Single B-Cell Genomic Analyses Differentiate Vitreoretinal Lymphoma from Chronic Inflammation.

PURPOSE: To test whether analyzing DEPArray (Menarini Silicon Biosystems) isolated single B cells from the vitreous fluid can reveal crucial genomic and clinicopathological features to distinguish patients with vitreoretinal lymphoma (VRL) from those with chronic inflammation using immunoglobulin heavy chain (IGH), disease biomarker myeloid differentiation primary response 88 (MYD88)L265P mutation, and copy number profiling. DESIGN: A single-center, retrospective study. PARTICIPANTS: Remnant vitreous biopsies from 7 patients with VRL and 4 patients with chronic inflammation were acquired for molecular analysis. METHODS: Vitreous fluid samples were prefixed in PreservCyt (Hologic) and underwent cytologic analysis and immunohistochemistry examination. Single cells were isolated using the DEPArray NxT system, followed by downstream genomic analysis. MAIN OUTCOME MEASURES: The frequencies of the dominant IGH and MYD88L265P mutation and the genome-wide copy number aberration (CNA) profiles of individual vitreous-isolated B cells were characterized. RESULTS: An average of 10 to 13 vitreous B cells were used in the single-cell IGH and MYD88 analyses. Higher frequencies of dominant IGH (88.8% ± 13.2%) and MYD88L265P mutations (35.0% ± 31.3%) were detected in patients with VRL than in patients with chronic inflammation (65.9% ± 13.4% and 1.5% ± 2.6% for IGH and MYD88L265P, respectively). In a cytology-proven VRL case, all 15 vitreous isolated B cells were derived from the same clone with 100% paired IGH: immunoglobulin light chain (IGK) sequences. Genome-wide copy number profiling revealed a high degree of similarity between B cells from the same patient with VRL, with extensive gains and losses at the same areas across the whole genome. In addition, 14 of 15 B cells showed a BCL2/JH t(14;18) translocation, confirming cellular malignancy with a clonal origin. Clustering analysis of the copy number profiles revealed that malignant B cells derived from different patients with VRL had no common genome-wide signatures. CONCLUSIONS: Single B-cell genomic characterization of the IGH, MYD88L265P mutation, and copy number profile enables VRL diagnosis. Because our study involved only a small cohort, these meaningful proof-of-concept data now warrant further investigation in a larger patient cohort.

Targeting Epstein-Barr virus-transformed B lymphoblastoid cells using antibodies with T-cell receptor-like specificities.

Epstein-Barr virus (EBV) is an oncovirus associated with several human malignancies including posttransplant lymphoproliferative disease in immunosuppressed patients. We show here that anti-EBV T-cell receptor-like monoclonal antibodies (TCR-like mAbs) E1, L1, and L2 bound to their respective HLA-A*0201-restricted EBV peptides EBNA1562-570, LMP1125-133, and LMP2A426-434 with high affinities and specificities. These mAbs recognized endogenously presented targets on EBV B lymphoblastoid cell lines (BLCLs), but not peripheral blood mononuclear cells, from which they were derived. Furthermore, these mAbs displayed similar binding activities on several BLCLs, despite inherent heterogeneity between different donor samples. A single weekly administration of the naked mAbs reduced splenomegaly, liver tumor spots, and tumor burden in BLCL-engrafted immunodeficient NOD-SCID/Il2rg(-/-) mice. In particular, mice that were treated with the E1 mAb displayed a delayed weight loss and significantly prolonged survival. In vitro, these TCR-like mAbs induced early apoptosis of BLCLs, thereby enhancing their Fc-dependent phagocytic uptake by macrophages. These data provide evidence for TCR-like mAbs as potential therapeutic modalities to target EBV-associated diseases.

Rational design of fluorescent biosensor for cyclic di-GMP.

Messenger bagged: The design of a fluorophore-labeled protein biosensor for the bacterial messenger cyclic di-GMP is described. The biosensor responds to c-di-GMP with sub-micromolar sensitivity in a real-time fashion. The biosensor can be used for enzyme assays for diguanylate cyclases and c-di-GMP phosphodiesterases as well as the high-throughput screening of inhibitors.

PreservCyt Is an Optimal Fixative that Permits Cytologic and Molecular Analyses of Vitreoretinal Lymphoma Biopsies.

