Identification of novel candidate genes associated with non-syndromic tooth agenesis in Mongolian families

OBJECTIVES

This study aimed to identify genetic variants associated with non-syndromic tooth agenesis (TA) in nine families from Mongolia using whole-exome sequencing (WES) and bioinformatics analysis.

MATERIAL AND METHODS

The study enrolled 41 participants, including three inherited and six non-inherited families. WES analysis was performed on 14 saliva samples from individuals with non-syndromic TA. The potential candidate genes were identified through variant filtering and segregation analysis. The filtered variants were then analyzed in silico mutation impact analysis.

RESULTS

WES analysis identified 21 variants associated with TA, and 5 of these variants met all filtering criteria. These variants were located in the exome region of MAST4, ITGA6, PITX2, CACNA1S, and CDON genes. The variant in PITX2 was found in eight participants from inherited and non-inherited families, while the MAST4 variant was identified in 6 participants from inherited families.

CONCLUSIONS

The study identified various genetic variant candidates associated with TA in different family groups, with PITX2 being the most commonly identified. Our findings suggest that MAST4 may also be a novel candidate gene for TA due to its association with the Wnt signaling pathway. Additionally, we found that five candidate genes related to focal adhesion and calcium channel complex were significant and essential in tooth development.

CLINICAL RELEVANCE

Identifying new pathogenic genes associated with TA can improve our understanding of the molecular mechanisms underlying the disease, leading to better diagnosis, prevention, and treatment. Early detection of TA based on biomarkers can improve dental management and facilitate orthodontic and prosthetic treatment.

Identification of potential key variants in mandibular premolar hypodontia through whole-exome sequencing

Determining genotype-phenotype correlations in patients with hypodontia is important for understanding disease pathogenesis, although only a few studies have elucidated it. We aimed to identify genetic variants linked to non-syndromic bilateral mandibular second premolar hypodontia in a Korean population for the first time by specifying the phenotype of hypodontia. Twenty unrelated individuals with non-syndromic bilateral mandibular second premolar hypodontia were enrolled for whole-exome sequencing. Using a tooth agenesis gene set panel consisting of 112 genes based on literature, potential candidate variants were screened through variant filtering and prioritization. We identified 13 candidate variants in 12 genes, including a stop-gain variant (c.4750C>T) in LAMA3. Through the functional enrichment analysis of the prioritized genes, several terms related to tooth development were enriched in a protein-protein interaction network of candidate genes for mandibular premolar hypodontia. The hypodontia group also had approximately 2-fold as many mutated variants in all four genes related to these key terms, which are CDH1, ITGB4, LAMA3, LAMB3, as those in the 100 healthy control group individuals. The relationship between enriched terms and pathways and mandibular premolar hypodontia was also investigated. In addition, we identified some known oligodontia variants in patients with hypodontia, strengthening the possibility of synergistic effects in other genes. This genetic investigation may be a worthwhile preliminary attempt to reveal the pathogenesis of tooth agenesis and sets a background for future studies.

Development of bioinformatics and multi-omics analyses in organoids

Pre-clinical models are critical in gaining mechanistic and biological insights into disease progression. Recently, patient-derived organoid models have been developed to facilitate our understanding of disease development and to improve the discovery of therapeutic options by faithfully recapitulating in vivo tissues or organs. As technological developments of organoid models are rapidly growing, computational methods are gaining attention in organoid researchers to improve the ability to systematically analyze experimental results. In this review, we summarize the recent advances in organoid models to recapitulate human diseases and computational advancements to analyze experimental results from organoids. [BMB Reports 2023; 56(1): 43-48].

Impact of mental disease on the risk of atrial fibrillation in patients with diabetes mellitus: a nationwide population-based study

Background

Diabetes mellitus (DM) is known to increase the risk of mental disorders, which increases the health care burden in these patients. Also, DM is one of the risk factors leading to atrial fibrillation (AF), and the presence of concomitant AF and DM adds to the increased risks of stroke and death. It is uncertain whether mental disease is an independent risk factor of incident AF in patients with DM.

Purpose

To investigate whether diabetic patients with mental disease have an increased risk of AF.

Methods

Using the Korea National Health Insurance Service database, we enrolled 2,512,690 patients diagnosed with DM without AF between 2009 and 2021. Newly diagnosed AF was identified during the follow-up period. We compared the risk of AF between patients with mental disease and those without.

