[論文紹介] 古代の伝染性がん系統の体細胞進化と世界的拡大 (Somatic evolution and global expansion of an ancient transmissible cancer lineage)
•
0 likes•100 views
論文紹介 (2019) Somatic evolution and global expansion of an ancient transmissible cancer lineage 古代の伝染性がん系統の体細胞進化と世界的拡大 ※なぜか文字が表示されない場合は全画面表示や保存をすると表示されるようです。
Recommended
Recommended
More Related Content
What's hot
What's hot (20)
Similar to [論文紹介] 古代の伝染性がん系統の体細胞進化と世界的拡大 (Somatic evolution and global expansion of an ancient transmissible cancer lineage)
Similar to [論文紹介] 古代の伝染性がん系統の体細胞進化と世界的拡大 (Somatic evolution and global expansion of an ancient transmissible cancer lineage) (20)
More from Shohei Nagata
More from Shohei Nagata (8)
Recently uploaded
Recently uploaded (20)
[論文紹介] 古代の伝染性がん系統の体細胞進化と世界的拡大 (Somatic evolution and global expansion of an ancient transmissible cancer lineage)
- 1. 古代の伝染性がん系統の体細胞進化と世界的拡大 令和元年十月八日 PMID: 31371581 M2 永田 祥平 RESEARCH ARTICLE ◥ CANCER EVOLUTION Somatic evolution and global expansion of an ancient transmissible cancer lineage Adrian Baez-Ortega1 , Kevin Gori1 *, Andrea Strakova1 *, Janice L. Allen2 , Karen M. Allum3 , Leontine Bansse-Issa4 , Thinlay N. Bhutia5 , Jocelyn L. Bisson1,6 , Cristóbal Briceño7 , Artemio Castillo Domracheva8 , Anne M. Corrigan9 , Hugh R. Cran10 , Jane T. Crawford11 , Eric Davis12 , Karina F. de Castro13 , Andrigo B. de Nardi14 , Anna P. de Vos15 , Laura Delgadillo Keenan16 , Edward M. Donelan2 , Adela R. Espinoza Huerta17 , Ibikunle A. Faramade18 , Mohammed Fazil19 , Eleni Fotopoulou20 , Skye N. Fruean21 , Fanny Gallardo-Arrieta22 , Olga Glebova23 , Pagona G. Gouletsou24 , Rodrigo F. Häfelin Manrique25 , Joaquim J. G. P. Henriques26 , Rodrigo S. Horta27 , Natalia Ignatenko28 , Yaghouba Kane29 , Cathy King3 , Debbie Koenig3 , Ada Krupa30 , Steven J. Kruzeniski17 , Young-Mi Kwon1 , Marta Lanza-Perea9 , Mihran Lazyan31 , Adriana M. Lopez Quintana32 , Thibault Losfelt33 , Gabriele Marino34 , Simón Martínez Castañeda35 , Mayra F. Martínez-López36,37 , Michael Meyer38 , Edward J. Migneco39 , Berna Nakanwagi40 , Karter B. Neal41 , Winifred Neunzig3 , Máire Ní Leathlobhair1 , Sally J. Nixon42 , Antonio Ortega-Pacheco43 , Francisco Pedraza-Ordoñez44 , Maria C. Peleteiro45 , Katherine Polak46 , Ruth J. Pye47 , John F. Reece48 , Jose Rojas Gutierrez49 , Haleema Sadia50 , Sheila K. Schmeling51 , Olga Shamanova52 , Alan G. Sherlock47 , Maximilian Stammnitz1 , Audrey E. Steenland-Smit4 , Alla Svitich53 , Lester J. Tapia Martínez17 , Ismail Thoya Ngoka54 , Cristian G. Torres55 , Elizabeth M. Tudor56 , Mirjam G. van der Wel57 , Bogdan A. Vi ălaru58 , Sevil A. Vural59 , Oliver Walkinton47 , Jinhong Wang1 , Alvaro S. Wehrle-Martinez60 , Sophie A. E. Widdowson61 , Michael R. Stratton62 , Ludmil B. Alexandrov63 , Iñigo Martincorena62 , Elizabeth P. Murchison1 † The canine transmissible venereal tumor (CTVT) is a cancer lineage that arose countries during the 20th century owing to the management andremoval of free-roamingdogs (4). Similar to cancers that remain in a single in- dividual, CTVT accumulates somatic mutations. These result from the activities of endogenous and exogenous mutational processes, and genet- ically imprint a cancer’s history of mutagenic exposures (5). Thus, the CTVT genome can be considered a living biomarker that records the changing mutagenic environments experienced by this cancer throughout millennia and across continents. Although most somatic mutations in cancer have no functional effect and are con- sidered neutral “passenger” mutations, a subset of mutations are positively selected “driver” muta- tions that confer the proliferation and survival advantages that spur cancer growth (6). Ordinary cancers, which remain in