Genomic data analysis workflows for tumors from patient-derived xenografts (PDXs): challenges and guidelines

BACKGROUND

Patient-derived xenograft (PDX) models are in vivo models of human cancer that have been used for translational cancer research and therapy selection for individual patients. The Jackson Laboratory (JAX) PDX resource comprises 455 models originating from 34 different primary sites (as of 05/08/2019). The models undergo rigorous quality control and are genomically characterized to identify somatic mutations, copy number alterations, and transcriptional profiles. Bioinformatics workflows for analyzing genomic data obtained from human tumors engrafted in a mouse host (i.e., Patient-Derived Xenografts; PDXs) must address challenges such as discriminating between mouse and human sequence reads and accurately identifying somatic mutations and copy number alterations when paired non-tumor DNA from the patient is not available for comparison.

RESULTS

We report here data analysis workflows and guidelines that address these challenges and achieve reliable identification of somatic mutations, copy number alterations, and transcriptomic profiles of tumors from PDX models that lack genomic data from paired non-tumor tissue for comparison. Our workflows incorporate commonly used software and public databases but are tailored to address the specific challenges of PDX genomics data analysis through parameter tuning and customized data filters and result in improved accuracy for the detection of somatic alterations in PDX models. We also report a gene expression-based classifier that can identify EBV-transformed tumors. We validated our analytical approaches using data simulations and demonstrated the overall concordance of the genomic properties of xenograft tumors with data from primary human tumors in The Cancer Genome Atlas (TCGA).

CONCLUSIONS

The analysis workflows that we have developed to accurately predict somatic profiles of tumors from PDX models that lack normal tissue for comparison enable the identification of the key oncogenic genomic and expression signatures to support model selection and/or biomarker development in therapeutic studies. A reference implementation of our analysis recommendations is available at https://github.com/TheJacksonLaboratory/PDX-Analysis-Workflows .

Abstract 1075: Genomic data analysis workflows for tumors from patient-derived xenografts (PDXs): Challenges and guidelines

Patient-derived xenograft (PDX) models are in vivo models of human cancer that have been used for translational cancer research and therapy selection for individual patients. The Jackson Laboratory (JAX) PDX resource has over 450 models representing more than 20 different types of cancer. The models undergo rigorous quality control and are genomically characterized to identify somatic mutations, copy number alterations, and transcriptional profiles. Bioinformatics workflows for analyzing genomic data obtained from human tumors engrafted in a mouse host (i.e., Patient-Derived Xenografts; PDXs) must address challenges such as discriminating between mouse and human sequence reads and accurately identifying somatic mutations and copy number alterations when paired non-tumor DNA from the patient is not available for comparison.

Here we describe bioinformatics analysis workflows and guidelines (https://github.com/TheJacksonLaboratory/PDX-Analysis-Workflows) that we developed specifically for the analysis of genomic data generated from PDX tumors. Our workflows incorporate commonly used software and public databases but are tailored to address the specific challenges of PDX genomics data analysis through parameter tuning and customized data filters and result in improved accuracy for the detection of somatic alterations in PDX models. We also report a gene expression-based classifier that can identify EBV-transformed tumors. Finally, to demonstrate the effectiveness of our workflows, we show the overall concordance of the genomic and transcriptomic profiles of the PDX models in the JAX PDX resource with relevant tumor types from The Cancer Genome Atlas (TCGA).

Using the reliable results obtained from the PDX genomics data analysis, we are able to compare the patient tumor with different PDX passages, perform classification analysis to verify the annotations of PDX tumors, as well as associate genomic signatures of each PDX tumor with results from dosing studies.

Acknowledgements

The data analysis workflows reported in this publication were partially supported by the National Cancer Institute of the National Institutes of Health under Award Number P30CA034196. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. The public portal for JAX PDX data is supported by R01CA089713.

Citation Format: Xing Yi Woo, Anuj Srivastava, Joel H. Graber, Vinod Yadav, Vishal Kumar Sarsani, Al Simons, Glen Beane, Stephen Grubb, Guruprasad Ananda, Grace Stafford, Jeffrey H. Chuang, Susan D. Airhart, R. Krishna Karuturi, Joshy George, Carol J. Bult. Genomic data analysis workflows for tumors from patient-derived xenografts (PDXs): Challenges and guidelines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1075.

