Heterozygous Germline Mutations Research Articles

#1193 Tracking kidney cancer initiation via somatic mutation analysis of pre-cancer cells from Von Hippel Lindau cancer predisposition syndrome

Abstract Background and Aims Somatic mutations promote the transition from a normal cell to a cancer clone. Little is known about the factors that promote mutation in normal tissues, but whole genome sequencing of pre-cancer cells, followed by mutational pattern analyses, is a revolutionary tool to understand somatic mutation mechanisms active during an individual's lifetime. In the kidney, we have shown that normal kidney tubule epithelial cells (TEC) derived from damaged PT display an excess of somatic mutations and a peculiar enrichment of mutations in exons and highly transcribed DNA compared to other cell types [1]. However, the direct contribution of this PT-specific mutational process to carcinogenesis needs further demonstration. Here, we have analyzed normal TEC that are genetically predisposed to evolve into clear cell renal cell carcinoma (ccRCC), as they harbor a germline heterozygous mutation in the tumor suppressor Von Hippel Lindau, VHL. Using this genetic model of tumor predisposition, we have tracked the PT-specific mutational process from normal cells to overt ccRCC. This study sheds light on the etiology of this mutational process, as well as its causative role in ccRCC. Method We detected somatic mutations in single genomes from normal kidney TEC from 8 control individuals and 7 VHL-disease patients in the age range 24-70. Different from our previous study [1], we isolated kidney tubule cells from the urine. Multiple TECs per individual were subjected to in vitro clonal expansion, followed by whole genome sequencing (WGS), a golden-standard method to obtain high confidence somatic mutation data. We analyzed concomitant somatic mutation- and gene expression-data from 58 clones, and expression data from 154 TEC clones. Results First, we compared our newly generated dataset (TECs obtained from urines) with our previous dataset (TECs obtained from kidney biopsies). QPCR measurements of marker gene expression and somatic mutational pattern analyses showed that the same two populations could be clonally expanded from both urines and kidney biopsies. One population expressed markers of proximal tubule (AQP1, SLC17A3) and tubule damage (VCAM1, KIM1), and showed an excess of somatic single base substitutions (SBSs). This TEC population was defined: VCAM1-PT cells. We characterized the types of SBSs that are more frequently found in VCAM1-PT genomes. The mutation spectrum was different from that induced by exposure to common mutagens, e.g. aristolochic acid, reactive oxygen species and tobacco. Normal cells, including TEC, fat and blood progenitors, showed mutation depletion in highly transcribed genes, in agreement with more efficient repair. Instead, VCAM1-PT cells showed an enrichment of specific SBS types, distinct from those induced by another transcription-coupled mutational process described in the liver. In vitro exposure of TECs to the alkylating agent ENU recapitulates some features of the spectrum of mutations observed in vivo, suggesting that VCAM1-PT cells might fail to repair damage induced by endogenous alkylating agents. The VCAM1-PT-specific mutational signature was observed in ccRCC, but not found in a variety of non-kidney cell-types and cancers. Importantly, the impact of the mutational signature was more evident in VCAM1-PT genomes from VHL-disease patients compared to similar samples from control individuals. Moreover, VCAM1-PT cells were more common (8-fold increase, chi squared test P = .026) in the urines of VHL-disease patients than in the urines of controls. Conclusion Our data show that TECs derived from damaged PTs are subjected to a specific somatic mutation process during adult life. The process is a distinctive feature of kidney cancer (ccRCC) genomes, and is more evident in patients affected by VHL-cancer predisposition syndrome. These data suggest that heterozygous loss of VHL facilitates a PT-specific, somatic mutation process involved in cancer initiation.

Pediatric-type high-grade gliomas with PDGFRA amplification in adult patients with Li-Fraumeni syndrome: clinical and molecular characterization of three cases

Li-Fraumeni syndrome (LFS) is an autosomal dominant tumor predisposition syndrome caused by heterozygous germline mutations or deletions in the TP53 tumor suppressor gene. Central nervous system tumors, such as choroid plexus tumors, medulloblastomas, and diffuse gliomas, are frequently found in patients with LFS. Although molecular profiles of diffuse gliomas that develop in pediatric patients with LFS have been elucidated, those in adults are limited. Recently, diffuse gliomas have been divided into pediatric- and adult-type gliomas, based on their distinct molecular profiles. In the present study, we investigated the molecular profiles of high-grade gliomas in three adults with LFS. These tumors revealed characteristic histopathological findings of high-grade glioma or glioblastoma and harbored wild-type IDH1/2 according to whole exome sequencing (WES). However, these tumors did not exhibit the key molecular alterations of glioblastoma, IDH-wildtype such as TERT promoter mutation, EGFR amplification, or chromosome 7 gain and 10 loss. Although WES revealed no other characteristic gene mutations or copy number alterations in high-grade gliomas, such as those in histone H3 genes, PDGFRA amplification was found in all three cases together with uniparental disomy of chromosome 17p, where the TP53 gene is located. DNA methylation analyses revealed that all tumors exhibited DNA methylation profiles similar to those of pediatric-type high-grade glioma H3-wildtype and IDH-wildtype (pHGG H3-/IDH-wt), RTK1 subtype. These data suggest that high-grade gliomas developed in adult patients with LFS may be involved in pHGG H3-/IDH-wt. PDGFRA and homozygous alterations in TP53 may play pivotal roles in the development of this type of glioma in adult patients with LFS.

Familial isolated pituitary adenoma is independent of Ahr genotype in a novel mouse model of disease

Human familial isolated pituitary adenoma (FIPA) has been linked to germline heterozygous mutations in the gene encoding the aryl hydrocarbon receptor-interacting protein (AIP, also known as ARA9, XAP2, FKBP16, or FKBP37). To investigate the hypothesis that AIP is a pituitary adenoma tumor suppressor via its role in aryl hydrocarbon receptor (AHR) signaling, we have compared the pituitary phenotype of our global null Aip (AipΔC) mouse model with that of a conditional null Aip model (Aipfx/fx) carrying the same deletion, as well as pituitary phenotypes of Ahr global null and Arnt conditional null animals. We demonstrate that germline AipΔC heterozygosity results in a high incidence of pituitary tumors in both sexes, primarily somatotropinomas, at 16 months of age. Biallelic deletion of Aip in Pit-1 cells (Aipfx/fx:rGHRHRcre) increased pituitary tumor incidence and also accelerated tumor progression, supporting a loss-of-function/loss-of-heterozygosity model of tumorigenesis. Tumor development exhibited sexual dimorphism in wildtype and Aipfx/fx:rGHRHRcre animals. Despite the role of AHR as a tumor suppressor in other cancers, the observation that animals lacking AHR in all tissues, or ARNT in Pit-1 cells, do not develop somatotropinomas argues against the hypothesis that pituitary tumorigenesis in AIP-associated FIPA is related to decreased activities of either the Ahr or Arnt gene products.

