1
|
Mehta A, Bi L, Al'Khafaji A, Jankowiak M, Parikh M, Babadi M, Bloemendal A, Schwartz M, Munson G, Chan J, Burdziak C, Donnard E, Park R, Lu C, Rigollet P, Aguirre A, Subramanian V, Jones R, Lander ES, Ting DT, Pe'er D, Hacohen N. Abstract B016: Quantifying and dissecting pancreatic cancer cell phenotypic plasticity using lineage tracing, single-cell multiomics and CRISPR perturbations reveals novel regulators of plastic states. Cancer Res 2022. [DOI: 10.1158/1538-7445.panca22-b016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Abstract
Pancreatic cancer is a lethal disease in part because tumor cells exist in distinct transcriptional phenotypes (e.g. basal and classical states), each with a selective ability to evade current chemotherapy regimens. Two major mechanisms have been suggested for treatment evasion: 1) intrinsic resistance of certain phenotypes to particular chemotherapy regimens and 2) plasticity of treatment sensitive phenotypes to adopt more resistant phenotypes. However, the relative contribution of these mechanisms to treatment resistance is still poorly understood. Whereas previous work has described the redistribution of tumor cell states under selective treatment pressure, there is no direct evidence that tumor cells exhibit phenotypic plasticity at steady state or with treatment. By leveraging technological advancements in single-cell methods, lineage tracing and functional genomics, we have now shown direct evidence of phenotypic state switching in human pancreatic cancer cell lines. By performing single-cell RNA-seq on 5 barcoded PDAC cell lines over a steady state timecourse and under chemotherapy selective pressure (>600k cells total), we identify unique plasticity phenotypes within these cell lines and infer regulators of these plastic states. We validate the role of several of these regulators using bulk phenotypic CRISPRi screens in these cell lines. We next perform CRISPRi perturbations along with lineage tracing and single-cell multiomics (>300k cells) to dissect the regulatory relationships that underlie these cell states. We identify several novel epithelial and mesenchymal biasing factors, including those with unique roles in the most plastic clones. Collectively, we nominate several regulators that bias PDAC cell states thus posing a paradigm whereby perturbations may be used to homogenize tumor populations towards treatment-sensitive phenotypes. We believe this approach combined with current chemotherapy regimens could benefit pancreatic cancer patients by targeting residual, resistant tumor cells in the localized and metastatic disease settings to improve patient survival.
Citation Format: Arnav Mehta, Lynn Bi, Aziz Al'Khafaji, Martin Jankowiak, Milan Parikh, Mehrtash Babadi, Alex Bloemendal, Marc Schwartz, Glen Munson, Joeseph Chan, Cassandra Burdziak, Elisa Donnard, Ryan Park, Chen Lu, Philippe Rigollet, Andrew Aguirre, Vidya Subramanian, Ray Jones, Eric S. Lander, David T. Ting, Dana Pe'er, Nir Hacohen. Quantifying and dissecting pancreatic cancer cell phenotypic plasticity using lineage tracing, single-cell multiomics and CRISPR perturbations reveals novel regulators of plastic states [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr B016.
Collapse
Affiliation(s)
- Arnav Mehta
- 1Broad Institute of MIT and Harvard, Cambridge, MA,
| | - Lynn Bi
- 1Broad Institute of MIT and Harvard, Cambridge, MA,
| | | | | | - Milan Parikh
- 1Broad Institute of MIT and Harvard, Cambridge, MA,
| | | | | | | | - Glen Munson
- 1Broad Institute of MIT and Harvard, Cambridge, MA,
| | - Joeseph Chan
- 2Memorial Sloan Kettering Cancer Center, New York, NY,
| | | | | | - Ryan Park
- 1Broad Institute of MIT and Harvard, Cambridge, MA,
| | - Chen Lu
- 3Massachusetts Institute of Technology, Cambridge, MA,
| | | | | | | | - Ray Jones
- 1Broad Institute of MIT and Harvard, Cambridge, MA,
| | | | | | - Dana Pe'er
- 2Memorial Sloan Kettering Cancer Center, New York, NY,
| | - Nir Hacohen
- 1Broad Institute of MIT and Harvard, Cambridge, MA,
| |
Collapse
|
2
|
Shin M, Chan IL, Cao Y, Gruntman AM, Lee J, Sousa J, Rodríguez TC, Echeverria D, Devi G, Debacker AJ, Moazami MP, Krishnamurthy PM, Rembetsy-Brown JM, Kelly K, Yukselen O, Donnard E, Parsons TJ, Khvorova A, Sontheimer EJ, Maehr R, Garber M, Watts JK. Intratracheally administered LNA gapmer antisense oligonucleotides induce robust gene silencing in mouse lung fibroblasts. Nucleic Acids Res 2022; 50:8418-8430. [PMID: 35920332 PMCID: PMC9410908 DOI: 10.1093/nar/gkac630] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/29/2022] [Accepted: 07/28/2022] [Indexed: 11/12/2022] Open
Abstract
