Article
Biochemistry & Molecular Biology
Xueqi Qu, Li Lin, Wanying Yi, Changyu Sun, Yuewen Chen, Yu Chen
Summary: This study investigates the transcriptomic changes in synaptodendrosomes during the progression of Alzheimer's disease. It reveals an increased number of differentially expressed genes in the mRNA reservoir as AD advances, with enrichment in mitochondrial biogenesis and metabolic activity. Three representative genes involved in mitochondrial and metabolic pathways are identified, which regulate dendritic spine density and morphology in neurons.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Daniel Bakopoulos, Sofya Golenkina, Callum Dark, Elizabeth L. Christie, Besaiz J. Sanchez-Sanchez, Brian M. Stramer, Louise Y. Cheng
Summary: This study shows that insulin and TGF-beta signalling converge via a BMP antagonist sog to regulate ECM remodelling in adipose tissue. In tumour bearing animals, Sog also modulates TGF-beta signalling to regulate ECM accumulation. Activation of insulin signalling, inhibition of TGF-beta signalling, or modulation of ECM levels can rescue tissue wasting in the presence of tumor.
Article
Plant Sciences
Yan Ao, Qi Wu, Chi Zhang, Jiqing Zheng, Guisheng Zhou, Shiqin Yang, Liang Zhang, Miaoyan Yang
Summary: This study demonstrates the importance of transcription factor NF-YC1 in the salt tolerance response in Arabidopsis, and identifies several genes associated with salt tolerance.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2023)
Article
Biochemical Research Methods
Xiaokang Wang, Jinfeng Liu, Danwen Wang, Maohui Feng, Xiongzhi Wu
Summary: This study identified four molecular subtypes of colorectal cancer patients based on epigenetically regulated gene expression profiles, each with distinct clinical and molecular features. These subtypes provide valuable information for further research on treatment and prognosis in CRC.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Cell Biology
Yongsheng Huang, Sijia Liu, Mengjie Shan, Sophie C. Hagenaars, Wilma E. Mesker, Danielle Cohen, Lin Wang, Zhi Zheng, Peter Devilee, Rob A. E. M. Tollenaar, Zhangfu Li, Yongmei Song, Long Zhang, Dan Li, Peter Ten Dijke
Summary: RNF12, overexpressed in invasive breast cancers, promotes migration and invasion of breast cancer cells through its interaction with the AKT signaling pathway. Phosphorylation of AKT induces nuclear localization of RNF12 and accelerates the degradation of SMAD7 mediated by RNF12. Moreover, RNF12 expression is positively correlated with phosphorylated AKT and phosphorylated SMAD2 levels.
CELL DEATH & DISEASE
(2022)
Article
Medical Laboratory Technology
Madison E. Calvert, Bhanu Kalra, Amita Patel, Ajay Kumar, Natalie D. Shaw
Summary: This study successfully measured the GDF-9/BMP-15 heterodimer in serum and demonstrated the ability to non-invasively measure GDF-15 in urine samples. This has important implications for monitoring female reproductive health and during pregnancy.
CLINICA CHIMICA ACTA
(2022)
Article
Cell & Tissue Engineering
Dongsheng Cai, Xiaochen Wang, Yaxun Sun, Hangping Fan, Jingjun Zhou, Zongkuai Yang, Hangyuan Qiu, Jue Wang, Jun Su, Tingyu Gong, Chenyang Jiang, Ping Liang
Summary: Aberrant activation of Wnt/β-catenin signaling contributes to the pathogenesis of SCN5A-related BrS, suggesting it as a potential therapeutic target.
STEM CELL RESEARCH & THERAPY
(2023)
Article
Oncology
Paula Reichelt, Stephan Bernhart, Franziska Wilke, Sebastian Schwind, Michael Cross, Uwe Platzbecker, Gerhard Behre
Summary: This study aims to identify differential pathways between chemo-sensitive and -resistant AML as potential therapeutic targets using next-generation sequencing-based microRNA expression profiling and pathway analysis. The study found significant differences in microRNA expression profiles between chemo-sensitive and chemo-resistant AML cells, reflecting differences in intracellular signaling cascades. Alterations in signaling pathway activities contribute to treatment resistance and thereby represent potential drug targets.
