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3. Abstract B024: Immune exhaustion and reversal of progestin-related immune modulation in adaptive resistance to levonorgestrel intrauterine device for treatment of atypical hyperplasia and early endometrial cancer

Author

Bowen, Mikayla B., primary, Melendez, Brenda, additional, Zhang, Qian, additional, Yang, Richard, additional, Fellman, Bryan, additional, Lawson, Barrett, additional, Adjei, Naomi, additional, Celestino, Joseph, additional, Nguyen, Tri, additional, Wani, Khalida, additional, Singh, Bhavana, additional, Straub, Christof, additional, Zhang, Liang, additional, Tan, Cheryl, additional, New, Felicia, additional, Urbauer, Diana, additional, Lazar, Alexander, additional, Lu, Karen, additional, Wargo, Jennifer, additional, Westin, Shannon N., additional, and Yates, Melinda S., additional

Published
2024
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4. Spatial Transcriptomics Resolve an Emphysema-specific Lymphoid Follicle B Cell Signature in COPD

Author

Rojas-Quintero, Joselyn, primary, Ochsner, Scott A, additional, New, Felicia, additional, Divakar, Prajan, additional, Yang, Chen Xi, additional, Wu, Tianshi David, additional, Robinson, Jerid, additional, Shimoga Chandrashekar, Darshan, additional, Banovich, Nicholas E, additional, Rosas, Ivan O., additional, Sauler, Maor, additional, Kheradmand, Farrah, additional, Gaggar, Amit, additional, Margaroli, Camilla, additional, San Jose Estepar, Raul, additional, McKenna, Neil J, additional, and Polverino, Francesca, additional

Published
2023
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5. Ultra High‐Plex Spatial Proteogenomic Investigation of Giant Cell Glioblastoma Multiforme Immune Infiltrates Reveals Distinct Protein and RNA Expression Profiles

Author

Bonnett, Shilah, primary, Rosenbloom, Alyssa, additional, Ong, Giang, additional, Conner, Mark, additional, Newhouse, Daniel, additional, New, Felicia, additional, Sato, Hiromi, additional, Phan, Chi, additional, Ilcisin, Saskia, additional, Lyssand, John, additional, Geiss, Gary, additional, and Beechem, Joseph M., additional

Published
2023
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6. Single nuclei chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestry

Author

Nakshatri, Harikrishna, primary, Bhat-Nakshatri, Poornima, additional, Gao, Hongyu, additional, Khatpe, Aditi, additional, McGuire, Patrick, additional, Erdogan, Cihat, additional, Chen, Duojiao, additional, Jiang, Guanglong, additional, New, Felicia, additional, German, Rana, additional, Storniolo, Anna Maria, additional, and Liu, Yunlong, additional

Published
2023
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7. Single nuclei chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestry

Author

Bhat-Nakshatri, Poornima, primary, Gao, Hongyu, additional, Khatpe, Aditi S, additional, McGuire, Patrick C, additional, Erdogan, Cihat, additional, Chen, Duojiao, additional, Jiang, Guanglong, additional, New, Felicia, additional, German, Rana, additional, Storniolo, Anna Maria, additional, Liu, Yunlong, additional, and Nakshatri, Harikrishna, additional

Published
2023
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8. Spatial Transcriptomics Resolve an Emphysema-Specific Lymphoid Follicle B Cell Signature in Chronic Obstructive Pulmonary Disease.

Author

Rojas-Quintero, Joselyn, Ochsner, Scott A., New, Felicia, Divakar, Prajan, Chen Xi Yang, Wu, Tianshi David, Robinson, Jerid, Chandrashekar, Darshan Shimoga, Banovich, Nicholas E., Rosas, Ivan O., Sauler, Maor, Kheradmand, Farrah, Gaggar, Amit, Margaroli, Camilla, Estepar, Raul San Jose, McKenna, Neil J., and Polverino, Francesca

Subjects
CHRONIC obstructive pulmonary disease, B cells, TRANSCRIPTOMES, GENE regulatory networks, GENE expression
Abstract

