bioinfo12-文献精读01-不同癌症进化模式及临床治疗

• Date : [[2022-06-29_Wed]]
• Tags : #文献解读 #肿瘤 #进化
• 参考：
  • Tumor Evolutionary Principles: How Intratumor Heterogeneity Influences Cancer Treatment and Outcome

1-肿瘤内部异质性和突变消融理论

基因组不稳定性与突变比例正相关，而这也导致了获得不同亚克隆的机会，从而造成内部异质性。

Chromosomal instability (CIN) 是基因组不稳定最显著的特征之一，refers to the rate of acquiring whole-chromosome or segmental chromosomal aneuploidies

杂合敲除gene centrosome-associated protein E (Cenp-e)【中心体相关蛋白】，杂合缺失提升CIN 水平。1）杂合敲除有更多的脾脏、肺癌，而2），genetically (through homozygous p19ARF deletion) and chemically (through 7,12dimethylbenz[a]anthracene exposure) induced tumorigenesis，则相对肿瘤反而少了。

This study supports the mutational meltdown theory postulated by Lynch et al regarding deleterious mutations in asexual populations

查了以下，发现mutational meltdown theory 理论还挺有趣的，参考：The mutational meltdown in asexual populations - PubMed (nih.gov)[1]突变增多>> 有害突变增多 >> 无法适应环境 >> 种群数量减少，甚至灭绝。

不过这里有个假设，就是通过自然选择的无性物种（asexual polulations），会保留其携带的有害突变（当然也假设了有害突变也是存在其中的），这样反复迭代，只会越来越无法适应环境，直至灭绝。

该理论考虑到了群体数量这个因素，假设有某个阈值，刚刚好够自然选择筛选那些存在有利突变的个体。但如果低于该阈值，则类似滚雪球般，下一代有1个有害，2个有害，直到完全无法适应环境：

This irreversible mechanism, long recognized by evolutionary biologists, is known as Muller s ratchet, for the ratchet-like, one-way accumulation of harmful mutations in a population. This process is traditionally viewed as being the result of genetic drift, a random evolutionary process, but under high mutation rate regimes these "clicks of the ratchet" may be driven by mutation itself.

如果利用这个特点来开发药物呢？

还有关于covid19 早期的评论：Mutational meltdown: Can we push SARS CoV-2 off an evolutionary cliff? | ASU News[2]

Over time, mutations accumulate, and if natural selection fails to eliminate these harmful mutations, each generation may become less fit than the preceding. In this way, the most fit genome carries more and more deleterious mutations over time. This phenomenon, known as Muller’s ratchet, sets the viral population on a one-way path to extinction

虽然我们无法控制新冠的繁殖速度，但如果加速它的突变发生的概率，打破这个有害突变累积和自然选择清除的平衡呢？

The drug favipiravir is one such mutation-enhancing candidate, which has already shown promise in this regard in a number of RNA viruses, including Ebola, yellow fever, chikungunya, enterovirus and notovirus.

关于favipiravir 新冠治疗有效性的综述：Favipiravir: A new and emerging antiviral option in COVID-19 - PMC (nih.gov)[3]

回到正题，既然病毒适用，同为asexual polulations 的癌细胞按理也同样适用，有意思的来了：

0 We found, in different cancer types, that patients with tumors containing intermediate levels of CIN had the worst prognosis, whereas tumors with high levels of CIN were associated with improved prognosis (Fig. 1).

这是不是有点像“走火入魔”？

• Roylance R, Endesfelder D, Gorman P, et al. Relationship of extreme chromosomal instability with long-term survival in a retrospective analysis of primary breast cancer. Cancer Epidemiol Biomarkers Prev. 2011;20:2183-2194.
• Birkbak NJ, Eklund AC, Li Q, et al. Paradoxical relationship between chromosomal instability and survival outcome in cancer. Cancer Res. 2011;71:3447-3452.

不过这个阈值该如何把控呢？

这种进化有两种途径：1）microevolution，不断地点突变累计（SNP, INDEL?）; 2）macroevolution，染色体的显著改变（拷贝数变化？）、基因断裂？

The influence of specific somatic alterations on the rate of evolution has been subject to investigation. Genomic aberrations in cancer may accumulate either gradually such as through point mutations (microevolution), or in a punctuated manner through processes such as chromoplexy,26 or in a single catastrophic event such as through chromothripsis (macroevolution).

