Article
Multidisciplinary Sciences
Wren E. Michaels, Cecilia Pena-Rasgado, Rusudan Kotaria, Robert J. Bridges, Michelle L. Hastings
Summary: Mutations in the CFTR gene result in cystic fibrosis, and skipping exon 23 can partially restore CFTR function, showing therapeutic potential for CF treatment.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Pachamuthu Kandasamy, Graham McClorey, Mamoru Shimizu, Nayantara Kothari, Rowshon Alam, Naoki Iwamoto, Jayakanthan Kumarasamy, Gopal R. Bommineni, Adam Bezigian, Onanong Chivatakarn, David C. D. Butler, Michael Byrne, Katarzyna Chwalenia, Kay E. Davies, Jigar Desai, Juili Dilip Shelke, Ann F. Durbin, Ruth Ellerington, Ben Edwards, Jack Godfrey, Andrew Hoss, Fangjun Liu, Kenneth Longo, Genliang Lu, Subramanian Marappan, Jacopo Oieni, Ik-Hyeon Paik, Erin Purcell Estabrook, Chikdu Shivalila, Maeve Tischbein, Tomomi Kawamoto, Carlo Rinaldi, Joana Rajao-Saraiva, Snehlata Tripathi, Hailin Yang, Yuan Yin, Xiansi Zhao, Cong Zhou, Jason Zhang, Luciano Apponi, Matthew J. A. Wood, Chandra Vargeese
Summary: By engineering chimeric stereopure oligonucleotides, significant improvements in pharmacology and efficacy have been achieved, leading to an extended median survival in a mouse model of muscular dystrophy.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Karima Relizani, Lucia Echevarria, Faouzi Zarrouki, Cecile Gastaldi, Chloe Dambrune, Philippine Aupy, Adrian Haeberli, Marek Komisarski, Thomas Tensorer, Thibaut Larcher, Fedor Svinartchouk, Cyrille Vaillend, Luis Garcia, Aurelie Goyenvalle
Summary: Tricyclo-DNA (tcDNA) is a promising oligonucleotide analog with therapeutic potential, especially when conjugated with palmitic acid for improved delivery to muscle tissues. This conjugation enhances the potency of tcDNA-ASO, resulting in functional improvement in dystrophic mice with significantly reduced dose, while also showing a promising safety profile for clinical development in neuromuscular diseases.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Biochemistry & Molecular Biology
Florian Malard, Cameron D. Mackereth, Sebastien Campagne
Summary: This article discusses the early stage of spliceosome assembly in eukaryotes, focusing on the factors that influence U1 snRNP's selection of splice sites in pre-mRNA. It also includes examples of diseases that affect this selection and recent therapeutic advances.
Review
Pharmacology & Pharmacy
Dianyang Li, Wenying Yu, Maode Lai
Summary: Serine-and arginine-rich splicing factors play important roles in regulating splicing by binding to cis-acting elements in precursor mRNAs and facilitating spliceosome assembly. SR proteins also have diverse functions in RNA metabolism as they shuttle between the nucleus and cytoplasm. Overexpression and/or hyperactivation of SR proteins have been associated with tumorigenesis, suggesting their potential as therapeutic targets. This review highlights the physiological and pathological roles of SR proteins and discusses small molecules and oligonucleotides that can modulate SR protein function for future studies.
DRUG DISCOVERY TODAY
(2023)
Article
Biochemistry & Molecular Biology
Minghui Xu, Suyang Wang, Qin Zhan, Ying Lin
Summary: Conditional protein splicing is a powerful tool to control the activity of target proteins. In this study, we demonstrated a novel approach using SUMO protease to induce splicing of a split intein. The splicing efficiency was significantly increased by the addition of SUMO protease. This engineered split intein-mediated protein trans-splicing has great potential for controlling protein structure and function in vitro.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Oncology
Ping Ye, Yan Yang, Liqiang Zhang, Guixi Zheng
Summary: This study identified 2,212 AS events significantly associated with overall survival in esophageal carcinoma patients from TCGA database. Prognostic signatures based on these AS events were established through multivariate analysis, with risk score proving to be an independent survival factor. The interaction network between AS events and splicing factors revealed hub genes and AS events warranting further investigation, providing novel insights into tumorigenesis and progression mechanisms of esophageal carcinoma.
