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Blood
Molecular and Cellular Features of CTLA-4 Blockade for Relapsed Myeloid Malignancies After Transplantation
Penter L, Zhang Y, Savell A, Huang T, Cieri N, Thrash EM, Jhaveri A, Fu J, Ranasinghe S, Li S,
Zhang W, Hathaway ES, Nazzaro M, Kim HT, Severgnini M, Cibulskis C, Gabriel S, Livak KJ, Cutler C, Antin JH, Nikiforow S, Koreth J, Ho VT, Armand P, Ritz J, Neuberg D, Hodi FS, Soiffer RJ, Liu XS, Davids MS, Bachireddy P, Wu CJ
Relapsed myeloid disease after allogeneic stem cell transplantation (HSCT) remains largely incurable. We previously demonstrated the potent activity of immune checkpoint blockade in this clinical setting with ipilimumab or nivolumab. To define the molecular and cellular pathways by which CTLA-4 blockade with ipilimumab can reinvigorate an effective graft-versus-leukemia (GVL) response, we integrated transcriptomic analysis of leukemic biopsies with immunophenotypic profiling of matched peripheral blood samples collected from patients treated with ipilimumab following HSCT on the Experimental Therapeutics Clinical Trials Network 9204 trial. Response to ipilimumab was associated with transcriptomic evidence of increased local CD8+ T-cell infiltration and activation. Systemically, ipilimumab decreased na?Øve and increased memory T-cell populations and increased expression of markers of T-cell activation and costimulation such as PD-1, HLA-DR, and ICOS, irrespective of response. However, responding patients were characterized by higher turnover of T-cell receptor sequences in peripheral blood and showed increased expression of proinflammatory chemokines in plasma that was further amplified by ipilimumab. Altogether, these data highlight the compositional T-cell shifts and inflammatory pathways induced by ipilimumab both locally and systemically that associate with successful GVL outcomes. This trial was registered at www.clinicaltrials.gov as #NCT01822509.
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Cancer Discovery
Longitudinal Single-Cell Dynamics of Chromatin Accessibility and Mitochondrial Mutations in Chronic Lymphocytic Leukemia Mirror Disease History
Penter L, Gohil SH, Parry EM, Huang T, Li S, Zhang W, Livitz D, Leshchiner I, Getz G, Brown JR, Davids MS, Neuberg DS, Livak KJ, Sankaran VG, Wu CJ
While cancers evolve during disease progression and in response to therapy, temporal dynamics remain difficult to study in humans due to the lack of consistent barcodes marking individual clones in vivo. We employ mitochondrial single-cell assay for transposase-accessible chromatin with sequencing to profile 163,279 cells from 9 patients with chronic lymphocytic leukemia (CLL) collected across disease course and utilize mitochondrial DNA (mtDNA) mutations as natural genetic markers of cancer clones. We observe stable propagation of mtDNA mutations over years in the absence of strong selective pressure indicating clonal persistence, but dramatic changes following tight bottlenecks including disease transformation and relapse post-therapy, paralleled by acquisition of copy number variants, changes in chromatin accessibility and gene expression. Furthermore, we link CLL subclones to distinct chromatin states, providing insight into non-genetic sources of relapse. mtDNA mutations thus mirror disease history and provide naturally-occurring genetic barcodes to enable patient-specific study of cancer subclonal dynamics.
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Cancer Discovery
Therapeutically Increasing MHC-I Expression Potentiates Immune Checkpoint Blockade
Gu SS, Zhang W, Wang X, Traugh N, Li Z, Meyer C, Stewig B, Xie Y, Bu X, Manos MP, Font-Tello A, Gjini E, Lako A, Lim K, Conway J, Tewari AK, Zeng Z, Sahu AD, Tokheim C, Weirather JL, Fu J,
Zhang Y, Liang JH, Cejas P, Freeman GJ, Rodig S, Long HW, Gewurz BE, Hodi FS, Brown M, Liu XS
Immune checkpoint blockade (ICB) therapy revolutionized cancer treatment, but many patients with impaired MHC-I expression remain refractory. Here, we combined FACS-based genome-wide CRISPR screens with a data-mining approach to identify drugs that can upregulate MHC-I without inducing PD-L1. CRISPR screening identified TRAF3, a suppressor of the NFŒ?B pathway, as a negative regulator of MHC-I but not PD-L1. The Traf3-knockout gene expression signature is associated with better survival in ICB-na?Øve patients with cancer and better ICB response. We then screened for drugs with similar transcriptional effects as this signature and identified Second Mitochondria-derived Activator of Caspase (SMAC) mimetics. We experimentally validated that the SMAC mimetic birinapant upregulates MHC-I, sensitizes cancer cells to T cell-dependent killing, and adds to ICB efficacy. Our findings provide preclinical rationale for treating tumors expressing low MHC-I expression with SMAC mimetics to enhance sensitivity to immunotherapy. The approach used in this study can be generalized to identify other drugs that enhance immunotherapy efficacy.
