Integrative Study of a High-Grade B-Cell Lymphoma Cohort of 45 Patients: A Single Institution Real Life Study

Background : High grade B cell lymphoma (HGBL) either Not Otherwise Specified (NOS) or either Double Hit (DH MYC/BCL2 or DH MYC/BCL6) or Triple Hit (TH) have been considered as separate entities from Diffuse Large B-Cell Lymphoma (DLBCL) NOS in the 2016 WHO classification. Until now, treatment of these particularly aggressive histological sybtypes remains unclear and most of patients (pts) still have a poor outcome because of chemoresistance or early relapse. Except IPI score, prognosis factors are not completely clarified. Since few years, treatment with Chimeric Antigen Receptor T (CAR-T) cells has changed the prognosis of relapsed refractory DLBCL and could represent a promising therapeutic approach - early in the course of the disease - to improve survival of HGBL. The aim of the present study is to describe a « real life » cohort of pts treated in our institution and to evaluate the prognostic impact of clinical, histological, genetic and imaging characteristics and treatment. Methods : We collected data of 45 pts diagnosed between January 2009 and October 2020. BCL2, BCL6 and MYC break were analyzed by Interphase Fluorescence In Situ Hybridization (FISH) with break-apart probes. When MYC was rearranged, MYC partner gene was analyzed with double fusion probes (MYC/IgH, MYC/IgL, MYC/IgK). Total metabolic tumor volume (TMTV) was calculated using fully automatic segmentation of lymphoma lesions by an artificial intelligence (P. Blanc-Durand, Eur J Nucl Med Mol Imaging, 2021). All pts were treated with rituximab R-CHOP/CHOP-like regimens. Treatment was reinforced (intensive regimen) with high dose methotrexate (14 pts treated with RCOPADM and one with R-ACVBP) when they were considered fit enough. Autologous stem cell transplantation at 1st relapse was performed in 3 pts and 5 pts were treated with CAR-T cells at 2 nd relapse. Results : Baseline characteristics were as follows: median age 60 y (28-80), IPI 3-5 : n=33 (73%), CNS localization : n=8/42 (19%), bone marrow involvement : n=10/34 (22%). Twenty-seven pts were DH lymphoma (MYC/BCL2: 18; MYC/BCL6: 9), 8 patients were TH-lymphoma and 10 were HGBL-NOS. MYC rearrangement was detected in 40 cases with an immunoglobulin partner gene (IgH, IgL or IgK) in 14 (52%) of 27 evaluable cases. TMTV was calculated for 29 pts with a median TMTV of 1019 ml (2-4536 ml). Fifteen pts were treated with an intensive regimen. With a median follow-up of alive pts of 17 months, 2-y progression-free survival (PFS) and overall survival (OS) were 42% [26.4 ; 56.8] and 62% [43.7 ; 75.5] respectively. PFS and OS were significantly affected by IPI 3-5 (PFS: p= 0.006, HR=3.37 ; OS: p= 0.01, HR=3.71) and CNS involvement (PFS : p=0.006, HR=6.93 ; OS: p=0.006, HR=7.44). TMTV>1000ml (PFS: p=0.051, HR 2.99 ; OS: p=0.033, HR=4.13) was associated with a significantly inferior OS. Prognosis of HGBL DH/TH and HGBL-NOS was similar (PFS: p= 0.89, HR=0.93 ; OS: p=0.64, HR=1.32). Immunoglobulin as MYC partner gene had no significant impact on prognosis (PFS: p=0.47, HR=1.48 ; OS: p=0.32, HR=1.73). Intensive regimens did not improve significantly prognosis (PFS: p=0.26, HR=1.71 ; OS: p=0.08, HR=2.86). Conclusion: This monocentric study confirms previous reports on the poor prognosis of HGBL (DH/TH and NOS) especially for patients for both high IPI or high TMTV and in case of initial CNS involvement. We confirm that intensive regimen don't improve prognosis supporting the need of alternative strategies incorporating bispecific monoclonal antibodies or consolidative CAR-T cells in very high risk pts. Disclosures Roulin: Janssen: Other: Travel and meetings. Lemonnier: Institut Roche: Research Funding; Gilead: Other: travel grant. Le Bras: Novartis: Honoraria; Takeda: Honoraria, Research Funding; Kite Gilead: Honoraria; Celgene BMS: Research Funding. Gaulard: Innate Pharma: Research Funding; Sanofi: Research Funding; Alderaan: Research Funding; Gilead: Consultancy; Takeda: Consultancy, Honoraria. Haioun: Miltenyi: Honoraria, Research Funding; Gilead: Honoraria, Research Funding; Janssen: Honoraria, Research Funding; Novartis: Honoraria, Research Funding; F. Hoffmann-La Roche Ltd: Honoraria, Research Funding; Servier: Honoraria, Research Funding; Takeda: Honoraria, Research Funding; Celgene: Honoraria, Research Funding; Amgen: Honoraria, Research Funding.

