From Pathology to Precision Medicine in Anaplastic Large Cell Lymphoma Expressing Anaplastic Lymphoma Kinase (ALK+ ALCL)

Characteristics and clinical outcomes of patients with ALK-positive anaplastic large cell lymphoma: Report from the prospective international T-cell lymphoma project

The T-cell Lymphoma Project is an international registry prospective study that enrolled patients with newly diagnosed peripheral T-cell and NK-cell lymphomas (PTCL). The main objective was to define the clinical features and outcomes, establishing a robust benchmark for future clinical trials. Seventy-four institutions from 14 countries in North America, South America, Europe, and Asia collected data on patients diagnosed and treated at their respective centers between September 2006 and February 2018. Among 1553 PTCL patients, 131 (8.4% of the total cohort) were confirmed to have anaplastic large cell lymphoma - kinase positive (ALCL, ALK+). The median age of the patients was 39 years (18-84). Sixty-five patients (66%) had advanced-stage disease, although majority (45 patients, 54%) had a low-risk International Prognostic Index (IPI) score (0-1). Of 97 patients treated with chemotherapy, 97% received anthracycline-containing regimens. The overall response rate was 81%, with 69 patients (70%) achieving complete remission. Estimated OS and PFS at 3 years were 77% (95% CI: 54%-99%) and 68% (95% CI: 46%-90%), respectively, and at 5 years were very similar, 77% of OS (95% CI: 62%-92%) and 64% of PFS (95% CI: 34%-94%). Multivariate analysis for PFS showed advanced stage (hazard ratios [HR]: 4.72, 95% CI: 1.43-23.9, p = 0.015), elevated lactate dehidrogenade (LDH) (HR 4.85; 95% CI: 1.73-13.60, p = 0.001), and Eastern Cooperative Oncology Group Performance Status scale (ECOG-PS) ≥2 (HR: 5.25; 95% CI: 1.68-16.4, p = 0.024). For OS, elevated LDH (HR: 3.77; 95% CI: 1.98-14.17, p = 0.014) and ECOG-PS ≥2 (HR: 4.59; 95% CI: 1.46-14.39, p = 0.004) were identified. In summary, although the outcome of ALK+ ALCL is superior to that of other PTCLs, it remains sufficiently favorable, given the young median age of the patients. Our results confirm the usefulness of both IPI and Prognostic Index for T-cell Lymphoma (PIT) in identifying groups of patients with different outcomes. Clinical Trials ID: NCT01142674.

Quantitative Acetylomics Uncover Acetylation-Mediated Pathway Changes Following Histone Deacetylase Inhibition in Anaplastic Large Cell Lymphoma

Histone deacetylases (HDACs) target acetylated lysine residues in histone and non-histone proteins. HDACs are implicated in the regulation of genomic stability, cell cycle, cell death and differentiation and thus critically involved in tumorigenesis. Further, HDACs regulate T-cell development and HDAC inhibitors (HDACis) have been approved for clinical use in some T-cell malignancies. Still, the exact targets and mechanisms of HDAC inhibition in cancer are understudied. We isolated tumor cell lines from a transgenic mouse model of anaplastic large cell lymphoma (ALCL), a rare T-cell lymphoma, and abrogated HDAC activity by treatment with the HDACis Vorinostat and Entinostat or Cre-mediated deletion of Hdac1. Changes in overall protein expression as well as histone and protein acetylation were measured following Hdac1 deletion or pharmacological inhibition using label-free liquid chromatography mass spectrometry (LC-MS/MS). We found changes in overall protein abundance and increased acetylation of histones and non-histone proteins, many of which were newly discovered and associated with major metabolic and DNA damage pathways. For non-histone acetylation, we mapped a total of 1204 acetylated peptides corresponding to 603 proteins, including chromatin modifying proteins and transcription factors. Hyperacetylated proteins were involved in processes such as transcription, RNA metabolism and DNA damage repair (DDR). The DDR pathway was majorly affected by hyperacetylation following HDAC inhibition. This included acetylation of H2AX, PARP1 and previously unrecognized acetylation sites in TP53BP1. Our data provide a comprehensive view of the targets of HDAC inhibition in malignant T cells with general applicability and could have translational impact for the treatment of ALCL with HDACis alone or in combination therapies.

Aberrant expression and genetic alteration of c-MYC in anaplastic large cell lymphoma

PURPOSE

c-MYC plays an important role in regulating cellular growth and apoptosis, and it is aberrantly expressed in many human malignancies. Although c-MYC has been extensively investigated in Burkitt lymphoma and diffuse large B cell lymphoma, little has been reported in anaplastic large cell lymphoma (ALCL). The aim of this study was to investigate the expression and genetic alterations of c-MYC in primary systemic ALCL, characterize its clinicopathologic features and immunophenotypes, and discuss their implications in prognosis.

METHODS

Tissue microarrays using samples from 85 ALCL patients were used to evaluate expression of c-MYC and anaplastic lymphoma kinase (ALK). c-MYC and ALK genetic alterations were detected using fluorescence in situ hybridization. The Kaplan-Meier and multivariate Cox regression methods were used for survival analysis.

