Genomic Methylation Profiles Research Articles

Diagnosis of acute lymphoblastic leukaemia: an overview of the current genomic classification, diagnostic approaches, and future directions.

B-acute lymphoblastic leukaemia (B-ALL) is a haematological disease resulting from haematopoietic system dysfunction, leading to the unchecked growth of immature B lymphoblasts. The disease's complexity is underscored by the spectrum of genetic aberrations that underlie B-ALL entities, necessitating advanced genetic analyses for precise classification and risk determination. Prior to the adoption of next-generation sequencing into standard diagnostic practices, up to 30% of B-ALL cases were not assigned to specific entities due to the limitations of traditional diagnostic methods. The advent of comprehensive genomic analysis, especially whole-genome transcriptome sequencing, has significantly enhanced our understanding of B-ALL's molecular heterogeneity, paving the way for the exploration of novel, tailored treatment strategies. Furthermore, recent technological innovations, such as optical genome mapping, methylation profiling, and single-cell sequencing, have propelled forward the fields of cancer research and B-ALL management. These innovations introduce novel diagnostic approaches and prognostic markers, facilitating a deeper, more nuanced understanding of individual patient disease profiles. This review focuses on the latest diagnostic standards and assays for B-ALL, the importance of new technologies and biomarkers in enhancing diagnostic accuracy, and the expected role of innovative advancements in the future diagnosis and treatment of B-ALL.

Abstract LB206: The progression of chromosomal instability and aberrant DNA methylation during colorectal cancer development

Abstract Chromosomal instability (CIN) and aberrant DNA methylation play a pivotal role in the pathogenesis of colorectal cancer (CRC). Mapping both of these cancer hallmarks during the progression of the disease can help identify potential targets for pharmacological intervention and improve the management of CRC metastasis. In a set of 27 patients diagnosed with either high-grade colorectal adenoma or advanced metastatic CRC disease, high-throughput DNA methylation and/or DNA somatic copy number alterations (SCNAs) analyses were performed. Global genome methylation profiles and the most frequent hot-spot regions harboring SCNAs, identified in the patients' DNA, were verified in a validation set of eight CRC patients through whole-exome sequencing, genome-wide DNA methylation measurement, and gene expression profiling.The study is currently ongoing; however, a panel of 29 cancer-relevant genes, amplified in more than 50% of investigated adenoma tissues (such as PTK6, SRC, MALAT1, BRCA2), was identified. Chromosomal loci amplified in primary tumors were highly concordant with those in liver metastases. An increase in CIN was detected in all metastases, representing mostly gains of Chr7q, 8q, 13q, 20q, and the small arm of ChrX, while the lost chromosomal loci included Chr8p, 17p, and the entire Chr18. A gain unique to metastases was located on Chr6 (p25.1-p22.3), encoding the oncogene DEK. All metastases exhibited an increase in hypomethylated and a decrease in hypermethylated CpGs. The gene enrichment analysis of the differently methylated gene promoters showed the olfactory receptors pathway as the most frequently represented (FDR-adjusted P value=1.06E-8), with all the identified promoters (n=120) less methylated in metastases. Taken together, several genomic hot-spot regions with SCNAs, possibly important during the development of adenoma and also during the metastatic process, were identified. Furthermore, a decrease in methylation within promoters of odorant receptors was the most prominent epigenetic alteration occurring in our set of metastases. The study was funded by the Ministry of Health of the Czech Republic (NU22J-03-00028) and GACR 21-27902S. Citation Format: Katerina Saskova, Mattias Landfors, Josef Horak, Katerina Honkova, Kristyna Tomasova, Jana Drabova, Fernanda Schäfer Hackenhaar, Jitka Pavlikova, Ludmila Vodickova, Torbjörn Nilsson, Sanja Farkas, Veronika Vymetalkova, Pavel Vodicka, Sofie Degerman, Michal Kroupa. The progression of chromosomal instability and aberrant DNA methylation during colorectal cancer development [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB206.

Abstract 1738: Precise detection of benign and malignant renal tumor via epigenetic characteristics of urinary cell-free DNA