Article
Biochemistry & Molecular Biology
Mohammad Asad, Abdus Sabur, Mohd Kamran, Md Shadab, Sonali Das, Nahid Ali
Summary: The study reveals the important role of IL-17 in the progression of Leishmania donovani infection in a murine model of VL, and highlights the regulatory functions of CD4(+)CD25(+) T cells and their secretion of TGF-beta and IL-35 in modulating IL-17 levels during chronic VL.
Article
Oncology
Giovanni Marchi, Anna Rajavuori, Mai T. N. Nguyen, Kaisa Huhtinen, Sinikka Oksa, Sakari Hietanen, Sampsa Hautaniemi, Johanna Hynninen, Jaana Oikkonen
Summary: The study shows that ctDNA can adequately represent high-grade serous ovarian carcinoma (HGSC), and the mutations observed at relapse suggest personalized therapy options.
TRANSLATIONAL ONCOLOGY
(2024)
Article
Gastroenterology & Hepatology
Junyan Yan, Baowei Hu, Wenjie Shi, Xiaoyi Wang, Jiayuan Shen, Yaping Chen, Huarong Huang, Lifang Jin
Summary: In this study, Gli2 was shown to regulate HSC activation and liver fibrosis through TGF-beta signaling. Conditional deletion of Gli2 in HSCs reduced liver fibrosis and HSC activation in a mouse model. Additionally, Gli2 promoted HSC activation by upregulating cyclin expression and TGF-beta signaling activity. These findings support further research on Gli2 inhibition as a potential therapy for slowing liver fibrosis progression in humans.
AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Yanan Min, Long Hao, Xinguang Liu, Shuai Tan, Hui Song, Hao Ni, Zi Sheng, Natalie Jooss, Xuena Liu, Rickard E. Malmstrom, Yang Sun, Jianguo Liu, Hua Tang, Hao Zhang, Chunhong Ma, Jun Peng, Ming Hou, Nailin Li
Summary: This study investigated the mechanisms underlying the regulation of effector responses of naive CD4(+) T (Tn) cells by platelets. The results showed that platelets exert sophisticated regulation on various types of T helper cells and regulatory T cells in a time-, concentration-, and organ-dependent manner, in cooperation with transforming growth factor beta (TGF beta) and platelet factor 4 (PF4). This study highlights the importance of platelet-targeted interventions for T cell immunity.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Zhi Chai, Yafei Lyu, Qiuyan Chen, Cheng-Hsin Wei, Lindsay M. Snyder, Veronika Weaver, Aswathy Sebastian, Istvan Albert, Qunhua Li, Margherita T. Cantorna, A. Catharine Ross
Summary: This study investigated the impact of preexisting vitamin A deficiency on gene expression patterns in the intestines using a mouse model, and identified novel target genes in vitamin A-related biological pathways. The results revealed significant effects of vitamin A deficiency on gene expression patterns in the small intestine, suggesting potential new candidate genes, while in the colon, cell division was the only enriched category negatively associated with vitamin A.
JOURNAL OF NUTRITIONAL BIOCHEMISTRY
(2021)
Article
Endocrinology & Metabolism
Christian Hagel, Ulrich Schueller, Jorg Flitsch, Ulrich J. Knappe, Udo Kellner, Markus Bergmann, Rolf Buslei, Michael Buchfelder, Thomas Ruediger, Jochen Herms, Wolfgang Saeger
Summary: Multiple pituitary adenomas can have different hormone expressions and molecular features, suggesting they may originate from distinct cell types. The immunohistochemical analysis of double adenomas with diverse lineage revealed various combinations of hormone expressions and distinct copy number changes in multiple lesions that were molecularly analyzed. This study expands our understanding of multiple pituitary adenomas and their potential origins.
Article
Oncology
Rukayat Aromokeye, Hongwei Si
Summary: This study demonstrates that the combination of luteolin and curcumin at low dosages synergistically inhibits colon cancer growth by suppressing cell proliferation, migration, and promoting necrosis through the Notch1 and TGF-beta pathways. These findings suggest that consuming foods with high levels of luteolin and curcumin may be a practical approach for the prevention and treatment of colon cancer.
