Diagnostic Antibodies Research Articles

Development of anti-aflatoxin B1 nanobodies from a novel mutagenesis-derived synthetic library for traditional Chinese medicine and foods safety testing

BackgroundThe main commercially available methods for detecting small molecules of mycotoxins in traditional Chinese medicine (TCM) and functional foods are enzyme-linked immunosorbent assay and mass spectrometry. Regarding the development of diagnostic antibody reagents, effective methods for the rapid preparation of specific monoclonal antibodies are inadequate.MethodsIn this study, a novel synthetic phage-displayed nanobody Golden Glove (SynaGG) library with a glove-like cavity configuration was established using phage display technology in synthetic biology. We applied this unique SynaGG library on the small molecule aflatoxin B1 (AFB1), which has strong hepatotoxicity, to isolate specific nanobodies with high affinity for AFB1.ResultThese nanobodies exhibit no cross-reactivity with the hapten methotrexate, which is recognized by the original antibody template. By binding to AFB1, two nanobodies can neutralize AFB1-induced hepatocyte growth inhibition. Using molecular docking, we found that the unique non-hypervariable complementarity-determining region 4 (CDR4) loop region of the nanobody was involved in the interaction with AFB1. Specifically, the CDR4’s positively charged amino acid arginine directed the binding interaction between the nanobody and AFB1. We then rationally optimized the interaction between AFB1 and the nanobody by mutating serine at position 2 into valine. The binding affinity of the nanobody to AFB1 was effectively improved, and this result supported the use of molecular structure simulation for antibody optimization.ConclusionIn summary, this study revealed that the novel SynaGG library, which was constructed through computer-aided design, can be used to isolate nanobodies that specifically bind to small molecules. The results of this study could facilitate the development of nanobody materials to detect small molecules for the rapid screening of TCM materials and foods in the future.

Altered somatic hypermutation patterns in COVID-19 patients classifies disease severity.

The success of the human body in fighting SARS-CoV2 infection relies on lymphocytes and their antigen receptors. Identifying and characterizing clinically relevant receptors is of utmost importance. We report here the application of a machine learning approach, utilizing B cell receptor repertoire sequencing data from severely and mildly infected individuals with SARS-CoV2 compared with uninfected controls. In contrast to previous studies, our approach successfully stratifies non-infected from infected individuals, as well as disease level of severity. The features that drive this classification are based on somatic hypermutation patterns, and point to alterations in the somatic hypermutation process in COVID-19 patients. These features may be used to build and adapt therapeutic strategies to COVID-19, in particular to quantitatively assess potential diagnostic and therapeutic antibodies. These results constitute a proof of concept for future epidemiological challenges.

A procedure for producing an anti-AXL nanobody in E. coli

As one of the receptors of the TAM family, AXL plays a vital role in stem cell maintenance, angiogenesis, immune escape of viruses and drug resistance against tumors. In this study, the truncated extracellular segment containing two immunoglobulin-like domains of human AXL (AXL-IG), which has been confirmed to bind growth arrest specific 6 (GAS6) by structural studies [1], was expressed in a prokaryotic expression system and then purified. Immunizing camelid with the purified AXL-IG as antigen could lead to the production of unique nanobodies composed of only variable domain of heavy chain of heavy-chain antibody (VHH), which are around 15 kD and stable. We screened out a nanobody A-LY01 specific binding to AXL-IG. We further determined the affinity of A-LY01 to AXL-IG and revealed that A-LY01 could specifically recognize full-length AXL on the surface of HEK 293T/17 cells. Our study provides appropriate support for the development of diagnostic reagents and antibody therapeutics targeting AXL.

Abstract 3300: Development of a diagnostic antibody for anti-BTN1A1 therapy, a novel immune checkpoint inhibitor mutually exclusive of PD-L1/PD-1

