Validation and clinical application of transactivation assays for RUNX1 variant classification

Familial platelet disorder with associated myeloid malignancies (RUNX1-FPD) is caused by heterozygous pathogenic germline variants of RUNX1. In the present study, we evaluate the applicability of transactivation assays to investigate RUNX1 variants in different regions of the protein. We studied 11 variants to independently validate transactivation assays supporting variant classification following the ClinGen Myeloid Malignancies variant curation expert panel guidelines. Variant classification is key for the translation of genetic findings. We showed that new assays need to be developed to assess C-terminal RUNX1 variants. Two variants of uncertain significance (VUS) were reclassified to likely pathogenic. Additionally, our analyses supported the (likely) pathogenic classification of two other variants. We demonstrated functionality of four VUS, but reclassification to (likely) benign was challenging and suggested the need to reevaluate current classification guidelines. Finally, clinical utility of our assays was illustrated in the context of seven families. Our data confirmed RUNX1-FPD suspicion in three families with RUNX1-FPD-specific family history. Whereas for three variants identified in non RUNX1-FPD-typical families, no functional defect was detected. Applying functional assays to support RUNX1 variant classification can be essential for adequate care of index patients and their relatives at risk. It facilitates translation of genetic data into personalized medicine.

Genomic Landscape of RUNX1-Familial Platelet Disorder with Myeloid Malignancies Reveals Rising Clonal Hematopoiesis

Familial platelet disorder with associated myeloid malignancies (FPDMM) is a rare autosomal dominant disease caused by germline RUNX1 mutations. FPDMM patients have defective megakaryocytic development, low platelet counts, prolonged bleeding times, and a life-long risk (20-50%) of developing hematological malignancies. FPDMM is a rare genetic disease in need of comprehensive clinical and genomic studies. In early 2019 we launched a longitudinal natural history study of patients with FPDMM at the NIH Clinical Center and by May 2021 we have enrolled 98 patients and 100 family controls from 55 unrelated families. Genomic data have been generated from 56 patients in 24 families, including whole exome sequencing (WES), RNA-seq, and single-nucleotide polymorphism (SNP) array. We have identified 21 different germline RUNX1 variants among these 24 families, which include lost-of-function mutations throughout the RUNX1 gene, but pathogenic/likely pathogenic missense mutations are mostly clustered in the runt-homology domain (RHD). As an important form of RUNX1 germline mutations, five splice site variants located between exon 4-5 and exon 5-6 were identified in 6 families, which led to the productions of novel transcript forms that are predicted to generate truncated RUNX1 proteins. Large deletions affecting the RUNX1 gene are also common, ranging from 50 Kb to 1.5Mb, which were detected in 8 of the 55 enrolled families. Besides RUNX1, copy number variation (CNV) analysis from both SNP array and WES showed limited CNV events in non-malignant FPDMM patients. In addition, fusion gene analysis did not detect any in-frame fusion gene in these patients, indicating a relatively stable chromosome status in FPDMM patients. Somatic mutation landscape shows that the overall mutation burden in non-malignant FPDMM patients is lower than AML or other cancer types. However, in 13 of the 44 non-malignant patients (30%), somatic mutations were detected in at least one of the reported clonal hematopoiesis of indeterminate potential (CHIP) genes, significantly higher than the general population (4.3%). Moreover, 85% of our patients who carried CHIP mutations are under 65 years of age; in the general population, only 10% of people above 65 years of age and 1% of people under 50 were reported to carry CHIP mutations. Among mutated genes related to clonal hematopoiesis, BCOR is the most frequently mutated gene (5/44) in our FPDMM cohort, which is not a common CHIP gene among the general population. Mutations in known CHIP genes including SF3B1, TET2, and DNMT3A were also found in more than one patient. In addition, sequencing of 5 patients who already developed myeloid malignancies detected somatic mutations in BCOR, TET2, NRAS, KRAS, CTCF, KMT2D, PHF6, and SUZ12. Besides reported CHIP genes or leukemia driver genes, 3 unrelated patients carried somatic mutations in the NFE2 gene, which is essential for regulating erythroid and megakaryocytic maturation and differentiation. Two of the NFE2 mutations are nonsense mutations, and the other is a missense mutation in the important functional domain. NFE2 somatic mutations may play important roles in developing malignancy because 2 of the 3 patients already developed myeloid malignancies. For multiple patients in our cohort, we have sequenced their DNA on multiple timepoints. We have observed patients with expanding clones carrying FKBP8, BCOR or FOXP1 mutations. We have also observed a patient with relatively stable clone(s) with somatic BCOR, DNMT3A, and RUNX1T1, who have been sampled over more than four years. We will follow these somatic mutations through sequencing longitudinally and correlate the findings with clinical observations to see if the dynamic changes of CHIP clones harboring the mutations give rise to MDS or leukemia. In summary, the genomic analysis of our new natural history study demonstrated diverse types of germline RUNX1 mutations and high frequency of somatic mutations related to clonal hematopoiesis in FPDMM patients. These findings indicate that monitoring the dynamic changes of these CHIP mutations prospectively will benefit patients' clinical management and help us understand possible mechanisms for the progression from FPDMM to myeloid malignancies. Disclosures No relevant conflicts of interest to declare.

