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Dighe A, Maziarz J, Ibrahim-Hashim A, Gatenby RA, Kshitiz, Levchenko A, Wagner GP. Experimental and phylogenetic evidence for correlated gene expression evolution in endometrial and skin fibroblasts. iScience 2024; 27:108593. [PMID: 38174318 PMCID: PMC10762354 DOI: 10.1016/j.isci.2023.108593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/12/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024] Open
Abstract
Gene expression change is a dominant mode of evolution. Mutations, however, can affect gene expression in multiple cell types. Therefore, gene expression evolution in one cell type can lead to similar gene expression changes in another cell type. Here, we test this hypothesis by investigating dermal skin fibroblasts (SFs) and uterine endometrial stromal fibroblasts (ESFs). The comparative dataset consists of transcriptomes from cultured SF and ESF of nine mammalian species. We find that evolutionary changes in gene expression in SF and ESF are highly correlated. The experimental dataset derives from a SCID mouse strain selected for slow cancer growth leading to substantial gene expression changes in SFs. We compared the gene expression profiles of SF with that of ESF and found a significant correlation between them. We discuss the implications of these findings for the evolutionary correlation between placental invasiveness and vulnerability to metastatic cancer.
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Affiliation(s)
- Anasuya Dighe
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Systems Biology Institute, Yale University, West Haven, CT, USA
| | - Jamie Maziarz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Systems Biology Institute, Yale University, West Haven, CT, USA
| | | | | | - Kshitiz
- Biomedical Engineering, University of Connecticut, Farmington, CT, USA
| | - Andre Levchenko
- Systems Biology Institute, Yale University, West Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Günter P. Wagner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Systems Biology Institute, Yale University, West Haven, CT, USA
- Department of Evolutionary Biology, University of Vienna, Djerassi Platz 1, Vienna A-1030, Austria
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2
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Evo-devo perspectives on cancer. Essays Biochem 2022; 66:797-815. [PMID: 36250956 DOI: 10.1042/ebc20220041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 12/13/2022]
Abstract
The integration of evolutionary and developmental approaches into the field of evolutionary developmental biology has opened new areas of inquiry- from understanding the evolution of development and its underlying genetic and molecular mechanisms to addressing the role of development in evolution. For the last several decades, the terms 'evolution' and 'development' have been increasingly linked to cancer, in many different frameworks and contexts. This mini-review, as part of a special issue on Evolutionary Developmental Biology, discusses the main areas in cancer research that have been addressed through the lenses of both evolutionary and developmental biology, though not always fully or explicitly integrated in an evo-devo framework. First, it briefly introduces the current views on carcinogenesis that invoke evolutionary and/or developmental perspectives. Then, it discusses the main mechanisms proposed to have specifically evolved to suppress cancer during the evolution of multicellularity. Lastly, it considers whether the evolution of multicellularity and development was shaped by the threat of cancer (a cancer-evo-devo perspective), and/or whether the evolution of developmental programs and life history traits can shape cancer resistance/risk in various lineages (an evo-devo-cancer perspective). A proper evolutionary developmental framework for cancer, both as a disease and in terms of its natural history (in the context of the evolution of multicellularity and development as well as life history traits), could bridge the currently disparate evolutionary and developmental perspectives and uncover aspects that will provide new insights for cancer prevention and treatment.
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Mika K, Whittington CM, McAllan BM, Lynch VJ. Gene expression phylogenies and ancestral transcriptome reconstruction resolves major transitions in the origins of pregnancy. eLife 2022; 11:e74297. [PMID: 35770963 PMCID: PMC9275820 DOI: 10.7554/elife.74297] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 06/29/2022] [Indexed: 11/13/2022] Open
Abstract
Structural and physiological changes in the female reproductive system underlie the origins of pregnancy in multiple vertebrate lineages. In mammals, the glandular portion of the lower reproductive tract has transformed into a structure specialized for supporting fetal development. These specializations range from relatively simple maternal nutrient provisioning in egg-laying monotremes to an elaborate suite of traits that support intimate maternal-fetal interactions in Eutherians. Among these traits are the maternal decidua and fetal component of the placenta, but there is considerable uncertainty about how these structures evolved. Previously, we showed that changes in uterine gene expression contributes to several evolutionary innovations during the origins of pregnancy (Mika et al., 2021b). Here, we reconstruct the evolution of entire transcriptomes ('ancestral transcriptome reconstruction') and show that maternal gene expression profiles are correlated with degree of placental invasion. These results indicate that an epitheliochorial-like placenta evolved early in the mammalian stem-lineage and that the ancestor of Eutherians had a hemochorial placenta, and suggest maternal control of placental invasiveness. These data resolve major transitions in the evolution of pregnancy and indicate that ancestral transcriptome reconstruction can be used to study the function of ancestral cell, tissue, and organ systems.
