Juno Krahn - Academia.edu (original) (raw)

Papers by Juno Krahn

Research paper thumbnail of Molecular basis for processing of topoisomerase 1-triggered DNA damage by Apn2/APE2

Research paper thumbnail of Additional file 1: Table S1. of A comprehensive genomic pan-cancer classification using The Cancer Genome Atlas gene expression data

â Normalâ (normal-adjacent-to-tumor) tissue types and number of TCGA RNA-seq samples used in the ... more â Normalâ (normal-adjacent-to-tumor) tissue types and number of TCGA RNA-seq samples used in the analysis. (DOCX 18 kb)

Research paper thumbnail of Additional file 10: Figure S6. of A comprehensive genomic pan-cancer classification using The Cancer Genome Atlas gene expression data

Heatmap representation of the expression patterns of the top 50 genes selected by XGBoost across ... more Heatmap representation of the expression patterns of the top 50 genes selected by XGBoost across all 602 â normalâ samples taken adjacent to tumors from 17 tumor types. Each row (gene) was centered by the median expression value across all samples. A hierarchical clustering analysis was carried out for both samples and genes using the Euclidean distance as the similarity metric. (DOCX 15 kb)

Research paper thumbnail of Additional file 8: Figure S4. of A comprehensive genomic pan-cancer classification using The Cancer Genome Atlas gene expression data

Heatmap representation of the expression patterns of the top 50 genes across all 602 â normalâ sa... more Heatmap representation of the expression patterns of the top 50 genes across all 602 â normalâ samples taken adjacent to tumors from 17 tumor types. Each row (gene) was centered by the median expression value across all samples. A hierarchical clustering analysis was carried out for both samples and genes using the Euclidean distance as the similarity metric. (DOCX 16 kb)

Research paper thumbnail of Additional file 15: Table S5. of A comprehensive genomic pan-cancer classification using The Cancer Genome Atlas gene expression data

Mean and median of for Ď cc values for each tumor type from full female dataset, full male datase... more Mean and median of for Ď cc values for each tumor type from full female dataset, full male dataset, and the corresponding mean (sd) from the eight â matchedâ male datasets. (DOCX 283 kb)

Research paper thumbnail of Additional file 6: Figure S2. of A comprehensive genomic pan-cancer classification using The Cancer Genome Atlas gene expression data

Heatmap representation of the expression patterns of the top 50 genes across all (a) ACC, (b) BLC... more Heatmap representation of the expression patterns of the top 50 genes across all (a) ACC, (b) BLCA, (c) BRCA, (d) KIRC, (e) KIRP, (f) LGG, and (g) PAAD samples. See Fig. 3 legend for details. The colors of the horizontal bar represent the subgroups identified by k-means clustering analysis. (DOCX 60 kb)

Research paper thumbnail of Additional file 5: of A comprehensive genomic pan-cancer classification using The Cancer Genome Atlas gene expression data

Research paper thumbnail of Additional file 12: Table S4. of A comprehensive genomic pan-cancer classification using The Cancer Genome Atlas gene expression data

Genes ranked among the top 100 from either females and males. (DOCX 389 kb)

Research paper thumbnail of Additional file 2: Table S2. of A comprehensive genomic pan-cancer classification using The Cancer Genome Atlas gene expression data

Hyper-parameters used for XGBoost. (DOCX 196 kb)

Research paper thumbnail of Additional file 7: Figure S3. of A comprehensive genomic pan-cancer classification using The Cancer Genome Atlas gene expression data

Post-procurement survival probability for patients in the three subtypes of (a) ACC, (b) BLCA, (c... more Post-procurement survival probability for patients in the three subtypes of (a) ACC, (b) BLCA, (c) BRCA, (d) KIRC, (e) KIRP, (f) LGG, and (g) PAAD tumors identified by k-means analysis based on RNA-seq expression data of the top 50 genes. (DOCX 15 kb)

