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Shirokawa Y. Evolutionary stability of developmental commitment. Biosystems 2024; 244:105309. [PMID: 39151881 DOI: 10.1016/j.biosystems.2024.105309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 08/12/2024] [Accepted: 08/13/2024] [Indexed: 08/19/2024]
Abstract
Evolution of unicellular to multicellular organisms must resolve conflicts in reproductive interests between individual cells and the group. The social amoeba Dictyostelium discoideum is a soil-living eukaryote with facultative sociality. While cells grow in the presence of nutrients, cells aggregate under starvation to form fruiting bodies containing spores and altruistic stalk cells. Once cells socially committed, they complete formation of fruiting bodies, even if a new source of nutrients becomes available. The persistence of this social commitment raises questions as it inhibits individual cells from swiftly returning to solitary growth. I hypothesize that traits enabling premature de-commitment are hindered from being selected. Recent work has revealed outcomes of the premature de-commitment through forced refeeding; The de-committed cells take an altruistic prestalk-like position due to their reduced cohesiveness through interactions with socially committed cells. I constructed an evolutionary model assuming their division of labor. The results revealed a valley in the fitness landscape that prevented invasion of de-committing mutants, indicating evolutionary stability of the social commitment. The findings provide a general scheme that maintains multicellularity by evolving a specific division of labor, in which less cohesive individuals become altruists.
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Affiliation(s)
- Yuka Shirokawa
- Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan.
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2
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Shirokawa Y, Shimada M, Shimada N, Sawai S. Prestalk-like positioning of de-differentiated cells in the social amoeba Dictyostelium discoideum. Sci Rep 2024; 14:7677. [PMID: 38561423 PMCID: PMC10985001 DOI: 10.1038/s41598-024-58277-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 03/27/2024] [Indexed: 04/04/2024] Open
Abstract
The social amoeba Dictyostelium discoideum switches between solitary growth and social fruitification depending on nutrient availability. Under starvation, cells aggregate and form fruiting bodies consisting of spores and altruistic stalk cells. Once cells socially committed, they complete fruitification, even if a new source of nutrients becomes available. This social commitment is puzzling because it hinders individual cells from resuming solitary growth quickly. One idea posits that traits that facilitate premature de-commitment are hindered from being selected. We studied outcomes of the premature de-commitment through forced refeeding. Our results show that when refed cells interacted with non-refed cells, some of them became solitary, whereas a fraction was redirected to the altruistic stalk, regardless of their original fate. The refed cells exhibited reduced cohesiveness and were sorted out during morphogenesis. Our findings provide an insight into a division of labor of the social amoeba, in which less cohesive individuals become altruists.
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Affiliation(s)
- Yuka Shirokawa
- Graduate School of Arts and Sciences, University of Tokyo, Tokyo, 153-8902, Japan.
| | - Masakazu Shimada
- Graduate School of Arts and Sciences, University of Tokyo, Tokyo, 153-8902, Japan
| | - Nao Shimada
- Graduate School of Arts and Sciences, University of Tokyo, Tokyo, 153-8902, Japan
| | - Satoshi Sawai
- Graduate School of Arts and Sciences, University of Tokyo, Tokyo, 153-8902, Japan
- Research Center for Complex Systems Biology, Universal Biology Institute, University of Tokyo, Tokyo, 153-8902, Japan
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3
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Katoh-Kurasawa M, Hrovatin K, Hirose S, Webb A, Ho HI, Zupan B, Shaulsky G. Transcriptional milestones in Dictyostelium development. Genome Res 2021; 31:1498-1511. [PMID: 34183452 PMCID: PMC8327917 DOI: 10.1101/gr.275496.121] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/23/2021] [Indexed: 02/02/2023]
Abstract
Dictyostelium development begins with single-cell starvation and ends with multicellular fruiting bodies. Developmental morphogenesis is accompanied by sweeping transcriptional changes, encompassing nearly half of the 13,000 genes in the genome. We performed time-series RNA-sequencing analyses of the wild type and 20 mutants to explore the relationships between transcription and morphogenesis. These strains show developmental arrest at different stages, accelerated development, or atypical morphologies. Considering eight major morphological transitions, we identified 1371 milestone genes whose expression changes sharply between consecutive transitions. We also identified 1099 genes as members of 21 regulons, which are groups of genes that remain coordinately regulated despite the genetic, temporal, and developmental perturbations. The gene annotations in these groups validate known transitions and reveal new developmental events. For example, DNA replication genes are tightly coregulated with cell division genes, so they are expressed in mid-development although chromosomal DNA is not replicated. Our data set includes 486 transcriptional profiles that can help identify new relationships between transcription and development and improve gene annotations. We show its utility by showing that cycles of aggregation and disaggregation in allorecognition-defective mutants involve dedifferentiation. We also show sensitivity to genetic and developmental conditions in two commonly used actin genes, act6 and act15, and robustness of the coaA gene. Finally, we propose that gpdA is a better mRNA quantitation standard because it is less sensitive to external conditions than commonly used standards. The data set is available for democratized exploration through the web application dictyExpress and the data mining environment Orange.
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Affiliation(s)
- Mariko Katoh-Kurasawa
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Karin Hrovatin
- Faculty of Computer and Information Science, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Shigenori Hirose
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Amanda Webb
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Hsing-I Ho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Blaž Zupan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Faculty of Computer and Information Science, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Gad Shaulsky
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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4
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Boler AK, Akhtar S, Bandyopadhyay A, Roy S. A report of two cases of dedifferentiated endometrioid carcinoma: A newly described underrecognized tumor of poor prognosis. INDIAN J PATHOL MICR 2020; 63:S91-S93. [PMID: 32108637 DOI: 10.4103/ijpm.ijpm_23_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Dedifferentiated endometrioid carcinoma or dedifferentiated endometrioid adenocarcinoma (DEAC) is defined by the presence of undifferentiated carcinoma with endometrioid carcinoma. Undifferentiated component can be misinterpreted as solid component of high-grade endometrioid carcinoma or sarcomatous component of malignant mixed mullerian tumor. We present two cases of DEAC. Two postmenopausal women underwent hysterectomy for vaginal bleeding. Microscopically, sections from the endometrial tumors showed a biphasic growth consisting of an undifferentiated component and a glandular component with sharp transition between the two components. The undifferentiated component showed focal positivity for cytokeratin and vimentin, while glandular component was diffusely positive for cytokeratin and negative for vimentin expression.
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Affiliation(s)
- Anup K Boler
- Department of Pathology, Burdwan Medical College and Hospital, Burdwan, West Bengal, India
| | - Sana Akhtar
- Department of Pathology, Burdwan Medical College and Hospital, Burdwan, West Bengal, India
| | - Arghya Bandyopadhyay
- Department of Pathology, Burdwan Medical College and Hospital, Burdwan, West Bengal, India
| | - Shreosee Roy
- Department of Pathology, Burdwan Medical College and Hospital, Burdwan, West Bengal, India
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5
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Nichols JME, Antolović V, Reich JD, Brameyer S, Paschke P, Chubb JR. Cell and molecular transitions during efficient dedifferentiation. eLife 2020; 9:e55435. [PMID: 32255425 PMCID: PMC7190356 DOI: 10.7554/elife.55435] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/06/2020] [Indexed: 01/16/2023] Open
Abstract
Dedifferentiation is a critical response to tissue damage, yet is not well understood, even at a basic phenomenological level. Developing Dictyostelium cells undergo highly efficient dedifferentiation, completed by most cells within 24 hr. We use this rapid response to investigate the control features of dedifferentiation, combining single cell imaging with high temporal resolution transcriptomics. Gene expression during dedifferentiation was predominantly a simple reversal of developmental changes, with expression changes not following this pattern primarily associated with ribosome biogenesis. Mutation of genes induced early in dedifferentiation did not strongly perturb the reversal of development. This apparent robustness may arise from adaptability of cells: the relative temporal ordering of cell and molecular events was not absolute, suggesting cell programmes reach the same end using different mechanisms. In addition, although cells start from different fates, they rapidly converged on a single expression trajectory. These regulatory features may contribute to dedifferentiation responses during regeneration.
