scholarly journals Genomic Classification and Clinical Outcome in Rhabdomyosarcoma: A Report From an International Consortium

2021 ◽  
pp. JCO.20.03060
Author(s):  
Jack F. Shern ◽  
Joanna Selfe ◽  
Elisa Izquierdo ◽  
Rajesh Patidar ◽  
Hsien-Chao Chou ◽  
...  

PURPOSE Rhabdomyosarcoma is the most common soft tissue sarcoma of childhood. Despite aggressive therapy, the 5-year survival rate for patients with metastatic or recurrent disease remains poor, and beyond PAX-FOXO1 fusion status, no genomic markers are available for risk stratification. We present an international consortium study designed to determine the incidence of driver mutations and their association with clinical outcome. PATIENTS AND METHODS Tumor samples collected from patients enrolled on Children's Oncology Group trials (1998-2017) and UK patients enrolled on malignant mesenchymal tumor and RMS2005 (1995-2016) trials were subjected to custom-capture sequencing. Mutations, indels, gene deletions, and amplifications were identified, and survival analysis was performed. RESULTS DNA from 641 patients was suitable for analyses. A median of one mutation was found per tumor. In FOXO1 fusion-negative cases, mutation of any RAS pathway member was found in > 50% of cases, and 21% had no putative driver mutation identified. BCOR (15%), NF1 (15%), and TP53 (13%) mutations were found at a higher incidence than previously reported and TP53 mutations were associated with worse outcomes in both fusion-negative and FOXO1 fusion-positive cases. Interestingly, mutations in RAS isoforms predominated in infants < 1 year (64% of cases). Mutation of MYOD1 was associated with histologic patterns beyond those previously described, older age, head and neck primary site, and a dismal survival. Finally, we provide a searchable companion database ( ClinOmics ), containing all genomic variants, and clinical annotation including survival data. CONCLUSION This is the largest genomic characterization of clinically annotated rhabdomyosarcoma tumors to date and provides prognostic genetic features that refine risk stratification and will be incorporated into prospective trials.

2019 ◽  
Vol 1 (Supplement_2) ◽  
pp. ii16-ii16
Author(s):  
Takaaki Yanagisawa ◽  
Takaya Honda ◽  
Masatada Yamaoka ◽  
Masaharu Akiyama ◽  
Kohei Fukuoka ◽  
...  

Abstract BACKGROUND Brainstem tumours account for 10–15% of brain tumors in childhood. Diffuse intrinsic pontine glioma (DIPG) accounts for 60–80% of them and are diagnosed based on clinical findings and radiologic features. All the rest of tumours excluding DIPG are very rare, heterogeneous group of tumours including low-grade glioma and malignant embryonal tumors. It is often difficult to diagnose and decide treatment strategy for their rarity. METHODS To present our experience with atypical brainstem tumours, a retrospective chart review was conducted to identify eligible cases treated over a ten-year period. All tumors involving brainstem, felt not to be DIPGs for absence of clinical/neuroimaging features were included. Demographic information, pathological findings, neuroimaging characteristics, surgical and nonsurgical management plans, and survival data were collected for analysis. RESULTS Between April 2007 and March 2017, 16 patients (14 initial and 2 recurrent) aged from 3 to 20 years were identified. 14 of them were symptomatic and 4 of them were asymptomatic at reference. Of 10 symptomatic cases, 10 were biopsied and pathological diagnosis was low-grade glioma in 8, glioblastoma in 2 cases. They had treatment depending on the pathological diagnosis. Of 4 asymptomatic cases, one with small focal tumour, with no findings suggesting malignant tumour with 11C-methioninePET or MRS, progressed to show typical clinical and image findings of DIPG in a year. For other three, they remain asymptomatic without progression with no treatment for 25months, 60months, and 65 months respectively. Malignant transformation was observed in one with biopsy-conformed oligoastrocytoma with no K27M-H3 mutations treated with chemotherapy and another with pilocytic astrocytoma treated with chemotherapy and radiotherapy. CONCLUSIONS Though molecular findings such as K27M-H3 mutations can predict clinical outcome in some cases, it still remains difficult to diagnose and find treatment strategy of atypical brainstem tumours. The need and usefulness of nationwide registry study is warranted.


Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 1599-1599 ◽  
Author(s):  
Yoseph Elala ◽  
Terra L. Lasho ◽  
Naseema Gangat ◽  
Christy Finke ◽  
A Kamel Abou Hussein ◽  
...  

