Cell Gene Rearrangement Research Articles

Composite Lymphoma Comprising of BCL2 Rearrangement Negative, CD23 Positive Follicle Center Cell Lymphoma and Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma: A Case Report

Abstract Introduction/Objective BCL2 rearrangement negative, CD23-positive follicle center cell lymphoma (BCL2 neg CD23 pos FCL) is a rare, recently described provisional entity in International Consensus Classification (2022). It has a predominantly diffuse growth pattern and often involves inguinal region. The molecular profile includes a high frequency of STAT6 and CREBBP co-mutation as well as 1q gain and a recurrent 1p36 loss/TNFRS14 abnormalities. We describe a composite tumor comprising of a rare entity BCL2 neg CD23 pos FCL and Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma (CLL/SLL). To the best of our knowledge this is the first reported case description of this co-occurrence. Methods/Case Report A 59 y/o woman presented with right cervical and axillary lymphadenopathy (upto 1.6 cm). Sections showed partial effacement of nodal architecture by interfollicular and diffuse proliferation of atypical lymphoid cells. The interfollicular areas were comprised of a monotonous population of small lymphocytes. Immunohistochemical stains performed showed that the interfollicular CD20+ PAX5+ atypical lymphoid cells coexpressed CD5, CD23, BCL2 and LEF1 and were negative for CD10, BCL6, CD3, and SOX11, with MIB1 of 5-10%. Based on these, a diagnosis of CLL/SLL was made. Admixed with the CLL/SLL, a second neoplastic B-cell component that distorted nodal architecture was also identified. It composed of a diffuse proliferation of intermediate sized lymphoid cells with a centrocytic/centroblastic morphology. This smaller population of small to intermediate sized B cells expressed CD10, BCL6, and CD23 with a MIB1 proliferation index of ~30%. This population was CD5 and BCL2 negative. CD21 showed residual follicular dendritic cell meshworks. SOX11 and BCL1 were negative. Therefore, a diagnosis of BCL2 neg CD23 pos FCL was made. Flow cytometry showed two distinct populations of monotypic B-cells, one CD5-positive and the other CD10-positive. FISH studies were negative for BCL2 and BCL6 rearrangements as well as del1p36. Cytogenetics was positive for trisomy 12, supporting CLL/SLL. Next Generation Sequencing showed Tier 1 / 2 mutations in STAT6, TNFRSF14, CREBBP, and FOXO1, supporting BCL2 neg CD23 pos FCL. Hence, this represents a unique case of composite CLL/SLL and BCL2 neg CD23 pos FCL. B cell gene rearrangement showed 2 distinct clones confirming 2 separate B cell lymphomas. Results (if a Case Study enter NA) NA Conclusion Here, we describe a composite CLL/SLL and BCL2 rearrangement negative, CD23 positive, FCL never previously described in literature.

WT1 And DNMT3A Mutations in Prognostic Significance of Acute Myeloid Leukemia: A Meta-Analysis.

Background: Adult acute leukemia most commonly manifests as acute myeloid leukemia (AML), a highly heterogeneous malignant tumor of the blood system. The application of genetic diagnostic technology is currently prevalent in numerous clinical sectors. According to recent research, the presence of specific gene mutations or rearrangements in leukemia cells is the primary cause of the disease. As different types of leukemia are caused by atypical mutated genes, testing for these mutations or rearrangements can help diagnose leukemia and identify the disease's molecular targets for treatment. Methods: Using the search fields "WT1," "DNMT3A," "Acute myeloid leukemia," and "survival," the CBM, Cochrane Library, Scopus, EMBASE, and PUBMED databases were separately reviewed. The methodology for evaluating the risk of bias developed by the Cochrane Collaboration was used in conjunction with a methodical evaluation of pertinent literature. Excluded studies with the following characteristics: (1) incomplete and repetitive publications, (2) unable to retrieve or convert data, (3) non-English or Chinese articles. Results: This analysis included 13 studies covering a total of 3478 subjects. The frequency of Wilms' Tumor 1 (WT1) mutations is 6.7%-35.73%, and the frequency of DNMT3A mutations is 12.06%-51.1%. The remission rate of patients with WT1 mutations was less than that of patients without WT1 mutations (OR = 0.22; 95% confidence interval [CI]: 0.14, 0.36; p < 0.00001; I2 = 55%). The DNMT3A mutation has no statistical significance for the prognosis of AML (OR = 1.21; 95% CI: 0.93, 1.58; p = 0.16; I2 = 80%). After removing one study, the heterogeneity of the indicator (mitigation rate) among other studies of DNMT3A mutation was dramatically reduced (OR = 0.63; 95% CI: 0.43, 0.93; p = 0.02; I2 = 0%). Conclusions: Our meta-analysis shows that WT1 mutations hurt the remission rate of AML. Moreover, the impact of DNMT3A mutations on AML needs to be treated with caution. Gene diagnosis is critical for the prognosis and clinical management of AML.

