Homopolymer switches mediate adaptive mutability in mismatch repair-deficient colorectal cancer.

Mismatch repair (MMR)-deficient cancer evolves through the stepwise erosion of coding homopolymers in target genes. Curiously, the MMR genes MutS homolog 6 (MSH6) and MutS homolog 3 (MSH3) also contain coding homopolymers, and these are frequent mutational targets in MMR-deficient cancers. The impact of incremental MMR mutations on MMR-deficient cancer evolution is unknown. Here we show that microsatellite instability modulates DNA repair by toggling hypermutable mononucleotide homopolymer runs in MSH6 and MSH3 through stochastic frameshift switching. Spontaneous mutation and reversion modulate subclonal mutation rate, mutation bias and HLA and neoantigen diversity. Patient-derived organoids corroborate these observations and show that MMR homopolymer sequences drift back into reading frame in the absence of immune selection, suggesting a fitness cost of elevated mutation rates. Combined experimental and simulation studies demonstrate that subclonal immune selection favors incremental MMR mutations. Overall, our data demonstrate that MMR-deficient colorectal cancers fuel intratumor heterogeneity by adapting subclonal mutation rate and diversity to immune selection.

Tumor evolution metrics predict recurrence beyond 10 years in locally advanced prostate cancer.

Cancer evolution lays the groundwork for predictive oncology. Testing evolutionary metrics requires quantitative measurements in controlled clinical trials. We mapped genomic intratumor heterogeneity in locally advanced prostate cancer using 642 samples from 114 individuals enrolled in clinical trials with a 12-year median follow-up. We concomitantly assessed morphological heterogeneity using deep learning in 1,923 histological sections from 250 individuals. Genetic and morphological (Gleason) diversity were independent predictors of recurrence (hazard ratio (HR) = 3.12 and 95% confidence interval (95% CI) = 1.34-7.3; HR = 2.24 and 95% CI = 1.28-3.92). Combined, they identified a group with half the median time to recurrence. Spatial segregation of clones was also an independent marker of recurrence (HR = 2.3 and 95% CI = 1.11-4.8). We identified copy number changes associated with Gleason grade and found that chromosome 6p loss correlated with reduced immune infiltration. Matched profiling of relapse, decades after diagnosis, confirmed that genomic instability is a driving force in prostate cancer progression. This study shows that combining genomics with artificial intelligence-aided histopathology leads to the identification of clinical biomarkers of evolution.

Immune evasion impacts the landscape of driver genes during cancer evolution.

BACKGROUND: Carcinogenesis is driven by interactions between genetic mutations and the local tumor microenvironment. Recent research has identified hundreds of cancer driver genes; however, these studies often include a mixture of different molecular subtypes and ecological niches and ignore the impact of the immune system. RESULTS: In this study, we compare the landscape of driver genes in tumors that escaped the immune system (escape +) versus those that did not (escape -). We analyze 9896 primary tumors from The Cancer Genome Atlas using the ratio of non-synonymous to synonymous mutations (dN/dS) and find 85 driver genes, including 27 and 16 novel genes, in escape - and escape + tumors, respectively. The dN/dS of driver genes in immune escaped tumors is significantly lower and closer to neutrality than in non-escaped tumors, suggesting selection buffering in driver genes fueled by immune escape. Additionally, we find that immune evasion leads to more mutated sites, a diverse array of mutational signatures and is linked to tumor prognosis. CONCLUSIONS: Our findings highlight the need for improved patient stratification to identify new therapeutic targets for cancer treatment.

NeuroSense: A non-invasive and configurable somatosensory stimulator with OPENVIBE communication.

Understanding the somatosensory system and its abnormalities requires the development of devices that can accurately stimulate the human skin. New methods for assessing the somatosensory system can enhance the diagnosis, treatments, and prognosis for individuals with somatosensory impairments. Therefore, the design of NeuroSense, a tactile stimulator that evokes three types of daily life sensations (touch, air and vibration) is described in this work. The prototype aims to evoke quantitative assessments to evaluate the functionality of the somatosensory system and its abnormal conditions that affect the quality of life. In addition, the device has proven to have varying intensities and onset latencies that produces somatosensory evoked potentials and energy desynchronization on somatosensory cortex.

