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Mendis M, Abeyrathna W, Halwatura R, Amarasekara H, Somadewa R, Jayasinghe R. Accumulate and consolidate the traditional vernacular timber preservation technologies through a field survey. Heliyon 2024; 10:e23907. [PMID: 38223715 PMCID: PMC10787270 DOI: 10.1016/j.heliyon.2023.e23907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 01/16/2024] Open
Abstract
There are remarks on diverse types of timber structures in the tropics. This paper examines several case histories in Sri Lanka, focusing on the culturally varied and ecologically diverse traditional buildings with wood used for construction. The main objective was to gather data and document the knowledge on wood preservation. Information was gathered through face-to-face interviews with 270 individuals' reference to 138 structures. A holistic analysis was performed to understand the techniques used to overcome the degradation mechanisms and state of conservation. The demographic profile of the informants was evaluated and cross-relationships on the tabulated data were analyzed by SPSS statistical software following the snow-balling sampling technique. There were three main preservation techniques identified from the open-ended questions namely, wood kept under smoke pits, wood kept under paddy field mud, and wood kept under the river banks. Preserving wood by keeping it under paddy field mud (49.62 %) was the highest recorded answer. The most obtained material matrix of preservation was plant origins (48.88 %). For generations, people have transmitted traditional and cultural practices through oral knowledge. The results conclude this knowledge places a high value on protecting construction technologies and applications while preserving biodiversity. Unfortunately, by today this technology has started extinct. The results revealed the importance of social norms and cultural perceptions as a set of valuable information that was practiced with a great history in a tropical country.
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Affiliation(s)
- M.S. Mendis
- Faculty of Engineering, NSBM Green University, Sri Lanka
| | | | - R.U. Halwatura
- Faculty of Engineering, University of Moratuwa, Sri Lanka
| | - H.S. Amarasekara
- Department of Forestry and Environment Science, University of Sri Jayewardenepura, Sri Lanka
| | - R. Somadewa
- Postgraduate Institute of Archaeology, University of Kelaniya, Sri Lanka
| | - R. Jayasinghe
- Faculty of Technology, University of Sri Jayewardenepura, Sri Lanka
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2
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Dang HX, Saha D, Jayasinghe R, Zhao S, Coonrod E, Mudd J, Goedegebuure S, Fields R, Ding L, Maher C. Single-cell transcriptomics reveals long noncoding RNAs associated with tumor biology and the microenvironment in pancreatic cancer. NAR Cancer 2023; 5:zcad055. [PMID: 38023733 PMCID: PMC10664695 DOI: 10.1093/narcan/zcad055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 10/31/2023] [Accepted: 11/09/2023] [Indexed: 12/01/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is highly heterogeneous and lethal. Long noncoding RNAs (lncRNAs) are an important class of genes regulating tumorigenesis and progression. Prior bulk transcriptomic studies in PDAC have revealed the dysregulation of lncRNAs but lack single-cell resolution to distinguish lncRNAs in tumor-intrinsic biology and the tumor microenvironment (TME). We analyzed single-cell transcriptome data from 73 multiregion samples in 21 PDAC patients to evaluate lncRNAs associated with intratumoral heterogeneity and the TME in PDAC. We found 111 cell-specific lncRNAs that reflected tumor, immune and stromal cell contributions, associated with outcomes, and validated across orthogonal datasets. Single-cell analysis of tumor cells revealed lncRNAs associated with TP53 mutations and FOLFIRINOX treatment that were obscured in bulk tumor analysis. Lastly, tumor subcluster analysis revealed widespread intratumor heterogeneity and intratumoral lncRNAs associated with cancer hallmarks and tumor processes such as angiogenesis, epithelial-mesenchymal transition, metabolism and immune signaling. Intratumoral subclusters and lncRNAs were validated across six datasets and showed clinically relevant associations with patient outcomes. Our study provides the first comprehensive assessment of the lncRNA landscape in PDAC using single-cell transcriptomic data and can serve as a resource, PDACLncDB (accessible at https://www.maherlab.com/pdaclncdb-overview), to guide future functional studies.
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Affiliation(s)
- Ha X Dang
- Department of Internal Medicine, Washington University in St Louis, St Louis, MO 63110, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO 63110, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO 63108, USA
| | - Debanjan Saha
- Department of Internal Medicine, Washington University in St Louis, St Louis, MO 63110, USA
- MD–PhD Program, Washington University in St Louis, St Louis, MO 63110, USA
| | - Reyka Jayasinghe
- Department of Internal Medicine, Washington University in St Louis, St Louis, MO 63110, USA
| | - Sidi Zhao
- Department of Internal Medicine, Washington University in St Louis, St Louis, MO 63110, USA
| | - Emily Coonrod
- Department of Internal Medicine, Washington University in St Louis, St Louis, MO 63110, USA
| | - Jacqueline Mudd
- Department of Surgery, Washington University in St Louis, St Louis, MO 63110, USA
| | - S Peter Goedegebuure
- Department of Surgery, Washington University in St Louis, St Louis, MO 63110, USA
| | - Ryan Fields
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO 63110, USA
- Department of Surgery, Washington University in St Louis, St Louis, MO 63110, USA
| | - Li Ding
- Department of Internal Medicine, Washington University in St Louis, St Louis, MO 63110, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO 63110, USA
| | - Christopher A Maher
- Department of Internal Medicine, Washington University in St Louis, St Louis, MO 63110, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO 63110, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO 63108, USA
- Department of Biomedical Engineering, Washington University in St Louis, St Louis, MO 63130, USA
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3
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Danushka PGN, Jayasinghe R, Munsinghe M. A late presentation of acute iatrogenic aortic dissection following percutaneous coronary intervention: A case report. SAGE Open Med Case Rep 2023; 11:2050313X231211714. [PMID: 37954541 PMCID: PMC10638864 DOI: 10.1177/2050313x231211714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 10/17/2023] [Indexed: 11/14/2023] Open
Abstract
Acute iatrogenic aortic dissection following percutaneous coronary intervention is a rare but sinister cause of post-procedure morbidity and mortality. Delayed diagnosis increases the mortality significantly. We present a case of a 52-year-old male who presented with an iatrogenic aortic dissection following percutaneous coronary intervention for an inferior ST-elevation myocardial infarction. Although the diagnosis was initially missed by conventional imaging for a period of 5 months, it was later diagnosed assisted by cardiac computed tomography. The patient underwent aortic repair with a Dacron graft and had an uneventful recovery. The case highlights the importance of early diagnosis and selection of appropriate imaging for this rare but serious iatrogenic sequel following percutaneous coronary intervention to minimize morbidity.
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Affiliation(s)
- PGN Danushka
- Department of Surgery, National Hospital of Sri Lanka, Colombo, Sri Lanka
| | - R Jayasinghe
- Department of Surgery, National Hospital of Sri Lanka, Colombo, Sri Lanka
| | - M Munsinghe
- Department of Surgery, National Hospital of Sri Lanka, Colombo, Sri Lanka
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4
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Rimando JC, Chendamarai E, Rettig MP, Jayasinghe R, Christopher MJ, Ritchey JK, Christ S, Kim MY, Bonvini E, DiPersio JF. Flotetuzumab and other T-cell immunotherapies upregulate MHC class II expression on acute myeloid leukemia cells. Blood 2023; 141:1718-1723. [PMID: 36563336 PMCID: PMC10273090 DOI: 10.1182/blood.2022017795] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/27/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022] Open
Abstract
Acute myeloid leukemia (AML) relapse is one of the most common and significant adverse events following allogeneic hematopoietic cell transplantation (HCT). Downregulation of major histocompatibility class II (MHC-II) surface expression on AML blasts may represent a mechanism of escape from the graft-versus-malignancy effect and facilitate relapse. We hypothesized that T-cell immunotherapies targeting AML antigens would upregulate MHC-II surface expression via localized release of interferon gamma (IFN-γ), a protein known to upregulate MHC-II expression via JAK-STAT signaling. We demonstrate that flotetuzumab (FLZ), a CD123 × CD3 bispecific DART molecule, and chimeric antigen receptor expressing T cells targeting CD123, CD33, or CD371 upregulate MHC-II surface expression in vitro on a THP-1 AML cell line with intermediate MHC-II expression and 4 primary AML samples from patients relapsing after HCT with low MHC-II expression. We additionally show that FLZ upregulates MHC-II expression in a patient-derived xenograft model and in patients with relapsed or refractory AML who were treated with FLZ in a clinical trial. Finally, we report that FLZ-induced MHC-II upregulation is mediated by IFN-γ. In conclusion, we provide evidence that T-cell immunotherapies targeting relapsed AML can kill AML via both MHC-independent mechanisms and by an MHC-dependent mechanism through local release of IFN-γ and subsequent upregulation of MHC-II expression.
