Clonal Characterization Research Articles

Comprehensive Genomic Characterization of Antibiotic Resistance, Virulence, and Clonality in Salmonella Isolates from Wild Animals in Algeria.

This study investigated Salmonella spp. in wild animals in Algeria, focusing on their prevalence, serotypes, antibiotic resistance, and virulence profiles. From fecal samples collected between May 2021 and June 2022, 1.9% showed Salmonella shedding. The identified serotypes included S. Bredeney, S. Enteritidis, S. Altona, and S. Virchow. Except for S. Altona, all isolates were resistant to quinolones, with S. Bredeney strains, exhibiting multidrug resistance. Whole-genome sequencing revealed various resistance genes and mutations in gyrA or parC genes. Additionally, plasmids IncX1 and ColpVC were detected in several isolates. A comprehensive analysis identified 201 virulence genes. These findings contribute to understanding Salmonella in wild animal populations and their potential impact on public health.

Characterization of B-cell receptor clonality and immunoglobulin gene usage at multiple time points during active SARS-CoV-2 infection.

Although monoclonal antibodies to the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) are known, B-cell receptor repertoire and its change in patients during coronavirus disease-2019 (COVID-19) progression is underreported. We aimed to study this molecularly. We used immunoglobulin heavy chain (IGH) variable region (IGHV) spectratyping and next-generation sequencing of peripheral blood B-cell genomic DNA collected at multiple time points during disease evolution to study B-cell response to SARS-CoV-2 infection in 14 individuals with acute COVID-19. We found a broad distribution of responding B-cell clones. The IGH gene usage was not significantly skewed but frequencies of individual IGH genes changed repeatedly. We found predominant usage of unmutated and low mutation-loaded IGHV rearrangements characterizing naïve and extrafollicular B cells among the majority of expanded peripheral B-cell clonal lineages at most tested time points in most patients. IGH rearrangement usage showed no apparent relation to anti-SARS-CoV-2 antibody titers. Some patients demonstrated mono/oligoclonal populations carrying highly mutated IGHV rearrangements indicating antigen experience at some of the time points tested, including even before anti-SARS-CoV-2 antibodies were detected. We present evidence demonstrating that the B-cell response to SARS-CoV-2 is individual and includes different lineages of B cells at various time points during COVID-19 progression.

Temporal and clonal characterization of neural stem cell niche recruitment in the medaka neuromast

Stem cell populations are defined by their capacity to self-renew and to generate differentiated progeny. These unique characteristics largely depend on the stem cell micro-environment, the so-called stem cell niche. Niches were identified for most adult stem cells studied so far, but we know surprisingly little about how somatic stem cells and their niche come together during organ formation. Using the neuromasts of teleost fish, we have previously reported that neural stem cells recruit their niche from neighboring epithelial cells, which go through a morphological and molecular transformation. Here, we tackle quantitative, temporal, and clonal aspects of niche formation in neuromasts by using 4D imaging in transgenic lines, and lineage analysis in mosaic fish. We show that niche recruitment happens in a defined temporal window during the formation of neuromasts in medaka, and after that, the niche is enlarged mainly by the proliferation of niche cells. Niche recruitment is a non-clonal process that feeds from diverse epithelial cells that do not display a preferential position along the circumference of the forming neuromast. Additionally, we cover niche formation and expansion in zebrafish to show that distant species show common features during organogenesis in the lateral line system. Overall, our findings shed light on the process of niche formation, fundamental for the maintenance of stem cells not only in medaka but also in many other multicellular organisms.

Exploring the impact of clonal definition on B-cell diversity: implications for the analysis of immune repertoires.

The adaptive immune system has the extraordinary ability to produce a broad range of immunoglobulins that can bind a wide variety of antigens. During adaptive immune responses, activated B cells duplicate and undergo somatic hypermutation in their B-cell receptor (BCR) genes, resulting in clonal families of diversified B cells that can be related back to a common ancestor. Advances in high-throughput sequencing technologies have enabled the high-throughput characterization of B-cell repertoires, however, the accurate identification of clonally related BCR sequences remains a major challenge. In this study, we compare three different clone identification methods on both simulated and experimental data, and investigate their impact on the characterization of B-cell diversity. We observe that different methods lead to different clonal definitions, which affects the quantification of clonal diversity in repertoire data. Our analyses show that direct comparisons between clonal clusterings and clonal diversity of different repertoires should be avoided if different clone identification methods were used to define the clones. Despite this variability, the diversity indices inferred from the repertoires' clonal characterization across samples show similar patterns of variation regardless of the clonal identification method used. We find the Shannon entropy to be the most robust in terms of the variability of diversity rank across samples. Our analysis also suggests that the traditional germline gene alignment-based method for clonal identification remains the most accurate when the complete information about the sequence is known, but that alignment-free methods may be preferred for shorter sequencing read lengths. We make our implementation freely available as a Python library cdiversity.

