Genomic Status Research Articles

Pan-cancer analysis of ARID family members as novel biomarkers for immune checkpoint inhibitor therapy

ABSTRACT Although immune checkpoint inhibitors (ICIs) have greatly improved cancer treatment, the accuracy of predictive biomarkers for ICI outcomes, such as PD-L1, TMB (tumor mutation burden) or MMR (mismatch repair) deficiency, have not been satisfactory. ARID family members are essential for maintaining the basic process of genomic stability and may serve as novel biomarkers for ICI therapy. A total of 1660 cancer patients who received ICI therapy were included in this pan-cancer analysis. The basic information and TMB values of each patient were collected. Survival analysis based on the Kaplan-Meier (KM) method was performed to explore the relationships between mutations in ARID family members and prognosis in pan-cancer as well as cancer subtypes. Genetic alterations in ARID1A (12%), ARID1B (5%), ARID2 (6%) and ARID5B (2.6%) were identified in multiple cancer types. Patients harboring mutated ARID family members benefited more from ICI therapy (P = .0003). Mutated ARID1A (P = .01), ARID1B (P = .0097) and ARID2 (P = .0054) all serve as compelling biomarkers in predicting the prognosis of ICI treatment. In addition, members of the ARID family were found to be strongly related to the abundance of CD4 + T cells and CD8 + T cells, the expression of PD-L1 and the TMB value in various cancers. Specifically, members of the ARID family could serve as novel biomarkers in multiple malignancies, especially gastrointestinal cancers. ARID family members serve as novel biomarkers for ICI therapy in malignancies. Testing the genomic status of ARID family members could help identify the definite subpopulation that benefits most from ICI treatment. Abbreviations: AT-rich interactive domain (ARID)Switch/sucrose nonfermenting (SWI/SNF)Non-small cell lung cancer (NSCLC)Immune checkpoint inhibitors (ICIs)Tumor microenvironment (TME)Programmed death-ligand 1 (PD-L1)Tumor mutational burden (TMB)

Mitonuclear incompatibility as a hidden driver behind the genome ancestry of African admixed cattle

BackgroundAfrica is an important watershed in the genetic history of domestic cattle, as two lineages of modern cattle, Bos taurus and B. indicus, form distinct admixed cattle populations. Despite the predominant B. indicus nuclear ancestry of African admixed cattle, B. indicus mitochondria have not been found on the continent. This discrepancy between the mitochondrial and nuclear genomes has been previously hypothesized to be driven by male-biased introgression of Asian B. indicus into ancestral African B. taurus. Given that this hypothesis mandates extreme demographic assumptions relying on random genetic drift, we propose a novel hypothesis of selection induced by mitonuclear incompatibility and assess these hypotheses with regard to the current genomic status of African admixed cattle.ResultsBy analyzing 494 mitochondrial and 235 nuclear genome sequences, we first confirmed the genotype discrepancy between mitochondrial and nuclear genome in African admixed cattle: the absence of B. indicus mitochondria and the predominant B. indicus autosomal ancestry. We applied approximate Bayesian computation (ABC) to assess the posterior probabilities of two selection hypotheses given this observation. The results of ABC indicated that the model assuming both male-biased B. indicus introgression and selection induced by mitonuclear incompatibility explains the current genomic discrepancy most accurately. Subsequently, we identified selection signatures at autosomal loci interacting with mitochondria that are responsible for integrity of the cellular respiration system. By contrast with B. indicus-enriched genome ancestry of African admixed cattle, local ancestries at these selection signatures were enriched with B. taurus alleles, concurring with the key expectation of selection induced by mitonuclear incompatibility.ConclusionsOur findings support the current genome status of African admixed cattle as a potential outcome of male-biased B. indicus introgression, where mitonuclear incompatibility exerted selection pressure against B. indicus mitochondria. This study provides a novel perspective on African cattle demography and supports the role of mitonuclear incompatibility in the hybridization of mammalian species.