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Affiliation(s)
- Joseph C. Rimando
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Ezhilarasi Chendamarai
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Michael P. Rettig
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Reyka Jayasinghe
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Matthew J. Christopher
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Julie K. Ritchey
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Stephanie Christ
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Miriam Y. Kim
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | | | - John F. DiPersio
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
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5
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Wells D, Gelev K, Thunuguntla P, Jayasinghe R, Ding L, Shao J, Ma C, Silva-Fisher J. Abstract P2-22-01: Nuclear long non-coding RNA LINC00355 expression and treatment using antisense oligonucleotides in Estrogen Receptor positive late-stage relapse breast cancer. Cancer Res 2023. [DOI: 10.1158/1538-7445.sabcs22-p2-22-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Abstract
Late-stage relapse also known as late recurrence breast cancer is a metastatic disease that occurs more than five years after initial adjuvant endocrine therapy treatment. The 5-year relative survival rate is less than 30% and there are limited treatment options for patients with late-stage relapse because of poor performance status. We hypothesize that long non-coding RNA (lncRNA) protein interactions regulate genes to promote late-stage relapse and these interactions can be targeted using RNA therapeutics. To address this, we used RNA-sequencing to identify LINC00355 to be up-regulated in 24 late-stage relapse samples compared to a unique cohort of 72 primary breast cancer samples. Analysis of 480 primary breast cancer samples from The Cancer Genome Atlas (TCGA) also shows decrease expression of LINC00355 compared to late-stage relapse. To better assess LINC00355 cell type expression, we analyzed 26 publicly available primary breast cancer single cell sequencing data samples and detected 0.90% or less of cells expressing LINC00355, which was restricted to cancer epithelial cells. Due to cellular localization playing an important role in lncRNA function, we isolated nuclear and cytoplasmic lysates and orthogonally validated with RNAscope in situ hybridization (RNA-ISH) to show that LINC00355 is located in the nucleus of MCF7 long-term estrogen deprived (MCF7 LTED) cells. LTED cells are deprived of estrogen for longer than three years meant to recapitulate the acquired resistance to aromatase inhibitors. Next, we determined that LINC00355 binds to MENIN protein to regulate p27KIP expression to promote proliferation with UV crosslinking immunoprecipitation and chromatin immunoprecipitation qPCR of LINC00355 overexpression and mutant constructs. Furthermore, RNA-ISH assays validated high nuclear expression of LINC00355 and RNA-ISH protein co-detection assays showed co-localization of LINC00355-MENIN interaction in a panel of late-stage relapse breast cancer patient tissues compared to primary tissues. Lastly to determine clinical significance, we treated MCF7 LTED cells with two locked nucleic acid antisense oligos (ASOs) targeting LINC00355 to observe a significant decrease in proliferation, cell viability, and invasion. Overall, this is the first study to show the importance of lncRNA-protein interactions and therapeutically target lncRNAs with ASOs in late-stage relapse breast cancer. Moving forward, we intend to further understand how LINC00355 contributes to the progression of late-stage relapse with the intent of creating novel cancer diagnostics and therapies.
Citation Format: DeAnna Wells, Kyla Gelev, Prasanth Thunuguntla, Reyka Jayasinghe, Li Ding, Jieya Shao, Cynthia Ma, Jessica Silva-Fisher. Nuclear long non-coding RNA LINC00355 expression and treatment using antisense oligonucleotides in Estrogen Receptor positive late-stage relapse breast cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-22-01.
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Affiliation(s)
- DeAnna Wells
- 1Washington University in St.Louis, Saint Louis, Missouri
| | - Kyla Gelev
- 2Washington University School of Medicine
| | | | | | - Li Ding
- 5Washington University School of Medicine
| | - Jieya Shao
- 6Washington University School of Medicine
| | - Cynthia Ma
- 7Washington University in St. Louis, St. Louis, MO
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Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vázquez-García I, Haase K, Jerman L, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD, Spellman PT, Wedge DC, Van Loo P, Tarabichi M, Wintersinger J, Deshwar AG, Yu K, Gonzalez S, Rubanova Y, Macintyre G, Adams DJ, Anur P, Beroukhim R, Boutros PC, Bowtell DD, Campbell PJ, Cao S, Christie EL, Cmero M, Cun Y, Dawson KJ, Demeulemeester J, Donmez N, Drews RM, Eils R, Fan Y, Fittall M, Garsed DW, Getz G, Ha G, Imielinski M, Jerman L, Ji Y, Kleinheinz K, Lee J, Lee-Six H, Livitz DG, Malikic S, Markowetz F, Martincorena I, Mitchell TJ, Mustonen V, Oesper L, Peifer M, Peto M, Raphael BJ, Rosebrock D, Sahinalp SC, Salcedo A, Schlesner M, Schumacher S, Sengupta S, Shi R, Shin SJ, Spiro O, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Stein LD, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Vázquez-García I, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Vembu S, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Wheeler DA, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Yang TP, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Yao X, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Yuan K, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Zhu H, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Wang W, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Morris QD, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Spellman PT, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Wedge DC, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Van Loo P, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Spellman PT, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Wedge DC, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Van Loo P, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Aaltonen LA, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Abascal F, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Abeshouse A, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Aburatani H, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Adams DJ, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Agrawal N, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Ahn KS, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Ahn SM, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Aikata H, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Akbani R, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Akdemir KC, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Al-Ahmadie H, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Al-Sedairy ST, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Al-Shahrour F, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Alawi M, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Albert M, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Aldape K, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Alexandrov LB, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Ally A, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Alsop K, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Alvarez EG, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Amary F, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Amin SB, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Aminou B, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Ammerpohl O, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Anderson MJ, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Ang Y, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, Antonello D, von Mering C, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, Dueso-Barroso A, Dunford AJ, Dunn M, Dursi LJ, Duthie FR, Dutton-Regester K, Eagles J, Easton DF, Edmonds S, Edwards PA, Edwards SE, Eeles RA, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu SMG, Estivill X, Etemadmoghadam D, Eyfjord JE, Faltas BM, Fan D, Fan Y, Faquin WC, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson ML, Ferretti V, Feuerbach L, Field MA, Fink JL, Finocchiaro G, Fisher C, Fittall MW, Fitzgerald A, Fitzgerald RC, Flanagan AM, Fleshner NE, Flicek P, Foekens JA, Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, 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Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen 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Author Correction: The evolutionary history of 2,658 cancers. Nature 2023; 614:E42. [PMID: 36697833 PMCID: PMC9931577 DOI: 10.1038/s41586-022-05601-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK. .,European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany. .,Wellcome Sanger Institute, Cambridge, UK.
| | - Clemency Jolly
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Ignaty Leshchiner
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Stefan C. Dentro
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK
| | - Santiago Gonzalez
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Daniel Rosebrock
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Thomas J. Mitchell
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Yulia Rubanova
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Pavana Anur
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - Kaixian Yu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Maxime Tarabichi
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Amit Deshwar
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Jeff Wintersinger
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Kortine Kleinheinz
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Heidelberg University, Heidelberg, Germany
| | - Ignacio Vázquez-García
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Kerstin Haase
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Lara Jerman
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK ,grid.8954.00000 0001 0721 6013University of Ljubljana, Ljubljana, Slovenia
| | - Subhajit Sengupta
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA
| | - Geoff Macintyre
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Salem Malikic
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Nilgun Donmez
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Dimitri G. Livitz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Marek Cmero
- grid.1008.90000 0001 2179 088XUniversity of Melbourne, Melbourne, Victoria Australia ,grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute, Melbourne, Victoria Australia
| | - Jonas Demeulemeester
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.5596.f0000 0001 0668 7884University of Leuven, Leuven, Belgium
| | - Steven Schumacher
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Yu Fan
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Xiaotong Yao
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Juhee Lee
- grid.205975.c0000 0001 0740 6917University of California Santa Cruz, Santa Cruz, CA USA
| | - Matthias Schlesner
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul C. Boutros
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.419890.d0000 0004 0626 690XOntario Institute for Cancer Research, Toronto, Ontario Canada ,grid.19006.3e0000 0000 9632 6718University of California, Los Angeles, CA USA
| | - David D. Bowtell
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, Melbourne, Victoria Australia
| | - Hongtu Zhu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Gad Getz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.32224.350000 0004 0386 9924Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA USA ,grid.32224.350000 0004 0386 9924Department of Pathology, Massachusetts General Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Marcin Imielinski
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Rameen Beroukhim
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - S. Cenk Sahinalp
- grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada ,grid.411377.70000 0001 0790 959XIndiana University, Bloomington, IN USA
| | - Yuan Ji
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA ,grid.170205.10000 0004 1936 7822The University of Chicago, Chicago, IL USA
| | - Martin Peifer
- grid.6190.e0000 0000 8580 3777University of Cologne, Cologne, Germany
| | - Florian Markowetz
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ville Mustonen
- grid.7737.40000 0004 0410 2071University of Helsinki, Helsinki, Finland
| | - Ke Yuan
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK ,grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Wenyi Wang
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Quaid D. Morris
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | | | - Paul T. Spellman
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - David C. Wedge
- grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK ,grid.454382.c0000 0004 7871 7212Oxford NIHR Biomedical Research Centre, Oxford, UK
| | - Peter Van Loo
- The Francis Crick Institute, London, UK. .,University of Leuven, Leuven, Belgium.
