Article
Multidisciplinary Sciences
Raquel Garcia-Perez, Paula Esteller-Cucala, Gloria Mas, Irene Lobon, Valerio Di Carlo, Meritxell Riera, Martin Kuhlwilm, Arcadi Navarro, Antoine Blancher, Luciano Di Croce, Jose Luis Gomez-Skarmeta, David Juan, Tomas Marques-Bonet
Summary: This study highlights the importance of epigenetic regulation in gene expression evolution across primates. The research reveals that epigenetic conservation in primates is dependent on the activity state of regulatory elements, with most changes occurring in weakly active elements. Human-specific regulatory elements with weak activities are enriched in genes associated with human adaptation, suggesting their role in recent human evolution.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Haizhu Zhang, Zhaoyu Qin, Xuetong Yue, Yang Liu, Xiaogang Sun, Jinwen Feng, Ziyan Xu, Jiangyan Zhao, Kai Li, Jiange Qiu, Wenjun Yang, Fuchu He, Chen Ding
Summary: ATAC-MS is a method to identify transcriptional protein complexes assembled on accessible chromatin, providing insight into the protein machinery in open chromatin. Combined with ATAC-seq, it allows for high-resolution profiling of chromatin-transcriptional machinery. Additionally, the fusion protein ctATAC-MS enables systematic pinpointing of the transcriptional machinery at specific open chromatin regions.
Article
Multidisciplinary Sciences
Chunyu Liu, Jessica L. Fetterman, Xianbang Sun, Kaiyu Yan, Poching Liu, Yan Luo, Jun Ding, Jun Zhu, Daniel Levy
Summary: This study compared mtDNA sequence variants between LCL and whole blood samples. The results showed that most homoplasmic variants were present in both LCL and blood samples, while most heteroplasmic variants were unique to either LCL or blood samples. LCL samples had a higher number of heteroplasmic variants compared to whole blood samples, but a similar number of homoplasmic variants. Additionally, LCL samples tended to have lower levels of heteroplasmy.
SCIENTIFIC REPORTS
(2022)
Article
Biotechnology & Applied Microbiology
Ziyue Qin, Wencan Wang, Malik Ahsan Ali, Yihan Wang, Yan Zhang, Ming Zhang, Guangbin Zhou, Jian-Dong Yang, Changjun Zeng
Summary: This study revealed the dynamic m(6)A modification of mRNAs in boar sperm during cryopreservation, which may affect mRNA expression and are closely related to sperm motility, apoptosis, and metabolism.
Article
Multidisciplinary Sciences
Kexuan Deng, Huan Yin, Fangjie Xiong, Li Feng, Pan Dong, Maozhi Ren
Summary: The study identified potential TOR-miRNA-mRNA regulatory networks in TOR signaling in potato. TOR inhibition led to significant differential expression of 2,899 genes in potato, mainly enriched in multiple metabolic processes. In addition, TOR suppression resulted in up-regulation of 41 miRNAs and down-regulation of 45 miRNAs, suggesting a crucial role of TOR in miRNA regulatory network. Integrated mRNA and miRNA expression profiling revealed involvement of these miRNAs in large-scale metabolic processes in the TOR signal pathway in potato.
Article
Biochemistry & Molecular Biology
Yi Zeng, Benjamin J. Fair, Huilin Zeng, Aiswarya Krishnamohan, Yichen Hou, Johnathon M. Hall, Alexander J. Ruthenburg, Yang Li, Jonathan P. Staley
Summary: Previous studies suggested that most vertebrate genes require exon definition for splicing, where spliceosome assembly occurs on exons rather than introns. However, our research found that 90% of introns, including long introns, can splice before the transcription of a downstream exon, indicating that exon definition is not necessary for most human introns. Additionally, splicing timing varies greatly among introns and is influenced by various genetic elements.
Article
Immunology
Fergal J. Duffy, Nina Hertoghs, Ying Du, Maxwell L. Neal, Damian Oyong, Suzanne McDermott, Nana Minkah, Jason Carnes, Katharine V. Schwedhelm, M. Juliana McElrath, Stephen C. De Rosa, Evan Newell, John D. Aitchison, Ken Stuart
Summary: This study provides detailed immunological profiling of a radiation-attenuated sporozoite (RAS) vaccine trial for malaria. The results reveal multiple immune processes induced by vaccination and associated with protection, including inflammatory and proliferative responses, as well as changes in specific cell subsets. Interferon responses differ between protected and non-protected individuals and are correlated with abundance of different monocyte populations.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Nutrition & Dietetics
Meiming Su, Wenqi Zhao, Yujie Li, Hong Li, Suowen Xu, Jianping Weng
Summary: Atherosclerosis is a chronic inflammatory vascular disease in which endothelial cells play a crucial role. Resveratrol, a polyphenol, prevents cardiovascular disease by regulating multiple signaling pathways. The study suggests that resveratrol may serve as a shear stress mimetic drug for combating atherosclerosis.
