Debugging and consolidating multiple synthetic chromosomes reveals combinatorial genetic interactions.

The Sc2.0 project is building a eukaryotic synthetic genome from scratch. A major milestone has been achieved with all individual Sc2.0 chromosomes assembled. Here, we describe the consolidation of multiple synthetic chromosomes using advanced endoreduplication intercrossing with tRNA expression cassettes to generate a strain with 6.5 synthetic chromosomes. The 3D chromosome organization and transcript isoform profiles were evaluated using Hi-C and long-read direct RNA sequencing. We developed CRISPR Directed Biallelic URA3-assisted Genome Scan, or "CRISPR D-BUGS," to map phenotypic variants caused by specific designer modifications, known as "bugs." We first fine-mapped a bug in synthetic chromosome II (synII) and then discovered a combinatorial interaction associated with synIII and synX, revealing an unexpected genetic interaction that links transcriptional regulation, inositol metabolism, and tRNASerCGA abundance. Finally, to expedite consolidation, we employed chromosome substitution to incorporate the largest chromosome (synIV), thereby consolidating >50% of the Sc2.0 genome in one strain.

Design, construction, and functional characterization of a tRNA neochromosome in yeast.

Here, we report the design, construction, and characterization of a tRNA neochromosome, a designer chromosome that functions as an additional, de novo counterpart to the native complement of Saccharomyces cerevisiae. Intending to address one of the central design principles of the Sc2.0 project, the ∼190-kb tRNA neochromosome houses all 275 relocated nuclear tRNA genes. To maximize stability, the design incorporates orthogonal genetic elements from non-S. cerevisiae yeast species. Furthermore, the presence of 283 rox recombination sites enables an orthogonal tRNA SCRaMbLE system. Following construction in yeast, we obtained evidence of a potent selective force, manifesting as a spontaneous doubling in cell ploidy. Furthermore, tRNA sequencing, transcriptomics, proteomics, nucleosome mapping, replication profiling, FISH, and Hi-C were undertaken to investigate questions of tRNA neochromosome behavior and function. Its construction demonstrates the remarkable tractability of the yeast model and opens up opportunities to directly test hypotheses surrounding these essential non-coding RNAs.

Systematic Immunotherapy Target Discovery Using Genome-Scale In Vivo CRISPR Screens in CD8 T Cells.

CD8 T cells play essential roles in anti-tumor immune responses. Here, we performed genome-scale CRISPR screens in CD8 T cells directly under cancer immunotherapy settings and identified regulators of tumor infiltration and degranulation. The in vivo screen robustly re-identified canonical immunotherapy targets such as PD-1 and Tim-3, along with genes that have not been characterized in T cells. The infiltration and degranulation screens converged on an RNA helicase Dhx37. Dhx37 knockout enhanced the efficacy of antigen-specific CD8 T cells against triple-negative breast cancer in vivo. Immunological characterization in mouse and human CD8 T cells revealed that DHX37 suppresses effector functions, cytokine production, and T cell activation. Transcriptomic profiling and biochemical interrogation revealed a role for DHX37 in modulating NF-κB. These data demonstrate high-throughput in vivo genetic screens for immunotherapy target discovery and establishes DHX37 as a functional regulator of CD8 T cells.

Overall Survival with Osimertinib in Resected EGFR-Mutated NSCLC.

BACKGROUND: Among patients with resected, epidermal growth factor receptor (EGFR)-mutated, stage IB to IIIA non-small-cell lung cancer (NSCLC), adjuvant osimertinib therapy, with or without previous adjuvant chemotherapy, resulted in significantly longer disease-free survival than placebo in the ADAURA trial. We report the results of the planned final analysis of overall survival. METHODS: In this phase 3, double-blind trial, we randomly assigned eligible patients in a 1:1 ratio to receive osimertinib (80 mg once daily) or placebo until disease recurrence was observed, the trial regimen was completed (3 years), or a discontinuation criterion was met. The primary end point was investigator-assessed disease-free survival among patients with stage II to IIIA disease. Secondary end points included disease-free survival among patients with stage IB to IIIA disease, overall survival, and safety. RESULTS: Of 682 patients who underwent randomization, 339 received osimertinib and 343 received placebo. Among patients with stage II to IIIA disease, the 5-year overall survival was 85% in the osimertinib group and 73% in the placebo group (overall hazard ratio for death, 0.49; 95.03% confidence interval [CI], 0.33 to 0.73; P<0.001). In the overall population (patients with stage IB to IIIA disease), the 5-year overall survival was 88% in the osimertinib group and 78% in the placebo group (overall hazard ratio for death, 0.49; 95.03% CI, 0.34 to 0.70; P<0.001). One new serious adverse event, pneumonia related to coronavirus disease 2019, was reported after the previously published data-cutoff date (the event was not considered by the investigator to be related to the trial regimen, and the patient fully recovered). Adjuvant osimertinib had a safety profile consistent with that in the primary analysis. CONCLUSIONS: Adjuvant osimertinib provided a significant overall survival benefit among patients with completely resected, EGFR-mutated, stage IB to IIIA NSCLC. (Funded by AstraZeneca; ADAURA ClinicalTrials.gov number, NCT02511106.).

