Molecular Aberrations Research Articles

SEAMARK: phase II study of first-line encorafenib and cetuximab plus pembrolizumab for MSI-H/dMMR BRAFV600E-mutant mCRC.

Patients with both BRAF V600E mutations and microsatellite instability-high (MSI-H)/mismatch repair-deficient (dMMR) metastatic colorectal cancer (mCRC) have poor prognosis. Currently, there are no specifically targeted first-line treatment options indicated for patients with mCRC whose tumors harbor both molecular aberrations. Pembrolizumab is a checkpoint inhibitor approved for the treatment of MSI-H/dMMR mCRC, and the BRAF inhibitor encorafenib, in combination with cetuximab, is approved for previously treated BRAF V600E-mutant mCRC. Combination of pembrolizumab with encorafenib and cetuximab may synergistically enhance antitumor activity in patients with BRAF V600E-mutant, MSI-H/dMMR mCRC. SEAMARK is a randomized phase II study comparing the efficacy of the combination of pembrolizumab with encorafenib and cetuximab versus pembrolizumab alone in patients with previously untreated BRAF V600E-mutant, MSI-H/dMMR mCRC.

Patient-derived organoid culture in epithelial ovarian cancers-Techniques, applications, and future perspectives.

Epithelial ovarian cancer (EOC) is a heterogeneous disease composed of different cell types with different molecular aberrations. Traditional cell lines and mice models cannot recapitulate the human tumor biology and tumor microenvironment (TME). Patient-derived organoids (PDOs) are freshly derived from patients' tissues and are then cultured with extracellular matrix and conditioned medium. The high concordance of epigenetic, genomic, and proteomic landscapes between the parental tumors and PDOs suggests that PDOs can provide more reliable results in studying cancer biology, allowing high throughput drug screening, and identifying their associated signaling pathways and resistance mechanisms. However, despite having a heterogeneity of cells in PDOs, some cells in TME will be lost during the culture process. Next-generation organoids have been developed to circumvent some of the limitations. Genetically engineered organoids involving targeted gene editing can facilitate the understanding of tumorigenesis and drug response. Co-culture systems where PDOs are cultured with different cell components like immune cells can allow research using immunotherapy which is otherwise impossible in conventional cell lines. In this review, the limitations of the traditional in vitro and in vivo assays, the use of PDOs, the challenges including some tips and tricks of PDO generation in EOC, and the future perspectives, will be discussed.

Different gene alterations in patients with non-small-cell lung cancer between the eastern and southern China

Geographical differences are conspicuous in lung cancer, and the distinct molecular features of lung tumor between Western patients and Asian patients have been demonstrated. However, the etiology of non-small-cell lung cancer (NSCLC) and the distribution of associated molecular aberrations in China have not been fully elucidated. The mutational profiles of 12 lung cancer-related genes were investigated in 85 patients from eastern China and 88 patients from southern China who had been histologically confirmed NSCLC. Overall, 93.6% (162/173) of tumor samples harbored at least one somatic alteration. The most frequently mutated genes were TP53 (56.1%), EGFR (50.3%), and KRAS (14.5%). We found that EGFR mutated much more frequently (60.0% vs 40.9%, P = 0.012) and TP53 mutations had significantly lower incidence (47.1% vs 64.8%, P = 0.019) in eastern cohort than that in southern cohort. Mutational signature analysis revealed a region-related mutagenesis mechanism characterized by a high prevalence of C to T transitions mainly occurring at CpG dinucleotides in southern patients. This study reveals the difference in the mutational features between NSCLC patients in eastern and southern China. The distinct patterns of gene mutation could provide clues for the mechanism of carcinogenesis of lung cancer, offering opportunities to stratify patients into optimal treatment plans based on genomic profiles.

Clear Cell Adenocarcinoma of Urethra: Clinical and Pathologic Implications and Characterization of Molecular Aberrations.

This study aimed to evaluate the molecular features of clear cell adenocarcinoma (CCA) of the urinary tract and investigate its pathogenic pathways and possible actionable targets. We retrospectively collected the data of patients with CCA between January 1999 and December 2016; the data were independently reviewed by two pathologists. We selected five cases of urinary CCA, based on the clinicopathological features. We analyzed these five cases by whole exome sequencing (WES) and subsequent bioinformatics analyses to determine the mutational spectrum and possible pathogenic pathways. All patients were female with a median age of 62 years. All tumors were located in the urethra and showed aggressive behavior with disease progression. WES revealed several genetic alterations, including driver gene mutations (AMER1, ARID1A, CHD4, KMT2D, KRAS, PBRM1, and PIK3R1) and mutations in other important genes with tumor-suppressive and oncogenic roles (CSMD3, KEAP1, SMARCA4, and CACNA1D). We suggest putative pathogenic pathways (chromatin remodeling pathway, mitogen-activated protein kinase signaling pathway, phosphoinositide 3-kinase/AKT/mammalian target of rapamycin pathway, and Wnt/β-catenin pathway) as candidates for targeted therapies. Our findings shed light on the molecular background of this extremely rare tumor with poor prognosis and can help improve treatment options.

