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Marjanovic ND, Hofree M, Chan JE, Canner D, Wu K, Trakala M, Hartmann GG, Smith OC, Kim JY, Evans KV, Hudson A, Ashenberg O, Porter CBM, Bejnood A, Subramanian A, Pitter K, Yan Y, Delorey T, Phillips DR, Shah N, Chaudhary O, Tsankov A, Hollmann T, Rekhtman N, Massion PP, Poirier JT, Mazutis L, Li R, Lee JH, Amon A, Rudin CM, Jacks T, Regev A, Tammela T. Emergence of a High-Plasticity Cell State during Lung Cancer Evolution. Cancer Cell 2020; 38:229-246.e13. [PMID: 32707077 PMCID: PMC7745838 DOI: 10.1016/j.ccell.2020.06.012] [Citation(s) in RCA: 236] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 03/13/2020] [Accepted: 06/18/2020] [Indexed: 12/13/2022]
Abstract
Tumor evolution from a single cell into a malignant, heterogeneous tissue remains poorly understood. Here, we profile single-cell transcriptomes of genetically engineered mouse lung tumors at seven stages, from pre-neoplastic hyperplasia to adenocarcinoma. The diversity of transcriptional states increases over time and is reproducible across tumors and mice. Cancer cells progressively adopt alternate lineage identities, computationally predicted to be mediated through a common transitional, high-plasticity cell state (HPCS). Accordingly, HPCS cells prospectively isolated from mouse tumors and human patient-derived xenografts display high capacity for differentiation and proliferation. The HPCS program is associated with poor survival across human cancers and demonstrates chemoresistance in mice. Our study reveals a central principle underpinning intra-tumoral heterogeneity and motivates therapeutic targeting of the HPCS.
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Research Support, N.I.H., Extramural |
5 |
236 |
2
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Schenkel JM, Herbst RH, Canner D, Li A, Hillman M, Shanahan SL, Gibbons G, Smith OC, Kim JY, Westcott P, Hwang WL, Freed-Pastor WA, Eng G, Cuoco MS, Rogers P, Park JK, Burger ML, Rozenblatt-Rosen O, Cong L, Pauken KE, Regev A, Jacks T. Conventional type I dendritic cells maintain a reservoir of proliferative tumor-antigen specific TCF-1 + CD8 + T cells in tumor-draining lymph nodes. Immunity 2021; 54:2338-2353.e6. [PMID: 34534439 PMCID: PMC8604155 DOI: 10.1016/j.immuni.2021.08.026] [Citation(s) in RCA: 160] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 05/22/2021] [Accepted: 08/20/2021] [Indexed: 12/28/2022]
Abstract
In tumors, a subset of CD8+ T cells expressing the transcription factor TCF-1 drives the response to immune checkpoint blockade. We examined the mechanisms that maintain these cells in an autochthonous model of lung adenocarcinoma. Longitudinal sampling and single-cell sequencing of tumor-antigen specific TCF-1+ CD8+ T cells revealed that while intratumoral TCF-1+ CD8+ T cells acquired dysfunctional features and decreased in number as tumors progressed, TCF-1+ CD8+ T cell frequency in the tumor draining LN (dLN) remained stable. Two discrete intratumoral TCF-1+ CD8+ T cell subsets developed over time-a proliferative SlamF6+ subset and a non-cycling SlamF6- subset. Blocking dLN egress decreased the frequency of intratumoral SlamF6+ TCF-1+ CD8+ T cells. Conventional type I dendritic cell (cDC1) in dLN decreased in number with tumor progression, and Flt3L+anti-CD40 treatment recovered SlamF6+ T cell frequencies and decreased tumor burden. Thus, cDC1s in tumor dLN maintain a reservoir of TCF-1+ CD8+ T cells and their decrease contributes to failed anti-tumor immunity.
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Research Support, N.I.H., Extramural |
4 |
160 |
3
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Ferrari A, Stark D, Peccatori FA, Fern L, Laurence V, Gaspar N, Bozovic-Spasojevic I, Smith O, De Munter J, Derwich K, Hjorth L, van der Graaf WTA, Soanes L, Jezdic S, Blondeel A, Bielack S, Douillard JY, Mountzios G, Saloustros E. Adolescents and young adults (AYA) with cancer: a position paper from the AYA Working Group of the European Society for Medical Oncology (ESMO) and the European Society for Paediatric Oncology (SIOPE). ESMO Open 2021; 6:100096. [PMID: 33926710 PMCID: PMC8103533 DOI: 10.1016/j.esmoop.2021.100096] [Citation(s) in RCA: 136] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 12/17/2022] Open
Abstract
It is well recognised that adolescents and young adults (AYA) with cancer have inequitable access to oncology services that provide expert cancer care and consider their unique needs. Subsequently, survival gains in this patient population have improved only modestly compared with older adults and children with cancer. In 2015, the European Society for Medical Oncology (ESMO) and the European Society for Paediatric Oncology (SIOPE) established the joint Cancer in AYA Working Group in order to increase awareness among adult and paediatric oncology communities, enhance knowledge on specific issues in AYA and ultimately improve the standard of care for AYA with cancer across Europe. This manuscript reflects the position of this working group regarding current AYA cancer care, the challenges to be addressed and possible solutions. Key challenges include the lack of specific biological understanding of AYA cancers, the lack of access to specialised centres with age-appropriate multidisciplinary care and the lack of available clinical trials with novel therapeutics. Key recommendations include diversifying interprofessional cooperation in AYA care and specific measures to improve trial accrual, including centralising care where that is the best means to achieve trial accrual. This defines a common vision that can lead to improved outcomes for AYA with cancer in Europe.
