Functional genomic landscape of cancer-intrinsic evasion of killing by T cells.

The genetic circuits that allow cancer cells to evade destruction by the host immune system remain poorly understood1-3. Here, to identify a phenotypically robust core set of genes and pathways that enable cancer cells to evade killing mediated by cytotoxic T lymphocytes (CTLs), we performed genome-wide CRISPR screens across a panel of genetically diverse mouse cancer cell lines that were cultured in the presence of CTLs. We identify a core set of 182 genes across these mouse cancer models, the individual perturbation of which increases either the sensitivity or the resistance of cancer cells to CTL-mediated toxicity. Systematic exploration of our dataset using genetic co-similarity reveals the hierarchical and coordinated manner in which genes and pathways act in cancer cells to orchestrate their evasion of CTLs, and shows that discrete functional modules that control the interferon response and tumour necrosis factor (TNF)-induced cytotoxicity are dominant sub-phenotypes. Our data establish a central role for genes that were previously identified as negative regulators of the type-II interferon response (for example, Ptpn2, Socs1 and Adar1) in mediating CTL evasion, and show that the lipid-droplet-related gene Fitm2 is required for maintaining cell fitness after exposure to interferon-γ (IFNγ). In addition, we identify the autophagy pathway as a conserved mediator of the evasion of CTLs by cancer cells, and show that this pathway is required to resist cytotoxicity induced by the cytokines IFNγ and TNF. Through the mapping of cytokine- and CTL-based genetic interactions, together with in vivo CRISPR screens, we show how the pleiotropic effects of autophagy control cancer-cell-intrinsic evasion of killing by CTLs and we highlight the importance of these effects within the tumour microenvironment. Collectively, these data expand our knowledge of the genetic circuits that are involved in the evasion of the immune system by cancer cells, and highlight genetic interactions that contribute to phenotypes associated with escape from killing by CTLs.

Predicting the recurrence risk of renal cell carcinoma after nephrectomy: potential role of CT-radiomics for adjuvant treatment decisions.

OBJECTIVES: Previous trial results suggest that only a small number of patients with non-metastatic renal cell carcinoma (RCC) benefit from adjuvant therapy. We assessed whether the addition of CT-based radiomics to established clinico-pathological biomarkers improves recurrence risk prediction for adjuvant treatment decisions. METHODS: This retrospective study included 453 patients with non-metastatic RCC undergoing nephrectomy. Cox models were trained to predict disease-free survival (DFS) using post-operative biomarkers (age, stage, tumor size and grade) with and without radiomics selected on pre-operative CT. Models were assessed using C-statistic, calibration, and decision curve analyses (repeated tenfold cross-validation). RESULTS: At multivariable analysis, one of four selected radiomic features (wavelet-HHL_glcm_ClusterShade) was prognostic for DFS with an adjusted hazard ratio (HR) of 0.44 (p = 0.02), along with American Joint Committee on Cancer (AJCC) stage group (III versus I, HR 2.90; p = 0.002), grade 4 (versus grade 1, HR 8.90; p = 0.001), age (per 10 years HR 1.29; p = 0.03), and tumor size (per cm HR 1.13; p = 0.003). The discriminatory ability of the combined clinical-radiomic model (C = 0.80) was superior to that of the clinical model (C = 0.78; p < 0.001). Decision curve analysis revealed a net benefit of the combined model when used for adjuvant treatment decisions. At an exemplary threshold probability of ≥ 25% for disease recurrence within 5 years, using the combined versus the clinical model was equivalent to treating 9 additional patients (per 1000 assessed) who would recur without treatment (i.e., true-positive predictions) with no increase in false-positive predictions. CONCLUSION: Adding CT-based radiomic features to established prognostic biomarkers improved post-operative recurrence risk assessment in our internal validation study and may help guide decisions regarding adjuvant therapy. KEY POINTS: In patients with non-metastatic renal cell carcinoma undergoing nephrectomy, CT-based radiomics combined with established clinical and pathological biomarkers improved recurrence risk assessment. Compared to a clinical base model, the combined risk model enabled superior clinical utility if used to guide decisions on adjuvant treatment.

Constructing inverse probability weights for institutional comparisons in healthcare.

