Publications

2024

• REliable PIcking by Consensus (REPIC): a consensus methodology for harnessing multiple cryo-EM particle pickersCameron C, Seager S, Sigworth F, Tagare H, Gerstein M. REliable PIcking by Consensus (REPIC): a consensus methodology for harnessing multiple cryo-EM particle pickers. Communications Biology 2024, 7: 1421. PMID: 39482410, PMCID: PMC11528043, DOI: 10.1038/s42003-024-07045-0.
• Single-cell transcriptomic and proteomic analysis of Parkinson’s disease brainsZhu B, Park J, Coffey S, Russo A, Hsu I, Wang J, Su C, Chang R, Lam T, Gopal P, Ginsberg S, Zhao H, Hafler D, Chandra S, Zhang L. Single-cell transcriptomic and proteomic analysis of Parkinson’s disease brains. Science Translational Medicine 2024, 16: eabo1997. PMID: 39475571, DOI: 10.1126/scitranslmed.abo1997.
• CDK9 phosphorylates RUNX1 to promote megakaryocytic fate in megakaryocytic-erythroid progenitorsKwon N, Lu Y, Thompson E, Mancuso R, Wang L, Zhang P, Krause D. CDK9 phosphorylates RUNX1 to promote megakaryocytic fate in megakaryocytic-erythroid progenitors. Blood 2024, 144: 1800-1812. PMID: 39102635, PMCID: PMC11530366, DOI: 10.1182/blood.2024023963.
• Image-based 3D genomics through chromatin tracingYang T, Wang S. Image-based 3D genomics through chromatin tracing. Nature Reviews Methods Primers 2024, 4: 76. DOI: 10.1038/s43586-024-00354-y.
• Analysis of Powassan Virus Genome Sequences from Human Cases Reveals Substantial Genetic Diversity with Implications for Molecular Assay DevelopmentKlontz E, Chowdhury N, Holbrook N, Solomon I, Telford S, Aliota M, Vogels C, Grubaugh N, Helgager J, Hughes H, Velez J, Piantadosi A, Chiu C, Lemieux J, Branda J. Analysis of Powassan Virus Genome Sequences from Human Cases Reveals Substantial Genetic Diversity with Implications for Molecular Assay Development. Viruses 2024, 16: 1653. DOI: 10.3390/v16111653.
• Machine-guided design of cell-type-targeting cis-regulatory elementsGosai S, Castro R, Fuentes N, Butts J, Mouri K, Alasoadura M, Kales S, Nguyen T, Noche R, Rao A, Joy M, Sabeti P, Reilly S, Tewhey R. Machine-guided design of cell-type-targeting cis-regulatory elements. Nature 2024, 634: 1211-1220. PMID: 39443793, PMCID: PMC11525185, DOI: 10.1038/s41586-024-08070-z.
• Epitope-anchored contrastive transfer learning for paired CD8+ T cell receptor–antigen recognitionZhang Y, Wang Z, Jiang Y, Littler D, Gerstein M, Purcell A, Rossjohn J, Ou H, Song J. Epitope-anchored contrastive transfer learning for paired CD8+ T cell receptor–antigen recognition. Nature Machine Intelligence 2024, 1-15. DOI: 10.1038/s42256-024-00913-8.
• Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships.Kudron M, Gewirtzman L, Victorsen A, Lear B, Vafeados D, Gao J, Xu J, Samanta S, Frink E, Tran-Pearson A, Hyunh C, Hammonds A, Fisher W, Wall M, Wesseling G, Hernandez V, Lin Z, Kasparian M, White K, Allada R, Gerstein M, Hillier L, Celniker S, Reinke V, Waterston R. Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships. Genome Research 2024, gr.279037.124. PMID: 39438113, DOI: 10.1101/gr.279037.124.
• All the sites we cannot see: Sources and mitigation of false negatives in RNA modification studiesOberdoeffer S, Gilbert W. All the sites we cannot see: Sources and mitigation of false negatives in RNA modification studies. Nature Reviews Molecular Cell Biology 2024, 1-12. PMID: 39433914, DOI: 10.1038/s41580-024-00784-2.
