Article
Immunology
Jinze Li, Dehong Cao, Yin Huang, Qiao Xiong, Daqing Tan, Liangren Liu, Tianhai Lin, Qiang Wei
Summary: This pooled analysis found that an elevated preoperative SII is significantly associated with worse survival outcomes and adverse pathological features in patients with bladder cancer.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Jiange Zhang, Caisheng Huang, Rirong Yang, Xiang Wang, Bo Fang, Junhao Mi, Hao Yuan, Zengnan Mo, Yihai Sun
Summary: This study explored the relationship between BLCA and immunity, identified 13 prognosis-related immune genes, and constructed an immune-related prognosis model. The low-risk group had better survival outcomes, and a nomogram based on clinicopathological information and risk scores was established. The research provided potential targets for BLCA treatment.
Article
Oncology
Shuai Liu, Yu Yao, Zhan-Kun Wang, Li-Jiang Sun, Gui-Ming Zhang
Summary: Sarcomatoid carcinoma of the bladder is a rare disease with limited knowledge about the prognostic impact of its components. This study aimed to assess the prognostic value of the proportion of sarcomatoid components and validate the worse survival outcomes of sarcomatoid carcinomas. Propensity score matching was used to compare the survival rates of patients with sarcomatoid and non-sarcomatoid carcinomas. The results showed that patients with sarcomatoid carcinoma had worse 5-year cancer-specific survival and recurrence-free survival rates, especially in the subgroup with muscle invasion. A higher proportion of sarcomatoid components was associated with poorer survival.
Article
Oncology
Ji-Qing Chen, Lucas A. Salas, John K. Wiencke, Devin C. Koestler, Annette M. Molinaro, Angeline S. Andrew, John D. Seigne, Margaret R. Karagas, Karl T. Kelsey, Brock C. Christensen
Summary: This study used DNA methylation profiles and cell type analysis to identify that increasing CD4T and CD8T cell proportions were associated with a decreased hazard of tumor recurrence or death in NMIBC patients, while increasing monocyte proportion and mdNLR were associated with an increased hazard. Additionally, 2528 CpGs associated with tumor recurrence or death were identified through epigenome-wide association study.
CLINICAL EPIGENETICS
(2022)
Article
Cell Biology
Yi Jiang, Zhenhao Zeng, Situ Xiong, Ming Jiang, Gaomin Huang, Chiyu Zhang, Xiaoqing Xi
Summary: The study identified two distinct immune clusters in BLCA patients, characterized by high and low ImmuneScores. CD96 and IBSP were identified as prognostic genes. ImmuneScoreH showed inactivation of innate immune cell chemotaxis, while ImmuneScoreL exhibited low tumor antigen load as a potential immune escape mechanism.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Oncology
Jedrzej Borowczak, Krzysztof Szczerbowski, Mateusz Maniewski, Marek Zdrenka, Piotr Slupski, Paulina Antosik, Sylwia Kolodziejska, Marta Sekielska-Domanowska, Mariusz Dubiel, Magdalena Bodnar, Lukasz Szylberg
Summary: This article investigates the prognostic role of cyclin-dependent kinase 9 expression in urothelial carcinoma. The results show that high CDK9 expression is associated with a better prognosis, tumor grade, stage, and invasiveness, contradicting previous findings. CDK9 may play a crucial role in the early stages of urothelial carcinoma.
Article
Immunology
Yuchen Bai, Qi Zhang, Feng Liu, Jing Quan
Summary: A novel cuproptosis-related lncRNA signature was identified that could predict the prognosis and immune landscape of BLCA. This signature not only had a higher diagnostic efficiency compared to other clinical features, but also had a good performance in predicting the 1-year, 3-year, and 5-year overall survival rate in BLCA. Patients with a low risk score seemed to be associated with an inflamed tumor immune microenvironment and had a higher TMB level than those with a high risk score.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Genetics & Heredity
Yongsheng Zhang, Yunlong Wang, Jichuang Wang, Kaixiang Zhang
Summary: BLCA patients with high ICI scores and high TMB have the best prognosis, suggesting that combining TMB and ICI scores can provide more accurate survival predictions for BLCA patients.
FRONTIERS IN GENETICS
(2022)
Article
Immunology
Miaoyan Wei, Jin Xu, Jie Hua, Qingcai Meng, Chen Liang, Jiang Liu, Bo Zhang, Wei Wang, Xianjun Yu, Si Shi
Summary: Immune infiltration in Pan-NETs is heterogeneous, with T lymphocytes and macrophages being predominant. The ISpnet model, consisting of six immune features, showed significant prognostic value in predicting postsurgical recurrence-free survival, with potential for aiding in clinical decision-making and identifying patients who may benefit from immunotherapy.