In comparing quality of care between hospitals, disease-specific quality indicators measure structural, process, or outcome elements related to the care of a particular condition. Such comparisons can be framed in terms of causal contrasts, answering the question of whether a patient (or a population of patients on average) would receive different care if treated at the care level of a different hospital. Fair comparisons have to be adjusted for patient case-mix, which is equivalent to controlling for confounding by the patient-level factors, including demographic factors, comorbidities, and disease progression. The methodological choice for such comparisons is usually between direct and indirect standardization methods. In this article, we discuss the alternative of inverse probability weighting as a tool for standardization in hospital comparisons. This involves fitting multinomial logistic hospital assignment models and using these to construct the inverse probability weights. The challenge in the present context is the presence of large number of hospitals being compared, many of which have a small patient volume. We propose methods to include small categories in the weighted analysis, as well as metrics and visualizations for checking the positivity/overlap and covariate balance in constructing such weights. The methods are illustrated in a running example using linked administrative data on surgical treatment of kidney cancer patients in Ontario.

Association between PD-L1 status and immune checkpoint inhibitor response in advanced malignancies: a systematic review and meta-analysis of overall survival data.

BACKGROUND: Targeting the programmed death ligand 1 (PD-L1) pathway has become standard for many advanced malignancies. Whether PD-L1 expression predicts response is unclear. We assessed the association between PD-L1 expression and immunotherapy response using stratified meta-analysis. METHODS: We performed a systematic review of randomized clinical trials published prior to October 2018 comparing overall survival (OS) in patients with advanced solid organ malignancies treated with immunotherapy or standard treatment. Pooled hazard ratios were calculated among patients with high and low PD-L1 levels independently. Differences between the two estimates were assessed using meta-analysis of study-level differences. Our primary analysis assessed a 1% threshold while secondary analyses utilized 5, 10 and 50%. RESULTS: 14 eligible trials reporting on 8887 patients were included. While there was a significant OS benefit for immunotherapy compared with standard treatment for all patients, the magnitude of benefit was significantly larger among those with high PD-L1 expression (P = 0.006). This finding persisted regardless of threshold used and across subgroup analyses according to PD-L1 assay type, tumor histology, line of therapy, type of inhibitor and study methodology. CONCLUSIONS: PD-L1 levels have important predictive value in determining the response to immunotherapy. However, patients with low PD-L1 levels also experience improved survival with immunotherapy compared with standard treatment.

Hospital Quality Metrics for Radical Cystectomy: Disease Specific and Correlated to Mortality Outcomes.

PURPOSE: Measuring quality is a high priority for health care systems globally. Despite the high perioperative morbidity, mortality, expenditures and performance variation of radical cystectomy there is a paucity of validated bladder cancer quality metrics. We aimed to create a hospital quality scoring system for radical cystectomy which is disease specific and associated with patient centered outcomes. MATERIALS AND METHODS: We used the National Cancer Database to identify hospitals where radical cystectomy was performed from 2004 to 2014. Mixed effects models were constructed to assess variation in hospital performance across 7 quality indicators. Indirect standardization was used to case mix adjust hospital performance. We assessed associations between quality indicators as well as the novel BC-QS (Bladder Cancer Quality Score) composite hospital quality metric with 30-day, 90-day and overall mortality using logistic and Cox regression, respectively. RESULTS: At 1,200 facilities radical cystectomy was performed in a total of 48,341 patients from 2004 to 2014. Mixed effects models demonstrated significant between hospital variation across all quality indicators after case mix adjustment. The composite BC-QS metric was composed of the hospital positive margin rate, the lymph node dissection rate and the neoadjuvant chemotherapy rate. Better BC-QS performance was associated with lower 30-day and 90-day mortality (adjusted OR 0.78, 95% CI 0.64-0.96, and OR 0.84, 95% CI 0.72-0.97, respectively) and overall mortality (HR 0.86, 95% CI 0.81-0.92). Hospitals with a higher BC-QS had higher volume and more were affiliated with an academic institution than hospitals with a lower BC-QS (p <0.0001). CONCLUSIONS: The BC-QS captures variations in the hospital performance of radical cystectomy and it shows an association of higher quality with lower patient mortality. Our validation of this quality metric provides support for its potential use by policy makers and payers in efforts to measure hospital quality for high cost surgeries.

Causal Mediation Analysis for Standardized Mortality Ratios.

