Somatic Gene Research Articles

PD10-11 DISTINCT CLINICAL GENOMIC VARIATIONS AMONG MEN WITH LOCALIZED VS METASTATIC PROSTATE CANCER

You have accessJournal of UrologyCME1 Apr 2023PD10-11 DISTINCT CLINICAL GENOMIC VARIATIONS AMONG MEN WITH LOCALIZED VS METASTATIC PROSTATE CANCER Ahmed El-shafie, Mohammed Al-Toubat, Allison H. Feibus, SeyedBehzad Jazayeri, Soroush Bazargani, Devon Thomas, Mark Bandyk, and K.C. Balaji Ahmed El-shafieAhmed El-shafie More articles by this author , Mohammed Al-ToubatMohammed Al-Toubat More articles by this author , Allison H. FeibusAllison H. Feibus More articles by this author , SeyedBehzad JazayeriSeyedBehzad Jazayeri More articles by this author , Soroush BazarganiSoroush Bazargani More articles by this author , Devon ThomasDevon Thomas More articles by this author , Mark BandykMark Bandyk More articles by this author , and K.C. BalajiK.C. Balaji More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000003250.11AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: Our objective was to identify unique genetic mutations associated with metastatic prostate cancer (PCa) by comparing next generation sequencing (NGS) data between men with localized and metastatic disease METHODS: We queried the American Association for Cancer Research Project Genomics Evidence Neoplasia Information Exchange (GENIE) registry for men diagnosed with PCa. Patients were categorized into localized (m0) and metastatic (m1) groups. The difference in the frequency of genetic mutations between the two groups and the prognostic significance of the differentially expressed genes were analysed using SPSS V24. We included frequency rates of >5% and p values <0.05 were considered statistically significant to maintain over 95% true positive detection rate. RESULTS: A total of 1,027 patients, with localized (n=459) and metastatic PCa (n=568) were included in the study. Patients were mostly non-Hispanic White men (89%) with a median age of 61 years (IQR 56-66 years). 421 (41%) of our cohort had Gleason grade group (GG) 2 disease, 277 (27%) had GG3 disease, and 267 (26%) had GG4 or GG5 disease. We identified alterations in 89 genes in our analyses. Patients with M1PCa had significantly higher genomic aberrations in TMPRSS2 (31.51% vs 11.14%, p<0.001); ERG fusion (23.59% vs 13.13%, p<0.001); PTEN loss (25.7% vs 16.16%, p<0.001); TP53 mutation (38.73% vs 12.23%, p<0.001); FOXA1 (17.43% vs 6.33%, p<0.001); KMT2C (9.51% vs 6.11%, p=0.02) (Figure 1). We then isolated the signalling pathways most likely to be affected by these mutations, and found that the androgen receptor was most often impacted (Figure 2). Patients with alterations in all 6 of the genes listed above had the worst progression-free survival (p = <0.01, log rank test) (Figure 1). CONCLUSIONS: In M1PCa, patients had significantly higher frequency of TMPRSS2, ERG, PTEN loss, TP53, FOXA1, and KMT2C somatic gene mutations compared to samples from patients with m0PCa. Additionally, patients who had mutations in all 6 of these genes harboured more aggressive cancer and poorer outcomes. Source of Funding: None © 2023 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 209Issue Supplement 4April 2023Page: e330 Advertisement Copyright & Permissions© 2023 by American Urological Association Education and Research, Inc.MetricsAuthor Information Ahmed El-shafie More articles by this author Mohammed Al-Toubat More articles by this author Allison H. Feibus More articles by this author SeyedBehzad Jazayeri More articles by this author Soroush Bazargani More articles by this author Devon Thomas More articles by this author Mark Bandyk More articles by this author K.C. Balaji More articles by this author Expand All Advertisement PDF downloadLoading ...

