Cell cycle arrest and p53 prevent ON-target megabase-scale rearrangements induced by CRISPR-Cas9.

The CRISPR-Cas9 system has revolutionized our ability to precisely modify the genome and has led to gene editing in clinical applications. Comprehensive analysis of gene editing products at the targeted cut-site has revealed a complex spectrum of outcomes. ON-target genotoxicity is underestimated with standard PCR-based methods and necessitates appropriate and more sensitive detection methods. Here, we present two complementary Fluorescence-Assisted Megabase-scale Rearrangements Detection (FAMReD) systems that enable the detection, quantification, and cell sorting of edited cells with megabase-scale loss of heterozygosity (LOH). These tools reveal rare complex chromosomal rearrangements caused by Cas9-nuclease and show that LOH frequency depends on cell division rate during editing and p53 status. Cell cycle arrest during editing suppresses the occurrence of LOH without compromising editing. These data are confirmed in human stem/progenitor cells, suggesting that clinical trials should consider p53 status and cell proliferation rate during editing to limit this risk by designing safer protocols.

CRISPR-Cas9 globin editing can induce megabase-scale copy-neutral losses of heterozygosity in hematopoietic cells.

CRISPR-Cas9 is a promising technology for gene therapy. However, the ON-target genotoxicity of CRISPR-Cas9 nuclease due to DNA double-strand breaks has received little attention and is probably underestimated. Here we report that genome editing targeting globin genes induces megabase-scale losses of heterozygosity (LOH) from the globin CRISPR-Cas9 cut-site to the telomere (5.2 Mb). In established lines, CRISPR-Cas9 nuclease induces frequent terminal chromosome 11p truncations and rare copy-neutral LOH. In primary hematopoietic progenitor/stem cells, we detect 1.1% of clones (7/648) with acquired megabase LOH induced by CRISPR-Cas9. In-depth analysis by SNP-array reveals the presence of copy-neutral LOH. This leads to 11p15.5 partial uniparental disomy, comprising two Chr11p15.5 imprinting centers (H19/IGF2:IG-DMR/IC1 and KCNQ1OT1:TSS-DMR/IC2) and impacting H19 and IGF2 expression. While this genotoxicity is a safety concern for CRISPR clinical trials, it is also an opportunity to model copy-neutral-LOH for genetic diseases and cancers.

Lymphomatoid papulosis types D and E: a multicentre series of the French Cutaneous Lymphomas Study Group.

BACKGROUND: Lymphomatoid papulosis (LyP) type D (LyP D) and type E (LyP E) have recently been described in small series of cases or isolated case reports. AIM: To further describe the clinical and histological features of LyP D and E based on a retrospective multicentre study. METHODS: The clinical and histopathological features of 29 patients with an initial diagnosis of LyP D or LyP E were retrospectively assessed using standardized forms. RESULTS: After exclusion of 5 cases, 24 patients (14 LyP D, 10 LyP E) were enrolled in the study. The median follow-up was 2.5 years (range 1 month to 13 years). LyP D was characterized by multiple recurrent self-regressing small papules that developed central erosion or necrosis, whereas LyP E presented as papulonodular lesions that rapidly evolved into necrotic eschar-like lesions > 10 mm in size. Epidermal changes were more frequent in LyP D, whereas dermal infiltrates were deeper in LyP E. Anaplastic cytology was rare and the DUSP22 rearrangement was never observed. Two patients (8%) had an associated cutaneous lymphoma. CONCLUSION: LyP D and E have distinct clinical findings and may be associated with other cutaneous lymphomas.

PTEN, ATM, IDH1 mutations and MAPK pathway activation as modulators of PFS and OS in patients treated by first line EGFR TKI, an ancillary study of the French Cooperative Thoracic Intergroup (IFCT) Biomarkers France project.

