Article
Biochemical Research Methods
Shouliang Guan, Huihui Tian, Yinan Yang, Mengcheng Liu, Jianfei Ding, Jinfen Wang, Ying Fang
Summary: The authors describe the fabrication, assembly, and long-term implantation of ultraflexible neural probes for simultaneous recording of neural activity and neuromodulation in rodents. These ultraflexible microelectrode arrays (MEAs) can stably record from a large number of neurons after chronic implantation, providing opportunities for understanding neural circuit mechanisms and developing next-generation brain-computer interfaces. The protocol outlines the process of preparing elastocapillary self-assembled ultraflexible MEAs, integrating them with optogenetic tools to form an optrode probe, and conducting in vivo experimental use in rodents' brains, enabling long-term electrophysiological recordings and optical modulation of neuronal activity. The protocol can be completed within 3 weeks and requires expertise in clean room facilities.
Article
Biology
Kitae Kim, Myeongsu Na, Kyoungjoon Oh, Eunji Cho, Seung Seok Han, Sunghoe Chang
Summary: OptiMuS is an optical clearing method that achieves rapid and high transparency of brain tissues and other intact organs while preserving tissue size and fluorescent signal. It is also compatible with the use of lipophilic dyes to reveal vascular structures and can be applied to pathological analysis of kidneys.
COMMUNICATIONS BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Anuj K. Yadav, Michael C. Lee, Melissa Y. Lucero, Shengzhang Su, Christopher J. Reinhardt, Jefferson Chan
Summary: NO's role in tumors is context-dependent, and the development of BL660-NO as an ABS probe for NIR bioluminescence imaging has provided valuable insights into the impact of diet on tumor progression.
ACS CENTRAL SCIENCE
(2022)
Article
Materials Science, Biomaterials
Fang Fan, Li Zhang, Xinguang Zhou, Fangya Mu, Guoyue Shi
Summary: A sensitive near-infrared probe was designed for the detection and real-time imaging of beta-galactosidase activity in ovarian tumors, showing high sensitivity and a low detection limit. It could serve as a highly sensitive sensor for real-time tracking of beta-galactosidase activity in vivo and ovarian tumor imaging.
JOURNAL OF MATERIALS CHEMISTRY B
(2021)
Article
Multidisciplinary Sciences
Jung Min Lee, Young-Woo Pyo, Yeon Jun Kim, Jin Hee Hong, Yonghyeon Jo, Wonshik Choi, Dingchang Lin, Hong-Gyu Park
Summary: This study presents an ultra-thin, minimally invasive neural probe called NeuroWeb, which combines the advantages of surface electrode arrays and implantable multi-electrode arrays. In vivo experiments demonstrate its ability to detect stable single-unit activity of neurons with high signal-to-noise ratios. The researchers also investigate neural interactions between brain regions using transparent dual NeuroWebs and optical stimulation. This study provides insights into complex brain networks through optical and electrophysiological mapping.
NATURE COMMUNICATIONS
(2023)
Review
Pharmacology & Pharmacy
Stephanie Heinzlmeir, Susanne Mueller
Summary: Selective chemical modulators are important tools for studying protein function, but the development of specific chemical probes has been hindered by the poor ligandability of many proteins. However, the emergence of covalent inhibitors and activity-based protein profiling tools has enhanced our understanding of difficult-to-target proteins and improved the accuracy of selectivity evaluation for small molecule modulators.
