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Exploring the role of exosomal and non-exosomal non-coding RNAs in Kawasaki disease: Implications for diagnosis and therapeutic strategies against coronary artery aneurysms

IF 2.3 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochemistry and Biophysics Reports

Pub Date : 2025-03-06 DOI: 10.1016/j.bbrep.2025.101970

Negar Jafari , Ali Zolfi Gol , Venus Shahabi Rabori , Mohammadreza Saberiyan

Kawasaki disease (KD) is an acute vasculitis primarily affecting children, with a potential risk of developing coronary artery aneurysms (CAAs) and cardiovascular complications. The emergence of non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), has provided insights into Kawasaki disease pathogenesis and opened new avenues for diagnosis and therapeutic intervention. Furthermore, polymorphism analysis of ncRNA genes offers significant insights into genetic predisposition to Kawasaki disease, facilitating tailored treatment approaches and risk assessment to improve patient outcomes. Exosomal ncRNAs, which are ncRNAs encapsulated within extracellular vesicles, have garnered significant attention as potential biomarkers for Kawasaki disease and CAA due to their stability and accessibility in biological fluids. This review comprehensively discusses the biogenesis, components, and potential of exosomal and non-exosomal ncRNAs in Kawasaki disease diagnosis and prognosis prediction. It also highlights the roles of non-exosomal ncRNAs, such as miRNAs, lncRNAs, and circRNAs, in Kawasaki disease pathogenesis and their implications as therapeutic targets. Additionally, the review explores the current diagnostic and therapeutic approaches for Kawasaki disease and emphasizes the need for further research to validate these ncRNA-based biomarkers in diverse populations and clinical settings.

{"title":"Exploring the role of exosomal and non-exosomal non-coding RNAs in Kawasaki disease: Implications for diagnosis and therapeutic strategies against coronary artery aneurysms","authors":"Negar Jafari , Ali Zolfi Gol , Venus Shahabi Rabori , Mohammadreza Saberiyan","doi":"10.1016/j.bbrep.2025.101970","DOIUrl":"10.1016/j.bbrep.2025.101970","url":null,"abstract":"<div><div>Kawasaki disease (KD) is an acute vasculitis primarily affecting children, with a potential risk of developing coronary artery aneurysms (CAAs) and cardiovascular complications. The emergence of non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), has provided insights into Kawasaki disease pathogenesis and opened new avenues for diagnosis and therapeutic intervention. Furthermore, polymorphism analysis of ncRNA genes offers significant insights into genetic predisposition to Kawasaki disease, facilitating tailored treatment approaches and risk assessment to improve patient outcomes. Exosomal ncRNAs, which are ncRNAs encapsulated within extracellular vesicles, have garnered significant attention as potential biomarkers for Kawasaki disease and CAA due to their stability and accessibility in biological fluids. This review comprehensively discusses the biogenesis, components, and potential of exosomal and non-exosomal ncRNAs in Kawasaki disease diagnosis and prognosis prediction. It also highlights the roles of non-exosomal ncRNAs, such as miRNAs, lncRNAs, and circRNAs, in Kawasaki disease pathogenesis and their implications as therapeutic targets. Additionally, the review explores the current diagnostic and therapeutic approaches for Kawasaki disease and emphasizes the need for further research to validate these ncRNA-based biomarkers in diverse populations and clinical settings.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"42 ","pages":"Article 101970"},"PeriodicalIF":2.3,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143549568","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Alterations of renal polyamine metabolism in mice with folic acid-induced chronic kidney disease

IF 2.3 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochemistry and Biophysics Reports

Pub Date : 2025-03-05 DOI: 10.1016/j.bbrep.2025.101967

Cheng Xue , Jiaxin Chen , Xinming Li , Chenchen Zhou , Zhiguo Mao

Chronic kidney disease (CKD) often follows acute kidney injury, leading to renal fibrosis and progressive renal failure. Spermine, a polyamine with antioxidant and anti-inflammatory properties, helps reduce renal fibrosis and may serve as a biomarker for CKD progression. We used spatially resolved metabonomic analysis with AFADESI-MSI to examine polyamine distribution in kidneys of a folic acid (FA)-induced CKD mouse model. Results showed decreased spermine and increased spermidine levels, associated with elevated spermine oxidase (SMOX) and spermidine/spermine N1-acetyltransferase (SSAT) enzyme expression in CKD. These findings suggest that altered polyamine metabolism contributes to CKD progression and may provide targets for polyamine-based therapies.