Assessing Outcomes of Patients Subject to Intensive Care to Facilitate Organ Donation: A Spanish Multicenter Prospective Study.

Intensive Care to facilitate Organ Donation (ICOD) consists of the initiation or continuation of intensive care measures in patients with a devastating brain injury (DBI) in whom curative treatment is deemed futile and death by neurological criteria (DNC) is foreseen, to incorporate organ donation into their end-of-life plans. In this study we evaluate the outcomes of patients subject to ICOD and identify radiological and clinical factors associated with progression to DNC. In this first prospective multicenter study we tested by multivariate regression the association of clinical and radiological severity features with progression to DNC. Of the 194 patients, 144 (74.2%) patients fulfilled DNC after a median of 25 h (95% IQR: 17-44) from ICOD onset. Two patients (1%) shifted from ICOD to curative treatment, both were alive at discharge. Factors associated with progression to DNC included: age below 70 years, clinical score consistent with severe brain injury, instability, intracranial hemorrhage, midline shift ≥5 mm and certain types of brain herniation. Overall 151 (77.8%) patients progressed to organ donation. Based on these results, we conclude that ICOD is a beneficial and efficient practice that can contribute to the pool of deceased donors.

CRISPRi-induced transcriptional regulation of IAH1 gene and its influence on volatile compounds profile in Kluyveromyces marxianus DU3.

Mezcal is a traditional Mexican distilled beverage, known for its marked organoleptic profile, which is influenced by several factors, such as the fermentation process, where a wide variety of microorganisms are present. Kluyveromyces marxianus is one of the main yeasts isolated from mezcal fermentations and has been associated with ester synthesis, contributing to the flavors and aromas of the beverage. In this study, we employed CRISPR interference (CRISPRi) technology, using dCas9 fused to the Mxi1 repressor factor domain, to down-regulate the expression of the IAH1 gene, encoding for an isoamyl acetate-hydrolyzing esterase, in K. marxianus strain DU3. The constructed CRISPRi plasmid successfully targeted the IAH1 gene, allowing for specific gene expression modulation. Through gene expression analysis, we assessed the impact of IAH1 down-regulation on the metabolic profile of volatile compounds. We also measured the expression of other genes involved in volatile compound biosynthesis, including ATF1, EAT1, ADH1, and ZWF1 by RT-qPCR. Results demonstrated successful down-regulation of IAH1 expression in K. marxianus strain DU3 using the CRISPRi system. The modulation of IAH1 gene expression resulted in alterations in the production of volatile compounds, specifically ethyl acetate, which are important contributors to the beverage's aroma. Changes in the expression levels of other genes involved in ester biosynthesis, suggesting that the knockdown of IAH1 may generate intracellular alterations in the balance of these metabolites, triggering a regulatory response. The application of CRISPRi technology in K. marxianus opens the possibility of targeted modulation of gene expression, metabolic engineering strategies, and synthetic biology in this yeast strain.

Cardiogenic shock as a health issue. Physiology, classification, and detection.

Cardiogenic shock (CS) is a heterogeneous syndrome with high mortality and a growing incidence. It is characterized by an imbalance between the tissue oxygen demands and the capacity of the cardiovascular system to meet these demands, due to acute cardiac dysfunction. Historically, acute coronary syndromes have been the primary cause of CS. However, non-ischemic cases have seen a rise in incidence. The pathophysiology involves ischemic damage of the myocardium and a sympathetic, renin-angiotensin-aldosterone system and inflammatory response, perpetuating the situation of tissue hypoperfusion and ultimately leading to multiorgan dysfunction. The characterization of CS patients through a triaxial assessment and the widespread use of the Society for Cardiovascular Angiography and Interventions (SCAI) scale has allowed standardization of the severity stratification of CS; this, coupled with early detection and the "hub and spoke" approach, could contribute to improving the prognosis of these patients.

