Characterization of metabolic phenotypes and distinctive genes in mice with low-weight gain.

Being overweight exacerbates various metabolic diseases, necessitating the identification of target molecules for obesity control. In the current study, we investigated common physiological features related to metabolism in mice with low weight gain: (1) G protein-coupled receptor, family C, group 5, member B-knockout; (2) gastric inhibitory polypeptide receptor-knockout; and (3) Iroquois-related homeobox 3-knockout. Moreover, we explored genes involved in metabolism by analyzing differentially expressed genes (DEGs) between low-weight gain mice and the respective wild-type control mice. The common characteristics of the low-weight gain mice were low inguinal white adipose tissue (iWAT) and liver weight despite similar food intake along with lower blood leptin levels and high energy expenditure. The DEGs of iWAT, epididymal (gonadal) WAT, brown adipose tissue, muscle, liver, hypothalamus, and hippocampus common to these low-weight gain mice were designated as candidate genes associated with metabolism. One such gene tetraspanin 7 (Tspan7) from the iWAT was validated using knockout and overexpressing mouse models. Mice with low Tspan7 expression gained more weight, while those with high Tspan7 expression gained less weight, confirming the involvement of the Tspan7 gene in weight regulation. Collectively, these findings suggest that the candidate gene list generated in this study contains potential target molecules for obesity regulation. Further validation and additional data from low-weight gain mice will aid in understanding the molecular mechanisms associated with obesity.

HaloTag-based conjugation of proteins to barcoding-oligonucleotides.

Highly sensitive protein quantification enables the detection of a small number of protein molecules that serve as markers/triggers for various biological phenomena, such as cancer. Here, we describe the development of a highly sensitive protein quantification system called HaloTag protein barcoding. The method involves covalent linking of a target protein to a unique molecule counting oligonucleotide at a 1:1 conjugation ratio based on an azido-cycloalkyne click reaction. The sensitivity of the HaloTag-based barcoding was remarkably higher than that of a conventional luciferase assay. The HaloTag system was successfully validated by analyzing a set of protein-protein interactions, with the identification rate of 44% protein interactions between positive reference pairs reported in the literature. Desmoglein 3, the target antigen of pemphigus vulgaris, an IgG-mediated autoimmune blistering disease, was used in a HaloTag protein barcode assay to detect the anti-DSG3 antibody. The dynamic range of the assay was over 104-times wider than that of a conventional enzyme-linked immunosorbent assay (ELISA). The technology was used to detect anti-DSG3 antibody in patient samples with much higher sensitivity compared to conventional ELISA. Our detection system, with its superior sensitivity, enables earlier detection of diseases possibly allowing the initiation of care/treatment at an early disease stage.

Mapping adipocyte interactome networks by HaloTag-enrichment-mass spectrometry.

Mapping protein interaction complexes in their natural state in vivo is arguably the Holy Grail of protein network analysis. Detection of protein interaction stoichiometry has been an important technical challenge, as few studies have focused on this. This may, however, be solved by artificial intelligence (AI) and proteomics. Here, we describe the development of HaloTag-based affinity purification mass spectrometry (HaloMS), a high-throughput HaloMS assay for protein interaction discovery. The approach enables the rapid capture of newly expressed proteins, eliminating tedious conventional one-by-one assays. As a proof-of-principle, we used HaloMS to evaluate the protein complex interactions of 17 regulatory proteins in human adipocytes. The adipocyte interactome network was validated using an in vitro pull-down assay and AI-based prediction tools. Applying HaloMS to probe adipocyte differentiation facilitated the identification of previously unknown transcription factor (TF)-protein complexes, revealing proteome-wide human adipocyte TF networks and shedding light on how different pathways are integrated.

Multifaceted analysis of cross-tissue transcriptomes reveals phenotype-endotype associations in atopic dermatitis.