a single host, often ac- quire additional driver mutations during tumor progression (7); however, it is unknown whether transmissible cancers that survive for hundreds or thousands of years similarly continue to adapt. It seems possible that the evolution of long-lived cancers such as CTVT may instead be dominated by negative selection acting to remove deleterious mutations. Finally, in addition to recording a his- tory of exposures and signatures of selection, so- matic mutations provide a tool for tracing CTVT phylogeography, potentially revealing how dogs, together with humans, moved around the world over the past centuries. Here, we use somatic mu- tations extracted from the protein-coding ge- nomes (exomes) of 546 globally distributed CTVT tumors to trace the history, spread, diversity, mu- tational exposures, and evolution of the CTVT clone. CTVT phylogeny We sequenced the exomes (43.6 megabases, Mb; mean sequencing depth ~132×) of 546 CTVT tumors collected between 2003 and 2016 from RESEARCH onSeptehttp://science.sciencemag.org/Downloadedfrom RESEARCH ARTICLE ◥ CANCER EVOLUTION Somatic evolution and global expansion of an ancient transmissible cancer lineage Adrian Baez-Ortega1 , Kevin Gori1 *, Andrea Strakova1 *, Janice L. Allen2 , Karen M. Allum3 , Leontine Bansse-Issa4 , Thinlay N. Bhutia5 , Jocelyn L. Bisson1,6 , Cristóbal Briceño7 , Artemio Castillo Domracheva8 , Anne M. Corrigan9 , Hugh R. Cran10 , Jane T. Crawford11 , Eric Davis12 , Karina F. de Castro13 , Andrigo B. de Nardi14 , Anna P. de Vos15 , Laura Delgadillo Keenan16 , Edward M. Donelan2 , Adela R. Espinoza Huerta17 , Ibikunle A. Faramade18 , Mohammed Fazil19 , Eleni Fotopoulou20 , Skye N. Fruean21 , Fanny Gallardo-Arrieta22 , Olga Glebova23 , Pagona G. Gouletsou24 , Rodrigo F. Häfelin Manrique25 , Joaquim J. G. P. Henriques26 , Rodrigo S. Horta27 , Natalia Ignatenko28 , Yaghouba Kane29 , Cathy King3 , Debbie Koenig3 , Ada Krupa30 , Steven J. Kruzeniski17 , Young-Mi Kwon1 , Marta Lanza-Perea9 , Mihran Lazyan31 , Adriana M. Lopez Quintana32 , Thibault Losfelt33 , Gabriele Marino34 , Simón Martínez Castañeda35 , Mayra F. Martínez-López36,37 , Michael Meyer38 , Edward J. Migneco39 , Berna Nakanwagi40 , Karter B. Neal41 , Winifred Neunzig3 , Máire Ní Leathlobhair1 , Sally J. Nixon42 , Antonio Ortega-Pacheco43 , Francisco Pedraza-Ordoñez44 , Maria C. Peleteiro45 , Katherine Polak46 , Ruth J. Pye47 , John F. Reece48 , Jose Rojas Gutierrez49 , Haleema Sadia50 , Sheila K. Schmeling51 , Olga Shamanova52 , Alan G. Sherlock47 , Maximilian Stammnitz1 , Audrey E. Steenland-Smit4 , Alla Svitich53 , Lester J. Tapia Martínez17 , Ismail Thoya Ngoka54 , Cristian G. Torres55 , Elizabeth M. Tudor56 , Mirjam G. van der Wel57 , Bogdan A. Vi ălaru58 , Sevil A. Vural59 , Oliver Walkinton47 , Jinhong Wang1 , Alvaro S. Wehrle-Martinez60 , Sophie A. E. Widdowson61 , Michael R. Stratton62 , Ludmil B. Alexandrov63 , Iñigo Martincorena62 , Elizabeth P. Murchison1 † The canine transmissible venereal tumor (CTVT) is a cancer lineage that arose countries during the 20th century owing to the management andremoval offree-roamingdogs (4). Similar to cancers that remain in a single in- dividual, CTVT accumulates somatic mutations. These result from the activities of endogenous and exogenous mutational processes, and genet- ically imprint a cancer’s history of mutagenic exposures (5). Thus, the CTVT genome can be considered a living biomarker that records the changing mutagenic environments experienced by this cancer throughout millennia and across continents. Although most somatic mutations in cancer have no functional effect and are con- sidered neutral “passenger” mutations, a