Use of genome-wide DNA methylation analysis to identify prognostic CpG site markers associated with longer survival time in dogs with multicentric high-grade B-cell lymphoma.

BACKGROUND: DNA methylation analysis might identify prognostic CpG sites in CHOP-treated dogs with multicentric high-grade B-cell lymphoma (MHGL) with heterogenous prognosis. OBJECTIVE: To identify prognostic CpG sites of MHGL through genome-wide DNA methylation analysis with pyrosequencing validation. ANIMALS: Test group: 24 dogs. Validation group: 100 dogs. All client-owned dogs were diagnosed with MHGL and treated with CHOP chemotherapy. METHODS: Cohort study. DNA was extracted from lymph node samples obtained via FNA. Genome-wide DNA methylation analysis using Digital Restriction Enzyme Analysis of Methylation (DREAM) was performed on the test group to identify differentially methylated CpG sites (DMCs). Bisulfite pyrosequencing was used to measure methylation status of candidate DMCs in the validation group. Median survival times (MST) were analyzed using Kaplan-Meier (log-rank) product limit method. RESULTS: DREAM analyzed 101 576 CpG sites. Hierarchical clustering of 16 262 CpG sites in test group identified group with better prognosis (MST = 55-477 days vs 10-301 days, P = .007). Volcano plot identified 1371 differentially methylated CpG sites (DMCs). DMC near the genes of FAM213A (DMC-F) and PHLPP1 (DMC-P) were selected as candidates. Bisulfite-pyrosequencing performed on validation group showed group with methylation level of DMC-F < 40% had favorable prognosis (MST = 11-1072 days vs 8-1792 days, P = .01), whereas group with the methylation level combination of DMC-F < 40% plus DMC-P < 10% had excellent prognosis (MST = 18-1072 days vs 8-1792 days, P = .009). CONCLUSION AND CLINICAL IMPORTANCE: Methylation status of prognostic CpG sites delineate canine MGHL cases with longer MST, providing owners with information on expectations of potential improved treatment outcomes.

Lymphocyte stimulation test for diagnosing hen's egg yolk-induced enterocolitis syndrome.

Background: There is currently little research into factors predicting the results of an initial diagnostic oral food challenge (OFC) test for food protein-induced enterocolitis syndrome (FPIES). Objective: The present study aimed to identify predictors of the diagnosis of hen's egg yolk-induced FPIES (HEY-FPIES). Methods: The present monocentric study was performed at Tokyo Metropolitan Children's Medical Center and included patients who underwent hen's egg yolk OFC (HEY-OFC) between March 2018 and March 2023 to assess for HEY-FPIES. The baseline characteristics of the groups and HEY-OFC positivity or negativity were then compared. Univariate analysis was conducted by using the Mann-Whitney U test or Fisher exact test. Receiver operator characteristic analysis was used to create probability curves. Results: In total, 35 patients were analyzed; of these, 17 were HEY-OFC-positive. No significant difference was observed between the HEY-OFC-positive and HEY-OFC-negative groups in terms of background factors except for the HEY-LST value, which was significantly higher in the HEY-LST group (P = .027). Receiver operator characteristic analysis demonstrated that the area under the curve for HEY-OFC positivity using the HEY-LST value was 0.719 (95% CI = 0.541-0.897). The statistically optimal cutoff value for the HEY-LST was 610%, which had a clinical sensitivity and specificity of 64.7% and 83.3%, respectively. Conclusions: The present study demonstrated that the HEY-LST may be a useful predictor of the result of an initial OFC for HEY-FPIES.

Diverse genome-wide DNA methylation alterations in canine hepatocellular tumours.

BACKGROUND: Canine hepatocellular tumours (HCTs) are common primary liver tumours. However, the exact mechanisms of tumourigenesis remain unclear. Although some genetic mutations have been reported, DNA methylation alterations in canine HCT have not been well studied. OBJECTIVES: In this study, we aimed to analyse the DNA methylation status of canine HCT. METHODS: Tissues from 33 hepatocellular carcinomas, 3 hepatocellular adenomas, 1 nodular hyperplasia, 21 non-tumour livers from the patients and normal livers from 5 healthy dogs were used. We analysed the DNA methylation levels of 72,367 cytosine-guanine dinucleotides (CpG sites) in all 63 samples. RESULTS AND CONCLUSIONS: Although a large fraction of CpG sites that were highly methylated in the normal liver became hypomethylated in tumours from most patients, we also found some patients with less remarkable change or no change in DNA methylation. Hierarchical clustering analysis revealed that 32 of 37 tumour samples differed from normal livers, although the remaining 5 tumour livers fell into the same cluster as normal livers. In addition, the number of hypermethylated genes in tumour livers varied among tumour cases, suggesting various DNA methylation patterns in different tumour groups. However, patient and clinical parameters, such as age, were not associated with DNA methylation status. In conclusion, we found that HCTs undergo aberrant and diverse patterns of genome-wide DNA methylation compared with normal liver tissue, suggesting a complex epigenetic mechanism in canine HCT.

