{"paper_id":"97322197-4bf4-4fbf-9354-d9d8a6323720","body_text":"A genome-wide CRISPR base-editing resource for functional genomics and drug-response mapping in Leishmania mexicana | bioRxiv /* */ /* */ <!-- <!-- /*! * yepnope1.5.4 * (c) WTFPL, GPLv2 */ (function(a,b,c){function d(a){return\"[object Function]\"==o.call(a)}function e(a){return\"string\"==typeof a}function f(){}function g(a){return!a||\"loaded\"==a||\"complete\"==a||\"uninitialized\"==a}function h(){var a=p.shift();q=1,a?a.t?m(function(){(\"c\"==a.t?B.injectCss:B.injectJs)(a.s,0,a.a,a.x,a.e,1)},0):(a(),h()):q=0}function i(a,c,d,e,f,i,j){function k(b){if(!o&&g(l.readyState)&&(u.r=o=1,!q&&h(),l.onload=l.onreadystatechange=null,b)){\"img\"!=a&&m(function(){t.removeChild(l)},50);for(var d in y[c])y[c].hasOwnProperty(d)&&y[c][d].onload()}}var j=j||B.errorTimeout,l=b.createElement(a),o=0,r=0,u={t:d,s:c,e:f,a:i,x:j};1===y[c]&&(r=1,y[c]=[]),\"object\"==a?l.data=c:(l.src=c,l.type=a),l.width=l.height=\"0\",l.onerror=l.onload=l.onreadystatechange=function(){k.call(this,r)},p.splice(e,0,u),\"img\"!=a&&(r||2===y[c]?(t.insertBefore(l,s?null:n),m(k,j)):y[c].push(l))}function j(a,b,c,d,f){return q=0,b=b||\"j\",e(a)?i(\"c\"==b?v:u,a,b,this.i++,c,d,f):(p.splice(this.i++,0,a),1==p.length&&h()),this}function k(){var a=B;return a.loader={load:j,i:0},a}var l=b.documentElement,m=a.setTimeout,n=b.getElementsByTagName(\"script\")[0],o={}.toString,p=[],q=0,r=\"MozAppearance\"in l.style,s=r&&!!b.createRange().compareNode,t=s?l:n.parentNode,l=a.opera&&\"[object Opera]\"==o.call(a.opera),l=!!b.attachEvent&&!l,u=r?\"object\":l?\"script\":\"img\",v=l?\"script\":u,w=Array.isArray||function(a){return\"[object Array]\"==o.call(a)},x=[],y={},z={timeout:function(a,b){return b.length&&(a.timeout=b[0]),a}},A,B;B=function(a){function b(a){var a=a.split(\"!\"),b=x.length,c=a.pop(),d=a.length,c={url:c,origUrl:c,prefixes:a},e,f,g;for(f=0;f<d;f++)g=a[f].split(\"=\"),(e=z[g.shift()])&&(c=e(c,g));for(f=0;f<b;f++)c=x[f](c);return c}function g(a,e,f,g,h){var i=b(a),j=i.autoCallback;i.url.split(\".\").pop().split(\"?\").shift(),i.bypass||(e&&(e=d(e)?e:e[a]||e[g]||e[a.split(\"/\").pop().split(\"?\")[0]]),i.instead?i.instead(a,e,f,g,h):(y[i.url]?i.noexec=!0:y[i.url]=1,f.load(i.url,i.forceCSS||!i.forceJS&&\"css\"==i.url.split(\".\").pop().split(\"?\").shift()?\"c\":c,i.noexec,i.attrs,i.timeout),(d(e)||d(j))&&f.load(function(){k(),e&&e(i.origUrl,h,g),j&&j(i.origUrl,h,g),y[i.url]=2})))}function h(a,b){function c(a,c){if(a){if(e(a))c||(j=function(){var a=[].slice.call(arguments);k.apply(this,a),l()}),g(a,j,b,0,h);else if(Object(a)===a)for(n in m=function(){var b=0,c;for(c in a)a.hasOwnProperty(c)&&b++;return b}(),a)a.hasOwnProperty(n)&&(!c&&!--m&&(d(j)?j=function(){var a=[].slice.call(arguments);k.apply(this,a),l()}:j[n]=function(a){return function(){var b=[].slice.call(arguments);a&&a.apply(this,b),l()}}(k[n])),g(a[n],j,b,n,h))}else!c&&l()}var h=!!a.test,i=a.load||a.both,j=a.callback||f,k=j,l=a.complete||f,m,n;c(h?a.yep:a.nope,!!i),i&&c(i)}var i,j,l=this.yepnope.loader;if(e(a))g(a,0,l,0);else if(w(a))for(i=0;i (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0];var j=d.createElement(s);var dl=l!='dataLayer'?'