Article
Biology
Elliott D. SoRelle, Joanne Dai, Emmanuela N. Bonglack, Emma M. Heckenberg, Jeffrey Y. Zhou, Stephanie N. Giamberardino, Jeffrey A. Bailey, Simon G. Gregory, Cliburn Chan, Micah A. Luftig
Summary: The study characterized single-cell transcriptomic profiles of five LCLs, revealing substantial phenotypic heterogeneity within and across LCLs likely due to intrinsic variance in primary B cells and host-pathogen dynamics. Stochastic simulations demonstrate that factors such as initial primary cell heterogeneity, random sampling, time in culture, and phenotype-specific fitness differences can contribute substantially to dynamic diversity in populations of nominally clonal cells.
Article
Plant Sciences
Moumita Roy Chowdhury, Ranjit Prasad Bahadur, Jolly Basak
Summary: This study predicted and validated miRNAs, their targets, and lncRNAs in the genome of cauliflower, providing insights into their roles in post-transcriptional gene regulation.
Article
Biology
Rebeca San Martin, Priyojit Das, Jacob T. Sanders, Ashtyn M. Hill, Rachel Patton McCord
Summary: The expression of a mutant Lamin A, progerin, in Hutchinson-Gilford Progeria Syndrome leads to various alterations in cells, such as changes in genome architecture, nuclear morphology, epigenetic states, and altered phenotypes. This study comprehensively analyzed the transcriptional status of patient-derived HGPS fibroblasts and found abnormal transcriptional signatures, related to DNA maintenance, bone development, blood vessel maturation, lipid management, and muscle growth. The study also revealed misregulation of genes involved in endochondral ossification and chondrogenic commitment in children aged 4-7 years old. Hi-C measurements indicated changes in genome compartmentalization and TAD strength in patient fibroblasts.
Article
Microbiology
Joshua M. Wang, Andrew L. Woodruff, Matthew J. Dunn, Robert J. Fillinger, Richard J. Bennett, Matthew Z. Anderson
Summary: The research on 21 clinical isolates of Candida albicans showed extensive genetic and phenotypic variation, with strain-specific gene expression patterns and linkages between gene expression and phenotypic traits. The study highlights the importance of transcriptional profiling in understanding the genetic basis for phenotypic diversity and identifies new genes and pathways associated with pathogenic processes. These findings underscore the need for personalized treatment strategies based on individual strains of infectious fungi.
Article
Engineering, Environmental
Cheng-Wei Qiu, Yue Ma, Zi-Feng Gao, Jakkrit Sreesaeng, Shuo Zhang, Wenxing Liu, Imrul Mosaddek Ahmed, Shengguan Cai, Yizhou Wang, Guoping Zhang, Feibo Wu
Summary: This study provides a comprehensive examination of genetic variation in aluminum-tolerant Tibetan wild barley through genome-wide profiling. The identification of key genes related to aluminum tolerance in barley and the strategy of manipulating these genes offer potential for developing more aluminum-tolerant barley cultivars.
JOURNAL OF HAZARDOUS MATERIALS
(2024)
Article
Clinical Neurology
Amber Yaqub, Michelle M. J. Mens, Jaco M. Klap, Gerrit Jan Weverling, Paul Klatser, Just P. J. Brakenhoff, Gennady Roshchupkin, Mohammad Kamran Ikram, Mohsen Ghanbari, Mohammad Arfan Ikram
Summary: We conducted a study to identify circulating miRNAs in plasma associated with cognition and incident dementia. Four miRNAs were found to be commonly associated with both cognition and dementia, and their target genes were expressed in the brain, suggesting their potential involvement in dementia pathways.
ALZHEIMERS & DEMENTIA
(2023)
Article
Biochemistry & Molecular Biology
Nathan G. Walworth, Josh L. Espinoza, Phoebe A. Argyle, Jana Hinners, Naomi M. Levine, Martina A. Doblin, Chris L. Dupont, Sinead Collins
Summary: This study reveals repeated evolutionary divergence within diatom populations in a constant environment through experimental evolution and transcriptome analysis. Most of the transcriptional divergence can be captured on a reduced set of axes and is associated with core metabolic pathways. The study shows that gene networks can diverge even in the absence of environmental change, suggesting their central role in generating phenotypic diversity.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Pharmacology & Pharmacy
Paul Y. Takahashi, Euijung Ryu, Suzette J. Bielinski, Matthew Hathcock, Gregory D. Jenkins, James R. Cerhan, Janet E. Olson
Summary: This study found no association between 10 well-established pharmacogenomics phenotypes and hospitalization or ED visits. Traditional risk factors like age and self-rated health were more predictive of hospitalization and/or ED visits than pharmacogenomics information.