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Review |
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136 |
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Tekkis PP, Heriot AG, Smith O, Smith JJ, Windsor ACJ, Nicholls RJ. Long-term outcomes of restorative proctocolectomy for Crohn's disease and indeterminate colitis. Colorectal Dis 2005; 7:218-23. [PMID: 15859957 DOI: 10.1111/j.1463-1318.2005.00800.x] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION The present study aims to evaluate the short-term and long-term outcomes of patients undergoing restorative proctocolectomy (RPC) for Crohn's disease (CD) and Indeterminate colitis (IC) and to identify factors associated with adverse outcomes. METHODS A descriptive study of 52 patients with CD or IC from a total of 1652 patients undergoing primary or salvage RPC in a single tertiary referral centre between 1978 and 2003. Primary outcomes were ileal pouch failure (excision or indefinite diversion), adverse events and functional outcomes (bowel frequency, urgency and continence). RESULTS Patients with IC or IC favouring ulcerative colitis (Group 1, n = 26) had a pouch failure rate of 11.5%vs 57.5% for patients with CD or IC favouring CD (Group 2, n = 26). Pouch salvage surgery was undertaken in 15 patients with a 13.3% failure rate. Patients in Group 2 were 2.6 times more likely (95% CI: 0.96-7. No significant differences were evident between CD and IC patients with regards to pelvic sepsis (19.2%vs 15.4%), anastomotic stricture (23.1%vs 21.7%), small bowel obstruction (26.9%vs 26.9%) or pouchitis (15.4%vs 11.5%). The 24-h bowel frequency (7.5 vs 8), faecal urgency, daytime or night time incontinence were similar between patients with CD or IC..17) to develop a pouch-related fistula than patients in Group 1. DISCUSSION Crohn's disease and to a great extent indeterminate colitis favouring CD were both associated with high failure rates and postoperative pouch-related fistula rates. Despite these problems, functional outcomes for patients with CD or IC were similar. Patients with IC should remain candidates for RPC but careful pre-operative assessment is advised to exclude clinical signs favouring the diagnosis of CD. The complications associated with failure are extensive and the option of reconstructive surgery in patients with CD should be questioned.
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Comparative Study |
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Westcott PMK, Sacks NJ, Schenkel JM, Ely ZA, Smith O, Hauck H, Jaeger AM, Zhang D, Backlund CM, Beytagh MC, Patten JJ, Elbashir R, Eng G, Irvine DJ, Yilmaz OH, Jacks T. Low neoantigen expression and poor T-cell priming underlie early immune escape in colorectal cancer. NATURE CANCER 2021; 2:1071-1085. [PMID: 34738089 PMCID: PMC8562866 DOI: 10.1038/s43018-021-00247-z] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 07/16/2021] [Indexed: 02/08/2023]
Abstract
Immune evasion is a hallmark of cancer, and therapies that restore immune surveillance have proven highly effective in cancers with high tumor mutation burden (TMB) (e.g., those with microsatellite instability (MSI)). Whether low TMB cancers, which are largely refractory to immunotherapy, harbor potentially immunogenic neoantigens remains unclear. Here, we show that tumors from all patients with microsatellite stable (MSS) colorectal cancer (CRC) express clonal predicted neoantigens despite low TMB. Unexpectedly, these neoantigens are broadly expressed at lower levels compared to those in MSI CRC. Using a versatile platform for modulating neoantigen expression in CRC organoids and transplantation into the distal colon of mice, we show that low expression precludes productive cross priming and drives immediate T cell dysfunction. Strikingly, experimental or therapeutic rescue of priming rendered T cells capable of controlling tumors with low neoantigen expression. These findings underscore a critical role of neoantigen expression level in immune evasion and therapy response.
