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Hughes EP, Syage AR, Mehrabad EM, Lane TE, Spike BT, Tantin D. OCA-B promotes autoimmune demyelination through control of stem-like CD4 + T cells. bioRxiv 2024:2023.11.29.569210. [PMID: 38076925 PMCID: PMC10705450 DOI: 10.1101/2023.11.29.569210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Stem-like T cell populations can selectively contribute to autoimmunity, but the activities that promote and sustain these populations are incompletely understood. Here, we show that T cell-intrinsic loss of the transcription cofactor OCA-B protects mice from experimental autoimmune encephalomyelitis (EAE) while preserving responses to CNS infection. In adoptive transfer EAE models driven by multiple antigen encounters, OCA-B deletion nearly eliminates CNS infiltration, proinflammatory cytokine production and clinical disease. OCA-B-expressing CD4 + T cells within the CNS of mice with EAE comprise a minority of the population but display a memory phenotype and preferentially confer disease. In a relapsing-remitting EAE model, OCA-B T cell deficiency specifically protects mice from relapse. During remission, OCA-B promotes the expression of Tcf7 , Slamf6 , and Sell in proliferating T cell populations. At relapse, OCA-B loss results in both the accumulation of an immunomodulatory CD4 + T cell population expressing Ccr9 and Bach2 , and the loss of pro-inflammatory gene expression from Th17 cells. These results identify OCA-B as a driver of pathogenic stem-like T cells.
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Balcioglu O, Gates BL, Freeman DW, Hagos BM, Mehrabad EM, Ayala-Talavera D, Spike BT. Mcam stabilizes luminal progenitor breast cancer phenotypes via Ck2 control and Src/Akt/Stat3 attenuation. bioRxiv 2024:2023.05.10.540211. [PMID: 38562809 PMCID: PMC10983870 DOI: 10.1101/2023.05.10.540211] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Breast cancers are categorized into subtypes with distinctive therapeutic vulnerabilities and prognoses based on their expression of clinically targetable receptors and gene expression patterns mimicking different cell types of the normal gland. Here, we tested the role of Mcam in breast cancer cell state control and tumorigenicity in a luminal progenitor-like murine tumor cell line (Py230) that exhibits lineage and tumor subtype plasticity. Mcam knockdown Py230 cells show augmented Stat3 and Pi3K/Akt activation associated with a lineage state switch away from a hormone-sensing/luminal progenitor state toward alveolar and basal cell related phenotypes that were refractory to growth inhibition by the anti-estrogen therapeutic, tamoxifen. Inhibition of Stat3, or the upstream activator Ck2, reversed these cell state changes. Mcam binds Ck2 and acts as a regulator of Ck2 substrate utilization across multiple mammary tumor cell lines. In Py230 cells this activity manifests as increased mesenchymal morphology, migration, and Src/Fak/Mapk/Paxillin adhesion complex signaling in vitro, in contrast to Mcam's reported roles in promoting mesenchymal phenotypes. In vivo, Mcam knockdown reduced tumor growth and take rate and inhibited cell state transition to Sox10+/neural crest like cells previously been associated with tumor aggressiveness. This contrasts with human luminal breast cancers where MCAM copy number loss is highly coupled to Cyclin D amplification, increased proliferation, and the more aggressive Luminal B subtype. Together these data indicate a critical role for Mcam and its regulation of Ck2 in control of breast cancer cell state plasticity with implications for progression, evasion of targeted therapies and combination therapy design.
