A tuneable genetic switch for tight control of tac promoters in Escherichia coli boosts expression of synthetic injectisomes.

Biosafety of engineered bacteria as living therapeutics requires a tight regulation to control the specific delivery of protein effectors, maintaining minimum leakiness in the uninduced (OFF) state and efficient expression in the induced (ON) state. Here, we report a three repressors (3R) genetic circuit that tightly regulates the expression of multiple tac promoters (Ptac) integrated in the chromosome of E. coli and drives the expression of a complex type III secretion system injectisome for therapeutic protein delivery. The 3R genetic switch is based on the tetracycline repressor (TetR), the non-inducible lambda repressor cI (ind-) and a mutant lac repressor (LacIW220F ) with higher activity. The 3R switch was optimized with different protein translation and degradation signals that control the levels of LacIW220F . We demonstrate the ability of an optimized switch to fully repress the strong leakiness of the Ptac promoters in the OFF state while triggering their efficient activation in the ON state with anhydrotetracycline (aTc), an inducer suitable for in vivo use. The implementation of the optimized 3R switch in the engineered synthetic injector E. coli (SIEC) strain boosts expression of injectisomes upon aTc induction, while maintaining a silent OFF state that preserves normal growth in the absence of the inducer. Since Ptac is a commonly used promoter, the 3R switch may have multiple applications for tight control of protein expression in E. coli. In addition, the modularity of the 3R switch may enable its tuning for the control of Ptac promoters with different inducers.

Interval between balloon removal and oxytocin administration in cervical ripening with double-balloon in singleton pregnancies: An observational study.

OBJECTIVE: To analyze the influence of the resting interval after removal of a double-balloon for cervical ripening and oxytocin administration on the time to onset of active labor in singleton pregnancies. METHODS: A retrospective cohort study of women who required a cervical ripening with double-balloon was conducted between January 2019 and December 2022. We collected data for cervical ripening balloon insertion and removal, oxytocin administration, suspicious or pathological cardiotocographic trace, mode of delivery, maternal and neonatal complications, neonatal outcomes. Proportional hazards model comparing resting interval between double-balloon cervical ripening removal and oxytocin administration. RESULTS: A total of 403 singleton pregnancies were recruited and 213 pregnant women experienced a rest of 12 h between cervical balloon removal and oxytocin administration (resting group). Oxytocin was administered immediately after balloon removal in 190 women (non-resting group). Median insertion-to-active labor interval and insertion-to-delivery interval were significantly shorter in the non-resting group: 18.5 versus 24.0 h, HR 2.59 (CI 95%: 1.97-3.41) and 24.0 versus 29.0 h, HR 2.38 (CI 95%: 1.85-3.05) respectively. Bishop score change and mode of delivery between were similar in both groups. No differences in maternal nor neonatal complications between both groups were found. CONCLUSIONS: Oxytocin administration immediately after removal of a double-balloon for cervical ripening compared with 12 h delayed interval resulted in a shortened time from insertion to active labor onset and to delivery interval without increasing maternal or neonatal adverse outcomes.

Time-course Changes of Field- and Laboratory-based Performance Indicators in Junior Cyclists Through a Season.

This study aimed to assess the seasonal evolution of field-based and laboratory-based performance indicators in cyclists. Thirteen Junior male road cyclists (age 17.4±0.5 years) were followed up during a season, which was divided in three phases: early season (involving mainly training sessions), mid-season (including the first competitions), and late season (including the major competitions of the season). During each phase, field-based power output data were registered for the assessment of maximum mean power values, and laboratory-based endurance (ramp test and simulated 8-minute time trial), muscle strength/power (squat, lunge, hip thrust) and body composition indicators (dual-energy X-ray absorptiometry) were also assessed. A progressive (p<0.01) increase in maximum mean power values (e.g., 3.8±0.3 and 4.5±0.4 watts/kg in early and late season, respectively, for 60-minute efforts) and on 8-minute time trial performance (i.e., 5.3±0.3 and 5.6±0.4 watts/kg, respectively) was observed through the season. Yet, more "traditional" endurance indicators (i.e., ventilatory threshold, respiratory compensation point, or maximum oxygen uptake) seemed to show a ceiling effect beyond the mid-season. In addition, neither peak power output, body composition, nor muscle strength indicators followed a similar pattern to the aforementioned field-based indicators. In summary, in Junior cyclists field-based indicators seem more sensitive to monitor endurance cyclists' changes in actual fitness and performance capacity than more "traditional" laboratory-based markers in Junior cyclists.