EBV positive plasmacytoma in immunocompetent patients: A diagnostically challenging rare entity

Abstract Introduction/Objective Epstein-Barr Virus (EBV)-positive plasmacytoma is a rare entity that shows morphological and immunophenotypic overlap with plasmablastic lymphoma and can cause a diagnostic dilemma. Here we discuss a unique case of EBER-positive plasmacytoma arising from nasal polyps. Methods/Case Report A 61-year-old immunocompetent male presented with nasal polyps, right maxillary sinus lesions, and an enlarging sternal lesion. Multiple biopsies were obtained which revealed a diffuse infiltration by atypical plasma cells, that were positive for CD138, MUM1, CD79a, CD56, lambda-in situ hybridization, and Ki67- proliferation index of 20-30%. In situ, hybridization for EBV-encoded viral RNA (EBER) was positive in the neoplastic cells. B- and T- cell markers were negative. The flow cytometry studies detected monotypic lambda-restricted CD38/CD138 positive plasma cells with an aberrant expression of CD56 and CD117. Molecular studies for B-and T- cell gene rearrangement were also negative. A final diagnosis of EBER-positive plasmacytoma was made. The patient was treated with cyclophosphamide, vincristine, doxorubicin, and carboplatin followed by four cycles of RVD, and is doing well. Results (if a Case Study enter NA) NA Conclusion EBER-positive plasmacytoma poses a diagnostic challenge with plasmablastic lymphoma, specifically in immunocompetent individuals. The useful differentiating clues pointing towards EBER positive plasmacytoma could be a spectrum of morphology ranging from mature to anaplastic, low Ki67 proliferation index, aberrant CD56 and CD117 positivity, and high M- spike on protein studies. Comprehensive clinical, morphologic phenotypic, and genetic investigations are necessary to make a specific diagnosis as the two entities differ in their management.

Clear Cell Sarcoma masquerading as Malignant Melanoma: A Case Report

Abstract Introduction/Objective Clear cell sarcoma (CCS) is a rare and diagnostically challenging soft tissue tumor that can mimic other malignancies with melanocytic differentiation. Histologically it shows diffuse sheets of clear cells with scattered melanin pigment in a subset of cases. Other morphologies have been described but contain atleast a portion of clear cell features. We report a case of CCS with unusual histomorphology, highlighting the importance of incorporating cytogenetic and immunohistochemical studies to accurately diagnose this tumor. Methods/Case Report We present a case of a 49-year-old male with a left lateral knee mass associated with pain and swelling for one year. A core biopsy revealed a diffuse proliferation of pleomorphic spindle and atypical epithelioid cells. These atypical cells exhibited intranuclear vacuoles, variable prominent nucleoli, abundant dusky cytoplasm, and increased mitotic activity. Immunohistochemical studies were positive for S100, SOX10, and Melan-A (patchy), suggesting a melanocytic differentiation. However, no expression of Preferentially Expressed Antigen in Melanoma (PRAME) or BRAF V600E mutation was noted. Given the clinical history and lack of cutaneous melanocytic lesion, clear cell sarcoma was considered in the differential diagnosis. Fluorescence in situ hybridization (FISH) studies revealed Ewing sarcoma region 1 (EWSR1) gene rearrangement in neoplastic cells, confirming the diagnosis of CCS. Results (if a Case Study enter NA) NA Conclusion The tumor lacked definitive histologic features including clear cell features, demonstrating the variability in histomorphology that can be encountered with CCS. Distinction of CCS from melanoma is of clinical significance as treatment significantly differs. Accurate diagnosis requires the incorporation of cytogenetic and immunohistochemical studies to differentiate it from melanocytic neoplasms. Variability in histomorphology of CCS can pose, as is evident in our case, as a diagnostic pitfall, and CCS should be considered in the differential diagnosis of unusual non-cutaneous melanocytic proliferations that lack clear cell features and show compelete spindle and epithelioid morphology.