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Affiliation(s)
- Ozlen Balcioglu
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112 USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112 USA
| | - Brooke L. Gates
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112 USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112 USA
| | - David W. Freeman
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112 USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112 USA
| | - Berhane M. Hagos
- Current Address: Emergency Medicine, Oregon Health & Science University School of Medicine, Portland, OR 97239 USA
| | | | - David Ayala-Talavera
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112 USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112 USA
| | - Benjamin T. Spike
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112 USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112 USA
- School of Computing, University of Utah, Salt Lake City, UT 84112 USA
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Cottone G, Spike BT, Mehrabad EM, Khan SA, Clare S. Abstract P3-09-16: Validating alternative splicing events between bulk and scRNA sequencing data: A bioinformatic approach. Cancer Res 2022. [DOI: 10.1158/1538-7445.sabcs21-p3-09-16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: As bulk and single-cell RNA (scRNA) sequencing studies and data continue to accrue to publicly accessible databases, bioinformatic tools continue being developed to analyze these datasets. The resulting pipelines often focus on either bulk or scRNA sequencing but rarely both. scRNA sequencing allows for in-depth characterization of transcription level events in distinct cell populations while bulk data offers a more global view, and for now, is more widely available in databases. Alternative splicing events in particular have been underexplored in a single-cell genomic architecture. The purpose of this study was to develop a bioinformatic pipeline to employ both bulk and single-cell mammary datasets to identify and validate alternative splicing events.Methods: Bulk fastq’s were utilized to identify AS events in luminal progenitor (LP) and mouse mammary stem cell (MSC) lineages in ovariectomized FVB mice that had been randomized into three treatment groups (SHAM [C], estradiol + progesterone [EP], EP + the selective progesterone receptor inhibitor telapristone acetate, TPA [EPT]). scRNA sequencing data from (Bach et al., 2017) was downloaded from the Gene Expression Omnibus (GEO) and utilized for validation of the AS events identified in the bulk data. To separate the data by progesterone level, the scRNA data was parsed into nulliparous, gestational, lactational, and post-involution groups. Further, to determine cell lineage level effects, the data was parsed into luminal and basal compartments using krt18 and krt5 expression. To accomplish the overall comparison between bulk and scRNA sequencing data, we developed a pipeline that would process and parse the scRNA data, identify the alternative splicing in bulk sequencing using rMATS and in the scRNA data using Outrigger (part of the Expedition suite). The resulting data from rMATS [bulk] LP/MSC: CvEP, CvEPT, & EPvEPT were filtered for events meeting statistical significance (p-value < 0.05, FDR < 0.01). After filtering, the events from each treatment comparison were then filtered so only events unique to LP or MSC CvEP, respectively, remain. The remaining significant and unique AS events are then compared to the Krt18-high and Krt5-high Outrigger results from each development stage based on genomic event coordinates (with a buffer +/- 20 base pairs).Results: 12 alternative splicing (AS) events were identified to be shared between the bulk and scRNA sequencing data in the context of increased progesterone exposure (EP and gestational, respectively) as well as cell lineage (LP and luminal respectively). Among the genes identified as having been alternatively spiced with an exact nucleotide match for the splice were Eif4a2, Pik3c2a, Brd4, Cdh1, and Enah. Conclusions: Alternative splicing events can be identified and validated between genomic sequencing methods, specifically bulk and single-cell RNA seq. We hypothesize that as scRNA-seq becomes more developed and quantification errors caused by short-read lengths fixed by full length scRNA seq methods currently in development, comparing data between single-cell and bulk may be made easier. However, we have shown that, when orthogonal methods for validation may not be feasible, events as specific as alternative splices can be validated using publicly available data and in-silico methods.
Citation Format: Gannon Cottone, Benjamin T Spike, Elnaz Mirzaei Mehrabad, Seema A Khan, Susan Clare. Validating alternative splicing events between bulk and scRNA sequencing data: A bioinformatic approach [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P3-09-16.
