Biology subjects

Kondo, J.

Publications and source records attributed to Kondo, J..

13 recordsLinked to original sources

bioRxiv2026

Hypoxia reduces induced LRIG1 protein despite sustained mRNA induction in colorectal cancer organoids

LRIG1 is a negative regulator of receptor tyrosine kinase (RTK) signaling that promotes tumor suppression by driving degradation of EGFR and other RTKs. Inducing LRIG1 expression has therefore been proposed as a strategy to limit cancer cell survival under hypoxia. However, whether hypoxia itself affects LRIG1 expression remains unclear. Here, we investigated how hypoxia affects LRIG1 expression and protein abundance in human cancer datasets and colorectal cancer organoids. Analysis of The Cancer Genome Atlas data across gastrointestinal and other cancers revealed an inverse association between LRIG1 mRNA expression and a hypoxia gene signature that persisted after adjustment for global gene expression. We previously showed that BMPR inhibition induces LRIG1 and suppresses colorectal cancer organoid growth through LRIG1. Under hypoxia, this growth inhibition in colorectal cancer organoids was attenuated, and LRIG1 protein accumulation was reduced despite sustained mRNA induction. Pre-induced LRIG1 protein declined within 3 h of hypoxic exposure in organoids, and ectopically expressed LRIG1 similarly decreased in HEK293 cells. Pharmacological HIF1 inhibition did not prevent LRIG1 protein loss under hypoxia, whereas HIF1 stabilization did not reproduce it under normoxia, suggesting limited HIF1 involvement. Bafilomycin A1 restored LRIG1 protein levels, whereas chloroquine and the proteasome inhibitor MG132 did not, implicating a bafilomycin A1-sensitive lysosomal process. Notably, the hypoxia-induced decrease in LRIG1 was not accompanied by a decrease in total EGFR. These findings suggest that hypoxia limits LRIG1 protein induction, potentially constraining strategies that rely on LRIG1 induction in cancer treatment.

biochemistry↗

bioRxiv2026

Prohaptoglobin Promotes Pancreatic Cancer Progression by sustaining YAP Activity

Background & AimsProhaptoglobin (proHp), a precursor of haptoglobin (Hp), has recently emerged as a cancer-associated biomarker, but its functional role in pancreatic cancer remains unclear. We investigated whether proHp promotes malignant phenotypes of pancreatic cancer and explored signaling pathways involved. MethodsSerum proHp was examined in patients with pancreatic cancer and healthy controls. HP expression in pancreatic tumors and cell lines was analyzed using transcriptomic datasets. ProHp function was evaluated using PSN1 HP knockout (HPKO) cells, exogenous proHp supplementation, xenograft models, and RNA sequencing of PSN1 wild-type and HPKO cells. YAP activity was assessed by target gene expression, subcellular localization, YAP overexpression, and inhibition of YAP-TEAD interaction. ResultsSerum proHp was significantly elevated in patients with pancreatic cancer, and a subset of tumors and pancreatic cancer cell lines showed HP expression comparable to liver, indicating a tumor-derived source of proHp. In PSN1 cells, HPKO reduced motility, whereas exogenous proHp partially rescued this defect and enhanced motility in additional pancreatic cancer cell lines. Wild-type PSN1 cells continued to proliferate beyond confluence and formed rapidly growing xenograft tumors, which were abolished in HPKO cells. At high density, wild-type cells maintained YAP-related gene expression and nuclear YAP despite Hippo activation, whereas HPKO exhibited reduced nuclear YAP, indicating noncanonical YAP regulation by proHp. YAP restoration in HPKO cells rescued high-density proliferation and cell motility, while a YAP-TEAD inhibitor selectively reduced high-density proliferation of wild-type but not HPKO cells. ConclusionProHp promotes pancreatic cancer progression in a context-dependent manner by sustaining YAP activity and enabling cells to partially overcome contact-dependent growth inhibition. SynopsisProhaptoglobin, a precursor of haptoglobin, is elevated in pancreatic cancer and produced by tumor cells. It promotes cell motility, supports tumor growth under high-density conditions, and maintains YAP-dependent transcription that overrides contact-dependent growth inhibition. What You Need to Know BackgroundProhaptoglobin, a precursor of haptoglobin, is elevated in pancreatic cancer, but its tumor-derived origin and functional role are unknown. We examined whether prohaptoglobin drives progression by sustaining YAP signaling. ImpactWe show that tumor-derived prohaptoglobin sustains nuclear YAP activity, allowing pancreatic cancer cells to bypass contact inhibition and proliferate, revealing prohaptoglobin as a context-dependent driver rather than a passive biomarker. Future DirectionsDefining how prohaptoglobin engages upstream Hippo-YAP regulators and whether prohaptoglobin-YAP signaling is targetable in vivo may uncover new biomarkers and therapeutic vulnerabilities for pancreatic cancer.