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Affiliation(s)
- Katelyn Mika
- Department of Human Genetics, University of ChicagoChicagoUnited States
- Department of Organismal Biology and Anatomy, University of ChicagoChicagoUnited States
| | | | | | - Vincent J Lynch
- Department of Biological Sciences, University at Buffalo, State University of New YorkBuffalo,NewyorkUnited States
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Liu S, Suhail Y, Novin A, Perpetua L, Kshitiz. Metastatic Transition of Pancreatic Ductal Cell Adenocarcinoma Is Accompanied by the Emergence of Pro-Invasive Cancer-Associated Fibroblasts. Cancers (Basel) 2022; 14:2197. [PMID: 35565326 PMCID: PMC9104173 DOI: 10.3390/cancers14092197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/24/2022] [Accepted: 04/25/2022] [Indexed: 02/08/2023] Open
Abstract
Cancer-associated fibroblasts (CAFs) are now appreciated as key regulators of cancer metastasis, particularly in cancers with high stromal content, e.g., pancreatic ductal cell carcinoma (PDAC). However, it is not yet well understood if fibroblasts are always primed to be cooperative in PDAC transition to metastasis, if they undergo transformation which ensures their cooperativity, and if such transformations are cancer-driven or intrinsic to fibroblasts. We performed a fibroblast-centric analysis of PDAC cancer, as it transitioned from the primary site to trespass stromal compartment reaching the lymph node using published single-cell RNA sequencing data by Peng et al. We have characterized the change in fibroblast response to cancer from a normal wound healing response in the initial stages to the emergence of subclasses with myofibroblast and inflammatory fibroblasts such as signatures. We have previously posited "Evolved Levels of Invasibility (ELI)", a framework describing the evolution of stromal invasability as a selected phenotype, which explains the large and correlated reduction in stromal invasion by placental trophoblasts and cancer cells in certain mammals. Within PDAC samples, we found large changes in fibroblast subclasses at succeeding stages of PDAC progression, with the emergence of specific subclasses when cancer trespasses stroma to metastasize to proximal lymph nodes (stage IIA to IIB). Surprisingly, we found that the initial metastatic transition is accompanied by downregulation of ELI-predicted pro-resistive genes, and the emergence of a subclass of fibroblasts with ELI-predicted increased invasibility. Interestingly, this trend was also observed in stellate cells. Using a larger cohort of bulk RNAseq data from The Cancer Genome Atlas for PDAC cancers, we confirmed that genes describing this emergent fibroblast subclass are also correlated with lymph node metastasis of cancer cells. Experimental testing of selected genes characterizing pro-resistive and pro-invasive fibroblast clusters confirmed their contribution in regulating stromal invasability as a phenotype. Our data confirm that the complexity of stromal response to cancer is really a function of stage-wise emergence of distinct fibroblast clusters, characterized by distinct gene sets which confer initially a predominantly pro-resistive and then a pro-invasive property to the stroma. Stromal response therefore transitions from being tumor-limiting to a pro-metastatic state, facilitating stromal trespass and the onset of metastasis.
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Affiliation(s)
- Shaofei Liu
- Department of Biomedical Engineering, University of Connecticut Health, Farmington, CT 06030, USA; (S.L.); (Y.S.); (A.N.)
- Center for Cell Analysis and Modeling, University of Connecticut Health, Farmington, CT 06030, USA
| | - Yasir Suhail
- Department of Biomedical Engineering, University of Connecticut Health, Farmington, CT 06030, USA; (S.L.); (Y.S.); (A.N.)
- Center for Cell Analysis and Modeling, University of Connecticut Health, Farmington, CT 06030, USA
| | - Ashkan Novin
- Department of Biomedical Engineering, University of Connecticut Health, Farmington, CT 06030, USA; (S.L.); (Y.S.); (A.N.)
| | - Lorrie Perpetua
- Research Tissue Repository, University of Connecticut Health, Farmington, CT 06030, USA;
| | - Kshitiz
- Department of Biomedical Engineering, University of Connecticut Health, Farmington, CT 06030, USA; (S.L.); (Y.S.); (A.N.)