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Affiliation(s)
- Gannon Cottone
- Department of Surgery, Lurie Cancer Center, Northwestern University, Feinberg School of Medicine, Chicago, IL
| | - Benjamin T Spike
- Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, UT
| | | | - Seema A Khan
- Department of Surgery, Lurie Cancer Center, Northwestern University, Feinberg School of Medicine, Chicago, IL
| | - Susan Clare
- Department of Surgery, Lurie Cancer Center, Northwestern University, Feinberg School of Medicine, Chicago, IL
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Ranjan M, Lee O, Cottone G, Mirzaei Mehrabad E, Spike BT, Zeng Z, Yadav S, Chatterton R, Kim JJ, Clare SE, Khan SA. Progesterone receptor antagonists reverse stem cell expansion and the paracrine effectors of progesterone action in the mouse mammary gland. Breast Cancer Res 2021; 23:78. [PMID: 34344445 PMCID: PMC8330021 DOI: 10.1186/s13058-021-01455-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 10/07/2019] [Accepted: 07/09/2021] [Indexed: 12/13/2022] Open
Abstract
Background The ovarian hormones estrogen and progesterone (EP) are implicated in breast cancer causation. A specific consequence of progesterone exposure is the expansion of the mammary stem cell (MSC) and luminal progenitor (LP) compartments. We hypothesized that this effect, and its molecular facilitators, could be abrogated by progesterone receptor (PR) antagonists administered in a mouse model. Methods Ovariectomized FVB mice were randomized to 14 days of treatment: sham, EP, EP + telapristone (EP + TPA), EP + mifepristone (EP + MFP). Mice were then sacrificed, mammary glands harvested, and mammary epithelial cell lineages separated by flow cytometry using cell surface markers. RNA from each lineage was sequenced and differential gene expression was analyzed using DESeq. Quantitative PCR was performed to confirm the candidate genes discovered in RNA seq. ANOVA with Tukey post hoc analysis was performed to compare relative expression. Alternative splicing events were examined using the rMATs multivariate analysis tool. Results Significant increases in the MSC and luminal mature (LM) cell fractions were observed following EP treatment compared to control (p < 0.01 and p < 0.05, respectively), whereas the LP fraction was significantly reduced (p < 0.05). These hormone-induced effects were reversed upon exposure to TPA and MFP (p < 0.01 for both). Gene Ontology analysis of RNA-sequencing data showed EP-induced enrichment of several pathways, with the largest effect on Wnt signaling in MSC, significantly repressed by PR inhibitors. In LP cells, significant induction of Wnt4 and Rankl, and Wnt pathway intermediates Lrp2 and Axin2 (confirmed by qRTPCR) were reversed by TPA and MFP (p < 0.0001). Downstream signaling intermediates of these pathways (Lrp5, Mmp7) showed similar effects. Expression of markers of epithelial-mesenchymal transition (Cdh1, Cdh3) and the induction of EMT regulators (Zeb1, Zeb2, Gli3, Snai1, and Ptch2) were significantly responsive to progesterone. EP treatment was associated with large-scale alternative splicing events, with an enrichment of motifs associated with Srsf, Esrp, and Rbfox families. Exon skipping was observed in Cdh1, Enah, and Brd4. Conclusions PR inhibition reverses known tumorigenic pathways in the mammary gland and suppresses a previously unknown effect of progesterone on RNA splicing events. In total, our results strengthen the case for reconsideration of PR inhibitors for breast cancer prevention. Supplementary Information The online version contains supplementary material available at 10.1186/s13058-021-01455-2.
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Affiliation(s)
- Manish Ranjan
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Oukseub Lee
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Gannon Cottone
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | | | - Benjamin T Spike
- Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, UT, 84112, USA
| | - Zexian Zeng
- Division of Health and Biomedical Informatics, Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Shivangi Yadav
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Robert Chatterton
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, 60611, USA
| | - J Julie Kim
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, 60611, USA
| | - Susan E Clare
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
| | - Seema A Khan
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA. .,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, 60611, USA.