引用次数: 0

Designing of an efficient DC-inducing multi-epitope vaccine against Epstein Barr virus targeting the GP350 using immunoinformatics and molecular dynamic simulation

IF 2.3 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochemistry and Biophysics Reports

Pub Date : 2025-03-03 DOI: 10.1016/j.bbrep.2025.101966

Golzar Fatahi , Maasoume Abdollahi , Zahra Nashtahosseini , Shima Minoo , Mehrnaz Mostafavi , Kholoud Saeidi

The findings underscore the critical role of Epstein-Barr virus (EBV) in the onset of various cancers. In response to the lack of effective treatments or vaccines for EBV infection, this investigation employed immunoinformatics approaches to develop a potent vaccine targeting multiple epitopes of the EBV glycoprotein 350 (Gp350), a key surface protein. Utilizing computational methods, we designed a comprehensive multi-epitope vaccine featuring 11 CTL and HTL epitopes, totaling 324 amino acids and covering five distinct EBV strains such as B95-8, P3HR-1, GD1, AG876, and Akata. To enhance immunogenicity, the 50S ribosomal protein L7/L12 (rplL) was included as an adjuvant at the vaccine's N-terminal. The vaccine was evaluated for its physicochemical and immunological properties, demonstrating stability, potency, solubility, hydrophilicity, non-allergenicity, and non-toxicity. Molecular docking studies have shown that the vaccine interacts with Toll-like receptor 4 (TLR4). Simulations performed using GROMACS confirmed the stability of the system over 100ns. Immune simulations indicated that the vaccine elicited robust humoral and cellular responses, activating both innate and adaptive immunity. The findings indicate that the multi-epitope vaccine is highly immunogenic and shows significant potential for further experimental validation.

{"title":"Designing of an efficient DC-inducing multi-epitope vaccine against Epstein Barr virus targeting the GP350 using immunoinformatics and molecular dynamic simulation","authors":"Golzar Fatahi , Maasoume Abdollahi , Zahra Nashtahosseini , Shima Minoo , Mehrnaz Mostafavi , Kholoud Saeidi","doi":"10.1016/j.bbrep.2025.101966","DOIUrl":"10.1016/j.bbrep.2025.101966","url":null,"abstract":"<div><div>The findings underscore the critical role of Epstein-Barr virus (EBV) in the onset of various cancers. In response to the lack of effective treatments or vaccines for EBV infection, this investigation employed immunoinformatics approaches to develop a potent vaccine targeting multiple epitopes of the EBV glycoprotein 350 (Gp350), a key surface protein. Utilizing computational methods, we designed a comprehensive multi-epitope vaccine featuring 11 CTL and HTL epitopes, totaling 324 amino acids and covering five distinct EBV strains such as B95-8, P3HR-1, GD1, AG876, and Akata. To enhance immunogenicity, the 50S ribosomal protein L7/L12 (rplL) was included as an adjuvant at the vaccine's N-terminal. The vaccine was evaluated for its physicochemical and immunological properties, demonstrating stability, potency, solubility, hydrophilicity, non-allergenicity, and non-toxicity. Molecular docking studies have shown that the vaccine interacts with Toll-like receptor 4 (TLR4). Simulations performed using GROMACS confirmed the stability of the system over 100ns. Immune simulations indicated that the vaccine elicited robust humoral and cellular responses, activating both innate and adaptive immunity. The findings indicate that the multi-epitope vaccine is highly immunogenic and shows significant potential for further experimental validation.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"42 ","pages":"Article 101966"},"PeriodicalIF":2.3,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143534807","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Intestinal antibody repertoire is altered by diabetes and varies depending on the pathogenesis