• Rab6a enables BICD2/dynein-mediated trafficking of human papillomavirus from the trans-Golgi network during virus entry.Choi J, Speckhart K, Tsai B, DiMaio D. Rab6a enables BICD2/dynein-mediated trafficking of human papillomavirus from the trans-Golgi network during virus entry. MBio 2024, e0281124. PMID: 39431827, DOI: 10.1128/mbio.02811-24.
• A TRilogy of ATR’s Non-Canonical Roles Throughout the Cell Cycle and Its Relation to CancerJoo Y, Ramirez C, Kabeche L. A TRilogy of ATR’s Non-Canonical Roles Throughout the Cell Cycle and Its Relation to Cancer. Cancers 2024, 16: 3536. PMID: 39456630, PMCID: PMC11506335, DOI: 10.3390/cancers16203536.
• SDePER: a hybrid machine learning and regression method for cell-type deconvolution of spatial barcoding-based transcriptomic dataLiu Y, Li N, Qi J, Xu G, Zhao J, Wang N, Huang X, Jiang W, Wei H, Justet A, Adams T, Homer R, Amei A, Rosas I, Kaminski N, Wang Z, Yan X. SDePER: a hybrid machine learning and regression method for cell-type deconvolution of spatial barcoding-based transcriptomic data. Genome Biology 2024, 25: 271. PMID: 39402626, PMCID: PMC11475911, DOI: 10.1186/s13059-024-03416-2.
• Ataxin-2 polyglutamine expansions aberrantly sequester TDP-43 ribonucleoprotein condensates disrupting mRNA transport and local translation in neuronsWijegunawardana D, Nayak A, Vishal S, Venkatesh N, Gopal P. Ataxin-2 polyglutamine expansions aberrantly sequester TDP-43 ribonucleoprotein condensates disrupting mRNA transport and local translation in neurons. Developmental Cell 2024 PMID: 39419034, DOI: 10.1016/j.devcel.2024.09.023.
• Splicing the Difference: Harnessing the Complexity of the Transcriptome in HematopoiesisMaul-Newby H, Halene S. Splicing the Difference: Harnessing the Complexity of the Transcriptome in Hematopoiesis. Experimental Hematology 2024, 140: 104655. PMID: 39393608, DOI: 10.1016/j.exphem.2024.104655.
• Somatic mosaicism in schizophrenia brains reveals prenatal mutational processesMaury E, Jones A, Seplyarskiy V, Nguyen T, Rosenbluh C, Bae T, Wang Y, Abyzov A, Khoshkhoo S, Chahine Y, Zhao S, Venkatesh S, Root E, Voloudakis G, Roussos P, Network B, Park P, Akbarian S, Brennand K, Reilly S, Lee E, Sunyaev S, Walsh C, Chess A. Somatic mosaicism in schizophrenia brains reveals prenatal mutational processes. Science 2024, 386: 217-224. PMID: 39388546, PMCID: PMC11490355, DOI: 10.1126/science.adq1456.
• Steering research on mRNA splicing in cancer towards clinical translationAnczukow O, Allain F, Angarola B, Black D, Brooks A, Cheng C, Conesa A, Crosse E, Eyras E, Guccione E, Lu S, Neugebauer K, Sehgal P, Song X, Tothova Z, Valcárcel J, Weeks K, Yeo G, Thomas-Tikhonenko A. Steering research on mRNA splicing in cancer towards clinical translation. Nature Reviews Cancer 2024, 1-19. PMID: 39384951, DOI: 10.1038/s41568-024-00750-2.
• Tumor-specific antigen delivery for T-cell therapy via a pH-sensitive peptide conjugate.Yurkevicz A, Liu Y, Katz S, Glazer P. Tumor-specific antigen delivery for T-cell therapy via a pH-sensitive peptide conjugate. Molecular Cancer Therapeutics 2024, of1-of13. PMID: 39382073, DOI: 10.1158/1535-7163.mct-23-0809.
