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Hama Faraj GS, Hussen BM, Abdullah SR, Fatih Rasul M, Hajiesmaeili Y, Baniahmad A, Taheri M. Advanced approaches of the use of circRNAs as a replacement for cancer therapy. Noncoding RNA Res 2024; 9:811-830. [PMID: 38590433 PMCID: PMC10999493 DOI: 10.1016/j.ncrna.2024.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/18/2024] [Accepted: 03/29/2024] [Indexed: 04/10/2024] Open
Abstract
Cancer is a broad name for a group of diseases in which abnormal cells grow out of control and are characterized by their complexity and recurrence. Although there has been progress in cancer therapy with the entry of precision medicine and immunotherapy, cancer incidence rates have increased globally. Non-coding RNAs in the form of circular RNAs (circRNAs) play crucial roles in the pathogenesis, clinical diagnosis, and therapy of different diseases, including cancer. According to recent studies, circRNAs appear to serve as accurate indicators and therapeutic targets for cancer treatment. However, circRNAs are promising candidates for cutting-edge cancer therapy because of their distinctive circular structure, stability, and wide range of capabilities; many challenges persist that decrease the applications of circRNA-based cancer therapeutics. Here, we explore the roles of circRNAs as a replacement for cancer therapy, highlight the main challenges facing circRNA-based cancer therapies, and discuss the key strategies to overcome these challenges to improve advanced innovative therapies based on circRNAs with long-term health effects.
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Affiliation(s)
- Goran Sedeeq Hama Faraj
- Department of Medical Laboratory Science, Komar University of Science and Technology, Sulaymaniyah, 46001, Iraq
| | - Bashdar Mahmud Hussen
- Department of Biomedical Sciences, College of Science, Cihan University-Erbil, Erbil, Kurdistan Region, 44001, Iraq
- Department of Clinical Analysis, College of Pharmacy, Hawler Medical University, Erbil, Kurdistan Region, 44001, Iraq
| | - Snur Rasool Abdullah
- Medical Laboratory Science, Lebanese French University, Erbil, Kurdistan Region, 44001, Iraq
| | - Mohammed Fatih Rasul
- Department of Pharmaceutical Basic Science, Faculty of Pharmacy, Tishk International University, Erbil, Kurdistan Region, Iraq
| | | | - Aria Baniahmad
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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2
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Wang XS, Chen Y, Zhao YW, Chen MW, Wang H. Assessing the association between a sedentary lifestyle and prevalence of primary osteoporosis: a community-based cross-sectional study among Chinese population. BMJ Open 2024; 14:e080243. [PMID: 38834324 PMCID: PMC11163664 DOI: 10.1136/bmjopen-2023-080243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 05/21/2024] [Indexed: 06/06/2024] Open
Abstract
OBJECTIVES To reveal the association between a sedentary lifestyle and the prevalence of primary osteoporosis (POP). DESIGN A community-based cross-sectional study was conducted. SETTING This study was conducted in communities in Hefei city, Anhui province, China. PARTICIPANTS A total of 1346 residents aged 40 and above underwent POP screening via calcaneus ultrasound bone mineral density (BMD) testing and completed a questionnaire survey. OUTCOME MEASURES The average daily sitting time was included in the study variable and used to assess sedentary behaviour. The 15 control variables included general information, dietary information and life behaviour information. Logistic regression was used to analyse the association between the POP prevalence and study or control variables in different models. RESULTS 1346 participants were finally included in the study. According to the 15 control variables, the crude model and 4 models were established. The analysis revealed that the average daily sitting time showed a significant correlation with the prevalence of POP in the crude model (OR=2.02, 95% CI=1.74 to 2.36, p<0.001), Model 1 (OR=2.65, 95% CI=2.21 to 3.17, p<0.001), Model 2 (OR=2.63, 95% CI=2.19 to 3.15, p<0.001), Model 3 (OR=2.62, 95% CI=2.18 to 3.15, p<0.001) and Model 4 (OR=2.58, 95% CI=2.14 to 3.11, p<0.001). Besides, gender, age and body mass index showed a significant correlation with the POP prevalence in all models. CONCLUSIONS This study suggests a potential association between a sedentary lifestyle and the prevalence of POP within the Chinese population. Modifying sedentary behaviours could contribute to a reduction in POP risk. However, longitudinal cohort studies are necessary to confirm this hypothesis in the future.
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Affiliation(s)
- Xiao-Song Wang
- Center for Big Data and Population Health of IHM, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Department of Epidemiology and Biostatistics, Anhui Medical University, Hefei, Anhui, China
| | - Yong Chen
- Department of Social Medicine and Health Management, Anhui Medical University, Hefei, Anhui, China
| | - Yun-Wu Zhao
- Center for Big Data and Population Health of IHM, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Ming-Wei Chen
- Center for Big Data and Population Health of IHM, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Heng Wang
- Center for Big Data and Population Health of IHM, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Department of Epidemiology and Biostatistics, Anhui Medical University, Hefei, Anhui, China
- Department of Social Medicine and Health Management, Anhui Medical University, Hefei, Anhui, China
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3
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Zinati Y, Takiddeen A, Emad A. GRouNdGAN: GRN-guided simulation of single-cell RNA-seq data using causal generative adversarial networks. Nat Commun 2024; 15:4055. [PMID: 38744843 DOI: 10.1038/s41467-024-48516-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 05/01/2024] [Indexed: 05/16/2024] Open
Abstract
We introduce GRouNdGAN, a gene regulatory network (GRN)-guided reference-based causal implicit generative model for simulating single-cell RNA-seq data, in silico perturbation experiments, and benchmarking GRN inference methods. Through the imposition of a user-defined GRN in its architecture, GRouNdGAN simulates steady-state and transient-state single-cell datasets where genes are causally expressed under the control of their regulating transcription factors (TFs). Training on six experimental reference datasets, we show that our model captures non-linear TF-gene dependencies and preserves gene identities, cell trajectories, pseudo-time ordering, and technical and biological noise, with no user manipulation and only implicit parameterization. GRouNdGAN can synthesize cells under new conditions to perform in silico TF knockout experiments. Benchmarking various GRN inference algorithms reveals that GRouNdGAN effectively bridges the existing gap between simulated and biological data benchmarks of GRN inference algorithms, providing gold standard ground truth GRNs and realistic cells corresponding to the biological system of interest.
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Affiliation(s)
- Yazdan Zinati
- Department of Electrical and Computer Engineering, McGill University, Montreal, QC, Canada
| | - Abdulrahman Takiddeen
- Department of Electrical and Computer Engineering, McGill University, Montreal, QC, Canada
| | - Amin Emad
- Department of Electrical and Computer Engineering, McGill University, Montreal, QC, Canada.
- Mila, Quebec AI Institute, Montreal, QC, Canada.
- The Rosalind and Morris Goodman Cancer Institute, Montreal, QC, Canada.
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4
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Kaur G, Pippin JA, Chang S, Redmond J, Chesi A, Wells AD, Maerz T, Grant SFA, Coleman RM, Hankenson KD, Wagley Y. Osteoporosis GWAS-implicated DNM3 locus contextually regulates osteoblastic and chondrogenic fate of mesenchymal stem/progenitor cells through oscillating miR-199a-5p levels. JBMR Plus 2024; 8:ziae051. [PMID: 38686038 PMCID: PMC11056323 DOI: 10.1093/jbmrpl/ziae051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 02/15/2024] [Accepted: 04/11/2024] [Indexed: 05/02/2024] Open
Abstract
Genome wide association study (GWAS)-implicated bone mineral density (BMD) signals have been shown to localize in cis-regulatory regions of distal effector genes using 3D genomic methods. Detailed characterization of such genes can reveal novel causal genes for BMD determination. Here, we elected to characterize the "DNM3" locus on chr1q24, where the long non-coding RNA DNM3OS and the embedded microRNA MIR199A2 (miR-199a-5p) are implicated as effector genes contacted by the region harboring variation in linkage disequilibrium with BMD-associated sentinel single nucleotide polymorphism, rs12041600. During osteoblast differentiation of human mesenchymal stem/progenitor cells (hMSC), miR-199a-5p expression was temporally decreased and correlated with the induction of osteoblastic transcription factors RUNX2 and Osterix. Functional relevance of miR-199a-5p downregulation in osteoblastogenesis was investigated by introducing miR-199a-5p mimic into hMSC. Cells overexpressing miR-199a-5p depicted a cobblestone-like morphological change and failed to produce BMP2-dependent extracellular matrix mineralization. Mechanistically, a miR-199a-5p mimic modified hMSC propagated normal SMAD1/5/9 signaling and expressed osteoblastic transcription factors RUNX2 and Osterix but depicted pronounced upregulation of SOX9 and enhanced expression of essential chondrogenic genes ACAN, COMP, and COL10A1. Mineralization defects, morphological changes, and enhanced chondrogenic gene expression associated with miR-199a-5p mimic over-expression were restored with miR-199a-5p inhibitor suggesting specificity of miR-199a-5p in chondrogenic fate specification. The expression of both the DNM3OS and miR-199a-5p temporally increased and correlated with hMSC chondrogenic differentiation. Although miR-199a-5p overexpression failed to further enhance chondrogenesis, blocking miR-199a-5p activity significantly reduced chondrogenic pellet size, extracellular matrix deposition, and chondrogenic gene expression. Taken together, our results indicate that oscillating miR-199a-5p levels dictate hMSC osteoblast or chondrocyte terminal fate. Our study highlights a functional role of miR-199a-5p as a BMD effector gene at the DNM3 BMD GWAS locus, where patients with cis-regulatory genetic variation which increases miR-199a-5p expression could lead to reduced osteoblast activity.
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Affiliation(s)
- Gurcharan Kaur
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - James A Pippin
- Center for Spatial and Functional Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
| | - Solomon Chang
- Department of Orthopaedic Surgery, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Justin Redmond
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI 48109, United States
- Department of Orthopaedic Surgery, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Alessandra Chesi
- Center for Spatial and Functional Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Andrew D Wells
- Center for Spatial and Functional Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Tristan Maerz
- Department of Orthopaedic Surgery, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Struan F A Grant
- Center for Spatial and Functional Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
- Division of Diabetes and Endocrinology, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
- Institute of Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Rhima M Coleman
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI 48109, United States
- Department of Orthopaedic Surgery, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Kurt D Hankenson
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI 48109, United States
- Department of Orthopaedic Surgery, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Yadav Wagley
- Department of Orthopaedic Surgery, University of Michigan Medical School, Ann Arbor, MI 48109, United States
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Kim M, Wang P, Clow PA, Chien I(E, Wang X, Peng J, Chai H, Liu X, Lee B, Ngan CY, Yue F, Milenkovic O, Chuang JH, Wei CL, Casellas R, Cheng AW, Ruan Y. Multifaceted roles of cohesin in regulating transcriptional loops. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.25.586715. [PMID: 38585764 PMCID: PMC10996690 DOI: 10.1101/2024.03.25.586715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Cohesin is required for chromatin loop formation. However, its precise role in regulating gene transcription remains largely unknown. We investigated the relationship between cohesin and RNA Polymerase II (RNAPII) using single-molecule mapping and live-cell imaging methods in human cells. Cohesin-mediated transcriptional loops were highly correlated with those of RNAPII and followed the direction of gene transcription. Depleting RAD21, a subunit of cohesin, resulted in the loss of long-range (>100 kb) loops between distal (super-)enhancers and promoters of cell-type-specific genes. By contrast, the short-range (<50 kb) loops were insensitive to RAD21 depletion and connected genes that are mostly housekeeping. This result explains why only a small fraction of genes are affected by the loss of long-range chromatin interactions due to cohesin depletion. Remarkably, RAD21 depletion appeared to up-regulate genes located in early initiation zones (EIZ) of DNA replication, and the EIZ signals were amplified drastically without RAD21. Our results revealed new mechanistic insights of cohesin's multifaceted roles in establishing transcriptional loops, preserving long-range chromatin interactions for cell-specific genes, and maintaining timely order of DNA replication.
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Affiliation(s)
- Minji Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- Present address: Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
- Equal contributions
| | - Ping Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Evanston, IL, 60201, USA
- Equal contributions
| | - Patricia A. Clow
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- Equal contributions
| | - I (Eli) Chien
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61820, USA
| | - Xiaotao Wang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Reproduction and Development, Shanghai, China
| | - Jianhao Peng
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61820, USA
| | - Haoxi Chai
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Xiyuan Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Eye hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, 325027, P.R. China
| | - Byoungkoo Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Chew Yee Ngan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Evanston, IL, 60201, USA
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Olgica Milenkovic
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61820, USA
| | - Jeffrey H. Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, 06030, USA
| | - Chia-Lin Wei
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Rafael Casellas
- Hematopoietic Biology and Malignancy, MD Anderson Cancer Center, Houston, TX, 77054, USA
| | - Albert W. Cheng
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, 85281, USA
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang Province, 310058, P.R. China
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6
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Conery M, Pippin JA, Wagley Y, Trang K, Pahl MC, Villani DA, Favazzo LJ, Ackert-Bicknell CL, Zuscik MJ, Katsevich E, Wells AD, Zemel BS, Voight BF, Hankenson KD, Chesi A, Grant SF. GWAS-informed data integration and non-coding CRISPRi screen illuminate genetic etiology of bone mineral density. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.585778. [PMID: 38562830 PMCID: PMC10983984 DOI: 10.1101/2024.03.19.585778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Over 1,100 independent signals have been identified with genome-wide association studies (GWAS) for bone mineral density (BMD), a key risk factor for mortality-increasing fragility fractures; however, the effector gene(s) for most remain unknown. Informed by a variant-to-gene mapping strategy implicating 89 non-coding elements predicted to regulate osteoblast gene expression at BMD GWAS loci, we executed a single-cell CRISPRi screen in human fetal osteoblast 1.19 cells (hFOBs). The BMD relevance of hFOBs was supported by heritability enrichment from cross-cell type stratified LD-score regression involving 98 cell types grouped into 15 tissues. 24 genes showed perturbation in the screen, with four (ARID5B, CC2D1B, EIF4G2, and NCOA3) exhibiting consistent effects upon siRNA knockdown on three measures of osteoblast maturation and mineralization. Lastly, additional heritability enrichments, genetic correlations, and multi-trait fine-mapping revealed that many BMD GWAS signals are pleiotropic and likely mediate their effects via non-bone tissues that warrant attention in future screens.
