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1. Exploratory analysis of the cervix tumoral HPV antigen-specific T-cell repertoire during chemoradiation and after brachytherapy

Author

Manzar, Gohar S., Alam, Molly B. El, Lynn, Erica J., Karpinets, Tatiana V., Harris, Timothy, Lo, David, Yoshida-Court, Kyoko, Napravnik, Tatiana Cisneros, Sammouri, Julie, Lin, Daniel, Andring, Lauren M., Bronk, Julianna, Wu, Xiaogang, Sims, Travis T., Mathew, Geena, Schmeler, Kathleen M., Eifel, Patricia J., Jhingran, Anuja, Lin, Lilie L., Joyner, Melissa M., Zhang, Jianhua, Futreal, Andrew, Klopp, Ann H., and Colbert, Lauren E.

Published
2024
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2. Tumor-resident Lactobacillus iners confer chemoradiation resistance through lactate-induced metabolic rewiring

Author

Colbert, Lauren E., El Alam, Molly B., Wang, Rui, Karpinets, Tatiana, Lo, David, Lynn, Erica J., Harris, Timothy A., Elnaggar, Jacob H., Yoshida-Court, Kyoko, Tomasic, Katarina, Bronk, Julianna K., Sammouri, Julie, Yanamandra, Ananta V., Olvera, Adilene V., Carlin, Lily G., Sims, Travis, Delgado Medrano, Andrea Y., Napravnik, Tatiana Cisneros, O’Hara, Madison, Lin, Daniel, Abana, Chike O., Li, Hannah X., Eifel, Patricia J., Jhingran, Anuja, Joyner, Melissa, Lin, Lilie, Ramondetta, Lois M., Futreal, Andrew M., Schmeler, Kathleen M., Mathew, Geena, Dorta-Estremera, Stephanie, Zhang, Jianhua, Wu, Xiaogang, Ajami, Nadim J., Wong, Matthew, Taniguchi, Cullen, Petrosino, Joseph F., Sastry, K. Jagannadha, Okhuysen, Pablo C., Martinez, Sara A., Tan, Lin, Mahmud, Iqbal, Lorenzi, Philip L., Wargo, Jennifer A., and Klopp, Ann H.

Published
2023
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3. Circulating neutrophils and tumor-associated myeloid cells function as a powerful biomarker for response to chemoradiation in locally advanced cervical cancer

Author

Gjyshi, Olsi, Grippin, Adam, Andring, Lauren, Jhingran, Anuja, Lin, Lilie L., Bronk, Julianna, Eifel, Patricia J., Joyner, Melissa M., Sastry, Jagannadha K., Yoshida-Court, Kyoko, Solley, Travis N., Napravnik, Tatiana Cisneros, O'Hara, Madison P., Hegde, Venkatesh L, Colbert, Lauren E., and Klopp, Ann H

Published
2023
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4. Metagenomes of rectal swabs in larger, advanced stage cervical cancers have enhanced mucus degrading functionalities and distinct taxonomic structure

Author

Karpinets, Tatiana V., Wu, Xiaogang, Solley, Travis, El Alam, Molly B., Sims, Travis T., Yoshida-Court, Kyoko, Lynn, Erica, Ahmed-Kaddar, Mustapha, Biegert, Greyson, Yue, Jingyan, Song, Xingzhi, Sun, Huandong, Petrosino, Joseph F., Mezzari, Melissa P., Okhuysen, Pablo, Eifel, Patricia J., Jhingran, Anuja, Lin, Lilie L., Schmeler, Kathleen M., Ramondetta, Lois, Ajami, Nadim, Jenq, Robert R., Futreal, Andrew, Zhang, Jianhua, Klopp, Ann H., and Colbert, Lauren E.

Published
2022
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6. Microbial Diversity and Composition Is Associated with Patient-Reported Toxicity during Chemoradiation Therapy for Cervical Cancer

Author

Mitra, Aparna, Grossman Biegert, Greyson Willis, Delgado, Andrea Y., Karpinets, Tatiana V., Solley, Travis N., Mezzari, Melissa P., Yoshida-Court, Kyoko, Petrosino, Joe F., Mikkelson, Megan D., Lin, Lilie, Eifel, Patricia, Zhang, Jianhua, Ramondetta, Lois M., Jhingran, Anuja, Sims, Travis T., Schmeler, Kathleen, Okhuysen, Pablo, Colbert, Lauren E., and Klopp, Ann H.

