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333 results on '"Spakowicz, Daniel"'

1. Obesity-associated microbiomes instigate visceral adipose tissue inflammation by recruitment of distinct neutrophils

Author

Shantaram, Dharti, Hoyd, Rebecca, Blaszczak, Alecia M., Antwi, Linda, Jalilvand, Anahita, Wright, Valerie P., Liu, Joey, Smith, Alan J., Bradley, David, Lafuse, William, Liu, YunZhou, Williams, Nyelia F., Snyder, Owen, Wheeler, Caroline, Needleman, Bradley, Brethauer, Stacy, Noria, Sabrena, Renton, David, Perry, Kyle A., Nagareddy, Prabha, Wozniak, Daniel, Mahajan, Sahil, Rana, Pranav S. J. B., Pietrzak, Maciej, Schlesinger, Larry S., Spakowicz, Daniel J., and Hsueh, Willa A.

Published
2024
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3. Metabolic Dysregulation Explains the Diverse Impacts of Obesity in Males and Females with Gastrointestinal Cancers.

Author

Rosario, Spencer, Dong, Bowen, Zhang, Yali, Hsiao, Hua-Hsin, Isenhart, Emily, Wang, Jianmin, Siegel, Erin, Owen, Dwight, Dey, Prasenjit, Tabung, Fred, Spakowicz, Daniel, Edge, Stephen, Yendamuri, Sai, Ibrahimi, Sami, Kolesar, Jill, McDonald, Patsy, Vadehra, Deepak, Churchman, Michelle, Liu, Song, Kalinski, Pawel, Mukherjee, Sarbajit, Monjazeb, Arta, and Murphy, William

Subjects
cancer, gender disparity, immunity, metabolism, obesity, omics, Male, Female, Humans, Kynurenine, Tryptophan, Leukocytes, Mononuclear, Obesity, Gastrointestinal Neoplasms, Adenocarcinoma
Abstract

The prevalence of obesity, defined as the body mass index (BMI) ≥ 30 kg/m2, has reached epidemic levels. Obesity is associated with an increased risk of various cancers, including gastrointestinal ones. Recent evidence has suggested that obesity disproportionately impacts males and females with cancer, resulting in varied transcriptional and metabolic dysregulation. This study aimed to elucidate the differences in the metabolic milieu of adenocarcinomas of the gastrointestinal (GI) tract both related and unrelated to sex in obesity. To demonstrate these obesity and sex-related effects, we utilized three primary data sources: serum metabolomics from obese and non-obese patients assessed via the Biocrates MxP Quant 500 mass spectrometry-based kit, the ORIEN tumor RNA-sequencing data for all adenocarcinoma cases to assess the impacts of obesity, and publicly available TCGA transcriptional analysis to assess GI cancers and sex-related differences in GI cancers specifically. We applied and integrated our unique transcriptional metabolic pipeline in combination with our metabolomics data to reveal how obesity and sex can dictate differential metabolism in patients. Differentially expressed genes (DEG) analysis of ORIEN obese adenocarcinoma as compared to normal-weight adenocarcinoma patients resulted in large-scale transcriptional reprogramming (4029 DEGs, adj. p < 0.05 and |logFC| > 0.58). Gene Set Enrichment and metabolic pipeline analysis showed genes enriched for pathways relating to immunity (inflammation, and CD40 signaling, among others) and metabolism. Specifically, we found alterations to steroid metabolism and tryptophan/kynurenine metabolism in obese patients, both of which are highly associated with disease severity and immune cell dysfunction. These findings were further confirmed using the TCGA colorectal adenocarcinoma (CRC) and esophageal adenocarcinoma (ESCA) data, which showed similar patterns of increased tryptophan catabolism for kynurenine production in obese patients. These patients further showed disparate alterations between males and females when comparing obese to non-obese patient populations. Alterations to immune and metabolic pathways were validated in six patients (two obese and four normal weight) via CD8+/CD4+ peripheral blood mononuclear cell RNA-sequencing and paired serum metabolomics, which showed differential kynurenine and lipid metabolism, which corresponded with altered T-cell transcriptome in obese populations. Overall, obesity is associated with differential transcriptional and metabolic programs in various disease sites. Further, these alterations, such as kynurenine and tryptophan metabolism, which impact both metabolism and immune phenotype, vary with sex and obesity together. This study warrants further in-depth investigation into obesity and sex-related alterations in cancers that may better define biomarkers of response to immunotherapy.

