The assessment of circulating tumor DNA (ctDNA), released by tumor cells undergoing apoptosis or ... more The assessment of circulating tumor DNA (ctDNA), released by tumor cells undergoing apoptosis or necrosis, has established utility in solid tumors due to the advantage of a non-invasive "liquid biopsy" replacing multiple site-specific biopsies. However, its role in acute myeloid leukemia (AML) is uncertain, where a significant proportion of variants detected in the bone marrow (BM) may not be detected in ctDNA (Short, Blood Adv 2020). We have previously demonstrated the possibility of comprehensive genomic characterization of lymphoid malignancy from ctDNA using a single targeted next generation sequencing (NGS) hybridization-based panel (Blombery, BJH 2017). We aimed to assess the performance of this same genomic approach in ctDNA and to compare it against BM in AML. In addition, we aimed to assess the integration of a sensitive variant caller (Mutect2; Benjamin, bioRxiv 2019) to the bioinformatics suite in an attempt to improve low-level variant detection. Nineteen patie...
Cancer and Blood Diseases Institute, Cincinnati Children’s Hospital Medical Center, University of... more Cancer and Blood Diseases Institute, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH; College of Nursing, University of Cincinnati, Cincinnati, OH; Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH; Systems Biology of Signal Transduction, German Cancer Research Center, Center for Molecular Biology Alliance, Heidelberg, Germany; and Department of Pediatrics, Center for Pediatric Biomedical Research, University of Rochester Medical Center, Rochester, NY
Zebrafish are an important model for studying phagocyte function, but rigorous experimental syste... more Zebrafish are an important model for studying phagocyte function, but rigorous experimental systems to distinguish whether phagocyte-dependent effects are neutrophil or macrophage specific have been lacking. We have developed and validated transgenic lines that enable superior demonstration of cell-autonomous neutrophil and macrophage genetic requirements. We coupled well-characterized neutrophil- and macrophage-specific Gal4 driver lines with UAS:Cas9 transgenes for selective expression of Cas9 in either neutrophils or macrophages. Efficient gene editing, confirmed by both Sanger and next-generation sequencing, occurred in both lineages following microinjection of efficacious synthetic guide RNAs into zebrafish embryos. In proof-of-principle experiments, we demonstrated molecular and/or functional evidence of on-target gene editing for several genes (mCherry, lamin B receptor, trim33) in either neutrophils or macrophages as intended. These new UAS:Cas9 tools provide an improved res...
Richter syndrome (RS), an aggressive lymphoma occurring in the context of chronic lymphocytic leu... more Richter syndrome (RS), an aggressive lymphoma occurring in the context of chronic lymphocytic leukaemia/small lymphocytic lymphoma, is associated with poor prognosis when treated with conventional immunochemotherapy, therefore, improved treatments are required. Immune checkpoint blockade has shown efficacy in some B‐cell malignancies and modest responses in early clinical trials for RS. We investigated the immune checkpoint profile of RS as a basis to inform rational therapeutic investigations in RS.
The molecular profile of clonal hematopoiesis in patients (pts) with idiopathic aplastic anaemia ... more The molecular profile of clonal hematopoiesis in patients (pts) with idiopathic aplastic anaemia (iAA) has been shown to predict response to immunosuppressive therapy (IST). Moreover, clonal evolution is associated with transformation of iAA to aggressive myeloid malignancies such as myelodysplastic syndrome (MDS) and acute myeloid leukaemia (AML). Detection of somatic mutations may help identify pts more likely to respond to IST and also those at increased risk of transformation however the predictive value of detecting mutations at a single timepoint is limited. Longitudinal detection of changes in mutation profile over time may improve prediction of transformation risk, however due to bone marrow hypocellularity DNA quality and quantity from pts with iAA is frequently suboptimal. Serial mutation analysis of cell-free DNA (cfDNA) is one approach that may overcome this problem as the majority of cfDNA originates from hematopoietic cells and mutations detected in this compartment ha...