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Research Support, N.I.H., Extramural |
4 |
81 |
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Boublikova L, Kalinova M, Ryan J, Quinn F, O'Marcaigh A, Smith O, Browne P, Stary J, McCann SR, Trka J, Lawler M. Wilms' tumor gene 1 (WT1) expression in childhood acute lymphoblastic leukemia: a wide range of WT1 expression levels, its impact on prognosis and minimal residual disease monitoring. Leukemia 2005; 20:254-63. [PMID: 16341043 DOI: 10.1038/sj.leu.2404047] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Wilms' tumor gene 1 (WT1) is overexpressed in the majority (70-90%) of acute leukemias and has been identified as an independent adverse prognostic factor, a convenient minimal residual disease (MRD) marker and potential therapeutic target in acute leukemia. We examined WT1 expression patterns in childhood acute lymphoblastic leukemia (ALL), where its clinical implication remains unclear. Using a real-time quantitative PCR designed according to Europe Against Cancer Program recommendations, we evaluated WT1 expression in 125 consecutively enrolled patients with childhood ALL (106 BCP-ALL, 19 T-ALL) and compared it with physiologic WT1 expression in normal and regenerating bone marrow (BM). In childhood B-cell precursor (BCP)-ALL, we detected a wide range of WT1 levels (5 logs) with a median WT1 expression close to that of normal BM. WT1 expression in childhood T-ALL was significantly higher than in BCP-ALL (P<0.001). Patients with MLL-AF4 translocation showed high WT1 overexpression (P<0.01) compared to patients with other or no chromosomal aberrations. Older children (> or =10 years) expressed higher WT1 levels than children under 10 years of age (P<0.001), while there was no difference in WT1 expression in patients with peripheral blood leukocyte count (WBC) > or =50 x 10(9)/l and lower. Analysis of relapsed cases (14/125) indicated that an abnormal increase or decrease in WT1 expression was associated with a significantly increased risk of relapse (P=0.0006), and this prognostic impact of WT1 was independent of other main risk factors (P=0.0012). In summary, our study suggests that WT1 expression in childhood ALL is very variable and much lower than in AML or adult ALL. WT1, thus, will not be a useful marker for MRD detection in childhood ALL, however, it does represent a potential independent risk factor in childhood ALL. Interestingly, a proportion of childhood ALL patients express WT1 at levels below the normal physiological BM WT1 expression, and this reduced WT1 expression appears to be associated with a higher risk of relapse.
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Galligan L, Livingstone W, Volkov Y, Hokamp K, Murphy C, Lawler M, Fukudome K, Smith O. Characterization of protein C receptor expression in monocytes. Br J Haematol 2001; 115:408-14. [PMID: 11703343 DOI: 10.1046/j.1365-2141.2001.03187.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Many sequelae associated with endotoxaemic-induced shock result from excessive production of the cytokine mediators, tumour necrosis factor alpha (TNF-alpha), interleukin 1 (IL-1) and IL-6 from lipopolysaccharide (LPS)-activated monocytes. Protein C (PC)/activated protein C (APC) has potent cytokine-modifying properties and is protective in animal models and human clinical trials of sepsis. The precise mechanism by which this anti-inflammatory response is achieved remains unknown; however, the recently described endothelial protein C receptor (EPCR) appears to be essential for this function. The pivotal role that monocytes play in the pathophysiology of septic shock led us to investigate the possible expression of a protein C receptor on the monocyte membrane. We used similarity algorithms to screen human sequence databases for paralogues of the EPCR but found none. However, using reverse transcription-polymerase chain reaction (RT-PCR), we detected an mRNA transcribed in primary human monocytes and THP1 cells that was identical to human EPCR mRNA. We also used immunocytochemical analysis to demonstrate the expression of a protein C receptor on the surface of monocytes encoded by the same gene as EPCR. These results confirm a new member of the protein C pathway involving primary monocytes. Further characterization will be necessary to compare and contrast its biological properties with those of EPCR.
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Ljung R, Aronis-Vournas S, Kurnik-Auberger K, van den Berg M, Chambost H, Claeyssens S, van Geet C, Glomstein A, Hann I, Hill F, Kobelt R, Kreuz W, Mancuso G, Muntean W, Petrini P, Rosado L, Scheibel E, Siimes M, Smith O, Tusell J. Treatment of children with haemophilia in Europe: a survey of 20 centres in 16 countries. Haemophilia 2000; 6:619-24. [PMID: 11122385 DOI: 10.1046/j.1365-2516.2000.00427.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A survey was made of the current status of treatment of haemophilic boys at 20 centres in 16 European countries and includes approximately 1500 of the estimated 6500 haemophiliacs in the participating countries. Many mild haemophiliacs are not seen, or seen infrequently, at haemophilia centres and this requires study. Nine of 18 centres provide continuous prophylaxis to 80-100% of their patients, five centres provide it to 55-80% and the remaining four centres to 15-40% of the boys. The median dose given was 6240 U kg-1 year-1 (range 3120-7800). Four centres administered only recombinant concentrates to children with severe haemophilia A, while seven centres administered recombinant concentrates to 75-90% and the remaining centres to less than 50% of the boys (two centres < 10%). When asked for the choice of concentrate for a newly diagnosed boy with severe haemophilia A, all but one centre preferred recombinant concentrate. Most boys below 6 years received concentrates via a peripheral vein but three centres preferred a central venous line for 80-100% of the boys. Thirteen of 18 centres applied home treatment to 84-100% of the boys and the remaining five centres to 57-77% of the boys.
