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Abstract
This review delves into the rapidly evolving landscape of liquid biopsy technologies based on cell-free DNA (cfDNA) and cell-free RNA (cfRNA) and their increasingly prominent role in precision medicine. With the advent of high-throughput DNA sequencing, the use of cfDNA and cfRNA has revolutionized noninvasive clinical testing. Here, we explore the physical characteristics of cfDNA and cfRNA, present an overview of the essential engineering tools used by the field, and highlight clinical applications, including noninvasive prenatal testing, cancer testing, organ transplantation surveillance, and infectious disease testing. Finally, we discuss emerging technologies and the broadening scope of liquid biopsies to new areas of diagnostic medicine.
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Affiliation(s)
- Conor Loy
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA;
| | - Lauren Ahmann
- Department of Pathology, Stanford University, Stanford, California, USA;
| | - Iwijn De Vlaminck
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA;
| | - Wei Gu
- Department of Pathology, Stanford University, Stanford, California, USA;
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Garcia-Flores V, Romero R, Tarca AL, Peyvandipour A, Xu Y, Galaz J, Miller D, Chaiworapongsa T, Chaemsaithong P, Berry SM, Awonuga AO, Bryant DR, Pique-Regi R, Gomez-Lopez N. Deciphering maternal-fetal cross-talk in the human placenta during parturition using single-cell RNA sequencing. Sci Transl Med 2024; 16:eadh8335. [PMID: 38198568 PMCID: PMC11238316 DOI: 10.1126/scitranslmed.adh8335] [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: 03/16/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024]
Abstract
Labor is a complex physiological process requiring a well-orchestrated dialogue between the mother and fetus. However, the cellular contributions and communications that facilitate maternal-fetal cross-talk in labor have not been fully elucidated. Here, single-cell RNA sequencing (scRNA-seq) was applied to decipher maternal-fetal signaling in the human placenta during term labor. First, a single-cell atlas of the human placenta was established, demonstrating that maternal and fetal cell types underwent changes in transcriptomic activity during labor. Cell types most affected by labor were fetal stromal and maternal decidual cells in the chorioamniotic membranes (CAMs) and maternal and fetal myeloid cells in the placenta. Cell-cell interaction analyses showed that CAM and placental cell types participated in labor-driven maternal and fetal signaling, including the collagen, C-X-C motif ligand (CXCL), tumor necrosis factor (TNF), galectin, and interleukin-6 (IL-6) pathways. Integration of scRNA-seq data with publicly available bulk transcriptomic data showed that placenta-derived scRNA-seq signatures could be monitored in the maternal circulation throughout gestation and in labor. Moreover, comparative analysis revealed that placenta-derived signatures in term labor were mirrored by those in spontaneous preterm labor and birth. Furthermore, we demonstrated that early in gestation, labor-specific, placenta-derived signatures could be detected in the circulation of women destined to undergo spontaneous preterm birth, with either intact or prelabor ruptured membranes. Collectively, our findings provide insight into the maternal-fetal cross-talk of human parturition and suggest that placenta-derived single-cell signatures can aid in the development of noninvasive biomarkers for the prediction of preterm birth.
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Affiliation(s)
- Valeria Garcia-Flores
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, MD 20892 and Detroit, MI 48201, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Roberto Romero
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, MD 20892 and Detroit, MI 48201, USA
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI 48824, USA
| | - Adi L Tarca
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, MD 20892 and Detroit, MI 48201, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
- Department of Computer Science, Wayne State University College of Engineering, Detroit, MI 48201, USA
| | - Azam Peyvandipour
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, MD 20892 and Detroit, MI 48201, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
| | - Yi Xu
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, MD 20892 and Detroit, MI 48201, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Jose Galaz
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, MD 20892 and Detroit, MI 48201, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Division of Obstetrics and Gynecology, School of Medicine, Faculty of Medicine, Pontificia Universidad Catolica de Chile, Santiago 8330024, Chile
| | - Derek Miller
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, MD 20892 and Detroit, MI 48201, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Tinnakorn Chaiworapongsa
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, MD 20892 and Detroit, MI 48201, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Piya Chaemsaithong
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, MD 20892 and Detroit, MI 48201, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Department of Obstetrics and Gynecology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Stanley M Berry
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, MD 20892 and Detroit, MI 48201, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Awoniyi O Awonuga
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - David R Bryant
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Roger Pique-Regi
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, MD 20892 and Detroit, MI 48201, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
| | - Nardhy Gomez-Lopez
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, MD 20892 and Detroit, MI 48201, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI 48201, USA
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Zhou S, Li J, Yang W, Xue P, Yin Y, Wang Y, Tian P, Peng H, Jiang H, Xu W, Huang S, Zhang R, Wei F, Sun HX, Zhang J, Zhao L. Noninvasive preeclampsia prediction using plasma cell-free RNA signatures. Am J Obstet Gynecol 2023; 229:553.e1-553.e16. [PMID: 37211139 DOI: 10.1016/j.ajog.2023.05.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 05/02/2023] [Accepted: 05/14/2023] [Indexed: 05/23/2023]
Abstract
BACKGROUND Preeclampsia, especially preterm preeclampsia and early-onset preeclampsia, is a life-threating pregnancy disorder, and the heterogeneity and complexity of preeclampsia make it difficult to predict risk and to develop treatments. Plasma cell-free RNA carries unique information from human tissue and may be useful for noninvasive monitoring of maternal, placental, and fetal dynamics during pregnancy. OBJECTIVE This study aimed to investigate various RNA biotypes associated with preeclampsia in plasma and to develop classifiers to predict preterm preeclampsia and early-onset preeclampsia before diagnosis. STUDY DESIGN We performed a novel, cell-free RNA sequencing method termed polyadenylation ligation-mediated sequencing to investigate the cell-free RNA characteristics of 715 healthy pregnancies and 202 pregnancies affected by preeclampsia before symptom onset. We explored differences in the abundance of different RNA biotypes in plasma between healthy and preeclampsia samples and built preterm preeclampsia and early-onset preeclampsia prediction classifiers using machine learning methods. Furthermore, we validated the performance of the classifiers using the external and internal validation cohorts and assessed the area under the curve and positive predictive value. RESULTS We detected 77 genes, including messenger RNA (44%) and microRNA (26%), that were differentially expressed in healthy mothers and mothers with preterm preeclampsia before symptom onset, which could separate participants with preterm preeclampsia from healthy samples and that played critical functional roles in preeclampsia physiology. We developed 2 classifiers for predicting preterm preeclampsia and early-onset preeclampsia before diagnosis based on 13 cell-free RNA signatures and 2 clinical features (in vitro fertilization and mean arterial pressure), respectively. Notably, both classifiers showed enhanced performance when compared with the existing methods. The preterm preeclampsia prediction model achieved 81% area under the curve and 68% positive predictive value in an independent validation cohort (preterm, n=46; control, n=151); the early-onset preeclampsia prediction model had an area under the curve of 88% and a positive predictive value of 73% in an external validation cohort (early-onset preeclampsia, n=28; control, n=234). Furthermore, we demonstrated that downregulation of microRNAs may play vital roles in preeclampsia through the upregulation of preeclampsia-relevant target genes. CONCLUSION In this cohort study, a comprehensive transcriptomic landscape of different RNA biotypes in preeclampsia was presented and 2 advanced classifiers with substantial clinical importance for preterm preeclampsia and early-onset preeclampsia prediction before symptom onset were developed. We demonstrated that messenger RNA, microRNA, and long noncoding RNA can simultaneously serve as potential biomarkers of preeclampsia, holding the promise of prevention of preeclampsia in the future. Abnormal cell-free messenger RNA, microRNA, and long noncoding RNA molecular changes may help to elucidate the pathogenic determinants of preeclampsia and open new therapeutic windows to effectively reduce pregnancy complications and fetal morbidity.
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Affiliation(s)
- Si Zhou
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; BGI Genomics, BGI-Shenzhen, Shenzhen, China; Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Shijiazhuang BGI Genomics Co, Ltd, Shijiazhuang, Hebei Province, China; Shijiazhuang BGI Clinical Laboratory Co, Ltd, Shijiazhuang, Hebei Province, China
| | - Jie Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; BGI-Shenzhen, Shenzhen, China; BGI-Beijing, Beijing, China
| | - Wenzhi Yang
- Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Shijiazhuang BGI Genomics Co, Ltd, Shijiazhuang, Hebei Province, China; Shijiazhuang BGI Clinical Laboratory Co, Ltd, Shijiazhuang, Hebei Province, China
| | - Penghao Xue
- Shijiazhuang BGI Clinical Laboratory Co, Ltd, Shijiazhuang, Hebei Province, China
| | - Yanning Yin
- Shijiazhuang BGI Clinical Laboratory Co, Ltd, Shijiazhuang, Hebei Province, China
| | - Yunfang Wang
- Shijiazhuang BGI Clinical Laboratory Co, Ltd, Shijiazhuang, Hebei Province, China
| | | | | | | | - Wenqiu Xu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Shang Huang
- Shenzhen Children's Hospital of China Medical University, Shenzhen, China
| | - Rui Zhang
- Division of Maternal-Fetal Medicine, Jinan University-affiliated Shenzhen Baoan Women's and Children's Hospital, Shenzhen, China.
| | - Fengxiang Wei
- Genetics Laboratory, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City, Shenzhen, China.
| | - Hai-Xi Sun
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; BGI-Shenzhen, Shenzhen, China; BGI-Beijing, Beijing, China.
| | - Jianguo Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China; Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Shijiazhuang BGI Genomics Co, Ltd, Shijiazhuang, Hebei Province, China; Shijiazhuang BGI Clinical Laboratory Co, Ltd, Shijiazhuang, Hebei Province, China.
| | - Lijian Zhao
- BGI Genomics, BGI-Shenzhen, Shenzhen, China; Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Shijiazhuang BGI Genomics Co, Ltd, Shijiazhuang, Hebei Province, China; Medical Technology College of Hebei Medical University, Shijiazhuang, China.
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Xue VW, Ng SSM, Tsang HF, Wong HT, Leung WW, Wong YN, Wong YKE, Yu ACS, Yim AKY, Cho WCS, Tai WCS, Wong SCC. The non-invasive diagnosis of colorectal cancer via a SOX9-based gene panel. Clin Exp Med 2023; 23:2421-2432. [PMID: 36637582 DOI: 10.1007/s10238-022-00970-6] [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: 10/30/2022] [Accepted: 12/01/2022] [Indexed: 01/14/2023]
Abstract
Colorectal cancer (CRC) threatens human health seriously. Early diagnosis of CRC is critical to improving patient survival. Meanwhile, non-invasive detection through tumor-circulating markers can be an important auxiliary diagnosis. In this study, we performed targeted RNA sequencing in paired tumor and adjacent normal fresh frozen tissues from 68 patients, and we also measured circulating mRNA levels in 4 time-point plasma samples collected before and after operation or chemotherapy. Our results showed that SOX9 (6.73-fold with adjusted p value < 1 × 10-45), MYC (20.59-fold with adjusted p value < 1 × 10-57), and MMP7 (131.94-fold with adjusted p value < 1 × 10-78) highly expressed in tumor compared with adjacent normal tissues. Besides, the circulating mRNA of SOX9 (41.14-fold with adjusted p value < 1 × 10-13) in CRC was significantly higher than in the normal control as well. Moreover, a SOX9-based 9-gene panel (SOX9, GSK3A, FZD4, LEF1, DVL1, FZD7, NFATC1, KRT19, and RUVBL1) showed the non-invasive diagnostic value of CRC (AUC: 0.863 (0.766-0.960), TPR: 0.92, TNR: 0.87). In summary, SOX9 expression consistently increases in tumor and plasma samples from CRC patients, which indicates the important role of SOX9 in CRC progression and its potential in non-invasive diagnosis of CRC.
