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Introduction: The SARS-CoV-2 pandemic has had a widespread and severe impact on society, yet there have also been instances of remarkable recovery, even in critically ill patients., Materials and Methods: In this study, we used single-cell RNA sequencing to analyze the immune responses in recovered and deceased COVID-19 patients during moderate and critical stages., Results: Expanded T cell receptor (TCR) clones were predominantly SARS-CoV-2-specific, but represented only a small fraction of the total repertoire in all patients. In contrast, while deceased patients exhibited monoclonal B cell receptor (BCR) expansions without COVID-19 specificity, survivors demonstrated diverse and specific BCR clones. These findings suggest that neither TCR diversity nor BCR monoclonal expansions are sufficient for viral clearance and subsequent recovery. Differential gene expression analysis revealed that protein biosynthetic processes were enriched in survivors, but that potentially damaging mitochondrial ATP metabolism was activated in the deceased., Conclusion: This study underscores that BCR repertoire diversity, but not TCR diversity, correlates with favorable outcomes in COVID-19., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Paran, Oyama, Khasawneh, Ai, Ismanto, Sherif, Saputri, Ono, Saita, Takei, Horiuchi, Yagi, Matsuura, Okazaki, Takahashi, Standley, Tabe and Naito.)

Liquid biopsies based on peripheral blood offer a minimally invasive alternative to solid tissue biopsies for the detection of diseases, primarily cancers. However, such tests currently consider only the serum component of blood, overlooking a potentially rich source of biomarkers: adaptive immune receptors (AIRs) expressed on circulating B and T cells. Machine learning-based classifiers trained on AIRs have been reported to accurately identify not only cancers but also autoimmune and infectious diseases as well. However, when using the conventional "clonotype cluster" representation of AIRs, individuals within a disease or healthy cohort exhibit vastly different features, limiting the generalizability of these classifiers. This study aimed to address the challenge of classifying specific diseases from circulating B or T cells by developing a novel representation of AIRs based on similarity networks constructed from their antigen-binding regions (paratopes). Features based on this novel representation, paratope cluster occupancies (PCOs), significantly improved disease classification performance for infectious disease, autoimmune disease, and cancer. Under identical methodological conditions, classifiers trained on PCOs achieved a mean AUC of 0.893 when applied to new individuals, outperforming clonotype cluster-based classifiers (AUC 0.714) and the best-performing published classifier (AUC 0.777). Surprisingly, for cancer patients, we observed that "healthy-biased" AIRs were predicted to target known cancer-associated antigens at dramatically higher rates than healthy AIRs as a whole (Z scores >75), suggesting an overlooked reservoir of cancer-targeting immune cells that could be identified by PCOs., (© The Author(s) 2024. Published by Oxford University Press.)

Background/aim: Hematotoxicity is a life-threatening condition that has become the major cause of drug discontinuation in patients with acute lymphoblastic leukemia (ALL). The nudix hydrolase 15 (NUDT15) gene polymorphism (c.415C>T) is reported to have an association with the hematotoxicity of 6-mercaptopurine (6-MP) as maintenance therapy in patients with ALL. However, the prevalence of this genetic polymorphism in the Indonesian population is unknown. This study aimed to assess the frequency of NUDT15 polymorphism among Indonesian pediatric patients with ALL and its association with the hematotoxicity of 6-MP., Patients and Methods: A total of 101 stored DNA samples from pediatric patients with ALL receiving 6-MP treatment were used for genetic testing. Direct sequencing was conducted to determine the NUDT15 c.415C>T genotype. Chi-square or Fisher's exact test were employed to examine the association between the NUDT15 c.415C>T genotype and hematotoxicity., Results: All (100%) of the DNA samples from patients with ALL treated with 6-MP exhibited a homozygous variant of the NUDT15 c.415C>T genotype, 70.3% of which showed hematotoxicity to some extent. We found no significant differences in NUDT15 gene polymorphism among patients with ALL with different states of hematotoxicity., Conclusion: The observed high frequency of NUDT15 c.415C>T in our study population might explain the elevated prevalence of 6-MP-associated hematotoxicity in pediatric patients with ALL within the Indonesian population. Our study provides new insight regarding the NUDT15 gene polymorphism and its relation to hematotoxicity. Further studies are required to determine the necessity of adjusting the initial dose of 6-MP for Indonesian pediatric patients with ALL., (Copyright © 2024, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.)

