Journal: bioRxiv

Article Title: A predisposing effect of HLA class II genes in celiac disease by skewing the naïve CD4 + T-cell receptor repertoire

doi: 10.1101/2025.07.15.663863

Figure Lengend Snippet: Approach, sample cohort characteristics and sequencing statistics. ( a ) An illustration of our overall approach. ( b,c ) Cohort characteristics of control and CeD subjects, showing age at time of sample collection ( b ) and biological sex distribution ( c ). ( d,e ) AIRR-seq metrics for naïve CD4 + T cells isolated from peripheral blood of control and CeD subjects, showing RNA concentration used for preparation of sequencing libraries ( d ) and number of unique TRA and TRB sequences after processing ( e ). ( f ) Genotyping and HLA typing approach for control and CeD subjects. ( g ) HLA allele inference probability reported by the Axiom HLA Analysis tool. Statistical significance was calculated with a Wilcoxon rank sum test ( b , d,e ).

Article Snippet: These cells had already been thawed once and depleted for CD4 + effector memory T cells using the human CD4+ Effector Memory T Cell Isolation Kit (Miltenyi).

Techniques: Sequencing, Control, Isolation, Concentration Assay, Immunopeptidomics

Journal: bioRxiv

Article Title: A predisposing effect of HLA class II genes in celiac disease by skewing the naïve CD4 + T-cell receptor repertoire

doi: 10.1101/2025.07.15.663863

Figure Lengend Snippet: Cis -guQTL analysis of TRA and TRB gene usage in naïve CD4 + T cells of control subjects. ( a ) Manhattan plots showing SNP associations across V, D and J genes within 1 Mb of the TRA (left) and TRB (right) loci. Dashed lines indicate Bonferroni-corrected significance thresholds. Lower tracks show tested SNPs/10 Kb. ( b ) Significance of lead cis -guQTLs for each gene. ( c ) Examples of cis -mediated effects of lead guQTL genotype on gene expression. ( d ) Fold-change in expression between subjects homozygous for the REF or ALT lead guQTL variant for each gene. ( e ) guQTLs associated with one or more TRA or TRB gene (upper) and biggest networks of TRA (middle) and TRB (lower) genes associated with the same guQTLs. Gene tracks indicate positions of guQTLs, affected genes and tested SNPs for each network. ( f,g ) Examples of location of lead guQTLs with respect to their affected TRB ( f ) or TRA ( g ) genes.

Article Snippet: These cells had already been thawed once and depleted for CD4 + effector memory T cells using the human CD4+ Effector Memory T Cell Isolation Kit (Miltenyi).

Techniques: Control, Gene Expression, Expressing, Variant Assay

Journal: bioRxiv

Article Title: A predisposing effect of HLA class II genes in celiac disease by skewing the naïve CD4 + T-cell receptor repertoire

doi: 10.1101/2025.07.15.663863

Figure Lengend Snippet: Trans -guQTL analysis of the influence of the HLA region on TRA and TRB gene usage in the naïve CD4 + TCR repertoire of control subjects. ( a ) Manhattan plots showing SNP associations for V, D and J genes with SNPs located on the entire chromosome 6 (left) or limited to 1 Mb before and after the HLA region (right). Dashed horizontal lines indicate significance threshold determined by Bonferroni correction. The lower tracks show number of tested SNPs along the chromosome. ( b ) Significance of the lead guQTL for each gene tested in ( a ). Black/grey bars correspond to the analysis including SNPs spanning the entire chromosome 6, blue bars correspond to the HLA-restricted analysis. ( c ) Examples of trans- mediated effects of lead guQTL genotype on TRA and TRB gene expression. Statistical significance was calculated using a Wilcoxon rank sum test followed by Bonferroni correction within each subfigure. Non-significant differences are not indicated. ( d ) Fold-change in expression between subjects with REF/REF and ALT/ALT genotype at lead trans -guQTL for each gene. ( e ) guQTLs associated with one or more TRA or TRB gene (left) and biggest networks of TRA genes and TRB genes associated to the same significant trans -guQTLs (right). ( f ) Location of significant lead trans- guQTLs within the HLA region of chromosome 6.