- Center for Cell Analysis and Modeling, University of Connecticut Health, Farmington, CT 06030, USA
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Tracing the cis-regulatory changes underlying the endometrial control of placental invasion. Proc Natl Acad Sci U S A 2022; 119:2111256119. [PMID: 35110402 PMCID: PMC8832988 DOI: 10.1073/pnas.2111256119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2021] [Indexed: 11/18/2022] Open
Abstract
Among eutherian (placental) mammals, placental embedding into the maternal endometrium exhibits great differences, from being deeply invasive (e.g., humans) to noninvasive (e.g., cattle). The degree of invasion of placental trophoblasts is positively correlated with the rate of cancer malignancy. Previously, we have shown that fibroblasts from different species offer different levels of resistance to the invading trophoblasts as well as to cancer cell invasion. Here we present a comparative genomic investigation revealing cis-regulatory elements underlying these interspecies differences in invasibility. We identify transcription factors that regulate proinvasibility and antiinvasibility genes in stromal cells. Using an in vitro invasibility assay combined with CRISPR-Cas9 gene knockout, we found that the transcription factors GATA2 and TFDP1 strongly influence the invasibility of endometrial and skin fibroblasts. This work identifies genomic mechanisms explaining species differences in stromal invasibility, paving the way to therapies targeting stromal characteristics to regulate placental invasion, wound healing, and cancer dissemination.
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Ma X, Dighe A, Maziarz J, Neumann E, Erkenbrack E, Hei YY, Liu Y, Suhail Y, Pak I, Levchenko A, Wagner GP. Evolution of higher mesenchymal CD44 expression in the human lineage. Evol Med Public Health 2022; 10:447-462. [PMID: 36148042 PMCID: PMC9487634 DOI: 10.1093/emph/eoac036] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 08/21/2022] [Indexed: 12/24/2022] Open
Abstract
CD44 is an extracellular matrix receptor implicated in cancer progression. CD44 increases the invasibility of skin (SF) and endometrial stromal fibroblasts (ESF) by cancer and trophoblast cells. We reasoned that the evolution of CD44 expression can affect both, the fetal–maternal interaction through CD44 in ESF as well as vulnerability to malignant cancer through expression in SF. We studied the evolution of CD44 expression in mammalian SF and ESF and demonstrate that in the human lineage evolved higher CD44 expression. Isoform expression in cattle and human is very similar suggesting that differences in invasibility are not due to the nature of expressed isoforms. We then asked whether the concerted gene expression increase in both cell types is due to shared regulatory mechanisms or due to cell type-specific factors. Reporter gene experiments with cells and cis-regulatory elements from human and cattle show that the difference of CD44 expression is due to cis effects as well as cell type-specific trans effects. These results suggest that the concerted expression increase is likely due to selection acting on both cell types because the evolutionary change in cell type-specific factors requires selection on cell type-specific functions. This scenario implies that the malignancy enhancing effects of elevated CD44 expression in humans likely evolved as a side-effect of positive selection on a yet unidentified other function of CD44. A possible candidate is the anti-fibrotic effect of CD44 but there are no reliable data showing that humans and primates are less fibrotic than other mammals.