The lung is a complex organ with various cell types having distinct roles. Antisense oligonucleotides (ASOs) have been studied in the lung, but it has been challenging to determine their effectiveness in each cell type due to the lack of appropriate analytical methods. We employed three distinct approaches to study silencing efficacy within different cell types. First, we used lineage markers to identify cell types in flow cytometry, and simultaneously measured ASO-induced silencing of cell-surface proteins CD47 or CD98. Second, we applied single-cell RNA sequencing (scRNA-seq) to measure silencing efficacy in distinct cell types; to the best of our knowledge, this is the first time scRNA-seq has been applied to measure the efficacy of oligonucleotide therapeutics. In both approaches, fibroblasts were the most susceptible to locally delivered ASOs, with significant silencing also in endothelial cells. Third, we confirmed that the robust silencing in fibroblasts is broadly applicable by silencing two targets expressed mainly in fibroblasts, Mfap4 and Adam33. Across independent approaches, we demonstrate that intratracheally administered LNA gapmer ASOs robustly induce gene silencing in lung fibroblasts. ASO-induced gene silencing in fibroblasts was durable, lasting 4-8 weeks after a single dose. Thus, lung fibroblasts are well aligned with ASOs as therapeutics.
Collapse
Affiliation(s)
- Minwook Shin
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Io Long Chan
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Yuming Cao
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Alisha M Gruntman
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.,Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.,Department of Clinical Sciences, Cummings School of Veterinary Medicine at Tufts University, N. Grafton, MA 01536, USA
| | - Jonathan Lee
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Jacquelyn Sousa
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Tomás C Rodríguez
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Gitali Devi
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Alexandre J Debacker
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Michael P Moazami
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | | | - Julia M Rembetsy-Brown
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Karen Kelly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Onur Yukselen
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Elisa Donnard
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Teagan J Parsons
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.,Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.,Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.,Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.,Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - René Maehr
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.,Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Manuel Garber
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.,Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Jonathan K Watts
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.,Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.,Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| |
Collapse
|
3
|
Donnard E, Shu H, Garber M. Single cell transcriptomics reveals dysregulated cellular and molecular networks in a fragile X syndrome model. PLoS Genet 2022; 18:e1010221. [PMID: 35675353 PMCID: PMC9212148 DOI: 10.1371/journal.pgen.1010221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 06/21/2022] [Accepted: 04/27/2022] [Indexed: 02/07/2023] Open
Abstract
Despite advances in understanding the pathophysiology of Fragile X syndrome (FXS), its molecular basis is still poorly understood. Whole brain tissue expression profiles have proved surprisingly uninformative, therefore we applied single cell RNA sequencing to profile an FMRP deficient mouse model with higher resolution. We found that the absence of FMRP results in highly cell type specific gene expression changes that are strongest among specific neuronal types, where FMRP-bound mRNAs were prominently downregulated. Metabolic pathways including translation and respiration are significantly upregulated across most cell types with the notable exception of excitatory neurons. These effects point to a potential difference in the activity of mTOR pathways, and together with other dysregulated pathways, suggest an excitatory-inhibitory imbalance in the Fmr1-knock out cortex that is exacerbated by astrocytes. Our data demonstrate that FMRP loss affects abundance of key cellular communication genes that potentially affect neuronal synapses and provide a resource for interrogating the biological basis of this disorder. Fragile X syndrome is a leading genetic cause of inherited intellectual disability and autism spectrum disorder. It results from the inactivation of a single gene, FMR1 and hence the loss of its encoded protein FMRP. Despite decades of intensive research, we still lack an overview of the molecular and biological consequences of the disease. Using single cell RNA sequencing, we profiled cells from the brain of healthy mice and of knock-out mice lacking the FMRP protein, a common model for this disease, to identify molecular changes that happen across different cell types. We find neurons are the most impacted cell type, where genes in multiple pathways are similarly impacted. This includes transcripts known to be bound by FMRP, which are collectively decreased only in neurons but not in other cell types. Our results show how the loss of FMRP affects the intricate interactions between different brain cell types, which could provide new perspectives to the development of therapeutic interventions.
