Shiva Dahal-Koirala

• Funsten, Matthew C.; Yurkovetskiy, Leonid A.; Kuznetsov, Andrey; Reiman, Derek; Hansen, Camilla H.F. & Senter, Katharine I. [Show all 15 contributors for this article] (2023). Microbiota-dependent proteolysis of gluten subverts diet-mediated protection against type 1 diabetes. Cell Host and Microbe. ISSN 1931-3128. 31(2), p. 213–227.e9. doi: 10.1016/j.chom.2022.12.009.
• Chlubnova, Marketa; Christophersen, Asbjørn Otto; Sandve, Geir Kjetil Ferkingstad; Lundin, Knut Erik Aslaksen; Jahnsen, Jørgen & Dahal-Koirala, Shiva [Show all 7 contributors for this article] (2023). Identification of gluten T cell epitopes driving celiac disease. Science Advances. ISSN 2375-2548. 9(4), p. 1–8. doi: 10.1126/sciadv.ade5800. Full text in Research Archive
• Zhou, Chunyan; Østerbye, Thomas; Bach, Emil; Dahal-Koirala, Shiva; Høydahl, Lene Støkken & Steinsbø, Øyvind [Show all 11 contributors for this article] (2022). Focused B cell response to recurring gluten motif with implications for epitope spreading in celiac disease. Cell reports. ISSN 2211-1247. 41:111541(4), p. 1–16. doi: 10.1016/j.celrep.2022.111541. Full text in Research Archive
• Ciacchi, Laura; Farenc, Carine; Dahal-Koirala, Shiva; Petersen, Jan; Sollid, Ludvig Magne & Reid, Hugh H. [Show all 7 contributors for this article] (2022). Structural basis of T cell receptor specificity and cross-reactivity of two HLA-DQ2.5-restricted gluten epitopes in celiac disease. Journal of Biological Chemistry. ISSN 0021-9258. 298:101619(3), p. 1–11. doi: 10.1016/j.jbc.2022.101619. Full text in Research Archive
• Christophersen, Asbjørn Otto; Dahal-Koirala, Shiva; Chlubnova, Marketa; Jahnsen, Jørgen; Lundin, Knut & Sollid, Ludvig Magne (2022). Phenotype-Based Isolation of Antigen-Specific CD4+ T Cells in Autoimmunity: A Study of Celiac Disease. Advanced Science. ISSN 2198-3844. 9(10), p. 1–10. doi: 10.1002/advs.202104766. Full text in Research Archive
• Dahal-Koirala, Shiva; Balaban, Gabriel; Neumann, Ralf Stefan; Scheffer, Lonneke; Lundin, Knut & Greiff, Victor [Show all 9 contributors for this article] (2022). TCRpower: quantifying the detection power of T-cell receptor sequencing with a novel computational pipeline calibrated by spike-in sequences. Briefings in Bioinformatics. ISSN 1467-5463. 23(2), p. 1–14. doi: 10.1093/bib/bbab566. Full text in Research Archive Show summary

  T-cell receptor (TCR) sequencing has enabled the development of innovative diagnostic tests for cancers, autoimmune diseases and other applications. However, the rarity of many T-cell clonotypes presents a detection challenge, which may lead to misdiagnosis if diagnostically relevant TCRs remain undetected. To address this issue, we developed TCRpower, a novel computational pipeline for quantifying the statistical detection power of TCR sequencing methods. TCRpower calculates the probability of detecting a TCR sequence as a function of several key parameters: in-vivo TCR frequency, T-cell sample count, read sequencing depth and read cutoff. To calibrate TCRpower, we selected unique TCRs of 45 T-cell clones (TCCs) as spike-in TCRs. We sequenced the spike-in TCRs from TCCs, together with TCRs from peripheral blood, using a 5′ RACE protocol. The 45 spike-in TCRs covered a wide range of sample frequencies, ranging from 5 per 100 to 1 per 1 million. The resulting spike-in TCR read counts and ground truth frequencies allowed us to calibrate TCRpower. In our TCR sequencing data, we observed a consistent linear relationship between sample and sequencing read frequencies. We were also able to reliably detect spike-in TCRs with frequencies as low as one per million. By implementing an optimized read cutoff, we eliminated most of the falsely detected sequences in our data (TCR α-chain 99.0% and TCR β-chain 92.4%), thereby improving diagnostic specificity. TCRpower is publicly available and can be used to optimize future TCR sequencing experiments, and thereby enable reliable detection of disease-relevant TCRs for diagnostic applications.