Rationale: Within chronic obstructive pulmonary disease (COPD), emphysema is characterized by a significant yet partially understood B cell immune component. Objectives: To characterize the transcriptomic signatures from lymphoid follicles (LFs) in ever-smokers without COPD and patients with COPD with varying degrees of emphysema. Methods: Lung sections from 40 patients with COPD and eversmokers were used for LF proteomic and transcriptomic spatial profiling. Formalin- and O.C.T.-fixed lung samples obtained from biopsies or lung explants were assessed for LF presence. Emphysema measurements were obtained from clinical chest computed tomographic scans. High-confidence transcriptional target intersection analyses were conducted to resolve emphysema-induced transcriptional networks. Measurements and Main Results: Overall, 115 LFs from eversmokers andGlobal Initiative for ChronicObstructive LungDisease (GOLD) 1-2 andGOLD3-4 patients were analyzed. No LFs were found in never-smokers. Differential gene expression analysis revealed significantly increased expression of LF assembly and B cellmarker genes in subjects with severe emphysema. High-confidence transcriptional analysis revealed activation of an abnormal B cell activity signature in LFs (q-value= 2.56E-111). LFs frompatients withGOLD 1-2 COPDwith emphysema showed significantly increased expression of genes associated with antigen presentation, inflammation, and B cell activation and proliferation. LFs frompatients with GOLD1-2COPD without emphysema showed an antiinflammatory profile. The extent of centrilobular emphysema was significantly associated with genes involved in B cellmaturation and antibody production. Protein-RNA network analysis showed that LFs in emphysema have a unique signature skewed toward chronic B cell activation. Conclusions: An off-targeted B cell activation within LFs is associated with autoimmune-mediated emphysema pathogenesis. [ABSTRACT FROM AUTHOR]

Published
2024
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9. FIGURE 2 from Ultra High-plex Spatial Proteogenomic Investigation of Giant Cell Glioblastoma Multiforme Immune Infiltrates Reveals Distinct Protein and RNA Expression Profiles

Author

Bonnett, Shilah A., primary, Rosenbloom, Alyssa B., primary, Ong, Giang T., primary, Conner, Mark, primary, Rininger, Aric B.E., primary, Newhouse, Daniel, primary, New, Felicia, primary, Phan, Chi Q., primary, Ilcisin, Saskia, primary, Sato, Hiromi, primary, Lyssand, John S., primary, Geiss, Gary, primary, and Beechem, Joseph M., primary

Published
2023
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10. FIGURE 5 from Ultra High-plex Spatial Proteogenomic Investigation of Giant Cell Glioblastoma Multiforme Immune Infiltrates Reveals Distinct Protein and RNA Expression Profiles

Author

Bonnett, Shilah A., primary, Rosenbloom, Alyssa B., primary, Ong, Giang T., primary, Conner, Mark, primary, Rininger, Aric B.E., primary, Newhouse, Daniel, primary, New, Felicia, primary, Phan, Chi Q., primary, Ilcisin, Saskia, primary, Sato, Hiromi, primary, Lyssand, John S., primary, Geiss, Gary, primary, and Beechem, Joseph M., primary

Published
2023
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11. FIGURE 6 from Ultra High-plex Spatial Proteogenomic Investigation of Giant Cell Glioblastoma Multiforme Immune Infiltrates Reveals Distinct Protein and RNA Expression Profiles

Author

Bonnett, Shilah A., primary, Rosenbloom, Alyssa B., primary, Ong, Giang T., primary, Conner, Mark, primary, Rininger, Aric B.E., primary, Newhouse, Daniel, primary, New, Felicia, primary, Phan, Chi Q., primary, Ilcisin, Saskia, primary, Sato, Hiromi, primary, Lyssand, John S., primary, Geiss, Gary, primary, and Beechem, Joseph M., primary

Published
2023
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12. Supplementary Tables S1-S6 from Ultra High-plex Spatial Proteogenomic Investigation of Giant Cell Glioblastoma Multiforme Immune Infiltrates Reveals Distinct Protein and RNA Expression Profiles

Author

Bonnett, Shilah A., primary, Rosenbloom, Alyssa B., primary, Ong, Giang T., primary, Conner, Mark, primary, Rininger, Aric B.E., primary, Newhouse, Daniel, primary, New, Felicia, primary, Phan, Chi Q., primary, Ilcisin, Saskia, primary, Sato, Hiromi, primary, Lyssand, John S., primary, Geiss, Gary, primary, and Beechem, Joseph M., primary

Published
2023
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13. FIGURE 7 from Ultra High-plex Spatial Proteogenomic Investigation of Giant Cell Glioblastoma Multiforme Immune Infiltrates Reveals Distinct Protein and RNA Expression Profiles

Author

Bonnett, Shilah A., primary, Rosenbloom, Alyssa B., primary, Ong, Giang T., primary, Conner, Mark, primary, Rininger, Aric B.E., primary, Newhouse, Daniel, primary, New, Felicia, primary, Phan, Chi Q., primary, Ilcisin, Saskia, primary, Sato, Hiromi, primary, Lyssand, John S., primary, Geiss, Gary, primary, and Beechem, Joseph M., primary

