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Smith K, Moore A, Popov S, Adams M, Folaranmi E, Sekaran P. 671 Fetus-In-Fetu Found at Excision of An Antenatally Diagnosed Abdominal Mass: Multi-Disciplinary Approach. Br J Surg 2021. [DOI: 10.1093/bjs/znab259.681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
We present a case of antenatally detected abdominal mass and an alternative diagnostic course for suspected neonatal neuroblastoma as a result of investigative findings. A female infant presented antenatally with a left upper quadrant mass initially managed as a suspected neonatal neuroblastoma; further cross-sectional imaging suggested a wider differential including teratoma and aided surgical planning. The multi-disciplinary team (MDT) decision was for an early excision at 31 days and post-operative histology identified a diagnosis of fetus-in-fetu (FIF). We describe this case as a compliment to the current literature and an example of a necessary variation to recognised diagnostic and treatment pathways as a result of investigative findings.
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O'Leary C, Monkman J, Kirkby B, Matigian N, Kulasinghe A, McCaffrey E, Richard D, Adams M, O'Byrne K. 1797P Polo-like kinase-1 as a biomarker in resected non-small cell lung cancer. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.08.1739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Abazov VM, Abbott B, Acharya BS, Adams M, Adams T, Agnew JP, Alexeev GD, Alkhazov G, Alton A, Alves GA, Antchev G, Askew A, Aspell P, Assis Jesus ACS, Atanassov I, Atkins S, Augsten K, Aushev V, Aushev Y, Avati V, Avila C, Badaud F, Baechler J, Bagby L, Baldenegro Barrera C, Baldin B, Bandurin DV, Banerjee S, Barberis E, Baringer P, Barreto J, Bartlett JF, Bassler U, Bazterra V, Bean A, Begalli M, Bellantoni L, Berardi V, Beri SB, Bernardi G, Bernhard R, Berretti M, Bertram I, Besançon M, Beuselinck R, Bhat PC, Bhatia S, Bhatnagar V, Blazey G, Blessing S, Bloom K, Boehnlein A, Boline D, Boos EE, Borchsh V, Borissov G, Borysova M, Bossini E, Bottigli U, Bozzo M, Brandt A, Brandt O, Brochmann M, Brock R, Bross A, Brown D, Bu XB, Buehler M, Buescher V, Bunichev V, Burdin S, Burkhardt H, Buszello CP, Cafagna FS, Camacho-Pérez E, Carvalho W, Casey BCK, Castilla-Valdez H, Catanesi MG, Caughron S, Chakrabarti S, Chan KM, Chandra A, Chapon E, Chen G, Cho SW, Choi S, Choudhary B, Cihangir S, Claes D, Clutter J, Cooke M, Cooper WE, Corcoran M, Couderc F, Cousinou MC, Csanád M, Csörgő T, Cuth J, Cutts D, da Motta H, Das A, Davies G, Deile M, de Jong SJ, De La Cruz-Burelo E, De Leonardis F, Déliot F, Demina R, Denisov D, Denisov SP, De Oliveira Martins C, Desai S, Deterre C, DeVaughan K, Diehl HT, Diesburg M, Ding PF, Dominguez A, Doubek M, Drutskoy A, Druzhkin D, Dubey A, Dudko LV, Duperrin A, Dutt S, Eads M, Edmunds D, Eggert K, Ellison J, Elvira VD, Enari Y, Eremin V, Evans H, Evdokimov A, Evdokimov VN, Fauré A, Feng L, Ferbel T, Ferro F, Fiedler F, Fiergolski A, Filthaut F, Fisher W, Fisk HE, Forthomme L, Fortner M, Fox H, Franc J, Fuess S, Garbincius PH, Garcia F, Garcia-Bellido A, García-González JA, Gavrilov V, Geng W, Georgiev V, Gerber CE, Gershtein Y, Giani S, Ginther G, Gogota O, Golovanov G, Grannis PD, Greder S, Greenlee H, Grenier G, Gris P, Grivaz JF, Grohsjean A, Grünendahl S, Grünewald MW, Grzanka L, Guillemin T, Gutierrez G, Gutierrez P, Haley J, Hammerbauer J, Han L, Harder K, Harel A, Hauptman JM, Hays J, Head T, Hebbeker T, Hedin D, Hegab H, Heinson AP, Heintz U, Hensel C, Heredia-De La Cruz I, Herner K, Hesketh G, Hildreth MD, Hirosky R, Hoang T, Hobbs JD, Hoeneisen B, Hogan J, Hohlfeld M, Holzbauer JL, Howley I, Hubacek Z, Hynek V, Iashvili I, Ilchenko Y, Illingworth R, Isidori T, Ito AS, Ivanchenko V, Jabeen S, Jaffré M, Janda M, Jayasinghe A, Jeong MS, Jesik R, Jiang P, Johns K, Johnson E, Johnson M, Jonckheere A, Jonsson P, Joshi J, Jung AW, Juste A, Kajfasz E, Karev A, Karmanov D, Kašpar J, Katsanos I, Kaur M, Kaynak B, Kehoe R, Kermiche S, Khalatyan N, Khanov A, Kharchilava A, Kharzheev