Dana-Farber Research Publication, 8.1.2021

Blood Activation of the MAPK Pathway Mediates Resistance to PI3K Inhibitors in Chronic Lymphocytic Leukemia Murali I, Kasar S, Naeem A, Tyekucheva S, Khalsa JK, Thrash EM, Itchaki G, Livitz D, Leshchiner I, Fernandes SM, Getz G, Brown JR Inhibitors of Bruton tyrosine kinase (BTK) and phosphatidylinositol 3-kinase d (PI3Kd) that target the B-cell receptor (BCR) signaling pathway have revolutionized the treatment of chronic lymphocytic leukemia (CLL). Mutations associated with resistance to BTK inhibitors have been identified, but limited data are available on mechanisms of resistance to PI3Kd inhibitors. Here we present findings from longitudinal whole-exome sequencing of cells from patients with multiply relapsed CLL (N = 28) enrolled in trials of PI3K inhibitors. The nonresponder subgroup was characterized by baseline activating mutations in MAP2K1, BRAF, and KRAS genes in 60% of patients. PI3Kd inhibition failed to inhibit ERK phosphorylation (pERK) in nonresponder CLL cells with and without mutations, whereas treatment with a MEK inhibitor rescued ERK inhibition. Overexpression of MAP2K1 mutants in vitro led to increased basal and inducible pERK and resistance to idelalisib. These data demonstrate that MAPK/ERK activation plays a key role in resistance to PI3Kd inhibitors in CLL and provide a rationale for therapy with a combination of PI3Kδ and ERK inhibitors.

Cancer Cell Artificial Intelligence for Clinical Oncology Kann BH, Hosny A, Aerts HJWL Clinical oncology is experiencing rapid growth in data that are collected to enhance cancer care. With recent advances in the field of artificial intelligence (AI), there is now a computational basis to integrate and synthesize this growing body of multi-dimensional data, deduce patterns, and predict outcomes to improve shared patient and clinician decision making. While there is high potential, significant challenges remain. In this perspective, we propose a pathway of clinical cancer care touchpoints for narrow-task AI applications and review a selection of applications. We describe the challenges faced in the clinical translation of AI and propose solutions. We also suggest paths forward in weaving AI into individualized patient care, with an emphasis on clinical validity, utility, and usability. By illuminating these issues in the context of current AI applications for clinical oncology, we hope to help advance meaningful investigations that will ultimately translate to real-world clinical use.

Gastroenterology Familial Burden and Other Clinical Factors Associated With Various Types of Cancer in Individuals With Lynch Syndrome Biller LH, Horiguchi M, Uno H, Ukaegbu C, Syngal S, Yurgelun MB BACKGROUND & AIMS: Lynch syndrome (LS) is associated with increased risks of various gastrointestinal, gynecologic, genitourinary, and other cancers. Many clinical practice guidelines recommend that LS carriers' screening strategies be devised based on their family history of various cancers, in addition to age-, sex-, and gene-specific considerations. The aim of this study was to examine the association between family history and other clinical factors with LS carriers' histories of various cancers. METHODS: Two cohorts of LS carriers were analyzed: a laboratory-based cohort of consecutively ascertained individuals undergoing germline LS testing and a clinic-based cohort of LS carriers undergoing clinical care at an academic medical center. Multivariable logistic regression was performed to assess clinical factors associated with LS carriers' histories of various cancers/neoplasms. Familial burden was defined as LS carriers' aggregate number of first-/second-degree relatives with a history of a given malignancy. RESULTS: Multivariable analysis of the laboratory-based cohort (3828 LS carriers) identified familial burden as being incrementally associated with LS carriers' personal history of endometrial (odds ratio [OR], 1.37 per affected first-/second-degree relative; 95% confidence interval [CI], 1.21-1.56), urinary tract (OR, 2.72; 95% CI, 2.02-3.67), small bowel (OR, 3.17; 95% CI, 1.65-6.12), gastric (OR, 1.93; 95% CI, 1.24-3.02), and pancreaticobiliary cancers (OR, 2.10; 95% CI, 1.21-3.65) and sebaceous neoplasms (OR, 7.39; 95% CI, 2.71-20.15). Multivariable analysis of the clinic-based cohort (607 LS carriers) confirmed a significant association of familial burden of endometrial and urinary tract cancers. CONCLUSIONS: Familial burden - in addition to age, sex, and specific LS gene - should be used to assess LS carriers' risks of specific cancers and guide decision-making about organ-specific surveillance.

Journal of Clinical Oncology Adjuvant Versus Early Salvage Radiation Therapy for Men at High Risk for Recurrence Following Radical Prostatectomy for Prostate Cancer and the Risk of Death D'Amico AV PURPOSE: Adjuvant compared with early salvage radiation therapy (sRT) following radical prostatectomy (RP) has not been shown to reduce progression-free survival in randomized controlled trials. However, these trials might have missed a benefit in men with adverse pathology at RP given that these men were under-represented and immortal time bias might have been present; herein, we investigate this possibility. METHODS: We evaluated the impact of adjuvant versus early sRT on all-cause mortality (ACM) risk in men with adverse pathology defined as positive pelvic lymph nodes (pN1) or pGleason score 8-10 prostate cancer (PC) and disease extending beyond the prostate (pT3/4). We used a treatment propensity score to minimize potential treatment selection bias when estimating the causal effect of adjuvant versus early sRT on ACM risk and a sensitivity analysis to assess the impact that varying definitions of adverse pathology had on ACM risk adjusting for age at RP, PC prognostic factors, site, and the time-dependent use of post-RP androgen deprivation therapy. RESULTS: After a median follow-up (interquartile range) of 8.16 (6.00-12.10) years, of the 26,118 men in the study cohort, 2,104 (8.06%) died, of which 539 (25.62%) were from PC. After excluding men with a persistent prostate-specific antigen, adjuvant compared with early sRT was associated with a significantly lower ACM risk among men with adverse pathology at RP when men with pN1 PC were excluded (0.33 [0.13-0.85]; P = .02) or included (0.66 [0.44-0.99]; P = .04). CONCLUSION: Adjuvant radiation therapy should be considered in men with pN1 or pGleason score 8 to 10 and pT3/4 PC given the possibility that a significant reduction in ACM risk exists.

