Clinical characterization of the mutational landscape of 24,639 real-world samples from patients with myeloid malignancies.

Myeloid neoplasms represent a broad spectrum of hematological disorders for which somatic mutation status in key driver genes is important for diagnosis, prognosis and treatment. Here we summarize the findings of a targeted, next generation sequencing laboratory developed test in 24,639 clinical myeloid samples. Data were analyzed comprehensively and as part of individual cohorts specific to acute myeloid leukemia (AML), myelodysplastic syndrome (MDS), and myeloproliferative neoplasms (MPN). Overall, 48,015 variants were detected, and variants were found in all 50 genes in the panel. The mean number of mutations per patient was 1.95. Mutation number increased with age (Spearman's rank correlation coefficient, ρ = 0.29, P < 0.0001) and was higher in patients with AML than MDS or MPN (Student's t-test, P < 0.0001). TET2 was the most common mutation detected (19.1% of samples; 4,695/24,639) including 7.7% (1,908/24,639) with multi-hit TET2 mutations. Mutation frequency was correlated between patients with cytopenias and MDS (Spearman's, ρ = 0.97, P < 2.2×10-16) with the MDS diagnostic gene SF3B1 being the only notable outlier. This large retrospective study shows the utility of NGS testing to inform clinical decisions during routine clinical care and highlights the mutational landscape of a broad population of myeloid patients.

RNA Sequencing Identifies Novel NRG1 Fusions in Solid Tumors that Lack Co-Occurring Oncogenic Drivers.

NRG1 gene fusions are rare, therapeutically relevant, oncogenic drivers that occur across solid tumor types. To understand the landscape of NRG1 gene fusions, 4397 solid tumor formalin-fixed, paraffin-embedded samples consecutively tested by comprehensive genomic and immune profiling during standard care were analyzed. Nineteen NRG1 fusions were found in 17 unique patients, across multiple tumor types, including non-small-cell lung (n = 7), breast (n = 2), colorectal (n = 3), esophageal (n = 2), ovarian (n = 1), pancreatic (n = 1), and unknown primary (n = 1) carcinomas, with a cumulative incidence of 0.38%. Fusions were identified with breakpoints across four NRG1 introns spanning 1.4 megabases, with a mixture of known (n = 8) and previously unreported (n = 11) fusion partners. Co-occurring driver alterations in tumors with NRG1 fusions were uncommon, except colorectal carcinoma, where concurrent alterations in APC, BRAF, and ERBB2 were present in a subset of cases. The overall lack of co-occurring drivers highlights the importance of identifying NRG1 gene fusions, as these patients are unlikely to harbor other targetable alterations. In addition, RNA sequencing is important to identify NRG1 gene fusions given the variety of fusion partners and large genomic areas where breakpoints can occur.

Formin 2 Regulates Lysosomal Degradation of Wnt-Associated ß-Catenin in Neural Progenitors.

Although neural progenitor proliferation along the ventricular zone is regulated by ß-catenin through Wnt signaling, the cytoskeletal mechanisms that regulate expression and localization of these proteins are not well understood. Our prior studies have shown that loss of the actin-binding Filamin A (FlnA) and actin-nucleating protein Formin 2 (Fmn2) impairs endocytosis of low-density-lipoprotein-receptor-related protein 6 (Lrp6), thereby disrupting ß-catenin activation, resulting in decreased brain size. Here, we report that activated RhoA-GTPase disengages Fmn2 N- to C-terminal binding to promote Fmn2 activation and redistribution into lysosomal vesicles. Fmn2 colocalizes with ß-catenin in lysosomes and promotes its degradation. Further, Fmn2 binds the E3 ligase Smurf2, enhances Smurf2-dependent ubiquitination, and degradation of Dishevelled-2 (Dvl2), thereby initiates ß-catenin degradation. Finally, Fmn2 overexpression disrupts neuroepithelial integrity, neuronal migration, and proliferation-phenotypes in E13 mouse embryos, as seen with loss of Fmn2+FlnA function. Conversely, co-expression of Dvl2 with Fmn2 rescues the proliferation defect due to Fmn2 overexpression in mouse embryos. These findings suggest that there is a homeostatic feedback mechanism in the cytoskeletal-dependent regulation of neural proliferation within the cerebral cortex. Upstream, Fmn2 promotes proliferation by stabilizing the Lrp6 receptor, leading to ß-catenin activation. Downstream, RhoA-activated Fmn2 promotes lysosomal degradation of Dvl2, leading to ß-catenin degradation.