Abstract 1410: An effect of Phenylalanine hydroxylase (PAH) deficiency on cancer development in kidney

Abstract Several studies have noted the importance of amino acid metabolism in cancer progression. Preliminary research using public cancer multi-omics data has revealed associations between heterozygous germline mutations in genes associated with amino acid metabolism and cancer development. In particular, the heterozygous status of the PAH gene enhances the risk of developing kidney cancer by more than three times. Phenylalanine hydroxylase (PAH) is an enzyme that converts phenylalanine to tyrosine. It is highly expressed in the liver and kidneys. Analysis of the blood metabolome in prospectively collected PAH heterozygous carriers indicates that heterozygous status causes metabolome fluctuations in the body. By the way, renal cell carcinoma (RCC) is an immunogenic tumor mainly infiltrated by T cells. Accordingly, we suggest that defects in the PAH gene change the metabolites in the body, leading to a reduction in immune function and an increased risk of developing kidney cancer. First, the expression of the PAH protein was confirmed through immunohistochemistry in a tissue microarray from RCC patients, and the results were then compared with clinical information. Next, we simulated the environment of PAH deficiency in vitro by treating the cells with phenylalanine (Phe) and its metabolite, phenylpyruvate (PRA), which accumulates during PAH dysfunction. The cytotoxicity of Phe and PPA was investigated using the WST assay. The Jurkat T cell line was cultured long-term in a medium containing Phe or PPA and then stimulated with PHA/PMA. Cytokine secretion was confirmed in these supernatants. In addition, purified primary human pan T cells were stimulated with Anti-CD3/CD28 in the medium containing either Phe or PPA. Proliferation was evaluated using CFSE staining. The IHC was performed on 467 tissues from RCC patients aged 29 to 101 years. We classified the cases into three scale scores based on the percentage of PAH intensity. Approximately 73% of cases were PAH-negative, and only 27% were positive (score 1+ or 2+). A comparison of IHC results with clinical information showed that lower PAH expression was associated with a lower relapse-free survival rate. Next, Phe and PPA exhibited minimal cytotoxicity. The secretion of representative proinflammatory cytokines IL-2 and TNF- α were dose-dependent and significantly decreased with Phe and PPA treatment. Additionally, cell proliferation, a critical step in acquiring effector functions of T cells, was inhibited by treatment with Phe and PPA, particularly in the CD8+ T cell population compared to CD4+ T cells. These results suggest that metabolite changes within the tissue microenvironment of the kidney, caused by Pah defects, may suppress anti-tumor immunity by impairing the function of immune cells. This novel discovery may contribute to the importance of the PAH gene as a new biomarker for diagnosing kidney cancer and to the development of kidney cancer therapy. Citation Format: Seojeong Kim, Jihyun Park, Jeongmin Park, Chaelin Kang, Kyung Chul Moon, Seung Seok Han, Youngil Koh, Sung-Soo Yoon. An effect of Phenylalanine hydroxylase (PAH) deficiency on cancer development in kidney [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1410.

Abstract 1468: Low exposures to amphibole or serpentine asbestos in germline Bap1-mutant mice induce mesotheliomacharacterized by an immunosuppressive tumor microenvironment

Abstract The purpose of this study was to determine if minimal exposures to amphibole (crocidolite) and serpentine (chrysotile) asbestos fibers significantly increase the incidence and rate of malignant mesothelioma (MM) onset in mice with a germline heterozygous Bap1 mutation, and to assess the effect of the resulting gene × environment interactions on the tumor immune microenvironment (TIME). The studies were carried out by chronically injecting intraperitoneally Bap1+/- and Bap1+/+ (wild-type, WT) mice with minimal doses of asbestos (in some experiments, as low as 0.0125 mg x 8 injections; total, 0.1 mg/mouse) and then monitoring the mice for tumor formation for up to 90 weeks. Pro-inflammatory and pro-tumorigenic factors in the TIME were evaluated by immunohistochemistry (IHC) and immunofluorescence (IF) for immune cell markers. With either type of asbestos and at each dose tested, MMs occurred at a significantly higher rate and earlier onset time in Bap1-mutant mice than in WT littermates. MMs from mice injected with chrysotile, but less so with crocidolite, had widespread adhesions in the peritoneal cavity owing to an overwhelming immune response, particularly at the higher dose used. IHC staining demonstrated an increased number of immune cells in granulomas and MMs. In particular, pro-inflammatory M1 macrophages were found mainly in granulomas, whereas pro-tumorigenic M2 macrophages were predominant in MMs. IF staining revealed that the relative number of M2 macrophages was strikingly greater in chrysotile-induced than crocidolite-induced MMs, suggesting that chrysotile induces a more profound immune response. MMs from Bap1-mutant mice showed upregulation of both CD39/CD73-adenosine and Ccl2/Ccr2 pathways, which collectively are known to mechanistically create favorable conditions for neoplastic transformation, invasion, and the development of an immunosuppressive TIME, in part by attracting M2 macrophages. This implies that chemoprevention and immunotherapy strategies targeting these pro-tumorigenic immune pathways could be beneficial in BAP1 mutation carriers. In conclusion, we provide evidence that low-level exposures to either chrysotile or crocidolite in germline Bap1 heterozygous mice result in a markedly increased risk of MM characterized by an immunosuppressive tumor microenvironment. Drawing parallels to humans, these experimental findings suggest that exposure of BAP1 mutation carriers to even minimal doses of different forms of asbestos may be associated with significantly enhanced susceptibility to MM. Citation Format: Yuwaraj Kadariya, Eleonora Sementino, Maggie Ruan, Mitchell Cheung, Andres J. Klein-Szanto, Kathy Cai, Joseph R. Testa. Low exposures to amphibole or serpentine asbestos in germline Bap1-mutant mice induce mesotheliomacharacterized by an immunosuppressive tumor microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1468.