Published
2023

4. Resiliency among older adults receiving lung cancer treatment (ROAR-LCT): A novel supportive care intervention for older adults with advanced lung cancer

Author

Presley, Carolyn J., Grogan, Madison, Compston, Amy, Hock, Karen, Knauss, Brittany, Redder, Elyse, Arrato, Nicole A., Lo, Stephen B., Janse, Sarah, Benedict, Jason, Hoyd, Rebecca, Williams, Nyelia, Hayes, Scott, Wells-Di Gregorio, Sharla, Gill, Thomas M., Allore, Heather, Focht, Brian, Quist, Morten, Carbone, David P., Spakowicz, Daniel, Paskett, Electra D., and Andersen, Barbara L.

Published
2024
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5. Mean platelet volume, thrombocytosis, and survival in non-small cell lung cancer patients treated with first-line pembrolizumab alone or with chemotherapy

Author

Li, Mingjia, Zhao, Songzhu, Lopez, Gabrielle, Secor, Austin, Das, Parthib, Surya, Nitya, Grogan, Madison, Patel, Sandip, Chakravarthy, Karthik, Miah, Abdul, Spakowicz, Daniel, Tinoco, Gabriel, Li, Zihai, Wei, Lai, He, Kai, Bertino, Erin, Alahmadi, Asrar, Memmott, Regan, Kaufman, Jacob, Shields, Peter G., Carbone, David P., Presley, Carolyn J., Otterson, Gregory A., and Owen, Dwight H.

Published
2023
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7. Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease

Author

Zhou, Xin, Shen, Xiaotao, Johnson, Jethro S., Spakowicz, Daniel J., Agnello, Melissa, Zhou, Wenyu, Avina, Monica, Honkala, Alexander, Chleilat, Faye, Chen, Shirley Jingyi, Cha, Kexin, Leopold, Shana, Zhu, Chenchen, Chen, Lei, Lyu, Lin, Hornburg, Daniel, Wu, Si, Zhang, Xinyue, Jiang, Chao, Jiang, Liuyiqi, Jiang, Lihua, Jian, Ruiqi, Brooks, Andrew W., Wang, Meng, Contrepois, Kévin, Gao, Peng, Rose, Sophia Miryam Schüssler-Fiorenza, Tran, Thi Dong Binh, Nguyen, Hoan, Celli, Alessandra, Hong, Bo-Young, Bautista, Eddy J., Dorsett, Yair, Kavathas, Paula B., Zhou, Yanjiao, Sodergren, Erica, Weinstock, George M., and Snyder, Michael P.

Published
2024
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9. The FITNESS study: longitudinal geriatric assessment, treatment toxicity, and biospecimen collection to assess functional disability among older adults with lung cancer

Author

Grogan, Madison, primary, Hoyd, Rebecca, additional, Benedict, Jason, additional, Janse, Sarah, additional, Williams, Nyelia, additional, Naughton, Michelle, additional, Burd, Christin E., additional, Paskett, Electra D., additional, Rosko, Ashley, additional, Spakowicz, Daniel J., additional, and Presley, Carolyn J., additional

Published
2024
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11. Comparative analysis of the tumor microbiome, molecular profiles, and immune cell abundances by HPV status in mucosal head and neck cancers and their impact on survival

Author

Upadhyay, Rituraj, primary, Dhakal, Aastha, additional, Wheeler, Caroline, additional, Hoyd, Rebecca, additional, Jagjit Singh, Malvenderjit, additional, Karivedu, Vidhya, additional, Bhateja, Priyanka, additional, Bonomi, Marcelo, additional, Valentin, Sasha, additional, Gamez, Mauricio E., additional, Konieczkowski, David J., additional, Baliga, Sujith, additional, Grecula, John C., additional, Blakaj, Dukagjin M., additional, Gogineni, Emile, additional, Mitchell, Darrion L., additional, Denko, Nicholas C., additional, Spakowicz, Daniel, additional, and Jhawar, Sachin R., additional

Published
2024
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12. Bridging the Gap from Bench to Bedside: A Call for In Vivo Preclinical Models to Advance Endometrial Cancer and Cervical Cancer Immuno-Oncology Research

Author

Chambers, Laura, primary, Haight, Paulina, additional, Chalif, Julia, additional, Mehra, Yogita, additional, Spakowicz, Daniel, additional, Backes, Floor J., additional, Cosgrove, Casey M., additional, O'Malley, David M., additional, Vargas, Roberto, additional, Corr, Bradley R., additional, Bae-Jump, Victoria L., additional, and Arend, Rebecca C., additional

Published
2024
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14. Longitudinal multi-omics of host-microbe dynamics in prediabetes.

