Katie Seo

Human Responses to Influenza Vaccination Show Seroconversion Signatures and Convergent Antibody Rearrangements

B cells produce a diverse antibody repertoire by undergoing gene rearrangements. Pathogen exposure induces the clonal expansion of B cells expressing antibodies that can bind the infectious agent. To assess human B cell responses to trivalent seasonal influenza and monovalent pandemic H1N1 vaccination, we sequenced gene rearrangements encoding the immunoglobulin heavy chain, a major determinant of epitope recognition. The magnitude of B cell clonal expansions correlates with an individuals secreted antibody response to the vaccine, and the expanded clones are enriched with those expressing influenza-specific monoclonal antibodies. Additionally, B cell responses to pandemic influenza H1N1 vaccination and infection in different people show a prominent family of convergent antibody heavy chain gene rearrangements specific to influenza antigens. These results indicate that microbes can induce specific signatures of immunoglobulin gene rearrangements and that pathogen exposure can potentially be assessed from B cell repertoires.

Effects of Aging, Cytomegalovirus Infection, and EBV Infection on Human B Cell Repertoires

Elderly humans show decreased humoral immunity to pathogens and vaccines, yet the effects of aging on B cells are not fully known. Chronic viral infection by CMV is implicated as a driver of clonal T cell proliferations in some aging humans, but whether CMV or EBV infection contributes to alterations in the B cell repertoire with age is unclear. We have used high-throughput DNA sequencing of IGH gene rearrangements to study the BCR repertoires over two successive years in 27 individuals ranging in age from 20 to 89 y. Some features of the B cell repertoire remain stable with age, but elderly subjects show increased numbers of B cells with long CDR3 regions, a trend toward accumulation of more highly mutated IgM and IgG Ig genes, and persistent clonal B cell populations in the blood. Seropositivity for CMV or EBV infection alters B cell repertoires, regardless of the individual’s age: EBV infection correlates with the presence of persistent clonal B cell expansions, whereas CMV infection correlates with the proportion of highly mutated Ab genes. These findings isolate effects of aging from those of chronic viral infection on B cell repertoires and provide a baseline for understanding human B cell responses to vaccination or infectious stimuli.

Evaluation of B-cell Clonality Using the Biomed-2 Pcr Method Effectively Distinguishes Cutaneous B-cell Lymphoma From Benign Lymphoid Infiltrates

Primary cutaneous B-cell lymphomas (CBCL) are a diverse group of lymphomas that are limited to the skin at the time of diagnosis. Recently, standardized polymerase chain reaction protocols for immunoglobulin (Ig) rearrangement in nodal malignancies using the BIOMED-2 method have been studied extensively. However, reports of investigations of Ig clonality in CBCL using the BIOMED-2 method have been scant. We hypothesized that clonality detection in CBCL with the BIOMED-2 method could effectively distinguish malignant from benign B-cell-rich infiltrates in the skin. Formalin-fixed tissue samples from 26 patients with CBCL and 23 with benign lymphoid infiltrates were analyzed for Ig clonality using standardized BIOMED-2 polymerase chain reaction protocols. The (14;18) translocation was also assessed. A clone was detected in 22 (85%) of the 26 patients with CBCL [12/15 (80%) marginal zone B-cell lymphoma; 10/11 (91%) follicle center lymphoma] and in 1 (4%) of the 23 patients with benign infiltrates. The (14;18) translocation was present in 3 (12%) of the 26 patients with CBCL [1/15 (7%) marginal zone B-cell lymphoma; 2/11 (18%) follicle center lymphoma]. Our preliminary data indicate that Ig clonality can be detected in formalin-fixed samples of CBCL with meaningful sensitivity (85%) and high specificity (96%) using the BIOMED-2 method. This study forms the basis for further investigating the role of Ig clonality in distinguishing CBCL from benign lymphoid infiltrates that may pose a challenge in morphologic diagnosis.

