Modular pooled discovery of synthetic knockin sequences to program durable cell therapies

Chronic stimulation can cause T cell dysfunction and limit the efficacy of cellular immunotherapies. Improved methods are required to compare large numbers of synthetic knockin (KI) sequences to reprogram cell functions. Here, we developed modular pooled KI screening (ModPoKI), an adaptable platform for modular construction of DNA KI libraries using barcoded multicistronic adaptors. We built two ModPoKI libraries of 100 transcription factors (TFs) and 129 natural and synthetic surface receptors (SRs). Over 30 ModPoKI screens across human TCR- and CAR-T cells in diverse conditions identified a transcription factor AP4 (TFAP4) construct that enhanced fitness of chronically stimulated CAR-T cells and anti-cancer function in vitro and in vivo. ModPoKI's modularity allowed us to generate an ∼10,000-member library of TF combinations. Non-viral KI of a combined BATF-TFAP4 polycistronic construct enhanced fitness. Overexpressed BATF and TFAP4 co-occupy and regulate key gene targets to reprogram T cell function. ModPoKI facilitates the discovery of complex gene constructs to program cellular functions.

CRISPR screens decode cancer cell pathways that trigger γδ T cell detection

γδ T cells are potent anticancer effectors with the potential to target tumours broadly, independent of patient-specific neoantigens or human leukocyte antigen background1-5. γδ T cells can sense conserved cell stress signals prevalent in transformed cells2,3, although the mechanisms behind the targeting of stressed target cells remain poorly characterized. Vγ9Vδ2 T cells-the most abundant subset of human γδ T cells4-recognize a protein complex containing butyrophilin 2A1 (BTN2A1) and BTN3A1 (refs. 6-8), a widely expressed cell surface protein that is activated by phosphoantigens abundantly produced by tumour cells. Here we combined genome-wide CRISPR screens in target cancer cells to identify pathways that regulate γδ T cell killing and BTN3A cell surface expression. The screens showed previously unappreciated multilayered regulation of BTN3A abundance on the cell surface and triggering of γδ T cells through transcription, post-translational modifications and membrane trafficking. In addition, diverse genetic perturbations and inhibitors disrupting metabolic pathways in the cancer cells, particularly ATP-producing processes, were found to alter BTN3A levels. This induction of both BTN3A and BTN2A1 during metabolic crises is dependent on AMP-activated protein kinase (AMPK). Finally, small-molecule activation of AMPK in a cell line model and in patient-derived tumour organoids led to increased expression of the BTN2A1-BTN3A complex and increased Vγ9Vδ2 T cell receptor-mediated killing. This AMPK-dependent mechanism of metabolic stress-induced ligand upregulation deepens our understanding of γδ T cell stress surveillance and suggests new avenues available to enhance γδ T cell anticancer activity.

Genome-wide CRISPR screens reveal metabolic and transcriptional regulation of BTN3A and cancer susceptibility to Vγ9Vδ2 T cell targeting

γδ T cells are potent anti-cancer effectors with potential to target tumors broadly, independent of neoantigens or HLA-background. γδ T cells can sense conserved cell stress signals prevalent in transformed cells, although the mechanisms governing how γδ T cells sense and kill stressed target cells remain poorly characterized. Vγ9Vδ2 T cells – the most abundant subset of human γδ T cells – recognize a protein complex containing butyrophilin 3A1 (BTN3A1), a ubiquitously expressed cell surface protein that is activated by phosphoantigens abundantly produced by tumor cells. Here we performed genome-wide CRISPR screens in target cancer cells to identify pathways that regulate: (1) γδ T cell activity with a functional co-culture killing screen, and (2) BTN3A1 cell surface expression in a phenotypic screen. Multilayered regulation of BTN3A1 expression was uncovered: transcriptional regulation (IRF1, CTBP1, ZNF217, RUNX1), intracellular trafficking, sialylation, oxidative phosphorylation (OXPHOS), purine metabolism, and other metabolic pathways. Consistent with these results, we found upregulated BTN3A1 on cells undergoing an energy crisis due to glucose deprivation, glycolysis inhibition, or OXPHOS inhibition. Furthermore, we discovered that this BTN3A1 upregulation was induced by activation of the AMP-activated protein kinase (AMPK). Also, CRISPR screen-derived gene expression signatures correlated with higher survival in low-grade glioma patients whose tumors had high Vγ9Vδ2 T cell infiltration. Uncovering this AMPK-dependent mechanism of metabolic stress-induced ligand activation deepens our understanding of γδ T cell stress surveillance and suggests new avenues to enhance γδ T cell anti-cancer activity.

