Biology subjects

Kamada, K.

Publications and source records attributed to Kamada, K..

7 recordsLinked to original sources

bioRxiv2026

Spatial Transcriptomics Reveals Region-Specific Remodeling in Vein Grafts After Peripheral Arterial Bypass

BackgroundVein graft failure due to intimal hyperplasia and maladaptive remodeling remains a major limitation of peripheral bypass surgery. Although vascular remodeling is recognized as a multilayered process, layer-specific molecular mechanisms that distinguish adaptive from negative remodeling remain incompletely understood. We aimed to investigate the vascular microenvironment of patent and stenotic grafts using spatial transcriptomics. MethodsVein specimens were obtained from three patients undergoing revision surgery. For each patient, a matched set of three samples was collected: unused saphenous vein (Denovo), normally healed vein graft (Non-stenosed), and stenosed vein graft (Stenosed) (n = 3 patients). GeoMx Digital Spatial Profiling with the Human Whole Transcriptome Atlas was used to map gene expression across intima, medial, and adventitial layers. Differential expression, gene ontology, spatial deconvolution, and immunohistochemistry were integrated for analysis. ResultsNon-stenosed and Stenosed grafts shared transcriptional features distinct from Denovo veins, particularly in pathways related to cell proliferation. Non-stenosed grafts showed increased expression of CDKN1A across all vascular layers, whereas Stenosed grafts exhibited enhanced mitogen-activated protein kinase (MAPK) pathway activity, reduced DUSP1-mediated regulation, and increased macrophage accumulation. ECM remodeling showed layer-specific organization, with VCAN and ACAN enriched in the intima and DCN in the adventitia, while Stenosed grafts demonstrated a trend toward collagen-dominant remodeling. Cell deconvolution suggested a shift toward vascular smooth muscle cell (VSMC)-dominant architecture after arterialization, with modest enrichment of synthetic VSMC signatures in stenotic regions. ConclusionsVein graft stenosis appears to be associated with layer-specific alterations in cell cycle regulation, inflammatory signaling, extracellular matrix remodeling, and VSMC phenotype. Spatial transcriptomic analysis reveals molecular heterogeneity not captured by bulk approaches and provides preliminary insight into graft remodeling. These findings may inform future studies to improve long-term graft patency.

pathology↗

bioRxiv2024

Comparative genomic analysis of multidrug-resistant clinical isolates of Mycobacterium abscessus revealed worldwide horizontal plasmid transfer

Genetic epidemiological analysis of mobile genetic elements, such as plasmids, has rarely been carried out in Mycobacterium abscessus, regardless of its usefulness in speculating the past contact between bacteria. In this study, through whole genome sequencing analysis of clinical isolates of M. abscessus sequentially collected from the same patient, we identified a single nucleotide variant that could cause antibiotic resistance, and three plasmids (pMAB625-1, pMAB625-2 and pMAB625-3) not found in the type strain. We investigated the distribution of plasmids previously identified in M. abscessus, including pMAB625 plasmids, in 462 clinical isolates worldwide in silico. pMAB625-3 was detected in the largest number of isolates. Furthermore, phylogenetic tree analysis revealed that these plasmids transferred beyond regions and subspecies and acquired unique mutations. These results indicate that transmission of plasmids increases the genomic diversity in M. abscessus, and plasmid epidemiology is useful for estimating the past contact between bacteria.

genomics↗

bioRxiv2023

Spatiotemporal coordination of Rac1 and Cdc42 at the whole cell level during cell ruffling

Rho-GTPases are central regulators within a complex signaling network that controls the cytoskeletal organization and cell movement. This network includes multiple GTPases, such as the most studied Rac1, Cdc42, and RhoA, and their numerous effectors that provide mutual regulation and feedback loops. Here we investigate the temporal and spatial relationship between Rac1 and Cdc42 during membrane ruffling using a simulation model which couples GTPase signaling with cell morphodynamics to capture the GTPase behavior observed with FRET-based biosensors. We show that membrane velocity is regulated by the kinetic rate of GTPase activation rather than the concentration of active GTPase. Our model captures both uniform and polarized ruffling. We also show that cell-type specific time delays between Rac1 and Cdc42 activation can be reproduced with a single signaling motif, in which the delay is controlled by feedback from Cdc42 to Rac1. The resolution of our simulation output matches those of the time-lapsed recordings of cell dynamics and GTPase activity. This approach allows us to validate simulation results with quantitative precision using the same pipeline for the analysis of simulated and experimental data.

cell biology↗

bioRxiv2022

Fc-modified SARS-CoV-2 neutralizing antibodies with therapeutic effects in two animal models.

