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Yan J, Wang X. Machine learning bridges omics sciences and plant breeding. Trends Plant Sci 2023; 28:199-210. [PMID: 36153276 DOI: 10.1016/j.tplants.2022.08.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 08/15/2022] [Accepted: 08/23/2022] [Indexed: 06/16/2023]
Abstract
Some of the biological knowledge obtained from fundamental research will be implemented in applied plant breeding. To bridge basic research and breeding practice, machine learning (ML) holds great promise to translate biological knowledge and omics data into precision-designed plant breeding. Here, we review ML for multi-omics analysis in plants, including data dimensionality reduction, inference of gene-regulation networks, and gene discovery and prioritization. These applications will facilitate understanding trait regulation mechanisms and identifying target genes potentially applicable to knowledge-driven molecular design breeding. We also highlight applications of deep learning in plant phenomics and ML in genomic selection-assisted breeding, such as various ML algorithms that model the correlations among genotypes (genes), phenotypes (traits), and environments, to ultimately achieve data-driven genomic design breeding.
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Affiliation(s)
- Jun Yan
- National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100094, China; Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing 100094, China
| | - Xiangfeng Wang
- National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100094, China; Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing 100094, China.
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Madan I, Than NG, Romero R, Chaemsaithong P, Miranda J, Tarca AL, Bhatti G, Draghici S, Yeo L, Mazor M, Hassan SS, Chaiworapongsa T. The peripheral whole-blood transcriptome of acute pyelonephritis in human pregnancya. J Perinat Med 2014; 42:31-53. [PMID: 24293448 PMCID: PMC5881913 DOI: 10.1515/jpm-2013-0085] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
OBJECTIVE Human pregnancy is characterized by activation of the innate immune response and suppression of adaptive immunity. The former is thought to provide protection against infection for the mother, and the latter, tolerance against paternal antigens expressed in fetal cells. Acute pyelonephritis is associated with an increased risk of acute respiratory distress syndrome and sepsis in pregnant (vs. nonpregnant) women. The objective of this study was to describe the gene expression profile (transcriptome) of maternal whole blood in acute pyelonephritis. METHOD A case-control study was conducted to include pregnant women with acute pyelonephritis (n=15) and women with a normal pregnancy (n=34). Affymetrix HG-U133 Plus 2.0 arrays (Affymetrix, Santa Clara, CA, USA) were used for gene expression profiling. A linear model was used to test the association between the presence of pyelonephritis and gene expression levels while controlling for white blood cell count and gestational age. A fold change of 1.5 was considered significant at a false discovery rate of 0.1. A subset of differentially expressed genes (n=56) was tested with real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR) (cases, n=19; controls, n=59). Gene ontology and pathway analyses were applied. RESULTS A total of 983 genes were differentially expressed in acute pyelonephritis: 457 were upregulated and 526 were downregulated. Significant enrichment of 300 biological processes and 63 molecular functions was found in pyelonephritis. Significantly impacted pathways in pyelonephritis included (a) cytokine-cytokine receptor interaction, (b) T-cell receptor signaling, (c) Jak-STAT signaling, and (d) complement and coagulation cascades. Of 56 genes tested by qRT-PCR, 48 (85.7%) had confirmation of differential expression. CONCLUSION This is the first study of the transcriptomic signature of whole blood in pregnant women with acute pyelonephritis. Acute infection during pregnancy is associated with the increased expression of genes involved in innate immunity and the decreased expression of genes involved in lymphocyte function.