YN, Kiselevich I, Kohli JM, Kopal J, Kozelov AV, Kraus J, Kumar A, Kundrát V, Kupco A, Kurča T, Kuzmin VA, Lami S, Lammers S, Latino G, Lebrun P, Lee HS, Lee SW, Lee WM, Le X, Lellouch J, Li D, Li H, Li L, Li QZ, Lim JK, Lincoln D, Lindsey C, Linhart R, Linnemann J, Lipaev VV, Lipton R, Liu H, Liu Y, Lobodenko A, Lokajicek M, Lokajíček MV, Lopes de Sa R, Losurdo L, Lucas Rodríguez F, Luna-Garcia R, Lyon AL, Maciel AKA, Macrí M, Madar R, Magaña-Villalba R, Malawski M, Malbouisson HB, Malik S, Malyshev VL, Mansour J, Martínez-Ortega J, McCarthy R, McGivern CL, Meijer MM, Melnitchouk A, Menezes D, Mercadante PG, Merkin M, Meyer A, Meyer J, Miconi F, Minafra N, Minutoli S, Molina J, Mondal NK, Mulhearn M, Mundim L, Naaranoja T, Nagy E, Narain M, Nayyar R, Neal HA, Negret JP, Nemes F, Neustroev P, Nguyen HT, Niewiadomski H, Novák T, Nunnemann T, Oguri V, Oliveri E, Oljemark F, Orduna J, Oriunno M, Osman N, Österberg K, Pal A, Palazzi P, Parashar N, Parihar V, Park SK, Partridge R, Parua N, Pasechnik R, Passaro V, Patwa A, Penning B, Perfilov M, Peroutka Z, Peters Y, Petridis K, Petrillo G, Pétroff P, Pleier MA, Podstavkov VM, Popov AV, Prado da Silva WL, Prewitt M, Price D, Procházka J, Prokopenko N, Qian J, Quadt A, Quinn B, Quinto M, Raben TG, Radermacher E, Radicioni E, Rangel M, Ratoff PN, Ravotti F, Razumov I, Ripp-Baudot I, Rizatdinova F, Robutti E, Rodrigues RF, Rominsky M, Ross A, Royon C, Rubinov P, Ruchti R, Ruggiero G, Saarikko H, Sajot G, Samoylenko VD, Sánchez-Hernández A, Sanders MP, Santoro A, Santos AS, Savage G, Savitskyi M, Sawyer L, Scanlon T, Schamberger RD, Scheglov Y, Schellman H, Schott M, Schwanenberger C, Schwienhorst R, Scribano A, Sekaric J, Severini H, Shabalina E, Shary V, Shaw S, Shchukin AA, Shkola O, Simak V, Siroky J, Skubic P, Slattery P, Smajek J, Snoeys W, Snow GR, Snow J, Snyder S, Söldner-Rembold S, Sonnenschein L, Soustruznik K, Stark J, Stefaniuk N, Stefanovitch R, Ster A, Stoyanova DA, Strauss M, Suter L, Svoisky P, Szanyi I, Sziklai J, Taylor C, Tcherniaev E, Titov M, Tokmenin VV, Tsai YT, Tsybychev D, Tuchming B, Tully C, Turini N, Urban O, Uvarov L, Uvarov S, Uzunyan S, Vacek V, Van Kooten R, van Leeuwen WM, Varelas N, Varnes EW, Vasilyev IA, Vavroch O, Verkheev AY, Vertogradov LS, Verzocchi M, Vesterinen M, Vilanova D, Vokac P, Wahl HD, Wang C, Wang MHLS, Warchol J, Watts G, Wayne M, Weichert J, Welti J, Welty-Rieger L, Williams J, Williams MRJ, Wilson GW, Wobisch M, Wood DR, Wyatt TR, Xie Y, Yamada R, Yang S, Yasuda T, Yatsunenko YA, Ye W, Ye Z, Yin H, Yip K, Youn SW, Yu JM, Zennamo J, Zhao TG, Zhou B, Zhu J, Zich J, Zielinski K, Zielinski M, Zieminska D, Zivkovic L. Odderon Exchange from Elastic Scattering Differences between pp and pp[over ¯] Data at 1.96 TeV and from pp Forward Scattering Measurements. PHYSICAL REVIEW LETTERS 2021; 127:062003. [PMID: 34420329 DOI: 10.1103/physrevlett.127.062003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/19/2021] [Accepted: 06/10/2021] [Indexed: 06/13/2023]
Abstract
We describe an analysis comparing the pp[over ¯] elastic cross section as measured by the D0 Collaboration at a center-of-mass energy of 1.96 TeV to that in pp collisions as measured by the TOTEM Collaboration at 2.76, 7, 8, and 13 TeV using a model-independent approach. The TOTEM cross sections, extrapolated to a center-of-mass energy of sqrt[s]=1.96 TeV, are compared with the D0 measurement in the region of the diffractive minimum and the second maximum of the pp cross section. The two data sets disagree at the 3.4σ level and thus provide evidence for the t-channel exchange of a colorless, C-odd gluonic compound, also known as the odderon. We combine these results with a TOTEM analysis of the same C-odd exchange based on the total cross section and the ratio of the real to imaginary parts of the forward elastic strong interaction scattering amplitude in pp scattering for which the significance is between 3.4σ and 4.6σ. The combined significance is larger than 5σ and is interpreted as the first observation of the exchange of a colorless, C-odd gluonic compound.