Purpose: Vitreoretinal lymphoma (VRL) is a potentially fatal intraocular malignancy. Diagnosis is hampered by poor preservation of morphology and DNA/RNA integrity, which precludes adjunctive molecular analysis. We aimed to determine the optimum fixative protocol for VRL biopsies that permits cytology, IHC/flow cytometry and molecular analyses.Methods: Six fixatives were compared on cultured Pfeiffer cells used as a cellular model. Cells were fixed and evaluated on cellular morphology, antibody staining, DNA/RNA amount and integrity. VRL clinical cases were used as validation and proof-of-concept.Results: PreservCyt was the best fixative for preserving cellular morphology and high-quality RNA/DNA from vitreous fluid biopsies. Cells from clinical VRL cases fixed with PreservCyt showed adequate cellular morphology and IHC positivity. Sufficient DNA was obtained for IgH clonality and MYD88 mutation detection using remnant cytological fluid.Conclusions: PreservCyt maintains good morphology and RNA/DNA integrity suggesting that it is a suitable fixative for VRL diagnosis and molecular analysis.

Characterization and Establishment of a Novel EBV Strain Simultaneously Associated With Nasopharyngeal Carcinoma and B-Cell Lymphoma.

Epstein-Barr virus (EBV)-the prototypical human tumor virus-is responsible for 1-2% of the global cancer burden, but divergent strains seem to exist in different geographical regions with distinct predilections for causing lymphoid or epithelial malignancies. Here we report the establishment and characterization of Yu103, an Asia Pacific EBV strain with a highly remarkable provenance of being derived from nasopharyngeal carcinoma biopsy but subsequently propagated in human B-lymphoma cells and xenograft models. Unlike previously characterized EBV strains which are either predominantly B-lymphotropic or epitheliotropic, Yu103 evinces an uncanny capacity to infect and transform both B-lymphocytes and nasopharyngeal epithelial cells. Genomic and phylogenetic analyses indicated that Yu103 EBV lies midway along the spectrum of EBV strains known to drive lymphomagenesis or carcinogenesis, and harbors molecular features which likely account for its unusual properties. To our knowledge, Yu103 EBV is currently the only EBV isolate shown to drive human nasopharyngeal carcinoma and B-lymphoma, and should therefore provide a powerful novel platform for research on EBV-driven hematological and epithelial malignancies.

Cytologic and Molecular Diagnostics for Vitreoretinal Lymphoma: Current Approaches and Emerging Single-Cell Analyses.

Vitreoretinal lymphoma (VRL) is a rare ocular malignancy that manifests as diffuse large B-cell lymphoma. Early and accurate diagnosis is essential to prevent mistreatment and to reduce the high morbidity and mortality associated with VRL. The disease can be diagnosed using various methods, including cytology, immunohistochemistry, cytokine analysis, flow cytometry, and molecular analysis of bulk vitreous aspirates. Despite these options, VRL diagnosis remains challenging, as samples are often confounded by low cellularity, the presence of debris and non-target immunoreactive cells, and poor cytological preservation. As such, VRL diagnostic accuracy is limited by both false-positive and false-negative outcomes. Missed or inappropriate diagnosis may cause delays in treatment, which can have life-threatening consequences for patients with VRL. In this review, we summarize current knowledge and the diagnostic modalities used for VRL diagnosis. We also highlight several emerging molecular techniques, including high-resolution single cell-based analyses, which may enable more comprehensive and precise VRL diagnoses.

Applying Single-Cell Technology in Uveal Melanomas: Current Trends and Perspectives for Improving Uveal Melanoma Metastasis Surveillance and Tumor Profiling.

Uveal melanoma (UM) is the most common primary adult intraocular malignancy. This rare but devastating cancer causes vision loss and confers a poor survival rate due to distant metastases. Identifying clinical and molecular features that portend a metastatic risk is an important part of UM workup and prognostication. Current UM prognostication tools are based on determining the tumor size, gene expression profile, and chromosomal rearrangements. Although we can predict the risk of metastasis fairly accurately, we cannot obtain preclinical evidence of metastasis or identify biomarkers that might form the basis of targeted therapy. These gaps in UM research might be addressed by single-cell research. Indeed, single-cell technologies are being increasingly used to identify circulating tumor cells and profile transcriptomic signatures in single, drug-resistant tumor cells. Such advances have led to the identification of suitable biomarkers for targeted treatment. Here, we review the approaches used in cutaneous melanomas and other cancers to isolate single cells and profile them at the transcriptomic and/or genomic level. We discuss how these approaches might enhance our current approach to UM management and review the emerging data from single-cell analyses in UM.

