# Functional Genomics Publications ## Acknowledging ICCB-L in Publications Researchers using the services of ICCB-L staff or equipment agree to acknowledge the support of '*ICCB-Longwood Screening Facility at Harvard Medical School*' in publications arising from your use of the facility. If an ICCB-L member has made an important intellectual contribution to the project, as determined by generally accepted criteria for academic collaborations, then that person should be considered for authorship on the publication. If your project was supported by a grant that also directly supports the ICCB-L, please consult the ICCB-L Director regarding the appropriate grant citation. Please notify Jen Smith upon public release of your publication. Below is a list of publications that have resulted from RNAi screening efforts at ICCB-Longwood. Please notify us of your publications that involve use of the ICCB-Longwood Screening Facility. Download 87 citations download- [BibTeX](/bibcite/export?pager_style=standard_pager&number_of_items=30&sort_field=bibcite_year--desc&taxonomy_filters%5Bfield_hwp_c_publicationcategory%5D%5B0%5D%5Btarget_id%5D=110776&&&format=bibtex) - [EndNote X3 XML](/bibcite/export?pager_style=standard_pager&number_of_items=30&sort_field=bibcite_year--desc&taxonomy_filters%5Bfield_hwp_c_publicationcategory%5D%5B0%5D%5Btarget_id%5D=110776&&&format=endnote8) - [EndNote 7 XML](/bibcite/export?pager_style=standard_pager&number_of_items=30&sort_field=bibcite_year--desc&taxonomy_filters%5Bfield_hwp_c_publicationcategory%5D%5B0%5D%5Btarget_id%5D=110776&&&format=endnote7) - [Endnote tagged](/bibcite/export?pager_style=standard_pager&number_of_items=30&sort_field=bibcite_year--desc&taxonomy_filters%5Bfield_hwp_c_publicationcategory%5D%5B0%5D%5Btarget_id%5D=110776&&&format=tagged) - [Marc](/bibcite/export?pager_style=standard_pager&number_of_items=30&sort_field=bibcite_year--desc&taxonomy_filters%5Bfield_hwp_c_publicationcategory%5D%5B0%5D%5Btarget_id%5D=110776&&&format=marc) - [PubMedId](/bibcite/export?pager_style=standard_pager&number_of_items=30&sort_field=bibcite_year--desc&taxonomy_filters%5Bfield_hwp_c_publicationcategory%5D%5B0%5D%5Btarget_id%5D=110776&&&format=pubmed_id) - [RIS](/bibcite/export?pager_style=standard_pager&number_of_items=30&sort_field=bibcite_year--desc&taxonomy_filters%5Bfield_hwp_c_publicationcategory%5D%5B0%5D%5Btarget_id%5D=110776&&&format=ris) ### 2025 Li W, Sparks RP, Sun C, Yang Y, Pantano L, Kirchner R, Arghiani N, Weilheimer A, Toles BJ, Chen JY, Moran SP, Barrera V, Li Z, Zhou P, Brassil ML, Wrobel D, Sui SJH, Aspnes G, Schuler M, Smith J, Medoff BD, Zhou C, Boustany-Kari CM, Rippmann JF, Santos DM, Doerner JF, Mullen AC. [Screening the human druggable genome identifies ABHD17B as an anti-fibrotic target in hepatic stellate cells.](https://pmc.ncbi.nlm.nih.gov/articles/PMC11873113/) Nature communications. 2025;16(1):2109. PMID: 40025044 Li W, Sparks RP, Sun C, Yang Y, Pantano L, Kirchner R, Arghiani N, Weilheimer A, Toles BJ, Chen JY, Moran SP, Barrera V, Li Z, Zhou P, Brassil ML, Wrobel D, Sui SJH, Aspnes G, Schuler M, Smith J, Medoff BD, Zhou C, Boustany-Kari CM, Rippmann JF, Santos DM, Doerner JF, Mullen AC. [Screening the human druggable genome identifies ABHD17B as an anti-fibrotic target in hepatic stellate cells.](https://pmc.ncbi.nlm.nih.gov/articles/PMC11873113/) Nature communications. 