Sex Differences in the Load-Velocity Profiles of Three Different Row Exercises.

This study examined the force-velocity profile differences between men and women in three variations of row exercises. Twenty-eight participants (14 men and 14 women) underwent maximum dynamic strength assessments in the free prone bench row (PBR), bent-over barbell row (BBOR), and Smith machine bent-over row (SMBOR) in a randomized order. Subjects performed a progressive loading test from 30 to 100% of 1-RM (repetition maximum), and the mean propulsive velocity was measured in all attempts. Linear regression analyses were conducted to establish the relationships between the different measures of bar velocity and % 1-RM. The ANOVAs applied to the mean velocity achieved in each % 1-RM tested revealed significantly higher velocity values for loads < 65% 1-RM in SMBOR compared to BBOR (p < 0.05) and higher velocities for loads < 90% 1-RM in SMBOR compared to PBR (p < 0.05) for both sexes. Furthermore, men provided significantly higher velocity values than women (PBR 55-100% 1-RM; BBOR and SMBOR < 85% 1-RM; p < 0.05) and significant differences were found between exercises and sex for 30-40% 1-RM. These results confirm that men have higher velocities at different relative loads (i.e., % 1-RM) compared to women during upper-body rowing exercises.

Loss of p53-DREAM-mediated repression of cell cycle genes as a driver of lymph node metastasis in head and neck cancer.

BACKGROUND: The prognosis for patients with head and neck cancer (HNC) is poor and has improved little in recent decades, partially due to lack of therapeutic options. To identify effective therapeutic targets, we sought to identify molecular pathways that drive metastasis and HNC progression, through large-scale systematic analyses of transcriptomic data. METHODS: We performed meta-analysis across 29 gene expression studies including 2074 primary HNC biopsies to identify genes and transcriptional pathways associated with survival and lymph node metastasis (LNM). To understand the biological roles of these genes in HNC, we identified their associated cancer pathways, as well as the cell types that express them within HNC tumor microenvironments, by integrating single-cell RNA-seq and bulk RNA-seq from sorted cell populations. RESULTS: Patient survival-associated genes were heterogenous and included drivers of diverse tumor biological processes: these included tumor-intrinsic processes such as epithelial dedifferentiation and epithelial to mesenchymal transition, as well as tumor microenvironmental factors such as T cell-mediated immunity and cancer-associated fibroblast activity. Unexpectedly, LNM-associated genes were almost universally associated with epithelial dedifferentiation within malignant cells. Genes negatively associated with LNM consisted of regulators of squamous epithelial differentiation that are expressed within well-differentiated malignant cells, while those positively associated with LNM represented cell cycle regulators that are normally repressed by the p53-DREAM pathway. These pro-LNM genes are overexpressed in proliferating malignant cells of TP53 mutated and HPV + ve HNCs and are strongly associated with stemness, suggesting that they represent markers of pre-metastatic cancer stem-like cells. LNM-associated genes are deregulated in high-grade oral precancerous lesions, and deregulated further in primary HNCs with advancing tumor grade and deregulated further still in lymph node metastases. CONCLUSIONS: In HNC, patient survival is affected by multiple biological processes and is strongly influenced by the tumor immune and stromal microenvironments. In contrast, LNM appears to be driven primarily by malignant cell plasticity, characterized by epithelial dedifferentiation coupled with EMT-independent proliferation and stemness. Our findings postulate that LNM is initially caused by loss of p53-DREAM-mediated repression of cell cycle genes during early tumorigenesis.

Laboratory-based determinants of simulated time trial performance in cyclists.

Different laboratory-based variables are individually associated with cycling performance, but scarce evidence exists on which of them, when all assessed in combination, could best explain cycling performance. The present study aimed to examine the combined association between laboratory-based endurance, strength/power and body composition indicators with time trial performance in high-level cyclists. Ninety-four male cyclists were recruited (age: 20 ± 3.5 years, maximum oxygen uptake [V̇O2max]: 77.7 ± 5.4 ml · kg-1 · min-1). Participants performed a maximal incremental cycling test for the assessment of endurance indicators (peak power output [PPO], V̇O2max, ventilatory threshold [VT] and respiratory compensation point [RCP]), and an incremental loading test to assess muscle strength and power-related outcomes (1-repetition maximum, mean maximal power) in the squat, lunge and hip-thrust exercises. Body composition was assessed by dual energy X-ray absorptiometry. On a separate visit, participants performed a simulated 8-minute time trial to assess cycling performance (determined as the mean power output attained). Strong-to-very-strong correlations were found between all endurance indicators and time trial performance (most r-values ranging between 0.68-0.92), whereas weaker correlations were found for strength/power (r-values < 0.5) or body composition (r-values < 0.7) indicators. Multivariate regression analyses revealed that VT, RCP and PPO explained together 92% of the variance in time trial performance (p < 0.001), with no significant contribution of the remaining variables. Although different endurance, strength/power and body composition individually correlate with simulated time trial performance in high-level cyclists, the former (and particularly VT, RCP and PPO) show the strongest association when all studied in combination. These findings underscore the importance of endurance capabilities (above strength/power or body composition) for maximizing time trial performance.

