Formalin-fixed Paraffin-embedded Lymph Node Research Articles

Exploratory Analyses of Lymph Node Tissue, Serum, and Peripheral Blood Mononuclear Cells Do Not Reveal Pathogen Signatures in Idiopathic Multicentric Castleman Disease

Background : Castleman disease (CD) encompasses a group of hematologic disorders that share characteristic histopathological features. Unicentric CD (UCD) involves a solitary enlarged lymph node with typically mild symptoms. Multicentric CD (MCD) involves generalized lymphadenopathy and often severe cytokine-driven multi-organ dysfunction. MCD is further subdivided into cases caused by Human Herpesvirus-8 (HHV-8-associated MCD) infection, POEMS syndrome (POEMS-associated MCD), and those with an idiopathic cause (iMCD). The underlying pathological mechanisms and etiologies of UCD and iMCD are not well understood. Given that a viral pathogen, HHV-8, causes HHV-8-associated MCD, we pursued multiple approaches to identify potential pathogens that may trigger iMCD and UCD. Methods: We used 2 distinct detection methods to identify potential pathogens in CD. PathoChIP is a microarray-based assay that uses ~60,000 DNA/RNA probes to detect 4,000+ pathogens associated with human diseases. Viral Track is a computational method that can be applied to unmapped next-generation sequencing (NGS) reads to search for the presence of viral RNA. Formalin-fixed paraffin-embedded (FFPE) lymph node tissue was analyzed by PathoChIP from iMCD (n=6), UCD (n=8), HHV8-associated MCD (n=1, HHV8-MCD), EBV-driven post-transplant lymphoproliferative disorder (n=1, EBV-PTLD), reactive samples without a clear etiology (n=1), and POEMS-associated MCD (n=2) patients. We also analyzed serum from iMCD patients (n=2) and healthy donors (n=8). A ‘positive’ probe for a given microorganism was defined as exceeding the 95 th percentile on a per-probe basis of the optical signal captured across all probes in the dataset. Data from single-cell RNA sequencing of cryopreserved peripheral blood mononuclear cells (iMCD, n=4; EBV, n=2; HHV8, n=1; healthy donor, n=2) and bulk RNA sequencing of FFPE lymph node tissue (iMCD, n=9; sentinel, n=7; systemic lupus erythematosus (SLE), n=3; Diffuse large B-cell lymphoma (DLBCL), n=3) were used as input into the Viral Track program. To detect a positive viral signal, standard thresholds were required: >50 uniquely mapped reads to a given virus, a read complexity threshold >1.2, and >10% coverage of the length of the respective viral genome. Results: After quality control, 49,657 probes from the PathoCHIP assay were mapped to 4,000+ known pathogens. As expected, the HHV-8 MCD and EBV-PTLD samples identified significantly more positive probes compared to the rest of the cohort for HHV-8 (65/259 vs 1/259) and EBV (38/235 vs 1/235), respectively. Importantly, no other microorganisms were detected in UCD or MCD lymph nodes or serum samples at a significantly increased rate than controls. For Viral Track, human endogenous retrovirus K113 and Escherichia phages were detected at low levels throughout all results. Excluding these viruses, positive controls including HHV-8-MCD, and EBV solely identified their respective predicted virally mapped NGS reads and no viral signature was detected in healthy donors. Importantly, there was no significant viral signature specific to CD in PBMCs or LN tissue. Interestingly, 1 iMCD sample did contain a significant number of NGS sequencing reads mapping to HHV5. These results were confirmed with clinical data reporting a positive IgG, negative PCR, and negative IgM test within 2 weeks of the biopsy date, suggesting that the HHV5 positive result was likely detecting a previous, now latent infection rather than a potential pathological driver of CD. Conclusions: Although there are limitations to this study, including small cohorts and viral mRNA single-cell capture limitations, we were able to use 2 orthogonal pathogen detection methods on multiple tissue types from iMCD patients. Taken together, our results suggest that an active infectious agent is unlikely to be a major contributor or pathological mechanism driving UCD or iMCD. The continued search for potential causative microorganisms in iMCD patients should continue, but our results suggest that alternative hypotheses related to the pathology and etiology of iMCD and UCD should be prioritized.

Establishment of a Novel Anti-Human CCR6 Monoclonal Antibody C6Mab-19 with the High Binding Affinity in Flow Cytometry.

CC chemokine receptor 6 (CCR6) is a member of the G-protein-coupled receptor family that is highly expressed in B lymphocytes, effector and memory T cells, regulatory T cells, and immature dendritic cells. CCR6 has been revealed to have important functions in many pathological conditions, such as cancer, intestinal bowel disease, psoriasis, and autoimmune diseases. The only CCR6 chemokine ligand, CC motif chemokine ligand 20 (CCL20), is also involved in pathogenesis by interacting with CCR6. The CCL20/CCR6 axis is drawing attention as an attractive therapeutic target for various diseases. In this study, we developed novel monoclonal antibodies (mAbs) against human CCR6 (hCCR6) using the peptide immunization method, which are applicable to flow cytometry and immunohistochemistry. The established anti-hCCR6 mAb, clone C6Mab-19 (mouse IgG1, kappa), reacted with hCCR6-overexpressed Chinese hamster ovary-K1 (CHO/hCCR6), human liver carcinoma (HepG2), and human differentiated hepatoma (HuH-7) cells in flow cytometry. The dissociation constant (KD) of C6Mab-19 was determined as 3.0 × 10-10 M for CHO/hCCR6, 6.9 × 10-10 M for HepG2, and 1.8 × 10-10 M for HuH-7. Thus, C6Mab-19 could bind to exogenously and endogenously expressed hCCR6 with extremely high affinity. Furthermore, C6Mab-19 could stain formalin-fixed paraffin-embedded lymph node tissues from a patient with non-Hodgkin lymphoma by immunohistochemistry. Therefore, C6Mab-19 is suitable for detecting hCCR6-expressing cells and tissues and could be useful for pathological analysis and diagnosis.