SIGNIFICANCE: MHC-I loss or downregulation in cancer cells is a major mechanism of resistance to T cell-based immunotherapies. Our study reveals that birinapant may be used for patients with low baseline MHC-I to enhance ICB response. This represents promising immunotherapy opportunities given the biosafety profile of birinapant from multiple clinical trials.This article is highlighted in the In This Issue
feature, p. 1307.
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Cancer Discovery
Treatment Decisions for Patients with Cancer during the COVID-19 Pandemic
Labaki C, Choueiri TK
Patients with cancer have been disproportionally affected by the COVID-19 pandemic, with high rates of severe outcomes and death. Similarly, treatment decisions in this vulnerable population have been altered to a major degree during the past year, with significant disruption of care reported. Although complex, therapeutic choices in patients with cancer in times of COVID-19 are critical, as they may save thousands of lives. A mounting body of evidence, in addition to clear recommendations by multiple international societies, can help oncologists decide appropriately the necessity to administer antineoplastic regimens, helping to avoid a surge in cancer-related deaths in the upcoming months. |
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Cell
Death in the Fas, ELANE
Letai A
In this issue of Cell, Cui et al. demonstrate a previously unknown capacity for neutrophils to selectively kill cancer cells. How this killing is effected unfolds as a story of classical biochemistry, novel cell biology, and innate and adaptive immunity. |
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Elife
You Can Keep Your Coat On
Bedwell GJ, Engelman AN
High-resolution imaging techniques reveal new insights into the actions of the retrovirus HIV-1 inside host cells. |
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Gastroenterology
Hybrid Stomach-Intestinal Chromatin States Underlie Human Barrett's Metaplasia
Singh H, Hornick JL, Madha S, Cejas P, Jajoo K, Singh P, Shivdasani RA
Background & aims: Tissue metaplasia is uncommon in adults because established cis-element programs resist rewiring. In Barrett's esophagus, the distal esophageal mucosa acquires predominantly intestinal character, with notable gastric features, and is predisposed to develop invasive cancers. We sought to understand the chromatin underpinnings of Barrett's metaplasia and why it commonly displays simultaneous gastric and intestinal properties.
Methods: We profiled cis-regulatory elements with active histone modifications in primary human biopsy materials using chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq). Mutations in Barrett's esophagus were examined in relation to tissue-specific enhancer landscapes using a random-forest machine learning algorithm. We also profiled open chromatin at single-cell resolution in primary Barrett's biopsy specimens using the assay for transposase-accessible chromatin (ATAC-seq). We used one- and two-color immunohistochemistry to examine protein expression of tissue-restricted genes.
Results: Barrett's esophagus bears epigenome fingerprints of human stomach and intestinal columnar, but not esophageal squamous, epithelia. Mutational patterns were best explained as arising on the epigenome background of active gastric cis-elements, supporting the view that adjoining stomach epithelium is a likely tissue source. Individual cells in Barrett's metaplasia co-express gastric and intestinal genes, reflecting concomitant chromatin access at enhancers ordinarily restricted to one or the other epithelium. Protein expression of stomach-specific mucins, CLDN18, and a novel gastric marker, ANXA10, revealed extensive tissue and sub-clonal heterogeneity of dual stomach-intestinal cell states.
Conclusions: These findings reveal mixed and dynamic tissue-restricted chromatin states and phenotypic heterogeneity in Barrett's esophagus. Pervasive intra-gland variation argues against stem-cell governance of this phenotype.
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Journal of Clinical Oncology
Adjuvant Trastuzumab Emtansine Versus Paclitaxel in Combination With Trastuzumab for Stage I HER2-Positive Breast Cancer (ATEMPT): A Randomized Clinical Trial
Tolaney SM, Tayob N, Isakoff SJ, Faggen M, Mulvey T, Hu J, Weckstein D, Constantine M, Briccetti F, Tung N, Zheng Y, Rosenberg SM, Gelber RD, Trippa L, Barry W, DeMeo M, Burstein H, Partridge A, Winer EP, Krop I
PURPOSE: The ATEMPT trial was designed to determine if treatment with trastuzumab emtansine (T-DM1) caused less toxicity than paclitaxel plus trastuzumab (TH) and yielded clinically acceptable invasive disease-free
survival (iDFS) among patients with stage I human epidermal growth factor receptor 2-positive (HER2+) breast cancer (BC).
