biomarker_id	biomarker	assessed_biomarker_entity	assessed_biomarker_entity_id	assessed_entity_type	condition	condition_id	exposure_agent	exposure_agent_id	best_biomarker_role	specimen	specimen_id	loinc_code	evidence_source	evidence	tag	vocab_pattern	biomarker_controlled_vocab	component_group	flags
BB3816-1	absence of glycosylation on CD274	Programmed cell death 1 ligand 1	UPKB:Q9NZQ7	protein	triple-receptor negative breast cancer	DOID:0060081				tissue	UBERON:0000479		PubMed:40651655	After deglycosylation, 84.31 % of the initially PD-L1-negative cases were reclassified as PD-L1 positive, indicating that glycosylation led to a 27.92 % false-negative rate in the TNBC samples. Notably, higher PD-L1 levels post-de-glycosylation were significantly associated with favorable responses to ICB treatments, particularly among patients receiving pembrolizumab and atezolizumab. Receiver operating characteristic (ROC) analysis demonstrated a stronger correlation between deglycosylated PD-L1 and treatment response, with an area under the curve (AUC) of 0.860, compared to 0.648 for non-deglycosylated PD-L1. Incorporating deglycosylation into PD-L1 assessment protocols may improve treatment outcomes for TNBC patients and establish deglycosylated PD-L1 as a more reliable biomarker for ICB therapy response.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		absence of glycosylation on CD274 [biomarker_term_in_review]	200263	not_mapped
BB3817-1	increased level of GlcNAc on KLK3	KLK3	UPKB:Q546G3	protein	prostate cancer	DOID:10283				tissue	UBERON:0000479		PubMed:40635354	Especially Erythrina cristagalli (ECL), succinylated wheat germ (WGAsucc), Griffonia simplicifolia I (GSL I) and Vicia villosa (VVA) lectins showed no or weak staining of PSA in benign samples, while several cancer samples showed strong staining (p < 0.05 for all). Based on the preliminary experiments above we selected three of the lectins showing the most pronounced difference in PSA‐glycoform staining between cancer and adjacent benign tissues, that is, ECL, WGAsucc, and VVA, for PSA‐glycoform stainings in a larger prostate cancer TMA, consisting of cancer and adjacent benign tissue samples from patients with Grade Group 2–4 prostate cancers. Contrary to ECL, strong staining (score 3) of WGAsucc and VVA reactive PSA was undetectable in adjacent benign tissues, while in 5.0% and 6.9% of cancerous tissues strong staining was observed for WGAsucc and VVA reactive PSA, respectively. Weaker staining was observed in some benign samples, but the overall staining of WGAsucc and VVA reactive PSA was strongly associated with cancer as compared to adjacent benign tissues (p < 10−4 and p < 10−8, respectively) (Figure 3). Instead, our results suggest that PSA‐glycoforms that react with succinylated wheat germ lectin (WGAsucc) and Vicia villosa lectin (VVA) are highly enriched in cancerous prostate as compared to adjacent benign prostatic tissue, irrespective of the fact that in benign prostate the total PSA staining was more pronounced. WGAsucc and VVA recognize epitopes with GlcNAc and terminal GalNAc, respectively [30, 46, 47]. However, this is not likely to explain our results with WGAsucc and VVA lectins since, in in situ proximity ligation, those showed much more pronounced staining in cancer as compared to adjacent benign tissue, while opposite was observed for total PSA staining. Our results further prove that glycosylation of PSA is changed in prostate cancer and identify lectins that can be used in conjunction with a PSA‐antibody for the establishment of a serological diagnostic assay selective for cancer‐associated PSA‐glycoforms.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen	change_type:increased;aspect_type:level	Increased level of protein KLK3/UPKB:Q546G3	200264	
BB3818-1	increased level of terminal GalNAc on KLK3	KLK3	UPKB:Q546G3	protein	prostate cancer	DOID:10283				tissue	UBERON:0000479		PubMed:40635354	Especially Erythrina cristagalli (ECL), succinylated wheat germ (WGAsucc), Griffonia simplicifolia I (GSL I) and Vicia villosa (VVA) lectins showed no or weak staining of PSA in benign samples, while several cancer samples showed strong staining (p < 0.05 for all). Based on the preliminary experiments above we selected three of the lectins showing the most pronounced difference in PSA‐glycoform staining between cancer and adjacent benign tissues, that is, ECL, WGAsucc, and VVA, for PSA‐glycoform stainings in a larger prostate cancer TMA, consisting of cancer and adjacent benign tissue samples from patients with Grade Group 2–4 prostate cancers. Contrary to ECL, strong staining (score 3) of WGAsucc and VVA reactive PSA was undetectable in adjacent benign tissues, while in 5.0% and 6.9% of cancerous tissues strong staining was observed for WGAsucc and VVA reactive PSA, respectively. Weaker staining was observed in some benign samples, but the overall staining of WGAsucc and VVA reactive PSA was strongly associated with cancer as compared to adjacent benign tissues (p < 10−4 and p < 10−8, respectively) (Figure 3). Instead, our results suggest that PSA‐glycoforms that react with succinylated wheat germ lectin (WGAsucc) and Vicia villosa lectin (VVA) are highly enriched in cancerous prostate as compared to adjacent benign prostatic tissue, irrespective of the fact that in benign prostate the total PSA staining was more pronounced. WGAsucc and VVA recognize epitopes with GlcNAc and terminal GalNAc, respectively [30, 46, 47]. However, this is not likely to explain our results with WGAsucc and VVA lectins since, in in situ proximity ligation, those showed much more pronounced staining in cancer as compared to adjacent benign tissue, while opposite was observed for total PSA staining. Our results further prove that glycosylation of PSA is changed in prostate cancer and identify lectins that can be used in conjunction with a PSA‐antibody for the establishment of a serological diagnostic assay selective for cancer‐associated PSA‐glycoforms.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		increased level of terminal GalNAc on KLK3 [biomarker_term_in_review]	200265	not_mapped
BB3819-1	β-glucans associated with immunoglobulin M	Immunoglobulin J chain	UPKB:P01591	protein	candidiasis	DOID:1508				blood serum	UBERON:0001977		PubMed:40996794	IgM antibodies directed toward β-glucans were observed shortly after infection, and after a longer time of infection, IgM and IgG antibodies that preferentially recognize mannans.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		β-glucans associated with immunoglobulin M [biomarker_term_in_review]	200266	not_mapped
BB3820-1	β-glucans associated with immunoglobulin M	Immunoglobulin J chain	UPKB:P01592	protein	candidiasis	DOID:1508				blood serum	UBERON:0001977		PubMed:40996794	IgM antibodies directed toward β-glucans were observed shortly after infection, and after a longer time of infection, IgM and IgG antibodies that preferentially recognize mannans.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		β-glucans associated with immunoglobulin M [biomarker_term_in_review]	200267	not_mapped
BB3821-1	mannans associated with immunoglobulin M	Immunoglobulin J chain	UPKB:P01591	protein	candidiasis	DOID:1508				blood serum	UBERON:0001977		PubMed:40996794	IgM antibodies directed toward β-glucans were observed shortly after infection, and after a longer time of infection, IgM and IgG antibodies that preferentially recognize mannans.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		mannans associated with immunoglobulin M [biomarker_term_in_review]	200268	not_mapped
BB3822-1	mannans associated with immunoglobulin M	Immunoglobulin J chain	UPKB:P01592	protein	candidiasis	DOID:1508				blood serum	UBERON:0001977		PubMed:40996794	IgM antibodies directed toward β-glucans were observed shortly after infection, and after a longer time of infection, IgM and IgG antibodies that preferentially recognize mannans.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		mannans associated with immunoglobulin M [biomarker_term_in_review]	200269	not_mapped
BB3823-1	decreased level of agalactosylated glycan on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	cystinosis	DOID:1064				blood serum	UBERON:0001977		PubMed:40843950	Interestingly, all agalactosylated glycan species (structures lacking galactose, e.g. A2, also called G0) are decreased in the NC cohort (boxplots in Fig. 3C and linear regression 4D, GP1-GP4). The glycan peak GP3 containing the most abundant agalactosylated glycan, FA2, displayed different abundances between the two NC status at a 10% significance level (P = 0.092). For IgG N-glycosylation, the NC status neared significance for several glycan peaks and traits, most notably those associated with the absence of galactosylation (G0).	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		decreased level of agalactosylated glycan on immunoglobulin G [biomarker_term_in_review]	200270	not_mapped
BB3824-1	decreased level of FA2 on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	cystinosis	DOID:1064				blood serum	UBERON:0001977		PubMed:40843950	The glycan peak GP3 containing the most abundant agalactosylated glycan, FA2, displayed different abundances between the two NC status at a 10% significance level (P = 0.092). For IgG N-glycosylation, the NC status neared significance for several glycan peaks and traits, most notably those associated with the absence of galactosylation (G0).	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		decreased level of FA2 on immunoglobulin G [biomarker_term_in_review]	200271	not_mapped
