Michael V. Gormally

Purpose:The clinical implications of distinct SMARCA4 alteration classes remain incompletely defined. We performed a pan-cancer analysis to characterize SMARCA4 mutation classes and their associations with allelic status, genomic context, and therapeutic outcomes. Experimental Design:We analyzed 68,920 tumor–normal paired samples sequenced with the MSK-IMPACT next-generation sequencing assay between 2015 and 2023. We curated oncogenic or likely oncogenic SMARCA4 alterations using OncoKB and classified them based on prior functional and structural literature. Allele-specific copy number, ploidy, fraction of genome altered, loss of heterozygosity, and whole-genome doubling were calculated. Clinical outcomes were evaluated in selected tumor cohorts treated with platinum-based therapy or immune checkpoint blockade. Results:SMARCA4 alterations were most frequent in thymic epithelial tumors (10.7%), non–small cell lung cancer (7.1%), bladder cancer (5.6%), and cervical cancer (5%). Class 1 and 2 alterations occurred in 2.9% and 0.7% of tumors, respectively. Distinct patterns of genomic complexity, co-occurring alterations, and mutational signatures were observed across tumor types based on SMARCA4 alteration allelic state and class. In a phase I trial of the BRM degrader PRT3789, patients with monoallelic class 2 SMARCA4 alterations and preserved BRG1 expression saw clinical benefit, including 1 who attained a complete response. Conclusions:SMARCA4 alteration class and allelic status define biologically and clinically distinct subsets of tumors. These findings support incorporating allelic status and functional mutation class into patient selection strategies for emerging BRM-targeted therapies.

Purpose: The clinical implications of distinct SMARCA4 alteration classes remain incompletely defined. We performed a pan-cancer analysis to characterize SMARCA4 mutation classes and their associations with allelic status, genomic context, and therapeutic outcomes. Experimental Design: We analyzed 68,920 tumor–normal paired samples sequenced with the MSK-IMPACT next-generation sequencing assay between 2015 and 2023. We curated oncogenic or likely oncogenic SMARCA4 alterations using OncoKB and classified them based on prior functional and structural literature. Allele-specific copy number, ploidy, fraction of genome altered, loss of heterozygosity, and whole-genome doubling were calculated. Clinical outcomes were evaluated in selected tumor cohorts treated with platinum-based therapy or immune checkpoint blockade. Results: SMARCA4 alterations were most frequent in thymic epithelial tumors (10.7%), non–small cell lung cancer (7.1%), bladder cancer (5.6%), and cervical cancer (5%). Class 1 and 2 alterations occurred in 2.9% and 0.7% of tumors, respectively. Distinct patterns of genomic complexity, co-occurring alterations, and mutational signatures were observed across tumor types based on SMARCA4 alteration allelic state and class. In a phase I trial of the BRM degrader PRT3789, patients with monoallelic class 2 SMARCA4 alterations and preserved BRG1 expression saw clinical benefit, including 1 who attained a complete response. Conclusions: SMARCA4 alteration class and allelic status define biologically and clinically distinct subsets of tumors. These findings support incorporating allelic status and functional mutation class into patient selection strategies for emerging BRM-targeted therapies.

T-cell receptors (TCRs) recognize antigens derived from fragments of somatically expressed proteins that are degraded by the proteasome and presented by specific human leukocyte antigen (HLA) molecules. Recent therapeutic advances using the TCR as a tumor-targeting moiety have focused attention on HLA loss of heterozygosity (LOH) as a potential resistance mechanism. Allele-specific LOH, rather than allele-agnostic, is particularly pertinent, but rarely evaluated. Using a real-world dataset comprising 78,418 cases, we demonstrate that allele-specific LOH occurs at a relatively low frequency (HLA LOH in cancers harboring associated neoantigen driver mutations (eg, KRAS or TP53 mutations), but the overall frequency remained consistently low. Furthermore, using an orthogonal dataset, we integrated clinical outcomes with HLA LOH and identified distinct impacts on overall survival in colorectal cancer (CRC) and non-small cell lung cancer (NSCLC) cohorts. For instance, A*02:01-specific LOH was linked to worse survival in CRC (HR 0.5355, 95% CI 0.2991 to 0.9589, p=0.0094) but showed a trend toward improved survival in NSCLC (HR 1.249, 95% CI 0.7778 to 2.005). These findings underscore the relevance of allele-specific HLA LOH assessments and reveal nuanced differences in its clinical implications, which should be accounted for in the optimization of TCR-based immunotherapies.

Prenatal cell-free DNA (cfDNA) sequencing is a screening method that utilizes circulating cfDNA in maternal blood to identify fetal chromosomal abnormalities. Beyond its primary application in prenatal care, cfDNA sequencing can detect occult maternal malignancies before they manifest clinically, presenting a critical window for early therapeutic intervention. Here we report a single case in detail from the Incidental DEtection of maternal Neoplasia Through non-Invasive cell-Free DNA analysis (IDENTIFY) study, in which an abnormal cfDNA sequencing result from an asymptomatic pregnant woman identified locally advanced cholangiocarcinoma. Her disease was successfully treated with a multi-modal approach, and she achieved an ongoing complete response.