Journal of Clinical Oncology Efficacy and Toxicity of Pegaspargase and Calaspargase Pegol in Childhood Acute Lymphoblastic Leukemia: Results of DFCI 11-001 Vrooman LM, Blonquist TM, Stevenson KE, Supko JG, Hunt SK, Cronholm SM, Koch V, Kay-Green S, Harris MH, Place AE, Neuberg DS, Sallan SE, Silverman LB PURPOSE: Dana-Farber Cancer Institute Acute Lymphoblastic Leukemia (ALL) Consortium Protocol 11-001 assessed efficacy and toxicity of calaspargase pegol (calaspargase), a novel pegylated asparaginase formulation with longer half-life, compared with the standard formulation pegaspargase. METHODS: Patients age 1 to 21 years with newly diagnosed ALL or lymphoblastic lymphoma were randomly assigned to intravenous pegaspargase or calaspargase, 2,500 IU/m2/dose. Patients received one induction dose. Beginning week 7, pegaspargase was administered every 2 week for 15 doses and calaspargase every 3 week for 10 doses (30 weeks). Serum asparaginase activity (SAA) (0.1 IU/mL considered therapeutic) was assessed 4, 11, 18, and 25 days after the induction dose and before each postinduction dose. RESULTS: Between 2012 and 2015, 239 eligible patients enrolled (230 ALL, nine lymphoblastic lymphoma); 120 were assigned to pegaspargase and 119 to calaspargase. After the induction dose, SAA was 0.1 IU/mL in 95% of patients on both arms 18 days after dosing. At day 25, more patients had SAA 0.1 IU/mL with calaspargase (88% v 17%; P .001). Postinduction, median nadir SAAs were similar (1.0 IU/mL) for both arms. Of 230 evaluable patients, 99% of pegaspargase and 95% of calaspargase patients achieved complete remission (P = .12), with no difference in frequency of high end-induction minimal residual disease among evaluable patients with B acute lymphoblastic leukemia (B-ALL). There were no differences in frequencies of asparaginase allergy, pancreatitis, thrombosis, or hyperbilirubinemia. With 5.3 years median follow-up, 5-year event-free survival for pegaspargase was 84.9% (SE 3.4%) and 88.1% (SE 3.0%) for calaspargase (P = .65). CONCLUSION: Every 3-week calaspargase had similar nadir SAA, toxicity, and survival outcomes compared with every 2-week pegaspargase. The high nadir SAA observed for both preparations suggest dosing strategies can be further optimized.

Journal of Clinical Oncology Radiation and Androgen Deprivation Therapy with or Without Docetaxel in the Management of Nonmetastatic Unfavorable-Risk Prostate Cancer: A Prospective Randomized Trial D'Amico AV, Xie W, McMahon E, Loffredo M, Medeiros S, Bubley G PURPOSE: Although docetaxel is not recommended when managing men with unfavorable-risk prostate cancer (PC) given negative or inconclusive results from previous randomized trials, unstudied benefits may exist. METHODS: Between September 21, 2005, and January 13, 2015, we randomly assigned 350 men 1:1 with T1c-4N0M0 unfavorable-risk PC to receive radiation therapy (RT) and androgen deprivation therapy (ADT) plus docetaxel (60 mg/m2 once every 3 weeks for three cycles before RT and 20 mg/m2 once weekly during RT) versus ADT + RT. We evaluated the treatment effect of adding docetaxel to ADT + RT on the primary end point of overall survival (OS) and the incidence of RT-induced cancers and explored whether the impact of the treatment effect on OS differed within prostate-specific antigen (PSA) subgroups (< 4, > 20 v 4-20 ng/mL) using the interaction test for heterogeneity adjusted for age and PC prognostic factors. RESULTS: After a median follow-up of 10.2 years, 89 men died (25.43%); of these, 42 from PC (47.19%). Although OS was not significantly increased in the docetaxel arm (the restricted mean survival time over 10 years was 9.11 v 8.82 years; P = .22), significantly fewer RT-induced cancers were observed (10-year estimates: 0.61% v 4.90%; age-adjusted hazard ratio of 0.13; 95% CI, 0.02 to 0.97; P = .046). The treatment effect of adding docetaxel to ADT + RT on OS significantly differed in men with a PSA < 4 ng/mL versus 4-20 ng/mL (adjusted hazard ratio: 0.27 and 1.51, respectively) because of less PC-specific mortality on the docetaxel arm (0.00% v 28.57%) among men with PSA < 4 ng/mL. CONCLUSION: Adding docetaxel to ADT + RT did not prolong OS in men with unfavorable-risk PC, but decreased RT-induced cancer incidence, and may prolong OS in the subgroup of men with a PSA < 4 ng/mL by reducing PC-specific mortality.

