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Dcunha N, Sakhti D, Sigamani E, Chandramohan J, Korula A, George B, Manipadam MT, Pai R. Utility of reverse transcriptase - Multiplex ligation-dependant probe amplification ( RT-MLPA) in the molecular classification of Diffuse Large B cell lymphoma (DLBCL) by cell-of-origin (COO). INDIAN J PATHOL MICR 2023; 66:714-719. [PMID: 38084521 DOI: 10.4103/ijpm.ijpm_326_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Classifying diffuse large B cell lymphomas, not otherwise specified (DLBCL, NOS), is based on their cell-of-origin (COO) which is included in the WHO classification (2016), is essential to characterize them better in context of prognostication. While gene expression profiling (GEP) considered the gold standard and more recently, the Nanostring-based approach, classify these tumors accurately, many laboratories with limited resources and instrumentation need an alternate approach that is reliable, inexpensive, and with a reasonable turnaround. The Reverse Transcriptase Multiplex Ligation Dependant Probe Amplification (RT-MLPA) to subtype DLBCL, NOS cases, as designed by CALYM group appears to provide a good alternative but needs to be validated in other centres. Therefore, this study evaluated DLBCL, NOS and compared the results of RT-MLPA to that obtained by immunohistochemistry using the Hans algorithm. Materials and Methods Sixty-five DLBCL, NOS cases were included and the RT-MLPA was set up and standardized using probes that were designed by the CALYM study group. Briefly, RNA was extracted converted to cDNA and the 21-gene expression classifier that also included probes to detect MYD88 mutations and EBER mRNA was performed by MLPA. The results were analyzed by the open home grown software designed by the same group and compared to the results obtained by IHC. Results Forty-four of the sixty-five cases provided concordant results (k = 0.35) and if the MYD88 results were to be used as a classifier the concordance would have improved from 67.7% to 82%. The 21 discordant cases were divided into five categories to provide a possible explanation for the discordance. Further 26% and 31% of the samples tested were positive for MYD88 mutations and EBER mRNA, respectively. The test had a turnaround of three days. Conclusion The test provided moderate (67.7%) concordance when compared with IHC and perhaps would have provided higher concordance if compared with GEP. The test also has the advantage of providing information on the MYD88 and EBV infection status. It was found to be reliable, easy to perform and standardize, requiring only routine instruments available in most molecular laboratories. The RT-MLPA assay therefore provides an alternative for laboratories that would require subtyping of DLBCL, NOS cases in the absence of an access to GEP or other instrument intensive methods.
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Affiliation(s)
- Nicholas Dcunha
- Department of Pathology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Dhananjayan Sakhti
- Department of Pathology, Christian Medical College, Vellore, Tamil Nadu, India
| | | | - Jagan Chandramohan
- Department of Pathology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Anu Korula
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Biju George
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, India
| | | | - Rekha Pai
- Department of Pathology, Christian Medical College, Vellore, Tamil Nadu, India
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Sesboue C, Galtier J, Jeanneau M, Chauvel A, Laharanne E, Amintas S, Merlio JP, Bouabdallah K, Gros FX, de Leval L, Gros A, Parrens M. Combined Reverse-Transcriptase Multiplex Ligation-Dependent Probe Amplification and Next-Generation Sequencing Analyses to Assign Unclassified BCL2 -/BCL6 - Nonrearranged Small B-Cell Lymphoid Neoplasms as Follicular or Nodal Marginal Zone Lymphoma. Mod Pathol 2023; 36:100043. [PMID: 36853790 DOI: 10.1016/j.modpat.2022.100043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 09/30/2022] [Accepted: 10/12/2022] [Indexed: 01/11/2023]
Abstract