COVID-19 Vaccination in Adults with Immune Thrombocytopenia (ITP): Data from the Platelet Disorder Support Association (PDSA) Patient Registry

BACKGROUND AND AIMS Immune thrombocytopenia (ITP) is an autoimmune bleeding disorder causing low platelet counts (PC) and increased bleeding. COVID-19 vaccines are a major concern for ITP patients who fear vaccination might exacerbate their thrombocytopenia. To assess these concerns, PDSA developed a survey to explore how COVID-19 vaccinations impact individuals with ITP. Methods Data was collected using the ITP-COVID-19 web-based survey part of the Platelet Disorder Support Association's ITP Natural History Study. As of June 2021, 338 adult ITP patients had completed the survey. Data was analyzed with descriptive statistics and chi-squared tests. Results The majority of the 338 participants were female (78%) between 18-64 years of age (83%); 118 (35%) participants reported they were in remission, and 79 (24%) reported they had undergone splenectomy. Viral Disease: Forty participants (12%) were diagnosed with COVID-19: 7 (18%) reported their PC increased from baseline, 20 (50%) reported their PC was unaffected, and 13 (32%) reported their PC decreased. Of the 20 participants who reported a PC change (increase or decrease) following a positive COVID-19 test, 13 (65%) reported their PC returned to baseline within four weeks following vaccination. Four patients (10%), all between the ages of 41-50 years, were hospitalized: 2 received dexamethasone, 1 received IVIG, and 1 required oxygen. Two of the 4 had been treated for ITP with corticosteroids within the last 6 months. Three out of 4 were female, and no additional autoimmune conditions were reported however, and 2 out of 4 reported co-morbid conditions including increased blood pressure, under-active thyroid, and allergies. No deaths occurred. Vaccination impacts: 267 (79%) participants reported receiving at least one vaccine dose at survey completion, and 137 (41%) of participants reported they were fully vaccinated: Pfizer (45%), Moderna (38%), other (17%). Following at least one vaccine dose, platelet increases were reported by 37 (15%), 127 (53%) reported no change, and decreases were reported by 77 (32%); 26 did not answer. Of the 114 participants who reported a PC change following dose 1 (D1), 82 addressed the time for their PC to return to baseline; 69 (84%) reported their PC returned to baseline within four weeks. Following dose two (D2), PC increases were reported by 18 (13%), 82 (60%) were unchanged, and 37 (27%) saw a decrease. Of 55 participants who reported a PC change following D2, 44 addressed the time for their PC to return to baseline with 31(71%) indicating their PC returned to their normal within four weeks. Changes in PC following receipt of D1 vs D2 were not statistically significantly (X 2=1.01, p=.31). Following at least D1, three participants reported bleeding symptoms including epistaxis, wet purpura, petechiae, bruising, and a gastrointestinal internal bleed in an asplenic 64-year-old female with alpha-gal allergy. Twenty-four (9%) participants of 262 who answered the question, reported adverse effects other than bleeding including chills and fever. Two women, aged 35 and 47, developed a blood clot after receiving the Pfizer vaccine, despite reporting no past personal or family history of hypercoagulability. Fourteen participants (13 females; 1 male) reported platelet decreases >100,000/µL following vaccination, but only one received rescue treatment. Two had a pre-existing autoimmune disorder and eight a previous splenectomy. Eight received the Pfizer vaccine, five Moderna, and one AstraZeneca. Thirty (21%) participants reported a past change in platelets following a non-COVID vaccine; 23/30 shared their experience following receipt of D1 of a COVID-19 vaccine including 11 (48%) who experienced a platelet decrease, 4(17%) an increase, and 8 (35%) reporting no change. Conclusion The results are very reassuring for ITP patients that the risks of aggravated thrombocytopenia due specifically to getting COVID-19 infection or vaccine are small. There were only three cases of bleeding and two of clotting; all were well-treated. Decreases in PC following viral infection and vaccine receipt did occur, but they were rarely substantial and most resolved within four weeks. These very positive findings should reduce vaccine hesitancy among ITP patients and encourage them to be vaccinated. Disclosures MacWhirter - DiRaimo: JD has not personally received any payment personally, but PDSA has received grants and consultancy fees from Novartis, grant and honorarium from Amgen, grant and consultancy fees from Pfizer and UCB, and grants from Argenx, Principia, Rigel, and CSL Behr: Consultancy, Honoraria, Other. Kruse: CK has not personally received payment but reports that PDSA received grants and consultancy fees from Novartis, grant and honorarium from Amgen, grant and consultancy fees from Pfizer and UCB, and grants from Argenx, Principia, Rigel, and CSL Behring: Consultancy, Honoraria, Other. Bussel: UCB: Consultancy, Membership on an entity's Board of Directors or advisory committees, Other: DSMB; CSL: Other: DSMB; Momenta/Janssen: Consultancy, Membership on an entity's Board of Directors or advisory committees; Amgen: Consultancy, Membership on an entity's Board of Directors or advisory committees; Novartis: Consultancy, Membership on an entity's Board of Directors or advisory committees; Argenx: Consultancy, Membership on an entity's Board of Directors or advisory committees; UptoDate: Honoraria; Principia/Sanofi: Consultancy, Membership on an entity's Board of Directors or advisory committees; Rigel: Consultancy, Membership on an entity's Board of Directors or advisory committees; Dova/Sobi: Consultancy, Membership on an entity's Board of Directors or advisory committees; RallyBio: Consultancy, Membership on an entity's Board of Directors or advisory committees. Kruse: Alex has not personally received any payment but reports that PDSA received grants and consultancy fees from Novartis, grant and honorarium from Amgen, grant and consultancy fees from Pfizer and UCB, and grants from Argenx, Principia, Rigel, and CSL Behri: Consultancy, Honoraria, Other.