Journal of the National Cancer Institute Timing of Aspirin Use in Colorectal Cancer Chemoprevention: A Prospective Cohort Study Zhang Y, Chan AT, Meyerhardt JA, Giovannucci EL BACKGROUND: Prior epidemiological and intervention studies have not been able to separate independent effects of dose, timing, and duration of aspirin use in colorectal cancer (CRC) chemoprevention. We examined aspirin-based CRC chemoprevention according to timing in the Nurses' Health Study and Health Professionals Follow-Up Study. METHODS: The exposures include cumulative average dose and total duration of aspirin use in more than 10 years before follow-up started (remote period) and in the immediate 10 years before follow-up started (recent period). Cox models were used to estimate hazard ratios (HRs) and 95% confidence intervals (CIs) for exposures and CRC risk. RESULTS: Aspirin use of longer than 10 years before follow-up started (HR = 0.88, 95% CI = 0.83 to 0.94) per 5-year increment and the immediate 10 years before follow-up started (HR = 0.90, 95% CI = 0.84 to 0.96) were similarly important in CRC chemoprevention, though a 5-year lag was required for a clear benefit in the recent period. In the remote period, the association was not dose dependent; compared with less than 0.5 standard-dose (325mg) tablets per week; hazard ratios were 0.78 (95% CI = 0.63 to 0.98), 0.81 (95% CI = 0.72 to 0.91), and 0.74 (95% CI = 0.64 to 0.86) for doses of 0.5 to less than 1.5, 1.5 to less than 5, and 5 and more tablets per week, respectively. However, there was dose dependency in the recent period (with respective HR = 0.91, 95% CI = 0.79 to 1.06; HR = 0.87, 95% CI = 0.77 to 0.98; and HR = 0.76, 95% CI = 0.64 to 0.91). CONCLUSIONS: A suggestive benefit necessitates at least 6-10 years and most clearly after approximately 10‚Äâyears since initiation of aspirin. Remote use and use within the previous 10 years both contribute independently to decrease risk, though a lower dose may be required for a benefit with longer term use.

JAMA Oncology Association of Combination of Conformation-Specific KIT Inhibitors With Clinical Benefit in Patients With Refractory Gastrointestinal Stromal Tumors: A Phase 1b/2a Nonrandomized Clinical Trial Wagner AJ IMPORTANCE: Many cancer subtypes, including KIT-mutant gastrointestinal stromal tumors (GISTs), are driven by activating mutations in tyrosine kinases and may initially respond to kinase inhibitors but frequently relapse owing to outgrowth of heterogeneous subclones with resistance mutations. KIT inhibitors commonly used to treat GIST (eg, imatinib and sunitinib) are inactive-state (type II) inhibitors. OBJECTIVE: To assess whether combining a type II KIT inhibitor with a conformation-complementary, active-state (type I) KIT inhibitor is associated with broad mutation coverage and global disease control. DESIGN, SETTING, AND PARTICIPANTS: A highly selective type I inhibitor of KIT, PLX9486, was tested in a 2-part phase 1b/2a trial. Part 1 (dose escalation) evaluated PLX9486 monotherapy in patients with solid tumors. Part 2e (extension) evaluated PLX9486-sunitinib combination in patients with GIST. Patients were enrolled from March 2015 through February 2019; data analysis was performed from May 2020 through July 2020. INTERVENTIONS: Participants received 250, 350, 500, and 1000 mg of PLX9486 alone (part 1) or 500 and 1000 mg of PLX9486 together with 25 or 37.5 mg of sunitinib (part 2e) continuously in 28-day dosing cycles until disease progression, treatment discontinuation, or withdrawal. MAIN OUTCOMES AND MEASURES: Pharmacokinetics, safety, and tumor responses were assessed. Clinical efficacy end points (progression-free survival and clinical benefit rate) were supplemented with longitudinal monitoring of KIT mutations in circulating tumor DNA. RESULTS: A total of 39 PLX9486-naive patients (median age, 57 years [range, 39-79 years]; 22 men [56.4%]; 35 [89.7%] with refractory GIST) were enrolled in the dose escalation and extension parts. The recommended phase 2 dose of PLX9486 was 1000 mg daily. At this dose, PLX9486 could be safely combined with 25 or 37.5 mg daily of sunitinib continuously. Patients with GIST who received PLX9486 at a dose of 500 mg or less, at the recommended phase 2 dose, and with sunitinib had median (95% CI) progression-free survivals of 1.74 (1.54-1.84), 5.75 (0.99-11.0), and 12.1 (1.34-NA) months and clinical benefit rates (95% CI) of 14% (0%-58%), 50% (21%-79%), and 80% (52%-96%), respectively. CONCLUSIONS AND RELEVANCE: In this phase 1b/2a nonrandomized clinical trial, type I and type II KIT inhibitors PLX9486 and sunitinib were safely coadministered at the recommended dose of both single agents in patients with refractory GIST. Results suggest that cotargeting 2 complementary conformational states of the same kinase was associated with clinical benefit with an acceptable safety profile. TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT02401815.