• Early Release - Dengue Outbreak Caused by Multiple Virus Serotypes and Lineages, Colombia, 2023–2024 - Volume 30, Number 11—November 2024 - Emerging Infectious Diseases journal - CDCGrubaugh N, Torres-Hernández D, Murillo-Ortiz M, Dávalos D, Lopez P, Hurtado I, Breban M, Bourgikos E, Hill V, López-Medina E. Early Release - Dengue Outbreak Caused by Multiple Virus Serotypes and Lineages, Colombia, 2023–2024 - Volume 30, Number 11—November 2024 - Emerging Infectious Diseases journal - CDC. Emerging Infectious Diseases 2024, 30: 2391-2395. PMID: 39378873, PMCID: PMC11521178, DOI: 10.3201/eid3011.241031.
• CUTS: A Deep Learning and Topological Framework for Multigranular Unsupervised Medical Image SegmentationLiu C, Amodio M, Shen L, Gao F, Avesta A, Aneja S, Wang J, Del Priore L, Krishnaswamy S. CUTS: A Deep Learning and Topological Framework for Multigranular Unsupervised Medical Image Segmentation. Lecture Notes In Computer Science 2024, 15008: 155-165. DOI: 10.1007/978-3-031-72111-3_15.
• CCR2+ monocytes are dispensable to resolve acute pulmonary Pseudomonas aeruginosa infections in WT and Cystic Fibrosis miceÖz H, Braga C, Gudneppanavar R, Di Pietro C, Huang P, Zhang P, Krause D, Egan M, Murray T, Bruscia E. CCR2+ monocytes are dispensable to resolve acute pulmonary Pseudomonas aeruginosa infections in WT and Cystic Fibrosis mice. Journal Of Leukocyte Biology 2024, qiae218. PMID: 39365279, DOI: 10.1093/jleuko/qiae218.
• Targeting Pseudomonas aeruginosa biofilm with an evolutionary trained bacteriophage cocktail exploiting phage resistance trade-offsKunisch F, Campobasso C, Wagemans J, Yildirim S, Chan B, Schaudinn C, Lavigne R, Turner P, Raschke M, Trampuz A, Gonzalez Moreno M. Targeting Pseudomonas aeruginosa biofilm with an evolutionary trained bacteriophage cocktail exploiting phage resistance trade-offs. Nature Communications 2024, 15: 8572. PMID: 39362854, PMCID: PMC11450229, DOI: 10.1038/s41467-024-52595-w.
• Keratin 17 and A2ML1 are negative prognostic biomarkers in non-small cell lung cancerBabu S, Horowitz M, Delgado-Coka L, Roa-Peña L, Akalin A, Escobar-Hoyos L, Shroyer K. Keratin 17 and A2ML1 are negative prognostic biomarkers in non-small cell lung cancer. Pathology - Research And Practice 2024, 263: 155643. PMID: 39413460, DOI: 10.1016/j.prp.2024.155643.
• INTERACTIONS BETWEEN MITOCHONDRIAL DNA AND TOLL-LIKE RECEPTOR 9 MEDIATES PULMONARY FIBROSISLEE C, TRUJILLO G, REGUEIRO-REN A, LIU C, HU B, SUN Y, KHOURY J, KHOURY J, AHANGARI F, ISHIKAWA G, WALIA A, PIVARNIK T, YU S, WOO S, FIORINI V, MCGOVERN J, AL JUMAILY K, SUN H, PENG X, ANTIN-OZERKIS D, SAULER M, KAMINSKI N, HERZOG E. INTERACTIONS BETWEEN MITOCHONDRIAL DNA AND TOLL-LIKE RECEPTOR 9 MEDIATES PULMONARY FIBROSIS. CHEST Journal 2024, 166: a3384-a3386. DOI: 10.1016/j.chest.2024.06.2020.
