Liu, Yuanhang

AbstractObjectiveThe health benefits of exercise are well documented, but several exercise‐response parameters are attenuated in individuals with obesity. The goal of this pilot study was to identify molecular mechanisms that may influence exercise response with obesity.MethodsA multi‐omics comparison of the transcriptome, proteome, and phosphoproteome in muscle from a preliminary cohort of lean individuals (n = 4) and individuals with obesity (n = 4) was performed, before and after a single bout of 30 minutes of unilateral cycling at 70% maximal oxygen uptake (VO2 peak). Mass spectrometry and RNA sequencing were used to interrogate the proteome, phosphoproteome, and transcriptome from muscle biopsy tissue.ResultsThe main findings are that individuals with obesity exhibited transcriptional and proteomic signatures consistent with reduced mitochondrial function, protein synthesis, and glycogen synthesis. Furthermore, individuals with obesity demonstrated markedly different transcriptional, proteomic, and phosphoproteomic responses to exercise, particularly biosynthetic pathways of glycogen synthesis and protein synthesis. Casein kinase II subunit alpha and glycogen synthase kinase‐3β signaling was identified as exercise‐response pathways that were notably altered by obesity.ConclusionsOpportunities to enhance exercise responsiveness by targeting specific molecular pathways that are disrupted in skeletal muscle from individuals with obesity await a better understanding of the precise molecular mechanisms that may limit exercise‐response pathways in obesity.

Abstract BackgroundFormalin-fixed, paraffin-embedded (FFPE) tissues have many advantages for identification of risk biomarkers, including wide availability and potential for extended follow-up endpoints. However, RNA derived from archival FFPE samples has limited quality. Here we identified parameters that determine which FFPE samples have the potential for successful RNA extraction, library preparation, and generation of usable RNAseq data.MethodsWe optimized library preparation protocols designed for use with FFPE samples using seven FFPE and Fresh Frozen replicate pairs, and tested optimized protocols using a study set of 130 FFPE biopsies from women with benign breast disease. Metrics from RNA extraction and preparation procedures were collected and compared with bioinformatics sequencing summary statistics. Finally, a decision tree model was built to learn the relationship between pre-sequencing lab metrics and qc pass/fail status as determined by bioinformatics metrics.ResultsSamples that failed bioinformatics qc tended to have low median sample-wise correlation within the cohort (Spearman correlation < 0.75), low number of reads mapped to gene regions (< 25 million), or low number of detectable genes (11,400 # of detected genes with CPM > 2). The median RNA concentration and pre-capture library Qubit values for qc failed samples were 18.7 ng/ul and 1.68 ng/ul respectively, which were significantly lower than those of qc pass samples (40.8 ng/ul and 5.58 ng/ul). We built a decision tree model based on input RNA concentration, input library qubit values, and achieved an F score of 0.803 in predicting QC status (pass/fail) of FFPE samples. ConclusionsWe provide a bioinformatics quality control recommendation for FFPE samples from breast tissue by evaluating bioinformatic and sample metrics. Our results suggest a minimum concentration of 25 ng/ul FFPE-extracted RNA for library preparation and 1.8 ng/ul pre-capture library output to achieve adequate RNA-seq data for downstream bioinformatics analysis.

Objectives Pancreatic acinar cell carcinoma (ACC) is a rare pancreatic cancer. The advancement of treatment is hampered because of the limited knowledge of its molecular mechanism. Methods Whole-exome sequencing was performed on DNA extracted from 11 pure ACC surgical samples. Potential germline variants were removed on the basis of polymorphic databases, alternative allele frequency, coverage depth, and Catalogue of Somatic Mutations in Cancer (COSMIC) annotations after variant calling procedure. Mutation profiles and signatures were assessed through the Mutational Patterns package. Results A median of 34 somatic mutations were detected (range, 19–60). Three novel recurrent small deletions were identified. Common pancreatic ductal adenocarcinoma mutations or neuroendocrine tumor mutants were not found. FAT atypical cadherin 4, mucin 5B, titin, and zinc finger homeobox 3 were consistently mutated across 4 independent ACC studies. A high contribution of COSMIC mutational signature 1 was seen in ACC, indicating deamination of 5-methylcytosine. The majority of the patients had COSMIC signatures 6, 15, or 20, relating to defective DNA mismatch repair. Six patients showed COSMIC mutational signature 10 because of the altered activity of DNA polymerase epsilon. Conclusions Distinct mutational signatures pathways were found in ACC and targeting them may improve clinical outcome.

