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22 results on '"Semenkovich, Nicholas P."'

2. Supplementary Table S3 from Sensitive MRD Detection from Lymphatic Fluid after Surgery in HPV-Associated Oropharyngeal Cancer

Author

Earland, Noah, primary, Semenkovich, Nicholas P., primary, Ramirez, Ricardo J., primary, Gerndt, Sophie P., primary, Harris, Peter K., primary, Gu, Zhuosheng, primary, Hearn, Andrew I., primary, Inkman, Matthew, primary, Szymanski, Jeffrey J., primary, Whitfield, Damion, primary, Wahle, Benjamin M., primary, Xu, Zhongping, primary, Chen, Kevin, primary, Alahi, Irfan, primary, Ni, Gabris, primary, Chen, Andrew, primary, Winckler, Wendy, primary, Zhang, Jin, primary, Chaudhuri, Aadel A., primary, and Zevallos, Jose P., primary

Published
2024
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3. Data from Sensitive MRD Detection from Lymphatic Fluid after Surgery in HPV-Associated Oropharyngeal Cancer

Author

Earland, Noah, primary, Semenkovich, Nicholas P., primary, Ramirez, Ricardo J., primary, Gerndt, Sophie P., primary, Harris, Peter K., primary, Gu, Zhuosheng, primary, Hearn, Andrew I., primary, Inkman, Matthew, primary, Szymanski, Jeffrey J., primary, Whitfield, Damion, primary, Wahle, Benjamin M., primary, Xu, Zhongping, primary, Chen, Kevin, primary, Alahi, Irfan, primary, Ni, Gabris, primary, Chen, Andrew, primary, Winckler, Wendy, primary, Zhang, Jin, primary, Chaudhuri, Aadel A., primary, and Zevallos, Jose P., primary

Published
2024
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4. Supplementary Figure S5 from Sensitive MRD Detection from Lymphatic Fluid after Surgery in HPV-Associated Oropharyngeal Cancer

Author

Earland, Noah, primary, Semenkovich, Nicholas P., primary, Ramirez, Ricardo J., primary, Gerndt, Sophie P., primary, Harris, Peter K., primary, Gu, Zhuosheng, primary, Hearn, Andrew I., primary, Inkman, Matthew, primary, Szymanski, Jeffrey J., primary, Whitfield, Damion, primary, Wahle, Benjamin M., primary, Xu, Zhongping, primary, Chen, Kevin, primary, Alahi, Irfan, primary, Ni, Gabris, primary, Chen, Andrew, primary, Winckler, Wendy, primary, Zhang, Jin, primary, Chaudhuri, Aadel A., primary, and Zevallos, Jose P., primary

Published
2024
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5. Supplementary Methods S1 from Sensitive MRD Detection from Lymphatic Fluid after Surgery in HPV-Associated Oropharyngeal Cancer

Author

Earland, Noah, primary, Semenkovich, Nicholas P., primary, Ramirez, Ricardo J., primary, Gerndt, Sophie P., primary, Harris, Peter K., primary, Gu, Zhuosheng, primary, Hearn, Andrew I., primary, Inkman, Matthew, primary, Szymanski, Jeffrey J., primary, Whitfield, Damion, primary, Wahle, Benjamin M., primary, Xu, Zhongping, primary, Chen, Kevin, primary, Alahi, Irfan, primary, Ni, Gabris, primary, Chen, Andrew, primary, Winckler, Wendy, primary, Zhang, Jin, primary, Chaudhuri, Aadel A., primary, and Zevallos, Jose P., primary

Published
2024
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7. Effects of a gut pathobiont in a gnotobiotic mouse model of childhood undernutrition

Author

Wagner, Vitas E, Dey, Neelendu, Guruge, Janaki, Hsiao, Ansel, Ahern, Philip P, Semenkovich, Nicholas P, Blanton, Laura V, Cheng, Jiye, Griffin, Nicholas, Stappenbeck, Thaddeus S, Ilkayeva, Olga, Newgard, Christopher B, Petri, William, Haque, Rashidul, Ahmed, Tahmeed, and Gordon, Jeffrey I