Published
2020
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7. Exploratory analysis of the cervix tumoral HPV antigen-specific T-cell repertoire during chemoradiation and after brachytherapy

Author

Manzar, Gohar S., primary, Alam, Molly B. El, additional, Lynn, Erica J., additional, Karpinets, Tatiana V., additional, Harris, Timothy, additional, Lo, David, additional, Yoshida-Court, Kyoko, additional, Napravnik, Tatiana Cisneros, additional, Sammouri, Julie, additional, Lin, Daniel, additional, Andring, Lauren M., additional, Bronk, Julianna, additional, Wu, Xiaogang, additional, Sims, Travis T., additional, Mathew, Geena, additional, Schmeler, Kathleen M., additional, Eifel, Patricia J., additional, Jhingran, Anuja, additional, Lin, Lilie L., additional, Joyner, Melissa M., additional, Zhang, Jianhua, additional, Futreal, Andrew, additional, Klopp, Ann H., additional, and Colbert, Lauren E., additional

Published
2023
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9. Gut microbiome diversity is an independent predictor of survival in cervical cancer patients receiving chemoradiation

Author

Sims, Travis T., El Alam, Molly B., Karpinets, Tatiana V., Dorta-Estremera, Stephanie, Hegde, Venkatesh L., Nookala, Sita, Yoshida-Court, Kyoko, Wu, Xiaogang, Biegert, Greyson W. G., Delgado Medrano, Andrea Y., Solley, Travis, Ahmed-Kaddar, Mustapha, Chapman, Bhavana V., Sastry, K. Jagannadha, Mezzari, Melissa P., Petrosino, Joseph F., Lin, Lilie L., Ramondetta, Lois, Jhingran, Anuja, Schmeler, Kathleen M., Ajami, Nadim J., Wargo, Jennifer, Colbert, Lauren E., and Klopp, Ann H.

Published
2021
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11. Supplemental Tables from Expansion of Candidate HPV-Specific T Cells in the Tumor Microenvironment during Chemoradiotherapy Is Prognostic in HPV16+ Cancers

Author

Colbert, Lauren E., primary, El, Molly B., primary, Lynn, Erica J., primary, Bronk, Julianna, primary, Karpinets, Tatiana V., primary, Wu, Xiaogang, primary, Chapman, Bhavana V., primary, Sims, Travis T., primary, Lin, Daniel, primary, Kouzy, Ramez, primary, Sammouri, Julie, primary, Biegert, Greyson, primary, Delgado Medrano, Andrea Y., primary, Olvera, Adilene, primary, Sastry, K. Jagannadha, primary, Eifel, Patricia J., primary, Jhingran, Anuja, primary, Lin, Lilie, primary, Ramondetta, Lois M., primary, Futreal, Andrew P., primary, Jazaeri, Amir A., primary, Schmeler, Kathleen M., primary, Yue, Jingyan, primary, Mitra, Aparna, primary, Yoshida-Court, Kyoko, primary, Wargo, Jennifer A., primary, Solley, Travis N., primary, Hegde, Venkatesh, primary, Nookala, Sita S., primary, Yanamandra, Ananta V., primary, Dorta-Estremera, Stephanie, primary, Mathew, Geena, primary, Kavukuntla, Rohit, primary, Papso, Cassidy, primary, Ahmed-Kaddar, Mustapha, primary, Kim, Minsoo, primary, Zhang, Jianhua, primary, Reuben, Alexandre, primary, Holliday, Emma B., primary, Minsky, Bruce D., primary, Koong, Albert C., primary, Koay, Eugene J., primary, Das, Prajnan, primary, Taniguchi, Cullen M., primary, and Klopp, Ann, primary

Published
2023
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12. Data from Expansion of Candidate HPV-Specific T Cells in the Tumor Microenvironment during Chemoradiotherapy Is Prognostic in HPV16+ Cancers

Author

Colbert, Lauren E., primary, El, Molly B., primary, Lynn, Erica J., primary, Bronk, Julianna, primary, Karpinets, Tatiana V., primary, Wu, Xiaogang, primary, Chapman, Bhavana V., primary, Sims, Travis T., primary, Lin, Daniel, primary, Kouzy, Ramez, primary, Sammouri, Julie, primary, Biegert, Greyson, primary, Delgado Medrano, Andrea Y., primary, Olvera, Adilene, primary, Sastry, K. Jagannadha, primary, Eifel, Patricia J., primary, Jhingran, Anuja, primary, Lin, Lilie, primary, Ramondetta, Lois M., primary, Futreal, Andrew P., primary, Jazaeri, Amir A., primary, Schmeler, Kathleen M., primary, Yue, Jingyan, primary, Mitra, Aparna, primary, Yoshida-Court, Kyoko, primary, Wargo, Jennifer A., primary, Solley, Travis N., primary, Hegde, Venkatesh, primary, Nookala, Sita S., primary, Yanamandra, Ananta V., primary, Dorta-Estremera, Stephanie, primary, Mathew, Geena, primary, Kavukuntla, Rohit, primary, Papso, Cassidy, primary, Ahmed-Kaddar, Mustapha, primary, Kim, Minsoo, primary, Zhang, Jianhua, primary, Reuben, Alexandre, primary, Holliday, Emma B., primary, Minsky, Bruce D., primary, Koong, Albert C., primary, Koay, Eugene J., primary, Das, Prajnan, primary, Taniguchi, Cullen M., primary, and Klopp, Ann, primary