FRONTIERS IN ONCOLOGY
(2021)
Article
Oncology
Wai Kit Ma, Dillon M. Voss, Juergen Scharner, Ana S. H. Costa, Kuan-Ting Lin, Hyun Yong Jeon, John E. Wilkinson, Michaela Jackson, Frank Rigo, C. Frank Bennett, Adrian R. Krainer
Summary: The upregulation of the M2 pyruvate kinase (PKM2) isoform in most cancers, which is involved in the Warburg effect, can be inhibited by antisense oligonucleotides (ASO), leading to apoptosis in liver cancer cells. This ASO-based splicing therapy shows potential as a targeted treatment for hepatocellular carcinoma (HCC) by altering glucose metabolism and inhibiting tumor growth.
Review
Oncology
Maram Arafat, Ruth Sperling
Summary: Splicing and alternative splicing are important in regulating gene expression and their misregulation can lead to diseases, including cancer. This review summarizes a quality control mechanism called Suppression of Splicing (SOS) that protects cells from splicing at unused intronic splice sites and its relevance to cancer. SOS is abrogated in stress and cancer, resulting in the expression of aberrant nonsense mRNAs that may be toxic to cells. These findings suggest the potential of aberrant isoforms as novel targets for cancer diagnosis and therapies.
Article
Pharmacology & Pharmacy
Amina Jbara, Zahava Siegfried, Rotem Karni
Summary: RNA splicing modulation, as a therapy for genetic diseases, may be applicable to cancer treatment. Two promising approaches being investigated are splice-switching oligonucleotides and CRISPR technology. These methods offer potential for new therapeutic strategies but also have challenges and limitations to overcome.
CURRENT OPINION IN PHARMACOLOGY
(2021)
Article
Oncology
Jun-Xian Du, Yi-Hong Luo, Si-Jia Zhang, Biao Wang, Cong Chen, Gui-Qi Zhu, Ping Zhu, Cheng-Zhe Cai, Jing-Lei Wan, Jia-Liang Cai, Shi-Ping Chen, Zhi Dai, Wei Zhu
Summary: The study revealed that SRSF1 is upregulated in breast cancer and correlates with tumor grade, Ki-67 index, and poor prognosis in HR+ patients. By regulating PTPMT1 AS, SRSF1 exerts oncogenic roles in breast cancer.
JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Francisco Carranza, Hossein Shenasa, Klemens J. Hertel
Summary: Alternative splicing is a highly combinatorial mechanism that allows higher eukaryotes to increase mRNA diversity. The selection of alternative splice sites is influenced by sequence, cis-regulatory elements, exon and intron length, and RNA secondary structures. The study showed that the mode of splice site recognition, either intron or exon definition, plays a role in alternative splicing decisions.
Article
Multidisciplinary Sciences
Josep Biayna, Helena Mazuelas, Bernat Gel, Ernest Terribas, Gabrijela Dumbovic, Inma Rosas, Juana Fernandez-Rodriguez, Ignacio Blanco, Elisabeth Castellanos, Meritxell Carrio, Conxi Lazaro, Eduard Serra
Summary: Neurofibromatosis Type 1 (NF1) is a genetic condition with cognitive impairment possibly related to alternative splicing of the NF1 gene. Modulation of the ratio between type I and type II isoforms can disrupt neuronal differentiation and deregulate signaling pathways. The study suggests a feedback loop involving neurofibromin-related signaling pathways.
SCIENTIFIC REPORTS
(2021)
Article
Chemistry, Multidisciplinary
Suyog Padgaonkar, Christopher T. Eckdahl, Jakub K. Sowa, Rafael Lopez-Arteaga, Dana E. Westmoreland, Eliot F. Woods, Shawn Irgen-Gioro, Benjamin Nagasing, Tamar Seideman, Mark C. Hersam, Julia A. Kalow, Emily A. Weiss
Summary: This paper describes reversible on-off switching of the photoluminescence intensity of CdSe quantum dots mediated by photochromic furylfulgide carboxylate molecules chemisorbed to the QDs' surfaces. The switching is enabled by different rates and yields of PL-quenching photoinduced electron transfer from the QDs to the isomers, consistent with cyclic voltammetry measurements and density functional calculations. This work demonstrates fatigue-resistant modulation of the PL of a QD-molecule complex through remote control of PET, enabling potential applications like all-optical memory, sensing, and imaging with a fast, tunable, and reversible response to light stimuli.
Review
Geriatrics & Gerontology
Giuseppe Biamonti, Angela Amato, Elisa Belloni, Anna Di Matteo, Lucia Infantino, Davide Pradella, Claudia Ghigna
Summary: Alzheimer's disease is the most common neurodegenerative disorder in the elderly, with approximately 20% of people over 80 affected. Recent studies have shown that Alternative Splicing is involved in gene expression reprogramming and splicing abnormalities in AD tissues. While the molecular causes of AD are still poorly understood, therapeutic approaches targeting aberrant AS regulation offer potential new treatments.