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Podnar JW, Pantano L, Zeller MJ, Kolling FW, Zhang Y, Alekseyev YO, Niece J, Deiderick H, Fan J, Xuei X, Kieleczawa J, Levine SS, Herbert ZT, Adams M. Cross-Site Evaluation of Commercial Sanger Sequencing Chemistries. J Biomol Tech 2021; 31:88-93. [PMID: 32831655 DOI: 10.7171/jbt.20-3103-002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Sanger sequencing remains an essential tool utilized by researchers. Despite competition from commercial sequencing providers, many academic sequencing core facilities continue to offer these services based on a model of competitive pricing, knowledgeable technical support, and rapid turnaround time. In-house Sanger sequencing remains a viable core service and, until recently, Applied Biosystems BigDye Terminator chemistry was the only commercially available solution for Sanger DNA sequencing on Applied Biosystems (ABI) instruments; however, several new products employing novel dye chemistries and reaction configurations have entered the market. As a result, there is a need to benchmark the performance of these new chemistries on various DNA templates, including difficult-to-sequence templates, and their amenability to commonly employed cost-saving measures, such as dye dilution and reaction miniaturization. To evaluate these new reagents, a study was designed to compare the quality of Sanger sequencing data produced by ABI BigDye and commercially available kits from 2 other vendors using both control and difficult-to-sequence DNA templates under various reaction conditions. This study will serve as a valuable resource to core facilities conducting Sanger sequencing that wish to evaluate the use of an alternative chemistry in their sequencing core.
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Morrison J, Koeman JM, Johnson BK, Foy KK, Beddows I, Zhou W, Chesla DW, Rossell LL, Siegwald EJ, Adams M, Shen H. Evaluation of whole-genome DNA methylation sequencing library preparation protocols. Epigenetics Chromatin 2021; 14:28. [PMID: 34147133 PMCID: PMC8214260 DOI: 10.1186/s13072-021-00401-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/27/2021] [Indexed: 12/18/2022] Open
Abstract
Background With rapidly dropping sequencing cost, the popularity of whole-genome DNA methylation sequencing has been on the rise. Multiple library preparation protocols currently exist. We have performed 22 whole-genome DNA methylation sequencing experiments on snap frozen human samples, and extensively benchmarked common library preparation protocols for whole-genome DNA methylation sequencing, including three traditional bisulfite-based protocols and a new enzyme-based protocol. In addition, different input DNA quantities were compared for two kits compatible with a reduced starting quantity. In addition, we also present bioinformatic analysis pipelines for sequencing data from each of these library types. Results An assortment of metrics were collected for each kit, including raw read statistics, library quality and uniformity metrics, cytosine retention, and CpG beta value consistency between technical replicates. Overall, the NEBNext Enzymatic Methyl-seq and Swift Accel-NGS Methyl-Seq kits performed quantitatively better than the other two protocols. In addition, the NEB and Swift kits performed well at low-input amounts, validating their utility in applications where DNA is the limiting factor. Results The NEBNext Enzymatic Methyl-seq kit appeared to be the best option for whole-genome DNA methylation sequencing of high-quality DNA, closely followed by the Swift kit, which potentially works better for degraded samples. Further, a general bioinformatic pipeline is applicable across the four protocols, with the exception of extra trimming needed for the Swift Biosciences’s Accel-NGS Methyl-Seq protocol to remove the Adaptase sequence. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00401-y.
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Herbert ZT, Thimmapuram J, Xie S, Kershner JP, Kolling FW, Ringelberg CS, LeClerc A, Alekseyev YO, Fan J, Podnar JW, Stevenson HS, Sommerville G, Gupta S, Berkeley M, Koeman J, Perera A, Scott AR, Grenier JK, Malik J, Ashton JM, Pivarski KL, Wang X, Kuffel G, Mesa TE, Smith AT, Shen J, Takata Y, Volkert TL, Love JA, Zhang Y, Wang J, Xuei X, Adams M, Levine SS. Multisite Evaluation of Next-Generation Methods for Small RNA Quantification. J Biomol Tech 2021; 31:47-56. [PMID: 31966025 DOI: 10.7171/jbt.20-3102-001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Small RNAs (smRNAs) are important regulators of many biologic processes and are now most frequently characterized using Illumina sequencing. However, although standard RNA sequencing library preparation has become routine in most sequencing facilities, smRNA sequencing library preparation has historically been challenging because of high input requirements, laborious protocols involving gel purifications, inability to automate, and a lack of benchmarking standards. Additionally, studies have suggested that many of these methods are nonlinear and do not accurately reflect the amounts of smRNAs in vivo. Recently, a number of new kits have become available that permit lower input amounts and less laborious, gel-free protocol options. Several of these new kits claim to reduce RNA ligase-dependent sequence bias through novel adapter modifications and to lessen adapter-dimer contamination in the resulting libraries. With the increasing number of smRNA kits available, understanding the relative strengths of each method is crucial for appropriate experimental design. In this study, we systematically compared 9 commercially available smRNA library preparation kits as well as NanoString probe hybridization across multiple study sites. Although several of the new methodologies do reduce the amount of artificially over- and underrepresented microRNAs (miRNAs), we observed that none of the methods was able to remove all of the bias in the library preparation. Identical samples prepared with different methods show highly varied levels of different miRNAs. Even so, many methods excelled in ease of use, lower input requirement, fraction of usable reads, and reproducibility across sites. These differences may help users select the most appropriate methods for their specific question of interest.
