Forensic transcriptome analysis using massively parallel sequencing

Haas, Cordula; Neubauer, Jacqueline; Salzmann, Andrea Patrizia; Hanson, Erin; Ballantyne, Jack

doi:10.1016/j.fsigen.2021.102486

Cited by 37 publications

(20 citation statements)

References 167 publications

(161 reference statements)

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“…This field of study can be explored in forensic sciences (e.g. determination of the cause of death; estimation of post-mortem interval; identification of body fluids) 13 and in medical sciences (e.g. quality control for organ transplantation) 2 , 18 .…”

Section: Discussionmentioning

confidence: 99%

“…Hence, there is consensus that the environment can influence mRNA transcription dynamics, mostly through epigenetic regulators 10 , 11 . The degradation rate of mRNAs is influenced by intrinsic factors, such as gender, age and health conditions during the antemortem period; and also external factors, such as temperature, humidity, sunlight exposure and microbiota interaction in the post-mortem period 12 , 13 . Therefore, it is reasonable to think that mRNA degradation and gene expression could be altered depending on the circumstances in which the cadaver was deposited.…”

Section: Introductionmentioning

confidence: 99%

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Insights into how environment shapes post-mortem RNA transcription in mouse brain

Bonadio

Nunes

Moretti

et al. 2021

Sci Rep

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Most biological features that occur on the body after death were already deciphered by traditional medicine. However, the molecular mechanisms triggered in the cellular microenvironment are not fully comprehended yet. Previous studies reported gene expression alterations in the post-mortem condition, but little is known about how the environment could influence RNA degradation and transcriptional regulation. In this work, we analysed the transcriptome of mouse brain after death under three concealment simulations (air exposed, buried, and submerged). Our analyses identified 2,103 genes differentially expressed in all tested groups 48 h after death. Moreover, we identified 111 commonly upregulated and 497 commonly downregulated genes in mice from the concealment simulations. The gene functions shared by the individuals from the tested environments were associated with RNA homeostasis, inflammation, developmental processes, cell communication, cell proliferation, and lipid metabolism. Regarding the altered biological processes, we identified that the macroautophagy process was enriched in the upregulated genes and lipid metabolism was enriched in the downregulated genes. On the other hand, we also described a list of biomarkers associated with the submerged and buried groups, indicating that these environments can influence the post-mortem RNA abundance in its particular way.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Insights into how environment shapes post-mortem RNA transcription in mouse brain

Bonadio

Nunes

Moretti

et al. 2021

Sci Rep

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“…Real time PCR (qPCR) has also been used [116,117] but is somewhat limited by the number of markers that can be multiplexed together (restricted by the availability of fluorescent dyes) and the difficulty in identifying appropriate housekeeping genes, applicable to all included body fluids of interest. More recently, massively parallel sequencing (MPS) has been used to detect multiplexed markers [118][119][120] reflecting a shift towards this technology in forensic science [121]. The main advantages of MPS is the high multiplexing capacity, that amplicons can have overlapping (small) sizes and that nucleotide variation is detected.…”

Section: Messenger Rnamentioning

confidence: 99%

“…Environmental and physiological factors may cause variation between people and over time (an infection will increase the number of white blood cells and the mRNAs these cells contain). Thus, it appears inevitable that the sensitivity of markers targeting either the same or different body fluids will vary [121] despite careful marker selection and assay optimization. An extreme example is semen from an azoospermic male, which will provide RNA and proteins for seminal fluid but little DNA (or spermatozoa mRNAs/ proteins).…”

Section: Sensitivity Specificity and Degradation Issues Affecting Interpretationmentioning

confidence: 99%

On the Identification of Body Fluids and Tissues: A Crucial Link in the Investigation and Solution of Crime

Sijen

Harbison

2021

Genes

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Body fluid and body tissue identification are important in forensic science as they can provide key evidence in a criminal investigation and may assist the court in reaching conclusions. Establishing a link between identifying the fluid or tissue and the DNA profile adds further weight to this evidence. Many forensic laboratories retain techniques for the identification of biological fluids that have been widely used for some time. More recently, many different biomarkers and technologies have been proposed for identification of body fluids and tissues of forensic relevance some of which are now used in forensic casework. Here, we summarize the role of body fluid/ tissue identification in the evaluation of forensic evidence, describe how such evidence is detected at the crime scene and in the laboratory, elaborate different technologies available to do this, and reflect real life experiences. We explain how, by including this information, crucial links can be made to aid in the investigation and solution of crime.

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“…An erroneous PMI estimation can falsify the outcome of forensic investigations in the event of homicides, suicides, and unintentional deaths [ 8 , 9 ]. The term PMI refers to the time elapsed between the time of death and the discovery and examination of the body [ 1 , 2 , 4 , 10 ]. The estimation of the PMI can be an extremely complicated process, as it can be influenced by various endogenous and exogenous factors (environmental temperature or humidity, or health status at the time of death) [ 4 , 6 ].…”

Section: Introductionmentioning

confidence: 99%

New Trends in Immunohistochemical Methods to Estimate the Time since Death: A Review

et al. 2022

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The identification of a reliable and accurate post-mortem interval (PMI) is a major challenge in the field of forensic sciences and criminal investigation. Several laboratory techniques have recently been developed that offer a better contribution to the estimation of PMI, in addition to the traditional physical or physico-chemical (body cooling, lividity, radiocarbon dating, rigor mortis), chemical (autolysis), microbiological (putrefaction), entomological, as well as botanical parameters. Molecular biology (degradation pattern of macromolecules such as proteins, DNA, RNA), biochemical analysis of biological fluids (such as blood, cerebrospinal fluid, and vitreous humor), and immunohistochemistry are some of the most recent technological innovations. A systematic review of the literature was performed with the aim of presenting an up-to-date overview on the correlation between the immunohistochemical (IHC) expression of specific antigenic markers at different PMIs. The systematic review was performed according to PRISMA guidelines. Scopus and PubMed were used as search engines from January 1, 1998 to March 1, 2022 to evaluate the effectiveness of immunohistochemistry in estimating PMI. The following keywords were used: (immunohistochemical) OR (immunohistochemistry) AND (time since death) OR (post-mortem interval) OR (PMI). A total of 6571 articles were collected. Ultimately, 16 studies were included in this review. The results of this systematic review highlighted that IHC techniques, in association with traditional methods, add, in Bayesian terms, additional information to define a more accurate time of death and PMI. However, current IHC results are numerically limited and more data and studies are desirable in the near future.

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Forensic transcriptome analysis using massively parallel sequencing

Cited by 37 publications

References 167 publications

Insights into how environment shapes post-mortem RNA transcription in mouse brain

Insights into how environment shapes post-mortem RNA transcription in mouse brain

On the Identification of Body Fluids and Tissues: A Crucial Link in the Investigation and Solution of Crime

New Trends in Immunohistochemical Methods to Estimate the Time since Death: A Review

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