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Affiliation(s)
- Ichchha Madan
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, MD, and Detroit, MI, USA,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Nandor Gabor Than
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, MD, and Detroit, MI, USA,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Roberto Romero
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, MD, and Detroit, MI, USA,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA,Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA
| | - Piya Chaemsaithong
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, MD, and Detroit, MI, USA,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Jezid Miranda
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, MD, and Detroit, MI, USA,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Adi L. Tarca
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, MD, and Detroit, MI, USA,Department of Computer Science, Wayne State University, Detroit, MI, USA
| | - Gaurav Bhatti
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, MD, and Detroit, MI, USA,Department of Computer Science, Wayne State University, Detroit, MI, USA
| | - Sorin Draghici
- Department of Computer Science, Wayne State University, Detroit, MI, USA
| | - Lami Yeo
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, MD, and Detroit, MI, USA,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Moshe Mazor
- Department of Obstetrics and Gynecology, Soroka University Medical Center, School of Medicine, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Sonia S. Hassan
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, MD, and Detroit, MI, USA,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Tinnakorn Chaiworapongsa
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, MD, and Detroit, MI, USA,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
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Varkonyi T, Nagy B, Fule T, Tarca AL, Karaszi K, Schonleber J, Hupuczi P, Mihalik N, Kovalszky I, Rigo J, Meiri H, Papp Z, Romero R, Than NG. Microarray profiling reveals that placental transcriptomes of early-onset HELLP syndrome and preeclampsia are similar. Placenta 2011; 32 Suppl:S21-9. [PMID: 20541258 PMCID: PMC3917714 DOI: 10.1016/j.placenta.2010.04.014] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Revised: 04/23/2010] [Accepted: 04/29/2010] [Indexed: 02/05/2023]
Abstract
BACKGROUND The involvement of the placenta in the pathogenesis of preeclampsia and HELLP syndrome is well established, and placental lesions are also similar in these two syndromes. Here we aimed to examine the placental transcriptome and to identify candidate biomarkers in early-onset preeclampsia and HELLP syndrome. METHODS Placental specimens were obtained at C-sections from women with early-onset preeclampsia and HELLP syndrome, and from controls who delivered preterm or at term. After histopathological examination, fresh-frozen placental specimens were used for microarray profiling and validation by qRT-PCR. Differential expression was analysed using log-linear models while adjusting for gestational age. Gene ontology and pathway analyses were used to interpret gene expression changes. Tissue microarrays were constructed from paraffin-embedded placental specimens and immunostained. RESULTS Placental gene expression was gestational age-dependent among preterm and term controls. Out of the 350 differentially expressed genes in preeclampsia and 554 genes in HELLP syndrome, 224 genes (including LEP, CGB, LHB, INHA, SIGLEC6, PAPPA2, TREM1, and FLT1) changed in the same direction (elevated or reduced) in both syndromes. Many of these encode proteins that have been implicated as biomarkers for preeclampsia. Enrichment analyses revealed similar biological processes, cellular compartments and biological pathways enriched in early-onset preeclampsia and HELLP syndrome; however, some processes and pathways (e.g., cytokine-cytokine receptor interaction) were over-represented only in HELLP syndrome. CONCLUSION High-throughput transcriptional and tissue microarray expression profiling revealed that placental transcriptomes of early-onset preeclampsia and HELLP syndrome largely overlap, underlying a potential common cause and pathophysiologic processes in these syndromes. However, gene expression changes may also suggest a more severe placental pathology and pronounced inflammatory response in HELLP syndrome than in preeclampsia.
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Affiliation(s)
- T Varkonyi
- First Department of Obstetrics and Gynecology, Semmelweis University, Budapest, Hungary
| | - B Nagy
- First Department of Obstetrics and Gynecology, Semmelweis University, Budapest, Hungary
| | - T Fule
- First Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - AL Tarca
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
| | - K Karaszi
- First Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - J Schonleber
- First Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - P Hupuczi
- First Department of Obstetrics and Gynecology, Semmelweis University, Budapest, Hungary
| | - N Mihalik
- First Department of Obstetrics and Gynecology, Semmelweis University, Budapest, Hungary
- First Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - I Kovalszky
- First Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - J Rigo
- First Department of Obstetrics and Gynecology, Semmelweis University, Budapest, Hungary
| | - H Meiri
- Diagnostic Technologies, Yokneam, Israel
| | - Z Papp
- First Department of Obstetrics and Gynecology, Semmelweis University, Budapest, Hungary
| | - R Romero
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
| | - NG Than
- First Department of Obstetrics and Gynecology, Semmelweis University, Budapest, Hungary
- Wayne State University, Detroit, MI, USA
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