Pharmacologic modulation of RNA splicing enhances anti-tumor immunity.

Although mutations in DNA are the best-studied source of neoantigens that determine response to immune checkpoint blockade, alterations in RNA splicing within cancer cells could similarly result in neoepitope production. However, the endogenous antigenicity and clinical potential of such splicing-derived epitopes have not been tested. Here, we demonstrate that pharmacologic modulation of splicing via specific drug classes generates bona fide neoantigens and elicits anti-tumor immunity, augmenting checkpoint immunotherapy. Splicing modulation inhibited tumor growth and enhanced checkpoint blockade in a manner dependent on host T cells and peptides presented on tumor MHC class I. Splicing modulation induced stereotyped splicing changes across tumor types, altering the MHC I-bound immunopeptidome to yield splicing-derived neoepitopes that trigger an anti-tumor T cell response in vivo. These data definitively identify splicing modulation as an untapped source of immunogenic peptides and provide a means to enhance response to checkpoint blockade that is readily translatable to the clinic.

Mechanisms of Resistance to Noncovalent Bruton's Tyrosine Kinase Inhibitors.

BACKGROUND: Covalent (irreversible) Bruton's tyrosine kinase (BTK) inhibitors have transformed the treatment of multiple B-cell cancers, especially chronic lymphocytic leukemia (CLL). However, resistance can arise through multiple mechanisms, including acquired mutations in BTK at residue C481, the binding site of covalent BTK inhibitors. Noncovalent (reversible) BTK inhibitors overcome this mechanism and other sources of resistance, but the mechanisms of resistance to these therapies are currently not well understood. METHODS: We performed genomic analyses of pretreatment specimens as well as specimens obtained at the time of disease progression from patients with CLL who had been treated with the noncovalent BTK inhibitor pirtobrutinib. Structural modeling, BTK-binding assays, and cell-based assays were conducted to study mutations that confer resistance to noncovalent BTK inhibitors. RESULTS: Among 55 treated patients, we identified 9 patients with relapsed or refractory CLL and acquired mechanisms of genetic resistance to pirtobrutinib. We found mutations (V416L, A428D, M437R, T474I, and L528W) that were clustered in the kinase domain of BTK and that conferred resistance to both noncovalent BTK inhibitors and certain covalent BTK inhibitors. Mutations in BTK or phospholipase C gamma 2 (PLCγ2), a signaling molecule and downstream substrate of BTK, were found in all 9 patients. Transcriptional activation reflecting B-cell-receptor signaling persisted despite continued therapy with noncovalent BTK inhibitors. CONCLUSIONS: Resistance to noncovalent BTK inhibitors arose through on-target BTK mutations and downstream PLCγ2 mutations that allowed escape from BTK inhibition. A proportion of these mutations also conferred resistance across clinically approved covalent BTK inhibitors. These data suggested new mechanisms of genomic escape from established covalent and novel noncovalent BTK inhibitors. (Funded by the American Society of Hematology and others.).

COVID-19 update: the first 6 months of the pandemic.

The COVID-19 pandemic is sweeping the world and will feature prominently in all our lives for months and most likely for years to come. We review here the current state 6 months into the declared pandemic. Specifically, we examine the role of the pathogen, the host and the environment along with the possible role of diabetes. We also firmly believe that the pandemic has shown an extraordinary light on national and international politicians whom we should hold to account as performance has been uneven. We also call explicitly on competent leadership of international organizations, specifically the WHO, UN and EU, informed by science. Finally, we also condense successful strategies for dealing with the current COVID-19 pandemic in democratic countries into a developing pandemic playbook and chart a way forward into the future. This is useful in the current COVID-19 pandemic and, we hope, in a very distant future again when another pandemic might arise.

Systematic evaluation of AML-associated antigens identifies anti-U5 SNRNP200 therapeutic antibodies for the treatment of acute myeloid leukemia.