OBJECTIVES: Tumor mutation screening is standard of care for patients with stage IV NSCLC. Since a couple of years, widespread NGS approaches used in routine diagnostics to detect driver mutations such as EGFR, KRAS, BRAF or MET allows the identification of other alterations that could modulated the intensity or duration of response to targeted therapies. The prevalence of co-occurring alterations that could affect response or prognosis as not been largely analyzed in clinical settings and large cohorts of patients. Thanks to the IFCT program "Biomarkers France", a collection of samples and data at a nation-wide level was available to test the impact of co-mutations on first line EGFR TKI in patients with EGFR mutated cancers. MATERIALS AND METHODS: Targeted NGS was assessed on available (n = 208) samples using the Ion AmpliSeq™ Cancer Hotspot Panel v2 to screen for mutations in 50 different cancer genes. RESULTS: This study showed that PTEN inactivating mutations, ATM alterations, IDH1 mutations and complex EGFR mutations were predictors of short PFS in patients with a stage 4 lung adenocarcinoma receiving first line EGFR TKI and that PTEN, ATM, IDH1 and KRAS mutations as well as alterations in the MAPK pathway were related to shorter OS. CONCLUSION: These findings may lead to new treatment options in patients with unfavorable genotypes to optimize first line responses.

Clinical and molecular characteristics of non-small-cell lung cancer (NSCLC) harboring EGFR mutation: results of the nationwide French Cooperative Thoracic Intergroup (IFCT) program.

BACKGROUND: EGFR mutations cause inconsistent response to EGFR tyrosine-kinase inhibitors (TKI). To better understand these features, we reviewed all cases of EGFR-mutated non-small-cell lung cancer collected in the Biomarkers France database. PATIENTS AND METHODS: Of 17 664 patients, 1837 (11%) with EGFR-mutated non-small-cell lung cancer were retrospectively analyzed for clinical and molecular characteristics. Results were correlated with survival and treatment response for the 848 stage IV patients. RESULTS: EGFR exon 18, 19, 20 and 21 mutations were found in 102 (5.5%), 931 (51%), 102 (5.5%) and 702 (38%) patients, respectively. Over 50% of exon 18 and 20 mutated patients were smokers. The median follow-up was 51.7 months. EGFR mutation type was prognostic of overall survival (OS) versus wild-type {exon 19: hazard ratio (HR)=0.51 [95% confidence interval (CI): 0.41-0.64], P < 0.0001; exon 21: HR = 0.76 (95% CI: 0.61-0.95), P = 0.002; exon 20: HR = 1.56 (95% CI: 1.02-2.38), P = 0.004}. EGFR mutation type was prognostic of progression-free survival versus wild-type [exon 19: HR = 0.62 (95% CI: 0.49-0.78), P < 0.0001; exon 20: HR = 1.46 (95% CI: 0.96-2.21), P = 0.07]. First-line treatment choice did not influence OS in multivariate analysis. First-line TKI predicted improved progression-free survival versus chemotherapy [HR = 0.67 (95% CI: 0.53-0.85), P = 0.001]. OS was longer for del19 versus L858R, which was associated with better OS compared with other exon 21 mutations, including L861Q. TKI improved survival in patients with exon 18 mutations, while chemotherapy was more beneficial for exon 20-mutated patients. CONCLUSION: EGFR mutation type can inform the most appropriate treatment. Therapeutic schedule had no impact on OS in our study, although TKI should be prescribed in first-line considering the risk of missing the opportunity to use this treatment.

Assessment of diagnostic criteria between primary cutaneous anaplastic large-cell lymphoma and CD30-rich transformed mycosis fungoides; a study of 66 cases.