Expression of IDO1 and PD-L2 in Patients with Benign Lymphadenopathies and Association with Autoimmune Diseases.

The expression patterns of IDO1 and PD-L2 have not been thoroughly investigated in benign lymphadenopathies. The aim with this study was to elucidate how IDO1 and PD-L2 are expressed in benign lymphadenopathies in patients with autoimmune diseases (AD) compared to patients without AD. Formalin-fixed paraffin-embedded lymph nodes from 22 patients with AD and 57 patients without AD were immunohistochemically stained to detect IDO1 and PD-L2. The material was previously stained with EBER in situ hybridization to detect cells harboring the Epstein-Barr virus (EBV). IDO1 and PD-L2 were generally expressed by leukocytes to low degrees, while follicular IDO1+ cells were very rare. IDO1+ cells in single germinal centers were detected in five patients, and there was a high co-occurrence of follicular EBV+ cells in these cases (three of five patients). There were also significant correlations between interfollicular EBV+ cells and interfollicular IDO1+ cells (Spearman rho = 0.32, p = 0.004) and follicular IDO1+ cells (Spearman rho = 0.34, p = 0.004). High or low amounts of IDO1+ or PD-L2+ cells were not statistically significantly associated with patients with AD. However, the lymphadenopathy with the highest amount of interfollicular IDO1+ cells, which was also the only lymphadenopathy in which endothelial cells expressed IDO1, was in a patient with sarcoidosis. This study further supports that the EBV induces the expression of IDO1 and our findings should be recognized by future studies on IDO1 and PD-L2 in inflammatory and malignant conditions.

Predictive value of topoisomerase IIα immunoreactivity in canine diffuse large B-cell lymphoma (DLBCL) and peripheral T-cell lymphoma (PTCL) treated with a doxorubicin-based chemotherapy protocol

Topoisomerase IIα (TOPIIα) plays a key role in DNA replication and is a molecular target for TOPIIα inhibitor chemotherapy. A doxorubicin-based chemotherapy remains the most effective treatment for canine lymphoma, but there are no clear indications for its use in individual patients. The aim of this study was to assess the predictive value of TOPIIα expression in the treatment of canine lymphomas with TOPIIα inhibitors. Samples of formalin-fixed paraffin-embedded lymph nodes from 14 dogs with diffuse large B-cell lymphoma (DLBCL) and 5 dogs with peripheral T-cell lymphoma (PTCL) treated with a CHOP protocol were immunohistochemically labelled with anti-TOPIIα. Progression-free survival time (PFS) and overall survival time (OS) were estimated and compared with TOPIIα expression. Dogs with DLBCL had a higher level of TOPIIα expression compared to dogs with PTCL. The median PFS for dogs with DLBCL was significantly longer (260 days) than it was for dogs with PTCL (60 days). In DLBCL dogs with a high TOPIIα expression level, the median PFS was significantly longer (310 days) then it was in dogs with week or medium TOPIIα expression (51 days). The results of the study indicate that the immunohistochemical assessment of TOPIIα expression may be a valuable predictive indicator for anthracycline-based treatment of dogs with malignant lymphoma.

Differential Phosphoproteomics Deciphers Physiopathology of High-Risk Mantle Cell Lymphoma

Background: Mantle cell lymphoma (MCL) is a rare adult-onset non-Hodgkin lymphoma of which genetic hallmark is CCND1 translocation with IG genes, although CCND2, CCND3 or CCNE translocations are alternatives. The median survival of patients with MCL has lately increased due to improved therapies. However, the identification of high-risk MCLs characterized by pleomorphic or blastoid appearance, high proliferation index and TP53 deletions/mutations, remains mandatory due to their highly aggressive features and dismal clinical course even with intensified regimens. Therefore, specific therapeutic approaches are still warranted for such patients, but clinical and biological data are scarce since high-risk MCLs represent only 10-20% of all MCLs. A valuable source of rare samples for clinical/translational research is archived collections of formalin-fixed paraffin-embedded (FFPE) tissue blocks which enable retrospective studies to be performed. However, FFPE samples remain challenging for omics studies, especially phosphoproteomics. Here we implemented an original process to overcome this technical roadblock and took full advantage of FFPE samples to investigate biological processes differentially involved in high-risk and classical MCL (cMCL) to highlight rationale for innovative targeted therapies for these aggressive forms. Material and methods: We employed an unbiased differential label-free phosphoproteomic approach using archived FFPE MCL samples. Briefly, archived FFPE lymph nodes conclusive for cMCL or blastoid MCL (bMCL) diagnoses were retrieved from the Biological Resource Center of Strasbourg University Hospital from 1996 to 2016. H&E slides were reevaluated, and areas enriched in tumoral cells were selected to be punched from FFPE blocks. Our original sample preparation procedure entailed 1/ xylene-based deparaffinization, 2/ protein extraction with high content SDS-based lysis buffer, 3/ sample reduction/alkylation followed by cleanup and protein digestion on carboxylate paramagnetic beads and Lys-C/trypsin proteolytic enzyme mix, 4/ phosphopeptide enrichment on the AssayMap Bravo platform (Agilent) using IMAC Fe(III)-NTA cartridges. All samples were then analyzed on a NanoElute coupled to a TimsTOF Pro mass spectrometer (Bruker). Label-free quantification was performed using MaxQuant with the human database downloaded from SwissProt in April 2022. Further bioinformatics analyses were conducted in Perseus and Prostar. Data were functionally annotated with Reactome Pathway Database and STRING for association networks. Results: For this monocentric study we retrieved 30 FFPE blocks of lymph node biopsies conclusive for MCL diagnosis, including 15 bMCL and 15 cMCL. Although FFPE samples represented a challenge to work with for phosphoproteomics, we extracted enough protein from three 2mm-punches to proceed to the phosphopeptide enrichment according to our original sample preparation procedure. Overall, we successfully identified and quantified 7,220 class I phosphosites, i.e., sites of phosphorylation for which the probability of the phosphate group localization is greater than 0.75. No significant difference was found considering neither the archived period length of FFPE blocks nor the MCL subtypes (bMCL or cMCL). Differential analysis of bMCL and cMCL identified 180 differentially phosphorylated phosphosites (p-value < 0.05) corresponding to 103 proteins. Among these phosphosites, 139 were more phosphorylated in bMCL. Functional annotation of their corresponding proteins highlighted an over-representation of proteins involved in cell cycle, DNA repair and RNA metabolism within bMCL differential phosphoproteome (Fig.1). In addition, the kinase enrichment analysis of these differentially phosphorylated proteins predicted an increased activity of cyclin-dependent kinases in bMCL compared to cMCL. Conclusion: Here we performed for the first time phosphoproteomics from archived FFPE MCL samples. Differential analysis revealed that high-risk MCLs are characterized by an increased phosphorylation of proteins involved in cell cycle and an increased activity of cyclin-dependent kinases. Further studies are mandatory to fully understand to which extent cyclin-dependent kinases could be suitable targeted therapeutic candidates for patients with high-risk MCL. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Kikuchi-Fujimoto disease is mediated by an aberrant type I interferon response