Guidelines for genetic testing of healthy adults who deposit samples and related data in bioresource collections and biobanks

Currently, a significant part of research in the fields of human and medical genetics is carried out using tissue samples, genealogical, population, medical and personal data. Their use is of particular relevance in the “genome era”, since only joint analysis of genomic data and health status of the population is crucial for understanding how genes are associated with health and disease. Genetic studies of adults without symptoms of diseases are carried out to obtain data on a possible predisposition to multifactorial diseases, to establish the carrier status of autosomal recessive mutations as part of preconception care and to assess individual sensitivity to drugs. In addition, healthy individuals can be tested to detect an inherited disease at presymptomatic stage. This situation increasingly emphasizes the importance of storing data on genome sequencing or any other patient tests for subsequent data reanalysis, as well as their safety, including biosamples from an individual and one’s family. The review article, based on international experience, summarizes guidelines for genetic testing of healthy individuals. The options for storing biological samples and related data are considered.

Comparative methylomics and chromatin accessibility analysis in Osmanthus fragrans uncovers regulation of genic transcription and mechanisms of key floral scent production.

Linalool and ionone are two important aromatic components in sweet osmanthus petals, and the regulatory mechanisms that produce these two components remain unclear. In this study, we employed whole-genome methylation sequencing and ATAC-seq technology to analyze the genomic DNA methylation status and chromatin accessibility of the sweet osmanthus cultivars ‘Zaohuang’ and ‘Chenghong Dangui’. Results showed that the promoter region of TPS2, a key gene in the linalool synthesis pathway, was less methylated in ‘Chenghong Dangui’ than in ‘Zaohuang’. The chromatin was more accessible in ‘Chenghong Dangui’ than in ‘Zaohuang’, which resulted in a much stronger expression of this gene in ‘Chenghong Dangui’ than in ‘Zaohuang’. This eventually led to a high quantity of linalool and its oxides in the petals of ‘Chenghong Dangui’, but there were lower levels present in the petals of ‘Zaohuang’. These results suggest that DNA methylation and chromatin accessibility play major roles in linalool synthesis in sweet osmanthus. The methylation level of the promoter region of CCD4, a key gene for ionone synthesis, was higher in ‘Zaohuang’ than in ‘Chenghong Dangui’. The chromatin accessibility was lower in ‘Zaohuang’ than in ‘Chenghong Dangui’, although the expression of this gene was significantly higher in ‘Zaohuang’ than in ‘Chenghong Dangui’. ChIP-seq analysis and a series of experiments showed that the differential expression of CCD4 and CCD1 in the two cultivars may predominantly be the result of regulation by ERF2 and other transcription factors. However, a 183-bp deletion involving the CCD4 promoter region in ‘Chenghong Dangui’ may be the main reason for the low expression of this gene in its petals. This study provides an important theoretical basis for improving selective breeding of key floral fragrance components in sweet osmanthus.

The impact of radiomics in diagnosis and staging of pancreatic cancer.

Introduction:Pancreatic cancer (PC) is one of the most aggressive tumours, and better risk stratification among patients is required to provide tailored treatment. The meaning of radiomics and texture analysis as predictive techniques are not already systematically assessed. The aim of this study is to assess the role of radiomics in PC.Methods:A PubMed/MEDLINE and Embase systematic review was conducted to assess the role of radiomics in PC. The search strategy was ‘radiomics [All Fields] AND (“pancreas” [MeSH Terms] OR “pancreas” [All Fields] OR “pancreatic” [All Fields])’ and only original articles referred to PC in humans in the English language were considered.Results:A total of 123 studies and 183 studies were obtained using the mentioned search strategy on PubMed and Embase, respectively. After the complete selection process, a total of 56 papers were considered eligible for the analysis of the results. Radiomics methods were applied in PC for assessment technical feasibility and reproducibility aspects analysis, risk stratification, biologic or genomic status prediction and treatment response prediction.Discussion:Radiomics seems to be a promising approach to evaluate PC from diagnosis to treatment response prediction. Further and larger studies are required to confirm the role and allowed to include radiomics parameter in a comprehensive decision support system.

