Pub Date : 2024-04-22Epub Date: 2024-04-02DOI: 10.1016/j.crmeth.2024.100741
Matthew Waas, Amanda Khoo, Pirashaanthy Tharmapalan, Curtis W McCloskey, Meinusha Govindarajan, Bowen Zhang, Shahbaz Khan, Paul D Waterhouse, Rama Khokha, Thomas Kislinger
Deep proteomic profiling of rare cell populations has been constrained by sample input requirements. Here, we present DROPPS (droplet-based one-pot preparation for proteomic samples), an accessible low-input platform that generates high-fidelity proteomic profiles of 100-2,500 cells. By applying DROPPS within the mammary epithelium, we elucidated the connection between mitochondrial activity and clonogenicity, identifying CD36 as a marker of progenitor capacity in the basal cell compartment. We anticipate that DROPPS will accelerate biology-driven proteomic research for a multitude of rare cell populations.
{"title":"Droplet-based proteomics reveals CD36 as a marker for progenitors in mammary basal epithelium.","authors":"Matthew Waas, Amanda Khoo, Pirashaanthy Tharmapalan, Curtis W McCloskey, Meinusha Govindarajan, Bowen Zhang, Shahbaz Khan, Paul D Waterhouse, Rama Khokha, Thomas Kislinger","doi":"10.1016/j.crmeth.2024.100741","DOIUrl":"https://doi.org/10.1016/j.crmeth.2024.100741","url":null,"abstract":"<p><p>Deep proteomic profiling of rare cell populations has been constrained by sample input requirements. Here, we present DROPPS (droplet-based one-pot preparation for proteomic samples), an accessible low-input platform that generates high-fidelity proteomic profiles of 100-2,500 cells. By applying DROPPS within the mammary epithelium, we elucidated the connection between mitochondrial activity and clonogenicity, identifying CD36 as a marker of progenitor capacity in the basal cell compartment. We anticipate that DROPPS will accelerate biology-driven proteomic research for a multitude of rare cell populations.</p>","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11045875/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140859236","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Intracellular signaling plays essential roles in various cell types. In the central nervous system, signaling cascades are strictly regulated in a spatiotemporally specific manner to govern brain function; for example, presynaptic cyclic adenosine monophosphate (cAMP) can enhance the probability of neurotransmitter release. In the last decade, channelrhodopsin-2 has been engineered for subcellular targeting using localization tags, but optogenetic tools for intracellular signaling are not well developed. Therefore, we engineered a selective presynaptic fusion tag for photoactivated adenylyl cyclase (bPAC-Syn1a) and found its high localization at presynaptic terminals. Furthermore, an all-optical electrophysiological method revealed rapid and robust short-term potentiation by bPAC-Syn1a at brain stem-amygdala synapses in acute brain slices. Additionally, bPAC-Syn1a modulated mouse immobility behavior. These results indicate that bPAC-Syn1a can manipulate presynaptic cAMP signaling in vitro and in vivo. The all-optical manipulation technique developed in this study can help further elucidate the dynamic regulation of various cellular functions.