METHODS: Patients with stage I centrally confirmed HER2+ BC were randomly assigned 3:1 to T-DM1 or TH and received T-DM1 3.6 mg/kg IV every 3 weeks for 17 cycles or T 80 mg/m2 IV with H once every week ?ó 12 weeks (4 mg/kg load 2 mg/kg), followed by H ?ó 39 weeks (6 mg/kg once every 3 weeks). The co-primary objectives were to compare the incidence of clinically relevant toxicities (CRTs) in patients treated with T-DM1 versus TH and to evaluate iDFS in patients receiving T-DM1.
RESULTS: The analysis population includes all 497 patients who initiated protocol therapy (383 T-DM1 and 114 TH). CRTs were experienced by 46% of patients on T-DM1 and 47% of patients on TH (P = .83). The 3-year iDFS for T-DM1 was 97.8% (95% CI, 96.3 to 99.3), which rejected the null hypothesis (P < .0001). Serially collected patient-reported outcomes indicated that patients treated with T-DM1 had less neuropathy and alopecia and better work productivity compared with patients on TH.
CONCLUSION: Among patients with stage I HER2+ BC, one year of adjuvant T-DM1 was associated with excellent 3-year iDFS, but was not associated with fewer CRT compared with TH.
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Journal of Clinical Oncology
Biologic Assignment Trial of Reduced-Intensity Hematopoietic Cell Transplantation Based on Donor Availability in Patients 50-75 Years of Age with Advanced Myelodysplastic Syndrome
Cutler C
PURPOSE: Allogeneic hematopoietic cell transplantation (HCT) is the only potentially curative therapy for myelodysplastic syndromes (MDS), although it is infrequently offered to older patients. The relative benefits of HCT over non-HCT therapy in older patients with higher-risk MDS have not been defined.
METHODS: We conducted a multicenter biologic assignment trial comparing reduced-intensity HCT to hypomethylating therapy or best supportive care in subjects 50-75 years of age with intermediate-2 or high-risk de novo MDS. The primary outcome was overall survival probability at 3 years. Between January 2014 and November 2018, we enrolled 384 subjects at 34 centers. Subjects were assigned to the Donor or No-Donor arms according to the availability of a matched donor within 90 days of study registration.
RESULTS: The median follow-up time for surviving subjects was 34.2 months (range: 2.3-38 months) in the Donor arm and 26.9 months (range: 2.4-37.2 months) in the No-Donor arm. In an intention-to-treat analysis, the adjusted overall survival rate at 3 years in the Donor arm was 47.9% (95% CI, 41.3 to 54.1) compared with 26.6% (95% CI, 18.4 to 35.6) in the No-Donor arm (P = .0001) with an absolute difference of 21.3% (95% CI, 10.2 to 31.8). Leukemia-free survival at 3 years was greater in the Donor arm (35.8%; 95% CI, 29.8 to 41.8) compared with the No-Donor arm (20.6%; 95% CI, 13.3 to 29.1; P = .003). The survival benefit was seen across all subgroups examined.
CONCLUSION: We observed a significant survival advantage in older subjects with higher-risk MDS who have a matched donor identified and underwent reduced-intensity HCT, when compared with those without a donor. HCT should be included as an integral part of MDS management plans in fit older adults with higher-risk MDS.
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Journal of Clinical Oncology
Elective Pelvic Lymph Node Radiation in Prostate Cancer Revisited
Yang DD, Nguyen PL, D'Amico AV
The benefit of elective pelvic lymph node (LN) radiation in node-negative prostate cancer is controversial. As such, we applaud Murthy et al on successfully undertaking the POP-RT randomized trial. The authors demonstrated that for a cohort of men with node-negative disease and an estimated nodal risk ? 20% (by the Roach formula), pelvic LN radiation significantly improved the primary end point of 5-year biochemical failure-free survival (BFFS; 95.0% v 81.2%) and, on exploratory analysis, was associated with improved distant metastasis-free survival (5-year DMFS 95.9% v 89.2%). |
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Journal of Clinical Oncology
Immune Checkpoint Inhibitors in Ovarian Cancer: Can We Bridge the Gap Between IMagynation and Reality?
Konstantinopoulos PA, Cannistra SA
Epithelial ovarian cancer (EOC) was among the first tumor types in which evidence of cell-mediated, antitumor immunity was associated with improved outcome. In a seminal paper almost 20 years ago, Zhang et al demonstrated that the presence of either CD3+ or CD8+ tumor-infiltrating lymphocytes (TILs) in EOC was associated with improved overall survival (OS) and increased tumor expression of interferon gamma and other lymphocyte-attracting cytokines. Ovarian cancer was also among the first tumor types where the paradigm of regulatory T-cell (Treg)–mediated immunosuppression in human malignancies was defined. In that regard, Curiel et al demonstrated that Tregs suppress tumor-specific T-cell immunity, contribute to tumor growth in vivo, and are associated with poor OS in this disease.