To Mars and Beyond: Engineering Life as a Moral Duty

To Mars and Beyond: Engineering Life as a Moral Duty

MP17-19 GENE MUTATIONS AMONG PROSTATE CANCER PATIENTS WITH A SMOKING HISTORY

You have accessJournal of UrologyCME1 Apr 2023MP17-19 GENE MUTATIONS AMONG PROSTATE CANCER PATIENTS WITH A SMOKING HISTORY Ahmed El-shafie, Allison H. Feibus, Mohammed Al-Toubat, Navid Lelani, SeyedBehzad Jazayeri, Kashyap Koul, Robert A. Marino, Mark Bandyk, Joseph Costa, and K. C. Balaji Ahmed El-shafieAhmed El-shafie More articles by this author , Allison H. FeibusAllison H. Feibus More articles by this author , Mohammed Al-ToubatMohammed Al-Toubat More articles by this author , Navid LelaniNavid Lelani More articles by this author , SeyedBehzad JazayeriSeyedBehzad Jazayeri More articles by this author , Kashyap KoulKashyap Koul More articles by this author , Robert A. MarinoRobert A. Marino More articles by this author , Mark BandykMark Bandyk More articles by this author , Joseph CostaJoseph Costa More articles by this author , and K. C. BalajiK. C. Balaji More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000003237.19AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: Tobacco smoking has been established as a risk factor for a majority of cancers, representing one of the most important modifiable risk factors. However, the association between smoking and prostate cancer (PCa) remains unclear. We compared gene mutations using a next generation sequencing (NGS) database of smokers and non-smokers with PCa. METHODS: Data is derived from the American Association for Cancer Research Project Genomics Evidence Neoplasia Information Exchange (GENIE) registry. We included 1832 men with PCa in our study cohort, categorized as either smokers or non/never smokers. We compared the frequency of mutations (point mutations, copy number variations and structural variants) of 47 genes between the 2 groups. We also studied the association of the gene mutations with overall survival. Univariate and multivariate logistic regression analyses were conducted to identify factors associated with mortality. RESULTS: Within the study cohort, 1007 (55%) patients were non-smokers and the remaining 825 (45%) were smokers. Patients with a smoking history had a higher percentage of somatic mutations in PREX2 (p=0.018), PTEN (p=0.02), AGO2 (p=0.03), and KMT2C (p=0.04) compared to non-smokers. In contrast, non-smokers had a higher percentage of somatic mutations in APC (p=0.02) and KMT2A (p=0.04) compared to smokers. The mortality rate was significantly higher among the smoker population (p=0.006). The presence of metastatic disease at the time of diagnosis (OR 2.26, p<0.001), smoking history (OR 1.32, p=0.02), and PTEN somatic gene mutation (OR 1.89, p<0.001) were independent predictors of mortality among patients diagnosed with PCa (Table 1). CONCLUSIONS: PCa patients with a tobacco smoking history had significantly higher somatic mutations of PREX2, KMT2C, AGO2, and PTEN genes. Moreover, PTEN somatic gene mutation is linked to mortality among patients with PCa (Figure 1). Source of Funding: none © 2023 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 209Issue Supplement 4April 2023Page: e220 Advertisement Copyright & Permissions© 2023 by American Urological Association Education and Research, Inc.MetricsAuthor Information Ahmed El-shafie More articles by this author Allison H. Feibus More articles by this author Mohammed Al-Toubat More articles by this author Navid Lelani More articles by this author SeyedBehzad Jazayeri More articles by this author Kashyap Koul More articles by this author Robert A. Marino More articles by this author Mark Bandyk More articles by this author Joseph Costa More articles by this author K. C. Balaji More articles by this author Expand All Advertisement PDF downloadLoading ...

Ganglioglioma with adverse clinical outcome and atypical histopathological features were defined by alterations in PTPN11/KRAS/NF1 and other RAS-/MAP-Kinase pathway genes

Exome-wide sequencing studies recently described PTPN11 as a novel brain somatic epilepsy gene. In contrast, germline mutations of PTPN11 are known to cause Noonan syndrome, a multisystem disorder characterized by abnormal facial features, developmental delay, and sporadically, also brain tumors. Herein, we performed a deep phenotype-genotype analysis of a comprehensive series of ganglioglioma (GG) with brain somatic alterations of the PTPN11/KRAS/NF1 genes compared to GG with common MAP-Kinase signaling pathway alterations, i.e., BRAFV600E. Seventy-two GG were submitted to whole exome sequencing and genotyping and 84 low grade epilepsy associated tumors (LEAT) to DNA-methylation analysis. In 28 tumours, both analyses were available from the same sample. Clinical data were retrieved from hospital files including disease onset, age at surgery, brain localization, and seizure outcome. A comprehensive histopathology staining panel was available in all cases. We identified eight GG with PTPN11 alterations, copy number variant (CNV) gains of chromosome 12, and the commonality of additional CNV gains in NF1, KRAS, FGFR4 and RHEB, as well as BRAFV600E alterations. Histopathology revealed an atypical glio-neuronal phenotype with subarachnoidal tumor spread and large, pleomorphic, and multinuclear cellular features. Only three out of eight patients with GG and PTPN11/KRAS/NF1 alterations were free of disabling-seizures 2 years after surgery (38% had Engel I). This was remarkably different from our series of GG with only BRAFV600E mutations (85% had Engel I). Unsupervised cluster analysis of DNA methylation arrays separated these tumours from well-established LEAT categories. Our data point to a subgroup of GG with cellular atypia in glial and neuronal cell components, adverse postsurgical outcome, and genetically characterized by complex alterations in PTPN11 and other RAS-/MAP-Kinase and/or mTOR signaling pathways. These findings need prospective validation in clinical practice as they argue for an adaptation of the WHO grading system in developmental, glio-neuronal tumors associated with early onset focal epilepsy.

Incomplete hippocampal inversion in patients with mutations in genes involved in sonic hedgehog signaling

Sonic hedgehog (Shh) signaling pathways are known to play an important role in the morphological development of the hippocampus in vivo, but their actual roles in humans have not been clarified. Hypothalamic hamartoma (HH) is known to be associated with germline or somatic gene mutations of Shh signaling. We hypothesized that patients with HH and mutations of Shh-related genes also show hippocampal maldevelopment and an abnormal hippocampal infolding angle (HIA). We analyzed 45 patients (age: 1–37 years) with HH who underwent stereotactic radiofrequency thermocoagulation and found Shh-related gene mutations in 20 patients. In addition, 44 pediatric patients without HH (age: 2–25 years) who underwent magnetic resonance imaging (MRI) examinations under the same conditions during the same period were included in this study as a control group. HIA evaluated on MRI was compared between patients with gene mutations and the control group. The median HIA at the cerebral peduncle slice in patients with the gene mutation was 74.36° on the left and 76.11° on the right, and these values were significantly smaller than the corresponding values in the control group (80.46° and 80.56°, respectively, p < 0.01). Thus, mutations of Shh-related genes were correlated to incomplete hippocampal inversion. The HIA, particularly at the cerebral peduncle slice, is a potential indicator of abnormalities of the Shh-signaling pathway.