Kinetics of lisinopril intramolecular cyclization in solid phase monitored by Fourier transform infrared microscopy.

The solid-state intramolecular cyclization of lisinopril to diketopiperazine was investigated by in situ Fourier transform infrared (FT-IR) microscopy. Using a controllable heating cell, the isothermal transformation was monitored in situ at 147.5, 150, 152.5, 155, and 157.5 degrees C. The collected time-dependent FT-IR spectra at each isothermal temperature were preprocessed and analyzed using a multivariate chemometric approach. The pure component spectra of the observable component (lisinopril and diketopiperazine) were resolved and their time-dependent relative contributions were also determined. Model-free and various model fitting methods were implemented in the kinetic analysis to estimate the activation energy of the intramolecular cyclization reaction. Arrhenius plots indicate that the activation energy is circa 327 kJ/mol.

TCR-like antibodies mediate complement and antibody-dependent cellular cytotoxicity against Epstein-Barr virus-transformed B lymphoblastoid cells expressing different HLA-A*02 microvariants.

Epstein-Barr virus (EBV) is a common gammaherpesvirus associated with various human malignancies. Antibodies with T cell receptor-like specificities (TCR-like mAbs) provide a means to target intracellular tumor- or virus-associated antigens by recognising their processed peptides presented on major histocompatibility complex (MHC) class I (pMHC) complexes. These antibodies are however thought to be relevant only for a single HLA allele. Here, we show that HLA-A*02:01-restricted EBV antigenic peptides EBNA1562-570, LMP1125-133 and LMP2A426-434 display binding degeneracy towards HLA-A*02 allelic microvariants, and that these pMHC complexes are recognised by anti-EBV TCR-like mAbs E1, L1 and L2 raised in the context of HLA-A*02:01. These antibodies bound endogenously derived pMHC targets on EBV-transformed human B lymphoblastoid cell lines expressing A*02:01, A*02:03, A*02:06 and A*02:07 alleles. More importantly, these TCR-like mAbs mediated both complement-dependent and antibody-dependent cellular cytotoxicity of these cell lines in vitro. This finding suggests the utility of TCR-like mAbs against target cells of closely related HLA subtypes, and the potential applicability of similar reagents within populations of diverse HLA-A*02 alleles.

The other side of the coin: Leveraging Epstein-Barr virus in research and therapy.

Epstein-Barr virus is (EBV) a ubiquitous virus prevalent in 90% of the human population. Transmitted through infected saliva, EBV is the causative agent of infectious mononucleosis (IM) and is further implicated in malignancies of lymphoid and epithelial origins. In the past few decades, research efforts primarily focused on dissecting the mechanism of EBV-induced oncogenesis. Here, we present an alternate facet of the oncovirus EBV, on its applications in research and therapy. Finally, discussions on the prospective utilization of EBV in nasopharyngeal carcinoma (NPC) diagnosis and therapy will also be presented.

Multivariate chemometric approach to thermal solid-state FT-IR monitoring of pharmaceutical drug compound.

The study of thermal-related solid-state reaction monitored by spectroscopic method needs the use of advanced multivariate chemometric approach. It is because visual inspection of spectral data on particular functional groups or spectral bands is difficult to reveal the complete physical and chemical information. The spectral contributions from various species involved in the solid-state changes are generally highly overlapping and the spectral differences between reactant and product are usually quite minute. In this article, we demonstrate the use of multivariate chemometric approach to resolve the in situ thermal-dependent Fourier-transform infrared (FT-IR) mixture spectra of lisinopril dihydrate when it was heated from 24 to 170 degrees C. The collected FT-IR mixture spectra were first subjected to singular value decomposition (SVD) to obtain the right singular vectors. The right singular vectors were rotated into a set of pure component spectral estimates based on entropy minimization and spectral dissimilarity objective functions. The resulting pure component spectral estimates were then further refined using alternating least squares (ALS). In current study, four pure component spectra, that is, lisinopril dihydrate, monohydrate, anhydrate, and diketopiperazine (DKP) were all resolved and the relative thermal-dependent contributions of each component were also obtained. These relative contributions revealed the critical temperature for each transformation and degradation. This novel approach provides better interpretation of the pathway of dehydration and intramolecular cyclization of lisinopril dihydrate in the solid state. In addition, it can be used to complement the information obtained from differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA).