BBA Advances最新文献

{"title":"Introduction to a special issue, “Expanded glycomics: A bridge over future glycomics”","authors":"Jun Hirabayashi , Yann Guerardel","doi":"10.1016/j.bbadva.2025.100167","DOIUrl":"10.1016/j.bbadva.2025.100167","url":null,"abstract":"","PeriodicalId":34672,"journal":{"name":"BBA Advances","volume":"8 ","pages":"Article 100167"},"PeriodicalIF":3.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145736181","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The future of plant lectinology: Advanced technologies and computational tools","authors":"Vinicius J.S. Osterne ,&nbsp;Kyria S. Nascimento ,&nbsp;Benildo S. Cavada ,&nbsp;Els J.M. Van Damme","doi":"10.1016/j.bbadva.2025.100145","DOIUrl":"10.1016/j.bbadva.2025.100145","url":null,"abstract":"<div><div>Lectins play crucial roles in many biological processes and serve as tools in fields ranging from agriculture to biomedicine. While classical methods for lectin discovery and characterization were foundational for the field, they often lack sensitivity and throughput, limiting the detection of less abundant or weakly binding lectins, such as the stress-inducible or monovalent lectins. This review focuses on recent advancements in plant lectin research, particularly novel technologies that complement traditional approaches. Techniques such as glycan microarrays allow rapid assessment of lectin specificity across a diverse range of glycans by evaluating interactions with immobilized glycans on solid surfaces. Phage display libraries enable the identification of carbohydrate-mimetic peptides and the development of ligands for lectins by presenting diverse peptide libraries on bacteriophages. Genomic and transcriptomic analyses facilitate the exploration of the lectome in various plant species by scanning entire datasets to identify genes that contain lectin motifs—specific conserved amino acid sequences involved in carbohydrate recognition—and lectin domains, the larger structural regions that facilitate and stabilize these interactions. Additionally, computational methods—including molecular docking, molecular dynamics simulations, and machine learning pipelines—support predictions of lectin structures and binding properties, underpinning experimental efforts. These advanced techniques bring increased efficiency, accuracy, and a broader scope to lectin studies, with potential impacts across multiple fields. However, challenges such as data complexity and the need for experimental validation for computational methods remain. The future of lectin research will depend on the integration of these methods and the strengthening of interdisciplinarity to unlock the full potential of lectins.</div></div>","PeriodicalId":34672,"journal":{"name":"BBA Advances","volume":"7 ","pages":"Article 100145"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143170982","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}

{"title":"Toward spatial glycomics and glycoproteomics: Innovations and applications","authors":"Patcharaporn Boottanun ,&nbsp;Sayaka Fuseya ,&nbsp;Atsushi Kuno","doi":"10.1016/j.bbadva.2025.100146","DOIUrl":"10.1016/j.bbadva.2025.100146","url":null,"abstract":"<div><div>In this mini review, we provide an overview of the challenging field of spatial glycomics/glycoproteomics. Owing to their complexity, sophisticated analytical methods and innovative technologies are needed to advance this field. An agile development approach enables unraveling aberrant glycosylations, glycobiomarkers, and glycotargets for spatial imaging, diagnosis, and therapeutic purposes. We discuss glycopathology and tissue glycomic profiling using highly sensitive lectin-based analyses and introduce deep visual proteomics for glycomic/glycoproteomic sample preparation. Additionally, we highlight the importance of leveraging laser microdissection and artificial intelligence-driven visual software for cell-type assignment and automation techniques, which are crucial for advancing glycomics/glycoproteomics.</div></div>","PeriodicalId":34672,"journal":{"name":"BBA Advances","volume":"7 ","pages":"Article 100146"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143376930","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}