BACKGROUND: Transformed mycosis fungoides (TMF) large cells may express CD30 antigen, and because of this, the differential diagnosis between CD30-rich TMF and primary cutaneous anaplastic large-cell lymphoma (cALCL) may be difficult, and especially in distinguishing cALCL associated with MF vs. CD30-rich TMF. OBJECTIVES: To find clinical, histological and molecular diagnostic features useful for differential diagnosis between cALCL and CD30-rich TMF. To analyse and compare the prognostic value of clinical and pathological factors in these two diseases. MATERIAL AND METHODS: We conducted a retrospective study (1999-2012) of 32 patients with cALCL and 34 with CD30-rich TMF, seen in reference centres of the French Study Group of Cutaneous Lymphoma. Clinical, histological and molecular features were analysed and compared to determine their diagnostic and prognostic value. RESULTS: Comparison of the two groups showed that age ˃ 60 years, ≥ 5 skin lesions, early progression, absence of spontaneous regression and trunk involvement were significantly associated with the diagnosis of TMF. Abnormal T-cell phenotype and perforin expression were significantly more frequent in cALCL (both P < 0·001). Overall survival (OS) at 5 years was 77·4% for cALCL and 20·7% for CD30-rich TMF. Stage T3, ≥ 5 skin lesions, lower limb involvement for cALCL and stage T4, extracutaneous involvement, B symptoms, high levels of lactate dehydrogenase for CD30-rich TMF were associated with poor OS and progression-free survival. DUSP22 gene rearrangement had no diagnostic or prognostic value. CONCLUSIONS: Clinical features and outcome are the most discriminative to differentiate the two entities. Even histological and molecular markers were not fully specific; abnormal vs. normal T-cell phenotype and perforin expression may constitute helpful tools.

IGHV gene features and MYD88 L265P mutation separate the three marginal zone lymphoma entities and Waldenström macroglobulinemia/lymphoplasmacytic lymphomas.

To clarify the relationships between marginal zone lymphomas (MZLs) and Waldenström macroglobulinemia/lymphoplasmacytic lymphomas (WM/LPLs), immunoglobulin heavy chain variable gene (IGHV) features were analyzed and the occurrence of MYD88 L265P mutations was identified in a series of 123 patients: 53 MZLs from the spleen (SMZLs), 11 from lymph nodes (NMZLs), 28 mucosa-associated lymphatic tissue (MALT) lymphomas and 31 WM/LPLs. SMZLs were characterized by overrepresentation of IGHV1-2 gene rearrangements with a canonical motif, without selection pressure and with long CDR3 segments. NMZLs had increased frequencies of IGHV3 genes. The IGHV gene was unmutated in most cases, often with long CDR3 segments. MALT lymphomas were usually associated with a mutated IGHV gene, but with the absence of selection pressure. WM/LPLs were associated with an IGHV3-23 overrepresentation and high IGHV mutation rate, with features of selection pressure and short CDR3 segments. MYD88 L265P mutations were almost restricted exclusively to WM/LPL patients. Taken all diagnoses together, all patients with MYD88 L265P mutations had an immunoglobulin M peak and almost all patients except one had bone marrow infiltration. These results demonstrate that the history of antigen exposure of the four entities studied was different and MYD88 L265P was specifically associated with WM/LPLs. WM/LPL may thus be functionally associated with constitutive nuclear factor-κB activation.

Diagnostic value of immunohistochemistry for the detection of the BRAFV600E mutation in primary lung adenocarcinoma Caucasian patients.

BACKGROUND: Non-small-cell lung carcinoma (NSCLC) patients with a BRAF(V600E) mutation benefit from targeted therapy. The usefulness of immunohistochemistry (IHC) as an alternative approach for the detection of BRAF(V600E) in NSCLC patients has not been evaluated until now. This study compared the specificity and sensitivity of IHC with other methods for the detection of BRAF(V600E) in primary lung adenocarcinoma. PATIENTS AND METHODS: BRAF mutations were analysed by DNA sequencing of a Caucasian subpopulation of selected 450 of 1509 (30%) EGFR, KRAS, PI3KA, Her2 and EML4-ALK wild-type (wt) primary lung adenocarcinomas. Detection of the BRAF(V600E) mutation was carried out by IHC using the VE1 clone antibody and compared with the results of other molecular methodologies. RESULTS: Of 450 (9%) of tumours, 40 harboured a BRAF mutation, which corresponded to either a BRAF(V600E) or a non-BRAF(V600E) mutation in 21 of 450 (5%) and 19 of 450 (4%) cases, respectively. The IHC VE1 assay was positive in 19 of 21 (90%) BRAF(V600E)-mutated tumours and negative in all BRAF(nonV600E)-mutated tumours. CONCLUSION: IHC using the VE1 clone is a specific and sensitive method for the detection of BRAF(V600E) and may be an alternative to molecular biology for the detection of mutations in NSCLC.

