Targeted Sequencing of Pancreatic Adenocarcinomas from Patients with Metachronous Pulmonary Metastases

. 2020 Nov 24 ; 11 (12) : . [epub] 20201124

Jazyk angličtina Země Švýcarsko Médium electronic

Typ dokumentu časopisecké články, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/pmid33255265

Mutation spectra of 250 cancer driver, druggable, and actionable genes were analyzed in surgically resected pancreatic ductal adenocarcinoma (PDAC) patients who developed metachronous pulmonary metastases. Targeted sequencing was performed in DNA from blood and archival samples of 15 primary tumors and three paired metastases. Results were complemented with the determination of G12V mutation in KRAS by droplet digital PCR. The median number of protein-changing mutations was 52 per patient. KRAS and TP53 were significantly enriched in fractions of mutations in hotspots. Individual gene mutation frequencies or mutational loads accounting separately for drivers, druggable, or clinically actionable genes, did not significantly associate with patients' survival. LRP1B was markedly mutated in primaries of patients who generalized (71%) compared to those developing solitary pulmonary metastases (0%). FLG2 was mutated exclusively in primary tumors compared to paired metastases. In conclusion, signatures of prognostically differing subgroups of PDAC patients were generated for further utilization in precision medicine.

Zobrazit více v PubMed

Bray F., Ferlay J., Soerjomataram I., Siegel R.L., Torre L.A., Jemal A. Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J. Clin. 2018;68:394–424. doi: 10.3322/caac.21492. PubMed DOI

Rahib L., Smith B.D., Aizenberg R., Rosenzweig A.B., Fleshman J.M., Matrisian L.M. Projecting Cancer Incidence and Deaths to 2030: The Unexpected Burden of Thyroid, Liver, and Pancreas Cancers in the United States. Cancer Res. 2014;74:2913–2921. doi: 10.1158/0008-5472.CAN-14-0155. PubMed DOI

Strobel O., Neoptolemos J.P., Jäger D., Büchler M.W. Optimizing the outcomes of pancreatic cancer surgery. Nat. Rev. Clin. Oncol. 2019;16:11–26. doi: 10.1038/s41571-018-0112-1. PubMed DOI

Jameson G.S., Borazanci E., Babiker H.M., Poplin E., Niewiarowska A.A., Gordon M.S., Barrett M.T., Rosenthal A., Stoll-D’Astice A., Crowley J., et al. Response Rate Following Albumin-Bound Paclitaxel Plus Gemcitabine Plus Cisplatin Treatment Among Patients With Advanced Pancreatic Cancer. JAMA Oncol. 2020;6:125–132. doi: 10.1001/jamaoncol.2019.3394. PubMed DOI PMC

Conroy T., Hammel P., Hebbar M., Ben Abdelghani M., Wei A.C., Raoul J.-L., Choné L., Francois E., Artru P., Biagi J.J., et al. FOLFIRINOX or Gemcitabine as Adjuvant Therapy for Pancreatic Cancer. N. Engl. J. Med. 2018;379:2395–2406. doi: 10.1056/NEJMoa1809775. PubMed DOI

Neoptolemos J.P., Palmer D.H., Ghaneh P., Psarelli E.E., Valle J.W., Halloran C.M., Faluyi O., O’Reilly D.A., Cunningham D., Wadsley J., et al. Comparison of adjuvant gemcitabine and capecitabine with gemcitabine monotherapy in patients with resected pancreatic cancer (ESPAC-4): A multicentre, open-label, randomised, phase 3 trial. Lancet. 2017;389:1011–1024. doi: 10.1016/S0140-6736(16)32409-6. PubMed DOI

Claire D., Marine G., Aurélie A., Olivier T., Sandrine O.-T., Flora P., Marc G., Patrice V., Juan I., Raoul J.L. Heterogeneity of metastatic pancreatic adenocarcinoma: Lung metastasis show better prognosis than liver metastasis—A case control study. Oncotarget. 2016;7:45649–45655. doi: 10.18632/oncotarget.9861. PubMed DOI PMC

Katz M.H.G., Hwang R.F., Fleming J.B., Sun C.C., Wolff R.A., Varadhachary G., Abbruzzese J.L., Crane C.H., Krishnan S., Vauthey J.-N., et al. Long-Term Survival After Multidisciplinary Management of Resected Pancreatic Adenocarcinoma. Ann. Surg. Oncol. 2009;16:836–847. doi: 10.1245/s10434-008-0295-2. PubMed DOI PMC