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Affiliation(s)
- Vivian Weiwen Xue
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Department of Pharmacology, Shenzhen University Health Science Center, Shenzhen, China
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China
| | - Simon Siu Man Ng
- Department of Surgery, Faculty of Medicine, The Chinese University of Hong Kong, Kowloon, Hong Kong Special Administrative Region, China
| | - Hin Fung Tsang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China
| | - Heong Ting Wong
- Department of Pathology, Kiang Wu Hospital, Santo António, Macau Special Administrative Region, China
| | - Wing Wa Leung
- Department of Surgery, Faculty of Medicine, The Chinese University of Hong Kong, Kowloon, Hong Kong Special Administrative Region, China
| | - Yee Ni Wong
- Department of Surgery, Faculty of Medicine, The Chinese University of Hong Kong, Kowloon, Hong Kong Special Administrative Region, China
| | - Yin Kwan Evelyn Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China
| | - Allen Chi Shing Yu
- Codex Genetics Limited, Kowloon, Hong Kong Special Administrative Region, China
| | - Aldrin Kay Yuen Yim
- Codex Genetics Limited, Kowloon, Hong Kong Special Administrative Region, China
| | - William Chi Shing Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong Special Administrative Region, China
| | - William Chi Shing Tai
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China
| | - Sze Chuen Cesar Wong
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China.
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Jin H, Zhang Y, Fan Z, Wang X, Rui C, Xing S, Dong H, Wang Q, Tao F, Zhu Y. Identification of novel cell-free RNAs in maternal plasma as preterm biomarkers in combination with placental RNA profiles. J Transl Med 2023; 21:256. [PMID: 37046301 PMCID: PMC10100253 DOI: 10.1186/s12967-023-04083-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: 01/07/2023] [Accepted: 03/25/2023] [Indexed: 04/14/2023] Open
Abstract
BACKGROUND Preterm birth (PTB) is the main driver of newborn deaths. The identification of pregnancies at risk of PTB remains challenging, as the incomplete understanding of molecular mechanisms associated with PTB. Although several transcriptome studies have been done on the placenta and plasma from PTB women, a comprehensive description of the RNA profiles from plasma and placenta associated with PTB remains lacking. METHODS Candidate markers with consistent trends in the placenta and plasma were identified by implementing differential expression analysis using placental tissue and maternal plasma RNA-seq datasets, and then validated by RT-qPCR in an independent cohort. In combination with bioinformatics analysis tools, we set up two protein-protein interaction networks of the significant PTB-related modules. The support vector machine (SVM) model was used to verify the prediction potential of cell free RNAs (cfRNAs) in plasma for PTB and late PTB. RESULTS We identified 15 genes with consistent regulatory trends in placenta and plasma of PTB while the full term birth (FTB) acts as a control. Subsequently, we verified seven cfRNAs in an independent cohort by RT-qPCR in maternal plasma. The cfRNA ARHGEF28 showed consistence in the experimental validation and performed excellently in prediction of PTB in the model. The AUC achieved 0.990 for whole PTB and 0.986 for late PTB. CONCLUSIONS In a comparison of PTB versus FTB, the combined investigation of placental and plasma RNA profiles has shown a further understanding of the mechanism of PTB. Then, the cfRNA identified has the capacity of predicting whole PTB and late PTB.
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Affiliation(s)
- Heyue Jin
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China
- MOE Key Laboratory of Population Health Across Life Cycle, No 81 Meishan Road, Hefei, Anhui, China
- Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, Anhui, China
| | - Yimin Zhang
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China
- MOE Key Laboratory of Population Health Across Life Cycle, No 81 Meishan Road, Hefei, Anhui, China
- Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, Anhui, China
| | - Zhigang Fan
- Department of Neonatology, Ma'anshan Maternal and Child Health Hospital, Ma'anshan, Anhui, China
| | - Xianyan Wang
- Department of Toxicology, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, Hefei, Anhui, China
| | - Chen Rui
- Department of Toxicology, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, Hefei, Anhui, China
| | - Shaozhen Xing
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Hongmei Dong
- Department of Obstetrics, Ma'anshan Maternal and Child Health Hospital, Ma'anshan, Anhui, China
| | - Qunan Wang
- Department of Toxicology, School of Public Health, Anhui Medical University, Hefei, Anhui, China.
- Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, Hefei, Anhui, China.
| | - Fangbiao Tao
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China.
- MOE Key Laboratory of Population Health Across Life Cycle, No 81 Meishan Road, Hefei, Anhui, China.
- Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China.
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, Anhui, China.
| | - Yumin Zhu
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China.
- MOE Key Laboratory of Population Health Across Life Cycle, No 81 Meishan Road, Hefei, Anhui, China.
- Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China.
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, Anhui, China.
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Reappraisal of evolving methods in non-invasive prenatal screening: Discovery, biology and clinical utility. Heliyon 2023; 9:e13923. [PMID: 36879971 PMCID: PMC9984859 DOI: 10.1016/j.heliyon.2023.e13923] [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: 07/10/2022] [Revised: 01/16/2023] [Accepted: 02/15/2023] [Indexed: 02/24/2023] Open
Abstract
Non-invasive prenatal screening (NIPS) offers an opportunity to screen or determine features associated with the fetus. Earlier, prenatal testing was done with cytogenetic procedures like karyotyping or fluorescence in-situ hybridization, which necessitated invasive methods such as fetal blood sampling, chorionic villus sampling or amniocentesis. Over the last two decades, there has been a paradigm shift away from invasive prenatal diagnostic methods to non-invasive ones. NIPS tests heavily rely on cell-free fetal DNA (cffDNA). This DNA is released into the maternal circulation by placenta. Like cffDNA, fetal cells such as nucleated red blood cells, placental trophoblasts, leukocytes, and exosomes or fetal RNA circulating in maternal plasma, have enormous potential in non-invasive prenatal testing, but their use is still limited due to a number of limitations. Non-invasive approaches currently use circulating fetal DNA to assess the fetal genetic milieu. Methods with an acceptable detection rate and specificity such as sequencing, methylation, or PCR, have recently gained popularity in NIPS. Now that NIPS has established clinical significance in prenatal screening and diagnosis, it is critical to gain insights into and comprehend the genesis of NIPS de novo. The current review reappraises the development and emergence of non-invasive prenatal screen/test approaches, as well as their clinical application, with a focus, on the scope, benefits, and limitations.
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The amniotic fluid proteome changes with term labor and informs biomarker discovery in maternal plasma. Sci Rep 2023; 13:3136. [PMID: 36823217 PMCID: PMC9950459 DOI: 10.1038/s41598-023-28157-3] [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: 08/17/2022] [Accepted: 01/13/2023] [Indexed: 02/25/2023] Open
Abstract
The intra-uterine components of labor, namely, myometrial contractility, cervical ripening, and decidua/membrane activation, have been extensively characterized and involve a local pro-inflammatory milieu of cellular and soluble immune mediators. Targeted profiling has demonstrated that such processes extend to the intra-amniotic space, yet unbiased analyses of the proteome of human amniotic fluid during labor are lacking. Herein, we utilized an aptamer-based platform to characterize 1,310 amniotic fluid proteins and found that the proteome undergoes substantial changes with term labor (251 proteins with differential abundance, q < 0.1, and fold change > 1.25). Proteins with increased abundance in labor are enriched for immune and inflammatory processes, consistent with prior reports of labor-associated changes in the intra-uterine space. By integrating the amniotic fluid proteome with previously generated placental-derived single-cell RNA-seq data, we demonstrated the labor-driven upregulation of signatures corresponding to stromal-3 and decidual cells. We also determined that changes in amniotic fluid protein abundance are reflected in the maternal plasma proteome. Collectively, these findings provide novel insights into the amniotic fluid proteome in term labor and support its potential use as a source of biomarkers to distinguish between true and false labor by using maternal blood samples.
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Li N, Gu Y, Tang J, Li Y, Chen D, Xu Z. Circulating Non-coding RNAs and Exosomes: Liquid Biopsies for Monitoring Preeclampsia. Methods Mol Biol 2023; 2695:263-277. [PMID: 37450125 DOI: 10.1007/978-1-0716-3346-5_18] [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: 07/18/2023]
Abstract
Preeclampsia (PE) remains a leading cause of maternal and fetal mortality, due to ineffective treatment and diagnostic strategies, compounded by the lack of clarity on the etiology of the disorder. The early prediction or accurate diagnosis of PE is a concern of researchers. Liquid biopsy can be analyzed for cell-free nucleic acids and exosomes. Because circulating non-coding RNAs (ncRNAs) and peripheral blood exosomes can be detected in the peripheral blood of women in early pregnancy, these vesicles and their contents have become the focus of research on early predictive and diagnostic biomarkers for preeclampsia. In this review, we focus on recent studies addressing the roles of circulating ncRNAs and exosomes in PE, with particular attention paid to the potential application value of placenta-derived exosomes and circulating ncRNAs as PE-specific biomarkers.
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Affiliation(s)
- Na Li
- Lab of Perinatal Medicine, Wuxi Maternity and Child Health Care Hospital, Wuxi, Jiangsu, China
| | - Ying Gu
- Lab of Perinatal Medicine, Wuxi Maternity and Child Health Care Hospital, Wuxi, Jiangsu, China
| | - Jiaqi Tang
- Institute for Fetology, First Hospital of Soochow University, Suzhou, China
| | - Yongmei Li
- Department of Obstetrics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, China
| | - Daozhen Chen
- Lab of Perinatal Medicine, Wuxi Maternity and Child Health Care Hospital, Wuxi, Jiangsu, China
| | - Zhice Xu
- Lab of Perinatal Medicine, Wuxi Maternity and Child Health Care Hospital, Wuxi, Jiangsu, China
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9
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Tao Y, Gao C, Qian D, Cao D, Han L, Yang L. Regulatory mechanism of fibrosis-related genes in patients with heart failure. Front Genet 2022; 13:1032572. [DOI: 10.3389/fgene.2022.1032572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/06/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Heart failure (HF) is a complex clinical syndrome characterized by the inability to match cardiac output with metabolic needs. Research on regulatory mechanism of fibrosis-related genes in patients with HF is very limited. In order to understand the mechanism of fibrosis in the development and progression of HF, fibrosis -related hub genes in HF are screened and verified.Methods: RNA sequencing data was obtained from the Gene Expression Omnibus (GEO) cohorts to identify differentially expressed genes (DEGs). Thereafter, fibrosis-related genes were obtained from the GSEA database and that associated with HF were screened out. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis was carried out to analyze the biological function of fibrosis-related DEGs. The protein-protein interaction (PPI) network of hub genes was constructed via the STRING database. Moreover, the diagnostic value of hub genes for HF was confirmed using ROC curves and expression analysis. Finally, quantitative real time PCR was used to detect the expression levels of mRNAs.Results: A total of 3, 469 DEGs were identified closely related to HF, and 1, 187 fibrosis-related DEGs were obtained and analyzed for GO and KEGG enrichment. The enrichment results of fibrosis-related DEGs were consistent with that of DEGs. A total of 10 hub genes (PPARG, KRAS, JUN, IL10, TLR4, STAT3, CXCL8, CCL2, IL6, IL1β) were selected via the PPI network. Receiver operating characteristic curve analysis was estimated in the test cohort, and 6 genes (PPARG, KRAS, JUN, IL10, TLR4, STAT3) with AUC more than 0.7 were identified as diagnosis genes. Moreover, miRNA-mRNA and TF-mRNA regulatory networks were constructed. Finally, quantitative real time PCR revealed these 6 genes may be used as the potential diagnostic biomarkers of HF.Conclusion: In this study, 10 fibrosis-related hub genes in the HF were identified and 6 of them were demonstrated as potential diagnostic biomarkers for HF.