Kikuchi-Fujimoto disease (KFD) is a reactive lymphadenitis of unclear etiology. To understand the pathogenesis of KFD, we performed targeted RNA sequencing of a well-characterized cohort of 15 KFD specimens with 9 non-KFD lymphadenitis controls. Two thousand and three autoimmunity-related genes were evaluated from archived formalin-fixed paraffin-embedded lymph node tissue and analyzed by a bioinformatics approach. Differential expression analysis of KFD cases compared to controls revealed 44 significantly upregulated genes in KFD. Sixty-eight percent of these genes were associated with the type I interferon (IFN) response pathway. Key component of the pathway including nucleic acid sensors, IFN regulatory factors, IFN-induced antiviral proteins, IFN transcription factors, IFN-stimulated genes, and IFN-induced cytokines were significantly upregulated. Unbiased gene expression pathway analysis revealed enrichment of IFN signaling and antiviral pathways in KFD. Protein–protein interaction analysis and a molecular complex detection algorithm identified a densely interacting 15-gene module of type I IFN pathway genes. Apoptosis regulator IFI6 was identified as a key seed gene. Transcription factor target analysis identified enrichment of IFN-response elements and IFN-response factors. T-cell-associated genes were upregulated while myeloid and B-cell-associated genes were downregulated in KFD. CD123+ plasmacytoid dendritic cells (PDCs) and activated T cells were noted in KFD. In conclusion, KFD is mediated by an aberrant type I interferon response that is likely driven by PDCs and T cells.

Molecular Diagnosis of Cat Scratch Disease: a 25-Year Retrospective Comparative Analysis of Various Clinical Specimens and Different PCR Assays.

ABSTRACTCat-scratch disease (CSD), caused primarily by Bartonella henselae, is a common etiology of infectious regional lymphadenopathy. Lymphadenopathy is preceded by a primary inoculation lesion and may progress to suppuration. Laboratory diagnosis of CSD is hampered by the limitations of available confirmatory tests. PCR, in general, is highly sensitive and specific; however, clinical sensitivity in CSD varies greatly between studies. We aimed to identify clinical specimens and PCR assays best suited for CSD diagnosis using a national CSD registry and a uniform case definition. Different clinical specimens and PCR assays, including conventional and real-time PCR, were evaluated. PCR was positive in 335/390 (86%) CSD patients and 425/482 (88%) PCR tests. The highest PCR sensitivity was achieved in lymph node pus aspirates (96%; n = 278 tests) followed by primary lesions (88%; n = 50), lymph node fine needle aspirations (85%; n = 46), lymph node biopsy specimens (73%; n = 91) and paraffin-embedded lymph nodes (59%; n = 17), (P < 0.001). Sensitivity was similar in all types of PCR assays studied. PCR negative predictive value of pus aspirate and lymph node biopsy specimen patient groups was 82% and 72%, respectively. Specificity was 100% based on 125 non-CSD patients with negative PCR. In conclusion, the specimen type rather than the PCR assay type has a major impact on CSD molecular diagnosis. We assume that the inadequate sensitivity of the biopsy specimens was due to sampling errors or the presence of inhibitory factors. Primary lesions should be sampled more frequently for CSD diagnosis. Physicians should be aware of the low PCR negative predictive value of lymph node biopsy specimens.IMPORTANCE Polymerase chain reaction (PCR) for the detection of Bartonella henselae is an important tool for the diagnosis of cat scratch disease (CSD); however, clinical sensitivity varies greatly between studies. The current study shows that the specimen type, with pus aspiration, fine needle aspiration, and primary inoculation lesion having significantly higher sensitivity than fresh or formalin-fixed paraffin-embedded lymph node biopsy specimen, rather than the type of the PCR assay, whether a conventional or a real-time assay, has a major impact on the performance of diagnostic PCR for CSD. The new data provide new tools for the clinical microbiologist when interpreting the results of the PCR assays. Primary inoculation lesions, although easily accessible, are often neglected and should be sampled more frequently for molecular diagnosis of CSD. Physicians should be aware that negative PCR, particularly if performed on fresh or paraffin-embedded lymph node biopsy specimens, does not exclude CSD.

