Academic literature on the topic 'FFPE bone marrow'

Abstract Background Chemo-immunotherapy remains the backbone of therapy for patients with chronic lymphocytic leukaemia (CLL), with evidence pointing towards long term remission and even cure in patients with mutated IGHV status receiving this therapy frontline (1). However, relapse is common especially in those harbouring abnormalities in TP53 or ATM, unmutated IGHV status or a complex karyotype (2). It has become increasingly apparent that the bone marrow (BM) and lymph node (LN) play important roles in promoting the survival and proliferation of CLL cells. Signalling pathways triggered by interactions within these niches, such as the B cell receptor (BCR) pathway, and intracellular proteins such as Bcl-2 are vitally important in the biology of CLL. Novel therapeutic agents, such as ibrutinib, which target components of the BCR pathway, and the Bcl-2 inhibitor venetoclax, have demonstrated the potential of targeted therapies in CLL (3, 4). Novel therapeutic approaches must target the proliferative, drug-resistant compartments of disease within these microenvironments. The NanoString® nCounter platform enables mRNA profiling of archival samples, including formalin-fixed, paraffin-embedded tissue (FFPE). We have previously demonstrated the utility of this technology by comparing the mRNA expression profile of CLL cells derived from the peripheral blood (PB), archival BM and LN tissue as well as PB-derived CLL cells following in vitro co-culture with a human stromal cell line under either normoxic or hypoxic conditions. Here we present an update on our previous work with increased sample numbers in each of the tissues or culture conditions. Methods RNA was extracted from FFPE BM trephines (n = 5) and LN sections (n = 5), using the QIAGEN RNeasy FFPE Kit. All biopsies analysed were comprised of > 80 % lymphocytes, as determined by microscopic review. RNA from PBMC fractions (n = 5) was isolated either immediately or following co-culture with HS5 stromal cells for 24 h under normoxic (n = 5) or hypoxic (n = 5) conditions using the QIAGEN RNeasy Mini Kit. RNA from all preparations was quantified using a NanoDrop™ spectrophotometer. A total of 200ng of FFPE-derived RNA and 100ng of PBMC-derived RNA was analysed per sample on the NanoString® platform using a 260 gene panel. Three-fold changes in mRNA expression were considered significant. Results Of the 260 genes profiled, 89 were upregulated in the BM samples and 52 in the LN samples compared to expression in PB-derived CLL cells. Changes were seen in genes encoding for proteins involved in chemotaxis (CXCL9), the regulation of apoptosis (BCL2L1), surface receptors (FLT3) and genes associated with intracellular signalling, metabolism and cell division. 35 genes were downregulated in the LN samples and 31 in the BM samples. These changes were seen in genes coding for surface receptors (ROR1 and CXCR4), genes coding for intracellular signalling proteins (RAF1) and genes coding for transcription factors (JUN and FOS). Co-culture of PBMCs with HS5 cells induced similar changes to those observed in our comparison of the PBMCs and BM samples; genes coding for 61.5% and 50.0% of the mRNA expression changes observed in the LN were observed in PBMCs cultured under normoxic and hypoxic conditions respectively. A similar comparison of the BM samples identified concordant changes in expression of 46.5% and 39.2% of genes under normoxic and hypoxic conditions respectively. Importantly, changes observed in genes coding for the anti-apoptotic protein MCL1, the surface receptors CXCR4 and ROR1 and the transcription factors ATF, FOS and JUN were consistent across samples from LN, BM and the in vitro model. In summary, we have utilised the NanoString® nCounter platform to profile PB, BM and LN-derived CLL cells and have identified panels of genes that are either up or down-regulated in cells derived from these microenvironments. Furthermore, the high concordance between RNA changes in the in vitro model and the primary tissue suggest the HS5 co-culture system mimics aspects of the tumour microenvironment. These data provide a better understanding of how CLL cells populate and proliferate in the tumour microenvironment and may lead to novel therapeutic strategies. Disclosures No relevant conflicts of interest to declare.