Enhancing the efficacy of glycolytic blockade in cancer cells via RAD51 inhibition

Targeting the early steps of the glycolysis pathway in cancers is a well-established therapeutic strategy; however, the doses required to elicit a therapeutic effect on the cancer can be toxic to the patient. Consequently, numerous preclinical and clinical studies have combined glycolytic blockade with other therapies. However, most of these other therapies do not specifically target cancer cells, and thus adversely affect normal tissue. Here we first show that a diverse number of cancer models – spontaneous, patient-derived xenografted tumor samples, and xenografted human cancer cells – can be efficiently targeted by 2-deoxy-D-Glucose (2DG), a well-known glycolytic inhibitor. Next, we tested the cancer-cell specificity of a therapeutic compound using the MEC1 cell line, a chronic lymphocytic leukemia (CLL) cell line that expresses activation induced cytidine deaminase (AID). We show that MEC1 cells, are susceptible to 4,4ʹ-Diisothiocyano-2,2ʹ-stilbenedisulfonic acid (DIDS), a specific RAD51 inhibitor. We then combine 2DG and DIDS, each at a lower dose and demonstrate that this combination is more efficacious than fludarabine, the current standard- of- care treatment for CLL. This suggests that the therapeutic blockade of glycolysis together with the therapeutic inhibition of RAD51-dependent homologous recombination can be a potentially beneficial combination for targeting AID positive cancer cells with minimal adverse effects on normal tissue.

Implications: Combination therapy targeting glycolysis and specific RAD51 function shows increased efficacy as compared to standard of care treatments in leukemias.

Abstract 3842: Comprehensive genomic analysis demonstrates concordance of PDX models and patient tumor cohorts

The Jackson Laboratory has established more than 400 unique patient-derived xenograft (PDX) cancer models from patient tumors in the immunocompromised NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (aka, NSGTM) mouse strain, spanning across more than 30 tumor types. At low passages, these engrafted models are known to retain similar molecular characteristics and heterogeneity to the originating human tumor. As such, PDX models offer an excellent preclinical platform to test drug responses of novel cancer therapeutics and a powerful resource for conducting preclinical cancer pharmacogenomic studies. To aid the selection of suitable PDX models for preclinical studies and for the research purpose to understand tumor biology and response or resistance to a given treatment, we have characterized the PDX models for their transcriptomic, mutational and copy number profiles using sequencing and array approaches. We have established a compendium of PDX-tailored computational pipelines as the analysis of genomic data from PDX models could be challenging due to a) the contamination of PDX sample with mouse stroma, which complicates downstream bioinformatics analyses as mouse genome is almost 90% homologous to the human genome, and b) the lack of matched normal material to call somatic events. Our pipelines incorporate various filters to identify tumor specific single nucleotide variants, indels, copy number changes and expression profile in the PDX model. For the purpose of validating the accuracy of our analysis pipelines and demonstrating that the JAX PDX models are indeed representative of patient tumors, we compared JAX’s PDX cohort with patient cohorts in TCGA for mutations, copy number aberrations and RNA expression concordance. Using gene sets representative of each tumor type, we found that the overall genomic profile of each PDX tumor type is more correlated to the same tumor type in TCGA than other tumor types. In addition, an integrative analysis across all data types reveals that there are more common affected pathways between the same tumor type in PDX and TCGA. This comprehensive analysis revealed that the PDX and patient cohorts exhibit similar molecular characteristics, hence establishing the suitability of JAX PDX models as in vivo models to study fundamental tumor biology as well as to carry out preclinical studies of cancer drugs, including identification of biomarkers of response or resistance.

Citation Format: Xing Yi Woo, Vinod Yadav, Al Simons, Anuj Srivastava, Guruprasad Ananda, Vishal Kumar Sarsani, Roger Liu, Grace Stafford, Joel Graber, Krishna Karuturi, Susie Airhart, Joshy George, Carol Bult. Comprehensive genomic analysis demonstrates concordance of PDX models and patient tumor cohorts [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3842. doi:10.1158/1538-7445.AM2017-3842

Clinical outcome following primary total hip or knee replacement in nonagenarians