JAMA Oncology Use of Total Neoadjuvant Therapy for Locally Advanced Rectal Cancer: Initial Results from the Pembrolizumab Arm of a Phase 2 Randomized Clinical Trial Rahma OE, Hong TS IMPORTANCE: Total neoadjuvant therapy (TNT) is often used to downstage locally advanced rectal cancer (LARC) and decrease locoregional relapse; however, more than one-third of patients develop recurrent metastatic disease. As such, novel combinations are needed. OBJECTIVE: To assess whether the addition of pembrolizumab during and after neoadjuvant chemoradiotherapy can lead to an improvement in the neoadjuvant rectal (NAR) score compared with treatment with FOLFOX (5-fluorouracil, leucovorin, and oxaliplatin) and chemoradiotherapy alone. DESIGN, SETTING, AND PARTICIPANTS: In this open-label, phase 2, randomized clinical trial (NRG-GI002), patients in academic and private practice settings were enrolled. Patients with stage II/III LARC with distal location (cT3-4 ? 5cm from anal verge, any N), with bulky disease (any cT4 or tumor within 3 mm of mesorectal fascia), at high risk for metastatic disease (cN2), and/or who were not candidates for sphincter-sparing surgery (SSS) were stratified based on clinical tumor and nodal stages. Trial accrual opened on August 1, 2018, and ended on May 31, 2019. This intent-to-treat analysis is based on data as of August 2020. INTERVENTIONS: Patients were randomized (1:1) to neoadjuvant FOLFOX for 4 months and then underwent chemoradiotherapy (capecitabine with 50.4 Gy) with or without intravenous pembrolizumab administered at a dosage of 200 mg every 3 weeks for up to 6 doses before surgery. MAIN OUTCOMES AND MEASURES: The primary end point was the NAR score. Secondary end points included pathologic complete response (pCR) rate, SSS, disease-free survival, and overall survival. This report focuses on end points available after definitive surgery (NAR score, pCR, SSS, clinical complete response rate, margin involvement, and safety). RESULTS: A total of 185 patients (126 [68.1%] male; mean [SD] age, 55.7 [11.1] years) were randomized to the control arm (CA) (n=95) or the pembrolizumab arm (PA) (n=90). Of these patients, 137 were evaluable for NAR score (68 CA patients and 69 PA patients). The mean (SD) NAR score was 11.53 (12.43) for the PA patients (95% CI, 8.54-14.51) vs 14.08 (13.82) for the CA patients (95% CI, 10.74-17.43) (P=.26). The pCR rate was 31.9% in the PA vs 29.4% in the CA (P=.75). The clinical complete response rate was 13.9% in the PA vs 13.6% in the CA (P=.95). The percentage of patients who underwent SSS was 59.4% in the PA vs 71.0% in the CA (P=.15). Grade 3 to 4 adverse events were slightly increased in the PA (48.2%) vs the CA (37.3%) during chemoradiotherapy. Two deaths occurred during FOLFOX: sepsis (CA) and pneumonia (PA). No differences in radiotherapy fractions, FOLFOX, or capecitabine doses were found. CONCLUSIONS AND RELEVANCE: Pembrolizumab added to chemoradiotherapy as part of total neoadjuvant therapy was suggested to be safe; however, the NAR score difference does not support further study. TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT02921256.

Lancet Ipatasertib Plus Abiraterone and Prednisolone in Metastatic Castration-Resistant Prostate Cancer (IPATential150): A Multicentre, Randomised, Double-Blind, Phase 3 Trial Sweeney C BACKGROUND: The PI3K/AKT and androgen-receptor pathways are dysregulated in metastatic castration-resistant prostate cancers (mCRPCs); tumours with functional PTEN-loss status have hyperactivated AKT signalling. Dual pathway inhibition with AKT inhibitor ipatasertib plus abiraterone might have greater benefit than abiraterone alone. We aimed to compare ipatasertib plus abiraterone with placebo plus abiraterone in patients with previously untreated mCRPC with or without tumour PTEN loss. METHODS: We did a randomised, double-blind, phase 3 trial at 200 sites across 26 countries or regions. Patients aged 18 years or older with previously untreated asymptomatic or mildly symptomatic mCRPC who had progressive disease and Eastern Collaborative Oncology Group performance status of 0 or 1 were randomly assigned (1:1; permuted block method) to receive ipatasertib (400 mg once daily orally) plus abiraterone (1000 mg once daily orally) and prednisolone (5 mg twice a day orally) or placebo plus abiraterone and prednisolone (with the same dosing schedule). Patients received study treatment until disease progression, intolerable toxicity, withdrawal from the study, or study completion. Stratification factors were previous taxane-based therapy for hormone-sensitive prostate cancer, type of progression, presence of visceral metastasis, and tumour PTEN-loss status by immunohistochemistry. Patients, investigators, and the study sponsor were masked to the treatment allocation. The coprimary endpoints were investigator-assessed radiographical progression-free survival in the PTEN-loss-by-immunohistochemistry population and in the intention-to-treat population. This study is ongoing and is registered with ClinicalTrials.gov, NCT03072238. FINDINGS: Between June 30, 2017, and Jan 17, 2019, 1611 patients were screened for eligibility and 1101 (68%) were enrolled; 554 (50%) were assigned to the placebo-abiraterone group and 547 (50%) to the ipatasertib-abiraterone group. At data cutoff (March 16, 2020), median follow-up duration was 19 months (range 0-33). In the 521 (47%) patients who had tumours with PTEN loss by immunohistochemistry (261 in the placebo-abiraterone group and 260 in the ipatasertib-abiraterone group), median radiographical progression-free survival was 16×5 months (95% CI 13×9-17×0) in the placebo-abiraterone group and 18×5 months (16×3-22×1) in the ipatasertib-abiraterone group (hazard ratio [HR] 0×77 [95% CI 0×61-0×98]; p=0×034; significant at (a=0×04). In the intention-to-treat population, median progression-free survival was 16×6 months (95% CI 15×6-19×1) in the placebo-abiraterone group and 19×2 months (16×5-22×3) in the ipatasertib-abiraterone group (HR 0×84 [95% CI 0×71-0×99]; p=0×043; not significant at a=0×01). Grade 3 or higher adverse events occurred in 213 (39%) of 546 patients in the placebo-abiraterone group and in 386 (70%) of 551 patients in the ipatasertib-abiraterone group; adverse events leading to discontinuation of placebo or ipatasertib occurred in 28 (5%) in the placebo-abiraterone group and 116 (21%) in the ipatasertib-abiraterone group. Deaths due to adverse events deemed related to treatment occurred in two patients (<1%; acute myocardial infarction [n=1] and lower respiratory tract infection [n=1]) in the placebo-abiraterone group and in two patients (<1%; hyperglycaemia [n=1] and chemical pneumonitis [n=1]) in the ipastasertb-abiraterone group. INTERPRETATION: Ipatasertib plus abiraterone significantly improved radiographical progression-free survival compared with placebo plus abiraterone among patients with mCRPC with PTEN-loss tumours, but there was no significant difference between the groups in the intention-to-treat population. Adverse events were consistent with the known safety profiles of each agent. These data suggest that combined AKT and androgen-receptor signalling pathway inhibition with ipatasertib and abiraterone is a potential treatment for men with PTEN-loss mCRPC, a population with a poor prognosis. FUNDING: F Hoffmann-La Roche and Genentech.