Published
2023
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13. Supplemental Table Legends from Expansion of Candidate HPV-Specific T Cells in the Tumor Microenvironment during Chemoradiotherapy Is Prognostic in HPV16+ Cancers

Author

Colbert, Lauren E., primary, El, Molly B., primary, Lynn, Erica J., primary, Bronk, Julianna, primary, Karpinets, Tatiana V., primary, Wu, Xiaogang, primary, Chapman, Bhavana V., primary, Sims, Travis T., primary, Lin, Daniel, primary, Kouzy, Ramez, primary, Sammouri, Julie, primary, Biegert, Greyson, primary, Delgado Medrano, Andrea Y., primary, Olvera, Adilene, primary, Sastry, K. Jagannadha, primary, Eifel, Patricia J., primary, Jhingran, Anuja, primary, Lin, Lilie, primary, Ramondetta, Lois M., primary, Futreal, Andrew P., primary, Jazaeri, Amir A., primary, Schmeler, Kathleen M., primary, Yue, Jingyan, primary, Mitra, Aparna, primary, Yoshida-Court, Kyoko, primary, Wargo, Jennifer A., primary, Solley, Travis N., primary, Hegde, Venkatesh, primary, Nookala, Sita S., primary, Yanamandra, Ananta V., primary, Dorta-Estremera, Stephanie, primary, Mathew, Geena, primary, Kavukuntla, Rohit, primary, Papso, Cassidy, primary, Ahmed-Kaddar, Mustapha, primary, Kim, Minsoo, primary, Zhang, Jianhua, primary, Reuben, Alexandre, primary, Holliday, Emma B., primary, Minsky, Bruce D., primary, Koong, Albert C., primary, Koay, Eugene J., primary, Das, Prajnan, primary, Taniguchi, Cullen M., primary, and Klopp, Ann, primary

Published
2023
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14. Supplementary Data from Expansion of Candidate HPV-Specific T Cells in the Tumor Microenvironment during Chemoradiotherapy Is Prognostic in HPV16+ Cancers

Author

Colbert, Lauren E., primary, El, Molly B., primary, Lynn, Erica J., primary, Bronk, Julianna, primary, Karpinets, Tatiana V., primary, Wu, Xiaogang, primary, Chapman, Bhavana V., primary, Sims, Travis T., primary, Lin, Daniel, primary, Kouzy, Ramez, primary, Sammouri, Julie, primary, Biegert, Greyson, primary, Delgado Medrano, Andrea Y., primary, Olvera, Adilene, primary, Sastry, K. Jagannadha, primary, Eifel, Patricia J., primary, Jhingran, Anuja, primary, Lin, Lilie, primary, Ramondetta, Lois M., primary, Futreal, Andrew P., primary, Jazaeri, Amir A., primary, Schmeler, Kathleen M., primary, Yue, Jingyan, primary, Mitra, Aparna, primary, Yoshida-Court, Kyoko, primary, Wargo, Jennifer A., primary, Solley, Travis N., primary, Hegde, Venkatesh, primary, Nookala, Sita S., primary, Yanamandra, Ananta V., primary, Dorta-Estremera, Stephanie, primary, Mathew, Geena, primary, Kavukuntla, Rohit, primary, Papso, Cassidy, primary, Ahmed-Kaddar, Mustapha, primary, Kim, Minsoo, primary, Zhang, Jianhua, primary, Reuben, Alexandre, primary, Holliday, Emma B., primary, Minsky, Bruce D., primary, Koong, Albert C., primary, Koay, Eugene J., primary, Das, Prajnan, primary, Taniguchi, Cullen M., primary, and Klopp, Ann, primary

Published
2023
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15. Cervicovaginal Microbiota Profiles in Precancerous Lesions and Cervical Cancer among Ethiopian Women

Author

Teka, Brhanu, primary, Yoshida-Court, Kyoko, additional, Firdawoke, Ededia, additional, Chanyalew, Zewditu, additional, Gizaw, Muluken, additional, Addissie, Adamu, additional, Mihret, Adane, additional, Colbert, Lauren E., additional, Napravnik, Tatiana Cisneros, additional, El Alam, Molly B., additional, Lynn, Erica J., additional, Mezzari, Melissa, additional, Anuja, Jhingran, additional, Kantelhardt, Eva Johanna, additional, Kaufmann, Andreas M., additional, Klopp, Ann H., additional, and Abebe, Tamrat, additional

Published
2023
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16. Immune environment and antigen specificity of the T cell receptor repertoire of malignant ascites in ovarian cancer