DRUG DISCOVERY TODAY
(2022)
Article
Biochemistry & Molecular Biology
Christine Mehner, Alexandra Hockla, Mathew Coban, Benjamin Madden, Rosendo Estrada, Derek C. Radisky, Evette S. Radisky
Summary: Ovarian clear cell carcinoma (OCCC) is an understudied and poor prognosis subtype of ovarian cancer. In this study, researchers found that inhibitors of trypsin-like serine proteases can suppress the malignant features of OCCC cell lines. They also identified tissue plasminogen activator and urokinase-type plasminogen activator as active proteases involved in cancer cell invasion and proliferation of OCCC cells. These findings suggest that these proteases could be potential targets for new therapeutic strategies in OCCC.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Review
Engineering, Biomedical
Natalie Landon-Brace, Nancy T. Li, Alison P. Mcguigan
Summary: Modeling the heterogeneity of the tumor microenvironment (TME) in vitro is crucial for understanding cancer biology and developing effective treatment strategies. The use of patient-derived organoids (PDOs) and advanced 3D in vitro models, combined with single-cell omics analysis, provides a new avenue for studying tumor heterogeneity. This review discusses the current application of PDOs in 3D in vitro models of the TME and explores the integration of single-cell analysis. The ultimate goal is to identify novel therapeutic targets that consider the complex interactions between tumors and the microenvironment.
ADVANCED HEALTHCARE MATERIALS
(2023)
Article
Chemistry, Multidisciplinary
Fumihiro Ishikawa, Natsumi Tsukumo, Erika Morishita, Shumpei Asamizu, Saaya Kusuhara, Shinsuke Marumoto, Katsuki Takashima, Hiroyasu Onaka, Genzoh Tanabe
Summary: We present a method called activity-based protein profiling for studying the adenylation domains of non-ribosomal peptide synthetases (ABPP-NRPS) in bacterial proteomes. This method allows substrate tolerance towards non-proteinogenic amino acids by using a range of non-proteinogenic amino acid sulfamoyladenosines in a competitive format. Additionally, we demonstrate successful incorporation of a non-proteinogenic amino acid (O-allyl-L-serine) into gramicidin S using precursor-directed biosynthesis.
CHEMICAL COMMUNICATIONS
(2023)
Article
Oncology
Huan Wee Chan, Christopher Uff, Aabir Chakraborty, Neil Dorward, Jeffrey Colin Bamber
Summary: The study aimed to determine the accuracy of SWE in detecting residual brain tumors using post-operative MRI scans as the gold standard. Results showed that SWE had a higher sensitivity but lower specificity compared to the surgeons' detection. Combining SWE with surgeons' opinions may optimize the detection of residual tumors and improve the extent of brain tumor resection.
FRONTIERS IN ONCOLOGY
(2021)
Review
Oncology
Yirizhati Aili, Nuersimanguli Maimaitiming, Hu Qin, Wenyu Ji, Guofeng Fan, Zengliang Wang, Yongxin Wang
Summary: Metastasis is an important feature of malignant tumors and affects prognosis. Understanding the mechanisms of tumor cell growth and invasion in the central nervous system is crucial for the prevention and treatment of brain metastases. Exosomes play a key role in the brain metastasis microenvironment.
FRONTIERS IN ONCOLOGY
(2022)
Article
Spectroscopy
Minglu Li, Hui Han, Shengmei Song, Shaomin Shuang, Chuan Dong
Summary: Fluorescent probes with different substituents show varying sensitivity and emission spectrum changes in detecting peroxynitrite. Among them, the ADB probe with aggregation-induced emission (AIE) process demonstrates good sensitivity for detecting peroxynitrite and can quantitatively detect ONOO- concentrations within 20 seconds.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2021)
Article
Chemistry, Medicinal
Chen Shao, Yuling Wang, Guofan Jin
Summary: The study successfully designed and synthesized novel BODIPY fluorescent probes with good biocompatibility and potential tumor targeting properties, which had certain hydrophilicity due to ethylenediamine bridging and oxygen-rich sulfonyl groups. These probes showed a certain inhibitory effect on cancer cells, and exhibited excellent biocompatibility and potential tumor targeting properties in cell and mice imaging. This research is of great significance for the rational design of novel targeted BODIPY probes with good hydrophilicity and biocompatibility.
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS
(2021)
Article
Materials Science, Biomaterials
Yifan Zhao, Yandong Xie, Yuyang Liu, Xianglong Tang, Sheng Cui
Summary: In this study, stable long-wavelength red-light emission carbon dots (R-CDs) were successfully synthesized and used for the visualization of GBM through a liposome delivery system. The optical behaviors of R-CDs were found to vary in different environments. In vitro and in vivo experiments demonstrated the excellent properties of R-CDs, suggesting their potential for deep tissue imaging and other applications.