Leukaemia hijacks a neural mechanism to invade the central nervous system.

Acute lymphoblastic leukaemia (ALL) has a marked propensity to metastasize to the central nervous system (CNS). In contrast to brain metastases from solid tumours, metastases of ALL seldom involve the parenchyma but are isolated to the leptomeninges, which is an infrequent site for carcinomatous invasion. Although metastasis to the CNS occurs across all subtypes of ALL, a unifying mechanism for invasion has not yet been determined. Here we show that ALL cells in the circulation are unable to breach the blood-brain barrier in mice; instead, they migrate into the CNS along vessels that pass directly between vertebral or calvarial bone marrow and the subarachnoid space. The basement membrane of these bridging vessels is enriched in laminin, which is known to coordinate pathfinding of neuronal progenitor cells in the CNS. The laminin receptor α6 integrin is expressed in most cases of ALL. We found that α6 integrin-laminin interactions mediated the migration of ALL cells towards the cerebrospinal fluid in vitro. Mice with ALL xenografts were treated with either a PI3Kδ inhibitor, which decreased α6 integrin expression on ALL cells, or specific α6 integrin-neutralizing antibodies and showed significant reductions in ALL transit along bridging vessels, blast counts in the cerebrospinal fluid and CNS disease symptoms despite minimally decreased bone marrow disease burden. Our data suggest that α6 integrin expression, which is common in ALL, allows cells to use neural migratory pathways to invade the CNS.

Afadin controls cell polarization and mitotic spindle orientation in developing cortical radial glia.

BACKGROUND: In developing tissues, cell polarity and tissue architecture play essential roles in the regulation of proliferation and differentiation. During cerebral cortical development, adherens junctions link highly polarized radial glial cells in a neurogenic niche that controls their behavior. How adherens junctions regulate radial glial cell polarity and/or differentiation in mammalian cortical development is poorly understood. RESULTS: Conditional deletion of Afadin, a protein required for formation and maintenance of epithelial tissues, leads to abnormalities in radial glial cell polarity and subsequent loss of adherens junctions. We observed increased numbers of obliquely-oriented progenitor cell divisions, increased exit from the ventricular zone neuroepithelium, and increased production of intermediate progenitors. CONCLUSIONS: Together, these findings indicate that Afadin plays an essential role in regulating apical-basal polarity and adherens junction integrity of radial glial cells, and suggest that epithelial architecture plays an important role in radial glial identity by regulating mitotic orientation and preventing premature exit from the neurogenic niche.

Filamin A- and formin 2-dependent endocytosis regulates proliferation via the canonical Wnt pathway.

Actin-associated proteins regulate multiple cellular processes, including proliferation and differentiation, but the molecular mechanisms underlying these processes are unclear. Here, we report that the actin-binding protein filamin A (FlnA) physically interacts with the actin-nucleating protein formin 2 (Fmn2). Loss of FlnA and Fmn2 impairs proliferation, thereby generating multiple embryonic phenotypes, including microcephaly. FlnA interacts with the Wnt co-receptor Lrp6. Loss of FlnA and Fmn2 impairs Lrp6 endocytosis, downstream Gsk3ß activity, and ß-catenin accumulation in the nucleus. The proliferative defect in Flna and Fmn2 null neural progenitors is rescued by inhibiting Gsk3ß activity. Our findings thus reveal a novel mechanism whereby actin-associated proteins regulate proliferation by mediating the endocytosis and transportation of components in the canonical Wnt pathway. Moreover, the Fmn2-dependent signaling in this pathway parallels that seen in the non-canonical Wnt-dependent regulation of planar cell polarity through the Formin homology protein Daam. These studies provide evidence for integration of actin-associated processes in directing neuroepithelial proliferation.