Nature cGAS-Like Receptors Sense RNA and Control 3'2'-cGAMP Signaling in Drosophila Slavik KM, Morehouse BR, Ragucci AE, Zhou W, Lee ASY, Kranzusch PJ Cyclic GMP-AMP synthase (cGAS) is a cytosolic DNA sensor that produces the second messenger 2'3'-cGAMP and controls activation of innate immunity in mammalian cells1-5. Animal genomes typically encode multiple proteins with predicted homology to cGAS6-10, but the function of these uncharacterized enzymes is unknown. Here we show that cGAS-like receptors (cGLRs) are innate immune sensors capable of recognizing divergent molecular patterns and catalyzing synthesis of distinct nucleotide second messenger signals. Crystal structures of human and insect cGLRs reveal a nucleotidyltransferase signaling core shared with cGAS and a diversified primary ligand-binding surface modified with significant insertions and deletions. We demonstrate that cGLR surface remodeling enables altered ligand specificity and use a forward biochemical screen to identify cGLR1 as a double-stranded RNA sensor in the model organism Drosophila melanogaster. Surprisingly, RNA recognition activates Drosophila cGLR1 to synthesize the novel product cG[3'-5']pA[2'-5']p (3'2'-cGAMP). A crystal structure of Drosophila Stimulator of Interferon Genes (STING) in complex with 3'2'-cGAMP explains selective isomer recognition and we demonstrate that 3'2'-cGAMP induces an enhanced antiviral state in vivo that protects from viral infection. Similar to radiation of Toll-like receptors in pathogen immunity, our results establish cGLRs as a diverse family of metazoan pattern recognition receptors.

Nature Communications High-Resolution Characterization of Gene Function Using Single-Cell CRISPR Tiling Screen Delaney CD, Wang X, Chen KY, Feng Z, Hoshii T, Armstrong SA, Chen CW Identification of novel functional domains and characterization of detailed regulatory mechanisms in cancer-driving genes is critical for advanced cancer therapy. To date, CRISPR gene editing has primarily been applied to defining the role of individual genes. Recently, high-density mutagenesis via CRISPR tiling of gene-coding exons has been demonstrated to identify functional regions in genes. Furthermore, breakthroughs in combining CRISPR library screens with single-cell droplet RNA sequencing (sc-RNAseq) platforms have revealed the capacity to monitor gene expression changes upon genetic perturbations at single-cell resolution. Here, we present "sc-Tiling," which integrates a CRISPR gene-tiling screen with single-cell transcriptomic and protein structural analyses. Distinct from other reported single-cell CRISPR screens focused on observing gene function and gene-to-gene/enhancer-to-gene regulation, sc-Tiling enables the capacity to identify regulatory mechanisms within a gene-coding region that dictate gene activity and therapeutic response.