Author

Yoshida-Court, Kyoko, primary, Karpinets, Tatiana V., additional, Mitra, Aparna, additional, Solley, Travis N., additional, Dorta-Estremera, Stephanie, additional, Sims, Travis T., additional, Delgado Medrano, Andrea Y., additional, El Alam, Molly B., additional, Ahmed-Kaddar, Mustapha, additional, Lynn, Erica J., additional, Sastry, K. Jagannadha, additional, Zhang, Jianhua, additional, Futreal, Andrew, additional, Nick, Alpa, additional, Lu, Karen, additional, Colbert, Lauren E., additional, and Klopp, Ann H., additional

Published
2023
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17. 674 IMMUNOCERV, an ongoing phase II trial combining PDS0101, an HPV-specific T cell immunotherapy, with chemotherapy and radiation for treatment of locally advanced cervical cancers

Author

Yoshida-Court, Kyoko, primary, Gjyshi, Olsi, additional, O’Hara, Madison, additional, Lin, Lilie, additional, Jhingran, Anuja, additional, Joyner, Melissa, additional, Napravnik, Tatiana Cisneros, additional, Lynn, Erica, additional, Colbert, Lauren, additional, Sastry, Jagannadha K, additional, and Klopp, Ann, additional

Published
2022
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18. Cancer-associated Lactobacillus iners are genetically distinct and associated with chemoradiation resistance in cervical cancer

Author

Colbert, Lauren E., primary, Karpinets, Tatiana, additional, El Alam, Molly B., additional, Lynn, Erica J., additional, Sammouri, Julie, additional, Lo, David, additional, Elnaggar, Jacob H, additional, Wang, Rui, additional, Harris, Timothy A, additional, Yoshida-Court, Kyoko, additional, Tomasic, Katarina, additional, Bronk, Julianna K., additional, Yanamandra, Ananta V., additional, Olvera, Adilene V., additional, Carlin, Lily G., additional, Sims, Travis, additional, Delgado Medrano, Andrea Y., additional, Solley, Travis, additional, Eifel, Patricia J., additional, Jhingran, Anuja, additional, Joyner, Melissa, additional, Lin, Lilie, additional, Ramondetta, Lois M., additional, Futreal, Andrew M., additional, Schmeler, Kathleen M., additional, Mathew, Geena, additional, Dorta-Estremera, Stephanie, additional, Zhang, Jianhua, additional, Wu, Xiaogang, additional, Ajami, Nadim J., additional, Taniguchi, Cullen, additional, Petrosino, Joseph F., additional, Wargo, Jennifer, additional, Sastry, K. Jagannadha, additional, Okhuysen, Pablo C., additional, and Klopp, Ann H., additional

Published
2022
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19. Additional file 1 of Metagenomes of rectal swabs in larger, advanced stage cervical cancers have enhanced mucus degrading functionalities and distinct taxonomic structure

Author

Karpinets, Tatiana V., Wu, Xiaogang, Solley, Travis, El Alam, Molly B., Sims, Travis T., Yoshida-Court, Kyoko, Lynn, Erica, Ahmed-Kaddar, Mustapha, Biegert, Greyson, Yue, Jingyan, Song, Xingzhi, Sun, Huandong, Petrosino, Joseph F., Mezzari, Melissa P., Okhuysen, Pablo, Eifel, Patricia J., Jhingran, Anuja, Lin, Lilie L., Schmeler, Kathleen M., Ramondetta, Lois, Ajami, Nadim, Jenq, Robert R., Futreal, Andrew, Zhang, Jianhua, Klopp, Ann H., and Colbert, Lauren E.