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Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z, Wu K, Yang H, Fonseca NA, Kahles A, Lehmann KV, Urban L, Soulette CM, Shiraishi Y, Liu F, He Y, Demircioğlu D, Davidson NR, Calabrese C, Zhang J, Perry MD, Xiang Q, Greger L, Li S, Liu D, Stark SG, Zhang F, Amin SB, Bailey P, Chateigner A, Cortés-Ciriano I, Craft B, Erkek S, Frenkel-Morgenstern M, Goldman M, Hoadley KA, Hou Y, Huska MR, Khurana E, Kilpinen H, Korbel JO, Lamaze FC, Li C, Li X, Li X, Liu X, Marin MG, Markowski J, Nandi T, Nielsen MM, Ojesina AI, Pan-Hammarström Q, Park PJ, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Pedamallu CS, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pedersen JS, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Siebert R, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Su H, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Tan P, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Teh BT, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Wang J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Waszak SM, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Xiong H, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Yakneen S, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Ye C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Yung C, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Zhang X, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Zheng L, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Zhu J, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Zhu S, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Awadalla P, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Creighton CJ, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Meyerson M, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Ouellette BFF, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Wu K, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Yang H, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Göke J, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Schwarz RF, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Stegle O, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Zhang Z, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Brazma A, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Rätsch G, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Brooks AN, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Brazma A, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Brooks AN, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, 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Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, 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Author Correction: Genomic basis for RNA alterations in cancer. Nature 2023; 614:E37. [PMID: 36697831 PMCID: PMC9931574 DOI: 10.1038/s41586-022-05596-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
| | - Claudia Calabrese
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Natalie R. Davidson
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medical College, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Deniz Demircioğlu
- grid.4280.e0000 0001 2180 6431National University of Singapore, Singapore, Singapore ,grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Nuno A. Fonseca
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Yao He
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - André Kahles
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Kjong-Van Lehmann
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Fenglin Liu
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Yuichi Shiraishi
- grid.26999.3d0000 0001 2151 536XThe University of Tokyo, Minato-ku, Japan
| | - Cameron M. Soulette
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Lara Urban
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Liliana Greger
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Siliang Li
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Dongbing Liu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Marc D. Perry
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.266102.10000 0001 2297 6811University of California, San Francisco, San Francisco, CA USA
| | - Qian Xiang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Fan Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Junjun Zhang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Peter Bailey
- grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Serap Erkek
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Katherine A. Hoadley
- grid.10698.360000000122483208The University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Yong Hou
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Matthew R. Huska
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Helena Kilpinen
- grid.83440.3b0000000121901201University College London, London, UK
| | - Jan O. Korbel
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Maximillian G. Marin
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Julia Markowski
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Tannistha Nandi
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Qiang Pan-Hammarström
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.4714.60000 0004 1937 0626Karolinska Institutet, Stockholm, Sweden
| | - Chandra Sekhar Pedamallu
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Reiner Siebert
- grid.410712.10000 0004 0473 882XUlm University and Ulm University Medical Center, Ulm, Germany
| | - Stefan G. Stark
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Hong Su
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Patrick Tan
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Singapore, Singapore
| | - Sebastian M. Waszak
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Christina Yung
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Shida Zhu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Philip Awadalla
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada
| | - Chad J. Creighton
- grid.39382.330000 0001 2160 926XBaylor College of Medicine, Houston, TX USA
| | - Matthew Meyerson
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | | | - Kui Wu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Huanming Yang
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China
| | | | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
| | - Angela N. Brooks
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA ,grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - Jonathan Göke
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745National Cancer Centre Singapore, Singapore, Singapore
| | - Gunnar Rätsch
- ETH Zurich, Zurich, Switzerland. .,Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Weill Cornell Medical College, New York, NY, USA. .,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,University Hospital Zurich, Zurich, Switzerland.
| | - Roland F. Schwarz
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), partner site Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver Stegle
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zemin Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
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8
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Wang JT, Fiala M, Fortier J, Liu R, Jayasinghe R, Vij R, Ding L. Abstract 3815: Investigating the role of bone marrow microenvironment dysregulation at remission in disease outlook of multiple myeloma. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Multiple myeloma (MM) is a cancer characterized by the unchecked proliferation of antibody-secreting plasma cells (PCs), which to date remains incurable despite therapeutic advancements. The idea that deeper tumor clearance leads to better outcomes is widely accepted in MM treatment: minimal residual disease (MRD) testing, whereby ultra-sensitive sequencing or fluorescence-based cytometric detection of the clonal immunoglobulin secreted by tumor PCs, has been found to be the strongest independent prognostic factor when predicting survival. However, MRD status remains an imperfect predictor. As PCs have a well-defined physiological niche within the bone marrow (BM), and patients often exhibit immunosuppressive BM dysregulation, we investigate the presence of BM microenvironment signatures present at remission that may influence clinical outcomes insufficiently explained by tumor risk strata or MRD status. We conducted 3’ single-cell RNA sequencing of 36 remission, 8 primary diagnosis, and 3 relapse whole BM aspirates taken from 35 patients enrolled in an ongoing clinical trial evaluating a treatment regimen consisting of ixazomib, lenalidomide, and dexamethasone (IRD). 19 of 35 patients were MRD+ at remission; among these, 6 have been reported as having poor outcome (PO; progression-free survival <2.5yrs post sample collection), 12 have had average outcomes (AO; PFS >2.5yrs), and 1 is awaiting assessment. The remaining 16 patients were MRD- at remission, 6 of whom had poor outcome, 7 average, and 3 awaiting assessment. Preliminary analysis of 43 samples have yielded an average capture of 8,620 cells per sample with 1,247 median genes per cell. In comparing 3 PO to 8 AO MRD- remission samples, we see clear polarity between PO and AO cells in every major immune lineage, with a majority of clusters being predominantly (>80%) made of either PO or AO cells. Surprisingly, T, NK, and B cells from AO samples exhibit FOS/JUN upregulation relative to those from PO samples, indicative of AP-1 transcription factor activity that is typically associated with cell proliferation. PO samples also exhibited signs of active cytotoxicity, including upregulated granzymes H and B and IL7R in T and NK cells. Sizeable PC populations were detected in several MRD- remission samples with subpopulation heterogeneity in the expression of MM marker genes; comparison against PCs isolated from healthy donor BM suggests possible persistence of disease phenotypes not captured by MRD testing. We further investigate BM microenvironment evolution between primary diagnosis, remission, and relapse timepoints to elucidate changes in response to tumor clearance. Overall, this study enhances our understanding of how immune surveillance and interaction may influence treatment response in MM.
Citation Format: Julia T. Wang, Mark Fiala, Julie Fortier, Ruiyang Liu, Reyka Jayasinghe, Ravi Vij, Li Ding. Investigating the role of bone marrow microenvironment dysregulation at remission in disease outlook of multiple myeloma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3815.
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Affiliation(s)
- Julia T. Wang
- 1Washington University School of Medicine, Saint Louis, MO
| | - Mark Fiala
- 1Washington University School of Medicine, Saint Louis, MO
| | - Julie Fortier
- 1Washington University School of Medicine, Saint Louis, MO
| | - Ruiyang Liu
- 1Washington University School of Medicine, Saint Louis, MO
| | | | - Ravi Vij
- 1Washington University School of Medicine, Saint Louis, MO
| | - Li Ding
- 1Washington University School of Medicine, Saint Louis, MO
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9
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Kim MY, Jayasinghe R, Devenport JM, Ritchey JK, Rettig MP, O'Neal J, Staser KW, Kennerly KM, Carter AJ, Gao F, Lee BH, Cooper ML, DiPersio JF. A long-acting interleukin-7, rhIL-7-hyFc, enhances CAR T cell expansion, persistence, and anti-tumor activity. Nat Commun 2022; 13:3296. [PMID: 35697686 PMCID: PMC9192727 DOI: 10.1038/s41467-022-30860-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/23/2022] [Indexed: 12/16/2022] Open
Abstract
Chimeric antigen receptor (CAR) T cell therapy is routinely used to treat patients with refractory hematologic malignancies. However, a significant proportion of patients experience suboptimal CAR T cell cytotoxicity and persistence that can permit tumor cell escape and disease relapse. Here we show that a prototype pro-lymphoid growth factor is able to enhance CAR T cell efficacy. We demonstrate that a long-acting form of recombinant human interleukin-7 (IL-7) fused with hybrid Fc (rhIL-7-hyFc) promotes proliferation, persistence and cytotoxicity of human CAR T cells in xenogeneic mouse models, and murine CAR T cells in syngeneic mouse models, resulting in long-term tumor-free survival. Thus, rhIL-7-hyFc represents a tunable clinic-ready adjuvant for improving suboptimal CAR T cell activity.