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10
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Žarković M, Hufsky F, Markert UR, Marz M. The Role of Non-Coding RNAs in the Human Placenta. Cells 2022; 11:cells11091588. [PMID: 35563893 PMCID: PMC9104507 DOI: 10.3390/cells11091588] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/01/2022] [Accepted: 05/03/2022] [Indexed: 12/11/2022] Open
Abstract
Non-coding RNAs (ncRNAs) play a central and regulatory role in almost all cells, organs, and species, which has been broadly recognized since the human ENCODE project and several other genome projects. Nevertheless, a small fraction of ncRNAs have been identified, and in the placenta they have been investigated very marginally. To date, most examples of ncRNAs which have been identified to be specific for fetal tissues, including placenta, are members of the group of microRNAs (miRNAs). Due to their quantity, it can be expected that the fairly larger group of other ncRNAs exerts far stronger effects than miRNAs. The syncytiotrophoblast of fetal origin forms the interface between fetus and mother, and releases permanently extracellular vesicles (EVs) into the maternal circulation which contain fetal proteins and RNA, including ncRNA, for communication with neighboring and distant maternal cells. Disorders of ncRNA in placental tissue, especially in trophoblast cells, and in EVs seem to be involved in pregnancy disorders, potentially as a cause or consequence. This review summarizes the current knowledge on placental ncRNA, their transport in EVs, and their involvement and pregnancy pathologies, as well as their potential for novel diagnostic tools.
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Affiliation(s)
- Milena Žarković
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany; (M.Ž.); (F.H.)
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
- Placenta Lab, Department of Obstetrics, University Hospital Jena, Am Klinikum 1, 07747 Jena, Germany;
| | - Franziska Hufsky
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany; (M.Ž.); (F.H.)
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
| | - Udo R. Markert
- Placenta Lab, Department of Obstetrics, University Hospital Jena, Am Klinikum 1, 07747 Jena, Germany;
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany; (M.Ž.); (F.H.)
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
- FLI Leibniz Institute for Age Research, Beutenbergstraße 11, 07745 Jena, Germany
- Aging Research Center (ARC), 07745 Jena, Germany
- Correspondence:
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11
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Vong JSL, Ji L, Heung MMS, Cheng SH, Wong J, Lai PBS, Wong VWS, Chan SL, Chan HLY, Jiang P, Chan KCA, Chiu RWK, Lo YMD. Single Cell and Plasma RNA Sequencing for RNA Liquid Biopsy for Hepatocellular Carcinoma. Clin Chem 2021; 67:1492-1502. [PMID: 34463757 DOI: 10.1093/clinchem/hvab116] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 06/08/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND Human plasma contains RNA transcripts released by multiple cell types within the body. Single-cell transcriptomic analysis allows the cellular origin of circulating RNA molecules to be elucidated at high resolution and has been successfully utilized in the pregnancy context. We explored the application of a similar approach to develop plasma RNA markers for cancer detection. METHODS Single-cell RNA sequencing was performed to decipher transcriptomic profiles of single cells from hepatocellular carcinoma (HCC) samples. Cell-type-specific transcripts were identified and used for deducing the cell-type-specific gene signature (CELSIG) scores of plasma RNA from patients with and without HCC. RESULTS Six major cell clusters were identified, including hepatocyte-like, cholangiocyte-like, myofibroblast, endothelial, lymphoid, and myeloid cell clusters based on 4 HCC tumor tissues as well as their paired adjacent nontumoral tissues. The CELSIG score of hepatocyte-like cells was significantly increased in preoperative plasma RNA samples of patients with HCC (n = 14) compared with non-HCC participants (n = 49). The CELSIG score of hepatocyte-like cells declined in plasma RNA samples of patients with HCC within 3 days after tumor resection. Compared with the discriminating power between patients with and without HCC using the abundance of ALB transcript in plasma [area under curve (AUC) 0.72)], an improved performance (AUC: 0.84) was observed using the CELSIG score. The hepatocyte-specific transcript markers in plasma RNA were further validated by ddPCR assays. The CELSIG scores of hepatocyte-like cell and cholangiocyte trended with patients' survival. CONCLUSIONS The combination of single-cell transcriptomic analysis and plasma RNA sequencing represents an approach for the development of new noninvasive cancer markers.
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Affiliation(s)
- Joaquim S L Vong
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Lu Ji
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
| | - Macy M S Heung
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
| | - Suk Hang Cheng
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
| | - John Wong
- Department of Surgery, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Paul B S Lai
- Department of Surgery, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Vincent W S Wong
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Institute of Digestive Diseases, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Stephen L Chan
- Department of Clinical Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China.,State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Henry L Y Chan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Institute of Digestive Diseases, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Peiyong Jiang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
| | - K C Allen Chan
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China.,State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Rossa W K Chiu
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
| | - Y M Dennis Lo
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China.,State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
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12
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Gomez-Lopez N, Romero R, Galaz J, Bhatti G, Done B, Miller D, Ghita C, Motomura K, Farias-Jofre M, Jung E, Pique-Regi R, Hassan SS, Chaiworapongsa T, Tarca AL. Transcriptome changes in maternal peripheral blood during term parturition mimic perturbations preceding spontaneous Preterm birth†. Biol Reprod 2021; 106:185-199. [PMID: 34686873 DOI: 10.1093/biolre/ioab197] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/30/2021] [Accepted: 10/20/2021] [Indexed: 11/14/2022] Open
Abstract
The complex physiologic process of parturition includes the onset of labor, which requires the orchestrated stimulation of a common pathway involving uterine contractility, cervical ripening, and chorioamniotic membrane activation. However, the labor-specific processes taking place in these tissues have limited use as predictive biomarkers unless they can be probed in non-invasive samples, such as the peripheral blood. Herein, we utilized a transcriptomic dataset to assess labor-specific changes in the peripheral blood of women who delivered at term. We identified a set of genes that were differentially expressed with labor and enriched for immunological processes, and these gene expression changes were strongly correlated with results from prior studies, providing in silico validation of our findings. We then identified significant correlations between labor-specific transcriptomic changes in the maternal circulation and those reported in the chorioamniotic membranes, myometrium, and cervix of women at term, demonstrating that tissue-specific labor signatures are partly mirrored in the peripheral blood. Last, we demonstrated a significant overlap between the peripheral blood transcriptomic changes in term parturition and those observed in asymptomatic women prior to the diagnosis of preterm prelabor rupture of membranes who delivered preterm. Collectively, we provide evidence that the normal process of labor at term is characterized by a unique immunological expression signature, which may serve as a useful tool for assessing labor status and potentially identifying women at risk for preterm birth.
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Affiliation(s)
- Nardhy Gomez-Lopez
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (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 Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Roberto Romero
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (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.,Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA.,Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA.,Detroit Medical Center, Detroit, MI, USA.,Department of Computer Science, Wayne State University College of Engineering, Detroit, MI, USA
| | - Jose Galaz
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS); Bethesda, MD, and Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Gaurav Bhatti
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS); Bethesda, MD, and Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Bogdan Done
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS); Bethesda, MD, and Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Derek Miller
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS); Bethesda, MD, and Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Corina Ghita
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS); Bethesda, MD, and Detroit, MI, USA
| | - Kenichiro Motomura
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS); Bethesda, MD, and Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Marcelo Farias-Jofre
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS); Bethesda, MD, and Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Eunjung Jung
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS); Bethesda, MD, and Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Roger Pique-Regi
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS); Bethesda, MD, and Detroit, MI, USA.,Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
| | - Sonia S Hassan
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Tinnakorn Chaiworapongsa
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (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, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (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 Computer Science, Wayne State University College of Engineering, Detroit, MI, USA
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13
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Sadeghi S, Rahaie M, Ostad-Hasanzadeh B. Nanostructures in non-invasive prenatal genetic screening. Biomed Eng Lett 2021; 12:3-18. [DOI: 10.1007/s13534-021-00208-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/22/2021] [Accepted: 10/02/2021] [Indexed: 11/24/2022] Open
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14
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Tang X, Chen X, Liao Y, Yan B, Hu H, Ming Z, Liu L, Li L, Mao Z, Xiao X. Self-Internal-Reference Probe System for Control-Free Quantification of Mutation Abundance. Anal Chem 2021; 93:13274-13283. [PMID: 34546716 DOI: 10.1021/acs.analchem.1c02877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Gene mutations are important biomarkers for the diagnosis, classification, monitoring, and prognosis evaluation of cancers and genetic diseases. Both personalized cancer treatment and noninvasive prenatal testing require methods to accurately determine the abundance of mutation. At present, the widely adopted and convenient methods for measuring mutation abundance are mainly based on relative quantification, which requires negative samples and strict control of the analyte amounts. The development of DNA-probe-based methods that can determine the mutation abundance without negative samples nor control of analyte amount is highly preferred. The key to solving this bottleneck lies in whether the probe's response to mutation abundance can be completely independent of the number of targeted DNA strands. Herein, we propose the design of a self-internal-reference probe system. We established a theoretical model of this system and used the model to guide the design of probes. In this model, we provided quantitative corrections to the test results from the internal reference, thereby eliminating the influence of substrate amount. Therefore, the purification and quantification processes toward polymerase chain reaction (PCR) amplicons can be omitted. We applied this system to analyze unquantified PCR products aimed at cancer mutation detection and noninvasive prenatal testing.
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Affiliation(s)
- Xiaofeng Tang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China
| | - Xin Chen
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China
| | - Yangwei Liao
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China
| | - Bei Yan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China
| | - Hao Hu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China
| | - Zhihao Ming
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China
| | - Liquan Liu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China
| | - Longjie Li
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China.,School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, P. R. China
| | - Zenghui Mao
- Center of Reproductive Medicine, Changsha Hospital for Maternal and Child Health Care of Hunan Normal University, Changsha 410007, P. R. China
| | - Xianjin Xiao
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China
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15
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Munchel S, Rohrback S, Randise-Hinchliff C, Kinnings S, Deshmukh S, Alla N, Tan C, Kia A, Greene G, Leety L, Rhoa M, Yeats S, Saul M, Chou J, Bianco K, O'Shea K, Bujold E, Norwitz E, Wapner R, Saade G, Kaper F. Circulating transcripts in maternal blood reflect a molecular signature of early-onset preeclampsia. Sci Transl Med 2021; 12:12/550/eaaz0131. [PMID: 32611681 DOI: 10.1126/scitranslmed.aaz0131] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 11/07/2019] [Accepted: 06/08/2020] [Indexed: 12/13/2022]
Abstract
Circulating RNA (C-RNA) is continually released into the bloodstream from tissues throughout the body, offering an opportunity to noninvasively monitor all aspects of pregnancy health from conception to birth. We asked whether C-RNA analysis could robustly detect aberrations in patients diagnosed with preeclampsia (PE), a prevalent and potentially fatal pregnancy complication. As an initial examination, we sequenced the circulating transcriptome from 40 pregnancies at the time of severe, early-onset PE diagnosis and 73 gestational age-matched controls. Differential expression analysis identified 30 transcripts with gene ontology annotations and tissue expression patterns consistent with the placental dysfunction, impaired fetal development, and maternal immune and cardiovascular system dysregulation characteristic of PE. Furthermore, machine learning identified combinations of 49 C-RNA transcripts that classified an independent cohort of patients (early-onset PE, n = 12; control, n = 12) with 85 to 89% accuracy. C-RNA may thus hold promise for improving the diagnosis and identification of at-risk pregnancies.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Emmanuel Bujold
- Department of Obstetrics and Gynecology and Department of Social and Preventive Medicine, Faculty of Medicine, Université Laval, Quebec City, Quebec G1V 086, Canada
| | - Errol Norwitz
- Department of Obstetrics and Gynecology and the Mother Infant Research Institute, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Ronald Wapner
- Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY 10032, USA
| | - George Saade
- Department of Obstetrics and Gynecology, University of Texas Medical Branch, Galveston, TX 77555, USA
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16
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Function Follows Form: Gene Expression and Prenatal Screening. Trends Mol Med 2021; 27:725-727. [PMID: 34175229 PMCID: PMC10040215 DOI: 10.1016/j.molmed.2021.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 11/22/2022]
Abstract
To date, prenatal testing has relied on imaging to determine fetal 'form' (anatomy). 'Function', as ascertained by measuring fetal or placental mRNA transcripts in maternal blood, has the potential to more precisely determine which pregnancies need closer monitoring and which babies should be delivered in special care settings.