Epigenome and early selection determine the tumour-immune evolutionary trajectory of colorectal cancer.

Immune system control is a major hurdle that cancer evolution must circumvent. The relative timing and evolutionary dynamics of subclones that have escaped immune control remain incompletely characterized, and how immune-mediated selection shapes the epigenome has received little attention. Here, we infer the genome- and epigenome-driven evolutionary dynamics of tumour-immune coevolution within primary colorectal cancers (CRCs). We utilise our existing CRC multi-region multi-omic dataset that we supplement with high-resolution spatially-resolved neoantigen sequencing data and highly multiplexed imaging of the tumour microenvironment (TME). Analysis of somatic chromatin accessibility alterations (SCAAs) reveals frequent somatic loss of accessibility at antigen presenting genes, and that SCAAs contribute to silencing of neoantigens. We observe that strong immune escape and exclusion occur at the outset of CRC formation, and that within tumours, including at the microscopic level of individual tumour glands, additional immune escape alterations have negligible consequences for the immunophenotype of cancer cells. Further minor immuno-editing occurs during local invasion and is associated with TME reorganisation, but that evolutionary bottleneck is relatively weak. Collectively, we show that immune evasion in CRC follows a "Big Bang" evolutionary pattern, whereby genetic, epigenetic and TME-driven immune evasion acquired by the time of transformation defines subsequent cancer-immune evolution.

Role of ultrasound in acute respiratory failure and in the weaning of mechanical ventilation.

Comprehensive ultrasound assessment has become an essential tool to facilitate the diagnosis and therapeutic management of critically ill patients with acute respiratory failure (ARF). There is evidence supporting the use of ultrasound for the diagnosis of pneumothorax, acute respiratory distress syndrome, cardiogenic pulmonary edema, pneumonia and acute pulmonary thromboembolism, and in patients with COVID-19. In addition, in recent years, the use of ultrasound to evaluate responses to treatment in critically ill patients with ARF has been developed, providing a noninvasive tool for titrating positive end-expiratory pressure, monitoring recruitment maneuvers and response to prone position, as well as for facilitating weaning from mechanical ventilation. The objective of this review is to summarize the basic concepts on the utility of ultrasound in the diagnosis and monitoring of critically ill patients with ARF.

Binaural Beat Effects on Attention: A Study Based on the Oddball Paradigm.

The impact of binaural beats (BBs) on human cognition and behavior remains and various methods have been used to measure their effect, including neurophysiological, psychometric, and human performance evaluations. The few approaches where the level of neural synchronicity and connectivity were measured by neuroimaging techniques have only been undertaken in spontaneous mode. The present research proposes an approach based on the oddball paradigm to study BB effect by estimating the level of attention induced by BBs. Evoked activity of 25 young adults between 19 and 24 years old with no hearing impairments nor clinical neurological history were analyzed. The experiment was conducted in two different sessions of 24.5 min. The first part consisted of 20-min BB stimulation in either theta (BBθ) or beta (BBß). After the BB stimulation, an oddball paradigm was applied in each BB condition to assess the attentional effect induced by BBs. Attention enhancement is expected for BBß with respect to BBθ. Target event related potentials (ERPs) were mainly analyzed in the time and time-frequency domains. The frequency analysis was based on continuous wavelet transform (CWT), event-related spectral perturbation (ERSP), and inter-trial phase coherence (ITPC). The study revealed that the P300 component was not significantly different between conditions (BBθ vs. BBß). However, the target grand average ERP in BBθ condition was mainly composed of 8 Hz-frequency components, appearing before 400 ms post-stimulus, and mainly on the centro-parietal regions. In contrast, the target grand average ERP in BBß condition was mainly composed of frequency components below 6 Hz, mainly appearing at 400 ms post-stimulus on the parieto-occipital regions. Furthermore, ERPs in the BBθ condition were more phase locked than the BBß condition.

Association between diastolic dysfunction and fluid balance in critically ill patients during weaning from mechanical ventilation.

