Biology subjects

Ma, B.

Publications and source records attributed to Ma, B..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Transplant immunosuppressant therapies induce unique functional changes in lymph node and re-shape gut immune homeostasis

BackgroundLifelong immunosuppressive therapy is required to prevent allograft rejection in organ transplantation. Current immunosuppressants effectively suppress adaptive and innate immune responses, but their broad, antigen-non-specific effects often result in severe off-target complications. It remains a significant unmet medical need in transplant medicine. ResultsIn this study we investigated immunosuppressant effects of four major immunosuppressant classes, including tacrolimus, prednisone, mycophenolate mofetil (MMF), and fingolimod (FTY), on the gut microbiome, metabolic pathways, lymphoid architecture and lymphocyte trafficking after up to 30-day chronic exposure. Despite their distinct mechanisms of action and not designed to target the gut, all immunosuppressive drugs induced profound and time-dependent alterations in both intestine gene expression and gut microbiome composition. Progressive alterations from moderate early, drug-specific changes to a strikingly convergent microbial dysbiosis, marked by significant expansion of pathobionts of Muribaculaceae, occurred across all drug classes. Concurrently, all drugs uniformly induced significant suppression of mucosal immunity including B cell, immunoglobulin, and antigen recognition. Time-dependent changes in lymph node (LN) reorganization and cellular composition were also observed, marked by a progressive shift toward pro-inflammatory phenotypes in gut-draining mesenteric LNs and a gradual loss of tolerogenic architecture in peripheral LNs. Drug-specific metabolic alterations and distinct phases of intestinal transcriptional responses were also characterized. Notably, MMF and FTY demonstrated the most robust immunomodulatory properties, and were able to suppress alloantigen-induced inflammation through mediating regulatory T cell distribution and LN remodeling. ConclusionsTogether, these findings highlight the underappreciated complexity and temporal dynamics immunosuppressants effects, particularly their impact on the gut and compartmentalized regulation of alloimmune in lymphoid tissues. Understanding these relationships offers new opportunities for refining immunosuppressive strategies to reduce treatment-related off-target complications and improve long-term organ transplant outcomes.

immunology↗

bioRxiv2024

The genetic diversity and populational specificity of the human gut virome at single nucleotide resolution

Large-scale characterization of gut viral genomes provides strain-resolved insights into host-microbe interactions. However, existing viral genomes are mainly derived from Western populations, limiting our understanding of global gut viral diversity and functional variations necessary for personalized medicine and addressing regional health disparities. Here, we introduce the Chinese Gut Viral Reference (CGVR) set, consisting of 120,568 viral genomes from 3,234 deeply sequenced fecal samples collected nationwide, covering 72,751 viral species-level clusters (VSCs), nearly 90% of which are absent from current databases. Analysis of single nucleotide variations (SNVs) in 233 globally prevalent VSCs revealed that 18.9% showed significant genetic stratification between Chinese and non-Chinese populations, potentially linked to bacterial infection susceptibility. The predicted bacterial hosts of population-stratified viruses exhibit distinct genetic components associated with health-related functions, including multidrug resistance. Additionally, viral strain diversity at the SNV level correlated with human phenotypic traits, such as age and gastrointestinal issues like constipation. Our analysis also indicates that the human gut bacteriome is specifically shaped by the virome, which mediates associations with human phenotypic traits. This foundational resource underscores the unique genetic makeup of the gut virome across populations and emphasizes the importance of recognizing gut viral genetic heterogeneity for deeper insights into regional health implications.

microbiology↗

bioRxiv2024

Population comparisons reveal more social interactions are correlated with larger brains in the Lake Tanganyikan cichlid Neolamprologus brevis

The Social Brain Hypothesis (SBH) proposes that complex social environments drive the evolution of larger brains and specific neuroanatomical adaptations. This relationship can be difficult to study in the wild, because species that differ in social organization may also diverge in morphology, ecology, phylogeny, and other life history parameters. Here we use two populations of the shell-dwelling cichlid Neolamprologus brevis with contrasting social environments to test whether increased social complexity is associated with larger brain sizes or specific regional adaptations. Behavioral observations revealed similarly low feeding rates in both populations, but significantly more frequent social interaction frequencies in the population one of the populations. This population had larger total brain volumes relative to body size, with a disproportionately larger telencephalon and a smaller hypothalamus, suggesting region-specific adaptations to social demands. By integrating behavioral quantification and neuroanatomical analysis, our study highlights the importance of sociality as a driver of brain evolution and demonstrates the utility of cichlid fish as a model for testing the SBH in non-mammalian systems. These findings provide empirical support for the SBH and underscore the value of combining behavioral and morphological data in evolutionary neuroethology.