Abstract

Additional file 1: Figure S1. Workflow for quantification and analysis of known functions in WGS dataset. a Computational pipeline for assembly and annotation of each metagenome. b Computational workflow for merging of metagenomes into MFA table. c MFA table analysis. Figure S2. A toy example explaining a quantification of molecular functions using WGS dataset. The quantity of a molecular function in the metagenome is referred as Metagenome Function Abundance (MFA). The Figure shows 2 sequenced Metagenomes, A and B, populated by 18 and 19 bacterial cells respectively that belong to 4 different species: read, green yellow and blue colored shapes. Circles have Function1 (F1) in the genome, and ovals have Function 2 (F2). We propose to calculate MFA as the total number of DNA sequencing reads covering known functions in all bacterial cells. In the depicted example, each bacterial cell shown as an ovals has a gene that encode F1, but doesn’t have genes encoding F2. Vice versa, each bacterial cell shown as a circle has a gene that encode F2, but not F1. In both cases, ovals and circles, cells belong to 2 different species shown by color. For simplicity, we suggest that all genes in each cell is covered by 1 read after WGS. Therefore, MFA of F1 may be calculated just as number of circles in each metagenome, which is 4 for metagenome A and 16x for metagenome B, MFA ofF2 will be equal 14 and 4 respectively for A and B. The produced MFA values are integrated into MFA table where columns are metagenomes in the study and rows are unique known functions found in the metagenomes. The quantification is based on the following 2 conditions: (1) We ignore which of the species implement the function and calculate the Metagenome Function Abundance (MFA) as the total number of reads that cover the function in each cell of the metagenome, (2) If we don’t know what function the gene implement, we just ignore the gene. One important advantage of the quantification is that the MFA profile calculated this way for all unique function identified in the metagenome is like the profile of gene abundances calculated from RNA-seq data and can be analyzed in a similar way. Figure S3. KEGG pathways associated with quick proliferation of microbial cells are enriched “ST KO cluster” (Fig. 1c). a Ribosome biogenesis. b DNA repair. c Oxidative phosphorylation. KEGG orthologous groups found in the clusters are labeled by rose color. Figure S4. Quorum sensing was enriched in metagenomes of “LT KO cluster” (Fig. 1c). Total 19 KOs were annotated by the pathway in the cluster with the most complete known pathways similar to Staphylococcus aureus and Enterococcus faecalis. Figure S5. Overlap of KOs involved in galactose, fructose and mannose metabolism with KOs found in “LT KO cluster” (Fig. 1c). Overlapping KOs are colored in rose. Figure S6. Overlap of genes involved in pentose phosphate pathway in “LT KO cluster” (Fig. 1c). Overlapping genes are colored in rose. Figure S7. Overlap of genes involved in bacterial chemotaxis (a) and flagella assembly (b) with KOs found in “LT KO cluster” (Fig. 1c). Overlapping KO are colored in rose color. Figure S8. Overlap of enzymes involved in galactose, arginine and proline metabolism with differentially abundant KOs between LT- and ST-groups of metagenomes. (Fig. 2j). Overlapping KO are colored in rose color. Metabolic routs involved in production of glutamate from arginine and in putrescine and spermidine metabolism are framed in red. Figure S9. Overlap of enzymes involved in 2-oxocarboxylic acid metabolism with differentially abundant KOs between LT- and ST-groups of metagenomes. (Fig. 2j). Overlapping KO are colored in rose color and framed in red. They represent the complete set of enzymes involved production of ornithine from glutamate. Figure S10. Association of clinicopathological characteristics with the progression free survival probability. Categorization of patients into the low (blue color) and high (rose color) group in terms of the continues characteristics, such as Age, BMI and Tumor size, was done according to the maximally selected rank statistics as described in the Methods section. Characteristics significantly associated with the progression free survival according to log-rank test are in red color. Figure S11. Increased activity of Ribosome biogenesis pathway in metagenomes of patients with stage I/II tumors. Figure S12. Taxonomic structure of metagenomes in LT- and ST-groups at the Class level. Figure S13. Taxonomic structure of metagenomes in LT- and ST-groups at the Order level. Figure S14. Taxonomic structure of metagenomes in LT- and ST-groups at the Family level. Figure S15. Differentially abundant taxa between Large (L) and Small (S) tumor groups (a) and cladogram of the taxa (b) identified by LDA Effect Size (LEfSe) Figure S16. Relative abundance of selected taxa differentially abundant in ST-group (a) and in LT-group (b) according to LEfSe analysis. Figure S17. Pairwise Person correlation coefficients between the Glycan Degradation pathway score and the abundance profile of the taxa (order level) encoding enzymes of the pathway. Coefficients identified as significant (P

Published
2022
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20. Expansion of Candidate HPV-Specific T Cells in the Tumor Microenvironment during Chemoradiotherapy Is Prognostic in HPV16+ Cancers

Author

Colbert, Lauren E., primary, El, Molly B., additional, Lynn, Erica J., additional, Bronk, Julianna, additional, Karpinets, Tatiana V., additional, Wu, Xiaogang, additional, Chapman, Bhavana V., additional, Sims, Travis T., additional, Lin, Daniel, additional, Kouzy, Ramez, additional, Sammouri, Julie, additional, Biegert, Greyson, additional, Delgado Medrano, Andrea Y., additional, Olvera, Adilene, additional, Sastry, K. Jagannadha, additional, Eifel, Patricia J., additional, Jhingran, Anuja, additional, Lin, Lilie, additional, Ramondetta, Lois M., additional, Futreal, Andrew P., additional, Jazaeri, Amir A., additional, Schmeler, Kathleen M., additional, Yue, Jingyan, additional, Mitra, Aparna, additional, Yoshida-Court, Kyoko, additional, Wargo, Jennifer A., additional, Solley, Travis N., additional, Hegde, Venkatesh, additional, Nookala, Sita S., additional, Yanamandra, Ananta V., additional, Dorta-Estremera, Stephanie, additional, Mathew, Geena, additional, Kavukuntla, Rohit, additional, Papso, Cassidy, additional, Ahmed-Kaddar, Mustapha, additional, Kim, Minsoo, additional, Zhang, Jianhua, additional, Reuben, Alexandre, additional, Holliday, Emma B., additional, Minsky, Bruce D., additional, Koong, Albert C., additional, Koay, Eugene J., additional, Das, Prajnan, additional, Taniguchi, Cullen M., additional, and Klopp, Ann, additional