Rhesus Macaques As a Preclinical Model Organism for RUNX1-FPD

Germline loss-of-function (LOF) heterozygous mutations in the central hematopoietic transcription factor RUNX1 gene cause the marrow failure/malignancy predisposition syndrome Familial Platelet Disorder with associated Myeloid Malignancies (FPDMM, or FPD). Patients with FPD have defective megakaryocytic development, low platelet counts, and a very high (35-50%) life-long risk of hematological malignancies, particularly MDS/AML. Murine heterozygous gene knockout models do not recapitulate the human phenotype in terms of thrombocytopenia or myeloid leukemia progression. Although gene correction of the RUNX1 mutation in hematopoietic stem and progenitor cells (HSPCs) is being considered as a possible treatment approach, it is unknown whether mutation-corrected HSPCs will have the hoped for advantage over RUNX1 mutant HSCs in vivo, likely necessary to significantly lower leukemia risk. In order to study the relative function of wildtype and RUNX1-mutated HSPCs in vivo in a model with close hematopoietic similarity to humans, we generated a rhesus macaque FPD competitive repopulation model via CRISPR/Cas9 NHEJ editing of the RUNX1 gene versus the AAVS1 safe-harbor control locus. We transplanted mixtures of autologous HSPCs edited at the two loci: 75% RUNX1-edited/25% AAVS1- edited CD34+ HSPCs in animal 1 and 25% RUNX1-edited/75% AAVS1-edited CD34+ HSPCs in animal 2, following conditioning with total body irradiation. Both animals engrafted tri-lineage hematopoiesis promptly following transplantation. However, platelet numbers remained below the normal range long-term in animal 1 receiving a higher ration of RUNX1-edited HSPCS and below counts of macaques receiving HSPCs edited at other loci (Figure 1). Bone marrow morphology at 6 months was normal. To assess the HSPC function of RUNX1 mutant versus AAV1 control and unedited WT cells we tracked RUNX1 and AAVS1-mutated allele frequencies in blood cells over time via deep sequencing (Figure 2). In the infusion products (IP), allele fractions reflected the desired ratios. In both animals, AAVS1-edited cells dominated compared to RUNX1-edited cells. However, in animal 1, RUNX1-mutated cells expanded over time eventually exceeding the ratio in the IP, and in animal 2, levels of RUNX1 and AAVS1-mutated cells were equivalent long-term. Marrow analyzed at 6 months showed heterozygous RUNX1-mutated CFU at levels concordant with mutation frequencies in the blood, but no homozygous RUNX1 mutated CFU, suggesting homozygous LOF is not compatible with long-term HSPC function. In conclusion, we have created pre-clinical model for FPD via CRISPR/Cas editing of HSPCs in rhesus macaques. The lack of a competitive advantage for wildtype or control-locus edited HSPCs over RUNX1 heterozygous-mutated HSPCs long-term in our model suggests that gene correction approaches for FPD will be challenging, particularly to reverse the MDS/AML predisposition phenotype. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.