Preserved striatal innervation maintains motor function despite severe loss of nigral dopaminergic neurons.

Degeneration of dopaminergic neurons in the substantia nigra and their striatal axon terminals causes cardinal motor symptoms of Parkinson's disease. In idiopathic cases, high levels of mitochondrial DNA alterations, leading to mitochondrial dysfunction, are a central feature of these vulnerable neurons. Here we present a mouse model expressing the K320E variant of the mitochondrial helicase Twinkle in dopaminergic neurons, leading to accelerated mitochondrial DNA mutations. These K320E-TwinkleDaN mice showed normal motor function at 20 months of age, although ∼70% of nigral dopaminergic neurons had perished. Remaining neurons still preserved ∼75% of axon terminals in the dorsal striatum and enabled normal dopamine release. Transcriptome analysis and viral tracing confirmed compensatory axonal sprouting of the surviving neurons. We conclude that a small population of substantia nigra dopaminergic neurons is able to adapt to the accumulation of mitochondrial DNA mutations and maintain motor control.

Quantitative Measurement of HER2 Expression in Non-Small Cell Lung Cancer With a High-Sensitivity Assay.

Recently, low human epidermal growth factor receptor 2 (HER2) protein expression has been proposed as a predictive biomarker for response to the antibody-drug conjugate trastuzumab deruxtecan (T-DXd) in metastatic breast cancer. HER2 expression in non-small cell lung cancer (NSCLC) patients has never been carefully measured, and little is known about the frequency of cases with unamplified but detectable levels of the protein. Although some HER2-targeted therapies have been studied in NSCLC patients, they have been restricted to those with genomic ERBB2 gene alterations, which only represent relatively rare cases of NSCLC. Still, emerging investigations of T-DXd in NSCLC have shown promise in patients with unamplified HER2. Taken together, we hypothesize that there may be many cases of NSCLC with levels of HER2 protein expression comparable with levels seen in breast cancer that benefit from T-DXd. Here, we used a previously validated, analytic, quantitative immunofluorescence (QIF) assay that is more sensitive than legacy clinical HER2 immunohistochemistry assays. We measured HER2 protein levels in NSCLC cases to determine the proportion of cases with detectable HER2 expression. Using cell line calibration microarrays alongside our QIF method enabled us to convert HER2 signal into units of attomoles per mm2. We found that over 63% of the 741 analyzed NSCLC cases exhibited HER2 expression above the limit of detection, with more than 17% of them exceeding the lower limit of quantification. Although the threshold for response to T-DXd in breast cancer is still unknown, many cases of NSCLC have expression in a range comparable to breast cancer cases with immunohistochemistry scores of 1+ or 2+. Our assay could potentially select NSCLC cases with a detectable target (ie, HER2) that might benefit from HER2 antibody-drug conjugates, irrespective of ERBB2 genomic alterations.

Long-Term Outcomes After Lung Transplantation in Children With Intellectual Disabilities.

