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Mamrot J, Hall NE, Lindley RA. Predicting clinical outcomes using cancer progression associated signatures. Oncotarget 2021; 12:845-858. [PMID: 33889305 PMCID: PMC8057277 DOI: 10.18632/oncotarget.27934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 03/22/2021] [Indexed: 12/09/2022] Open
Abstract
Somatic mutation signatures are an informative facet of cancer aetiology, however they are rarely useful for predicting patient outcome. The aim of this study is to evaluate the utility of a panel of 142 mutation-signature–associated metrics (P142) for predicting cancer progression in patients from a ‘TCGA PanCancer Atlas’ cohort. The P142 metrics are comprised of AID/APOBEC and ADAR deaminase associated SNVs analyzed for codon context, strand bias, and transitions/transversions. TCGA tumor-normal mutation data was obtained for 10,437 patients, representing 31 of the most prevalent forms of cancer. Stratified random sampling was used to split patients into training, tuning and validation cohorts for each cancer type. Cancer specific machine learning (XGBoost) models were built using the output from the P142 panel to predict patient Progression Free Survival (PFS) status as either “High PFS” or “Low PFS”. Predictive performance of each model was evaluated using the validation cohort. Models accurately predicted PFS status for several cancer types, including adrenocortical carcinoma, glioma, mesothelioma, and sarcoma. In conclusion, the P142 panel of metrics successfully predicted cancer progression status in patients with some, but not all cancer types analyzed. These results pave the way for future studies on cancer progression associated signatures.
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Affiliation(s)
- Jared Mamrot
- GMDx Group Ltd, Melbourne, Victoria, Australia.,Department of Obstetrics and Gynaecology, Monash University, Clayton, VIC, Australia
| | | | - Robyn A Lindley
- GMDx Group Ltd, Melbourne, Victoria, Australia.,Department of Clinical Pathology, The Victorian Comprehensive Cancer Centre, Faculty of Medicine, Dentistry & Health Sciences, University of Melbourne, VIC, Australia
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Mamrot J, Balachandran S, Steele EJ, Lindley RA. Molecular model linking Th2 polarized M2 tumour-associated macrophages with deaminase-mediated cancer progression mutation signatures. Scand J Immunol 2019; 89:e12760. [PMID: 30802996 PMCID: PMC6850162 DOI: 10.1111/sji.12760] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 02/19/2019] [Indexed: 12/11/2022]
Abstract
A new and diverse range of somatic mutation signatures are observed in late‐stage cancers, but the underlying reasons are not fully understood. We advance a “combinatorial association model” for deaminase binding domain (DBD) diversification to explain the generation of previously observed cancer‐progression associated mutation signatures. We also propose that changes in the polarization of tumour‐associated macrophages (TAMs) are accompanied by the expression of deaminases with a new and diverse range of DBDs, and thus accounting for the generation of new somatic mutation signatures. The mechanism proposed is molecularly reminiscent of combinatorial association of heavy (H) and light (L) protein chains following V(D)J recombination of immunoglobulin molecules (and similarly for protein chains in heterodimers α/β and γ/δ of V(D)Js of T Cell Receptors) required for pathogen antigen recognition by B cells and T cells, respectively. We also discuss whether extracellular vesicles (EVs) emanating from tumour enhancing M2‐polarized macrophages represent a likely source of the de novo deaminase DBDs. We conclude that M2‐polarized macrophages extruding EVs loaded with deaminase proteins or deaminase‐specific transcription/translation regulatory factors and like information may directly trigger deaminase diversification within cancer cells, and thus account for the many new somatic mutation signatures that are indicative of cancer progression. This hypothesis now has a plausible evidentiary base, and it is worth direct testing in future investigations. A long‐term objective would be to identify molecular biomarkers predicting cancer progression (or metastatic disease) and to support the development of new drug targets before metastatic pathways are activated.
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Affiliation(s)
| | - Siddharth Balachandran
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Edward J Steele
- CYO'Connor ERADE Village Foundation, Perth, Western Australia, Australia.,Melville Analytics Pty Ltd, Melbourne, Victoria, Australia
| | - Robyn A Lindley
- GMDxCo Pty Ltd, Melbourne, Victoria, Australia.,Faculty of Medicine, Dentistry & Health Sciences, Department of Clinical Pathology, University of Melbourne, Melbourne, Victoria, Australia
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Mamrot J, Legaie R, Ellery SJ, Wilson T, Seemann T, Powell DR, Gardner DK, Walker DW, Temple-Smith P, Papenfuss AT, Dickinson H. De novo transcriptome assembly for the spiny mouse (Acomys cahirinus). Sci Rep 2017; 7:8996. [PMID: 28827620 PMCID: PMC5566366 DOI: 10.1038/s41598-017-09334-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 07/17/2017] [Indexed: 12/21/2022] Open
Abstract
Spiny mice of the genus Acomys display several unique physiological traits, including menstruation and scar-free wound healing; characteristics that are exceedingly rare in mammals, and of considerable interest to the scientific community. These unique attributes, and the potential for spiny mice to accurately model human diseases, are driving increased use of this genus in biomedical research, however little genetic information is accessible for this species. This project aimed to generate a draft transcriptome for the Common spiny mouse (Acomys cahirinus). Illumina sequencing of RNA from 15 organ types (male and female) produced 451 million, 150 bp paired-end reads (92.4Gbp). An extensive survey of de novo transcriptome assembly approaches using Trinity, SOAPdenovo-Trans, and Oases at multiple kmer lengths was conducted, producing 50 single-kmer assemblies from this dataset. Non-redundant transcripts from all assemblies were merged into a meta-assembly using the EvidentialGene tr2aacds pipeline, producing the largest gene catalogue to date for Acomys cahirinus. This study provides the first detailed characterization of the spiny mouse transcriptome. It validates use of the EvidentialGene tr2aacds pipeline in mammals to augment conventional de novo assembly approaches, and provides a valuable scientific resource for further investigation into the unique physiological characteristics inherent in the genus Acomys.