Single-Cell Genomic Analysis Identifies Prognostically Significant Gene Expression Programs in Infant Acute Lymphoblastic Leukemia

Introduction: Infant acute lymphoblastic leukemia (ALL) is an aggressive subtype of leukemia with low rates of survival. Rearrangements involving the KMT2A gene are associated with poor prognosis for infants with this cancer. Although many patients with KMT2A rearrangements (KMT2A-r) ultimately relapse, some do not. The molecular basis for this distinction has not yet been determined. There is evidence to suggest that cancers with distinct KMT2A fusion partners show distinct patterns of gene expression, though these differences have not previously been linked to prognostic outcomes. Here we utilize single-cell genomic analysis for infant ALL samples with and without KMT2A-r taken at diagnosis to explore transcriptional dynamics and identify gene expression programs with potential prognostic value. Methods: We performed 10x Chromium single-cell multiome sequencing to obtain both gene expression (scRNA-seq) and chromatin accessibility (scATAC-seq) data for blood and/or bone marrow samples obtained from a total of 34 infant ALL patients at time of diagnosis. Of these, 19 KMT2A-r patients later relapsed, 6 KMT2A-r patients did not relapse, and 9 patients did not show KMT2A rearrangement. Sequencing data were processed and aggregated with cellranger-arc, with normalization and differential gene expression performed using the Seurat package for gene expression analysis. Differential gene expression was performed between the three groups described above, (KMT2A-r + relapse, KMT2A-r no relapse, no KMT2A-r), then further subdivided for KMT2A-r cases based on the KMT2A partner gene (MLLT1 n=13 or AFF1 n=12). Results: In preliminary scRNA- and scATAC-seq in infant ALL patients, we had observed that cancer cells from individual patients tend to cluster separately, while non-blast cell populations showed similar interindividual patterns, suggesting a high degree of divergence among blast cell transcriptional programs. We replicated this finding here in larger patient samples, demonstrating no overt similarity based on KMT2A-r status or whether patients later relapsed. Strikingly, samples did broadly cluster according to KMT2A rearrangement partner gene, indicating that this appears to be a major driver of the transcriptional program in infant ALL patients. Differential expression analysis within the KMT2A-MLLT1 and KMT2A-AFF1 samples separately revealed expression of other genes associated with particular KMT2A fusion genes. Specifically, we observed that expression of HOXA genes was mostly restricted to KMT2A-MLLT1 samples. Consistent with previous results, we observed that within KMT2A-AFF1 samples there were two distinct groups of cells with mutually exclusive expression of HOXA9 or IRX1. Furthermore, the limited HOX gene expression observed in KMT2A-AFF1 samples was enriched in patients who did not relapse, supporting previous observations that the KMT2A-AFF1 samples expressing IRX1 comprise a more aggressive leukemia. Conclusions: Utilizing a single-cell transcriptomic approach enabled us to identify gene expression programs associated with good and poor prognosis in KMT2A-r infant ALL cases. We found that the KMT2A fusion partner gene appears to drive a large portion of the transcriptional heterogeneity observed across KMT2A-r samples. By treating the KMT2A-MLLT1 and KMT2A-AFF1 samples separately and exploring transcriptional dynamics within these groups, we identified transcriptional differences between patients who did and did not relapse in the presence of a KMT2A-AFF1 fusion. We are continuing to explore these data to identify prognostic markers in KMT2A-MLLT1 patients. Figure 1. Mutually exclusive gene expression programs distinguish subsets of infant ALL samples. A) Uniform manifold approximation and projection (UMAP) visualization of gene expression in individual cells across all patient samples at diagnosis, each color corresponding to a single patient (n=34). B) Cells colored according to KMT2A-r status and relapse or lack thereof. C) Cells colored according to KMT2A fusion partner gene. D) HOXA9 expression among KMT2A-AFF1 patients is strongly biased to patients that do not relapse. E) In KMT2A-AFF1 samples, HOXA9 and IRX1 show mutually exclusive expression patterns. Figure 1 Figure 1. Disclosures Brown: Novartis: Membership on an entity's Board of Directors or advisory committees; Takeda: Membership on an entity's Board of Directors or advisory committees; Amgen: Membership on an entity's Board of Directors or advisory committees; Kura: Membership on an entity's Board of Directors or advisory committees; KIte: Membership on an entity's Board of Directors or advisory committees.