AML with CEBPA mutations: A comparison of ICC and WHO-HAEM5 criteria in patients with 20% or more blasts

AML with CEBPA mutation and AML with in-frame bZIP CEBPA mutations define favorable-risk disease entities in the proposed 5th edition of the World Health Organization Classification (WHO-HAEM5) and the International Consensus Classification (ICC), respectively. However, the impact of these new classifications on clinical practice remains unclear. We sought to assess the differences between the ICC and WHO-HAEM5 for AML with CEBPA mutation. 741 AML patients were retrospectively analyzed. Cox proportional-hazard regression was used to identify factors predictive of outcome. A validation cohort from the UK-NCRI clinical trials was used to confirm our findings. 81 (11%) AML patients had CEBPA mutations. 39 (48%) patients met WHO-HAEM5 criteria for AML with CEBPA mutation, among which 30 (77%) had biallelic CEBPA mutations and 9 (23%) had a single bZIP mutation. Among the 39 patients who met WHO-HAEM5 criteria, 25 (64%) also met ICC criteria. Compared to patients only meeting WHO-HAEM5 criteria, patients with in-frame bZIP CEBPA mutations (ie. meeting both WHO-HAEM5 and ICC criteria) were younger, had higher bone marrow blast percentages and CEBPA mutation burden, infrequently harboured 2022 ELN high-risk genetic features and co-mutations in other genes, and had superior outcomes. The associations in clinicopathological features and outcomes between the CEBPA-mutated groups were validated in the UK-NCRI cohort. Our study indicates that in-frame bZIP CEBPA mutations are the critical molecular aberrations associated with favorable outcomes in AML patients treated with curative intent chemotherapy. Compared to WHO-HAEM5, the ICC identifies a more homogenous group of CEBPA-mutated AML patients with favorable outcomes.

Mutational landscape of cancer-driver genes across human cancers

The genetic mutations that contribute to the transformation of healthy cells into cancerous cells have been the subject of extensive research. The molecular aberrations that lead to cancer development are often characterised by gain-of-function or loss-of-function mutations in a variety of oncogenes and tumour suppressor genes. In this study, we investigate the genomic sequences of 20,331 primary tumours representing 41 distinct human cancer types to identify and catalogue the driver mutations present in 727 known cancer genes. Our findings reveal significant variations in the frequency of cancer gene mutations across different cancer types and highlight the frequent involvement of tumour suppressor genes (94%), oncogenes (93%), transcription factors (72%), kinases (64%), cell surface receptors (63%), and phosphatases (22%), in cancer. Additionally, our analysis reveals that cancer gene mutations are predominantly co-occurring rather than exclusive in all types of cancer. Notably, we discover that patients with tumours displaying different combinations of gene mutation patterns tend to exhibit variable survival outcomes. These findings provide new insights into the genetic landscape of cancer and bring us closer to a comprehensive understanding of the underlying mechanisms driving the development of various forms of cancer.

Molecular genetic aberrations in the pathogenesis of multiple myeloma.

Multiple myeloma (MM) is the second most common form of blood cancer characterized by clonal expansion of malignant plasma cells within the bone marrow. MM is a complex, progressive, and highly heterogeneous malignancy, which occurs via a multistep transformation process involving primary and secondary oncogenic events. Recent advances in molecular techniques have further expanded our understanding of the mutational landscape, clonal composition, and dynamic evolution patterns of MM. The first part of this review describes the key oncogenic events involved in the initiation and progression of MM, together with their prognostic impact. The latter part highlights the most prominent findings concerning genomic aberrations promoted by gene expression profiling (GEP) and next-generation sequencing (NGS) in MM. This review provides a concise understanding of the molecular pathogenesis of the MM genome and the importance of adopting emerging molecular technology in future clinical management of MM.

Investigation of Clinically Significant Molecular Aberrations in Patients with Prostate Cancer: Implications for Personalized Treatment, Prognosis and Genetic Testing.

