Genomic technologies for detecting structural variations in hematologic malignancies.

Genomic structural variations in myeloid, lymphoid, and plasma cell neoplasms can provide key diagnostic, prognostic, and therapeutic information while elucidating the underlying disease biology. Several molecular diagnostic approaches play a central role in evaluating hematological malignancies. Traditional cytogenetic diagnostic assays, such as chromosome banding and fluorescence in situ hybridization, are essential components of the current diagnostic workup that guide clinical care for most hematologic malignancies. However, each assay has inherent limitations, including limited resolution for detecting small structural variations and low coverage, and can only detect alterations in the target regions. Recently, the rapid expansion and increasing availability of novel and comprehensive genomic technologies have led to their use in clinical laboratories for clinical management and translational research. This review aims to describe the clinical relevance of structural variations in hematologic malignancies and introduce genomic technologies that may facilitate personalized tumor characterization and treatment.

Clinical, Mutational, and Transcriptomic Characteristics in Elderly Korean Individuals With Clonal Hematopoiesis Driver Mutations.

Background: Clonal hematopoiesis of indeterminate potential (CHIP), which is defined as the presence of blood cells originating from somatically mutated hematopoietic stem cells, is common among the elderly and is associated with an increased risk of hematologic malignancies. We investigated the clinical, mutational, and transcriptomic characteristics in elderly Korean individuals with CHIP mutations. Methods: We investigated CHIP in 90 elderly individuals aged ≥60 years with normal complete blood counts at a tertiary-care hospital in Korea between June 2021 and February 2022. Clinical and laboratory data were prospectively obtained. Targeted next-generation sequencing of 49 myeloid malignancy driver genes and massively parallel RNA sequencing were performed to explore the molecular spectrum and transcriptomic characteristics of CHIP mutations. Results: We detected 51 mutations in 10 genes in 37 (41%) of the study individuals. CHIP prevalence increased with age. CHIP mutations were observed with high prevalence in DNMT3A (26 individuals) and TET2 (eight individuals) and were also found in various other genes, including KDM6A, SMC3, TP53, BRAF, PPM1D, SRSF2, STAG1, and ZRSR2. Baseline characteristics, including age, confounding diseases, and blood cell parameters, showed no significant differences. Using mRNA sequencing, we characterized the altered gene expression profile, implicating neutrophil degranulation and innate immune system dysregulation. Conclusions: Somatic CHIP driver mutations are common among the elderly in Korea and are detected in various genes, including DNMT3A and TET2. Our study highlights that chronic dysregulation of innate immune signaling is associated with the pathogenesis of various diseases, including hematologic malignancies.

Dikkopf-1 promotes matrix mineralization of osteoblasts by regulating Ca+-CAMK2A- CREB1 pathway.

Dickkopf-1 (DKK1) is a secreted protein that acts as an antagonist of the canonical WNT/ß-catenin pathway, which regulates osteoblast differentiation. However, the role of DKK1 on osteoblast differentiation has not yet been fully clarified. Here, we investigate the functional role of DKK1 on osteoblast differentiation. Primary osteoprogenitor cells were isolated from human spinal bone tissues. To examine the role of DKK1 in osteoblast differentiation, we manipulated the expression of DKK1, and the cells were differentiated into mature osteoblasts. DKK1 overexpression in osteoprogenitor cells promoted matrix mineralization of osteoblast differentiation but did not promote matrix maturation. DKK1 increased Ca+ influx and activation of the Ca+/calmodulin-dependent protein kinase II Alpha (CAMK2A)-cAMP response element-binding protein 1 (CREB1) and increased translocation of p-CREB1 into the nucleus. In contrast, stable DKK1 knockdown in human osteosarcoma cell line SaOS2 exhibited reduced nuclear translocation of p-CREB1 and matrix mineralization. Overall, we suggest that manipulating DKK1 regulates the matrix mineralization of osteoblasts by Ca+-CAMK2A-CREB1, and DKK1 is a crucial gene for bone mineralization of osteoblasts. [BMB Reports 2022; 55(12): 627-632].