RESULTS

c-MYC was expressed in 24 of 85 samples (28.2%), and ALK was expressed in 54 (63.5%). c-MYC and ALK were co-expressed in 16 samples (18.8%). c-MYC expression and c-MYC and ALK co-expression increased with ALCL clinical stages and the International Prognostic Index (IPI) score (p < 0.05). Fifty of the samples (58.8%) had ALK rearrangement, and 18 (22.1%) had aneuploidy. c-MYC rearrangement was not detected, but aneuploidy was observed in 19 cases (22.4%). c-MYC aneuploidy was significantly different based on c-MYC expression and the IPI score (p < 0.05). c-MYC was a significant independent prognostic factor for progression-free survival and overall survival in patients with ALCL.

CONCLUSION

c-MYC protein expression and c-MYC aneuploidy could predict worse survival in patients with ALCL.

IL10RA modulates crizotinib sensitivity in NPM1-ALK+ anaplastic large cell lymphoma

Anaplastic large cell lymphoma (ALCL) is a T-cell malignancy predominantly driven by a hyperactive anaplastic lymphoma kinase (ALK) fusion protein. ALK inhibitors, such as crizotinib, provide alternatives to standard chemotherapy with reduced toxicity and side effects. Children with lymphomas driven by nucleophosmin 1 (NPM1)-ALK fusion proteins achieved an objective response rate to ALK inhibition therapy of 54% to 90% in clinical trials; however, a subset of patients progressed within the first 3 months of treatment. The mechanism for the development of ALK inhibitor resistance is unknown. Through genome-wide clustered regularly interspaced short palindromic repeats (CRISPR) activation and knockout screens in ALCL cell lines, combined with RNA sequencing data derived from ALK inhibitor-relapsed patient tumors, we show that resistance to ALK inhibition by crizotinib in ALCL can be driven by aberrant upregulation of interleukin 10 receptor subunit alpha (IL10RA). Elevated IL10RA expression rewires the STAT3 signaling pathway, bypassing otherwise critical phosphorylation by NPM1-ALK. IL-10RA expression does not correlate with response to standard chemotherapy in pediatric patients, suggesting that a combination of crizotinib and chemotherapy could prevent ALK inhibitor resistance-specific relapse.

High Levels of miR-7-5p Potentiate Crizotinib-Induced Cytokilling and Autophagic Flux by Targeting RAF1 in NPM-ALK Positive Lymphoma Cells

Simple Summary

Anaplastic lymphoma kinase positive anaplastic large cell lymphomas are a pediatric disease, which still needs treatment improvement. Crizotinib was the first ALK-targeted inhibitor used in clinics, but relapses are now known to occur. Current research efforts indicate that combined therapies could represent a superior strategy to eradicate malignant cells and prevent tumor recurrence. Autophagy is a self-digestion cellular process, known to be induced upon diverse cancer therapies. Our present work demonstrates that the potentiation of the crizotinib-induced autophagy flux, through the serine/threonine kinase RAF1 downregulation, drives ALK+ ALCL cells to death. These results should encourage further investigations on the therapeutic modulation of autophagy in this particular cancer settings and other ALK-related malignancies.

Abstract

Anaplastic lymphoma kinase positive anaplastic large cell lymphomas (ALK+ ALCL) are an aggressive pediatric disease. The therapeutic options comprise chemotherapy, which is efficient in approximately 70% of patients, and targeted therapies, such as crizotinib (an ALK tyrosine kinase inhibitor (TKI)), used in refractory/relapsed cases. Research efforts have also converged toward the development of combined therapies to improve treatment. In this context, we studied whether autophagy could be modulated to improve crizotinib therapy. Autophagy is a vesicular recycling pathway, known to be associated with either cell survival or cell death depending on the cancer and therapy. We previously demonstrated that crizotinib induced cytoprotective autophagy in ALK+ lymphoma cells and that its further intensification was associated with cell death. In line with these results, we show here that combined ALK and Rapidly Accelerated Fibrosarcoma 1 (RAF1) inhibition, using pharmacological (vemurafenib) or molecular (small interfering RNA targeting RAF1 (siRAF1) or microRNA-7-5p (miR-7-5p) mimics) strategies, also triggered autophagy and potentiated the toxicity of TKI. Mechanistically, we found that this combined therapy resulted in the decrease of the inhibitory phosphorylation on Unc-51-like kinase-1 (ULK1) (a key protein in autophagy initiation), which may account for the enforced autophagy and cytokilling effect. Altogether, our results support the development of ALK and RAF1 combined inhibition as a new therapeutic approach in ALK+ ALCL.