animal behavior and cognition↗

bioRxiv2024

Multiple within species comparisons show Tanganyikan cichlid fish have larger brains in less structurally complex habitats

Many studies have found a link between higher habitat structural complexity and increased relative brain size in vertebrates. Here we explore this relationship in a multi-species comparison, comparing ten species of wild cichlids that differ in their social and territorial behaviour, but which occur across four ecologically similar but structurally diverse rocky habitats. This design allows us to perform repeated intra-specific comparisons, avoiding confounds associated with comparisons across species boundaries. We sampled 147 fish, analysing brain size and architecture while controlling for body mass and species-specific variability and compared this with habitat complexity, quantified using underwater video and three-dimensional reconstructions. Our results challenge the Clever Foraging Hypothesis (CFH), which posits that greater habitat complexity correlates with larger brain sizes. Contrary to CFH, fish from the least complex habitat had significantly larger brains. Additionally, brain architecture analysis indicated a significant enlargement of the cerebellum in fish from less complex habitats, whereas the hypothalamus showed a non-significant negative trend. Taken together, these results indicate that lower habitat complexity may impose higher cognitive demands on spatial memory and navigation due to limited refuges and increased predation risk. This study highlights the need to reconsider the assumed linear positive relationship between environmental complexity and brain development, suggesting that simpler environments might also impose significant cognitive and ecological challenges that drive brain evolution. Our findings underscore the importance of considering intra-species variability and the specific ecological and cognitive demands of different habitats in studies of brain evolution.

evolutionary biology↗

bioRxiv2024

Cardiolipin-mimic lipid nanoparticles without antibody modification delivered senolytic in-vivo CAR-T therapy for inflamm-aging

mRNA-based in vivo CAR T cell engineering offers advantages over ex vivo therapies, including streamlined manufacturing and transient expression. However, current delivery requires antibody-modified vehicles with manufacturing challenges. In this study, inspired by cardiolipin, we identified a cardiolipin-like di-phosphoramide lipid that improved T cell transfection without targeting ligands, both in vivo and in vitro. The T cell-favored tropism is likely due to the lipids packing, shape, and rigidity. Encapsulating circular RNA further prolonged mRNA expression in the spleen and T cells. Using PL40 lipid nanoparticles, we delivered mRNA encoding a CAR targeting the senolytic and inflammatory antigen urokinase-type plasminogen activator receptor (uPAR), alleviating uPAR-related liver fibrosis and rheumatoid arthritis (RA). Single cell sequencing in humans confirmed uPARs relevance to senescence and inflammation in RA. To further enhance clinical translation, we screened and humanized scFvs against uPAR, establishing PL40 mRNA encoding a circular human uPAR CAR, with potential for treating aging-inflamed disorders. One Sentence SummaryWeve developed a unique class of Cardiolipin-mimic lipids that facilitate mRNA delivery to T cells in vivo without the need for antibody modification, enhancing the treatment of liver fibrosis and rheumatoid arthritis through circular CAR uPAR RNA and propelling the clinical application of humanized CAR against human uPAR.

bioengineering↗

bioRxiv2024

ABA increases fatty acids levels in apple roots to boost colonization by arbuscular mycorrhizal fungi

The roots of most land plants are in symbiosis with arbuscular mycorrhizal (AM) fungi. The fungus promotes nutrient uptake from the soil while receiving plant photosynthate as lipids and sugars. Nutrient exchange must be regulated by both partners, but the mechanisms underlying the regulation of lipid supplement from the plant to the AM fungus remain elusive. Here, we conducted a molecular study on the role of increased abscisic acid (ABA) levels during AM fungus infection in the roots of apple (Malus spp.). AM fungus induced the expression of two ABA synthesis genes, MdNCED3.1 and 3.2, in apple roots and increased the ABA content, which promoted the growth of the AM fungus. The effect of ABA on symbiosis was confirmed in transgenic apple roots either overexpressing or silencing MdNCED3.1 or MdNCED3.2. Transcriptome analysis and transgenic manipulation revealed that the transcription factor MdABF2 played a key role in the ABA-mediated formation of symbiosis during AM infection and that MdABF2 could regulate the expression levels of genes related to fatty acid (FA) synthesis (e.g., MdKASIII) and translocation (such as MdSTR2) in apple roots. Activation of these genes boosted the levels of available fatty acids in the roots and increased the AM fungal colonization and arbuscule development in the roots. These results revealed a molecular pathway in which positive regulation of FA synthesis and transport by the ABA signaling pathway increases supplementation to AM fungi and promotes AM symbiosis.