Gardnerella vaginalis in Recurrent Urinary Tract Infection Is Associated with Dysbiosis of the Bladder Microbiome.

Recent studies on the urine microbiome have highlighted the importance of the gut-vagina-bladder axis in recurrent urinary tract infection (rUTI). In particular, the role of Gardnerella as a covert pathogen that activates E. coli in animal experiments has been reported. Herein, we conducted a human bladder microbiome study to investigate the effect of Gardnerella on rUTI. Urine 16S ribosomal RNA gene sequencing via transurethral catheterization was conducted in the normal control group (NC) (n = 18) and rUTI group (n = 78). The positive detection rate of Gardnerella species did not differ between the NC and rUTI groups (22.2% vs. 18.0%, p = 0.677). In addition, the Gardnerella-positive NC and Gardnerella-positive rUTI groups showed similar levels of microbiome diversity. The Gardnerella-positive group was categorized into three subgroups: the Escherichia-dominant group, Gardnerella-dominant group, and Lactobacillus-dominant group. All of the Escherichia-dominant groups were associated with rUTI. The Gardnerella-dominant or Lactobacillus-dominant groups expressed rUTI with symptoms when risk factors such as the degree of Gardnerella proliferation or causative agents of bacterial vaginosis were present. The presence of Gardnerella in the urine is considered to be related to rUTI depending on other risk factors. New guideline recommendations regarding antibiotic selection based on a novel method to detect the cause of rUTI may be required to reduce antibiotic resistance.

Recent insights regarding the molecular basis of myeloproliferative neoplasms.

Myeloproliferative neoplasms (MPNs) are a heterogeneous group of clonal disorders characterized by the overproduction of mature blood cells that have an increased risk of thrombosis and progression to acute myeloid leukemia. Next-generation sequencing studies have provided key insights regarding the molecular mechanisms of MPNs. MPN driver mutations in genes associated with the JAK-STAT pathway include JAK2 V617F, JAK2 exon 12 mutations and mutations in MPL, CALR, and CSF3R. Cooperating driver genes are also frequently detected and also mutated in other myeloid neoplasms; these driver genes are involved in epigenetic methylation, messenger RNA splicing, transcription regulation, and signal transduction. In addition, other genetic factors such as germline predisposition, order of mutation acquisition, and variant allele frequency also influence disease initiation and progression. This review summarizes the current understanding of the genetic basis of MPN, and demonstrates how molecular pathophysiology can improve both our understanding of MPN heterogeneity and clinical practice.

Clinical impact of CD5 expression in Korean patients with diffuse large B-cell lymphoma.

BACKGROUND: CD5-positive diffuse large B-cell lymphoma (CD5+ DLBCL) accounts for 5-10% of DLBCL cases and has poor patient outcomes. However, most studies on CD5+ DLBCL were performed in Japanese patients and only few data are available for Korean population. In this study, we investigated the clinical characteristics and prognostic impact of CD5 expression in Korean patients with bone marrow (BM) involvement of DLBCL. METHODS: Patients who were initially diagnosed with BM involvement of de novo DLBCL from 2005 to 2013 were included. Clinicopathological features and outcomes of patients were compared between CD5+ and CD5 negative (CD5-) DLBCL. RESULTS: Among a total of 57 patients, the number of patients with CD5+ and CD5- DLBCL were 13 and 44, respectively. Clinical and laboratory features of CD5+ DLBCL were not significantly different from those of CD5- DLBCL. The 3-year overall survival (OS) rates for CD5+ and CD5- DLBCL were 20.2% and 59.0%, respectively (P=0.031), and 3-year progression-free survival (PFS) rates for CD5+ and CD5- DLBCL were 23.1% and 50.1%, respectively (P=0.055). CONCLUSION: CD5+ DLBCL with BM involvement showed an inferior survival tendency compared to CD5- DLBCL, and thorough evaluation of CD5 expression might be helpful to predict the prognosis of patients with DLBCL.

Frequency and significance of rare RNF213 variants in patients with adult moyamoya disease.