2025;16(1):2109. PMID: 40025044 - add\_circle do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://www.nature.com/articles/s41467-025-56900-z) Hepatic stellate cells (HSCs) are activated with chronic liver injury and transdifferentiate into myofibroblasts, which produce excessive extracellular matrices that form the fibrotic scar. While the progression of fibrosis is understood to be the cause... - [ descriptionPublisher's Version](https://www.nature.com/articles/s41467-025-56900-z) Chong SJF, Lu J, Valentin R, Lehmberg TZ, Eu JQ, Wang J, Zhu F, Kong LR, Fernandes SM, Zhang J, Herbaux C, Goh BC, Brown JR, Niemann CU, Huber W, Zenz T, Davids MS. [BCL-2 dependence is a favorable predictive marker of response to therapy for chronic lymphocytic leukemia.](https://pmc.ncbi.nlm.nih.gov/articles/PMC11874845/) Molecular cancer. 2025;24(1):62. PMID: 40025512 Chong SJF, Lu J, Valentin R, Lehmberg TZ, Eu JQ, Wang J, Zhu F, Kong LR, Fernandes SM, Zhang J, Herbaux C, Goh BC, Brown JR, Niemann CU, Huber W, Zenz T, Davids MS. [BCL-2 dependence is a favorable predictive marker of response to therapy for chronic lymphocytic leukemia.](https://pmc.ncbi.nlm.nih.gov/articles/PMC11874845/) Molecular cancer. 2025;24(1):62. PMID: 40025512 - add\_circle do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://link.springer.com/article/10.1186/s12943-025-02260-7) **BACKGROUND:** Established genetic biomarkers in chronic lymphocytic leukemia (CLL) have been useful in predicting response to chemoimmunotherapy but are less predictive of response to targeted therapies. With several such targeted therapies now approved for... - [ descriptionPublisher's Version](https://link.springer.com/article/10.1186/s12943-025-02260-7) ### 2024 Chang KC, Silvestri F, Oliphant MUJ, Martinez-Gakidis A, Orgill DP, Garber JE, Dillon DD, Brugge JS. [Breast organoid suspension cultures maintain long-term estrogen receptor expression and responsiveness.](https://pmc.ncbi.nlm.nih.gov/articles/PMC11659324/) NPJ breast cancer. 2024;10(1):107. PMID: 39702422 Chang KC, Silvestri F, Oliphant MUJ, Martinez-Gakidis A, Orgill DP, Garber JE, Dillon DD, Brugge JS. [Breast organoid suspension cultures maintain long-term estrogen receptor expression and responsiveness.](https://pmc.ncbi.nlm.nih.gov/articles/PMC11659324/) NPJ breast cancer. 2024;10(1):107. PMID: 39702422 - add\_circle do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://www.nature.com/articles/s41523-024-00714-7) Organoid cultures offer a powerful technology to investigate many different aspects of development, physiology, and pathology of diverse tissues. Unlike standard tissue culture of primary breast epithelial cells, breast organoids preserve the epithelial... - [ descriptionPublisher's Version](https://www.nature.com/articles/s41523-024-00714-7) Kilgas S, Syed A, Toolan-Kerr P, Swift ML, Roychoudhury S, Sarkar A, Wilkins S, Quigley M, Poetsch AR, Botuyan MV, Cui G, Mer G, Ule J, Drané P, Chowdhury D. [NEAT1 modulates the TIRR/53BP1 complex to maintain genome integrity.](https://pmc.ncbi.nlm.nih.gov/articles/PMC11443056/) Nature communications. 2024;15(1):8438. PMID: 39349456 Kilgas S, Syed A, Toolan-Kerr P, Swift ML, Roychoudhury S, Sarkar A, Wilkins S, Quigley M, Poetsch AR, Botuyan MV, Cui G, Mer G, Ule J, Drané P, Chowdhury D. [NEAT1 modulates the TIRR/53BP1 complex to maintain genome integrity.](https://pmc.ncbi.nlm.nih.gov/articles/PMC11443056/) Nature communications. 