FRONTIERS IN IMMUNOLOGY
(2021)
Review
Multidisciplinary Sciences
Wentao Zhang, Fuhan Yang, Shiyu Mao, Ruiliang Wang, Haotian Chen, Yuefei Ran, Shenghua Liu, Pengfei Wu, Yang Yan, Wei Li, Junfeng Zhang, Xudong Yao
Summary: Recent evidence suggests that the genitourinary microbiome plays a significant role in the development and progression of urological tumors, including bladder cancer. However, there is limited information available about the interaction between bladder cancer and the genitourinary microbiome, compared to the gut microbiota and gastrointestinal tumors. This expanding field merits further investigation for its potential impact on bladder cancer diagnosis, prevention, and treatment prospects.
Article
Cell Biology
Li Yang, Aitian Li, Fengsen Liu, Qitai Zhao, Shaofei Ji, Wen Zhu, Weina Yu, Ru Zhang, Yaqing Liu, Wencai Li, Yi Zhang
Summary: The study conducted immune profiling of UBC and identified four immune subtypes, with the hot tumor subtype showing a high correlation with patient survival. The hot tumor subtype had significant immune cell infiltration, but the cells exhibited an exhaustion phenotype. CCL4 may play a key role in immune cell infiltration in the hot tumor subtype.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Yi Wang, Hong Cheng, Tengyue Zeng, Shuqiu Chen, Qianwei Xing, Bingye Zhu
Summary: A novel prognostic signature based on apoptosis-related genes (ARGs) was developed for predicting overall survival (OS) in bladder cancer (BC) patients and its association with immune infiltrates was examined.
Article
Oncology
Suk Kyun Hong, Kwang-Woong Lee, Su young Hong, Sanggyun Suh, Kwangpyo Hong, Eui Soo Han, Jeong-Moo Lee, YoungRok Choi, Nam-Joon Yi, Kyung-Suk Suh
Summary: This study identified prognostic factors and recommended therapeutic strategies for patients with single large HCC and good performance status. Resection as an initial treatment should be considered, particularly for patients with low platelet count, low sodium level, and large tumor diameter. However, caution should be exercised in patients with these risk factors.
FRONTIERS IN ONCOLOGY
(2021)
Article
Oncology
Zhenghong Liu, Li Sun, Bin Zheng, Heng Wang, Xiaowen Qin, Pu Zhang, Qijun Wo, Haichang Li, Yixuan Mou, Dahong Zhang, Shuai Wang
Summary: This study found that abnormal overexpression of ATAD3A in bladder cancer tissues is associated with pathological features and prognosis of patients. ATAD3A overexpression is correlated with patient age, tumor characteristics, and stage. High expression of ATAD3A indicates reduced survival rate in bladder cancer patients.
Review
Oncology
Lina Liu, Zhongyi Shi, Xingdong Qiu
Summary: This study aimed to investigate the impact of bone metastasis on the prognosis of non-small cell lung cancer (NSCLC) patients treated with immune checkpoint inhibitors (ICIs). The findings showed that bone metastasis was associated with poor overall survival (OS) in NSCLC patients treated with ICIs, but it did not affect progression-free survival (PFS). Therefore, clinicians should prioritize the management of NSCLC patients with bone metastasis and explore combination therapies for better outcomes.
CLINICAL & TRANSLATIONAL ONCOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Fu-Ying Tian, Elizabeth M. Kennedy, Karen Hermetz, Amber Burt, Todd M. Everson, Tracy Punshon, Brian P. Jackson, Ke Hao, Jia Chen, Margaret R. Karagas, Devin C. Koestler, Carmen Marsit
Summary: Selenium is essential for fetal development, and its influence on placental microRNA expression was examined in this study. The results suggest a non-monotonic association between selenium concentration and the expression of the miR-216a-5p/miR-217-5p cluster in the placenta.
Article
Multidisciplinary Sciences
Arjun Bhattacharya, Anastasia N. Freedman, Vennela Avula, Rebeca Harris, Weifang Liu, Calvin Pan, Aldons J. Lusis, Robert M. Joseph, Lisa Smeester, Hadley J. Hartwell, Karl C. K. Kuban, Carmen J. Marsit, Yun Li, T. Michael O'Shea, Rebecca C. Fry, Hudson P. Santos
Summary: The placenta plays a vital role in the Developmental Origins of Health and Disease (DOHaD) hypothesis, but its study has been historically neglected. In this research, we investigate placental genetrait associations (GTAs) for 40 traits across different stages of life. By analyzing placental multi-omics data, we identify 248 GTAs, mainly related to neonatal and metabolic traits, and enriched in cell growth and immunological pathways. We find that genetic effects mediated by placental gene expression significantly contribute to early-life traits, but not later-in-life traits. We also discover hypotheses for distal regulation of GTAs through distal genetic variants.