Combined use of PCR-based TCRG and TCRB clonality tests on paraffin-embedded skin tissue in the differential diagnosis of mycosis fungoides and inflammatory dermatoses.

The distinction between mycosis fungoides (MF) and inflammatory dermatoses (ID) by clinicopathologic criteria can be challenging. There is limited information regarding the performance characteristics and utility of TCRG and TCRB clonality assays in diagnosis of MF and ID from paraffin-embedded tissue sections. In this study, PCR tests were performed with both TCRG and TCRB BIOMED-2 clonality methods followed by capillary electrophoresis and Genescan analysis using DNA samples from 35 MF and 96 ID patients with 69 and 133 paraffin-embedded specimens, respectively. Performance characteristics were determined for each test individually and in combination. TCRG and TCRB tests demonstrated identical sensitivity (64%) and specificity (84%) when analyzed as individual assays. The positive predictive value, negative predictive value, and change of posttest MF probability over a range of MF pretest probabilities were obtained. These data were used to construct an algorithm for sequential use of TCRG and TCRB. As single tests, commercially available BIOMED-2 PCR-based TCRG and TCRB clonality tests on paraffin-embedded tissue have no significant difference in terms of sensitivity and specificity. Combined use of the two tests in patients with intermediate pretest probabilities as proposed in the algorithm could improve test utility.

The Frequency of Immunoglobulin Heavy Chain Gene and T-Cell Receptor γ-Chain Gene Rearrangements and Epstein-Barr Virus in ALK+ and ALK− Anaplastic Large Cell Lymphoma and Other Peripheral T-Cell Lymphomas

We previously identified a relatively high frequency of B-cell proliferations along with simultaneous T-cell receptor gamma-chain gene (TRG) and immunoglobulin heavy chain gene (IGH) rearrangements in a series of angioimmunoblastic T-cell lymphoma and peripheral T-cell lymphoma, unspecified. Here, we report on a series of 74 peripheral T-cell lymphoma (PTCL) cases composed entirely of specific PTCL subtypes, including 28 cases of ALK+ anaplastic large-cell lymphoma (ALCL), 35 cases of ALK- ALCL, and 11 cases that represent other specific PTCL subtypes. We performed IGH and TRG gene rearrangement studies and in situ hybridization for Epstein-Barr virus (EBV) to determine the frequency of IGH clonality and to investigate the relationship between EBV, clonality, and associated B-cell proliferations. Using BIOMED-2 PCR assays, we detected TRG clones in 64 of 74 (86%) cases and IGH clones in 6 of 74 (8%) cases, with all IGH-positive cases exhibiting a concurrent TRG clone. Despite the detection of occasional IGH clones, there was no correlation between IGH clonality and EBV, and B-cell proliferations were not identified in any of the cases. These findings suggest that other factors contribute to IGH clonality and demonstrate that, in the absence of an associated B-cell proliferation, IGH clonality occurs infrequently (8%) in specific PTCL subtypes.

A Comparison of Two Methods for Screening CEBPA Mutations in Patients with Acute Myeloid Leukemia

The goal of the study was to compare the performance of a fluorescence-based multiplex PCR fragment analysis to a direct sequencing method for detecting CEBPA mutations in patients with acute myeloid leukemia. Thirty-three samples were selected from a larger study of 107 cases of acute myeloid leukemia by screening for CEBPA mutations by sequence analysis. Of ten identified mutations, six (insertions and deletions) were detected by both sequencing and fragment methods. The fragment analysis method did not detect the remaining four base substitutions because the method cannot detect changes that result in identically sized products. The multiplex PCR fragment length analysis method therefore failed to detect substitution mutations accounting for 40% of total CEBPA mutations in our patient set. Our results indicate that fragment length analysis should not be used in isolation, and that direct sequencing is required to evaluate CEBPA gene mutational status in acute myeloid leukemia. A combination of the two assays may offer some advantages, chiefly in permitting more sensitive detection by fragment length analysis of insertions and deletions.