PURPOSE: Moyamoya disease (MMD) is a rare cerebrovascular disorder characterized by stenosis of the internal carotid arteries with compensatory development of collateral vessels. Although a founder variant of RNF213, p.Arg4810Lys (c.14429G>A, rs112735431), is a major genetic risk factor for MMD in East Asians, the frequency and disease susceptibility of other variants in this gene remain largely unknown. In the present study, we investigated the association of RNF213 variants with MMD in Korean patients and population controls. METHODS: For all RNF213 variants listed in the Human Gene Mutation Database (HGMD) as disease-causing or likely disease-causing mutations for MMD, genotyping was performed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Genetic data from 264 adult patients with MMD were analyzed and compared with two control populations comprised of 622 and 1,100 Korean individuals, respectively. RESULTS: Among the 30 RNF213 variants that were listed in the HGMD, p.Arg4810Lys was identified in 67.4% (178/264) of patients with MMD and showed a significantly higher allele frequency than in the controls, giving an odds ratio of 63.29 (95% confidence interval, 33.11-120.98) for the 622 controls and 48.55 (95% confidence interval, 31.00-76.03) for the 1100 controls. One additional variant, p.Ala5021Val (c.15062C>T, rs138130613), was identified in 0.8% (2/264) of patients; however, the allele frequencies were not significantly different from those in the controls. CONCLUSIONS: These results suggest that, in our cohort of Korean patients, the p.Arg4810Lys is the only variant that is strongly associated with MMD among the 30 RNF213 variants listed in the HGMD.

Identification and characterization of NF1 splicing mutations in Korean patients with neurofibromatosis type 1.

Neurofibromatosis type I (NF1) is an autosomal dominant genetic disorder caused by NF1 mutations. Although mutations affecting mRNA splicing are the most common molecular defects in NF1, few studies have analyzed genomic DNA (gDNA)-mRNA correlations in Korean NF1 patients. In this study, we investigated 28 unrelated NF1 patients who showed splicing alterations in reverse transcription-PCR of NF1 mRNA and identified 24 different NF1 splicing mutations, 9 of which were novel. These mutations can be categorized into five groups: exon skipping resulting from mutations at authentic 5' and 3' splice sites (type I, 46%), cryptic exon inclusion caused by deep intronic mutations (type II, 8%), creation of new splice sites causing loss of exonic sequences (type III, 8%), activation of cryptic splice sites due to disruption of authentic splice sites (type IV, 25%) and exonic sequence alterations causing exon skipping (type V, 13%). In total, 42% of all splicing mutations did not involve the conserved AG/GT dinucleotides of the splice sites, making it difficult to identify the correct mutation sites at the gDNA level. These results add to the mutational spectrum of NF1 and further elucidate the gDNA-mRNA correlations of NF1 mutations.

Differences in Factors Associated with Albuminuria according to Gender and Comorbidities of Hypertension and Diabetes.

BACKGROUND: This study examined the differences in factors associated with albuminuria according to gender and comorbidities of hypertension (HTN) and diabetes mellitus (DM). METHODS: We included 3,859 participants aged 20 to 79 years (55% female) from the 5th Korea National Health and Nutrition Examination Survey. Participants were excluded if they took antihypertensive or anti-diabetic medication, had chronic renal failure, had malignant tumor, were pregnant or menstruating during the health examination, or had missing urine albumin data. Albuminuria was defined by the participant's urine albumin-creatinine ratio (uACR). Relationships between dependent and independent variables were analyzed using the Pearson's correlation test and simple linear regression. Due to possible muticollinearity, multiple linear regression analysis was used to determine whether the association between the dependent and independent variables of interest remained significant after adjustment for other potentially confounding independent variables. RESULTS: The variables significantly correlated with uACR were different between the genders and between subjects with HTN or DM as a comorbidity. In the multiple linear regression models, hemoglobin A1c (P=0.01) was positively associated with uACR in men without HTN and DM. In men with HTN or DM, systolic blood pressure and fasting glucose (P<0.01) were positively associated with uACR. In women with HTN or DM, waist circumference (P=0.011) and gamma-glutamyl transpeptidase (P<0.001) were positively correlated with uACR (P<0.05) and glucose level (P=0.019) was negatively correlated with uACR. CONCLUSION: The study suggested factors correlated with albuminuria were different for men and women according to comorbidities such as HTN and DM.