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Journal of Clinical Oncology
Phase II Trial of Costimulation Blockade with Abatacept for Prevention of Acute GVHD
Bratrude B, Betz K, Yu A, Tkachev V, Duncan C, Horan JT, Kean LS
PURPOSE: Severe (grade 3-4) acute graft-versus-host disease (AGVHD) is a major cause of death after unrelated-donor (URD) hematopoietic cell transplant (HCT), resulting in particularly high mortality after HLA-mismatched transplantation. There are no approved agents for AGVHD prevention, underscoring the critical unmet need for novel therapeutics. ABA2 was a phase II trial to rigorously assess safety, efficacy, and immunologic effects of adding T-cell costimulation blockade with abatacept to calcineurin inhibitor (CNI)/methotrexate (MTX)-based GVHD prophylaxis, to test whether abatacept could decrease AGVHD.
METHODS: ABA2 enrolled adults and children with hematologic malignancies under two strata: a randomized, double-blind, placebo-controlled stratum (8/8-HLA-matched URD), comparing CNI/MTX plus abatacept with CNI/MTX plus placebo, and a single-arm stratum (7/8-HLA-mismatched URD) comparing CNI/MTX plus abatacept versus CNI/MTX CIBMTR controls. The primary end point was day +100 grade 3-4 AGVHD, with day +180 severe-AGVHD-free-survival (SGFS) a key secondary end point. Sample sizes were calculated using a higher type-1 error (0.2) as recommended for phase II trials, and were based on predicting that abatacept would reduce grade 3-4 AGVHD from 20% to 10% (8/8s) and 30% to 10% (7/8s). ABA2 enrolled 142 recipients (8/8s, median follow-up = 716 days) and 43 recipients (7/8s, median follow-up = 708 days).
RESULTS: In 8/8s, grade 3-4 AGVHD was 6.8% (abatacept) versus 14.8% (placebo) (P = .13, hazard ratio = 0.45). SGFS was 93.2% (CNI/MTX plus abatacept) versus 82% (CNI/MTX plus placebo, P = .05). In the smaller 7/8 cohort, grade 3-4 AGVHD was 2.3% (CNI/MTX plus abatacept, intention-to-treat population), which compared favorably with a nonrandomized matched cohort of CNI/MTX (30.2%, P < .001), and the SGFS was better (97.7% v 58.7%, P < .001). Immunologic analysis revealed control of T-cell activation in abatacept-treated patients.
CONCLUSION: Adding abatacept to URD HCT was safe, reduced AGVHD, and improved SGFS. These results suggest that abatacept may substantially improve AGVHD-related transplant outcomes, with a particularly beneficial impact on HLA-mismatched HCT.
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Journal of Clinical Oncology
Treating Inflammation and Fibrosis in Chronic GVHD: Two Birds, One ROCK
Cutler C
Chronic graft-versus-host disease (cGVHD) is the most serious long-term complication of allogeneic stem-cell transplantation, leading to lifelong morbidity, a reduction in quality of life, and excess mortality. The biology of cGVHD is thought to progress between three stages, characterized initially by tissue injury and acute inflammation. In the absence of thymic negative selection and in the context of a relative deficiency of regulatory T cells (TREG), there is expansion of alloreactive donor TH17 cells in the germinal center, where pathogenic B cell expansion similarly occurs. Following this is a variable period of chronic inflammation and dysregulated immunity; unless successfully treated, a final stage of aberrant tissue repair and fibrosis ensues. Although all initial clinical manifestations of cGVHD are inflammatory, the morbidity of cGVHD is primarily related to this terminal hallmark fibrosis. Skin and soft-tissue fasciitis with fibrosis leads to disfiguring and disabling joint contractions; ocular cGVHD, marked by subtarsal and subconjunctival fibrosis, leads to vision loss, whereas bronchiolitis obliterans, the pulmonary manifestation of cGVHD, is characterized histologically by loss of small airways and a fibrotic lung interstitium, leading to eventual respiratory failure.
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Journal of the National Cancer Institute
Prevalence and Outcome of COVID-19 Infection in Cancer Patients: A National Veterans Affairs Study
Fillmore NR, Szalat RE, Tuck DP, Munshi NC
BACKGROUND: Emerging data suggest variability in susceptibility and outcome to coronavirus disease 2019 (COVID-19) infection. Identifying risk factors associated with infection and outcomes in cancer patients is necessary to develop healthcare recommendations.
METHODS: We analyzed electronic health records of the US Veterans Affairs
Healthcare System and assessed the prevalence of COVID-19 infection in cancer patients. We evaluated the proportion of cancer patients tested for COVID-19 who were positive, as well as outcome attributable to COVID-19, and stratified by clinical characteristics including demographics, comorbidities, cancer treatment, and cancer type. All statistical tests are 2-sided.
