Forensic bone proteomics: novel biomarkers and technologies for estimating the postmortem interval (a review)

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Abstract

Bone proteomics is a rapidly evolving field in forensic medicine aimed at determining the postmortem interval. Unlike traditional approaches, this method enables quantitative and molecular-level analysis of protein composition changes in bone tissue. Highly degradation-resistant proteins are considered reliable biomarkers for estimating the postmortem interval, providing more accurate and objective results. Mass spectrometry, in combination with modern bioinformatics tools and machine learning technologies, allows for a detailed investigation of postmortem protein degradation processes and the identification of time-dependent molecular patterns. However, environmental factors such as humidity, temperature, soil composition, and microbial activity significantly affect protein preservation in bone tissue, underscoring the need for standardized analytical protocols.

This review summarizes key methods of bone proteomic analysis, prospects for its integration with metabolomics and lipidomics, and the potential of machine learning in postmortem interval estimation. Further research in this field should aim at validating biomarkers, standardizing techniques, and integrating these methods into forensic practice.

The development of forensic bone proteomics opens new possibilities, offering more precise data in complex medico-legal cases.

About the authors

Gulgena R. Mustafina

Bashkir State Medical University

Email: gulgenarm@mail.ru
ORCID iD: 0000-0003-2534-6385
SPIN-code: 8904-2046

MD, Cand. Sci. (Medicine), Assistant Professor

Russian Federation, Ufa

Airat A. Khalikov

Bashkir State Medical University

Email: airat.expert@mail.ru
ORCID iD: 0000-0003-1045-5677
SPIN-code: 1895-7300

MD, Dr. Sci. (Medicine), Professor

Russian Federation, Ufa

Kirill O. Kuznetsov

Ufa University of Science and Technology; Bureau of Forensic Medical Examination

Author for correspondence.
Email: kuznetsovarticles@mail.ru
ORCID iD: 0000-0002-2405-1801
SPIN-code: 3053-3773