Abstract BACKGROUND: Bone marrow fibrosis in myelofibrosis (MF) is the result of a complex and poorly understood interaction between megakaryocytes, fibroblasts, endothelial cells, cytokines and marrow stroma. Preclinical studies support a pathobiological role of TGF-β. It is overexpressed by megakaryocytes in MF and the TGF-β signature is upregulated and has been targeted in MF animal models. However TGF-β is a pleiotropic cytokine implicated in many cellular processes. CCN proteins are a group of 6 matricellular proteins important in fibrotic diseases and injury repair. CCN1 (CYR61) and CCN2 (CTGF) are transcriptionally activated by mitogenic growth factors such as PDGF, FGF2 and TGF-β. Recombinant CCN2 induces differentiation of human bone marrow mesenchymal stem cells into fibroblasts (Lee et al. JCI 2010). Levels of CCN2 in biologic fluids correlate with severity of fibrosis in scleroderma, liver cirrhosis and nephropathy. Given the proven role of CCN2 as a measurable serum biomarker in pro-fibrotic diseases and a downstream effector of TGF-β, in this retrospective study we examined CCN2 expression in myelofibrosis. We studied its correlation with clinical response following allogeneic stem cell transplant (ASCT), the only therapeutic modality to date which can consistently reverse fibrosis. METHODS: Patients diagnosed with MF at our institution from 1998 to 2015 were identified by diagnostic code (IRB#2013-0896). Bone marrow (BM) specimens at diagnosis and 1 year following ASCT were retrieved. Staging bone marrows from lymphoma patients, read as normal, were used as negative controls. CCN2 localization and expression was assessed by IHC (Abcam 5097). The slides were scored from 0-100% for megakaryocyte cytoplasmic staining by a blinded hematopathologist. RNA was extracted and reverse transcribed from frozen fixed paraffin embedded (FFPE) BM samples using the Qiagen RNeasy FFPE RNA Purification Kit. Assays for CCN1, CCN2 and CCN3 (NOV) and endogenous controls RPLPO and GAPDH were performed using Taqman quantitative PCR assays. mRNA data were analyzed using the software package DataAssist (v3.01; Life Technologies). RESULTS: CCN2 expression is upregulated in myelofibrosis compared to healthy bone marrow. mRNA analysis showed a 27 fold increase (p=0.19) in CCN2 mRNA expression in patients with MF when compared to healthy controls. IHC data also showed increased expression in megakaryocytes of MF patients compared to controls (63% vs 40%, p=0.28). Exploratory analysis showed a 36 fold increase in CCN2 mRNA expression in JAK2 negative (n=3) MF patients compared to JAK2 positive (n=7) patients (p=0.06), suggesting expression may depend on the molecular profile. CCN2 expression in the bone marrow of myelofibrosis patients is significantly downregulated at 1 year after allogeneic stem cell transplant. 13 pre-treatment cases of MF were compared with 6 post-transplant cases. The mean percentage of megakaryocyte with cytoplasmic expression of CCN2 by IHC in MF at diagnosis was 63%, compared to 22% in post-transplant specimens, (p= 0.01). mRNA extracted from the post-transplant marrows showed 0.01 fold expression of CCN2 compared to pre-transplant (p= 0.18). This decrease in CCN2 correlated with clinical and pathologic resolution of disease. The average DIPSS score pre-transplant was 2 (range 0-5) which improved to 0 for all patients post-transplant. The mean BM cellularity pre-transplant was 82% (range 50%-95%) and post-transplant was 48% (range 35%-65%). The average decrease in cellularity after transplant was 29%. Reticulin fibrosis ranged from grade 2-3 in the pre-transplant MF bone marrow samples which improved to grade 0-1 post-transplant. CONCLUSIONS: CCN2 is a downstream effector of TGF-β and a measurable biomarker of fibrosis in fibroproliferative diseases. We show that CCN2 expression in myelofibrosis decreases significantly after ASCT, suggesting its role as a biomarker of fibrosis in this disease. This paralleled clinical and pathologic resolution of disease. This will need to be validated in a larger number of paired patient samples where in addition to bone marrow expression, serum CCN2 levels will be measured by ELISA. Disclosures No relevant conflicts of interest to declare.