M.R.M. is a Cancer Research Institute (CRI) Irvington Fellow supported by CRI and was funded by the Human Vaccines Project Michelson Prize for Human Immunology.

Constrained chromatin accessibility in PU.1-mutated agammaglobulinemia patients

The pioneer transcription factor (TF) PU.1 controls hematopoietic cell fate by decompacting stem cell heterochromatin and allowing nonpioneer TFs to enter otherwise inaccessible genomic sites. PU.1 deficiency fatally arrests lymphopoiesis and myelopoiesis in mice, but human congenital PU.1 disorders have not previously been described. We studied six unrelated agammaglobulinemic patients, each harboring a heterozygous mutation (four de novo, two unphased) of SPI1, the gene encoding PU.1. Affected patients lacked circulating B cells and possessed few conventional dendritic cells. Introducing disease-similar SPI1 mutations into human hematopoietic stem and progenitor cells impaired early in vitro B cell and myeloid cell differentiation. Patient SPI1 mutations encoded destabilized PU.1 proteins unable to nuclear localize or bind target DNA. In PU.1-haploinsufficient pro–B cell lines, euchromatin was less accessible to nonpioneer TFs critical for B cell development, and gene expression patterns associated with the pro– to pre–B cell transition were undermined. Our findings molecularly describe a novel form of agammaglobulinemia and underscore PU.1’s critical, dose-dependent role as a hematopoietic euchromatin gatekeeper.

Polymer-stabilized Cas9 nanoparticles and modified repair templates increase genome editing efficiency

Versatile and precise genome modifications are needed to create a wider range of adoptive cellular therapies1-5. Here we report two improvements that increase the efficiency of CRISPR-Cas9-based genome editing in clinically relevant primary cell types. Truncated Cas9 target sequences (tCTSs) added at the ends of the homology-directed repair (HDR) template interact with Cas9 ribonucleoproteins (RNPs) to shuttle the template to the nucleus, enhancing HDR efficiency approximately two- to fourfold. Furthermore, stabilizing Cas9 RNPs into nanoparticles with polyglutamic acid further improves editing efficiency by approximately twofold, reduces toxicity, and enables lyophilized storage without loss of activity. Combining the two improvements increases gene targeting efficiency even at reduced HDR template doses, yielding approximately two to six times as many viable edited cells across multiple genomic loci in diverse cell types, such as bulk (CD3+) T cells, CD8+ T cells, CD4+ T cells, regulatory T cells (Tregs), γδ T cells, B cells, natural killer cells, and primary and induced pluripotent stem cell-derived6 hematopoietic stem progenitor cells (HSPCs).

[The analysis of health effects of exposure to occupational hazards on works in gypsum mining enterprise]

Objective: To investigate the health of gypsum miners in Hubei province and analyze the health effects of occupational disease hazards exposure on gypsum miners. Methods: In April 2017, occupational disease hazard factors were tested on the site of a gypsum mine, and 500 workers were selected by random sampling to conduct questionnaires, relevant data such as occupational health examination was collected, and descriptive statistical analysis was performed. Results: The main occupational hazards of gypsum miners were gypsum dust and noise. The time-weighted average concentration of 8 h in the workplace was 4.32 to 9.34 mg/m(3), and the post pass rate was 69.2% (9/13) ; Respiratory dust 0.13-5.15 mg/m(3), post pass rate 75.0% (3/4). Gypsum miners had finger dysfunction and muscle numbness, joint pain (29.2%, 88/301) and chest pain and breathing difficulties (17.6%, 53/301). Followed by tinnitus, auricle pus, running water (4.7%, 14/301), abnormal muscle tension (2.7%, 8/301). The exposure of occupational disease hazards was associated with respiratory, auditory and neurological symptoms of gypsum miners. Conclusion: The long-term exposure of gypsum workers to gypsum dust, noise and other harmful factors may result in obvious symptoms of respiratory system and other health damage.

Relationship of changes in cardiac output to changes in heart rate in medical ICU patients

OBJECTIVE

To determine whether changes in cardiac output are correlated with changes in other commonly measured covariables (heart rate, respiratory rate, mean arterial pressure, mean pulmonary artery pressure, pulmonary artery occlusion pressure, and temperature).

DESIGN

Case series.

SETTING

Medical intensive care unit (ICU) in a Veterans Administration Medical Center.

PATIENTS

Twenty-three patients with Swan-Ganz catheters placed by the primary care team were studied on 25 occasions. Patients were managed by the primary team as clinically indicated.

INTERVENTIONS

Thermodilution cardiac output and covariables were determined at baseline and at hourly intervals for the next 5 h. Each cardiac output measurement was calculated by averaging the last four of five individual measurements at each time point.

RESULTS

The mean cardiac output (9.21/min), heart rate (107/min), and pulmonary artery occlusion pressure (19 mmHg) were elevated. The hourly mean change in cardiac output was 10.2%. Using least-squares linear regression analysis, we found clinically significant changes in cardiac output (> 6.4%) to be most closely correlated with changes in heart rate (R2 = 0.29, p < 0.001). Stepwise linear regression analysis showed that none of the other covariables added significantly to this relationship. No significant relationship was found between changes in cardiac output and changes in pulmonary artery occlusion pressure. Despite these correlations clinically significant changes in cardiac output were accompanied by changes in heart rate in the same direction only 62% of the time.

CONCLUSION

Changes in cardiac output were best correlated with changes in heart rate. Changes in pulmonary artery occlusion pressure were not correlated with changes in cardiac output in this population of medical ICU patients. A change in any of the covariables (alone or in combination) cannot be reliably used to indicate a simultaneous change in cardiac output.

Arterial oxygenation time after an FIO2 increase in mechanically ventilated patients

The time for arterial PO2 to reach equilibrium after a 0.2 increase in the fraction of inspired oxygen (FIO2) was studied, using arterial blood gases measured at 1, 2, 3, 4, 5, 7, 9, and 11 min in 30 stable, mechanically ventilated medical intensive care unit (ICU) patients. Eight patients also underwent a 0.4 increase in FIO2. Each patient's rise in PO2 over time [PO2(t)] was fit to the following exponential equation: PO2(t) = PO2i + (PO2f-PO2i) (1-e-kt), where t refers to time, PO2i and PO2f refer to the initial and final equilibrated PO2. The time constant k and PO2f were determined by a nonlinear curve fitting technique. The 90% oxygenation times (t90%), defined as the time required to reach 90% of the final equilibrated PO2, were calculated. The mean t90% (+/- SD) was 6.0 (+/- 3.4) min for all patients (range 1.7 to 14.3 min); 7.1 +/- 2.1 min for 18 patients with chronic obstructive pulmonary disease (COPD) and 4.4 +/- 2.0 min for 12 patients without COPD (p < 0.05). In the subgroup of patients undergoing both an FIO2 increase of 0.2 and 0.4, there was no significant difference in the mean t90%'s for the two FIO2 changes (7.7 versus 7.7 min). We conclude that after a 0.2 or 0.4 increase of FIO3, a 15-min equilibration time period is adequate for 90% of the increase in PO2 to occur, in stable, mechanically ventilated medical ICU patients.

Performance of a patient-dedicated, on-demand blood gas monitor in medical ICU patients

We examined the performance characteristics of a new bedside blood gas monitor. This monitor's fluorescent pH, PCO2, and PO2 sensors are embedded in a cassette, which is calibrated in vitro and then inserted into the patient's radial artery tubing set. In 50 medical ICU patients, 683 paired monitor and conventional blood gas analyzer values were obtained. Performance was assessed via calculations of bias (mean monitor and analyzer difference) and its standard deviation (SD), plots of monitor and analyzer differences against the means (of monitor and analyzer), and linear regression analysis of the sequential changes in monitor values versus the corresponding sequential changes in analyzer values. The ex vivo calibration, assessed using the initial paired blood samples, showed a bias +/- SD of 0.02 +/- 0.02 for pH, -0.1 +/- 1.9 mm Hg for PCO2, and 4.3 +/- 6.0 mm Hg for PO2. For all paired samples (n = 683), the biases +/- SD were 0.004 +/- 0.023 for pH, 0.6 +/- 2.4 mm Hg for PCO2, and 2.7 +2- 6.4 mm HG for PO2. The PO2 bias increased as PO2 increased. The standard deviations (imprecision) of both PCO2 and PO2 also increased as the magnitudes of these variables increased. Sequential changes in monitor values versus the corresponding sequential changes in analyzer values revealed regression lines close to the line of identity. Serum sodium had no effect on pH bias. Daily drift of the sensors was inconsequential, with values of -0.01/d for pH, 1.7 mm Hg/d for PCO2, and 1.1 mm Hg/d for PO2. We conclude that the performance of this monitor is comparable to that of conventional blood gas analyzers.