cancer biology↗

bioRxiv2026

Enterococcus faecalis is involved in the progression of the early stages of latent chronic pancreatitis surrounding pancreatic cancer tissue

(Objective) In our previous research, we identified latent chronic pancreatitis in the normal tissue surrounding pancreatic cancer. We also discovered the presence of Enterococcus faecalis (E. faecalis), a type of intestinal bacterium, in the pancreatic fluid and tissue of pancreatic cancer patients, suggesting it may be one of the factors contributing to the development of latent chronic pancreatitis. In this study, we performed pathological analyses to investigate its characteristics and investigate a possibility of E. faecalis infection. (Methods) Pathological analyses were performed, using 16 cases of pancreatic cancer and intraductal papillary mucinous neoplasia (IPMN) involving lesions in the pancreas tail. The involvement of E. faecalis was investigated with immunohistochemical analysis and serological methods. (Results) All cases exhibited inflammatory changes in pancreatic tissue without a clinical diagnosis of chronic pancreatitis, along with macrophage infiltration. These changes did not significantly differ according to preoperative treatment. DNA encoding E. faecalis 16s ribosomal RNA was detected in many cases, however, a positive immunostaining to E. faecalis was observed in only a few cases. Serum capsular polysaccharide (CPS) antibody levels exceeding the mean values were observed in patients with established chronic pancreatitis, while the level was not correlated with E. faecalis immunostaining. (Conclusion) These results suggest the E. faecalis infection is involved in the early stage of the progression of chronic latent pancreatitis and the diagnostic technology incorporating novel multi-biomarkers may be useful for identifying high-risk individuals for future pancreatic cancer development.

cancer biology↗

bioRxiv2026

FUT8 mediated core fucosylation modulates growth related functions of LRP1 in liver cancer cells

Fucosylation is a cancer-associated glycosylation change, and core fucosylation of N-glycans catalyzed by the 1,6-fucosyltransferase FUT8, has been closely linked to tumor progression, metastasis, drug resistance, and poor prognosis. However, the core-fucosylated proteins that directly support hepatocarcinogenesis are not fully defined. In a KRAS-G12D-driven mouse liver cancer model, we observed increased fucosylation and FUT8 upregulation, and glycoproteomic analysis of fucose-enriched fractions identified low-density lipoprotein receptor-related protein 1 (LRP1) as a prominent core-fucosylated protein in tumor tissue. In immortalized mouse hepatocytes, genetic or pharmacological inhibition of FUT8 markedly increased Lrp1 mRNA and protein, indicating that loss of core fucosylation is accompanied by robust upregulation of LRP1. In human HepG2 cells, LRP1 knockout suppressed cell proliferation and markedly altered colony morphology, leading to compact rounded clusters instead of the typical polygonal pattern. It also reduced EGFR protein and further inhibited proliferation of HepG2 cell. These findings identify LRP1 as a FUT8-dependent core-fucosylated receptor in experimental hepatocarcinogenesis and suggest that the FUT8-LRP1 axis contributes to the maintenance of proliferative signaling in hepatoma cells.