Organization of the human intestine at single-cell resolution.

The intestine is a complex organ that promotes digestion, extracts nutrients, participates in immune surveillance, maintains critical symbiotic relationships with microbiota and affects overall health1. The intesting has a length of over nine metres, along which there are differences in structure and function2. The localization of individual cell types, cell type development trajectories and detailed cell transcriptional programs probably drive these differences in function. Here, to better understand these differences, we evaluated the organization of single cells using multiplexed imaging and single-nucleus RNA and open chromatin assays across eight different intestinal sites from nine donors. Through systematic analyses, we find cell compositions that differ substantially across regions of the intestine and demonstrate the complexity of epithelial subtypes, and find that the same cell types are organized into distinct neighbourhoods and communities, highlighting distinct immunological niches that are present in the intestine. We also map gene regulatory differences in these cells that are suggestive of a regulatory differentiation cascade, and associate intestinal disease heritability with specific cell types. These results describe the complexity of the cell composition, regulation and organization for this organ, and serve as an important reference map for understanding human biology and disease.

Bacteria-instructed B cells cross-prime naïve CD8+ T cells triggering effective cytotoxic responses.

In addition to triggering humoral responses, conventional B cells have been described in vitro to cross-present exogenous antigens activating naïve CD8+ T cells. Nevertheless, the way B cells capture these exogenous antigens and the physiological roles of B cell-mediated cross-presentation remain poorly explored. Here, we show that B cells capture bacteria by trans-phagocytosis from previously infected dendritic cells (DC) when they are in close contact. Bacterial encounter "instructs" the B cells to acquire antigen cross-presentation abilities, in a process that involves autophagy. Bacteria-instructed B cells, henceforth referred to as BacB cells, rapidly degrade phagocytosed bacteria, process bacterial antigens and cross-prime naïve CD8+ T cells which differentiate into specific cytotoxic cells that efficiently control bacterial infections. Moreover, a proof-of-concept experiment shows that BacB cells that have captured bacteria expressing tumor antigens could be useful as novel cellular immunotherapies against cancer.

Should We Use the Men Load-Velocity Profile for Women in Deadlift and Hip Thrust?

Injuries are common in team sports and can impact both team and individual performance. In particular, hamstring strain injuries are some of the most common injuries. Furthermore, hamstring injury ratios, in number of injuries and total absence days, have doubled in the last 21 seasons in professional soccer. Weakness in hip extensor strength has been identified as a risk factor in elite-level sprinters. In addition, strength imbalances of the hamstring muscle group seem to be a common cause of hamstring strain injuries. In this regard, velocity-based training has been proposed to analyze deficits in the force-velocity profile. Previous studies have shown differences between men and women, since there are biomechanical and neuromuscular differences in the lower limbs between sexes. Therefore, the aim of this study was to compare the load-velocity profile between males and females during two of the most important hip extension exercises: the hip thrust and the deadlift. Sixteen men and sixteen women were measured in an incremental loading test following standard procedures for the hip thrust and deadlift exercises. Pearson's correlation (r) was used to measure the strength of the correlation between movement velocity and load (%1RM). The differences in the load-velocity relationship between the men and the women were assessed using a 2 (sex) × 15 (load) repeated-measures ANOVA. The main findings revealed that: (I) the load-velocity relationship was always strong and linear in both exercises (R2 range: 0.88-0.94), (II) men showed higher velocities for light loads (30-50%1RM; effect size: 0.9-0.96) than women for the deadlift, but no significant differences were found for the hip thrust. Based on the results of this study, the load-velocity equations seem to be sex-specific. Therefore, we suggest that using sex-specific equations to analyze deficits in the force-velocity profile would be more effective to control intensity in the deadlift exercise.

Pre-sleep protein supplementation in professional cyclists during a training camp: a three-arm randomized controlled trial.