Clinical Characteristics of Cryopyrin-Associated Periodic Syndrome and Long-Term Real-World Efficacy and Tolerability of Canakinumab in Japan: Results of a Nationwide Survey.

We assess the clinical characteristics of patients with cryopyrin-associated periodic syndrome (CAPS) in Japan and evaluate the real-world efficacy and safety of interleukin-1 (IL-1) inhibitors, primarily canakinumab. Clinical information was collected retrospectively, and serum concentrations of canakinumab and cytokines were analyzed. A total of 101 patients were included, with 86 and 15 carrying heterozygous germline and somatic mosaic mutations, respectively. We identified 39 mutation types, and the common CAPS-associated symptoms corresponded with those in previous reports. Six patients (5.9% of all patients) died, with four of the deaths caused by CAPS-associated symptoms. Notably, 73.7% of patients (100%, 79.6%, and 44.4% of familial cold autoinflammatory syndrome, Muckle-Wells syndrome, and chronic infantile neurological cutaneous articular syndrome/neonatal onset multisystem inflammatory disease, respectively) achieved complete remission with canakinumab, and early therapeutic intervention was associated with better auditory outcomes. In some patients, canakinumab treatment stabilized the progression of epiphysial overgrowth and improved height gain, visual acuity, and renal function. However, 23.7% of patients did not achieve inflammatory remission with crucial deterioration of organ damage, with two dying while receiving high-dose canakinumab treatment. Serological analysis of canakinumab and cytokine concentrations revealed that the poor response was not related to canakinumab shortage. Four inflammatory nonremitters developed inflammatory bowel disease (IBD)-unclassified during canakinumab treatment. Dual biologic therapy with canakinumab and anti-tumor necrosis factor-α agents was effective for IBD- and CAPS-associated symptoms not resolved by canakinumab monotherapy. This study provides one of the largest epidemiologic data sets for CAPS. Although early initiation of anti-IL-1 treatment with canakinumab is beneficial for improving disease prognosis, some patients do not achieve remission despite a high serum concentration of canakinumab. Moreover, IBD may develop in CAPS after canakinumab treatment.

Germline variants of DNA repair and immune genes in lymphoma from lymphoma-cancer families.

The genetic predisposition to lymphoma is not fully understood. We identified 13 lymphoma-cancer families (2011-2021), in which 27 individuals developed lymphomas and 26 individuals had cancers. Notably, male is the predominant gender in lymphoma patients, whereas female is the predominant gender in cancer patients (p = .019; OR = 4.72, 95% CI, 1.30-14.33). We collected samples from 18 lymphoma patients, and detected germline variants through exome sequencing. We found that germline protein truncating variants (PTVs) were enriched in DNA repair and immune genes. Totally, we identified 31 heterozygous germline mutations (including 12 PTVs) of 25 DNA repair genes and 19 heterozygous germline variants (including 7 PTVs) of 14 immune genes. PTVs of ATM and PNKP were found in two families, respectively. We performed whole genome sequencing of diffuse large B cell lymphomas (DLBCLs), translocations at IGH locus and activation of oncogenes (BCL6 and MYC) were verified, and homologous recombination deficiency was detected. In DLBCLs with germline PTVs of ATM, deletion and insertion in CD58 were further revealed. Thus, in lymphoma-cancer families, we identified germline defects of both DNA repair and immune genes in lymphoma patients.

Case Report: Unusual pulmonary involvement in a patient with Costello syndrome

Costello syndrome (CS) is a rare disease with intellectual disability, characterized by failure to thrive, short stature, joint laxity, loose soft skin, and distinctive facial features. This disease is caused by heterozygous germline mutations in the HRAS proto-oncogene. Cardiac and neurological abnormalities are the most common. Cardiovascular manifestations include valvular pulmonary stenosis, arrhythmia and hypertrophic cardiomyopathy. Neurological manifestations are dominated by hydrocephalus, seizures, and tethered spinal cord. Respiratory system manifestations have been reported in people with CS, but a full description of the different lung involvement and respiratory symptoms in these patients is not available. We report the case of a 19-year-old non-smoking man, followed for a Costello syndrome since the age of 8 months, who complained of exertional dyspnea and chest pain for over 18 months. The chest CT scan showed bullous emphysema of the left lung with a giant bulla in the left upper lobe measured than 20 cm long axis responsible for passive atelectasis. Pulmonary function tests revealed a severe non-reversible obstructive ventilatory defect. Faced with the worsening of his dyspnea despite treatment with bronchodilators and recurrent respiratory infections, it was decided to surgically remove the the giant emphysematous bulla. After bullectomy, a clinical and functional respiratory improvement was noted.

Exploiting Synthetic Lethality between Germline BRCA1 Haploinsufficiency and PARP Inhibition in JAK2V617F-Positive Myeloproliferative Neoplasms.

Myeloproliferative neoplasms (MPN) are rare hematologic disorders characterized by clonal hematopoiesis. Familial clustering is observed in a subset of cases, with a notable proportion exhibiting heterozygous germline mutations in DNA double-strand break repair genes (e.g., BRCA1). We investigated the therapeutic potential of targeting BRCA1 haploinsufficiency alongside the JAK2V617F driver mutation. We assessed the efficacy of combining the PARP inhibitor olaparib with interferon-alpha (IFNα) in CRISPR/Cas9-engineered Brca1+/- Jak2V617F-positive 32D cells. Olaparib treatment induced a higher number of DNA double-strand breaks, as demonstrated by γH2AX analysis through Western blot (p = 0.024), flow cytometry (p = 0.013), and confocal microscopy (p = 0.071). RAD51 foci formation was impaired in Brca1+/- cells compared to Brca1+/+ cells, indicating impaired homologous recombination repair due to Brca1 haploinsufficiency. Importantly, olaparib enhanced apoptosis while diminishing cell proliferation and viability in Brca1+/- cells compared to Brca1+/+ cells. These effects were further potentiated by IFNα. Olaparib induced interferon-stimulated genes and increased endogenous production of IFNα in Brca1+/- cells. These responses were abrogated by STING inhibition. In conclusion, our findings suggest that the combination of olaparib and IFNα presents a promising therapeutic strategy for MPN patients by exploiting the synthetic lethality between germline BRCA1 mutations and the JAK2V617F MPN driver mutation.