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Affiliation(s)
- Miriam Y Kim
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Reyka Jayasinghe
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Jessica M Devenport
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Julie K Ritchey
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Michael P Rettig
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Julie O'Neal
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Karl W Staser
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Division of Dermatology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Krista M Kennerly
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Alun J Carter
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Feng Gao
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Matthew L Cooper
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - John F DiPersio
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
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10
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Mok D, Weaver M, Hughes I, Jayasinghe R, Hattingh L. Evaluation of the Emergency Cardiology Coordinator, a Senior Nursing Role Within the Emergency Department. Heart Lung Circ 2022. [PMCID: PMC9345560 DOI: 10.1016/j.hlc.2022.06.427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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11
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Gao GF, Parker JS, Reynolds SM, Silva TC, Wang LB, Zhou W, Akbani R, Bailey M, Balu S, Berman BP, Brooks D, Chen H, Cherniack AD, Demchok JA, Ding L, Felau I, Gaheen S, Gerhard DS, Heiman DI, Hernandez KM, Hoadley KA, Jayasinghe R, Kemal A, Knijnenburg TA, Laird PW, Mensah MKA, Mungall AJ, Robertson AG, Shen H, Tarnuzzer R, Wang Z, Wyczalkowski M, Yang L, Zenklusen JC, Zhang Z, Liang H, Noble MS. Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons' Data. Cell Syst 2020; 9:24-34.e10. [PMID: 31344359 DOI: 10.1016/j.cels.2019.06.006] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 03/18/2019] [Accepted: 06/13/2019] [Indexed: 01/09/2023]
Abstract
We present a systematic analysis of the effects of synchronizing a large-scale, deeply characterized, multi-omic dataset to the current human reference genome, using updated software, pipelines, and annotations. For each of 5 molecular data platforms in The Cancer Genome Atlas (TCGA)-mRNA and miRNA expression, single nucleotide variants, DNA methylation and copy number alterations-comprehensive sample, gene, and probe-level studies were performed, towards quantifying the degree of similarity between the 'legacy' GRCh37 (hg19) TCGA data and its GRCh38 (hg38) version as 'harmonized' by the Genomic Data Commons. We offer gene lists to elucidate differences that remained after controlling for confounders, and strategies to mitigate their impact on biological interpretation. Our results demonstrate that the hg19 and hg38 TCGA datasets are very highly concordant, promote informed use of either legacy or harmonized omics data, and provide a rubric that encourages similar comparisons as new data emerge and reference data evolve.
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Affiliation(s)
- Galen F Gao
- Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; The University of Texas Southwestern Medical School, Dallas, TX 75390, USA
| | - Joel S Parker
- Department of Genetics, Lineberger Comprehensive Cancer Center, the University of North Carolin at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Tiago C Silva
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14.040-905, Brazil
| | - Liang-Bo Wang
- Department of Medicine, Washington University in St Louis, Saint Louis, MO 63108, USA; McDonnell Genome Institute, Washington University in St Louis, Saint Louis, MO 63108, USA; Siteman Cancer Center, Washington University in St Louis, Saint Louis, MO 63108, USA
| | - Wanding Zhou
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Rehan Akbani
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Matthew Bailey
- Department of Medicine, Washington University in St Louis, Saint Louis, MO 63108, USA; McDonnell Genome Institute, Washington University in St Louis, Saint Louis, MO 63108, USA; Siteman Cancer Center, Washington University in St Louis, Saint Louis, MO 63108, USA
| | - Saianand Balu
- Lineberger Comprehensive Cancer Center, Bioinformatics Core, the University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Benjamin P Berman
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Faculty of Medicine, Department of Developmental Biology and Cancer Research, the Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Denise Brooks
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada
| | - Hu Chen
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andrew D Cherniack
- Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Li Ding
- Department of Medicine, Washington University in St Louis, Saint Louis, MO 63108, USA; McDonnell Genome Institute, Washington University in St Louis, Saint Louis, MO 63108, USA; Siteman Cancer Center, Washington University in St Louis, Saint Louis, MO 63108, USA
| | - Ina Felau
- National Cancer Institute, Bethesda, MD 20892, USA
| | - Sharon Gaheen
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | | | - David I Heiman
- Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Kyle M Hernandez
- Department of Pediatrics, the University of Chicago, Chicago, IL 60637, USA; Center for Research Informatics, the University of Chicago, Chicago, IL 60637, USA
| | - Katherine A Hoadley
- Department of Genetics, Lineberger Comprehensive Cancer Center, the University of North Carolin at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Reyka Jayasinghe
- Department of Medicine, Washington University in St Louis, Saint Louis, MO 63108, USA
| | - Anab Kemal
- National Cancer Institute, Bethesda, MD 20892, USA
| | | | - Peter W Laird
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | | | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada
| | - A Gordon Robertson
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada
| | - Hui Shen
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | | | - Zhining Wang
- National Cancer Institute, Bethesda, MD 20892, USA
| | - Matthew Wyczalkowski
- Department of Medicine, Washington University in St Louis, Saint Louis, MO 63108, USA; McDonnell Genome Institute, Washington University in St Louis, Saint Louis, MO 63108, USA; Siteman Cancer Center, Washington University in St Louis, Saint Louis, MO 63108, USA
| | - Liming Yang
- National Cancer Institute, Bethesda, MD 20892, USA
| | | | - Zhenyu Zhang
- Center for Translational Data Science, the University of Chicago, Chicago, IL 60615, USA
| | | | - Han Liang
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA; Department of Systems Biology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Michael S Noble
- Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA.
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Godec A, Jayasinghe R, Chrisinger JSA, Prudner B, Ball T, Wang Y, Srihari D, Kaushal M, Dietz H, Zhang X, Pekmezci M, Dahiya S, Tao Y, Luo J, Van Tine BA, Ding L, Gutmann DH, Hirbe AC. Whole exome sequencing reveals the maintained polyclonal nature from primary to metastatic malignant peripheral nerve sheath tumor in two patients with NF1. Neurooncol Adv 2020; 2:i75-i84. [PMID: 32642734 PMCID: PMC7317063 DOI: 10.1093/noajnl/vdz026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive soft tissue sarcomas with high metastatic rates and poor overall patient survival. There are currently no effective therapies, underscoring the pressing need to define the molecular etiologies that underlie MPNST progression. The aim of this study was to examine clonal progression and identify the molecular events critical for MPNST spread. METHODS In two patients with temporally and spatially distinct metastatic lesions, we employed whole exome sequencing (WES) to elucidate the genetic events of clonal progression, thus identifying the molecular events critical for MPNST spread. RESULTS First, we demonstrated shared clonal origins for the metastatic lesions relative to the primary tumors, which were maintained throughout the course of MPNST progression, supporting the conclusion that cancer cells with metastatic potential already exist in the primary neoplasm. Second, we discovered TRIM23, a member of the Tripartite Motif family of proteins, as a regulator of MPNST lung metastatic spread in vivo. CONCLUSIONS The ability to track the genomic evolution from primary to metastatic MPNST offers new insights into the sequence of genetic events required for tumor progression and has identified TRIM23 as a novel target for future study in this rare cancer.
