1
|
Das B, Evrard YA, Chen L, Patidar R, Vilimas T, McCutcheon JN, Peach AL, Nair NV, Forbes TD, Fullmer BA, Fong AJL, Romero LE, Chapman AK, Conley KA, Harrington RD, Jiwani SS, Wang P, Gottholm-Ahalt MM, Cantu EN, Rivera G, Dutko LM, Benauer KM, Kannan VR, Bonomi CA, Dougherty KM, Geraghty JP, Gibson MV, Styers SS, Walke AJ, Moyer JE, Wade A, Baldwin ML, Arthur KA, Plater KJ, Stockwin L, Murphy MR, Mullendore ME, Newton DL, Hollingshead MG, Karlovich CA, Williams PM, Doroshow JH. Abstract 3916: Patient-derived organoid and cell culture models from the NCI Patient-Derived Models Repository (NCI PDMR) preserve genomic stability and heterogeneity of patient tumor specimens. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-3916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: The National Cancer Institute (NCI) has developed a Patient-Derived Models Repository (PDMR; https://pdmr.cancer.gov) of preclinical models including patient-derived xenografts (PDX), organoids (PDOrg) and patient-derived cell cultures (PDC). Extensive clinical annotation and genomic datasets are available for these preclinical models. However, it is unclear if the molecular profiles of the corresponding patient tumors are stably propagated in these models. We have previously demonstrated that PDX models from the NCI PDMR faithfully represent the patient tumors both in terms of genomic stability and tumor heterogeneity. Here, we conduct an in-depth investigation of genomic representation of patient tumors in the PDOrgs and PDCs.
Methods: PDOrgs (n=64) and PDCs (n=94) were established from tumor fragments (i.e., initiator specimens) obtained either from patient specimens or from PDX specimens of early passage. For some models (n=19), both PDOrgs and PDCs were generated from the same tumor tissue; in fewer cases (n=4), PDCs were established from organoids derived from patient specimens. Whole Exome Sequencing and RNA-Seq were performed on all PDCs and PDOrgs, and data were compared with patient specimens or early passage PDXs.
Results: A majority of the PDOrgs and PDCs have stably inherited the genome of the corresponding patient specimens based on the following observations: (1) >87% of PDOrgs and PDCs maintained similar copy number alteration profiles compared with the initiator specimens of the preclinical model; (2) the variant allele frequency (VAF) of clinically relevant mutations remained consistent between the PDOrgs, PDCs, and the initiator specimens, with none of the PDCs or PDOrgs deviating by >15% VAF; and (3) clinically relevant biomarkers (e.g., MSI, LOH, mutational signatures etc.) are concordant amongst the PDOrgs, PDCs, and the initiator specimens. We observed that the majority of SNVs and indels present in the initiator specimens were also found in the PDOrgs and PDCs, suggesting almost all the tumor heterogeneity was preserved in these preclinical models.
Conclusions: This large and histologically diverse set of PDOrgs and PDCs from the NCI PDMR exhibited genomic stability and faithfully represented the tumor heterogeneity observed in corresponding patient specimens. These preclinical models thus represent a valuable resource for researchers interested in pre-clinical drug or other studies.
Citation Format: Biswajit Das, Yvonne A. Evrard, Li Chen, Rajesh Patidar, Tomas Vilimas, Justine N. McCutcheon, Amanda L. Peach, Nikitha V. Nair, Thomas D. Forbes, Brandie A. Fullmer, Anna J. Lee Fong, Luis E. Romero, Alyssa K. Chapman, Kelsey A. Conley, Robin D. Harrington, Shahanawaz S. Jiwani, Peng Wang, Michelle M. Gottholm-Ahalt, Erin N. Cantu, Gloryvee Rivera, Lindsay M. Dutko, Kelly M. Benauer, Vishnuprabha R. Kannan, Carrie A. Bonomi, Kelly M. Dougherty, Joseph P. Geraghty, Marion V. Gibson, Savanna S. Styers, Abigail J. Walke, Jenna E. Moyer, Anna Wade, Mariah L. Baldwin, Kaitlyn A. Arthur, Kevin J. Plater, Luke Stockwin, Matthew R. Murphy, Michael E. Mullendore, Dianne L. Newton, Melinda G. Hollingshead, Chris A. Karlovich, Paul M. Williams, James H. Doroshow. Patient-derived organoid and cell culture models from the NCI Patient-Derived Models Repository (NCI PDMR) preserve genomic stability and heterogeneity of patient tumor specimens [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3916.