cancer biology↗

bioRxiv2025

IGF2BP3 is essential for the growth heterogeneity of colorectal adenoma cells by regulating MYC

Adenoma is a major precancerous lesion in colorectal cancer (CRC), and the adenoma-carcinoma sequence is a well-known multistep progression to CRC caused by the accumulation of genetic mutations. On the other hand, the non-genetic mechanisms in the adenoma-carcinoma sequence remain largely unknown. In this study, organoids were established from 31 colorectal adenomas from 19 patients. Some adenomas showed heterogeneity in the proliferative potential of single cells, and this heterogeneity was regulated by non-genetic mechanisms. IGF2BP3 was identified as a differentially expressed gene between organoids with different growth patterns. IGF2BP3 positively regulated MYC expression at the transcriptional level and negatively regulated it at the translational level. This promoted high proliferative potential with high levels of oxidative phosphorylation, while allowing cells to avoid MYC-induced cell death. IGF2BP3 affected the tumorigenicity of mouse adenomas in vivo. Intra-tumor heterogeneity in growth potential is acquired at the precancerous stage in the adenoma-carcinoma sequence of colorectal carcinogenesis, and IGF2BP3 plays an important role in regulating MYC levels. These findings provide new insights into the non-genetic regulation of adenomas during CRC development.

cancer biology↗

bioRxiv2025

Functional Impact of Glycosylation and Splicing Variants of LRIG1 on EGFR Proteostasis in Cancer

LRIG1, a membrane glycoprotein, has emerged as a significant stem cell marker and negative regulator of receptor tyrosine kinases (RTKs), including EGFR. Glycosylation is a major post-translational modification, which plays a crucial role in protein function and stability. In cancer biology, abnormal glycosylation can serve as a biomarker and contribute to pathogenesis. We aimed to investigate the effects of glycosylation on LRIG1 functions. Through database analysis and experimental approaches, we focused on evolutionarily conserved glycosylation sites of LRIG1, particularly N74 in humans. We found that a mutation of the N74 glycosylation site (N74Q) enhances LRIG1s binding to EGFR and promotes EGFR degradation. Furthermore, we identified a naturally occurring splice variant of LRIG1 lacking exon 2, which includes the N74 site, that shows similar enhanced EGFR binding and degradation. Analysis of TCGA data revealed that exon 2 skipping in LRIG1 occurs in various cancers, with higher levels correlating with poorer survival in breast and ovarian cancers. Our findings suggest that the absence of glycosylation at N74 enhances LRIG1-EGFR binding, providing an example of glycosylation negatively regulating protein-protein interaction. This mechanism, achieved through alternative splicing, provides insights into the importance of glycosylation deficiency in cancer biology.

biochemistry↗

bioRxiv2022

Inhibition of the BMP pathway suppresses tumor growth via downregulation of EGFR in MEK/ERK-dependent colorectal cancer

The bone morphogenetic protein (BMP) pathway promotes differentiation and induces apoptosis in normal colorectal epithelial cells. However, the effect of the BMP pathway in colorectal cancer (CRC) is controversial; it can either be tumor promoting or tumor suppressing, depending on the study. In this study, we found that CRC cells reside in a BMP-rich environment based on RNA-sequencing database analysis. Suppression of BMP using a specific BMP inhibitor, LDN193189, suppresses the growth of organoids in some CRC cases. CRC organoids treated with LDN193189 exhibited a decrease in epidermal growth factor receptor, which was, at least in part, mediated by protein degradation induced by leucine-rich repeats and immunoglobulin-like domains protein 1 (LRIG1). Among CRC organoid panels from 18 different patients, suppression of organoid growth by BMP inhibition correlated with the induction of LRIG1 gene expression. Notably, knockdown of LRIG1 in organoids diminished the growth-suppressive effect of LDN193189. Furthermore, simultaneous treatment with LDN192189 and trametinib, an FDA-approved MEK inhibitor, resulted in a combination effect in both in vivo and in vitro xenograft tumor treatment in CRC organoids, which are susceptible to growth suppression by LDN193189. Taken together, the simultaneous inhibition of BMP and MEK can be a novel treatment option in CRC cases, and evaluating in vitro growth suppression and LRIG1 induction by BMP inhibition using patient-derived organoids could offer functional biomarkers for predicting potential responders.

