Re: Cell Reports Methods: March 2024 (Volume 4, Issue 3)

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Mar 25, 2024 Vol. 4, Iss. 3 Open Access Website Table of Contents Online Now Archive

Highlights Announcements Meet with a Cell Reports Methods editor Our editors are available to chat! Book a virtual meeting with them to discuss your research. Learn more about the Cell Reports Portfolio Publishing cutting-edge multidisciplinary research and methodologies. Trends in Biotechnology: Now publishing original research Learn more and submit your research ideas for editorial feedback. Call for papers: Microbial genomics Joint special issue from Cell Reports, Cell Reports Methods, Cell Reports Medicine, and Cell Genomics. On the cover On the cover: In this issue, Shinde et al. present CMI-PB, a data resource and challenge contest to develop computational models predicting vaccine responses. The cover image draws inspiration from the "blind man and elephant" parable, showing blindfolded scientists each bringing their own expertise to solve a multifaceted systems biology problem represented by the elephant and involving the multi-omics datatypes represented at the top. Courtesy: Unsplash (Wolfgang Hasselmann) and BioRender.

Table of Contents Reports GAUSS-EM, guided accumulation of ultrathin serial sections with a static magnetic field for volume electron microscopy Kara A. Fulton, Paul V. Watkins, Kevin L. Briggman Fulton et al. present a simple and inexpensive method to collect ultrathin tissue sections for volumetric electron microscopy. They demonstrate improved sample preparation that allows high-throughput acquisition of sections using static magnetic fields. After collection, sections are reordered and assembled into high-resolution datasets that can be used for further analysis. Live-cell biosensors based on the fluorescence lifetime of environment-sensing dyes Brian P. Mehl, Pothiappan Vairaprakash, Li Li, Elizabeth Hinde, Christopher J. MacNevin, Chia-Wen Hsu, Enrico Gratton, Bei Liu, Klaus M. Hahn Mehl et al. construct biosensors based on dyes whose fluorescence lifetimes respond to their solvent environment. Lifetime changes of a biosensor reflect the changing level and location of Cdc42 activation during cell protrusion and enable quantitation of the activated concentration in cells. Articles A tangible method to assess native ferroptosis suppressor activity Toshitaka Nakamura, Junya Ito, André Santos Dias Mourão, Adam Wahida, Kiyotaka Nakagawa, Eikan Mishima, Marcus Conrad Lipid peroxidation triggers ferroptosis, a promising therapeutic target. Nakamura et al. present a tangible method that utilizes affinity-purified GPX4 and FSP1 to obtain a snapshot of native anti-ferroptotic activity. This assay opens up avenues for evaluating alternative ferroptosis regulatory mechanisms and for screening ferroptosis-inducing agents targeting key suppressors. An integrative platform for detection of RNA 2′-O-methylation reveals its broad distribution on mRNA Yao Tang, Yifan Wu, Sainan Wang, Xiaolan Lu, Xiangwen Gu, Yong Li, Fan Yang, Ruilin Xu, Tao Wang, Zichen Jiao, Yan Wu, Liwei Liu, Jian-Qun Chen, Qiang Wang, Qihan Chen Tang et al. present an integrative platform for detection of RNA 2′-O-methylation (Nm), including high-throughput and site-specific Nm detection technologies. Using these methods in tandem, they identify precise mRNA Nm sites and ratios and explore molecular mechanisms and disease-related occurrences. Detecting differential transcript usage in complex diseases with SPIT Beril Erdogdu, Ales Varabyou, Stephanie C. Hicks, Steven L. Salzberg, Mihaela Pertea Erdogdu et al. present SPIT, a tool that advances differential transcript usage analysis by navigating population structure and genetic complexity in populations with complex disease. SPIT’s precision in subgroup identification and false discovery rate control makes it a robust tool for revealing intricate transcriptomic variation. Epigenomic tomography for probing spatially defined chromatin state in the brain Zhengzhi Liu, Chengyu Deng, Zirui Zhou, Ya Xiao, Shan Jiang, Bohan Zhu, Lynette B. Naler, Xiaoting Jia, Danfeng (Daphne) Yao, Chang Lu Liu et al. develop an approach, referred to as epigenomic tomography, to map the spatial epigenome of mouse brain at a span of 1 cm with a resolution