A rare case of cervical gastric-type adenocarcinoma mimicking bilateral ovarian malignancy in a genetically confirmed Peutz-Jeghers syndrome without known polyposis

Abstract Introduction/Objective Cervical gastric-type adenocarcinoma (GAS) is rare and accounts for 2-4% of cervical cancer. GAS is usually sporadic but can be associated with Peutz-Jeghers syndrome (PJS), a rare autosomal dominant disorder caused by germline STK11 mutations and characterized by hamartomatous polyposis in the gastrointestinal (GI) tract, mucocutaneous pigmentation, and cancer predisposition. Although cases of GAS may occur in patients with PJS associated with polyposis, our patient with GAS has an unusual and perhaps unique association with the PJS mutation that is unassociated with polyposis. Methods/Case Report A 33-year-old female presented with abdominal pain, abnormal uterine bleeding, vaginal discharge, weight loss, and fatigue for one year. Pigmentations were noted on lips, gum, tongue, and hands. She had a family history of maternal ovarian and pancreatic cancers. Computerized tomography revealed large bilateral multiloculated complex cystic adnexal masses, thickened endometrium extending into the endocervix, and ascites. Tumor markers showed increased CA19-9 and CA125, suggesting either a primary ovarian malignancy or possible metastatic GI tract cancer to both ovaries. Her PAP smear demonstrated atypical glandular cells that favored endocervical origin. HPV was not detected. A cervical biopsy showed bland gastric-type glands without obvious stromal invasion. Given the clinical concern for malignancy, a cervical cone biopsy was performed, demonstrating unequivocal invasion by gastric-appearing glands. The tumor cells were positive for CK7, CEA, and PAX8, and were negative for CK20, CDX2, and p16. The pathologic diagnosis confirmed a primary GAS with a spread to bilateral ovaries. Although the upper GI tract and left colon were free of polyps or masses by endoscopic exam, the genetic evaluation revealed a germline heterozygous STK11 mutation consistent with PJS. Results (if a Case Study enter NA) NA Conclusion To our knowledge, this is the first case of occult PJS (confirmed by genetic analysis) presenting with widely advanced metastatic GAS without known polyposis.

Conserved and Unique Regulatory Mechanisms of RUNX1 in Hematopoietic Stem/Progenitor Cell Subpopulations in Both Normal Hematopoiesis and FPD/AML Development

RUNX1 is a RUNT domain core-binding factor indispensable for the establishment of definitive hematopoiesis in vertebrate. In humans, heterozygous RUNX1 germline mutations are closely associated with Familial Platelet Disorder with propensity to develop AML (FPD/AML), a rare autosomal dominant disorder characterized by thrombocytopenia, platelet dysfunction, and markedly elevated risk for myelodysplastic syndrome and leukemia. RUNX1 regulates hematopoietic genes directly or indirectly, acting as a context-dependent activator or repressor of gene transcription. Here we have examined how RUNX1 regulates various subpopulations of hematopoietic stem/progenitor cells (HSPCs) to provide important insights into its physiologic and pathogenic roles and mechanisms.We used two complementary mouse models: a conditional RUNX1 knockout mouse, i,e, Mx-Cre;Runx1flox/flox, and a tetracycline-inducible FPD/AML patient derived RUNX1 S291fsX300 mutation knock-in crossed to a MLL-PTD knock-in mouse, i.e. MLL-PTD;RUNX1 S291fsX300. We monitored hematopoiesis and/or disease progression in both models by tracking CBCs in peripheral blood and analyzing bone marrow cells by flow cytometry. The bone marrow samples were sorted by flow cytometry to yield HSPC subpopulations: HSC (LSK CD34-Flt3-), GMP (LK FCRII/III+CD34+), and MEP (LK FCRII/III-CD34-). Cells were analyzed for transcriptome by deep RNA-seq, epigenetics by ATAC-seq, and gene targets by anti-RUNX1 CHIP-seq. Focusing on the HSC, GMP, and MEP subpopulations, we found that RUNX1 deletion in the hematopoietic system causes thrombocytopenia and HSC engraftment defects, and dramatic changes in HSPC subpopulations: RUNX1 deficiency resulted in an increase MegaK-primed HSCs via blocking their direct differentiation to megakaryocytes leading to thrombocytopenia, and caused a marked increase of GMPs and a significant decrease of MEPs. Induction of RUNX1 S291fsX300 mutant in MLL-PTD;RUNX1 S291fsX300 mice mimicked that of RUNX1 deletion, resulting similarly in thrombocytopenia, an expansion of Mega-HSCs, increased GMPs, and decreased MEPs. “Correction” of the RUNX1S291fsX300 mutation by doxycycline withdraw reversed the FPD phenotype as well as the cellular distribution changes in HSCs, GMPs and MEPs. RNA-seq analyses of DEGs found that RUNX1 acts both as an activator and a suppressor in gene transcription in HSPCs. In HSCs, among 1879 DEGs, 608 are upregulated and 1271 are downregulated in Runx1 -/- compared with WT cells. In GMPs, 2042 DEGs were seen, among which 908 are upregulated and 1134 are downregulated whereas in MEPs, 316 transcripts were upregulated and 1214 were downregulated amongst 1530 DEGs in Runx1 -/- cells. Combining the DEGs from RNA-seq with annotated ATAC-seq peaks, we discovered through gene ontology analyses that a set of systemic development genes are commonly regulated by RUNX1 via chromosome accessibility in all HSPC subpopulations, with potentially shared targets such as Jam2, Bcar1, Irf4 Insrr , Cxcl12, Tnfsf4, Rap1gap, Aldh1a1. In contrast, in HSCs, a unique set of hemostasis/platelet regulatory genes such as Itga2b, Gp5, Pdgfb and Vwf were seen as potential targets, consistent with our recent findings ( Blood Adv 7:2590). In GMPs, RUNX1 appears to specifically regulate inflammatory and innate immunity genes with potential targets such as Gfi1b, Ets1, Tnfrsf11a while in MEP, RUNX1 specifically regulates cell motility and migration gene sets affecting targets such as Notch1, Ifitm1, Hoxa7, Cd300a Cxcl10 Fut7, suggesting a role of RUNX1 in modulating MEP movement/location in the bone marrow. RUNX1 CHIP-seq analyses are under way to further clarify the potential targets in each HSPC subpopulation. Our studies indicate that RUNX1 regulates common as well as distinct transcriptional events in various HSPC subpopulations by context-dependent activation and suppression mechanisms. RUNX1 plays a universal role in the systemic developmental program of various HSPC subpopulations but appears to engage in unique lineage specific factors to deliver subpopulation-specific functions such as mega-K cell fate-priming of HSCs, inflammatory program in GMPs, and bone marrow location signals in MEPs. Ongoing analyses of the FPD/AML mouse genomic data in this context are expected to reveal contributions of patient RUNX1 mutations to the disease development.