Correction
Cell Biology
Jian Carrot-Zhang, Xiaotong Yao, Siddhartha Devarakonda, Aditya Deshpande, Jeffrey S. Damrauer, Tiago Chedraoui Silva, Christopher K. Wong, Hyo Young Choi, Ina Felau, A. Gordon Robertson, Mauro A. A. Castro, Lisui Bao, Esther Rheinbay, Eric Minwei Liu, Tuan Trieu, David Haan, Christina Yau, Toshinori Hinoue, Yuexin Liu, Ofer Shapira, Kiran Kumar, Karen L. Mungall, Hailei Zhang, Jake June-Koo Lee, Ashton Berger, Galen F. Gao, Binyamin Zhitomirsky, Wen-Wei Liang, Meng Zhou, Sitapriya Moorthi, Alice H. Berger, Eric A. Collisson, Michael C. Zody, Li Ding, Andrew D. Cherniack, Gad Getz, Olivier Elemento, Christopher C. Benz, Josh Stuart, J. C. Zenklusen, Rameen Beroukhim, Jason C. Chang, Joshua D. Campbell, D. Neil Hayes, Lixing Yang, Peter W. Laird, John N. Weinstein, David J. Kwiatkowski, Ming S. Tsao, William D. Travis, Ekta Khurana, Benjamin P. Berman, Katherine A. Hoadley, Nicolas Robine, Matthew Meyerson, Ramaswamy Govindan, Marcin Imielinski
Article
Cell Biology
Jian Carrot-Zhang, Xiaotong Yao, Siddhartha Devarakonda, Aditya Deshpande, Jeffrey S. Damrauer, Tiago Chedraoui Silva, Christopher K. Wong, Hyo Young Choi, Ina Felau, A. Gordon Robertson, Mauro A. A. Castro, Lisui Bao, Esther Rheinbay, Eric Minwei Liu, Tuan Trieu, David Haan, Christina Yau, Toshinori Hinoue, Yuexin Liu, Ofer Shapira, Kiran Kumar, Karen L. Mungall, Hailei Zhang, Jake June-Koo Lee, Ashton Berger, Galen F. Gao, Binyamin Zhitomirsky, Wen-Wei Liang, Meng Zhou, Sitapriya Moorthi, Alice H. Berger, Eric A. Collisson, Michael C. Zody, Li Ding, Andrew D. Cherniack, Gad Getz, Olivier Elemento, Christopher C. Benz, Josh Stuart, J. C. Zenklusen, Rameen Beroukhim, Jason C. Chang, Joshua D. Campbell, D. Neil Hayes, Lixing Yang, Peter W. Laird, John N. Weinstein, David J. Kwiatkowski, Ming S. Tsao, William D. Travis, Ekta Khurana, Benjamin P. Berman, Katherine A. Hoadley, Nicolas Robine, Matthew Meyerson, Ramaswamy Govindan, Marcin Imielinski
Summary: Alterations in the RTK/RAS/RAF pathway are a characteristic feature of lung adenocarcinoma (LUAD). A study using whole-genome sequencing of 85 cases initially identified as RPA(-) revealed that around 33% of cases were actually RPA(+). The remaining cases showed genetic mutations associated with tumor suppressor deletions and genome instability.
Article
Oncology
Ping-Chieh Chou, Hyun Ho Choi, Yizhi Huang, Enrique Fuentes-Mattei, Guermarie Velazquez-Torres, Fanmao Zhang, Liem Phan, Jaehyuk Lee, Yanxia Shi, James A. Bankson, Yun Wu, Huamin Wang, Ruiying Zhao, Sai-Ching Jim Yeung, Mong-Hong Lee
Summary: The study established a mouse model that mimics diabetic patients with HER2(+) breast cancer and demonstrated the pathogenic role of diabetes in breast cancer progression.
CANCER COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Harsha Doddapaneni, Sara Javornik Cregeen, Richard Sucgang, Qingchang Meng, Xiang Qin, Vasanthi Avadhanula, Hsu Chao, Vipin Menon, Erin Nicholson, David Henke, Felipe-Andres Piedra, Anubama Rajan, Zeineen Momin, Kavya Kottapalli, Kristi L. Hoffman, Fritz J. Sedlazeck, Ginger Metcalf, Pedro A. Piedra, Donna M. Muzny, Joseph F. Petrosino, Richard A. Gibbs
Summary: A capture sequencing methodology was developed to obtain SARS-CoV-2 genomic and transcriptome sequences from infected patients. Analysis of samples with varying viral titers revealed differential transcriptional activity and allelic frequencies. Hybridization-based capture proved to be effective and scalable for sequencing SARS-CoV-2 from patient samples.