Collapse
Affiliation(s)
- Elisa Donnard
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail: (ED); (HS); (MG)
| | - Huan Shu
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail: (ED); (HS); (MG)
| | - Manuel Garber
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Department of Dermatology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail: (ED); (HS); (MG)
| |
Collapse
|
4
|
Wang IH, Murray E, Andrews G, Jiang HC, Park SJ, Donnard E, Durán-Laforet V, Bear DM, Faust TE, Garber M, Baer CE, Schafer DP, Weng Z, Chen F, Macosko EZ, Greer PL. Spatial transcriptomic reconstruction of the mouse olfactory glomerular map suggests principles of odor processing. Nat Neurosci 2022; 25:484-492. [PMID: 35314823 PMCID: PMC9281876 DOI: 10.1038/s41593-022-01030-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 02/07/2022] [Indexed: 12/14/2022]
Abstract
The olfactory system's ability to detect and discriminate between the vast array of chemicals present in the environment is critical for an animal's survival. In mammals, the first step of this odor processing is executed by olfactory sensory neurons, which project their axons to a stereotyped location in the olfactory bulb (OB) to form glomeruli. The stereotyped positioning of glomeruli in the OB suggests an importance for this organization in odor perception. However, because the location of only a limited subset of glomeruli has been determined, it has been challenging to determine the relationship between glomerular location and odor discrimination. Using a combination of single-cell RNA sequencing, spatial transcriptomics and machine learning, we have generated a map of most glomerular positions in the mouse OB. These observations significantly extend earlier studies and suggest an overall organizational principle in the OB that may be used by the brain to assist in odor decoding.
Collapse
Affiliation(s)
- I-Hao Wang
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Evan Murray
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Greg Andrews
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Hao-Ching Jiang
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Sung Jin Park
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Elisa Donnard
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Violeta Durán-Laforet
- Department of Neurobiology and Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Daniel M Bear
- Department of Psychology, Stanford University, Palo Alto, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Palo Alto, CA, USA
| | - Travis E Faust
- Department of Neurobiology and Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Manuel Garber
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Christina E Baer
- Sanderson Center for Optical Imaging and Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
| | - Dorothy P Schafer
- Department of Neurobiology and Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Fei Chen
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Evan Z Macosko
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Paul L Greer
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.
| |
Collapse
|
5
|
Abstract
Fragile X syndrome (FXS) is caused by inactivation of the FMR1 gene and loss of encoded FMRP, an RNA binding protein that represses translation of some of its target transcripts. Here we use ribosome profiling and RNA sequencing to investigate the dysregulation of translation in the mouse brain cortex. We find that most changes in ribosome occupancy on hundreds of mRNAs are largely driven by dysregulation in transcript abundance. Many down-regulated mRNAs, which are mostly responsible for neuronal and synaptic functions, are highly enriched for FMRP binding targets. RNA metabolic labeling demonstrates that, in FMRP-deficient cortical neurons, mRNA down-regulation is caused by elevated degradation and is correlated with codon optimality. Moreover, FMRP preferentially binds mRNAs with optimal codons, suggesting that it stabilizes such transcripts through direct interactions via the translational machinery. Finally, we show that the paradigm of genetic rescue of FXS-like phenotypes in FMRP-deficient mice by deletion of the Cpeb1 gene is mediated by restoration of steady-state RNA levels and consequent rebalancing of translational homeostasis. Our data establish an essential role of FMRP in codon optimality-dependent mRNA stability as an important factor in FXS.
Collapse
Affiliation(s)
- Huan Shu
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605;
| | - Elisa Donnard
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Botao Liu
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605
| | - Suna Jung
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605
| | - Ruijia Wang
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605
| | - Joel D Richter
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605
| |
Collapse
|
6
|
Rinaldi VD, Donnard E, Gellatly K, Rasmussen M, Kucukural A, Yukselen O, Garber M, Sharma U, Rando OJ. An atlas of cell types in the mouse epididymis and vas deferens. eLife 2020; 9:e55474. [PMID: 32729827 PMCID: PMC7426093 DOI: 10.7554/elife.55474] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 07/27/2020] [Indexed: 12/12/2022] Open
Abstract
Following testicular spermatogenesis, mammalian sperm continue to mature in a long epithelial tube known as the epididymis, which plays key roles in remodeling sperm protein, lipid, and RNA composition. To understand the roles for the epididymis in reproductive biology, we generated a single-cell atlas of the murine epididymis and vas deferens. We recovered key epithelial cell types including principal cells, clear cells, and basal cells, along with associated support cells that include fibroblasts, smooth muscle, macrophages and other immune cells. Moreover, our data illuminate extensive regional specialization of principal cell populations across the length of the epididymis. In addition to region-specific specialization of principal cells, we find evidence for functionally specialized subpopulations of stromal cells, and, most notably, two distinct populations of clear cells. Our dataset extends on existing knowledge of epididymal biology, and provides a wealth of information on potential regulatory and signaling factors that bear future investigation.