PHARMACOGENOMICS & PERSONALIZED MEDICINE
(2021)
Article
Oncology
Joshua C. Pritchett, Zhi-Zhang Yang, Hyo Jin Kim, Jose C. Villasboas, Xinyi Tang, Shahrzad Jalali, James R. Cerhan, Andrew L. Feldman, Stephen M. Ansell
Summary: AITL is an aggressive lymphoid malignancy with a unique tumor microenvironment characterized by a minority population of malignant TFH cells and a diverse infiltrate of immune cells. Non-malignant populations within the TME, such as B cells and CD8+ T cells, are increasingly recognized for their potential role in AITL biology. These non-malignant populations exhibit specific expression patterns that may contribute to the understanding of AITL pathogenesis.
Editorial Material
Hematology
James R. Cerhan
Summary: In this article, Williams et al. provide a clearer perspective on the additional burden of neurocognitive, psychosocial, and quality of life impairments faced by long-term survivors of childhood Hodgkin lymphoma. The authors also identify potentially modifiable factors that could help prevent or reduce adverse outcomes.
Article
Oncology
Sophia S. Wang, Claire M. Vajdic, Martha S. Linet, Susan L. Slager, Jenna Voutsinas, Alexandra Nieters, Delphine Casabonne, James R. Cerhan, Wendy Cozen, Graciela Alarcon, Otoniel Martinez-Maza, Elizabeth E. Brown, Paige M. Bracci, Jennifer Turner, Henrik Hjalgrim, Parveen Bhatti, Yawei Zhang, Brenda M. Birmann, Christopher R. Flowers, Ora Palliel, Elizabeth A. Holly, Eleanor Kane, Dennis Weisenburger, Marc Maynadie, Pierluigi Cocco, Lenka Foretova, Elizabeth Crabb Breen, Qing Lan, Angela Brooks-Wilson, Anneclaire J. De Roos, Martyn T. Smith, Eve Roman, Paoloa Boffetta, Anne Kricker, Tongzhang Zheng, Christine F. Skibola, Jacqueline Clavel, Alain Monnereau, Stephen J. Chanock, Nathaniel Rothman, Yolanda Benavente, Patricia Hartge, Karin E. Smedby
Summary: This study suggests that polygenic risk scores (PRS) constructed from currently known subtype-specific loci may not capture biological pathways shared with autoimmune conditions. Targeted genetic screening (PRS) among populations with autoimmune conditions may help identify individuals at highest risk for DLBCL and enable early detection.
CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION
(2022)
Article
Oncology
Sanjal H. Desai, Levi D. Pederson, Betsy Laplant, Raphael Mwangi, Matthew J. Maurer, Jason R. Young, William R. Macon, Rebecca L. King, Yucai Wang, James R. Cerhan, Andrew L. Feldman, David J. Inwards, Ivana N. Micallef, Patrick B. Johnston, Luis F. Porrata, Stephen M. Ansell, Thomas M. Habermann, Thomas E. Witzig, Grzegorz S. Nowakowski
Summary: This study found that PET2 after two cycles of chemotherapy can predict the risk of disease progression and death in patients with diffuse large B cell lymphoma. PET2-guided risk-adapted strategies may improve outcomes for these patients.
BLOOD CANCER JOURNAL
(2022)
Article
Oncology
Surbhi Sidana, Cristine Allmer, Melissa C. Larson, Amylou Dueck, Kathleen Yost, Rahma Warsame, Gita Thanarajasingam, James R. Cerhan, Jonas Paludo, S. Vincent Rajkumar, Thomas M. Habermann, Grzegorz S. Nowakowski, Yi Lin, Morie A. Gertz, Thomas Witzig, Angela Dispenzieri, Wilson Gonsalves, Stephen M. Ansell, Carrie A. Thompson, Shaji K. Kumar
Summary: Patients treated on CTs reported similar QoL and quality of care compared to the non-CT group, but both groups experienced increasing financial burden over time.
JCO ONCOLOGY PRACTICE
(2022)
Review
Hematology
Grzegorz Nowakowski, Matthew J. Maurer, James R. Cerhan, Debarshi Dey, Laurie H. Sehn
Summary: Comparative effectiveness studies using real-world data can provide complementary evidence on treatment effectiveness. By balancing baseline covariates using propensity score methods, closely matched patient-level cohorts can be generated for robust comparative analyses.