Distribution and prognostic impact of EGFR and KRAS mutations according to histological subtype and tumor invasion status in pTis-3N0M0 lung adenocarcinoma

BackgroundThe prognostic impact of EGFR mutation as major targetable somatic gene variant on lung adenocarcinoma is controversial. KRAS is another major somatic variant in lung adenocarcinoma, and a therapeutic agent for KRAS G12C became available in clinical settings. These mutations represent clinicopathological features of lung adenocarcinoma and can guide the treatment choice after recurrence. We evaluated the prognostic impact of EGFR and KRAS mutations by considering other clinicopathological recurrence risks in resected pTis-3N0M0 lung adenocarcinoma.MethodsClinicopathological features related to recurrence and genetic status were estimated in consecutive 877 resected cases. Recurrence-free survival (RFS), cumulative recurrence rate (CRR), and overall survival (OS) were compared. Uni- and multivariate analyses for RFS were performed after excluding cases with little or no recurrence risks.ResultsEGFR mutation was more likely to be harbored in female, never-smoker, or patients accompanied by > 5% lepidic component. KRAS mutation was more likely to be harbored in patients with current/ex-smoking history, International Association for the Study of Lung Cancer (IASLC) grade 3, or accompanied lymphatic or vascular invasion. In IASLC grade 2 and 3 patients, EGFR or KRAS mutation cases had significantly worse 5-year RFS than wild type patients (76.9% vs. 85.0%, hazard ratio [HR] = 1.55, 95% confidence interval [CI] = 1.62–6.41, P < 0.001). EGFR or KRAS mutation cases had significantly higher 5-year CRR than wild type patients (17.7% vs. 9.8%, HR = 1.69, 95% CI = 1.44–6.59, P = 0.0038). KRAS mutation cases had higher 5-year CRR than EGFR mutation cases (16.7% vs. 21.4%, HR = 1.62, 95% CI = 0.96–7.19, P = 0.061). There was no significant difference in OS between cohorts. Multivariate analysis revealed that a positive EGFR/KRAS mutation status was risk factor for worse RFS (HR = 2.007, 95% CI = 1.265–3.183, P = 0.003).ConclusionPositive EGFR and KRAS mutation statuses were risk factors for recurrence in resected IASLC grade 2 and 3 patients. KRAS mutations were more likely to be confirmed in cases with an increased risk of recurrence. EGFR and KRAS mutation statuses should be evaluated simultaneously when assessing the risk of recurrence.

Correlation between ARID1B gene mutation (p.A460, p.V215G) and prognosis of high-risk refractory neuroblastoma.

In a few reports, ARID1B/A mutation was found in neuroblastoma. We analyzed the clinical characteristics, clinical efficacy, and prognosis of three children with high-risk refractory neuroblastoma (NB) with somatic ARID1B gene mutation. The whole exon sequencing results showed that there were involved in transcription, DNA synthesis, and repair of ARID1B gene mutations. All mutation sites were located in the promoter region of the exon: ARID1B (p.A460) mutation was found in cases 1 and 2, and ARID1B (p.V215G) mutation was found in cases 1 and 3. The nucleic acid site of ARID1B (p.A460) mutation was c.1379 (exon1) C > G, and the nucleic acid site of ARID1B (p.V215G) mutation was c.644 (exon1) T > G. The meningeal metastasis in case 1 turned negative after 4 cycles of intrathecal injection combined with chemotherapy. However, the child died of agranulocytosis combined with sepsis during the 5th cycle of chemotherapy. Case 2 achieved complete remission (CR). Case 3 achieved CR after chemotherapy, surgery, metaiodobenzylguanidine, and 3F-8 (Naxitamab) immunotherapy after the initial diagnosis. The mediastinum and lymph node metastasis occurred during the 6-month observation period after stopping treatment. He achieved very good partial remission after individualized chemotherapy and surgical treatment. ARID1B is a component protein of the SWI/SNF chromatin-remodeling complex that participates in the occurrence of a variety of tumors by regulating DNA repair and synthesis. ARID1B nucleic acid mutation (p.A460, p.V215G) in the promoter region of three children may contribute to the poor prognosis of NB children.

Identification and Validation of a Necroptosis-Related Prognostic Signature for Kidney Renal Clear Cell Carcinoma.

Necroptosis is progressively becoming an important focus of research because of its role in the pathogenesis of cancer and other inflammatory diseases. Our study is designed to anticipate the survival time of kidney renal clear cell carcinoma (KIRC) by constructing a prognostic signature of necroptosis-related genes. Clinical information and RNA-seq data were acquired from Renal Cell Cancer-European Union (RECA-EU) and The Cancer Genome Atlas- (TCGA-) KIRC, respectively. ConsensusClusterPlus was used to identify molecular subtypes, and the distribution of immune cell infiltration, anticancer drug sensitivity, and somatic gene mutations was studied in these subtypes. Subsequently, LASSO-Cox regression and univariate Cox regression were also carried out to construct a necroptosis-related signature. Cox regression, survival analysis, clinicopathological characteristic correlation analysis, nomogram, cancer stem cell analysis, and receiver operating characteristic (ROC) curve were some tools employed to study the prognostic power of the signature. Based on the expression patterns of 66 survival-related necroptosis genes, we classified the KIRC into three subtypes (C1, C2, and C3) that are associated with necroptosis, which had significantly different tumor stem cell components. Among these, C2 patients had a longer survival time and enhanced immune status and were more sensitive to conventional chemotherapeutic drugs. Moreover, in order to predict the prognosis of KIRC patients, five genes (BMP8A, TLCD1, CLGN, GDF7, and RARB) were used to develop a necroptosis-related prognostic signature, which had an acceptable predictive potency. The results from Cox regression and stratified survival analysis revealed that the signature was an independent prognostic factor, whereas the nomogram and calibration curve demonstrated satisfactory survival time prediction based on the risk score. Three molecular subtypes and five necroptosis-related genes were discovered in KIRC using data from TCGA-KIRC and RECA-EU. Thus, a new biomarker and a potentially effective therapeutic approach for KIRC patients were provided in the current study.