The use of therapeutic neutralizing antibodies against SARS-CoV-2 infection has been highly effective. However, there remain few practical antibodies against viruses that are acquiring mutations. In this study, we created 494 monoclonal antibodies from COVID-19-convalescent patients, and identified antibodies that exhibited comparable neutralizing ability to clinically used antibodies in the neutralization assay using pseudovirus and authentic virus including variants of concerns. These antibodies have different profiles against various mutations, which were confirmed by cell-based assay and cryo-electron microscopy. To prevent antibody-dependent enhancement, N297A modification was introduced, and showed a reduction of lung viral RNAs by therapeutic administration in a hamster model. In addition, an antibody cocktail consisting of three antibodies was also administered therapeutically to a macaque model, which resulted in reduced viral titers of swabs and lungs and reduced lung tissue damage scores. These results showed that our antibodies have sufficient antiviral activity as therapeutic candidates.

microbiology↗

bioRxiv2021

Bovine serum albumin as a resuscitation promoting factor for viable but non-culturable Mycobacterium tuberculosis via the activation of protein kinase A-dependent cellular processes

We investigated the mechanisms underlying the fetal bovine serum (FBS)-induced reactivation of the viable but non-culturable (VBNC) state of Mycobacterium tuberculosis (Mtb) using the H37Rv strain. We found that bovine serum albumin (BSA), a major component of FBS, could reactivate the VBNC state of Mtb cells without other reactivation-promoting agents. Human serum albumin also had a restorative effect similar to BSA, but mouse serum albumin and egg-white albumin (ovalbumin) did not, suggesting that a common protein structure between bovine and human serum albumin is essential for reactivation. In addition, antioxidative agents, such as N-acetyl-L-cysteine, showed no restorative effect, suggesting that the restoration of culturability might not be due to the antioxidative property of BSA. BSA-mediated reactivation is inhibited by H89 and staurosporine. These inhibitors are known to inhibit multiple protein kinases, including serine/threonine protein kinases, in Mtb, suggesting the involvement of mycobacterial protein kinases in cell division during reactivation. These findings provide new insights into the mechanisms of Mtb reactivation, and may contribute to the development of novel strategies for the treatment of latent tuberculosis. ImportanceReactivation of dormant, including viable but non-culturable (VBNC) Mycobacterium tuberculosis (Mtb) cells, represents a critical step in the progression from latent infection to active tuberculosis. However, the molecular mechanisms that trigger this transition are not yet fully understood. We herein report that bovine serum albumin (BSA), a major component of fetal bovine serum, can restore the culturability of VBNC Mtb cells. Human serum albumin showed a similar effect, whereas mouse and egg-white albumins did not, suggesting that the specific structural features shared between bovine and human albumins are essential for reactivation. The lack of reactivation by the antioxidant N-acetyl-L-cysteine indicates that the mechanism is not related to redox balance. Inhibition of BSA-induced reactivation by H89 and staurosporine implicates mycobacterial serine/threonine protein kinases in this process. These findings highlight the previously unrecognized role of albumin-kinase signaling in Mtb reactivation and suggest new molecular targets for preventing tuberculosis relapse.

microbiology↗

bioRxiv2020

Efficacy of a novel SARS-CoV-2 detection kit without RNA extraction and purification

Rapid detection of SARS-CoV-2 is critical for the diagnosis of coronavirus disease 2019 (COVID-19) and preventing the spread of the virus. A novel "2019 Novel Coronavirus Detection Kit (nCoV-DK)" halves detection time by eliminating the steps of RNA extraction and purification. We evaluated concordance between the nCoV-DK and direct PCR. The virus was detected in 53/71 fresh samples by the direct method and 55/71 corresponding frozen samples by the nCoV-DK. The overall concordance rate of the virus detection between the two methods was 94.4% (95% CI, 86.2-98.4). Concordance rates were 95.2% (95% CI, 83.8-99.4), 95.5% (95% CI, 77.2-99.9), 85.7% (95% CI, 42.1-99.6) in nasopharyngeal swab, saliva, and sputum samples, respectively. These results indicate that the nCoV-DK effectively detects SARS-CoV-2 in all types of the samples including saliva, while reducing time required for detection, labor, and risk of human error.

microbiology↗

bioRxiv2020

Lab-on-a-graphene-FET detection of key molecular events underpinning influenza virus infection and effect of antiviral drugs

Small solid-state devices are candidates for accelerating biomedical assays/drug discovery, however their potential remains unfulfilled. Here, we demonstrate that graphene-field effect transistors (FET) can be used to successfully detect the key molecular events underlying viral infections and the effect of antiviral drugs. Our device success is achieved by bio-mimicking the host-cell surface during an influenza infection at the graphene channel. In-situ AFM confirms the biological interactions at the sialic acid-functionalized graphene: viral hemagglutinin (HA) binds to sialic acid, and neuraminidase (NA) reacts with the sialic acid-HA complex. The graphene-FET detects HA binding to sialic acid, and NA cleavage of sialic acid. The inhibitory effect of the drug "zanamivir" on NA-sialic acid interactions is monitored in real-time; the reaction rate constant of NA-sialic acid reaction was successfully determined. We demonstrate that graphene-FETs are powerful platforms for measurement of biomolecular interactions and contribute to future deployment of solid-state devices in drug discovery/biosensing.

bioengineering↗