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Li A, Herbst RH, Canner D, Schenkel JM, Smith OC, Kim JY, Hillman M, Bhutkar A, Cuoco MS, Rappazzo CG, Rogers P, Dang C, Jerby-Arnon L, Rozenblatt-Rosen O, Cong L, Birnbaum M, Regev A, Jacks T. IL-33 Signaling Alters Regulatory T Cell Diversity in Support of Tumor Development. Cell Rep 2020; 29:2998-3008.e8. [PMID: 31801068 PMCID: PMC6990979 DOI: 10.1016/j.celrep.2019.10.120] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 09/07/2019] [Accepted: 10/29/2019] [Indexed: 02/08/2023] Open
Abstract
Regulatory T cells (Tregs) can impair anti-tumor immune responses and are associated with poor prognosis in multiple cancer types. Tregs in human tumors span diverse transcriptional states distinct from those of peripheral Tregs, but their contribution to tumor development remains unknown. Here, we use single-cell RNA sequencing (RNA-seq) to longitudinally profile dynamic shifts in the distribution of Tregs in a genetically engineered mouse model of lung adenocarcinoma. In this model, interferon-responsive Tregs are more prevalent early in tumor development, whereas a specialized effector phenotype characterized by enhanced expression of the interleukin-33 receptor ST2 is predominant in advanced disease. Treg-specific deletion of ST2 alters the evolution of effector Treg diversity, increases infiltration of CD8+ T cells into tumors, and decreases tumor burden. Our study shows that ST2 plays a critical role in Treg-mediated immunosuppression in cancer, highlighting potential paths for therapeutic intervention.
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Research Support, Non-U.S. Gov't |
5 |
58 |
10
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Burton JL, Lidbury EA, Gillespie AM, Tidy JA, Smith O, Lawry J, Hancock BW, Wells M. Over-diagnosis of hydatidiform mole in early tubal ectopic pregnancy. Histopathology 2001; 38:409-17. [PMID: 11422477 DOI: 10.1046/j.1365-2559.2001.01151.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS Tubal ectopic hydatidiform moles are rare lesions, and only 40 cases have been reported in the world literature. We investigated the apparently high incidence of tubal ectopic hydatidiform moles in women referred for treatment to a Supraregional Trophoblastic Tumour Screening and Treatment Centre between 1986 and 1996. METHODS AND RESULTS Of 4261 women referred during the study period, 25 (0.6%) had a suspected tubal ectopic hydatidiform mole and paraffin-embedded tissue was available in 20 (80%) of these. Each case was reviewed by two pathologists and DNA flow cytometric analysis was undertaken when the histological diagnosis was initially deemed equivocal or suggestive of hydatidiform mole. On review, 17 cases (85%) showed no evidence of hydatidiform mole (circumferential trophoblastic proliferation, hydrops, scalloped villi, and stromal karyorrhexis). Of these, 11 cases (65%) showed features of early placentation and six (35%) showed hydropic abortion. DNA flow cytometry was performed in 14 (82%) of these cases and revealed a diploid population in each case. Three cases of molar pregnancy (15%) were identified. Each of these cases had the histological features of an early complete hydatidiform mole. Sufficient tissue was available for DNA flow cytometric analysis in two of these cases and confirmed the presence of diploidy in each. CONCLUSION Our results show that tubal ectopic hydatidiform mole is a rare entity and demonstrate that it is over-diagnosed. Polar trophoblastic proliferation and hydropic villi are features of early placentation and of hydropic abortion. Sheets of extravillous trophoblast may be particularly prominent in tubal ectopic gestation. In the absence of circumferential trophoblastic proliferation combined with hydropic change a diagnosis of gestational trophoblastic disease should be avoided.