Genome-wide DNA methylation profile in feline haematological tumours: A preliminary study.

Although DNA methylation has been analysed in few studies for a limited number of loci in cats with diseases, genome-wide profile of DNA methylation has never been addressed. The hypothesis for this study is that next-generation sequencing with sequential digestion of genomic DNA with SmaI and XmaI enzymes could provide highly quantitative information on methylation levels in cats. Using blood from four healthy control cats and two disease cats as well as three feline lymphoma/leukemia cell lines, approximately 74-94 thousand CpG sites across the cat genome could be analysed. CpG sites in CpG island (CGI) were broadly either methylated or unmethylated in normal blood, while CpG sites in non-CpG islands (NCGI) are largely methylated. Lymphoma cell lines showed thousands of CpG sites with gain of methylation at normally unmethylated CGI sites and loss of methylation at normally methylated NCGI sites. Hypermethylated CpG sites located at promoter regions included genes annotated with 'developmental process' and 'anatomical structure morphogenesis' such as HOXD10. This highly quantitative method would be suitable for studies of DNA methylation changes not only in cancer but also in other common diseases in cats.

Obese status is associated with accelerated DNA methylation change in peripheral blood of senior dogs.

Obesity and its associated comorbidities constitute a major and growing health problem worldwide not only involved with people but also dogs and cats. Although few genetic mutations have been associated with obesity in dogs, molecular mechanism remains to be clearly understood. Given the fact that DNA methylation leads to gene expression variability and has plasticity affected by metabolic phenotypes such as obesity in human, the objective of this study is to identify obesity-associated differentially methylated cytosine-phosphate-guanine (CpG) dinucleotide sites in dogs. With genome-wide DNA methylation analysis using next-generation sequencing for blood samples from fourteen Miniature dachshunds with body condition score (BCS) 4-5 and BCS ≥6, over 100,000 sites could be analysed to identify genomic locations of differentially methylated CpG sites. As a result, 191 differentially methylated CpG sites (89 CpG sites were hypermethylated in BCS ≥6 and 102 were hypermethylated in BCS 4-5) were identified. These sites included promoter regions of Kisspeptin receptor (KISS1R) and Calcyphosine 2 (CAPS2) genes which were subsequently validated by bisulfite-pyrosequencing for another set of 157 dog blood samples. KISS1R methylation levels were found to be higher in BCS ≥6 group than BCS 4-5 in senior (>84 months) dogs. Especially male dogs but not female dogs as well as uncastrated male dogs but not castrated male dogs showed this trend. DNA methylation of KISS1R gene will be useful for understanding of comprehensive epigenetic change in obese dogs.

Genome-wide DNA methylation analysis of dogs with high lead exposure living near a lead mining area in Kabwe, Zambia.

Lead (Pb) is a heavy metal that has been proven to be toxic to both animals and humans. Genom-wide DNA methylation in domestic dogs exposed to high levels of Pb in Kabwe, Zambia was analyzed in this study. Using next-generation sequencing on samples from 20 domestic dogs (mean blood Pb concentration: 43.6 µg/dL and 7.2 µg/dL in the high and low exposure groups), a digital restriction enzyme analysis of methylation was performed to identify the genomic locations of differentially methylated CpG sites. A validation study on an additional 20 dogs followed (blood Pb concentration: 4.9-29.7 µg/dL). The cluster analysis resolved two broad clusters indicating high and low Pb exposure. The study identified 827 (1.2%) CpG sites with differences in methylation (101 CpG sites were hypermethylated in the low exposure group and 726 were hypermethylated in the high exposure group). The sites corresponded to 26 genes with differentially methylated CpG sites at their promoter regions, including the NGF gene. The methylation of four CpG sites was validated using bisulfite pyrosequencing. The results indicate that aberrant hypermethylation is prevalent in dogs exposed to Pb. The altered DNA methylation of the genes identified in this study contributes to a greater understanding of the epigenetic changes caused by Pb exposure and highlights novel biomarker discoveries across species.