Survival Outcomes, Efficacy and Tolerability of a Pediatric-Inspired Regimen (MASPORE) for Philadelphia-Negative Acute Lymphoblastic Leukemia in Young Adults at a Tertiary Hospital in Singapore

Introduction: Recent evidence has emerged to support the use of pediatric-inspired regimen as a standard of care in Adolescents and Young Adults (AYA) patients diagnosed with Philadelphia-negative acute lymphoblastic leukemia (Ph- ALL). The backbone of the pediatric regimen is high cumulative doses of steroids, asparaginase, vincristine and more intensive CNS prophylaxis. Most literature, however, has been in the western population, with few data reported in Asia. MASPORE protocol is a locally designed pediatric-inspired regimen for treatment of ALL in AYA. The protocol uses a 3- or 4-drugs induction regimen (L-asparaginase, Vincristine, Dexamethasone +/- Daunorubicin) based on standard or high-risk disease. PCR-based measurable residual disease (MRD) marker was utilized for disease monitoring and dynamic risk stratification, which led to subsequent intensification of regimen as needed. Methods: In this IRB approved retrospective analysis, patients aged 18-39 years old with Ph- ALL who received MASPORE regimen from January 2009 to December 2021 at the National University Hospital Singapore were identified via our institution database. Treatment outcomes, including measurable residual disease (MRD) monitoring, and toxicity profile were analyzed. Survival outcomes were estimated using Kaplan-Meier method. High risk disease at diagnosis was defined as high white blood cell (&amp;gt;30x10 9/L for B-ALL, &amp;gt;100x10 9/L for T-ALL), hypodiploidy, t(4;11) and other MLL gene rearrangement. Results: 32 patients were identified during the study period; 3 patients were excluded due to incomplete data. The median age was 23 years old (range 18-33 years) with majority being male (86.2%). 16 patients (55.2%) had B-ALL and 13 (44.8%) had T-ALL. High risk disease was present in 7 (43.8%) B-ALL patients and 8 (61.5%) in T-ALL patients. 2 patients in B-ALL group had CNS involvement at diagnosis. The majority (96.5%) achieved complete remission after the induction phase. 1 patient died within first 1 month of treatment due to pancreatitis. 5 patients in high risk group received allogenic stem cell transplantation (alloSCT), whereas 2 patients with standard risk required alloSCT due to relapse and persistent MRD positivity. MRD result was available for 26 patients. In the entire cohort, MRD negativity was achieved in 22 patients (75.9%). Subtype was not associated with achievement of MRD negativity (80% in B-ALL vs 90.9% in T-ALL). High risk patients however had a lower odds of achieving MRD negativity after induction (OR 0.114 95% CI 0.017-0.742, p=0.021). The median follow-up for survivors was 41 months (range 27 to 89 months). Relapse and mortality rate was low at 13.8% each. 5-year OS for patients with B-ALL and T-ALL were 92.3% and 75.2%, respectively (Figure 1a). 5-year OS for patients with standard and high-risk disease were 84.4% and 84.0%, respectively (Figure 1b). Delayed achievement of MRD negativity (i.e. after induction) was not associated with inferior survival outcomes, albeit our sample size was small. In terms of adverse events, Asparaginase-related toxicities included 11 patients (37.9%) with thrombotic events (4 cerebral venous thrombosis and 7 deep vein thrombosis), and 5 patients (17.2%) with grade 2 or more pancreatitis. 7 patients (24.1%) had at least 1 episode of grade 3 or 4 transaminitis. 7 patients (24.1%) had grade 3 or 4 sepsis during the course of treatment. 2 patients developed osteonecrosis of the hip requiring operation and cessation of steroids. Conclusion: Our locally designed MASPORE protocol tailored in accordance to risk stratification demonstrated promising survival outcomes. Similar outcomes observed in standard and high-risk disease suggests the benefit of such an approach. Toxicities were mainly related to L-asparaginase use. Individualized dosing based on drug level monitoring will help to further optimize the treatment intensity with reduced toxicities.