Tracing and Targeting the Origins of Childhood Cancer

Despite the success of treating childhood cancers with cytotoxic agents, novel therapeutic strategies are required to achieve the next leap in cure rates. A promising avenue may be to target the origin of childhood cancers. Here, we review recent advances in tracing the origins of pediatric tumors. Cancer-to-normal cell comparisons by single-cell mRNA sequencing reveal the fetal state of cancer cells, as well as their cell of origin. Recent phylogenetic analyses have uncovered large tissue-resident precursor clones to childhood cancers, which already possess key genomic alterations leading to tumor formation. Both the transcriptional fetalness and genomic status of the premalignant tissue bed provide further avenues for targeted therapy. Overall, these advances begin to describe the precise origins of pediatric tumors and pave the way for novel methods in detecting, treating, and perhaps even preventing childhood cancers.

DNA Methylation Basis in the Effect of White Matter Integrity Deficits on Cognitive Impairments and Psychopathological Symptoms in Drug-Naive First-Episode Schizophrenia.

Background: Mounting evidence from diffusion tensor imaging (DTI) and epigenetic studies, respectively, confirmed the abnormal alterations of brain white matter integrity and DNA methylation (DNAm) in schizophrenia. However, few studies have been carried out in the same sample to simultaneously explore the WM pathology relating to clinical behaviors, as well as the DNA methylation basis underlying the WM deficits.Methods: We performed DTI scans in 42 treatment-naïve first-episode schizophrenia patients and 38 healthy controls. Voxel-based method of fractional anisotropy (FA) derived from DTI was used to assess WM integrity. Participants' peripheral blood genomic DNAm status, quantified by using Infinium® Human Methylation 450K BeadChip, was examined in parallel with DTI scanning. Participants completed Digit Span test and Trail Making test, as well as Positive and Negative Syndrome Scale measurement. We acquired genes that are differentially expressed in the brain regions with abnormal FA values according to the Allen anatomically comprehensive atlas, obtained DNAm levels of the corresponding genes, and then performed Z-test to compare the differential epigenetic-imaging associations (DEIAs) between the two groups.Results: Significant decreases of FA values in the patient group were in the right middle temporal lobe WM, right cuneus WM, right anterior cingulate WM, and right inferior parietal lobe WM, while the significant increases were in the bilateral middle cingulate WM (Ps < 0.01, GRF correction). Abnormal FA values were correlated with patients' clinical symptoms and cognitive impairments. In the DEIAs, patients showed abnormal couple patterns between altered FA and DNAm components, for which the enriched biological processes and pathways could be largely grouped into three biological procedures: the neurocognition, immune, and nervous system.Conclusion: Schizophrenia may not cause widespread neuropathological changes, but subtle alterations affecting local cingulum WM, which may play a critical role in positive symptoms and cognitive impairments. This imaging-epigenetics study revealed for the first time that DNAm of genes enriched in neuronal, immunologic, and cognitive processes may serve as the basis in the effect of WM deficits on clinical behaviors in schizophrenia.

Genomic attributes of homology-directed DNA repair deficiency in metastatic prostate cancer.

Cancers with homology-directed DNA repair (HRR) deficiency exhibit high response rates to poly(ADP-ribose) polymerase inhibitors (PARPi) and platinum chemotherapy. Though mutations disrupting BRCA1 and BRCA2 associate with HRR deficiency (HRRd), patterns of genomic aberrations and mutation signatures may be more sensitive and specific indicators of compromised repair. Here, we evaluated whole-exome sequences from 418 metastatic prostate cancers (mPCs) and determined that one-fifth exhibited genomic characteristics of HRRd that included Catalogue Of Somatic Mutations In Cancer mutation signature 3. Notably, a substantial fraction of tumors with genomic features of HRRd lacked biallelic loss of a core HRR-associated gene, such as BRCA2. In this subset, HRRd associated with loss of chromodomain helicase DNA binding protein 1 but not with mutations in serine-protein kinase ATM, cyclin dependent kinase 12, or checkpoint kinase 2. HRRd genomic status was strongly correlated with responses to PARPi and platinum chemotherapy, a finding that supports evaluating biomarkers reflecting functional HRRd for treatment allocation.

