Comprehensive RNA-sequencing analysis of colorectal cancer in a Korean cohort.

Considering the recent increase in the number of colorectal cancer (CRC) cases in South Korea, we aimed to clarify the molecular characteristics of CRC unique to the Korean population. To gain insights into the complexities of CRC and promote the exchange of critical data, RNA-sequencing analysis was performed to reveal the molecular mechanisms that drive the development and progression of CRC; this analysis is critical for developing effective treatment strategies. We performed RNA-sequencing analysis of CRC and adjacent normal tissue samples from 214 Korean participants (comprising a total of 381 including 169 normal and 212 tumor samples) to investigate differential gene expression between the groups. We identified 19,575 genes expressed in CRC and normal tissues, with 3,830 differentially expressed genes (DEGs) between the groups. Functional annotation analysis revealed that the upregulated DEGs were significantly enriched in pathways related to the cell cycle, DNA replication, and IL-17, whereas the downregulated DEGs were enriched in metabolic pathways. We also analyzed the relationship between clinical information and subtypes using the Consensus Molecular Subtype (CMS) classification. Furthermore, we compared groups clustered within our dataset to CMS groups and performed additional analysis of the methylation data between DEGs and CMS groups to provide comprehensive biological insights from various perspectives. Our study provides valuable insights into the molecular mechanisms underlying CRC in Korean patients and serves as a platform for identifying potential target genes for this disease. The raw data and processed results have been deposited in a public repository for further analysis and exploration.

Comprehensive profiling of DNA methylation in Korean patients with colorectal cancer.

Alterations in DNA methylation play an important pathophysiological role in the development and progression of colorectal cancer. We comprehensively profiled DNA methylation alterations in 165 Korean patients with colorectal cancer (CRC), and conducted an in-depth investigation of cancer-specific methylation patterns. Our analysis of the tumor samples revealed a significant presence of hypomethylated probes, primarily within the gene body regions; few hypermethylated sites were observed, which were mostly enriched in promoter-like and CpG island regions. The CpG Island Methylator PhenotypeHigh (CIMP-H) exhibited notable enrichment of microsatellite instability-high (MSI-H). Additionally, our findings indicated a significant correlation between methylation of the MLH1 gene and MSI-H status. Furthermore, we found that the CIMP-H had a higher tendency to affect the right-side of the colon tissues and was slightly more prevalent among older patients. Through our methylome profile analysis, we successfully verified the thylation patterns and clinical characteristics of Korean patients with CRC. This valuable dataset lays a strong foundation for exploring novel molecular insights and potential therapeutic targets for the treatment of CRC. [BMB Reports 2024; 57(2): 110-115].

Exploring the DNA methylome of Korean patients with colorectal cancer consolidates the clinical implications of cancer-associated methylation markers.

Aberrant DNA methylation plays a critical role in the development and progression of colorectal cancer (CRC), which has high incidence and mortality rates in Korea. Various CRC-associated methylation markers for cancer diagnosis and prognosis have been developed; however, they have not been validated for Korean patients owing to the lack of comprehensive clinical and methylome data. Here, we obtained reliable methylation profiles for 228 tumor, 103 adjacent normal, and two unmatched normal colon tissues from Korean patients with CRC using an Illumina Infinium EPIC array; the data were corrected for biological and experiment biases. A comparative methylome analysis confirmed the previous findings that hypermethylated positions in the tumor were highly enriched in CpG island and promoter, 5' untranslated, and first exon regions. However, hypomethylated positions were enriched in the open-sea regions considerably distant from CpG islands. After applying a CpG island methylator phenotype (CIMP) to the methylome data of tumor samples to stratify the CRC patients, we consolidated the previously established clinicopathological findings that the tumors with high CIMP signatures were significantly enriched in the right colon. The results showed a higher prevalence of microsatellite instability status and MLH1 methylation in tumors with high CMP signatures than in those with low or non-CIMP signatures. Therefore, our methylome analysis and dataset provide insights into applying CRC-associated methylation markers for Korean patients regarding cancer diagnosis and prognosis. [BMB Reports 2024; 57(3): 161-166].

Deciphering the DNA methylation landscape of colorectal cancer in a Korean cohort.

