Biology subjects

Kitagawa, M.

Publications and source records attributed to Kitagawa, M..

6 recordsLinked to original sources

bioRxiv2025

Proteomic profiling of bacterial extracellular vesicles for exploring ovarian cancer biomarkers

Extracellular vesicles (EVs) are present in body fluids and act as disease biomarkers. Emerging evidence has proven that EVs are released not only from mammalian cells but also from bacteria. Ovarian cancer has a dismal prognosis because of difficulties in early detection. This study aimed to identify bacterial EV (BEV) proteins associated with ovarian cancer. Fifteen patients with ovarian cancer or benign tumors were recruited, and EVs were isolated from the ascites. BEVs were recovered from seven in vitro-cultured strains of bacteria present in the vaginal microbiota, and LC-MS/MS analysis was performed. The detected peptide data were annotated to both human and bacterial references, and the human data showed that the profiles of cancer EVs were distinct from those of patients with benign tumors. As analyzed by bacterial proteins, P15636_Protease1 was found as the BEV-associated protein highly expressed in patients with cancer. To distinguish patients with cancer, the area under the curve was 0.88 (95% CI, 0.64-1.00). In addition, homology analysis showed that P15636_Protease1 is a unique protein only detected in bacteria. In this study, ovarian cancer-specific bacterial proteins were identified on EVs, and BEVs in bodily fluids are promising in the discovery of disease biomarkers.

cancer biology↗

bioRxiv2025

Ubiquilin-2 liquid droplets catalyze α-synuclein fibril formation

Liquid-liquid phase separation (LLPS) and subsequent liquid-gel/solid transition are considered common aggregation mechanisms of proteins linked to neurodegenerative diseases. -synuclein (-syn), the main component of Parkinsons disease pathology, has been reported to undergo LLPS, thereby accelerating aggregate formation. However, the precise molecular events involved in the early stages of -syn aggregation remain controversial. In this study, we show that -syn aggregation is promoted by droplets formed by ubiquilin-2 (UBQLN2), rather than by -syn LLPS itself. During the liquid-gel/solid transition of UBQLN2 droplets, -syn within the droplets transformed into pathogenic fibrils both in vitro and in cells. Immunohistochemistry of brain sections from sporadic Parkinsons disease patients revealed UBQLN2 in substantia nigra Lewy bodies, implicating UBQLN2 in -syn aggregation in vivo. Furthermore, the small compound SO286 inhibited both UBQLN2 self-association and its interaction with -syn by binding to the STI1 domain, thereby suppressing -syn aggregation. These findings demonstrate that UBQLN2 droplets catalyze -syn fibrillization and suggest that small molecules targeting fibril-catalyzing proteins such as UBQLN2 may represent a novel therapeutic approach for neurodegenerative diseases.

biochemistry↗

bioRxiv2023

Identification of novel autophagy inducers by accelerating lysosomal clustering against Parkinson's disease

Autophagy-lysosome pathway plays an indispensable role in the intracellular protein quality control system, degrading abnormal organelles and proteins. Among these proteins is -Synuclein (Syn), which is associated with the pathogenesis of Parkinsons disease (PD). However, the activation of this lysosome-dependent degradation strategy is restricted by enzyme complementation. In this study, we focused on the phase of autophagosome-lysosome fusion around the microtubule organizing center (MTOC) that leads to Syn degradation. Through high-throughput chemical screening, we identified six clinically available drugs that enhance autophagy and can accumulate lysosomes around the MTOC from approximately 1,200 drugs screened. We further demonstrated that these compounds induce lysosomal clustering through a JIP4-TRPML1-dependent mechanism, which is associated with autophagy induction. Among these, the lysosomal clustering compound albendazole was observed to promote the autophagy-dependent degradation of Triton-X-insoluble proteasome inhibitor-induced aggregates (p62). In a cellular PD model, albendazole boosted the degradation of insoluble Syn, an effect that was reversed upon the addition of bafilomycin A1. Our results suggest that lysosomal clustering can facilitate the breakdown of protein aggregates. Therefore, compounds that promote lysosomal clustering may offer a promising therapeutic strategy against neurodegenerative diseases characterized by the presence of aggregate-prone proteins.

cell biology↗

bioRxiv2022

Indirect CRISPR screening with photoconversion revealed key factors of drug resistance with cell-cell interactions

Comprehensive screenings to clarify indirect cell-cell interactions, such as those in the tumor microenvironment, especially comprehensive assessments of supporting cells effects, are challenging. Therefore, in this study, indirect CRISPR screening for drug resistance with cell-cell interactions was invented. The photoconvertible fluorescent protein Dendra2 was inducted to determine the drug resistance responsible factors of supporting cells with CRISPR screenings. Random mutated supporting cells co-cultured with leukemic cells induced drug resistance with cell- cell interactions. Supporting cells responsible for drug resistance were isolated with green-to-red photoconversion, and 39 candidate genes were identified. Knocking out C9orf89, MAGI2, MLPH, or RHBDD2 in supporting cells reduced the ratio of apoptosis of cancer cells. In addition, the low expression of RHBDD2 in supporting cells, specifically fibroblasts, of clinical pancreatic cancer showed a shortened prognosis, and a negative correlation with CXCL12 was observed. Indirect CRISPR screening was established to isolate the responsible elements of cell-cell interactions. This screening method could reveal new mechanisms in all kinds of cell-cell interactions by revealing live phenotype-inducible cells, and it could be a new platform for discovering new targets of drugs for conventional chemotherapies.

cancer biology↗

bioRxiv2020

Rapid expression of COVID-19 proteins by transient expression in tobacco.

In 2020 we suffered from a major global pandemic caused by the SARS-CoV-2 coronavirus. Efforts to contain the virus include the development of rapid tests and vaccines, which require a ready supply of viral proteins. Here we report the production of two SARS-CoV-2 proteins by transient transformation of tobacco, leading to high expression within three days, and subsequent purification of the intact proteins. Such efforts may help to develop testing resources to alleviate the major impacts of this global pandemic.

plant biology↗

bioRxiv2019

Control of Shoot Meristem Size by an Aminoacyl tRNA Synthetase, OKI1, in Arabidopsis

In plants, the stem cells that form the shoot system reside within the shoot apical meristem (SAM), which is regulated by feedback signaling between the WUSCHEL (WUS) homeobox protein and CLAVATA (CLV) peptides and receptors. WUS-CLV feedback signaling can be modulated by various endogenous or exogenous factors such as chromatin state, hormone signaling, reactive oxygen species (ROS) signaling and nutrition, leading to a dynamic control of SAM size corresponding to meristem activity. Despite these insights, however, the knowledge of genes that control stem cell fate is still limited, and in particular the regulation by ROS signaling is only beginning to be comprehended. Here, we report a new regulator of SAM size, OKINA KUKI (OKI1), which is expressed in the SAM and encodes a mitochondrial aspartyl tRNA synthetase (AspRS). oki1 mutants display enlarged SAMs with abnormal expression of WUS and CLV3, and overaccumulation of ROS in the meristem. Our findings support the importance of normal AspRS function in the maintenance of the WUS-CLV3 feedback loop and SAM size.

plant biology↗