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Affiliation(s)
- John ME Nichols
- MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Vlatka Antolović
- MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Jacob D Reich
- MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | | | - Peggy Paschke
- CRUK Beatson Institute, Garscube Estate, Switchback Road, BearsdenGlasgowUnited Kingdom
| | - Jonathan R Chubb
- MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
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6
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Hamamoto Y, Harada H, Suzuki M, Fujii T, Nakatsuka SI. Salivary Duct Carcinoma of the Parotid Gland Originating from an Epithelial-Myoepithelial Carcinoma: Report of a Rare Case. Head Neck Pathol 2019; 14:283-289. [PMID: 30937832 PMCID: PMC7021872 DOI: 10.1007/s12105-019-01034-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/20/2019] [Indexed: 11/29/2022]
Abstract
Salivary duct carcinoma (SDC) is a high-grade carcinoma with poor prognosis, especially among various salivary carcinomas. In this study, we report a rare case of SDC of the parotid gland originating from an epithelial-myoepithelial carcinoma (EMC). A 71-year-old Japanese man presented with swelling of the right parotid region and a right facial nerve paralysis for 10 months. He underwent extended total parotidectomy and chemoradiotherapy after the surgery. Histologically, a major part of the tumor was an androgen receptor (AR)-positive, human epidermal growth factor receptor 2 (HER2)-positive, gross cystic disease fluid protein-15 (GCDFP-15)-positive SDC, with a focus of a typical EMC component at the periphery of the lesion. In the transitional area of the two components, inner ductal cells of double-layered ducts showed similar morphology and immunophenotype to SDC. These findings suggest that SDC originated from the inner ductal cells of EMC. Because the tumor included an EMC as a low-grade carcinoma and an SDC as a high-grade carcinoma, we can consider our case as a dedifferentiated carcinoma as well as a hybrid tumor.
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Affiliation(s)
- Yuichiro Hamamoto
- Department of Diagnostic Pathology and Cytology, Osaka International Cancer Institute, 3-1-69 Otemae, Chuo-ku, Osaka, Osaka 541-8567 Japan
| | - Hiroshi Harada
- Department of Diagnostic Pathology and Cytology, Osaka International Cancer Institute, 3-1-69 Otemae, Chuo-ku, Osaka, Osaka 541-8567 Japan ,Department of Diagnostic Pathology, Seichokai Fuchu Hospital, 1-10-17, Hiko-Town, Izumi-City, Osaka 594-0076 Japan
| | - Motoyuki Suzuki
- Department of Otorhinolaryngology-Head and Neck Surgery, Osaka University Graduate School of Medicine, 2-2, Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Takashi Fujii
- Department of Head and Neck Surgery, Osaka International Cancer Institute, 3-1-69 Otemae, Chuo-ku, Osaka, Osaka 541-8567 Japan
| | - Shin-ichi Nakatsuka
- Department of Diagnostic Pathology and Cytology, Osaka International Cancer Institute, 3-1-69 Otemae, Chuo-ku, Osaka, Osaka 541-8567 Japan
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Miyazaki M, Aoki M, Koga K, Hamasaki M, Sugiyama Y, Midorikawa K, Hamatake D, Masaki M, Takamatsu Y, Iwasaki A, Sakata T, Nagao T, Nabeshima K. Adenoid cystic carcinoma with high-grade transformation forming spindle cell component of the submandibular gland. Auris Nasus Larynx 2019; 46:934-939. [PMID: 30777403 DOI: 10.1016/j.anl.2019.01.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 01/22/2019] [Accepted: 01/31/2019] [Indexed: 10/27/2022]
Abstract
Adenoid cystic carcinoma (AdCC) with high-grade transformation (AdCC-HGT) is rare, and AdCC-HGT with spindle cell component is particularly rare. The patient was a 65-year-old man with a 5 cm sized swelling of the right submandibular gland. Submandibular sialoadenectomy was performed. Histopathological findings mainly showed conventional AdCC, and minorly showed two other components: (1) the pleomorphic component, a proliferation of atypical pleomorphic epithelial cells forming solid or small clusters and accompanied by necrosis; (2) the spindle cell component, containing atypical spindle cells invading the stroma. Postoperative chemoradiotherapy was performed. Multiple right lung nodular lesions were found on the contrast-enhanced chest CT one month after the surgery. Thoracoscopic pulmonary resection was performed. The lung tumors exhibited a proliferation of atypical spindle cells, accompanied by necrosis. We considered that the spindle cell component of the AdCC-HGT of the submandibular gland developed lung metastases. The patient died seven months after submandibular sialoadenectomy due to respiratory failure. Although rare, our case highlights the importance of recognising spindle cell components in conventional AdCC; even if the area is small, these high-grade transformation areas can metastasise and become prognostic factors.
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Affiliation(s)
- Masaru Miyazaki
- Department of Pathology, Fukuoka University, School of Medicine, Japan; Department of Otorhinolaryngology and Head & Neck Surgery, Fukuoka University, School of Medicine, Japan
| | - Mikiko Aoki
- Department of Pathology, Fukuoka University, School of Medicine, Japan.
| | - Kaori Koga
- Department of Pathology, Fukuoka University, School of Medicine, Japan
| | - Makoto Hamasaki
- Department of Pathology, Fukuoka University, School of Medicine, Japan
| | - Yoshikazu Sugiyama
- Department of Otorhinolaryngology and Head & Neck Surgery, Fukuoka University, School of Medicine, Japan
| | - Kensuke Midorikawa
- Department of Thoracic, Breast, Endocrine, and Pediatric Surgery, Fukuoka University, School of Medicine, Japan
| | - Daisuke Hamatake
- Department of Thoracic, Breast, Endocrine, and Pediatric Surgery, Fukuoka University, School of Medicine, Japan
| | - Michio Masaki
- Department of Medical Oncology, Hematology and Infectious Diseases, Fukuoka University, School of Medicine, Japan
| | - Yasushi Takamatsu
- Department of Medical Oncology, Hematology and Infectious Diseases, Fukuoka University, School of Medicine, Japan
| | - Akinori Iwasaki
- Department of Thoracic, Breast, Endocrine, and Pediatric Surgery, Fukuoka University, School of Medicine, Japan
| | - Toshifumi Sakata
- Department of Otorhinolaryngology and Head & Neck Surgery, Fukuoka University, School of Medicine, Japan
| | - Toshitaka Nagao
- Department of Anatomic Pathology, Tokyo Medical University, School of Medicine, Japan
| | - Kazuki Nabeshima
- Department of Pathology, Fukuoka University, School of Medicine, Japan
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8
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Biological active matter aggregates: Inspiration for smart colloidal materials. Adv Colloid Interface Sci 2019; 263:38-51. [PMID: 30504078 DOI: 10.1016/j.cis.2018.11.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 11/02/2018] [Accepted: 11/20/2018] [Indexed: 12/16/2022]
Abstract
Aggregations of social organisms exhibit a remarkable range of properties and functionalities. Multiple examples, such as fire ants or slime mold, show how a population of individuals is able to overcome an existential threat by gathering into a solid-like aggregate with emergent functionality. Surprisingly, these aggregates are driven by simple rules, and their mechanisms show great parallelism among species. At the same time, great effort has been made by the scientific community to develop active colloidal materials, such as microbubbles or Janus particles, which exhibit similar behaviors. However, a direct connection between these two realms is still not evident, and it would greatly benefit future studies. In this review, we first discuss the current understanding of living aggregates, point out the mechanisms in their formation and explore the vast range of emergent properties. Second, we review the current knowledge in aggregated colloidal systems, the methods used to achieve the aggregations and their potential functionalities. Based on this knowledge, we finally identify a set of over-arching principles commonly found in biological aggregations, and further suggest potential future directions for the creation of bio-inspired colloid aggregations.