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17
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Gai W, Zhou Z, Agbor-Enoh S, Fan X, Lian S, Jiang P, Cheng SH, Wong J, Chan SL, Jang MK, Yang Y, Liang RH, Chan WK, Ma ES, Leung TY, Chiu RW, Valantine H, Chan KA, Lo YD. Applications of genetic-epigenetic tissue mapping for plasma DNA in prenatal testing, transplantation and oncology. eLife 2021; 10:64356. [PMID: 33752803 PMCID: PMC7997656 DOI: 10.7554/elife.64356] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 03/10/2021] [Indexed: 01/02/2023] Open
Abstract
We developed genetic-epigenetic tissue mapping (GETMap) to determine the tissue composition of plasma DNA carrying genetic variants not present in the constitutional genome through comparing their methylation profiles with relevant tissues. We validated this approach by showing that, in pregnant women, circulating DNA carrying fetal-specific alleles was entirely placenta-derived. In lung transplant recipients, we showed that, at 72 hr after transplantation, the lung contributed only a median of 17% to the plasma DNA carrying donor-specific alleles, and hematopoietic cells contributed a median of 78%. In hepatocellular cancer patients, the liver was identified as the predominant source of plasma DNA carrying tumor-specific mutations. In a pregnant woman with lymphoma, plasma DNA molecules carrying cancer mutations and fetal-specific alleles were accurately shown to be derived from the lymphocytes and placenta, respectively. Analysis of tissue origin for plasma DNA carrying genetic variants is potentially useful for noninvasive prenatal testing, transplantation monitoring, and cancer screening.
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Affiliation(s)
- Wanxia Gai
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China.,State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong, China
| | - Ze Zhou
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Sean Agbor-Enoh
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, United States.,Division of Pulmonary and Critical Care Medicine, The Johns Hopkins School of Medicine, Baltimore, United States.,Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, United States
| | - Xiaodan Fan
- Department of Statistics, The Chinese University of Hong Kong, Hong Kong, China
| | - Sheng Lian
- Department of Statistics, The Chinese University of Hong Kong, Hong Kong, China
| | - Peiyong Jiang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China.,State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong, China
| | - Suk Hang Cheng
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - John Wong
- Department of Surgery, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Stephen L Chan
- Department of Clinical Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Moon Kyoo Jang
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, United States.,Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, United States
| | - Yanqin Yang
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, United States.,Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, United States
| | - Raymond Hs Liang
- Comprehensive Oncology Centre, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Wai Kong Chan
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Edmond Sk Ma
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Tak Y Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Rossa Wk Chiu
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Hannah Valantine
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, United States.,Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, United States
| | - Kc Allen Chan
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China.,State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong, China
| | - Ym Dennis Lo
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China.,State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong, China
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18
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Martins C, Lima J, Cambridge G, Ângelo-Dias M, Leandro M, Miguel Borrego L. Serum markers of B-cell activation in pregnant women with atopic asthma. Am J Reprod Immunol 2021; 86:e13414. [PMID: 33682259 PMCID: PMC8365761 DOI: 10.1111/aji.13414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 03/02/2021] [Indexed: 11/28/2022] Open
Abstract
PROBLEM As maternal atopy represents a risk factor for the development of atopy in offspring, we aimed to assess how pregnancy affects B-cell activation markers in women with atopic asthma and whether they correlate with risk manifestations for allergy in newborns from mothers with atopic asthma. METHOD OF STUDY Pregnant women with atopic asthma (AP) in the third trimester of gestation and nonpregnant women with atopic asthma (ANP) were prospectively recruited and compared to respective healthy counterparts (HP and HNP). All pregnant women were also assessed during the postpartum period until 6 weeks after delivery (HP/PP and AP/PP). Newborns were clinically evaluated at the age of 6 months. Peripheral blood samples were taken from each woman at each time point. Soluble CD23 (sCD23), B-cell activating factor (BAFF), IgA, IgG, IgM, kappa (κ), and lambda (λ) free light chains (FLC) were quantified in serum samples. RESULTS The AP group presented increased sCD23 (p < 0.05) and BAFF (p < 0.001) levels compared to the ANP group and even higher levels of sCD23 during the postpartum period (p < 0.001). Moreover, the cutoffs of 6.74 g/L for IgG (sensitivity 90.9%, specificity 77.8%) and of 11.30 mg/L for λ FLC (sensitivity 81.8%, specificity 88.9%) in the AP group were predictive factors for the manifestation of allergy in their offspring. CONCLUSIONS After delivery, the dynamics of sCD23 and BAFF changed significantly in the AP group. Furthermore, we found novel predictive factors for allergy manifestations in the children of these women, with potential clinical application.
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Affiliation(s)
- Catarina Martins
- CEDOC, NOVA Medical School, Nova University of Lisbon. Campo dos Mártires da Pátria, Lisbon, Portugal.,Comprehensive Health Research Centre (CHRC), NOVA Medical School, Nova University of Lisbon, Lisbon, Portugal
| | - Jorge Lima
- CEDOC, NOVA Medical School, Nova University of Lisbon. Campo dos Mártires da Pátria, Lisbon, Portugal.,Comprehensive Health Research Centre (CHRC), NOVA Medical School, Nova University of Lisbon, Lisbon, Portugal.,Department of Obstetrics and Gynecology, CUF Descobertas Hospital, Lisbon, Portugal
| | - Geraldine Cambridge
- Centre for Rheumatology and Bloomsbury Rheumatology Unit, Division of Medicine, University College London, London, UK
| | - Miguel Ângelo-Dias
- CEDOC, NOVA Medical School, Nova University of Lisbon. Campo dos Mártires da Pátria, Lisbon, Portugal.,Comprehensive Health Research Centre (CHRC), NOVA Medical School, Nova University of Lisbon, Lisbon, Portugal
| | - Maria Leandro
- Centre for Rheumatology and Bloomsbury Rheumatology Unit, Division of Medicine, University College London, London, UK
| | - Luís Miguel Borrego
- CEDOC, NOVA Medical School, Nova University of Lisbon. Campo dos Mártires da Pátria, Lisbon, Portugal.,Comprehensive Health Research Centre (CHRC), NOVA Medical School, Nova University of Lisbon, Lisbon, Portugal.,Department of Imunoallergy, LUZ SAÚDE, Hospital da Luz, Lisbon, Portugal
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19
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Oudejans C, Manders V, Visser A, Keijser R, Min N, Poutsma A, Mulders J, van den Berkmortel T, Wigman DJ, Blanken B, Jongejan A, Pajkrt E, de Boer M, Sistermans EA, Sie D, Best MG, Würdinger T, Afink G. Circular RNA Sequencing of Maternal Platelets: A Novel Tool for the Identification of Pregnancy-Specific Biomarkers. Clin Chem 2021; 67:508-517. [PMID: 33257975 DOI: 10.1093/clinchem/hvaa249] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 09/29/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND In the first trimester of pregnancy, the maternal platelet is directly involved in a positive feedback mechanism that facilitates invasion of the extravillous trophoblast into the maternal spiral arteries. Dysfunctional trophoblast invasion with defective deep placentation is primordial in the etiology of the "great obstetrical syndromes." METHODS In this proof-of-concept study, using transcriptome analysis of circular RNA (circRNA) following RNA sequencing of maternal platelets, we tested whether pregnancy-specific circRNA markers could be identified in the first trimester of normal pregnancies. Differential transcript expression analysis of circRNAs, as predicted by Accurate CircRNA Finder Suite, CircRNA Identifier (version 2), and Known and Novel Isoform Explorer, was done using thromboSeq.R with variation of multiple settings. Test performance was checked for (a) de novo circRNA identification using the novel platelet-specific Plt-circR4 as a positive control, (b) complete segregation of groups (pregnant vs nonpregnant) after heat map-dendrogram clustering, (c) identification of pregnancy-specific circRNA markers at a false discovery rate (FDR) <0.05, and (d) confirmation of differentially expressed circRNA markers with an FDR <0.05 by an independent method, reverse transcription-quantitative PCR. RESULTS Of the differentially expressed circRNAs with P values <0.05, 41 circRNAs were upregulated (logFC >2), and 52 circRNAs were downregulated (logFC less than -2) in first-trimester platelet RNA. Of these, nuclear receptor-interacting protein 1 circRNA covering exons 2 and 3 of the 5'-untranslated region was pregnancy specific with upregulation in first-trimester maternal platelets compared to nonpregnant controls. CONCLUSION CircRNA sequencing of first-trimester maternal platelets permits the identification of novel pregnancy-specific RNA biomarkers. Future use could include the assessment of maternal and fetal well-being.
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Affiliation(s)
- Cees Oudejans
- Department of Clinical Chemistry, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands
| | - Vera Manders
- Department of Clinical Chemistry, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands.,Reproductive Biology Laboratory, Amsterdam UMC, Academic Medical Center, Amsterdam, the Netherlands
| | - Allerdien Visser
- Department of Clinical Chemistry, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands
| | - Remco Keijser
- Reproductive Biology Laboratory, Amsterdam UMC, Academic Medical Center, Amsterdam, the Netherlands
| | - Naomi Min
- Department of Clinical Chemistry, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands.,Reproductive Biology Laboratory, Amsterdam UMC, Academic Medical Center, Amsterdam, the Netherlands
| | - Ankie Poutsma
- Department of Clinical Chemistry, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands
| | - Joyce Mulders
- Department of Clinical Chemistry, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands
| | - Tarah van den Berkmortel
- Department of Clinical Chemistry, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands
| | - Di-Jan Wigman
- Department of Clinical Chemistry, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands
| | - Britt Blanken
- Department of Clinical Chemistry, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands
| | - Aldo Jongejan
- Department of Clinical Epidemiology, Biostatistics, and Bioinformatics, Amsterdam UMC, Academic Medical Center, the Netherlands
| | - Eva Pajkrt
- Department of Obstetrics/Gynecology, Amsterdam UMC, Academic Medical Center, Amsterdam, the Netherlands
| | - Marjon de Boer
- Department of Obstetrics/Gynecology, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands
| | - Erik A Sistermans
- Department of Clinical Genetics, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands
| | - Daoud Sie
- Department of Clinical Genetics, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands
| | - Myron G Best
- Department of Neurosurgery, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands.,Department of Pathology, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands.,Brain Tumor Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands
| | - Tom Würdinger
- Department of Neurosurgery, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands.,Brain Tumor Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands
| | - Gijs Afink
- Reproductive Biology Laboratory, Amsterdam UMC, Academic Medical Center, Amsterdam, the Netherlands
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20
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The bivariate NRIP1/ZEB2 RNA marker permits non-invasive presymptomatic screening of pre-eclampsia. Sci Rep 2020; 10:21857. [PMID: 33318568 PMCID: PMC7736279 DOI: 10.1038/s41598-020-79008-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 12/02/2020] [Indexed: 12/15/2022] Open
Abstract
Using genome-wide transcriptome analysis by RNA sequencing of first trimester plasma RNA, we tested whether the identification of pregnancies at risk of developing pre-eclampsia with or without preterm birth or growth restriction is possible between weeks 9–14, prior to the appearance of clinical symptoms. We implemented a metaheuristic approach in the self-learning SVM algorithm for differential gene expression analysis of normal pregnancies (n = 108), affected pregnancies (n = 34) and non-pregnant controls (n = 19). Presymptomatic candidate markers for affected pregnancies were validated by RT-qPCR in first trimester samples (n = 34) from an independent cohort. PRKG1 was significantly downregulated in a subset of pregnancies with birth weights below the 10thpercentile as shared symptom. The NRIP1/ZEB2 ratio was found to be upregulated in pregnancies with pre-eclampsia or trisomy 21. Complementary quantitative analysis of both the linear and circular forms of NRIP1 permitted discrimination between pre-eclampsia and trisomy 21. Pre-eclamptic pregnancies showed an increase in linear NRIP1 compared to circular NRIP1, while trisomy 21 pregnancies did not.
