Journal Article10.1158/2159-8290.CD-22-1427
Late-Stage Metastatic Melanoma Emerges through a Diversity of Evolutionary Pathways
Lavinia Spain,Alexander Coulton,Irene Lobon,Andrew Rowan,Desiree Schnidrig,Scott Shepherd,B. Shum,Fiona Byrne,M. Goicoechea,Lewis Au,Kim Edmonds,Eleanor Carlyle,Nikki Hunter,Alexandra Renn,Christina Messiou,Peta Hughes,Floris Foijer,H. van den Bos,René Wardenaar,Diana C.J. Spierings,Charlotte Spencer,Andreas M. Schmitt,Z Tippu,Karla Lingard,Lauren Grostate,Kema Peat,Kayleigh Kelly,Sarah Sarker,Mary Mangwende,L Pavlis Terry,Denise Kelly,Jennifer Biano,Aida Murra,Justine Korteweg,Charlotte B. Lewis,Anne-Laure Cattin,Max Emmerich,Camille L. Gerard,Husayn A. Pallikonda,Joanna Lynch,Robert Mason,Aljosja Rogiers,Hang Xu,Ariana Huebner,Nicholas McGranahan,Maise Al Bakir,Jun Murai,Cristina Naceur-Lombardelli,Elaine Borg,Miriam Mitchison,David D. Moore,Mary Falzon,Ian Proctor,Gordon Stamp,Emma Nye,Kate Young,Andrew Furness,Lisa Pickering,Ruby Stewart,Ula Mahadeva,Anna Green,James Larkin,Kevin Litchfield,Charles Swanton,Mariam Jamal-Hanjani,Samra Turajlic +65 more
TL;DR: In this paper , a detailed analysis of melanoma evolution was presented through research autopsy and extensive multi-omic profiling and revealed the diverse routes to treatment resistance, including extensive copy-number alterations, mutations in key drivers, and extrachromosomal DNA.
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Abstract: Metastatic melanoma evolution was illustrated through research autopsy and extensive multiomic profiling and revealed the diverse routes to treatment resistance, including extensive copy-number alterations, mutations in key drivers, and extrachromosomal DNA.
read more
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Cancer cell-intrinsic mechanisms driving acquired immune tolerance.
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Whole-genome doubling in tissues and tumors.
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microDNA and ecDNA: Current methods and single-cell sequencing
TL;DR: Extrachromosomal circular DNA (eccDNA) is a class of circular DNA molecules that originate from genomic DNA but are separate from chromosomes as mentioned in this paper , and it has been used extensively in cancer development, progression, evolution and drug resistance.
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Tumour-wide RNA splicing aberrations generate actionable public neoantigens.
Darwin Kwok,Nicholas O. Stevers,Inaki Etxeberria,Takahide Nejo,Maggie Colton Cove,Lee H. Chen,Jangham Jung,K. Okada,Senthilnath Lakshmanachetty,M. Gallus,Abhilash Barpanda,Gary Chan,Jerry Liu,Samuel H. Wu,Emilio Ramos,Akane Yamamichi,Payal Watchmaker,Hirokazu Ogino,A. Saijo,Aidan Du,Nadia Grishanina,James Woo,Aaron Diaz,Shawn L. Hervey-Jumper,Susan Marina Chang,Arun P Wiita,Christopher A. Klebanoff,Joseph F Costello,Hideo Okada +28 more
TL;DR: Researchers identify a new class of cancer-specific antigens, "public neoantigens," generated by aberrant RNA splicing in various cancers, which can be targeted by T cells to trigger cancer cell eradication and overcome intratumoural heterogeneity.
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Bcl-2 dependent modulation of Hippo pathway in cancer cells
Simona D'Aguanno,Matteo Brignone,Stefano Scalera,Martina Chiacchiarini,Marta Di Martile,Elisabetta Valentini,Francesca De Nicola,Alessia Ricci,Fabio Pelle,Claudio Botti,Marcello Maugeri-Saccà,Donatella Del Bufalo +11 more
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TL;DR: This study reveals that Bcl-2 modulates the Hippo pathway in cancer cells, promoting cell migration, adaptation to high stiffness, and fibroblast activation, suggesting Bcl-2 inhibitors as a potential therapeutic strategy to counteract cancer progression.
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TL;DR: The Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure outperforms other aligners by a factor of >50 in mapping speed.
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TL;DR: The revised RECIST includes a new imaging appendix with updated recommendations on the optimal anatomical assessment of lesions, and a section on detection of new lesions, including the interpretation of FDG-PET scan assessment is included.
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Signatures of mutational processes in human cancer
Ludmil B. Alexandrov,Serena Nik-Zainal,Serena Nik-Zainal,David C. Wedge,Samuel Aparicio,Sam Behjati,Sam Behjati,Andrew V. Biankin,Graham R. Bignell,Niccolo Bolli,Niccolo Bolli,Åke Borg,Anne Lise Børresen-Dale,Anne Lise Børresen-Dale,Sandrine Boyault,Birgit Burkhardt,Adam Butler,Carlos Caldas,Helen Davies,Christine Desmedt,Roland Eils,Jorunn E. Eyfjord,John A. Foekens,Mel Greaves,Fumie Hosoda,Barbara Hutter,Tomislav Ilicic,Sandrine Imbeaud,Sandrine Imbeaud,Marcin Imielinsk,Natalie Jäger,David T. W. Jones,David T. Jones,Stian Knappskog,Stian Knappskog,Marcel Kool,Sunil R. Lakhani,Carlos López-Otín,Sancha Martin,Nikhil C. Munshi,Nikhil C. Munshi,Hiromi Nakamura,Paul A. Northcott,Marina Pajic,Elli Papaemmanuil,Angelo Paradiso,John V. Pearson,Xose S. Puente,Keiran Raine,Manasa Ramakrishna,Andrea L. Richardson,Andrea L. Richardson,Julia Richter,Philip Rosenstiel,Matthias Schlesner,Ton N. Schumacher,Paul N. Span,Jon W. Teague,Yasushi Totoki,Andrew Tutt,Rafael Valdés-Mas,Marit M. van Buuren,Laura van ’t Veer,Anne Vincent-Salomon,Nicola Waddell,Lucy R. Yates,Icgc PedBrain,Jessica Zucman-Rossi,Jessica Zucman-Rossi,P. Andrew Futreal,Ultan McDermott,Peter Lichter,Matthew Meyerson,Matthew Meyerson,Sean M. Grimmond,Reiner Siebert,Elias Campo,Tatsuhiro Shibata,Stefan M. Pfister,Stefan M. Pfister,Peter J. Campbell,Peter J. Campbell,Peter J. Campbell,Michael R. Stratton,Michael R. Stratton +84 more
TL;DR: It is shown that hypermutation localized to small genomic regions, ‘kataegis’, is found in many cancer types, and this results reveal the diversity of mutational processes underlying the development of cancer.
Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response
Peng Jiang,Shengqing Gu,Deng Pan,Jingxin Fu,Avinash Das Sahu,Xihao Hu,Ziyi Li,Nicole Traugh,Xia Bu,Bo Li,Bo Li,Jun Liu,Gordon J. Freeman,Myles Brown,Kai W. Wucherpfennig,X. Shirley Liu +15 more
TL;DR: An algorithm-selected gene signature focused on tumor immune evasion and suppression predicts response to immune checkpoint blockade in melanoma, exceeding the accuracy of current clinical biomarkers.
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