Abstract Butyrophilin 1A1 (BTN1A1) is currently undergoing investigation in Phase 1 clinical trials as a novel immune checkpoint protein for the treatment of solid tumors. BTN1A1 exhibits a mutually exclusive expression pattern to that of PD-1/PD-L1, making anti-BTN1A1 antibody therapy an attractive option for cancer patients with PD-L1 refractory or relapsed disease. While current cancer immunotherapies have shown some efficacy against late-stage disease, there remains a major unmet medical need as a large number of patients fail to respond to current treatments. BTN1A1 has been studied at length in preclinical models to characterize its immunomodulatory functions, revealing its ability to inhibit the proliferation of activated T cells and the ability of these cells to kill tumor cells in vitro. In vivo, BTN1A1-overexpressing tumor models exhibit accelerated growth, whereas the growth of BTN1A1-deficient tumors is impaired in immunocompetent settings, supporting a role for this protein in the regulation of immune evasion. Here in, we present the development of a diagnostic antibody for use in the anti-BTN1A1 therapy clinical trials to enable the immunohistochemical (IHC) detection of human BTN1A1. A high-quality BTN1A1 antibody may help predict which patients are more likely to respond to BTN1A1 antibody-based cancer therapy, similar to the PD-L1 companion diagnostic test for anti-PD-L1/PD-1 therapy. The characterization of the developed BTN1A1 antibody was conducted via ELISA, Western blotting, confocal microscopy, and flow cytometry to demonstrate its overall performance. Validation was performed using formalin-fixed paraffin-embedded human tumor tissue samples to determine the analytical sensitivity and specificity of the IHC assay. This antibody was also found to be of value for imaging mass cytometry and flow cytometry experiments elucidating applicable clinical features of both human tumor tissues and immune cells. Specifically, the developed antibody can detect the robust expression of BTN1A1 on both cancer cells and immune cells, while also revealing the mutually exclusive expression of BTN1A1 and PD-L1. Finally, we demonstrate the capability of a BTN1A1 antibody that can be used to identify BTN1A1-positive patients with a high degree of analytical sensitivity and specificity. Citation Format: Stephen S. Yoo. Development of a diagnostic antibody for anti-BTN1A1 therapy, a novel immune checkpoint inhibitor mutually exclusive of PD-L1/PD-1 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3300.

Limitations on knowledge of autoimmune encephalitis and barriers to its treatment among neurologists: a survey from western China

BackgroundAutoimmune encephalitis (AE) is a group of severe antibody-mediated brain diseases. The understanding of clinical management of AE has developed rapidly. However, the knowledge level of AE and barriers to effective treatment among neurologists remains unstudied.MethodsWe conducted a questionnaire survey among neurologist in western China on knowledge of AE, treatment practices, and perspectives on barriers to treatment.ResultsA total of 1113 neurologists were invited and 690 neurologists from 103 hospitals completed the questionnaire with a response rate of 61.9%. Respondents correctly answered 68.3% of medical questions about AE. Some respondents (12.4%) never assayed for diagnostic antibodies if patients had suspected AE. Half (52.3%) never prescribed immunosuppressants for AE patients, while another 7.6% did not know whether they should do so. Neurologists who never prescribed immunosuppressants were more likely to have less education, a less senior job title, and to practice in a smaller setting. Neurologists who did not know whether to prescribe immunosuppressants were associated with less AE knowledge. The most frequent barrier to treatment, according to respondents, was financial cost. Other barriers to treatment included patient refusal, insufficient AE knowledge, lack of access to AE guidelines, drugs or diagnostic test, etc.ConclusionNeurologists in western China lack AE knowledge. Medical education around AE is urgent needed and should be more targeted to individuals with less educated level or working in non-academic hospitals. Policies should be developed to increase the availability of AE related antibody testing or drugs and reduce the economic burden of disease.

Abstract P6-04-04: Clinical Relevance of PD-L1 and CD8 Expression in Triple Negative Breast Cancer