Subjects
Medical Biotechnology, Biomedical and Clinical Sciences, Nutrition, Prevention, Zero Hunger, Animals, Bacteroides fragilis, Bangladesh, Cachexia, Child Nutrition Disorders, Child, Preschool, Diet, Disease Models, Animal, Feces, Female, Gastrointestinal Microbiome, Gene Expression Regulation, Bacterial, Germ-Free Life, Humans, Infant, Male, Mice, Phenotype, Biological Sciences, Medical and Health Sciences, Medical biotechnology, Biomedical engineering
Abstract

To model how interactions among enteropathogens and gut microbial community members contribute to undernutrition, we colonized gnotobiotic mice fed representative Bangladeshi diets with sequenced bacterial strains cultured from the fecal microbiota of two 24-month-old Bangladeshi children: one healthy and the other underweight. The undernourished donor's bacterial collection contained an enterotoxigenic Bacteroides fragilis strain (ETBF), whereas the healthy donor's bacterial collection contained two nontoxigenic strains of B. fragilis (NTBF). Analyses of mice harboring either the unmanipulated culture collections or systematically manipulated versions revealed that ETBF was causally related to weight loss in the context of its native community but not when introduced into the healthy donor's community. This phenotype was transmissible from the dams to their offspring and was associated with derangements in host energy metabolism manifested by impaired tricarboxylic acid cycle activity and decreased acyl-coenzyme A utilization. NTBF reduced ETBF's expression of its enterotoxin and mitigated the effects of ETBF on the transcriptomes of other healthy donor community members. These results illustrate how intraspecific (ETBF-NTBF) and interspecific interactions influence the effects of harboring B. fragilis.

Published
2016

8. Sensitive MRD Detection from Lymphatic Fluid after Surgery in HPV-Associated Oropharyngeal Cancer

Author

Earland, Noah, primary, Semenkovich, Nicholas P., additional, Ramirez, Ricardo J., additional, Gerndt, Sophie P., additional, Harris, Peter K., additional, Gu, Zhuosheng, additional, Hearn, Andrew I., additional, Inkman, Matthew, additional, Szymanski, Jeffrey J., additional, Whitfield, Damion, additional, Wahle, Benjamin M., additional, Xu, Zhongping, additional, Chen, Kevin, additional, Alahi, Irfan, additional, Ni, Gabris, additional, Chen, Andrew, additional, Winckler, Wendy, additional, Zhang, Jin, additional, Chaudhuri, Aadel A., additional, and Zevallos, Jose P., additional

Published
2023
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13. Emerging Roles of Circulating Tumor DNA for Increased Precision and Personalization in Radiation Oncology.

Author

Earland, Noah, Chen, Kevin, Semenkovich, Nicholas P., Chauhan, Pradeep S., Zevallos, Jose P., and Chaudhuri, Aadel A.

Abstract

Recent breakthroughs in circulating tumor DNA (ctDNA) technologies present a compelling opportunity to combine this emerging liquid biopsy approach with the field of radiogenomics, the study of how tumor genomics correlate with radiotherapy response and radiotoxicity. Canonically, ctDNA levels reflect metastatic tumor burden, although newer ultrasensitive technologies can be used after curative-intent radiotherapy of localized disease to assess ctDNA for minimal residual disease (MRD) detection or for post-treatment surveillance. Furthermore, several studies have demonstrated the potential utility of ctDNA analysis across various cancer types managed with radiotherapy or chemoradiotherapy, including sarcoma and cancers of the head and neck, lung, colon, rectum, bladder, and prostate. Additionally, because peripheral blood mononuclear cells are routinely collected alongside ctDNA to filter out mutations associated with clonal hematopoiesis, these cells are also available for single nucleotide polymorphism analysis and could potentially be used to detect patients at high risk for radiotoxicity. Lastly, future ctDNA assays will be utilized to better assess locoregional MRD in order to more precisely guide adjuvant radiotherapy after surgery in cases of localized disease, and guide ablative radiotherapy in cases of oligometastatic disease. [ABSTRACT FROM AUTHOR]

Published
2023
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14. Human papillomavirus DNA resides in surgical drain fluid exosomes from HPV+ oropharyngeal squamous cell carcinoma patients and can be spread to neighboring HPV-negative cells.