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9
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Alibardi L. Ultrastructural analysis of early regenerating lizard tail suggests that a process of dedifferentiation is involved in the formation of the regenerative blastema. J Morphol 2018; 279:1171-1184. [DOI: 10.1002/jmor.20838] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 04/18/2018] [Accepted: 04/20/2018] [Indexed: 01/29/2023]
Affiliation(s)
- Lorenzo Alibardi
- Comparative Histolab, Padova, and Department of Biology; University of Bologna; Bologna Italy
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10
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Palatal Polymorphous Adenocarcinoma with High-Grade Transformation: A Case Report and Literature Review. Head Neck Pathol 2018; 13:131-139. [PMID: 29594833 PMCID: PMC6513909 DOI: 10.1007/s12105-018-0916-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 03/26/2018] [Indexed: 01/05/2023]
Abstract
Polymorphous adenocarcinoma (PAC) is the second most common intraoral malignant neoplasm of the minor salivary glands. However, it is very rare for PAC to show high-grade transformation (HGT) and to our knowledge, the English literature only seven reported cases. HGT tends to be observed when PAC recurs, and it is extremely rare to be seen at initial presentation. Here we report a 43-year-old Japanese male patient with PAC of the right palate showing HGT at initial presentation. Histopathologically, the tumor was characterized by a prominent solid and papillary-cystic growth pattern, with nuclear atypia and necrosis in area of HGT. The immunohistochemical staining pattern was consistent with PAC, as the tumor cells showed diffuse positivity for cytokeratin, vimentin and S-100, and focal positivity for bcl-2, ɑ-SMA and EMA. The tumor cells in HGT areas were markedly positive for AR and Ki-67 (about 40%/HPF), and also focally positive for cyclin D1 and p53, whereas HER2/neu, ER, PgR, p63, D2-40, GCDFP-15, and mitochondria were negative. Here we present a very rare case of palatal PAC with HGT at initial presentation.
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11
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Pfeuty B, Kaneko K. Requirements for efficient cell-type proportioning: regulatory timescales, stochasticity and lateral inhibition. Phys Biol 2016; 13:026007. [PMID: 27172110 DOI: 10.1088/1478-3975/13/2/026007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The proper functioning of multicellular organisms requires the robust establishment of precise proportions between distinct cell types. This developmental differentiation process typically involves intracellular regulatory and stochastic mechanisms to generate cell-fate diversity as well as intercellular signaling mechanisms to coordinate cell-fate decisions at tissue level. We thus surmise that key insights about the developmental regulation of cell-type proportion can be captured by the modeling study of clustering dynamics in population of inhibitory-coupled noisy bistable systems. This general class of dynamical system is shown to exhibit a very stable two-cluster state, but also metastability, collective oscillations or noise-induced state hopping, which can prevent from timely and reliably reaching a robust and well-proportioned clustered state. To circumvent these obstacles or to avoid fine-tuning, we highlight a general strategy based on dual-time positive feedback loops, such as mediated through transcriptional versus epigenetic mechanisms, which improves proportion regulation by coordinating early and flexible lineage priming with late and firm commitment. This result sheds new light on the respective and cooperative roles of multiple regulatory feedback, stochasticity and lateral inhibition in developmental dynamics.
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Affiliation(s)
- B Pfeuty
- Université de Lille, CNRS, Laboratoire de Physique des Lasers, Atomes, et Molécules, F-59000, Lille, France
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12
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Katoh-Kurasawa M, Santhanam B, Shaulsky G. The GATA transcription factor gene gtaG is required for terminal differentiation in Dictyostelium. J Cell Sci 2016; 129:1722-1733. [PMID: 26962009 DOI: 10.1242/jcs.181545] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The GATA transcription factor GtaG is conserved in Dictyostelids and essential for terminal differentiation in Dictyostelium discoideum, but its function is not well understood. Here we show that gtaG is expressed in prestalk cells at the anterior region of fingers and in the extending stalk during culmination. The gtaG- phenotype is cell-autonomous in prestalk cells and non-cell-autonomous in prespore cells. Transcriptome analyses reveal that GtaG regulates prestalk gene expression during cell differentiation before culmination and is required for progression into culmination. GtaG-dependent genes include genetic suppressors of the Dd-STATa-defective phenotype as well as Dd-STATa target-genes, including extra cellular matrix genes. We show that GtaG may be involved in the production of two culmination-signaling molecules, cyclic di-GMP and the spore differentiation factor SDF-1 and that addition of c-di-GMP rescues the gtaG- culmination and spore formation deficiencies. We propose that GtaG is a regulator of terminal differentiation that functions in concert with Dd-STATa and controls culmination through regulating c-di-GMP and SDF-1 production in prestalk cells.
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Affiliation(s)
- Mariko Katoh-Kurasawa
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030, USA
| | - Balaji Santhanam
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030, USA
| | - Gad Shaulsky
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030, USA
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13
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Epigenomic Reprogramming of Adult Cardiomyocyte-Derived Cardiac Progenitor Cells. Sci Rep 2015; 5:17686. [PMID: 26657817 PMCID: PMC4677315 DOI: 10.1038/srep17686] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 10/14/2015] [Indexed: 01/01/2023] Open
Abstract
It has been believed that mammalian adult cardiomyocytes (ACMs) are terminally-differentiated and are unable to proliferate. Recently, using a bi-transgenic ACM fate mapping mouse model and an in vitro culture system, we demonstrated that adult mouse cardiomyocytes were able to dedifferentiate into cardiac progenitor-like cells (CPCs). However, little is known about the molecular basis of their intrinsic cellular plasticity. Here we integrate single-cell transcriptome and whole-genome DNA methylation analyses to unravel the molecular mechanisms underlying the dedifferentiation and cell cycle reentry of mouse ACMs. Compared to parental cardiomyocytes, dedifferentiated mouse cardiomyocyte-derived CPCs (mCPCs) display epigenomic reprogramming with many differentially-methylated regions, both hypermethylated and hypomethylated, across the entire genome. Correlated well with the methylome, our transcriptomic data showed that the genes encoding cardiac structure and function proteins are remarkably down-regulated in mCPCs, while those for cell cycle, proliferation, and stemness are significantly up-regulated. In addition, implantation of mCPCs into infarcted mouse myocardium improves cardiac function with augmented left ventricular ejection fraction. Our study demonstrates that the cellular plasticity of mammalian cardiomyocytes is the result of a well-orchestrated epigenomic reprogramming and a subsequent global transcriptomic alteration.
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14
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Abstract
UNLABELLED Understanding the composition of gene lists that result from high-throughput experiments requires elaborate processing of gene annotation lists. In this article we present GOAT (Gene Ontology Analysis Tool), a tool based on the statistical software 'R' for analysing Gene Ontologytrade mark (GO) term enrichment in gene lists. Given a gene list, GOAT calculates the enrichment and statistical significance of every GO term and generates graphical presentations of significantly enriched terms. GOAT works for any organism with a genome-scale GO annotation and allows easy updates of ontologies and annotations. AVAILABILITY GOAT is freely available from http://dictygenome.org/software/GOAT/ CONTACT: Gad Shaulsky (gadi@bcm.tmc.edu).
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Affiliation(s)
- Qikai Xu
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas, USADepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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15
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Santhanam B, Cai H, Devreotes PN, Shaulsky G, Katoh-Kurasawa M. The GATA transcription factor GtaC regulates early developmental gene expression dynamics in Dictyostelium. Nat Commun 2015; 6:7551. [PMID: 26144553 PMCID: PMC4506546 DOI: 10.1038/ncomms8551] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 05/20/2015] [Indexed: 12/11/2022] Open
Abstract
In many systems, including the social amoeba Dictyostelium discoideum, development is often marked by dynamic morphological and transcriptional changes orchestrated by key transcription factors. However, efforts to examine sequential genome-wide changes of gene regulation in developmental processes have been fairly limited. Here we report the developmental regulatory dynamics of GtaC, a GATA-type zinc-finger transcription factor, through the analyses of serial ChIP- and RNA-sequencing data. GtaC is essential for developmental progression, decoding extracellular cAMP pulses during early development and may play a role in mediating cell-type differentiation at later stages. We find that GtaC exhibits temporally distinctive DNA-binding patterns concordant with each developmental stage. We identify direct GtaC targets and observe cotemporaneous GtaC-binding and developmental expression regulation. Our results suggest that GtaC regulates multiple physiological processes as Dictyostelium transitions from a group of unicellular amoebae to an integrated multicellular organism. Development involves dynamic transcriptional changes. By serial ChIP- and RNA-sequencing, here, the authors show that GtaC, a GATA type transcription factor, exhibits temporally distinctive DNA binding and regulation of gene expression concordant with the development in the social amoeba Dictyostelium discoideum.
