we show that naturally occurring S mutations can reduce or enhance cell entry via ACE2 and TMPRSS2. A SARS-CoV-2 S-pseudotyped lentivirus exhibits substantially lower entry than SARS-CoV S. Among S variants, the D614G mutant shows the highest cell entry, as supported by structural observations. Nevertheless, the D614G mutant remains susceptible to neutralization by antisera against prototypic viruses. Taken together, these data indicate that the D614G mutation enhances viral infectivity while maintaining neutralization susceptibility.

microbiology↗