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Gupta R, Leimanis ML, Adams M, Bachmann AS, Uhl KL, Bupp CP, Hartog NL, Kort EJ, Olivero R, Comstock SS, Sanfilippo DJ, Lunt SY, Prokop JW, Rajasekaran S. Balancing precision versus cohort transcriptomic analysis of acute and recovery phase of viral bronchiolitis. Am J Physiol Lung Cell Mol Physiol 2021; 320:L1147-L1157. [PMID: 33851876 DOI: 10.1152/ajplung.00440.2020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Viral infections affecting the lower respiratory tract place enormous burdens on hospitals. As neither vaccines nor antiviral agents exist for many viruses, understanding risk factors and outcomes in each patient using minimally invasive analysis, such as blood, can lead to improved health care delivery. A cohort of PAXgene RNA sequencing of infants admitted with moderate or severe acute bronchiolitis and respiratory syncytial virus were compared with case-control statistical analysis and cohort-based outlier mapping for precision transcriptomics. Patients with severe bronchiolitis had signatures connected to the immune system, interferon signaling, and cytokine signaling, with marked sex differences in XIST, RPS4Y1, KDM5D, and LINC00278 for severity. Several patients had unique secondary infections, cytokine activation, immune responses, biological pathways, and immune cell activation, highlighting the need for defining patient-level transcriptomic signatures. Balancing relative contributions of cohort-based biomarker discoveries with patient's biological responses is needed to understand the totality of mechanisms of adverse outcomes in viral bronchiolitis.
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Suraweera A, Duijf P, Tang M, Jekimovs C, Schrobback K, Liu C, Adams M, Richard D, O'Byrne K. 216P COMMD1 in non-small cell lung cancer: A novel DNA repair protein as a therapeutic target and diagnostic biomarker. J Thorac Oncol 2021. [DOI: 10.1016/s1556-0864(21)02058-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Dorkenoo A, Kouassi K, Afanyibo YG, Gbada K, Yakpa K, Têko M, Koura A, Katawa G, Adams M, Merkel M. [External Quality Assessment of Thick and Thin Blood Smear Slides for the Diagnosis of Malaria in the Lomé and Gulf Health Districts of Togo]. MEDECINE TROPICALE ET SANTE INTERNATIONALE 2021; 1:S1SQ-3476. [PMID: 35586643 PMCID: PMC9022756 DOI: 10.48327/s1sq-3476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 02/12/2021] [Indexed: 11/24/2022]
Abstract
Objective In sub-Saharan Africa where 90% of malaria cases are concentrated, the control of this disease constitutes a major challenge whose diagnosis by thick and thin smear deserves to be exact and reproducible. The purpose of this study is to assess the performance of thick/thin blood smear in order to improve its implementation process. Material and methods This was a descriptive and analytical study that took place from May to June 2017 and involved participating laboratories (PL) coming from public, liberal and confessional sectors in Lomé. A set of 13 blood smear slides of variable parasite densities (PD) with assigned values (AV) of parasite densities and the Plasmodium species assigned was used. The criterion for establishing the parasite densities compliance interval was assigned values ± 25% and the performance rates were compared to the 80% recommended by the WHO for Africa region. Results 41.9% (13/31) of the PLs had a compliance rate greater than 80% including four with a performance of 100% for the ability to identify the Plasmodium species. For the parasitaemia < 100/μl, 51.6% of participating laboratories had a performance rate less than 80% and for parasitaemia > 2000/μl, 100% of these laboratories had a performance rate greater than 80%. Conclusion The evaluated laboratories had insufficient ability for the identification of Plasmodium falciparum and the correct estimation of low parasitaemia. A need to strength the technical skills, adapted to the context of low parasitaemia are essential to improve the biological diagnosis of malaria in Togo.