Article
Cell Biology
Bingbing Dai, Jithesh J. Augustine, Ya'an Kang, David Roife, Xinqun Li, Jenying Deng, Lin Tan, Leona A. Rusling, John N. Weinstein, Philip L. Lorenzi, Michael P. Kim, Jason B. Fleming
Summary: This study identified a novel compound NSLC01 that selectively targets NRF2-activated pancreatic cancer cells, inducing significant anticancer effects, especially in cells with high NRF2 activation. NSLC01 induces apoptosis in cancer cells by inhibiting protein translation and suppressing de novo synthesis of amino acids, leading to synthetic lethal effects in NRF2-activated pancreatic cancers.
CELL DEATH & DISEASE
(2021)
Article
Multidisciplinary Sciences
Tamar Sofer, Xiuwen Zheng, Cecelia A. Laurie, Stephanie M. Gogarten, Jennifer A. Brody, Matthew P. Conomos, Joshua C. Bis, Timothy A. Thornton, Adam Szpiro, Jeffrey R. O'Connell, Ethan M. Lange, Yan Gao, L. Adrienne Cupples, Bruce M. Psaty, Kenneth M. Rice
Summary: Pooling participant-level genetic data into a single analysis can result in variance stratification, reducing statistical performance. The authors developed variant-specific inflation factors to assess variance stratification and apply this to pooled individual-level data from whole genome sequencing.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Ali R. Keramati, Ming-Huei Chen, Benjamin A. T. Rodriguez, Lisa R. Yanek, Arunoday Bhan, Brady J. Gaynor, Kathleen Ryan, Jennifer A. Brody, Xue Zhong, Qiang Wei, Kai Kammers, Kanika Kanchan, Kruthika Iyer, Madeline H. Kowalski, Achilleas N. Pitsillides, L. Adrienne Cupples, Bingshan Li, Thorsten M. Schlaeger, Alan R. Shuldiner, Jeffrey R. O'Connell, Ingo Ruczinski, Braxton D. Mitchell, Nauder Faraday, Margaret A. Taub, Lewis C. Becker, Joshua P. Lewis, Rasika A. Mathias, Andrew D. Johnson
Summary: Platelet aggregation is associated with myocardial infarction and stroke. A whole genome sequencing study identified a locus in RGS18, suggesting an effect on haematopoeitic lineage transcription factors.
NATURE COMMUNICATIONS
(2021)
Review
Genetics & Heredity
Liem Minh Phan, Abdol-Hossein Rezaeian
Summary: ATM is a critical initiator and coordinator of the DNA-damage response, regulating important cellular processes. Despite being considered a major tumor suppressor, increased ATM signaling in some cancer cells provides significant advantages for cancer cell survival.
Article
Medicine, General & Internal
Timothy Farinholt, Harsha Doddapaneni, Xiang Qin, Vipin Menon, Qingchang Meng, Ginger Metcalf, Hsu Chao, Marie-Claude Gingras, Vasanthi Ayadhanula, Paige Farinholt, Charu Agrawal, Donna M. Muzny, Pedro A. Piedra, Richard A. Gibbs, Joseph Petrosino
Summary: This study identified a cluster of 6 vaccinated patients infected with the delta variant, suggesting immune evasion in patients who received the Pfizer BNT162b2, Moderna mRNA-1273, and Covaxin BBV152 vaccines. The delta variant may pose the highest risk among currently circulating SARS-CoV-2 variants, with increased transmissibility over the alpha variant and potential vaccine breakthrough.
Article
Cell Biology
Shuyun Rao, Xiaochun Yang, Kazufumi Ohshiro, Sobia Zaidi, Zhanhuai Wang, Kirti Shetty, Xiyan Xiang, Md Imtaiyaz Hassan, Taj Mohammad, Patricia S. Latham, Bao-Ngoc Nguyen, Linda Wong, Herbert Yu, Yousef Al-Abed, Bibhuti Mishra, Michele Vacca, Gareth Guenigault, Michael E. D. Allison, Antonio Vidal-Puig, Jihane N. Benhammou, Marcus Alvarez, Paivi Pajukanta, Joseph R. Pisegna, Lopa Mishra
Summary: The study found that SPTBN1 promotes the development of NASH and liver cancer, and intervention in SPTBN1 can protect mice from damage caused by a high-fat diet, making it a potential therapeutic target.