The role of adherens junctions in the developing neocortex.

The disproportional enlargement of the neocortex through evolution has been instrumental in the success of vertebrates, in particular mammals. The neocortex is a multilayered sheet of neurons generated from a simple proliferative neuroepithelium through a myriad of mechanisms with substantial evolutionary conservation. This developing neuroepithelium is populated by progenitors that can generate additional progenitors as well as post-mitotic neurons. Subtle alterations in the production of progenitors vs. differentiated cells during development can result in dramatic differences in neocortical size. This review article will examine how cadherin adhesion proteins, in particular α-catenin and N-cadherin, function in regulating the neural progenitor microenvironment, cell proliferation, and differentiation in cortical development.

Clonality assessment of cutaneous B-cell lymphoid proliferations: a comparison of flow cytometry immunophenotyping, molecular studies, and immunohistochemistry/in situ hybridization and review of the literature.

Cutaneous lymphoid infiltrates are diagnostically challenging. Although ancillary techniques to assess clonality can help distinguish between reactive lymphoid hyperplasia and lymphoma, one of the most widely used techniques in hematopathology, flow cytometry immunophenotyping (FCI), has not been routinely applied to skin specimens. We performed FCI on 73 skin specimens from 67 patients clinically suspected of having a cutaneous B-cell lymphoma (CBCL) and compared the results with those obtained from immunoglobulin heavy chain (IGH) gene molecular studies (58 cases, primarily by polymerase chain reaction) and either immunohistochemistry (IHC) or in situ hybridization to evaluate for light chain restriction (22 and 2 cases, respectively). Sufficient quantity of CD45 (leukocyte common antigen)-positive cells and staining quality were achieved in 88% of cases by FCI, and clonality was detected in 68% of CBCLs versus molecular studies showing sufficient DNA quality in 74% and only 39% clonality detection, and interpretable/contributory IHC results in 84% of cases with 55% clonality detection. Clonality was documented more frequently in secondary rather than primary CBCLs by all 3 techniques. Therefore, FCI is feasible and appears to be more reliable than molecular studies or IHC/in situ hybridization for detecting clonality in CBCLs and can provide additional prognostically and therapeutically relevant information. The exception is cases with plasmacytic differentiation such as marginal zone lymphoma for which IHC might be a superior tool. We have also shown that a large subset of primary cutaneous follicle center lymphomas express CD10 and/or BCL2 by FCI. Recent advances in FCI beg the question of applicability to cutaneous T-cell and NK-cell lymphomas.

Cadherin-11 regulates motility in normal cortical neural precursors and glioblastoma.

Metastasizing tumor cells undergo a transformation that resembles a process in normal development when non-migratory epithelial cells modulate the expression of cytoskeletal and adhesion proteins to promote cell motility. Here we find a mesenchymal cadherin, Cadherin-11 (CDH11), is increased in cells exiting the ventricular zone (VZ) neuroepithelium during normal cerebral cortical development. When overexpressed in cortical progenitors in vivo, CDH11 causes premature exit from the neuroepithelium and increased cell migration. CDH11 expression is elevated in human brain tumors, correlating with higher tumor grade and decreased patient survival. In glioblastoma, CDH11-expressing tumor cells can be found localized near tumor vasculature. Endothelial cells stimulate TGFß signaling and CDH11 expression in glioblastoma cells. TGFß promotes glioblastoma cell motility, and knockdown of CDH11 expression in primary human glioblastoma cells inhibits TGFß-stimulated migration. Together, these findings show that Cadherin-11 can promote cell migration in neural precursors and glioblastoma cells and suggest that endothelial cells increase tumor aggressiveness by co-opting mechanisms that regulate normal neural development.

AKT activation by N-cadherin regulates beta-catenin signaling and neuronal differentiation during cortical development.