molecular biology↗

bioRxiv2024

Genomic diversity and underlying metabolic variations of the human gut microbiome between populations at single nucleotide resolution

BackgroundA comprehensive and representative reference database is crucial for accurate taxonomic and functional profiling of the human gut microbiome in population-level studies. However, with 70% of current microbial reference data derived from Europeans and the Americans, East Asia, especially China, remain underrepresented. MethodsWe constructed the human Gut Microbiome Reference (GMR), comprising 478,588 high-quality microbial genomes from Chinese (247,134) and non-Chinese (231,454) populations. Species-level clustering and protein annotations were performed to characterize microbial diversity and function. We further integrated novel genomes into taxonomic profiling database and validated the improvements using independent cohort data. ResultsThe GMR dataset spans 6,664 species, including 26.4% newly classified species, and encodes over 20 million unique proteins, with 47% lacking known functional annotations. Notably, we observed that 35.35% and 32.46% of species unique to Chinese and non-Chinese populations, respectively. For 2,145 species shared between populations, 74% of 304 species with balanced prevalence between populations exhibited population-specific phylogenetic stratification, involving health relevant functionalities such as antibiotic resistance. Integration of novel genomes into taxonomic improved population-level species profiling by up to 23% and uncovered replicable associations between novel species and host physiological traits. ConclusionsOur study largely expands the compositional and functional landscape of the human gut microbiome, providing a crucial resource for studying the role of gut microbiome for regional health disparities.

genomics↗

bioRxiv2024

Rapamycin Immunomodulation Utilizes Time-Dependent Alterations of Lymph Node Architecture, Leukocyte Trafficking, and Gut Microbiome

Transplant recipients require lifelong, multimodal immunosuppression to prevent rejection by reducing alloreactive immunity. Rapamycin, a mechanistic target of rapamycin (mTOR) inhibitor, is known to modulate adaptive and innate immunity, while the full spectrum of its immunosuppressive mechanisms remains incompletely understood. Given the broad expression of mTOR, we investigated the understudied effects of rapamycin on lymph node (LN) architecture, leukocyte trafficking, and the gut microbiome and metabolism after 3, 7, and 30 days of rapamycin treatment, to characterize the early, intermediate, and late changes. Rapamycin significantly reduced CD4+ T cells, CD8+ T cells, and regulatory T (Treg) cells in peripheral LNs, mesenteric LNs, and the spleen over time. Rapamycin induced early pro-inflammation transition to pro-tolerogenic status, by modulating the LN laminin 4:5 expression ratios through LN stromal cells laminin 5 expression and by adjusting Treg numbers and distribution. Additionally, rapamycin significantly altered gut microbiota composition and metabolic functions, shifting the Bacteroides to Firmicutes ratio and increasing amino acid bioavailability in the gut lumen. These effects were evident by 7 days and became most pronounced by 30 days in naive mice, with notable changes as early as 3 days in allogeneic splenocyte-stimulated mice. These findings reveal a novel mechanism of rapamycins action through time-dependent modulation of LN architecture and gut microbiome, which orchestrates changes in immune cell trafficking, providing a new framework for understanding and optimizing immunosuppressive therapies.