The NKL-code for innate lymphoid cells reveals deregulated expression of NKL homeobox genes HHEX and HLX in anaplastic large cell lymphoma (ALCL)

NKL homeobox genes encode developmental transcription factors and display an NKL-code according to their physiological expression pattern in hematopoiesis. Here, we analyzed public transcriptome data from primary innate lymphoid cells (ILCs) for NKL homeobox gene activities and found that ILC3 expressed exclusively HHEX while in ILC1 and ILC2 these genes were silenced. Deregulation of the NKL-code promotes hematopoietic malignancies, including anaplastic large cell lymphoma (ALCL) which reportedly may derive from ILC3. Accordingly, we analyzed NKL homeobox gene activities in ALCL cell lines and investigated their role in this malignancy. Transcriptome analyses demonstrated low expression levels of HHEX but powerfully activated HLX. Forced expression of HHEX in ALCL cell lines induced genes involved in apoptosis and ILC3 differentiation, indicating tumor suppressor activity. ALCL associated NPM1-ALK and JAK-STAT3-signalling drove enhanced expression of HLX while discounting HHEX. Genomic profiling revealed copy number gains at the loci of HLX and STAT3 in addition to genes encoding both STAT3 regulators (AURKA, BCL3, JAK3, KPNB1, NAMPT, NFAT5, PIM3, ROCK1, SIX1, TPX2, WWOX) and targets (BATF3, IRF4, miR135b, miR21, RORC). Transcriptome data of ALCL cell lines showed absence of STAT3 mutations while MGA was mutated and downregulated, encoding a novel potential STAT3 repressor. Furthermore, enhanced IL17F-signalling activated HLX while TGFbeta-signalling inhibited HHEX expression. Taken together, our data extend the scope of the NKL-code for ILCs and spotlight aberrant expression of NKL homeobox gene HLX in ALCL. HLX represents a direct target of ALCL hallmark factor STAT3 and deregulates cell survival and differentiation in this malignancy.

[Clinical characteristics and prognostic factors of 40 cases of primary systemic anaplastic large cell lymphoma]

Objective: To analyze the clinical features and prognostic factors of primary systemic anaplastic large cell lymphoma (ALCL) . Methods: 40 ALCL cases treated in the First Affiliated Hospital of Zhejiang University from January 2013 to December 2018 were retrospectively analyzed. Results: ① With a median age of 41 (14-67) years, there were 29 males and 11 females, 36 patients (90.0%) had Ann Arbor stage Ⅲ-Ⅳ tumors, 23 patients (57.5%) were in high-intermediate or high international prognostic index (IPI) risk group. 25 patients (62.5%) had B symptoms, such as fever, emaciation and night sweat.38 patients (95.0%) had extranodal invasion, 25 patients (62.5%) had higher LDH level, and 25 patients (62.5%) had high expression of Ki-67 (80% or more) . With 22 ALK(+) patients (55.0%) and 18 ALK(-) patients (45.0%) , there was a significantly difference in the median age of the two groups [29 (14-67) years old vs 51.5 (19-67) years old, P=0.003]. ② All patients received chemotherapy, 18 cases were treated with CHOP (cyclophosphamide, doxorubicin, vindesine, prednisone) , 12 cases with ECHOP (cyclophosphamide, doxorubicin, vindesine, prednisone, etoposide) , 10 cases with other treatments and 26 patients (65.0%) obtained complete remission (CR) . ALK(-) (P=0.029, OR=13.458) and Ki-67 expression of 80% or more (P=0.04, OR=14.453) were independent factors of CR rate, the CR rate of ECHOP chemotherapy was higher than CHOP chemotherapy (P=0.026) . ③ LDH level, IPI score, ALK expression and chemotherapy regimen had significantly effect on progression free survival (PFS) and overall survival (OS) (P<0.05) . Conclusion: The study shows that primary systemic ALCL usually occurs in males, the average age of ALK(+) patients were younger than ALK(-) patients. Most patients are in stage Ⅲ-Ⅳ with extranodal invasion, more than half of the patients have B symptoms, elevated LDH, and high expression of Ki-67. The expression level of Ki-67, ALK expression, and chemotherapy regimen have prognostic value for CR rate, the LDH level, IPI score, ALK expression and chemotherapy regimen for PFS and OS. ECHOP is a better choice with improved prognosis.

The γ-secretase inhibitor GSI-I interacts synergistically with the proteasome inhibitor bortezomib to induce ALK+ anaplastic large cell lymphoma cell apoptosis

Single agent treatment of the γ-secretase inhibitor (GSI-I) or proteasome inhibitor in anaplastic lymphoma kinase positive anaplastic large cell lymphoma (ALK+ ALCL) shows limited response and considerable toxicity. Here, we examined the effects of the combination of low dose GSI-I and the proteasome inhibitor bortezomib (BTZ) in ALK+ ALCL cells in vivo and in vitro. We found that ALK+ ALCL cells treated with the BTZ and GSI-I combination treatment showed elevated apoptosis, consistent with increased caspase activation, compared with BTZ or GSI-I alone. The combination treatment also inhibited AKT and extracellular signal-related kinase pathways, as well as stress-related cascades, including the c-jun N-terminal kinase and stress-activated kinases. Moreover, combined treatment in a murine xenograft model resulted in increased apoptosis in tumor tissues and reduced tumor growth. Our results reveal the synergistic anti-tumor effects of low dose inhibitors against γ-secretase and the proteasome and suggest the potential application of the tolerable BTZ/GSI-I combined agents in treating ALK+ ALCL in future clinical treatment.