• Christophersen, Asbjørn Otto; Zühlke, Stephanie; Lund, Eivind Gard; Snir, Omri; Dahal-Koirala, Shiva & Risnes, Louise Fremgaard [Show all 9 contributors for this article] (2021). Pathogenic T cells in celiac disease change phenotype on gluten challenge: Implications for T-cell-directed therapies. Advanced Science. ISSN 2198-3844. 8(21), p. 1–11. doi: 10.1002/advs.202102778.
• Risnes, Louise Fremgaard; Eggesbø, Linn Margrethe; Zühlke, Stephanie; Dahal-Koirala, Shiva; Neumann, Ralf Stefan & Lundin, Knut Erik Aslaksen [Show all 8 contributors for this article] (2021). Circulating CD103+ γδ and CD8+ T cells are clonally shared with tissue-resident intraepithelial lymphocytes in celiac disease. Mucosal Immunology. ISSN 1933-0219. 14(4), p. 842–851. doi: 10.1038/s41385-021-00385-8. Full text in Research Archive
• Dahal-Koirala, Shiva; Risnes, Louise Fremgaard; Neumann, Ralf Stefan; Christophersen, Asbjørn; Lundin, Knut E. A. & Sandve, Geir Kjetil [Show all 8 contributors for this article] (2021). Comprehensive Analysis of CDR3 Sequences in Gluten-Specific T-Cell Receptors Reveals a Dominant R-Motif and Several New Minor Motifs. Frontiers in Immunology. ISSN 1664-3224. 12:639672, p. 1–13. doi: 10.3389/fimmu.2021.639672. Full text in Research Archive
• Qiao, Shuo-Wang; Dahal-Koirala, Shiva; Eggesbø, Linn Margrethe; Lundin, Knut E. A. & Sollid, Ludvig Magne (2021). Frequency of Gluten-Reactive T Cells in Active Celiac Lesions Estimated by Direct Cell Cloning. Frontiers in Immunology. ISSN 1664-3224. 12:646163, p. 1–8. doi: 10.3389/fimmu.2021.646163. Full text in Research Archive
• Ting, Yi Tian; Dahal-Koirala, Shiva; Kim, Hui Shi Keshia; Qiao, Shuo Wang; Neumann, Ralf Stefan & Lundin, Knut Erik Aslaksen [Show all 10 contributors for this article] (2020). A molecular basis for the T cell response in HLA-DQ2.2 mediated celiac disease. Proceedings of the National Academy of Sciences of the United States of America. ISSN 0027-8424. 117(6), p. 3063–3073. doi: 10.1073/pnas.1914308117. Full text in Research Archive
• Dahal-Koirala, Shiva; Neumann, Ralf Stefan; Jahnsen, Jørgen; Lundin, Knut Erik Aslaksen & Sollid, Ludvig Magne (2019). On the immune response to barley in celiac disease: Biased and public T-cell receptor usage to a barley unique and immunodominant gluten epitope. European Journal of Immunology. ISSN 0014-2980. p. 1–14. doi: 10.1002/eji.201948253. Full text in Research Archive
• Zühlke, Stephanie; Risnes, Louise Fremgaard; Dahal-Koirala, Shiva; Christophersen, Asbjørn; Sollid, Ludvig Magne & Lundin, Knut Erik Aslaksen (2019). CD38 expression on gluten-specific T cells is a robust marker of gluten re-exposure in coeliac disease . United European Gastroenterology Journal (UEG Journal). ISSN 2050-6406. 7(10), p. 1337–1344. doi: 10.1177/2050640619874183.
• Frick, Rahel; Gunnarsen, Kristin Støen; Dahal-Koirala, Shiva; Risnes, Louise Fremgaard; Sollid, Ludvig Magne & Sandlie, Inger [Show all 8 contributors for this article] (2019). A TRAV26-1-encoded recognition motif focuses the biased T cell response in celiac disease. European Journal of Immunology. ISSN 0014-2980. 50, p. 142–145. doi: 10.1002/eji.201948235. Full text in Research Archive
• Christophersen, Asbjørn; Risnes, Louise Fremgaard; Dahal-Koirala, Shiva & Sollid, Ludvig Magne (2019). Therapeutic and diagnostic implications of T cell scarring in celiac disease and beyond. Trends in Molecular Medicine. ISSN 1471-4914. 25(10), p. 836–852. doi: 10.1016/j.molmed.2019.05.009. Full text in Research Archive
