Review
Urology & Nephrology
Stuart J. Shankland, Yuliang Wang, Andrey S. Shaw, Joshua C. Vaughan, Jeffrey W. Pippin, Oliver Wessely
Summary: Aging has negative effects on kidney health, especially with regard to podocytes. This review discusses the mechanisms of podocyte aging, its impact in age-related kidney diseases, strategies to mitigate podocyte damage, and the role of cellular growth pathways in confounding aging processes in humans and rodents.
JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
(2021)
Article
Biology
Bokang Ko, Jeremy M. Van Raamsdonk
Summary: Gene expression studies provide valuable insights into biological processes, such as aging. This study shows that pooling individual RNA samples before sequencing can yield similar results as sequencing them individually, reducing the cost of experiments. Analysis of gene expression changes across the genome is a powerful and unbiased tool for understanding molecular mechanisms.
Article
Plant Sciences
Tao Yan, Meng Sun, Rui Su, Xiaozhong Wang, Xuedan Lu, Yunhua Xiao, Huabing Deng, Xiong Liu, Wenbang Tang, Guilian Zhang
Summary: Cold stress has a significant impact on the growth and development of rice, particularly the susceptible indica cultivar. This study identified genes and transcription factors associated with cold responsiveness in indica rice and revealed the molecular mechanisms underlying cold responses, providing important insights for enhancing cold tolerance in susceptible varieties.
Article
Genetics & Heredity
Sarah Rashid, Scott G. Wilson, Kun Zhu, John P. Walsh, Jiake Xu, Benjamin H. Mullin
Summary: This study analyzed the transcriptome of human peripheral blood mononuclear cells and their differentiated osteoclast-like cells in culture, identifying differentially expressed genes and associated biological pathways in the progression of osteoporosis. Several well-established osteoclast genes were significantly upregulated in osteoporosis, and the upregulated genes were involved in cell division, migration, adhesion, as well as oxidative phosphorylation, glycolysis, lysosome, and focal adhesion pathways.
Article
Biotechnology & Applied Microbiology
Yong Liu, Jing Huang, Rajan Pandey, Pengyuan Liu, Bhavika Therani, Qiongzi Qiu, Sridhar Rao, Aron M. Geurts, Allen W. Cowley Jr, Andrew S. Greene, Mingyu Liang
Summary: This study found that in order to accurately identify differentially expressed genes (DEGs) with various characteristics in single-cell clusters, there need to be at least 2000 cells. However, for the majority of DEGs with extremely small p values or transcript abundance greater than a few hundred transcripts per million in bulk RNA-seq analysis, clusters with as few as 50-100 cells may be sufficient.
Article
Cell Biology
Xue-Min Cao, Sheng-Long Li, Yu-Qi Cao, Ye-Hua Lv, Ya-Xian Wang, Bin Yu, Chun Yao
Summary: The initial mechanical damage of a spinal cord injury triggers a complex secondary injury cascade involving multiple systems and cells. This study analyzed the differences in gene expression between rostral and caudal regions after injury and identified distinct biological process alterations in these two segments, providing new insights into the pathology of SCI.
NEURAL REGENERATION RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Byeong Hee Kang, Woon Ji Kim, Sreeparna Chowdhury, Chang Yeok Moon, Sehee Kang, Seong-Hoon Kim, Sung-Hwan Jo, Tae-Hwan Jun, Kyung Do Kim, Bo-Keun Ha
Summary: This study identified genes related to salt stress in cowpea by comparing germplasms with contrasting salt tolerance. The results provide useful information for the development of molecular markers in cowpea breeding programs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Medicine, Research & Experimental
Emel Rothzerg, Jiake Xu, David Wood, Sulev Koks
Summary: The TARGET project aims to identify molecular changes driving childhood cancers, including osteosarcoma, and develop novel therapies by analyzing gene expression. A study identified 5758 differentially expressed genes between deceased and alive patients, with only 217 associated with overall survival. Eight downregulated genes and four upregulated genes were selected as potential independent prognostic candidate genes.