OBJECTIVE: To assess the role of diastolic dysfunction and fluid balance in weaning failure. DESIGN: Prospective, observational, single center. SETTING: Intensive care unit of a university hospital. PATIENTS: Adult patients on mechanical ventilation for more than 48 h who underwent a spontaneous breathing trial (SBT). INTERVENTIONS: Echocardiography was performed immediately before and at the end of SBT. Patients were classified into two groups according to weaning outcome. MAIN VARIABLE OF INTEREST: Weaning failure. RESULTS: Among 89 patients included, weaning failure occurred in 33 patients (37%). Isolated diastolic dysfunction at the end of the SBT was more frequent in the failure group (39.3% vs. 17.8%, p = 0.025). Average daily fluid balance from ICU admission until first SBT was less negative in patients who failed than in those who succeed in the weaning (-648 mL [-884 to -138] vs. -893 mL [-1284 to -501], p = 0.007). Average daily fluid balance from the first SBT until the ICU discharge was more negative in the weaning failure than in the success group (-973 mL [-1493 to -201] vs. -425 mL [-1065 to 12], p = 0.034). Cox regression analysis showed that diastolic dysfunction was not an independent factor related to weaning failure but needed the association of positive fluid balance and age. CONCLUSIONS: Weaning failure due to diastolic dysfunction is highly related to fluid balance, and the deleterious effect of fluid balance on diastolic function is associated with age The timing of fluid removal could play a key role in this scenario.

LIPRNAseq: a method to discover lipid interacting RNAs by sequencing.

BACKGROUND: Current biological research extensively describes the interactions of molecules such as RNA with other nucleic acids or proteins. However, the relatively recent discovery of nuclear phospholipids playing biologically relevant processes outside membranes, as well as, RNA-lipid interactions shows the need for new methods to explore the identity of these RNAs. METHODS AND RESULTS: In this study, we describe the method for LIPID-RNA isolation followed by sequencing and analysis of the RNA that has the ability to interact with the selected lipids. Here we utilized specific phospholipid coated beads for selective RNA binding. We tested RNA from organisms belonging to different realms (human, plant, and yeast), and tested their ability to bind a specific lipid. CONCLUSIONS: The results show several RNAs differentially enriched in the pull-down of phosphatidyl Inositol 4,5 bisphosphate coated beads. This method is helpful to screen lipid-binding RNA, which may have relevant biological functions. The method can be used with different lipids and comparison of pull-downs and can narrow the selection of RNAs that interact with a particular lipid for further studies.

Current research on viral proteins that interact with fibrillarin.

The nucleolus is a multifunctional nuclear domain primarily dedicated to ribosome biogenesis. Certain viruses developed strategies to manipulate host nucleolar proteins to facilitate their replication by modulating ribosomal RNA (rRNA) processing. This association interferes with nucleolar functions resulting in overactivation or arrest of ribosome biogenesis, induction or inhibition of apoptosis, and affecting stress response. The nucleolar protein fibrillarin (FBL) is an important target of some plant and animal viruses. FBL is an essential and highly conserved S-adenosyl methionine (SAM) dependent methyltransferase, capable of rRNA degradation by its intrinsically disordered region (IDR), the glycine/arginine-rich (GAR) domain. It forms a ribonucleoprotein complex that directs 2'-O-methylations in more than 100 sites of pre-rRNAs. It is involved in multiple cellular processes, including initiation of transcription, oncogenesis, and apoptosis, among others. The interaction with animal viruses, including human viruses, triggered its redistribution to the nucleoplasm and cytoplasm, interfering with its role in pre-rRNA processing. Viral-encoded proteins with IDRs as nucleocapsids, matrix, Tat protein, and even a viral snoRNA, can associate with FBL, forcing the nucleolar protein to undergo atypical functions. Here we review the molecular mechanisms employed by animal and human viruses to usurp FBL functions and the effect on cellular processes, particularly in ribosome biogenesis.

Immune selection determines tumor antigenicity and influences response to checkpoint inhibitors.