[Management of cutaneous T-cell lymphomas: Recommendations of the French Cutaneous Lymphoma Group]. / Prise en charge des lymphomes T cutanés : recommandations du Groupe français d'étude des lymphomes cutanés.

BACKGROUND: Classification of diagnostic methods, of initial staging and of the treatment of primary cutaneous T-cell lymphomas, particularly the most common epidermotropic forms, constitutes an essential step in rationalising therapeutic practice and in evaluating the results of treatment. PATIENTS AND METHODS: We carried out an analysis of the literature and of existing recommendations in order to create recommendations regarding the diagnosis, initial staging and treatment of primary T-cell lymphomas. RESULTS: We present the key elements of diagnosis and initial staging. The selected therapeutic strategy, which necessarily changes over time, must avoid both unnecessarily aggressive early treatment as well as an overly timid therapeutic approach that could allow lesions to rapidly progress towards more advanced stages. Regular reassessment of the benefit/risk ratio is necessary and involves the use of first- and second-line measures, in which it is difficult to establish any hierarchy, with the current tendency favouring in particular combined therapy as second-line treatment in order to limit the toxicity of each individual constituent drug within the combination. The creation of a national SPC marks significant progress in difficult cases. CONCLUSION: As a result of the offer, limited level of proof in existing studies, which are generally unsatisfactory in terms of methodology, the new recommendations described herein are timely and should be updated regularly in accordance with advances in knowledge. The organisation of clinical trials and validation of the scoring systems currently being developed should be encouraged.

[Optimized protocols for interphase FISH analysis of imprints and sections using split signal probes]. / Application de la technique de FISH interphasique avec des sondes encadrantes dites de <> à différents types de préparations histologiques et cytologiques.

Fluorescent in situ hybridization (FISH) analysis is a molecular technique allowing the detection of recurrent translocations in cancer. Several hybridization protocols were assayed in order to evaluate their performances for interphase FISH analysis of histological sections and imprints using split probes. Adult and foetal lymphoid tissues were selected. Touch imprints of fresh (EF) or frozen (EC) tissues, sections (CF) and isolated nuclei (NI) of formol-fixed paraffin-embedded tissues were performed. The cut-off values of the IGH, IGlambda, BCL-2, BCL-6, CCND1 and MYC DNA FISH split signal probes were calculated for adult reactive lymph nodes on the different histological preparations (EC, CF, CC, NI) and on several tissues for the IGH and BCL-6 probes. In reactive lymph nodes, the cut-off values of the probes were between 3 and 13% and found independent of the preparation type. Conversely, slight but significant variations of the cut-off level were observed when different foetal control tissues were assayed with the same probe set. Finally, this study provided optimized-protocols for FISH analysis of either fresh/frozen imprints or formalin-fixed paraffin-embedded sections using split signal DNA probes.

Splitting bone marrow trephines into frozen and fixed fragments allows parallel histological and molecular detection of B cell malignant infiltrates.

Clonality analysis of the immunoglobulin heavy chain (IgH) gene is helpful in identifying malignant B cell infiltrates in the bone marrow and is usually carried out on separate aspirates or on the same formalin-fixed decalcified bone marrow specimen. To determine whether the removal of the decalcification step would improve the molecular analysis, we first studied 12 bone marrow specimens with lymphoma infiltration split into a fixed and a small frozen fragment. Both the detection rate of IgH gene monoclonality and DNA quality were found to be superior in the frozen part than in the fixed part. Conversely, to evaluate whether the split would compromise histological analysis, we selected a series of 134 bone marrow specimens obtained from patients with small B cell lymphoma and showing IgH monoclonality on the frozen part. The histological detection rate of infiltrated or suspicious infiltrates (95%) on the fixed part was not altered by saving a frozen part.

Blastoid and common variants of mantle cell lymphoma exhibit distinct immunophenotypic and interphase FISH features.