Author

Xu, Zhongping, primary, Earland, Noah, additional, Harris, Peter K., additional, Gerndt, Sophie P., additional, Ramirez, Ricardo J., additional, Hearn, Andrew I., additional, Semenkovich, Nicholas P., additional, Chaudhuri, Aadel A, additional, and Zevallos, Jose P., additional

Published
2022
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17. Going viral: next generation sequencing applied to human gut phage populations

Author

Reyes, Alejandro, Semenkovich, Nicholas P., Whiteson, Katrine, Rohwer, Forest, and Gordon, Jeffrey I.

Subjects
Complementary Therapies, Gastrointestinal Tract, Biological Products, Bacteria, viruses, High-Throughput Nucleotide Sequencing, Humans, Bacteriophages, Bacterial Infections, Biodiversity, human activities, Biota, Article
Abstract

Over the past decade, researchers have begun to characterize viral diversity using metagenomic methods. These studies have shown that viruses, the majority of which infect bacteria, are probably the most genetically diverse components of the biosphere. Here, we briefly review the incipient rise of a phage biology renaissance, which has been catalysed by advances in next-generation sequencing. We explore how work characterizing phage diversity and lifestyles in the human gut is changing our view of ourselves as supra-organisms. Finally, we discuss how a renewed appreciation of phage dynamics may yield new applications for phage therapies designed to manipulate the structure and functions of our gut microbiomes.

Published
2012

20. Identification of Racial Inequities in Access to Specialized Inpatient Heart Failure Care at an Academic Medical Center