Development of Diagnostic Recommendations for Vitreoretinal Lymphoma

ABSTRACT Purpose To develop diagnostic recommendations for diffuse large B-cell vitreoretinal lymphoma (VRL) in Chinese patients. Methods Retrospective observational case series. Seventy-three eyes of 40 VRL patients and 8 control patients were analyzed. Eighteen patients from Beijing Tongren Hospital and 46 patients from literature were involved as validations. Results Diagnostic methods included (1) typical clinical manifestations; (2) vitreous cytology; (3) immunohistochemical examination of vitreous or choroid/retina; (4) aqueous humor or vitreous cytokine; (5) vitreous cell gene rearrangement; (6) vitreous flow cytometry. If patients meet (1)+(2)+(3), or if they meet (1), and two of (4), (5), (6) are positive, they can be diagnosed as VRL. The sensitivity and specificity values for accurate diagnosis were 0.975 and 1.00. One hundred percent eyes from Beijing Tongren Hospital and 92.7% eyes from literature can be diagnosed. Conclusion We developed diagnostic recommendations for diffuse large B-cell VRL through vitreous cytology combined with multiple auxiliary examinations.

Primary breast T cell lymphoma – a rare case report

Primary breast lymphomas (PBL) are an exceptionally rare form of extranodal non-Hodgkin lymphoma (NHL), occurring in less than 0.5% of all breast malignancies.1 Primary breast T-cell lymphoma (TCL) is an even rarer entity, accounting for only 6% of breast lymphomas. It has an aggressive but poorly understood clinical course, and non-specific features that can mimic inflammatory breast carcinoma (oedema, skin changes and mastalgia).1 Currently, there is no standard treatment protocol for PBL, but a multimodal approach using diagnostic lumpectomy combined with chemotherapy and/or radiation therapy is recommended, versus radical mastectomy alone with no overall survival benefit and higher all-cause mortality rates.2 We present a case of a 64 year old female with a 12 month history of right breast pain with skin changes. Clinical and radiological examination (mammogram and ultrasound) revealed no focal lesion or lymphadenopathy. Multiple biopsies showed no evidence of malignancy. The patient was also treated with IV antibiotics with no improvement. Due to persistent symptoms and concern of inflammatory breast carcinoma, a mastectomy was performed. Haematoxylin and eosin (H&E) stained sections and molecular testing (immunohistochemistry and T cell gene rearrangement) confirmed primary breast T cell lymphoma.

HYPEREOSINOPHILIA LEADS TO PRIMARY IMMUNODEFICIENCY DIAGNOSIS

<h3>Introduction</h3> In the absence of prior infections, idiopathic hypereosinophilia should prompt consideration of a primary immunodeficiency (PID). <h3>Case Description</h3> We present an 8-month-old previously healthy male admitted for persistent hypoxia and suspected bronchiolitis. This patient did not present with fever, weight loss, adenopathy, chronic rash, GI symptoms, or medication use. There was no travel history, sick contacts, or pertinent family history. Laboratory results were significant for negative viral panel and absolute eosinophil count > 34,000. Chest CT showed scattered ground glass opacities without cavitation or bronchiectasis. Bone marrow biopsy was negative for malignancy. T cell (beta) and B cell gene rearrangement studies were negative, as well as FIP1L1-PDFGFRA, FISH studies, and myelodysplastic panels. Cardiac workup, infectious/parasitic tests, tryptase, and B12 levels were normal. The patient was started on systemic steroids with dramatically improved hypereosinophilia. Workup revealed low IgG/IgA levels, with normal IgM. Vaccine titers to tetanus, diphtheria and Hib were absent, despite up-to-date immunizations. Genetic testing revealed a pathogenic mutation in the CD40L gene, indicating X-linked hyper IgM syndrome (HIGM). Pneumocystic jirovecii was confirmed with bronchoscopy. TMP-SMX treatment allowed for weaning off steroids. The patient was started on IVIG and is awaiting bone marrow transplant. <h3>Discussion</h3> HIGM often presents in infancy with increased susceptibility to sinopulmonary infections. Unlike other PIDs with clinical manifestations of atopy, HIGM does not often present with eosinophilia. Opportunistic infections, including PJP, may drive eosinophil production through antigenic stimulation of TH2 cells. This case illustrates the importance of immunologic considerations in patients with unexplained hypereosinophilia, even without a significant infectious history.