AIMS: The recognition of blastoid variant (BV) of mantle cell lymphoma (MCL) is based on morphological criteria. Our aim was to analyse 18 MCL cases including four BV-MCL for their clinicopathological features, proliferation index, cyclin D1 and CDK4 expression and interphase fluorescence in-situ hybridization (FISH) pattern. METHODS AND RESULTS: BV-MCL versus common MCL was characterized by a shorter overall duration of response after first-line therapy (11 months versus 28 months) and shorter overall survival (20 months versus 42 months). Interphase FISH showed a t(11;14) fusion pattern in all MCL tested cases. However, the four blastoid cases were characterized by extra copies of CCND1 signals. Using additional probes of chromosomes 11, 18, 21, these signals were shown to be the result of hypotetraploidy and not of a specific amplification of the normal or the translocated CCND1 allele. Moreover, the BV-MCL cases were characterized by a combined high percentage of cells expressing cyclin D1 and/or CDK4 with a proliferation (MIB-1-Ki67) index above 50%. Such features allowed the recognition of areas of large cell transformation in the case of secondary BV-MCL. CONCLUSIONS: Since distinction between BV and common MCL is of clinical relevance, our data underline the need to add phenotypic and cytogenetic criteria to cytomorphology for a better recognition of BV-MCL.

Detection of circulating cells expressing chromogranin A gene transcripts in patients with lung neuroendocrine carcinoma.

High grade lung neuroendocrine carcinomas, like small and large cell neuroendocrine carcinomas, pose therapeutic problems. Most initially respond to chemotherapeutic agents, but early relapses are frequent and are resistant to the presently available treatments. Our study reports for the first time the development and evaluation of a test for detecting the presence of circulating tumour cells by measuring chromogranin A gene transcripts with reverse transcriptase-polymerase chain reaction (RT-PCR) and Southern blotting. The test is specific and sensitive (detection of 10 cancer cells/ml blood), and only minimally invasive. Positivity is statistically correlated to high grade neuroendocrine carcinomas and to a poor prognosis with a 3-fold higher lethal risk. The test now needs to be assessed for its usefulness as a tool in the initial staging procedures and follow-up by comparison with the recent immunoradiometric assay (RIA) for detection of chromogranin A in the serum.

Combined analysis of T cell receptor gamma and immunoglobulin heavy chain gene rearrangements at the single-cell level in lymphomas with dual genotype.

By prospectively studying immunoglobulin heavy chain gene (IgH) and T cell receptor gamma (TCRgamma) gene rearrangements in 398 lymphoma cases, a dual genotype was observed in 13% of B cell and 11% of T cell lymphomas. According to histological subtype, the highest incidence was observed for mantle cell lymphomas (32%) and lymphoplasmacytic lymphoma (21%) among B cell lymphomas, and for angioimmunoblastic lymphoma (AILT) (46%) and Sézary syndrome (SS) (50%) among T cell lymphomas. To determine whether the dual genotype corresponds to the presence of two distinct monoclonal populations or to the presence of both rearrangements within the same lymphoma cells, single-cell microdissection was used after immunohistochemistry and a single-cell combined IgH and TCRgamma gene analysis was designed after a whole-genome amplification step. This protocol was applied to the study of two nodal B cell lymphomas (one diffuse large B cell lymphoma and one mantle cell lymphoma) and two cutaneous T cell lymphomas (one AILT and one SS). Two cases (SS and mantle cell lymphoma) were true bigenotypic lymphomas, as both IgH and TCRgamma monoclonal rearrangements were detected in the same cells. Conversely, in the diffuse large B cell lymphoma and AILT cases, large CD22+ single cells exhibited only the monoclonal IgH rearrangement but not the TCRgamma gene that was detected in CD3+ single cells. Such an approach allows the identification of true bigenotypic lymphoma among dual genotypic lymphoma. Specific genetic alterations may be further amplified from microdissected cryopreserved material, such as the t(11;14) breakpoint detected in bigenotypic B cells of the mantle cell lymphoma case.

[Interphase FISH analysis of frozen or fixed tissues for the detection of t(11;14) (q13;q32) in mantle cell lymphoma]. / Analyse par FISH interphasique de tissus congelés ou fixés pour la détection de la t(11;14)(q13;q32) dans les lymphomes du manteau.