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Wilson MR, Reske JJ, Holladay J, Neupane S, Ngo J, Cuthrell N, Wegener M, Rhodes M, Adams M, Sheridan R, Hostetter G, Alotaibi FT, Yong PJ, Anglesio MS, Lessey BA, Leach RE, Teixeira JM, Missmer SA, Fazleabas AT, Chandler RL. ARID1A Mutations Promote P300-Dependent Endometrial Invasion through Super-Enhancer Hyperacetylation. Cell Rep 2020; 33:108366. [PMID: 33176148 PMCID: PMC7682620 DOI: 10.1016/j.celrep.2020.108366] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 09/16/2020] [Accepted: 10/16/2020] [Indexed: 12/12/2022] Open
Abstract
Endometriosis affects 1 in 10 women and is characterized by the presence of abnormal endometrium at ectopic sites. ARID1A mutations are observed in deeply invasive forms of the disease, often correlating with malignancy. To identify epigenetic dependencies driving invasion, we use an unbiased approach to map chromatin state transitions accompanying ARID1A loss in the endometrium. We show that super-enhancers marked by high H3K27 acetylation are strongly associated with ARID1A binding. ARID1A loss leads to H3K27 hyperacetylation and increased chromatin accessibility and enhancer RNA transcription at super-enhancers, but not typical enhancers, indicating that ARID1A normally prevents super-enhancer hyperactivation. ARID1A co-localizes with P300 at super-enhancers, and genetic or pharmacological inhibition of P300 in ARID1A mutant endometrial epithelia suppresses invasion and induces anoikis through the rescue of super-enhancer hyperacetylation. Among hyperactivated super-enhancers, SERPINE1 (PAI-1) is identified as an essential target gene driving ARID1A mutant endometrial invasion. Broadly, our findings provide rationale for therapeutic strategies targeting super-enhancers in ARID1A mutant endometrium.
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Reske JJ, Wilson MR, Holladay J, Wegener M, Adams M, Chandler RL. SWI/SNF inactivation in the endometrial epithelium leads to loss of epithelial integrity. Hum Mol Genet 2020; 29:3412-3430. [PMID: 33075803 PMCID: PMC7749707 DOI: 10.1093/hmg/ddaa227] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 10/01/2020] [Accepted: 10/12/2020] [Indexed: 12/14/2022] Open
Abstract
Although ARID1A mutations are a hallmark feature, mutations in other SWI/SNF (SWItch/Sucrose Non-Fermentable) chromatin remodeling subunits are also observed in endometrial neoplasms. Here, we interrogated the roles of Brahma/SWI2-related gene 1 (BRG1, SMARCA4), the SWI/SNF catalytic subunit, in the endometrial epithelium. BRG1 loss affects more than one-third of all active genes and highly overlaps with the ARID1A gene regulatory network. Chromatin immunoprecipitation studies revealed widespread subunit-specific differences in transcriptional regulation, as BRG1 promoter interactions are associated with gene activation, while ARID1A binding is associated with gene repression. However, we identified a physiologically relevant subset of BRG1 and ARID1A co-regulated epithelial identity genes. Mice were genetically engineered to inactivate BRG1 specifically in the endometrial epithelium. Endometrial glands were observed embedded in uterine myometrium, indicating adenomyosis-like phenotypes. Molecular similarities were observed between BRG1 and ARID1A mutant endometrial cells in vivo, including loss of epithelial cell adhesion and junction genes. Collectively, these studies illustrate overlapping contributions of multiple SWI/SNF subunit mutations in the translocation of endometrium to distal sites, with loss of cell integrity being a common feature in SWI/SNF mutant endometrial epithelia.
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Poole J, Bentley J, Barraud L, Samish I, Dalkas G, Matheson A, Clegg P, Euston S, Kauffman Johnson J, Haacke C, Westphal L, Molina Beato L, Adams M, Spiro A. Rising to the challenges: Solution‐based case studies highlighting innovation and evolution in reformulation. NUTR BULL 2020. [DOI: 10.1111/nbu.12456] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Giovannetti O, Forster A, Tomalty D, Hannan J, Szell N, Komisaruk B, Goldstein S, Goldstein I, Adams M. 023 Investigation of Sensory Innervation in the Surgical Field of Mid-Urethral Sling and Loop Electrosurgical Excision Procedures in Periurethral and Cervical Tissues Using Immunohistochemistry. J Sex Med 2020. [DOI: 10.1016/j.jsxm.2020.04.259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Tomalty D, Giovannetti O, Hannan J, Komisaruk B, Goldstein S, Goldstein I, Szell N, Adams M. 073 Characterization of Female Periurethral Glandular Tissue in the Periurethral Space Negatively Impacted by Mid-Urethral Sling Surgery. J Sex Med 2020. [DOI: 10.1016/j.jsxm.2020.04.309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Abbas Y, Abdelkader M, Adams M, Addison A, Advani R, Ahmed T, Alexander V, Alexander V, Alli B, Alvi S, Amiraraghi N, Ashman A, Balakumar R, Bewick J, Bhasker D, Bola S, Bowles P, Campbell N, Can Guru Naidu N, Caton N, Chapman J, Chawdhary G, Cherko M, Coates M, Conroy K, Coyle P, Cozar O, Cresswell M, Dalton L, Danino J, Daultrey C, Davies K, Carrie S, Dick D, Dimitriadis PA, Doddi N, Dowling M, Easto R, Edmiston R, Ellul D, Erskine S, Evans A, Farboud A, Forde