Interconnections between DDX41-Dependent Post-Transcriptional and GATA Factor-Instigated Transcriptional Mechanisms That Govern Hematopoiesis

Heterozygous DDX41 germline mutations occur in familial myelodysplastic syndrome (MDS)/acute myeloid leukemia (AML) and acute erythroid leukemia (AEL). DDX41 encodes an RNA helicase that regulates RNA splicing, cGAS-Sting signaling in innate immunity, and maintains genome stability in erythropoiesis. We described the innovation of a facile genetic rescue system to compare RNA-regulatory activities of wild type and disease-associated DDX41 variants in engineered HoxB8-immortalized (hi) murine myeloid progenitor cells (hi-Ddx41+/+ and Ddx41+/- cells) (Kim et al., Leukemia 2023). We identified DDX41-regulated transcripts and membrane proteins as quantitative metrics of DDX41 activity that discriminate benign from pathogenic DDX41 alleles. As these transcripts and the cognate proteins were not known to be components of GATA2 genetic networks that govern hematopoietic stem/progenitor cell (HSPC) transitions, we hypothesized that DDX41 mechanisms in progenitors operate in parallel with or independent of GATA2 mechanisms. Considering the biological and pathological importance of DDX41 and many unanswered questions on how clinical variants impact DDX41 activity, we instituted studies to discover DDX41-regulated transcript isoforms. The datasets are being used to unveil how DDX41 controls cellular functions, how clinical variants derail mechanisms, and to establish interconnections or independence with GATA factor mechanisms. To develop a broader perspective, we extended the myeloid data by innovating a rescue system to analyze DDX41 structure/function in G1E-ER-GATA1 erythroblasts that express a conditionally active ER-GATA1 allele. We used CRISPR/Cas9 to generate Ddx41 +/- clonal lines that expressed ~50% lower levels of DDX41 protein. A comparable system is being generated in human HUDEP2 erythroid precursor cells. We compared DDX41 with two disease-associated germline variants: G173R and K331deletion. G1E-ER-GATA1- Ddx41 +/-cells were infected with retrovirus expressing GFP, or GFP and DDX41 (WT, G173R, or K331del), GFP + cells were sorted, and total RNA was analyzed by RNA-seq. Differential expression analysis revealed 138 Ddx41-regulated transcripts (P < 0.05), with 63 elevated and 75 decreased. Disease-associated variants failed to regulate these transcripts. To establish relationships between DDX41-regulated and GATA1-regulated transcripts in erythroblasts, we compared DDX41-regulated transcripts with our GATA1 transcriptomic data (Tanimura et al., EMBO Rep. 2016; Dev. Cell 2018; Liao et al., Cell Rep. 2020), which revealed 78 transcripts co-regulated by DDX41 and GATA1. The RNA analysis is being extended to the proteome. To investigate similarities between DDX41-dependent post-transcriptional and GATA1-dependent transcriptional mechanisms, we analyzed the genes encoding the 78 co-regulated transcripts using gene ontology and pathway analyses. The gene signatures included downregulation of apoptosis (p=0.0006). We are testing the hypothesis that DDX41 and GATA1 operate additively or synergistically to control levels of transcripts encoding apoptotic regulators in developing erythroblasts, thus establishing a balance between pro-apoptotic and anti-apoptotic factors. We compared myeloid and erythroid DDX41-regulated transcript datasets to identify common and cell type-specific DDX41-regulated transcripts. This analysis unveiled 11 transcripts that are DDX41-regulated in both systems. One transcript encodes CLK3, a member of Cdc2-like kinase family that phosphorylates splicing factors. DDX41 increased intron 3 retention in Clk3 mRNA in both systems. By quantifying exon-intron junctions, we demonstrated that DDX41 promoted intron 3 retention in hi- Ddx41 +/- cells 1.7-fold (P = 0.0002) and in G1E-ER-GATA1- Ddx41 +/- cells 3.3-fold (P = 0.0002). We are testing models to explain the functional significance of DDX41-regulated Clk3 intron retention and discovered DDX41 regulates intron retention at other loci. We are assessing how DDX41 controls alternative splicing globally in the erythroid and myeloid systems and elucidating the biological and pathological consequences of corrupting these mechanisms. In aggregate, these studies established a system to discriminate pathogenic from benign DDX41 variants, and mechanistic insights that provide the basis for new myeloid and erythroid paradigms.