Research paper thumbnail of Additional file 3: Table S3. of A comprehensive genomic pan-cancer classification using The Cancer Genome Atlas gene expression data

Schematic of proportion of times samples in the test set were assigned to each of the 31 tumor ty... more Schematic of proportion of times samples in the test set were assigned to each of the 31 tumor types and the category of â unclassifiableâ across 1000 GA/KNN runs for each of two training/testing partitions (2000 runs total). Only four tumor types (ACC, BLCA, BRCA, and UVM) are shown with sample names denoted generically as S1 through Sn, where n is the number of samples available for that tumor type. The column containing the proportion correctly classified (Ď cc) is shown in boldface. (DOCX 21 kb)

Research paper thumbnail of Additional file 14: Figure S9. of A comprehensive genomic pan-cancer classification using The Cancer Genome Atlas gene expression data

Boxplot BNC1 expression data in the 23 sex non-specific tumors from males (blue) and females (pin... more Boxplot BNC1 expression data in the 23 sex non-specific tumors from males (blue) and females (pink). (DOCX 126 kb)

Research paper thumbnail of Additional file 11: Figure S7. of A comprehensive genomic pan-cancer classification using The Cancer Genome Atlas gene expression data

Proportion of test-set samples predicted to be each of the 23 sex non-specific tumor types in mal... more Proportion of test-set samples predicted to be each of the 23 sex non-specific tumor types in male patients. Y-axis lists the 23 actual tumor types; X-axis lists the 24 possible classification categories (23 tumor types plus â unclassifiedâ [UC]). Each bar represents one of the 24 proportions that samples from the actual tumor type were predicted to be. The 24 plotted proportions represent averages from the corresponding proportions for all samples of the actual tumor type. (DOCX 1745 kb)

Research paper thumbnail of Additional file 13: Figure S8. of A comprehensive genomic pan-cancer classification using The Cancer Genome Atlas gene expression data

Heatmap representations of the expression patterns of the top genes across all male and female sa... more Heatmap representations of the expression patterns of the top genes across all male and female samples. Each row (gene) was centered by the median expression value across all samples. A hierarchical clustering analysis was carried out for both samples and genes using the Euclidean distance as the similarity metric. (DOCX 15 kb)

Research paper thumbnail of Additional file 9: Figure S5. of A comprehensive genomic pan-cancer classification using The Cancer Genome Atlas gene expression data

Classification accuracies between GA/KNN and XGBoost for 10 testing sets. (DOCX 560 kb)

Research paper thumbnail of Additional file 4: Figure S1. of A comprehensive genomic pan-cancer classification using The Cancer Genome Atlas gene expression data

Scatterplots of expression levels of PA2G4 and PA2G4P4 across all tumor types. (DOCX 383 kb)

Research paper thumbnail of Characterization of SARS2 Nsp15 nuclease activity reveals it's mad about U

Nucleic Acids Research, 2021

Nsp15 is a uridine specific endoribonuclease that coronaviruses employ to cleave viral RNA and ev... more Nsp15 is a uridine specific endoribonuclease that coronaviruses employ to cleave viral RNA and evade host immune defense systems. Previous structures of Nsp15 from across Coronaviridae revealed that Nsp15 assembles into a homo-hexamer and has a conserved active site similar to RNase A. Beyond a preference for cleaving RNA 3′ of uridines, it is unknown if Nsp15 has any additional substrate preferences. Here, we used cryo-EM to capture structures of Nsp15 bound to RNA in pre- and post-cleavage states. The structures along with molecular dynamics and biochemical assays revealed critical residues involved in substrate specificity, nuclease activity, and oligomerization. Moreover, we determined how the sequence of the RNA substrate dictates cleavage and found that outside of polyU tracts, Nsp15 has a strong preference for purines 3′ of the cleaved uridine. This work advances our understanding of how Nsp15 recognizes and processes viral RNA, and will aid in the development of new anti-vir...

