Khang Le Quy

• Chernigovskaya, Maria; Quy, Khang Le; Stensland, Maria; Singh, Sachin; Nelson, Rowan & Yilmaz, Melih [Show all 19 contributors for this article] (2025). Systematic benchmarking of mass spectrometry-based antibody sequencing reveals methodological biases. Cell Systems. ISSN 2405-4712. 16(11). doi: 10.1016/j.cels.2025.101449. Full text in Research Archive Show summary

  The circulating antibody (Ab) repertoire is crucial for immune protection, holding significant immunological and biotechnological value. While bottom-up mass spectrometry (MS) is widely used for profiling the sequence diversity of circulating Abs (Ab repertoire sequencing [Ab-seq]), it has not been thoroughly benchmarked. We quantified the replicability and robustness of Ab-seq using six monoclonal Ab spike-ins in 70 combinations of concentration and oligoclonality, with and without polyclonal serum immunoglobulin G (IgG) background. Each combination underwent four protease treatments and was analyzed across four experimental and three technical replicates, totaling 3,360 liquid chromatography-tandem MS (LC-MS/MS) runs. We quantified the dependence of Ab-seq identification on Ab sequence, concentration, protease, presence of background IgGs, and bioinformatics methods. Integrating the data from experimental replicates, proteases, and bioinformatics tools enhanced Ab identification. De novo sequencing performed similarly to database-dependent methods at higher Ab concentrations, but de novo Ab reconstruction remains challenging. Our work provides a foundational resource for the field of MS-based Ab profiling. A record of this paper’s transparent peer review process is included in the supplemental information

• Le, Quy Khang; Chernigovskaia, Mariia; Stensland, Maria; Singh, Sachin; Leem, Jinwoo & Revale, Santiago [Show all 14 contributors for this article] (2024). Benchmarking and integrating human B-cell receptor genomic and antibody proteomic profiling. npj Systems Biology and Applications. 10. doi: 10.1038/s41540-024-00402-z. Full text in Research Archive Show summary

  Immunoglobulins (Ig), which exist either as B-cell receptors (BCR) on the surface of B cells or as antibodies when secreted, play a key role in the recognition and response to antigenic threats. The capability to jointly characterize the BCR and antibody repertoire is crucial for understanding human adaptive immunity. From peripheral blood, bulk BCR sequencing (bulkBCR-seq) currently provides the highest sampling depth, single-cell BCR sequencing (scBCR-seq) allows for paired chain characterization, and antibody peptide sequencing by tandem mass spectrometry (Ab-seq) provides information on the composition of secreted antibodies in the serum. Yet, it has not been benchmarked to what extent the datasets generated by these three technologies overlap and complement each other. To address this question, we isolated peripheral blood B cells from healthy human donors and sequenced BCRs at bulk and single-cell levels, in addition to utilizing publicly available sequencing data. Integrated analysis was performed on these datasets, resolved by replicates and across individuals. Simultaneously, serum antibodies were isolated, digested with multiple proteases, and analyzed with Ab-seq. Systems immunology analysis showed high concordance in repertoire features between bulk and scBCR-seq within individuals, especially when replicates were utilized. In addition, Ab-seq identified clonotype-specific peptides using both bulk and scBCR-seq library references, demonstrating the feasibility of combining scBCR-seq and Ab-seq for reconstructing paired-chain Ig sequences from the serum antibody repertoire. Collectively, our work serves as a proof-of-principle for combining bulk sequencing, single-cell sequencing, and mass spectrometry as complementary methods towards capturing humoral immunity in its entirety.

