Chronic Lymphocytic Leukemia IGHV Somatic Hypermutation Detection by Targeted Capture Next-Generation Sequencing.

BACKGROUND: Somatic hypermutation (SHM) status of the immunoglobulin heavy variable (IGHV) gene plays a crucial role in determining the prognosis and treatment of patients with chronic lymphocytic leukemia (CLL). A common approach for determining SHM status is multiplex polymerase chain reaction and Sanger sequencing of the immunoglobin heavy locus; however, this technique is low throughput, is vulnerable to failure, and does not allow multiplexing with other diagnostic assays. METHODS: Here we designed and validated a DNA targeted capture approach to detect immunoglobulin heavy variable somatic hypermutation (IGHV SHM) status as a submodule of a larger next-generation sequencing (NGS) panel that also includes probes for ATM, BIRC3, CHD2, KLHL6, MYD88, NOTCH1, NOTCH2, POT1, SF3B1, TP53, and XPO1. The assay takes as input FASTQ files and outputs a report containing IGHV SHM status and V allele usage following European Research Initiative on CLL guidelines. RESULTS: We validated the approach on 35 CLL patient samples, 34 of which were characterized using Sanger sequencing. The NGS panel identified the IGHV SHM status of 34 of 35 CLL patients. We showed 100% sensitivity and specificity among the 33 CLL samples with both NGS and Sanger sequencing calls. Furthermore, we demonstrated that this panel can be combined with additional targeted capture panels to detect prognostically important CLL single nucleotide variants, insertions/deletions, and copy number variants (TP53 copy number loss). CONCLUSIONS: A targeted capture approach to IGHV SHM detection can be integrated into broader sequencing panels, allowing broad CLL prognostication in a single molecular assay.

Multisite clinical cross-validation and variant interpretation of a next generation sequencing panel for lymphoid cancer prognostication.

AIMS: Genomic sequencing of lymphomas is under-represented in routine clinical testing despite having prognostic and predictive value. Clinical implementation is challenging due to a lack of consensus on reportable targets and a paucity of reference samples. We organised a cross-validation study of a lymphoma-tailored next-generation sequencing panel between two College of American Pathologists (CAP)-accredited clinical laboratories to mitigate these challenges. METHODS: A consensus for the genomic targets was discussed between the two institutes based on recurrence in diffuse large B-cell lymphoma, follicular lymphoma, mantle cell lymphoma, chronic lymphocytic leukaemia and T-cell lymphomas. Using the same genomic targets, each laboratory ordered libraries independently and a cross-validation study was designed to exchange samples (8 cell lines and 22 clinical samples) and their FASTQ files. RESULTS: The sensitivity of the panel when comparing different library preparation and bioinformatic workflows was between 97% and 99% and specificity was 100% when a 5% limit of detection cut-off was applied. To evaluate how the current standards for variant classification of tumours apply to lymphomas, the Association for Molecular Pathology/American Society of Clinical Oncology/CAP and OncoKB classification systems were applied to the panel. The majority of variants were assigned a possibly actionable class or likely pathogenic due to more limited evidence in the literature. CONCLUSIONS: The cross-validation study highlights the benefits of sample and data exchange for clinical validation and provided a framework for reporting the findings in lymphoid malignancies.

Case Report: Identification of a novel STAT3 mutation in EBV-positive inflammatory follicular dendritic cell sarcoma.

EBV-positive inflammatory follicular dendritic cell sarcoma (EBV+ IFDCS) is an uncommon disease primarily observed in Asia. It is characterized by the development of tumors believed to originate from follicular dendritic cells (FDC). The consistent association between this condition and clonal EBV infection suggests EBV's involvement as an etiological factor. However, diagnosing EBV+ IFDCS can be challenging due to its morphological variability and diverse immunohistochemical staining patterns. The genetic characteristics of EBV+ IFDCS remain insufficiently understood. To address this knowledge gap, we present a case study of a 47-year-old male patient diagnosed with EBV+ IFDCS. We utilized a Next-generation sequencing (NGS) platform to investigate the genetic profile of the tumor cells. We identified a single pathogenic mutation (G618R) in the STAT3 gene. This finding provides valuable insights into the genetic alterations associated with EBV+ IFDCS and potentially contributes to our understanding of the disease's pathogenesis.