Chimeric antigen receptor (CAR)-engineered T and NK cells can cause durable remission of B-cell malignancies; however, limited persistence restrains the full potential of these therapies in many patients. The FAS ligand (FAS-L)/FAS pathway governs naturally-occurring lymphocyte homeostasis, yet knowledge of which cells express FAS-L in patients and whether these sources compromise CAR persistence remains incomplete. Here, we constructed a single-cell atlas of diverse cancer types to identify cellular subsets expressing FASLG , the gene encoding FAS-L. We discovered that FASLG is limited primarily to endogenous T cells, NK cells, and CAR-T cells while tumor and stromal cells express minimal FASLG . To establish whether CAR-T/NK cell survival is regulated through FAS-L, we performed competitive fitness assays using lymphocytes modified with or without a FAS dominant negative receptor (ΔFAS). Following adoptive transfer, ΔFAS-expressing CAR-T and CAR-NK cells became enriched across multiple tissues, a phenomenon that mechanistically was reverted through FASLG knockout. By contrast, FASLG was dispensable for CAR-mediated tumor killing. In multiple models, ΔFAS co-expression by CAR-T and CAR-NK enhanced antitumor efficacy compared with CAR cells alone. Together, these findings reveal that CAR-engineered lymphocyte persistence is governed by a FAS-L/FAS auto-regulatory circuit.

Background: Coronavirus disease 2019 (COVID-19), a multi-system disorder resulting from infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has affected 5.0 million individuals in the United States (US) resulting in more than 160,000 deaths. There is currently no proven effective therapy for SARS-CoV-2 infection beyond supportive care. Convalescent plasma (CP), collected from individuals who have recovered from SARS-CoV-2 infection, has been safely used to transfer virus-neutralizing antibodies to patients hospitalized with COVID-19. Herein we report on the clinical course and outcomes of patients who received CP for the treatment of COVID-19 across our health system. Methods: Hospitalized patients ≥ 18 years of age at 5 hospitals in the Yale-New Haven Health System with confirmed SARS-CoV-2 infection and severe or life-threatening disease (Figure 1) were enrolled in the US COVID-19 Expanded Access Program (EAP) and transfused 1 unit of CP. Patient outcomes were assessed at 7, 14, and 28 days after CP transfusion. Furthermore, we sought to determine mortality predictors in this patient cohort. Results: 105 patients enrolled in the EAP were transfused CP from 4/12/2020 to 6/14/2020. Median age was 62 years (28-88 years). 62.9% of patients were male. Individuals of a non-white race comprised 56.2% of our cohort and 33.3% identified as Hispanic or Latinx. 47.6% of patients had a body mass index greater than 30, with 13.3% classified as extremely obese. Diabetes mellitus, hypertension, and hyperlipidemia were highly prevalent in our population. Concomitant therapy for COVID-19 included hydroxychloroquine (79.0%), tocilizumab (79.0%), and remdesivir (23.8%) (Table 1). 91 patients required the intensive care unit (ICU) during their hospital course, with 87 patients in the ICU at the time of CP transfusion. 42.9% of patients had an improvement in their World Health Organization (WHO) Ordinal Scale score by day 7 post-CP transfusion (median 4 days to improvement), while 9.5% demonstrated an increase in their WHO score indicating worsening oxygenation during the 7 days following CP (Figure 2). Mortality was 10.48% at 7 days, 20.95% at 14 days, and 28.57% at 28 days post-CP transfusion (Figure 2). Of the patients in the ICU at the time of CP, 56 (64.4%) de-escalated to non-ICU care after a median of 8 days from transfusion and 55 (63.2%) were ultimately discharged from the hospital. The median time from CP transfusion to discharge in survivors was 14 days (2-103 days), while median time from CP to death in non-survivors was 10 days (1-76 days). The mean time in days both from hospital admission to CP and from positive SARS-CoV-2 polymerase chain reaction (PCR) to CP trended slightly longer in non-survivors when compared to survivors (8.6 vs 6.9 days, p=0.218 and 9.7 vs 7.3 days, p=0.85, respectively). D-dimer levels >5 milligrams per liter fibrinogen equivalent units (mg/L FEU) were associated with increased mortality at 24 (OR 2.79, 95% CI 1.18-6.72), 48 (OR 3.64, 95% CI 1.44-9.70), and 72 hours (OR 2.99, 95% CI 1.23-7.66) post-CP transfusion (Figure 3). Twelve patients (11.4%) on prophylactic or intermediate dose anticoagulation were subsequently escalated to therapeutic dosing during the 7 days after CP transfusion. Furthermore, a ferritin level of >3000 nanograms per milliliter (ng/mL) on the day of CP was associated with increased mortality (OR 5.14, 95% CI 1.34-19.68). Conclusions: CP therapy was administered through the EAP to COVID-19 patients with severe disease and with advanced age, high frequency of obesity, and extensive co-morbidity. In this COVID-19 population with high expected mortality, 42.9% of patients improved by WHO Ordinal Scale score within 7 days of CP transfusion and 52.4% were alive and discharged at 28 days. Baseline ferritin and d-dimer levels at 24, 48, and 72 hours post-CP were predictors of mortality, the latter raising the possibility that the increased thrombotic risk associated with COVID-19 may be exacerbated by administration of blood products from donors potentially in a residual procoagulant state. Further studies by our group are underway to assess hemostatic balance in donor CP, to estimate associations with outcomes by comparing patients who received CP with a matched control cohort of COVID-19 patients who did not receive CP, and to evaluate efficacy of CP in a randomized, placebo-controlled clinical trial.

Non-coding RNAs are crucial regulators for a vast array of cellular processes and have been implicated in human disease. These biological processes represent a hitherto untapped resource in our fight against disease. In this work we identify small molecule inhibitors of a non-coding RNA uridylylation pathway. The TUTase family of enzymes is important for modulating non-coding RNA pathways in both human cancer and pathogen systems. We demonstrate that this new class of drug target can be accessed with traditional drug discovery techniques. Using the Trypanosoma brucei TUTase, RET1, we identify TUTase inhibitors and lay the groundwork for the use of this new target class as a therapeutic opportunity for the under-served disease area of African Trypanosomiasis. In a broader sense this work demonstrates the therapeutic potential for targeting RNA post-transcriptional modifications with small molecules in human disease.