Indirectly standardized mortality ratios (SMR) are often used to compare patient outcomes between health care providers as indicators of quality of care. Observed differences in the outcomes raise the question of whether these could be causally attributable to earlier processes or outcomes in the pathway of care that the patients received. Such pathways can be naturally addressed in a causal mediation analysis framework. Adopting causal mediation models allows the total provider effect on outcome to be decomposed into direct and indirect (mediated) effects. This in turn enables quantification of the improvement in patient outcomes due to a hypothetical intervention on the mediator. We formulate the effect decomposition for the indirectly standardized SMR when comparing to a health care system-wide average performance, propose novel model-based and semiparametric estimators for the decomposition, study the properties of these through simulations, and demonstrate their use through application to Ontario kidney cancer data.

Multi-ancestry genome-wide association study of kidney cancer identifies 63 susceptibility regions.

Here, in a multi-ancestry genome-wide association study meta-analysis of kidney cancer (29,020 cases and 835,670 controls), we identified 63 susceptibility regions (50 novel) containing 108 independent risk loci. In analyses stratified by subtype, 52 regions (78 loci) were associated with clear cell renal cell carcinoma (RCC) and 6 regions (7 loci) with papillary RCC. Notably, we report a variant common in African ancestry individuals ( rs7629500 ) in the 3' untranslated region of VHL, nearly tripling clear cell RCC risk (odds ratio 2.72, 95% confidence interval 2.23-3.30). In cis-expression quantitative trait locus analyses, 48 variants from 34 regions point toward 83 candidate genes. Enrichment of hypoxia-inducible factor-binding sites underscores the importance of hypoxia-related mechanisms in kidney cancer. Our results advance understanding of the genetic architecture of kidney cancer, provide clues for functional investigation and enable generation of a validated polygenic risk score with an estimated area under the curve of 0.65 (0.74 including risk factors) among European ancestry individuals.

Cystic Renal Masses: Old and New Paradigms.

Cystic renal masses describe a spectrum of lesions with benign and/or malignant features. Cystic renal masses are most often identified incidentally with the Bosniak classification system stratifying their malignant potential. Solid enhancing components most often represent clear cell renal cell carcinoma yet display an indolent natural history relative to pure solid renal masses. This has led to an increased adoption of active surveillance as a management strategy in those who are poor surgical candidates. This article provides a contemporary overview of historical and emerging clinical paradigms in the diagnosis and management of this distinct clinical entity.

PBRM1, SETD2 and BAP1 - the trinity of 3p in clear cell renal cell carcinoma.

Biallelic inactivation of the tumour suppressor gene Von Hippel-Lindau (VHL) occurs in the vast majority of clear cell renal cell carcinoma (ccRCC) instances, disrupting cellular oxygen-sensing mechanisms to yield a state of persistent pseudo-hypoxia, defined as a continued hypoxic response despite the presence of adequate oxygen levels. However, loss of VHL alone is often insufficient to drive oncogenesis. Results from genomic studies have shown that co-deletions of VHL with one (or more) of three genes encoding proteins involved in chromatin modification and remodelling, polybromo-1 gene (PBRM1), BRCA1-associated protein 1 (BAP1) and SET domain-containing 2 (SETD2), are common and important co-drivers of tumorigenesis. These genes are all located near VHL on chromosome 3p and are often altered following cytogenetic rearrangements that lead to 3p loss and precede the establishment of ccRCC. These three proteins have multiple roles in the regulation of crucial cancer-related pathways, including protection of genomic stability, antagonism of polycomb group (PcG) complexes to maintain a permissive transcriptional landscape in physiological conditions, and regulation of genes that mediate responses to immune checkpoint inhibitor therapy. An improved understanding of these mechanisms will bring new insights regarding cellular drivers of ccRCC growth and therapy response and, ultimately, will support the development of novel translational therapeutics.

Surgeon-level versus hospital-level quality variance in kidney cancer surgery.

PURPOSE: To determine whether variance in kidney cancer surgery quality indicators (QIs) is most impacted by surgeon-level or hospital-level factors in order to inform quality improvement initiatives. MATERIALS AND METHODS: The ICES and Veterans Affairs (VA) databases were queried for patients undergoing surgery for localized kidney cancer. Kidney cancer surgery QIs were defined within each cohort. Quality of care was benchmarked at a surgeon- vs. hospital-level to identify statistical outliers, using available clinicopathological data to adjust for differences in case-mix. Variance between surgeons and hospitals was calculated for each QI using a random-effects model. RESULTS: The QI with the greatest amount of variance explained by hospital and surgeon-level factors was proportion of cases performed with minimally invasive surgery (MIS). The majority of this variance was due to surgeon-level factors for both the VA and ICES cohorts. The proportion of cases performed using an MIS approach was also the QI with the greatest number of outlier hospitals and surgeons compared to the average performance. The proportion of partial nephrectomies performed for patients at risk of chronic kidney disease was the QI with the greatest amount of variance due to hospital-level factors for the ICES cohort. CONCLUSIONS: The proportion of localized kidney cancer cases performed using an MIS approach is the QI requiring the greatest attention. Quality improvement initiatives should focus on surgeon-level factors to increase the number of MIS cases being performed for patients with localized renal masses.