Prognostic significance of CD163- and CD68-expressing macrophages in nodular sclerosis Hodgkin lymphoma

The objective of the study was to determine the clinical and morphological criteria and prognostic significance of CD163- and CD68-expressing macrophages in formalin-fixed paraffin-embedded (FFPE) lymph node samples of nodular sclerosis Hodgkin lymphoma.Materials and methods. We have studied clinical and laboratory characteristics and treatment results of 52 patients with newly diagnosed nodular sclerosis Hodgkin lymphoma. The treatment efficacy was assessed after 2–4 courses of chemotherapy by positron emission tomography combined with computed tomography scan (PET-CT) according to the Deauville scale.Results. In FFPE lymph node samples, differences in the localization and relative number of CD163-positive macrophages in patients of both study groups were determined. Morphometric counting of CD68-positive cells did not reveal statistically significant intergroup differences. The threshold of CD163-positive cells has been established. The relationship between the CD68 expression level and the response to frontline therapy was not revealed. The ratio of tumorassociated macrophages in each patient was assessed by the CD163/CD68 index. The threshold of the index was determined, which allows predicting the course of nodular sclerosis Hodgkin lymphoma.Conclusion. The following parameters could be used as additional morphological criteria for predicting the response to frontline therapy in patients with nodular sclerosis Hodgkin lymphoma: tissue distribution pattern and quantitative calculation of macrophage-histiocytic microenvironment subpopulation composition. The results could be used to risk group stratification of patients with nodular sclerosis Hodgkin lymphoma in order to predict the response to initial phase of therapy, as well as to determine personalized treatment approaches.

Evaluation of the Proliferative Activity of Diffuse Large B-Cell Lymphoma (DLBCL) in Dogs with Respect to Patient Eligibility for Anthracycline-Based Chemotherapy.

Simple SummaryCanine lymphomas usually have aggressive behavior, but respond well to chemotherapy. Despite proper diagnosis and numerous available therapeutic regimens, it is difficult to determine the prognosis and choose the optimal method of treatment in each individual patient. Diffuse large B-cell lymphoma is the most commonly diagnosed histological subtype of canine lymphoma and is treated with anthracyclines alone or in combination with other chemotherapeutics. A new diagnostic marker of prognostic and predictive value is topoisomerase IIα, which also constitutes a molecular target for anti-cancer drugs belonging to the group of topoisomerase IIα inhibitors including anthracyclines. Proliferative activity was estimated in samples of enlarged lymph nodes in dogs with diffuse large B-cell lymphoma based on mitotic count and immunohistochemical evaluation of topoisomerase IIα and Ki67 antigen expression with a view to qualifying patients for anthracycline-base chemotherapy. It has been shown that higher levels of topoisomerase IIα expression corresponded to a higher mitotic count but not to Ki67 index. These results indicate that an immunohistochemical evaluation of topoisomerase IIα expression can be used to develop a diagnostic-clinical protocol for the treatment of dogs with diffuse large B-cell lymphoma using anthracycline-based chemotherapy.Different types of canine lymphoma respond differently to chemotherapy and have different prognoses. Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoma in dogs. Topoisomerase II alpha (TOPIIα) protein has been shown to be a proliferation marker associated with prognostic significance. The aim of the study was to determine the relationship between TOPIIα expression, mitotic count (MC), and Ki67 antigen index in DLBCL in dogs, taking into account the applicability of these parameters to select the chemotherapy protocol with emphasis on the use of anthracycline drugs. Samples of formalin-fixed paraffin-embedded lymph nodes from 34 dogs with DLBCL were immunohistochemically labelled with anti-TOPIIα and Ki67. The number of positive cells and the intensity of the reaction were taken into account in order to assess TOPIIα expression. MC was estimated in the hematoxylin and eosin-stained slides in the area of 2.37 mm2. Positive association between TOPIIα and MC, but no association between TOPIIα and Ki67 was found. It can be concluded that the immunohistochemical determination of TOPIIα as a molecular target for drugs from the anthracycline group may be used in association with MC to establish a diagnostic-clinical protocol for selecting dogs with DLBCL for treatment with anthracycline drugs.

Study of DNA topoisomerase IIa expression in canine lymphomas and its potential role as a marker of sensitivity to anthracycline-based chemotherapy in dogs.

Canine lymphoma remains one of the most chemotherapy-responsive neoplasia in dogs. Many factors affect the prognosis in dogs treated for lymphoma, but indications for a specific treatment regimen in individual animals with lymphoma are poorly defined. Topoisomerase IIα (TOPIIα) is a key enzyme in DNA replication and a molecular target for TOPIIα inhibitors, including anthracyclines. The aim of this study was to determine the expression of TOPIIα in canine malignant lymphomas. The relationship between TOPIIα expression in canine lymphomas and potential sensitivity of neoplastic cells to anthracycline-based chemotherapy is discussed. Samples of formalin-fixed paraffin-embedded lymph nodes from 47 dogs with different subtypes of non-Hodgkin's (34 B-cell and 13 T-cell) lymphoma were immunohistochemically labeled with anti-TOPIIα. The number of positive cells and the intensity of the reaction were taken into account in order to assess TOPIIα expression. TOPIIα expression was evident in all cases, although differences in the number of positive cells and intensity of the reaction were demonstrated between B-cell and T-cell lymphoma groups as well as within individual groups. Based on the established scoring system, in the B-cell lymphoma group statistically higher expression of TOPIIα was found compared to the T-cell lymphoma group (P = 0.006). In B-cell lymphoma group moderate (41.18%) and strong (32.35%) TOPIIα expression predominated, whereas among T-cell lymphoma group the majority were cases with a weak (46.15%) TOPIIα expression. These preliminary results indicate that further studies are needed to determine the prognostic value of TOPIIα expression with regard to the sensitivity of canine B-cell lymphomas to anthracycline-based chemotherapy regimen. Nevertheless, this study indicates the possibility of choosing the appropriate treatment of canine lymphoma based on TOPIIa expression.