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Affiliation(s)
- Balaji Santhanam
- 1] Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA [2] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Huaqing Cai
- Department of Cell Biology, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Peter N Devreotes
- Department of Cell Biology, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Gad Shaulsky
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Mariko Katoh-Kurasawa
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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Park SY, Park MH, Ko HS, Cha EJ, Sohn JS, Jung US, Kim CJ, Kim JS. Dedifferentiated endometrioid adenocarcinoma of the uterus: highly aggressive and poor prognostic tumor. KOREAN JOURNAL OF PATHOLOGY 2014; 48:327-30. [PMID: 25214869 PMCID: PMC4160600 DOI: 10.4132/koreanjpathol.2014.48.4.327] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 09/27/2013] [Accepted: 09/27/2013] [Indexed: 11/17/2022]
Affiliation(s)
- Shin Young Park
- Department of Pathology, Konyang University College of Medicine, Daejeon, Korea
| | - Moon Hyang Park
- Department of Pathology, Konyang University College of Medicine, Daejeon, Korea
| | - Hyoung Suk Ko
- Department of Pathology, Konyang University College of Medicine, Daejeon, Korea
| | - Eun Jung Cha
- Department of Pathology, Konyang University College of Medicine, Daejeon, Korea
| | - Jang Sihn Sohn
- Department of Pathology, Konyang University College of Medicine, Daejeon, Korea
| | - Un Suk Jung
- Department of Obstetrics and Gynecology, Konyang University College of Medicine, Daejeon, Korea
| | - Chul Jung Kim
- Department of Obstetrics and Gynecology, Konyang University College of Medicine, Daejeon, Korea
| | - Jin Suk Kim
- Department of Nuclear Medicine, Konyang University College of Medicine, Daejeon, Korea
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Thennavan A, Rao L, Radhakrishnan R. Polymorphous low-grade adenocarcinoma of maxillary alveolus metastasising to the abdomen: the role of immunomarkers in diagnosis. BMJ Case Rep 2013; 2013:bcr2013009633. [PMID: 23661663 PMCID: PMC3669867 DOI: 10.1136/bcr-2013-009633] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Polymorphous low-grade adenocarcinoma (PLGA) originating mostly in the minor salivary glands of the posterior hard and soft palate is characterised by its indolent growth and a slower rate of metastasis. Seldom does the PLGA present an aggressive behaviour and demonstrate distant metastasis, as in the present case where a 73-year-old female patient with a swelling in the maxillary alveolus was diagnosed as PLGA exhibiting high-grade transformation, subsequently metastasizing to the abdomen and lungs. The importance of immunomarkers, c-kit and ki-67 in deciphering the clinical behaviour of this PLGA is highlighted. Distant metastasis to the abdomen has not yet been reported; hence, this case of PLGA emphasises the importance of immunohistochemistry in assessing its aggressiveness and understanding a novel aspect of its pathogenesis.
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Affiliation(s)
- Aatish Thennavan
- Department of Oral and Maxillofacial Pathology, Manipal College of Dental Sciences, Manipal, Karnataka, India
| | - Lakshmi Rao
- Department of Pathology, Kasturba Medical College, Manipal, Karnataka, India
| | - Raghu Radhakrishnan
- Department of Oral and Maxillofacial Pathology, Manipal College of Dental Sciences, Manipal, Karnataka, India
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Tian X, Strassmann JE, Queller DC. Dictyostelium development shows a novel pattern of evolutionary conservation. Mol Biol Evol 2013; 30:977-84. [PMID: 23329689 DOI: 10.1093/molbev/mst007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
von Baer's law states that early stages of animal development are the most conserved. More recent evidence supports a modified "hourglass" pattern in which an early but somewhat later stage is most conserved. Both patterns have been explained by the relative complexity of either temporal or spatial interactions; the greatest conservation and lowest evolvability occur at the time of the most complex interactions, because these cause larger effects that are harder for selection to alter. This general kind of explanation might apply universally across independent multicellular systems, as supported by the recent finding of the hourglass pattern in plants. We use RNA-seq expression data from the development of the slime mold Dictyostelium to demonstrate that it does not follow either of the two canonical patterns but instead tends to show the strongest conservation and weakest evolvability late in development. We propose that this is consistent with a version of the spatial constraints model, modified for organisms that never achieve a high degree of developmental modularity.
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Affiliation(s)
- Xiangjun Tian
- Department of Biology, Washington University in St. Louis, St. Louis, USA
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19
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Abstract
Heterogeneity is an omnipresent feature of mammalian cells in vitro and in vivo. It has been recently realized that even mouse and human embryonic stem cells under the best culture conditions are heterogeneous containing pluripotent as well as partially committed cells. Somatic stem cells in adult organs are also heterogeneous, containing many subpopulations of self-renewing cells with distinct regenerative capacity. The differentiated progeny of adult stem cells also retain significant developmental plasticity that can be induced by a wide variety of experimental approaches. Like normal stem cells, recent data suggest that cancer stem cells (CSCs) similarly display significant phenotypic and functional heterogeneity, and that the CSC progeny can manifest diverse plasticity. Here, I discuss CSC heterogeneity and plasticity in the context of tumor development and progression, and by comparing with normal stem cell development. Appreciation of cancer cell plasticity entails a revision to the earlier concept that only the tumorigenic subset in the tumor needs to be targeted. By understanding the interrelationship between CSCs and their differentiated progeny, we can hope to develop better therapeutic regimens that can prevent the emergence of tumor cell variants that are able to found a new tumor and distant metastases.
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Huang E, Talukder S, Hughes TR, Curk T, Zupan B, Shaulsky G, Katoh-Kurasawa M. BzpF is a CREB-like transcription factor that regulates spore maturation and stability in Dictyostelium. Dev Biol 2011; 358:137-46. [PMID: 21810415 PMCID: PMC3180911 DOI: 10.1016/j.ydbio.2011.07.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Revised: 07/08/2011] [Accepted: 07/13/2011] [Indexed: 12/31/2022]
Abstract
The cAMP response element-binding protein (CREB) is a highly conserved transcription factor that integrates signaling through the cAMP-dependent protein kinase A (PKA) in many eukaryotes. PKA plays a critical role in Dictyostelium development but no CREB homologue has been identified in this system. Here we show that Dictyostelium utilizes a CREB-like protein, BzpF, to integrate PKA signaling during late development. bzpF(-) mutants produce compromised spores, which are extremely unstable and germination defective. Previously, we have found that BzpF binds the canonical CRE motif in vitro. In this paper, we determined the DNA binding specificity of BzpF using protein binding microarray (PBM) and showed that the motif with the highest specificity is a CRE-like sequence. BzpF is necessary to activate the transcription of at least 15 PKA-regulated, late-developmental target genes whose promoters contain BzpF binding motifs. BzpF is sufficient to activate two of these genes. The comparison of RNA sequencing data between wild type and bzpF(-) mutant revealed that the mutant fails to express 205 genes, many of which encode cellulose-binding and sugar-binding proteins. We propose that BzpF is a CREB-like transcription factor that regulates spore maturation and stability in a PKA-related manner.
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Affiliation(s)
- Eryong Huang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030, USA
| | - Shaheynoor Talukder
- Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Timothy R. Hughes
- Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Tomaz Curk
- Faculty of Computer and Information Science, University of Ljubljana, Trzaska cesta 25, SI-1001 Ljubljana, Slovenia
| | - Blaz Zupan
- Faculty of Computer and Information Science, University of Ljubljana, Trzaska cesta 25, SI-1001 Ljubljana, Slovenia
| | - Gad Shaulsky
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030, USA
| | - Mariko Katoh-Kurasawa
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030, USA
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21
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Costa AF, Altemani A, Hermsen M. Current concepts on dedifferentiation/high-grade transformation in salivary gland tumors. PATHOLOGY RESEARCH INTERNATIONAL 2011; 2011:325965. [PMID: 21876843 PMCID: PMC3160012 DOI: 10.4061/2011/325965] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Accepted: 05/09/2011] [Indexed: 12/16/2022]
Abstract
The concept of dedifferentiation had previously been used in salivary gland carcinomas. Recently, the term “high-grade transformation” was introduced for adenoid cystic carcinoma, acinic cell carcinoma, epithelial-myoepithelial carcinoma, and polymorphous low-grade adenocarcinoma and may better reflect this phenomenon, although transformation into moderately differentiated adenocarcinoma (i.e., not “high grade”) has also been described. Among the immunohistochemical markers, Ki-67 seems to be the only one that can help distinguish between the conventional and transformed components; however, the combination of morphological criteria is still sovereign. The overexpression of p53 was observed in the transformed component in all tumor types studied, despite few cases having been demonstrated to carry mutations or deletions in TP53 gene. Genetic studies in salivary gland tumors with dedifferentiation/high-grade transformation are rare and deserve further investigation. This paper aims at providing an overview on the recent concepts in histopathological classification of salivary gland tumors, complemented by immunohistochemical and genetic findings.