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Durham ND, Agrawal A, Waltari E, Croote D, Zanini F, Fouch M, Davidson E, Smith O, Carabajal E, Pak JE, Doranz BJ, Robinson M, Sanz AM, Albornoz LL, Rosso F, Einav S, Quake SR, McCutcheon KM, Goo L. Broadly neutralizing human antibodies against dengue virus identified by single B cell transcriptomics. eLife 2019; 8:e52384. [PMID: 31820734 PMCID: PMC6927745 DOI: 10.7554/elife.52384] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 12/09/2019] [Indexed: 12/23/2022] Open
Abstract
Eliciting broadly neutralizing antibodies (bNAbs) against the four dengue virus serotypes (DENV1-4) that are spreading into new territories is an important goal of vaccine design. To define bNAb targets, we characterized 28 antibodies belonging to expanded and hypermutated clonal families identified by transcriptomic analysis of single plasmablasts from DENV-infected individuals. Among these, we identified J9 and J8, two somatically related bNAbs that potently neutralized DENV1-4. Mutagenesis studies showed that the major recognition determinants of these bNAbs are in E protein domain I, distinct from the only known class of human bNAbs against DENV with a well-defined epitope. B cell repertoire analysis from acute-phase peripheral blood suggested that J9 and J8 followed divergent somatic hypermutation pathways, and that a limited number of mutations was sufficient for neutralizing activity. Our study suggests multiple B cell evolutionary pathways leading to DENV bNAbs targeting a new epitope that can be exploited for vaccine design.
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Research Support, N.I.H., Extramural |
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44 |
12
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Adamson PA, Smith O, Tropper GJ. Incision and scar analysis in open (external) rhinoplasty. ARCHIVES OF OTOLARYNGOLOGY--HEAD & NECK SURGERY 1990; 116:671-5. [PMID: 2340118 DOI: 10.1001/archotol.1990.01870060029003] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Open (external) rhinoplasty is becoming increasingly popular. Two of its disadvantages most frequently espoused are the difficulty in making the external incision atraumatically and the resulting scar. To diminish these concerns, different incision lines and methods of exposure have been proposed by various authors. These are reviewed along with our preferred technique. We reviewed 100 consecutive cases of open rhinoplasty, yielding 81 patients who underwent subjective and objective scar analysis. There was 1 subjective failure (1.2%), and 2 minor objective failures (2.5%). Recommendations are made to minimize difficulties in performing the open approach and to maximize scar cosmesis.
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Bloch SE, Clark R, Gottlieb SS, Wood LK, Shah N, Mak SM, Lorigan JG, Johnson J, Davis-Richardson AG, Williams L, McKellar M, Soriano D, Petersen M, Horton A, Smith O, Wu L, Tung E, Broglie R, Tamsir A, Temme K. Biological nitrogen fixation in maize: optimizing nitrogenase expression in a root-associated diazotroph. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4591-4603. [PMID: 32267497 PMCID: PMC7382387 DOI: 10.1093/jxb/eraa176] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 04/09/2020] [Indexed: 05/04/2023]
Abstract
Plants depend upon beneficial interactions between roots and root-associated microorganisms for growth promotion, disease suppression, and nutrient availability. This includes the ability of free-living diazotrophic bacteria to supply nitrogen, an ecological role that has been long underappreciated in modern agriculture for efficient crop production systems. Long-term ecological studies in legume-rhizobia interactions have shown that elevated nitrogen inputs can lead to the evolution of less cooperative nitrogen-fixing mutualists. Here we describe how reprogramming the genetic regulation of nitrogen fixation and assimilation in a novel root-associated diazotroph can restore ammonium production in the presence of exogenous nitrogen inputs. We isolated a strain of the plant-associated proteobacterium Kosakonia sacchari from corn roots, characterized its nitrogen regulatory network, and targeted key nodes for gene editing to optimize nitrogen fixation in corn. While the wild-type strain exhibits repression of nitrogen fixation in conditions replete with bioavailable nitrogen, such as fertilized greenhouse and field experiments, remodeled strains show elevated levels in the rhizosphere of corn in the greenhouse and field even in the presence of exogenous nitrogen. Such strains could be used in commercial applications to supply fixed nitrogen to cereal crops.
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research-article |
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Xia W, Smith O, Zmora N, Xu S, Zohar Y. Comprehensive analysis of GnRH2 neuronal projections in zebrafish. Sci Rep 2014; 4:3676. [PMID: 24419253 PMCID: PMC3891355 DOI: 10.1038/srep03676] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 12/13/2013] [Indexed: 11/26/2022] Open
Abstract
The presence and conservation of GnRH2 across vertebrate species suggest important biological roles. However, the function of GnRH2 remains unclear. A good research model for GnRH2 functional studies is still lacking largely due to the absence of GnRH2 in the widely used mouse model. Hence, we used the zebrafish, for which powerful genetic tools are available, and developed a transgenic (Tg) line expressing enhanced green fluorescence protein (eGFP). The high sensitivity of eGFP, which can diffuse throughout the neuron, enables us to document the complete projectome of GnRH2 neurons at different developmental stages. Fine projection structures were observed without sacrificing the fish. Crossed with the GnRH3:tdTomato Tg line, the GnRH2:eGFP Tg line provides us with an opportunity to visualize the entire GnRH system simultaneously in one organism. This work will provide a framework to understand the function of the highly-conserved GnRH2 system.