Results

Among the total population, 828,929 (32.99%; mean age 61.58±11.28; 56.71% female) patients were diagnosed with mental diseases (Figure 1). Anxiety (564,786 patients, 68.13%) was the most common mental disease, while depression was the second most common (313,773 patients, 37.85%). Diabetic patients with mental diseases had a higher percentage of women, hypertension, dyslipidemia, chronic kidney failure, congestive heart failure, obstructive sleep apnea, and thyroid disease. During a median 7.0 years (IQR 5.93–8.07) follow-up, 34,523 were diagnosed new-onset AF (4.66 per 1,000 person-year). In multivariate analysis, diabetic patients with mental disorders showed a higher risk of new-onset AF (HR 1.19; 95% CI 1.17–1.21; p-value <0.0001) (Figure 2). Among mental diseases, depression, insomnia, and anxiety were associated with increased risks of new-onset AF (HR 1.15; 95% CI 1.12–1.17; HR 1.15; 95% CI 1.13–1.18; and HR 1.19; 95% CI, 1.67–1.21; all p-value <0.0001, respectively), whereas bipolar disorder and schizophrenia showed non-statistically significant trends (due to small numbers). Subgroup analyses showed that younger age had significant interactions with depression, insomnia, and anxiety.

Conclusion

Mental diseases, especially depression, insomnia, and anxiety, showed an increased risk of AF in patients with DM. Awareness and prompt diagnosis and management of AF would be necessary for these high-risk populations at risk of incident AF.

Funding Acknowledgement

Type of funding sources: None.

Enzyme activity engineering based on sequence co-evolution analysis

The utility of engineering enzyme activity is expanding with the development of biotechnology. Conventional methods have limited applicability as they require high-throughput screening or three-dimensional structures to direct target residues of activity control. An alternative method uses sequence evolution of natural selection. A repertoire of mutations was selected for fine-tuning enzyme activities to adapt to varying environments during the evolution. Here, we devised a strategy called sequence co-evolutionary analysis to control the efficiency of enzyme reactions (SCANEER), which scans the evolution of protein sequences and direct mutation strategy to improve enzyme activity. We hypothesized that amino acid pairs for various enzyme activity were encoded in the evolutionary history of protein sequences, whereas loss-of-function mutations were avoided since those are depleted during the evolution. SCANEER successfully predicted the enzyme activities of beta-lactamase and aminoglycoside 3'-phosphotransferase. SCANEER was further experimentally validated to control the activities of three different enzymes of great interest in chemical production: cis-aconitate decarboxylase, α-ketoglutaric semialdehyde dehydrogenase, and inositol oxygenase. Activity-enhancing mutations that improve substrate-binding affinity or turnover rate were found at sites distal from known active sites or ligand-binding pockets. We provide SCANEER to control desired enzyme activity through a user-friendly webserver.

P10.01 Anti-migration and anti-invasion effects of curcumin via suppression of fascin expression in glioblastoma cells

BACKGROUND

The natural compound Curcumin was known to inhibit migration and invasion of glioblastoma (GBM) cells. Fascin, a kind of actin-binding proteins, is correlated with migration and invasion of GBM cells. The purpose of this study was to investigate anti-migration and anti-invasion effects of Curcumin via suppression of fascin expression in GBM cells.

MATERIAL AND METHODS

U87 cell line was used as an experimental model of GBM. Fascin was quantified by Western blot analysis. And, the signal transducer and activator of transcription 3 (STAT3), known to play an important role in migration and invasion of tumor cells, were analyzed by sandwich-ELISA. Migration and invasion capacities were assessed by attachment, migration and invasion assays. Cellular morphology was demonstrated by immunofluorescence.

RESULTS

At various concentrations of curcumin and exposure times, fascin expression decreased. After temporarily exposure to 10μM/L Curcumin during 6 hours as less invasive concentration and time, fascin expression temporarily decreased at 12 hours (18.4%, p=0.024), and since then recovered. And, the change of phosphrylated STAT3 level also reflected the temporarily decreased pattern of fascin expression at 12 hours (19.7%, p=0.010). Attachment, migration, and invasion capacities consistently decreased at 6, 12, and 24 hours. And, immunofluorescence showed the change of shape and the reduction of filopodia formation in cells.