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Affiliation(s)
- Ana Flávia Costa
- Department of Pathology, University of Campinas, (UNICAMP), 13083-887 Campinas, SP, Brazil
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22
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Roberge-White E, Katoh-Kurasawa M. Plasticity in the development and dedifferentiation of Dictyostelium discoideum. Dev Growth Differ 2011; 53:587-96. [DOI: 10.1111/j.1440-169x.2011.01256.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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23
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Blagg SL, Battom SE, Annesley SJ, Keller T, Parkinson K, Wu JMF, Fisher PR, Thompson CRL. Cell type-specific filamin complex regulation by a novel class of HECT ubiquitin ligase is required for normal cell motility and patterning. Development 2011; 138:1583-93. [PMID: 21389049 PMCID: PMC3062426 DOI: 10.1242/dev.063800] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2011] [Indexed: 11/20/2022]
Abstract
Differential cell motility, which plays a key role in many developmental processes, is perhaps most evident in examples of pattern formation in which the different cell types arise intermingled before sorting out into discrete tissues. This is thought to require heterogeneities in responsiveness to differentiation-inducing signals that result in the activation of cell type-specific genes and 'salt and pepper' patterning. How differential gene expression results in cell sorting is poorly defined. Here we describe a novel gene (hfnA) that provides the first mechanistic link between cell signalling, differential gene expression and cell type-specific sorting in Dictyostelium. HfnA defines a novel group of evolutionarily conserved HECT ubiquitin ligases with an N-terminal filamin domain (HFNs). HfnA expression is induced by the stalk differentiation-inducing factor DIF-1 and is restricted to a subset of prestalk cells (pstO). hfnA(-) pstO cells differentiate but their sorting out is delayed. Genetic interactions suggest that this is due to misregulation of filamin complex activity. Overexpression of filamin complex members phenocopies the hfnA(-) pstO cell sorting defect, whereas disruption of filamin complex function in a wild-type background results in pstO cells sorting more strongly. Filamin disruption in an hfnA(-) background rescues pstO cell localisation. hfnA(-) cells exhibit altered slug phototaxis phenotypes consistent with filamin complex hyperactivity. We propose that HfnA regulates filamin complex activity and cell type-specific motility through the breakdown of filamin complexes. These findings provide a novel mechanism for filamin regulation and demonstrate that filamin is a crucial mechanistic link between responses to differentiation signals and cell movement in patterning based on 'salt and pepper' differentiation and sorting out.
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Affiliation(s)
- Simone L. Blagg
- Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Suzanne E. Battom
- Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Sarah J. Annesley
- Department of Microbiology, La Trobe University, VIC 3086, Australia
| | - Thomas Keller
- Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Katie Parkinson
- Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Jasmine M. F. Wu
- Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Paul R. Fisher
- Department of Microbiology, La Trobe University, VIC 3086, Australia
| | - Christopher R. L. Thompson
- Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
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24
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Parikh A, Huang E, Dinh C, Zupan B, Kuspa A, Subramanian D, Shaulsky G. New components of the Dictyostelium PKA pathway revealed by Bayesian analysis of expression data. BMC Bioinformatics 2010; 11:163. [PMID: 20356373 PMCID: PMC2873529 DOI: 10.1186/1471-2105-11-163] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Accepted: 03/31/2010] [Indexed: 11/30/2022] Open
Abstract
Background Identifying candidate genes in genetic networks is important for understanding regulation and biological function. Large gene expression datasets contain relevant information about genetic networks, but mining the data is not a trivial task. Algorithms that infer Bayesian networks from expression data are powerful tools for learning complex genetic networks, since they can incorporate prior knowledge and uncover higher-order dependencies among genes. However, these algorithms are computationally demanding, so novel techniques that allow targeted exploration for discovering new members of known pathways are essential. Results Here we describe a Bayesian network approach that addresses a specific network within a large dataset to discover new components. Our algorithm draws individual genes from a large gene-expression repository, and ranks them as potential members of a known pathway. We apply this method to discover new components of the cAMP-dependent protein kinase (PKA) pathway, a central regulator of Dictyostelium discoideum development. The PKA network is well studied in D. discoideum but the transcriptional networks that regulate PKA activity and the transcriptional outcomes of PKA function are largely unknown. Most of the genes highly ranked by our method encode either known components of the PKA pathway or are good candidates. We tested 5 uncharacterized highly ranked genes by creating mutant strains and identified a candidate cAMP-response element-binding protein, yet undiscovered in D. discoideum, and a histidine kinase, a candidate upstream regulator of PKA activity. Conclusions The single-gene expansion method is useful in identifying new components of known pathways. The method takes advantage of the Bayesian framework to incorporate prior biological knowledge and discovers higher-order dependencies among genes while greatly reducing the computational resources required to process high-throughput datasets.
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Affiliation(s)
- Anup Parikh
- Graduate Program in Structural Computational Biology and Molecular Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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25
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Rot G, Parikh A, Curk T, Kuspa A, Shaulsky G, Zupan B. dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface. BMC Bioinformatics 2009; 10:265. [PMID: 19706156 PMCID: PMC2738683 DOI: 10.1186/1471-2105-10-265] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Accepted: 08/25/2009] [Indexed: 11/25/2022] Open
Abstract
Background Bioinformatics often leverages on recent advancements in computer science to support biologists in their scientific discovery process. Such efforts include the development of easy-to-use web interfaces to biomedical databases. Recent advancements in interactive web technologies require us to rethink the standard submit-and-wait paradigm, and craft bioinformatics web applications that share analytical and interactive power with their desktop relatives, while retaining simplicity and availability. Results We have developed dictyExpress, a web application that features a graphical, highly interactive explorative interface to our database that consists of more than 1000 Dictyostelium discoideum gene expression experiments. In dictyExpress, the user can select experiments and genes, perform gene clustering, view gene expression profiles across time, view gene co-expression networks, perform analyses of Gene Ontology term enrichment, and simultaneously display expression profiles for a selected gene in various experiments. Most importantly, these tasks are achieved through web applications whose components are seamlessly interlinked and immediately respond to events triggered by the user, thus providing a powerful explorative data analysis environment. Conclusion dictyExpress is a precursor for a new generation of web-based bioinformatics applications with simple but powerful interactive interfaces that resemble that of the modern desktop. While dictyExpress serves mainly the Dictyostelium research community, it is relatively easy to adapt it to other datasets. We propose that the design ideas behind dictyExpress will influence the development of similar applications for other model organisms.
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Affiliation(s)
- Gregor Rot
- Faculty of Computer and Information Science, University of Ljubljana, SI-1000 Ljubljana, Slovenia.
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26
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Abstract
Cellular slime molds are eukaryotic microorganisms in the soil. They feed on bacteria as solitary amoebae but conditionally construct multicellular forms in which cell differentiation takes place. Therefore, they are attractive for the study of fundamental biological phenomena such as phagocytosis, cell division, chemotactic movements, intercellular communication, cell differentiation, and morphogenesis. The most widely used species, Dictyostelium discoideum, is highly amenable to experimental manipulation and can be used with most recent molecular biological techniques. Its genome and cDNA analyses have been completed and well-annotated data are publicly available. A larger number of orthologues of human disease-related genes were found in D. discoideum than in yeast. Moreover, some pathogenic bacteria infect Dictyostelium amoebae. Thus, this microorganism can also offer a good experimental system for biomedical research. The resources of cellular slime molds, standard strains, mutants, and genes are maintained and distributed upon request by the core center of the National BioResource Project (NBRP-nenkin) to support Dictyostelium community users as well as new users interested in new platforms for research and/or phylogenic consideration.