Collapse
Affiliation(s)
- Biswajit Das
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Yvonne A. Evrard
- 2Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Li Chen
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Rajesh Patidar
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Tomas Vilimas
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Justine N. McCutcheon
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Amanda L. Peach
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Nikitha V. Nair
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Thomas D. Forbes
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Brandie A. Fullmer
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Anna J. Lee Fong
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Luis E. Romero
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Alyssa K. Chapman
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Kelsey A. Conley
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Robin D. Harrington
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Shahanawaz S. Jiwani
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Peng Wang
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Michelle M. Gottholm-Ahalt
- 3Biological Testing Branch, Developmental Therapeutics Program, National Cancer Institute at Frederick, Frederick, MD
| | - Erin N. Cantu
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Gloryvee Rivera
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Lindsay M. Dutko
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Kelly M. Benauer
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Vishnuprabha R. Kannan
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Carrie A. Bonomi
- 2Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | | | | | - Marion V. Gibson
- 2Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Savanna S. Styers
- 2Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Abigail J. Walke
- 2Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Jenna E. Moyer
- 2Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Anna Wade
- 2Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Mariah L. Baldwin
- 2Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Kaitlyn A. Arthur
- 2Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Kevin J. Plater
- 2Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Luke Stockwin
- 2Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Matthew R. Murphy
- 2Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | | | - Dianne L. Newton
- 2Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Melinda G. Hollingshead
- 3Biological Testing Branch, Developmental Therapeutics Program, National Cancer Institute at Frederick, Frederick, MD
| | - Chris A. Karlovich
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Paul M. Williams
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - James H. Doroshow
- 4Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD
| |
Collapse
|
2
|
Patidar R, Chen L, Karlovich CA, Das B, Evrard YA, Vilimas T, McCutcheon JN, Peach AL, Nair NV, Forbes TD, Fullmer BA, Fong AJL, Romero LE, Chapman AK, Conley KA, Harrington RD, Jiwani SS, Wang P, Ahalt MMG, Cantu EN, Rivera G, Dutko LM, Benauer KM, Kannan VR, Borgel SD, Carter JP, Stottlemyer JM, Miner TL, Breen DR, Delaney ET, McGlynn CA, Mallow CN, Radzyminski M, Uzelac SN, Alcoser SY, Grinnage-Pulley TL, Eugeni MA, Newton DL, Hollingshead MG, Williams PM, Doroshow JH. Abstract 3554: Genomic landscape of acquired uniparental disomy in NCI PDMR patient derived xenograft models. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-3554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Acquired Uniparental Disomy (aUPD) is relatively common in cancer. Occurrence of aUPD is more frequent in some tumor histologies (e.g., serous ovarian, colorectal) and may be relevant for choice of therapy. The Patient-Derived Models Repository (PDMR; https://pdmr.cancer.gov) developed by The National Cancer Institute (NCI) includes patient-derived xenograft (PDX) models from multiple tumor histologies with different passages and lineages. The associated clinical annotation and genomic data make it possible to assess the prevalence of aUPD in the PDMR cohort and the stability of aUPD in different passages and lineages within a PDX model.
Methods: High tumor purity in the PDX specimens (after removal of mouse reads representing the stroma) enabled highly accurate assessment of loss of heterozygosity (LOH). Variants called by GATK Haplotype caller from whole exome sequencing (WES) data were used to identify segments of homozygosity using BCFtools/RoH (runs of homozygosity). The RoH segments were then intersected with the bed file for chromosome arms to get %LOH at the arm level. If %LOH on a chromosome arm was >90%, we considered the sample to have aUPD at the arm level. WES was also used to look for associations between DNA damage repair (DDR) pathway alterations and aUPD.