Aberrant DNA methylation plays a pivotal role in the onset and progression of colorectal cancer (CRC), a disease with high incidence and mortality rates in Korea. Several CRC-associated diagnostic and prognostic methylation markers have been identified; however, due to a lack of comprehensive clinical and methylome data, these markers have not been validated in the Korean population. Therefore, in this study, we aimed to obtain the CRC methylation profile using 172 tumors and 128 adjacent normal colon tissues of Korean patients with CRC. Based on the comparative methylome analysis, we found that hypermethylated positions in the tumor were predominantly concentrated in CpG islands and promoter regions, whereas hypomethylated positions were largely found in the open-sea region, notably distant from the CpG islands. In addition, we stratified patients by applying the CpG island methylator phenotype (CIMP) to the tumor methylome data. This stratification validated previous clinicopathological implications, as tumors with high CIMP signatures were significantly correlated with the proximal colon, higher prevalence of microsatellite instability status, and MLH1 promoter methylation. In conclusion, our extensive methylome analysis and the accompanying dataset offers valuable insights into the utilization of CRC-associated methylation markers in Korean patients, potentially improving CRC diagnosis and prognosis. Furthermore, this study serves as a solid foundation for further investigations into personalized and ethnicity-specific CRC treatments. [BMB Reports 2023; 56(10): 569-574].

Epigenetic insights into colorectal cancer: comprehensive genome-wide DNA methylation profiling of 294 patients in Korea.

DNA methylation regulates gene expression and contributes to tumorigenesis in the early stages of cancer. In colorectal cancer (CRC), CpG island methylator phenotype (CIMP) is recognized as a distinct subset that is associated with specific molecular and clinical features. In this study, we investigated the genomewide DNA methylation patterns among patients with CRC. The methylation data of 1 unmatched normal, 142 adjacent normal, and 294 tumor samples were analyzed. We identified 40,003 differentially methylated positions with 6,933 (79.8%) hypermethylated and 16,145 (51.6%) hypomethylated probes in the genic region. Hypermethylated probes were predominantly found in promoter-like regions, CpG islands, and N shore sites; hypomethylated probes were enriched in open-sea regions. CRC tumors were categorized into three CIMP subgroups, with 90 (30.6%) in the CIMP-high (CIMP-H), 115 (39.1%) in the CIMP-low (CIMP-L), and 89 (30.3%) in the non-CIMP group. The CIMP-H group was associated with microsatellite instabilityhigh tumors, hypermethylation of MLH1, older age, and rightsided tumors. Our results showed that genome-wide methylation analyses classified patients with CRC into three subgroups according to CIMP levels, with clinical and molecular features consistent with previous data. [BMB Reports 2023; 56(10): 563-568].

Dissection of activation parameters in the bell-shaped α-effect following solvent modulation (DMSO-H2O media).

This paper comprises results of our investigation of the α-effect phenomenon for the reaction of O-p-nitrophenyl thionobenzoate (PNPTB) with butane-2,3-dione monoximate (Ox(-), α-nucleophile) and p-chlorophenoxide (p-ClPhO(-), normal-nucleophile) in DMSO-H2O mixtures of varying compositions at 15.0 °C, 25.0 °C, and 35.0 °C. The reactivity of Ox(-) and p-ClPhO(-) increases significantly as the DMSO content in the medium increases, although the effects of medium on reactivity are not the same for the reactions with Ox(-) and p-ClPhO(-). Ox(-) exhibits the α-effect in all solvent compositions and temperatures. The α-effect increases up to 50 mol % DMSO and then decreases thereafter, resulting in a bell-shaped α-effect profile. Dissection of the activation parameters (i.e., ΔH(‡) and TΔS(‡)) has revealed that the bell-shaped α-effect behavior is due to entropy of activation differences rather than enthalpy terms, although the enthalpy term controls almost entirely the solvent dependence of the reaction rate. Differences in the transition-state (TS) structures for the reactions with Ox(-) (a six-membered cyclic TS) and p-ClPhO(-) (an acyclic TS) are consistent with the entropy-dependent α-effect behavior.

Kinetic study on Michael-type reactions of ß-nitrostyrenes with cyclic secondary amines in acetonitrile: transition-state structures and reaction mechanism deduced from negative enthalpy of activation and analyses of LFERs.

A kinetic study is reported for the Michael-type reactions of X-substituted ß-nitrostyrenes (1a-j) with a series of cyclic secondary amines in MeCN. The plots of pseudo-first-order rate constant k(obsd) vs [amine] curve upward, indicating that the reactions proceed through catalyzed and uncatalyzed routes. The dissection of k(obsd) into Kk2 and Kk3 (i.e., the rate constants for the uncatalyzed and catalyzed routes, respectively) revealed that Kk3 is much larger than Kk2, implying that the reactions proceed mainly through the catalyzed route when [amine] > 0.01 M. Strikingly, the reactivity of ß-nitrostyrene (1g) toward piperidine decreases as the reaction temperature increases. Consequently, a negative enthalpy of activation is obtained, indicating that the reaction proceeds through a relatively stable intermediate. The Brønsted-type plots for the reactions of 1g are linear with ß(nuc) = 0.51 and 0.61, and the Hammett plots for the reactions of 1a-j are also linear with ρX = 0.84 and 2.10 for the uncatalyzed and catalyzed routes, respectively. The reactions are concluded to proceed through six-membered cyclic transition states for both the catalyzed and uncatalyzed routes. The effects of the substituent X on reactivity and factors influencing ß(nuc) and ρX obtained in this study are discussed.