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Affiliation(s)
- Hideko Urushihara
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
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27
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Abstract
Chronic kidney disease (CKD) is increasing at the rate of 6-8% per annum in the US alone. At present, dialysis and transplantation remain the only treatment options. However, there is hope that stem cells and regenerative medicine may provide additional regenerative options for kidney disease. Such new treatments might involve induction of repair using endogenous or exogenous stem cells or the reprogramming of the organ to reinitiate development. This review addresses the current state of understanding with respect to the ability of non-renal stem cell sources to influence renal repair, the existence of endogenous renal stem cells and the biology of normal renal repair in response to damage. It also examines the remaining challenges and asks the question of whether there is one solution for all forms of renal disease.
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Affiliation(s)
- C Hopkins
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, Australia
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28
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Liao X, Siu MKY, Au CWH, Wong ESY, Chan HY, Ip PPC, Ngan HYS, Cheung ANY. Aberrant activation of hedgehog signaling pathway in ovarian cancers: effect on prognosis, cell invasion and differentiation. Carcinogenesis 2008; 30:131-40. [PMID: 19028702 PMCID: PMC7109814 DOI: 10.1093/carcin/bgn230] [Citation(s) in RCA: 158] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Aberrant activation of hedgehog (HH) pathway has been implicated in the development of human malignancies. This study aimed at investigating the role of HH molecules in human ovarian carcinogenesis. The expression profiles of HH molecules were examined in ovarian tumor samples and ovarian cancer cell lines and the in vitro effects of HH molecules on cell proliferation, apoptosis, migration, invasion and cell differentiation as well as related downstream target genes were assessed. Overexpression of Patched and Gli1 protein in ovarian cancers correlated with poor survival of the patients (P = 0.008; P = 0.004). Significantly elevated expression of Sonic hedgehog messenger RNA was observed in ovarian cancers compared with normal tissues and benign ovarian tumors and such differential expression was specific to histological types (P < 0.05). Ectopic Gli1 overexpression in ovarian cancer cells conferred increased cell proliferation, cell mobility, invasiveness and change in differentiation in association with increased expression of E-cadherin, vimentin, Bcl-2, caspases as well as beta1 integrin, membrane type 1 matrix metalloproteinase (MT1-MMP) and vascular endothelial growth factor (VEGF). Treatment with 3-keto-N-(aminoethyl-aminocaproyl-dihydrocinnamoyl)-cyclopamine induced cancer cell apoptosis, suppressed cell growth, mobility and invasiveness and induced cancer cell dedifferentiation with decreased expression of E-cadherin, cytokeratin 7, Snail, calretinin, vimentin, Bcl-2, caspases, beta1 integrin, MT1-MMP and VEGF. Our data suggested that abnormal HH signaling activation plays important roles in the development and progression of ovarian cancers. Gli1 expression is an independent prognostic marker. Inhibition of the HH pathway molecules might be a valid therapeutic strategy for ovarian cancers.
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Affiliation(s)
- Xiaoyun Liao
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
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29
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Urushihara H. Developmental biology of the social amoeba: history, current knowledge and prospects. Dev Growth Differ 2008; 50 Suppl 1:S277-81. [PMID: 18482401 DOI: 10.1111/j.1440-169x.2008.01013.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The cellular slime molds are known as the social amoebae because they conditionally construct multicellular forms in which cell differentiation takes place. Among them, Dictyostelium discoideum has many advantages as an experimental system and is widely used as a model organism. This review aims to reconsider how it has contributed to the understanding of developmental mechanisms and what should be done in the future. Chemotaxis, cell differentiation, genome and transcriptome, and the ecological and evolutionary implications of development are discussed.
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Affiliation(s)
- Hideko Urushihara
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8572, Japan.
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30
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Katoh M, Chen G, Roberge E, Shaulsky G, Kuspa A. Developmental commitment in Dictyostelium discoideum. EUKARYOTIC CELL 2007; 6:2038-45. [PMID: 17905919 PMCID: PMC2168402 DOI: 10.1128/ec.00223-07] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Upon starvation, Dictyostelium discoideum cells halt cell proliferation, aggregate into multicellular organisms, form migrating slugs, and undergo morphogenesis into fruiting bodies while differentiating into dormant spores and dead stalk cells. At almost any developmental stage cells can be forced to dedifferentiate when they are dispersed and diluted into nutrient broth. However, migrating slugs can traverse lawns of bacteria for days without dedifferentiating, ignoring abundant nutrients and continuing development. We now show that developing Dictyostelium cells revert to the growth phase only when bacteria are supplied during the first 4 to 6 h of development but that after this time, cells continue to develop regardless of the presence of food. We postulate that the cells' inability to revert to the growth phase after 6 h represents a commitment to development. We show that the onset of commitment correlates with the cells' loss of phagocytic function. By examining mutant strains, we also show that commitment requires extracellular cyclic AMP (cAMP) signaling. Moreover, cAMP pulses are sufficient to induce both commitment and the loss of phagocytosis in starving cells, whereas starvation alone is insufficient. Finally, we show that the inhibition of development by food prior to commitment is independent of contact between the cells and the bacteria and that small soluble molecules, probably amino acids, inhibit development during the first few hours and subsequently the cells become unable to react to the molecules and commit to development. We propose that commitment serves as a checkpoint that ensures the completion of cooperative aggregation of developing Dictyostelium cells once it has begun, dampening the response to nutritional cues that might inappropriately block development.
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Affiliation(s)
- Mariko Katoh
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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31
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Van Driessche N, Alexander H, Min J, Kuspa A, Alexander S, Shaulsky G. Global transcriptional responses to cisplatin in Dictyostelium discoideum identify potential drug targets. Proc Natl Acad Sci U S A 2007; 104:15406-11. [PMID: 17878305 PMCID: PMC2000517 DOI: 10.1073/pnas.0705996104] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Dictyostelium discoideum is a useful model for studying mechanisms of cisplatin drug sensitivity. Our previous findings, that mutations in sphingolipid metabolism genes confer cisplatin resistance in D. discoideum and in human cells, raised interest in the resistance mechanisms and their implications for cisplatin chemotherapy. Here we used expression microarrays to monitor physiological changes and to identify pathways that are affected by cisplatin treatment of D. discoideum. We found >400 genes whose regulation was altered by cisplatin treatment of wild-type cells, including groups of genes that participate in cell proliferation and in nucleotide and protein metabolism, showing that the cisplatin response is orderly and multifaceted. Transcriptional profiling of two isogenic cisplatin-resistant mutants, impaired in different sphingolipid metabolism steps, showed that the effect of cisplatin treatment was greater than the effect of the mutations, indicating that cisplatin resistance in the mutants is due to specific abilities to overcome the drug effects rather than to general drug insensitivity. Nevertheless, the mutants exhibited significantly different responses to cisplatin compared with the parent, and >200 genes accounted for that difference. Mutations in five cisplatin response genes (sgkB, csbA, acbA, smlA, and atg8) resulted in altered drug sensitivity, implicating novel pathways in cisplatin response. Our data illustrate how modeling complex cellular responses to drugs in genetically stable and tractable systems can uncover new targets with the potential for improving chemotherapy.
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Affiliation(s)
| | - Hannah Alexander
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211
| | - Junxia Min
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211
| | - Adam Kuspa
- Departments of *Molecular and Human Genetics and
- Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030; and
| | - Stephen Alexander
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211
- To whom correspondence may be addressed. E-mail: or
| | - Gad Shaulsky
- Departments of *Molecular and Human Genetics and
- To whom correspondence may be addressed. E-mail: or
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32
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Williams MD, Hanna EY, El-Naggar AK. Anaplastic ameloblastic fibrosarcoma arising from recurrent ameloblastic fibroma: restricted molecular abnormalities of certain genes to the malignant transformation. ACTA ACUST UNITED AC 2007; 104:72-5. [PMID: 17577546 DOI: 10.1016/j.tripleo.2006.07.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2006] [Revised: 06/30/2006] [Accepted: 07/17/2006] [Indexed: 12/17/2022]
Abstract
A rare case of anaplastic ameloblastic fibrosarcoma (AS) arising in an ameloblastic fibroma (AF) of the maxilla of a 48-year-old patient 10 years after the primary excision is presented. The recurrent tumor retained focal areas of AF but manifested heterogeneous malignant features ranging from low-grade spindle to highly pleomorphic sarcomas. Biomarker analysis showed alterations of the p53 and c-KIT genes restricted to the sarcomatous component. The biological implications of these findings in the future management of these tumors are discussed.