Atopic dermatitis (AD) is a skin disease that is heterogeneous both in terms of clinical manifestations and molecular profiles. It is increasingly recognized that AD is a systemic rather than a local disease and should be assessed in the context of whole-body pathophysiology. Here we show, via integrated RNA-sequencing of skin tissue and peripheral blood mononuclear cell (PBMC) samples along with clinical data from 115 AD patients and 14 matched healthy controls, that specific clinical presentations associate with matching differential molecular signatures. We establish a regression model based on transcriptome modules identified in weighted gene co-expression network analysis to extract molecular features associated with detailed clinical phenotypes of AD. The two main, qualitatively differential skin manifestations of AD, erythema and papulation are distinguished by differential immunological signatures. We further apply the regression model to a longitudinal dataset of 30 AD patients for personalized monitoring, highlighting patient heterogeneity in disease trajectories. The longitudinal features of blood tests and PBMC transcriptome modules identify three patient clusters which are aligned with clinical severity and reflect treatment history. Our approach thus serves as a framework for effective clinical investigation to gain a holistic view on the pathophysiology of complex human diseases.

Development of an efficient and durable photocatalytic system for hydride reduction of an NAD(P)+ model compound using a ruthenium(II) complex based on mechanistic studies.

The mechanism of photocatalytic reduction of 1-benzylnicotinamidium cation (BNA(+)) to the 1,4-dihydro form (1,4-BNAH) using [Ru(tpy)(bpy)(L)](2+) (Ru-L(2+), where tpy = 2,2':6',2''-terpyridine, bpy = 2,2'-bipyridine, and L = pyridine and MeCN) as a photocatalyst and NEt(3) as a reductant has been clarified. On the basis of this mechanistic study, an efficient and durable photocatalytic system for selective hydride reduction of an NAD(P)(+) model compound has been developed. The photocatalytic reaction is initiated by the formation of [Ru(tpy)(bpy)(NEt(3))](2+) (Ru-NEt(3)(2+)) via the photochemical ligand substitution of Ru-L(2+). For this reason, the production rate of 1,4-BNAH using [Ru(tpy)(bpy)(MeCN)](2+) (Ru-MeCN(2+)) as a photocatalyst, from which the quantum yield of photoelimination of the MeCN ligand is greater than that of the pyridine ligand from [Ru(tpy)(bpy)(pyridine)](2+) (Ru-py(2+)), was faster than that using Ru-py(2+), especially in the first stage of the photocatalytic reduction. The photoexcitation of Ru-NEt(3)(2+) yields [Ru(tpy)(bpy)H](+) (Ru-H(+)), which reacts with BNA(+) to give 1:1 adduct [Ru(tpy)(bpy)(1,4-BNAH)](2+) (Ru-BNAH(2+)). In the presence of excess NEt(3) in the reaction solution, a deprotonation of the carbamoyl group in Ru-BNAH(2+) proceeds rapidly, mainly forming [Ru(tpy)(bpy)(1,4-BNAH-H(+))](+) (Ru-(BNAH-H(+))(+)). Although photocleavage of the adduct yields 1,4-BNAH and the cycle is completed by the re-coordination of a NEt(3) molecule to the Ru(II) center, this process competes with hydride abstraction from Ru-(BNAH-H(+))(+) by BNA(+) giving 1,4-BNAH and [Ru(tpy)(bpy)(BNA(+)-H(+))](2+). This adduct was observed as the major complex in the reaction solution after the photocatalysis was depressed and is a dead-end product because of its stability. Based on the information about the reaction mechanism and the deactivation process, we have successfully developed a new photocatalytic system using Ru-MeCN(2+) with 2 M of NEt(3) as a reductant, which could reduce more than 59 equivalent amounts of an NAD(P)(+) model, 1-benzyl-N,N-diethylnicotinamidium cation, selectively to the corresponding 1,4-dihydro form in a 6 x 10(-4) quantum yield using 436-nm light.

Quantitative photochemical formation of [Ru(tpy)(bpy)H]+.

