Spatial and clonality-resolved 3D cancer genome alterations reveal enhancer-hijacking as a potential prognostic marker for colorectal cancer.

The regulatory effect of non-coding large-scale structural variations (SVs) on proto-oncogene activation remains unclear. This study investigated SV-mediated gene dysregulation by profiling 3D cancer genome maps from 40 patients with colorectal cancer (CRC). We developed a machine learning-based method for spatial characterization of the altered 3D cancer genome. This revealed a frequent establishment of "de novo chromatin contacts" that can span multiple topologically associating domains (TADs) in addition to the canonical TAD fusion/shuffle model. Using this information, we precisely identified super-enhancer (SE)-hijacking and its clonal characteristics. Clonal SE-hijacking genes, such as TOP2B, are recurrently associated with cell-cycle/DNA-processing functions, which can potentially be used as CRC prognostic markers. Oncogene activation and increased drug resistance due to SE-hijacking were validated by reconstructing the patient's SV using CRISPR-Cas9. Collectively, the spatial and clonality-resolved analysis of the 3D cancer genome reveals regulatory principles of large-scale SVs in oncogene activation and their clinical implications.

Hi-C as a molecular rangefinder to examine genomic rearrangements.

The mammalian genome is highly packed into the nucleus. Over the past decade, the development of Hi-C has contributed significantly to our understanding of the three-dimensional (3D) chromatin structure, uncovering the principles and functions of higher-order chromatin organizations. Recent studies have repositioned its property in spatial proximity measurement to address challenging problems in genome analyses including genome assembly, haplotype phasing, and the detection of genomic rearrangements. In particular, the power of Hi-C in detecting large-scale structural variations (SVs) in the cancer genome has been demonstrated, which is challenging to be addressed solely with short-read-based whole-genome sequencing analyses. In this review, we first provide a comprehensive view of Hi-C as an intuitive and effective SV detection tool. Then, we introduce recently developed bioinformatics tools utilizing Hi-C to investigate genomic rearrangements. Finally, we discuss the potential application of single-cell Hi-C to address the heterogeneity of genomic rearrangements and sub-population identification in the cancer genome.

Development and validation of a HILIC-MS/MS method for the quantitation of fructose in human urine in support of clinical programs.

In a previous publication [1], a 20-minute UPLC®-MS/MS method, employing a surrogate analyte approach, was developed and validated to measure fructose and sorbitol, as mechanistic biomarkers, in human plasma to support first-in-human (FIH) studies. Different from plasma which maintains its homeostasis, urine has no such homeostasis mechanisms [2], therefore it is expected to be able to accommodate more changes. Here we describe the development and validation of a LC-MS/MS method for the quantiation of fructose in human urine to support clinical trials. A hydrophilic interaction chromatography (HILIC) method using an Asahipak NH2P-50 column (Shodex, 4.6 × 250 mm, 5 µm) was developed. Acetone precipitation was utilized to extract fructose from urine. For validation, stable isotope-labeled 13C6-fructose was used as the surrogate analyte for fructose in the preparation of calibration curves. QCs were prepared using both the surrogate analyte (13C6-fructose) and the authentic analyte (fructose). Difficulties were encountered for post-extraction stability experiments especially for authentic fructose QCs at low concentrations. Extensive troubleshooting revealed that fructose's chromatography improved as the column aged. As a result, the response factor of fructose increased over time for low concentration samples, leading to failed post-extraction stability experiments. A column cleaning procedure was implemented to ensure consistency in chromatography performance. The HILIC-MS/MS method was successfully validated and applied to analyze clinical samples with a 91% overall run passing rate.

Molecular laterality encodes stress susceptibility in the medial prefrontal cortex.