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Affiliation(s)
- Michelle D Williams
- Department of Pathology, University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA.
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Mendoza MC, Booth EO, Shaulsky G, Firtel RA. MEK1 and protein phosphatase 4 coordinate Dictyostelium development and chemotaxis. Mol Cell Biol 2007; 27:3817-27. [PMID: 17353263 PMCID: PMC1899987 DOI: 10.1128/mcb.02194-06] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2006] [Revised: 01/22/2007] [Accepted: 03/06/2007] [Indexed: 11/20/2022] Open
Abstract
The MEK and extracellular signal-regulated kinase/mitogen-activated protein kinase proteins are established regulators of multicellular development and cell movement. By combining traditional genetic and biochemical assays with a statistical analysis of global gene expression profiles, we discerned a genetic interaction between Dictyostelium discoideum mek1, smkA (named for its role in the suppression of the mek1(-) mutation), and pppC (the protein phosphatase 4 catalytic subunit gene). We found that during development and chemotaxis, both mek1 and smkA regulate pppC function. In other organisms, the protein phosphatase 4 catalytic subunit, PP4C, functions in a complex with the regulatory subunits PP4R2 and PP4R3 to control recovery from DNA damage. Here, we show that catalytically active PP4C is also required for development, chemotaxis, and the expression of numerous genes. The product of smkA (SMEK) functions as the Dictyostelium PP4R3 homolog and positively regulates a subset of PP4C's functions: PP4C-mediated developmental progression, chemotaxis, and the expression of genes specifically involved in cell stress responses and cell movement. We also demonstrate that SMEK does not control the absolute level of PP4C activity and suggest that SMEK regulates PP4C by controlling its localization to the nucleus. These data define a novel genetic pathway in which mek1 functions upstream of pppC-smkA to control multicellular development and chemotaxis.
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Affiliation(s)
- Michelle C Mendoza
- Natural Sciences Building, Room 6316, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0380, USA
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Kuzdzal-Fick JJ, Foster KR, Queller DC, Strassmann JE. Exploiting new terrain: an advantage to sociality in the slime mold Dictyostelium discoideum. Behav Ecol 2007. [DOI: 10.1093/beheco/arl102] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Booth EO, Van Driessche N, Zhuchenko O, Kuspa A, Shaulsky G. Microarray phenotyping in Dictyostelium reveals a regulon of chemotaxis genes. Bioinformatics 2005; 21:4371-7. [PMID: 16234315 DOI: 10.1093/bioinformatics/bti726] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Coordinate regulation of gene expression can provide information on gene function. To begin a large-scale analysis of Dictyostelium gene function, we clustered genes based on their expression in wild-type and mutant strains and analyzed their functions. RESULTS We found 17 modes of wild-type gene expression and refined them into 57 submodes considering mutant data. Annotation analyses revealed correlations between co-expression and function and an unexpected correlation between expression and function of genes involved in various aspects of chemotaxis. Co-regulation of chemotaxis genes was also found in published data from neutrophils. To test the predictive power of the analysis, we examined the phenotypes of mutations in seven co-regulated genes that had no published role in chemotaxis. Six mutants exhibited chemotaxis defects, supporting the idea that function can be inferred from co-expression. The clustering and annotation analyses provide a public resource for Dictyostelium functional genomics.
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Affiliation(s)
- Ezgi O Booth
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
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36
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Cheung SW, Shaw CA, Yu W, Li J, Ou Z, Patel A, Yatsenko SA, Cooper ML, Furman P, Stankiewicz P, Stankiewicz P, Lupski JR, Chinault AC, Beaudet AL. Development and validation of a CGH microarray for clinical cytogenetic diagnosis. Genet Med 2005; 7:422-32. [PMID: 16024975 DOI: 10.1097/01.gim.0000170992.63691.32] [Citation(s) in RCA: 204] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
PURPOSE We developed a microarray for clinical diagnosis of chromosomal disorders using large insert genomic DNA clones as targets for comparative genomic hybridization (CGH). METHODS The array contains 362 FISH-verified clones that span genomic regions implicated in over 40 known human genomic disorders and representative subtelomeric clones for each of the 41 clinically relevant human chromosome telomeres. Three or four clones from almost all deletion or duplication genomic regions and three or more clones for each subtelomeric region were included. We tested chromosome microarray analysis (CMA) in a masked fashion by examining genomic DNA from 25 patients who were previously ascertained in a genetic clinic and studied by conventional cytogenetics. A novel software package implemented in the R statistical programming language was developed for normalization, visualization, and inference. RESULTS The CMA results were entirely consistent with previous cytogenetic and FISH findings. For clone by clone analysis, the sensitivity was estimated to be 96.7% and the specificity was 99.1%. Major advantages of this selected human genome array include the following: interrogation of clinically relevant genomic regions, the ability to test for a wide range of duplication and deletion syndromes in a single analysis, the ability to detect duplications that would likely be undetected by metaphase FISH, and ease of confirmation of suspected genomic changes by conventional FISH testing currently available in the cytogenetics laboratory. CONCLUSION The array is an attractive alternative to telomere FISH and locus-specific FISH, but it does not include uniform coverage across the arms of each chromosome and is not intended to substitute for a standard karyotype. Limitations of CMA include the inability to detect both balanced chromosome changes and low levels of mosaicism.
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Affiliation(s)
- Sau W Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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37
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Eichinger L, Pachebat J, Glöckner G, Rajandream MA, Sucgang R, Berriman M, Song J, Olsen R, Szafranski K, Xu Q, Tunggal B, Kummerfeld S, Madera M, Konfortov BA, Rivero F, Bankier AT, Lehmann R, Hamlin N, Davies R, Gaudet P, Fey P, Pilcher K, Chen G, Saunders D, Sodergren E, Davis P, Kerhornou A, Nie X, Hall N, Anjard C, Hemphill L, Bason N, Farbrother P, Desany B, Just E, Morio T, Rost R, Churcher C, Cooper J, Haydock S, van Driessche N, Cronin A, Goodhead I, Muzny D, Mourier T, Pain A, Lu M, Harper D, Lindsay R, Hauser H, James K, Quiles M, Babu MM, Saito T, Buchrieser C, Wardroper A, Felder M, Thangavelu M, Johnson D, Knights A, Loulseged H, Mungall K, Oliver K, Price C, Quail M, Urushihara H, Hernandez J, Rabbinowitsch E, Steffen D, Sanders M, Ma J, Kohara Y, Sharp S, Simmonds M, Spiegler S, Tivey A, Sugano S, White B, Walker D, Woodward J, Winckler T, Tanaka Y, Shaulsky G, Schleicher M, Weinstock G, Rosenthal A, Cox E, Chisholm RL, Gibbs R, Loomis WF, Platzer M, Kay RR, Williams J, Dear PH, Noegel AA, Barrell B, Kuspa A. The genome of the social amoeba Dictyostelium discoideum. Nature 2005; 435:43-57. [PMID: 15875012 PMCID: PMC1352341 DOI: 10.1038/nature03481] [Citation(s) in RCA: 960] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2004] [Accepted: 02/17/2005] [Indexed: 02/07/2023]
Abstract
The social amoebae are exceptional in their ability to alternate between unicellular and multicellular forms. Here we describe the genome of the best-studied member of this group, Dictyostelium discoideum. The gene-dense chromosomes of this organism encode approximately 12,500 predicted proteins, a high proportion of which have long, repetitive amino acid tracts. There are many genes for polyketide synthases and ABC transporters, suggesting an extensive secondary metabolism for producing and exporting small molecules. The genome is rich in complex repeats, one class of which is clustered and may serve as centromeres. Partial copies of the extrachromosomal ribosomal DNA (rDNA) element are found at the ends of each chromosome, suggesting a novel telomere structure and the use of a common mechanism to maintain both the rDNA and chromosomal termini. A proteome-based phylogeny shows that the amoebozoa diverged from the animal-fungal lineage after the plant-animal split, but Dictyostelium seems to have retained more of the diversity of the ancestral genome than have plants, animals or fungi.