Published
2023
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14. Supplementary Methods S1 from Ultra High-plex Spatial Proteogenomic Investigation of Giant Cell Glioblastoma Multiforme Immune Infiltrates Reveals Distinct Protein and RNA Expression Profiles

Author

Bonnett, Shilah A., primary, Rosenbloom, Alyssa B., primary, Ong, Giang T., primary, Conner, Mark, primary, Rininger, Aric B.E., primary, Newhouse, Daniel, primary, New, Felicia, primary, Phan, Chi Q., primary, Ilcisin, Saskia, primary, Sato, Hiromi, primary, Lyssand, John S., primary, Geiss, Gary, primary, and Beechem, Joseph M., primary

Published
2023
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15. FIGURE 3 from Ultra High-plex Spatial Proteogenomic Investigation of Giant Cell Glioblastoma Multiforme Immune Infiltrates Reveals Distinct Protein and RNA Expression Profiles

Author

Bonnett, Shilah A., primary, Rosenbloom, Alyssa B., primary, Ong, Giang T., primary, Conner, Mark, primary, Rininger, Aric B.E., primary, Newhouse, Daniel, primary, New, Felicia, primary, Phan, Chi Q., primary, Ilcisin, Saskia, primary, Sato, Hiromi, primary, Lyssand, John S., primary, Geiss, Gary, primary, and Beechem, Joseph M., primary

Published
2023
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16. Supplementary Figures S10-S15 from Ultra High-plex Spatial Proteogenomic Investigation of Giant Cell Glioblastoma Multiforme Immune Infiltrates Reveals Distinct Protein and RNA Expression Profiles

Author

Bonnett, Shilah A., primary, Rosenbloom, Alyssa B., primary, Ong, Giang T., primary, Conner, Mark, primary, Rininger, Aric B.E., primary, Newhouse, Daniel, primary, New, Felicia, primary, Phan, Chi Q., primary, Ilcisin, Saskia, primary, Sato, Hiromi, primary, Lyssand, John S., primary, Geiss, Gary, primary, and Beechem, Joseph M., primary

Published
2023
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17. FIGURE 4 from Ultra High-plex Spatial Proteogenomic Investigation of Giant Cell Glioblastoma Multiforme Immune Infiltrates Reveals Distinct Protein and RNA Expression Profiles

Author

Bonnett, Shilah A., primary, Rosenbloom, Alyssa B., primary, Ong, Giang T., primary, Conner, Mark, primary, Rininger, Aric B.E., primary, Newhouse, Daniel, primary, New, Felicia, primary, Phan, Chi Q., primary, Ilcisin, Saskia, primary, Sato, Hiromi, primary, Lyssand, John S., primary, Geiss, Gary, primary, and Beechem, Joseph M., primary

Published
2023
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18. Ultra High-plex Spatial Proteogenomic Investigation of Giant Cell Glioblastoma Multiforme Immune Infiltrates Reveals Distinct Protein and RNA Expression Profiles

Author

Bonnett, Shilah A., primary, Rosenbloom, Alyssa B., additional, Ong, Giang T., additional, Conner, Mark, additional, Rininger, Aric B.E., additional, Newhouse, Daniel, additional, New, Felicia, additional, Phan, Chi Q., additional, Ilcisin, Saskia, additional, Sato, Hiromi, additional, Lyssand, John S., additional, Geiss, Gary, additional, and Beechem, Joseph M., additional

Published
2023
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19. Data from Ultra High-plex Spatial Proteogenomic Investigation of Giant Cell Glioblastoma Multiforme Immune Infiltrates Reveals Distinct Protein and RNA Expression Profiles

Author

Bonnett, Shilah A., primary, Rosenbloom, Alyssa B., primary, Ong, Giang T., primary, Conner, Mark, primary, Rininger, Aric B.E., primary, Newhouse, Daniel, primary, New, Felicia, primary, Phan, Chi Q., primary, Ilcisin, Saskia, primary, Sato, Hiromi, primary, Lyssand, John S., primary, Geiss, Gary, primary, and Beechem, Joseph M., primary

Published
2023
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20. Supplementary Figures S10-S15 from Ultra High-Plex Spatial Proteogenomic Investigation of Giant Cell Glioblastoma Multiforme Immune Infiltrates Reveals Distinct Protein and RNA Expression Profiles

Author

Bonnett, Shilah A, primary, Rosenbloom, Alyssa B, primary, Ong, Giang T, primary, Conner, Mark, primary, Rininger, Aric BE, primary, Newhouse, Daniel, primary, New, Felicia, primary, Phan, Chi Q., primary, Ilcisin, Saskia, primary, Sato, Hiromi, primary, Lyssand, John S, primary, Geiss, Gary, primary, and Beechem, Joseph M., primary