EXPERIMENTAL BIOLOGY AND MEDICINE
(2021)
Article
Medical Laboratory Technology
Reza Najafipour, Davood Mohammadi, Zohreh Estaki, Kiana Zarabadi, Manijeh Jalilvand, Sahar Moghbelinejad
Summary: The COVID-19 pandemic has caused high mortality and poses a significant threat worldwide. This study used small RNA deep-sequencing to analyze differentially expressed microRNAs in blood and bronchoalveolar fluid samples from patients with acute respiratory distress syndrome (ARDS). The results provide valuable insights into the molecular mechanisms of the host response and may guide anti-inflammatory medication.
JOURNAL OF CLINICAL LABORATORY ANALYSIS
(2022)
Article
Biochemical Research Methods
Lihong Zhao, Cong Yan, Shuzhen Kong, Tao Jia, Zhaowei Chu, Li Yang, Jian Wu, Songmei Geng, Kun Guo
Summary: CAP has more significant biological effects on melanoma cells than on HaCaT cells by inhibiting proliferation and promoting apoptosis. CAP can selectively kill melanoma cells and has good biosafety cytologically. Besides apoptosis, CAP can induce cell death via autophagy and necroptosis.
JOURNAL OF BIOPHOTONICS
(2022)
Article
Biochemistry & Molecular Biology
Valentina Di Salvatore, Elena Crispino, Avisa Maleki, Giulia Nicotra, Giulia Russo, Francesco Pappalardo
Summary: This study used RNA sequencing data to evaluate the expression differences of specific human genes in COVID-19 patients with different severity, and to determine the molecular origins of different responses to SARS-CoV-2 infection. The study identified a small group of genes that were up-regulated in the severe form of the disease, potentially serving as biomarkers for severe COVID-19.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Pharmacology & Pharmacy
Xiaoxiao Xue, Jiayu Yu, Cheng Li, Fang Wang, Yatao Guo, Yongwen Li, Huijuan Shi
Summary: This study aimed to explore the genes and pathways involved in the therapeutic effects of oxymatrine on psoriasis. The results showed that oxymatrine can alter the abnormal expression of certain genes and pathways in psoriasis patients, and multi-pathway and multi-target therapy can effectively treat psoriasis.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Neurosciences
Jiyeon K. Denninger, Logan A. Walker, Xi Chen, Altan Turkoglu, Alex Pan, Zoe Tapp, Sakthi Senthilvelan, Raina Rindani, Olga N. Kokiko-Cochran, Ralf Bundschuh, Pearlly Yan, Elizabeth D. Kirby
Summary: This study compared bulk sequencing and single cell sequencing and found that differentially expressed genes (DEGs) identified in single cell sequencing were derived from genes with higher transcript counts and exhibited smaller fold changes. To facilitate the identification of disease-relevant genes, an RNA-input threshold suitable for single cell sequencing was determined, and a corresponding workflow was established.
FRONTIERS IN MOLECULAR NEUROSCIENCE
(2022)
Article
Plant Sciences
Shiqi Liu, Xuqian Peng, Xiaojing Wang, Weibing Zhuang
Summary: In this study, the effects of heavy metals cadmium and arsenic on tea plants were investigated. Transcriptomic analysis of tea roots revealed candidate genes involved in tolerance and accumulation of cadmium and arsenic. The results identified potential genes that may play important roles in enhancing tolerance to cadmium and arsenic stresses, providing potential targets for genetic engineering to improve multi-metal tolerance.
