Placental transcriptome co-expression analysis reveals conserved regulatory programs across gestation

Buckberry, Sam; Bianco‐Miotto, Tina; Bent, Stephen J.; Clifton, Vicki L.; Shoubridge, Cheryl; Shankar, Kartik; Roberts, Claire T.

doi:10.1186/s12864-016-3384-9

Cited by 34 publications

(43 citation statements)

References 53 publications

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“…Additionally, I would like to recognize the effort made by K. W. Witwer on examination of the methodology and critical reviewing a recent publication by Liu and colleagues in 2017 1 . Here Liu et al report plant cross kingdom RNAi in two human sRNA plasma sequencing studies.…”

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confidence: 99%

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Alternative miRNAs? Human sequences misidentified as plant miRNAs in plant studies and in human plasma

Witwer

2018

F1000Res

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Background: A 2017 study reported that “Plant miRNAs found in human circulating system provide evidences of cross kingdom RNAi”. Analysis of two human blood plasma sequencing datasets was said to provide evidence for uptake of plant miRNAs into human plasma. The results were also purportedly inconsistent with contamination. Methods: Sequences from public datasets and miRNA databases were compared with results downloaded from the website of the reporting journal. Results: Only one putative plant miRNA (“peu-MIR2910) mapped consistently above background, and this sequence is found with 100% identity in a human rRNA. Several other rarer but consistently mapped putative plant miRNAs also have 100% or near 100% matches to human transcripts or genomic sequences, and some do not appear to map to plant genomes at all. Conclusions: Reanalysis of public data suggests that dietary plant xenomiR uptake is not supported, but instead confirms previous findings that detection of rare plant miRNAs in mammalian sequencing datasets is artifactual. Some putative plant miRNAs, including MIR2910 and MIR2911, may represent human sequence contamination or other artifacts in plant studies, emphasizing the need for rigorous controls and data filtering strategies when assessing possible xenomiRNAs.

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confidence: 99%

“…Here, Witwer has a closer look at the article ‘Plant miRNAs found in human circulating system provide evidence of cross kingdom RNAi’ by Liu et al 2017 3 . Liu et al 2017 claim that the plant miRNAs are not contamination, but only checked whether they contain sequencing adapters.…”

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confidence: 99%

Alternative miRNAs? Human sequences misidentified as plant miRNAs in plant studies and in human plasma

Witwer

2018

F1000Res

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“…However, to put the problem in context, there are over 2000 described β-lactamase gene sequences responsible for multiresistance to β-lactam antibiotics such as penicillins, cephalosporins, and carbapenems [23] . Whilst β-lactam resistance in some pathogens, including S. pneumoniae , can be predicted through, for example, penicillin-binding protein (PBP) typing and machine-learning-based approaches [24] , the general problem of reliably assigning resistance phenotype based on many described gene sequences is commonplace.…”

Section: Predicting Phenotypes From Wgsmentioning

confidence: 99%

“…Additionally, with some notable exceptions, such as the pneumococci [24] , most AMR profile predictions from WGS data are qualitative, simply predicting whether an isolate is expected to be resistant or susceptible against a compound despite AMR generally being a continuous and often complex trait. The level of resistance of a strain to a drug can be affected by multiple epistatic AMR elements or mutations [25] , the copy number variation of these elements [26] , the function of the genetic background of the strain 27 , 28 , 29 , and modulating effects by the environment [30] .…”

Section: Predicting Phenotypes From Wgsmentioning

confidence: 99%

From Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic

Balloux

Brynildsrud

Dorp

et al. 2018

Trends in Microbiology

133

102

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Hospitals worldwide are facing an increasing incidence of hard-to-treat infections. Limiting infections and providing patients with optimal drug regimens require timely strain identification as well as virulence and drug-resistance profiling. Additionally, prophylactic interventions based on the identification of environmental sources of recurrent infections (e.g., contaminated sinks) and reconstruction of transmission chains (i.e., who infected whom) could help to reduce the incidence of nosocomial infections. WGS could hold the key to solving these issues. However, uptake in the clinic has been slow. Some major scientific and logistical challenges need to be solved before WGS fulfils its potential in clinical microbial diagnostics. In this review we identify major bottlenecks that need to be resolved for WGS to routinely inform clinical intervention and discuss possible solutions.

