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1. Molecular classification and biomarkers of clinical outcome in breast ductal carcinoma in situ: Analysis of TBCRC 038 and RAHBT cohorts

Author

Strand, Siri H., Rivero-Gutiérrez, Belén, Houlahan, Kathleen E., Seoane, Jose A., King, Lorraine M., Risom, Tyler, Simpson, Lunden A., Vennam, Sujay, Khan, Aziz, Cisneros, Luis, Hardman, Timothy, Harmon, Bryan, Couch, Fergus, Gallagher, Kristalyn, Kilgore, Mark, Wei, Shi, DeMichele, Angela, King, Tari, McAuliffe, Priscilla F., Nangia, Julie, Lee, Joanna, Tseng, Jennifer, Storniolo, Anna Maria, Thompson, Alastair M., Gupta, Gaorav P., Burns, Robyn, Veis, Deborah J., DeSchryver, Katherine, Zhu, Chunfang, Matusiak, Magdalena, Wang, Jason, Zhu, Shirley X., Tappenden, Jen, Ding, Daisy Yi, Zhang, Dadong, Luo, Jingqin, Jiang, Shu, Varma, Sushama, Anderson, Lauren, Straub, Cody, Srivastava, Sucheta, Curtis, Christina, Tibshirani, Rob, Angelo, Robert Michael, Hall, Allison, Owzar, Kouros, Polyak, Kornelia, Maley, Carlo, Marks, Jeffrey R., Colditz, Graham A., Hwang, E. Shelley, and West, Robert B.

Published
2022
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3. Single Cell Expression Analysis of Ductal Carcinoma in Situ Identifies Alterations in Epithelial Integrity

Author

Qin, Xiaodi, primary, Strand, Siri H, additional, Lee, Marissa R., additional, van Ijzendoorn, David G. P., additional, Zhu, ChunFang, additional, Vennam, Sujay, additional, Varma, Sushama, additional, Hall, Allison, additional, King, Lorraine, additional, Simpson, Lunden, additional, Luo, Xiaoke, additional, Colditz, Graham A., additional, Jiang, Shu, additional, Hwang, E. Shelley, additional, Marks, Jeffrey R., additional, Owzar, Kouros, additional, and West, Robert B., additional

Published
2023
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6. Reproductive investment in a phyletic giant, the Caribbean king crab Damithrax spinosissimus: exploring egg production costs in large brooding marine inertebrates

Author

Baeza, J. Antonio, Simpson, Lunden, Ambrosio, L.J., Gueron, Rodrigo, Mora, Nathalia, and Owen, Dallas

Subjects
King crabs -- Economic aspects, Agricultural productivity -- Management, Company business management, Biological sciences, Zoology and wildlife conservation
Abstract

ABSTRACT The Caribbean king crab Damithrax spinosissimus, a phyletic giant and the largest crab in the western Atlantic, was used to explore the costs of brooding, in terms of reproductive [...]

Published
2015
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7. Abstract GS4-07: The Breast PreCancer Atlas DCIS genomic signatures define biology and correlate with clinical outcomes: An analysis of TBCRC 038 and RAHBT cohorts

Author

Strand, Siri H, primary, Rivero-Gutiérrez, Belén, additional, Houlahan, Kathleen E, additional, Seoane, Jose A, additional, King, Lorraine M, additional, Risom, Tyler, additional, Simpson, Lunden, additional, Vennam, Sujay, additional, Khan, Aziz, additional, Hardman, Timothy, additional, Harmon, Bryan E, additional, Couch, Fergus J, additional, Gallagher, Kristalyn, additional, Kilgore, Mark, additional, Wei, Shi, additional, DeMichele, Angela, additional, King, Tari, additional, McAuliffe, Priscilla F, additional, Nangia, Julie, additional, Lee, Joanna, additional, Tseng, Jennifer, additional, Storniolo, Anna Maria, additional, Thompson, Alastair, additional, Gupta, Gaorav, additional, Burns, Robyn, additional, Veis, Deborah J, additional, DeSchryver, Katherine, additional, Zhu, Chunfang, additional, Matusiak, Magdalena, additional, Wang, Jason, additional, Zhu, Shirley X, additional, Tappenden, Jen, additional, Ding, Daisy Yi, additional, Zhang, Dadong, additional, Luo, Jingqin, additional, Jiang, Shu, additional, Varma, Sushama, additional, Straub, Cody, additional, Srivastava, Sucheta, additional, Curtis, Christina, additional, Tibshirani, Rob, additional, Angelo, Robert Michael, additional, Hall, Allison, additional, Owzar, Kouros, additional, Polyak, Kornelia, additional, Maley, Carlo, additional, Marks, Jeffrey R, additional, Colditz, Graham A, additional, Hwang, E Shelley, additional, and West, Robert B, additional