Abstract Background: Splenic diffuse red pulp lymphoma (SDRPL) is a rare small B cell neoplasm provisionally included in a category of unclassifiable splenic B-cell lymphoma/leukemias in the 2008 WHO classification. SDRPL is characterized by a diffuse pattern of involvement of the splenic red pulp by small monomorphous B lymphocytes. Patients are normally diagnosed at stage IV when spleen, bone marrow and peripheral blood are involved. This indolent but incurable disease is more common in aged males and it shows with splenomegaly and moderate lymphocytosis. The differential diagnosis with other splenic lymphomas such as marginal zone lymphoma, hairy cell lymphoma and its variant is not always easy, due to the similar clinical presentation and the absence of specific molecular markers. Here we studied the mutational status of 15 SDRPL patients using Whole Exome Next Generation Sequencing. Methods: Genomic DNA was extracted from FFPE/FF splenic tumor or bone marrow samples. When available, DNA from oral mucosa was obtained as the corresponding non-tumor control. Whole exome sequencing was performed at CNAG (Barcelona, Spain) following standard protocols for high-throughput paired-end sequencing on the Illumina HiSeq2000 instruments (Illumina Inc., San Diego, CA). Validation of variants was performed by PCR based targeted resequencing using a MiSeq instrument (Illumina Inc., San Diego, CA). We performed paired-end-76pb whole exome sequencing on DNA from 15 SDRPL patients. The corresponding normal counterpart from 3 of the patients was sequenced. From one patient FFPE and bone marrow DNA was available for comparison. In total 9 FFPE tissue samples, 3 FF tissue samples, and 4 bone marrow samples were sequenced. Almost 95% of the selected variants were validated by PCR based resequencing in 9 of the patients, while from 6 of the patients no tissue was available for validation. Results: 290 substitutions and 26 indels were obtained after filtering. Whole exome sequencing permitted us to identify variations in several genes of relevant pathways in lymphomas, such as NFkB pathway (IkBKB, TRAF, TANK, SYK), Apoptosis (BAD, DCPS, BCLAF1), MAPK (CXCR4, TCF3, NF1, MAP3K5), Cell cycle (CCND3, POLD3, BUB1), Chromatin (CREBBP, ARID1A, ARID1B, ARID3A, MLL3), MYC regulators (AKAP10, CTCF, EP400) or WNT signaling (SALL1, WNT5B, GPC6). Moreover, CCND3 and MLL3 were recurrently mutated in 2 different patients. Genes specifically found mutated in other splenic malignancies, such as NOTCH2, BRAF, MAP2K1, and KLF2 were not found mutated in this series of SDRPL patients. Conclusions: SDRPL samples contain somatic mutations involving genes regulating relevant pathways for cell survival, such as NFkB, apoptosis, cell cycle, chromatin, or WNT. The mutational signature of the series studied here may indicate that SDRPL is a distinct entity with specific molecular features different to other lymphoid splenic malignancies. Disclosures No relevant conflicts of interest to declare.

