Specialized short term crisis intervention for patients with personality disorder: Effects on coercion and length of stay.

BACKGROUND: Acute crises in patients with personality disorders (PD) are often accompanied by suicidal and self-harming behavior. Their management is challenging, as both coercive measures and prolonged inpatient-treatment are known to be counterproductive. Only in crises that cannot be controlled by outpatient means, inpatient treatment is to be taken into account. This treatment should be time-limited and not involve coercion. AIMS: The aim of this study was to assess if the introduction of a specialized crisis intervention track is associated with a reduction of coercive measures as well as a shorter in-hospital stay in PD patients. METHODS: In this 8-year, hospital-wide, longitudinal, observational study, we investigated the frequency of coercive measures and the median length of in-hospital stay in 1,752 inpatient-cases with PD admitted to the Adult Psychiatry, UPK, Basel, Switzerland, between 01.01.2012 and 31.12.2019. By means of an interrupted-time-series analysis, we compared the period before and after the implementation of a specialized crisis intervention track for PD patients. RESULTS: Our data show a significant decrease in the median length of in-hospital stay and no significant reduction in the incidence rate of coercion among PD patients after the intervention. The latter is likely due to a floor effect, since there was a significant decrease in coercive measures over the entire observation period, already reaching very low rates before the intervention. CONCLUSIONS: Our study underlines the clinical importance of specialized short-term crisis management in PD, which comes along with shorter lengths of in-hospital stays and a stable low rate of coercive measure.

ADP-heptose attenuates Helicobacter pylori-induced dendritic cell activation.

Sophisticated immune evasion strategies enable Helicobacter pylori (H. pylori) to colonize the gastric mucosa of approximately half of the world's population. Persistent infection and the resulting chronic inflammation are a major cause of gastric cancer. To understand the intricate interplay between H. pylori and host immunity, spatial profiling was used to monitor immune cells in H. pylori infected gastric tissue. Dendritic cell (DC) and T cell phenotypes were further investigated in gastric organoid/immune cell co-cultures and mechanistic insights were acquired by proteomics of human DCs. Here, we show that ADP-heptose, a bacterial metabolite originally reported to act as a bona fide PAMP, reduces H. pylori-induced DC maturation and subsequent T cell responses. Mechanistically, we report that H. pylori uptake and subsequent DC activation by an ADP-heptose deficient H. pylori strain depends on TLR2. Moreover, ADP-heptose attenuates full-fledged activation of primary human DCs in the context of H. pylori infection by impairing type I IFN signaling. This study reveals that ADP-heptose mitigates host immunity during H. pylori infection.

COVID-19 and mental distress among health professionals in eight European countries during the third wave: a cross-sectional survey.

Even during the third wave of the COVID-19 pandemic health professionals were facing mental health challenges. The aim of this study was to examine the mental health of doctors, nurses and other professional groups in Europe and to identify differences between the professional groups. We conducted a cross-sectional online survey in 8 European countries. We asked for demographic data, whether the participants were exposed to COVID-19 at work, for main information sources about the pandemic, the Depression Anxiety Stress Scales (DASS-21), and major stressors. A MANCOVA was carried out to find predictors of mental health among health care professionals. The sample (N = 1398) consisted of 237 physicians, 459 nurses, and 351 other healthcare professionals and 351 non-medical professionals with no direct involvement in patient care. The mean mental health of all groups was affected to a mild degree. Major predictors for depression and anxiety were the profession group with higher scores especially in the group of the nurses and working directly with COVID-patients. In the third wave of the COVID-19 pandemic, the psychological burden on health professionals has remained high, with being nurse and working directly with COVID19 patients being particular risk factors for mental distress. We found as a main result that nurses scored significantly higher on depression and anxiety than practitioners.

Global and risk-group stratified well-being and mental health during the COVID-19 pandemic in adults: Results from the international COH-FIT Study.