Clonal Characterization and Somatic Hypermutation Assessment by Next-Generation Sequencing in Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma: A Detailed Description of the Technical Performance, Clinical Utility, and Platform Comparison

Somatic hypermutation status of the IGHV gene is essential for treating patients with chronic lymphocytic leukemia/small lymphocytic lymphoma. Unlike the conventional low-throughput method, assessment of somatic hypermutation by next-generation sequencing (NGS) has potential for uniformity and scalability. However, it lacks standardization or guidelines for routine clinical use. We critically assessed the performance of an amplicon-based NGS assay across 458 samples. Using a validation cohort (35 samples), the comparison of two platforms (Ion Torrent versus Illumina) and two primer sets [leader versus framework region 1 (FR1)] in their ability to identify clonotypic IGHV rearrangement(s) revealed 97% concordance. The mutation rates were identical by both platforms when using the same primer set (FR1), whereas a slight overestimation bias (+0.326%) was found when comparing FR1 with leader primers. However, for nearly all patients this did not affect the stratification into mutated or unmutated categories, suggesting that use of FR1 may provide comparable results if leader sequencing is not available and allowing for a simpler NGS laboratory workflow. In routine clinical practice (423 samples), the productive rearrangement was successfully detected by either primer set (leader, 97.7%; FR1, 94.7%), and a combination of both in problematic cases reduced the failure rate to 1.2%. Higher sensitivity of the NGS-based analysis also detected a higher frequency of double IGHV rearrangements (19.1%) compared with traditional approaches.

Transcriptional and Clonal Characterization of Cytotoxic T Cells in Crescentic Glomerulonephritis.

T-cell infiltration is a hallmark of crescentic GN (cGN), often caused by ANCA-associated vasculitis. Pathogenic T-cell subsets, their clonality, and downstream effector mechanisms leading to kidney injury remain to be fully elucidated. Single-cell RNA sequencing and T-cell receptor sequencing revealed activated, clonally expanded cytotoxic CD4 + and CD8 + T cells in kidneys from patients with ANCA-associated cGN. In experimental cGN, kidney-infiltrating CD8 + T cells expressed the cytotoxic molecule, granzyme B (GzmB), which induced apoptosis in renal tissue cells by activation of procaspase-3, and aggravated disease pathology. These findings describe a pathogenic function of (clonally expanded) cytotoxic T cells in cGN and identify GzmB as a mediator and potential therapeutic target in immune-mediated kidney disease. Crescentic GN (cGN) is an aggressive form of immune-mediated kidney disease that is an important cause of end stage renal failure. Antineutrophilic cytoplasmic antibody (ANCA)-associated vasculitis is a common cause. T cells infiltrate the kidney in cGN, but their precise role in autoimmunity is not known. Combined single-cell RNA sequencing and single-cell T-cell receptor sequencing were conducted on CD3 + T cells isolated from renal biopsies and blood of patients with ANCA-associated cGN and from kidneys of mice with experimental cGN. Functional and histopathological analyses were performed with Cd8a-/- and GzmB-/- mice. Single-cell analyses identified activated, clonally expanded CD8 + and CD4 + T cells with a cytotoxic gene expression profile in the kidneys of patients with ANCA-associated cGN. Clonally expanded CD8 + T cells expressed the cytotoxic molecule, granzyme B (GzmB), in the mouse model of cGN. Deficiency of CD8 + T cells or GzmB ameliorated the course of cGN. CD8 + T cells promoted macrophage infiltration and GzmB activated procaspase-3 in renal tissue cells, thereby increasing kidney injury. Clonally expanded cytotoxic T cells have a pathogenic function in immune-mediated kidney disease.