Research paper thumbnail of Cryo-EM Structures of the SARS-CoV-2 Endoribonuclease Nsp15

New therapeutics are urgently needed to inhibit SARS-CoV-2, the virus responsible for the on-goin... more New therapeutics are urgently needed to inhibit SARS-CoV-2, the virus responsible for the on-going Covid-19 pandemic. Nsp15, a uridine-specific endoribonuclease found in all coronaviruses, processes viral RNA to evade detection by RNA-activated host defense systems, making it a promising drug target. Previous work with SARS-CoV-1 established that Nsp15 is active as a hexamer, yet how Nsp15 recognizes and processes viral RNA remains unknown. Here we report a series of cryo-EM reconstructions of SARS-CoV-2 Nsp15. The UTP-bound cryo-EM reconstruction at 3.36 Å resolution provides molecular details into how critical residues within the Nsp15 active site recognize uridine and facilitate catalysis of the phosphodiester bond, whereas the apo-states reveal active site conformational heterogeneity. We further demonstrate the specificity and mechanism of nuclease activity by analyzing Nsp15 products using mass spectrometry. Collectively, these findings advance understanding of how Nsp15 proce...

Research paper thumbnail of Predicting Tumor Response to Drugs based on Gene-Expression Biomarkers of Sensitivity Learned from Cancer Cell Lines

SUMMARYHuman cancer cell line profiling and drug sensitivity studies provide valuable information... more SUMMARYHuman cancer cell line profiling and drug sensitivity studies provide valuable information about the therapeutic potential of drugs and their possible mechanisms of action. The goal of those studies is to translate the findings from in vitro studies of cancer cell lines into in vivo therapeutic relevance and, eventually, patients’ care. Tremendous progress has been made. In this work, we built predictive models for 453 drugs using data on gene expression and drug sensitivity (IC50) from cancer cell lines. We identified many known drug-gene interactions and uncovered several potentially novel drug-gene associations. Importantly, we further applied these predictive models to ∼17,000 bulk RNA-seq samples from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) database to predict drug sensitivity for both normal and tumor tissues. We created a web site for users to visualize and download our predicted data (https://edelgene.niehs.nih.gov/cancerRxTissue). Usi...

Research paper thumbnail of Cryo-EM reveals active site coordination within a multienzyme pre-rRNA processing complex

Nature Structural & Molecular Biology, 2019

Ribosome assembly is a complex process reliant on the coordination of transacting enzymes to prod... more Ribosome assembly is a complex process reliant on the coordination of transacting enzymes to produce functional ribosomal subunits and secure the translational capacity of the cell. Las1 is a recently discovered endoribonuclease that assembles into a multienzyme complex with the Grc3 polynucleotide kinase to orchestrate the targeted removal of a transcribed spacer (ITS2) from precursor ribosomal RNA (pre-rRNA). The essential Las1 endoribonuclease cleaves the ITS2 spacer at a defined site to initiate pre-rRNA processing. The Grc3 polynucleotide kinase subsequently phosphorylates the resulting 5'-hydroxyl RNA to signal for 5'-and 3'-exoribonucleases to degrade the ITS2. Disruption of mammalian Las1-Grc3 has been linked to congenital lethal motor neuron disease and X-linked intellectual disability disorders, thus highlighting its importance in human health; yet, its mechanism of action remains unclear. Here we report that the Las1 endoribonuclease assembles into a higher-order tetrameric complex with its binding partner the Grc3 polynucleotide kinase, which is essential for the activation of its nuclease and kinase functions. To understand how Las1-Grc3 achieves its strict nuclease specificity and coordinates its dual enzymes, we determined a series of high-resolution cryo-EM structures of Las1-Grc3 in multiple conformational states. Structural characterization of Las1-Grc3 reveals its molecular architecture harboring a composite nuclease active site flanked by two discrete RNA kinase sites. Coupled with functional studies, we identify molecular features crucial for RNA specificity and two molecular switches that coordinate nuclease and kinase function. Together, our structures and corresponding functional studies establish how Las1-Grc3 couples its enzymatic functions to drive ribosome assembly.