BACKGROUND: The United Network for Organ Sharing (UNOS) started recording data on intellectual disability status in 2008. This study aimed to characterize the long-term outcomes for children with intellectual disabilities (IDs) undergoing lung transplantation. METHODS: All pediatric patients (under 18 years old) undergoing bilateral lung transplantation were identified using the UNOS database. The patients were grouped into the following categories: no cognitive delay, possible cognitive delay, and definite cognitive delay. The primary endpoint was graft survival at 3-year posttransplantation. Multivariate Cox proportional hazards modeling was used to estimate the independent effect of cognitive disability on graft survival. RESULTS: Five hundred four pediatric patients who underwent lung transplantation between March 2008 and December 2022 were retrospectively analyzed. 59 had a definite cognitive delay (12%), 23 had a possible delay (5%), and 421 had no delay (83%). When comparing these three groups, there was no significant difference in 60-day graft survival (p = 0.4), 3-year graft survival (p = 0.6), 3-year graft survival for patients who survived at least 60-day posttransplantation (p = 0.9), distribution of causes of death (p = 0.24), nor distribution treatment of rejection within 1-year posttransplantation (p = 0.06). CONCLUSIONS: Intellectual disability does not impact long-term outcomes after bilateral lung transplantation. Intellectual disability should not be a contraindication to bilateral lung transplantation on the basis of inferior graft survival.

The biology and management of non-small cell lung cancer.

Important advancements in the treatment of non-small cell lung cancer (NSCLC) have been achieved over the past two decades, increasing our understanding of the disease biology and mechanisms of tumour progression, and advancing early detection and multimodal care. The use of small molecule tyrosine kinase inhibitors and immunotherapy has led to unprecedented survival benefits in selected patients. However, the overall cure and survival rates for NSCLC remain low, particularly in metastatic disease. Therefore, continued research into new drugs and combination therapies is required to expand the clinical benefit to a broader patient population and to improve outcomes in NSCLC.

Acceptability, validity and responsiveness of inertial measurement units for assessing motor recovery after gene therapy in infants with early onset spinal muscular atrophy: a prospective cohort study.

BACKGROUND: Onasemnogene abeparvovec gene replacement therapy (GT) has changed the prognosis of patients with spinal muscular atrophy (SMA) with variable outcome regarding motor development in symptomatic patients. This pilot study evaluates acceptability, validity and clinical relevance of Inertial Measurement Units (IMU) to monitor spontaneous movement recovery in early onset SMA patients after GT. METHODS: Clinical assessments including CHOPINTEND score (the gold standard motor score for infants with SMA) and IMU measurements were performed before (M0) and repeatedly after GT. Inertial data was recorded during a 25-min spontaneous movement task, the child lying on the back, without (10 min) and with a playset (15 min) wearing IMUs. Two commonly used parameters, norm acceleration 95th centile (||A||_95) and counts per minute (||A||_CPM) were computed for each wrist, elbow and foot sensors. RESULTS: 23 SMA-patients were included (mean age at diagnosis 8 months [min 2, max 20], 19 SMA type 1, three type 2 and one presymptomatic) and 104 IMU-measurements were performed, all well accepted by families and 84/104 with a good child participation (evaluated with Brazelton scale). ||A||_95 and ||A||_CPM showed high internal consistency (without versus with a playset) with interclass correlation coefficient for the wrist sensors of 0.88 and 0.85 respectively and for the foot sensors of 0.93 and 0.91 respectively. ||A||_95 and ||A||_CPM were strongly correlated with CHOPINTEND (r for wrist sensors 0.74 and 0.67 respectively and for foot sensors 0.61 and 0.68 respectively, p-values < 0.001). ||A||_95 for the foot, the wrist, the elbow sensors and ||A||_CPM for the foot, the wrist, the elbow sensors increased significantly between baseline and the 12 months follow-up visit (respective p-values: 0.004, < 0.001, < 0.001, 0.006, < 0.001, < 0.001). CONCLUSION: IMUs were well accepted, consistent, concurrently valid, responsive and associated with unaided sitting acquisition especially for the elbow sensors. This study is the first reporting a large set of inertial sensor derived data after GT in SMA patients and paves the way for IMU-based follow-up of SMA patients after treatment.

When knowing the activity is not enough to predict gaze.