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Affiliation(s)
- Abigail Godec
- Division of Medical Oncology, Department of Medicine Washington University School of Medicine, St. Louis, Missouri
| | - Reyka Jayasinghe
- Division of Medical Oncology, Department of Medicine Washington University School of Medicine, St. Louis, Missouri
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - John S A Chrisinger
- Siteman Cancer Center, Washington University School of Medicine, Saint Louis, Missouri
- Department of Immunology and Pathology, Washington University School of Medicine, Saint Louis, Missouri
| | - Bethany Prudner
- Division of Medical Oncology, Department of Medicine Washington University School of Medicine, St. Louis, Missouri
| | - Tyler Ball
- Division of Medical Oncology, Department of Medicine Washington University School of Medicine, St. Louis, Missouri
| | - Yuxi Wang
- Division of Medical Oncology, Department of Medicine Washington University School of Medicine, St. Louis, Missouri
| | - Divya Srihari
- Division of Medical Oncology, Department of Medicine Washington University School of Medicine, St. Louis, Missouri
| | - Madhurima Kaushal
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Hilary Dietz
- Division of Medical Oncology, Department of Medicine Washington University School of Medicine, St. Louis, Missouri
| | - Xiaochun Zhang
- Division of Medical Oncology, Department of Medicine Washington University School of Medicine, St. Louis, Missouri
| | - Melike Pekmezci
- Department of Pathology, University of California San Francisco School of Medicine, San Francisco, California
| | - Sonika Dahiya
- Siteman Cancer Center, Washington University School of Medicine, Saint Louis, Missouri
- Department of Immunology and Pathology, Washington University School of Medicine, Saint Louis, Missouri
| | - Yu Tao
- Cancer Center Biostatistics Shared Resource, Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, St. Louis, Missouri
| | - Jinqin Luo
- Cancer Center Biostatistics Shared Resource, Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, St. Louis, Missouri
| | - Brian A Van Tine
- Division of Medical Oncology, Department of Medicine Washington University School of Medicine, St. Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, Saint Louis, Missouri
| | - Li Ding
- Division of Medical Oncology, Department of Medicine Washington University School of Medicine, St. Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, Saint Louis, Missouri
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - David H Gutmann
- Siteman Cancer Center, Washington University School of Medicine, Saint Louis, Missouri
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri
- Neurofibromatosis Center, Washington University School of Medicine, St. Louis, Missouri
| | - Angela C Hirbe
- Division of Medical Oncology, Department of Medicine Washington University School of Medicine, St. Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, Saint Louis, Missouri
- Neurofibromatosis Center, Washington University School of Medicine, St. Louis, Missouri
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Aaltonen LA, Abascal F, Abeshouse A, Aburatani H, Adams DJ, Agrawal N, Ahn KS, Ahn SM, Aikata H, Akbani R, Akdemir KC, Al-Ahmadie H, Al-Sedairy ST, Al-Shahrour F, Alawi M, Albert M, Aldape K, Alexandrov LB, Ally A, Alsop K, Alvarez EG, Amary F, Amin SB, Aminou B, Ammerpohl O, Anderson MJ, Ang Y, Antonello D, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, Dueso-Barroso A, Dunford AJ, Dunn M, Dursi LJ, Duthie FR, Dutton-Regester K, Eagles J, Easton DF, Edmonds S, Edwards PA, Edwards SE, Eeles RA, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu SMG, Estivill X, Etemadmoghadam D, Eyfjord JE, Faltas BM, Fan D, Fan Y, Faquin WC, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson ML, Ferretti V, Feuerbach L, Field MA, Fink JL, Finocchiaro G, Fisher C, Fittall MW, Fitzgerald A, Fitzgerald RC, Flanagan AM, Fleshner NE, Flicek P, Foekens JA, Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, von Mering C. Pan-cancer analysis of whole genomes. Nature 2020; 578:82-93. [PMID: 32025007 PMCID: PMC7025898 DOI: 10.1038/s41586-020-1969-6] [Citation(s) in RCA: 1435] [Impact Index Per Article: 358.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 12/11/2019] [Indexed: 02/07/2023]
Abstract
Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.
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Oldfield K, Jayasinghe R, Niranjan S, Howes L. 173 Takotsubo Syndrome and Diabetic Ketoacidosis Secondary to Immune Checkpoint Inhibitors: A Case Report and Literature Review. Heart Lung Circ 2020. [DOI: 10.1016/j.hlc.2020.09.180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Wang C, Dang S, Har P, Mok D, Jayasinghe R. 083 Audit of the Uptake of Empagliflozin in Diabetic Patients Attending Heart Failure Clinic at a Single Centre. Heart Lung Circ 2020. [DOI: 10.1016/j.hlc.2020.09.090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Huang KL, Mashl RJ, Wu Y, Ritter DI, Wang J, Oh C, Paczkowska M, Reynolds S, Wyczalkowski MA, Oak N, Scott AD, Krassowski M, Cherniack AD, Houlahan KE, Jayasinghe R, Wang LB, Zhou DC, Liu D, Cao S, Kim YW, Koire A, McMichael JF, Hucthagowder V, Kim TB, Hahn A, Wang C, McLellan MD, Al-Mulla F, Johnson KJ, Lichtarge O, Boutros PC, Raphael B, Lazar AJ, Zhang W, Wendl MC, Govindan R, Jain S, Wheeler D, Kulkarni S, Dipersio JF, Reimand J, Meric-Bernstam F, Chen K, Shmulevich I, Plon SE, Chen F, Ding L. Pathogenic Germline Variants in 10,389 Adult Cancers. Cell 2019; 173:355-370.e14. [PMID: 29625052 DOI: 10.1016/j.cell.2018.03.039] [Citation(s) in RCA: 501] [Impact Index Per Article: 100.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 02/24/2018] [Accepted: 03/15/2018] [Indexed: 12/20/2022]
Abstract
We conducted the largest investigation of predisposition variants in cancer to date, discovering 853 pathogenic or likely pathogenic variants in 8% of 10,389 cases from 33 cancer types. Twenty-one genes showed single or cross-cancer associations, including novel associations of SDHA in melanoma and PALB2 in stomach adenocarcinoma. The 659 predisposition variants and 18 additional large deletions in tumor suppressors, including ATM, BRCA1, and NF1, showed low gene expression and frequent (43%) loss of heterozygosity or biallelic two-hit events. We also discovered 33 such variants in oncogenes, including missenses in MET, RET, and PTPN11 associated with high gene expression. We nominated 47 additional predisposition variants from prioritized VUSs supported by multiple evidences involving case-control frequency, loss of heterozygosity, expression effect, and co-localization with mutations and modified residues. Our integrative approach links rare predisposition variants to functional consequences, informing future guidelines of variant classification and germline genetic testing in cancer.
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Affiliation(s)
- Kuan-Lin Huang
- Department of Medicine, Washington University in St. Louis, Saint Louis, MO 63108, USA; McDonnell Genome Institute, Washington University in St. Louis, Saint Louis, MO 63108, USA
| | - R Jay Mashl
- Department of Medicine, Washington University in St. Louis, Saint Louis, MO 63108, USA; McDonnell Genome Institute, Washington University in St. Louis, Saint Louis, MO 63108, USA
| | - Yige Wu
- Department of Medicine, Washington University in St. Louis, Saint Louis, MO 63108, USA; McDonnell Genome Institute, Washington University in St. Louis, Saint Louis, MO 63108, USA
| | - Deborah I Ritter
- Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | - Jiayin Wang
- School of Management, Xi'an Jiaotong University, Xi'an, Shanxi, China
| | - Clara Oh
- Department of Medicine, Washington University in St. Louis, Saint Louis, MO 63108, USA
| | - Marta Paczkowska
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Matthew A Wyczalkowski
- Department of Medicine, Washington University in St. Louis, Saint Louis, MO 63108, USA; McDonnell Genome Institute, Washington University in St. Louis, Saint Louis, MO 63108, USA
| | - Ninad Oak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Adam D Scott
- Department of Medicine, Washington University in St. Louis, Saint Louis, MO 63108, USA; McDonnell Genome Institute, Washington University in St. Louis, Saint Louis, MO 63108, USA
| | - Michal Krassowski
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Kathleen E Houlahan
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Reyka Jayasinghe
- Department of Medicine, Washington University in St. Louis, Saint Louis, MO 63108, USA; McDonnell Genome Institute, Washington University in St. Louis, Saint Louis, MO 63108, USA
| | - Liang-Bo Wang
- Department of Medicine, Washington University in St. Louis, Saint Louis, MO 63108, USA; McDonnell Genome Institute, Washington University in St. Louis, Saint Louis, MO 63108, USA
| | - Daniel Cui Zhou
- Department of Medicine, Washington University in St. Louis, Saint Louis, MO 63108, USA; McDonnell Genome Institute, Washington University in St. Louis, Saint Louis, MO 63108, USA
| | - Di Liu
- Department of Medicine, Washington University in St. Louis, Saint Louis, MO 63108, USA
| | - Song Cao
- Department of Medicine, Washington University in St. Louis, Saint Louis, MO 63108, USA; McDonnell Genome Institute, Washington University in St. Louis, Saint Louis, MO 63108, USA
| | - Young Won Kim
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Amanda Koire
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joshua F McMichael
- McDonnell Genome Institute, Washington University in St. Louis, Saint Louis, MO 63108, USA
| | | | - Tae-Beom Kim
- Departments of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Abigail Hahn
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Chen Wang
- Department of Health Sciences Research and Department of Obstetrics and Gynecology, Mayo Clinic College of Medicine, Rochester, MN 55905 USA
| | - Michael D McLellan
- McDonnell Genome Institute, Washington University in St. Louis, Saint Louis, MO 63108, USA
| | - Fahd Al-Mulla
- Dasman Diabetes Institute and Molecular Pathology Laboratory, Kuwait University, Kuwait
| | - Kimberly J Johnson
- Brown School Master of Public Health Program, Washington University in St. Louis, Saint Louis, MO 63108, USA
| | | | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Paul C Boutros
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Benjamin Raphael
- Lewis-Sigler Institute, Princeton University, Princeton, NJ 08544, USA
| | - Alexander J Lazar
- Departments of Pathology and Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Wei Zhang
- Department of Cancer Biology and Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston Salem, NC 27157 USA
| | - Michael C Wendl
- McDonnell Genome Institute, Washington University in St. Louis, Saint Louis, MO 63108, USA; Department of Genetics, Washington University in St. Louis, Saint Louis, MO 63108, USA; Department of Mathematics, Washington University in St. Louis, Saint Louis, MO 63108, USA
| | - Ramaswamy Govindan
- Department of Medicine, Washington University in St. Louis, Saint Louis, MO 63108, USA
| | - Sanjay Jain
- Department of Medicine, Washington University in St. Louis, Saint Louis, MO 63108, USA
| | - David Wheeler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shashikant Kulkarni
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - John F Dipersio
- Department of Medicine, Washington University in St. Louis, Saint Louis, MO 63108, USA; Siteman Cancer Center, Washington University in St. Louis, Saint Louis, MO 63108, USA
| | - Jüri Reimand
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ken Chen
- Departments of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Sharon E Plon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Feng Chen
- Department of Medicine, Washington University in St. Louis, Saint Louis, MO 63108, USA; Siteman Cancer Center, Washington University in St. Louis, Saint Louis, MO 63108, USA.