• Next-generation cell-penetrating antibodies for tumor targeting and RAD51 inhibitionRackear M, Quijano E, Ianniello Z, Colón-Ríos D, Krysztofiak A, Abdullah R, Liu Y, Rogers F, Ludwig D, Dwivedi R, Bleichert F, Glazer P. Next-generation cell-penetrating antibodies for tumor targeting and RAD51 inhibition. Oncotarget 2024, 15: 699-713. PMID: 39352803, PMCID: PMC11444335, DOI: 10.18632/oncotarget.28651.
• Emerging and re-emerging themes in co-transcriptional pre-mRNA splicingCarrocci T, Neugebauer K. Emerging and re-emerging themes in co-transcriptional pre-mRNA splicing. Molecular Cell 2024, 84: 3656-3666. PMID: 39366353, PMCID: PMC11463726, DOI: 10.1016/j.molcel.2024.08.036.
• Modern Photon-Based Craniospinal Irradiation in Leptomeningeal DiseaseKeit E, Peterson J, Johnstone P, Robinson T, Figura N. Modern Photon-Based Craniospinal Irradiation in Leptomeningeal Disease. International Journal Of Radiation Oncology • Biology • Physics 2024, 120: e242. DOI: 10.1016/j.ijrobp.2024.07.542.
• Patterns of CNS Failures in Relapse/Refractory Large B-Cell Lymphoma (LBCL) Patients with Secondary CNS Disease Following Chimeric Antigen Receptor T-Cell (CAR T) TherapyNakashima J, Khatri V, Cruz-Chamorro R, Zhou J, Patra P, Gaballa S, Khimani F, Mirza S, Shah B, Saeed H, Chavez J, Locke F, Nishihori T, Liu H, Dong N, Lazaryan A, Robinson T, Freeman C, Jain M, Figura N. Patterns of CNS Failures in Relapse/Refractory Large B-Cell Lymphoma (LBCL) Patients with Secondary CNS Disease Following Chimeric Antigen Receptor T-Cell (CAR T) Therapy. International Journal Of Radiation Oncology • Biology • Physics 2024, 120: e646-e647. DOI: 10.1016/j.ijrobp.2024.07.1421.
• SENESCENT CELL CLEARANCE PROTECTS THE OVARIAN RESERVE IN AGING MICEZhang J, Lopez J, Liang J, Sela M, Kallen A. SENESCENT CELL CLEARANCE PROTECTS THE OVARIAN RESERVE IN AGING MICE. Fertility And Sterility 2024, 122: e21. DOI: 10.1016/j.fertnstert.2024.07.121.
• F91. MAPPING THE EFFECTS OF OPIOID USE DISORDER GENETIC ASSOCIATED VARIANTS IN BRAIN PATHWAYS AT A SINGLE CELL LEVELRivera-Hernández M, Martínez-Magaña J, Brennand K, Montalvo-Ortiz J. F91. MAPPING THE EFFECTS OF OPIOID USE DISORDER GENETIC ASSOCIATED VARIANTS IN BRAIN PATHWAYS AT A SINGLE CELL LEVEL. European Neuropsychopharmacology 2024, 87: 254. DOI: 10.1016/j.euroneuro.2024.08.502.
• 42. STRESS EXPOSURE DYNAMICALLY REGULATES EQTL ACTIVITY IN THE POST-MORTEM BRAIN AND IN HIPSC-DERIVED NEURONSSeah C, Signer R, Young H, Hicks E, Rusielewicz T, Bader H, Xu C, Breen M, Paull D, Yehuda R, Girgenti M, Brennand K, Huckins L. 42. STRESS EXPOSURE DYNAMICALLY REGULATES EQTL ACTIVITY IN THE POST-MORTEM BRAIN AND IN HIPSC-DERIVED NEURONS. European Neuropsychopharmacology 2024, 87: 71-72. DOI: 10.1016/j.euroneuro.2024.08.156.