CONCLUSION

Curcumin is likely to suppress the fascin expression in GBM cells, and this might be a possible mechanism for anti-migration and anti-invasion effects of Curcumin via inhibition of STAT3 phosphorylation.

Entecavir and tenofovir reduce hepatitis B virus-related hepatocellular carcinoma recurrence more effectively than other antivirals

Nucleos(t)ide analogues (NAs) have been shown to decrease the risk of hepatocellular carcinoma (HCC) recurrence. This study evaluated whether high-potency NAs (entecavir and tenofovir disoproxil fumarate [TDF]) reduce the risk of tumour recurrence more potently than low-potency NAs after curative treatment of hepatitis B virus (HBV)-related HCC. This study included 607 consecutive HBV-related HCC patients treated with surgical resection or radiofrequency ablation. The patients were categorized into three groups according to antiviral treatment: group A (no antiviral; n = 261), group B (low-potency NA; n = 90) and group C (high-potency NA; n = 256). The primary end-point was recurrence-free survival (RFS). During the duration of follow-up, the median RFS was 29.4, 25.1, and 88.2 months in groups A, B and C, respectively (P < .001, log-rank test). The multivariate Cox analysis indicated that group C had a significantly longer RFS than both group A (adjusted hazard ratio [HR] = 0.39, P < .001) and group B (adjusted HR = 0.47, P < .001). When baseline characteristics were balanced using inverse probability weighting, group C still had a significantly longer RFS than group A (adjusted HR = 0.46, P < .001) and group B (adjusted HR = 0.59, P = .007). Group C had significantly lower risk of viral breakthrough than group B (HR = 0.19, P < .001). Viral breakthrough was an independent risk factor for shorter RFS among groups B and C (adjusted HR = 2.03, P = .007, time-dependent Cox analysis). Antiviral agents with high genetic barrier to resistance (entecavir and TDF) reduced the risk of HCC recurrence compared with other antivirals and no antiviral treatment, especially in patients with high baseline viral load.

An Accelerator Mass Spectrometry-Enabled Microtracer Study to Evaluate the First-Pass Effect on the Absorption of YH4808

¹⁴ C-labeled YH4808, a novel potassium-competitive acid blocker, was intravenously administered as a microtracer at 80 μg (11.8 kBq or 320 nCi) concomitantly with the nonradiolabeled oral drug at 200 mg to determine the absolute bioavailability and to assess the effect of pharmacogenomics on the oral absorption of YH4808. The absolute bioavailability was low and highly variable (mean, 10.1%; range, 2.3-19.3%), and M3 and M8, active metabolites of YH4808, were formed 22.6- and 38.5-fold higher after oral administration than intravenous administration, respectively. The product of the fraction of an oral YH4808 dose entering the gut wall and the fraction of YH4808 passing on to the portal circulation was larger in subjects carrying the variants of the CHST3, SLC15A1, and SULT1B1 genes. A combined LC+AMS is a useful tool to construct a rich and highly informative pharmacokinetic knowledge core in early clinical drug development at a reasonable cost.

Clinical significance of subclinical varicocelectomy in male infertility: systematic review and meta-analysis

Recent meta-analysis by the Cochrane collaboration concluded that treatment of varicocele may improve an infertile couple's chance of pregnancy. However, there has been no consensus on the management of subclinical varicocele. Therefore, we determine the impact of varicocele treatment on semen parameters and pregnancy rate in men with subclinical varicocele. The randomised controlled trials that assessed the presence and/or treatment of subclinical varicocele were included for systematic review and meta-analysis. Random effect model was used to calculate the weighted mean difference of semen parameters and odds ratio of pregnancy rates. Seven trials with 548 participants, 276 in subclinical varicocelectomy and 272 in no-treatment or clomiphene citrate subjects, were included. Although there was also no statistically significant difference in pregnancy rate (OR 1.29, 95% CI 0.99-1.67), surgical treatment resulted in statistically significant improvements on forward progressive sperm motility (MD 3.94, 95% CI 1.24-6.65). However, the evidence is not enough to allow final conclusions because the quality of included studies is very low and further research is needed.