Abstract Early detection of clear cell renal cell carcinoma (ccRCC) and accurate differentiation between malignant and benign lesions pose clinical challenges. Profiling the epigenetic pattern of patients through liquid biopsy offers a promising strategy for non-invasive cancer identification. This study utilizes the methylation characteristics of urinary cell-free DNA to enhance the precise diagnosis of ccRCC. In this study, 32 patients with malignant RCC, 20 patients with benign kidney lesions, and 28 age- and sex-matched healthy donors were enrolled. Urine samples were collected and applied by PredicineEPIC assay to analyze the whole genome methylation profiles. We assessed the methylation differences on cancer-specific altered regions and constructed a machine learning model for malignant and benign classification. Beta values were calculated for differentially methylated regions identified through literature mining and our current work. These features carry methylation signals that are recognized by gradient boosting machine and used for classification training. The leave-one-out cross-validation method compensated for the shotage of sample size. The sensitivity and specificity of the optimal model in the training set are both greater than 0.97, and it can achieve an accuracy of 0.95 on the validation set. This performance surpasses traditional diagnostic methods such as contrast-enhanced CT and MRI. This study demonstrated the technical feasibility of leveraging epigenetics profiles to discriminate malignant from benign lesions, suggesting a promising liquid biopsy-based approach for the precise detection of renal cell carcinoma. Citation Format: Wen Kong, Hang Dong, Haoran Tang, Pan Du, Shidong Jia, Jin Zhang. Precise detection of benign and malignant renal tumor via epigenetic characteristics of urinary cell-free DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1738.

The streptococcal phase-variable type I restriction modification system SsuCC20p dictates the methylome of Streptococcus suis impacting the transcriptome and virulence in a zebrafish larvae infection model.

Phase variation allows a single strain to produce phenotypic diverse subpopulations. Phase-variable restriction modification (RM) systems are systems that allow for such phase variation via epigenetic regulation of gene expression levels. The phase-variable RM system SsuCC20p was found in multiple streptococcal species and was acquired by an emerging zoonotic lineage of Streptococcus suis. We show that the phase variability of SsuCC20p is dependent on a recombinase encoded within the SsuCC20p locus. We characterized the genome methylation profiles of the different phases of SsuCC20p and demonstrated the consequential impact on the transcriptome and virulence in a zebrafish infection model. Acquiring mobile genetic elements containing epigenetic regulatory systems, like phase-variable RM systems, enables bacterial pathogens to produce diverse phenotypic subpopulations that are better adapted to specific (host) environments encountered during infection.

Genomic analysis of spermatocytic tumors demonstrates recurrent molecular alterations in cases with malignant clinical behavior.

Spermatocytic tumor (ST) is a rare type of germ cell tumor that occurs exclusively in the postpubertal testis and typically affects elderly men. Most STs are benign, but rare cases exhibit aggressive clinical behavior, often in association with transition to sarcomatoid histology. Limited molecular analyses have been performed on STs; therefore, their genomic and epigenomic features remain incompletely described. Twenty-seven samples from 25 individual patients were analyzed with a combination of DNA sequencing panels, genomic methylation profiling, SNP array, isochromosome (12p) [i(12p)] FISH, and immunohistochemistry. The series included five metastasizing tumors (three with sarcomatoid transformation, one anaplastic, and one conventional) and 20 non-metastasizing tumors (14 anaplastic and six conventional). Anaplastic tumors comprised a monomorphic population of intermediate-sized neoplastic cells, as previously described. Multiomic analyses demonstrated that there were two genomic subgroups of STs: one with diploid genomes and hotspot RAS/RAF variants and the other with global ploidy shift and absence of recurrent mutations. Relative gain of chromosome 9 was a consistent finding in both subgroups. A comparison of metastasizing and non-metastasizing cases demonstrated that aggressive behavior was associated with the acquisition of pathogenic TP53 mutations and/or relative gains of 12p/i(12p). In cases with sarcomatoid transformation, TP53 mutations seem to underlie the transition to sarcomatoid histology. Genomic methylation analysis demonstrated that aggressive cases with gains of 12p cluster closer to pure seminomas than to STs without gains of 12p. In conclusion, STs include two genomic subgroups, characterized by global ploidy shifts without recurrent mutations and diploid genomes with RAS/RAF hotspot mutations, respectively. Biologic progression was associated with relative gains of 12p and TP53 mutations. The findings in STs with relative gains of 12p suggest that they may exhibit biologic characteristics akin to those seen in germ cell neoplasia in situ-related germ cell tumors rather than non-germ cell neoplasia in situ-derived STs. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Hippocampal and peripheral blood DNA methylation signatures correlate at the gene and pathway level in a mouse model of autism.