• Christophersen, Asbjørn; Lund, Eivind Gard; Snir, Omri; Solà, Elsa; Kanduri, Srinivasa Kalyana Chakravarthi & Dahal-Koirala, Shiva [Show all 15 contributors for this article] (2019). Distinct phenotype of CD4+ T cells driving celiac disease identified in multiple autoimmune conditions. Nature Medicine. ISSN 1078-8956. 25(5), p. 734–737. doi: 10.1038/s41591-019-0403-9. Full text in Research Archive
• Dahal-Koirala, Shiva; Ciacchi, Laura; Petersen, Jan; Risnes, Louise Fremgaard; Neumann, Ralf Stefan & Christophersen, Asbjørn [Show all 11 contributors for this article] (2018). Discriminative T-cell receptor recognition of highly homologous HLA-DQ2-bound gluten epitopes . Journal of Biological Chemistry. ISSN 0021-9258. 294(3), p. 941–952. doi: 10.1074/jbc.RA118.005736. Full text in Research Archive
• Risnes, Louise Fremgaard; Christophersen, Asbjørn; Dahal-Koirala, Shiva; Neumann, Ralf Stefan; Sandve, Geir Kjetil & Sarna, Vikas Kumar [Show all 9 contributors for this article] (2018). Disease-driving CD4+ T cell clonotypes persist for decades in celiac disease. Journal of Clinical Investigation. ISSN 0021-9738. 128(6), p. 2642–2650. doi: 10.1172/JCI98819. Full text in Research Archive
• Sarna, Vikas Kumar; Skodje, Gry Irene; Reims, Henrik Mikael; Risnes, Louise Fremgaard; Dahal-Koirala, Shiva & Sollid, Ludvig Magne [Show all 7 contributors for this article] (2017). HLA-DQ:gluten tetramer test in blood gives better detection of coeliac patients than biopsy after 14-day gluten challenge. Gut. ISSN 0017-5749. 67(9), p. 1606–1613. doi: 10.1136/gutjnl-2017-314461. Full text in Research Archive
• Raki, Melinda; Dahal-Koirala, Shiva; Yu, Hao; Korponay-Szabó, Ilma R.; Gyimesi, Judit & Castillejo, Gemma [Show all 9 contributors for this article] (2017). Similar Responses of Intestinal T Cells From Untreated Children and Adults With Celiac Disease to Deamidated Gluten Epitopes. Gastroenterology. ISSN 0016-5085. 153(3), p. 787–798.e4. doi: 10.1053/j.gastro.2017.05.016.
• Gunnarsen, Kristin Støen; Høydahl, Lene Støkken; Risnes, Louise Fremgaard; Dahal-Koirala, Shiva; Neumann, Ralf Stefan & Bergseng, Elin [Show all 15 contributors for this article] (2017). A TCRα framework–centered codon shapes a biased T cell repertoire through direct MHC and CDR3β interactions. JCI Insight. ISSN 2379-3708. 2(17). doi: 10.1172/jci.insight.95193. Full text in Research Archive
• Fykerud, Tone Aase; Knudsen, Lars Mørland; Totland, Max; Sørensen, Vigdis; Dahal-Koirala, Shiva & Lothe, Ragnhild A [Show all 8 contributors for this article] (2016). Mitotic cells form actin-based bridges with adjacent cells to provide intercellular communication during rounding. Cell Cycle. ISSN 1538-4101. 15(21), p. 2943–2957. doi: 10.1080/15384101.2016.1231280. Full text in Research Archive
• Dahal-Koirala, Shiva; Risnes, Louise Fremgaard; Christophersen, Asbjørn; Sarna, Vikas Kumar; Lundin, Knut Erik Aslaksen & Sollid, Ludvig Magne [Show all 7 contributors for this article] (2016). TCR sequencing of single cells reactive to DQ2.5-glia-α2 and DQ2.5-glia-ω2 reveals clonal expansion and epitope-specific V-gene usage. Mucosal Immunology. ISSN 1933-0219. 9(3), p. 587–596. doi: 10.1038/mi.2015.147. Full text in Research Archive

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• Risnes, Louise Fremgaard; Chlubnova, Marketa; Magistrelli, Elio; Kemppainen, Esko; Hervonen, Kaisa & Mansikka, Eriika [Show all 10 contributors for this article] (2022). Phenotypic Analysis of Disease-Relevant T Cells in Dermatitis Herpetiformis. Journal of Investigative Dermatology. ISSN 0022-202X. 143(1), p. 163–166. doi: 10.1016/j.jid.2022.07.007. Full text in Research Archive

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