In cancer, evolutionary forces select for clones that evade the immune system. Here we analyzed >10,000 primary tumors and 356 immune-checkpoint-treated metastases using immune dN/dS, the ratio of nonsynonymous to synonymous mutations in the immunopeptidome, to measure immune selection in cohorts and individuals. We classified tumors as immune edited when antigenic mutations were removed by negative selection and immune escaped when antigenicity was covered up by aberrant immune modulation. Only in immune-edited tumors was immune predation linked to CD8 T cell infiltration. Immune-escaped metastases experienced the best response to immunotherapy, whereas immune-edited patients did not benefit, suggesting a preexisting resistance mechanism. Similarly, in a longitudinal cohort, nivolumab treatment removes neoantigens exclusively in the immunopeptidome of nonimmune-edited patients, the group with the best overall survival response. Our work uses dN/dS to differentiate between immune-edited and immune-escaped tumors, measuring potential antigenicity and ultimately helping predict response to treatment.

Domestic Violence From a Child Perspective: Impact of an Immersive Virtual Reality Experience on Men With a History of Intimate Partner Violent Behavior.

Domestic violence has long-term negative consequences on children. In this study, men with a history of partner aggression and a control group of non-offenders were embodied in a child's body from a first-person perspective in virtual reality (VR). From this perspective, participants witnessed a scene of domestic violence where a male avatar assaulted a female avatar. We evaluated the impact of the experience on emotion recognition skills and heart rate deceleration responses. We found that the experience mainly impacted the recognition of angry facial expressions. The results also indicate that males with a history of partner aggression had larger physiological responses during an explicit violent event (when the virtual abuser threw a telephone) compared with controls, while their physiological reactions were less pronounced when the virtual abuser invaded the victim's personal space. We show that embodiment from a child's perspective during a conflict situation in VR impacts emotion recognition, physiological reactions, and attitudes towards violence. We provide initial evidence of the potential of VR in the rehabilitation and neuropsychological assessment of males with a history of domestic violence, especially in relation to children.

Cardiogenic shock code 2023. Expert document for a multidisciplinary organization that allows quality care.

Despite the efforts made to improve the care of cardiogenic shock (CS) patients, including the development of mechanical circulatory support (MCS), the prognosis of these patients continues to be poor. In this context, CS code initiatives arise, based on providing adequate, rapid, and quality care to these patients. In this multidisciplinary document we try to justify the need to implement the SC code, defining its structure/organization, activation criteria, patient flow according to care level, and quality indicators. Our specific purposes are: a) to present the peculiarities of this condition and the lessons of infarction code and previous experiences in CS; b) to detail the structure of the teams, their logistics and the bases for the management of these patients, the choice of the type of MCS, and the moment of its implantation, and c) to address challenges to SC code implementation, including the uniqueness of the pediatric SC code. There is an urgent need to develop protocolized, multidisciplinary, and centralized care in hospitals with a large volume and experience that will minimize inequity in access to the MCS and improve the survival of these patients. Only institutional and structural support from the different administrations will allow optimizing care for CS.

Evaluation of Natural Pigments Production in Response to Various Stress Signals in Cell Lines of Stenocereus queretaroensis.

Stenocereus queretaroensis (F.A.C. Weber ex Mathes.) Buxb is a cactus that has long been used as a source food in central and northern México. Its fruits, commonly called pitayas, biosynthesize high amounts of betalains. These molecules are water-soluble nitrogenous compounds; that compared to other pigments, such as anthocyanins or carotenoids, stand out for their physicochemical stability in industrial processes. Due to genetic and environmental factors involved in the biosynthesis and accumulation of secondary metabolites in plants, we tested different stress-inducing agents (elicitor, osmotic, salt, and temperature) to induce betalains accumulation in cell culture from fruits of Stenocereus queretaroensis. This work aimed to understand stress conditions that induce the metabolic pathways required for the accumulation of betalains. The results show how betacyanin concentration increases under high sugar conditions, thus affecting the expression of L-DOPA 4, 5 dioxygenase resulting in a strong dark red coloration. This suggests this enzyme is part of a rate-limiting step in betalain production. In addition, we found that betalains accumulation occurs under particular stress conditions. Cells that have a high level of betacyanins show better resistance to stress in the cell culture, as well as an overall different behavior including cell aggregation and alterations in nuclear size. Together the results shown here may provide new strategies to manipulate and mass produce the pigments from Stenocereus queretaroensis in cell culture.