Autism spectrum disorders (ASD) are polygenic multifactorial disorders influenced by environmental factors. ASD-related differential DNA methylation has been found in human peripheral tissues, such as placenta, paternal sperm, buccal epithelium, and blood. However, these data lack direct comparison of DNA methylation levels with brain tissue from the same individual to determine the extent that peripheral tissues are surrogates for behavior-related disorders. Here, whole genome methylation profiling at all the possible sites throughout the mouse genome (>25 million) from both brain and blood tissues revealed novel insights into the systemic contributions of DNA methylation to ASD. Sixty-six differentially methylated regions (DMRs) share the same genomic coordinates in these two tissues, many of which are linked to risk genes for neurodevelopmental disorders and intellectual disabilities (e.g. Prkch, Ptn, Hcfc1, Mid1, and Nfia). Gene ontological pathways revealed a significant number of common terms between brain and blood (N = 65 terms), and nearly half (30/65) were associated with brain/neuronal development. Furthermore, seven DMR-associated genes among these terms contain methyl-sensitive transcription factor sequence motifs within the DMRs of both tissues; four of them (Cux2, Kcnip2, Fgf13, and Mrtfa) contain the same methyl-sensitive transcription factor binding sequence motifs (HES1/2/5, TBX2 and TFAP2C), suggesting DNA methylation influences the binding of common transcription factors required for gene expression. Together, these findings suggest that peripheral blood is a good surrogate tissue for brain and support that DNA methylation contributes to altered gene regulation in the pathogenesis of ASD.

The Association between Deoxyribonucleic Acid Hypermethylation in Intron VII and Human Leukocyte Antigen-C∗07 Expression in Patients with Endometriosis.

Endometriosis, which is a common disease affecting approximately 10% of women of reproductive age, usually causes dysmenorrhea and infertility, thus seriously harming the patients' physical and mental health. However, there is a mean delay of 6.7 years between the onset of the symptoms and the surgical diagnosis of endometriosis. There is an increasing amount of evidence that suggests that epigenetic aberrations, including deoxyribonucleic acid (DNA) methylation, play a definite role in the pathogenesis of endometriosis. This study aimed to explore the noninvasive or minimally invasive biomarkers of this disease. Six patients with surgically confirmed ovarian endometriosis and six patients who received IUD implantation for contraception without endometriosis were recruited in the East Hospital of Tongji University in 2018. The genome methylation profiling of the eutopic and ectopic endometrium of ovarian endometriosis patients and normal endometrial specimens from healthy women was determined using a methylation microarray test. The test screened methylation-differentiated 5'-C-phosphate-G-3' (CpG) sites and then located the target genes affected by these sites following sequence alignment. Then, an additional 22 patients and 26 healthy controls were enrolled to further verify the difference in the selected genes between endometriosis patients and healthy women. The differential DNA methylation of the selected genes was validated via direct bisulfite sequencing and analysis of their messenger ribonucleic acid (mRNA) levels using quantitative reverse transcription polymerase chain reaction (qRT-PCR). Fifteen differentially methylated CpG sites were found among the patients and healthy women, and five CpG sites were mapped to the introns of the human leukocyte antigen-C (HLA-C) gene; these were highly polymorphic between different HLA-C alleles and were HLA-C∗07 specific. The results indicated that the HLA-C∗07 carrier patients exhibited significantly higher DNA methylation levels at the intron VII of HLA-C compared to the HLA-C∗07 carrier healthy controls. High HLA-C∗07 mRNA levels were also observed using qRT-PCR with HLA-C∗07-specific primers, which indicated that the hypermethylation of CpG in intron VII might suppress a silencer that regulates HLA-C∗07 expressions. Deoxyribonucleic acid hypermethylation in the intron VII of the HLA-C∗07 gene appears to regulate the expression of HLA-C∗07. The aberrant DNA methylation in this region was positively correlated with the occurrence of endometriosis.

Docetaxel targets aggressive methylation profiles and serves as a radiosensitizer in high-risk meningiomas.

Meningioma is the most common primary intracranial tumor in adults. A subset of these tumors recur and invade the brain, even after surgery and radiation, resulting in significant disability. There is currently no standard-of-care chemotherapy for meningiomas. As genomic DNA methylation profiling can prognostically stratify these lesions, we sought to determine whether any existing chemotherapies might be effective against meningiomas with high-risk methylation profiles. A previously published dataset of meningioma methylation profiles was used to screen for clinically significant CpG methylation events and associated cellular pathways. Based on these results, patient-derived meningioma cell lines were used to test candidate drugs in vitro and in vivo, including efficacy in conjunction with radiotherapy. We identified 981 genes for which methylation of mapped CpG sites was related to progression-free survival in meningiomas. Associated molecular pathways were cross-referenced with FDA-approved cancer drugs, which nominated Docetaxel as a promising candidate for further preclinical analyses. Docetaxel arrested growth in 17 meningioma cell sources, representing all tumor grades, with a clinically favorable IC50 values ranging from 0.3 nM to 10.7 mM. The inhibitory effects of this medication scaled with tumor doubling time, with maximal benefit in fast-growing lesions. The combination of Docetaxel and radiation therapy increased markers of apoptosis and double-stranded DNA breaks, and extended the survival of mice engrafted with meningioma cells relative to either modality alone. Global patterns of DNA methylation may be informative for the selection of chemotherapies against meningiomas, and existing drugs may enhance radiation sensitivity in high-risk cases.