subset of mutations are positively selected “driver” muta- tions that confer the proliferation and survival advantages that spur cancer growth (6). Ordinary cancers, which remain in a single host, often ac- quire additional driver mutations during tumor progression (7); however, it is unknown whether transmissible cancers that survive for hundreds or thousands of years similarly continue to adapt. It seems possible that the evolution of long-lived cancers such as CTVT may instead be dominated by negative selection acting to remove deleterious mutations. Finally, in addition to recording a his- tory of exposures and signatures of selection, so- matic mutations provide a tool for tracing CTVT phylogeography, potentially revealing how dogs, together with humans, moved around the world over the past centuries. Here, we use somatic mu- tations extracted from the protein-coding ge- nomes (exomes) of 546 globally distributed CTVT tumors to trace the history, spread, diversity, mu- tational exposures, and evolution of the CTVT clone. CTVT phylogeny We sequenced the exomes (43.6 megabases, Mb; mean sequencing depth ~132×) of 546 CTVT tumors collected between 2003 and 2016 from RESEARCH onSephttp://science.sciencemag.org/Downloadedfrom ※写真はただのイメージです。本文の内容と一切の関係はありません。
- 2. 2 要旨 (全文) 可移植性性器腫瘍 (CTVT)は、数千年前に発生し、細胞移植により宿主間で「転 移」することにより生存するがん系統である。 このがんの体細胞変異は、その系 統地理学と進化の歴史を記録している。 本研究では，546個のCTVTエクソームから時間分解された系統発生を構築し、 系統の世界的な拡大について解明した。 変異曝露の変動を調べることにより高度 にコンテキスト特異的な変異プロセスを特定し，これはがんの進化の初期に作動 したがその後消失し、紫外線変異誘発と緯度と相関した。また内因性変異プロセ スの遺伝的多動性を有する腫瘍について解明した。 CTVTは進行中の正の選択 (positive selection)の証拠をほとんど示さず、負の 選択 (negative selection)は必須遺伝子でのみ検出可能であった。 長寿命のク ローン生物が変化する変異原性環境をどのように捕捉するかを示し、中立的な遺 伝的浮動 (genetic drift)が長期的ながんの進化の主要な特徴であることを明らか にした
- 3. 3 要旨 背景 可移植性性器腫瘍 (canine transmissible venereal tumor;CTVT)は細胞移植によってイヌ科宿主間 を転移して感染していくがん細胞である。数千年前に発生したと考えているがその起源やどのように して世界中へ拡大したかは明らかにされていなかった。 対象と手法 世界中のCTVTサンプルのタンパク質コード領域をシーケンスし，蓄積された変異をもとに感染拡大 経路と変異プロセスを解明した。 結果 • CTVTは約6,000年前に中央アフリカで発生し，500年前頃からアメリカ，その後世界各地へと移 入した。 • CTVTに非常に特徴的な変異シグネチャを特定した。 • 長期に渡ってがんを支配するのは中立進化であることが示唆された。(短命なヒトのがんとは対照的) 展望 イヌと数千年に渡ってある種の共存をしているがん細胞の変異プロセスを理解することで，ヒトがが ん細胞を根絶ではなく制御して共存していくという新たな治療アプローチに繋がると期待される。
- 4. 4 可移植性性器腫瘍 (CTVT)とは 可移植性性器腫瘍 (canine transmissible venereal tumor; CTVT) イヌ科において発生する感染性のがん。主に交尾により伝染し外性器などに腫瘍を形成する。 がん細胞が直接イヌからイヌに「転移する」ことで伝染する。 数千年前に個々の「始祖犬 (founder dog)」で最初に発生し，その後，交尾中に生きているがん 細胞を新しい宿主に移すことで生き残っている。 Introduction WHAT IS CTVT? Canine Transmissible Venereal Tumour (CTVT), also called TVT or Sticker s sarcoma is a transmissible cancer hich arose around 11,000 years ago and has been transmitted by living cancer cells during coitus between individual dogs. https://www.tcg.vet.cam.ac.uk/pdfs/ctvt-project-information.pdf
- 5. 5 本研究の流れ INTRODUCTION: The canine transmissible venereal tumor (CTVT) is a sexually transmitted cancer that manifests as genital tumors in dogs. This cancer first arose in an individual “founder dog” several thousand years ago and has since survived by transfer of living cancer cells to new hosts during coitus. Today, CTVT affects dogs around the world and is the oldest and most prolific known cancer lineage. CTVT thus pro- vides an opportunity to explore the evolution of cancer over the long term and to track the unusual biological transition from multicel- lular organism to obligate conspecific asexual parasite. Furthermore, the CTVT genome, act- ing as a living biomarker, has recorded the changing mutagenic environments experienced by this cancer throughout millennia and across continents. RATIONALE: To capture the genetic diversity of the CTVT lineage, we analyzed somatic muta- tions extracted from the protein-coding