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Affiliation(s)
- Mitchell Conery
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James A. Pippin
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yadav Wagley
- Department of Orthopaedic Surgery, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Khanh Trang
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Matthew C. Pahl
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - David A. Villani
- Colorado Program for Musculoskeletal Research, University of Colorado Anschutz Medical Campus, Aurora, CO
- Cell Biology, Stems Cells and Development Ph.D. Program, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Lacey J. Favazzo
- Colorado Program for Musculoskeletal Research, University of Colorado Anschutz Medical Campus, Aurora, CO
- Department of Orthopedics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
- University of Colorado Interdisciplinary Joint Biology Program, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Cheryl L. Ackert-Bicknell
- Colorado Program for Musculoskeletal Research, University of Colorado Anschutz Medical Campus, Aurora, CO
- Department of Orthopedics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
- University of Colorado Interdisciplinary Joint Biology Program, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Michael J. Zuscik
- Colorado Program for Musculoskeletal Research, University of Colorado Anschutz Medical Campus, Aurora, CO
- Department of Orthopedics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
- University of Colorado Interdisciplinary Joint Biology Program, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Eugene Katsevich
- Department of Statistics and Data Science, The Wharton School, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew D. Wells
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Babette S. Zemel
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Benjamin F. Voight
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute of Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kurt D. Hankenson
- Department of Orthopaedic Surgery, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Alessandra Chesi
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Struan F.A. Grant
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute of Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
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7
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Patel R, Menon J, Kumar S, Nóbrega MB, Patel DA, Sakure AA, Vaja MB. Modern day breeding approaches for improvement of castor. Heliyon 2024; 10:e27048. [PMID: 38463846 PMCID: PMC10920369 DOI: 10.1016/j.heliyon.2024.e27048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 02/12/2024] [Accepted: 02/22/2024] [Indexed: 03/12/2024] Open
Abstract
Castor (Ricinus communis L.) is an industrially important oil producing crop belongs to Euphorbiaceae family. Castor oil has unique chemical properties make it industrially important crop. It is a member of monotypic genus even though it has ample amount of variability. Using this variability, conventionally many varieties and hybrids have been developed. But, like other crops, the modern and unconventional methods of crop improvement has not fully explored in castor. This article discusses the use of polyploidy induction, distant/wide hybridization and mutation breeding as tools for generating variety. Modern approaches accelerate the speed of crop breeding as an alternative tool. To achieve this goal, molecular markers are employed in breeding to capture the genetic variability through molecular analysis and population structuring. Allele mining is used to trace the evolution of alleles, identify new haplotypes and produce allele specific markers for use in marker aided selection using Genome wide association studies (GWAS) and quantitative trait loci (QTL) mapping. Plant genetic transformation is a rapid and effective mode of castor improvement is also discussed here. The efforts towards developing stable regeneration protocol provide a wide range of utility like embryo rescue in distant crosses, development of somaclonal variation, haploid development using anther culture and callus development for stable genetic transformation has reviewed in this article. Omics has provided intuitions to the molecular mechanisms of (a)biotic stress management in castor along with dissected out the possible genes for improving the yield. Relating genes to traits offers additional scientific inevitability leading to enhancement and sympathetic mechanisms of yield improvement and several stress tolerance.
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Affiliation(s)
- Rumit Patel
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand, 388110, India
- Department of Genetics & Plant Breeding, B. A. College of Agriculture, Anand Agricultural University, Anand, 388110, India
| | - Juned Menon
- Department of Genetics & Plant Breeding, B. A. College of Agriculture, Anand Agricultural University, Anand, 388110, India
| | - Sushil Kumar
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand, 388110, India
| | - Márcia B.M. Nóbrega
- Embrapa Algodão, Rua Oswaldo Cruz, nº 1.143, Centenário, CEP 58428-095, Campina Grande, PB, Brazil
| | - Dipak A. Patel
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand, 388110, India
| | - Amar A. Sakure
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand, 388110, India
| | - Mahesh B. Vaja
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand, 388110, India
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8
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Gálvez-Silva M, Arros P, Berríos-Pastén C, Villamil A, Rodas PI, Araya I, Iglesias R, Araya P, Hormazábal JC, Bohle C, Chen Y, Gan YH, Chávez FP, Lagos R, Marcoleta AE. Carbapenem-resistant hypervirulent ST23 Klebsiella pneumoniae with a highly transmissible dual-carbapenemase plasmid in Chile. Biol Res 2024; 57:7. [PMID: 38475927 DOI: 10.1186/s40659-024-00485-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND The convergence of hypervirulence and carbapenem resistance in the bacterial pathogen Klebsiella pneumoniae represents a critical global health concern. Hypervirulent K. pneumoniae (hvKp) strains, frequently from sequence type 23 (ST23) and having a K1 capsule, have been associated with severe community-acquired invasive infections. Although hvKp were initially restricted to Southeast Asia and primarily antibiotic-sensitive, carbapenem-resistant hvKp infections are reported worldwide. Here, within the carbapenemase production Enterobacterales surveillance system headed by the Chilean Public Health Institute, we describe the isolation in Chile of a high-risk ST23 dual-carbapenemase-producing hvKp strain, which carbapenemase genes are encoded in a single conjugative plasmid. RESULTS Phenotypic and molecular tests of this strain revealed an extensive resistance to at least 15 antibiotic classes and the production of KPC-2 and VIM-1 carbapenemases. Unexpectedly, this isolate lacked hypermucoviscosity, challenging this commonly used hvKp identification criteria. Complete genome sequencing and analysis confirmed the K1 capsular type, the KpVP-1 virulence plasmid, and the GIE492 and ICEKp10 genomic islands carrying virulence factors strongly associated with hvKp. Although this isolate belonged to the globally disseminated hvKp clonal group CG23-I, it is unique, as it formed a clade apart from a previously reported Chilean ST23 hvKp isolate and acquired an IncN KPC-2 plasmid highly disseminated in South America (absent in other hvKp genomes), but now including a class-I integron carrying blaVIM-1 and other resistance genes. Notably, this isolate was able to conjugate the double carbapenemase plasmid to an E. coli recipient, conferring resistance to 1st -5th generation cephalosporins (including combinations with beta-lactamase inhibitors), penicillins, monobactams, and carbapenems. CONCLUSIONS We reported the isolation in Chile of high-risk carbapenem-resistant hvKp carrying a highly transmissible conjugative plasmid encoding KPC-2 and VIM-1 carbapenemases, conferring resistance to most beta-lactams. Furthermore, the lack of hypermucoviscosity argues against this trait as a reliable hvKp marker. These findings highlight the rapid evolution towards multi-drug resistance of hvKp in Chile and globally, as well as the importance of conjugative plasmids and other mobile genetic elements in this convergence. In this regard, genomic approaches provide valuable support to monitor and obtain essential information on these priority pathogens and mobile elements.
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Affiliation(s)
- Matías Gálvez-Silva
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Las Palmeras, Ñuñoa, Santiago, 3425, Chile
| | - Patricio Arros
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Las Palmeras, Ñuñoa, Santiago, 3425, Chile
| | - Camilo Berríos-Pastén
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Las Palmeras, Ñuñoa, Santiago, 3425, Chile
| | - Aura Villamil
- Instituto de Salud Pública Marathon, Ñuñoa, Santiago, 1000, Chile
| | - Paula I Rodas
- Instituto de Salud Pública Marathon, Ñuñoa, Santiago, 1000, Chile
| | - Ingrid Araya
- Instituto de Salud Pública Marathon, Ñuñoa, Santiago, 1000, Chile
| | - Rodrigo Iglesias
- Instituto de Salud Pública Marathon, Ñuñoa, Santiago, 1000, Chile
| | - Pamela Araya
- Instituto de Salud Pública Marathon, Ñuñoa, Santiago, 1000, Chile
| | | | | | - Yahua Chen
- Yong Loo Lin School of Medicine, National University of Singapore, MD7, 8 Medical Drive, Singapore, Singapore
| | - Yunn-Hwen Gan
- Yong Loo Lin School of Medicine, National University of Singapore, MD7, 8 Medical Drive, Singapore, Singapore
| | - Francisco P Chávez
- Laboratorio de Microbiología de Sistemas, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Las Palmeras, Ñuñoa, Santiago, 3425, Chile
| | - Rosalba Lagos
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Las Palmeras, Ñuñoa, Santiago, 3425, Chile
| | - Andrés E Marcoleta
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Las Palmeras, Ñuñoa, Santiago, 3425, Chile.
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9
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Trang KB, Pahl MC, Pippin JA, Su C, Littleton SH, Sharma P, Kulkarni NN, Ghanem LR, Terry NA, O’Brien JM, Wagley Y, Hankenson KD, Jermusyk A, Hoskins JW, Amundadottir LT, Xu M, Brown KM, Anderson SA, Yang W, Titchenell PM, Seale P, Cook L, Levings MK, Zemel BS, Chesi A, Wells AD, Grant SF. 3D genomic features across >50 diverse cell types reveal insights into the genomic architecture of childhood obesity. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.08.30.23294092. [PMID: 37693606 PMCID: PMC10491377 DOI: 10.1101/2023.08.30.23294092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
The prevalence of childhood obesity is increasing worldwide, along with the associated common comorbidities of type 2 diabetes and cardiovascular disease in later life. Motivated by evidence for a strong genetic component, our prior genome-wide association study (GWAS) efforts for childhood obesity revealed 19 independent signals for the trait; however, the mechanism of action of these loci remains to be elucidated. To molecularly characterize these childhood obesity loci we sought to determine the underlying causal variants and the corresponding effector genes within diverse cellular contexts. Integrating childhood obesity GWAS summary statistics with our existing 3D genomic datasets for 57 human cell types, consisting of high-resolution promoter-focused Capture-C/Hi-C, ATAC-seq, and RNA-seq, we applied stratified LD score regression and calculated the proportion of genome-wide SNP heritability attributable to cell type-specific features, revealing pancreatic alpha cell enrichment as the most statistically significant. Subsequent chromatin contact-based fine-mapping was carried out for genome-wide significant childhood obesity loci and their linkage disequilibrium proxies to implicate effector genes, yielded the most abundant number of candidate variants and target genes at the BDNF, ADCY3, TMEM18 and FTO loci in skeletal muscle myotubes and the pancreatic beta-cell line, EndoC-BH1. One novel implicated effector gene, ALKAL2 - an inflammation-responsive gene in nerve nociceptors - was observed at the key TMEM18 locus across multiple immune cell types. Interestingly, this observation was also supported through colocalization analysis using expression quantitative trait loci (eQTL) derived from the Genotype-Tissue Expression (GTEx) dataset, supporting an inflammatory and neurologic component to the pathogenesis of childhood obesity. Our comprehensive appraisal of 3D genomic datasets generated in a myriad of different cell types provides genomic insights into pediatric obesity pathogenesis.