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Affiliation(s)
- L. Eichinger
- Center for Biochemistry and Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
| | - J.A. Pachebat
- Center for Biochemistry and Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
| | - G. Glöckner
- Genome Analysis, Institute for Molecular Biotechnology, Beutenbergstr. 11, D-07745 Jena, Germany
| | - M.-A. Rajandream
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - R. Sucgang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
| | - M. Berriman
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - J. Song
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
| | - R. Olsen
- Section of Cell and Developmental Biology, Division of Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - K. Szafranski
- Genome Analysis, Institute for Molecular Biotechnology, Beutenbergstr. 11, D-07745 Jena, Germany
| | - Q. Xu
- Dept. of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston TX 77030, USA
| | - B. Tunggal
- Center for Biochemistry and Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
| | - S. Kummerfeld
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
| | - M. Madera
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
| | - B. A. Konfortov
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
| | - F. Rivero
- Center for Biochemistry and Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
| | - A. T. Bankier
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
| | - R. Lehmann
- Genome Analysis, Institute for Molecular Biotechnology, Beutenbergstr. 11, D-07745 Jena, Germany
| | - N. Hamlin
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - R. Davies
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - P. Gaudet
- dictyBase, Center for Genetic Medicine, Northwestern University, 303 E Chicago Ave, Chicago, IL 60611, USA
| | - P. Fey
- dictyBase, Center for Genetic Medicine, Northwestern University, 303 E Chicago Ave, Chicago, IL 60611, USA
| | - K. Pilcher
- dictyBase, Center for Genetic Medicine, Northwestern University, 303 E Chicago Ave, Chicago, IL 60611, USA
| | - G. Chen
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
| | - D. Saunders
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - E. Sodergren
- Dept. of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - P. Davis
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - A. Kerhornou
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - X. Nie
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
| | - N. Hall
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - C. Anjard
- Section of Cell and Developmental Biology, Division of Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - L. Hemphill
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
| | - N. Bason
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - P. Farbrother
- Center for Biochemistry and Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
| | - B. Desany
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
| | - E. Just
- dictyBase, Center for Genetic Medicine, Northwestern University, 303 E Chicago Ave, Chicago, IL 60611, USA
| | - T. Morio
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - R. Rost
- Adolf-Butenandt-Institute/Cell Biology, Ludwig-Maximilians-University, 80336 Munich, Germany
| | - C. Churcher
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - J. Cooper
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - S. Haydock
- Biochemistry Department, University of Cambridge, Cambridge CB2 1QW, UK
| | - N. van Driessche
- Dept. of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - A. Cronin
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - I. Goodhead
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - D. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - T. Mourier
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - A. Pain
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - M. Lu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
| | - D. Harper
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - R. Lindsay
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
| | - H. Hauser
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - K. James
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - M. Quiles
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - M. Madan Babu
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
| | - T. Saito
- Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810 Japan
| | - C. Buchrieser
- Unité de Genomique des Microorganismes Pathogenes, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - A. Wardroper
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
- Department of Biology, University of York, York YO10 5YW, UK
| | - M. Felder
- Genome Analysis, Institute for Molecular Biotechnology, Beutenbergstr. 11, D-07745 Jena, Germany
| | - M. Thangavelu
- MRC Cancer Cell Unit, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 2XZ, UK
| | - D. Johnson
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - A. Knights
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - H. Loulseged
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - K. Mungall
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - K. Oliver
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - C. Price
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - M.A. Quail
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - H. Urushihara
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - J. Hernandez
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - E. Rabbinowitsch
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - D. Steffen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - M. Sanders
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - J. Ma
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Y. Kohara
- Centre for Genetic Resource Information, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - S. Sharp
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - M. Simmonds
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - S. Spiegler
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - A. Tivey
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - S. Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Minato, Tokyo 108-8639, Japan
| | - B. White
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - D. Walker
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - J. Woodward
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - T. Winckler
- Institut für Pharmazeutische Biologie, Universität Frankfurt (Biozentrum), Frankfurt am Main, 60439, Germany
| | - Y. Tanaka
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - G. Shaulsky
- Dept. of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston TX 77030, USA
| | - M. Schleicher
- Adolf-Butenandt-Institute/Cell Biology, Ludwig-Maximilians-University, 80336 Munich, Germany
| | - G. Weinstock
- Dept. of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - A. Rosenthal
- Genome Analysis, Institute for Molecular Biotechnology, Beutenbergstr. 11, D-07745 Jena, Germany
| | - E.C. Cox
- Department of Molecular Biology, Princeton University, Princeton, NJ08544-1003, USA
| | - R. L. Chisholm
- dictyBase, Center for Genetic Medicine, Northwestern University, 303 E Chicago Ave, Chicago, IL 60611, USA
| | - R. Gibbs
- Dept. of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - W. F. Loomis
- Section of Cell and Developmental Biology, Division of Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - M. Platzer
- Genome Analysis, Institute for Molecular Biotechnology, Beutenbergstr. 11, D-07745 Jena, Germany
| | - R. R. Kay
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
| | - J. Williams
- School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - P. H. Dear
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
| | - A. A. Noegel
- Center for Biochemistry and Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
| | - B. Barrell
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - A. Kuspa
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
- Dept. of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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Van Driessche N, Demsar J, Booth EO, Hill P, Juvan P, Zupan B, Kuspa A, Shaulsky G. Epistasis analysis with global transcriptional phenotypes. Nat Genet 2005; 37:471-7. [PMID: 15821735 DOI: 10.1038/ng1545] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2004] [Accepted: 02/10/2005] [Indexed: 11/09/2022]
Abstract
Classical epistasis analysis can determine the order of function of genes in pathways using morphological, biochemical and other phenotypes. It requires knowledge of the pathway's phenotypic output and a variety of experimental expertise and so is unsuitable for genome-scale analysis. Here we used microarray profiles of mutants as phenotypes for epistasis analysis. Considering genes that regulate activity of protein kinase A in Dictyostelium, we identified known and unknown epistatic relationships and reconstructed a genetic network with microarray phenotypes alone. This work shows that microarray data can provide a uniform, quantitative tool for large-scale genetic network analysis.
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Affiliation(s)
- Nancy Van Driessche
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
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Xu Q, Ibarra M, Mahadeo D, Shaw C, Huang E, Kuspa A, Cotter D, Shaulsky G. Transcriptional transitions during Dictyostelium spore germination. EUKARYOTIC CELL 2005; 3:1101-10. [PMID: 15470238 PMCID: PMC522591 DOI: 10.1128/ec.3.5.1101-1110.2004] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Many protozoa form spores in response to adversity; therefore, spore germination is a key process in their life cycle. Dictyostelium discoideum sporulates in response to starvation following a developmental program. Germination is characterized by two visible changes, spore swelling and the emergence of amoeba from the spore capsule. Several studies have indicated that an additional process termed spore activation is also required, but the physiological changes that characterize the three phases are largely uncharacterized. We used microarrays to monitor global transcriptional transitions as a surrogate measure of the physiological changes that occur during germination. Using two independent methods to induce germination, we identified changes in mRNA levels that characterized the germination process rather than changes that resulted from the induction method. We found that germination is characterized by three transitions. The first transition occurs during activation, while the spores appear dormant, the largest transition occurs when swelling begins, and the third transition occurs when emergence begins. These findings indicate that activation and swelling are not passive occurrences, such as dilution of inhibitors or spore rehydration, but are active processes that are accompanied by dramatic events in mRNA degradation and de novo transcription. These findings confirm and extend earlier reports that genes such as celA are regulated during spore germination. We also found by mutation analysis that the unconventional myosin gene myoI, which is induced during early germination, plays roles in the maintenance of dormancy and in spore swelling. This finding suggests that some of the observed transcriptional changes are required for spore germination.
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Affiliation(s)
- Qikai Xu
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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40
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Wells WA. How to become a generalist again. J Biophys Biochem Cytol 2004. [PMCID: PMC2249964 DOI: 10.1083/jcb1654rr3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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