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21
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Brummaier T, Kabeer BSA, Chaussabel D, Utzinger J, McGready R, Paris DH. Blood gene transcript signature profiling in pregnancies resulting in preterm birth: A systematic review. Eur J Obstet Gynecol Reprod Biol X 2020; 8:100118. [PMID: 33024956 PMCID: PMC7528201 DOI: 10.1016/j.eurox.2020.100118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/16/2020] [Accepted: 09/21/2020] [Indexed: 01/15/2023] Open
Abstract
OBJECTIVE To pursue a systematic review and summarise the current evidence for the potential of transcriptome molecular profiling in investigating the preterm phenotype. STUDY DESIGN We systematically reviewed the literature, using readily available electronic databases (i.e. PubMed/Medline, Embase, Scopus and Web of Science) from inception until March 2020 to identify investigations of maternal blood-derived RNA profiling in preterm birth (PTB). Studies were included if circulating coding or non-coding RNA was analysed in maternal blood during pregnancy and/or at delivery. Interventional trials were not included. The primary outcome was the availability of whole genome expression patterns evaluated in pregnancies resulting in preterm deliveries. RESULTS A total of 35 articles were included in the final analysis. Most of the studies were conducted in high-income countries and published in the last decade. Apart from spontaneous PTB, a variety of phenotypes leading to preterm delivery were reported. Differences in sampling methods, target gene selection and laboratory protocols severely limited any quantitative comparisons. Most of the studies revealed that gene expression profiling during pregnancy has high potential for identifying women at risk of spontaneous and/or non-spontaneous PTB as early as in the first trimester. CONCLUSION Assessing maternal blood-derived transcriptional signatures for PTB risk in pregnant women holds promise as a screening approach. However, longitudinally followed, prospective pregnancy cohorts are lacking. These are relevant for identifying causes leading to PTB and whether prediction of spontaneous PTB or co-morbidities associated with PTB is achievable. More emphasis on widely employed standardised protocols is required to ensure comparability of results.
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Key Words
- ANC, antenatal care
- Antenatal screening
- DNA, deoxyribonucleic acid
- EGA, estimated gestational age
- FGR, fetal growth restriction
- Gene expression profiling
- HIC, high-income country
- LIC, low-income country
- LMP, last menstrual period
- MIC, middle-income country
- NGS, next generation sequencing
- PCR, polymerase chain reaction
- PICo, Population phenomenon of Interest and Context
- PPROM, preterm premature rupture of membranes
- PROSPERO, Prospective Register of Systematic Reviews
- PTB, preterm birth
- PTL, preterm labour
- PoA, proportion of agreement
- Preterm birth
- RIN, RNA integrity number
- RNA, Ribonucleic acid
- SDG, Sustainable Development Goal
- SGA, small for gestational age
- Systematic review
- Transcriptome
- WBC, white blood cells
- WHO, World Health Organization
- mRNA, messenger RNA
- miRNA, microRNA
- sPTB, spontaneous preterm birth
- sPTL, spontaneous preterm labour
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Affiliation(s)
- Tobias Brummaier
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | | | | | - Jürg Utzinger
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Rose McGready
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Daniel H Paris
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
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22
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Extracellular RNA: Emerging roles in cancer cell communication and biomarkers. Cancer Lett 2020; 495:33-40. [PMID: 32916182 DOI: 10.1016/j.canlet.2020.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/15/2020] [Accepted: 09/02/2020] [Indexed: 01/05/2023]
Abstract
Extracellular RNAs (exRNAs) are a type of RNA molecules that present in various biological fluids. exRNAs are heterogenous populations including small (e.g., miRNA) and long non-coding RNAs and coding RNAs (e.g., mRNA). They can exist in a free form or associate with carriers range from lipo- and ribo-proteins to extracellular vesicles such as exosomes in the extracellular fluids. exRNAs participate in cell-to-cell communication to regulate a broad array of physiological and pathological processes. exRNAs have been widely studied as a biomarker for cancer and other diseases. In this review, we will discuss the sorts of exRNAs with potential carriers as well as their roles in cancer.
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23
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Wang L, Wang J, Jia E, Liu Z, Ge Q, Zhao X. Plasma RNA sequencing of extracellular RNAs reveals potential biomarkers for non-small cell lung cancer. Clin Biochem 2020; 83:65-73. [PMID: 32526228 DOI: 10.1016/j.clinbiochem.2020.06.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 06/05/2020] [Accepted: 06/06/2020] [Indexed: 01/31/2023]
Abstract
BACKGROUND Lung cancer is one of the most common malignancies, and it has extremely high incidence and mortality rates. Although there have been many studies focused on lung cancer biomarkers, few have reported the extracellular RNA profiles of lung cancer. In this study, we used RNA-seq technology to analyze extracellular RNAs in low volume peripheral blood plasma; we compared the differentially expressed genes from the plasma of non-small cell lung cancer (NSCLC) patients with that of healthy controls. METHODS We used RNA-seq technology and bioinformatics to analyze the extracellular RNA (exRNA) sequences of 12 human plasma samples (500 μl per sample), 6 from NSCLC patients and 6 from healthy controls. Subsequently, we used gene ontology (GO) enrichment, KEGG analysis and coexpression experiments to compare the differentially expressed genes (DEGs) and identify tumor biomarkers that were highly correlated with NSCLC. These DEGs were further verified by quantitative PCR. RESULTS Approximately 20 million clean reads were produced for each plasma sample; 50-80% of the reads aligned to the human references, and hundreds of thousands of reads were counted in each plasma sample. In addition, a total of 640 genes (368 upregulated and 272 downregulated) were differentially expressed between NSCLC plasma and normal plasma. Further, we identified 7 key DEGs that are highly correlated with lung tumorigenesis: COX1, COX2, COX3, ND1, ND2, ND4L, and ATP6. CONCLUSION exRNA-seq from a small amount (400-500 μl) of plasma opens new possibilities for exploring lung cancer biomarkers in the plasma.
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Affiliation(s)
- Liujing Wang
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Jun Wang
- Nanjing Med Univ, Jiangsu Prov Peoples Hosp, Dept Thorac Surg, Nanjing, Jiangsu, China.
| | - Erteng Jia
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Zhiyu Liu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Xiangwei Zhao
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China.
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24
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Leung OM, Li J, Li X, Chan VW, Yang KY, Ku M, Ji L, Sun H, Waldmann H, Tian XY, Huang Y, Lau J, Zhou B, Lui KO. Regulatory T Cells Promote Apelin-Mediated Sprouting Angiogenesis in Type 2 Diabetes. Cell Rep 2020; 24:1610-1626. [PMID: 30089270 DOI: 10.1016/j.celrep.2018.07.019] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 06/27/2018] [Accepted: 07/05/2018] [Indexed: 12/13/2022] Open
Abstract
The role of CD4+ T cells in the ischemic tissues of T2D patients remains unclear. Here, we report that T2D patients' vascular density was negatively correlated with the number of infiltrating CD4+ T cells after ischemic injury. Th1 was the predominant subset, and Th1-derived IFN-γ and TNF-α directly impaired human angiogenesis. We then blocked CD4+ T cell infiltration into the ischemic tissues of both Leprdb/db and diet-induced obese T2D mice. Genome-wide RNA sequencing shows an increased proliferative and angiogenic capability of diabetic ECs in ischemic tissues. Moreover, wire myography shows enhanced EC function and laser Doppler imaging reveals improved post-ischemic blood reperfusion. Mechanistically, functional revascularization after CD4 coreceptor blockade was mediated by Tregs. Genetic lineage tracing via Cdh5-CreER and Apln-CreER and coculture assays further illustrate that Tregs increased vascular density and induced de novo sprouting angiogenesis in a paracrine manner. Taken together, our results reveal that Th1 impaired while Tregs promoted functional post-ischemic revascularization in obesity and diabetes.
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Affiliation(s)
- Oscar M Leung
- Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jiatao Li
- Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Xisheng Li
- Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Vicken W Chan
- Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kevin Y Yang
- Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Manching Ku
- Next Generation Sequencing Core, Salk Institute for Biological Studies, La Jolla, CA, USA; Department of Paediatrics and Adolescent Medicine, Division of Paediatric Hematology and Oncology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Lu Ji
- Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hao Sun
- Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Herman Waldmann
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Xiao Yu Tian
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China; Institute of Vascular Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yu Huang
- Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China; School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China; Institute of Vascular Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - James Lau
- Department of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Bin Zhou
- The State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Kathy O Lui
- Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China.
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25
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Moufarrej MN, Wong RJ, Shaw GM, Stevenson DK, Quake SR. Investigating Pregnancy and Its Complications Using Circulating Cell-Free RNA in Women's Blood During Gestation. Front Pediatr 2020; 8:605219. [PMID: 33381480 PMCID: PMC7767905 DOI: 10.3389/fped.2020.605219] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/12/2020] [Indexed: 12/11/2022] Open
Abstract
In recent years, there have been major advances in the application of non-invasive techniques to predict pregnancy-related complications, for example by measuring cell-free RNA (cfRNA) in maternal blood. In contrast to cell-free DNA (cfDNA), which is already in clinical use to diagnose fetal aneuploidy, circulating RNA levels can correspond with tissue-specific gene expression and provide a snapshot of prenatal health across gestation. Here, we review the physiologic origins of cfRNA and its novel applications and corresponding challenges to monitor fetal and maternal health and predict pregnancy-related complications.
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Affiliation(s)
- Mira N Moufarrej
- Departments of Bioengineering and Applied Physics, Stanford University, and Chan Zuckerberg Biohub, Stanford, CA, United States
| | - Ronald J Wong
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States
| | - Gary M Shaw
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States
| | - David K Stevenson
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States
| | - Stephen R Quake
- Departments of Bioengineering and Applied Physics, Stanford University, and Chan Zuckerberg Biohub, Stanford, CA, United States
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26
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Xue VW, Cheung MT, Chan PT, Luk LLY, Lee VH, Au TC, Yu AC, Cho WCS, Tsang HFA, Chan AK, Wong SCC. Non-invasive Potential Circulating mRNA Markers for Colorectal Adenoma Using Targeted Sequencing. Sci Rep 2019; 9:12943. [PMID: 31506480 PMCID: PMC6736954 DOI: 10.1038/s41598-019-49445-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 08/22/2019] [Indexed: 12/22/2022] Open
Abstract
We have developed an optimized protocol for plasma targeted mRNA sequencing in our previous study. Here, we performed plasma targeted mRNA sequencing for 40 colorectal adenoma patients and 39 colonoscopy-proven normal controls in order to find potential circulating mRNA markers for colorectal adenoma. Results showed that GSK3A and RHOA were differential expressed genes identified by a cut-off of fold change >2 and adjusted P value < 0.05. More detailed analysis showed that the expression of both GSK3A (0.01-fold with adjusted P < 1 × 10-6) and RHOA (0.35-fold with adjusted P < 0.01) in adenoma patients was significantly lower than those in normal healthy subjects. Based on the enrichment analysis of biological process for potential markers, we found that the regulation of programmed cell death (GO: 0043067; GO: 0043069), regulation of cell death (GO: 0010941; GO: 0060548) and cell differentiation (GO: 0021861) were the main processes involved in adenoma formation. In summary, this study is a cutting-edge research on the detection of plasma mRNA in colorectal adenoma patients and normal healthy subjects.