• Deletion of miR‐33, a regulator of the ABCA1–APOE pathway, ameliorates neuropathological phenotypes in APP/PS1 miceTate M, Wijeratne H, Kim B, Philtjens S, You Y, Lee D, Gutierrez D, Sharify D, Wells M, Perez‐Cardelo M, Doud E, Fernandez‐Hernando C, Lasagna‐Reeves C, Mosley A, Kim J. Deletion of miR‐33, a regulator of the ABCA1–APOE pathway, ameliorates neuropathological phenotypes in APP/PS1 mice. Alzheimer's & Dementia 2024 PMID: 39345217, DOI: 10.1002/alz.14243.
• An efficient multiplex approach to CRISPR/Cas9 gene editing in citrusSagawa C, Thomson G, Mermaz B, Vernon C, Liu S, Jacob Y, Irish V. An efficient multiplex approach to CRISPR/Cas9 gene editing in citrus. Plant Methods 2024, 20: 148. PMID: 39342225, PMCID: PMC11438372, DOI: 10.1186/s13007-024-01274-4.
• PIWI-interacting RNAs: who, what, when, where, why, and howHaase A, Ketting R, Lai E, van Rij R, Siomi M, Svoboda P, van Wolfswinkel J, Wu P. PIWI-interacting RNAs: who, what, when, where, why, and how. The EMBO Journal 2024, 1-5. PMID: 39327528, DOI: 10.1038/s44318-024-00253-8.
• Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissuesBai Z, Zhang D, Gao Y, Tao B, Zhang D, Bao S, Enninful A, Wang Y, Li H, Su G, Tian X, Zhang N, Xiao Y, Liu Y, Gerstein M, Li M, Xing Y, Lu J, Xu M, Fan R. Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues. Cell 2024 PMID: 39353436, DOI: 10.1016/j.cell.2024.09.001.
• Single-cell CAR T atlas reveals type 2 function in 8-year leukaemia remissionBai Z, Feng B, McClory S, de Oliveira B, Diorio C, Gregoire C, Tao B, Yang L, Zhao Z, Peng L, Sferruzza G, Zhou L, Zhou X, Kerr J, Baysoy A, Su G, Yang M, Camara P, Chen S, Tang L, June C, Melenhorst J, Grupp S, Fan R. Single-cell CAR T atlas reveals type 2 function in 8-year leukaemia remission. Nature 2024, 634: 702-711. PMID: 39322664, PMCID: PMC11485231, DOI: 10.1038/s41586-024-07762-w.
• The type 2 cytokine Fc–IL-4 revitalizes exhausted CD8+ T cells against cancerFeng B, Bai Z, Zhou X, Zhao Y, Xie Y, Huang X, Liu Y, Enbar T, Li R, Wang Y, Gao M, Bonati L, Peng M, Li W, Tao B, Charmoy M, Held W, Melenhorst J, Fan R, Guo Y, Tang L. The type 2 cytokine Fc–IL-4 revitalizes exhausted CD8+ T cells against cancer. Nature 2024, 634: 712-720. PMID: 39322665, PMCID: PMC11485240, DOI: 10.1038/s41586-024-07962-4.
• Alternative translation initiation produces synaptic organizer proteoforms with distinct localization and functionsLee P, Sun Y, Soares A, Fai C, Picciotto M, Guo J. Alternative translation initiation produces synaptic organizer proteoforms with distinct localization and functions. Molecular Cell 2024, 84: 3967-3978.e8. PMID: 39317199, PMCID: PMC11490368, DOI: 10.1016/j.molcel.2024.08.032.