New Genetic Technologies in Diagnosis and Treatment of Cancer of Unknown Primary.

Cancer of unknown primary (CUP) represents a rare oncological and heterogeneous disease in which one or more metastases are present, but the location of the primary site is unknown. Pathological diagnosis, using immunohistochemistry, of such metastatic materials is challenging and frequently does not allow for determining the tissue of origin (ToO). The selection of systemic therapy in patients with CUP is usually based on empiric grounds, and the prognosis is generally unfavourable. New molecular techniques could identify the tissue of origin and be used to select systemic agnostic therapies in various malignancies with specific molecular abnormalities. Targetable driver mutations or gene rearrangements in cancer cells may be identified using various molecular assays, of which particularly valuable are next-generation sequencing techniques. These assays may identify tumour sources and allow personalized treatments. However, current guidelines for CUP management do not recommend routine testing of gene expression and epigenetic factors. This is mainly due to the insufficient evidence supporting the improvement of CUP's prognosis by virtue of this approach. This review summarizes the advantages and disadvantages of new genetic techniques in CUP diagnostics and proposes updating the recommendations for CUP management.

CloneRetriever: An Automated Algorithm to Identify Clonal B and T Cell Gene Rearrangements by Next-Generation Sequencing for the Diagnosis of Lymphoid Malignancies.

Clonal immunoglobulin and T-cell receptor rearrangements serve as tumor-specific markers that have become mainstays of the diagnosis and monitoring of lymphoid malignancy. Next-generation sequencing (NGS) techniques targeting these loci have been successfully applied to lymphoblastic leukemia and multiple myeloma for minimal residual disease detection. However, adoption of NGS for primary diagnosis remains limited. We addressed the bioinformatics challenges associated with immune cell sequencing and clone detection by designing a novel web tool, CloneRetriever (CR), which uses machine-learning principles to generate clone classification schemes that are customizable, and can be applied to large datasets. CR has 2 applications-a "validation" mode to derive a clonality classifier, and a "live" mode to screen for clones by applying a validated and/or customized classifier. In this study, CR-generated multiple classifiers using 2 datasets comprising 106 annotated patient samples. A custom classifier was then applied to 36 unannotated samples. The optimal classifier for clonality required clonal dominance ≥4.5× above background, read representation ≥8% of all reads, and technical replicate agreement. Depending on the dataset and analysis step, the optimal algorithm yielded sensitivities of 81%-90%, specificities of 97%-100%, areas under the curve of 91%-94%, positive predictive values of 92-100%, and negative predictive values of 88%-98%. Customization of the algorithms yielded 95%-100% concordance with gold-standard clonality determination, including rescue of indeterminate samples. Application to a set of unknowns showed concordance rates of 83%-96%. CR is an out-of-the-box ready and user-friendly software designed to identify clonal rearrangements in large NGS datasets for the diagnosis of lymphoid malignancies.

Jiyuan Oridonin A Overcomes Differentiation Blockade in Acute Myeloid Leukemia Cells With MLL Rearrangements via Multiple Signaling Pathways.

Differentiation therapy with all-trans-retinoic acid (ATRA) in acute promyelocytic leukemia (APL), a subtype of acute myeloid leukemia (AML), has been extremely successful in inducing clinical remission in APL patients. However, the differentiation therapy of ATRA-based treatment has not been effective in other subtypes of AML. In this study, we evaluated a small molecule of ent-kaurene diterpenoid, Jiyuan oridonin A (JOA), on the differentiation blockade in AML cells with the mixed lineage leukemia (MLL) gene rearrangements (MLLr) in MV4-11, MOLM-13 and THP-1 cells. We found that JOA could significantly inhibit the proliferation of MOLM-13, MV4-11 and THP-1 cells. Moreover, JOA promoted cell differentiation coupled with cell-cycle exit at G0/G1 and inhibited the colony- forming capacity of these cells. We showed that the anti-proliferative effect of JOA attributed to cell differentiation is most likely through the martens tretinoin response up pathway in the MOLM-13 cell line, and the hematopoietic cell lineage pathway by the inhibition of c-KIT expression and cell adhesion pathway in the THP-1 cell line. Our findings suggest that JOA could be a novel therapeutic agent against human MLLr acute myeloid leukemia.

