The path towards consensus genome classification of diffuse large B-cell lymphoma for use in clinical practice

Diffuse large B-cell lymphoma (DLBCL) is a widely heterogeneous disease in presentation, treatment response and outcome that results from a broad biological heterogeneity. Various stratification approaches have been proposed over time but failed to sufficiently capture the heterogeneous biology and behavior of the disease in a clinically relevant manner. The most recent DNA-based genomic subtyping studies are a major step forward by offering a level of refinement that could serve as a basis for exploration of personalized and targeted treatment for the years to come. To enable consistent trial designs and allow meaningful comparisons between studies, harmonization of the currently available knowledge into a single genomic classification widely applicable in daily practice is pivotal. In this review, we investigate potential avenues for harmonization of the presently available genomic subtypes of DLBCL inspired by consensus molecular classifications achieved for other malignancies. Finally, suggestions for laboratory techniques and infrastructure required for successful clinical implementation are described

Large B-cell Lymphomas of Immune-Privileged Sites Relapse via Parallel Clonal Evolution from a Common Progenitor B Cell

Large B-cell lymphoma of immune-privileged sites (LBCL-IP) arise in immune sanctuaries including the testis and central nervous system (CNS). After initially reaching complete response, relapses occur in almost 50% of patients, typically at other immune-privileged sites. Resolution of the clonal relationships and evolutionary patterns of LBCL-IP is required to understand the unique clinical behavior. We collected a unique set of 33 primary-relapse LBCL-IP sample pairs and performed next-generation sequencing for copy number, mutation, translocation, and immunoglobulin clonality analysis. All LBCL-IP sample pairs were clonally related, and both tumors developed from a common progenitor cell (CPC) with MYD88 and TBL1XR1 mutations and/or BCL6 translocations in 30/33 cases, indicating that these are early genetic events. This was succeeded by intermediate genetic events including shared, as well as unique alterations in targets of aberrant somatic hypermutation (aSHM), CD79B mutations, and 9p21.3/CDKN2A loss. Genetic alterations in genes involved in immune escape (HLA, CD274/PDCD1LG2) were predominantly unique in primary and relapse samples and thus considered late genetic events. Together, this study indicates that primary and relapsed LBCL-IP follow an early parallel evolutionary pattern where the CPC contains genetic alterations that support prolonged survival/proliferation and retention in a memory B-cell state, followed by germinal center reentry, aSHM and immune escape. SIGNIFICANCE: Genomic analyses reveal that primary and relapse LBCL-IP originate from a common progenitor cell with a small set of genetic alterations, followed by extensive parallel diversification, elucidating the clonal evolution of LBCL-IP

An Acquired Vulnerability of Drug-Resistant Melanoma with Therapeutic Potential

BRAF(V600E) mutant melanomas treated with inhibitors of the BRAF and MEK kinases almost invariably develop resistance that is frequently caused by reactivation of the mitogen activated protein kinase (MAPK) pathway. To identify novel treatment options for such patients, we searched for acquired vulnerabilities of MAPK inhibitor-resistant melanomas. We find that resistance to BRAF+MEK inhibitors is associated with increased levels of reactive oxygen species (ROS). Subsequent treatment with the histone deacetylase inhibitor vorinostat suppresses SLC7A11, leading to a lethal increase in the already-elevated levels of ROS in drug-resistant cells. This causes selective apoptotic death of only the drug-resistant tumor cells. Consistently, treatment of BRAF inhibitor-resistant melanoma with vorinostat in mice results in dramatic tumor regression. In a study in patients with advanced BRAF+MEK inhibitor-resistant melanoma, we find that vorinostat can selectively ablate drug-resistant tumor cells, providing clinical proof of concept for the novel therapy identified here

An Acquired Vulnerability of Drug-Resistant Melanoma with Therapeutic Potential

BRAF(V600E) mutant melanomas treated with inhibitors of the BRAF and MEK kinases almost invariably develop resistance that is frequently caused by reactivation of the mitogen activated protein kinase (MAPK) pathway. To identify novel treatment options for such patients, we searched for acquired vulnerabilities of MAPK inhibitor-resistant melanomas. We find that resistance to BRAF+MEK inhibitors is associated with increased levels of reactive oxygen species (ROS). Subsequent treatment with the histone deacetylase inhibitor vorinostat suppresses SLC7A11, leading to a lethal increase in the already-elevated levels of ROS in drug-resistant cells. This causes selective apoptotic death of only the drug-resistant tumor cells. Consistently, treatment of BRAF inhibitor-resistant melanoma with vorinostat in mice results in dramatic tumor regression. In a study in patients with advanced BRAF+MEK inhibitor-resistant melanoma, we find that vorinostat can selectively ablate drug-resistant tumor cells, providing clinical proof of concept for the novel therapy identified here

Chromosome 20 loss is characteristic of breast implant-associated anaplastic large cell lymphoma

