Article
Chemistry, Multidisciplinary
Sarah Viola Heel, Karolina Bartosik, Fabian Juen, Christoph Kreutz, Ronald Micura, Kathrin Breuker
Summary: Understanding how ligands bind to ribonucleic acids (RNA) is crucial in studying RNA recognition and drug development. This study used mass spectrometry (MS) to investigate neomycin B binding to neomycin-sensing riboswitch aptamer constructs. The MS data revealed the binding site and ligand interactions, providing valuable insights for RNA recognition by aminoglycosides.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Multidisciplinary Sciences
Yang Pan, John W. Phillips, Beatrice D. Zhang, Miyako Noguchi, Eric Kutschera, Jami McLaughlin, Pavlo A. Nesterenko, Zhiyuan Mao, Nathanael J. Bangayan, Robert Wang, Wendy Tran, Harry T. Yang, Yuanyuan Wang, Yang Xu, Matthew B. Obusan, Donghui Cheng, Alex H. Lee, Kathryn E. Kadash-Edmondson, Ameya Champhekar, Cristina Puig-Saus, Antoni Ribas, Robert M. Prins, Christopher S. Seet, Gay M. Crooks, Owen N. Witte, Yi Xing
Summary: This study describes a computational platform called IRIS that can discover tumor antigens derived from alternative splicing, providing potential targets for TCR and CAR-T immunotherapies. Through the analysis of transcriptomics and immuno-peptidomics data, the study demonstrates that the predicted targets by IRIS can bind with HLA molecules. The study illustrates the contribution of alternative splicing to the repertoire of tumor antigens and demonstrates the utility of IRIS in discovering AS-derived antigens and expanding cancer immunotherapies.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Chemistry, Multidisciplinary
Zhao Gao, Lulu Shi, Fei Yan, Yifei Han, Wei Yuan, Wei Tian
Summary: We report the synthesis of well-regulated 2D supramolecular polymers (2DSPs) through an aromatics-selective recognition strategy. These polymers exhibit enhanced photocatalytic hydrogen evolution activity and ordered 2D structures.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Review
Plant Sciences
Junfei Ma, Ying Wang
Summary: RNAs play essential roles in coordinating plant growth, and their subcellular localization and intercellular/systemic trafficking are crucial for their functions. The study on viroids as a model for RNA movement regulation has revealed multiple RNA 3D motifs responsible for trafficking across diverse cellular boundaries in plants.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Casey S. Jacobsen, Prince Salvador, John F. Yung, Sabrina Kragness, Herra G. Mendoza, Gail Mandel, Peter A. Beal
Summary: Adenosine deaminases acting on RNA (ADARs) catalyze the hydrolytic deamination of adenosine to inosine in duplex RNA, resulting in an effective A-to-G edit. ADAR editing can lead to recoding events and alterations in RNA function. One limitation of ADAR is its preference for editing adenosines with specific neighboring nucleotides, but new strategies and approaches are being developed to overcome this.
ACS CHEMICAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Maya Ron, Igor Ulitsky
Summary: The post-transcriptional fate of long RNAs is determined by the specific sequence elements, the splicing status, and the presence of terminal features unique to linear RNAs in a combinatorial manner, which is strongly dependent on the form (linear or circular) and splicing status (spliced or unspliced) of the host RNA.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Samuel G. Chamberlain, Andrea Gohlke, Arooj Shafiq, Iolo J. Squires, Darerca Owen, Helen R. Mott
Summary: The study reveals that in vivo, CaM interacts exclusively with the C terminus of RaIA and binding of CaM leads to removal of RaIA from its membrane environment. These findings provide important clues to understand how CaM regulates the function of RaIA.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Oncology
Xueyan Xi, Yang Guo, Min Zhu, Fen Qiu, Feifei Lei, Gang Li, Boyu Du
Summary: The research team identified a new peptide and protein antigen recognized by gamma delta T cells in hepatocellular carcinoma, providing a new potential therapeutic target for immunotherapy.