Comprehensive characterization of clonality of driver genes revealing their clinical relevance in colorectal cancer

BackgroundGenomic studies of colorectal cancer have revealed the complex genomic heterogeneity of the tumor. The acquisition and selection of genomic alterations may be critical to understanding the initiation and progression of this disease.MethodsIn this study, we have systematically characterized the clonal architecture of 97 driver genes in 536 colorectal cancer patients from TCGA.ResultsA high proportion of clonal mutations in 93 driver genes were observed. 40 genes showed significant associations between their clonality and multiple clinicopathologic factors. Kaplan–Meier analysis suggested that the mutation clonality of ANK1, CASP8, SMAD2, and ARID1A had a significant impact on the CRC patients' outcomes. Multivariable analysis revealed that subclonal ANK1 mutations, clonal CASP8 mutations, and clonal SMAD2 mutations independently predicted for shorter overall survival after adjusting for clinicopathological factors. The poor outcome of the subclonal ANK1 mutation may be caused by upregulation of IL4I1, IDO1, IFNG and MAPK12 which showed potential roles in tumor immune evasion through accumulation of immunosuppressive cells such as regulatory T cells and myeloid derived suppressor cells.ConclusionThese results suggested that the clonality of driver genes could act as prognostic markers and potential therapeutic targets in human colorectal cancer.

Abstract 3794: Comprehensive clonal and molecular profiling of primary tumors and distant lung metastases in an amputation model of osteosarcoma

Abstract An important feature of osteosarcoma is relapse which occurs in more than 30% of patients and metastasis to the lungs. It has been revealed that the metastatic ability and resistance to chemotherapy might be due to the presence of a subset of cells within the intra-tumorally heterogeneous population. However, tracking the rare genetic subpopulations that play a critical role in cancer recurrence, metastasis and resistance and the lack of a defined in vivo model to recapitulate clonal evolution has been a challenge. To further understand clonal dynamics and intra-tumoral heterogeneity a new barcoded PDX (OS17) derived cell line was established by stably transducing the cell line with a lentiviral vector-based system. The highly complex barcode library of ten million enabled labelling each of the cells with a unique molecular identifier and clonally tracking more than one million cells in vitro. Following seventeen passages in vitro and transplant for three generations in vivo, flow cytometry, nested PCR and next generation sequencing showed that the barcoded cells retained the sequence in vitro and in vivo suggesting that it was possible to track cell populations and their clonal lineages both at the genomic DNA and RNA level. The barcoded M17 PDX cells were injected in 25 SCID and NSG mice intratibially to monitor tumor growth and clonally track the cells in both the primary tumors and the lungs. Seventeen (68%) of the mice developed primary tumors. Tumor latency and growth was 61.82 ±34.5 and 51.24 ± 23 days respectively. Seven (35%) of the primary tumor bearing mice had lung metastasis. Limb amputations were performed in 5 mice with 2 surviving the surgery. The results not only show a diversity in clonal subpopulations between the mice injected on different dates but also the primary tumor and matched lung metastatic samples. An in-depth clonal characterization further revealed a high degree of similarity in the subclonal populations between the lung nodules and the primary tumor samples. In vitro, a proportion of the barcodes were very reduced or lost in the early six passages however, these slowly expanded in the late passages suggesting that in a more favorable environment in vivo, these clones can maintain tumorigenic potential. These results suggest a clonal evolutionary dynamic model where pre-existing clones have a fitness for persistence and dissemination. This advantage might include long term tumorigenic and proliferative potential and the ability to grow in different micro-environments. Conclusion: It has been demonstrated that the barcoded PDX models have inter and intra-tumoral heterogeneity of osteosarcoma both in vitro and in vivo and can potentially be used in tracking tumor colonization at the primary and metastatic sites. Using this model will therefore advance our understanding of osteosarcoma lung metastasis which is the critical clinical challenge for these patients. Citation Format: Sylvester Jusu, Sankaranarayanan Kannan, Sahil Seth, Michael D. Peoples, Zhongting Zhang, Wendong Zhang, Zhaohui Xu, Yifei Wang, Xin Zhou, Yizheng Tu, Giuseppe Longo, Michael Roth, Jonathan B. Gill, Richard Gorlick. Comprehensive clonal and molecular profiling of primary tumors and distant lung metastases in an amputation model of osteosarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3794.