RESULTS: Of 22 914 cancer patients tested for COVID-19, 1794 (7.8%) were positive. The prevalence of COVID-19 was similar across age. Higher prevalence was observed in African American (15.0%) compared with White (5.5%; P < .001) and in patients with hematologic malignancy compared with those with solid tumors (10.9% vs 7.8%; P < .001). Conversely, prevalence was lower in current smokers and patients who recently received cancer therapy (
CONCLUSION: Preexistence of cancer affects both susceptibility to COVID-19 infection and eventual outcome. The overall COVID-19-attributable mortality in cancer patients is affected by age, comorbidity, and specific cancer types; however, race or recent treatment including immunotherapy do not impact outcome.
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Journal of the National Cancer Institute
Racial and Ethnic Variation in PSA Testing and Prostate Cancer Incidence Following the 2012 USPSTF Recommendation
Kensler KH, Pernar CH, Mahal BA, Nguyen PL, Trinh QD, Kibel AS, Rebbeck TR
BACKGROUND: The 2012 US Preventive Services Task Force recommendation against routine prostate-specific antigen (PSA) testing led to a decrease in prostate cancer screening, but the heterogeneity of its impact by race and ethnicity remains unclear.
METHODS: The proportion of 40- to 74-year-old men who self-reported receiving a routine PSA test in the past year was estimated in the Behavioral Risk Factor Surveillance System (2012-2018). Odds ratios (ORs) of undergoing screening by race and ethnicity were estimated, adjusting for healthcare-related factors. Prostate cancer incidence rates and rate ratios (IRRs) by race and ethnicity were estimated using Surveillance, Epidemiology, and End Results registry data (2004-2017).
RESULTS: PSA testing frequencies were 32.3% (95% confidence interval [CI] = 31.7% to 32.8%) among non-Hispanic White (NHW), 30.3% (95% CI = 28.3% to 32.3%) among non-Hispanic Black (NHB), 21.8% (95% CI = 19.9% to 23.7%) among Hispanic, and 17.7% (95% CI = 14.1% to 21.3%) among Asian and Pacific Islander men in 2012. The absolute screening frequency declined by 9.5% from 2012 to 2018, with a larger decline among NHB (11.6%) than NHW men (9.3%). The relative annual decrease was greater among NHB (OR 0.86, 95% CI = 0.84 to 0.88) than NHW men (OR 0.89, 95% CI = 0.89 to 0.90; Pheterogeneity = .005), driven by a larger decline among NHB men ages 40-54 years. The NHB to NHW IRR for total prostate cancer increased from 1.73 (95% CI = 1.69 to 1.76) in 2011 to 1.87 (95% CI = 1.83 to 1.92) in 2012 and has remained elevated, driven by differences in localized tumor incidence. Metastatic disease incidence is rising across all racial and ethnic groups.
CONCLUSIONS: The frequency of prostate cancer screening varies by race and ethnicity, and there was a modestly steeper decline in PSA testing among younger NHB men relative to NHW men since 2012. The NHB to NHW IRR for localized prostate cancer modestly increased following 2012.
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Journal of the National Cancer Institute
Racial Disparities in Colorectal Cancer Recurrence and Mortality: Equitable Care, Inequitable Outcomes?
Manz CR, Schrag D
Racial disparities in cancer survival have persisted over decades, and colorectal cancer is no exception. Colorectal cancer occurs in 46 per 100?000 Black Americans compared with 39 per 100?000 non-Hispanic White Americans, with a more pronounced disparity in colorectal cancer deaths at 19 per 100?000 Black Americans vs 14 per 100?000 White Americans. Racial disparities in cancer outcomes can occur as the result of differences in social determinants of health, comorbid conditions, and severity of disease presentation, treatment, and biological factors. Disentangling the relative contributions of each of these features is critically important because it prioritizes strategies for eliminating disparities.
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Nature Biotechnology
Noncanonical Open Reading Frames Encode Functional Proteins Essential for Cancer Cell Survival
Prensner JR, Enache OM, Luria V, Krug K, Clauser KR, Dempster JM, Karger A, Wang L,
Stumbraite K, Wang VM, Botta G, Lyons NJ, Goodale A, Kalani Z, Fritchman B, Brown A, Alan D, Green T, Yang X, Jaffe JD, Roth JA, Piccioni F, Kirschner MW, Root DE, Golub TR
Although genomic analyses predict many noncanonical open reading frames (ORFs) in the human genome, it is unclear whether they encode biologically active proteins. Here we experimentally interrogated 553 candidates selected from noncanonical ORF datasets. Of these, 57 induced viability defects when knocked out in human cancer cell lines. Following ectopic expression, 257 showed evidence of protein expression and 401 induced gene expression changes. Clustered regularly interspaced short palindromic repeat (CRISPR) tiling and start codon mutagenesis indicated that their biological effects required translation as opposed to RNA-mediated effects. We found that one of these ORFs, G029442-renamed glycine-rich extracellular protein-1 (GREP1)-encodes a secreted protein highly expressed in breast cancer, and its knockout in 263 cancer cell lines showed preferential essentiality in breast cancer-derived lines. The secretome of GREP1-expressing cells has an increased abundance of the oncogenic cytokine GDF15, and GDF15 supplementation mitigated the growth-inhibitory effect of GREP1 knockout. Our experiments suggest that noncanonical ORFs can express biologically active proteins that are potential therapeutic targets.