Abstract Cisplatin chemotherapy, although efficacious in resolution of cancer, potentiates cognitive impairments (known as chemobrain) affecting approximately 14 million cancer survivors in the United States. Cisplatin is a frontline chemotherapy used to treat ovarian, testicular, breast and brain cancers. Despite the high prevalence of clinical reports of cognitive impairments during and following chemotherapy, there is little information on how learning/memory are detrimentally affected and no known cure. To elucidate the mechanisms by which chemobrain impairs cognition, we implemented a mouse model resembling intermittent cisplatin chemotherapy in humans. Our preliminary studies revealed that repeated intermittent cisplatin treatment detrimentally affects the structure of neuronal brain cells in the hippocampus, a brain region known for its ability to control learning/memory, emotional behaviors and motor function. Although the molecular pathways vulnerable to cisplatin in the brain remain elusive, gene sequencing from the hippocampus of mice administered cisplatin identified the adenosine A2A receptor (Adora2a) protein was concentrated in elevated quantities in this brain region. Importantly, the Adora2a receptor protein is known for its critical role in learning/memory and has been found to play a role in neurodegenerative conditions. To investigate Adora2a functionality in cisplatin-induced chemobrain, we assessed the efficacy of the non-selective Adora2a antagonist caffeine, in preventing cisplatin-induced cognitive dysfunction. Caffeine was selected as a therapeutic due to its safe pharmacological profile, its universal availability, and low cost. Our translational approach employing the non-selective Adora2a antagonist caffeine, protected against cisplatin-induced body weight deficits and motor dysfunction, both of which are common clinical symptoms of chemotherapy. Interestingly, relative to cisplatin alone, mice treated with caffeine in combination with cisplatin exhibited improved dendritic spine densities in the hippocampus, suggesting improved neuronal morphology by caffeine. Given that Adora2a antagonists are known to enhance anti-tumor activity while also showing neuroprotective promise in neurodegenerative conditions, inhibiting Adora2a during cancer treatment may have far-reaching synergistic effects on quality of life improvement for cancer survivors. Citation Format: Alfredo Oliveros, Ana M. Corujo-Ramirez, Ki-Hyun Yoo, Jason Tang, Danielle Brogren, Mohammad A. Rashid, Yuanhang Liu, Mi-Hyeon Jang. Adora2a inhibition via caffeine as a novel therapeutic target for cisplatin-induced chemobrain [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 3115.

Abstract Benign breast disease (BBD) is an established risk factor for development of breast cancer (BC). However, little is known about the prevalence of somatic genetic alterations at the time of BBD diagnosis and relationship to subsequent BC. To characterize DNA variants in BBD and investigate association with BC risk, we isolated DNA from formalin-fixed paraffin-embedded (FFPE) BBD biopsies and assessed mutations using a panel of 93 breast cancer predisposition genes (Qiagen GeneRead). The study set consisted of 120 BBD patients from three age-matched groups defined based on 16 years of BC follow-up: BBD-controls (cancer-free after 16 years), BBD-ER+, or BBD-ER- breast cancer (within 16 years). Bioinformatics quality checks included comparisons of paired fresh-frozen and FFPE replicates to reduce false variant calls induced by FFPE artifacts. Gene-level variant burden differences among study groups were assessed using 12 statistical approaches, adjusted for patient age, year of biopsy, and histology. To investigate possible immune implications of increased variant burden, extent of leukocytes in the BBD biopsies was assessed using CD45 immunohistochemistry. To assess variant profile changes during the progression from BBD to BC, we also performed targeted sequencing of 12 BBD-matched subsequent tumor samples (six ER+ and six ER-) developed within 5 years of BBD diagnosis. Gene-level association results showed consistently skewed distributions suggesting a higher variant burden in BBD controls: among the top 10 genes associated with case-status (p&lt;0.05), all had BC-risk odds ratio estimates less than 1.0. Immune infiltrates, assessed by CD45 H-scores, were positively associated with overall variant burden (r=0.42, p=0.0031), and noticeably higher in cancer-free controls (r=0.50, p=0.005). Comparison of mutation variants in 12 BBD cases that developed cancer within 5 years of diagnosis and their subsequent tumors revealed that more than half of the non-SNP variants were shared between the BBD and the subsequent tumor (54.6%), whereas less than one quarter were unique to the tumor (20.6%) or unique to the BBD (24.9%). Through BBD-BC paired variant analysis, three subjects were found with newly emergent clones uniquely appearing in the tumors and four subjects had loss of clones in the tumor that were present in the BBD. These results show that somatic variant burden is lower in patients with BBD that progress to BC, mutation profiles of BC progression are heterogeneous, and BBD tissues with reduced variant burden also show reduced immune infiltrate. This implicates a potential protective role for immune activation in BBD. Future directions will define the characteristics of the potentially protective immune response and its role in variant heterogeneity in a larger sample set, integrated with paired RNA sequencing to better understand the pathways involved and the relationship to immune infiltration. Citation Format: Stacey J. Winham, Julie M. Cunningham, Yuanhang Liu, Aditya V. Bhagwate, Ethan P. Heinzen, Samantha J. McDonough, Melody L. Stallings-Mann, Robert A. Vierkant, Jodi M. Carter, Mark E. Sherman, Derek C. Radisky, Amy C. Degnim, Chen Wang. Somatic variant burdenin benign breast disease and association with risk of subsequent breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2274.