Abstract LB079: Pancreatic clonal replica tumors display functional heterogeneity in response to KRAS pharmacological inhibition and reveal unique epigenetic vulnerabilities to overcome resistance

Abstract Introduction: Pre-existing tumor heterogeneity may allow tumors to escape treatment via selection and expansion of drug-resistant clones. Recent discovery of KRAS targeted therapies (e.g. SOS1i, KRASG12Ci, etc.) has dramatically changed the clinical outlook for patients with KRAS mutant tumors. Here, we generated and utilized pancreatic clonal replica tumors (CRTs) to identify drug-resistant clones of KRAS inhibitors (e.g. SOS1i and MEKi, KRASG12Di). Deep clonal characterization of KRAS inhibition revealed a novel epigenetic vulnerability which may inform on unbiased combination strategies to prolong responses for pancreatic cancer patients. Experimental procedures: Our CRT platform combines high-complexity in vivo lineage tracing with quantitative assessments of adaptive responses to therapeutics. In this study we generated a KRASG12D-driven CRT xenograft model of pancreatic ductal adenocarcinoma and treated the CRTs with MEKi, SOSi, and MEKi + SOSi. Upon comprehensive analysis of the clonal composition associated with each drug treatment, we identified, isolated, and validated a collection of clones with differential response to MEKi + SOS1i or KRASG12Di. Deep molecular characterization of sensitive and resistance clones identified novel combination strategies to overcome resistance to KRAS inhibitors. Results: We found that KRAS inhibition greatly impacted CRT clonal composition and tumor heterogeneity. Well-controlled reconstitution experiments with CRT-informed treatment-naïve clones confirmed the pre-existing nature of the differential clonal response to KRAS inhibitors in pancreatic cancer. Transcriptomic profiling of clonal diversity further revealed a BRD3-driven molecular plasticity in resistant clones that may drive resistance to MEKi + SOS1i or KRASG12Di. Pharmacological combination of MEKi (trametinib) + SOS1i (BI-3406) or KRASG12Di (MRTX1133) with BETi (BI 894999 and dBET6) exhibited combination benefits in preclinical pancreatic cancer models. Conclusions: Our study suggests that pre-existing heterogeneous subclones with epigenetic plasticity contribute to escaping direct KRAS inhibition in pancreatic cancer and provides a new avenue to overcome such resistance by combining KRAS inhibitors with BET inhibitors. Citation Format: Hengyu Lyu, Rosalba Minelli, Charles E. Deckard, Sahil Seth, Justin Huang, Hong Jiang, Michael D. Peoples, Meggie Lam, Christopher A. Bristow, Daniel Gerlach, Ulrike Tontsch-Grunt, Chieh-Yuan Li, I-Lin Ho, Christopher P. Vellano, Marco H. Hofmann, Timothy P. Heffernan, Joseph R. Marszalek, Andrea Viale, Alessandro Carugo. Pancreatic clonal replica tumors display functional heterogeneity in response to KRAS pharmacological inhibition and reveal unique epigenetic vulnerabilities to overcome resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB079.

Sequencing Independent Molecular Typing of Staphylococcus aureus Isolates: Approach for Infection Control and Clonal Characterization.

ABSTRACTStaphylococcus aureus is a major bacterial human pathogen that causes a wide variety of clinical manifestations. The main aim of the presented study was to determine and optimize a novel sequencing independent approach that enables molecular typing of S. aureus isolates and elucidates the transmission of emergent clones between patients. In total, 987 S. aureus isolates including both methicillin-resistant S. aureus (MRSA) and methicillin-sensitive S. aureus (MSSA) isolates were used to evaluate the novel typing approach combining high-resolution melting (HRM) analysis of multilocus sequence typing (MLST) genes (mini-MLST) and spa gene (spa-HRM). The novel approach’s discriminatory ability was evaluated by whole-genome sequencing (WGS). The clonal relatedness of tested isolates was set by the BURP and BURST approach using spa and MLST data, respectively. Mini-MLST classified the S. aureus isolates into 38 clusters, followed by spa-HRM classifying the isolates into 101 clusters. The WGS proved HRM-based methods to effectively differentiate between related S. aureus isolates. Visualizing evolutionary relationships among different spa-types provided by the BURP algorithm showed comparable results to MLST/mini-MLST clonal clusters. We proved that the combination of mini-MLST and spa-HRM is rapid, reproducible, and cost-efficient. In addition to high discriminatory ability, the correlation between spa evolutionary relationships and mini-MLST clustering allows the variability in population structure to be monitored.IMPORTANCE Rapid and cost-effective molecular typing tools for Staphylococcus aureus epidemiological applications such as transmission tracking, source attribution and outbreak investigations are highly desirable. High-resolution melting based methods are effective alternative to those based on sequencing. Their good reproducibility and easy performance allow prospective typing of large set of isolates while reaching great discriminatory power. In this study, we established a new epidemiological approach to S. aureus typing. This scheme has the potential to greatly improve epidemiological investigations of S. aureus.