MD

Russian Federation, Ufa; Ufa

Elmira M. Nazarova

Bashkir State Medical University

Email: egevan@list.ru
ORCID iD: 0000-0002-1160-7241
SPIN-code: 6340-5202

MD, Cand. Sci. (Medicine), Assistant Professor

Russian Federation, Ufa

References

  1. Kumar S, Singh P. Proteomics: A Prospective New Tool in Forensic Investigations. Forensic Sci Rev. 2021;33(2):145–150. Available from: http://forensicsciencereview.com/Abstract/
  2. Parker GJ, Leppert T, Anex DS, et al. Demonstration of Protein-Based Human Identification Using the Hair Shaft Proteome. PLOS ONE. 2016;11(9):e0160653. doi: 10.1371/journal.pone.0160653 EDN: XTZYCV
  3. Goecker ZC, Salemi MR, Karim N, et al. Optimal Processing for Proteomic Genotyping Of Single Human Hairs. Forensic Science International: Genetics. 2020;47:102314. doi: 10.1016/j.fsigen.2020.102314 EDN: VPWLXQ
  4. Marcus K, Lelong C, Rabilloud T. What Room for Two-Dimensional Gel-Based Proteomics in a Shotgun Proteomics World? Proteomes. 2020;8(3):17. doi: 10.3390/PROTEOMES8030017 EDN: JYJNQG
  5. Zhao L, Cong X, Zhai L, et al. Comparative Evaluation of Label-Free Quantification Strategies. Journal of Proteomics. 2020;215:103669. doi: 10.1016/j.jprot.2020.103669 EDN: RQEZYB
  6. Jiang P, Peng W, Zhao J, et al. Glycan/Protein-Stable Isotope Labeling in Cell Culture for Enabling Concurrent Quantitative Glycomics/Proteomics/Glycoproteomics. Analytical Chemistry. 2023;95(44):16059–16069. doi: 10.1021/acs.analchem.3c00247 EDN: HDPVBM
  7. Wolters DA, Washburn MP, Yates JR. An Automated Multidimensional Protein Identification Technology for Shotgun Proteomics. Analytical Chemistry. 2001;73(23):5683–5690. doi: 10.1021/ac010617e
  8. Bian Y, Zheng R, Bayer FP, et al. Robust, Reproducible and Quantitative Analysis of Thousands of Proteomes by Micro-Flow LC–MS/MS. Nature Communications. 2020;11(1):157. doi: 10.1038/s41467-019-13973-x EDN: SDQBNF
  9. Adav SS, Leung CY, Ng KW. Profiling of Hair Proteome Revealed Individual Demographics. Forensic Science International: Genetics. 2023;66:102914. doi: 10.1016/j.fsigen.2023.102914 EDN: SZDFOX
  10. Mickleburgh HL, Schwalbe EC, Bonicelli A, et al. Human Bone Proteomes before and after Decomposition: Investigating the Effects of Biological Variation and Taphonomic Alteration on Bone Protein Profiles and the Implications for Forensic Proteomics. Journal of Proteome Research. 2021;20(5):2533–2546. doi: 10.1021/acs.jproteome.0c00992 EDN: YGTMFO
  11. Li Y, Xun D, Li L, et al. Deep Dive on the Proteome of Human Body Fluids: A Valuable Data Resource for Biomarker Discovery. Cancer Genomics and Proteomics. 2021;18(4):549–568. doi: 10.21873/cgp.20280 EDN: SXLVTB
  12. Parker GJ, McKiernan HE, Legg KM, Goecker ZC. Forensic Proteomics. Forensic Science International: Genetics. 2021;54:102529. doi: 10.1016/j.fsigen.2021.102529 EDN: XBXXJV
  13. Bonicelli A, Di Nunzio A, Di Nunzio C, Procopio N. Insights into the Differential Preservation of Bone Proteomes in Inhumed and Entombed Cadavers from Italian Forensic Caseworks. Journal of Proteome Research. 2022;21(5):1285–1298. doi: 10.1021/acs.jproteome.1c00904 EDN: BTQOIH
  14. Franceschetti L, Amadasi A, Bugelli V, et al. Estimation of Late Postmortem Interval: Where Do We Stand? A Literature Review. Biology. 2023;12(6):783. doi: 10.3390/biology12060783 EDN: NJVWJN
  15. Brockbals L, Garrett-Rickman S, Fu S, et al. Estimating the Time of Human Decomposition Based on Skeletal Muscle Biopsy Samples Utilizing an Untargeted LC–MS/MS-based Proteomics Approach. Analytical and Bioanalytical Chemistry. 2023;415(22):5487–5498. doi: 10.1007/s00216-023-04822-4 EDN: SXNXAY
  16. Mizukami H, Hathway B, Procopio N. Aquatic Decomposition of Mammalian Corpses: A Forensic Proteomic Approach. Journal of Proteome Research. 2020;19(5):2122–2135. doi: 10.1021/acs.jproteome.0c00060 EDN: TOEFBK