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, Saint Louis, MO 63108, USA; McDonnell Genome Institute, Washington University in St. Louis, Saint Louis, MO 63108, USA; Department of Genetics, Washington University in St. Louis, Saint Louis, MO 63108, USA; Siteman Cancer Center, Washington University in St. Louis, Saint Louis, MO 63108, USA.
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Huang KL, Xie M, Wu Y, Jayasinghe R, Varghese R, Mashl RJ, Cao S, Wyczalkowski M, Liang WW, Wendel MC, Fields R, McLellan MD, Link DC, Chen F, Ding L. Abstract 3424: Genomic alterations in clonal hematopoiesis. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-3424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cancer development is an incremental process. Mutations that initiate clonal hematopoiesis often arise in individuals many years before disease symptoms are apparent. We discovered blood somatic mutations in 8,612 germline blood samples in The Cancer Genome Atlas, drawing fundamental distinctions between these events and germline variants. In a preliminary scan of 5,949 samples, 13,345 blood-specific mutations were identified, preferentially distributed across 26 genes, including ones frequently mutated in hematologic malignancies (e.g., DNMT3A, ASXL1, TET2, JAK2, IDH2, SF3B1, MLL3, and KDM6A) and genes rarely mutated in primary hematologic tumors, including EGFR, PIK3CA, NOTCH2, and PPM1D. Further, we utilized both exome sequencing and SNP array data to conduct the first large-scale survey of blood somatic copy number variation, discovering potentially oncogenic events such as JAK2 amplification. Finally, elderly individuals and smokers have increased likelihoods of undergoing clonal expansion. Our analysis of genomic alterations reveals the origins of hematologic malignancies and can facilitate advancement in early detection and prevention.
Citation Format: Kuan-Lin Huang, Mingchao Xie, Yige Wu, Reyka Jayasinghe, Rajees Varghese, R. Jay Mashl, Song Cao, Matthew Wyczalkowski, Wen-wei Liang, Michael C. Wendel, Ryan Fields, Michael D. McLellan, Daniel C. Link, Feng Chen, Li Ding. Genomic alterations in clonal hematopoiesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3424.
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Affiliation(s)
| | | | - Yige Wu
- Washington Univ. St. Louis, Saint Louis, MO
| | | | | | | | - Song Cao
- Washington Univ. St. Louis, Saint Louis, MO
| | | | | | | | | | | | | | - Feng Chen
- Washington Univ. St. Louis, Saint Louis, MO
| | - Li Ding
- Washington Univ. St. Louis, Saint Louis, MO
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Ding L, Bailey MH, Porta-Pardo E, Thorsson V, Colaprico A, Bertrand D, Gibbs DL, Weerasinghe A, Huang KL, Tokheim C, Cortés-Ciriano I, Jayasinghe R, Chen F, Yu L, Sun S, Olsen C, Kim J, Taylor AM, Cherniack AD, Akbani R, Suphavilai C, Nagarajan N, Stuart JM, Mills GB, Wyczalkowski MA, Vincent BG, Hutter CM, Zenklusen JC, Hoadley KA, Wendl MC, Shmulevich L, Lazar AJ, Wheeler DA, Getz G. Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics. Cell 2018; 173:305-320.e10. [PMID: 29625049 PMCID: PMC5916814 DOI: 10.1016/j.cell.2018.03.033] [Citation(s) in RCA: 210] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 02/20/2018] [Accepted: 03/13/2018] [Indexed: 12/21/2022]
Abstract
The Cancer Genome Atlas (TCGA) has catalyzed systematic characterization of diverse genomic alterations underlying human cancers. At this historic junction marking the completion of genomic characterization of over 11,000 tumors from 33 cancer types, we present our current understanding of the molecular processes governing oncogenesis. We illustrate our insights into cancer through synthesis of the findings of the TCGA PanCancer Atlas project on three facets of oncogenesis: (1) somatic driver mutations, germline pathogenic variants, and their interactions in the tumor; (2) the influence of the tumor genome and epigenome on transcriptome and proteome; and (3) the relationship between tumor and the microenvironment, including implications for drugs targeting driver events and immunotherapies. These results will anchor future characterization of rare and common tumor types, primary and relapsed tumors, and cancers across ancestry groups and will guide the deployment of clinical genomic sequencing.
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Affiliation(s)
- Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA.
| | - Matthew H Bailey
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Eduard Porta-Pardo
- Barcelona Supercomputing Centre, 08034 Barcelona, Spain; Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | | | - Antonio Colaprico
- Machine Learning Group (MLG), Département d'Informatique, Université Libre de Bruxelles, 1050 Brussels, Belgium; Department of Human Genetics, University of Miami, Miami, FL 33136, USA
| | - Denis Bertrand
- Computational and Systems Biology, Genome Institute of Singapore, Singapore, 13862
| | - David L Gibbs
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Amila Weerasinghe
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Kuan-Lin Huang
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Collin Tokheim
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Isidro Cortés-Ciriano
- Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Boston, MA 02115, USA; Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Reyka Jayasinghe
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Feng Chen
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Lihua Yu
- H3 Biomedicine Inc., Cambridge, MA 02139, USA
| | - Sam Sun
- Department of Radiation Oncology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Catharina Olsen
- Machine Learning Group (MLG), Département d'Informatique, Université Libre de Bruxelles, 1050 Brussels, Belgium
| | - Jaegil Kim
- Broad Institute, Cambridge, MA 02142, USA
| | - Alison M Taylor
- Broad Institute, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Andrew D Cherniack
- Broad Institute, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Rehan Akbani
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77498, USA
| | - Chayaporn Suphavilai
- Computational and Systems Biology, Genome Institute of Singapore, Singapore, 13862
| | - Niranjan Nagarajan
- Computational and Systems Biology, Genome Institute of Singapore, Singapore, 13862
| | - Joshua M Stuart
- Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Gordon B Mills
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77498, USA
| | - Matthew A Wyczalkowski
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Carolyn M Hutter
- National Human Genome Research Institute, Bethesda, MD 20892, USA
| | | | - Katherine A Hoadley
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Michael C Wendl
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63110, USA
| | | | - Alexander J Lazar
- Departments of Pathology, Genomic Medicine, and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77498, USA
| | - David A Wheeler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Gad Getz
- Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Massachusetts General Hospital, Boston, MA 02114, USA.