RBIO-03. INITIAL RESULT OF DEVELOP ROBUST DEEP LEARNING MODEL FOR DETECTING GENOMIC STATUS IN GLIOMAS AGAINST IMAGE DIFFERENCES AMONG FACILITIES

Abstract BACKGROUND The importance of detecting the genomic status of gliomas is increasingly recognized and IDH (isocitrate dehydrogenase) mutation and TERT (telomerase reverse transcriptase) promoter mutation have a significant impact on treatment decisions. Noninvasive prediction of these genomic statuses in gliomas is a challenging problem; however, a deep learning model using magnetic resonance imaging (MRI) can be a solution. The image differences among facilities causing performance degradation, called domain shift, have also been reported in other tasks such as brain tumor segmentation. We investigated whether a deep learning model could predict the gene status, and if so, to what extent it would be affected by domain shift. METHOD We used the Multimodal Brain Tumor Segmentation Challenge (BraTS) data and the Japanese cohort (JC) dataset consisted of brain tumor images collected from 544 patients in 10 facilities in Japan. We focused on IDH mutation and TERT promoter mutation. The deep learning models to predict the statuses of these genes were trained by the BraTS dataset or the training portion of the JC dataset, and the test portion of the JC dataset evaluated the accuracy of the models. RESULTS The IDH mutation predicting model trained by the BraTS dataset showed 80.0% accuracy for the validation portion of the BraTS dataset; however, only 67.3% for the test portion of the JC dataset. The TERT promoter mutation predicting model trained by the training portion of the JC dataset showed only 49% accuracy for the test portion of the JC dataset. CONCLUSION IDH mutation can be predicted by deep learning models using MRI, but the performance degeneration by domain shift was significant. On the other hand, TERT promoter mutation could not be predicted accurately enough by current deep learning techniques. In both mutations, further studies are needed.

Does Microfluidic Sperm Sorting Affect Embryo Euploidy Rates in Couples with High Sperm DNA Fragmentation?

Male infertility contributes as the main factor in 30-50% of infertility cases. Conventional methods for sperm preparation have induced questioning of sperm recovery rates. The microfluidic sperm sorting (MSS) technique selects highly motile sperm with lower levels of SDF (sperm DNA fragmentation) compared to conventional sperm sorting techniques. This study aimed to determine whether utilizing this technique will reveal better embryo quality and euploidy rates in couples with repeated implantation failure (RIF) and high SDF in a new PGT-A (preimplantation genetic testing for aneuploidies) cycle. This retrospective study included couples referred to PGT-A for previous repeated ART (assisted reproductive techniques) cycle failures and with high SDF. In their new cycles, couples who accepted the technique were assigned to the MSS group, and the rest were managed with DGC (density-gradient centrifugation). Two groups were compared in terms of fertilization and euploidy rates, clinical miscarriage and live birth rates, the total number of blastocysts, and top quality blastocysts. There was no difference between the groups regarding fertilization rates, euploidy rates, clinical miscarriage, and live birth rates. The total number of blastocysts and top quality blastocysts were significantly higher in the MSS group. The MSS technique provides a higher number of top-quality blastocysts than DGC; however, neither euploidy nor live birth rates improved. Studies focusing on confounding factors to embryonic genomic status in the presence of high SDF are needed.

Genomic Landscape in Neoplasm-Like Stroma Reveals Distinct Prognostic Subtypes of Pancreatic Ductal Adenocarcinoma.