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Zewdu R, Mehrabad EM, Ingram K, Fang P, Gillis KL, Camolotto SA, Orstad G, Jones A, Mendoza MC, Spike BT, Snyder EL. An NKX2-1/ERK/WNT feedback loop modulates gastric identity and response to targeted therapy in lung adenocarcinoma. eLife 2021; 10:e66788. [PMID: 33821796 PMCID: PMC8102067 DOI: 10.7554/elife.66788] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/05/2021] [Indexed: 12/13/2022] Open
Abstract
Cancer cells undergo lineage switching during natural progression and in response to therapy. NKX2-1 loss in human and murine lung adenocarcinoma leads to invasive mucinous adenocarcinoma (IMA), a lung cancer subtype that exhibits gastric differentiation and harbors a distinct spectrum of driver oncogenes. In murine BRAFV600E-driven lung adenocarcinoma, NKX2-1 is required for early tumorigenesis, but dispensable for established tumor growth. NKX2-1-deficient, BRAFV600E-driven tumors resemble human IMA and exhibit a distinct response to BRAF/MEK inhibitors. Whereas BRAF/MEK inhibitors drive NKX2-1-positive tumor cells into quiescence, NKX2-1-negative cells fail to exit the cell cycle after the same therapy. BRAF/MEK inhibitors induce cell identity switching in NKX2-1-negative lung tumors within the gastric lineage, which is driven in part by WNT signaling and FoxA1/2. These data elucidate a complex, reciprocal relationship between lineage specifiers and oncogenic signaling pathways in the regulation of lung adenocarcinoma identity that is likely to impact lineage-specific therapeutic strategies.
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Affiliation(s)
- Rediet Zewdu
- Huntsman Cancer InstituteSalt Lake CityUnited States
- Department of Pathology, University of UtahSalt Lake CityUnited States
| | - Elnaz Mirzaei Mehrabad
- Huntsman Cancer InstituteSalt Lake CityUnited States
- School of Computing, University of UtahSalt Lake CityUnited States
| | - Kelley Ingram
- Huntsman Cancer InstituteSalt Lake CityUnited States
- Department of Oncological Sciences, University of UtahSalt Lake CityUnited States
| | - Pengshu Fang
- Huntsman Cancer InstituteSalt Lake CityUnited States
- Department of Oncological Sciences, University of UtahSalt Lake CityUnited States
| | - Katherine L Gillis
- Huntsman Cancer InstituteSalt Lake CityUnited States
- Department of Oncological Sciences, University of UtahSalt Lake CityUnited States
| | - Soledad A Camolotto
- Huntsman Cancer InstituteSalt Lake CityUnited States
- Department of Pathology, University of UtahSalt Lake CityUnited States
| | - Grace Orstad
- Huntsman Cancer InstituteSalt Lake CityUnited States
- Department of Oncological Sciences, University of UtahSalt Lake CityUnited States
| | - Alex Jones
- Huntsman Cancer InstituteSalt Lake CityUnited States
- Department of Pathology, University of UtahSalt Lake CityUnited States
| | - Michelle C Mendoza
- Huntsman Cancer InstituteSalt Lake CityUnited States
- Department of Oncological Sciences, University of UtahSalt Lake CityUnited States
| | - Benjamin T Spike
- Huntsman Cancer InstituteSalt Lake CityUnited States
- Department of Oncological Sciences, University of UtahSalt Lake CityUnited States
| | - Eric L Snyder
- Huntsman Cancer InstituteSalt Lake CityUnited States
- Department of Pathology, University of UtahSalt Lake CityUnited States
- Department of Oncological Sciences, University of UtahSalt Lake CityUnited States
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Balcioglu O, Heinz RE, Freeman DW, Gates BL, Hagos BM, Booker E, Mirzaei Mehrabad E, Diesen HT, Bhakta K, Ranganathan S, Kachi M, Leblanc M, Gray PC, Spike BT. CRIPTO antagonist ALK4 L75A-Fc inhibits breast cancer cell plasticity and adaptation to stress. Breast Cancer Res 2020; 22:125. [PMID: 33187540 PMCID: PMC7664111 DOI: 10.1186/s13058-020-01361-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 10/20/2020] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND CRIPTO is a multi-functional signaling protein that promotes stemness and oncogenesis. We previously developed a CRIPTO antagonist, ALK4L75A-Fc, and showed that it causes loss of the stem cell phenotype in normal mammary epithelia suggesting it may similarly inhibit CRIPTO-dependent plasticity in breast cancer cells. METHODS We focused on two triple negative breast cancer cell lines (MDA-MB-231 and MDA-MB-468) to measure the effects of ALK4L75A-Fc on cancer cell behavior under nutrient deprivation and endoplasmic reticulum stress. We characterized the proliferation and migration of these cells in vitro using time-lapse microscopy and characterized stress-dependent changes in the levels and distribution of CRIPTO signaling mediators and cancer stem cell markers. We also assessed the effects of ALK4L75A-Fc on proliferation, EMT, and stem cell markers in vivo as well as on tumor growth and metastasis using inducible lentiviral delivery or systemic administration of purified ALK4L75A-Fc, which represents a candidate therapeutic approach. RESULTS ALK4L75A-Fc inhibited adaptive responses of breast cancer cells under conditions of nutrient and ER stress and reduced their proliferation, migration, clonogenicity, and expression