JOURNAL OF MATERIALS CHEMISTRY B
(2022)
Article
Biochemistry & Molecular Biology
Alyson M. Curry, Elizabeth Barton, Wenjia Kang, Daniel V. Mongeluzi, Yana Cen
Summary: This study developed simple activity-based chemical probes for investigating active sirtuin content and successfully enabled cell imaging of sirtuin activity change, providing new tools for future drug discovery strategies.
Editorial Material
Behavioral Sciences
Nathan T. Cohen
EPILEPSY & BEHAVIOR
(2021)
Article
Clinical Neurology
Natrujee Wiwattanadittakul, Sirorat Suwannachote, Xiaozhen You, Nathan T. Cohen, Tan Tran, Rochana Phuackchantuck, Tammy N. Tsuchida, Dewi F. Depositario-Cabacar, Tesfaye Zelleke, John M. Schreiber, Joan A. Conry, Amy Kao, Luca Bartolini, Chima Oluigbo, M. Isabel Almira-Suarez, Kathryn Havens, Matthew T. Whitehead, William Davis Gaillard
Summary: This study investigated the association of lesion volume and location with age of seizure onset in pediatric patients with CD undergoing epilepsy surgery. Larger CD lesions were associated with earlier onset epilepsy, with CD commonly occurring within the DMN and Limbic network. The percentage of CD overlapping the motor cortex correlated with earlier seizure onset.
Article
Biochemistry & Molecular Biology
Neri Amara, Madison P. Cooper, Maria A. Voronkova, Bradley A. Webb, Eric M. Lynch, Justin M. Kollman, Taylur Ma, Kebing Yu, Zijuan Lai, Dewakar Sangaraju, Nobuhiko Kayagaki, Kim Newton, Matthew Bogyo, Steven T. Staben, Vishva M. Dixit
Summary: The study demonstrates that small-molecule LDC7559 and its potent analog NA-11 inhibit the NOX2-dependent oxidative burst in neutrophils by activating PFKL, reducing inflammation and tissue damage. This provides a potential tool for selectively activating PFKL, the main isoform expressed in immune cells.
Review
Biochemistry & Molecular Biology
Ryan K. Muir, Matteo Guerra, Matthew M. Bogyo
Summary: This review highlights recent methodologies employed in activity-based diagnostics for detecting various diseases by leveraging the dysregulated enzyme expression and activity. These methods exhibit exquisite signal sensitivity and specificity in complex biological systems, and some have advanced into clinical trials.
ACS CHEMICAL BIOLOGY
(2022)
Article
Clinical Neurology
Konrad Wagstyl, Kirstie Whitaker, Armin Raznahan, Jakob Seidlitz, Petra E. Vertes, Stephen Foldes, Zachary Humphreys, Wenhan Hu, Jiajie Mo, Marcus Likeman, Shirin Davies, Matteo Lenge, Nathan T. Cohen, Yingying Tang, Shan Wang, Mathilde Ripart, Aswin Chari, Martin Tisdall, Nuria Bargallo, Estefania Conde-Blanco, Jose Carlos Pariente, Saul Pascual-Diaz, Ignacio Delgado-Martinez, Carmen Perez-Enriquez, Ilaria Lagorio, Eugenio Abela, Nandini Mullatti, Jonathan O'Muircheartaigh, Katy Vecchiato, Yawu Liu, Maria Caligiuri, Ben Sinclair, Lucy Vivash, Anna Willard, Jothy Kandasamy, Ailsa McLellan, Drahoslav Sokol, Mira Semmelroch, Ane Kloster, Giske Opheim, Clarissa Yasuda, Kai Zhang, Khalid Hamandi, Carmen Barba, Renzo Guerrini, William Davis Gaillard, Xiaozhen You, Irene Wang, Sofia Gonzalez-Ortiz, Mariasavina Severino, Pasquale Striano, Domenico Tortora, Reetta Kalviainen, Antonio Gambardella, Angelo Labate, Patricia Desmond, Elaine Lui, Terry O'Brien, Jay Shetty, Graeme Jackson, John S. Duncan, Gavin P. Winston, Lars Pinborg, Fernando Cendes, Judith Helen Cross, Torsten Baldeweg, Sophie Adler
Summary: The study revealed that FCDs are unevenly distributed across the cerebral cortex and different lesion locations have significant impact on surgical outcomes. Lesions in the temporal and occipital lobes tend to be larger than frontal lobe lesions, leading to varying rates of seizure freedom post surgery.