CANCER IMMUNOLOGY IMMUNOTHERAPY
(2021)
Article
Microbiology
Han Xiao, Emanuel Wyler, Miha Milek, Bastian Grewe, Philipp Kirchner, Arif Ekici, Ana Beatriz Oliveira Villela Silva, Doris Jungnickl, Florian Full, Marco Thomas, Markus Landthaler, Armin Ensser, Klaus Ueberla
Summary: The HIV-1 Rev protein is crucial for nuclear export of unspliced and incompletely spliced HIV-1 RNAs. Depletion of proteins like CRNKL1 can significantly enhance levels of unspliced HIV-1 RNA in the cytoplasm, potentially revealing a cellular mechanism exploited by HIV-1 to regulate its complex splicing pattern.
Article
Biochemistry & Molecular Biology
S. Pankivskyi, D. Pastre, E. Steiner, V Joshi, A. Rynditch, L. Hamon
Summary: SAM68 is an mRNA-binding protein involved in mRNA processing in the nucleus, and its interaction with ITSN1 can enhance its solubility, regulating the processing of a fraction of nuclear mRNAs. ITSN1 and mRNA may act together to promote SAM68 solubilization, which is important for SAM68-controlled splicing events related to higher neuronal functions or cancer progression.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2021)
Article
Virology
Sriram Yandrapally, Satarupa Sarkar, Sharmistha Banerjee
Summary: The study focuses on understanding the molecular mechanisms behind the differential regulation of HIV proliferation in astrocytes and CD4+ T lymphocytes. It reveals that HIV-1 Tat regulates hnRNPA2 expression in CD4+ T lymphocytes, but not in astrocytes, leading to increased levels of unspliced/partially spliced viral RNA and viral propagation in CD4+ T lymphocytes. This study uncovers a new mechanism imposed by HIV on host cells that determines the fate of infection.
JOURNAL OF VIROLOGY
(2023)
Article
Biochemistry & Molecular Biology
Louise Chambon, Francois-Xavier Gillet, Maha Chieb, David Cobessi, Thomas Pfannschmidt, Robert Blanvillain
Summary: Chloroplast biogenesis relies on a complex transcriptional program that involves coordinated expression of plastid and nuclear genes. The researchers discovered that some plastid-encoded RNA polymerase subunits (PAPs) are present in the nucleus and may play a nuclear function in efficient chloroplast formation. They also found that PAP8 can form a large nuclear subcomplex with other subunits of the plastid-encoded RNA polymerase. Additionally, PAP8 exhibits structural homology with a rhinoviral RNA-dependent RNA polymerase. This study provides insights into the important role of PAP8 in chloroplast formation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Shouxiong Huang, Adam Shahine, Tan-Yun Cheng, Yi-Ling Chen, Soo Weei Ng, Gautham R. Balaji, Rachel Farquhar, Stephanie Gras, Clare S. Hardman, John D. Altman, Nabil Tahiri, Adriaan J. Minnaard, Graham S. Ogg, Jacob A. Mayfield, Jamie Rossjohn, D. Branch Moody
Summary: The study identified the lipid profiles of four human CD1 antigen-presenting molecules, revealing a broad presentation of self-sphingolipids and phospholipids. Each type of CD1 protein displayed distinct capture motifs based on lipid length and chemical composition.
Article
Multidisciplinary Sciences
Norimasa Iwanami, Andreas S. Richter, Katarzyna Sikora, Thomas Boehm
Summary: Unconventional T cells, such as iNKT cells, play an important role in vertebrate immune defenses. The study suggests that Tnpo3 is involved in regulating the splicing of pre-mRNA encoding the characteristic TCR alpha chain of iNKT cells.