Next Generation Sequencing (NGS) Based IGH and TCR Clonality Assays Provide Excellent Specificity and Sensitivity for Routine Clonal Characterization and Monitoring of Lymphoproliferative Disorders

Background:IGH and TCR gamma clonality testing is an important component in the diagnosis of lymphoproliferative disorders. Capillary electrophoresis (CE) of multiplexed PCR products is currently considered the gold standard method of analysis. Although robust, simple and highly reproducible, it does not provide full characterization of clonal sequences and lacks sensitivity and specificity to track clones in subsequent samples. Here we describe our clinical implementation of an NGS based assay for routine assessment of lymphoproliferative disorders and outline the clinical utility for initial clonal characterization and minimal residual disease monitoring through patient specific clone tracking.Methods:Blood, bone marrow and FFPE tissue samples submitted for routine clonality assessment during Jan 2016 to March 2017 were identified. DNA was extracted and tested using both standard CE and LymphoTrack® IGH + TRG - MiSeq assays (InvivoScribe). Results were analyzed using an in-house developed software (LymphoClone) as well as proprietary InvivoScribe software. The lymphoma classification at the time of initial diagnosis, disease status and results of ancillary studies, including morphologic assessment, immunohistochemical analysis, flow cytometry (FC) and molecular test results were recorded for each case.Results:A total of 716 samples were analyzed, including 534 samples at the time of initial diagnosis (Dx) for clonal characterization and 182 follow up samples for disease monitoring. The case distribution is outlined in table 1. Sensitivity for initial clonal characterization was superior for the NGS assays, allowing clonal detection down to 1% tumor content, compared to 5-10% for the CE assays. Clonal rearrangement was detected in 94% of Dx cases by NGS (502/534) vs 89% CE (475/534). For monitoring samples with a previously characterized clone, NGS was equivalent to FC for detection of plasma cell neoplasms (PCN) but showed distinct advantages in disease monitoring for B-ALL, B and T cell lymphomas. Among 182 monitoring samples, NGS testing allowed residual disease detection in 25 (14%) more cases (137/182 vs 112/182) compared to flow cytometry. In all cases, residual disease was confirmed by an ancillary method (qPCR for a molecular marker) or a subsequent sample with higher disease level. The sensitivity for MRD detection for NGS has been established as 1x10-5. Sensitivity for FC ranged between 1x10-4 to 1x10-5 (1x10-4 for T and B-ALL and 1x10-5 for PCN and B cell lymphomas). Higher sensitivities may be attained by NGS with increasing DNA input. The NGS assay provided additional information on distinct clonal tumor population behavior, including suppression and/or re-emergence of subpopulations following treatment. In the current study, turnaround time (TAT) was higher for NGS vs FC, 9 days vs 1 day, respectively.Conclusions:Routine assessment of clonality by NGS methods is feasible and provides significant improvement over existing CE clonality assays, enabling comprehensive clonal characterization and disease monitoring with high sensitivity which is similar and often superior than FC. Based on current technology and protocols, TAT is longer for NGS compared to both CE and FC assays, which could limit its use as a stand-alone test in select clinical settings. Further protocol optimization is in progress to reduce this time to ~7 days. The NGS assays further define behaviors of clonal tumor populations and should therefore be considered in the routine assessment of lymphoid malignancies in conjunction with FC and other ancillary molecular tests. [Display omitted] DisclosuresArcila:Raindance Tecnologies: Honoraria; Invivoscribe: Honoraria; Archer: Honoraria. Park:Amgen: Consultancy. Dogan:Seattle Genetics: Consultancy, Membership on an entity's Board of Directors or advisory committees; Peer Review Institute: Consultancy; Novartis: Consultancy, Membership on an entity's Board of Directors or advisory committees; Roche Pharmaceuticals: Consultancy; Celgene: Consultancy.

