Sachs, Zohar

Abstract Acute myeloid leukemia (AML) with TP53 mutations (TP53Mut) has poor clinical outcomes. We investigated whether this AML subtype harbors a distinct gene expression profile (GEP) and whether this GEP is prognostic in TP53 wild type (TP53WT) AML. We applied a supervised machine-learning approach to detect the TP53Mut GEP. We divided the samples in the Beat-AML dataset into training and testing datasets. The TCGA LAML dataset was used as a validation dataset. We trained a ridge regression machine learning model to classify TP53Mut and TP53WT cases. This model was highly accurate in distinguishing TP53Mut versus TP53WT cases in both the test and validation datasets. Additionally, we identified TP53WT samples with high ridge regression scores. These high-scoring TP53WT samples also have poor overall survival, suggesting they share clinical and GEP features with TP53Mut AML. We defined these TP53WT samples as TP53Mut-like. Using drug sensitivity data in the Beat AML dataset, we found TP53Mut-like AMLs have distinct drug sensitivity patterns that phenocopy TP53Mut cases. Finally, we identified a 25-gene signature that can identify TP53Mut-like AML. This signature could be used clinically to identify this novel subset of poor-prognosis AML.

ImportanceSystematic data on the association between anticancer therapies and thromboembolic events (TEEs) in patients with COVID-19 are lacking.ObjectiveTo assess the association between anticancer therapy exposure within 3 months prior to COVID-19 and TEEs following COVID-19 diagnosis in patients with cancer.Design, Setting, and ParticipantsThis registry-based retrospective cohort study included patients who were hospitalized and had active cancer and laboratory-confirmed SARS-CoV-2 infection. Data were accrued from March 2020 to December 2021 and analyzed from December 2021 to October 2022.ExposureTreatments of interest (TOIs) (endocrine therapy, vascular endothelial growth factor inhibitors/tyrosine kinase inhibitors [VEGFis/TKIs], immunomodulators [IMiDs], immune checkpoint inhibitors [ICIs], chemotherapy) vs reference (no systemic therapy) in 3 months prior to COVID-19.Main Outcomes and MeasuresMain outcomes were (1) venous thromboembolism (VTE) and (2) arterial thromboembolism (ATE). Secondary outcome was severity of COVID-19 (rates of intensive care unit admission, mechanical ventilation, 30-day all-cause mortality following TEEs in TOI vs reference group) at 30-day follow-up.ResultsOf 4988 hospitalized patients with cancer (median [IQR] age, 69 [59-78] years; 2608 [52%] male), 1869 had received 1 or more TOIs. Incidence of VTE was higher in all TOI groups: endocrine therapy, 7%; VEGFis/TKIs, 10%; IMiDs, 8%; ICIs, 12%; and chemotherapy, 10%, compared with patients not receiving systemic therapies (6%). In multivariable log-binomial regression analyses, relative risk of VTE (adjusted risk ratio [aRR], 1.33; 95% CI, 1.04-1.69) but not ATE (aRR, 0.81; 95% CI, 0.56-1.16) was significantly higher in those exposed to all TOIs pooled together vs those with no exposure. Among individual drugs, ICIs were significantly associated with VTE (aRR, 1.45; 95% CI, 1.01-2.07). Also noted were significant associations between VTE and active and progressing cancer (aRR, 1.43; 95% CI, 1.01-2.03), history of VTE (aRR, 3.10; 95% CI, 2.38-4.04), and high-risk site of cancer (aRR, 1.42; 95% CI, 1.14-1.75). Black patients had a higher risk of TEEs (aRR, 1.24; 95% CI, 1.03-1.50) than White patients. Patients with TEEs had high intensive care unit admission (46%) and mechanical ventilation (31%) rates. Relative risk of death in patients with TEEs was higher in those exposed to TOIs vs not (aRR, 1.12; 95% CI, 0.91-1.38) and was significantly associated with poor performance status (aRR, 1.77; 95% CI, 1.30-2.40) and active/progressing cancer (aRR, 1.55; 95% CI, 1.13-2.13).Conclusions and RelevanceIn this cohort study, relative risk of developing VTE was high among patients receiving TOIs and varied by the type of therapy, underlying risk factors, and demographics, such as race and ethnicity. These findings highlight the need for close monitoring and perhaps personalized thromboprophylaxis to prevent morbidity and mortality associated with COVID-19–related thromboembolism in patients with cancer.