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Affiliation(s)
- Khanh B. Trang
- Center for Spatial and Functional Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Matthew C. Pahl
- Center for Spatial and Functional Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - James A. Pippin
- Center for Spatial and Functional Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Chun Su
- Center for Spatial and Functional Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sheridan H. Littleton
- Center for Spatial and Functional Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Prabhat Sharma
- Center for Spatial and Functional Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Nikhil N. Kulkarni
- Center for Spatial and Functional Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Louis R. Ghanem
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, PA, USA
| | - Natalie A. Terry
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, PA, USA
| | - Joan M. O’Brien
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, PA, USA
- Penn Medicine Center for Ophthalmic Genetics in Complex Disease
| | - Yadav Wagley
- Department of Orthopedic Surgery University of Michigan Medical School Ann Arbor, MI, USA
| | - Kurt D. Hankenson
- Department of Orthopedic Surgery University of Michigan Medical School Ann Arbor, MI, USA
| | - Ashley Jermusyk
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jason W. Hoskins
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Laufey T. Amundadottir
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Mai Xu
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Kevin M Brown
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Stewart A. Anderson
- Department of Child and Adolescent Psychiatry, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Wenli Yang
- Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Paul M. Titchenell
- Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Patrick Seale
- Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Laura Cook
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Department of Critical Care, Melbourne Medical School, University of Melbourne, Melbourne, VIC, Australia
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Megan K. Levings
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
| | - Babette S. Zemel
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alessandra Chesi
- Center for Spatial and Functional Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew D. Wells
- Center for Spatial and Functional Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Struan F.A. Grant
- Center for Spatial and Functional Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division Endocrinology and Diabetes, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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10
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Rodrick E, Kindler JM. Bone mass accrual in children. Curr Opin Endocrinol Diabetes Obes 2024; 31:53-59. [PMID: 38010050 PMCID: PMC11015822 DOI: 10.1097/med.0000000000000849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
PURPOSE OF REVIEW Bone accrual during childhood and adolescence is critical for the attainment of peak bone mass and is a major contributing factor towards osteoporosis in later life. Bone mass accrual is influenced by nonmodifiable factors, such as genetics, sex, race, ethnicity, and puberty, as well as modifiable factors, such as physical activity and diet. Recent progress in bone imaging has allowed clinicians and researchers to better measure the morphology, density, and strength of the growing skeleton, thereby encompassing key characteristics of peak bone strength. In this review, the patterning of bone accrual and contributors to these changes will be described, as well as new techniques assessing bone mass and strength in pediatric research and clinical settings. RECENT FINDINGS This review discusses factors influencing peak bone mass attainment and techniques used to assess the human skeleton. SUMMARY The rate of bone accrual and the magnitude of peak bone mass attainment occurs in specific patterns varying by sex, race, ethnicity, longitudinal growth, and body composition. Physical activity, diet, and nutritional status impact these processes. There is a need for longitudinal studies utilizing novel imaging modalities to unveil factors involved in the attainment and maintenance of peak bone strength.
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Affiliation(s)
- Eugene Rodrick
- University of Georgia, Department of Nutritional Sciences, Athens, Georgia, USA
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11
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Gutierrez-Castillo DE, Barrett E, Roberts R. A recently collected Xanthomonas translucens isolate encodes TAL effectors distinct from older, less virulent isolates. Microb Genom 2024; 10:001177. [PMID: 38189214 PMCID: PMC10868612 DOI: 10.1099/mgen.0.001177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/19/2023] [Indexed: 01/09/2024] Open
Abstract
Xanthomonas translucens, the causal agent of bacterial leaf streak disease (BLS) in cereals, is a re-emerging pathogen that is becoming increasingly destructive across the world. While BLS has caused yield losses in the past, there is anecdotal evidence that newer isolates may be more virulent. We observed that two X. translucens isolates collected from two sites in Colorado, USA, are more aggressive on current wheat and barley varieties compared to older isolates, and we hypothesize that genetic changes between recent and older isolates contribute to the differences in isolate aggressiveness. To test this, we phenotyped and genetically characterized two X. translucens isolates collected from Colorado in 2018, which we designated CO236 (from barley) and CO237 (from wheat). Using pathovar-specific phenotyping and PCR primers, we determined that CO236 belongs to pathovar translucens (Xtt) and CO237 belongs to pathovar undulosa (Xtu). We sequenced the full genomes of the isolates using Oxford Nanopore long-read sequencing, and compared their whole genomes against published X. translucens genomes. This analysis confirmed our pathovar designations for Xtt CO236 and Xtu CO237, and showed that, at the whole-genome level, there were no obvious genomic structural changes between Xtt CO236 and Xtu CO237 and other respective published pathovar genomes. Focusing on pathovar undulosa (Xtu CO237), we then compared putative type III effectors among all available Xtu isolate genomes and found that they were highly conserved. However, there were striking differences in the presence and sequence of various transcription activator-like effectors between Xtu CO237 and published undulosa genomes, which correlate with isolate virulence. Here, we explore the potential implications of the differences in these virulence factors, and provide possible explanations for the increased virulence of recently emerged isolates.
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Affiliation(s)
| | - Emma Barrett
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Robyn Roberts
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
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12
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Sapoval N, Tanevski M, Treangen TJ. KombOver: Efficient k-core and K-truss based characterization of perturbations within the human gut microbiome. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2024; 29:506-520. [PMID: 38160303 PMCID: PMC10764071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
The microbes present in the human gastrointestinal tract are regularly linked to human health and disease outcomes. Thanks to technological and methodological advances in recent years, metagenomic sequencing data, and computational methods designed to analyze metagenomic data, have contributed to improved understanding of the link between the human gut microbiome and disease. However, while numerous methods have been recently developed to extract quantitative and qualitative results from host-associated microbiome data, improved computational tools are still needed to track microbiome dynamics with short-read sequencing data. Previously we have proposed KOMB as a de novo tool for identifying copy number variations in metagenomes for characterizing microbial genome dynamics in response to perturbations. In this work, we present KombOver (KO), which includes four key contributions with respect to our previous work: (i) it scales to large microbiome study cohorts, (ii) it includes both k-core and K-truss based analysis, (iii) we provide the foundation of a theoretical understanding of the relation between various graph-based metagenome representations, and (iv) we provide an improved user experience with easier-to-run code and more descriptive outputs/results. To highlight the aforementioned benefits, we applied KO to nearly 1000 human microbiome samples, requiring less than 10 minutes and 10 GB RAM per sample to process these data. Furthermore, we highlight how graph-based approaches such as k-core and K-truss can be informative for pinpointing microbial community dynamics within a myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) cohort. KO is open source and available for download/use at: https://github.com/treangenlab/komb.
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Affiliation(s)
- Nicolae Sapoval
- Department of Computer Science, Rice University, Houston, TX 77005, USA,
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13
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Drag MH, Debes KP, Franck CS, Flethøj M, Lyhne MK, Møller JE, Ludvigsen TP, Jespersen T, Olsen LH, Kilpeläinen TO. Nanopore sequencing reveals methylation changes associated with obesity in circulating cell-free DNA from Göttingen Minipigs. Epigenetics 2023; 18:2199374. [PMID: 37032646 PMCID: PMC10088973 DOI: 10.1080/15592294.2023.2199374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/29/2023] [Accepted: 03/08/2023] [Indexed: 04/11/2023] Open
Abstract
Profiling of circulating cell-free DNA (cfDNA) by tissue-specific base modifications, such as 5-methylcytosines (5mC), may enable the monitoring of ongoing pathophysiological processes. Nanopore sequencing allows genome-wide 5mC detection in cfDNA without bisulphite conversion. The aims of this study were: i) to find differentially methylated regions (DMRs) of cfDNA associated with obesity in Göttingen minipigs using Nanopore sequencing, ii) to validate a subset of the DMRs using methylation-specific PCR (MSP-PCR), and iii) to compare the cfDNA DMRs with those from whole blood genomic DNA (gDNA). Serum cfDNA and gDNA were obtained from 10 lean and 7 obese Göttingen Minipigs both with experimentally induced myocardial infarction and sequenced using Oxford Nanopore MinION. A total of 1,236 cfDNA DMRs (FDR<0.01) were associated with obesity. In silico analysis showed enrichment of the adipocytokine signalling, glucagon signalling, and cellular glucose homoeostasis pathways. A strong cfDNA DMR was discovered in PPARGC1B, a gene linked to obesity and type 2 diabetes. The DMR was validated using MSP-PCR and correlated significantly with body weight (P < 0.05). No DMRs intersected between cfDNA and gDNA, suggesting that cfDNA originates from body-wide shedding of DNA. In conclusion, nanopore sequencing detected differential methylation in minute quantities (0.1-1 ng/µl) of cfDNA. Future work should focus on translation into human and comparing 5mC from somatic tissues to pinpoint the exact location of pathology.
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Affiliation(s)
- Markus Hodal Drag
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Conservation, Copenhagen Zoo, Frederiksberg, Denmark
| | | | - Clara Sandkamm Franck
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mette Flethøj
- Research & Early Development, Novo Nordisk A/S, Måløv, Denmark
| | - Mille Kronborg Lyhne
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jacob Eifer Møller
- Department of Cardiology, Copenhagen University Hospital and Odense University Hospital, Odense, Denmark
| | | | - Thomas Jespersen
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lisbeth Høier Olsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tuomas O. Kilpeläinen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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14
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Yan G, Song D, Li JJ. scReadSim: a single-cell RNA-seq and ATAC-seq read simulator. Nat Commun 2023; 14:7482. [PMID: 37980428 PMCID: PMC10657386 DOI: 10.1038/s41467-023-43162-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 11/02/2023] [Indexed: 11/20/2023] Open
Abstract
Benchmarking single-cell RNA-seq (scRNA-seq) and single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) computational tools demands simulators to generate realistic sequencing reads. However, none of the few read simulators aim to mimic real data. To fill this gap, we introduce scReadSim, a single-cell RNA-seq and ATAC-seq read simulator that allows user-specified ground truths and generates synthetic sequencing reads (in a FASTQ or BAM file) by mimicking real data. At both read-sequence and read-count levels, scReadSim mimics real scRNA-seq and scATAC-seq data. Moreover, scReadSim provides ground truths, including unique molecular identifier (UMI) counts for scRNA-seq and open chromatin regions for scATAC-seq. In particular, scReadSim allows users to design cell-type-specific ground-truth open chromatin regions for scATAC-seq data generation. In benchmark applications of scReadSim, we show that UMI-tools achieves the top accuracy in scRNA-seq UMI deduplication, and HMMRATAC and MACS3 achieve the top performance in scATAC-seq peak calling.
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Affiliation(s)
- Guanao Yan
- Department of Statistics, University of California, Los Angeles, CA 90095-1554, USA
| | - Dongyuan Song
- Bioinformatics Interdepartmental Ph.D. Program, University of California, Los Angeles, CA, 90095-7246, USA
| | - Jingyi Jessica Li
- Department of Statistics, University of California, Los Angeles, CA 90095-1554, USA.
- Bioinformatics Interdepartmental Ph.D. Program, University of California, Los Angeles, CA, 90095-7246, USA.
- Department of Human Genetics, University of California, Los Angeles, CA, 90095-7088, USA.
- Department of Computational Medicine, University of California, Los Angeles, CA, 90095-1766, USA.
- Department of Biostatistics, University of California, Los Angeles, CA, 90095-1772, USA.
- Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA, 02138, USA.
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15
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Hou R, Hon CC, Huang Y. CamoTSS: analysis of alternative transcription start sites for cellular phenotypes and regulatory patterns from 5' scRNA-seq data. Nat Commun 2023; 14:7240. [PMID: 37945584 PMCID: PMC10636040 DOI: 10.1038/s41467-023-42636-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 10/16/2023] [Indexed: 11/12/2023] Open
Abstract
Five-prime single-cell RNA-seq (scRNA-seq) has been widely employed to profile cellular transcriptomes, however, its power of analysing transcription start sites (TSS) has not been fully utilised. Here, we present a computational method suite, CamoTSS, to precisely identify TSS and quantify its expression by leveraging the cDNA on read 1, which enables effective detection of alternative TSS usage. With various experimental data sets, we have demonstrated that CamoTSS can accurately identify TSS and the detected alternative TSS usages showed strong specificity in different biological processes, including cell types across human organs, the development of human thymus, and cancer conditions. As evidenced in nasopharyngeal cancer, alternative TSS usage can also reveal regulatory patterns including systematic TSS dysregulations.
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Affiliation(s)
- Ruiyan Hou
- School of Biomedical Sciences, University of Hong Kong, Hong Kong, SAR, China
| | - Chung-Chau Hon
- RIKEN Center for Integrative Medical Sciences, Yokohama City, Kanagawa, 230-0045, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Yuanhua Huang
- School of Biomedical Sciences, University of Hong Kong, Hong Kong, SAR, China.
- Department of Statistics and Actuarial Science, University of Hong Kong, Hong Kong, AR, China.
- Center for Translational Stem Cell Biology, Hong Kong Science and Technology Park, Hong Kong, SAR, China.
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16
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Zhu YJ, Liao ML, Dong YW. Exploring the adaptability of the secondary structure of mRNA to temperature in intertidal snails based on SHAPE experiments. J Exp Biol 2023; 226:jeb246544. [PMID: 37767692 DOI: 10.1242/jeb.246544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023]
Abstract
RNA-based thermal regulation is an important strategy for organisms to cope with temperature changes. Inhabiting the intertidal rocky shore, a key interface of the ocean, atmosphere and terrestrial environments, intertidal species have developed variable thermal adaptation mechanisms; however, adaptions at the RNA level remain largely uninvestigated. To examine the relationship between mRNA structural stability and species distribution, in the present study, the secondary structure of cytosolic malate dehydrogenase (cMDH) mRNA of Echinolittorina malaccana, Echinolittorina radiata and Littorina brevicula was determined using selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE), and the change in folding free energy of formation (ΔGfold) was calculated. The results showed that ΔGfold increased as the temperature increased. The difference in ΔGfold (ΔΔGfold) between two specific temperatures (25 versus 0°C, 37 versus 0°C and 57 versus 0°C) differed among the three species, and the ΔΔGfold value of E. malaccana was significantly lower than those of E. radiata and L. brevicula. The number of stems of cMDH mRNA of the snails decreased with increasing temperature, and the breakpoint temperature of E. malaccana was the highest among these. The number of loops was also reduced with increasing temperature, while the length of the loop structure increased accordingly. Consequently, these structural changes can potentially affect the translational efficiency of mRNA. These results imply that there were interspecific differences in the thermal stability of RNA secondary structures in intertidal snails, and these differences may be related to snail distribution.