BACKGROUND: During cerebral cortical development, neural precursor-precursor interactions in the ventricular zone neurogenic niche coordinate signaling pathways that regulate proliferation and differentiation. Previous studies with shRNA knockdown approaches indicated that N-cadherin adhesion between cortical precursors regulates ß-catenin signaling, but the underlying mechanisms remained poorly understood. RESULTS: Here, with conditional knockout approaches, we find further supporting evidence that N-cadherin maintains ß-catenin signaling during cortical development. Using shRNA to N-cadherin and dominant negative N-cadherin overexpression in cell culture, we find that N-cadherin regulates Wnt-stimulated ß-catenin signaling in a cell-autonomous fashion. Knockdown or inhibition of N-cadherin with function-blocking antibodies leads to reduced activation of the Wnt co-receptor LRP6. We also find that N-cadherin regulates ß-catenin via AKT, as reduction of N-cadherin causes decreased AKT activation and reduced phosphorylation of AKT targets GSK3ß and ß-catenin. Inhibition of AKT signaling in neural precursors in vivo leads to reduced ß-catenin-dependent transcriptional activation, increased migration from the ventricular zone, premature neuronal differentiation, and increased apoptotic cell death. CONCLUSIONS: These results show that N-cadherin regulates ß-catenin signaling through both Wnt and AKT, and suggest a previously unrecognized role for AKT in neuronal differentiation and cell survival during cortical development.

Expansion of a clonal CD8+CD57+ large granular lymphocyte population after autologous stem cell transplant in multiple myeloma.

Clonal expansions of large granular lymphocytes (LGLs) have been identified in patients following stem cell transplants and may represent posttransplant LGL leukemias or reactive immune responses. To differentiate between these 2 possibilities, we assessed peripheral blood and bone marrow of patients with myeloma after autologous stem cell transplant. All patients examined shortly after autologous stem cell transplant had significant increases in the LGLs in the peripheral blood and bone marrow (71% of lymphocytes) as compared with controls (39%). This increase was detectable years after transplant. The LGLs had a reproducible immunophenotype of CD8+CD57+ T cells without phenotypic abnormalities in 19 of 20 patients. Sixty-five percent of the post-autologous stem cell transplant patients had clonal T-cell receptor gene rearrangements in the bone marrow, yet no patients had neutropenia or splenomegaly. Although the LGL expansions were clonal and persistent, the lack of clinical sequelae suggests the clonal LGL expansion is a reactive, potentially beneficial, immune response to autologous stem cell transplant.

Early posttransplant lymphoproliferative disease: clinicopathologic features and correlation with mTOR signaling pathway activation.

Early posttransplant lymphoproliferative disorders (EPTLDs) represent the first changes in posttransplant lymphoproliferative disorders (PTLDs) morphologic spectrum. EPTLD data are available mostly from case reports and series that include other types of PTLD. Fifteen EPTLDs were reviewed retrospectively. Clinical data, histopathology, clonality, and Epstein- Barr virus (EBV) status were correlated with staining intensity to an antibody for phosphorylated S6 (pS6) ribosomal protein, a downstream effector of mammalian target of rapamycin (mTOR). Median time from transplantation to EPTLD was 50 months (range, 7-135 mo). EPTLDs involved tonsil and/or adenoids (n = 11) and lymph nodes (n = 4), all of which were nonclonal and EBV-encoded RNA-positive. Most (n = 11) were plasmacytic hyperplasia and florid follicular hyperplasia (n = 4). All regressed with reduced immunosuppression, and had increased pS6 staining compared with normal tonsil (P = .002, F test). EPTLDs developed later than previously reported, involved mostly tonsils/adenoids, were EBV-encoded RNA (EBER) positive, showed increased pS6, and had excellent clinical outcome with reduction of immunosuppression.

Hierarchical clustering of gene expression patterns in the Eomes + lineage of excitatory neurons during early neocortical development.