Despite recent advances in the treatment of acute myeloid leukemia (AML), there has been limited success in targeting surface antigens in AML, in part due to shared expression across malignant and normal cells. Here, high-density immunophenotyping of AML coupled with proteogenomics identified unique expression of a variety of antigens, including the RNA helicase U5 snRNP200, on the surface of AML cells but not on normal hematopoietic precursors and skewed Fc receptor distribution in the AML immune microenvironment. Cell membrane localization of U5 snRNP200 was linked to surface expression of the Fcγ receptor IIIA (FcγIIIA, also known as CD32A) and correlated with expression of interferon-regulated immune response genes. Anti-U5 snRNP200 antibodies engaging activating Fcγ receptors were efficacious across immunocompetent AML models and were augmented by combination with azacitidine. These data provide a roadmap of AML-associated antigens with Fc receptor distribution in AML and highlight the potential for targeting the AML cell surface using Fc-optimized therapeutics.

Modulation of RNA splicing enhances response to BCL2 inhibition in leukemia.

Therapy resistance is a major challenge in the treatment of cancer. Here, we performed CRISPR-Cas9 screens across a broad range of therapies used in acute myeloid leukemia to identify genomic determinants of drug response. Our screens uncover a selective dependency on RNA splicing factors whose loss preferentially enhances response to the BCL2 inhibitor venetoclax. Loss of the splicing factor RBM10 augments response to venetoclax in leukemia yet is completely dispensable for normal hematopoiesis. Combined RBM10 and BCL2 inhibition leads to mis-splicing and inactivation of the inhibitor of apoptosis XIAP and downregulation of BCL2A1, an anti-apoptotic protein implicated in venetoclax resistance. Inhibition of splicing kinase families CLKs (CDC-like kinases) and DYRKs (dual-specificity tyrosine-regulated kinases) leads to aberrant splicing of key splicing and apoptotic factors that synergize with venetoclax, and overcomes resistance to BCL2 inhibition. Our findings underscore the importance of splicing in modulating response to therapies and provide a strategy to improve venetoclax-based treatments.

Moving the needle on time to resuscitation: An EAST prospective multicenter study of vascular access in hypotensive injured patients using trauma video review.

BACKGROUND: Vascular access in hypotensive trauma patients is challenging. Little evidence exists on the time required and success rates of vascular access types. We hypothesized that intraosseous (IO) access would be faster and more successful than peripheral intravenous (PIV) and central venous catheter (CVC) access in hypotensive patients. METHODS: An EAST prospective multicenter trial was performed; 19 centers provided data. Trauma video review was used to evaluate the resuscitations of hypotensive (systolic blood pressure ≤90 mm Hg) trauma patients. Highly granular data from video recordings were abstracted. Data collected included vascular access attempt type, location, success rate, and procedural time. Demographic and injury-specific variables were obtained from the medical record. Success rates, procedural durations, and time to resuscitation were compared among access strategies (IO vs. PIV vs. CVC). RESULTS: There were 1,410 access attempts that occurred in 581 patients with a median age of 40 years (27-59 years) and an Injury Severity Score of 22 [10-34]. Nine hundred thirty-two PIV, 204 IO, and 249 CVC were attempted. Seventy percent of access attempts were successful but were significantly less likely to be successful in females (64% vs. 71%, p = 0.01). Median time to any access was 5.0 minutes (3.2-8.0 minutes). Intraosseous had higher success rates than PIV or CVC (93% vs. 67% vs. 59%, p < 0.001) and remained higher after subsequent failures (second attempt, 85% vs. 59% vs. 69%, p = 0.08; third attempt, 100% vs. 33% vs. 67%, p = 0.002). Duration varied by access type (IO, 36 [23-60] seconds; PIV, 44 [31-61] seconds; CVC 171 [105-298]seconds) and was significantly different between IO versus CVC ( p < 0.001) and PIV versus CVC ( p < 0.001) but not PIV versus IO. Time to resuscitation initiation was shorter in patients whose initial access attempt was IO, 5.8 minutes versus 6.7 minutes ( p = 0.015). This was more pronounced in patients arriving to the hospital with no established access (5.7 minutes vs. 7.5 minutes, p = 0.001). CONCLUSION: Intraosseous is as fast as PIV and more likely to be successful compared with other access strategies in hypotensive trauma patients. Patients whose initial access attempt was IO were resuscitated more expeditiously. Intraosseous access should be considered a first line therapy in hypotensive trauma patients. LEVEL OF EVIDENCE: Therapeutic/Care Management; Level II.

Medical Certification for Utility Shut-Off Protection and Health-Related Social Needs.