Abstract Eph receptors are the largest subgroup of the receptor tyrosine kinases (RTK). Unlike other RTK, these function principally during development. Quiescent in postembryonic tissues, Eph expression by adult tissues is abnormal and implicated in tumor initiation, invasion and metastasis. Aberrant EphA3 expression is seen in solid and hematologic tumors, particularly advanced stage lymphoproliferative and myeloproliferative diseases. In this regard, targeting EphA3 may constitute a novel treatment for hematological malignancy. With clinical utility in mind, i.e., patient selection for anti-EphA3 therapy, a panel of commercial and proprietary (KaloBios) antibodies was screened by Western Blot for reactivity to recombinant Eph receptors (EphA3, EphA4, EphA5, EphA7, EphB2, EphB3). Those with EphA3 binding selectivity were further screened (QualTek) by immunohistochemistry (IHC) using formalin-fixed paraffin-embedded (FFPE) normal and diseased human bone marrow (NLBM, AML) as well the LK63 pre-B-ALL cell line from which EphA3 was originally isolated. Different tissue pretreatments were used for antigen/epitope retrieval of EphA3, including steam-heating in citrate-based or Tris & chelator-based buffers, subsequent/or protease digestion, or neither. Following each antigen/epitope retrieval procedure, antibody reactivity for EphA3 was assessed by light microscopy using enzymatic biotin, tyramide and polymer-based detection techniques. In each instance, the location of the EphA3/antibody complex was visualized with 3,3-diaminobenzidine that precipitates a discrete insoluble reaction product in presence of enzyme (HRP). Nuclei were counterstained with hematoxylin to assess cell/tissue morphology. From this screen, one antibody (with an epitope in the cytoplasmic CT-domain of EphA3) was chosen for further assay optimization based on its selective reactivity towards LK63 and AML and low selective reactivity towards NLBM. Assay optimization included, amongst other aspects, evaluation of EphA3 expression in a panel of NLBM and hematopoietic tumors (200+ specimens inclusive of acute & chronic leukemia, peripheral T-cell & B-cell neoplasm, Hodgkin & non-Hodgkin lymphoma, multiple myeloma, myelodysplasic syndrome, myeloproliferative neoplasm) by a board-certified hematopathologist. In NLBM, the frequency of EphA3+ immature-blast cells (CD34+ or CD117+) was insignificant. Less than 10% CD34+/CD117+ cells were EphA3+. Elevated EphA3 expression (percentage EphA3+ nucleated cells) was observed in most hematopoietic tumors. For example, in multiple myeloma, tumor cells were typically EphA3+/CD138+ plasma cells. For AML, leukemic CD34+ or CD117+ blasts/initiating cells were typically EphA3+. Some CD138- plasma cells or leukemic CD34-/CD117- cells were also EphA3+. Correlation was made between EphA3 expression and specific tumor maturation stages, differentiation status and/or tumor aggressiveness. Tumors in blast crisis presented elevated EphA3 expression, e.g., CML in accelerated or blastic crisis but not chronic phase. Elevated EphA3 expression was noted in pre-B-ALL & pro-B-ALL (early pre-B-ALL) rather than mature B-cell ALL. EphA3 expression for some peripheral B-cell neoplasms correlated well with tumor grade: high grade, poorly differentiated (typically aggressive) B-cell lymphomas or follicular lymphomas were EphA3+. A similar relationship was noted for non-Hodgkin lymphoma (Hodgkin lymphoma was EphA3-). Preclinical screening also provided evidence for EphA3 expression by stroma/fibroblast (mostly lymphoma) and vasculature/endothelium, further rationale for development of reliable tools for profiling EphA3 in hematologic tumors and other malignancies. Using well-characterized normal and diseased FFPE bone marrow biopsies, this IHC assay for EphA3 has subsequently been validated (QualTek) to provide data that is not directly available from routine histopathology review and that supports use of the assay for profiling EphA3 in specific hematologic tumors and for patient selection in early Phase clinical trial/s of an anti-EphA3 monoclonal antibody (KB004, KaloBios). Beyond this, EphA3 targeted therapy with KB004 is anticipated for treatment of solid tumors. Recent genome-wide surveys identify EphA3 amongst the most frequently overexpressed genes in pancreatic, colon and lung carcinoma, melanoma and glioblastoma. Disclosures: Locke: QualTek Molecular Labs: Employment. Bernstein:QualTek Molecular Laboratories: Employment, Equity Ownership. Lynch:QualTek Molecular Laboratories: Employment, Equity Ownership. Siami-Namini:QualTek Molecular Laboratories: Consultancy. Walling:KaloBios: Consultancy; Corcept Therapeutics: Consultancy; Prothena: Consultancy; New Gen Therapeutics: Consultancy; Valent Technologies: Consultancy; LBC Pharmaceuticals: Consultancy; Amgen: Equity Ownership; BioMarin: Equity Ownership; Crown BioScience: Membership on an entity’s Board of Directors or advisory committees. Yonker:KaloBios: Employment, Equity Ownership. Yarranton:KaloBios: Employment, Equity Ownership; Glaxo: Equity Ownership; EnGen: Equity Ownership, Science Advisor, Science Advisor Other; StemLine Therapeutics: Equity Ownership.