BB3825-1	increased level of galactosylated glycans on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	cystinosis	DOID:1064				blood serum	UBERON:0001977		PubMed:40843950	Additionally, the galactosylated glycans (Gal, P = 0.059) and individual GPs associated with galactosylation (GP10 (P = 0.057), GP13 (P = 0.081), and GP16 (P = 0.081)) are all only partially statistically relevant. For IgG N-glycosylation, the NC status neared significance for several glycan peaks and traits, most notably those associated with the absence of galactosylation (G0).	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		increased level of galactosylated glycans on immunoglobulin G [biomarker_term_in_review]	200272	not_mapped
BB3826-1	increased level of Tn-MUC1 on MUC1	Mucin-1	UPKB:P15941	protein	salivary gland carcinoma	DOID:0050904				tissue	UBERON:0000479		PubMed:40844495	We determined the expression of the transmembrane glycoprotein mucin 1 with Tn antigen (GalNAc), Tn‐MUC1, using 20 clinical SDC specimens. GalNAc, to which VVL binds, formed Tn‐MUC1 via glycosylation with N‐acetylgalactosaminyltransferases (GALNTs). GALNT7 was highly expressed in SDC. Analysis of clinical SDC specimens revealed that Tn‐MUC1 was also positive in the SDC tumor cells, suggesting its potential as a cell surface target for SDC. Notably, GalNAc and fucose were detected only in malignant tumors, suggesting their potential as malignant tumor cell surface markers (Figure 1C). VVL was strongly stained in SDC (Figure 2A). VVL was more positive in malignant tumors than in benign tumors, particularly SDC (Figure 2). Notably, VVL was specifically positive in SDC tumor cells but negative in vascular endothelial cells in SDC tumor tissue, suggesting its mutually exclusive expression (Figure 2C,D). GALNT7 was highly expressed in SDC (Figure 3A). These data indicate that GALNT7 influences O‐glycosylation in SDC more than the other GALNT family genes (Figure 3B). To validate the high expression of GALNT7 at the protein level in SDC, we performed immunohistochemistry on 24 FFPE SDC samples using a GALNT7‐specific antibody. Out of 24 SDC cases, 12 cases (50%) showed strong positive (3+) staining, 6 cases (25%) showed moderate positive (2+) staining, 5 cases (20.8%) showed weak positive (1+) staining, and only 1 case (4.2%) showed negative (0) staining for GALNT7 (Figure 3D). These results demonstrate that GALNT7 is frequently and highly expressed at the protein level in SDC, consistent with our mRNA expression data. This finding further supports the notion that GALNT7 plays a significant role in O‐glycosylation and potentially in Tn‐MUC1 formation in SDC. Based on the fact that VVL lectin staining specifically recognizes Tn‐MUC1, Tn‐MUC1 and VVL lectin expression were evaluated using clinical specimens from 20 SDC cases. Notably, in all cases, Tn‐MUC1 and VVL were positive only in the same tumor regions. VVL and Tn‐MUC1 were strongly positive, as in case 12, and weakly positive, as in case 6 (Figure 4B). These data suggest that VVL expression is a surrogate of Tn‐MUC1 expression in SDC tumors. In other words, Tn‐MUC1 may be positive even in HER2‐negative SDC (Figure 4D). Thus, Tn‐MUC1 may be a therapeutic target for HER2‐negative SDC. In general, Tn‐MUC1 expression is associated with poor prognosis and high malignancy. This study revealed that Tn‐MUC1 was expressed in SDC tumor cells, suggesting its potential as a new diagnostic marker for SDC. Tn‐MUC1, which is formed by GalNAc specifically bound to VVL, was also highly expressed in SDC. In addition, it was suggested that GALNT7 is involved in the formation of Tn‐MUC1 in SDC. These results suggest that Tn‐MUC1 may be a novel potential marker for the diagnosis of SDC.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen	change_type:increased;aspect_type:level	Increased level of protein MUC1/UPKB:P15941	200273	
BB3827-1	decreased level of galactosylation on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	lung non-small cell carcinoma	DOID:3908				blood serum	UBERON:0001977		PubMed:40680951	Compared with controls, NSCLC patients exhibited distinct IgG glycosylation patterns, including decreased galactosylation, monosialylation, and bisecting N-acetylglucosamine, alongside increased agalactosylation. The lectin-based assay confirmed the reductions in IgG galactosylation and sialylation.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		decreased level of galactosylation on immunoglobulin G [biomarker_term_in_review]	200274	not_mapped
BB3828-1	decreased level of monosialylation on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	lung non-small cell carcinoma	DOID:3908				blood serum	UBERON:0001977		PubMed:40680951	Compared with controls, NSCLC patients exhibited distinct IgG glycosylation patterns, including decreased galactosylation, monosialylation, and bisecting N-acetylglucosamine, alongside increased agalactosylation. The lectin-based assay confirmed the reductions in IgG galactosylation and sialylation.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		decreased level of monosialylation on immunoglobulin G [biomarker_term_in_review]	200275	not_mapped
BB3829-1	decreased level of bisecting N-acetylglucosamine on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	lung non-small cell carcinoma	DOID:3908				blood serum	UBERON:0001977		PubMed:40680951	Compared with controls, NSCLC patients exhibited distinct IgG glycosylation patterns, including decreased galactosylation, monosialylation, and bisecting N-acetylglucosamine, alongside increased agalactosylation.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		decreased level of bisecting N-acetylglucosamine on immunoglobulin G [biomarker_term_in_review]	200276	not_mapped
BB3830-1	increased level of agalactosylation on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	lung non-small cell carcinoma	DOID:3908				blood serum	UBERON:0001977		PubMed:40680951	Compared with controls, NSCLC patients exhibited distinct IgG glycosylation patterns, including decreased galactosylation, monosialylation, and bisecting N-acetylglucosamine, alongside increased agalactosylation.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		increased level of agalactosylation on immunoglobulin G [biomarker_term_in_review]	200277	not_mapped
BB3831-1	decreased level of sialylation on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	lung non-small cell carcinoma	DOID:3908				blood serum	UBERON:0001977		PubMed:40680951	The lectin-based assay confirmed the reductions in IgG galactosylation and sialylation.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		decreased level of sialylation on immunoglobulin G [biomarker_term_in_review]	200278	not_mapped
BB3832-1	decreased level of FS1/FS2 ratio on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	lung non-small cell carcinoma	DOID:3908				blood serum	UBERON:0001977		PubMed:40680951	MR analysis further revealed an inverse association between the IgG FS1/FS2 ratio and NSCLC risk.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		decreased level of FS1/FS2 ratio on immunoglobulin G [biomarker_term_in_review]	200279	not_mapped
BB3833-1	fucosylated IgG associated with immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	COVID-19	DOID:0080600				cerebrospinal fluid	UBERON:0001359		PubMed:40157461	Fucosylated IgG were associated with Spike IgG, CSF protein, and soluble CD14, whereas afucosylated bisecting IgG were inversely correlated with Spike IgG.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		fucosylated IgG associated with immunoglobulin G [biomarker_term_in_review]	200280	not_mapped
BB3834-1	afucosylated bisecting IgG associated with immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	COVID-19	DOID:0080600				cerebrospinal fluid	UBERON:0001359		PubMed:40157461	Fucosylated IgG were associated with Spike IgG, CSF protein, and soluble CD14, whereas afucosylated bisecting IgG were inversely correlated with Spike IgG.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		afucosylated bisecting IgG associated with immunoglobulin G [biomarker_term_in_review]	200281	not_mapped
BB3835-1	sialic acid containing IgG associated with immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	COVID-19	DOID:0080600				cerebrospinal fluid	UBERON:0001359		PubMed:40157461	Sialic acid containing IgG were positively correlated with IL1β and TNFα.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		sialic acid containing IgG associated with immunoglobulin G [biomarker_term_in_review]	200282	not_mapped
BB3836-1	agalactosylated fucosylated IgG (G0F) associated with immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	COVID-19	DOID:0080600				cerebrospinal fluid	UBERON:0001359		PubMed:40157461	Inflammatory agalactosylated fucosylated IgG (G0F) were associated with infiltrating CD4 + T cells in the brains of COVID-19 donors.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		agalactosylated fucosylated IgG (G0F) associated with immunoglobulin G [biomarker_term_in_review]	200283	not_mapped
BB3826-2	increased level of TnMUC1 on MUC1	Mucin-1	UPKB:P15941	protein	lung non-small cell carcinoma	DOID:3908				tissue	UBERON:0000479		PubMed:40562040	EGFR TKI exposure resulted in a more than 2-fold increase in TnMUC1 cell surface expression compared with untreated controls (Figures 3O, S7D, and S7E). Quantitative IHC scoring revealed a 3-fold elevation in TnMUC1 protein levels following EGFR TKI administration (Figures 3P, 3Q, S4D, and S4E). IHC analysis of the subcutaneous tumors revealed that both itraconazole and osimertinib downregulated C1GALT1 expression and upregulated TnMUC1 expression.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen	change_type:increased;aspect_type:level	Increased level of protein MUC1/UPKB:P15941	200284	