Results: We made the following observations: a) aUPD was observed most frequently in chr18q (75/427, 17.6%) and chr3p (69/427, 16%) of PDX models; b) aUPD was observed more frequently in certain tumor histologies, e.g., clear cell renal cell carcinoma (6/8), small cell lung cancer (3/4) and non-small cell lung cancer (25/38); c) extensive aUPD was observed in 4 PDMR models (>50% of evaluated chromosome arms in these models have aUPD); d) aUPD was not observed in some tumor histologies, i.e., synovial sarcoma, uterine endometrioid carcinoma; e) in the vast majority of PDMR models (>90%), aUPD is maintained faithfully across lineages and through multiple passaging; f) subclonal aUPD events were observed in some models across different lineages; g) significant enrichment of double strand DNA break repair (DSBR) pathway alterations was observed in PDMR models without aUPD (p=0.0007, Fisher's exact test) suggesting defects in DSBR are not associated with aUPD; and h) aUPD was rarely observed in MSI-high models (1/30) suggesting mutual exclusivity of mismatch repair (MMR) pathway defects and aUPD.
Conclusion: We observed a relatively high frequency of UPD in the PDMR models (at least 1 arm of a chromosome). UPD was more frequently observed in specific chromosomal arms. The frequency of aUPD was higher in some tumor histologies and absent in others. aUPD was stably maintained across passages and lineages, although some heterogeneity was observed. Our data suggest aUPD is not associated with defects in DSBR and MMR pathways. Preclinical drug studies using NCI PDMR models may suggest appropriate therapeutic options for cancers with aUPD.
Citation Format: Rajesh Patidar, Li Chen, Chris A. Karlovich, Biswajit Das, Yvonne A. Evrard, Tomas Vilimas, Justine N. McCutcheon, Amanda L. Peach, Nikitha V. Nair, Thomas D. Forbes, Brandie A. Fullmer, Anna J. Lee Fong, Luis E. Romero, Alyssa K. Chapman, Kelsey A. Conley, Robin D. Harrington, Shahanawaz S. Jiwani, Peng Wang, Michelle M. Gottholm Ahalt, Erin N. Cantu, Gloryvee Rivera, Lindsay M. Dutko, Kelly M. Benauer, Vishnuprabha R. Kannan, Suzanne D. Borgel, John P. Carter, Jesse M. Stottlemyer, Tiffanie L. Miner, Devynn R. Breen, Emily T. Delaney, Chelsea A. McGlynn, Candace N. Mallow, Marianne Radzyminski, Shannon N. Uzelac, Sergio Y. Alcoser, Tara L. Grinnage-Pulley, Michelle A. Eugeni, Dianne L. Newton, Melinda G. Hollingshead, Paul M. Williams, James H. Doroshow. Genomic landscape of acquired uniparental disomy in NCI PDMR patient derived xenograft models [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3554.
Collapse
Affiliation(s)
- Rajesh Patidar
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Li Chen
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Chris A. Karlovich
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Biswajit Das
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Yvonne A. Evrard
- 2Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Tomas Vilimas
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Justine N. McCutcheon
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Amanda L. Peach
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Nikitha V. Nair
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Thomas D. Forbes
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Brandie A. Fullmer
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Anna J. Lee Fong
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Luis E. Romero
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Alyssa K. Chapman
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Kelsey A. Conley
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Robin D. Harrington
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Shahanawaz S. Jiwani
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Peng Wang
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Michelle M. Gottholm Ahalt
- 3Biological Testing Branch, Developmental Therapeutics Program, National Cancer Institute at Frederick, Frederick, MD
| | - Erin N. Cantu
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Gloryvee Rivera
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Lindsay M. Dutko
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Kelly M. Benauer
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Vishnuprabha R. Kannan
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Suzanne D. Borgel
- 2Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - John P. Carter
- 2Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | | | - Tiffanie L. Miner
- 2Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Devynn R. Breen
- 2Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Emily T. Delaney
- 2Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | | | - Candace N. Mallow
- 2Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | | | - Shannon N. Uzelac
- 2Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Sergio Y. Alcoser
- 3Biological Testing Branch, Developmental Therapeutics Program, National Cancer Institute at Frederick, Frederick, MD
| | - Tara L. Grinnage-Pulley
- 3Biological Testing Branch, Developmental Therapeutics Program, National Cancer Institute at Frederick, Frederick, MD
| | - Michelle A. Eugeni
- 3Biological Testing Branch, Developmental Therapeutics Program, National Cancer Institute at Frederick, Frederick, MD
| | - Dianne L. Newton
- 2Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - Melinda G. Hollingshead
- 3Biological Testing Branch, Developmental Therapeutics Program, National Cancer Institute at Frederick, Frederick, MD
| | - Paul M. Williams
- 1Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research (NCI), Frederick, MD
| | - James H. Doroshow
- 4Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD
| |
Collapse
|