  17. Merkley ED, Wunschel DS, Wahl KL, Jarman KH. Applications and Challenges of Forensic Proteomics. Forensic Science International. 2019;297:350–363. doi: 10.1016/j.forsciint.2019.01.022 EDN: RVBHXU
  18. Halikov AA, Kildyushov EM, Kuznetsov KO, et al. Use of microRNA to Estimate Time Science Death: Review. Russian Journal of Forensic Medicine. 2021;7(3):132–138. doi: 10.17816/fm412 EDN: FHYOZZ
  19. Kildyushov EM, Ermakova YV, Tumanov EV, Kuznetsova GS. Estimation of Time Since Death in the Late Postmortem Period in Forensic Medicine (Literature Review). Russian Journal of Forensic Medicine. 2018;4(1):34–38. doi: 10.19048/2411-8729-2018-4-1-34-38 EDN: YWDARF
  20. Indiaminov SI, Zhumanov ZE, Blinova SA. Problems of Establishing the Prescription of Death. Forensic Medical Expertise. 2020;63(6):45–50. doi: 10.17116/sudmed20206306145 EDN: FXLSCS
  21. Ferreira MT, Cunha E. Can we Infer Post Mortem Interval on the Basis of Decomposition Rate? A Case from a Portuguese Cemetery. Forensic Science International. 2013;226(1-3):298.e1–298.e6. doi: 10.1016/j.forsciint.2013.01.006
  22. Jellinghaus K, Hachmann C, Hoeland K, et al. Correction to: Collagen Degradation as a Possibility to Determine the Post-Mortem Interval (PMI) of Animal Bones: A Validation Study Referring to an Original Study of Boaks et al. (2014). International Journal of Legal Medicine. 2018;132(3):765–765. doi: 10.1007/s00414-018-1782-z
  23. Zelentsova EA, Yanshole LV, Melnikov AD, et al. Post-Mortem Changes in Metabolomic Profiles of Human Serum, Aqueous Humor and Vitreous Humor. Metabolomics. 2020;16(7):80. doi: 10.1007/s11306-020-01700-3 EDN: YHUAPI
  24. Wu H, Liu FF, Wu JD, Xie Y. Research Progress on Estimation of Postmortem Interval Based on Ocular Tissues Structure. Fa Yi Xue Za Zhi. 2023;39(1):50–56. doi: 10.12116/j.issn.1004-5619.2021.410602
  25. Zissler A, Stoiber W, Geissenberger J, et al. Influencing Factors on Postmortem Protein Degradation for PMI Estimation: A Systematic Review. Diagnostics. 2021;11(7):1146. doi: 10.3390/diagnostics11071146 EDN: LGHYTE
  26. Martin C, Verheggen F. Odour Profile of Human Corpses: A Review. Forensic Chemistry. 2018;10:27–36. doi: 10.1016/j.forc.2018.07.002
  27. Procopio N, Hopkins RJA, Harvey VL, Buckley M. Proteome Variation with Collagen Yield in Ancient Bone. Journal of Proteome Research. 2021;20(3):1754–1769. doi: 10.1021/acs.jproteome.0c01014 EDN: BZKNHN
  28. Qi F, Tan Y, Yao A, et al. Psoriasis to Psoriatic Arthritis: The Application of Proteomics Technologies. Frontiers in Medicine. 2021;8:681172. doi: 10.3389/fmed.2021.681172 EDN: NPHHJX
  29. Sacco MA, Aquila I. Proteomics: A New Research Frontier in Forensic Pathology. International Journal of Molecular Sciences. 2023;24(13):10735. doi: 10.3390/ijms241310735 EDN: LHPKWV
  30. Duong VA, Park JM, Lim HJ, Lee H. Proteomics in Forensic Analysis: Applications for Human Samples. Applied Sciences. 2021;11(8):3393. doi: 10.3390/app11083393 EDN: ACJCEU
  31. Rose JP, Schurman CA, King CD, et al. Deep Coverage and Quantification of the Bone Proteome Provides Enhanced Opportunities for New Discoveries in Skeletal Biology and Disease. PLOS ONE. 2023;18(10):e0292268. doi: 10.1371/journal.pone.0292268 EDN: XCZVTY
  32. Creecy A, Damrath JG, Wallace JM. Control of Bone Matrix Properties by Osteocytes. Frontiers in Endocrinology. 2021;11:578477. doi: 10.3389/fendo.2020.578477 EDN: CUSLVW
  33. Volk SW, Shah SR, Cohen AJ, et al. Type III Collagen Regulates Osteoblastogenesis and the Quantity of Trabecular Bone. Calcified Tissue International. 2014;94(6):621–631. doi: 10.1007/s00223-014-9843-x EDN: BXNINO
  34. Ivanova VP, Krivchenko AI. Current Viewpoint on Structure and on Evolution of Collagens. II. Fibril-Associated Collagens. Journal of Evolutionary Biochemistry and Physiology. 2014;50(4):273–285. doi: 10.1134/S0022093014040012 EDN: UFPNRJ