Article Snippet: These cells had already been thawed once and depleted for CD4 + effector memory T cells using the human CD4+ Effector Memory T Cell Isolation Kit (Miltenyi).

Techniques: Control, Gene Expression, Expressing

Journal: bioRxiv

Article Title: A predisposing effect of HLA class II genes in celiac disease by skewing the naïve CD4 + T-cell receptor repertoire

doi: 10.1101/2025.07.15.663863

Figure Lengend Snippet: TRA and TRB gene usage frequencies in the naïve CD4 + TCR repertoire of CeD compared to control subjects. ( a ) Distribution of HLA-DQ allotypes in CeD subjects, with heatmap indicating number of subjects with each combination of allotypes. ( b ) Highly biased HLA-DQ allotype distribution in CeD compared to control individuals, with most CeD subjects expressing the DQ2.5 allotype ( c ) Log-fold change in expression of V, D and J genes between CeD and control subjects. Positive log-fold-change indicates more frequent usage in CeD subjects compared to controls. An absolute log2 fold-change of 0.1 is indicated with dashed vertical lines. Genes most commonly used by DQ2.5-restricted gluten-reactive effector T cells in CeD are highlighted in green. ( d ) Distribution of gene usage frequency for most highly expressed TRAV (left) and TRBV (right) genes in CeD subjects compared to controls. ( e ) Frequency of potentially gluten-reactive TRA (left) and TRB (right) sequences for CeD subjects compared to controls, based on a database of DQ2.5-restricted gluten-reactive TCR sequences from 50 CeD subjects . Frequency is further conditioned by HLA-DQ2.5 allotype, with number of subjects in each group indicated on the graph. Statistical significance was calculated for each gene ( d ) or subfigure ( e ) using a Wilcoxon rank sum test and Bonferroni correction within each subfigure. Non-significant differences are not shown.

Article Snippet: These cells had already been thawed once and depleted for CD4 + effector memory T cells using the human CD4+ Effector Memory T Cell Isolation Kit (Miltenyi).

Techniques: Control, Expressing

Journal: bioRxiv

Article Title: A predisposing effect of HLA class II genes in celiac disease by skewing the naïve CD4 + T-cell receptor repertoire

doi: 10.1101/2025.07.15.663863

Figure Lengend Snippet: Approach, sample cohort characteristics and sequencing statistics. ( a ) An illustration of our overall approach. ( b,c ) Cohort characteristics of control and CeD subjects, showing age at time of sample collection ( b ) and biological sex distribution ( c ). ( d,e ) AIRR-seq metrics for naïve CD4 + T cells isolated from peripheral blood of control and CeD subjects, showing RNA concentration used for preparation of sequencing libraries ( d ) and number of unique TRA and TRB sequences after processing ( e ). ( f ) Genotyping and HLA typing approach for control and CeD subjects. ( g ) HLA allele inference probability reported by the Axiom HLA Analysis tool. Statistical significance was calculated with a Wilcoxon rank sum test ( b , d,e ).

Article Snippet: These cells had already been thawed once and depleted for CD4 + effector memory T cells using the human CD4+ Effector Memory T Cell Isolation Kit (Miltenyi).

Techniques: Sequencing, Control, Isolation, Concentration Assay, Immunopeptidomics

Journal: bioRxiv

Article Title: A predisposing effect of HLA class II genes in celiac disease by skewing the naïve CD4 + T-cell receptor repertoire

doi: 10.1101/2025.07.15.663863

Figure Lengend Snippet: Cis -guQTL analysis of TRA and TRB gene usage in naïve CD4 + T cells of control subjects. ( a ) Manhattan plots showing SNP associations across V, D and J genes within 1 Mb of the TRA (left) and TRB (right) loci. Dashed lines indicate Bonferroni-corrected significance thresholds. Lower tracks show tested SNPs/10 Kb. ( b ) Significance of lead cis -guQTLs for each gene. ( c ) Examples of cis -mediated effects of lead guQTL genotype on gene expression. ( d ) Fold-change in expression between subjects homozygous for the REF or ALT lead guQTL variant for each gene. ( e ) guQTLs associated with one or more TRA or TRB gene (upper) and biggest networks of TRA (middle) and TRB (lower) genes associated with the same guQTLs. Gene tracks indicate positions of guQTLs, affected genes and tested SNPs for each network. ( f,g ) Examples of location of lead guQTLs with respect to their affected TRB ( f ) or TRA ( g ) genes.