Background: The effects of pre-sleep protein supplementation on endurance athletes remain unclear, particularly whether its potential benefits are due to the timing of protein intake or solely to an increased total protein intake. We assessed the effects of pre-sleep protein supplementation in professional cyclists during a training camp accounting for the influence of protein timing. Methods: Twenty-four professional U23 cyclists (19 ± 1 years, peak oxygen uptake: 79.8 ± 4.9 ml/kg/min) participated in a six-day training camp. Participants were randomized to consume a protein supplement (40 g of casein) before sleep (n = 8) or in the afternoon (n = 8), or an isoenergetic placebo (40 g of carbohydrates) before sleep (n = 8). Indicators of fatigue/recovery (Hooper index, Recovery-Stress Questionnaire for Athletes, countermovement jump), body composition, and performance (1-, 5-, and 20-minute time trials, as well as the estimated critical power) were assessed as study outcomes. Results: The training camp resulted in a significant (p < 0.001) increase in training loads (e.g. training stress score of 659 ± 122 per week during the preceding month versus 1207 ± 122 during the training camp), which induced an increase in fatigue indicators (e.g. time effect for Hooper index p < 0.001) and a decrease in performance (e.g. time effect for critical power p = 0.002). Protein intake was very high in all the participants (>2.5 g/kg on average), with significantly higher levels found in the two protein supplement groups compared to the placebo group (p < 0.001). No significant between-group differences were found for any of the analyzed outcomes (all p > 0.05). Conclusions: Protein supplementation, whether administered before sleep or earlier in the day, exerts no beneficial effects during a short-term strenuous training period in professional cyclists, who naturally consume a high-protein diet.

Molecular Characterization of Acquired Resistance to KRASG12C-EGFR Inhibition in Colorectal Cancer.

With the combination of KRASG12C and EGFR inhibitors, KRAS is becoming a druggable target in colorectal cancer. However, secondary resistance limits its efficacy. Using cell lines, patient-derived xenografts, and patient samples, we detected a heterogeneous pattern of putative resistance alterations expected primarily to prevent inhibition of ERK signaling by drugs at progression. Serial analysis of patient blood samples on treatment demonstrates that most of these alterations are detected at a low frequency except for KRASG12C amplification, a recurrent resistance mechanism that rises in step with clinical progression. Upon drug withdrawal, resistant cells with KRASG12C amplification undergo oncogene-induced senescence, and progressing patients experience a rapid fall in levels of this alteration in circulating DNA. In this new state, drug resumption is ineffective as mTOR signaling is elevated. However, our work exposes a potential therapeutic vulnerability, whereby therapies that target the senescence response may overcome acquired resistance. SIGNIFICANCE: Clinical resistance to KRASG12C-EGFR inhibition primarily prevents suppression of ERK signaling. Most resistance mechanisms are subclonal, whereas KRASG12C amplification rises over time to drive a higher portion of resistance. This recurrent resistance mechanism leads to oncogene-induced senescence upon drug withdrawal and creates a potential vulnerability to senolytic approaches. This article is highlighted in the In This Issue feature, p. 1.

MACHETE identifies interferon-encompassing chromosome 9p21.3 deletions as mediators of immune evasion and metastasis.

The most prominent homozygous deletions in cancer affect chromosome 9p21.3 and eliminate CDKN2A/B tumor suppressors, disabling a cell-intrinsic barrier to tumorigenesis. Half of 9p21.3 deletions, however, also encompass a type I interferon (IFN) gene cluster; the consequences of this co-deletion remain unexplored. To functionally dissect 9p21.3 and other large genomic deletions, we developed a flexible deletion engineering strategy, MACHETE (molecular alteration of chromosomes with engineered tandem elements). Applying MACHETE to a syngeneic mouse model of pancreatic cancer, we found that co-deletion of the IFN cluster promoted immune evasion, metastasis and immunotherapy resistance. Mechanistically, IFN co-deletion disrupted type I IFN signaling in the tumor microenvironment, leading to marked changes in infiltrating immune cells and escape from CD8+ T-cell surveillance, effects largely driven by the poorly understood interferon epsilon. These results reveal a chromosomal deletion that disables both cell-intrinsic and cell-extrinsic tumor suppression and provide a framework for interrogating large deletions in cancer and beyond.

Neurophysiological Findings in Critical COVID-19 Patients With Peripheral Nervous System Manifestations.