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Vaishnav M, Oldfield K, Nguyen BT, Jayasinghe R. Retrospective Analysis of Anomalous Origin Coronary Arteries. Heart Lung Circ 2018. [DOI: 10.1016/j.hlc.2018.06.670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Vaishnav M, Jayasinghe R, Oldfield K, Adsett G, Appleby A, Nguyen BT. Retrospective Analysis of Lipid Control With Evolocumab. Heart Lung Circ 2018. [DOI: 10.1016/j.hlc.2018.06.671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Saraswat A, Singh K, Jayasinghe R. Patent Foramen Ovale Closure Compared to Medical Therapy for Prevention of Stroke Recurrence in Cryptogenic Stroke Population: Systematic Review and Meta-Analysis. Heart Lung Circ 2018. [DOI: 10.1016/j.hlc.2018.06.958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Vaishnav M, Jayasinghe R, Rashid M, Reza A. Percutaneous Closure of a Left Anterior Descending Artery-Pulmonary Artery Fistula Using Onyx (Ethylene-Vinyl Alcohol Copolymer). Heart Lung Circ 2018. [DOI: 10.1016/j.hlc.2018.06.960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Lwin M, Ngo C, Jayasinghe R. Audit on Stent Choice and Baseline Clinical Characteristics of Patients in a Tertiary Centre. Heart Lung Circ 2018. [DOI: 10.1016/j.hlc.2018.06.578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Saraswat A, Malawaraarachchi N, Stroebel A, Jayasinghe R. Unruptured Left Sinus of Valsalva Aneurysm Compressing the Left Anterior Descending Artery: Case Report. Heart Lung Circ 2018. [DOI: 10.1016/j.hlc.2018.06.535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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25
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Marshall AD, Bailey CG, Champ K, Vellozzi M, O'Young P, Metierre C, Feng Y, Thoeng A, Richards AM, Schmitz U, Biro M, Jayasinghe R, Ding L, Anderson L, Mardis ER, Rasko JEJ. CTCF genetic alterations in endometrial carcinoma are pro-tumorigenic. Oncogene 2017; 36:4100-4110. [PMID: 28319062 PMCID: PMC5519450 DOI: 10.1038/onc.2017.25] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 12/21/2016] [Accepted: 01/05/2017] [Indexed: 12/14/2022]
Abstract
CTCF is a haploinsufficient tumour suppressor gene with diverse normal functions in genome structure and gene regulation. However the mechanism by which CTCF haploinsufficiency contributes to cancer development is not well understood. CTCF is frequently mutated in endometrial cancer. Here we show that most CTCF mutations effectively result in CTCF haploinsufficiency through nonsense-mediated decay of mutant transcripts, or loss-of-function missense mutation. Conversely, we identified a recurrent CTCF mutation K365T, which alters a DNA binding residue, and acts as a gain-of-function mutation enhancing cell survival. CTCF genetic deletion occurs predominantly in poor prognosis serous subtype tumours, and this genetic deletion is associated with poor overall survival. In addition, we have shown that CTCF haploinsufficiency also occurs in poor prognosis endometrial clear cell carcinomas and has some association with endometrial cancer relapse and metastasis. Using shRNA targeting CTCF to recapitulate CTCF haploinsufficiency, we have identified a novel role for CTCF in the regulation of cellular polarity of endometrial glandular epithelium. Overall, we have identified two novel pro-tumorigenic roles (promoting cell survival and altering cell polarity) for genetic alterations of CTCF in endometrial cancer.
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Affiliation(s)
- A D Marshall
- Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, New South Wales, Australia.,Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - C G Bailey
- Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, New South Wales, Australia.,Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - K Champ
- Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, New South Wales, Australia.,Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - M Vellozzi
- Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, New South Wales, Australia.,Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - P O'Young
- Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, New South Wales, Australia.,Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - C Metierre
- Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, New South Wales, Australia.,Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Y Feng
- Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, New South Wales, Australia.,Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - A Thoeng
- Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, New South Wales, Australia.,Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - A M Richards
- Gynaecological Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - U Schmitz
- Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, New South Wales, Australia.,Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - M Biro
- Cell Motility and Mechanobiology, School of Medical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - R Jayasinghe
- Cancer Genomics, McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA.,Division of Oncology, Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - L Ding
- Cancer Genomics, McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA.,Division of Oncology, Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - L Anderson
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia.,Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - E R Mardis
- Cancer Genomics, McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA.,Division of Oncology, Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - J E J Rasko
- Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, New South Wales, Australia.,Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia.,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
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26
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Dashwood A, Mclaughlin L, O’brolchain G, Chyeteck S, Batra R, Jayasinghe R, Sivakumar P. A Single Centre Experience of Triple and Dual Anti Thrombotic Therapy in Cardiovascular Disease. Heart Lung Circ 2017. [DOI: 10.1016/j.hlc.2017.06.562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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27
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Lwin M, Jayasinghe R, Dashwood A, Hunt S, Manawaar S. A Case of Giant Cell Myocarditis Presenting with Rapidly Progressive Conduction Disease and Heart Failure. Heart Lung Circ 2017. [DOI: 10.1016/j.hlc.2017.06.189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Vaishnav M, Semasinghe Bandaralage S, Jayasinghe R. Epidemiological Analysis of Infective Endocarditis at the Gold Coast Health Service. Heart Lung Circ 2016. [DOI: 10.1016/j.hlc.2016.06.628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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30
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Habibian M, Sweeny A, Batra R, Jayasinghe R, Kapadia V, Gunter H, Milne J, Niranjan S, Rahman A. Time to Angiography for NSTEMI Patients. 72% within 72hours, but We Can Still do Better! Heart Lung Circ 2016. [DOI: 10.1016/j.hlc.2016.06.153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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31
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Habibian M, Gahan L, Lwin M, Sweeny A, Batra R, Jayasinghe R, Rahman A. A Review of Complication Rates Following Cardiac Implantable Electrophysiological Devices in a Major Hospital Centre. Heart Lung Circ 2016. [DOI: 10.1016/j.hlc.2016.06.326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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32
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Huang KL, Wang J, Cao S, Xie M, Jayasinghe R, Ning J, McLellan M, Wendl M, Scott A, Johnson K, Davies S, Fenyö D, Townsend R, Chen F, Parvin J, Ellis M, Ding L. Abstract 1939: Discovery and proteogenomic investigation of genetic variants in human cancers. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-1939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
A significant fraction of cancers have a heritable component, and require an interplay between somatic and germline variants. Common and rare germline variants have been investigated by previous GWAS and family based studies. However, a comprehensive analysis of both somatic and germline variants in cancer using high throughput sequencing data to discover genetic variants of functional relevance is lacking. Herein, we investigated the potential role of somatic and germline variants from over 20 major cancer types from large-scale studies such as TCGA and ICGC and discovered thousands of somatic and germline variants in cancer genomes. To link these genetic variants to cancer phenotypes, we analyzed the proteomics data in breast, ovarian and colorectal cancers generated by the Clinical Proteomic Tumour Analysis Consortium (CPTAC) using a PepScan pipeline that can detect whether a genomic variant is observed at the peptide level. The pipeline incorporated QUILTS to construct patient-specific protein database and MS-GF+ to identify peptide sequences in the database from MS spectra. Our analysis validated roughly 2% of non-synonymous genetic variants in peptides with matched spectra. We correlated the effect of genetic mutations on proteomic subtypes based on global protein expression levels. Additionally, we assessed the role of genetic variations in kinase genes using phosphoproteome profiles, and identified downstream markers that may be candidate targets for diagnosis or treatment. This analysis also helped us prioritize kinase variants that are likely functional candidates for experimental validation. In conclusion, the comprehensive study of genetic variants utilizing an integrated proteogenomic approach revealed genetic variants with potential functional impacts in cancer.
Citation Format: Kuan-lin Huang, Jaiyin Wang, Song Cao, Mingchao Xie, Reyka Jayasinghe, Jie Ning, Michael McLellan, Michael Wendl, Adam Scott, Kimberly Johnson, Sherri Davies, David Fenyö, Reid Townsend, Feng Chen, Jeffrey Parvin, Matthew Ellis, Li Ding. Discovery and proteogenomic investigation of genetic variants in human cancers. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1939. doi:10.1158/1538-7445.AM2015-1939
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Affiliation(s)
- Kuan-lin Huang
- 1The Genome Institute, Washington University in St. Louis, St. Louis, MO
| | - Jaiyin Wang
- 1The Genome Institute, Washington University in St. Louis, St. Louis, MO
| | - Song Cao
- 1The Genome Institute, Washington University in St. Louis, St. Louis, MO
| | - Mingchao Xie
- 1The Genome Institute, Washington University in St. Louis, St. Louis, MO
| | - Reyka Jayasinghe
- 1The Genome Institute, Washington University in St. Louis, St. Louis, MO
| | - Jie Ning
- 2Department of Medicine, Washington University in St. Louis, St. Louis, MO
| | - Michael McLellan
- 1The Genome Institute, Washington University in St. Louis, St. Louis, MO
| | - Michael Wendl
- 1The Genome Institute, Washington University in St. Louis, St. Louis, MO
| | - Adam Scott
- 1The Genome Institute, Washington University in St. Louis, St. Louis, MO
| | - Kimberly Johnson
- 3Brown School Master of Public Health Program, Washington University in St. Louis, St. Louis, MO
| | - Sherri Davies
- 2Department of Medicine, Washington University in St. Louis, St. Louis, MO
| | - David Fenyö
- 4Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, NY
| | - Reid Townsend
- 2Department of Medicine, Washington University in St. Louis, St. Louis, MO
| | - Feng Chen
- 2Department of Medicine, Washington University in St. Louis, St. Louis, MO
| | - Jeffrey Parvin
- 5Department of Biomedical Informatics, The Ohio State University, Columbia, OH
| | - Matthew Ellis
- 2Department of Medicine, Washington University in St. Louis, St. Louis, MO
| | - Li Ding
- 1The Genome Institute, Washington University in St. Louis, St. Louis, MO
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Jayasinghe R, Narasimhan S, Tran TH, Paskaranandavadivel A. Rapid rule out of myocardial infarction with the use of copeptin as a biomarker for cardiac injury. Intern Med J 2015; 44:921-4. [PMID: 25201424 DOI: 10.1111/imj.12526] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Accepted: 05/05/2014] [Indexed: 12/17/2022]
Abstract
Copeptin is a non-specific marker of an endogenous stress response. A dual biomarker marker approach involving the simultaneous use of troponin and copeptin assays may assist early exclusion of acute coronary syndrome in Australian emergency departments. The utility and limitations of this approach are discussed.