Modeling the relationship between gene expression and mutational signature.

Mutational signatures computed from somatic mutations, allow an in-depth understanding of tumorigenesis and may illuminate early prevention strategies. Many studies have shown the regulation effects between somatic mutation and gene expression dysregulation. We hypothesized that there are potential associations between mutational signature and gene expression. We capitalized upon RNA-seq data to model 49 established mutational signatures in 33 cancer types. Both accuracy and area under the curve were used as performance measures in five-fold cross-validation. A total of 475 models using unconstrained genes, and 112 models using protein-coding genes were selected for future inference purposes. An independent gene expression dataset on lung cancer smoking status was used for validation which achieved over 80% for both accuracy and area under the curve. These results demonstrate that the associations between gene expression and somatic mutations can translate into the associations between gene expression and mutational signatures.

Abstract P2-26-06: Association between CK+/CD45+ circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) alterations in advanced breast cancer patients

Abstract Background: Circulating tumor cells (CTCs) in breast cancer (BC) are commonly defined as epithelial cells (EPCAM and cytokeratin (CK) positive), lacking the universal blood cell marker CD45. Nonetheless, CTCs expressing both CK and CD45 (= dual-positive, DP cells) can be observed in the blood of cancer patients. Early evidence suggests that DP cells might derive from the fusion of tumor cells and macrophages, and we have previously demonstrated that they present aberrant genomes and are associated with worse prognosis in BC [1,2]. Here, to further investigate the mechanisms/pathways underlying their presence, we analyzed the association between DP cells and circulating tumor DNA (ctDNA) alterations. Methods: Blood samples were collected from patients with advanced BC (aBC), before starting a new line of therapy. All patients were enrolled in a prospective clinical trial. For CTC and DP cells analysis, 7.5 ml of blood collected in CellSave® tubes was processed with the FDA-approved CellSearch® platform (positivity cutoffs were ≥1 cell for DPcells and ≥5 cells for CTCs). For ctDNA analysis, plasma was collected from Streck stabilizing tubes and analyzed with the Guardant360™ NGS platform for the detection of somatic single nucleotide variants (SNVs), insertions/deletions (indels), gene fusions/rearrangements and copy number variations (CNVs), which were then classified into pathways based on previously defined profiles generated on the Cancer Genome Atlas database (RTK, RAS, RAF, MEK, NRF2, ER, WNT, MYC, P53, cell cycle, notch, PI3K). Associations between ctDNA-detected gene alterations and circulating cell types were analyzed through chi square test, while mutant allele frequency (MAF) and number of detected alterations (NDA) were tested by Mann Whitney test. Results: We analyzed blood samples from 169 patients with luminal-like (n=80), HER2+ (n=34) and triple-negative (n=52) aBC. DPcells were detected in 85 patients (50.3 %, range 0-53), of which 40 (47 %) were CTC-positive and 45 (53%) CTC-negative. Somatic ctDNA alterations were detected in all analyzed samples. In the overall population, the presence of ≥1 DPcell was associated with SNVs in the cell cycle pathway (p = 0.043), a numerically higher incidence was also observed for CNVs in this pathway. SNVs and CNVs in the cell cycle pathway were associated with CTCs ≥ 5 as well (p = 0.005 and p = 0.003, respectively). Moreover, associations with CTCs ≥ 5 were observed for RTK SNVs and CNVs (p = 0.041 and p = 0.046, respectively), PI3K SNVs and CNVs (p = 0.006 and p = 0.007, respectively), MYC SNVs and CNVs (p = 0.042). No associations were observed in terms of MAF and NDA. In the luminal-like subgroup an association was highlighted for CNVs in the cell cycle pathway, p = 0.038. CTCs ≥ 5 were associated with PI3K SNVs (p = 0.031). In the triple-negative subgroup DPcells were associated with SNVs in the RAF pathway (p = 0.041), whereas CTCs ≥ 5 were associated with PI3K SNVs and CNVs (p = 0.044 and p = 0.024, respectively) and RTK SNVs (p = 0.008). In the HER2 positive subgroup, a higher MAF and number of detected SNVs was observed for samples with ≥1 DPcell (p = 0.0286 and p = 0.0099, respectively). Conclusions: The study analyzed ctDNA features associated with canonical and CK+/CD45+ CTCs, showing differential gene alteration profiles. Cell cycle pathway SNVs were common in both CTC populations, while other pathways (RTK, PI3K, MYC and RAF) were significantly altered in a mutually exclusive pattern. These results suggest that DPcells might have a different biological meaning compared to canonical CTCs. More studies need to be conducted to better characterize this understudied CTC subpopulation and understand their specific contribution to cancer progression.