ge- nomes (exomes) of 546 globally distributed CTVT tumors. We inferred a time-resolved phyloge- netic tree for the clone and used this to trace the worldwide spread of the disease and to select subsets of mutations acquired at known geo- graphical locations and time periods. Computa- tionalmethodswereappliedtoextractmutational signatures and to measure their exposures across time and space. In addition, we assessed the activity of selection using ratios of nonsynon- ymous and synonymous variants. RESULTS: The CTVT phylogeny reveals that the lineage first arose from its founder dog 4000 to 8500 years ago, likely in Asia, with the most recent common ancestor of modern glob- ally distributed tumors occurring ~1900 years ago. CTVT underwent a rapid global expansion within the past 500 years, likely aided by in- tensification of human maritime travel. We identify a highly specific mutational signature dominated by C>T mutations at GTCCA penta- nucleotide contexts, which operated in CTVT up until ~1000 years ago. The number of mu- tations caused by ultraviolet light exposure is correlated with latitude of tumor collection, described in human can- cers. The identification of a highly context-specific mutational process that operated in the past but subsequently vanished, as well as correlation of ultra- violet light–induced DNA damage with latitude, highlight the potential for long-lived, widespread clonal organisms to act as biomarkers for muta- genic exposures. Our results suggest that neu- tral genetic drift is the dominant evolutionary force operating on cancer over the long term, in contrast to the ongoing positive selection that is often observed in short-lived human cancers. The weakness of negative selection in this asexual lineage may be expected to lead to the pro- gressive accumulation of deleterious mutations, invoking Muller’s ratchet and raising the pos- sibility that CTVT may be declining in fitness despite its global success. ▪ Transcribed strand Untranscribed strand Early drivers PTEN RB1 CDKN2A MYC SETD2 546 CTVT exomes (148,030 somatic SNVs) Somatic phylogeny Phylogeography Mutational signatures Selection CTVT founder tumor (4000–8500 BP) Neutral drift Basal trunk (prior to ~1900 BP) Signature A (unknown early process) Signature 7 (UV light) GTCCA C>T Cancer evolution over thousands of years. The canine transmissi- ble venereal tumor (CTVT) is an ancient contagious cancer with a global distribution. We sequenced the exomes of 546 CTVT tumors insights into the cancer’s phylogeography, mutational processes, and signatures of selection across thousands of years. Notably, a highly context-specific mutational pattern named signature A ON OUR WEBSITE ◥ Read the full article at http://dx.doi. org/10.1126/ science.aau9923 .................................................. The list of authors and their affiliations is available in the full article online. Cite this article as A. Baez-Ortega et al., Science 365, eaau9923 (2019). DOI: 10.1126/science.aau9923 onSeptember17,2019http://science.sciencemag.org/Downloadedfrom データセット ・2003年から2016年に渡り，世界各国から546のCTVTサンプルを取得 ・タンパク質コード領域をシークエンス (Exome sequencing) Fig. 1. 地理情報を合わせた系統解析と年代推定により，CTVTの起源と世界的移入の経路を解明した。 Fig. 2. 変異パターンの分析により，CTVTに非常に特徴的な変異シグネチャを特定した。 Fig. 3. CTCV遺伝子にかかる自然選択圧を算出することで，CTCVの進化を支配している中立進化である ことを示唆した。