BACKGROUND: Cortical neurons display dynamic patterns of gene expression during the coincident processes of differentiation and migration through the developing cerebrum. To identify genes selectively expressed by the Eomes + (Tbr2) lineage of excitatory cortical neurons, GFP-expressing cells from Tg(Eomes::eGFP) Gsat embryos were isolated to > 99% purity and profiled. RESULTS: We report the identification, validation and spatial grouping of genes selectively expressed within the Eomes + cortical excitatory neuron lineage during early cortical development. In these neurons 475 genes were expressed ≥ 3-fold, and 534 genes ≤ 3-fold, compared to the reference population of neuronal precursors. Of the up-regulated genes, 328 were represented at the Genepaint in situ hybridization database and 317 (97%) were validated as having spatial expression patterns consistent with the lineage of differentiating excitatory neurons. A novel approach for quantifying in situ hybridization patterns (QISP) across the cerebral wall was developed that allowed the hierarchical clustering of genes into putative co-regulated groups. Forty four candidate genes were identified that show spatial expression with Intermediate Precursor Cells, 49 candidate genes show spatial expression with Multipolar Neurons, while the remaining 224 genes achieved peak expression in the developing cortical plate. CONCLUSIONS: This analysis of differentiating excitatory neurons revealed the expression patterns of 37 transcription factors, many chemotropic signaling molecules (including the Semaphorin, Netrin and Slit signaling pathways), and unexpected evidence for non-canonical neurotransmitter signaling and changes in mechanisms of glucose metabolism. Over half of the 317 identified genes are associated with neuronal disease making these findings a valuable resource for studies of neurological development and disease.

Rapid quantitative detection of the T315I mutation in patients with chronic myelogenous leukemia.

Acquired resistance to tyrosine kinase inhibitors (TKIs) in the treatment of chronic myelogenous leukemia (CML) is frequently caused by point mutations in the ABL kinase domain of the BCR-ABL fusion gene. The T315I mutation is the most common mutation found in the kinase domain and leads to complete resistance to existing TKIs. Sensitive and specific approaches for detecting this mutation in patient specimens can provide valuable information to guide treatment decisions and monitor their effectiveness. Here, we describe an allele-specific real-time polymerase chain reaction method to distinguish and quantify wild type or T315I mutant ABL transcripts. This approach has high specificity in identifying mutant transcripts and shows minimal interference from wild-type transcripts. As few as 5 copies of the T315I mutant transcript or 0.025% (2.5×10(-4)) T315I mutant transcripts could be detected by this method. This approach requires no additional specialized reagents other than those used in standard real-time polymerase chain reaction and therefore may be easily incorporated as an effective strategy for the early detection and monitoring of TKI resistance in patients with CML.

Clinical, morphologic, immunophenotypic, and molecular cytogenetic assessment of CD4-/CD8-γδ T-cell large granular lymphocytic leukemia.

γδ T-cell large granular lymphocytic (T-LGL) leukemia of the CD4-/CD8- subtype is rare, and data are limited in the literature. This study evaluated the clinical, morphologic, immunophenotypic, and molecular cytogenetic features of 7 cases of CD4-/CD8- γδ T-LGL leukemia. Although this variant shares several clinical and morphologic features with the more common T-LGL leukemias, the incidences of autoimmune hemolytic anemia and pure red cell aplasia are higher. Another striking feature observed in our study was the lack of increased large granular lymphocytes in the peripheral blood in the majority of cases despite prominent bone marrow or splenic involvement. CD4-/CD8- γδ T-LGL leukemia also displays an immunophenotype and pattern of splenic involvement overlapping with hepatosplenic T-cell lymphoma. Clinically, this variant of T-LGL leukemia shows an overall indolent course, but treatment is often required in the initial stages of the disease. Awareness of these features is important for early recognition and accurate diagnosis of patients with CD4-/CD8- γδ T-LGL leukemia.

Beta-catenin signaling negatively regulates intermediate progenitor population numbers in the developing cortex.

Intermediate progenitor cells constitute a second proliferative cell type in the developing mammalian cerebral cortex. Little is known about the factors that govern the production of intermediate progenitors. Although persistent expression of stabilized beta-catenin was found to delay the maturation of radial glial progenitors into intermediate progenitors, the relationship between beta-catenin signaling and intermediate progenitors remains poorly understood. Using a transgenic reporter mouse for Axin2, a direct target of Wnt/beta-catenin signaling, we observed that beta-catenin signaling is decreased in intermediate progenitor cells relative to radial glial progenitors. Conditional deletion of beta-catenin from mouse cortical neural progenitors increased intermediate progenitor numbers, while conditional expression of stabilized beta-catenin reduced the intermediate progenitor population. Together, these findings provide evidence that beta-catenin signaling in radial progenitors negatively regulates intermediate progenitor cell number during cortical development.