Bone marrow failure (BMF) related to hypoplasia of hematopoietic elements in the bone marrow is a... more Bone marrow failure (BMF) related to hypoplasia of hematopoietic elements in the bone marrow is a heterogeneous clinical entity with a broad differential diagnosis including both inherited and acquired causes. Accurate diagnostic categorization is critical to optimal patient care and detection of genomic variants in these patients may provide this important diagnostic and prognostic information. We performed real-time, accredited (ISO15189) comprehensive genomic characterization including targeted sequencing and whole exome sequencing in 115 patients with BMF syndrome (median age 24 years, range 3 months - 81 years). In patients with clinical diagnoses of inherited BMF syndromes, acquired BMF syndromes or clinically unclassifiable BMF we detected variants in 52% (12/23), 53% (25/47) and 56% (25/45) respectively. Genomic characterization resulted in a change of diagnosis in 30/115 (26%) including the identification of germline causes for 3/47 and 16/45 cases with pre-test diagnoses o...
Richter syndrome (RS) is the transformation of chronic lymphocytic leukemia (CLL) to a high-grade... more Richter syndrome (RS) is the transformation of chronic lymphocytic leukemia (CLL) to a high-grade B-cell lymphoma and is associated with an aggressive clinical course and poor prognosis. Conventional treatment options for RS are generally associated with low response rates and limited durability making this entity an area of significant unmet therapeutic need. Immune checkpoint inhibitor therapy has shown promise in the treatment of some aggressive lymphoma subtypes. In RS, modest benefits have been reported in small phase two trials of anti-PD-1 monotherapy and in combination with ibrutinib, however larger scale studies are lacking (Ding et al Blood, 2017; Jain et al Blood, 2016). We sought to characterise the immune-evasion phenotype of RS focussing on potential genetic biomarkers which may inform the selection of patients who are most likely to benefit from immune-directed therapies. We first assessed the gene expression of immune-checkpoint molecules given their potential clinic...
The number of genomics and proteomics experiments is growing rapidly, producing an ever-increasin... more The number of genomics and proteomics experiments is growing rapidly, producing an ever-increasing amount of data that are awaiting functional interpretation. A number of function prediction algorithms were developed and improved to enable fast and automatic function annotation. With the well-defined structure and manual curation, Gene Ontology (GO) is the most frequently used vocabulary for representing gene functions. To understand relationship and similarity between GO annotations of genes, it is important to have a convenient pipeline that quantifies and visualizes the GO function analyses in a systematic fashion. NaviGO is a web-based tool for interactive visualization, retrieval, and computation of functional similarity and associations of GO terms and genes. Similarity of GO terms and gene functions is quantified with six different scores including protein-protein interaction and context based association scores we have developed in our previous works. Interactive navigation ...
The detection of copy number abnormalities (CNAs) is of significant clinical relevance in hematol... more The detection of copy number abnormalities (CNAs) is of significant clinical relevance in hematological malignancy (e.g. TP53 CN loss in chronic lymphocytic leukemia). Whilst detection of CNAs is typically performed by FISH or SNP array, it is also possible from next generation sequencing (NGS) data. Given the rapid and global expansion of targeted sequencing for the diagnosis and management of hematological malignancy, we aimed to develop a copy number (CN) analysis tool specifically suited to reporting CN in hematological malignancy in the diagnostic laboratory. We describe CNspectorX, a comprehensive CNA solution from FASTQ to interactive whole genome CN visualization with significant advantages over existing bioinformatics tools. Detecting CNAs sensitively and specifically from NGS data requires a diploid baseline with minimal random variation (noise) and with non-random variation which can correct for systematic biases. An optimal baseline requires representation of recurrent t...
IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM, Jan 25, 2015
Proteins carry out their function in a cell through interactions with other proteins. A large sca... more Proteins carry out their function in a cell through interactions with other proteins. A large scale Protein-Protein Interaction (PPI) network of an organism provides static yet an essential structure of interactions, which is valuable clue for understanding the functions of proteins and pathways. PPIs are determined primarily by experimental methods; however, computational PPI prediction methods can supplement or verify PPIs identified by experiment. Here we developed a novel scoring method for predicting PPIs from Gene Ontology (GO) annotations of proteins. Unlike existing methods that consider functional similarity as an indication of interaction between proteins, the new score, named the protein-protein Interaction Association Score (IAS), was computed from GO term associations of known interacting protein pairs in 49 organisms. IAS was evaluated on PPI data of six organisms and found to outperform existing GO term-based scoring methods. Moreover, consensus scoring methods that c...