Abstract Background: Immune checkpoint inhibitors such as PD-L1 are promising therapy targets in triple negative breast cancer (TNBC). In the present study, we examined the clinical relevance of PD-L1 and CD8 expression in TNBC patients treated with adjuvant chemotherapy. Methods: FFPE tumor material from 118 patients with early TNBC treated between 1999 and 2012 was included in our analysis. Immunohistochemical (IHC) expression of PD-L1 was determined by immune score using the diagnostic antibody SP142 (Ventana). CD8 IHC was performed using the SP57 antibody (Ventana). Follow-up data were available for all 118 patients with a median follow up time of 19.4 years. Biomarkers were examined as continuous or categorical variable (predefined cutoffs). Invasive disease-free survival (IDFS) and overall survival (OS) were analyzed using Cox regression models. Results: The median PD-L1 immune score was 1% and PD-L1 expression was classified as positive in 79/116 (68.1%, cutoff ≥1%) cases. Median CD8 expression was 10% and was scored as positive in 51/115 (44.3%, cutoff >10%) samples. Significant associations were observed between PD-L1 expression and tumor grade, Ki67, and CD8 expression. PD-L1-positive tumors were more frequently in the G3 group (p=0.006) and had higher Ki67 (p< 0.001) and higher CD8 expression (p< 0.001). PD-L1 but not CD8 expression was associated with IDFS or OS. Univariate Cox regression analyses showed that PD-L1-negative patients had a shorter IDFS (HR 0.52, 95%CI 0.30-0.89, p=0.02) and showed a trend towards shorter OS (HR 0.56, 95%CI 0.30-1.03, p=0.06). CD8 expression was neither associated with IDFS (HR 0.74, 95%CI 0.43-1.27, p=0.27) nor with OS (HR 0.87, 95%CI 0.48-1.60, p=0.66). In multivariate analyses, PD-L1 expression was an independent prognostic factor for IDFS (HR 0.51, 95%CI 0.29-0.88, p=0.016) but not for OS (HR 0.53, 95%CI 0.28-1.01, p=0.052). Conclusions: Our results suggest that PD-L1 but not CD8 expression assessed by IHC predicted outcome in TNBC. Further analysis of larger, suitable patient cohorts is warranted to further assess the prognostic and predictive value of PD-L1 expression. Citation Format: Zsuzsanna Bago-Horvath, Maximilian Marhold, Ulrike Heber, Rupert Bartsch, Florian Fitzal, Christian F. Singer, Martin Filipits. Clinical Relevance of PD-L1 and CD8 Expression in Triple Negative Breast Cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P6-04-04.

Advancing Luciferase-Based Antibody Immunoassays to Next-Generation Mix and Read Testing

Antibody measurements play a central role in the diagnosis of many autoimmune and infectious diseases. One antibody detection technology, Luciferase Immunoprecipitation Systems (LIPS), utilizes genetically encoded recombinant luciferase antigen fusion proteins in an immunoglobulin capture format to generate robust antibody measurement with high diagnostic sensitivity and specificity. The LIPS technology has been highly useful in detecting antibodies for research diagnostics and the discovery of new autoantigens. The methodology of the assay requires immunoglobulin binding reagents such as protein A/G beads and washing steps to process the immune complex before antibody levels are measured by light production with a luminometer. Recently, simplified mix and read immunoassays based on split components of the nanoluciferase enzyme in a complementation format have been developed for antibody measurements without requiring immunoglobulin-capturing beads or washing steps. The mix and read immunoassays utilize two or three nanoluciferase fragments which when reconstituted via antigen-specific antibody binding generate a functional enzyme. At present, these split luciferase tests have been developed mainly for detecting SARS-CoV-2 antibodies. Here, we describe the traditional LIPS technology and compare it to the new split luciferase methodologies focusing on their technical features, strengths, limitations, and future opportunities for diagnostic research, and clinical applications.

Epitope mapping of diagnostic anti-rabies monoclonal antibodies provide structural insight into rabies variant identification in infected wildlife.

Rabies virus is a member of the lyssavirus family and causes over 60,000 deaths a year. There are currently five strains of rabies virus circulating throughout the continental United States. In order to better control the spread of rabies virus, the Center of Disease Control monitors the prevalence and host range of different rabies virus variants (RVV) throughout the United States. This surveillance relies on a panel of monoclonal antibodies that are known to differentially bind to the nucleoprotein of RVV in a direct fluorescent antibody test (DFA). While these tests are known to accurately distinguish RVV, it is unknown where these antibodies bind to the rabies nucleoprotein. To better understand the fundamental principles of this assay, the epitopes of three monoclonal antibodies from the current panel, which are suspected to have conformational epitopes, were determined using hydrogen-deuterium mass spectrometry. We determined these antibodies bind to distinct surface-exposed epitopes of the nucleoprotein, one of which makes contacts with multiple subunits of the 11-mer ring that is formed by the nucleoprotein. After determining the epitopes, a multiple sequence alignment was examined to look at the conservation of the amino acids in each epitope to determine how these antibodies distinguish between RVV. By determining epitopes, we can now predict how viral mutations could change the specificity and/or sensitivity of a rabies DFA. The results of this work can be used to help further develop rapid immunoassays for more economical RVV diagnostics in the field, in regions that may lack access to microscopy-based DFA diagnostics.