Cortical neural precursors inhibit their own differentiation via N-cadherin maintenance of beta-catenin signaling.

Little is known about the architecture of cellular microenvironments that support stem and precursor cells during tissue development. Although adult stem cell niches are organized by specialized supporting cells, in the developing cerebral cortex, neural stem/precursor cells reside in a neurogenic niche lacking distinct supporting cells. Here, we find that neural precursors themselves comprise the niche and regulate their own development. Precursor-precursor contact regulates beta-catenin signaling and cell fate. In vivo knockdown of N-cadherin reduces beta-catenin signaling, migration from the niche, and neuronal differentiation in vivo. N-cadherin engagement activates beta-catenin signaling via Akt, suggesting a mechanism through which cells in tissues can regulate their development. These results suggest that neural precursor cell interactions can generate a self-supportive niche to regulate their own number.

Nestin reporter transgene labels multiple central nervous system precursor cells.

Embryonic neuroepithelia and adult subventricular zone (SVZ) stem and progenitor cells express nestin. We characterized a transgenic line that expresses enhanced green fluorescent protein (eGFP) specified to neural tissue by the second intronic enhancer of the nestin promoter that had several novel features. During embryogenesis, the dorsal telencephalon contained many and the ventral telencephalon few eGFP+ cells. eGFP+ cells were found in postnatal and adult neurogenic regions. eGFP+ cells in the SVZ expressed multiple phenotype markers, glial fibrillary acidic protein, Dlx, and neuroblast-specific molecules suggesting the transgene is expressed through the lineage. eGFP+ cell numbers increased in the SVZ after cortical injury, suggesting this line will be useful in probing postinjury neurogenesis. In non-neurogenic regions, eGFP was strongly expressed in oligodendrocyte progenitors, but not in astrocytes, even when they were reactive. This eGFP+ mouse will facilitate studies of proliferative neuroepithelia and adult neurogenesis, as well as of parenchymal oligodendrocytes.

Beta-catenin signaling levels in progenitors influence the laminar cell fates of projection neurons.

The mechanisms underlying the timing of the laminar fate decisions during cortical neurogenesis remain poorly understood. Here we show that beta-catenin signaling in cortical neural precursors can regulate the laminar fate of their daughters. In ventricular zone neural precursors, beta-catenin signaling is higher when deep-layer neurons are being generated and lower when upper-layer neurons are being generated. Overactivation of beta-catenin in cortical precursors midway through corticogenesis increased the relative production of deep-layer neurons, while inhibition of signaling increased the relative production of upper-layer neurons. Furthermore, in late-gestation upper-layer precursors, overactive beta-catenin signaling was able to partially restore production of deep-layer neurons. These observations suggest that increased beta-catenin signaling can reset the timing of cortical precursors to promote the production of deep-layer neurons, while inhibition of beta-catenin signaling advances the timing to promote upper-layer production.

Activity of the beta-catenin phosphodestruction complex at cell-cell contacts is enhanced by cadherin-based adhesion.

It is well established that cadherin protein levels impact canonical Wnt signaling through binding and sequestering beta-catenin (beta-cat) from T-cell factor family transcription factors. Whether changes in intercellular adhesion can affect beta-cat signaling and the mechanism through which this occurs has remained unresolved. We show that axin, APC2, GSK-3beta and N-terminally phosphorylated forms of beta-cat can localize to cell-cell contacts in a complex that is molecularly distinct from the cadherin-catenin adhesive complex. Nonetheless, cadherins can promote the N-terminal phosphorylation of beta-cat, and cell-cell adhesion increases the turnover of cytosolic beta-cat. Together, these data suggest that cadherin-based cell-cell adhesion limits Wnt signals by promoting the activity of a junction-localized beta-cat phosphodestruction complex, which may be relevant to tissue morphogenesis and cell fate decisions during development.