BACKGROUND AND OBJECTIVES: Children in families facing energy insecurity have greater odds of poor health and developmental problems. In this study of families who requested and received medical certification for utility shut-off protection and were contacted by our Medical Legal Partnership (MLP), we aimed to assess concurrent health-related social needs related to utilities, housing, finances, and nutrition. METHODS: After medical certificates were completed at our academic pediatric center, our MLP office contacted families and assessed utility concerns as well as other health, social, and legal needs. In this observational study, we present descriptive analyses of patients who received certificates from September 2019 to May 2020 via data collected through the MLP survey during the coronavirus disease 2019 pandemic (June 2020-December 2021). RESULTS: Of 167 families who received utility shut-off protection from September 2019 to May 2020, 84 (50.3%) parents and guardians were successfully contacted. Most (93%) found the medical certificate helpful. Additionally, 68% had applied for Energy Assistance, and 69% reported they were on utility company payment plans. Most (78%) owed arrearages, ranging from under $500 to over $20 000, for gas, electric, and/or water bills. Food, housing, and financial insecurity screening positivity rates were 65%, 85%, and 74%, respectively. CONCLUSIONS: Patients who were contacted by an MLP after receiving medical certification for utility shutoff protection were found to have challenges paying for utilities and faced multiple food, housing, and financial stressors. Through consultation and completion of medical forms for utility shutoff protection, pediatricians and MLPs can provide resources and advocacy to support families' physical, emotional, and psychosocial needs.

Synthetic introns enable splicing factor mutation-dependent targeting of cancer cells.

Many cancers carry recurrent, change-of-function mutations affecting RNA splicing factors. Here, we describe a method to harness this abnormal splicing activity to drive splicing factor mutation-dependent gene expression to selectively eliminate tumor cells. We engineered synthetic introns that were efficiently spliced in cancer cells bearing SF3B1 mutations, but unspliced in otherwise isogenic wild-type cells, to yield mutation-dependent protein production. A massively parallel screen of 8,878 introns delineated ideal intronic size and mapped elements underlying mutation-dependent splicing. Synthetic introns enabled mutation-dependent expression of herpes simplex virus-thymidine kinase (HSV-TK) and subsequent ganciclovir (GCV)-mediated killing of SF3B1-mutant leukemia, breast cancer, uveal melanoma and pancreatic cancer cells in vitro, while leaving wild-type cells unaffected. Delivery of synthetic intron-containing HSV-TK constructs to leukemia, breast cancer and uveal melanoma cells and GCV treatment in vivo significantly suppressed the growth of these otherwise lethal xenografts and improved mouse host survival. Synthetic introns provide a means to exploit tumor-specific changes in RNA splicing for cancer gene therapy.

Impaired Proteolysis of Noncanonical RAS Proteins Drives Clonal Hematopoietic Transformation.

Recently, screens for mediators of resistance to FLT3 and ABL kinase inhibitors in leukemia resulted in the discovery of LZTR1 as an adapter of a Cullin-3 RING E3 ubiquitin ligase complex responsible for the degradation of RAS GTPases. In parallel, dysregulated LZTR1 expression via aberrant splicing and mutations was identified in clonal hematopoietic conditions. Here we identify that loss of LZTR1, or leukemia-associated mutants in the LZTR1 substrate and RAS GTPase RIT1 that escape degradation, drives hematopoietic stem cell (HSC) expansion and leukemia in vivo. Although RIT1 stabilization was sufficient to drive hematopoietic transformation, transformation mediated by LZTR1 loss required MRAS. Proteolysis targeting chimeras (PROTAC) against RAS or reduction of GTP-loaded RAS overcomes LZTR1 loss-mediated resistance to FLT3 inhibitors. These data reveal proteolysis of noncanonical RAS proteins as novel regulators of HSC self-renewal, define the function of RIT1 and LZTR1 mutations in leukemia, and identify means to overcome drug resistance due to LZTR1 downregulation. SIGNIFICANCE: Here we identify that impairing proteolysis of the noncanonical RAS GTPases RIT1 and MRAS via LZTR1 downregulation or leukemia-associated mutations stabilizing RIT1 enhances MAP kinase activation and drives leukemogenesis. Reducing the abundance of GTP-bound KRAS and NRAS overcomes the resistance to FLT3 kinase inhibitors associated with LZTR1 downregulation in leukemia. This article is highlighted in the In This Issue feature, p. 2221.