&l='+l:'';j.src='//www.googletagmanager.com/gtm.js?id='+i+dl;j.type='text/javascript';j.async=true;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-M677548'); Skip to main content Home About Submit ALERTS / RSS Search for this keyword Advanced Search New Results A genome-wide CRISPR base-editing resource for functional genomics and drug-response mapping in Leishmania mexicana Jorge Arias del Angel , Fabian Link , Nicole Herrmann May , Ilkem Ekici , Konstantin Wawra , Simon Schwind , Simon Zorn , Jennifer Haggarty , Stefan K Weidt , Ryan Ritchie , Michael P Barrett , Ger van Zandbergen , View ORCID Profile Tom Beneke doi: https://doi.org/10.1101/2025.06.16.659792 Jorge Arias del Angel 1 Department of Cell and Developmental Biology, Biocentre, University of Wuerzburg, Wuerzburg, Germany; Division of Immunology, Paul-Ehrlich-Institut, Langen, Germany; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Fabian Link 2 Department of Cell and Developmental Biology, Biocentre, University of Wuerzburg, Wuerzburg, Germany; Division of Immunology, Paul-Ehrlich-Institut, Langen, Germany; Current Affiliation: Fraunhofer Institute for Translational Medicine and Pharmacology ITM; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Nicole Herrmann May 3 Department of Cell and Developmental Biology, Biocentre, University of Wuerzburg, Wuerzburg, Germany; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Ilkem Ekici 3 Department of Cell and Developmental Biology, Biocentre, University of Wuerzburg, Wuerzburg, Germany; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Konstantin Wawra 3 Department of Cell and Developmental Biology, Biocentre, University of Wuerzburg, Wuerzburg, Germany; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Simon Schwind 3 Department of Cell and Developmental Biology, Biocentre, University of Wuerzburg, Wuerzburg, Germany; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Simon Zorn 3 Department of Cell and Developmental Biology, Biocentre, University of Wuerzburg, Wuerzburg, Germany; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Jennifer Haggarty 4 Shared Research Facilities (SRF), MVLS, University of Glasgow, Glasgow, United Kingdom; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Stefan K Weidt 4 Shared Research Facilities (SRF), MVLS, University of Glasgow, Glasgow, United Kingdom; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Ryan Ritchie 5 School of Infection and Immunity, University of Glasgow, Glasgow, United Kingdom; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Michael P Barrett 5 School of Infection and Immunity, University of Glasgow, Glasgow, United Kingdom; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Ger van Zandbergen 6 Division of Immunology, Paul-Ehrlich-Institut, Langen, Germany Find this author on Google Scholar Find this author on PubMed Search for this author on this site Tom Beneke 3 Department of Cell and Developmental Biology, Biocentre, University of Wuerzburg, Wuerzburg, Germany; Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Tom Beneke For correspondence: tom.beneke{at}uni-wuerzburg.de Abstract Info/History Metrics Supplementary material Data/Code Preview PDF Abstract We present a CRISPR/Cas9 cytosine base editing library for genome-wide loss-of-function screening in L. mexicana and apply it to dissect the genetics of Leishmania drug response. The results, accessible at www.LeishBASEeditDB.net, revealed novel response biomarkers for SbIII, miltefosine, amphotericin B, pentamidine, and the arylmethylaminosteroid 1c. We identified hundreds of loci linked to altered drug responses, including opposing effects among paralogs, cross-resistance, and collateral sensitivity. Among 41 validated candidates, we identified sterol defects in two novel amphotericin B markers, discovered a regulator of intracellular miltefosine transporter complex localization, and uncovered evidence that flagellar-associated defects reduce drug sensitivity. Parallel viability and motility screens revealed, for the first