Dual Antigen T Cell Engagers Targeting CA9 as an Effective Immunotherapeutic Modality for Targeting CA9 in Solid Tumors.

Glioblastomas (GBM), the most common malignant primary adult brain tumors, are uniformly lethal and are in need of improved therapeutic modalities. GBM contain extensive regions of hypoxia and are enriched in therapy resistant brain tumor-initiating cells (BTICs). Carbonic anhydrase 9 (CA9) is a hypoxia-induced cell surface enzyme that plays an important role in maintenance of stem cell survival and therapeutic resistance. Here we demonstrate that CA9 is highly expressed in patient-derived BTICs. CA9+ GBM BTICs showed increased self-renewal and proliferative capacity. To target CA9, we developed dual antigen T cell engagers (DATEs) that were exquisitely specific for CA9-positive patient-derived clear cell Renal Cell Carcinoma (ccRCC) and GBM cells. Combined treatment of either ccRCC or GBM cells with the CA9 DATE and T cells resulted in T cell activation, increased release of pro-inflammatory cytokines and enhanced cytotoxicity in a CA9-dependent manner. Treatment of ccRCC and GBM patient-derived xenografts markedly reduced tumor burden and extended survival. These data suggest that the CA9 DATE could provide a novel therapeutic strategy for patients with solid tumors expressing CA9 to overcome treatment resistance. .

A Novel Metric for Hospital Quality in Kidney Cancer Surgery: A Veterans Affairs National Health System Validation of Concept.

INTRODUCTION: We aimed to develop and validate a Compound Quality Score (CQS) as a metric for hospital-level quality of surgical care in kidney cancer at the Veterans Affairs National Health System. METHODS: A retrospective review of 8,965 patients with kidney cancer treated at Veterans Affairs (2005-2015) was performed. Two previously validated process quality indicators (QIs) were explored: the proportion of patients with 1) T1a tumors undergoing partial nephrectomy and 2) T1-T2 tumors undergoing minimally invasive radical nephrectomy. Demographics/comorbidity/tumor characteristics/treatment year were used for case mix adjustments at hospital level. The predicted versus observed ratio of cases was calculated per hospital to generate QI scores using indirect standardization and multivariable regression models. CQS represents the sum of both scores. A total of 96 hospitals were grouped by CQS, and short-term patient-level outcomes were regressed on CQS levels to assess for length of stay (LOS), 30-day complications/readmission, 90-day mortality and total cost of surgical admission. RESULTS: CQS identified 25/33/38 hospitals with higher/lower/average performance, respectively. High performance hospitals had higher nephrectomy volumes (p <0.01). Total CQS independently associated with LOS (ß=-0.04, p <0.01, predicted LOS 0.84 days shorter for CQS=2 versus CQS=-2), 30-day surgical complications (OR=0.88, p <0.01) or 30-day medical complications (OR=0.93, p <0.01) and total cost of surgical admission (ß =-0.014, p <0.01, predicted 12% lower cost for CQS=2 versus CQS=-2). No association was found between CQS and 30-day readmissions or 90-day mortality (all p >0.05), although low event rates were observed (8.9% and 1.7%, respectively). CONCLUSIONS: Variability in quality of surgical care at hospital level can be captured with the CQS among patients with kidney cancer. CQS is associated with relevant short-term perioperative outcomes and surgical cost. QIs should be used to identify, audit and implement quality improvement strategies across health systems.

High-content CRISPR screening.