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Affiliation(s)
- R Jayasinghe
- Cardiology Department, Gold Coast University Hospital, Southport, Queensland, Australia; School of Medicine, Griffith University, Southport, Queensland, Australia
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Latona J, Jayasinghe R, Niranjan S. Restrictive cardiomyopathy as a result of endomyocardial fibrosis from hypereosinophilia. Intern Med J 2015; 45:115-7. [DOI: 10.1111/imj.12639] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 06/26/2014] [Indexed: 11/28/2022]
Affiliation(s)
- J. Latona
- Gold Coast University Hospital - Cardiology; Southport Queensland Australia
| | - R. Jayasinghe
- Gold Coast University Hospital; Southport Queensland Australia
| | - S. Niranjan
- Gold Coast University Hospital; Southport Queensland Australia
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35
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Hanna J, Erian A, Donoghue H, Jayasinghe R. Cardiac catheterisation laboratory complications in an Australian tertiary hospital. Heart Lung Circ 2015. [DOI: 10.1016/j.hlc.2015.06.364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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36
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Murdoch D, Mason R, Basavaraj A, Tromp D, Markham R, Jayasinghe R. Gender Based Differences in the Clinical Utility of Computed-Tomography Coronary Angiography (CTCA). Heart Lung Circ 2013. [DOI: 10.1016/j.hlc.2013.05.430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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37
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Mason R, Murdoch D, Tromp D, Basavaraj A, Markham R, Jayasinghe R. Real-world Clinical Application of Computed-tomography Coronary Angiography: A Single-centre Audit of 439 Consecutive Cases. Heart Lung Circ 2013. [DOI: 10.1016/j.hlc.2013.05.462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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38
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Jayasinghe R, Weerasooriya S, Kapadia N. Non-invasive investigation of chronic stable angina--a practical overview for medical practitioners. Med J Malaysia 2012; 67:236-240. [PMID: 22822658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
How does one decide on the best non-invasive test to investigate stable coronary ischaemia? This is a very common question faced by many medical practitioners. Chronic stable angina is a common presentation encountered in general practitice. Upon clinical assessment and risk stratification the patient needs to be investigated further to confirm the diagnosis. The first investigational modality involves a non-invasive test. It is important that practitioners possess a practical knowledge of the array of different tests that are available so that the best suited one for each patient can be chosen. This article aims to compare the efficacy and accuracy and the practical utility of the different non-invasive tests for coronary ischaemia and aid the practitioner in making sound decisions in this regard.
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Affiliation(s)
- R Jayasinghe
- Griffith University, Gold Coast Hospital, Queensland, Australia.
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39
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Yudi M, Omera L, McCubbery N, Dick S, Jayasinghe R, Hamilton-Craig I. Suboptimal consideration and management of potential familial hypercholesterolaemia in patients with suspected premature coronary artery disease. Singapore Med J 2012; 53:174-178. [PMID: 22434290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
INTRODUCTION Familial hypercholesterolaemia (FH) is caused by an autosomal dominant mutation of the low density lipoprotein (LDL) receptor gene, resulting in high levels of LDL cholesterol and premature coronary artery disease (P-CAD). Studies have shown low detection rates of FH in patients admitted with P-CAD and suboptimal therapy at discharge. METHODS Males aged ≤ 55 years and females aged ≤ 60 years who were admitted with P-CAD to the Gold Coast Hospital during a 12-month period were included in the study. The demographics, cardiovascular risk factors, examination findings, admission and discharge cardiac medications and provisional diagnoses were recorded. Diagnosis of FH was made according to internationally accepted criteria. RESULTS 210 patients were included in the study; 60% were male and 40% female (mean age 48 and 50 years, respectively). Only 96 (46%) patients' fasting lipid levels were documented (LDL-C 2.75 ± 1.0 mmol/L), and FH was considered in three (1%) cases. According to the Dutch Lipid Network criteria, three (1%) patients had probable FH, 50 (24%) had possible FH and 60 (29%) had unlikely FH. Of the 53 patients with probable or possible FH, 12 (23%) were discharged without statin therapy and 13 (25%) on the maximum recommended statin dose. CONCLUSION Our study has found inadequate documentation and screening for FH and suboptimal therapy in patients admitted with P-CAD. We propose a simple screening tool that can be applied to all patients admitted with suspected P-CAD in order to improve the detection rate of FH and its management.
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Affiliation(s)
- M Yudi
- Cardiology Department, Gold Coast Hospital, Queensland, Australia.
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Murdoch D, Yudi M, Sweeny A, Trikilis M, Jayasinghe R. Treatment Delay Components for STEMI Patients Undergoing Primary PCI: Four Years of Progress. Heart Lung Circ 2012. [DOI: 10.1016/j.hlc.2012.05.133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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41
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Gaikwad N, Aroney G, Jayasinghe R, Comadira G, Fields J. Out of Hospital Arrests Admitted to the ICU at the Gold Coast Hospital Over 12 Years. Heart Lung Circ 2012. [DOI: 10.1016/j.hlc.2012.05.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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42
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Singbal Y, Trikilis M, Jayasinghe R. A Grading System for Chronic Total Occlusions. Heart Lung Circ 2011. [DOI: 10.1016/j.hlc.2011.05.281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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43
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Yudi M, Jayasinghe R, Jayasinghe S. Efficacy and Safety of Eptifibatide vs Abciximab in ST Elevation Myocardial Infarction. Heart Lung Circ 2011. [DOI: 10.1016/j.hlc.2011.05.309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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44
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Hatton R, Ng K, Hayes P, Bhagwandeen R, Collins N, Jayasinghe R. Percutaneous Device Closure Utilising the Premere Patent Foramen Ovale Occluder. Heart Lung Circ 2010. [DOI: 10.1016/j.hlc.2010.06.1010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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45
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Wright S, Jayasinghe R. Primary Percutaneous Coronary Intervention (PCI) Outcomes in the Elderly. Heart Lung Circ 2010. [DOI: 10.1016/j.hlc.2010.06.1018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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46
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Murdoch D, Jayasinghe R, Buchanan C. A Successful Urban Indigenous Heart Health Screening Clinic. Heart Lung Circ 2010. [DOI: 10.1016/j.hlc.2010.06.623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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47
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McKenzie S, Trikilis M, Rahman A, Batra R, Essack N, Aroney G, Kapadia V, Jayasinghe R. The Frequency and Manner of Presentation of Anomalous Coronary Artery Origin in an Unselected Australian Population Undergoing Coronary Angiography. Heart Lung Circ 2010. [DOI: 10.1016/j.hlc.2010.06.750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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48
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Buchanan C, Manion T, Jayasinghe R. Heart Health Screening Clinics. Heart Lung Circ 2009. [DOI: 10.1016/j.hlc.2009.05.442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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49
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Batra R, Mishra A, Jayasinghe R, Bissessor N, Kapadia V, Rahman A, Aroney G, Sedgwick J. Results in complex multivessel and multilesion percutaneous coronary intervention in patients treated with a combination of drug eluting stents and bare metal stents in real world practice. Cardiovascular Revascularization Medicine 2008. [DOI: 10.1016/j.carrev.2008.02.078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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50
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Bissessor N, Jayasinghe R, Mishra A, Sedgwick J, Batra R. N-terminal pro-B-type natriuretic peptide predicts impaired functional capacity in chronic mixed heart valve disease. Cardiovascular Revascularization Medicine 2008. [DOI: 10.1016/j.carrev.2008.02.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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