The Origin and Composition of Korean Ethnicity Analyzed by Ancient and Present-Day Genome Sequences

Elucidating immunological characteristics of the adenoma-carcinoma sequence in colorectal cancer patients in South Korea using a bioinformatics approach

Colorectal cancer (CRC) is one of the top five most common and life-threatening malignancies worldwide. Most CRC develops from advanced colorectal adenoma (ACA), a precancerous stage, through the adenoma-carcinoma sequence. However, its underlying mechanisms, including how the tumor microenvironment changes, remain elusive. Therefore, we conducted an integrative analysis comparing RNA-seq data collected from 40 ACA patients who visited Dongguk University Ilsan Hospital with normal adjacent colons and tumor samples from 18 CRC patients collected from a public database. Differential expression analysis identified 21 and 79 sequentially up- or down-regulated genes across the continuum, respectively. The functional centrality of the continuum genes was assessed through network analysis, identifying 11 up- and 13 down-regulated hub-genes. Subsequently, we validated the prognostic effects of hub-genes using the Kaplan-Meier survival analysis. To estimate the immunological transition of the adenoma-carcinoma sequence, single-cell deconvolution and immune repertoire analyses were conducted. Significant composition changes for innate immunity cells and decreased plasma B-cells with immunoglobulin diversity were observed, along with distinctive immunoglobulin recombination patterns. Taken together, we believe our findings suggest underlying transcriptional and immunological changes during the adenoma-carcinoma sequence, contributing to the further development of pre-diagnostic markers for CRC.

Comparative Analysis of Allogeneic Bone Marrow Transplantation Outcomes Between Japanese and Non-Japanese Populations

BACKGROUND

As the Japanese population may have less genetic diversity than other ethnic groups, treatment outcomes may be affected when allogeneic hematopoietic cell transplantation is performed in other races. However, evidence explaining the effect of racial differences is limited.

METHODS

We used the Japanese National Database to examine the outcomes of first allogeneic bone marrow transplantations (BMTs) performed between Japanese and non-Japanese patients from 1996 to 2021. We performed propensity score matching using sex, age group, underlying disease group, HLA mismatch, conditioning regimen intensity, and BMT implementation age to select Japanese-to-Japanese BMT patients as the controls.

RESULTS

The numbers of non-Japanese-to-Japanese and Japanese-to-non-Japanese BMT cases included in the analysis were 48 and 75, respectively, and the following outcomes were compared: overall survival, non-relapse mortality, acute graft-vs-host disease (GVHD) ≥ grade II, chronic GVHD, and engraftment of neutrophils and platelets. Most parameters did not differ when comparing BMTs according to ethnicity; only platelet engraftment was delayed in Japanese-to-non-Japanese BMT but not in non-Japanese-to-Japanese BMT.

CONCLUSIONS

The results of this study suggested that BMT performed in Japanese and non-Japanese patients has little effect on treatment outcomes. The results of this study may be useful for donor selection in Japan, where internationalization has progressed in recent years.

Origin and population structure of native dog breeds in the Korean peninsula and East Asia

To study the ancestry and phylogenetic relationships of native Korean dog breeds to other Asian dog populations, we analyzed nucleotide variations in whole-genome sequences of 205 canid individuals. Sapsaree, Northern Chinese indigenous dog, and Tibetan Mastiff were largely related to West Eurasian ancestry. Jindo, Donggyeongi, Shiba, Southern Chinese indigenous (SCHI), Vietnamese indigenous dogs (VIET), and Indonesian indigenous dogs were related to Southeast and East Asian ancestry. Among East Asian dog breeds, Sapsaree presented the highest haplotype sharing with German Shepherds, indicating ancient admixture of European ancestry to modern East Asian dog breeds. SCHI showed greater haplotype sharing with New Guinea singing dogs, VIET, and Jindo than with other Asian breeds. The predicted divergence time of East Asian populations from their common ancestor was approximately 2,000 to 11,000 years ago. Our results expand understanding of the genetic history of dogs in the Korean peninsula to the Asian continent and Oceanic region.