Abstract Background: Benign breast disease (BBD) is a risk factor for breast cancer (BC); however, little is known about the genetic alterations present at the time of BBD diagnosis, and how these relate to risk of incident BC. Methods: A subset of a long-term BBD cohort was selected to examine DNA variation across three BBD groups (42 future estrogen receptor-positive (ER+) BC, 36 future estrogen receptor-negative (ER-) BC and 42 controls cancer-free for at least 16 years post-BBD). DNA extracted from archival formalin fixed, paraffin-embedded (FFPE) tissue blocks was tested and analyzed for presence of DNA alterations using a targeted panel of 93 BC-associated genes. To address artifacts frequently observed in FFPE tissues (e.g., C>T changes), we applied three filtering strategies based on alternative allele frequencies and nucleotide substitution context. Gene-level associations were performed using two burden tests, SKAT-O and logistic regression, and adjusted for clinical and technical covariates including epithelial percentage, histologic impression, patient age and year of BBD biopsy. Results: After filtering, the variant frequency of SNPs in our samples was highly consistent with population allele frequencies reported in 1KG/ExAC (0.986, p <1e-16). Ten genes were found to be associated with later cancer status by four of 12 association methods, with nominal p-values <0.05: MED12, MSH2, BRIP1, PMS1, GATA3, MUC16, FAM175A, EXT2, MLH1 and TGFB1. Additionally, analysis revealed 11 and 19 gene-level associations with p-values <0.05 and OR<1 for all cancer cases and ER- cases, respectively. Comparing between the three case groups, BBD ER+ cases were closer to controls in mutation profile, while BBD ER- cases were distinct. Notably, the variant burden was significantly higher in controls than in either ER+ or ER- cases. CD45 expression was associated with mutational burden (p=0.003).Conclusions: Somatic mutations were more frequent in benign breast tissue from women who did not develop cancer, opening questions of clonal diversity or immune-mediated restraint on future cancer development. CD45 expression was positively associated with mutational burden, most strongly in controls. Further studies in both normal and premalignant tissues are needed to better understand the role of somatic gene mutations and their contribution to future cancer development.

Abstract Background: Traditionally, mutational burden and mutational signatures have been assessed by tumor-normal pair DNA sequencing. The requirement of having both normal and tumor samples is not always feasible from a clinical perspective, and led us to investigate the efficacy of using RNA sequencing of only the tumor sample to determine the mutational burden and signatures, and subsequently molecular cause of the cancer. The potential advantages include reducing the cost of testing, and simultaneously providing information on the gene expression profile and gene fusions present in the tumor. Results: In this study, we devised supervised and unsupervised learning methods to determine mutational signatures from tumor RNA-seq data. As applications, we applied the methods to a training set of 587 TCGA uterine cancer RNA-seq samples, and examined in an independent testing set of 521 TCGA colorectal cancer RNA-seq samples. Both diseases are known associated with microsatellite instable high (MSI-H) and driver defects in DNA polymerase ɛ (POLɛ). From RNA-seq called variants, we found majority (>95%) are likely germline variants, leading to C>T enriched germline variants (dbSNP) widely applicable in tumor and normal RNA-seq samples. We found significant associations between RNA-derived mutational burdens and MSI/POLɛ status, and insignificant relationship between RNA-seq total coverage and derived mutational burdens. Additionally we found that over 80% of variants could be explained by using the COSMIC mutational signature-5, -6 and -10, which are implicated in natural aging, MSI-H, and POLɛ, respectively. For classifying tumor type, within UCEC we achieved a recall of 0.56 and 0.78, and specificity of 0.66 and 0.99 for MSI and POLɛ respectively. By applying learnt RNA signatures from UCEC to COAD, we were able to improve our classification of both MSI and POLɛ. Conclusions: Taken together, our work provides a novel method to detect RNA-seq derived mutational signatures with effective procedures to remove likely germline variants. It can leads to accurate classification of underlying driving mechanisms of DNA damage deficiency.