Functional lateralization of the prefrontal cortex has been implicated in stress and emotional disorders, yet underlying gene expression changes remains unknown. Here, we report molecular signatures lateralized by chronic social defeats between the two medial prefrontal cortices (mPFCs). Stressed mice show 526 asymmetrically expressed genes between the mPFCs. This cortical asymmetry selectively occurs in stressed mice with depressed social activity, but not in resilient mice with normal behavior. We have isolated highly asymmetric genes including connective tissue growth factor (CTGF), a molecule that modulates wound healing at the periphery. Knockdown of CTGF gene in the right mPFC by shRNA led to a stress-resistant behavioral phenotype. Overexpression of CTGF in the right mPFC using viral transduction induces social avoidance while the left mPFC thereof prevent stress-induced social avoidance. Our study provides a molecular window into the mechanism of stress-induced socioemotional disorders, which can pave the way for new interventions by targeting cortical asymmetry.

3DIV update for 2021: a comprehensive resource of 3D genome and 3D cancer genome.

Three-dimensional (3D) genome organization is tightly coupled with gene regulation in various biological processes and diseases. In cancer, various types of large-scale genomic rearrangements can disrupt the 3D genome, leading to oncogenic gene expression. However, unraveling the pathogenicity of the 3D cancer genome remains a challenge since closer examinations have been greatly limited due to the lack of appropriate tools specialized for disorganized higher-order chromatin structure. Here, we updated a 3D-genome Interaction Viewer and database named 3DIV by uniformly processing ∼230 billion raw Hi-C reads to expand our contents to the 3D cancer genome. The updates of 3DIV are listed as follows: (i) the collection of 401 samples including 220 cancer cell line/tumor Hi-C data, 153 normal cell line/tissue Hi-C data, and 28 promoter capture Hi-C data, (ii) the live interactive manipulation of the 3D cancer genome to simulate the impact of structural variations and (iii) the reconstruction of Hi-C contact maps by user-defined chromosome order to investigate the 3D genome of the complex genomic rearrangement. In summary, the updated 3DIV will be the most comprehensive resource to explore the gene regulatory effects of both the normal and cancer 3D genome. '3DIV' is freely available at http://3div.kr.

Development and validation of a quantitative ultra performance LC® hydrophilic interaction liquid chromatography MS/MS method to measure fructose and sorbitol in human plasma.

AIM: Fructose and sorbitol are utilized as biomarkers for nonalcoholic steatohepatitis. Measurement of fructose and sorbitol levels helps understanding disease progression, drug response and underlying mechanism. MATERIALS & METHODS: Stable isotope-labeled fructose and sorbitol were used as surrogate standards and internal standards. Human plasma samples were processed and analyzed by ultra performance LC®-MS/MS via chromatographic separation on a hydrophilic interaction liquid chromatography analytical column without derivatization. Assay was validated with biomarker fit-for-purpose concept. RESULTS: A 12-min ultra performance LC®-MS/MS method was developed and validated to directly measure fructose and sorbitol in human plasma with acceptable intra- and inter-assay precision and accuracy. CONCLUSION: This sensitive, selective, and high-throughput assay with suitable dynamic ranges was successfully applied to clinical studies to provide reliable fructose and sorbitol biomarker data.

The Australian Aged Care and Its Implications for the Korean Aging Crisis.

The Australian aged care system has evolved for >50 years to support frail older adults and allow them to make informed decisions about their care. Hospitals provide streamlined geriatric services from visits at the Emergency Department to discharges from acute and subacute geriatric care units. Moreover, nonhospital aged care services, including Transition Care Program, Commonwealth Home Support Program, Home Care Packages Program, and Residential Care (nursing home) are provided under the auspices of the Australian Government. These various specialized hospital and nonhospital services are integrated and coordinated by the multidisciplinary assessment team called ACAT (Aged Care Assessment Team). Korea does not have a similar amount of time to prepare a well-organized aged care system because of a rapidly increasing older population. The Korean government and aged care experts should exert vigorous efforts to improve the last journeys of the Korean older population.

Development of a Consensus List of Potentially Inappropriate Medications for Korean Older Adults.