Author

Zhou, Wenyu, Sailani, M Reza, Contrepois, Kévin, Zhou, Yanjiao, Ahadi, Sara, Leopold, Shana R, Zhang, Martin J, Rao, Varsha, Avina, Monika, Mishra, Tejaswini, Johnson, Jethro, Lee-McMullen, Brittany, Chen, Songjie, Metwally, Ahmed A, Tran, Thi Dong Binh, Nguyen, Hoan, Zhou, Xin, Albright, Brandon, Hong, Bo-Young, Petersen, Lauren, Bautista, Eddy, Hanson, Blake, Chen, Lei, Spakowicz, Daniel, Bahmani, Amir, Salins, Denis, Leopold, Benjamin, Ashland, Melanie, Dagan-Rosenfeld, Orit, Rego, Shannon, Limcaoco, Patricia, Colbert, Elizabeth, Allister, Candice, Perelman, Dalia, Craig, Colleen, Wei, Eric, Chaib, Hassan, Hornburg, Daniel, Dunn, Jessilyn, Liang, Liang, Rose, Sophia Miryam Schüssler-Fiorenza, Kukurba, Kim, Piening, Brian, Rost, Hannes, Tse, David, McLaughlin, Tracey, Sodergren, Erica, Weinstock, George M, and Snyder, Michael

Subjects
Humans, Respiratory Tract Infections, Diabetes Mellitus, Type 2, Prediabetic State, Insulin Resistance, Inflammation, Insulin, Glucose, Proteome, Influenza Vaccines, Anti-Bacterial Agents, Vaccination, Cohort Studies, Longitudinal Studies, Computational Biology, Adult, Aged, Middle Aged, Female, Male, Stress, Physiological, Transcriptome, Healthy Volunteers, Microbiota, Datasets as Topic, Biomarkers, Gastrointestinal Microbiome, Host Microbial Interactions, Diabetes Mellitus, Type 2, Stress, Physiological, General Science & Technology
Abstract

Type 2 diabetes mellitus (T2D) is a growing health problem, but little is known about its early disease stages, its effects on biological processes or the transition to clinical T2D. To understand the earliest stages of T2D better, we obtained samples from 106 healthy individuals and individuals with prediabetes over approximately four years and performed deep profiling of transcriptomes, metabolomes, cytokines, and proteomes, as well as changes in the microbiome. This rich longitudinal data set revealed many insights: first, healthy profiles are distinct among individuals while displaying diverse patterns of intra- and/or inter-personal variability. Second, extensive host and microbial changes occur during respiratory viral infections and immunization, and immunization triggers potentially protective responses that are distinct from responses to respiratory viral infections. Moreover, during respiratory viral infections, insulin-resistant participants respond differently than insulin-sensitive participants. Third, global co-association analyses among the thousands of profiled molecules reveal specific host-microbe interactions that differ between insulin-resistant and insulin-sensitive individuals. Last, we identified early personal molecular signatures in one individual that preceded the onset of T2D, including the inflammation markers interleukin-1 receptor agonist (IL-1RA) and high-sensitivity C-reactive protein (CRP) paired with xenobiotic-induced immune signalling. Our study reveals insights into pathways and responses that differ between glucose-dysregulated and healthy individuals during health and disease and provides an open-access data resource to enable further research into healthy, prediabetic and T2D states.

Published
2019

15. Serum Albumin: Early Prognostic Marker of Benefit for Immune Checkpoint Inhibitor Monotherapy But Not Chemoimmunotherapy

Author

Guo, Yizhen, Wei, Lai, Patel, Sandip H., Lopez, Gabrielle, Grogan, Madison, Li, Mingjia, Haddad, Tyler, Johns, Andrew, Ganesan, Latha P., Yang, Yiping, Spakowicz, Daniel J., Shields, Peter G., He, Kai, Bertino, Erin M., Otterson, Gregory A., Carbone, David P., Presley, Carolyn, Kulp, Samuel K., Mace, Thomas A., Coss, Christopher C., Phelps, Mitch A., and Owen, Dwight H.

Published
2022
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16. Chemotoxicity and Associated Risk Factors in Colorectal Cancer: A Systematic Review and Meta-Analysis.

Author

Han, Claire J., Ning, Xia, Burd, Christin E., Spakowicz, Daniel J., Tounkara, Fode, Kalady, Matthew F., Noonan, Anne M., McCabe, Susan, and Von Ah, Diane

Subjects
DRUG toxicity, RISK assessment, MEDICAL information storage & retrieval systems, DIARRHEA, RESEARCH funding, DRUG side effects, MALNUTRITION, CINAHL database, FRAIL elderly, GUT microbiome, SEX distribution, COLORECTAL cancer, META-analysis, DISEASE prevalence, DESCRIPTIVE statistics, TUMOR markers, AGE distribution, CANCER chemotherapy, SYSTEMATIC reviews, MEDLINE, ODDS ratio, MEDICAL databases, NUTRITIONAL status, ANALYSIS of variance, QUALITY of life, ONLINE information services, CONFIDENCE intervals, DATA analysis software, TELOMERES, PSYCHOLOGY information storage & retrieval systems, REGRESSION analysis, NEUTROPENIA
Abstract