Clonal diversity and genomic characterization of Panton-valentine Leukocidin (PVL)-positive Staphylococcus aureus in Tehran, Iran

BackgroundSome Staphylococcus aureus strains produce Panton-Valentine leukocidin (PVL), a bi-component pore-forming toxin, which causes leukocyte lysis and tissue necrosis. Currently, there is very limited information on the molecular epidemiology of PVL-encoding S. aureus strains in Iran. This study aimed to determine the molecular epidemiology and genetic background of PVL-positive S. aureus clinical strains isolated from Iranian patients.MethodsA total of 28 PVL-positive S. aureus strains were detected from 600 S. aureus isolates between February 2015 and March 2018 from different hospitals in Tehran, Iran. Antimicrobial susceptibility testing was performed according to the Clinical and Laboratory Standards Institute (CLSI) guidelines. Molecular genotyping was performed using SCCmec and accessory gene regulator (agr) typing, PVL haplotyping, multilocus sequence typing (MLST), and pulsed-field gel electrophoresis (PFGE).ResultsThe highest antibiotic resistance rate was found to be against erythromycin (57.1%), followed by ciprofloxacin (42.8%) and clindamycin (35.7%). Moreover, 19 (67.9%) out of 28 S. aureus isolates were identified as MRSA, including CA-MRSA (14/19, 73.7%) and HA-MRSA (5/19, 26.3%). SCCmec type IVa was detected as the predominant type (10/19, 52.6%), followed by type III (5/19, 26.3%) and type V (4/19, 21.1%). The agr type I was identified as the most common type (14/28, 50%), and H and R haplotype groups were observed at frequencies of 67.9 and 32.1%, respectively. Among H variants, the predominant variant was H2 (78/9%). The isolates encompassed 21 different sequence types (STs), including 16 new STs (ST5147 to ST5162). Based on eBURST analysis, the isolates were clustered into five CCs, including CC30, CC22, CC1, CC8, and CC5 (ST5160), and nine singletons. PFGE typing showed that 24 isolates were clustered into A (4 pulsotypes), B (9 pulsotypes), and C (11 pulsotypes) clusters.ConclusionsA high prevalence of PVL-positive CA-MRSA strains was detected in Iran. The majority of PVL-positive isolates were of H (mostly H2) variant, while R variant was harbored by 100% of PVL-positive MRSA strains. Also, CC8, CC22, and CC30 were identified as the dominant clones among PVL-encoding S. aureus strains. This study promotes a better understanding of the molecular epidemiology and evolution of PVL-positive S. aureus strains in Iran.

A target enrichment high throughput sequencing system for characterization of BLV whole genome sequence, integration sites, clonality and host SNP

Bovine leukemia virus (BLV) is an oncogenic retrovirus which induces malignant lymphoma termed enzootic bovine leukosis (EBL) after a long incubation period. Insertion sites of the BLV proviral genome as well as the associations between disease progression and polymorphisms of the virus and host genome are not fully understood. To characterize the biological coherence between virus and host, we developed a DNA-capture-seq approach, in which DNA probes were used to efficiently enrich target sequence reads from the next-generation sequencing (NGS) library. In addition, enriched reads can also be analyzed for detection of proviral integration sites and clonal expansion of infected cells since the reads include chimeric reads of the host and proviral genomes. To validate this DNA-capture-seq approach, a persistently BLV-infected fetal lamb kidney cell line (FLK-BLV), four EBL tumor samples and four non-EBL blood samples were analyzed to identify BLV integration sites. The results showed efficient enrichment of target sequence reads and oligoclonal integrations of the BLV proviral genome in the FLK-BLV cell line. Moreover, three out of four EBL tumor samples displayed multiple integration sites of the BLV proviral genome, while one sample displayed a single integration site. In this study, we found the evidence for the first time that the integrated provirus defective at the 5′ end was present in the persistent lymphocytosis cattle. The efficient and sensitive identification of BLV variability, integration sites and clonal expansion described in this study provide support for use of this innovative tool for understanding the detailed mechanisms of BLV infection during the course of disease progression.