{"title":"Identification of aberrant α-2,3 sialylation of cartilage associated with osteonecrosis of the femoral head based on integrated multi-omics analyses","authors":"Xueliang Lu ,&nbsp;Xu Wang ,&nbsp;Mingyue Xiong ,&nbsp;Pengbo Wang ,&nbsp;Yingkang Zhu ,&nbsp;Xiangyu Wang ,&nbsp;Xia Liu ,&nbsp;Hanjie Yu ,&nbsp;Ruiyu Liu","doi":"10.1016/j.bbadva.2025.100175","DOIUrl":"10.1016/j.bbadva.2025.100175","url":null,"abstract":"<div><h3>Purpose</h3><div>Osteonecrosis of the femoral head (ONFH) is one of the most common and devastating articular cartilage diseases worldwide. The role of glycosylation in cartilage degeneration of ONFH is not yet fully understood.</div></div><div><h3>Patients and methods</h3><div>The expression of glycogens in cartilage from ONFH patients was determined using our own whole-genome expression dataset. Moreover, the altered glycosylation associated with ONFH cartilage and methylprednisolone (MPS)-induced cell models was investigated by lectin microarrays. The synthesis of α-2,3 sialylation was repressed by silencing ST3GAL2, and the effect of α-2,3-sialylation on ONFH-associated molecular events was assessed.</div></div><div><h3>Results</h3><div>Our findings revealed that the expression of 18 glycogens (including ST3GAL2) were significantly changed in ONFH cartilage compared with those in fracture control cartilage. Moreover, the level of α-2,3 sialylation, which is catalyzed by ST3GAL2, was significantly increased in ONFH cartilage and cell models compared to their corresponding controls. Silencing the expression of ST3GAL2 not only reduced the level of α-2,3 sialylation but also suppressed the expression of proinflammatory cytokines, reduced apoptosis-related proteins, and inactivated the NF-κB signaling pathway.</div></div><div><h3>Conclusion</h3><div>Our study highlighted the important role of α-2,3 sialylation in the development of ONFH, providing valuable insights into the molecular mechanisms underlying the pathogenesis of ONFH.</div></div>","PeriodicalId":34672,"journal":{"name":"BBA Advances","volume":"8 ","pages":"Article 100175"},"PeriodicalIF":3.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145614525","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of a permethylation-based detection method for oligo/polysialic acid structures via tandem MALDI-TOF mass spectrometry","authors":"Kai Suzuki ,&nbsp;Di Wu ,&nbsp;Ken Kitajima ,&nbsp;Nao Yamakawa ,&nbsp;Takayuki Omoto ,&nbsp;Masaya Hane ,&nbsp;Chihiro Sato","doi":"10.1016/j.bbadva.2025.100155","DOIUrl":"10.1016/j.bbadva.2025.100155","url":null,"abstract":"<div><div>Oligo/polysialic acid (oligo/polySia) refers to a class of linear polymers composed of Sias, found extensively at the non-reducing ends of glycans across various organisms, from bacteria to vertebrates. Different types of oligo/polySia have been characterized, varying in Sia composition, α-ketosidic linkages to penultimate Sia residues, and degree of polymerization. Detection of oligo/polySia-capped glycans is typically achieved through western blotting or ELISA using specific antibodies or endo-N-acylneuraminidase. Additionally, a sensitive chemical approach involving the direct labeling of oligo/polySia with 1,2-diamino-4,5-methylenedioxybenzene, followed by separation and quantification via anion-exchange high-performance liquid chromatography, has been developed. However, detection through mass spectrometry (MS) has remained challenging due to the multiple negative charges and structural instability of these glycans. In this study, we applied a permethylation technique to convert carboxyl group of Sias into methyl esters, thereby neutralizing their negative charges, which allowed for improved MS analysis of sialylated glycans. We optimized both the permethylation and glycan purification processes. Consequently, we achieved the first successful detection of polySia structures using MALDI-TOF MS. There are more in-source decay ions in the MS profiling of permethylated α2,9-linked polySias compared to α2,8-linked polySias. Furthermore, we present the first examples of oligo/polySia sequencing by collision-induced dissociation on a TOF/TOF instrument, enabling us to differentiate between α2,8- and α2,9-linked polySias. We extended this approach to analyze oligo/polySia structures with <em>O</em>-linked glycans in polysialoglycoprotein from salmonid eggs. For the first time, the analysis of intact oligo/polySia structures with <em>O</em>-linked glycans were successfully detected using MALDI-TOF/TOF MS/MS with this optimized permethylation method.</div></div>","PeriodicalId":34672,"journal":{"name":"BBA Advances","volume":"7 ","pages":"Article 100155"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143642499","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}