Extract-Shaped Immune Repertoires as Source for Nanobody-Based Human IgE in Grass Pollen Allergy.

The presence of allergen-specific IgE in serum is a biomarker for allergic disease. Specific IgE antibodies for research and diagnostics, however, remain scarce. In contrast to prototypic antibodies, camelid species have evolved single domains as moiety for antigen recognition. These so-called nanobodies represent a versatile platform for the development of diagnostic and therapeutic approaches. In this study, we aimed for generating nanobodies and derived IgE formats from an extract-shaped immune repertoire. Timothy grass pollen represents a complex, but well-defined mixture of individual allergens. Therefore, a repertoire library from a timothy grass pollen extract immunised llama was established. The selection by phage display yielded 3 nanobodies with immunoreactivity to the extract. IgE-like nanobody-based human IgE (nb-hIgE) antibodies were produced in mammalian cells and assessed in different immunoassays and commercial platforms. Immunoblotting and diagnostic ImmunoCap analysis of single timothy grass pollen allergens identified the major allergens Phl p 6 and Phl p 4 as targets. Assessment of immunoreactivity further documented significant molecular cross-reactivity with pollen extract of different grass species and variant presence of allergens within extracts of Pooideae grasses. In summary, our study shows that extract-based immunisation enables the generation of allergen-specific nanobodies and derived nb-hIgE formats linking nanobody technologies with allergological applications.

In-Vitro Diagnostic Reagent Evaluation of Commercially Available Cardiac Troponin I Assay Kits Using H/D Exchange Mass Spectrometry for Antibody-Epitope Mapping.

Cardiac troponin I (cTnI) is the biomarker of choice and considered a gold standard for the diagnosis of acute myocardial infarction. However, the quantitative results of cTnI assay kits from different manufacturers are not comparable. Based on the H/D exchange mass spectrometry (HDX-MS) workflow, we developed an in-vitro diagnostic reagent antibody evaluation strategy to analyze the interactions of epitopes and antibody cocktails─(R195, F12, S13) and (D1, D2, pAb2). The HDX results indicate that the quantitative result bias of the different reagents originates from the ability of antibodies to recognize various cTnI complex forms, such as free cTnI, hydrolyzed cTnI, and cTnI combined with cTnT or TnC as binary or ternary complexes (cTnIC, cTnTIC), in blood based on different epitopes. The data obtained from the peptide HDX of interest after treatment with various antibody cocktails clearly indicated epitope specificity. The consistency of quantitative results can be improved by a thorough investigation into the epitopes recognized by the antibodies of various diagnostic kits, which will lead to the standardization of cTnI diagnosis.

Antibody Selection in Solution Using Magnetic Beads.

Antibody phage display is a valuable in vitro technology to generate recombinant, sequence-defined antibodies for research, diagnostics, and therapy. Up to now (autumn 2022), 14 FDA/EMA-approved therapeutic antibodies were developed using phage display, including the world best-selling antibody adalimumab. Additionally, recombinant, sequence-defined antibodies have significant advantages over their polyclonal counterparts.For a successful in vitro antibody generation by phage display, a suitable panning strategy is highly important. We present in this book chapter the panning in solution and its advantages over panning with immobilized antigens and give detailed protocols for the panning and screening procedure.

Construction of Human Immune and Naive scFv Phage Display Libraries.

Antibody phage display is a widely used in vitro selection technology for the generation of human recombinant antibodies and has yielded thousands of useful antibodies for research, diagnostics, and therapy. In order to successfully generate antibodies using phage display, the basis is the construction of high-quality antibody gene libraries. Here, we describe detailed methods for the construction of such high-quality immune and naive scFv gene libraries of human origin. These protocols were used to develop human naive (e.g., HAL9/10) and immune libraries, which resulted in thousands of specific antibodies for all kinds of applications.