IgH sequences in common variable immune deficiency reveal altered B cell development and selection

Deep sequence analysis of the IgH repertoires of common variable immune deficiency patients highlights phenotypic features of the disorder and potential disease mechanisms. Not immune to memory problems Although elderly patients typically lament loss of memory, Roskin et al. now highlight a different kind of memory problem plus developmental difficulties that bedevils the immune systems of children and young adults with common variable immune deficiency (CVID). These aberrations may drive a variety of outcomes, including impaired antibody responses to foreign antigens, generation of autoimmune responses, and lymphoid cancers. As the most common symptomatic primary immune deficiency, CVID affects nearly one in 25,000 persons, but the biological basis for the constellation of clinical phenotypes remains hazy. Genetic recombination in the V(D)J regions of immunoglobulin (Ig) genes, which occurs in developing lymphocytes during the early stages of B cell maturation, gives rise to the diverse repertoire of antibodies produced by activated B lymphocytes. This so-called Ig gene rearrangement—a seminal component of the adaptive immune system—gives rise to a broad range of amino acid sequences in the antigen-binding regions of Igs, which permits the recognition of antigens from many pathogens and abnormal cells (such as cancer cells) and subsequent activation of the immune response. The authors first used high-throughput genomic DNA sequencing to explore Ig heavy chain gene rearrangements in B cells from CVID patients versus control subjects. CVID patients displayed abnormal VDJ rearrangement and thus abnormal formation of complementarity determining region 3 (CDR3), which are part of the Ig variable chains and central to the ability of B cells to recognize a wide range of antigens. The authors then sorted B cell populations to retrieve, specifically, the naïve and memory B cells. They detected decreased selection against antibodies with long CDR3 regions in CVID memory repertoires and fewer of the antibody gene mutations that accompany the formation of immune memory. The unmutated naïve B cell pool displayed decreased diversity and abnormal clonal expansion. Together, these alterations could explain the immune deficiencies and autoimmune reactions detected in CVID patients, and suggest that CVID phenotypes stem from aberrant generation and selection of B cell repertoires. Common variable immune deficiency (CVID) is the most common symptomatic primary immune deficiency, affecting ~1 in 25,000 persons. These patients suffer from impaired antibody responses, autoimmunity, and susceptibility to lymphoid cancers. To explore the cellular basis for these clinical phenotypes, we conducted high-throughput DNA sequencing of immunoglobulin heavy chain gene rearrangements from 93 CVID patients and 105 control subjects and sorted naïve and memory B cells from 13 of the CVID patients and 10 of the control subjects. The CVID patients showed abnormal VDJ rearrangement and abnormal formation of complementarity-determining region 3 (CDR3). We observed a decreased selection against antibodies with long CDR3s in memory repertoires and decreased variable gene replacement, offering possible mechanisms for increased patient autoreactivity. Our data indicate that patient immunodeficiency might derive from both decreased diversity of the naïve B cell pool and decreased somatic hypermutation in memory repertoires. The CVID patients also exhibited an abnormal clonal expansion of unmutated B cells relative to the controls. Although impaired B cell germinal center activation is commonly viewed as causative in CVID, these data indicate that CVID B cells diverge from controls as early as the pro–B stage, cell and suggest possible explanations for the increased incidence of autoimmunity, immunodeficiency, and lymphoma CVID patients.

The prognostic value of CXCR4 in acute myeloid leukemia.