Abstract Background : In essential thrombocythemia (ET) , ̴ 85% of patients harbor one of three "driver" mutations, with mutational frequencies of approximately 58%, 23% and 4%, for JAK2, CALR and MPL, respectively; ̴ 15% are wild type for all three mutations and are operationally referred to as "triple negative" (Blood. 2014;124:2507). In one of the original descriptions on CALR mutations, CALR -mutated patients with ET, compared to their JAK2-mutated counterparts, were reported to have better survival (NEJM. 2013;369:2379). However, this observation was not supported by subsequent studies while other reports suggested differential prognostic effect from distinct CALR variants in myelofibrosis (Blood. 2014;124:2465). In this study, we sought to clarify the impact of all three mutations, and CALR variants, on overall (OS), myelofibrosis-free (MFS) and leukemia-free (LFS) survival. Methods: Patientswere selected from our institutional database of myeloproliferative neoplasms, based on availability of mutational status inforomation. ET diagnosis was according to WHO criteria (Blood. 2009;114:937). Published methods were used for CALR, JAK2 and MPL mutation analyses and determination of CALR variants (Blood. 2014;124:2465). Kaplan-Meier survival analysis was considered from the date of diagnosis to date of death or last contact. MFS and LFS calculations considered fibrotic or leukemic transformation events as uncensored variables, respectively. Cox proportional hazard regression model was used for multivariable analysis. Results : A total of 502 patients (median age 59 year; 61% females) met study eligibility criteria. Median levels of hemoglobin, platelet count and leukocyte counts were 13.7 g/dL, 893 x 10 (9)/L and 8.8 x 10(9)/L, respectively. All patients were annotated for JAK2/CALR/MPL mutations as well as CALR variants; 324 harbored JAK2, 111 CALR and 13 MPL mutations; 54 patients were triple-negative. The 111 CALR-mutated patients included type 1 (n=55), type 2 (n=41) or other (n=15) CALR variants. At a median follow-up time of 9.9 years, 172 (34.3%) deaths, 42 (8.4%) fibrotic progressions, 15 (3%) blast transformations and 12 (2.4%) polycythemic conversions were documented. In univariate analysis, survival data appeared significantly better in "triple negative" patients (median not reached) and inferior in MPL-mutated cases (median 8.5 years) whereas median survival times were similar for JAK2 (18.5 years) and CALR (22.1 years) mutated cases (Figure 1; p=0.0006). However, the difference in survival was no longer apparent (p=0.60) during multivariable analysis that included age and sex, which are known to differentially cluster with specific driver mutations; in the current study, median age/sex distributions for "triple-negative", CALR, JAK2 and MPL mutated cases were 44 years/72% females, 48 years/46% females, 60 years/65% females, 70 years/46% females, respectively (p=<0.0001/0.0007). Of note, both age and sex were independently predictive of shortened survival. OS data remained unchanged when CALR-mutated patients were further stratified into type 1 vs type 2 vs other CALR variants, with similar survival data between the three CALR mutation groups (p=0.98). In univariate analysis, MPL-mutated patients were significantly more prone to fibrotic progression (Figure 2; p=0.0083). The prognostic relevance of MPL mutations to MFS remained significant when age and sex were included in multivariable analysis (p=0.008). In the current cohort, univariate analysis identified lower hemoglobin and lower platelet count as the only other risk factors for fibrotic progression. Multivariable analysis confirmed the independent prognostic relevance of MPL mutations (p=0.003), lower hemoglobin level (p=0.0009) and lower platelet count (p=0.0094) for MFS. There was no significant difference in LFS among the four driver mutational categories (p=0.9): 9 events in JAK2, 6 in CALR, none in triple negative and none in MPL mutated cases. Among the 6 leukemic transformations in CALR-mutated cases, three were type 1, two type 2, and one other CALR variants. Conclusions : Age- and sex-adjusted survival is similar among ET patients with JAK2 vs CALR vs MPL vs "triple-negative" mutational status. Survival is also similar between patients with distinct CALR variants. MPL -mutated patients with ET might be at a higher risk of fibrotic progression. Figure 1. Figure 1. Figure 2. Figure 2. Disclosures Pardanani: Stemline: Research Funding.