Nature Genetics Genome-Scale Screens Identify Factors Regulating Tumor Cell Responses to Natural Killer Cells Sheffer M, Lowry E, Borah M, Amara SN, Mader CC, Roth JA, Tsherniak A, Freeman SS, Dashevsky O, Gandolfi S, Bender S, Bryan JG, Zhu C, Wang L, Tariq I, Simoes RM, Dhimolea E, Yu C, Hu Y, Giannakis M, Fraenkel E, Golub T, Romee R, Culhane AC, Mitsiades CS To systematically define molecular features in human tumor cells that determine their degree of sensitivity to human allogeneic natural killer (NK) cells, we quantified the NK cell responsiveness of hundreds of molecularly annotated 'DNA-barcoded' solid tumor cell lines in multiplexed format and applied genome-scale CRISPR-based gene-editing screens in several solid tumor cell lines, to functionally interrogate which genes in tumor cells regulate the response to NK cells. In these orthogonal studies, NK cell-sensitive tumor cells tend to exhibit 'mesenchymal-like' transcriptional programs; high transcriptional signature for chromatin remodeling complexes; high levels of B7-H6 (NCR3LG1); and low levels of HLA-E/antigen presentation genes. Importantly, transcriptional signatures of NK cell-sensitive tumor cells correlate with immune checkpoint inhibitor (ICI) resistance in clinical samples. This study provides a comprehensive map of mechanisms regulating tumor cell responses to NK cells, with implications for future biomarker-driven applications of NK cell immunotherapies.

New England Journal of Medicine Lenvatinib plus Pembrolizumab for Renal Cell Carcinoma Reply Choueiri TK To the Editor: In the phase 3 CLEAR trial investigating first-line treatment strategies for advanced renal cell carcinoma, the combination of lenvatinib plus pembrolizumab improved overall survival as compared with sunitinib (hazard ratio for death, 0.66; 95% confidence interval [CI], 0.49 to 0.88; P=0.005). However, in the IMDC (International Metastatic Renal Cell Carcinoma Database Consortium) favorable-risk group that represented one third of the patients, improvement in progression-free survival did not translate into an overall survival benefit.

American Journal of Hematology Cell-Free DNA Analysis for Detection of MYD88(L265P) and CXCR4(S338X) Mutations in Waldenström Macroglobulinemia Demos MG, Hunter ZR, Xu L, Tsakmaklis N, Kofides A, Munshi M, Liu X, Guerrera ML, Leventoff CR, White TP, Flynn CA, Meid K, Patterson CJ, Yang G, Branagan AR, Sarosiek S, Castillo JJ, Treon SP, Gustine JN

American Journal of Hematology Complete Response to Pembrolizumab and Radiation in a Patient with HIV-Negative, EBV-Positive Plasmablastic Lymphoma Castillo JJ, Lamacchia J, Flynn CA, Sarosiek S

American Journal of Hematology Pretreatment Clinical and Genetic Factors Predict Early Post-Treatment Mortality in Fit AML Patients Following Induction Haydu JE, Flamand Y, Vedula RS, Versluis J, Charles A, Copson KM, Stone RM, DeAngelo DJ, Neuberg D, Lindsley RC, Luskin MR

American Journal of Hematology The Evaluation and Management of Monoclonal Gammopathy of Renal Significance and Monoclonal Gammopathy of Neurological Significance Castillo JJ

American Journal of Reproductive Immunology Triaging Abnormal Cervical Cancer Screening Tests Using p16INK4a Detection by ELISA on Fresh Cervical Samples Leung SOA, Feldman S, Kalyanaraman R, Shanmugam V, Worley MJ, Berkowitz RS, Horowitz NS, Feltmate CM, Muto MG, Lee LJ, King MT, Einarsson JI, Ajao MO, Elias KM

Angewandte Chemie International Edition Discovery of a Potent Degrader for Fibroblast Growth Factor Receptor 1/2 Du G, Jiang J, Wu Q, Henning NJ, Donovan KA, Yue H, Che J, Lu W, Fischer ES, Bardeesy N

Bioinformatics CUT&RUNTools 2.0: A Pipeline for Single-Cell and Bulk-Level CUT&RUN and CUT&Tag Data Analysis Yu F, Sankaran VG, Yuan GC

Bioinformatics Robustifying Genomic Classifiers to Batch Effects via Ensemble Learning Parmigiani G

Blood Cancer Discovery Finding the Optimal Partner to Pair with Bispecific Antibody Therapy for Multiple Myeloma Louvet C, Nadeem O, Smith EL

Blood Cancer Discovery Lysine Demethylase 5A is Required for MYC Driven Transcription in Multiple Myeloma Park PMC, Wang T, Ogiya D, Kurata K, Zhang X, Li D, Pei C, Wimalasena VK, Samur MK, Tai YT, Munshi NC, Anderson KC, Hideshima T, Qi J

British Journal of Haematology Subgroup Analysis of ICARIA-MM Study in Relapsed/Refractory Multiple Myeloma Patients with High-Risk Cytogenetics Richardson P

Breast Cancer Research and Treatment Correction To: Factors Associated with Late Risks of Breast Cancer Specific Mortality in the SEER Registry Leone JP, Hassett MJ, Graham N, Tayob N, Freedman RA, Tolaney SM, Winer EP, Lin NU

Cancer Interdisciplinary Care of Pediatric Oncology Patients in Central America and the Caribbean Mack JW

Cancer Prostate-Specific Antigen Levels of 4 and >4 ng/mL and Risk of Prostate Cancer-Specific Mortality in Men with Biopsy Gleason Score 9 to 10 Prostate Cancer Kim DW, D'Amico AV

Cancer Race, Ethnicity, and Goal-Concordance of End-of-Life Palliative Care in Pediatric Oncology Umaretiya PJ, Li A, McGovern A, Ma C, Wolfe J, Bona K