International studies measuring wellbeing/multidimensional mental health before/ during the COVID-19 pandemic, including representative samples for >2 years, identifying risk groups and coping strategies are lacking. COH-FIT is an online, international, anonymous survey measuring changes in well-being (WHO-5) and a composite psychopathology P-score, and their associations with COVID-19 deaths/restrictions, 12 a-priori defined risk individual/cumulative factors, and coping strategies during COVID-19 pandemic (26/04/2020-26/06/2022) in 30 languages (representative, weighted non-representative, adults). T-test, χ2, penalized cubic splines, linear regression, correlation analyses were conducted. Analyzing 121,066/142,364 initiated surveys, WHO-5/P-score worsened intra-pandemic by 11.1±21.1/13.2±17.9 points (effect size d=0.50/0.60) (comparable results in representative/weighted non-probability samples). Persons with WHO-5 scores indicative of depression screening (<50, 13% to 32%) and major depression (<29, 3% to 12%) significantly increased. WHO-5 worsened from those with mental disorders, female sex, COVID-19-related loss, low-income country location, physical disorders, healthcare worker occupations, large city location, COVID-19 infection, unemployment, first-generation immigration, to age=18-29 with a cumulative effect. Similar findings emerged for P-score. Changes were significantly but minimally related to COVID-19 deaths, returning to near-pre-pandemic values after >2 years. The most subjectively effective coping strategies were exercise and walking, internet use, social contacts. Identified risk groups, coping strategies and outcome trajectories can inform global public health strategies.

Targeting NLRP3 inhibits AML progression by inducing PERK/eIF2-mediated apoptosis.

BACKGROUND: Acute myeloid leukemia (AML) is characterized by the abnormal proliferation of myeloid precursor cells and presents significant challenges in treatment due to its heterogeneity. Recently, the NLRP3 inflammasome has emerged as a potential contributor to AML pathogenesis, although its precise mechanisms remain poorly understood. METHODS: Public genome datasets were utilized to evaluate the expression of NLRP3 inflammasome-related genes (IL-1ß, IL-18, ASC, and NLRP3) in AML patients compared to healthy individuals. CRISPR/Cas9 technology was employed to generate NLRP3-deficient MOLM-13 AML cells, followed by comprehensive characterization using real-time PCR, western blotting, FACS analysis, and transmission electron and immunofluorescence microscopy. Proteomic analyses were conducted to identify NLRP3-dependent alterations in protein levels, with a focus on the eIF2 kinase PERK-mediated signaling pathways. Additionally, in vivo studies were performed using a leukemic mouse model to elucidate the pathogenic role of NLRP3 in AML. RESULTS: Elevated expression of NLRP3 was significantly associated with diminished overall survival in AML patients. Genetic deletion, pharmacological inhibition and silencing by RNA interference of NLRP3 led to decreased AML cell survival through the induction of apoptosis. Proteomic analyses uncovered NLRP3-dependent alterations in protein translation, characterized by enhanced eIF2α phosphorylation in NLRP3-deficient AML cells. Moreover, inhibition of PERK-mediated eIF2α phosphorylation reduced apoptosis by downregulating pro-apoptotic Bcl-2 family members. In vivo studies demonstrated reduced leukemic burden in mice engrafted with NLRP3 knockout AML cells, as evidenced by alleviated leukemic symptoms. CONCLUSION: Our findings elucidate the involvement of the NLRP3/PERK/eIF2 axis as a novel driver of AML cell survival. Targeting NLRP3-induced signaling pathways, particularly through the PERK/eIF2 axis, presents a promising therapeutic strategy for AML intervention. These insights into the role of the NLRP3 inflammasome offer potential avenues for improving the prognosis and treatment outcomes of AML patients.

Individualized pretest risk estimates to guide treatment decisions in patients with clinical high risk for psychotic disorders.