Developing human pluripotent stem cell-based cerebral organoids with a controllable microglia ratio for modeling brain development and pathology.

Microglia play critical roles in brain development, homeostasis, and disease. Microglia in animal models cannot accurately model human microglia due to notable transcriptomic and functional differences between human and other animal microglia. Incorporating human pluripotent stem cell (hPSC)-derived microglia into brain organoids provides unprecedented opportunities to study human microglia. However, an optimized method that integrates appropriate amounts of microglia into brain organoids at a proper time point, resembling in vivo brain development, is still lacking. Here, we report a new brain region-specific, microglia-containing organoid model by co-culturing hPSC-derived primitive neural progenitor cells and primitive macrophage progenitors. In the organoids, the number of human microglia can be controlled, and microglia exhibit phagocytic activity and synaptic pruning function. Furthermore, human microglia respond to Zika virus infection of the organoids. Our findings establish a new microglia-containing brain organoid model that will serve to study human microglial function in a variety of neurological disorders.

Depression predicts long-term cognitive impairment in survivors of critical illness.

INTRODUCTION: Intensive care unit (ICU) survivorship is associated with long-term cognitive impairment (LTCI). Our work has found post-ICU depression in up to 30% and posttraumatic stress disorder (PTSD) in up to 10% of ICU survivors. We hypothesized that post-ICU depression and PTSD are independently associated with LTCI in ICU survivors. METHODS: This is a five-center nested prospective cohort of critically ill patients admitted to medical and surgical ICUs who underwent neuropsychological assessments at 3 and 12 months posthospital discharge. Our primary outcome was global cognition using the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS) and Trail Making Test, Part B, a test of executive functioning, at 3- and 12-month follow-up. Our independent variables were Beck Depression Inventory II and the PTSD Checklist-Specific Version measured at 3 and 12 months. We performed multivariable linear regression models controlling for covariates such as age, years of education, preexisting cognitive impairment, comorbidities, ventilator days, hypoxemia episodes, and days of delirium or coma. RESULTS: Of 1,047 patients in the combined cohort, 679 were alive and available for follow-up at 3 months. A total of 590 (87%) ICU survivors completed at least one 3-month assessment, and of the 554 who survived to 12 months, 519 (94%) completed both a 3- and 12-month assessment with a median age of 61 years (52-70 years) and mean daily Sequential Organ Failure Assessment score of 6 (4-8), 520 (88%) were mechanically ventilated, and 420 (71%) were with delirium. Of these, 113 (19%) had PTSD and 187 (32%) had depression at 3 months with similar rates at 12 months. Depression at 3 months was associated with lower 3-month RBANS (coefficient, -2.25; -3.10 to -1.39) and lower Trails B scores at both 3 months (odds ratio, 0.69; 0.56-0.85) and 12 months (odds ratio, 0.66; 0.52-0.84). Posttraumatic stress disorder at 3 months had no association with RBANS or Trails B scores at 3 or 12 months. CONCLUSION: Early post-ICU depression, but not PTSD, is independently associated with coexisting LTCI, even when controlling for past ICU delirium. Treatment for early depression represents a novel intervention area for LTCI prevention in ICU survivors. LEVEL OF EVIDENCE: Prognostic/epidemiological, level III.

Mutant SF3B1 promotes AKT- and NF-κB-driven mammary tumorigenesis.

Mutations in the core RNA splicing factor SF3B1 are prevalent in leukemias and uveal melanoma, but hotspot SF3B1 mutations are also seen in epithelial malignancies such as breast cancer. Although hotspot mutations in SF3B1 alter hematopoietic differentiation, whether SF3B1 mutations contribute to epithelial cancer development and progression is unknown. Here, we identify that SF3B1 mutations in mammary epithelial and breast cancer cells induce a recurrent pattern of aberrant splicing leading to activation of AKT and NF-κB, enhanced cell migration, and accelerated tumorigenesis. Transcriptomic analysis of human cancer specimens, MMTV-cre Sf3b1K700E/WT mice, and isogenic mutant cell lines identified hundreds of aberrant 3' splice sites (3'ss) induced by mutant SF3B1. Consistently between mouse and human tumors, mutant SF3B1 promoted aberrant splicing (dependent on aberrant branchpoints as well as pyrimidines downstream of the cryptic 3'ss) and consequent suppression of PPP2R5A and MAP3K7, critical negative regulators of AKT and NF-κB. Coordinate activation of NF-κB and AKT signaling was observed in the knockin models, leading to accelerated cell migration and tumor development in combination with mutant PIK3CA but also hypersensitizing cells to AKT kinase inhibitors. These data identify hotspot mutations in SF3B1 as an important contributor to breast tumorigenesis and reveal unique vulnerabilities in cancers harboring them.