VARIATION IN PHYTOLITHS MORPHOLOGY OF ERIANTHUS ARUNDINACEUS

Five improved Erianthus arundinaceus clones were studied for variations in phytoliths present in leaves. Phytoliths were extracted by acid digestion and the morphology was studied by light microscopy. Phytoliths belonging to three classes viz., Eupanicoid, Festucoid and Chloridoid were identified in the samples. Variations in type and shape were observed among the clones studied. The results indicate that phytolith characteristics may be an important and reliable trait for clonal characterization in improved Erianthus clones and also there is a possibility of using this trait as a tool for the identification of species, hybrids and their parentage in sugarcane and their related genera.

Routine Evaluation of Minimal Residual Disease in Myeloma Using Next-Generation Sequencing Clonality Testing: Feasibility, Challenges, and Direct Comparison with High-Sensitivity Flow Cytometry

The 2016 International Myeloma Working Group consensus recommendations emphasize high-sensitivity methods for minimal residual disease (MRD) detection, treatment response assessment, and prognostication. Next-generation sequencing (NGS) of IGH gene rearrangements is highly specific and sensitive, but its description in routine clinical practice and performance comparison with high-sensitivity flow cytometry (hsFC) remain limited. In this large, single-institution study including 438 samples from 251 patients, the use of NGS targeting the IGH and IGK genes for clonal characterization and monitoring, with comparison to hsFC, is described. The index clone characterization success rate was 93.6% (235/251), which depended on plasma cell (PC) cellularity, reaching 98% when PC ≥10% and below 80% when PC <5%. A total of 85% of cases were successfully characterized using leader and FR1 primer sets, and most clones showed high somatic hypermutation rates (median, 8.1%). Among monitoring samples from 124 patients, 78.6% (147/187) had detectable disease by NGS. Concordance with hsFC was 92.9% (170/183). Discordant cases encompassed 8 of 124 hsFC MRD+/NGS MRD− patients (6.5%) and 4 of 124 hsFC MRD−/NGS MRD+ patients (3.2%), all with low-level disease near detection limits for both assays. Among concordant hsFC MRD−/NGS MRD− cases, only 5 of 24 patients (20.8%) showed subsequent overt relapse at 3-year follow-up. HsFC and NGS showed similar operational sensitivity, and the choice of test may depend on practical, rather than test performance, considerations.

Frontline Sequential Immunochemotherapy Plus Lenalidomide for Mantle Cell Lymphoma Incorporating MRD Evaluation: Phase II, Investigator-Initiated, Single-Center Study

Frontline Sequential Immunochemotherapy Plus Lenalidomide for Mantle Cell Lymphoma Incorporating MRD Evaluation: Phase II, Investigator-Initiated, Single-Center Study

Transcriptomic and clonal characterization of T cells in the human central nervous system.

T cells provide critical immune surveillance to the central nervous system (CNS), and the cerebrospinal fluid (CSF) is thought to be a main route for their entry. Further characterization of the state of T cells in the CSF in healthy individuals is important for understanding how T cells provide protective immune surveillance without damaging the delicate environment of the CNS and providing tissue-specific context for understanding immune dysfunction in neuroinflammatory disease. Here, we have profiled T cells in the CSF of healthy human donors and have identified signatures related to cytotoxic capacity and tissue adaptation that are further exemplified in clonally expanded CSF T cells. By comparing profiles of clonally expanded T cells obtained from the CSF of patients with multiple sclerosis (MS) and healthy donors, we report that clonally expanded T cells from the CSF of patients with MS have heightened expression of genes related to T cell activation and cytotoxicity.

TCR clonality and Treg frequency as predictors of outcome in stage III NSCLC treated with durvalumab.