time, genome-wide fitness contributions of unique and multi-copy genes in Leishmania promastigotes. Our approach enables powerful reverse genetic screens across Leishmania species, advancing drug mechanism studies and guiding combination therapy designs. The library is available for others to screen a multitude of additional loss-of-function phenotypes. Competing Interest Statement The authors have declared no competing interest. Footnotes We have improved the previous version of the manuscript as follows: 1. Re-analysed the screening data and improved data visualization to better highlight the strengths of the approach, particularly for the fitness screen 2. Added extensive quality control analyses and datasets to further demonstrate the robustness of the method and screen 3. Repeated the MTF screen at lower drug concentrations and expanded the discussion of dose-dependent effects 4. Demonstrated that the library can be cryopreserved and revived, establishing it as a valuable and distributable community resource 5. Included data from newly generated L. major AQP1 null mutants 6. Expanded the Methods section to improve reproducibility and facilitate adoption by other researchers http://www.leishbaseeditdb.net/ Funder Information Declared LOEWE Center DRUID , Project D3, B3 Deutsche Forschungsgemeinschaft , project 532631727 European Molecular Biology Organization , ALTF 727-2021 European Commission , 101064428 – LeishMOM Biotechnology and Biological Sciences Research Council , BB/Y007360/1 Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license . View the discussion thread. Back to top Previous Next Posted May 24, 2026. Download PDF Supplementary Material Data/Code Email Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. 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Share A genome-wide CRISPR base-editing resource for functional genomics and drug-response mapping in Leishmania mexicana Jorge Arias del Angel , Fabian Link , Nicole Herrmann May , Ilkem Ekici , Konstantin Wawra , Simon Schwind , Simon Zorn , Jennifer Haggarty , Stefan K Weidt , Ryan Ritchie , Michael P Barrett , Ger van Zandbergen , Tom Beneke bioRxiv 2025.06.16.659792; doi: https://doi.org/10.1101/2025.06.16.659792 Share This Article: Copy Citation Tools A genome-wide CRISPR base-editing resource for functional genomics and drug-response mapping in Leishmania mexicana Jorge Arias del Angel , Fabian Link , Nicole Herrmann May , Ilkem Ekici , Konstantin Wawra , Simon Schwind , Simon Zorn , Jennifer Haggarty , Stefan K Weidt , Ryan Ritchie , Michael P Barrett , Ger van Zandbergen , Tom Beneke bioRxiv 2025.06.16.659792; doi: https://doi.org/10.1101/2025.06.16.659792 Citation Manager Formats BibTeX Bookends EasyBib EndNote (tagged) EndNote 8 (xml) Medlars Mendeley Papers RefWorks Tagged Ref Manager RIS Zotero Tweet Widget Facebook Like Google Plus One Subject Area Microbiology Subject Areas All Articles Animal Behavior and Cognition (7636) Biochemistry (17704) Bioengineering (13898) Bioinformatics (41967) Biophysics (21460) Cancer Biology (18599) Cell Biology (25525) Clinical Trials (138) Developmental Biology (13384) Ecology (19909) Epidemiology (2067) Evolutionary Biology (24326) Genetics (15613) Genomics (22512) Immunology (17740) Microbiology (40423) Molecular Biology (17191) Neuroscience (88645) Paleontology (667) Pathology (2835) Pharmacology and Toxicology (4825) Physiology (7646) Plant Biology (15158) Scientific Communication and Education (2046) Synthetic Biology (4302) Systems Biology (9825) Zoology (2271)","source_license":"CC-BY-4.0","license_restricted":false}