Parameter sensitivities in tilted-pulse-front based terahertz setups and their implications for high-energy terahertz source design and optimization.

Despite the popularity and ubiquity of the tilted-pulse-front technique for single-cycle terahertz (THz) pulse generation, there is a deficit of experimental studies comprehensively mapping out the dependence of the performance on key setup parameters. The most critical parameters include the pulse-front tilt, the effective length of the pump pulse propagation within the crystal as well as effective length over which the THz beam interacts with the pump before it spatially walks off. Therefore, we investigate the impact of these parameters on the conversion efficiency and the shape of the THz beam via systematically scanning the 5D parameter space spanned by pump fluence, pulse-front-tilt, crystal-position (2D), and the pump size experimentally. We verify predictions so far only made by theory regarding the optimum interaction lengths and map out the impact of cascading on the THz radiation generation process. Furthermore, distortions imposed on the spatial THz beam profile for larger than optimum interaction lengths are observed. Finally, we identify the most sensitive parameters and, based on our findings, propose a robust optimization strategy for tilted-pulse-front THz setups. These findings are relevant for all THz strong-field applications in high demand of robust high-energy table-top single-cycle THz sources such as THz plasmonics, high-harmonic generation in solids as well as novel particle accelerators and beam manipulators.

The co-evolution of the genome and epigenome in colorectal cancer.

Colorectal malignancies are a leading cause of cancer-related death1 and have undergone extensive genomic study2,3. However, DNA mutations alone do not fully explain malignant transformation4-7. Here we investigate the co-evolution of the genome and epigenome of colorectal tumours at single-clone resolution using spatial multi-omic profiling of individual glands. We collected 1,370 samples from 30 primary cancers and 8 concomitant adenomas and generated 1,207 chromatin accessibility profiles, 527 whole genomes and 297 whole transcriptomes. We found positive selection for DNA mutations in chromatin modifier genes and recurrent somatic chromatin accessibility alterations, including in regulatory regions of cancer driver genes that were otherwise devoid of genetic mutations. Genome-wide alterations in accessibility for transcription factor binding involved CTCF, downregulation of interferon and increased accessibility for SOX and HOX transcription factor families, suggesting the involvement of developmental genes during tumourigenesis. Somatic chromatin accessibility alterations were heritable and distinguished adenomas from cancers. Mutational signature analysis showed that the epigenome in turn influences the accumulation of DNA mutations. This study provides a map of genetic and epigenetic tumour heterogeneity, with fundamental implications for understanding colorectal cancer biology.

Phenotypic plasticity and genetic control in colorectal cancer evolution.

Genetic and epigenetic variation, together with transcriptional plasticity, contribute to intratumour heterogeneity1. The interplay of these biological processes and their respective contributions to tumour evolution remain unknown. Here we show that intratumour genetic ancestry only infrequently affects gene expression traits and subclonal evolution in colorectal cancer (CRC). Using spatially resolved paired whole-genome and transcriptome sequencing, we find that the majority of intratumour variation in gene expression is not strongly heritable but rather 'plastic'. Somatic expression quantitative trait loci analysis identified a number of putative genetic controls of expression by cis-acting coding and non-coding mutations, the majority of which were clonal within a tumour, alongside frequent structural alterations. Consistently, computational inference on the spatial patterning of tumour phylogenies finds that a considerable proportion of CRCs did not show evidence of subclonal selection, with only a subset of putative genetic drivers associated with subclone expansions. Spatial intermixing of clones is common, with some tumours growing exponentially and others only at the periphery. Together, our data suggest that most genetic intratumour variation in CRC has no major phenotypic consequence and that transcriptional plasticity is, instead, widespread within a tumour.