Cancer Risk of Cardiovascular Mortality with Androgen Deprivation Therapy in Prostate Cancer: A Secondary Analysis of the Prostate, Lung, Colorectal, and Ovarian (PLCO) Randomized Controlled Trial Butler SS, Mahal BA, Nohria A, Dee EC, Makkar R, Whitbeck A, Wangoe J, Mouw KW, Nguyen PL, Muralidhar V

Cancer Validating the Patient-Reported Outcomes Measurement Information System Short Form v1.0-Anxiety 8a in a Sample of Young Adult Cancer Survivors: Comparison with a Structured Clinical Diagnostic Interview Recklitis CJ, Blackmon JE, Chevalier LL, Chang G

Cancer Research Cell line-specific network models of ER+ breast cancer identify potential PI3Ka inhibitor resistance mechanisms and drug combinations Gomez Tejeda Zanudo J, Mao P, Kowalski K, Johnson GN, Letai A, Wagle N

Cell Reports Extracellular Domain Shedding of the ALK Receptor Mediates Neuroblastoma Cell Migration Huang H, Dries R, Sharma B, Debruyne DN, Harlow M, Sengupta S, Yeung CM, Wang W, George RE

Clinical Cancer Research CDKN2A Alterations and Response to Immunotherapy in Solid Tumors Adib E, Nassar AH, Akl EW, Abou Alaiwi S, Nuzzo PV, Sonpavde G, Haddad RI, Mouw KW, Giannakis M, Hodi FS, Shukla SA, Gusev A, Braun DA, Choueiri TK, Kwiatkowski DJ

Clinical Cancer Research First-in-Human Phase I Study of ABBV-085, an Antibody-Drug Conjugate Targeting LRRC15, in Sarcomas and Other Advanced Solid Tumors Demetri GD

Clinical Cancer Research Phase II Multicenter Study of Enzalutamide in Metastatic Castration-Resistant Prostate Cancer to Identify Mechanisms Driving Resistance McKay RR, Kwak L, Crowdis JP, Xie W, Werner L, Lis RT, Zhang Z, Wei XX, Van Allen EM, Bhatt RS, Bubley GJ, Taplin ME

Clinical Cancer Research Thirty Years of HER3: From Basic Biology to Therapeutic Interventions Haikala HM, Jänne PA

Clinical Gastroenterology and Hepatology Validation of the Updated Hepatocellular Carcinoma Early Detection Screening Algorithm in a Community-Based Cohort of Patients with Cirrhosis of Multiple Etiologies Tayob N

Cold Spring Harbor Perspectives in Medicine Biological and Translational Considerations regarding the Recent Therapeutic Successes and Upcoming Challenges for Multiple Myeloma Mitsiades CS

Current Treatment Options in Oncology Role of Radiation Therapy for Newly Diagnosed Retroperitoneal Sarcoma Lam MB, Baldini EH, DeLaney TF

Cytometry Part A High-Throughput Image Cytometry Detection Method for CAR-T Transduction, Cell Proliferation, and Cytotoxicity Assays Wang Y, Grimaud M, Fayed A, Zhu Q, Marasco WA

European Journal of Medicinal Chemistry A Biphenyl Inhibitor of eIF4E Targeting an Internal Binding Site Enables the Design of Cell-Permeable PROTAC-Degraders Fischer PD, Papadopoulos E, Dempersmier JM, Wang ZF, Nowak RP, Donovan KA, Kalabathula J, Gorgulla C, Kabha E, Dimitrakakis N, Mitsiades C, Fischer ES, Wagner G, Arthanari H

Future Oncology Immune-Related Adverse Events with PD-1 Versus PD-L1 Inhibitors: A Meta-Analysis of 8730 Patients from Clinical Trials Sonpavde GP

Genome Medicine Haplotype-Resolved Germline and Somatic Alterations in Renal Medullary Carcinomas Tan KT, Kim H, Carrot-Zhang J, Zhang Y, Kim WJ, Kugener G, Howard TP, Beroukhim R, Li H, Alper SL, Mullen EA, Hahn WC, Meyerson M

Gynecologic Oncology Sequential Phase II Clinical Trials Evaluating CRLX101 as Monotherapy and in Combination with Bevacizumab in Recurrent Ovarian Cancer Krasner CN, Campos SM, Young CL, Chadda KR, Lee H, Horowitz NS, Konstantinopoulos PA, D'Ascanio AM, Matulonis UA, Penson RT

Immunology and Cell Biology CD44 v5 Domain Inhibition Represses the Polarization of Th2 Cells by Interfering with the IL-4/IL-4R Signaling Pathway Yang C, Lin J, Xue L, Kwart A, Jiang M, Jiang X, Munshi NC

International Journal of Gynecologic Cancer Definitive Radiotherapy for Vaginal Recurrence of Early-Stage Endometrial Cancer: Survival Outcomes and Effect of Mismatch Repair Status Alban G, Cheng T, Adleman J, Buzurovic I, Pretz J, Singer L, King M, Lee L

International Journal of Radiation Oncology, Biology, Physics Clinical Natural Language Processing for Radiation Oncology: A Review and Practical Primer Bitterman DS, Miller TA, Mak RH, Savova GK

International Journal of Radiation Oncology, Biology, Physics Radiation Therapy in a Patient with Dermatomyositis and Delayed Wound Healing Bellon JR, Recht A

Investigational New Drugs Phase 1 Dose Escalation Study of Seribantumab (MM-121), an Anti-HER3 Monoclonal Antibody, in Patients with Advanced Solid Tumors Shapiro GI