As a main component of the tumor microenvironment, the stroma is critical in development, progression, and metastasis of pancreatic ductal adenocarcinoma (PDAC). The genomic status and its relationship of neoplastic and stromal components remain unclear in PDAC. We performed targeted sequencing for 1,021 cancer-suspected genes on parallel microdissected stromal and neoplastic components from 50 operable PDAC patients. Clonality analysis of mutations was conducted to reconstruct the evolutionary trajectory, and then molecular subtypes were established. Multi-lineage differentiation potential and mesenchymal transformation of KRAS-mutant cell line Panc1 were evaluated using RT-PCR and immunofluorescence staining. In this study, 39 (78.0%) were genomically altered in stroma, with KRAS (71.8%), TP53 (61.5%), and CDKN2A (23.1%) as the most commonly mutated genes. The majority of stromal mutations (89.8%) were detected in matched neoplastic components. Patients with KRAS/TP53-mut stroma demonstrated a higher tumor cell fraction (TCF) than did those with wild-type (WT) stroma (p = 0.0371, p = 0.0014). In both components, mutants KRAS and TP53 often occurred as clonal events, and the allele frequencies presented linear correlation in the same specimen. All neoplasm-like stroma (characterized with all or initial neoplastic clones and driver events in stroma) harbored KRAS or TP53 mutations. Neoplasm-like and KRAS-mutant stroma was associated with shorter disease-free survival. It is a new finding for the existence of driver gene mutations in PDAC stroma. These data suggest that genomic features of stromal components may serve as prognostic biomarkers in resectable PDAC and might help to guide a more precise treatment paradigm in therapeutic options.

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.

CTLA4 Mediates Immunosuppersion in the Tumor Microenvironment via Macrophage Recruitment for Glioblastoma Immunotherapy

Background: CTLA4 has been widely reported to contribute to downregulation of immune responses to anti-tumor activity. Anti-CTLA4 provides a novel strategy to improve the outcome of cancer immunotherapy, but the role of CTLA4 needs to be addressed in glioblastoma (GBM). To investigate the role of CTLA4 in GBM, we analyzed the sequencing data of CTLA4 and evaluated its clinical prognostic value. Methods: 467 GBM cases were enrolled into this study from 4 cohorts. In their works, the Cancer Genome Atlas (TCGA) cohort was divided into training set and the Chinese Glioma Genome Atlas (CGGA) cohort, REMBRANDT, and GSE84465 cohorts were divided into validation set. Then, the role of CTLA4 in tumor microenvironment (TME) of GBM was comprehensively investigated. Findings: Significant differences exist in immunological characteristics between low and high CTLA4 expression groups. Mutation analysis found distinct genomic patterns associated with CTLA4 expression. Next, network analysis found the module named c1-1562 including CTLA4 correlated with over survival (OS) in GBM. We also developed a predictive model to calculate the risk score of every GBM case and the risk score was independently related to OS. Furthermore, expression of CTLA4 was positively related to the infiltration level and function of macrophage in GBM TME based on seven independent algorithms and single cell RNA-seq data. Interpretation: This study confirmed that CTLA4 plays an obviously key role in clinical, genomic, and TME status. This will contribute to stratifying clinical treatment and enhancing the efficiency of cancer immunotherapy. Funding Information: This project was supported by National Natural Science Foundation of China (No. 82071996, No. 81802483 and No. 82003075), the Beijing Municipal Health Commission of China (No. PXM2019_026280_000002), the Capital’s Funds for Health Improvement and Research (No. 2018-1-1071), and Beijing Hospitals Authority Youth Program (No. QML20190507) Declaration of Interests: The authors have declared that no competing interest exists. Ethics Approval Statement: The study was conducted in accordance with good clinical practice guidelines and the declaration of Helsinki, which has been approved by Capital Medical University Institutional Review Board.

Malignant Tumor Purity Reveals the Driven and Prognostic Role of CD3E in Low-Grade Glioma Microenvironment.