Collapse
Affiliation(s)
- Vera D Rinaldi
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Elisa Donnard
- Department of Bioinformatics and Integrative Biology, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Kyle Gellatly
- Department of Bioinformatics and Integrative Biology, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Morten Rasmussen
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Alper Kucukural
- Department of Bioinformatics and Integrative Biology, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Onur Yukselen
- Department of Bioinformatics and Integrative Biology, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Manuel Garber
- Department of Bioinformatics and Integrative Biology, University of Massachusetts Medical SchoolWorcesterUnited States
- Program in Molecular Medicine, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Upasna Sharma
- Department of Molecular, Cell and Developmental Biology, University of California Santa CruzSanta CruzUnited States
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical SchoolWorcesterUnited States
| |
Collapse
|
7
|
Bettoni F, Masotti C, Corrêa BR, Donnard E, Dos Santos FF, São Julião GP, Vailati BB, Habr-Gama A, Galante PAF, Perez RO, Camargo AA. The Effects of Neoadjuvant Chemoradiation in Locally Advanced Rectal Cancer-The Impact in Intratumoral Heterogeneity. Front Oncol 2019; 9:974. [PMID: 31612112 PMCID: PMC6776613 DOI: 10.3389/fonc.2019.00974] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 09/13/2019] [Indexed: 12/22/2022] Open
Abstract
Purpose: Intratumoral genetic heterogeneity (ITGH) is a common feature of solid tumors. However, little is known about the effect of neoadjuvant chemoradiation (nCRT) in ITGH of rectal tumors that exhibit poor response to nCRT. Here, we examined the impact of nCRT in the mutational profile and ITGH of rectal tumors and its adjacent irradiated normal mucosa in the setting of incomplete response to nCRT. Methods and Materials: To evaluate ITGH in rectal tumors, we analyzed whole-exome sequencing (WES) data from 79 tumors obtained from The Cancer Genome Atlas (TCGA). We also compared matched peripheral blood cells, irradiated normal rectal mucosa and pre and post-treatment tumor samples (PRE-T and POS-T) from one individual to examine the iatrogenic effects of nCRT. Finally, we performed WES of 7 PRE-T/POST-T matched samples to examine how nCRT affects ITGH. ITGH was assessed by quantifying subclonal mutations within individual tumors using the Mutant-Allele Tumor Heterogeneity score (MATH score). Results: Rectal tumors exhibit remarkable ITGH that is ultimately associated with disease stage (MATH score stage I/II 35.54 vs. stage III/IV 44.39, p = 0.047) and lymph node metastasis (MATH score N0 35.87 vs. N+ 45.79, p = 0.026). We also showed that nCRT does not seem to introduce detectable somatic mutations in the irradiated mucosa. Comparison of PRE-T and POST-T matched samples revealed a significant increase in ITGH in 5 out 7 patients and MATH scores were significantly higher after nCRT (median 41.7 vs. 28.8, p = 0.04). Finally, we were able to identify a subset of “enriched mutations” with significant changes in MAFs between PRE-T and POST-T samples. These “enriched mutations” were significantly more frequent in POST-T compared to PRE-T samples (92.9% vs. 7.1% p < 0.00001) and include mutations in genes associated with genetic instability and drug resistance in colorectal cancer, indicating the expansion of tumor cell subpopulations more prone to resist to nCRT. Conclusions: nCRT increases ITGH and may result in the expansion of resistant tumor cell populations in residual tumors. The risk of introducing relevant somatic mutations in the adjacent mucosa is minimal but non-responsive tumors may have potentially worse biological behavior when compared to their untreated counterparts. This was an exploratory study, and due to the limited number of samples analyzed, our results need to be validated in larger cohorts.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Anamaria A Camargo
- Hospital Sírio Libanês, São Paulo, Brazil.,Ludwig Institute for Cancer Research, São Paulo, Brazil
| |
Collapse
|
8
|
Chou HJ, Donnard E, Gustafsson HT, Garber M, Rando OJ. Transcriptome-wide Analysis of Roles for tRNA Modifications in Translational Regulation. Mol Cell 2017; 68:978-992.e4. [PMID: 29198561 DOI: 10.1016/j.molcel.2017.11.002] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/19/2017] [Accepted: 10/31/2017] [Indexed: 12/17/2022]
Abstract
Covalent nucleotide modifications in noncoding RNAs affect a plethora of biological processes, and new functions continue to be discovered even for well-known modifying enzymes. To systematically compare the functions of a large set of noncoding RNA modifications in gene regulation, we carried out ribosome profiling in budding yeast to characterize 57 nonessential genes involved in tRNA modification. Deletion mutants exhibited a range of translational phenotypes, with enzymes known to modify anticodons, or non-tRNA substrates such as rRNA, exhibiting the most dramatic translational perturbations. Our data build on prior reports documenting translational upregulation of the nutrient-responsive transcription factor Gcn4 in response to numerous tRNA perturbations, and identify many additional translationally regulated mRNAs throughout the yeast genome. Our data also uncover unexpected roles for tRNA-modifying enzymes in regulation of TY retroelements, and in rRNA 2'-O-methylation. This dataset should provide a rich resource for discovery of additional links between tRNA modifications and gene regulation.