Author

Eberly, Lauren A., Richterman, Aaron, Beckett, Anne G., Wispelwey, Bram, Marsh, Regan H., Cleveland Manchanda, Emily C., Chang, Cindy Y., Glynn, Robert J., Brooks, Katherine C., Boxer, Robert, Kakoza, Rose, Goldsmith, Jennifer, Loscalzo, Joseph, Morse, Michelle, Lewis, Eldrin F., Abel, Samantha, Adams, Ayrenne, Anaya, Joseph, Andrews, Erik H, Atkinson, Benjamin, Avutu, Viswatej, Bachorik, Alexandra, Badri, Omar, Bailey, Mariel, Baird, Katie, Bakshi, Salina, Balaban, Denis, Barshop, Kenneth, Baumrin, Emily, Bayomy, Omar, Beamesderfer, Julia, Becker, Nora, Berg, David D., N., Adam, Berman, Blum, Steven M., Boardman, Alexander P., Boden, Kaeleen, Bonacci, Robert A, Brown, Sarah, Campbell, Kirsti, Case, Siobhan, Cetrone, Emily, Charrow, Alexandra, Chiang, David, Clark, Devin, Cohen, Aaron J., Cooper, Alissa, Cordova, Tomas, Cuneo, C. Nicholas, de Feria, Alsina Alejandro, Deffenbacher, Karen, DeFilippis, Ersilia M., DeGregorio, Geneva, Deutsch, Aaron J., Diephuis, Bradford, Divakaran, Sanjay, Dorschner, Peter, Downing, Nicholas, Drescher, Caitlin, D’Silva, Kristin M., Dunbar, Peter, Duong, David, Earp, Sarah, Eckhardt, Christine, Elman, Scott A., England, Ross, Everett, Kay, Fedotova, Natalie, Feingold-Link, Tamara, Ferreira, Mark, Fisher, Herrick, Foo, Patricia, Foote, Michael, Franco, Idalid, Gilliland, Thomas, Greb, Jacqueline, Greco, Katherine, Grewal, Sungat, Grin, Benjamin, Growdon, Matthew E., Guercio, Brendan, Hahn, Cynthia K., Hasselfeld, Brian, Haydu, Erika J, Hermes, Zachary, Hildick-Smith, Gordon, Holcomb, Zachary, Holroyd, Kathryn, Horton, Laura, Huang, George, Jablonski, Stanley, Jacobs, Douglas, Jain, Nina, Japa, Sohan, Joseph, Richard, Kalashnikova, Mariya, Kalwani, Neil, Kang, Daniel, Karan, Abraar, Katz, Joel T, Kellner, Daniel, Kidia, Khameer, Kim, June-Ho, Knowles, Scott M, Kolbe, Laura, Kore, Idil, Koullias, Yiannis, Kuye, Ifedayo, Lang, Joshua, Lawlor, Matthew, Lechner, Melissa G., Lee, Ken, Lee, Scott, Lee, Zachary, Limaye, Neha, Lin-Beckford, Stephanie, Lipsyc, Marla, Little, Jessica, Loewenthal, Julia, Logaraj, Ranjani, Lopez, Diana M, Loriaux, Daniel, Lu, Yi, Ma, Kevin, Marukian, Nareh, Matias, Wilfredo, Mayers, Jared R., McConnell, Ian, McLaughlin, Michael, Meade, Christina, Meador, Catherine, Mehta, Anish, Messenger, Elizabeth, Michaelidis, Constantinos, Mirsky, Jacob, Mitten, Emilie, Mueller, Alisa, Mullur, Jyotsna, Munir, Amir, Murphy, Emily, Nagami, Ellen, Natarajan, Abirami, Nsahlai, Michelle, Nze, Chijioke, Okwara, Noreen, Olds, Peter, Paez, Rafael, Pardo, Michael, Patel, Siddharth, Petersen, Alec, Phelan, Laura, Pimenta, Erica, Pipilas, Daniel, Plovanich, Molly, Pong, Denise, Powers, Brian W., Rao, Anita, Ramirez Batlle, Haiyan, Ramsis, Mattheus, Reichardt, Anna, Reiger, Sheridan, Rengarajan, Michelle, Rico, Stephanie, Rome, Benjamin N., Rosales, Rachael, Rotenstein, Lisa, Roy, Alexis, Royston, Sarah, Rozansky, Hallie, Rudder, Meghan, Ryan, Christine E., Salgado, Sanjay, Sanchez, Pablo, Schulte, Jennifer, Sekar, Aswin, Semenkovich, Nicholas, Shannon, Evan, Shaw, Neil, Shorten, Andrew Ben, Shrauner, William, Sinnenberg, Lauren, Smithy, James W., Snyder, Gregory, Sreekrishnan, Anirudh, Stabenau, Hans, Stavrou, Eleni, Stergachis, Andrew, Stern, Robert, Stone, Alexander, Tabrizi, Shervin, Tanyos, Sam, Thomas, Cristina, Thun, Haley, Torres-Lockhart, Kristine, Tran, An, Treasure, Carolyn, Tsai, Frederick D., Tsaur, Stephen, Tschirhart, Evan, Tuwatananurak, Justin, Venkateswaran, Ramkumar V., Vishnevetsky, Anastasia, Wahl, Lindsay, Wall, April, Wallace, Frances, Walsh, Elisa, Wang, Priscilla, Ward, Heather B., Warner, Lindsay N., Weeks, Lachelle D., Weiskopf, Kipp, Wengrod, Jordan, Williams, Jessica N., Winkler, Marisa, Wong, Jeffrey L., Worster, Devin, Wright, Aileen, Wunsch, Caroline, Wynter, Jamila S., Yarbrough, Chase, Yau, Wai-Ying, Yazdi, Daniel, Yeh, Jennifer, Yialamas, Maria A., Yozamp, Nicholas, Zambrotta, Marina, and Zon, Rebecca

Abstract

Supplemental Digital Content is available in the text.

Published
2019
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21. Sensitive MRD Detection from Lymphatic Fluid after Surgery in HPV-Associated Oropharyngeal Cancer.

Author

Earland N, Semenkovich NP, Ramirez RJ, Gerndt SP, Harris PK, Gu Z, Hearn AI, Inkman M, Szymanski JJ, Whitfield D, Wahle BM, Xu Z, Chen K, Alahi I, Ni G, Chen A, Winckler W, Zhang J, Chaudhuri AA, and Zevallos JP

Subjects
Humans, Human Papillomavirus Viruses, Neoplasm, Residual pathology, Prognosis, Neoplasm Staging, Squamous Cell Carcinoma of Head and Neck diagnosis, Squamous Cell Carcinoma of Head and Neck genetics, Squamous Cell Carcinoma of Head and Neck surgery, Retrospective Studies, Papillomavirus Infections complications, Papillomavirus Infections diagnosis, Papillomavirus Infections surgery, Oropharyngeal Neoplasms diagnosis, Oropharyngeal Neoplasms surgery, Oropharyngeal Neoplasms pathology, Head and Neck Neoplasms pathology
Abstract