INTRODUCTION: Clinical high risk for psychosis (CHR) states are associated with an increased risk of transition to psychosis. However, the predictive value of CHR screening interviews is dependent on pretest risk enrichment in referred patients. This poses a major obstacle to CHR outreach campaigns since they invariably lead to risk dilution through enhanced awareness. A potential compensatory strategy is to use estimates of individual pretest risk as a 'gatekeeper' for specialized assessment. We aimed to test a risk stratification model previously developed in London, UK (OASIS) and to train a new predictive model for the Swiss population. METHOD: The sample was composed of 513 individuals referred for CHR assessment from six Swiss early psychosis detection services. Sociodemographic variables available at referral were used as predictors whereas the outcome variable was transition to psychosis. RESULTS: Replication of the risk stratification model developed in OASIS resulted in poor performance (Harrel's c=0.51). Retraining resulted in moderate discrimination (Harrel's c=0.67) which significantly differentiated between different risk groups. The lowest risk group had a cumulative transition incidence of 6.4% (CI: 0-23.1%) over two years. CONCLUSION: Failure to replicate the OASIS risk stratification model might reflect differences in the public health care systems and referral structures between Switzerland and London. Retraining resulted in a model with adequate discrimination performance. The developed model in combination with CHR assessment result, might be useful for identifying individuals with high pretest risk, who might benefit most from specialized intervention.

Collaborative outcomes study on health and functioning during infection times (COH-FIT): Insights on modifiable and non-modifiable risk and protective factors for wellbeing and mental health during the COVID-19 pandemic from multivariable and network analyses.

There is no multi-country/multi-language study testing a-priori multivariable associations between non-modifiable/modifiable factors and validated wellbeing/multidimensional mental health outcomes before/during the COVID-19 pandemic. Moreover, studies during COVID-19 pandemic generally do not report on representative/weighted non-probability samples. The Collaborative Outcomes study on Health and Functioning during Infection Times (COH-FIT) is a multi-country/multi-language survey conducting multivariable/LASSO-regularized regression models and network analyses to identify modifiable/non-modifiable factors associated with wellbeing (WHO-5)/composite psychopathology (P-score) change. It enrolled general population-representative/weighted-non-probability samples (26/04/2020-19/06/2022). Participants included 121,066 adults (age=42±15.9 years, females=64 %, representative sample=29 %) WHO-5/P-score worsened (SMD=0.53/SMD=0.74), especially initially during the pandemic. We identified 15 modifiable/nine non-modifiable risk and 13 modifiable/three non-modifiable protective factors for WHO-5, 16 modifiable/11 non-modifiable risk and 10 modifiable/six non-modifiable protective factors for P-score. The 12 shared risk/protective factors with highest centrality (network-analysis) were, for non-modifiable factors, country income, ethnicity, age, gender, education, mental disorder history, COVID-19-related restrictions, urbanicity, physical disorder history, household room numbers and green space, and socioeconomic status. For modifiable factors, we identified medications, learning, internet, pet-ownership, working and religion as coping strategies, plus pre-pandemic levels of stress, fear, TV, social media or reading time, and COVID-19 information. In multivariable models, for WHO-5, additional non-modifiable factors with |B|>1 were income loss, COVID-19 deaths. For modifiable factors we identified pre-pandemic levels of social functioning, hobbies, frustration and loneliness, and social interactions as coping strategy. For P-scores, additional non-modifiable/modifiable factors were income loss, pre-pandemic infection fear, and social interactions as coping strategy. COH-FIT identified vulnerable sub-populations and actionable individual/environmental factors to protect well-being/mental health during crisis times. Results inform public health policies, and clinical practice.

Testing times: disentangling admixture histories in recent and complex demographies using ancient DNA.