Development of a comprehensive approach to adult hereditary cancer testing in Ontario.

BACKGROUND: Genetic testing for hereditary cancer susceptibility has advanced over time due to the discovery of new risk genes, improved technology and decreased cost. In the province of Ontario, testing eligibility criteria were initially developed to include hereditary breast, ovarian and colorectal cancer syndromes. The rapid evolution of genetic technologies has facilitated the ability to interrogate a large number of genes concurrently. This, coupled with new knowledge about risk genes, necessitated a coordinated approach to expanding the scope of genes and indications tested and synchronisation of access and test utilisation across the province as required in a publicly funded universal healthcare system. METHODS: Ontario Health-Cancer Care Ontario convened expert working groups to develop a standardised and comprehensive cancer gene list for adults and accompanying hereditary cancer testing (HCT) criteria using an evidence-based framework and broad laboratory and clinical genetics engagement. RESULTS: A standardised 76-cancer-gene panel, organised into 13 larger disease site panels and 25 single/small gene panels, was developed and endorsed by the working groups. Provincial genetic testing eligibility criteria were updated to align with the new panels and to guide clinical decision-making. In the first year following the implementation of these changes, 10 564 HCT panels were performed with an overall mutation detection rate of 12.2%. CONCLUSION: Using an evidence framework and broad clinical engagement to develop and endorse an updated guidance document, cancer genetic testing for adults in Ontario is now standardised and coordinated across the province.

Consensus Recommendations for MRD Testing in Adult B-Cell Acute Lymphoblastic Leukemia in Ontario.

Measurable (minimal) residual disease (MRD) is an established, key prognostic factor in adult B-cell acute lymphoblastic leukemia (B-ALL), and testing for MRD is known to be an important tool to help guide treatment decisions. The clinical value of MRD testing depends on the accuracy and reliability of results. Currently, there are no Canadian provincial or national guidelines for MRD testing in adult B-ALL, and consistent with the absence of such guidelines, there is no uniform Ontario MRD testing consensus. Moreover, there is great variability in Ontario in MRD testing with respect to where, when, and by which technique, MRD testing is performed, as well as in how the results are interpreted. To address these deficiencies, an expert multidisciplinary working group was convened to define consensus recommendations for improving the provision of such testing. The expert panel recommends that MRD testing should be implemented in a centralized manner to ensure expertise and accuracy in testing for this low volume indication, thereby to provide accurate, reliable results to clinicians and patients. All adult patients with B-ALL should receive MRD testing after induction chemotherapy. Philadelphia chromosome (Ph)-positive patients should have ongoing monitoring of MRD during treatment and thereafter, while samples from Ph-negative B-ALL patients should be tested at least once later during treatment, ideally at 12 to 16 weeks after treatment initiation. In Ph-negative adult B-ALL patients, standardized, ideally centralized, protocols must be used for MRD testing, including both flow cytometry and immunoglobulin (Ig) heavy chain and T-cell receptor (TCR) gene rearrangement analysis. For Ph-positive B-ALL patients, MRD testing using a standardized protocol for reverse transcription real-time quantitative PCR (RT-qPCR) for the BCR-ABL1 gene fusion transcript is recommended, with Ig/TCR gene rearrangement analysis done in parallel likely providing additional clinical information.

Molecular profiling for precision cancer therapies.

