scholarly journals RARE-26. WHOLE GENOME SEQUENCING OF AN OSSEOUS METASTASIS DURING CHECKPOINT-CONTROLLED INTRACRANIAL GLIOBLASTOMA REVEALS NEW INSIGHTS INTO POTENTIAL MECHANISMS OF IMMUNE ESCAPE

2019 ◽  
Vol 21 (Supplement_6) ◽  
pp. vi227-vi227
Author(s):  
Malte Mohme ◽  
Cecile Maire ◽  
Simon Schliffke ◽  
Simon Joosse ◽  
Malik Alawi ◽  
...  
Keyword(s):  
T Cell ◽  
Bone Metastasis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Cell Response ◽  
Immune Escape ◽  
T Cell Response ◽  
Molecular Profile ◽  
Whole Genome ◽  
Checkpoint Inhibition

Abstract Glioblastoma (GBM) has a devastating prognosis and recent advances in the treatment of a variety of cancer entities, e.g. through checkpoint inhibition, could so far not be translated into improved outcome in newly-diagnosed GBM. Characterizing rare cases of peripheral metastases which succeeded in overcoming immune control, can help to understand the mechanisms of immune escape. Here we describe the first reported case of a detailed genetic and immunological characterization of a peripheral bone metastasis from a GBM which was controlled intracranially by anti-PD1 checkpoint inhibition We performed whole genome sequencing (WGS) of the primary- and recurrent tumor, as well as the bone metastasis. Genomic data was analyzed for copy number variations and mutational profiles. In addition, immune monitoring with flow cytometric phenotyping and next-generation sequencing of the peripheral T-cell repertoire was used. A 70-year old patient developed multiple osseous metastases in the spine, while his IDHwt GBM recurrence was immunologically controlled with checkpoint inhibition. Biopsy confirmed peripheral GBM metastases. Immunophenotyping reflected the effective activation of the peripheral T-cell response, with, however, simultaneous upregulation of regulatory T-cells during disease progression. WGS sequencing demonstrated a distinct molecular profile of the GBM metastasis, with amplifications in chromosome 3 and 9, as well as genomic loss on chromosomes 4, 10 and 11. The peripheral metastasis was distinguished by mutations in mismatch repair genes, such as MSH4 and MLH1, associated with a hypermutated phenotype. Among the mutated genes we found potential candidates involved in immune escape of circulating tumor cells. This case represents a unique opportunity to analyze potential mechanisms of GBM-mediated immune escape during immune activation with anti-PD1 checkpoint therapy. It highlights the fact, that although an effective, disinhibited immune response can control the cranial GBM disease, hypermutated tumor clones can evade the tumor-specific T-cell response and disseminate to distant organs.

Discovery of Novel Recurrent Mutations in Childhood Early T-Cell Precursor Acute Lymphoblastic Leukemia by Whole Genome Sequencing - a Report From the St Jude Children's Research Hospital - Washington University Pediatric Cancer Genome Project

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 68-68
Author(s):  
Jinghui Zhang ◽  
Li Ding ◽  
Linda Holmfeldt ◽  
Gang Wu ◽  
Susan L. Heatley ◽  
...  
Keyword(s):  
Gene Expression ◽  
Acute Lymphoblastic Leukemia ◽  
T Cell ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Lymphoblastic Leukemia ◽  
Whole Genome ◽  
Structural Variants ◽  
Cell Precursor ◽  
Recurrent Mutations