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Affiliation(s)
- Vivian W Xue
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Moon T Cheung
- Department of Surgery, Queen Elizabeth Hospital, Kowloon, Hong Kong, China
| | - Pak T Chan
- Department of Surgery, Queen Elizabeth Hospital, Kowloon, Hong Kong, China
| | - Lewis L Y Luk
- Department of Surgery, Queen Elizabeth Hospital, Kowloon, Hong Kong, China
| | - Vivian H Lee
- Department of Surgery, Queen Elizabeth Hospital, Kowloon, Hong Kong, China
| | - Thomas C Au
- State Key Laboratory in Oncology in South China, Sir YK Pao Centre for Cancer, Department of Clinical Oncology, Hong Kong Cancer Institute and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong, China
| | - Allen C Yu
- Department of Computer Science, University of Oxford, Oxford, United Kingdom
| | - William C S Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong, China
| | - Hin Fung Andy Tsang
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Amanda K Chan
- Department of Pathology, Queen Elizabeth Hospital, Kowloon, Hong Kong, China
| | - S C Cesar Wong
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Kowloon, Hong Kong, China. .,Department of Pathology, Queen Elizabeth Hospital, Kowloon, Hong Kong, China.
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Jiang P, Chan KCA, Lo YMD. Liver-derived cell-free nucleic acids in plasma: Biology and applications in liquid biopsies. J Hepatol 2019; 71:409-421. [PMID: 31004682 DOI: 10.1016/j.jhep.2019.04.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 04/01/2019] [Accepted: 04/05/2019] [Indexed: 02/09/2023]
Abstract
There is much global research interest surrounding the use of cell-free DNA (cfDNA) for liquid biopsies. cfDNA-based non-invasive prenatal testing for foetal chromosomal aneuploidies was the first successful application of cfDNA technology that transformed clinical practice - it has since been rapidly adopted in dozens of countries and is used by millions of pregnant women every year. Prompted by such developments, efforts to use cfDNA in other fields, especially for cancer detection and monitoring have been actively pursued in recent years. Cancer-associated aberrations including single nucleotide mutations, copy number aberrations, aberrations in methylation and alterations in DNA fragmentation patterns have been detected in the cfDNA of patients suffering from a wide variety of cancers. In addition, the analysis of methylation and fragmentomic patterns has enabled the tissue origin of cfDNA to be determined. In this review, different approaches for detecting circulating liver-derived nucleic acids and cancer-associated aberrations, as well as their potential clinical applications for the detection, monitoring and management of hepatocellular carcinoma, will be discussed.
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Affiliation(s)
- Peiyong Jiang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region; Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong Special Administrative Region; State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong Special Administrative Region
| | - K C Allen Chan
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region; Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong Special Administrative Region; State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong Special Administrative Region
| | - Y M Dennis Lo
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region; Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong Special Administrative Region; State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong Special Administrative Region.
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Heitzer E, Haque IS, Roberts CES, Speicher MR. Current and future perspectives of liquid biopsies in genomics-driven oncology. Nat Rev Genet 2019; 20:71-88. [PMID: 30410101 DOI: 10.1038/s41576-018-0071-5] [Citation(s) in RCA: 782] [Impact Index Per Article: 156.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Precision oncology seeks to leverage molecular information about cancer to improve patient outcomes. Tissue biopsy samples are widely used to characterize tumours but are limited by constraints on sampling frequency and their incomplete representation of the entire tumour bulk. Now, attention is turning to minimally invasive liquid biopsies, which enable analysis of tumour components (including circulating tumour cells and circulating tumour DNA) in bodily fluids such as blood. The potential of liquid biopsies is highlighted by studies that show they can track the evolutionary dynamics and heterogeneity of tumours and can detect very early emergence of therapy resistance, residual disease and recurrence. However, the analytical validity and clinical utility of liquid biopsies must be rigorously demonstrated before this potential can be realized.
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Affiliation(s)
- Ellen Heitzer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria. .,BioTechMed-Graz, Graz, Austria. .,Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Graz, Austria.
| | | | | | - Michael R Speicher
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria.,BioTechMed-Graz, Graz, Austria
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Lima J, Cambridge G, Vilas‐Boas A, Martins C, Borrego L, Leandro M. Serum markers of B-cell activation in pregnancy during late gestation, delivery, and the postpartum period. Am J Reprod Immunol 2019; 81:e13090. [PMID: 30624814 PMCID: PMC6590212 DOI: 10.1111/aji.13090] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 11/30/2018] [Accepted: 01/07/2019] [Indexed: 12/17/2022] Open
Abstract
PROBLEM B cells are vital for the normal evolution of pregnancy due to their humoral and possible regulatory activities. Our group and others have documented that circulating B-cell subsets undergo changes from normal late pregnancy to the postpartum period. However, the underlying mechanisms are poorly understood. Therefore, this study examined the degree of B-cell activation in normal pregnancy by analyzing the levels of serum markers in healthy pregnant women during the third trimester of pregnancy, the day of delivery, and the postpartum period. METHOD OF STUDY A prospective study including pregnant and non-pregnant women attending routine care was undertaken at a hospital clinic. Sociodemographic and clinical data were collected, along with peripheral blood samples. The serum levels of soluble CD23 (sCD23), B-cell-activating factor (BAFF), kappa (κ) and lambda (λ) free light chains (FLC), IgA, IgG, and IgM were quantified. RESULTS Our study included 43 third trimester pregnant and 35 non-pregnant women. In the pregnant women, the median levels of sCD23, BAFF, IgG, and κ FLC were significantly higher during the postpartum period than during the third trimester of pregnancy. Compared to the non-pregnant women, the third trimester pregnant women had higher median BAFF levels and lower sCD23, IgA, IgG, and FLC levels. CONCLUSION Changes in serum markers of B-cell kinetics that occur during pregnancy often persist into the postpartum period and affect the secretion of immunoglobulins from different classes. Further studies are needed to clarify the biological significance of our observations.
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Affiliation(s)
- Jorge Lima
- Department of Obstetrics and GynecologyCUF Descobertas HospitalLisbonPortugal
- Department of Immunology, Chronic Diseases Research Center (CEDOC), Faculty of Medical SciencesNOVA Medical SchoolLisbonPortugal
| | - Geraldine Cambridge
- Centre for Rheumatology and Bloomsbury Rheumatology Unit, Division of MedicineUniversity College LondonLondonUK
| | - Andreia Vilas‐Boas
- Centre for Rheumatology and Bloomsbury Rheumatology Unit, Division of MedicineUniversity College LondonLondonUK
| | - Catarina Martins
- Department of Immunology, Chronic Diseases Research Center (CEDOC), Faculty of Medical SciencesNOVA Medical SchoolLisbonPortugal
| | - Luís‐Miguel Borrego
- Department of Immunology, Chronic Diseases Research Center (CEDOC), Faculty of Medical SciencesNOVA Medical SchoolLisbonPortugal
- Department of ImmunoallergyCUF Descobertas HospitalLisbonPortugal
| | - Maria Leandro
- Centre for Rheumatology and Bloomsbury Rheumatology Unit, Division of MedicineUniversity College LondonLondonUK
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Oudejans CBM. Presymptomatic Noninvasive Assessment of Fetal Well-being by Genome-wide RNA Sequencing. Clin Chem 2018; 65:228-229. [PMID: 30327300 DOI: 10.1373/clinchem.2018.294199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 09/14/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Cees B M Oudejans
- Amsterdam University Medical Centers, VU University Medical Center, Department of Clinical Chemistry, Amsterdam, the Netherlands.
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31
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Zhou F, Liu S, Wang H. Noninvasively diagnosing for fetal trisomy 21 by examining heterozygous single nucleotide polymorphisms in the placental specific genes on chromosome 21. Eur J Obstet Gynecol Reprod Biol 2018; 233:19-25. [PMID: 30544028 DOI: 10.1016/j.ejogrb.2018.09.015] [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: 05/28/2018] [Revised: 09/03/2018] [Accepted: 09/10/2018] [Indexed: 10/28/2022]
Abstract
OBJECTIVE Noninvasive prenatal diagnosing for fetal trisomy 21 could help to avoid unnecessary amniocentesis. It is feasible to target the cell-free placental-specific mRNA in maternal plasma, thus eliminating the interference from the maternal genetic background. STUDY DESIGN In this study, placental-specific genes on chromosome 21 were identified by searching the TiGER database and reviewing the published literature. These cell-free placental-specific mRNA fragments in maternal plasma were amplified and sequenced. Then, the allelic ratio of heterozygous single-nucleotide polymorphisms(SNPs) was analyzed. RESULTS Four placental-specific genes (DNMT3L, KRTAP26-1, PLAC4, DSCR4) were identified. This study included 42 cases of normal pregnancies and 19 cases of trisomy 21 pregnancies. The probability density function showed that the allelic ratio of heterozygous SNPs in normal pregnancy reached a peak at 1.0, and that in the trisomy 21 pregnancy was a double-peaked curve in both 0.5 and 2.0. However, the allelic ratio of heterozygous SNPs demonstrated no statistical difference between the normal and trisomy 21 pregnancies. CONCLUSION Fetal trisomy 21 could not be diagnosed by examining the heterozygous SNPs of cell-free placental-specific mRNA on chromosome 21. This might be because the low quantity and quality of cell-free placental-specific mRNA fragments in maternal plasma, and the limited available heterozygous SNPs on the placental-specific genes.
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Affiliation(s)
- Fan Zhou
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Shanling Liu
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - He Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China.
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Xue VW, Ng SSM, Leung WW, Ma BBY, Cho WCS, Au TCC, Yu ACS, Tsang HFA, Wong SCC. The Effect of Centrifugal Force in Quantification of Colorectal Cancer-Related mRNA in Plasma Using Targeted Sequencing. Front Genet 2018; 9:165. [PMID: 29868115 PMCID: PMC5963087 DOI: 10.3389/fgene.2018.00165] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 04/26/2018] [Indexed: 12/24/2022] Open
Abstract
In our previous study, we detected the effects of centrifugal forces on plasma RNA quantification by quantitative reverse transcription PCR. The aims of this study were to perform targeted mRNA sequencing and data analysis in healthy donors' plasma prepared by two centrifugation protocols and to investigate the effects of centrifugal forces on plasma mRNA quality and quantity. Targeted mRNA sequencing was performed using a custom panel with 108 colorectal cancer-related genes in 18 healthy donors' plasma that prepared by (1) 3,500 g for 10 min at 4°C and (2) 1,600 g for 10 min at 4°C followed by 16,000 g for 10 min at 4°C. Results showed that plasma ribosomal RNA was detected in 16/18 (88.9%) 3,500 g and 6/18 (33.3%) 1,600 g followed by 16,000 g centrifuged plasma. For targeted sequencing, 75/108 (69.4%) and 86/108 (79.6%) genes were detected in 3,500 and 1,600 g followed by 16,000 g, respectively, while 16/108 (14.8%) genes were not detected in both centrifugations. Detailed analysis showed that 2 of 108 (1.85%) genes showed lower expressions in 3,500 g than in 1,600 g followed by 16,000 g. The median expressions of genes in 3,500 g were positively correlated with the expressions in 1,600 g followed by 16,000 g (R2 = 0.9471, P < 0.0001, Spearman rank correlation). Meanwhile, plasma samples were not distinctively clustered based on centrifugal forces according to hierarchical clustering. Targeted mRNA sequencing and subsequent data analysis were performed in this study to investigate the effects of two different centrifugal forces that are commonly used in plasma collection. Our targeted sequencing results help to understand the centrifugal force effects on plasma mRNA, and these findings show that the centrifugation protocol for plasma mRNA research using targeted sequencing can be standardized which facilitates multicenter studies for comparison and quality assurance in the future.