The data on tumor molecular profiling of European patients with prostate cancer is limited. Our aim was to evaluate the prevalence and prognostic and predictive values of gene alterations in unselected patients with prostate cancer. The presence of gene alterations was assessed in patients with histologically confirmed prostate cancer using the ForeSENTIA® Prostate panel (Medicover Genetics), targeting 36 clinically relevant genes and microsatellite instability testing. The primary endpoint was the prevalence of gene alterations in homologous recombination repair (HRR) genes. Overall, 196 patients with prostate cancer were evaluated (median age 72.2 years, metastatic disease in 141 (71.9%) patients). Gene alterations were identified in 120 (61%) patients, while alteration in HRR genes were identified in 34 (17.3%) patients. The most commonly mutated HRR genes were ATM (17, 8.7%), BRCA2 (9, 4.6%) and BRCA1 (4, 2%). The presence of HRR gene alterations was not associated with advanced stage (p = 0.21), age at diagnosis (p = 0.28), Gleason score (p = 0.17) or overall survival (HR 0.72; 95% CI: 0.41-1.26; p = 0.251). We identified clinically relevant somatic gene alterations in European patients with prostate cancer. These molecular alterations have prognostic significance and therapeutic implications and/or may trigger genetic testing in selected patients. In the era of precision medicine, prospective research on the predictive role of these alterations for innovative treatments or their combinations is warranted.

Uterine leiomyoma with RAD51B::NUDT3 fusion: a report of 2 cases

Three main uterine leiomyoma molecular subtypes include tumors with MED12 mutation, molecular aberrations leading to HMGA2 overexpression, and biallelic loss of FH. These aberrations are mutually exclusive and can be found in approximately 80–90% of uterine leiomyoma, in which they seem to be a driver event. Approximately 10% of uterine leiomyoma, however, does not belong to any of these categories. Uterine leiomyoma with HMGA2 overexpression is the most common subtype in cellular and second most common category of usual leiomyoma. In some of these tumors, rearrangement of HMGA2 gene is present. The most common fusion partner of HMGA2 gene is RAD51B. Limited data suggests that RAD51B fusions with other genes may be present in uterine leiomyoma. In our study, we described two cases of uterine leiomyoma with RAD51B::NUDT3 fusion, which occur in one case of usual and one case of highly cellular leiomyoma. In both cases, no other driver molecular aberrations were found. The results of our study showed that RAD51::NUDT3 fusion can occur in both usual and cellular leiomyoma. RAD51B may be a fusion partner of multiple genes other than HMGA2 and HMGA1. In these cases, RAD51B fusion seems to be mutually exclusive with other driver aberrations defining molecular leiomyoma subtypes. RAD51B::NUDT3 fusion should be added to the spectrum of fusions which may occur in uterine leiomyoma, which can be of value especially in cellular leiomyoma in the context of differential diagnosis against endometrial stromal tumors.

P-328 Endometrial receptivity in women with endometriosis undergoing Assisted Reproductive Technology (ART) after frozen embryo transfer: a matched pair case-control study

Abstract Study question Does endometriosis affect endometrial receptivity in frozen/thawed embryo transfer (FET) cycles? Summary answer Stage III/IV endometriosis-patients undergoing ART submitted to FET cycles have implantation, pregnancy and live-birth rates, as well as pregnancy outcomes, similar to control women. What is known already The increased infertility rate observed in women with endometriosis is supposed to be linked, among other factors, to molecular alterations already documented in the endometrial tissue of these affected women. These alterations might influence the interaction between the embryo and the endometrium, leading to a compromised implantation; however, data from the literature are controversial and do not always corroborate the hypothesis of a lower implantation rate in women with endometriosis. Study design, size, duration This is a retrospective matched case-control study including 101 women diagnosed with stage III/IV endometriosis. They were matched in a 1:1 ratio with patients undergoing frozen embryo transfers after ART treatments for other infertility-related indications at the Fondazione IRCCS Ca’Granda Ospedale Maggiore Policlinico di Milano, between 2015 and 2022. Participants/materials, setting, methods Patients (n = 202) were submitted to ovarian stimulation according to standard protocols and only single embryo transfer cases and the 1st ART cycle with freeze-all protocol were included. To match, it was considered the women's age ( ± 1 year), and the number ( = ) and quality ( ± 1 top vs low) of blastocysts obtained in each cycle, considering the Istanbul consensus as the embryo standard assessment protocol. The main outcome evaluated in this study was implantation rate. Main results and the role of chance Baseline characteristics did not significantly vary between the two study groups, except for AMH levels, which was considerably lower in the endometriosis group compared to control (4.0 [2.7 - 5.4] vs 4.6 [3.7 - 6.5], respectively; p = 0.03). Considering the treatment outcomes, the number of oocytes inseminated/injected in each cycle was similar between endometriosis and control group (8 [7 - 10] vs 9 [7 - 11], respectively; p = 0.26). In line with the matching performed, the number of blastocysts generated did not differ between women with and without endometriosis (3 [2 - 4] vs 3 [2 - 4], respectively; p = 1.00), as well as the number of top-quality blastocysts (2 [1 - 3] vs 2 [1 - 3], respectively; p = 0.76). In regard to our main outcome evaluated, implantation rate in women with endometriosis and their controls were similar (36% vs 40%, respectively; p = 0.52). There was also no difference between the endometriosis group and controls considering cumulative pregnancy outcomes, such as pregnancy rate (58% vs 65%, respectively; p = 0.39), cumulative live birth rate (51% vs 59%, respectively; p = 0.26), pregnancy complications (6% vs 14%, respectively; p = 0.34), and pregnancy loss (16% vs 19%, respectively; p = 0.70). Limitations, reasons for caution As it is a retrospective study, our reports might be subjected to misclassification bias. Also, some of the women in the control group may have asymptomatic undiagnosed endometriosis; however, considering the incidence of this disease, it should not compromise our evaluation. Wider implications of the findings Our present findings give support to the idea that endometriosis does not influence the implantation rate in women with endometriosis undergoing ART submitted to FET. Considering fertility, this finding raises doubts about the clinical relevance of the molecular aberrations detected in the endometrium of women affected by endometriosis. Trial registration number not applicable