Published
2022
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8. DCIS genomic signatures define biology and clinical outcome: Human Tumor Atlas Network (HTAN) analysis of TBCRC 038 and RAHBT cohorts

Author

Strand, Siri H, primary, Rivero-Gutiérrez, Belén, additional, Houlahan, Kathleen E, additional, Seoane, Jose A, additional, King, Lorraine M, additional, Risom, Tyler, additional, Simpson, Lunden A, additional, Vennam, Sujay, additional, Khan, Aziz, additional, Cisneros, Luis, additional, Hardman, Timothy, additional, Harmon, Bryan, additional, Couch, Fergus, additional, Gallagher, Kristalyn, additional, Kilgore, Mark, additional, Wei, Shi, additional, DeMichele, Angela, additional, King, Tari, additional, McAuliffe, Priscilla F, additional, Nangia, Julie, additional, Lee, Joanna, additional, Tseng, Jennifer, additional, Storniolo, Anna Maria, additional, Thompson, Alastair M, additional, Gupta, Gaorav P, additional, Burns, Robyn, additional, Veis, Deborah J, additional, DeSchryver, Katherine, additional, Zhu, Chunfang, additional, Matusiak, Magdalena, additional, Wang, Jason, additional, Zhu, Shirley X, additional, Tappenden, Jen, additional, Ding, Daisy Yi, additional, Zhang, Dadong, additional, Luo, Jingqin, additional, Jiang, Shu, additional, Varma, Sushama, additional, Anderson, Lauren, additional, Straub, Cody, additional, Srivastava, Sucheta, additional, Curtis, Christina, additional, Tibshirani, Rob, additional, Angelo, Robert Michael, additional, Hall, Allison, additional, Owzar, Kouros, additional, Polyak, Kornelia, additional, Maley, Carlo, additional, Marks, Jeffrey R, additional, Colditz, Graham A, additional, Hwang, E Shelley, additional, and West, Robert B, additional

Published
2021
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9. Molecular classification and biomarkers of clinical outcome in breast ductal carcinoma in situ: Analysis of TBCRC 038 and RAHBT cohorts

Author

Strand, Siri H., Rivero-Gutiérrez, Belén, Houlahan, Kathleen E., Seoane, Jose A., King, Lorraine M., Risom, Tyler, Simpson, Lunden A., Vennam, Sujay, Khan, Aziz, Cisneros, Luis, Hardman, Timothy, Harmon, Bryan, Couch, Fergus, Gallagher, Kristalyn, Kilgore, Mark, We, Shi, DeMichele, Angela, King, Tari, McAuliffe, Priscilla F., Nangia, Julie, Lee, Joanna, Tseng, Jennifer, Storniolo, Anna Maria, Thompson, Alastair M., Gupta, Gaorav P., Burns, Robyn, Veis, Deborah J., DeSchryver, Katherine, Zhu, Chunfang, Matusiak, Magdalena, Wang, Jason, Zhu, Shirley X., Tappenden, Jen, Ding, Daisy Yi, Zhang, Dadong, Luo, Jingqin, Jiang, Shu, Varma, Sushama, Anderson, Lauren, Straub, Cody, Srivastava, Sucheta, Curtis, Christina, Tibshirani, Rob, Angelo, Robert Michael, Hall, Allison, Owzar, Kouros, Polyak, Kornelia, Maley, Carlo, Marks, Jeffrey R., Colditz, Graham A., Hwang, E. Shelley, and West, Robert B.