IF 2.3 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochemistry and Biophysics Reports

Pub Date : 2025-03-02 DOI: 10.1016/j.bbrep.2025.101964

Miho Chikazawa, Ken-Ichiro Minato

Intestinal immunity is an important system for host defense and it is influenced by various factors such as diet and diseases. To elucidate the relationship between intestinal immunity and type 2 diabetes, we analyzed the effects of diabetes on intestinal antibody production and IgA repertoire using high-fat diet-fed mice and genetically diabetic KK-A^y mice model. The antibody level in the small intestine increased only in KK-A^y mice. We also confirmed that the IgA repertoire in both models experienced significant changes when compared to that in control mice, and no shared characteristics were observed between the two diabetic models. Antibody production in the intestine is influenced by stimuli associated with the onset of diabetes, and the types of induced IgA would differ depending on the process of disease onset.

引用次数: 0

A novel anti-mouse CXCR1 monoclonal antibody, Cx1Mab-8, demonstrates nanomolar affinity in flow cytometry

IF 2.3 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochemistry and Biophysics Reports

Pub Date : 2025-03-01 DOI: 10.1016/j.bbrep.2025.101965

Guanjie Li, Hiroyuki Suzuki, Tomohiro Tanaka, Hiroyuki Satofuka, Mika K. Kaneko, Yukinari Kato

CXC chemokine receptor 1 (CXCR1) is an important regulator for neutrophil granulocyte activation through binding to the ligand interleukin-8 (IL-8). Upon binding to IL-8, CXCR1 activates downstream signaling, critical for innate and adaptive immune responses. The IL-8-CXCR1 axis also plays an important role in tumor progression, especially in the tumor microenvironment. CXCR1 antagonists or anti-IL-8 monoclonal antibodies (mAbs) have been developed and evaluated in clinical trials for inflammatory diseases and tumors. In this study, we developed novel mAbs for mouse CXCR1 (mCXCR1) using the N-terminal peptide immunization. Among the established anti-mCXCR1 mAbs, Cx₁Mab-8 (rat IgG_2b, kappa) recognized mCXCR1-overexpressed Chinese hamster ovary-K1 (CHO/mCXCR1) and mCXCR1-overexpressed LN229 (LN229/mCXCR1) by flow cytometry. The dissociation constant (K_D) values of Cx₁Mab-8 for CHO/mCXCR1 and LN229/mCXCR1 were determined as 4.1 × 10⁻¹⁰ M and 1.5 × 10⁻⁹ M, respectively. These results indicated that Cx₁Mab-8 is useful for detecting mCXCR1 by flow cytometry with high affinity and could contribute to obtaining the proof of concept in preclinical studies.