Simple Summary: Chemotoxicity in colorectal cancer (CRC) patients impacts treatment compliance, survival, and quality of life. While clinician-reported chemotoxicity predicts rehospitalization and survival, a comprehensive understanding is lacking. This systematic review and meta-analysis studied chemotoxicity in CRC patients. The study found that 45.7% of patients experienced overall moderate-to-severe toxicities, with gastrointestinal toxicity (22.9%) and neuropathy or neutropenia (17.9%) being the most common. Risk factors included malnutrition, frailty, impaired immune or hepato-renal functions, short telomere lengths, low gut lactobacillus levels, age, female sex, aggressive chemotherapy, and low quality of life. Age was linked to neutropenia and gastrointestinal toxicity. Older adults had higher overall and gastrointestinal toxicities but lower neutropenia than younger adults. The study underscores the need for close monitoring and management of chemotoxicity in CRC patients. Community contributions have been instrumental in raising awareness about these issues, advocating for patient support, and future research to improve treatment toxicities in CRC. Background: Colorectal cancer (CRC) patients experience multiple types of chemotoxicity affecting treatment compliance, survival, and quality of life (QOL). Prior research shows clinician-reported chemotoxicity (i.e., grading scales or diagnostic codes) predicts rehospitalization and cancer survival. However, a comprehensive synthesis of clinician-reported chemotoxicity is still lacking. Objectives: We conducted a systematic review and meta-analysis to determine chemotoxicity's prevalence and risk factors in CRC. Methods: A systematic search from 2009 to 2024 yielded 30 studies for review, with 25 included in the meta-analysis. Results: Pooled prevalences of overall, non-hematological, and hematological moderate-to-severe toxicities were 45.7%, 39.2%, and 25.3%, respectively. The most common clinician-reported chemotoxicities were gastrointestinal (GI) toxicity (22.9%) and neuropathy or neutropenia (17.9%). Significant risk factors at baseline were malnutritional status, frailty, impaired immune or hepato-renal functions, short telomere lengths, low gut lactobacillus levels, age, female sex, aggressive chemotherapy, and low QOL. Age was associated with neutropenia (β: −1.44) and GI toxicity (β:1.85) (p-values < 0.01). Older adults (>65 y.o.) had higher prevalences of overall (OR: 1.14) and GI (OR: 1.65) toxicities, but a lower prevalence of neutropenia (OR: 0.65) than younger adults (p-values < 0.05). Conclusions. Our findings highlight the importance of closely monitoring and managing chemotoxicity in CRC patients receiving chemotherapy. [ABSTRACT FROM AUTHOR]

Published
2024
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17. Supplementary Table 3 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

Author

Wang, Cankun, primary, Ma, Anjun, primary, Li, Yingjie, primary, McNutt, Megan E., primary, Zhang, Shiqi, primary, Zhu, Jiangjiang, primary, Hoyd, Rebecca, primary, Wheeler, Caroline E., primary, Robinson, Lary A., primary, Chan, Carlos H.F., primary, Zakharia, Yousef, primary, Dodd, Rebecca D., primary, Ulrich, Cornelia M., primary, Hardikar, Sheetal, primary, Churchman, Michelle L., primary, Tarhini, Ahmad A., primary, Singer, Eric A., primary, Ikeguchi, Alexandra P., primary, McCarter, Martin D., primary, Denko, Nicholas, primary, Tinoco, Gabriel, primary, Husain, Marium, primary, Jin, Ning, primary, Osman, Afaf E.G., primary, Eljilany, Islam, primary, Tan, Aik Choon, primary, Coleman, Samuel S., primary, Denko, Louis, primary, Riedlinger, Gregory, primary, Schneider, Bryan P., primary, Spakowicz, Daniel, primary, and Ma, Qin, primary

Published
2024
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18. FIGURE 2 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

Author

Wang, Cankun, primary, Ma, Anjun, primary, Li, Yingjie, primary, McNutt, Megan E., primary, Zhang, Shiqi, primary, Zhu, Jiangjiang, primary, Hoyd, Rebecca, primary, Wheeler, Caroline E., primary, Robinson, Lary A., primary, Chan, Carlos H.F., primary, Zakharia, Yousef, primary, Dodd, Rebecca D., primary, Ulrich, Cornelia M., primary, Hardikar, Sheetal, primary, Churchman, Michelle L., primary, Tarhini, Ahmad A., primary, Singer, Eric A., primary, Ikeguchi, Alexandra P., primary, McCarter, Martin D., primary, Denko, Nicholas, primary, Tinoco, Gabriel, primary, Husain, Marium, primary, Jin, Ning, primary, Osman, Afaf E.G., primary, Eljilany, Islam, primary, Tan, Aik Choon, primary, Coleman, Samuel S., primary, Denko, Louis, primary, Riedlinger, Gregory, primary, Schneider, Bryan P., primary, Spakowicz, Daniel, primary, and Ma, Qin, primary