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Nature Chemical Biology
Acute Pharmacological Degradation of Helios Destabilizes Regulatory T Cells
Wang ES, Verano AL, Nowak RP, Yuan JC, Donovan KA, Eleuteri NA, Yue H, Ngo KH, Lizotte PH, Gokhale PC, Gray NS, Fischer ES
The zinc-finger transcription factor Helios is critical for maintaining the identity, anergic phenotype and suppressive activity of regulatory T (Treg) cells. While it is an attractive target to enhance the efficacy of currently approved immunotherapies, no existing approaches can directly modulate Helios activity or abundance. Here, we report the structure-guided development of small molecules that recruit the E3 ubiquitin ligase substrate receptor cereblon to Helios, thereby promoting its degradation. Pharmacological Helios degradation destabilized the anergic phenotype and reduced the suppressive activity of Treg cells, establishing a route towards Helios-targeting therapeutics. More generally, this study provides a framework for the development of small-molecule degraders for previously unligandable targets by reprogramming E3 ligase substrate specificity.
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Nature Chemical Biology
Discovery and Resistance Mechanism of a Selective CDK12 Degrader
Jiang B, Gao Y, Che J, Lu W, Kalocsay M, Berberich MJ, Jiang J, You I, Kwiatkowski N, Sorger PK, Geyer M, Zhang T, Gray NS
Cyclin-dependent kinase 12 (CDK12) is an emerging therapeutic target due to its role in regulating transcription of DNA-damage response (DDR) genes. However, development of selective small molecules targeting CDK12 has been challenging due to the high degree of homology between kinase domains of CDK12 and other transcriptional CDKs, most notably CDK13. In the present study, we report the rational design and characterization of a CDK12-specific degrader, BSJ-4-116. BSJ-4-116 selectively degraded CDK12 as assessed through quantitative proteomics. Selective degradation of CDK12 resulted in premature cleavage and poly(adenylation) of DDR genes. Moreover, BSJ-4-116 exhibited potent antiproliferative effects, alone and in combination with the poly(ADP-ribose) polymerase inhibitor olaparib, as well as when used as a single agent against cell lines resistant to covalent CDK12 inhibitors. Two point mutations in CDK12 were identified that confer resistance to BSJ-4-116, demonstrating a potential mechanism that tumor cells can use to evade bivalent degrader molecules.
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Nature Chemical Biology
Peroxisomal-Derived Ether Phospholipids Link Nucleotides to Respirasome Assembly
Bennett CF, O'Malley KE, Perry EA, Balsa E, Latorre-Muro P, Riley CL, Luo C, Jedrychowski M,
Gygi SP, Puigserver P
The protein complexes of the mitochondrial electron transport chain exist in isolation and in higher order assemblies termed supercomplexes (SCs) or respirasomes (SC I+III2+IV). The association of complexes I, III and IV into the respirasome is regulated by unknown mechanisms. Here, we designed a nanoluciferase complementation reporter for complex III and IV proximity to determine in vivo respirasome levels. In a chemical screen, we found that inhibitors of the de novo pyrimidine synthesis enzyme dihydroorotate dehydrogenase (DHODH) potently increased respirasome assembly and activity. By-passing DHODH inhibition via uridine supplementation decreases SC assembly by altering mitochondrial phospholipid composition, specifically elevated peroxisomal-derived ether phospholipids. Cell growth rates upon DHODH inhibition depend on ether lipid synthesis and SC assembly. These data reveal that nucleotide pools signal to peroxisomes to modulate synthesis and transport of ether phospholipids to mitochondria for SC assembly, which are necessary for optimal cell growth in conditions of nucleotide limitation.
