A5035216019- Lymphoma Diagnosis and Treatment
- Hepatocellular Carcinoma Treatment and Prognosis
- vaccines and immunoinformatics approaches
- Cancer, Hypoxia, and Metabolism
- Cancer Genomics and Diagnostics
- Chronic Lymphocytic Leukemia Research
- Immune Cell Function and Interaction
- Cancer Immunotherapy and Biomarkers
- Ferroptosis and cancer prognosis
- Liver physiology and pathology
- Monoclonal and Polyclonal Antibodies Research
- Microtubule and mitosis dynamics
- Genetic Associations and Epidemiology
- RNA modifications and cancer
- T-cell and B-cell Immunology
- Viral-associated cancers and disorders
- Immunotherapy and Immune Responses
- Cancer-related molecular mechanisms research
- Acute Lymphoblastic Leukemia research
- Circular RNAs in diseases
- T-cell and Retrovirus Studies
- Bladder and Urothelial Cancer Treatments
- MicroRNA in disease regulation
- Glioma Diagnosis and Treatment
- Mathematical Biology Tumor Growth
Icahn School of Medicine at Mount Sinai
2016-2023
Adaptive Biotechnologies (United States)
2019-2022
Seattle University
2022
Universitat de Barcelona
2020
Consorci Institut D'Investigacions Biomediques August Pi I Sunyer
2020
Beckley VA Medical Center
2018
University of California, Berkeley
2010-2017
Berkeley Public Health Division
2010-2014
Abstract Clonal evolution of a tumor ecosystem depends on different selection pressures that are principally immune and treatment mediated. We integrate RNA-seq, DNA sequencing, TCR-seq SNP array data across multiple regions liver cancer specimens to map spatio-temporal interactions between cells. investigate how these reflect intra-tumor heterogeneity (ITH) by correlating regional neo-epitope viral antigen burden with the adaptive response. Regional expression passenger mutations dominantly...
Genome-wide association studies (GWAS) have identified hundreds of cardiometabolic disease (CMD) risk loci. However, they contribute little to genetic variance, and most downstream gene-regulatory mechanisms are unknown. We genotyped RNA-sequenced vascular metabolic tissues from 600 coronary artery patients in the Stockholm-Tartu Atherosclerosis Reverse Networks Engineering Task study (STARNET). Gene expression traits associated with CMD single-nucleotide polymorphism (SNPs) by GWAS were...
Hepatoblastoma (HB) is a rare disease. Nevertheless, it the predominant pediatric liver cancer, with limited therapeutic options for patients aggressive tumors. Herein, we aimed to uncover mechanisms of HB pathobiology and identify new biomarkers targets in move towards precision medicine advanced HB.We performed comprehensive genomic, transcriptomic epigenomic characterization 159 clinically annotated samples from 113 HB, using high-throughput technologies.We discovered widespread...
The clonoSEQ® Assay (Adaptive Biotechnologies Corporation, Seattle, USA) identifies and tracks unique disease-associated immunoglobulin (Ig) sequences by next-generation sequencing of IgH, IgK, IgL rearrangements IgH-BCL1/2 translocations in malignant B cells. Here, we describe studies to validate the analytical performance assay using patient samples cell lines.Sensitivity specificity were established defining limit detection (LoD), quantitation (LoQ) blank (LoB) genomic DNA (gDNA) from 66...
Inter‐individual differences in arsenic metabolism have been linked to arsenic‐related disease risks. Arsenic (+3) methyltransferase (AS3MT) is the primary enzyme involved metabolism, and we previously demonstrated vitro that N‐6 adenine‐specific DNA 1 (N6AMT1) also methylates toxic inorganic (iAs) metabolite, monomethylarsonous acid (MMA), less dimethylarsonic (DMA). Here, evaluated whether AS3MT N6AMT1 gene polymorphisms alter methylation impact iAs‐related cancer We assessed urinary...
Management of hepatoblastoma (HB), the most frequent pediatric liver cancer, is based on surgical resection and perioperative chemotherapy regimens. In this study, we aimed to identify actionable targets in HB assess efficacy molecular therapies preclinical models HB. Paired tumor adjacent tissues from 31 HBs a validation set 50 were analyzed using RNA-seq, SNP, methylation arrays. IGF2 overexpression was identified as top targetable driver, present 71% (22/31). IGF2high tumors displayed...
Follicular lymphoma (FL) is an indolent, sometimes, fatal disease characterized by recurrence at progressively shorter intervals and frequently refractive to therapy. Genome‐wide association studies have identified single nucleotide polymorphisms (SNPs) in the human leukocyte antigen (HLA) region on chromosome 6p21.32‐33 that are statistically significantly associated with FL risk. Low medium resolution typing of or multiple HLA genes has provided incomplete picture total genetic risk...