Collapse
Affiliation(s)
- Hsin-Jung Chou
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Elisa Donnard
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - H Tobias Gustafsson
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Manuel Garber
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| |
Collapse
|
9
|
Diehl WE, Lin AE, Grubaugh ND, Carvalho LM, Kim K, Kyawe PP, McCauley SM, Donnard E, Kucukural A, McDonel P, Schaffner SF, Garber M, Rambaut A, Andersen KG, Sabeti PC, Luban J. Ebola Virus Glycoprotein with Increased Infectivity Dominated the 2013-2016 Epidemic. Cell 2017; 167:1088-1098.e6. [PMID: 27814506 PMCID: PMC5115602 DOI: 10.1016/j.cell.2016.10.014] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/23/2016] [Accepted: 10/06/2016] [Indexed: 11/18/2022]
Abstract
The magnitude of the 2013–2016 Ebola virus disease (EVD) epidemic enabled an unprecedented number of viral mutations to occur over successive human-to-human transmission events, increasing the probability that adaptation to the human host occurred during the outbreak. We investigated one nonsynonymous mutation, Ebola virus (EBOV) glycoprotein (GP) mutant A82V, for its effect on viral infectivity. This mutation, located at the NPC1-binding site on EBOV GP, occurred early in the 2013–2016 outbreak and rose to high frequency. We found that GP-A82V had heightened ability to infect primate cells, including human dendritic cells. The increased infectivity was restricted to cells that have primate-specific NPC1 sequences at the EBOV interface, suggesting that this mutation was indeed an adaptation to the human host. GP-A82V was associated with increased mortality, consistent with the hypothesis that the heightened intrinsic infectivity of GP-A82V contributed to disease severity during the EVD epidemic. Ebola glycoprotein mutant GP-A82V arose early and dominated the West African epidemic GP-A82V infects human cells more efficiently than does the ancestral glycoprotein The increased infectivity of GP-A82V is specific for primate cells GP-A82V was weakly associated with increased mortality during the epidemic
Collapse
Affiliation(s)
- William E Diehl
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA
| | - Aaron E Lin
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Nathan D Grubaugh
- Department of Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Luiz Max Carvalho
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, Scotland, UK
| | - Kyusik Kim
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA
| | - Pyae Phyo Kyawe
- Department of Medicine, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01605, USA
| | - Sean M McCauley
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA
| | - Elisa Donnard
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA; Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Alper Kucukural
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA; Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Patrick McDonel
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA; Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Stephen F Schaffner
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Manuel Garber
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA; Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, Scotland, UK
| | - Kristian G Andersen
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Department of Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Scripps Translational Science Institute, 3344 North Torrey Pines Court, La Jolla, CA 92037, USA.
| | - Pardis C Sabeti
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA.
| | - Jeremy Luban
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA.