EPEN-03. ZFTA/C11ORF95 FUSIONS DRIVE SUPRATENTORIAL EPENDYMOMA VIA SHARED ONCOGENIC MECHANISMS

The majority of supratentorial ependymomas (ST-EPN) are driven by fusion genes between RELA and zinc finger translocation associated, ZFTA, previously named C11orf95. Apart from fusions with a portion of the Hippo effector YAP1, which affects a small group of infant patients, the oncogenic mechanism of remaining ST-EPNs remains unclear. Aiming at refining the molecular classification of ST-EPNs, we have analyzed methylation profiles, RNA and DNA sequencing results as well as clinical data in a cohort of 613 ST-EPNs. An unbiased approach revealed distinct methylation clusters composed of tumors with ependymal but also various other histological features containing alternative translocations that shared ZFTA as a partner gene. Tumors within these additional clusters were characterized by fusions of ZFTA to numerous fusion partners different from RELA, e.g. MAML2, MAML3, NCOA2 and SS18, implying a general role of ZFTA in tumorigenesis of ST-EPN. Indeed, the transforming capacity of newly identified fusion genes was validated using an electroporation-based in vivo gene transfer technology in mice. All fusion genes themselves were sufficient to drive malignant transformation in the developing cerebral cortex and resulting tumors faithfully recapitulated molecular characteristics of their human counterparts. We found that both, the partner gene and the zinc finger DNA binding domain of ZFTA, were essential to exert tumorigenesis. Together with two additional studies, we performed a comprehensive analysis across datasets to derive a 93 gene signature of ZFTA-RELA-driven tumors, in which the Sonic Hedgehog effector gene GLI2 was identified as a promising downstream target. Subsequent co-expression of ZFTA:RELA and a dominant negative form of Gli2 indeed hampered tumorigenesis. Targeting GLI2 with arsenic trioxide caused extended survival of tumor-bearing animals, indicating GLI2 as a critical regulator of ZFTA fusion-positive tumorigenesis as well as a potential therapeutic vulnerability in these tumors.

The characterization of MCEF : an AFF transcription factor associated with acute lymphoglastic leukemia and HIV-1

Acute Lymphoblastic Leukemia (ALL) results from environmentally-triggered in utero translocations between the Mixed Lineage Leukemia (MLL) gene and partner genes. In the most frequent cases of ALL, this partner gene is one of the AF4 family (AFF) of transcription factors. The newest AFF member to be discovered and cloned is AFF-4/AF5q31/MCEF. MCEF interacts with a transcription factor necessary for transcription of HIV-1. In addition, evidence suggests that male knockout mice are azoospermic. Therefore, the characterization of MCEF is clinically and theoretically important. The purpose of my research was to further characterize MCEF. In this paper, I first review the AFF members, focusing on MCEF. I then show a series of experimental results addressing MCEF isoforms and HIV-1 repression domains, as well as the generation of anti-MCEF antisera. Finally, I highlight intriguing results with live virus replication assays that suggest how MCEF could be exploited as a therapeutic target for AIDS.