- 6. 6 CTVTはいつ頃生まれどのように世界に広がったのか？ ~1,000 BP Likely region of origin 4000–8500 BP ~2,000 BP ~1,,0000000000000 BBBBBBBPPPPPPPPPPPPPPPPPPP ~2,00000 B 54 56 55 1 5758 56 54 53 51 50 49 47 46 52 46 46 46 52 52 4948 2223324 26 27728 2825 31 30 34 33 436 37 41 43 44 45 22 17 1716 13 6 5 5 4 43 7 15 ~500 BP 10 11 11 5 2 10 14 12 454 19 200 21 39 4 338 040 414 18 9 3 42 3 303 322 29 45 43 433 434 43 35 Early expansion (prior to ~500 BP) Late expansion (from ~500 BP) Sublineage 1 Sublineage 2 B C D A Years before present (BP) 010002000300040005000600070008000 22,632 SNVs A1 Founder tumor Earliest divergence India Nicaragua Mexico Belize–Mexico Mexico– United States Nicaragua Nicaragua Nicaragua Belize Nicaragua– Guat.–Hond. Mexico– United States Colombia– Panama Ecuador Nicaragua– Colombia Ecuador Chile Paraguay– Uruguay The Gambia Suriname Grenada Grenada India Pakistan India India Thailand India India Brazil Brazil–Uruguay Brazil Brazil South Africa South Africa South Africa Lesotho– South Africa Italy Venezuela Venezuela Grenada Reunion– Senegal Paraguay Gr.–Tur.–Ken.– Tan.–Uganda Mauritius Suriname– C.V.–Portugal Tan.–Tur.– Rom.–Russia United States Australia Australia Colombia Malawi Rom.–Ukraine– Russia Russia Russia–Ukraine Ukraine Armenia–Tur. India India 2 4 5 6 7 8 1 3 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 Sublineage2Sublineage1 3289 SNVs A2 5964 SNVs A3 RESEARCH | RESEARCH ARTICLE onSeptember17,2019http://science.sciencemag.org/Downloadedfrom (A) 分子系統樹を作成し年代情報を推定 ・6,220年前頃 (4,000-8,500年前)に最初の CTVT細胞が発生 ・3つの配列変異グループ (A1-A3) (B) 2,000年前くらいから西へ広がる ・インド系統との分離 ( 2,000年前) ・東ヨーロッパ・黒海領域へ ( 1,000年前) (C, D) 500年前頃から世界中へ爆発的に拡大 ・サブ系統 1 赤：白人の入植と共にアメリカ大陸への流入 ( 500年前) 黒：アフリカへの移入 (少なくとも5回)とヨー ロッパ・アジアへの再移入 ( 300年前) ・サブ系統 2 オーストラリア・太平洋側への移入 ( 500年前) CTVTは中央アジアで約6,000年前に発生し， 約2,000年前から西へ広がっていき，500年前 頃から世界中へ爆発的に感染が広がった。 Fig.1 SNV: 一塩基多様性
- 7. 7 CTVTではどのような変異が発生しているのか？ A B C D E C>A C>G C>T T>A T>C T>G TCC NCGCCC Grenada Mauritius 0.15 Signature 1 NCG Signature 5 0.05 0.30 Signature 2* TCT TCA 0.02 0.04 C>T GTCCA CTCCA ATCCAGGCCA 0.40 C>TC> Signature A NCC Transcribed strand Untranscribed strand Mutationprobability C>T 0.02 0.04 NCCCN NCCTN NTCCN NTCTN 0.15 C>T Signature 7 TCC TCT CCC CCT 0 500 1000 1500 2000 2500 Mutations Transcribed strand Untranscribed strand Transcribed strand Untranscribed strand solutemeanlatitude A2 A3 A1 Signature 7 Signature A Mutationprobability 20 30 40 50 Prediction for A1 (Basal trunk) India Russia–Ukraine South Africa Nicaragua−Colombia RESEARCH | RESEARCH ARTICLE onSeptembhttp://science.sciencemag.org/Downloadedfrom Fig.2 (A) CTVTに特徴的な変異パターンを分析したところ，ほとんどがC>T変異であった。 A B C D E C>A C>G C>T T>A T>C T>G TCC NCGCCC 0.15 Signature 1 NCG Signature 5 0.05 0.30 Signature 2* TCT TCA 0.02 0.04 C>T GTCCA CTCCA ATCCAGGCCA 0.40 C>TC> Signature A NCC Transcribed strand Untranscribed strand Mutationprobability C>T 0.02 0.04 NCCCN NCCTN NTCCN NTCTN 0.15 C>T Signature 7 TCC TCT CCC CCT 0 500 1000 1500 2000 2500 Mutations Transcribed strand Untranscribed strand Transcribed strand Untranscribed strand A2 A3 A1 Signature 7 Signature A Mutationprobability Russia–Ukraine RESEARCH | RESEARCH ARTICLE http://science.sciencemagDownloadedfrom (B) 特徴的な変異プロセスが5つ抽出された。 Signature 1, 5: 内因性変異プロセス Signature 2*: APOBEC酵素 Signature 7: 紫外線への暴露 Signature A: 既知の変異パターンと不一致 COSMIC signatures: COSMIC, the Catalogue Of Somatic Mutations In Cancer, is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer. トリヌクレオチド (3塩基) トリヌクレオチド (3塩基)