Frequency of the moyamoya-related RNF213 p.Arg4810Lys variant in 1,516 Korean individuals.

BACKGROUND: Moyamoya disease (MMD) is a progressive steno-occlusive vasculopathy that involves large intracranial arteries accompanied by abnormal collateral vessels. Recently, RNF213 was identified as a susceptibility gene for MMD and p.Arg4810Lys (rs112735431) is the most common variant in East Asian MMD patients. Interestingly, many studies have reported that a certain proportion of the general population in Japan, Korea, and China also has this variant. In this study, we investigated the frequency of this variant and estimated an odds ratio of MMD using two different Korean populations. METHODS: A total of 1,516 anonymous DNA samples, 799 from an umbilical cord blood bank and 717 from routine health-checked adults, were genotyped using targeted Sanger sequencing. RESULTS: The p.Arg4810Lys variant was detected at genotype frequencies of 2.25% (18/799; 95% confidence interval (CI), 1.43-3.53%) in cord blood samples and 2.65% (19/717; 95% CI, 1.70-4.10%) in adult samples, respectively. This variant showed a strong association with MMD (P < 0.001), giving an odds ratio of 162.7 (95% CI, 65.5-403.9) and 137.8 (95% CI, 55.8-339.9) based on the cord blood and adults samples, respectively. CONCLUSIONS: These results confirm that the RNF213 p.Arg4810Lys variant is not uncommon in the general Korean population and provide reference data for the association of this variant and MMD.

Time to First Cigarette and Hypertension in Korean Male Smokers.

BACKGROUND: Morning blood pressure surge affects to cardiovascular disease risk. Short time to first cigarette (TTFC) after waking can enhance morning blood pressure surge, and accelerate atherosclerosis. METHODS: We investigated that the relationship between TTFC and blood pressure. The study subjects included male current smokers (n=211) who had health check-up in Hallym University Sacred Heart Hospital from July to September, 2014. We categorized the subjects into 2 groups according to TTFC; early TTFC (TTFC <30 minutes) and late TTFC (TTFC ≥30 minutes), and the subjects who were taking antihypertensive medications or had a high blood pressure (>140 mm Hg or 90 mm Hg) were defined as hypertensive group. Multivariate logistic regression was performed to estimate the odds ratio and 95% confidence interval to investigate the association between TTFC and hypertensive group. RESULTS: Compared with late TTFC, early TTFC had higher odds (odds ratio [OR], 3.87; 95% confidence interval [CI], 1.89-7.94) for hypertensive group. After adjusting confounding factors, early TTFC was significantly associated with an increased risk of hypertension (OR, 4.43; 95% CI, 1.84-10.70). CONCLUSION: early TTFC after waking is associated with hypertension. It suggests delaying TTFC might help to control of blood pressure among the current smokers who are not ready to immediately quit smoking.

The t(11;14)(q13;q32) translocation as a poor prognostic parameter for autologous stem cell transplantation in myeloma patients with extramedullary plasmacytoma.