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Journal Article |
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Williams Y, Lynch S, McCann S, Smith O, Feighery C, Whelan A. Correlation of platelet Fc gammaRIIA polymorphism in refractory idiopathic (immune) thrombocytopenic purpura. Br J Haematol 1998; 101:779-82. [PMID: 9674755 DOI: 10.1046/j.1365-2141.1998.00802.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Fc gammaRIIA, a low affinity receptor for IgG, is a polymorphic molecule: Fc gammaRIIA-HH131, Fc gammaRIIA-HR131 and Fc gammaRIIA-RR131. This polymorphism influences the efficiency of the receptor to bind with IgG2. Recent reports on altered distribution amongst individuals with heparin-induced thrombocytopenia (HIT) prompted us to examine the Fc gammaRIIA polymorphism in a cohort of patients with refractory idiopathic (immune) thrombocytopenic purpura (ITP), in whom severe disease had required them to undergo splenectomy. 29 post splenectomy ITP individuals and 61 normal controls were investigated. Polymerase chain reaction (PCR) and a Southern blotting technique were used to determine the Fc gammaRII polymorphism. Although the distribution of the allotypes of Fc gammaRIIA in the control population was similar to that found in other European studies of Caucasian populations (15 (25%) HH131; 35 (57%) HR131; 11 (18%) RR131), the patient group was skewed towards the RR131 allotype which has least efficiency for IgG2 binding (3 (10%) HH131; 12 (42%) HR131; 14 (48%) RR131; P<0.005). These findings suggest that Fc gammaRIIA polymorphisms may be implicated in the pathophysiology of ITP or may be responsible for modulating the immune response in this heterogeneous autoimmune disease.
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Abstract
Fifty patients who primarily desired cosmetic improvement underwent nasal airflow studies using posterior rhinomanometry before and after reduction rhinoplasty. There was no significant difference in nasal resistance before and after surgery. This study demonstrates that neither subjective nor objective nasal obstruction follows reduction rhinoplasty, despite the potential for a decreased cross-sectional area of the valve region.
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Al-Abdulhadi SA, Helms PJ, Main M, Smith O, Christie G. Preferential transmission and association of the -403 G --> A promoter RANTES polymorphism with atopic asthma. Genes Immun 2005; 6:24-30. [PMID: 15592421 DOI: 10.1038/sj.gene.6364151] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Asthma is a complex inherited disease. The study was undertaken to identify the association of RANTES promoter polymorphisms with atopy and asthma using family-based association tests (FBATs) and generation-specific case-control analyses. We identified 154 nuclear families (453 individuals) in whom we established RANTES promoter status using the RFLP-PCR method. Of the two known promoter polymorphisms -403G/A and -28C/G, only the former appeared with a clinically relevant frequency. A total of 61 families were eligible for assessment of transmission of the allele with asthma and atopy by the pedigree disequilibrium test (PDT). Overall, allele frequency for -403A was 38.3% and 84 of 89 (94.3%) alleles were transmitted with physician diagnosed asthma (PDA) (P=0.001). All 89 children with atopy received the mutant allele, which was more than expected following Mendelian Laws of transmission (P=0.0001). In 303 unrelated parents, significant associations of the mutant allele were for atopy with or without asthma (P=0.001). In 150 unrelated children, significant associations were for atopy alone (P=0.001) and asthma (P=0.001). No associations were found for bronchial hyper-responsiveness (BHR). The -403 G --> A is transmitted with atopy and atopic asthma, although its contribution appears to relate more to atopy than asthma and BHR.
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Journal Article |
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Lin F, Murphy R, White B, Kelly J, Feighery C, Doyle R, Pittock S, Moroney J, Smith O, Livingstone W, Keenan C, Jackson J. Circulating levels of beta2-glycoprotein I in thrombotic disorders and in inflammation. Lupus 2006; 15:87-93. [PMID: 16539279 DOI: 10.1191/0961203306lu2270oa] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Beta2-glycoprotein I (beta2GPI) is a plasma protein suspected to have a role in inhibition of thrombosis. This suspicion is reinforced by the observation that beta2GPI is the major target for autoantibodies in the antiphospholipid syndrome. However, little is known about its circulating levels in common thrombotic diseases or inflammation. We measured beta2GPI levels in 344 healthy controls, 58 normal pregnancies, 102 patients with non-haemorrhagic stroke, 121 patients with acute coronary syndrome and 200 patients with elevated C-reactive protein (CRP). In healthy individuals, we found a strong positive correlation between age and beta2GPI concentration (r = 0.274, P < 0.001) and that beta2GPI levels fall significantly after the eighth week of pregnancy (P = 0.002). We also found significantly reduced levels of beta2GPI in patients with stroke and in elderly patients with myocardial syndrome (P = 0.013 and 0.043). However, in neither group did beta2GPI levels change in the following six months, suggesting that the reduced levels were not a transient post-event phenomenon. In patients with inflammation, beta2GPI levels showed a significant negative correlation with CRP (r = -0.284, P < 0.001) and positively correlated with albumin and transferrin (r = 0.372 and 0.453, respectively with P < 0.001 for both). Furthermore, the largest reduction in beta2GPI levels occurred in patients with the highest CRP values (P < 0.001).