Molecular and immune landscape of hepatocellular carcinoma to guide therapeutic decision-making.

Liver cancer, primarily HCC, exhibits highly heterogeneous histological and molecular aberrations across tumors and within individual tumor nodules. Such intertumor and intratumor heterogeneities may lead to diversity in the natural history of disease progression and various clinical disparities across the patients. Recently developed multimodality, single-cell, and spatial omics profiling technologies have enabled interrogation of the intertumor/intratumor heterogeneity in the cancer cells and the tumor immune microenvironment. These features may influence the natural history and efficacy of emerging therapies targeting novel molecular and immune pathways, some of which had been deemed undruggable. Thus, comprehensive characterization of the heterogeneities at various levels may facilitate the discovery of biomarkers that enable personalized and rational treatment decisions, and optimize treatment efficacy while minimizing the risk of adverse effects. Such companion biomarkers will also refine HCC treatment algorithms across disease stages for cost-effective patient management by optimizing the allocation of limited medical resources. Despite this promise, the complexity of the intertumor/intratumor heterogeneity and ever-expanding inventory of therapeutic agents and regimens have made clinical evaluation and translation of biomarkers increasingly challenging. To address this issue, novel clinical trial designs have been proposed and incorporated into recent studies. In this review, we discuss the latest findings in the molecular and immune landscape of HCC for their potential and utility as biomarkers, the framework of evaluation and clinical application of predictive/prognostic biomarkers, and ongoing biomarker-guided therapeutic clinical trials. These new developments may revolutionize patient care and substantially impact the still dismal HCC mortality.

MDB-35. RECURRENT MEDULLOBLASTOMA A RARE COMPLETE RESPONSE IN EXTRA NEURAL DISEASE

Abstract Extra-neural metastasis in recurrent medulloblastoma, carries a potentially fatal outcome. No robust salvageable therapeutic strategy is present, for these clinical phenotypes. We present an 18-year male, who presented at the age of 8 years as a standard risk medulloblastoma and was treated with chemotherapy (as per ACNS0331) followed by craniospinal radiation. At first recurrence in the thoracic spine, he underwent a gross total resection of the tumor, followed by high-dose stem cell chemotherapy and focal radiation. The 2nd recurrence which occurred in the thecal sac 9 years later was treated with metronomic anti angiogenic chemotherapy with outcome a complete radiographic response. Third recurrence occurred in the liver, bone marrow, multiple bones of axial skeleton and sacrum. Molecular interrogation of the lesions showed a (non-WNT / non-SHH subtype) with absence of MYC or MYCN amplification or any other clinically significant biological aberration. He received local radiation to tumors, following which he developed severe myelosuppression. A bone marrow aspirate and biopsy showed greater than 95% involvement with medulloblastoma cells. He was treated with irinotecan and temozolomide. A dramatic response was noted after one cycle (with PET and MRI), with bone marrow involvement of less than 1%. He continues with that therapy. To-date no defined molecular profile is predictive of extra neural metastasis, and has been likened to a fatal outcome, most patients being declared for hospice care. Our patient with this unique clinical outcome, warrants extensive evaluation of these rare clinical phenotypes including methylation profiling and RNA sequencing, which might suggest, certain molecular aberrations which correlates with good response, even in these biologically aggressive variants.