The biological relevance of chimeric RNA alignments is now well established. Chimera arising as chromosomal fusions are often drivers cancer and recently discovered circular (circRNA) only being characterized. While software already exists for fusion discovery quantitation, high false positive rates run-times hamper scalable on large datasets. Furthermore, available circRNA detection quantification limited.Here, we present STAR Chimeric Post (STARChip), a novel package that processes from...
In a recent genome-wide association study of follicular lymphoma (FL), we identified novel risk alleles on chromosome 6p21.33 that appeared to be part an extended haplotype including HLA-DRB1*0101, DQA1*0101, and DQB1*0501. To follow up these findings, obtained 2–4 digit HLA-DQB1 allelotypes subset 265 cases FL 757 controls using assay applies multiplexed ligation-dependent probe amplification (MLPA). We confirmed positive between the HLA-DQB1*05 allele group (OR = 1.70, 95% CI 1.28–2.27;...
300 Background: Somatic mut in DDR genes have been associated with increased sensitivity to cisplatin UC. Higher load has correlated response immune checkpoint blockade. We hypothesized that result higher and UC may be particularly sensitive both chemotherapy Methods: Three cohorts were utilized: (1) TCGA cohort (n = 389), (2) Mount Sinai (MS) 67) of (cystectomy) specimens subjected targeted exome sequencing for 341 (MSK-IMPACT), (3) Phase 2 trial gemcitabine, cisplatin, plus ipilimumab...
Genetic loss-of-function variants (LoFs) associated with disease traits are increasingly recognized as critical evidence for the selection of therapeutic targets. We integrated analysis genetic and clinical data from 10,511 individuals in Mount Sinai BioMe Biobank to identify genes significantly cardiovascular (CVD) traits, used RNA-sequence seven metabolic vascular tissues isolated 600 CVD patients Stockholm-Tartu Atherosclerosis Reverse Network Engineering Task (STARNET) study validation....
Abstract Recently proposed tumor fitness measures, based on profiling neoepitopes for reactive viral epitope similarity, have been to predict response immune checkpoint inhibitors in melanoma and small-cell lung cancer. Here we applied these measures the matched treatment naive Cancer Genome Atlas (TCGA) samples where cytolytic activity (CYT) imparts a known survival benefit. We observed no significant predictive power beyond that of overall patient mutation burden, furthermore, found...
Abstract Motivation The biological relevance of chimeric RNA alignments is now well established. Chimera arising as chromosomal fusions are often drivers cancer, and recently discovered circular only being characterized. While software already exists for fusion discovery quantitation, high false positive rates run-times hamper scalable on large datasets. Furthermore, very little available detection quantification. Results Here we present STAR Chimeric Post (STARChip), a novel package that...
Abstract Background: The clonoSEQ® Assay (Adaptive Biotechnologies Corporation, Seattle, USA) identifies and tracks unique disease-associated immunoglobulin (Ig) sequences by next-generation sequencing of IgH, IgK, IgL rearrangements IgH-BCL1/2 translocations in malignant B cells. Here, we describe studies to validate the analytical performance assay using patient samples cell lines.Methods: Sensitivity specificity were established defining limit detection (LoD), quantitation (LoQ) blank...
Many effective options exist to accurately type DNA for human leukocyte antigen ( HLA ) alleles. However, most of the existing methods are excessively costly in terms overall monetary costs, requirements, and proprietary software. We present a novel assay capable resolving heterozygous HLA‐DQB1 allelotypes at two digits, with even greater specificity HLA‐DQB1*06 allele family, by using multiplexed ligation‐dependent probe amplification technology. This provides more specific data than...
Abstract Background and aims: Clonal evolution of a tumor ecosystem depends not only on somatic mutations driving uncontrolled growth, but full array selection pressures, principally immune resource mediated. We aimed at mapping the spatio-temporal interactions between cancer cells in hepatocellular carcinoma (HCC) by quantifying regional adaptive editing, how this impacts clonal evolution. Methods: integrated data from RNAseq, targeted DNA sequencing, SNP histological evaluation multiple...
Abstract Recently proposed tumor fitness measures, based on profiling neoepitopes for reactive viral epitope similarity, have been to predict response immune checkpoint inhibitors in melanoma and small-cell lung cancer. Here we apply these measures the matched treatment naive TCGA samples where cytolytic activity imparts a known survival benefit. We observed no significant predictive power beyond that of overall patient mutation burden, furthermore, found association between T-cell...