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Affiliation(s)
- Ya-Jie Zhu
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao 266003, PR China
| | - Ming-Ling Liao
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao 266003, PR China
| | - Yun-Wei Dong
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao 266003, PR China
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17
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Lazaros K, Vlamos P, Vrahatis AG. Methods for cell-type annotation on scRNA-seq data: A recent overview. J Bioinform Comput Biol 2023; 21:2340002. [PMID: 37743364 DOI: 10.1142/s0219720023400024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The evolution of single-cell technology is ongoing, continually generating massive amounts of data that reveal many mysteries surrounding intricate diseases. However, their drawbacks continue to constrain us. Among these, annotating cell types in single-cell gene expressions pose a substantial challenge, despite the myriad of tools at our disposal. The rapid growth in data, resources, and tools has consequently brought about significant alterations in this area over the years. In our study, we spotlight all note-worthy cell type annotation techniques developed over the past four years. We provide an overview of the latest trends in this field, showcasing the most advanced methods in taxonomy. Our research underscores the demand for additional tools that incorporate a biological context and also predicts that the rising trend of graph neural network approaches will likely lead this research field in the coming years.
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Affiliation(s)
- Konstantinos Lazaros
- Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, 49100 Corfu, Greece
| | - Panagiotis Vlamos
- Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, 49100 Corfu, Greece
| | - Aristidis G Vrahatis
- Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, 49100 Corfu, Greece
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18
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Kim EY, Kim JE, Chung SH, Park JE, Yoon D, Min HJ, Sung Y, Lee SB, Kim SW, Chang EJ. Concomitant induction of SLIT3 and microRNA-218-2 in macrophages by toll-like receptor 4 activation limits osteoclast commitment. Cell Commun Signal 2023; 21:213. [PMID: 37596575 PMCID: PMC10436635 DOI: 10.1186/s12964-023-01226-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/12/2023] [Indexed: 08/20/2023] Open
Abstract
BACKGROUND Toll-like receptor 4 (TLR4) conducts a highly regulated inflammatory process by limiting the extent of inflammation to avoid toxicity and tissue damage, even in bone tissues. Thus, it is plausible that strategies for the maintenance of normal bone-immunity to prevent undesirable bone damage by TLR4 activation can exist, but direct evidence is still lacking. METHODS Osteoclast precursors (OCPs) obtained from WT or Slit3-deficient mice were differentiated into osteoclast (OC) with macrophage colony-stimulating factor (M-CSF), RANK ligand (RANKL) and lipopolysaccharide (LPS) by determining the number of TRAP-positive multinuclear cells (TRAP+ MNCs). To determine the alteration of OCPs population, fluorescence-activated cell sorting (FACS) was conducted in bone marrow cells in mice after LPS injection. The severity of bone loss in LPS injected WT or Slit3-deficient mice was evaluated by micro-CT analysis. RESULT We demonstrate that TLR4 activation by LPS inhibits OC commitment by inducing the concomitant expression of miR-218-2-3p and its host gene, Slit3, in mouse OCPs. TLR4 activation by LPS induced SLIT3 and its receptor ROBO1 in BMMs, and this SLIT3-ROBO1 axis hinders RANKL-induced OC differentiation by switching the protein levels of C/EBP-β isoforms. A deficiency of SLIT3 resulted in increased RANKL-induced OC differentiation, and the elevated expression of OC marker genes including Pu.1, Nfatc1, and Ctsk. Notably, Slit3-deficient mice showed expanded OCP populations in the bone marrow. We also found that miR-218-2 was concomitantly induced with SLIT3 expression after LPS treatment, and that this miRNA directly suppressed Tnfrsf11a (RANK) expression at both gene and protein levels, linking it to a decrease in OC differentiation. An endogenous miR-218-2 block rescued the expression of RANK and subsequent OC formation in LPS-stimulated OCPs. Aligned with these results, SLIT3-deficient mice displayed increased OC formation and reduced bone density after LPS challenge. CONCLUSION Our findings suggest that the TLR4-dependent concomitant induction of Slit3 and miR-218-2 targets RANK in OCPs to restrain OC commitment, thereby avoiding an uncoordinated loss of bone through inflammatory processes. These observations provide a mechanistic explanation for the role of TLR4 in controlling the commitment phase of OC differentiation. Video Abstract.
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Affiliation(s)
- Eun-Young Kim
- Department of Biochemistry and Molecular Biology, Asan Medical Center and AMIST, University of Ulsan College of Medicine, 88, Olympic-Ro 43-Gil, Songpa-Gu, Seoul, 05505, Korea
- Stem Cell Immunomodulation Research Center, University of Ulsan College of Medicine, Seoul, 05505, Korea
| | - Ji-Eun Kim
- Department of Biochemistry and Molecular Biology, Asan Medical Center and AMIST, University of Ulsan College of Medicine, 88, Olympic-Ro 43-Gil, Songpa-Gu, Seoul, 05505, Korea
- Stem Cell Immunomodulation Research Center, University of Ulsan College of Medicine, Seoul, 05505, Korea
| | - Soo-Hyun Chung
- Department of Biochemistry and Molecular Biology, Asan Medical Center and AMIST, University of Ulsan College of Medicine, 88, Olympic-Ro 43-Gil, Songpa-Gu, Seoul, 05505, Korea
- Stem Cell Immunomodulation Research Center, University of Ulsan College of Medicine, Seoul, 05505, Korea
| | - Ji-Eun Park
- Department of Biochemistry and Molecular Biology, Asan Medical Center and AMIST, University of Ulsan College of Medicine, 88, Olympic-Ro 43-Gil, Songpa-Gu, Seoul, 05505, Korea
| | - Dohee Yoon
- Department of Biochemistry and Molecular Biology, Asan Medical Center and AMIST, University of Ulsan College of Medicine, 88, Olympic-Ro 43-Gil, Songpa-Gu, Seoul, 05505, Korea
- Stem Cell Immunomodulation Research Center, University of Ulsan College of Medicine, Seoul, 05505, Korea
| | - Hyo-Jin Min
- Department of Biochemistry and Molecular Biology, Asan Medical Center and AMIST, University of Ulsan College of Medicine, 88, Olympic-Ro 43-Gil, Songpa-Gu, Seoul, 05505, Korea
- Stem Cell Immunomodulation Research Center, University of Ulsan College of Medicine, Seoul, 05505, Korea
| | - Yoolim Sung
- Department of Biochemistry and Molecular Biology, Asan Medical Center and AMIST, University of Ulsan College of Medicine, 88, Olympic-Ro 43-Gil, Songpa-Gu, Seoul, 05505, Korea
- Stem Cell Immunomodulation Research Center, University of Ulsan College of Medicine, Seoul, 05505, Korea
| | - Soo Been Lee
- Department of Biochemistry and Molecular Biology, Asan Medical Center and AMIST, University of Ulsan College of Medicine, 88, Olympic-Ro 43-Gil, Songpa-Gu, Seoul, 05505, Korea
- Stem Cell Immunomodulation Research Center, University of Ulsan College of Medicine, Seoul, 05505, Korea
| | - Seong Who Kim
- Department of Biochemistry and Molecular Biology, Asan Medical Center and AMIST, University of Ulsan College of Medicine, 88, Olympic-Ro 43-Gil, Songpa-Gu, Seoul, 05505, Korea.
- Stem Cell Immunomodulation Research Center, University of Ulsan College of Medicine, Seoul, 05505, Korea.
| | - Eun-Ju Chang
- Department of Biochemistry and Molecular Biology, Asan Medical Center and AMIST, University of Ulsan College of Medicine, 88, Olympic-Ro 43-Gil, Songpa-Gu, Seoul, 05505, Korea.
- Stem Cell Immunomodulation Research Center, University of Ulsan College of Medicine, Seoul, 05505, Korea.
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19
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Tang Y, Li X, Shi M. LIDER: cell embedding based deep neural network classifier for supervised cell type identification. PeerJ 2023; 11:e15862. [PMID: 37601262 PMCID: PMC10439717 DOI: 10.7717/peerj.15862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/17/2023] [Indexed: 08/22/2023] Open
Abstract
Background Automatic cell type identification has been an urgent task for the rapid development of single-cell RNA-seq techniques. Generally, the current approach for cell type identification is to generate cell clusters by unsupervised clustering and later assign labels to each cell cluster with manual annotation. Methods Here, we introduce LIDER (celL embeddIng based Deep nEural netwoRk classifier), a deep supervised learning method that combines cell embedding and deep neural network classifier for automatic cell type identification. Based on a stacked denoising autoencoder with a tailored and reconstructed loss function, LIDER identifies cell embedding and predicts cell types with a deep neural network classifier. LIDER was developed upon a stacked denoising autoencoder to learn encoder-decoder structures for identifying cell embedding. Results LIDER accurately identifies cell types by using stacked denoising autoencoder. Benchmarking against state-of-the-art methods across eight types of single-cell data, LIDER achieves comparable or even superior enhancement performance. Moreover, LIDER suggests comparable robust to batch effects. Our results show a potential in deep supervised learning for automatic cell type identification of single-cell RNA-seq data. The LIDER codes are available at https://github.com/ShiMGLab/LIDER.
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Affiliation(s)
- Yachen Tang
- Hefei University of Technology, Hefei, China
| | - Xuefeng Li
- Hefei University of Technology, Hefei, China
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20
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Stamp J, DenAdel A, Weinreich D, Crawford L. Leveraging the genetic correlation between traits improves the detection of epistasis in genome-wide association studies. G3 (BETHESDA, MD.) 2023; 13:jkad118. [PMID: 37243672 PMCID: PMC10484060 DOI: 10.1093/g3journal/jkad118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 01/11/2023] [Accepted: 05/23/2023] [Indexed: 05/29/2023]
Abstract
Epistasis, commonly defined as the interaction between genetic loci, is known to play an important role in the phenotypic variation of complex traits. As a result, many statistical methods have been developed to identify genetic variants that are involved in epistasis, and nearly all of these approaches carry out this task by focusing on analyzing one trait at a time. Previous studies have shown that jointly modeling multiple phenotypes can often dramatically increase statistical power for association mapping. In this study, we present the "multivariate MArginal ePIstasis Test" (mvMAPIT)-a multioutcome generalization of a recently proposed epistatic detection method which seeks to detect marginal epistasis or the combined pairwise interaction effects between a given variant and all other variants. By searching for marginal epistatic effects, one can identify genetic variants that are involved in epistasis without the need to identify the exact partners with which the variants interact-thus, potentially alleviating much of the statistical and computational burden associated with conventional explicit search-based methods. Our proposed mvMAPIT builds upon this strategy by taking advantage of correlation structure between traits to improve the identification of variants involved in epistasis. We formulate mvMAPIT as a multivariate linear mixed model and develop a multitrait variance component estimation algorithm for efficient parameter inference and P-value computation. Together with reasonable model approximations, our proposed approach is scalable to moderately sized genome-wide association studies. With simulations, we illustrate the benefits of mvMAPIT over univariate (or single-trait) epistatic mapping strategies. We also apply mvMAPIT framework to protein sequence data from two broadly neutralizing anti-influenza antibodies and approximately 2,000 heterogeneous stock of mice from the Wellcome Trust Centre for Human Genetics. The mvMAPIT R package can be downloaded at https://github.com/lcrawlab/mvMAPIT.
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Affiliation(s)
- Julian Stamp
- Center for Computational Molecular Biology, Brown University, Providence, RI 02906, USA
| | - Alan DenAdel
- Center for Computational Molecular Biology, Brown University, Providence, RI 02906, USA
| | - Daniel Weinreich
- Center for Computational Molecular Biology, Brown University, Providence, RI 02906, USA
- Department of Ecology, Evolution, and Organismal Biology, Brown University, Providence, RI 02906, USA
| | - Lorin Crawford
- Center for Computational Molecular Biology, Brown University, Providence, RI 02906, USA
- Department of Biostatistics, Brown University, Providence, RI 02903, USA
- Microsoft Research New England, Cambridge, MA 02142, USA
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21
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Xu X, Qi Z, Han X, Xu A, Geng Z, He X, Ren Y, Duo Z. Predicting anticancer drug sensitivity on distributed data sources using federated deep learning. Heliyon 2023; 9:e18615. [PMID: 37593639 PMCID: PMC10427996 DOI: 10.1016/j.heliyon.2023.e18615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/12/2023] [Accepted: 07/24/2023] [Indexed: 08/19/2023] Open
Abstract
Drug sensitivity prediction plays a crucial role in precision cancer therapy. Collaboration among medical institutions can lead to better performance in drug sensitivity prediction. However, patient privacy and data protection regulation remain a severe impediment to centralized prediction studies. For the first time, we proposed a federated drug sensitivity prediction model with high generalization, combining distributed data sources while protecting private data. Cell lines are first classified into three categories using the waterfall method. Focal loss for solving class imbalance is then embedded into the horizontal federated deep learning framework, i.e., HFDL-fl is presented. Applying HFDL-fl to homogeneous and heterogeneous data, we obtained HFDL-Cross and HFDL-Within. Our comprehensive experiments demonstrated that (i) collaboration by HFDL-fl outperforms private model on local data, (ii) focal loss function can effectively improve model performance to classify cell lines in sensitive and resistant categories, and (iii) HFDL-fl is not significantly affected by data heterogeneity. To summarize, HFDL-fl provides a valuable solution to break down the barriers between medical institutions for privacy-preserving drug sensitivity prediction and therefore facilitates the development of cancer precision medicine and other privacy-related biomedical research.
