破解肺癌和黑色素瘤之基因組

作者：Roxanne Nelson  
出處：WebMD醫學新聞

　　December 23, 2009 — 根據線上發表於12月16日自然(Nature)期刊的新研究，首次完成癌症基因組的綜合分析，英國劍橋Wellcome Trust Sanger研究中心的研究人員，將惡性黑色素瘤和肺癌的整個基因組定序。
　　
　　研究作者指出，癌症由突變誘發，所有癌症細胞的基因突變都不會遺傳，但是會累積而使細胞發病。目前有100多種不同的癌症，但是只有一件事情相同：全部都是一個人一生之細胞體突變增加所致。
　　
　　對於這兩種癌症，研究者指出，他們已經可以在腫瘤變得明顯之前幾年，清楚揭露這些環境誘導有機體突變物質在DNA上的痕跡。
　　
　　研究者表示，其中的一些體細胞改變，稱為「駕駛員突變」，提供選擇性無性系生長幫助，與癌症發生有關。其他的是「乘客」突變，與腫瘤形成無關，不過，這些「乘客突變」有突變機轉的痕跡，因此可提供關於癌症原因和病理的有價值線索。
　　
　　Wellcome Trust Sanger研究中心副主任、這兩篇研究的共同作者、英國皇家病理科醫學院榮譽院士、英國醫療科學協會會員、Michael R. Stratton醫師解釋，關鍵在於我們真正需朝向辨識個別癌症的所有「駕駛員突變」，這是瞭解每個癌症之演化的基礎，也將成為瞭解如何治療的基礎。
　　
　　惡性黑色素瘤與肺癌是工業化國家常見的兩種癌症，已知其主要致癌曝露原因。對於肺癌，主因是抽菸；對於惡性黑色素瘤，是曝曬紫外線。Stratton醫師向Medscape Oncology表示，我們在目前特別研究這兩個癌症，是因為我們有興趣知道是否有完整的體細胞突變清單，可讓我們瞭解紫外線和抽菸對於癌症DNA的影響。
　　
　　同時也是癌症基因組計畫(Cancer Genome Project)共同負責人的Stratton醫師表示，事實證明我們可以看見這兩個外部誘導突變物質的影響，且在這兩個癌症發現的不同體細胞突變模式中有相當的敏銳度。現在，我們可以繼續研究環境曝露因素不清楚的其他癌症，看是否有無法解釋的謎題。
　　
　　發現這個資訊將誘導出有關癌症起源和發展的大量訊息。他表示，發現的突變也將告訴我們關於驅使每個癌症之突變的基因。在每個案例中，在未來知道所有的癌症基因，將可讓我們做出更多告知選項，哪種藥物對哪個病患有效、對哪些病患無效。
　　
　　【肺癌基因組】
　　根據研究作者，抽菸者發生肺癌的風險是未抽菸者的20倍以上，其他惡性疾病的風險也增加。終究，抽菸含有60種以上的誘導突變物質，會和DNA結合且產生化學影響，因此讓肺癌基因組產生有特徵的突變模式。
　　
　　此次分析中，Stratton醫師等人定序NCI-H209，在一個55歲、骨髓轉移的小細胞肺癌病患進行化療之前取得的細胞線。目標是找出與抽菸有關的突變負擔。雖然沒有病患的抽菸史資料，研究者指出，樣本顯示為組織上典型的、有傳統神經內分泌特徵的小細胞，這些特徵的腫瘤有超過97%與抽菸有關。
　　
　　使用「大量同時定序科技」，總共辨識22,910個體細胞替代，包括134個位於基因編碼外顯子，研究者可以辨識許多清楚的點突變模式，反映出「抽菸的混合型致癌因子」，以及修補DNA損傷的細胞監控機轉所達到之部份成功嘗試的特徵。
　　
　　肺癌一般發生在抽菸50年(包數-年= 7300根香菸)之後。如果多數的突變是來自與抽菸有關的致癌物質，最後在一生中，將會變成惡性的細胞群落，研究作者指出，平均每抽15根菸產生一個突變。如果這是局部細胞群聚案例，每根香菸在整個支氣管樹的後天突變數量將很明顯。
　　
　　【定序惡性黑色素瘤】
　　研究者定序的另一個癌症是惡性黑色素瘤，雖僅佔3%的皮膚癌案例，但是引起四分之三的皮膚癌死亡。在此次分析中，他們定序COLO-829，一個永久公開的癌細胞線，在治療前得自一個43歲惡性黑色素瘤轉移男性。
　　
　　總共辨識33,345鹽基體細胞替代，首次提供個別癌症的體細胞突變的綜合清單。根據研究作者，體細胞突變的清單代表所有發生在細胞分裂世系突變事件的累積紀錄，始於受精卵而終於癌細胞。
　　
　　此清單包括出現在COLO-829的絕大多數突變，也帶有以前紫外線誘發DNA傷害的痕跡，以及附屬的、獨立的傷害機轉的證據。
　　
　　研究者寫道，已知紫外線曝露是發生黑色素瘤的環境風險因素，這明顯的突變特徵反映出此因素引起的DNA傷害。也有試圖修補DNA的證據，其中多數為駕駛員突變，提供此黑色素瘤選擇性生長優勢。
　　
　　Stratton醫師指出，此計畫將繼續定序癌症，他表示，我們將繼續這些研究，我們自己以及全球的研究夥伴，將以同樣的方法對上百種癌症進行研究。
　　
　　肺癌研究的作者們宣告有各種財務關係，完整記載於原始文章。黑色素瘤研究的作者們皆宣告沒有相關財務關係。
　　
　　Nature.線上發表於2009年12月16日。


Genomes for Lung Cancer and Melanoma Deciphered

By Roxanne Nelson
Medscape Medical News

December 23, 2009 — The first comprehensive analyses of cancer genomes have been completed, according to new research published in the December 16 online issue of Nature. Led by researchers from the Wellcome Trust Sanger Institute in Cambridge, the United Kingdom, the entire genome of malignant melanoma and lung cancer has been sequenced.