Abstract PD17-02: ctDNA Molecular Response based on breast cancer driver mutations predicts progression in aromatase inhibitor-sensitive first line treatment of oestrogen receptor-positive (ER+) HER2-negative (HER2-) advanced breast cancer

Abstract Background: The combination of a CDK4/6 inhibitor and an aromatase inhibitor (AI) is the gold standard for AI-sensitive first line treatment of ER+ HER2- advanced breast cancer. Nevertheless, some patients progress rapidly and may benefit from alternative strategies. Early ctDNA dynamics have been shown to predict disease course in several clinical situations. Here, we use samples from the PADA-1 trial to assess this strategy for patients receiving AI and palbociclib as first line treatment. PADA-1 was designed to assess the clinical utility of sequential analysis of ctDNA for emerging ESR1 mutations to trigger an early switch from AI plus palbociclib to fulvestrant plus palbociclib treatment. The study included 1,017 patients and was positive on its primary end-point. The objective of this translational study was to analyze the predictive value of 4-week molecular response (MR) for patient progression. Material &amp; Method: First, a CLIA-validated targeted next-generation sequencing-based test (Guardant360 Response) was used to characterize changes in ctDNA level via detection of somatic single-nucleotide variants (SNVs), insertion/deletion mutations (indels), and gene fusions in 74 genes frequently mutated in cancer. A second analysis was restricted to cancer-associated mutations in 11 genes commonly mutated in breast cancer (PIK3CA, GATA3, TP53, AKT1, ERBB2, BRCA1, BRCA2, ATM, ESR1, PALB2 and RB1). The threshold for molecular response was defined as ≥ 50% decrease in ctDNA (MR score &amp;lt; 0.5). Subjects with ctDNA levels below the test’s limit of quantitation (ctDNA-low) were considered molecular responders. Results: 372 subjects with matched baseline and 4-weeks samples were available for analysis. Of these, 134 subjects (36%) were ctDNA-low, and 238 subjects (64%) quantifiable. Among the quantifiable subjects, 183 (77%) were molecular responders (MR+, MR &amp;lt; 0.5), and 55 (23%) were not (MR–, MR ≥ 0.5). PFS was moderately improved for both MR+ and ctDNA-low relative to MR– (HR=0.61 (95%CI 0.44-0.85), p&amp;lt; 0.01) over the full 29 months of follow up. Differential PFS event rate was observed only in the first 8 months following ctDNA assessment; during this time MR+ and ctDNA-low were associated with more significantly decreased risk of progression (HR 0.24, 95% CI 0.13 – 0.43, p=0.0001). Limiting ctDNA assessment to genes commonly mutated in breast cancer enhanced the predictive power of MR (HR=0.08, 95% CI 0.04 0.17, p&amp;lt; 0.001, for MR+ and ctDNA-low vs. MR– across 8 months post-assessment); however, fewer samples were quantifiable by this method (169 [45%] quantifiable; 203 [55%] ctDNA-low). Combining MR status with additional molecular features (e.g.tumor mutational burden and maximum mutation allele fraction) did not improve prediction of non-response. Conclusion: Changes in ctDNA fraction during the first weeks of treatment are predictive of long term clinical benefit on an individual patient basis, particularly during the first year of therapy. Adjusting the MR threshold and/or limiting to genes known to be relevant in the specific tumor can tailor the assessment of ctDNA change to specific clinical scenarios where greater sensitivity or specificity may be required. The identification of patients at high risk for early clinical failure at the onset of treatment may allow for therapy escalation and/or change to improve outcome in this population. Funding: Pfizer and Guardant Health Citation Format: Caroline Bailleux, Thomas Bachelot, Francois-Clement Bidard, Anne-Claire Hardy-Bessard, Ivan Bièche, Anne Pradines, Florian Clatot, thibault DE LA MOTTE ROUGE, Jean-Luc Canon, Barbara Pistilli, Kyle Chang, Katie J. Quinn, Heather L. Gustafson, Florence Dalenc, Cyril Foa, Hanifa Ammarguellat, Chantal Bernard-Marty, Brigitte Lucas, Sophie Barthier, Fabrice Lorchel, Olivier Gisserot, Laurent Arnould, Marjorie Mauduit, Jérôme Lemonnier, Frédérique Berger, Suzette Delaloge, Fabrice Andre. ctDNA Molecular Response based on breast cancer driver mutations predicts progression in aromatase inhibitor-sensitive first line treatment of oestrogen receptor-positive (ER+) HER2-negative (HER2-) advanced breast cancer. [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD17-02.

Abstract PD5-01: PD5-01 Genomic and epigenomic BRCA alterations predict adaptive resistance and response to platinum-based therapy in triple negative breast cancer and ovarian carcinoma