NATURE COMMUNICATIONS
(2023)
Review
Immunology
Peter M. Kloetzel
Summary: Proteasome generates spliced peptides through a reverse proteolysis reaction, potentially holding therapeutic and immune relevance. However, there is controversy surrounding the frequency, abundance, and therapeutic applicability of spliced peptides. Nevertheless, the search for tumor and patient-specific neosplicetopes still seems valuable.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Endocrinology & Metabolism
Emily Chan Brodowsky, Akshay Sood, Mohit Butaney, Sami E. Majdalany, Alex Stephens, Nicholas Corsi, Austin J. Piontkowski, Ivan Rakic, Marcus Jamil, Deepansh Dalela, James O. Peabody, Craig G. Rogers, Firas Abdollah
Summary: The prognostic significance of a second biochemical recurrence (sBCR) after salvage radiation therapy (sRT) with/without hormonal therapy following primary radical prostatectomy has not been examined. The study found that a shorter time to sBCR is associated with worse cancer control outcomes. These findings are important for guiding subsequent treatments and counseling patients.
Article
Biochemistry & Molecular Biology
Xiaoran Li, Yanping Zhong, Xudong Zhang, Anil K. K. Sood, Jinsong Liu
Summary: By studying the dynamics of different cellular components during the formation of high-grade serous carcinoma organoids, we discovered that polyploid giant cancer cells (PGCCs) can develop through various modes of nuclear replication. PGCCs undergo processes like asymmetric mitosis, endoreplication, multipolar endomitosis, nuclear fusion, and karyokinesis without cytokinesis. This leads to an increase in nuclear contents and heterogeneity, resulting in the formation of complex tissue structures. These findings suggest that PGCCs play a central role in malignant histogenesis, intratumoral heterogeneity, immune escape, and macroevolution.
Article
Oncology
Patrick J. Hensley, Zhigang Duan, Kelly Bree, Akshay Sood, Hui Zhao, Niyati Lobo, Roberto Contieri, Matthew T. Campbell, Charles C. Guo, Neema Navai, Stephen B. Williams, Colin P. Dinney, Ashish M. Kamat
Summary: In this retrospective cohort study, we found that second primary nonurothelial cancers (SNUC) have a high incidence in patients with muscle-invasive bladder cancer (BC) who underwent radical cystectomy (RC). The most common SNUC types were lung cancer and colon cancer. Surveillance imaging for BC can aid in the early detection of SNUC.
UROLOGIC ONCOLOGY-SEMINARS AND ORIGINAL INVESTIGATIONS
(2023)
Article
Oncology
Katherine I. Foster, Kenna R. M. Shaw, Jeff Jin, Shannon N. Westin, Timothy A. Yap, Deanna M. Glassman, Amir A. Jazaeri, Jose A. Rauh-Hain, Sanghoon Lee, Bryan M. Fellman, Zhenlin Ju, Yuexin Liu, Nicole D. Fleming, Anil K. Sood
Summary: This study assessed the clinical relevance of tumor-based next-generation sequencing in patients with ovarian cancer. It found that tumor-based next-generation sequencing often provides clinically relevant information, helping to identify therapeutic targets and guide the development of clinical decision support tools.
Article
Biochemistry & Molecular Biology
Santosh K. K. Dasari, Robiya Joseph, Sujanitha Umamaheswaran, Lingegowda S. S. Mangala, Emine Bayraktar, Cristian Rodriguez-Aguayo, Yutuan Wu, Nghi Nguyen, Reid T. T. Powell, Mary Sobieski, Yuan Liu, Mamur A. A. Chowdhury, Paola Amero, Clifford Stephan, Gabriel Lopez-Berestein, Shannon N. N. Westin, Anil K. K. Sood
Summary: EphA2 tyrosine kinase is upregulated in many cancers and correlated with poor patient survival. A chemical screen identified Wee1 kinase inhibitor as a synergistic partner to EphA2-targeted therapeutics. Combination treatment showed enhanced anti-tumor response in endometrial cancer, suggesting the potential of Wee1 inhibition in improving EphA2-targeted therapy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Ophthalmology
Xiaole Li, Manav Nayeni, Monali S. S. Malvankar-Mehta
Summary: This study systematically compared different interventions for treating HSK and their patient outcomes. The results showed that corticosteroids and antivirals were most effective when used together. Oral acyclovir was as effective as its ointment counterpart. Tapering corticosteroid use and using it for at least 10 weeks could lead to greater therapeutic benefits. Anti-inflammatory drugs like flurbiprofen, cyclosporine-A, and tacrolimus were safe and effective for treating HSK. Long-term follow-up and randomized controlled trials could provide further insights on these potential alternatives.