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Affiliation(s)
- Xiaolu Xu
- School of Computer and Artificial Intelligence, Liaoning Normal University, Dalian 116029, China
| | - Zitong Qi
- Department of Statistics, University of Washington, Seattle, WA 98195, USA
| | - Xiumei Han
- College of Artificial Intelligence, Dalian Maritime University, Dalian 116026, China
| | - Aiguo Xu
- Department of Oncology, The Second People's Hospital of Lianyungang, Lianyungang 222023, China
| | - Zhaohong Geng
- Department of Cardiology, Second Affiliated Hospital of Dalian Medical University, Dalian 116023, China
| | - Xinyu He
- School of Computer and Artificial Intelligence, Liaoning Normal University, Dalian 116029, China
| | - Yonggong Ren
- School of Computer and Artificial Intelligence, Liaoning Normal University, Dalian 116029, China
| | - Zhaojun Duo
- School of Computer and Artificial Intelligence, Liaoning Normal University, Dalian 116029, China
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22
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Magdy Mohamed Abdelaziz Barakat S, Sallehuddin R, Yuhaniz SS, R. Khairuddin RF, Mahmood Y. Genome assembly composition of the String "ACGT" array: a review of data structure accuracy and performance challenges. PeerJ Comput Sci 2023; 9:e1180. [PMID: 37547391 PMCID: PMC10403225 DOI: 10.7717/peerj-cs.1180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 04/27/2023] [Indexed: 08/08/2023]
Abstract
Background The development of sequencing technology increases the number of genomes being sequenced. However, obtaining a quality genome sequence remains a challenge in genome assembly by assembling a massive number of short strings (reads) with the presence of repetitive sequences (repeats). Computer algorithms for genome assembly construct the entire genome from reads in two approaches. The de novo approach concatenates the reads based on the exact match between their suffix-prefix (overlapping). Reference-guided approach orders the reads based on their offsets in a well-known reference genome (reads alignment). The presence of repeats extends the technical ambiguity, making the algorithm unable to distinguish the reads resulting in misassembly and affecting the assembly approach accuracy. On the other hand, the massive number of reads causes a big assembly performance challenge. Method The repeat identification method was introduced for misassembly by prior identification of repetitive sequences, creating a repeat knowledge base to reduce ambiguity during the assembly process, thus enhancing the accuracy of the assembled genome. Also, hybridization between assembly approaches resulted in a lower misassembly degree with the aid of the reference genome. The assembly performance is optimized through data structure indexing and parallelization. This article's primary aim and contribution are to support the researchers through an extensive review to ease other researchers' search for genome assembly studies. The study also, highlighted the most recent developments and limitations in genome assembly accuracy and performance optimization. Results Our findings show the limitations of the repeat identification methods available, which only allow to detect of specific lengths of the repeat, and may not perform well when various types of repeats are present in a genome. We also found that most of the hybrid assembly approaches, either starting with de novo or reference-guided, have some limitations in handling repetitive sequences as it is more computationally costly and time intensive. Although the hybrid approach was found to outperform individual assembly approaches, optimizing its performance remains a challenge. Also, the usage of parallelization in overlapping and reads alignment for genome assembly is yet to be fully implemented in the hybrid assembly approach. Conclusion We suggest combining multiple repeat identification methods to enhance the accuracy of identifying the repeats as an initial step to the hybrid assembly approach and combining genome indexing with parallelization for better optimization of its performance.
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Affiliation(s)
| | - Roselina Sallehuddin
- Computer Science, School of Computing, Faculty of Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Siti Sophiayati Yuhaniz
- Advanced Informatics Department, Razak Faculty of Technology and Informatics, Universiti Teknologi Malaysia, Kuala Lumpur, Kuala Lumpur, Malaysia
| | | | - Yasir Mahmood
- Faculty of Information Technology, The University of Lahore, Lahore, Lahore, Pakistan
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23
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Li L, Zheng X, Wang J, Zhang X, He X, Xiong L, Song S, Su J, Diao Y, Yuan Z, Zhang Z, Hu Z. Joint analysis of phenotype-effect-generation identifies loci associated with grain quality traits in rice hybrids. Nat Commun 2023; 14:3930. [PMID: 37402793 DOI: 10.1038/s41467-023-39534-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 06/16/2023] [Indexed: 07/06/2023] Open
Abstract
Genetic improvement of grain quality is more challenging in hybrid rice than in inbred rice due to additional nonadditive effects such as dominance. Here, we describe a pipeline developed for joint analysis of phenotypes, effects, and generations (JPEG). As a demonstration, we analyze 12 grain quality traits of 113 inbred lines (male parents), five tester lines (female parents), and 565 (113×5) of their hybrids. We sequence the parents for single nucleotide polymorphisms calling and infer the genotypes of the hybrids. Genome-wide association studies with JPEG identify 128 loci associated with at least one of the 12 traits, including 44, 97, and 13 loci with additive effects, dominant effects, and both additive and dominant effects, respectively. These loci together explain more than 30% of the genetic variation in hybrid performance for each of the traits. The JEPG statistical pipeline can help to identify superior crosses for breeding rice hybrids with improved grain quality.
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Affiliation(s)
- Lanzhi Li
- Hunan Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-making, College of Plant Protection, Hunan Agricultural University, 410128, Changsha, Hunan, China
| | - Xingfei Zheng
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crop Institute, Hubei Academy of Agricultural Sciences, 430064, Wuhan, Hubei, China
- State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, 430072, Wuhan, Hubei, China
| | - Jiabo Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Ministry of Education and Sichuan province, Southwest Minzu University, 610041, Chengdu, Sichuan, China
| | - Xueli Zhang
- Hunan Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-making, College of Plant Protection, Hunan Agricultural University, 410128, Changsha, Hunan, China
| | - Xiaogang He
- Hunan Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-making, College of Plant Protection, Hunan Agricultural University, 410128, Changsha, Hunan, China
| | - Liwen Xiong
- Hunan Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-making, College of Plant Protection, Hunan Agricultural University, 410128, Changsha, Hunan, China
| | - Shufeng Song
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, 410125, Changsha, Hunan, China
| | - Jing Su
- Hunan Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-making, College of Plant Protection, Hunan Agricultural University, 410128, Changsha, Hunan, China
| | - Ying Diao
- School of Life Science and Technology, Wuhan Polytechnic University, 430023, Wuhan, Hubei, China
| | - Zheming Yuan
- Hunan Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-making, College of Plant Protection, Hunan Agricultural University, 410128, Changsha, Hunan, China
| | - Zhiwu Zhang
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA.
| | - Zhongli Hu
- State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, 430072, Wuhan, Hubei, China.
- School of Life Science and Technology, Wuhan Polytechnic University, 430023, Wuhan, Hubei, China.
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24
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Rundell TB, Brunelli M, Alvi A, Safian G, Capobianco C, Tu W, Subedi S, Fiumera A, Musselman LP. Polygenic adaptation to overnutrition reveals a role for cholinergic signaling in longevity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.14.544888. [PMID: 37398379 PMCID: PMC10312690 DOI: 10.1101/2023.06.14.544888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Overnutrition by high-sugar (HS) feeding reduces both the lifespan and healthspan across taxa. Pressuring organisms to adapt to overnutrition can highlight genes and pathways important for the healthspan in stressful environments. We used an experimental evolution approach to adapt four replicate, outbred population pairs of Drosophila melanogaster to a HS or control diet. Sexes were separated and aged on either diet until mid-life, then mated to produce the next generation, allowing enrichment for protective alleles over time. All HS-selected populations increased their lifespan and were therefore used as a platform to compare allele frequencies and gene expression. Pathways functioning in the nervous system were overrepresented in the genomic data and showed evidence for parallel evolution, although very few genes were the same across replicates. Acetylcholine-related genes, including the muscarinic receptor mAChR-A, showed significant changes in allele frequency in multiple selected populations and differential expression on a HS diet. Using genetic and pharmacological approaches, we show that cholinergic signaling affects Drosophila feeding in a sugar-specific fashion. Together, these results suggest that adaptation produces changes in allele frequencies that benefit animals under conditions of overnutrition and that it is repeatable at the pathway level.
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25
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Kumasaka N, Rostom R, Huang N, Polanski K, Meyer KB, Patel S, Boyd R, Gomez C, Barnett SN, Panousis NI, Schwartzentruber J, Ghoussaini M, Lyons PA, Calero-Nieto FJ, Göttgens B, Barnes JL, Worlock KB, Yoshida M, Nikolić MZ, Stephenson E, Reynolds G, Haniffa M, Marioni JC, Stegle O, Hagai T, Teichmann SA. Mapping interindividual dynamics of innate immune response at single-cell resolution. Nat Genet 2023; 55:1066-1075. [PMID: 37308670 PMCID: PMC10260404 DOI: 10.1038/s41588-023-01421-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 04/27/2023] [Indexed: 06/14/2023]
Abstract
Common genetic variants across individuals modulate the cellular response to pathogens and are implicated in diverse immune pathologies, yet how they dynamically alter the response upon infection is not well understood. Here, we triggered antiviral responses in human fibroblasts from 68 healthy donors, and profiled tens of thousands of cells using single-cell RNA-sequencing. We developed GASPACHO (GAuSsian Processes for Association mapping leveraging Cell HeterOgeneity), a statistical approach designed to identify nonlinear dynamic genetic effects across transcriptional trajectories of cells. This approach identified 1,275 expression quantitative trait loci (local false discovery rate 10%) that manifested during the responses, many of which were colocalized with susceptibility loci identified by genome-wide association studies of infectious and autoimmune diseases, including the OAS1 splicing quantitative trait locus in a COVID-19 susceptibility locus. In summary, our analytical approach provides a unique framework for delineation of the genetic variants that shape a wide spectrum of transcriptional responses at single-cell resolution.
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Affiliation(s)
- Natsuhiko Kumasaka
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Medical Support Center of Japan Environment and Children's Study (JECS), National Center for Child Health and Development, Tokyo, Japan
| | - Raghd Rostom
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Ni Huang
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Sharad Patel
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Rachel Boyd
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Celine Gomez
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Sam N Barnett
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | - Jeremy Schwartzentruber
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Open Targets, Wellcome Genome Campus, Hinxton, UK
| | - Maya Ghoussaini
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Open Targets, Wellcome Genome Campus, Hinxton, UK
| | - Paul A Lyons
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | - Berthold Göttgens
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Josephine L Barnes
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Kaylee B Worlock
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Masahiro Yoshida
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Marko Z Nikolić
- UCL Respiratory, Division of Medicine, University College London, London, UK
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Emily Stephenson
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Gary Reynolds
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
- NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Department of Dermatology, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - John C Marioni
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Oliver Stegle
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center, Heidelberg, Germany
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Tzachi Hagai
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, Cambridge, UK.
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Kong Y, Mead EA, Fang G. Navigating the pitfalls of mapping DNA and RNA modifications. Nat Rev Genet 2023; 24:363-381. [PMID: 36653550 PMCID: PMC10722219 DOI: 10.1038/s41576-022-00559-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2022] [Indexed: 01/19/2023]
Abstract
Chemical modifications to nucleic acids occur across the kingdoms of life and carry important regulatory information. Reliable high-resolution mapping of these modifications is the foundation of functional and mechanistic studies, and recent methodological advances based on next-generation sequencing and long-read sequencing platforms are critical to achieving this aim. However, mapping technologies may have limitations that sometimes lead to inconsistent results. Some of these limitations are technical in nature and specific to certain types of technology. Here, however, we focus on common (yet not always widely recognized) pitfalls that are shared among frequently used mapping technologies and discuss strategies to help technology developers and users mitigate their effects. Although the emphasis is primarily on DNA modifications, RNA modifications are also discussed.
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Affiliation(s)
- Yimeng Kong
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edward A Mead
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gang Fang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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27
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Pielawski N, Andersson A, Avenel C, Behanova A, Chelebian E, Klemm A, Nysjö F, Solorzano L, Wählby C. TissUUmaps 3: Improvements in interactive visualization, exploration, and quality assessment of large-scale spatial omics data. Heliyon 2023; 9:e15306. [PMID: 37131430 PMCID: PMC10149187 DOI: 10.1016/j.heliyon.2023.e15306] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/30/2023] [Accepted: 04/03/2023] [Indexed: 05/04/2023] Open
Abstract
Background and objectives Spatially resolved techniques for exploring the molecular landscape of tissue samples, such as spatial transcriptomics, often result in millions of data points and images too large to view on a regular desktop computer, limiting the possibilities in visual interactive data exploration. TissUUmaps is a free, open-source browser-based tool for GPU-accelerated visualization and interactive exploration of 107+ data points overlaying tissue samples. Methods Herein we describe how TissUUmaps 3 provides instant multiresolution image viewing and can be customized, shared, and also integrated into Jupyter Notebooks. We introduce new modules where users can visualize markers and regions, explore spatial statistics, perform quantitative analyses of tissue morphology, and assess the quality of decoding in situ transcriptomics data. Results We show that thanks to targeted optimizations the time and cost associated with interactive data exploration were reduced, enabling TissUUmaps 3 to handle the scale of today's spatial transcriptomics methods. Conclusion TissUUmaps 3 provides significantly improved performance for large multiplex datasets as compared to previous versions. We envision TissUUmaps to contribute to broader dissemination and flexible sharing of largescale spatial omics data.