It is reasonable to assume that where people look in the world is largely determined by what they are doing. The reasoning is that the activity determines where it is useful to look at each moment in time. Assuming that it is vital to accurately judge the positions of the steps when navigating a staircase, it is surprising that people differ a lot in the extent to which they look at the steps. Apparently, some people consider the accuracy of peripheral vision, predictability of the step size, and feeling the edges of the steps with their feet to be good enough. If so, occluding part of the view of the staircase and making it more important to place one's feet gently might make it more beneficial to look directly at the steps before stepping onto them, so that people will more consistently look at many steps. We tested this idea by asking people to walk on staircases, either with or without a tray with two cups of water on it. When carrying the tray, people walked more slowly, but they shifted their gaze across steps in much the same way as they did when walking without the tray. They did not look at more steps. There was a clear positive correlation between the fraction of steps that people looked at when walking with and without the tray. Thus, the variability in the extent to which people look at the steps persists when one makes walking on the staircase more challenging.

Representative design: A realistic alternative to (systematic) integrative design.

We disagree with Almaatouq et al. that no realistic alternative exists to the "one-at-a-time" paradigm. Seventy years ago, Egon Brunswik introduced representative design, which offers a clear path to commensurability and generality. Almaatouq et al.'s integrative design cannot guarantee the external validity and generalizability of results which is sorely needed, while representative design tackles the problem head on.

Large eye-head gaze shifts measured with a wearable eye tracker and an industrial camera.

We built a novel setup to record large gaze shifts (up to 140 ∘ ). The setup consists of a wearable eye tracker and a high-speed camera with fiducial marker technology to track the head. We tested our setup by replicating findings from the classic eye-head gaze shift literature. We conclude that our new inexpensive setup is good enough to investigate the dynamics of large eye-head gaze shifts. This novel setup could be used for future research on large eye-head gaze shifts, but also for research on gaze during e.g., human interaction. We further discuss reference frames and terminology in head-free eye tracking. Despite a transition from head-fixed eye tracking to head-free gaze tracking, researchers still use head-fixed eye movement terminology when discussing world-fixed gaze phenomena. We propose to use more specific terminology for world-fixed phenomena, including gaze fixation, gaze pursuit, and gaze saccade.

What is a blink? Classifying and characterizing blinks in eye openness signals.

Blinks, the closing and opening of the eyelids, are used in a wide array of fields where human function and behavior are studied. In data from video-based eye trackers, blink rate and duration are often estimated from the pupil-size signal. However, blinks and their parameters can be estimated only indirectly from this signal, since it does not explicitly contain information about the eyelid position. We ask whether blinks detected from an eye openness signal that estimates the distance between the eyelids (EO blinks) are comparable to blinks detected with a traditional algorithm using the pupil-size signal (PS blinks) and how robust blink detection is when data quality is low. In terms of rate, there was an almost-perfect overlap between EO and PS blink (F1 score: 0.98) when the head was in the center of the eye tracker's tracking range where data quality was high and a high overlap (F1 score 0.94) when the head was at the edge of the tracking range where data quality was worse. When there was a difference in blink rate between EO and PS blinks, it was mainly due to data loss in the pupil-size signal. Blink durations were about 60 ms longer in EO blinks compared to PS blinks. Moreover, the dynamics of EO blinks was similar to results from previous literature. We conclude that the eye openness signal together with our proposed blink detection algorithm provides an advantageous method to detect and describe blinks in greater detail.

GlassesValidator: A data quality tool for eye tracking glasses.

According to the proposal for a minimum reporting guideline for an eye tracking study by Holmqvist et al. (2022), the accuracy (in degrees) of eye tracking data should be reported. Currently, there is no easy way to determine accuracy for wearable eye tracking recordings. To enable determining the accuracy quickly and easily, we have produced a simple validation procedure using a printable poster and accompanying Python software. We tested the poster and procedure with 61 participants using one wearable eye tracker. In addition, the software was tested with six different wearable eye trackers. We found that the validation procedure can be administered within a minute per participant and provides measures of accuracy and precision. Calculating the eye-tracking data quality measures can be done offline on a simple computer and requires no advanced computer skills.

A field test of computer-vision-based gaze estimation in psychology.