Modern Japanese ancestry-derived variants reveal the formation process of the current Japanese regional gradations

Modern Japanese people have two major ancestral populations: indigenous Jomon hunter-gatherers and continental East Asian farmers. To determine the formation process of the current Japanese population, we developed a detection method for variants derived from ancestral populations using a summary statistic, the ancestry marker index (AMI). We applied AMI to modern Japanese population samples and identified 208,648 single nucleotide polymorphisms (SNPs) that were likely derived from the Jomon people (Jomon-derived variants). Analysis of Jomon-derived variants in 10,842 modern Japanese individuals recruited from all over Japan revealed that the admixture proportions of the Jomon people varied between prefectures, probably owing to the prehistoric population size difference. The estimated allele frequencies of genome-wide SNPs in the ancestral populations of the modern Japanese suggested their adaptive phenotypic characteristics to their respective livelihoods. Based on our findings, we propose a formation model for the genotypic and phenotypic gradations of the current Japanese archipelago populations.

Biogeographic origin and genetic characteristics of the peopling of Jeju Island based on lineage markers

BACKGROUND

Jeju Island is the largest island of South Korea, located southwest far from the mainland of Korea, and has a unique history and its own cultures that are distinguished from those of the other regions of the Korean mainland. However, the Jeju population has not been deeply investigated to date to understand their genetic structure, which may reflect their historical and geographical background.

OBJECTIVE

To identify the genetic characteristics and biogeographic origin of people of Jeju Island based on the statistical analysis of genetic data using lineage markers.

METHODS

17 Y-STRs data for 615 unrelated males and mitochondrial DNA haplogroup data for 799 unrelated individuals residing on Jeju Island were generated, and analyzed to investigate genetic diversity and genetic characteristics using statistical methods including pairwise Fst or Rst, Analysis of molecular variance (AMOVA) and Multidimensional scaling (MDS).

RESULTS

For male individuals of Jeju Island, unique genetic characteristics were observed in the analysis of Y-STRs, including low haplotype diversity, strong association with surnames, genetic difference from other regions of Korea, and common genetic variation of the Y-STR loci known to be predominant in Northern populations, such as Mongolians. Statistical analysis of the mitochondrial DNA haplogroups also revealed similar results that showed low haplogroup diversity and high frequency of haplogroup Y prevalent mostly in ethnic populations around the Sea of Okhotsk in Northeastern Asia. All these results suggest that Jeju Island is genetically distinct from other regions of Korea, possibly being a subpopulation in Korea, and related closely to Northern Asian populations.

CONCLUSION

The findings in the genetic approach could support understanding of the historical background of Jeju Island that is consistent with evidence from other multidisciplinary studies.

The genetic structure and admixture of Manchus and Koreans in northeast China

BACKGROUND

The fine-scale genetic profiles and population history of Manchus and Koreans remain unclear.

AIM

To infer a fine-scale genetic structure and admixture of Manchu and Korean populations.

SUBJECTS AND METHODS

We collected and genotyped 16 Manchus from Liaoning and 18 Koreans from Jilin province with about 700K genome-wide SNPs. We analysed the data using principal component analysis (PCA), ADMIXTURE, Fst, TreeMix, f-statistics, qpWave, and qpAdm.

RESULTS

Manchus and Koreans showed a genetic affinity with northern East Asians. Chinese Koreans showed a long-term genetic continuity with Bronze Age populations from the West Liao River and had a strong affinity with Koreans in South Korea and Japan. Manchus had a different genetic profile compared with other Tungusic populations since the Manchus received additional genetic influence from the southern Chinese but didn't have West Eurasian-related admixture.

CONCLUSIONS

The genetic formation of Manchus involving southern Chinese was consistent with the extensive interactions between Manchus and populations from central and southern China. The large-scale genetic continuity between ancient West Liao River farmers and Koreans highlighted the role farming expansion played in the peopling of the Korean Peninsula.