Cancer is driven by mutation, the study authors note, and all cancer cells carry genetic mutations that are not inherited but have accumulated as the cell progresses to disease. There are more than 100 different types of cancer, but all have one thing in common: they all develop as a result of the acquisition of somatic mutations throughout the lifetime of an individual.

For both types of cancer, the researchers note that they have been able to clearly uncover imprints of these environmental mutagens on DNA, which occur years before the tumor becomes evident.

Some of these somatic alterations, called driver mutations, confer selective clonal growth advantage and are implicated in cancer development, say the researchers. The remaining mutations are "passengers," in that they do not contribute to oncogenesis. However, these passenger mutations have the imprints of the mutational mechanisms that have generated them and thus can provide valuable insights into the cause and pathogenesis of cancer.

That is fundamental to understanding the evolution of each cancer

The key thing that we really need to be moving toward is to identify all the driver mutations for individual cancers, explained Michael R. Stratton, FRCPath, FMedSci, FRS, deputy director of the Wellcome Trust Sanger Institute, and who is a coauthor of both studies. "That is fundamental to understanding the evolution of each cancer and will become fundamental to understanding how we should treat them."

Malignant melanoma and lung cancer are 2 common cancers in industrialized nations, for which the primary carcinogenic exposure is known. For lung cancer, it is cigarette smoke; for malignant melanoma, it is exposure to ultraviolet light. "We studied these two cancers in particular at this stage, because we were interested in knowing whether having a complete catalogue of somatic mutations would allow us to see the effects of ultraviolet light and tobacco smoke on DNA of the cancer," Dr. Stratton told Medscape Oncology.

"It turned out that we could see the effects of these two external mutagens with remarkable acuity in the different patterns of somatic mutation that were found in the two cancers," said Dr. Stratton, who is also joint head of the Cancer Genome Project. "Now, we can go on to other cancer types in which the environmental exposure is not known and see whether there are mysterious patterns that have no explanation."

Uncovering this information will divulge a great deal of information about the origins and development of cancer. "The mutations found will also tell us about the cancer genes that are mutated and that are driving each individual cancer," he said. "Knowing all the cancer genes in future, in each case, will allow us to make much more informed choices as to which drugs will work in the individual patient and which ones will not."

Knowing all the cancer genes in future...will allow us to make much more informed choices

Lung Cancer Genome

Smokers have more than 20 times the risk for the development of lung cancer than nonsmokers, according to the study authors, as well as an increased risk for other types of malignant diseases. Tobacco smoke contains more than 60 mutagens that will bind to and, eventually, chemically modify DNA and thus brand the lung cancer genome with characteristic mutational patterns.

In this analysis, Dr. Stratton and colleagues sequenced NCI-H209, a small-cell lung cancer cell line derived from a bone marrow metastasis of a 55-year-old man before he was treated with chemotherapy. The goal was to explore the mutational burden associated with tobacco smoking. Although the smoking history of the patient was not available, the researchers point out that the sample showed "histologically typical small cells with classic neuroendocrine features," and more than 97% of tumors with these characteristics are associated with tobacco smoking.

With use of massively parallel sequencing technology, a total of 22,910 somatic substitutions were identified, including 134 in coding exons. The investigators were able to identify many distinct point mutation patterns, which reflects the "cocktail of carcinogens present in cigarette smoke," along with signatures of the partially successful attempts made by the cell's surveillance mechanisms to repair DNA damage.

an average of one mutation for every 15 cigarettes smoked,

Lung cancer typically develops after 50 pack-years of smoking (pack-year = 7300 cigarettes). If the majority of mutations are derived from the combination of mutagens present in tobacco smoke, then the clone of cells that ultimately becomes malignant would acquire, during its lifetime, "an average of one mutation for every 15 cigarettes smoked," the study authors note. "And if this is the case for a localized cluster of cells, then the number of mutations acquired across the whole bronchial tree from even one cigarette must be substantial."

Sequencing Malignant Melanoma

The second cancer that the researchers sequenced was malignant melanoma, which comprises only 3% of skin cancer cases but causes three quarters of death due to skin cancer. In this analysis, they sequenced COLO-829, an immortal, publicly available cancer cell line that was derived, before therapy, from a metastasis of a malignant melanoma in a 43-year-old man.

A total of 33,345 base somatic substitutions were identified, providing "the first comprehensive catalogue of somatic mutations from an individual cancer." The catalogue of somatic mutations represents a cumulative record of all mutational events that have occurred during the lineage of cell divisions, beginning with the fertilized egg and ending in the cancer cell, according to the study authors.

This catalogue included the overwhelming majority of mutations present in COLO-829 and also carried the imprint of past ultraviolet-light–induced DNA damage along with evidence for auxiliary, independent mechanisms of damage.

Ultraviolet light exposure is a known environmental risk factor for the development of melanoma and the dominant mutational signature reflected DNA damage due to this factor, the study authors write. There was also evidence of attempts to repair the DNA, and "buried within it are most of the driver mutations that have conferred selective growth advantage on this melanoma."

Dr. Stratton noted that the plan is to continue sequencing cancers. "We intend to continue these studies ultimately doing thousands of cancers in the same way ourselves and together with colleagues around the globe," he said.

The authors in the lung cancer study have disclosed various financial relationships. A complete description is available in the original article. The authors in the melanoma study have disclosed no relevant financial relationships.

Nature. Published online December 16, 2009.