  35. Vavilov AY, Khalikov AA, Rykunov IA, et al. Determination of the Corpse’s Stay in the Water Duration According to Maceration Degree of its Skin. Forensic Medical Expertise. 2023;66(3):64–68. doi: 10.17116/sudmed20236603164 EDN: BOUGOE
  36. Procopio N, Chamberlain AT, Buckley M. Exploring Biological and Geological Age-related Changes through Variations in Intra- and Intertooth Proteomes of Ancient Dentine. Journal of Proteome Research. 2018;17(3):1000–1013. doi: 10.1021/acs.jproteome.7b00648 EDN: YGDOTJ
  37. Holtz A, Basisty N, Schilling B. Quantification and Identification of Post-Translational Modifications Using Modern Proteomics Approaches. In; Marcus K, Eisenacher M, Sitek D, editors. Quantitative Methods in Proteomics. Methods in Molecular Biology. Humana, New York: Springer Protocols; 2021; P. 225–235. ISBN: 978-1-0716-1024-4 doi: 10.1007/978-1-0716-1024-4_16
  38. Donaldson AE, Lamont IL. Biochemistry Changes That Occur after Death: Potential Markers for Determining Post-Mortem Interval. PLoS ONE. 2013;8(11):e82011. doi: 10.1371/journal.pone.0082011
  39. Aslam B, Basit M, Nisar MA, et al. Proteomics: Technologies and Their Applications. Journal of Chromatographic Science. 2016;55(2):182–196. doi: 10.1093/chromsci/bmw167
  40. Rhein M, Hagemeier L, Klintschar M, et al. DNA Methylation Results Depend on DNA Integrity—Role of Post Mortem Interval. Frontiers in Genetics. 2015;6:182. doi: 10.3389/fgene.2015.00182
  41. Pittner S, Ehrenfellner B, Zissler A, et al. First Application of a Protein-Based Approach for Time Since Death Estimation. International Journal of Legal Medicine. 2016;131(2):479–483. doi: 10.1007/s00414-016-1459-4 EDN: LILOFA
  42. Marrone A, La Russa D, Barberio L, et al. Forensic Proteomics for the Discovery of New post mortem Interval Biomarkers: A Preliminary Study. International Journal of Molecular Sciences. 2023;24(19):14627. doi: 10.3390/ijms241914627 EDN: NFNVVZ
  43. Sidorova NA, Popov VL, Lavrukova OS. Features of Physiological Groups of Microorganisms — Participants in the Diagenesis of Bone Remains. Forensic Medical Expertise. 2021;64(5):41–45. doi: 10.17116/sudmed20216405141 EDN: BOBKCX
  44. Procopio N, Mein CA, Starace S, et al. Bone Diagenesis in Short Timescales: Insights from an Exploratory Proteomic Analysis. Biology. 2021;10(6):460. doi: 10.3390/biology10060460 EDN: DFDWGZ
  45. Ahmad A, Imran M, Ahsan H. Biomarkers as Biomedical Bioindicators: Approaches and Techniques for the Detection, Analysis, and Validation of Novel Biomarkers of Diseases. Pharmaceutics. 2023;15(6):1630. doi: 10.3390/pharmaceutics15061630 EDN: ZQCYIE
  46. Jellinghaus K, Urban PK, Hachmann C, et al. Collagen Degradation as a Possibility to Determine the Post-Mortem Interval (PMI) of Human Bones in a Forensic Context – A Survey. Legal Medicine. 2019;36:96–102. doi: 10.1016/j.legalmed.2018.11.009
  47. Boaks A, Siwek D, Mortazavi F. The Temporal Degradation of Bone Collagen: A Histochemical Approach. Forensic Science International. 2014;240:104–110. doi: 10.1016/j.forsciint.2014.04.008
  48. Sacco MA, Cordasco F, Scalise C, et al. Systematic Review on Post-Mortem Protein Alterations: Analysis of Experimental Models and Evaluation of Potential Biomarkers of Time of Death. Diagnostics. 2022;12(6):1490. doi: 10.3390/diagnostics12061490 EDN: NNVJXN
  49. Kram V, Shainer R, Jani P, et al. Biglycan in the Skeleton. Journal of Histochemistry & Cytochemistry. 2020;68(11):747–762. doi: 10.1369/0022155420937371 EDN: DIMWEJ
  50. Prieto-Bonete G, Pérez-Cárceles MD, Maurandi-López A, et al. Association Between Protein Profile and Postmortem Interval in Human Bone Remains. Journal of Proteomics. 2019;192:54–63. doi: 10.1016/j.jprot.2018.08.008 EDN: YKLYPJ
  51. Procopio N, Williams A, Chamberlain AT, Buckley M. Forensic Proteomics for the Evaluation of the Post-Mortem Decay in Bones. Journal of Proteomics. 2018;177:21–30. doi: 10.1016/j.jprot.2018.01.016