Computer-vision-based gaze estimation refers to techniques that estimate gaze direction directly from video recordings of the eyes or face without the need for an eye tracker. Although many such methods exist, their validation is often found in the technical literature (e.g., computer science conference papers). We aimed to (1) identify which computer-vision-based gaze estimation methods are usable by the average researcher in fields such as psychology or education, and (2) evaluate these methods. We searched for methods that do not require calibration and have clear documentation. Two toolkits, OpenFace and OpenGaze, were found to fulfill these criteria. First, we present an experiment where adult participants fixated on nine stimulus points on a computer screen. We filmed their face with a camera and processed the recorded videos with OpenFace and OpenGaze. We conclude that OpenGaze is accurate and precise enough to be used in screen-based experiments with stimuli separated by at least 11 degrees of gaze angle. OpenFace was not sufficiently accurate for such situations but can potentially be used in sparser environments. We then examined whether OpenFace could be used with horizontally separated stimuli in a sparse environment with infant participants. We compared dwell measures based on OpenFace estimates to the same measures based on manual coding. We conclude that OpenFace gaze estimates may potentially be used with measures such as relative total dwell time to sparse, horizontally separated areas of interest, but should not be used to draw conclusions about measures such as dwell duration.

Atezolizumab for First-Line Treatment of PD-L1-Selected Patients with NSCLC.

BACKGROUND: The efficacy and safety of the anti-programmed death ligand 1 (PD-L1) monoclonal antibody atezolizumab, as compared with those of platinum-based chemotherapy, as first-line treatment for patients with metastatic non-small-cell lung cancer (NSCLC) with PD-L1 expression are not known. METHODS: We conducted a randomized, open-label, phase 3 trial involving patients with metastatic nonsquamous or squamous NSCLC who had not previously received chemotherapy and who had PD-L1 expression on at least 1% of tumor cells or at least 1% of tumor-infiltrating immune cells as assessed by the SP142 immunohistochemical assay. Patients were assigned in a 1:1 ratio to receive atezolizumab or chemotherapy. Overall survival (primary end point) was tested hierarchically according to PD-L1 expression status among patients in the intention-to-treat population whose tumors were wild-type with respect to EGFR mutations or ALK translocations. Within the population with EGFR and ALK wild-type tumors, overall survival and progression-free survival were also prospectively assessed in subgroups defined according to findings on two PD-L1 assays as well as by blood-based tumor mutational burden. RESULTS: Overall, 572 patients were enrolled. In the subgroup of patients with EGFR and ALK wild-type tumors who had the highest expression of PD-L1 (205 patients), the median overall survival was longer by 7.1 months in the atezolizumab group than in the chemotherapy group (20.2 months vs. 13.1 months; hazard ratio for death, 0.59; P = 0.01). Among all the patients who could be evaluated for safety, adverse events occurred in 90.2% of the patients in the atezolizumab group and in 94.7% of those in the chemotherapy group; grade 3 or 4 adverse events occurred in 30.1% and 52.5% of the patients in the respective groups. Overall and progression-free survival favored atezolizumab in the subgroups with a high blood-based tumor mutational burden. CONCLUSIONS: Atezolizumab treatment resulted in significantly longer overall survival than platinum-based chemotherapy among patients with NSCLC with high PD-L1 expression, regardless of histologic type. (Funded by F. Hoffmann-La Roche/Genentech; IMpower110 ClinicalTrials.gov number, NCT02409342.).

Osimertinib in Resected EGFR-Mutated Non-Small-Cell Lung Cancer.

BACKGROUND: Osimertinib is standard-of-care therapy for previously untreated epidermal growth factor receptor (EGFR) mutation-positive advanced non-small-cell lung cancer (NSCLC). The efficacy and safety of osimertinib as adjuvant therapy are unknown. METHODS: In this double-blind, phase 3 trial, we randomly assigned patients with completely resected EGFR mutation-positive NSCLC in a 1:1 ratio to receive either osimertinib (80 mg once daily) or placebo for 3 years. The primary end point was disease-free survival among patients with stage II to IIIA disease (according to investigator assessment). The secondary end points included disease-free survival in the overall population of patients with stage IB to IIIA disease, overall survival, and safety. RESULTS: A total of 682 patients underwent randomization (339 to the osimertinib group and 343 to the placebo group). At 24 months, 90% of the patients with stage II to IIIA disease in the osimertinib group (95% confidence interval [CI], 84 to 93) and 44% of those in the placebo group (95% CI, 37 to 51) were alive and disease-free (overall hazard ratio for disease recurrence or death, 0.17; 99.06% CI, 0.11 to 0.26; P<0.001). In the overall population, 89% of the patients in the osimertinib group (95% CI, 85 to 92) and 52% of those in the placebo group (95% CI, 46 to 58) were alive and disease-free at 24 months (overall hazard ratio for disease recurrence or death, 0.20; 99.12% CI, 0.14 to 0.30; P<0.001). At 24 months, 98% of the patients in the osimertinib group (95% CI, 95 to 99) and 85% of those in the placebo group (95% CI, 80 to 89) were alive and did not have central nervous system disease (overall hazard ratio for disease recurrence or death, 0.18; 95% CI, 0.10 to 0.33). Overall survival data were immature; 29 patients died (9 in the osimertinib group and 20 in the placebo group). No new safety concerns were noted. CONCLUSIONS: In patients with stage IB to IIIA EGFR mutation-positive NSCLC, disease-free survival was significantly longer among those who received osimertinib than among those who received placebo. (Funded by AstraZeneca; ADAURA ClinicalTrials.gov number, NCT02511106.).