Abstract Abstract 68 Early T-cell precursor acute lymphoblastic leukemia (ETP ALL) is characterized by an immature T-lineage immunophenotype (cCD3+, CD1a-, CD8- and CD5dim) aberrant expression of myeloid and stem cell markers, a distinct gene expression profile and very poor outcome. The underlying genetic basis of this form of leukemia is unknown. Here we report results of whole genome sequencing (WGS) of tumor and normal DNA from 12 children with ETP ALL. Genomes were sequenced to 30-fold haploid coverage using the Illumina GAIIx platform, and all putative somatic sequence and structural variants were validated. The frequency of mutations in 43 genes was assessed in a recurrence cohort of 52 ETP and 42 non-ETP T-ALL samples from patients enrolled in St Jude, Children's Oncology Group and AEIOP trials. Transcriptomic resequencing was performed for two WGS cases, and whole exome sequencing for three ETP ALL cases in the recurrence cohort. We identified 44 interchromosomal translocations (mean 4 per patient, range 0–12), 32 intrachromosomal translocations (mean 3, 0–7), 53 deletions (mean 4, 0–10) and 16 insertions (mean 1, 0–5). Three cases exhibited a pattern of complex rearrangements suggestive of a single cellular catastrophe (“chromothripsis”), two of which had mutations targeting mismatch and DNA repair (MLH3 and DCLRE1C). While no single chromosomal alteration was present in all cases, 10 of 12 ETP ALLs harbored chromosomal rearrangements, several of which involved complex multichromosomal translocations and resulted in the expression of chimeric in-frame novel fusion genes disrupting hematopoietic regulators, including ETV6-INO80D, NAP1L1-MLLT10, RUNX1-EVX1 and NUP214-SQSTM1, each occurring in a single case. An additional ETP case with the ETV6-INO80D fusion was identified in the recurrence cohort. Additionally, 51% of structural variants had breakpoints in genes, including those with roles in hematopoiesis and leukemogenesis, and genes also targeted by mutation in other cases (MLH3, SUZ12, RUNX1). We identified a high frequency of activating mutations in genes regulating cytokine receptor and Ras signalling in ETP ALL (67.2% of ETP compared to 19% of non-ETP T-ALL) including NRAS (17%), FLT3 (14%), JAK3 (9%), SH2B3 (or LNK; 9%), IL7R (8%), JAK1 (8%), KRAS (3%), and BRAF (2%). Seven cases (5 ETP, 2 non-ETP) harbored in frame insertion mutations in the transmembrane domain of IL7R, which were transforming when expressed in the murine cell lines, and resulted in enhanced colony formation when expressed in primary murine hematopoietic cells. The IL7R mutations resulted in constitutive Jak-Stat activation in these cell lines and primary leukemic cells expressing these mutations. Fifty-eight percent of ETP cases (compared to 17% of non-ETP cases) harbored mutations known or predicted to disrupt hematopoietic and lymphoid development, including ETV6 (33%), RUNX1 (16%), IKZF1 (14%), GATA3 (10%), EP300 (5%) and GATA2 (2%). GATA3 regulates early T cell development, and mutations in this gene were observed exclusively in ETP ALL. The mutations were commonly biallelic, and were clustered at R276, a residue critical for binding of GATA3 to DNA. Strikingly, mutations disrupting chromatin modifying genes were also highly enriched in ETP ALL. Genes encoding the the polycomb repressor complex 2 (EZH2, SUZ12 and EED), that mediates histone 3 lysine 27 (H3K27) trimethylation were deleted or mutated in 42% of ETP ALL compared to 12% of non-ETP T-ALL. In addition, alterations of the H3K36 trimethylase SETD2 were observed in 5 ETP cases, but not in non-ETP ALL. We also identified recurrent mutations in genes that have not previously been implicated in hematopoietic malignancies including RELN, DNM2, ECT2L, HNRNPA1 and HNRNPR. Using gene set enrichment analysis we demonstrate that the gene expression profile of ETP ALL shares features not only with normal human hematopoietic stem cells, but also with leukemic initiating cells (LIC) purified from patients with acute myeloid leukemia (AML). These results indicate that mutations that drive proliferation, impair differentiation and disrupt histone modification cooperate to induce an aggressive leukemia with an aberrant immature phenotype. The similarity of the gene expression pattern with that observed in the LIC of AML raises the possibility that myeloid-directed therapies might improve the outcome of ETP ALL. Disclosures: Evans: St. Jude Children's research Hospital: Employment, Patents & Royalties; NIH & NCI: Research Funding; Aldagen: Membership on an entity's Board of Directors or advisory committees.

scholarly journals Whole-Genome Genomics Correlates of Response to Anti-PD1 Therapy in Relapsed/Refractory Natural Killer/T Cell Lymphoma

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 2915-2915
Author(s):  
Jing Quan Lim ◽  
Tiffany Tang ◽  
Daryl Tan ◽  
Yurike Laurensia ◽  
Burton Chia Kuan Hui ◽  
...  
Keyword(s):  
T Cell ◽  
Whole Genome Sequencing ◽  
Natural Killer ◽  
Genome Sequencing ◽  
Progressive Disease ◽  
Whole Genome ◽  
Natural Killer T Cell ◽  
Pd1 Blockade ◽  
Killer T Cell ◽  
Natural Killer T