BACKGROUND: Korea has recently attained the aged society status and the growth rate of the aging population will be among the most rapid worldwide. The objective of this study was to develop a credible list of potentially inappropriate medications (PIMs) for Korean older adults. METHODS: A new Korean PIMs list was produced through a comprehensive structured expert survey (modified Delphi method). To generate an expert panel, we invited the nomination of experts in geriatric medication from the Korean Geriatric Society, the Korean Academy of Clinical Geriatrics, the Korean Academy of Family Medicine, the Korean Association for Geriatric Psychiatry, and the Korean Association of Geriatric Hospitals. Based on their recommendation, the expert panel consisted of 14 geriatric specialists, including 10 geriatricians (7 family medicine doctors and 3 internal medicine doctors), 3 geriatric psychiatrists, and 1 clinical pharmacist. After 4 rounds, the new Korean PIMs list was finalized. RESULTS: Sixty-two drugs were classified as PIMs for older adults irrespective of comorbidities, including antipsychotics, tricyclic antidepressants, benzodiazepines, non-steroidal anti-inflammatory drugs, and first-generation antihistamines. Forty-eight drugs or drug categories were classified as PIMs for 18 specific conditions that older adults encounter frequently. The expert panel presented the rationale and comments including preferred therapeutic alternatives and exceptional situations for each item. CONCLUSION: We presented a "user-friendly" PIMs list for Korean older adults. Further prospective studies to validate its usefulness in clinical settings and regular updating of the list are required. It is also important to disseminate this list to doctors who prescribe medication to older people.

Association between Living Arrangements and Influenza Vaccination Rates among Elderly South Korean People: The Fifth Korea National Health and Nutrition Examination Survey (KNHANES V-2).

BACKGROUND: This study aimed to investigate the association between living arrangements and influenza vaccination among elderly South Korean subjects. METHODS: We used data from the fifth Korean National Health and Nutrition Examination Survey. Participants older than 65 years were included and categorized into 4 groups according to the type of living arrangement as follows: (1) living alone group; (2) living with a spouse group; (3) living with offspring (without spouse) group; and (4) living with other family members group. A total of 1,435 participants were included in this cross-sectional analysis. RESULTS: A lower vaccination rate was observed in the living with offspring (without spouse) group, whereas the living with a spouse group had higher rates of both seasonal and H1N1 influenza vaccination. After adjusting for age, sex, region, education level, income level, and number of comorbidities, the living with offspring (without spouse) group had a higher H1N1 vaccination non-receipt rate than the living alone group (odds ratio, 2.03; 95% confidence interval, 1.08-3.82). CONCLUSION: Influenza vaccination rates differed according to the type of living arrangement. Particularly, those living with offspring (without spouse) had the lowest H1N1 influenza vaccination rate compared to those with other living arrangements, and this difference was significant. Interventions to improve influenza vaccination coverage should target not only elderly persons who live alone, but also those living with offspring.

Hemoglobin concentration and risk of cardiovascular disease in Korean men and women - the Korean heart study.

This study investigated the relationship between hemoglobin concentration and the incidence of cardiovascular diseases (CVD). A total of 407,858 subjects (256,851 men, aged 30-94 yr), who underwent physical examination at 17 Korean nationwide health examination centers, was included in this study. Data regarding CVD incidence were obtained from the Korean National Health Insurance database. In Cox proportional hazard models, men with lower or higher hemoglobin level showed higher hazard ratios (HR) with total CVD (HR, 1.14; 95% Confidence interval [CI], 1.08-1.21 for the 1st quintile; HR, 1.14; 95% CI, 1.09-1.21 for the 5th quintile), ischemic heart disease (HR, 1.16; 95% CI, 1.07-1.26 for the 1st quintile; HR, 1.16; 95% CI, 1.07-1.25 for the 5th quintile), and stroke (HR, 1.13; 95% CI, 1.02-1.25 for the 1st quintile; HR, 1.18; 95% CI, 1.07-1.30 for the 5th quintile) compared to those with mid-level of hemoglobin (3rd quintile). Women with higher hemoglobin level showed higher HR with total CVD (HR, 1.15; 95% CI, 1.01-1.31 for pre-menopausal women; HR, 1.08; 95% CI, 1.01-1.16 for post-menopausal women). We found an independent U-shaped association between hemoglobin level and CVD incidence in Korean population.

The use of complementary and alternative medicine (CAM) in children: a telephone-based survey in Korea.