BB3837-1	increased level of TnMUC1 on MUC1	Mucin-1	UPKB:Q02496	protein	lung non-small cell carcinoma	DOID:3908				tissue	UBERON:0000479		PubMed:40562040	We further confirmed this upregulation in vivo through IHC analysis of tumor bulks. Quantitative IHC scoring revealed a 3-fold elevation in TnMUC1 protein levels following EGFR TKI administration (Figures 3P, 3Q, S4D, and S4E). The observed TnMUC1 induction demonstrated model-independent consistency, which manifested in both CDXs and preclinical PDXs.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen	change_type:increased;aspect_type:level	Increased level of protein mucin-1/UPKB:Q02496	200285	
BB3837-1	increased level of TnMUC1 on MUC1	Mucin-1	UPKB:Q02496	protein	lung non-small cell carcinoma	DOID:3908				tissue	UBERON:0000479		PubMed:40562040	Notably, the combination therapy induced near-complete tumor regression, demonstrating its superior antitumor activity (Figures S4B and S4C). Quantitative IHC scoring revealed a 3-fold elevation in TnMUC1 protein levels following EGFR TKI administration (Figures 3P, 3Q, S4D, and S4E).	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen	change_type:increased;aspect_type:level	Increased level of protein mucin-1/UPKB:Q02496	200285	
BB3837-1	increased level of TnMUC1 on MUC1	Mucin-1	UPKB:Q02496	protein	lung non-small cell carcinoma	DOID:3908				tissue	UBERON:0000479		PubMed:40562040	IHC analysis of the subcutaneous tumors revealed that both itraconazole and osimertinib downregulated C1GALT1 expression and upregulated TnMUC1 expression. We observed the most pronounced effect in the combination treatment group (Figures 6N and 6O).	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen	change_type:increased;aspect_type:level	Increased level of protein mucin-1/UPKB:Q02496	200285	
BB3837-1	increased level of TnMUC1 on MUC1	Mucin-1	UPKB:Q02496	protein	lung non-small cell carcinoma	DOID:3908				tissue	UBERON:0000479		PubMed:40562040	We observed the most pronounced effect in the combination treatment group (Figures 6N and 6O).	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen	change_type:increased;aspect_type:level	Increased level of protein mucin-1/UPKB:Q02496	200285	
BB3838-1	increased level of MUCST on MUC1	Mucin-1	UPKB:P15941	protein	luminal breast carcinoma A	DOID:0060548				breast epithelium	UBERON:0008367		PubMed:40492697	The results for core 2, and the four sialylated epitopes (Table 1a, Table S6) show a significant upregulation in MUC6St and MUCdST concentrations and smaller upregulation in MUCST concentration at 80 h. This indicates a clear shift towards tumour-associated core 1-glycan biosynthesis in luminal A breast cancer compared to MUC1 in healthy breast epithelial tissue. The network demonstrates a 32% upregulation of MUCST, which, albeit significant, is smaller than the values for the MUC6ST and MUCdST, ranging between 55%–70%. This can be attributed to the simultaneous overexpression of ST3GAL1 and ST6GALNAC2. Although the increased ST3GAL1 activity brings about an enhanced rate in MUCST synthesis, this is counteracted by the increased enzyme activity of ST6GALNAC2 partaking in two reactions. The first reaction, denoted by ST6GALNAC2_a catalyses the α2,6 sialylation of the MUC1 T-antigen GalNAc residue, thereby limiting the amount of MUC1 T-antigen available for α-2,3-Sialylation at the Gal residue. The second reaction, denoted by ST6GALNAC2_b, catalyses the α2,6 sialylation of the GalNAc residue on MUCST, hence resulting in MUCST consumption. Nevertheless, a 32% upregulation of MUCST in luminal A breast cancer is substantial enough to investigate the influence of increased MUCST binding on the CXCL5 synthesis pathway in monocyte-derived macrophages.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen	change_type:increased;aspect_type:level	Increased level of MUCST on protein MUC1/UPKB:P15941	200286	
BB3839-1	increased level of core 1-glycan on MUC1	Mucin-1	UPKB:P15941	protein	luminal breast carcinoma A	DOID:0060548				breast epithelium	UBERON:0008367		PubMed:40492697	This indicates a clear shift towards tumour-associated core 1-glycan biosynthesis in luminal A breast cancer compared to MUC1 in healthy breast epithelial tissue.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		increased level of core 1-glycan on MUC1 [biomarker_term_in_review]	200287	not_mapped
BB3840-1	decreased level of MUCST on MUC1	Mucin-1	UPKB:P15941	protein	luminal breast carcinoma A	DOID:0060548				breast epithelium	UBERON:0008367		PubMed:40492697	The effects of 10 μM Soyasaponin introduction on the TCGA-based luminal A network (Table 2a, Tables S9-S11) results in a 26.6% decrease in MUCST. The largest change is observed for MUCST in line with the expectations since the drug primarily targets ST3Gal1, the enzyme catalysing MUCST production. The substantial decrease in MUCST leads to an associated decrease in MUCdST by 20.7%.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		decreased level of MUCST on MUC1 [biomarker_term_in_review]	200288	not_mapped
BB3841-1	increased level of MUCT on MUC1	Mucin-1	UPKB:P15941	protein	luminal breast carcinoma A	DOID:0060548				breast epithelium	UBERON:0008367		PubMed:40492697	In addition, there is an increase of 2.2% in MUCT levels at t = 80 h is observed, despite the inhibitor tangentially acting on C1GALT1 due to a weak binding affinity of the inhibitor to the enzyme.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen	change_type:increased;aspect_type:level	Increased level of MUCT on protein MUC1/UPKB:P15941	200289	
BB3842-1	increased level of core 2 on MUC1	Mucin-1	UPKB:P15941	protein	luminal breast carcinoma A	DOID:0060548				breast epithelium	UBERON:0008367		PubMed:40492697	Furthermore, increases below 2% do occur with other core structures, such as core 2, MUC6ST, and MUCTGlcNAc.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		increased level of core 2 on MUC1 [biomarker_term_in_review]	200290	not_mapped
BB3843-1	increased level of fucosylated N-glycan on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	antisynthetase syndrome	DOID:0080744				blood plasma	UBERON:0001969		PubMed:40607430	Notably, we observed increased fucosylation (p<0.0001) and decreased N-acetylneuraminic acid (p<0.05) in ASS patients. As shown in Figure 2 , in comparison with those in HCs, 2 N-glycans were increased ( Figures 2A, B ) and 7 were decreased ( Figures 2C-I ) among patients with ASS. In addition, we selected N-glycans containing F (fucose) and A (N-acetylneuraminic acid) from the 11 highly reliable and reproducible N-glycans, added them and found that fucose was significantly increased, whereas N-acetylneuraminic acid was significantly decreased in ASS patients ( Figure 3 ). In contrast to previous findings that afucosylation promotes inflammation in in-vitro models, some studies have reported an increase in fucosylation among JO-1+ myositis patients (25), SLE patients (32) and RA patients (33), which is consistent with our study. Moreover, studies have reported elevated fucosylation levels in JO-1 positive patients compared with both healthy controls and JO-1 negative patients (25), a finding that aligns with our own study. Notable disease-specific changes included elevated fucosylation (p<0.0001) and reduced N-acetylneuraminic acid (p<0.05).	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		increased level of fucosylated N-glycan on immunoglobulin G [biomarker_term_in_review]	200291	not_mapped
BB3844-1	decreased level of N-acetylneuraminic acid on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	antisynthetase syndrome	DOID:0080744				blood plasma	UBERON:0001969		PubMed:40607430	Notably, we observed increased fucosylation (p<0.0001) and decreased N-acetylneuraminic acid (p<0.05) in ASS patients. In addition, we selected N-glycans containing F (fucose) and A (N-acetylneuraminic acid) from the 11 highly reliable and reproducible N-glycans, added them and found that fucose was significantly increased, whereas N-acetylneuraminic acid was significantly decreased in ASS patients ( Figure 3 ). Our study also revealed a reduction in sialylation among ASS patients, which is in line with findings from other studies on autoimmune diseases (14, 15). Notable disease-specific changes included elevated fucosylation (p<0.0001) and reduced N-acetylneuraminic acid (p<0.05).	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		decreased level of N-acetylneuraminic acid on immunoglobulin G [biomarker_term_in_review]	200292	not_mapped
BB3845-1	decreased level of sialylated IgG on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	antisynthetase syndrome	DOID:0080744				blood plasma	UBERON:0001969		PubMed:40607430	Our study also revealed a reduction in sialylation among ASS patients, which is in line with findings from other studies on autoimmune diseases (14, 15).	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		decreased level of sialylated IgG on immunoglobulin G [biomarker_term_in_review]	200293	not_mapped
BB3846-1	increased level of N-glycolylneuraminic acid on MUC1	Mucin-1	UPKB:P15941	protein	breast cancer	DOID:1612				blood serum	UBERON:0001977		PubMed:40148706	A genetically engineered lectin (SubB2M) that specifically binds N-glycolylneuraminic acid (Neu5Gc) was used as a detection reagent in a CA15-3 capture antibody-lectin sandwich (neuCA15-3) assay. Classification accuracy and AUC for neuCA15-3 were 81% and 0.886 ± 0.015 (standard error, n = 567) and for Elecsys CA15-3 II, 55% and 0.642 ± 0.023 (n = 558), respectively. At a threshold cut-off serum concentration of 23.6 units/ml, overall breast cancer classification accuracy of the neuCA15-3 was 81% (compared to 55% for the comparator assay, p < 0.001). The diagnostic performance of neuCA15-3 was substantially improved by specifically targeting both a CA15-3 protein epitope and a pan-cancer glycan (Neu5Gc) epitope (the specific binding target of SubB2M). The reporter signal generated depends on the colocalization of the cancer antigen protein epitope and the aberrant sialylation of the protein, thus increasing the assay specificity. The presence of multiple Neu5Gc lectin-binding sites per glycoprotein molecule increases signal generation and assay sensitivity.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		increased level of N-glycolylneuraminic acid on MUC1 [biomarker_term_in_review]	200294	not_mapped