Article Snippet: These cells had already been thawed once and depleted for CD4 + effector memory T cells using the human CD4+ Effector Memory T Cell Isolation Kit (Miltenyi).

Techniques: Control, Gene Expression, Expressing, Variant Assay

Journal: bioRxiv

Article Title: A predisposing effect of HLA class II genes in celiac disease by skewing the naïve CD4 + T-cell receptor repertoire

doi: 10.1101/2025.07.15.663863

Figure Lengend Snippet: Trans -guQTL analysis of the influence of the HLA region on TRA and TRB gene usage in the naïve CD4 + TCR repertoire of control subjects. ( a ) Manhattan plots showing SNP associations for V, D and J genes with SNPs located on the entire chromosome 6 (left) or limited to 1 Mb before and after the HLA region (right). Dashed horizontal lines indicate significance threshold determined by Bonferroni correction. The lower tracks show number of tested SNPs along the chromosome. ( b ) Significance of the lead guQTL for each gene tested in ( a ). Black/grey bars correspond to the analysis including SNPs spanning the entire chromosome 6, blue bars correspond to the HLA-restricted analysis. ( c ) Examples of trans- mediated effects of lead guQTL genotype on TRA and TRB gene expression. Statistical significance was calculated using a Wilcoxon rank sum test followed by Bonferroni correction within each subfigure. Non-significant differences are not indicated. ( d ) Fold-change in expression between subjects with REF/REF and ALT/ALT genotype at lead trans -guQTL for each gene. ( e ) guQTLs associated with one or more TRA or TRB gene (left) and biggest networks of TRA genes and TRB genes associated to the same significant trans -guQTLs (right). ( f ) Location of significant lead trans- guQTLs within the HLA region of chromosome 6.

Article Snippet: These cells had already been thawed once and depleted for CD4 + effector memory T cells using the human CD4+ Effector Memory T Cell Isolation Kit (Miltenyi).

Techniques: Control, Gene Expression, Expressing

Journal: bioRxiv

Article Title: A predisposing effect of HLA class II genes in celiac disease by skewing the naïve CD4 + T-cell receptor repertoire

doi: 10.1101/2025.07.15.663863

Figure Lengend Snippet: TRA and TRB gene usage frequencies in the naïve CD4 + TCR repertoire of CeD compared to control subjects. ( a ) Distribution of HLA-DQ allotypes in CeD subjects, with heatmap indicating number of subjects with each combination of allotypes. ( b ) Highly biased HLA-DQ allotype distribution in CeD compared to control individuals, with most CeD subjects expressing the DQ2.5 allotype ( c ) Log-fold change in expression of V, D and J genes between CeD and control subjects. Positive log-fold-change indicates more frequent usage in CeD subjects compared to controls. An absolute log2 fold-change of 0.1 is indicated with dashed vertical lines. Genes most commonly used by DQ2.5-restricted gluten-reactive effector T cells in CeD are highlighted in green. ( d ) Distribution of gene usage frequency for most highly expressed TRAV (left) and TRBV (right) genes in CeD subjects compared to controls. ( e ) Frequency of potentially gluten-reactive TRA (left) and TRB (right) sequences for CeD subjects compared to controls, based on a database of DQ2.5-restricted gluten-reactive TCR sequences from 50 CeD subjects . Frequency is further conditioned by HLA-DQ2.5 allotype, with number of subjects in each group indicated on the graph. Statistical significance was calculated for each gene ( d ) or subfigure ( e ) using a Wilcoxon rank sum test and Bonferroni correction within each subfigure. Non-significant differences are not shown.

Article Snippet: These cells had already been thawed once and depleted for CD4 + effector memory T cells using the human CD4+ Effector Memory T Cell Isolation Kit (Miltenyi).

Techniques: Control, Expressing