Published
2024
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19. Supplementary Table 5 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

Author

Wang, Cankun, primary, Ma, Anjun, primary, Li, Yingjie, primary, McNutt, Megan E., primary, Zhang, Shiqi, primary, Zhu, Jiangjiang, primary, Hoyd, Rebecca, primary, Wheeler, Caroline E., primary, Robinson, Lary A., primary, Chan, Carlos H.F., primary, Zakharia, Yousef, primary, Dodd, Rebecca D., primary, Ulrich, Cornelia M., primary, Hardikar, Sheetal, primary, Churchman, Michelle L., primary, Tarhini, Ahmad A., primary, Singer, Eric A., primary, Ikeguchi, Alexandra P., primary, McCarter, Martin D., primary, Denko, Nicholas, primary, Tinoco, Gabriel, primary, Husain, Marium, primary, Jin, Ning, primary, Osman, Afaf E.G., primary, Eljilany, Islam, primary, Tan, Aik Choon, primary, Coleman, Samuel S., primary, Denko, Louis, primary, Riedlinger, Gregory, primary, Schneider, Bryan P., primary, Spakowicz, Daniel, primary, and Ma, Qin, primary

Published
2024
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20. Supplementary Table 1 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

Author

Wang, Cankun, primary, Ma, Anjun, primary, Li, Yingjie, primary, McNutt, Megan E., primary, Zhang, Shiqi, primary, Zhu, Jiangjiang, primary, Hoyd, Rebecca, primary, Wheeler, Caroline E., primary, Robinson, Lary A., primary, Chan, Carlos H.F., primary, Zakharia, Yousef, primary, Dodd, Rebecca D., primary, Ulrich, Cornelia M., primary, Hardikar, Sheetal, primary, Churchman, Michelle L., primary, Tarhini, Ahmad A., primary, Singer, Eric A., primary, Ikeguchi, Alexandra P., primary, McCarter, Martin D., primary, Denko, Nicholas, primary, Tinoco, Gabriel, primary, Husain, Marium, primary, Jin, Ning, primary, Osman, Afaf E.G., primary, Eljilany, Islam, primary, Tan, Aik Choon, primary, Coleman, Samuel S., primary, Denko, Louis, primary, Riedlinger, Gregory, primary, Schneider, Bryan P., primary, Spakowicz, Daniel, primary, and Ma, Qin, primary

Published
2024
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21. Supplementary Figure 1 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

Author

Wang, Cankun, primary, Ma, Anjun, primary, Li, Yingjie, primary, McNutt, Megan E., primary, Zhang, Shiqi, primary, Zhu, Jiangjiang, primary, Hoyd, Rebecca, primary, Wheeler, Caroline E., primary, Robinson, Lary A., primary, Chan, Carlos H.F., primary, Zakharia, Yousef, primary, Dodd, Rebecca D., primary, Ulrich, Cornelia M., primary, Hardikar, Sheetal, primary, Churchman, Michelle L., primary, Tarhini, Ahmad A., primary, Singer, Eric A., primary, Ikeguchi, Alexandra P., primary, McCarter, Martin D., primary, Denko, Nicholas, primary, Tinoco, Gabriel, primary, Husain, Marium, primary, Jin, Ning, primary, Osman, Afaf E.G., primary, Eljilany, Islam, primary, Tan, Aik Choon, primary, Coleman, Samuel S., primary, Denko, Louis, primary, Riedlinger, Gregory, primary, Schneider, Bryan P., primary, Spakowicz, Daniel, primary, and Ma, Qin, primary

Published
2024
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22. FIGURE 1 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

Author

Wang, Cankun, primary, Ma, Anjun, primary, Li, Yingjie, primary, McNutt, Megan E., primary, Zhang, Shiqi, primary, Zhu, Jiangjiang, primary, Hoyd, Rebecca, primary, Wheeler, Caroline E., primary, Robinson, Lary A., primary, Chan, Carlos H.F., primary, Zakharia, Yousef, primary, Dodd, Rebecca D., primary, Ulrich, Cornelia M., primary, Hardikar, Sheetal, primary, Churchman, Michelle L., primary, Tarhini, Ahmad A., primary, Singer, Eric A., primary, Ikeguchi, Alexandra P., primary, McCarter, Martin D., primary, Denko, Nicholas, primary, Tinoco, Gabriel, primary, Husain, Marium, primary, Jin, Ning, primary, Osman, Afaf E.G., primary, Eljilany, Islam, primary, Tan, Aik Choon, primary, Coleman, Samuel S., primary, Denko, Louis, primary, Riedlinger, Gregory, primary, Schneider, Bryan P., primary, Spakowicz, Daniel, primary, and Ma, Qin, primary