Published
2023
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10. Abstract PD5-08: The human tumor atlas network (HTAN) breast pre cancer atlas: A multi-omic integrative analysis of ductal carcinoma in situ (DCIS) and correlation with clinical outcomes

Author

Hwang, Shelley, primary, Strand, Siri H, additional, Rivero, Belen, additional, King, Lorraine, additional, Risom, Tyler, additional, Harmon, Bryan, additional, Couch, Fergus, additional, Gallagher, Kristalyn, additional, Kilgore, Mark, additional, Wei, Shi, additional, DeMichele, Angela, additional, King, Tari, additional, McAuliffe, Priscilla, additional, Nangia, Julie, additional, Storniolo, Ana Maria, additional, Thompson, Alastair, additional, Gupta, Gaorav, additional, Lee, Joanna, additional, Tseng, Jennifer, additional, Burns, Robyn, additional, Zhu, ChunFang, additional, Matusiak, Magda, additional, Zhu, Shirley X, additional, Wang, Jason, additional, Seoane, Jose, additional, Tappenden, Jen, additional, Ding, Daisy, additional, Zhang, Dadong, additional, Luo, Jingqin, additional, Vennam, Sujay, additional, Varma, Sushama, additional, Simpson, Lunden, additional, Cisneros, Luis, additional, Hardman, Timmothy, additional, Anderson, Lauren, additional, Straub, Cody, additional, Srivastava, Sucheta, additional, Veis, Deb J, additional, Curtis, Christina, additional, Tibshirani, Rob, additional, Angelo, Robert Michael, additional, Hall, Allison, additional, Owzar, Kouros, additional, Polyak, Kornelia, additional, Maley, Carlo, additional, Marks, Jeff, additional, Colditz, Graham, additional, and West, Robert B, additional

Published
2021
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11. The Human Tumor Atlas Network (HTAN) Breast Precancer Atlas: A Multi-Omic Integrative Analysis of Ductal Carcinoma in situ With Clinical Outcomes

Author

Strand, Siri H., primary, Rivero-Gutiérrez, Belén, additional, Houlahan, Kathleen E., additional, Seoane, Jose A., additional, King, Lorraine, additional, Risom, Tyler, additional, Simpson, Lunden A., additional, Vennam, Sujay, additional, Kahn, Aziz, additional, Cisneros, Luis, additional, Hardman, Timothy, additional, Harmon, Bryan, additional, Couch, Fergus, additional, Gallagher, Kristalyn, additional, Kilgore, Mark, additional, Rocque, Gabrielle B., additional, DeMichele, Angela, additional, King, Tari, additional, McAuliffe, Priscilla, additional, Nangia, Julie, additional, Lee, Joanna, additional, Tseng, Jennifer, additional, Storniolo, Ana Maria, additional, Thompson, Alastair, additional, Gupta, Gaorav, additional, Burns, Robyn, additional, Veis, Deborah J., additional, DeSchryver, Katherine, additional, Zhu, Chunfang, additional, Matusiak, Magdalena, additional, Wang, Jason, additional, Zhu, Shirley X., additional, Tappenden, Jen, additional, Ding, Daisy Yi, additional, Zhang, Dadong, additional, Luo, Jingqin, additional, Jiang, Shu, additional, Varma, Sushama, additional, Anderson, Lauren, additional, Straub, Cody, additional, Srivastava, Sucheta, additional, Curtis, Christina, additional, Tibshirani, Rob, additional, Angelo, Robert Michael, additional, Hall, Allison, additional, Owzar, Kouros, additional, Polyak, Kornelia, additional, Maley, Carlo, additional, Marks, Jeffrey R., additional, Colditz, Graham A., additional, Hwang, E. Shelley, additional, and West, Robert B., additional

Published
2021
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12. Abstract PR02: Inferring the evolutionary dynamics of ductal carcinoma in situ through multi-regional sequencing and mathematical modeling

Author

Ryser, Marc D., primary, Sorribes, Inmaculada C., additional, Greenwald, Matthew, additional, Wu, Ethan, additional, Hall, Allison, additional, Mallo, Diego, additional, King, Lorraine M., additional, Hardman, Timothy, additional, Simpson, Lunden, additional, Maley, Carlo C., additional, Marks, Jeffrey R., additional, Shibata, Darryl, additional, and Hwang, E. Shelley, additional

Published
2020
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13. Abstract 2683: Ductal carcinoma in situ is a multiclonal disease

Author

Ryser, Marc D., primary, Sorribes, Inmaculada C., additional, Greenwald, Matthew, additional, Hall, Allison, additional, Mallo, Diego, additional, King, Lorraine M., additional, Hardman, Timothy, additional, Simpson, Lunden, additional, Maley, Carlo C., additional, Marks, Jeffrey R., additional, Shibata, Darryl, additional, and Hwang, E. Shelley, additional

Published
2020
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18. Sexual dimorphism and allometric growth in the enigmatic pygmy crab Petramithrax pygmaeus(Bell, 1836) (Decapoda: Brachyura: Mithracidae), with a formal test of Rensch’s rule in spider crabs (superfamily Majoidea)

Author

Simpson, Lunden A., Simpson, Lunden A., and Simpson, Lunden A.