Homoharringtonine and Mebendazole Are Preferentially Lethal Against Models of Myeloid Malignancy Associated with Germline Mutant RUNX1

RUNX1 is a master-transcriptional regulator involved in normal and malignant hematopoiesis. Majority of mono-allelic germline mutations in RUNX1 are missense, large deletions or truncation mutations, behaving mostly as loss of function (LOF) mutations. They are ~40%-penetrant and cause Familial Platelet Disorder (RUNX1-FPD) that has a propensity to evolve into myeloid malignancy (FPD-MM), i.e., MDS or AML. FPD-MM harbors co-mutations, most commonly on the second allele of RUNX1, and on BCOR, PHF6, K-RAS, WT1 or TET2, which confer relative resistance to standard therapy for MDS or AML. Although curative in some patients with FPD-MM, allogeneic transplantation from matched, un-related donors carries risk of graft versus host disease and frequent AML relapse. This creates a strong rationale and an unmet need to develop novel targeted therapies for FPD-MM. We previously reported on utilizing the RNA-Seq signature of RUNX1 knockdown, which exerted more lethality in AML cells with mutant (mt) RUNX1 compared to AML harboring two copies of wild-type RUNX1, for conducting LINCS1000-CMap analysis. This identified several expression mimickers (EMs), including the protein synthesis inhibitor homoharringtonine (HHT or omacetaxine) and anthelmintic fenbendazole (analog of mebendazole). Present studies demonstrate that treatment with HHT or mebendazole (MB) dose-dependently induced significantly greater loss of viability in four patient-derived (PD) bone marrow aspirate (BMA) samples of FPD-MM (3 AML and 1 MDS) compared to RUNX1-FPD (3 samples) or in normal CD34+ progenitor cells. In a patient with RUNX1-FPD (expressing mtRUNX1 K194N), who developed FPD-MM, following co-mutations were documented by NGS: BCOR A1437fs, PHF6 L324fs, SF3B1 D781G and SRSF2 P95R/L. From BMA of this patient, we successfully established the first ever, continuously cultured cell line (GMR-AML1) expressing the same germline mtRUNX1. GMR-AML1 cells were cytogenetically diploid and lacked MYC or MLL1 rearrangement, or any copy number gains or losses on array CGH. However whole exome sequencing (WES) identified additional mutations in TP53 (P72R), AIM2 (K340fs), NELFB (L523F), CEP152 (Y370X), SUGP2 (H23L), RRM2B (R71fs), TADA3 (T27R), SPDYE6 (G292C) and PRDM9 (S814R) with % VAF ranging between 33 to 55%. GMR-AML1 cells exhibited high surface expression of CD117 (c-KIT), CD123 (IL3R), CD86 and CD33, but without expression of CD34, CD14, CD11b, MPO or CD135 (FLT3). Compared to the AML OCI-AML5 cells with somatic mtRUNX1, GMR-AML1 cells demonstrated markedly reduced protein expression of RUNX1, RUNX2, PU.1, c-Myb, GFI1, GFI1B, FLT3, MEIS1 and CEBPα (p42), but much higher protein expression of RUNX3 and NOTCH (p120). CRISPR-Cas9 knockout of RUNX3 in GMR-AML1 cells restored RUNX1 expression, while significantly increasing % of differentiated cells. Although dose-dependently sensitive to daunorubicin, etoposide, cytarabine and panobinostat (class I and II HDAC inhibitor), GMR-AML1 cells were relatively insensitive to venetoclax, A1155463 (Bcl-xL inhibitor), AZD-5991 (MCL1 inhibitor), azacytidine or decitabine. Notably, treatment with HHT or MB dose-dependently induced loss of viability of GMR-AML1 cells (LD50: 40 and 330 nM, respectively). Additionally, co-treatment with HHT and venetoclax synergistically induced apoptosis in GMR-AML1 cells, as determined by the SynergyFinder algorithm. This synergy in GMR-AML1 cells was associated with abrogation of venetoclax-induced