C, Fussey J, Gaunt A, Gilchrist J, Gohil R, Gosnell E, Grech Marguerat D, Green R, Grounds R, Hall A, Hardman J, Harris A, Harrison L, Hone R, Hoskison E, Howard J, Ioannidis D, Iqbal I, Janjua N, Jolly K, Kamal S, Kanzara T, Keates N, Kelly A, Khan H, Korampalli T, Kuet M, Kul‐loo P, Lakhani R, Lambert A, Lancer H, Leonard C, Lloyd G, Lowe E, Mair J, Maughan E, Gao C, Mayberry T, McCadden L, McClenaghan F, McKenzie G, Mcleod R, Meghji S, Mian M, Millington A, Mirza O, Mistry S, Molena E, Morris J, Myuran T, Navaratnam A, Noon E, Okonkwo O, Oremule B, Pabla L, Papesch E, Puranik V, Roplekar R, Ross E, Rudd J, Schechter E, Senior A, Sethi N, Sharma S, Sharma R, Shelton F, Sherazi Z, Tahir A, Tikka T, Tkachuk Hlinicanova O, To K, Tse A, Toll E, Ubayasiri K, Unadkat S, Upile N, Vijendren A, Walijee H, Wilkie M, Williams R, Williams M, Wilson G, Wong W, Wong G, Xie C, Yao A, Zhang H, Ellis M, Mehta N, Milinis K, Tikka T, Slovick A, Swords C, Hutson K, Smith ME, Hopkins C, Ng Kee Kwong F. Nasal Packs for Epistaxis: Predictors of Success. Clin Otolaryngol 2020; 45:659-666. [DOI: 10.1111/coa.13555] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 03/08/2020] [Accepted: 04/13/2020] [Indexed: 11/30/2022]
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Prokop JW, Shankar R, Gupta R, Leimanis ML, Nedveck D, Uhl K, Chen B, Hartog NL, Van Veen J, Sisco JS, Sirpilla O, Lydic T, Boville B, Hernandez A, Braunreiter C, Kuk CC, Singh V, Mills J, Wegener M, Adams M, Rhodes M, Bachmann AS, Pan W, Byrne-Steele ML, Smith DC, Depinet M, Brown BE, Eisenhower M, Han J, Haw M, Madura C, Sanfilippo DJ, Seaver LH, Bupp C, Rajasekaran S. Virus-induced genetics revealed by multidimensional precision medicine transcriptional workflow applicable to COVID-19. Physiol Genomics 2020; 52:255-268. [PMID: 32437232 PMCID: PMC7303726 DOI: 10.1152/physiolgenomics.00045.2020] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 05/20/2020] [Accepted: 05/20/2020] [Indexed: 12/26/2022] Open
Abstract
Precision medicine requires the translation of basic biological understanding to medical insights, mainly applied to characterization of each unique patient. In many clinical settings, this requires tools that can be broadly used to identify pathology and risks. Patients often present to the intensive care unit with broad phenotypes, including multiple organ dysfunction syndrome (MODS) resulting from infection, trauma, or other disease processes. Etiology and outcomes are unique to individuals, making it difficult to cohort patients with MODS, but presenting a prime target for testing/developing tools for precision medicine. Using multitime point whole blood (cellular/acellular) total transcriptomics in 27 patients, we highlight the promise of simultaneously mapping viral/bacterial load, cell composition, tissue damage biomarkers, balance between syndromic biology versus environmental response, and unique biological insights in each patient using a single platform measurement. Integration of a transcriptome workflow yielded unexpected insights into the complex interplay between host genetics and viral/bacterial specific mechanisms, highlighted by a unique case of virally induced genetics (VIG) within one of these 27 patients. The power of RNA-Seq to study unique patient biology while investigating environmental contributions can be a critical tool moving forward for translational sciences applied to precision medicine.
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Mische SM, Fisher NC, Meyn SM, Sol-Church K, Hegstad-Davies RL, Weis-Garcia F, Adams M, Ashton JM, Delventhal KM, Dragon JA, Holmes L, Jagtap P, Kubow KE, Mason CE, Palmblad M, Searle BC, Turck CW, Knudtson KL. A Review of the Scientific Rigor, Reproducibility, and Transparency Studies Conducted by the ABRF Research Groups. J Biomol Tech 2020; 31:11-26. [PMID: 31969795 PMCID: PMC6959150 DOI: 10.7171/jbt.20-3101-003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Shared research resource facilities, also known as core laboratories (Cores), are responsible for generating a significant and growing portion of the research data in academic biomedical research institutions. Cores represent a central repository for institutional knowledge management, with deep expertise in the strengths and limitations of technology and its applications. They inherently support transparency and scientific reproducibility by protecting against cognitive bias in research design and data analysis, and they have institutional responsibility for the conduct of research (research ethics, regulatory compliance, and financial accountability) performed in their Cores. The Association of Biomolecular Resource Facilities (ABRF) is a FASEB-member scientific society whose members are scientists and administrators that manage or support Cores. The ABRF Research Groups (RGs), representing expertise for an array of cutting-edge and established technology platforms, perform multicenter research studies to determine and communicate best practices and community-based standards. This review provides a summary of the contributions of the ABRF RGs to promote scientific rigor and reproducibility in Cores from the published literature, ABRF meetings, and ABRF RGs communications.