INTRODUCTION: Coronavirus disease 2019 patients hospitalized in intensive care units develop neuromuscular manifestations. However, to our knowledge, a study describing the neurophysiological findings in these patients has not been reported. The objective of this study was to diagnose the cause of neuromuscular deficit in severe coronavirus disease 2019 patients, through neurophysiological examination. METHODS: This is a retrospective, observational case series. Data were collected from April 13, 2020, to May 31, 2020. Twenty-two coronavirus disease 2019 patients with generalized neuromuscular deficit during intensive care unit hospitalization were studied. Neurophysiological examinations included motor and sensory peripheral nerve conductions, needle electromyography, F waves, and repetitive nerve stimulation. RESULTS: The subjects were 14 men (63.6%) and eight women, ranged from 35 to 74 years old (58.0, interquartile ranges 50.7-66.2). Intensive care unit hospitalization time ranged from 14 to 82 days (median 37.5, interquartile ranges 22.7-55.0). Through neurophysiological examination, myopathy was diagnosed in 17 patients (77.3%) and polyneuropathy in four (18.2%). Focal neuropathies were diagnosed in 12 patients (54.6%), with a total of 19 affected nerves. Common peroneal nerve lesions at the fibular head (68.4%) and ulnar nerve lesions at the elbow level (21.1%) were the most frequent locations. No significant differences were established between neurophysiological findings and clinical or analytical data. CONCLUSIONS: In critical coronavirus disease 2019 patients with neuromuscular complaints, neurophysiological examination provides an accurate diagnosis-useful to select treatment measures and establish the prognosis of recovery. Neurophysiological findings are similar to those described for critical illness neuromuscular disease, with myopathy being the most frequent diagnosis.

Transit-amplifying cells control R-spondins in the mouse crypt to modulate intestinal stem cell proliferation.

Intestinal epithelium regenerates rapidly through proliferation of intestinal stem cells (ISCs), orchestrated by potent mitogens secreted within the crypt niche. However, mechanisms regulating these mitogenic factors remain largely unknown. Here, we demonstrate that transit-amplifying (TA) cells, marked by unconventional prefoldin RPB5 interactor (URI), control R-spondin production to guide ISC proliferation. Genetic intestinal URI ablation in mice injures TA cells, reducing their survival capacity, leading to an inflamed tissue and subsequently decreasing R-spondin levels, thereby causing ISC quiescence and disruption of intestinal structure. R-spondin supplementation or restoration of R-spondin levels via cell death inhibition by c-MYC elimination or the suppression of inflammation reinstates ISC proliferation in URI-depleted mice. However, selective c-MYC and p53 suppression are required to fully restore TA cell survival and differentiation capacity and preserve complete intestinal architecture. Our data reveal an unexpected role of TA cells, which represent a signaling platform instrumental for controlling inflammatory cues and R-spondin production, essential for maintaining ISC proliferation and tissue regeneration.

Comparative analysis of endurance, strength and body composition indicators in professional, under-23 and junior cyclists.

Purpose: To compare endurance, strength and body composition indicators between cyclists of three different competition age categories. Methods: Fifty-one male road cyclists classified as either junior (n = 13, age 16.4 ± 0.5 years), under-23 [(U23), n = 24, 19.2 ± 1.3 years] or professional (n = 14, 26.1 ± 4.8 years) were studied. Endurance (assessed through a maximal incremental test and an 8-minute time-trial), strength/power (assessed through incremental loading tests for the squat, lunge and hip thrust exercises) and body composition (assessed through dual energy X-ray absorptiometry) were determined on three different testing sessions. Results: U23 and, particularly professional, cyclists attained significantly (p < 0.05) higher values than juniors for most of the analyzed endurance indicators [time-trial performance, maximum oxygen uptake (VO2max), peak power output (PPO), respiratory compensation point (RCP), and ventilatory threshold (VT)]. Significant differences (p < 0.05) between U23 and professionals were also found for time-trial performance, PPO and VT, but not for other markers such as VO2max or RCP. Professional cyclists also showed significantly (p < 0.05) lower relative fat mass and higher muscle mass levels than U23 and, particularly, juniors. No consistent differences between age categories were found for muscle strength/power indicators. Conclusion: Endurance (particularly time-trial performance, PPO and VT) and body composition (fat and muscle mass) appear as factors that best differentiate between cyclists of different age categories, whereas no consistent differences are found for muscle strength/power. These findings might help in performance prediction and/or talent identification and may aid in guiding coaches in the design of training programs focused on improving those variables that appear more determinant.

Peripheral blood DNA methylation profiles predict future development of B-cell Non-Hodgkin Lymphoma.

