Stability of gene expression and epigenetic profiles highlights the utility of patient-derived paediatric acute lymphoblastic leukaemia xenografts for investigating molecular mechanisms of drug resistance

Background

Patient-derived tumour xenografts are an attractive model for preclinical testing of anti-cancer drugs. Insights into tumour biology and biomarkers predictive of responses to chemotherapeutic drugs can also be gained from investigating xenograft models. As a first step towards examining the equivalence of epigenetic profiles between xenografts and primary tumours in paediatric leukaemia, we performed genome-scale DNA methylation and gene expression profiling on a panel of 10 paediatric B-cell precursor acute lymphoblastic leukaemia (BCP-ALL) tumours that were stratified by prednisolone response.

Results

We found high correlations in DNA methylation and gene expression profiles between matching primary and xenograft tumour samples with Pearson’s correlation coefficients ranging between 0.85 and 0.98. In order to demonstrate the potential utility of epigenetic analyses in BCP-ALL xenografts, we identified DNA methylation biomarkers that correlated with prednisolone responsiveness of the original tumour samples. Differential methylation of CAPS2, ARHGAP21, ARX and HOXB6 were confirmed by locus specific analysis. We identified 20 genes showing an inverse relationship between DNA methylation and gene expression in association with prednisolone response. Pathway analysis of these genes implicated apoptosis, cell signalling and cell structure networks in prednisolone responsiveness.

Conclusions

The findings of this study confirm the stability of epigenetic and gene expression profiles of paediatric BCP-ALL propagated in mouse xenograft models. Further, our preliminary investigation of prednisolone sensitivity highlights the utility of mouse xenograft models for preclinical development of novel drug regimens with parallel investigation of underlying gene expression and epigenetic responses associated with novel drug responses.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-416) contains supplementary material, which is available to authorized users.     

Are special read alignment strategies necessary and cost-effective when handling sequencing reads from patient-derived tumor xenografts?

Background

Patient-derived tumor xenografts in mice are widely used in cancer research and have become important in developing personalized therapies. When these xenografts are subject to DNA sequencing, the samples could contain various amounts of mouse DNA. It has been unclear how the mouse reads would affect data analyses. We conducted comprehensive simulations to compare three alignment strategies at different mutation rates, read lengths, sequencing error rates, human-mouse mixing ratios and sequenced regions. We also sequenced a nasopharyngeal carcinoma xenograft and a cell line to test how the strategies work on real data.

Results

We found the "filtering" and "combined reference" strategies performed better than aligning reads directly to human reference in terms of alignment and variant calling accuracies. The combined reference strategy was particularly good at reducing false negative variants calls without significantly increasing the false positive rate. In some scenarios the performance gain of these two special handling strategies was too small for special handling to be cost-effective, but it was found crucial when false non-synonymous SNVs should be minimized, especially in exome sequencing.

Conclusions

Our study systematically analyzes the effects of mouse contamination in the sequencing data of human-in-mouse xenografts. Our findings provide information for designing data analysis pipelines for these data.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1172) contains supplementary material, which is available to authorized users.     

Monoclonal antibody uptake in B-cell lymphomas: Experimental studies in nude mouse xenografts

Accumulation of radiolabelled monoclonal antibodies (mAb) in human B-lymphoma xenografts was found to result in two distinct patterns. The basic elements leading to these patterns were elucidated by autoradiographic and immunohistological analysis applied to the nude mouse xenografts BJAB and OCI.LY1. With BJAB, accumulation occurred exclusively in peripheral cell layers of the lymphoma nodule, while central areas were not accessible irrespective of mAb dose. This feature was the consequence of an inefficient transport across intratumoral vessels together with peripheral mAb supply through a subcapsular pseudosinus. With OCI.LY1, intratumoral vessels showed generalized leakiness. Furthermore, interstitial transport was operative to a fair extent, such that in early images multiple sites of mAb extravasation were obvious, which coalesced during the course of prolonged uptake. The pattern of peripheral mAb uptake resulted in a low overall tumour uptake, while multifocal uptake yielded substantial accumulation values.     

A Simple Guide Screw Method for Intracranial Xenograft Studies in Mice

The grafting of human tumor cells into the brain of immunosuppressed mice is an established method for the study of brain cancers including glioblastoma (glioma) and medulloblastoma. The widely used stereotactic approach only allows for the injection of a single animal at a time, is labor intensive and requires highly specialized equipment. The guide screw method, initially developed by Lal et al.,¹ was developed to eliminate cumbersome stereotactic procedures. We now describe a modified guide screw approach that is rapid and exceptionally safe; both of which are critical ethical considerations. Notably, our procedure now incorporates an infusion pump that allows up to 10 animals to be simultaneously injected with tumor cells.To demonstrate the utility of this procedure, we established human U87MG glioma cells as intracranial xenografts in mice, which were then treated with AMG102; a fully human antibody directed to HGF/scatter factor currently undergoing clinical evaluation^2-5. Systemic injection of AMG102 significantly prolonged the survival of all mice with intracranial U87MG xenografts and resulted in a number of complete cures. This study demonstrates that the guide screw method is an inexpensive, highly reproducible approach for establishing intracranial xenografts. Furthermore, it provides a relevant physiological model for validating novel therapeutic strategies for the treatment of brain cancers.     