- 8. 8 CTVTではどのような変異が発生しているのか？ Fig.2 Fig.2 (C) GTCCAの塩基配列の並びに変異が入り，既知のコンテキスト固有変異よりも顕著な配列嗜好性がある。 2,000年前頃までの間に変異しており，A1枝間での変異の35%を占める (Fig. S5)。 →創立犬 (founder)が居た環境のみで外来的要因によって発生していた変異の可能性 (逆の可能性もある) Fig. S5 Mutational signature exposures across the CTVT phylogeny. Phylogenetic mutational signature exposures in the 61 defined phylogenetic mutation groups Coloured triangles represent the collapsed tree branches of tumour groups coloured according to geographic expansion movements as shown in Fig. numbers, and coloured bars representing group-specific signature exposures, a next to each group. Signature exposures in each group are expressed in normali (the ratio between the number of group-unique SNVs attributed to a signatur number of group-unique C>T changes at CpG dinucleotides). Three groups of somatic variation (A1, A2, A3) are indicated in the tree, with signature displayed at the bottom. 22,632 SNVs A1Founder tumour Earliest divergence 8 2 55 33 56 27 54 28 44 32 31 16 42 40 37 11 3 36 51 12 26 14 9 13 20 43 34 24 10 48 18 49 22 4 45 1 15 7 57 47 38 53 46 29 58 17 19 6 23 39 21 41 5 50 25 35 52 30 Signature 1 Signature 5 Signature 7 Signature 2* Signature A 0 2 4 6 8 10 Normalised SNVs A1 A2 A3 Ancestral somatic variants 3,289 SNVs A2 5,964 SNVs A3 Fig. S5 (D, E) 紫外線の強い地域ほどSignature 7が多いのでは？ → 緯度とCC>TT変異数の関係をもとにCTVT始祖犬集団の緯度を推定 B C D E Grenada Mauritius 0.15 Signature 1 NCG Signature 5 0.05 0.30 Signature 2* TCT TCA 0.02 0.04 C>T GTCCA CTCCA ATCCAGGCCA 0.40 C>TC> Signature A NCC Mutationprobability C>T 0.02 0.04 NCCCN NCCTN NTCCN NTCTN 0.15 C>T Signature 7 TCC TCT CCC CCT F Transcribed strand Untranscribed strand Transcribed strand Untranscribed strand G0.10 Grenada (20) 0.10 Grenada (21) 12–16 20 40 Normalized CC>TT mutations Absolutemeanlatitude A2 A3 A1 Signature 7 Signature A MutationprobabilityMutationprobability 0 10 20 30 40 50 0.0 0.1 0.2 0.3 0.4 Prediction for A1 (Basal trunk) India Suriname Ecuador Russia–Ukraine South Africa Colombia Nicaragua−Colombia Australia utational processes in CTVT. (A) Trinucleotide-context al spectrum of somatic SNVs in a single CTVT tumor. l axis presents 96 mutation types displayed in pyrimidine Relevant mutation contexts are indicated. (B) Mutational f extracted mutational signatures with relevant mutation represent the ratio between group-specific CC>TT mutations and group-specific C>T changes at CpG dinucleotides. The black line and shadowed area indicate the regression curve and associated 95% HPDI. The orange dot and bars represent predicted absolute mean latitude and associated 90% prediction interval for the basal trunk ancestral onSeptember17,2019http://science.sciencemag.org/Downloadedfrom ペンタヌクレオチド (5塩基)
- 9. 9 補足: dN/dSについて 同義置換 (Synonymous substitution): コードされるアミノ酸が変わらない塩基置換 非同義置換 (Non-synonymous substitution): コードされるアミノ酸が変わる塩基置換 非同義置換率 (dN)と同義置換率 (dS)の比 → 自然選択の強さを表す指標 dN/dS > 1 → 正の自然選択 (positive selection) その遺伝子には非同義置換が入りやすい。その遺伝子が適応度を高めるような変異をどんどん獲得している。 dN/dS = 1 → 自然選択がかかっていない. 中立的な進化 同義置換も非同義置換も同じ意味。 dN/dS < 1 → 負の自然選択 (negative selection) その遺伝子には非同義置換が入りにくい。アミノ酸配列の変化が生存に不利になる場合が多い。機能的制約がか かっている。 複数のコドンが同一のアミノ酸を指定する
- 10. 10 CTVTの遺伝子にはどのような選択が働いているのか？ of minimal benefit, such that they were insuffi- cienttoovercometheneutraleffectsofdrift.Notably, since the 1980s, CTVT has been routinely treated with vincristine, a cytotoxic microtubule inhibitor (32). Despite the strong selection pressure imposed by vincristine treatment, we find no evidence of convergent evolution of vincristine resistance mechanisms in CTVT at the level of point mu- prevalent in signature A, accumulating in the human germ line between 15,000 and 2000 years ago. If this human mutation pulse is due to signa- ture A, it could indicate a shared environmental exposure that was once widespread but has now disappeared. However, we find no evidence of an excess of C>T mutations at GTCCA penta- nucleotides in the dog germ line, suggesting that lineage known in nature; it has spread through- out the globe and has seeded its tumors in many thousands of dogs. Here, we have traced this cancer’s route through the steppes of Asia and Europe and as an unwelcome stowaway on global voyages. We have observed the patterns in its mutational profiles