of EMT and cancer stem cell markers. ALK4L75A-Fc also inhibited proliferation of human breast cancer cells in stressed tumor microenvironments in xenografts and reduced both primary tumor size and metastatic burden. CONCLUSIONS Cancer cell adaptation to stresses such as nutrient deprivation, hypoxia, and chemotherapy can critically contribute to dormancy, metastasis, therapy resistance, and recurrence. Identifying mechanisms that govern cellular adaptation, plasticity, and the emergence of stem-like cancer cells may be key to effective anticancer therapies. Results presented here indicate that targeting CRIPTO with ALK4L75A-Fc may have potential as such a therapy since it inhibits breast cancer cell adaptation to microenvironmental challenges and associated stem-like and EMT phenotypes.
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Affiliation(s)
- Ozlen Balcioglu
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112, USA
| | - Richard E Heinz
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112, USA
| | - David W Freeman
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, 84112, USA
| | - Brooke L Gates
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, 84112, USA
| | - Berhane M Hagos
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112, USA
| | - Evan Booker
- Peptide Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | | | - Hyrum T Diesen
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, 84112, USA
| | - Kishan Bhakta
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, 84112, USA
| | - Supraja Ranganathan
- Department of Biochemistry, University of Utah, Salt Lake City, UT, 84112, USA
| | - Masami Kachi
- Peptide Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Mathias Leblanc
- Peptide Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Peter C Gray
- Peptide Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Present Address: Biotheranostics Inc., San Diego, CA, 92121, USA
| | - Benjamin T Spike
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112, USA.
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, 84112, USA.
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Wahl GM, Ma Z, Chung C, Dravis C, Spike BT, Giraddi RT, Balcioglu O, Fan C, Hagos B, Heinz R, Herrera-Valdez J, Hou X, Hwang J, Lasken R, Luna G, Lytle NE, Mehrabad EM, Novotny M, Perou CM, Poirion O, Preissl S, Ren B, Reya T, Trejo CL, Varley KT. Abstract ES10-2: Understanding breast cancer using a developmental perspective. Cancer Res 2020. [DOI: 10.1158/1538-7445.sabcs19-es10-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Parallels among embryonic development, stem cells, and cancer have long been recognized. We identified, isolated, and characterized stem cells that first become committed to a mammary fate during embryogenesis; we refer to these cells as fetal mammary stem cells (fMaSCs). Lineage tracing, in vitro sphere formation, and in vivo transplantation studies by our group and many others all confirm that cells in the embryo are the bipotent progenitors of the mammary gland. There is debate, however, on whether such bipotent cells persist into the adult, or whether the luminal and basal lineages are maintained by unipotent progenitors. To gain insight into the relationships between fMaSCs and breast cancer, and to investigate their potential persistence in the adult, we have applied bulk and single cell RNA-sequencing (sc-RNA-seq) and single nucleus ATAC-sequencing (snATAC-seq) throughout mammary development. The results to be discussed demonstrate that fMaSC transcriptomes are heterogeneous, but all share co-expression of genes associated with luminal and basal cell fates. This fits a model in which the bipotent state is created by a balance of lineage specifiers. We also find that the fMaSC transcriptome is highly enriched in basal-like human breast cancers and identify potential embryonic pathways that correlate with poor prognosis. We used a variety of computational tools to infer the gene expression programs that ensue when fMaSCs commit to luminal and basal states. The data from scRNA-seq and snATAC-seq demonstrate that the transitions are gradual, not precipitous, and that luminal and basal cells exhibit significant transcriptomic and epigenetic heterogeneity. This challenges the notion that the mammary gland consists of discrete cell types defined by rigid transcriptomic parameters, and reveals a potential for intrinsic phenotypic plasticity of normal mammary cells. Using the combined databases, we identified Sox10 as a significantly differentially expressed cell state regulator. We show that tumors are heterogeneous with regard to Sox10 expression, and that locally invasive cells tend to express high Sox10 levels. Elevated Sox10 correlates with acquisition of a neural-crest like, EMT-related state. Implications for interception of metastasis by targeting neural crest-like cells will be discussed. Finally, we have generated a web resource that is available to the scientific community to enable the transcription and epigenetic characteristics of any gene of interest to be tracked through mammary development (https://wahl-labsalk.shinyapps.io/Mammary_snATAC/).