ImportanceCytokine storm due to COVID-19 can cause high morbidity and mortality and may be more common in patients with cancer treated with immunotherapy (IO) due to immune system activation.ObjectiveTo determine the association of baseline immunosuppression and/or IO-based therapies with COVID-19 severity and cytokine storm in patients with cancer.Design, Setting, and ParticipantsThis registry-based retrospective cohort study included 12 046 patients reported to the COVID-19 and Cancer Consortium (CCC19) registry from March 2020 to May 2022. The CCC19 registry is a centralized international multi-institutional registry of patients with COVID-19 with a current or past diagnosis of cancer. Records analyzed included patients with active or previous cancer who had a laboratory-confirmed infection with SARS-CoV-2 by polymerase chain reaction and/or serologic findings.ExposuresImmunosuppression due to therapy; systemic anticancer therapy (IO or non-IO).Main Outcomes and MeasuresThe primary outcome was a 5-level ordinal scale of COVID-19 severity: no complications; hospitalized without requiring oxygen; hospitalized and required oxygen; intensive care unit admission and/or mechanical ventilation; death. The secondary outcome was the occurrence of cytokine storm.ResultsThe median age of the entire cohort was 65 years (interquartile range [IQR], 54-74) years and 6359 patients were female (52.8%) and 6598 (54.8%) were non-Hispanic White. A total of 599 (5.0%) patients received IO, whereas 4327 (35.9%) received non-IO systemic anticancer therapies, and 7120 (59.1%) did not receive any antineoplastic regimen within 3 months prior to COVID-19 diagnosis. Although no difference in COVID-19 severity and cytokine storm was found in the IO group compared with the untreated group in the total cohort (adjusted odds ratio [aOR], 0.80; 95% CI, 0.56-1.13, and aOR, 0.89; 95% CI, 0.41-1.93, respectively), patients with baseline immunosuppression treated with IO (vs untreated) had worse COVID-19 severity and cytokine storm (aOR, 3.33; 95% CI, 1.38-8.01, and aOR, 4.41; 95% CI, 1.71-11.38, respectively). Patients with immunosuppression receiving non-IO therapies (vs untreated) also had worse COVID-19 severity (aOR, 1.79; 95% CI, 1.36-2.35) and cytokine storm (aOR, 2.32; 95% CI, 1.42-3.79).Conclusions and RelevanceThis cohort study found that in patients with cancer and COVID-19, administration of systemic anticancer therapies, especially IO, in the context of baseline immunosuppression was associated with severe clinical outcomes and the development of cytokine storm.Trial RegistrationClinicalTrials.gov Identifier: NCT04354701

Purpose: Acute myeloid leukemia (AML) is the most common acute leukemia in adults, affecting approximately 20,000 patients annually in the United States. AML genetic subtypes, as defined by the World Health Organization (WHO), are identified through fluorescence in situ hybridization (FISH), conventional chromosome analysis, and sequencing techniques. Mate pair sequencing (MPseq) is a next generation sequencing (NGS) technology optimized to detect genome wide structural variants and copy number alterations at high resolution. Our study goal was to investigate the prognostic value of MPseq in comparison to FISH, chromosome, and sequencing studies in the evaluation of AML patients. Methods: We performed a prospective study using blood and bone marrow samples from 105 patients with a diagnosis of AML, using MPseq, along with chromosome, FISH, and NGS or PCR studies to detect small mutations. Cytogenetic and molecular genetic results were correlated with MPseq findings. We also analyzed the MPseq data for chromoplexy, chromothripsis, and progressive complexity. Junction and copy number burden, the incidence of structural variation in the genome and the percent of the genome with aberrant copy number, were evaluated. Overall survival statistics were stratified by AML subtypes and observed anomalies. Results: Although structural variants in AML were characterized at a high resolution using MPseq when compared to conventional cytogenetic methods, risk stratification using current European Leukemia Net (ELN) guidelines was not improved by MPseq. The cohorts involving 5q and/or 7q deletions exhibited high levels of genomic complexity when compared to normal karyotype AML (NK-AML). The incidence of copy number gains, losses and junctions was greatest in 5q and 7q co-deletions (5q/7q) (16.5, 25.0, 69.3) and 5q deletions (5q) (9.8, 16.7, 31.6) subtypes compared to 7q deletions (3.4, 7.0, 6.7) and NK-AML (2.6, 4.3, 3.8) (p<0.001) subtypes. Chromoplexy, chromothripsis, and progressive structural complexity were detected in most samples with 5q deletions and 5q/7q co-deletions, but absent in samples with 7q or NK-AML. Biallelic inactivation of TP53 by sequencing mutation and/or deletion was common in the 5q/7q co-deletion (14/18 cases) and 5q deletion cohorts (7/10 cases), rare in the 7q deletion cohort (1/11 cases), and absent in the NK-AML (n=44) cohort. The median OS was significantly worse for patients with 5q/7q deletions (122.5 days) and 5q deletions (248 days) compared to NK-AML (413.5 days; p<0.001 and p=0.017, respectively) and between 5q/7q deletions and 7q deletions (370.5 days; p<0.001). No significant difference was observed between 5q/7q and 5q deletion subtypes, between NK and 7q deletion subtypes and between 5q and 7q deletion subtypes. The median OS was also significantly shorter for patients with TP53 alterations compared to patients with normal TP53 status. Patients with chromoplexy, chromothripsis and/or progressive structural complexity identified by MPseq had a significantly shorter median OS compared to patients without these features. (p<0.0001) Discussion: Risk stratifications based on current guidelines using cytogenetic and sequencing results were not adjusted due to MPseq results, which is not surprising when primary abnormalities are observed by conventional cytogenetic methods. NK-AML cases did not appear to benefit from a high resolution genomic evaluation. However, MPseq added value when structural variation required additional characterization, detecting novel rearrangements, such as a KAT6A/SORBS3 fusion. Lastly, we recognized common mischaracterizations made by conventional chromosome studies - including missed TP53 deletions in 7 cases, 5q/7q deletions misinterpreted as monosomies, cryptic NUP98 rearrangements, and unappreciated genomic complexity correlating with poor OS. These mischaracterizations challenge the use of conventional chromosome studies as a gold standard without accompanying FISH or MPseq studies. MPseq, similar to other structural methodologies such as optical mapping and long read sequencing, should be considered important complements to standard cytologic techniques given the important additional genomic information obtained. The additional structural variant characterization will be critical in paving the way for genomic discovery with the overall goal of improving prognostication for patient care. Figure Disclosures Vasmatzis: WholeGenome LLC.: Other: Owner; Mayo Clinic: Membership on an entity's Board of Directors or advisory committees, Research Funding.