| |
Collapse
|
10
|
Carpinetti P, Donnard E, Bettoni F, Asprino P, Koyama F, Rozanski A, Sabbaga J, Habr-Gama A, Parmigiani RB, Galante PAF, Perez RO, Camargo AA. The use of personalized biomarkers and liquid biopsies to monitor treatment response and disease recurrence in locally advanced rectal cancer after neoadjuvant chemoradiation. Oncotarget 2016; 6:38360-71. [PMID: 26451609 PMCID: PMC4742005 DOI: 10.18632/oncotarget.5256] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 09/24/2015] [Indexed: 12/18/2022] Open
Abstract
Neoadjuvant chemoradiotherapy (nCRT) followed by surgery is the mainstay treatment for locally advanced rectal cancer. Variable degrees of tumor regression are observed after nCRT and alternative treatment strategies, including close surveillance without immediate surgery, have been investigated to spare patients with complete tumor regression from potentially adverse outcomes of radical surgery. However, clinical and radiological assessment of response does not allow accurate identification of patients with complete response. In addition, surveillance for recurrence is similarly important for these patients, as early detection of recurrence allows salvage resections and adjuvant interventions. We report the use of liquid biopsies and personalized biomarkers for monitoring treatment response to nCRT and detecting residual disease and recurrence in patients with rectal cancer. We sequenced the whole-genome of four rectal tumors to identify patient-specific chromosomal rearrangements that were used to monitor circulating tumor DNA (ctDNA) in liquid biopsies collected at diagnosis and during nCRT and follow-up. We compared ctDNA levels to clinical, radiological and pathological response to nCRT. Our results indicate that personalized biomarkers and liquid biopsies may not be sensitive for the detection of microscopic residual disease. However, it can be efficiently used to monitor treatment response to nCRT and detect disease recurrence, preceding increases in CEA levels and radiological diagnosis. Similar good results were observed when assessing tumor response to systemic therapy and disease progression. Our study supports the use of personalized biomarkers and liquid biopsies to tailor the management of rectal cancer patients, however, replication in a larger cohort is necessary to introduce this strategy into clinical practice.
Collapse
Affiliation(s)
- Paola Carpinetti
- Ludwig Institute for Cancer Research, São Paulo, SP, Brazil.,Centro de Oncologia Molecular Hospital Sírio Libanês, São Paulo, SP, Brazil.,Programa de Pós Graduação em Bioquímica, Instituto de Química, Universidade de São Paulo, SP, Brazil
| | - Elisa Donnard
- Ludwig Institute for Cancer Research, São Paulo, SP, Brazil.,Centro de Oncologia Molecular Hospital Sírio Libanês, São Paulo, SP, Brazil.,Programa de Pós Graduação em Bioquímica, Instituto de Química, Universidade de São Paulo, SP, Brazil
| | - Fabiana Bettoni
- Centro de Oncologia Molecular Hospital Sírio Libanês, São Paulo, SP, Brazil
| | - Paula Asprino
- Centro de Oncologia Molecular Hospital Sírio Libanês, São Paulo, SP, Brazil
| | | | - Andrei Rozanski
- Centro de Oncologia Molecular Hospital Sírio Libanês, São Paulo, SP, Brazil
| | - Jorge Sabbaga
- Centro de Oncologia Clínica, Hospital Sírio Libanês, São Paulo, SP, Brazil
| | - Angelita Habr-Gama
- Angelita & Joaquim Gama Institute, São Paulo, SP, Brazil.,University of São Paulo, School of Medicine, São Paulo, SP, Brazil
| | | | - Pedro A F Galante
- Centro de Oncologia Molecular Hospital Sírio Libanês, São Paulo, SP, Brazil
| | - Rodrigo O Perez
- Ludwig Institute for Cancer Research, São Paulo, SP, Brazil.,Angelita & Joaquim Gama Institute, São Paulo, SP, Brazil.,University of São Paulo, School of Medicine, São Paulo, SP, Brazil
| | - Anamaria A Camargo
- Ludwig Institute for Cancer Research, São Paulo, SP, Brazil.,Centro de Oncologia Molecular Hospital Sírio Libanês, São Paulo, SP, Brazil
| |
Collapse
|
11
|
Donnard E, Asprino PF, Correa BR, Bettoni F, Koyama FC, Navarro FC, Perez RO, Mariadason J, Sieber OM, Strausberg RL, Simpson AJ, Jardim DL, Reis LFL, Parmigiani RB, Galante PA, Camargo AA. Mutational analysis of genes coding for cell surface proteins in colorectal cancer cell lines reveal novel altered pathways, druggable mutations and mutated epitopes for targeted therapy. Oncotarget 2014; 5:9199-213. [PMID: 25193853 PMCID: PMC4253428 DOI: 10.18632/oncotarget.2374] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 08/20/2014] [Indexed: 12/14/2022] Open
Abstract
We carried out a mutational analysis of 3,594 genes coding for cell surface proteins (Surfaceome) in 23 colorectal cancer cell lines, searching for new altered pathways, druggable mutations and mutated epitopes for targeted therapy in colorectal cancer. A total of 3,944 somatic non-synonymous substitutions and 595 InDels, occurring in 2,061 (57%) Surfaceome genes were catalogued. We identified 48 genes not previously described as mutated in colorectal tumors in the TCGA database, including genes that are mutated and expressed in >10% of the cell lines (SEMA4C, FGFRL1, PKD1, FAM38A, WDR81, TMEM136, SLC36A1, SLC26A6, IGFLR1). Analysis of these genes uncovered important roles for FGF and SEMA4 signaling in colorectal cancer with possible therapeutic implications. We also found that cell lines express on average 11 druggable mutations, including frequent mutations (>20%) in the receptor tyrosine kinases AXL and EPHA2, which have not been previously considered as potential targets for colorectal cancer. Finally, we identified 82 cell surface mutated epitopes, however expression of only 30% of these epitopes was detected in our cell lines. Notwithstanding, 92% of these epitopes were expressed in cell lines with the mutator phenotype, opening new venues for the use of "general" immune checkpoint drugs in this subset of patients.