Germline MPL Mutations May be a Rare Cause of “Triple-Negative” Thrombocytosis

Background Rare cases of primary thrombocytosis are related to inherited genetic abnormalities and are called hereditary thrombocytosis (HT). HT has clinical features resembling sporadic essential thrombocythemia (ET) but has usually an autosomal dominant (AD) inheritance with variable penetrance. To date, germline mutation involving the MPL, THPO, JAK2 genes have been associated with HT. Methods The study included 933 patients evaluated at our Division because of persistent isolated thrombocytosis for whom secondary reactive causes were excluded. Patients were screened for the three canonical somatic driver mutations associated with myeloproliferative neoplasms: JAK2 V617F mutation, CALR exon 9 mutations, MPL exon 10 mutations. Triple-negative cases with unexplained isolated thrombocytosis which also resulted negative for non-canonical exon 10 MPL mutations were analyzed using next generation sequencing (NGS) to test a panel of 80 myeloid genes. Results Of 933 patients with isolated thrombocytosis screened, 567 were JAK2-mutated, 255 CALR-mutated, 41 MPL-mutated, 2 double-mutated and 68 triple-negative. Two MPL-mutated patients carried a non-canonical mutation located in exon 10: MPL W515* and MPL V501A. Of the 68 triple-negative patients, 32 were evaluated by NGS and one of them showed another non-canonical mutation of MPL located outside exon 10: MPL R102P. These 3 non-canonical MPL mutations resulted to be germline as they were detected also in DNA extracted from T lymphocytes and from hair roots. Due to the germline nature of the mutations, a study of the family was carried out. In 2 out of 3 pedigrees at least a second relative carried the same germline mutation discovered in the proband; these 2 pedigrees are shown in the figure. Patient MPC17_15 was an 80 years-old patient with a history of thrombocytosis. She resulted JAK2- and CALR- wild-type while HRM screening was positive for exon 10 MPL mutations; Sanger sequencing identified the MPL W515* mutation in DNA from granulocytes, T-lymphocytes and hair roots, confirming its germline nature. Her children showed a normal complete blood count (CBC) and were MPL wild-type, thus confirming a segregation between mutation and clinical phenotype. Patient MPC14_674 (panel A) was a 36 years-old women with a history of mild thrombocytosis never investigated before. She was referred to our clinic by Pediatricians after the delivery because her baby (MPC17_167) showed persistent isolated thrombocytosis (826 x10 9/L) during the first months of life despite the exclusion of the most common reactive causes of thrombocytosis. Sanger sequencing identified the MPL V501A mutation in granulocyte and in T-lymphocyte in both cases. To evaluate the segregation of MPL V501A with the disease phenotype, we evaluated the CBC and MPL mutation in the other relatives. Both proband's father (MPC23_597) and sister (MPC23_602) carried germline heterozygous MPL V501A mutation associated with a PLT count above or at the upper limit of normal range (570 x10 9/L and 355 x10 9/L, respectively). Conversely, the husband (MPC17_495), the second son (MPC18_43) and the mother (MPC23_603) of the proband showed a normal CBC and were MPL wild-type, confirming an AD inheritance. Patient MPC07_130 (panel B) was a 44 years-old women with triple-negative isolated thrombocytosis lasting since 2007. NGS analysis showed the presence of a heterozygous germline MPL R102P mutation. As this mutation is located in exon 3, it was not detected through HRM and Sanger sequencing which target only exon 10. Her son (MPC13_672), 18 years-old, was completely asymptomatic but the CBC showed mild thrombocytosis (472 x 10 9/L). He tested negative for the 3 driver mutations but Sanger sequencing of MPL exon 3 identified the heterozygous germline MPL R102P mutation. Conclusions We identified 3 non-canonical germline MPL mutations in 3 different unrelated subjects with isolated thrombocytosis: MPL W515*, MPL R102P, and MPL V501A. Germline MPL mutations may underly HT and should be evaluated by sequencing of the whole exon 10 of MPL gene or by NGS in cases with isolated thrombocytosis negative for the three canonical somatic driver mutations. Namely, patients with HT might present as sporadic cases, and in the initial workup they might be inappropriately diagnosed with triple-negative ET. A correct diagnosis is pivotal to avoid unnecessary treatments.

Familial Thrombocytopenia-Associated Germline ETV6 P214L Mutation Results in XPO1-Mediated Nuclear Export

In recent years, a number of heterozygous germline mutations in ETV6 have been associated with familial thrombocytopenia and predisposition to hematologic malignancies. While most of these missense mutations occur in the DNA-binding-domain of ETV6, the recurrent P214L mutation is unique in that it occurs in the central disordered region of the protein. The ETV6 P214L mutation has previously been shown to disrupt the nuclear localization of ETV6 and the ability of ETV6 to act as a transcriptional repressor. Unexpectedly, we have found that the P214L missense mutation creates a recognition motif for the nuclear export protein XPO1. We have demonstrated in cellular and protein reconstitution assays that XPO1 directly engages the P214L but not the wild-type ETV6 construct. Consistent with this mechanism, we are able to fully rescue the nuclear localization of ETV6 P214L in mammalian cells with small molecule XPO1 inhibitors. We have also found that once localized to the nucleus, the P214L mutant construct exhibits functional consequences indistinguishable from wild-type ETV6 in Ba/F3 transformation assays. When looking at the evolutionary conservation of the ETV6 amino acid sequence involved in the XPO1 recognition motif, we observed that the synonymous P216L mutation in the mouse ETV6 ortholog does not create a nuclear export signal. In order to study XPO1-mediated export of ETV6 P214L and its impact on hematopoiesis, we have generated a mouse model in which two point mutations (P216L and S211I) have been introduced into a single endogenous ETV6 allele, which precisely matches the sequence of this region in human P214L carriers. Using CRISPR-Cas9, we generated 3 transgenic mouse lines: Etv6 P216L, Etv6 S211I, and Etv6 S211IP216L. Immunofluorescence of fixed bone marrow shows that ETV6 is only mislocalized in megakaryocytes from ETV6 S211I P216L mice. Complete blood counts revealed a significant decrease in platelet counts in ETV6 S211I P216L heterozygotes (485 x 10 3/µL) compared to ETV6 S211I heterozygotes (1140 x 10 3/µL, p<0.0001), ETV6 P216L heterozygotes (1065 x 10 3/µL, p<0.0006), and wild-type littermates (1254 x 10 3/µL, p<0.0001). Flow cytometry phenotyping of bone marrow from the three transgenic lines and wild-type littermates shows a significant decrease in the absolute numbers of hematopoietic stem cells (HSCs) and megakaryocyte precursors (MkPs) in ETV6 S211I P216L mice. In summary, we have determined that XPO1-mediated nuclear export is the mechanistic basis for ETV6 P214L mislocalization. We developed a mouse model that recapitulates this export signal in the endogenous ETV6 allele and found that this model demonstrates a thrombocytopenic phenotype as seen in human patients. Reductions in HSCs and MkPs suggest both a decreased fitness of HSCs, as well as dysregulated megakaryopoiesis in this model.