Variability of arterial blood gas values over time in stable medical ICU patients

The spontaneous variability of arterial blood gas and pH values (ABGs) was examined in a group of 28 typical stable medical ICU patients under a variety of ventilatory conditions. In each patient, 13 ABG specimens were measured at 5-min intervals during a 1-h study period using a new bedside, extravascular fluorescent blood gas monitor. For all patients, the mean coefficient of variation (C) was 6.1 percent for PO2 and 4.7 percent for PCO2. The average SD for pH was 0.012. We conclude that the spontaneous variability for ABG values over a 1-h period is substantial and that this variability should be taken into account when making clinical decisions based on ABG values.

Development of a patient-dedicated, on-demand, blood gas monitor

A new monitor (CDI 2000) that brings blood gas measurements to the patient's bedside has been developed. To measure blood gases, blood is drawn into the patient's arterial pressure-monitoring line past in-line fluorescent-based sensors. After measurement, the blood is returned to the patient, avoiding blood loss and delays in sample turnaround and reducing the risk of infection to both patient and operator. We assessed this system's performance in vitro with tonometered bovine blood. Bias (mean difference between monitor and tonometered gas or measured pH values) +/- the standard deviation (SD) were 0.01 +/- 0.02 at pH = 7.39; 0.0 +/- 0.7 mm Hg at Pco2 = 39 mm Hg; and 2.4 +/- 3.2 mm Hg at a Po2 = 100 mm Hg (n = 54). Changes in hematocrit, blood temperature, or serum sodium concentration did not have clinically significant effects on system performance. Studies in normal volunteers, in whom large changes in blood gases were induced, showed a bias (mean difference between monitor and IL 1306 values) +/- SD of 0.00 +/- 0.02 for pH, -0.4 +/- 2.0 mm Hg for Pco2, and -3.6 +/- 7.7 mm Hg for Po2 (n = 69). We conclude from the present study that the performance of this system is comparable to that of conventional blood gas analyzers.

Variability of cardiac output over time in medical intensive care unit patients

OBJECTIVES

To determine the amount of spontaneous variability of cardiac output over time in critically ill patients, and to determine the effect of mechanical ventilation on cardiac output variability over time.

DESIGN

Case series.

SETTING

Medical intensive care unit in a Veterans Affairs Medical Center.

PATIENTS

Twenty-two patients with indwelling pulmonary artery flotation catheters were studied. Two patients were studied twice.

INTERVENTIONS

During a 1-hr time period in which no interventions were required or made, thermodilution cardiac output was determined at baseline and then every 15 mins for 1 hr. At each time point, five individual cardiac output measurements were made and a mean was computed. The covariables of heart rate, respiration rate, mean arterial pressure, mean pulmonary arterial pressure, pulmonary artery occlusion pressure, and temperature were also recorded at each time point.

MEASUREMENTS AND MAIN RESULTS

The variability of the five cardiac output measurements made at each time point was expressed by calculating for each patient a coefficient of variation of the measurements. The overall mean coefficient of variation of the measurements was 5.8%. The variability of the cardiac output measurements over time was expressed by calculating for each patient a coefficient of variation over time. The overall mean coefficient of variation over time was 7.7%. A subgroup of 15 "covariable stable" patients (defined as those patients with covariables within +/- 5% of the mean covariable values during the hour) had a mean coefficient of variation over time of 6.4%, whereas "covariable unstable" patients (with > +/- 5% changes in any covariable) had a mean coefficient of variation over time of 9.9% (p < .05). Patients breathing spontaneously had a mean coefficient of variation over time of 10.1%, whereas mechanically ventilated patients had a mean coefficient of variation over time of 6.3% (p < .05).

CONCLUSIONS

The spontaneous variability of cardiac output should be considered when interpreting two cardiac output determinations made at separate times. Due to spontaneous variability alone, a patient with a baseline cardiac output of 10.0 L/min would be expected (95% confidence interval) to have a cardiac output range of 9.2 to 10.8 L/min if covariables were stable, and a range of at least 8.8 to 11.2 L/min if covariables were unstable. Patients who were mechanically ventilated displayed less variability than patients who were breathing spontaneously.

Oxygen Fick and modified carbon dioxide Fick cardiac outputs

OBJECTIVE

To compare cardiac outputs estimated from the classical oxygen Fick and modified CO2 Fick methods with thermodilution cardiac output. The modified CO2 Fick cardiac output was obtained by replacing the oxygen uptake (VO2) in the Fick equation with the CO2 production (VCO2) divided by either an assumed or measured value of the respiratory exchange ratio or with an independently determined constant (Crit Care Med 1991; 19:1270-1277).