The tumor microenvironment (TME) contributes to the initiation and progression of many neoplasms. However, the impact of low-grade glioma (LGG) purity on carcinogenesis remains to be elucidated. We selected 509 LGG patients with available genomic and clinical information from the TCGA database. The percentage of tumor infiltrating immune cells and the tumor purity of LGG were evaluated using the ESTIMATE and CIBERSORT algorithms. Stromal-related genes were screened through Cox regression, and protein-protein interaction analyses and survival-related genes were selected in 487 LGG patients from GEO database. Hub genes involved in LGG purity were then identified and functionally annotated using bioinformatics analyses. Prognostic implications were validated in 100 patients from an Asian real-world cohort. Elevated tumor purity burden, immune scores, and stromal scores were significantly associated with poor outcomes and increased grade in LGG patients from the TCGA cohort. In addition, CD3E was selected with the most significant prognostic value (Hazard Ratio=1.552, P<0.001). Differentially expressed genes screened according to CD3E expression were mainly involved in stromal related activities. Additionally, significantly increased CD3E expression was found in 100 LGG samples from the validation cohort compared with adjacent normal brain tissues. High CD3E expression could serve as an independent prognostic indicator for survival of LGG patients and promotes malignant cellular biological behaviors of LGG. In conclusion, tumor purity has a considerable impact on the clinical, genomic, and biological status of LGG. CD3E, the gene for novel membrane immune biomarker deeply affecting tumor purity, may help to evaluate the prognosis and develop individual immunotherapy strategies for LGG patients. Evaluating the ratio of differential tumor purity and CD3E expression levels may provide novel insights into the complex structure of the LGG microenvironment and targeted drug development.

740P Olaparib maintenance monotherapy for non-germline BRCA1/2-mutated (non-gBRCAm) platinum-sensitive relapsed ovarian cancer (PSR OC): Exploratory biomarker analyses of the phase IIIb OPINION study

Maintenance olaparib is a standard of care for PSR OC patients (pts), including those without a BRCA1 and/or BRCA2 mutation (BRCAm). The OPINION (NCT03402841) primary analysis showed clinical benefit with maintenance olaparib monotherapy in non-gBRCAm pts, and by homologous recombination deficiency (HRD) genomic instability status, compared with historical placebo controls (Poveda et al. ASCO 2021). Here, we assessed exploratory biomarkers beyond HRD that may be predictive of response in non-gBRCAm PSR OC.

Low THRB (thyroid hormone receptor beta) Promoter Methylation Levels in Peripheral Blood Leukocytes Induced By Systematic Inflammation Are Involved in Low Thyroid Hormone Function in Metabolic Syndrome.

[Figure: see text].

The complete chloroplast genome of Libocedrus chevalieri, a Critically Endangered species in New Caledonia

Libocedrus chevalieri is a rare endemic conifer from New Caledonia, and it is evaluated as Critically Endangered in the IUCN Red List of Threatened Species. To take conservation actions more effectively, a survey of its genomic background and evolutionary status is of great significance. Illumina paired-end reads were used to character the chloroplast (cp) genome of L. chevalieri. The circular genome is 122,068 bp in length, containing 115 genes, in which include 83 protein-coding genes, four ribosomal RNA genes, and 28 transfer RNA genes. Nine genes (atpF, rpoC1, ndhB, ndhA, rpl2, petB, rpl16, petD, rps12) have one intron, whilst one gene (ycf3) has two introns. Inverted repeat (IR) sequence doesn’t exist in the genome. The GC content of the cp genome is 34.1%. The phylogenetic analysis demonstrates that L. chevalieri has a close relationship with L. plumosa.

Dual germline and somatic testing in women with high-grade epithelial ovarian, tubal, and peritoneal cancer: a prospective systemic quality improvement initiative