MDB-04. SINGLE-CELL TRANSCRIPTOMIC ANALYSIS REVEALS DISTINCT GENOMIC LANDSCAPES, CELL TRAJECTORIES, AND TUMOUR-MICROENVIRONMENT INTERACTIONS IN FOUR SUBTYPES OF MEDULLOBLASTOMA

Abstract Medulloblastoma is the most common paediatric high-grade brain tumour, which comprises four different molecular subtypes (SHH, Wnt, Group 3, and Group 4), each defined by different molecular characteristics, genomic aberrations, and prognosis. High levels of inter- and intra-tumoural heterogeneity, together with the detrimental side effects caused by the current medulloblastoma treatments, need to be addressed in order to develop more personalised treatments and improve the quality of life of these patients. In this study, we analysed single-cell RNA sequencing data from 14 medulloblastoma patients, comprising all four molecular subtypes. We found that these tumours exhibit great levels of heterogeneity with regard to their copy number variation (CNV) profiles analysed using Numbat, as well as immune cell infiltration and composition within these tumours. Tumour-infiltrating immune cells represented a heterogeneous population comprised of monocytes, M1- and M2-like macrophages, dendritic cells, and microglia. Our ligand-receptor analysis also identified a subset of immune cells that send EGF signals to the tumour clusters, potentially contributing to the tumour growth. In addition, we showed that the tissue of origin of the immune cells found within the tumour microenvironment and their medulloblastoma subgroup specificity greatly influence their clustering when projected onto a UMAP. We also found that the clustering of tumour cells is influenced by their CNV levels. Finally, we performed RNA velocity analysis and identified subgroup-specific cell trajectories for each medulloblastoma subtype. As predicted, identified cell trajectories demonstrated that cells move in a direction of increasing CNV levels, making it possible to visualise and track the tumour progression and identify genetic markers specific to either earlier or later tumour stages. Overall, our study underlines high levels of inter-tumoural heterogeneity in medulloblastoma. It also provides opportunities for the identification of subgroup-specific biomarkers for the early stages of medulloblastoma, potentially contributing to the discovery of novel drug targets.

Primary testicular lymphoma demonstrates overexpression of the Wilms tumor 1 gene and different mRNA and miRNA expression profiles compared to nodal diffuse large B-cell lymphoma.

Diffuse large B-cell lymphoma (DLBCL) shows a high degree of clinical and biological heterogeneity. Primary testicular lymphoma (PTL) is an extranodal variant of DLBCL associated with a higher risk of recurrence, including contralateral testicles and central nervous system sanctuary sites. Several molecular aberrations, including somatic mutation of MYD88, CD79B, and upregulation of NF-kB, PDL-1, and PDL-2, are thought to contribute to the pathogenesis and poor prognosis of PTL. However, additional biomarkers are needed that may improve the prognosis and help understand the PTL biology and lead to new therapeutic targets. RNA from diagnostic tissue biopsies of the PTL-ABC subtype and matched nodal DLBCL-ABC subtype patients was evaluated by mRNA and miRNA expression. Screening of 730 essential oncogenic genes was performed, and their epigenetic connections were examined using the nCounter PAN-cancer pathway, and Human miRNA assays with the nCounter System (NanoString Technologies). PTL and nodal DLBCL patients were comparable in age, gender, and putative cell of origin (p>0.05). Wilms tumor 1 (WT1) expression in PTL exceeded that in nodal DLBCL (>6-fold; p=0.01, FDR <0.01) and WT1 associated pathway genes THBS4, PTPN5, PLA2G2A, and IFNA17 were upregulated in PTL (>2.0-fold, p<0.01, FDR <0.01). Additionally, miRNAs targeting WT1 (hsa15a-5p, hsa-miR-16-5p, has-miR-361-5p, has-miR-27b-3p, has-miR-199a-5p, has-miR-199b-5p, has-miR-132-3p, and hsa-miR-128-3p) showed higher expression in PTL compared to nodal DLBCL (≥2.0-fold; FDR 0.01). Lower expression of BMP7, LAMB3, GAS1, MMP7, and LAMC2 (>2.0-fold, p<0.01) was observed in PTL compared to nodal DLBCL. This research revealed higher WT1 expression in PTL relative to nodal DLBCL, suggesting that a specific miRNA subset may target WT1 expression and impact the PI3k/Akt pathway in PTL. Further investigation is needed to explore WT1's biological role in PTL and its potential as a therapeutic target.

Third-Line Palliative Systemic Therapy for Advanced Biliary Tract Cancer: Multicentre Review of Patterns of Care and Outcomes.