increase in MCL1 and Bcl-xL levels, as well as greater decline in levels of RUNX3, PU.1, c-Myb, c-Myc, MPL and CDK4/6. Tail vein infusion and engraftment of luciferase-transduced GMR-AML1 (10 6 cells) caused marked splenomegaly and 100% mortality of NSG mice by day-18, post-infusion. We will present at the ASH meeting findings of ongoing in vivo studies determining effects of treatment with HHT and/or venetoclax, versus vehicle control, on AML burden and overall survival of NSG mice engrafted with GMR-AML1 cells. Overall, preclinical findings presented here highlight the molecular and genetic features associated with progression of RUNX1-FPD to FPD-MM, especially in the newly established GMR-AML1 cell line. They also demonstrate that HHT or MB are preferentially more lethal against FPD-MM versus RUNX1-FPD cells and exert synergistic lethality with venetoclax against GMR-AML1 cells. Disclosures DiNardo: GlaxoSmithKline: Membership on an entity's Board of Directors or advisory committees; Novartis: Honoraria; AbbVie: Consultancy, Research Funding; Agios/Servier: Consultancy, Honoraria, Research Funding; Notable Labs: Current holder of stock options in a privately-held company, Membership on an entity's Board of Directors or advisory committees; Bristol Myers Squibb: Honoraria, Research Funding; Takeda: Honoraria; ImmuneOnc: Honoraria, Research Funding; Forma: Honoraria, Research Funding; Foghorn: Honoraria, Research Funding; Celgene, a Bristol Myers Squibb company: Honoraria, Research Funding. Takahashi: GSK: Consultancy; Celgene/BMS: Consultancy; Symbio Pharmaceuticals: Consultancy, Membership on an entity's Board of Directors or advisory committees; Novartis: Consultancy. Khoury: Stemline Therapeutics: Research Funding; Angle: Research Funding; Kiromic: Research Funding.

SARS-CoV-2 Vaccination and Immune Thrombocytopenia in de novo and pre-existing ITP patients

Cases of de novo immune thrombocytopenia (ITP) - including a fatality - following SARS-CoV-2 vaccination in previously healthy recipients led to studying its impact in pre-existing ITP. In this study, four data sources were analyzed: the Vaccine Adverse Events Reporting System (VAERS) for cases of de novo ITP; a ten-center retrospective study of adults with pre-existing ITP receiving SARS-CoV-2 vaccination; and surveys distributed by the Platelet Disorder Support Association (PDSA, United States) and the United Kingdom (UK) ITP Support Association. Seventy-seven de novo ITP cases were identified in VAERS, presenting with median platelet count of 3 [1-9] x109/L approximately 1-week post-vaccination. Of 28 patients with available data, 26 responded to treatment with corticosteroids and/or intravenous immunoglobulin (IVIG), and/or platelet transfusions. Among 109 patients with pre-existing ITP who received a SARS-CoV-2 vaccine, 19 experienced an ITP exacerbation (any of: ≥50% decline in platelet count, nadir platelet count <30x109/L with >20% decrease from baseline, and/or use of rescue therapy) following the first dose and 14 of 70 after a second dose. Splenectomized persons and those who received 5 or more prior lines of therapy were at highest risk of ITP exacerbation. Fifteen patients received and responded to rescue treatment. In surveys of both 57 PDSA and 43 UK ITP patients, prior splenectomy was associated with worsened thrombocytopenia. ITP may worsen in pre-existing ITP or be identified de novo post-SARS-CoV2-vaccination; both situations responded well to treatment. Proactive monitoring of patients with known ITP, especially those post-splenectomy and with more refractory disease, is indicated.