OPHTHALMIC EPIDEMIOLOGY
(2023)
Article
Radiology, Nuclear Medicine & Medical Imaging
Piyush Aggarwal, Anupriya Anwariya, Anwin Joseph Kavanal, Ashwani Sood, Santosh Ranjan Jena, Bhagwant Rai Mittal
Summary: Peptide receptor radionuclide therapy (PRRT) is an effective treatment for patients with inoperable and/or metastatic neuroendocrine tumors that overexpress somatostatin receptor type 2 (SSTR-2). The post-therapy Lu-177-DOTATATE whole-body scan provides a comprehensive assessment of disease status and dosimetry, but it may also show abnormal radiotracer uptake that requires further imaging for accurate diagnosis. This report presents two cases of hot emboli in post-therapy Lu-177-DOTATATE scans, which has not been previously described.
NUCLEAR MEDICINE AND MOLECULAR IMAGING
(2023)
Article
Radiology, Nuclear Medicine & Medical Imaging
Ritanshu Solanki, Parikshaa Gupta, Ashwani Sood, Bhagwant Rai Mittal
Summary: This case report describes an unusual presentation of metastasis to the breast in addition to liver, pancreas, and lymph nodal metastases in a patient with ileal neuroendocrine tumor who was operated upon 5 years back. The metastases were detected by somatostatin receptor-based imaging and post-therapy scan confirmed by cytology and immunocytochemistry.
NUCLEAR MEDICINE AND MOLECULAR IMAGING
(2023)
Article
Biochemistry & Molecular Biology
Si Hoon Park, Juhyun Han, Byung-Cheon Jeong, Ju Han Song, Se Hwan Jang, Hyeongseop Jeong, Bong Heon Kim, Young-Gyu Ko, Zee-Yong Park, Kyung Eun Lee, Jaekyung Hyun, Hyun Kyu Song
Summary: By studying TRIM72 protein, we have revealed the importance of its interaction with phosphatidylserine-enriched membranes for its function. We have also proposed a molecular model of TRIM72, providing further insights into its role in cell membrane repair and ubiquitination.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Meeting Abstract
Urology & Nephrology
Ivan Rakic, Matthew Davis, Nicholas Corsi, Alexander Stephens, Sohrab Arora, Nikola Rakic, Taylor Malchow, Chase Morrison, Rafe Affas, Akshay Sood, Craig Rogers, Firas Abdollah
JOURNAL OF UROLOGY
(2023)
Meeting Abstract
Urology & Nephrology
Ivan Rakic, Matthew Davis, Nicholas Corsi, Alexander Stephens, Sohrab Arora, Taylor Malchow, Rafe Affas, Akshay Sood, Alexander Cole, Quoc-Dienh Trinh, Firas Abdollah
JOURNAL OF UROLOGY
(2023)
Meeting Abstract
Urology & Nephrology
Akshay Sood, Jan Rudzinski, Alberto Martini, Come Tholomier, Sharada Mokkapati, Colin Dinney
JOURNAL OF UROLOGY
(2023)
Meeting Abstract
Urology & Nephrology
Akshay Sood, Ralph Grauer, Mireya Diaz-Insua, Firas Abdollah, Mani Menon
JOURNAL OF UROLOGY
(2023)
Meeting Abstract
Urology & Nephrology
Niyati Lobo, Akshay Sood, Zhigang Duan, Wei Shen Tan, Valentina Grajales, Sia Viborg Lindskrog, Lars Dyrskjot, Hui Zhao, Sharon Giordano, Stephen B. Williams, Ashish M. Kamat
JOURNAL OF UROLOGY
(2023)
Meeting Abstract
Urology & Nephrology
Matthew Davis, Alexander Stephens, Sohrab Arora, Eric Williams, Chase Morrison, Nicholas Corsi, Ivan Rakic, Rafe Affas, Akshay Sood, Craig Rogers, Firas Abdollah
JOURNAL OF UROLOGY
(2023)