The number of druggable tumor-specific molecular aberrations has grown substantially in the past decade, with a significant survival benefit obtained from biomarker matching therapies in several cancer types. Molecular pathology has therefore become fundamental not only to inform on tumor diagnosis and prognosis but also to drive therapeutic decisions in daily practice. The introduction of next-generation sequencing technologies and the rising number of large-scale tumor molecular profiling programs across institutions worldwide have revolutionized the field of precision oncology. As comprehensive genomic analyses become increasingly available in both clinical and research settings, healthcare professionals are faced with the complex tasks of result interpretation and translation. This review summarizes the current and upcoming approaches to implement precision cancer medicine, highlighting the challenges and potential solutions to facilitate the interpretation and to maximize the clinical utility of molecular profiling results. We describe novel molecular characterization strategies beyond tumor DNA sequencing, such as transcriptomics, immunophenotyping, epigenetic profiling, and single-cell analyses. We also review current and potential applications of liquid biopsies to evaluate blood-based biomarkers, such as circulating tumor cells and circulating nucleic acids. Last, lessons learned from the existing limitations of genotype-derived therapies provide insights into ways to expand precision medicine beyond genomics.

Stable transmission of an unbalanced chromosome 21 derived from chromoanasynthesis in a patient with a SYNGAP1 likely pathogenic variant.

BACKGROUND: Complex genomic structural variations, involving chromoanagenesis, have been implicated in multiple congenital anomalies and abnormal neurodevelopment. Familial inheritance of complex chromosomal structural alteration resulting from germline chromoanagenesis-type mechanisms are limited. CASE PRESENTATION: We report a two-year eleven-month old male presenting with epilepsy, ataxia and dysmorphic features of unknown etiology. Chromosomal microarray identified a complex unbalanced rearrangement involving chromosome 21. G-banding and FISH for targeted regions of chromosome 21 revealed that the copy number imbalances were limited to gains dispersed throughout the long arm of chromosome 21, characteristic of a chromosome derived from chromoanagenesis. Family studies showed that the unbalanced chromosome had been stably inherited, as it was present in both his healthy mother and maternal grandfather. Further molecular testing for non-syndromic intellectual disability genes found a likely pathogenic mutation in SYNGAP1 (NM_006772.2:c.3722_3723del). CONCLUSIONS: This study indicates that complex rearrangements involving an unbalanced chromosome derived from chromoanasynthesis can be familial and should be not be presumed pathogenic.

Danon Disease Due to a Novel LAMP2 Microduplication.

Danon disease is a rare X-linked disorder comprising hypertrophic cardiomyopathy, skeletal myopathy, intellectual disability, and retinopathy; mutations of the lysosome-associated membrane protein gene LAMP2 are responsible. Most affected persons exhibit "private" point mutations; small locus rearrangements have recently been reported in four cases. Here, we describe the clinical, pathologic, and molecular features of a male proband and his affected mother with Danon disease and a small LAMP2 microduplication. The proband presented at age 12 years with exercise intolerance, hypertrophic cardiomyopathy, and increased creatine kinase. Endomyocardial biopsy findings were nonspecific, showing myocyte hypertrophy and reactive mitochondrial changes. Quadriceps muscle biopsy demonstrated the characteristic autophagic vacuoles with sarcolemma-like features. LAMP2 tissue immunostaining was absent; however, LAMP2 sequencing was normal. Deletion/duplication testing by multiplex ligation-dependent probe amplification (MLPA) assay revealed a 1.5kb microduplication containing LAMP2 exons 4 and 5. RT-PCR studies were consistent with the inclusion of these two duplicated exons in the final spliced transcript, resulting in a frameshift. The proband's mother, who had died following cardiac transplantation due to suspected myocarditis at age 35, was reviewed and was shown to be affected upon immunostaining of banked myocardial tissue. This case constitutes the second report of a pathogenic microduplication in Danon disease, and illustrates a number of potential diagnostic pitfalls. Firstly, given the imperfect sensitivity of LAMP2 sequencing, tissue immunostaining and/or MLPA should be considered as a diagnostic adjunct in the workup for this disorder. Secondly, the pathological findings in myocardium may be falsely indicative of relatively common conditions such as myocarditis.

Type VIII collagen signals via ß1 integrin and RhoA to regulate MMP-2 expression and smooth muscle cell migration.