cancer biology↗

bioRxiv2022

Hepatocyte Differentiation From Mouse Liver Ductal Organoids By Transducing Four Liver-Specific Transcription Factors

Background & AimsHepatocyte sources that are expandable in vitro are required for liver regenerative medicine and to elucidate the mechanisms underlying the physiological functions of the liver. Liver ductal organoids (LDOs) comprise liver tissue stem cells with a bipotential capacity to differentiate into hepatocyte and cholangiocyte lineages, and can thus serve as a hepatocyte source. However, using current differentiation methods LDOs differentiate into immature hepatocytes while retaining strong cholangiocyte characteristics. We thus investigated an alternative differentiation method for LDOs to achieve hepatocyte maturation. MethodsWe extracted 12 candidate transcription factors to induce hepatocyte differentiation by comparing their gene expression in LDOs and liver tissues. After evaluating the effects of these transcription factors on LDOs, we analyzed the comprehensive gene expression profile, protein expression, and hepatic function in the transduced organoids. ResultsWe identified a combination of four transcription factors, Hnf4a, Foxa1, Prox1, and Hlf, which upregulated hepatic lineage markers and downregulated cholangiocyte markers. Differentiation-induced LDOs showed more hepatocyte-specific characteristics than those with the conventional method, enhancing the transition from cholangiocyte to hepatocyte lineage and hepatic functions, such as liver-specific protein synthesis, lipid droplet deposition, and ammonia detoxification. ConclusionTransduction of the four transcription factors (Hnf4a, Foxa1, Prox1, Hlf) is a promising strategy to promote the differentiation of LDOs to obtain mature hepatocyte-like cells with better functionality.

cell biology↗

bioRxiv2021

Distinct and interchangeable growing patterns in colorectal cancer stem-like cells are regulated by Musashi-1

The dynamic and heterogeneous features of cancer stem-like cells (CSCs) have been widely recognized, but their nongenetic cellular plasticity mechanisms remain elusive. By using colorectal cancer organoids, we phenotypically tracked their spheroid formation and growth capacity to a single-cell resolution, and we discovered that the spheroid-forming cells exhibit a heterogeneous growth pattern, consisting of slow- and fast-growing spheroids. The isolated fast-growing spheroids seem to preserve a dual-growing pattern through multiple passages, whereas the isolated slow-growing spheroids are restricted to a slow-growing pattern. Notably, the spheroids of both patterns were tumorigenic. Moreover, the expression of CSC markers varied among the subpopulations with different growth patterns. The isolated slow-growing spheroids adopted the dual-growing pattern by various extrinsic triggers, in which Musashi-1 plays a key role. The slow-growing fraction was resistant to chemotherapy, and its successful isolation can provide an in vitro platform allowing us to elucidate their role in drug resistance.

cancer biology↗

bioRxiv2021

Liver ductal organoids reconstruct intrahepatic biliary trees in decellularized liver grafts.

Three-dimensional scaffolds decellularized from native organs are a promising technique to establish engineered liver grafts and overcome the current shortage of donor organs. However, limited sources of bile duct cells and inappropriate cell distribution in bioengineered liver grafts have hindered their practical application. Organoid technology is anticipated to be an excellent tool for the advancement of regenerative medicine. In the present study, we reconstructed intrahepatic bile ducts in a rat decellularized liver graft by recellularization with liver ductal organoids. Using an ex vivo perfusion culture system, we demonstrated the biliary characteristics of repopulated mouse liver organoids, which maintained bile duct markers and reconstructed biliary tree-like networks with luminal structures. We also established a method for the co-recellularization with engineered bile ducts and primary hepatocytes, revealing the appropriate cell distribution to mimic the native liver. We then utilized this model in human organoids to demonstrate the reconstructed bile ducts. Our results show that liver ductal organoids are a potential cell source for bile ducts from bioengineered liver grafts using three-dimensional scaffolds.