Introduction The Elective Orthopaedic Centre in Epsom has an established patient reported outcome measures programme, into which all patients are enrolled. Postoperative complications, Oxford hip/knee scores (OHS/OKS) and EQ-5D™ (EuroQol, Rotterdam, Netherlands) scores are collected up to the second postoperative year. Our population is ageing and the number of joint replacements being performed on the very elderly is rising. The aim of this study was to investigate the outcome of joint replacements in a nonagenarian population. Methods Our dataset was reviewed retrospectively for a cohort of nonagenarians undergoing either a primary total hip replacement (THR) or total knee replacement (TKR) between April 2008 and October 2011. Postoperative complications, mortality rates and functional outcomes were compared with those of a time matched 70-79-year-old cohort. Results Nonagenarians requiring a THR presented with a lower preoperative OHS (p=0.020) but made a greater improvement in the first postoperative year than the younger cohort (p=0.040). The preoperative OKS was lower for nonagenarians than for the control group (p=0.022). At one and two years after TKR, however, there was no significant difference between the age groups. The nonagenarians had a greater risk of requiring a blood transfusion following both THR (p=0.027; 95% confidence interval [CI]: 1.11-5.75) and TKR (p=0.037; 95% CI: 1.08-16.65) while the latter cohort also required a longer stay than their younger counterparts (p=0.001). Mortality rates were higher in the nonagenarian group but these were in keeping with the life expectancy projections identified by the Office for National Statistics. Conclusions Over a two-year period, the functional outcome and satisfaction rates achieved by nonagenarians following a THR or TKR are comparable with 70-79-year-olds.

Development and validation of the JAX Cancer Treatment Profile™ for detection of clinically actionable mutations in solid tumors

BACKGROUND

The continued development of targeted therapeutics for cancer treatment has required the concomitant development of more expansive methods for the molecular profiling of the patient's tumor. We describe the validation of the JAX Cancer Treatment Profile™ (JAX-CTP™), a next generation sequencing (NGS)-based molecular diagnostic assay that detects actionable mutations in solid tumors to inform the selection of targeted therapeutics for cancer treatment.

METHODS

NGS libraries are generated from DNA extracted from formalin fixed paraffin embedded tumors. Using hybrid capture, the genes of interest are enriched and sequenced on the Illumina HiSeq 2500 or MiSeq sequencers followed by variant detection and functional and clinical annotation for the generation of a clinical report.

RESULTS

The JAX-CTP™ detects actionable variants, in the form of single nucleotide variations and small insertions and deletions (≤50 bp) in 190 genes in specimens with a neoplastic cell content of ≥10%. The JAX-CTP™ is also validated for the detection of clinically actionable gene amplifications.

CONCLUSIONS

There is a lack of consensus in the molecular diagnostics field on the best method for the validation of NGS-based assays in oncology, thus the importance of communicating methods, as contained in this report. The growing number of targeted therapeutics and the complexity of the tumor genome necessitate continued development and refinement of advanced assays for tumor profiling to enable precision cancer treatment.

Sialic acid, periodontal pathogens and Tannerella forsythia: stick around and enjoy the feast!

Periodontal pathogens, like any other human commensal or pathogenic bacterium, must possess both the ability to acquire the necessary growth factors and the means to adhere to surfaces or reside and survive in their environmental niche. Recent evidence has suggested that sialic acid containing host molecules may provide both of these requirements in vivo for several periodontal pathogens but most notably for the red complex organism Tannerella forsythia. Several other periodontal pathogens also possess sialic acid scavenging enzymes - sialidases, which can also expose adhesive epitopes, but might also act as adhesins in their own right. In addition, recent experimental work coupled with the release of several genome sequences has revealed that periodontal bacteria have a range of sialic acid uptake and utilization systems while others may also use sialic acid as a cloaking device on their surface to mimic host and avoid immune recognition. This review will focus on these systems in a range of periodontal bacteria with a focus on Ta. forsythia.

Blockade of parathyroid hormone-related protein prevents joint destruction and granuloma formation in streptococcal cell wall-induced arthritis

OBJECTIVE

To determine whether parathyroid hormone-related protein (PTHrP), an interleukin-1beta-inducible, bone-resorbing peptide that is produced in increasing amounts by the synovium in rheumatoid arthritis (RA), may play a role in the pathophysiology of joint destruction in RA.

METHODS

PTHrP expression and the effect of PTHrP 1-34 neutralizing antibody on disease progression were tested in streptococcal cell wall (SCW)-induced arthritis, an animal model of RA.