Purpose: Our goal was to demonstrate that lymphatic drainage fluid (lymph) has improved sensitivity in quantifying postoperative minimal residual disease (MRD) in locally advanced human papillomavirus (HPV)-associated oropharyngeal squamous cell carcinoma (OPSCC) compared with plasma, and leverage this novel biofluid for patient risk stratification., Experimental Design: We prospectively collected lymph samples from neck drains of 106 patients with HPV (+) OPSCC, along with 67 matched plasma samples, 24 hours after surgery. PCR and next-generation sequencing were used to quantify cancer-associated cell-free HPV (cf-HPV) and tumor-informed variants in lymph and plasma. Next, lymph cf-HPV and variants were compared with TNM stage, extranodal extension (ENE), and composite definitions of high-risk pathology. We then created a machine learning model, informed by lymph MRD and clinicopathologic features, to compare with progression-free survival (PFS)., Results: Postoperative lymph was enriched with cf-HPV compared with plasma (P < 0.0001) and correlated with pN2 stage (P = 0.003), ENE (P < 0.0001), and trial-defined pathologic risk criteria (mean AUC = 0.78). In addition, the lymph mutation number and variant allele frequency were higher in pN2 ENE (+) necks than in pN1 ENE (+) (P = 0.03, P = 0.02) or pN0-N1 ENE (-) (P = 0.04, P = 0.03, respectively). The lymph MRD-informed risk model demonstrated inferior PFS in high-risk patients (AUC = 0.96, P < 0.0001)., Conclusions: Variant and cf-HPV quantification, performed in 24-hour postoperative lymph samples, reflects single- and multifeature high-risk pathologic criteria. Incorporating lymphatic MRD and clinicopathologic feature analysis can stratify PFS early after surgery in patients with HPV (+) head and neck cancer. See related commentary by Shannon and Iyer, p. 1223., (©2023 The Authors; Published by the American Association for Cancer Research.)

Published
2024
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22. Pre-radiotherapy ctDNA liquid biopsy for risk stratification of oligometastatic non-small cell lung cancer.

Author

Semenkovich NP, Samson PP, Badiyan SN, Vlacich G, Stowe HB, Wang YE, Star R, Devarakonda S, Govindan R, Waqar SN, Robinson CG, Pellini B, and Chaudhuri AA

Abstract

The optimal treatment for patients with oligometastatic non-small cell lung cancer (NSCLC) remains unclear. Some patients with oligometastatic disease can experience prolonged remission after locally consolidative radiation therapy (RT), while others harbor micrometastatic disease (below current limits of detection by imaging) that may benefit from further prioritization of systemic therapy. To better risk-stratify this population and identify the patients most likely to benefit from locally consolidative radiation therapy, we performed a multi-institutional cohort study of patients with oligometastatic NSCLC undergoing liquid biopsy analysis of circulating tumor DNA (ctDNA). Among this real-world cohort of 1,487 patients undergoing analysis (using the Tempus xF assay), a total of 1,880 ctDNA liquid biopsies along with paired clinical data were obtained across various timepoints. Approximately 20% (n=309) of patients had ctDNA obtained prior to RT and after their diagnosis of oligometastatic disease. Samples were de-identified and analyzed for mutational burden and variant frequencies of detectable deleterious (or likely deleterious) mutations in plasma. Patients with undetectable ctDNA before RT had significantly improved progression-free survival and overall survival compared to patients with detectable ctDNA prior to RT. In patients that received RT, 598 pathogenic (or likely deleterious) variants were identified. ctDNA mutational burden pre-RT and ctDNA maximum variant allele frequency (VAF) pre-RT were both significantly inversely correlated with both progression-free (P = 0.0031 for mutational burden, P = 0.0084 for maximum VAF) and overall survival (P = 0.045 for mutational burden, P = 0.0073 for maximum VAF). Patients without detectable ctDNA prior to RT had significantly improved progression-free survival (P = 0.004) and overall survival (P = 0.03) compared to patients with detectable ctDNA prior to RT. These data suggest that in patients with oligometastatic NSCLC, pre-radiotherapy ctDNA analysis can potentially identify the patients most likely to benefit from locally consolidative RT and experience prolonged progression-free and overall survival. Similarly, ctDNA may be useful to identify those patients with undiagnosed micrometastatic disease, in whom it may be appropriate to prioritize systemic therapy.

Published
2023
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