Cytogenetic analyses have revealed that mantle cell lymphomas (MCL) are closely associated with the t(11;14)(q13;q32). This translocation juxtaposes the immunoglobulin heavy chain gene (IGH) sequences with the BCL-1 locus, leading to up-regulation of the CCND1 gene and consequently to an overexpression of cyclin D1 protein. We studied 27 MCL with characteristic morphological and immunological (CD5+, CD10-, CD20+, CD23-) features and 2 controls (reactionnal lymphadenitis) to evaluate the feasibility and the interest of FISH analysis on interphase cells from frozen or paraffin-embedded tissues. Sections (CC) and touch preparations (EC) of frozen tissues and sections of paraffin-embedded tissues (CF) were successfully hybridized with the Vysis LSI IgH/CCND1 dual color dual fusion translocation probe. The touch preparations presented a lower cellularity than sections, therefore allowing an easier analysis. Hybridization spots intensities were found stronger in CC and EC than in CF. The percentages of t(11;14) positive cells were similar in CC, EC and CF from a same patient. The percentage of non hybridized cells, analogous in CC and EC, was higher in CF. However, the CF were directly analysed on microscope without the need of any numerical picture treatment. The t(11;14) was detected in all the cases (27/27) and positive cells percentages were always higher than the probe cut-off (5%). The FISH analysis on interphase cells appears a performing and rapid technique to detect t(11;14) in MCL on both frozen and paraffin-embedded tissue, thus extending its practical and diagnostic use.

Evidence that an identical T cell clone in skin and peripheral blood lymphocytes is an independent prognostic factor in primary cutaneous T cell lymphomas.

The monoclonality of the T cell receptor gamma-chain gene was analyzed by polymerase chain reaction in skin and blood specimens of 85 patients with cutaneous T cell lymphomas including 67 mycosis fungoides, seven Sézary syndromes, and 11 CD30- nonepidermotropic cutaneous T cell lymphomas. A cutaneous T cell clone was detected in 69% of mycosis fungoides and 100% of Sézary syndromes. This frequency varied according to the clinical stage: 57% in early stages (Ia-IIa) to 96% in advanced stages (IIb-IV, Sézary syndrome). A peripheral blood T cell clone was detected in 42% of early stages and in 74% of late stages but was identical to the cutaneous one in 15% and in 63%, respectively. A significant association between initial clinical stage and T cell monoclonality was observed. In nonepidermotropic cutaneous T cell lymphomas, T cell monoclonality was detected in 55% of skin and 36% of blood samples. Univariate and multivariate analyses showed that, besides the initial clinical stage, an identical cutaneous and blood T cell clone was an independent prognostic factor for disease progression of mycosis fungoides/Sézary syndrome (hazard ratio 3.4, 95% confidence interval 1.4-9.9). Parallel polymerase chain reaction study of skin and blood specimens may therefore provide an initial prognostic marker that could help to monitor therapeutic strategies. A fully prospective study, with simultaneous therapeutic trials, needs to be done to confirm our findings and to include treatment variables in the statistical analysis.

Sodium valproate-induced cutaneous pseudolymphoma followed by recurrence with carbamazepine.

We report a patient with a sodium valproate-induced cutaneous pseudolymphoma, presenting with an erythematous papule, histologically mimicking a non-epidermotropic T-cell lymphoma. Polymerase chain reaction study of the skin biopsy revealed monoclonal rearrangement of the T-cell receptor gamma gene. Withdrawal of sodium valproate was followed by regression of the lesion, but 5 months after substitution by carbamazepine, two further papules appeared, with similar histological features and a T-cell clone identical to the initial one. Carbamazepine was stopped and the lesions disappeared without relapse over a 4-year follow-up. Sodium valproate is very rarely responsible for a hypersensitivity syndrome, and our case is the first report of sodium valproate-induced cutaneous pseudolymphoma. The recurrence with carbamazepine may be due to a common effect on T-cell lymphocyte function. The return of the same monoclonal population shows that the recurrence of monoclonal T cells may be observed in benign conditions and is not an exclusive hallmark of cutaneous lymphoma.