Article
Pharmacology & Pharmacy
Taraswi Mitra Ghosh, Jason White, Joshua Davis, Suman Mazumder, Teeratas Kansom, Elena Skarupa, Grafton S. Barnett, Gary A. Piazza, R. Curtis Bird, Amit K. Mitra, Clayton Yates, Brian S. Cummings, Robert D. Arnold
Summary: Low-dose metronomic administration of topotecan (TOPO) is more effective than conventional dosing in treating aggressive prostate cancer, and has been associated with increased survival rates for PCa patients. Through analysis of different PCa cell lines, candidate pharmacogenomic biomarkers and novel pathways related to METRO-TOPO therapy have been identified, with findings suggesting that ethnic differences may impact drug response and gene expression patterns in patients.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Materials Science, Biomaterials
Ryan J. Nagao, Raluca Marcu, Yu Jung Shin, Daniel Lih, Jun Xue, Nadia Arang, Ling Wei, Shreeram Akilesh, Alexis Kaushansky, Jonathan Himmelfarb, Ying Zheng
Summary: The study revealed that CsA inhibited NFAT1 activation and impaired VEGF signaling in kidney-specific microvascular endothelial cells, leading to microvascular injury characterized by impairment of fenestrae and cell adhesion, membrane swelling, and erythrocyte adhesion and extravasation. This underscores the importance of targeting VEGF-related pathways for therapy during CsA treatment and leveraging species and organ-specific cells to better understand human pathophysiology and injury response.
ACS BIOMATERIALS SCIENCE & ENGINEERING
(2022)
Article
Urology & Nephrology
Nicole K. Andeen, Shahad Abdulameer, Vivek Charu, Jonathan E. Zuckerman, Megan Troxell, Neeraja Kambham, Charles E. Alpers, Behzad Najafian, Roberto F. Nicosia, Kelly D. Smith, Vanderlene L. Kung, Rupali S. Avasare, Anusha Vallurupalli, J. Ashley Jefferson, Douglas Hecox, Leah Swetnam, Michifumi Yamashita, Mercury Lin, Mei Lin Bissonnette, Shreeram Akilesh, Jean Hou
Summary: Limited studies have been conducted on kidney biopsy findings in patients with mantle cell lymphoma (MCL). This retrospective study aimed to analyze kidney biopsy findings in MCL patients. The study identified 30 MCL patients who underwent kidney biopsies, with 70% of those with active MCL presenting with acute kidney injury, proteinuria, hematuria, and biopsy findings potentially linked to lymphoma. The study also found diverse monoclonal and polyclonal glomerular and extra-glomerular immune complex (IC) and complement-mediated (C3) diseases associated with MCL.
KIDNEY INTERNATIONAL REPORTS
(2022)
Article
Urology & Nephrology
Kevin A. Lidberg, Selvaraj Muthusamy, Mohamed Adil, Anish Mahadeo, Jade Yang, Ranita S. Patel, Lu Wang, Theo K. Bammler, Jonathan Reichel, Catherine K. Yeung, Jonathan Himmelfarb, Edward J. Kelly, Shreeram Akilesh
Summary: This study confirmed the damaging effect of serum proteins on kidney tubules, showing that serum proteins induced tubular injury and secretion of proinflammatory cytokines. The epigenomic approach revealed canonical stress-inducible regulation of injured genes, providing new pathways for intervention.
JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
(2022)
Article
Urology & Nephrology
Kelly D. Smith, David K. Prince, Kammi J. Henriksen, Roberto F. Nicosia, Charles E. Alpers, Shreeram Akilesh
Summary: Collapsing glomerulopathy is a histologically distinct variant of focal and segmental glomerulosclerosis that presents with heavy proteinuria and poor prognosis. This disease can be triggered by viral infections such as HIV or SARS-CoV-2. Digital spatial profiling (DSP) technology provides a powerful method to analyze the transcriptional programs of pathologically discernible kidney lesions.