BB3847-1	increased level of Neu5Gc on MUC1	Mucin-1	UPKB:P15941	protein	breast cancer	DOID:1612				blood serum	UBERON:0001977		PubMed:40148706	A genetically engineered lectin (SubB2M) that specifically binds N-glycolylneuraminic acid (Neu5Gc) was used as a detection reagent in a CA15-3 capture antibody-lectin sandwich (neuCA15-3) assay. Classification accuracy and AUC for neuCA15-3 were 81% and 0.886 ± 0.015 (standard error, n = 567) and for Elecsys CA15-3 II, 55% and 0.642 ± 0.023 (n = 558), respectively. At a threshold cut-off serum concentration of 23.6 units/ml, overall breast cancer classification accuracy of the neuCA15-3 was 81% (compared to 55% for the comparator assay, p < 0.001). The diagnostic performance of neuCA15-3 was substantially improved by specifically targeting both a CA15-3 protein epitope and a pan-cancer glycan (Neu5Gc) epitope (the specific binding target of SubB2M). The reporter signal generated depends on the colocalization of the cancer antigen protein epitope and the aberrant sialylation of the protein, thus increasing the assay specificity. The presence of multiple Neu5Gc lectin-binding sites per glycoprotein molecule increases signal generation and assay sensitivity.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen	change_type:increased;aspect_type:level	Increased level of Neu5Gc on protein MUC1/UPKB:P15941	200295	
BB3848-1	decreased level of 6-O-su-Le^c on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	ovarian cancer	DOID:2394				blood serum	UBERON:0001977		PubMed:39947417	Blood serum samples from patients (n = 203) with ovarian cancer (OvaCan) and healthy volunteers were analyzed using a glycan microarray containing 63 immobilized glycans to determine changes in anti-glycan IgG and IgM antibody profiles in OvaCan. Levels of anti-glycan IgG and IgM antibodies in OvaCan statistically differed from levels in healthy donors: the most prominent statistically significant difference for anti-glycan IgG antibodies was found for 6-O-su-Le<sup>c</sup> (AUC = 0.657, Se = 48.0 %, and Sp = 73.3 %).	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		decreased level of 6-O-su-Le^c on immunoglobulin G [biomarker_term_in_review]	200296	not_mapped
BB3849-1	decreased level of Le^y on immunoglobulin M	B-cell antigen receptor complex-associated protein beta chain	UPKB:P40259	protein	ovarian cancer	DOID:2394				blood serum	UBERON:0001977		PubMed:39947417	Blood serum samples from patients (n = 203) with ovarian cancer (OvaCan) and healthy volunteers were analyzed using a glycan microarray containing 63 immobilized glycans to determine changes in anti-glycan IgG and IgM antibody profiles in OvaCan. The AUC values for certain glycans investigated in diagnosing OvaCan indicated a fingerprint consisting of IgM antibodies to specific glycans, and the most specific anti-glycan IgM antibodies were Le<sup>y</sup> (AUC = 0.625, Se = 98.0 % and Sp = 45.0 %).	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		decreased level of Le^y on immunoglobulin M [biomarker_term_in_review]	200297	not_mapped
BB3850-1	decreased level of digalactosylated on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	echinococcosis	DOID:1496				blood serum	UBERON:0001977		PubMed:40200705	In this work, the galactosylation level of serum IgG was analyzed by Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF-MS) in a cohort comprising patients, including 100 diagnosed with CE, 27 with AE and 29 with HCC. The relative quantification of IgG digalactosylated (G2), monogalactosylated (G1), and agalactosylated (G0) N-glycans with the formula G0/(G1 + G2 × 2) (IgG Gal-ratio) was obtained and found to effectively distinguish between echinococcosis patients, CE and AE patients, and healthy controls, respectively. Thus, the results demonstrate that the IgG Gal-ratio has the potential to be a biomarker for diagnosis and discrimination of echinococcosis, which also needs to be verified in further studies.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		decreased level of digalactosylated on immunoglobulin G [biomarker_term_in_review]	200298	not_mapped
BB3851-1	increased level of agalactosylated on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	echinococcosis	DOID:1496				blood serum	UBERON:0001977		PubMed:40200705	In this work, the galactosylation level of serum IgG was analyzed by Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF-MS) in a cohort comprising patients, including 100 diagnosed with CE, 27 with AE and 29 with HCC. The relative quantification of IgG digalactosylated (G2), monogalactosylated (G1), and agalactosylated (G0) N-glycans with the formula G0/(G1 + G2 × 2) (IgG Gal-ratio) was obtained and found to effectively distinguish between echinococcosis patients, CE and AE patients, and healthy controls, respectively. Thus, the results demonstrate that the IgG Gal-ratio has the potential to be a biomarker for diagnosis and discrimination of echinococcosis, which also needs to be verified in further studies.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		increased level of agalactosylated on immunoglobulin G [biomarker_term_in_review]	200299	not_mapped
BB3851-2	increased level of agalactosylated on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	cystic echinococcosis	DOID:1495				blood serum	UBERON:0001977		PubMed:40200705	The relative quantification of IgG digalactosylated (G2), monogalactosylated (G1), and agalactosylated (G0) N-glycans with the formula G0/(G1 + G2 × 2) (IgG Gal-ratio) was obtained and found to effectively distinguish between echinococcosis patients, CE and AE patients, and healthy controls, respectively. Meanwhile, the IgG Gal-ratio was evidently related to different types of CE (from CE1 to CE5) and the follow-up CE disease progress.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		increased level of agalactosylated on immunoglobulin G [biomarker_term_in_review]	200300	not_mapped
BB3851-3	increased level of agalactosylated on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	alveolar echinococcosis	DOID:12148				blood serum	UBERON:0001977		PubMed:40200705	The relative quantification of IgG digalactosylated (G2), monogalactosylated (G1), and agalactosylated (G0) N-glycans with the formula G0/(G1 + G2 × 2) (IgG Gal-ratio) was obtained and found to effectively distinguish between echinococcosis patients, CE and AE patients, and healthy controls, respectively. Furthermore, the IgG Gal-ratio shows the potential differential diagnosis of AE and HCC.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		increased level of agalactosylated on immunoglobulin G [biomarker_term_in_review]	200301	not_mapped
BB3852-1	increased level of H3N2 on CEACAM5	Carcinoembryonic antigen-related cell adhesion molecule 5	UPKB:P06731	protein	lung adenocarcinoma	DOID:3910				tissue	UBERON:0000479		PubMed:40175289	For example, the increase of N197/553 H3N2 and H5N2 on CEAM5 in tumor regions can be partially due to the overexpression of CEAM5 itself; on the other hand, the decrease of IQGA1 N1449 F1H5N4S1 is likely affected only by N-glycosylation events. 50 In our results, CEAM5 was highly (more than 10 times higher) and CEAM6 was moderately overexpressed in tumor tissue, while we also found changes in the abundance of 3 N-glycopeptides. For CEAM5 N-glycopeptides, the large increase in abundance is likely due to the increase in glycoprotein expression, but for CEAM6 N197 H5N2 the increase in N-glycopeptide abundance is much greater than for the glycoprotein.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen	change_type:increased;aspect_type:level	Increased level of H3N2 on protein CEACAM5/UPKB:P06731	200302	
BB3853-1	increased level of H5N2 on CEACAM5	Carcinoembryonic antigen-related cell adhesion molecule 5	UPKB:P06731	protein	lung adenocarcinoma	DOID:3910				tissue	UBERON:0000479		PubMed:40175289	For example, the increase of N197/553 H3N2 and H5N2 on CEAM5 in tumor regions can be partially due to the overexpression of CEAM5 itself; on the other hand, the decrease of IQGA1 N1449 F1H5N4S1 is likely affected only by N-glycosylation events. 50 In our results, CEAM5 was highly (more than 10 times higher) and CEAM6 was moderately overexpressed in tumor tissue, while we also found changes in the abundance of 3 N-glycopeptides. For CEAM5 N-glycopeptides, the large increase in abundance is likely due to the increase in glycoprotein expression, but for CEAM6 N197 H5N2 the increase in N-glycopeptide abundance is much greater than for the glycoprotein. For example, it has been reported that targeting high-mannose-type glycans in the glycocalyx with lectibodies shows anticancer activity, and in our data set, we found the N190 H5N2 peptide of CEAM6, a glycoprotein known to be located in the apical plasma membrane, elevated in tumor tissue. This suggests differential N-glycosylation with potential functional consequences, especially as the increase of high-mannose-type glycans have been previously linked to cancers and specifically targeting them in the glycocalyx with lectibodies showed anticancer activity and a potential druggable target.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen	change_type:increased;aspect_type:level	Increased level of H5N2 on protein CEACAM5/UPKB:P06731	200303	