Importance: Determining antigen and epitope specificity is an essential step in the discovery of therapeutic antibodies as well as in the analysis adaptive immune responses to disease or vaccination. Despite extensive efforts, deciphering antigen specificity solely from BCR amino acid sequence remains a challenging task, requiring a combination of experimental and computational approaches. Here, we describe and experimentally validate a simple and straightforward approach for grouping antibodies that share antigen and epitope specificities based on their CDR sequence similarity. This approach allows us to identify the specificities of a large number of antibodies whose antigen targets are unknown, using a small fraction of antibodies with well-annotated binding specificities., Competing Interests: We wish to disclose that we are in the process of applying for a patent describing the antibody clustering method.

Antibody and TCR modeling are becoming important as more and more sequence data becomes available to the public. One of the pressing questions now is how to use such data to understand adaptive immune responses to disease. Infectious disease is of particular interest because the antigens driving such responses are often known to some extent. Here, we describe tips for gathering data and cleaning it for use in downstream analysis. We present a method for high-throughput structural modeling of antibodies or TCRs using Repertoire Builder and its extensions. AbAdapt is an extension of Repertoire Builder for antibody-antigen docking from antibody and antigen sequences. ImmuneScape is a corresponding extension for TCR-pMHC 3D modeling. Together, these pipelines can help researchers to understand immune responses to infection from a structural point of view., (© 2023. Springer Science+Business Media, LLC, part of Springer Nature.)

Antibodies make up an important and growing class of compounds used for the diagnosis or treatment of disease. While traditional antibody discovery utilized immunization of animals to generate lead compounds, technological innovations have made it possible to search for antibodies targeting a given antigen within the repertoires of B cells in humans. Here we group these innovations into four broad categories: cell sorting allows the collection of cells enriched in specificity to one or more antigens; BCR sequencing can be performed on bulk mRNA, genomic DNA or on paired (heavy-light) mRNA; BCR repertoire analysis generally involves clustering BCRs into specificity groups or more in-depth modeling of antibody-antigen interactions, such as antibody-specific epitope predictions; validation of antibody-antigen interactions requires expression of antibodies, followed by antigen binding assays or epitope mapping. Together with innovations in Deep learning these technologies will contribute to the future discovery of diagnostic and therapeutic antibodies directly from humans., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Xu, Ismanto, Zhou, Saputri, Sugihara and Standley.)

Sacha inchi is a source of quality commercial oil in Taiwan. Oil extraction results in sacha inchi residue have not been utilized and not much investigated. Different edible seeds and nuts have different levels of nutrients. This study aims (a) to determine the oil, moisture, ash, protein, carbohydrate, type of fatty acid, resveratrol, and type of sugar in edible seeds and nuts, including sacha inchi residue, and (b) to determine the model to predict the five macronutrients using NIR spectroscopy. The samples used were candlenut, peanut, sesame, sunflower, sacha inchi residue, and black bean. Determination was conducted using NIR spectroscopy, NMR spectroscopy, LC-MS/MS, and HPLC-ELSD. NIR spectroscopy prediction results show that candlenut is rich in oil, and sacha inchi residue is rich in minerals, protein, and moisture. The correct prediction model for oil and moisture is principal component regression, while partial least squares are for ash, protein, and carbohydrates. NMR spectroscopy results showed that all samples were rich in polyunsaturated fatty acids. Sacha inchi residue is rich in omega 3. LC-MS/MS results showed that all samples contained resveratrol, and its highest level was found in sesame. HPLC-ELSD results showed eight types of sugars in the samples. High sucrose was found in sacha inchi residue, sunflower, sesame, and candlenut. The results are expected to provide information on nutrient levels in seeds and nuts to consumers and people who deal with nutrition. Also, results are expected to increase the economic value of sacha inchi residue as a source of diversification of food products in Taiwan., Competing Interests: The authors declare that they have no conflicts of interest., (Copyright © 2022 Sahri Yanti et al.)