PharmaKoVariome database for supporting genetic testing

Pharmacogenomics (PGx) provides information about routine precision medicine, based on the patient's genotype. However, many of the available information about human allele frequencies, and about clinical drug-gene interactions, is based on American and European populations. PharmaKoVariome database was constructed to support genetic testing for safe prescription and drug development. It consolidated and stored 2507 diseases, 11 459 drugs and 61 627 drug-target or druggable genes from public databases. PharmaKoVariome precomputed ethnic-specific abundant variants for approximately 120 M single-nucleotide variants of drug-target or druggable genes. A user can search by gene symbol, drug name, disease and reference SNP ID number (rsID) to statistically analyse the frequency of ethnical variations, such as odds ratio and P-values for related genes. In an example study, we observed five Korean-enriched variants in the CYP2B6 and CYP2D6 genes, one of which (rs1065852) is known to be incapable of metabolizing drug. It is also shown that 4-6% of North and East Asians have risk factors for drugs metabolized by the CYP2D6 gene. Therefore, PharmaKoVariome is a useful database for pharmaceutical or diagnostic companies for developing diagnostic technologies that can be applied in the Asian PGx industry. Database URL: http://www.pharmakovariome.com/.

Pathogenic variants of the mitochondrial aspartate/glutamate carrier causing citrin deficiency

Citrin deficiency is a pan-ethnic and highly prevalent mitochondrial disease with three different stages: neonatal intrahepatic cholestasis (NICCD), a relatively mild adaptation stage, and type II citrullinemia in adulthood (CTLN2). The cause is the absence or dysfunction of the calcium-regulated mitochondrial aspartate/glutamate carrier 2 (AGC2/SLC25A13), also called citrin, which imports glutamate into the mitochondrial matrix and exports aspartate to the cytosol. In citrin deficiency, these missing transport steps lead to impairment of the malate-aspartate shuttle, gluconeogenesis, amino acid homeostasis, and the urea cycle. In this review, we describe the geological spread and occurrence of citrin deficiency, the metabolic consequences and use our current knowledge of the structure to predict the impact of the known pathogenic mutations on the calcium-regulatory and transport mechanism of citrin.

Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae, Korea

The genetic history of prehistoric and protohistoric Korean populations is not well understood because only a small number of ancient genomes are available. Here, we report the first paleogenomic data from the Korean Three Kingdoms period, a crucial point in the cultural and historic formation of Korea. These data comprise eight shotgun-sequenced genomes from ancient Korea (0.7×-6.1× coverage). They were derived from two archeological sites in Gimhae: the Yuha-ri shell mound and the Daesung-dong tumuli, the latter being the most important funerary complex of the Gaya confederacy. All individuals are from between the 4th and 5th century CE and are best modeled as an admixture between a northern China Bronze Age genetic source and a source of Jomon-related ancestry that shares similarities with the present-day genomes from Japan. The observed substructure and proportion of Jomon-related ancestry suggest the presence of two genetic groups within the population and diversity among the Gaya population. We could not correlate the genomic differences between these two groups with either social status or sex. All the ancient individuals' genomic profiles, including phenotypically relevant SNPs associated with hair and eye color, facial morphology, and myopia, imply strong genetic and phenotypic continuity with modern Koreans for the last 1,700 years.

Real-World Long-Term Clinical Outcomes of Ultrathin Strut Biodegradable Polymer Drug-Eluting Stents in Korean ST-Segment-Elevation Myocardial Infarction (STEMI) Patients with or without Acute Heart Failure Undergoing Primary Percutaneous Coronary Intervention

Biodegradable polymers (BDPs) and ultrathin struts were recently introduced to drug-eluting stents (DES) to further improve outcomes. In this study, we analyzed and compared the effect of the ultrathin strut BDP-DES (UBDP-DES) with the conventional durable polymer-DES (DP-DES) in patients with ST-segment elevation myocardial infarction (STEMI) who underwent primary percutaneous coronary intervention (PPCI). A total of 356 STEMI patients (n = 160 in the UBDP-DES group and n = 196 in the DP-DES group) were enrolled. The primary endpoint was target lesion failure (TLF), including cardiac death, target vessel myocardial infarction, and ischemic-driven, target lesion revascularization (ID-TLR). The mean age was 60.3 ± 12.7 years (male 81.7%), and the median follow-up duration was 63.8 months. TLF was numerically more frequent in the UBDP-DES group (8.1% vs. 4.1%; HR 2.14; 95% CI 0.89-5.18; p = 0.091). Propensity score matching (PSM) was performed to balance discrepancies in the baseline characteristics due to patients in the UBDP-DES group initially having more unstable vital signs. However, after PSM (n = 116 in each group), there was no significant difference in TLF (5.3% vs. 5.3%; HR 1.04, 95% CI 0.34-3.22; p = 0.947) or other secondary endpoints including ID-TLR. In the subgroup analysis, subjects with initial acute heart failure (AHF), defined as Killip class ≥ 3, were associated with 13.6% chance of 30-day mortality (9-fold of those without AHF), although chances of repeat revascularization were low (3.0%). Among patients with AHF, the UBDP-DES group was associated with a numerically higher chance of TLF compared with the DP-DES group. There was no difference in TLF between groups in patients without AHF. This study showed that UBDP-DES has long-term clinical outcomes similar to those of conventional DP-DES in real-world Korean STEMI patients receiving PPCI, especially in those without initial AHF.