The characterization of MCEF : an AFF transcription factor associated with acute lymphoglastic leukemia and HIV-1

Acute Lymphoblastic Leukemia (ALL) results from environmentally-triggered in utero translocations between the Mixed Lineage Leukemia (MLL) gene and partner genes. In the most frequent cases of ALL, this partner gene is one of the AF4 family (AFF) of transcription factors. The newest AFF member to be discovered and cloned is AFF-4/AF5q31/MCEF. MCEF interacts with a transcription factor necessary for transcription of HIV-1. In addition, evidence suggests that male knockout mice are azoospermic. Therefore, the characterization of MCEF is clinically and theoretically important. The purpose of my research was to further characterize MCEF. In this paper, I first review the AFF members, focusing on MCEF. I then show a series of experimental results addressing MCEF isoforms and HIV-1 repression domains, as well as the generation of anti-MCEF antisera. Finally, I highlight intriguing results with live virus replication assays that suggest how MCEF could be exploited as a therapeutic target for AIDS.

A Cryptic BCR-PDGFRB Fusion Resulting in a Chronic Myeloid Neoplasm With Monocytosis and Eosinophilia: A Novel Finding With Treatment Implications

RNA-seq was used to identify the partner gene and confirm the presence of a BCR-PDGFRB fusion. Identification of this fusion product resulted in successful treatment and long-term remission of this myeloid neoplasm. Based on our results, we suggest that despite current WHO recommendations, screening for PDGFRB rearrangement in cases of leukocytosis with eosinophilia and no other etiologic explanation is necessary, even if the karyotype is normal.

Gene of the month: GLI-1

The Glioma-associated homologue-1 (GLI-1) gene was first discovered to be amplified in glioblastoma multiforme. It encodes for a zinc-finger transcription factor in the Kruppel family of proteins and is important in the sonic hedgehog signalling pathway. GLI-1 also plays a role in several other pathways and is important for proliferation, migration, invasion, growth and angioinvasion, and cancer stem cell self-renewal in a variety of malignancies. GLI-1 is amplified in several malignancies, including an epithelioid, pericytomatous soft tissue neoplasm that can exhibit malignant behaviour. More recently, GLI-1 fusions with other partner genes have been found in three rare tumours: a pericytomatous tumour with a t(7;12) translocation, where it partners with Actin beta 1, and gastroblastoma and plexiform fibromyxoma, where the partner gene is metastasis-associated lung adenocarcinoma transcript 1, respectively.

Prognostic Significance of MYC Rearrangement and Translocation Partner in Diffuse Large B-Cell Lymphoma: A Study by the Lunenburg Lymphoma Biomarker Consortium

PURPOSE MYC rearrangement ( MYC-R) occurs in approximately 10% of diffuse large B-cell lymphomas (DLBCLs) and has been associated with poor prognosis in many studies. The impact of MYC-R on prognosis may be influenced by the MYC partner gene (immunoglobulin [IG] or a non-IG gene). We evaluated a large cohort of patients through the Lunenburg Lymphoma Biomarker Consortium to validate the prognostic significance of MYC-R (single-, double-, and triple-hit status) in DLBCL within the context of the MYC partner gene. METHODS The study cohort included patients with histologically confirmed DLBCL morphology derived from large prospective trials and patient registries in Europe and North America who were uniformly treated with rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone therapy or the like. Fluorescence in situ hybridization for the MYC, BCL2, BCL6, and IG heavy and light chain loci was used, and results were correlated with clinical outcomes. RESULTS A total of 5,117 patients were identified of whom 2,383 (47%) had biopsy material available to assess for MYC-R. MYC-R was present in 264 (11%) of 2,383 patients and was associated with a significantly shorter progression-free and overall survival, with a strong time-dependent effect within the first 24 months after diagnosis. The adverse prognostic impact of MYC-R was only evident in patients with a concurrent rearrangement of BCL2 and/or BCL6 and an IG partner (hazard ratio, 2.4; 95% CI, 1.6 to 3.6; P < .001). CONCLUSION The negative prognostic impact of MYC-R in DLBCL is largely observed in patients with MYC double hit/triple-hit disease in which MYC is translocated to an IG partner, and this effect is restricted to the first 2 years after diagnosis. Our results suggest that diagnostic strategies should be adopted to identify this high-risk cohort, and risk-adjusted therapeutic approaches should be refined further.