Collapse
Affiliation(s)
- Elisa Donnard
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
- Programa de Pós Graduação do Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Paula F. Asprino
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Bruna R. Correa
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Fabiana Bettoni
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Fernanda C. Koyama
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
- Laboratory of Molecular Biology and Genomics, Ludwig Institute for Cancer Research, São Paulo, Brazil
| | - Fabio C.P. Navarro
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
- Programa de Pós Graduação do Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Rodrigo O. Perez
- Laboratory of Molecular Biology and Genomics, Ludwig Institute for Cancer Research, São Paulo, Brazil
- Instituto Angelita & Joaquim Gama, São Paulo, Brazil
| | - John Mariadason
- Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Melbourne, Australia
| | - Oliver M. Sieber
- Colorectal Cancer Genetics Laboratory, Systems Biology and Personalised Medicine Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville, Australia
| | | | | | - Denis L.F. Jardim
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
| | | | | | - Pedro A.F. Galante
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Anamaria A. Camargo
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
- Laboratory of Molecular Biology and Genomics, Ludwig Institute for Cancer Research, São Paulo, Brazil
| |
Collapse
|
12
|
Donnard E, Queiroz EM, Ortega JM, Gietz RD. Yeast two-hybrid liquid screening. Methods Mol Biol 2014; 1163:97-107. [PMID: 24841301 DOI: 10.1007/978-1-4939-0799-1_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Yeast two-hybrid (YTH) method consists of a genetic trap that selects for "prey" cDNA products within a library that interact with a "bait" protein of interest. Here, we provide a protocol for YTH screening using a liquid medium screening method, which improves the sensitivity of this technique and streamlines the laborious classic screening in solid medium plates. The method uses a simple series of dilutions with established yeast strains transformed with diverse baits and complex cDNA libraries. This allows for prompt detection of positive clones revealed by liquid growth, due to activation of HIS3 reporter gene. Activation of a second reporter gene and reconstruction of the YTH interaction is highly reproducible using this system. This approach can either be performed using culture flasks or deep-well 96-well plates and the number of interactions obtained is similar, when compared to the classic method. In addition, the liquid screening method is faster and more economical for YTH screening and has the added benefit of automation if 96-well plates are used.
Collapse
Affiliation(s)
- Elisa Donnard
- Departamento de Bioquímica e Imunologia, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Brasil
| | | | | | | |
Collapse
|
13
|
Carpinetti P, Donnard E, Asprino P, Bettoni F, Koyama F, Habr-Gama A, Parmigiani R, Galante P, Perez R, Camargo AA. Abstract A33: The use of personalized biomarkers for accessing tumor regression and defining surgical approach in rectal cancer patients treated with neoadjuvant chemoradiation. Mol Cancer Ther 2013. [DOI: 10.1158/1535-7163.targ-13-a33] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Neoadjuvant chemoradiation (nCRT) is the preferred initial treatment for locally advanced rectal cancer due to improved local disease control, lower toxicity and significant tumor regression. Response to nCRT varies substantially among patients and complete tumor regression can be observed in up to 42% of the patients. To avoid unnecessary postoperative morbidity associated with radical surgery, patients exhibiting significant tumor regression have been referred for conservative surgical approaches or even no immediate surgery with strict follow-up (Wait and Watch approach). However, assessment of treatment response remains a significant challenge due to the subjectivity of the clinical assessment and limitations of available radiological studies. In this context, identification of biomarkers capable of accessing tumor regression and complete response to nCRT would allow accurate selection of patients for alternative treatment strategies without immediate radical surgery after nCRT. Circulating DNA carrying tumor-specific genetic alterations can be found in the cell-free fraction of the blood (circulating tumor DNA - ctDNA) and has been successfully used to monitor tumor dynamics in both hematological and solid tumors. Recent advances in sequencing technologies have enabled the rapid and cost effective identification of genetic alterations in individual tumors. These alterations, in special tumor-specific chromosomal rearrangements, can then be used as personalized biomarkers to monitor treatment response and detect minimal residual disease, overcoming the problem imposed by the absence of a universally recurrent genetic alteration in solid tumors. In the present work, we sequenced the whole genome of 6 rectal tumors using mate-pair reads and identified tumor-specific chromosomal rearrangements (TSCR) that were subsequently validated by Sanger sequencing. Personalized assays were then designed to monitor these TSCR in serum samples collected at different time points during nCRT. TSCRs were detected in all pre-treatment serum samples and in post-treatment serum samples from patients presenting marginal tumor regression after nCRT. Post-treatment samples from patients with significant or complete tumor regression were mainly negative for the presence of TSCR. Our preliminary results suggest that personalized biomarkers can be used in the clinics for accessing tumor regression and defining the best surgical approach in rectal cancer patients treated with neoadjuvant chemoradiation.