Research paper thumbnail of Molecular basis for processing of topoisomerase 1-triggered DNA damage by Apn2/APE2

Research paper thumbnail of Additional file 1: Table S1. of A comprehensive genomic pan-cancer classification using The Cancer Genome Atlas gene expression data

â Normalâ (normal-adjacent-to-tumor) tissue types and number of TCGA RNA-seq samples used in the ... more â Normalâ (normal-adjacent-to-tumor) tissue types and number of TCGA RNA-seq samples used in the analysis. (DOCX 18 kb)

Research paper thumbnail of Additional file 10: Figure S6. of A comprehensive genomic pan-cancer classification using The Cancer Genome Atlas gene expression data

Heatmap representation of the expression patterns of the top 50 genes selected by XGBoost across ... more Heatmap representation of the expression patterns of the top 50 genes selected by XGBoost across all 602 â normalâ samples taken adjacent to tumors from 17 tumor types. Each row (gene) was centered by the median expression value across all samples. A hierarchical clustering analysis was carried out for both samples and genes using the Euclidean distance as the similarity metric. (DOCX 15 kb)

Research paper thumbnail of Additional file 8: Figure S4. of A comprehensive genomic pan-cancer classification using The Cancer Genome Atlas gene expression data

Heatmap representation of the expression patterns of the top 50 genes across all 602 â normalâ sa... more Heatmap representation of the expression patterns of the top 50 genes across all 602 â normalâ samples taken adjacent to tumors from 17 tumor types. Each row (gene) was centered by the median expression value across all samples. A hierarchical clustering analysis was carried out for both samples and genes using the Euclidean distance as the similarity metric. (DOCX 16 kb)

Research paper thumbnail of Additional file 15: Table S5. of A comprehensive genomic pan-cancer classification using The Cancer Genome Atlas gene expression data

Mean and median of for Ď cc values for each tumor type from full female dataset, full male datase... more Mean and median of for Ď cc values for each tumor type from full female dataset, full male dataset, and the corresponding mean (sd) from the eight â matchedâ male datasets. (DOCX 283 kb)

Research paper thumbnail of Additional file 6: Figure S2. of A comprehensive genomic pan-cancer classification using The Cancer Genome Atlas gene expression data

Heatmap representation of the expression patterns of the top 50 genes across all (a) ACC, (b) BLC... more Heatmap representation of the expression patterns of the top 50 genes across all (a) ACC, (b) BLCA, (c) BRCA, (d) KIRC, (e) KIRP, (f) LGG, and (g) PAAD samples. See Fig. 3 legend for details. The colors of the horizontal bar represent the subgroups identified by k-means clustering analysis. (DOCX 60 kb)

Research paper thumbnail of Additional file 5: of A comprehensive genomic pan-cancer classification using The Cancer Genome Atlas gene expression data

Research paper thumbnail of Additional file 12: Table S4. of A comprehensive genomic pan-cancer classification using The Cancer Genome Atlas gene expression data

Genes ranked among the top 100 from either females and males. (DOCX 389 kb)

Research paper thumbnail of Additional file 2: Table S2. of A comprehensive genomic pan-cancer classification using The Cancer Genome Atlas gene expression data

Hyper-parameters used for XGBoost. (DOCX 196 kb)

Research paper thumbnail of Additional file 7: Figure S3. of A comprehensive genomic pan-cancer classification using The Cancer Genome Atlas gene expression data

Post-procurement survival probability for patients in the three subtypes of (a) ACC, (b) BLCA, (c... more Post-procurement survival probability for patients in the three subtypes of (a) ACC, (b) BLCA, (c) BRCA, (d) KIRC, (e) KIRP, (f) LGG, and (g) PAAD tumors identified by k-means analysis based on RNA-seq expression data of the top 50 genes. (DOCX 15 kb)

Research paper thumbnail of Additional file 3: Table S3. of A comprehensive genomic pan-cancer classification using The Cancer Genome Atlas gene expression data