• Bashour, Habib; Smorodina, Eva; Pariset, Matteo; Zhong, Jahn; Akbar, Rahmad & Chernigovskaia, Maria [Show all 15 contributors for this article] (2024). Biophysical cartography of the native and human-engineered antibody landscapes quantifies the plasticity of antibody developability. Communications Biology. 7(1), p. 1–25. doi: 10.1038/s42003-024-06561-3. Full text in Research Archive Show summary

  Designing effective monoclonal antibody (mAb) therapeutics faces a multi-parameter optimization challenge known as “developability”, which reflects an antibody’s ability to progress through development stages based on its physicochemical properties. While natural antibodies may provide valuable guidance for mAb selection, we lack a comprehensive understanding of natural developability parameter (DP) plasticity (redundancy, predictability, sensitivity) and how the DP landscapes of human-engineered and natural antibodies relate to one another. These gaps hinder fundamental developability profile cartography. To chart natural and engineered DP landscapes, we computed 40 sequence- and 46 structure-based DPs of over two million native and human-engineered single-chain antibody sequences. We find lower redundancy among structure-based compared to sequence-based DPs. Sequence DP sensitivity to single amino acid substitutions varied by antibody region and DP, and structure DP values varied across the conformational ensemble of antibody structures. We show that sequence DPs are more predictable than structure-based ones across different machine-learning tasks and embeddings, indicating a constrained sequence-based design space. Human-engineered antibodies localize within the developability and sequence landscapes of natural antibodies, suggesting that human-engineered antibodies explore mere subspaces of the natural one. Our work quantifies the plasticity of antibody developability, providing a fundamental resource for multi-parameter therapeutic mAb design.

• Mhanna, Vanessa; Bashour, Habib; Quy, Khang Le; Barennes, Pierre; Rawat, Puneet & Greiff, Victor [Show all 7 contributors for this article] (2024). Adaptive immune receptor repertoire analysis. Nature Reviews Disease Primers. 4(1), p. 1–25. doi: 10.1038/s43586-023-00284-1. Full text in Research Archive
• Heimli, Marte; Flåm, Siri Tennebø; Hjorthaug, Hanne Sagsveen; Bjørnstad, Pål Marius; Chernigovskaia, Maria & Le, Quy Khang [Show all 9 contributors for this article] (2023). Human thymic putative CD8αα precursors exhibit a biased TCR repertoire in single cell AIRR-seq. Scientific Reports. 13:17714(1), p. 1–13. doi: 10.1038/s41598-023-44693-4. Full text in Research Archive Show summary

  Thymic T cell development comprises T cell receptor (TCR) recombination and assessment of TCR avidity towards self-peptide-MHC complexes presented by antigen-presenting cells. Self-reactivity may lead to negative selection, or to agonist selection and differentiation into unconventional lineages such as regulatory T cells and CD8 T cells. To explore the effect of the adaptive immune receptor repertoire on thymocyte developmental decisions, we performed single cell adaptive immune receptor repertoire sequencing (scAIRR-seq) of thymocytes from human young paediatric thymi and blood. Thymic PDCD1+ cells, a putative CD8 T cell precursor population, exhibited several TCR features previously associated with thymic and peripheral ZNF683+ CD8 T cells, including enrichment of large and positively charged complementarity-determining region 3 (CDR3) amino acids. Thus, the TCR repertoire may partially explain the decision between conventional vs. agonist selected thymocyte differentiation, an aspect of importance for the development of therapies for patients with immune-mediated diseases.

• Elster, Christin; Ommer-Bläsius, Miriam; Lang, Alexander; Vajen, Tanja; Pfeiler, Susanne & Feige, Milena [Show all 16 contributors for this article] (2023). Application and challenges of TCR and BCR sequencing to investigate T- and B-cell clonality in elastase-induced experimental murine abdominal aortic aneurysm. Frontiers in Cardiovascular Medicine. 10:1221620, p. 1–15. doi: 10.3389/fcvm.2023.1221620. Full text in Research Archive Show summary