Systematic Mapping of Gene-Editable Mutations in GATA2 and SAMD9/SAMD9L Syndromes

Germline predisposition to bone marrow failure (BMF) and myelodysplastic syndromes (MDS) cause substantial economic and psychosocial burden and early mortality in affected individuals. Due to the limitations and risks of hematopoietic stem cell transplantation, there is an urgent need for new and innovative treatment approaches. Conventional lentiviral-based gene therapy is not feasible for most BMF/MDS predisposing genes because their uncontrolled overexpression is detrimental and lentiviral vectors might cause insertional mutagenesis. However, new technologies that precisely modify the endogenous allele can overcome these limitations. Base editing (BE) using cytosine base editors (CBE) and adenine base editors (ABE) as well as prime editing (PE) are advanced gene editing techniques with great therapeutic promise. The goal of this project is to develop a comprehensive map of gene-editable mutations in the GATA2, SAMD9, and SAMD9L genes as a preclinical effort to facilitate gene editing trials. Germline heterozygous mutations in these key predisposing genes lead to highly penetrant disorders characterized by progressive immunodeficiency and BMF/MDS risk, with particularly high prevalence in children, as recently reported by us (Sahoo, Nature Medicine 2021) and others. For in depth analysis, we focused on the 5 most recurrent mutations in respective genes and devise strategies to correct mutations in cellular models. We first created a comprehensive database encompassing reported and unpublished pathogenic mutations (single nucleotide variants [SNVs] and <20bp insertion/deletions[indels]). In total, we annotated 506 cases with GATA2, 195 cases with SAMD9, and 187 cases with SAMD9L mutations. SNVs were detected in 83.2% (421/506), 94.4% (184/195), and 93.1% (174/187) patients with GATA2, SAMD9, SAMD9L mutations, respectively, while remaining cases had indels. Among all GATA2 cases, 59.9% (303/506) mutations are editable by ABE, 4.5% (23/506) by CBE, while remaining 35.6% (180/506) can be “rescued” by PE ( Fig. 1A). For SAMD9, 34.4% (67/195) cases were found to be amenable to editing by ABE, 30.3% (59/195) by CBE, and 35.4% (69/195) using PE. For SAMD9L, 47.1% (88/187) are editable by ABE, 20.3% (38/187) by CBE, and 32.6% (61/187) using PE. Having a well-annotated mutation list, we proceeded to identify the top 5 most common mutations in each gene ( Fig. 1B). Remarkably, all 5 mutations in both GATA2 and SAMD9 and 4 out of 5 top mutations in SAMD9L and amenable to BE. Next, we explored in depth the target editing window, protospacer adjacent motif (PAM) sites, and bystander editing effect (utilizing BE that recognize the canonical [NGG], and non-canonical PAM sequences [NG and near PAMless SpRY-NRN/NYN]. This stepwise approach resulted in successful identification of at least one potential guide RNA for each mutation with predicted low bystander editing. Ongoing work includes guide RNA validation, off-target analysis, and assessment of gene-editing efficiency using model cell lines. In conclusion, we have undertaken a systematic analysis of the gene editing landscape for frequent germline driver mutations in BMF/MDS. Our findings reveal promising editing strategies for the majority of prevalent mutations in key predisposing genes GATA2, SAMD9 and SAMD9L using CBE, ABE, or PE editors, and lay a groundwork to enable future clinical translation.

Analysis of Turkish Breast Cancer Patients With ATM-Heterozygous Germline Mutation According to Clinicopathological Features.

The ATM gene is one of the most common breast cancer (BC) susceptibility genes after BRCA1/2 and has been shown to be a moderate BC susceptibility gene. The association between ATM germline mutation and clinical features of BC is now unknown. In this article, clinicopathological features of BC patients with ATM germline heterozygous mutation were investigated. Patients admitted to the Medical Genetics departmentof a tertiary hospital between January 2020 and December 2022 were examined. Only invasive BC patients with pathogenic mutation, likely pathogenic mutation, or variants of uncertain significance (VUS) were included in the study. In all, 121 patients were included in the study. The median age at the first cancer diagnosis of the patients was 44 years. Of the total number of patients, 75.2% (91) had the histological subtype of infiltrating ductal carcinoma, and 43% (52) had Luminal B molecular subtype features. At a median follow-up of 16 months, 5.8% (7) of patients developed cancer in the contralateral breast. In addition, 7.4% (9) of the patients developed a second primary cancer during follow-up. When the patients were compared according to ATM variant classification, the localization, histologic types, and molecular subtypes of the BC were not different between all groups (respectively; p=0.68, p=0.65, p=0.32). To the best of our knowledge, this is the first publication that evaluates the clinical and pathological characteristics of BC patients with germline heterozygous ATM mutations in the Turkish population. When patients were compared according to variant classifications of ATM mutation, patients' histological and molecular subtypes were similar.

FRI188 Exploratory Genomic Analysis From A Brazilian PMAH-Family With ARMC5 Alteration With Insidious Pattern Progression Of The Disease