SNAIL regulates gastric carcinogenesis through CCN3 and NEFL.

Among cancer cells, there are specific cell populations of whose activities are comparable to those of stem cells in normal tissues, and for whom the levels of cell dedifferentiation are reported to correlate with poor prognosis. Information concerning the mechanisms that modulate the stemness like traits of cancer cells is limited. Therefore, we examined five gastric cancer cell lines and isolated gastric oncospheres from three gastric cancer cell lines. The gastric cancer cells that expanded in the spheres expressed relatively elevated proportion of CD44, which is a marker of gastric cancer stem cells (CSCs), and displayed many properties of CSCs, for example: chemoresistance, tumorigenicity and epithelial-mesenchymal transition (EMT) acquisition. SNAIL, which is a key factor in EMT, was highly expressed in the gastric spheres. Microarray analysis in gastric cancer cell line HGC27 showed that CCN3 and NEFL displayed the greatest differential expression by knocking down of SNAIL; the former was upregulated and the latter downregulated, respectively. Downregulation of CCN3 and upregulation of NEFL gene expression impaired the SNAIL-dependent EMT activity: high tumorigenicity, and chemoresistance in gastric cancer cells. Thus, approach that disrupts SNAIL/CCN3/NEFL axis may be credible in inhibiting gastric cancer development.

Promoter-Level Transcriptome Identifies Stemness Associated With Relatively High Proliferation in Pancreatic Cancer Cells.

Both pancreatic intraepithelial neoplasia (PanIN), a frequent precursor of pancreatic cancer, and intraductal papillary mucinous neoplasm (IPMN), a less common precursor, undergo several phases of molecular conversions and finally develop into highly malignant solid tumors with negative effects on the quality of life. We approached this long-standing issue by examining the following PanIN/IPMN cell lines derived from mouse models of pancreatic cancer: Ptf1a-Cre; KrasG12D; p53f/+ and Ptf1a-Cre; KrasG12D; and Brg1f/f pancreatic ductal adenocarcinomas (PDAs). The mRNA from these cells was subjected to a cap analysis of gene expression (CAGE) to map the transcription starting sites and quantify the expression of promoters across the genome. Two RNA samples extracted from three individual subcutaneous tumors generated by the transplantation of PanIN or IPMN cancer cell lines were used to generate libraries and Illumina Seq, with four RNA samples in total, to depict discrete transcriptional network between IPMN and PanIN. Moreover, in IPMN cells, the transcriptome tended to be enriched for suppressive and inhibitory biological processes. In contrast, the transcriptome of PanIN cells exhibited properties of stemness. Notably, the proliferation capacity of the latter cells in culture was only minimally constrained by well-known chemotherapy drugs such as GSK690693 and gemcitabine. The various transcriptional factor network systems detected in PanIN and IPMN cells reflect the distinct molecular profiles of these cell types. Further, we hope that these findings will enhance our mechanistic understanding of the characteristic molecular alterations underlying pancreatic cancer precursors. These data may provide a promising direction for therapeutic research.

Synthesis and In Vitro Assessment of pH-Sensitive Human Serum Albumin Conjugates of Pirarubicin.

In a previous study, we reported on the development of a synthetic polymer conjugate of pirarubicin (THP) that was formed via an acid-labile hydrazone bond between the polymer and the THP. However, the synthetic polymer itself was non-biodegradable, which could lead to unexpected adverse effects. Human serum albumin (HSA), which has a high biocompatibility and good biodegradability, is also a potent carrier for delivering antitumor drugs. The objective of this study was to develop pH-sensitive HSA conjugates of THP (HSA-THP), and investigate the release of THP and the cytotoxicity under acidic conditions in vitro for further clinical development. HSA-THP was synthesized by conjugating maleimide hydrazone derivatives of THP with poly-thiolated HSA using 2-iminothiolane, via a thiol-maleimide coupling reaction. We synthesized two types of HSA-THP that contained different amounts of THP (HSA-THP2 and HSA-THP4). Free THP was released from both of the HSA conjugates more rapidly at an acidic pH, and the rates of release for HSA-THP2 and HSA-THP4 were similar. Moreover, both HSA-THPs exhibited a higher cytotoxicity at acidic pH than at neutral pH, which is consistent with the effective liberation of free THP under acidic conditions. These findings suggest that these types of HSA-THPs are promising candidates for further development.