RandomizEd phase II trial of Sunitinib four weeks on and two weeks off versus Two weeks on and One week off in metastatic clear-cell type REnal cell carcinoma: RESTORE trial

BACKGROUND

The standard sunitinib schedule, 4 weeks on, followed by 2 weeks off (4/2 schedule), is associated with troublesome toxicities, and maintenance of adequate sunitinib dosing and drug levels, which are essential for achieving an optimal treatment outcome, is challenging. The objective of this study was to investigate the efficacy and safety of an alternative sunitinib dosing schedule of 2 weeks on and 1 week off (2/1 schedule) compared with the standard sunitinib schedule of 4 weeks on and 2 weeks off (4/2 schedule).

PATIENTS AND METHODS

In this multicenter, randomized, open-label, phase II trial, treatment-naïve patients with clear-cell type metastatic renal cell carcinoma (mRCC) were randomly assigned to 4/2 or 2/1 schedules after stratification by Memorial Sloan Kettering Cancer Center risk group and the presence or absence of measurable lesions. The primary end point was the 6-month failure-free survival (FFS) rate, determined by intention-to-treat analysis.

RESULTS

From November 2007 to February 2014, 76 patients were accrued, and 74 were eligible. FFS rates at 6 months were 44% with the 4/2 schedule (N = 36) and 63% with the 2/1 schedule (N = 38). Neutropenia (all grades, 61% versus 37%; grade 3-4, 28% versus 11%) and fatigue (all grades, 83% versus 58%) were more frequently observed with schedule 4/2. There was a strong tendency toward a lower incidence of stomatitis, hand-foot syndrome, and rash with schedule 2/1. Objective response rates (ORRs) were 47% in schedule 2/1 and 36% in schedule 4/2. With a median follow-up of 30.0 months, the median time to progression (TTP) was 12.1 months in schedule 2/1 and 10.1 months in schedule 4/2.

CONCLUSION

Sunitinib administered with a 2/1 schedule is associated with less toxicity and higher FFS at 6 months than a 4/2 schedule, without compromising the efficacy in terms of ORR and TTP (NCT00570882).

Histogram analysis of apparent diffusion coefficient at 3.0t: Correlation with prognostic factors and subtypes of invasive ductal carcinoma

PURPOSE

To evaluate apparent diffusion coefficient (ADC) histogram parameters that show correlations with prognostic factors and subtypes of breast cancer.

MATERIALS AND METHODS

At 3.0T, various ADC histogram parameters were calculated including the entire tumor volume in 173 invasive ductal carcinomas: the minimum, 10th percentile, mean, median, 90th percentile, and maximum. ADC parameters were correlated with prognostic factors and subtype.

RESULTS

The mean ADCmedian value was significantly higher in the group with lymph node metastasis, HER2 positivity, and a Ki-67 value <14% than in the group with negativity for lymph node metastasis, HER2 negativity, and a Ki-67 value ≥14% (0.907, 0.978, and 0.941 vs. 0.735, 0.778, and 0.761 × 10(-3) mm(2) /s, respectively) (P < 0.01). There was no significant correlation between ADCmedian and tumor size, histologic grade, estrogen receptor expression, and progesterone receptor expression (P = 0.272, 0.113, 0.261, and 0.181, respectively). For most ADC parameters except for ADCmin , the mean of variable ADC parameters of HER2-positive, luminal A, luminal B-HER2(+), triple-negative, and luminal B-HER2(-) diseases were arranged in descending order (1.175, 0.936, 0.863, 0.811, and 0.665 × 10(-3) mm(2) /s in ADCmedian , respectively) with statistical significant difference (P < 0.001). In multivariate analysis, histologic grade, the Ki-67 index, and HER2 expression were statistically significant explanatory prognostic factors for ADCmedian and the Ki-67 index had the most robust effects on ADC parameters (standardized coefficient = -0.317).

CONCLUSION

Various ADC parameters were correlated with prognostic factors and subtype, except for ADCmin . HER2 positivity showed high ADC values and high Ki-67 index revealed low ADC values.

Phase II study of pemetrexed in combination with cisplatin in patients with advanced urothelial cancer: the PECULIAR study (KCSG 10-17)

Background:

Pemetrexed has shown a favourable response rate of about 30% with minimal toxicity when used as a single agent for treatment of advanced urothelial carcinoma. This phase II study evaluated the efficacy and safety of pemetrexed plus cisplatin in advanced urothelial carcinoma.

Methods:

This multicentre, single-arm, open-label, phase II clinical trial enrolled patients who had advanced urothelial carcinoma, ECOG PS 0–2, and measurable disease. Pemetrexed 500 mg m⁻² with cisplatin 70 mg m⁻² on day 1 were administered every 3 weeks. The primary endpoint was the objective response rate (ORR). Secondary endpoints were progression-free survival (PFS), overall survival (OS), and toxicity.