Editorial Material
Chemistry, Physical
Matthew Bogyo
Summary: This nanosensor probe combines a tumour-targeting peptide, a diagnostic reporter, and an imaging contrast agent to enable early diagnosis, precision imaging, disease stratification, and downstream therapeutic response monitoring of metastatic cancer.
Editorial Material
Biochemical Research Methods
Markus Lakemeyer, Matthew Bogyo
Article
Clinical Neurology
Nathan T. Cohen, Xiaozhen You, Manu Krishnamurthy, Leigh N. Sepeta, Anqing Zhang, Chima Oluigbo, Matthew T. Whitehead, Taha Gholipour, Torsten Baldeweg, Konrad Wagstyl, Sophie Adler, William D. Gaillard
Summary: This study found that co-localization of FCD with distributed functional cortical networks is associated with age of epilepsy onset, with sensory neural networks (such as somatomotor and visual) linked to earlier onset and cognitive networks linked to later onset.
ANNALS OF NEUROLOGY
(2022)
Article
Clinical Neurology
Hannah Spitzer, Mathilde Ripart, Kirstie Whitaker, Felice D'Arco, Kshitij Mankad, Andrew A. Chen, Antonio Napolitano, Luca De Palma, Alessandro De Benedictis, Stephen Foldes, Zachary Humphreys, Kai Zhang, Wenhan Hu, Jiajie Mo, Marcus Likeman, Shirin Davies, Christopher Guttler, Matteo Lenge, Nathan T. Cohen, Yingying Tang, Shan Wang, Aswin Chari, Martin Tisdall, Nuria Bargallo, Estefania Conde-Blanco, Jose Carlos Pariente, Saul Pascual-Diaz, Ignacio Delgado-Martinez, Carmen Perez-Enriquez, Ilaria Lagorio, Eugenio Abela, Nandini Mullatti, Jonathan O'Muircheartaigh, Katy Vecchiato, Yawu Liu, Maria Eugenia Caligiuri, Ben Sinclair, Lucy Vivash, Anna Willard, Jothy Kandasamy, Ailsa McLellan, Drahoslav Sokol, Mira Semmelroch, Ane G. Kloster, Giske Opheim, Leticia Ribeiro, Clarissa Yasuda, Camilla Rossi-Espagnet, Khalid Hamandi, Anna Tietze, Carmen Barba, Renzo Guerrini, William Davis Gaillard, Xiaozhen You, Irene Wang, Sofia Gonzalez-Ortiz, Mariasavina Severino, Pasquale Striano, Domenico Tortora, Reetta Kalviainen, Antonio Gambardella, Angelo Labate, Patricia Desmond, Elaine Lui, Terence O'Brien, Jay Shetty, Graeme Jackson, John S. Duncan, Gavin P. Winston, Lars H. Pinborg, Fernando Cendes, Fabian J. Theis, Russell T. Shinohara, J. Helen Cross, Torsten Baldeweg, Sophie Adler, Konrad Wagstyl
Summary: One of the challenges in applying machine learning to diagnostic biomedical imaging is the interpretability of algorithms. This study developed an open-source and interpretable machine-learning algorithm to automatically identify FCDs from structural MRI data, improving the confidence of physicians in identifying subtle MRI lesions in individuals with epilepsy.