Abstract Background. Homologous recombination deficiency (HRD), induced by germline and somatic BRCA1 or BRCA2 gene mutations (BRCAmut) and by BRCA1 promoter methylation (BRCA1meth), has been associated with better response to platinum agents in both triple negative breast cancer (TNBC) and ovarian carcinoma (OvCa). A major conundrum arising from recent studies is why patients with BRCA1meth cancers do more poorly compared to those with BRCAmut cancers given the biologically equivalent HRD in both states. Here, we address this question by performing detailed genomic analyses of primary TNBC and OvCa cohorts and through patient-derived xenografts (PDXs) and their derivative cell lines. Methods. Both new and publicly available cohorts of primary TNBC and OvCa encompassing 499 individuals treated with a combination of platinum and taxane chemotherapy were analyzed by whole genome and transcriptome sequencing as well as limited epigenetic analyses. A cohort of 43 PDX models of TNBC was genomically characterized and responses to both single agent platinum and docetaxel were evaluated in vivo. PDX longitudinal studies were performed to assess the dynamics of BRCA1 methylation following treatment. Results. Genomic analyses revealed that BRCA1mut and BRCA1meth cancers share the same pattern of BRCA1-linked genomic rearrangements. Nonetheless, in all four primary cancer cohorts examined we found that patients with BRCAmut cancers, but not those with BRCA1meth cancers, had significantly better response outcomes compared to those with BRCA proficient cancers. A separate analysis of PDX TNBCs with BRCA1 promoter methylation showed that PDXs derived from treatment naïve cancers had complete methylation of the BRCA1 promoter, whereas those derived from post-treatment cancers invariably had only partial methylation. Compared to PDXs with complete methylation, those with partial methylation had a lower response rate to in vivo platinum-based therapy, but not to docetaxel. Using single cell clonal expansions from BRCA1meth PDX models, we confirmed that partial methylation was the result of demethylation of one of the BRCA1 promoter alleles and not of the outgrowth of a non-methylated clone. Exposure of TNBC PDXs with complete methylation to a single course of platinum therapy resulted in the emergence of an unmethylated BRCA1 promoter allele, which associated with an increase in BRCA1 expression. We confirmed that platinum treatment results in progressive loss of BRCA1 methylation and restoration of BRCA1 expression in the clinical setting, by studying the BRCA1 status of a longitudinal series of four TNBC PDX models established from the same patient at different stages of her clinical history. Differential gene expression analysis revealed an increased immune transcriptional signal, especially an elevated M1 macrophage signature, associated with enhanced response to platinum therapy only in patients with BRCA proficient cancers, in both TNBC and OvCa. Integrating both the strength of this cancer immune signature and the presence of BRCA mutations resulted in more accurate predictions of response when compared to either HRD or BRCA status alone. Conclusions. These results suggest that unlike BRCAmut cancers, where BRCA deficiency is more genetically stable, BRCA1meth cancers are highly adaptive to genotoxin exposure resulting in demethylation of one allele, recovery of BRCA1 expression and acquired insensitivity to platinum. On the other end, a high immune transcriptional signature identifies patients with BRCA proficient cancers that are more likely to benefit from platinum therapy. Taken together, our study underscores the importance of characterizing molecular heterogeneity to optimize predictive precision in assigning response probabilities in TNBC and OvCa. Citation Format: Francesca Menghi, Kalyan Banda, Pooja Kumar, Robert Straub, Lacey E. Dobrolecki, Isabel Rodriguez, Susan E. Yost, Harshpreet Chandok, Marc Radke, George Somlo, Yuan Yuan, Michael T. Lewis, Elizabeth Swisher, Edison Liu. PD5-01 Genomic and epigenomic BRCA alterations predict adaptive resistance and response to platinum-based therapy in triple negative breast cancer and ovarian carcinoma [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD5-01.

Abstract P1-06-07: Interrogating the Molecular Profile of Breast Cancer Tumors in Hispanics Living in Puerto Rico (PRH)

Abstract Breast cancer (BC) has the highest incidence and mortality rates among Puerto Rican women. However, the representation of Hispanics living in Puerto Rico (PRH) in breast cancer clinical trials may be limited due to the lack of a defined genetic profile from BC tumors in Puerto Rican patients. Mutations in genes associated with tumor suppressors, tumor progression, and genome stability are shared among all BCs. Nonetheless, differences in the frequency of these mutations have been observed among racial/ethnic groups. This study aims to characterize the genomic landscape of BC tumors in PRH and identify the most common genetic mutations. We conducted secondary data analysis to evaluate the mutational profile of 189 BC tumors from PRH who underwent NGS testing from 2015 to 2020 and compared the prevalence of breast tumor somatic mutations and gene amplifications with profiles reported for other races/ethnicities available through The Cancer Genome Atlas (TCGA) and the AACR Genomics Evidence Neoplasia Information Exchange (GENIE). The most mutated genes among PRH breast tumors were TP53, PIK3CA, ARID1A, NF1, and RB1, while the most frequent gene amplifications were FGF19, H3F3B, ZN703, MCL1, and ADGRA2. H1047R and E545K were the most frequent specific mutations in PRH for PIK3CA; R248Q and R273C for TP53 and Q1212*, S634* and Q557fs for ARID1A. Statistically significant differences were found between populations. This study reports a unique mutational profile of BC tumors in PRH and makes comparisons with non-Hispanic and USH populations, providing novel knowledge to increase Hispanic representation in future BC studies and treatments. Citation Format: Norianne Martinez-Viota, Xavier Bittman-Soto, Ingrid M. Montes-Rodriguez, Kelvin Carrasquillo, Hilmaris Centeno-Girona, Marcia Cruz-Correa. Interrogating the Molecular Profile of Breast Cancer Tumors in Hispanics Living in Puerto Rico (PRH) [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P1-06-07.

Abstract P3-05-10: Disease features, genomic profiles and outcomes of younger vs. older Chinese hormone receptor positive (HR+), HER2 negative (HER2-) metastatic breast cancer (MBC) patients