Citation Format: GM Wahl, Z Ma, C Chung, C Dravis, BT Spike, RR Giraddi, O Balcioglu, C Fan, B Hagos, R Heinz, Herrera-Valdez J, X Hou, J Hwang, R Lasken, G Luna, NE Lytle, EM Mehrabad, M Novotny, CM Perou, O Poirion, S Preissl, B Ren, T Reya, CL Trejo, KT Varley. Understanding breast cancer using a developmental perspective [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr ES10-2.
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Affiliation(s)
- GM Wahl
- 1Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA
| | - Z Ma
- 1Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA
| | - C Chung
- 2Gene Expression Laboratory, Salk Institute for Biological Studies; Current address: Pfizer Inc., San Diego, CA 92121, La Jolla, CA
| | - C Dravis
- 1Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA
| | - BT Spike
- 3Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, UT
| | - RT Giraddi
- 2Gene Expression Laboratory, Salk Institute for Biological Studies; Current address: Pfizer Inc., San Diego, CA 92121, La Jolla, CA
| | - O Balcioglu
- 3Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, UT
| | - C Fan
- 4Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - B Hagos
- 3Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, UT
| | - R Heinz
- 5Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake Sity, UT
| | - J Herrera-Valdez
- 1Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA
| | - X Hou
- 6Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, School of Medicine, La Jolla, CA
| | - J Hwang
- 3Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, UT
| | - R Lasken
- 7J. Craig Venter Institute, La Jolla, CA
| | - G Luna
- 1Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA
| | - NE Lytle
- 1Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA
| | - EM Mehrabad
- 3Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, UT
| | - M Novotny
- 7J. Craig Venter Institute, La Jolla, CA
| | - CM Perou
- 4Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - O Poirion
- 6Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, School of Medicine, La Jolla, CA
| | - S Preissl
- 6Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, School of Medicine, La Jolla, CA
| | - B Ren
- 8Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, School of Medicine; Ludwig Institute for Cancer Research, La Jolla, CA
| | - T Reya
- 9Sanford Consortium for Regenerative Medicine; Departments of Pharmacology and Medicine, Moores Cancer Center, University of California San Diego School of Medicine, La Jolla, CA
| | - CL Trejo
- 1Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA
| | - KT Varley
- 3Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, UT
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Giraddi RR, Chung CY, Heinz RE, Balcioglu O, Novotny M, Trejo CL, Dravis C, Hagos BM, Mehrabad EM, Rodewald LW, Hwang JY, Fan C, Lasken R, Varley KE, Perou CM, Wahl GM, Spike BT. Single-Cell Transcriptomes Distinguish Stem Cell State Changes and Lineage Specification Programs in Early Mammary Gland Development. Cell Rep 2020; 24:1653-1666.e7. [PMID: 30089273 PMCID: PMC6301014 DOI: 10.1016/j.celrep.2018.07.025] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [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: 07/11/2017] [Revised: 05/29/2018] [Accepted: 07/06/2018] [Indexed: 01/23/2023] Open
Abstract
The mammary gland consists of cells with gene expression patterns
reflecting their cellular origins, function, and spatiotemporal context.