Endogenous reference RNAs for microRNA quantitation in formalin-fixed, paraffin-embedded lymph node tissue

Lymph node metastasis is one of the most important factors for tumor dissemination. Quantifying microRNA (miRNA) expression using real-time PCR in formalin-fixed, paraffin-embedded (FFPE) lymph node can provide valuable information regarding the biological research for cancer metastasis. However, a universal endogenous reference gene has not been identified in FFPE lymph node. This study aimed to identify suitable endogenous reference genes for miRNA expression analysis in FFPE lymph node. FFPE lymph nodes were obtained from 41 metastatic cancer and from 16 non-cancerous tissues. We selected 10 miRNAs as endogenous reference gene candidates using the global mean method. The stability of candidate genes was assessed by the following four statistical tools: BestKeeper, geNorm, NormFinder, and the comparative ΔCt method. miR-103a was the most stable gene among candidate genes. However, the use of a single miR-103a was not recommended because its stability value exceeded the reference value. Thus, we combined stable genes and investigated the stability and the effect of gene normalization. The combination of miR-24, miR-103a, and let-7a was identified as one of the most stable sets of endogenous reference genes for normalization in FFPE lymph node. This study may provide a basis for miRNA expression analysis in FFPE lymph node tissue.

New Molecular Assay for the Proliferation Signature in Mantle Cell Lymphoma Applicable to Formalin-Fixed Paraffin-Embedded Biopsies.

Purpose Mantle cell lymphoma is an aggressive B-cell neoplasm that displays heterogeneous outcomes after treatment. In 2003, the Lymphoma/Leukemia Molecular Profiling Project described a powerful biomarker-the proliferation signature-using gene expression in fresh frozen material. Herein, we describe the training and validation of a new assay that measures the proliferation signature in RNA derived from routinely available formalin-fixed paraffin-embedded (FFPE) biopsies. Methods Forty-seven FFPE biopsies were used to train an assay on the NanoString platform, using microarray gene expression data of matched fresh frozen biopsies as a gold standard. The locked assay was applied to pretreatment FFPE lymph node biopsies from an independent cohort of 110 patients uniformly treated with rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone. Seventeen biopsies were tested across three laboratories to assess assay reproducibility. Results The MCL35 assay, which contained a 17-gene proliferation signature, yielded gene expression of sufficient quality to assign an assay score and risk group in 108 (98%) of 110 archival FFPE biopsies. The MCL35 assay assigned patients to high-risk (26%), standard-risk (29%), and low-risk (45%) groups, with different lengths of overall survival (OS): a median of 1.1, 2.6, and 8.6 years, respectively (log-rank for trend, P < .001). In multivariable analysis, these risk groups and the Mantle Cell Lymphoma International Prognostic Index were independently associated with OS ( P < .001 for both variables). Concordance of risk assignment across the three independent laboratories was 100%. Conclusion The newly developed and validated MCL35 assay for FFPE biopsies uses the proliferation signature to define groups of patients with significantly different OS independent of the Mantle Cell Lymphoma International Prognostic Index. Importantly, the analytic and clinical validity of this assay defines it as a reliable biomarker to support risk-adapted clinical trials.

Abstract A81: Immune-cancer interactions in tumors and tumor-draining lymph nodes: Novel prognostic indicators for breast cancer

Abstract It is becoming clear that immune cells play many important but sometimes conflicting roles in cancer., and iImmune profile changes at sites of immune–cancer interactions, such as the tumor microenvironment and tumor-draining lymph nodes (TDLNs), may represent a sensitive predictor of local and distant tumor metastasis. However, standard pathologic analysis of tumor sections has remained at the visual assessment of one marker per serial section level; it would be extremely useful to be able to visualize the distributions of multiple phenotyped immune and other cells in-situ in solid tumors to dissect the complex interplay between immune/stromal cells and cancer cells within tumors, tumor-draining lymph nodes (TDLNs), and blood. We generate immune profiles that include complete immunophenotyping and identification of cellular spatial relationships within and between the tumor microenvironment and TDLNs from formalin-fixed paraffin-embedded lymph node and tumor specimens from cancer patients using a combination of multiplexed IHC/IF, multispectral imaging, and automated image analysis which delivers quantitative per-cell measures of each marker. These per-cell intensities are then translated into a phenotype for each cell. We have found that immune cell populations as well as their spatial distributions and clustering patterns have strong correlation with clinical outcome. Citation Format: James Mansfield, Peter Lee. Immune-cancer interactions in tumors and tumor-draining lymph nodes: Novel prognostic indicators for breast cancer. [abstract]. In: Proceedings of the AACR Special Conference: Tumor Immunology and Immunotherapy: A New Chapter; December 1-4, 2014; Orlando, FL. Philadelphia (PA): AACR; Cancer Immunol Res 2015;3(10 Suppl):Abstract nr A81.

Accuracy of microRNAs as markers for the detection of neck lymph node metastases in patients with head and neck squamous cell carcinoma.