AGING CLINICAL AND EXPERIMENTAL RESEARCH
(2021)
Article
Biochemical Research Methods
Amy Ryan, Olivia Shade, Anirban Bardhan, Aleksander Bartnik, Alexander Deiters
Summary: This article describes a novel method for quantifying protein bioconjugation in cells. By selectively installing a small and bioorthogonally reactive handle onto the surface of a protein through unnatural amino acid mutagenesis, the authors utilized inverse electron-demand Diels-Alder cycloadditions to evaluate different reactions. Quantification of bioconjugation was achieved through simple western blot analysis. This versatile tool allows for quick and accurate determination of bioconjugation efficiency in different proteins.
BIOCONJUGATE CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Jenny W. Cheung, William D. Kinney, Joshua S. Wesalo, Megan Reed, Eve M. Nicholson, Alexander Deiters, T. Ashton Cropp
Summary: The use of light to control protein function is a critical tool in chemical biology. In this paper, we describe the addition of a photocaged histidine to the genetic code, allowing for the optical control of enzymes. By genetically encoding photocaged histidine in mammalian cells, we were able to successfully manipulate and control firefly and Renilla luciferases using light.
Article
Chemistry, Multidisciplinary
Wes Brown, Joshua Wesalo, Michael Tsang, Alexander Deiters
Summary: Precise temporal regulation of protein function is important for embryo development. The zebrafish embryo is an excellent model for studying development, but there is a lack of small molecule switches for protein function control. Genetic code expansion was used to incorporate unnatural amino acids with caging groups into proteins, allowing for conditional control through small molecules. This method was successfully used to activate enzymes in zebrafish embryos with temporal precision, leading to insights into heart defect development and control of DNA and protein cleavage events.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Wes Brown, Jason D. Galpin, Carolyn Rosenblum, Michael Tsang, Christopher A. Ahern, Alexander Deiters
Summary: Genetic code expansion has allowed the incorporation of unnatural amino acids into proteins. In this study, chemically acylating tRNAs were used to site-specifically incorporate unnatural amino acids into proteins in zebrafish embryos. This approach was successful in incorporating a photocaged histidine analogue that could not be achieved through enzyme engineering. Additionally, optical control over different enzymes in live embryos was demonstrated by installing photocaged histidine into their active sites.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Kristie E. Darrah, Savannah Albright, Rohan Kumbhare, Michael Tsang, James K. Chen, Alexander Deiters
Summary: The structure and mechanism of the bacterial enzyme beta-lactamase, which is clinically important for antibiotic resistance, have been extensively studied. Beta-lactamase can hydrolyze the beta-lactam ring of the cephalosporin scaffold, leading to self-immolation. This study presents a circular caged morpholino oligonucleotide (cMO) activated by beta-lactamase-mediated cleavage of a cephalosporin motif, showing potential for silencing gene expression and eliciting observable phenotypes in aquatic embryos.
ACS CHEMICAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Wes Brown, Joshua Wesalo, Subhas Samanta, Ji Luo, Steven E. Caldwell, Michael Tsang, Alexander Deiters
Summary: The technique of strategically placing unnatural amino acids into kinases and phosphatases' active sites has resulted in the development of photocaged signaling proteins, enabling precise light control over pathway activation. However, applying this technology to study cell signaling in embryonic development has been limited. In this study, we demonstrate light-induced activation of Protein Kinase A and a RASopathy mutant of NRAS in zebrafish embryos using a novel light-activated amino acid. This approach provides insights into the roles of these proteins in gastrulation and heart development, opening up possibilities for further investigation of RASopathy mutant proteins in animals.
ACS CHEMICAL BIOLOGY
(2023)
Article
Developmental Biology
Daniel A. Zuppo, Maria A. Missinato, Lucas Santana-Santos, Guang Li, Panayiotis Benos, Michael Tsang
Summary: The poor regenerative capacity of the mammalian heart may be due to the inability of adult cardiomyocytes to proliferate at sufficient levels. However, research has shown that the transcription factor Foxm1 can induce cardiomyocyte proliferation after injury through regulation of cell cycle genes.
Article
Multidisciplinary Sciences
Elisa Ruffo, Adam A. Butchy, Yaniv Tivon, Victor So, Michael Kvorjak, Avani Parikh, Eric L. Adams, Natasa Miskov-Zivanov, Olivera J. Finn, Alexander Deiters, Jason Lohmueller
Summary: This study introduces engineered cell-surface receptors called chimeric antigen receptors (CARs) and synthetic Notch (synNotch) receptors, which can sense target antigens and respond accordingly. The authors develop universal receptor systems that can be post-translationally directed to specific antigens through covalent attachment of BG-conjugated antibodies. They demonstrate successful targeting of SNAP-CAR and SNAP-synNotch receptors using clinically relevant BG-conjugated antibodies, showing anti-tumor activity in a human tumor xenograft mouse model. A mathematical model is also developed to better understand the parameters affecting universal receptor signaling.