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Affiliation(s)
- Xinghong Ma
- Systems Biology Institute, Yale University , West Haven, CT 06516, USA
- Department of Ecology and Evolutionary Biology, Yale University , New Haven, CT 06520, USA
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Sciences, Northeast Agricultural University , Harbin, China
| | - Anasuya Dighe
- Systems Biology Institute, Yale University , West Haven, CT 06516, USA
- Department of Ecology and Evolutionary Biology, Yale University , New Haven, CT 06520, USA
| | - Jamie Maziarz
- Systems Biology Institute, Yale University , West Haven, CT 06516, USA
- Department of Ecology and Evolutionary Biology, Yale University , New Haven, CT 06520, USA
| | - Edwin Neumann
- Systems Biology Institute, Yale University , West Haven, CT 06516, USA
| | - Eric Erkenbrack
- Systems Biology Institute, Yale University , West Haven, CT 06516, USA
- Department of Ecology and Evolutionary Biology, Yale University , New Haven, CT 06520, USA
| | - Yuan-Yuan Hei
- Cancer Biology Institute, Yale University , West Haven, CT 06516, USA
- Department of Pharmacology, Yale Medical School , New Haven, CT 06510, USA
| | - Yansheng Liu
- Cancer Biology Institute, Yale University , West Haven, CT 06516, USA
- Department of Pharmacology, Yale Medical School , New Haven, CT 06510, USA
| | - Yasir Suhail
- Department of Biomedical Engineering, University of Connecticut Health Center , Farmington, CT 06030, USA
| | - Irene Pak
- Systems Biology Institute, Yale University , West Haven, CT 06516, USA
- Department of Ecology and Evolutionary Biology, Yale University , New Haven, CT 06520, USA
| | - Andre Levchenko
- Systems Biology Institute, Yale University , West Haven, CT 06516, USA
- Department of Biomedical Engineering, Yale University , New Haven, CT 06520, USA
| | - Günter P Wagner
- Systems Biology Institute, Yale University , West Haven, CT 06516, USA
- Department of Ecology and Evolutionary Biology, Yale University , New Haven, CT 06520, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale Medical School , New Haven, CT 06510, USA
- Department of Obstetrics and Gynecology, Wayne State University , Detroit, MI 48202, USA
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Abstract
Analogies between placentation, in particular the behavior of trophoblast cells, and cancer have been noted since the beginning of the twentieth century. To what degree these can be explained as a consequence of the evolution of placentation has been unclear. In this review, we conclude that many similarities between trophoblast and cancer cells are shared with other, phylogenetically older processes than placentation. The best candidates for cancer hallmarks that can be explained by the evolution of eutherian placenta are mechanisms of immune evasion. Another dimension of the maternal accommodation of the placenta with an impact on cancer malignancy is the evolution of endometrial invasibility. Species with lower degrees of placental invasion tend to have lower vulnerability to cancer malignancy. We finally identify several areas in which one could expect to see coevolutionary changes in placental and cancer biology but that, to our knowledge, have not been explored. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Günter P Wagner
- Systems Biology Institute, Yale University, West Haven, Connecticut, USA; , , .,Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University, New Haven, Connecticut, USA.,Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan, USA
| | - Kshitiz
- Department of Biomedical Engineering, University of Connecticut Health, Storrs, Connecticut, USA;
| | - Anasuya Dighe
- Systems Biology Institute, Yale University, West Haven, Connecticut, USA; , , .,Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
| | - Andre Levchenko
- Systems Biology Institute, Yale University, West Haven, Connecticut, USA; , , .,Department of Biomedical Engineering, Yale University, New Haven, Connecticut, USA
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Suhail Y, Afzal J. Evolved Resistance to Placental Invasion Secondarily Confers Increased Survival in Melanoma Patients. J Clin Med 2021; 10:jcm10040595. [PMID: 33562461 PMCID: PMC7915120 DOI: 10.3390/jcm10040595] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/29/2021] [Accepted: 02/02/2021] [Indexed: 12/25/2022] Open
Abstract
Mammals exhibit large differences in rates of cancer malignancy, even though the tumor formation rates may be similar. In placental mammals, rates of malignancy correlate with the extent of placental invasion. Our Evolved Levels of Invasibility (ELI) framework links these two phenomena identifying genes that potentially confer resistance in stromal fibroblasts to limit invasion, from trophoblasts in the endometrium, and from disseminating melanoma in the skin. Herein, using patient data from The Cancer Genome Atlas (TCGA), we report that these anti-invasive genes may be crucial in melanoma progression in human patients, and that their loss is correlated with increased cancer spread and lowered survival. Our results suggest that, surprisingly, these anti-invasive genes, which have lower expression in humans compared to species with non-invasive placentation, may potentially prevent stromal invasion, while a further reduction in their levels increases the malignancy and lethality of melanoma. Our work links evolution, comparative biology, and cancer progression across tissues, indicating new avenues for using evolutionary medicine to prognosticate and treat human cancers.
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Affiliation(s)
- Yasir Suhail
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA;
- Cancer Systems Biology (CaSB@Yale), Yale West Campus, West Haven, CT 06477, USA
- Center for Cell Analysis and Modeling, University of Connecticut Health, Farmington, CT 06032, USA
| | - Junaid Afzal
- Department of Cardiology, University of California, San Francisco, CA 94143, USA;
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