The extracellular matrix signals and regulates the behavior of vascular cells during the pathogenesis of atherosclerosis. Type VIII collagen, a short chain collagen, is scarcely present in normal arteries, but is dramatically upregulated in atherosclerosis and after other types of vascular injury. Cell culture studies have revealed that this protein supports smooth muscle cell (SMC) adhesion and stimulates migration, however little is known about the signaling or the mechanisms by which this occurs. SMCs isolated from wild-type C57BL/6 and type VIII collagen deficient mice were studied using assays to measure chemotactic and haptotactic migration, and remodeling and contraction of 3-dimensional type I collagen gels. Col8(-/-) SMCs exhibited impairments in migration, and a strongly adhesive phenotype with prominent stress fibers, stable microtubules and pronounced central basal focal adhesions. The addition of exogenous type VIII collagen to the Col8(-/-) SMCs rescued the impairments in migration, and restored cytoskeletal architecture so that it was similar to Col8(+/+) cells. We measured elevated levels of active GTP-RhoA in the Col8(-/-) cells, and this too was reversed by treatment with exogenous type VIII collagen. We showed that type VIII collagen normally suppresses RhoA activation through a beta-1 integrin dependent mechanism. MMP-2 levels were reduced in the Col8(-/-) SMCs, and knockdown of MMP-2 in Col8(+/+) SMCs partially recapitulated the decreases in migration and 3D gel contraction seen in Col8(-/-) cells, showing that type VIII collagen-stimulated migration was dependent on MMP-2. Inhibition of Rho restored MMP-2 activity in the Col8(-/-) cells, and partially rescued migration, demonstrating that the elevations in RhoA activity were responsible for the suppression of migration of these cells. In conclusion, we have shown that type VIII collagen signals through beta-1 integrin receptors to suppress RhoA, allowing optimal configuration of the cytoskeleton, and the stimulation of MMP-2-dependent cell migration.

Cadherins at cell-autonomous membrane contacts control macropinocytosis.

Cadherins aggregate and stabilize cell-cell junctions through interactions with adjacent cells. In addition, N-cadherin and E-cadherin concentrate at free edges or at the lamellipodia of migrating cells and are found within large vesicles called macropinosomes, which develop from membrane ruffles. The binding properties of cadherins have not previously been associated with the localization of cadherins at membrane ruffles; however, we report that the dorsal, ventral and lateral membrane contacts that occur as a result of the overlap of membrane ruffles aggregate N-cadherin, and that both N-cadherin and E-cadherin promote macropinosome closure and fluid-phase uptake in macropinosomes. These data reveal a previously unsuspected function for cadherin-mediated cell-cell adhesion molecules in the closure of cell-autonomous membrane contacts at membrane ruffles, resulting in macropinocytosis.

Homotypic and endothelial cell adhesions via N-cadherin determine polarity and regulate migration of vascular smooth muscle cells.

Migration of smooth muscle cells from the arterial media to the intima is central to several vascular pathologies including restenosis. This study demonstrates that, like directional migration of other cells, smooth muscle migration is accompanied by a dramatic, polarized reorganization of the cell cytoskeleton that is accompanied by activation of the Rho GTPase Cdc42 and inactivation of glycogen synthase kinase-3beta. We also show, for the first time, that signals generated at the posterior-lateral aspects of wound edge cells by the cell-cell adhesion molecule N-cadherin are required for polarization and rapid migration of vascular smooth muscle. Importantly, when a cohort of migrating smooth muscle cells encounter CHO cells or the A10 smooth muscle cell line, neither of which expresses N-cadherin, polarity is only slightly suppressed. However, when smooth muscle cells encounter stably transfected, N-cadherin-expressing A10 cells or (N-cadherin-expressing) vascular endothelium, they rapidly lose their polarized phenotype. The latter finding indicates that endothelial signaling to innermost smooth muscle cells via N-cadherin may be critical to normal vessel wall stability. We infer that asymmetrical distribution of N-cadherin is necessary for the establishment of cell polarity during migration and that N-cadherin ligation is highly effective in abrogating polarized migration. Finally, we showed that endothelial cell polarity does not depend on N-cadherin; therefore, this molecule may be an attractive target for therapies to prevent restenosis without suppressing endothelial repair and risking late thrombosis.