of 0.5 mm. As a proof of principle, epigenomic tomography data reveal striking changes in the frontal cortex due to kainic-acid-induced seizure. DESP demixes cell-state profiles from dynamic bulk molecular measurements Ahmed Youssef, Indranil Paul, Mark Crovella, Andrew Emili Youssef et al. present DESP, an algorithm addressing the limited exploration of quantitative proteomics data at the cell-state level due to experimental constraints. DESP accurately deciphers cell-state contributions to parallel quantitative proteomics, providing a generalizable computational framework for studying cell-state-level proteomes within conventional bulk-level workflows. Anchored-fusion enables targeted fusion search in bulk and single-cell RNA sequencing data Xilu Yuan, Haishuai Wang, Zhongquan Sun, Chunpeng Zhou, Simon Chong Chu, Jiajun Bu, Ning Shen Yuan et al. present Anchored-fusion, a method for detecting fusion genes with high sensitivity from paired-end RNA-seq. Anchoring a gene of interest avoids over-filtering, and a deep learning model removes false positives. Anchored-fusion demonstrates superior sensitivity in various scenarios, particularly in detecting fusion genes from single-cell RNA-seq. Pooled CRISPR screening of high-content cellular phenotypes using ghost cytometry Asako Tsubouchi, Yuri An, Yoko Kawamura, Yuichi Yanagihashi, Hirofumi Nakayama, Yuri Murata, Kazuki Teranishi, Soh Ishiguro, Hiroyuki Aburatani, Nozomu Yachie, Sadao Ota Tsubouchi et al. present multimodal ghost cytometry for pooled CRISPR screening. Their approach, combining both fluorescence and label-free phenotyping, allows rapid, large-scale gene perturbation analysis. This method successfully identifies genes involved in kinase signaling and macrophage polarization and significantly expands the possibilities for designing perturbation screens. Discontinuity third harmonic generation microscopy for label-free imaging and quantification of intraepidermal nerve fibers Pei-Jhe Wu, Hsiao-Chieh Tseng, Chi-Chao Chao, Yi-Hua Liao, Chen-Tung Yen, Wen-Ying Lin, Sung-Tsang Hsieh, Wei-Zen Sun, Chi-Kuang Sun Wu et al. present discontinuity third harmonic generation microscopy (dTHGM), a method that allows for three-dimensional visualization of intraepidermal nerve endings. This label-free, section-free methodology assesses epidermal nerve fibers noninvasively, providing an intraepidermal nerve fiber index for clinical small-fiber neuropathy (SFN) diagnosis. It holds significance for noninvasive SFN diagnosis, including cases of diabetic peripheral neuropathy. An autologous ex vivo model for exploring patient-specific responses to viro-immunotherapy in glioblastoma Eftychia Stavrakaki, Wouter B.L. van den Bossche, Lisette B. Vogelezang, Cristina Teodosio, Dana M. Mustafa, Jacques J.M. van Dongen, Clemens M.F. Dirven, Rutger K. Balvers, Martine L. Lamfers Stavrakaki et al. present a co-culture model designed to investigate the interactions between oncolytic virus-infected glioblastoma cells and immune cells derived from the same patient. This model serves as a valuable tool to explore individual patient responses to virus-based immunotherapy. SOX17/ETV2 improves the direct reprogramming of adult fibroblasts to endothelial cells Alexander Grath, Guohao Dai Grath et al. develop an improved method of directly reprogramming adult human dermal fibroblasts into vascular endothelial cells using SOX17 and ETV2. This approach enhances reprogramming efficiency and endothelial cell characteristics, such as eNOS expression. Resource A multi-omics systems vaccinology resource to develop and test computational models of immunity Pramod Shinde, Ferran Soldevila, Joaquin Reyna, Minori Aoki, Mikkel Rasmussen, Lisa Willemsen, Mari Kojima, Brendan Ha, Jason A. Greenbaum, James A. Overton, Hector Guzman-Orozco, Somayeh Nili, Shelby Orfield, Jeremy P. Gygi, Ricardo da Silva Antunes, Alessandro Sette, Barry Grant, Lars Rønn Olsen, Anna Konstorum, Leying Guan, Ferhat Ay, Steven H. Kleinstein, Bjoern Peters Shinde et al. establish a community resource to compare patients' vaccine responses and to host annual contests to predict vaccination outcomes. They find specifically trained multi-omics models and simple age-based models outperformed. They aim to engage the community with a public prediction contest starting August 2024.