Abstract Background: Breast cancer in younger women has been characterized as a more aggressive disease with relatively poor outcomes compared to breast cancer in older women. This pattern has been attributed to a variety of clinicopathologic characteristics including the enrichment of aggressive HER2+ and TNBC subtypes in younger patients. However, similar to older breast cancer patients, the majority of young breast cancer patients are HR+/HER2-. Here we have evaluated the clinicopathologic characteristics and genomic profiles of real-world HR+/HER2- MBC patients to examine the determinants of outcome for younger vs. older patients in this subtype. Patients and Methods: This study included 65 Chinese patients presenting with HR+/HER2- MBC at the Peking University Cancer Hospital. Blood samples were collected upon metastatic disease diagnosis before treatment and profiled with the targeted 152-gene PredicineCARETM sequencing panel. Fourteen patients were &amp;lt; 40 years, 19 were 40-50 years, and 32 were &amp;gt; 50 years at the time of primary cancer diagnosis. Kaplan-Meier survival analysis was performed to analyze outcomes including overall survival (OS), disease free survival (DFS) and progression free survival (PFS) in association with clinicopathologic and genomic variables. OS was also evaluated in association with age in separate multivariate models using Cox proportional hazards regression. Results: Significant variation across age groups was observed for several clinicopathological features, including molecular subtype classification (p = 0.045), de novo Stage IV disease (p = 0.011), type of adjuvant endocrine therapy (p = 5.56E-06), resistance to adjuvant endocrine therapy (p = 0.015) and receipt of adjuvant chemotherapy (p = 0.042). Luminal B status was most frequent in patients &amp;lt; 40 years (92.31%), whereas de novo Stage IV disease was more prevalent in patients &amp;gt; 50 years (37.5%). Aromatase inhibitors (AIs) were administered as adjuvant endocrine therapy (ET) to 73.68% of women &amp;gt; 50 years vs. 16.67% and 0% of women aged 40-50 years and &amp;lt; 40 years, respectively. Resistance to adjuvant ET was observed in 23.08% of patients &amp;lt; 40 years but was not observed in the other age groups. Adjuvant chemotherapy was received by a higher proportion of patients in the 40-50 year age group (94.44%) compared to patients &amp;lt; 40 years (69.23%) and patients &amp;gt; 50 years (60%). No differences in somatic gene alteration frequencies were observed across age groups, menopausal status, germline mutation status or tumor grade. However, a higher frequency of FGFR1 alterations was observed in patients classified as Luminal B vs. A (p = 0.048). Comparison of profiles across women who received adjuvant ET revealed a higher prevalence of FGFR1 (p = 0.012), ATM (p = 0.047) and CCND2 (p = 0.04) alterations in patients treated with AIs vs. SERMS. In addition, a higher frequency of APC alterations was observed in patients with high (≥ 20%) vs. low (&amp;lt; 20%) Ki67 index (p = 0.035). At the univariate level OS was significantly associated with age (p = 0.039). OS was shortest in patients &amp;gt; 50 years, intermediate in patients &amp;lt; 40 years, and longest in patients 40-50 years. Across all patients, shorter OS was also associated with de novo Stage IV disease (p = 0.0001), Luminal B subtype (p = 0.008), adjuvant ET with AIs vs SERMS (p = 0.028) and the presence of an FGFR1 (p = 0.028) or CCND2 (p = 0.033) alteration. In multivariate analyses, OS remained significantly longer for patients aged 40-50 years after adjustment for de novo Stage IV disease, Luminal B subtype and FGFR1 status (all p &amp;lt; 0.05). Conclusions: In this group of real-world HR+/HER2- MBC breast cancer patients, younger age was not associated with worse outcomes. While current guidelines recommend treatment decisions based on tumor biology rather than age, young HR+ breast cancer patients are more likely to receive chemotherapy. Our findings support the development of biomarker-driven treatment strategies for these patients. Citation Format: Jinhao Wang, Yaxin Liu, Bin Shao, Hang Dong, Tiantian Zheng, Pan Du, Shidong Jia, Bonnie King, Jing Wang, Xiaoran Liu, Huiping Li. Disease features, genomic profiles and outcomes of younger vs. older Chinese hormone receptor positive (HR+), HER2 negative (HER2-) metastatic breast cancer (MBC) patients [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P3-05-10.

Low expression of E-Cadherin and CDH1 variants associated with diffuse gastric cancer.

Reduced or null expression of E-cadherin protein is a frequent cause of diffuse gastric cancer (DGC). More than 50% of patients with DGC present somatic variants in CDH1 gene. The objectives of this study were to study E-cadherin expression and identify variants in the CDH1 gene in gastric tumors of patients with DGC. We studied 18 Mexican DGC patients who attended a hospital of the Mexican Social Security Institute; E-cadherin expression was determined by immunohistochemistry, and variants were identified by Sanger sequencing in promoter and coding regions. Predictive analysis was performed using PolyPhen-2 and HOPE software. We found that 56% of DGC patients showed reduced expression of E-cadherin. All patients carried CDH1 variants; overall, 12 different CDH1 variants were identified. Predictive analysis revealed that the rs114265540 variant was probably damaging, with a value of 0.985, indicating a functional impact on the E-cadherin protein. Variants rs34939176 and rs33964119 were identified as risk factors for DGC (odds' ratios [OR] = 31.3, 95% CI 6.3-154.0, p < 0.001; OR = 6.1, 95% CI 2.0-19.0, p < 0.001, respectively) given their elevated frequency and by comparing it with those reported for MXL population in the 1000 Genomes Project database. In this Mexican population, the percentage of diffuse gastric tumors with reduced expression of E-cadherin was similar to that reported in other populations. All gastric tumors of DGC patients studied had somatic CDH1 gene variants; however, the rs114265540, rs34939176, and rs33964119 variants were importantly related to DGC.

A phase II single-arm trial of niraparib in platinum-sensitive metastatic castration-resistant prostate cancer with DNA repair defects (PLATPARP).