Abstract

Rensch’s rule, a well-studied macroevolutionary pattern of sexual size dimorphism (SSD), predicts, in monophyletic taxa in which males are the larger sex, that as the body size of the species in the clade increases, SSD increases as well. We tested Rensch’s rule in the superfamily Majoidea, a diverse clade of ‘spider crabs.’ Considering that having the widest range of data available is important when testing macroevolutionary hypotheses, we first explored SSD in the pygmy spider crab Petramithrax pygmaeus(Bell, 1836), one of the smallest spider crabs in the superfamily. Petramithrax pygmaeusexhibits an unusual pattern of sexual dimorphism, with females displaying a larger average carapace width than males, yet males attain a larger overall body size. This type of SSD is unusual for spider crabs, with most species displaying male-biased sexual size dimorphism for both mean and overall body size. Hierarchical cluster and discriminant analyses demonstrated the existence of two distinct ontogenetic phases in P. pygmaeus(juvenile/prepubertal and adult/postpubertal). We used our data on body size of P. pygmaeusalong with previously published body-size data for 11 other species within the superfamily Majoidea to test for Rensch’s rule. Using raw data, phylogenetic independent contrasts generated from maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees, and reduced major axis regression analyses, we determined that for the tested species in the Majoidea that the predictions of Rensch’s rule were not upheld. Macroevoultionary patterns such as Rensch’s rule are not well studied in marine invertebrate systems; looking at how these rules compare between vertebrate and invertebrate and terrestrial and aquatic animals will help us to understand the differences and factors that could influence size and growth in these systems.

Published
2016
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19. Reproductive Investment in a Phyletic Giant, the Caribbean King Crab Damithrax spinosissimus: Exploring Egg Production Costs in Large Brooding Marine Inertebrates.

Author

A, J. Antonio Baez, Simpson, Lunden, Ambrosio, L. J., Guéron, Rodrigo, Mora, Nathalia, and Owen, Dallas

Abstract

The Caribbean king crab Damithrax spinosissimus, a phyletie giant and the largest crab in the western Atlantic, was used to explore the costs of brooding, in terms of reproductive investment, in marine invertebrates. Given (i) the theoretical allometry between gamete production and brooding surfaces and (ii) increased physiological costs with increased brood mass, it was expected that larger broods from larger crabs should suffer higher mortality and brood loss than smaller broods from smaller crabs. It was also expected that smaller females should allocate disproportionably more resources to egg production than larger females. In D. spinosissimus, fecundity in females carrying early and late embryos varied, respectively, between 5.170 and 26.024 eggs/crab (mean ± SD = 16.569 ± 4.899) and between 1.966 and 26.906 eggs/crab (15.147 ± 7.003). In disagreement with expectation, females did not experience brood loss during embryo development. Egg mortality in females carrying early and late eggs varied, respectively, between 0% and 69% (4.71 ± 15.37) and between 2% and 100% (27.17 ± 33.99). Also in disagreement with expectations, egg mortality did not increase disproportionably with parental female body size. Reproductive output varied between 10.45% and 43.79% (34.02% ± 7.4) of crab body dry weight. Finally, in agreement with expectations, the slope ( b = 0.54 ± 0.17) of the line describing the relationship between brood and parental female dry weight was significantly less than unity. Overall, most of the results disagree with the notion that the allometry of gamete production and increased physiological costs with increased brood size explain the association between brooding and small body size in marine invertebrates. Comparative studies on the reproductive investment of brooding species pertaining to monophyletic clades with extensive disparity in body size are warranted to further our understanding about the evolution of brooding in marine invertebrates. [ABSTRACT FROM AUTHOR]

Published
2015
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20. Carcinonemertes conanobrieni - A Nemertean Parasite Infecting the Caribbean Spiny Lobster, Panulirus argus. Species Description, Host-Use, and Effect on Host Reproductive Health

Author

Simpson, Lunden A.