BACKGROUND: The purpose of this study was to estimate the prevalence and patterns of CAM use in Korean children via a telephone based survey. We also investigated parent satisfaction, a proxy for their child, with CAM therapy and determined the factors affecting satisfaction with CAM use. METHODS: This study used a landline telephone-based survey to examine a random sample representative of Korean children, aged 0 to 18 years. We assigned and surveyed 2,000 subjects according to age group, gender, and geographical distributions by proportionate quota and systematic sampling of children throughout Korea in 2010. A household of 1,184 with a 18.6% response rate was projected to yield 2,077 completed data. We performed statistical analyses using sampling weight. RESULTS: The prevalence of CAM use was 65.3% for the Korean children in our sample population. The most commonly used CAM category was natural products (89.3%). More than half of CAM user's parents reported satisfaction with their therapies (52.7%), but only 29.1% among them had consulted a Western trained doctor regarding the CAM therapies used. Doctor visits were associated with lower satisfaction with CAM use but not with consultation rate with a doctor. CONCLUSIONS: Our study suggests that CAM is widely used among children in Korea. Medical doctors should actively discuss the use of CAM therapies with their patients and provide information on the safety and efficacy of diverse CAM modalities to guide the choices of CAM users.

Sex differences in the relationship between metabolic syndrome and pulmonary function: the 2007 Korean National Health and Nutrition Examination Survey.

Pulmonary function impairment has a connection with abdominal obesity, type 2 diabetes, and insulin resistance. Sex differences in lifestyle factors, and pulmonary structure and function may affect pulmonary function in different manners. This study focused on sex differences in the relationship of MetS and its component with pulmonary function. Among 2,614 Korean adults (1,059 men; 1,555 women), pulmonary function was measured by the percentage of predicted forced vital capacity (FVC (%)) and a ratio between forced expiratory volume in 1 second (FEV(1))/FVC. FVC (%) and FEV(1)/FVC were compared according to the presence of MetS and its components. Multiple linear regression analysis was conducted to assess the association between FVC (%), FEV(1)/FVC and clinical variables. We found sex differences in the relationship of MetS and its components with pulmonary function. FVC (%) was significantly lower in subjects with MetS than in those without MetS in both men and women, and FEV(1)/FVC was lower in subjects with MetS only in women. Among components of MetS, waist circumference, blood pressure and fasting plasma glucose, and HDL-cholesterol were independently related to FVC (%) in men, whereas waist circumference was significantly associated with FVC (%) in women. Blood pressure was found to be an independent factor of FEV(1)/FVC in men, whereas blood pressure, fasting plasma glucose and HDL-cholesterol independently determined FEV(1)/FVC in women. These findings suggest that sex-specific association between MetS and lung function measures should be considered in clinical practice.

Leukocyte mitochondrial DNA (mtDNA) content is associated with depression in old women.

The purpose of this study was to investigate whether mitochondrial DNA (mtDNA) content of peripheral blood leukocyte is related to depression in community-dwelling old women. A total of 142 community-dwelling women, older than 60 years, were included in the study. The mtDNA copy number, which represents the mtDNA content, was measured using real-time PCR methods. Patients with depression defined as the subjects whose 15-question geriatric depression scale (GDS) score was ≥ 8 or who were taking anti-depressant medication. We also measured cognitive function, physical performances (gait speed, chair-stand times, tandem standing times) and metabolic parameters. The depression group had a significantly lower mtDNA copy number than the control group (71.5 vs. 107.3; interquartile range (IQR) = 42.7-116.0 vs. 51.7-202.1; p = 0.028). The Korean version of the mini mental state examination (K-MMSE) score and physical performance score were significantly lower in the depression group than in the control group (p = 0.041, and p = 0.002, respectively). After adjustment for confounding factors using multiple logistic regression analysis, mtDNA copy number was significantly related to depression (p = 0.025). We demonstrated that low leukocyte mtDNA content is related to depression in community dwelling old women. This finding suggests that mitochondrial dysfunction could be a mechanism of geriatric depression.