Distinguishing between follicular lymphoma (FL) and nodal marginal zone lymphoma (NMZL) can be difficult when morphologic and phenotypic features are unusual and characteristic cytogenetic rearrangements are absent. We evaluated the diagnostic contribution of ancillary techniques-including fluorescence in situ hybridization (FISH)-detected 1p36 deletion; reverse-transcriptase, multiplex, ligation-dependent probe amplification (RT-MLPA); and next-generation sequencing (NGS)-for tumors that remain unclassified according to standard criteria. After review, 50 CD5-negative small B-cell lymphoid neoplasms without BCL2 and BCL6 FISH rearrangements were diagnosed as FLs (n = 27), NMZLs (n = 5), or unclassified (n = 18) based on the 2016 World Health Organization Classification of Tumours of Haematopoietic and Lymphoid Tissues. FISH helped identify the 1p36 deletion in 3 FLs and 1 unclassified tumor. Most classified FLs had an RT-MLPA germinal center B-cell (GCB) signature (93%) or were noncontributive (7%). Classified NMZLs had an RT-MLPA activated B-cell signature (20%), had an unassigned signature (40%), or were noncontributive (40%). Among unclassified tumors, the RT-MLPA GCB signature was associated with mutations most commonly found in FLs (CREBBP, EZH2, STAT6, and/or TNFRSF14) (90%). An RT-MLPA-detected GCB signature and/or NGS-detected gene mutations were considered as FL identifiers for 13 tumors. An activated B-cell signature or NOTCH2 mutation supported NMZL diagnosis in 3 tumors. Combining the RT-MLPA and NGS findings successfully discriminated 89% of unclassified tumors in favor of one or the other diagnosis. NGS-detected mutations may be of therapeutic interest. Herein, we detected 3 EZH2 and 8 CREBBP mutations that might be eligible for targeted therapies.
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Affiliation(s)
- Come Sesboue
- Pathology Department, University Hospital of Bordeaux, Pessac, France.
| | - Jean Galtier
- Hematology and Cell Therapy Department, University Hospital of Bordeaux, Pessac, France
| | - Marie Jeanneau
- Pathology Department, University Hospital of Bordeaux, Pessac, France
| | - Annick Chauvel
- Pathology Department, University Hospital of Bordeaux, Pessac, France
| | - Elodie Laharanne
- Tumor Bank and Tumor Biology Laboratory, University Hospital of Bordeaux, Pessac, France; BRIC INSERM U1312, Trio 2, University of Bordeaux, Bordeaux, France
| | - Samuel Amintas
- Tumor Bank and Tumor Biology Laboratory, University Hospital of Bordeaux, Pessac, France; BRIC INSERM U1312, BioGo, University of Bordeaux, Bordeaux, France
| | - Jean-Philippe Merlio
- Tumor Bank and Tumor Biology Laboratory, University Hospital of Bordeaux, Pessac, France; BRIC INSERM U1312, Trio 2, University of Bordeaux, Bordeaux, France
| | - Krimo Bouabdallah
- Hematology and Cell Therapy Department, University Hospital of Bordeaux, Pessac, France
| | - François-Xavier Gros
- Hematology and Cell Therapy Department, University Hospital of Bordeaux, Pessac, France
| | | | - Audrey Gros
- Tumor Bank and Tumor Biology Laboratory, University Hospital of Bordeaux, Pessac, France; BRIC INSERM U1312, Trio 2, University of Bordeaux, Bordeaux, France
| | - Marie Parrens
- Pathology Department, University Hospital of Bordeaux, Pessac, France; BRIC INSERM U1312, Trio 2, University of Bordeaux, Bordeaux, France
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Taslimi Y, Masoudzadeh N, Bahrami F, Rafati S. Cutaneous leishmaniasis: multiomics approaches to unravel the role of immune cells checkpoints. Expert Rev Proteomics 2022; 19:213-225. [PMID: 36191333 DOI: 10.1080/14789450.2022.2131545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Cutaneous leishmaniasis (CL) is the most frequent form of leishmaniases, associated with skin inflammation and ulceration. Understanding the interaction of different phagocytic cells in the recognition and uptake of different Leishmania species is critical for controlling the infection. Phagocytic cells have a pivotal role as professional antigen-presenting cells that bridge the innate and adaptive immunity and shape the outcome of the disease. AREAS COVERED Here we reviewed new technologies with high-throughput data collection capabilities along with systems biology approaches which are recently being used to decode the paradox of CL immunology. EXPERT OPINION We emphasized on the crosstalk between DC and T-cells while focusing on the immune checkpoints interactions between the human immune system and the Leishmania species. Further, we discussed omics technologies including bulk RNA sequencing, reverse transcriptase-multiplex ligation dependent probe amplification (RT-MLPA), and proximity extension assay (PEA) in studies on human blood or tissue-driven samples from CL patients in which we have so far been involved.