DESIGN

Criterion standard study.

SETTING

The medical and surgical intensive care unit (ICU) in a Veterans Affairs Medical Center.

PATIENTS

A total of 17 patients (26 studies) and 11 surgical patients (13 studies), predominantly mechanically ventilated using the intermittent mandatory ventilation mode, were studied over a period of 4.3 hrs.

MEASUREMENTS

A respiratory gas exchange monitor was used to measure VO2, VCO2, and respiratory exchange ratio at 3-min intervals. Calculations were performed with arterial and venous oxygen saturations measured with both a laboratory cooximeter and bedside pulse and venous reflectance oximeters. In the oxygen Fick method, cardiac output was calculated from VO2 together with arterial and venous oxygen saturations. In the modified CO2 Fick methods, cardiac output values were calculated from arterial and venous oxygen saturations with VCO2, divided by either: a) an assumed value of the respiratory exchange ratio equal to 0.8 for all patients (method 1); b) the patient's measured value of the respiratory exchange ratio (method 2); or c) a constant, determined from an initial, simultaneous measurement of thermodilution cardiac output, VCO2, and oximetry saturations. Data were examined by linear regression analysis and bias and precision calculations.

MAIN RESULTS

Thermodilution cardiac output was more related to cardiac outputs calculated with the 3 modified CO2 Fick methods than to the oxygen Fick cardiac output. Thermodilution cardiac output was closely related to the modified CO2 Fick cardiac output calculated via method 3. For this method, with pulse and venous reflectance oximetry saturations, linear regression yielded an r2 = .85, a standard error of the estimate of 0.88 L/min (n = 111) and a bias and precision of 0.11 and 0.97 L/min, respectively. Thermodilution cardiac output was less closely related to oxygen Fick cardiac output, which, when calculated with pulse and venous reflectance oximetry saturations, yielded an r2 = .50, a standard error of the estimate of 1.47 L/min (n = 128), and a bias and precision of 0.01 and 1.85 L/min, respectively.

CONCLUSIONS

We conclude from this study that thermodilution cardiac output is more closely related to cardiac output calculated from modified CO2 Fick methods than to oxygen Fick cardiac output. Since cardiac output calculated with the modified CO2 Fick method 3 obviates the difficulties associated with measuring VO2 accurately and requires neither an assumption of nor measurement of the respiratory exchange ratio, method 3 may prove to be clinically useful for continuous cardiac output monitoring via oximetry in ICU patients.

Relationship of thermodilution cardiac output to metabolic measurements and mixed venous oxygen saturation

To determine the individual contributions of variables in the Fick equation to cardiac output, we simultaneously measured oxygen uptake (VO2), carbon dioxide production (VCO2), venous oxygen saturation (SvO2) and thermodilution cardiac output (Qth) in 28 medical and surgical ICU patients. Patients were intubated and ventilated with the intermittent mandatory ventilation mode. VO2 and VCO2 (averaged over 3 min) were obtained from a metabolic cart. SvO2 was measured with fiberoptic reflectance oximetry (and COoximetry). Thirty-nine studies (average duration, 4.3 h) with 151 Qth measurements were performed. The relationships between Qth and VO2, Qth and VCO2, Qth and SvO2, and 1/Qth and SvO2, as well as between the sequential changes in these variables were analyzed by least squares linear regression. The ability of changes in the variables VO2, VCO2, and SvO2 to predict changes in Qth were analyzed by receiver operating characteristic (ROC) curves. Qth was weakly related to VO2 (r = 0.45), VCO2 (r = 0.45), or SvO2 (r = 0.36). Changes in Qth were weakly related to changes in VCO2 (r = 0.40), and even less to changes in VO2 (r = 0.18) and SvO2 (r = 0.13). The areas under the ROC curves for increases in Qth > 10 percent were as follows: 0.66 for VCO2, 0.50 for VO2, and 0.55 for SvO2. The areas for decreases in Qth < 10 percent were as follows: 0.78 for VCO2, 0.65 for VO2, and 0.49 for SvO2. None of the above oximetry relationships were substantially altered by use of COoximetry venous oxygen saturations. We conclude that Qth cannot be predicted well solely from VO2, VCO2, or SvO2 nor can changes in Qth be predicted well solely from changes in VO2, VCO2, or SvO2. Of the metabolic variables, changes in VCO2 best predicted changes in Qth.