Comparison of the Clinical Profile and Severity Factors of COVID-19 during the First 4 Waves in a Paediatric Population of Yaounde

Introduction: COVID-19 is an infectious disease that has been causing a global pandemic since 2019. Although clinical forms are generally less severe in children than in adults, children nevertheless present polymorphous clinical forms and severe cases that can lead to death. Objective: To describe the clinical presentations found in the different waves of COVID-19, and to highlight the different factors of severity. Materials and Methods: We conducted a cross-sectional study with retrospective and prospective data collection which lasted 7 months (from November 2021 to June 2022) and covered a study period from 6 March 2020 to 22 June 2022, i.e. 27 months. All patients aged 0 to 18 years, suspected of having COVID-19, confirmed by real-time RT-PCR or an antigenic Rapid Diagnostic Test or antibody were included. These patients were to be managed in the Mother and Child Centre of the Chantal Biya Foundation, as well as in the Specialised Centre for the Management of COVID patients, annex number II of the Yaoundé Central Hospital. The results were analysed using IBM SPSS.23 software. Results: We included 163 patients in our study. No paediatric patients were registered during the 3rd wave. The mean age of the patients in the study population was 13 ± 5 years with extremes from 15 days to 18 years. We had a female predominance with a sex ratio of 0.83. The most common comorbidity was asthma. The first wave presented mainly with respiratory symptoms such as dry cough and signs of respiratory distress. The second wave presented mainly with digestive symptoms such as diarrhoea, abdominal pain and vomiting. The fourth wave presented with ENT signs such as sore throat, and rhinorrhea. Factors associated with severity were mainly age less than five years (OR = 17.69), vomiting (OR = 6.50), presence of comorbidities (OR = 3.39), and alteration of vital parameters such as bradypnoea (OR = 19.68), bradycardia (OR = 6.34), tachycardia (OR = 3.73), oxygen saturation Conclusion: Clinical presentations varied between waves and the main risk factor was age under 5 years. The fourth wave was less severe than the second wave, which in turn was less severe than the first. (4th nd st) which allows us to humbly recommend more screening for patients under 18 years of age with respiratory, ENT and digestive signs and special attention for those under 5 years of age.

Plurality of diagnostic and prophylactic antibodies to rabies virus - A boon...!

Plurality of diagnostic and prophylactic antibodies to rabies virus - A boon...!

SARS-CoV-2 multi-variant rapid detector based on graphene transistor functionalized with an engineered dimeric ACE2 receptor

Reliable point-of-care (POC) rapid tests are crucial to detect infection and contain the spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The emergence of several variants of concern (VOC) can reduce binding affinity to diagnostic antibodies, limiting the efficacy of the currently adopted tests, while showing unaltered or increased affinity for the host receptor, angiotensin converting enzyme 2 (ACE2). We present a graphene field-effect transistor (gFET) biosensor design, which exploits the Spike-ACE2 interaction, the crucial step for SARS-CoV-2 infection. Extensive computational analyses show that a chimeric ACE2-Fragment crystallizable (ACE2-Fc) construct mimics the native receptor dimeric conformation. ACE2-Fc functionalized gFET allows in vitro detection of the trimeric Spike protein, outperforming functionalization with a diagnostic antibody or with the soluble ACE2 portion, resulting in a sensitivity of 20 pg/mL. Our miniaturized POC biosensor successfully detects B.1.610 (pre-VOC), Alpha, Beta, Gamma, Delta, Omicron (i.e., BA.1, BA.2, BA.4, BA.5, BA.2.75 and BQ.1) variants in isolated viruses and patient’s clinical nasopharyngeal swabs. The biosensor reached a Limit Of Detection (LOD) of 65 cps/mL in swab specimens of Omicron BA.5. Our approach paves the way for a new and reusable class of highly sensitive, rapid and variant-robust SARS-CoV-2 detection systems.

A Mycobacterium tuberculosis fingerprint in human breath allows tuberculosis detection

An estimated one-third of tuberculosis (TB) cases go undiagnosed or unreported. Sputum samples, widely used for TB diagnosis, are inefficient at detecting infection in children and paucibacillary patients. Indeed, developing point-of-care biomarker-based diagnostics that are not sputum-based is a major priority for the WHO. Here, in a proof-of-concept study, we tested whether pulmonary TB can be detected by analyzing patient exhaled breath condensate (EBC) samples. We find that the presence of Mycobacterium tuberculosis (Mtb)-specific lipids, lipoarabinomannan lipoglycan, and proteins in EBCs can efficiently differentiate baseline TB patients from controls. We used EBCs to track the longitudinal effects of antibiotic treatment in pediatric TB patients. In addition, Mtb lipoarabinomannan and lipids were structurally distinct in EBCs compared to ex vivo cultured bacteria, revealing specific metabolic and biochemical states of Mtb in the human lung. This provides essential information for the rational development or improvement of diagnostic antibodies, vaccines and therapeutic drugs. Our data collectively indicate that EBC analysis can potentially facilitate clinical diagnosis of TB across patient populations and monitor treatment efficacy. This affordable, rapid and non-invasive approach seems superior to sputum assays and has the potential to be implemented at point-of-care.