The landscape of common genetic drivers and DNA methylation in low-grade (epilepsy-associated) neuroepithelial tumors: A review.

Low-grade neuroepithelial tumors (LNETs) represent an important group of central nervous system neoplasms, some of which may be associated to epilepsy. The concept of long-term epilepsy-associated tumors (LEATs) includes a heterogenous group of low-grade, cortically based tumors, associated to drug-resistant epilepsy, often requiring surgical treatment. LEATs entities can sometimes be poorly discriminated by histological features, precluding a confident classification in the absence of additional diagnostic tools. This study aimed to provide an updated review on the genomic findings and DNA methylation profiling advances in LNETs, including histological entities of LEATs. A comprehensive search strategy was conducted on PubMed, Embase, and Web of Science Core Collection. High-quality peer-reviewed original manuscripts and review articles with full-text in English, published between 2003 and 2022, were included. Results were screened based on titles and abstracts to determine suitability for inclusion, and when addressed the topic of the review was screened by full-text reading. Data extraction was performed through a qualitative content analysis approach. Most LNETs appear to be driven mainly by a single genomic abnormality and respective affected signaling pathway, including BRAF p.V600E mutations in ganglioglioma, FGFR1 abnormalities in dysembryoplastic neuroepithelial tumor, MYB alterations in angiocentric glioma, BRAF fusions in pilocytic astrocytoma, PRKCA fusions in papillary glioneuronal tumor, between others. However, these molecular alterations are not exclusive, with some overlap amongst different tumor histologies. Also, clustering analysis of DNA methylation profiles allowed the identification of biologically similar molecular groups that sometimes transcend conventional histopathological classification. The exciting developments on the molecular basis of these tumors reinforce the importance of an integrative histopathological and (epi)genetic classification, which can be translated into precision medicine approaches.

Abstract 6084: Recurrent genomic patterns of MPNST evolution correlate with clinical outcome

Abstract Neurofibromatosis type 1 (NF1) is the most common tumor predisposition syndrome, and is associated with an aggressive soft-tissue sarcoma, malignant peripheral nerve sheath tumours (MPNSTs), the greatest cause of mortality in people with NF1. The only potentially curative therapy involves en bloc resection with negative margins, which is not always appropriate. Even therapy with curative intent is associated with poor overall survival for both sporadic and NF1-related MPNSTs. The development of novel therapies has been largely hindered by a poor understanding of the molecular events underpinning MPNST pathogenesis. We report a comprehensive multi-omic study of MPNST evolution based on whole genome sequencing, transcriptomic and methylation profiling data on 95 tumors (64 NF1-related; 31 sporadic). In all cases, the early events in MPNST evolution involve biallelic inactivation of NF1 followed by inactivation of CDKN2A, as well as mutations in TP53 or PRC2 complex genes in a subset of cases. Analysis of the genomic architecture revealed distinct pathways of tumor evolution that can be identified through H3K27 trimethylation (H3K27me3) status. Integration of these data allows us to propose several mechanistic tumor evolution models. Tumors with H3K27me3 loss evolve through extensive copy number aberrations (CNAs) including haploidization followed by whole genome doubling and chromosome 8 amplifications, whereas tumors with H3K27me3 retention evolve through extensive chromosome instability and chromothripsis. Taken together, these genome-wide CNA profiles act as a surrogate for the loss of H3K27me3 status and correlate with prognosis, suggesting that CNA profiling of cell-free DNA could be incorporated in clinical decision-making. Citation Format: Isidro Cortes Ciriano, Chris D. Steele, Katherine Piculell, Alyaa Al-Ibraheemi, Vanessa Eulo, Marilyn M. Bui, Aikaterini Chatzipli, Brendan C. Dickson, Dana C. Borcherding, Alon Galor, Jesse Hart, Andrew Feber, Kevin B. Jones, Justin T. Jordan, Raymond H. Kim, Daniel Lindsay, Colin Miller, Yoshihiro Nishida, Jonathan Serrano, Nicole J. Ullrich, David Viskochil, Xia Wang, Matija Snuderl, Paula Proszek, Peter J. Park, Adrienne M. Flanagan, Angela C. Hirbe, Nischalan Pillay, David T. Miller, The Genomics of MPNST (GeM) Consortium. Recurrent genomic patterns of MPNST evolution correlate with clinical outcome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6084.