Article
Oncology
Gregory T. Kennedy, David E. Holt, Feredun S. Azari, Elizabeth Bernstein, Bilal Nadeem, Ashley Chang, Neil T. Sullivan, Alix Segil, Charuhas Desphande, Eric Bensen, John T. Santini Jr, John C. Kucharczuk, Edward J. Delikatny, Matthew Bogyo, A. J. Matthew Egan, Charles W. Bradley, Evgeniy Eruslanov, Jason D. Lickliter, Gavin Wright, Sunil Singhal
Summary: This study successfully translated a cathepsin activity-based probe (VGT-309) for fluorescence-guided surgery and conducted human research. The results showed that VGT-309 has good specificity and feasibility, and it can successfully label tumors during tumor resection.
CLINICAL CANCER RESEARCH
(2022)
Article
Oncology
Ethan Walker, Daan G. J. Linders, Eric Abenojar, Xinning Wang, Hans Marten Hazelbag, Marieke E. Straver, Okker D. Bijlstra, Taryn L. March, Alexander L. Vahrmeijer, Agata Exner, Matthew Bogyo, James P. Basilion, Brian Straight
Summary: A formulation of a fluorescent molecular probe has been developed to enhance the resection quality for solid-tumor cancers. This formulation can be topically applied immediately after surgery and activates in the presence of residual cancer, providing a strong fluorescent signal to precisely delineate any remaining cancer cells. The utilization of this formulation has the potential to reduce re-excisions and improve patient quality of life.
Article
Clinical Neurology
Nathan T. Cohen, Phat Chang, Xiaozhen You, Anqing Zhang, Kathryn A. Havens, Chima O. Oluigbo, Matthew T. Whitehead, Taha Gholipour, William D. Gaillard
Summary: This study aimed to evaluate the prevalence and risk factors for pharmacoresistance in pediatric FCD-related epilepsy.
Review
Clinical Neurology
Nathan T. Cohen, Hua Xie, Taha Gholipour, William D. Gaillard
Summary: This article summarizes the evidence to date on the network basis of FCD-related epilepsy, and highlights the potential applications of rsfMRI in the diagnosis and treatment of FCD-related epilepsy. Numerous studies have shown a global disruption of cortical functional networks in FCD-related epilepsy, and the underlying pathological subtypes of FCD influence overall functional network patterns.
Article
Clinical Neurology
Nathan T. Cohen, Phat Chang, Taha Gholipour, Chima Oluigbo, L. Gilbert Vezina, Hua Xie, Anqing Zhang, William D. Gaillard
Summary: This study evaluated the role of focal cortical dysplasia co-localization to cortical functional networks in the development of pharmacoresistance. A total of 136 focal cortical dysplasia patients with 3.0 T or 1.5 T MRI were identified from clinical databases at Children's National Hospital. Clinical, radiological, and pathological factors were determined, and it was found that limbic network co-localization and focal to bilateral tonic-clonic seizures predicted pharmacoresistance. These findings provide important markers for clinicians to identify high-risk patients and facilitate earlier evaluation for epilepsy surgery.
ANNALS OF CLINICAL AND TRANSLATIONAL NEUROLOGY
(2023)
Article
Biochemistry & Molecular Biology
Brett M. Babin, Laura J. Keller, Yishay Pinto, Veronica L. Li, Andrew S. Eneim, Summer E. Vance, Stephanie M. Terrell, Ami S. Bhatt, Jonathan Z. Long, Matthew Bogyo
Summary: The increasing incidence of antibiotic-resistant Mycobacterium tuberculosis infections is a global health threat. In this study, researchers screened a narrow-spectrum inhibitor that successfully suppressed the growth of Mycobacterium tuberculosis. Analyses revealed that the inhibition of SH enzymes was linked to defects in cell envelope biogenesis. It was also found that resistance was primarily developed through the synthesis of mycocerates rather than mutations to SH targets.
CELL CHEMICAL BIOLOGY
(2022)