3050 Background: Novel blood-based biomarkers evaluating T-cell receptor (TCR) clonality as well as the frequency/activation of immune populations hold significant potential for predicting response and elucidating the biology of anti-tumor immunity in stage 3 NSCLC treated with durvalumab. In this study, we sought to characterize clinical and immunologic predictors of durable response to therapy with a specific focus on TCR clonality and peripheral immune populations. Methods: Stage 3 NSCLC patients undergoing chemoradiation (CRT) and durvalumab were prospectively recruited and underwent baseline and serial blood collections. TCR repertoire analysis was performed on cfDNA using hybrid-capture TCR sequencing and TCR diversity estimated using Shannon’s entropy index. Viably preserved peripheral blood mononuclear cells (PBMC) were analyzed by high-dimensional flow cytometry using validated panels to evaluate T/B/NK-cell, Treg and myeloid populations. Correlations between cell populations were examined using linear and cox regression. Results: 134 stage 3 NSCLC patients who received durvalumab had a median PFS was 15.4 months, with worse PFS in patients with PD-L1 1-49% (HR 2.4, p = 0.03) and PD-L1 &lt; 1% (HR 2.6, p = 0.03). Smoking and EGFR/ALK mutations were not predictors of PFS. Immune profiling was performed in a pilot of 19 patients. Baseline TCR diversity did not associate with clinical factors or outcome. However, lack of clonal expansion after CRT indicated by a higher Shannon’s index was significantly associated with increased frequency of Tregs after durvalumab (p &lt; 0.05). In turn, this elevation in Tregs was associated with significantly reduced PFS in EGFR/ALK wt patients (p = 0.03) and a trend towards reduced PFS in the overall cohort (HR 5.2, p = 0.1). Conclusions: Clonal expansion of T cells after CRT may influence the likelihood of an anti-tumor immune response following PD-L1 blockade in stage 3 NSCLC. Similarly, expansion of peripheral Treg populations is associated with increased likelihood of disease recurrence. Further characterization of TCR clonality, minimal residual disease and T cell subpopulations using serially collected blood is ongoing.

Transcriptional and clonal characterization of B cell plasmablast diversity following primary and secondary natural DENV infection

Abstract Antibody-mediated humoral immunity is thought to play a central role in mediating the immunopathogenesis of acute DENV infection, but limited data are available on the molecular-level diversity, specificity, and functionality of the antibody response elicited by primary or secondary DENV infection. In order to close this functional gap in our understanding of DENV-specific humoral immunity, we utilized high-throughput single cell RNA sequencing to investigate B cells circulating in both primary and secondary natural DENV infections. We captured full-length paired immunoglobulin receptor sequence data from 9,027 B cells from a total of 6 subjects, including 2,717 plasmablasts. Unexpectedly, we found a high proportion of the DENV-elicited plasmablasts expressing IgA, principally in individuals with primary DENV infections. These IgA class-switched cells were extensively hypermutated and appeared to be derived from memory B cells, even in individuals with a serologically confirmed primary DENV infection. Utilizing a combination of conventional proteomics and high-throughput shotgun mutagenesis, we determined that DENV-reactive IgA class-switched antibodies represent a significant fraction of DENV-reactive and DENV-neutralizing Igs generated in response to DENV infection, and that they exhibit a comparable epitope specificity to DENV-reactive IgG antibodies. These results identify a heretofore unappreciated role for DENV-reactive IgA in the humoral response to DENV infection, and may offer insight into the differential pathogenesis associated with primary and secondary DENV infections.

Transcriptional and clonal characterization of B cell plasmablast diversity following primary and secondary natural DENV infection.

Antibody-mediated humoral immunity is thought to play a central role in mediating the immunopathogenesis of acute DENV infection, but limited data are available on the diversity, specificity, and functionality of the antibody response at the molecular level elicited by primary or secondary DENV infection. In order to close this functional gap in our understanding of DENV-specific humoral immunity, we utilized high-throughput single cell RNA sequencing to investigate B cells circulating in both primary and secondary natural DENV infections. We captured full-length paired immunoglobulin receptor sequence data from 9,027 B cells from a total of 6 subjects, including 2,717 plasmablasts. In addition to IgG and IgM class-switched cells, we unexpectedly found a high proportion of the DENV-elicited plasmablasts expressing IgA, principally in individuals with primary DENV infections. These IgA class-switched cells were extensively hypermutated even in individuals with a serologically confirmed primary DENV infection. Utilizing a combination of conventional biochemical assays and high-throughput shotgun mutagenesis, we determined that DENV-reactive IgA class-switched antibodies represent a significant fraction of DENV-reactive Igs generated in response to DENV infection, and that they exhibit a comparable epitope specificity to DENV-reactive IgG antibodies. These results provide insight into the molecular-level diversity of DENV-elicited humoral immunity and identify a heretofore unappreciated IgA plasmablast response to DENV infection.