Single-Cell Multi-Omics of Peripheral Blood Reveals Tiding and Evolution of Responsive and Resistant Clones upon Daratumumab-Based Treatments in Multiple Myeloma and Plasma Cell Leukemia

Background: Treatment with anti-CD38 antibodies is a standard of care in newly diagnosed and relapsed/refractory multiple myeloma (MM). Clonal tiding and evolution as well as genomic heterogeneity are major drivers towards drug-resistant disease. However, modes of resistance to anti-CD38 directed therapies are currently unknown and might include loss of antigen expression and/or exhaustion of the immune system. We performed longitudinal single-cell multi-omic analyses of circulating tumor cells (CTC) and non-malignant cells to decipher clonal heterogeneity and tiding upon response and resistance to daratumumab (Dara)-based therapies in MM and plasma cell leukemia (PCL). Methods: Peripheral blood mononuclear cells (MNCs) were isolated from 7 patients (PCL n=5, MM n=2) before and after exposure to Dara. Samples were collected at four different time points: 1. before administration of Dara (CD38-naïve). 2. Four days after first application of Dara (CD38-exposed). 3. After relapse from Dara (CD38-refractory). 4. After an additional line of non-CD38 targeted therapy following relapse from Dara. In total, we analyzed 17 PB samples. To demonstrate that results from PB are comparable to bone marrow (BM), four paired PB and BM samples were included (21 samples in total). MNCs were subjected to single cell RNA (scRNAseq), B-cell (scBCRseq), and T-cell receptor sequencing (scTCRseq). Surface protein expression was measured using a custom panel of 57 DNA-barcoded antibodies. Sequencing files were processed with CellRanger (10x Genomics) and data were analyzed with the Seurat toolkit for single cell sequencing. Cell types were annotated with SingleR based on the Human Primary Cell Atlas built-in references. ScRepertoire was used for longitudinal scTCRseq and scBCRseq data. Copy number variations (CNVs) in CTCs were detected with inferCNV, and cellular interactions were investigated with CellPhoneDB. Results: In total, we sequenced 130.038 MNCs (PB: 108.236, range 414-8700/patient; BM: 21802, range 3375-8516/patient, Figure 1A). Malignant plasma cells were identified using scBCRseq and restricted light chain expression from scRNAseq. Even in MM patients without morphological evidence for CTC, we could identify and characterize single malignant plasma cells in PB. By inferring genome-wide CNVs from scRNAseq, we were able to characterize intra-patient genomic heterogeneity. Longitudinal tracking of CTC revealed tiding of clones characterized by distinct CNV profiles and transcriptomes upon Dara-exposure and resistance. Early transcriptional changes in CTCs upon Dara-exposure included inflammatory signaling (e.g. upregulation of IFI6, IFI35, IFIT1, IFITM1). Analysis of CD38 protein surface expression using DNA-barcoded antibodies showed significantly decreased levels after Dara exposure. To rule out that this might have resulted from competitive binding of the diagnostic antibody and Dara, we repeated analyses after discontinuing Dara and after application of a further line of therapy. In contrast to CD38 RNA expression, surface protein expression decreased significantly upon exposure and relapse, but recovered after an additional line of therapy. Expression of other druggable antigens (BCMA, SLAMF7, GPRCD5, FcRL5, Figure 1B) was not affected by treatment with Dara. Next, we investigated co-evolution of non-malignant cells. Longitudinal scTCRseq showed concomitant expansion and stagnation of TCRs. Receptor-ligand interaction analyses demonstrated that exposure to Dara resulted in significant differences in CD38-PECAM1-mediated interactions between CTCs with non-malignant B-cells and CD8+ T-cells. We detected recurrently increased immunosuppressive receptor-ligand interactions between malignant plasma cells and CD4+, CD8+, and regulatory T-cells via CD86-CTLA4 and NECTIN3-TIGIT axis upon Dara exposure. Conclusion: We demonstrate that single-cell multi-omic analyses of PB provide a minimal invasive approach to study genomic heterogeneity and evolution of malignant plasma cells and non-malignant cells of the immune system. Longitudinal analyses reveal different patterns of response and resistance to targeted myeloma therapies and might affect future therapeutic decision-making. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Structural Basis for Rabbit Hemorrhagic Disease Virus Antibody Specificity.