BackgroundThe presence of metastatic disease in cervical lymph nodes of head and neck squamous cell carcinoma (HNSCC) patients is a very important determinant in therapy choice and prognosis, with great impact in overall survival. Frequently, routine lymph node staging cannot detect occult metastases and the post-surgical histologic evaluation of resected lymph nodes is not sensitive in detecting small metastatic deposits. Molecular markers based on tissue-specific microRNA expression are alternative accurate diagnostic markers. Herein, we evaluated the feasibility of using the expression of microRNAs to detect metastatic cells in formalin-fixed paraffin-embedded (FFPE) lymph nodes and in fine-needle aspiration (FNA) biopsies of HNSCC patients.MethodsAn initial screening compared the expression of 667 microRNAs in a discovery set comprised by metastatic and non-metastatic lymph nodes from HNSCC patients. The most differentially expressed microRNAs were validated by qRT-PCR in two independent cohorts: i) 48 FFPE lymph node samples, and ii) 113 FNA lymph node biopsies. The accuracy of the markers in identifying metastatic samples was assessed through the analysis of sensitivity, specificity, accuracy, negative predictive value, positive predictive value, and area under the curve values.ResultsSeven microRNAs highly expressed in metastatic lymph nodes from the discovery set were validated in FFPE lymph node samples. MiR-203 and miR-205 identified all metastatic samples, regardless of the size of the metastatic deposit. Additionally, these markers also showed high accuracy when FNA samples were examined.ConclusionsThe high accuracy of miR-203 and miR-205 warrant these microRNAs as diagnostic markers of neck metastases in HNSCC. These can be evaluated in entire lymph nodes and in FNA biopsies collected at different time-points such as pre-treatment samples, intraoperative sentinel node biopsy, and during patient follow-up. These markers can be useful in a clinical setting in the management of HNSCC patients from initial disease staging and therapy planning to patient surveillance.Electronic supplementary materialThe online version of this article (doi:10.1186/s12916-015-0350-3) contains supplementary material, which is available to authorized users.

Prognostic Significance Of a 4-Microrna Signature Targeting JAK2 In Classical Hodgkin Lymphoma

IntroductionThe behavior of classical Hodgkin lymphoma (cHL) is determined by both the intrinsic features of the Hodgkin/Reed Sternberg (HRS) cells and the characteristics of the microenvironment, making the analysis of entire lymph nodes an effective approach to understanding the disease. One of the genetic lesions most frequently found in HRS cells involves members of the JAK/STAT signaling pathway. However, few studies have identified microRNAs (miRNAs) that target JAK2 in cHL. In a previous study, our group identified miR-135a as a JAK2 regulator and showed the prognostic impact of this miRNA in a small set (n=89) of cHL patients (Navarro A. et al. Blood 2009). In the present study, we have examined novel miRNAs targeting JAK2 and evaluated the prognostic impact of their expression levels in 170 lymph nodes of cHL patients. MethodsTargetScan and miRbase were used to identify JAK2-related miRNAs. The conserved miRNAs with higher scores were selected and further validated by Renilla-Luciferase assay and Western Blot. We performed a Renilla-Luciferase assay with a modified expression vector psiChecK-2 containing the complete 3'UTR region of JAK2 cloned in the 3'UTR region of Renilla luciferase gene. For Renilla-Luciferase assay, 100nM of the pre-miRNAs of interest or pre-miR negative control were transfected in the HDMYZ cHL cell line together with 1μM of modified psicheck2 vector using Lipofectamine 2000, and luminescence was read at 24 hours. Further validation of the miRNA target was performed by Western Blot in three cHL cell lines (L428, L-1236 and HDMYZ). The expression levels of the miRNAs identified as targeting JAK2 were then assessed in lymph nodes from 170 cHL patients (median age, 33 years; male, 51%; EBV, 43.8%; HIV, 12%) diagnosed and treated in a single institution. Moreover, 15 reactive lymph nodes (RLN) were used as normal controls. RNA was purified from formalin-fixed paraffin-embedded lymph nodes using RecoverAll Total Nucleic Acid Isolation kit. The miRNA expression was analyzed using TaqMan microRNA assays. Statistical analyses were performed using R v2.13 and PASW Statistics 18. ResultsThe bioinformatic analysis identified seven microRNAs as possible regulators of JAK2 (miR-34a, miR-101, miR-135a, miR-204, miR-216a, miR-216b and miR-375). The Renilla-Luciferase assay confirmed that in addition to miR-135a, miR-101 (61%; p=0.01), miR-204 (46%; p=0.003) and miR-216a (64.8%; p=0.02) also targeted JAK2. These findings were confirmed by Western Blot analysis of JAK2 levels after transfection with pre-miRNAs (median % of protein reduction in the 3 cell lines of 21.1%, 46.7% and 24%, respectively). The analysis of these miRNAs in RLN showed that miR-101, miR-135a and miR-204 were significantly downregulated in lymph nodes of cHL patients (p<0.001, p<0.001 and p=0.02 respectively) in comparison with RLN used as control. In contrast, miR-216 did not show significant differences in comparison with RLN. Interestingly, the analysis of the expression levels of these 4 miRNA in the patient lymph nodes had an impact on prognosis. First, low expression levels of miR-135a was associated with lower rate of complete response to first line treatment (76% vs 89%, p=0.012) and a trend was observed for miR-216(p=0.077). Secondly, patients with low expression levels of miR-101 or miR-204 had shorter disease-free survival (DFS) (151 vs 109 months, p=0.020; and 149.2 vs 105.5 months, p=0.055). Finally, patients with low levels of miR-135a, miR-204 or miR-216 had shorter overall survival (OS) (158 vs 136 months; p=0.039; and 157.5 vs 110 months, p=0.025; and 165 vs 140 moths, p=0.011 respectively). Since all four miRNAs showed prognostic impact (DFS, OS or treatment response), we decide to analyze the prognostic impact of the combination of the 4 miRNAs. Patients were then classified in two subgroups according to the expression levels of all four miRNAs. Patients with low expression of more than 2 miRNAs had shorter OS (163 vs 132 months; p=0.012). The multivariate analysis identified the combination of the four miRNAs as an independent prognostic marker of OS (OR, 7.6; 95% CI, 1.1-57.2; p=0.048) together with Age≥45years (OR, 5.9; 95% CI, 2.4-14.4; p<0.001) and B symptoms (OR, 2.6; 95% CI, 1.09-6.3; p=0.03). ConclusionsMiR-101, miR-135a, miR-204 and miR-216 regulate JAK2 and are independent prognostic factors in cHL. AcknowledgmentsSDCSD of School of Medicine of UB. AC is an APIF-UB fellow. Disclosures:No relevant conflicts of interest to declare.