A kinetic study on nucleophilic displacement reactions of aryl benzenesulfonates with potassium ethoxide: role of K+ ion and reaction mechanism deduced from analyses of LFERs and activation parameters.

Pseudofirst-order rate constants (k(obsd)) have been measured spectrophotometrically for the nucleophilic substitution reactions of 2,4-dinitrophenyl X-substituted benzenesulfonates 4a-f and Y-substituted phenyl benzenesulfonates 5a-k with EtOK in anhydrous ethanol. Dissection of k(obsd) into k(EtO(-)) and k(EtOK) (i.e., the second-order rate constants for the reactions with the dissociated EtO(-) and ion-paired EtOK, respectively) shows that the ion-paired EtOK is more reactive than the dissociated EtO(-), indicating that K(+) ion catalyzes the reaction. The catalytic effect exerted by K(+) ion (e.g., the k(EtOK)/k(EtO(-)) ratio) decreases linearly as the substituent X in the benzenesulfonyl moiety changes from an electron-donating group (EDG) to an electron-withdrawing group (EWG), but it is independent of the electronic nature of the substituent Y in the leaving group. The reactions have been concluded to proceed through a concerted mechanism from analyses of the kinetic data through linear free energy relationships (e.g., the Brønsted-type, Hammett, and Yukawa-Tsuno plots). K(+) ion catalyzes the reactions by increasing the electrophilicity of the reaction center through a cyclic transition state (TS) rather than by increasing the nucleofugality of the leaving group. Activation parameters (e.g., ΔH(‡) and ΔS(‡)) determined from the reactions performed at five different temperatures further support the proposed mechanism and TS structures.

Effects of Inter-electrode Distance on Delayed Onset Muscle Soreness in Microcurrent Therapy.

[Purpose] This study examined the effect of the distance between the two electrodes on delayed onset muscle soreness during microcurrent therapy. [Methods] In this study 24 healthy women who hadn't exercised regularly for six months were selected and randomly divided into two groups. Delayed onset muscle soreness (DOMS) was induced and experimental Group 1 were given microcurrent treatment with the electrodes attached at a close distance evaluated. Experimental Group 2 received the same treatment with the electrodes attached at a greater distance apart. Visual analogue scale pain and the RIII reflex were evaluated after inducing DOMS and after one day, two days, three days and four days of microcurrent treatment. [Results] The visual analogue scale and amplitude of RIII amplitude only showed significant differences with the length of time of the treatment. [Conclusion] This study found that difference of interelectrode distance has no influence on VAS pain and the RIII reflex of DOMS. Although there were no significant differences in RIII amplitude, we suspect that it may be influenced by current parameters such as frequency and intensity.

Mechanistic assessment of S(N)Ar displacement of halides from 1-halo-2,4-dinitrobenzenes by selected primary and secondary amines: Brønsted and Mayr analyses.

Pseudo-first-order rate constants (k(obsd)) have been measured spectrophotometrically for nucleophilic substitution reactions of 1-X-2,4-dinitrobenzenes (1a-d, X = F, Cl, Br, I) with various primary and secondary amines in MeCN and H(2)O at 25.0 ± 0.1 °C. The plots of k(obsd) vs [amine] curve upward for reactions of 1a (X = F) with secondary amines in MeCN. In contrast, the corresponding plots for the other reactions of 1b-d with primary and secondary amines in MeCN and H(2)O are linear. The Brønsted-type plots for reactions of 1a-d with a series of secondary amines are linear with ß(nuc) = 1.00 for the reaction of 1a and 0.52 ± 0.01 for those of 1b-d. Factors governing reaction mechanisms (e.g., solvent, halogen atoms, H-bonding interactions, amine types) have been discussed. Kinetic data were also analyzed in terms of the Mayr nucleophilicity parameter for the amines with each aromatic substrate. Provisional Mayr electrophilicity parameter (E) values for 1-X-2,4-dinitrobenzenes have been determined: E = -14.1 for X = F, E = -17.6 for X = Cl and Br, and E = -18.3 for X = I. These values are consistent with the range and order of E values for heteroaromatic superelectrophiles and normal 6-π aromatic electrophiles.