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Affiliation(s)
- Nicolas Pielawski
- Department of Information Technology and SciLifeLab BioImage Informatics Facility, Uppsala University, Uppsala, Sweden
| | - Axel Andersson
- Department of Information Technology and SciLifeLab BioImage Informatics Facility, Uppsala University, Uppsala, Sweden
| | - Christophe Avenel
- Department of Information Technology and SciLifeLab BioImage Informatics Facility, Uppsala University, Uppsala, Sweden
| | - Andrea Behanova
- Department of Information Technology and SciLifeLab BioImage Informatics Facility, Uppsala University, Uppsala, Sweden
| | - Eduard Chelebian
- Department of Information Technology and SciLifeLab BioImage Informatics Facility, Uppsala University, Uppsala, Sweden
| | - Anna Klemm
- Department of Information Technology and SciLifeLab BioImage Informatics Facility, Uppsala University, Uppsala, Sweden
| | - Fredrik Nysjö
- Department of Information Technology and SciLifeLab BioImage Informatics Facility, Uppsala University, Uppsala, Sweden
| | - Leslie Solorzano
- Department of Information Technology and SciLifeLab BioImage Informatics Facility, Uppsala University, Uppsala, Sweden
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Carolina Wählby
- Department of Information Technology and SciLifeLab BioImage Informatics Facility, Uppsala University, Uppsala, Sweden
- Corresponding author.
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28
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Ahlmann-Eltze C, Huber W. Comparison of transformations for single-cell RNA-seq data. Nat Methods 2023; 20:665-672. [PMID: 37037999 PMCID: PMC10172138 DOI: 10.1038/s41592-023-01814-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 02/11/2023] [Indexed: 04/12/2023]
Abstract
The count table, a numeric matrix of genes × cells, is the basic input data structure in the analysis of single-cell RNA-sequencing data. A common preprocessing step is to adjust the counts for variable sampling efficiency and to transform them so that the variance is similar across the dynamic range. These steps are intended to make subsequent application of generic statistical methods more palatable. Here, we describe four transformation approaches based on the delta method, model residuals, inferred latent expression state and factor analysis. We compare their strengths and weaknesses and find that the latter three have appealing theoretical properties; however, in benchmarks using simulated and real-world data, it turns out that a rather simple approach, namely, the logarithm with a pseudo-count followed by principal-component analysis, performs as well or better than the more sophisticated alternatives. This result highlights limitations of current theoretical analysis as assessed by bottom-line performance benchmarks.
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Affiliation(s)
- Constantin Ahlmann-Eltze
- Genome Biology Unit, EMBL, Heidelberg, Germany.
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.
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29
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Rogalska ME, Vivori C, Valcárcel J. Regulation of pre-mRNA splicing: roles in physiology and disease, and therapeutic prospects. Nat Rev Genet 2023; 24:251-269. [PMID: 36526860 DOI: 10.1038/s41576-022-00556-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2022] [Indexed: 12/23/2022]
Abstract
The removal of introns from mRNA precursors and its regulation by alternative splicing are key for eukaryotic gene expression and cellular function, as evidenced by the numerous pathologies induced or modified by splicing alterations. Major recent advances have been made in understanding the structures and functions of the splicing machinery, in the description and classification of physiological and pathological isoforms and in the development of the first therapies for genetic diseases based on modulation of splicing. Here, we review this progress and discuss important remaining challenges, including predicting splice sites from genomic sequences, understanding the variety of molecular mechanisms and logic of splicing regulation, and harnessing this knowledge for probing gene function and disease aetiology and for the design of novel therapeutic approaches.
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Affiliation(s)
- Malgorzata Ewa Rogalska
- Genome Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Claudia Vivori
- Genome Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- The Francis Crick Institute, London, UK
| | - Juan Valcárcel
- Genome Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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30
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Wang D, Hu X, Ye H, Wang Y, Yang Q, Liang X, Wang Z, Zhou Y, Wen M, Yuan X, Zheng X, Ye W, Guo B, Yusuyin M, Russinova E, Zhou Y, Wang K. Cell-specific clock-controlled gene expression program regulates rhythmic fiber cell growth in cotton. Genome Biol 2023; 24:49. [PMID: 36918913 PMCID: PMC10012527 DOI: 10.1186/s13059-023-02886-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 02/26/2023] [Indexed: 03/16/2023] Open
Abstract
BACKGROUND The epidermis of cotton ovule produces fibers, the most important natural cellulose source for the global textile industry. However, the molecular mechanism of fiber cell growth is still poorly understood. RESULTS Here, we develop an optimized protoplasting method, and integrate single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq) to systematically characterize the cells of the outer integument of ovules from wild type and fuzzless/lintless (fl) cotton (Gossypium hirsutum). By jointly analyzing the scRNA-seq data from wildtype and fl, we identify five cell populations including the fiber cell type and construct the development trajectory for fiber lineage cells. Interestingly, by time-course diurnal transcriptomic analysis, we demonstrate that the primary growth of fiber cells is a highly regulated circadian rhythmic process. Moreover, we identify a small peptide GhRALF1 that circadian rhythmically controls fiber growth possibly through oscillating auxin signaling and proton pump activity in the plasma membrane. Combining with scATAC-seq, we further identify two cardinal cis-regulatory elements (CREs, TCP motif, and TCP-like motif) which are bound by the trans factors GhTCP14s to modulate the circadian rhythmic metabolism of mitochondria and protein translation through regulating approximately one third of genes that are highly expressed in fiber cells. CONCLUSIONS We uncover a fiber-specific circadian clock-controlled gene expression program in regulating fiber growth. This study unprecedentedly reveals a new route to improve fiber traits by engineering the circadian clock of fiber cells.
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Affiliation(s)
- Dehe Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiao Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Hanzhe Ye
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Yue Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Qian Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Xiaodong Liang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Zilin Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Yifan Zhou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Miaomiao Wen
- Institute for Advanced Studies, Wuhan University, Wuhan, China.,TaiKang Center for Life and Medical Sciences, RNA Institute, Remin Hospital, Wuhan University, Wuhan, China
| | - Xueyan Yuan
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiaomin Zheng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Wen Ye
- Medical Research Institute, Frontier Science Center for Immunology and Metabolism, School of Medicine, Wuhan University, Wuhan, China
| | - Boyu Guo
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Mayila Yusuyin
- Research Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Eugenia Russinova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Yu Zhou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China. .,Institute for Advanced Studies, Wuhan University, Wuhan, China. .,TaiKang Center for Life and Medical Sciences, RNA Institute, Remin Hospital, Wuhan University, Wuhan, China. .,Medical Research Institute, Frontier Science Center for Immunology and Metabolism, School of Medicine, Wuhan University, Wuhan, China.
| | - Kun Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China. .,Hubei Hongshan Laboratory, Wuhan, China. .,Institute for Advanced Studies, Wuhan University, Wuhan, China.
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31
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Welsh H, Batalha CMPF, Li W, Mpye KL, Souza-Pinto NC, Naslavsky MS, Parra EJ. A systematic evaluation of normalization methods and probe replicability using infinium EPIC methylation data. Clin Epigenetics 2023; 15:41. [PMID: 36906598 PMCID: PMC10008016 DOI: 10.1186/s13148-023-01459-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 02/24/2023] [Indexed: 03/13/2023] Open
Abstract
BACKGROUND The Infinium EPIC array measures the methylation status of > 850,000 CpG sites. The EPIC BeadChip uses a two-array design: Infinium Type I and Type II probes. These probe types exhibit different technical characteristics which may confound analyses. Numerous normalization and pre-processing methods have been developed to reduce probe type bias as well as other issues such as background and dye bias. METHODS This study evaluates the performance of various normalization methods using 16 replicated samples and three metrics: absolute beta-value difference, overlap of non-replicated CpGs between replicate pairs, and effect on beta-value distributions. Additionally, we carried out Pearson's correlation and intraclass correlation coefficient (ICC) analyses using both raw and SeSAMe 2 normalized data. RESULTS The method we define as SeSAMe 2, which consists of the application of the regular SeSAMe pipeline with an additional round of QC, pOOBAH masking, was found to be the best performing normalization method, while quantile-based methods were found to be the worst performing methods. Whole-array Pearson's correlations were found to be high. However, in agreement with previous studies, a substantial proportion of the probes on the EPIC array showed poor reproducibility (ICC < 0.50). The majority of poor performing probes have beta values close to either 0 or 1, and relatively low standard deviations. These results suggest that probe reliability is largely the result of limited biological variation rather than technical measurement variation. Importantly, normalizing the data with SeSAMe 2 dramatically improved ICC estimates, with the proportion of probes with ICC values > 0.50 increasing from 45.18% (raw data) to 61.35% (SeSAMe 2).
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Affiliation(s)
- H Welsh
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, Canada.
| | - C M P F Batalha
- Department of Biochemistry, University of São Paulo, São Paulo, Brazil
| | - W Li
- The Centre for Applied Genomics, Hospital for Sick Children, Toronto, Canada
| | - K L Mpye
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, Canada
| | - N C Souza-Pinto
- Department of Biochemistry, University of São Paulo, São Paulo, Brazil
| | - M S Naslavsky
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, Brazil
| | - E J Parra
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, Canada
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32
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Zhu J, Shang L, Zhou X. SRTsim: spatial pattern preserving simulations for spatially resolved transcriptomics. Genome Biol 2023; 24:39. [PMID: 36869394 PMCID: PMC9983268 DOI: 10.1186/s13059-023-02879-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 02/16/2023] [Indexed: 03/05/2023] Open
Abstract
Spatially resolved transcriptomics (SRT)-specific computational methods are often developed, tested, validated, and evaluated in silico using simulated data. Unfortunately, existing simulated SRT data are often poorly documented, hard to reproduce, or unrealistic. Single-cell simulators are not directly applicable for SRT simulation as they cannot incorporate spatial information. We present SRTsim, an SRT-specific simulator for scalable, reproducible, and realistic SRT simulations. SRTsim not only maintains various expression characteristics of SRT data but also preserves spatial patterns. We illustrate the benefits of SRTsim in benchmarking methods for spatial clustering, spatial expression pattern detection, and cell-cell communication identification.
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Affiliation(s)
- Jiaqiang Zhu
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Lulu Shang
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA.
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA.
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33
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Yan X, Zheng R, Wu F, Li M. CLAIRE: contrastive learning-based batch correction framework for better balance between batch mixing and preservation of cellular heterogeneity. Bioinformatics 2023; 39:7055295. [PMID: 36821425 PMCID: PMC9985174 DOI: 10.1093/bioinformatics/btad099] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/27/2022] [Accepted: 02/22/2023] [Indexed: 02/24/2023] Open
Abstract
MOTIVATION Integration of growing single-cell RNA sequencing datasets helps better understand cellular identity and function. The major challenge for integration is removing batch effects while preserving biological heterogeneities. Advances in contrastive learning have inspired several contrastive learning-based batch correction methods. However, existing contrastive-learning-based methods exhibit noticeable ad hoc trade-off between batch mixing and preservation of cellular heterogeneities (mix-heterogeneity trade-off). Therefore, a deliberate mix-heterogeneity trade-off is expected to yield considerable improvements in scRNA-seq dataset integration. RESULTS We develop a novel contrastive learning-based batch correction framework, CIAIRE, which achieves superior mix-heterogeneity trade-off. The key contributions of CLAIRE are proposal of two complementary strategies: construction strategy and refinement strategy, to improve the appropriateness of positive pairs. Construction strategy dynamically generates positive pairs by augmenting inter-batch mutual nearest neighbors (MNN) with intra-batch k-nearest neighbors (KNN), which improves the coverage of positive pairs for the whole distribution of shared cell types between batches. Refinement strategy aims to automatically reduce the potential false positive pairs from the construction strategy, which resorts to the memory effect of deep neural networks. We demonstrate that CLAIRE possesses superior mix-heterogeneity trade-off over existing contrastive learning-based methods. Benchmark results on six real datasets also show that CLAIRE achieves the best integration performance against eight state-of-the-art methods. Finally, comprehensive experiments are conducted to validate the effectiveness of CLAIRE. AVAILABILITY AND IMPLEMENTATION The source code and data used in this study can be found in https://github.com/CSUBioGroup/CLAIRE-release. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Xuhua Yan
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, China
| | - Ruiqing Zheng
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, China
| | - Fangxiang Wu
- Division of Biomedical Engineering, Department of Computer Science, Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, SK S7N 5A9, Canada
| | - Min Li
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, China
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34
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Noya SB, Sehgal A. Variant-to-gene, gene-to-trait: finding new sleep genes through GWAS. Trends Genet 2023; 39:338-339. [PMID: 36858881 DOI: 10.1016/j.tig.2023.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023]
Abstract
Distilling insomnia genome-wide association study (GWAS) variants, Palermo and colleagues identified several genes that participate in sleep regulation in two different model organisms. This workflow sets off an innovative strategy to extract biological relevance from large human genomic databases.