{"title":"A novel anti-mouse CXCR1 monoclonal antibody, Cx1Mab-8, demonstrates nanomolar affinity in flow cytometry","authors":"Guanjie Li, Hiroyuki Suzuki, Tomohiro Tanaka, Hiroyuki Satofuka, Mika K. Kaneko, Yukinari Kato","doi":"10.1016/j.bbrep.2025.101965","DOIUrl":"10.1016/j.bbrep.2025.101965","url":null,"abstract":"<div><div>CXC chemokine receptor 1 (CXCR1) is an important regulator for neutrophil granulocyte activation through binding to the ligand interleukin-8 (IL-8). Upon binding to IL-8, CXCR1 activates downstream signaling, critical for innate and adaptive immune responses. The IL-8-CXCR1 axis also plays an important role in tumor progression, especially in the tumor microenvironment. CXCR1 antagonists or anti-IL-8 monoclonal antibodies (mAbs) have been developed and evaluated in clinical trials for inflammatory diseases and tumors. In this study, we developed novel mAbs for mouse CXCR1 (mCXCR1) using the N-terminal peptide immunization. Among the established anti-mCXCR1 mAbs, Cx<sub>1</sub>Mab-8 (rat IgG<sub>2b</sub>, kappa) recognized mCXCR1-overexpressed Chinese hamster ovary-K1 (CHO/mCXCR1) and mCXCR1-overexpressed LN229 (LN229/mCXCR1) by flow cytometry. The dissociation constant (<em>K</em><sub>D</sub>) values of Cx<sub>1</sub>Mab-8 for CHO/mCXCR1 and LN229/mCXCR1 were determined as 4.1 × 10<sup>−10</sup> M and 1.5 × 10<sup>−9</sup> M, respectively. These results indicated that Cx<sub>1</sub>Mab-8 is useful for detecting mCXCR1 by flow cytometry with high affinity and could contribute to obtaining the proof of concept in preclinical studies.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"42 ","pages":"Article 101965"},"PeriodicalIF":2.3,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143521306","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Corrigendum to “A non-invasive screening method using Caenorhabditis elegans for early detection of multiple cancer types: A prospective clinical study” [Biochem. and Biophys. Rep. 39 (2024) 101778]

IF 2.3 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochemistry and Biophysics Reports

Pub Date : 2025-03-01 DOI: 10.1016/j.bbrep.2024.101883

Hideyuki Hatakeyama, Masayo Morishita, Aya Hasan Alshammari, Umbhorn Ungkulpasvich, Junichi Yamaguchi, Takaaki Hirotsu, Eric di Luccio

引用次数: 0

The C-terminal end of PLIN1 displays structural disorder

IF 2.3 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochemistry and Biophysics Reports

Pub Date : 2025-02-28 DOI: 10.1016/j.bbrep.2025.101963

Edgar D. Páez-Pérez , Miriam Livier Llamas-García , Gabriela M. Montero-Morán , Samuel Lara-González

Lipid droplets (LDs) serve as crucial organelles for lipid storage and metabolism, with their proteome significantly influencing their regulation. Perilipins (PLINs), in particular PLIN1, play vital role in LD metabolism by orchestrating lipolysis. The C-terminal end of PLIN1 regulates lipolysis through interactions with coactivators such as the CGI-58 protein. Despite its importance, the structural characterization of this domain remains limited. Here, we present a comprehensive bioinformatic and biophysical analysis of the C-terminal end of mouse PLIN1 (mPLIN1C). Our findings suggest that mPLIN1C behaves as an intrinsically disordered region (IDR), exhibiting context-dependent properties of the coil-like or pre-molten globule type. Structural analysis reveals a predominance of disordered secondary structure, with circular dichroism spectroscopy indicating a high coil content. Interaction studies with SDS micelles suggest a conformational transition towards a pre-molten globule state. Furthermore, the analysis of molecular recognition features (MoRFs) identifies the EPESE sequence spanning residues 413–417 as a potential binding site for partner molecules. Overall, our findings shed light on the structural properties and potential interaction mechanisms of mPLIN1C, providing insight into its functional role in LD metabolism.