Abstract The genetic landscape of Natural killer/T-cell nasal-type lymphoma (NKTL) has been recently unraveled by discoveries describing recurring mutations altering the JAK-STAT pathway, epigenetic modifiers, the DDX3X gene and genetic predisposition in the HLA-DPB1 gene but none has employed whole-genome sequencing (WGS). Whole-genome sequencing was performed for 11 pairs of tumor-blood samples to study the association between somatic mutations and response to pembrolizumab. Interestingly, recurrent PD-L1 SRs were validated in four of the seven complete responders (CR) cases. JAK3-activating (p.A573V) mutations were also validated in another two pembrolizumab-treated patients who have achieved CR. Lastly, we also found a homozygous 3 bp insertion (p.Q131_H132insQ) in the ARID1B gene, a chromatin remodeler gene and a subunit in the SWI/SNF complex in the last remaining CR case. A recent study has also reported PBRM1-deficient and ARID2-deficient tumors correlated with better response to anti-PD1/PD-L1 therapy renal cell carcinoma. There seems to be a relationship between truncating alterations in the subunits of the SWI/SNF complex and response to PD1/PD-L1 therapy. However, the exact mechanisms behind these associations remain to be elucidated for NKTL. Analysis of the WGS data from the four remaining progressive disease (PD) patients' tumors did not reveal similar alterations in the PD-L1 and JAK3 genes. A careful inspection was also carried out on the genes associated with major histocompatibility complex and interferon gamma pathways, which are known to associate with resistance to immune checkpoint blockade in melanoma, but no further mutation in these groups of genes was found in our cohort. Furthermore, a TP53 (p.W14X) stop-gain mutation, a hallmark tumor suppressor gene, was detected in a patient who had progressive disease after given pembrolizumab. We went on to check if PD-L1 IHC staining could explain the response of these NKTL patients to pembrolizumab. In this study, tumors were stained and assessed for PD-L1 positivity by the same pathologist. All cases, except two cases, have greater than 20% of tumor cells stained positive for PD-L1. Interesting, both cases are CR. In addition, all four PD cases were strongly stained for PD-L1 with an average of 69% PD-L1 positive cells (range, 50% - 90%) but their outcomes were dismal. This suggests that there could be a companion biomarker that could be added to PD-L1 IHC positivity for better predictive power of response to PD1 blockade therapy. Here we report retrospectively, for the first time, the genomic mutational profiles of anti-PD1 blockade in 11 relapsed/refractory NKTL patients using WGS data, which provide proof-of-concept data that the response to anti-PD1 is relevant and correlates with recurrent PD-L1 and JAK3 genomic alterations in this malignancy. Disclosures No relevant conflicts of interest to declare.

Whole Genome and Exome Sequencing Defines The Genetic Landscape Of Hepatosplenic T-Cell Lymphoma

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 842-842
Author(s):  
Paula Scotland ◽  
Philippe Gaulard ◽  
Cassandra L Love ◽  
Virginie Fataccioli ◽  
Marion Travert ◽  
...  
Keyword(s):  
T Cell ◽  
Whole Genome Sequencing ◽  
Exome Sequencing ◽  
Genome Sequencing ◽  
Cell Lymphoma ◽  
T Cell Lymphoma ◽  
Chromosome 7 ◽  
Whole Genome ◽  
Hepatosplenic T Cell Lymphoma ◽  
Isochromosome 7Q