前列腺癌tp53 突变多 << tp53 失活导致基因不稳定容忍增大、转移事件增多：

For example, prostate cancer metastases were enriched for TP53 mutations, whereas this mutation was subclonal in the primary tumor.29 Conceivably, metastasis may be enhanced by lossof-function of TP53, possibly allowing for greater tolerance of genome instability and the subsequent gain of a metastasis-driving event.

读到这我算是明白了突变和癌症的一些关系，不过最后这个提到的转移耐药性的形成我还是有点懵逼：

Unfortunately, the clinical effect of targeted therapeutic drugs has been limited by the rapid acquisition of drug resistance in the metastatic setting. There are now multiple reports suggesting that drug-resistant subclones reside within the tumor at low frequency prior to therapy in melanoma,30 prostate cancer,31 colorectal cancer,32,33 ovarian cancer,21 and medulloblastoma.34 We recently reported in a study of nine cancer types that mutations in many driver genes can be subclonal across multiple different tumor types. These data suggest that targeting founder events present in every tumor cell may facilitate a more effective drug development process.35

所以耐药性的形成，与突变、基因不稳定，是什么关系呢？

2-肿瘤进化模式

肿瘤的形成过程（从突变进化来看），包括1）癌基因的激活，2）抑癌基因的失活，以及3）由最佳克隆（fittest clone）主导的克隆清除（clonal sweep）。

从之前的进化选择来看，这部分克隆也就是携带有最具适应性的，最能够适应选择的那部分肿瘤克隆：

而什么是clonal sweep 呢？参考：CLONAL EVOLUTION IN CANCER - PMC (nih.gov)[4]

In 1976 Peter Nowell3 published a landmark perspective on cancer as an evolutionary process, driven by stepwise, somatic cell mutations with sequential, sub-clonal selection. The implicit parallel was to Darwinian natural selection with cancer equivalent to an asexually reproducing, unicellular, quasi-species. The modern era of cancer biology and genomics has validated the fundamentals of cancer as a complex, Darwinian, adaptive system The traditional model of clonal evolution posits a series of clonal expansions that grow to dominate the neoplasm (‘selective sweeps’)

这里又对应上了上面提到的，癌细胞也是一种asexual polulations。而克隆清除，则对应具有高适应性的突变的癌细胞迅速增殖，成为肿瘤群体中占据主导（数目最多）的克隆。

作者这里整理市面上的进化类型，以及不同癌症已经有报道的进化模式。

2.1-达尔文进化

2.1.1-分支进化与线性进化

类似在多为点策略中，存在trunk、shared（branch）、private：

个人觉得，在达尔文进化模型中，我们也可以简化的认为，多为点的肿瘤的进化，也是从trunk、shared、private。

在癌症的开始阶段，肿瘤都来自某一个克隆，也就都具有相同的突变。虽然在bulk 测序中，我们无法得知这些突变来自哪个细胞，但我们有理由相信，这些不同位点的肿瘤所公有的突变，极其可能是肿瘤开始时的克隆所携带的。

• 分支进化 分支进化是癌症进化最多的模式之一：

Deep sequencing analysis of hematologic and solid tumors indicate that cancer is usually of clonal origin and often follows a branched tumor evolutionary pattern

某个克隆可能会发展成不同的亚克隆，而这些亚克隆又可能会进化出新的克隆。

这些克隆、亚克隆，亚克隆的亚克隆，在癌症的不同时期，也会发生clonal sweep，从而改变各个克隆的占比，甚至“消灭”其他的克隆，比如下图：

来自timescape结果，(14条消息) Topic 9. 克隆进化之 TimeScape_桓峰基因的博客-CSDN博客[5]

在chemo 的阶段的克隆，在relapse 阶段，几乎全部进化成了新的克隆。这种进化模式，叫做线性进化。

另外，广义上的线性进化模型也指，如果最终（最后事件）被检测到只存在一个克隆，也可以称为线程进化。

Reports suggest that branched evolution is common in cancer, as there may be one or more subclonal/branched driver events present within distinct subclones of a tumor. Nevertheless, in several cancer types, cases of linear evolution have been documented such as in acute myeloid leukemia,46,47 chronic lymphocytic leukemia,48 and VHL-associated ccRCC.4