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2015
Proteins carry out their function in a cell through interactions with other proteins. A large sca... more Proteins carry out their function in a cell through interactions with other proteins. A large scale Protein-Protein Interaction (PPI) network of an organism provides static yet an essential structure of interactions, which is valuable clue for understanding the functions of proteins and pathways. PPIs are determined primarily by experimental methods; however, computational PPI prediction methods can supplement or verify PPIs identified by experiment. Here we developed a novel scoring method for predicting PPIs from Gene Ontology (GO) annotations of proteins. Unlike existing methods that consider functional similarity as an indication of interaction between proteins, the new score, named the protein-protein Interaction Association Score (IAS), was computed from GO term associations of known interacting protein pairs in 49 organisms. IAS was evaluated on PPI data of six organisms and found to outperform existing GO term-based scoring methods. Moreover, consensus scoring methods that combine different scores further improved performance of PPI prediction.
RhoA GTPase has been shown in vitro in cell lines and in vivo in non-mammalian organisms to regul... more RhoA GTPase has been shown in vitro in cell lines and in vivo in non-mammalian organisms to regulate cell division, particularly during cytokinesis and abscission, when two daughter cells partition through coordinated actomyosin and microtubule machineries. In order to investigate the role of this GTPase in the rapidly proliferating mammalian erythroid lineage, we developed a mouse model with erythroid-specific deletion of RhoA. This model was proved embryonic lethal due to severe anemia by embryonic day 16.5 (E16.5). The primitive red blood cells were enlarged, poikilocytic, and frequently multinucleated but were able to sustain life despite experiencing cytokinesis failure. In contrast, definitive erythropoiesis failed and the mice died by E16.5 with profound reduction of maturing erythroblast populations within the fetal liver. RhoA was required to activate myosin-regulatory light chain and localized at the site of the midbody formation in dividing wild-type erythroblasts. Cytokinesis failure due to RhoA deficiency resulted in p53 activation and p21-transcriptional upregulation with associated cell cycle arrest, increased DNA damage, and cell death. Our findings demonstrate the role of RhoA as a critical regulator for efficient erythroblast proliferation and the p53 pathway as a powerful quality control mechanism in erythropoiesis.
The assessment of circulating tumor DNA (ctDNA), released by tumor cells undergoing apoptosis or ... more The assessment of circulating tumor DNA (ctDNA), released by tumor cells undergoing apoptosis or necrosis, has established utility in solid tumors due to the advantage of a non-invasive "liquid biopsy" replacing multiple site-specific biopsies. However, its role in acute myeloid leukemia (AML) is uncertain, where a significant proportion of variants detected in the bone marrow (BM) may not be detected in ctDNA (Short, Blood Adv 2020). We have previously demonstrated the possibility of comprehensive genomic characterization of lymphoid malignancy from ctDNA using a single targeted next generation sequencing (NGS) hybridization-based panel (Blombery, BJH 2017). We aimed to assess the performance of this same genomic approach in ctDNA and to compare it against BM in AML. In addition, we aimed to assess the integration of a sensitive variant caller (Mutect2; Benjamin, bioRxiv 2019) to the bioinformatics suite in an attempt to improve low-level variant detection. Nineteen patie...
Cancer and Blood Diseases Institute, Cincinnati Children’s Hospital Medical Center, University of... more Cancer and Blood Diseases Institute, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH; College of Nursing, University of Cincinnati, Cincinnati, OH; Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH; Systems Biology of Signal Transduction, German Cancer Research Center, Center for Molecular Biology Alliance, Heidelberg, Germany; and Department of Pediatrics, Center for Pediatric Biomedical Research, University of Rochester Medical Center, Rochester, NY
Zebrafish are an important model for studying phagocyte function, but rigorous experimental syste... more Zebrafish are an important model for studying phagocyte function, but rigorous experimental systems to distinguish whether phagocyte-dependent effects are neutrophil or macrophage specific have been lacking. We have developed and validated transgenic lines that enable superior demonstration of cell-autonomous neutrophil and macrophage genetic requirements. We coupled well-characterized neutrophil- and macrophage-specific Gal4 driver lines with UAS:Cas9 transgenes for selective expression of Cas9 in either neutrophils or macrophages. Efficient gene editing, confirmed by both Sanger and next-generation sequencing, occurred in both lineages following microinjection of efficacious synthetic guide RNAs into zebrafish embryos. In proof-of-principle experiments, we demonstrated molecular and/or functional evidence of on-target gene editing for several genes (mCherry, lamin B receptor, trim33) in either neutrophils or macrophages as intended. These new UAS:Cas9 tools provide an improved res...