Alkali-metal-ion catalysis and inhibition in the nucleophilic displacement reaction of y-substituted phenyl diphenylphosphinates and diphenylphosphinothioates with alkali-metal ethoxides: effect of changing the electrophilic center from P=O to P=S.

A kinetic study of the nucleophilic substitution reaction of Y-substituted phenyl diphenylphosphinothioates 2 a-g with alkali-metal ethoxides (MOEt; M = Li, Na, K) in anhydrous ethanol at (25.0±0.1) °C is reported. Plots of pseudo-first-order rate constants (k(obsd)) versus [MOEt], the alkali ethoxide concentration, show distinct upward (KOEt) and downward (LiOEt) curvatures, respectively, pointing to the importance of ion-pairing phenomena and a differential reactivity of dissociated EtO(-) and ion-paired MOEt. Based on ion-pairing treatment of the kinetic data, the k(obsd) values were dissected into k EtO - and k(MOEt), the second-order rate constants for the reaction with the dissociated EtO(-) and ion-paired MOEt, respectively. The reactivity of MOEt toward 2 b (Y = 4-NO(2)) increases in the order LiOEtNaOEt>KOEt>EtO(-). The current study based on Yukawa-Tsuno analysis has revealed that the reactions of 2 a-g (P=S) and Y-substituted phenyl diphenylphosphinates 1 a-g (P=O) with MOEt proceed through the same concerted mechanism, which indicates that the contrasting selectivity patterns are not due to a difference in reaction mechanism. The P=O compounds 1 a-g are approximately 80-fold more reactive than the P=S compounds 2 a-g toward the dissociated EtO(-) (regardless of the electronic nature of substituent Y) but are up to 3.1×10(3)-fold more reactive toward ion-paired LiOEt. The origin of the contrasting selectivity patterns is further discussed on the basis of competing electrostatic effects and solvational requirements as a function of anionic electric field strength and cation size (Eisenman's theory).

Hydrolysis of 1-(X-substituted-benzoyl)-4-aminopyridinium ions: effect of substituent X on reactivity and reaction mechanism.

A kinetic study is reported for hydrolysis of 1-(X-substituted-benzoyl)-4-aminopyridinium ions 2a-i, which were generated in situ from the nucleophilic substitution reaction of 2,4-dinitrophenyl X-substituted-benzoates 1a-i with 4-aminopyridine in 80 mol% H(2)O/20 mol% DMSO at 25.0 ± 0.1 °C. The plots of pseudo-first-order rate constants k(obsd) vs. pyridine concentration are linear with a large positive intercept, indicating that the hydrolysis of 2a-i proceeds through pyridine-catalyzed and uncatalyzed pathways with the rate constant k(cat) and k(o), respectively. The Hammett plots for k(cat) and k(o) consist of two intersecting straight lines, which might be taken as evidence for a change in the rate-determining step (RDS). However, it has been proposed that the nonlinear Hammett plots are not due to a change in the RDS but are caused by stabilization of 2a-i in the ground state through a resonance interaction between the π-electron-donor substituent X and the carbonyl functionality. This is because the corresponding Yukawa-Tsuno plots exhibit excellent linear correlations with ρ(X) = 1.45 and r = 0.76 for k(cat) while ρ(X) = 1.39 and r = 0.72 for k(o). A possibility that the hydrolysis of 2a-i proceeds through a concerted mechanism has been ruled out on the basis of the large ρ(X) values. Thus, the reaction has been concluded to proceed through a stepwise mechanism in which the leaving group departs after the RDS since OH(-) is more basic and a poorer nucleofuge than 4-aminopyridine.

Ultrathin carbon support films for high-resolution electron microscopy of nanoparticles.

We introduce a simple preparation method for ultrathin carbon support films that is especially useful for high-resolution electron microscopy (HREM) of nanoparticles. Oxidized iron nanoparticles were used as a test sample in a demonstration of this method. The film qualities are discussed on the basis of electron-energy-loss spectroscopy (EELS) and image analysis techniques such as thickness maps and histograms. We carried out a comparison between the homemade and commercial film qualities. The relative thickness of the homemade support films was 0.6 times less than that of the commercial films, which was calculated from the EELS analysis, whereas the thicknesses of both carbon support films varied within about 3%. The percentage of the observable area was about 67 +/- 7.6% of the support film. This was about twice as large as the commercial film (32 +/- 9.3%). The HREM image of the sample prepared with our support film improved 9% in brightness and 15% in contrast compared with images obtained with the commercial support.