INTRODUCTION: Fluorescence in-situ hybridization (FISH)-detected abnormalities, including del(17p), del(13q), and t(4;14), have been associated with inferior prognosis. However, there are few data about the prognostic significance of cytogenetic abnormalities for autologous stem cell transplantation (ASCT) in multiple myeloma (MM) patients with extramedullary plasmacytoma (EMP). PATIENTS AND METHODS: Between April 2004 and December 2012, 290 MM patients underwent ASCT at 3 centers. FISH data for bone marrow samples obtained at diagnosis were available for 58 patients who had EMP at diagnosis or during treatment. RESULTS: The t(11;14), t(4;14), del(13q), and 1q gain abnormalities were seen in 14.9%, 6.3%, 25.6%, and 42.9%, respectively. No t(14;16) or del(17p) cytogenetic abnormality was detected in the examined patients. Patients with t(11;14) had a lower response rate compared to patients with other cytogenetic abnormalities. EMP-specific relapse was higher in patients with t(11;14) than in patients with other cytogenetic abnormalities (42.9% vs. 10%-33.3%). Each of the 4 cytogenetic abnormalities predicted shorter median progression-free survival (6-12 months vs. 27-37 months) and shorter overall survival (16-22 months vs. 68 months or not reached) compared to no cytogenetic abnormality. The t(11;14) translocation was an important prognostic factor for both progression-free survival (hazard ratio, 25.154; P < .001) and overall survival (hazard ratio, 7.484; P = .024) in the multivariate analysis. CONCLUSION: In the current study, t(11;14), t(4;14), del(13q), and 1q gain were associated with worse survival in MM patients with EMP. The role of t(11;14) as a prognostic parameter for ASCT in MM patients with EMP should be confirmed with a large, well-designed study.

Asp58Ala is the predominant mutation of the TTR gene in Korean patients with hereditary transthyretin-related amyloidosis.

Hereditary transthyretin (TTR)-related amyloidosis (ATTR) seems to be a rare autosomal-dominant inherited form of systemic amyloidosis. Studies indicate considerable heterogeneity in the disease's presentation and genotype; however, there is little data from Korea, where the prevalence of hereditary ATTR is very low. In this study, we investigated the phenotypic and genotypic spectra of hereditary ATTR in Korea. Direct sequencing analysis was performed to detect TTR gene mutations in amyloidosis patients whose results of TTR immunohistochemical staining were positive or equivocal. Clinical presentation was categorized as exclusively cardiac, exclusively neurologic, or mixed phenotype. Of 12 genetic tests performed, seven were positive for TTR mutations. D58A (c.173A>C) was the most common mutation in this study (57%, 4/7). The majority of those patients with hereditary ATTR had the mixed phenotype (86%, 6/7). The patients with D58A mutation had older ages of disease onset (median, 61 years vs. 42 years; P = 0.08), and a higher incidence of gastrointestinal involvement (75% vs. 0%; P = 0.03) than those with other identified TTR mutations. A significant male predominance was also noted in this study (P = 0.01).

Mutations in DDX58, which encodes RIG-I, cause atypical Singleton-Merten syndrome.

Singleton-Merten syndrome (SMS) is an autosomal-dominant multi-system disorder characterized by dental dysplasia, aortic calcification, skeletal abnormalities, glaucoma, psoriasis, and other conditions. Despite an apparent autosomal-dominant pattern of inheritance, the genetic background of SMS and information about its phenotypic heterogeneity remain unknown. Recently, we found a family affected by glaucoma, aortic calcification, and skeletal abnormalities. Unlike subjects with classic SMS, affected individuals showed normal dentition, suggesting atypical SMS. To identify genetic causes of the disease, we performed exome sequencing in this family and identified a variant (c.1118A>C [p.Glu373Ala]) of DDX58, whose protein product is also known as RIG-I. Further analysis of DDX58 in 100 individuals with congenital glaucoma identified another variant (c.803G>T [p.Cys268Phe]) in a family who harbored neither dental anomalies nor aortic calcification but who suffered from glaucoma and skeletal abnormalities. Cys268 and Glu373 residues of DDX58 belong to ATP-binding motifs I and II, respectively, and these residues are predicted to be located closer to the ADP and RNA molecules than other nonpathogenic missense variants by protein structure analysis. Functional assays revealed that DDX58 alterations confer constitutive activation and thus lead to increased interferon (IFN) activity and IFN-stimulated gene expression. In addition, when we transduced primary human trabecular meshwork cells with c.803G>T (p.Cys268Phe) and c.1118A>C (p.Glu373Ala) mutants, cytopathic effects and a significant decrease in cell number were observed. Taken together, our results demonstrate that DDX58 mutations cause atypical SMS manifesting with variable expression of glaucoma, aortic calcification, and skeletal abnormalities without dental anomalies.