Published
2024
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23. Supplementary Table 6 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

Author

Wang, Cankun, primary, Ma, Anjun, primary, Li, Yingjie, primary, McNutt, Megan E., primary, Zhang, Shiqi, primary, Zhu, Jiangjiang, primary, Hoyd, Rebecca, primary, Wheeler, Caroline E., primary, Robinson, Lary A., primary, Chan, Carlos H.F., primary, Zakharia, Yousef, primary, Dodd, Rebecca D., primary, Ulrich, Cornelia M., primary, Hardikar, Sheetal, primary, Churchman, Michelle L., primary, Tarhini, Ahmad A., primary, Singer, Eric A., primary, Ikeguchi, Alexandra P., primary, McCarter, Martin D., primary, Denko, Nicholas, primary, Tinoco, Gabriel, primary, Husain, Marium, primary, Jin, Ning, primary, Osman, Afaf E.G., primary, Eljilany, Islam, primary, Tan, Aik Choon, primary, Coleman, Samuel S., primary, Denko, Louis, primary, Riedlinger, Gregory, primary, Schneider, Bryan P., primary, Spakowicz, Daniel, primary, and Ma, Qin, primary

Published
2024
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24. Supplementary Table 4 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

Author

Wang, Cankun, primary, Ma, Anjun, primary, Li, Yingjie, primary, McNutt, Megan E., primary, Zhang, Shiqi, primary, Zhu, Jiangjiang, primary, Hoyd, Rebecca, primary, Wheeler, Caroline E., primary, Robinson, Lary A., primary, Chan, Carlos H.F., primary, Zakharia, Yousef, primary, Dodd, Rebecca D., primary, Ulrich, Cornelia M., primary, Hardikar, Sheetal, primary, Churchman, Michelle L., primary, Tarhini, Ahmad A., primary, Singer, Eric A., primary, Ikeguchi, Alexandra P., primary, McCarter, Martin D., primary, Denko, Nicholas, primary, Tinoco, Gabriel, primary, Husain, Marium, primary, Jin, Ning, primary, Osman, Afaf E.G., primary, Eljilany, Islam, primary, Tan, Aik Choon, primary, Coleman, Samuel S., primary, Denko, Louis, primary, Riedlinger, Gregory, primary, Schneider, Bryan P., primary, Spakowicz, Daniel, primary, and Ma, Qin, primary

Published
2024
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25. Supplementary Table 2 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

Author

Wang, Cankun, primary, Ma, Anjun, primary, Li, Yingjie, primary, McNutt, Megan E., primary, Zhang, Shiqi, primary, Zhu, Jiangjiang, primary, Hoyd, Rebecca, primary, Wheeler, Caroline E., primary, Robinson, Lary A., primary, Chan, Carlos H.F., primary, Zakharia, Yousef, primary, Dodd, Rebecca D., primary, Ulrich, Cornelia M., primary, Hardikar, Sheetal, primary, Churchman, Michelle L., primary, Tarhini, Ahmad A., primary, Singer, Eric A., primary, Ikeguchi, Alexandra P., primary, McCarter, Martin D., primary, Denko, Nicholas, primary, Tinoco, Gabriel, primary, Husain, Marium, primary, Jin, Ning, primary, Osman, Afaf E.G., primary, Eljilany, Islam, primary, Tan, Aik Choon, primary, Coleman, Samuel S., primary, Denko, Louis, primary, Riedlinger, Gregory, primary, Schneider, Bryan P., primary, Spakowicz, Daniel, primary, and Ma, Qin, primary

Published
2024
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26. Data from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

Author

Wang, Cankun, primary, Ma, Anjun, primary, Li, Yingjie, primary, McNutt, Megan E., primary, Zhang, Shiqi, primary, Zhu, Jiangjiang, primary, Hoyd, Rebecca, primary, Wheeler, Caroline E., primary, Robinson, Lary A., primary, Chan, Carlos H.F., primary, Zakharia, Yousef, primary, Dodd, Rebecca D., primary, Ulrich, Cornelia M., primary, Hardikar, Sheetal, primary, Churchman, Michelle L., primary, Tarhini, Ahmad A., primary, Singer, Eric A., primary, Ikeguchi, Alexandra P., primary, McCarter, Martin D., primary, Denko, Nicholas, primary, Tinoco, Gabriel, primary, Husain, Marium, primary, Jin, Ning, primary, Osman, Afaf E.G., primary, Eljilany, Islam, primary, Tan, Aik Choon, primary, Coleman, Samuel S., primary, Denko, Louis, primary, Riedlinger, Gregory, primary, Schneider, Bryan P., primary, Spakowicz, Daniel, primary, and Ma, Qin, primary