Quantitative photochemical production of [Ru(tpy)(bpy)H](+) (Ru-H(+)) was achieved by irradiation of [Ru(tpy)(bpy)(DMF)](2+) (Ru-DMF(2+); DMF = N,N-dimethylformamide) in a tetrahydrofuran (THF) solution containing excess triethylamine (NEt(3)). The mechanism of the Ru-H(+) formation was investigated in detail. A photochemical ligand substitution reaction of Ru-DMF(2+) in THF proceeded to give [Ru(tpy)(bpy)(THF)](2+) (Ru-THF(2+)) with a quantum yield of (7.6 +/- 0.7) x 10(-2). In the presence of NEt(3), a similar photochemical ligand substitution reaction also proceeded quickly, but the products were an equilibrium mixture of Ru-THF(2+) and [Ru(tpy)(bpy)(NEt(3))](2+) (Ru-NEt(3)(2+)) with a considerable amount of Ru-H(+) even in the first stage of the photochemical reaction. The equilibrium constant between Ru-THF(2+) and Ru-NEt(3)(2+) was determined as 6.9 +/- 2.1. Irradiation to Ru-NEt(3)(2+) gave Ru-H(+) with a quantum yield of (9.1 +/- 0.5) x 10(-3). An important intermediate, Ru-NEt(3)(2+), was isolated, and its properties were investigated in detail.

Solution structure of the kinase-associated domain 1 of mouse microtubule-associated protein/microtubule affinity-regulating kinase 3.

Microtubule-associated protein/microtubule affinity-regulating kinases (MARKs)/PAR-1 are common regulators of cell polarity that are conserved from nematode to human. All of these kinases have a highly conserved C-terminal domain, which is termed the kinase-associated domain 1 (KA1), although its function is unknown. In this study, we determined the solution structure of the KA1 domain of mouse MARK3 by NMR spectroscopy. We found that approximately 50 additional residues preceding the previously defined KA1 domain are required for its proper folding. The newly defined KA1 domain adopts a compact alpha+beta structure with a betaalphabetabetabetabetaalpha topology. We also found a characteristic hydrophobic, concave surface surrounded by positively charged residues. This concave surface includes the highly conserved Glu-Leu-Lys-Leu motif at the C terminus, indicating that it is important for the function of the KA1 domain.

Hepatocellular carcinoma incidentally detected at second hepatectomy for repeated colorectal liver metastasis in a patient with hepatitis C virus-related cirrhosis: a case report.

BACKGROUND: It has been reported that liver metastasis rarely occurs in a cirrhotic/hepatitic liver. Thus, coexistence of liver metastasis and hepatocellular carcinoma has been scarcely reported. To the best of our knowledge, there are no cases with hepatocellular carcinoma, which developed during an observational period after hepatectomy for colorectal liver metastasis, in the worldwide English literature. Here we present a case of hepatocellular carcinoma which occurred during a period between the first and second hepatectomy for repeated colorectal liver metastasis. CASE PRESENTATION: A 65-year-old Japanese woman underwent rectal resection for advanced rectal cancer. Hepatitis C cirrhosis was diagnosed at that time and antiviral therapy was offered but rejected because of socioeconomic reasons. At the age of 68, she developed two colorectal liver metastases originating from the rectal cancer, which were treated by local ablation and partial hepatectomy. At the age of 71, solitary recurrent colorectal liver metastasis was observed adjacent to the previously ablated lesion in segment 4, and thus segmentectomy 4 was performed. During surgery, a small tumor in segment 8 was incidentally identified. Taking into account her history, the tumor was considered to be recurrent colorectal liver metastasis and it was extirpated by partial hepatectomy. However, the segment 4 tumor was diagnosed as recurrent colorectal liver metastasis on the basis of histological findings and the segment 8 tumor was diagnosed as hepatocellular carcinoma. Although she had a cut surface abscess postoperatively, she was discharged from hospital 21 days after the surgery and is currently doing well 18 months after the second hepatectomy. She is currently receiving interferon and ribavirin therapy to eliminate hepatitis C virus. CONCLUSIONS: If antiviral therapy was performed earlier for the present case and viral elimination was achieved, hepatocellular carcinoma might not have developed. This case reemphasizes the importance of antiviral therapy for preventing carcinogenesis of hepatocellular carcinoma in patients with viral hepatitis even if they have other cancers.