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Affiliation(s)
- Sara B Noya
- Chronobiology and Sleep Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Amita Sehgal
- Chronobiology and Sleep Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Howard Hughes Medical Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
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35
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Quantifying portable genetic effects and improving cross-ancestry genetic prediction with GWAS summary statistics. Nat Commun 2023; 14:832. [PMID: 36788230 PMCID: PMC9929290 DOI: 10.1038/s41467-023-36544-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 02/07/2023] [Indexed: 02/16/2023] Open
Abstract
Polygenic risk scores (PRS) calculated from genome-wide association studies (GWAS) of Europeans are known to have substantially reduced predictive accuracy in non-European populations, limiting their clinical utility and raising concerns about health disparities across ancestral populations. Here, we introduce a statistical framework named X-Wing to improve predictive performance in ancestrally diverse populations. X-Wing quantifies local genetic correlations for complex traits between populations, employs an annotation-dependent estimation procedure to amplify correlated genetic effects between populations, and combines multiple population-specific PRS into a unified score with GWAS summary statistics alone as input. Through extensive benchmarking, we demonstrate that X-Wing pinpoints portable genetic effects and substantially improves PRS performance in non-European populations, showing 14.1%-119.1% relative gain in predictive R2 compared to state-of-the-art methods based on GWAS summary statistics. Overall, X-Wing addresses critical limitations in existing approaches and may have broad applications in cross-population polygenic risk prediction.
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36
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Kumar A, Schrader AW, Boroojeny AE, Asadian M, Lee J, Song YJ, Zhao SD, Han HS, Sinha S. Intracellular Spatial Transcriptomic Analysis Toolkit (InSTAnT). RESEARCH SQUARE 2023:rs.3.rs-2481749. [PMID: 36747718 PMCID: PMC9901031 DOI: 10.21203/rs.3.rs-2481749/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Imaging-based spatial transcriptomics technologies such as MERFISH offer snapshots of cellular processes in unprecedented detail, but new analytic tools are needed to realize their full potential. We present InSTAnT, a computational toolkit for extracting molecular relationships from spatial transcriptomics data at the intra-cellular resolution. InSTAnT detects gene pairs and modules with interesting patterns of mutual co-localization within and across cells, using specialized statistical tests and graph mining. We showcase the toolkit on datasets profiling a human cancer cell line and hypothalamic preoptic region of mouse brain. We performed rigorous statistical assessment of discovered co-localization patterns, found supporting evidence from databases and RNA interactions, and identified subcellular domains associated with RNA-colocalization. We identified several novel cell type-specific gene co-localizations in the brain. Intra-cellular spatial patterns discovered by InSTAnT mirror diverse molecular relationships, including RNA interactions and shared sub-cellular localization or function, providing a rich compendium of testable hypotheses regarding molecular functions.
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Affiliation(s)
- Anurendra Kumar
- College of Computing, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Alex W. Schrader
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | | | - Marisa Asadian
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Juyeon Lee
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - You Jin Song
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sihai Dave Zhao
- Department of Statistics, University of Illinois Urbana-Champaign, Urbana, IL, 61820, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Hee-Sun Han
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Saurabh Sinha
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- H. Milton Stewart School of Industrial & Systems Engineering, Georgia Institute of Technology, Atlanta, GA, 30318, USA
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Cohesin controls X chromosome structure remodeling and X-reactivation during mouse iPSC-reprogramming. Proc Natl Acad Sci U S A 2023; 120:e2213810120. [PMID: 36669113 PMCID: PMC9942853 DOI: 10.1073/pnas.2213810120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Reactivation of the inactive X chromosome is a hallmark epigenetic event during reprogramming of mouse female somatic cells to induced pluripotent stem cells (iPSCs). This involves global structural remodeling from a condensed, heterochromatic into an open, euchromatic state, thereby changing a transcriptionally inactive into an active chromosome. Despite recent advances, very little is currently known about the molecular players mediating this process and how this relates to iPSC-reprogramming in general. To gain more insight, here we perform a RNAi-based knockdown screen during iPSC-reprogramming of mouse fibroblasts. We discover factors important for X chromosome reactivation (XCR) and iPSC-reprogramming. Among those, we identify the cohesin complex member SMC1a as a key molecule with a specific function in XCR, as its knockdown greatly affects XCR without interfering with iPSC-reprogramming. Using super-resolution microscopy, we find SMC1a to be preferentially enriched on the active compared with the inactive X chromosome and that SMC1a is critical for the decompacted state of the active X. Specifically, depletion of SMC1a leads to contraction of the active X both in differentiated and in pluripotent cells, where it normally is in its most open state. In summary, we reveal cohesin as a key factor for remodeling of the X chromosome from an inactive to an active structure and that this is a critical step for XCR during iPSC-reprogramming.
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38
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Palermo J, Chesi A, Zimmerman A, Sonti S, Pahl MC, Lasconi C, Brown EB, Pippin JA, Wells AD, Doldur-Balli F, Mazzotti DR, Pack AI, Gehrman PR, Grant SF, Keene AC. Variant-to-gene mapping followed by cross-species genetic screening identifies GPI-anchor biosynthesis as a regulator of sleep. SCIENCE ADVANCES 2023; 9:eabq0844. [PMID: 36608130 PMCID: PMC9821868 DOI: 10.1126/sciadv.abq0844] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 12/05/2022] [Indexed: 05/13/2023]
Abstract
Genome-wide association studies (GWAS) in humans have identified loci robustly associated with several heritable diseases or traits, yet little is known about the functional roles of the underlying causal variants in regulating sleep duration or quality. We applied an ATAC-seq/promoter focused Capture C strategy in human iPSC-derived neural progenitors to carry out a "variant-to-gene" mapping campaign that identified 88 candidate sleep effector genes connected to relevant GWAS signals. To functionally validate the role of the implicated effector genes in sleep regulation, we performed a neuron-specific RNA interference screen in the fruit fly, Drosophila melanogaster, followed by validation in zebrafish. This approach identified a number of genes that regulate sleep including a critical role for glycosylphosphatidylinositol (GPI)-anchor biosynthesis. These results provide the first physical variant-to-gene mapping of human sleep genes followed by a model organism-based prioritization, revealing a conserved role for GPI-anchor biosynthesis in sleep regulation.
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Affiliation(s)
- Justin Palermo
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Alessandra Chesi
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Amber Zimmerman
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Sleep Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, PA 19104, USA
| | - Shilpa Sonti
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Matthew C. Pahl
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Chiara Lasconi
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Elizabeth B. Brown
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - James A. Pippin
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Andrew D. Wells
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Sleep Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, PA 19104, USA
| | - Fusun Doldur-Balli
- Division of Sleep Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, PA 19104, USA
| | - Diego R. Mazzotti
- Division of Medical Informatics, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS 66103, USA
- Division of Pulmonary Critical Care and Sleep Medicine, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS 66103, USA
| | - Allan I. Pack
- Division of Sleep Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, PA 19104, USA
| | - Phillip R. Gehrman
- Division of Sleep Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, PA 19104, USA
| | - Struan F.A. Grant
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Divisions of Human Genetics and Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alex C. Keene
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
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SPICEMIX enables integrative single-cell spatial modeling of cell identity. Nat Genet 2023; 55:78-88. [PMID: 36624346 PMCID: PMC9840703 DOI: 10.1038/s41588-022-01256-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 11/01/2022] [Indexed: 01/11/2023]
Abstract
Spatial transcriptomics can reveal spatially resolved gene expression of diverse cells in complex tissues. However, the development of computational methods that can use the unique properties of spatial transcriptome data to unveil cell identities remains a challenge. Here we introduce SPICEMIX, an interpretable method based on probabilistic, latent variable modeling for joint analysis of spatial information and gene expression from spatial transcriptome data. Both simulation and real data evaluations demonstrate that SPICEMIX markedly improves on the inference of cell types and their spatial patterns compared with existing approaches. By applying to spatial transcriptome data of brain regions in human and mouse acquired by seqFISH+, STARmap and Visium, we show that SPICEMIX can enhance the inference of complex cell identities, reveal interpretable spatial metagenes and uncover differentiation trajectories. SPICEMIX is a generalizable analysis framework for spatial transcriptome data to investigate cell-type composition and spatial organization of cells in complex tissues.
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40
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Toneyan S, Tang Z, Koo PK. Evaluating deep learning for predicting epigenomic profiles. NAT MACH INTELL 2022. [DOI: 10.1038/s42256-022-00570-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Liu L, Yang Y, Deng Y, Zhang T. Nanopore long-read-only metagenomics enables complete and high-quality genome reconstruction from mock and complex metagenomes. MICROBIOME 2022; 10:209. [PMID: 36457010 PMCID: PMC9716684 DOI: 10.1186/s40168-022-01415-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 11/07/2022] [Indexed: 05/31/2023]
Abstract
BACKGROUND The accurate and comprehensive analyses of genome-resolved metagenomics largely depend on the reconstruction of reference-quality (complete and high-quality) genomes from diverse microbiomes. Closing gaps in draft genomes have been approaching with the inclusion of Nanopore long reads; however, genome quality improvement requires extensive and time-consuming high-accuracy short-read polishing. RESULTS Here, we introduce NanoPhase, an open-source tool to reconstruct reference-quality genomes from complex metagenomes using only Nanopore long reads. Using Kit 9 and Q20+ chemistries, we first evaluated the feasibility of NanoPhase using a ZymoBIOMICS gut microbiome standard (including 21 strains), then sequenced the complex activated sludge microbiome and reconstructed 275 MAGs with median completeness of ~ 90%. As a result, NanoPhase improved the MAG contiguity (median MAG N50: 735 Kb, 44-86X compared to conventional short-read-based methods) while maintaining high accuracy, allowing for a full and accurate investigation of target microbiomes. Additionally, leveraging these high-contiguity reference-quality genomes, we identified 165 prophages within 111 MAGs, with 5 as active prophages, indicating the prophage was a neglected source of genetic diversity within microbial populations and influencer in shaping microbial composition in the activated sludge microbiome. CONCLUSIONS Our results demonstrated that NanoPhase enables reference-quality genome reconstruction from complex metagenomes directly using only Nanopore long reads. Furthermore, besides the 16S rRNA genes and biosynthetic gene clusters, the generated high-accuracy and high-contiguity MAGs improved the host identification of critical mobile genetic elements, e.g., prophage, serving as a genomic blueprint to investigate the microbial potential and ecology in the activated sludge ecosystem. Video Abstract.
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Affiliation(s)
- Lei Liu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China
| | - Yu Yang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China
| | - Yu Deng
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China
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42
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Abstract
Semidwarfing genes have greatly increased wheat yields globally, yet the widely used gibberellin (GA)-insensitive genes Rht-B1b and Rht-D1b have disadvantages for seedling emergence. Use of the GA-sensitive semidwarfing gene Rht13 avoids this pleiotropic effect. Here, we show that Rht13 encodes a nucleotide-binding site/leucine-rich repeat (NB-LRR) gene. A point mutation in the semidwarf Rht-B13b allele autoactivates the NB-LRR gene and causes a height reduction comparable with Rht-B1b and Rht-D1b in diverse genetic backgrounds. The autoactive Rht-B13b allele leads to transcriptional up-regulation of pathogenesis-related genes including class III peroxidases associated with cell wall remodeling. Rht13 represents a new class of reduced height (Rht) gene, unlike other Rht genes, which encode components of the GA signaling or metabolic pathways. This discovery opens avenues to use autoactive NB-LRR genes as semidwarfing genes in a range of crop species, and to apply Rht13 in wheat breeding programs using a perfect genetic marker.
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David JK, Maden SK, Wood MA, Thompson RF, Nellore A. Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads. Genome Biol 2022; 23:240. [PMID: 36369064 PMCID: PMC9652823 DOI: 10.1186/s13059-022-02789-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 10/10/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND There is growing interest in retained introns in a variety of disease contexts including cancer and aging. Many software tools have been developed to detect retained introns from short RNA-seq reads, but reliable detection is complicated by overlapping genes and transcripts as well as the presence of unprocessed or partially processed RNAs. RESULTS We compared introns detected by 8 tools using short RNA-seq reads with introns observed in long RNA-seq reads from the same biological specimens. We found significant disagreement among tools (Fleiss' [Formula: see text]) such that 47.7% of all detected intron retentions were not called by more than one tool. We also observed poor performance of all tools, with none achieving an F1-score greater than 0.26, and qualitatively different behaviors between general-purpose alternative splicing detection tools and tools confined to retained intron detection. CONCLUSIONS Short-read tools detect intron retention with poor recall and precision, calling into question the completeness and validity of a large percentage of putatively retained introns called by commonly used methods.
