Rosai-Dorfman disease in the central nervous system with two isolated lesions originated from a single clone: a case report

Background Rosai–Dorfman disease (RDD) is a rare, benign, idiopathic non-Langerhans cell histiocytosis. Cases of RDD in the CNS are extremely rare but lethal. RDD is thought to represent a reactive process. Recent studies proposed a subset of RDD cases that had a clonal nature. However, its clone origin is poorly understood. Case presentation We present a rare case of RDD in the CNS with two isolated lesions. These two lesions were removed successively after two operations. No seizure nor recurrence appears to date (2 years follow-up). Morphological and immunohistochemical profiles of these two lesions support the diagnosis of RDD. Based on the whole-exome sequencing (WES) data, we found the larger lesion has a higher tumor mutational burden (TMB) and more driver gene mutations than the smaller lesion. We also found seven common truncal mutations in these two lesions, raising the possibility that they might stem from the same ancestor clone. Conclusions Overall, this is the first report about clonal evolution of RDD in the CNS with two isolated lesions. Our findings contribute to the pathology of RDD, and support the notion that a subset of cases with RDD is a clonal histiocytic disorder driven by genetic alterations.

Molecular investigations on a chimeric strain of Staphylococcus aureus sequence type 80

An Eritrean patient was admitted with suspected tuberculous cervical lymphadenitis. While no mycobacteria were detected in pus from this process, culture yielded PVL-positive, methicillin-susceptible Staphylococcus aureus. Microarray hybridisation assigned the isolate to clonal complex (CC) 80 but revealed unusual features, including the presence of the ORF-CM14 enterotoxin homologue and of an ACME-III element as well as the absence of etD and edinB. The isolate was subjected to both, Illumina and Nanopore sequencing allowing characterisation of deviating regions within the strain’s genome. Atypical features of this strain were attributable to the presence of two genomic regions that originated from other S. aureus lineages and that comprised, respectively, 3% and 1.4% of the genome. One deviating region extended from walJ to sirB. It comprised ORF-CM14 and the ACME-III element. A homologous, but larger fragment was also found in an atypical S. aureus CC1/ST567 strain whose lineage might have served as donor of this genomic region. This region itself is a chimera comprising fragments from CC1 as well as fragments of unknown origin. The other region of another 3% of the genome comprised the region from htsB to ecfA2. It was very similar to CC1 sequences. This suggests either an incorporation of CC1 DNA into the study strain, or it might alternatively suggest a recombination event affecting “canonical” CC80. As the study strain bears witness of several recombination events, such complex and large-scale events cannot be rare and exceptional, despite a mainly clonal nature of S. aureus. Although the exact mechanism is not yet clear, chimerism seems to be an additional pathway in the evolution of S. aureus, possibly being responsible for the transmission also of virulence and resistance factors. An organism that can shuffle, swap or exchange major parts of its genome by a yet unknown mechanism would have an evolutionary advantage compared to a strictly clonal organism.

Histiocytosis

The histiocytoses are disorders derived from the dendritic cell and monocyte/macrophage lineages, with the classification of this group of disorders relating to the underlying cell of origin. Dendritic cell disorders—there has been much debate about the nature of these conditions, and their status as neoplastic or primary inflammatory diseases; for Langerhans’ cell histiocytosis in particular, there is increasing evidence of their clonal nature, as manifest by recurrent BRAF mutations. Clinical features and diagnosis—these are highly variable and dependent on the sites affected by histiocytic infiltration. Symptoms and signs may include rashes, bony pain, lymphadenopathy, hepatomegaly and splenomegaly, cough and dyspnoea, features of marrow failure, and endocrine presentations (classically diabetes insipidus). Diagnosis typically follows imaging and biopsy, with the demonstration of a histiocytic infiltrate confirmed by immunostaining. Treatment and prognosis—the rarity and heterogeneity of these diseases has made it difficult to achieve a consensus on treatment. For localized disease, curettage, steroid injections, or targeted radiotherapy may be helpful. For more systemic disease, combination chemotherapy is typically used. Treatment schedules differ between adults and children. Prognosis is dependent mainly on the site(s) of involvement. Our expanding appreciation of the molecular basis of these conditions also provides some justification for the use of BRAF inhibitors and other targeted small molecule therapies. Macrophage-related disorders—these include haemophagocytic lymphohistiocytosis, a collection of macrophage-activating syndromes which may be either reactive to underlying inflammatory, infective, or neoplastic disease, or consequent upon a primary genetic lesion affecting cytotoxic T-cell killing function. Rosai–Dorfman disease is a separate macrophage proliferation syndrome, thought to be non-neoplastic, which causes massive cervical lymphadenopathy, usually in children.