immunology↗

bioRxiv2024

Gas1-Mediated Suppression of Hepatoblastoma Tumorigenesis

Background and AimsHepatoblastoma (HB), the most common pediatric liver cancer, often dysregulates the Wnt/{beta}-catenin, Hippo and NFE2L2/NRF2 pathways. Pairwise combinations of oncogenically active forms of the terminal transcription factor effectors of these pathways, namely {beta}-catenin (B), YAP (Y) and NRF2 (N) generate HBs in mice, with the triple combination (B+Y+N) being particularly potent. Each tumor group alters the expression of thousands of B-,Y- and N-driven unique and common target genes. Identifying those most responsible for transformation is thus an important question as it might reveal new mechanistic insights and therapeutic opportunities. Approach and ResultsTranscriptional profiling of >60 murine HBs driven by the above oncogenic combinations and different B mutants and in genetic backgrounds that impair tumor growth rates but not initiation has revealed a common set of 22 "BYN genes" that are similarly deregulated in all cases. Many are associated with multiple "Cancer Hallmarks" and their expression levels often correlate with survival in human HBs, hepatocellular carcinomas and other cancers. Among the most down-regulated of these is Gas1, which encodes a Glycosylphosphatidylinositol (GPI)-linked outer membrane protein. We show here that restoring Gas1 expression impairs B+Y+N-driven HB tumor growth in vivo and in HB-derived immortalized cell lines in vitro in a manner than requires membrane anchoring of the protein via its GPI moiety. ConclusionsOur findings implicate Gas1 as a proximal mediator of HB pathogenesis and validate the BYN gene set as one deserving of closer additional scrutiny in future studies.

cancer biology↗

bioRxiv2024

Efficient Derivation of Immortalized, Isogenic Cell Lines from Genetically Defined Murine Hepatoblastomas

Background & AimsMolecularly, hepatoblastoma (HB), the most common childhood liver cancer, is the simplest of all human neoplasms, with the vast majority deregulating the Wnt/{beta}-catenin, Hippo and/or NFE2/NRF2 signaling pathways. Murine HBs can be generated by over-expressing any pairwise or triple combination of mutant forms of these pathways terminal effectors, namely {beta}-catenin (B), YAP (Y) and NFE2L2/NRF (N). Each molecular subtypes displays distinct features resembling those of human HBs. However, research has been hampered by a paucity of established cell lines of any species. MethodsWe show here that immortalized cell lines can be routinely established from murine HBs that over-express B+Y and B+Y+N. This is facilitated by the concurrent in vivo, Crispr-mediated inactivation of the Cdkn2a tumor suppressor locus. ResultsEight BY and 3 BYN cell lines have been generated and characterized and are available to the HB research community. Ten of these lines can be regrown as subcutaneous and metastatic lung tumors in the immuno-competent mice from which they originated while retaining their original histologic features. During maintenance as spheroids in vitro, or during in vivo propagation, tumor cells express endothelial cell markers, particularly in regions that are hypoxic and/or in proximity to incipient blood vessels. ConclusionsThe ability to generate isogenic HB cell lines with defined oncogenic drivers should facilitate studies that are best performed in vitro. The approach may also be useful for deriving HB cell lines associated with less common molecular drivers and from human tumors. SynopsisThe derivation of multiple immortalized murine hepatoblastoma cell lines driven by defined oncogenes is described. These lines are isogenic, retain their tumorigenicity in immuno-competent mice, readily form spheroids and express endothelial markers in response to hypoxia. They will allow studies that have heretofore been difficult or impossible to perform in vivo.

cancer biology↗

bioRxiv2024

Modulating DNA Polα Enhances Cell Reprogramming Across Species

As a fundamental biological process, DNA replication ensures the accurate copying of genetic information. However, the impact of this process on cellular plasticity in multicellular organisms remains elusive. Here, we find that reducing the level or activity of a replication component, DNA Polymerase (Pol), facilitates cell reprogramming in diverse stem cell systems across species. In Drosophila male and female germline stem cell lineages, reducing Pol levels using heterozygotes significantly enhances fertility of both sexes, promoting reproductivity during aging without compromising their longevity. Consistently, in C. elegans the pola heterozygous hermaphrodites exhibit increased fertility without a reduction in lifespan, suggesting that this phenomenon is conserved. Moreover, in male germline and female intestinal stem cell lineages of Drosophila, pol heterozygotes exhibit increased resistance to tissue damage caused by genetic ablation or pathogen infection, leading to enhanced regeneration and improved survival during post-injury recovery, respectively. Additionally, fine tuning of an inhibitor to modulate Pol activity significantly enhances the efficiency of reprogramming human embryonic fibroblasts into induced pluripotent cells. Together, these findings unveil novel roles of a DNA replication component in regulating cellular reprogramming potential, and thus hold promise for promoting tissue health, facilitating post-injury rehabilitation, and enhancing healthspan.

developmental biology↗

bioRxiv2024

ProtRNA: A Protein-derived RNA Language Model by Cross-Modality Transfer Learning