{"title":"The C-terminal end of PLIN1 displays structural disorder","authors":"Edgar D. Páez-Pérez , Miriam Livier Llamas-García , Gabriela M. Montero-Morán , Samuel Lara-González","doi":"10.1016/j.bbrep.2025.101963","DOIUrl":"10.1016/j.bbrep.2025.101963","url":null,"abstract":"<div><div>Lipid droplets (LDs) serve as crucial organelles for lipid storage and metabolism, with their proteome significantly influencing their regulation. Perilipins (PLINs), in particular PLIN1, play vital role in LD metabolism by orchestrating lipolysis. The C-terminal end of PLIN1 regulates lipolysis through interactions with coactivators such as the CGI-58 protein. Despite its importance, the structural characterization of this domain remains limited. Here, we present a comprehensive bioinformatic and biophysical analysis of the C-terminal end of mouse PLIN1 (mPLIN1C). Our findings suggest that mPLIN1C behaves as an intrinsically disordered region (IDR), exhibiting context-dependent properties of the coil-like or pre-molten globule type. Structural analysis reveals a predominance of disordered secondary structure, with circular dichroism spectroscopy indicating a high coil content. Interaction studies with SDS micelles suggest a conformational transition towards a pre-molten globule state. Furthermore, the analysis of molecular recognition features (MoRFs) identifies the EPESE sequence spanning residues 413–417 as a potential binding site for partner molecules. Overall, our findings shed light on the structural properties and potential interaction mechanisms of mPLIN1C, providing insight into its functional role in LD metabolism.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"42 ","pages":"Article 101963"},"PeriodicalIF":2.3,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143510839","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Development and analytical performance of a new research use only (RUO) GP73 automated immunoassay

IF 2.3 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochemistry and Biophysics Reports

Pub Date : 2025-02-25 DOI: 10.1016/j.bbrep.2025.101961

Shaohua Ning , Enfu Liu , Fanju Meng , Fei Chen , James Hartnett , Zhihong Lin , Bailin Tu , David J. Hawksworth , Bryan C. Tieman , De Yu Mao , Ryan Piktel , Amit Kumar , You Pan , Philip M. Hemken

Golgi protein 73 (GP73) is a serum marker with potential applications in the assessment of chronic liver disease progression. We developed a research use only (RUO) GP73 immunoassay to detect serum GP73 concentration. A pair of internal antibodies that most effectively capture and detect GP73 were used to develop a prototype assay. An internal recombinant GP73 standard was used to prepare the assay calibrator and controls. The stability performance of the antibodies and GP73 calibrator were evaluated. We analyzed assay performance on the automated Alinity i system, including precision, sensitivity, linearity, endogenous interference, and HAMA/RF interference. The RUO Alinity i GP73 immunoassay showed good stability when the reagent kit was stored on board the instrument for more than 30 days without recalibration. The internal GP73 calibrator was stable at 2–8 °C for 28 days. Total %CV for 20 days was ≤3 %. The limit of quantitation (LoQ) at 20 % CV was 0.20 ng/mL or lower. Dilution analysis yielded a linear result within the range of 2.1 ng/mL – 1000.0 ng/mL. No interference was observed from common endogenous interferents at each test interference level. These findings support the reliability and robustness of the RUO Alinity i GP73 immunoassay for measuring serum GP73 concentration.

{"title":"Development and analytical performance of a new research use only (RUO) GP73 automated immunoassay","authors":"Shaohua Ning , Enfu Liu , Fanju Meng , Fei Chen , James Hartnett , Zhihong Lin , Bailin Tu , David J. Hawksworth , Bryan C. Tieman , De Yu Mao , Ryan Piktel , Amit Kumar , You Pan , Philip M. Hemken","doi":"10.1016/j.bbrep.2025.101961","DOIUrl":"10.1016/j.bbrep.2025.101961","url":null,"abstract":"<div><div>Golgi protein 73 (GP73) is a serum marker with potential applications in the assessment of chronic liver disease progression. We developed a research use only (RUO) GP73 immunoassay to detect serum GP73 concentration. A pair of internal antibodies that most effectively capture and detect GP73 were used to develop a prototype assay. An internal recombinant GP73 standard was used to prepare the assay calibrator and controls. The stability performance of the antibodies and GP73 calibrator were evaluated. We analyzed assay performance on the automated Alinity i system, including precision, sensitivity, linearity, endogenous interference, and HAMA/RF interference. The RUO Alinity i GP73 immunoassay showed good stability when the reagent kit was stored on board the instrument for more than 30 days without recalibration. The internal GP73 calibrator was stable at 2–8 °C for 28 days. Total %CV for 20 days was ≤3 %. The limit of quantitation (LoQ) at 20 % CV was 0.20 ng/mL or lower. Dilution analysis yielded a linear result within the range of 2.1 ng/mL – 1000.0 ng/mL. No interference was observed from common endogenous interferents at each test interference level. These findings support the reliability and robustness of the RUO Alinity i GP73 immunoassay for measuring serum GP73 concentration.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"41 ","pages":"Article 101961"},"PeriodicalIF":2.3,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143480166","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