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Flores G, Everett JH, Boguslawski EA, Oswald BM, Madaj ZB, Beddows I, Dikalov S, Adams M, Klumpp-Thomas CA, Kitchen-Goosen SM, Martin SE, Caplen NJ, Helman LJ, Grohar PJ. CDK9 Blockade Exploits Context-dependent Transcriptional Changes to Improve Activity and Limit Toxicity of Mithramycin for Ewing Sarcoma. Mol Cancer Ther 2020; 19:1183-1196. [PMID: 32127464 DOI: 10.1158/1535-7163.mct-19-0775] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 12/17/2019] [Accepted: 02/19/2020] [Indexed: 11/16/2022]
Abstract
There is a need to develop novel approaches to improve the balance between efficacy and toxicity for transcription factor-targeted therapies. In this study, we exploit context-dependent differences in RNA polymerase II processivity as an approach to improve the activity and limit the toxicity of the EWS-FLI1-targeted small molecule, mithramycin, for Ewing sarcoma. The clinical activity of mithramycin for Ewing sarcoma is limited by off-target liver toxicity that restricts the serum concentration to levels insufficient to inhibit EWS-FLI1. In this study, we perform an siRNA screen of the druggable genome followed by a matrix drug screen to identify mithramycin potentiators and a synergistic "class" effect with cyclin-dependent kinase 9 (CDK9) inhibitors. These CDK9 inhibitors enhanced the mithramycin-mediated suppression of the EWS-FLI1 transcriptional program leading to a shift in the IC50 and striking regressions of Ewing sarcoma xenografts. To determine whether these compounds may also be liver protective, we performed a qPCR screen of all known liver toxicity genes in HepG2 cells to identify mithramycin-driven transcriptional changes that contribute to the liver toxicity. Mithramycin induces expression of the BTG2 gene in HepG2 but not Ewing sarcoma cells, which leads to a liver-specific accumulation of reactive oxygen species (ROS). siRNA silencing of BTG2 rescues the induction of ROS and the cytotoxicity of mithramycin in these cells. Furthermore, CDK9 inhibition blocked the induction of BTG2 to limit cytotoxicity in HepG2, but not Ewing sarcoma cells. These studies provide the basis for a synergistic and less toxic EWS-FLI1-targeted combination therapy for Ewing sarcoma.
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Ni M, Adams M, Huddy J, Carr R, Fotheringham I, Wilson C, Tsang M, Hanna G. A multi-centred, prospective, observational study of a first-generation novel human lipase pH test for siting nasogastric feeding tubes in adult patients. Clin Nutr ESPEN 2020. [DOI: 10.1016/j.clnesp.2019.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Scasta JD, Adams M, Gibbs R, Fleury B. Free-ranging horse management in Australia, New Zealand and the United States: socio-ecological dimensions of a protracted environmental conflict. RANGELAND JOURNAL 2020. [DOI: 10.1071/rj19019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Management of free-ranging horses (Equus ferus caballus) is a complex socio-ecological issue in Australia (AU), New Zealand (NZ), and the United States (US). In these countries, horses are the results of colonial introductions and occupy very harsh rangeland environments exerting a grazing disturbance that has generated ecological concerns. Although many social and ecological concerns are similar, each country also has nuances. In 2018, we conducted a field-based comparison of AU, NZ, and US using an inductive approach to identify similarities, differences, and emerging themes through conversations with >100 individuals from New South Wales Australia, the North Island of New Zealand, and the western US. Additional data sources included field observations and archival documents. Consistent emergent themes identified included: strong public emotion, politicization of management, population growth concerns, negative ecological impact concerns, agreement that horses should be treated humanely, disagreement as to what practices were the most humane, interest and scepticism about fertility control, the need for transparency, compromise to accommodating horses and acknowledgement of social values, and recognition that collaboration is the only means to achieve both healthy rangelands and healthy horses. Unique themes identified included: NZ empowering advocate groups to become part of the solution, conflict between horses and livestock is a mostly US conflict, equids originated in the US, concern about the sustainability of adoption programs, different expectations/options for management on private lands, cultural history such as brumby running in AU, permanent branding of horses in the US, litigation as a uniquely US strategy (although a judgement on recent AU litigation is pending), government data accepted to guide removals in NZ but not always in AU or US, and complex heterogeneous land surface ownership patterns makes management difficult in the US. The difficulty of horse management in these countries is attributed to social intricacies rather than biological/ecological gaps of knowledge.