Published
2024
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27. FIGURE 3 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

Author

Wang, Cankun, primary, Ma, Anjun, primary, Li, Yingjie, primary, McNutt, Megan E., primary, Zhang, Shiqi, primary, Zhu, Jiangjiang, primary, Hoyd, Rebecca, primary, Wheeler, Caroline E., primary, Robinson, Lary A., primary, Chan, Carlos H.F., primary, Zakharia, Yousef, primary, Dodd, Rebecca D., primary, Ulrich, Cornelia M., primary, Hardikar, Sheetal, primary, Churchman, Michelle L., primary, Tarhini, Ahmad A., primary, Singer, Eric A., primary, Ikeguchi, Alexandra P., primary, McCarter, Martin D., primary, Denko, Nicholas, primary, Tinoco, Gabriel, primary, Husain, Marium, primary, Jin, Ning, primary, Osman, Afaf E.G., primary, Eljilany, Islam, primary, Tan, Aik Choon, primary, Coleman, Samuel S., primary, Denko, Louis, primary, Riedlinger, Gregory, primary, Schneider, Bryan P., primary, Spakowicz, Daniel, primary, and Ma, Qin, primary

Published
2024
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28. Supplementary Table 7 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

Author

Wang, Cankun, primary, Ma, Anjun, primary, Li, Yingjie, primary, McNutt, Megan E., primary, Zhang, Shiqi, primary, Zhu, Jiangjiang, primary, Hoyd, Rebecca, primary, Wheeler, Caroline E., primary, Robinson, Lary A., primary, Chan, Carlos H.F., primary, Zakharia, Yousef, primary, Dodd, Rebecca D., primary, Ulrich, Cornelia M., primary, Hardikar, Sheetal, primary, Churchman, Michelle L., primary, Tarhini, Ahmad A., primary, Singer, Eric A., primary, Ikeguchi, Alexandra P., primary, McCarter, Martin D., primary, Denko, Nicholas, primary, Tinoco, Gabriel, primary, Husain, Marium, primary, Jin, Ning, primary, Osman, Afaf E.G., primary, Eljilany, Islam, primary, Tan, Aik Choon, primary, Coleman, Samuel S., primary, Denko, Louis, primary, Riedlinger, Gregory, primary, Schneider, Bryan P., primary, Spakowicz, Daniel, primary, and Ma, Qin, primary

Published
2024
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29. Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease

Author

Zhou, Xin, primary, Shen, Xiaotao, additional, Johnson, Jethro, additional, Spakowicz, Daniel, additional, Agnello, Melissa, additional, Zhou, Wenyu, additional, Avina, Monica, additional, Honkala, Alexander, additional, Chleilat, Faye, additional, Chen, Shirley Jingyi, additional, Cha, Kexin, additional, Leopold, Shana, additional, Zhu, Chenchen, additional, Chen, Lei, additional, Lyu, Lin, additional, Hornburg, Daniel, additional, Wu, Si, additional, Zhang, Xinyue, additional, Jiang, Chao, additional, Jiang, Liuyiqi, additional, jiang, lihua, additional, Jian, Ruiqi, additional, Brooks, Andrew W, additional, Wang, Meng, additional, Contrepois, Kevin, additional, Gao, Peng, additional, Schussler-Fiorenza Rose, Sophia Miryam, additional, Tran, Thi Dong Binh, additional, Nguyen, Hoan, additional, Celli, Alessandra, additional, Hong, Bo-Young, additional, Bautista, Eddy J, additional, Dorsett, Yair, additional, Kavathas, Paula, additional, zhou, yanjiao, additional, Sodergren, Erica, additional, Weinstock, George M, additional, and Snyder, Michael P, additional

Published
2024
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30. A bioinformatics tool for identifying intratumoral microbes from the ORIEN dataset

Author

Wang, Cankun, primary, Ma, Anjun, additional, Li, Yingjie, additional, McNutt, Megan E., additional, Zhang, Shiqi, additional, Zhu, Jiangjiang, additional, Hoyd, Rebecca, additional, Wheeler, Caroline E, additional, Robinson, Lary A, additional, Chan, Carlos H.F., additional, Zakharia, Yousef, additional, Dodd, Rebecca D., additional, Ulrich, Cornelia M, additional, Hardikar, Sheetal, additional, Churchman, Michelle L, additional, Tarhini, Ahmad A, additional, Singer, Eric A, additional, Ikeguchi, Alexandra P, additional, McCarter, Martin D., additional, Denko, Nicholas, additional, Tinoco, Gabriel, additional, Husain, Marium, additional, Jin, Ning, additional, Osman, Afaf E.G., additional, Eljilany, Islam, additional, Tan, Aik Choon, additional, Coleman, Samuel S, additional, Denko, Louis, additional, Riedlinger, Gregory, additional, Schneider, Bryan P., additional, Spakowicz, Daniel, additional, and Ma, Qin, additional

Published
2024
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31. Sex-based differences in the transcriptomic metabolic profiling in young onset colorectal cancer (YOCRC).