2024;15(1):8438. PMID: 39349456 - add\_circle do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://www.nature.com/articles/s41467-024-52862-w) Tudor Interacting Repair Regulator (TIRR) is an RNA-binding protein (RBP) that interacts directly with 53BP1, restricting its access to DNA double-strand breaks (DSBs) and its association with p53. We utilized iCLIP to identify RNAs that directly bind to... - [ descriptionPublisher's Version](https://www.nature.com/articles/s41467-024-52862-w) Chidley C, Darnell A, Gaudio B, Lien E, Barbeau A, Vander-Heiden M, Sorger P. [A CRISPRi/a screening platform to study cellular nutrient transport in diverse microenvironments](https://pubmed.ncbi.nlm.nih.gov/38605144/). Nat Cell Biol. 2024;(11 April). Chidley C, Darnell A, Gaudio B, Lien E, Barbeau A, Vander-Heiden M, Sorger P. [A CRISPRi/a screening platform to study cellular nutrient transport in diverse microenvironments](https://pubmed.ncbi.nlm.nih.gov/38605144/). Nat Cell Biol. 2024;(11 April). - [ descriptionPublisher's Version](https://www.nature.com/articles/s41556-024-01402-1) - [ descriptionPublisher's Version](https://www.nature.com/articles/s41556-024-01402-1) ### 2023 Durall R, Huang J, Wojenski L, Huang Y, Gokhale P, Leeper B, Nash J, Ballester P, Davidson S, Shlien A, Sotirakis E, Bertaux F, Dubus V, Luo J, Wu C, Keskin D, Eagen K, Shapiro G, French C. [The BRD4-NUT fusion alone drives malignant transformation of NUT carcinoma](https://pubmed.ncbi.nlm.nih.gov/37819236/). Cancer Res. 2023;(Oct 11). Durall R, Huang J, Wojenski L, Huang Y, Gokhale P, Leeper B, Nash J, Ballester P, Davidson S, Shlien A, Sotirakis E, Bertaux F, Dubus V, Luo J, Wu C, Keskin D, Eagen K, Shapiro G, French C. [The BRD4-NUT fusion alone drives malignant transformation of NUT carcinoma](https://pubmed.ncbi.nlm.nih.gov/37819236/). Cancer Res. 2023;(Oct 11). - [ descriptionPublisher's Version](https://aacrjournals.org/cancerres/article/doi/10.1158/0008-5472.CAN-23-2545/729540/The-BRD4-NUT-fusion-alone-drives-malignant) - [ descriptionPublisher's Version](https://aacrjournals.org/cancerres/article/doi/10.1158/0008-5472.CAN-23-2545/729540/The-BRD4-NUT-fusion-alone-drives-malignant) Chen DY, Chin C, Kenney D, Tavares A, Khan N, Conway H, Liu G, Choudhary M, Gertje H, O’Connell A, Adams S, Kotton D, Herrmann A, Ensser A, Connor J, Bosmann M, Li J, Gack M, Baker S, Kirchdoerfer R, Kataria Y, Crossland N, Douam F, Saeed M. [Spike and nsp6 are key determinants of SARS-CoV-2 Omicron BA.1 attenuation](https://pubmed.ncbi.nlm.nih.gov/36630998/). Nature. 2023;615:143–150. Chen DY, Chin C, Kenney D, Tavares A, Khan N, Conway H, Liu G, Choudhary M, Gertje H, O’Connell A, Adams S, Kotton D, Herrmann A, Ensser A, Connor J, Bosmann M, Li J, Gack M, Baker S, Kirchdoerfer R, Kataria Y, Crossland N, Douam F, Saeed M. [Spike and nsp6 are key determinants of SARS-CoV-2 Omicron BA.1 attenuation](https://pubmed.ncbi.nlm.nih.gov/36630998/). Nature. 2023;615:143–150. - [ descriptionPublisher's Version](https://www.nature.com/articles/s41586-023-05697-2) - [ descriptionPublisher's Version](https://www.nature.com/articles/s41586-023-05697-2) Schmaier A, Anderson P, Chen S, El-Darzi E, Aivasovsky I, Kaushik M, Sack K, Hartzell H, Parikh S, Flaumenhaft, Schulman S. [TMEM16E regulates endothelial cell procoagulant activity and thrombosis](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10231993/). J Clin Invest. 2023;133(11):e163808. Schmaier A, Anderson P, Chen S, El-Darzi E, Aivasovsky I, Kaushik M, Sack K, Hartzell H, Parikh S, Flaumenhaft, Schulman S. [TMEM16E regulates endothelial cell procoagulant activity and thrombosis](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10231993/). J Clin Invest. 