Results:

A total of 42 patients were enrolled (median age, 66 years; ECOG 0–1, 100% visceral metastasis, 54.8% recurrent disease, 57.1%). Twenty-seven partial responses for an ORR of 64.3% (95% CI, 49.2%–77.0%) were documented. Seven patients had stable disease. Median PFS and OS were 6.9 (95% CI, 6.2–7.6) and 14.4 (95% CI, 10.4–18.4) months, respectively. Grade 3 or 4 neutropenia was observed in 28.6% of patients. No patients experienced febrile neutropenia.

Conclusion:

The combination of pemetrexed and cisplatin is active, and well tolerated in patients with advanced urothelial cancer as a first-line treatment.

The incidence of Fever after subinguinal microsurgical varicocelectomy

PURPOSE

In the present study, we aimed to identify the incidence of fever in patients after subinguinal microsurgical varicocelectomy and to evaluate the clinical factors associated with the occurrence of the fever.

MATERIALS AND METHODS

We retrospectively reviewed the cases of patients who underwent subinguinal microsurgical varicocelectomy (group A) under spinal anesthesia. In addition, we reviewed the cases of patients who underwent microsurgical vasovasostomy under spinal anesthesia as a control group (group B). The incidence of fever in each group was compared. We investigated the clinical factors influencing the occurrence of fever in the patients of group A.

RESULTS

The incidence of fever in group A was significantly higher than that in group B (32.5% [53/163] vs. 0.4% [1/284]; p<0.001). Clinical factors such as age, varicocele grade, weight, height, operation time, number of ligated veins, usage of immediate postoperative analgesics, presence of postoperative hematoma, and duration of hospital stay were not significantly associated with the occurrence of fever.

CONCLUSIONS

We found that one-third of the patients developed transient fever after subinguinal microsurgical varicocelectomy, and therefore, this information should be provided during preoperative counseling.

Reasons for delayed orchiopexies in a korean tertiary care hospital

PURPOSE

Since the 1990s, it has been well known that orchiopexies should be performed by no later than 2 years of age. Nevertheless, studies from other countries report a substantial number of delayed orchiopexies. On the basis of an analysis of a tertiary care hospital database, we aimed to investigate the incidence of delayed orchiopexies performed in patients after 5 years of age and to understand the causes of such delays and the possible consequences.

MATERIALS AND METHODS

We retrospectively analyzed the surgical database of Seoul National University Hospital between 2004 and 2012 and detected patients who underwent orchiopexy later than 5 years of age. Reasons for delayed orchiopexies were studied and the possible consequences of delayed orchiopexies were assessed with respect to surgical difficulty and testicular volume.

RESULTS

We found 160 cases of delayed orchiopexies, which accounted for about 15% of all orchiopexies performed. Two major reasons for delay were related to the parents of the child: parental delay and parental request for the treatment of persistent retractile testis. Acquired cryptorchidism was found in 21 cases (13.1%), mainly associated with hypospadias. Surgical difficulty, especially owing to a short testicular cord, was encountered in 48 cases (30.2%), and a comparison with age-matched normative values showed substantially smaller testicular volume.

CONCLUSIONS

Despite well-established guidelines for the optimal age of surgery, 15% of orchiopexies were not performed at a proper time. Improved propagation of an optimal age limit is necessary to reduce the rate of delayed orchiopexies considering increases in surgical difficulty and potential testicular growth retardation.

Successful Removal of an Intravesical Electrical Wire Cable

A few previous reports have described cases wherein electrical wire cables were inserted into the male urethra and bladder. Electrical wire cables are available at home and are easy to insert. However, after they coil in the patient's bladder, they are difficult to remove. In February 2013, a 30-year-old man presented to the emergency room of SMG-SNU Boramae Medical Center with a urethral foreign body. He had inserted an electrical wire cable into his urethra for the purpose of masturbation, despite having a regular sex partner and no underlying disease. A kidney-ureter-bladder radiography showed a tangled wire in his bladder and urethra. On the next day, we tried to remove the wire cystoscopically, but this proved to be impossible because of complex coiling and the slippery surface of the wire. A Pfannenstiel incision was made to remove the foreign body. No postoperative complications were noted.