Phase 3 trials have established standard first-line (1L) and 2L systemic therapy options for patients with advanced biliary cancer (ABC). However, a standard 3L treatment remains undefined. Clinical practice and outcomes for 3L systemic therapy in patients with ABC were therefore evaluated from three academic centres. Included patients were identified using institutional registries; demographics, staging, treatment history, and clinical outcomes were collected. Kaplan-Meier methods were used to assess progression-free survival (PFS) and overall survival (OS). Ninety-seven patients, treated between 2006 and 2022, were included; 61.9% had intrahepatic cholangiocarcinoma. At the time of analysis, there had been 91 deaths. Median PFS from initiating 3L palliative systemic therapy (mPFS3) was 3.1 months (95%CI 2.0-4.1), while mOS3 was 6.4 months (95%CI 5.5-7.3); mOS1 was 26.9 months (95%CI 23.6-30.2). Among patients with a therapy-targeted molecular aberration (10.3%; n = 10; all received in 3L), mOS3 was significantly improved versus all other included patients (12.5 vs. 5.9 months; p = 0.02). No differences in OS1 were demonstrated between anatomical subtypes. Fourth-line systemic therapy was received by 19.6% of patients (n = 19). This international multicentre analysis documents systemic therapy use in this select patient group, and provides a benchmark of outcomes for future trial design.

Phase II study of niraparib in patients with advanced melanoma with genetic homologous recombination (HR) mutation/alteration.

TPS9596 Background: There are a limited number of therapeutic options available for metastatic melanoma patients progressing on the checkpoint inhibitor(s) and BRAF-targeting drugs. PARP inhibitors have been approved in the setting of BRCA1/2 germline mutations, and have demonstrated activity in the setting of HR deficiency in other cancers. Documentation of PARP inhibitors in melanoma would have clear clinical impact. We have previously shown that 21-34% of metastatic melanomas harbor at least 1 molecular aberration in the HR pathway, considered pathogenic, and likely leading to HR deficiency. Previously, we demonstrated dramatic regression of tumors harboring HR mutation(s) with PARP inhibitor treatment in a PDX model. These findings provide a strong rationale to evaluate the clinical efficacy of a PARP inhibitor in patients with advanced melanoma with HR deficiency. Methods: This is a single arm, open-label, multi-center phase II trial. The primary objective of the study is: To evaluate the clinical efficacy of niraparib in advanced melanoma patients with HR deficiency. The secondary objectives is to evaluate PFS, OS, and safety profile of niraparib. The key eligibility criteria: Advanced melanoma patients with mutation in any of the following: ARID1A/B, ARID2, ATM, ATR, ATRX, BARD1, BRCA1/2, BAP1, BRIP1, CHEK2, FANCD2, MRN11A, RAD50, RAD51, RAD54B, PALB2 (requires a genetic analysis result performed at any CLIA-certified laboratory) disease progression on PD1-antibody therapy and if BRAF mutant, BRAF/MEK inhibitors ≥ 18 years of age; ECOG PS ≤ 1; prior systemic cytotoxic therapy ≤1 regimen; no limit on number of prior immunotherapy or targeted therapy regimens. No symptomatic brain metastasis; active brain lesions ≥6 mm size, or requiring steroid treatment Patients will be treated with oral niraparib once daily (28-day cycle); the dose will be 300 mg (if weight ≥77 kg and platelet counts of ≥150,000 µL); otherwise 200 mg RECIST 1.1 will be used to evaluate clinical response every 8 weeks. Adverse events will be recorded according to CTCAE version 4.03. The primary study endpoint is overall response rate. Simon’s optimal 2-stage design is proposed. With significance level of5% and 80% power, our null hypothesis that the true response rate is 0.10 will be tested against a one-sided alternative: H0: p ≤ 10%, a response rate of no real interest VS H1: p ≥ 30%, a response rate that would be of considerable interest 10 patients will be analyzed for a response evaluation in the first stage of the study, and 19 in the second stage, for a total of 29 patients. If the response rate is 10% (1/10) or less at the end of the first stage, further accrual will be terminated. With 2 or more responses in the first stage, accrual will continue to a total of 29 patients for this cohort. The null hypothesis will be rejected if ≥6 responses are observed in a cohort of 29 subjects. Clinical trial information: NCT03925350 .