Our knowledge of human evolutionary history has been greatly advanced by paleogenomics. Since the 2020s, the study of ancient DNA has increasingly focused on reconstructing the recent past. However, the accuracy of paleogenomic methods in resolving questions of historical and archaeological importance amidst the increased demographic complexity and decreased genetic differentiation remains an open question. We evaluated the performance and behavior of two commonly used methods, qpAdm and the f3-statistic, on admixture inference under a diversity of demographic models and data conditions. We performed two complementary simulation approaches-firstly exploring a wide demographic parameter space under four simple demographic models of varying complexities and configurations using branch-length data from two chromosomes-and secondly, we analyzed a model of Eurasian history composed of 59 populations using whole-genome data modified with ancient DNA conditions such as SNP ascertainment, data missingness, and pseudohaploidization. We observe that population differentiation is the primary factor driving qpAdm performance. Notably, while complex gene flow histories influence which models are classified as plausible, they do not reduce overall performance. Under conditions reflective of the historical period, qpAdm most frequently identifies the true model as plausible among a small candidate set of closely related populations. To increase the utility for resolving fine-scaled hypotheses, we provide a heuristic for further distinguishing between candidate models that incorporates qpAdm model P-values and f3-statistics. Finally, we demonstrate a significant performance increase for qpAdm using whole-genome branch-length f2-statistics, highlighting the potential for improved demographic inference that could be achieved with future advancements in f-statistic estimations.

Sustainability initiatives in inpatient psychiatry: tackling food waste.

Background: Food plays a dual role in promoting human health and environmental sustainability. Yet, current food systems jeopardize both. Food waste poses a major global challenge due to its significant economic, social, and environmental impacts. Healthcare facilities generate the largest amounts of food waste compared to other forms of catering provision. Food waste correlates with environmental unsustainability and diminished patient satisfaction, compounding the prevalent challenge of hospital malnutrition and contributing to suboptimal patient outcomes. Materials and methods: In a three-year interventional study (2020-2022) at a psychiatric tertiary care center, we assessed and mitigated food waste using evidence-based measures. We conducted systematic food wastage audits over three years (2020-2022) in May and June, each lasting four weeks. Costs were analyzed comprehensively, covering food, staff, infrastructure, and disposal. Environmental impact was assessed using Umweltbelastungspunkte (UBP) and CO2e/kg emissions, alongside water usage (H2O - l/kg). Results: Economic losses due to food wastage were substantial, primarily from untouched plates and partially consumed dinners, prompting meal planning adjustments. Despite a >3% increase in meals served, both food waste mass and costs decreased by nearly 6%. Environmental impact indicators showed a reduction >20%. Vegetables, salad, and fruits constituted a significant portion of waste. Overproduction minimally contributed to waste, validating portion control efficacy. Conclusion: Our study highlights significant economic and environmental losses due to hospital food waste, emphasizing the importance of resource efficiency. The strategies outlined offer promising avenues for enhanced efficiency. The decrease in food waste observed over the three-year period underscores the potential for improvement.

Patient-reported experience measures (PREMs) in outpatient psychiatry - is there an association to perceived discrimination and devaluation?

Patient-Reported Experience Measures (PREMs) are gaining significance in the field of psychiatry, with patient satisfaction being a key measure. However, it is unclear if patient satisfaction in psychiatry is influenced by variables outside the treatment setting. This brief report thus examines the possible impact of perceived discrimination and devaluation (PDD) on patient satisfaction in the psychiatric outpatient setting. Data from 1,126 individuals who were undergoing or had recently completed treatment at 15 outpatient centers of the Psychiatric University Clinic in Basel, Switzerland, was analyzed. Patient satisfaction was assessed using the Münsterlingen Patient Satisfaction Questionnaire (MüPF), and perceived stigma was measured with the Perceived Discrimination Devaluation Scale. The results revealed a positive small effect size relationship between MüPF and PDD, suggesting that patients who perceived less stigma report higher treatment satisfaction. This relationship may affect most ratings, with the total MüPF score remaining relatively robust against this potential influence. Linear regression analysis indicated that a one-unit increase in PDD score could lead to a maximum change of 1.8 points on the 7-point Likert scale for the MüPF item correlating highest with PDD and 0.4 points on the total MüPF score. These findings highlight the importance of considering perceived stigma when evaluating patient satisfaction with psychiatric outpatient treatment. Future research should investigate associations between stigma, patient satisfaction, treatment outcome, as well as other external factors that may influence patient satisfaction in psychiatric settings.