Richter syndrome (RS), an aggressive lymphoma occurring in the context of chronic lymphocytic leu... more Richter syndrome (RS), an aggressive lymphoma occurring in the context of chronic lymphocytic leukaemia/small lymphocytic lymphoma, is associated with poor prognosis when treated with conventional immunochemotherapy, therefore, improved treatments are required. Immune checkpoint blockade has shown efficacy in some B‐cell malignancies and modest responses in early clinical trials for RS. We investigated the immune checkpoint profile of RS as a basis to inform rational therapeutic investigations in RS.
The molecular profile of clonal hematopoiesis in patients (pts) with idiopathic aplastic anaemia ... more The molecular profile of clonal hematopoiesis in patients (pts) with idiopathic aplastic anaemia (iAA) has been shown to predict response to immunosuppressive therapy (IST). Moreover, clonal evolution is associated with transformation of iAA to aggressive myeloid malignancies such as myelodysplastic syndrome (MDS) and acute myeloid leukaemia (AML). Detection of somatic mutations may help identify pts more likely to respond to IST and also those at increased risk of transformation however the predictive value of detecting mutations at a single timepoint is limited. Longitudinal detection of changes in mutation profile over time may improve prediction of transformation risk, however due to bone marrow hypocellularity DNA quality and quantity from pts with iAA is frequently suboptimal. Serial mutation analysis of cell-free DNA (cfDNA) is one approach that may overcome this problem as the majority of cfDNA originates from hematopoietic cells and mutations detected in this compartment ha...
Bone marrow failure (BMF) related to hypoplasia of hematopoietic elements in the bone marrow is a... more Bone marrow failure (BMF) related to hypoplasia of hematopoietic elements in the bone marrow is a heterogeneous clinical entity with a broad differential diagnosis including both inherited and acquired causes. Accurate diagnostic categorization is critical to optimal patient care and detection of genomic variants in these patients may provide this important diagnostic and prognostic information. We performed real-time, accredited (ISO15189) comprehensive genomic characterization including targeted sequencing and whole exome sequencing in 115 patients with BMF syndrome (median age 24 years, range 3 months - 81 years). In patients with clinical diagnoses of inherited BMF syndromes, acquired BMF syndromes or clinically unclassifiable BMF we detected variants in 52% (12/23), 53% (25/47) and 56% (25/45) respectively. Genomic characterization resulted in a change of diagnosis in 30/115 (26%) including the identification of germline causes for 3/47 and 16/45 cases with pre-test diagnoses o...
Richter syndrome (RS) is the transformation of chronic lymphocytic leukemia (CLL) to a high-grade... more Richter syndrome (RS) is the transformation of chronic lymphocytic leukemia (CLL) to a high-grade B-cell lymphoma and is associated with an aggressive clinical course and poor prognosis. Conventional treatment options for RS are generally associated with low response rates and limited durability making this entity an area of significant unmet therapeutic need. Immune checkpoint inhibitor therapy has shown promise in the treatment of some aggressive lymphoma subtypes. In RS, modest benefits have been reported in small phase two trials of anti-PD-1 monotherapy and in combination with ibrutinib, however larger scale studies are lacking (Ding et al Blood, 2017; Jain et al Blood, 2016). We sought to characterise the immune-evasion phenotype of RS focussing on potential genetic biomarkers which may inform the selection of patients who are most likely to benefit from immune-directed therapies. We first assessed the gene expression of immune-checkpoint molecules given their potential clinic...
The number of genomics and proteomics experiments is growing rapidly, producing an ever-increasin... more The number of genomics and proteomics experiments is growing rapidly, producing an ever-increasing amount of data that are awaiting functional interpretation. A number of function prediction algorithms were developed and improved to enable fast and automatic function annotation. With the well-defined structure and manual curation, Gene Ontology (GO) is the most frequently used vocabulary for representing gene functions. To understand relationship and similarity between GO annotations of genes, it is important to have a convenient pipeline that quantifies and visualizes the GO function analyses in a systematic fashion. NaviGO is a web-based tool for interactive visualization, retrieval, and computation of functional similarity and associations of GO terms and genes. Similarity of GO terms and gene functions is quantified with six different scores including protein-protein interaction and context based association scores we have developed in our previous works. Interactive navigation ...