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Journal Article |
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Bavin EP, Smith O, Baird AEG, Smith LC, Guest DJ. Equine Induced Pluripotent Stem Cells have a Reduced Tendon Differentiation Capacity Compared to Embryonic Stem Cells. Front Vet Sci 2015; 2:55. [PMID: 26664982 PMCID: PMC4672282 DOI: 10.3389/fvets.2015.00055] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 10/30/2015] [Indexed: 12/23/2022] Open
Abstract
Tendon injuries occur commonly in horses and their repair through scar tissue formation predisposes horses to a high rate of re-injury. Pluripotent stem cells may provide a cell replacement therapy to improve tendon tissue regeneration and lower the frequency of re-injury. We have previously demonstrated that equine embryonic stem cells (ESCs) differentiate into the tendon cell lineage upon injection into the damaged horse tendon and can differentiate into functional tendon cells in vitro to generate artificial tendons. Induced pluripotent stem cells (iPSCs) have now been derived from horses but, to date, there are no reports on their ability to differentiate into tendon cells. As iPSCs can be produced from adult cell types, they provide a more accessible source of cells than ESCs, which require the use of horse embryos. The aim of this study was to compare tendon differentiation by ESCs and iPSCs produced through two independent methods. In two-dimensional differentiation assays, the iPSCs expressed tendon-associated genes and proteins, which were enhanced by the presence of transforming growth factor-β3. However, in three-dimensional (3D) differentiation assays, the iPSCs failed to differentiate into functional tendon cells and generate artificial tendons. These results demonstrate the utility of the 3D in vitro tendon assay for measuring tendon differentiation and the need for more detailed studies to be performed on equine iPSCs to identify and understand their epigenetic differences from pluripotent ESCs prior to their clinical application.
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Guerin J, Smith O, White B, Sweetman G, Feighery C, Jackson J. Antibodies to prothrombin in antiphospholipid syndrome and inflammatory disorders. Br J Haematol 1998; 102:896-902. [PMID: 9734636 DOI: 10.1046/j.1365-2141.1998.00876.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Antiphospholipid antibodies associated with the antiphospholipid syndrome (APS) have been shown to bind plasma proteins, particularly beta 2-glycoprotein I (beta2-GPI). In this study the incidence of antibodies to solid-phase prothrombin was examined in patients with antiphospholipid syndrome and a variety of other inflammatory disorders. Significantly elevated levels of IgG anti-prothrombin (anti-PT) antibodies were detected in 63% of patients with APS (n = 27, median 22 arbitrary units: AU), 33% with SLE (n = 92, median 14 AU). 45% with rheumatoid factor (n = 22, median 16 AU), 21% with carotid artery stenosis (n = 21, median 15 AU), 32% with stroke (n = 38, median 13 AU). 67% of patients with a false positive serology for syphilis (n = 21, median 24 AU), 37% with HIV (n = 30, median 14 AU), 29% with syphilis (n = 14, median 19 AU) and 3% with infectious mononucleosis (n= 30, median 9 AU). In addition, a group of lupus anticoagulant (LA) positive patients (n = 48) was examined for antibodies to prothrombin, beta2-GPI and cardiolipin. 10 (21%) patients had raised levels of IgG anti-PT antibodies, 30 (62%) had significantly elevated levels of anti-beta2-GPI antibodies and 15 (31%) had elevated levels of anticardiolipin antibodies (ACA). Of the LA-positive patients, 15 (43%) were identified with definite APS, eight (23%) with probable APS, two (6%) with possible APS and 10 (28%) patients had no clinical evidence of APS. In conclusion, antibodies to prothrombin were found in a variety of inflammatory disorders and were therefore not specific for the APS. However, identification of the plasma proteins recognized by antibodies from patients with APS may provide insight into the pathogenic mechanisms involved in the heterogenous clinical manifestations of the APS.
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Chen C, Smith OC, McChesney J. Biosynthesis and cytokinin activity of 8-hydroxy and 2,8-dihydroxy derivatives of zeatin and N-6(increment-2-isopentenyl)adenine. Biochemistry 1975; 14:3088-93. [PMID: 1148191 DOI: 10.1021/bi00685a008] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
8-Hydroxy and 2,8-dihydroxy derivatives of the cytokinins, 6-(4-hydroxy-3-methyl-trans-2-butenylamino)purine and N-6-(increment -2-isopentenyl)adenine, have been biosynthesized by xanthine oxidase oxidation. 8-Hydroxy derivatives have been shown to be the major intermdeiates. These compounds were tested for cytokinin activity in the tobacco bioassay. The results suggest that substitution of the 8 position with a hydroxyl group causes less decrease of cytokinin activity than substitution of both the 2 and 8 positions with hydroxyl groups.