Assessing DcR3 expression in relation to survivin and other prognostic factors in B cell non-Hodgkin’s lymphoma

The soluble decoy receptor 3 (DcR3) is a member of the tumor necrosis factor receptor superfamily whose overexpression has been observed in several human malignancies. Survivin is one of the inhibitors of apoptosis proteins that are thought to play an important role in the pathogenesis of malignancies. We aimed to evaluate the expression of DcR3 in relation to survivin in B cell non-Hodgkin`s lymphoma (NHL) and then we focused on patients with diffuse large B cell non-Hodgkin's lymphoma (DLBCL) (50 cases) and correlated DcR3 expression with survivin expression and other prognostic parameters. Fifteen subjects with reactive lymphoid hyperplasia were included as controls. The expression of DcR3 and survivin were analyzed by immunohistochemistry on formalin-fixed paraffin-embedded lymph node sections from 80 cases of B cell NHL and 15 controls. Bone marrow biopsy sections of patients were also immunostained with the previous markers. DcR3 expression was found in 32.5% of B cell NHL patients versus 6.7% of controls (p <0.001) and was associated with the aggressive/highly aggressive subtypes. DcR3 was strongly expressed in 30% of DLBCL patients, where it was associated with survivin expression, high international prognostic index (IPI), the presence of extra nodal disease, ECOG performance status >1, reduced remission rates and shorter event-free survival. The expression of survivin was 40% in B cell NHL patients versus 13.3% in the control group (p <0.001). The expression of survivin in aggressive/highly aggressive B cell NHL was significantly higher than that in indolent B cell NHL. Survivin expression has been detected in 44% of the DLBCL patients and was associated with their clinical stage and shorter event-free survival (p = 0.026). Bone marrow biopsy sections from DLBCL patients showed significant DcR3 and survivin over expressions in sections with infiltration by lymphoma cells than sections with no infiltration. DcR3 expression was associated with other prognostic factors including survivin, reduced remission rates, and shorter event-free survival. Survivin is closely related to aggressive/highly aggressive subtypes of B cell NHL and is associated with shorter event-free survival. Both DcR3 and survivin expressions on bone marrow sections can be of help in diagnosing bone marrow infiltration.

Imaging of Metastatic Lymph Nodes by X-ray Phase-Contrast Micro-Tomography

Invasive cancer causes a change in density in the affected tissue, which can be visualized by x-ray phase-contrast tomography. However, the diagnostic value of this method has so far not been investigated in detail. Therefore, the purpose of this study was, in a blinded manner, to investigate whether malignancy could be revealed by non-invasive x-ray phase-contrast tomography in lymph nodes from breast cancer patients. Seventeen formalin-fixed paraffin-embedded lymph nodes from 10 female patients (age range 37–83 years) diagnosed with invasive ductal carcinomas were analyzed by X-ray phase-contrast tomography. Ten lymph nodes had metastatic deposits and 7 were benign. The phase-contrast images were analyzed according to standards for conventional CT images looking for characteristics usually only visible by pathological examinations. Histopathology was used as reference. The result of this study was that the diagnostic sensitivity of the image analysis for detecting malignancy was 100% and the specificity was 87%. The positive predictive value was 91% for detecting malignancy and the negative predictive value was 100%. We conclude that x-ray phase-contrast imaging can accurately detect density variations to obtain information regarding lymph node involvement previously inaccessible with standard absorption x-ray imaging.

95P Comparison of Expression Levels of Twist, Snail and Slug in Primary Tumors and Lymph Node Metastases in Breast Cancer Patients

ABSTRACT Introduction The expression of prognostic markers including the regulators of epithelial to mesenchymal transition (EMT) can change during the course of the disease. Therefore, reassessment of these markers at the time of disease progression might help to optimize their prognostic value. In this context, characterization of metastatic tissue could be of relevance. The aim of this study was to evaluate and compare the expression of master regulators of EMT TWIST, SNAIL and SLUG in primary breast cancer tumors and their corresponding lymph node metastases. Materials and methods Fresh-frozen or formalin-fixed paraffin-embedded (FFPE) primary tumor samples and their corresponding FFPE lymph node metastases from 21, stage II-III breast cancer patients were examined. Expression of TWIST, SNAIL and SLUG was measured by RT-qPCR method using Ct approach. Based on the median gene expression level samples were classified as positive or negative for a particular marker. Results from primary tumor samples and metastases were compared. Expression levels of transcription factors (TFs) in lymph node metastases were correlated with patients' outcome. Results FFPE samples from lymph node metastases showed elevated levels of all TFs when compared to FFPE primary tumor samples. Ratios between the average expression levels were 7:1, 6:1 and 3:1 for TWIST, SNAIL and SLUG, respectively. Primary tumors paired with corresponding lymph node metastases were concordant in 52% for each gene. In lymph node metastases elevated expression of TWIST and SNAIL was associated with decreased overall survival (p = 0.045 and p = 0.022, respectively) and disease free survival (p = 0.02 and p = 0.01, respectively). Conclusions All TFs had elevated expression levels in lymph node metastases when compared to primary tumors, with TWIST being most significantly upregulated. These findings could be explicable by recent studies showing the critical role of TWIST in the development of metastases. TWIST and SNAIL expression in lymph node metastases was found to be marker of poor prognosis in accordance to the fact that EMT is thought to confer aggressive behavior of the tumor. Disclosure All authors have declared no conflicts of interest.