CRISPR screens are a powerful source of biological discovery, enabling the unbiased interrogation of gene function in a wide range of applications and species. In pooled CRISPR screens, various genetically encoded perturbations are introduced into pools of cells. The targeted cells proliferate under a biological challenge such as cell competition, drug treatment or viral infection. Subsequently, the perturbation-induced effects are evaluated by sequencing-based counting of the guide RNAs that specify each perturbation. The typical results of such screens are ranked lists of genes that confer sensitivity or resistance to the biological challenge of interest. Contributing to the broad utility of CRISPR screens, adaptations of the core CRISPR technology make it possible to activate, silence or otherwise manipulate the target genes. Moreover, high-content read-outs such as single-cell RNA sequencing and spatial imaging help characterize screened cells with unprecedented detail. Dedicated software tools facilitate bioinformatic analysis and enhance reproducibility. CRISPR screening has unravelled various molecular mechanisms in basic biology, medical genetics, cancer research, immunology, infectious diseases, microbiology and other fields. This Primer describes the basic and advanced concepts of CRISPR screening and its application as a flexible and reliable method for biological discovery, biomedical research and drug development - with a special emphasis on high-content methods that make it possible to obtain detailed biological insights directly as part of the screen.

Single-cell profiling of healthy human kidney reveals features of sex-based transcriptional programs and tissue-specific immunity.

Knowledge of the transcriptional programs underpinning the functions of human kidney cell populations at homeostasis is limited. We present a single-cell perspective of healthy human kidney from 19 living donors, with equal contribution from males and females, profiling the transcriptome of 27677 cells to map human kidney at high resolution. Sex-based differences in gene expression within proximal tubular cells were observed, specifically, increased anti-oxidant metallothionein genes in females and aerobic metabolism-related genes in males. Functional differences in metabolism were confirmed in proximal tubular cells, with male cells exhibiting higher oxidative phosphorylation and higher levels of energy precursor metabolites. We identified kidney-specific lymphocyte populations with unique transcriptional profiles indicative of kidney-adapted functions. Significant heterogeneity in myeloid cells was observed, with a MRC1+LYVE1+FOLR2+C1QC+ population representing a predominant population in healthy kidney. This study provides a detailed cellular map of healthy human kidney, and explores the complexity of parenchymal and kidney-resident immune cells.

Hospital-level Effects Contribute to Variations in Prostate Cancer Quality of Care.

A paucity of real-world data exists highlighting whether variations in prostate cancer quality of care occur at a hospital level, independent of differences in case mix. To overcome this knowledge gap, we benchmarked hospital-level quality (n = 1245 hospitals) across a broad multidisciplinary panel of previously reported disease-specific, expert-defined quality indicators (QIs), adjusting for differences in patient case mix by indirect standardization. A composite measure of prostate cancer quality-the prostate cancer quality score (PC-QS)-was derived, and associations between PC-QS and hospital volume, academic status, and location as well as patient all-cause mortality were determined. After adjusting for the case mix, of the total of 1245 hospitals evaluated, 2-37% were identified as those performing significantly below the national average for a given QI. Hospitals with a higher PC-QS displayed larger patient volumes, were more commonly academic affiliated, and had lower overall mortality. Collectively, our data-driven benchmarking analysis reveals that widespread hospital-level variations exist in prostate cancer quality of care after adjusting for differences in case mix, with the PC-QS serving as a novel, validated, quality benchmarking tool. PATIENT SUMMARY: Our statistical benchmarking method shows that the quality of prostate cancer care varies between hospitals, after accounting for differences in patient characteristics. The prostate cancer quality score is a novel, validated, quality benchmarking tool.

Establishing a global quality of care benchmark report.

BACKGROUND: The Movember funded TrueNTH Global Registry (TNGR) aims to improve care by collecting and analysing a consistent dataset to identify variation in disease management, benchmark care delivery in accordance with best practice guidelines and provide this information to those in a position to enact change. We discuss considerations of designing and implementing a quality of care report for TNGR. METHODS: Eleven working group sessions were held prior to and as reports were being built with representation from clinicians, data managers and investigators contributing to TNGR. The aim of the meetings was to understand current data display approaches, share literature review findings and ideas for innovative approaches. Preferred displays were evaluated with two surveys (survey 1: 5 clinicians and 5 non-clinicians, 83% response rate; survey 2: 17 clinicians and 18 non-clinicians, 93% response rate). RESULTS: Consensus on dashboard design and three data-display preferences were achieved. The dashboard comprised two performance summary charts; one summarising site's relative quality indicator (QI) performance and another to summarise data quality. Binary outcome QIs were presented as funnel plots. Patient-reported outcome measures of function score and the extent to which men were bothered by their symptoms were presented in bubble plots. Time series graphs were seen as providing important information to supplement funnel and bubble plots. R Markdown was selected as the software program principally because of its excellent analytic and graph display capacity, open source licensing model and the large global community sharing program code enhancements. CONCLUSIONS: International collaboration in creating and maintaining clinical quality registries has allowed benchmarking of process and outcome measures on a large scale. A registry report system was developed with stakeholder engagement to produce dynamic reports that provide user-specific feedback to 132 participating sites across 13 countries.