Abstract Background: Traditionally, mutational burden and mutational signatures have been assessed by tumor-normal pair DNA sequencing. The requirement of having both normal and tumor samples is not always feasible from a clinical perspective, and led us to investigate the efficacy of using RNA sequencing of only the tumor sample to determine the mutational burden and signatures, and subsequently molecular cause of the cancer. The potential advantages include reducing the cost of testing, and simultaneously providing information on the gene expression profile and gene fusions present in the tumor. Results: In this study, we devised supervised and unsupervised learning methods to determine mutational signatures from tumor RNA-seq data. As applications, we applied the methods to a training set of 587 TCGA uterine cancer RNA-seq samples, and examined in an independent testing set of 521 TCGA colorectal cancer RNA-seq samples. Both diseases are known associated with microsatellite instable high (MSI-H) and driver defects in DNA polymerase ɛ (POLɛ).From RNA-seq called variants, we found majority (>95%) are likely germline variants, leading to C>T enriched germline variants (dbSNP) widely applicable in tumor and normal RNA-seq samples. We found significant associations between RNA-derived mutational burdens and MSI/POLɛ status, and insignificant relationship between RNA-seq total coverage and derived mutational burdens. Additionally we found that over 80% of variants could be explained by using the COSMIC mutational signature-5, -6 and -10, which are implicated in natural aging, MSI-H, and POLɛ, respectively. For classifying tumor type, within UCEC we achieved a recall of 0.56 and 0.78, and specificity of 0.66 and 0.99 for MSI and POLɛ respectively. By applying learnt RNA signatures from UCEC to COAD, we were able to improve our classification of both MSI and POLɛ. Conclusions: Taken together, our work provides a novel method to detect RNA-seq derived mutational signatures with effective procedures to remove likely germline variants. It can leads to accurate classification of underlying driving mechanisms of DNA damage deficiency.

Abstract Cisplatin chemotherapy, although efficacious in positive resolution of cancer, adversely potentiates off-target cognitive dysfunction and affects approximately 14 million cancer survivors in the United States alone. Despite the high prevalence of chemotherapy induced cognitive impairments (known as chemobrain), there is little information on how memory and learning are impaired and no known cure. To elucidate the mechanisms by which chemobrain impairs cognition, we implement a novel experimental mouse model resembling clinical cisplatin-chemotherapy. Our results reveal that repeated cisplatin administration impairs hippocampal neuronal functional morphology, while inducing significant emotional and memory deficits. Although the molecular targets and pathways vulnerable to cisplatin in the central nervous system (CNS) are currently unknown, RNA-sequencing derived from mice administered cisplatin or vehicle revealed the G-protein coupled adenosine A2A receptor (Adora2a) known to be critical for synaptic plasticity and memory, as a promising therapeutic target for chemobrain. Bioinformatic analysis and qRT-PCR validation revealed significant induction of Adora2a mRNA expression by cisplatin in the adult hippocampus, a brain structure critical for learning and memory. Interestingly, while Adora2a is known to be expressed by neurons, astrocytes and other brain glia, confocal microscopy demonstrates that cisplatin specifically increases Adora2a expression in hippocampal neurons without affecting astrocytes, indicating that Adora2a expressing neurons are particularly vulnerable. To mechanistically determine whether elevated neuronal Adora2a functionality are implicated in cisplatin-induced chemobrain, we assessed the efficacy of Istradefylline (KW-6002), a selective Adora2a inhibitor, in preventing cisplatin-induced chemobrain. Our results indicate that selective pharmacological inhibition of Adora2a prevented cisplatin induced anxiety and cognitive impairments in the elevated plus maze, the Morris water maze and novel object recognition test. In addition, our translational approach employing the non-specific Adora2a antagonist caffeine, protected against cisplatin-induced impairments in body weight, motor learning and motor function. Therefore, our results suggest a critical regulatory role for Adora2a in cisplatin-induced cognitive and motor dysfunction. Given that Adora2a antagonists are proven to be safe and neuroprotective in neurodegeneration as well as in enhancing anti-tumor activity, inhibiting Adora2a may have far-reaching synergistic effects on cancer treatment and chemobrain. This work was supported by Mayo Clinic Breast SPORE (R50CA116201) and Regenerative Medicine Minnesota (RMM 091718 DS 005) to M.H.J. and the Bosarge Family Foundation-Waun Ki Hong Scholar Award to A.O. Citation Format: Alfredo Oliveros, Ki-Hyun Yoo, jun Tang, Ana M. Corujo, Danielle Brogren, Yuanhang Liu, Mi-Hyeon Jang. Adora2a inhibition as a novel therapeutic target for cisplatin chemobrain-induced cognitive dysfunction [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 4141.