• Contemporary Approach to the Diagnosis and Classification of Myelodysplastic Neoplasms/Syndromes—Recommendations From the International Consortium for Myelodysplastic Neoplasms/Syndromes (MDS [icMDS])Aakash F, Gisriel S, Zeidan A, Bennett J, Bejar R, Bewersdorf J, Borate U, Boultwood J, Brunner A, Buckstein R, Carraway H, Churpek J, Daver N, DeZern A, Efficace F, Fenaux P, Figueroa M, Garcia-Manero G, Gore S, Greenberg P, Griffiths E, Halene S, Hourigan C, Kim T, Kim N, Komrokji R, Kutchroo V, List A, Little R, Majeti R, Nazha A, Nimer S, Odenike O, Padron E, Patnaik M, Platzbecker U, Della Porta M, Roboz G, Sallman D, Santini V, Sanz G, Savona M, Sekeres M, Stahl M, Starczynowski D, Steensma D, Taylor J, Abdel-Wahab O, Wei A, Xie Z, Xu M, Hasserjian R, Loghavi S. Contemporary Approach to the Diagnosis and Classification of Myelodysplastic Neoplasms/Syndromes—Recommendations From the International Consortium for Myelodysplastic Neoplasms/Syndromes (MDS [icMDS]). Modern Pathology 2024, 37: 100615. PMID: 39322118, DOI: 10.1016/j.modpat.2024.100615.
• IL-1β Induces Human Endothelial Surface Expression of IL-15 by Relieving let-7c-3p Suppression of Protein Translation.Mullan C, Summer L, Lopez-Giraldez F, Tobiasova Z, Manes T, Yasothan S, Song G, Jane-Wit D, Saltzman W, Pober J. IL-1β Induces Human Endothelial Surface Expression of IL-15 by Relieving let-7c-3p Suppression of Protein Translation. The Journal Of Immunology 2024, 213: 1338-1348. PMID: 39302113, PMCID: PMC11493510, DOI: 10.4049/jimmunol.2400331.
• Diagnostic values of BALF metagenomic next-generation sequencing, BALF real-time PCR and serum BDG for Pneumocystis jirovecii pneumonia in HIV-infected patientsChen Q, Chen X, Mo P, Chen L, Du Q, Hu W, Jiang Q, Zhang Z, Zhang Y, Guo Q, Xiong Y, Deng L. Diagnostic values of BALF metagenomic next-generation sequencing, BALF real-time PCR and serum BDG for Pneumocystis jirovecii pneumonia in HIV-infected patients. Frontiers In Microbiology 2024, 15: 1421660. PMID: 39372273, PMCID: PMC11449763, DOI: 10.3389/fmicb.2024.1421660.
• A comparative roadmap of PIWI-interacting RNAs across seven species reveals insights into de novo piRNA-precursor formation in mammalsKonstantinidou P, Loubalova Z, Ahrend F, Friman A, Almeida M, Poulet A, Horvat F, Wang Y, Losert W, Lorenzi H, Svoboda P, Miska E, van Wolfswinkel J, Haase A. A comparative roadmap of PIWI-interacting RNAs across seven species reveals insights into de novo piRNA-precursor formation in mammals. Cell Reports 2024, 43: 114777. PMID: 39302833, DOI: 10.1016/j.celrep.2024.114777.
• Protocol for detecting glycoRNAs using metabolic labeling and northwestern blotLi L, Zhang N, Pantoja C, Wang Y, Lu J. Protocol for detecting glycoRNAs using metabolic labeling and northwestern blot. STAR Protocols 2024, 5: 103321. PMID: 39298321, PMCID: PMC11426122, DOI: 10.1016/j.xpro.2024.103321.
• Improved methods for genetic manipulation of the alkaliphile Halalkalibacterium haloduransWencker F, Lyon S, Breaker R. Improved methods for genetic manipulation of the alkaliphile Halalkalibacterium halodurans. Frontiers In Microbiology 2024, 15: 1465811. PMID: 39360312, PMCID: PMC11445130, DOI: 10.3389/fmicb.2024.1465811.
• Genome-wide association study between SARS-CoV-2 single nucleotide polymorphisms and virus copies during infectionsLi K, Chaguza C, Stamp J, Chew Y, Chen N, Ferguson D, Pandya S, Kerantzas N, Schulz W, Initiative Y, Hahn A, Ogbunugafor C, Pitzer V, Crawford L, Weinberger D, Grubaugh N. Genome-wide association study between SARS-CoV-2 single nucleotide polymorphisms and virus copies during infections. PLOS Computational Biology 2024, 20: e1012469. PMID: 39288189, PMCID: PMC11432881, DOI: 10.1371/journal.pcbi.1012469.