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Affiliation(s)
- Julianne K. David
- grid.5288.70000 0000 9758 5690Computational Biology Program, Oregon Health & Science University, Portland, OR USA ,grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR USA ,Present Address: Base5 Genomics, Inc., Mountain View, CA USA
| | - Sean K. Maden
- grid.5288.70000 0000 9758 5690Computational Biology Program, Oregon Health & Science University, Portland, OR USA ,grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR USA ,grid.21107.350000 0001 2171 9311Present Address: Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | - Mary A. Wood
- grid.5288.70000 0000 9758 5690Computational Biology Program, Oregon Health & Science University, Portland, OR USA ,grid.429936.30000 0004 5914 210XPortland VA Research Foundation, Portland, OR USA ,Present Address: Phase Genomics, Inc., Seattle, WA USA
| | - Reid F. Thompson
- grid.5288.70000 0000 9758 5690Computational Biology Program, Oregon Health & Science University, Portland, OR USA ,grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR USA ,grid.484322.bDivision of Hospital and Specialty Medicine, VA Portland Healthcare System, Portland, OR USA ,grid.5288.70000 0000 9758 5690Department of Medical Informatics & Clinical Epidemiology, Oregon Health & Science University, Portland, OR USA ,grid.5288.70000 0000 9758 5690Department of Radiation Medicine, Oregon Health & Science University, Portland, OR USA
| | - Abhinav Nellore
- grid.5288.70000 0000 9758 5690Computational Biology Program, Oregon Health & Science University, Portland, OR USA ,grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR USA ,grid.5288.70000 0000 9758 5690Department of Surgery, Oregon Health & Science University, Portland, OR USA
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DaDalt AA, Bonham CA, Lotze GP, Luiso AA, Vacratsis PO. Src-mediated phosphorylation of the ribosome biogenesis factor hYVH1 affects its localization, promoting partitioning to the 60S ribosomal subunit. J Biol Chem 2022; 298:102679. [PMID: 36370849 PMCID: PMC9731860 DOI: 10.1016/j.jbc.2022.102679] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 10/22/2022] [Accepted: 10/25/2022] [Indexed: 11/11/2022] Open
Abstract
Yeast VH1-related phosphatase (YVH1) (also known as DUSP12) is a member of the atypical dual-specificity phosphatase subfamily. Although no direct substrate has been firmly established, human YVH1 (hYVH1) has been shown to protect cells from cellular stressors, regulate the cell cycle, disassemble stress granules, and act as a 60S ribosome biogenesis factor. Despite knowledge of hYVH1 function, further research is needed to uncover mechanisms of its regulation. In this study, we investigate cellular effects of a Src-mediated phosphorylation site at Tyr179 on hYVH1. We observed that this phosphorylation event attenuates localization of hYVH1 to stress granules, enhances shuttling of hYVH1 to the nucleus, and promotes hYVH1 partitioning to the 60S ribosomal subunit. Quantitative proteomics reveal that Src coexpression with hYVH1 reduces formation of ribosomal species that represent stalled intermediates through the alteration of associating factors that mediate translational repression. Collectively, these results implicate hYVH1 as a novel Src substrate and provide the first demonstrated role of tyrosine phosphorylation regulating the activity of a YVH1 ortholog. Moreover, the ribosome proteome alterations point to a collaborative function of hYVH1 and Src in maintaining translational fitness.
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Linder J, Koplik SE, Kundaje A, Seelig G. Deciphering the impact of genetic variation on human polyadenylation using APARENT2. Genome Biol 2022; 23:232. [PMID: 36335397 PMCID: PMC9636789 DOI: 10.1186/s13059-022-02799-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 10/19/2022] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND 3'-end processing by cleavage and polyadenylation is an important and finely tuned regulatory process during mRNA maturation. Numerous genetic variants are known to cause or contribute to human disorders by disrupting the cis-regulatory code of polyadenylation signals. Yet, due to the complexity of this code, variant interpretation remains challenging. RESULTS We introduce a residual neural network model, APARENT2, that can infer 3'-cleavage and polyadenylation from DNA sequence more accurately than any previous model. This model generalizes to the case of alternative polyadenylation (APA) for a variable number of polyadenylation signals. We demonstrate APARENT2's performance on several variant datasets, including functional reporter data and human 3' aQTLs from GTEx. We apply neural network interpretation methods to gain insights into disrupted or protective higher-order features of polyadenylation. We fine-tune APARENT2 on human tissue-resolved transcriptomic data to elucidate tissue-specific variant effects. By combining APARENT2 with models of mRNA stability, we extend aQTL effect size predictions to the entire 3' untranslated region. Finally, we perform in silico saturation mutagenesis of all human polyadenylation signals and compare the predicted effects of [Formula: see text] million variants against gnomAD. While loss-of-function variants were generally selected against, we also find specific clinical conditions linked to gain-of-function mutations. For example, we detect an association between gain-of-function mutations in the 3'-end and autism spectrum disorder. To experimentally validate APARENT2's predictions, we assayed clinically relevant variants in multiple cell lines, including microglia-derived cells. CONCLUSIONS A sequence-to-function model based on deep residual learning enables accurate functional interpretation of genetic variants in polyadenylation signals and, when coupled with large human variation databases, elucidates the link between functional 3'-end mutations and human health.
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Affiliation(s)
| | | | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, USA
- Department of Computer Science, Stanford University, Stanford, USA
| | - Georg Seelig
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, USA
- Department of Electrical and Computer Engineering, University of Washington, Seattle, USA
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46
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Hoberecht L, Perampalam P, Lun A, Fortin JP. A comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies. Nat Commun 2022; 13:6568. [PMID: 36323688 PMCID: PMC9630310 DOI: 10.1038/s41467-022-34320-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
The success of CRISPR-mediated gene perturbation studies is highly dependent on the quality of gRNAs, and several tools have been developed to enable optimal gRNA design. However, these tools are not all adaptable to the latest CRISPR modalities or nucleases, nor do they offer comprehensive annotation methods for advanced CRISPR applications. Here, we present a new ecosystem of R packages, called crisprVerse, that enables efficient gRNA design and annotation for a multitude of CRISPR technologies. This includes CRISPR knockout (CRISPRko), CRISPR activation (CRISPRa), CRISPR interference (CRISPRi), CRISPR base editing (CRISPRbe) and CRISPR knockdown (CRISPRkd). The core package, crisprDesign, offers a user-friendly and unified interface to add off-target annotations, rich gene and SNP annotations, and on- and off-target activity scores. These functionalities are enabled for any RNA- or DNA-targeting nucleases, including Cas9, Cas12, and Cas13. The crisprVerse ecosystem is open-source and deployed through the Bioconductor project ( https://github.com/crisprVerse ).
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Affiliation(s)
- Luke Hoberecht
- Genentech Research and Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | | | - Aaron Lun
- Genentech Research and Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Jean-Philippe Fortin
- Genentech Research and Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.
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47
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Hämälä T, Ning W, Kuittinen H, Aryamanesh N, Savolainen O. Environmental response in gene expression and DNA methylation reveals factors influencing the adaptive potential of Arabidopsis lyrata. eLife 2022; 11:83115. [PMID: 36306157 PMCID: PMC9616567 DOI: 10.7554/elife.83115] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/12/2022] [Indexed: 11/13/2022] Open
Abstract
Understanding what factors influence plastic and genetic variation is valuable for predicting how organisms respond to changes in the selective environment. Here, using gene expression and DNA methylation as molecular phenotypes, we study environmentally induced variation among Arabidopsis lyrata plants grown at lowland and alpine field sites. Our results show that gene expression is highly plastic, as many more genes are differentially expressed between the field sites than between populations. These environmentally responsive genes evolve under strong selective constraint – the strength of purifying selection on the coding sequence is high, while the rate of adaptive evolution is low. We find, however, that positive selection on cis-regulatory variants has likely contributed to the maintenance of genetically variable environmental responses, but such variants segregate only between distantly related populations. In contrast to gene expression, DNA methylation at genic regions is largely insensitive to the environment, and plastic methylation changes are not associated with differential gene expression. Besides genes, we detect environmental effects at transposable elements (TEs): TEs at the high-altitude field site have higher expression and methylation levels, suggestive of a broad-scale TE activation. Compared to the lowland population, plants native to the alpine environment harbor an excess of recent TE insertions, and we observe that specific TE families are enriched within environmentally responsive genes. Our findings provide insight into selective forces shaping plastic and genetic variation. We also highlight how plastic responses at TEs can rapidly create novel heritable variation in stressful conditions.
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Affiliation(s)
- Tuomas Hämälä
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Weixuan Ning
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Helmi Kuittinen
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Nader Aryamanesh
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Outi Savolainen
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
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48
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Rodriguez Gallo MC, Li Q, Mehta D, Uhrig RG. Genome-scale analysis of Arabidopsis splicing-related protein kinase families reveals roles in abiotic stress adaptation. BMC PLANT BIOLOGY 2022; 22:496. [PMID: 36273172 PMCID: PMC9587599 DOI: 10.1186/s12870-022-03870-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 10/04/2022] [Indexed: 05/24/2023]
Abstract
Nearly 60 - 80 % of intron-containing plant genes undergo alternative splicing in response to either stress or plant developmental cues. RNA splicing is performed by a large ribonucleoprotein complex called the spliceosome in conjunction with associated subunits such as serine arginine (SR) proteins, all of which undergo extensive phosphorylation. In plants, there are three main protein kinase families suggested to phosphorylate core spliceosome subunits and related splicing factors based on orthology to human splicing-related kinases: the SERINE/ARGININE PROTEIN KINASES (SRPK), ARABIDOPSIS FUS3 COMPLEMENT (AFC), and Pre-mRNA PROCESSING FACTOR 4 (PRP4K) protein kinases. To better define the conservation and role(s) of these kinases in plants, we performed a genome-scale analysis of the three families across photosynthetic eukaryotes, followed by extensive transcriptomic and bioinformatic analysis of all Arabidopsis thaliana SRPK, AFC, and PRP4K protein kinases to elucidate their biological functions. Unexpectedly, this revealed the existence of SRPK and AFC phylogenetic groups with distinct promoter elements and patterns of transcriptional response to abiotic stress, while PRP4Ks possess no phylogenetic sub-divisions, suggestive of functional redundancy. We also reveal splicing-related kinase families are both diel and photoperiod regulated, implicating different orthologs as discrete time-of-day RNA splicing regulators. This foundational work establishes a number of new hypotheses regarding how reversible spliceosome phosphorylation contributes to both diel plant cell regulation and abiotic stress adaptation in plants.
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Affiliation(s)
- M C Rodriguez Gallo
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Q Li
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - D Mehta
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - R G Uhrig
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.
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49
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Suh S, Choi EH, Raguram A, Liu DR, Palczewski K. Precision genome editing in the eye. Proc Natl Acad Sci U S A 2022; 119:e2210104119. [PMID: 36122230 PMCID: PMC9522375 DOI: 10.1073/pnas.2210104119] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
CRISPR-Cas-based genome editing technologies could, in principle, be used to treat a wide variety of inherited diseases, including genetic disorders of vision. Programmable CRISPR-Cas nucleases are effective tools for gene disruption, but they are poorly suited for precisely correcting pathogenic mutations in most therapeutic settings. Recently developed precision genome editing agents, including base editors and prime editors, have enabled precise gene correction and disease rescue in multiple preclinical models of genetic disorders. Additionally, new delivery technologies that transiently deliver precision genome editing agents in vivo offer minimized off-target editing and improved safety profiles. These improvements to precision genome editing and delivery technologies are expected to revolutionize the treatment of genetic disorders of vision and other diseases. In this Perspective, we describe current preclinical and clinical genome editing approaches for treating inherited retinal degenerative diseases, and we discuss important considerations that should be addressed as these approaches are translated into clinical practice.
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Affiliation(s)
- Susie Suh
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA 92697
| | - Elliot H. Choi
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA 92697
| | - Aditya Raguram
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138
| | - David R. Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA 92697
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697
- Department of Chemistry, University of California, Irvine, CA 92697
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697
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50
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Treppner M, Binder H, Hess M. Interpretable generative deep learning: an illustration with single cell gene expression data. Hum Genet 2022; 141:1481-1498. [PMID: 34988661 PMCID: PMC9360114 DOI: 10.1007/s00439-021-02417-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/06/2021] [Indexed: 11/26/2022]
Abstract
Deep generative models can learn the underlying structure, such as pathways or gene programs, from omics data. We provide an introduction as well as an overview of such techniques, specifically illustrating their use with single-cell gene expression data. For example, the low dimensional latent representations offered by various approaches, such as variational auto-encoders, are useful to get a better understanding of the relations between observed gene expressions and experimental factors or phenotypes. Furthermore, by providing a generative model for the latent and observed variables, deep generative models can generate synthetic observations, which allow us to assess the uncertainty in the learned representations. While deep generative models are useful to learn the structure of high-dimensional omics data by efficiently capturing non-linear dependencies between genes, they are sometimes difficult to interpret due to their neural network building blocks. More precisely, to understand the relationship between learned latent variables and observed variables, e.g., gene transcript abundances and external phenotypes, is difficult. Therefore, we also illustrate current approaches that allow us to infer the relationship between learned latent variables and observed variables as well as external phenotypes. Thereby, we render deep learning approaches more interpretable. In an application with single-cell gene expression data, we demonstrate the utility of the discussed methods.
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Affiliation(s)
- Martin Treppner
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Stefan-Meier-Str. 26, Freiburg, 79104, Germany.
| | - Harald Binder
- Freiburg Center for Data Analysis and Modeling, University of Freiburg, Freiburg, 79104, Germany
| | - Moritz Hess
- Freiburg Center for Data Analysis and Modeling, University of Freiburg, Freiburg, 79104, Germany
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