reflecting the dynamics of its exogenous and endogenous environment. Further, Homozygous deletion Upstream LINE-1 element integration Hemizygous essential splice-site Hemizygous nonsense Hemizygous nonsense CDKN2A MYC PTEN RB1 SETD2 A D Basal trunk ancestral variation (A1) 22,632 somatic SNVs C 0.0 0.2 0.4 0.6 0.8 1.0 1.2 dN/dS All genes Essential genes Genes per copy number state Genes per gene expression quintile category CN = 1 CN > 1 CN = 1 CN = 2 CN > 2 19,381 genes 269 genes 1520 genes 2585 genes 10,624 genes 1457 genes 3866 genes 3858 genes 3874 genes 3886 genes 3893 genes Missense Nonsense SomaticSNVprevalence (SNVsperMb) 0.01 0.1 1 10 100 1000 B ALL Lung squamous Melanoma CTVT Prostate Head and neck Neuroblastoma 0 20 40 60 80 100 Coding genes (%) Low High Fig. 3. Selection in CTVT. (A) Somatic SNV prevalence across six human cancer types and CTVT. Dots represent individual tumors; red lines indicate median SNV prevalence. ALL, acute lymphoblastic leukemia. (B) Bars showing the percentage of protein-coding genes in the CTVT genome harboring ≥1 nonsynonymous somatic mutation (SNV or indel; 14,412 genes) and ≥1 somatic protein-truncating somatic mutation (5704 genes). (C) Diagram presenting the putative driver events found in the set of basal trunk ancestral variants (group A1, Fig. 1A). A description of each somatic alteration is shown next to the corresponding gene symbol. (D) Exome-wide dN/dS ratios esti- mated for somatic SNVs in all protein-coding genes (left) and in sets of genes defined according to gene essentiality, copy number state, and expression level. Estimates of dN/dS are presented for missense (blue) and nonsense (orange) mutations in each gene group. The dashed line indicates dN/dS = 1 (neutrality); error bars indicate 95% confidence intervals. RESEARCH | RESEARCH ARTICLE onSeptember17,2019http://science.sciencemag.org/Downloadedfrom Fig.3 (A) ヒトがん細胞と比べ，CTVTには圧倒的に多くの変異が蓄積している。 (B) 546サンプルのうち，73%の遺伝子には非同義変異が入っており，29%にはタンパク質欠損変異が入っていた。 (C) 初期にCTVTの移植能を高める等をしてCTVTを引き起こしたと考えられるドライバー遺伝子は5つだった。 PTE, BRC1はヒトがん細胞で頻繁にドライバー変異を有しており，CTVTが伝染するために獲得した特殊な遺伝子は見つからなかった。 (D) CTVTのdN/dS比を算出したところ，ほとんどが中立進化だった。 数十年が寿命のヒトがん細胞では強い正の選択 (dN/dS > 1)がほとんどであり，大きく異なる傾向。 短命なヒトのがんとは対照的に，長期に渡ってがんを支配するのは中立進化であることが示唆された。 CTVTは初期に可移植性がんとしての最適化をほとんど終えており，その後は変えるリスクのほうが大きい可能性。 Fig.3 ヒトがん細胞
- 11. 11 総括 掲載理由 本研究は数千年に渡って進化してきた最古のがん系統の歴史を追跡し，特徴的な変異プロセスがあるこ とと長命ながんでは中立進化が支配的であることを明らかにした。ヒトががん細胞を制御して共存して いくという新たな治療アプローチに繋がると期待される。 感想 • エキソン以外のnon-coding領域はどうなっているんだろう • 比較的長命なヒトがん系統 (HeLaとか)と比較してみたい • 腫瘍を制御し共存するという新しい道へ expansion of an ancient transmissible cancer lineage Adrian Baez-Ortega et al. INTRODUCTION: The canine transmissible venereal tumor (CTVT) is a sexually transmitted cancer that manifests as genital tumors in dogs. This cancer first arose in an individual “founder dog” several thousand years ago and has since survived by transfer of living cancer cells to new hosts during coitus. Today, CTVT affects dogs around the world and is the oldest and most prolific known cancer lineage. CTVT thus pro- vides an opportunity to explore the evolution of cancer over the long term and to track the unusual biological transition from multicel- lular organism to obligate conspecific asexual parasite. Furthermore, the CTVT genome, act- ing as a living biomarker, has recorded the changing mutagenic environments experienced by this cancer throughout millennia and across continents. RATIONALE: To capture the genetic diversity of the CTVT lineage, we analyzed somatic muta- tions extracted from the protein-coding ge- nomes (exomes) of 546 globally distributed CTVT tumors. We inferred a time-resolved phyloge- netic tree for the clone and