Visioning synthetic futures for yeast research within the context of current global techno-political trends.

Yeast research is entering into a new period of scholarship, with new scientific tools, new questions to ask and new issues to consider. The politics of emerging and critical technology can no longer be separated from the pursuit of basic science in fields, such as synthetic biology and engineering biology. Given the intensifying race for technological leadership, yeast research is likely to attract significant investment from government, and that it offers huge opportunities to the curious minded from a basic research standpoint. This article provides an overview of new directions in yeast research with a focus on Saccharomyces cerevisiae, and places these trends in their geopolitical context. At the highest level, yeast research is situated within the ongoing convergence of the life sciences with the information sciences. This convergent effect is most strongly pronounced in areas of AI-enabled tools for the life sciences, and the creation of synthetic genomes, minimal genomes, pan-genomes, neochromosomes and metagenomes using computer-assisted design tools and methodologies. Synthetic yeast futures encompass basic and applied science questions that will be of intense interest to government and nongovernment funding sources. It is essential for the yeast research community to map and understand the context of their research to ensure their collaborations turn global challenges into research opportunities.

Assessing acceptance and effects of child feeding counselling on nutritional status of children aged 6-23 months in a semi-urban community.

In Bangladesh, only 34 % of the children aged 18-23 months old are given minimum acceptable diets of complementary foods. Objective of the study was to find the effects of complementary feeding counselling on nutritional status among 6-23 months old children of poor families. This was a community-based randomised control trial. A total of 192 children in two groups were randomly selected. Nutrition education was given for a period of 4 months with post-intervention follow-up for 2 months. After 4 months of intervention, the difference in height for age Z score, weight for height Z score and weight for age Z score were significantly higher in the intervention group than in the control group (1·01 ± 0·31 v. 0·19 ± 0·01, P =< 0·001; 1·34 ± 0·15 v 0·72 ± 0·11, P =< 0·001; 1·5 ± 0·24 v. 0·62 ± 0·04, P =< 0·001). Mid-upper arm circumference Z score also improved in the intervention group than in the control group (0·95 ± 0·03 v. 0·57 ± 0·12, P =< 0·001). Morbidity of the children in the intervention group significantly reduced than in the control group (49 % v 80·20 %, P =< 0·001). Higher feeding frequency (3-4 times) (71·9 % v. 45·8 %) and energy intake increased in the intervention group than in the control group. Promotion of complementary feeding from the family foods can improve the nutritional status of 6-23 months old children of poor families within a short period.

Frameworks for estimating causal effects in observational settings: comparing confounder adjustment and instrumental variables.

To estimate causal effects, analysts performing observational studies in health settings utilize several strategies to mitigate bias due to confounding by indication. There are two broad classes of approaches for these purposes: use of confounders and instrumental variables (IVs). Because such approaches are largely characterized by untestable assumptions, analysts must operate under an indefinite paradigm that these methods will work imperfectly. In this tutorial, we formalize a set of general principles and heuristics for estimating causal effects in the two approaches when the assumptions are potentially violated. This crucially requires reframing the process of observational studies as hypothesizing potential scenarios where the estimates from one approach are less inconsistent than the other. While most of our discussion of methodology centers around the linear setting, we touch upon complexities in non-linear settings and flexible procedures such as target minimum loss-based estimation and double machine learning. To demonstrate the application of our principles, we investigate the use of donepezil off-label for mild cognitive impairment. We compare and contrast results from confounder and IV methods, traditional and flexible, within our analysis and to a similar observational study and clinical trial.