Journal of Adolescent Health Adolescent Shared Decision-Making: Where We Have Been and Where We are Going Marron JM

Journal of Pain and Symptom Management Children at the Intersection of Pediatric Palliative Care and Child Maltreatment: A Vulnerable and Understudied Population Cleveland RW, Ullrich C

Journal of Pain and Symptom Management Weighing Distress and Benefit: Understanding the Research Participation Experiences of Bereaved Parents of Children with Complex Chronic Conditions Deming RS, Wolfe J, DeCourcey DD

Journal of Palliative Medicine Meeting and Exceeding Hospice and Palliative Medicine Milestones in a Pandemic Thomas JD, Doyle KP

Journal of Proteome Research A Compendium of Murine (Phospho)Peptides Encompassing Different Isobaric Labeling and Data Acquisition Strategies Popow O, Liu X, Haigis KM, Gygi SP, Paulo JA

Journal of Thoracic Oncology SMARCA4 and Other SWItch/Sucrose NonFermentable Family Genomic Alterations in NSCLC: Clinicopathologic Characteristics and Outcomes to Immune Checkpoint Inhibition Alessi JV, Ricciuti B, Spurr LF, Gupta H, Li YY, Nishino M, Cherniack AD, Lindsay J, Sharma B, Felt KD, Rodig SJ, Cheng ML, Sholl LM, Awad MM

Journal of Urology Results of a Randomized Phase II Trial of Intense Androgen Deprivation Therapy Prior to Radical Prostatectomy in Men with High-Risk Localized Prostate Cancer Xie W, Fennessy FM, Zhang Z, Lis R, Calagua C, Bubley GJ, Einstein DJ, Chang PK, Wagner AA, Preston MA, Kilbridge K, Chang SL, Choudhury AD, Pomerantz MM, Trinh QD, Kibel AS, Taplin ME

Lung Cancer Rates of Invasive Disease and Outcomes in NSCLC Patients with Biopsy Suggestive of Carcinoma In Situ White AA, Kozono DE, Singer L, Sands JM, Sholl LM, Mak RH, Kann BH

Molecular Cancer Research NF-kB Blockade with Oral Administration of Dimethylaminoparthenolide (DMAPT), Delays Prostate Cancer Resistance to Androgen Receptor (AR) Inhibition and Inhibits AR Variants Morel KL, Hamid AA, Clohessy JG, Pandell N, Ellis L, Sweeney CJ

Nature Reviews Clinical Oncology Cancer Therapies Based on Targeted Protein Degradation - Lessons Learned with Lenalidomide Jan M, Sperling AS, Ebert BL

Nature Reviews Drug Discovery Kinase Drug Discovery 20 Years After Imatinib: Progress and Future Directions Jänne PA

Oncology Nursing Forum Symptom Clusters in Patients with Gynecologic Cancer Receiving Chemotherapy Pozzar RA, Hammer MJ

Oncologist Clinical Results and Biomarker Analyses of Axitinib and TRC105 versus Axitinib Alone in Patients with Advanced or Metastatic Renal Cell Carcinoma (TRAXAR) Choueiri TK, Walsh M

Physics in Medicine and Biology Improvements in Beam's Eye View Fiducial Tracking Using a Novel Multilayer Imager Harris TC, Jacobson MW, Myronakis ME, Valencia Lozano I, Mamon HJ, Mancias JD, Martin NE, Berbeco RI

Practical Radiation Oncology Association Between Travel Distance and Use of Postoperative Radiation Therapy Among Men with Organ-Confined Prostate Cancer: Does Geography Influence Treatment Decisions? Arega MA, Yang DD, Mahal BA, Dee EC, Butler SS, Mouw KW, Nguyen PL, Muralidhar V

Practical Radiation Oncology Development and Implementation of an Online Adaptive Stereotactic Body Radiation Therapy Workflow for Treatment of Intracardiac Metastasis Shi DD, Liu KX, Hacker F, Hanna GJ, Kwong RY, Cagney DN, Mak RH, Singer L

Prostate A Polymorphism in the Promoter of FRAS1 is a Candidate SNP Associated with Metastatic Prostate Cancer Wang V, Gerke T, Penney KL, Markt SC, Freedman M, Pomerantz M, Lee GM, Rana H, Börnigen D, Rebbeck TR, Huttenhower C, Mucci L, Sweeney CJ

Seminars in Nuclear Medicine FDG PET for Assessment of Autologous Stem Cell Transplantation Jacene HA

Supportive Care in Cancer Quantitative-Qualitative Analyses of Patient-Reported Pain Response After Palliative Radiation Therapy Shi DD, Balboni TA, Krishnan MS, Spektor A, Huynh MA, Shiloh RY, Zaslowe-Dude C, Hertan LM

Transfusion Peri-Transfusion Quality-of-Life Assessment for Patients with Myelodysplastic Syndromes Abel GA, Magnavita ES, Jaung T, Lu W, Hantel A, Bahl NE, Winer ES

Transplant Cell Therapy National Institutes of Health Consensus Development Project on Criteria for Clinical Trials in Chronic Graft-versus-Host Disease: IIa. The 2020 Clinical Implementation and Early Diagnosis Working Group Report Luo ZK, Cutler C

Trends in Biochemical Sciences Histone PTM Crosstalk Stimulates Dot1 Methyltransferase Activity Cutler JA, Perner F, Armstrong SA