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Arnold R, Amos D, Lowe H, Elder A, Martin S, Moss S, McMaster K, Juergens C, Ryan E, Larnach G, Adams M. 472 Development of a Rural NSW Cardiac Catheter and Coronary Intervention Service Over 14 Years: Impacts on Service and 30 Day AMI Mortality. Heart Lung Circ 2020. [DOI: 10.1016/j.hlc.2020.09.479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Moss S, Arnold R, Lowe H, Elder A, Juergens C, McMaster K, Roach A, Larnach G, Adams M, Amos D. 436 A Rural 24/7 Cardiac Catheter Lab Service in Western NSW Local Health District (WNSWLHD): Locally Based Acute Coronary Syndrome (ACS) Care With Low Mortality Over 5 Years. Heart Lung Circ 2020. [DOI: 10.1016/j.hlc.2020.09.443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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George JW, Fan H, Johnson B, Carpenter TJ, Foy KK, Chatterjee A, Patterson AL, Koeman J, Adams M, Madaj ZB, Chesla D, Marsh EE, Triche TJ, Shen H, Teixeira JM. Integrated Epigenome, Exome, and Transcriptome Analyses Reveal Molecular Subtypes and Homeotic Transformation in Uterine Fibroids. Cell Rep 2019; 29:4069-4085.e6. [PMID: 31851934 PMCID: PMC6956710 DOI: 10.1016/j.celrep.2019.11.077] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 09/20/2019] [Accepted: 11/19/2019] [Indexed: 11/29/2022] Open
Abstract
Uterine fibroids are benign myometrial smooth muscle tumors of unknown etiology that, when symptomatic, are the most common indication for hysterectomy in the United States. Unsupervised clustering of results from DNA methylation analyses segregates normal myometrium from fibroids and further segregates the fibroids into subtypes characterized by MED12 mutation or activation of either HMGA2 or HMGA1 expression. Upregulation of HMGA2 expression does not always appear to be dependent on translocation but is associated with hypomethylation in the HMGA2 gene body. HOXA13 expression is upregulated in fibroids and correlates with expression of typical uterine fibroid genes. Significant overlap of differentially expressed genes is observed between cervical stroma and uterine fibroids compared with normal myometrium. These analyses show a possible role of DNA methylation in fibroid biology and suggest that homeotic transformation of myometrial cells to a more cervical stroma phenotype could be an important mechanism for etiology of the disease.
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Adams M, Burgess J, Richard D, O'Byrne K. P1.01-01 Clinical Relevance of Targeting Proteins Required for Mitotic Progression to Improve Chemotherapy Response in Non-Small Cell Lung Cancer. J Thorac Oncol 2019. [DOI: 10.1016/j.jtho.2019.08.716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Asch FM, Poilvert N, Abraham T, Jankowski M, Cleve J, Adams M, Romano N, Hong H, Mor-Avi V, Lang RM. P4347Automated echocardiographic quantification of left ventricular ejection fraction without volume measurements using a machine learning algorithm mimicking a human expert. Eur Heart J 2019. [DOI: 10.1093/eurheartj/ehz745.0755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Echocardiographic quantification of left ventricular (LV) ejection fraction (EF) relies on either manual or automated identification of endocardial boundaries followed by standard calculation of model-based end-systolic and end-diastolic LV volumes. Recent developments in artificial intelligence resulted in computer algorithms that allow near automated detection of endocardial boundaries and measurement of LV volumes and function. However, boundary identification is still prone to errors limiting accuracy in certain patients. We hypothesized that a fully automated machine learning algorithm could be developed, which circumvents border detection and instead estimates the degree of ventricular contraction, similar to a human expert trained on tens of thousands of images.
Purpose
This study was designed to test the feasibility and accuracy of this approach.
Methods
Machine learning algorithm was developed and trained on a database of >50,000 echocardiographic studies, including multiple apical 2- and 4-chamber views, to automatically estimate LVEF (AutoEF, BayLabs). Testing was performed on an independent group of 99 unselected patients, whose automated EF values were compared to reference values obtained by averaging measurements by 3 experts using conventional volume-based technique. Inter-technique agreement was assessed using linear regression and Bland-Altman analysis of bias and limits of agreement (LOA). Consistency was assessed by mean absolute deviation (MAD) among automated estimates based on different combinations of apical views. Finally, sensitivity and specificity of detecting of EF≤35% was calculated. These metrics were compared side-by-side against the same reference standard to those obtained from conventional EF measurements by clinical readers.
Results
Automated estimation of LVEF was feasible in all 99 patients. AutoEF values showed high consistency (MAD=2.9%) and excellent agreement with the reference values: r=0.95, bias=1.0%, LOA=±11.8%, with sensitivity 0.90 and specificity 0.92 for detection of EF≤35%. This was similar to clinicians' measurements: r=0.94, bias=1.4%, LOA=±13.4%,sensitivity 0.93, specificity 0.87.
Conclusions
Machine learning algorithm for volume-independent LVEF estimation is highly feasible and similar in accuracy to conventional volume-based measurements, when compared to reference values provided by an expert panel.
Acknowledgement/Funding
Bay Labs, Inc.
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