Immunologic and Osteogeneic Properties of Xenogeneic and Allogeneic Demineralized Bone Transplants

Xenografting is increasingly being developed as a response to the shortage of human tissues. However, antigenic components of bone material eliciting immune responses – particularly of cellular nature – are blamed for the reduction of the osteoinductive properties of bone and bone-derived implants. The aim of our study was to compare the immunologic response and osteogenesis induced by antigen-depleted allogeneic and xenogeneic bone-derived implants to that induced by partially antigen-depleted material heterotopically placed (muscular pouch) in rats. Wistar rats received bone-derived implants of different antigeneic condition, from both xenogeneic (rabbit) and allogeneic (rat) origin. After sacrifice, animals were evaluated for osteogenesis and immune response. New bone formation was observed around all bone-derived implants, whether fully or partially antigen-extracted, and from both xenogeneic and allogeneic origin. No significant humoral response resulted following bone implantation. Cellular response showed a similar pattern in partial and fully antigen-extracted bone of both allogeneic and xenogeneic origin. Xenogeneic antigen-extracted bone from safe donor sources could be a suitable solution to human tissue shortage in a near future.     

Harnessing genetically engineered mouse models for preclinical testing

Recent studies cast doubt on the value of traditionally used models as tools for testing therapies for human cancer. Although the standard practice of xenografting tumors into immunocompromised mice generates reproducible tumors, drug testing in these models has low predictive power when compared to the clinical responses in Phase II trials. The use of tumor-bearing genetically engineered mouse models holds promise for improving preclinical testing. These models recapitulate specific molecular pathways in tumor initiation or progression and provide a biological system in which to study the disease process for assessing efficacy of new therapies and proof-of-principle for testing molecularly targeted drugs. In this review, we discuss the advantages and limitations of genetically engineered mice and plausible solutions for adapting these valuable tumors for wider use in preclinical testing by transplantation into na?ve recipients. We also provide examples of comparative molecular analysis of mammary tumors from MMTV-Polyoma Middle-T antigen and MMTV-wnt1 models as tools for finding clinical correlates, validating existing models and guiding the development of new genetically engineered mouse models for cancer.     

Experimental Boron Neutron Capture Therapy for Melanoma: Systemic Delivery of Boron to Melanotic and Amelanotic Melanoma

The boron-containing melanin precursor analogue p-boronophenylalanine (BPA) has previously been shown to selectively deliver boron to pigmented murine melanomas when administered in a single intragastric dose. If boron neutron capture therapy is to become a clinically useful method of radiation therapy for human malignant melanoma, the boron carrier must be capable of delivering useful amounts of boron to remote tumor sites (metastases) and to poorly pigmented melanomas. We have now determined the ability of BPA to accumulate in several nonpigmented melanoma models including human melanoma xenografts in nude mice. The absolute amount of boron in the nonpigmented melanomas was about 50% of that observed in the pigmented counterparts but was still selectively concentrated in the tumor relative to normal tissues in amounts sufficient for effective neutron capture therapy. Single intragastric doses of BPA resulted in selective localization of boron in the amelanotic Greene melanoma carried in the anterior chamber of the rabbit eye and in a pigmented murine melanoma growing in the lungs. The ratio of the boron concentration in these tumors to the boron concentration in the immediately adjacent normal tissue was in the range of 3:1 to 4:1. These distribution studies support the proposal that boron neutron capture therapy may be useful as a regional therapy for malignant melanoma.     

胰腺癌裸鼠皮下异种移植动物模型建立研究

目的:用人体胰腺癌细胞株,建立小鼠胰腺癌细胞株(pGHAM-1)移植性胰腺癌模型,并研究其生物学特性。方法:将pGHAM-1细胞培养后配成1×107/ml,取0.2mL接种于小鼠皮下。于接种后20、30、40天观察肿瘤的生长、转移及腹水量。接种40天后处死动物,解剖取出移植瘤,用游标卡尺测量肿瘤大小,再进行HE染色的组织病理学检查,免疫组织化学检测血管内皮细胞生长因子(VEGF)及肿瘤转移相关蛋白(nm23-H1)的表达。结果:分别于20、30、40天测量肿瘤体积为84.1±21.9 mm3,413.7±208.4 mm3,2187.3±1882.8 mm3,后者与10 d前比较差异均具有统计学意义(P<0.01)。HE染色结果显示肿瘤组织呈条索状或小梁状排列,肿瘤组织与正常组织交界处有少量淋巴细胞浸润,肿瘤组织中血管生成罕见。免疫组织结果显示VEGF和nm23-H1蛋白在肿瘤组织中均呈阴性表达。结论:异位裸鼠人胰腺癌移植瘤模型易复制,时间短,成功率高,为胰腺癌体内研究提供了理想的动物模型。     

Influence of the CNS Environment on Chromaffin Cell Survival and Catecholamine Secretion Patterns

Abstract: Chromaffin cells implanted into the CNS have been used as a potential source of sustained catecholamine delivery, although their survival and continued catecholamine secretion are controversial. In addition, chromaffin cells exhibit a high degree of neurochemical plasticity in response to environmental factors. The present aims were to determine whether the CNS provides a supportive environment for sustained catecholamine production in transplanted chromaffin cells and to assess whether this novel environment alters patterns of catecholamine secretion. Catecholamine release from bovine chromaffin cells implanted into the rat midbrain was determined in brain slices. In addition, alterations in catecholamine secretion patterns, particularly adrenaline/noradrenaline ratios, were compared in vitro versus in transplants. Results indicated that brain slices containing chromaffin cell implants released high basal and nicotine-stimulated levels of adrenaline and noradrenaline. It is surprising that although adrenaline/noradrenaline ratios steadily declined in culture, this did not occur when cells were transplanted to the CNS in the early postharvesting phases. However, if cells were transplanted following longer periods in culture, adrenaline/noradrenaline ratios remained low. Together, these results suggest that the CNS can provide a supportive environment for chromaffin cell survival and that the pattern of catecholamine secretion can be optimized by prior in vitro manipulation.