Causal variance decompositions for institutional comparisons in healthcare.

There is increasing interest in comparing institutions delivering healthcare in terms of disease-specific quality indicators (QIs) that capture processes or outcomes showing variations in the care provided. Such comparisons can be framed in terms of causal models, where adjusting for patient case-mix is analogous to controlling for confounding, and exposure is being treated in a given hospital, for instance. Our goal here is to help identify good QIs rather than comparing hospitals in terms of an already chosen QI, and so we focus on the presence and magnitude of overall variation in care between the hospitals rather than the pairwise differences between any two hospitals. We consider how the observed variation in care received at patient level can be decomposed into that causally explained by the hospital performance adjusting for the case-mix, the case-mix itself, and residual variation. For this purpose, we derive a three-way variance decomposition, with particular attention to its causal interpretation in terms of potential outcome variables. We propose model-based estimators for the decomposition, accommodating different link functions and either fixed or random effect models. We evaluate their performance in a simulation study and demonstrate their use in a real data application.

Long-term outcomes after radical or partial nephrectomy for T1a renal cell carcinoma: A population-based study.

INTRODUCTION: The benefit of partial nephrectomy (PN) compared to radical nephrectomy (RN) for T1a renal cell carcinoma (RCC) remains uncertain, with observational studies conflicting with level 1 evidence. Therefore, the purpose of this population-based study was to compare long-term outcomes in patients undergoing PN or RN for T1a RCC. METHODS: We studied 5670 patients in Ontario, Canada undergoing PN or RN for T1a RCC. The primary outcome was overall survival (OS). Secondary outcomes were cancer-specific survival (CSS), chronic kidney disease (CKD), renal replacement therapy, and myocardial infarction (MI). We used multivariable Cox proportional hazard models to evaluate the association between PN or RN and these outcomes. A sensitivity analysis was performed in patients with a preoperative serum creatinine available. RESULTS: Median followup was 77 months. Compared to RN, PN was associated with significantly improved OS (hazard ratio [HR] 0.73, 95% confidence interval [CI] 0.63-0.84), reduced risk of CKD (HR 0.18, 95% CI 0.12-0.27), and improved CSS (HR 0.45, 95% CI 0.30-0.65). The risk of MI was not significantly different between groups (HR 0.91, 95% CI 0.62-1.34). Few patients (n=15) required renal replacement therapy. In the sensitivity analysis, the association between type of surgery and OS and CKD persisted, while the association with CSS did not. CONCLUSIONS: Our study found that in patients undergoing surgery for T1a RCC, PN was associated with improved OS and reduced risk of CKD compared to RN. However, few patients in either group required renal replacement therapy.

Systematic mapping of genetic interactions for de novo fatty acid synthesis identifies C12orf49 as a regulator of lipid metabolism.

The de novo synthesis of fatty acids has emerged as a therapeutic target for various diseases, including cancer. Because cancer cells are intrinsically buffered to combat metabolic stress, it is important to understand how cells may adapt to the loss of de novo fatty acid biosynthesis. Here, we use pooled genome-wide CRISPR screens to systematically map genetic interactions (GIs) in human HAP1 cells carrying a loss-of-function mutation in fatty acid synthase (FASN), whose product catalyses the formation of long-chain fatty acids. FASN-mutant cells show a strong dependence on lipid uptake that is reflected in negative GIs with genes involved in the LDL receptor pathway, vesicle trafficking and protein glycosylation. Further support for these functional relationships is derived from additional GI screens in query cell lines deficient in other genes involved in lipid metabolism, including LDLR, SREBF1, SREBF2 and ACACA. Our GI profiles also identify a potential role for the previously uncharacterized gene C12orf49 (which we call LUR1) in regulation of exogenous lipid uptake through modulation of SREBF2 signalling in response to lipid starvation. Overall, our data highlight the genetic determinants underlying the cellular adaptation associated with loss of de novo fatty acid synthesis and demonstrate the power of systematic GI mapping for uncovering metabolic buffering mechanisms in human cells.