Abstract Background Hepatosplenic T-cell lymphoma (HSTL) is a rare form of lymphoma, comprising less than 1% of the cases. However, HSTL extracts a highly disproportionate toll on patients with a median age of diagnosis of 35 years and an expected median survival of less than two years. The vast majority of HSTL patients eventually succumb to their disease. The genetic basis of the disease is largely unknown. Although abnormalities of chromosome 7, including isochromosome 7q occur commonly in the disease, the role of specific genes and genetic mutations to the disease remains essentially unknown. Methods In this study, we sought to define the genetic features of HSTL through the whole genome sequencing and exome sequencing of 32 HSTL tumors and germline DNA (where available) from the same patients. Exome enrichment of DNA was carried out using the Agilent solution-based system of exon capture, which uses RNA baits to target all protein coding genes as well as ∼700 human microRNAs. Both whole genome and exome sequencing were performed using the Illumina platform. Results We identified 28 candidate cancer genes that were recurrently mutated in HSTL. Commonly implicated biological processes comprising these genes included signal transduction (e.g. PIK3CD, KRAS) and chromatin modification (e.g. TET1, SETD2 and MLL3), accounting for 16% and 23% of the total genetic events, respectively. Nearly all of these genes have been implicated in HSTL for the first time and provide new insights into the pathogenesis of the disease and potential targets for therapy. Whole genome sequencing confirmed isochromosome 7q as the most common recurrent chromosomal abnormality in HSTL and additional structural genetic alterations in chromosome 7. Conclusion Our study provides the most comprehensive genetic portrait of HSTL to date, and is a significant step in defining the genetic causes of this disease. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Whole-Genome Immunoinformatic Analysis of F. tularensis: Predicted CTL Epitopes Clustered in Hotspots Are Prone to Elicit a T-Cell Response

PLoS ONE ◽  
2011 ◽  
Vol 6 (5) ◽  
pp. e20050 ◽  
Author(s):  
Anat Zvi ◽  
Shahar Rotem ◽  
Erez Bar-Haim ◽  
Ofer Cohen ◽  
Avigdor Shafferman
Keyword(s):  
T Cell ◽  
Cell Response ◽  
T Cell Response ◽  
Whole Genome ◽  
Ctl Epitopes

scholarly journals Whole-genome sequencing identifies responders to Pembrolizumab in relapse/refractory natural-killer/T cell lymphoma

Leukemia ◽  
2020 ◽  
Vol 34 (12) ◽  
pp. 3413-3419 ◽  
Author(s):  
Jing Quan Lim ◽  
Dachuan Huang ◽  
Tiffany Tang ◽  
Daryl Tan ◽  
Yurike Laurensia ◽  
...  
Keyword(s):  
T Cell ◽  
Whole Genome Sequencing ◽  
Natural Killer ◽  
Genome Sequencing ◽  
Cell Lymphoma ◽  
T Cell Lymphoma ◽  
Whole Genome ◽  
Natural Killer T Cell ◽  
Killer T Cell ◽  
Natural Killer T

scholarly journals Whole-genome Sequencing of Angioimmunoblastic T-Cell Lymphoma Combined With Plasma Cell Leukemia: A Case Report and Review of the Literature

2021 ◽  
Author(s):  
Yang Yang ◽  
Enfan Zhang ◽  
Zhen Cai ◽  
Jingsong He
Keyword(s):  
T Cell ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Molecular Mechanisms ◽  
Plasma Cells ◽  
Cell Lymphoma ◽  
Whole Genome ◽  
Review Of The Literature ◽  
Cell Leukemia ◽  
Angioimmunoblastic T Cell Lymphoma

Abstract Purpose Angioimmunoblastic T-cell lymphoma (AITL) is a distinct subtype of peripheral T-cell lymphomas, sometimes involves proliferation of plasma cells. Currently, only 7 cases of AITL with monoclonal plasmacytosis have been reported. However, the molecular mechanisms underlying the interaction between monoclonal plasma cells and T cells have not been identified. We describe a rare case of AITL with plasma cell leukemia (PCL) in this report. Methods The patient was a 67-year-old female diagnosed with AITL and PCL. CD138 positive plasma cells and CD138-negative mixed bone marrow populations of this patient were collected for whole-genome sequencing (WGS). A review of the literature on AITL cases with monoclonal plasma cells is presented.Results WGS showed that the two cell populatoins shared 282 non-synonymous single nucleotide variants (SNVs) and excess of G to A and C to T transitions. We identified 14 potential driver genes in this patient. Functional enriched analysis of mutant genes confirmed several significantly enriched pathways, including VEGF signaling. The patient was treated with one cycle of PD (combined Bortezomib and Dexamethasone) and Chidamide. However, the patient developed severe pneumonia and pancytopenia, refused to receive further treatment, and died one week after discharge. Conclusion Being aware of the coexistence of PCL and AITL is important for accurate diagnosis and appropriate treatment. In addition, our results suggested the involvement of a group of genes and pathways in AITL with coexisting PCL, providing valuable information for further exploration of the underlying molecular mechanisms.

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