Lovecek M., Skalicky P., Chudacek J., Szkorupa M., Svebisova H., Lemstrova R., Ehrmann J., Melichar B., Yogeswara T., Klos D., et al. Different clinical presentations of metachronous pulmonary metastases after resection of pancreatic ductal adenocarcinoma: Retrospective study and review of the literature. World J. Gastroenterol. 2017;23:6420–6428. doi: 10.3748/wjg.v23.i35.6420. PubMed DOI PMC

Bailey P., Chang D.K., Nones K., Johns A.L., Patch A.M., Gingras M.C., Miller D.K., Christ A.N., Bruxner T.J., Quinn M.C., et al. Genomic analyses identify molecular subtypes of pancreatic cancer. Nature. 2016;531:47–52. doi: 10.1038/nature16965. PubMed DOI

Biankin A.V., Waddell N., Kassahn K.S., Gingras M.C., Muthuswamy L.B., Johns A.L., Miller D.K., Wilson P.J., Patch A.M., Wu J., et al. Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes. Nat. Cell Biol. 2012;491:399–405. doi: 10.1038/nature11547. PubMed DOI PMC

Jones S., Zhang X., Parsons D.W., Lin J.C.-H., Leary R.J., Angenendt P., Mankoo P., Carter H., Kamiyama H., Jimeno A., et al. Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses. Science. 2008;321:1801–1806. doi: 10.1126/science.1164368. PubMed DOI PMC

Waddell N., Pajic M., Patch A.-M., Chang D.K., Kassahn K.S., Bailey P., Johns A.L., Miller D., Nones K., Quek K., et al. Whole genomes redefine the mutational landscape of pancreatic cancer. Nature. 2015;518:495–501. doi: 10.1038/nature14169. PubMed DOI PMC

Makohon-Moore A.P., Zhang M., Reiter J.G., Bozic I., Allen B., Kundu D., Chatterjee K., Wong F., Jiao Y., Kohutek Z.A., et al. Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer. Nat. Genet. 2017;49:358–366. doi: 10.1038/ng.3764. PubMed DOI PMC

Yachida S., Jones S., Bozic I., Antal T., Leary R.J., Fu B., Kamiyama M., Hruban R.H., Eshleman J.R., Nowak M.A., et al. Distant metastasis occurs late during the genetic evolution of pancreatic cancer. Nat. Cell Biol. 2010;467:1114–1117. doi: 10.1038/nature09515. PubMed DOI PMC

Pishvaian M.J., Bender R.J., Halverson D., Rahib L., Hendifar A., Mikhail S., Chung V., Picozzi V.J., Sohal D., Blais E.M., et al. Molecular Profiling of Patients with Pancreatic Cancer: Initial Results from the Know Your Tumor Initiative. Clin. Cancer Res. 2018;24:5018–5027. doi: 10.1158/1078-0432.CCR-18-0531. PubMed DOI

Topić E., Gluhak J. Isolation of restrictible DNA. Eur. J. Clin. Chem. Clin. Biochem. 1991;29:1892954. PubMed

Hlaváč V., Kovacova M., Elsnerova K., Brynychova V., Kozevnikovova R., Raus K., Kopeckova K., Mestakova S., Vrána D., Gatek J., et al. Use of Germline Genetic Variability for Prediction of Chemoresistance and Prognosis of Breast Cancer Patients. Cancers. 2018;10:511. doi: 10.3390/cancers10120511. PubMed DOI PMC

Bolger A.M., Lohse M., Usadel B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–2120. doi: 10.1093/bioinformatics/btu170. PubMed DOI PMC

Li H. Toward better understanding of artifacts in variant calling from high-coverage samples. Bioinformatics. 2014;30:2843–2851. doi: 10.1093/bioinformatics/btu356. PubMed DOI PMC

Van Der Auwera G.A., Carneiro M.O., Hartl C., Poplin R., Del Angel G., Levy-Moonshine A., Jordan T., Shakir K., Roazen D., Thibault J., et al. From FastQ Data to High-Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline. Curr. Protoc. Bioinform. 2013;43:11.10.1–11.10.33. doi: 10.1002/0471250953.bi1110s43. PubMed DOI PMC