However, knowledge of developmental kinetics and mechanisms of lineage
specification is lacking. We address this significant knowledge gap by
generating a single-cell transcriptome atlas encompassing embryonic, postnatal,
and adult mouse mammary development. From these data, we map the chronology of
transcriptionally and epigenetically distinct cell states and distinguish fetal
mammary stem cells (fMaSCs) from their precursors and progeny. fMaSCs show
balanced co-expression of factors associated with discrete adult lineages and a
metabolic gene signature that subsides during maturation but reemerges in some
human breast cancers and metastases. These data provide a useful resource for
illuminating mammary cell heterogeneity, the kinetics of differentiation, and
developmental correlates of tumorigenesis. Single-cell RNA sequencing of developing mouse mammary epithelia reveals
the timing of lineage specification. Giraddi et al. find that fetal mammary stem
cells co-express factors that define distinct lineages in their progeny and bear
functionally relevant metabolic program signatures that change with
differentiation and are resurrected in human breast cancers and metastases.
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Affiliation(s)
- Rajshekhar R Giraddi
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Chi-Yeh Chung
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Richard E Heinz
- Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Ozlen Balcioglu
- Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Mark Novotny
- J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Christy L Trejo
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Christopher Dravis
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Berhane M Hagos
- Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Elnaz Mirzaei Mehrabad
- Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Luo Wei Rodewald
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jae Y Hwang
- Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Cheng Fan
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Roger Lasken
- J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Katherine E Varley
- Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Charles M Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Geoffrey M Wahl
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
| | - Benjamin T Spike
- Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA.
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Mirzaei Mehrabad E, Hassanzadeh R, Eslahchi C. PMLPR: A novel method for predicting subcellular localization based on recommender systems. Sci Rep 2018; 8:12006. [PMID: 30104743 PMCID: PMC6089892 DOI: 10.1038/s41598-018-30394-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [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: 11/25/2016] [Accepted: 07/30/2018] [Indexed: 12/16/2022] Open
Abstract
The importance of protein subcellular localization problem is due to the importance of protein's functions in different cell parts. Moreover, prediction of subcellular locations helps to identify the potential molecular targets for drugs and has an important role in genome annotation. Most of the existing prediction methods assign only one location for each protein. But, since some proteins move between different subcellular locations, they can have multiple locations. In recent years, some multiple location predictors have been introduced. However, their performances are not accurate enough and there is much room for improvement. In this paper, we introduced a method, PMLPR, to predict locations for a protein. PMLPR predicts a list of locations for each protein based on recommender systems and it can properly overcome the multiple location prediction problem. For evaluating the performance of PMLPR, we considered six datasets RAT, FLY, HUMAN, Du et al., DBMLoc and Höglund. The performance of this algorithm is compared with six state-of-the-art algorithms, YLoc, WOLF-PSORT, prediction channel, MDLoc, Du et al. and MultiLoc2-HighRes. The results indicate that our proposed method is significantly superior on RAT and Fly proteins, and decent on HUMAN proteins. Moreover, on the datasets introduced by Du et al., DBMLoc and Höglund, PMLPR has comparable results. For the case study, we applied the algorithms on 8 proteins which are important in cancer research. The results of comparison with other methods indicate the efficiency of PMLPR.
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Affiliation(s)
- Elnaz Mirzaei Mehrabad
- Department of Computer Science, Faculty of Mathematical Sciences, Shahid Beheshti University, Tehran, Iran
| | - Reza Hassanzadeh
- Department of Engineering Sciences, Faculty of Advanced Technologies, University of Mohaghegh Ardabili, Namin, Iran
- Department of Bioinformatics, Faculty of Computer Engineering and Information Technology, Sabalan University of Advanced Technologies (SUAT), Namin, Iran
| | - Changiz Eslahchi
- Department of Computer Science, Faculty of Mathematical Sciences, Shahid Beheshti University, Tehran, Iran.
- School of Biological Science, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran.
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