Rabbit hemorrhagic disease virus (RHDV) typically causes a fatal disease in rabbits. In Australia, RHDV was imported to control the feral rabbit population, while it poses a severe threat to native rabbits in other countries. RHDV variants are genetically diverse and serological studies using antibodies isolated from infected rabbits or raised against RHDV virus-like particles (VLPs) have found RHDV variants antigenically distinct. In this study, we determined the X-ray crystal structure of an RHDV GI.2 (N11 strain) protruding (P) domain in complex with a diagnostic monoclonal antibody (2D9) Fab. We showed that 2D9 interacted with conserved and variable residues on top of the P domain with nanomolar affinity. To better illustrate 2D9 specificity, we determined the X-ray crystal structure of an RHDV GI.1b (Ast89 strain) that was a 2D9 non-binder. Structural analysis indicated that amino acid substitutions on the GI.1b P domain likely restricted 2D9 binding. Interestingly, a model of the GI.2 P domain-Fab complex superimposed onto a cryo-EM structure of an RHDV VLP revealed that 2D9 Fab molecules clashed with neighboring Fabs and indicated that there was a reduced antibody binding occupancy. Moreover, the RHDV GI.2 histo-blood group antigen (HBGA) co-factor binding site appeared obstructed when 2D9 was modeled on the VLP and suggested that 2D9 might also function by blocking HBGA attachment. Overall, this new data provides the first structural basis of RHDV antibody specificity and explains how amino acid variation at the binding site likely restricts 2D9 cross-reactivity. IMPORTANCE Isolated RHDV antibodies have been used for decades to distinguish between antigenic variants, monitor temporal capsid evolution, and examine neutralizing capacities. In this study, we provided the structural basis for an RHDV GI.2 specific diagnostic antibody (2D9) binding and reveal that a small number of amino acid substitutions at the binding site could differentiate between RHDV GI.2 and GI.1b. This novel structural information provides a framework for understanding how RHDV displays a specific antigenic epitope and engages an antibody at the atomic level. Importantly, part of the 2D9 binding region was earlier reported to contain a neutralizing epitope and our structural modeling as well as recent human norovirus antibody-mediated neutralization studies, suggest that the 2D9 antibody has the potential to block HBGA attachment. These new findings should aid in characterizing antigenic variants and advance the development of novel monoclonal antibodies for diagnostics and therapeutics.

Development and verification of new monoclonal orthopedia homeobox (OTP) specific antibodies for pulmonary carcinoid diagnostics

Orthopedia homeobox (OTP) has shown to be a useful prognostic marker to predict outcome in pulmonary carcinoids, which is also supported by the World Health Organization. However, the discontinuation of the initially used polyclonal antibody and absence of a reliable routinely applicable monoclonal OTP antibody hampers implementation in routine diagnostics. Here, new monoclonal antibodies directed against OTP were developed and verified on formalin-fixed paraffin-embedded tissue of pulmonary neuroendocrine tumors (NETs) for clinical diagnostics. OTP specific monoclonal antibodies were produced from mice immunised with a recombinant human OTP protein fragment. Enzyme-linked immunosorbent assay (ELISA) positive hybridomas were evaluated using immunohistochemistry (IHC). Following epitope-mapping and isotyping, purified monoclonal antibodies were validated for IHC in formalin-fixed paraffin-embedded tissues, the optimal dilution was determined, and results were cross validated with the OTP polyclonal antibody (HPA039365, Atlas Antibodies). Staining protocols were optimized on two automated staining platforms and performance was harmonized using a tissue microarray (TMA). Two clones (CL11222 and CL11225) were selected for purified monoclonal antibody (mAb) production. Intratumor heterogeneity assessment revealed similar performance for both clones. While clone CL11225 displayed a unique epitope compared to those present in the polyclonal antibody, this clone performed most similar to the polyclonal antibody. Cross-platform assessment revealed an excellent agreement for clone CL11225 while clone CL11222 showed somewhat discordant results on Dako. New monoclonal OTP specific antibodies have been developed and verified on different automated immunohistochemical staining platforms. The OTP specific monoclonal antibodies showed excellent agreement with the often-used polyclonal antibody allowing application in routine diagnostics.

Advances in antibody discovery from human BCR repertoires.

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.