BERNARD SOULIER SYNDROME IN PREGNANCY

Bernard-Soulier syndrome is an inherited platelet disorder, transmitted in an autosomal recessive pattern. Thrombocytopenia and large defective platelets are characteristics, often presents early with bleeding symptoms, such as epistaxis, ecchymosis, menometrorrhagia, and gingival or gastrointestinal bleeding. Diagnosis can be conrmed by platelet aggregation studies and ow cytometry. Differential diagnosis includes other inherited giant platelet disorders, as well as von Willebrand disease and immune thrombocytopenic purpura. During pregnancy, it can present as recurrent rst trimester miscarriages, antepartum, intrapartum and postpartum haemorrhage. Treatment remains generally supportive with platelet transfusions and recombinant factor VII has also been described in literature.

B-cell acute lymphoblastic leukemia in patients with germline RUNX1 mutations

Germline RUNX1 mutations underlie a syndrome, RUNX1-familial platelet disorder (RUNX1-FPD), characterized by bleeding symptoms that result from quantitative and/or qualitative defect in platelets and a significantly increased risk for developing hematologic malignancies. Myeloid neoplasms are the most commonly diagnosed hematologic malignancies, followed by lymphoid malignancies of T-cell origin. Here, we describe the first 2 cases of B-cell acute lymphoblastic leukemia (B-ALL) in patients with confirmed germline RUNX1 mutations. While 1 of the patients had a known diagnosis of RUNX1-FPD with a RUNX1 p.P240Hfs mutation, the other was the index patient of a kindred with a novel RUNX1 variant, RUNX1 c.587C>T (p.T196I), noted on a targeted genetic testing of the B-ALL diagnostic sample. We discuss the clinical course, treatment approaches, and the outcome for the 2 patients. Additionally, we describe transient resolution of the mild thrombocytopenia and bleeding symptoms during therapy, as well as the finding of clonal hematopoiesis with a TET2 mutant clone in 1 of the patients. It is critical to consider testing for germline RUNX1 mutations in patients presenting with B-ALL who have a personal or family history of thrombocytopenia, bleeding symptoms, or RUNX1 variants identified on genetic testing at diagnosis.

Platelet dysfunction in platelet-type von Willebrand disease due to the constitutive triggering of the Lyn-PECAM1 inhibitory pathway

Platelet-type von Willebrand disease (PT-VWD) is an inherited platelet disorder characterized by macrothrombocytopenia and mucocutaneous bleeding, of variable severity, due to gain-of-function variants of GP1BA conferring to glycoprotein Ibα (GPIbα) enhanced affinity for von Willebrand factor (VWF). The bleeding tendency is conventionally attributed to thrombocytopenia and large VWF-multimers depletion. Some clues, however, suggest that platelet dysfunction may contribute to the bleeding phenotype but no information on its characteristics and causes are available. Aim of the present study was to characterize platelet dysfunction in PT-VWD and shed light on its mechanism. Platelets from a PT-VWD patient carrying the p.M239V variant and from PT-VWD mice carrying the p.G233V variant showed a remarkable platelet function defect, with impaired aggregation, defective granule secretion and reduced adhesion under static and flow conditions. VWF-binding to GPIbα is known to trigger intracellular signaling involving Src-family kinases (SFKs). We found that constitutive phosphorylation of the platelet SFK Lyn induces a negative-feedback loop downregulating platelet activation through phosphorylation of PECAM1 on Tyr686 and that this is triggered by the constitutive binding of VWF to GPIbα binding. These data show for the first time that the abnormal triggering of inhibitory signals mediated by Lyn and PECAM1 may lead to platelet dysfunction.In conclusion, our study unravels the mechanism of platelet dysfunction in PT-VWD caused by deranged inhibitory signaling triggered by the constitutive binding of VWF to GPIbα which may significantly contribute to the bleeding phenotype of these patients.