An exogenous encoding sequence based on DNA data storage technology and its application in assisted reproductive technology

IF 2.3 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochemistry and Biophysics Reports

Pub Date : 2025-02-24 DOI: 10.1016/j.bbrep.2025.101962

Zhiqing Huang , Taoli Ding , Zixuan Ni , Yujie Zheng , Na Liu , Tuan Li , Wenchang Lian , Beihong Zheng , Yan Sun

Safety and ethical issues are the primary concerns for assisted reproductive technology (ART). However, confusion and contamination of samples are common problems in embryo laboratories, preimplantation genetic test (PGT) laboratories, and third-party medical testing laboratories due to large sample numbers and complex procedures. Once these problems occur, they are often difficult to trace, posing risks and ethical challenges to hospital reproductive centers, third-party medical testing laboratories, and patient families. Therefore, it is necessary to establish an effective and feasible tracing system to ensure sample safety. In this study, we designed an exogenous encoding sequence (EES) based on DNA data storage technology, which provide a unique identification code for each in vitro cultured embryo, effectively avoiding potential risks and ethical problems caused by sample confusion and contamination. This exogenous encoding sequence is a DNA molecule that is non-toxic and structurally stable. We verified that a small amount of exogenous encoding sequence (6∗109 copies/uL) can be amplified together with embryo biopsy cells and detected by various sequencing methods without affecting copy number variants (CNVs). Furthermore, if there is contamination from other samples at a proportion of more than 5 %, it can also be identified through the encoding information of the exogenous encoding sequence. Our study proves that the exogenous encoding sequence designed based on DNA data storage technology is effective and reliable, and can be applied in hospital reproductive centers and third-party medical testing laboratories to improve the safety of in vitro cultured embryos and avoid potential ethical problems in the future.

{"title":"An exogenous encoding sequence based on DNA data storage technology and its application in assisted reproductive technology","authors":"Zhiqing Huang , Taoli Ding , Zixuan Ni , Yujie Zheng , Na Liu , Tuan Li , Wenchang Lian , Beihong Zheng , Yan Sun","doi":"10.1016/j.bbrep.2025.101962","DOIUrl":"10.1016/j.bbrep.2025.101962","url":null,"abstract":"<div><div>Safety and ethical issues are the primary concerns for assisted reproductive technology (ART). However, confusion and contamination of samples are common problems in embryo laboratories, preimplantation genetic test (PGT) laboratories, and third-party medical testing laboratories due to large sample numbers and complex procedures. Once these problems occur, they are often difficult to trace, posing risks and ethical challenges to hospital reproductive centers, third-party medical testing laboratories, and patient families. Therefore, it is necessary to establish an effective and feasible tracing system to ensure sample safety. In this study, we designed an exogenous encoding sequence (EES) based on DNA data storage technology, which provide a unique identification code for each in vitro cultured embryo, effectively avoiding potential risks and ethical problems caused by sample confusion and contamination. This exogenous encoding sequence is a DNA molecule that is non-toxic and structurally stable. We verified that a small amount of exogenous encoding sequence (6∗109 copies/uL) can be amplified together with embryo biopsy cells and detected by various sequencing methods without affecting copy number variants (CNVs). Furthermore, if there is contamination from other samples at a proportion of more than 5 %, it can also be identified through the encoding information of the exogenous encoding sequence. Our study proves that the exogenous encoding sequence designed based on DNA data storage technology is effective and reliable, and can be applied in hospital reproductive centers and third-party medical testing laboratories to improve the safety of in vitro cultured embryos and avoid potential ethical problems in the future.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"41 ","pages":"Article 101962"},"PeriodicalIF":2.3,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143480165","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Development of a novel anti-erythropoietin-producing hepatocellular receptor B6 monoclonal antibody Eb6Mab-3 for flow cytometry