Published
2023
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21. Data from Ultra High-Plex Spatial Proteogenomic Investigation of Giant Cell Glioblastoma Multiforme Immune Infiltrates Reveals Distinct Protein and RNA Expression Profiles

Author

Bonnett, Shilah A, primary, Rosenbloom, Alyssa B, primary, Ong, Giang T, primary, Conner, Mark, primary, Rininger, Aric BE, primary, Newhouse, Daniel, primary, New, Felicia, primary, Phan, Chi Q., primary, Ilcisin, Saskia, primary, Sato, Hiromi, primary, Lyssand, John S, primary, Geiss, Gary, primary, and Beechem, Joseph M., primary

Published
2023
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22. Supplementary Tables S1-S6 from Ultra High-Plex Spatial Proteogenomic Investigation of Giant Cell Glioblastoma Multiforme Immune Infiltrates Reveals Distinct Protein and RNA Expression Profiles

Author

Bonnett, Shilah A, primary, Rosenbloom, Alyssa B, primary, Ong, Giang T, primary, Conner, Mark, primary, Rininger, Aric BE, primary, Newhouse, Daniel, primary, New, Felicia, primary, Phan, Chi Q., primary, Ilcisin, Saskia, primary, Sato, Hiromi, primary, Lyssand, John S, primary, Geiss, Gary, primary, and Beechem, Joseph M., primary

Published
2023
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23. Supplementary Methods S1 from Ultra High-Plex Spatial Proteogenomic Investigation of Giant Cell Glioblastoma Multiforme Immune Infiltrates Reveals Distinct Protein and RNA Expression Profiles

Author

Bonnett, Shilah A, primary, Rosenbloom, Alyssa B, primary, Ong, Giang T, primary, Conner, Mark, primary, Rininger, Aric BE, primary, Newhouse, Daniel, primary, New, Felicia, primary, Phan, Chi Q., primary, Ilcisin, Saskia, primary, Sato, Hiromi, primary, Lyssand, John S, primary, Geiss, Gary, primary, and Beechem, Joseph M., primary

Published
2023
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24. Abstract 4310: Ultra high-plex spatial proteogenomic investigation of giant cell glioblastoma multiforme immune infiltrates reveals distinct protein and RNA expression profiles

Author

Bonnett, Shilah, primary, Rosenbloom, Alyssa, additional, Ong, Giang, additional, Conner, Mark, additional, Newhouse, Daniel, additional, New, Felicia, additional, Sato, Hiromi, additional, Pha, Chi, additional, Ilcisin, Saskia, additional, Lyssand, John, additional, Geiss, Gary, additional, and Beechem, Joseph M., additional

Published
2023
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25. Ultra High-Plex Spatial Proteogenomic Investigation of Giant Cell Glioblastoma Multiforme Immune Infiltrates Reveals Distinct Protein and RNA Expression Profiles

Author

Bonnett, Shilah A., primary, Rosenbloom, Alyssa, additional, Ong, Giang, additional, Conner, Mark, additional, Rininger, Aric, additional, Newhouse, Daniel, additional, New, Felicia, additional, Phan, Chi, additional, Ilcisin, Saskia, additional, Sato, Hiromi, additional, Lyssand, John, additional, Geiss, Gary, additional, and Beechem, Joseph M., additional

Published
2022
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35. A Large Panel of Drosophila simulans Reveals an Abundance of Common Variants.

Author

Signor, Sarah A., New, Felicia N., and Nuzhdin, Sergey

Subjects
*DROSOPHILA genetics, *GENOTYPES, *POPULATION genetics, *GENETIC polymorphisms, *DNA analysis
Abstract

The rapidly expanding availability of large NGS data sets provides an opportunity to investigate population genetics at an unprecedented scale. Drosophila simulans is the sister species of the model organism Drosophila melanogaster, and is often presumed to share similar demographic history. However, previous population genetic and ecological work suggests very different signatures of selection and demography. Here, we sequence a new panel of 170 inbred genotypes of a North American population of D. simulans, a valuable complement to the DGRP and other D. melanogaster panels. We find some unexpected signatures of demography, in the form of excess intermediate frequency polymorphisms. Simulations suggest that this is possibly due to a recent population contraction and selection. We examine the outliers in the D. simulans genome determined by a haplotype test to attempt to parse the contribution of demography and selection to the patterns observed in this population. Untangling the relative contribution of demography and selection to genomic patterns of variation is challenging, however, it is clear that although D. melanogaster was thought to share demographic history with D. simulans different forces are at work in shaping genomic variation in this population of D. simulans. [ABSTRACT FROM AUTHOR]

Published
2018
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