bioengineering↗

bioRxiv2021

Enterococcus spp. have higher fitness for survival, in a pH-dependent manner, in pancreatic juice among duodenal bacterial flora

ObjectivesBacterial infection is involved in the progression of many gastrointestinal diseases, including cancer; however, how and which bacteria colonize in pancreatic juice and tissue have yet to be elucidated. Recently, we reported that Enterococcus faecalis exists in the pancreatic juice and tissues of patients with chronic pancreatic disease. Here, we investigated the survival of E. faecalis in duodenal juice with different pH conditions. MethodsPancreatic juice samples from 62 patients with cancers of the duodeno-pancreato-biliary region were evaluated for the presence of E. faecalis. 16S ribosomal RNA PCR and 16S-based metagenome analyses were performed to determine the bacterial composition. The survival of E. faecalis in various pancreatic juice conditions was evaluated. ResultsOf 62 samples, 27% (17/62) were positive for Enterococcus spp., among which 71% (12/17) contained E. faecalis. Enterococcus spp. showed the highest fitness for survival in alkaline pancreatic juice among various bacterial species. The microbiome of pancreatic juice from patients with pancreatic and bile duct cancer showed diversity, but Enterococcus spp. were enriched among duodenal tumors and intraductal papillary mucinous neoplasms. ConclusionsAlkalinity is important for the selective survival of E. faecalis among microbiota. E. faecalis may induce pancreatic inflammation with changes in pancreatic juice conditions.

microbiology↗

bioRxiv2021

Functional annotation-driven unsupervised clustering of single-cell transcriptomes

MotivationSingle-cell RNA sequencing (scRNA-seq) analysis reveals heterogeneity and dynamic cell transitions. However, conventional gene-based analyses require intensive manual curation to interpret the biological implications of computational results. Hence, a theory for efficiently annotating individual cells is necessary. ResultsWe present ASURAT, a computational pipeline for simultaneously performing unsupervised clustering and functional annotation of disease, cell type, biological process, and signaling pathway activity for single-cell transcriptomic data, using correlation graph-based decomposition of genes based on database-derived functional terms. We validated the usability and clustering performance of ASURAT using scRNA-seq datasets for human peripheral blood mononuclear cells, which required fewer manual curations than existing methods. Moreover, we applied ASURAT to scRNA-seq and spatial transcriptome datasets for small cell lung cancer and pancreatic ductal adenocarcinoma, identifying previously overlooked subpopulations and differentially expressed genes. ASURAT is a powerful tool for dissecting cell subpopulations and improving biological interpretability of complex and noisy transcriptomic data. AvailabilityA GPLv3-licensed implementation of ASURAT is on GitHub (https://github.com/keita-iida/ASURAT).

bioinformatics↗

bioRxiv2019

Dear Editorial manager PLoS ONEA survey of vaccine-induced measles IgG antibody titer and the verification of changes in temporal differences of measles vaccination in young adults

In Japan, sporadic measles cases increased rapidly in 2019 compared to that in past 6 years. To clarify the persistence of immunity against measles in young adult, this study explored the prevalence of IgG antibody titer against measles virus in 18-to 24-year-old young adult participants. Measles-specific IgG antibody titers determined by enzyme immunoassay in serum samples collected from 506 participants between 18 to 24 years were assessed through statistical analyses. Multiple regression analysis revealed that the distribution of measles IgG antibody titers was significantly correlated with medical history (P < 0.05), while there was no significant difference among the number of vaccinations related to measles IgG titers. Further, measles IgG titers were significantly different, which was determined by the temporal change that elapsed period after last vaccination (P < 0.05). These results indicate that periodic vaccination against measles is required for young and older adults to prevent even sporadic measles infection.

microbiology↗