2.1.2-趋同进化

We have studied four clonally independent primary kidney cancers in the context of a germline VHL mutation.49 Several observations were made from this patient: (1) the tumors were polyclonal, (2) the tumors shared no other mutations apart from the germline VHL mutation highlighting independent evolutionary trajectories despite similar microenvironments, and (3) the tumors showed signs of evolutionary constraints shown by the absence of branched evolution and the presence of convergent evolution toward the PI3K-Akt-mTOR pathway (Fig. 2C)

趋同进化，表示的是一个病人相互独立的肿瘤（不同的原发灶），在相似的环境选择压力下，可能会产生相同的功能或突变：

而在物种进化上来看，趋同进化，即源自不同祖先的生物，由于相似的生活方式，整体或部分形态结构向着同一方向改变。

参考：Clone 2. 肿瘤克隆进化之不同进化模式 (qq.com)

不同类型的具有耐药的癌症，彼此间是否有某些相似的特征？

2.1.3-平行进化

parallel evolution refers to subclones derived from the same parental clone acquiring (epi)genetic alterations in similar genes, protein complexes, or signaling pathways (Fig. 2D).50,51 Although many tumors follow a branched evolutionary pattern, presumably many of these tumors experience common selective pressures from the microenvironment or constraints inherited from the parental founder cell, which force the different subclones to independently converge on similar cellular processes. The level of convergent and parallel evolution is of emerging interest because of developments in the use of multiregion and single cell sequencing (Table 1).

ps：作者文中的说明有点模糊。

从图中来看，平行进化似乎是彼此独立的克隆独立地进化发展。

上面提到，在分支进化中，存在clonal sweep 的现象，同样在平行进化中，不同的克隆之间也可能会彼此之间发生相互作用：

它们可以是协同的，也可以是竞争的。（怎么有点儿打仗那味道了呢？会不会一旦击败了宿主，又要开始“内战”了呢？）

Marusyk et al elegantly demonstrated in a mouse model that a minor subclone with inferior fitness drove tumor growth in a non–cell-autonomous fashion through the secretion of a specific ligand.56 This enabled the tumor to maintain growth, clonal diversity, and even metastatic potential. These tumor phenotypes could be abrogated once the driving subclones were omitted from the tumor, highlighting the importance of examining minor subclones in addition to dominant subclones

不同的克隆从肿瘤整体来看，似乎也是各有分工，比如某个minor subclone，却可以左右肿瘤的成长。

Marusyk A, Tabassum DP, Altrock PM, et al. Non-cell-autonomous driving of tumour growth supports sub-clonal heterogeneity. Nature. 2014;514:54-58.

ps：研究肿瘤各个亚克隆的功能，感觉也是个有意思的课题。

Gatenby et al hypothesized that a tumor may consist of chemotherapy-sensitive cells that have a higher fitness in the absence of chemotherapeutic pressure and suppress the outgrowth of less fit chemotherapyresistant subpopulation.‘ They demonstrated that adapting the chemotherapy dose according to tumor dynamics—that is, higher doses upon tumor growth and lower doses upon tumor reduction—was able to stabilize the tumor and prevent the resistant subpopulation from reaching lethal proportions.

通过对化疗剂量的动态调整，来稳固住肿瘤的发展，控制住比如耐药细胞在内的亚克隆的比例（适当的保证一定比例的非耐药的亚克隆，让克隆之间保持竞争）

ps：Adaptive therapy？让癌症内部自行竞争，好可怕啊。

Gatenby RA, Silva AS, Gillies RJ, et al. Adaptive therapy. Cancer Res. 2009;69:4894-4903.

ps：如何把握这种dose 的平衡呢？可否介入其他的治疗手段，先消除resistant subclone，再一鼓作气消灭sensitive subclone？

2.1.4-序贯进化

治疗策略，不一定是调整药物的剂量，很多时候，也会使用不同的药物以进行治疗。比如根据肿瘤的耐药进化情况进行药物治疗策略的调整，选择新的药物。

肿瘤内部，不仅有更适宜选择压力下的克隆进化，而且也会在这种选择压力下发展出新的突变，新的亚克隆：

肿瘤os：好家伙，换药是吧，那我也发展出新的小伙伴。ps：癌症细胞这种无性增值，每一代都会有很多不同的突变，选择压力下自然是挑选出一代的强者，累积下来，也就形成了能够抵抗药物治疗的新一代的王者了。

2.1.5-转移

. Studies by Gundem et al and Hong et al in prostate cancer show that the following patterns of metastasis occur frequently Kim MY, Oskarsson T, Acharyya S, et al. Tumor self-seeding by circulating cancer cells. Cell. 2009;139:1315-1326.