Abstract 5686: Integrative genomic analysis reveals hypermethylation triggered GPER1 loss is associated with genomic instability of endometrial cancer

Abstract Objective: Endometrial cancer is a common gynecologic malignancy, yet carcinogenesis remains elusive. Evidence showed that aberrant genomic methylation profiling contributes to the development of endometrial cancer. G protein-coupled estrogen receptor (GPER1), a membrane-associated estrogen receptor, was reported to play a multifaceted role in tumors. Its function in endometrial cancer is little known. Here, we conducted an integrated analysis of RNA expression, DNA methylation, and somatic mutations data from TCGA to investigate GPER1 upstream regulator and its influence in endometrial cancer biological process. Methods: RNA-seq, DNA methylation, and clinical information of endometrial cancer (n=554) and normal control (n=33) were obtained from TCGA database. RNA-seq profiles of GPER1 low and high groups were analyzed by R 4.1.0 software. KEGG and GSEA based on GPER1 expression were conducted. Correlation analysis of GPER1 and genomic instability were displayed. G1, the GPER1 agonist, was added to observe cell viability and metastatic ability in vitro. DNA methylation data was analyzed. Results: GPER1 expression was decreased in endometrial cancer compared with normal tissues. GPER1 was associated with poor overall survival (HR=0.52, p=0.003) (Figure 1). Low expression group showed a more frequent mutation landscape, higher tumor mutation burden (TMB), and micro-satellite instability (MSI) (Figure 2). Several hypermethylation loci on GPER1 CpG island were revealed. Methylation status is negatively correlative to RNA expression of GPER1 (Figure 3). P-value <0.05 and log2FC >1.5, 473 up-regulated and 114 down-regulated genes were screened. Up-regulated DEGs enriched in the Estrogen signaling pathway, Endometrial cancer, wnt signaling pathway, etc. Down-regulated DEGs enriched in Cell cycle, p53 signaling pathway, etc. (Figure 4). GSEA analysis showed that GPER1 low expression group was enriched in several biological processes including cell cycle checkpoint, Recombinational repair, etc. G1 inhibited endometrial cancer cell growth in a dose-dependent manner, and reduced cell metastatic ability (Figure 5). Conclusions: GPER1 exhibited decreased expression in endometrial cancer and DNA hypermethylation in promoter CpG island locus. The low GPER1 expression group showed prominent genomic instability. GPER1 agonists inhibit endometrial cancer cell growth and metastasis, which may serve as a therapeutic target. Citation Format: Xuan Feng, Ting Huang, Boqiang Shen, Juan Hao, Jiaqi Wang, Yangyang Dong, Jingyi Zhou, Jianliu Wang. Integrative genomic analysis reveals hypermethylation triggered GPER1 loss is associated with genomic instability of endometrial cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5686.

MEDB-57.GNAS inactivation as a driver for sonic hedgehog-activated medulloblastoma

INTRODUCTION: Sonic hedgehog (SHH)-activated medulloblastoma is one of the four consensus molecular subgroups of medulloblastoma and is typically associated with PTCH1, SUFU, and/or SMO mutations. GNAS inactivating mutations are a less commonly recognized tumorigenic driver for SHH pathway activation. CASE PRESENTATION: We report the case of an 11-month-old male who presented with a large posterior fossa mass, cerebellar tonsillar herniation, and obstructive hydrocephalus. Following a successful gross total resection, pathology was consistent with desmoplastic/nodular medulloblastoma. Tumor molecular profiling using a DNA-based, next-generation sequencing platform detected a pathogenic frameshift mutation in the GNAS gene (p.D189Mfs*14, NM_000516.4:c.565_568del) at a variant allele frequency of 81%, suggestive of biallelic GNAS inactivation. The same mutation was detected from a buccal swab sample, confirming germline GNAS inactivation. Whole genome methylation profiling was consistent with medulloblastoma subclass SHH B (infant). Concurrent with this brain tumor evaluation, a skin biopsy was performed of scattered subcutaneous, plate-like nodules distributed over the patient’s back and extremities. This revealed metaplastic-appearing cancellous bone within the dermis and subcutaneous tissue consistent with plate-like osteoma cutis. He was treated with high-dose chemotherapy followed by autologous stem cell rescue and remains disease-free 15 months from diagnosis. DISCUSSION: There have been scattered case reports describing germline loss-of-function GNAS mutations acting as tumorigenic drivers of SHH medulloblastoma. However, GNAS alterations are not covered by most standard diagnostic molecular sequencing panels for medulloblastoma. Other phenotypic manifestations of germline inactivating GNAS mutations include pseudohypoparathyroidism, pseudopseudohypoparathyroidism, progressive osseous heteroplasia, and osteoma cutis. CONCLUSION: Knowledge of the possible association between germline GNAS inactivating mutations and the development of childhood SHH-activated medulloblastoma is essential for prompt diagnosis and treatment initiation. As such, consideration should be given for inclusion of GNAS alterations in diagnostic medulloblastoma sequencing panels, especially in the setting of osteoma cutis or other endocrinopathies.