Minor intron retention drives clonal hematopoietic disorders and diverse cancer predisposition.

Most eukaryotes harbor two distinct pre-mRNA splicing machineries: the major spliceosome, which removes >99% of introns, and the minor spliceosome, which removes rare, evolutionarily conserved introns. Although hypothesized to serve important regulatory functions, physiologic roles of the minor spliceosome are not well understood. For example, the minor spliceosome component ZRSR2 is subject to recurrent, leukemia-associated mutations, yet functional connections among minor introns, hematopoiesis and cancers are unclear. Here, we identify that impaired minor intron excision via ZRSR2 loss enhances hematopoietic stem cell self-renewal. CRISPR screens mimicking nonsense-mediated decay of minor intron-containing mRNA species converged on LZTR1, a regulator of RAS-related GTPases. LZTR1 minor intron retention was also discovered in the RASopathy Noonan syndrome, due to intronic mutations disrupting splicing and diverse solid tumors. These data uncover minor intron recognition as a regulator of hematopoiesis, noncoding mutations within minor introns as potential cancer drivers and links among ZRSR2 mutations, LZTR1 regulation and leukemias.

Does Intentional Support of Degree Programs in General Surgery Residency Affect Research Productivity or Pursuit of Academic Surgery? A Multi-Institutional Study.

OBJECTIVE: To determine whether pursuit of an advanced degree during dedicated research time (DRT) in a general surgery residency training program impacts a resident's research productivity. DESIGN: A retrospective, multi-institutional cohort study. SETTING: General surgery residency programs that were approved to graduate more than 5 categorical residents per year and that offered at least 1 year of DRT were contacted for participation in the study. A total of 10 general surgery residency programs agreed to participate in the study. PARTICIPANTS: Residents who started their residency between 2000 and 2012 and spent at least one full year in DRT (n = 511) were included. Those who completed an advanced degree were compared on the following parameters to those who did not complete one: total number of papers, first-author papers, the Journal Citation Reports impact factors of publication (2018, or most recent), and first position after residency or fellowship training. RESULTS: During DRT, 87 (17%) residents obtained an advanced degree. The most common degree obtained was a Master of Public Health (MPH, n = 42 (48.8%)). Residents who did not obtain an advanced degree during DRT published fewer papers (median 8, [interquartile range 4-12]) than those who obtained a degree (9, [6-17]) (p = 0.002). They also published fewer first author papers (3, [2-6]) vs (5, [2-9]) (p = 0.002) than those who obtained a degree. Resident impact factor (RIF) was calculated using Journal Citation Reports impact factor and author position. Those who did not earn an advanced degree had a lower RIF (adjusted RIF, 84 ± 4 vs 134 ± 5, p < 0.001) compared to those who did. There was no association between obtaining a degree and pursuit of academic surgery (p = 0.13) CONCLUSIONS: Pursuit of an advanced degree during DRT is associated with increased research productivity but is not associated with pursuit of an academic career.

Activating mutations in CSF1R and additional receptor tyrosine kinases in histiocytic neoplasms.

Histiocytoses are clonal hematopoietic disorders frequently driven by mutations mapping to the BRAF and MEK1 and MEK2 kinases. Currently, however, the developmental origins of histiocytoses in patients are not well understood, and clinically meaningful therapeutic targets outside of BRAF and MEK are undefined. In this study, we uncovered activating mutations in CSF1R and rearrangements in RET and ALK that conferred dramatic responses to selective inhibition of RET (selpercatinib) and crizotinib, respectively, in patients with histiocytosis.