  52. Office of the Surgeon General (US). Bone Health and Osteoporosis: A Report of the Surgeon General. Rockville (MD): Office of the Surgeon General (US); 2004. Available from: https://www.ncbi.nlm.nih.gov/books/NBK45513/
  53. Procopio N, Buckley M. Minimizing Laboratory-Induced Decay in Bone Proteomics. Journal of Proteome Research. 2016;16(2):447–458. doi: 10.1021/acs.jproteome.6b00564 EDN: YXOVPR
  54. Procopio N, Chamberlain AT, Buckley M. Intra- and Interskeletal Proteome Variations in Fresh and Buried Bones. Journal of Proteome Research. 2017;16(5):2016–2029. doi: 10.1021/acs.jproteome.6b01070
  55. Wadsworth C, Buckley M. Proteome Degradation in Fossils: Investigating the Longevity of Protein Survival in Ancient Bone. Rapid Communications in Mass Spectrometry. 2014;28(6):605–615. doi: 10.1002/rcm.6821
  56. Ntasi G, Palomo IR, Marino G, et al. Molecular Signatures Written in Bone Proteins of 79 AD Victims from Herculaneum and Pompeii. Scientific Reports. 2022;12(1):8401. doi: 10.1038/s41598-022-12042-6 EDN: ZZGORT
  57. Mukherjee A, Rotwein P. Insulin-Like Growth Factor-Binding Protein-5 Inhibits Osteoblast Differentiation and Skeletal Growth by Blocking Insulin-Like Growth Factor Actions. Molecular Endocrinology. 2008;22(5):1238–1250. doi: 10.1210/me.2008-0001
  58. Shuken SR. An Introduction to Mass Spectrometry-Based Proteomics. Journal of Proteome Research. 2023;22(7):2151–2171. doi: 10.1021/acs.jproteome.2c00838 EDN: LYMSIJ
  59. Zhang HW, Lv C, Zhang LJ, et al. Application of Omics- and Multi-Omics-Based Techniques for Natural Product Target Discovery. Biomedicine & Pharmacotherapy. 2021;141:111833. doi: 10.1016/j.biopha.2021.111833 EDN: GDUUZU
  60. Pascovici D, Wu JX, McKay MJ, et al. Clinically Relevant Post-Translational Modification Analyses—Maturing Workflows and Bioinformatics Tools. International Journal of Molecular Sciences. 2018;20(1):16. doi: 10.3390/ijms20010016 EDN: KJCYCE
  61. Chen X, Wei S, Ji Y, et al. Quantitative Proteomics Using SILAC: Principles, Applications, and Developments. Proteomics. 2015;15(18):3175–3192. doi: 10.1002/pmic.201500108
  62. Wang X, He Y, Ye Y, et al. SILAC–Based Quantitative MS Approach for Real-Time Recording Protein-Mediated Cell-Cell Interactions. Scientific Reports. 2018;8(1):8441. doi: 10.1038/s41598-018-26262-2 EDN: DKDQCP
  63. Swan AL, Mobasheri A, Allaway D, et al. Application of Machine Learning to Proteomics Data: Classification and Biomarker Identification in Postgenomics Biology. OMICS: A Journal of Integrative Biology. 2013;17(12):595–610. doi: 10.1089/omi.2013.0017 EDN: MTRVWU
  64. Chen C, Hou J, Tanner JJ, Cheng J. Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis. International Journal of Molecular Sciences. 2020;21(8):2873. doi: 10.3390/ijms21082873 EDN: QVSXLB
  65. Wilke C. Proteomics Offers New Clues for Forensic Investigations. ACS Central Science. 2021;7(10):1595–1598. doi: 10.1021/acscentsci.1c01232 EDN: QWAWGY
  66. Broadbelt KG, Rivera KD, Paterson DS, et al. Brainstem Deficiency of the 14-3-3 Regulator of Serotonin Synthesis: A Proteomics Analysis in the Sudden Infant Death Syndrome. Molecular & Cellular Proteomics. 2012;11(1):M111.009530. doi: 10.1074/mcp.M111.009530
  67. Sawafuji R, Cappellini E, Nagaoka T, et al. Proteomic Profiling of Archaeological Human Bone. Royal Society Open Science. 2017;4(6):161004. doi: 10.1098/rsos.161004 EDN: YFCEBR
  68. Wadsworth C, Procopio N, Anderung C, et al. Comparing Ancient DNA Survival and Proteome Content in 69 Archaeological Cattle Tooth and Bone Samples From Multiple European Sites. Journal of Proteomics. 2017;158:1–8. doi: 10.1016/j.jprot.2017.01.004 EDN: YYBWPN
  69. Bonicelli A, Mickleburgh HL, Chighine A, et al. The ‘ForensOMICS’ Approach for Postmortem Interval Estimation From Human Bone by Integrating Metabolomics, Lipidomics, and Proteomics. eLife. 2022;11:e83658. doi: 10.7554/eLife.83658 EDN: ZASEWN

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