WS02.01 Decreased fertility in female cystic fibrosis patients: peering into the endometrial factor using cutting-edge organoid models

Female CF patients suffer from sub-to infertility, often facing problems to become pregnant. Underlying reasons remain understudied. In particular, it is largely unknown whether dysfunction of the endometrium is involved, the womb’s inner lining and key tissue for embryo implantation and development. This gap is mainly due to lack of appropriate study models. Therefore, we develop and apply tissue-mimicking organoid models to indetail decipher molecular and functional aberrations in fertility-deficient CF endometrium as compared to healthy (fertile) endometrium. First, we established endometrial organoids (EMO) from the Cftrtm1Eur mouse model. These organoids show a smaller lumen than wildtype (WT) EMO, and do not swell in the FIS assay, both validating the CFTR defect. Currently, we are comparing expression of endometrial functionality/fertility markers in CF versus WT EMO, as well as their responsiveness to estrogen (E2) and progesterone (P4), which in vivo regulate the estrous cycle. Second, we develop(ed) organoids from CF patient endometrium. Before, we have shown that EMO from healthy endometrium can reliably reproduce all menstrual cycle phases under defined E2/P4 exposure. Currently, we are deciphering whether and how menstrual cycle phases, including the receptivity stage, are different between CF and healthy EMO. We already observed dissimilarities in the proliferative (E2) and secretory (P4) phase, such as increased apoptosis and decreased fertility marker expression, respectively. Taken together, we establish(ed) organoid models from CF endometrium as novel and powerful tools to gain insight into the endometrial factor in CF fertility deficiency. Importantly, the organoids will be highly apt to explore the impact of new-era CFTR modulators on the endometrium, at present unknown. Moreover, our study has the potential to reveal paths toward restoring reproductive fitness in CF patients, which can be tested using the organoids as (drug) screening platform.

Tumor mutational burden as a predictive biomarker for molecularly matched therapy in two independent pan-cancer cohorts.

3066 Background: Personalized cancer therapy based on molecular tumor aberrations has shown efficacy in a subset of tumors. Novel biomarkers are warranted to help extend this benefit to a larger patient population. Tumor mutational burden (TMB) is an established predictive biomarker for immune checkpoint inhibition. Its role for molecularly matched therapy is unknown. Methods: Comprehensive molecular profiling including whole-exome and RNA-sequencing was performed in 104 patients with advanced cancer within the DKTK MASTER program. 55 patients received a systemic therapy excluding immunotherapy. TMB and survival were analyzed in patients receiving molecularly matched therapy (n=34) or non-molecularly matched therapy (n=21) as well as in an independent published cohort of patients receiving molecularly matched (n=68) or non-molecularly matched (n=40) therapy (excluding immunotherapy). TMB and co-occurring driver mutations were analyzed in the DKTK MASTER cohort. Results: The median TMB of 1.68 mutations per megabase (mut/Mb) in the 34 patients receiving molecularly matched therapy was used to stratify patients into TMB-high and -low groups. Median overall survival (OS) and progression-free survival (PFS) were significantly shorter in the TMB-high than in the TMB-low group (OS: 4 months [95% CI, 3.3 to 7.6] versus 19 months [95%CI, 10.0 to not reached] p &lt; 0.001, Hazard Ratio (HR) 4.4 [95%CI, 1.9 to 10.2], p&lt;0.001; PFS 1.8 months [95%CI, 1.1 to 3.6] versus 8.5 months [95% CI, 2.8 to 17.0] p = 0.004, HR 2.9 [95%CI, 1.4 to 6.2], p=0.005). No significant differences were observed in patients receiving non-molecularly informed systemic therapy (OS HR 0.7 [95%CI, 0.2 to 2.6], p=0.635 and PFS HR 1.2 [95%CI, 0.4 to 3.5] p=0.701). In the validation cohort, shorter progression-free survival was also identified in the TMB-high group (median TMB cut-off of 4 mut/Mb; HR 2.2 [95%CI, 1.3 to 3.7] p=0.005) treated with molecularly matched therapy but not with non-molecularly informed therapy (HR 1.1 [95%CI, 0.5 to 2.2] p=0.848). TMB was associated with co-occurring driver mutations (n=104, r = 0.78 [95%CI, 0.68 to 0.85], p&lt;0.001). Conclusions: High TMB was previously established as a positive predictive biomarker associated with efficacy of immune checkpoint inhibitor treatments. Our study reveals high TMB as a negative predictive biomarker associated with low efficacy of molecularly informed systemic therapy, potentially due to co-occurring driver mutations. Thus, TMB is a candidate predictive pan-cancer biomarker for combined precision oncology and immunotherapy programs.