Myocarditis as a Manifestation of a T Cell Lymphoproliferative Disorder in a Patient Undergoing Left Ventricular Assistance Device Implantation

<h3>Introduction</h3> Left ventricular assist device (LVAD) core pathology may provide definitive cardiomyopathy etiology and guide management. We present a case of progressive cardiomyopathy concerning for myocarditis in a patient with cutaneous T cell lymphoma (CTCL) undergoing LVAD implantation. <h3>Case Report</h3> A 63-year-old man presented with mildly reduced left ventricular ejection fraction (LVEF) and ventricular tachycardia (VT). He had an extensive history of Gulf War Syndrome, heavy metal exposure, chronic kidney disease, hypercalcemia and cutaneous T cell lymphoma, managed with ultraviolet light therapy and methotrexate. Cardiac magnetic resonance (CMR) imaging demonstrated anteroseptal and inferolateral wall delayed gadolinium enhancement (DGE). Coronary angiography showed no coronary artery disease. Fluorodeoxyglucose-positron emission tomography (FDG-PET) showed reduced lateral and inferior wall perfusion but no myocardial FDG uptake or evidence of systemic CTCL. Endomyocardial biopsy demonstrated mild hypertrophy and marked interstitial fibrosis, however no evidence of sarcoidosis or myocarditis. Over the next 2 years, his cardiomyopathy progressed (LVEF 15-20%, LVDd 7.2cm). Upon readmission for VT and heart failure (HF), repeat FDG-PET showed myocardial FDG uptake - perfusion mismatch pattern prompting oral prednisone initiation. Durable LVAD was implanted 5 days later given clinical progression. LVAD core pathology showed myocardial T cell infiltration with a clonal T cell gene rearrangement (Figure 1). Peripheral blood and PET markers remained otherwise negative for CTCL. After LVAD, his HF and VT stabilized, and he is undergoing treatment plan for systemic T cell lymphoproliferative disorder. <h3>Summary</h3> We present a case of myocardial T cell lymphoproliferative disorder presenting as progressive cardiomyopathy and highlight the role of LVAD core pathology in diagnosis.

Evaluation of Somatic Hypermutation Status in Chronic Lymphocytic Leukemia (CLL) in the Era of Next Generation Sequencing.

Somatic hypermutation (SHM) status provides an important prognostic indicator for chronic lymphocytic leukemia (CLL), a very common type of mature B-cell leukemia. Owing to the adverse prognosis associated with an unmutated immunoglobulin heavy chain variable (IGHV) status, SHM testing is performed as a standard of care in CLL. Conventionally, SHM testing has been performed using labor intensive and primarily analog Sanger sequencing method following PCR amplification of the clonal immunoglobulin heavy chain gene rearrangements in CLL cells. In comparison, recent availability of next generation sequencing (NGS) allows more versatile detection and direct identification of clonal immunoglobulin gene rearrangements in neoplastic B-cell populations. The ability to identify specific clonal IGHV signature(s) in both baseline (diagnostic) and post-treatment settings enables unique clinical applications of NGS such as determination of SHM status, minimal residual disease (MRD) monitoring, clonal heterogeneity and B cell receptor IG stereotypy. We provide a review of current practices and recommendations for SHM determination using NGS including examples of difficult cases.

Gene rearrangements of MLL and RUNX1 sporadically occur in normal CD34+ cells under cytokine stimulation.