BB3854-1	decreased level of F1H5N4S1 on IQGAP1	Ras GTPase-activating-like protein IQGAP1	UPKB:P46940	protein	lung adenocarcinoma	DOID:3910				tissue	UBERON:0000479		PubMed:40175289	For example, the increase of N197/553 H3N2 and H5N2 on CEAM5 in tumor regions can be partially due to the overexpression of CEAM5 itself; on the other hand, the decrease of IQGA1 N1449 F1H5N4S1 is likely affected only by N-glycosylation events. 57 We have not detected changes in IQGA1 expression, but we have found that the abundance of the N-glycopeptide N1449 F1H5N4S1 decreased substantially in TWT LUAD. Additionally, the novel glycosylation site of IQGAP1 protein (N1449) where a decrease in glycopeptide abundance was observed is also interesting as a possible intervention point as this glycoprotein can be linked with sustained proliferative signaling, an important hallmark of cancer. We confirmed and detected changes in glycosylation on previously unconfirmed N-glycosylation sites, for example the substantial decrease of the N-glycopeptide N1449 F1H5N4S1 of IQGA1, a glycoprotein with high oncogenic potential.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		decreased level of F1H5N4S1 on IQGAP1 [biomarker_term_in_review]	200304	not_mapped
BB3855-1	decreased level of H5N4S1 on HP (Haptoglobin)	HP (Haptoglobin)	UPKB:Q6NSB4	protein	lung adenocarcinoma	DOID:3910				tissue	UBERON:0000479		PubMed:40175289	53 In our study, HPT was underexpressed in TWT LUAD, and we also identified decreased levels of H5N4S1 on the N184 N-glycosylation site that is reported to carry complex type glycans54 in line with our results.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		decreased level of H5N4S1 on HP (Haptoglobin) [biomarker_term_in_review]	200305	not_mapped
BB3856-1	increased level of high-mannose-type glycans on CEACAM6	Cell adhesion molecule CEACAM6	UPKB:P40199	protein	lung adenocarcinoma	DOID:3910				tissue	UBERON:0000479		PubMed:40175289	This suggests differential N-glycosylation with potential functional consequences, especially as the increase of high-mannose-type glycans have been previously linked to cancers and specifically targeting them in the glycocalyx with lectibodies showed anticancer activity and a potential druggable target. For example, it has been reported that targeting high-mannose-type glycans in the glycocalyx with lectibodies shows anticancer activity, and in our data set, we found the N190 H5N2 peptide of CEAM6, a glycoprotein known to be located in the apical plasma membrane, elevated in tumor tissue.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		increased level of high-mannose-type glycans on CEACAM6 [biomarker_term_in_review]	200306	not_mapped
BB3857-1	sialylated HPT associated with HP (Haptoglobin)	HP (Haptoglobin)	UPKB:Q6NSB4	protein	lung cancer	DOID:1324				blood serum	UBERON:0001977		PubMed:40175289	Haptoglobin (HPT) has been suggested as a serum marker for lung cancer in combination with other proteins,52 and HPT N-glycoforms, specifically sialylated and fucosylated HPT were also identified as potential lung cancer markers.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		sialylated HPT associated with HP (Haptoglobin) [biomarker_term_in_review]	200307	not_mapped
BB3858-1	fucosylated HPT associated with HP (Haptoglobin)	HP (Haptoglobin)	UPKB:Q6NSB4	protein	lung cancer	DOID:1324				blood serum	UBERON:0001977		PubMed:40175289	Haptoglobin (HPT) has been suggested as a serum marker for lung cancer in combination with other proteins,52 and HPT N-glycoforms, specifically sialylated and fucosylated HPT were also identified as potential lung cancer markers.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		fucosylated HPT associated with HP (Haptoglobin) [biomarker_term_in_review]	200308	not_mapped
BB3859-1	increased level of fucosylation on ITGA2	ITGA2	UPKB:L0R6I3	protein	head and neck squamous cell carcinoma	DOID:5520				tissue	UBERON:0000479		PubMed:40287842	In accordance, we observed high expression of fucosylated ITGA3, ITGA6, and ITGB4 recognized by UEA lectin in cell lines and in sera of HNSCC patients, whereas in tissue samples, high fucosylation was restricted to three of the six investigated ITGs, namely, ITGA2, ITGA3, and ITGB1.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen	change_type:increased;aspect_type:level	Increased level of fucosylation on protein ITGA2/UPKB:L0R6I3	200309	
BB3860-1	increased level of fucosylation on ITGA3	ITGA3	UPKB:Q86SW1	protein	head and neck squamous cell carcinoma	DOID:5520				blood serum	UBERON:0001977		PubMed:40287842	In accordance, we observed high expression of fucosylated ITGA3, ITGA6, and ITGB4 recognized by UEA lectin in cell lines and in sera of HNSCC patients, whereas in tissue samples, high fucosylation was restricted to three of the six investigated ITGs, namely, ITGA2, ITGA3, and ITGB1.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen	change_type:increased;aspect_type:level	Increased level of protein iTGA3/UPKB:Q86SW1	200310	
BB3861-1	increased level of GalNAc–glycan structure on ITGA3	ITGA3	UPKB:Q86SW1	protein	head and neck squamous cell carcinoma	DOID:5520				tissue	UBERON:0000479		PubMed:40287842	The largest effect sizes were estimated in ITGA6–ConA (γ = 1.09; 95% CI 0.49 to 1.67, p < 0.001) and ITGA3–WFL (γ = 0.98; 95% CI 0.40 to 1.53, p < 0.001) assays (Table S1). In ROC analysis, especially ITGA3–WFL demonstrated remarkable performance in discriminating between tumor and normal tissues (Figure 2B). Remarkable differences between normal and tumor tissues in GalNAc‐specific WFL assays were observed in ITGA3 and ITGB1. While the signal differences of the WFL assays between normal and tumor tissues were relatively low as compared to other lectin assays, suggesting only minor changes in GalNAc structures of these six ITGs, the ITGA3–WFL assay resulted in high discrimination between tumor and normal tissues.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		increased level of GalNAc–glycan structure on ITGA3 [biomarker_term_in_review]	200311	not_mapped
BB3862-1	increased level of mannose on ITGA2	ITGA2	UPKB:L0R6I3	protein	head and neck squamous cell carcinoma	DOID:5520				tissue	UBERON:0000479		PubMed:40287842	Mannose‐binding ConA assays yielded high S/B ratios with ITGA2, ITGB1, and ITGB4.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen	change_type:increased;aspect_type:level	Increased level of mannose on protein ITGA2/UPKB:L0R6I3	200312	
BB3863-1	decreased level of fucosylation on ITGA2	ITGA2	UPKB:L0R6I3	protein	head and neck squamous cell carcinoma	DOID:5520				blood serum	UBERON:0001977		PubMed:40287842	However, interestingly, low signal levels in two lectin assays from serum, namely, ITGA2–UEA and ITGB4–MAA, were significantly associated with both tumor recurrence and poor radiotherapy response in ROC analysis as well (Figure 4D). In the present study, low signal levels of ITGA2–UEA and ITGB4–MAA assays from serum were significantly associated with both tumor recurrence and negative radiotherapy response. Therefore, ITGA2–UEA is suggested to be a potential predictive biomarker for HNSCC radiotherapy response and tumor recurrence, but naturally, further studies including validation by functional analysis would be needed to confirm its role as a biomarker.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		decreased level of fucosylation on ITGA2 [biomarker_term_in_review]	200313	not_mapped
BB3864-1	decreased level of G1F on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	background diabetic retinopathy	DOID:13208				blood serum	UBERON:0001977		PubMed:40204274	Significant differences in 9 DSIgG N-glycopeptide ratios (DSIgG1: G1F/G0F, G1FN/G0FN, G2F/G0F, G2F/G1F; DSIgG2: G1F/G0F, G1FN/G0FN, G2/G1, G2F/G0F, G2F/G1F) were found between NDR, NPDR and PDR groups and are displayed in Figure 2. Eight glycopeptide ratios (DSIgG1: G1F/G0F, G1FN/G0FN, G2F/G0F; DSIgG2: G1F/G0F, G1FN/G0FN, G2/G1, G2F/G0F, G2F/G1F) were found to be significantly different between NDR and NPDR groups. Six glycopeptide ratios (DSIgG1: G1F/G0F, G2F/G0F; DSIgG2: G1F/G0F, G2/G1, G2F/G0F, G2F/G1F) were found to be significantly different between NDR and PDR groups. It was found that patients with NDR have the highest tendency of galactosylation, while patients with NPDR have the lowest. Patients with severe NPDR have a lower tendency of galactosylation and a higher tendency for fucosylation, demonstrating that patients with severe NPDR manifest a higher status of inflammatory response. Nine DSIgG N-glycopeptide ratios were found to be significantly different among the NDR, NPDR, and PDR groups in this study.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen	change_type:presence of;mod_type:sequence variation	Presence of bmkb_I::G1F sequence variation in protein IGHV4-59/NCBI:	200314	check_entity
BB3865-1	decreased level of G1FN on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	background diabetic retinopathy	DOID:13208				blood serum	UBERON:0001977		PubMed:40204274	Significant differences in 9 DSIgG N-glycopeptide ratios (DSIgG1: G1F/G0F, G1FN/G0FN, G2F/G0F, G2F/G1F; DSIgG2: G1F/G0F, G1FN/G0FN, G2/G1, G2F/G0F, G2F/G1F) were found between NDR, NPDR and PDR groups and are displayed in Figure 2. Eight glycopeptide ratios (DSIgG1: G1F/G0F, G1FN/G0FN, G2F/G0F; DSIgG2: G1F/G0F, G1FN/G0FN, G2/G1, G2F/G0F, G2F/G1F) were found to be significantly different between NDR and NPDR groups. Two glycopeptide ratios (DSIgG1: G1FN/G0FN, G2F/G1F) were found to be significantly different between NPDR and PDR groups. Six glycopeptide ratios (DSIgG1 G1FN/G0FN, G1FN/G1F, G2F/G0F, G2F/G1F; DSIgG2 G1F/G1, G2F/G1F) were found to be significantly different between mild, moderate NPDR patients compared with severe NPDR patients and shown in Figure 3. Nine DSIgG N-glycopeptide ratios were found to be significantly different among the NDR, NPDR, and PDR groups in this study.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		decreased level of G1FN on immunoglobulin G [biomarker_term_in_review]	200315	not_mapped