Breast implant-associated anaplastic large cell lymphoma (BIA-ALCL) is a very rare type of T-cell lymphoma that is uniquely caused by a single environmental stimulus. Here, we present a comprehensive genetic analysis of a relatively large series of BIA-ALCL (n = 29), for which genome-wide chromosomal copy number aberrations (CNAs) and mutational profiles for a subset (n = 7) were determined. For comparison, CNAs for anaplastic lymphoma kinase (ALK)- nodal anaplastic large cell lymphomas (ALCLs; n = 24) were obtained. CNAs were detected in 94% of BIA-ALCLs, with losses at chromosome 20q13.13 in 66% of the samples. Loss of 20q13.13 is characteristic of BIA-ALCL compared with other classes of ALCL, such as primary cutaneous ALCL and systemic type ALK+ and ALK- ALCL. Mutational patterns confirm that the interleukin-6-JAK1-STAT3 pathway is deregulated. Although this is commonly observed across various types of T-cell lymphomas, the extent of deregulation is significantly higher in BIA-ALCL, as indicated by phosphorylated STAT3 immunohistochemistry. The characteristic loss of chromosome 20 in BIA-ALCL provides further justification to recognize BIA-ALCL as a separate disease entity. Moreover, CNA analysis may serve as a parameter for future diagnostic assays for women with breast implants to distinguish seroma caused by BIA-ALCL from other causes of seroma accumulation, such as infection or trauma

Genetic and Microenvironment Features Do Not Distinguish Follicular Lymphoma Patients Requiring Immediate or Deferred Treatment

International audienc

Genomic and microenvironmental landscape of stage I follicular lymphoma, compared with stage III/IV

Although the genomic and immunemicroenvironmental landscape of follicular lymphoma (FL) has been extensively investigated, little is known about the potential biological differences between stage I and stage III/IV disease. Using next-generation sequencing and immunohistochemistry, 82 FL nodal stage I caseswere analyzed and comparedwith 139 FL stage III/IV nodal cases.Many similarities in mutations, chromosomal copy number aberrations, and microenvironmental cell populationswere detected. However, therewere also significant differences inmicroenvironmental and genomic features. CD8- T cells (P= .02) and STAT6 mutations (false discovery rate [FDR],0.001)weremore frequent in stage I FL. In contrast, programmed cell death protein 1-positive T cells, CD68-/CD163- macrophages (P<.001), BCL2 translocation (BCL2trl-) (P< .0001), and KMT2D (FDR= 0.003) and CREBBP (FDR= 0.04) mutationswere foundmore frequently in stage III/IV FL. Using clustering,we identified 3 clusters within stage I, and 2 clusterswithin stage III/IV. The BLC2trl- stage I clusterwas comparable to the BCL2trl- cluster in stage III/IV. The two BCL2trl- stage I clusters were unique for stage I. One was enriched for CREBBP (95%) andSTAT6 (64%)mutations,without BLC6 translocation (BCL6trl), whereas the BCL2trl- stage III/IV cluster contained BCL6trl (64%)with fewer CREBBP (45%) andSTAT6 (9%)mutations. The other BCL2trl- stage I clusterwas relatively heterogeneouswith more copy number aberrations and linker histonemutations. This exploratory study shows that stage I FL is genetically heterogeneouswith different underlying oncogenic pathways. Stage I FL BCL2trl- is likely STAT6 driven,whereas BCL2trl- stage III/IV appears to bemore BCL6trl driven

Genomic and microenvironmental landscape of stage I follicular lymphoma, compared with stage III/IV

Although the genomic and immunemicroenvironmental landscape of follicular lymphoma (FL) has been extensively investigated, little is known about the potential biological differences between stage I and stage III/IV disease. Using next-generation sequencing and immunohistochemistry, 82 FL nodal stage I caseswere analyzed and comparedwith 139 FL stage III/IV nodal cases.Many similarities in mutations, chromosomal copy number aberrations, and microenvironmental cell populationswere detected. However, therewere also significant differences inmicroenvironmental and genomic features. CD8- T cells (P= .02) and STAT6 mutations (false discovery rate [FDR],0.001)weremore frequent in stage I FL. In contrast, programmed cell death protein 1-positive T cells, CD68-/CD163- macrophages (P<.001), BCL2 translocation (BCL2trl-) (P< .0001), and KMT2D (FDR= 0.003) and CREBBP (FDR= 0.04) mutationswere foundmore frequently in stage III/IV FL. Using clustering,we identified 3 clusters within stage I, and 2 clusterswithin stage III/IV. The BLC2trl- stage I clusterwas comparable to the BCL2trl- cluster in stage III/IV. The two BCL2trl- stage I clusters were unique for stage I. One was enriched for CREBBP (95%) andSTAT6 (64%)mutations,without BLC6 translocation (BCL6trl), whereas the BCL2trl- stage III/IV cluster contained BCL6trl (64%)with fewer CREBBP (45%) andSTAT6 (9%)mutations. The other BCL2trl- stage I clusterwas relatively heterogeneouswith more copy number aberrations and linker histonemutations. This exploratory study shows that stage I FL is genetically heterogeneouswith different underlying oncogenic pathways. Stage I FL BCL2trl- is likely STAT6 driven,whereas BCL2trl- stage III/IV appears to bemore BCL6trl driven