Abstract CALR mutations are present in 70-84% of JAK2 wild-type myeloproliferative neoplasms (MPN) and 67% and 88% of essential thrombocytopenia (ET) and primary myelofibrosis (PMF) respectively. Most cases of MPN are apparently sporadic, but 7-11% have evidence of familial predisposition. While germline mutations in ET-associated genes, MPL and JAK2, have been described in hereditary thrombocytosis, germline mutations in CALR have not been described in any setting. Two types of CALR mutations are common in MPN: a 52-base pair deletion (bp) and a 5 bp insertion, both in exon 9. With rare exceptions, CALR mutations are generally mutually exclusive with JAK2 or MPL mutations and have very rarely been reported in conjunction with the BCR-ABL1translocation. Here, we report a patient with a germline CALR mutation, thrombocytosis, and subsequent development of BCR-ABL+ CML. A 67-year-old female with no significant medical history presented with severe abdominal pain and nausea. Peripheral blood analysis revealed a marked leukocytosis composed of 66% neutrophils, 16% myelocytes, 6.5% monocytes, 3.5% basophils, 2.5% promyelocytes, 2.5% metamyelocytes, 1.5% lymphocytes, 1.5% blasts, and no eosinophils. The patient was non-anemic and had a normal platelet count (340,000/mm3). Bone marrow biopsy revealed a hypercellular marrow with myeloid predominant trilineage hematopoiesis and 1-2% blasts with morphology consistent with chronic myelogenous leukemia (CML). Fluorescence in-situ hybridization analysis of peripheral blood identified a BCR-ABL1fusion in 98.5% of interphase cells. After 3 months of standard imatinib therapy, quantitative RT-PCR showed a reduction of BCR-ABL1/ABL1 in the peripheral blood, however platelet count was elevated at 539,000/mm3. Thrombocytosis persisted over 2 years with a maximal platelet count of 584,000/mm3. Given the patient's thrombocytosis, her peripheral blood was subjected to a next generation sequencing of JAK2, MPL, and CALR genes. A 52-bp out-of-frame deletion in exon 9 of the CALR gene was detected (52% allele frequency) in peripheral blood. In addition, the same 52-bp CALR deletion (63% allele frequency) was present at the time of diagnosis and within a buccal specimen (47% allele frequency) when the BCR-ABL1 transcript was 1% in the peripheral blood. Immunostain of the buccal sample was strongly positive for cytokeratin (CK) AE1/AE3 but CD45 was not detected indicating no leukocyte contamination. This case reports the first instance of a germline CALR mutation associated with thrombocytosis and is the fourth report of the co-occurrence of BCR-ABL1 and CALR mutation in a single patient. Evolution to BCR-ABL1+ CML suppressed the CALR-mutant thrombocytosis phenotype, emphasizing the effect of these genes on lineage determination in abnormal myeloid proliferation. Disclosures No relevant conflicts of interest to declare.

Key Points Buccal epithelial cells harbor an MPN-associated CALR mutation in a patient with CALR-mutant essential thrombocytosis, Ph+ CML, and no germ line CALR mutation.