McLaren W., Gil L., Hunt S.E., Riat H.S., Ritchie G.R.S., Thormann A., Flicek P., Cunningham F. The Ensembl Variant Effect Predictor. Genome Biol. 2016;17:1–14. doi: 10.1186/s13059-016-0974-4. PubMed DOI PMC

Tamborero D., Lopez-Bigas N., Gonzalez-Perez A. OncodriveCLUST: Exploiting the positional clustering of somatic mutations to identify cancer genes. Bioinformatics. 2013;29:2238–2244. doi: 10.1093/bioinformatics/btt395. PubMed DOI

Lawrence M.S., Stojanov P., Polak P., Kryukov G.V., Cibulskis K., Sivachenko A., Carter S.L., Stewart C., Mermel C.H., Roberts S.A., et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nat. Cell Biol. 2013;499:214–218. doi: 10.1038/nature12213. PubMed DOI PMC

Broad_Institute_TCGA_Genome_Data_Analysis_Center . PAAD-TP Mutation Analysis (MutSig 2CV v3.1) Broad Institute of MIT and Harvard; Cambridge, MA, USA: 2016. DOI

Broad_Institute_TCGA_Genome_Data_Analysis_Center . LUAD-TP Mutation Analysis (MutSig 2CV v3.1) Broad Institute of MIT and Harvard; Cambridge, MA, USA: 2016. DOI

Grüning B., Bioconda The Bioconda Team. Dale R., Sjödin A., Chapman B.A., Rowe J., Tomkins-Tinch C.H., Valieris R., Köster J. Bioconda: Sustainable and comprehensive software distribution for the life sciences. Nat. Methods. 2018;15:475–476. doi: 10.1038/s41592-018-0046-7. PubMed DOI PMC

Mayakonda A., Lin D.-C., Assenov Y., Plass C., Koeffler H.P. Maftools: Efficient and comprehensive analysis of somatic variants in cancer. Genome Res. 2018;28:1747–1756. doi: 10.1101/gr.239244.118. PubMed DOI PMC

Robinson J.T., Thorvaldsdóttir H., Wenger A.M., Zehir A., Mesirov J.P. Variant Review with the Integrative Genomics Viewer. Cancer Res. 2017;77:e31–e34. doi: 10.1158/0008-5472.CAN-17-0337. PubMed DOI PMC

Benjamini Y., Hochberg Y. Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. J. R. Stat. Soc. Ser. B. 1995;57:289–300. doi: 10.1111/j.2517-6161.1995.tb02031.x. DOI

Shyr C., Tarailo-Graovac M., Gottlieb M., Lee J.J.Y., Van Karnebeek C.D.M., Wasserman W.W. FLAGS, frequently mutated genes in public exomes. BMC Med. Genom. 2014;7:64. doi: 10.1186/s12920-014-0064-y. PubMed DOI PMC

Bailey M.H., Tokheim C., Porta-Pardo E., Sengupta S., Bertrand D., Weerasinghe A., Colaprico A., Wendl M.C., Kim J., Reardon B., et al. Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell. 2018;173:371–385.e18. doi: 10.1016/j.cell.2018.02.060. PubMed DOI PMC

Buchhalter I., Rempel E., Endris V., Allgäuer M., Neumann O., Volckmar A.-L., Kirchner M., Leichsenring J., Lier A., Von Winterfeld M., et al. Size matters: Dissecting key parameters for panel-based tumor mutational burden analysis. Int. J. Cancer. 2019;144:848–858. doi: 10.1002/ijc.31878. PubMed DOI

Huang J., Löhr J.-M., Nilsson M., Segersvärd R., Matsson H., Verbeke C., Heuchel R., Kere J., Iafrate A.J., Zheng Z., et al. Variant Profiling of Candidate Genes in Pancreatic Ductal Adenocarcinoma. Clin. Chem. 2015;61:1408–1416. doi: 10.1373/clinchem.2015.238543. PubMed DOI

Guo S., Shi X., Shen J., Gao S., Wang H., Shen S., Pan Y., Li B., Xu X., Shao Z., et al. Preoperative detection of KRAS G12D mutation in ctDNA is a powerful predictor for early recurrence of resectable PDAC patients. Br. J. Cancer. 2020;122:857–867. doi: 10.1038/s41416-019-0704-2. PubMed DOI PMC