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Affiliation(s)
- Jared Mamrot
- The Ritchie Centre, Hudson Institute of Medical Research, Melbourne, Australia
- Department of Obstetrics and Gynaecology, Monash University, Melbourne, Australia
| | - Roxane Legaie
- MHTP node - Monash Bioinformatics Platform, Monash University, Melbourne, Australia
| | - Stacey J Ellery
- The Ritchie Centre, Hudson Institute of Medical Research, Melbourne, Australia
- Department of Obstetrics and Gynaecology, Monash University, Melbourne, Australia
| | - Trevor Wilson
- MHTP Medical Genomics Facility, Melbourne, Australia
| | - Torsten Seemann
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, Australia
| | - David R Powell
- Monash Bioinformatics Platform, Monash University, Melbourne, Australia
| | - David K Gardner
- School of BioSciences, University of Melbourne, Melbourne, Australia
| | - David W Walker
- The Ritchie Centre, Hudson Institute of Medical Research, Melbourne, Australia
- Department of Obstetrics and Gynaecology, Monash University, Melbourne, Australia
- RMIT University, Bundoora Campus, Bundoora, Australia
| | - Peter Temple-Smith
- Department of Obstetrics and Gynaecology, Monash University, Melbourne, Australia
- Education Program in Reproduction and Development, Monash University, Melbourne, Australia
| | - Anthony T Papenfuss
- Bioinformatics Division, Walter and Eliza Hall Institute, Parkville, Australia
- Computational Cancer Biology Program, Peter MacCallum Cancer Centre, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Hayley Dickinson
- The Ritchie Centre, Hudson Institute of Medical Research, Melbourne, Australia.
- Department of Obstetrics and Gynaecology, Monash University, Melbourne, Australia.
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Bellofiore N, Ellery SJ, Mamrot J, Walker DW, Temple-Smith P, Dickinson H. First evidence of a menstruating rodent: the spiny mouse (Acomys cahirinus). Am J Obstet Gynecol 2017; 216:40.e1-40.e11. [PMID: 27503621 DOI: 10.1016/j.ajog.2016.07.041] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 07/14/2016] [Accepted: 07/15/2016] [Indexed: 12/13/2022]
Abstract
BACKGROUND Advances in research relating to menstruation and associated disorders (eg, endometriosis and premenstrual syndrome) have been hindered by the lack of an appropriate animal model. Menstruation, the cyclical shedding of the decidualized endometrium in the absence of pregnancy, is believed to be limited to 78 higher-order primates (human beings and Old World monkeys), 4 species of bat, and the elephant shrew. This represents only 1.5% of the known 5502 mammalian species and <0.09% of these are nonprimates. Thus, many aspects of menstruation remain poorly understood, limiting the development of effective treatments for women with menstrual disorders. Menstruation occurs as a consequence of progesterone priming of the endometrial stroma and a spontaneous decidual reaction. At the end of each infertile cycle as progesterone levels decline the uterus is unable to maintain this terminally differentiated stroma and the superficial endometrium is shed. True menstruation has never been reported in rodents. OBJECTIVE Here we describe the first observation of menstruation in a rodent, the spiny mouse (Acomys cahirinus). STUDY DESIGN Virgin female spiny mice (n = 14) aged 12-16 weeks were sampled through daily vaginal lavage for 2 complete reproductive cycles. Stage-specific collection of reproductive tissue and plasma was used for histology, prolactin immunohistochemistry, and enzyme-linked immunosorbent assay of progesterone (n = 4-5/stage of the menstrual cycle). Normally distributed data are reported as the mean ± SE and significant differences calculated using a 1-way analysis of variance. Nonnormal data are displayed as the median values of replicates (with interquartile range) and significant differences calculated using Kruskal-Wallis test. RESULTS Mean menstrual cycle length was 8.7 ± 0.4 days with red blood cells observed in the lavages over 3.0 ± 0.2 days. Cyclic endometrial shedding and blood in the vaginal canal concluding with each infertile cycle was confirmed in all virgin females. The endometrium was thickest during the luteal phase at 322.6 μm (254.8, 512.2), when plasma progesterone peaked at 102.1 ng/mL (70.1, 198.6) and the optical density for prolactin immunoreactivity was strongest (0.071 ± 0.01 arbitrary units). CONCLUSION The spiny mouse undergoes spontaneous decidualization, demonstrating for the first time menstruation in a rodent. The spiny mouse provides a readily accessible nonprimate model to study the mechanisms of menstrual shedding and repair, and may therefore be useful in furthering studies of human menstrual and pregnancy-associated disorders.
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Mamrot J, Pangestu M, Walker D, Gardner DK, Dickinson H. Confirmed dioestrus in pseudopregnant mice using vaginal exfoliative cytology improves embryo transfer implantation rate. Reprod Biomed Online 2015; 31:538-43. [DOI: 10.1016/j.rbmo.2015.06.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 06/17/2015] [Accepted: 06/17/2015] [Indexed: 11/28/2022]
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