NATURE COMMUNICATIONS
(2023)
Article
Anesthesiology
Gareth R. Tibbs, Rajendra Uprety, J. David Warren, Nicole P. Beyer, Rebecca L. Joyce, Matthew A. Ferrer, Wilfredo Mellado, Victor S. C. Wong, David C. Goldberg, Melanie W. Cohen, Christopher J. Costa, Zhucui Li, Guoan Zhang, Noah E. Dephoure, Dipti N. Barman, Delin Sun, Helgi I. Ingolfsson, Anthony A. Sauve, Dianna E. Willis, Peter A. Goldstein
Summary: This study presents a new class of compounds, anchor-tethered drugs, for the treatment of membrane-targeting disorders. Through molecular dynamics simulation and in vitro and in vivo experiments, BP4L-18:1:1 was identified as a well-tolerated and selective HCN1 inverse agonist with oral availability and antihyperalgesic effects. This compound showed poor penetration across the blood-brain barrier and cardiac sparing.
BRITISH JOURNAL OF ANAESTHESIA
(2023)
Article
Chemistry, Multidisciplinary
Savannah Albright, Mary Cacace, Yaniv Tivon, Alexander Deiters
Summary: Covalent aptamers are innovative biochemical tools that can transfer labels to target proteins quickly and selectively. Equipped with cleavable electrophiles, these nucleic acid probes allow for the installation of functional handles on native proteins. Their high affinity and specificity enable covalent labeling that can compete with nuclease-mediated degradation. In this study, we successfully applied covalent aptamers to modify a specific cell surface protein, protein tyrosine kinase 7 (PTK7), by transferring biotin to specific lysine residues on its extracellular domain. This enabled us to track PTK7 expression, localization, and cellular internalization. These findings validate the programmability of covalent aptamers and demonstrate their applicability in a cellular context for protein and small molecule delivery.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Organic
Brittany M. Klootwyk, Amy E. Ryan, Arbil Lopez, Mitchell J. R. McCloskey, Chasity P. Janosko, Alexander Deiters, Paul E. Floreancig
Summary: Phosphate mono- and diesters can be efficiently released from boryl allyloxy (BAO) and related phosphotriesters by H2O2. This method was successfully applied to release a phosphorylated serine derivative and the nucleotide analogue AZT monophosphate. The release of nucleotides in the presence of ATP and a kinase leads to the formation of diphosphate, demonstrating the potential application of this method in biological processes.
Article
Biochemical Research Methods
Michael Kvorjak, Elisa Ruffo, Yaniv Tivon, Victor So, Avani Parikh, Alexander Deiters, Jason Lohmueller
Summary: Engineered T cell therapies as living drugs have unique functional capabilities that revolutionize disease treatment. However, they have limitations such as unpredictable behavior, toxicities, and nontraditional pharmacokinetics. To address these issues, we have developed OFF-switch adaptors that can conditionally control CAR T cell activity, enhancing the programmability and potential safety of universal CAR T cells.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Chasity P. Janosko, Olivia Shade, Taylor M. Courtney, Trevor J. Horst, Melinda Liu, Sagar D. Khare, Alexander Deiters
Summary: An arylazopyrazole was studied as an enhanced photoswitchable amino acid for genetic code expansion. This new unnatural amino acid was successfully incorporated into proteins in bacterial and mammalian cells. Although pulsed irradiations were required for photocontrol of translation, complete selectivity for the trans-configuration was achieved by the pyrrolysyl tRNA synthetase, demonstrating the selective control of gene expression through light exposure.
Article
Chemistry, Organic
Steven E. Caldwell, Chasity P. Janosko, Alexander Deiters
Summary: In this study, a light-activated STING agonist was developed to selectively activate the STING pathway by blocking a key interaction. This finding expands the toolbox of conditionally controlled STING agonists and provides a potential solution to avoid systemic immune activation.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Wenyuan Zhou, Amy Ryan, Chasity P. Janosko, Karsen E. Shoger, Jason M. Haugh, Rachel A. Gottschalk, Alexander Deiters
Summary: Evolution has diversified the mammalian proteome through the generation of protein isoforms, but it is difficult to differentiate between these isoforms in cellular contexts. This study presents a method for the precise light control of individual isoforms of the mitogen-activated protein kinase (MAPK) p38, revealing a novel point of crosstalk between two MAPK pathways.
RSC CHEMICAL BIOLOGY
(2023)