A typology of evaluative health platforms: Commercial interests and their implications for patient voice.

Interactions in the healthcare system today involve an important new set of actors: evaluative health platforms (EHPs). These platforms are not neutral intermediaries, but active moderators of how patients express opinions, choose providers, and consume health-related information. This paper adds to our understanding of the varied and evolving commercial interests of EHPs and the implications these have for patient voice. We analyze 71 platforms in the USA, UK, and Germany and identify five ideal types: subscribers, analyzers, advertisers, regulators, and scammers. Each platform type enacts a unique competitive strategy through an evaluative infrastructure which constrains but also generates possibilities for patient voice. Based on our typology, we develop three contributions. First, we nuance universalizing claims about the consequences of platform capitalism by specifying the diverse strategies underpinning competition between EHPs in different countries, and showing how each strategy leads evaluative infrastructures to develop in ways that impact patient voice. Second, we show how patients can navigate the challenges of a complex EHP space by exercising their ability to choose between platforms. Finally, we outline the conditions platforms need to fulfil to become empowering. Overall, this study highlights the varied and complex relationship between platform business models and user voice, which exists not only in healthcare, but also in many other fields.

Treatment-seeking threshold and accessibility of psychiatric outpatient services in Switzerland: the relationship with stigma and self-esteem.

Perceived stigmatization and low self-esteem are linked to poorer mental health outcomes, but their impact on treatment-seeking thresholds and the importance of outpatient service location remain unclear. The study included 525 outpatients of the University Psychiatric Clinic (UPK) Basel, Switzerland, of whom 346 were treated at inner city services and 179 at services located on the main site of the UPK at the outer city limits. Perceived discrimination and devaluation (PDD), self-esteem (SE), treatment-seeking threshold (TST), and accessibility were measured via a self-reported questionnaire. The PDD consisted of 12 items evaluating beliefs about the level of stigma towards individuals with mental illness in the general population on a 5-point Likert scale. SE, TST and accessibility were assessed through single-item 7-point Likert scales. PDD and SE were positively correlated (p < 0.001), suggesting that lower perceived stigma was linked to higher self-esteem, and were not associated with TST. The relationship between PDD and SE remained consistent after controlling for age, gender, and nationality. Age was negatively correlated with TST (p = 0.022), while gender did not significantly influence any of the variables. There was little variation regarding PDD, with emergencies at the site of the psychiatric clinic and substance use disorder (SUD) patients reporting higher levels of stigmatization. Emergency patients and those with SUD and personality disorder reported the lowest SE ratings. TST showed a broad range and was highest for emergency services and transcultural psychiatry patients. Differences in accessibility were mainly linked to the location, with outpatient service users in the inner city reporting better accessibility (p < 0.001) and higher SE (p = 0.009). In comparison to patients using services with planned contacts only, patients in emergency settings differed by higher TST (p = 0.018) and better ratings of accessibility (p = 0.004). In conclusion, there was a relevant amount of stigmatization, impaired self-esteem, and, for some outpatient services, high thresholds to seek treatment. Future research should explore other factors influencing TST. The findings highlight the need to address stigmatization and accessibility when planning mental health services.

Pathways to care in youth and young adults at clinical high risk for psychosis in Switzerland: Current situation and clinical implementation of the PsyYoung project.