Transition metal complexes coordinated by an NAD(P)H model compound and their enhanced hydride-donating abilities in the presence of a base.

The ruthenium(II) and rhenium(I) complexes containing an NAD(P)H model compound, 1-benzyl-1,4-dihydronicotinamide (BNAH), as ligand, [Ru(tpy)(bpy)(BNAH)]2+ (1 a) and [Re(bpy)(CO)3(BNAH)]+ (1 b), were quantitatively produced by the reaction of the corresponding metal hydrido complexes with BNA(+) (1-benzylnicotinamidium cation). In the presence of base with pK(a) = 8.9, 1 a and 1 b have much greater reducing power than "free" BNAH. The oxidation potentials of 1 a in the absence and the presence of triethylamine were 0.55 V and -0.04 V, respectively, versus Ag/AgNO(3), whereas that of "free" BNAH was 0.30 V. Spectroscopic results clearly showed that the base extracts a proton from the carbamoyl group on 1 a and 1 b to give the deprotonated BNAH coordinating to the transition-metal complexes [Ru(tpy)(bpy)(BNAH-H+)]+ (3 a) and [Re(bpy)(CO)3(BNAH-H+)] (3 b); this deprotonation underlies the enhancement in reducing ability. The deprotonated forms 3 a and 3 b can efficiently reduce other NAD(P) models to give the corresponding 1,4-dihydro form, resulting in the deprotonated BNA+ being coordinated to the metal complexes [Ru(tpy)(bpy)(BNA(+)-H+)]2+ (2 a) and [Re(bpy)(CO)3(BNA+-H+)]+ (2 b); "free" BNAH and the protonated adducts 1 a and 1 b cannot act in this way. X-ray crystallography was performed on the PF6- salt of 2 a, and showed that the deprotonated nitrogen atom on the carbamoyl group coordinates to the ruthenium(II) metal center with a bond length of 2.086(3) Angstroms. Infrared spectral data suggested that the deprotonated carbamoyl group on the reduced forms 3 a and 3 b is converted to the imido group, and that the oxygen atom coordinates to the metal center.

Solution structure of the SEA domain from the murine homologue of ovarian cancer antigen CA125 (MUC16).

Human CA125, encoded by the MUC16 gene, is an ovarian cancer antigen widely used for a serum assay. Its extracellular region consists of tandem repeats of SEA domains. In this study we determined the three-dimensional structure of the SEA domain from the murine MUC16 homologue using multidimensional NMR spectroscopy. The domain forms a unique alpha/beta sandwich fold composed of two alpha helices and four antiparallel beta strands and has a characteristic turn named the TY-turn between alpha1 and alpha2. The internal mobility of the main chain is low throughout the domain. The residues that form the hydrophobic core and the TY-turn are fully conserved in all SEA domain sequences, indicating that the fold is common in the family. Interestingly, no other residues are conserved throughout the family. Thus, the sequence alignment of the SEA domain family was refined on the basis of the three-dimensional structure, which allowed us to classify the SEA domains into several subfamilies. The residues on the surface differ between these subfamilies, suggesting that each subfamily has a different function. In the MUC16 SEA domains, the conserved surface residues, Asn-10, Thr-12, Arg-63, Asp-75, Asp-112, Ser-115, and Phe-117, are clustered on the beta sheet surface, which may be functionally important. The putative epitope (residues 58-77) for anti-MUC16 antibodies is located around the beta2 and beta3 strands. On the other hand the tissue tumor marker MUC1 has a SEA domain belonging to another subfamily, and its GSVVV motif for proteolytic cleavage is located in the short loop connecting beta2 and beta3.