Abstract Disclosure: H.L. Charchar: None. A.W. Kuhn: None. B.M. Mariani: None. M.Y. Nishi: None. F.L. Ledesma: None. M.C. Zerbini: None. F.Y. Tanno: None. V. Srougi: None. J.L. Chambo: None. M.Q. Almeida: None. B.B. Mendonca: None. M.C. Fragoso: None. Background: The clinical evolution of primary macronodular adrenal hyperplasia (PMAH) is usually slow over many years and is related to the insidious progression of hypercortisolism. The disease presents an autosomal dominant inheritance pattern with incomplete penetrance. Germline heterozygous mutations in the ARMC5 are present in 10% to 55% of the patients. The long-term follow-up of patients harboring germline ARMC5 pathogenic variants with normal evaluation will provide us with important insights regarding the outcomes. Clinical case: A 53-year-old man (index-case) was referred by the cardiologist to our service in October 2012, due to resistant hypertension (HTA), type 2 diabetes mellitus, dyslipidemia, and BMI of 32.4 kg/m2. Hormonal data: low ACTH (<5 pg/mL) and no suppression of cortisol after the overnight DST-1mg (22.7 µg/dL); late-night salivary cortisol, urinary free cortisol, aldosterone/renin ratio and plasma metanephrines were in the normal range. A CT scan showed bilateral enlargement of the adrenals associated with multiple macronodules. He underwent an adrenal-sparing surgery (total adrenalectomy of the left adrenal and partial adrenalectomy of the right adrenal). The macroscopic and histological appearance was consistent with PMAH. Leucocyte DNA genotyping identified the germline heterozygous ARMC5 pathogenic variant in exon 1 c.280del, p.(Ser94Argfs*43). This variant was identified in 3 of the 10 relatives investigated (son#1, daughter#2 and grandson#3). In 2021, the 37-year-old son#1 presented with a BMI of 32.6 kg/m2. Autonomous cortisol secretion was confirmed (cortisol after DST-1mg = 6.7 µg/dL). CT scan showed bilateral enlargement of the adrenals, similar to his father (index-case), with a larger left adrenal. Unilateral left adrenalectomy was performed, and PMAH was histologically confirmed. In 2018, the 21-year-old daugher#2 had normal adrenal function. More recently, in December 2022, she presented with an important weight gain (44kg in 4 years), without any specific signs and symptoms of hypercortisolism. Hormonal investigation showed a possible autonomous cortisol secretion (cortisol after DST-1mg = 2.2 µg/dL); the CT scan demonstrated an adrenal diffusely thickened with several nodules, especially on the left side, as the other relatives. Up to now, she has been using ketoconazole. All of them did not present meningioma of CNS. The grandson#3 with 11-year-old, is asymptomatic so far. Clinical Lesson: PMAH is a heterogenous and underdiagnosed disorder and is more genetically associated than previously thought. Therefore, a careful hormonal-genetic-clinical-radiological study of the relatives of index cases permits the diagnosis of many unsuspected familial-cases, including asymptomatic patients. Surgical or medical treatment should be considered for these patients to avoid progression to a possible overt Cushing syndrome. Presentation: Friday, June 16, 2023

Combined germline and somatic human FADD mutations cause autoimmune lymphoproliferative syndrome

The autoimmune lymphoproliferative syndrome (ALPS) is a noninfectious and nonmalignant lymphoproliferative disease frequently associated with autoimmune cytopenia resulting from defective FAS signaling. We previously described germline monoallelic FAS (TNFRSF6) haploinsufficient mutations associated with somatic events, such as loss of heterozygosity on the second allele of FAS, as a cause of ALPS-FAS. These somatic events were identified by sequencing FAS in DNA from double-negative (DN) T cells, the pathognomonic T-cell subset in ALPS, in which the somatic events accumulated. We sought to identify whether a somatic event affecting the FAS-associated death domain (FADD) gene could be related to the disease onset in 4 unrelated patients with ALPS carrying a germline monoallelic mutation of the FADD protein inherited from a healthy parent. We sequenced FADD and performed array-based comparative genomic hybridization using DNA from sorted CD4+ or DN T cells. We found homozygous FADD mutations in the DN T cells from all 4 patients, which resulted from uniparental disomy. FADD deficiency caused by germline heterozygous FADD mutations associated with a somatic loss of heterozygosity was a phenocopy of ALPS-FAS without the more complex symptoms reported in patients with germline biallelic FADD mutations. The association of germline and somatic events affecting the FADD gene is a new genetic cause of ALPS.

A novel RBBP8(p.E281*) germline mutation is a predisposing mutation in familial hereditary cancer syndrome.

Screening tumor susceptibility genes helps in identifying powerful biomarkers for hereditary cancer monitoring, prevention, and diagnosis, providing opportunities for understanding potential molecular mechanisms and biomarkers for the precise treatment of hereditary cancer syndromes. Whole-exome sequencing of blood and bioinformatics analysis uncovered a novel RBBP8(p.E281*) germline mutation in a family with hereditary cancer syndrome, which was verified by Sanger sequencing. Cell proliferation, colony formation, cell migration, and in vivo tumorigenesis were investigated by CCK8, colony formation, Transwell, and in vivo xenograft assays. Protein localization and interaction were detected by immunofluorescence, nuclear and cytoplasmic protein extraction kits, and Co-IP. A new heterozygous germline mutation of the RBBP8(p.E281*) gene was found to be associated with familial hereditary cancer syndrome. RBBP8-WT was mainly detected in the nucleus and interacts with BRCA1. In contrast, RBBP8(p.E281*) is mainly located in the cytoplasm, with no interaction with BRCA1. RBBP8(p.E281*) variant plays an oncogenic role in the cytoplasm in addition to its loss of function in the nucleus, which promotes breast cancer proliferation, in vivo tumorigenesis, and migration. Compared with the control group, RBBP8(p.E281*) showed elevated cell death in response to cisplatin and olaparib treatment. A novel RBBP8(p.E281*) germline mutation was identified from familial hereditary cancer syndrome. RBBP8(p.E281*) is not able to enter the nucleus or interact with BRCA1 through the lost binding motif, and RBBP8(p.E281*) variant appears to promote tumorigenesis in the cytoplasm in addition to its loss of function in the nucleus. RBBP8(p.E281*) variant may promote tumor susceptibility and serve as a precision medicine biomarker in familial hereditary cancer syndrome. KEY MESSAGES: RBBP8(p.E281*) is a susceptibility gene in this familial hereditary cancer syndrome RBBP8(p.E281*) lost its ability to enter the nucleus and the BRCA1 binding motif A novel RBBP8(p.E281*) germline mutation promotes breast cancer tumorigenesis Patients with RBBP8(p.E281*) germline mutation may benefit from Olaparib, Cisplatin.

Mutation spectrum of retinoblastoma patients in Vietnam.

Retinoblastoma (RB), an intraocular malignancy commonly diagnosed in children, is mostly caused by inactivating mutations of both alleles of the RB1 gene. Early genetic screening for RB1 gene mutations would greatly improve treatment outcomes and patient management. In this study, both somatic and germline mutations were detected in blood and tumour samples of 42 RB patients using direct sequencing and multiplex ligation-dependent probe amplification. In total, 34 different mutations were found in 36 patients, including 1 SNP, 4 large deletions, 5 splicing sites, 1 missense, 7 frameshifts and 17 nonsense mutations. There were five novel mutations and one unreported which have not been found in large databases such as Leiden Open Variation Database (LOVD) and ClinVar. A higher rate of RB patients carrying heterozygous germline mutation and highly prevalent with pathogenic truncated mutation, hence, early detection of RB is essential for vision salvation and genetic counselling.