RESULTS

As has been reported in RA, while serum levels of PTHrP did not change during SCW-induced arthritis, PTHrP expression dramatically increased in the arthritic synovium. Treatment with PTHrP neutralizing antibody (versus control antibody) did not affect joint swelling in SCW-treated animals. However, PTHrP antibody significantly inhibited SCW-induced joint destruction, as measured by its ability to block increases in serum pyridinoline (a marker of cartilage and bone destruction), erosion of articular cartilage, decreases in femoral bone mineral density, and increases in the numbers of osteoclasts in eroded bone. Unexpectedly, granuloma formation at sites of SCW deposition in the liver and spleen was also inhibited by PTHrP antibody, an effect associated with significant decreases in the tissue influx of PTH/PTHrP receptor-positive neutrophils and in SCW-induced neutrophilia. In vitro, neutrophil chemotaxis was stimulated by PTHrP 1-34.

CONCLUSION

These findings suggest that PTHrP, consistent with its previously described osteolytic effects in metastatic bone disease, can also be an important mediator of joint destruction in inflammatory bone disorders, such as RA. Moreover, this study reveals heretofore unknown effects of PTHrP peptides on neutrophil function that could have important implications in the pathogenesis of inflammatory granulomatous disorders.

Parathyroid hormone-related protein (PTHrP) induction in reactive astrocytes following brain injury: a possible mediator of CNS inflammation

PTHrP, a peptide induced in parenchymal organs during endotoxemia and in the synovium in rheumatoid arthritis, has recently been shown to be expressed in immature or transformed human astrocytes, but not in normal cells. This finding has led us to postulate that PTHrP might also be induced in reactive astrocytes in inflamed brain and, thus, act as a mediator of CNS inflammation. To test this hypothesis, PTHrP expression was examined following cortical stab wound injury in rats, a classical model of reactive gliosis. To determine whether PTHrP was induced in glia by TNF-alpha, a known mediator of inflammation in brain and of PTHrP induction in peripheral tissues, and to determine whether PTHrP, in turn, mediated inflammatory changes in glia, in vitro studies with rat astrocytes and glial-enriched mixed brain cells were also undertaken. Consistent with previous reports of PTHrP expression in normal brain, neurons were the primary site of immunoreactive PTHrP expression in the injured cortex 1 day after stab wound injury. Over the subsequent 3 days, specific immunostaining for PTHrP and for GFAP, a marker of reactive astrocytes, appeared in reactive astrocytes at the wound edge and in perivascular astrocytes, reaching a maximum level of expression at the last time point examined (day 4). TNF-alpha induced PTHrP expression in astrocyte and glial-enriched brain cells in vitro, suggesting that this pro-inflammatory peptide was a possible mediator of PTHrP expression in CNS inflammation. PTHrP(1-34) acted in an additive fashion with TNF-alpha to induced astrocyte expression of IL-6, a cytokine with demonstrated neuroprotective effects. Astrocyte proliferation was inhibited by PTHrP(1-34) and PTHrP(1-141), acting via a PTH/PTHrP receptor cAMP signaling pathway. These studies suggest that PTHrP, analogous to its regulatory functions in other non-CNS models of inflammation, may be an important mediator of the inflammatory response in brain.

Allograft aortic root replacement in 418 patients over a span of 15 years: 1985 to 2000

Allograft aortic root replacement for primary aortic valve or ascending aortic root pathology is the favored method of technical implantation. Results in 418 patients over 15 years demonstrate exceedingly low early mortality (<1%), complete eradication of preoperative endocarditis but poor long-term durability in the young age group of 20 years or less.

Differential expression and mutation of NME genes in autologous cultured human melanoma cells with different metastatic potentials

The putative metastasis suppressor genes, NME1(nm23-1) and NME2(nm23-2), were examined in a model system we developed to approximate the dissemination of melanoma from a primary skin tumor. We utilized two autologous human melanoma cell lines, IV Cl 1 and IV Cl 3, which displayed qualitatively different metastatic phenotypes following subdermal inoculation into nude mice. Highly metastatic IV Cl 1 cells expressed approximately 5 fold lower levels of protein encoded by NME genes than non-metastatic IV Cl 3 cells. Similar differences in NME protein levels were observed in tumors induced by the two cell lines in nude mice. There were no differences in NME mRNA levels between these two cell lines, suggesting that expression of these proteins is regulated at a post-transcriptional level. We found a ser122-pro mutation in the NME2 gene of metastatic IV Cl 1 cells. A similar ser120-gly mutation in NME1 has been found in human neuroblastoma, suggesting that mutation in this region may be a general phenomenon related to tumor progression. These mutations may have functional consequences since they eliminate potential phosphorylation sites and may affect the tertiary structure of mature protein complexes.