• A new lineage nomenclature to aid genomic surveillance of dengue virusHill V, Cleemput S, Pereira J, Gifford R, Fonseca V, Tegally H, Brito A, Ribeiro G, de Souza V, Brcko I, Ribeiro I, De Lima I, Slavov S, Sampaio S, Elias M, Tran V, Kien D, Huynh T, Yacoub S, Dieng I, Salvato R, Wallau G, Gregianini T, Godinho F, Vogels C, Breban M, Leguia M, Jagtap S, Roy R, Hapuarachchi C, Mwanyika G, Giovanetti M, Alcantara L, Faria N, Carrington C, Hanley K, Holmes E, Dumon W, Lima A, de Oliveira T, Grubaugh N. A new lineage nomenclature to aid genomic surveillance of dengue virus. PLOS Biology 2024, 22: e3002834. PMID: 39283942, PMCID: PMC11426435, DOI: 10.1371/journal.pbio.3002834.
• Abstract PR-05: Endocrine beta-cell stress promotes pancreatic ductal adenocarcinoma through endocrine-exocrine cell crosstalkGarcia C, Venkat A, McQuaid D, Agabiti S, Tong A, Cardone R, Kibbey R, Krishnaswamy S, Muzumdar M. Abstract PR-05: Endocrine beta-cell stress promotes pancreatic ductal adenocarcinoma through endocrine-exocrine cell crosstalk. Cancer Research 2024, 84: pr-05-pr-05. DOI: 10.1158/1538-7445.pancreatic24-pr-05.
• Abstract PR-01: Systemic targeting of therapeutic RNA to pancreatic ductal adenocarcinoma via a novel, cell-penetrating, and nucleic acid-binding monoclonal antibodyMartinez-Saucedo D, Quijano E, Ianniello Z, Rackear M, Liu Y, Hegan D, Chen H, Shan X, Tseng R, Yugawa D, Pinto-Medici N, Chowdhury S, Bindra R, Robert M, Saltzman W, Escobar-Hoyos L, Glazer P. Abstract PR-01: Systemic targeting of therapeutic RNA to pancreatic ductal adenocarcinoma via a novel, cell-penetrating, and nucleic acid-binding monoclonal antibody. Cancer Research 2024, 84: pr-01-pr-01. DOI: 10.1158/1538-7445.pancreatic24-pr-01.
• Abstract C030: Evolutionary and epistatic analyses reveal genic interactions with KRAS during malignant progression of pancreatic ductal adenocarcinomaFisk N, Song D, Moore M, Jensen C, Cannataro V, Nagib M, Mandell J, Escobar-Hoyos L, Kunstman J, Townsend J. Abstract C030: Evolutionary and epistatic analyses reveal genic interactions with KRAS during malignant progression of pancreatic ductal adenocarcinoma. Cancer Research 2024, 84: c030-c030. DOI: 10.1158/1538-7445.pancreatic24-c030.
• Abstract PR-11: Altered mRNA splicing mimics chromosome loss and drives pancreatic cancerMedici N, Martinez-Saucedo D, Lee D, Chu T, Tseng R, Cannataro V, Townsend J, Iacobuzio-Donahue C, Robert M, Abdel-Wahab O, Leach S, Escobar-Hoyos L. Abstract PR-11: Altered mRNA splicing mimics chromosome loss and drives pancreatic cancer. Cancer Research 2024, 84: pr-11-pr-11. DOI: 10.1158/1538-7445.pancreatic24-pr-11.