2023;133(11):e163808. - [ descriptionPublisher's Version](https://www.jci.org/articles/view/163808) - [ descriptionPublisher's Version](https://www.jci.org/articles/view/163808) Jovanović B, Temko D, Stevens L, Seehawer M, Fassl A, Murphy K, Anand J, Garza K, Gulvady A, Qiu X, Harper N, Daniels V, Xiao-Yun H, Ge J, Alečković M, Pyrdol J, Hinohara K, Egri S, Papanastasiou M, Vadhi R, Font-Tello A, Witwicki R, Peluffo G, Trinh A, Shu S, Diciaccio B, Ekram M, Subedee A, Herbert Z, Wucherpfennig K, Letai A, Jaffe J, Sicinski P, Brown M, Dillon D, Long H, Michor, Polyak K. [Heterogeneity and transcriptional drivers of triple-negative breast cancer](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10842760/). Cell Rep. 2023;42(12):113564. Jovanović B, Temko D, Stevens L, Seehawer M, Fassl A, Murphy K, Anand J, Garza K, Gulvady A, Qiu X, Harper N, Daniels V, Xiao-Yun H, Ge J, Alečković M, Pyrdol J, Hinohara K, Egri S, Papanastasiou M, Vadhi R, Font-Tello A, Witwicki R, Peluffo G, Trinh A, Shu S, Diciaccio B, Ekram M, Subedee A, Herbert Z, Wucherpfennig K, Letai A, Jaffe J, Sicinski P, Brown M, Dillon D, Long H, Michor, Polyak K. [Heterogeneity and transcriptional drivers of triple-negative breast cancer](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10842760/). Cell Rep. 2023;42(12):113564. - [ descriptionPublisher's Version](https://www.cell.com/cell-reports/fulltext/S2211-1247(23)01576-0?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2211124723015760%3Fshowall%3Dtrue) - [ descriptionPublisher's Version](https://www.cell.com/cell-reports/fulltext/S2211-1247(23)01576-0?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2211124723015760%3Fshowall%3Dtrue) Park D, Nguyen S, Isenhart R, Shah P, Kim W, Barnett R, Chandra A, Luppino J, Harke J, Wai M, Walsh P, Abdill R, Yang R, Lan Y, Yoon S, Yunker R, Kanemaki M, Vahedi G, Phillips-Cremins J, Jain R, Joyce E. [High-throughput Oligopaint screen identifies druggable 3D genome regulators](https://pubmed.ncbi.nlm.nih.gov/37438531/). Nature. 2023;620:209–217. Park D, Nguyen S, Isenhart R, Shah P, Kim W, Barnett R, Chandra A, Luppino J, Harke J, Wai M, Walsh P, Abdill R, Yang R, Lan Y, Yoon S, Yunker R, Kanemaki M, Vahedi G, Phillips-Cremins J, Jain R, Joyce E. [High-throughput Oligopaint screen identifies druggable 3D genome regulators](https://pubmed.ncbi.nlm.nih.gov/37438531/). Nature. 2023;620:209–217. ### 2022 Martínez-Noël, Szajner, Kramer R, Boyland K, Sheikh, Smith J, Howley P. [Identification of MicroRNAs That Stabilize p53 in Human Papillomavirus-Positive Cancer Cells](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8865425/). J Virol. 2022;96(4). Martínez-Noël, Szajner, Kramer R, Boyland K, Sheikh, Smith J, Howley P. [Identification of MicroRNAs That Stabilize p53 in Human Papillomavirus-Positive Cancer Cells](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8865425/). J Virol. 2022;96(4). Vora S, Fontana P, Mao T, Leger V, Zhang Y, Fu TM, Lieberman, Gehrke L, Shi M, Wang L, Iwasaki A, Wu. [Targeting stem-loop 1 of the SARS-CoV-2 5’ UTR to suppress viral translation and Nsp1 evasion](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8892331/). Proc Natl Acad Sci U S A. 2022;119(9):e2117198119. Vora S, Fontana P, Mao T, Leger V, Zhang Y, Fu TM, Lieberman, Gehrke L, Shi M, Wang L, Iwasaki A, Wu. [Targeting stem-loop 1 of the SARS-CoV-2 5’ UTR to suppress viral translation and Nsp1 evasion](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8892331/). Proc Natl Acad Sci U S A. 2022;119(9):e2117198119. - [ descriptionPublisher's Version](https://www.pnas.org/doi/full/10.1073/pnas.2117198119) - [ descriptionPublisher's Version](https://www.pnas.org/doi/full/10.1073/pnas.2117198119) Jutzi J, Marneth A, Ciboddo M, Guerra-Moreno A, Jiménez-Santos M, Kosmidou A, Dressman J, Liang H, Hamel R, Lozano P, Rumi E, Doench J, Gotlib J, Krishnan A, Elf S, Al-Shahrour F, Mullally A. [Whole-genome CRISPR screening identifies N-glycosylation as a genetic and therapeutic vulnerability in CALR-mutant MPNs](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9479036/). Blood. 