A study of the cells in the explanted viable cryopreserved allograft valve

From June 1975 to December 1987, 231 patients underwent aortic valve replacement with a viable cryopreserved allograft aortic valve. Throughout this era, a uniform procurement and preservation was used to maintain leaflet fibroblast viability. The allograft valve was obtained from coroner's autopsies within 24 hours of death, and more recently from organ donors, incubated for 24 hours in low dose antibiotic solution followed immediately by cryopreservation (mean time interval 39 hours after donor death). Viability was ensured by monitoring glucose utilization of the aortic and pulmonary valves and by demonstrating fibroblast growth in tissue cultured from the pulmonary valve. A uniform protocol for valve preparation was used during the entire experience. Nine allograft aortic valves have been obtained by eight reoperations (two were for leaflet degeneration) and one autopsy. The time intervals from implantation to explantation were 2 months, 10 months, 20 months, 22 months, 2.2 years, 5 years, 8.3 years, 9.2 years, and 10.8 years. Histologic examination of the leaflet tissue disclosed a variable degree of cellularity, ranging from a highly cellular matrix (9.2 years) to minimal cellularity (20 months). Within the same valve (10 months), one leaflet was completely acellular with a moderate degree of cellularity in the other two leaflets. The competent valve recovered at autopsy (8.2 years) was essentially acellular. Fibroblasts could consistently be cultured from leaflets in which viable cells were seen histologically. Chromosomal analysis of cultured cells from a valve leaflet (9.2 years) that was implanted with a donor and recipient sex mismatch demonstrated persistence of donor cells.(ABSTRACT TRUNCATED AT 250 WORDS)

The viable cryopreserved allograft aortic valve

One hundred and twenty-four patients underwent aortic valve replacement with a nonviable 4 degrees C refrigerated aortic allograft valve. One hundred and eighty-four patients underwent aortic valve replacement with a viable cryopreserved aortic allograft valve in a later era. The longest follow-up was 16 years for the group with the nonviable valve and 11 years for the group with the viable valves. Within this time frame, reoperation was required in 23 patients with nonviable valves for leaflet perforation or rupture whereas no patients in the group with viable valves developed this complication (p less than 0.0001). The prevalence of endocarditis and thromboembolism was very low in both groups. Viability of leaflet tissue is associated with an important improvement in durability over nonviable allograft valves. Consequently, long-term follow-up results of allograft valves might be best expressed in terms of viability. The current evidence suggests that the viable cells are donor in origin. The viable cryopreserved aortic allograft valve offers significant advantages over current nonviable allograft valves, mechanical valves, and bioprostheses.

Traumatic rupture of the thoracic aorta

Eleven patients with aortic rupture secondary to non-penetrating thoracic trauma, recent in four patients and of longer standing in seven, have been operated upon. Every patient with an acute injury had a widened mediastinum in the chest skiagram. The diagnosis of traumatic rupture was made by aortography in each case. The operative procedure involved cardiopulmonary bypass, left heart bypass or aorta to aorta bypass shunt. There was one postoperative death. It is recommended that in the acute stage a rupture of the aorta secondary to trauma should be repaired as soon as possible, while ruptures of long standing should be electively repaired.

Q fever endocarditis in Queensland

Thirteen patients with proven Q fever endocarditis and three additional patients with probable endocarditis are reviewed. The most helpful diagnostic test is the demonstration of a high complement fixing antibody titre to Phase 1 antigen of Coxiella burneti. The macroscopic pathology of the aortic valve is described and includes aneurysmal pockets in the aortic wall and valve annulus which are demonstrable angiographically. Evidence is presented that the infection may be controlled by prolonged tetracycline therapy and that this is accompanied by a falling antibody titre to Phase 1 antigen. Valve replacement is undertaken only for symptomatic and hemodynamic indications. The combined tetracycline therapy and valve replacement have produced a fall in titres with eradication of infection and palliation of the cardiac disability in all patients followed for long periods.