Treatment phase stratified outcomes of core binding factor acute myeloid leukemia.

e19055 Background: Mutations in core binding factor (CBF) are associated with a favorable prognosis in acute myeloid leukemia (AML). However, between 30-40% of patients with CBF-AML relapse, and relative outcomes with each subsequent line of therapy remain unclear. Additionally, the overall survival of CBF-AML compared to other favorable risk molecular aberrations — such as NPM1mut and CEBPA — is unknown in light of the addition of monoallelic CEBPA in ELN 2022. Therefore, the purpose of this study was to clarify the outcomes of CBF-AML relative to other favorable risk aberrations and to determine the relative overall survival associated with each subsequent relapse. Methods: We retrospectively analyzed 46 consecutive patients with CBF-AML treated from January 2013 to January 2022 at VCU Massey Cancer Center that underwent intensive chemotherapy (IC) with or without gemtuzumab ozogamicin. During the same study period, we analyzed a comparison cohort of 272 consecutive patients: 103 ELN 2017 intermediate-risk patients, 111 adverse-risk patients, eight patients with mono- or biallelic mutations in CEBPA, and 50 with ELN 2017 favorable-risk NPM1mut. All patients were treated with front-line IC. We analyzed survival by the Kaplan-Meier method and compared groups with the log-rank test. Results: We analyzed 46 patients with CBF-AML across 136 treatment phases. Patients with CBF-AML had superior overall survival compared to patients with NPM1mut (median overall survival not reached at a median follow-up time of 5.0 years versus 21.0 m., p = 0.028). There were no differences in survival between CBF-AML and AML with monoallelic or biallelic mutations in CEBPA at a median follow-up time of 3.7 years (not reached, p = 0.976). Expectedly, the overall survival for CBF-AML was superior to ELN 2017 intermediate (30.1 m., p = 0.011) and adverse (10.9 m., p &lt; 0.0001) risk disease. Next, we analyzed survival trends in the relapsed or refractory setting for CBF-AML by lines of therapy, using ELN 2017 intermediate and adverse risk cohorts as a comparison. During the first relapse, CBF-AML was associated with a significantly superior overall survival compared to the adverse cohort (19.1 m. versus 10.0 m., p = 0.024) but not the intermediate cohort (14.5 m., p = 0.734). The absence of KITmut was not associated with improved survival compared to the ELN 2017 intermediate category at the first relapse ( p = 0.610). At the second relapse, the survival disparity disappeared between the CBF-AML and adverse risk groups (7.7 m. vs 4.0 m., p = 0.964). Conclusions: CBF-AML was associated with similar survival to mono- or biallelic mutations in CEBPA, and significantly prolonged overall survival compared to NPM1mut. Relative to a matched cohort of adverse-risk AML at the time of the first relapse, outcomes of relapsed CBF-AML remain favorable. The relative overall survival benefit of CBF-AML disappeared at the time of the second relapse.

Patterns of actionable biomarker testing in lung cancer patients: Disparity or an opportunity for improvement.

e21211 Background: In 2018, lung cancer represented about 13% of new cancer diagnosis but was still the leading cause of cancer deaths at 25%. In the last five years, rates of new cases of lung cancer have decreased by 11% and survival has increased 21% nationally; largely due to advancements in screening, diagnosis and expanding treatment modalities, including targeted therapies geared toward specific molecular alterations. Despite these advancements, there are still shortcomings in terms of next generation sequencing (NGS) utilization for detection of molecular aberrations. A recent query of 37,925 patients with stage IV non-small cell lung cancer (NSCLC), diagnosed between 2010 and 2018 discovered that only 22% of all patients had any molecular testing. Only 3% of these patients received any form of targeted therapy. This further illustrates the ongoing gap between molecular diagnostics and its clinical utilization. Methods: Our project serves to assess this shortcoming in our patient population. In this retrospective chart review and quality improvement project, the goal was to identify the limitations that led to delays or omittance of timely NGS in patients with newly diagnosed NSCLC. Under an IRB approval, a system was created where once a biopsy was confirmed to be NSCLC, tissue was sent for NGS. Prior to this intervention, molecular testing had to be ordered by an Oncologist after the patient was seen in clinic, generally during their first outpatient appointment or when discussed in multidisciplinary meetings. Additionally, testing was shifted from individual molecular studies, which would frequently exhaust tissue sample, to only comprehensive panels. Results: The charts of 194 patients with newly diagnosed NSCLC between 2014 and 2022 were analyzed. Of these patients, 125 patients (64.4%) had completion of at least one molecular test. 36 patients (18.6%) had only been tested for programmed death-ligand 1 (PDL1) and 33 patients (17.0%) had no immunohistochemical or molecular testing following biopsy results. The time from biopsy to completion of molecular testing was compared to 34 patients following implementation of our protocol. The median time from biopsy to availability of results was 29 days before our intervention and decreased to 23 days afterwards. Additionally, molecular testing increased to 100% in our newly diagnosed NSCLC patient population. Conclusions: As the genomic revolution continues and the importance of targeted therapy for NSCLC in both the adjuvant and metastatic setting progresses, timely next generation sequencing will be paramount for optimal treatment selection. Our project shows that through the implementation of systems codeveloped between medical oncology and anatomic pathology, turnaround times of molecular testing can be greatly improved and widely implemented.