2022;140(11):1291–1304. Jutzi J, Marneth A, Ciboddo M, Guerra-Moreno A, Jiménez-Santos M, Kosmidou A, Dressman J, Liang H, Hamel R, Lozano P, Rumi E, Doench J, Gotlib J, Krishnan A, Elf S, Al-Shahrour F, Mullally A. [Whole-genome CRISPR screening identifies N-glycosylation as a genetic and therapeutic vulnerability in CALR-mutant MPNs](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9479036/). Blood. 2022;140(11):1291–1304. - [ descriptionPublisher's Version](https://ashpublications.org/blood/article/140/11/1291/485707/Whole-genome-CRISPR-screening-identifies-N) - [ descriptionPublisher's Version](https://ashpublications.org/blood/article/140/11/1291/485707/Whole-genome-CRISPR-screening-identifies-N) Coverdell T, Abraham-Fan RJ, Wu C, Abbott S, Campbell J. [Genetic encoding of an esophageal motor circuit](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9255432/). Cell Rep. 2022;39(11):110962. Coverdell T, Abraham-Fan RJ, Wu C, Abbott S, Campbell J. [Genetic encoding of an esophageal motor circuit](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9255432/). Cell Rep. 2022;39(11):110962. - [ descriptionPublisher's Version](https://www.sciencedirect.com/science/article/pii/S2211124722007446?via%3Dihub) - [ descriptionPublisher's Version](https://www.sciencedirect.com/science/article/pii/S2211124722007446?via%3Dihub) Boekell K, Brown B, Talbot B, Schlondorff J. [Trpc6 gain-of-function disease mutation enhances phosphatidylserine exposure in murine platelets](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9231752/). PLoS One. 2022;17(6):e0270431. Boekell K, Brown B, Talbot B, Schlondorff J. [Trpc6 gain-of-function disease mutation enhances phosphatidylserine exposure in murine platelets](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9231752/). PLoS One. 2022;17(6):e0270431. - [ descriptionPublisher's Version](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0270431) - [ descriptionPublisher's Version](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0270431) ### 2021 Chu V, Feng Q, Lim Y, Shao S. [Selective destabilization of polypeptides synthesized from NMD-targeted transcripts](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8694075/). Mol Biol Cell. 2021;32(22):ar38. Chu V, Feng Q, Lim Y, Shao S. [Selective destabilization of polypeptides synthesized from NMD-targeted transcripts](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8694075/). Mol Biol Cell. 2021;32(22):ar38. - [ descriptionPublisher's Version](https://www.molbiolcell.org/doi/10.1091/mbc.E21-08-0382) - [ descriptionPublisher's Version](https://www.molbiolcell.org/doi/10.1091/mbc.E21-08-0382) Tasdemir-Yilmaz O, Druckenbrod N, Olukoya O, Dong W, Yung A, Bastille I, Pazyra-Murphy M, Sitko A, Hale E, Vigneau S, Gimelbrant A, Kharchenko P, Goodrich L, Segal R. [Diversity of developing peripheral glia revealed by single-cell RNA sequencing](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8442251/). Dev Cell. 2021;56(17):2516–2535. Tasdemir-Yilmaz O, Druckenbrod N, Olukoya O, Dong W, Yung A, Bastille I, Pazyra-Murphy M, Sitko A, Hale E, Vigneau S, Gimelbrant A, Kharchenko P, Goodrich L, Segal R. [Diversity of developing peripheral glia revealed by single-cell RNA sequencing](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8442251/). 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