2013 ◽  
Vol 31 (15_suppl) ◽  
pp. e14639-e14639
Author(s):  
Anna Koutoulaki ◽  
Zafeiris Zafeiriou ◽  
Dimitra Skalidaki ◽  
Despoina Aggouraki ◽  
Kiriaki E Vetsika ◽  
...  

e14639 Background: Immune suppressive cells,Myeloid-Derived Suppressor Cells (MDSCs) and T Regulatory Cells (Tregs) have been identified as negative prognostic biomarkers in distinct solid tumors. In colorectal cancer (CRC), increased peripheral levels of MDSCs have been correlated to worse survival (Solito S et al.; Blood 2011). Although Tregs infiltrated in tumors have been associated with favourable clinical outcome (Salama P et al.; JCO 2009), their significance in peripheral blood remains unclear. The aim of the present study was to evaluate the role of these cells in the peripheral blood as a prognostic marker in CRC patients. Methods: Blood sample was collected from 49 CRC naïve patients (Stage IV) prior to 1st line treatment and 33 healthy donors. Flow cytometric analysis of MDSCs (HLA-DR-Lin-/lowCD33+CD11b+) and Tregs (CD3+CD4+CD25 highCD127low/-FoxP3+CD39+) was performed in fresh samples. MDSC and Treg levels of patients and normal controls were analyzed by using unpaired t-test. ROC analysis (area = 0.8539) was used to define high versus low MDSC levels, whereas the median value of Tregs in normal controls was used as a cut-off. Among patients that relapsed, Kaplan-Meier analysis was used to compare time to tumor progression (TTP) with high and low levels of MDSCs and Tregs. Results: The median percentages of MDSCs and Tregs in patients were significantly increased compared to controls (Mann Whitney test: p < 0.0001; p = 0.0111, respectively). MDSCs were positively correlated to Treg levels (Spearman's r2 = +0.408; p = 0.048). Patients with high levels of MDSCs at baseline, but not Tregs (p = 0.7165), relapsed earlier to those with low levels (p= 0.0348; 9.83 vs. 4.93 months, respectively). Conclusions: CRC patients have elevated peripheral levels of immunosuppressive cells. MDSCs seem to be an independent prognostic factor for TTP. The significance of the observed correlation of MDSCs with Tregs and the suppressive mechanisms of these cells will be further investigated. Updated survival data will be presented in an increased cohort of patients.


2019 ◽  
Vol 37 (15_suppl) ◽  
pp. 11044-11044 ◽  
Author(s):  
Junaid Arshad ◽  
Ali Roberts ◽  
Jared Addison Cotta ◽  
Jonathan C. Trent

11044 Background: Leiomyosarcoma is a malignant mesenchymal tumor of cells of smooth muscle lineage arising commonly in retroperitoneum, uterus, large veins, and the limbs. In contrast to many sarcomas, the genetics of leiomyosarcomas are complex and there is very limited understanding of common driver mutations. Circulating Tumor DNA (ctDNA) offers a rapid and non-invasive method of next-generation sequencing (NGS) that could be utilized for diagnosis, therapy and detection of recurrence. Methods: ctDNA testing was performed using Guardant360, which detects single nucleotide variants, amplifications, fusions, and specific insertion/deletion mutations in 73 genes utilizing NGS. Blood samples from patients with leiomyosarcoma were analyzed, and results from December 2014-December 2018 were reviewed. Results: Of the 90 samples collected and analyzed, alterations were detected in 73 ctDNA samples. After exclusion of variants of uncertain significance (VUS), 63 ctDNA samples harbored cancer-associated genomic alterations. Of 73 patients, 59 were found to have one or more cancer-associated genomic alteration. 76% (45) were female with a median age of 63 (range, 38-87) years. All samples were designated metastatic. The following table shows common alterations and types of mutations. The other alterations included RAF1, ERBB2, MET, PTEN, TERT, APC and NOTCH1. In 24 of the 73 patients (33%) the genomic alterations detected by ctDNA are potentially targetable by an FDA-approved or clinical trial therapy. There were 4 (5%) patients who were found to have incidental germline TP53 mutations. Conclusions: NGS of ctDNA allows identification of genomic alterations in plasma from patients with leiomyosarcoma. Unfortunately, there is limited activity of targeted agents in leiomyosarcomas. These results suggest opportunities to develop therapy against TP53, cell cycle, and kinase signaling pathways. Further validation and prospective evaluation is warranted to investigate the clinical utility of ctDNA for patients with leiomyosarcoma.[Table: see text]


2021 ◽  
Author(s):  
Riku Klen ◽  
Disha Purohit ◽  
Ricardo Gomez-Huelgas ◽  
Jose Manuel Casas-Rojo ◽  
Juan Miguel Anton Santos ◽  
...  