Lack of accurate methods for early lymphoma detection limits the ability to cure patients. Since patients with Non-Hodgkin lymphomas (NHL) who present with advanced disease have worse outcomes, accurate and sensitive methods for early detection are needed to improve patient care. We developed a DNA methylation-based prediction tool for NHL, based on blood samples collected prospectively from 278 apparently healthy patients who were followed for up to 16 years to monitor for NHL development. A predictive score was developed using machine learning methods in a robust training/validation framework. Our predictive score incorporates CpG DNA methylation at 135 genomic positions, with higher scores predicting higher risk. It was 85% and 78% accurate for identifying patients at risk of developing future NHL, in patients with high or low epigenetic mitotic clock respectively, in a validation cohort. It was also sensitive at detecting active NHL (96.3% accuracy) and healthy status (95.6% accuracy) in additional independent cohorts. Scores optimized for specific NHL subtypes showed significant but lower accuracy for predicting other subtypes. Our score incorporates hyper-methylation of Polycomb and HOX genes, which have roles in NHL development, as well as PAX5 - a master transcriptional regulator of B-cell fate. Subjects with higher risk scores showed higher regulatory T-cells, memory B-cells, but lower naïve T helper lymphocytes fractions in the blood. Future prospective studies will be required to confirm the utility of our signature for managing patients who are at high risk for developing future NHL.

Are Unilateral Devices Valid for Power Output Determination in Cycling? Insights From the Favero Assioma Power Meter.

PURPOSE: Some power meters are available in both bilateral and unilateral versions. However, despite the popularity of the latter, their validity remains unknown. We aimed to analyze the validity of a unilateral pedal power meter for estimating actual ("bilateral") power output (PO). METHODS: Thirty-three male cyclists were assessed at different POs (steady cycling at 100-500 W, as well as all-out sprints), pedaling cadences (70, 85, and 100 repetitions·min-1), and cycling positions (seated and standing). The PO estimated by a left-only power meter (Favero Assioma Uno) was compared with the actual PO computed by a bilateral power meter (Favero Assioma Duo), and the level of bilateral asymmetry (most- vs least-powerful leg) with the latter system was also computed. RESULTS: Nonsignificant differences, high intraclass correlation coefficients (≥.90), and low coefficients of variation (consistently ≤5% except for low PO levels, ie, 5%-7% at 100 W) were found between Favero Assioma Uno and Favero Assioma Duo. However, although a strong intraclass correlation coefficient (.995) was found between both legs, asymmetry values of 4% to 6% were found for all conditions except when pedaling at the lowest PO (100 W), in which asymmetry increased up to 10% to 13%. CONCLUSIONS: Although cyclists tend to present some level of bilateral asymmetry during cycling (particularly at low PO), Favero Assioma Uno provides overall valid estimates of actual PO and is, therefore, an economical alternative to bilateral power meters. Caution is needed, however, when interpreting data at the individual level in cyclists with high levels of asymmetry.

An immunocompetent rectal cancer model to study radiation therapy.

We describe a mouse model of rectal cancer (RC) involving rapid tumor organoid engraftment via orthotopic transplantation in an immunocompetent setting. This approach uses simple mechanical disruption to allow engraftment, avoiding the use of dextran sulfate sodium. The resulting RC tumors invaded from the mucosal surface and metastasized to distant organs. Histologically, the tumors closely resemble human RC and mirror remodeling of the tumor microenvironment in response to radiation. This murine RC model thus recapitulates key aspects of human RC pathogenesis and presents an accessible approach for more physiologically accurate, preclinical efficacy studies.

Atlas of clinically distinct cell states and ecosystems across human solid tumors.

Determining how cells vary with their local signaling environment and organize into distinct cellular communities is critical for understanding processes as diverse as development, aging, and cancer. Here we introduce EcoTyper, a machine learning framework for large-scale identification and validation of cell states and multicellular communities from bulk, single-cell, and spatially resolved gene expression data. When applied to 12 major cell lineages across 16 types of human carcinoma, EcoTyper identified 69 transcriptionally defined cell states. Most states were specific to neoplastic tissue, ubiquitous across tumor types, and significantly prognostic. By analyzing cell-state co-occurrence patterns, we discovered ten clinically distinct multicellular communities with unexpectedly strong conservation, including three with myeloid and stromal elements linked to adverse survival, one enriched in normal tissue, and two associated with early cancer development. This study elucidates fundamental units of cellular organization in human carcinoma and provides a framework for large-scale profiling of cellular ecosystems in any tissue.