SCIENCE TRANSLATIONAL MEDICINE
(2021)
Article
Biology
Vipin K. Menon, Pablo C. Okhuysen, Cynthia L. Chappell, Medhat Mahmoud, Medhat Mahmoud, Qingchang Meng, Harsha Doddapaneni, Vanesa Vee, Yi Han, Sejal Salvi, Sravya Bhamidipati, Kavya Kottapalli, George Weissenberger, Hua Shen, Matthew C. Ross, Kristi L. Hoffman, Sara Javornik Cregeen, Donna M. Muzny, Ginger A. Metcalf, Richard A. Gibbs, Joseph F. Petrosino, Fritz J. Sedlazeck
Summary: This study provides a highly accurate and complete reference genome of Cryptosporidium parvum, based on Oxford Nanopore reads and improved using Illumina reads. The assembly includes 8 chromosomes and resolves 13 telomeres, with a high completion rate of 98.4% single-copy BUSCO genes. This high-quality reference genome will facilitate future comparative genomic studies across the Cryptosporidium clade.
Article
Virology
Anubama Rajan, Felipe-Andres Piedra, Letisha Aideyan, Trevor McBride, Matthew Robertson, Hannah L. Johnson, Gina Marie Aloisio, David Henke, Cristian Coarfa, Fabio Stossi, Vipin Kumar Menon, Harshavardhan Doddapaneni, Donna Marie Muzny, Sara Joan Javornik Cregeen, Kristi Louise Hoffman, Joseph Petrosino, Richard A. Gibbs, Vasanthi Avadhanula, Pedro A. Piedra
Summary: Respiratory syncytial virus (RSV) is a common cause of pediatric respiratory infection worldwide. This study characterized the infection of HEp-2 and A549 cells with four strains of RSV, including both major subgroups and historic and contemporary genotypes. The findings revealed differences in viral gene expression and host response between RSV subgroups, as well as the sensitivity of different cell lines to viral variation.
JOURNAL OF VIROLOGY
(2022)
Article
Peripheral Vascular Disease
Brandon M. Blobner, Annet Kirabo, Ossama B. Kashlan, Shaohu Sheng, Donna K. Arnett, Lewis C. Becker, Eric Boerwinkle, Jenna C. Carlson, Yan Gao, Richard A. Gibbs, Jiang He, Marguerite R. Irvin, Sharon L. R. Kardia, Tanika N. Kelly, Charles Kooperberg, Stephen T. McGarvey, Vipin K. Menon, May E. Montasser, Take Naseri, Susan Redline, Alexander P. Reiner, Muagututi'a S. Reupena, Jennifer A. Smith, Xiao Sun, Dhananjay Vaidya, Karine A. Viaud-Martinez, Daniel E. Weeks, Lisa R. Yanek, Xiaofeng Zhu, Ryan L. Minster, Thomas R. Kleyman
Summary: This study found an association between low-frequency and rare variants in ENaC subunits and blood pressure and kidney function.
Article
Biochemistry & Molecular Biology
Felipe-Andres Piedra, David Henke, Anubama Rajan, Donna M. Muzny, Harsha Doddapaneni, Vipin K. Menon, Kristi L. Hoffman, Matthew C. Ross, Sara J. Javornik J. Cregeen, Ginger Metcalf, Richard A. Gibbs, Joseph F. Petrosino, Vasanthi Avadhanula, Pedro A. Piedra
Summary: Infections by non-segmented negative-strand RNA viruses (NNSV) are believed to involve gradient gene expression, but recent studies on respiratory syncytial virus (RSV) show inconsistent mRNA levels. A biophysically reasonable model of NNSV transcription is proposed, integrating known and predicted phenomena. The model successfully captures observations of RSV and vesicular stomatitis virus (VSV) mRNA levels, suggesting the possibility of ejective polymerase-polymerase collisions and biased polymerase diffusion in NNSV transcription.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Adam C. English, Vipin K. Menon, Richard A. Gibbs, Ginger A. Metcalf, Fritz J. Sedlazeck
Summary: The fundamental challenge in multi-sample structural variant (SV) analysis is identifying when two SVs are the same. As SV detection becomes more precise, algorithms to preserve this refined signal are needed. This study introduces Truvari, a toolkit for SV comparison, annotation, and analysis, and demonstrates the impact of SV comparison choices by building population-level VCFs.