通常转移事件有以下特征：

• 不同的亚克隆可能在相同的转移灶播种（polyclonal seeding）；
• 这些被播种的多克隆，可能会发生共享亚克隆的组合；
• 一个转移灶内的亚克隆能够传播到其他转移灶（metastatic cross-seeding）；
• 转移灶内的克隆，还可能会返回原发灶（self-seeding）

通常的观点认为，转移发生在克隆选择阶段（角逐出最适宜环境的亚克隆），但也有研究发现，转移在癌症的早期，即trunk克隆向其他亚克隆分化的阶段也会发生：

Schwarz RF, Ng CK, Cooke SL, et al. Spatial and temporal heterogeneity in high-grade serous ovarian cancer: a phylogenetic analysis. PLoS Med. 2015;12:e1001789. Hong MK, Macintyre G, Wedge DC, et al. Tracking the origins and drivers of subclonal metastatic expansion in prostate cancer. Nat Commun. 2015;6:6605.

2.2-中性进化

neutral evolution，也叫大爆炸（big bang model），据说是由谢尔顿·李·库珀博士，哦不，由Sottoriva 提出：

Sottoriva etal termed the“bigbangmodel,” or neutral cancer evolution Sottoriva A, Kang H, Ma Z, et al. A Big Bang model of human colorectal tumor growth. Nat Genet. 2015;47:209-216.

在Sottoriva 研究中，他们发现了一部分肿瘤是克隆的，但意外的是，在相反的不同部位的肿瘤中，发现了等量数目的亚克隆突变 >> 细胞一形成肿瘤，亚克隆就迅速地累积产生 >> 这些细胞会产生迁移，而这种迁移也和肿瘤的生长有一定关系 >> 这些细胞的迁移距离也同样会被肿瘤的生长放大 >> 因此可能在肿瘤中发现四散的亚克隆（肿瘤变大了，本来彼此距离近的肿瘤细胞，被“拉”长了？）>> 因为这些亚克隆四散在肿瘤中，就像大爆炸一样，所以叫做big bang ？

ps：克隆是怎么一下子就形成了若干的亚克隆呢？

中性进化模式的最大区别在于，驱动基因突变是直接的还是选择的。并非是一步步自然选择形成了突变，而是一下子产生多个亚克隆，像大爆炸一样。

还有一种可能，其实迁移的就是相同的亚克隆，只是在四散迁移的过程中，形成了新的突变（产生了新的亚克隆？），不过这种可能比较牵强：

This is unlikely because these private mutations were clonal in individual tumor glands and it is improbable that a whole gland would migrate.

1）整个肿瘤不太可能全部都迁移；2）这些private 突变是克隆突变。

ps：亚克隆本身，并不一定是在克隆的基础上，形成新的突变吗？另外，如果都来自某个克隆，突变都是恰巧”分“得了克隆的某个亚克隆吗？

This model of neutral cancer evolution states that after malignant transformation, individual subclones grow at similar rates, despite showing distinct mutational patterns. In this context, the timing of a new mutation occurring is the major determinant of its prevalence within the tumor, rather than clonal selection for that mutation

ps：如何理解，突变的时机，而非克隆选择呢？在中性进化下，亚克隆就不会彼此竞争了？

However, once treatment has been initiated, it is likely that other forms of Darwinian cancer evolution take over and eventually force the selection of treatmentresistant subclones. ps：这两种模型的具体联系是什么呢？

3-基于肿瘤异质与进化的治疗策略

肿瘤通常是由于若干个驱动基因主导的。但是，肿瘤异质与进化的研究告诉我们，一个肿瘤，其内部是复杂的，可能有各种各样的克隆。

即使我们使用某个药物针对某个突变，可能也无法覆盖全部的克隆，从而导致最佳克隆占据上风。

一种策略是，针对克隆的驱动突变进行靶向，并且这一突变是trunk 形式（所有的克隆都具有该突变），

Yap TA, Gerlinger M, Futreal PA, et al. Intratumor heterogeneity: seeing the wood for the trees. Sci Transl Med. 2012;4:127ps10.

针对突变富集到的相同通路，也是个不错的思路：

Indeed, these observations were initially made in ccRCC, in which rapalogs worked exceptionally well in tumors that harbored multiple mutations that converged upon the mTOR pathway,68 suggesting that parallel evolution could pose as an Achilles heel of cancer.