BB3866-1	increased level of G2F on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	background diabetic retinopathy	DOID:13208				blood serum	UBERON:0001977		PubMed:40204274	Significant differences in 9 DSIgG N-glycopeptide ratios (DSIgG1: G1F/G0F, G1FN/G0FN, G2F/G0F, G2F/G1F; DSIgG2: G1F/G0F, G1FN/G0FN, G2/G1, G2F/G0F, G2F/G1F) were found between NDR, NPDR and PDR groups and are displayed in Figure 2. Eight glycopeptide ratios (DSIgG1: G1F/G0F, G1FN/G0FN, G2F/G0F; DSIgG2: G1F/G0F, G1FN/G0FN, G2/G1, G2F/G0F, G2F/G1F) were found to be significantly different between NDR and NPDR groups. Six glycopeptide ratios (DSIgG1: G1F/G0F, G2F/G0F; DSIgG2: G1F/G0F, G2/G1, G2F/G0F, G2F/G1F) were found to be significantly different between NDR and PDR groups. Six glycopeptide ratios (DSIgG1 G1FN/G0FN, G1FN/G1F, G2F/G0F, G2F/G1F; DSIgG2 G1F/G1, G2F/G1F) were found to be significantly different between mild, moderate NPDR patients compared with severe NPDR patients and shown in Figure 3. Nine DSIgG N-glycopeptide ratios were found to be significantly different among the NDR, NPDR, and PDR groups in this study.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen	change_type:presence of;mod_type:sequence variation	Presence of bmkb_I::G2F sequence variation in protein IGHV4-59/NCBI:	200316	check_entity
BB3867-1	decreased level of G2 on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	background diabetic retinopathy	DOID:13208				blood serum	UBERON:0001977		PubMed:40204274	Significant differences in 9 DSIgG N-glycopeptide ratios (DSIgG1: G1F/G0F, G1FN/G0FN, G2F/G0F, G2F/G1F; DSIgG2: G1F/G0F, G1FN/G0FN, G2/G1, G2F/G0F, G2F/G1F) were found between NDR, NPDR and PDR groups and are displayed in Figure 2. Eight glycopeptide ratios (DSIgG1: G1F/G0F, G1FN/G0FN, G2F/G0F; DSIgG2: G1F/G0F, G1FN/G0FN, G2/G1, G2F/G0F, G2F/G1F) were found to be significantly different between NDR and NPDR groups. Six glycopeptide ratios (DSIgG1: G1F/G0F, G2F/G0F; DSIgG2: G1F/G0F, G2/G1, G2F/G0F, G2F/G1F) were found to be significantly different between NDR and PDR groups. Nine DSIgG N-glycopeptide ratios were found to be significantly different among the NDR, NPDR, and PDR groups in this study.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		decreased level of G2 on immunoglobulin G [biomarker_term_in_review]	200317	not_mapped
BB3864-2	decreased level of G1F on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	proliferative diabetic retinopathy	DOID:13207				blood serum	UBERON:0001977		PubMed:40204274	Significant differences in 9 DSIgG N-glycopeptide ratios (DSIgG1: G1F/G0F, G1FN/G0FN, G2F/G0F, G2F/G1F; DSIgG2: G1F/G0F, G1FN/G0FN, G2/G1, G2F/G0F, G2F/G1F) were found between NDR, NPDR and PDR groups and are displayed in Figure 2. Six glycopeptide ratios (DSIgG1: G1F/G0F, G2F/G0F; DSIgG2: G1F/G0F, G2/G1, G2F/G0F, G2F/G1F) were found to be significantly different between NDR and PDR groups. Nine DSIgG N-glycopeptide ratios were found to be significantly different among the NDR, NPDR, and PDR groups in this study.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen	change_type:presence of;mod_type:sequence variation	Presence of bmkb_I::G1F sequence variation in protein IGHV4-59/NCBI:	200318	check_entity
BB3866-2	increased level of G2F on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	proliferative diabetic retinopathy	DOID:13207				blood serum	UBERON:0001977		PubMed:40204274	Significant differences in 9 DSIgG N-glycopeptide ratios (DSIgG1: G1F/G0F, G1FN/G0FN, G2F/G0F, G2F/G1F; DSIgG2: G1F/G0F, G1FN/G0FN, G2/G1, G2F/G0F, G2F/G1F) were found between NDR, NPDR and PDR groups and are displayed in Figure 2. Six glycopeptide ratios (DSIgG1: G1F/G0F, G2F/G0F; DSIgG2: G1F/G0F, G2/G1, G2F/G0F, G2F/G1F) were found to be significantly different between NDR and PDR groups. Nine DSIgG N-glycopeptide ratios were found to be significantly different among the NDR, NPDR, and PDR groups in this study.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen	change_type:presence of;mod_type:sequence variation	Presence of bmkb_I::G2F sequence variation in protein IGHV4-59/NCBI:	200319	check_entity
BB3867-2	decreased level of G2 on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	proliferative diabetic retinopathy	DOID:13207				blood serum	UBERON:0001977		PubMed:40204274	Significant differences in 9 DSIgG N-glycopeptide ratios (DSIgG1: G1F/G0F, G1FN/G0FN, G2F/G0F, G2F/G1F; DSIgG2: G1F/G0F, G1FN/G0FN, G2/G1, G2F/G0F, G2F/G1F) were found between NDR, NPDR and PDR groups and are displayed in Figure 2. Six glycopeptide ratios (DSIgG1: G1F/G0F, G2F/G0F; DSIgG2: G1F/G0F, G2/G1, G2F/G0F, G2F/G1F) were found to be significantly different between NDR and PDR groups. Nine DSIgG N-glycopeptide ratios were found to be significantly different among the NDR, NPDR, and PDR groups in this study.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		decreased level of G2 on immunoglobulin G [biomarker_term_in_review]	200320	not_mapped
BB3865-2	decreased level of G1FN on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	proliferative diabetic retinopathy	DOID:13207				blood serum	UBERON:0001977		PubMed:40204274	Significant differences in 9 DSIgG N-glycopeptide ratios (DSIgG1: G1F/G0F, G1FN/G0FN, G2F/G0F, G2F/G1F; DSIgG2: G1F/G0F, G1FN/G0FN, G2/G1, G2F/G0F, G2F/G1F) were found between NDR, NPDR and PDR groups and are displayed in Figure 2. Two glycopeptide ratios (DSIgG1: G1FN/G0FN, G2F/G1F) were found to be significantly different between NPDR and PDR groups. Nine DSIgG N-glycopeptide ratios were found to be significantly different among the NDR, NPDR, and PDR groups in this study.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		decreased level of G1FN on immunoglobulin G [biomarker_term_in_review]	200321	not_mapped
BB3865-3	decreased level of G1FN on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	severe nonproliferative diabetic retinopathy	DOID:8946				blood serum	UBERON:0001977		PubMed:40204274	Six glycopeptide ratios (DSIgG1 G1FN/G0FN, G1FN/G1F, G2F/G0F, G2F/G1F; DSIgG2 G1F/G1, G2F/G1F) were found to be significantly different between mild, moderate NPDR patients compared with severe NPDR patients and shown in Figure 3. Patients with severe NPDR have a lower tendency of galactosylation and a higher tendency for fucosylation, demonstrating that patients with severe NPDR manifest a higher status of inflammatory response. Combined Biomarker 3 used six DSIgG N-glycopeptide ratios to successfully determine whether patients had mild and moderate NDPR or severe NPDR (AUC = 0.8059, sensitivity = 85.71%, specificity = 73.91%).	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		decreased level of G1FN on immunoglobulin G [biomarker_term_in_review]	200322	not_mapped
BB3866-3	increased level of G2F on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	severe nonproliferative diabetic retinopathy	DOID:8946				blood serum	UBERON:0001977		PubMed:40204274	Six glycopeptide ratios (DSIgG1 G1FN/G0FN, G1FN/G1F, G2F/G0F, G2F/G1F; DSIgG2 G1F/G1, G2F/G1F) were found to be significantly different between mild, moderate NPDR patients compared with severe NPDR patients and shown in Figure 3. Patients with severe NPDR have a lower tendency of galactosylation and a higher tendency for fucosylation, demonstrating that patients with severe NPDR manifest a higher status of inflammatory response. Combined Biomarker 3 used six DSIgG N-glycopeptide ratios to successfully determine whether patients had mild and moderate NDPR or severe NPDR (AUC = 0.8059, sensitivity = 85.71%, specificity = 73.91%).	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen	change_type:presence of;mod_type:sequence variation	Presence of bmkb_I::G2F sequence variation in protein IGHV4-59/NCBI:	200323	check_entity
BB3867-3	decreased level of G2 on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	severe nonproliferative diabetic retinopathy	DOID:8946				blood serum	UBERON:0001977		PubMed:40204274	Six glycopeptide ratios (DSIgG1 G1FN/G0FN, G1FN/G1F, G2F/G0F, G2F/G1F; DSIgG2 G1F/G1, G2F/G1F) were found to be significantly different between mild, moderate NPDR patients compared with severe NPDR patients and shown in Figure 3. Patients with severe NPDR have a lower tendency of galactosylation and a higher tendency for fucosylation, demonstrating that patients with severe NPDR manifest a higher status of inflammatory response. Combined Biomarker 3 used six DSIgG N-glycopeptide ratios to successfully determine whether patients had mild and moderate NDPR or severe NPDR (AUC = 0.8059, sensitivity = 85.71%, specificity = 73.91%).	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		decreased level of G2 on immunoglobulin G [biomarker_term_in_review]	200324	not_mapped
BB3868-1	decreased level of G2F on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	diabetic macular edema	DOID:9191				blood serum	UBERON:0001977		PubMed:40204274	Analysis using the Mann-Whitney U test revealed that DSIgG1: G2F/G1F; DSIgG2: G1FN/G0FN, G2F/G0F, and G2F/G1F were significantly lower in the DME(+) group compared to the DME(−) group as shown in Figure 3. Lastly, Combined Biomarker 4 consists of nine DSIgG N-glycopeptide ratios (AUC = 0.7846, sensitivity = 70.59%, specificity = 75.56%) and performed superbly in identifying the presence of DME in patients.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen	change_type:presence of;mod_type:sequence variation	Presence of bmkb_I::G2F sequence variation in protein IGHV4-59/NCBI:	200325	check_entity