Force-induced polarized mitosis of endothelial and smooth muscle cells in arterial remodeling.

Arteries display highly directional growth and remodeling that are specific to increases in the mechanical loads imposed on them by blood pressure, blood flow, and lengthwise tensile forces that are transmitted from the tissues to which they are attached. This study examined the effect of mechanical forces on the direction in which mitosis delivers daughter cells, as a mechanism for directional growth. Lateral forces were imposed on surface integrins of cultured endothelial cells by seeding the cells with arginine-glycine-aspartate peptide-coated magnetic microspheres and applying a magnetic field. Video images revealed that the mitotic axis of dividing cells became highly biased in the direction of applied force. Distribution of cortactin, which participates in polarized mitoses driven by other stimuli, was highly sensitive to mechanical loading and interfering with cortactin function arrested cell growth. Smooth muscle cell mitoses also proved to be sensitive to mechanical force: when lengthwise force imposed on rabbit carotid arteries was altered by excision of a vessel segment and reanastomosis of the cut ends, direction of mitosis was dramatically altered. These findings indicate that influences of mechanical force can modulate the manner in which mitosis of vascular cells contributes to reorganization of arterial wall tissue.

Localization of insulin-like growth factor-I in lung tissues of patients with fibroproliferative acute respiratory distress syndrome.

Insulin-like growth factor-I (IGF-I) is elevated in human fibrotic lung diseases and in animal models of pulmonary fibrosis, implicating IGF-I in the pathogenesis of fibrotic lung disease. We questioned whether IGF-I protein levels were enhanced in fibroproliferative acute respiratory distress syndrome (FP-ARDS). Serial lung tissue sections from a biopsy database were immunohistochemically stained for IGF-I, IGF-I receptor, CD68, alpha-smooth muscle actin, collagens I and III, and proliferating cell nuclear antigen. Our results show enhanced staining of IGF-I and IGF-I receptor, collagens I and III, smooth muscle actin, CD68, and proliferating cell nuclear antigen in FP-ARDS compared with control lung sections. In FP-ARDS specimens, prominent staining of IGF-I and IGF-I receptor was seen in alveolar and interstitial macrophages as well as in a variety of mesenchymal cells. There was a correlation between IGF-I staining and CD68-positive cells, suggesting macrophages as a potential source of the IGF-I protein present in lungs. IGF-I also correlated with enhanced collagen I, collagen III, and proliferating cell nuclear antigen immunoreactivity, suggesting that IGF-I may play a role in the extracellular matrix protein deposition and cellular proliferation seen in the lungs of individuals with FP-ARDS. Our results indicate that IGF-I is increased in FP-ARDS and may be an important mediator in the progression of acute lung injury to FP-ARDS.

N-cadherin upregulation and function in response of smooth muscle cells to arterial injury.

OBJECTIVE: Smooth muscle cell migration is critical to neointimal formation after arterial injury. The purpose of this study was to elucidate the regulation and functional significance of cell-cell adhesion via adherens junctions during this process. METHODS AND RESULTS: Using balloon catheter injury of rat carotid artery, we showed that neointimal formation is accompanied by dramatic but transient upregulation of intimal N-cadherin and associated catenins, proteins that mediate adhesion at adherens junctions. Upregulation was demonstrated by immunofluorescence microscopy and by immunoblotting, and it coincided with evidence of phenotypic modulation of smooth muscle cells. Similar upregulation was observed when postconfluent cultures of porcine aortic smooth muscle cells were subjected to linear denuding injuries. Furthermore, treatment of wounded cultures with a blocking antibody against the extracellular domain of the N-cadherin protein significantly suppressed the repair of wounds. CONCLUSIONS: N-cadherin and associated proteins are dynamically regulated during neointimal formation and provide evidence that this regulation is important for migratory repair. Therefore, N-cadherin may provide a novel target for therapies that are directed toward intimal proliferative disorders, including restenosis and vascular bypass graft failure.