KIDNEY INTERNATIONAL
(2022)
Article
Medicine, Research & Experimental
Yong Li, Yurong Cheng, Francesco Consolato, Guglielmo Schiano, Michael R. Chong, Maik Pietzner, Ngoc Quynh H. Nguyen, Nora Scherer, Mary L. Biggs, Marcus E. Kleber, Stefan Haug, Burulca Goecmen, Marie Pigeyre, Peggy Sekula, Inga Steinbrenner, Pascal Schlosser, Christina B. Joseph, Jennifer A. Brody, Morgan E. Grams, Caroline Hayward, Ulla T. Schultheiss, Bernhard K. Kraemer, Florian Kronenberg, Annette Peters, Jochen Seissler, Dominik Steubl, Cornelia Then, Matthias Wuttke, Winfried Maerz, Kai-Uwe Eckardt, Christian Gieger, Eric Boerwinkle, Bruce M. Psaty, Josef Coresh, Peter J. Oefner, Guillaume Pare, Claudia Langenberg, Jurgen E. Scherberich, Bing Yu, Shreeram Akilesh, Olivier Devuyst, Luca Rampoldi, Anna Koettgen
Summary: Uromodulin (UMOD) is a major risk gene for kidney disease and is highly abundant in urine. This study identified genetic variants associated with circulating uromodulin and found an upstream variant in the UMOD locus that affects its synthesis in kidney cells. The study also found shared association patterns between UMOD and complex traits like chronic kidney disease. Furthermore, the study revealed the role of glycan marks and their enzymes and receptors in uromodulin glycosylation.
Letter
Urology & Nephrology
Kevin Lidberg, Jonathan Himmelfarb, Edward Kelly, Shreeram Akilesh
JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
(2022)
Article
Oncology
Yuexin Xu, Alicia J. Morales, Andrea M. H. Towlerton, Shreeram Akilesh, Chris P. Miller, Scott S. Tykodi, Edus H. Warren
Summary: This study provides insights into the characteristics of clonally expanded T cells in metastatic renal cell carcinoma (RCC), showing their higher density in tumors and their potential for effective immune therapy. The study also reveals different phenotypes of clonally expanded T cell subpopulations, which may play a significant role in immune therapy.
FRONTIERS IN ONCOLOGY
(2022)
Article
Materials Science, Biomaterials
Chelsea L. Fortin, Tara N. McCray, Sarah H. Saxton, Fredrik Johansson, Christian B. Andino, Jonathan Mene, Yuliang Wang, Kelly R. Stevens
Summary: This study successfully constructed engineered human liver tissues and observed the expression of human liver metabolic genes and proteins in these tissues at different stages post-implantation. Furthermore, the grafted engineered tissues exhibited zonation expression similar to the native liver.
Article
Anatomy & Morphology
Christopher P. Miller, Farinaz Shokri, Shreeram Akilesh, Yuexin Xu, Edus H. Warren, Scott S. Tykodi, Maria Tretiakova
Summary: 5T4 is a cancer/testis antigen highly expressed in renal cell carcinoma (RCC) and other cancers, but rarely in normal tissues. This study identified 3 monoclonal antibodies with 5T4 specificity and demonstrated high staining consistency in 263 renal tumors. These findings provide valuable reagents for detecting 5T4 in formalin-fixed, paraffin-embedded tissues and reveal heterogeneity in patient and histologic subtypes.
APPLIED IMMUNOHISTOCHEMISTRY & MOLECULAR MORPHOLOGY
(2023)
Article
Immunology
Michael A. Davis, Kathleen Voss, J. Bryan Turnbull, Andrew T. Gustin, Megan Knoll, Antonio Muruato, Tien-Ying Hsiang, Kenneth H. Dinnon, Sarah R. Leist, Katie Nickel, Ralph S. Baric, Warren Ladiges, Shreeram Akilesh, Kelly D. Smith, Michael Gale
Summary: We conducted a comprehensive analysis of SARS-CoV-2 infection and recovery in mice and found that it closely resembles the acute human disease. Disease severity and infection kinetics were influenced by age and sex, with older mice and males exhibiting higher mortality rates and slower viral clearance. The pathological features observed in mice, including virus positivity in bronchial epithelial cells and lung damage, parallel those seen in humans. Our findings suggest that C57BL/6 mice can serve as a useful model for studying SARS-CoV-2 and other emerging coronaviruses.