• Abstract B083: The splicing factor SMNDC1 facilitates alternative RNA splicing, contributing to therapy resistance in pancreatic cancerSiraj M, Zhang Y, Yugawa D, Giri G, Chakraborty P, Goda G, Rao G, Dominguez D, Kubicek S, Bhattacharya R, Escobar-Hoyos L, Mukherjee P. Abstract B083: The splicing factor SMNDC1 facilitates alternative RNA splicing, contributing to therapy resistance in pancreatic cancer. Cancer Research 2024, 84: b00-b00. DOI: 10.1158/1538-7445.pancreatic24-b083.
• Abstract B079: Disassembly of embryonic keratin filaments promotes pancreatic cancer metastasesYugawa D, Kawalerski R, Gonçalves M, Pan C, Tseng R, Roa-Pena L, Leiton C, Torre-Healy L, Boyle T, Chowdhury S, Snider N, Shroyer K, Escobar-Hoyos L. Abstract B079: Disassembly of embryonic keratin filaments promotes pancreatic cancer metastases. Cancer Research 2024, 84: b079-b079. DOI: 10.1158/1538-7445.pancreatic24-b079.
• Abstract C031: Keratin 17 promotes pancreatic cancer chemoresistance through mitochondrial translocation and stabilization of dihydroorotate dehydrogenase (DHODH)Lyu Y, Ghosh M, Pan C, Sarkar S, Rajacharya G, Chen B, Marchenko N, Singh P, Shroyer K, Escobar-Hoyos L. Abstract C031: Keratin 17 promotes pancreatic cancer chemoresistance through mitochondrial translocation and stabilization of dihydroorotate dehydrogenase (DHODH). Cancer Research 2024, 84: c031-c031. DOI: 10.1158/1538-7445.pancreatic24-c031.
• Abstract C070: Keratin 17 and GATA6 correlate with diffusely infiltrative versus gland-forming components of PDAC: Uncovering the transitional state in pancreatic ductal adenocarcinomaDelgado- Coka L, Nelson B, Horowitz M, Sarkar S, Marchenko N, Powers S, Escobar-Hoyos L, Shroyer K. Abstract C070: Keratin 17 and GATA6 correlate with diffusely infiltrative versus gland-forming components of PDAC: Uncovering the transitional state in pancreatic ductal adenocarcinoma. Cancer Research 2024, 84: c070-c070. DOI: 10.1158/1538-7445.pancreatic24-c070.
• Organization of a functional glycolytic metabolon on mitochondria for metabolic efficiencyWang H, Vant J, Zhang A, Sanchez R, Wu Y, Micou M, Luczak V, Whiddon Z, Carlson N, Yu S, Jabbo M, Yoon S, Abushawish A, Ghassemian M, Masubuchi T, Gan Q, Watanabe S, Griffis E, Hammarlund M, Singharoy A, Pekkurnaz G. Organization of a functional glycolytic metabolon on mitochondria for metabolic efficiency. Nature Metabolism 2024, 6: 1712-1735. PMID: 39261628, DOI: 10.1038/s42255-024-01121-9.
• HIV-1 usurps mixed-charge domain-dependent CPSF6 phase separation for higher-order capsid binding, nuclear entry and viral DNA integrationJang S, Bedwell G, Singh S, Yu H, Arnarson B, Singh P, Radhakrishnan R, Douglas A, Ingram Z, Freniere C, Akkermans O, Sarafianos S, Ambrose Z, Xiong Y, Anekal P, Llopis P, KewalRamani V, Francis A, Engelman A. HIV-1 usurps mixed-charge domain-dependent CPSF6 phase separation for higher-order capsid binding, nuclear entry and viral DNA integration. Nucleic Acids Research 2024, 52: 11060-11082. PMID: 39258548, PMCID: PMC11472059, DOI: 10.1093/nar/gkae769.
• RluA is the major mRNA pseudouridine synthase in Escherichia coliSchaening-Burgos C, LeBlanc H, Fagre C, Li G, Gilbert W. RluA is the major mRNA pseudouridine synthase in Escherichia coli. PLOS Genetics 2024, 20: e1011100. PMID: 39241085, PMCID: PMC11421799, DOI: 10.1371/journal.pgen.1011100.
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