Author

Vadehra, Deepak, primary, Rosario, Spencer, additional, Wang, Jianmin, additional, Zhang, Yali, additional, Isenhart, Emily, additional, Kolesar, Jill, additional, Ibrahimi, Sami, additional, Singer, Eric A., additional, Spakowicz, Daniel, additional, Owen, Dwight Hall, additional, Churchman, Michelle L., additional, and Mukherjee, Sarbajit, additional

Published
2024
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48. Gut Microbiota Richness and Diversity Track With T Cell Aging in Healthy Adults.

Author

Madison, Annelise A, Burd, Christin E, Andridge, Rebecca, Wilson, Stephanie J, Bailey, Michael T, Belury, Martha A, Spakowicz, Daniel J, Malarkey, William B, and Kiecolt-Glaser, Janice K

Subjects
CELLULAR aging, T cells, GUT microbiome, SLEEP quality, ADULTS
Abstract

Background This study examined how gut microbiota diversity and richness relate to T cell aging among 96 healthy adults of all ages. It also explored whether these links differed throughout the lifespan. Methods Peripheral blood was obtained from 96 study participants (N =  96, aged 21–72) to assess mRNA markers of T cell aging (p16 ink4a , p14 ARF , B3gat1, Klrg1) and DNA methylation. T cell aging mRNA markers were combined into an aging index, and the Horvath epigenetic clock algorithm was used to calculate epigenetic age based on DNA methylation status of over 500 loci. Participants also collected a stool sample from which the V4 region of the 16S rRNA gene was sequenced to derive the Shannon and Simpson diversity indices, and the total count of observed operational taxonomic units (richness). Models controlled for BMI, comorbidities, sex, dietary quality, smoking status, physical activity, and sleep quality. Results Lower microbiota richness was associated with higher T cell age based on mRNA markers, but when probing the region of significance, this relationship was only significant among adults 45 years and older (p = .03). Lower Shannon diversity (p = .05) and richness (p = .07) marginally correlated with higher epigenetic age (ie, greater T cell DNA methylation). Conclusions Gut microbiota complexity may correspond with the rate of T cell aging, especially in mid-to-late life. These results suggest an interplay between the gut microbiome and immunological aging that warrants further experimental work. [ABSTRACT FROM AUTHOR]

Published
2024
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50. Emerging Immunotherapy Approaches for Advanced Clear Cell Renal Cell Carcinoma.

Author

Meng, Lingbin, Collier, Katharine A., Wang, Peng, Li, Zihai, Monk, Paul, Mortazavi, Amir, Hu, Zhiwei, Spakowicz, Daniel, Zheng, Linghua, and Yang, Yuanquan

Subjects
BISPECIFIC antibodies, RENAL cell carcinoma, IMMUNE checkpoint inhibitors, PROGRAMMED cell death 1 receptors, CHIMERIC antigen receptors, IMMUNOTHERAPY, IMMUNOMODULATORS
Abstract

The most common subtype of renal cell carcinoma is clear cell renal cell carcinoma (ccRCC). While localized ccRCC can be cured with surgery, metastatic disease has a poor prognosis. Recently, immunotherapy has emerged as a promising approach for advanced ccRCC. This review provides a comprehensive overview of the evolving immunotherapeutic landscape for metastatic ccRCC. Immune checkpoint inhibitors (ICIs) like PD-1/PD-L1 and CTLA-4 inhibitors have demonstrated clinical efficacy as monotherapies and in combination regimens. Combination immunotherapies pairing ICIs with antiangiogenic agents, other immunomodulators, or novel therapeutic platforms such as bispecific antibodies and chimeric antigen receptor (CAR) T-cell therapy are areas of active research. Beyond the checkpoint blockade, additional modalities including therapeutic vaccines, cytokines, and oncolytic viruses are also being explored for ccRCC. This review discusses the mechanisms, major clinical trials, challenges, and future directions for these emerging immunotherapies. While current strategies have shown promise in improving patient outcomes, continued research is critical for expanding and optimizing immunotherapy approaches for advanced ccRCC. Realizing the full potential of immunotherapy will require elucidating mechanisms of response and resistance, developing predictive biomarkers, and rationally designing combination therapeutic regimens tailored to individual patients. Advances in immunotherapy carry immense promise for transforming the management of metastatic ccRCC. [ABSTRACT FROM AUTHOR]

Published
2024
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