Identification of endogenous phosphorylation sites of bovine medium and low molecular weight neurofilament proteins by tandem mass spectrometry.

Neurofilament proteins (NFP) are intermediate filaments found in the neuronal cytoskeleton. They are highly phosphorylated, a condition that is believed to be responsible for the assembly and stability of the filaments. Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) shows molecular masses for bovine NFP subunits of 63, 105, and 125 kDa for NFL, NFM, and NFH. Mass spectrometric de novo sequencing was used to determine the N-terminal sequence of bovine NFM (115 amino acids), which was previously unknown. Molecular mass information shows that there is one-half equivalent phosphate group on NFL and 24 on NFM. For the first time, it is shown that bovine NFL has three phosphorylation sites (Ser(55), Ser(66), and Ser(472)) and NFM has 22 (Ser(512), Ser(546), Ser(554), Ser(560), Thr(627), Ser(629), Ser(634), Ser(639), Thr(646), Ser(649), Ser(654), Ser(664), Ser(669), Thr(676), Ser(679), Ser(684), Ser(694), Ser(726), Ser(750), Ser(756), Ser(770), and Ser(846)) and two tentative sites (Ser(659)/Thr(661) and Thr(840)). Ser(66) was previously not known to be phosphorylated in NFL of other species, while two sites (Ser(55) and Ser(472)) are consistent with the phosphorylations observed in other mammalian NFLs. The three sites, Ser(55), Ser(66), Ser(472), are heterogeneously phosphorylated. Phosphorylation in bovine NFM occurs mainly in the Lys-Ser-Pro (KSP) region, but the Val-Ser-Pro and Ser-Glu-Lys motifs are also phosphorylated. Most of the phosphorylation sites are in accordance with those previously identified in other mammalian NFMs. In bovine NFM, 16 out of the 22 sites are always phosphorylated (Ser(512), Thr(627), Ser(629), Ser(634), Ser(639), Thr(646), Ser(649), Ser(654), Ser(664), Ser(669), Thr(676), Ser(679), Ser(684), Ser(694), Ser(726), and Ser(750)), all of which are contained in the KSP region, and six are sometimes phosphorylated (Ser(546), Ser(554), Ser(560), Ser(756), Ser(770), and Ser(846)). The NFPs have other modifications, including deamidation, oxidation, and N-terminal acetylation. Pyroglutamic acid formation also occurs.

Conformational changes in chemically modified Escherichia coli thioredoxin monitored by H/D exchange and electrospray ionization mass spectrometry.

Hydrogen/deuterium (H/D) exchange in combination with electrospray ionization mass spectrometry and near-ultraviolet (UV) circular dichroism (CD) was used to study the conformational properties and thermal unfolding of Escherichia coli thioredoxin and its Cys32-alkylated derivatives in 1% acetic acid (pH 2.7). Thermal unfolding of oxidized (Oxi) and reduced (Red) -thioredoxin (TRX) and Cys-32-ethylglutathionyl (GS-ethyl-TRX) and Cys-32-ethylcysteinyl (Cys-ethyl-TRX), which are derivatives of Red-TRX, follow apparent EX1 kinetics as charge-state envelopes, H/D mass spectral exchange profiles, and near-UV CD appear to support a two-state folding/unfolding model. Minor mass peaks in the H/D exchange profiles and nonsuperimposable MS- and CD-derived melting curves, however, suggest the participation of unfolding intermediates leading to the conclusion that the two-state model is an oversimplification of the process. The relative stabilities as measured by melting temperatures by both CD and mass spectral charge states are, Oxi-TRX, GS-ethyl-TRX, Cys-ethyl-TRX, and Red-TRX. The introduction of the Cys-32-ethylglutathionyl group provides extra stabilization that results from additional hydrogen bonding interactions between the ethylglutathionyl group and the protein. Near-UV CD data show that the local environment near the active site is perturbed to almost an identical degree regardless of whether alkylation at Cys-32 is by the ethylglutathionyl group, or the smaller, nonhydrogen-bonding ethylcysteinyl group. Mass spectral data, however, indicate a tighter structure for GS-ethyl-TRX.