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Affiliation(s)
- Yasaman Taslimi
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran Iran
| | - Nasrin Masoudzadeh
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran Iran
| | - Fariborz Bahrami
- Department of Immunology, Pasteur Institute of Iran, Tehran, Iran
| | - Sima Rafati
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran Iran
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Toledano MN, Desbordes P, Banjar A, Gardin I, Vera P, Ruminy P, Jardin F, Tilly H, Becker S. Combination of baseline FDG PET/CT total metabolic tumour volume and gene expression profile have a robust predictive value in patients with diffuse large B-cell lymphoma. Eur J Nucl Med Mol Imaging 2018; 45:680-688. [PMID: 29344718 DOI: 10.1007/s00259-017-3907-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 12/03/2017] [Indexed: 01/12/2023]
Abstract
PURPOSE This study evaluated the predictive significance of total metabolic tumour volume (TMTV) measured on baseline FDG PET/CT and its value in addition to gene expression profiling using a new method of gene analysis (rapid reverse transcriptase multiplex ligation-dependent probe amplification assay, RT-MLPA) in patients with diffuse large B-cell lymphoma treated with R-CHOP or R-CHOP-like chemotherapies. METHODS The analysis included 114 patients. TMTV was measured using a 41% SUVmax threshold and tumours were classified into GCB or ABC subtypes according to the RT-MLPA assay. RESULTS The median follow-up was 40 months. the 5-year progression-free survival (PFS) was 54% and the 5-year overall survival (OS) was 62%. The optimal TMTV cut-off value was 261 cm3. In 59 patients with a high TMTV the 5-year PFS and OS were 37% and 39%, respectively, in comparison with 72% and 83%, respectively, in 55 patients with a low TMTV (p = 0.0002 for PFS, p < 0.0001 for OS). ABC status was significantly associated with a worse prognosis. TMTV combined with molecular data identified three groups with very different outcomes: (1) patients with a low TMTV whatever their phenotype (n = 55), (2) patients with a high TMTV and GCB phenotype (n = 33), and (3) patients with a high TMTV and ABC phenotype (n = 26). In the three groups, 5-year PFS rates were 72%, 51% and 17% (p < 0.0001), and 5-year OS rates were 83%, 55% and 17% (p < 0.0001), respectively. In multivariate analysis, TMTV, ABC/GCB phenotype and International Prognostic Index were independent predictive factors for both PFS and OS (p < 0.05 for both). CONCLUSIONS This integrated risk model could lead to more accurate selection of patients that would allow better individualization of therapy.
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Affiliation(s)
- Mathieu Nessim Toledano
- Nuclear Medicine Department, Henri Becquerel Cancer Centre and Rouen University Hospital, Rouen, France. .,QuantIF-LITIS (EA 4108-FR CNRS 3638), Faculty of Medicine, University of Rouen, Rouen, France.