Validation of Whole Genome Methylation Profiling Classifier for Central Nervous System Tumors

The 2021 WHO Classification of Tumors of the Central Nervous System includes several tumor types and subtypes for which the diagnosis is at least partially reliant on utilization of whole genome methylation profiling. The current approach to array DNA methylation profiling utilizes a reference library of tumor DNA methylation data, and a machine learning-based tumor classifier. This approach was pioneered and popularized by the German Cancer Research Network (DKFZ) and University Hospital Heidelberg. This research group has kindly made their classifier for central nervous system tumors freely available as a research tool via a web-based portal. However, their classifier is not maintained in a clinical testing environment. Therefore, the Northwestern Medicine (NM) classifier was developed and validated. The NM classifier was validated using the same training and validation data sets as the DKFZ group. Using the DKFZ validation data set, the NM classifier's performance showed high concordance (92%) and comparable accuracy (specificity 94.0% versus 84.9% for DKFZ, sensitivity 88.6% versus 94.7% for DKFZ). Receiver-operator characteristic curves showed areas under the curve of 0.964 versus 0.966 for NM and DKFZ classifiers, respectively. In addition, in-house validation was performed and performance was compared using both classifiers. The NM classifier performed comparably well and is currently offered for clinical testing.

A molecular approach integrating genomic and DNA methylation profiling for tissue of origin identification in lung-specific cancer of unknown primary

BackgroundDetermining the tissue of origin (TOO) is essential for managing cancer of unknown primary (CUP). In this study, we evaluated the concordance between genome profiling and DNA methylation analysis in determining TOO for lung-specific CUP and assessed their performance by comparing the clinical responses and survival outcomes of patients predicted with multiple primary or with metastatic cancer.MethodsWe started by retrospectively screening for CUP patients who presented with both intra- and extrathoracic tumors. Tumor samples from included patients were analyzed with targeted sequencing with a 520-gene panel and targeted bisulfite sequencing. TOO inferences were made in parallel via an algorithm using genome profiles and time interval between tumors and via machine learning-based classification of DNA methylation profiles.ResultsFour hundred patients were screened retrospectively. Excluding patients definitively diagnosed with conventional diagnostic work-up or without available samples, 16 CUP patients were included. Both molecular approaches alone enabled inference of clonality for all analyzed patients. Genome profile enabled TOO inference for 43.8% (7/16) patients, and the percentage rose to 68.8% (11/16) after considering inter-tumor time lag. On the other hand, DNA methylation analysis was conclusive for TOO prediction for 100% (14/14) patients with available samples. The two approaches gave 100% (9/9) concordant inferences regarding clonality and TOO identity. Moreover, patients predicted with metastatic disease showed significantly shorter overall survival than those with multiple primary tumors.ConclusionsGenome and DNA methylation profiling have shown promise as individual analysis for TOO identification. This study demonstrated the feasibility of incorporating the two methods and proposes an integrative scheme to facilitate diagnosing and treating lung-specific CUPs.

Methylation Profiling Improves the Care of Pediatric Brain Tumor Patients

Abstract We describe a pediatric patient with an intra-axial tumor; histopathologic examination of the resected specimen was unable to establish a precise diagnosis. While the initial targeted next-generation sequencing (NGS) panel was also nondiagnostic, genomic DNA methylation profiling indicated that the tumor was an astroblastoma, MN1-altered. A more comprehensive NGS panel was then run, which confirmed an MN1-BEND2 fusion. This case displays the limitations and pitfalls of a histological and immunohistochemical-based diagnosis in a case of an infrequently encountered pediatric brain tumor. Furthermore, it highlights the growing need for performing DNA methylation, paired with a comprehensive NGS panel, to ensure an accurate diagnosis in modern surgical neuropathology.

Whole Genome DNA Methylation Profiling of D2 Medium Spiny Neurons in Mouse Nucleus Accumbens Using Two Independent Library Preparation Methods.

DNA methylation plays essential roles in various cellular processes. Next-generation sequencing has enabled us to study the functional implication of DNA methylation across the whole genome. However, this approach usually requires a substantial amount of genomic DNA, which limits its application to defined cell types within a discrete brain region. Here, we applied two separate protocols, Accel-NGS Methyl-Seq (AM-seq) and Enzymatic Methyl-seq (EM-seq), to profile the methylome of D2 dopamine receptor-expressing medium spiny neurons (D2-MSNs) in mouse nucleus accumbens (NAc). Using 40 ng DNA extracted from FACS-isolated D2-MSNs, we found that both methods yielded comparably high-quality methylome data. Additionally, we identified numerous unmethylated regions (UMRs) as cell type-specific regulatory regions. By comparing the NAc D2-MSN methylome with the published methylomes of mouse prefrontal cortex excitatory neurons and neural progenitor cells (NPCs), we identified numerous differentially methylated CpG and non-CpG regions. Our study not only presents a comparison of these two low-input DNA whole genome methylation profiling protocols, but also provides a resource of DNA methylome of mouse accumbal D2-MSNs, a neuron type that has critical roles in addiction and other neuropsychiatric disorders.