{"title":"All-optical presynaptic plasticity induction by photoactivated adenylyl cyclase targeted to axon terminals.","authors":"Masashi Nagase, Takashi Nagashima, Shun Hamada, Mieko Morishima, Suguru Tohyama, Fumiko Arima-Yoshida, Kanae Hiyoshi, Tomoha Hirano, Toshihisa Ohtsuka, Ayako M Watabe","doi":"10.1016/j.crmeth.2024.100740","DOIUrl":"10.1016/j.crmeth.2024.100740","url":null,"abstract":"<p><p>Intracellular signaling plays essential roles in various cell types. In the central nervous system, signaling cascades are strictly regulated in a spatiotemporally specific manner to govern brain function; for example, presynaptic cyclic adenosine monophosphate (cAMP) can enhance the probability of neurotransmitter release. In the last decade, channelrhodopsin-2 has been engineered for subcellular targeting using localization tags, but optogenetic tools for intracellular signaling are not well developed. Therefore, we engineered a selective presynaptic fusion tag for photoactivated adenylyl cyclase (bPAC-Syn1a) and found its high localization at presynaptic terminals. Furthermore, an all-optical electrophysiological method revealed rapid and robust short-term potentiation by bPAC-Syn1a at brain stem-amygdala synapses in acute brain slices. Additionally, bPAC-Syn1a modulated mouse immobility behavior. These results indicate that bPAC-Syn1a can manipulate presynaptic cAMP signaling in vitro and in vivo. The all-optical manipulation technique developed in this study can help further elucidate the dynamic regulation of various cellular functions.</p>","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11045876/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140194731","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-04-01DOI: 10.1016/j.crmeth.2024.100758
Hratch M. Baghdassarian, Daniel Dimitrov, Erick Armingol, Julio Saez-Rodriguez, Nathan E. Lewis
{"title":"Combining LIANA and Tensor-cell2cell to decipher cell-cell communication across multiple samples.","authors":"Hratch M. Baghdassarian, Daniel Dimitrov, Erick Armingol, Julio Saez-Rodriguez, Nathan E. Lewis","doi":"10.1016/j.crmeth.2024.100758","DOIUrl":"https://doi.org/10.1016/j.crmeth.2024.100758","url":null,"abstract":"","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140760333","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-04-01DOI: 10.1016/j.crmeth.2024.100762
Bunyarit Meksiriporn, Jamie B. Spangler
{"title":"Directed-evolution approach to empower EGFR targeting for immunotherapy.","authors":"Bunyarit Meksiriporn, Jamie B. Spangler","doi":"10.1016/j.crmeth.2024.100762","DOIUrl":"https://doi.org/10.1016/j.crmeth.2024.100762","url":null,"abstract":"","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140763593","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-04-01DOI: 10.1016/j.crmeth.2024.100759
Sergii Domanskyi, Anuj Srivastava, Jessica Kaster, Haiyin Li, M. Herlyn, Jill C. Rubinstein, Jeffrey H. Chuang
{"title":"Nextflow pipeline for Visium and H&E data from patient-derived xenograft samples.","authors":"Sergii Domanskyi, Anuj Srivastava, Jessica Kaster, Haiyin Li, M. Herlyn, Jill C. Rubinstein, Jeffrey H. Chuang","doi":"10.1016/j.crmeth.2024.100759","DOIUrl":"https://doi.org/10.1016/j.crmeth.2024.100759","url":null,"abstract":"","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140768949","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-04-01DOI: 10.1016/j.crmeth.2024.100753
Vanessa Mhanna, Pierre Barennes, Hélène Vantomme, Gwladys Fourcade, Nicolas Coatnoan, A. Six, David Klatzmann, E. Mariotti-Ferrandiz
{"title":"Enhancing comparative T cell receptor repertoire analysis in small biological samples through pooling homologous cell samples from multiple mice.","authors":"Vanessa Mhanna, Pierre Barennes, Hélène Vantomme, Gwladys Fourcade, Nicolas Coatnoan, A. Six, David Klatzmann, E. Mariotti-Ferrandiz","doi":"10.1016/j.crmeth.2024.100753","DOIUrl":"https://doi.org/10.1016/j.crmeth.2024.100753","url":null,"abstract":"","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140797034","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-04-01DOI: 10.1016/j.crmeth.2024.100756
Pascal D. Vos, Andrianto P. Gandadireja, Giulia Rossetti, Stefan J. Siira, Jessica L. Mantegna, A. Filipovska, O. Rackham
{"title":"Mutational rescue of the activity of high-fidelity Cas9 enzymes.","authors":"Pascal D. Vos, Andrianto P. Gandadireja, Giulia Rossetti, Stefan J. Siira, Jessica L. Mantegna, A. Filipovska, O. Rackham","doi":"10.1016/j.crmeth.2024.100756","DOIUrl":"https://doi.org/10.1016/j.crmeth.2024.100756","url":null,"abstract":"","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140794974","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-04-01DOI: 10.1016/j.crmeth.2024.100763
Henrietta Holze, Laure Talarmain, K. A. Fennell, E. Lam, M. Dawson, Dane Vassiliadis
{"title":"Analysis of synthetic cellular barcodes in the genome and transcriptome with BARtab and bartools","authors":"Henrietta Holze, Laure Talarmain, K. A. Fennell, E. Lam, M. Dawson, Dane Vassiliadis","doi":"10.1016/j.crmeth.2024.100763","DOIUrl":"https://doi.org/10.1016/j.crmeth.2024.100763","url":null,"abstract":"","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140764041","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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