| | - P Desbordes
- QuantIF-LITIS (EA 4108-FR CNRS 3638), Faculty of Medicine, University of Rouen, Rouen, France
| | - A Banjar
- Nuclear Medicine Department, Henri Becquerel Cancer Centre and Rouen University Hospital, Rouen, France.,QuantIF-LITIS (EA 4108-FR CNRS 3638), Faculty of Medicine, University of Rouen, Rouen, France
| | - I Gardin
- Nuclear Medicine Department, Henri Becquerel Cancer Centre and Rouen University Hospital, Rouen, France.,QuantIF-LITIS (EA 4108-FR CNRS 3638), Faculty of Medicine, University of Rouen, Rouen, France
| | - P Vera
- Nuclear Medicine Department, Henri Becquerel Cancer Centre and Rouen University Hospital, Rouen, France.,QuantIF-LITIS (EA 4108-FR CNRS 3638), Faculty of Medicine, University of Rouen, Rouen, France
| | - P Ruminy
- INSERM U918, Centre Henri Becquerel, Rouen, France
| | - F Jardin
- INSERM U918, Centre Henri Becquerel, Rouen, France.,Hematology Department, Centre Henri Becquerel, Rouen, France
| | - H Tilly
- INSERM U918, Centre Henri Becquerel, Rouen, France.,Hematology Department, Centre Henri Becquerel, Rouen, France
| | - S Becker
- Nuclear Medicine Department, Henri Becquerel Cancer Centre and Rouen University Hospital, Rouen, France.,QuantIF-LITIS (EA 4108-FR CNRS 3638), Faculty of Medicine, University of Rouen, Rouen, France
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Elliott TOJP, Owolabi O, Donkor S, Kampmann B, Hill PC, Ottenhoff THM, Haks MC, Kaufmann SHE, Maertzdorf J, Sutherland JS. Dysregulation of Apoptosis Is a Risk Factor for Tuberculosis Disease Progression. J Infect Dis 2015; 212:1469-79. [PMID: 25895988 DOI: 10.1093/infdis/jiv238] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 03/25/2015] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND A major barrier to effective tuberculosis control is our limited understanding of risk factors for tuberculosis disease progression. This study examined the role of apoptosis in immunity to tuberculosis. METHODS Cell subsets from tuberculosis cases and tuberculin skin test-positive (TST(+)) and TST-negative (TST(-)) household contacts (HHCs) were analyzed for expression of annexin-V and propidium iodide by flow cytometry. RNA microarrays were used to determine differences in apoptotic gene expression levels and multiplex ligation-dependent probe amplification was used to analyze gene expression in HHCs who progressed to active tuberculosis. RESULTS T cells from TST(+)HHC exhibited higher levels of apoptosis than tuberculosis cases; however, tuberculosis cases had a higher proportion of late apoptotic cells within the CD3(+)PD-1(+) subset. Tuberculosis cases had reduced levels of antiapoptotic genes compared to HHCs with a significant reduction in BCL2 associated with disease progression at least 1 year prior to progression. CONCLUSIONS While T cells are clearly able to mount a robust immune response to Mycobacterium tuberculosis, there are increased levels of apoptosis seen in effector T cells from tuberculosis patients. Dysregulation of several apoptotic genes suggest that apoptosis is a major functional pathway that could be targeted for future host-directed therapeutics.
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Affiliation(s)
- Thomas O J P Elliott
- Vaccines & Immunity, Medical Research Council Unit, Fajara, The Gambia University of Manchester, United Kingdom
| | - Olumuyiwa Owolabi
- Vaccines & Immunity, Medical Research Council Unit, Fajara, The Gambia
| | - Simon Donkor
- Vaccines & Immunity, Medical Research Council Unit, Fajara, The Gambia
| | - Beate Kampmann
- Vaccines & Immunity, Medical Research Council Unit, Fajara, The Gambia
| | - Philip C Hill
- Vaccines & Immunity, Medical Research Council Unit, Fajara, The Gambia Centre for International Health, Department of Preventive and Social Medicine, Faculty of Medicine, University of Otago, Dunedin, New Zealand
| | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, The Netherlands
| | - Marielle C Haks
- Department of Infectious Diseases, Leiden University Medical Center, The Netherlands
| | - Stefan H E Kaufmann
- Department of Immunology, Max Planck Institute of Infection Biology, Berlin, Germany
| | - Jeroen Maertzdorf
- Department of Immunology, Max Planck Institute of Infection Biology, Berlin, Germany