Schematic of proportion of times samples in the test set were assigned to each of the 31 tumor ty... more Schematic of proportion of times samples in the test set were assigned to each of the 31 tumor types and the category of â unclassifiableâ across 1000 GA/KNN runs for each of two training/testing partitions (2000 runs total). Only four tumor types (ACC, BLCA, BRCA, and UVM) are shown with sample names denoted generically as S1 through Sn, where n is the number of samples available for that tumor type. The column containing the proportion correctly classified (Ď cc) is shown in boldface. (DOCX 21 kb)

Research paper thumbnail of Additional file 14: Figure S9. of A comprehensive genomic pan-cancer classification using The Cancer Genome Atlas gene expression data

Boxplot BNC1 expression data in the 23 sex non-specific tumors from males (blue) and females (pin... more Boxplot BNC1 expression data in the 23 sex non-specific tumors from males (blue) and females (pink). (DOCX 126 kb)

Research paper thumbnail of Additional file 11: Figure S7. of A comprehensive genomic pan-cancer classification using The Cancer Genome Atlas gene expression data

Proportion of test-set samples predicted to be each of the 23 sex non-specific tumor types in mal... more Proportion of test-set samples predicted to be each of the 23 sex non-specific tumor types in male patients. Y-axis lists the 23 actual tumor types; X-axis lists the 24 possible classification categories (23 tumor types plus â unclassifiedâ [UC]). Each bar represents one of the 24 proportions that samples from the actual tumor type were predicted to be. The 24 plotted proportions represent averages from the corresponding proportions for all samples of the actual tumor type. (DOCX 1745 kb)

Research paper thumbnail of Additional file 13: Figure S8. of A comprehensive genomic pan-cancer classification using The Cancer Genome Atlas gene expression data

Heatmap representations of the expression patterns of the top genes across all male and female sa... more Heatmap representations of the expression patterns of the top genes across all male and female samples. Each row (gene) was centered by the median expression value across all samples. A hierarchical clustering analysis was carried out for both samples and genes using the Euclidean distance as the similarity metric. (DOCX 15 kb)

Research paper thumbnail of Additional file 9: Figure S5. of A comprehensive genomic pan-cancer classification using The Cancer Genome Atlas gene expression data

Classification accuracies between GA/KNN and XGBoost for 10 testing sets. (DOCX 560 kb)

Research paper thumbnail of Additional file 4: Figure S1. of A comprehensive genomic pan-cancer classification using The Cancer Genome Atlas gene expression data

Scatterplots of expression levels of PA2G4 and PA2G4P4 across all tumor types. (DOCX 383 kb)

Research paper thumbnail of Characterization of SARS2 Nsp15 nuclease activity reveals it's mad about U

Nucleic Acids Research, 2021

Nsp15 is a uridine specific endoribonuclease that coronaviruses employ to cleave viral RNA and ev... more Nsp15 is a uridine specific endoribonuclease that coronaviruses employ to cleave viral RNA and evade host immune defense systems. Previous structures of Nsp15 from across Coronaviridae revealed that Nsp15 assembles into a homo-hexamer and has a conserved active site similar to RNase A. Beyond a preference for cleaving RNA 3′ of uridines, it is unknown if Nsp15 has any additional substrate preferences. Here, we used cryo-EM to capture structures of Nsp15 bound to RNA in pre- and post-cleavage states. The structures along with molecular dynamics and biochemical assays revealed critical residues involved in substrate specificity, nuclease activity, and oligomerization. Moreover, we determined how the sequence of the RNA substrate dictates cleavage and found that outside of polyU tracts, Nsp15 has a strong preference for purines 3′ of the cleaved uridine. This work advances our understanding of how Nsp15 recognizes and processes viral RNA, and will aid in the development of new anti-vir...