Subjects
Brood parasite, Carcinonemertes, Carcinonemertes conanobrieni, Caribbean spiny lobster, Nemertean, Panulirus argus
Abstract

Marine ecosystems are one of the world’s most heavily used and valuable natural systems. However, over the past decades, they have seen changes in the oceans’ pH, temperature, salinity, and other abiotic factors - all of which appear to have impacted the health of these systems, and there seems to be a global trend indicating that diseases in marine environments are emerging at an increased rate. Infection by a disease can result in a variety of negative effects on the health of a host, all of which are especially relevant in instances where commercially important hosts are infected. Disease can lead to changes in growth, longevity, reproduction, embryo survival, and marketability of a host. One ecologically and commercially important species that appears to have been impacted by this trend of increased disease emergence is the Caribbean spiny lobster, Panulirus argus. Panulirus argus plays host to a number of previously described and newly emergent pathogens. However, here, a new species of nemertean worm belonging to the genus Carcinonemertes is described from egg masses of P. argus from the Florida Keys, Florida, USA. Though P. argus ranges throughout the Caribbean, this worm has thus far only been observed infecting gravid female lobsters in the Florida Keys. This is the first species of Carcinonemertes reported to infect P. argus or any other lobster species in the greater Caribbean and western Atlantic Ocean. To determine the host use, infection prevalence, and infection intensity of this new parasite on P. argus, male, non-gravid female, and gravid female lobsters were captured along the Florida Key reef tract from and examined for infection. Furthermore, infected gravid females were also used in estimating the impact that infection by this nemertean had on three levels of reproductive performance (reproductive output, fecundity, and brood mortality).

Published
2018

21. Single Cell Expression Analysis of Ductal Carcinoma in Situ Identifies Complex Genotypic-Phenotypic Relationships Altering Epithelial Composition.

Author

Qin X, Strand SH, Lee MR, Saraswathibhatla A, van IJzendoorn DGP, Zhu C, Vennam S, Varma S, Hall A, Factor RE, King L, Simpson L, Luo X, Colditz GA, Jiang S, Chaudhuri O, Hwang ES, Marks JR, Owzar K, and West RB

Abstract

To identify mechanisms underlying the growth of ductal carcinoma in situ (DCIS) and properties that lead to progression to invasive cancer, we performed single-cell RNA-sequencing (scRNA-seq) on DCIS lesions and matched synchronous normal breast tissue. Using inferred copy number variations (CNV), we identified neoplastic epithelial cells from the clinical specimens which contained a mixture of DCIS and normal ducts. Phylogenetic analysis based on the CNVs demonstrated intratumoral clonal heterogeneity was associated with significant gene expression differences. We also classified epithelial cells into mammary cell states and found that individual genetic clones contained a mixture of cell states suggesting an ongoing pattern of differentiation after neoplastic transformation. Cell state proportions were significantly different based on estrogen receptor (ER) expression with ER-DCIS more closely resembling the distribution in the normal breast, particularly with respect to cells with basal characteristics. Using deconvolution from bulk RNA-seq in archival DCIS specimens, we show that specific alterations in cell state proportions are associated with progression to invasive cancer. Loss of an intact basement membrane (BM) is the functional definition of invasive breast cancer (IBC) and scRNA-seq data demonstrated that ongoing transcription of key BM genes occurs in specific subsets of epithelial cell states. Examining BM in archival microinvasive breast cancers and an in vitro model of invasion, we found that passive loss of BM gene expression due to cell state proportion alterations is associated with loss of the structural integrity of the duct leading to an invasive phenotype. Our analyses provide detailed insight into DCIS biology., Significance: Single cell analysis reveals that preinvasive breast cancer is comprised of multiple genetic clones and there is substantial phenotypic diversity both within and between these clones. Ductal carcinoma in situ (DCIS) of the breast is a non-invasive condition commonly identified through mammographic screening. A primary diagnosis of DCIS carries little mortality risk on its own, but its presence is a risk factor for subsequent clonally related invasive breast cancer (IBC) (1-5).

Published
2024
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