Summary: Background More contagious SARS-CoV-2 virus variants, breakthrough infections, waning immunity, and differential access to COVID-19 vaccines account for the worst yet numbers of hospitalization and deaths during the COVID-19 pandemic, particularly in resource-limited countries. There is an urgent need for clinically valuable, generalizable, and parsimonious triage tools assisting the appropriate allocation of hospital resources during the pandemic. We aimed to develop and extensively validate a machine learning-based tool for accurately predicting the clinical outcome of hospitalized COVID-19 patients. Methods: CODOP was built using modified stable iterative variable selection and linear regression with lasso regularisation. To avoid generalization problems, CODOP was trained and tested with three time-sliced and geographically distinct cohorts encompassing 40 511 blood-based analyses of COVID-19 patients from more than 110 hospitals in Spain and the USA during 2020-21. We assessed the discriminative ability of the model using the Area Under the Receiving Operative Curve (AUROC) as well as horizon and Kaplan-Meier risk stratification analyses. To reckon the fluctuating pressure levels in hospitals through the pandemic, we offer two online CODOP calculators suited for undertriage or overtriage scenarios. We challenged their generalizability and clinical utility throughout an evaluation with datasets gathered in five hospitals from three Latin American countries. Findings: CODOP uses 12 clinical parameters commonly measured at hospital admission and associated with the pathophysiology of COVID-19. CODOP reaches high discriminative ability up to nine days before clinical resolution (AUROC: 0.90-0.96, 95% CI 0.879-0.970), it is well calibrated, and it enables an effective dynamic risk stratification during hospitalization. The two CODOP online calculators predicted the clinical outcome of the majority of patients (73-100% sensitivity and 84-100% specificity) from the distinctive Latin American evaluation cohort. Interpretation: The high predictive performance of CODOP in geographically disperse patient cohorts and the easiness-of-use, strongly suggest its clinical utility as a global triage tool, particularly in resource-limited countries.


2021 ◽  
Author(s):  
Nicole Thomas ◽  
Kostiantyn Dreval ◽  
Daniela S. Gerhard ◽  
Laura K. Hilton ◽  
Jeremy S. Abramson ◽  
...  

AbstractBurkitt lymphoma (BL) accounts for the majority of pediatric non-Hodgkin lymphomas (NHL) and is relatively rare but significantly more lethal when diagnosed in adults. The global incidence is highest in Sub-Saharan Africa, where Epstein-Barr virus (EBV) positivity is observed in 95% of all tumors. Both pediatric (pBL) and adult (aBL) cases are known to share some driver mutations, for example MYC translocations, which are seen in > 90% of cases. Sequencing efforts have identified many common somatic alterations that cooperate with MYC in lymphomagenesis with approximately 30 significantly mutated genes (SMG) reported thus far. Recent analyses revealed non-coding mutation patterns in pBL that were attributed to aberrant somatic hypermutation (aSHM). We sought to identify genomic and molecular features that may explain clinical disparities within and between aBL and pBL in an effort to delineate BL subtypes that may allow for the stratification of patients with shared pathobiology. Through comprehensive sequencing of BL genomes, we found additional SMGs, including more genetic features that associate with tumor EBV status, and established three new genetic subgroups that span pBL and aBL. Direct comparisons between pBL and aBL revealed only marginal differences and the mutational profiles were consistently better explained by EBV status. Using an unsupervised clustering approach to identify subgroupings within BL and diffuse large B-cell lymphoma (DLBCL), we have defined three genetic subgroups that predominantly comprise BL tumors. Akin to the recently defined DLBCL subgroups, each BL subgroup is characterized by combinations of common driver mutations and non-coding mutations caused by aSHM. Two of these subgroups and their prototypical genetic features (ID3 and TP53) had significant associations with patient outcomes that were different among the aBL and pBL cohorts. These findings highlight not only a shared pathogenesis between aBL and pBL, but also establish genetic subtypes within BL that serve to delineate tumors with distinct molecular features, providing a new framework for epidemiological studies, and diagnostic and therapeutic strategies.


2019 ◽  
Vol 65 (1) ◽  
pp. 69-76
Author(s):  
Foat Akhmetzyanov ◽  
Sergey Petrov ◽  
Dinar Khalikov

In this review presented the most relevant scientific information on the molecular and genetic features of gastrointestinal stromal tumors (GISTs). GISTs is a heterogeneous group of mesenchymal neoplasms of the gastrointestinal tract, which according to modern ideas originate from the interstitial cells of Cajal. It was found that this disease is largely somatic mutations: in the overwhelming majority of cases, activating mutations in kit or PDGFRA genes that encode effector tyrosine kinases are found in tumor cells. Constitutive activation of these enzymes triggers a complex cascade of intracellular reactions, the result of which is the enhancement of cell proliferation and tumor growth. In the absence of the above-mentioned driver mutations, the GISTs is referred to as a “wild type”. The profile of mutations affects the aggressiveness of the GISTs flow and the sensitivity to target antitumor drugs. Thus, carrying out a mutational analysis in the case of a GISTs is of great prognostic significance.


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