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Affiliation(s)
- Vivian Weiwen Xue
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Simon Siu Man Ng
- Department of Surgery, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Wing Wa Leung
- Department of Surgery, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Brigette Buig Yue Ma
- State Key Laboratory in Oncology in South China, Sir YK Pao Centre for Cancer, Department of Clinical Oncology, Hong Kong Cancer Institute and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | | | - Thomas Chi Chuen Au
- State Key Laboratory in Oncology in South China, Sir YK Pao Centre for Cancer, Department of Clinical Oncology, Hong Kong Cancer Institute and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Allen Chi Shing Yu
- Department of Computer Science, University of Oxford, Oxford, United Kingdom
| | - Hin Fung Andy Tsang
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Sze Chuen Cesar Wong
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Kowloon, Hong Kong
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Chen L, Guan J, Wei Q, Yuan Z, Zhang M. Potential role of "omics" technique in prenatal diagnosis of congenital heart defects. Clin Chim Acta 2018; 482:185-190. [PMID: 29649453 DOI: 10.1016/j.cca.2018.04.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/04/2018] [Accepted: 04/06/2018] [Indexed: 02/08/2023]
Abstract
Congenital heart defect (CHD) is one of the most common birth defects and is the leading cause of neonatal death. Currently, there are no biomarkers available for prenatal diagnosis of CHD. Clinical strategies to diagnose CHD mostly depend on fetal echocardiography. Recent advances in "omics" techniques have opened up new possibilities for biomarker discoveries. In this review, we discuss recent advances in prenatal detection of CHD using biomarkers obtained by "omics" approaches, including genomics, proteomics, metabolomics, and others. There is great potential in obtaining various kinds of parameters using "omics" studies to facilitate early and accurate diagnosis of CHD.
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Affiliation(s)
- Lizhu Chen
- Department of Ultrasound, Shengjing Hospital, China Medical University, Shenyang 110004, China; Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang 110004, China
| | - Johnny Guan
- Department of Urology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Qiuju Wei
- Department of Obstetrics and Gynecology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Zhengwei Yuan
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang 110004, China.
| | - Mo Zhang
- Department of Urology, Shengjing Hospital, China Medical University, Shenyang 110004, China..
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Abstract
Fetal growth restriction (FGR) continues to be a leading cause of preventable stillbirth and poor neurodevelopmental outcomes in offspring, and furthermore is strongly associated with the obstetrical complications of iatrogenic preterm birth and pre-eclampsia. The terms small for gestational age (SGA) and FGR have, for too long, been considered equivalent and therefore used interchangeably. However, the delivery of improved clinical outcomes requires that clinicians effectively distinguish fetuses that are pathologically growth-restricted from those that are constitutively small. A greater understanding of the multifactorial pathogenesis of both early- and late-onset FGR, especially the role of underlying placental pathologies, may offer insight into targeted treatment strategies that preserve placental function. The new maternal blood biomarker placenta growth factor offers much potential in this context. This review highlights new approaches to effective screening for FGR based on a comprehensive review of: etiology, diagnosis, antenatal surveillance and management. Recent advances in novel imaging methods provide the basis for stepwise multi-parametric testing that may deliver cost-effective screening within existing antenatal care systems.
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Wang X, Chen Y, Du L, Li X, Li X, Chen D. Evaluation of circulating placenta-related long noncoding RNAs as potential biomarkers for preeclampsia. Exp Ther Med 2018; 15:4309-4317. [PMID: 29725373 PMCID: PMC5920431 DOI: 10.3892/etm.2018.5968] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 10/23/2017] [Indexed: 12/12/2022] Open
Abstract
Increasing evidence has indicated that circulating placental RNAs may reflect the pathophysiology of the placenta. In the current study, circulating placenta-related long noncoding RNAs (lncRNAs) were evaluated as potential biomarkers for preeclampsia (PE). Two parts of the case-control study were simultaneously executed, including the following sets: 52 patients with late-onset PE (LOPE) (diagnosed after 34 weeks) and 52 gestational age (GA)-matched controls; 58 patients with early-onset PE (EOPE) (diagnosed before 34 weeks) and 58 GA-matched controls. LncRNA expression was detected in the placenta analysis part, and the participants were delivered by caesarean sections. The levels of circulating placenta-associated lncRNAs were measured in the plasma analysis part and all pregnant women were included. Using microarray analysis, 163 differentially expressed lncRNAs were identified in placental samples from patients with LOPE, some of which were also detected in plasma samples from pregnant women. There were significant positive correlations between plasma, and placental expression levels of NONHSAT116812 and NONHSAT145880, which in plasma provided high diagnostic efficiencies for LOPE and EOPE. The present study demonstrated that circulating placenta-associated lncRNAs, paticularly NONHSAT116812 and NONHSAT145880 have potential as biomarkers for PE.
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Affiliation(s)
- Xin Wang
- Department of Obstetrics and Gynecology, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510150, P.R. China.,Department of Obstetrics and Gynecology, Affiliated Hangzhou Hospital (Hangzhou First People's Hospital), Nanjing Medical University, Hangzhou, Zhejiang 310006, P.R. China
| | - Yanhong Chen
- Department of Obstetrics and Gynecology, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510150, P.R. China
| | - Lili Du
- Department of Obstetrics and Gynecology, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510150, P.R. China
| | - Xiaomei Li
- Department of Obstetrics and Gynecology, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510150, P.R. China
| | - Xiuying Li
- Department of Obstetrics and Gynecology, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510150, P.R. China
| | - Dunjin Chen
- Department of Obstetrics and Gynecology, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510150, P.R. China
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Stewart CM, Kothari PD, Mouliere F, Mair R, Somnay S, Benayed R, Zehir A, Weigelt B, Dawson SJ, Arcila ME, Berger MF, Tsui DW. The value of cell-free DNA for molecular pathology. J Pathol 2018; 244:616-627. [PMID: 29380875 DOI: 10.1002/path.5048] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/23/2018] [Accepted: 01/25/2018] [Indexed: 02/06/2023]
Abstract
Over the past decade, advances in molecular biology and genomics techniques have revolutionized the diagnosis and treatment of cancer. The technological advances in tissue profiling have also been applied to the study of cell-free nucleic acids, an area of increasing interest for molecular pathology. Cell-free nucleic acids are released from tumour cells into the surrounding body fluids and can be assayed non-invasively. The repertoire of genomic alterations in circulating tumour DNA (ctDNA) is reflective of both primary tumours and distant metastatic sites, and ctDNA can be sampled multiple times, thereby overcoming the limitations of the analysis of single biopsies. Furthermore, ctDNA can be sampled regularly to monitor response to treatment, to define the evolution of the tumour genome, and to assess the acquisition of resistance and minimal residual disease. Recently, clinical ctDNA assays have been approved for guidance of therapy, which is an exciting first step in translating cell-free nucleic acid research tests into clinical use for oncology. In this review, we discuss the advantages of cell-free nucleic acids as analytes in different body fluids, including blood plasma, urine, and cerebrospinal fluid, and their clinical applications in solid tumours and haematological malignancies. We will also discuss practical considerations for clinical deployment, such as preanalytical factors and regulatory requirements. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Caitlin M Stewart
- Marie-José and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Prachi D Kothari
- Marie-José and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Pediatric Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Florent Mouliere
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.,Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Richard Mair
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.,Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Cambridge, UK.,Division of Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, UK
| | - Saira Somnay
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sarah-Jane Dawson
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia.,Centre for Cancer Research, University of Melbourne, Victoria, Australia
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael F Berger
- Marie-José and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dana Wy Tsui
- Marie-José and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Huang J, Jin N, Qin H, Shi X, Liu Y, Cheung W, Wang CC, Chan TF, Li TC. Transcriptomic profiles in peripheral blood between women with unexplained recurrent implantation failure and recurrent miscarriage and the correlation with endometrium: A pilot study. PLoS One 2017; 12:e0189159. [PMID: 29216287 PMCID: PMC5720758 DOI: 10.1371/journal.pone.0189159] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/20/2017] [Indexed: 11/30/2022] Open
Abstract
Aim To study the transcriptome profiles in the blood of recurrent implantation failure (RIF), recurrent miscarriage (RM) and fertile women during the window of implantation, and further analysis the correlation of transcriptome profiles between blood and endometrium. Methods This is an observational prospective study. In total 9 subjects were recruited, 3 RIF, 3 RM, and 3 controls. Paired samples (endometrium and peripheral blood) from the same subjects were precisely timed on the 7th days after luteal hormone surge (LH+7). RNA sequencing was applied to investigate the transcriptome profiles. Results The results of transcriptome in peripheral blood cannot be used to characterize women with RIF and unexplained RM. There was a medium level correlation between transcriptome in peripheral blood and endometrium during the window of implantation. Conclusion The differential transcriptome patterns in blood are not representative of those in endometrium, and the blood transcriptome cannot differentiate among the women with RIF, RM or fertile.
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Affiliation(s)
- Jin Huang
- Department of Obstetrics and Gynaecology, the Chinese University of Hong Kong, Hong Kong SAR, China
| | - Nana Jin
- School of Life Sciences, the Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hao Qin
- School of Life Sciences, the Chinese University of Hong Kong, Hong Kong SAR, China
| | - Xiao Shi
- Department of Obstetrics and Gynaecology, the Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yingyu Liu
- Department of Obstetrics and Gynaecology, the Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wingching Cheung
- Department of Obstetrics and Gynaecology, the Chinese University of Hong Kong, Hong Kong SAR, China
| | - Chi Chiu Wang
- Department of Obstetrics and Gynaecology, the Chinese University of Hong Kong, Hong Kong SAR, China
- School of Biomedical Sciences, the Chinese University of Hong Kong, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, the Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ting Fung Chan
- School of Life Sciences, the Chinese University of Hong Kong, Hong Kong SAR, China
| | - Tin Chiu Li
- Department of Obstetrics and Gynaecology, the Chinese University of Hong Kong, Hong Kong SAR, China
- * E-mail:
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Integrative single-cell and cell-free plasma RNA transcriptomics elucidates placental cellular dynamics. Proc Natl Acad Sci U S A 2017; 114:E7786-E7795. [PMID: 28830992 DOI: 10.1073/pnas.1710470114] [Citation(s) in RCA: 192] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The human placenta is a dynamic and heterogeneous organ critical in the establishment of the fetomaternal interface and the maintenance of gestational well-being. It is also the major source of cell-free fetal nucleic acids in the maternal circulation. Placental dysfunction contributes to significant complications, such as preeclampsia, a potentially lethal hypertensive disorder during pregnancy. Previous studies have identified significant changes in the expression profiles of preeclamptic placentas using whole-tissue analysis. Moreover, studies have shown increased levels of targeted RNA transcripts, overall and placental contributions in maternal cell-free nucleic acids during pregnancy progression and gestational complications, but it remains infeasible to noninvasively delineate placental cellular dynamics and dysfunction at the cellular level using maternal cell-free nucleic acid analysis. In this study, we addressed this issue by first dissecting the cellular heterogeneity of the human placenta and defined individual cell-type-specific gene signatures by analyzing more than 24,000 nonmarker selected cells from full-term and early preeclamptic placentas using large-scale microfluidic single-cell transcriptomic technology. Our dataset identified diverse cellular subtypes in the human placenta and enabled reconstruction of the trophoblast differentiation trajectory. Through integrative analysis with maternal plasma cell-free RNA, we resolved the longitudinal cellular dynamics of hematopoietic and placental cells in pregnancy progression. Furthermore, we were able to noninvasively uncover the cellular dysfunction of extravillous trophoblasts in early preeclamptic placentas. Our work showed the potential of integrating transcriptomic information derived from single cells into the interpretation of cell-free plasma RNA, enabling the noninvasive elucidation of cellular dynamics in complex pathological conditions.