还可以利用自然选择，使用Adaptive therapy 或者让肿瘤往序贯进化的方向发展：

As cancer evolves during treatment, dynamic therapy strategies may allow the clinician to maintain a stable population of treatment-sensitive cells (adaptive therapy),58 or even force the tumor down a particular evolutionary route resulting in acquired sensitivity to a different drug (sequential therapy

ps：序贯进化不也是治标不治本吗？

The utility of sequential therapy has recently been demonstrated in a patient with an ALKrearranged non–small cell lung cancer, who sequentially responded to different generations of ALK inhibitors Shaw AT, Friboulet L, Leshchiner I, et al. Resensitization to Crizotinib by the Lorlatinib ALK Resistance Mutation L1198F. NEnglJMed. 2016;374:54-61.

ps：病人也没有钱折腾这一代代的药物吧。

从采样来看：

Liquid biopsy analysis of circulating tumor DNA or circulating tumor cells is a convenient way to monitor cancer genetic changes.

ps：ctDNA 或ctCells，和肿瘤部位直接取样，有什么区别呢？本质上的，或是技术上的？了解一下。

比如现在经常看的还是:

We collected 120 surgically resected FFPE tumor tissues from 40 patients (3 tumor regions in different quadrants for each patient) Multi-region exome sequencing reveals the intratumoral heterogeneity of surgically resected small cell lung cancer

ctDNA 或ctCells液体活检的优势在于：

Furthermore, liquid biopsy has the potential to detect subclonal events,71-74 minimal residual disease, and the acquisition of new somatic alterations associated with drug resistance,31,32,75 and it can be used to monitor response73,76 Crowley E, Di Nicolantonio F, Loupakis F, et al. Liquid biopsy: monitoring cancer-genetics in the blood. Nat Rev Clin Oncol. 2013;10:472-484. Krebs MG, Metcalf RL, Carter L, et al. Molecular analysis of circulating tumour cells-biology and biomarkers. Nat Rev Clin Oncol. 2014;11:129-144.

此外，针对肿瘤的基因组不稳定性，也是一个方向：

In addition to adapting treatment to the adapting cancer, it may be attractive to interfere with the causes of genome instability. Reducing genome instability may reduce the adaptability of cancer cells to treatments. Conversely, increasing genome instability may tip the cancer cell beyond the levels of tolerance, forcing cell-autonomous lethality. As there are many causes of genome instability (reviewed in Aguilera et al6 and Burrell et al12), identifying the mechanistic basis of micro- and macroevolutionary events may enable the therapeutic intervention and prevention of major resistance-forming events from occurring.

ps：突变数目和基因不稳定是正相关的，那么如果基于mutational meltdown theory 开发药物，岂不是和针对某一突变靶向的药物治疗相左了？

4-展望

TRACERx (TRAcking nonsmall cell lung Cancer Evolution through therapy [Rx]) is such a prospective study, which aims to define the evolutionary trajectories of non–small cell lung cancer.

Jamal-Hanjani M, Hackshaw A, Ngai Y, et al. Tracking genomic cancer evolution for precision medicine: the lung TRACERx study. PLoS Biol. 2014;12:e1001906

现在已经扩展到四个癌症的研究了：

TracerX | Tracking Cancer Evolution through study[6]

里面也罗列了Melanoma | TracerX[7]

参考资料

[1]

The mutational meltdown in asexual populations - PubMed (nih.gov): https://pubmed.ncbi.nlm.nih.gov/8409355/

[2]

Mutational meltdown: Can we push SARS CoV-2 off an evolutionary cliff? | ASU News: https://news.asu.edu/20200518-mutational-meltdown-can-we-push-sars-cov-2-evolutionary-cliff

[3]

Favipiravir: A new and emerging antiviral option in COVID-19 - PMC (nih.gov): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7467067/

[4]

CLONAL EVOLUTION IN CANCER - PMC (nih.gov): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3367003/

[5]

(14条消息) Topic 9. 克隆进化之 TimeScape_桓峰基因的博客-CSDN博客: https://blog.csdn.net/weixin_41368414/article/details/122346453

[6]

TracerX | Tracking Cancer Evolution through study: http://tracerx.co.uk/

[7]

Melanoma | TracerX: http://tracerx.co.uk/studies/melanoma/