Genomic drivers of large B-cell lymphoma resistance to CD19 CAR-T therapy

ABSTRACTChimeric antigen receptor-reprogrammed autologous T cells directed to CD19 are breakthrough immunotherapies for heavily pretreated patients with aggressive B-cell lymphomas but still fail to cure most patients. Host inflammatory and tumor microenvironmental factors associate with CAR-19 resistance, but the tumor-intrinsic factors underlying these phenomena remain undefined. To characterize genomic drivers of resistance, we interrogated whole genome sequencing of 30 tumor samples from 28 uniformly CAR-19-treated large-cell lymphoma patients. We reveal that patterns of genomic complexity (i.e., chromothripsis and APOBEC mutational activity), and distinct genomic alterations (deletions of RB1 or RHOA) associate with more exhausted immune microenvironments and poor outcome after CAR-19 therapy. Strikingly, pretreatment reduced expression or sub-clonal mutation of CD19 did not affect responses, suggesting CAR-19 therapy successes are due not only to direct antigen-dependent cytotoxicity but require surmounting immune exhaustion in tumor microenvironments to permit broader host responses that eliminate tumors.

Genomic based analyses reveal unique mutational profiling and identify prognostic biomarker for overall survival in Chinese small-cell lung cancer

Objective As an aggressive subtype of lung cancer, small-cell lung cancer (SCLC) presents a poor prognosis. Although molecular and clinical characteristics have been established for SCLC, limited investigation has been performed for predicting survival of SCLC patients. Methods Genomic alterations were profiled in Chinese SCLC patients (N = 37) using targeted sequencing. Clonal mutation burden (CMB) integrated the number of mutations with the clonal structure of the tumor. Specific pathways involving DNA damage repair (DDR) and cell cycle as well as CMB were studied as potential biomarkers for prognosis of SCLC. Results TP53 and RB1 gene mutations were the most common alterations (91.9% and 83.8%, respectively), followed by LRP1B, FAM135B, SPTA1, KMT2D, FAT1, and NOTCH3. Survival analysis revealed that mutation status of the DDR pathway was associated with worse OS in our cohort. Importantly, patients with higher CMB exhibited worse OS in our cohort and this observation was successfully validated in the cBioportal cohort. Moreover, multivariate analysis demonstrated CMB as a promising independent prognostic factor for OS in Chinese SCLC patients. Interestingly, patients with loss of function of RB1, validated by immunohistochemistry staining, appeared to have worse OS. Conclusions The mutational profiling of Chinese SCLC patients signified an ethnicity dependent component. CMB was firstly found to be associated with OS of Chinese SCLC patients and could be regarded as a prognostic marker for SCLC.

How many samples are needed to infer truly clonal mutations from heterogenous tumours?

BackgroundModern cancer treatment strategies aim to target tumour specific genetic (or epigenetic) alterations. Treatment response improves if these alterations are clonal, i.e. present in all cancer cells within tumours. However, the identification of truly clonal alterations is impaired by the tremendous intra-tumour genetic heterogeneity and unavoidable sampling biases.MethodsHere, we investigate the underlying causes of these spatial sampling biases and how the distribution and sizes of biopsies in sampling protocols can be optimized to minimize such biases.ResultsWe find that in the ideal case, less than a handful of samples can be enough to infer truly clonal mutations. The frequency of the largest sub-clone at diagnosis is the main factor determining the accuracy of truncal mutation estimation in structured tumours. If the first sub-clone is dominating the tumour, higher spatial dispersion of samples and larger sample size can increase the accuracy of the estimation. In such an improved sampling scheme, fewer samples will enable the detection of truly clonal alterations with the same probability.ConclusionsTaking spatial tumour structure into account will decrease the probability to misclassify a sub-clonal mutation as clonal and promises better informed treatment decisions.

New challenges in evaluating anemia in older persons in the era of molecular testing

Anemia is common in older persons, and often remains unexplained despite a thorough clinical history, physical examination, and focused laboratory testing, including marrow aspiration, biopsy, and karyotyping. The advent of molecular genetic testing panels in hematology clinical practice has complicated the evaluation of older patients with unexplained anemia. While the presence of a somatic mutation provides evidence of clonal hematopoiesis and may support a diagnosis of a hematologic neoplasm such as one of the myelodysplastic syndromes (MDS), with rare exceptions, individual mutations are not strongly associated with one specific diagnosis, nor are they by themselves diagnostic of neoplasia. A clonal mutation in a patient with cytopenias and a nondiagnostic bone marrow may indicate a syndrome with a similar natural history to MDS, but at present there are no clear criteria to distinguish cytopenias coincidentally seen in association with an unrelated clonal mutation from cytopenias that are directly caused by that mutation. Ongoing and planned analyses will help define when mutation patterns alone can identify a disorder equivalent to a morphologically defined myeloid neoplasm such as MDS, further clarifying the etiology and natural history of unexplained anemia in the elderly.

Comparative Analysis of Selective Clonal Mutation with Conventional GA Operators in Solar Tracking Environment

Genetic Algorithm (GA) belongs to elementary stochastic optimization algorithms inspired by evolution.It points out the ability of simple representations using bit strings to encode complicated structures and the power of simple transformations to reach the desired solution. Research shows that a new operator namely Selective Clonal Mutation (SCM) for better genetic solutions has been successfully developed so that faster convergence to the best desired solution could be obtained. This operator has produced the best fitness value as compared to the conventional genetic algorithm result within 50 generation, Selective Clonal Mutation (SCM) is able to produce the best fitness value at 0.01731 with optimum voltage 10.05V in solar tracking environment.

JAK2 Negative Polycythemia Vera

ABSTRACTPolycythemia vera (PV) is a stem cell disorder, characterized as a panhyperplastic, malignant, and neoplastic marrow disorder. Several reasons suggest that a mutation on the Janus kinase-2 gene (JAK2) is the most probable candidate gene involved in PV pathogenesis, as JAK2 is directly involved in intracellular signaling, following its exposure to cytokines, to which PV progenitor cells display hypersensitivity. A recurrent unique acquired clonal mutation in JAK2 was found in most patients with PV and other myeloproliferative diseases (MPDs). A female patient of age 50 years, presented with hemiplegia, diplopia, and had a consistent rise in hemoglobin and hematocrit. Serum Erythropoietin (Epo) was decreased. JAK2 mutation analysis was found to be negative. A diagnosis of polycythemia vera was made on the basis of the British Committee for Standards in Hematology (BCSH) guidelines.