used this to trace the worldwide spread of the disease and to select subsets of mutations acquired at known geo- graphical locations and time periods. Computa- tionalmethodswereappliedtoextractmutational signatures and to measure their exposures across time and space. In addition, we assessed the activity of selection using ratios of nonsynon- ymous and synonymous variants. RESULTS: The CTVT phylogeny reveals that the lineage first arose from its founder dog 4000 to 8500 years ago, likely in Asia, with the most recent common ancestor of modern glob- ally distributed tumors occurring ~1900 years ago. CTVT underwent a rapid global expansion within the past 500 years, likely aided by in- tensification of human maritime travel. We identify a highly specific mutational signature dominated by C>T mutations at GTCCA penta- nucleotide contexts, which operated in CTVT up until ~1000 years ago. The number of mu- tations caused by ultraviolet light exposure is correlated with latitude of tumor collection, CONCLUSION: We have traced the evolution of a transmissible cancer over several thousand years, tracking its spread across continents and contrasting the mutational processes and selec- tive forces that molded its genome with those described in human can- cers. The identification of a highly context-specific mutational process that operated in the past but subsequently vanished, as well as correlation of ultra- violet light–induced DNA damage with latitude, highlight the potential for long-lived, widespread clonal organisms to act as biomarkers for muta- genic exposures. Our results suggest that neu- tral genetic drift is the dominant evolutionary force operating on cancer over the long term, in contrast to the ongoing positive selection that is often observed in short-lived human cancers. The weakness of negative selection in this asexual lineage may be expected to lead to the pro- gressive accumulation of deleterious mutations, invoking Muller’s ratchet and raising the pos- sibility that CTVT may be declining in fitness despite its global success. ▪ Baez-Ortega et al., Science 365, 464 (2019) 2 August 2019 1 of 1 Transcribed strand Untranscribed strand Early drivers PTEN RB1 CDKN2A MYC SETD2 546 CTVT exomes (148,030 somatic SNVs) Somatic phylogeny Phylogeography Mutational signatures Selection CTVT founder tumor (4000–8500 BP) Neutral drift Basal trunk (prior to ~1900 BP) Signature A (unknown early process) Signature 7 (UV light) GTCCA C>T Cancer evolution over thousands of years. The canine transmissi- ble venereal tumor (CTVT) is an ancient contagious cancer with a global distribution. We sequenced the exomes of 546 CTVT tumors and identified somatic single-nucleotide variants (SNVs). These were used to construct a time-resolved phylogenetic tree, yielding insights into the cancer’s phylogeography, mutational processes, and signatures of selection across thousands of years. Notably, a highly context-specific mutational pattern named signature A was identified, which was active in the past but ceased to operate about 1000 years ago. BP, years before present. ON OUR WEBSITE ◥ Read the full article at http://dx.doi. org/10.1126/ science.aau9923 .................................................. The list of authors and their affiliations is available in the full article online. Cite this article as A. Baez-Ortega et al., Science 365, eaau9923 (2019). DOI: 10.1126/science.aau9923 onSeptember17,2019http://science.sciencemag.org/Downloadedfrom • CTVTは約6,000年前に中央アフリカで発生し，500年前頃からアメリカ，その後世界各地へと移入 した。 • 始祖たるCTVT細胞に発生した5つのドライバー遺伝子によって腫瘍となった。 • 現在のCTVT細胞になるまでに蓄積している変異の殆どは中立変異であり，長期に渡ってがんを支配 するするのは中立進化であることが示唆された。(短命なヒトのがんとは対照的) まとめ