Membrane Incorporation, Channel Formation, and Disruption of Calcium Homeostasis by Alzheimer's ß-Amyloid Protein.

Oligomerization, conformational changes, and the consequent neurodegeneration of Alzheimer's ß-amyloid protein (AßP) play crucial roles in the pathogenesis of Alzheimer's disease (AD). Mounting evidence suggests that oligomeric AßPs cause the disruption of calcium homeostasis, eventually leading to neuronal death. We have demonstrated that oligomeric AßPs directly incorporate into neuronal membranes, form cation-sensitive ion channels ("amyloid channels"), and cause the disruption of calcium homeostasis via the amyloid channels. Other disease-related amyloidogenic proteins, such as prion protein in prion diseases or α-synuclein in dementia with Lewy bodies, exhibit similarities in the incorporation into membranes and the formation of calcium-permeable channels. Here, based on our experimental results and those of numerous other studies, we review the current understanding of the direct binding of AßP into membrane surfaces and the formation of calcium-permeable channels. The implication of composition of membrane lipids and the possible development of new drugs by influencing membrane properties and attenuating amyloid channels for the treatment and prevention of AD is also discussed.

Syntheses of new model compounds related to an antigenic epitope from Bupleurum falcatum L. and their distributions in various ganglioside-phospholipid monolayers.

6-N-[2-(Tetradecyl)hexadecanamido]hexyl beta-D-glucopyranosyluronic acid-(1-->6)-beta-D-galactopyranosyl-(1-->6)-beta-D-galactopyranoside (1) and its clustering compound (2) carrying a tetravalent sugar unit, which are new model compounds related to a major antigenic epitope from antiulcer pectic polysaccharide of Bupleurum falcatum L., were synthesized and the distributions of 1 and 2 in mixed ganglioside (GM1, GD1a or GT1b)/phospholipid (DPPC) monolayers were observed using atomic force microscopy (AFM). AFM images showed that 1 was distributed in the GM1, GD1a and GT1b region of the mixed monolayers, in which 1 was miscible with GD1a. Specific distribution of 1 was observed in the mixed GM1/DPPC monolayer. Compound 2 was miscible with GM1, while 2 formed associations with GD1a and GT1b in the mixed monolayers. The distribution mode of 1 and 2 was different among the mixed ganglioside/DPPC monolayers.

Membrane properties of cationic liposomes composed of dipalmitoylphosphatidylcholine and dipalmityldimethylammonium bromide.

Cationic liposomes composed of dipalmitoylphosphatidylcholine (DPPC) and dipalmityldimethylammmonium bromide (DPAB) were prepared by the Bangham method and the effect of DPAB on the membrane properties was examined in terms of liposomal shape, particle size, trapping efficiency, surface potential and dispersibility. The dispersibility of the mixed DPPC/DPAB liposomes (the mole fraction of DPAB (XDPAB)>==0.05) was excellent and the dispersibility was maintained for 6 months, since the zeta-potential of the mixed liposomes was approximately +40 mV. The trapping efficiency of the mixed DPPC/DPAB liposomes (XDPAB=0.05) was 10 times greater than that of the DPPC liposomes, and the value was largest among the mixed liposomes (XDPAB=0-1.0). Freeze-fracture electron micrographs indicated that the shape of the mixed DPPC/DPAB liposomes (XDPAB=0.05) was that of large unilamellar vesicles (LUVs) with a diameter of approximately 2 microm, while the shape of the DPPC liposomes was that of multilamellar vesicles (MLVs). The mixed liposomes had, therefore, a high trapping efficiency. Furthermore, the shape of the mixed DPPC/DPAB liposomes (XDPAB=0.75) was also that of LUVs with a diameter of approximately 2 microm and these had a high trapping efficiency. Whereas, the particle size (500 nm) of the mixed DPPC/DPAB liposomes (XDPAB=0.25) was smaller than that of the former and had the minimum trapping efficiency. The phase transition temperature of the liposomal bilayer membranes indicated a maximum value at 0.25-0.30 mole fractions of DPAB. These facts were considered to be due to the fact that DPPC and DPAB, whose molar ratio was 7.5:2.5, were tightly packed in the liposomal bilayer membranes and that the curvature of the liposomal particle was resultantly large. Nevertheless, LUVs having a high trapping efficiency were easily obtained by mixing a small amount of DPAB with the DPPC.