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“…As the review is focussed on human placental studies, animal studies will not be referred to. Studies in other mammals ( Barreto et al , 2011 ; Buckberry et al , 2017 ; Carter, 2018 ) have undoubtedly provided additional valuable perspectives on placental health and disease and have added to knowledge on comparative placentation across species.…”

Section: Introductionmentioning

confidence: 99%

Current approaches and developments in transcript profiling of the human placenta

Yong

Chan

2020

Human Reproduction Update

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BACKGROUND The placenta is the active interface between mother and foetus, bearing the molecular marks of rapid development and exposures in utero. The placenta is routinely discarded at delivery, providing a valuable resource to explore maternal-offspring health and disease in pregnancy. Genome-wide profiling of the human placental transcriptome provides an unbiased approach to study normal maternal–placental–foetal physiology and pathologies. OBJECTIVE AND RATIONALE To date, many studies have examined the human placental transcriptome, but often within a narrow focus. This review aims to provide a comprehensive overview of human placental transcriptome studies, encompassing those from the cellular to tissue levels and contextualize current findings from a broader perspective. We have consolidated studies into overarching themes, summarized key research findings and addressed important considerations in study design, as a means to promote wider data sharing and support larger meta-analysis of already available data and greater collaboration between researchers in order to fully capitalize on the potential of transcript profiling in future studies. SEARCH METHODS The PubMed database, National Center for Biotechnology Information and European Bioinformatics Institute dataset repositories were searched, to identify all relevant human studies using ‘placenta’, ‘decidua’, ‘trophoblast’, ‘transcriptome’, ‘microarray’ and ‘RNA sequencing’ as search terms until May 2019. Additional studies were found from bibliographies of identified studies. OUTCOMES The 179 identified studies were classifiable into four broad themes: healthy placental development, pregnancy complications, exposures during pregnancy and in vitro placental cultures. The median sample size was 13 (interquartile range 8–29). Transcriptome studies prior to 2015 were predominantly performed using microarrays, while RNA sequencing became the preferred choice in more recent studies. Development of fluidics technology, combined with RNA sequencing, has enabled transcript profiles to be generated of single cells throughout pregnancy, in contrast to previous studies relying on isolated cells. There are several key study aspects, such as sample selection criteria, sample processing and data analysis methods that may represent pitfalls and limitations, which need to be carefully considered as they influence interpretation of findings and conclusions. Furthermore, several areas of growing importance, such as maternal mental health and maternal obesity are understudied and the profiling of placentas from these conditions should be prioritized. WIDER IMPLICATIONS Integrative analysis of placental transcriptomics with other ‘omics’ (methylome, proteome and metabolome) and linkage with future outcomes from longitudinal studies is crucial in enhancing knowledge of healthy placental development and function, and in enabling the underlying causal mechanisms of pregnancy complications to be identified. Such understanding could help in predicting risk of future adversity and in designing interventions that can improve the health outcomes of both mothers and their offspring. Wider collaboration and sharing of placental transcriptome data, overcoming the challenges in obtaining sufficient numbers of quality samples with well-defined clinical characteristics, and dedication of resources to understudied areas of pregnancy will undoubtedly help drive the field forward.

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Placental transcriptome co-expression analysis reveals conserved regulatory programs across gestation

Cited by 34 publications

References 53 publications

Alternative miRNAs? Human sequences misidentified as plant miRNAs in plant studies and in human plasma

Alternative miRNAs? Human sequences misidentified as plant miRNAs in plant studies and in human plasma

From Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic

Current approaches and developments in transcript profiling of the human placenta

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