Published
2022
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21. Tumor-Resident  Lactobacillus iners Confers Chemoradiation Resistance in Cervical Cancer Patients Through Acquired Metabolic Functions

Author

Colbert, Lauren, primary, El Alam, Molly B., additional, Karpinets, Tatiana, additional, Lynn, Erica J., additional, Lo, David, additional, Wang, Rui, additional, Harris, Timothy A., additional, Elnaggar, Jacob, additional, Yoshida-Court, Kyoko, additional, Tomasic, Katarina, additional, Bronk, Julianna K., additional, Sammouri, Julie, additional, Yanamandra, Ananta V., additional, Olvera, Adilene V., additional, Carlin, Lily G., additional, Sims, Travis, additional, Delgado Medrano, Andrea Y., additional, Lin, Daniel, additional, Abana, Chike O., additional, Eifel, Patricia J., additional, Jhingran, Anuja, additional, Joyner, Melissa, additional, Lin, Lilie, additional, Ramondetta, Lois M., additional, Futreal, Andrew M., additional, Schmeler, Kathleen, additional, Mathew, Geena, additional, Dorta-Estremera, Stephanie, additional, Zhang, Jianhua, additional, Wu, Xiaogang, additional, Ajami, Nadim J., additional, Taniguchi, Cullen M., additional, Petrosino, Joseph F., additional, Wargo, Jennifer, additional, Sastry, K. Jagannadha, additional, Okhuysen, Pablo, additional, and Klopp, Ann H., additional

Published
2022
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22. Diversity and composition of gut microbiome of cervical cancer patients: Do results of 16S rRNA sequencing and whole genome sequencing approaches align?

Author

Biegert, Greyson, primary, El Alam, Molly B., additional, Karpinets, Tatiana, additional, Wu, Xiaogang, additional, Sims, Travis T., additional, Yoshida-Court, Kyoko, additional, Lynn, Erica J., additional, Yue, Jingyan, additional, Medrano, Andrea Delgado, additional, Petrosino, Joseph, additional, Mezzari, Melissa P., additional, Ajami, Nadim J., additional, Solley, Travis, additional, Ahmed-Kaddar, Mustapha, additional, Klopp, Ann H., additional, and Colbert, Lauren E., additional

Published
2021
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23. Candidate HPV-Specific T-Cells Expand in the Tumor Microenvironment During Chemoradiotherapy

Author

Colbert, Lauren, primary, Alam, Molly El, additional, Lynn, Erica, additional, Edwards, Julianna, additional, Karpinets, Tatiana, additional, Wu, Xiaogang, additional, Chapman, Bhavana, additional, Sims, Travis, additional, Lin, Daniel, additional, Kouzy, Ramez, additional, Biegert, Greyson, additional, Medrano, Andrea Delgado, additional, Olvera, Adilene, additional, Sastry, K., additional, Eifel, Patricia, additional, Jhingran, Anuja, additional, Lin, Lilie, additional, Ramondetta, Lois, additional, Futreal, Andrew, additional, Jazaeri, Amir, additional, Schmeler, Kathleen, additional, Yue, Jingyan, additional, Mitra, Aparna, additional, Yoshida-Court, Kyoko, additional, Wargo, Jennifer, additional, Solley, Travis, additional, Hegde, Venkatesh, additional, Nookala, Sita, additional, Yanamandra, Ananta, additional, Dorta-Estremera, Stephanie, additional, Mathew, Geena, additional, Kavukuntla, Rohit, additional, Papso, Cassidy, additional, Ahmed-Kaddar, Mustapha, additional, Kim, Minsoo, additional, Zhang, Jianhua, additional, Reuben, Alexandre, additional, Holliday, Emma, additional, Minsky, Bruce, additional, Koong, Albert, additional, Koay, Eugene, additional, Das, Prajnan, additional, Taniguchi, Cullen, additional, and Klopp, Ann, additional

Published
2021
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24. A prospective study of the adaptive changes in the gut microbiome during standard-of-care chemoradiotherapy for gynecologic cancers