Review
Urology & Nephrology
Kelly D. Smith, Shreeram Akilesh
Summary: Collapsing glomerulopathy is a condition characterized by nephrotic syndrome and rapid loss of kidney function. It is associated with various clinical and genetic conditions, and its underlying mechanisms are being explored through animal models and patient studies.
CURRENT OPINION IN NEPHROLOGY AND HYPERTENSION
(2023)
Article
Genetics & Heredity
Pascal Schlosser, Nora Scherer, Franziska Grundner-Culemann, Sara Monteiro-Martins, Stefan Haug, Inga Steinbrenner, Burulca Uluvar, Matthias Wuttke, Yurong Cheng, Arif B. Ekici, Gergely Gyimesi, Edward D. Karoly, Fruzsina Kotsis, Johanna Mielke, Maria F. Gomez, Bing Yu, Morgan E. Grams, Josef Coresh, Eric Boerwinkle, Michael Kottgen, Florian Kronenberg, Heike Meiselbach, Robert P. Mohney, Shreeram Akilesh, Miriam Schmidts, Matthias A. Hediger, Ulla T. Schultheiss, Kai-Uwe Eckardt, Peter J. Oefner, Peggy Sekula, Yong Li, Anna Koettgen
Summary: The kidneys play a critical role in removing waste products and retaining valuable solutes in the body. Genetic studies of plasma and urine metabolites have identified important associations and provided insights into kidney function, such as glycerol transport and protein localization. Shared genetic determinants of metabolite-disease combinations offer potential for understanding metabolic diseases. Expanding genetic studies of the metabolome beyond plasma allows for a better understanding of processes at the interface of body compartments.
Review
Urology & Nephrology
Abbal Koirala, Negiin Pourafshar, Arvin Daneshmand, Christopher S. Wilcox, Sai Sudha Mannemuddhu, Nayan Arora
Summary: The development of peripheral edema can be a challenge for practitioners due to its association with various underlying disorders. Updated understanding of edema formation and the role of hypochloremia in diuretic resistance provide potential therapeutic targets. This article reviews the pathophysiology of edema formation and its implications for treatment.
ADVANCES IN KIDNEY DISEASE AND HEALTH
(2023)
Article
Oncology
Chris P. Miller, Megan Fung, Carla A. Jaeger-Ruckstuhl, Yuexin Xu, Edus H. Warren, Shreeram Akilesh, Scott S. Tykodi
Summary: This study introduces a rapid and economical human microphysiological system (RCC-on-a-chip) for investigating therapies targeting metastatic renal cell carcinoma (RCC). The authors demonstrate that culturing RCC cell lines in a 3D collagen extracellular matrix (ECM) more accurately replicates the gene expression program of primary RCC tumors compared to traditional 2D cultures. They also show that the RCC-on-a-chip can be used to identify compounds that inhibit cellular migration without inducing cell death, and to study the killing of tumor spheroids by tumor-reactive T cells.
Article
Medicine, Research & Experimental
Jeffrey W. Pippin, Natalya Kaverina, Yuliang Wang, Diana G. Eng, Yuting Zeng, Uyen Tran, Carol J. Loretz, Anthony Chang, Shreeram Akilesh, Chetan Poudel, Hannah S. Perry, Christopher O'Connor, Joshua C. Vaughan, Markus Bitzer, Oliver Wessely, Stuart J. Shankland
Summary: With an aging population, kidney health becomes an important medical and socioeconomic factor. The study found that PD-1 signaling plays a crucial role in kidney aging and in the development of focal segmental glomerulosclerosis.
JOURNAL OF CLINICAL INVESTIGATION
(2022)