IF 2.3 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochemistry and Biophysics Reports

Pub Date : 2025-02-21 DOI: 10.1016/j.bbrep.2025.101960

Tomohiro Tanaka , Yu Kaneko , Haruto Yamamoto , Guanjie Li, Shiori Fujisawa, Hiroyuki Satofuka, Keisuke Shinoda, Takuya Nakamura, Mika K. Kaneko, Hiroyuki Suzuki, Yukinari Kato

Erythropoietin-producing hepatocellular receptor B6 (EphB6) is a member of the largest Eph subfamily of receptor tyrosine kinases. EphB6 is widely expressed in various tissues and regulates cellular homeostasis by interacting with its membrane-bound ephrin ligands and other receptors. EphB6 is involved in cancer pathology despite lacking kinase activity. Developing sensitive monoclonal antibodies (mAbs) for EphB6 has been desired for treatment, diagnosis, and further analysis of EphB6. This study established a novel specific and sensitive anti-human EphB6 mAb clone Eb₆Mab-3 (mouse IgG₁, kappa) by the Cell-Based Immunization and Screening (CBIS) method. In flow cytometry, Eb₆Mab-3 demonstrated reactivity with EphB6-overexpressed Chinese hamster ovary-K1 cells (CHO/EphB6) and endogenously EphB6-expressing DLD-1 colorectal cancer cells. Cross-reactivity of Eb₆Mab-3 was not observed. Eb₆Mab-3 demonstrated a moderate binding affinity (dissociation constant; K_D) for CHO/EphB6 (K_D: 2.6 ± 1.0 × 10⁻⁸ M) and a high binding affinity for DLD-1 (K_D: 3.4 ± 1.3 × 10⁻⁹ M). Eb₆Mab-3 can detect EphB6 protein in CHO/EphB6 lysate in Western blot. Eb₆Mab-3, established by the CBIS method, could be valuable for analyzing the EphB6-associated cellular functions and has potential applications in diagnosis and treatment with specificity and high affinity for cancer cells.

促红细胞生成素肝细胞受体 B6（EphB6）是最大的受体酪氨酸激酶 Eph 亚家族的成员。EphB6 广泛表达于各种组织，通过与其膜结合的ephrin 配体和其他受体相互作用来调节细胞的稳态。尽管 EphB6 缺乏激酶活性，但它与癌症病理有关。针对 EphB6 开发灵敏的单克隆抗体（mAbs）一直是治疗、诊断和进一步分析 EphB6 所需要的。本研究通过细胞免疫和筛选（CBIS）方法建立了一种新型特异性和敏感性抗人 EphB6 mAb 克隆 Eb6Mab-3（小鼠 IgG1，kappa）。在流式细胞术中，Eb6Mab-3 与过表达 EphB6 的中国仓鼠卵巢-K1 细胞（CHO/EphB6）和内源性表达 EphB6 的 DLD-1 大肠癌细胞有反应性。未观察到 Eb6Mab-3 的交叉反应。Eb6Mab-3 与 CHO/EphB6 的结合亲和力（解离常数；KD）适中（KD：2.6 ± 1.0 × 10-8 M），与 DLD-1 的结合亲和力较高（KD：3.4 ± 1.3 × 10-9 M）。在 Western 印迹中，Eb6Mab-3 可以检测 CHO/EphB6 裂解液中的 EphB6 蛋白。通过 CBIS 方法建立的 Eb6Mab-3 可用于分析与 EphB6 相关的细胞功能，其对癌细胞的特异性和高亲和力在诊断和治疗中具有潜在的应用价值。

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