Author

El Alam, Molly B., primary, Sims, Travis T., additional, Kouzy, Ramez, additional, Biegert, Greyson W. G., additional, Jaoude, Joseph A. B. I., additional, Karpinets, Tatiana V., additional, Yoshida-Court, Kyoko, additional, Wu, Xiaogang, additional, Delgado-Medrano, Andrea Y., additional, Mezzari, Melissa P., additional, Ajami, Nadim J., additional, Solley, Travis, additional, Ahmed-Kaddar, Mustapha, additional, Lin, Lilie L., additional, Ramondetta, Lois, additional, Jazaeri, Amir, additional, Jhingran, Anuja, additional, Eifel, Patricia J., additional, Schmeler, Kathleen M., additional, Wargo, Jennifer, additional, Klopp, Ann H., additional, and Colbert, Lauren E., additional

Published
2021
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25. Diversity and Composition of Gut Microbiome of Cervical Cancer Patients by 16S rRNA and Whole-metagenome Sequencing

Author

Biegert, Greyson, primary, Karpinets, Tatiana, additional, Wu, Xiaogang, additional, Alam, Molly B. El, additional, Sims, Travis T., additional, Yoshida-Court, Kyoko, additional, Lynn, Erica J., additional, Yue, Jingyan, additional, Medrano, Andrea Delgado, additional, Petrosino, Joseph, additional, Mezzari, Melissa P., additional, Ajami, Nadim J., additional, Solley, Travis, additional, Ahmed-Kaddar, Mustapha, additional, Colbert, Lauren E, additional, and Klopp, Ann H., additional

Published
2020
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26. Gut microbiome diversity is an independent predictor of survival in cervical cancer patients receiving chemoradiation

Author

Sims, Travis T., primary, El Alam, Molly B., additional, Karpinets, Tatiana V., additional, Dorta-Estremera, Stephanie, additional, Hegde, Venkatesh L., additional, Nookala, Sita, additional, Yoshida-Court, Kyoko, additional, Wu, Xiaogang, additional, Biegert, Greyson W.G., additional, Delgado Medrano, Andrea Y., additional, Solley, Travis, additional, Ahmed-Kaddar, Mustapha, additional, Chapman, Bhavana V., additional, Sastry, K. Jagannadha Jagannadha, additional, Mezzari, Melissa P., additional, Petrosino, Joseph F., additional, Lin, Lilie L., additional, Ramondetta, Lois, additional, Jhingran, Anuja, additional, Schmeler, Kathleen M., additional, Ajami, Nadim J., additional, Wargo, Jennifer, additional, Colbert, Lauren E., additional, and Klopp, Ann H., additional

Published
2020
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27. Gut microbiome diversity as an independent predictor of survival in cervical cancer patients receiving chemoradiation.

Author

Sims, Travis T., primary, Alam, Molly B., additional, Karpinets, Tatiana, additional, Yoshida-Court, Kyoko, additional, Biegert, Greyson W.G., additional, Ahmed-Kaddar, Mustapha, additional, Wu, Xiaogang, additional, Medrano, Andrea Delgado, additional, Chapman, Bhavana Sree Vangara, additional, Solley, Travis, additional, Aparna, Mitra, additional, Mezzari, Melissa P., additional, Ramondetta, Lois M., additional, Lin, Lilie L., additional, Jhingran, Anuja, additional, Schmeler, Kathleen M., additional, Ajami, Nadim J, additional, Wargo, Jennifer Ann, additional, Colbert, Lauren Elizabeth, additional, and Klopp, Ann, additional

Published
2020
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28. Adaptive changes in the gut microbiome during standard-of-care chemoradiotherapy for gynecologic cancers

Author

El Alam, Molly B., primary, Sims, Travis T., additional, Kouzy, Ramez, additional, Biegert, Greyson W. G., additional, Abi Jaoude, Joseph, additional, Karpinets, Tatiana V., additional, Yoshida-Court, Kyoko, additional, Wu, Xiaogang, additional, Delgado Medrano, Andrea Y., additional, Mezzari, Melissa P., additional, Ajami, Nadim J., additional, Solley, Travis, additional, Ahmed-Kaddar, Mustapha, additional, Lin, Lilie L., additional, Ramondetta, Lois, additional, Jazaeri, Amir, additional, Jhingran, Anuja, additional, Eifel, Patricia J., additional, Schmeler, Kathleen M., additional, Wargo, Jennifer, additional, Klopp, Ann H., additional, and Colbert, Lauren E., additional

Published
2020
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29. Dynamic evolution of cervical cancer mutations during chemoradiation using novel sampling approach

Author

Chapman, Bhavana V., primary, Karpinets, Tatiana, additional, Sims, Travis T., additional, Biegert, Greyson, additional, Wu, Xiaogang, additional, Delgado Medrano, Andrea Y., additional, Eifel, Patricia J., additional, Jhingran, Anuja, additional, Lin, Lilie L., additional, Ramondetta, Lois M., additional, Futreal, Andrew M., additional, Jazaeri, Amir A., additional, Frumovitz, Michael, additional, Schmeler, Kathleen M., additional, Yue, Jingyan, additional, Mitra, Aparna, additional, Yoshida-Court, Kyoko, additional, Solley, Travis, additional, Mathew, Geena, additional, Ahmed-Kaddar, Mustapha, additional, Zhang, Jianhua, additional, Klopp, Ann H., additional, and Colbert, Lauren E., additional

Published
2019
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30. Expansion of Candidate HPV-Specific T Cells in the Tumor Microenvironment during Chemoradiotherapy Is Prognostic in HPV16 + Cancers.