Assessment of the Molecular Heterogeneity of E-Cadherin Expression in Invasive Lobular Breast Cancer.

Simple SummaryInvasive lobular breast cancers (ILCs) are histologically classified by their discohesive growth pattern, due to loss of the cell adhesion glycoprotein E-cadherin (CDH1), which arises via mutation in CDH1 in around half of these tumours. A subset of these tumours, however, show mixed levels of E-cadherin expression. Here, we sought to address whether the distinct parts of individual tumours showing heterogeneous E-cadherin expression harbour distinct driver alterations. Using whole genome sequencing and methylation profiling of nine such cases, we identified that these tumours are clonally related, suggesting that they are part of the spectrum of ILC tumours. CDH1 mutant tumours showed a higher mutational burden indicative of APOBEC-mediated mutagenesis. In some cases, known clinically actionable driver mutations, such as PIK3CA, were exclusive to one component. Together, these results highlight the heterogeneity underpinning this special histological breast cancer.Mutations and loss of E-cadherin protein expression define the vast majority of invasive lobular carcinomas. In a subset of these cases, the heterogeneous expression of E-cadherin is observed either as wild-type (strong membranous) expression or aberrant expression (cytoplasmic expression). However, it is unclear as to whether the two components would be driven by distinct genetic or epigenetic alterations. Here, we used whole genome DNA sequencing and methylation array profiling of two separately dissected components of nine invasive lobular carcinomas with heterogeneous E-cadherin expression. E-cadherin negative and aberrant/positive components of E-cadherin heterogeneous tumours showed a similar mutational, copy number and promoter methylation repertoire, suggesting they arise from a common ancestor, as opposed to the collision of two independent tumours. We found that the majority of E-cadherin heterogeneous tumours harboured CDH1 mutations in both the E-cadherin negative and aberrant/positive components together with somatic mutations in additional driver genes known to be enriched in both pure invasive carcinomas of no special type and invasive lobular breast cancers, whereas these were less commonly observed in CDH1 wild-type tumours. CDH1 mutant tumours also exhibited a higher mutation burden as well as increased presence of APOBEC-dependent mutational signatures 2 and 13 compared to CDH1 wild-type tumours. Together, our results suggest that regardless of E-cadherin protein expression, tumours showing heterogeneous expression of E-cadherin should be considered as part of the spectrum of invasive lobular breast cancers.

Abstract CC07-01: Whole exome and whole genome methylation sequencing of low-input cfDNA to implement precision medicine in metastatic castration resistant prostate cancer

Abstract Purpose Liquid biopsy has become increasingly important in cancer diagnosis, personalized medicine, and disease progression monitoring. Conventional liquid biopsy relies on targeted cancer gene panels which often contain fewer than 500 genes. Despite the revolutionary impact of liquid biopsy on cancer research and patient care, targeted gene panels may miss key novel mutations involved in cancer development and drug response, and other novel genomic alternations underlining cancer development, such as whole genome structural or epigenetic changes. Additionally, current commonly used methodologies require relatively large amounts of cell free DNA (cfDNA) input material, thus limiting its application when only small amounts of cfDNA input is available. Experimental Design cfDNA was isolated from whole blood collected from commercially available prostate cancer patients or age-matched healthy donors and evaluated using Predicine’s platform for whole exome sequencing, plasma WES, and compared to the targeted 500 gene PredicineATLAS panel (cfDNA input 10 or 30 ng). Additionally, low-input cfDNA (cfDNA input 10 or 20 ng) was also evaluated for whole genome methylation sequencing using PredicineECM and compared with standard whole genome bisulfite sequencing (WGBS). Results Plasma WES profiling of 30 or 10 ng cfDNA detected variants with mutation allele frequency (MAF) of 1% and above in the entire exome region, which enabled more accurate genome wide copy number variation prediction. All mutations detected using the PredicineATLAS panel that were ≥1% allele frequency were also detected by plasma WES, although low input required greater depth (10 ng, 3,500x) compared with high input (30 ng, 2500x depth). Furthermore, plasma WES identified 1.5 to 15.3x additional mutations compared with the PredicineATLAS panel. PredicineECM methylation analysis was superior to WGBS in reducing DNA damage and GC bias, resulting in increased NGS read mapping rate and quality score. Profiling of 2.5, 5 and 10 ng cfDNA using PredicineECM showed higher mapping rate and quality compared with WGBS profiling of 10 ng cfDNA. Additionally, clustering analysis of CpG methylation using PredicineECM separated tumor samples from normal samples and may serve as additional markers for minimal residue disease (MRD) tracing or early cancer detection. Conclusion In conclusion, we have successfully developed a multi-omics analysis platform for low-input cfDNA that integrates whole exome mutation and whole genome methylation profiling to obtain a comprehensive picture of cancer genomics to enable precision medicine in prostate cancer. This technology can also be applied to other cancers. Citation Format: Raju Kandimalla, Binggang Xiang, Chao Dai, Amy Wang, Pan Du, Shujun Luo, Debbie Liao. Whole exome and whole genome methylation sequencing of low-input cfDNA to implement precision medicine in metastatic castration resistant prostate cancer [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr CC07-01.