Gene rearrangements of MLL/KMT2A or RUNX1 are the major cause of therapy‐related leukemia. Moreover, MLL rearrangements are the major cause of infant leukemia, and RUNX1 rearrangements are frequently detected in cord blood. These genes are sensitive to topoisomerase II inhibitors, and various genes have been identified as potential fusion partners. However, fetal exposure to these inhibitors is rare. Therefore, we postulated that even a proliferation signal itself might induce gene rearrangements in hematopoietic stem cells. To test this hypothesis, we detected gene rearrangements in etoposide‐treated or non–treated CD34+ cells cultured with cytokines using inverse PCR. In the etoposide‐treated cells, variable‐sized rearrangement bands were detected in the RUNX1 and MLL genes at 3 hours of culture, which decreased after 7 days. However, more rearrangement bands were detected in the non–treated cells at 7 days of culture. Such gene rearrangements were also detected in peripheral blood stem cells mobilized by cytokines for transplantation. However, none of these rearranged genes encoded the leukemogenic oncogene, and the cells with rearrangements did not expand. These findings suggest that MLL and RUNX1 rearrangements, which occur with very low frequency in normal hematopoietic progenitor cells, may be induced under cytokine stimulation. Most of the cells with gene rearrangements are likely eliminated, except for leukemia‐associated gene rearrangements, resulting in the low prevalence of leukemia development.

RAG-Mediated DNA Breaks Attenuate PU.1 Activity in Early B Cells through Activation of a SPIC-BCLAF1 Complex

SUMMARYEarly B cell development is regulated by stage-specific transcription factors. PU.1, an ETS-family transcription factor, is essential for coordination of early B cell maturation and immunoglobulin gene (Ig) rearrangement. Here we show that RAG DNA double-strand breaks (DSBs) generated during Ig light chain gene (Igl) rearrangement in pre-B cells induce global changes in PU.1 chromatin binding. RAG DSBs activate a SPIC/BCLAF1 transcription factor complex that displaces PU.1 throughout the genome and regulates broad transcriptional changes. SPIC recruits BCLAF1 to gene-regulatory elements that control expression of key B cell developmental genes. The SPIC/BCLAF1 complex suppresses expression of the SYK tyrosine kinase and enforces the transition from large to small pre-B cells. These studies reveal that RAG DSBs direct genome-wide changes in ETS transcription factor activity to promote early B cell development.

RAG-Mediated DNA Breaks Attenuate PU.1 Activity in Early B Cells Through Activation of a SPIC-BCLAF1 Complex

Early B cell development is regulated by stage-specific transcription factors. PU.1, an ETS family transcription factor, is essential for coordination of early B cell maturation and immunoglobulin gene (Ig) rearrangement. Here we show that RAG DNA double-strand breaks (DSBs) generated during Ig light chain gene (Igl) rearrangement in pre-B cells induce global changes in PU.1 chromatin binding. RAG DSBs activate a SPIC/BCLAF1 transcription factor complex that displaces PU.1 throughout the genome and regulates broad transcriptional changes. SPIC uniquely recruits BCLAF1 to gene regulatory elements that control expression of key B cell developmental genes. The SPIC/BCLAF1 complex suppresses expression of the SYK tyrosine kinase and enforces the transition from large to small pre-B cells. These studies reveal that RAG DSBs direct genome-wide changes in ETS transcription factor activity to promote early B cell development.

Epigenetic Enhancer Marks and Transcription Factor Binding Influence Vκ Gene Rearrangement in Pre-B Cells and Pro-B Cells.

To date there has not been a study directly comparing relative Igκ rearrangement frequencies obtained from genomic DNA (gDNA) and cDNA and since each approach has potential biases, this is an important issue to clarify. Here we used deep sequencing to compare the unbiased gDNA and RNA Igκ repertoire from the same pre-B cell pool. We find that ~20% of Vκ genes have rearrangement frequencies ≥2-fold up or down in RNA vs. DNA libraries, including many members of the Vκ3, Vκ4, and Vκ6 families. Regression analysis indicates Ikaros and E2A binding are associated with strong promoters. Within the pre-B cell repertoire, we observed that individual Vκ genes rearranged at very different frequencies, and also displayed very different Jκ usage. Regression analysis revealed that the greatly unequal Vκ gene rearrangement frequencies are best predicted by epigenetic marks of enhancers. In particular, the levels of newly arising H3K4me1 peaks associated with many Vκ genes in pre-B cells are most predictive of rearrangement levels. Since H3K4me1 is associated with long range chromatin interactions which are created during locus contraction, our data provides mechanistic insight into unequal rearrangement levels. Comparison of Igκ rearrangements occurring in pro-B cells and pre-B cells from the same mice reveal a pro-B cell bias toward usage of Jκ-distal Vκ genes, particularly Vκ10-96 and Vκ1-135. Regression analysis indicates that PU.1 binding is the highest predictor of Vκ gene rearrangement frequency in pro-B cells. Lastly, the repertoires of iEκ−/− pre-B cells reveal that iEκ actively influences Vκ gene usage, particularly Vκ3 family genes, overlapping with a zone of iEκ-regulated germline transcription. These represent new roles for iEκ in addition to its critical function in promoting overall Igκ rearrangement. Together, this study provides insight into many aspects of Igκ repertoire formation.