MRD evaluation of AML in clinical practice: are we there yet?

MRD technologies increase our ability to measure response in acute myeloid leukemia (AML) beyond the limitations of morphology. When applied in clinical trials, molecular and immunophenotypic MRD assays have improved prognostic precision, providing a strong rationale for their use to guide treatment, as well as to measure its effectiveness. Initiatives such as those from the European Leukemia Network now provide a collaborative knowledge-based framework for selection and implementation of MRD assays most appropriate for defined genetic subgroups. For patients with mutated-NPM1 AML, quantitative polymerase chain reaction (qPCR) monitoring of mutated-NPM1 transcripts postinduction and sequentially after treatment has emerged as a highly sensitive and specific tool to predict relapse and potential benefit from allogeneic transplant. Flow cytometric MRD after induction is prognostic across genetic risk groups and can identify those patients in the wild-type NPM1 intermediate AML subgroup with a very high risk for relapse. In parallel with these data, advances in genetic profiling have extended understanding of the etiology and the complex dynamic clonal nature of AML, as well as created the opportunity for MRD monitoring using next-generation sequencing (NGS). NGS AML MRD detection can stratify outcomes and has potential utility in the peri-allogeneic transplant setting. However, there remain challenges inherent in the NGS approach of multiplex quantification of mutations to track AML MRD. Although further development of this methodology, together with orthogonal testing, will clarify its relevance for routine clinical use, particularly for patients lacking a qPCR genetic target, established validated MRD assays can already provide information to direct clinical practice.

Within-host Mycobacterium tuberculosis evolution: a population genetics perspective

ABSTRACTThe within-host evolutionary dynamics of TB remain unclear, and underlying biological characteristics render standard population genetic approaches based upon the Wright-Fisher model largely inappropriate. In addition, the compact genome combined with an absence of recombination is expected to result in strong purifying selection effects. Thus, it is imperative to establish a biologically-relevant evolutionary framework incorporating these factors in order to enable an accurate study of this important human pathogen. Further, such a model is critical for inferring fundamental evolutionary parameters related to patient treatment, including mutation rates and the severity of infection bottlenecks. We here implement such a model and infer the underlying evolutionary parameters governing within-patient evolutionary dynamics. Results demonstrate that the progeny skew associated with the clonal nature of TB severely reduces genetic diversity and that the neglect of this parameter in previous studies has led to significant mis-inference of mutation rates. As such, our results suggest an underlying de novo mutation rate that is considerably faster than previously inferred, and a progeny distribution differing significantly from Wright-Fisher assumptions. This inference largely reconciles the seemingly contradictory observations of both rapid drug-resistance evolution but extremely low levels of genetic variation in both resistant and non-resistant populations.

The Biological Inferences from the Ranking of SF3B1 Mutations in the Clonal Hierarchy of Myeloid Neoplasia