AIM: We aim to give an insight into the current situation in Switzerland concerning the pathways to care of young people with clinical high risk of psychosis. In a second step we propose a procedure of optimizing pathways to care developed within the project PsyYoung. METHODS: A qualitative survey derived and adapted from Kotlicka-Antczak et al. (2020) was conducted in large early detection services of three Swiss cantons (Geneva, Basel-Stadt, Vaud) focusing on pathways to care. More specifically, using questionnaires delivered to the heads of participating services, information was collected on referral sources, on activities to implement outreach campaigns and on the use of a pre-screening tool. RESULTS: Main results on referral source indicated that sources were variable but seemed to come primarily from the medical sector and more so from the psychiatric sector. Very few referrals came from non-medical sectors. Outreach activities included the contact to other clinics as well as through brochures and posters. All services but one used the Prodromal Questionnaire - 16 as pre-screening tool. CONCLUSIONS: All in all, the results indicate a referral and care pathway system implemented mostly within the medical and particularly mental health sector. Accordingly, the PsyYoung project proposes a procedure for pathways to care which could help overcome the obstacle of referrals being restrained to a narrow field of mental health and to harmonize the referral process within services dedicated to the same aim of helping young people at high risk of developing a psychosis.

Comparing the latent state-trait structure of the PANSS in cariprazine-medicated and placebo-controlled patients with acute schizophrenia.

After over a hundred years of research, the question whether the symptoms of schizophrenia are rather trait-like (being a relatively stable quality of individuals) or state-like (being substance to change) is still unanswered. To assess the trait and the state component in patients with acute schizophrenia, one group receiving antipsychotic treatment, the other not. Data from four phase II/III, 6-week, randomized, double-blind, placebo-controlled trials of similar design that included patients with acute exacerbation of schizophrenia were pooled. In every trial, one treatment group received a third-generation antipsychotic, cariprazine, and the other group placebo. To assess symptoms of schizophrenia, the Positive and Negative Symptom Scale (PANSS) was applied. Further analyses were conducted using the five subscales as proposed by Wallwork and colleagues. A latent state-trait (LST) model was developed to estimate the trait and state components of the total variance of the observed scores. All symptom dimensions behaved more in a trait-like manner. The proportions of all sources of variability changed over the course of the observational period, with a bent around weeks 3 and 4. Visually inspected, no major differences were found between the two treatment groups regarding the LST structure of symptom dimensions. This high proportion of inter-individual stability may represent an inherent part of symptomatology that behaves independently from treatment status.

Implementation of a Budo group therapy for psychiatric in- and outpatients: a feasibility study.

Introduction: Physical exercise has been shown to have numerous health benefits on co-morbid somatic conditions in psychiatry and can also enhance mental health. Thus, it is not difficult to recommend physical training programs as part of an integrated and holistic treatment approach for mental health disorders. However, getting patients to participate and keeping them engaged is a major challenge. Programs based on martial arts training could be interventions improving physical and mental health with higher attachment rates. The structured discipline, holistic approach integrating physical and mental elements, and empowering activities, may explain higher participant attachment rates. Methods: Thus, the main objective of this feasibility study is to describe a newly established group therapy program incorporating interventions from martial arts training with its physical and philosophical parts including mindfulness and breath work. Results: During the 14-month study period from April 2021 to May 2022, a Budo group therapy was used by 215 individual persons with a total of 725 group therapy participations. Retention in the program was good across all settings and very good for persons who participated as outpatients. The mean age of the participants was 33.5 years with a range from 14 to 69 years of age, and about 41% of the participants were female. The therapy program was able to address patients over the whole spectrum of psychiatric diagnoses. Satisfaction and motivation were uniformly self-reported as very good. Patients self-reported improved mental and physical health after participating in a Budo session compared to pre-session. Discussion: Budo group therapy thus can be seen as a feasible, well-accepted and promising new transdiagnostic treatment approach, combining physical activation with resilience enhancement. With minimal contraindications, a broad spectrum of individuals seeking mental health support can engage in this group therapy.

Just Not Enough: Utilization of Outpatient Psychotherapy Provided by Clinical Psychologists for Patients With Psychosis and Bipolar Disorder in Switzerland.