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Sutherland JS, Loxton AG, Haks MC, Kassa D, Ambrose L, Lee JS, Ran L, van Baarle D, Maertzdorf J, Howe R, Mayanja-Kizza H, Boom WH, Thiel BA, Crampin AC, Hanekom W, Ota MOC, Dockrell H, Walzl G, Kaufmann SHE, Ottenhoff THM. Differential gene expression of activating Fcγ receptor classifies active tuberculosis regardless of human immunodeficiency virus status or ethnicity. Clin Microbiol Infect 2013; 20:O230-8. [PMID: 24205913 DOI: 10.1111/1469-0691.12383] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Revised: 08/07/2013] [Accepted: 08/30/2013] [Indexed: 12/19/2022]
Abstract
New diagnostics and vaccines for tuberculosis (TB) are urgently needed, but require an understanding of the requirements for protection from/susceptibility to TB. Previous studies have used unbiased approaches to determine gene signatures in single-site populations. The present study utilized a targeted approach, reverse transcriptase multiplex ligation-dependent probe amplification (RT-MLPA), to validate these genes in a multisite study. We analysed ex vivo whole blood RNA from a total of 523 participants across four sub-Saharan countries (Ethiopia, Malawi, South Africa, and The Gambia) with differences in TB and human immunodeficiency virus (HIV) status. We found a number of genes that were expressed at significantly lower levels in participants with active disease than in those with latent TB infection (LTBI), with restoration following successful TB treatment. The most consistent classifier of active disease was FCGR1A (high-affinity IgG Fc receptor 1 (CD64)), which was the only marker expressed at significantly higher levels in participants with active TB than in those with LTBI before treatment regardless of HIV status or genetic background. This is the first study to identify a biomarker for TB that is not affected by HIV status or geo-genetic differences. These data provide valuable clues for understanding TB pathogenesis, and also provide a proof-of-concept for the use of RT-MLPA in rapid and inexpensive validation of unbiased gene expression findings.
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Gologan S, Iacob R, Iancu D, Iacob S, Cotruta B, Vadan R, Catuneanu AM, Constantinescu I, Barbarii L, Gheorghe C, Diculescu M. Inflammatory gene expression profiles in Crohn's disease and ulcerative colitis: a comparative analysis using a reverse transcriptase multiplex ligation-dependent probe amplification protocol. J Crohns Colitis 2013; 7:622-30. [PMID: 23014361 DOI: 10.1016/j.crohns.2012.08.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Revised: 08/17/2012] [Accepted: 08/24/2012] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIMS Cytokines and their receptors play a critical role in the pathogenesis of the inflammatory bowel disease (IBD). The aim of this study was to investigate the expression profiles of inflammatory genes in inflamed and non-inflamed colonic tissue samples in patients with Crohn's disease (CD) and ulcerative colitis (UC), and to identify molecular signatures for different IBD phenotypes. METHODS Seventy-one patients diagnosed with IBD (38 CD, 33 UC) and 15 non-IBD controls have been included in the study. For each patient, biopsy samples were obtained during colonoscopy from inflamed (L) and healthy (N) mucosa. We investigated by commercially available reverse-transcriptase multiplex ligation-dependent probe amplification (RT-MLPA) kit the mRNA expression of a set of 40 genes involved in inflammation: cytokines, chemokines, receptors, signal transduction molecules and transcription factors. RESULTS In L biopsies from patients with CD, higher expression levels were found for IL-4 (p=0.009) and IL-12p35 (p=0.0005), whereas in L biopsy samples from patients with UC higher expression levels were found for IL-8 (p=0.03), chemokines SCYA3 (p=0.05), SCYA4 (p=0.01) and glutathione S-transferase P1 (p=0.01). In N biopsies of patients with CD higher expression levels were found for IL-1R (p=0.01) and IL-12p35 (p=0.007), whereas in N biopsies of patients with UC higher expression levels were found for IL-15 (p=0.009) and SCYA8 (p=0.001). The logistic regression analysis has indicated that low expression levels of IL-2 and IL-10, together with higher ASCA IgG titers were independently associated with penetrating/stricturing CD. CONCLUSIONS RT-MLPA is a sensitive and effective method for the evaluation of the profiles of inflammatory genes in IBD, with potential future applications for diagnosis, phenotypic stratification and targeted therapy.
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Affiliation(s)
- Serban Gologan
- Department of Gastroenterology and Hepatology, University of Medicine and Pharmacy Carol Davila, Bucharest, Romania
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