Comparison of the insertion patterns of the extensor hallucis longus muscle in Korean focusing on the regional difference

PURPOSE

From the evolutionary myology, the additional tendon of the extensor hallucis longus (EHL) muscle represents the sample of a new acquisition. We aimed to determine whether the insertion pattern of the EHL muscle differs in Koreans according to demographic populations, especially between Jeju islanders and the Korean Peninsula inhabitants.

METHODS

We used 69 Korean cadavers and classified the tendinous insertion of the EHL muscle as Pattern I, Pattern II, and Pattern III. The ratio of each Pattern in adult cadaveric samples was compared between demographic populations.

RESULTS

The proportion of Pattern I, Pattern II, and Pattern III of the EHL muscle was 30.43, 63.77, and 5.80%, respectively, further divided into 18.00 vs. 36.04%, 72.00 vs. 60.47%, 10.00 vs. 3.49% in Jeju islanders vs. peninsular Koreans. There was a considerable difference in the insertion patterns of the EHL muscle in each regional group (p = 0.032), but not in each gender, age, and body sides of lower limbs.

CONCLUSION

The findings of this study indicate that there was a higher incidence of the accessory tendon(s) of the EHL muscle in Koreans and the distributed insertion patterns of the EHL muscle was significantly different between Jeju islanders and peninsular Koreans.

Population genomics of East Asian ethnic groups

East Asia constitutes one-fifth of the global population and exhibits substantial genetic diversity. However, genetic investigations on populations in this region have been largely under-represented compared with European populations. Nonetheless, the last decade has seen considerable efforts and progress in genome-wide genotyping and whole-genome sequencing of the East-Asian ethnic groups. Here, we review the recent studies in terms of ancestral origin, population relationship, genetic differentiation, and admixture of major East- Asian groups, such as the Chinese, Korean, and Japanese populations. We mainly focus on insights from the whole-genome sequence data and also include the recent progress based on mitochondrial DNA (mtDNA) and Y chromosome data. We further discuss the evolutionary forces driving genetic diversity in East-Asian populations, and provide our perspectives for future directions on population genetics studies, particularly on underrepresented indigenous groups in East Asia.

Do Genes Associated with Dyslexia of Chinese Characters Evolve Neutrally?

Dyslexia, or reading disability, is found to have a genetic basis, and several related genes have been reported. We investigated whether natural selection has acted on single nucleotide polymorphisms (SNPs) that were reported to be associated with risk/non-risk for the reading disability of Chinese characters. We applied recently developed 2D SFS-based statistics to SNP data of East Asian populations to examine whether there is any sign of selective sweep. While neutrality was not rejected for most SNPs, significant signs of selection were detected for two linkage disequilibrium (LD) regions containing the reported SNPs of GNPTAB and DCDC2. Furthermore, we searched for a selection target site among the SNPs in these LD regions, because a causal site is not necessarily a reported SNP but could instead be a tightly linked site. In both LD regions, we found candidate target sites, which may have an effect on expression regulation and have been selected, although which genes these SNPs affect remains unknown. Because most people were not engaged in reading until recently, it is unlikely that there has been selective pressure on reading ability itself. Consistent with this, our results suggest a possibility of genetic hitchhiking, whereby alleles of the reported SNPs may have increased in frequency together with the selected target, which could have functions for other genes and traits apart from reading ability.