Treatment guidelines state that evidence-based psychotherapy is effective for people with psychosis and bipolar disorder and should be offered during every phase of the treatment process. However, research has indicated a lack of outpatient psychotherapeutic services for this patient group, for example, in the United States or Germany. We extend this finding by presenting survey data from Switzerland. We surveyed 112 inpatients with a diagnosis of a schizophrenia spectrum disorder or bipolar disorder and assessed outpatient treatment over the 5 years prior to their index hospitalization by using retrospective self-reports. The survey focused on psychotherapy provided by clinical psychologists. Results indicate that only 23.2% of participants retrospectively reported having utilized any outpatient psychotherapy within the reporting period and only 8% of participants reported having received a number of outpatient sessions that reaches recommended levels of psychotherapy. Exploratory analyses did not detect a significant association between self-reported utilization of outpatient psychotherapy sessions and most demographic, psychiatric, and psychological attributes, but patients with a bipolar disorder diagnosis (vs schizophrenia spectrum diagnosis) reported having utilized outpatient treatment more often. These findings are preliminary. When replicated they highlight the need for increased access to outpatient psychotherapy and better alignment between guideline recommendations and outpatient supply.

Population genetic simulation: Benchmarking frameworks for non-standard models of natural selection.

Population genetic simulation has emerged as a common tool for investigating increasingly complex evolutionary and demographic models. Software capable of handling high-level model complexity has recently been developed, and the advancement of tree sequence recording now allows simulations to merge the efficiency and genealogical insight of coalescent simulations with the flexibility of forward simulations. However, frameworks utilizing these features have not yet been compared and benchmarked. Here, we evaluate various simulation workflows using the coalescent simulator msprime and the forward simulator SLiM, to assess resource efficiency and determine an optimal simulation framework. Three aspects were evaluated: (1) the burn-in, to establish an equilibrium level of neutral diversity in the population; (2) the forward simulation, in which temporally fluctuating selection is acting; and (3) the final computation of summary statistics. We provide typical memory and computation time requirements for each step. We find that the fastest framework, a combination of coalescent and forward simulation with tree sequence recording, increases simulation speed by over twenty times compared to classical forward simulations without tree sequence recording, although it does require six times more memory. Overall, using efficient simulation workflows can lead to a substantial improvement when modelling complex evolutionary scenarios-although the optimal framework ultimately depends on the available computational resources.

Selectivity and Resolving Power of Hydrophobic Interaction Chromatography Targeting the Separation of Monoclonal Antibody Variants.

This study presents a comprehensive investigation of the mechanistic understanding of retention and selectivity in hydrophobic interaction chromatography. It provides valuable insights into crucial method-development parameters involved in achieving chromatographic resolution for profiling molecular variants of trastuzumab. Retention characteristics have been assessed for three column chemistries, i.e., butyl, alkylamide, and long-stranded multialkylamide ligands, while distinguishing column hydrophobicity and surface area. Salt type and specifically chloride ions proved to be the key driver for improving chromatographic selectivity, and this was attributed to the spatial distribution of ions at the protein surface, which is ion-specific. The effect was notably more pronounced on the multialkylamide column, as proteins intercalated between the multiamide polymer strands, enabling steric effects. Column coupling proved to be an effective approach for maximizing resolution between molecular variants present in the trastuzumab reference sample and trastuzumab variants induced by forced oxidation. Liquid chromatography-mass spectrometry (LC-MS)/MS peptide mapping experiments after fraction collection indicate that the presence of chloride in the mobile phase enables the selectivity of site-specific deamidation (N30) situated at the heavy chain. Moreover, site-specific oxidation of peptides (M255, W420, and M431) was observed for peptides situated at the Fc region close to the CH2-CH3 interface, previously reported to activate unfolding of trastuzumab, increasing the accessible surface area and hence resulting in an increase in chromatographic retention.

The Promise of Inferring the Past Using the Ancestral Recombination Graph.