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Sanfilippo JS, Yussman MA, Smith O. Hysterosalpingography in the evaluation of infertility: a six-year review. Fertil Steril 1978; 30:636-43. [PMID: 729824 DOI: 10.1016/s0015-0282(16)43689-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A series of 505 consecutive hysterosalpingograms (HSG) for the evaluation of infertility is reviewed. Two hundred and seventy-five (54.3%) were interpreted as normal. A tubal abnormality was found in 188 (37.2%) and a uterine abnormality in 42 (8.5%). The literature is reviewed. Hysterosalpingographic abnormalities in the present series are compared with those reported in studies previously published. Complications and advantages of the procedure are outlined. Analysis of the results shows a low morbidity and high return (45.7% abnormal), making HSG one of the most valuable tools in the initial evaluation of the infertile couple.
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Wyld L, Smith O, Lawry J, Reed MW, Brown NJ. Cell cycle phase influences tumour cell sensitivity to aminolaevulinic acid-induced photodynamic therapy in vitro. Br J Cancer 1998; 78:50-5. [PMID: 9662250 PMCID: PMC2062939 DOI: 10.1038/bjc.1998.441] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Photodynamic therapy (PDT) is a form of cancer treatment based on the destruction of cells by the interaction of light, oxygen and a photosensitizer. Aminolaevulinic acid (ALA) is the prodrug of the photosensitizer protoporphyrin IX (PpIX). ALA-induced PDT depends on the rate of cellular synthesis of PpIX, which may vary with cell cycle phase. This study has investigated the relationship between cell cycle phase, PpIX generation and phototoxicity in synchronized and unsynchronized bladder cancer cells (HT1197). In unsynchronized cells, relative PpIX fluorescence values (arbitrary units) were significantly different between cell cycle phases after a 1-h ALA incubation (G1 24.8 +/- 0.7; S-phase, 32.7 +/- 0.8, P < 0.05; G2 35.4 +/- 0.8, P < 0.05). In synchronized cells after a 1-h ALA incubation, cells in G1 produced less PpIX than those in S-phase or G2 [6.65 +/- 1.1 ng per 10(5) cells compared with 15.5 +/- 2.1 (P < 0.05), and 8.1 +/- 1.8 ng per 10(5) cells (not significant) respectively] and were significantly less sensitive to ALA-induced PDT (% survival, G1 76.2 +/- 8.3; S-phase 49.7 +/- 4.6, P < 0.05; G2 44.2 +/- 2.4, P < 0.05). This differential response in tumour cells may have implications for clinical PDT, resulting in treatment resistance and possible failure in complete tumour response.
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research-article |
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Abstract
Recent research suggests that cells respond to electromagnetic fields in the same ways as they do to other environmental stresses.
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Review |
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Thompson SA, Smith O, Linn DM, Linn CL. Acetylcholine neuroprotection against glutamate-induced excitotoxicity in adult pig retinal ganglion cells is partially mediated through alpha4 nAChRs. Exp Eye Res 2006; 83:1135-45. [PMID: 16928373 DOI: 10.1016/j.exer.2006.05.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2006] [Revised: 05/21/2006] [Accepted: 05/31/2006] [Indexed: 01/10/2023]
Abstract
In the mammalian retina, excess glutamate release has been shown to be involved in retinal ganglion cell (RGC) death associated with various diseases. Recent studies have determined that activation of alpha7 nicotinic acetylcholine receptors (nAChRs) partially protect isolated RGCs from glutamate-induced excitotoxicity. In this study, we further classify the types of nAChRs involved in neuroprotection against glutamate-induced excitotoxicity using isolated adult pig RGCs. Cells were isolated with a modified two-step immunoselective panning technique designed to isolate RGCs from other retinal neurons. Once isolated, nAChR subunits were identified using a combination of pharmacological and immunocytochemical techniques. In cell culture experiments, a variety of alpha4 nAChR specific agonists were found to have a partial neuroprotective against glutamate-induced excitotoxicity. This neuroprotection was abolished in the presence of the alpha4 nAChR antagonist, dihydro-beta-erythroidine (DHbetaE). Immunocytochemical results localized several nAChR subunits on isolated adult pig RGCs; in particular alpha4, alpha7 and beta2 nAChR subunits. Large RGCs exclusively immunostained with antibodies against alpha7 nAChR subunits whereas alpha4 and beta2 subunits exclusively immunostained only small RGCs. Double label experiments provided evidence that alpha4 and beta2 subunits co-localize on small RGCs. Knowledge of the receptor subtypes responsible for neuroprotection may lead to treatments associated with glutamate-induced excitotoxicity.
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Research Support, U.S. Gov't, Non-P.H.S. |
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