Noninvasive Molecular Monitoring in Multiple Myeloma Patients Using Cell-Free Tumor DNA: A Pilot Study

Novel treatments for multiple myeloma (MM) have increased rates of complete response, raising interest in more accurate methods to evaluate residual disease. Cell-free tumor DNA (cfDNA) analysis may represent a minimally invasive approach complementary to multiparameter flow cytometry (MFC) and molecular methods on bone marrow aspirates. A sequencing approach using the Ion Torrent Personal Genome Machine was applied to identify clonal IGH gene rearrangements in tumor plasma cells (PCs) and in serial plasma samples of 25 patients with MM receiving second-line therapy. The same clonal IGH rearrangement identified in tumor PCs was detected in paired plasma samples, and levels of IGH cfDNA correlated with outcome and mirrored tumor dynamics evaluated using conventional laboratory parameters. In addition, IGH cfDNA levels reflected the number of PCs enumerated by MFC immunophenotyping even in the complete response context. Patients determined by MFC to be free of minimal residual disease were characterized by low frequencies of tumor clonotypes in cfDNA and longer survival. This pilot study supports the clinical applicability of the noninvasive monitoring of tumor levels in plasma samples of patients with MM by IGH sequencing.

Primary mediastinal large B-cell lymphoma: a clinicopathologic study of 27 cases

Objective: To study the clinicopathologic characteristics and diagnostic criteria of primary mediastinal B-cell lymphoma (PMBL), and to distinguish PMBL from classic Hodgkin lymphoma(CHL) and systemic diffuse large B-cell lymphoma(DLBCL). Methods: The clinical features, histologic findings, results of immunohistochemical study and prgnosis in 27 PMBL cases were analyzed, with review of literature. Results: The age of patients ranged from 19 to 82 years (median age 34 years). All cases were located in the mediastinum and frequently accompanied by superior vein cava syndrome. Histologically, the tumor cells were pleomorphic and diffusely distributed. Clear cytoplasm and spindle tumor cells were seen in some cases. Varying amount of sclerosing stroma with collagen deposition was seen.Immunohistochemical study showed that the tumor cells were positive for CD20(100%, 27/27), CD30 (64.0%, 16/25), CD23 (77.3%, 17/22) and p63 (16/19). Clonal B cell gene rearrangement was seen. Conclusions: PMBL is a subtype of diffuse large B-cell lymphoma with various histomorphology. Immunohistochemistry can help to confirm the diagnosis, and the prognosis is better than diffuse large B cell lymphoma, not otherwise specified.

Specificity, Privacy, and Degeneracy in the CD4 T Cell Receptor Repertoire Following Immunization.

T cells recognize antigen using a large and diverse set of antigen-specific receptors created by a complex process of imprecise somatic cell gene rearrangements. In response to antigen-/receptor-binding-specific T cells then divide to form memory and effector populations. We apply high-throughput sequencing to investigate the global changes in T cell receptor sequences following immunization with ovalbumin (OVA) and adjuvant, to understand how adaptive immunity achieves specificity. Each immunized mouse contained a predominantly private but related set of expanded CDR3β sequences. We used machine learning to identify common patterns which distinguished repertoires from mice immunized with adjuvant with and without OVA. The CDR3β sequences were deconstructed into sets of overlapping contiguous amino acid triplets. The frequencies of these motifs were used to train the linear programming boosting (LPBoost) algorithm LPBoost to classify between TCR repertoires. LPBoost could distinguish between the two classes of repertoire with accuracies above 80%, using a small subset of triplet sequences present at defined positions along the CDR3. The results suggest a model in which such motifs confer degenerate antigen specificity in the context of a highly diverse and largely private set of T cell receptors.