NATURE COMMUNICATIONS
(2022)
Article
Health Care Sciences & Services
Brittney O. Baumert, Nancy Fiedler, Tippawan Prapamontol, Panrapee Suttiwan, Warangkana Naksen, Parinya Panuwet, Supattra Sittiwang, Chayada Dokjunyam, Melissa M. Smarr, Carmen J. Marsit, P. Barry Ryan, Wattasit Siriwong, Mark G. Robson, Dana Boyd Barr
Summary: This study aims to investigate the impact of prenatal exposure to pesticides on neurodevelopment in children and identify early predictors. The study cohort consists of participants from farming districts in Thailand and will undergo long-term follow-up and neurodevelopmental tests. The findings will contribute to the development of risk assessment standards for pregnant women in Thailand and other countries.
JMIR RESEARCH PROTOCOLS
(2022)
Article
Environmental Sciences
Pei Wen Tung, Amber Burt, Margaret Karagas, Brian P. Jackson, Tracy Punshon, Barry Lester, Carmen J. Marsit
Summary: The study found that toxic metals such as cadmium and lead measured in placental tissue may adversely impact newborn neurobehavior, suggesting the potential negative effects of prenatal exposure to these metals on newborn health.
ENVIRONMENTAL RESEARCH
(2022)
Article
Engineering, Environmental
Jessie P. Buckley, Jordan R. Kuiper, Deborah H. Bennett, Emily S. Barrett, Tracy Bastain, Carrie Breton, Sridhar Chinthakindi, Anne L. Dunlop, Shohreh F. Farzan, Julie B. Herbstman, Margaret R. Karagas, Carmen J. Marsit, John D. Meeker, Rachel Morello-Frosch, Thomas G. O'Connor, Megan E. Romano, Susan Schantz, Rebecca J. Schmidt, Deborah J. Watkins, Hongkai Zhu, Edo D. Pellizzari, Kurunthachalam Kannan, Tracey J. Woodruff
Summary: Prenatal chemical exposures can affect maternal and child health, but routine biomonitoring does not cover many industrial chemicals. A study of 171 pregnant women in the US and Puerto Rico found widespread exposures to both common and understudied chemicals in this diverse population, with higher concentrations of certain chemicals in Hispanic women.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Fasil Tekola-Ayele, Xuehuo Zeng, Suvo Chatterjee, Marion Ouidir, Corina Lesseur, Ke Hao, Jia Chen, Markos Tesfaye, Carmen J. Marsit, Tsegaselassie Workalemahu, Ronald Wapner
Summary: Abnormal birthweight is associated with increased risk for cardiometabolic diseases in later life. This study integrated placental methylation and gene expression data with genetic loci associated with birthweight to identify functional genes involved in fetal growth regulation.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Maya A. Deyssenroth, Shouneng Peng, Ke Hao, Carmen J. Marsit, Jia Chen
Summary: This study presents the first genome-wide characterization of placental transcript usage and its association with intrauterine metal exposure and fetal growth restriction. The results highlight the importance of interrogating the transcriptome at a finer-scale transcript-level resolution to identify novel placental biomarkers of exposure-induced outcomes.
FRONTIERS IN GENETICS
(2022)
Article
Environmental Sciences
Daniel A. Enquobahrie, James MacDonald, Michael Hussey, Theo K. Bammler, Christine T. Loftus, Alison G. Paquette, Nora Byington, Carmen J. Marsit, Adam Szpiro, Joel D. Kaufman, Kaja Z. LeWinn, Nicole R. Bush, Frances Tylavsky, Catherine J. Karr, Sheela Sathyanarayana
Summary: This study identified an association between prenatal exposure to PM2.5 and placental gene expression, particularly in the first half of pregnancy. Offspring sex may also play a role in modulating this association, with a positive correlation observed in males and a negative correlation in females.
ENVIRONMENT INTERNATIONAL
(2022)
Article
Pediatrics
Lauren A. Eaves, Adam E. Enggasser, Marie Camerota, Semsa Gogcu, William A. Gower, Hadley Hartwell, Wesley M. Jackson, Elizabeth Jensen, Robert M. Joseph, Carmen J. Marsit, Kyle Roell, Hudson P. Santos, Jeffrey S. Shenberger, Lisa Smeester, Diana Yanni, Karl C. K. Kuban, T. Michael O'Shea, Rebecca C. Fry
Summary: This study investigated the relationship between CpG methylation in the placenta and neonatal blood and neonatal inflammation in extremely preterm infants. The study found that placental CpG methylation was strongly associated with sustained systemic inflammation (ISSI), while neonatal blood CpG methylation was associated with day-one inflammation (DOI).