CD68+ Tumor-Associated Macrophages Predict Unfavorable Treatment Outcomes in Classic Hodgkin's Lymphoma in Correlation with Early FDG-PET Assessment Results

Abstract 1558 Background:The tumor microenvironment is an important factor in the development and progression of classic Hodgkin's Lymphoma (HL). A recent study (Steidl et al 2010) demonstrated that increased number of CD68+ tumor-associated macrophages was correlated with adverse survival in HL. Moreover the result of the early FDG-PET assessment after the first 2 courses of chemotherapy (early PET) is a major prognostic criterion in treatment of HL. The purpose of this study was to evaluate the relationship between CD68 expression and: 1) The clinical outcome in general practice for all patients treated for HL, 2) The results of initial and early PET. Patients and methods:Our retrospective study included 151 patients (pts) initially diagnosed and treated at our center from February 1995 to March 2011 and who had a formalin-fixed paraffin-embedded lymph node biopsy available. The slides were stained for CD68 by a single pathologist (MDC) using the PG-M1 antibody (Dako®) and analyzed by immunochemistry. CD68 staining was scored 1: CD68+ cells < 5%, 2: CD68+ cells from 5% to 25% and 3: CD68+ cells >25% relative to overall cellularity. FDG-PET is available in our center since 1999. A total of 100 pts (66%) had initial evaluation and follow up by FDG-PET. Clinical and laboratory data available on presentation and follow-up were recorded. Sex ratio was 1.16, median age was 39 years [18–85], histological subtypes in WHO classification were nodular sclerosis in 123 pts (81.46%), mixed cellularity in 21 (13.91%), lymphocyte-rich in 6 (3.97%), lymphocyte-depleted in 1 (0.66%). The Ann Arbor Stage was I-II in 78 pts (52%), and III-IV in 73 (48%). B symptoms were present in 68 pts (45%). Treatment protocols were as follows: ABVD in 100 pts (66.22%), MOPP/ABV in 26 (17.22%), BEACOPP in 8 (5.30%), ABVD-like in 8 (5.30%), other in 9 (6%). Additional radiotherapy was performed in 76 pts (50%). Mean follow-up was 75.6 months [1.87–194.5]. Results:The CD68 percentage was: group 1: <5% in 49 pts (32.45%); group 2: 5 to 25% in 67 (44.37%); group 3: >25% in 35 (23.17%). We found like Steidl a correlation between progression free survival (PFS) and initial tumor CD68 expression in accordance with the 3 groups. Group 1: Median PFS not reached, PFS at 5 years=79.8%, group 2: median PFS not reached, PFS at 5 years=69.4%, group 3: median PFS=52.5 month, PFS at 5 years=39.5 % (p<0.0068). Overall survival (OS) was not statistically different (p= 0.77) using these 3 groups, but it was the case when we mixed groups 1 and 2 (0 to 25% CD68+cells) compared to group 3 (>25%) for OS (p=0.0247) and for PFS (p=0.0026). Thus, these 2 groups with CD68 low (CD68≤25%) and CD68 high (CD68>25%) were used for the other statistical analysis. There was a correlation between B symptoms and CD68 expression (63% in the CD68 high group versus 40% in the CD68 low group) (p=0.016). We also found a correlation between the Ann Arbor stage and CD68 expression. Indeed, CD68 was high in 71% of pts in the stage III-IV versus 29% in the stage I-II (p=0.0016). FDG-TEP SUV-max and SUV-mean calculation is available since September 2007 (n=58). We did not find any correlation between CD68 and initial pre-therapeutic SUV-max or SUV-mean (Anova test). Furthermore, no correlation exists between CD68 and erythrocyte sedimentation rate (ESR). Since 2004, pts have an early PET. In the 62 pts assessed to date, the rate of FDG-PET positive was significantly higher after two treatments in pts CD 68 high (9 PET+/14=64%) compared to pts CD68 low (13PET+/48=27%) (p<0.012). Combining CD68 low and early negative PET (35 pts/62=56%) allowed us to define a very good prognosis group with a 100% OS and an 80% PFS with a median follow up of 31.12 months whatever the initial stage was. Conclusion:We found a strong correlation between initial Ann Arbor stages and CD68 expression. We also observe a correlation between CD68 expression and B symptoms at diagnosis. We confirm the experience of Steidl with adverse outcomes (PFS) when number of CD68 is increased. In our experience there are a worse PFS and OS when CD68 cells are >25% independently from initial clinical presentation. Our results show a strong correlation between CD68 expression and the results of early PET with an excellent PFS for the CD68 low/early PET negative group. The prognostic relevance of CD 68+ tumor-associated macrophages in HL should be validated prospectively to contribute in combination with FDG-PET to a better risk stratification of pts to adapted treatment in classical HL. Disclosures:No relevant conflicts of interest to declare.

Gene expression in formalin-fixed paraffin-embedded lymph nodes

Elucidation of molecular pathways involved in development of human lymphoma requires efficient methods for tackling gene expression in lymph nodes. Expression studies of transcription factors in these malignancies facilitate understanding the changes occurring in neoplastic transformation and lymphoma development. Excised lymph nodes are routinely fixed in formalin and embedded in paraffin for diagnosis and stored in many hospitals' pathology archives. These tissues represent a precious resource for research since they allow retrospective studies to cover a broad range of human lymphoma even the less frequent types. Reverse transcription polymerase chain reaction (RT-PCR) is a commonly used method for gene expression analysis and a reproducible protocol for RNA isolation from lymph nodes is an inevitable requirement for these studies. However, formalin fixation and paraffin-embedding interfere with the quality of RNA especially when isolated from lymph nodes being the most fragile lymphatic tissues. We present here a simple and fast method for RNA isolation from formalin-fixed paraffin-embedded lymph nodes that can be successfully applied for RT-PCR as well as for quantitative RT-PCR analysis. We tested diverse isolation reagents and combined a range of factors in order to get a high quality RNA for retrospective studies of gene expression in human lymphoma samples. Our modified method of RNA extraction from FFPE provides superior yields and purity based on qPCR data.