Schlitter A.M., Segler A., Steiger K., Michalski C.W., Jäger C., Konukiewitz B., Pfarr N., Endris V., Bettstetter M., Kong B., et al. Molecular, morphological and survival analysis of 177 resected pancreatic ductal adenocarcinomas (PDACs): Identification of prognostic subtypes. Sci. Rep. 2017;7:srep41064. doi: 10.1038/srep41064. PubMed DOI PMC

Yokose T., Kitago M., Matsuda S., Sasaki Y., Masugi Y., Nakamura Y., Shinoda M., Yagi H., Abe Y., Oshima G., et al. Combination of KRAS and SMAD4 mutations in formalin-fixed paraffin-embedded tissues as a biomarker for pancreatic cancer. Cancer Sci. 2020;111:2174–2182. doi: 10.1111/cas.14425. PubMed DOI PMC

Connor A.A., Denroche R.E., Jang G.H., Lemire M., Zhang A., Chan-Seng-Yue M., Wilson G., Grant R.C., Merico D., Lungu I., et al. Integration of Genomic and Transcriptional Features in Pancreatic Cancer Reveals Increased Cell Cycle Progression in Metastases. Cancer Cell. 2019;35:267–282.e7. doi: 10.1016/j.ccell.2018.12.010. PubMed DOI PMC

Sinn M., Sinn B.V., Treue D., Keilholz U., Damm F., Schmuck R.B., Lohneis P., Klauschen F., Striefler J.K., Bahra M., et al. TP53 mutations predict sensitivity to adjuvant gemcitabine in patients with pancreatic ductal adenocarcinoma: Next-generation sequencing results from the CONKO-001 trial. Clin. Cancer Res. 2020;26:3732–3739. doi: 10.1158/1078-0432.CCR-19-3034. PubMed DOI

Cerami E., Gao J., Dogrusoz U., Gross B.E., Sumer S.O., Aksoy B.A., Jacobsen A., Byrne C.J., Heuer M.L., Larsson E., et al. The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data. Cancer Discov. 2012;2:401–404. doi: 10.1158/2159-8290.CD-12-0095. PubMed DOI PMC

Gao J., Aksoy B.A., Dogrusoz U., Dresdner G., Gross B., Sumer S.O., Sun Y., Jacobsen A., Sinha R., Larsson E., et al. Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal. Sci. Signal. 2013;6:pl1. doi: 10.1126/scisignal.2004088. PubMed DOI PMC

Liu C.X., Musco S., Lisitsina N.M., Forgacs E., Minna J.D., Lisitsyn N.A. LRP-DIT, a putative endocytic receptor gene, is frequently inactivated in non-small cell lung cancer cell lines. Cancer Res. 2000;60:1961–1967. PubMed

Ni S., Hu J., Duan Y., Shi S., Li R., Wu H., Qu Y., Li Y. Down expression ofLRP1Bpromotes cell migration via RhoA/Cdc42 pathway and actin cytoskeleton remodeling in renal cell cancer. Cancer Sci. 2013;104:817–825. doi: 10.1111/cas.12157. PubMed DOI PMC

Ge W., Hu H., Cai W., Xu J., Hu W., Weng X., Qin X., Huang Y., Han W., Hu Y., et al. High-risk Stage III colon cancer patients identified by a novel five-gene mutational signature are characterized by upregulation of IL-23A and gut bacterial translocation of the tumor microenvironment. Int. J. Cancer. 2020;146:2027–2035. doi: 10.1002/ijc.32775. PubMed DOI

Ali S.M., Yao M., Yao J., Wang J., Cheng Y., Schrock A.B., Chirn G.-W., Chen H., Mu S., Gay L.M., et al. Comprehensive genomic profiling of different subtypes of nasopharyngeal carcinoma reveals similarities and differences to guide targeted therapy. Cancer. 2017;123:3628–3637. doi: 10.1002/cncr.30781. PubMed DOI

Johnson D.B., Frampton G.M., Rioth M.J., Yusko E., Xu Y., Guo X., Ennis R.C., Fabrizio D., Chalmers Z.R., Greenbowe J., et al. Targeted Next Generation Sequencing Identifies Markers of Response to PD-1 Blockade. Cancer Immunol. Res. 2016;4:959–967. doi: 10.1158/2326-6066.CIR-16-0143. PubMed DOI PMC