TPS291 Background: Platinum-based chemotherapy, either as monotherapy or in combination with taxanes, is increasingly used for patients with metastatic castration-resistant prostate cancer (mCRPC) harboring germline and/or somatic homologous recombination repair gene mutations (HRRm). However, clinical responses with platinum-based therapy are often of limited duration and limited by cumulative toxicities. The PARP inhibitor (PARPi) olaparib is approved for the treatment of mCRPC patients with pathogenic HRRm after progression on enzalutamide or abiraterone. Importantly, sensitivity to platinum-based chemotherapy may predict improved clinical outcomes with PARPi, and ‘maintenance’ PARPi strategies are routinely used in patients with advanced ovarian and pancreatic malignancies with HRRm with initial clinical response to platinum chemotherapy. We hypothesize that maintenance niraparib, a PARPi with demonstrated activity in mCRPC with HRRm, will prolong clinical responses to platinum-based chemotherapy with acceptable toxicity in mCRPC patients harboring germline and/or somatic HRRm. Methods: We are conducting an open-label, single-arm, phase II study to evaluate the clinical benefit of maintenance niraparib in biomarker-defined, platinum-sensitive mCRPC patients. Eligible subjects harbor a pathogenic germline and/or somatic mutation in BRCA1/2, ATM, FANCA, CDK12, RAD51B, RAD54L, PALB2, CHEK2, HDAC2, or BRIP1 and have received at least 3 cycles (or minimum 9 weeks) of platinum-based chemotherapy for the treatment of mCRPC per investigator discretion. Following ³4 weeks since completion of chemotherapy, subjects without evidence of clinical or radiographic disease progression receive investigational treatment with maintenance niraparib (starting dose 200 mg daily). The primary objective is an improvement in 6 month PFS rate (PFS6) (H0: PFS6 rate 25%; H1: PFS6 rate 50%; power 0.77 with one-sided α = 0.05). Serial plasma samples are obtained for correlative analyses of markers of response and/or resistance to maintenance niraparib. Eight of a planned total of 18 subjects have enrolled (N=3 germline BRCA2; N=2 somatic BRCA2; N=1 germline PALB2; N=1 germline ATM; N=1 germline CHEK2). This study incorporates a novel, combined genetic and clinical patient-selection approach for PARPi therapy to optimize clinical outcomes. Clinical trial information: NCT04288687 .

Gene Therapy for Ataxias

Ataxias are progressive diseases that are usually the result of cerebellar degeneration. Ataxias are divided into genetic, sporadic degenerative and acquired (secondary) forms. While there are established therapies for acquired (secondary) ataxias, genetic and sporadic degenerative ataxias are currently not medically treatable. For these ataxias, the development of somatic gene therapies is a promising avenue. The goals of gene therapies for genetic ataxias are to inactivate deleterious genes by gene silencing or to replace or correct a non-functional gene. Another option, which may also be considered for sporadic degenerative ataxias, are therapies that involve transferring new or modified genes. Gene therapies are being actively developed for the more common ataxias, such as Friedreich's ataxia, certain spinocerebellar ataxias, and multiple system atrphy, and initial phase I trials are underway.

A fair experimental comparison of neural network architectures for latent representations of multi-omics for drug response prediction

BackgroundRecent years have seen a surge of novel neural network architectures for the integration of multi-omics data for prediction. Most of the architectures include either encoders alone or encoders and decoders, i.e., autoencoders of various sorts, to transform multi-omics data into latent representations. One important parameter is the depth of integration: the point at which the latent representations are computed or merged, which can be either early, intermediate, or late. The literature on integration methods is growing steadily, however, close to nothing is known about the relative performance of these methods under fair experimental conditions and under consideration of different use cases.ResultsWe developed a comparison framework that trains and optimizes multi-omics integration methods under equal conditions. We incorporated early integration, PCA and four recently published deep learning methods: MOLI, Super.FELT, OmiEmbed, and MOMA. Further, we devised a novel method, Omics Stacking, that combines the advantages of intermediate and late integration. Experiments were conducted on a public drug response data set with multiple omics data (somatic point mutations, somatic copy number profiles and gene expression profiles) that was obtained from cell lines, patient-derived xenografts, and patient samples. Our experiments confirmed that early integration has the lowest predictive performance. Overall, architectures that integrate triplet loss achieved the best results. Statistical differences can, overall, rarely be observed, however, in terms of the average ranks of methods, Super.FELT is consistently performing best in a cross-validation setting and Omics Stacking best in an external test set setting.ConclusionsWe recommend researchers to follow fair comparison protocols, as suggested in the paper. When faced with a new data set, Super.FELT is a good option in the cross-validation setting as well as Omics Stacking in the external test set setting. Statistical significances are hardly observable, despite trends in the algorithms’ rankings. Future work on refined methods for transfer learning tailored for this domain may improve the situation for external test sets. The source code of all experiments is available under https://github.com/kramerlab/Multi-Omics_analysis

Impact of genome and epigenome on intratumor heterogeneity in colorectal cancer

Impact of genome and epigenome on intratumor heterogeneity in colorectal cancer

Engineered biocontainable RNA virus vectors for non-transgenic genome editing across crop species and genotypes

CRISPR/Cas genome-editing tools provide unprecedented opportunities for basic plant biology research and crop breeding. However, the lack of robust delivery methods has limited the widespread adoption of these revolutionary technologies in plant science. Here, we report an efficient, non-transgenic CRISPR/Cas delivery platform based on the engineered tomato spotted wilt virus (TSWV), an RNA virus with a host range of over 1000 plant species. We eliminated viral elements essential for insect transmission to liberate genome space for accommodating large genetic cargoes without sacrificing the ability to infect plant hosts. The resulting non-insect-transmissible viral vectors enabled effective and stable in planta delivery of Cas12a and Cas9 nucleases as well as adenine and cytosine base editors. In systemically infected plant tissues, the deconstructed TSWV-derived vectors induced efficient somatic gene mutations and base conversions in multiple crop species with little genotype dependency. Plants with heritable, bi-allelic mutations could be readily regenerated by culturing the virus-infected tissues in vitro without antibiotic selection. Moreover, we showed that antiviral treatment with ribavirin during tissue culture cleared the viral vectors in 100% of regenerated plants and further augmented the recovery of heritable mutations. Because many plants are recalcitrant to stable transformation, the viral delivery system developed in this work provides a promising tool to overcome gene delivery bottlenecks for genome editing in various crop species and elite varieties.