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Manokhina I, Del Gobbo GF, Konwar C, Wilson SL, Robinson WP. Review: placental biomarkers for assessing fetal health. Hum Mol Genet 2017; 26:R237-R245. [DOI: 10.1093/hmg/ddx210] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 06/01/2017] [Indexed: 12/26/2022] Open
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40
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Vermeesch JR, Voet T, Devriendt K. Prenatal and pre-implantation genetic diagnosis. Nat Rev Genet 2017; 17:643-56. [PMID: 27629932 DOI: 10.1038/nrg.2016.97] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The past decade has seen the development of technologies that have revolutionized prenatal genetic testing; that is, genetic testing from conception until birth. Genome-wide single-cell arrays and high-throughput sequencing analyses are dramatically increasing our ability to detect embryonic and fetal genetic lesions, and have substantially improved embryo selection for in vitro fertilization (IVF). Moreover, both invasive and non-invasive mutation scanning of the genome are helping to identify the genetic causes of prenatal developmental disorders. These advances are changing clinical practice and pose novel challenges for genetic counselling and prenatal care.
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Affiliation(s)
- Joris Robert Vermeesch
- Centre for Human Genetics, Department of Human Genetics, University of Leuven, 49 Herestraat, Leuven 3000, Belgium
| | - Thierry Voet
- Centre for Human Genetics, Department of Human Genetics, University of Leuven, 49 Herestraat, Leuven 3000, Belgium
| | - Koenraad Devriendt
- Centre for Human Genetics, Department of Human Genetics, University of Leuven, 49 Herestraat, Leuven 3000, Belgium
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41
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Abstract
Characterizing and monitoring tumor genomes with blood samples could achieve significant improvements in precision medicine. As tumors shed parts of themselves into the circulation, analyses of circulating tumor cells, circulating tumor DNA, and tumor-derived exosomes, often referred to as "liquid biopsies", may enable tumor genome characterization by minimally invasive means. Indeed, multiple studies have described how molecular information about parent tumors can be extracted from these components. Here, we briefly summarize current technologies and then elaborate on emerging novel concepts that may further propel the field. We address normal and detectable mutation levels in the context of our current knowledge regarding the gradual accumulation of mutations during aging and in light of technological limitations. Finally, we discuss whether liquid biopsies are ready to be used in routine clinical practice.
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Affiliation(s)
- Samantha Perakis
- Institute of Human Genetics, Medical University of Graz, Harrachgasse 21/8, A-8010, Graz, Austria
| | - Michael R Speicher
- Institute of Human Genetics, Medical University of Graz, Harrachgasse 21/8, A-8010, Graz, Austria. .,BioTechMed, Graz, Austria.
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Placental Up-Regulation of Leptin and ARMS2 is Associated with Growth Discordance in Monochorionic Diamniotic Twin Pregnancies. Twin Res Hum Genet 2017; 20:169-179. [DOI: 10.1017/thg.2017.11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Fetal growth discordance is a relatively common complication of monochorionic diamniotic (MCDA) twin pregnancies and is caused by a combination of maternal and placental factors. The aim of the study was to survey placental gene expression patterns and identify genes associated with growth discordance. Clinical samples comprised eight growth-discordant MCDA twin placentas (31+3–34+4 weeks gestational age) and six growth-concordant twin placentas (31+2–37 weeks gestational age). Gene expression libraries were constructed from placental biopsy samples and analyzed by RNA-sequencing. The distribution and relative abundance of mRNA transcripts expressed in the smaller and larger placentas from growth-discordant and concordant MCDA twins was remarkably similar. However, leptin (LEP) and age-related maculopathy susceptibility 2 (ARMS2) mRNA levels were exclusively up-regulated in all of the eight smaller growth-discordant twin placentas. Quantitative real-time PCR of independent biopsy samples confirmed the levels of differential mRNA expression for both genes. Immunohistochemical analysis of tissue sections from matching twin placentas showed increased leptin expression in 5–10% of blood vessel cells of the smaller placenta and marginally higher levels of ARMS2 expression in the microvillous membrane of the smaller placenta. Based on these findings, we speculate that up-regulation of leptin and ARMS2 forms part of an important survival mechanism to compensate for placental growth discordance. Since, leptin and ARMS2 are both expressed as soluble proteins, they may have clinical potential as measurable biomarkers for predicting the onset of growth discordance in MCDA twin pregnancies.
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44
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Measuring circulating placental RNAs to non-invasively assess the placental transcriptome and to predict pregnancy complications. Prenat Diagn 2016; 36:997-1008. [DOI: 10.1002/pd.4934] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 09/08/2016] [Accepted: 09/30/2016] [Indexed: 11/07/2022]
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46
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Byron SA, Van Keuren-Jensen KR, Engelthaler DM, Carpten JD, Craig DW. Translating RNA sequencing into clinical diagnostics: opportunities and challenges. Nat Rev Genet 2016; 17:257-71. [PMID: 26996076 PMCID: PMC7097555 DOI: 10.1038/nrg.2016.10] [Citation(s) in RCA: 439] [Impact Index Per Article: 54.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RNA-based measurements have the potential for application across diverse areas of human health, including disease diagnosis, prognosis and therapeutic selection. Current clinical applications include infectious diseases, cancer, transplant medicine and fetal monitoring. RNA sequencing (RNA-seq) allows for the detection of a wide variety of RNA species, including mRNA, non-coding RNA, pathogen RNA, chimeric gene fusions, transcript isoforms and splice variants, and provides the capability to quantify known, pre-defined RNA species and rare RNA transcript variants within a sample. In addition to differential expression and detection of novel transcripts, RNA-seq also supports the detection of mutations and germline variation for hundreds to thousands of expressed genetic variants, facilitating assessment of allele-specific expression of these variants. Circulating RNAs and small regulatory RNAs, such as microRNAs, are very stable. These RNA species are vigorously being tested for their potential as biomarkers. However, there are currently few agreed upon methods for isolation or quantitative measurements and a current lack of quality controls that can be used to test platform accuracy and sample preparation quality. Analytical, bioinformatic and regulatory challenges exist, and ongoing efforts toward the establishment of benchmark standards, assay optimization for clinical conditions and demonstration of assay reproducibility are required to expand the clinical utility of RNA-seq.
RNA sequencing (RNA-seq) is a powerful approach for comprehensive analyses of transcriptomes. This Review describes the widespread potential applications of RNA-seq in clinical medicine, such as detecting disease-associated mutations and gene expression disruptions, as well as characteristic non-coding RNAs, circulating extracellular RNAs or pathogen RNAs. The authors also highlight the challenges in adopting RNA-seq routinely into clinical practice. With the emergence of RNA sequencing (RNA-seq) technologies, RNA-based biomolecules hold expanded promise for their diagnostic, prognostic and therapeutic applicability in various diseases, including cancers and infectious diseases. Detection of gene fusions and differential expression of known disease-causing transcripts by RNA-seq represent some of the most immediate opportunities. However, it is the diversity of RNA species detected through RNA-seq that holds new promise for the multi-faceted clinical applicability of RNA-based measures, including the potential of extracellular RNAs as non-invasive diagnostic indicators of disease. Ongoing efforts towards the establishment of benchmark standards, assay optimization for clinical conditions and demonstration of assay reproducibility are required to expand the clinical utility of RNA-seq.
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Affiliation(s)
- Sara A Byron
- Center for Translational Innovation, Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | | | - David M Engelthaler
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, Arizona 86001, USA
| | - John D Carpten
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - David W Craig
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
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47
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Abstract
Cell-free fetal DNA screening for Down syndrome has gained rapid acceptance over the past few years with increasing market penetration. Three main laboratory methodologies are currently used: a massive parallel shotgun sequencing (MPSS), a targeted massive parallel sequencing (t-MPS) and a single nucleotide polymorphism (SNP) based approach. Although each of these technologies has its own advantages and disadvantages, the performance of all was shown to be comparable and superior to that of traditional first-trimester screening for the detection of trisomy 21 in a routine prenatal population. Differences in performance were predominantly shown for chromosomal anomalies other than trisomy 21. Understanding the limitations and benefits of each technology is essential for proper counseling to patients. These technologies, as well as few investigational technologies described in this review, carry a great potential beyond screening for the common aneuploidies.
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Affiliation(s)
- Pe'er Dar
- Department of Obstetrics & Gynecology and Women's Health, Montefiore Medical Center, Albert Einstein College of Medicine, 1695 Eastchester Road, Bronx, New York 10461, USA
| | - Hagit Shani
- Department of Obstetrics & Gynecology and Women's Health, Montefiore Medical Center, Albert Einstein College of Medicine, 1695 Eastchester Road, Bronx, New York 10461, USA
| | - Mark I Evans
- Department of Obstetrics and Gynecology, Mt. Sinai School of Medicine, New York, NY, USA; Comprehensive Genetics and Fetal Medicine Foundation of America, 131 East 65th Street, New York, NY 10065, USA.
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48
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Wang WT, Sun YM, Huang W, He B, Zhao YN, Chen YQ. Genome-wide Long Non-coding RNA Analysis Identified Circulating LncRNAs as Novel Non-invasive Diagnostic Biomarkers for Gynecological Disease. Sci Rep 2016; 6:23343. [PMID: 26987697 PMCID: PMC4796908 DOI: 10.1038/srep23343] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 03/02/2016] [Indexed: 12/11/2022] Open
Abstract
Increasing evidence indicates that long non-coding RNAs (lncRNAs) play important roles in human diseases. This study aimed to investigate the tissue and serum lncRNAs that are differentially expressed between patients with endometriosis, a gynecological disease, to evaluate the potential of these lncRNAs as non-invasive markers for the disease. The differentially expressed lncRNAs as competing endogenous RNAs (ceRNAs) were also analyzed to predict their functions in disease development. Genome-wide profiling of lncRNA expression patterns revealed that many lncRNAs were abnormally expressed between sera and tissuesof the patient samples. A set of aberrant differentially expressed lncRNAs were further validated in a validation cohort of 110 serum and 24 tissue samples. Functional analysis predicted that differentially expressed lncRNAs may participate in disease development through crosstalk between the ceRNAs of miRNAs and may be involved in a range of cellular pathways including steroid or hormone responses. We also found a unique set of lncRNAs that were associated with disease severity and progression, and their diagnostic values were also investigated. Our study demonstrated that lncRNAs could potentially serve as non-invasive biomarkers for the diagnosis of endometriosis and as important regulators in the progression of this disease.
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Affiliation(s)
- Wen-Tao Wang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou 510275, China
| | - Yu-Meng Sun
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou 510275, China
| | - Wei Huang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou 510275, China
| | - Bo He
- Dept of Obst &Gyn, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Ya-Nan Zhao
- Dept of Obst &Gyn, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Yue-Qin Chen
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou 510275, China
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49
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Affiliation(s)
- Felix C.K. Wong
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, and
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China; ,
| | - Y.M. Dennis Lo
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, and
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China; ,
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50
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Abstract
Cell-free DNA (cfDNA) testing has recently become indispensable in diagnostic testing and screening. In the prenatal setting, this type of testing is often called noninvasive prenatal testing (NIPT). With a number of techniques, using either next-generation sequencing or single nucleotide polymorphism-based approaches, fetal cfDNA in maternal plasma can be analyzed to screen for rhesus D genotype, common chromosomal aneuploidies, and increasingly for testing other conditions, including monogenic disorders. With regard to screening for common aneuploidies, challenges arise when implementing NIPT in current prenatal settings. Depending on the method used (targeted or nontargeted), chromosomal anomalies other than trisomy 21, 18, or 13 can be detected, either of fetal or maternal origin, also referred to as unsolicited or incidental findings. For various biological reasons, there is a small chance of having either a false-positive or false-negative NIPT result, or no result, also referred to as a "no-call." Both pre- and posttest counseling for NIPT should include discussing potential discrepancies. Since NIPT remains a screening test, a positive NIPT result should be confirmed by invasive diagnostic testing (either by chorionic villus biopsy or by amniocentesis). As the scope of NIPT is widening, professional guidelines need to discuss the ethics of what to offer and how to offer. In this review, we discuss the current biochemical, clinical, and ethical challenges of cfDNA testing in the prenatal setting and its future perspectives including novel applications that target RNA instead of DNA.
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