<h3>Objectives:</h3> Germline and somatic genetic testing can have significant implications for women with ovarian, fallopian tube or peritoneal carcinoma, including therapeutic decisions, prognostic counseling and cascade testing. However, there are obstacles to universal implementation of testing when it is dependent on clinician initiative. Therefore, we implemented a prospective quality improvement (QI) initiative that aimed to assure universal germline and somatic testing in women with newly diagnosed advanced stage, high grade disease. <h3>Methods:</h3> A systematic program was established to ensure that all patients with newly diagnosed, advanced stage ovarian, tubal or peritoneal carcinoma who were scheduled for formal genetics consultation underwent dual Myriad MyRisk multigene germline testing and Myriad MyChoice somatic testing for <i>BRCA1/2</i> mutations and genomic instability. The primary objective was to compare the frequency of germline and somatic testing between the pre-initiative (1/1/2015 - 3/31/2018) and post-initiative (4/1/2018- 7/1/2020) periods. Secondary objectives included comparison of time intervals between diagnosis and testing, incidence of ‘insufficient samples' for somatic testing, and clinical utilization of results. Descriptive statistics were used. Paired Student's T test was used to compare continuous variables; chi-square test was used to compare discrete variables. <h3>Results:</h3> There were 209 women in this study: 122 in the pre-intervention cohort and 87 in the post-intervention cohort. Among women in the pre-intervention group, 90 (74%) and 48 (39%) underwent germline and somatic testing, respectively, compared to 77 (89%) and 66 (76%) in the post-intervention cohort. Implementation of a systemic referral system with dual testing doubled the rate of somatic testing (p<0.01). Among all women who underwent germline testing, 10.1% had a g<i>BRCA1</i> mutation and 2.4% a g<i>BRCA2</i> mutation. Of all who underwent somatic testing, 6.2% had a s<i>BRCA1</i> mutation and 4.3% a s<i>BRCA2</i> mutation. All germline <i>BRCA1</i> and <i>BRCA2</i> mutations were also identified on somatic testing. There were 20 cases (9.5%) with negative germline multigene panels also lacking somatic <i>BRCA1/2</i> mutations that were found to have genomic instability. Among the 114 patients who received somatic testing, 29 (25.4%) had biomarkers (<i>BRCA1/2</i> mutation or genomic instability) predictive of major benefit from poly-ADP ribose polymerase inhibitors (PARPi) despite lacking germline mutations. Median time from diagnosis to germline testing decreased to 3.7 months in the post-intervention compared to 6.2 months in the pre-intervention cohort. <h3>Conclusions:</h3> Systematic referral for both germline and somatic genetic testing significantly increased the frequency of somatic testing, and results were obtained sooner in patients with advanced ovarian, fallopian tube and peritoneal cancers. In patients who underwent dual testing and lacked germline mutations, 25% had either a somatic <i>BRCA1</i> or <i>BRCA2</i> mutation or genomic instability that could help direct therapy. Since both germline and somatic mutations and genomic instability status increasingly play a role in directing therapy, earlier and consistent testing is of the upmost importance.

Prophylactic or Preemptive Low-Dose Azacitidine and Donor Lymphocyte Infusion to Prevent Disease Relapse following Allogeneic Transplantation in Patients with High-Risk Acute Myelogenous Leukemia or Myelodysplastic Syndrome

Because of the persistently high rates of relapse of patients with high-risk acute myelogenous leukemia (AML) and myelodysplastic syndrome (MDS) following allogeneic hematopoietic stem cell transplantation (allo-HSCT), post-transplantation maintenance therapy has been proposed. We previously initiated a Phase II trial in which epigenetic therapy was combined with immunotherapy in an attempt to reduce disease relapse. In that study, low-dose azacitidine (AZA) and escalating doses of donor lymphocyte infusion (DLI) were given as post-allo-HSCT maintenance treatment. In the present study, we retrospectively analyze a larger cohort of patients receiving post-transplantation maintenance therapy and provide updates on some patients of the earlier study. The objectives of the present study were to analyze the cumulative incidence of relapse (CIR), overall survival (OS), and progression-free survival (PFS) and the incidence of acute and chronic graft-versus-host disease (GVHD) of patients with high-risk AML or MDS receiving post-transplantation maintenance treatment with AZA with or without DLI. We retrospectively analyzed 77 patients (54 with AML, 23 with MDS) considered at high risk based on either their genomic or clinical status at transplantation. Following allogeneic transplantation, they received at least 1 cycle of prophylactic or preemptive low-dose AZA with or without escalating doses of DLI to prevent disease relapse. Almost one-half of the patients (47%) were able to receive the full 12 cycles of scheduled AZA, and a majority (79%) received at least 1 DLI. With a median follow-up of 24 months, 19 patients (25%; 16 with AML, 3 with MDS) relapsed, at a median of 9.8 months (range, 4 to 58.6 months), giving a 22% CIR at 24 months. OS and PFS at 24 months were 70.8% and 68.3%, respectively. The cumulative incidences of grade II-IV acute GVHD and chronic GVHD were 27.4% and 45%, respectively. Only a minority of patients (11%) required delayed administration of AZA. These findings confirm that AZA-DLI maintenance is both tolerable and effective in reducing the risk of post-transplantation relapse.