Author

Colbert LE, El MB, Lynn EJ, Bronk J, Karpinets TV, Wu X, Chapman BV, Sims TT, Lin D, Kouzy R, Sammouri J, Biegert G, Delgado Medrano AY, Olvera A, Sastry KJ, Eifel PJ, Jhingran A, Lin L, Ramondetta LM, Futreal AP, Jazaeri AA, Schmeler KM, Yue J, Mitra A, Yoshida-Court K, Wargo JA, Solley TN, Hegde V, Nookala SS, Yanamandra AV, Dorta-Estremera S, Mathew G, Kavukuntla R, Papso C, Ahmed-Kaddar M, Kim M, Zhang J, Reuben A, Holliday EB, Minsky BD, Koong AC, Koay EJ, Das P, Taniguchi CM, and Klopp A

Subjects
Chemoradiotherapy, Female, Human papillomavirus 16, Humans, Papillomavirus E7 Proteins, Prognosis, Repressor Proteins, T-Lymphocytes, Tumor Microenvironment, Oncogene Proteins, Viral, Papillomavirus Infections, Uterine Cervical Neoplasms
Abstract

Human papillomavirus (HPV) infection causes 600,000 new cancers worldwide each year. HPV-related cancers express the oncogenic proteins E6 and E7, which could serve as tumor-specific antigens. It is not known whether immunity to E6 and E7 evolves during chemoradiotherapy or affects survival. Using T cells from 2 HPV16 + patients, we conducted functional T-cell assays to identify candidate HPV-specific T cells and common T-cell receptor motifs, which we then analyzed across 86 patients with HPV-related cancers. The HPV-specific clones and E7-related T-cell receptor motifs expanded in the tumor microenvironment over the course of treatment, whereas non-HPV-specific T cells did not. In HPV16 + patients, improved recurrence-free survival was associated with HPV-responsive T-cell expansion during chemoradiotherapy., (©2022 American Association for Cancer Research.)

Published
2022
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31. Longitudinal characterization of the tumoral microbiome during radiotherapy in HPV-associated oropharynx cancer.

Author

Bahig H, Fuller CD, Mitra A, Yoshida-Court K, Solley T, Ping Ng S, Abu-Gheida I, Elgohari B, Delgado A, Rosenthal DI, Garden AS, Frank SJ, Reddy JP, Colbert L, and Klopp A

Abstract

Purpose: To describe the baseline and serial tumor microbiome in HPV-associated oropharynx cancer (OPC) over the course of radiotherapy (RT)., Methods: Patients with newly diagnosed HPV-associated OPC treated with definitive radiotherapy +/- concurrent chemotherapy were enrolled in this prospective study. Using 16S rRNA gene sequencing, dynamic changes in the tumor site microbiome during RT were investigated. Surface tumor samples were obtained before RT and at week 1, 3 and 5 of RT. Radiological primary tumor response at mid-treatment was categorized as complete (CR) or partial (PR)., Results: Ten patients were enrolled, but 9 patients were included in the final analysis. Mean age was 62 years (range: 51-71). As per AJCC 8th Ed, 56%, 22% and 22% of patients had stage I, II and III, respectively. At 4-weeks, 6 patients had CR and 3 patients had PR; at follow-up imaging post treatment, all patients had CR. The baseline diversity of the tumoral versus buccal microbiome was not statistically different. For the entire cohort, alpha diversity was significantly decreased over the course of treatment (p = 0.04). There was a significant alteration in the bacterial community within the first week of radiation. Baseline tumor alpha diversity of patients with CR was significantly higher than those with PR (p = 0.03). While patients with CR had significant reduction in diversity over the course of radiation (p = 0.01), the diversity remained unchanged in patients with PR. Patients with history of smoking had significantly increased abundance of   Kingella  (0.05) and lower abundance of  Stomatobaculum  (p = 0.03) compared to never smokers., Conclusions: The tumor microbiome of HPV-associated OPC exhibits reduced alpha diversity and altered taxa abundance over the course of radiotherapy. The baseline bacterial profiles of smokers vs. non-smokers were inherently different. Baseline tumor alpha diversity of patients with CR was higher than patients with PR, suggesting that the microbiome deserves further investigation as a biomarker of radiation response., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2020 The Authors.)

Published
2020
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