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Nature Communications
BRCA1 Binds TERRA RNA and Suppresses R-Loop-Based Telomeric DNA Damage
Vohhodina J, Goehring LJ, Liu B, Kong Q, Botchkarev VV Jr, Huynh M, Liu Z, Abderazzaq FO,
Clark AP, Ficarro SB, Marto JA, Hatchi E, Livingston DM
R-loop structures act as modulators of physiological processes such as
transcription termination, gene regulation, and DNA repair. However, they can cause transcription-replication conflicts and give rise to genomic instability, particularly at telomeres, which are prone to forming DNA secondary structures. Here, we demonstrate that BRCA1 binds TERRA RNA, directly and physically via its N-terminal nuclear localization sequence, as well as telomere-specific shelterin proteins in an R-loop-, and a cell cycle-dependent manner. R-loop-driven BRCA1 binding to CpG-rich TERRA promoters represses TERRA transcription, prevents TERRA R-loop-associated damage, and promotes its repair, likely in association with SETX and XRN2. BRCA1 depletion upregulates TERRA expression, leading to overly abundant TERRA R-loops, telomeric replication stress, and signs of telomeric aberrancy. Moreover, BRCA1 mutations within the TERRA-binding region lead to an excess of TERRA-associated R-loops and telomeric abnormalities. Thus, normal BRCA1/TERRA binding suppresses telomere-centered genome instability.
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Nature Communications
Replicate Sequencing Libraries are Important for Quantification of Allelic Imbalance
Mendelevich A, Vinogradova S, Gupta S, Sunyaev SR, Gimelbrant AA
A sensitive approach to quantitative analysis of transcriptional regulation in diploid organisms is analysis of allelic imbalance (AI) in RNA sequencing (RNA-seq) data. A near-universal practice in such studies is to prepare and sequence only one library per RNA sample. We present theoretical and experimental evidence that data from a single RNA-seq library is insufficient for reliable quantification of the contribution of technical noise to the observed AI signal; consequently, reliance on one-replicate experimental design can lead to unaccounted-for variation in error rates in allele-specific analysis. We develop a computational approach, Qllelic, that accurately accounts for technical noise by making use of replicate RNA-seq libraries. Testing on new and existing datasets shows that application of Qllelic greatly decreases false positive rate in allele-specific analysis while conserving appropriate signal, and thus greatly improves reproducibility of AI estimates. We explore sources of technical overdispersion in observed AI signal and conclude by discussing design of RNA-seq studies addressing two biologically important questions: quantification of transcriptome-wide AI in one sample, and differential analysis of allele-specific expression between samples.
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Nature Genetics
Chromothripsis as an On-Target Consequence of CRISPR-Cas9 Genome Editing
Leibowitz ML, Papathanasiou S, Blaine LJ, Sun L, Zhang CZ, Pellman D
Genome editing has therapeutic potential for treating genetic diseases and cancer. However, the currently most practicable approaches rely on the generation of DNA double-strand breaks (DSBs), which can give rise to a poorly characterized spectrum of chromosome structural abnormalities. Here, using model cells and single-cell whole-genome sequencing, as well as by editing at a clinically relevant locus in clinically relevant cells, we show that CRISPR-Cas9 editing generates structural defects of the nucleus, micronuclei and chromosome bridges, which initiate a mutational process called chromothripsis. Chromothripsis is extensive chromosome rearrangement restricted to one or a few chromosomes that can cause human congenital disease and cancer. These results demonstrate that chromothripsis is a previously unappreciated on-target consequence of CRISPR-Cas9-generated DSBs. As genome editing is implemented in the clinic, the potential for extensive chromosomal rearrangements should be considered and monitored.
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Nature Genetics
Reprogramming of the Esophageal Squamous Carcinoma Epigenome by SOX2 Promotes ADAR1 Dependence
Wu Z, Zhou J, Zhang X, Zhang Z, Xie Y, Liu JB, Ho ZV, Panda A, Qiu X, Cejas P, Canadas I, Akarca FG, McFarland JM, Nagaraja AK, Goss LB, Kesten N, Si L, Lim K, Zhang Y, Baek JY, Liu Y, Patil DT, Hai J, Bao C, Stachler M, Qi J, Ishizuka JJ, Meyerson M, Barbie DA, Brown M, Long H, Bass AJ
Esophageal squamous cell carcinomas (ESCCs) harbor recurrent chromosome 3q amplifications that target the transcription factor SOX2. Beyond its role as an oncogene in ESCC, SOX2 acts in development of the squamous esophagus and maintenance of adult esophageal precursor cells. To compare Sox2 activity in normal and malignant tissue, we developed engineered murine esophageal organoids spanning normal esophagus to Sox2-induced squamous cell carcinoma and mapped Sox2 binding and the epigenetic and transcriptional landscape with evolution from normal to cancer. While oncogenic Sox2 largely maintains actions observed in normal tissue, Sox2 overexpression with p53 and p16 inactivation promotes chromatin remodeling and evolution of the Sox2 cistrome. With Klf5, oncogenic Sox2 acquires new binding sites and enhances activity of oncogenes such as Stat3. Moreover, oncogenic Sox2 activates endogenous retroviruses, inducing expression of double-stranded RNA and dependence on the RNA editing enzyme ADAR1. These data reveal SOX2 functions in ESCC, defining targetable vulnerabilities.