As the highest yield crop worldwide, citrus peels that possess bioactive compounds were discarded as a futile by-product. Ultrasonication with environmentally friendly solvent (50% ethanol and ddH 2 O) were used in the present study to extract flavonoids from Citrus depressa Hayata peels with extraction period and fruit maturity as other variables. DPPH scavenging activity was investigated. Qualitative flavonoid content analysis was done by UV/Vis and FTIR-ATR spectra. Quantification of flavonoid using LC-MS/MS found that solvent type, fruit maturity, and ultrasonication period significantly affect the extracted flavonoid yield (p < 0.05). Extraction using 50% ethanol showed a higher yield than ddH 2 O. Flavonoid content was also higher in unripe than ripe samples. Nobiletin, tangeretin, and rutin were dominant among the identified compounds in all sample treatments. Flavonoid content in Citrus depressa Hayata extract was found to negatively correlate to DPPH scavenging activity, which needs further research to identify other bioactivities of these flavonoids., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2022 The Author(s).)

To assess the frequency of SARS-CoV-2 infection in the general population, we searched over 64 million heavy chain antibody sequences from healthy unvaccinated, healthy BNT162b2 vaccinated and COVID-19 patient repertoires for sequences similar to 11 previously reported enhancing antibodies. Although the distribution of sequence identities was similar in all three groups of repertoires, the COVID-19 and healthy vaccinated hits were significantly more clonally expanded than healthy unvaccinated hits. Furthermore, among the tested hits, 17 out of 94 from COVID-19 and 9 out of 59 from healthy vaccinated, compared with only 2 out of 96 from healthy unvaccinated, bound to the enhancing epitope. A total of 9 of the 28 epitope-binding antibodies enhanced ACE2 receptor binding to the spike protein. Together, this study revealed that infection enhancing-like antibodies are far more frequent in COVID-19 patients or healthy vaccinated donors than in healthy unvaccinated donors, but a reservoir of potential enhancing antibodies exists in healthy donors that could potentially mature to actual enhancing antibodies upon infection., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2022 The Author(s).)

The SARS-CoV-2 S protein is a major point of interaction between the virus and the human immune system. As a consequence, the S protein is not a static target but undergoes rapid molecular evolution. In order to more fully understand the selection pressure during evolution, we examined residue positions in the S protein that vary greatly across closely related viruses but are conserved in the subset of viruses that infect humans. These "evolutionarily important" residues were not distributed evenly across the S protein but were concentrated in two domains: the N-terminal domain and the receptor-binding domain, both of which play a role in host cell binding in a number of related viruses. In addition to being localized in these two domains, evolutionary importance correlated with structural flexibility and inversely correlated with distance from known or predicted host receptor-binding residues. Finally, we observed a bias in the composition of the amino acids that make up such residues toward more human-like, rather than virus-like, sequence motifs., (Copyright © 2020 Saputri, Li, van Eerden, Rozewicki, Xu, Ismanto, Davila, Teraguchi, Katoh and Standley.)

B cell receptors (BCRs) and T cell receptors (TCRs) make up an essential network of defense molecules that, collectively, can distinguish self from non-self and facilitate destruction of antigen-bearing cells such as pathogens or tumors. The analysis of BCR and TCR repertoires plays an important role in both basic immunology as well as in biotechnology. Because the repertoires are highly diverse, specialized software methods are needed to extract meaningful information from BCR and TCR sequence data. Here, we review recent developments in bioinformatics tools for analysis of BCR and TCR repertoires, with an emphasis on those that incorporate structural features. After describing the recent sequencing technologies for immune receptor repertoires, we survey structural modeling methods for BCR and TCRs, along with methods for clustering such models. We review downstream analyses, including BCR and TCR epitope prediction, antibody-antigen docking and TCR-peptide-MHC Modeling. We also briefly discuss molecular dynamics in this context., (© 2020 The Author(s).)