PEDIATRIC RESEARCH
(2023)
Article
Mathematical & Computational Biology
Roland Albert A. Romero, Mariefel Nicole Y. Deypalan, Suchit Mehrotra, John Titus Jungao, Natalie E. Sheils, Elisabetta Manduchi, Jason H. Moore
Summary: This study aims to ascertain and compare the performances of Automated Machine Learning (AutoML) tools on large, highly imbalanced healthcare datasets. The results show that the AutoML tools did not differ significantly from each other and all models performed poorly in predicting disease outcomes. The study provides a specific use-case to illustrate the selection of an optimal prediction threshold and highlights the challenges of healthcare datasets for AutoML tools.
Article
Genetics & Heredity
Patricia Caetano Mota, Miguel Luz Soares, Carlos Daniel Vasconcelos, Antonio Carlos Ferreira, Bruno A. Lima, Elisabetta Manduchi, Jason H. Moore, Natalia Melo, Helder Novais-Bastos, Jose Miguel Pereira, Susana Guimaraes, Conceicao Souto Moura, Jose Agostinho Marques, Antonio Morais
Summary: In this study, the association between idiopathic pulmonary fibrosis (IPF) and single-nucleotide polymorphisms (SNPs) of certain candidate genes was investigated. The MUC5B rs35705950 SNP was found to be significantly associated with IPF susceptibility, while the MUC5B-TOLLIP T-C-T-C haplotype was associated with improved survival in IPF patients. These findings could be valuable for prognosis and stratification of IPF patients.
JOURNAL OF MOLECULAR MEDICINE-JMM
(2022)
Article
Multidisciplinary Sciences
Patryk Orzechowski, Jason H. Moore
Summary: Understanding the strengths and weaknesses of machine learning algorithms is crucial for determining their applicability. The DIGEN benchmark provides a collection of synthetic datasets and 40 mathematical functions for comprehensive and interpretable testing of binary classification ML algorithms. It facilitates evaluation and comparison of new methods by maximizing the diversity of performance among popular ML algorithms.
Article
Multidisciplinary Sciences
Gianluca Ursini, Pasquale Di Carlo, Sreya Mukherjee, Qiang Chen, Shizhong Han, Jiyoung Kim, Maya Deyssenroth, Carmen J. Marsit, Jia Chen, Ke Hao, Giovanna Punzi, Daniel R. Weinberger
Summary: Our previous research indicates that genomic risk for schizophrenia is influenced by early life complications and sex-biased neurodevelopmental trajectories. In this study, we identify specific genes and potential mechanisms in the placenta that may mediate these outcomes. Through analysis of healthy term placentae and fetal brain, we highlight 139 placenta and schizophrenia-specific risk genes, many of which are sex-biased, and suggest a connection with nutrient-sensing capabilities of placenta and trophoblast invasiveness. These findings also implicate the Coronavirus-pathogenesis pathway and its association with SARS-CoV-2-positive pregnancies.
NATURE COMMUNICATIONS
(2023)
Article
Public, Environmental & Occupational Health
Michael Mortillo, Carmen J. Marsit
Summary: The purpose of this review is to summarize recent literature on the effects of early-life environmental exposures on placental DNA methylation, identify how variation in placental methylation is regulated in an exposure-specific manner, and encourage further research in this area. Multiple studies have found associations between prenatal environmental exposures and placental methylation at both gene-specific and epigenome-wide levels. Different exposures lead to unique patterns of methylation, and cross-exposure assessments have identified certain genes that consistently show differential placental methylation. Studies focusing on exposures such as air pollution, maternal smoking, environmental contaminants, and trace metals are more abundant, while studies on socioeconomic adversity and circadian disruption are scarce but show significant effects. Understanding the impacts of early-life environmental exposures on placental methylation is crucial for establishing the link between the maternal environment, epigenetic variation, and long-term health. Future studies should incorporate repeated measures of exposure throughout pregnancy to determine critical windows of heavy placental methylation effects. Methylation-based scores and sequencing technology could provide insights into epigenetic gestational age and identify more genomic regions affected by methylation. Studies on the impact of other exposures such as pesticides, alcohol, and other chemicals are also necessary.
CURRENT ENVIRONMENTAL HEALTH REPORTS
(2023)
Article
Biochemical Research Methods
Hyunjun Choi, Jay Moran, Nicholas Matsumoto, Miguel E. Hernandez, Jason H. Moore
Summary: Aliro is an open-source software package that automates machine learning analysis through a clean web interface. By leveraging the power of large language models, users can interact with their data and quickly discover new insights. It also includes a pre-trained machine learning recommendation system for automated algorithm and hyperparameter selection, as well as visualization of the evaluated model and data.