The detection of copy number abnormalities (CNAs) is of significant clinical relevance in hematol... more The detection of copy number abnormalities (CNAs) is of significant clinical relevance in hematological malignancy (e.g. TP53 CN loss in chronic lymphocytic leukemia). Whilst detection of CNAs is typically performed by FISH or SNP array, it is also possible from next generation sequencing (NGS) data. Given the rapid and global expansion of targeted sequencing for the diagnosis and management of hematological malignancy, we aimed to develop a copy number (CN) analysis tool specifically suited to reporting CN in hematological malignancy in the diagnostic laboratory. We describe CNspectorX, a comprehensive CNA solution from FASTQ to interactive whole genome CN visualization with significant advantages over existing bioinformatics tools. Detecting CNAs sensitively and specifically from NGS data requires a diploid baseline with minimal random variation (noise) and with non-random variation which can correct for systematic biases. An optimal baseline requires representation of recurrent t...
IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM, Jan 25, 2015
Proteins carry out their function in a cell through interactions with other proteins. A large sca... more Proteins carry out their function in a cell through interactions with other proteins. A large scale Protein-Protein Interaction (PPI) network of an organism provides static yet an essential structure of interactions, which is valuable clue for understanding the functions of proteins and pathways. PPIs are determined primarily by experimental methods; however, computational PPI prediction methods can supplement or verify PPIs identified by experiment. Here we developed a novel scoring method for predicting PPIs from Gene Ontology (GO) annotations of proteins. Unlike existing methods that consider functional similarity as an indication of interaction between proteins, the new score, named the protein-protein Interaction Association Score (IAS), was computed from GO term associations of known interacting protein pairs in 49 organisms. IAS was evaluated on PPI data of six organisms and found to outperform existing GO term-based scoring methods. Moreover, consensus scoring methods that c...
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2015
Proteins carry out their function in a cell through interactions with other proteins. A large sca... more Proteins carry out their function in a cell through interactions with other proteins. A large scale Protein-Protein Interaction (PPI) network of an organism provides static yet an essential structure of interactions, which is valuable clue for understanding the functions of proteins and pathways. PPIs are determined primarily by experimental methods; however, computational PPI prediction methods can supplement or verify PPIs identified by experiment. Here we developed a novel scoring method for predicting PPIs from Gene Ontology (GO) annotations of proteins. Unlike existing methods that consider functional similarity as an indication of interaction between proteins, the new score, named the protein-protein Interaction Association Score (IAS), was computed from GO term associations of known interacting protein pairs in 49 organisms. IAS was evaluated on PPI data of six organisms and found to outperform existing GO term-based scoring methods. Moreover, consensus scoring methods that combine different scores further improved performance of PPI prediction.
RhoA GTPase has been shown in vitro in cell lines and in vivo in non-mammalian organisms to regul... more RhoA GTPase has been shown in vitro in cell lines and in vivo in non-mammalian organisms to regulate cell division, particularly during cytokinesis and abscission, when two daughter cells partition through coordinated actomyosin and microtubule machineries. In order to investigate the role of this GTPase in the rapidly proliferating mammalian erythroid lineage, we developed a mouse model with erythroid-specific deletion of RhoA. This model was proved embryonic lethal due to severe anemia by embryonic day 16.5 (E16.5). The primitive red blood cells were enlarged, poikilocytic, and frequently multinucleated but were able to sustain life despite experiencing cytokinesis failure. In contrast, definitive erythropoiesis failed and the mice died by E16.5 with profound reduction of maturing erythroblast populations within the fetal liver. RhoA was required to activate myosin-regulatory light chain and localized at the site of the midbody formation in dividing wild-type erythroblasts. Cytokinesis failure due to RhoA deficiency resulted in p53 activation and p21-transcriptional upregulation with associated cell cycle arrest, increased DNA damage, and cell death. Our findings demonstrate the role of RhoA as a critical regulator for efficient erythroblast proliferation and the p53 pathway as a powerful quality control mechanism in erythropoiesis.
Uploads
Papers by Satwica Yerneni