Dynamic changes of genomic methylation profiles at different growth stages in Chinese Tan sheep

BackgroundTan sheep, an important local sheep breed in China, is famous for their fur quality. One-month-old Tan sheep have white, curly hair with beautiful flower spikes, commonly known as “nine bends”, which has high economic value. However, the “nine bends” characteristic gradually disappears with age; consequently, the economic value of the Tan sheep decreases. Age-related changes in DNA methylation have been reported and may be responsible for age-induced changes in gene expression. Until now, no genome-wide surveys have been conducted to identify potential DNA methylation sites involved in different sheep growth stages. In this study we investigated the dynamic changes of genome-wide DNA methylation profiles in Tan sheep using DNA from skin and deep whole-genome bisulfite sequencing, and compared the DNA methylation levels at three different growth stages: 1, 24, and 48 months old (mon1, mon24, and mon48, respectively).ResultsIn this study, 11 skin samples from three growth stages (four for mon1, four for mon24, and three for mon48) were used for DNA methylation analysis and gene expression profiling. There were 52, 288 and 236 differentially methylated genes (DMGs) identified between mon1 and mon24, mon1 and mon48, and mon24 and mon48, respectively. Of the differentially methylated regions, 1.11%, 7.61%, and 7.65% were in the promoter in mon1 vs. mon24, mon24 vs. mon48, and mon1 vs. mon48, respectively. DMGs were enriched in the MAPK and WNT signaling pathways, which are related to age growth and hair follicle morphogenesis processes. There were 51 DMGs associated with age growth and curly fleece formation. Four DMGs between mon1 and mon48 (KRT71, CD44, ROR2 and ZDHHC13) were further validated by bisulfite sequencing.ConclusionsThis study revealed dynamic changes in the genomic methylation profiles of mon1, mon24, and mon48 sheep, and the percentages of methylated cytosines were 3.38%, 2.85% and 4.17%, respectively. Of the DMGs, KRT71 and CD44 were highly methylated in mon1, and ROR2 and ZDHHC13 were highly methylated in mon48. These findings provide foundational information that may be used to develop strategies for potentially retaining the lamb fur and thus improving the economic value of Tan sheep.

P59.08 Identifying the Origin of Lung-Specific Cancer of Unknown Primary Based on Comprehensive Genomic Profiling Optimized With DNA Methylation

Precise diagnosis of the tissue origin for metastatic carcinoma is essential to decide the treatment scheme and improve outcome. The purpose of this study is to predict the primary site for lung-specific cancer of unknown primary (CUP) through genomic and DNA methylation profiles. Comprehensive genomic profiling (CGP) was performed to determine the genomic status within individual paired samples, and targeted bisulfite sequencing was exploited to interrogate their methylation status. Model training subjects were consisted of lung cancer and another type of cancer to compute the prediction signature weights for each DMR feature. A total of 300 patients with multi-site malignancies including lung and other organ lesions were screened retrospectively. Excluding individuals clearly diagnosed with imaging modalities and IHC staining, 40 patients needed further differential diagnosis. Among them, 26 cases were identified with novel molecular events like EGFR or ALK alterations; the remaining 14 lung-specific CUPs were located with another type of caners in stomach (n=5), intestine (n=5) and cervix (n=4). Of the 14 CUP cases, mutation spectrum analyses could distinguish metastatic disease from multiple primary tumors, while it was hard to determine the origin of metastatic cancers. However, methylation profiles not only predicted the consistent results with mutation spectrum, but also identified the origin of tumors through our train classification models (AUC>0.98), which can be confirmed with patients’ clinical efficacy who received treatments guided by prediction signature. Collectively, compared with genomic profiles, DNA methylation demonstrated better tumor traceability to determine the primary site of CUPs. The signature based on within-sample CGP testing optimized with DNA methylation could exactly identify the origin of lung-specific CUPs.