{"title":"Total cell N-glycosylation is altered during differentiation of induced pluripotent stem cells to neural stem cells and is disturbed by trisomy 21","authors":"Ana Cindrić ,&nbsp;Frano Vučković ,&nbsp;Aoife Murray ,&nbsp;Thomas S. Klarić ,&nbsp;Ivan Alić ,&nbsp;Jasminka Krištić ,&nbsp;Dean Nižetić ,&nbsp;Gordan Lauc","doi":"10.1016/j.bbadva.2024.100137","DOIUrl":"10.1016/j.bbadva.2024.100137","url":null,"abstract":"<div><div>Down syndrome (DS), a genetic condition caused by trisomy 21 (T21), manifests various neurological symptoms, including intellectual disability, early neurodegeneration, and early-onset dementia. N-glycosylation is a protein modification that plays a critical role in numerous neurobiological processes and whose dysregulation is associated with a range of neurological disorders. However, whether N-glycosylation of neural glycoproteins is affected in DS has not been studied. To better understand how T21 affects N-glycosylation during neural differentiation, we utilized an isogenic in vitro induced pluripotent stem cell (iPSC) model of T21 in which both T21 and euploid disomic karyotype (D21) clones were obtained from a single individual with mosaic DS. We comprehensively characterized and compared the total N-glycomes of iPSCs and their neural stem cell (NSC) derivatives. N-glycomics analysis of whole cell lysates was performed using liquid chromatography coupled with tandem mass spectrometry to determine N-glycan structures. Our results show that neural differentiation of iPSCs to NSCs is characterized by an increase in the abundance of complex N-glycans at the expense of minimally processed mannosidic N-glycans. Moreover, we found differences in N-glycosylation patterns between D21 and T21 cells. Notably, the abundance of pseudohybrid N-glycans was significantly higher in T21 cells which also exhibited a significantly lower abundance of a specific hybrid monoantennary fucosylated N-glycan (H6N3F1). Overall, our data define the total N-glycome of both D21 and T21 iPSCs and NSCs and show that T21 already impacts N-glycosylation patterns in the stem cell state in a manner consistent with aberrantly premature neural differentiation of T21 cells.</div></div>","PeriodicalId":34672,"journal":{"name":"BBA Advances","volume":"7 ","pages":"Article 100137"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11751427/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143025144","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}

{"title":"Porphyrin-based electrospun nanomaterials for life science applications","authors":"Ana C. Mendes ,&nbsp;Nuno M.M. Moura ,&nbsp;M. Amparo F․ Faustino ,&nbsp;M. Graça P.M.S. Neves ,&nbsp;Ioannis S. Chronakis","doi":"10.1016/j.bbadva.2025.100160","DOIUrl":"10.1016/j.bbadva.2025.100160","url":null,"abstract":"<div><div>Porphyrins are renowned for their utility in photocatalysis, electronics, sensors, solar cell dyes, and environmental remediation. However, their potential in life sciences applications remains underexplored, particularly in the context of encapsulation via electrospinning. This review examines recent advancements (2000–2025) in electrospinning techniques for encapsulating porphyrins, highlighting their unique properties, bioactivities, and versatile applications in life sciences. By combining the strengths of porphyrins and electrospinning technology, researchers can unlock transformative solutions for various life-science challenges, which include photodynamic therapy (PDT), composite materials for anti-microbial applications, sensors, and drug delivery. These efforts could push porphyrin-encapsulated materials from research concepts to applied societal solutions, addressing critical needs in healthcare and beyond to other fields.