The ancestral recombination graph (ARG) is a structure that represents the history of coalescent and recombination events connecting a set of sequences (Hudson RR. In: Futuyma D, Antonovics J, editors. Gene genealogies and the coalescent process. In: Oxford Surveys in Evolutionary Biology; 1991. p. 1 to 44.). The full ARG can be represented as a set of genealogical trees at every locus in the genome, annotated with recombination events that change the topology of the trees between adjacent loci and the mutations that occurred along the branches of those trees (Griffiths RC, Marjoram P. An ancestral recombination graph. In: Donnelly P, Tavare S, editors. Progress in population genetics and human evolution. Springer; 1997. p. 257 to 270.). Valuable insights can be gained into past evolutionary processes, such as demographic events or the influence of natural selection, by studying the ARG. It is regarded as the "holy grail" of population genetics (Hubisz M, Siepel A. Inference of ancestral recombination graphs using ARGweaver. In: Dutheil JY, editors. Statistical population genomics. New York, NY: Springer US; 2020. p. 231-266.) since it encodes the processes that generate all patterns of allelic and haplotypic variation from which all commonly used summary statistics in population genetic research (e.g. heterozygosity and linkage disequilibrium) can be derived. Many previous evolutionary inferences relied on summary statistics extracted from the genotype matrix. Evolutionary inferences using the ARG represent a significant advancement as the ARG is a representation of the evolutionary history of a sample that shows the past history of recombination, coalescence, and mutation events across a particular sequence. This representation in theory contains as much information, if not more, than the combination of all independent summary statistics that could be derived from the genotype matrix. Consistent with this idea, some of the first ARG-based analyses have proven to be more powerful than summary statistic-based analyses (Speidel L, Forest M, Shi S, Myers SR. A method for genome-wide genealogy estimation for thousands of samples. Nat Genet. 2019:51(9):1321 to 1329.; Stern AJ, Wilton PR, Nielsen R. An approximate full-likelihood method for inferring selection and allele frequency trajectories from DNA sequence data. PLoS Genet. 2019:15(9):e1008384.; Hubisz MJ, Williams AL, Siepel A. Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph. PLoS Genet. 2020:16(8):e1008895.; Fan C, Mancuso N, Chiang CWK. A genealogical estimate of genetic relationships. Am J Hum Genet. 2022:109(5):812-824.; Fan C, Cahoon JL, Dinh BL, Ortega-Del Vecchyo D, Huber C, Edge MD, Mancuso N, Chiang CWK. A likelihood-based framework for demographic inference from genealogical trees. bioRxiv. 2023.10.10.561787. 2023.; Hejase HA, Mo Z, Campagna L, Siepel A. A deep-learning approach for inference of selective sweeps from the ancestral recombination graph. Mol Biol Evol. 2022:39(1):msab332.; Link V, Schraiber JG, Fan C, Dinh B, Mancuso N, Chiang CWK, Edge MD. Tree-based QTL mapping with expected local genetic relatedness matrices. bioRxiv. 2023.04.07.536093. 2023.; Zhang BC, Biddanda A, Gunnarsson ÁF, Cooper F, Palamara PF. Biobank-scale inference of ancestral recombination graphs enables genealogical analysis of complex traits. Nat Genet. 2023:55(5):768-776.). As such, there has been significant interest in the field to investigate 2 main problems related to the ARG: (i) How can we estimate the ARG based on genomic data, and (ii) how can we extract information of past evolutionary processes from the ARG? In this perspective, we highlight 3 topics that pertain to these main issues: The development of computational innovations that enable the estimation of the ARG; remaining challenges in estimating the ARG; and methodological advances for deducing evolutionary forces and mechanisms using the ARG. This perspective serves to introduce the readers to the types of questions that can be explored using the ARG and to highlight some of the most pressing issues that must be addressed in order to make ARG-based inference an indispensable tool for evolutionary research.