BB3865-4	decreased level of G1FN on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	diabetic macular edema	DOID:9191				blood serum	UBERON:0001977		PubMed:40204274	Analysis using the Mann-Whitney U test revealed that DSIgG1: G2F/G1F; DSIgG2: G1FN/G0FN, G2F/G0F, and G2F/G1F were significantly lower in the DME(+) group compared to the DME(−) group as shown in Figure 3. Lastly, Combined Biomarker 4 consists of nine DSIgG N-glycopeptide ratios (AUC = 0.7846, sensitivity = 70.59%, specificity = 75.56%) and performed superbly in identifying the presence of DME in patients.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		decreased level of G1FN on immunoglobulin G [biomarker_term_in_review]	200326	not_mapped
BB3869-1	decreased level of O-GlcNAcylated MYC on MYC	Myc proto-oncogene protein	UPKB:P01108	protein	hepatocellular carcinoma	DOID:684				liver parenchyma	UBERON:0001280		PubMed:38975812	A significant decrease in the level of O-GlcNAcylated MYC was found in tumor liver samples from MYC-REG3A mice compared to that in MYC mice (Figures 3F, G), consistent with lower MYC accumulation.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		decreased level of O-GlcNAcylated MYC on MYC [biomarker_term_in_review]	200327	not_mapped
BB3870-1	increased level of Tn antigen on FN1	FN1	UPKB:Q14327	protein	hepatocellular carcinoma	DOID:684				blood serum	UBERON:0001977		PubMed:40162478	Here, we communicate that site-specific O-glycosylation in the oncofetal fibronectin creates cancer stage-specific serum biomarkers for hepatocellular carcinoma (HCC) by quantitative MS-based glycoproteomic approach. We found site-specific O-glycoform alteration from T/sialyl T antigens to Tn/sialyl Tn antigens at the consecutive threonine residues <sup>2155</sup>Thr-Thr-Ala<sup>2157</sup> within this fragment during cancer progression. Surprisingly, this dynamic glycoform alteration is observed specifically in the patient sera diagnosed newly as stage 2-4 groups not in the normal control and stage 1 patient groups.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		increased level of Tn antigen on FN1 [biomarker_term_in_review]	200328	not_mapped
BB3871-1	increased level of sialyl Tn antigen on FN1	FN1	UPKB:Q14327	protein	hepatocellular carcinoma	DOID:684				blood serum	UBERON:0001977		PubMed:40162478	Here, we communicate that site-specific O-glycosylation in the oncofetal fibronectin creates cancer stage-specific serum biomarkers for hepatocellular carcinoma (HCC) by quantitative MS-based glycoproteomic approach. We found site-specific O-glycoform alteration from T/sialyl T antigens to Tn/sialyl Tn antigens at the consecutive threonine residues <sup>2155</sup>Thr-Thr-Ala<sup>2157</sup> within this fragment during cancer progression. Surprisingly, this dynamic glycoform alteration is observed specifically in the patient sera diagnosed newly as stage 2-4 groups not in the normal control and stage 1 patient groups.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		increased level of sialyl Tn antigen on FN1 [biomarker_term_in_review]	200329	not_mapped
BB3872-1	decreased level of T antigen on FN1	FN1	UPKB:Q14327	protein	hepatocellular carcinoma	DOID:684				blood serum	UBERON:0001977		PubMed:40162478	Here, we communicate that site-specific O-glycosylation in the oncofetal fibronectin creates cancer stage-specific serum biomarkers for hepatocellular carcinoma (HCC) by quantitative MS-based glycoproteomic approach. We found site-specific O-glycoform alteration from T/sialyl T antigens to Tn/sialyl Tn antigens at the consecutive threonine residues <sup>2155</sup>Thr-Thr-Ala<sup>2157</sup> within this fragment during cancer progression. Surprisingly, this dynamic glycoform alteration is observed specifically in the patient sera diagnosed newly as stage 2-4 groups not in the normal control and stage 1 patient groups.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		decreased level of T antigen on FN1 [biomarker_term_in_review]	200330	not_mapped
BB3873-1	decreased level of sialyl T antigen on FN1	FN1	UPKB:Q14327	protein	hepatocellular carcinoma	DOID:684				blood serum	UBERON:0001977		PubMed:40162478	Here, we communicate that site-specific O-glycosylation in the oncofetal fibronectin creates cancer stage-specific serum biomarkers for hepatocellular carcinoma (HCC) by quantitative MS-based glycoproteomic approach. We found site-specific O-glycoform alteration from T/sialyl T antigens to Tn/sialyl Tn antigens at the consecutive threonine residues <sup>2155</sup>Thr-Thr-Ala<sup>2157</sup> within this fragment during cancer progression. Surprisingly, this dynamic glycoform alteration is observed specifically in the patient sera diagnosed newly as stage 2-4 groups not in the normal control and stage 1 patient groups.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		decreased level of sialyl T antigen on FN1 [biomarker_term_in_review]	200331	not_mapped
BB3874-1	increased level of Galβ3GalNAc on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	systemic lupus erythematosus	DOID:9074				blood serum	UBERON:0001977		PubMed:40187773	Compared to DC and HC groups, the IgG glycan level of Galβ3GalNAc (binding Jacalin (11.3%) and Maclura pomifera lectin (14.4%)) was significantly increased, whereas most IgG glycan levels were significantly decreased, including core fucose, high mannose, GlcNAc, GalNAc and Galβ4GlcNAc in the SLE group (all p<0.05). Interestingly, only one IgG glycan level of Galβ3GalNAc (binding Jacalin (11.3%) and MPL (14.4%)) was significantly increased in SLE compared with HC and DC. 28 Our study found higher levels of Galβ3GalNAc in patients with SLE than in non-lupus patients. Patients with SLE showed disease-specific alterations in serum IgG glycosylation. Aberrant Galβ3GalNAc, galactose and GalNAc glycosylation may offer potential diagnostic value for SLE and NPSLE.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		increased level of Galβ3GalNAc on immunoglobulin G [biomarker_term_in_review]	200332	not_mapped
BB3875-1	decreased level of core fucose on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	systemic lupus erythematosus	DOID:9074				blood serum	UBERON:0001977		PubMed:40187773	Compared to DC and HC groups, the IgG glycan level of Galβ3GalNAc (binding Jacalin (11.3%) and Maclura pomifera lectin (14.4%)) was significantly increased, whereas most IgG glycan levels were significantly decreased, including core fucose, high mannose, GlcNAc, GalNAc and Galβ4GlcNAc in the SLE group (all p<0.05). For patients with SLE compared with HC and DC, most IgG glycan levels were significantly decreased, including core fucose (Fuc, binding PSA), high mannose (Man, binding NPL, GNL (1%), HHL (0%) and VVA), N-Acetylglucosamine (GlcNAc, binding UDA and PWM), N-Acetylgalactosamine (GalNAc, binding Black bean crude) and Galβ4GlcNAc (binding PHA-E).	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		decreased level of core fucose on immunoglobulin G [biomarker_term_in_review]	200333	not_mapped
BB3876-1	decreased level of high mannose on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	systemic lupus erythematosus	DOID:9074				blood serum	UBERON:0001977		PubMed:40187773	Compared to DC and HC groups, the IgG glycan level of Galβ3GalNAc (binding Jacalin (11.3%) and Maclura pomifera lectin (14.4%)) was significantly increased, whereas most IgG glycan levels were significantly decreased, including core fucose, high mannose, GlcNAc, GalNAc and Galβ4GlcNAc in the SLE group (all p<0.05). For patients with SLE compared with HC and DC, most IgG glycan levels were significantly decreased, including core fucose (Fuc, binding PSA), high mannose (Man, binding NPL, GNL (1%), HHL (0%) and VVA), N-Acetylglucosamine (GlcNAc, binding UDA and PWM), N-Acetylgalactosamine (GalNAc, binding Black bean crude) and Galβ4GlcNAc (binding PHA-E).	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		decreased level of high mannose on immunoglobulin G [biomarker_term_in_review]	200334	not_mapped
BB3877-1	decreased level of GlcNAc on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	systemic lupus erythematosus	DOID:9074				blood serum	UBERON:0001977		PubMed:40187773	Compared to DC and HC groups, the IgG glycan level of Galβ3GalNAc (binding Jacalin (11.3%) and Maclura pomifera lectin (14.4%)) was significantly increased, whereas most IgG glycan levels were significantly decreased, including core fucose, high mannose, GlcNAc, GalNAc and Galβ4GlcNAc in the SLE group (all p<0.05). For patients with SLE compared with HC and DC, most IgG glycan levels were significantly decreased, including core fucose (Fuc, binding PSA), high mannose (Man, binding NPL, GNL (1%), HHL (0%) and VVA), N-Acetylglucosamine (GlcNAc, binding UDA and PWM), N-Acetylgalactosamine (GalNAc, binding Black bean crude) and Galβ4GlcNAc (binding PHA-E).	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		decreased level of GlcNAc on immunoglobulin G [biomarker_term_in_review]	200335	not_mapped
BB3878-1	decreased level of Galβ4GlcNAc on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	systemic lupus erythematosus	DOID:9074				blood serum	UBERON:0001977		PubMed:40187773	Compared to DC and HC groups, the IgG glycan level of Galβ3GalNAc (binding Jacalin (11.3%) and Maclura pomifera lectin (14.4%)) was significantly increased, whereas most IgG glycan levels were significantly decreased, including core fucose, high mannose, GlcNAc, GalNAc and Galβ4GlcNAc in the SLE group (all p<0.05). For patients with SLE compared with HC and DC, most IgG glycan levels were significantly decreased, including core fucose (Fuc, binding PSA), high mannose (Man, binding NPL, GNL (1%), HHL (0%) and VVA), N-Acetylglucosamine (GlcNAc, binding UDA and PWM), N-Acetylgalactosamine (GalNAc, binding Black bean crude) and Galβ4GlcNAc (binding PHA-E).	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		decreased level of Galβ4GlcNAc on immunoglobulin G [biomarker_term_in_review]	200336	not_mapped