Background:CXC chemokine receptor (CXCR4) has been shown to be expressed in a subset of acute myeloid leukemia (AML) patients and is correlated with a poor prognosis. CXCR4 expression appears to be an independent prognostic factor for survival in a heterogeneous group of AML patients. To better assess its significance, we analyzed CXCR4 expression in a group of AML patients. Methods:The prognostic value of CXCR4 expression in 53 patients with AML presenting between 2003 and 2008 was analyzed. Formalin-fixed, paraffin-embedded bone marrow biopsy or clot sections were stained using immunohistochemical methods. Results:CXCR4 was expressed in 26 patients (49.1%). A patient age of less than 60 years (P=0.023), achievement of complete remission after induction therapy (P<0.001), and no CXCR4 expression (P=0.010) were all associated with better progression-free survival (PFS). Among mutations of NPM1, CEBPA, FLT3 ITD, and FLT3 D835 and expression of CXCR4, only CXCR4 expression was associated with PFS (P=0.010; by log-rank test). By multivariate analysis, CXCR4 expression was an independent prognostic factor (P=0.001 for PFS and P=0.001 for overall survival). CXCR4 expression in patients with a normal karyotype was detected in 15 of 22 patients (68.2%, relative ratio 4.46, P=0.035). Expression of CXCR4 in normal-karyotype AML showed inferior PFS (median 2.0 vs. 10.7 mo, P=0.026) and had a trend toward inferior overall survival (median 10.8 vs. 14.0 mo, P=0.058). Conclusions:These results suggest that CXCR4 expression is associated with poor prognosis in patients with AML. Specifically, CXCR4 expression is common in normal-karyotype AML and is a marker of more aggressive disease in this population. CXCR4 expression could be incorporated into the risk assessment of patients with AML.

Clonal identity and differences in primary cutaneous B-cell lymphoma occurring at different sites or time points in the same patient.

Abstract:Primary cutaneous B-cell lymphomas (PCBCL) are rare. Marginal zone lymphomas and follicle center lymphomas (FCL) represent a majority of these cases, and a significant number of cases present with multiple lesions. It is unclear whether multiple lesions in PCBCL represent dissemination of a single clone or multiple new primary lymphomas. In the current study, we analyzed paired samples from 20 PCBCL patients at more than 1 site (16) or at the same site at different time points (4) and 12 patients with benign lymphoid infiltrates to investigate for the presence or absence of a clone, and if present, whether the clones were identical. Both IGH@ and IGK@ rearrangements were tested using the BIOMED-2 protocol. We identified a clone (IGH@ and/or IGK@) in 19 of 20 (95%) PCBCL patients and 2 of 12 (17%) benign lymphoid infiltrate patients. The B-cell clones were proven to be identical in 11 of 20 (55%) PCBCL patients, including 7 of 16(44%) biopsies from patients with 2 different sites and 4 of 4 biopsies (100%) from patients at the same site but different time points. In 4 cases (3 FCL and 1 marginal zone lymphoma), different clones were detected at different sites, suggesting the possibility of a second simultaneous primary lymphoma. Our results indicate that the presence of identical clones is highly suggestive of lymphoma. To our knowledge, this is the first report to investigate the detection of identical clones in 2 distinct biopsies in PCBCL patients. Although the study is small and the results need to be confirmed in a larger study, these findings suggest that a subset of PCBCL at different sites may represent different primary tumors rather than occurrence of a single disease.

Acute Myeloid Leukemia With Monosomal Karyotype Morphologic, Immunophenotypic, and Molecular Findings

OBJECTIVES Acute myeloid leukemia (AML) with monosomal karyotype (MK) recently has been reported to be associated with worse outcome than the traditional complex karyotype. METHODS In this retrospective study of 111 patients with AML, we identified 14 patients with MK (13% of all patients with AML) using the definition proposed by Breems et al. RESULTS Five (36%) of these 14 patients had a loss of a single chromosome in the presence of other structural abnormalities, and nine (64%) had a loss of two or more autosomal chromosomes. Patients with AML-MK presented at an older age, with lower bone marrow blasts, and their blasts less frequently expressed CD34. Most patients with AML-MK had morphologic multilineage dysplasia and were predominantly subclassified as having AML with myelodysplasia-related changes (AML-MRC). Molecular analysis showed a significant absence of NPM1 and FLT3 in patients with AML-MK. CONCLUSIONS Outcome data showed that patients with AML-MK had significantly worse overall survival, disease-free survival, and complete response compared with the rest of the patients with AML as well as within the AML-MRC group.