Penetration of bovine serum albumin into dipalmitoylphosphatidylglycerol monolayers: direct observation by atomic force microscopy.

The penetration of bovine serum albumin (BSA) into dipalmitoylphosphatidylglycerol (DPPG) monolayers was observed using atomic force microscopy (AFM) and surface pressure measurements. The effects of surface pressure, amount of BSA and the addition of ganglioside GM1 (GM1) were investigated. The surface pressure of the DPPG monolayer was increased by the penetration of BSA, and the increase in surface pressure was greater in the liquid-expanded film than that in the liquid-condensed film. The AFM images indicated that BSA penetrated into the DPPG monolayer. The amount of BSA that penetrated into the DPPG monolayer increased with time and with the amount of BSA added. On the contrary, the AFM image showed that BSA penetration into the mixed DPPG/GM1 (9 : 1) monolayer scarcely occurred. GM1 inhibited the penetration of BSA into the DPPG monolayer.

Membrane properties of binary and ternary systems of ganglioside GM1/dipalmitoylphosphatidylcholine/dioleoylphosphatidylcholine.

The membrane properties of the ganglioside GM1 (GM1)/dioleoylphosphatidylcholine (DOPC) binary system and GM1/dipalmitoylphosphatidylcholine (DPPC)/DOPC ternary system were investigated using surface pressure measurements and atomic force microscopy (AFM), and the effect of surface pressure on the properties of the membranes was examined. Mixed GM1/DPPC/DOPC monolayers were deposited on mica using the Langmuir-Blodgett technique for AFM. GM1 and DOPC were immiscible and phase-separated. The AFM image of the GM1/DOPC (1:1) monolayer showed island-like GM1 domains embedded in the DOPC matrix. There was no morphological change on varying surface pressure. The surface pressure-area isotherm of the GM1/DPPC/DOPC (2:9:9) monolayer showed a two-step collapse as in the DPPC/DOPC (1:1) monolayer. The AFM image for the GM1/DPPC/DOPC monolayer showed DPPC and GM1 domains in the DOPC matrix, and the DPPC-rich phase containing GM1 showed a percolation pattern the same as the GM1/DPPC (1:9) monolayer. The percolation pattern in the GM1/DPPC/DOPC monolayer changed as the surface pressure was varied. The surface pressure-responsive change in morphology of GM1 was affected by the surrounding environment, suggesting that the GM1 localized in each organ has a specific role.

Effect of membrane composition on surface states of ganglioside GM1/dipalmitoylphosphatidylcholine/dioleoylphosphatidylcholine monolayers.

The surface states of ganglioside GM1 (GM1)/dipalmitoylphosphatidylcholine (DPPC)/dioleoylphosphatidylcholine (DOPC) monolayers having various compositions were investigated using atomic force microscopy (AFM), and the effect of the composition on the surface states of the membrane was examined. The AFM images for the ternary system showed a DPPC-rich phase containing GM1 in the DOPC matrix, which indicated that the morphology varied as the composition of the monolayers changed. The AFM images for the GM1/DPPC/DOPC monolayers having (2:9:9) and (4:18:9) molar ratios showed a percolation pattern similar to that observed for the GM1/DPPC (1:9) monolayer. The AFM image for the GM1/DPPC/DOPC (2:18:9) monolayer showed a dotted pattern with a high topography. Monolayers having a higher content of DOPC than DPPC and/or having a higher content of GM1 showed dot-like domains in the DPPC-rich phase containing GM1. In conclusion, the surface states of GM1/DPPC/DOPC monolayers changed depending on the composition. These results may be related to a diversity of GM1 in various organs.

Controlled release of vitamin E from thermo-responsive polymeric physico-gel.

Thermo-sensitive copolymer consists of poly(2-ethoxyethyl vinyl ether) and poly(hydroxyethyl vinyl ether) (EOVE200-HOVE400), whose sol-gel transition temperature was 20.5 degrees C, was synthesized and its applicability to a drug delivery system was examined. Vitamin E (VE) was enclosed in EOVE200-HOVE400 and the release of VE was measured by varying the temperature 10<-->30 degrees C. There was no release of VE from EOVE200-HOVE400 at 30 degrees C, while VE was released when the temperature was reduced to 10 degrees C.