Deep sequencing of DNA from urine of kidney allograft recipients to estimate donor/recipient-specific DNA fractions.
Deep sequencing of DNA from urine of kidney allograft recipients to estimate donor/recipient-specific DNA fractions.
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DOI：
10.1371/journal.pone.0249930
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发表时间：
2021
期刊：
影响因子：
3.7
通讯作者：
Suhre K
中科院分区：
文献类型：
--
作者：
Belkadi A;Thareja G;Dadhania D;Lee JR;Muthukumar T;Snopkowski C;Li C;Halama A;Abdelkader S;Abdulla S;Mahmoud Y;Malek J;Suthanthiran M;Suhre K
肾移植是终末期肾功能衰竭患者的首选治疗方法，但移植的同种异体移植物可能受到病毒和细菌感染以及免疫排斥反应的影响。诊断肾移植急性病变的标准试验是肾活检。然而，非侵入性测试是可取的。移植界已经开发了使用不同技术的各种方法。但这些方法需要改进。在这里，我们提出了一个具有成本效益的方法，肾排斥反应的诊断，估计捐助者/受者特定的DNA分数在受体尿液中测序尿细胞DNA。我们假设在无病理阶段，受体尿液中存在的最大组织类型是供体肾细胞，并且在排斥反应的情况下，将观察到大量的受体免疫细胞。广泛的计算机模拟用于调整测序参数：变体数量和覆盖深度。对2个健康个体的DNA混合物测序表明，该方法具有高度的预测性（最大误差< 0.04）。然后，我们使用内部和公共数据库证明了家庭关系和种族的微不足道的影响。最后，我们对来自32个活检匹配样本的尿细胞团进行了深度DNA测序，这些样本代表两个病理组：急性排斥（AR，11个样本）和急性肾小管损伤（ATI，12个样本）以及9个无病理的样本。我们发现两个病理组与无病理组相比，供体/供体特异性DNA分数之间存在显著相关性（AR组P = 0.0064，ATI组P = 0.026）。我们的结论是，肾移植受者尿细胞的深度DNA测序提供了一种非侵入性的方法来诊断人类肾移植的急性病理。
Kidney transplantation is the treatment of choice for patients with end-stage kidney failure, but transplanted allograft could be affected by viral and bacterial infections and by immune rejection. The standard test for the diagnosis of acute pathologies in kidney transplants is kidney biopsy. However, noninvasive tests would be desirable. Various methods using different techniques have been developed by the transplantation community. But these methods require improvements. We present here a cost-effective method for kidney rejection diagnosis that estimates donor/recipient-specific DNA fraction in recipient urine by sequencing urinary cell DNA. We hypothesized that in the no-pathology stage, the largest tissue types present in recipient urine are donor kidney cells, and in case of rejection, a larger number of recipient immune cells would be observed. Extensive in-silico simulation was used to tune the sequencing parameters: number of variants and depth of coverage. Sequencing of DNA mixture from 2 healthy individuals showed the method is highly predictive (maximum error < 0.04). We then demonstrated the insignificant impact of familial relationship and ethnicity using an in-house and public database. Lastly, we performed deep DNA sequencing of urinary cell pellets from 32 biopsy-matched samples representing two pathology groups: acute rejection (AR, 11 samples) and acute tubular injury (ATI, 12 samples) and 9 samples with no pathology. We found a significant association between the donor/recipient-specific DNA fraction in the two pathology groups compared to no pathology (P = 0.0064 for AR and P = 0.026 for ATI). We conclude that deep DNA sequencing of urinary cells from kidney allograft recipients offers a noninvasive means of diagnosing acute pathologies in the human kidney allograft.
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影响因子：
16.6
作者：
Burnham P;Dadhania D;Heyang M;Chen F;Westblade LF;Suthanthiran M;Lee JR;De Vlaminck I
通讯作者：
De Vlaminck I
影响因子：
3.7
作者：
Macher HC;Suárez-Artacho G;Guerrero JM;Gómez-Bravo MA;Álvarez-Gómez S;Bernal-Bellido C;Dominguez-Pascual I;Rubio A
通讯作者：
Rubio A
影响因子：
3.6
作者：
Gordon PM;Khan A;Sajid U;Chang N;Suresh V;Dimnik L;Lamont RE;Parboosingh JS;Martin SR;Pon RT;Weatherhead J;Wegener S;Isaac D;Greenway SC
通讯作者：
Greenway SC
影响因子：
17.1
作者：
De Vlaminck I;Valantine HA;Snyder TM;Strehl C;Cohen G;Luikart H;Neff NF;Okamoto J;Bernstein D;Weisshaar D;Quake SR;Khush KK
通讯作者：
Khush KK
影响因子：
3
作者：
Kwon S;Lee B;Yoon S
通讯作者：
Yoon S