BB3874-2	increased level of Galβ3GalNAc on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	lupus erythematosus	DOID:8857				blood serum	UBERON:0001977		PubMed:40187773	The IgG glycan levels were elevated in GalNAc and galactose patterns in the NPSLE group compared to the WMOI group, as well as higher Galβ3GalNAc and galactose patterns in NPSLE and LN compared to HCs. Looking into differences of each subgroup compared with HC (with no difference between WMOI vs HC), the glycan levels of lgG galactose (binding GSL I-B4 and PNA (13.3% and 28.3%)), Galβ3GalNAc (binding MPL) were significantly higher in NPSLE and LN vs HC, while IgG core fucose (binding PSA) and Galβ4GlcNAc (binding PHA-E) levels were significantly reduced within NPSLE versus HC. Aberrant Galβ3GalNAc, galactose and GalNAc glycosylation may offer potential diagnostic value for SLE and NPSLE.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		increased level of Galβ3GalNAc on immunoglobulin G [biomarker_term_in_review]	200337	not_mapped
BB3874-3	increased level of Galβ3GalNAc on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	lupus nephritis	DOID:0080162				blood serum	UBERON:0001977		PubMed:40187773	The IgG glycan levels were elevated in GalNAc and galactose patterns in the NPSLE group compared to the WMOI group, as well as higher Galβ3GalNAc and galactose patterns in NPSLE and LN compared to HCs. Looking into differences of each subgroup compared with HC (with no difference between WMOI vs HC), the glycan levels of lgG galactose (binding GSL I-B4 and PNA (13.3% and 28.3%)), Galβ3GalNAc (binding MPL) were significantly higher in NPSLE and LN vs HC, while IgG core fucose (binding PSA) and Galβ4GlcNAc (binding PHA-E) levels were significantly reduced within NPSLE versus HC.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		increased level of Galβ3GalNAc on immunoglobulin G [biomarker_term_in_review]	200338	not_mapped
BB3879-1	increased level of galactose on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	lupus erythematosus	DOID:8857				blood serum	UBERON:0001977		PubMed:40187773	The IgG glycan levels were elevated in GalNAc and galactose patterns in the NPSLE group compared to the WMOI group, as well as higher Galβ3GalNAc and galactose patterns in NPSLE and LN compared to HCs. Looking into differences of each subgroup compared with HC (with no difference between WMOI vs HC), the glycan levels of lgG galactose (binding GSL I-B4 and PNA (13.3% and 28.3%)), Galβ3GalNAc (binding MPL) were significantly higher in NPSLE and LN vs HC, while IgG core fucose (binding PSA) and Galβ4GlcNAc (binding PHA-E) levels were significantly reduced within NPSLE versus HC. In our study, we found that the IgG glycan levels were higher for galactose in the NPSLE versus WMOI group. Our article found that compared with the WMOI group, the NPSLE group had patients who might experience higher IgG glycan levels of galactose. Aberrant Galβ3GalNAc, galactose and GalNAc glycosylation may offer potential diagnostic value for SLE and NPSLE.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		increased level of galactose on immunoglobulin G [biomarker_term_in_review]	200339	not_mapped
BB3879-2	increased level of galactose on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	lupus nephritis	DOID:0080162				blood serum	UBERON:0001977		PubMed:40187773	The IgG glycan levels were elevated in GalNAc and galactose patterns in the NPSLE group compared to the WMOI group, as well as higher Galβ3GalNAc and galactose patterns in NPSLE and LN compared to HCs. Looking into differences of each subgroup compared with HC (with no difference between WMOI vs HC), the glycan levels of lgG galactose (binding GSL I-B4 and PNA (13.3% and 28.3%)), Galβ3GalNAc (binding MPL) were significantly higher in NPSLE and LN vs HC, while IgG core fucose (binding PSA) and Galβ4GlcNAc (binding PHA-E) levels were significantly reduced within NPSLE versus HC.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		increased level of galactose on immunoglobulin G [biomarker_term_in_review]	200340	not_mapped
BB3875-2	decreased level of core fucose on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	lupus erythematosus	DOID:8857				blood serum	UBERON:0001977		PubMed:40187773	Looking into differences of each subgroup compared with HC (with no difference between WMOI vs HC), the glycan levels of lgG galactose (binding GSL I-B4 and PNA (13.3% and 28.3%)), Galβ3GalNAc (binding MPL) were significantly higher in NPSLE and LN vs HC, while IgG core fucose (binding PSA) and Galβ4GlcNAc (binding PHA-E) levels were significantly reduced within NPSLE versus HC.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		decreased level of core fucose on immunoglobulin G [biomarker_term_in_review]	200341	not_mapped
BB3878-2	decreased level of Galβ4GlcNAc on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	lupus erythematosus	DOID:8857				blood serum	UBERON:0001977		PubMed:40187773	Looking into differences of each subgroup compared with HC (with no difference between WMOI vs HC), the glycan levels of lgG galactose (binding GSL I-B4 and PNA (13.3% and 28.3%)), Galβ3GalNAc (binding MPL) were significantly higher in NPSLE and LN vs HC, while IgG core fucose (binding PSA) and Galβ4GlcNAc (binding PHA-E) levels were significantly reduced within NPSLE versus HC.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		decreased level of Galβ4GlcNAc on immunoglobulin G [biomarker_term_in_review]	200342	not_mapped
BB3880-1	decreased level of galactose on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	systemic lupus erythematosus	DOID:9074				blood serum	UBERON:0001977		PubMed:40187773	As for the WMOI group, glycan levels of lgG galactose (binding GHA), GalNAc (binding CSA) and Galβ4GlcNAc (binding MAL I) were significantly lower than NPSLE and HC. For patients WMOI, lower binding levels were verified for GHA (preferred to Gal) than in NPSLE, and CSA (preferred to GalNAc) than in NPSLE or PAH.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		decreased level of galactose on immunoglobulin G [biomarker_term_in_review]	200343	not_mapped
BB3881-1	decreased level of GalNAc on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	systemic lupus erythematosus	DOID:9074				blood serum	UBERON:0001977		PubMed:40187773	As for the WMOI group, glycan levels of lgG galactose (binding GHA), GalNAc (binding CSA) and Galβ4GlcNAc (binding MAL I) were significantly lower than NPSLE and HC. For patients WMOI, lower binding levels were verified for GHA (preferred to Gal) than in NPSLE, and CSA (preferred to GalNAc) than in NPSLE or PAH.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		decreased level of GalNAc on immunoglobulin G [biomarker_term_in_review]	200344	not_mapped
BB3878-1	decreased level of Galβ4GlcNAc on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	systemic lupus erythematosus	DOID:9074				blood serum	UBERON:0001977		PubMed:40187773	As for the WMOI group, glycan levels of lgG galactose (binding GHA), GalNAc (binding CSA) and Galβ4GlcNAc (binding MAL I) were significantly lower than NPSLE and HC.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		decreased level of Galβ4GlcNAc on immunoglobulin G [biomarker_term_in_review]	200336	not_mapped
BB3879-3	increased level of galactose on immunoglobulin G	Immunoglobulin heavy variable 4-59	UPKB:P01825	protein	systemic lupus erythematosus	DOID:9074				blood serum	UBERON:0001977		PubMed:40187773	A higher binding level of PNA (preferred to Gal) was confirmed in patients with SLE than in HCs, pSS and RA. Among these, PNA binding levels in the lectin microarray analysis provided better differentiation conditions between SLE and pSS with a sensitivity of 92.8, specificity of 65.0% and area under the curve value of 0.775 (95% CI: 0.676 to 0.874, p<0.001), though it just showed medium potential.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen		increased level of galactose on immunoglobulin G [biomarker_term_in_review]	200345	not_mapped
BB3882-1	increased level of N4H5 on fibrinogen	Fibrinogen alpha chain	UPKB:P02671	protein	atrial fibrillation	DOID:0060224				blood plasma	UBERON:0001969		PubMed:40099449	Application to 181 atrial fibrillation (AF) patients and 52 healthy controls identified three gamma chain glycoforms significantly associated with AF. Most notably, increased levels of the asialylated N4H5, known to enhance fibrin bundle thickness and promote clot formation, suggest a potential mechanism linking glycosylation changes to the prothrombotic state in AF. Regression analysis identified three glycopeptides significantly associated with AF, all of which were lower-abundance glycopeptides from the Gamma glycosylation site (Table 3). Specifically, Gamma. MISS-N4H5, Gamma. MISS-N4H5S1F1, and Gamma. MISS-N4H5S2F1 were found to be more abundant in AF patients compared to the controls. The most notable finding was an increase in the level of Gamma. MISS-N4H5, an asialylated glycoform. Asialylated fibrinogen is known to enhance clot formation, producing fibrin bundles with greater thickness compared to those formed by fibrinogen with disialylated glycans. 24 Given that AF patients are predisposed to clot formation and routinely prescribed anticoagulants,46 these glycosylation changes could have functional implications in the prothrombotic state associated with AF. Notably, an increase in the asialylated glycoform Gamma. MISS-N4H5 was observed in AF patients, which may contribute to the prothrombotic state seen under this condition.	assessed_biomarker_entity_id;assessed_biomarker_entiy;assessed_entity_type;biomarker;condition;specimen	change_type:increased;aspect_type:level	Increased level of protein FGA/UPKB:P02671	200346