Citation Information: Mol Cancer Ther 2013;12(11 Suppl):A33.
Citation Format: Paola Carpinetti, Elisa Donnard, Paula Asprino, Fabiana Bettoni, Fernanda Koyama, Angelita Habr-Gama, Raphael Parmigiani, Pedro Galante, Rodrigo Perez, Anamaria A. Camargo. The use of personalized biomarkers for accessing tumor regression and defining surgical approach in rectal cancer patients treated with neoadjuvant chemoradiation. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr A33.
Collapse
Affiliation(s)
- Paola Carpinetti
- 1Centro de Oncologia Molecular Hospital Sírio Libanês, Sao Paulo, Brazil
| | - Elisa Donnard
- 1Centro de Oncologia Molecular Hospital Sírio Libanês, Sao Paulo, Brazil
| | - Paula Asprino
- 1Centro de Oncologia Molecular Hospital Sírio Libanês, Sao Paulo, Brazil
| | - Fabiana Bettoni
- 1Centro de Oncologia Molecular Hospital Sírio Libanês, Sao Paulo, Brazil
| | - Fernanda Koyama
- 2Instituto Ludwig de Pesquisa sobre o Câncer, Sao Paulo, Brazil
| | | | - Raphael Parmigiani
- 1Centro de Oncologia Molecular Hospital Sírio Libanês, Sao Paulo, Brazil
| | - Pedro Galante
- 1Centro de Oncologia Molecular Hospital Sírio Libanês, Sao Paulo, Brazil
| | - Rodrigo Perez
- 2Instituto Ludwig de Pesquisa sobre o Câncer, Sao Paulo, Brazil
| | | |
Collapse
|
14
|
Donnard E, Barbosa-Silva A, Guedes RLM, Fernandes GR, Velloso H, Kohn MJ, Andrade-Navarro MA, Ortega JM. Preimplantation development regulatory pathway construction through a text-mining approach. BMC Genomics 2011; 12 Suppl 4:S3. [PMID: 22369103 PMCID: PMC3287586 DOI: 10.1186/1471-2164-12-s4-s3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background The integration of sequencing and gene interaction data and subsequent generation of pathways and networks contained in databases such as KEGG Pathway is essential for the comprehension of complex biological processes. We noticed the absence of a chart or pathway describing the well-studied preimplantation development stages; furthermore, not all genes involved in the process have entries in KEGG Orthology, important information for knowledge application with relation to other organisms. Results In this work we sought to develop the regulatory pathway for the preimplantation development stage using text-mining tools such as Medline Ranker and PESCADOR to reveal biointeractions among the genes involved in this process. The genes present in the resulting pathway were also used as seeds for software developed by our group called SeedServer to create clusters of homologous genes. These homologues allowed the determination of the last common ancestor for each gene and revealed that the preimplantation development pathway consists of a conserved ancient core of genes with the addition of modern elements. Conclusions The generation of regulatory pathways through text-mining tools allows the integration of data generated by several studies for a more complete visualization of complex biological processes. Using the genes in this pathway as “seeds” for the generation of clusters of homologues, the pathway can be visualized for other organisms. The clustering of homologous genes together with determination of the ancestry leads to a better understanding of the evolution of such process.
Collapse
Affiliation(s)
- Elisa Donnard
- Laboratório Biodados, Dept. de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte - MG, Brazil
| | | | | | | | | | | | | | | |
Collapse
|