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Nature Immunology
Inflammatory Stromal Cells in the Myeloma Microenvironment
Sklavenitis-Pistofidis R, Haradhvala NJ, Getz G, Ghobrial IM
Single-cell RNA sequencing identifies an inflammatory subpopulation of mesenchymal stromal cells in patients with multiple myeloma. Multiple myeloma (MM) is a deadly plasma cell malignancy of the bone marrow that reoccurs after treatment. Recent sequencing endeavors have unveiled many of the key genomic drivers acquired by MM, yet the majority of these also occur in patients at the asymptomatic precursor stages of the disease that may never progress to overt MM. Mounting evidence, such as the consistent growth of these precursors following transplant in mice, suggests that tumor-extrinsic mechanisms are probably key regulators of disease formation. Indeed, the immune microenvironment is significantly altered in MM, and immune dysregulation is established early at the monoclonal gammopathy of undetermined significance (MGUS) stage. The nonimmune microenvironment (mesenchymal stromal cells, MSCs) has been shown to support MM growth and induce drug resistance and immunomodulation. Despite great scientific interest in the role of MSCs in MM disease progression, investigation of their role has been hampered by the low frequency of these cells in bone marrow aspirate samples and by challenges related to their in vitro expansion, which is often required to obtain sufficient numbers for experimentation. In this issue of Nature Immunology, de Jong et al. present the first study using single-cell RNA sequencing to profile natural MSCs, as well as immune and tumor cells, from individuals with MM (n = 13) and healthy donors (n = 7) to comprehensively characterize the nonimmune microenvironment in MM and its interactions with immune and tumor cells.
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British Journal of Cancer
Essential Role of the Histone Lysine Demethylase KDM4A in the Biology of Malignant Pleural Mesothelioma (MPM)
Lapidot M, Case AE, Weisberg EL, Meng C, Garg S, Ni W, Hung YP, Carrasco RD, Knott A,
Gokhale PC, Frank DA, Griffin JD, Saladi SV, Bueno R, Sattler M
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Breast Cancer Research and Treatment
Chemotherapy-Related Amenorrhea (CRA) After Adjuvant Ado-Trastuzumab Emtansine (T-DM1) Compared to Paclitaxel in Combination with Trastuzumab (TH) (TBCRC033: ATEMPT Trial)
Zheng Y, Tayob N, Hu J, Isakoff SJ, Faggen MG, Mulvey TM, Sella T, Constantine M, Briccetti FM, Tung NM, Rosenberg S, DeMeo MK, Burstein HJ, Winer EP, Krop IE, Partridge AH, Tolaney SM
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Cancer Research
Gene Fusions Create Partner and Collateral Dependencies Essential to Cancer Cell Survival
Gillani R, Seong BKA, Crowdis J, Conway JR, Haas BJ, Park J, Dietlein F, He MX, Imamovic A, Ma C, Bassik MC, Boehm JS, Vazquez F, Gusev A, Liu D, Janeway KA, McFarland JM, Stegmaier K, Van Allen EM
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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
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JCI Insight
The Impact of Tumor Epithelial and Microenvironmental Heterogeneity on Treatment Responses in HER2+ Breast Cancer
Janiszewska M, Stein S, Metzger Filho O, Kingston NL, Harper NW, Aleckovic M, Trinh A,
Murphy KC, Cristea S, Oakes B, Winer EP, Krop IE, Michor F, Polyak K
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Oral Oncology
A Phase II Trial of All-Trans Retinoic Acid (ATRA) in Advanced Adenoid Cystic Carcinoma
Hanna GJ, ONeill A, Cutler JM, Flynn M, Vijaykumar T, Clark JR, Wirth LJ, Lorch JH, Park JC,
Mito JK, Lohr JG, Zon LI, Haddad RI
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Science Advances
ERK Signaling Mediates Resistance to Immunomodulatory Drugs in the Bone Marrow Microenvironment
Liu J, Hideshima T, Xing L, Wang S, Samur MK, Sewastianik T, Ogiya D, Bianchi G, Wen K, Tai YT, Munshi N, Richardson P, Carrasco R, Anderson KC
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Science Signaling
Metabolic Perturbations Sensitize Triple-Negative Breast Cancers to Apoptosis Induced by BH3 Mimetics
Daniels VW, Zoeller JJ, van Gastel N, McQueeney KE, Parvin S, Potter DS, Fell GG, Ferreira VG, Yilma B, Gupta R, Spetz J, Bhola PD, Endress JE, Harris IS, Sarosiek KA, Scadden DT, Brugge JS, Letai A
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