Protein language models (PLM), such as the highly successful ESM-2, have proven particularly effective. However, language models designed for RNA continue to face challenges. A key question is: can the information derived from PLMs be harnessed and transferred to RNA? To investigate this, a model termed ProtRNA has been developed by cross-modality transfer learning strategy for addressing the challenges posed by RNAs limited and less conserved sequences. By leveraging the evolutionary and physicochemical information encoded in protein sequences, the ESM-2 model is adapted to processing "low-resource" RNA sequence data. The results show comparable or superior performance in various RNA downstream tasks, with only 1/8 the trainable parameters and 1/6 the training data employed by the primary reference baseline RNA language model. This approach highlights the potential of cross-modality transfer learning in biological language models.

bioinformatics↗

bioRxiv2024

MYC Binding Near Transcriptional End Sites Regulates Basal Gene Expression, Read-Through Transcription and Intragenic Contacts

The MYC oncoprotein regulates numerous genes involved in cellular processes such as cell cycle and mitochondrial and ribosomal structure and function. This requires heterodimerization with its partner, MAX, and binding to specific promoter and enhancer elements. Here, we show that MYC and MAX also bind near transcriptional end sites (TESs) of over one-sixth of all annotated genes. These interactions are dose-dependent, evolutionarily conserved, stabilize the normally short-lived MYC protein and regulate expression both in concert with and independent of MYCs binding elsewhere. MYCs TES binding occurs in association with other transcription factors, alters the chromatin landscape, increases nuclease susceptibility and can alter transcriptional read-through, particularly in response to certain stresses. MYC-bound TESs can directly contact promoters and may fine-tune gene expression in response to both physiologic and pathologic stimuli. Collectively, these findings support a previously unrecognized role for MYC in regulating transcription and its read-through via direct intragenic contacts between TESs and promoters.

molecular biology↗

bioRxiv2024

Deep learning of protein energy landscape and conformational dynamics from experimental structures in PDB

Protein structure prediction has reached revolutionary levels of accuracy on single structures, implying biophysical energy function can be learned from known protein structures. However apart from single static structure, conformational distributions and dynamics often control protein biological functions. In this work, we tested a hypothesis that protein energy landscape and conformational dynamics can be learned from experimental structures in PDB and coevolution data. Towards this goal, we develop DeepConformer, a diffusion generative model for sampling protein conformation distributions from a given amino acid sequence. Despite the lack of molecular dynamics (MD) simulation data in training process, DeepConformer captured conformational flexibility and dynamics (RMSF and covariance matrix correlation) similar to MD simulation and reproduced experimentally observed conformational variations. Our study demonstrated that DeepConformer learned energy landscape can be used to efficiently explore protein conformational distribution and dynamics.

biophysics↗

bioRxiv2024

LooMS: a novel peptide identification tools for data independent acquisition

Advancements in mass spectrometry (MS)-based proteomics have produced large-scale datasets, necessitating the development of effective tools for peptide identification. Here, we present LooMS, a novel tool specifically designed for identifying peptides in data-independent acquisition (DIA) datasets. LooMS employs an innovative approach, using an unbiased generation strategy for positive and negative samples, which reduces the risk of overfitting in peptide identification with deep learning models. Additionally, LooMS addresses various critical aspects of DIA mass spectra data analysis, constructing a comprehensive set of 43 features for training deep learning models, which cover different stages of DIA data analysis. Notably, we propose a false discovery rate (FDR) control strategy that integrates results from both LooMS and DiaNN, another leading peptide identification tool. Our results demonstrate significant improvements in peptide identification performance, with enhancements of 40.61% and 26.60% at the unique peptide level for human and mouse datasets, respectively. HighlightsO_LILooMS is a novel tool for identifying peptides in DIA datasets that adopts an innovative unbiased positive and negative sample generation strategy, which aim to avoid the overfilling in peptide identification with deep learning model. C_LIO_LILooMS comprehensively considers various aspects of data analysis for DIA mass spectra and builds 43 useful features for training deep learning models, which involve different stages of DIA data analysis. C_LIO_LIA FDR control strategy for integration of results from both LooMS and DiaNN is proposed, which can significantly improve the identification of peptides due to the differences in the features involved in peptide detection during their respective design. C_LI

bioinformatics↗

bioRxiv2024

Neural basis of cognitive control signals in anterior cingulate cortex during delay discounting

