XPA is a central scaffold protein that coordinates the assembly of repair complexes in the global genome (GG-NER) and transcription-coupled nucleotide excision repair (TC-NER) subpathways. Inactivating mutations in XPA cause xeroderma pigmentosum (XP), which is characterized by extreme UV sensitivity and a highly elevated skin cancer risk. Here, we describe two Dutch siblings in their late forties carrying a homozygous H244R substitution in the C-terminus of XPA. They present with mild cutaneous manifestations of XP without skin cancer but suffer from marked neurological features, including cerebellar ataxia. We show that the mutant XPA protein has a severely weakened interaction with the transcription factor IIH (TFIIH) complex leading to an impaired association of the mutant XPA and the downstream endonuclease ERCC1-XPF with NER complexes. Despite these defects, the patient-derived fibroblasts and reconstituted knockout cells carrying the XPA-H244R substitution show intermediate UV sensitivity and considerable levels of residual GG-NER (~50%), in line with the intrinsic properties and activities of the purified protein. By contrast, XPA-H244R cells are exquisitely sensitive to transcription-blocking DNA damage, show no detectable recovery of transcription after UV irradiation, and display a severe deficiency in TC-NER-associated unscheduled DNA synthesis. Our characterization of a new case of XPA deficiency that interferes with TFIIH binding and primarily affects the transcription-coupled subpathway of nucleotide excision repair, provides an explanation of the dominant neurological features in these patients, and reveals a specific role for the C-terminus of XPA in TC-NER.

Country-of-origin violations have occurred in which some merchants have fraudulently sold cheap Japanese yellowtail (Seriola quinqueradiata) by presenting them as domestic Korean products. There are many methods for determining the origins of marine organisms, such as molecular genetic methods and isotope analysis. However, this study aimed to develop a method for determining the origins of aquatic products using metabolite analysis technology. Ten yellowtail each from Korea and Japan were analyzed by capillary electrophoresis–time of flight/mass spectrometry (CETOF/MS). Hierarchical cluster analysis (HCA) and principal component analysis (PCA) results showed highly differing aspects between the Korean and Japanese samples. In the tricarboxylic acid (TCA) cycle, citric, malic, oxaloglutaric, and fumaric acids exhibited significant differences between Korean and Japanese yellowtail. Sixteen of the twenty essential amino acids analyzed as metabolites also differed significantly. All amino acids were involved in protein digestion, absorption, and metabolism. All 16 amino acid contents were higher in Japanese yellowtail than in Korean yellowtail, except for glutamine. The fasting period was found to be the biggest factor contributing to the difference in amino acid contents, in addition to environmental factors (including feeding habits). These significant differences indicated that metabolomics could be used to determine geographical origin.

Red seabream (Pagrus major), a migratory fish, is characterized by high protein levels in the muscle. South Korean and Japanese red seabreams have a general distribution pattern; however, distinguishing them based on their geographical origin is difficult. In this study, we used capillary electrophoresis time-of-flight mass spectrometry (CE-TOF/MS) to analyze the red seabream muscle metabolome to investigate how can distinguish the origin of the fish. The metabolites were extracted using 50% acetonitrile in water. Chromatographic separation was successfully used to classify the metabolite profiles of Japanese and South Korean red seabream. Principal component analysis and hierarchical cluster analysis showed good ability to categorize the samples according to their origin. Amino acids showed the greatest quantitative difference in South Korean and Japanese muscle samples. Specifically, the L-alanine, L-glutamic acid, L-isoleucine, dimethylglycine, and L-valine levels in Japanese red seabream samples were significantly higher than those in South Korean samples. In contrast, the levels of trimethylamine N-oxide and inosine monophosphate in South Korean muscle samples were significantly higher than those in Japanese red muscle samples. The monitored metabolite profiles suggest that South Korean and Japanese red seabreams can be identified on the basis of amino acid levels.

Red seabream (Pagrus major) is widely consumed in East Asia. As nuclear wastewater is discharged into Japanese waterbodies, the country of origin of marine products must be accurately labeled. Here, we aimed to discover candidate metabolite biomarkers to discriminate between Korean and Japanese red seabream using LC-Orbitrap mass spectrometry. In total, 95 and 138 putative metabolites were detected via chromatographic separation of fish sampled in the warm and cold seasons, respectively. The spectrometric and chromatographic data were analyzed using principal component analysis and orthogonal partial least squares discriminant analysis. We identified 12 and 19 influential metabolites to discriminate between each origin fish in the warm and cold seasons, respectively, using variable importance in projection scores and p values. Anserine was further selected as a candidate biomarker based on receiver operating characteristic curve analysis. This study provides a basis for using anserine to determine the geographic origin of red seabream.

Mud loach (Misgurnus mizolepis) has long been consumed in Korea. Recently, Chinese mud loaches were replaced with expensive Korean mud loaches, owing to taste and preference. Such issues occur in aquatic food distribution processes, leading to inferior food delivery. Previously, a study was conducted to confirm the origin of mud loaches using genetic analysis. However, untargeted metabolites profiling of mud loaches has not been reported. Untargeted metabolomics provides information on the overall metabolic profiling of a sample, allowing the identification of new metabolites. Here, we analyzed the metabolites of mud loaches of different geographical origins using liquid chromatography (LC)-quadrupole-time-of-flight mass spectrometry (MS). Orthogonal partial least squares discriminant analysis from LC/MS datasets showed a clear distinction between Korean and Chinese mud loaches, and univariate statistical analysis showed significantly different metabolites between them. N-acetylhistidine and anserine were selected as biomarkers for geographical origin discrimination using the receiver operating characteristic curve. N-acetylhistidine and anserine levels were significantly higher in Chinese than in Korean mud loaches. These results indicate that metabolic analysis can be used to discriminate between the geographical origins of mud loaches, curtailing the inadvertent substitution of mud loaches from different regions.