</div></div>","PeriodicalId":34672,"journal":{"name":"BBA Advances","volume":"7 ","pages":"Article 100160"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143874824","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unravelling lipid heterogeneity: Advances in single-cell lipidomics in cellular metabolism and disease","authors":"Sutanu Sarkar,&nbsp;Rajgourab Ghosh","doi":"10.1016/j.bbadva.2025.100169","DOIUrl":"10.1016/j.bbadva.2025.100169","url":null,"abstract":"<div><div>Recent advancements in single-cell analysis have revolutionized our understanding of cellular heterogeneity, particularly in lipid metabolism. Single-cell lipidomics, enabled by ultra-sensitive mass spectrometry techniques such as Orbitrap and Fourier-transform ion cyclotron resonance (FT-ICR), provides unprecedented insights into lipid-mediated cellular functions. Unlike bulk analyses, single-cell approaches capture real-time metabolic changes, highlighting lipid species' roles in cell differentiation, signal transduction, and disease progression. Mass spectrometry imaging (MSI), including MALDI-MSI and SIMS, further delineates lipid distributions within tissues, revealing spatial heterogeneity critical to cellular function. Emerging evidence suggests that lipid alterations significantly impact developmental mechanisms, stem cell niches, and disease pathogenesis, challenging conventional bulk-level assumptions. However, a key challenge remains in deciphering how lipid networks coordinate cellular differentiation and transcriptional regulation. Future research must integrate lipidomic, proteomic, and genomic data to unravel lipid-mediated signaling and epigenetic modifications. Understanding these dynamics will advance regenerative medicine and therapeutic interventions, enabling precise targeting of lipid-driven pathways in disease contexts.</div></div>","PeriodicalId":34672,"journal":{"name":"BBA Advances","volume":"8 ","pages":"Article 100169"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144522814","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CaF2 nanoparticles deliver siRNA targeting STAT6 and PPAR- γ to depolarise tumour-associated macrophages","authors":"Hamed Al-Busaidi ,&nbsp;Won Fen Wong ,&nbsp;Lakshmi Selvaratnam ,&nbsp;Ezharul Hoque Chowdhury","doi":"10.1016/j.bbadva.2025.100170","DOIUrl":"10.1016/j.bbadva.2025.100170","url":null,"abstract":"<div><div>Breast cancer is a leading cause of death in women, partly due to challenges posed by constituents of the tumour-microenvironment, such as tumour-associated macrophages (TAMs). Polarisation of macrophages to a pro-tumour phenotype usually involves STAT6 and PPAR- <span><math><mi>γ</mi></math></span> pathways. In this study, CaF₂ nanoparticles were developed and bound to siRNA to inhibit the expression of STAT6 and PPAR-<span><math><mi>γ</mi></math></span> in an in vitro model of TAMs. CaF₂ nanoparticles were synthesised by precipitation reactions and characterised by spectrophotometry, dynamic light scattering, FTIR, electron microscopy and MTT assay. Their binding affinity to siRNA was confirmed, as was the cellular uptake by TAMs. CaF₂-bound siRNAs targeting STAT6 and PPAR-<span><math><mi>γ</mi></math></span> were found to reduce the expression of M2 phenotype when assessed by PCR and microscopy. These findings open the possibility of using nanoparticle-bound siRNA to target genes associated with pro-tumour polarisation in macrophages, with further potential to repolarise them to a more inflammatory phenotype.</div></div>","PeriodicalId":34672,"journal":{"name":"BBA Advances","volume":"8 ","pages":"Article 100170"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144522813","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tools for structural lectinomics: From structures to lectomes","authors":"Frédérique Lisacek ,&nbsp;Boris Schnider ,&nbsp;Anne Imberty","doi":"10.1016/j.bbadva.2025.100154","DOIUrl":"10.1016/j.bbadva.2025.100154","url":null,"abstract":"<div><div>Lectins are ubiquitous proteins that interact with glycans in a variety of molecular processes and as such, also play a role in diseases, whether infectious, chronic or cancer-related. The systematic study of lectins is therefore essential, in particular for understanding cell-cell communication. Accumulated protein three-dimensional structural data in the past decades boosted advance in AI-based prediction and opened up new options to characterise lectins that are known to often be multimeric and multivalent. This article reviews the methods to obtain structures of lectins, the current data available for lectin 3D structures and their interactions, how this knowledge is used to classify these proteins and shows that the combination of an array of bioinformatics tools should make the prediction of binding specificity possible in a near future.</div></div>","PeriodicalId":34672,"journal":{"name":"BBA Advances","volume":"7 ","pages":"Article 100154"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143629259","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}