Cognitive control involves allocating cognitive effort according to internal needs and task demands. The anterior cingulate cortex (ACC) is hypothesized to play a central role in this process. We investigated the neural basis of cognitive control in the ACC of rats performing an adjusting-amount delay discounting task, with a 4s or 8s delay between lever choice and reward. A reinforcement learning model indicated that decision making on this task can be guided by either a value tracking strategy, requiring a resource-based form of cognitive control or a delay-lever biased strategy requiring a resistance-based form of cognitive control. This was then tested in vivo by multiple single unit recordings and local field potentials acquired from male rats performing the task. On this task, the behavioral manifestation of resistance-based control is an excessive focus on delayed lever choices which was observed during a substantial portion of 4s but not 8s delay sessions. On a neural level, this was associated with an increase in Theta (6-12Hz) oscillations prior to delay choices which was present exclusively on 4s delay sessions. By contrast, evidence of a resource-based control signal was found in spike trains that closely tracked lever value prior to choice, and was far more prevalent on 8s delay sessions. These data provide candidate neural signatures of resource-based versus resistance-based forms of cognitive control. While mediated by distinct neural mechanisms, either form could be engaged by individual subjects under different task conditions.

neuroscience↗

bioRxiv2024

Discovery and Synthesis of GS-7682, a Novel Prodrug of a 4'-CN-4-Aza-7,9-Dideazaadenosine C-Nucleoside with Broad-Spectrum Potency Against Pneumo- and Picornaviruses and Efficacy in RSV-Infected African Green Monkeys.

Acute respiratory viral infections (ARVI), such as pneumovirus and respiratory picornavirus infections, exacerbate disease in COPD and asthma patients. A research program targeting respiratory syncytial virus (RSV) led to the discovery of GS-7682 (1) a novel phosphoramidate prodrug of a 4'-CN-4-aza-7,9-dideazaadenosine C-nucleoside GS-646089 (2) with broad antiviral activity against RSV EC50 = 3-46 nM, human metapneumovirus (hMPV) EC50 = 210 {+/-} 50 nM, human rhinovirus (RV) EC50 = 54-61 nM, and enterovirus (EV) EC50 = 83-90 nM. Prodrug optimization for cellular potency and lung cell metabolism identified the 5-methyl((S)-hydroxy(phenoxy)phosphoryl)-L-alaninate in combination with 2,3-diisobutyrate promoieties as optimal for high intracellular triphosphate formation in vitro and in vivo. 1 demonstrated significant reductions of viral loads in the lower respiratory tract of RSV-infected African green monkeys when administered once daily via intratracheal nebulized aerosol. Together these finding support additional evaluation of 1 and its analogs as a potential therapeutic for pneumo- and picornaviruses.

biochemistry↗

bioRxiv2024

de Novo Sequencing of Antibodies for Identification of Neutralizing Antibodies in Human Plasma Post SARS-CoV-2 Vaccination

We present a method for sequencing polyclonal IgG enriched from human plasma, employing a combination of de novo sequencing, proteomics, bioinformatics, protein separation, sequencing, and peptide separations. Our study analyzes a single patients IgG antibody response triggered by the Moderna Spikevax mRNA COVID-19 vaccine. From the sequencing data of the natural polyclonal response to vaccination, we generated 12 recombinant antibodies. Six derived recombinant antibodies, including four generated with de novo sequencing, exhibited similar or higher binding affinities than the original natural polyclonal antibody. Our neutralization tests revealed that the six antibodies possess neutralizing capabilities against the target antigen. This research provides insights into sequencing polyclonal IgG antibodies while highlighting the effectiveness and potential of our approach in generating recombinant antibodies with robust binding affinity and neutralization capabilities. Our proposed approach is an advancement in characterizing the IgG response by directly investigating the circulating pool of IgG without relying exclusively on the B-cell repertoire or population. This is crucial as the B-cell analysis may not accurately represent the circulating antibodies. Interestingly, a large proportion (80 to 90%) of the human antibody sequences generated against SARS-CoV-2 in the literature have been derived solely from B-cell analysis. Therefore, the ability to offer a different perspective is crucial in gaining a comprehensive understanding of the IgG response. Significance StatementWe investigate human IgG targeting the receptor binding domain using de novo proteomics. The peripheral B-cell repertoire may not adequately cover all the circulating IgG for human IgG sequencing. Our approach overcomes this limitation by using a de novo protein sequencing on top of standard proteomics. We obtained distinct de novo sequences, showcasing our methods potential. The recombinant proteins we generate possess traits comparable to or surpassing the naturally occurring polyclonal antibodies (pAbs). This study highlights similarities and differences between IgG populations in blood and circulating B-cells, which is crucial for future biologics development.

immunology↗