Abstract 2055: Evaluation of DNA damage repair gene alterations, microsatellite instability status, and tumor mutational burden as predictive biomarkers of olaparib sensitivity in gastric cancer

Abstract One of the many causes of cancer is a dysfunction of the DNA damage repair (DDR) pathway. Cancers with alterations in homologous recombination (HR) genes are known to be increased the sensitivity of PARP inhibitors and genomic instability. Besides, cancers with alterations in other DDR genes like mismatch repair (MMR), have been recently reported to have similar features. Furthermore, some studies suggested that hypermutated cancers, such as microsatellite instability-high (MSI-H) or tumor mutational burden (TMB) high, have DDR gene alterations. Nevertheless, many studies still have focused on HR-related gene alteration as a predictor of olaparib. Here, we aim to determine if the DDR gene alteration and genomic instability markers can predict olaparib efficacy in 49 gastric cancer cell lines. First, we profiled the genomic status of 48 DDR genes, MSI status, and TMB using targeted sequencing (524 genes). BRCA1, RAD51C, and MLH1 methylation were detected by bisulfite sequencing. If cell lines had the deleterious mutation, homozygous deletion, or methylation in DDR genes, it was categorized as an alteration group. To determine the efficacy of olaparib, cell lines were treated with olaparib for 5 days and assessed by CCK-8 assay. IC50 values were determined by the CalcuSyn software and cell lines were classified as a sensitive group when the IC50 was less than 10µM. MMR-related and PARP1 protein expression was determined by western blot. As a result, 17 cell lines had the alteration in one or more of the 18 DDR-related genes. In our cell line panel, the expression of PARP1 protein was varied, and 12 cell lines were sensitive to olaparib. DDR alteration group was more sensitive to olaparib than the DDR wild type group (median of IC50 = 14.08µM vs &amp;gt; 20µM, p = 0.034). In detail, cell lines with alterations in the HR and MMR were significantly sensitive among the subtype of DDR pathways (p = 0.011, p = 0.009). TMB was widely distributed among the GC cell lines (range = 4.36 to 21.80, median = 10.90), and the DDR alteration group had higher TMB than DDR wild type group (median = 11.63 vs 10.90, p = 0.029). Interestingly, the olaparib sensitive group had higher TMB than the resistant group (median = 15.3 vs 10.9, p &amp;lt; 0.0001). Four cell lines (SNU-1, SNU-638, IM95m, and NUGC-3) were MSI-H, and all of them were no MLH1 protein expression. MSI-H cell lines had significantly higher TMB than other cell lines (median=19.3, p &amp;lt; 0.0001). Three MSI-H cell lines were sensitive to olaparib, but NUGC-3 with the lowest TMB (13.8) among MSI-H cell lines was resistant. In our result, the olaparib sensitive group had the alteration in DDR genes and high TMB. MSI-H cell lines were sensitive to olaparib when it had high TMB. MSI status and TMB could predict olaparib sensitivity in gastric cancer as well as DDR gene alterations. Citation Format: Jihyun Hwang, Woo sun Kwon, Juin Park, Hyun Joo Bae, Inhye Jeong, Sun Kyoung Kang, Tae Soo Kim, Jingmin Che, Hyun Cheol Chung, Sun Young Rha. Evaluation of DNA damage repair gene alterations, microsatellite instability status, and tumor mutational burden as predictive biomarkers of olaparib sensitivity in gastric 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 2055.