Chromosomal abnormalities can be founder lesions (e.g., t (8; 21), inv (16), inv (3)), initiate or advance disease progression (both founder and secondary hits e.g., ASXL1, TP53, RUNX1) or can be obligatory secondary hits (FLT3, NPM1). Hence, the rank of these mutations may determine the biological properties and clinical outcomes. However, while many mechanistic studies have been undertaken without identifying the key pathogenetic factors resulting from SF3B1 mutations, important biological clues can be derived from the consequences of SF3B1 alterations in the context of the clonal architecture of myeloid neoplasia (MN). SF3B1 mutant patients often have a homogeneous phenotype with isolated erythroid dysplasia, ring sideroblasts (RS) and favorable prognoses. Studies in primary MDS cells have suggested that SF3B1 mutations are initiating lesions and provide a marked clonal advantage to MDS-RS cells by propagating from rare lympho-myeloid hematopoietic stem cells. However, there is significant diversity of clinical phenotypes and outcomes including the observation that the disappearance of RS can be observed during the disease course of clonal MN and might suggest cellular shifts due to acquisition of additional hits. In such scenarios, the cell's fate in the context of SF3B1 mutations is pre-defined by the predominance of expanded hits. We took advantage of our detailed database of molecularly and clinical annotated cases with MN to study the SF3B1 mutatome and describe whether the clonal nature (ancestral vs. secondary) might change the clinical and phenotypic trajectories of MDS cells and whether the concatenation of mutations decreases the competitiveness of SF3B1 clones, leading to the dominance of other driver genes and subsequently to clonal evolution. The clonal hierarchy was resolved using our in-house designed VAF-based bioanalytic method and confirmed by the PyClone pipeline, which showed a high level of concordance. We first assigned clonal hierarchy to SF3B1 mutations by using VAFs (adjusted for copy number and zygosity) and classifying the mutations into dominant (if a cutoff of at least 5% difference between VAFs existed), secondary (any subsequent sub-clonal hit) and co-dominant hits (if the difference of VAFs between two mutations was <5%). In total, we identified 140 dominant (SF3B1DOM), 121 secondary (SF3B1SEC) and 74 co-dominant SF3B1 mutations. For the purpose of this study, we set aside co-dominant SF3B1 mutations. Focusing on SF3B1DOM and SF3B1SEC, SF3B1DOM were often associated with a normocellular bone marrow compared to SF3B1SEC (n=42 vs. 26; P=0.02) and were less likely enriched in multi-dysplastic myeloid cells (29% vs. 53%; P=0.01). As such, SF3B1DOM tended to be more frequently detected in lower-risk MDS (P=0.05) in the subtypes of MDS-RS and MLD-RS (RS≥15%: 67% vs. 41%; P=0.01) compared to other disease subtypes. Twenty-three percent of patients with SF3B1SEC had secondary acute myeloid leukemia (sAML) (P=0.03). SF3B1SEC patients tended to have a lower median platelet count than patients with SF3B1DOM (97 vs. 130 x 109/L; P=0.05). SF3B1SEC was also more associated with bi-cytopenia compared to SF3B1DOM (52% vs. 36%; P=0.01). No specific association was found between SF3B1 clonal nature and cytogenetic abnormalities, suggesting that additional mutations might be the main contributors in the evolution of MDS to AML. Of note, patients with SF3B1SEC had half OS compared to patients with SF3B1DOM (SF3B1SECvs. SF3B1DOM: 15.9 mo. vs. 39.7 mo., P= 0.0001), suggesting that in cases evolving to AML, expanding hits might have dramatically skewed the favorable nature of SF3B1 mutations. Indeed, mutations preceding SF3B1 mainly affected lineage-restricted genes associated with repression of erythroid programs (RUNX1, 23%), terminal monocytic differentiation (TET2, 9%), transcriptional corepressors (BCOR/L1, 8%) and development of leukemia (DNMT3A, 8%). In conclusion, our study of the clonal architecture of SF3B1 mutations highlights that clonal progression of cases with MN harboring SF3B1 mutations might be inferred by the rank of additional genetic lesions cooperating with SF3B1. Disclosures Meggendorfer: MLL Munich Leukemia Laboratory: Employment. Advani:Abbvie: Research Funding; Macrogenics: Research Funding; Pfizer: Honoraria, Research Funding; Amgen: Research Funding; Glycomimetics: Consultancy, Research Funding; Kite Pharmaceuticals: Consultancy. Nazha:Tolero, Karyopharma: Honoraria; Novartis: Speakers Bureau; MEI: Other: Data monitoring Committee; Daiichi Sankyo: Consultancy; Jazz Pharmacutical: Research Funding; Incyte: Speakers Bureau; Abbvie: Consultancy. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Sekeres:Syros: Membership on an entity's Board of Directors or advisory committees; Millenium: Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees. Maciejewski:Alexion: Consultancy; Novartis: Consultancy.