Tucker M.D., Zhu J., Marin D., Gupta R.T., Gupta S., Berry W.R., Ramalingam S., Zhang T., Harrison M., Wu Y., et al. Pembrolizumab in men with heavily treated metastatic castrate-resistant prostate cancer. Cancer Med. 2019;8:4644–4655. doi: 10.1002/cam4.2375. PubMed DOI PMC

Reiter J.G., Baretti M., Gerold J.M., Makohon-Moore A.P., Daud A.I., Iacobuzio-Donahue C.A., Azad N.S., Kinzler K.W., Nowak M.A., Vogelstein B. An analysis of genetic heterogeneity in untreated cancers. Nat. Rev. Cancer. 2019;19:639–650. doi: 10.1038/s41568-019-0185-x. PubMed DOI PMC

Zhang J.N., Huang J.Y., Chen Y.N., Yuan F., Zhang H., Yan F.H., Wang M.J., Wang G., Su M., Lu G., et al. Whole genome and transcriptome sequencing of matched primary and peritoneal metastatic gastric carcinoma. Sci. Rep. 2015;5:1–12. doi: 10.1038/srep13750. PubMed DOI PMC

Gorlov I., Gorlova O.Y., Amos C.I. Untouchable genes in the human genome: Identifying ideal targets for cancer treatment. Cancer Genet. 2019;232:67–79. doi: 10.1016/j.cancergen.2019.01.005. PubMed DOI PMC

Sausen M., Phallen J., Adleff V., Jones S., Leary R.J., Barrett M.T., Anagnostou V., Parpart-Li S., Murphy D., Li Q.K., et al. Clinical implications of genomic alterations in the tumour and circulation of pancreatic cancer patients. Nat. Commun. 2015;6:1–6. doi: 10.1038/ncomms8686. PubMed DOI PMC

Williams C., Pontén F., Moberg C., Söderkvist P., Uhlén M., Pontén J., Sitbon G., Lundeberg J. A High Frequency of Sequence Alterations Is Due to Formalin Fixation of Archival Specimens. Am. J. Pathol. 1999;155:1467–1471. doi: 10.1016/S0002-9440(10)65461-2. PubMed DOI PMC

Do H., Wong S.Q., Li J., Dobrovic A. Reducing Sequence Artifacts in Amplicon-Based Massively Parallel Sequencing of Formalin-Fixed Paraffin-Embedded DNA by Enzymatic Depletion of Uracil-Containing Templates. Clin. Chem. 2013;59:1376–1383. doi: 10.1373/clinchem.2012.202390. PubMed DOI

Peng Q., Satya R.V., Lewis M., Randad P., Wang Y. Reducing amplification artifacts in high multiplex amplicon sequencing by using molecular barcodes. BMC Genom. 2015;16:1–12. doi: 10.1186/s12864-015-1806-8. PubMed DOI PMC

Mariani S., Bertero L., Coppola V., Saracco G., Arezzo A., Di Celle P.F., Metovic J., Marchiò C., Cassoni P. Awareness of mutational artefacts in suboptimal DNA samples: Possible risk for therapeutic choices. Expert Rev. Mol. Diagn. 2018;18:467–475. doi: 10.1080/14737159.2018.1468254. PubMed DOI

Kresse S.H., Namløs H.M., Lorenz S., Berner J.-M., Myklebost O., Bjerkehagen B., Meza-Zepeda L.A. Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples. PLoS ONE. 2018;13:e0197456. doi: 10.1371/journal.pone.0197456. PubMed DOI PMC

Robbe P., Popitsch N., Knight F.S.J.L., Antoniou P., Becq J., Henderson S., Kanapin A., Samsonova A., Vavoulis D.V., Ross M.T., et al. Clinical whole-genome sequencing from routine formalin-fixed, paraffin-embedded specimens: Pilot study for the 100,000 Genomes Project. Genet. Med. 2018;20:1196–1205. doi: 10.1038/gim.2017.241. PubMed DOI PMC

Najít záznam

Citační ukazatele

Nahrávání dat ...

Možnosti archivace

Nahrávání dat ...