AMERICAN JOURNAL OF HEMATOLOGY
(2023)
Article
Hematology
Juan Pablo Alderuccio, Isildinha M. Reis, Thomas M. Habermann, Brian K. Link, Catherine Thieblemont, Annarita Conconi, Melissa C. Larson, Luciano Cascione, Wei Zhao, James R. Cerhan, Emanuele Zucca, Izidore S. Lossos
Summary: The study developed and validated a new prognostic index, the Revised mucosa-associated lymphoid tissue International Prognostic Index (Revised MALT-IPI), which is centered on disease characteristics and provides robust risk stratification, identifying a group of patients characterized by earlier progression of EMZL.
AMERICAN JOURNAL OF HEMATOLOGY
(2022)
Article
Oncology
Terry Boyle, Geffen Kleinstern, Paige M. Bracci, James R. Cerhan, Yolanda Benavente, Delphine Casabonne, Brian C-H Chiu, Thomas M. Habermann, Elizabeth A. Holly, Mark Liebow, Aaron Norman, Ora Paltiel, Dennis Robinson, Nathaniel Rothman, Rania Abu Seir, Susan L. Slager, Paul J. Villeneuve, Sophia S. Wang, Dennis D. Weisenburger, John J. Spinelli
Summary: This study, which pooled data from nine case-control studies, found that moderate-to-vigorous intensity physical activity can reduce the risk of non-Hodgkin lymphoma.
INTERNATIONAL JOURNAL OF CANCER
(2023)
Article
Hematology
Sanjal H. Desai, Raphael Mwangi, Wern Lynn Ng, Rebecca L. King, Matthew J. Maurer, James R. Cerhan, Andrew L. Feldman, Umar Farooq, Eric Mou, Thomas M. Habermann, Carrie A. Thompson, Yucai Wang, Thomas E. Witzig, Grzegorz S. Nowakowski
Summary: This observational study found that patients with DLBCL who underwent CNB had poor-risk features, worse outcomes, and inadequate tissue for molecular analyses compared to those who underwent EB. The increasing tissue requirements of biomarker-driven clinical trials may result in the exclusion of high-risk DLBCL patients who need novel agents.
Letter
Oncology
Sameer A. Parikh, Sara J. Achenbach, Kari G. Rabe, Aaron D. Norman, Nicholas J. Boddicker, Janet E. Olson, Timothy G. Call, James R. Cerhan, Celine M. Vachon, Neil E. Kay, Esteban Braggio, Curtis A. Hanson, Susan L. Slager, Tait D. Shanafelt
BLOOD CANCER JOURNAL
(2022)
Article
Oncology
Cristina Correia, Matthew J. J. Maurer, Samantha J. J. McDonough, Paula A. A. Schneider, Paige E. E. Ross, Anne J. J. Novak, Andrew L. L. Feldman, James R. R. Cerhan, Susan L. L. Slager, Thomas E. E. Witzig, Bruce W. W. Eckloff, Hu Li, Grzegorz S. S. Nowakowski, Scott H. H. Kaufmann
Summary: The identification of follicular lymphoma (FL) patients with low disease burden but high risk for early progression is unclear. In a study on newly diagnosed FLs, BCL2 mutations with high variant allele frequency (VAF) were found to be associated with increased transformation risk and shorter event-free survival. However, other sequenced genes did not contribute significantly to the prognostic value of the panel. Nonsynonymous BCL2 mutations with VAF = 20% were consistently associated with decreased event-free survival and overall survival.
BLOOD CANCER JOURNAL
(2023)
Article
Oncology
Travis J. Gates, Ce Yuan, Mihir Shetty, Thomas Kaiser, Andrew C. Nelson, Aastha Chauhan, Timothy K. Starr, Christopher Staley, Subbaya Subramanian
Summary: Inflammation of the colon (colitis) increases the risk of colorectal cancers, and gut microbiota may be involved in cancer development. Manipulating the bacteria community in the colon could be a potential way to prevent cancer. A study using mice found that transferring bacteria from healthy mice to those with colitis increased the presence of Akkermansia, which may alleviate colon inflammation, while untreated mice had an increase in other bacteria types, such as Anaeroplasma and Alistipes, which could contribute to inflammation. These findings suggest that specific bacteria types may help reduce colon inflammation and prevent cancer.
Article
Environmental Sciences
Joseph Boyle, Mary H. Ward, James R. Cerhan, Nathaniel Rothman, David C. Wheeler
Summary: Many studies have found associations between neighborhood deprivation and disease, emphasizing the importance of social determinants of health. However, when studying diseases with long latency periods such as cancers, considering the timing of exposures for deprivation becomes more important.
ENVIRONMENTAL RESEARCH
(2023)
Editorial Material
Oncology
Xianda Zhao, Timothy Starr, Subbaya Subramanian