Research paper thumbnail of Cryo-EM Structures of the SARS-CoV-2 Endoribonuclease Nsp15

New therapeutics are urgently needed to inhibit SARS-CoV-2, the virus responsible for the on-goin... more New therapeutics are urgently needed to inhibit SARS-CoV-2, the virus responsible for the on-going Covid-19 pandemic. Nsp15, a uridine-specific endoribonuclease found in all coronaviruses, processes viral RNA to evade detection by RNA-activated host defense systems, making it a promising drug target. Previous work with SARS-CoV-1 established that Nsp15 is active as a hexamer, yet how Nsp15 recognizes and processes viral RNA remains unknown. Here we report a series of cryo-EM reconstructions of SARS-CoV-2 Nsp15. The UTP-bound cryo-EM reconstruction at 3.36 Å resolution provides molecular details into how critical residues within the Nsp15 active site recognize uridine and facilitate catalysis of the phosphodiester bond, whereas the apo-states reveal active site conformational heterogeneity. We further demonstrate the specificity and mechanism of nuclease activity by analyzing Nsp15 products using mass spectrometry. Collectively, these findings advance understanding of how Nsp15 proce...

Research paper thumbnail of Predicting Tumor Response to Drugs based on Gene-Expression Biomarkers of Sensitivity Learned from Cancer Cell Lines

SUMMARYHuman cancer cell line profiling and drug sensitivity studies provide valuable information... more SUMMARYHuman cancer cell line profiling and drug sensitivity studies provide valuable information about the therapeutic potential of drugs and their possible mechanisms of action. The goal of those studies is to translate the findings from in vitro studies of cancer cell lines into in vivo therapeutic relevance and, eventually, patients’ care. Tremendous progress has been made. In this work, we built predictive models for 453 drugs using data on gene expression and drug sensitivity (IC50) from cancer cell lines. We identified many known drug-gene interactions and uncovered several potentially novel drug-gene associations. Importantly, we further applied these predictive models to ∼17,000 bulk RNA-seq samples from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) database to predict drug sensitivity for both normal and tumor tissues. We created a web site for users to visualize and download our predicted data (https://edelgene.niehs.nih.gov/cancerRxTissue). Usi...

Research paper thumbnail of Cryo-EM reveals active site coordination within a multienzyme pre-rRNA processing complex

Nature Structural & Molecular Biology, 2019

Ribosome assembly is a complex process reliant on the coordination of transacting enzymes to prod... more Ribosome assembly is a complex process reliant on the coordination of transacting enzymes to produce functional ribosomal subunits and secure the translational capacity of the cell. Las1 is a recently discovered endoribonuclease that assembles into a multienzyme complex with the Grc3 polynucleotide kinase to orchestrate the targeted removal of a transcribed spacer (ITS2) from precursor ribosomal RNA (pre-rRNA). The essential Las1 endoribonuclease cleaves the ITS2 spacer at a defined site to initiate pre-rRNA processing. The Grc3 polynucleotide kinase subsequently phosphorylates the resulting 5'-hydroxyl RNA to signal for 5'-and 3'-exoribonucleases to degrade the ITS2. Disruption of mammalian Las1-Grc3 has been linked to congenital lethal motor neuron disease and X-linked intellectual disability disorders, thus highlighting its importance in human health; yet, its mechanism of action remains unclear. Here we report that the Las1 endoribonuclease assembles into a higher-order tetrameric complex with its binding partner the Grc3 polynucleotide kinase, which is essential for the activation of its nuclease and kinase functions. To understand how Las1-Grc3 achieves its strict nuclease specificity and coordinates its dual enzymes, we determined a series of high-resolution cryo-EM structures of Las1-Grc3 in multiple conformational states. Structural characterization of Las1-Grc3 reveals its molecular architecture harboring a composite nuclease active site flanked by two discrete RNA kinase sites. Coupled with functional studies, we identify molecular features crucial for RNA specificity and two molecular switches that coordinate nuclease and kinase function. Together, our structures and corresponding functional studies establish how Las1-Grc3 couples its enzymatic functions to drive ribosome assembly.