  Background An abdominal aortic aneurysm (AAA) is a life-threatening cardiovascular disease. Although its pathogenesis is still poorly understood, recent evidence suggests that AAA displays autoimmune disease characteristics. Particularly, T cells responding to AAA-related antigens in the aortic wall may contribute to an initial immune response. Single-cell RNA (scRNA) T cell receptor (TCR) and B cell receptor (BCR) sequencing is a powerful tool for investigating clonality. However, difficulties such as limited numbers of isolated cells must be considered during implementation and data analysis, making biological interpretation challenging. Here, we perform a representative single-cell immune repertoire analysis in experimental murine AAA and show a reliable bioinformatic processing pipeline highlighting opportunities and limitations of this approach. Methods We performed scRNA TCR and BCR sequencing of isolated lymphocytes from the infrarenal aorta of male C57BL/6J mice 3, 7, 14, and 28 days after AAA induction via elastase perfusion of the aorta. Sham-operated mice at days 3 and 28 and non-operated mice served as controls. Results Comparison of complementarity-determining region (CDR3) length distribution of 179 B cells and 796 T cells revealed neither differences between AAA and control nor between the disease stages. We found no clonal expansion of B cells in AAA. For T cells, we identified several clones in 11 of 16 AAA samples and one of eight control samples. Immune receptor repertoire comparison indicated that only a few clones were shared between the individual AAA samples. The most frequently used V-genes in the TCR beta chain in AAA were TRBV3, TRBV19, and the splicing variant TRBV12-2 + TRBV13-2. Conclusion We found no clonal expansion of B cells but evidence for clonal expansion of T cells in elastase-induced AAA in mice. Our findings imply that a more precise characterization of TCR and BCR distribution requires a more extensive number of lymphocytes to prevent undersampling and potentially detect rare clones. Thus, further experiments are necessary to confirm our findings. In summary, this paper examines TCR and BCR sequencing results, identifies limitations and pitfalls, and offers guidance for future studies.

• Snapkov, Igor; Chernigovskaia, Maria; Sinitcyn, Pavel; Le, Quy Khang; Nyman, Tuula Anneli & Greiff, Victor (2021). Progress and challenges in mass spectrometry-based analysis of antibody repertoires. Trends in Biotechnology. ISSN 0167-7799. 00, p. 1–19. doi: 10.1016/j.tibtech.2021.08.006. Full text in Research Archive Show summary

  Humoral immunity is divided into the cellular B cell and protein-level antibody responses. High-throughput sequencing has advanced our understanding of both these fundamental aspects of B cell immunology as well as aspects pertaining to vaccine and therapeutics biotechnology. Although the protein-level serum and mucosal antibody repertoire make major contributions to humoral protection, the sequence composition and dynamics of antibody repertoires remain underexplored. This limits insight into important immunological and biotechnological parameters such as the number of antigen-specific antibodies, which are for example, relevant for pathogen neutralization, microbiota regulation, severity of autoimmunity, and therapeutic efficacy. High-resolution mass spectrometry (MS) has allowed initial insights into the antibody repertoire. We outline current challenges in MS-based sequence analysis of antibody repertoires and propose strategies for their resolution.

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• Quy, Khang Le; Greiff, Victor & Snapkov, Igor (2025). Integrative system immunology approaches to characterize immunoglobulin repertoires in health and disease. Universitetet i Oslo. ISSN 9788234806735. Full text in Research Archive Show summary

  B-cell receptors and antibodies are essential elements of the adaptive immune system, pivotal in pathogen recognition and neutralization, and widely utilized in diagnostics and therapeutic development. Their broad diversity, generated through various processes during immune cell development, demands effective profiling and characterization. High-throughput sequencing has emerged as a leading technique to capture B-cell receptor diversity, with single-cell sequencing further enhancing resolution and context for understanding immune responses. Despite the potential of these technologies, challenges such as undersampling and data preprocessing persist. Concurrently, mass spectrometry offers a unique lens to explore the effector antibody repertoire, complementing sequencing yet remains underutilized with uncertainties surrounding its analytical performance in antibody samples. In this thesis, Khang Le Quy focused on evaluating sequencing methodologies, particularly single-cell sequencing, delineating its capabilities and limitations. A novel integration of antibody bottom-up mass spectrometry data with sequencing datasets is introduced, presenting a complementary approach that broadens analytical scope in immune repertoire studies. Large-scale benchmarking of bottom-up mass spectrometry using ground-truth data is conducted, delivering insights into performance and future recommendations. Applying these methodologies, the thesis examines immune imprinting phenomena via sequential influenza infections, shedding light on how prior exposures influence immune responses. Collectively, this work highlights the transformative impact of merging advanced sequencing and mass spectrometry techniques on immunological research. paving the way for advancing the precision and scope of immune system analysis necessary for future biomedical breakthroughs.

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